Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold149
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: 1065560
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.30
Warning! 107426 characters in sequence are not A, C, G, or T
File 3 of 4
Found at i:387435 original size:15 final size:15
Alignment explanation
Indices: 387415--387448 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
387405 GTTCAAATCT
387415 CATAGCATACCATAC
1 CATAGCATACCATAC
*
387430 CATAGCATAGCATAC
1 CATAGCATACCATAC
387445 CATA
1 CATA
387449 TAATTAAACT
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:0.29, G:0.09, T:0.21
Consensus pattern (15 bp):
CATAGCATACCATAC
Found at i:390128 original size:11 final size:11
Alignment explanation
Indices: 390114--390138 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
390104 TAAAATGTAG
390114 AAAAAATAAAT
1 AAAAAATAAAT
390125 AAAAAATAAAT
1 AAAAAATAAAT
390136 AAA
1 AAA
390139 TTCGAGCTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAAAATAAAT
Found at i:392270 original size:75 final size:74
Alignment explanation
Indices: 392179--392343 Score: 258
Period size: 75 Copynumber: 2.2 Consensus size: 74
392169 ATTTCTCTTT
*
392179 GATATAGAGAAAGAGACTATAGTACTTTTACTATATTGAGTCTGTCATACGTAAGAGAGAGAGAG
1 GATATAGAGAAAGAGACTATAGTACTTTTACTATATTGAGTCTGTCATACGTAAGAAAGAGAGAG
392244 AGAGAGAGA
66 AGAGAGAGA
* *
392253 GNATATAGAGAAAGAGACTATAGTACTTTTACTATATTGAGTCTGTCATTCGTAAGAAAGATAGA
1 G-ATATAGAGAAAGAGACTATAGTACTTTTACTATATTGAGTCTGTCATACGTAAGAAAGAGAGA
*
392318 TAGAGAGAGA
65 GAGAGAGAGA
* * *
392328 GAGAGAGAGAGAGAGA
1 GATATAGAGAAAGAGA
392344 GAGAGATTGA
Statistics
Matches: 83, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
74 13 0.16
75 70 0.84
ACGTcount: A:0.41, C:0.07, G:0.27, T:0.24
Consensus pattern (74 bp):
GATATAGAGAAAGAGACTATAGTACTTTTACTATATTGAGTCTGTCATACGTAAGAAAGAGAGAG
AGAGAGAGA
Found at i:392326 original size:2 final size:2
Alignment explanation
Indices: 392319--392349 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
392309 AAAGATAGAT
392319 AG AG 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 AG AG A
392350 TTGAAAGCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:393547 original size:2 final size:2
Alignment explanation
Indices: 393542--393595 Score: 67
Period size: 2 Copynumber: 28.0 Consensus size: 2
393532 TTTATATATG
* * *
393542 CA CA CA CA CA CA CA CA CA CC CA CA CC CA CA CC CA CA C- CA -A
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
393582 CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA
393596 TTACATGTAC
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
1 2 0.05
2 42 0.95
ACGTcount: A:0.44, C:0.56, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:395976 original size:17 final size:17
Alignment explanation
Indices: 395950--395983 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
395940 GATATATTGT
*
395950 TTTATAATTAAATTAAA
1 TTTATAATTAAAATAAA
*
395967 TTTATTATTAAAATAAA
1 TTTATAATTAAAATAAA
395984 AAAGTCATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TTTATAATTAAAATAAA
Found at i:398082 original size:4 final size:4
Alignment explanation
Indices: 398073--398144 Score: 144
Period size: 4 Copynumber: 18.0 Consensus size: 4
398063 ATATAATCAA
398073 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
398121 TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC
398145 CGTCCGTCCG
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 68 1.00
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.50
Consensus pattern (4 bp):
TATC
Found at i:400442 original size:2 final size:2
Alignment explanation
Indices: 400435--400472 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
400425 AGACTGAAAA
400435 TC 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 TC
400473 ATGCTTTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:404810 original size:141 final size:140
Alignment explanation
Indices: 404556--404836 Score: 553
Period size: 141 Copynumber: 2.0 Consensus size: 140
404546 AGATTAATAT
404556 TATTTGTAAAGGTAAAACGGACTCAATTTGCACATCAAAATACAGAAAGTTAAATTATAAGGAAT
1 TATTTGTAAAGGTAAAACGGACTCAATTTGCACATCAAAATACAGAAAGTTAAATTATAAGGAAT
404621 ATATTCAATATTTACCCAATTTGTACTCGTATAACCTGGGTTGGAGCAATTTCCGCTTTTTTATA
66 ATATTCAATATTTACCCAATTTGTACTCGTATAACCTGGGTTGGAGCAATTTCCGCTTTTTTATA
404686 ATCTGCTTCC
131 ATCTGCTTCC
404696 NTATTTGTAAAGGTAAAACGGACTCAATTTGCACATCAAAATACAGAAAGTTAAATTATAAGGAA
1 -TATTTGTAAAGGTAAAACGGACTCAATTTGCACATCAAAATACAGAAAGTTAAATTATAAGGAA
404761 TATATTCAATATTTACCCAATTTGTACTCGTATAACCTGGGTTGGAGCAATTTCCGCTTTTTTAT
65 TATATTCAATATTTACCCAATTTGTACTCGTATAACCTGGGTTGGAGCAATTTCCGCTTTTTTAT
404826 AATCTGCTTCC
130 AATCTGCTTCC
404837 ACAGGATGAA
Statistics
Matches: 140, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
141 140 1.00
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.35
Consensus pattern (140 bp):
TATTTGTAAAGGTAAAACGGACTCAATTTGCACATCAAAATACAGAAAGTTAAATTATAAGGAAT
ATATTCAATATTTACCCAATTTGTACTCGTATAACCTGGGTTGGAGCAATTTCCGCTTTTTTATA
ATCTGCTTCC
Found at i:404940 original size:11 final size:11
Alignment explanation
Indices: 404910--404941 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
404900 TAAAGACGAT
*
404910 CTTTAAGCCAC
1 CTTTAAGCTAC
404921 CTTTAAGCTAC
1 CTTTAAGCTAC
404932 CTTTAAGCTA
1 CTTTAAGCTA
404942 TANNNNNNNN
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.28, C:0.28, G:0.09, T:0.34
Consensus pattern (11 bp):
CTTTAAGCTAC
Found at i:415763 original size:11 final size:11
Alignment explanation
Indices: 415747--415812 Score: 69
Period size: 11 Copynumber: 6.0 Consensus size: 11
415737 TCCCATTTTT
*
415747 CCGTGCGTTTA
1 CCGTGCGTTCA
*
415758 CCGTGCGCTCA
1 CCGTGCGTTCA
*
415769 CAGTGCGTTCA
1 CCGTGCGTTCA
* *
415780 CTGTGCGCTCA
1 CCGTGCGTTCA
* *
415791 CAGTGCGTACA
1 CCGTGCGTTCA
415802 CCGTGCGTTCA
1 CCGTGCGTTCA
415813 TTTGCGATCT
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 44 1.00
ACGTcount: A:0.14, C:0.33, G:0.27, T:0.26
Consensus pattern (11 bp):
CCGTGCGTTCA
Found at i:415775 original size:22 final size:22
Alignment explanation
Indices: 415749--415808 Score: 93
Period size: 22 Copynumber: 2.7 Consensus size: 22
415739 CCATTTTTCC
*
415749 GTGCGTTTACCGTGCGCTCACA
1 GTGCGTTCACCGTGCGCTCACA
*
415771 GTGCGTTCACTGTGCGCTCACA
1 GTGCGTTCACCGTGCGCTCACA
*
415793 GTGCGTACACCGTGCG
1 GTGCGTTCACCGTGCG
415809 TTCATTTGCG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.13, C:0.32, G:0.30, T:0.25
Consensus pattern (22 bp):
GTGCGTTCACCGTGCGCTCACA
Found at i:417083 original size:11 final size:11
Alignment explanation
Indices: 417028--417111 Score: 69
Period size: 11 Copynumber: 7.6 Consensus size: 11
417018 CAAATTCCGT
*
417028 TCAGCGTGCGC
1 TCAGAGTGCGC
** *
417039 TCACCGTTCGC
1 TCAGAGTGCGC
417050 TCAGAGTGCGC
1 TCAGAGTGCGC
** *
417061 TCACCGTACGC
1 TCAGAGTGCGC
*
417072 TTAGAGTGCGC
1 TCAGAGTGCGC
** *
417083 TCATTGTACGC
1 TCAGAGTGCGC
417094 TCAGAGTGCGC
1 TCAGAGTGCGC
417105 TCAGAGT
1 TCAGAGT
417112 TCACTCACCG
Statistics
Matches: 54, Mismatches: 19, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
11 54 1.00
ACGTcount: A:0.17, C:0.31, G:0.29, T:0.24
Consensus pattern (11 bp):
TCAGAGTGCGC
Found at i:417118 original size:22 final size:22
Alignment explanation
Indices: 417028--417107 Score: 115
Period size: 22 Copynumber: 3.6 Consensus size: 22
417018 CAAATTCCGT
* *
417028 TCAGCGTGCGCTCACCGTTCGC
1 TCAGAGTGCGCTCACCGTACGC
417050 TCAGAGTGCGCTCACCGTACGC
1 TCAGAGTGCGCTCACCGTACGC
* **
417072 TTAGAGTGCGCTCATTGTACGC
1 TCAGAGTGCGCTCACCGTACGC
417094 TCAGAGTGCGCTCA
1 TCAGAGTGCGCTCA
417108 GAGTTCACTC
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.16, C:0.33, G:0.28, T:0.24
Consensus pattern (22 bp):
TCAGAGTGCGCTCACCGTACGC
Found at i:420735 original size:4 final size:4
Alignment explanation
Indices: 420728--420796 Score: 138
Period size: 4 Copynumber: 17.2 Consensus size: 4
420718 AATATTTCTT
420728 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
420776 TATC TATC TATC TATC TATC T
1 TATC TATC TATC TATC TATC T
420797 TTTTTCTATT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 65 1.00
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.51
Consensus pattern (4 bp):
TATC
Found at i:434843 original size:16 final size:16
Alignment explanation
Indices: 434822--434856 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
434812 AAAATGCCCG
434822 GTAATTTGTGAAACTA
1 GTAATTTGTGAAACTA
434838 GTAATTTGTGAAACTA
1 GTAATTTGTGAAACTA
434854 GTA
1 GTA
434857 TTTTTAGCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.37, C:0.06, G:0.20, T:0.37
Consensus pattern (16 bp):
GTAATTTGTGAAACTA
Found at i:435495 original size:12 final size:12
Alignment explanation
Indices: 435480--435514 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
435470 CCGTTTTCCC
*
435480 TTCCGTTCTGCT
1 TTCCGTTCCGCT
*
435492 TTCCGTTCCGTT
1 TTCCGTTCCGCT
435504 TTCCGTTCCGC
1 TTCCGTTCCGC
435515 GTTTTAGCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.00, C:0.37, G:0.17, T:0.46
Consensus pattern (12 bp):
TTCCGTTCCGCT
Found at i:438558 original size:2 final size:2
Alignment explanation
Indices: 438551--438592 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
438541 GTAAAAGTGA
438551 TC TC TC 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 TC TC TC
438593 AGGGAGAGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:461857 original size:2 final size:2
Alignment explanation
Indices: 461852--461910 Score: 109
Period size: 2 Copynumber: 29.5 Consensus size: 2
461842 ATCAGAATAC
*
461852 CT CT CT CT CT CT CT CT CT CC CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
461894 CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT C
461911 CAGTTTAATA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:472889 original size:16 final size:16
Alignment explanation
Indices: 472870--472906 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
472860 TATCACCTAG
472870 TTTTTTTTTTTTTGTT
1 TTTTTTTTTTTTTGTT
472886 TTTTTTTTTTTTTGTT
1 TTTTTTTTTTTTTGTT
472902 TTTTT
1 TTTTT
472907 ACCTTTTTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.05, T:0.95
Consensus pattern (16 bp):
TTTTTTTTTTTTTGTT
Found at i:472914 original size:1 final size:1
Alignment explanation
Indices: 472870--472906 Score: 56
Period size: 1 Copynumber: 37.0 Consensus size: 1
472860 TATCACCTAG
* *
472870 TTTTTTTTTTTTTGTTTTTTTTTTTTTTTGTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
472907 ACCTTTTTGC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.05, T:0.95
Consensus pattern (1 bp):
T
Found at i:479576 original size:29 final size:29
Alignment explanation
Indices: 479540--479619 Score: 151
Period size: 29 Copynumber: 2.8 Consensus size: 29
479530 AAATATGAAC
479540 AAGCAAAGGAAGATAACTCCATAATGAGA
1 AAGCAAAGGAAGATAACTCCATAATGAGA
479569 AAGCAAAGGAAGATAACTCCATAATGAGA
1 AAGCAAAGGAAGATAACTCCATAATGAGA
*
479598 AAGCAAAGGAAGATAATTCCAT
1 AAGCAAAGGAAGATAACTCCAT
479620 TAACTGTTAC
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.51, C:0.14, G:0.20, T:0.15
Consensus pattern (29 bp):
AAGCAAAGGAAGATAACTCCATAATGAGA
Found at i:488406 original size:2 final size:2
Alignment explanation
Indices: 488401--488425 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
488391 ACACACACAC
488401 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
488426 NNNNNNNNNN
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:488661 original size:39 final size:39
Alignment explanation
Indices: 488584--488663 Score: 126
Period size: 40 Copynumber: 2.1 Consensus size: 39
488574 CCACACACAC
*
488584 AAAAATTAACCGTTTTCATAATTTTGGTATTATCCAAAA
1 AAAAATTAACCGTTTTCATAATTTTGGCATTATCCAAAA
*
488623 AAAAATTGAACTGTTTTCATAATTTTGGCATTAT-CAAAA
1 AAAAATT-AACCGTTTTCATAATTTTGGCATTATCCAAAA
488662 AA
1 AA
488664 GATTTTTTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
39 14 0.37
40 24 0.63
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.38
Consensus pattern (39 bp):
AAAAATTAACCGTTTTCATAATTTTGGCATTATCCAAAA
Found at i:494480 original size:4 final size:4
Alignment explanation
Indices: 494473--494506 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
494463 GGGTGGGTGG
494473 GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GT
1 GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GT
494507 CAAGGTTCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.00, C:0.24, G:0.50, T:0.26
Consensus pattern (4 bp):
GTGC
Found at i:497608 original size:40 final size:40
Alignment explanation
Indices: 497551--498174 Score: 489
Period size: 40 Copynumber: 15.4 Consensus size: 40
497541 GAATAATACN
* *
497551 TCACCACCGAGTCTTACCCTTACTGTACTATGGTTCTTCG
1 TCACCACCGAGTGTTACCCTTACTGTACTAAGGTTCTTCG
* *
497591 TCACCACCGAGTGTTACCCCTACTGTACTAAGGTTCGTCG
1 TCACCACCGAGTGTTACCCTTACTGTACTAAGGTTCTTCG
** * *
497631 TCAATACCGAGTGTTACCCTTACTGTACTATGGTTCGTCG
1 TCACCACCGAGTGTTACCCTTACTGTACTAAGGTTCTTCG
* * *
497671 TCACCACCGAGTGTAACCCTTACTGAACTAAGGTTCGTCG
1 TCACCACCGAGTGTTACCCTTACTGTACTAAGGTTCTTCG
* * * *
497711 TCACCACCGAGTGTAACCCTTACTGAACTAAGTTTCGTCG
1 TCACCACCGAGTGTTACCCTTACTGTACTAAGGTTCTTCG
* *
497751 TCACCACCGAGTGTTACCCTTACTGTACTAAGGTTCGTCA
1 TCACCACCGAGTGTTACCCTTACTGTACTAAGGTTCTTCG
* * *
497791 TCACTACCGAGTGTTACCCTTACTGTACTATGGTTCGTACCG
1 TCACCACCGAGTGTTACCCTTACTGTACTAAGGTTC-T-TCG
* * * ** * * *
497833 ACTCTAATGAGTCTTA-CCTTAATGTACTAAGGTACGTGTCG
1 TCACCACCGAGTGTTACCCTTACTGTACTAAGGTTC-T-TCG
* * *
497874 TCA-CACCAGAGCGTTACCCTTACTGTACTAGGGTTCGTCG
1 TCACCACC-GAGTGTTACCCTTACTGTACTAAGGTTCTTCG
** * * *
497914 TCATTACAGAGTGTTACCCTTACTGTTCTAA-GATCGTGTCG
1 TCACCACCGAGTGTTACCCTTACTGTACTAAGGTTC-T-TCG
* * ** * * *
497955 ACTCCAATGAGTGTTA-CCTTAATGTATTAAGGTTCGAATCG
1 TCACCACCGAGTGTTACCCTTACTGTACTAAGGTTC--TTCG
* * * *
497996 TCTCCACCGAGTGTTATCCC--ACTGTATTTAGGTTTGTGTCG
1 TCACCACCGAGTGTTA-CCCTTACTGTACTAAGG-TTCT-TCG
* *
498037 TCACCACCAAGTGTTA-CCTTGCTGTACTAAGGTT-TGTACCG
1 TCACCACCGAGTGTTACCCTTACTGTACTAAGGTTCT-T--CG
* ** *
498078 ACTTCACCGAGTGTTATCCC--ACTGTACTAAGGTTTGTGTCG
1 TCACCACCGAGTGTTA-CCCTTACTGTACTAAGG-TTCT-TCG
*
498119 TCACCACCGAGTGTTATCCC--ACTGTACTAAGGTTTGTGTCG
1 TCACCACCGAGTGTTA-CCCTTACTGTACTAAGG-TTCT-TCG
498160 TCACCACCGAGTGTT
1 TCACCACCGAGTGTT
498175 TCCCCACTGT
Statistics
Matches: 480, Mismatches: 83, Indels: 41
0.79 0.14 0.07
Matches are distributed among these distances:
39 8 0.02
40 256 0.53
41 177 0.37
42 32 0.07
43 7 0.01
ACGTcount: A:0.21, C:0.27, G:0.20, T:0.32
Consensus pattern (40 bp):
TCACCACCGAGTGTTACCCTTACTGTACTAAGGTTCTTCG
Found at i:497695 original size:80 final size:80
Alignment explanation
Indices: 497551--498174 Score: 561
Period size: 80 Copynumber: 7.7 Consensus size: 80
497541 GAATAATACN
* * * *
497551 TCACCACCGAGTCTTACCCTTACTGTACTATGGTTCTTCGTCACCACCGAGTGTTACCCCTACTG
1 TCACCACCGAGTGTTACCCTTACTGTACTAAGGTTCGTCGTCACCACCGAGTGTTACCCTTACTG
497616 TACTAAGGTTCGTCG
66 TACTAAGGTTCGTCG
** * *
497631 TCAATACCGAGTGTTACCCTTACTGTACTATGGTTCGTCGTCACCACCGAGTGTAACCCTTACTG
1 TCACCACCGAGTGTTACCCTTACTGTACTAAGGTTCGTCGTCACCACCGAGTGTTACCCTTACTG
*
497696 AACTAAGGTTCGTCG
66 TACTAAGGTTCGTCG
* * *
497711 TCACCACCGAGTGTAACCCTTACTGAACTAAGTTTCGTCGTCACCACCGAGTGTTACCCTTACTG
1 TCACCACCGAGTGTTACCCTTACTGTACTAAGGTTCGTCGTCACCACCGAGTGTTACCCTTACTG
*
497776 TACTAAGGTTCGTCA
66 TACTAAGGTTCGTCG
* * * * * ** * *
497791 TCACTACCGAGTGTTACCCTTACTGTACTATGGTTCGTACCGACTCTAATGAGTCTTA-CCTTAA
1 TCACCACCGAGTGTTACCCTTACTGTACTAAGGTTCGT--CGTCACCACCGAGTGTTACCCTTAC
*
497855 TGTACTAAGGTACGTGTCG
64 TGTACTAAGGTTC--GTCG
* * ** *
497874 TCA-CACCAGAGCGTTACCCTTACTGTACTAGGGTTCGTCGTCATTACAGAGTGTTACCCTTACT
1 TCACCACC-GAGTGTTACCCTTACTGTACTAAGGTTCGTCGTCACCACCGAGTGTTACCCTTACT
* *
497938 GTTCTAA-GATCGT-G
65 GTACTAAGGTTCGTCG
** * * *
497952 TCGACTCCAATGAGTGTTA-CCTTAATGTATTAAGGTTCGAATCGTCTCCACCGAGTGTTATCCC
1 TC-A--CCACCGAGTGTTACCCTTACTGTACTAAGGTTCG--TCGTCACCACCGAGTGTTA-CCC
* * *
498016 --ACTGTATTTAGGTTTGTGTCG
60 TTACTGTACTAAGG-TT-CGTCG
* * * * **
498037 TCACCACCAAGTGTTA-CCTTGCTGTACTAAGGTTTGTACCGACTTCACCGAGTGTTATCCC--A
1 TCACCACCGAGTGTTACCCTTACTGTACTAAGGTTCGT--CGTCACCACCGAGTGTTA-CCCTTA
*
498099 CTGTACTAAGGTTTGTGTCG
63 CTGTACTAAGG-TT-CGTCG
*
498119 TCACCACCGAGTGTTATCCC--ACTGTACTAAGGTTTGTGTCGTCACCACCGAGTGTT
1 TCACCACCGAGTGTTA-CCCTTACTGTACTAAGG-TT-CGTCGTCACCACCGAGTGTT
498175 TCCCCACTGT
Statistics
Matches: 447, Mismatches: 74, Indels: 44
0.79 0.13 0.08
Matches are distributed among these distances:
78 3 0.01
79 3 0.01
80 195 0.44
81 45 0.10
82 150 0.34
83 40 0.09
84 8 0.02
85 3 0.01
ACGTcount: A:0.21, C:0.27, G:0.20, T:0.32
Consensus pattern (80 bp):
TCACCACCGAGTGTTACCCTTACTGTACTAAGGTTCGTCGTCACCACCGAGTGTTACCCTTACTG
TACTAAGGTTCGTCG
Found at i:498022 original size:41 final size:41
Alignment explanation
Indices: 497993--498185 Score: 255
Period size: 41 Copynumber: 4.7 Consensus size: 41
497983 AAGGTTCGAA
* * *
497993 TCGTCTCCACCGAGTGTTATCCCACTGTATTTAGGTTTGTG
1 TCGTCACCACCGAGTGTTATCCCACTGTACTAAGGTTTGTG
* ** *
498034 TCGTCACCACCAAGTGTTA-CCTTGCTGTACTAAGGTTTGTA
1 TCGTCACCACCGAGTGTTATCC-CACTGTACTAAGGTTTGTG
* * **
498075 CCGACTTCACCGAGTGTTATCCCACTGTACTAAGGTTTGTG
1 TCGTCACCACCGAGTGTTATCCCACTGTACTAAGGTTTGTG
498116 TCGTCACCACCGAGTGTTATCCCACTGTACTAAGGTTTGTG
1 TCGTCACCACCGAGTGTTATCCCACTGTACTAAGGTTTGTG
498157 TCGTCACCACCGAGTGTT-TCCCCACTGTA
1 TCGTCACCACCGAGTGTTAT-CCCACTGTA
498186 TTATGGTCCG
Statistics
Matches: 130, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
40 3 0.02
41 125 0.96
42 2 0.02
ACGTcount: A:0.19, C:0.27, G:0.21, T:0.33
Consensus pattern (41 bp):
TCGTCACCACCGAGTGTTATCCCACTGTACTAAGGTTTGTG
Found at i:498185 original size:123 final size:119
Alignment explanation
Indices: 497551--498174 Score: 519
Period size: 123 Copynumber: 5.1 Consensus size: 119
497541 GAATAATACN
* * * * *
497551 TCACCACCGAGTCTTACCCTTACTGTACTATGGTTCTTCGTCACCACCGAGTGTTACCCCTACTG
1 TCACCACCGAGTGTTACCCTTACTGTACTAAGGTTCGTCGACTCCACCGAGTGTTA-CCC-ACTG
** *
497616 TACTAAGG-TT-CGTCGTCAATACCGAGTGTTACCCTTACTGTACTATGGTTCGTCG
64 TACTAAGGTTTGCGTCGTCACCACCGAGTGTTACCC-TACTGTACTAAGGTTCGTCG
* * * * *
497671 TCACCACCGAGTGTAACCCTTACTGAACTAAGGTTCGTCGTCACCACCGAGTGTAACCCTTACTG
1 TCACCACCGAGTGTTACCCTTACTGTACTAAGGTTCGTCGACTCCACCGAGTGTTACCC--ACTG
* *
497736 AACTAA-GTTT-CGTCGTCACCACCGAGTGTTACCCTTACTGTACTAAGGTTCGTCA
64 TACTAAGGTTTGCGTCGTCACCACCGAGTGTTACCC-TACTGTACTAAGGTTCGTCG
* * * ** * * *
497791 TCACTACCGAGTGTTACCCTTACTGTACTATGGTTCGTACCGACTCTAATGAGTCTTACCTTAAT
1 TCACCACCGAGTGTTACCCTTACTGTACTAAGGTTCGT--CGACTCCACCGAGTGTTACC-CACT
** * * *
497856 GTACTAAGGTACGTGTCGTCA-CACCAGAGCGTTACCCTTACTGTACTAGGGTTCGTCG
63 GTACTAAGGTTTGCGTCGTCACCACC-GAGTGTTACCC-TACTGTACTAAGGTTCGTCG
** * * * ** * *
497914 TCATTACAGAGTGTTACCCTTACTGTTCTAA-GATCGTGTCGACTCCAATGAGTGTTACCTTAAT
1 TCACCACCGAGTGTTACCCTTACTGTACTAAGGTTC--GTCGACTCCACCGAGTGTTACC-CACT
* * ** * * * *
497978 GTATTAAGGTTCGAATCGTCTCCACCGAGTGTTATCCC-ACTGTATTTAGGTTTGTGTCG
63 GTACTAAGGTTTGCGTCGTCACCACCGAGTGTTA-CCCTACTGTACTAAGG-TT-CGTCG
* * * *
498037 TCACCACCAAGTGTTA-CCTTGCTGTACTAAGGTTTGTACCGACTTCACCGAGTGTTATCCCACT
1 TCACCACCGAGTGTTACCCTTACTGTACTAAGGTTCGT--CGACTCCACCGAGTGTTA-CCCACT
* *
498101 GTACTAAGGTTTGTGTCGTCACCACCGAGTGTTATCCC-ACTGTACTAAGGTTTGTGTCG
63 GTACTAAGGTTTGCGTCGTCACCACCGAGTGTTA-CCCTACTGTACTAAGG-TT-CGTCG
498160 TCACCACCGAGTGTT
1 TCACCACCGAGTGTT
498175 TCCCCACTGT
Statistics
Matches: 417, Mismatches: 69, Indels: 33
0.80 0.13 0.06
Matches are distributed among these distances:
119 4 0.01
120 137 0.33
121 19 0.05
122 82 0.20
123 171 0.41
124 4 0.01
ACGTcount: A:0.21, C:0.27, G:0.20, T:0.32
Consensus pattern (119 bp):
TCACCACCGAGTGTTACCCTTACTGTACTAAGGTTCGTCGACTCCACCGAGTGTTACCCACTGTA
CTAAGGTTTGCGTCGTCACCACCGAGTGTTACCCTACTGTACTAAGGTTCGTCG
Found at i:498199 original size:82 final size:82
Alignment explanation
Indices: 497964--498201 Score: 275
Period size: 82 Copynumber: 2.9 Consensus size: 82
497954 GACTCCAATG
* * * * *
497964 AGTGTTACCTTAATGTATTAAGGTTCGAATCGTCTCCACCGAGTGTTATCCCACTGTATT-TAGG
1 AGTGTTACCTCACTGTACTAAGGTTTGTATCGTCTCCACCGAGTGTTATCCCACTGTATTAT-GG
498028 TTTGTGTCGTCACCACCA
65 TTTGTGTCGTCACCACCA
** * * * * *
498046 AGTGTTACCTTGCTGTACTAAGGTTTGTACCGACTTCACCGAGTGTTATCCCACTGTACTAAGGT
1 AGTGTTACCTCACTGTACTAAGGTTTGTATCGTCTCCACCGAGTGTTATCCCACTGTATTATGGT
*
498111 TTGTGTCGTCACCACCG
66 TTGTGTCGTCACCACCA
* *
498128 AGTGTTATCC-CACTGTACTAAGGTTTGTGTCGTCACCACCGAGTGTT-TCCCCACTGTATTATG
1 AGTGTTA-CCTCACTGTACTAAGGTTTGTATCGTCTCCACCGAGTGTTAT-CCCACTGTATTATG
**
498191 GTCCGTGTCGT
64 GTTTGTGTCGT
498202 ATTGCAGCTT
Statistics
Matches: 131, Mismatches: 22, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
81 1 0.01
82 128 0.98
83 2 0.02
ACGTcount: A:0.19, C:0.25, G:0.21, T:0.34
Consensus pattern (82 bp):
AGTGTTACCTCACTGTACTAAGGTTTGTATCGTCTCCACCGAGTGTTATCCCACTGTATTATGGT
TTGTGTCGTCACCACCA
Found at i:499046 original size:8 final size:8
Alignment explanation
Indices: 499033--499063 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
499023 ATTTCTATGG
499033 TGATTTAT
1 TGATTTAT
499041 TGATTTTAT
1 TGA-TTTAT
499050 TGATTTAT
1 TGATTTAT
499058 TGATTT
1 TGATTT
499064 TAAAATCTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 14 0.64
9 8 0.36
ACGTcount: A:0.23, C:0.00, G:0.13, T:0.65
Consensus pattern (8 bp):
TGATTTAT
Found at i:499050 original size:9 final size:9
Alignment explanation
Indices: 499036--499065 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
499026 TCTATGGTGA
499036 TTTATTGAT
1 TTTATTGAT
499045 TTTATTGA-
1 TTTATTGAT
499053 TTTATTGAT
1 TTTATTGAT
499062 TTTA
1 TTTA
499066 AAATCTGAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (9 bp):
TTTATTGAT
Found at i:499053 original size:17 final size:17
Alignment explanation
Indices: 499033--499065 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
499023 ATTTCTATGG
499033 TGATTTATTGATTTTAT
1 TGATTTATTGATTTTAT
499050 TGATTTATTGATTTTA
1 TGATTTATTGATTTTA
499066 AAATCTGAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (17 bp):
TGATTTATTGATTTTAT
Found at i:502222 original size:2 final size:2
Alignment explanation
Indices: 502215--502271 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
502205 AATATAAAGC
*
502215 AG AG AG AG AG AG AG AG AG GG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
502257 AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG A
502272 ATTAGACAGC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:505560 original size:2 final size:2
Alignment explanation
Indices: 505553--505600 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
505543 GTGAATATAA
505553 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
505595 AG AG AG
1 AG AG AG
505601 TCGAATTGAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:516833 original size:10 final size:11
Alignment explanation
Indices: 516797--516832 Score: 54
Period size: 11 Copynumber: 3.1 Consensus size: 11
516787 TTTAACTAAA
516797 TTATTTTGTTATT
1 TTATTTT-TT-TT
516810 TTATTTTTTTT
1 TTATTTTTTTT
516821 TTATTTTTTTT
1 TTATTTTTTTT
516832 T
1 T
516833 AAACATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 14 0.61
12 2 0.09
13 7 0.30
ACGTcount: A:0.11, C:0.00, G:0.03, T:0.86
Consensus pattern (11 bp):
TTATTTTTTTT
Found at i:519692 original size:65 final size:66
Alignment explanation
Indices: 519526--519729 Score: 277
Period size: 65 Copynumber: 3.1 Consensus size: 66
519516 CAAATTTATT
* * * * * *
519526 AAAAAAAATCTGTGAAAATATTACACTATAACGACAGGTGTTTAGTGGAGATCATCACAAAATAT
1 AAAAAAAATCTATGAAAATATTACACTCTAACGTCTGGTTTTTAGTGG-GGTCATCACAAAATAT
519591 AA
65 AA
*
519593 AAAAAAAATTCTATAAAAATATTACACTCTAACGTCTGGTTTTTAGTGGGCGTCATCACAAAAT-
1 AAAAAAAA-TCTATGAAAATATTACACTCTAACGTCTGGTTTTTAGTGGG-GTCATCACAAAATA
519657 T-A
64 TAA
*
519659 AAAAAAAATCTATGAAAATATTACACTCTAACGTCTGGTTTTTTGTGGGGGTCATCACAAAATAT
1 AAAAAAAATCTATGAAAATATTACACTCTAACGTCTGGTTTTTAGT-GGGGTCATCACAAAATAT
*
519724 TA
65 AA
519726 AAAA
1 AAAA
519730 TACACCAACT
Statistics
Matches: 123, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
65 49 0.40
66 13 0.11
67 15 0.12
68 46 0.37
ACGTcount: A:0.44, C:0.13, G:0.14, T:0.29
Consensus pattern (66 bp):
AAAAAAAATCTATGAAAATATTACACTCTAACGTCTGGTTTTTAGTGGGGTCATCACAAAATATA
A
Found at i:522294 original size:4 final size:4
Alignment explanation
Indices: 522285--522323 Score: 60
Period size: 4 Copynumber: 9.8 Consensus size: 4
522275 ACTGAAGTGG
* *
522285 GACA GACA GACG GACG GACA GACA GACA GACA GACA GAC
1 GACA GACA GACA GACA GACA GACA GACA GACA GACA GAC
522324 GGACGGACGG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.44, C:0.26, G:0.31, T:0.00
Consensus pattern (4 bp):
GACA
Found at i:522304 original size:12 final size:12
Alignment explanation
Indices: 522284--522336 Score: 61
Period size: 12 Copynumber: 4.4 Consensus size: 12
522274 AACTGAAGTG
*
522284 GGACAGACAGAC
1 GGACGGACAGAC
522296 GGACGGACAGAC
1 GGACGGACAGAC
* *
522308 AGACAGACAGAC
1 GGACGGACAGAC
* *
522320 AGACGGACGGAC
1 GGACGGACAGAC
522332 GGACG
1 GGACG
522337 CAGAAGAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.38, C:0.25, G:0.38, T:0.00
Consensus pattern (12 bp):
GGACGGACAGAC
Found at i:522336 original size:8 final size:8
Alignment explanation
Indices: 522284--522335 Score: 59
Period size: 8 Copynumber: 6.5 Consensus size: 8
522274 AACTGAAGTG
522284 GGACAGAC
1 GGACAGAC
* *
522292 AGACGGAC
1 GGACAGAC
522300 GGACAGAC
1 GGACAGAC
*
522308 AGACAGAC
1 GGACAGAC
*
522316 AGACAGAC
1 GGACAGAC
*
522324 GGACGGAC
1 GGACAGAC
522332 GGAC
1 GGAC
522336 GCAGAAGAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
8 37 1.00
ACGTcount: A:0.38, C:0.25, G:0.37, T:0.00
Consensus pattern (8 bp):
GGACAGAC
Found at i:525589 original size:2 final size:2
Alignment explanation
Indices: 525582--525617 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
525572 TTGAAACAAT
525582 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
525618 ACTAGTTTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:528627 original size:2 final size:2
Alignment explanation
Indices: 528620--528652 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
528610 TGTTAAAATC
528620 AG AG AG 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 AG AG AG A
528653 TGAATATTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:530384 original size:2 final size:2
Alignment explanation
Indices: 530379--530496 Score: 159
Period size: 2 Copynumber: 60.0 Consensus size: 2
530369 AGATGAGAAA
530379 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
* *
530421 AC -C AC AC AC AC -C AC AC AC AC AC AC AC AC AC AC AC AC TC TC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
* * * * *
530461 TC TC TC TC TC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
530497 TCTCTCTCTC
Statistics
Matches: 112, Mismatches: 2, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
1 2 0.02
2 110 0.98
ACGTcount: A:0.43, C:0.51, G:0.00, T:0.06
Consensus pattern (2 bp):
AC
Found at i:530501 original size:2 final size:2
Alignment explanation
Indices: 530496--530540 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
530486 CACACACACA
530496 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
530538 CT C
1 CT C
530541 AAAATAAAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:533326 original size:16 final size:16
Alignment explanation
Indices: 533305--533340 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
533295 AGAGGAAAAC
*
533305 TTCGAGGTATCAAGAG
1 TTCGAGCTATCAAGAG
*
533321 TTCGAGCTTTCAAGAG
1 TTCGAGCTATCAAGAG
533337 TTCG
1 TTCG
533341 GAATTTTCCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.31
Consensus pattern (16 bp):
TTCGAGCTATCAAGAG
Found at i:534079 original size:16 final size:17
Alignment explanation
Indices: 534040--534089 Score: 66
Period size: 16 Copynumber: 3.0 Consensus size: 17
534030 GTAGTTTGAC
* *
534040 CTCGAGAGATCGAGGGT
1 CTCGAGAGATCAAGAGT
534057 CTCGAGAGATCAAGAGT
1 CTCGAGAGATCAAGAGT
*
534074 -TCGAGAAATCAAGAGT
1 CTCGAGAGATCAAGAGT
534090 AATTTTGCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
16 15 0.50
17 15 0.50
ACGTcount: A:0.34, C:0.16, G:0.32, T:0.18
Consensus pattern (17 bp):
CTCGAGAGATCAAGAGT
Found at i:534174 original size:15 final size:15
Alignment explanation
Indices: 534137--534186 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 15
534127 CTAGACTCAC
*
534137 TTCGAGCGATCAAGAAC
1 TTCGAGCGATC--GAAG
534154 TTCGAGCGATCGAAG
1 TTCGAGCGATCGAAG
*
534169 TTCGAGCCATCGAGAG
1 TTCGAGCGATCGA-AG
534185 TT
1 TT
534187 ACCTGTACCT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
15 15 0.50
16 4 0.13
17 11 0.37
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22
Consensus pattern (15 bp):
TTCGAGCGATCGAAG
Found at i:535026 original size:21 final size:21
Alignment explanation
Indices: 535000--535065 Score: 89
Period size: 21 Copynumber: 3.1 Consensus size: 21
534990 GTAAAACGTA
535000 TGCAACGAATGCGAGAGCTCG
1 TGCAACGAATGCGAGAGCTCG
*
535021 TGCAACGTAA-GCGAGGGCTCG
1 TGCAACG-AATGCGAGAGCTCG
* *
535042 TGCAACGTATGCTAGAGCTCG
1 TGCAACGAATGCGAGAGCTCG
535063 TGC
1 TGC
535066 GAAGCTCAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
20 1 0.03
21 36 0.92
22 2 0.05
ACGTcount: A:0.24, C:0.24, G:0.33, T:0.18
Consensus pattern (21 bp):
TGCAACGAATGCGAGAGCTCG
Found at i:537459 original size:159 final size:158
Alignment explanation
Indices: 537242--537774 Score: 625
Period size: 159 Copynumber: 3.3 Consensus size: 158
537232 AATAAAAGCC
* *
537242 AGTAAAAATGTTTTAAATCTTAAAAAATCTTCTTCTCTACTCCCATTTAAATTTGTTAAAAACTA
1 AGTAAAAATGTATTAAATCTTAAAAAATCTTCTTCTCTACTCCCATATAAATTTGTTAAAAACTA
537307 AATGCATGAATATGATTTCCATGAGGCTCTCTACAAAAATTGTGAAATTCATGACCCCTGGGTCA
66 AATGCATGAATATGATTTCCATGAGGC-CTCTAC-AAAATTGTGAAATTCATGACCCCTGGGTCA
*
537372 GG-TCTAGGTTGGGGCTAATATGGCCATAT
129 GGCTCTAGGGTGGGGCTAATATGGCCATAT
* * *
537401 TGTAAAAATGTATTAAATCTTAGAAAATCTTCTTCTCTACT-CCACTATAAATTAGTTAAAAACT
1 AGTAAAAATGTATTAAATCTTAAAAAATCTTCTTCTCTACTCCCA-TATAAATTTGTTAAAAACT
* ** *
537465 AAATGCATGAATATGATTTTCATGAGGCCCTCTACCAAAATTGTGAAATAAATGACGCCTGGGTC
65 AAATGCATGAATATGATTTCCATGAGG-CCTCTA-CAAAATTGTGAAATTCATGACCCCTGGGTC
*
537530 AGGGGTTAGGCTCTAGGGTGGGGCTAATATGGCCATAC
128 -------AGGCTCTAGGGTGGGGCTAATATGGCCATAT
* * * *
537568 AGTTAAAATGTTTTAAATCTTAAAAAATCTTC-TC-C-ATTCCCATATATATTTGTTAAAAACTA
1 AGTAAAAATGTATTAAATCTTAAAAAATCTTCTTCTCTACTCCCATATAAATTTGTTAAAAACTA
* * **
537630 AATGCATGAATATGATTTCCATGAGGCC-CT-C-TAATTGTGAAA-TCTATGCTATCTGGGTCAG
66 AATGCATGAATATGATTTCCATGAGGCCTCTACAAAATTGTGAAATTC-ATG--A-C----CCCT
* *
537691 GGGTTCAGGCTCTAGGGTAGGGCCAATATGGCCATAT
123 GGG-TCAGGCTCTAGGGTGGGGCTAATATGGCCATAT
537728 AGTAAAAATGTATTAAATCTTAAAAAATCTTCTTCTCTACTCCCATA
1 AGTAAAAATGTATTAAATCTTAAAAAATCTTCTTCTCTACTCCCATA
537775 CATGTGGGCA
Statistics
Matches: 319, Mismatches: 31, Indels: 44
0.81 0.08 0.11
Matches are distributed among these distances:
158 3 0.01
159 125 0.39
160 61 0.19
161 3 0.01
162 4 0.01
163 10 0.03
164 45 0.14
165 4 0.01
166 9 0.03
167 55 0.17
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (158 bp):
AGTAAAAATGTATTAAATCTTAAAAAATCTTCTTCTCTACTCCCATATAAATTTGTTAAAAACTA
AATGCATGAATATGATTTCCATGAGGCCTCTACAAAATTGTGAAATTCATGACCCCTGGGTCAGG
CTCTAGGGTGGGGCTAATATGGCCATAT
Found at i:537854 original size:326 final size:325
Alignment explanation
Indices: 537170--537862 Score: 751
Period size: 326 Copynumber: 2.1 Consensus size: 325
537160 GTCCATGAAG
** * ** * *
537170 CCCTCTACCAAAATTGTGAAATTCATGACCCTTTTGT-TGGGGTTCAGGCTCTAGGGTGGGTC-A
1 CCCTCTACCAAAATTGTGAAATAAATGACCCCTGGGTCAGGGGTT-AGGCTCTAGGGTGGGGCTA
** *
537233 ATAAAAG-C---CAGTAAAAATGTTTTAAATCTTAAAAAATCTTCTTCTCTACTCCCATTTAAAT
65 AT-ATGGCCATACAGTAAAAATGTTTTAAATCTTAAAAAATCTTCTTCTCTACTCCCATATAAAT
537294 TTGTTAAAAACTAAATGCATGAATATGATTTCCATGAGGCTCTCTACAAAAATTGTGAAATTCAT
129 TTGTTAAAAACTAAATGCATGAATATGATTTCCATGAGGCTCTCTAC-AAAATTGTGAAATTCAT
** * * * * *
537359 GACCCCTGGGTCAGGTCTAGGTTGGGGCTAATATGGCCATATTGTAAAAATGTATTAAATCTTAG
193 GACCCAGGGGTCAGGTCTAGGGTAGGGCCAATATGGCCATATAGTAAAAATGTATTAAATCTTAA
** * ** *
537424 AAAATCTTCTTCTCTACTCCACTATAAATTAGTTAAAAACTAAATGCATGAATATGATTTTCATG
258 AAAATCTTCTTCTCTACTCCACTATAAATTAGGCAAAAACTAAATACATGAATACAATTTTCACG
*
537489 AGG
323 AGA
*
537492 CCCTCTACCAAAATTGTGAAATAAATGACGCCTGGGTCAGGGGTTAGGCTCTAGGGTGGGGCTAA
1 CCCTCTACCAAAATTGTGAAATAAATGACCCCTGGGTCAGGGGTTAGGCTCTAGGGTGGGGCTAA
* * *
537557 TATGGCCATACAGTTAAAATGTTTTAAATCTTAAAAAATCTTC-TC-C-ATTCCCATATATATTT
66 TATGGCCATACAGTAAAAATGTTTTAAATCTTAAAAAATCTTCTTCTCTACTCCCATATAAATTT
*
537619 GTTAAAAACTAAATGCATGAATATGATTTCCATGAGGC-C-CT-C-TAATTGTGAAA-TCTATGC
131 GTTAAAAACTAAATGCATGAATATGATTTCCATGAGGCTCTCTACAAAATTGTGAAATTC-ATG-
*
537679 TATCTGGGTCAGGGGTTCAGGCTCTAGGGTAGGGCCAATATGGCCATATAGTAAAAATGTATTAA
194 -A-C----CCAGGGG-TCAGG-TCTAGGGTAGGGCCAATATGGCCATATAGTAAAAATGTATTAA
* * * *
537744 ATCTTAAAAAATCTTCTTCTCTACTCC-C-ATACATGTGGGCAAAAACTGAATACAT-AGTTACA
251 ATCTTAAAAAATCTTCTTCTCTACTCCACTATAAAT-TAGGCAAAAACTAAATACATGA-ATACA
537806 A-TTTCTACGA-A
314 ATTTTC-ACGAGA
** *
537817 CTCCTCTACCTAAAA-TGTGAAATTCATGGCCCCTGGGTCAGGGGTT
1 C-CCTCTACC-AAAATTGTGAAATAAATGACCCCTGGGTCAGGGGTT
537863 CAGGACATGG
Statistics
Matches: 312, Mismatches: 38, Indels: 38
0.80 0.10 0.10
Matches are distributed among these distances:
317 2 0.01
318 13 0.04
320 2 0.01
321 3 0.01
322 50 0.16
323 61 0.20
324 1 0.00
325 17 0.05
326 94 0.30
327 69 0.22
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (325 bp):
CCCTCTACCAAAATTGTGAAATAAATGACCCCTGGGTCAGGGGTTAGGCTCTAGGGTGGGGCTAA
TATGGCCATACAGTAAAAATGTTTTAAATCTTAAAAAATCTTCTTCTCTACTCCCATATAAATTT
GTTAAAAACTAAATGCATGAATATGATTTCCATGAGGCTCTCTACAAAATTGTGAAATTCATGAC
CCAGGGGTCAGGTCTAGGGTAGGGCCAATATGGCCATATAGTAAAAATGTATTAAATCTTAAAAA
ATCTTCTTCTCTACTCCACTATAAATTAGGCAAAAACTAAATACATGAATACAATTTTCACGAGA
Found at i:539868 original size:13 final size:13
Alignment explanation
Indices: 539844--539877 Score: 59
Period size: 13 Copynumber: 2.5 Consensus size: 13
539834 TCTCGGTTTC
539844 TCTCTCCTTATTTT
1 TCTCT-CTTATTTT
539858 TCTCTCTTATTTT
1 TCTCTCTTATTTT
539871 TCTCTCT
1 TCTCTCT
539878 CTCTTTCGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 15 0.75
14 5 0.25
ACGTcount: A:0.06, C:0.29, G:0.00, T:0.65
Consensus pattern (13 bp):
TCTCTCTTATTTT
Found at i:540945 original size:17 final size:18
Alignment explanation
Indices: 540923--540963 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
540913 TTTTGTAAAG
*
540923 AAAAATCCTACCA-ATAT
1 AAAAATCATACCAGATAT
*
540940 AAAAATCATACCAGCTAT
1 AAAAATCATACCAGATAT
540958 AAAAAT
1 AAAAAT
540964 GTGTATAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.56, C:0.20, G:0.02, T:0.22
Consensus pattern (18 bp):
AAAAATCATACCAGATAT
Found at i:550910 original size:148 final size:144
Alignment explanation
Indices: 550632--550911 Score: 380
Period size: 148 Copynumber: 1.9 Consensus size: 144
550622 TTAACACCTT
* *
550632 ATGATGATATTCGTAGGCCTAAAGTAGGATTAATTTTTATTCCAGAAAGCAAAGTTCCTTAAAGA
1 ATGATGATATTCGTAGGCCTAAAGTAGGATTAATTTTTATTCCAGAAAGAAAACTTCCTTAAAGA
* *
550697 AGGAAACAATCAAAATTTCATTTAGAGGACATGATGCACTCACTTGTAAATGTTTGAAAAAAAAA
66 AGGAAACAATCAAAATTTCATTTAGAGAACATGATGCACTCAATTGTAAATGTTTG----AAAAA
550762 ACGATTCAACATTTAACA
127 ACGATTCAACATTTAACA
* * *
550780 ATGATGATCTTCGTAGGCCTAAAGTGGGATTAATTTTTATTCCAGAAAGAAAACTTTCTTAAAGA
1 ATGATGATATTCGTAGGCCTAAAGTAGGATTAATTTTTATTCCAGAAAGAAAACTTCCTTAAAGA
* * * *
550845 AGGAAACAATCAAATTTGTTTTTATTTTGGAGAACATGATGCTCTCAATTGTAAATGTTTGAAAA
66 AGGAAACAATCAAA----ATTTCA-TTTAGAGAACATGATGCACTCAATTGTAAATGTTTGAAAA
550910 AA
126 AA
550912 AAAAGATTTA
Statistics
Matches: 116, Mismatches: 11, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
148 74 0.64
149 6 0.05
152 4 0.03
153 32 0.28
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (144 bp):
ATGATGATATTCGTAGGCCTAAAGTAGGATTAATTTTTATTCCAGAAAGAAAACTTCCTTAAAGA
AGGAAACAATCAAAATTTCATTTAGAGAACATGATGCACTCAATTGTAAATGTTTGAAAAAACGA
TTCAACATTTAACA
Found at i:555059 original size:186 final size:187
Alignment explanation
Indices: 554729--555065 Score: 518
Period size: 186 Copynumber: 1.8 Consensus size: 187
554719 TTCATTTTGC
* *
554729 GTACATGCTTGTTTTATATGTGACATTTTATTTAATATATCTTTTAAAAATATGCTAAAATGCCT
1 GTACATGCTTGTTTTATATGTGACATTTTATTTAATATATCTTTTAAAAATATGCCAAAATGACT
* *
554794 CAAAATGTAGTTTGTATACCTCACGTAAAAAGCACGATGAAATGCATGAATCCCATTTAAATTCA
66 CAAAATGTAGTTTGTATACATCACGTAAAAAGCACGATGAAATGCACGAATCCCATTTAAATTCA
554859 TTCAAAACCCCC-AAAGTCAGAACGTTTAAATATATCTGTTAATGCCCTCTTTGTTT
131 TTCAAAACCCCCAAAAGTCAGAACGTTTAAATATATCTGTTAATGCCCTCTTTGTTT
*
554915 GTACATGCTTGTTTTATATGTGAC-TTTGTATTTAATATATCTTTTAAAACTATGCCAAAATGAC
1 GTACATGCTTGTTTTATATGTGACATTT-TATTTAATATATCTTTTAAAAATATGCCAAAATGAC
* * * * * ** *
554979 TCAAAATTTGGTTTGTATATATCACGTTGAAAAGCAGGATGAGTTGCACGAATCTCATTTAAATT
65 TCAAAATGTAGTTTGTATACATCACG-TAAAAAGCACGATGAAATGCACGAATCCCATTTAAATT
555044 CATTCAAAA-CCCCAAAAGTCAG
129 CATTCAAAACCCCCAAAAGTCAG
555066 GGCTGCGTTC
Statistics
Matches: 135, Mismatches: 13, Indels: 5
0.88 0.08 0.03
Matches are distributed among these distances:
185 3 0.02
186 83 0.61
187 49 0.36
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.36
Consensus pattern (187 bp):
GTACATGCTTGTTTTATATGTGACATTTTATTTAATATATCTTTTAAAAATATGCCAAAATGACT
CAAAATGTAGTTTGTATACATCACGTAAAAAGCACGATGAAATGCACGAATCCCATTTAAATTCA
TTCAAAACCCCCAAAAGTCAGAACGTTTAAATATATCTGTTAATGCCCTCTTTGTTT
Found at i:555673 original size:4 final size:4
Alignment explanation
Indices: 555664--555731 Score: 109
Period size: 4 Copynumber: 16.8 Consensus size: 4
555654 CGTGTTGATA
* *
555664 TATC TATC TATC TATC TATC TATC TATC TATC TAAC TATC TTTTC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC -TATC TATC
555713 TATC TATC TATC TATC TAT
1 TATC TATC TATC TATC TAT
555732 TGAAAATGAC
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
4 56 0.95
5 3 0.05
ACGTcount: A:0.25, C:0.24, G:0.00, T:0.51
Consensus pattern (4 bp):
TATC
Found at i:556108 original size:4 final size:4
Alignment explanation
Indices: 556101--556223 Score: 173
Period size: 4 Copynumber: 31.8 Consensus size: 4
556091 AGTAGCTTGC
* * *
556101 CTAT CTAT CGAT CGAT CGAT CTA- C-AT CTAT CTAT CTAT CTAT CTAT
1 CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT
556147 CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT
1 CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT
* *
556195 CTAT CTA- C-AT GTAT CTAT CCAT CTAT CTA
1 CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTA
556224 ATTCATTTTC
Statistics
Matches: 109, Mismatches: 6, Indels: 8
0.89 0.05 0.07
Matches are distributed among these distances:
2 2 0.02
3 3 0.03
4 104 0.95
ACGTcount: A:0.26, C:0.26, G:0.03, T:0.45
Consensus pattern (4 bp):
CTAT
Found at i:568019 original size:20 final size:20
Alignment explanation
Indices: 567996--568041 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
567986 ATTTACCTTT
567996 AAAAATA-AATATCCCATAGG
1 AAAAATATAAT-TCCCATAGG
*
568016 AAAATTATAATTCCCATAGG
1 AAAAATATAATTCCCATAGG
*
568036 AGAAAT
1 AAAAAT
568042 GATTCTCATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 19 0.86
21 3 0.14
ACGTcount: A:0.52, C:0.13, G:0.11, T:0.24
Consensus pattern (20 bp):
AAAAATATAATTCCCATAGG
Found at i:568941 original size:2 final size:2
Alignment explanation
Indices: 568934--568992 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
568924 AAGCTGTTTC
568934 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
568976 AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG A
568993 TGTGGGTAAC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:570465 original size:16 final size:16
Alignment explanation
Indices: 570444--570476 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
570434 TATTTTCGCC
570444 TGACACAGGTGAGATG
1 TGACACAGGTGAGATG
*
570460 TGACACAGGTGATATG
1 TGACACAGGTGAGATG
570476 T
1 T
570477 TTAGCAATTA
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:0.30, C:0.12, G:0.33, T:0.24
Consensus pattern (16 bp):
TGACACAGGTGAGATG
Found at i:571412 original size:2 final size:2
Alignment explanation
Indices: 571402--571437 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
571392 AGAGAGATCC
*
571402 CA CA AA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
571438 TACGTGTAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.47, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:572995 original size:2 final size:2
Alignment explanation
Indices: 572988--573033 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
572978 TTTTGTGTAC
572988 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
573030 CA CA
1 CA CA
573034 AATGGTTAGG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:574372 original size:2 final size:2
Alignment explanation
Indices: 574365--574416 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
574355 TTCTGCCCAC
*
574365 GA GA GA GA GA GA GC 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
574407 GA GA GA GA GA
1 GA GA GA GA GA
574417 TGCACTTGCA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.48, C:0.02, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:576281 original size:62 final size:62
Alignment explanation
Indices: 576184--576436 Score: 298
Period size: 62 Copynumber: 4.0 Consensus size: 62
576174 TTTCTAAAGA
* *
576184 AACAAACACAAACGAATGAACAGCATACTGATTATATACAGTTGTACTTGAGTAGCTTATTC
1 AACAAACACAAATGAATGAACAGCATACTGATTATATACAGTTGTACTTGAATAGCTTATTC
* * * * *
576246 AACAAACACAAATTAGTGAACAGCTTACTGATTATATACATGTACAGTTATACTTAAATAGC---
1 AACAAACACAAATGAATGAACAGCATACTGA-T-TAT--A--TACAGTTGTACTTGAATAGCTTA
576308 TTC
60 TTC
* * * *
576311 AACAAACACAAATGAATGAAAAGCATATTGATTATATACAGTTGTACCTGAATAGCTGATTC
1 AACAAACACAAATGAATGAACAGCATACTGATTATATACAGTTGTACTTGAATAGCTTATTC
* *
576373 AACAAACACAAGTGAATGAACAGCATACTGATCATATACAGTTGTACCTT-AATAGCTTATTC
1 AACAAACACAAATGAATGAACAGCATACTGATTATATACAGTTGTA-CTTGAATAGCTTATTC
576435 AA
1 AA
576437 AATGTGTATG
Statistics
Matches: 160, Mismatches: 21, Indels: 20
0.80 0.10 0.10
Matches are distributed among these distances:
59 17 0.11
61 1 0.01
62 85 0.53
63 6 0.04
64 4 0.03
65 29 0.18
66 1 0.01
68 17 0.11
ACGTcount: A:0.42, C:0.17, G:0.13, T:0.28
Consensus pattern (62 bp):
AACAAACACAAATGAATGAACAGCATACTGATTATATACAGTTGTACTTGAATAGCTTATTC
Found at i:576410 original size:127 final size:127
Alignment explanation
Indices: 576184--576412 Score: 359
Period size: 127 Copynumber: 1.8 Consensus size: 127
576174 TTTCTAAAGA
* * * *
576184 AACAAACACAAACGAATGAACAGCATACTGATTATATACAGTTGTACTTGAGTAGCTTATTCAAC
1 AACAAACACAAACGAATGAAAAGCATACTGATTATATACAGTTGTACCTGAATAGCTGATTCAAC
* * * *
576249 AAACACAAATTAGTGAACAGCTTACTGATTATATACATGTACAGTTATACTTAAATAGCTTC
66 AAACACAAATGAATGAACAGCATACTGATCATATACATGTACAGTTATACTTAAATAGCTTC
* *
576311 AACAAACACAAATGAATGAAAAGCATATTGATTATATACAGTTGTACCTGAATAGCTGATTCAAC
1 AACAAACACAAACGAATGAAAAGCATACTGATTATATACAGTTGTACCTGAATAGCTGATTCAAC
*
576376 AAACACAAGTGAATGAACAGCATACTGATCATATACA
66 AAACACAAATGAATGAACAGCATACTGATCATATACA
576413 GTTGTACCTT
Statistics
Matches: 91, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
127 91 1.00
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.27
Consensus pattern (127 bp):
AACAAACACAAACGAATGAAAAGCATACTGATTATATACAGTTGTACCTGAATAGCTGATTCAAC
AAACACAAATGAATGAACAGCATACTGATCATATACATGTACAGTTATACTTAAATAGCTTC
Found at i:582010 original size:2 final size:2
Alignment explanation
Indices: 582005--582035 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
581995 CACACACACA
582005 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
582036 CATCAAACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:584305 original size:2 final size:2
Alignment explanation
Indices: 584298--584332 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
584288 TCCAATACAA
584298 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
584333 CGTCTCCTAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:587349 original size:2 final size:2
Alignment explanation
Indices: 587342--587393 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
587332 CAGTTTAAGA
587342 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
587384 CT CT CT CT CT
1 CT CT CT CT CT
587394 TATACAAACG
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:588113 original size:2 final size:2
Alignment explanation
Indices: 588106--588155 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
588096 TTCTTACATC
588106 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
588148 AG AG AG AG
1 AG AG AG AG
588156 CATTCTAGGA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:601130 original size:2 final size:2
Alignment explanation
Indices: 601123--601157 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
601113 AACAAATTAC
601123 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
601158 CTATATACCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:608535 original size:4 final size:4
Alignment explanation
Indices: 608526--608566 Score: 73
Period size: 4 Copynumber: 10.2 Consensus size: 4
608516 AATGCTTTTC
*
608526 TATT TATT TATT TATT TATT TATC TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT T
608567 TATCACCCTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:616024 original size:8 final size:8
Alignment explanation
Indices: 616011--616035 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
616001 GGTATAGACA
616011 CGCATATC
1 CGCATATC
616019 CGCATATC
1 CGCATATC
616027 CGCATATC
1 CGCATATC
616035 C
1 C
616036 CAGACCAGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.40, G:0.12, T:0.24
Consensus pattern (8 bp):
CGCATATC
Found at i:620060 original size:26 final size:26
Alignment explanation
Indices: 620031--620086 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
620021 TAAATTGAAC
* *
620031 AAAACCAAGTATGTTATTTTGACAAA
1 AAAACAAAGTATGTTAATTTGACAAA
* *
620057 AAAATAAAGTATGTTAATTTGACAGA
1 AAAACAAAGTATGTTAATTTGACAAA
620083 AAAA
1 AAAA
620087 TAACACACGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.52, C:0.07, G:0.12, T:0.29
Consensus pattern (26 bp):
AAAACAAAGTATGTTAATTTGACAAA
Found at i:620087 original size:26 final size:26
Alignment explanation
Indices: 620037--620089 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
620027 GAACAAAACC
*
620037 AAGTATGTTATTTTGACAAAAAAATA
1 AAGTATGTTAATTTGACAAAAAAATA
*
620063 AAGTATGTTAATTTGACAGAAAAATA
1 AAGTATGTTAATTTGACAAAAAAATA
620089 A
1 A
620090 CACACGACTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.51, C:0.04, G:0.13, T:0.32
Consensus pattern (26 bp):
AAGTATGTTAATTTGACAAAAAAATA
Found at i:635455 original size:2 final size:2
Alignment explanation
Indices: 635448--635504 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
635438 ACTGCATTAA
635448 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
635490 CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT C
635505 CATAAATAAG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:636551 original size:18 final size:18
Alignment explanation
Indices: 636524--636575 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
636514 TAATTCTGCA
636524 TAAT-TTATGCAACATTG
1 TAATGTTATGCAACATTG
636541 TAATGTTATGCAACATTG
1 TAATGTTATGCAACATTG
* *
636559 TAATGTAATGTAACATT
1 TAATGTTATGCAACATT
636576 ATGTAAGATG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
17 4 0.12
18 28 0.88
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.40
Consensus pattern (18 bp):
TAATGTTATGCAACATTG
Found at i:636754 original size:4 final size:4
Alignment explanation
Indices: 636747--636787 Score: 82
Period size: 4 Copynumber: 10.2 Consensus size: 4
636737 AAGAAAAAAA
636747 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT A
1 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT A
636788 TAGTAATTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.24, T:0.24
Consensus pattern (4 bp):
AGAT
Found at i:645173 original size:1 final size:1
Alignment explanation
Indices: 645167--645192 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
645157 TGTATTTACT
645167 GGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGG
645193 AAANNNNNNN
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:645439 original size:98 final size:98
Alignment explanation
Indices: 645270--645465 Score: 392
Period size: 98 Copynumber: 2.0 Consensus size: 98
645260 NNNNNNNNNN
645270 AAATTATATGTAGCTGCTTTCATTATTCGTCGTAAAACGTGTTCTTCATCCAATGAACGGTACCA
1 AAATTATATGTAGCTGCTTTCATTATTCGTCGTAAAACGTGTTCTTCATCCAATGAACGGTACCA
645335 AAACCGCTTGTAGGTTCCCGACTAAAGTTTCAC
66 AAACCGCTTGTAGGTTCCCGACTAAAGTTTCAC
645368 AAATTATATGTAGCTGCTTTCATTATTCGTCGTAAAACGTGTTCTTCATCCAATGAACGGTACCA
1 AAATTATATGTAGCTGCTTTCATTATTCGTCGTAAAACGTGTTCTTCATCCAATGAACGGTACCA
645433 AAACCGCTTGTAGGTTCCCGACTAAAGTTTCAC
66 AAACCGCTTGTAGGTTCCCGACTAAAGTTTCAC
645466 TCCTATCTTA
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
98 98 1.00
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (98 bp):
AAATTATATGTAGCTGCTTTCATTATTCGTCGTAAAACGTGTTCTTCATCCAATGAACGGTACCA
AAACCGCTTGTAGGTTCCCGACTAAAGTTTCAC
Found at i:649528 original size:185 final size:185
Alignment explanation
Indices: 649216--649652 Score: 786
Period size: 185 Copynumber: 2.4 Consensus size: 185
649206 AGGAAATTCA
* *
649216 ATTTCCTTTAAGAAAACTACCTGTCTGAATTAAATTTCTACAGGAAATACTTTTTAAAGGTCTTA
1 ATTTCCTTTAAGAAAACTACCTGTCTGAATCAAATTTCTACAGGAAATACTTTTTAAAGATCTTA
* * *
649281 TATTAAGGTTGTTAATATTTCCTGAAGGAGAATCATTTATATGGGAATTATCATTTTCTTATAAT
66 TATTAAGGTTGTCAATATTTCCTGAAGAAGAATCATTTATATGGGAATTATCATTTTCTTATAAA
649346 ATATTAATTTTCAAAGGTAAATATCTCACTTGCCAGGTGAAACACACAATTCAAT
131 ATATTAATTTTCAAAGGTAAATATCTCACTTGCCAGGTGAAACACACAATTCAAT
649401 ATTTCCTTTAAGAAAACTACCTGTCTGAATCAAATTTCTACAGGAAATACTTTTTAAAGATCTTA
1 ATTTCCTTTAAGAAAACTACCTGTCTGAATCAAATTTCTACAGGAAATACTTTTTAAAGATCTTA
*
649466 TATTAAGGTTGTCAATATTTCCTGTAGAAGAATCATTTATATGGGAATTATCATTTTCTTATAAA
66 TATTAAGGTTGTCAATATTTCCTGAAGAAGAATCATTTATATGGGAATTATCATTTTCTTATAAA
649531 ATATTAATTTTCAAAGGTAAATATCTCACTTGCCAGGTGAAACACACAATTCAAT
131 ATATTAATTTTCAAAGGTAAATATCTCACTTGCCAGGTGAAACACACAATTCAAT
* *
649586 ATTTCCTTTAAGAAAACCACCTGTCTGAATCAAATTTCTACAGGAAATAC-TTTTAGAAAATCTT
1 ATTTCCTTTAAGAAAACTACCTGTCTGAATCAAATTTCTACAGGAAATACTTTTTA-AAGATCTT
649650 ATA
65 ATA
649653 AGATTGTCAA
Statistics
Matches: 243, Mismatches: 8, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
184 5 0.02
185 238 0.98
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (185 bp):
ATTTCCTTTAAGAAAACTACCTGTCTGAATCAAATTTCTACAGGAAATACTTTTTAAAGATCTTA
TATTAAGGTTGTCAATATTTCCTGAAGAAGAATCATTTATATGGGAATTATCATTTTCTTATAAA
ATATTAATTTTCAAAGGTAAATATCTCACTTGCCAGGTGAAACACACAATTCAAT
Found at i:660027 original size:21 final size:21
Alignment explanation
Indices: 659988--660029 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
659978 ATATTAAAAA
*
659988 TAATTTTTATAATGTAATAAC
1 TAATTTTTATAATGCAATAAC
660009 TAATTGTTTAT-ATGCAATAAC
1 TAATT-TTTATAATGCAATAAC
660030 GTATAACTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.45
Consensus pattern (21 bp):
TAATTTTTATAATGCAATAAC
Found at i:662354 original size:2 final size:2
Alignment explanation
Indices: 662347--662395 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
662337 ACGATAACGC
662347 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
662389 AG AG AG A
1 AG AG AG A
662396 TAGTTTGAGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:669046 original size:13 final size:13
Alignment explanation
Indices: 669028--669054 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
669018 TAGCGGAGAT
669028 GTATAAGTCCTTC
1 GTATAAGTCCTTC
669041 GTATAAGTCCTTC
1 GTATAAGTCCTTC
669054 G
1 G
669055 ACATTTAAAC
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:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (13 bp):
GTATAAGTCCTTC
Found at i:671518 original size:2 final size:2
Alignment explanation
Indices: 671511--671574 Score: 87
Period size: 2 Copynumber: 33.0 Consensus size: 2
671501 TTAAAAGCAT
*
671511 GA GA GA GA GA GA GA GA GA GA GG GA -A G- 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
* *
671551 GA GA AA GA GA GA GA GA GG GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA
671575 TTTTTTCCAG
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
1 2 0.04
2 52 0.96
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:677762 original size:19 final size:20
Alignment explanation
Indices: 677734--677771 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
677724 TGAAGAAGGA
677734 ATATTAATATTCA-TAATAT
1 ATATTAATATTCATTAATAT
*
677753 ATATTCATATTCATTAATA
1 ATATTAATATTCATTAATA
677772 ATCAATTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (20 bp):
ATATTAATATTCATTAATAT
Found at i:686591 original size:166 final size:167
Alignment explanation
Indices: 686229--686846 Score: 761
Period size: 166 Copynumber: 3.7 Consensus size: 167
686219 NNNNNNNNNN
686229 GGTCATGATTTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTT
1 GGTCATGATTTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTT
* * * *
686294 CCTG-GCTGATTAGTTTC-TGAGAAGAAGATTTTTAAAGATTTACTCT-T-TATTCCTATGTAAA
66 CCCGATCTTA-TAGGTTCATGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAA
*
686355 ACTTCGACTCCCCATTGTGGCCCCATCCTACTCCCGGG
130 ACTTCGACTCCCCATTGTGGCCCCATCCTACCCCCGGG
* * *
686393 GGTTATGATTTTCACAACTTTGAATCTACACTACC-GCAGGATGCTTTCACACAACTTTCAGCTT
1 GGTCATGATTTTCACAACTTTGAATCTACACTACCTG-AGGATGCTTCCACACAAGTTTCAGCTT
*
686457 TCCCGATCTTAT-GGTTCATGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCGTATGTAAA
65 TCCCGATCTTATAGGTTCATGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAA
*
686521 ACTTCGACTCCCCATTGTGGCCCCACCCTACCCCCGGG
130 ACTTCGACTCCCCATTGTGGCCCCATCCTACCCCCGGG
* * *
686559 GGTCATGATTTTCACAACTTTGAATCTACACTACCAGAGGATACTTCCACACAAGTTTCAGATTT
1 GGTCATGATTTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTT
* ** * *
686624 CCTGGCTGAT-TAGTTTCTGATCATGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTTT
66 CC---C-GATCT--TATAGGTTCATGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTAT
* * * ***
686688 GTTAAACTTCAACCCCCCCCCCAATTGTGGCCCCATCCTACCCCTAAG
125 GTAAAACTTCGA----CTCCCC-ATTGTGGCCCCATCCTACCCCCGGG
* * ** *
686736 GGTCACGATTTTCACAACTTTGTATCTACACTACCTGAATATGCTTTCACACAAGTTTCAGCTTT
1 GGTCATGATTTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTT
* *
686801 CCTGATCTTAT-GGTTCATGAAAAGAAGATTTTTGAAA-ATTT-CTCTA
66 CCCGATCTTATAGGTTCATGAGAAGAAGATTTTT-AAAGATTTACTCTA
686847 AAATTTTCAT
Statistics
Matches: 394, Mismatches: 40, Indels: 34
0.84 0.09 0.07
Matches are distributed among these distances:
163 5 0.01
164 93 0.24
165 4 0.01
166 109 0.28
167 1 0.00
169 2 0.01
170 8 0.02
171 25 0.06
172 58 0.15
173 3 0.01
174 1 0.00
176 5 0.01
177 80 0.20
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.34
Consensus pattern (167 bp):
GGTCATGATTTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTT
CCCGATCTTATAGGTTCATGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAA
CTTCGACTCCCCATTGTGGCCCCATCCTACCCCCGGG
Found at i:687012 original size:4 final size:4
Alignment explanation
Indices: 687003--687056 Score: 67
Period size: 4 Copynumber: 13.8 Consensus size: 4
686993 TGAAAAGTTT
* *
687003 ACAG ACAG AC-G AACAG ACAG ACGG ACTG ACAG ACAG ACAG ACAG AC-G
1 ACAG ACAG ACAG -ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG
687050 ACAG ACA
1 ACAG ACA
687057 AAATGTGTTC
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
3 4 0.09
4 39 0.89
5 1 0.02
ACGTcount: A:0.46, C:0.26, G:0.26, T:0.02
Consensus pattern (4 bp):
ACAG
Found at i:689143 original size:232 final size:230
Alignment explanation
Indices: 688732--689183 Score: 796
Period size: 232 Copynumber: 2.0 Consensus size: 230
688722 TAAAGTTAAA
688732 AATAATTTTTCTGATTTAAATGTTTACAGTGCTTCAGTAAGGCATTTTTAATAGACAACCAATTA
1 AATAATTTTTCTGATTTAAATGTTTACAGTGCTTCAGTAAGGCATTTTTAATAGACAACCAATTA
*
688797 AAATTTGAGTGTCATTTATTAAATCATCGGCAAGTTACAGAGCTTACAATGCCTAGCTATGTTAA
66 AAATTTGAGTGTCATTTATTAAATCATCGGCAAGTTACAGAGCTTACAATGCCTAGCTATGTAAA
*
688862 CAAAGCTAACAAAGTTTTATGCTTTTGTTAAAAATCATGAAGTAAAGATTCATCTATGCTCGATT
131 CAAAGCTAACAAAGTTTTATGCTTTTGTTAAAAATCATGAAGTAAAGATTCATCTATGATCGATT
*
688927 GGGCAGTATTTTTTAAAAGAGTTAATAGCTATACTGT
196 GGGCA-T-TATTTTAAAAGAGTTAATAGCTATACTGT
* *
688964 AATATTTTTTCTGATTTAAATGTTTACCGTGCTTCAGTAAGGCATTTTTAATAGACAACCAATTA
1 AATAATTTTTCTGATTTAAATGTTTACAGTGCTTCAGTAAGGCATTTTTAATAGACAACCAATTA
* * *
689029 AGATTTGAGTGTCATTTATTAAATCATCGGCGAGTTACAGAGCTTACAATGCCTGGCTATGTAAA
66 AAATTTGAGTGTCATTTATTAAATCATCGGCAAGTTACAGAGCTTACAATGCCTAGCTATGTAAA
*
689094 CAAAGCTGACAAAGTTTTATGCTTTTGTTAAAAATCATGAAGTAAAGATTCATCTATGATCGATT
131 CAAAGCTAACAAAGTTTTATGCTTTTGTTAAAAATCATGAAGTAAAGATTCATCTATGATCGATT
*
689159 GTGCATTATTTTAAAAGAGTTAATA
196 GGGCATTATTTTAAAAGAGTTAATA
689184 CGTACATGTA
Statistics
Matches: 210, Mismatches: 10, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
230 18 0.09
231 1 0.00
232 191 0.91
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (230 bp):
AATAATTTTTCTGATTTAAATGTTTACAGTGCTTCAGTAAGGCATTTTTAATAGACAACCAATTA
AAATTTGAGTGTCATTTATTAAATCATCGGCAAGTTACAGAGCTTACAATGCCTAGCTATGTAAA
CAAAGCTAACAAAGTTTTATGCTTTTGTTAAAAATCATGAAGTAAAGATTCATCTATGATCGATT
GGGCATTATTTTAAAAGAGTTAATAGCTATACTGT
Found at i:695714 original size:2 final size:2
Alignment explanation
Indices: 695709--695757 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
695699 CGCACACACA
695709 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
695751 CT CT CT C
1 CT CT CT C
695758 NTGTTAGAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:697060 original size:17 final size:17
Alignment explanation
Indices: 697031--697265 Score: 327
Period size: 17 Copynumber: 14.1 Consensus size: 17
697021 CTTCACGGTG
* *
697031 AGGATTTGATGGGGTTA
1 AGGATTGGATGGGATTA
*
697048 AGTATTGGATGGGATTA
1 AGGATTGGATGGGATTA
*
697065 AGGATTGGATAGGATTA
1 AGGATTGGATGGGATTA
* * *
697082 AGGACTGGATGAGTTTA
1 AGGATTGGATGGGATTA
697099 AGGATTGGATGGGATTA
1 AGGATTGGATGGGATTA
*
697116 AGGATTGGGTGGGATTA
1 AGGATTGGATGGGATTA
697133 AGGATTGGATGGGATTA
1 AGGATTGGATGGGATTA
697150 AGGATTGGATGGGATT-
1 AGGATTGGATGGGATTA
*
697166 A--A--GGATGGGATTG
1 AGGATTGGATGGGATTA
*
697179 AGGATTGGATAGGATTA
1 AGGATTGGATGGGATTA
697196 AGGATTGGATGGGATTA
1 AGGATTGGATGGGATTA
*
697213 AGGATTGGGTGGGATTA
1 AGGATTGGATGGGATTA
*
697230 AGGATTGGGTGGGATTA
1 AGGATTGGATGGGATTA
697247 AGGATTGGATGGGATTA
1 AGGATTGGATGGGATTA
697264 AG
1 AG
697266 AGTTATCATG
Statistics
Matches: 194, Mismatches: 19, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
12 10 0.05
13 1 0.01
14 1 0.01
15 1 0.01
16 1 0.01
17 180 0.93
ACGTcount: A:0.29, C:0.00, G:0.41, T:0.30
Consensus pattern (17 bp):
AGGATTGGATGGGATTA
Found at i:697183 original size:46 final size:47
Alignment explanation
Indices: 697124--697265 Score: 214
Period size: 46 Copynumber: 3.0 Consensus size: 47
697114 TAAGGATTGG
697124 GTGGGATTAAGGATTGGATGGGATTAAGGATTGGATGGGATTAAGGA
1 GTGGGATTAAGGATTGGATGGGATTAAGGATTGGATGGGATTAAGGA
* *
697171 -TGGGATTGAGGATTGGATAGGATTAAGGATTGGATGGGATTAAGGA
1 GTGGGATTAAGGATTGGATGGGATTAAGGATTGGATGGGATTAAGGA
*
697217 TTGGGTGGGATTAAGGATTGGGTGGGATTAAGGATTGGATGGGATTAAG
1 ----GTGGGATTAAGGATTGGATGGGATTAAGGATTGGATGGGATTAAG
697266 AGTTATCATG
Statistics
Matches: 85, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
46 44 0.52
51 41 0.48
ACGTcount: A:0.28, C:0.00, G:0.43, T:0.29
Consensus pattern (47 bp):
GTGGGATTAAGGATTGGATGGGATTAAGGATTGGATGGGATTAAGGA
Found at i:697204 original size:63 final size:63
Alignment explanation
Indices: 697105--697265 Score: 232
Period size: 63 Copynumber: 2.5 Consensus size: 63
697095 TTTAAGGATT
* *
697105 GGATGGGATTAAGGATTGGGTGGGATTAAGGATTGGATGGGATTAAGGATTGGATGGGATTAA
1 GGATGGGATTAAGGATTGGATAGGATTAAGGATTGGATGGGATTAAGGATTGGATGGGATTAA
* *
697168 GGATGGGATTGAGGATTGGATAGGATTAAGGATTGGATGGGATTAAGGATTGGGTGGGATTAA
1 GGATGGGATTAAGGATTGGATAGGATTAAGGATTGGATGGGATTAAGGATTGGATGGGATTAA
*
697231 GGATTGGGTGGGATTAAGGATTGGATGGGATTAAG
1 GGA-----TGGGATTAAGGATTGGATAGGATTAAG
697266 AGTTATCATG
Statistics
Matches: 87, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
63 62 0.71
68 25 0.29
ACGTcount: A:0.28, C:0.00, G:0.43, T:0.29
Consensus pattern (63 bp):
GGATGGGATTAAGGATTGGATAGGATTAAGGATTGGATGGGATTAAGGATTGGATGGGATTAA
Found at i:699893 original size:53 final size:53
Alignment explanation
Indices: 699836--699964 Score: 258
Period size: 53 Copynumber: 2.4 Consensus size: 53
699826 TTTCTCTTCC
699836 GACTGGTGACTTGGTGAGGTTGTTTCTGTGTAATTACTTTCTGTTTTCCTACA
1 GACTGGTGACTTGGTGAGGTTGTTTCTGTGTAATTACTTTCTGTTTTCCTACA
699889 GACTGGTGACTTGGTGAGGTTGTTTCTGTGTAATTACTTTCTGTTTTCCTACA
1 GACTGGTGACTTGGTGAGGTTGTTTCTGTGTAATTACTTTCTGTTTTCCTACA
699942 GACTGGTGACTTGGTGAGGTTGT
1 GACTGGTGACTTGGTGAGGTTGT
699965 CCCAGCAGCA
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 76 1.00
ACGTcount: A:0.15, C:0.14, G:0.28, T:0.43
Consensus pattern (53 bp):
GACTGGTGACTTGGTGAGGTTGTTTCTGTGTAATTACTTTCTGTTTTCCTACA
Found at i:700150 original size:46 final size:46
Alignment explanation
Indices: 700091--700303 Score: 264
Period size: 46 Copynumber: 4.6 Consensus size: 46
700081 CTTTATGGAC
*
700091 CATACAAAGCACAGGTAAATGTCAAGTGTGATAGGGAGTTATGAGA
1 CATACAAAGCACAGGTAAATGACAAGTGTGATAGGGAGTTATGAGA
*
700137 CATACAAAGCACAGGTAAATGTCAAGTGTGATAGGGAGTTATGAGA
1 CATACAAAGCACAGGTAAATGACAAGTGTGATAGGGAGTTATGAGA
* * * *
700183 CATACAAAGCACAGGTAAGTGACAGGTGTGGTAGAGAGTTATGAGA
1 CATACAAAGCACAGGTAAATGACAAGTGTGATAGGGAGTTATGAGA
* * * * * ** * *
700229 CATACAAGGAACAGGTAAGTGACAGGTGTGGTAGGGACATGTGAGG
1 CATACAAAGCACAGGTAAATGACAAGTGTGATAGGGAGTTATGAGA
* * *
700275 CATACAAGGCACAGGTAAGTGACAGGTGT
1 CATACAAAGCACAGGTAAATGACAAGTGT
700304 AAGGGGGACT
Statistics
Matches: 154, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 154 1.00
ACGTcount: A:0.37, C:0.12, G:0.32, T:0.20
Consensus pattern (46 bp):
CATACAAAGCACAGGTAAATGACAAGTGTGATAGGGAGTTATGAGA
Found at i:700959 original size:32 final size:30
Alignment explanation
Indices: 700899--701009 Score: 111
Period size: 30 Copynumber: 3.7 Consensus size: 30
700889 TACATATCAC
*
700899 TACAGTTATGCTGTTATTTTTGTAGGATGA
1 TACAGTTATACTGTTATTTTTGTAGGATGA
* *
700929 TACAGTTATACTTTTATTTTCTTGTAGGATGG
1 TACAGTTATACTGTTA-TTT-TTGTAGGATGA
* * *
700961 GATAGTTATACTGATATTTTTGTAGGATG-
1 TACAGTTATACTGTTATTTTTGTAGGATGA
* *
700990 --CTGTTATGCTGTTATTTTTG
1 TACAGTTATACTGTTATTTTTG
701010 CAGTTATGCT
Statistics
Matches: 68, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
27 16 0.24
30 24 0.35
31 6 0.09
32 22 0.32
ACGTcount: A:0.22, C:0.07, G:0.22, T:0.50
Consensus pattern (30 bp):
TACAGTTATACTGTTATTTTTGTAGGATGA
Found at i:701669 original size:34 final size:34
Alignment explanation
Indices: 701626--701693 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
701616 GGGTTAGGGG
701626 GTATGCATTTTTACATAGGAATATATAGAAAAAA
1 GTATGCATTTTTACATAGGAATATATAGAAAAAA
701660 GTATGCATTTTTACATAGGAATATATAGAAAAAA
1 GTATGCATTTTTACATAGGAATATATAGAAAAAA
701694 ATCATAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.47, C:0.06, G:0.15, T:0.32
Consensus pattern (34 bp):
GTATGCATTTTTACATAGGAATATATAGAAAAAA
Found at i:704479 original size:60 final size:60
Alignment explanation
Indices: 704410--704999 Score: 1072
Period size: 60 Copynumber: 9.8 Consensus size: 60
704400 TGCTTTACCT
*
704410 TTACAATCTATACATACAAAATACTGTTCTCTGTAATTGTTCATACCTACCTGTATATTA
1 TTACAATCTATGCATACAAAATACTGTTCTCTGTAATTGTTCATACCTACCTGTATATTA
* *
704470 TAACAATCTATGCATACAAAATACTGTTCTCTGTAACTGTTCATACCTACCTGTATATTA
1 TTACAATCTATGCATACAAAATACTGTTCTCTGTAATTGTTCATACCTACCTGTATATTA
704530 TTACAATCTATGCATACAAAATACTGTTCTCTGTAATTGTTCATACCTACCTGTATATTA
1 TTACAATCTATGCATACAAAATACTGTTCTCTGTAATTGTTCATACCTACCTGTATATTA
* *
704590 TTACAATCTATGCATACAAAATACTGTTCTCTGTAATTGTTCATACCTTCCTGTATTTTA
1 TTACAATCTATGCATACAAAATACTGTTCTCTGTAATTGTTCATACCTACCTGTATATTA
704650 TTACAAAATCTATGCATACAAAATACTGTTCTCTGTAATTGTTCATACCTACCTGTATATTA
1 TTAC--AATCTATGCATACAAAATACTGTTCTCTGTAATTGTTCATACCTACCTGTATATTA
* *
704712 TTACAATCTATGCATACAAAATACTGTTCTCTGTAATTGTTCATACCTTCCTGTATTTTA
1 TTACAATCTATGCATACAAAATACTGTTCTCTGTAATTGTTCATACCTACCTGTATATTA
704772 TTACAAAATCTATGCATACAAAATACTGTTCTCTGTAATTGTTCATACCTACCTGTATATTA
1 TTAC--AATCTATGCATACAAAATACTGTTCTCTGTAATTGTTCATACCTACCTGTATATTA
704834 TTACAATCTATGCATACAAAATACTGTTCTCTGTAATTGTTCATACCTACCTGTATATTA
1 TTACAATCTATGCATACAAAATACTGTTCTCTGTAATTGTTCATACCTACCTGTATATTA
704894 TTACAATCTATGCATACAAAATACTGTTCTCTGTAATTGTTCATACCTACCTGTATATTA
1 TTACAATCTATGCATACAAAATACTGTTCTCTGTAATTGTTCATACCTACCTGTATATTA
*
704954 TTACAATCTATGCATACAAAATACTGTTCTCTGTAACTGTTCATAC
1 TTACAATCTATGCATACAAAATACTGTTCTCTGTAATTGTTCATAC
705000 ATGTACATGT
Statistics
Matches: 512, Mismatches: 14, Indels: 8
0.96 0.03 0.01
Matches are distributed among these distances:
60 396 0.77
62 116 0.23
ACGTcount: A:0.32, C:0.20, G:0.08, T:0.40
Consensus pattern (60 bp):
TTACAATCTATGCATACAAAATACTGTTCTCTGTAATTGTTCATACCTACCTGTATATTA
Found at i:704715 original size:182 final size:181
Alignment explanation
Indices: 704410--704999 Score: 1067
Period size: 182 Copynumber: 3.3 Consensus size: 181
704400 TGCTTTACCT
* *
704410 TTACAATCTATACATACAAAATACTGTTCTCTGTAATTGTTCATACCTACCTGTATATTATAAC-
1 TTACAATCTATGCATACAAAATACTGTTCTCTGTAATTGTTCATACCTACCTGTATATTATTACA
*
704474 AATCTATGCATACAAAATACTGTTCTCTGTAACTGTTCATACCTACCTGTATATTATTACAATCT
66 AATCTATGCATACAAAATACTGTTCTCTGTAATTGTTCATACCTACCTGTATATTATTACAATCT
704539 ATGCATACAAAATACTGTTCTCTGTAATTGTTCATACCTACCTGTATATTA
131 ATGCATACAAAATACTGTTCTCTGTAATTGTTCATACCTACCTGTATATTA
* *
704590 TTACAATCTATGCATACAAAATACTGTTCTCTGTAATTGTTCATACCTTCCTGTATTTTATTACA
1 TTACAATCTATGCATACAAAATACTGTTCTCTGTAATTGTTCATACCTACCTGTATATTATTAC-
704655 AAATCTATGCATACAAAATACTGTTCTCTGTAATTGTTCATACCTACCTGTATATTATTACAATC
65 AAATCTATGCATACAAAATACTGTTCTCTGTAATTGTTCATACCTACCTGTATATTATTACAATC
* *
704720 TATGCATACAAAATACTGTTCTCTGTAATTGTTCATACCTTCCTGTATTTTA
130 TATGCATACAAAATACTGTTCTCTGTAATTGTTCATACCTACCTGTATATTA
704772 TTACAAAATCTATGCATACAAAATACTGTTCTCTGTAATTGTTCATACCTACCTGTATATTATTA
1 TTAC--AATCTATGCATACAAAATACTGTTCTCTGTAATTGTTCATACCTACCTGTATATTATTA
704837 C-AATCTATGCATACAAAATACTGTTCTCTGTAATTGTTCATACCTACCTGTATATTATTACAAT
64 CAAATCTATGCATACAAAATACTGTTCTCTGTAATTGTTCATACCTACCTGTATATTATTACAAT
704901 CTATGCATACAAAATACTGTTCTCTGTAATTGTTCATACCTACCTGTATATTA
129 CTATGCATACAAAATACTGTTCTCTGTAATTGTTCATACCTACCTGTATATTA
*
704954 TTACAATCTATGCATACAAAATACTGTTCTCTGTAACTGTTCATAC
1 TTACAATCTATGCATACAAAATACTGTTCTCTGTAATTGTTCATAC
705000 ATGTACATGT
Statistics
Matches: 394, Mismatches: 12, Indels: 8
0.95 0.03 0.02
Matches are distributed among these distances:
180 101 0.26
182 235 0.60
184 58 0.15
ACGTcount: A:0.32, C:0.20, G:0.08, T:0.40
Consensus pattern (181 bp):
TTACAATCTATGCATACAAAATACTGTTCTCTGTAATTGTTCATACCTACCTGTATATTATTACA
AATCTATGCATACAAAATACTGTTCTCTGTAATTGTTCATACCTACCTGTATATTATTACAATCT
ATGCATACAAAATACTGTTCTCTGTAATTGTTCATACCTACCTGTATATTA
Found at i:704716 original size:122 final size:120
Alignment explanation
Indices: 704410--704999 Score: 1072
Period size: 122 Copynumber: 4.9 Consensus size: 120
704400 TGCTTTACCT
* *
704410 TTACAATCTATACATACAAAATACTGTTCTCTGTAATTGTTCATACCTACCTGTATATTATAACA
1 TTACAATCTATGCATACAAAATACTGTTCTCTGTAATTGTTCATACCTACCTGTATATTATTACA
*
704475 ATCTATGCATACAAAATACTGTTCTCTGTAACTGTTCATACCTACCTGTATATTA
66 ATCTATGCATACAAAATACTGTTCTCTGTAATTGTTCATACCTACCTGTATATTA
704530 TTACAATCTATGCATACAAAATACTGTTCTCTGTAATTGTTCATACCTACCTGTATATTATTACA
1 TTACAATCTATGCATACAAAATACTGTTCTCTGTAATTGTTCATACCTACCTGTATATTATTACA
* *
704595 ATCTATGCATACAAAATACTGTTCTCTGTAATTGTTCATACCTTCCTGTATTTTA
66 ATCTATGCATACAAAATACTGTTCTCTGTAATTGTTCATACCTACCTGTATATTA
704650 TTACAAAATCTATGCATACAAAATACTGTTCTCTGTAATTGTTCATACCTACCTGTATATTATTA
1 TTAC--AATCTATGCATACAAAATACTGTTCTCTGTAATTGTTCATACCTACCTGTATATTATTA
* *
704715 CAATCTATGCATACAAAATACTGTTCTCTGTAATTGTTCATACCTTCCTGTATTTTA
64 CAATCTATGCATACAAAATACTGTTCTCTGTAATTGTTCATACCTACCTGTATATTA
704772 TTACAAAATCTATGCATACAAAATACTGTTCTCTGTAATTGTTCATACCTACCTGTATATTATTA
1 TTAC--AATCTATGCATACAAAATACTGTTCTCTGTAATTGTTCATACCTACCTGTATATTATTA
704837 CAATCTATGCATACAAAATACTGTTCTCTGTAATTGTTCATACCTACCTGTATATTA
64 CAATCTATGCATACAAAATACTGTTCTCTGTAATTGTTCATACCTACCTGTATATTA
704894 TTACAATCTATGCATACAAAATACTGTTCTCTGTAATTGTTCATACCTACCTGTATATTATTACA
1 TTACAATCTATGCATACAAAATACTGTTCTCTGTAATTGTTCATACCTACCTGTATATTATTACA
*
704959 ATCTATGCATACAAAATACTGTTCTCTGTAACTGTTCATAC
66 ATCTATGCATACAAAATACTGTTCTCTGTAATTGTTCATAC
705000 ATGTACATGT
Statistics
Matches: 460, Mismatches: 8, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
120 220 0.48
122 240 0.52
ACGTcount: A:0.32, C:0.20, G:0.08, T:0.40
Consensus pattern (120 bp):
TTACAATCTATGCATACAAAATACTGTTCTCTGTAATTGTTCATACCTACCTGTATATTATTACA
ATCTATGCATACAAAATACTGTTCTCTGTAATTGTTCATACCTACCTGTATATTA
Found at i:706629 original size:36 final size:36
Alignment explanation
Indices: 706577--706686 Score: 211
Period size: 36 Copynumber: 3.1 Consensus size: 36
706567 AAAAATTTGT
*
706577 CAATTAGCCAAGGACTAGTTCAAGAATGAAATATTA
1 CAATAAGCCAAGGACTAGTTCAAGAATGAAATATTA
706613 CAATAAGCCAAGGACTAGTTCAAGAATGAAATATTA
1 CAATAAGCCAAGGACTAGTTCAAGAATGAAATATTA
706649 CAATAAGCCAAGGACTAGTTCAAGAATGAAATATTA
1 CAATAAGCCAAGGACTAGTTCAAGAATGAAATATTA
706685 CA
1 CA
706687 GTGAGAAGTT
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
36 73 1.00
ACGTcount: A:0.46, C:0.15, G:0.16, T:0.23
Consensus pattern (36 bp):
CAATAAGCCAAGGACTAGTTCAAGAATGAAATATTA
Found at i:709357 original size:2 final size:2
Alignment explanation
Indices: 709350--709397 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
709340 ACAGTGTACA
709350 TC TC TC 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 TC TC TC
709392 TC TC TC
1 TC TC TC
709398 ACCTGGATAC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:709963 original size:39 final size:39
Alignment explanation
Indices: 709920--710253 Score: 487
Period size: 39 Copynumber: 8.6 Consensus size: 39
709910 CCTACCGGTA
709920 TGTTGATGAGATACTGATTT-TTGTTGAGATAGTTACCTG
1 TGTTGATGAGATACTGATTTGTT-TTGAGATAGTTACCTG
* * *
709959 TGTTGATGAGATACTTATTTGTTTTTAAATAGTTACCTG
1 TGTTGATGAGATACTGATTTGTTTTGAGATAGTTACCTG
* *
709998 TGTTGATGAAATACTGATTTGTTTTGAGGTAGTTACCTG
1 TGTTGATGAGATACTGATTTGTTTTGAGATAGTTACCTG
*
710037 TGTTGATGAGATACTTATTTGTTTTGAGGA-AGTTACCTG
1 TGTTGATGAGATACTGATTTGTTTTGA-GATAGTTACCTG
710076 TGTTGATGAGATACTGATTT-TTGTTGAGATAGTTACCTG
1 TGTTGATGAGATACTGATTTGTT-TTGAGATAGTTACCTG
* * *
710115 TGTTGATGAGATACTTATTTGTTTTTAAATAGTTACCTG
1 TGTTGATGAGATACTGATTTGTTTTGAGATAGTTACCTG
* * *
710154 TGTTGATGAAATACTGATTTGTTTTGAGGTATTTACCTG
1 TGTTGATGAGATACTGATTTGTTTTGAGATAGTTACCTG
*
710193 TGTTGATGAGATACTTATTTGTTTTGAGGA-AGTTACCTG
1 TGTTGATGAGATACTGATTTGTTTTGA-GATAGTTACCTG
710232 TGTTGATGAGATACTGATTTGT
1 TGTTGATGAGATACTGATTTGT
710254 GAGTCCTGGA
Statistics
Matches: 263, Mismatches: 26, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
38 4 0.02
39 253 0.96
40 6 0.02
ACGTcount: A:0.24, C:0.07, G:0.24, T:0.45
Consensus pattern (39 bp):
TGTTGATGAGATACTGATTTGTTTTGAGATAGTTACCTG
Found at i:710081 original size:18 final size:18
Alignment explanation
Indices: 710021--710081 Score: 50
Period size: 18 Copynumber: 3.2 Consensus size: 18
710011 CTGATTTGTT
*
710021 TTGAGGTAGTTACCTGTG
1 TTGAGGAAGTTACCTGTG
* ** *
710039 TTGATGAGATACTTATTTGTT
1 TTGA-G-GA-AGTTACCTGTG
710060 TTGAGGAAGTTACCTGTG
1 TTGAGGAAGTTACCTGTG
710078 TTGA
1 TTGA
710082 TGAGATACTG
Statistics
Matches: 31, Mismatches: 9, Indels: 6
0.67 0.20 0.13
Matches are distributed among these distances:
18 15 0.48
19 3 0.10
20 2 0.06
21 11 0.35
ACGTcount: A:0.21, C:0.08, G:0.28, T:0.43
Consensus pattern (18 bp):
TTGAGGAAGTTACCTGTG
Found at i:710174 original size:156 final size:156
Alignment explanation
Indices: 709920--710251 Score: 655
Period size: 156 Copynumber: 2.1 Consensus size: 156
709910 CCTACCGGTA
709920 TGTTGATGAGATACTGATTTTTGTTGAGATAGTTACCTGTGTTGATGAGATACTTATTTGTTTTT
1 TGTTGATGAGATACTGATTTTTGTTGAGATAGTTACCTGTGTTGATGAGATACTTATTTGTTTTT
709985 AAATAGTTACCTGTGTTGATGAAATACTGATTTGTTTTGAGGTAGTTACCTGTGTTGATGAGATA
66 AAATAGTTACCTGTGTTGATGAAATACTGATTTGTTTTGAGGTAGTTACCTGTGTTGATGAGATA
710050 CTTATTTGTTTTGAGGAAGTTACCTG
131 CTTATTTGTTTTGAGGAAGTTACCTG
710076 TGTTGATGAGATACTGATTTTTGTTGAGATAGTTACCTGTGTTGATGAGATACTTATTTGTTTTT
1 TGTTGATGAGATACTGATTTTTGTTGAGATAGTTACCTGTGTTGATGAGATACTTATTTGTTTTT
*
710141 AAATAGTTACCTGTGTTGATGAAATACTGATTTGTTTTGAGGTATTTACCTGTGTTGATGAGATA
66 AAATAGTTACCTGTGTTGATGAAATACTGATTTGTTTTGAGGTAGTTACCTGTGTTGATGAGATA
710206 CTTATTTGTTTTGAGGAAGTTACCTG
131 CTTATTTGTTTTGAGGAAGTTACCTG
710232 TGTTGATGAGATACTGATTT
1 TGTTGATGAGATACTGATTT
710252 GTGAGTCCTG
Statistics
Matches: 175, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
156 175 1.00
ACGTcount: A:0.24, C:0.08, G:0.23, T:0.45
Consensus pattern (156 bp):
TGTTGATGAGATACTGATTTTTGTTGAGATAGTTACCTGTGTTGATGAGATACTTATTTGTTTTT
AAATAGTTACCTGTGTTGATGAAATACTGATTTGTTTTGAGGTAGTTACCTGTGTTGATGAGATA
CTTATTTGTTTTGAGGAAGTTACCTG
Found at i:711112 original size:47 final size:47
Alignment explanation
Indices: 711059--711336 Score: 303
Period size: 47 Copynumber: 6.2 Consensus size: 47
711049 ATGTACGCAA
*
711059 GTAAGTGCTTTATCCTATTTACCTGTAATATTGTATAAGTAACACAG
1 GTAAGTGCTTTATCCTATTTACCTGTAATATTGTATAGGTAACACAG
* * * *
711106 GAAAGTGATTTATCCTATTTATCTGTTATATTGTATAGGTAACACAG
1 GTAAGTGCTTTATCCTATTTACCTGTAATATTGTATAGGTAACACAG
* * * *
711153 GAAAGTGCTTTATCCTATTTACC--T-ATA--CTAT---T-GCACAA
1 GTAAGTGCTTTATCCTATTTACCTGTAATATTGTATAGGTAACACAG
* * *
711191 GTAAGTGCTTTATCCTATTTATCTGTACTATTGTATAAGTAACACAG
1 GTAAGTGCTTTATCCTATTTACCTGTAATATTGTATAGGTAACACAG
* * *
711238 GTAAGTACTTTATCCTATTTACCTGTACTATTGTACAGGT---AC-G
1 GTAAGTGCTTTATCCTATTTACCTGTAATATTGTATAGGTAACACAG
* * *
711281 GTAAGTGGTTAATTCTATTTACCTGTAATATTGTATAGGTAACACAG
1 GTAAGTGCTTTATCCTATTTACCTGTAATATTGTATAGGTAACACAG
711328 GTAAGTGCT
1 GTAAGTGCT
711337 CGGTTGTTTG
Statistics
Matches: 191, Mismatches: 27, Indels: 26
0.78 0.11 0.11
Matches are distributed among these distances:
38 25 0.13
39 1 0.01
40 1 0.01
41 2 0.01
42 3 0.02
43 38 0.20
44 5 0.03
45 1 0.01
46 3 0.02
47 112 0.59
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.39
Consensus pattern (47 bp):
GTAAGTGCTTTATCCTATTTACCTGTAATATTGTATAGGTAACACAG
Found at i:711197 original size:38 final size:38
Alignment explanation
Indices: 711155--711232 Score: 120
Period size: 38 Copynumber: 2.1 Consensus size: 38
711145 TAACACAGGA
711155 AAGTGCTTTATCCTATTTACCTATACTATTGCACAAGT
1 AAGTGCTTTATCCTATTTACCTATACTATTGCACAAGT
* * * *
711193 AAGTGCTTTATCCTATTTATCTGTACTATTGTATAAGT
1 AAGTGCTTTATCCTATTTACCTATACTATTGCACAAGT
711231 AA
1 AA
711233 CACAGGTAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (38 bp):
AAGTGCTTTATCCTATTTACCTATACTATTGCACAAGT
Found at i:711251 original size:85 final size:86
Alignment explanation
Indices: 711108--711333 Score: 294
Period size: 85 Copynumber: 2.6 Consensus size: 86
711098 TAACACAGGA
* *
711108 AAGTGATTTATCCTATTTATCTGTTATATTGTATAGGTAACACAGGAAAGTGCTTTATCCTATTT
1 AAGTGATTTATCCTATTTATCTG-TATATTGTATAGGTAACACAGGTAAGTACTTTATCCTATTT
711173 ACCTATACTATTGCACA-A-GT
65 ACCTATACTATTGCACAGACGT
* *
711193 AAGTGCTTTATCCTATTTATCTGTACTATTGTATAAGTAACACAGGTAAGTACTTTATCCTATTT
1 AAGTGATTTATCCTATTTATCTGTA-TATTGTATAGGTAACACAGGTAAGTACTTTATCCTATTT
* *
711258 ACCTGTACTATTGTACAGGTACGGT
65 ACCTATACTATTGCACA-G-AC-GT
* * * *
711283 AAGTGGTTAATTCTATTTACCTGTAATATTGTATAGGTAACACAGGTAAGT
1 AAGTGATTTATCCTATTTATCTGT-ATATTGTATAGGTAACACAGGTAAGT
711334 GCTCGGTTGT
Statistics
Matches: 123, Mismatches: 11, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
84 2 0.02
85 73 0.59
88 1 0.01
90 46 0.37
91 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.39
Consensus pattern (86 bp):
AAGTGATTTATCCTATTTATCTGTATATTGTATAGGTAACACAGGTAAGTACTTTATCCTATTTA
CCTATACTATTGCACAGACGT
Found at i:713120 original size:13 final size:13
Alignment explanation
Indices: 713104--713266 Score: 132
Period size: 13 Copynumber: 12.5 Consensus size: 13
713094 TCAAAAAAAT
*
713104 GTGTGAGCATTGA
1 GTGTGAGCGTTGA
*
713117 GTGTGAGCATCTG-
1 GTGTGAGCGT-TGA
*
713130 GTGTCAGCGTTGA
1 GTGTGAGCGTTGA
* *
713143 ATGTGAGTGTTGA
1 GTGTGAGCGTTGA
*
713156 GTATGAGCGTTGA
1 GTGTGAGCGTTGA
* *
713169 GAGTGAGTGTTGA
1 GTGTGAGCGTTGA
*
713182 GTATGAGCGTTGA
1 GTGTGAGCGTTGA
* *
713195 GAGTGAGTGTTGA
1 GTGTGAGCGTTGA
* *
713208 GCGTGAGTC-TTAA
1 GTGTGAG-CGTTGA
* *
713221 GTGTTAGCATTGA
1 GTGTGAGCGTTGA
*
713234 GTGTGAGTGTTGA
1 GTGTGAGCGTTGA
* *
713247 GTGTTAGCTTTGA
1 GTGTGAGCGTTGA
713260 GTGTGAG
1 GTGTGAG
713267 TATCATTGCA
Statistics
Matches: 116, Mismatches: 30, Indels: 8
0.75 0.19 0.05
Matches are distributed among these distances:
12 3 0.03
13 111 0.96
14 2 0.02
ACGTcount: A:0.20, C:0.07, G:0.39, T:0.34
Consensus pattern (13 bp):
GTGTGAGCGTTGA
Found at i:713336 original size:76 final size:76
Alignment explanation
Indices: 713243--713415 Score: 303
Period size: 76 Copynumber: 2.3 Consensus size: 76
713233 AGTGTGAGTG
*
713243 TTGAGTGTTAGCT-TTGAGTGTGAGTATCATTGCATACCTTGCTGGAGGCCATGTCACTGACTGA
1 TTGAGTGTGAG-TGTTGAGTGTGAGTATCATTGCATACCTTGCTGGAGGCCATGTCACTGACTGA
713307 CCGGTGCGAGCA
65 CCGGTGCGAGCA
* *
713319 TTGAGTGTGAGTGTTGAGTGTGAGTATCTTTGCATACCTTGCTGGAGGCCATGTCATTGACTGAC
1 TTGAGTGTGAGTGTTGAGTGTGAGTATCATTGCATACCTTGCTGGAGGCCATGTCACTGACTGAC
713384 CGGTGCGAGCA
66 CGGTGCGAGCA
713395 TTGAGTGTGAGTGTTGAGTGT
1 TTGAGTGTGAGTGTTGAGTGT
713416 TAGTGTTGAG
Statistics
Matches: 93, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
75 1 0.01
76 92 0.99
ACGTcount: A:0.18, C:0.16, G:0.33, T:0.32
Consensus pattern (76 bp):
TTGAGTGTGAGTGTTGAGTGTGAGTATCATTGCATACCTTGCTGGAGGCCATGTCACTGACTGAC
CGGTGCGAGCA
Found at i:713337 original size:13 final size:13
Alignment explanation
Indices: 713319--713343 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
713309 GGTGCGAGCA
713319 TTGAGTGTGAGTG
1 TTGAGTGTGAGTG
713332 TTGAGTGTGAGT
1 TTGAGTGTGAGT
713344 ATCTTTGCAT
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:0.16, C:0.00, G:0.44, T:0.40
Consensus pattern (13 bp):
TTGAGTGTGAGTG
Found at i:713413 original size:13 final size:13
Alignment explanation
Indices: 713395--713432 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
713385 GGTGCGAGCA
713395 TTGAGTGTGAGTG
1 TTGAGTGTGAGTG
*
713408 TTGAGTGTTAGTG
1 TTGAGTGTGAGTG
713421 TTGAGTGTGAGT
1 TTGAGTGTGAGT
713433 ATCTTTGGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.16, C:0.00, G:0.42, T:0.42
Consensus pattern (13 bp):
TTGAGTGTGAGTG
Found at i:714579 original size:55 final size:55
Alignment explanation
Indices: 714441--714613 Score: 256
Period size: 55 Copynumber: 3.1 Consensus size: 55
714431 ACCAGGTTGG
* * * * *
714441 TATCTGTGGGTGGGGCAGTACAGAACAGAACAATATTCACTTGTTTATATAAAGTAGA
1 TATCTGTGGGTGGGGCAGTACAGAACAGTACAATATTGACCT-ATT-TAT-CAGTAGA
714499 TATCTGTGGGTGGGGCAGTACAGAACAGTACAATATTGACCTATTTATCAGTAGA
1 TATCTGTGGGTGGGGCAGTACAGAACAGTACAATATTGACCTATTTATCAGTAGA
* *
714554 TATCTGTGTGTGGGGCAGTATAGAACAGTACAATATTGACCTATTTATCAGTAGA
1 TATCTGTGGGTGGGGCAGTACAGAACAGTACAATATTGACCTATTTATCAGTAGA
714609 TATCT
1 TATCT
714614 ATGTGAGTGT
Statistics
Matches: 108, Mismatches: 7, Indels: 3
0.92 0.06 0.03
Matches are distributed among these distances:
55 64 0.59
56 3 0.03
57 2 0.02
58 39 0.36
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.31
Consensus pattern (55 bp):
TATCTGTGGGTGGGGCAGTACAGAACAGTACAATATTGACCTATTTATCAGTAGA
Found at i:716252 original size:13 final size:14
Alignment explanation
Indices: 716211--716252 Score: 68
Period size: 14 Copynumber: 3.1 Consensus size: 14
716201 CCGGAAAATA
716211 GTAAATCCTCAGGT
1 GTAAATCCTCAGGT
716225 GTAAATCCTCAGGT
1 GTAAATCCTCAGGT
*
716239 GTATATCC-CAGGT
1 GTAAATCCTCAGGT
716252 G
1 G
716253 AGATCTTGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
13 6 0.22
14 21 0.78
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (14 bp):
GTAAATCCTCAGGT
Found at i:721297 original size:26 final size:26
Alignment explanation
Indices: 721261--721315 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
721251 GGTCGGACAT
721261 CTAGCTGGGTTAGGTGGATACAAATA
1 CTAGCTGGGTTAGGTGGATACAAATA
721287 CTAGCTGGGTTAGGTGGATACAAATA
1 CTAGCTGGGTTAGGTGGATACAAATA
721313 CTA
1 CTA
721316 CTAACTTCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.31, C:0.13, G:0.29, T:0.27
Consensus pattern (26 bp):
CTAGCTGGGTTAGGTGGATACAAATA
Found at i:724489 original size:2 final size:2
Alignment explanation
Indices: 724482--724540 Score: 95
Period size: 2 Copynumber: 30.5 Consensus size: 2
724472 GAAGTTTCCA
724482 TC TC TC TC TC -C TC TC TC TC TC TC TC -C 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 TC TC TC
*
724522 TC TC TC TC TC TC TT TC TC T
1 TC TC TC TC TC TC TC TC TC T
724541 GAATGTCACC
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
1 2 0.04
2 51 0.96
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:725784 original size:17 final size:18
Alignment explanation
Indices: 725760--725801 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 18
725750 ACAAGAGAGA
725760 GAGAGAGATGAGAAAG-GGT
1 GAGAGAGA-G-GAAAGAGGT
725779 GAGAGAGAGGAAAGAGGT
1 GAGAGAGAGGAAAGAGGT
725797 -AGAGA
1 GAGAGA
725802 AAATGAGATG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 10 0.45
18 4 0.18
19 8 0.36
ACGTcount: A:0.45, C:0.00, G:0.48, T:0.07
Consensus pattern (18 bp):
GAGAGAGAGGAAAGAGGT
Found at i:725801 original size:19 final size:20
Alignment explanation
Indices: 725759--725801 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
725749 AACAAGAGAG
725759 AGAGAGAGATGAGAAAGGGT
1 AGAGAGAGATGAGAAAGGGT
725779 -GAGAGAGA-G-GAAAGAGGT
1 AGAGAGAGATGAGAAAG-GGT
725797 AGAGA
1 AGAGA
725802 AAATGAGATG
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 5 0.24
18 4 0.19
19 12 0.57
ACGTcount: A:0.47, C:0.00, G:0.47, T:0.07
Consensus pattern (20 bp):
AGAGAGAGATGAGAAAGGGT
Found at i:728711 original size:22 final size:22
Alignment explanation
Indices: 728686--728757 Score: 56
Period size: 23 Copynumber: 3.2 Consensus size: 22
728676 CTTTGACGTG
728686 GATACATGGAATTACTGGACAA
1 GATACATGGAATTACTGGACAA
* ** * * *
728708 GATA-TTCGGTGTTTAATTGACGCA
1 GATACAT-GG-AATTACTGGAC-AA
728732 GATACATGGAATTACTGGACAA
1 GATACATGGAATTACTGGACAA
728754 GATA
1 GATA
728758 TTCGGTGTCT
Statistics
Matches: 34, Mismatches: 12, Indels: 8
0.63 0.22 0.15
Matches are distributed among these distances:
21 1 0.03
22 11 0.32
23 14 0.41
24 7 0.21
25 1 0.03
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.28
Consensus pattern (22 bp):
GATACATGGAATTACTGGACAA
Found at i:728820 original size:46 final size:46
Alignment explanation
Indices: 728350--728811 Score: 861
Period size: 46 Copynumber: 10.0 Consensus size: 46
728340 GTTCCCTTAC
728350 GTCTCTTTGACGCAGATACATGGAATTACTGGACAAGATATTCGGT
1 GTCTCTTTGACGCAGATACATGGAATTACTGGACAAGATATTCGGT
728396 GTCTCTTTGACGCAGATACATGGAATTACTGGACAAGATATTCGGT
1 GTCTCTTTGACGCAGATACATGGAATTACTGGACAAGATATTCGGT
728442 GTCTCTTTGACGCAGATACATGGAATTACTGGACAAGATATTCGGT
1 GTCTCTTTGACGCAGATACATGGAATTACTGGACAAGATATTCGGT
728488 GTCTCTTTGACGCAGATACATGGAATTACTGGACAAGATATTCGGT
1 GTCTCTTTGACGCAGATACATGGAATTACTGGACAAGATATTCGGT
728534 GTCTCTTTGACGCAGATACATGGAATTACTGGACAAGATATTCGGT
1 GTCTCTTTGACGCAGATACATGGAATTACTGGACAAGATATTCGGT
728580 GTCTCTTTGACGCAGATACATGGAATTACTGGACAAGATATTCGGT
1 GTCTCTTTGACGCAGATACATGGAATTACTGGACAAGATATTCGGT
728626 GTCTCTTTGACGCAGATACATGGAATTACTGGACAAGATATTCGGT
1 GTCTCTTTGACGCAGATACATGGAATTACTGGACAAGATATTCGGT
**
728672 GTCTCTTTGACGTGGATACATGGAATTACTGGACAAGATATTCGGT
1 GTCTCTTTGACGCAGATACATGGAATTACTGGACAAGATATTCGGT
* **
728718 GTTTAATTGACGCAGATACATGGAATTACTGGACAAGATATTCGGT
1 GTCTCTTTGACGCAGATACATGGAATTACTGGACAAGATATTCGGT
* *
728764 GTCTCTTTGACGCGGATACATGGAATTACTGGACAAGATAATCGGT
1 GTCTCTTTGACGCAGATACATGGAATTACTGGACAAGATATTCGGT
728810 GT
1 GT
728812 TTAATTGACT
Statistics
Matches: 404, Mismatches: 12, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 404 1.00
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (46 bp):
GTCTCTTTGACGCAGATACATGGAATTACTGGACAAGATATTCGGT
Found at i:729244 original size:19 final size:19
Alignment explanation
Indices: 729220--729287 Score: 68
Period size: 21 Copynumber: 3.5 Consensus size: 19
729210 CCAAGTGCTT
729220 TATAATAATAATAATATAA
1 TATAATAATAATAATATAA
*
729239 TATAATTATAATTATATATAA
1 TATAATAATAA-TA-ATATAA
* *
729260 TATATATTATTATAAT-T-A
1 TATA-ATAATAATAATATAA
729278 TATAATAATA
1 TATAATAATA
729288 TAACACTGCT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
17 4 0.10
18 5 0.12
19 11 0.26
20 4 0.10
21 12 0.29
22 6 0.14
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TATAATAATAATAATATAA
Found at i:729249 original size:16 final size:15
Alignment explanation
Indices: 729220--729290 Score: 60
Period size: 16 Copynumber: 4.7 Consensus size: 15
729210 CCAAGTGCTT
729220 TATAATAATAA-TA-A
1 TATAAT-ATAATTATA
729234 TATAATATAATTATA
1 TATAATATAATTATA
729249 -ATTATATATAA-TATA
1 TA-TA-ATATAATTATA
*
729264 TATTATTATAATTATA
1 TA-TAATATAATTATA
729280 TAATAATATAA
1 T-ATAATATAA
729291 CACTGCTTAT
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
13 4 0.08
14 9 0.19
15 12 0.25
16 22 0.46
17 1 0.02
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATAATATAATTATA
Done.