Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold3
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: 1336734
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.30
Warning! 151046 characters in sequence are not A, C, G, or T
File 2 of 4
Found at i:5594 original size:17 final size:17
Alignment explanation
Indices: 5572--5605 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
5562 TAGGTTTTCC
5572 GGGGGGAAAACTGCTAT
1 GGGGGGAAAACTGCTAT
5589 GGGGGGAAAACTGCTAT
1 GGGGGGAAAACTGCTAT
5606 ACAACACCGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.12, G:0.41, T:0.18
Consensus pattern (17 bp):
GGGGGGAAAACTGCTAT
Found at i:29745 original size:2 final size:2
Alignment explanation
Indices: 29738--29802 Score: 94
Period size: 2 Copynumber: 32.5 Consensus size: 2
29728 GTTGTTTGCT
* *
29738 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA AA GA GA AA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
* *
29780 GA GA GG GA GA GA AA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA G
29803 TACTCATGTC
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:30151 original size:16 final size:16
Alignment explanation
Indices: 30130--30161 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
30120 CTTTCCTCTG
30130 CGTCCGTCAGTCTGTC
1 CGTCCGTCAGTCTGTC
*
30146 CGTCCGTCCGTCTGTC
1 CGTCCGTCAGTCTGTC
30162 TATCTGTCTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.03, C:0.41, G:0.25, T:0.31
Consensus pattern (16 bp):
CGTCCGTCAGTCTGTC
Found at i:34385 original size:21 final size:21
Alignment explanation
Indices: 34360--34427 Score: 84
Period size: 21 Copynumber: 3.3 Consensus size: 21
34350 AATTTAGATA
34360 TTGAATCTCGAATTTCGAATC
1 TTGAATCTCGAATTTCGAATC
*
34381 TTGAATCTCGTATTTCGAATC
1 TTGAATCTCGAATTTCGAATC
* * * *
34402 -TGTATTTTGAATCTCGAATC
1 TTGAATCTCGAATTTCGAATC
34422 TTGAAT
1 TTGAAT
34428 GATCCTTTTC
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 15 0.38
21 24 0.62
ACGTcount: A:0.26, C:0.16, G:0.15, T:0.43
Consensus pattern (21 bp):
TTGAATCTCGAATTTCGAATC
Found at i:34408 original size:13 final size:14
Alignment explanation
Indices: 34383--34417 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
34373 TTCGAATCTT
34383 GAATCTCGTATTTC
1 GAATCTCGTATTTC
*
34397 GAATCT-GTATTTT
1 GAATCTCGTATTTC
34410 GAATCTCG
1 GAATCTCG
34418 AATCTTGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.43
Consensus pattern (14 bp):
GAATCTCGTATTTC
Found at i:34422 original size:7 final size:7
Alignment explanation
Indices: 34362--34427 Score: 53
Period size: 7 Copynumber: 9.6 Consensus size: 7
34352 TTTAGATATT
34362 GAATCTC
1 GAATCTC
*
34369 GAATTTC
1 GAATCTC
*
34376 GAATCTT
1 GAATCTC
34383 GAATCTC
1 GAATCTC
* *
34390 GTATTTC
1 GAATCTC
34397 GAATCT-
1 GAATCTC
* * *
34403 GTATTTT
1 GAATCTC
34410 GAATCTC
1 GAATCTC
*
34417 GAATCTT
1 GAATCTC
34424 GAAT
1 GAAT
34428 GATCCTTTTC
Statistics
Matches: 44, Mismatches: 14, Indels: 2
0.73 0.23 0.03
Matches are distributed among these distances:
6 4 0.09
7 40 0.91
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41
Consensus pattern (7 bp):
GAATCTC
Found at i:34427 original size:14 final size:14
Alignment explanation
Indices: 34362--34427 Score: 64
Period size: 14 Copynumber: 4.8 Consensus size: 14
34352 TTTAGATATT
* *
34362 GAATCTCGAATTTC
1 GAATCTTGAATCTC
34376 GAATCTTGAATCTC
1 GAATCTTGAATCTC
*
34390 GTAT-TTCGAATCT-
1 GAATCTT-GAATCTC
* *
34403 GTATTTTGAATCTC
1 GAATCTTGAATCTC
34417 GAATCTTGAAT
1 GAATCTTGAAT
34428 GATCCTTTTC
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
13 12 0.27
14 32 0.73
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41
Consensus pattern (14 bp):
GAATCTTGAATCTC
Found at i:38317 original size:7 final size:7
Alignment explanation
Indices: 38305--38371 Score: 89
Period size: 7 Copynumber: 9.6 Consensus size: 7
38295 GAGAAGGATC
38305 ATTCGAG
1 ATTCGAG
38312 ATTCGAG
1 ATTCGAG
*
38319 ATTCGAA
1 ATTCGAG
*
38326 ATACGAG
1 ATTCGAG
*
38333 ATTCGAA
1 ATTCGAG
*
38340 ATACGAG
1 ATTCGAG
38347 ATTCGAG
1 ATTCGAG
*
38354 ATTCGAA
1 ATTCGAG
38361 ATTCGAG
1 ATTCGAG
38368 ATTC
1 ATTC
38372 AATATCTAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 50 1.00
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (7 bp):
ATTCGAG
Found at i:40114 original size:33 final size:32
Alignment explanation
Indices: 40023--40101 Score: 140
Period size: 32 Copynumber: 2.4 Consensus size: 32
40013 CCTAGCCATC
40023 TTTCCCCCCGGAAAAATGGCTATATAGCAGTT
1 TTTCCCCCCGGAAAAATGGCTATATAGCAGTT
*
40055 CTTCCCCCCGGAAAAATGGCTATATAGCAGTT
1 TTTCCCCCCGGAAAAATGGCTATATAGCAGTT
40087 TTTCCCCCACGGAAA
1 TTTCCCCC-CGGAAA
40102 GCTGACTATA
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 38 0.86
33 6 0.14
ACGTcount: A:0.28, C:0.29, G:0.18, T:0.25
Consensus pattern (32 bp):
TTTCCCCCCGGAAAAATGGCTATATAGCAGTT
Found at i:41379 original size:166 final size:150
Alignment explanation
Indices: 41103--41420 Score: 431
Period size: 166 Copynumber: 2.0 Consensus size: 150
41093 TTATAAATAT
* *
41103 ACAATTTTGAAAACGATGCTATATAAATCAGGATATACGATTCCATAACCTAAAAAAATTATACT
1 ACAATTTTGAAAACGATGCCATATAAATCAAGATATACGATTCCATAACCTAAAAAAATTATACT
41168 ATTTGTTTCATATTTTTGCAATAAAGATTTACTTGTGTACCATATTATTTCTTCGAACAATGAAA
66 ATTTGTTTCATATTTTTGCAATAAAGATTTACTTGTGTACCATATTATTTCTTCGAACAATGAAA
41233 CAAGGGTAATTAAAAAAAAA
131 CAAGGGTAATTAAAAAAAAA
*
41253 NNNNNNNNNNNNNACAATTTTGAAAACGATGCCATATAAATCAAGATATACGATT-CACTTACCT
1 -------------ACAATTTTGAAAACGATGCCATATAAATCAAGATATACGATTCCA-TAACCT
**
41317 AAAAATCGTATATTACTATTTGTTTCATATTTTTGCAATAAAGATTTACTTGTGTACCATATTAT
52 AAAAA-AAT-TA-TACTATTTGTTTCATATTTTTGCAATAAAGATTTACTTGTGTACCATATTAT
41382 TTCTTCGAACAATGAAACAAGGGTAATTAAAAAAAAA
114 TTCTTCGAACAATGAAACAAGGGTAATTAAAAAAAAA
41419 AC
1 AC
41421 GACCCCCCCC
Statistics
Matches: 146, Mismatches: 5, Indels: 18
0.86 0.03 0.11
Matches are distributed among these distances:
153 2 0.01
162 2 0.01
163 50 0.34
164 1 0.01
165 2 0.01
166 89 0.61
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.33
Consensus pattern (150 bp):
ACAATTTTGAAAACGATGCCATATAAATCAAGATATACGATTCCATAACCTAAAAAAATTATACT
ATTTGTTTCATATTTTTGCAATAAAGATTTACTTGTGTACCATATTATTTCTTCGAACAATGAAA
CAAGGGTAATTAAAAAAAAA
Found at i:54508 original size:45 final size:46
Alignment explanation
Indices: 54437--54524 Score: 133
Period size: 45 Copynumber: 1.9 Consensus size: 46
54427 TATTACACTC
* * * *
54437 TATTCCTTTTAAAAACTTTAGTTCAAAGTGGTTTGAAAAGAAGCTA
1 TATTCCCTTTAAAAACTTCAATTCAAAGTGGATTGAAAAGAAGCTA
54483 TATTCCCTTT-AAAACTTCAATTCAAAGTGGATTGAAAAGAAG
1 TATTCCCTTTAAAAACTTCAATTCAAAGTGGATTGAAAAGAAG
54525 TCAATGATGC
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
45 29 0.76
46 9 0.24
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34
Consensus pattern (46 bp):
TATTCCCTTTAAAAACTTCAATTCAAAGTGGATTGAAAAGAAGCTA
Found at i:56939 original size:8 final size:8
Alignment explanation
Indices: 56926--56974 Score: 73
Period size: 8 Copynumber: 6.2 Consensus size: 8
56916 TGAGAAGTTT
56926 ACGGACAG
1 ACGGACAG
56934 ACGGACAG
1 ACGGACAG
56942 ACGGACAG
1 ACGGACAG
*
56950 ACGGACGG
1 ACGGACAG
*
56958 ACGGACGG
1 ACGGACAG
56966 AC-GACAG
1 ACGGACAG
56973 AC
1 AC
56975 AAAATGTGAT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
7 6 0.15
8 33 0.85
ACGTcount: A:0.35, C:0.27, G:0.39, T:0.00
Consensus pattern (8 bp):
ACGGACAG
Found at i:56975 original size:4 final size:4
Alignment explanation
Indices: 56926--56968 Score: 59
Period size: 4 Copynumber: 10.8 Consensus size: 4
56916 TGAGAAGTTT
* * *
56926 ACGG ACAG ACGG ACAG ACGG ACAG ACGG ACGG ACGG ACGG ACG
1 ACGG ACGG ACGG ACGG ACGG ACGG ACGG ACGG ACGG ACGG ACG
56969 ACAGACAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.33, C:0.26, G:0.42, T:0.00
Consensus pattern (4 bp):
ACGG
Found at i:60060 original size:1 final size:1
Alignment explanation
Indices: 60044--60110 Score: 62
Period size: 1 Copynumber: 67.0 Consensus size: 1
60034 ATCTATTGGG
* * * * * * * *
60044 TTTTTTGTTTTGTTTTTTTGTTTGTTTGTTTTTTTTTTTTTGTTTTTTTTTATGTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
60109 TT
1 TT
60111 GCTTCGTCTT
Statistics
Matches: 50, Mismatches: 16, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 50 1.00
ACGTcount: A:0.01, C:0.00, G:0.10, T:0.88
Consensus pattern (1 bp):
T
Found at i:60060 original size:12 final size:11
Alignment explanation
Indices: 60044--60107 Score: 76
Period size: 12 Copynumber: 5.5 Consensus size: 11
60034 ATCTATTGGG
60044 TTTTTTGTTTTGT
1 TTTTTTG-TTT-T
60057 TTTTTTGTTTGT
1 TTTTTTGTTT-T
*
60069 TTGTTT-TTTT
1 TTTTTTGTTTT
60079 TTTTTTGTTTT
1 TTTTTTGTTTT
60090 TTTTTATGTTTT
1 TTTTT-TGTTTT
60102 TTTTTT
1 TTTTTT
60108 TTTGCTTCGT
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
10 6 0.13
11 13 0.28
12 21 0.45
13 7 0.15
ACGTcount: A:0.02, C:0.00, G:0.11, T:0.88
Consensus pattern (11 bp):
TTTTTTGTTTT
Found at i:60085 original size:30 final size:29
Alignment explanation
Indices: 60044--60110 Score: 100
Period size: 30 Copynumber: 2.3 Consensus size: 29
60034 ATCTATTGGG
*
60044 TTTTTTGTTTTGTTTTTTTGTT-TGTTTGTT
1 TTTTTTTTTTTGTTTTTTT-TTATGTTT-TT
60074 TTTTTTTTTTTGTTTTTTTTTATGTTTTT
1 TTTTTTTTTTTGTTTTTTTTTATGTTTTT
60103 TTTTTTTT
1 TTTTTTTT
60111 GCTTCGTCTT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
29 12 0.34
30 23 0.66
ACGTcount: A:0.01, C:0.00, G:0.10, T:0.88
Consensus pattern (29 bp):
TTTTTTTTTTTGTTTTTTTTTATGTTTTT
Found at i:66384 original size:14 final size:14
Alignment explanation
Indices: 66365--66445 Score: 74
Period size: 14 Copynumber: 5.8 Consensus size: 14
66355 ATATACGACA
*
66365 GCCAACTGCCTACT
1 GCCAACTGCTTACT
*
66379 GCCAACTGGTTACT
1 GCCAACTGCTTACT
** **
66393 GCTTACTGCCAACT
1 GCCAACTGCTTACT
*
66407 GCTTAA-TGCTTACT
1 GC-CAACTGCTTACT
66421 GCCAACTGCTTACT
1 GCCAACTGCTTACT
*
66435 GCCAAATGCTT
1 GCCAACTGCTT
66446 TCTTTACCTC
Statistics
Matches: 53, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
13 2 0.04
14 49 0.92
15 2 0.04
ACGTcount: A:0.22, C:0.32, G:0.16, T:0.30
Consensus pattern (14 bp):
GCCAACTGCTTACT
Found at i:66399 original size:21 final size:21
Alignment explanation
Indices: 66369--66436 Score: 109
Period size: 21 Copynumber: 3.2 Consensus size: 21
66359 ACGACAGCCA
* *
66369 ACTGCCTACTGCCAACTGGTT
1 ACTGCTTACTGCCAACTGCTT
66390 ACTGCTTACTGCCAACTGCTT
1 ACTGCTTACTGCCAACTGCTT
*
66411 AATGCTTACTGCCAACTGCTT
1 ACTGCTTACTGCCAACTGCTT
66432 ACTGC
1 ACTGC
66437 CAAATGCTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.21, C:0.32, G:0.16, T:0.31
Consensus pattern (21 bp):
ACTGCTTACTGCCAACTGCTT
Found at i:67830 original size:14 final size:14
Alignment explanation
Indices: 67797--67835 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
67787 GAGGTAAAGA
*
67797 AAGCATTTGGCAGT
1 AAGCAGTTGGCAGT
*
67811 -AGCAGTTGTCAGT
1 AAGCAGTTGGCAGT
67824 AAGCAGTTGGCA
1 AAGCAGTTGGCA
67836 CCTGAAAGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.28, C:0.15, G:0.31, T:0.26
Consensus pattern (14 bp):
AAGCAGTTGGCAGT
Found at i:67905 original size:13 final size:15
Alignment explanation
Indices: 67885--67922 Score: 62
Period size: 13 Copynumber: 2.7 Consensus size: 15
67875 GCGGGTAATG
67885 TATTTTTTTTATT-T
1 TATTTTTTTTATTAT
67899 T-TTTTTTTTATTAT
1 TATTTTTTTTATTAT
67913 TATTTTTTTT
1 TATTTTTTTT
67923 TGCAATGTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 11 0.50
14 3 0.14
15 8 0.36
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (15 bp):
TATTTTTTTTATTAT
Found at i:67912 original size:16 final size:16
Alignment explanation
Indices: 67887--67923 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
67877 GGGTAATGTA
67887 TTTTTTTTATT-TTTT
1 TTTTTTTTATTATTTT
67902 TTTTTTATTATTATTTT
1 TTTTTT-TTATTATTTT
67919 TTTTT
1 TTTTT
67924 GCAATGTTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 6 0.30
16 5 0.25
17 9 0.45
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (16 bp):
TTTTTTTTATTATTTT
Found at i:76680 original size:14 final size:14
Alignment explanation
Indices: 76661--76689 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
76651 TCAACAGAGG
76661 TTTTTTTTTTT-AA
1 TTTTTTTTTTTGAA
76674 TTTTTTTTTTTGAA
1 TTTTTTTTTTTGAA
76688 TT
1 TT
76690 ATCTTCATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.14, C:0.00, G:0.03, T:0.83
Consensus pattern (14 bp):
TTTTTTTTTTTGAA
Found at i:78877 original size:21 final size:21
Alignment explanation
Indices: 78833--78931 Score: 164
Period size: 21 Copynumber: 4.8 Consensus size: 21
78823 ATTCAAATAT
*
78833 TTGTACCTATCTTCAAAT-AA
1 TTGTACCTATCTTCAATTCAA
78853 TTGTACCTATCTTCAATTCAA
1 TTGTACCTATCTTCAATTCAA
*
78874 TTGTACCTGTCTTCAATTCAA
1 TTGTACCTATCTTCAATTCAA
*
78895 TTGTACTTATCTTCAATTCAA
1 TTGTACCTATCTTCAATTCAA
78916 TTGTACCTATCTTCAA
1 TTGTACCTATCTTCAA
78932 ATTGAATTAG
Statistics
Matches: 73, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
20 17 0.23
21 56 0.77
ACGTcount: A:0.28, C:0.22, G:0.06, T:0.43
Consensus pattern (21 bp):
TTGTACCTATCTTCAATTCAA
Found at i:78966 original size:43 final size:42
Alignment explanation
Indices: 78908--79002 Score: 120
Period size: 42 Copynumber: 2.2 Consensus size: 42
78898 TACTTATCTT
*
78908 CAATTCAATTGTACCTATCTTCAAATTGAATTAG-AGATAGGTA
1 CAATTCAATTATACCTATCTT-AAATT-AATTAGAAGATAGGTA
* * *
78951 CAATTCAATTATACCTATCTTTAATTCATTTGAAGATAGGTA
1 CAATTCAATTATACCTATCTTAAATTAATTAGAAGATAGGTA
*
78993 CAATTGAATT
1 CAATTCAATT
79003 GAAGATAGGT
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
41 4 0.09
42 22 0.48
43 20 0.43
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.38
Consensus pattern (42 bp):
CAATTCAATTATACCTATCTTAAATTAATTAGAAGATAGGTA
Found at i:78997 original size:21 final size:21
Alignment explanation
Indices: 78973--79073 Score: 103
Period size: 21 Copynumber: 4.6 Consensus size: 21
78963 ACCTATCTTT
*
78973 AATTCATTTGAAGATAGGTAC
1 AATTCAATTGAAGATAGGTAC
*
78994 AATTGAATTGAAGATAGGTAC
1 AATTCAATTGAAGATAGGTAC
*
79015 AAATGCAATGGATTGAAGATAGGTAC
1 -AATTC-A---ATTGAAGATAGGTAC
* *
79041 AATTGAATTAAAGATAGGTAC
1 AATTCAATTGAAGATAGGTAC
*
79062 AATTGAATTGAA
1 AATTCAATTGAA
79074 CCTATCTTCA
Statistics
Matches: 67, Mismatches: 8, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
21 44 0.66
22 3 0.04
23 1 0.01
24 1 0.01
25 3 0.04
26 15 0.22
ACGTcount: A:0.44, C:0.06, G:0.22, T:0.29
Consensus pattern (21 bp):
AATTCAATTGAAGATAGGTAC
Found at i:79373 original size:17 final size:17
Alignment explanation
Indices: 79351--79384 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
79341 GTATATACTG
79351 ACCCTAACTACGTCACT
1 ACCCTAACTACGTCACT
*
79368 ACCCTAACTCCGTCACT
1 ACCCTAACTACGTCACT
79385 TTTGGGGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.44, G:0.06, T:0.24
Consensus pattern (17 bp):
ACCCTAACTACGTCACT
Found at i:79648 original size:21 final size:21
Alignment explanation
Indices: 79616--79684 Score: 102
Period size: 21 Copynumber: 3.3 Consensus size: 21
79606 TAGATATGTC
*
79616 TGAATTGAACCTATCTTCAAA
1 TGAATTGTACCTATCTTCAAA
* *
79637 TCAATTGTACCTATCTTTAAA
1 TGAATTGTACCTATCTTCAAA
*
79658 TGAATTTTACCTATCTTCAAA
1 TGAATTGTACCTATCTTCAAA
79679 TGAATT
1 TGAATT
79685 AGAGATAGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.35, C:0.17, G:0.07, T:0.41
Consensus pattern (21 bp):
TGAATTGTACCTATCTTCAAA
Found at i:79712 original size:42 final size:42
Alignment explanation
Indices: 79666--79754 Score: 119
Period size: 42 Copynumber: 2.1 Consensus size: 42
79656 AATGAATTTT
79666 ACCTATCT-TCAAATGAATT-AGAGATAGGTATAATTCAATTGA
1 ACCTATCTGT-AAATGAATTGA-AGATAGGTATAATTCAATTGA
* * *
79708 ACCTATCTGTAATTGAATTGAAGATAGGTATAATTCATTTGT
1 ACCTATCTGTAAATGAATTGAAGATAGGTATAATTCAATTGA
79750 ACCTA
1 ACCTA
79755 GGTATAATTC
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
42 40 0.95
43 2 0.05
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (42 bp):
ACCTATCTGTAAATGAATTGAAGATAGGTATAATTCAATTGA
Found at i:79741 original size:21 final size:21
Alignment explanation
Indices: 79687--79784 Score: 70
Period size: 21 Copynumber: 4.7 Consensus size: 21
79677 AATGAATTAG
79687 AGATAGGTATAATTCAATTGA
1 AGATAGGTATAATTCAATTGA
** ** * *
79708 ACCTATCTGTAATTGAATTGA
1 AGATAGGTATAATTCAATTGA
* *
79729 AGATAGGTATAATTCATTTGT
1 AGATAGGTATAATTCAATTGA
** * *
79750 ACCTAGGTATAATTCATTTGT
1 AGATAGGTATAATTCAATTGA
**
79771 ACCTAGGTATAATT
1 AGATAGGTATAATT
79785 ATGTACACCT
Statistics
Matches: 61, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 61 1.00
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.39
Consensus pattern (21 bp):
AGATAGGTATAATTCAATTGA
Found at i:79816 original size:21 final size:21
Alignment explanation
Indices: 79791--79863 Score: 114
Period size: 21 Copynumber: 3.6 Consensus size: 21
79781 AATTATGTAC
79791 ACCTATCTTCAATTCAATTGT
1 ACCTATCTTCAATTCAATTGT
*
79812 ACCTATCTTCAA--AAATTGT
1 ACCTATCTTCAATTCAATTGT
*
79831 ACCTATCTTTAATTCAATTGT
1 ACCTATCTTCAATTCAATTGT
79852 ACCTATCTTCAA
1 ACCTATCTTCAA
79864 ATGATTTGAA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
19 17 0.37
21 29 0.63
ACGTcount: A:0.32, C:0.23, G:0.04, T:0.41
Consensus pattern (21 bp):
ACCTATCTTCAATTCAATTGT
Found at i:79892 original size:20 final size:20
Alignment explanation
Indices: 79861--79913 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
79851 TACCTATCTT
79861 CAAATGATTTGAAGATAGGTA
1 CAAAT-ATTTGAAGATAGGTA
*
79882 CAATTATTTGAAGATAGGTA
1 CAAATATTTGAAGATAGGTA
79902 CAAATATTTGAA
1 CAAATATTTGAA
79914 TATATGTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 26 0.87
21 4 0.13
ACGTcount: A:0.43, C:0.06, G:0.19, T:0.32
Consensus pattern (20 bp):
CAAATATTTGAAGATAGGTA
Found at i:89306 original size:69 final size:71
Alignment explanation
Indices: 89217--89363 Score: 217
Period size: 69 Copynumber: 2.0 Consensus size: 71
89207 TATCATATTA
*
89217 TATGTATATTGGTTACAACTTCCTAACTTCCTTGTAATATATTTA-TATGT-ATGTAGAATAATA
1 TATGTATATTGGTTACAACTTCCTAACATCCTTGTAATATATTTATTATGTAATGTAGAATAATA
89280 TACATG
66 TACATG
**
89286 TATGTATATTGGTTACAACTTTGTAACATCCTTGTAATATATTTATTTTTATGTACATGTAGAAT
1 TATGTATATTGGTTACAACTTCCTAACATCCTTGTAATATATTTA---TTATGTA-ATGTAGAAT
89351 AATATACATG
62 AATATACATG
89361 TAT
1 TAT
89364 ACCGTAACTT
Statistics
Matches: 69, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
69 42 0.61
73 5 0.07
75 22 0.32
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.45
Consensus pattern (71 bp):
TATGTATATTGGTTACAACTTCCTAACATCCTTGTAATATATTTATTATGTAATGTAGAATAATA
TACATG
Found at i:108527 original size:44 final size:43
Alignment explanation
Indices: 108464--108583 Score: 170
Period size: 44 Copynumber: 2.8 Consensus size: 43
108454 TCTTCACAAA
* * *
108464 AATTTT-TTGCATATTGTTCACAGCATTATTGCTGTTCTTCAC
1 AATTTTCTTGCATATTGTTCAGAGCATTATTACTGTTCTTAAC
*
108506 AATTTTCTTAGCATATTGTTCAGAGCATTATTATTGTTCTTAAC
1 AATTTTCTT-GCATATTGTTCAGAGCATTATTACTGTTCTTAAC
*
108550 AATTTTCTTTGCATATTGTTCAGAGCATTGTTAC
1 AATTTTC-TTGCATATTGTTCAGAGCATTATTAC
108584 CATAGTTACT
Statistics
Matches: 69, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
42 6 0.09
43 2 0.03
44 59 0.86
45 2 0.03
ACGTcount: A:0.24, C:0.16, G:0.12, T:0.47
Consensus pattern (43 bp):
AATTTTCTTGCATATTGTTCAGAGCATTATTACTGTTCTTAAC
Found at i:139375 original size:5 final size:5
Alignment explanation
Indices: 139365--139390 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
139355 TGGTACTTTG
139365 CGGAA CGGAA CGGAA CGGAA CGGAA C
1 CGGAA CGGAA CGGAA CGGAA CGGAA C
139391 CAGTTAAGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.23, G:0.38, T:0.00
Consensus pattern (5 bp):
CGGAA
Found at i:142671 original size:27 final size:27
Alignment explanation
Indices: 142641--142724 Score: 66
Period size: 27 Copynumber: 3.1 Consensus size: 27
142631 ATTTTTAGTC
142641 TATTTTGAGTATATGTGTTTGAGTCTG
1 TATTTTGAGTATATGTGTTTGAGTCTG
* * * *
142668 TATTGTCAGTACTATTTG-TTGAGGCTG
1 TATTTTGAGTA-TATGTGTTTGAGTCTG
* * *
142695 --TTTTGAGTACATGTATGTTGAATCTG
1 TATTTTGAGTATATGTGT-TTGAGTCTG
142721 TATT
1 TATT
142725 CAGTTCTATT
Statistics
Matches: 41, Mismatches: 11, Indels: 9
0.67 0.18 0.15
Matches are distributed among these distances:
24 3 0.07
25 7 0.17
26 7 0.17
27 17 0.41
28 7 0.17
ACGTcount: A:0.20, C:0.07, G:0.24, T:0.49
Consensus pattern (27 bp):
TATTTTGAGTATATGTGTTTGAGTCTG
Found at i:142734 original size:51 final size:51
Alignment explanation
Indices: 142643--142770 Score: 156
Period size: 51 Copynumber: 2.5 Consensus size: 51
142633 TTTTAGTCTA
*
142643 TTTTGAGTATATG-TGTTTGAGTCTGTATTGTCAGTACTATTTGTTGAGGCTG
1 TTTTGAGTACATGTTG-TTGAGTCTGTATTGTCAGTACTATTTGTTGAGGC-G
* * *
142695 TTTTGAGTACATGTATGTTGAATCTGTA-T-TCAGTTCTATTTGTTGAGTCG
1 TTTTGAGTACATGT-TGTTGAGTCTGTATTGTCAGTACTATTTGTTGAGGCG
142745 TTTTGAGTACTAT-TTGTTGAGTCTGT
1 TTTTGAGTAC-ATGTTGTTGAGTCTGT
142771 TTTGAGTAGA
Statistics
Matches: 68, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
49 11 0.16
50 12 0.18
51 20 0.29
52 13 0.19
53 10 0.15
54 2 0.03
ACGTcount: A:0.18, C:0.09, G:0.24, T:0.49
Consensus pattern (51 bp):
TTTTGAGTACATGTTGTTGAGTCTGTATTGTCAGTACTATTTGTTGAGGCG
Found at i:142778 original size:25 final size:25
Alignment explanation
Indices: 142582--142778 Score: 148
Period size: 25 Copynumber: 7.7 Consensus size: 25
142572 AGTCCATGCA
* * * * *
142582 TTGAGTCTGTTTTAAATACTGTCTA
1 TTGAGTCTGTTTTGAGTACTATTTG
** * *
142607 TTGAGTCTGTTTTGTTTACTTTTTATT
1 TTGAGTCTGTTTTGAGTAC-TATT-TG
* * *
142634 TTTAGTCTATTTTGAGTA-TATGTG
1 TTGAGTCTGTTTTGAGTACTATTTG
*
142658 TTTGAGTCTGTATTGTCAGTACTATTTG
1 -TTGAGTCTGT-TT-TGAGTACTATTTG
*
142686 TTGAGGCTGTTTTGAGTAC-ATGTATG
1 TTGAGTCTGTTTTGAGTACTAT-T-TG
* * * *
142712 TTGAATCTGTATTCAGTTCTATTTG
1 TTGAGTCTGTTTTGAGTACTATTTG
142737 TTGAGTC-GTTTTGAGTACTATTTG
1 TTGAGTCTGTTTTGAGTACTATTTG
142761 TTGAGTCTGTTTTGAGTA
1 TTGAGTCTGTTTTGAGTA
142779 GATGCAGAAG
Statistics
Matches: 134, Mismatches: 28, Indels: 20
0.74 0.15 0.11
Matches are distributed among these distances:
24 24 0.18
25 51 0.38
26 23 0.17
27 31 0.23
28 5 0.04
ACGTcount: A:0.18, C:0.09, G:0.21, T:0.52
Consensus pattern (25 bp):
TTGAGTCTGTTTTGAGTACTATTTG
Found at i:143673 original size:15 final size:15
Alignment explanation
Indices: 143649--143685 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
143639 CAGTTGCTAG
*
143649 TCTATGTGCAGACAA
1 TCTATATGCAGACAA
143664 TCTATATGCAGACAA
1 TCTATATGCAGACAA
143679 TCTATAT
1 TCTATAT
143686 TTTGTCAGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.32
Consensus pattern (15 bp):
TCTATATGCAGACAA
Found at i:150975 original size:35 final size:34
Alignment explanation
Indices: 150923--150992 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 34
150913 GTGTATATGC
*
150923 ATGAGGACAATTCTATACAATAATGCATATAGAT
1 ATGAGAACAATTCTATACAATAATGCATATAGAT
150957 ANTGAGAACAATTCTATACAATAATGCATATAGAT
1 A-TGAGAACAATTCTATACAATAATGCATATAGAT
150992 A
1 A
150993 ACCAAACTGG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 1 0.03
35 33 0.97
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.29
Consensus pattern (34 bp):
ATGAGAACAATTCTATACAATAATGCATATAGAT
Found at i:151082 original size:2 final size:2
Alignment explanation
Indices: 151077--151102 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
151067 AAAAAATAAA
151077 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
151103 TTATTTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:151638 original size:10 final size:10
Alignment explanation
Indices: 151614--151701 Score: 54
Period size: 10 Copynumber: 8.6 Consensus size: 10
151604 CAGGGGATGT
151614 CAGGGGCATGCA
1 CAGGGGCAT--A
*
151626 CAGGGGTATA
1 CAGGGGCATA
* *
151636 CAGTGGCCTA
1 CAGGGGCATA
151646 CAGGGG-ATGA
1 CAGGGGCAT-A
*
151656 CAGGGGCGTA
1 CAGGGGCATA
*
151666 CAGGGG-GTGA
1 CAGGGGCAT-A
*
151676 CAGGGGCTTA
1 CAGGGGCATA
* *
151686 CAGTGGCACA
1 CAGGGGCATA
151696 CAGGGG
1 CAGGGG
151702 TTGTGTACAG
Statistics
Matches: 60, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
9 3 0.05
10 47 0.78
11 2 0.03
12 8 0.13
ACGTcount: A:0.24, C:0.19, G:0.44, T:0.12
Consensus pattern (10 bp):
CAGGGGCATA
Found at i:151650 original size:20 final size:20
Alignment explanation
Indices: 151602--151688 Score: 86
Period size: 20 Copynumber: 4.2 Consensus size: 20
151592 TTAAAGACCG
* *
151602 TACAGGGGATGTCAGGGGCA
1 TACAGGGGATGACAGGGGCC
*
151622 TGCACAGGGGTAT-ACAGTGGCC
1 T--ACAGGGG-ATGACAGGGGCC
*
151644 TACAGGGGATGACAGGGGCG
1 TACAGGGGATGACAGGGGCC
* *
151664 TACAGGGGGTGACAGGGGCT
1 TACAGGGGATGACAGGGGCC
151684 TACAG
1 TACAG
151689 TGGCACACAG
Statistics
Matches: 56, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
19 2 0.04
20 38 0.68
22 14 0.25
23 2 0.04
ACGTcount: A:0.24, C:0.17, G:0.44, T:0.15
Consensus pattern (20 bp):
TACAGGGGATGACAGGGGCC
Found at i:151795 original size:21 final size:20
Alignment explanation
Indices: 151771--151820 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 20
151761 CAGGGGATGT
151771 ACAGGGGATGACAGTGAAAAC
1 ACAGGGGATGACAGTG-AAAC
* * *
151792 ACAGGGGGTGACAGTGGAAG
1 ACAGGGGATGACAGTGAAAC
151812 ACAGGGGAT
1 ACAGGGGAT
151821 TTTCATACGG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.36, C:0.12, G:0.42, T:0.10
Consensus pattern (20 bp):
ACAGGGGATGACAGTGAAAC
Found at i:155060 original size:13 final size:13
Alignment explanation
Indices: 155042--155067 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
155032 AAGTTTATTG
155042 GAATATGAATTAT
1 GAATATGAATTAT
155055 GAATATGAATTAT
1 GAATATGAATTAT
155068 AATTTCTGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.38
Consensus pattern (13 bp):
GAATATGAATTAT
Found at i:159821 original size:177 final size:180
Alignment explanation
Indices: 159474--159831 Score: 614
Period size: 182 Copynumber: 2.0 Consensus size: 180
159464 TTTAAGATTT
*
159474 TGAGGGCTTCATTGTTTTGCTCAGCTCTGAATAAAAGCTGAGTTTCCTGAATAAGGAACACTTAA
1 TGAGGGCTTCATTGCTTTGCTCAGCTCTGAATAAAAGCTGAGTTTCCTGAATAAGGAACACTTAA
*
159539 ATAAGTACTGAATAAGCCATGGTCAATCAGCCTGAATAAAGCTGCAACCATTACGTAACTTAAAA
66 ATAAGTACTGAATAAGCAATGGTCAATCAGCCTGAATAAAGCTGCAACCATTA--TAACTTAAAA
*
159604 CCTCCTAGCTAGAATAGGGATTCACTTTTTTACACCCTATATTTGATCCTTA
129 CCTCCTAGCCAGAATAGGGATTCACTTTTTTACACCCTATATTTGATCCTTA
* * *
159656 TGAGGGCTTCATTGCTTTGCTTAGCTCTGAATAAAAGCTGAGTTTCGTGAATAAGGAACGCTTAA
1 TGAGGGCTTCATTGCTTTGCTCAGCTCTGAATAAAAGCTGAGTTTCCTGAATAAGGAACACTTAA
*
159721 A-AAGTACTGAATAAGCAATGGTCAATCAGCCTGAATAAAGCTGTAACCA-T-TAACTTAAAACC
66 ATAAGTACTGAATAAGCAATGGTCAATCAGCCTGAATAAAGCTGCAACCATTATAACTTAAAACC
159783 TCCTAGCCAGAATAGGGATTCACTTTTTTACACCCTATATTTGATCCTT
131 TCCTAGCCAGAATAGGGATTCACTTTTTTACACCCTATATTTGATCCTT
159832 TGCTGATGCA
Statistics
Matches: 169, Mismatches: 7, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
177 60 0.36
180 1 0.01
181 46 0.27
182 62 0.37
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (180 bp):
TGAGGGCTTCATTGCTTTGCTCAGCTCTGAATAAAAGCTGAGTTTCCTGAATAAGGAACACTTAA
ATAAGTACTGAATAAGCAATGGTCAATCAGCCTGAATAAAGCTGCAACCATTATAACTTAAAACC
TCCTAGCCAGAATAGGGATTCACTTTTTTACACCCTATATTTGATCCTTA
Found at i:160317 original size:13 final size:13
Alignment explanation
Indices: 160299--160332 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
160289 CTTTTACCTT
160299 TTCATTTAAAATC
1 TTCATTTAAAATC
*
160312 TTCATTTACAATC
1 TTCATTTAAAATC
*
160325 TTCGTTTA
1 TTCATTTA
160333 TCAACCGCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.29, C:0.18, G:0.03, T:0.50
Consensus pattern (13 bp):
TTCATTTAAAATC
Found at i:166479 original size:12 final size:12
Alignment explanation
Indices: 166462--166501 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
166452 AGTTGCGTCT
166462 ACAGACAGACGG
1 ACAGACAGACGG
* *
166474 ACAGACGGATGG
1 ACAGACAGACGG
166486 ACAGACAGACGG
1 ACAGACAGACGG
166498 ACAG
1 ACAG
166502 GGTGAAACCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.40, C:0.23, G:0.35, T:0.03
Consensus pattern (12 bp):
ACAGACAGACGG
Found at i:168056 original size:2 final size:2
Alignment explanation
Indices: 168049--168080 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
168039 TTTGTTTCCA
168049 TC TC TC TC TC TC TC TC TC TC TC TC TC TC -C TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
168081 TCCTCATTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:168113 original size:2 final size:2
Alignment explanation
Indices: 168106--168158 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
168096 TTTGTTTCCA
*
168106 TC TC TC TC TC TT 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
168148 TC TC TC TC TC T
1 TC TC TC TC TC T
168159 TACGTGGCTT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:168113 original size:57 final size:58
Alignment explanation
Indices: 168025--168138 Score: 212
Period size: 57 Copynumber: 2.0 Consensus size: 58
168015 CATTTAGAGA
168025 CCTCATTAGTACATTTTGTTTCCATCTCTCTCTCTCTCTCTCTCTCTCTCTC-CTCTT
1 CCTCATTAGTACATTTTGTTTCCATCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTT
*
168082 CCTCATTAGTACATTTTGTTTCCATCTCTCTCTCTTTCTCTCTCTCTCTCTCTCTCT
1 CCTCATTAGTACATTTTGTTTCCATCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT
168139 CTCTCTCTCT
Statistics
Matches: 55, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
57 51 0.93
58 4 0.07
ACGTcount: A:0.09, C:0.38, G:0.04, T:0.50
Consensus pattern (58 bp):
CCTCATTAGTACATTTTGTTTCCATCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTT
Found at i:170134 original size:21 final size:21
Alignment explanation
Indices: 170095--170174 Score: 97
Period size: 21 Copynumber: 3.8 Consensus size: 21
170085 AATCAAAGGA
* *
170095 AAATCAGAAGGGAACCATGGG
1 AAATCACAAGGGAATCATGGG
* *
170116 GAATCACAAGGGAGTCATGGG
1 AAATCACAAGGGAATCATGGG
* *
170137 AAACCACAAGTGAATCATGGG
1 AAATCACAAGGGAATCATGGG
*
170158 AAATCACAAGGAAATCA
1 AAATCACAAGGGAATCA
170175 GAAGGGAATC
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.44, C:0.16, G:0.28, T:0.12
Consensus pattern (21 bp):
AAATCACAAGGGAATCATGGG
Found at i:170171 original size:32 final size:32
Alignment explanation
Indices: 170135--170199 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
170125 GGGAGTCATG
*
170135 GGAAACCACAAGTGAATCATGGGAAATCACAA
1 GGAAACCACAAGGGAATCATGGGAAATCACAA
* *
170167 GGAAATCAGAAGGGAATCATGGGAAATCACAA
1 GGAAACCACAAGGGAATCATGGGAAATCACAA
170199 G
1 G
170200 AGAATCATGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.46, C:0.15, G:0.26, T:0.12
Consensus pattern (32 bp):
GGAAACCACAAGGGAATCATGGGAAATCACAA
Found at i:170174 original size:53 final size:53
Alignment explanation
Indices: 170117--170228 Score: 161
Period size: 53 Copynumber: 2.1 Consensus size: 53
170107 AACCATGGGG
* *
170117 AATCACAAGGGAGTCATGGGAAACCACAAGTGAATCATGGGAAATCACAAGGA
1 AATCACAAGGGAATCATGGGAAACCACAAGAGAATCATGGGAAATCACAAGGA
* * * * *
170170 AATCAGAAGGGAATCATGGGAAATCACAAGAGAATCATGTGAAATCATAAGGG
1 AATCACAAGGGAATCATGGGAAACCACAAGAGAATCATGGGAAATCACAAGGA
170223 AATCAC
1 AATCAC
170229 TAAAGTTGAT
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.45, C:0.15, G:0.25, T:0.15
Consensus pattern (53 bp):
AATCACAAGGGAATCATGGGAAACCACAAGAGAATCATGGGAAATCACAAGGA
Found at i:170188 original size:74 final size:72
Alignment explanation
Indices: 170051--170227 Score: 216
Period size: 74 Copynumber: 2.4 Consensus size: 72
170041 GTCATAATTT
**
170051 ACAAGGGAATCATGGGAAATCACAAGGAA--ATGTCAATCAAAGGAAAATCAGAAGGGAACCATG
1 ACAAGGGAATCATGGGAAATCACAAGGAATCATGGAAATCAAAGGAAAATCAGAAGGGAACCATG
*
170114 GGGAATC
66 GGAAATC
* * *
170121 ACAAGGGAGTCATGGGAAACCACAAGTGAATCATGGGAAATCACAAGG-AAATCAGAAGGGAATC
1 ACAAGGGAATCATGGGAAATCACAAG-GAATCAT-GGAAATCA-AAGGAAAATCAGAAGGGAACC
170185 ATGGGAAATC
63 ATGGGAAATC
* * *
170195 ACAAGAGAATCATGTGAAATCATAAGGGAATCA
1 ACAAGGGAATCATGGGAAATCACAA-GGAATCA
170228 CTAAAGTTGA
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
70 24 0.27
71 3 0.03
73 2 0.02
74 56 0.62
75 5 0.06
ACGTcount: A:0.45, C:0.14, G:0.27, T:0.14
Consensus pattern (72 bp):
ACAAGGGAATCATGGGAAATCACAAGGAATCATGGAAATCAAAGGAAAATCAGAAGGGAACCATG
GGAAATC
Found at i:170191 original size:21 final size:21
Alignment explanation
Indices: 170167--170227 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 21
170157 GAAATCACAA
*
170167 GGAAATCAGAAGGGAATCATG
1 GGAAATCACAAGGGAATCATG
*
170188 GGAAATCACAAGAGAATCATG
1 GGAAATCACAAGGGAATCATG
* *
170209 TGAAATCATAAGGGAATCA
1 GGAAATCACAAGGGAATCA
170228 CTAAAGTTGA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.46, C:0.11, G:0.26, T:0.16
Consensus pattern (21 bp):
GGAAATCACAAGGGAATCATG
Found at i:171790 original size:20 final size:20
Alignment explanation
Indices: 171756--171797 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
171746 TGTCAAATAC
171756 ATGTTGACAATGACCTTGCAA
1 ATGTTGACAATGACCTTG-AA
171777 ATGTTGAC-ATGACCTTGAA
1 ATGTTGACAATGACCTTGAA
171796 AT
1 AT
171798 CAACTGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 4 0.19
20 9 0.43
21 8 0.38
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (20 bp):
ATGTTGACAATGACCTTGAA
Found at i:172759 original size:22 final size:22
Alignment explanation
Indices: 172734--172776 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
172724 GATTACGGCA
* *
172734 TCCATCAAACTGCATTTGTGCT
1 TCCATCAAAATGCAGTTGTGCT
172756 TCCATCAAAATGCAGTTGTGC
1 TCCATCAAAATGCAGTTGTGC
172777 AGCATCAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.33
Consensus pattern (22 bp):
TCCATCAAAATGCAGTTGTGCT
Found at i:176744 original size:180 final size:183
Alignment explanation
Indices: 176384--176784 Score: 497
Period size: 180 Copynumber: 2.2 Consensus size: 183
176374 GTGAAATAAA
* * * * * * *
176384 GTACCCCATATGCAATATTTTGCTAAAAAAAGACTTAGTTCAAAAGCTGGCATTTTTTTTTTATA
1 GTACCCTATATGCAATATTTTGCTAAAAAATGACTAACTTCAAAAGCTGG-ATATTTTTTTCACA
*
176449 AACAATCAGAAATAAAAATCCTAAAAATATTCACACCTCTGATATATACATGTACAATTAATCTG
65 AACAATCAGAAATAAAAATCCTAAAAATATGCACACCTCTGA-ATATA-ATGTACAATTAATCTG
* *
176514 CAAAAGAACAACTTTTTATCAATAAAACTGTAGTAATAGTTATCCGTACAATGAGG
128 CAAAAGAACAACTTCTTATCAATAAAACTGTAGTAAGAGTTATCCGTACAATGAGG
* *
176570 TTACCCTATATGCAATATTTTGCTAAAAATTGACTAACTTCAAAAGCTGG-TATTTTTTTCACAA
1 GTACCCTATATGCAATATTTTGCTAAAAAATGACTAACTTCAAAAGCTGGATATTTTTTTCACAA
** * * ** * *
176634 ATTATCAGTAATCAAAATCCTAGCAATATGCACACCTCTG-ATAT-ATGTATAATTGATCTGCAA
66 ACAATCAGAAATAAAAATCCTAAAAATATGCACACCTCTGAATATAATGTACAATTAATCTGCAA
* *
176697 AAGAACAACTTCTTATC-TTGAAAACTGTAAG-AGGAGTTATCCGTACAATGAGG
131 AAGAACAACTTCTTATCAAT-AAAACTGT-AGTAAGAGTTATCCGTACAATGAGG
* * *
176750 GTACCATATATGCAAAATTTTGCCAAAAAATGACT
1 GTACCCTATATGCAATATTTTGCTAAAAAATGACT
176785 TCTTTTTTTT
Statistics
Matches: 186, Mismatches: 27, Indels: 10
0.83 0.12 0.04
Matches are distributed among these distances:
179 1 0.01
180 91 0.49
181 2 0.01
182 4 0.02
184 44 0.24
186 44 0.24
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32
Consensus pattern (183 bp):
GTACCCTATATGCAATATTTTGCTAAAAAATGACTAACTTCAAAAGCTGGATATTTTTTTCACAA
ACAATCAGAAATAAAAATCCTAAAAATATGCACACCTCTGAATATAATGTACAATTAATCTGCAA
AAGAACAACTTCTTATCAATAAAACTGTAGTAAGAGTTATCCGTACAATGAGG
Found at i:176864 original size:39 final size:39
Alignment explanation
Indices: 176787--176865 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
176777 AAATGACTTC
176787 TTTTTTTTCATAAATTATCAGAAACCAAAATCCAAGCAA
1 TTTTTTTTCATAAATTATCAGAAACCAAAATCCAAGCAA
* * *
176826 TTTTTTTTCATAAATTATCAGTAACCAAACTCCTAGCAA
1 TTTTTTTTCATAAATTATCAGAAACCAAAATCCAAGCAA
176865 T
1 T
176866 AAGCACACCT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.39, C:0.19, G:0.05, T:0.37
Consensus pattern (39 bp):
TTTTTTTTCATAAATTATCAGAAACCAAAATCCAAGCAA
Found at i:188574 original size:4 final size:4
Alignment explanation
Indices: 188565--188590 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
188555 GTAACATACC
188565 TCAA TCAA TCAA TCAA TCAA TCAA TC
1 TCAA TCAA TCAA TCAA TCAA TCAA TC
188591 CATATCAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.46, C:0.27, G:0.00, T:0.27
Consensus pattern (4 bp):
TCAA
Found at i:191531 original size:16 final size:16
Alignment explanation
Indices: 191497--191528 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
191487 AACACAGAAA
191497 AATTAAGATATAAAGG
1 AATTAAGATATAAAGG
191513 AATTCAAGATATAAAG
1 AATT-AAGATATAAAG
191529 AATAAAATGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.56, C:0.03, G:0.16, T:0.25
Consensus pattern (16 bp):
AATTAAGATATAAAGG
Found at i:191728 original size:2 final size:2
Alignment explanation
Indices: 191721--191754 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
191711 TTAGTGCACT
191721 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
191755 AACTTTCAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:191993 original size:2 final size:2
Alignment explanation
Indices: 191986--192022 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
191976 TATGATGAAA
191986 CT 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 CT C
192023 CAGCTATGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:193717 original size:2 final size:2
Alignment explanation
Indices: 193710--193771 Score: 110
Period size: 2 Copynumber: 32.0 Consensus size: 2
193700 TTTTTGTGAG
193710 CT CT CT CT CT CT C- CT CT CT CT CT CT C- 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
193750 CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT
193772 AGTGACATTT
Statistics
Matches: 58, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 2 0.03
2 56 0.97
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:195408 original size:1 final size:1
Alignment explanation
Indices: 195402--195428 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
195392 TTGGTTTCAA
195402 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
195429 GTGAGTGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:195598 original size:17 final size:19
Alignment explanation
Indices: 195561--195598 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
195551 GGACATGGAG
*
195561 CTAAAATATTAACATGGAT
1 CTAAAATATTAACATGCAT
195580 CTAAAATA-T-ACATGCAT
1 CTAAAATATTAACATGCAT
195597 CT
1 CT
195599 TAGTTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 9 0.50
18 1 0.06
19 8 0.44
ACGTcount: A:0.45, C:0.16, G:0.08, T:0.32
Consensus pattern (19 bp):
CTAAAATATTAACATGCAT
Found at i:197009 original size:2 final size:2
Alignment explanation
Indices: 197002--197079 Score: 126
Period size: 2 Copynumber: 40.0 Consensus size: 2
196992 CCACCACATT
197002 TC TC TC TC TC -C TC TC TC TC TC AT- 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
197043 TC TC TC TC TC TC TC TC TC TC TC TC T- 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
197080 GTTTCATATC
Statistics
Matches: 72, Mismatches: 0, Indels: 8
0.90 0.00 0.10
Matches are distributed among these distances:
1 3 0.04
2 68 0.94
3 1 0.01
ACGTcount: A:0.01, C:0.49, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:197205 original size:2 final size:2
Alignment explanation
Indices: 197198--197231 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
197188 GTATGCACGA
*
197198 CT CT CT CT CT CT CT CT CT AT 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
197232 AACTTTTTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.03, C:0.47, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:200522 original size:20 final size:21
Alignment explanation
Indices: 200485--200523 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
200475 ACAAACATTC
**
200485 AAAATACTAAATTTATTCTGA
1 AAAATACTAAATAAATTCTGA
200506 AAAATACTAAA-AAATTCT
1 AAAATACTAAATAAATTCT
200524 TTATTTCACT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.54, C:0.10, G:0.03, T:0.33
Consensus pattern (21 bp):
AAAATACTAAATAAATTCTGA
Found at i:202988 original size:11 final size:11
Alignment explanation
Indices: 202974--202998 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
202964 TTGTAAAAAA
202974 AAAAAAAAAGC
1 AAAAAAAAAGC
202985 AAAAAAAAAGC
1 AAAAAAAAAGC
202996 AAA
1 AAA
202999 CATTTGAAAA
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:0.08, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAGC
Found at i:206612 original size:28 final size:28
Alignment explanation
Indices: 206573--206706 Score: 150
Period size: 27 Copynumber: 4.9 Consensus size: 28
206563 TTAATTGACT
* *
206573 CACAAAAATTGACTGAATGTGAAA-GAC
1 CACAAAATTTGACTGAATGAGAAAGGAC
**
206600 ACACAAAATTTGACTGAATGTTAAA-GAC
1 -CACAAAATTTGACTGAATGAGAAAGGAC
*
206628 TCACAAAATTTGACTGAATGAGAAAGGTC
1 -CACAAAATTTGACTGAATGAGAAAGGAC
* *
206657 C-CTAAATTTGACTGAATGAGAAAGGTC
1 CACAAAATTTGACTGAATGAGAAAGGAC
*
206684 C-CTAAATTTGACTGAATGAGAAA
1 CACAAAATTTGACTGAATGAGAAA
206707 ACTCACCGTT
Statistics
Matches: 98, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
27 48 0.49
28 48 0.49
29 2 0.02
ACGTcount: A:0.43, C:0.14, G:0.19, T:0.24
Consensus pattern (28 bp):
CACAAAATTTGACTGAATGAGAAAGGAC
Found at i:206631 original size:56 final size:55
Alignment explanation
Indices: 206569--206706 Score: 154
Period size: 56 Copynumber: 2.5 Consensus size: 55
206559 GAGGTTAATT
*
206569 GACTCACAAAAATTGACTGAATGTGAAA-GACACACAAAATTTGACTGAATGTTAAA
1 GACTCACAAAAATTGACTGAATGAGAAAGGAC-C-CAAAATTTGACTGAATGTTAAA
* * * **
206625 GACTCACAAAATTTGACTGAATGAGAAAGGTCCCTAAATTTGACTGAATGAGAAA
1 GACTCACAAAAATTGACTGAATGAGAAAGGACCCAAAATTTGACTGAATGTTAAA
* * * *
206680 G-GTCCCTAAATTTGACTGAATGAGAAA
1 GACTCACAAAAATTGACTGAATGAGAAA
206707 ACTCACCGTT
Statistics
Matches: 72, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
54 23 0.32
55 20 0.28
56 27 0.38
57 2 0.03
ACGTcount: A:0.43, C:0.14, G:0.19, T:0.24
Consensus pattern (55 bp):
GACTCACAAAAATTGACTGAATGAGAAAGGACCCAAAATTTGACTGAATGTTAAA
Found at i:207523 original size:2 final size:2
Alignment explanation
Indices: 207516--207545 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
207506 TTTTTGCTCG
207516 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
207546 GCCGTGGGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:215847 original size:21 final size:21
Alignment explanation
Indices: 215822--215921 Score: 103
Period size: 21 Copynumber: 4.8 Consensus size: 21
215812 TGACTTTTGC
*
215822 ATGGTACTGTTCGTTTTGTGA
1 ATGGTACGGTTCGTTTTGTGA
* **
215843 ATGGTACGGTACACTTTGTGA
1 ATGGTACGGTTCGTTTTGTGA
* *
215864 ATGGT-CAGTTTGTTTTGTGA
1 ATGGTACGGTTCGTTTTGTGA
* * *
215884 ACGGTACGGTACGCTTTGTGA
1 ATGGTACGGTTCGTTTTGTGA
*
215905 ACGGTACGGTTCGTTTT
1 ATGGTACGGTTCGTTTT
215922 AGAGGTGTAG
Statistics
Matches: 62, Mismatches: 16, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 14 0.23
21 48 0.77
ACGTcount: A:0.17, C:0.13, G:0.30, T:0.40
Consensus pattern (21 bp):
ATGGTACGGTTCGTTTTGTGA
Found at i:218640 original size:16 final size:16
Alignment explanation
Indices: 218619--218659 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
218609 TGGGAATCAG
218619 GGCAAACAGGGTCAAA
1 GGCAAACAGGGTCAAA
* *
218635 GGCAAACGGGGTCAAG
1 GGCAAACAGGGTCAAA
218651 GGCAAACAG
1 GGCAAACAG
218660 ACCAATTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.39, C:0.20, G:0.37, T:0.05
Consensus pattern (16 bp):
GGCAAACAGGGTCAAA
Found at i:234562 original size:46 final size:48
Alignment explanation
Indices: 234493--234593 Score: 161
Period size: 46 Copynumber: 2.1 Consensus size: 48
234483 TACACAGACT
234493 GGGTGTTTAACAATGTATCTAGCATGTACAGTGTTAC-A-TGGTGCTG
1 GGGTGTTTAACAATGTATCTAGCATGTACAGTGTTACTACTGGTGCTG
*
234539 GGGTGTTTAACAATGTATTTAGCATGTACAGTGTTACTTACGTGGTGCTG
1 GGGTGTTTAACAATGTATCTAGCATGTACAGTGTTAC-TAC-TGGTGCTG
234589 GGGTG
1 GGGTG
234594 CTGCTGACGG
Statistics
Matches: 50, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
46 36 0.72
48 1 0.02
50 13 0.26
ACGTcount: A:0.22, C:0.12, G:0.31, T:0.36
Consensus pattern (48 bp):
GGGTGTTTAACAATGTATCTAGCATGTACAGTGTTACTACTGGTGCTG
Found at i:234780 original size:24 final size:24
Alignment explanation
Indices: 234747--234835 Score: 90
Period size: 24 Copynumber: 3.7 Consensus size: 24
234737 GAAGCCATGG
*
234747 GTGGAGGACAGGGTTTGTGTTGGA
1 GTGGAAGACAGGGTTTGTGTTGGA
* *
234771 GTGGAAGACAGGCTTTTTGTTAGG-
1 GTGGAAGACAGGGTTTGTGTT-GGA
** *
234795 GTGGAAGATGGGGTTTGCGTTGGA
1 GTGGAAGACAGGGTTTGTGTTGGA
**
234819 GTGGAAGATGGGGTTTG
1 GTGGAAGACAGGGTTTG
234836 CATTGCAGTG
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
23 2 0.04
24 51 0.93
25 2 0.04
ACGTcount: A:0.18, C:0.04, G:0.47, T:0.30
Consensus pattern (24 bp):
GTGGAAGACAGGGTTTGTGTTGGA
Found at i:234836 original size:24 final size:24
Alignment explanation
Indices: 234757--234847 Score: 94
Period size: 24 Copynumber: 3.8 Consensus size: 24
234747 GTGGAGGACA
* **
234757 GGGTTTGTGTTGGAGTGGAAGACA
1 GGGTTTGCGTTGGAGTGGAAGATG
* **
234781 GGCTTTTTGTTAGG-GTGGAAGATG
1 GGGTTTGCGTT-GGAGTGGAAGATG
234805 GGGTTTGCGTTGGAGTGGAAGATG
1 GGGTTTGCGTTGGAGTGGAAGATG
* *
234829 GGGTTTGCATTGCAGTGGA
1 GGGTTTGCGTTGGAGTGGA
234848 GGAGACATCA
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
23 2 0.04
24 52 0.93
25 2 0.04
ACGTcount: A:0.18, C:0.05, G:0.45, T:0.32
Consensus pattern (24 bp):
GGGTTTGCGTTGGAGTGGAAGATG
Found at i:237377 original size:8 final size:8
Alignment explanation
Indices: 237364--237388 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
237354 TCAAATCTAA
237364 TGTTTTAT
1 TGTTTTAT
237372 TGTTTTAT
1 TGTTTTAT
237380 TGTTTTAT
1 TGTTTTAT
237388 T
1 T
237389 TAGAATCATA
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:0.12, C:0.00, G:0.12, T:0.76
Consensus pattern (8 bp):
TGTTTTAT
Found at i:242240 original size:2 final size:2
Alignment explanation
Indices: 242227--242268 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
242217 ACAGCTCTCG
*
242227 GA GA GA GC GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
242269 ATTTTGGAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.02, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:245462 original size:23 final size:22
Alignment explanation
Indices: 245415--245464 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
245405 TAAACAAATT
* *
245415 TTTTGCTTTGATGTTCCATACA
1 TTTTGCTTCGATGTTCCACACA
*
245437 TTTTGCTTCGATGTTTCACACA
1 TTTTGCTTCGATGTTCCACACA
*
245459 ATTTGC
1 TTTTGC
245465 AACAATTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.18, C:0.20, G:0.14, T:0.48
Consensus pattern (22 bp):
TTTTGCTTCGATGTTCCACACA
Found at i:260720 original size:2 final size:2
Alignment explanation
Indices: 260713--260781 Score: 129
Period size: 2 Copynumber: 34.5 Consensus size: 2
260703 TGCGATGCTT
*
260713 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA NA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
260755 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
260782 CATCAAAAAC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:265474 original size:16 final size:16
Alignment explanation
Indices: 265453--265483 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
265443 CTGAAGTGGG
*
265453 ACAGACAGACGGACGA
1 ACAGACAGACAGACGA
265469 ACAGACAGACAGACG
1 ACAGACAGACAGACG
265484 GACTGACGGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.26, G:0.29, T:0.00
Consensus pattern (16 bp):
ACAGACAGACAGACGA
Found at i:265885 original size:21 final size:21
Alignment explanation
Indices: 265861--265914 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
265851 TTCTTTAAAA
265861 TTCCAACTTTAATCTTGGAAT
1 TTCCAACTTTAATCTTGGAAT
265882 TTCCAACTTGT-ATCTTGGAAT
1 TTCCAACTT-TAATCTTGGAAT
265903 TTCCAACTTTAA
1 TTCCAACTTTAA
265915 AGTTGATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 1 0.03
21 29 0.94
22 1 0.03
ACGTcount: A:0.28, C:0.20, G:0.09, T:0.43
Consensus pattern (21 bp):
TTCCAACTTTAATCTTGGAAT
Found at i:277323 original size:16 final size:16
Alignment explanation
Indices: 277302--277333 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
277292 ATATGTCAAT
277302 GTTATCTGTTTATGCC
1 GTTATCTGTTTATGCC
277318 GTTATCTGTTTATGCC
1 GTTATCTGTTTATGCC
277334 AATGAGTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.19, G:0.19, T:0.50
Consensus pattern (16 bp):
GTTATCTGTTTATGCC
Found at i:283660 original size:18 final size:18
Alignment explanation
Indices: 283634--283676 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
283624 TTTCGATCCG
*
283634 GTGTTTATACATTTTTTA
1 GTGTTTATACATTATTTA
* *
283652 GTTTTTATATATTATTTA
1 GTGTTTATACATTATTTA
283670 GTGTTTA
1 GTGTTTA
283677 GTTTAGTGGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.23, C:0.02, G:0.12, T:0.63
Consensus pattern (18 bp):
GTGTTTATACATTATTTA
Found at i:284793 original size:32 final size:32
Alignment explanation
Indices: 284746--284816 Score: 133
Period size: 32 Copynumber: 2.2 Consensus size: 32
284736 ATAAACAATC
284746 AATTTCTGATTCACATGCAGAGTCGTGTGTACT
1 AATTT-TGATTCACATGCAGAGTCGTGTGTACT
284779 AATTTTGATTCACATGCAGAGTCGTGTGTACT
1 AATTTTGATTCACATGCAGAGTCGTGTGTACT
284811 AATTTT
1 AATTTT
284817 CTGTTTCTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 33 0.87
33 5 0.13
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.39
Consensus pattern (32 bp):
AATTTTGATTCACATGCAGAGTCGTGTGTACT
Found at i:294272 original size:18 final size:18
Alignment explanation
Indices: 294251--294288 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
294241 AATATTACAT
294251 ATAACAGCA-TTATTGTAA
1 ATAACAGCATTTA-TGTAA
*
294269 ATAATAGCATTTATGTAA
1 ATAACAGCATTTATGTAA
294287 AT
1 AT
294289 TGTGATATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.45, C:0.08, G:0.11, T:0.37
Consensus pattern (18 bp):
ATAACAGCATTTATGTAA
Found at i:295097 original size:12 final size:12
Alignment explanation
Indices: 295073--295106 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
295063 ATCACATTTT
295073 GTCTGTC-GTCC
1 GTCTGTCTGTCC
295084 GTCTGTCTGTCC
1 GTCTGTCTGTCC
*
295096 GTCTGTTTGTC
1 GTCTGTCTGTC
295107 TGTGAACTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 7 0.33
12 14 0.67
ACGTcount: A:0.00, C:0.29, G:0.26, T:0.44
Consensus pattern (12 bp):
GTCTGTCTGTCC
Found at i:301346 original size:2 final size:2
Alignment explanation
Indices: 301341--301372 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
301331 ACGTGTGTCT
301341 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
301373 ACTTACAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:308702 original size:10 final size:10
Alignment explanation
Indices: 308682--308710 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
308672 GAAAATGGTG
308682 GACAA-TTTT
1 GACAATTTTT
308691 GACAATTTTT
1 GACAATTTTT
308701 GACAATTTTT
1 GACAATTTTT
308711 TCAAAAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 5 0.26
10 14 0.74
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.48
Consensus pattern (10 bp):
GACAATTTTT
Found at i:310575 original size:11 final size:11
Alignment explanation
Indices: 310559--310601 Score: 77
Period size: 11 Copynumber: 3.9 Consensus size: 11
310549 GTCCAAACTT
310559 CTTTAAGCCAC
1 CTTTAAGCCAC
*
310570 CTTTAAGCTAC
1 CTTTAAGCCAC
310581 CTTTAAGCCAC
1 CTTTAAGCCAC
310592 CTTTAAGCCA
1 CTTTAAGCCA
310602 TTAAAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.28, C:0.33, G:0.09, T:0.30
Consensus pattern (11 bp):
CTTTAAGCCAC
Found at i:310722 original size:14 final size:14
Alignment explanation
Indices: 310694--310733 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
310684 TTTGTTCTAG
* *
310694 AAAATAAAATAAAA
1 AAAAAAAAACAAAA
310708 ACAAAAAAAACAAAA
1 A-AAAAAAAACAAAA
310723 AAAAAAAAACA
1 AAAAAAAAACA
310734 CGCCCACGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.88, C:0.07, G:0.00, T:0.05
Consensus pattern (14 bp):
AAAAAAAAACAAAA
Found at i:322378 original size:2 final size:2
Alignment explanation
Indices: 322371--322422 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
322361 GCTAGGTGAT
322371 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
322413 GA GA GA GA GA
1 GA GA GA GA GA
322423 CGATGTAAAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:322616 original size:4 final size:4
Alignment explanation
Indices: 322609--322637 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
322599 ACTCTCTCTG
322609 TGTC TGTC TGTC TGTC TGTC TGTC TGTC T
1 TGTC TGTC TGTC TGTC TGTC TGTC TGTC T
322638 CTCTCTCTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.00, C:0.24, G:0.24, T:0.52
Consensus pattern (4 bp):
TGTC
Found at i:322642 original size:2 final size:2
Alignment explanation
Indices: 322635--322672 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
322625 TGTCTGTCTG
322635 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
322673 ATATCGACAA
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:323199 original size:7 final size:7
Alignment explanation
Indices: 323184--323225 Score: 57
Period size: 7 Copynumber: 6.0 Consensus size: 7
323174 TTTAGATATT
323184 GAATCTC
1 GAATCTC
*
323191 GAATTTC
1 GAATCTC
323198 GAATCTC
1 GAATCTC
323205 GAATCTC
1 GAATCTC
* *
323212 GTATTTC
1 GAATCTC
323219 GAATCTC
1 GAATCTC
323226 TACTCATGAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.26, C:0.24, G:0.14, T:0.36
Consensus pattern (7 bp):
GAATCTC
Found at i:323209 original size:21 final size:21
Alignment explanation
Indices: 323184--323225 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
323174 TTTAGATATT
323184 GAATCTCGAATTTCGAATCTC
1 GAATCTCGAATTTCGAATCTC
*
323205 GAATCTCGTATTTCGAATCTC
1 GAATCTCGAATTTCGAATCTC
323226 TACTCATGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.24, G:0.14, T:0.36
Consensus pattern (21 bp):
GAATCTCGAATTTCGAATCTC
Found at i:326602 original size:2 final size:2
Alignment explanation
Indices: 326595--326671 Score: 127
Period size: 2 Copynumber: 38.5 Consensus size: 2
326585 CTAATTATTA
326595 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
* * *
326637 AG AG GG GG AT 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 AG A
326672 TCTTCCACTG
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.48, C:0.00, G:0.51, T:0.01
Consensus pattern (2 bp):
AG
Found at i:339920 original size:161 final size:159
Alignment explanation
Indices: 339578--340385 Score: 856
Period size: 161 Copynumber: 5.0 Consensus size: 159
339568 AGTCCACCAA
* * * * * ** *
339578 CAGTTTCCATTCATTTTCTTTGCAAAGCATGAAA-ATATTGAAAGGAAAATTAAGTATACAGGTT
1 CAGTTTCCACTCATTTTCTTCGCAGAGGAT-AAACATATTGAAATG-AAATTTGGTATACAGGTG
** * * * *
339642 TATGAGGATAATATCTAGGTCAAGTTCGATATTGGGTACGATCGAACAATTTT--C-GAGTTATC
64 TACCATGATAATATCTAGGTCAAGTTTGATATTGGGTACGATCGAGCAATTTTGACAGAGTTATG
* * * *
339704 GTCCTTGGGCGTAGAAAAATTCCAGTTATTTG
129 GCCCTTGGACGTA-AAAAAATCCAGATATTTG
* * *
339736 CAGTTTCCACTCATTTTCTTCGCAGAGGATAAACATATAGAAATGAAATTTGGTATAAAGGCGTA
1 CAGTTTCCACTCATTTTCTTCGCAGAGGATAAACATATTGAAATGAAATTTGGTATACAGGTGTA
* * * *
339801 CCATGATATTATCTGGGTCACGTTTGATATTTGGTACGATCGAGCAACTTTTGACAGAGTTATGG
66 CCATGATAATATCTAGGTCAAGTTTGATATTGGGTACGATCGAGCAA-TTTTGACAGAGTTATGG
339866 CCCTTGGACGTGAAAAAAATCCAGATATTTG
130 CCCTTGGACGT-AAAAAAATCCAGATATTTG
*
339897 CAGTTTCCACTCATTTTCTTCGCAGAGGTTAAACATATTGAAATGAAATTTGGTATACAGGTGTA
1 CAGTTTCCACTCATTTTCTTCGCAGAGGATAAACATATTGAAATGAAATTTGGTATACAGGTGTA
* * ***
339962 CCATGATTATATCTAGATCAAGTTTGATATTAATTACGATCGAGCAATTTTCGACAGAGTTATGG
66 CCATGATAATATCTAGGTCAAGTTTGATATTGGGTACGATCGAGCAATTTT-GACAGAGTTATGG
* *
340027 TCCTTGGACGTGAAAAAATCCAGATATTTG
130 CCCTTGGACGTAAAAAAATCCAGATATTTG
* *
340057 CAGTTTCCGCTCATTTTCTTCGCAGAGGATAAACATATTGAAATGAAA--TGGTATACAGGTTTA
1 CAGTTTCCACTCATTTTCTTCGCAGAGGATAAACATATTGAAATGAAATTTGGTATACAGGTGTA
* * *
340120 TCATGATAATATCTAGGTCACGTTTGATATTGGGTACGACCGAGCAATTTTTGACAGAGATATAT
66 CCATGATAATATCTAGGTCAAGTTTGATATTGGGTACGATCGAGCAA-TTTTGACAGAG---T-T
* * * *
340185 ATGACCCTTGGACGTAAAACCATTCCAGTTATTTG
126 ATGGCCCTTGGACGTAAAA-AAATCCAGATATTTG
* * * ** * ** *
340220 CATTTTCCGCTCATTTTCTTAGCAGAGGATGGACACATTGATTTGAAATTTGGTATACAGGTTTA
1 CAGTTTCCACTCATTTTCTTCGCAGAGGATAAACATATTGAAATGAAATTTGGTATACAGGTGTA
* * * * * * * * *
340285 TC-TAAATAATATCTAGGTCATGTTTGATTTTTGGTATGATAGAGCAATTTCCGACAGATTTATG
66 CCAT-GATAATATCTAGGTCAAGTTTGATATTGGGTACGATCGAGCAATTT-TGACAGAGTTATG
* * *
340349 CCCCTTGGACTTAAACAAAATTCCAAATATTTG
129 GCCCTTGGACGTAAA-AAAA-TCCAGATATTTG
340382 CAGT
1 CAGT
340386 CTACGTTCAC
Statistics
Matches: 552, Mismatches: 79, Indels: 34
0.83 0.12 0.05
Matches are distributed among these distances:
157 56 0.10
158 99 0.18
159 4 0.01
160 69 0.12
161 175 0.32
162 33 0.06
163 53 0.10
164 4 0.01
165 59 0.11
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.34
Consensus pattern (159 bp):
CAGTTTCCACTCATTTTCTTCGCAGAGGATAAACATATTGAAATGAAATTTGGTATACAGGTGTA
CCATGATAATATCTAGGTCAAGTTTGATATTGGGTACGATCGAGCAATTTTGACAGAGTTATGGC
CCTTGGACGTAAAAAAATCCAGATATTTG
Found at i:340280 original size:323 final size:320
Alignment explanation
Indices: 339649--340385 Score: 885
Period size: 323 Copynumber: 2.3 Consensus size: 320
339639 GTTTATGAGG
* * * *
339649 ATAATATCTAGGTCAAGTTCGATATTGGGTACGATCGAACAATTTT---C-GAGTTATCGTCCTT
1 ATAATATCTAGGTCAAGTTTGATATTAGGTACGATCGAGCAATTTTCGACAGAGTTATGGTCCTT
* * *
339710 GGGCGTAGAAAAATTCCAGTTATTTGCAGTTTCCACTCATTTTCTTCGCAGAGGATAAACATATA
66 GGACGT-GAAAAAATCCAGATATTTGCAGTTTCCACTCATTTTCTTCGCAGAGGATAAACATATA
* * *
339775 GAAATGAAATTTGGTATAAAGGCGTACCATGATATTATCTGGGTCACGTTTGATATTTGGTACGA
130 GAAATGAAA-TTGGTATAAAGGCGTACCATGATAATATCTAGGTCACGTTTGATATTGGGTACGA
* *
339840 TCGAGCAACTTTTGACAGAGTTATGGCCCTTGGACGTGAAAAAAATCCAGATATTTGCAGTTTCC
194 CCGAGCAACTTTTGACAGAGTTATGACCCTTGGACGTGAAAAAAATCCAGATATTTGCAGTTTCC
* * * *
339905 ACTCATTTTCTTCGCAGAGGTTAAACATATTGAAATGAAATTTGGTATACAGGTGTACC-ATG
259 ACTCATTTTCTTAGCAGAGGATAAACACATTGAAATGAAATTTGGTATACAGGTGTACCTA-A
* * **
339967 ATTATATCTAGATCAAGTTTGATATTAATTACGATCGAGCAATTTTCGACAGAGTTATGGTCCTT
1 ATAATATCTAGGTCAAGTTTGATATTAGGTACGATCGAGCAATTTTCGACAGAGTTATGGTCCTT
* *
340032 GGACGTGAAAAAATCCAGATATTTGCAGTTTCCGCTCATTTTCTTCGCAGAGGATAAACATATTG
66 GGACGTGAAAAAATCCAGATATTTGCAGTTTCCACTCATTTTCTTCGCAGAGGATAAACATATAG
* ** *
340097 AAATGAAA-TGGTATACAGGTTTATCATGATAATATCTAGGTCACGTTTGATATTGGGTACGACC
131 AAATGAAATTGGTATAAAGGCGTACCATGATAATATCTAGGTCACGTTTGATATTGGGTACGACC
* * * * *
340161 GAGCAATTTTTGACAGAGATATATATGACCCTTGGACGT-AAAACCATTCCAGTTATTTGCATTT
196 GAGCAACTTTTGACAGAG---T-TATGACCCTTGGACGTGAAAA-AAATCCAGATATTTGCAGTT
* ** ** * *
340225 TCCGCTCATTTTCTTAGCAGAGGATGGACACATTGATTTGAAATTTGGTATACAGGTTTATCTAA
256 TCCACTCATTTTCTTAGCAGAGGATAAACACATTGAAATGAAATTTGGTATACAGGTGTACCTAA
* * * * * * * **
340290 ATAATATCTAGGTCATGTTTGATTTTTGGTATGATAGAGCAATTTCCGACAGATTTATGCCCCTT
1 ATAATATCTAGGTCAAGTTTGATATTAGGTACGATCGAGCAATTTTCGACAGAGTTATGGTCCTT
* * *
340355 GGACTTAAACAAAATTCCAAATATTTGCAGT
66 GGACGTGAA-AAAA-TCCAGATATTTGCAGT
340386 CTACGTTCAC
Statistics
Matches: 353, Mismatches: 54, Indels: 17
0.83 0.13 0.04
Matches are distributed among these distances:
318 39 0.11
319 65 0.18
321 64 0.18
322 23 0.07
323 142 0.40
324 5 0.01
325 15 0.04
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.34
Consensus pattern (320 bp):
ATAATATCTAGGTCAAGTTTGATATTAGGTACGATCGAGCAATTTTCGACAGAGTTATGGTCCTT
GGACGTGAAAAAATCCAGATATTTGCAGTTTCCACTCATTTTCTTCGCAGAGGATAAACATATAG
AAATGAAATTGGTATAAAGGCGTACCATGATAATATCTAGGTCACGTTTGATATTGGGTACGACC
GAGCAACTTTTGACAGAGTTATGACCCTTGGACGTGAAAAAAATCCAGATATTTGCAGTTTCCAC
TCATTTTCTTAGCAGAGGATAAACACATTGAAATGAAATTTGGTATACAGGTGTACCTAA
Found at i:343503 original size:59 final size:56
Alignment explanation
Indices: 343406--343548 Score: 189
Period size: 59 Copynumber: 2.5 Consensus size: 56
343396 TTCACTGGAA
* * * * *
343406 GTTAGTAAATCCAGGATTTGCTAACCCCTATTGGGCGCATGCCTTAG-GTTTTCTTTGGG
1 GTTAGTAAATCCAGGATTTGCTAACCCCTATTGAGCGCACG-CGT-GCGCTGTCTTT--G
343465 GTTAGTAAATCCAGGATTTGCTAACCCCTATTGAGCGCACGCGTGCGCTGTCTTTG
1 GTTAGTAAATCCAGGATTTGCTAACCCCTATTGAGCGCACGCGTGCGCTGTCTTTG
*
343521 GTTAGTAAATCCAGGATTTACTAACCCC
1 GTTAGTAAATCCAGGATTTGCTAACCCC
343549 CCCCCCCCCC
Statistics
Matches: 77, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
56 28 0.36
57 1 0.01
58 9 0.12
59 39 0.51
ACGTcount: A:0.22, C:0.23, G:0.23, T:0.32
Consensus pattern (56 bp):
GTTAGTAAATCCAGGATTTGCTAACCCCTATTGAGCGCACGCGTGCGCTGTCTTTG
Found at i:345209 original size:2 final size:2
Alignment explanation
Indices: 345202--345249 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
345192 NNNNNNNNNN
345202 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
345244 AG AG AG
1 AG AG AG
345250 GAGTTAAAAC
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:347031 original size:57 final size:58
Alignment explanation
Indices: 346951--347066 Score: 216
Period size: 57 Copynumber: 2.0 Consensus size: 58
346941 CTTCGCTAGC
*
346951 GAAGGGTTTTTGGTCCATTTCGCTCCCCATAACCCTAGGGTTTAT-GGGGAGCGAAGT
1 GAAGGGTTTTTGGTCCACTTCGCTCCCCATAACCCTAGGGTTTATGGGGGAGCGAAGT
347008 GAAGGGTTTTTGGTCCACTTCGCTCCCCATAACCCTAGGGTTTATGGGGGAGCGAAGT
1 GAAGGGTTTTTGGTCCACTTCGCTCCCCATAACCCTAGGGTTTATGGGGGAGCGAAGT
347066 G
1 G
347067 GACCGAAAAC
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
57 44 0.77
58 13 0.23
ACGTcount: A:0.19, C:0.22, G:0.31, T:0.28
Consensus pattern (58 bp):
GAAGGGTTTTTGGTCCACTTCGCTCCCCATAACCCTAGGGTTTATGGGGGAGCGAAGT
Found at i:350058 original size:11 final size:11
Alignment explanation
Indices: 350042--350067 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
350032 CAGACAATCA
350042 TGTTACATAAG
1 TGTTACATAAG
350053 TGTTACATAAG
1 TGTTACATAAG
350064 TGTT
1 TGTT
350068 TATGACTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.31, C:0.08, G:0.19, T:0.42
Consensus pattern (11 bp):
TGTTACATAAG
Found at i:355394 original size:2 final size:2
Alignment explanation
Indices: 355389--355438 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
355379 AACAAATTGC
*
355389 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA AA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
355431 GA GA GA GA
1 GA GA GA GA
355439 TCTGACTAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:356565 original size:2 final size:2
Alignment explanation
Indices: 356558--356595 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
356548 CTGATACGTG
356558 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
356596 NNNNNNNNNN
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:361637 original size:166 final size:166
Alignment explanation
Indices: 361363--362163 Score: 1270
Period size: 166 Copynumber: 4.8 Consensus size: 166
361353 NNNNNNNNNN
* * *
361363 AAAACTTGATCCCCCAATTGTGGCCCCACCCTACCCACAGAGACTATGATTTGAACAAACTTGAA
1 AAAACTTGATCCCCTAATTGTGGCCCCACCCTACCCCCAGGGACTATGATTTGAACAAACTTGAA
361428 TCTACACTATCTGAGGATGCTTCCATTTTAATTTGAGCTTTCCTGGCCTAATAGTTTTTGAAAAG
66 TCTACACTATCTGAGGATGCTTCCATTTTAATTTGAGCTTTCCTGGCCTAATAGTTTTTGAAAAG
*
361493 AAGATTTTTAAAGATTTTCTCTATATATTCCTGTGT
131 AAGATTTTTAAAGATTTTCTCTATATATTCCTATGT
361529 AAAACTTGATCCCCTAATTGTGGCCCCACCCTACCCCCAGGGACTATGATTTGAACAAACTTGAA
1 AAAACTTGATCCCCTAATTGTGGCCCCACCCTACCCCCAGGGACTATGATTTGAACAAACTTGAA
*
361594 TCTACACTATCTGAGGATGCTTCCATTTTAATTTGAGCTTTCCTGGCCTAATAGTTTTTGAAAAA
66 TCTACACTATCTGAGGATGCTTCCATTTTAATTTGAGCTTTCCTGGCCTAATAGTTTTTGAAAAG
361659 AAGATTTTTAAAGATTTTCTCTATATATTCCTATGT
131 AAGATTTTTAAAGATTTTCTCTATATATTCCTATGT
361695 AAAACTTGATCCCCTAATTGTGGCCCCACCCTACCCCCAGGGACTATGATTTGAACAAACTTGAA
1 AAAACTTGATCCCCTAATTGTGGCCCCACCCTACCCCCAGGGACTATGATTTGAACAAACTTGAA
* *
361760 TCTACACTATCTGAGGATGCTTCCATTTTAATTTGAGCTTTCCTGGCCTAATAAATTTTTTAAAA
66 TCTACACTATCTGAGGATGCTTCCATTTTAATTTGAGCTTTCCTGGCCTAAT-AGTTTTTGAAAA
*
361825 GATGATTTTTAAAGATTTTCTCTATATATTCCTATGT
130 GAAGATTTTTAAAGATTTTCTCTATATATTCCTATGT
* *
361862 AAAACTTGATCCCCTAATTGTGGCCCCACCCTACCCCCGGGGACCATGATTTGAACAAACTTGAA
1 AAAACTTGATCCCCTAATTGTGGCCCCACCCTACCCCCAGGGACTATGATTTGAACAAACTTGAA
* * * * *
361927 TCTACACTATCTGAGGATGCTACCATTTTAATTTTAGCTTTTCTGGTCTATTAGTTTTTG---AG
66 TCTACACTATCTGAGGATGCTTCCATTTTAATTTGAGCTTTCCTGGCCTAATAGTTTTTGAAAAG
361989 AAGATTTTTAAAGATTTTCTCTATATATTCCTATGT
131 AAGATTTTTAAAGATTTTCTCTATATATTCCTATGT
* * * *
362025 AAAACTTGATCCCCCT-CTTGTGGCCCCTCCCTACCCCCGGGGACCATGATTTGAACAAACTTGA
1 AAAACTTGAT-CCCCTAATTGTGGCCCCACCCTACCCCCAGGGACTATGATTTGAACAAACTTGA
* * *** * * * * * *
362089 ATCTACACTACCTGAGGATGCCTCCA-CACAAGTTTAAGCTTTTCAGGCCGATTAGTTTTTGAGA
65 ATCTACACTATCTGAGGATGCTTCCATTTTAA-TTTGAGCTTTCCTGGCCTAATAGTTTTTGAAA
362153 AGAAGATTTTT
129 AGAAGATTTTT
362164 GAAAAATACC
Statistics
Matches: 598, Mismatches: 31, Indels: 12
0.93 0.05 0.02
Matches are distributed among these distances:
162 2 0.00
163 141 0.24
164 5 0.01
166 295 0.49
167 155 0.26
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.35
Consensus pattern (166 bp):
AAAACTTGATCCCCTAATTGTGGCCCCACCCTACCCCCAGGGACTATGATTTGAACAAACTTGAA
TCTACACTATCTGAGGATGCTTCCATTTTAATTTGAGCTTTCCTGGCCTAATAGTTTTTGAAAAG
AAGATTTTTAAAGATTTTCTCTATATATTCCTATGT
Found at i:361984 original size:333 final size:329
Alignment explanation
Indices: 361363--362114 Score: 1263
Period size: 333 Copynumber: 2.3 Consensus size: 329
361353 NNNNNNNNNN
* * *
361363 AAAACTTGATCCCCCAATTGTGGCCCCACCCTACCCACAGAGACTATGATTTGAACAAACTTGAA
1 AAAACTTGATCCCCTAATTGTGGCCCCACCCTACCCCCAGGGACTATGATTTGAACAAACTTGAA
*
361428 TCTACACTATCTGAGGATGCTTCCATTTTAATTTGAGCTTTCCTGGCCTAATAGTTTTTGAAAAG
66 TCTACACTATCTGAGGATGCTTCCATTTTAATTTGAGCTTTCCTGGCCTAATAATTTTTGAAAAG
*
361493 AAGATTTTTAAAGATTTTCTCTATATATTCCTGTGTAAAACTTGATCCCCTAATTGTGGCCCCAC
131 AAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAACTTGATCCCCTAATTGTGGCCCCAC
* *
361558 CCTACCCCCAGGGACTATGATTTGAACAAACTTGAATCTACACTATCTGAGGATGCTTCCATTTT
196 CCTACCCCCAGGGACCATGATTTGAACAAACTTGAATCTACACTATCTGAGGATGCTACCATTTT
361623 AATTTGAGCTTTCCTGGCCTAATAGTTTTTGAAAAAAAGATTTTTAAAGATTTTCTCTATATATT
261 AATTTGAGCTTTCCTGGCCTAATAGTTTTTG---AAAAGATTTTTAAAGATTTTCTCTATATATT
361688 CCTATGT
323 CCTATGT
361695 AAAACTTGATCCCCTAATTGTGGCCCCACCCTACCCCCAGGGACTATGATTTGAACAAACTTGAA
1 AAAACTTGATCCCCTAATTGTGGCCCCACCCTACCCCCAGGGACTATGATTTGAACAAACTTGAA
*
361760 TCTACACTATCTGAGGATGCTTCCATTTTAATTTGAGCTTTCCTGGCCTAATAAATTTTTTAAAA
66 TCTACACTATCTGAGGATGCTTCCATTTTAATTTGAGCTTTCCTGGCCTAAT-AATTTTTGAAAA
*
361825 GATGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAACTTGATCCCCTAATTGTGGCCCCA
130 GAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAACTTGATCCCCTAATTGTGGCCCCA
*
361890 CCCTACCCCCGGGGACCATGATTTGAACAAACTTGAATCTACACTATCTGAGGATGCTACCATTT
195 CCCTACCCCCAGGGACCATGATTTGAACAAACTTGAATCTACACTATCTGAGGATGCTACCATTT
* * * * *
361955 TAATTTTAGCTTTTCTGGTCTATTAGTTTTTGAGAAGATTTTTAAAGATTTTCTCTATATATTCC
260 TAATTTGAGCTTTCCTGGCCTAATAGTTTTTGAAAAGATTTTTAAAGATTTTCTCTATATATTCC
362020 TATGT
325 TATGT
* * * *
362025 AAAACTTGATCCCCCT-CTTGTGGCCCCTCCCTACCCCCGGGGACCATGATTTGAACAAACTTGA
1 AAAACTTGAT-CCCCTAATTGTGGCCCCACCCTACCCCCAGGGACTATGATTTGAACAAACTTGA
* *
362089 ATCTACACTACCTGAGGATGCCTCCA
65 ATCTACACTATCTGAGGATGCTTCCA
362115 CACAAGTTTA
Statistics
Matches: 397, Mismatches: 21, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
330 115 0.29
331 5 0.01
332 114 0.29
333 163 0.41
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (329 bp):
AAAACTTGATCCCCTAATTGTGGCCCCACCCTACCCCCAGGGACTATGATTTGAACAAACTTGAA
TCTACACTATCTGAGGATGCTTCCATTTTAATTTGAGCTTTCCTGGCCTAATAATTTTTGAAAAG
AAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAACTTGATCCCCTAATTGTGGCCCCAC
CCTACCCCCAGGGACCATGATTTGAACAAACTTGAATCTACACTATCTGAGGATGCTACCATTTT
AATTTGAGCTTTCCTGGCCTAATAGTTTTTGAAAAGATTTTTAAAGATTTTCTCTATATATTCCT
ATGT
Found at i:362354 original size:12 final size:12
Alignment explanation
Indices: 362333--362386 Score: 54
Period size: 12 Copynumber: 4.4 Consensus size: 12
362323 TGAAAAGTTT
*
362333 ACAACGACGACG
1 ACAACAACGACG
362345 ACAACAACGACG
1 ACAACAACGACG
* * *
362357 ACGACTACGACA
1 ACAACAACGACG
*
362369 ACGACAACGACAG
1 ACAACAACGAC-G
362382 ACAAC
1 ACAAC
362387 GGACAAATTG
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
12 30 0.88
13 4 0.12
ACGTcount: A:0.46, C:0.33, G:0.19, T:0.02
Consensus pattern (12 bp):
ACAACAACGACG
Found at i:364926 original size:14 final size:13
Alignment explanation
Indices: 364889--364935 Score: 58
Period size: 14 Copynumber: 3.5 Consensus size: 13
364879 GTTTTGATGT
*
364889 TTGTTGTTTGTTA
1 TTGTTGTTTTTTA
364902 TATGTTGTTTTTTA
1 T-TGTTGTTTTTTA
*
364916 GTTGTTGTTTTTTT
1 -TTGTTGTTTTTTA
364930 TTGTTG
1 TTGTTG
364936 CTATTTGTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 7 0.23
14 22 0.73
15 1 0.03
ACGTcount: A:0.06, C:0.00, G:0.21, T:0.72
Consensus pattern (13 bp):
TTGTTGTTTTTTA
Found at i:364946 original size:17 final size:17
Alignment explanation
Indices: 364882--364946 Score: 53
Period size: 17 Copynumber: 3.8 Consensus size: 17
364872 TCCTTCTGTT
* *
364882 TTGATGTTTGTTGTTTG
1 TTGATATTTGTTTTTTG
364899 TT-ATATGTTGTTTTTTAG
1 TTGATAT-TTGTTTTTT-G
* *
364917 TTGTTGTTT-TTTTTTG
1 TTGATATTTGTTTTTTG
*
364933 TTGCTATTTGTTTT
1 TTGATATTTGTTTT
364947 GCGTGTTTGT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
16 11 0.29
17 20 0.53
18 5 0.13
19 2 0.05
ACGTcount: A:0.08, C:0.02, G:0.20, T:0.71
Consensus pattern (17 bp):
TTGATATTTGTTTTTTG
Found at i:368088 original size:2 final size:2
Alignment explanation
Indices: 368083--368128 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
368073 CTACTTTTAG
368083 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
368125 GA GA
1 GA GA
368129 CTAACAATGT
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:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:391852 original size:17 final size:17
Alignment explanation
Indices: 391810--391858 Score: 66
Period size: 15 Copynumber: 3.0 Consensus size: 17
391800 TTTGCAAATT
*
391810 TTTACGGCTATAACGAA
1 TTTACGGATATAACGAA
391827 TTT--GGATATAACGAA
1 TTTACGGATATAACGAA
*
391842 TTTACGGATATAGCGAA
1 TTTACGGATATAACGAA
391859 CTGATTCTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 14 0.50
17 14 0.50
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (17 bp):
TTTACGGATATAACGAA
Found at i:392133 original size:16 final size:16
Alignment explanation
Indices: 392112--392142 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
392102 GAATTCGTTA
*
392112 TACGGATATAGCGAAT
1 TACGGATATAACGAAT
392128 TACGGATATAACGAA
1 TACGGATATAACGAA
392143 GTAAATCCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.13, G:0.23, T:0.23
Consensus pattern (16 bp):
TACGGATATAACGAAT
Found at i:394746 original size:11 final size:11
Alignment explanation
Indices: 394730--394754 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
394720 NNNNNNNNNN
394730 ATATAATATAT
1 ATATAATATAT
394741 ATATAATATAT
1 ATATAATATAT
394752 ATA
1 ATA
394755 ATTTTTATCC
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
ATATAATATAT
Found at i:396008 original size:1 final size:1
Alignment explanation
Indices: 396002--396043 Score: 66
Period size: 1 Copynumber: 42.0 Consensus size: 1
395992 CATTTCTCCC
**
396002 TTTTTTTTTTTTTTTTTTTTTTTTTTTTCCTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
396044 GGTTTTAGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.00, C:0.05, G:0.00, T:0.95
Consensus pattern (1 bp):
T
Found at i:396049 original size:20 final size:20
Alignment explanation
Indices: 396012--396049 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
396002 TTTTTTTTTT
**
396012 TTTTTTTTTTTTTTTTTTCC
1 TTTTTTTTTTTTGGTTTTCC
396032 TTTTTTTTTTTTGGTTTT
1 TTTTTTTTTTTTGGTTTT
396050 AGAACTCTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.00, C:0.05, G:0.05, T:0.89
Consensus pattern (20 bp):
TTTTTTTTTTTTGGTTTTCC
Found at i:405971 original size:334 final size:333
Alignment explanation
Indices: 405362--406028 Score: 1325
Period size: 334 Copynumber: 2.0 Consensus size: 333
405352 ACATTTCCGC
405362 AAAGAAATACTTACTCTGGATAAGACATGATGATATCAGTATCAAATCTTGGTTTTGCAAATGTA
1 AAAGAAATACTTACTCTGGATAAGACATGATGATATCAGTATCAAATCTTGGTTTTGCAAATGTA
405427 AAGTTGGTACAAGAGTTGTGGGCATGTGTGCTCATATTACCAGTGTGATTTGGTTCTTGGGTCTT
66 AAGTTGGTACAAGAGTTGTGGGCATGTGTGCTCATATTACCAGTGTGATTTGGTTCTTGGGTCTT
405492 GCTCGTCATGAGGAAAGTGGTGTCTGTGGTGTGCGCGATTGGTGTAGTTCTGTTGAGGATGCTGC
131 GCTCGTCATGAGGAAAGTGGTGTCTGTGGTGTGCGCGATTGGTGTAGTTCTGTTGAGGATGCTGC
405557 TGCACTCCCAATTGATGAATCAGAAAGTGAGGAAGAAAATGAAGAAAGATGTTCCATAACAGAAG
196 TGCACTCCCAATTGATGAATCAGAAAGTGAGGAAGAAAATGAAGAAAGATGTTCCATAACAGAAG
405622 AGGAGTGAATTTCAAAGTGACTCATCAGTCAATAAATCAGTCAACAAAACATGTTTGGTAGGAGA
261 AGGAGTGAATTTCAAAGTGACTCATCAGTCAATAAATCAGTCAACAAAACATGTTTGGTAGGAGA
405687 ATTTTTCT
326 ATTTTTCT
405695 NAAAGAAATACTTACTCTGGATAAGACATGATGATATCAGTATCAAATCTTGGTTTTGCAAATGT
1 -AAAGAAATACTTACTCTGGATAAGACATGATGATATCAGTATCAAATCTTGGTTTTGCAAATGT
405760 AAAGTTGGTACAAGAGTTGTGGGCATGTGTGCTCATATTACCAGTGTGATTTGGTTCTTGGGTCT
65 AAAGTTGGTACAAGAGTTGTGGGCATGTGTGCTCATATTACCAGTGTGATTTGGTTCTTGGGTCT
405825 TGCTCGTCATGAGGAAAGTGGTGTCTGTGGTGTGCGCGATTGGTGTAGTTCTGTTGAGGATGCTG
130 TGCTCGTCATGAGGAAAGTGGTGTCTGTGGTGTGCGCGATTGGTGTAGTTCTGTTGAGGATGCTG
405890 CTGCACTCCCAATTGATGAATCAGAAAGTGAGGAAGAAAATGAAGAAAGATGTTCCATAACAGAA
195 CTGCACTCCCAATTGATGAATCAGAAAGTGAGGAAGAAAATGAAGAAAGATGTTCCATAACAGAA
405955 GAGGAGTGAATTTCAAAGTGACTCATCAGTCAATAAATCAGTCAACAAAACATGTTTGGTAGGAG
260 GAGGAGTGAATTTCAAAGTGACTCATCAGTCAATAAATCAGTCAACAAAACATGTTTGGTAGGAG
406020 AATTTTTCT
325 AATTTTTCT
406029 GAAATTTAGT
Statistics
Matches: 333, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
334 333 1.00
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.30
Consensus pattern (333 bp):
AAAGAAATACTTACTCTGGATAAGACATGATGATATCAGTATCAAATCTTGGTTTTGCAAATGTA
AAGTTGGTACAAGAGTTGTGGGCATGTGTGCTCATATTACCAGTGTGATTTGGTTCTTGGGTCTT
GCTCGTCATGAGGAAAGTGGTGTCTGTGGTGTGCGCGATTGGTGTAGTTCTGTTGAGGATGCTGC
TGCACTCCCAATTGATGAATCAGAAAGTGAGGAAGAAAATGAAGAAAGATGTTCCATAACAGAAG
AGGAGTGAATTTCAAAGTGACTCATCAGTCAATAAATCAGTCAACAAAACATGTTTGGTAGGAGA
ATTTTTCT
Found at i:409830 original size:100 final size:100
Alignment explanation
Indices: 409718--409918 Score: 386
Period size: 100 Copynumber: 2.0 Consensus size: 100
409708 AGCAAAACTT
409718 TTGCGGCAACATCTTTCTGGCAATATTGCCGCAATCTCATTTGCATACGAAAAACGCTACTGCAG
1 TTGCGGCAACATCTTTCTGGCAATATTGCCGCAATCTCATTTGCATACGAAAAACGCTACTGCAG
409783 CAACATTGCCGCAATGTATTGCCAG-AAAGGTGTTG
66 CAACATTGCCGCAATGTATTGCC-GCAAAGGTGTTG
409818 TTGCGGCAACATCTTTCTGGCAATATTGCCGCAATCTCATTTGCATACGAAAAACGCTACTGCAG
1 TTGCGGCAACATCTTTCTGGCAATATTGCCGCAATCTCATTTGCATACGAAAAACGCTACTGCAG
409883 CAACATTGCCGCAATGTATTGCCGCAAAGGTGTTG
66 CAACATTGCCGCAATGTATTGCCGCAAAGGTGTTG
409918 T
1 T
409919 CGCAACATTA
Statistics
Matches: 100, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
99 1 0.01
100 99 0.99
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.27
Consensus pattern (100 bp):
TTGCGGCAACATCTTTCTGGCAATATTGCCGCAATCTCATTTGCATACGAAAAACGCTACTGCAG
CAACATTGCCGCAATGTATTGCCGCAAAGGTGTTG
Done.