Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold1836
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1164857
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.29
Warning! 152653 characters in sequence are not A, C, G, or T
File 3 of 4
Found at i:446170 original size:4 final size:4
Alignment explanation
Indices: 446155--446208 Score: 74
Period size: 4 Copynumber: 13.8 Consensus size: 4
446145 ATCACATTTT
* * *
446155 GTCC GT-C GTCC GTCC GTCC GTCC GTCT GTCC GTCC GTCT GTCC GTCT
1 GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC
446202 GTCC GTC
1 GTCC GTC
446209 TGTAAACTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
3 3 0.07
4 40 0.93
ACGTcount: A:0.00, C:0.43, G:0.26, T:0.31
Consensus pattern (4 bp):
GTCC
Found at i:448253 original size:49 final size:49
Alignment explanation
Indices: 448197--448580 Score: 615
Period size: 49 Copynumber: 7.8 Consensus size: 49
448187 GGAAGGCGGG
**
448197 GATCTCCAAACTGGTCTGTGCAGGTGGGTAATGTCAGAGTCTCAGAGAA
1 GATCTCCAAACTGGTCTGTGCAGGTGGGTAATGTCAGAGTCTGGGAGAA
* *
448246 GATCTCCACACTGGTCTGTGCTGGTGGGTAATGTCAGAGTCTGGGAGAA
1 GATCTCCAAACTGGTCTGTGCAGGTGGGTAATGTCAGAGTCTGGGAGAA
* *
448295 GATCTCCAAACTGGTCTGTGCAGGTGGGTAATGTCAAAGTCTGGGAGAG
1 GATCTCCAAACTGGTCTGTGCAGGTGGGTAATGTCAGAGTCTGGGAGAA
**
448344 GATCTCCAAACTGGTCTGTGCAGGTGGGTAATGTCAGAGTCTCAGAGAA
1 GATCTCCAAACTGGTCTGTGCAGGTGGGTAATGTCAGAGTCTGGGAGAA
* * **
448393 GATCTCCACACTGGTCTGTGCTGGTGGGTAATGTCAGAGTCTCAGAGAA
1 GATCTCCAAACTGGTCTGTGCAGGTGGGTAATGTCAGAGTCTGGGAGAA
* *
448442 GATCTCCACACTGGTCTGTGCTGGTGGGTAATGTCAGAGTCTGGGAGAA
1 GATCTCCAAACTGGTCTGTGCAGGTGGGTAATGTCAGAGTCTGGGAGAA
* *
448491 GATCTCCAAACTGGTCTGTGCAGGTGGGTAATGTCAAAGTCTGGGAGAG
1 GATCTCCAAACTGGTCTGTGCAGGTGGGTAATGTCAGAGTCTGGGAGAA
*
448540 GATCTCCAAACTGGTCTGTGCTGGTGGGTAATGTCAGAGTC
1 GATCTCCAAACTGGTCTGTGCAGGTGGGTAATGTCAGAGTC
448581 GCCGCAGCAC
Statistics
Matches: 313, Mismatches: 22, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 313 1.00
ACGTcount: A:0.23, C:0.18, G:0.33, T:0.26
Consensus pattern (49 bp):
GATCTCCAAACTGGTCTGTGCAGGTGGGTAATGTCAGAGTCTGGGAGAA
Found at i:449695 original size:49 final size:49
Alignment explanation
Indices: 449623--449718 Score: 165
Period size: 49 Copynumber: 2.0 Consensus size: 49
449613 CCGTGCTGCG
*
449623 TGGGAGAAGATCTCCAAACTGGTCTGTGCTGGGGGGTAATGTCAGAGTC
1 TGGGAGAAGATCTCCAAACTGGTCTGTGCAGGGGGGTAATGTCAGAGTC
* *
449672 TGGGAGAAGATCTCCACACTGGTCTGTGCAGGTGGGTAATGTCAGAG
1 TGGGAGAAGATCTCCAAACTGGTCTGTGCAGGGGGGTAATGTCAGAG
449719 ACTCAGGGGT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.23, C:0.17, G:0.36, T:0.24
Consensus pattern (49 bp):
TGGGAGAAGATCTCCAAACTGGTCTGTGCAGGGGGGTAATGTCAGAGTC
Found at i:452031 original size:40 final size:40
Alignment explanation
Indices: 451920--452019 Score: 157
Period size: 39 Copynumber: 2.5 Consensus size: 40
451910 TTAACATTTT
* *
451920 TAAGAACTATATTTATTTTGTTTTACGACTTCGCATTTCA
1 TAAGAACTATATTTATTTTGTTTTACGACTTCTCATCTCA
*
451960 T-AGAACTATATTTATTTTGTTTTACGACTTCTTATCTCA
1 TAAGAACTATATTTATTTTGTTTTACGACTTCTCATCTCA
*
451999 TAAGAACTGTATTTATTTTGT
1 TAAGAACTATATTTATTTTGT
452020 GACACGACTT
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
39 36 0.65
40 19 0.35
ACGTcount: A:0.27, C:0.13, G:0.10, T:0.50
Consensus pattern (40 bp):
TAAGAACTATATTTATTTTGTTTTACGACTTCTCATCTCA
Found at i:458723 original size:2 final size:2
Alignment explanation
Indices: 458716--458784 Score: 79
Period size: 2 Copynumber: 35.5 Consensus size: 2
458706 GCAGGTAATA
* *
458716 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TG TG TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * *
458758 -C TC TC TA TC TC TA TA TC TC T- TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
458785 TTACTATCCC
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
1 2 0.03
2 57 0.97
ACGTcount: A:0.04, C:0.42, G:0.03, T:0.51
Consensus pattern (2 bp):
TC
Found at i:460794 original size:11 final size:11
Alignment explanation
Indices: 460778--460814 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
460768 TCAATGGCAG
460778 TTATATAGATA
1 TTATATAGATA
460789 TTATATAGATA
1 TTATATAGATA
460800 TTATCAT-GATA
1 TTAT-ATAGATA
460811 TTAT
1 TTAT
460815 GGAAATGTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 23 0.92
12 2 0.08
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.49
Consensus pattern (11 bp):
TTATATAGATA
Found at i:461098 original size:13 final size:13
Alignment explanation
Indices: 461080--461104 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
461070 TTATGATTTG
461080 CTTTTTTTTTTTT
1 CTTTTTTTTTTTT
461093 CTTTTTTTTTTT
1 CTTTTTTTTTTT
461105 ACAATTTATC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (13 bp):
CTTTTTTTTTTTT
Found at i:467066 original size:2 final size:2
Alignment explanation
Indices: 467061--467087 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
467051 GGGCACTGAT
467061 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
467088 TATTTAACAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:473042 original size:106 final size:106
Alignment explanation
Indices: 472911--473128 Score: 436
Period size: 106 Copynumber: 2.1 Consensus size: 106
472901 GATTTACGCA
472911 CACTTTATATGAAAAAAGTGCAAACATTTAAATTGTTTACCTTCTACATTTCGTCAAATGCCGTA
1 CACTTTATATGAAAAAAGTGCAAACATTTAAATTGTTTACCTTCTACATTTCGTCAAATGCCGTA
472976 GCTTAGTTGAACTTAGAGCCTTTTCGAGTGCAGATATTTCT
66 GCTTAGTTGAACTTAGAGCCTTTTCGAGTGCAGATATTTCT
473017 CACTTTATATGAAAAAAGTGCAAACATTTAAATTGTTTACCTTCTACATTTCGTCAAATGCCGTA
1 CACTTTATATGAAAAAAGTGCAAACATTTAAATTGTTTACCTTCTACATTTCGTCAAATGCCGTA
473082 GCTTAGTTGAACTTAGAGCCTTTTCGAGTGCAGATATTTCT
66 GCTTAGTTGAACTTAGAGCCTTTTCGAGTGCAGATATTTCT
473123 CACTTT
1 CACTTT
473129 TTTAAACACG
Statistics
Matches: 112, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
106 112 1.00
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37
Consensus pattern (106 bp):
CACTTTATATGAAAAAAGTGCAAACATTTAAATTGTTTACCTTCTACATTTCGTCAAATGCCGTA
GCTTAGTTGAACTTAGAGCCTTTTCGAGTGCAGATATTTCT
Found at i:483818 original size:14 final size:15
Alignment explanation
Indices: 483799--483827 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
483789 CTCGTCGCAT
483799 TATATTTG-ATATAA
1 TATATTTGTATATAA
483813 TATATTTGTATATAA
1 TATATTTGTATATAA
483828 AATTGTATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (15 bp):
TATATTTGTATATAA
Found at i:485233 original size:2 final size:2
Alignment explanation
Indices: 485226--485277 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
485216 GAATATCATT
485226 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
485268 GA GA GA GA GA
1 GA GA GA GA GA
485278 CTCTTACCGC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:486601 original size:42 final size:42
Alignment explanation
Indices: 486411--486786 Score: 215
Period size: 42 Copynumber: 9.1 Consensus size: 42
486401 GTAATTTGTG
** * * *
486411 TTATTTGTATCCT-GATCGCAATCGTTTTGTGAGTCATTCTCT
1 TTATTTGTATCCTGGAT-GCAATCGTTGAGCGAGTCTTTCTCA
* * *
486453 TTATCTGTATCCTGAATGCAATCATT----GAGT-TGTTCT--
1 TTATTTGTATCCTGGATGCAATCGTTGAGCGAGTCT-TTCTCA
*
486489 TT-TTCTGTATCCT-GATCACAATCGTTGAGCGAGTCTTTCTCA
1 TTATT-TGTATCCTGGAT-GCAATCGTTGAGCGAGTCTTTCTCA
* * * * * **
486531 TTATCTGTAT-TTTGAGCGCATTTATTGAGCGAGTCTTTCTCA
1 TTATTTGTATCCTGGA-TGCAATCGTTGAGCGAGTCTTTCTCA
* * * *
486573 TTATTTGTATCCTGGGTGCAATCTTTGAGCGATTCTTTCTCT
1 TTATTTGTATCCTGGATGCAATCGTTGAGCGAGTCTTTCTCA
* * * *** * * * *
486615 TTATCTGCATCATCTTTGCAATCGTCGAGTGAAT-TATTCTCC
1 TTATTTGTATCCTGGATGCAATCGTTGAGCGAGTCT-TTCTCA
** * *
486657 CCATTTGAATCCT-GATTGCAATCGTTGAGCGAGTCTTTCTTA
1 TTATTTGTATCCTGGA-TGCAATCGTTGAGCGAGTCTTTCTCA
* * *
486699 TTATTTCTATCCT-GATCGCAATCGTTGAGCGAGTATTTCTTA
1 TTATTTGTATCCTGGAT-GCAATCGTTGAGCGAGTCTTTCTCA
* *
486741 TTATTTGTATCCT-GATCGCAATCTTTGAGCGAGTCTTTCTCT
1 TTATTTGTATCCTGGAT-GCAATCGTTGAGCGAGTCTTTCTCA
486783 TTAT
1 TTAT
486787 CTGCATCTGT
Statistics
Matches: 257, Mismatches: 58, Indels: 38
0.73 0.16 0.11
Matches are distributed among these distances:
35 3 0.01
36 17 0.07
38 8 0.03
40 8 0.03
41 4 0.02
42 211 0.82
43 6 0.02
ACGTcount: A:0.19, C:0.20, G:0.17, T:0.44
Consensus pattern (42 bp):
TTATTTGTATCCTGGATGCAATCGTTGAGCGAGTCTTTCTCA
Found at i:486603 original size:84 final size:83
Alignment explanation
Indices: 486411--486789 Score: 260
Period size: 84 Copynumber: 4.6 Consensus size: 83
486401 GTAATTTGTG
** * * * *
486411 TTATTTGTATCCT-GATCGCAATCGTTTTGTGAGTCATTCTCTTTATCTGTATCCTGAAT-GCAA
1 TTATTTGTATCCTGGAT-GCAATCGTTGAGCGAGTCTTTCTCATTATCTGTATCATG-ATCGCAA
*
486474 TCATT----GAGTTGTTCT--
64 TCGTTGAGCGAGTT-TTCTCA
* ** * *
486489 TT-TTCTGTATCCT-GATCACAATCGTTGAGCGAGTCTTTCTCATTATCTGTATTTTGAGCGCAT
1 TTATT-TGTATCCTGGAT-GCAATCGTTGAGCGAGTCTTTCTCATTATCTGTATCATGATCGCAA
**
486552 TTATTGAGCGAGTCTTTCTCA
64 TCGTTGAGCGAGT-TTTCTCA
* * * * * ** *
486573 TTATTTGTATCCTGGGTGCAATCTTTGAGCGATTCTTTCTCTTTATCTGCATCATCTTTGCAATC
1 TTATTTGTATCCTGGATGCAATCGTTGAGCGAGTCTTTCTCATTATCTGTATCATGATCGCAATC
* * * *
486638 GTCGAGTGAATTATTCTCC
66 GTTGAGCGAGTT-TTCTCA
** * * * * *
486657 CCATTTGAATCCT-GATTGCAATCGTTGAGCGAGTCTTTCTTATTATTTCTATCCTGATCGCAAT
1 TTATTTGTATCCTGGA-TGCAATCGTTGAGCGAGTCTTTCTCATTATCTGTATCATGATCGCAAT
*
486721 CGTTGAGCGAGTATTTCTTA
65 CGTTGAGCGAGT-TTTCTCA
* *
486741 TTATTTGTATCCT-GATCGCAATCTTTGAGCGAGTCTTTCTCTTTATCTG
1 TTATTTGTATCCTGGAT-GCAATCGTTGAGCGAGTCTTTCTCATTATCTG
486790 CATCTGTATC
Statistics
Matches: 228, Mismatches: 58, Indels: 24
0.74 0.19 0.08
Matches are distributed among these distances:
77 3 0.01
78 52 0.23
82 8 0.04
83 4 0.02
84 156 0.68
85 5 0.02
ACGTcount: A:0.19, C:0.20, G:0.17, T:0.44
Consensus pattern (83 bp):
TTATTTGTATCCTGGATGCAATCGTTGAGCGAGTCTTTCTCATTATCTGTATCATGATCGCAATC
GTTGAGCGAGTTTTCTCA
Found at i:490584 original size:36 final size:36
Alignment explanation
Indices: 490529--490605 Score: 120
Period size: 36 Copynumber: 2.1 Consensus size: 36
490519 TGTCATCATT
490529 GTTTTGTTCTCCTTCATTCACCACTTCCGATTTTTC
1 GTTTTGTTCTCCTTCATTCACCACTTCCGATTTTTC
* *
490565 GTTTTGTTCTTCTGT-ATTCACCACTTTCGATTTTTC
1 GTTTTGTTCTCCT-TCATTCACCACTTCCGATTTTTC
490601 GTTTT
1 GTTTT
490606 CACTTGTGTT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
36 37 0.97
37 1 0.03
ACGTcount: A:0.10, C:0.25, G:0.10, T:0.55
Consensus pattern (36 bp):
GTTTTGTTCTCCTTCATTCACCACTTCCGATTTTTC
Found at i:498501 original size:15 final size:15
Alignment explanation
Indices: 498481--498511 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
498471 TTCTCTGTAA
498481 CCATTTGAGGTACTT
1 CCATTTGAGGTACTT
*
498496 CCATTTTAGGTACTT
1 CCATTTGAGGTACTT
498511 C
1 C
498512 ATCCCGAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.23, G:0.16, T:0.42
Consensus pattern (15 bp):
CCATTTGAGGTACTT
Found at i:501100 original size:29 final size:29
Alignment explanation
Indices: 501068--501123 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
501058 CTCTGAGCCG
*
501068 CTTTTGTTTCTTTCGT-TCACTCTTCTTTA
1 CTTTTCTTTCTTTC-TCTCACTCTTCTTTA
*
501097 CTTTTCTTTCTTTCTCTCTCTCTTCTT
1 CTTTTCTTTCTTTCTCTCACTCTTCTT
501124 CATCTAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 1 0.04
29 23 0.96
ACGTcount: A:0.04, C:0.29, G:0.04, T:0.64
Consensus pattern (29 bp):
CTTTTCTTTCTTTCTCTCACTCTTCTTTA
Found at i:505007 original size:34 final size:34
Alignment explanation
Indices: 504959--505027 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
504949 TCAGAACACC
*
504959 TATATAGTTACTTACATAGTCCTCTATCAAGATG
1 TATAAAGTTACTTACATAGTCCTCTATCAAGATG
504993 TATAAAGTTACTTACATAGTCCTCTATCAAGATG
1 TATAAAGTTACTTACATAGTCCTCTATCAAGATG
505027 T
1 T
505028 CTGCTCCTCC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (34 bp):
TATAAAGTTACTTACATAGTCCTCTATCAAGATG
Found at i:510580 original size:21 final size:21
Alignment explanation
Indices: 510554--510595 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
510544 TCTCTTTATC
*
510554 AAGCGTCTTTCAGTAGGTGCA
1 AAGCGTCCTTCAGTAGGTGCA
510575 AAGCGTCCTTCAGTAGGTGCA
1 AAGCGTCCTTCAGTAGGTGCA
510596 GACTTTCACC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
AAGCGTCCTTCAGTAGGTGCA
Found at i:510776 original size:16 final size:16
Alignment explanation
Indices: 510753--510948 Score: 257
Period size: 16 Copynumber: 12.2 Consensus size: 16
510743 AAAACACAGA
510753 CCGATAACTCTCTTAC
1 CCGATAACTCTCTTAC
* *
510769 CTGATAACTCTCTAAC
1 CCGATAACTCTCTTAC
510785 CCGATAACTCTCTTAC
1 CCGATAACTCTCTTAC
* *
510801 CCAATAACTCTCTAAC
1 CCGATAACTCTCTTAC
510817 CCGATAACTCTCTTAC
1 CCGATAACTCTCTTAC
* * *
510833 CCAATAATTCTCTAAC
1 CCGATAACTCTCTTAC
*
510849 CAGATAACTCTCTTAC
1 CCGATAACTCTCTTAC
* * *
510865 CCAATAATTCTCTAAC
1 CCGATAACTCTCTTAC
510881 CCGATAACTCTCTTAC
1 CCGATAACTCTCTTAC
*
510897 CTGATAACTCTCTTAC
1 CCGATAACTCTCTTAC
*
510913 CTGATAACTCTCTTAC
1 CCGATAACTCTCTTAC
* *
510929 CCAATAACTCTCTAAC
1 CCGATAACTCTCTTAC
510945 CCGA
1 CCGA
510949 CCAAACAGAA
Statistics
Matches: 153, Mismatches: 27, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 153 1.00
ACGTcount: A:0.30, C:0.35, G:0.05, T:0.31
Consensus pattern (16 bp):
CCGATAACTCTCTTAC
Found at i:510794 original size:32 final size:32
Alignment explanation
Indices: 510753--510948 Score: 311
Period size: 32 Copynumber: 6.1 Consensus size: 32
510743 AAAACACAGA
**
510753 CCGATAACTCTCTTACCTGATAACTCTCTAAC
1 CCGATAACTCTCTTACCCAATAACTCTCTAAC
510785 CCGATAACTCTCTTACCCAATAACTCTCTAAC
1 CCGATAACTCTCTTACCCAATAACTCTCTAAC
*
510817 CCGATAACTCTCTTACCCAATAATTCTCTAAC
1 CCGATAACTCTCTTACCCAATAACTCTCTAAC
* *
510849 CAGATAACTCTCTTACCCAATAATTCTCTAAC
1 CCGATAACTCTCTTACCCAATAACTCTCTAAC
** *
510881 CCGATAACTCTCTTACCTGATAACTCTCTTAC
1 CCGATAACTCTCTTACCCAATAACTCTCTAAC
*
510913 CTGATAACTCTCTTACCCAATAACTCTCTAAC
1 CCGATAACTCTCTTACCCAATAACTCTCTAAC
510945 CCGA
1 CCGA
510949 CCAAACAGAA
Statistics
Matches: 150, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 150 1.00
ACGTcount: A:0.30, C:0.35, G:0.05, T:0.31
Consensus pattern (32 bp):
CCGATAACTCTCTTACCCAATAACTCTCTAAC
Found at i:516928 original size:35 final size:35
Alignment explanation
Indices: 516828--517461 Score: 654
Period size: 35 Copynumber: 18.3 Consensus size: 35
516818 GATAAACAAA
* *
516828 CTGAGAGGTAAGATAGGTGTATTGGAGTGAAATAC
1 CTGAGAGGTAAGATAGGTGTATTAGAGTGACATAC
** *
516863 CTGAGAGGT-ATTTCACGGTGTATTAGAGTGACATAT
1 CTGAGAGGTAAGAT-A-GGTGTATTAGAGTGACATAC
* *
516899 CTGAGAGGTAAGATAGGTGTATTAAAGTGACATAA
1 CTGAGAGGTAAGATAGGTGTATTAGAGTGACATAC
*
516934 CTGAGAGGTAAGATAGGTGTATTACAGTGACATAC
1 CTGAGAGGTAAGATAGGTGTATTAGAGTGACATAC
*
516969 CTGAGAGGTAAGATAGGTGTATTACAGTGACATAC
1 CTGAGAGGTAAGATAGGTGTATTAGAGTGACATAC
** *
517004 CTGAGAGGT-ATCTCACGGTGTATTAGAGTGACATAA
1 CTGAGAGGTAAGAT-A-GGTGTATTAGAGTGACATAC
* *
517040 CTGAGAGGTAAGATAGGTGTATTACAGTGACATAA
1 CTGAGAGGTAAGATAGGTGTATTAGAGTGACATAC
*
517075 CTGAGAGGTAAGATAAGTGTATTAGAGTGACATAC
1 CTGAGAGGTAAGATAGGTGTATTAGAGTGACATAC
** *
517110 CTGAGAGGT-ATTTCATGGTGTATTAGAGTGACATAA
1 CTGAGAGGTAAGAT-A-GGTGTATTAGAGTGACATAC
*
517146 CTGAGAGGTAAGATAGGTGTATTACAGTGACATAC
1 CTGAGAGGTAAGATAGGTGTATTAGAGTGACATAC
*
517181 CTGAGAGGTAAGATAGGTGTATTACAGTGACATAC
1 CTGAGAGGTAAGATAGGTGTATTAGAGTGACATAC
517216 CTGAGAGGTAAGATACTAGGTGTATTAGAGTGACATAC
1 CTGAGAGGTAAG--A-TAGGTGTATTAGAGTGACATAC
517254 CTGAGA-G---G-TA----TATTAGAGTGACATAC
1 CTGAGAGGTAAGATAGGTGTATTAGAGTGACATAC
* * *
517280 CTGAGATGTTAGTTAGGTGTATTAGAGTGACATA-
1 CTGAGAGGTAAGATAGGTGTATTAGAGTGACATAC
* ** * * * *
517314 CAG-GTACCTAAAATAGGTGTGTCAAAGTGACATAC
1 CTGAG-AGGTAAGATAGGTGTATTAGAGTGACATAC
* **
517349 CTGAGAGGTTAA-ATAGGTGTCTTAGAGTGATTTAC
1 CTGAGAGG-TAAGATAGGTGTATTAGAGTGACATAC
* * *
517384 CTGAGAGG-ATATATAGGTGCATTAGTGTGACATAC
1 CTGAGAGGTA-AGATAGGTGTATTAGAGTGACATAC
** * * * * *
517419 CTGAGATATAACACAGGCGTTTTA-AGTGATATAC
1 CTGAGAGGTAAGATAGGTGTATTAGAGTGACATAC
517453 CTGAGAGGT
1 CTGAGAGGT
517462 TATATTGGTG
Statistics
Matches: 508, Mismatches: 63, Indels: 57
0.81 0.10 0.09
Matches are distributed among these distances:
26 22 0.04
27 1 0.00
30 3 0.01
31 2 0.00
33 2 0.00
34 46 0.09
35 309 0.61
36 88 0.17
37 8 0.02
38 27 0.05
ACGTcount: A:0.33, C:0.10, G:0.28, T:0.28
Consensus pattern (35 bp):
CTGAGAGGTAAGATAGGTGTATTAGAGTGACATAC
Found at i:517024 original size:106 final size:105
Alignment explanation
Indices: 516826--517424 Score: 645
Period size: 106 Copynumber: 5.7 Consensus size: 105
516816 ATGATAAACA
** * ** *
516826 AACTGAGAGGTAAGATAGGTGTATTGGAGTGAAATACCTGAGAGGT-ATTTCACGGTGTATTAGA
1 AACTGAGAGGTAAGATAGGTGTATTACAGTGACATACCTGAGAGGTAAGAT-A-GGTGTATTACA
* ** *
516890 GTGACATATCTGAGAGGTAAGATAGGTGTATTAAAGTGACAT
64 GTGACATACCTGAGAGGTAATCTAGGTGTATTAGAGTGACAT
516932 AACTGAGAGGTAAGATAGGTGTATTACAGTGACATACCTGAGAGGTAAGATAGGTGTATTACAGT
1 AACTGAGAGGTAAGATAGGTGTATTACAGTGACATACCTGAGAGGTAAGATAGGTGTATTACAGT
516997 GACATACCTGAGAGGT-ATCTCACGGTGTATTAGAGTGACAT
66 GACATACCTGAGAGGTAATCT-A-GGTGTATTAGAGTGACAT
* * *
517038 AACTGAGAGGTAAGATAGGTGTATTACAGTGACATAACTGAGAGGTAAGATAAGTGTATTAGAGT
1 AACTGAGAGGTAAGATAGGTGTATTACAGTGACATACCTGAGAGGTAAGATAGGTGTATTACAGT
*
517103 GACATACCTGAGAGGT-ATTTCATGGTGTATTAGAGTGACAT
66 GACATACCTGAGAGGTAATCT-A-GGTGTATTAGAGTGACAT
517144 AACTGAGAGGTAAGATAGGTGTATTACAGTGACATACCTGAGAGGTAAGATAGGTGTATTACAGT
1 AACTGAGAGGTAAGATAGGTGTATTACAGTGACATACCTGAGAGGTAAGATAGGTGTATTACAGT
517209 GACATACCTGAGAGGTAAGATACTAGGTGTATTAGAGTGACAT
66 GACATACCTGAGAGGT-A-AT-CTAGGTGTATTAGAGTGACAT
* * * * * *
517252 ACCTGAGA-G---G-TA----TATTAGAGTGACATACCTGAGATGTTAGTTAGGTGTATTAGAGT
1 AACTGAGAGGTAAGATAGGTGTATTACAGTGACATACCTGAGAGGTAAGATAGGTGTATTACAGT
* ** ** * * *
517308 GACATA-CAG-GTACCTAAAATAGGTGTGTCAAAGTGACAT
66 GACATACCTGAG-AGGTAATCTAGGTGTATTAGAGTGACAT
* * * ** * * **
517347 ACCTGAGAGGTTAA-ATAGGTGTCTTAGAGTGATTTACCTGAGAGG-ATATATAGGTGCATTAGT
1 AACTGAGAGG-TAAGATAGGTGTATTACAGTGACATACCTGAGAGGTA-AGATAGGTGTATTACA
517410 GTGACATACCTGAGA
64 GTGACATACCTGAGA
517425 TATAACACAG
Statistics
Matches: 429, Mismatches: 43, Indels: 43
0.83 0.08 0.08
Matches are distributed among these distances:
95 25 0.06
96 2 0.00
97 2 0.00
98 4 0.01
99 45 0.10
100 2 0.00
103 2 0.00
104 43 0.10
105 31 0.07
106 241 0.56
107 3 0.01
108 25 0.06
109 3 0.01
110 1 0.00
ACGTcount: A:0.34, C:0.10, G:0.28, T:0.28
Consensus pattern (105 bp):
AACTGAGAGGTAAGATAGGTGTATTACAGTGACATACCTGAGAGGTAAGATAGGTGTATTACAGT
GACATACCTGAGAGGTAATCTAGGTGTATTAGAGTGACAT
Found at i:517082 original size:141 final size:138
Alignment explanation
Indices: 516828--517424 Score: 673
Period size: 141 Copynumber: 4.3 Consensus size: 138
516818 GATAAACAAA
* *
516828 CTGAGAGGTAAGATAGGTGTATTGGAGTGAAATACCTGAGAGGTATTTCACGGTGTATTAGAGTG
1 CTGAGAGGTAAGATAGGTGTATTAGAGTGACATACCTGAGAGGTA-TT-A-GGTGTATTAGAGTG
*
516893 ACATATCTGAGAGGTAAGATAGGTGTATTAAAGTGACATAACTGAGAGGTAAGATAGGTGTATTA
63 ACATAACTGAGAGGTAAGATAGGTGTATTAAAGTGACATAACTGAGAGGTAAGATAGGTGTATTA
*
516958 CAGTGACATAC
128 GAGTGACATAC
*
516969 CTGAGAGGTAAGATAGGTGTATTACAGTGACATACCTGAGAGGTATCTCACGGTGTATTAGAGTG
1 CTGAGAGGTAAGATAGGTGTATTAGAGTGACATACCTGAGAGGTAT-T-A-GGTGTATTAGAGTG
* *
517034 ACATAACTGAGAGGTAAGATAGGTGTATTACAGTGACATAACTGAGAGGTAAGATAAGTGTATTA
63 ACATAACTGAGAGGTAAGATAGGTGTATTAAAGTGACATAACTGAGAGGTAAGATAGGTGTATTA
517099 GAGTGACATAC
128 GAGTGACATAC
** * * *
517110 CTGAGAGGT-ATTTCATGGTGTATTAGAGTGACATAACTGAGAGGTAAGATAGGTGTATTACAGT
1 CTGAGAGGTAAGAT-A-GGTGTATTAGAGTGACATACCTGAGAGGT-A-TTAGGTGTATTAGAGT
* * *
517174 GACATACCTGAGAGGTAAGATAGGTGTATTACAGTGACATACCTGAGAGGTAAGATACTAGGTGT
62 GACATAACTGAGAGGTAAGATAGGTGTATTAAAGTGACATAACTGAGAGGTAAG--A-TAGGTGT
517239 ATTAGAGTGACATAC
124 ATTAGAGTGACATAC
*
517254 CTGAGA-G---G-TA----TATTAGAGTGACATACCTGAGATGTTAGTTAGGTGTATTAGAGTGA
1 CTGAGAGGTAAGATAGGTGTATTAGAGTGACATACCTGAGA-GGTA-TTAGGTGTATTAGAGTGA
* ** * * * * *
517310 CAT-ACAG-GTACCTAAAATAGGTGTGTCAAAGTGACATACCTGAGAGGTTAA-ATAGGTGTCTT
64 CATAACTGAG-AGGTAAGATAGGTGTATTAAAGTGACATAACTGAGAGG-TAAGATAGGTGTATT
**
517372 AGAGTGATTTAC
127 AGAGTGACATAC
* * *
517384 CTGAGAGG-ATATATAGGTGCATTAGTGTGACATACCTGAGA
1 CTGAGAGGTA-AGATAGGTGTATTAGAGTGACATACCTGAGA
517425 TATAACACAG
Statistics
Matches: 401, Mismatches: 35, Indels: 42
0.84 0.07 0.09
Matches are distributed among these distances:
130 25 0.06
131 2 0.00
132 1 0.00
133 34 0.08
134 45 0.11
135 4 0.01
139 21 0.05
140 4 0.01
141 206 0.51
142 28 0.07
143 4 0.01
144 27 0.07
ACGTcount: A:0.34, C:0.10, G:0.28, T:0.28
Consensus pattern (138 bp):
CTGAGAGGTAAGATAGGTGTATTAGAGTGACATACCTGAGAGGTATTAGGTGTATTAGAGTGACA
TAACTGAGAGGTAAGATAGGTGTATTAAAGTGACATAACTGAGAGGTAAGATAGGTGTATTAGAG
TGACATAC
Found at i:517295 original size:26 final size:26
Alignment explanation
Indices: 517233--517285 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
517223 GTAAGATACT
*
517233 AGGTGTATTAGAGTGACATACCTGAG
1 AGGTATATTAGAGTGACATACCTGAG
517259 AGGTATATTAGAGTGACATACCTGAG
1 AGGTATATTAGAGTGACATACCTGAG
517285 A
1 A
517286 TGTTAGTTAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.34, C:0.11, G:0.28, T:0.26
Consensus pattern (26 bp):
AGGTATATTAGAGTGACATACCTGAG
Found at i:517485 original size:69 final size:70
Alignment explanation
Indices: 517370--517528 Score: 216
Period size: 69 Copynumber: 2.3 Consensus size: 70
517360 AATAGGTGTC
* *
517370 TTAGAGTGATTTACCTGAGAGGATATATAGGTGCATTAGTGTGACATACCT-GAGATATAACACA
1 TTAGAGTGATATACCTGAGAGGATATATAGGTGCATAAGTGTGACATACCTAG-GATATAACACA
*
517434 GGCGTT
65 GGCGTG
* * *
517440 TTA-AGTGATATACCTGAGAGGTTATATTGGTGCATAATTGTGACATACCTAGGATATAACACAG
1 TTAGAGTGATATACCTGAGAGGATATATAGGTGCATAAGTGTGACATACCTAGGATATAACACAG
*
517504 GTGTG
66 GCGTG
517509 TTAGAGTGATA-ACCCTGAGA
1 TTAGAGTGATATA-CCTGAGA
517529 TATAAGACAG
Statistics
Matches: 79, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
69 61 0.77
70 18 0.23
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.30
Consensus pattern (70 bp):
TTAGAGTGATATACCTGAGAGGATATATAGGTGCATAAGTGTGACATACCTAGGATATAACACAG
GCGTG
Found at i:526519 original size:35 final size:35
Alignment explanation
Indices: 526460--526822 Score: 292
Period size: 35 Copynumber: 11.3 Consensus size: 35
526450 GTCCTATATA
526460 ACTGACACACTGTCAGCTAGAGGAGTCAAGGAGAG
1 ACTGACACACTGTCAGCTAGAGGAGTCAAGGAGAG
* * * * *
526495 ACTGACACATTGTCGGCTACAGGAGTCAAAGAGTG
1 ACTGACACACTGTCAGCTAGAGGAGTCAAGGAGAG
*
526530 ACTGATACACTCCGTCAGCTAGAGGAGTCAAGGAGAG
1 ACTGACACACT--GTCAGCTAGAGGAGTCAAGGAGAG
* *
526567 ACTGACACACTGTCAGCTAGAGGAATCAAGGACAG
1 ACTGACACACTGTCAGCTAGAGGAGTCAAGGAGAG
*
526602 ACTGACACACTATCAGCT-----AG---AGGAGAG
1 ACTGACACACTGTCAGCTAGAGGAGTCAAGGAGAG
*
526629 ACTGACACACTGTCAG-T---TG-G---AGGAGAG
1 ACTGACACACTGTCAGCTAGAGGAGTCAAGGAGAG
*
526656 ACTGATACACTGTCAGCTAGAGGAGTCAAGGAGA-
1 ACTGACACACTGTCAGCTAGAGGAGTCAAGGAGAG
* *
526690 AATGGACACACTGTCAGCT--A-G-G----GGAGAT
1 ACT-GACACACTGTCAGCTAGAGGAGTCAAGGAGAG
* *
526718 ACTGACACACTGTCAG-T----TAG---AGGAGAT
1 ACTGACACACTGTCAGCTAGAGGAGTCAAGGAGAG
*
526745 ACTGACACACTGTCAGCTAGAGGAGTCAA-AAGAG
1 ACTGACACACTGTCAGCTAGAGGAGTCAAGGAGAG
*
526779 ACTGACACATTGTCAGCT-GCAGGAGTCAAGGAGAG
1 ACTGACACACTGTCAGCTAG-AGGAGTCAAGGAGAG
526814 ACTGACACA
1 ACTGACACA
526823 AATATATGTA
Statistics
Matches: 273, Mismatches: 29, Indels: 52
0.77 0.08 0.15
Matches are distributed among these distances:
26 3 0.01
27 84 0.31
28 4 0.01
30 1 0.00
31 2 0.01
32 4 0.01
33 2 0.01
34 31 0.11
35 112 0.41
37 30 0.11
ACGTcount: A:0.34, C:0.20, G:0.29, T:0.17
Consensus pattern (35 bp):
ACTGACACACTGTCAGCTAGAGGAGTCAAGGAGAG
Found at i:526575 original size:72 final size:70
Alignment explanation
Indices: 526460--526822 Score: 238
Period size: 62 Copynumber: 5.6 Consensus size: 70
526450 GTCCTATATA
* * *
526460 ACTGACACACTGTCAGCTAGAGGAGTCAAGGAGAGACTGACACATTGTCGGCTACAGGAGTCAAA
1 ACTGACACACTGTCAGCTAGAGGAGTCAAGGAGAGACTGACACACTGTCAGCTACAGGAATCAAA
**
526525 GAGTG
66 GACAG
* *
526530 ACTGATACACTCCGTCAGCTAGAGGAGTCAAGGAGAGACTGACACACTGTCAGCTAGAGGAATCA
1 ACTGACACACT--GTCAGCTAGAGGAGTCAAGGAGAGACTGACACACTGTCAGCTACAGGAATCA
*
526595 AGGACAG
64 AAGACAG
* * *
526602 ACTGACACACTATCAGCT-----AG---AGGAGAGACTGACACACTGTCAG-T--TGG-----AG
1 ACTGACACACTGTCAGCTAGAGGAGTCAAGGAGAGACTGACACACTGTCAGCTACAGGAATCAAA
*
526651 GAGAG
66 GACAG
* *
526656 ACTGATACACTGTCAGCTAGAGGAGTCAAGGAGA-AATGGACACACTGTCAGCT--AGG------
1 ACTGACACACTGTCAGCTAGAGGAGTCAAGGAGAGACT-GACACACTGTCAGCTACAGGAATCAA
* * *
526712 GGAGAT
65 AGACAG
* * * *
526718 ACTGACACACTGTCAG-T-TA-GAG-----GAGATACTGACACACTGTCAGCTAGAGGAGTCAAA
1 ACTGACACACTGTCAGCTAGAGGAGTCAAGGAGAGACTGACACACTGTCAGCTACAGGAATCAAA
*
526775 -AGAG
66 GACAG
*
526779 ACTGACACATTGTCAGCT-GCAGGAGTCAAGGAGAGACTGACACA
1 ACTGACACACTGTCAGCTAG-AGGAGTCAAGGAGAGACTGACACA
526823 AATATATGTA
Statistics
Matches: 239, Mismatches: 25, Indels: 59
0.74 0.08 0.18
Matches are distributed among these distances:
54 41 0.17
55 2 0.01
56 3 0.01
59 7 0.03
60 1 0.00
61 22 0.09
62 63 0.26
63 4 0.02
64 3 0.01
65 2 0.01
69 13 0.05
70 16 0.07
72 62 0.26
ACGTcount: A:0.34, C:0.20, G:0.29, T:0.17
Consensus pattern (70 bp):
ACTGACACACTGTCAGCTAGAGGAGTCAAGGAGAGACTGACACACTGTCAGCTACAGGAATCAAA
GACAG
Found at i:526625 original size:27 final size:27
Alignment explanation
Indices: 526595--526769 Score: 188
Period size: 27 Copynumber: 6.2 Consensus size: 27
526585 AGAGGAATCA
* *
526595 AGGACAGACTGACACACTATCAGCTAG
1 AGGAGAGACTGACACACTGTCAGCTAG
* *
526622 AGGAGAGACTGACACACTGTCAGTTGG
1 AGGAGAGACTGACACACTGTCAGCTAG
*
526649 AGGAGAGACTGATACACTGTCAGCTAG
1 AGGAGAGACTGACACACTGTCAGCTAG
*
526676 AGGAGTCAAGGAGAAATGGACACACTGTCAGCTAG
1 A-G-G---A-GAG-ACT-GACACACTGTCAGCTAG
* * *
526711 GGGAGATACTGACACACTGTCAGTTAG
1 AGGAGAGACTGACACACTGTCAGCTAG
*
526738 AGGAGATACTGACACACTGTCAGCTAG
1 AGGAGAGACTGACACACTGTCAGCTAG
526765 AGGAG
1 AGGAG
526770 TCAAAAGAGA
Statistics
Matches: 125, Mismatches: 15, Indels: 16
0.80 0.10 0.10
Matches are distributed among these distances:
27 94 0.75
28 3 0.02
29 3 0.02
30 1 0.01
32 1 0.01
33 4 0.03
34 3 0.02
35 16 0.13
ACGTcount: A:0.34, C:0.19, G:0.30, T:0.17
Consensus pattern (27 bp):
AGGAGAGACTGACACACTGTCAGCTAG
Found at i:526716 original size:89 final size:89
Alignment explanation
Indices: 526560--526773 Score: 331
Period size: 89 Copynumber: 2.4 Consensus size: 89
526550 AGAGGAGTCA
* *
526560 AGGAGAGACTGACACACTGTCAGCTAGAGGAATCAAGGACAGACTGACACACTATCAGCTAGAGG
1 AGGAGAGACTGACACACTGTCAGCTAGAGGAGTCAAGGACAGAATGACACACTATCAGCTAGAGG
*
526625 AGAGACTGACACACTGTCAGTTGG
66 AGAGACTGACACACTGTCAGTTAG
* * * *
526649 AGGAGAGACTGATACACTGTCAGCTAGAGGAGTCAAGGAGA-AATGGACACACTGTCAGCTAGGG
1 AGGAGAGACTGACACACTGTCAGCTAGAGGAGTCAAGGACAGAAT-GACACACTATCAGCTAGAG
*
526713 GAGATACTGACACACTGTCAGTTAG
65 GAGAGACTGACACACTGTCAGTTAG
*
526738 AGGAGATACTGACACACTGTCAGCTAGAGGAGTCAA
1 AGGAGAGACTGACACACTGTCAGCTAGAGGAGTCAA
526774 AAGAGACTGA
Statistics
Matches: 114, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
88 2 0.02
89 112 0.98
ACGTcount: A:0.35, C:0.20, G:0.29, T:0.17
Consensus pattern (89 bp):
AGGAGAGACTGACACACTGTCAGCTAGAGGAGTCAAGGACAGAATGACACACTATCAGCTAGAGG
AGAGACTGACACACTGTCAGTTAG
Found at i:526793 original size:34 final size:35
Alignment explanation
Indices: 526745--526822 Score: 115
Period size: 34 Copynumber: 2.3 Consensus size: 35
526735 TAGAGGAGAT
526745 ACTGACACACTGTCAGCTAG-AGGAGTCAA-AAGAG
1 ACTGACACACTGTCAGCT-GCAGGAGTCAAGAAGAG
* *
526779 ACTGACACATTGTCAGCTGCAGGAGTCAAGGAGAG
1 ACTGACACACTGTCAGCTGCAGGAGTCAAGAAGAG
526814 ACTGACACA
1 ACTGACACA
526823 AATATATGTA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
33 1 0.03
34 26 0.65
35 13 0.32
ACGTcount: A:0.36, C:0.22, G:0.27, T:0.15
Consensus pattern (35 bp):
ACTGACACACTGTCAGCTGCAGGAGTCAAGAAGAG
Found at i:529715 original size:24 final size:24
Alignment explanation
Indices: 529603--529715 Score: 84
Period size: 24 Copynumber: 4.6 Consensus size: 24
529593 CCAGAACTGT
529603 CATTTTGGTGGTAGCCCCTGAAAGGA
1 CATTTTGGTGGTAGCCCCTG--AGGA
* * ** * *
529629 CATTTTGGTGATTGCATCAGGGGA
1 CATTTTGGTGGTAGCCCCTGAGGA
* * *
529653 CACTTTGGTGGTAGCCGCTG-GAA
1 CATTTTGGTGGTAGCCCCTGAGGA
* * *
529676 AAATTTGGATGATAGCCCCTGAGGA
1 CATTTTGG-TGGTAGCCCCTGAGGA
529701 CATTTTGGTGGTAGC
1 CATTTTGGTGGTAGC
529716 AGGTGGAAGA
Statistics
Matches: 64, Mismatches: 21, Indels: 6
0.70 0.23 0.07
Matches are distributed among these distances:
23 8 0.12
24 33 0.52
25 8 0.12
26 15 0.23
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.29
Consensus pattern (24 bp):
CATTTTGGTGGTAGCCCCTGAGGA
Found at i:547270 original size:41 final size:41
Alignment explanation
Indices: 547213--547295 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
547203 TGCTACAGTG
*
547213 ACTCGATCCAACTCATTTTGTCAGGTTGCGATAATAGGTGA
1 ACTCGATCCAACTCATTTTGACAGGTTGCGATAATAGGTGA
547254 ACTCGATCCAACTCATTTTGACAGGTTGCGATAATAGGTGA
1 ACTCGATCCAACTCATTTTGACAGGTTGCGATAATAGGTGA
547295 A
1 A
547296 GATCCTACAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (41 bp):
ACTCGATCCAACTCATTTTGACAGGTTGCGATAATAGGTGA
Found at i:548539 original size:22 final size:22
Alignment explanation
Indices: 548503--549167 Score: 654
Period size: 22 Copynumber: 30.2 Consensus size: 22
548493 AGAATACATT
548503 AAGTGAACAGACTAATGTTACA
1 AAGTGAACAGACTAATGTTACA
* * * *
548525 AAGTGAGCAGGCTAATATTACT
1 AAGTGAACAGACTAATGTTACA
* *
548547 CAGTGAAAAGACTAATGTTACA
1 AAGTGAACAGACTAATGTTACA
* *
548569 AAGTGAACAGACTAATATTCCA
1 AAGTGAACAGACTAATGTTACA
*
548591 CAGTGAACAGACTAATGTTACA
1 AAGTGAACAGACTAATGTTACA
*
548613 AAGTGAACAGACTAATATTACA
1 AAGTGAACAGACTAATGTTACA
* *
548635 CAGTGAAAAGACTAATGTTACA
1 AAGTGAACAGACTAATGTTACA
* *
548657 AAGTGAACAGACTAATATTACT
1 AAGTGAACAGACTAATGTTACA
* *
548679 CAGTGAAAAGACTAATGTTACA
1 AAGTGAACAGACTAATGTTACA
* * *
548701 AAGTGAGCAGGCTAATATTACA
1 AAGTGAACAGACTAATGTTACA
*
548723 CAGTGAACAGACTAATGTTACA
1 AAGTGAACAGACTAATGTTACA
* *
548745 AAGTGAACAGACTAATATTCCA
1 AAGTGAACAGACTAATGTTACA
*
548767 CAGTGAACAGACTAATGTTACA
1 AAGTGAACAGACTAATGTTACA
* *
548789 AAGTGAACAGACTAATATTACT
1 AAGTGAACAGACTAATGTTACA
* *
548811 CAGTGAACAGACTGATGTTACA
1 AAGTGAACAGACTAATGTTACA
*
548833 AAGTGAACAGACTAATATTACA
1 AAGTGAACAGACTAATGTTACA
*
548855 CAGTGAACAGACTAATGTTACA
1 AAGTGAACAGACTAATGTTACA
* *
548877 AAGTGAACAGACTAATATTACT
1 AAGTGAACAGACTAATGTTACA
* *
548899 CAGTGAAAAGACTAATGTTACA
1 AAGTGAACAGACTAATGTTACA
*
548921 AAGTGAACAGACTAATATTACA
1 AAGTGAACAGACTAATGTTACA
* *
548943 CAGTGAACAGACTAATGTTTCA
1 AAGTGAACAGACTAATGTTACA
*
548965 AATTGAACAGACTAATGTTA-A
1 AAGTGAACAGACTAATGTTACA
* *
548986 ATA-TAGAACA-AATAAATGTTATA
1 A-AGT-GAACAGACT-AATGTTACA
* * **
549009 AAGTGAACATATTAATGAAACA
1 AAGTGAACAGACTAATGTTACA
** *
549031 TGGTGTACAGACTAATGTTACA
1 AAGTGAACAGACTAATGTTACA
* * * * *
549053 TAGTGTACATATTAATGATACA
1 AAGTGAACAGACTAATGTTACA
* * *
549075 TAGTGTACATA-TCAATGTTACA
1 AAGTGAACAGACT-AATGTTACA
* * * *
549097 TAGTGTACATATTAATGTTACA
1 AAGTGAACAGACTAATGTTACA
** * * *
549119 TTGTGTACATATTAATGTTACA
1 AAGTGAACAGACTAATGTTACA
* * * *
549141 TAGTGTACAGGCTAAGGTTACA
1 AAGTGAACAGACTAATGTTACA
*
549163 TAGTG
1 AAGTG
549168 TACATATTAA
Statistics
Matches: 539, Mismatches: 96, Indels: 16
0.83 0.15 0.02
Matches are distributed among these distances:
21 6 0.01
22 527 0.98
23 6 0.01
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.27
Consensus pattern (22 bp):
AAGTGAACAGACTAATGTTACA
Found at i:548995 original size:44 final size:44
Alignment explanation
Indices: 548504--548980 Score: 801
Period size: 44 Copynumber: 10.8 Consensus size: 44
548494 GAATACATTA
* * *
548504 AGTGAACAGACTAATGTTACAAAGTGAGCAGGCTAATATTACTC
1 AGTGAACAGACTAATGTTACAAAGTGAACAGACTAATATTACAC
* *
548548 AGTGAAAAGACTAATGTTACAAAGTGAACAGACTAATATTCCAC
1 AGTGAACAGACTAATGTTACAAAGTGAACAGACTAATATTACAC
548592 AGTGAACAGACTAATGTTACAAAGTGAACAGACTAATATTACAC
1 AGTGAACAGACTAATGTTACAAAGTGAACAGACTAATATTACAC
* *
548636 AGTGAAAAGACTAATGTTACAAAGTGAACAGACTAATATTACTC
1 AGTGAACAGACTAATGTTACAAAGTGAACAGACTAATATTACAC
* * *
548680 AGTGAAAAGACTAATGTTACAAAGTGAGCAGGCTAATATTACAC
1 AGTGAACAGACTAATGTTACAAAGTGAACAGACTAATATTACAC
*
548724 AGTGAACAGACTAATGTTACAAAGTGAACAGACTAATATTCCAC
1 AGTGAACAGACTAATGTTACAAAGTGAACAGACTAATATTACAC
*
548768 AGTGAACAGACTAATGTTACAAAGTGAACAGACTAATATTACTC
1 AGTGAACAGACTAATGTTACAAAGTGAACAGACTAATATTACAC
*
548812 AGTGAACAGACTGATGTTACAAAGTGAACAGACTAATATTACAC
1 AGTGAACAGACTAATGTTACAAAGTGAACAGACTAATATTACAC
*
548856 AGTGAACAGACTAATGTTACAAAGTGAACAGACTAATATTACTC
1 AGTGAACAGACTAATGTTACAAAGTGAACAGACTAATATTACAC
*
548900 AGTGAAAAGACTAATGTTACAAAGTGAACAGACTAATATTACAC
1 AGTGAACAGACTAATGTTACAAAGTGAACAGACTAATATTACAC
* *
548944 AGTGAACAGACTAATGTTTCAAATTGAACAGACTAAT
1 AGTGAACAGACTAATGTTACAAAGTGAACAGACTAAT
548981 GTTAAATATA
Statistics
Matches: 406, Mismatches: 27, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 406 1.00
ACGTcount: A:0.44, C:0.15, G:0.17, T:0.24
Consensus pattern (44 bp):
AGTGAACAGACTAATGTTACAAAGTGAACAGACTAATATTACAC
Found at i:549085 original size:66 final size:66
Alignment explanation
Indices: 548559--549304 Score: 349
Period size: 66 Copynumber: 11.3 Consensus size: 66
548549 GTGAAAAGAC
* * * * * * * * * * * *
548559 TAATGTTACAAAGTGAACAGACTAATATTCCACAGTGAACAGACTAATGTTACAAAGTGAACAGA
1 TAATGTTACATAGTGTACAGACTAATGTTACATAGTGTACATATTAATGATACATAGTGTACATA
*
548624 C
66 T
* * * * * * * * * *
548625 TAATATTACACAGTGAAAAGACTAATGTTACAAAGTGAACAGACTAAT-ATTAC-TCAGTGAAAA
1 TAATGTTACATAGTGTACAGACTAATGTTACATAGTGTACATATTAATGA-TACAT-AGTGTACA
* *
548688 GAC
64 TAT
* * * * * * * * * * *
548691 TAATGTTACAAAGTG-AGCAGGCTAATATTACACAGTGAACAGACTAATGTTACAAAGTGAACAG
1 TAATGTTACATAGTGTA-CAGACTAATGTTACATAGTGTACATATTAATGATACATAGTGTACAT
*
548755 AC
65 AT
* * * * * * * * *
548757 TAATATTCCACAGTGAACAGACTAATGTTACAAAGTGAACAGACTAAT-ATTAC-TCAGTGAACA
1 TAATGTTACATAGTGTACAGACTAATGTTACATAGTGTACATATTAATGA-TACAT-AGTGTACA
* *
548820 GAC
64 TAT
* * * * * * * * * * * *
548823 TGATGTTACAAAGTGAACAGACTAATATTACACAGTGAACAGACTAATGTTACAAAGTGAACAGA
1 TAATGTTACATAGTGTACAGACTAATGTTACATAGTGTACATATTAATGATACATAGTGTACATA
*
548888 C
66 T
* * * * * * * * *
548889 TAATATTAC-TCAGTGAAAAGACTAATGTTACAAAGTGAACAGACTAAT-ATTACACAGTGAACA
1 TAATGTTACAT-AGTGTACAGACTAATGTTACATAGTGTACATATTAATGA-TACATAGTGTACA
* *
548952 GAC
64 TAT
* * * * * * * * * * * *
548955 TAATGTTTCAAATTGAACAGACTAATGTTAAATA-TAGAACAAATAAATGTTATAAAGTGAACAT
1 TAATGTTACATAGTGTACAGACTAATGTTACATAGT-GTACATATTAATGATACATAGTGTACAT
549019 AT
65 AT
** *
549021 TAATGAAACATGGTGTACAGACTAATGTTACATAGTGTACATATTAATGATACATAGTGTACATA
1 TAATGTTACATAGTGTACAGACTAATGTTACATAGTGTACATATTAATGATACATAGTGTACATA
549086 T
66 T
* * * * * **
549087 CAATGTTACATAGTGTACATATTAATGTTACATTGTGTACATATTAATGTTACATAGTGTACAGG
1 TAATGTTACATAGTGTACAGACTAATGTTACATAGTGTACATATTAATGATACATAGTGTACATA
*
549152 C
66 T
* * * * * * * * **
549153 TAAGGTTACATAGTGTACATATTAATGATACATGGTGTACAAAATAATGTAATATATAGTAAACA
1 TAATGTTACATAGTGTACAGACTAATGTTACATAGTGTACATATTAATG--ATACATAGTGTACA
*
549218 GAT
64 TAT
* * *
549221 GAATGATACATAGCGTACAGACTAATGTTACATAGTGTACATATTAATGATACATAGTGTACATA
1 TAATGTTACATAGTGTACAGACTAATGTTACATAGTGTACATATTAATGATACATAGTGTACATA
549286 T
66 T
*
549287 TAAT-TTACATGGTGTACA
1 TAATGTTACATAGTGTACA
549305 TATTAATGAA
Statistics
Matches: 549, Mismatches: 113, Indels: 37
0.79 0.16 0.05
Matches are distributed among these distances:
65 13 0.02
66 484 0.88
67 2 0.00
68 50 0.09
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.28
Consensus pattern (66 bp):
TAATGTTACATAGTGTACAGACTAATGTTACATAGTGTACATATTAATGATACATAGTGTACATA
T
Found at i:549168 original size:22 final size:22
Alignment explanation
Indices: 549000--549321 Score: 331
Period size: 22 Copynumber: 14.6 Consensus size: 22
548990 AGAACAAATA
* * *
549000 AATGTTATAAAGTGAACATATT
1 AATGTTACATAGTGTACATATT
** * * *
549022 AATGAAACATGGTGTACAGACT
1 AATGTTACATAGTGTACATATT
549044 AATGTTACATAGTGTACATATT
1 AATGTTACATAGTGTACATATT
* *
549066 AATGATACATAGTGTACATATC
1 AATGTTACATAGTGTACATATT
549088 AATGTTACATAGTGTACATATT
1 AATGTTACATAGTGTACATATT
*
549110 AATGTTACATTGTGTACATATT
1 AATGTTACATAGTGTACATATT
***
549132 AATGTTACATAGTGTACAGGCT
1 AATGTTACATAGTGTACATATT
*
549154 AAGGTTACATAGTGTACATATT
1 AATGTTACATAGTGTACATATT
* * * *
549176 AATGATACATGGTGTACAAAAT
1 AATGTTACATAGTGTACATATT
* ** * *
549198 AATGTAATATATAGTAAACAGATG
1 AATGT--TACATAGTGTACATATT
* * * *
549222 AATGATACATAGCGTACAGACT
1 AATGTTACATAGTGTACATATT
549244 AATGTTACATAGTGTACATATT
1 AATGTTACATAGTGTACATATT
*
549266 AATGATACATAGTGTACATATT
1 AATGTTACATAGTGTACATATT
*
549288 AAT-TTACATGGTGTACATATT
1 AATGTTACATAGTGTACATATT
**
549309 AATGAAACATAGT
1 AATGTTACATAGT
549322 TAAGAGAACG
Statistics
Matches: 241, Mismatches: 56, Indels: 6
0.80 0.18 0.02
Matches are distributed among these distances:
21 19 0.08
22 208 0.86
24 14 0.06
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (22 bp):
AATGTTACATAGTGTACATATT
Found at i:549486 original size:22 final size:22
Alignment explanation
Indices: 549461--549861 Score: 479
Period size: 22 Copynumber: 18.2 Consensus size: 22
549451 ATGATGCATG
* *
549461 GGACAAAGATTTATGATACAGA
1 GGACACAGACTTATGATACAGA
*
549483 GG--ACAGATTTATGATAAACACAGA
1 GGACACAGACTTATGAT----ACAGA
*
549507 GGACACAGACTTACGATACAGA
1 GGACACAGACTTATGATACAGA
**
549529 GGACACAGACTTATGATATGGA
1 GGACACAGACTTATGATACAGA
*
549551 GGACATAGACTTATGATACAGA
1 GGACACAGACTTATGATACAGA
* *
549573 AGACACAGACGTATGATACAGA
1 GGACACAGACTTATGATACAGA
** * *
549595 TAACATAGCCTTATGATACAGA
1 GGACACAGACTTATGATACAGA
549617 GGACACAGACTTATGATACAGA
1 GGACACAGACTTATGATACAGA
*
549639 AGACACAGACTTATGATACAGA
1 GGACACAGACTTATGATACAGA
* *
549661 AGACACAGACTTATGATACATA
1 GGACACAGACTTATGATACAGA
549683 GGACACAGACTTATGATACAGA
1 GGACACAGACTTATGATACAGA
* * * *
549705 TGACATAGCCTTATGATACAAA
1 GGACACAGACTTATGATACAGA
549727 GG--ACAGACTTATGATACAGA
1 GGACACAGACTTATGATACAGA
*
549747 AGACACAGACTTATGATACCA-A
1 GGACACAGACTTATGATA-CAGA
*
549769 GGACACAAACTTATGATACAGA
1 GGACACAGACTTATGATACAGA
*
549791 AGACACAGACTTATGATACAGA
1 GGACACAGACTTATGATACAGA
* **
549813 AGACACAGACTTATGATACCTA
1 GGACACAGACTTATGATACAGA
549835 GGACACAGACTTATGATACAGA
1 GGACACAGACTTATGATACAGA
*
549857 AGACA
1 GGACA
549862 ATTGGACAAA
Statistics
Matches: 325, Mismatches: 44, Indels: 20
0.84 0.11 0.05
Matches are distributed among these distances:
20 28 0.09
21 2 0.01
22 275 0.85
23 2 0.01
24 7 0.02
26 11 0.03
ACGTcount: A:0.43, C:0.17, G:0.20, T:0.20
Consensus pattern (22 bp):
GGACACAGACTTATGATACAGA
Found at i:552713 original size:45 final size:45
Alignment explanation
Indices: 552646--553102 Score: 564
Period size: 45 Copynumber: 10.1 Consensus size: 45
552636 AGATACTGGC
* **
552646 TGTACAACACATGATTAGAGATAGATATGCCACTCCCCCAGTAGT
1 TGTACAACACATGATTACAGATAGATACACCACTCCCCCAGTAGT
552691 TGTACAACACATGATTACAGATAGATACA-CATCTCCCCCAGTAGT
1 TGTACAACACATGATTACAGATAGATACACCA-CTCCCCCAGTAGT
* ** *
552736 TGTAAAACACATGATTACAGATAGATATGCCCCTCCCCCAGTAGT
1 TGTACAACACATGATTACAGATAGATACACCACTCCCCCAGTAGT
* * * *
552781 TGTTCAACACATGATTACAGATAGATATGTCTCTCTCCCCCCCCCCAGTAGT
1 TGTACAACACATGATTACAGATAGATA-------CACCACTCCCCCAGTAGT
* * * * *
552833 TGTACACCACATGATTACAGATGGATACACCTCTCCCCAAGAAGT
1 TGTACAACACATGATTACAGATAGATACACCACTCCCCCAGTAGT
*
552878 TGTACACCACATGATTACAGATAGATACA-C-CTCCCCCAGTAGT
1 TGTACAACACATGATTACAGATAGATACACCACTCCCCCAGTAGT
* * * *
552921 TGTACAACACATGATTACAGTTGGATACACCCCTCCCCCAGTGGT
1 TGTACAACACATGATTACAGATAGATACACCACTCCCCCAGTAGT
* *
552966 TGTAAAACACATGATTACAGATAGATACACCTCTCCCCCAGTAGT
1 TGTACAACACATGATTACAGATAGATACACCACTCCCCCAGTAGT
553011 TGTACAACACATGATTACAGATAGATACA-C-CTCCCCCAGTAGT
1 TGTACAACACATGATTACAGATAGATACACCACTCCCCCAGTAGT
* * * *
553054 TGTACAACACATGATTACAGTTGGATACACCCCTCCCCCAGTGGT
1 TGTACAACACATGATTACAGATAGATACACCACTCCCCCAGTAGT
553099 TGTA
1 TGTA
553103 NNNNNNNNNN
Statistics
Matches: 363, Mismatches: 36, Indels: 26
0.85 0.08 0.06
Matches are distributed among these distances:
43 77 0.21
44 6 0.02
45 240 0.66
46 1 0.00
52 39 0.11
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.25
Consensus pattern (45 bp):
TGTACAACACATGATTACAGATAGATACACCACTCCCCCAGTAGT
Found at i:552957 original size:88 final size:89
Alignment explanation
Indices: 552646--553102 Score: 587
Period size: 88 Copynumber: 5.0 Consensus size: 89
552636 AGATACTGGC
* ** *
552646 TGTACAACACATGATTAGAGATAGATATGCCACTCCCCCAGTAGTTGTACAACACATGATTACAG
1 TGTACAACACATGATTACAGATAGATACACCCCTCCCCCAGTAGTTGTACAACACATGATTACAG
552711 ATAGATACACATCTCCCCCAGTAGT
66 ATAGATACAC-TCTCCCCCAGTAGT
* ** *
552736 TGTAAAACACATGATTACAGATAGATATGCCCCTCCCCCAGTAGTTGTTCAACACATGATTACAG
1 TGTACAACACATGATTACAGATAGATACACCCCTCCCCCAGTAGTTGTACAACACATGATTACAG
*
552801 ATAGATATGTCTCTCTCCCCCCCCCCAGTAGT
66 ATAGATA---CACTCT-----CCCCCAGTAGT
* * * * * *
552833 TGTACACCACATGATTACAGATGGATACACCTCTCCCCAAGAAGTTGTACACCACATGATTACAG
1 TGTACAACACATGATTACAGATAGATACACCCCTCCCCCAGTAGTTGTACAACACATGATTACAG
552898 ATAGATACAC-CTCCCCCAGTAGT
66 ATAGATACACTCTCCCCCAGTAGT
* * * *
552921 TGTACAACACATGATTACAGTTGGATACACCCCTCCCCCAGTGGTTGTAAAACACATGATTACAG
1 TGTACAACACATGATTACAGATAGATACACCCCTCCCCCAGTAGTTGTACAACACATGATTACAG
552986 ATAGATACACCTCTCCCCCAGTAGT
66 ATAGATACA-CTCTCCCCCAGTAGT
553011 TGTACAACACATGATTACAGATAGATACA--CCTCCCCCAGTAGTTGTACAACACATGATTACAG
1 TGTACAACACATGATTACAGATAGATACACCCCTCCCCCAGTAGTTGTACAACACATGATTACAG
* * * *
553074 TTGGATACACCCCTCCCCCAGTGGT
66 ATAGATACA-CTCTCCCCCAGTAGT
553099 TGTA
1 TGTA
553103 NNNNNNNNNN
Statistics
Matches: 325, Mismatches: 32, Indels: 22
0.86 0.08 0.06
Matches are distributed among these distances:
88 134 0.41
89 1 0.00
90 108 0.33
92 3 0.01
93 4 0.01
94 2 0.01
97 73 0.22
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.25
Consensus pattern (89 bp):
TGTACAACACATGATTACAGATAGATACACCCCTCCCCCAGTAGTTGTACAACACATGATTACAG
ATAGATACACTCTCCCCCAGTAGT
Found at i:553012 original size:133 final size:133
Alignment explanation
Indices: 552646--553102 Score: 635
Period size: 133 Copynumber: 3.4 Consensus size: 133
552636 AGATACTGGC
* ** *
552646 TGTACAACACATGATTAGAGATAGATATGCCACTCCCCCAGTAGTTGTACAACACATGATTACAG
1 TGTACAACACATGATTACAGATAGATACACCCCTCCCCCAGTAGTTGTACAACACATGATTACAG
* * *
552711 ATAGATACACATCTCCCCCAGTAGTTGTAAAACACATGATTACAGATAGATATGCCCCTCCCCCA
66 ATAGATACACCTCTCCCCCAGTAGTTGTACAACACATGATTACAGATAGATA--CACCTCCCCCA
552776 GTAGT
129 GTAGT
* * * *
552781 TGTTCAACACATGATTACAGATAGATATGTCTCTCTCCCCCCCCCCAGTAGTTGTACACCACATG
1 TGTACAACACATGATTACAGATAGATA-------CACCCCTCCCCCAGTAGTTGTACAACACATG
* * * *
552846 ATTACAGATGGATACACCTCTCCCCAAGAAGTTGTACACCACATGATTACAGATAGATACACCTC
59 ATTACAGATAGATACACCTCTCCCCCAGTAGTTGTACAACACATGATTACAGATAGATACACCTC
552911 CCCCAGTAGT
124 CCCCAGTAGT
* * * *
552921 TGTACAACACATGATTACAGTTGGATACACCCCTCCCCCAGTGGTTGTAAAACACATGATTACAG
1 TGTACAACACATGATTACAGATAGATACACCCCTCCCCCAGTAGTTGTACAACACATGATTACAG
552986 ATAGATACACCTCTCCCCCAGTAGTTGTACAACACATGATTACAGATAGATACACCTCCCCCAGT
66 ATAGATACACCTCTCCCCCAGTAGTTGTACAACACATGATTACAGATAGATACACCTCCCCCAGT
553051 AGT
131 AGT
* * *
553054 TGTACAACACATGATTACAGTTGGATACACCCCTCCCCCAGTGGTTGTA
1 TGTACAACACATGATTACAGATAGATACACCCCTCCCCCAGTAGTTGTA
553103 NNNNNNNNNN
Statistics
Matches: 289, Mismatches: 26, Indels: 16
0.87 0.08 0.05
Matches are distributed among these distances:
133 146 0.51
135 25 0.09
140 39 0.13
142 79 0.27
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.25
Consensus pattern (133 bp):
TGTACAACACATGATTACAGATAGATACACCCCTCCCCCAGTAGTTGTACAACACATGATTACAG
ATAGATACACCTCTCCCCCAGTAGTTGTACAACACATGATTACAGATAGATACACCTCCCCCAGT
AGT
Found at i:554003 original size:45 final size:45
Alignment explanation
Indices: 553939--554086 Score: 271
Period size: 45 Copynumber: 3.3 Consensus size: 45
553929 NNNNNNNCCT
553939 CTCCCCCAGTAGTTGTACAACACATGATTACAGATAGATACACCC
1 CTCCCCCAGTAGTTGTACAACACATGATTACAGATAGATACACCC
*
553984 CTCCCCCAGTAGTTGTACAACACATGATTACAGATAGATACACCT
1 CTCCCCCAGTAGTTGTACAACACATGATTACAGATAGATACACCC
*
554029 CTCCCCCAGTAGTTGTACAACACATGATTACAGATAGATAC-GCC
1 CTCCCCCAGTAGTTGTACAACACATGATTACAGATAGATACACCC
554073 CTCCCCCAGTAGTT
1 CTCCCCCAGTAGTT
554087 TGTAGTACAC
Statistics
Matches: 100, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
44 15 0.15
45 85 0.85
ACGTcount: A:0.31, C:0.31, G:0.14, T:0.24
Consensus pattern (45 bp):
CTCCCCCAGTAGTTGTACAACACATGATTACAGATAGATACACCC
Found at i:554176 original size:56 final size:56
Alignment explanation
Indices: 554092--554228 Score: 202
Period size: 56 Copynumber: 2.4 Consensus size: 56
554082 TAGTTTGTAG
* * * *
554092 TACACCATGGCTTTCACTGTCACCGTAATGTTATAACAGACTCACCTGGTTTGCAA
1 TACAGCATGGCTTTGACTGGCACTGTAATGTTATAACAGACTCACCTGGTTTGCAA
* * * *
554148 TACAGTATGGCTTTGACTGGCACTGTAATGTTATAATAGACTCACCTGGTTTGTAG
1 TACAGCATGGCTTTGACTGGCACTGTAATGTTATAACAGACTCACCTGGTTTGCAA
554204 TACAGCATGGCTTTGACTGGCACTG
1 TACAGCATGGCTTTGACTGGCACTG
554229 GTTTAGCATC
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
56 72 1.00
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (56 bp):
TACAGCATGGCTTTGACTGGCACTGTAATGTTATAACAGACTCACCTGGTTTGCAA
Found at i:555948 original size:26 final size:26
Alignment explanation
Indices: 555919--556639 Score: 712
Period size: 26 Copynumber: 27.5 Consensus size: 26
555909 TTAGCCTTTA
* *
555919 TGACAAAACACTAATATTCCCCCTTC
1 TGACATAACACTAATATTCCCCCTCC
* * *
555945 TGACATTACACTAACTCTTACCCCTCC
1 TGACATAACACTAA-TATTCCCCCTCC
* **
555972 TGACATAATACTAATATTCCCATTCC
1 TGACATAACACTAATATTCCCCCTCC
* *
555998 TGACATAACACTAATATTCCTCCTTC
1 TGACATAACACTAATATTCCCCCTCC
* * *
556024 TGACATTACACTAACTCTTACCCCTCC
1 TGACATAACACTAA-TATTCCCCCTCC
*
556051 TGACATAACACTAATATTCCCACTCC
1 TGACATAACACTAATATTCCCCCTCC
*
556077 TGACATAACACTAATATTCCCACTCC
1 TGACATAACACTAATATTCCCCCTCC
**
556103 TGACATAACACTAATATTCCTACTCC
1 TGACATAACACTAATATTCCCCCTCC
* *
556129 TGACACAACACTAATATTCCCACTCC
1 TGACATAACACTAATATTCCCCCTCC
* *
556155 TGACATAACACTAATATTCCCACT-G
1 TGACATAACACTAATATTCCCCCTCC
**
556180 TGGACATAACACTAATATTCCCATTCC
1 T-GACATAACACTAATATTCCCCCTCC
* * *
556207 GGACATTACACTAATATTCCCACTCC
1 TGACATAACACTAATATTCCCCCTCC
* * *
556233 TAACATAACACTAATATTCCTCCTTC
1 TGACATAACACTAATATTCCCCCTCC
* * * *
556259 TGACATTACATTAACTCTTACCCCTCC
1 TGACATAACACTAA-TATTCCCCCTCC
* * **
556286 TGACAGT-ACACAAACTCTTAACCCTCC
1 TGACA-TAACACTAA-TATTCCCCCTCC
* *
556313 TGACAGT-ACACGAATATTCCCCCTTC
1 TGACA-TAACACTAATATTCCCCCTCC
* *
556339 TGACATAACACCAATATTCCCACTCC
1 TGACATAACACTAATATTCCCCCTCC
* * * *
556365 TGATATAACACTAATTTTCCCACACC
1 TGACATAACACTAATATTCCCCCTCC
* *
556391 TGACATAACACTTATATTCCCACTCC
1 TGACATAACACTAATATTCCCCCTCC
* * **
556417 TGACATAACCCTTATATTCCCCCTTT
1 TGACATAACACTAATATTCCCCCTCC
* * **
556443 TGACATTACACTAATTCTTAACCCTCC
1 TGACATAACACTAA-TATTCCCCCTCC
*
556470 TGACCA-AACACTAATATTCCCCCTTC
1 TGA-CATAACACTAATATTCCCCCTCC
* *
556496 TGACATAATACTAATATTCCCACTCC
1 TGACATAACACTAATATTCCCCCTCC
* * *
556522 TGACAAAATACTAATATTCCCCCTTC
1 TGACATAACACTAATATTCCCCCTCC
* * *
556548 TGACAAAACACTAATATTCTCCCTAC
1 TGACATAACACTAATATTCCCCCTCC
* * *
556574 TGACATAACACTAACTCTTTCTCCTCC
1 TGACATAACACTAA-TATTCCCCCTCC
*
556601 TGACATAACACTAATATTCCCACTCC
1 TGACATAACACTAATATTCCCCCTCC
556627 TGACATAACACTA
1 TGACATAACACTA
556640 GCATGTACCT
Statistics
Matches: 581, Mismatches: 103, Indels: 22
0.82 0.15 0.03
Matches are distributed among these distances:
25 4 0.01
26 451 0.78
27 123 0.21
28 3 0.01
ACGTcount: A:0.32, C:0.34, G:0.05, T:0.29
Consensus pattern (26 bp):
TGACATAACACTAATATTCCCCCTCC
Found at i:556362 original size:262 final size:258
Alignment explanation
Indices: 555920--556639 Score: 831
Period size: 262 Copynumber: 2.7 Consensus size: 258
555910 TAGCCTTTAT
* * *
555920 GACAAAACACTAATATTCCCCCTT-CTGACATTACACTAACTCTTACCCCTCCTGACATAATACT
1 GACATAACACTAATATT-ACCCTTCCTGACATTACACTAA-TATT-CCCCTCCTGACATAATACT
* * *
555984 AATATTCCCATTCCTGACATAACACTAATATTCCTCCTTCTGACATTACACTAACTCTTACCCCT
63 AATATTCCCCTT-CTGACATAACACTAATATTCC-CCTTCTGACAATACACTAACTCTTAACCCT
*
556049 CCTGACATAACACTAATATTCCCACTCCTGACATAACACTAATATTCCCACTCCTGACATAACAC
126 CCTGACATAACACTAATATTCCCCCTCCTGACATAACACTAATATTCCCACTCCTGACATAACAC
* *
556114 TAATATTCCTACTCCTGACACAACACTAATATTCCCACTCCTGACATAACACTAATATTCCCACT
191 TAATATTCCCACACCTGACACAACACTAATATTCCCACTCCTGACATAACACTAATATTCCCACT
556179 GTG
256 GTG
* * *
556182 GACATAACACTAATATT-CCCATTCCGGACATTACACTAATATTCCCACTCCTAACATAACACTA
1 GACATAACACTAATATTACCC-TTCCTGACATTACACTAATATTCCC-CTCCTGACATAATACTA
* * * * * *
556246 ATATTCCTCCTTCTGACATTACATTAACTCTTACCCCTCCTGACAGTACACAAACTCTTAACCCT
64 ATATTCC-CCTTCTGACATAACACTAA-TATT-CCCCTTCTGACAATACACTAACTCTTAACCCT
* * * *
556311 CCTGACAGT-ACACGAATATTCCCCCTTCTGACATAACACCAATATTCCCACTCCTGATATAACA
126 CCTGACA-TAACACTAATATTCCCCCTCCTGACATAACACTAATATTCCCACTCCTGACATAACA
* * * * * *
556375 CTAATTTTCCCACACCTGACATAACACTTATATTCCCACTCCTGACATAACCCTTATATTCCCCC
190 CTAATATTCCCACACCTGACACAACACTAATATTCCCACTCCTGACATAACACTAATATTCCCAC
* *
556440 TTTT
255 TGTG
* * * *
556444 GACATTACACTAATTCTTAACCC-TCCTGACCA-AACACTAATATTCCCCCTTCTGACATAATAC
1 GACATAACACTAA-TATT-ACCCTTCCTGA-CATTACACTAATATT-CCCCTCCTGACATAATAC
* * * * * **
556507 TAATATTCCCACTCCTGACAAAATACTAATATTCCCCCTTCTGACAAAACACTAA-TATTCTCCC
62 TAATATTCCC-CTTCTGACATAACACTAATATT-CCCCTTCTGACAATACACTAACTCTTAACCC
* * * *
556571 TACTGACATAACACTAACTCTTTCTCCTCCTGACATAACACTAATATTCCCACTCCTGACATAAC
125 TCCTGACATAACACTAA-TATTCCCCCTCCTGACATAACACTAATATTCCCACTCCTGACATAAC
556636 ACTA
189 ACTA
556640 GCATGTACCT
Statistics
Matches: 386, Mismatches: 57, Indels: 30
0.82 0.12 0.06
Matches are distributed among these distances:
260 7 0.02
261 59 0.15
262 256 0.66
263 56 0.15
264 5 0.01
265 3 0.01
ACGTcount: A:0.32, C:0.34, G:0.05, T:0.29
Consensus pattern (258 bp):
GACATAACACTAATATTACCCTTCCTGACATTACACTAATATTCCCCTCCTGACATAATACTAAT
ATTCCCCTTCTGACATAACACTAATATTCCCCTTCTGACAATACACTAACTCTTAACCCTCCTGA
CATAACACTAATATTCCCCCTCCTGACATAACACTAATATTCCCACTCCTGACATAACACTAATA
TTCCCACACCTGACACAACACTAATATTCCCACTCCTGACATAACACTAATATTCCCACTGTG
Found at i:558755 original size:16 final size:16
Alignment explanation
Indices: 558734--558766 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
558724 AACTAATTTC
*
558734 TGCCAAATATCATACA
1 TGCCAAATATAATACA
558750 TGCCAAATATAATACA
1 TGCCAAATATAATACA
558766 T
1 T
558767 TTACAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.45, C:0.21, G:0.06, T:0.27
Consensus pattern (16 bp):
TGCCAAATATAATACA
Found at i:561512 original size:34 final size:34
Alignment explanation
Indices: 561440--561580 Score: 115
Period size: 34 Copynumber: 4.1 Consensus size: 34
561430 CCTCAGCACT
* * * *
561440 TGATATCTTTGTATATCCACACTCA-TTGCAGCAC
1 TGATATCTATGTACATCCACACTCACAT-CAGTAC
* * *
561474 TGATATCTATGTACATCCACATTTACATCAGTAT
1 TGATATCTATGTACATCCACACTCACATCAGTAC
* ** *
561508 TGATATCTTTGTTTATCCACACTCACCTCAGTAC
1 TGATATCTATGTACATCCACACTCACATCAGTAC
** * *
561542 TGATATCTATGTTA-ATCTTCACTCACCTCAGCAC
1 TGATATCTATG-TACATCCACACTCACATCAGTAC
561576 TGATA
1 TGATA
561581 AACTGTTTTT
Statistics
Matches: 86, Mismatches: 19, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
34 84 0.98
35 2 0.02
ACGTcount: A:0.28, C:0.26, G:0.10, T:0.37
Consensus pattern (34 bp):
TGATATCTATGTACATCCACACTCACATCAGTAC
Found at i:561580 original size:68 final size:68
Alignment explanation
Indices: 561414--561580 Score: 176
Period size: 68 Copynumber: 2.4 Consensus size: 68
561404 ATTAAGTGTC
* * * *
561414 TGTATATCCAAACACACCTCAGCACTTGATATCTTTGTATATCCACACTCATTGCAGCACTGATA
1 TGTACATCCACACTCACCTCAGCAC-TGATATCTTTGTATATCCACACTCACTGCAGCACTGATA
561479 TCTA
65 TCTA
* * * * * * *
561483 TGTACATCCACATTTACATCAGTATTGATATCTTTGTTTATCCACACTCACCT-CAGTACTGATA
1 TGTACATCCACACTCACCTCAGCACTGATATCTTTGTATATCCACACTCA-CTGCAGCACTGATA
561547 TCTA
65 TCTA
**
561551 TGTTA-ATCTTCACTCACCTCAGCACTGATA
1 TG-TACATCCACACTCACCTCAGCACTGATA
561581 AACTGTTTTT
Statistics
Matches: 78, Mismatches: 18, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
68 58 0.74
69 20 0.26
ACGTcount: A:0.29, C:0.27, G:0.10, T:0.35
Consensus pattern (68 bp):
TGTACATCCACACTCACCTCAGCACTGATATCTTTGTATATCCACACTCACTGCAGCACTGATAT
CTA
Found at i:561926 original size:34 final size:34
Alignment explanation
Indices: 561883--561967 Score: 136
Period size: 34 Copynumber: 2.5 Consensus size: 34
561873 AAATGGTTCT
561883 ACCTCAGCACTGATATCAATGGTT-ATCTTCACTC
1 ACCTCAGCACTGATATCAAT-GTTCATCTTCACTC
* *
561917 ACCTCAGCACAGATATCAATGTTCATTTTCACTC
1 ACCTCAGCACTGATATCAATGTTCATCTTCACTC
561951 ACCTCAGCACTGATATC
1 ACCTCAGCACTGATATC
561968 CTTGTAGATC
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
33 3 0.06
34 44 0.94
ACGTcount: A:0.28, C:0.31, G:0.11, T:0.31
Consensus pattern (34 bp):
ACCTCAGCACTGATATCAATGTTCATCTTCACTC
Found at i:563947 original size:38 final size:38
Alignment explanation
Indices: 563905--563983 Score: 140
Period size: 38 Copynumber: 2.1 Consensus size: 38
563895 AGACGAATAA
*
563905 AAGATCATTGACTATGCTGAATAACCAGAGAGTGTTAT
1 AAGATCATTGACTATACTGAATAACCAGAGAGTGTTAT
*
563943 AAGATCATTGACTATACTGAATAACCAGCGAGTGTTAT
1 AAGATCATTGACTATACTGAATAACCAGAGAGTGTTAT
563981 AAG
1 AAG
563984 CAGATGTTAC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (38 bp):
AAGATCATTGACTATACTGAATAACCAGAGAGTGTTAT
Found at i:565894 original size:32 final size:32
Alignment explanation
Indices: 565871--567067 Score: 1966
Period size: 32 Copynumber: 37.6 Consensus size: 32
565861 TTGCCTATAA
565871 TAGATGGTTTGTAGTGTATTCCTTACCTAGAG
1 TAGATGGTTTGTAGTGTATTCCTTACCTAGAG
*
565903 TAGATAGTTT-TAGTGTATTCCTTACCTAGAG
1 TAGATGGTTTGTAGTGTATTCCTTACCTAGAG
565934 TAGATGGTTTGTAGTGTATTCCTTACCTAGAG
1 TAGATGGTTTGTAGTGTATTCCTTACCTAGAG
* *
565966 TTGATGGTTTGTAGTGTATTCCTTACGTAGAG
1 TAGATGGTTTGTAGTGTATTCCTTACCTAGAG
*
565998 TTGATGGTTTGTAGTGTATTCCTTACCTAGAG
1 TAGATGGTTTGTAGTGTATTCCTTACCTAGAG
566030 TAGATGGTTTGTAGTGTATTCCTTACCTAGAG
1 TAGATGGTTTGTAGTGTATTCCTTACCTAGAG
*
566062 TCGATGGTTTGTAGTGTATTCCTTACCTAGAG
1 TAGATGGTTTGTAGTGTATTCCTTACCTAGAG
566094 TAGATGGTTTGTAGTGTATTCCTTACCTAGAG
1 TAGATGGTTTGTAGTGTATTCCTTACCTAGAG
*
566126 TTGATGGTTTGTAGTGTATTCCTTACCTAGAG
1 TAGATGGTTTGTAGTGTATTCCTTACCTAGAG
*
566158 TTGATGGTTTGTAGTGTATTCCTTACCTAGAG
1 TAGATGGTTTGTAGTGTATTCCTTACCTAGAG
566190 TAGATGGTTTGTAGTGTATTCCTTACCTAGAG
1 TAGATGGTTTGTAGTGTATTCCTTACCTAGAG
*
566222 TAGATGGTTTGTAGTGTATTCCTTCCCTAGAG
1 TAGATGGTTTGTAGTGTATTCCTTACCTAGAG
*
566254 TAGATGGTTTGTAGTGTATTCCATACCTAGAG
1 TAGATGGTTTGTAGTGTATTCCTTACCTAGAG
566286 TCA-ATGGTTTGTAGTGTATTCCTTACCTAGAG
1 T-AGATGGTTTGTAGTGTATTCCTTACCTAGAG
566318 TAGATGGTTTGTAGTGTATTCCTTACCTAGAG
1 TAGATGGTTTGTAGTGTATTCCTTACCTAGAG
*
566350 TCA-ATGGTCTGTAGTGTATTCCTTACCTAGAG
1 T-AGATGGTTTGTAGTGTATTCCTTACCTAGAG
*
566382 TCGATGGTTTGTAGTGTATTCCTTACCTAGAG
1 TAGATGGTTTGTAGTGTATTCCTTACCTAGAG
** *
566414 TAGATGGTTTAAAGTATATTCCTTACCTAGAG
1 TAGATGGTTTGTAGTGTATTCCTTACCTAGAG
*
566446 TAGATGGTTTGTAGTGTATTCCTTCCCTAGAG
1 TAGATGGTTTGTAGTGTATTCCTTACCTAGAG
*
566478 TAAATGGTTTGTAGTGTATTCCTTACCTAGAG
1 TAGATGGTTTGTAGTGTATTCCTTACCTAGAG
566510 TAGATGGTTTGTAGTGTATTCCTTACCTAGAG
1 TAGATGGTTTGTAGTGTATTCCTTACCTAGAG
566542 TAGATGGTTTGTAGTGTATTCCTTACCTAGAG
1 TAGATGGTTTGTAGTGTATTCCTTACCTAGAG
* * *
566574 TTGATGGTCTGTTGTGTATTCCTTACCTAGAG
1 TAGATGGTTTGTAGTGTATTCCTTACCTAGAG
566606 TCA-ATGGTTTGTAGTGTATTCCTTACCTAGAG
1 T-AGATGGTTTGTAGTGTATTCCTTACCTAGAG
* *
566638 TAGATAGTTTGTAGTGTATTCCTTCCCTAGAG
1 TAGATGGTTTGTAGTGTATTCCTTACCTAGAG
* *
566670 TTGATGGTTTGTAGTGTATTCCTTCCCTAGAG
1 TAGATGGTTTGTAGTGTATTCCTTACCTAGAG
*
566702 TAGATGGTCTGTAGTGTATTCCTTACCTAGAG
1 TAGATGGTTTGTAGTGTATTCCTTACCTAGAG
*
566734 TCA-ATGTTTTGTAGTGTATTCCTTACCTAGAG
1 T-AGATGGTTTGTAGTGTATTCCTTACCTAGAG
*
566766 TAGATGGTTTGTAATGTATTCCTTACCTAGAG
1 TAGATGGTTTGTAGTGTATTCCTTACCTAGAG
*
566798 TAGATGGTTTGTAGTGTATTCCTGACCTAGAG
1 TAGATGGTTTGTAGTGTATTCCTTACCTAGAG
*
566830 TAGATGGTCTGTAGTGTATTCCTTACCTAGAG
1 TAGATGGTTTGTAGTGTATTCCTTACCTAGAG
566862 TAGATGGTTTGTAGTGTATTCCTTACCTAGAG
1 TAGATGGTTTGTAGTGTATTCCTTACCTAGAG
566894 TAGATGGTTTGTAGTGTATTCCTTACCTAGAG
1 TAGATGGTTTGTAGTGTATTCCTTACCTAGAG
566926 TAGATGGTTTGTAGTGTATTCCTTACCTAGAG
1 TAGATGGTTTGTAGTGTATTCCTTACCTAGAG
*
566958 TAGATGGTTTGTAGTGTATTCCTCACCTAGAG
1 TAGATGGTTTGTAGTGTATTCCTTACCTAGAG
* *
566990 TAGATAGTTTGTAGTGTATTCCGTACCT--AG
1 TAGATGGTTTGTAGTGTATTCCTTACCTAGAG
* * *
567020 -AG-T--TTTGTTGTTTATTCCTTACCTGGAG
1 TAGATGGTTTGTAGTGTATTCCTTACCTAGAG
*
567048 TAGATGTTTTGTAGTGTATT
1 TAGATGGTTTGTAGTGTATT
567068 ATTTTTTAAA
Statistics
Matches: 1091, Mismatches: 59, Indels: 30
0.92 0.05 0.03
Matches are distributed among these distances:
26 18 0.02
28 3 0.00
29 4 0.00
30 3 0.00
31 33 0.03
32 1027 0.94
33 3 0.00
ACGTcount: A:0.21, C:0.14, G:0.24, T:0.41
Consensus pattern (32 bp):
TAGATGGTTTGTAGTGTATTCCTTACCTAGAG
Found at i:567125 original size:32 final size:32
Alignment explanation
Indices: 567087--567147 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
567077 AAGGGAGTAG
* *
567087 TTGGTTTGCCGTGTATTTCTTACCTGGAGAAA
1 TTGGTTTGCAGTGTATTCCTTACCTGGAGAAA
567119 TTGGTTTGCAGTGTATTCCTTACCTGGAG
1 TTGGTTTGCAGTGTATTCCTTACCTGGAG
567148 TTTTCCGATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.16, C:0.16, G:0.26, T:0.41
Consensus pattern (32 bp):
TTGGTTTGCAGTGTATTCCTTACCTGGAGAAA
Found at i:567928 original size:32 final size:31
Alignment explanation
Indices: 567890--567990 Score: 100
Period size: 32 Copynumber: 3.3 Consensus size: 31
567880 GTTGTTACTC
*
567890 CTTACCTGGAGCAGATGGTTTGTAGTGTATA
1 CTTACCTGGAGTAGATGGTTTGTAGTGTATA
* * * *
567921 CTTTACCTGGAGTAGTTGATCTGT--TGT-TT
1 C-TTACCTGGAGTAGATGGTTTGTAGTGTATA
* *
567950 CTTACCTGTAGTAGATGGTTTGTAGTTTATA
1 CTTACCTGGAGTAGATGGTTTGTAGTGTATA
567981 CCTTACCTGG
1 -CTTACCTGG
567991 GTTTGTTGTT
Statistics
Matches: 53, Mismatches: 12, Indels: 9
0.72 0.16 0.12
Matches are distributed among these distances:
28 18 0.34
29 2 0.04
30 5 0.09
31 2 0.04
32 26 0.49
ACGTcount: A:0.19, C:0.15, G:0.25, T:0.42
Consensus pattern (31 bp):
CTTACCTGGAGTAGATGGTTTGTAGTGTATA
Found at i:567977 original size:28 final size:29
Alignment explanation
Indices: 567890--567978 Score: 90
Period size: 28 Copynumber: 3.0 Consensus size: 29
567880 GTTGTTACTC
*
567890 CTTACCTGGAGCAGATGGTTTGTAGTGTATA
1 CTTACCTGGAGTAGATGGTTTGTAGT-T-TA
* * * *
567921 CTTTACCTGGAGTAGTTGATCTGTTGTTT-
1 C-TTACCTGGAGTAGATGGTTTGTAGTTTA
*
567950 CTTACCTGTAGTAGATGGTTTGTAGTTTA
1 CTTACCTGGAGTAGATGGTTTGTAGTTTA
567979 TACCTTACCT
Statistics
Matches: 46, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
28 22 0.48
29 1 0.02
30 1 0.02
31 2 0.04
32 20 0.43
ACGTcount: A:0.19, C:0.12, G:0.26, T:0.43
Consensus pattern (29 bp):
CTTACCTGGAGTAGATGGTTTGTAGTTTA
Found at i:569590 original size:32 final size:32
Alignment explanation
Indices: 569549--569614 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
569539 TGCAAAGTGC
569549 GCGTTTTACCCAAGATTATTTACACAGAAATG
1 GCGTTTTACCCAAGATTATTTACACAGAAATG
569581 GCGTTTTACCCAAGATTATTTACACAGAAATG
1 GCGTTTTACCCAAGATTATTTACACAGAAATG
569613 GC
1 GC
569615 ATAAGAACAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (32 bp):
GCGTTTTACCCAAGATTATTTACACAGAAATG
Found at i:572970 original size:21 final size:21
Alignment explanation
Indices: 572946--573015 Score: 95
Period size: 21 Copynumber: 3.3 Consensus size: 21
572936 ACGCTTTGTC
*
572946 CGAAACGCTAAACGGTTTACA
1 CGAAACGCTAAACGGTTAACA
** * *
572967 CGAAACGCTTCACGATTCACA
1 CGAAACGCTAAACGGTTAACA
572988 CGAAACGCTAAACGGTTAACA
1 CGAAACGCTAAACGGTTAACA
573009 CGAAACG
1 CGAAACG
573016 TTTCTCGCAC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.39, C:0.27, G:0.19, T:0.16
Consensus pattern (21 bp):
CGAAACGCTAAACGGTTAACA
Found at i:574403 original size:2 final size:2
Alignment explanation
Indices: 574398--574433 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
574388 TTTTATAATA
574398 CT CT CT CT CT CT CT CT CT CT CT CT C- CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
574434 CGAGAGAAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:578628 original size:24 final size:24
Alignment explanation
Indices: 578596--578642 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
578586 AAGATTTTGT
578596 CTGGCACCAAGCATTCCAAGGAAA
1 CTGGCACCAAGCATTCCAAGGAAA
*
578620 CTGGCACCAAGCATTTCAAGGAA
1 CTGGCACCAAGCATTCCAAGGAA
578643 GGCTAACCTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.36, C:0.28, G:0.21, T:0.15
Consensus pattern (24 bp):
CTGGCACCAAGCATTCCAAGGAAA
Found at i:579327 original size:127 final size:127
Alignment explanation
Indices: 579101--579353 Score: 506
Period size: 127 Copynumber: 2.0 Consensus size: 127
579091 ATAAAGGTTT
579101 TGGCACATCTGTAAAAGGTCTCGATGGGTGAGTGGCATTATATATTATACTGTGGTCATCCTTCG
1 TGGCACATCTGTAAAAGGTCTCGATGGGTGAGTGGCATTATATATTATACTGTGGTCATCCTTCG
579166 AGGCATCAGAAAAGAGGCATCCGAAAACGCACTGTTTCCAAAATCTATTATACACAGATATG
66 AGGCATCAGAAAAGAGGCATCCGAAAACGCACTGTTTCCAAAATCTATTATACACAGATATG
579228 TGGCACATCTGTAAAAGGTCTCGATGGGTGAGTGGCATTATATATTATACTGTGGTCATCCTTCG
1 TGGCACATCTGTAAAAGGTCTCGATGGGTGAGTGGCATTATATATTATACTGTGGTCATCCTTCG
579293 AGGCATCAGAAAAGAGGCATCCGAAAACGCACTGTTTCCAAAATCTATTATACACAGATAT
66 AGGCATCAGAAAAGAGGCATCCGAAAACGCACTGTTTCCAAAATCTATTATACACAGATAT
579354 ATTGTAATCA
Statistics
Matches: 126, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
127 126 1.00
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.28
Consensus pattern (127 bp):
TGGCACATCTGTAAAAGGTCTCGATGGGTGAGTGGCATTATATATTATACTGTGGTCATCCTTCG
AGGCATCAGAAAAGAGGCATCCGAAAACGCACTGTTTCCAAAATCTATTATACACAGATATG
Found at i:583732 original size:38 final size:37
Alignment explanation
Indices: 583678--584303 Score: 689
Period size: 38 Copynumber: 16.5 Consensus size: 37
583668 ATCTACCTCG
583678 GATGACCTTGATATTTTCACTGTTTAAGCTTGACTTCA
1 GATGACCTTGATATTTTCACTGTTTAAGCTT-ACTTCA
* * * * * * *
583716 GATGACCTCGAAATTTTTACTGCTGAAGCTTTCCTTCT
1 GATGACCTTGATATTTTCACTGTTTAAGC-TTACTTCA
* * * **
583754 TATGACTTTAATATTTTCTTTGTTTAAGCTTTACTTCA
1 GATGACCTTGATATTTTCACTGTTTAAGC-TTACTTCA
*
583792 GATGACCTTGATATTTTCACTGTTTATGCCTTACTTCA
1 GATGACCTTGATATTTTCACTGTTTAAG-CTTACTTCA
* * * *
583830 AAGGACCTTGATATTTTCACTGTTAAAGCTTTGCTTCA
1 GATGACCTTGATATTTTCACTGTTTAAGC-TTACTTCA
* *
583868 GATGACCTTGATATTTTCACTGTTTATGCCTTCCTTCA
1 GATGACCTTGATATTTTCACTGTTTAAG-CTTACTTCA
* * * *
583906 GATGACCTTGGTATTTTCAGTGTTAAAGCTTTGCTTCA
1 GATGACCTTGATATTTTCACTGTTTAAGC-TTACTTCA
* *
583944 GATGACCTTGATATTTTCACTGTTAAAGCTTTACTGCA
1 GATGACCTTGATATTTTCACTGTTTAAGC-TTACTTCA
* *
583982 GATGACCTTGGTATTTTCACTGTTTATGCCTTACTTCA
1 GATGACCTTGATATTTTCACTGTTTAAG-CTTACTTCA
* *
584020 GATGACCTTGATATTTTCACTGTTTATGCCTTCCTTCA
1 GATGACCTTGATATTTTCACTGTTTAAG-CTTACTTCA
* * * *
584058 GATGACCTTGGTATTTTCAGTGTTAAAGCTTTGCTTCA
1 GATGACCTTGATATTTTCACTGTTTAAGC-TTACTTCA
* * *
584096 GATGACCTTGATATTTTCAGTGTTAAAGCTTTGCTTCA
1 GATGACCTTGATATTTTCACTGTTTAAGC-TTACTTCA
* *
584134 GATGACCTTGATATTTTCACTGTTAAAGCTTTGCTTCA
1 GATGACCTTGATATTTTCACTGTTTAAGC-TTACTTCA
*
584172 GATGACCTTGATATTTTCACTGTTTATGCCTTACTTCA
1 GATGACCTTGATATTTTCACTGTTTAAG-CTTACTTCA
584210 GATGACCTTGATATTTTCACTG-TTAATGCCTTACTTCA
1 GATGACCTTGATATTTTCACTGTTTAA-G-CTTACTTCA
* * *
584248 GACGACCTTGATATTTTCACTGTTAAAGCTCTACTACA
1 GATGACCTTGATATTTTCACTGTTTAAGCT-TACTTCA
584286 -ACTGACCTTGATAATTTT
1 GA-TGACCTTGAT-ATTTT
584304 GACAGTTTTT
Statistics
Matches: 510, Mismatches: 65, Indels: 25
0.85 0.11 0.04
Matches are distributed among these distances:
37 9 0.02
38 487 0.95
39 14 0.03
ACGTcount: A:0.23, C:0.19, G:0.15, T:0.43
Consensus pattern (37 bp):
GATGACCTTGATATTTTCACTGTTTAAGCTTACTTCA
Found at i:583882 original size:114 final size:114
Alignment explanation
Indices: 583678--584303 Score: 774
Period size: 114 Copynumber: 5.5 Consensus size: 114
583668 ATCTACCTCG
* * * * *
583678 GATGACCTTGATATTTTCACTGTTTAAG-CTTGACTTCAGATGACCTCGAAATTTTTACTGCTGA
1 GATGACCTTGATATTTTCACTGTTTAAGCCTT-ACTTCAGATGACCTTGATATTTTCACTGTTAA
* ** * * ** *
583742 AGCTTTCCTTCTTATGACTTTAATATTTTCTTTGTTTAAGCTTTACTTCA
65 AGCTTTACTTCAGATGACCTTGATATTTTCACTGTTTAAGCCTTACTTCA
* * *
583792 GATGACCTTGATATTTTCACTGTTTATGCCTTACTTCAAAGGACCTTGATATTTTCACTGTTAAA
1 GATGACCTTGATATTTTCACTGTTTAAGCCTTACTTCAGATGACCTTGATATTTTCACTGTTAAA
* * *
583857 GCTTTGCTTCAGATGACCTTGATATTTTCACTGTTTATGCCTTCCTTCA
66 GCTTTACTTCAGATGACCTTGATATTTTCACTGTTTAAGCCTTACTTCA
* * * * *
583906 GATGACCTTGGTATTTTCAGTGTTAAAGCTTTGCTTCAGATGACCTTGATATTTTCACTGTTAAA
1 GATGACCTTGATATTTTCACTGTTTAAGCCTTACTTCAGATGACCTTGATATTTTCACTGTTAAA
* * *
583971 GCTTTACTGCAGATGACCTTGGTATTTTCACTGTTTATGCCTTACTTCA
66 GCTTTACTTCAGATGACCTTGATATTTTCACTGTTTAAGCCTTACTTCA
* * * *
584020 GATGACCTTGATATTTTCACTGTTTATGCCTTCCTTCAGATGACCTTGGTATTTTCAGTGTTAAA
1 GATGACCTTGATATTTTCACTGTTTAAGCCTTACTTCAGATGACCTTGATATTTTCACTGTTAAA
* * * * *
584085 GCTTTGCTTCAGATGACCTTGATATTTTCAGTGTTAAAGCTTTGCTTCA
66 GCTTTACTTCAGATGACCTTGATATTTTCACTGTTTAAGCCTTACTTCA
* * * * *
584134 GATGACCTTGATATTTTCACTGTTAAAGCTTTGCTTCAGATGACCTTGATATTTTCACTGTTTAT
1 GATGACCTTGATATTTTCACTGTTTAAGCCTTACTTCAGATGACCTTGATATTTTCACTGTTAAA
*
584199 GCCTTACTTCAGATGACCTTGATATTTTCACTG-TTAATGCCTTACTTCA
66 GCTTTACTTCAGATGACCTTGATATTTTCACTGTTTAA-GCCTTACTTCA
* * *
584248 GACGACCTTGATATTTTCACTGTTAAAG-CTCTACTACA-ACTGACCTTGATAATTTT
1 GATGACCTTGATATTTTCACTGTTTAAGCCT-TACTTCAGA-TGACCTTGAT-ATTTT
584304 GACAGTTTTT
Statistics
Matches: 443, Mismatches: 64, Indels: 9
0.86 0.12 0.02
Matches are distributed among these distances:
113 5 0.01
114 430 0.97
115 8 0.02
ACGTcount: A:0.23, C:0.19, G:0.15, T:0.43
Consensus pattern (114 bp):
GATGACCTTGATATTTTCACTGTTTAAGCCTTACTTCAGATGACCTTGATATTTTCACTGTTAAA
GCTTTACTTCAGATGACCTTGATATTTTCACTGTTTAAGCCTTACTTCA
Found at i:583902 original size:152 final size:152
Alignment explanation
Indices: 583678--584303 Score: 860
Period size: 152 Copynumber: 4.1 Consensus size: 152
583668 ATCTACCTCG
* * * * * *
583678 GATGACCTTGATATTTTCACTGTTTAAGC-TTGACTTCAGATGACCTCGAAATTTTTACTGCTGA
1 GATGACCTTGATATTTTCACTGTTAAAGCTTTG-CTTCAGATGACCTTGATATTTTCACTGTTTA
* * ** * * ** *
583742 AGCTTTCCTTCTTATGACTTTAATATTTTCTTTGTTTAAGCTTTACTTCAGATGACCTTGATATT
65 TGCCTTCCTTCAGATGACCTTGATATTTTCAGTGTTAAAGCTTTACTTCAGATGACCTTGATATT
* * *
583807 TTCACTGTTTATGCCTTACTTCA
130 TTCACTGTTAAAGCTTTACTTCA
* *
583830 AAGGACCTTGATATTTTCACTGTTAAAGCTTTGCTTCAGATGACCTTGATATTTTCACTGTTTAT
1 GATGACCTTGATATTTTCACTGTTAAAGCTTTGCTTCAGATGACCTTGATATTTTCACTGTTTAT
* *
583895 GCCTTCCTTCAGATGACCTTGGTATTTTCAGTGTTAAAGCTTTGCTTCAGATGACCTTGATATTT
66 GCCTTCCTTCAGATGACCTTGATATTTTCAGTGTTAAAGCTTTACTTCAGATGACCTTGATATTT
*
583960 TCACTGTTAAAGCTTTACTGCA
131 TCACTGTTAAAGCTTTACTTCA
* * * * *
583982 GATGACCTTGGTATTTTCACTGTTTATGCCTTACTTCAGATGACCTTGATATTTTCACTGTTTAT
1 GATGACCTTGATATTTTCACTGTTAAAGCTTTGCTTCAGATGACCTTGATATTTTCACTGTTTAT
* *
584047 GCCTTCCTTCAGATGACCTTGGTATTTTCAGTGTTAAAGCTTTGCTTCAGATGACCTTGATATTT
66 GCCTTCCTTCAGATGACCTTGATATTTTCAGTGTTAAAGCTTTACTTCAGATGACCTTGATATTT
* *
584112 TCAGTGTTAAAGCTTTGCTTCA
131 TCACTGTTAAAGCTTTACTTCA
584134 GATGACCTTGATATTTTCACTGTTAAAGCTTTGCTTCAGATGACCTTGATATTTTCACTGTTTAT
1 GATGACCTTGATATTTTCACTGTTAAAGCTTTGCTTCAGATGACCTTGATATTTTCACTGTTTAT
* * * * *
584199 GCCTTACTTCAGATGACCTTGATATTTTCACTGTTAATGCCTTACTTCAGACGACCTTGATATTT
66 GCCTTCCTTCAGATGACCTTGATATTTTCAGTGTTAAAGCTTTACTTCAGATGACCTTGATATTT
* *
584264 TCACTGTTAAAGCTCTACTACA
131 TCACTGTTAAAGCTTTACTTCA
584286 -ACTGACCTTGATAATTTT
1 GA-TGACCTTGAT-ATTTT
584304 GACAGTTTTT
Statistics
Matches: 422, Mismatches: 49, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
151 1 0.00
152 413 0.98
153 8 0.02
ACGTcount: A:0.23, C:0.19, G:0.15, T:0.43
Consensus pattern (152 bp):
GATGACCTTGATATTTTCACTGTTAAAGCTTTGCTTCAGATGACCTTGATATTTTCACTGTTTAT
GCCTTCCTTCAGATGACCTTGATATTTTCAGTGTTAAAGCTTTACTTCAGATGACCTTGATATTT
TCACTGTTAAAGCTTTACTTCA
Found at i:584292 original size:76 final size:76
Alignment explanation
Indices: 583678--584303 Score: 779
Period size: 76 Copynumber: 8.2 Consensus size: 76
583668 ATCTACCTCG
* * * * * * *
583678 GATGACCTTGATATTTTCACTGTTTAAGCTTGACTTCAGATGACCTCGAAATTTTTACTGCTGAA
1 GATGACCTTGATATTTTCACTGTTAAAGCTTTACTTCAGATGACCTTGATATTTTCACTGTTTAA
* * *
583743 GCTTTCCTTCT
66 GCCTTACTTCA
* * * ** * *
583754 TATGACTTTAATATTTTCTTTGTTTAAGCTTTACTTCAGATGACCTTGATATTTTCACTGTTTAT
1 GATGACCTTGATATTTTCACTGTTAAAGCTTTACTTCAGATGACCTTGATATTTTCACTGTTTAA
583819 GCCTTACTTCA
66 GCCTTACTTCA
* * * *
583830 AAGGACCTTGATATTTTCACTGTTAAAGCTTTGCTTCAGATGACCTTGATATTTTCACTGTTTAT
1 GATGACCTTGATATTTTCACTGTTAAAGCTTTACTTCAGATGACCTTGATATTTTCACTGTTTAA
*
583895 GCCTTCCTTCA
66 GCCTTACTTCA
* * * *
583906 GATGACCTTGGTATTTTCAGTGTTAAAGCTTTGCTTCAGATGACCTTGATATTTTCACTGTTAAA
1 GATGACCTTGATATTTTCACTGTTAAAGCTTTACTTCAGATGACCTTGATATTTTCACTGTTTAA
* *
583971 GCTTTACTGCA
66 GCCTTACTTCA
* * * * *
583982 GATGACCTTGGTATTTTCACTGTTTATGCCTTACTTCAGATGACCTTGATATTTTCACTGTTTAT
1 GATGACCTTGATATTTTCACTGTTAAAGCTTTACTTCAGATGACCTTGATATTTTCACTGTTTAA
*
584047 GCCTTCCTTCA
66 GCCTTACTTCA
* * * * *
584058 GATGACCTTGGTATTTTCAGTGTTAAAGCTTTGCTTCAGATGACCTTGATATTTTCAGTGTTAAA
1 GATGACCTTGATATTTTCACTGTTAAAGCTTTACTTCAGATGACCTTGATATTTTCACTGTTTAA
* *
584123 GCTTTGCTTCA
66 GCCTTACTTCA
* *
584134 GATGACCTTGATATTTTCACTGTTAAAGCTTTGCTTCAGATGACCTTGATATTTTCACTGTTTAT
1 GATGACCTTGATATTTTCACTGTTAAAGCTTTACTTCAGATGACCTTGATATTTTCACTGTTTAA
584199 GCCTTACTTCA
66 GCCTTACTTCA
* * * *
584210 GATGACCTTGATATTTTCACTGTTAATGCCTTACTTCAGACGACCTTGATATTTTCACTGTTAAA
1 GATGACCTTGATATTTTCACTGTTAAAGCTTTACTTCAGATGACCTTGATATTTTCACTGTTTAA
*
584275 G-CTCTACTACA
66 GCCT-TACTTCA
584286 -ACTGACCTTGATAATTTT
1 GA-TGACCTTGAT-ATTTT
584304 GACAGTTTTT
Statistics
Matches: 480, Mismatches: 67, Indels: 5
0.87 0.12 0.01
Matches are distributed among these distances:
75 3 0.01
76 472 0.98
77 5 0.01
ACGTcount: A:0.23, C:0.19, G:0.15, T:0.43
Consensus pattern (76 bp):
GATGACCTTGATATTTTCACTGTTAAAGCTTTACTTCAGATGACCTTGATATTTTCACTGTTTAA
GCCTTACTTCA
Found at i:598953 original size:38 final size:38
Alignment explanation
Indices: 598902--599014 Score: 199
Period size: 38 Copynumber: 3.0 Consensus size: 38
598892 GAAACACAAC
*
598902 TAGGATTCATACGATGAAATCATCTATGCTGTTCAATG
1 TAGGATTCATACGATGAAATCATCTATGCTGATCAATG
598940 TAGGATTCATACGATGAAATCATCTATGCTGATCAATG
1 TAGGATTCATACGATGAAATCATCTATGCTGATCAATG
* *
598978 TAGGATTCGTATGATGAAATCATCTATGCTGATCAAT
1 TAGGATTCATACGATGAAATCATCTATGCTGATCAAT
599015 TAAAGAAATG
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
38 72 1.00
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.34
Consensus pattern (38 bp):
TAGGATTCATACGATGAAATCATCTATGCTGATCAATG
Found at i:604874 original size:16 final size:16
Alignment explanation
Indices: 604853--604892 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
604843 AGTATCTAGG
*
604853 TTAATGCAGAAATAAT
1 TTAATGAAGAAATAAT
604869 TTAATGAAGAAATAAT
1 TTAATGAAGAAATAAT
604885 TTAATGAA
1 TTAATGAA
604893 ACTATTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.53, C:0.03, G:0.12, T:0.33
Consensus pattern (16 bp):
TTAATGAAGAAATAAT
Found at i:610586 original size:2 final size:2
Alignment explanation
Indices: 610579--610631 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
610569 ATATTTTTAA
*
610579 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
610621 TC TC TC TC TC T
1 TC TC TC TC TC T
610632 GCTAATTCGT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:616612 original size:16 final size:17
Alignment explanation
Indices: 616579--616613 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
616569 GTGGGACACA
616579 TATTTCCTTGTATACAG
1 TATTTCCTTGTATACAG
616596 TATTTCCTTGT-TACAG
1 TATTTCCTTGTATACAG
616612 TA
1 TA
616614 CATTAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.23, C:0.17, G:0.11, T:0.49
Consensus pattern (17 bp):
TATTTCCTTGTATACAG
Found at i:624770 original size:317 final size:312
Alignment explanation
Indices: 624199--624827 Score: 1195
Period size: 317 Copynumber: 2.0 Consensus size: 312
624189 TTTAGGGTGG
* *
624199 GTATTCTTGGTATTGTACATTATTCATGAAACTTAAGGTACAATGGAGGTCTGAACAAAACTGGA
1 GTATTCTTGGTATTGAACATTAATCATGAAACTTAAGGTACAATGGAGGTCTGAACAAAACTGGA
624264 GGCATTGTCTGCTGCATTACATTGGATTGGTTATACAAGTAATTCATTTTATTTCTAAATACATG
66 GGCATTGTCTGCTGCATTACATTGGATTGGTTATACAAGTAATTCATTTTATTTCTAAATACATG
624329 GGTGTGGCATCTAAGTGATGTTCAAGATCAATGGTTTGACATGTTCTTGCCAAATATACTGTGCA
131 GGTGTGGCATCTAAGTGATGTTCAAGATCAATGGTTTGACATGTTCTTGCCAAATATACTGTGCA
624394 CTCTTTCTATTTCTAATATCTTTATGATCAGTTATATGCATCTTTTAATAATACTAAGCATTTTT
196 CTCTTTCTATTTCTAATATCTTTATGATCAGTTATATGCATCTTTTAATAATACTAAGCATTTTT
624459 GACTTTACATATTGTGAATTTATATAATGCGCAATGTATTTTGATTTTAAAA
261 GACTTTACATATTGTGAATTTATATAATGCGCAATGTATTTTGATTTTAAAA
624511 NGTATTCTTGGTATTGAACATTAATCATGAAACTTAAGGTACAATGGAGGTCTGAAATAACAAAA
1 -GTATTCTTGGTATTGAACATTAATCATGAAACTTAAGGTACAATGGAGGTCTG----AACAAAA
624576 CTGGAGGCATTGTCTGCTGCATTACATTGGATTGGTTATACAAGTAATTCATTTTATTTCTAAAT
61 CTGGAGGCATTGTCTGCTGCATTACATTGGATTGGTTATACAAGTAATTCATTTTATTTCTAAAT
624641 ACATGGGTGTGGCATCTAAGTGATGTTCAAGATCAATGGTTTGACATGTTCTTGCCAAATATACT
126 ACATGGGTGTGGCATCTAAGTGATGTTCAAGATCAATGGTTTGACATGTTCTTGCCAAATATACT
624706 GTGCACTCTTTCTATTTCTAATATCTTTATGATCAGTTATATGCATCTTTTAATAATACTAAGCA
191 GTGCACTCTTTCTATTTCTAATATCTTTATGATCAGTTATATGCATCTTTTAATAATACTAAGCA
624771 TTTTTGACTTTACATATTGTGAATTTATATAATGCGCAATGTATTTTGATTTTAAAA
256 TTTTTGACTTTACATATTGTGAATTTATATAATGCGCAATGTATTTTGATTTTAAAA
624828 TGAAAAACTC
Statistics
Matches: 310, Mismatches: 2, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
313 51 0.16
317 259 0.84
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.40
Consensus pattern (312 bp):
GTATTCTTGGTATTGAACATTAATCATGAAACTTAAGGTACAATGGAGGTCTGAACAAAACTGGA
GGCATTGTCTGCTGCATTACATTGGATTGGTTATACAAGTAATTCATTTTATTTCTAAATACATG
GGTGTGGCATCTAAGTGATGTTCAAGATCAATGGTTTGACATGTTCTTGCCAAATATACTGTGCA
CTCTTTCTATTTCTAATATCTTTATGATCAGTTATATGCATCTTTTAATAATACTAAGCATTTTT
GACTTTACATATTGTGAATTTATATAATGCGCAATGTATTTTGATTTTAAAA
Found at i:630849 original size:166 final size:167
Alignment explanation
Indices: 630575--630997 Score: 724
Period size: 167 Copynumber: 2.5 Consensus size: 167
630565 NNNNNNNNNN
* * * *
630575 GATTGGTACAAAAATACATCCCACGATATAGCATGCC-TATACAAATACTGTGTAAAAATTTCAA
1 GATTGGTACAAAAATATATCCCACGATATGGCATGCCTTA-ACAAACACTGTGTTAAAATTTCAA
* * *
630639 GCATCTGCGATAAACAGTTGCTTAGAATTCTTTGACGGAAATTTGTTTGAAAATTTTGGCT-AAA
65 GCATCTGCGATAAACAGTTGCTGAGAAATCTTTGACGAAAATTTGTTTGAAAATTTTGGCTAAAA
*
630703 AATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCT
130 AATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCC
630741 GATTGGTACAAAAATATATCCCACGATATGGCATGCCTTAACAAACACTGTGTTAAAATTTCAAG
1 GATTGGTACAAAAATATATCCCACGATATGGCATGCCTTAACAAACACTGTGTTAAAATTTCAAG
*
630806 CATCTGCGATAAACAGTTGCTGAGAAATCTTTGACGAAAATTTGTTTGAAAATTTTGGTTAAAAA
66 CATCTGCGATAAACAGTTGCTGAGAAATCTTTGACGAAAATTTGTTTGAAAATTTTGGCTAAAAA
*
630871 ATAAGCAAAGTCGTCATTTAACAGGAAGTTGACGTCC
131 ATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCC
630908 GATTGGTACAAAAATATATCCCACGATATGGCATGCCTTAACAAACACTGTGTTAAAATTTCAAG
1 GATTGGTACAAAAATATATCCCACGATATGGCATGCCTTAACAAACACTGTGTTAAAATTTCAAG
*
630973 CATCTGCGATAAATAGTTGCTGAGA
66 CATCTGCGATAAACAGTTGCTGAGA
630998 TAAATGCGAC
Statistics
Matches: 244, Mismatches: 11, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
166 114 0.47
167 130 0.53
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.29
Consensus pattern (167 bp):
GATTGGTACAAAAATATATCCCACGATATGGCATGCCTTAACAAACACTGTGTTAAAATTTCAAG
CATCTGCGATAAACAGTTGCTGAGAAATCTTTGACGAAAATTTGTTTGAAAATTTTGGCTAAAAA
ATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCC
Found at i:631041 original size:8 final size:8
Alignment explanation
Indices: 631028--631083 Score: 67
Period size: 8 Copynumber: 7.0 Consensus size: 8
631018 GTTACGGACG
631028 GACAGACA
1 GACAGACA
631036 GACAGACA
1 GACAGACA
* **
631044 GACGGAGG
1 GACAGACA
* *
631052 GACGGACG
1 GACAGACA
631060 GACAGACA
1 GACAGACA
631068 GACAGACA
1 GACAGACA
631076 GACAGACA
1 GACAGACA
631084 CACAAGGGTA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
8 42 1.00
ACGTcount: A:0.43, C:0.23, G:0.34, T:0.00
Consensus pattern (8 bp):
GACAGACA
Found at i:631045 original size:12 final size:12
Alignment explanation
Indices: 631028--631083 Score: 67
Period size: 12 Copynumber: 4.7 Consensus size: 12
631018 GTTACGGACG
631028 GACAGACAGACA
1 GACAGACAGACA
* **
631040 GACAGACGGAGG
1 GACAGACAGACA
* *
631052 GACGGACGGACA
1 GACAGACAGACA
631064 GACAGACAGACA
1 GACAGACAGACA
631076 GACAGACA
1 GACAGACA
631084 CACAAGGGTA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.43, C:0.23, G:0.34, T:0.00
Consensus pattern (12 bp):
GACAGACAGACA
Found at i:634185 original size:112 final size:113
Alignment explanation
Indices: 633989--634211 Score: 403
Period size: 112 Copynumber: 2.0 Consensus size: 113
633979 TGACACATTT
*
633989 AAAATAAAAAGATGGAGGTGATTTAAATAAATAGGAAAAAAATATGTGTAGAAAAGTTCTTTAGA
1 AAAATAAAAAGATGGAAGTGATTTAAATAAATAGGAAAAAAATATGTGTAGAAAAGTTCTTTAGA
*
634054 TGCAAAATGAATAGCTGATGAAAAGTTTTGTAGATAAACGAAACAATA
66 TGAAAAATGAATAGCTGATGAAAAGTTTTGTAGATAAACGAAACAATA
634102 AAAATAAAAAGATGGAAGTGATTTAAATAAATAGG-AAAAAATATGTGTAGAAAAGTTCTTTAGA
1 AAAATAAAAAGATGGAAGTGATTTAAATAAATAGGAAAAAAATATGTGTAGAAAAGTTCTTTAGA
* *
634166 TGAAAAATGAATGGCTGATGAAAAGTTTTGTAGATAAATGAAACAA
66 TGAAAAATGAATAGCTGATGAAAAGTTTTGTAGATAAACGAAACAA
634212 ATACTGTTAA
Statistics
Matches: 106, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
112 72 0.68
113 34 0.32
ACGTcount: A:0.51, C:0.04, G:0.20, T:0.26
Consensus pattern (113 bp):
AAAATAAAAAGATGGAAGTGATTTAAATAAATAGGAAAAAAATATGTGTAGAAAAGTTCTTTAGA
TGAAAAATGAATAGCTGATGAAAAGTTTTGTAGATAAACGAAACAATA
Found at i:635202 original size:2 final size:2
Alignment explanation
Indices: 635189--635264 Score: 129
Period size: 2 Copynumber: 39.0 Consensus size: 2
635179 TTCTAGTTTA
*
635189 TC TC TC TT TC TC TC TC TC TC TC TC -C TC TC TC TC TC TC -C TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
635229 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
635265 ATATAAGAAC
Statistics
Matches: 70, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
1 2 0.03
2 68 0.97
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:652350 original size:91 final size:90
Alignment explanation
Indices: 652195--652375 Score: 344
Period size: 91 Copynumber: 2.0 Consensus size: 90
652185 TTAATTTTTT
*
652195 TTTAAATATTTTCGAAGTACAAACGATGTGTCAGCTCCAAACTTGCCCTGTATTACTTATTGTCT
1 TTTAAATATTTTCGAAGTACAAACGATCTGTCAGCTCCAAACTTGCCCTGTATTACTTATTGTCT
652260 AACGTCCGTCTTGTCGAAATGTGTC
66 AACGTCCGTCTTGTCGAAATGTGTC
652285 NTTTAAATATTTTCGAAGTACAAACGATCTGTCAGCTCCAAACTTGCCCTGTATTACTTATTGTC
1 -TTTAAATATTTTCGAAGTACAAACGATCTGTCAGCTCCAAACTTGCCCTGTATTACTTATTGTC
652350 TAACGTCCGTCTTGTCGAAATGTGTC
65 TAACGTCCGTCTTGTCGAAATGTGTC
652376 GTTCAGCATT
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
91 89 1.00
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.36
Consensus pattern (90 bp):
TTTAAATATTTTCGAAGTACAAACGATCTGTCAGCTCCAAACTTGCCCTGTATTACTTATTGTCT
AACGTCCGTCTTGTCGAAATGTGTC
Found at i:663317 original size:21 final size:21
Alignment explanation
Indices: 663291--663403 Score: 108
Period size: 21 Copynumber: 5.4 Consensus size: 21
663281 AAAATATTTT
*
663291 TTTCGCAAATAAACGCGTAAC
1 TTTCGCGAATAAACGCGTAAC
*
663312 TTTCGCGAATAAAC-CTGAAAC
1 TTTCGCGAATAAACGC-GTAAC
* *
663333 TTTCGTG-ATATAACGCGTAAG
1 TTTCGCGAATA-AACGCGTAAC
* *
663354 TTTCGCGAATAAACGCGTTAG
1 TTTCGCGAATAAACGCGTAAC
*
663375 TTTCGTGAATAAACGCG-AA-
1 TTTCGCGAATAAACGCGTAAC
663394 TTTACGCGAA
1 TTT-CGCGAA
663404 ACTATTATAT
Statistics
Matches: 77, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
19 3 0.04
20 10 0.13
21 60 0.78
22 4 0.05
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.27
Consensus pattern (21 bp):
TTTCGCGAATAAACGCGTAAC
Found at i:663379 original size:42 final size:41
Alignment explanation
Indices: 663298--663403 Score: 119
Period size: 42 Copynumber: 2.5 Consensus size: 41
663288 TTTTTTCGCA
663298 AATAAACGCGTAACTTTCGCGAATAAACCTGAAACTTTCGTG
1 AATAAACGCGTAA-TTTCGCGAATAAACCTGAAACTTTCGTG
** *
663340 -ATATAACGCGTAAGTTTCGCGAATAAACGC-GTTAGTTTCGTG
1 AATA-AACGCGTAA-TTTCGCGAATAAAC-CTGAAACTTTCGTG
663382 AATAAACGCG-AATTTACGCGAA
1 AATAAACGCGTAATTT-CGCGAA
663404 ACTATTATAT
Statistics
Matches: 56, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
40 3 0.05
41 11 0.20
42 38 0.68
43 4 0.07
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (41 bp):
AATAAACGCGTAATTTCGCGAATAAACCTGAAACTTTCGTG
Found at i:664296 original size:21 final size:21
Alignment explanation
Indices: 664270--664519 Score: 263
Period size: 21 Copynumber: 11.9 Consensus size: 21
664260 ATTTATATTT
*
664270 AAGTTTCGCATTTATTCGCGA
1 AAGTTTCGCGTTTATTCGCGA
*
664291 AAGTTTTGCGTTTATTCGCGA
1 AAGTTTCGCGTTTATTCGCGA
* *
664312 AACTAAT-GCGTTATATT-GCGA
1 AAGT-TTCGCGTT-TATTCGCGA
664333 AAGTTTCGCGTTTATTCGCGA
1 AAGTTTCGCGTTTATTCGCGA
* * *
664354 AACTTACGCGTTTAATCGCGA
1 AAGTTTCGCGTTTATTCGCGA
*
664375 AAGTTTTGCGTTTATTCGCGA
1 AAGTTTCGCGTTTATTCGCGA
* **
664396 AACTCACGCG-TTATATCGCGA
1 AAGTTTCGCGTTTAT-TCGCGA
*
664417 AAGTTTCACGTTTATTCGCGA
1 AAGTTTCGCGTTTATTCGCGA
* *
664438 AAGTTACGCGTTTATTTGCGA
1 AAGTTTCGCGTTTATTCGCGA
* *
664459 AAGTTTCGCGTTCATTTGCGA
1 AAGTTTCGCGTTTATTCGCGA
* * *
664480 AACTTACGCGTTTAATCGCGA
1 AAGTTTCGCGTTTATTCGCGA
* *
664501 AAGTTTTGCATTTATTCGC
1 AAGTTTCGCGTTTATTCGC
664520 AAAAAAAAAA
Statistics
Matches: 187, Mismatches: 36, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
20 9 0.05
21 169 0.90
22 9 0.05
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (21 bp):
AAGTTTCGCGTTTATTCGCGA
Found at i:664334 original size:42 final size:41
Alignment explanation
Indices: 664280--664519 Score: 309
Period size: 42 Copynumber: 5.7 Consensus size: 41
664270 AAGTTTCGCA
* * *
664280 TTTATTCGCGAAAGTTTTGCGTTTATTCGCGAAACTAATGCG
1 TTTA-TCGCGAAAGTTTCGCGTTTATTCGCGAAACTTACGCG
*
664322 TTATATTGCGAAAGTTTCGCGTTTATTCGCGAAACTTACGCG
1 TT-TATCGCGAAAGTTTCGCGTTTATTCGCGAAACTTACGCG
* *
664364 TTTAATCGCGAAAGTTTTGCGTTTATTCGCGAAACTCACGCG
1 TTT-ATCGCGAAAGTTTCGCGTTTATTCGCGAAACTTACGCG
* *
664406 TTATATCGCGAAAGTTTCACGTTTATTCGCGAAAGTTACGCG
1 TT-TATCGCGAAAGTTTCGCGTTTATTCGCGAAACTTACGCG
* * *
664448 TTTATTTGCGAAAGTTTCGCGTTCATTTGCGAAACTTACGCG
1 TTTA-TCGCGAAAGTTTCGCGTTTATTCGCGAAACTTACGCG
* *
664490 TTTAATCGCGAAAGTTTTGCATTTATTCGC
1 TTT-ATCGCGAAAGTTTCGCGTTTATTCGC
664520 AAAAAAAAAA
Statistics
Matches: 172, Mismatches: 21, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
41 3 0.02
42 165 0.96
43 4 0.02
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.37
Consensus pattern (41 bp):
TTTATCGCGAAAGTTTCGCGTTTATTCGCGAAACTTACGCG
Found at i:664382 original size:84 final size:84
Alignment explanation
Indices: 664280--664519 Score: 347
Period size: 84 Copynumber: 2.9 Consensus size: 84
664270 AAGTTTCGCA
* *
664280 TTTATTCGCGAAAGTTTTGCGTTTATTCGCGAAACTAATGCGTTATATTGCGAAAGTTTCGCGTT
1 TTTATTCGCGAAAGTTTTGCGTTTATTCGCGAAACTAACGCGTTATATCGCGAAAGTTTCGCGTT
664345 TATTCGCGAAACTTACGCG
66 TATTCGCGAAACTTACGCG
* * *
664364 TTTAATCGCGAAAGTTTTGCGTTTATTCGCGAAACTCACGCGTTATATCGCGAAAGTTTCACGTT
1 TTTATTCGCGAAAGTTTTGCGTTTATTCGCGAAACTAACGCGTTATATCGCGAAAGTTTCGCGTT
*
664429 TATTCGCGAAAGTTACGCG
66 TATTCGCGAAACTTACGCG
* * * * * * *
664448 TTTATTTGCGAAAGTTTCGCGTTCATTTGCGAAACTTACGCGTT-TAATCGCGAAAGTTTTGCAT
1 TTTATTCGCGAAAGTTTTGCGTTTATTCGCGAAACTAACGCGTTAT-ATCGCGAAAGTTTCGCGT
664512 TTATTCGC
65 TTATTCGC
664520 AAAAAAAAAA
Statistics
Matches: 140, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
83 1 0.01
84 139 0.99
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.37
Consensus pattern (84 bp):
TTTATTCGCGAAAGTTTTGCGTTTATTCGCGAAACTAACGCGTTATATCGCGAAAGTTTCGCGTT
TATTCGCGAAACTTACGCG
Found at i:670614 original size:37 final size:37
Alignment explanation
Indices: 670505--671380 Score: 1334
Period size: 37 Copynumber: 24.4 Consensus size: 37
670495 TGGATGTTTG
*
670505 CTACATTACTTTTGTAC-A-AAA-TACATGTAATGCA
1 CTACATTACTCTTGTACAACAAACTACATGTAATGCA
670539 CTACATTACTCTTGTAC-A-AAA-TACAT-TAATGCA
1 CTACATTACTCTTGTACAACAAACTACATGTAATGCA
*
670572 CTACATTACTTTTGTACAACAAACTACATGTAATGCA
1 CTACATTACTCTTGTACAACAAACTACATGTAATGCA
* * *
670609 CTACATTACTTTTGTACAACAAAATACATGAAATGCA
1 CTACATTACTCTTGTACAACAAACTACATGTAATGCA
*
670646 CTACATTACTCTTGTACAACAAAATACATGTAATGCA
1 CTACATTACTCTTGTACAACAAACTACATGTAATGCA
*
670683 CTACATTACTCTTGTACAACAAAATACATGTAATGCA
1 CTACATTACTCTTGTACAACAAACTACATGTAATGCA
*
670720 CTACATTACTATTGTAC-A-AAA-TACATGTAATGCA
1 CTACATTACTCTTGTACAACAAACTACATGTAATGCA
* *
670754 CTACATTACTCTTGTACAACAAAATACATGAAATGCA
1 CTACATTACTCTTGTACAACAAACTACATGTAATGCA
* *
670791 CTACATTACTTTTGTACAACAAAATACATGTAATGCA
1 CTACATTACTCTTGTACAACAAACTACATGTAATGCA
*
670828 CTACATTACTCTTGTACAACAAAATACATGTAATGCA
1 CTACATTACTCTTGTACAACAAACTACATGTAATGCA
*
670865 CTACATTACTATTGTAC-A-AAA-TACATGTAATGCA
1 CTACATTACTCTTGTACAACAAACTACATGTAATGCA
*
670899 CTACATTACTTTTGTAC-A-AAA-TACATGTAATGCA
1 CTACATTACTCTTGTACAACAAACTACATGTAATGCA
*
670933 CTACATTACTCTTGTACAACAAAATACATGTAATGCA
1 CTACATTACTCTTGTACAACAAACTACATGTAATGCA
670970 CTACATTACTCTTGTAC-A-AAA-TACATGTAATGCA
1 CTACATTACTCTTGTACAACAAACTACATGTAATGCA
*
671004 CTACATTACTCTTGTACAACAAAATACATGTAATGCA
1 CTACATTACTCTTGTACAACAAACTACATGTAATGCA
*
671041 TTACATTACTCTTGT---ACAAACTACATGTAATGCA
1 CTACATTACTCTTGTACAACAAACTACATGTAATGCA
671075 CTACATTACTCTTGTACAACAAACTACATGTAATGCA
1 CTACATTACTCTTGTACAACAAACTACATGTAATGCA
671112 CTACATTACTCTTGTACAACAAACTACATGTAATGCA
1 CTACATTACTCTTGTACAACAAACTACATGTAATGCA
* *
671149 CTATATTACTTTTGTACAACAAACTACATGTAATGCA
1 CTACATTACTCTTGTACAACAAACTACATGTAATGCA
* * *
671186 CTTCATTACTTTTGTACAACAAACTACACGTAATGCA
1 CTACATTACTCTTGTACAACAAACTACATGTAATGCA
671223 CTACATTACTCTTGT---ACAAACTACATGTAATGCA
1 CTACATTACTCTTGTACAACAAACTACATGTAATGCA
*
671257 CTACATTAATCTTGTACAACAAACTACATGTAATGCA
1 CTACATTACTCTTGTACAACAAACTACATGTAATGCA
*
671294 CTACATTAATCTTGTACAACAAACTACATGTAATGCA
1 CTACATTACTCTTGTACAACAAACTACATGTAATGCA
*
671331 CTACATTAATCTTGTACAACAAACTACATGTAATGCA
1 CTACATTACTCTTGTACAACAAACTACATGTAATGCA
*
671368 CTACATTAATCTT
1 CTACATTACTCTT
671381 TTATTTCTTC
Statistics
Matches: 796, Mismatches: 27, Indels: 35
0.93 0.03 0.04
Matches are distributed among these distances:
33 23 0.03
34 211 0.27
35 15 0.02
36 17 0.02
37 530 0.67
ACGTcount: A:0.39, C:0.21, G:0.08, T:0.32
Consensus pattern (37 bp):
CTACATTACTCTTGTACAACAAACTACATGTAATGCA
Found at i:670774 original size:145 final size:148
Alignment explanation
Indices: 670520--671380 Score: 1334
Period size: 145 Copynumber: 6.0 Consensus size: 148
670510 TTACTTTTGT
670520 ACAAAATACATGTAATGCACTACATTACTCTTGT---ACAAAATACAT-TAATGCACTACATTAC
1 ACAAAATACATGTAATGCACTACATTACTCTTGTACAACAAAATACATGTAATGCACTACATTAC
* * *
670581 TTTTGTACAACAAACTACATGTAATGCACTACATTACTTTTGTACAACAAAATACATGAAATGCA
66 TATTGTACAACAAACTACATGTAATGCACTACATTACTCTTGTACAACAAAATACATGTAATGCA
670646 CTACATTACTCTTGTACA
131 CTACATTACTCTTGTACA
670664 ACAAAATACATGTAATGCACTACATTACTCTTGTACAACAAAATACATGTAATGCACTACATTAC
1 ACAAAATACATGTAATGCACTACATTACTCTTGTACAACAAAATACATGTAATGCACTACATTAC
*
670729 TATTGTAC-A-AAA-TACATGTAATGCACTACATTACTCTTGTACAACAAAATACATGAAATGCA
66 TATTGTACAACAAACTACATGTAATGCACTACATTACTCTTGTACAACAAAATACATGTAATGCA
*
670791 CTACATTACTTTTGTACA
131 CTACATTACTCTTGTACA
670809 ACAAAATACATGTAATGCACTACATTACTCTTGTACAACAAAATACATGTAATGCACTACATTAC
1 ACAAAATACATGTAATGCACTACATTACTCTTGTACAACAAAATACATGTAATGCACTACATTAC
*
670874 TATTGTAC-A-AAA-TACATGTAATGCACTACATTACTTTTGT---ACAAAATACATGTAATGCA
66 TATTGTACAACAAACTACATGTAATGCACTACATTACTCTTGTACAACAAAATACATGTAATGCA
670933 CTACATTACTCTTGTACA
131 CTACATTACTCTTGTACA
670951 ACAAAATACATGTAATGCACTACATTACTCTTGT---ACAAAATACATGTAATGCACTACATTAC
1 ACAAAATACATGTAATGCACTACATTACTCTTGTACAACAAAATACATGTAATGCACTACATTAC
* * * *
671013 TCTTGTACAACAAAATACATGTAATGCATTACATTACTCTTGT---ACAAACTACATGTAATGCA
66 TATTGTACAACAAACTACATGTAATGCACTACATTACTCTTGTACAACAAAATACATGTAATGCA
671075 CTACATTACTCTTGTACA
131 CTACATTACTCTTGTACA
* * *
671093 ACAAACTACATGTAATGCACTACATTACTCTTGTACAACAAACTACATGTAATGCACTATATTAC
1 ACAAAATACATGTAATGCACTACATTACTCTTGTACAACAAAATACATGTAATGCACTACATTAC
* * * * *
671158 TTTTGTACAACAAACTACATGTAATGCACTTCATTACTTTTGTACAACAAACTACACGTAATGCA
66 TATTGTACAACAAACTACATGTAATGCACTACATTACTCTTGTACAACAAAATACATGTAATGCA
671223 CTACATTACTCTTGT---
131 CTACATTACTCTTGTACA
* * * *
671238 ACAAACTACATGTAATGCACTACATTAATCTTGTACAACAAACTACATGTAATGCACTACATTAA
1 ACAAAATACATGTAATGCACTACATTACTCTTGTACAACAAAATACATGTAATGCACTACATTAC
* * *
671303 TCTTGTACAACAAACTACATGTAATGCACTACATTAATCTTGTACAACAAACTACATGTAATGCA
66 TATTGTACAACAAACTACATGTAATGCACTACATTACTCTTGTACAACAAAATACATGTAATGCA
*
671368 CTACATTAATCTT
131 CTACATTACTCTT
671381 TTATTTCTTC
Statistics
Matches: 676, Mismatches: 28, Indels: 25
0.93 0.04 0.03
Matches are distributed among these distances:
139 35 0.05
140 1 0.00
141 3 0.00
142 164 0.24
144 34 0.05
145 368 0.54
146 3 0.00
147 12 0.02
148 56 0.08
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.31
Consensus pattern (148 bp):
ACAAAATACATGTAATGCACTACATTACTCTTGTACAACAAAATACATGTAATGCACTACATTAC
TATTGTACAACAAACTACATGTAATGCACTACATTACTCTTGTACAACAAAATACATGTAATGCA
CTACATTACTCTTGTACA
Found at i:670777 original size:71 final size:71
Alignment explanation
Indices: 670505--671380 Score: 1220
Period size: 71 Copynumber: 12.2 Consensus size: 71
670495 TGGATGTTTG
*
670505 CTACATTACTTTTGTACAAAATACATGTAATGCACTACATTACTCTTGT---ACAAAATACAT-T
1 CTACATTACTCTTGTACAAAATACATGTAATGCACTACATTACTCTTGTACAACAAAATACATGT
670566 AATGCA
66 AATGCA
* *
670572 CTACATTACTTTTGTACAACAAACTACATGTAATGCACTACATTACTTTTGTACAACAAAATACA
1 CTACATTACTCTTGTAC-A-AAA-TACATGTAATGCACTACATTACTCTTGTACAACAAAATACA
*
670637 TGAAATGCA
63 TGTAATGCA
670646 CTACATTACTCTTGTACAACAAAATACATGTAATGCACTACATTACTCTTGTACAACAAAATACA
1 CTACATTACTCTTGT---ACAAAATACATGTAATGCACTACATTACTCTTGTACAACAAAATACA
670711 TGTAATGCA
63 TGTAATGCA
* *
670720 CTACATTACTATTGTACAAAATACATGTAATGCACTACATTACTCTTGTACAACAAAATACATGA
1 CTACATTACTCTTGTACAAAATACATGTAATGCACTACATTACTCTTGTACAACAAAATACATGT
670785 AATGCA
66 AATGCA
*
670791 CTACATTACTTTTGTACAACAAAATACATGTAATGCACTACATTACTCTTGTACAACAAAATACA
1 CTACATTACTCTTGT---ACAAAATACATGTAATGCACTACATTACTCTTGTACAACAAAATACA
670856 TGTAATGCA
63 TGTAATGCA
* *
670865 CTACATTACTATTGTACAAAATACATGTAATGCACTACATTACTTTTGT---ACAAAATACATGT
1 CTACATTACTCTTGTACAAAATACATGTAATGCACTACATTACTCTTGTACAACAAAATACATGT
670927 AATGCA
66 AATGCA
670933 CTACATTACTCTTGTACAACAAAATACATGTAATGCACTACATTACTCTTGT---ACAAAATACA
1 CTACATTACTCTTGT---ACAAAATACATGTAATGCACTACATTACTCTTGTACAACAAAATACA
670995 TGTAATGCA
63 TGTAATGCA
* *
671004 CTACATTACTCTTGTACAACAAAATACATGTAATGCATTACATTACTCTTGT---ACAAACTACA
1 CTACATTACTCTTGT---ACAAAATACATGTAATGCACTACATTACTCTTGTACAACAAAATACA
671066 TGTAATGCA
63 TGTAATGCA
*
671075 CTACATTACTCTTGTACAACAAACTACATGTAATGCACTACATTACTCTTGTACAACAAACTACA
1 CTACATTACTCTTGTAC-A-AAA-TACATGTAATGCACTACATTACTCTTGTACAACAAAATACA
671140 TGTAATGCA
63 TGTAATGCA
* * * * *
671149 CTATATTACTTTTGTACAACAAACTACATGTAATGCACTTCATTACTTTTGTACAACAAACTACA
1 CTACATTACTCTTGTAC-A-AAA-TACATGTAATGCACTACATTACTCTTGTACAACAAAATACA
*
671214 CGTAATGCA
63 TGTAATGCA
* * *
671223 CTACATTACTCTTGTACAAACTACATGTAATGCACTACATTAATCTTGTACAACAAACTACATGT
1 CTACATTACTCTTGTACAAAATACATGTAATGCACTACATTACTCTTGTACAACAAAATACATGT
671288 AATGCA
66 AATGCA
* * *
671294 CTACATTAATCTTGTACAACAAACTACATGTAATGCACTACATTAATCTTGTACAACAAACTACA
1 CTACATTACTCTTGTAC-A-AAA-TACATGTAATGCACTACATTACTCTTGTACAACAAAATACA
671359 TGTAATGCA
63 TGTAATGCA
*
671368 CTACATTAATCTT
1 CTACATTACTCTT
671381 TTATTTCTTC
Statistics
Matches: 754, Mismatches: 30, Indels: 43
0.91 0.04 0.05
Matches are distributed among these distances:
67 17 0.02
68 36 0.05
69 4 0.01
70 30 0.04
71 327 0.43
72 3 0.00
73 14 0.02
74 317 0.42
75 3 0.00
76 1 0.00
77 2 0.00
ACGTcount: A:0.39, C:0.21, G:0.08, T:0.32
Consensus pattern (71 bp):
CTACATTACTCTTGTACAAAATACATGTAATGCACTACATTACTCTTGTACAACAAAATACATGT
AATGCA
Found at i:671090 original size:21 final size:21
Alignment explanation
Indices: 671066--671127 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
671056 ACAAACTACA
671066 TGTAATGCACTACATTACTCT
1 TGTAATGCACTACATTACTCT
* *
671087 TGT-A--CA--ACA-AACTACA
1 TGTAATGCACTACATTACT-CT
671103 TGTAATGCACTACATTACTCT
1 TGTAATGCACTACATTACTCT
671124 TGTA
1 TGTA
671128 CAACAAACTA
Statistics
Matches: 30, Mismatches: 4, Indels: 14
0.62 0.08 0.29
Matches are distributed among these distances:
15 3 0.10
16 7 0.23
17 1 0.03
18 2 0.07
19 2 0.07
20 1 0.03
21 11 0.37
22 3 0.10
ACGTcount: A:0.34, C:0.23, G:0.10, T:0.34
Consensus pattern (21 bp):
TGTAATGCACTACATTACTCT
Found at i:673572 original size:34 final size:34
Alignment explanation
Indices: 673485--673609 Score: 137
Period size: 34 Copynumber: 3.6 Consensus size: 34
673475 CTGCCATTTG
673485 CCTGAAGTGACCTAGATATTCAGTGTGACATTAA
1 CCTGAAGTGACCTAGATATTCAGTGTGACATTAA
* * * *
673519 TCTGACAGTGACCTTGATATTCAGAGT-AGCATTCA
1 CCTGA-AGTGACCTAGATATTCAGTGTGA-CATTAA
* **
673554 CCTGAAGTGATCTAGATA-TCTAGTGTGACATTTG
1 CCTGAAGTGACCTAGATATTC-AGTGTGACATTAA
*
673588 CCTGAAGTGATCTAGATATTCA
1 CCTGAAGTGACCTAGATATTCA
673610 ACTTGACAGT
Statistics
Matches: 76, Mismatches: 10, Indels: 10
0.79 0.10 0.10
Matches are distributed among these distances:
33 2 0.03
34 43 0.57
35 31 0.41
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.32
Consensus pattern (34 bp):
CCTGAAGTGACCTAGATATTCAGTGTGACATTAA
Found at i:673733 original size:44 final size:44
Alignment explanation
Indices: 673685--673880 Score: 302
Period size: 44 Copynumber: 4.4 Consensus size: 44
673675 TTGCATATGA
673685 TATTTACCTGGCTATGACATATATATTCAGTGTGATCAATGTGG
1 TATTTACCTGGCTATGACATATATATTCAGTGTGATCAATGTGG
* * * * *
673729 TATTTACATGGCTATGACCTATATATTCATTGTGATAAATGTGA
1 TATTTACCTGGCTATGACATATATATTCAGTGTGATCAATGTGG
*
673773 TATTTACCTGGATATGACATATATATTTTCAGTGTGATCAATGTGG
1 TATTTACCTGGCTATGACATATATA--TTCAGTGTGATCAATGTGG
*
673819 TATTTACCTGGCTATGACCTATATATTCAGTGTGATCAATGTGG
1 TATTTACCTGGCTATGACATATATATTCAGTGTGATCAATGTGG
*
673863 TATTTACCTGGCTGTGAC
1 TATTTACCTGGCTATGAC
673881 TTTGATAGTC
Statistics
Matches: 136, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
44 97 0.71
46 39 0.29
ACGTcount: A:0.27, C:0.14, G:0.19, T:0.40
Consensus pattern (44 bp):
TATTTACCTGGCTATGACATATATATTCAGTGTGATCAATGTGG
Found at i:673811 original size:90 final size:88
Alignment explanation
Indices: 673682--673873 Score: 321
Period size: 90 Copynumber: 2.2 Consensus size: 88
673672 ACATTGCATA
*
673682 TGATATTTACCTGGCTATGACATATATATTCAGTGTGATCAATGTGGTATTTACATGGCTATGAC
1 TGATATTTACCTGGATATGACATATATATTCAGTGTGATCAATGTGGTATTTACATGGCTATGAC
*
673747 CTATATATTCATTGTGATAAATG
66 CTATATATTCAGTGTGATAAATG
*
673770 TGATATTTACCTGGATATGACATATATATTTTCAGTGTGATCAATGTGGTATTTACCTGGCTATG
1 TGATATTTACCTGGATATGACATATATA--TTCAGTGTGATCAATGTGGTATTTACATGGCTATG
*
673835 ACCTATATATTCAGTGTGATCAATG
64 ACCTATATATTCAGTGTGATAAATG
*
673860 TGGTATTTACCTGG
1 TGATATTTACCTGG
673874 CTGTGACTTT
Statistics
Matches: 97, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
88 27 0.28
90 70 0.72
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.40
Consensus pattern (88 bp):
TGATATTTACCTGGATATGACATATATATTCAGTGTGATCAATGTGGTATTTACATGGCTATGAC
CTATATATTCAGTGTGATAAATG
Found at i:675065 original size:22 final size:23
Alignment explanation
Indices: 675026--675070 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
675016 GTAAAATTGC
675026 AACATATGTTCAAAATAT-ATTA
1 AACATATGTTCAAAATATGATTA
* *
675048 AACATATGTTGAACATATGATTA
1 AACATATGTTCAAAATATGATTA
675071 CCACAATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.47, C:0.09, G:0.09, T:0.36
Consensus pattern (23 bp):
AACATATGTTCAAAATATGATTA
Found at i:675135 original size:24 final size:25
Alignment explanation
Indices: 675108--675167 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 25
675098 TGAGTCTGTA
* *
675108 ATATGTTTAAC-GTATTTTTCAAAC
1 ATATGTTTAACAATATATTTCAAAC
675132 ATATG-TTAACAATATATTTCAAAC
1 ATATGTTTAACAATATATTTCAAAC
*
675156 ATATGTTCAACA
1 ATATGTTTAACA
675168 TACTGTGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
23 5 0.16
24 21 0.68
25 5 0.16
ACGTcount: A:0.40, C:0.13, G:0.07, T:0.40
Consensus pattern (25 bp):
ATATGTTTAACAATATATTTCAAAC
Found at i:675159 original size:11 final size:12
Alignment explanation
Indices: 675125--675249 Score: 64
Period size: 11 Copynumber: 10.2 Consensus size: 12
675115 TAACGTATTT
675125 TTCAAACATATG
1 TTCAAACATATG
* *
675137 TTAACAATATAT-
1 TTCA-AACATATG
675149 TTCAAACATATG
1 TTCAAACATATG
675161 TTC-AACATACTG
1 TTCAAACATA-TG
**
675173 TGAAAAATTCATATG
1 T-TCAAA--CATATG
*
675188 TT-TAACATATG
1 TTCAAACATATG
*
675199 TTC-AACGTATG
1 TTCAAACATATG
675210 TTC-AACATATG
1 TTCAAACATATG
675221 TTACTCGAAACATATG
1 -T--TC-AAACATATG
*
675237 TT-GAACATATG
1 TTCAAACATATG
675248 TT
1 TT
675250 GCAATTTTAC
Statistics
Matches: 89, Mismatches: 11, Indels: 27
0.70 0.09 0.21
Matches are distributed among these distances:
11 47 0.53
12 13 0.15
13 9 0.10
14 4 0.04
15 4 0.04
16 12 0.13
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.37
Consensus pattern (12 bp):
TTCAAACATATG
Found at i:680892 original size:11 final size:11
Alignment explanation
Indices: 680872--680901 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
680862 AGATTTTGAT
680872 AAAAAA-AAAA
1 AAAAAAGAAAA
680882 AAAAAAGAAAA
1 AAAAAAGAAAA
680893 AAAAAAGAA
1 AAAAAAGAA
680902 GTATAATTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.32
11 13 0.68
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:687971 original size:20 final size:19
Alignment explanation
Indices: 687946--687998 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 19
687936 CTTCAATAAT
687946 TAATATGATATTGTATCAC
1 TAATATGATATTGTATCAC
*
687965 --ATA--ATATTGTATCATA
1 TAATATGATATTGTATCA-C
*
687981 TAATATGATATTCTATCA
1 TAATATGATATTGTATCA
687999 TACGATACAA
Statistics
Matches: 27, Mismatches: 2, Indels: 9
0.71 0.05 0.24
Matches are distributed among these distances:
15 11 0.41
17 3 0.11
18 3 0.11
20 10 0.37
ACGTcount: A:0.40, C:0.09, G:0.08, T:0.43
Consensus pattern (19 bp):
TAATATGATATTGTATCAC
Found at i:687973 original size:15 final size:15
Alignment explanation
Indices: 687953--687986 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
687943 AATTAATATG
687953 ATATTGTATCACATA
1 ATATTGTATCACATA
*
687968 ATATTGTATCATATA
1 ATATTGTATCACATA
687983 ATAT
1 ATAT
687987 GATATTCTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.44
Consensus pattern (15 bp):
ATATTGTATCACATA
Found at i:688476 original size:23 final size:23
Alignment explanation
Indices: 688432--688476 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
688422 TTTGATCTGA
**
688432 TGATCCGCGCCTGGAACTCCATG
1 TGATCCGCGCCTGGAAAGCCATG
*
688455 TGATCCGTGCCTGGAAAGCCAT
1 TGATCCGCGCCTGGAAAGCCAT
688477 CTCGTTTGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.31, G:0.27, T:0.22
Consensus pattern (23 bp):
TGATCCGCGCCTGGAAAGCCATG
Found at i:688505 original size:59 final size:60
Alignment explanation
Indices: 688413--688531 Score: 222
Period size: 59 Copynumber: 2.0 Consensus size: 60
688403 GGATCATGTT
688413 GCCATCTCGTTTGATCTGATGATCCGCGCCTGG-AACTCCATGTGATCCGTGCCTGGAAA
1 GCCATCTCGTTTGATCTGATGATCCGCGCCTGGAAACTCCATGTGATCCGTGCCTGGAAA
*
688472 GCCATCTCGTTTGATCTGATGATCCGTGCCTGGAAACTCCATGTGATCCGTGCCTGGAAA
1 GCCATCTCGTTTGATCTGATGATCCGCGCCTGGAAACTCCATGTGATCCGTGCCTGGAAA
688532 CTCCCCTTGG
Statistics
Matches: 58, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
59 32 0.55
60 26 0.45
ACGTcount: A:0.19, C:0.28, G:0.25, T:0.28
Consensus pattern (60 bp):
GCCATCTCGTTTGATCTGATGATCCGCGCCTGGAAACTCCATGTGATCCGTGCCTGGAAA
Found at i:689353 original size:6 final size:6
Alignment explanation
Indices: 689342--689366 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
689332 TCAAGGCAAC
689342 ACATGT ACATGT ACATGT ACATGT A
1 ACATGT ACATGT ACATGT ACATGT A
689367 TTTAACAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (6 bp):
ACATGT
Found at i:690351 original size:15 final size:15
Alignment explanation
Indices: 690327--690356 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
690317 GGTAAGTGAA
*
690327 GCGTCTGGATATCTG
1 GCGTCCGGATATCTG
690342 GCGTCCGGATATCTG
1 GCGTCCGGATATCTG
690357 AGGCTCCACT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.23, G:0.33, T:0.30
Consensus pattern (15 bp):
GCGTCCGGATATCTG
Found at i:690942 original size:27 final size:27
Alignment explanation
Indices: 690911--690974 Score: 128
Period size: 27 Copynumber: 2.4 Consensus size: 27
690901 TAACCTCCCC
690911 CAGCATCCAAAATTCATGGCCCAGATT
1 CAGCATCCAAAATTCATGGCCCAGATT
690938 CAGCATCCAAAATTCATGGCCCAGATT
1 CAGCATCCAAAATTCATGGCCCAGATT
690965 CAGCATCCAA
1 CAGCATCCAA
690975 GTTTTTATCC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.34, C:0.31, G:0.14, T:0.20
Consensus pattern (27 bp):
CAGCATCCAAAATTCATGGCCCAGATT
Found at i:691244 original size:17 final size:17
Alignment explanation
Indices: 691201--691244 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
691191 GAGCTGCAGC
*
691201 ACTTTCATTATTGTAAA
1 ACTTTCATTTTTGTAAA
*
691218 GCTTTCATTTTTGTAAA
1 ACTTTCATTTTTGTAAA
691235 ACTTTCATTT
1 ACTTTCATTT
691245 CAATTATAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.27, C:0.14, G:0.07, T:0.52
Consensus pattern (17 bp):
ACTTTCATTTTTGTAAA
Found at i:692547 original size:1 final size:1
Alignment explanation
Indices: 692541--692566 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
692531 TCGGATGGTC
692541 GGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGG
692567 AGAGNNNNNN
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:696489 original size:19 final size:19
Alignment explanation
Indices: 696465--697408 Score: 1009
Period size: 19 Copynumber: 51.3 Consensus size: 19
696455 NNNNNNNNNN
*
696465 TAAAACGGCCACAACATGA
1 TAAAACAGCCACAACATGA
* *
696484 TAAAACAGCTACAAAATGA
1 TAAAACAGCCACAACATGA
* ** *
696503 AAAAACAGCTTCACCATGA
1 TAAAACAGCCACAACATGA
* *
696522 TAAAACAGCCACAACACGC
1 TAAAACAGCCACAACATGA
*
696541 TAAAACAGCCACAACAGGA
1 TAAAACAGCCACAACATGA
* *
696560 CAAAACAGCCACAGCATGA
1 TAAAACAGCCACAACATGA
*
696579 TAAAACAGCCACAACGTGA
1 TAAAACAGCCACAACATGA
*
696598 T--AA-A---ACAACATGT
1 TAAAACAGCCACAACATGA
*
696611 TAGAACAGCCACAACATGA
1 TAAAACAGCCACAACATGA
* *
696630 TACAACAGCCACAACAGGA
1 TAAAACAGCCACAACATGA
696649 TAAAACAGCCACAACATGA
1 TAAAACAGCCACAACATGA
696668 TAAAACAGCCACAACATGA
1 TAAAACAGCCACAACATGA
*
696687 TAAAACAGCCATAACATGAA
1 TAAAACAGCCACAACATG-A
* * *
696707 AAAAACAGCTTA-ACCATGA
1 TAAAACAGC-CACAACATGA
*
696726 TAAAACAGCCACATCATGA
1 TAAAACAGCCACAACATGA
696745 TAAAACAGCCACAACATGA
1 TAAAACAGCCACAACATGA
696764 T--AA-A---ACAACATGA
1 TAAAACAGCCACAACATGA
696777 TAAAACAGCCACAACATGA
1 TAAAACAGCCACAACATGA
*
696796 TAAAACGGCCACAACATGA
1 TAAAACAGCCACAACATGA
* *
696815 TAAAACAGCTACAAAATGA
1 TAAAACAGCCACAACATGA
* ** *
696834 AAAAACAGCTTCACCATGA
1 TAAAACAGCCACAACATGA
*
696853 TAAAACAGCCACAACACGA
1 TAAAACAGCCACAACATGA
*
696872 TAAAACAGCCACAACAGGA
1 TAAAACAGCCACAACATGA
* *
696891 CAAAACAGCCACAGCATGA
1 TAAAACAGCCACAACATGA
*
696910 TAAAACAGCCACAACGTGA
1 TAAAACAGCCACAACATGA
*
696929 T--AA-A---ACAACATGT
1 TAAAACAGCCACAACATGA
696942 TAAAACAGCCACAACATGA
1 TAAAACAGCCACAACATGA
*
696961 T----NA---ACAACATGA
1 TAAAACAGCCACAACATGA
*
696973 TAAAACAGCCACAACATGT
1 TAAAACAGCCACAACATGA
696992 TAAAAC-GTCCACAACATGA
1 TAAAACAG-CCACAACATGA
* *
697011 TAAAACAGCTACAAAATGA
1 TAAAACAGCCACAACATGA
* ** *
697030 AAAAACAGCTTCACCATGA
1 TAAAACAGCCACAACATGA
* *
697049 TAAAACAGCCACAACACGC
1 TAAAACAGCCACAACATGA
*
697068 TAAAACAGCCACAACAGGA
1 TAAAACAGCCACAACATGA
* *
697087 CAAAACAGCCACAGCATGA
1 TAAAACAGCCACAACATGA
*
697106 TAAAACAGCCACAACGTGA
1 TAAAACAGCCACAACATGA
*
697125 T--AA-A---ACAACATGT
1 TAAAACAGCCACAACATGA
*
697138 TAAAACAGCCACAACAGGA
1 TAAAACAGCCACAACATGA
*
697157 TAAAACAGCCACAAAATGA
1 TAAAACAGCCACAACATGA
* * *
697176 CAAAACAGCCGCAGCATGA
1 TAAAACAGCCACAACATGA
*
697195 CAAAACAGCCACAACATGA
1 TAAAACAGCCACAACATGA
*
697214 TAAATCAGCCACAACATGA
1 TAAAACAGCCACAACATGA
*
697233 CAAAACAGCCACAACATGA
1 TAAAACAGCCACAACATGA
697252 TAAAACAGCCACAACATGA
1 TAAAACAGCCACAACATGA
* * * *
697271 TTAAACCGACACAACATGT
1 TAAAACAGCCACAACATGA
*
697290 TAAAACAGCCATAACATGA
1 TAAAACAGCCACAACATGA
*
697309 TAAAACAGACACAACATGA
1 TAAAACAGCCACAACATGA
*
697328 CAAAACAGCCACAACATGA
1 TAAAACAGCCACAACATGA
697347 TAAAACAGCCACAACATGA
1 TAAAACAGCCACAACATGA
* * * *
697366 TTAAACCGACACCACATGA
1 TAAAACAGCCACAACATGA
697385 TAAAACAGCCACAACATGA
1 TAAAACAGCCACAACATGA
697404 TAAAA
1 TAAAA
697409 TACCTGTAAT
Statistics
Matches: 767, Mismatches: 122, Indels: 72
0.80 0.13 0.07
Matches are distributed among these distances:
12 10 0.01
13 34 0.04
15 9 0.01
16 9 0.01
17 8 0.01
18 2 0.00
19 679 0.89
20 15 0.02
21 1 0.00
ACGTcount: A:0.51, C:0.26, G:0.12, T:0.11
Consensus pattern (19 bp):
TAAAACAGCCACAACATGA
Found at i:696773 original size:13 final size:13
Alignment explanation
Indices: 696755--696783 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
696745 TAAAACAGCC
696755 ACAACATGATAAA
1 ACAACATGATAAA
696768 ACAACATGATAAA
1 ACAACATGATAAA
696781 ACA
1 ACA
696784 GCCACAACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.62, C:0.17, G:0.07, T:0.14
Consensus pattern (13 bp):
ACAACATGATAAA
Found at i:697147 original size:32 final size:32
Alignment explanation
Indices: 697068--697163 Score: 104
Period size: 32 Copynumber: 2.8 Consensus size: 32
697058 CACAACACGC
*
697068 TAAAACAGCCACAACAGGACAAAACAGCCACAGCATGA
1 TAAAACAGCCACAACAGGA-TAAA-A--CA-A-CATGA
*
697106 TAAAACAGCCACAAC-GTGATAAAACAACATGT
1 TAAAACAGCCACAACAG-GATAAAACAACATGA
697138 TAAAACAGCCACAACAGGATAAAACA
1 TAAAACAGCCACAACAGGATAAAACA
697164 GCCACAAAAT
Statistics
Matches: 54, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
32 28 0.52
33 2 0.04
34 2 0.04
36 1 0.02
37 4 0.07
38 17 0.31
ACGTcount: A:0.52, C:0.25, G:0.14, T:0.09
Consensus pattern (32 bp):
TAAAACAGCCACAACAGGATAAAACAACATGA
Found at i:697881 original size:21 final size:21
Alignment explanation
Indices: 697855--697898 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
697845 TTTAGATTCT
*
697855 CACGAGCTCTCTCATGCGTTG
1 CACGAGCTCTCGCATGCGTTG
*
697876 CACGAGCTCTCGCATTCGTTG
1 CACGAGCTCTCGCATGCGTTG
697897 CA
1 CA
697899 TGCGTTTAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.34, G:0.23, T:0.27
Consensus pattern (21 bp):
CACGAGCTCTCGCATGCGTTG
Found at i:702874 original size:12 final size:12
Alignment explanation
Indices: 702857--702886 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
702847 ATGGTTACCA
702857 TGACCAATATTG
1 TGACCAATATTG
702869 TGACCAATATTG
1 TGACCAATATTG
702881 TGACCA
1 TGACCA
702887 TGGCCATAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (12 bp):
TGACCAATATTG
Found at i:703809 original size:174 final size:174
Alignment explanation
Indices: 703519--703859 Score: 664
Period size: 174 Copynumber: 2.0 Consensus size: 174
703509 ATTGGCTCAC
703519 GTGCAACTGTCCAATCACCAGATCACTCGCGCGATCCTATCGCTCTATCTTACAACACTCGCTTT
1 GTGCAACTGTCCAATCACCAGATCACTCGCGCGATCCTATCGCTCTATCTTACAACACTCGCTTT
*
703584 TCTTGTACAACAGTCGCATATAGACGAAATATATATATCGCGCAATGGTCGATTAAGATCGTGCA
66 TCTTGTACAACAGTCGCATATAGACGAAATATATATATCGCACAATGGTCGATTAAGATCGTGCA
703649 AATTTCTTACTTGCGATTATTTCGGCAACAGTTTACGTGCAACT
131 AATTTCTTACTTGCGATTATTTCGGCAACAGTTTACGTGCAACT
*
703693 GTGCAACTGTCCAATCACCAGATCACTCGCGCGATCCTATCGCTCTGTCTTACAACACTCGCTTT
1 GTGCAACTGTCCAATCACCAGATCACTCGCGCGATCCTATCGCTCTATCTTACAACACTCGCTTT
703758 TCTTGTACAACAGTCGCATATAGACGAAATATATATATCGCACAATGGTCGATTAAGATCGTGCA
66 TCTTGTACAACAGTCGCATATAGACGAAATATATATATCGCACAATGGTCGATTAAGATCGTGCA
703823 AATTTCTTACTTGCGATTATTTCGGCAACAGTTTACG
131 AATTTCTTACTTGCGATTATTTCGGCAACAGTTTACG
703860 ATCCAAATCT
Statistics
Matches: 165, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
174 165 1.00
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (174 bp):
GTGCAACTGTCCAATCACCAGATCACTCGCGCGATCCTATCGCTCTATCTTACAACACTCGCTTT
TCTTGTACAACAGTCGCATATAGACGAAATATATATATCGCACAATGGTCGATTAAGATCGTGCA
AATTTCTTACTTGCGATTATTTCGGCAACAGTTTACGTGCAACT
Found at i:705414 original size:99 final size:99
Alignment explanation
Indices: 705258--705457 Score: 364
Period size: 99 Copynumber: 2.0 Consensus size: 99
705248 ATTTCATTAA
*
705258 AATATTGCAGATTATTTTAGTTCAAGGTTAAATTTTTATTTCTTTAGACTGATTTAGTTTTAGGT
1 AATATTGCAGATTATTTTAGTTCAAGGTTAAATTTTTATTTCTTAAGACTGATTTAGTTTTAGGT
* *
705323 TAATTGTACACTATCTGCAATTACATTTACTAGT
66 TAATTGTACACTATCTGCAATTACAATTACAAGT
705357 AATATTGCAGATTATTTTAGTTCAAGGTTAAATTTTTATTTCTTAAGACTGATTTAGTTTTAGGT
1 AATATTGCAGATTATTTTAGTTCAAGGTTAAATTTTTATTTCTTAAGACTGATTTAGTTTTAGGT
*
705422 TAATTGTACACTATGTGCAATTACAATTACAAGT
66 TAATTGTACACTATCTGCAATTACAATTACAAGT
705456 AA
1 AA
705458 ATAATTAAAA
Statistics
Matches: 97, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
99 97 1.00
ACGTcount: A:0.32, C:0.10, G:0.14, T:0.46
Consensus pattern (99 bp):
AATATTGCAGATTATTTTAGTTCAAGGTTAAATTTTTATTTCTTAAGACTGATTTAGTTTTAGGT
TAATTGTACACTATCTGCAATTACAATTACAAGT
Found at i:706674 original size:30 final size:29
Alignment explanation
Indices: 706639--707221 Score: 470
Period size: 30 Copynumber: 19.4 Consensus size: 29
706629 CTGAGGTCAC
* * *
706639 ACAAAACAATCATCCAGGGACTGCAATCAA
1 ACAACACAATCATCCAGGCACTGGAAT-AA
* * * *
706669 ACAAAAAAAATCATCCAGGCACTAGAAAAA
1 AC-AACACAATCATCCAGGCACTGGAATAA
* *
706699 CACAACACAATCATCCAGGGACTGGAGTAA
1 -ACAACACAATCATCCAGGCACTGGAATAA
* * * *
706729 CACAAAACAGTCATCCAGGGACTGAAATTAA
1 -ACAACACAATCATCCAGGCACTGGAA-TAA
* * * * *
706760 ACAAGATAATCATCCACGCACTGGAACCAG
1 ACAACACAATCATCCAGGCACTGGAA-TAA
* ** * *
706790 ACAAGATGATCATCCAGGCACTGGAGTCAC
1 ACAACACAATCATCCAGGCACTGGAAT-AA
* * *
706820 ACAACACAATCATCCAGACACTAGAAAAA
1 ACAACACAATCATCCAGGCACTGGAATAA
*
706849 CACAACACAATCATCCAGGGACT-GAAGTAA
1 -ACAACACAATCATCCAGGCACTGGAA-TAA
* *
706879 CACAAAACAATCATCCAGACACT-GAAGTAA
1 -ACAACACAATCATCCAGGCACTGGAA-TAA
*** * *
706909 CACAACACAATCATTGGGGCCCTGAAATTAA
1 -ACAACACAATCATCCAGGCACTGGAA-TAA
* * * * *
706940 ACAAGATAATCATCCACGCACTGGAACCAG
1 ACAACACAATCATCCAGGCACTGGAA-TAA
* ** *
706970 ACAAGATGATCATCCAGACACT-GAAGTAA
1 ACAACACAATCATCCAGGCACTGGAA-TAA
*
706999 GACAACACAATCATCCAGGCACTGGAATCAC
1 -ACAACACAATCATCCAGGCACTGGAAT-AA
*
707030 ACAACACAATCATCCAGGCACTGGAATCAC
1 ACAACACAATCATCCAGGCACTGGAAT-AA
*
707060 ACAACACAATCATCCAGGCACTGGAGTAA
1 ACAACACAATCATCCAGGCACTGGAATAA
* * *
707089 CACAAAACAGTCATCCAGGCACTGGAATCAC
1 -ACAACACAATCATCCAGGCACTGGAAT-AA
*
707120 ACAACACAATCATCCAGGCACTGGAATCAC
1 ACAACACAATCATCCAGGCACTGGAAT-AA
*
707150 ACAACACAATCATCCAGGCACTGGAGTAA
1 ACAACACAATCATCCAGGCACTGGAATAA
*
707179 CACAACACAATCATCCAGGCACTGGAGTAA
1 -ACAACACAATCATCCAGGCACTGGAATAA
707209 CACAACACAATCA
1 -ACAACACAATCA
707222 CACAACACAA
Statistics
Matches: 457, Mismatches: 83, Indels: 26
0.81 0.15 0.05
Matches are distributed among these distances:
29 10 0.02
30 412 0.90
31 35 0.08
ACGTcount: A:0.43, C:0.28, G:0.15, T:0.14
Consensus pattern (29 bp):
ACAACACAATCATCCAGGCACTGGAATAA
Found at i:706814 original size:90 final size:90
Alignment explanation
Indices: 706637--707221 Score: 629
Period size: 90 Copynumber: 6.5 Consensus size: 90
706627 TACTGAGGTC
* * * * * * **
706637 ACACAAAACAATCATCCAGGGACTGCAATCAAACAAAAAAAATCATCCAGGCACTAGAAAAACAC
1 ACACAACACAATCATCCAGGCACTGAAATCAAAC-AACACAATCATCCAGGCACTGGAATCACAC
*
706702 AACACAATCATCCAGGGACTGGAGTA
65 AACACAATCATCCAGGCACTGGAGTA
* * * * * * * * *
706728 ACACAAAACAGTCATCCAGGGACTGAAATTAAACAAGATAATCATCCACGCACTGGAACCAGACA
1 ACACAACACAATCATCCAGGCACTGAAATCAAACAACACAATCATCCAGGCACTGGAATCACACA
* ** *
706793 AGATGATCATCCAGGCACTGGAGTC
66 ACACAATCATCCAGGCACTGGAGTA
* * *
706818 ACACAACACAATCATCCAGACACTAGAAA--AACACAACACAATCATCCAGGGACT-GAAGTAAC
1 ACACAACACAATCATCCAGGCACT-GAAATCAA-ACAACACAATCATCCAGGCACTGGAA-TCAC
* * *
706880 ACAAAACAATCATCCAGACACTGAAGTA
63 ACAACACAATCATCCAGGCACTGGAGTA
*** * * * * * * *
706908 ACACAACACAATCATTGGGGCCCTGAAATTAAACAAGATAATCATCCACGCACTGGAACCAGACA
1 ACACAACACAATCATCCAGGCACTGAAATCAAACAACACAATCATCCAGGCACTGGAATCACACA
* ** * *
706973 AGATGATCATCCAGACACTGAAGTA
66 ACACAATCATCCAGGCACTGGAGTA
* * *
706998 AGACAACACAATCATCCAGGCACTGGAATCACACAACACAATCATCCAGGCACTGGAATCACACA
1 ACACAACACAATCATCCAGGCACTGAAATCAAACAACACAATCATCCAGGCACTGGAATCACACA
707063 ACACAATCATCCAGGCACTGGAGTA
66 ACACAATCATCCAGGCACTGGAGTA
* * * *
707088 ACACAAAACAGTCATCCAGGCACTGGAATCACACAACACAATCATCCAGGCACTGGAATCACACA
1 ACACAACACAATCATCCAGGCACTGAAATCAAACAACACAATCATCCAGGCACTGGAATCACACA
707153 ACACAATCATCCAGGCACTGGAGTA
66 ACACAATCATCCAGGCACTGGAGTA
* *
707178 ACACAACACAATCATCCAGGCACTGGAGT-AACACAACACAATCA
1 ACACAACACAATCATCCAGGCACTGAAATCAA-ACAACACAATCA
707222 CACAACACAA
Statistics
Matches: 415, Mismatches: 72, Indels: 15
0.83 0.14 0.03
Matches are distributed among these distances:
89 10 0.02
90 365 0.88
91 40 0.10
ACGTcount: A:0.43, C:0.28, G:0.15, T:0.14
Consensus pattern (90 bp):
ACACAACACAATCATCCAGGCACTGAAATCAAACAACACAATCATCCAGGCACTGGAATCACACA
ACACAATCATCCAGGCACTGGAGTA
Found at i:707226 original size:13 final size:13
Alignment explanation
Indices: 707208--707234 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
707198 CACTGGAGTA
707208 ACACAACACAATC
1 ACACAACACAATC
707221 ACACAACACAATC
1 ACACAACACAATC
707234 A
1 A
707235 TCCAGGCACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.37, G:0.00, T:0.07
Consensus pattern (13 bp):
ACACAACACAATC
Found at i:707226 original size:43 final size:43
Alignment explanation
Indices: 707178--707264 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
707168 CACTGGAGTA
*
707178 ACACAACACAATCATCCAGGCACTGGAGTAACACAACACAATC
1 ACACAACACAATCATCCAGGCACTGAAGTAACACAACACAATC
707221 ACACAACACAATCATCCAGGCACTGAAGTAACACAACACAATC
1 ACACAACACAATCATCCAGGCACTGAAGTAACACAACACAATC
707264 A
1 A
707265 TCCAGGCACT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.46, C:0.32, G:0.10, T:0.11
Consensus pattern (43 bp):
ACACAACACAATCATCCAGGCACTGAAGTAACACAACACAATC
Found at i:707233 original size:73 final size:73
Alignment explanation
Indices: 707144--707293 Score: 273
Period size: 73 Copynumber: 2.1 Consensus size: 73
707134 CAGGCACTGG
* *
707144 AATCACACAACACAATCATCCAGGCACTGGAGTAACACAACACAATCATCCAGGCACTGGAGTAA
1 AATCACACAACACAATCATCCAGGCACTGAAGTAACACAACACAATCATCCAGGCACTGGAATAA
707209 CACAACAC
66 CACAACAC
*
707217 AATCACACAACACAATCATCCAGGCACTGAAGTAACACAACACAATCATCCAGGCACTGGAATCA
1 AATCACACAACACAATCATCCAGGCACTGAAGTAACACAACACAATCATCCAGGCACTGGAATAA
707282 CACAACAC
66 CACAACAC
707290 AATC
1 AATC
707294 TCTACACAGG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 74 1.00
ACGTcount: A:0.43, C:0.32, G:0.12, T:0.13
Consensus pattern (73 bp):
AATCACACAACACAATCATCCAGGCACTGAAGTAACACAACACAATCATCCAGGCACTGGAATAA
CACAACAC
Found at i:707314 original size:33 final size:30
Alignment explanation
Indices: 707217--707314 Score: 133
Period size: 30 Copynumber: 3.2 Consensus size: 30
707207 AACACAACAC
707217 AATCACACAACACAATCATCCAGGCACTGA
1 AATCACACAACACAATCATCCAGGCACTGA
* * *
707247 AGTAACACAACACAATCATCCAGGCACTGG
1 AATCACACAACACAATCATCCAGGCACTGA
*
707277 AATCACACAACACAATCTCTACACAGGCACTGA
1 AATCACACAACACAATC-AT-C-CAGGCACTGA
707310 AATCA
1 AATCA
707315 ATCATTCTTT
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
30 42 0.72
31 1 0.02
32 1 0.02
33 14 0.24
ACGTcount: A:0.43, C:0.32, G:0.11, T:0.14
Consensus pattern (30 bp):
AATCACACAACACAATCATCCAGGCACTGA
Found at i:708174 original size:79 final size:79
Alignment explanation
Indices: 708051--708203 Score: 236
Period size: 79 Copynumber: 1.9 Consensus size: 79
708041 GATTGGTATG
*
708051 AAAATAAATCCCACAATATTGCATGCCTAAACAAATAGTGTGTTAAAATTTTAAGCATCTGCAAT
1 AAAATAAATCCCACAATATTGCATGCCTAAACAAATAGTGTGTTAAAATTTCAAGCATCTGCAAT
708116 AAATAGTTGGTACA
66 AAATAGTTGGTACA
* * * * *
708130 AAAATATATCCCACTATA-TGCCGTGCCTGAACAAATAGTGTGTTAAAATTTCAAGCATCTGCGA
1 AAAATAAATCCCACAATATTG-CATGCCTAAACAAATAGTGTGTTAAAATTTCAAGCATCTGCAA
708194 TAAATAGTTG
65 TAAATAGTTG
708204 CTGAGAGATC
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
78 2 0.03
79 65 0.97
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.29
Consensus pattern (79 bp):
AAAATAAATCCCACAATATTGCATGCCTAAACAAATAGTGTGTTAAAATTTCAAGCATCTGCAAT
AAATAGTTGGTACA
Found at i:708403 original size:166 final size:166
Alignment explanation
Indices: 708122--708543 Score: 580
Period size: 166 Copynumber: 2.5 Consensus size: 166
708112 CAATAAATAG
** * * * *
708122 TTGGTACAAAAATATATCCCACTATATGCCGTGCCTGAACAAATAGTGTGTTAAAATTTCAAGCA
1 TTGGTACAAAAATATATCCCAAAATATGGCATGCCTAAACAAATAGTGTGTTAAAATTTCAAGTA
* *
708187 TCTGCGATAAATAGTTGCTGAGAGATCTTTAACAAAATTTTGTATGAAAATTTTGGCTAAAAATA
66 TCTGCGATAAATAATTGCTGAGAAATCTTTAACAAAATTTTGTATGAAAATTTTGGCTAAAAATA
* *
708252 AATAAAGTCGTCATTTAACAGGAAGTTGACGTCCGA
131 AACAAAGTCATCATTTAACAGGAAGTTGACGTCCGA
* *
708288 TTGGTACAAAAATATATCCCAAGATATGGCATGCCTAAACAAATAGTGTGTTTAAATTTCAAGTA
1 TTGGTACAAAAATATATCCCAAAATATGGCATGCCTAAACAAATAGTGTGTTAAAATTTCAAGTA
* * * * *
708353 TCTGCGATAAATATTTGCTGAGAAATCTTTGACGAAAA-TTTGTTTGAAAATTTTGGCTATAATT
66 TCTGCGATAAATAATTGCTGAGAAATCTTTAAC-AAAATTTTGTATGAAAATTTTGGCTAAAAAT
708417 AAACAAAGTCATCATTTAACAGGAAGTTGACGTCCGA
130 AAACAAAGTCATCATTTAACAGGAAGTTGACGTCCGA
** * * * **
708454 TTGGTGTAAAAGTATAT-TCAACAATATAGCATGCCTAAACAAATAGTGTGTTAAAATTTC-CTT
1 TTGGTACAAAAATATATCCCAA-AATATGGCATGCCTAAACAAATAGTGTGTTAAAATTTCAAGT
708517 CATCTGCGATAAATAATTGCTGAGAAA
65 -ATCTGCGATAAATAATTGCTGAGAAA
708544 AATGTGACAG
Statistics
Matches: 228, Mismatches: 25, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
165 4 0.02
166 220 0.96
167 4 0.02
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.32
Consensus pattern (166 bp):
TTGGTACAAAAATATATCCCAAAATATGGCATGCCTAAACAAATAGTGTGTTAAAATTTCAAGTA
TCTGCGATAAATAATTGCTGAGAAATCTTTAACAAAATTTTGTATGAAAATTTTGGCTAAAAATA
AACAAAGTCATCATTTAACAGGAAGTTGACGTCCGA
Found at i:718434 original size:42 final size:42
Alignment explanation
Indices: 718370--718764 Score: 499
Period size: 42 Copynumber: 9.2 Consensus size: 42
718360 CACATCATCA
*
718370 AGGATCTGAT--TAAGCGACACATCATTAAAACGGGAGCATTA
1 AGGATCTGATCGT-AGCGACACATCATTAAAACGGGAGCATTG
*
718411 AGGATCTGATCGTAGCGACACATCATTAAAATGGGAGCATTG
1 AGGATCTGATCGTAGCGACACATCATTAAAACGGGAGCATTG
718453 AGGATCTGATCGTAGCGACACATCATTAAAACGGGAGCATTG
1 AGGATCTGATCGTAGCGACACATCATTAAAACGGGAGCATTG
*
718495 AGGATCTGATCGTAGCGACACATCATTAAAACGGGAGCGTTG
1 AGGATCTGATCGTAGCGACACATCATTAAAACGGGAGCATTG
718537 AGGATCTGATCGTAGCGACACATCATTAAAACGGGAGCATTG
1 AGGATCTGATCGTAGCGACACATCATTAAAACGGGAGCATTG
718579 AGGATCTGATCGTAGCGACACATCATTAAAACGGGAGCATTG
1 AGGATCTGATCGTAGCGACACATCATTAAAACGGGAGCATTG
* * * * ** ** * *
718621 AGGATCTGATTGTAGCAATATGAGGATCTGATCGTAGCGAC-ATATCATTA
1 AGGATCTGATCGTAGC--GA-CA-CATC--AT--TA-AAACGGGAGCATTG
* **
718671 AGGATCTGATCGTAGCGACACATCATGAAAACGAAAGCATTG
1 AGGATCTGATCGTAGCGACACATCATTAAAACGGGAGCATTG
* * *
718713 AGGATCTGATCGTAGCGACATATCATTAAAACGGTAGCATGG
1 AGGATCTGATCGTAGCGACACATCATTAAAACGGGAGCATTG
*
718755 AGGATATGAT
1 AGGATCTGAT
718765 TTTAATCAGA
Statistics
Matches: 311, Mismatches: 31, Indels: 23
0.85 0.08 0.06
Matches are distributed among these distances:
41 12 0.04
42 260 0.84
43 1 0.00
44 3 0.01
45 1 0.00
46 6 0.02
47 1 0.00
48 3 0.01
50 22 0.07
51 2 0.01
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.23
Consensus pattern (42 bp):
AGGATCTGATCGTAGCGACACATCATTAAAACGGGAGCATTG
Found at i:718675 original size:28 final size:28
Alignment explanation
Indices: 718643--718696 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
718633 TAGCAATATG
*
718643 AGGATCTGATCGTAGCGACATATCATTA
1 AGGATCTGATCGTAGCGACACATCATTA
718671 AGGATCTGATCGTAGCGACACATCAT
1 AGGATCTGATCGTAGCGACACATCAT
718697 GAAAACGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.26
Consensus pattern (28 bp):
AGGATCTGATCGTAGCGACACATCATTA
Found at i:726612 original size:32 final size:32
Alignment explanation
Indices: 726571--726804 Score: 263
Period size: 32 Copynumber: 7.1 Consensus size: 32
726561 TGAATGGGAC
* *
726571 CTCACTACACAACAGGTAAGATACACAGGTAC
1 CTCACTACACAGCAGGTAAGATACACAGGTAA
* * *
726603 CTCAATACACTGCAGGTAAGATTACAAAGGTAA
1 CTCACTACACAGCAGGTAAGA-TACACAGGTAA
* * *
726636 CTCACTACAC-GTCACGTAAGACACACAAGTAA
1 CTCACTACACAG-CAGGTAAGATACACAGGTAA
* * *
726668 CTCCCAACACAGCAGGTAAGATATACAGGTAA
1 CTCACTACACAGCAGGTAAGATACACAGGTAA
* *
726700 CTCAGTTCACAGCAGGTAAGATTACACAGGTAA
1 CTCACTACACAGCAGGTAAGA-TACACAGGTAA
726733 CTCACTACACAGCAGGTAAGATTACACACTCGGGTAA
1 CTCACTACACAGCAGGTAAGA-TACACA----GGTAA
*
726770 CTCACTACACAGCAGGTAAGATACGCAGGTAA
1 CTCACTACACAGCAGGTAAGATACACAGGTAA
726802 CTC
1 CTC
726805 TCTATACCTT
Statistics
Matches: 170, Mismatches: 24, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
32 76 0.45
33 63 0.37
36 5 0.03
37 26 0.15
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.18
Consensus pattern (32 bp):
CTCACTACACAGCAGGTAAGATACACAGGTAA
Found at i:726683 original size:65 final size:65
Alignment explanation
Indices: 726571--726804 Score: 210
Period size: 65 Copynumber: 3.6 Consensus size: 65
726561 TGAATGGGAC
* * * * *
726571 CTCACTACACAACAGGTAAGAT-ACACAGGTACCTCA-ATACACTGCAGGTAAGATTACAAAGGT
1 CTCACTACACAGCACGTAAGATCACACAAGTAACTCACA-ACACAGCAGGTAAGATTAC-AAGGT
726634 AA
64 AA
*
726636 CTCACTACAC-GTCACGTAAGA-CACACAAGTAACTCCCAACACAGCAGGTAAGATATAC-AGGT
1 CTCACTACACAG-CACGTAAGATCACACAAGTAACTCACAACACAGCAGGTAAGAT-TACAAGGT
726698 AA
64 AA
* * * * * *
726700 CTCAGTTCACAGCAGGTAAGATTACACAGGTAACTCACTACACAGCAGGTAAGATTACACACTCG
1 CTCACTACACAGCACGTAAGATCACACAAGTAACTCACAACACAGCAGGTAAGATTACA-A----
726765 GGTAA
61 GGTAA
* * *
726770 CTCACTACACAGCAGGTAAGAT-ACGCAGGTAACTC
1 CTCACTACACAGCACGTAAGATCACACAAGTAACTC
726805 TCTATACCTT
Statistics
Matches: 141, Mismatches: 16, Indels: 20
0.80 0.09 0.11
Matches are distributed among these distances:
64 25 0.18
65 74 0.52
66 5 0.04
69 12 0.09
70 25 0.18
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.18
Consensus pattern (65 bp):
CTCACTACACAGCACGTAAGATCACACAAGTAACTCACAACACAGCAGGTAAGATTACAAGGTAA
Found at i:726717 original size:19 final size:18
Alignment explanation
Indices: 726693--726751 Score: 54
Period size: 19 Copynumber: 3.4 Consensus size: 18
726683 GTAAGATATA
726693 CAGGTAACTCAGTTCACAG
1 CAGGTAACTCA-TTCACAG
*
726712 CAGGTAA--GATT-ACA-
1 CAGGTAACTCATTCACAG
*
726726 CAGGTAACTCACTACACAG
1 CAGGTAACTCA-TTCACAG
726745 CAGGTAA
1 CAGGTAA
726752 GATTACACAC
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
14 7 0.22
15 3 0.09
16 3 0.09
17 2 0.06
18 3 0.09
19 14 0.44
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.19
Consensus pattern (18 bp):
CAGGTAACTCATTCACAG
Found at i:726752 original size:97 final size:99
Alignment explanation
Indices: 726571--726804 Score: 285
Period size: 97 Copynumber: 2.4 Consensus size: 99
726561 TGAATGGGAC
* * * *
726571 CTCACTACACAACAGGTAAGATACACAGGTACCTCAATACACTGCAGGTAAGATTACAAAGGTAA
1 CTCACAACACAGCAGGTAAGATACACAGGTAACTCAATACACAGCAGGTAAGATTACAAAGGTAA
726636 CTCACTACACGTCACGTAAG-ACACA-CAAGTAA
66 CTCACTACACGTCACGTAAGTACACACCAAGTAA
* * * * *
726668 CTCCCAACACAGCAGGTAAGATATACAGGTAACTCAGTTCACAGCAGGTAAGATTACACAGGTAA
1 CTCACAACACAGCAGGTAAGATACACAGGTAACTCAATACACAGCAGGTAAGATTACAAAGGTAA
* **
726733 CTCACTACACAG-CAGGTAAGATTACACACTCGGGTAA
66 CTCACTACAC-GTCACGTAAG--TACACAC-CAAGTAA
* *
726770 CTCACTACACAGCAGGTAAGATACGCAGGTAACTC
1 CTCACAACACAGCAGGTAAGATACACAGGTAACTC
726805 TCTATACCTT
Statistics
Matches: 115, Mismatches: 16, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
97 73 0.63
98 1 0.01
100 5 0.04
102 36 0.31
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.18
Consensus pattern (99 bp):
CTCACAACACAGCAGGTAAGATACACAGGTAACTCAATACACAGCAGGTAAGATTACAAAGGTAA
CTCACTACACGTCACGTAAGTACACACCAAGTAA
Found at i:726760 original size:17 final size:17
Alignment explanation
Indices: 726707--726760 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 17
726697 TAACTCAGTT
726707 CACAGCAGGTAAGATT-
1 CACAGCAGGTAAGATTA
* *
726723 -ACA-CAGGTAACTCACTA
1 CACAGCAGGTAA--GATTA
726740 CACAGCAGGTAAGATTA
1 CACAGCAGGTAAGATTA
726757 CACA
1 CACA
726761 CTCGGGTAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 9
0.69 0.10 0.21
Matches are distributed among these distances:
14 7 0.24
15 3 0.10
16 2 0.07
17 7 0.24
18 3 0.10
19 7 0.24
ACGTcount: A:0.41, C:0.24, G:0.19, T:0.17
Consensus pattern (17 bp):
CACAGCAGGTAAGATTA
Done.