Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold373
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3053563
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 20
Found at i:187487 original size:51 final size:50
Alignment explanation
Indices: 187397--187518 Score: 145
Period size: 51 Copynumber: 2.4 Consensus size: 50
187387 CCGATGAAAT
* * *
187397 AACGGAGTTGGAGTACCCCCGATTGTGAAAAATTAGTGTTTTGGAAATAA
1 AACGGAGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTAGAAATAA
* * * * *
187447 AATCGGAGTTGGAATATCCCTGATTATGGAGAATTGGTGTTTTAGAAATAA
1 AA-CGGAGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTAGAAATAA
*
187498 AACCGAGGTTGGAGTATCCCC
1 AACGGA-GTTGGAGTATCCCC
187519 TTGGAAATAA
Statistics
Matches: 59, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
50 5 0.08
51 54 0.92
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.29
Consensus pattern (50 bp):
AACGGAGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTAGAAATAA
Found at i:187571 original size:79 final size:79
Alignment explanation
Indices: 187458--187752 Score: 384
Period size: 79 Copynumber: 3.8 Consensus size: 79
187448 ATCGGAGTTG
* * * * * *
187458 GAATATCCCTGATTATGGAGAATTGGTGTTTTAGAAATAAAACCGAGGTTGGAGTATCCCCTTGG
1 GAATATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGAGGTTGGAGTATCCCCTCGA
187523 AAATAACGGGGTTA
66 AAATAACGGGGTTA
* *
187537 GAATATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAATCGGGGTTGGAGTATCCCCTCGA
1 GAATATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGAGGTTGGAGTATCCCCTCGA
*
187602 AAATAACGTGGTTA
66 AAATAACGGGGTTA
* * *
187616 GAGTAT-CCC--TTATGAAAAATTGATGTTTTAGAAATAAAACCGAGGTTGGCGTGTCCCCTCGA
1 GAATATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGAGGTTGGAGTATCCCCTCGA
*
187678 AAATAATGGGGTT-
66 AAATAACGGGGTTA
* * * *
187691 GAAGTATCCCCGATTATGAAAAGTCGATGTTTTGGAAATAAAATCG-GAGTTGGAGTATCCCC
1 GAA-TATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGAG-GTTGGAGTATCCCC
187753 GATTATGGAA
Statistics
Matches: 188, Mismatches: 23, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
75 2 0.01
76 63 0.34
77 3 0.02
78 4 0.02
79 116 0.62
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (79 bp):
GAATATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGAGGTTGGAGTATCCCCTCGA
AAATAACGGGGTTA
Found at i:187751 original size:51 final size:50
Alignment explanation
Indices: 187688--187864 Score: 214
Period size: 51 Copynumber: 3.5 Consensus size: 50
187678 AAATAATGGG
*
187688 GTTGAAGTATCCCCGATTATGAAAAGTCGATGTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAA-TCGATGTTTTGGAAATAAAATCGGA
* * *
187739 GTTGGAGTATCCCCGATTATGGAAAATGGGTGTTTTAGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTAT-GAAAATCGATGTTTTGGAAATAAAATCGGA
* * * * *
187790 GTTGGAGTATCCCCGATTAAGAAAAATTGACGTTTTGGAAATGAAACCGG-
1 GTTGGAGTATCCCCGATTATG-AAAATCGATGTTTTGGAAATAAAATCGGA
*
187840 GATTGGAGTATCCCCGA-GATGAAAA
1 G-TTGGAGTATCCCCGATTATGAAAA
187865 ATCTAGAAAT
Statistics
Matches: 110, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
49 4 0.04
50 4 0.04
51 97 0.88
52 5 0.05
ACGTcount: A:0.34, C:0.12, G:0.26, T:0.27
Consensus pattern (50 bp):
GTTGGAGTATCCCCGATTATGAAAATCGATGTTTTGGAAATAAAATCGGA
Found at i:190179 original size:20 final size:20
Alignment explanation
Indices: 190154--190223 Score: 82
Period size: 20 Copynumber: 3.9 Consensus size: 20
190144 AAAATGCCTA
190154 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGAGC
190174 AATGTATCG-----AT-A-C
1 AATGTATCGATACAATGAGC
*
190187 AATGTATCGATACAAGGAGC
1 AATGTATCGATACAATGAGC
190207 AATGTATCGATACAATG
1 AATGTATCGATACAATG
190224 CAAAAGGTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 14
0.72 0.04 0.25
Matches are distributed among these distances:
13 10 0.24
14 1 0.02
15 2 0.05
18 1 0.02
19 1 0.02
20 26 0.63
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (20 bp):
AATGTATCGATACAATGAGC
Found at i:190189 original size:13 final size:13
Alignment explanation
Indices: 190173--190201 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
190163 ATACAATGAG
190173 CAATGTATCGATA
1 CAATGTATCGATA
190186 CAATGTATCGATA
1 CAATGTATCGATA
190199 CAA
1 CAA
190202 GGAGCAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:190196 original size:33 final size:33
Alignment explanation
Indices: 190154--190223 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
190144 AAAATGCCTA
*
190154 AATGTATCGATACAATGAGCAATGTATCGATAC
1 AATGTATCGATACAAGGAGCAATGTATCGATAC
190187 AATGTATCGATACAAGGAGCAATGTATCGATAC
1 AATGTATCGATACAAGGAGCAATGTATCGATAC
190220 AATG
1 AATG
190224 CAAAAGGTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (33 bp):
AATGTATCGATACAAGGAGCAATGTATCGATAC
Found at i:190351 original size:21 final size:21
Alignment explanation
Indices: 190327--190381 Score: 110
Period size: 21 Copynumber: 2.6 Consensus size: 21
190317 GTTGGGGCCT
190327 TGTATCGATACATCAAGGGCA
1 TGTATCGATACATCAAGGGCA
190348 TGTATCGATACATCAAGGGCA
1 TGTATCGATACATCAAGGGCA
190369 TGTATCGATACAT
1 TGTATCGATACAT
190382 TTTAGTAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (21 bp):
TGTATCGATACATCAAGGGCA
Found at i:190995 original size:34 final size:36
Alignment explanation
Indices: 190925--190997 Score: 96
Period size: 36 Copynumber: 2.1 Consensus size: 36
190915 GATTAATAAA
*
190925 ATACTCCCATACAAAGGATCCTATTGTTTATCTGCC
1 ATACTCCCATACAAAGGATCCTATAGTTTATCTGCC
* * *
190961 ATACTCCCATACAAGGGAT-GTGTAG-TTATCTGCC
1 ATACTCCCATACAAAGGATCCTATAGTTTATCTGCC
190995 ATA
1 ATA
190998 ATATTGTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
34 12 0.36
35 3 0.09
36 18 0.55
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.32
Consensus pattern (36 bp):
ATACTCCCATACAAAGGATCCTATAGTTTATCTGCC
Found at i:198611 original size:51 final size:51
Alignment explanation
Indices: 198534--198643 Score: 186
Period size: 51 Copynumber: 2.2 Consensus size: 51
198524 AGATAACGGG
*
198534 GTTGGAGTATCCCCGATGGTGGAAAATCAGTATTTTAGAAATAAAATC-GA
1 GTTGGAGTATCCCCGATGGTGGAAAATCAATATTTTAGAAATAAAATCAGA
*
198584 GATTGGAGTATCCCCGATGGTGGAAAATTAATATTTTAGAAATAAAATCAGA
1 G-TTGGAGTATCCCCGATGGTGGAAAATCAATATTTTAGAAATAAAATCAGA
198636 GTTGGAGT
1 GTTGGAGT
198644 GTCTTCTCAG
Statistics
Matches: 56, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
50 1 0.02
51 52 0.93
52 3 0.05
ACGTcount: A:0.36, C:0.10, G:0.25, T:0.29
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATGGTGGAAAATCAATATTTTAGAAATAAAATCAGA
Found at i:198858 original size:158 final size:158
Alignment explanation
Indices: 198584--198980 Score: 435
Period size: 158 Copynumber: 2.5 Consensus size: 158
198574 ATAAAATCGA
* * *** * * **
198584 GATTGGAGTATCCCCGATGGTGGAAAATTAATATTTTAGAAATAAAATCAGAGTTGGAGTGTCTT
1 GATTGGAGTATCCCTGATGGTGAAAAATCGGTGTTTTAGAAATAAAATC-GGGTTGGAGTGTCCC
** * * * *
198649 CTC-AGAAATAATGGGGTTAAAGTATCCCCGATGGTGAAAAAAAGGTGTTTTAAAAATAAATCCG
65 CTCGA-AAATAACAGGGTTAAAGTATCCCCAATGGTGAAAAAAAGATATTTTAAAAATAAAACCG
*
198713 AGGTTGAAGT-ATCCACTCAAAAATAAC-GG
129 AGGTTGAAGTGATCC-CTCAAAAACAACAGG
*
198742 GATTGGAGTATCCCTGATGGTGAAAAATCGGTGTTTTAGAAATAAAATCGTGGTTAGAGTGTCCC
1 GATTGGAGTATCCCTGATGGTGAAAAATCGGTGTTTTAGAAATAAAATCG-GGTTGGAGTGTCCC
* * *** * *
198807 CTCGAAAATAACAGGGTTAGAGTATCCCTAATGGTGAAAATTTGATATTTTAGAAATAAAACTGA
65 CTCGAAAATAACAGGGTTAAAGTATCCCCAATGGTGAAAAAAAGATATTTTAAAAATAAAACCGA
* * *
198872 GGTTGGAGTGTTCCCTCGAAAACAACAGG
130 GGTTGAAGTGATCCCTCAAAAACAACAGG
*
198901 G-TTGGAGTATCCCTGATGGTGAAAAATCGAG-GTTTTAGAAATAAAATGGGGGTTGGAGTGTCC
1 GATTGGAGTATCCCTGATGGTGAAAAATCG-GTGTTTTAGAAATAAAAT-CGGGTTGGAGTGTCC
* *
198964 CTTTGAAAATAACAGGG
64 CCTCGAAAATAACAGGG
198981 CCTTTGGTGG
Statistics
Matches: 202, Mismatches: 31, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
157 1 0.00
158 192 0.95
159 9 0.04
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.28
Consensus pattern (158 bp):
GATTGGAGTATCCCTGATGGTGAAAAATCGGTGTTTTAGAAATAAAATCGGGTTGGAGTGTCCCC
TCGAAAATAACAGGGTTAAAGTATCCCCAATGGTGAAAAAAAGATATTTTAAAAATAAAACCGAG
GTTGAAGTGATCCCTCAAAAACAACAGG
Found at i:198937 original size:79 final size:77
Alignment explanation
Indices: 198586--198980 Score: 350
Period size: 79 Copynumber: 5.0 Consensus size: 77
198576 AAAATCGAGA
* * ** ** * *
198586 TTGGAGTATCCCCGATGGTGGAAAATTAATATTTTAGAAATAAAATCAGAGTTGGAGTGTCTTCT
1 TTGGAGTATCCCTGATGGTGAAAAATCGAGGTTTTAGAAATAAAATGAG-GTTGGAGTGTC-CCT
**
198651 C-AGAAATAATGGGG
64 CGA-AAATAACAGGG
** * ** * * *
198665 TTAAAGTATCCCCGATGGTGAAAAAAAG-GTGTTTTAAAAAT-AAATCCGAGGTTGAAGTATCCA
1 TTGGAGTATCCCTGATGGTGAAAAATCGAG-GTTTTAGAAATAAAAT--GAGGTTGGAGTGTCC-
*
198728 CTCAAAAATAAC-GGG
62 CTCGAAAATAACAGGG
* *
198743 ATTGGAGTATCCCTGATGGTGAAAAATCG-GTGTTTTAGAAATAAAATCGTGGTTAGAGTGTCCC
1 -TTGGAGTATCCCTGATGGTGAAAAATCGAG-GTTTTAGAAATAAAAT-GAGGTTGGAGTGT-CC
198807 CTCGAAAATAACAGGG
62 CTCGAAAATAACAGGG
* * * * **
198823 TTAGAGTATCCCTAATGGTGAAAATTTGATATTTTAGAAATAAAACTGAGGTTGGAGTGTTCCCT
1 TTGGAGTATCCCTGATGGTGAAAAATCGAGGTTTTAGAAATAAAA-TGAGGTTGGAGTG-TCCCT
*
198888 CGAAAACAACAGGG
64 CGAAAATAACAGGG
*
198902 TTGGAGTATCCCTGATGGTGAAAAATCGAGGTTTTAGAAATAAAATGGGGGTTGGAGTGTCCCTT
1 TTGGAGTATCCCTGATGGTGAAAAATCGAGGTTTTAGAAATAAAAT-GAGGTTGGAGTGTCCC-T
*
198967 TGAAAATAACAGGG
64 CGAAAATAACAGGG
198981 CCTTTGGTGG
Statistics
Matches: 259, Mismatches: 43, Indels: 28
0.78 0.13 0.08
Matches are distributed among these distances:
78 12 0.05
79 233 0.90
80 14 0.05
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.28
Consensus pattern (77 bp):
TTGGAGTATCCCTGATGGTGAAAAATCGAGGTTTTAGAAATAAAATGAGGTTGGAGTGTCCCTCG
AAAATAACAGGG
Found at i:201464 original size:20 final size:21
Alignment explanation
Indices: 201439--201493 Score: 85
Period size: 20 Copynumber: 2.7 Consensus size: 21
201429 AAAATTCTTG
**
201439 AATGTATCGATACAATGAA-A
1 AATGTATCGATACAAACAATA
201459 AATGTATCGATACAAACAATA
1 AATGTATCGATACAAACAATA
201480 AATGTATCGATACA
1 AATGTATCGATACA
201494 TTTGCTTGGC
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 17 0.53
21 15 0.47
ACGTcount: A:0.49, C:0.13, G:0.13, T:0.25
Consensus pattern (21 bp):
AATGTATCGATACAAACAATA
Found at i:204435 original size:22 final size:21
Alignment explanation
Indices: 204395--204435 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
204385 CCATTAGATT
**
204395 ATTTTTTTCCAAATTTTTAAA
1 ATTTTTTTCCAAAAATTTAAA
204416 ATTTTTTTCCTAAAAATTTA
1 ATTTTTTTCC-AAAAATTTA
204436 TTGCAATTCC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.34, C:0.10, G:0.00, T:0.56
Consensus pattern (21 bp):
ATTTTTTTCCAAAAATTTAAA
Found at i:217518 original size:2 final size:2
Alignment explanation
Indices: 217511--217540 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
217501 GCTAAATTTA
217511 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
217541 GTATGTACAC
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:219770 original size:16 final size:18
Alignment explanation
Indices: 219747--219782 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
219737 AGATATATAG
*
219747 ATTTTTTAA-AAAAATTA
1 ATTTTTAAATAAAAATTA
219764 ATTTTTAAATAAAAATTA
1 ATTTTTAAATAAAAATTA
219782 A
1 A
219783 AAATACAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATTTTTAAATAAAAATTA
Found at i:220866 original size:21 final size:21
Alignment explanation
Indices: 220842--220882 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
220832 ATTATTTTTA
220842 TATTTATTAA-GAAAAATAAAT
1 TATTT-TTAATGAAAAATAAAT
*
220863 TATTTTTAATTAAAAATAAA
1 TATTTTTAATGAAAAATAAA
220883 AAAATAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (21 bp):
TATTTTTAATGAAAAATAAAT
Found at i:221253 original size:34 final size:35
Alignment explanation
Indices: 221215--221281 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 35
221205 CCTTACAACA
221215 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
*
221249 CTATCTTTTTCAAAGGTTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
221282 AATCACTTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.41
37 12 0.41
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.34
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:221749 original size:22 final size:22
Alignment explanation
Indices: 221721--221764 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
221711 ATTGAATAGT
*
221721 ATGAACAGTGATGTATCGATAC
1 ATGAACAATGATGTATCGATAC
*
221743 ATGAACAATGATGTATTGATAC
1 ATGAACAATGATGTATCGATAC
221765 TCTGATGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (22 bp):
ATGAACAATGATGTATCGATAC
Found at i:221909 original size:13 final size:13
Alignment explanation
Indices: 221891--221915 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
221881 TGCTAATGCT
221891 ATGTATCGATACA
1 ATGTATCGATACA
221904 ATGTATCGATAC
1 ATGTATCGATAC
221916 TTAGCAAAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:222962 original size:20 final size:20
Alignment explanation
Indices: 222931--222987 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
222921 GTCAAAACCC
*
222931 TGAAAAGTATCGATACACAT
1 TGAAATGTATCGATACACAT
* *
222951 TTAAATGTATCGATACAGAT
1 TGAAATGTATCGATACACAT
* *
222971 TGCATTGTATCGATACA
1 TGAAATGTATCGATACA
222988 TTGTATCGAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.32
Consensus pattern (20 bp):
TGAAATGTATCGATACACAT
Found at i:222991 original size:13 final size:13
Alignment explanation
Indices: 222973--223001 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
222963 ATACAGATTG
222973 CATTGTATCGATA
1 CATTGTATCGATA
222986 CATTGTATCGATA
1 CATTGTATCGATA
222999 CAT
1 CAT
223002 GACCAAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:223014 original size:20 final size:21
Alignment explanation
Indices: 222989--223041 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
222979 ATCGATACAT
**
222989 TGTATCGATACATGACCAA-A
1 TGTATCGATACATGAAAAAGA
*
223009 TGTATCGATACTTGAAAAAGA
1 TGTATCGATACATGAAAAAGA
223030 TGTATCGATACA
1 TGTATCGATACA
223042 GGTCATTGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (21 bp):
TGTATCGATACATGAAAAAGA
Found at i:223130 original size:33 final size:32
Alignment explanation
Indices: 223073--223140 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 32
223063 GTAGCCAAAT
223073 TTGTATCGATACACACAATATGTATCGATACA
1 TTGTATCGATACACACAATATGTATCGATACA
*
223105 TTGTATGGATACACCACAA-ATTGTATCGATACA
1 TTGTATCGATACA-CACAATA-TGTATCGATACA
223138 TTG
1 TTG
223141 GCTTGTAACG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 13 0.39
33 20 0.61
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (32 bp):
TTGTATCGATACACACAATATGTATCGATACA
Found at i:224597 original size:15 final size:16
Alignment explanation
Indices: 224558--224615 Score: 52
Period size: 15 Copynumber: 3.9 Consensus size: 16
224548 ATGCAATTAA
*
224558 TTAT-AAATTATTA-A
1 TTATAAAATTATTATT
**
224572 TTATATTATTA-TATT
1 TTATAAAATTATTATT
*
224587 TTATAAAATTATTTTT
1 TTATAAAATTATTATT
224603 TTATAAAA-TATTA
1 TTATAAAATTATTA
224616 AAACAAAGCA
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
14 6 0.18
15 17 0.50
16 11 0.32
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TTATAAAATTATTATT
Found at i:224599 original size:18 final size:17
Alignment explanation
Indices: 224576--224615 Score: 57
Period size: 16 Copynumber: 2.4 Consensus size: 17
224566 TATTAATTAT
224576 ATTATTATATTTTATAAA
1 ATTATTAT-TTTTATAAA
224594 ATTATT-TTTTTATAAA
1 ATTATTATTTTTATAAA
224610 A-TATTA
1 ATTATTA
224616 AAACAAAGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 4 0.19
16 10 0.48
17 1 0.05
18 6 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
ATTATTATTTTTATAAA
Found at i:225572 original size:10 final size:10
Alignment explanation
Indices: 225538--225572 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
225528 ACATACTTAT
225538 TATTTATTATA
1 TATTTA-TATA
*
225549 TATATATATA
1 TATTTATATA
225559 TATTTATATA
1 TATTTATATA
225569 TATT
1 TATT
225573 GGACATTGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 17 0.77
11 5 0.23
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
TATTTATATA
Found at i:226132 original size:15 final size:15
Alignment explanation
Indices: 226112--226165 Score: 51
Period size: 15 Copynumber: 3.6 Consensus size: 15
226102 TTCGAATTTC
226112 AAAATATTTTTTATT
1 AAAATATTTTTTATT
226127 AAAATATTTATTTGA--
1 AAAATATTT-TTT-ATT
*
226142 AAAATA-TTATTATT
1 AAAATATTTTTTATT
226156 AAATATATTT
1 AAA-ATATTT
226166 AAATACAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 11
0.73 0.02 0.25
Matches are distributed among these distances:
12 1 0.03
13 2 0.06
14 5 0.16
15 18 0.56
16 5 0.16
17 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (15 bp):
AAAATATTTTTTATT
Found at i:226139 original size:29 final size:30
Alignment explanation
Indices: 226107--226166 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 30
226097 TCCAATTCGA
*
226107 ATTTC-AAAATATTTTTTATTAAA-ATATTT
1 ATTTCAAAAATA-TTATTATTAAATATATTT
*
226136 ATTTGAAAAATATTATTATTAAATATATTT
1 ATTTCAAAAATATTATTATTAAATATATTT
226166 A
1 A
226167 AATACAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 14 0.52
30 13 0.48
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (30 bp):
ATTTCAAAAATATTATTATTAAATATATTT
Found at i:226220 original size:26 final size:26
Alignment explanation
Indices: 226199--226249 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
226189 TAAAATGTAG
226199 TATTTTTAAAATATTATTAAATATAA
1 TATTTTTAAAATATTATTAAATATAA
* * *
226225 TATTTTTATATTATTTTTAAATATA
1 TATTTTTAAAATATTATTAAATATA
226250 TTTAAAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
TATTTTTAAAATATTATTAAATATAA
Found at i:226251 original size:12 final size:12
Alignment explanation
Indices: 226199--226262 Score: 51
Period size: 12 Copynumber: 5.2 Consensus size: 12
226189 TAAAATGTAG
226199 TATTTTTAAA-A
1 TATTTTTAAATA
*
226210 TATTATTAAATA
1 TATTTTTAAATA
*
226222 TAATATTTT-TATA
1 T-AT-TTTTAAATA
226235 TTATTTTTAAATA
1 -TATTTTTAAATA
**
226248 TATTTAAAAATA
1 TATTTTTAAATA
226260 TAT
1 TAT
226263 AAAATATAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
11 9 0.21
12 19 0.45
13 10 0.24
14 4 0.10
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TATTTTTAAATA
Found at i:226300 original size:52 final size:48
Alignment explanation
Indices: 226206--226304 Score: 128
Period size: 47 Copynumber: 2.0 Consensus size: 48
226196 TAGTATTTTT
* *
226206 AAAATATTATTAAATATAATATTTTTATATTATTTTTAAATATATTTA
1 AAAATATTATAAAATATAATATTTTGATATTATTTTTAAATATATTTA
226254 AAAATA-TATAAAATATAATATATTTGATAGTTAAATATTTTAAATATATTT
1 AAAATATTATAAAATATAATAT-TTTGATA-TT--AT-TTTTAAATATATTT
226305 TCAATATAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
47 14 0.32
48 12 0.27
49 2 0.05
51 2 0.05
52 14 0.32
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.49
Consensus pattern (48 bp):
AAAATATTATAAAATATAATATTTTGATATTATTTTTAAATATATTTA
Found at i:227424 original size:25 final size:24
Alignment explanation
Indices: 227396--227454 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 24
227386 TTGGATAAAA
* *
227396 AAATTTAAAATTTTGAAAATTTTTG
1 AAATTTAAAATTTT-AAAATATATG
*
227421 AAATTAATAAATTTTAAAATATATG
1 AAATTTA-AAATTTTAAAATATATG
227446 -AATTTAAAA
1 AAATTTAAAA
227455 ATTCAACACT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
23 3 0.10
24 5 0.17
25 14 0.48
26 7 0.24
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (24 bp):
AAATTTAAAATTTTAAAATATATG
Found at i:230937 original size:2 final size:2
Alignment explanation
Indices: 230930--230956 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
230920 TATAGTGTAC
230930 AT 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 AT A
230957 ATGATTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:231156 original size:30 final size:30
Alignment explanation
Indices: 231122--231412 Score: 129
Period size: 30 Copynumber: 9.5 Consensus size: 30
231112 TACAGCAGAG
231122 CCTCCACCTCCACCAAATCCTCCTCCTCCT
1 CCTCCACCTCCACCAAATCCTCCTCCTCCT
*
231152 CCTCCACCTCCACCAAAGCCTCCACCGAATCCTCCT
1 CCTCCACCTCCACCAAA---TCCTCC---TCCTCCT
* * * * *
231188 CCTCCTCCTCCGCCTACACCTCTACCAAATCCTGCT
1 CCTCCACCTCCACC-AAATC-CT-CC---TCCTCCT
* * * *
231224 CCTTCTCCTCCACC---TCCACCTCCACCAAAT
1 CCTCCACCTCCACCAAATCCTCCTCCTCC---T
* * *
231254 CCTCCTCCTCCTCC---TCCTCC-CGCTCCA
1 CCTCCACCTCCACCAAATCCTCCTC-CTCCT
231281 CCTCCACCTCCACCAAATCCTCCTCCTCCT
1 CCTCCACCTCCACCAAATCCTCCTCCTCCT
** *
231311 CCTCC-CGCTCCACC-TCTACCTCCTCCTCCA
1 CCTCCAC-CTCCACCAAAT-CCTCCTCCTCCT
* *
231341 CCTCCACCTCCACC---TCCACCTCCTCCC
1 CCTCCACCTCCACCAAATCCTCCTCCTCCT
* ** * *
231368 CCTACACCTTTACCAAATCCTGCTCCTTCT
1 CCTCCACCTCCACCAAATCCTCCTCCTCCT
231398 CCTCCACCTCCACCA
1 CCTCCACCTCCACCA
231413 CCACCAAATC
Statistics
Matches: 201, Mismatches: 37, Indels: 46
0.71 0.13 0.16
Matches are distributed among these distances:
27 37 0.18
28 1 0.00
29 3 0.01
30 106 0.53
31 3 0.01
32 1 0.00
33 5 0.02
34 1 0.00
35 1 0.00
36 41 0.20
37 2 0.01
ACGTcount: A:0.16, C:0.59, G:0.02, T:0.23
Consensus pattern (30 bp):
CCTCCACCTCCACCAAATCCTCCTCCTCCT
Found at i:231187 original size:42 final size:39
Alignment explanation
Indices: 231125--231444 Score: 230
Period size: 36 Copynumber: 8.0 Consensus size: 39
231115 AGCAGAGCCT
231125 CCACCTCCACCAAATCCTCCTCCTCCTCCTCCACCTCCA
1 CCACCTCCACCAAATCCTCCTCCTCCTCCTCCACCTCCA
* *
231164 CCAAAGCCTCCACCGAATCCTCCTCCTCCTCCTCCGCCT--A
1 CC--A-CCTCCACCAAATCCTCCTCCTCCTCCTCCACCTCCA
* * *
231204 -CACCTCTACCAAATCCTGCTCCTTCTCCTCCACCT---
1 CCACCTCCACCAAATCCTCCTCCTCCTCCTCCACCTCCA
*
231239 CCACCTCCACCAAATCCTCCTCCTCCTCCTCCTCCCGCTCCA
1 CCACCTCCACCAAATCCTCCTCCTCCTCCT-C-CAC-CTCCA
231281 CCTCCACCTCCACCAAATCCTCCTCCTCCTCCTCC-CGCTCCA
1 ---CCACCTCCACCAAATCCTCCTCCTCCTCCTCCAC-CTCCA
* ** * * *
231323 CCTCTACCTCCTCCTCCA-CCTCCACCTCCACCTCCACCTCCT
1 -C-C-ACCTCCACC-AAATCCTCCTCCTCCTCCTCCACCTCCA
* * *
231365 CCCCCTACACCTTTACCAAATCCTGCTCCTTCTCCTCCACCTCCA
1 CCACCT---CC---ACCAAATCCTCCTCCTCCTCCTCCACCTCCA
* *
231410 CCA---CCACCAAATCCTCCTCCTCCACTTCCACCTCC
1 CCACCTCCACCAAATCCTCCTCCTCCTCCTCCACCTCC
231445 TCCTCCACCT
Statistics
Matches: 225, Mismatches: 32, Indels: 51
0.73 0.10 0.17
Matches are distributed among these distances:
36 80 0.36
37 2 0.01
38 2 0.01
39 10 0.04
40 3 0.01
41 3 0.01
42 67 0.30
43 3 0.01
44 2 0.01
45 53 0.24
ACGTcount: A:0.16, C:0.59, G:0.02, T:0.23
Consensus pattern (39 bp):
CCACCTCCACCAAATCCTCCTCCTCCTCCTCCACCTCCA
Found at i:231192 original size:6 final size:6
Alignment explanation
Indices: 231181--231366 Score: 83
Period size: 6 Copynumber: 31.0 Consensus size: 6
231171 CTCCACCGAA
* * * *** * *
231181 TCCTCC TCCTCC TCCTCC GCCTAC ACCT-C TACCAAA TCCTGC TCCTTC
1 TCCTCC TCCTCC TCCTCC TCCTCC TCCTCC T-CCTCC TCCTCC TCCTCC
* * * ***
231229 TCCTCC ACCTCC ACCTCC ACCAAA TCCTCC TCCTCC TCCTCC TCC-CGC
1 TCCTCC TCCTCC TCCTCC TCCTCC TCCTCC TCCTCC TCCTCC TCCTC-C
* * * *** *
231277 TCCACC TCCACC TCCACC AAATCC TCCTCC TCCTCC TCC-CGC TCCACC
1 TCCTCC TCCTCC TCCTCC TCCTCC TCCTCC TCCTCC TCCTC-C TCCTCC
* * * *
231325 T-CTACC TCCTCC TCCACC TCCACC TCCACC TCCACC TCCTCC
1 TCCT-CC TCCTCC TCCTCC TCCTCC TCCTCC TCCTCC TCCTCC
231367 CCCTACACCT
Statistics
Matches: 143, Mismatches: 29, Indels: 16
0.76 0.15 0.09
Matches are distributed among these distances:
5 4 0.03
6 134 0.94
7 5 0.03
ACGTcount: A:0.13, C:0.61, G:0.02, T:0.24
Consensus pattern (6 bp):
TCCTCC
Found at i:231232 original size:45 final size:44
Alignment explanation
Indices: 231139--231408 Score: 172
Period size: 45 Copynumber: 6.2 Consensus size: 44
231129 CTCCACCAAA
* * * *
231139 TCCTCCTCCTCCTCCTCCACCTCCACCAAAGCCTCCACCGAATCCTCC
1 TCCTCCTCCTCC-CCTACACCTCTACCAAATCCTCCTCC---TCCTCC
*
231187 TCCTCCTCCTCCGCCTACACCTCTACCAAATCCTGCTCCT--T-C
1 TCCTCCTCCTCC-CCTACACCTCTACCAAATCCTCCTCCTCCTCC
* *
231229 TCCTCCACCT---C--CACCTCCACCAAATCCTCCTCCTCCTCC
1 TCCTCCTCCTCCCCTACACCTCTACCAAATCCTCCTCCTCCTCC
* *
231268 TCCTCC-CGCTCCACCTCCACCTCCACCAAATCCTCCTCCTCCTCC
1 TCCTCCTC-CTCC-CCTACACCTCTACCAAATCCTCCTCCTCCTCC
* * * * *
231313 TCC-CGCTCCACCTCTACCTCCTCCT-CC--A-CCTCCACCTCCACC
1 TCCTC-CTCCTCCCCTA-CACCT-CTACCAAATCCTCCTCCTCCTCC
* * * *
231355 TCCACCTCCTCCCCCTACACCTTTACCAAATCCTGCTCCTTCTCC
1 TCCTCCTCCT-CCCCTACACCTCTACCAAATCCTCCTCCTCCTCC
*
231400 TCCACCTCC
1 TCCTCCTCC
231409 ACCACCACCA
Statistics
Matches: 178, Mismatches: 24, Indels: 43
0.73 0.10 0.18
Matches are distributed among these distances:
36 21 0.12
38 3 0.02
39 9 0.05
41 1 0.01
42 35 0.20
43 9 0.05
44 4 0.02
45 61 0.34
46 2 0.01
48 33 0.19
ACGTcount: A:0.14, C:0.59, G:0.03, T:0.24
Consensus pattern (44 bp):
TCCTCCTCCTCCCCTACACCTCTACCAAATCCTCCTCCTCCTCC
Found at i:231430 original size:30 final size:30
Alignment explanation
Indices: 231268--231444 Score: 141
Period size: 30 Copynumber: 5.8 Consensus size: 30
231258 CTCCTCCTCC
231268 TCCTCC-CGCTCCACCTCCACCTCCACCAAA
1 TCCTCCTC-CTCCACCTCCACCTCCACCAAA
* **
231298 TCCTCCTCCTCCTCCTCC-CGCTCCACC-TC
1 TCCTCCTCCTCCACCTCCAC-CTCCACCAAA
231327 TACCTCCTCCTCCACCTCCACCTCCACC---
1 T-CCTCCTCCTCCACCTCCACCTCCACCAAA
* * * **
231355 TCCACCTCCTCCCCCTACACCTTTACCAAA
1 TCCTCCTCCTCCACCTCCACCTCCACCAAA
*
231385 TCCTGCTCCTTCTCCTCCACCTCCACCACCACCAAA
1 T-C--CT-C--CTCCTCCACCTCCACCTCCACCAAA
*
231421 TCCTCCTCCTCCACTTCCACCTCC
1 TCCTCCTCCTCCACCTCCACCTCC
231445 TCCTCCACCT
Statistics
Matches: 117, Mismatches: 17, Indels: 26
0.73 0.11 0.16
Matches are distributed among these distances:
27 21 0.18
28 1 0.01
29 2 0.02
30 63 0.54
31 3 0.03
32 1 0.01
33 3 0.03
34 1 0.01
35 1 0.01
36 21 0.18
ACGTcount: A:0.15, C:0.60, G:0.02, T:0.23
Consensus pattern (30 bp):
TCCTCCTCCTCCACCTCCACCTCCACCAAA
Found at i:231440 original size:36 final size:36
Alignment explanation
Indices: 231379--231453 Score: 96
Period size: 36 Copynumber: 2.1 Consensus size: 36
231369 CTACACCTTT
* * *
231379 ACCAAATCCTGCTCCTTCTCCTCCACCTCCACCACC
1 ACCAAATCCTCCTCCTCCACCTCCACCTCCACCACC
* * *
231415 ACCAAATCCTCCTCCTCCACTTCCACCTCCTCCTCC
1 ACCAAATCCTCCTCCTCCACCTCCACCTCCACCACC
231451 ACC
1 ACC
231454 TTTTCCAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.19, C:0.57, G:0.01, T:0.23
Consensus pattern (36 bp):
ACCAAATCCTCCTCCTCCACCTCCACCTCCACCACC
Found at i:231923 original size:96 final size:99
Alignment explanation
Indices: 231714--231923 Score: 243
Period size: 96 Copynumber: 2.2 Consensus size: 99
231704 GCACTACTAC
* * * * *
231714 TGCTTCCACTTCCGCCATTATTTCCACCAAGCCCTCCTCGTCCTCCTCTTATTCCACCTCCAGAA
1 TGCTTCCACTTCCACCATTATTTCCACCAAGACCTCCTCGTCCTCCTCTAACTCCACCTCCAAAA
* *
231779 CCAACGTTAACACCACTCCCACCATCAGCACTAG
66 CCAACGTTAACACCACTCCCACCATCAGCACCAA
* **
231813 TGCTTCCACTTCCACCATTATTTCCACCAAGACCTCCTTGTCCT-C-C-AACTCCACCTTTAAAA
1 TGCTTCCACTTCCACCATTATTTCCACCAAGACCTCCTCGTCCTCCTCTAACTCCACCTCCAAAA
231875 CCAACAG-TAACACCAC-CTCCACCAGT-AGCACCAA
66 CCAAC-GTTAACACCACTC-CCACCA-TCAGCACCAA
* *
231909 TGCTACCACCTCCAC
1 TGCTTCCACTTCCAC
231924 TACCTCCTGC
Statistics
Matches: 96, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
95 1 0.01
96 50 0.52
97 3 0.03
98 1 0.01
99 41 0.43
ACGTcount: A:0.25, C:0.44, G:0.07, T:0.24
Consensus pattern (99 bp):
TGCTTCCACTTCCACCATTATTTCCACCAAGACCTCCTCGTCCTCCTCTAACTCCACCTCCAAAA
CCAACGTTAACACCACTCCCACCATCAGCACCAA
Found at i:233680 original size:32 final size:31
Alignment explanation
Indices: 233605--233684 Score: 97
Period size: 33 Copynumber: 2.5 Consensus size: 31
233595 TTAAGAAATT
** *
233605 TGATCAAAGTTAACCAAAAGTGTACAATATC
1 TGATCAAAGTTAATAAAAAGTGTAAAATATC
*
233636 TAGGATCAAAGTTAATAAAAAGTGTATAAATATG
1 T--GATCAAAGTTAATAAAAAGTGTA-AAATATC
233670 TGATCAAAGTTAATA
1 TGATCAAAGTTAATA
233685 GCTTTAGAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
31 1 0.02
32 14 0.33
33 21 0.50
34 6 0.14
ACGTcount: A:0.47, C:0.09, G:0.15, T:0.29
Consensus pattern (31 bp):
TGATCAAAGTTAATAAAAAGTGTAAAATATC
Found at i:235265 original size:72 final size:74
Alignment explanation
Indices: 235100--235273 Score: 271
Period size: 74 Copynumber: 2.4 Consensus size: 74
235090 GACTAGGATG
* * *
235100 TTCCTACACGAGCAAAAAAATTATTAAATATTATTTAAATATTAAAATATATAATTAAAAAATTT
1 TTCCTACACGAGC-AAAAAATTATTGAATATTATTGAAATATTAAAATATATAATTAAAAAATAT
235165 TTTAATTTTT
65 TTTAATTTTT
* * *
235175 TTCTTACACAAGCAAAAAATTATTGAATATTATTGAAATATTGAAATATATAATTAAAAAA-ATT
1 TTCCTACACGAGCAAAAAATTATTGAATATTATTGAAATATTAAAATATATAATTAAAAAATATT
235239 TTAA-TTTT
66 TTAATTTTT
235247 TTCCTACACGAGCAAAAAATTATTGAA
1 TTCCTACACGAGCAAAAAATTATTGAA
235274 ATATATAATT
Statistics
Matches: 91, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
72 29 0.32
73 6 0.07
74 45 0.49
75 11 0.12
ACGTcount: A:0.48, C:0.08, G:0.05, T:0.39
Consensus pattern (74 bp):
TTCCTACACGAGCAAAAAATTATTGAATATTATTGAAATATTAAAATATATAATTAAAAAATATT
TTAATTTTT
Found at i:238175 original size:2 final size:2
Alignment explanation
Indices: 238170--238201 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
238160 TTGCATCTAC
238170 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
238202 CTTCTACGAA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:238332 original size:2 final size:2
Alignment explanation
Indices: 238325--238368 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
238315 TTTTGTCTCC
238325 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
238367 AT
1 AT
238369 TCTGCTAAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:238461 original size:166 final size:165
Alignment explanation
Indices: 238170--238472 Score: 552
Period size: 166 Copynumber: 1.8 Consensus size: 165
238160 TTGCATCTAC
*
238170 ATATATATATATATATATATATATATATATATCTTCTACGAAATTATTTTATTCAGGATTTAGTT
1 ATATATATATATATATATATATATATATATATATTCTACGAAATTATTTTATTCAGGATTTAGTT
* *
238235 CCCTTAATACCTTTTTCTAATTTCAATTTCTTTTTTGTTTCTTTTTCTAATGTTGACTTCTCTAT
66 CCCTTAATACCTTTTTCTAATTTCAATTTCTTTTTCGTTTCTTTTTCTAATGTTGACTTCTCAAT
238300 GGGCTAGCATCTACATTTTGTCTCCATATATATAT
131 GGGCTAGCATCTACATTTTGTCTCCATATATATAT
* *
238335 ATATATATATATATATATATATATATATATATATTCTGCTAAATTATTTTATTCAGGATTTAGTT
1 ATATATATATATATATATATATATATATATATATTCTACGAAATTATTTTATTCAGGATTTAGTT
238400 CCCCTTAATACCTTTTTCTAATTTCAATTTCTTTTTCGTTTCTTTTTCTAATGTTGACTTCTCAA
66 -CCCTTAATACCTTTTTCTAATTTCAATTTCTTTTTCGTTTCTTTTTCTAATGTTGACTTCTCAA
238465 TGGGCTAG
130 TGGGCTAG
238473 TTTCTAAGTA
Statistics
Matches: 132, Mismatches: 5, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
165 62 0.47
166 70 0.53
ACGTcount: A:0.27, C:0.14, G:0.08, T:0.51
Consensus pattern (165 bp):
ATATATATATATATATATATATATATATATATATTCTACGAAATTATTTTATTCAGGATTTAGTT
CCCTTAATACCTTTTTCTAATTTCAATTTCTTTTTCGTTTCTTTTTCTAATGTTGACTTCTCAAT
GGGCTAGCATCTACATTTTGTCTCCATATATATAT
Found at i:239966 original size:17 final size:17
Alignment explanation
Indices: 239946--239988 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
239936 AAAAGTGATA
*
239946 GAATAAAAAATGAGAAT
1 GAATAAAAAATGAGAAC
239963 GAATAAAAAATGAGAAC
1 GAATAAAAAATGAGAAC
*
239980 AAATAAAAA
1 GAATAAAAA
239989 GGGAGACGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.70, C:0.02, G:0.14, T:0.14
Consensus pattern (17 bp):
GAATAAAAAATGAGAAC
Found at i:240482 original size:21 final size:21
Alignment explanation
Indices: 240456--240515 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
240446 TACTCAAATA
*
240456 ATTGTATCGATACATTCTGGT
1 ATTGTATCGATACATTCTGGG
*
240477 ATTGTATCGATACATTATGGG
1 ATTGTATCGATACATTCTGGG
* * *
240498 ATTATATCAATAGATTCT
1 ATTGTATCGATACATTCT
240516 AAGTTTTTTG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.42
Consensus pattern (21 bp):
ATTGTATCGATACATTCTGGG
Found at i:242610 original size:16 final size:16
Alignment explanation
Indices: 242568--242610 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
242558 TTTTTATTTA
242568 TTAATAAAATTATAATT
1 TTAATAAAA-TATAATT
*
242585 TGACAT-AAATATAATT
1 TTA-ATAAAATATAATT
242601 TTAATAAAAT
1 TTAATAAAAT
242611 TTAGCTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
15 2 0.09
16 13 0.59
17 5 0.23
18 2 0.09
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (16 bp):
TTAATAAAATATAATT
Found at i:244433 original size:23 final size:23
Alignment explanation
Indices: 244401--244470 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
244391 GAATCTCTTT
*
244401 TTAGCATTGGCCAATTAAAAGAT
1 TTAGCATTGGCCAATTAAAAGAA
** * *
244424 TTAGTGTTGGCTAGTTAAAAGAA
1 TTAGCATTGGCCAATTAAAAGAA
*
244447 TTAGCATTGGCCGATTAAAAGAA
1 TTAGCATTGGCCAATTAAAAGAA
244470 T
1 T
244471 GAACCTTGTT
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.37, C:0.10, G:0.21, T:0.31
Consensus pattern (23 bp):
TTAGCATTGGCCAATTAAAAGAA
Found at i:252079 original size:21 final size:22
Alignment explanation
Indices: 252055--252095 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
252045 TTTTTAAAGG
252055 TCACCAA-ATCCTA-AAAATAAA
1 TCACCAAGAT-CTATAAAATAAA
252076 TCACCAAGATCTATAAAATA
1 TCACCAAGATCTATAAAATA
252096 CCAAAAATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.54, C:0.22, G:0.02, T:0.22
Consensus pattern (22 bp):
TCACCAAGATCTATAAAATAAA
Found at i:253746 original size:16 final size:15
Alignment explanation
Indices: 253725--253766 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
253715 GATAAAATGA
253725 TATTTATTTATTATTT
1 TATTTATTT-TTATTT
253741 TATTTATTTTTATTT
1 TATTTATTTTTATTT
*
253756 TTTTTCATTTT
1 TATTT-ATTTT
253767 CAAAAATTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (15 bp):
TATTTATTTTTATTT
Found at i:253868 original size:183 final size:183
Alignment explanation
Indices: 253594--254056 Score: 660
Period size: 183 Copynumber: 2.5 Consensus size: 183
253584 CCAAAAAAAA
* * *
253594 ATTTCATAGCTTAATGGAAAATCGAAAAGATACAAAAAGTTTTAAAGATTTCTATAGCCTTACGG
1 ATTTCATAGCTTAATGGAAAATCAAAAAGATACGAAAAGTTTTAAAGATTTCTATA-CCTTACGA
*
253659 ATGACCATAGGAATATTAAAAATCTTGAAAAATTAAGATAATAATTTTTATTTAGTGATAAAATG
65 ACGACCATAGGAATATTAAAAATCTTGAAAAATTAAGATAATAATTTTTATTTAGTGATAAAATG
* *
253724 ATATTTATTTATTATTTTATTTATTTTTA-TTTTTTTTCATTTTCAAAAATTTC
130 ATATTTATTTATTATTTTATTTATTTTTACTATATTTTCATTTTCAAAAATTTC
* * * * * * *
253777 ATTTCGTAGCTTAATGGAGAACCAAAAAGATACGAAAAGTATTGAAGATCTCTATACCATTATGA
1 ATTTCATAGCTTAATGGAAAATCAAAAAGATACGAAAAGTTTTAAAGATTTCTATACC-TTACGA
253842 ACGACCATAGGAATATTAAAAATCTTGAAAAATTAAGATAATAATTTTTATTTAGTGATAAAATG
65 ACGACCATAGGAATATTAAAAATCTTGAAAAATTAAGATAATAATTTTTATTTAGTGATAAAATG
** *
253907 ATATTTATTTATTATTTTATTTATTTTTACTATATTTTCATTTTGGAAATTTTC
130 ATATTTATTTATTATTTTATTTATTTTTACTATATTTTCATTTTCAAAAATTTC
* * * * *
253961 ATTTCATACCTTAATGGATAGTCAAAAAGATACGAAAAGTTTTAAAGATTTCTATACCCCTACTA
1 ATTTCATAGCTTAATGGAAAATCAAAAAGATACGAAAAGTTTTAAAGATTTCTATA-CCTTACGA
** * *
254026 AAAATCATAGGAATATTAAAAAT-TTAAAAAA
65 ACGACCATAGGAATATTAAAAATCTTGAAAAA
254057 AGAAATGACC
Statistics
Matches: 246, Mismatches: 31, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
182 2 0.01
183 152 0.62
184 90 0.37
185 2 0.01
ACGTcount: A:0.41, C:0.09, G:0.10, T:0.40
Consensus pattern (183 bp):
ATTTCATAGCTTAATGGAAAATCAAAAAGATACGAAAAGTTTTAAAGATTTCTATACCTTACGAA
CGACCATAGGAATATTAAAAATCTTGAAAAATTAAGATAATAATTTTTATTTAGTGATAAAATGA
TATTTATTTATTATTTTATTTATTTTTACTATATTTTCATTTTCAAAAATTTC
Found at i:254913 original size:9 final size:9
Alignment explanation
Indices: 254894--254929 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
254884 CGAAAGACCA
254894 TTTTA-TTT
1 TTTTATTTT
254902 TTTTATTTT
1 TTTTATTTT
*
254911 TTTTGTTTT
1 TTTTATTTT
254920 TTTTATTTT
1 TTTTATTTT
254929 T
1 T
254930 ATACTCTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
8 5 0.20
9 20 0.80
ACGTcount: A:0.08, C:0.00, G:0.03, T:0.89
Consensus pattern (9 bp):
TTTTATTTT
Found at i:255689 original size:163 final size:166
Alignment explanation
Indices: 255340--255711 Score: 373
Period size: 163 Copynumber: 2.3 Consensus size: 166
255330 ACAATATTAG
* * * **
255340 ATGAATTTTAAAAATTT-TAAATTAAGAAAAATCCGCTCGAAAACCTTTAAGAAATAGAAAACTC
1 ATGAATTTT-AAAATTTATAAATCAAGAAAAATCCCCTCAAAAACCAGTAAGAAATAGAAAACTC
* * ***
255404 GATTTTTTGAAAACAGTTGAATTTCAAAGAAAAACGAAAAAACTTATGAAAATAAATAAAATTTT
65 GATATTTCGAAAACAGGAAAATTTCAAAGAAAAACGAAAAAACTTATGAAAATAAATAAAATTTT
* * * * *
255469 TAAAATTGATTTACTATGAATTAAATAATGTTATCTC
130 TAAAACTAATTTAATATGAATTAAACAATGATATCTC
* * * * *
255506 ATGAATTCTAAAAATTATAAATCAAGAAAAATCCCCTCAAAAACCAGTACGAAATAGAAAATTCT
1 ATGAATTTTAAAATTTATAAATCAAGAAAAATCCCCTCAAAAACCAGTAAGAAATAGAAAACTCG
* * *
255571 ATATTTCG-AAATAGGAAAATTTC-AAGAAAAATG-AAAAA-TTCAT-AAAATAAA-AGAATTTT
66 ATATTTCGAAAACAGGAAAATTTCAAAGAAAAACGAAAAAACTT-ATGAAAATAAATA-AAATTT
* * * *
255630 TTCAAAACTAATTTAATTTGAATTAGACAGTGATATTTC
129 TT-AAAACTAATTTAATATGAATTAAACAATGATATCTC
* * *
255669 ATGAATTTTAAGATTTATAAA-CAAGTGAAAATCCTCTCAAAAA
1 ATGAATTTTAAAATTTATAAATCAAG-AAAAATCCCCTCAAAAA
255712 AAGTTTACGA
Statistics
Matches: 169, Mismatches: 32, Indels: 13
0.79 0.15 0.06
Matches are distributed among these distances:
161 1 0.01
162 21 0.12
163 67 0.40
164 9 0.05
165 17 0.10
166 54 0.32
ACGTcount: A:0.49, C:0.10, G:0.09, T:0.31
Consensus pattern (166 bp):
ATGAATTTTAAAATTTATAAATCAAGAAAAATCCCCTCAAAAACCAGTAAGAAATAGAAAACTCG
ATATTTCGAAAACAGGAAAATTTCAAAGAAAAACGAAAAAACTTATGAAAATAAATAAAATTTTT
AAAACTAATTTAATATGAATTAAACAATGATATCTC
Found at i:258091 original size:13 final size:13
Alignment explanation
Indices: 258073--258136 Score: 68
Period size: 13 Copynumber: 5.4 Consensus size: 13
258063 ACATTTCTTC
258073 ATGTATCGATACA
1 ATGTATCGATACA
258086 ATGTATCGATAC-
1 ATGTATCGATACA
*
258098 A--T-T-G-TACC
1 ATGTATCGATACA
258106 ATGTATCGATACA
1 ATGTATCGATACA
258119 ATGTATCGATACA
1 ATGTATCGATACA
*
258132 TTGTA
1 ATGTA
258137 CCATGTATCG
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
7 3 0.07
8 2 0.05
9 1 0.02
10 2 0.05
11 1 0.02
12 2 0.05
13 32 0.74
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:258091 original size:33 final size:33
Alignment explanation
Indices: 258053--258152 Score: 168
Period size: 33 Copynumber: 3.0 Consensus size: 33
258043 GTTACAAGCT
258053 ATGTATCGATACATT-T-CTTCATGTATCGATACA
1 ATGTATCGATACATTGTAC--CATGTATCGATACA
258086 ATGTATCGATACATTGTACCATGTATCGATACA
1 ATGTATCGATACATTGTACCATGTATCGATACA
258119 ATGTATCGATACATTGTACCATGTATCGATACA
1 ATGTATCGATACATTGTACCATGTATCGATACA
258152 A
1 A
258153 ATAGTAATAG
Statistics
Matches: 65, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
33 63 0.97
34 1 0.02
35 1 0.02
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (33 bp):
ATGTATCGATACATTGTACCATGTATCGATACA
Found at i:258111 original size:20 final size:20
Alignment explanation
Indices: 258086--258151 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
258076 TATCGATACA
258086 ATGTATCGATACATTGTACC
1 ATGTATCGATACATTGTACC
258106 ATGTATCGATAC-----A--
1 ATGTATCGATACATTGTACC
258119 ATGTATCGATACATTGTACC
1 ATGTATCGATACATTGTACC
258139 ATGTATCGATACA
1 ATGTATCGATACA
258152 AATAGTAATA
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 12 0.31
15 1 0.03
18 1 0.03
20 25 0.64
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACATTGTACC
Found at i:258207 original size:21 final size:21
Alignment explanation
Indices: 258181--258238 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
258171 CTGCCAGTTT
258181 CATGTATCGATACAATTTGTC
1 CATGTATCGATACAATTTGTC
*
258202 CATGTATCGATATAATTTGTC
1 CATGTATCGATACAATTTGTC
258223 CATGTATCGATACAAT
1 CATGTATCGATACAAT
258239 GTATCGATAC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (21 bp):
CATGTATCGATACAATTTGTC
Found at i:258242 original size:13 final size:13
Alignment explanation
Indices: 258224--258283 Score: 60
Period size: 13 Copynumber: 5.1 Consensus size: 13
258214 TAATTTGTCC
258224 ATGTATCGATACA
1 ATGTATCGATACA
258237 ATGTATCGATACA
1 ATGTATCGATACA
* *
258250 A---AGC-A-GC-
1 ATGTATCGATACA
258257 ATGTATCGATACA
1 ATGTATCGATACA
258270 ATGTATCGATACA
1 ATGTATCGATACA
258283 A
1 A
258284 AGCAGCATGT
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
7 1 0.03
8 1 0.03
9 1 0.03
10 4 0.11
11 1 0.03
12 1 0.03
13 28 0.76
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.27
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:258262 original size:20 final size:20
Alignment explanation
Indices: 258237--258302 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
258227 TATCGATACA
258237 ATGTATCGATACAAAGCAGC
1 ATGTATCGATACAAAGCAGC
258257 ATGTATCGAT----A-CA--
1 ATGTATCGATACAAAGCAGC
258270 ATGTATCGATACAAAGCAGC
1 ATGTATCGATACAAAGCAGC
258290 ATGTATCGATACA
1 ATGTATCGATACA
258303 TCTGGATGTG
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 10 0.26
15 2 0.05
16 1 0.03
17 1 0.03
18 2 0.05
20 23 0.59
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.24
Consensus pattern (20 bp):
ATGTATCGATACAAAGCAGC
Found at i:258265 original size:33 final size:33
Alignment explanation
Indices: 258223--258302 Score: 160
Period size: 33 Copynumber: 2.4 Consensus size: 33
258213 ATAATTTGTC
258223 CATGTATCGATACAATGTATCGATACAAAGCAG
1 CATGTATCGATACAATGTATCGATACAAAGCAG
258256 CATGTATCGATACAATGTATCGATACAAAGCAG
1 CATGTATCGATACAATGTATCGATACAAAGCAG
258289 CATGTATCGATACA
1 CATGTATCGATACA
258303 TCTGGATGTG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.25
Consensus pattern (33 bp):
CATGTATCGATACAATGTATCGATACAAAGCAG
Found at i:258903 original size:52 final size:52
Alignment explanation
Indices: 258845--258944 Score: 200
Period size: 52 Copynumber: 1.9 Consensus size: 52
258835 TCTCCCCTTT
258845 AAAAAATTCTCCCCCTTAAACGATTATCTTCTCCCCCTTATGTAAAAAATAA
1 AAAAAATTCTCCCCCTTAAACGATTATCTTCTCCCCCTTATGTAAAAAATAA
258897 AAAAAATTCTCCCCCTTAAACGATTATCTTCTCCCCCTTATGTAAAAA
1 AAAAAATTCTCCCCCTTAAACGATTATCTTCTCCCCCTTATGTAAAAA
258945 TTTATTTTCA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.37, C:0.28, G:0.04, T:0.31
Consensus pattern (52 bp):
AAAAAATTCTCCCCCTTAAACGATTATCTTCTCCCCCTTATGTAAAAAATAA
Found at i:269716 original size:20 final size:19
Alignment explanation
Indices: 269691--269728 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
269681 CTGCCAGTTT
269691 CATGTATCGATACAATTGTC
1 CATGTATCGATAC-ATTGTC
269711 CATGTATCGATACATTGT
1 CATGTATCGATACATTGT
269729 ATCGATACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (19 bp):
CATGTATCGATACATTGTC
Found at i:269731 original size:13 final size:13
Alignment explanation
Indices: 269713--269737 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
269703 CAATTGTCCA
269713 TGTATCGATACAT
1 TGTATCGATACAT
269726 TGTATCGATACA
1 TGTATCGATACA
269738 AAGCATAATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:270757 original size:17 final size:17
Alignment explanation
Indices: 270735--270768 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
270725 GAAGTGATTA
*
270735 ACTCTCAGATGGACGGT
1 ACTCTCAAATGGACGGT
270752 ACTCTCAAATGGACGGT
1 ACTCTCAAATGGACGGT
270769 GTCATTGAAG
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:0.24, G:0.26, T:0.24
Consensus pattern (17 bp):
ACTCTCAAATGGACGGT
Found at i:276787 original size:3 final size:3
Alignment explanation
Indices: 276779--276824 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
276769 TCCGACTCAC
*
276779 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CTT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
276825 TTTGATGGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.30, C:0.35, G:0.00, T:0.35
Consensus pattern (3 bp):
CAT
Found at i:278532 original size:19 final size:20
Alignment explanation
Indices: 278492--278538 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
278482 CAGTTTCATG
* *
278492 TATCGATACAATTATCCATA
1 TATCGATACAATGATACATA
278512 TATCGATACAATGA-ACATA
1 TATCGATACAATGATACATA
278531 TATCGATA
1 TATCGATA
278539 ATTATATCGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.43, C:0.17, G:0.09, T:0.32
Consensus pattern (20 bp):
TATCGATACAATGATACATA
Found at i:279513 original size:19 final size:19
Alignment explanation
Indices: 279489--279531 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
279479 AAAGAAATAT
279489 TTTTGTTTTCATTGACCTA
1 TTTTGTTTTCATTGACCTA
279508 TTTTGTTTTCATTGACCTA
1 TTTTGTTTTCATTGACCTA
279527 TTTTG
1 TTTTG
279532 CATTTTATGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.14, C:0.14, G:0.12, T:0.60
Consensus pattern (19 bp):
TTTTGTTTTCATTGACCTA
Found at i:284299 original size:44 final size:44
Alignment explanation
Indices: 284249--284346 Score: 169
Period size: 44 Copynumber: 2.2 Consensus size: 44
284239 GAAGAATTTT
* *
284249 GAAATTTTTTTAATATGATTTCATCGTCAAATTTATTATTTATA
1 GAAATTTTTTTAATATGATTTCACCATCAAATTTATTATTTATA
*
284293 GAAATTTTTTTAATATGATTTCACCATCAAATTTCTTATTTATA
1 GAAATTTTTTTAATATGATTTCACCATCAAATTTATTATTTATA
284337 GAAATTTTTT
1 GAAATTTTTT
284347 AAACCTCTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 51 1.00
ACGTcount: A:0.34, C:0.08, G:0.06, T:0.52
Consensus pattern (44 bp):
GAAATTTTTTTAATATGATTTCACCATCAAATTTATTATTTATA
Found at i:288279 original size:24 final size:24
Alignment explanation
Indices: 288247--288292 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
288237 GGGGTACATT
288247 GGTAAATTTTTGAATTCTTTAGTA
1 GGTAAATTTTTGAATTCTTTAGTA
288271 GGTAAATTTTTGAATTCTTTAG
1 GGTAAATTTTTGAATTCTTTAG
288293 AGTCACGAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.28, C:0.04, G:0.17, T:0.50
Consensus pattern (24 bp):
GGTAAATTTTTGAATTCTTTAGTA
Found at i:291851 original size:34 final size:32
Alignment explanation
Indices: 291769--291856 Score: 83
Period size: 34 Copynumber: 2.7 Consensus size: 32
291759 TTTAAATTAA
*
291769 ATTTAAATTTATT--TAATAATTTATTTTATT
1 ATTTAAATTTATTAATAATAATTTATATTATT
* *
291799 ATTTAAAATATTA-AAATAATATTTTTATATTATT
1 ATTT-AAAT-TTATTAATAATA-ATTTATATTATT
291833 ATTTATAATTTATTAATAAATAAT
1 ATTTA-AATTTATTAAT-AATAAT
291857 AATTTATTTC
Statistics
Matches: 45, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
30 4 0.09
31 4 0.09
32 3 0.07
33 9 0.20
34 21 0.47
35 4 0.09
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (32 bp):
ATTTAAATTTATTAATAATAATTTATATTATT
Found at i:292410 original size:20 final size:18
Alignment explanation
Indices: 292384--292434 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
292374 ATGATAATTA
292384 AATATTATAATTATATTT
1 AATATTATAATTATATTT
* *
292402 ATTATATTAAAAATATATTT
1 A--ATATTATAATTATATTT
292422 AATGATTATAATT
1 AAT-ATTATAATT
292435 TAAATTTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
18 3 0.12
19 7 0.27
20 16 0.62
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (18 bp):
AATATTATAATTATATTT
Found at i:292802 original size:2 final size:2
Alignment explanation
Indices: 292795--292819 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
292785 AACAGAAGGC
292795 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
292820 CACATGAAGT
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:293896 original size:19 final size:20
Alignment explanation
Indices: 293859--293899 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
293849 ATATATTTAA
293859 TATAAATATATTTAATTTTT
1 TATAAATATATTTAATTTTT
* *
293879 TATAAAT-TTTTTATTTTTT
1 TATAAATATATTTAATTTTT
293898 TA
1 TA
293900 AAAAATTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TATAAATATATTTAATTTTT
Found at i:294450 original size:13 final size:13
Alignment explanation
Indices: 294426--294459 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
294416 AACTTTACAG
294426 TAAATATCAGTTT
1 TAAATATCAGTTT
* *
294439 TGAATATTAGTTT
1 TAAATATCAGTTT
294452 TAAATATC
1 TAAATATC
294460 GATAATAAAA
Statistics
Matches: 17, Mismatches: 4, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (13 bp):
TAAATATCAGTTT
Found at i:295299 original size:25 final size:30
Alignment explanation
Indices: 295272--295327 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 30
295262 ATTAATATTT
295272 AAATATTA-TA-T-AATAA-AATTTAAATAA
1 AAATATTATTATTAAATAATAATTTAAAT-A
295299 AAATATTATTATTAAATAATAATTTAAAT
1 AAATATTATTATTAAATAATAATTTAAAT
295328 TATATCAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 8 0.32
28 2 0.08
29 1 0.04
30 5 0.20
31 9 0.36
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (30 bp):
AAATATTATTATTAAATAATAATTTAAATA
Found at i:295352 original size:15 final size:15
Alignment explanation
Indices: 295286--295353 Score: 50
Period size: 15 Copynumber: 4.5 Consensus size: 15
295276 ATTATATAAT
295286 AAAATTTAAA-TAAA
1 AAAATTTAAATTAAA
* *
295300 AATA-TTATTATTAAA
1 AAAATTTA-AATTAAA
*
295315 TAATAATTTAAATTATA
1 -AA-AATTTAAATTAAA
**
295332 TCAATTTAAATTAAA
1 AAAATTTAAATTAAA
295347 AAAATTT
1 AAAATTT
295354 TATTTAAAAT
Statistics
Matches: 39, Mismatches: 10, Indels: 9
0.67 0.17 0.16
Matches are distributed among these distances:
13 3 0.08
14 4 0.10
15 21 0.54
16 2 0.05
17 6 0.15
18 3 0.08
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (15 bp):
AAAATTTAAATTAAA
Found at i:296345 original size:23 final size:23
Alignment explanation
Indices: 296319--296362 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
296309 GTAACATATC
*
296319 ATTTTTTA-AATTTATATTTATTT
1 ATTTTTTATAA-TTAAATTTATTT
296342 ATTTTTTATAATTAAATTTAT
1 ATTTTTTATAATTAAATTTAT
296363 ATAAAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (23 bp):
ATTTTTTATAATTAAATTTATTT
Found at i:303979 original size:16 final size:16
Alignment explanation
Indices: 303958--304019 Score: 51
Period size: 16 Copynumber: 4.1 Consensus size: 16
303948 AGCTCAAATT
303958 ATTATTTAATTATAAA
1 ATTATTTAATTATAAA
**
303974 ATTATTT--TTATTTA
1 ATTATTTAATTATAAA
303988 A--ATTTAATTATAAA
1 ATTATTTAATTATAAA
* * *
304002 AATATATAAATATAAA
1 ATTATTTAATTATAAA
304018 AT
1 AT
304020 AAATATTTTA
Statistics
Matches: 35, Mismatches: 7, Indels: 8
0.70 0.14 0.16
Matches are distributed among these distances:
12 4 0.11
14 12 0.34
16 19 0.54
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATTATTTAATTATAAA
Found at i:304017 original size:28 final size:28
Alignment explanation
Indices: 303961--304017 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
303951 TCAAATTATT
* * ** *
303961 ATTTAATTATAAAATTATTTTTATTTAA
1 ATTTAATTATAAAAATATATAAATATAA
303989 ATTTAATTATAAAAATATATAAATATAA
1 ATTTAATTATAAAAATATATAAATATAA
304017 A
1 A
304018 ATAAATATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (28 bp):
ATTTAATTATAAAAATATATAAATATAA
Found at i:305147 original size:31 final size:32
Alignment explanation
Indices: 305096--305168 Score: 94
Period size: 31 Copynumber: 2.3 Consensus size: 32
305086 AAATTTAATA
*
305096 AATATTAAATAAAAATTATTTGTAAATATGAG
1 AATATTAAATAAAAATTATTTATAAATATGAG
* * *
305128 AATATTAAAT-ATAATTATTTATAAATTTGAT
1 AATATTAAATAAAAATTATTTATAAATATGAG
305159 AATCATTAAA
1 AAT-ATTAAA
305169 AAATTTAACT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
31 20 0.56
32 16 0.44
ACGTcount: A:0.52, C:0.01, G:0.05, T:0.41
Consensus pattern (32 bp):
AATATTAAATAAAAATTATTTATAAATATGAG
Found at i:307242 original size:20 final size:21
Alignment explanation
Indices: 307204--307243 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
307194 ATTTTTCTTT
* *
307204 TTTTTTTTCTTTTGTTTCCCC
1 TTTTTTTTCTTCTGCTTCCCC
307225 TTTTTTTTCTTCT-CTTCCC
1 TTTTTTTTCTTCTGCTTCCC
307244 TCCTATTCCC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.00, C:0.28, G:0.03, T:0.70
Consensus pattern (21 bp):
TTTTTTTTCTTCTGCTTCCCC
Found at i:307454 original size:11 final size:11
Alignment explanation
Indices: 307438--307494 Score: 55
Period size: 10 Copynumber: 5.2 Consensus size: 11
307428 TTATTACAAA
307438 AATTAATTTTT
1 AATTAATTTTT
*
307449 AATTAAATTTT
1 AATTAATTTTT
* *
307460 -ATTAAATTAT
1 AATTAATTTTT
307470 AATT-ATTTTT
1 AATTAATTTTT
307480 AATTTAAATTTTT
1 AA-TT-AATTTTT
307493 AA
1 AA
307495 ATTTTTAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
10 15 0.39
11 15 0.39
13 8 0.21
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
AATTAATTTTT
Found at i:307516 original size:7 final size:8
Alignment explanation
Indices: 307482--307515 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
307472 TTATTTTTAA
307482 TTTAAATT
1 TTTAAATT
307490 TTTAAATT
1 TTTAAATT
*
307498 TTTAAAAT
1 TTTAAATT
307506 TTTAAATT
1 TTTAAATT
307514 TT
1 TT
307516 AGGATCAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TTTAAATT
Found at i:310352 original size:79 final size:79
Alignment explanation
Indices: 310217--311006 Score: 757
Period size: 79 Copynumber: 10.1 Consensus size: 79
310207 TTTCAATGAT
** * * * *
310217 GATTTTATTTCTAAAATATCGGTTTTCCACCATCGGGGATACTCTAACCTTGTTATTTTTGAAGG
1 GATTTTATTTCTAAAATATCAATTTTTCACCATCGAGGATACTCCAACCCTGTTATTTTTGAAGG
*
310282 GATACTCTAACCCC
66 GATACTCCAACCCC
* * * * * *
310296 GATTTTATTTCTAAAATGTCAAATTTTCACCATTGAAGATACTCCAACCCTATTATTTTCG-AGG
1 GATTTTATTTCTAAAATATCAATTTTTCACCATCGAGGATACTCCAACCCTGTTATTTTTGAAGG
**
310360 GAATACTTTAACCCC
66 G-ATACTCCAACCCC
* ** * * * *
310375 GATTTTATTTCTAAAAAATTGATTTTCCACCATC-AGGATACTCTAACCCTATTA-TTTTCAATG
1 GATTTTATTTCTAAAATATCAATTTTTCACCATCGAGGATACTCCAACCCTGTTATTTTTGAA-G
310438 GGATACTCCAACCCC
65 GGATACTCCAACCCC
* ** * *
310453 GATTTTATTTCTAAAACA-CAGATTTTTCACCATCGAGGATACTCCAACCCCATTATTTTCGAGG
1 GATTTTATTTCTAAAATATCA-ATTTTTCACCATCGAGGATACTCCAACCCTGTTATTTTTGAAG
*
310517 GGATACTTCAACCCC
65 GGATACTCCAACCCC
* * * * ** *
310532 GGTTTTATTCCTAAAACACCAATTTTTCACTTTCGAGGATACTCCAACCCCGTTATTTTT-AAGG
1 GATTTTATTTCTAAAATATCAATTTTTCACCATCGAGGATACTCCAACCCTGTTATTTTTGAAGG
310596 AGATACTCCAACCCC
66 -GATACTCCAACCCC
* * * * * * * *
310611 GATTTTATTCCTAAAACATCGATTTTTCACCTTTGGGGATACTCTAACCCTGCTATTTTTGAAGG
1 GATTTTATTTCTAAAATATCAATTTTTCACCATCGAGGATACTCCAACCCTGTTATTTTTGAAGG
*
310676 AATAC-CCAACCCC
66 GATACTCCAACCCC
* *
310689 GATTTT-TTTCCTAAAATATCAATTTTTCACCATCGA-GATACTCCAACCCCGTTATTTCTG-AG
1 GATTTTATTT-CTAAAATATCAATTTTTCACCATCGAGGATACTCCAACCCTGTTATTTTTGAAG
* *
310751 AGGATACTCAAACCCT
65 -GGATACTCCAACCCC
* * * * * * * *
310767 GGTTTTATTTCTAACAT-TCGATTTTTTATCATCAAGGATACTCCAACTCC-GTTATTTTTTAGG
1 GATTTTATTTCTAAAATATCAATTTTTCACCATCGAGGATACTCCAAC-CCTGTTATTTTTGAAG
*
310830 GGATACTCCAACTCC
65 GGATACTCCAACCCC
* * * *
310845 AATTTTATTTCTAAAATATCAATTTTCCACCAACG-GGATACTCCAACCCTGTTATTTCTG-AGG
1 GATTTTATTTCTAAAATATCAATTTTTCACCATCGAGGATACTCCAACCCTGTTATTTTTGAAGG
* *
310908 AGACACTCCAACCTC
66 -GATACTCCAACCCC
* * * * * *
310923 -AGTTTTATTTCTAAAACATCGATTTTCCACCATCGGGGATACTCCAA-CCTCGTTGTTTTCGAA
1 GA-TTTTATTTCTAAAATATCAATTTTTCACCATCGAGGATACTCCAACCCT-GTTATTTTTGAA
310986 GGGATACTCCAACCCC
64 GGGATACTCCAACCCC
311002 G-TTTT
1 GATTTT
311007 CATCTTAAAA
Statistics
Matches: 585, Mismatches: 102, Indels: 49
0.79 0.14 0.07
Matches are distributed among these distances:
76 2 0.00
77 49 0.08
78 231 0.39
79 290 0.50
80 13 0.02
ACGTcount: A:0.28, C:0.25, G:0.12, T:0.35
Consensus pattern (79 bp):
GATTTTATTTCTAAAATATCAATTTTTCACCATCGAGGATACTCCAACCCTGTTATTTTTGAAGG
GATACTCCAACCCC
Found at i:310508 original size:157 final size:155
Alignment explanation
Indices: 310217--311006 Score: 741
Period size: 157 Copynumber: 5.0 Consensus size: 155
310207 TTTCAATGAT
** * * * *
310217 GATTTTATTTCTAAAATATCGGTTTTCCACCATCGGGGATACTCTAACCTTGTTATTTTTGAAGG
1 GATTTTATTTCTAAAATATCAATTTTCCACCATC-AGGATACTCCAACCCTGTTA-TTTTCAAGG
* ** * * * * *
310282 GATACTCTAACCCCGATTTTATTTCTAAAATGTCAAATTTTCACCATTGAAGATACTCCAACCCT
64 GATACTCCAACCCCGATTTTATTTCTAAAA-CACGATTTTTCACCATCGAGGATACTCCAACCCC
* **
310347 ATTATTTTCGAGGGAATACTTTAACCCC
128 GTTATTTTCGAGGGAATACTCCAACCCC
* ** * *
310375 GATTTTATTTCTAAAAAATTGATTTTCCACCATCAGGATACTCTAACCCTATTATTTTCAATGGG
1 GATTTTATTTCTAAAATATCAATTTTCCACCATCAGGATACTCCAACCCTGTTATTTTCAA-GGG
*
310440 ATACTCCAACCCCGATTTTATTTCTAAAACACAGATTTTTCACCATCGAGGATACTCCAACCCCA
65 ATACTCCAACCCCGATTTTATTTCTAAAACAC-GATTTTTCACCATCGAGGATACTCCAACCCCG
* *
310505 TTATTTTCGAGGGGATACTTCAACCCC
129 TTATTTTCGAGGGAATACTCCAACCCC
* * * * * ** * *
310532 GGTTTTATTCCTAAAACACCAATTTTTCACTTTCGAGGATACTCCAACCCCGTTATTTTTAAGGA
1 GATTTTATTTCTAAAATATCAATTTTCCACCATC-AGGATACTCCAACCCTGTTATTTTCAAGG-
* * * * * *
310597 GATACTCCAACCCCGATTTTATTCCTAAAACATCGATTTTTCACCTTTGGGGATACTCTAACCCT
64 GATACTCCAACCCCGATTTTATTTCTAAAACA-CGATTTTTCACCATCGAGGATACTCCAACCCC
* * *
310662 GCTATTTTTGAAGGAATAC-CCAACCCC
128 GTTATTTTCGAGGGAATACTCCAACCCC
* * *
310689 GATTTT-TTTCCTAAAATATCAATTTTTCACCATC-GAGATACTCCAACCCCGTTA-TTTCTGAG
1 GATTTTATTT-CTAAAATATCAATTTTCCACCATCAG-GATACTCCAACCCTGTTATTTTC-AAG
* * * * ** * * * *
310751 AGGATACTCAAACCCTGGTTTTATTTCTAACATTCGATTTTTTATCATCAAGGATACTCCAACTC
63 -GGATACTCCAACCCCGATTTTATTTCTAAAACACGATTTTTCACCATCGAGGATACTCCAACCC
** * *
310816 CGTTATTTTTTAGGGGATACTCCAACTCC
127 CGTTATTTTCGAGGGAATACTCCAACCCC
* * * *
310845 AATTTTATTTCTAAAATATCAATTTTCCACCAACGGGATACTCCAACCCTGTTA-TTTCTGAGGA
1 GATTTTATTTCTAAAATATCAATTTTCCACCATCAGGATACTCCAACCCTGTTATTTTC-AAGG-
* * * * *
310909 GACACTCCAACCTC-AGTTTTATTTCTAAAACATCGATTTTCCACCATCGGGGATACTCCAACCT
64 GATACTCCAACCCCGA-TTTTATTTCTAAAACA-CGATTTTTCACCATCGAGGATACTCCAACCC
*
310973 CGTTGTTTTCGAAGGG-ATACTCCAACCCC
127 CGTTATTTTCG-AGGGAATACTCCAACCCC
311002 G-TTTT
1 GATTTT
311007 CATCTTAAAA
Statistics
Matches: 521, Mismatches: 95, Indels: 34
0.80 0.15 0.05
Matches are distributed among these distances:
155 43 0.08
156 140 0.27
157 208 0.40
158 129 0.25
159 1 0.00
ACGTcount: A:0.28, C:0.25, G:0.12, T:0.35
Consensus pattern (155 bp):
GATTTTATTTCTAAAATATCAATTTTCCACCATCAGGATACTCCAACCCTGTTATTTTCAAGGGA
TACTCCAACCCCGATTTTATTTCTAAAACACGATTTTTCACCATCGAGGATACTCCAACCCCGTT
ATTTTCGAGGGAATACTCCAACCCC
Found at i:318219 original size:25 final size:25
Alignment explanation
Indices: 318185--318235 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
318175 AAAGAAACTG
318185 ACATAATTTTCTTATTCATATATAT
1 ACATAATTTTCTTATTCATATATAT
318210 ACATAATTTTCTTATTCATATATAT
1 ACATAATTTTCTTATTCATATATAT
318235 A
1 A
318236 TATATATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.37, C:0.12, G:0.00, T:0.51
Consensus pattern (25 bp):
ACATAATTTTCTTATTCATATATAT
Found at i:323128 original size:42 final size:40
Alignment explanation
Indices: 323081--323175 Score: 104
Period size: 42 Copynumber: 2.3 Consensus size: 40
323071 AAATTTTTCT
*
323081 TATTAATTATATAAATATAAATATAATAAAAATTATTAAACG
1 TATTAATTATATAAATATAAATATAAT--AAATTATTAAACA
* *
323123 TATTAAAATT-T-TAAATATAAATATAATATATTATTAAATA
1 TATT--AATTATATAAATATAAATATAATAAATTATTAAACA
323163 TATTATATTATAT
1 TATTA-ATTATAT
323176 TTATTATATT
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
38 1 0.02
39 3 0.07
40 15 0.33
41 1 0.02
42 20 0.44
43 1 0.02
44 4 0.09
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (40 bp):
TATTAATTATATAAATATAAATATAATAAATTATTAAACA
Found at i:323159 original size:23 final size:23
Alignment explanation
Indices: 323133--323181 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
323123 TATTAAAATT
323133 TTAAATATAAATATAATATA-TTA
1 TTAAATAT-AATATAATATATTTA
* *
323156 TTAAATATATTATATTATATTTA
1 TTAAATATAATATAATATATTTA
323179 TTA
1 TTA
323182 TATTATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TTAAATATAATATAATATATTTA
Found at i:323162 original size:17 final size:17
Alignment explanation
Indices: 323140--323173 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
323130 ATTTTAAATA
323140 TAAATATAATATATTAT
1 TAAATATAATATATTAT
*
323157 TAAATATATTATATTAT
1 TAAATATAATATATTAT
323174 ATTTATTATA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TAAATATAATATATTAT
Found at i:323187 original size:14 final size:14
Alignment explanation
Indices: 323163--323193 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
323153 TTATTAAATA
323163 TATTATATTATATT
1 TATTATATTATATT
*
323177 TATTATATTATTTT
1 TATTATATTATATT
323191 TAT
1 TAT
323194 ACACGTTCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TATTATATTATATT
Found at i:330121 original size:24 final size:26
Alignment explanation
Indices: 330088--330136 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 26
330078 GGATGATAAA
330088 AATATAATATAAAA-AAATA-ATTAT
1 AATATAATATAAAATAAATATATTAT
*
330112 AATATGATATAAAATAAATATATTA
1 AATATAATATAAAATAAATATATTA
330137 ACATTTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 13 0.59
25 5 0.23
26 4 0.18
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (26 bp):
AATATAATATAAAATAAATATATTAT
Found at i:330133 original size:21 final size:19
Alignment explanation
Indices: 330087--330133 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 19
330077 AGGATGATAA
330087 AAATATAATATAAAAAAAT
1 AAATATAATATAAAAAAAT
* *
330106 AATTATAATATGATATAAAAT
1 AAATATAATAT-A-AAAAAAT
330127 AAATATA
1 AAATATA
330134 TTAACATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 10 0.43
20 1 0.04
21 12 0.52
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (19 bp):
AAATATAATATAAAAAAAT
Found at i:330156 original size:33 final size:33
Alignment explanation
Indices: 330118--330200 Score: 89
Period size: 33 Copynumber: 2.5 Consensus size: 33
330108 TTATAATATG
*
330118 ATATAAAATAAATATATTAACATTTTAAAATTT
1 ATATAAAATAAATATATTAACATATTAAAATTT
* ** *
330151 ATATAATATAAAT-TATTAATGTATTGAAATTT
1 ATATAAAATAAATATATTAACATATTAAAATTT
*
330183 AAATAAATATAAA-ATATT
1 ATATAAA-ATAAATATATT
330201 TTAAATATAA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
32 20 0.49
33 21 0.51
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.42
Consensus pattern (33 bp):
ATATAAAATAAATATATTAACATATTAAAATTT
Found at i:331478 original size:18 final size:17
Alignment explanation
Indices: 331420--331480 Score: 54
Period size: 18 Copynumber: 3.5 Consensus size: 17
331410 CTATTATAGT
331420 AAAAAAATAATAGTTTA-
1 AAAAAAATAATA-TTTAG
*
331437 AGAAAAAATTAT-TTTAG
1 A-AAAAAATAATATTTAG
* *
331454 AAGAGAATAATATTTAG
1 AAAAAAATAATATTTAG
331471 AAAAAGAATA
1 AAAAA-AATA
331481 GATAATTTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
16 11 0.32
17 10 0.29
18 13 0.38
ACGTcount: A:0.61, C:0.00, G:0.11, T:0.28
Consensus pattern (17 bp):
AAAAAAATAATATTTAG
Found at i:332870 original size:5 final size:5
Alignment explanation
Indices: 332860--332898 Score: 62
Period size: 5 Copynumber: 8.0 Consensus size: 5
332850 ATAATTATAT
*
332860 AAATA AAATA AAATA AAATA AAAT- AATTA AAATA AAATA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA
332899 TGATACAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
4 3 0.10
5 28 0.90
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (5 bp):
AAATA
Found at i:332875 original size:14 final size:14
Alignment explanation
Indices: 332860--332898 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 14
332850 ATAATTATAT
332860 AAATAAAATAAAATA
1 AAATAAAAT-AAATA
*
332875 AAATAAAATAATTA
1 AAATAAAATAAATA
332889 AAATAAAATA
1 AAATAAAATA
332899 TGATACAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 14 0.61
15 9 0.39
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (14 bp):
AAATAAAATAAATA
Found at i:334460 original size:18 final size:18
Alignment explanation
Indices: 334437--334490 Score: 64
Period size: 16 Copynumber: 3.2 Consensus size: 18
334427 AAAATATTAT
334437 ATATTTATATAAATTTTA
1 ATATTTATATAAATTTTA
334455 ATATTT-TA-ATAA-TTT-
1 ATATTTATATA-AATTTTA
334470 A-ATTTATATAAATTTTA
1 ATATTTATATAAATTTTA
334487 ATAT
1 ATAT
334491 ATTTAAATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 12
0.71 0.00 0.29
Matches are distributed among these distances:
14 4 0.13
15 5 0.17
16 8 0.27
17 5 0.17
18 8 0.27
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATATTTATATAAATTTTA
Found at i:334486 original size:16 final size:16
Alignment explanation
Indices: 334439--334498 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 16
334429 AATATTATAT
334439 ATTTATATAAATTTTA
1 ATTTATATAAATTTTA
*
334455 ATATT-T-TAATAATTTA
1 AT-TTATATAA-ATTTTA
334471 ATTTATATAAATTTTA
1 ATTTATATAAATTTTA
* *
334487 ATATATTTAAAT
1 ATTTATATAAAT
334499 ATATATTATG
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
15 5 0.14
16 26 0.72
17 5 0.14
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
ATTTATATAAATTTTA
Found at i:334512 original size:26 final size:25
Alignment explanation
Indices: 334457--334504 Score: 71
Period size: 24 Copynumber: 1.9 Consensus size: 25
334447 AAATTTTAAT
*
334457 ATTTTAATA-ATTTAATTTATATAA
1 ATTTTAATATATTTAATATATATAA
334481 ATTTTAATATATTTAAATATATAT
1 ATTTTAATATATTT-AATATATAT
334505 TATGTTTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 9 0.43
25 4 0.19
26 8 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
ATTTTAATATATTTAATATATATAA
Found at i:334516 original size:11 final size:11
Alignment explanation
Indices: 334500--334534 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
334490 TATTTAAATA
*
334500 TATATTATGTT
1 TATATTATATT
334511 TATATTATATT
1 TATATTATATT
*
334522 TTTATTATATT
1 TATATTATATT
334533 TA
1 TA
334535 ATAATTTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (11 bp):
TATATTATATT
Found at i:335292 original size:5 final size:5
Alignment explanation
Indices: 335282--335438 Score: 74
Period size: 5 Copynumber: 31.2 Consensus size: 5
335272 AAAGATTATA
* * *
335282 AATAT AATAT AAAAAT AATTAA AATAT AATAT AATAT AAAAGT AATAT
1 AATAT AATAT -AATAT AA-TAT AATAT AATAT AATAT AATA-T AATAT
* * * * * *
335330 GATAT GATAT AATAT AA-AT -ATAT AAATAT ATTAA AAT-T TATAA AATAT
1 AATAT AATAT AATAT AATAT AATAT -AATAT AATAT AATAT AATAT AATAT
* * * * * *
335378 AAAAT ATTTT AAATAT AATTAT AATAT AA-AT AA-GT GATAA AATAT AATAT
1 AATAT AATAT -AATAT AA-TAT AATAT AATAT AATAT AATAT AATAT AATAT
335428 AA-AT ATATAT A
1 AATAT A-ATAT A
335439 TCATTAAATT
Statistics
Matches: 112, Mismatches: 28, Indels: 23
0.69 0.17 0.14
Matches are distributed among these distances:
3 1 0.01
4 15 0.13
5 70 0.62
6 26 0.23
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (5 bp):
AATAT
Found at i:335294 original size:11 final size:11
Alignment explanation
Indices: 335278--335438 Score: 87
Period size: 11 Copynumber: 15.4 Consensus size: 11
335268 TGACAAAGAT
335278 TATAAATATAA
1 TATAAATATAA
*
335289 TATAAAAATAA
1 TATAAATATAA
335300 T-TAAAATATAA
1 TAT-AAATATAA
335311 TAT-AATATAA
1 TATAAATATAA
* *
335321 AAGT-AATATGA
1 TA-TAAATATAA
*
335332 TAT-GATATAA
1 TATAAATATAA
335342 TAT-AA-AT-A
1 TATAAATATAA
*
335350 TATAAATATAT
1 TATAAATATAA
*
335361 TA-AAAT-TTA
1 TATAAATATAA
335370 TA-AAATATAA
1 TATAAATATAA
* * *
335380 AAT-ATTTTAAA
1 TATAAATAT-AA
*
335391 TATAATTATAA
1 TATAAATATAA
*
335402 TATAAATA-AG
1 TATAAATATAA
335412 TGATAAAATATAA
1 T-AT-AAATATAA
335425 TATAAATAT-A
1 TATAAATATAA
335435 TATA
1 TATA
335439 TCATTAAATT
Statistics
Matches: 117, Mismatches: 20, Indels: 27
0.71 0.12 0.16
Matches are distributed among these distances:
8 4 0.03
9 11 0.09
10 38 0.32
11 50 0.43
12 12 0.10
13 2 0.02
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (11 bp):
TATAAATATAA
Found at i:335334 original size:26 final size:27
Alignment explanation
Indices: 335282--335434 Score: 123
Period size: 27 Copynumber: 5.4 Consensus size: 27
335272 AAAGATTATA
335282 AATATAATATAAAAATAATTAAAATAT
1 AATATAATATAAAAATAATTAAAATAT
* *
335309 AATATAATATAAAAGTAATATGATATGATAT
1 AATATAATATAAAAATAAT-T-A-A-AATAT
*
335340 AATATAAATATATAAATATATTAAAAT-T
1 AATAT-AATATAAAAATA-ATTAAAATAT
* * * *
335368 TATAAAATAT-AAAATATTTTAAATAT
1 AATATAATATAAAAATAATTAAAATAT
*
335394 AATTATAATATAAATAAGTGA-TAAAATAT
1 AA-TATAATATAAA-AA-TAATTAAAATAT
335423 AATATAAATATA
1 AATAT-AATATA
335435 TATATCATTA
Statistics
Matches: 99, Mismatches: 15, Indels: 22
0.73 0.11 0.16
Matches are distributed among these distances:
25 6 0.06
26 7 0.07
27 30 0.30
28 10 0.10
29 20 0.20
30 3 0.03
31 10 0.10
32 11 0.11
33 2 0.02
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (27 bp):
AATATAATATAAAAATAATTAAAATAT
Found at i:335635 original size:15 final size:16
Alignment explanation
Indices: 335602--335634 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
335592 AAGTTAAAAT
335602 AATATTTTTATATTAA
1 AATATTTTTATATTAA
335618 AATATATTTTAT-TTAA
1 AATAT-TTTTATATTAA
335634 A
1 A
335635 TTTAATTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
AATATTTTTATATTAA
Found at i:336020 original size:32 final size:31
Alignment explanation
Indices: 335984--336108 Score: 109
Period size: 32 Copynumber: 4.0 Consensus size: 31
335974 TAGAAGTAAT
335984 TAAAAATATTATAAAATTTTTAT-ATAAAAATA
1 TAAAAATA-T-TAAAATTTTTATAATAAAAATA
* *
336016 TAAAAATATTAAAATTTATATAATATAAAT-
1 TAAAAATATTAAAATTTTTATAATAAAAATA
336046 TAATAATATATTAAAA--TTTAT-AT-AAAATA
1 TAA-AA-ATATTAAAATTTTTATAATAAAAATA
**
336075 TAAAAATAATTTAAATATAATTATAATAAAAATA
1 TAAAAAT-A-TTAAA-ATTTTTATAATAAAAATA
336109 ATTAACGTGG
Statistics
Matches: 77, Mismatches: 5, Indels: 20
0.75 0.05 0.20
Matches are distributed among these distances:
27 2 0.03
28 7 0.09
29 10 0.13
30 19 0.25
31 10 0.13
32 21 0.27
33 2 0.03
34 6 0.08
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (31 bp):
TAAAAATATTAAAATTTTTATAATAAAAATA
Found at i:336040 original size:17 final size:17
Alignment explanation
Indices: 336020--336070 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
336010 AAAATATAAA
336020 AATATTAAAATTTATAT
1 AATATTAAAATTTATAT
*
336037 AATA-T-AAATTAATA-
1 AATATTAAAATTTATAT
336051 ATATATTAAAATTTATAT
1 A-ATATTAAAATTTATAT
336069 AA
1 AA
336071 AATATAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 1 0.04
15 11 0.39
16 2 0.07
17 13 0.46
18 1 0.04
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AATATTAAAATTTATAT
Found at i:336265 original size:2 final size:2
Alignment explanation
Indices: 336258--336282 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
336248 CGCAAAATTC
336258 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
336283 ACACCTCATA
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:337227 original size:23 final size:24
Alignment explanation
Indices: 337201--337249 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
337191 GATATGCGAT
337201 ATTTTTAATATAAATATA-TTAAA
1 ATTTTTAATATAAATATATTTAAA
* * *
337224 ATTTTTATTTTTAATATATTTAAA
1 ATTTTTAATATAAATATATTTAAA
337248 AT
1 AT
337250 ATTATATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 15 0.68
24 7 0.32
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
ATTTTTAATATAAATATATTTAAA
Found at i:337254 original size:23 final size:24
Alignment explanation
Indices: 337213--337259 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
337203 TTTTAATATA
*
337213 AATATATTAAAATTTTTAT-TTTT
1 AATATATTAAAATTATTATATTTT
337236 AATATATTTAAAA-TATTATATTTT
1 AATATA-TTAAAATTATTATATTTT
337260 TTATTTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
AATATATTAAAATTATTATATTTT
Found at i:337257 original size:25 final size:23
Alignment explanation
Indices: 337213--337260 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 23
337203 TTTTAATATA
*
337213 AATATATTAAAATTTTTATTTTT
1 AATATATTAAAATTTATATTTTT
337236 AATATATTTAAAATATTATATTTTT
1 AATATA-TTAAAAT-TTATATTTTT
337261 TATTTATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 6 0.27
24 7 0.32
25 9 0.41
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
AATATATTAAAATTTATATTTTT
Found at i:337639 original size:29 final size:31
Alignment explanation
Indices: 337579--337639 Score: 74
Period size: 29 Copynumber: 2.0 Consensus size: 31
337569 AGATTTATCC
*
337579 AAATAAATAGTTGAAATTTATTTATCATTAAA
1 AAATAAATAGTT-AAATTTATTTATCAATAAA
337611 AAATAAATA-TT-AATTTA-TTATTCAATAAA
1 AAATAAATAGTTAAATTTATTTA-TCAATAAA
337640 TTATCCATGC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
28 3 0.11
29 13 0.48
31 2 0.07
32 9 0.33
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.41
Consensus pattern (31 bp):
AAATAAATAGTTAAATTTATTTATCAATAAA
Found at i:338040 original size:25 final size:26
Alignment explanation
Indices: 338023--338080 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
338013 ATATAAATTT
338023 AATAAAAAATTTAAAATATAAAATAA
1 AATAAAAAATTTAAAATATAAAATAA
* * *
338049 AATAAAATATTTAAATATTTAAAATAT
1 AATAAAAAATTTAAA-ATATAAAATAA
338076 AATAA
1 AATAA
338081 TAATATATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 14 0.50
27 14 0.50
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (26 bp):
AATAAAAAATTTAAAATATAAAATAA
Found at i:338088 original size:22 final size:23
Alignment explanation
Indices: 338046--338133 Score: 80
Period size: 22 Copynumber: 3.9 Consensus size: 23
338036 AAATATAAAA
* *
338046 TAAAATAAAATATTTAA-ATATT
1 TAAAATATAATATATAATATATT
338068 TAAAATATAATA-ATAATATA-T
1 TAAAATATAATATATAATATATT
338089 TAAATTTATATAAATATATAATAT-TT
1 TAAA---ATAT-AATATATAATATATT
338115 T-AAATATAAT-TATAATATA
1 TAAAATATAATATATAATATA
338134 AAAATATTTA
Statistics
Matches: 56, Mismatches: 2, Indels: 17
0.75 0.03 0.23
Matches are distributed among these distances:
20 8 0.14
21 11 0.20
22 18 0.32
24 4 0.07
25 6 0.11
26 9 0.16
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TAAAATATAATATATAATATATT
Found at i:338134 original size:11 final size:10
Alignment explanation
Indices: 338054--338133 Score: 50
Period size: 9 Copynumber: 8.6 Consensus size: 10
338044 AATAAAATAA
338054 AATAT-TTA-
1 AATATATTAT
*
338062 AATAT-TTAA
1 AATATATTAT
*
338071 AATATAATAAT
1 AATAT-ATTAT
338082 AATATATTA-
1 AATATATTAT
*
338091 AATTTA-TAT
1 AATATATTAT
338100 AA-ATA-TAT
1 AATATATTAT
*
338108 AATATTTTA-
1 AATATATTAT
338117 AATATAATTAT
1 AATAT-ATTAT
338128 AATATA
1 AATATA
338134 AAAATATTTA
Statistics
Matches: 57, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
8 17 0.30
9 19 0.33
10 9 0.16
11 12 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (10 bp):
AATATATTAT
Found at i:338761 original size:17 final size:16
Alignment explanation
Indices: 338721--338791 Score: 52
Period size: 17 Copynumber: 4.1 Consensus size: 16
338711 TAAAAAAATT
*
338721 TAAATAAATATATTAAA
1 TAAA-AAATAAATTAAA
*
338738 TTTAAAAATAAAATTAAA
1 -TAAAAAAT-AAATTAAA
* *
338756 TAAAAAATTAAATCTTAT
1 TAAAAAA-TAAAT-TAAA
*
338774 TTAAAAATAAATTAAA
1 TAAAAAATAAATTAAA
338790 TA
1 TA
338792 TTTATTTTAA
Statistics
Matches: 41, Mismatches: 9, Indels: 8
0.71 0.16 0.14
Matches are distributed among these distances:
16 3 0.07
17 19 0.46
18 19 0.46
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.35
Consensus pattern (16 bp):
TAAAAAATAAATTAAA
Found at i:338927 original size:23 final size:25
Alignment explanation
Indices: 338882--338928 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 25
338872 ATAAGATTAC
338882 ATTATATTAACTTTATATTTTATAT
1 ATTATATTAACTTTATATTTTATAT
*
338907 ATTATA-TAA-TTTTTATTTTATA
1 ATTATATTAACTTTATATTTTATA
338929 AAAAATACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 12 0.57
24 3 0.14
25 6 0.29
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (25 bp):
ATTATATTAACTTTATATTTTATAT
Found at i:338964 original size:55 final size:51
Alignment explanation
Indices: 338833--338966 Score: 121
Period size: 55 Copynumber: 2.6 Consensus size: 51
338823 TTATTTTATT
* * *
338833 ATTATATAATA-TAAAATATAAA-ATTAATATATTAATTTTATAAGATTAC
1 ATTATATAATATTATAATATAAATATTAATATATTAATTTTATAAAAATAC
* * * * *
338882 ATTATATTAACT-TTATATTTTATATATTATATAATTTTTATTTTATAAAAAATAC
1 ATTATA-TAA-TATTATAATATAAATATTA-AT-ATATTAATTTTAT-AAAAATAC
338937 ATATATATAATATTATAATATAAATATTAA
1 AT-TATATAATATTATAATATAAATATTAA
338967 AATTAAATTA
Statistics
Matches: 65, Mismatches: 11, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
49 6 0.09
50 3 0.05
51 8 0.12
52 4 0.06
53 2 0.03
54 13 0.20
55 25 0.38
56 4 0.06
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.48
Consensus pattern (51 bp):
ATTATATAATATTATAATATAAATATTAATATATTAATTTTATAAAAATAC
Found at i:339041 original size:15 final size:16
Alignment explanation
Indices: 339023--339060 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
339013 ATTAAATTAA
339023 TAAAAAT-TATATTTT
1 TAAAAATATATATTTT
339038 T-AAAATATATATTTT
1 TAAAAATATATATTTT
*
339053 CAAAAATA
1 TAAAAATA
339061 AATTATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 5 0.25
15 9 0.45
16 6 0.30
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (16 bp):
TAAAAATATATATTTT
Found at i:340432 original size:21 final size:21
Alignment explanation
Indices: 340391--340453 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 21
340381 TTTAAATTGT
* *
340391 TATTTTTTTAT-TAAATTAAA
1 TATTTATTTATATAATTTAAA
340411 T-TTTAATTTATATAATTTAAA
1 TATTT-ATTTATATAATTTAAA
*
340432 TAATTTTTTTA-ATAATTTAAA
1 T-ATTTATTTATATAATTTAAA
340453 T
1 T
340454 CATACTTGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
19 3 0.08
20 6 0.17
21 20 0.56
22 4 0.11
23 3 0.08
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TATTTATTTATATAATTTAAA
Done.