Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold34
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: 1758877
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 50 characters in sequence are not A, C, G, or T
File 2 of 12
Found at i:154090 original size:23 final size:22
Alignment explanation
Indices: 154077--154127 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 22
154067 TATTTATTTG
154077 ATATTTAATAATTTTATATATTA
1 ATATTT-ATAATTTTATATATTA
* *
154100 ATATTTATAATTTTA-AAATTT
1 ATATTTATAATTTTATATATTA
154121 ATATTTA
1 ATATTTA
154128 CATATATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 11 0.42
22 9 0.35
23 6 0.23
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
ATATTTATAATTTTATATATTA
Found at i:154093 original size:30 final size:30
Alignment explanation
Indices: 154033--154137 Score: 83
Period size: 30 Copynumber: 3.4 Consensus size: 30
154023 TTACTAATAA
*
154033 TAATATATTATATATTTTAAAATATTTTTATATT
1 TAATAT-TTATA-ATTTT--AATAATTTTATATT
*
154067 TATTTATTTGAT-A-TTTAATAATTTTATATAT
1 TA-ATATTT-ATAATTTTAATAATTTTATAT-T
154098 TAATATTTATAATTTTAA-AA-TTTATATT
1 TAATATTTATAATTTTAATAATTTTATATT
*
154126 TACATATATATA
1 TA-ATATTTATA
154138 TATATATATA
Statistics
Matches: 61, Mismatches: 4, Indels: 17
0.74 0.05 0.21
Matches are distributed among these distances:
28 3 0.05
29 17 0.28
30 20 0.33
31 8 0.13
32 3 0.05
33 1 0.02
34 4 0.07
35 5 0.08
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (30 bp):
TAATATTTATAATTTTAATAATTTTATATT
Found at i:154136 original size:2 final size:2
Alignment explanation
Indices: 154129--154159 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
154119 TTATATTTAC
154129 AT AT 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 AT AT A
154160 CATGCATATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:154599 original size:2 final size:2
Alignment explanation
Indices: 154592--154624 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
154582 AATTATTTTA
*
154592 AT AT AT AT AT AT AT AT AT AT AT CT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
154625 CAAAATGGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:154915 original size:2 final size:2
Alignment explanation
Indices: 154898--154935 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
154888 AATGATTCTA
* *
154898 AT AT AT AA AT AC 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
154936 GTCAAGGGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:155342 original size:18 final size:17
Alignment explanation
Indices: 155315--155348 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
155305 AAAATAATAG
*
155315 TATTAGTATAATATATTT
1 TATTAATATAA-ATATTT
155333 TATTAATATAAATATT
1 TATTAATATAAATATT
155349 AAACAAGTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
TATTAATATAAATATTT
Found at i:156378 original size:39 final size:39
Alignment explanation
Indices: 156324--156422 Score: 180
Period size: 39 Copynumber: 2.5 Consensus size: 39
156314 TGTTTGGGTT
*
156324 GCGTCCTACTCTTTGAGGACTAAAGGGCGAAAGAAGAGA
1 GCGTCCTGCTCTTTGAGGACTAAAGGGCGAAAGAAGAGA
156363 GCGTCCTGCTCTTTGAGGACTAAAGGGCGAAAGAAGAGA
1 GCGTCCTGCTCTTTGAGGACTAAAGGGCGAAAGAAGAGA
*
156402 GCGTCCTGCTCTTTGAAGACT
1 GCGTCCTGCTCTTTGAGGACT
156423 GGAAAGTGCC
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 58 1.00
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.21
Consensus pattern (39 bp):
GCGTCCTGCTCTTTGAGGACTAAAGGGCGAAAGAAGAGA
Found at i:156468 original size:55 final size:54
Alignment explanation
Indices: 156402--156591 Score: 251
Period size: 55 Copynumber: 3.5 Consensus size: 54
156392 AAAGAAGAGA
*
156402 GCGTCCTGCTCTTTGAAGACTGGAAAGTGCCACCAACTTGTGTGGGATTTAAAAG
1 GCGTCCTGCTCTTTGAAGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTAAAAG
* *
156457 GCGTCCTGCTCTTT-AAGGACTAAAAAATGCCACCAACTTGTGTGGGCTTTGAAAA-
1 GCGTCCTGCTCTTTGAA-GACT-GAAAGTGCCACCAACTTGTGTGGGCTTT-AAAAG
* * *
156512 GCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTATGGGCTTTGAAAG
1 GCGTCCTGCTCTTTGAAGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTAAAAG
*
156567 GCGTCCTGCTCTTTGAGGACT-AAAG
1 GCGTCCTGCTCTTTGAAGACTGAAAG
156592 GGTGAAATGA
Statistics
Matches: 121, Mismatches: 9, Indels: 12
0.85 0.06 0.08
Matches are distributed among these distances:
53 1 0.01
54 11 0.09
55 104 0.86
56 5 0.04
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.27
Consensus pattern (54 bp):
GCGTCCTGCTCTTTGAAGACTGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAG
Found at i:157698 original size:18 final size:17
Alignment explanation
Indices: 157675--157746 Score: 108
Period size: 18 Copynumber: 4.1 Consensus size: 17
157665 CTTTTCTCTC
* *
157675 TTTTTTCTTTGTTTTGT
1 TTTTTTTTTTGTTTTTT
157692 TTTTTTTTTTGTTTTTT
1 TTTTTTTTTTGTTTTTT
157709 TTTTGTTTTTTGTTTTTT
1 TTTT-TTTTTTGTTTTTT
157727 TTTGTTTTTTTGTTTTTT
1 TTT-TTTTTTTGTTTTTT
157745 TT
1 TT
157747 AAATGTGGGA
Statistics
Matches: 51, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
17 19 0.37
18 31 0.61
19 1 0.02
ACGTcount: A:0.00, C:0.01, G:0.10, T:0.89
Consensus pattern (17 bp):
TTTTTTTTTTGTTTTTT
Found at i:157737 original size:28 final size:27
Alignment explanation
Indices: 157675--157746 Score: 101
Period size: 28 Copynumber: 2.6 Consensus size: 27
157665 CTTTTCTCTC
*
157675 TTTTTTCTTTGTTTTGTTTTTTTTTTTG
1 TTTTTTTTTTGTTTT-TTTTTTTTTTTG
157703 TTTTTTTTTTGTTTTTTGTTTTTTTTTG
1 TTTTTTTTTTGTTTTTT-TTTTTTTTTG
*
157731 TTTTTTTGTT-TTTTTT
1 TTTTTTTTTTGTTTTTT
157747 AAATGTGGGA
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
27 8 0.20
28 33 0.80
ACGTcount: A:0.00, C:0.01, G:0.10, T:0.89
Consensus pattern (27 bp):
TTTTTTTTTTGTTTTTTTTTTTTTTTG
Found at i:157765 original size:1 final size:1
Alignment explanation
Indices: 157675--157746 Score: 72
Period size: 1 Copynumber: 72.0 Consensus size: 1
157665 CTTTTCTCTC
* * * * * * * *
157675 TTTTTTCTTTGTTTTGTTTTTTTTTTTGTTTTTTTTTTGTTTTTTGTTTTTTTTTGTTTTTTTGT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
157740 TTTTTTT
1 TTTTTTT
157747 AAATGTGGGA
Statistics
Matches: 55, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 55 1.00
ACGTcount: A:0.00, C:0.01, G:0.10, T:0.89
Consensus pattern (1 bp):
T
Found at i:170288 original size:79 final size:78
Alignment explanation
Indices: 170149--170450 Score: 331
Period size: 79 Copynumber: 3.8 Consensus size: 78
170139 TGGAGATAAC
* * *
170149 AACGGGGGTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTAAAAATAAAATTGGGGTTGGAGT
1 AACGGGGTTGGAGTATCCCCGATTATG-AAAATTGGTGTTTTGAAAATAAAATCGGGGTTGGAGT
170214 ATCTCCTCGGAAAT
65 ATCTCCTCGGAAAT
** * * *
170228 AATAGAGTTGGAGTATCCCTGATTATAGAAAATTGGTGTTTTGAAAATAAAATCAGGGTTGGAGT
1 AACGGGGTTGGAGTATCCCCGATTAT-GAAAATTGGTGTTTTGAAAATAAAATCGGGGTTGGAGT
* *
170293 ATCCCCTCGAAAAT
65 ATCTCCTCGGAAAT
* * * * * * **
170307 AACGGGGTTGGAGTATCCTCGATTGTGGGAAATCGATGCTTT-AGAAATAAGGTCGGGGTTGGAG
1 AACGGGGTTGGAGTATCCCCGATTAT-GAAAATTGGTGTTTTGA-AAATAAAATCGGGGTTGGAG
170371 TA--TCCTCGTGATAAT
64 TATCTCCTCG-GA-AAT
* * *
170386 AACGGGGTTGGAGTATCCCCGATTGTGAGAAATTGGTGTTTTGGAAATAAAATCGGAGTTGGAGT
1 AACGGGGTTGGAGTATCCCCGATTATGA-AAATTGGTGTTTTGAAAATAAAATCGGGGTTGGAGT
170451 GTCCCTAATT
Statistics
Matches: 182, Mismatches: 35, Indels: 12
0.79 0.15 0.05
Matches are distributed among these distances:
77 5 0.03
78 3 0.02
79 173 0.95
80 1 0.01
ACGTcount: A:0.30, C:0.11, G:0.29, T:0.29
Consensus pattern (78 bp):
AACGGGGTTGGAGTATCCCCGATTATGAAAATTGGTGTTTTGAAAATAAAATCGGGGTTGGAGTA
TCTCCTCGGAAAT
Found at i:170367 original size:158 final size:158
Alignment explanation
Indices: 170149--170455 Score: 379
Period size: 158 Copynumber: 1.9 Consensus size: 158
170139 TGGAGATAAC
* * * *
170149 AACGGGGGTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTAAAAATAAAATTGGGGTTGGAGT
1 AACGGGGGTGGAGTATCCCCGATTATGAAAAATCGATGCTTTAAAAATAAAATCGGGGTTGGAGT
* *
170214 ATCTCCTCG-GA-AATAATAGAGTTGGAGTATCCCTGATTAT-AGAAAATTGGTGTTTTGAAAAT
66 A--TCCTCGTGATAATAACAGAGTTGGAGTATCCCCGATTATGAG-AAATTGGTGTTTTGAAAAT
170276 AAAATCAGG-GTTGGAGTATCCCCTCGAAAAT
128 AAAATC-GGAGTTGGAGTATCCCCTCGAAAAT
* * * ** * **
170307 AACGGGGTTGGAGTATCCTCGATTGTGGGAAATCGATGCTTTAGAAATAAGGTCGGGGTTGGAGT
1 AACGGGGGTGGAGTATCCCCGATTATGAAAAATCGATGCTTTAAAAATAAAATCGGGGTTGGAGT
* * * *
170372 ATCCTCGTGATAATAACGGGGTTGGAGTATCCCCGATTGTGAGAAATTGGTGTTTTGGAAATAAA
66 ATCCTCGTGATAATAACAGAGTTGGAGTATCCCCGATTATGAGAAATTGGTGTTTTGAAAATAAA
*
170437 ATCGGAGTTGGAGTGTCCC
131 ATCGGAGTTGGAGTATCCC
170456 TAATTGTGAA
Statistics
Matches: 126, Mismatches: 19, Indels: 8
0.82 0.12 0.05
Matches are distributed among these distances:
156 6 0.05
157 4 0.03
158 114 0.90
159 2 0.02
ACGTcount: A:0.30, C:0.12, G:0.29, T:0.29
Consensus pattern (158 bp):
AACGGGGGTGGAGTATCCCCGATTATGAAAAATCGATGCTTTAAAAATAAAATCGGGGTTGGAGT
ATCCTCGTGATAATAACAGAGTTGGAGTATCCCCGATTATGAGAAATTGGTGTTTTGAAAATAAA
ATCGGAGTTGGAGTATCCCCTCGAAAAT
Found at i:170462 original size:51 final size:51
Alignment explanation
Indices: 170390--170507 Score: 159
Period size: 51 Copynumber: 2.3 Consensus size: 51
170380 GATAATAACG
* * *
170390 GGGTTGGAGTATCCCCGATTGTGAGAAA-TTGGTGTTTTGGAAATAAAATC-
1 GGGTTGGAGTATCCCCAATTGTGA-AAATTTGGTATTTTAGAAATAAAATCA
* *
170440 GGAGTTGGAGTGTCCCTAATTGTGAAAATTTGGTATTTTAGAAATAAAATCA
1 GG-GTTGGAGTATCCCCAATTGTGAAAATTTGGTATTTTAGAAATAAAATCA
170492 GGGTTGGAGTATCCCC
1 GGGTTGGAGTATCCCC
170508 TCGGAAATAA
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
50 5 0.09
51 51 0.88
52 2 0.03
ACGTcount: A:0.29, C:0.11, G:0.28, T:0.32
Consensus pattern (51 bp):
GGGTTGGAGTATCCCCAATTGTGAAAATTTGGTATTTTAGAAATAAAATCA
Found at i:170604 original size:108 final size:108
Alignment explanation
Indices: 170473--170722 Score: 319
Period size: 108 Copynumber: 2.3 Consensus size: 108
170463 GAAAATTTGG
* * *
170473 TATTTTAGAAATAAAATCAGGGTTGGAGTATCCCCTCGGAAATAA-CGGGATTGGAGTATCTCCG
1 TATTTTAGAAATAAAACCAGGGTTGGAGTATCCCCTCGGAAATAATAGGG-TTGGAGTATCCCCG
* *
170537 ATGACATAACGGGGTCGGAGTA-CCCCTGATTATGAAAAAATCAA
65 ATGAAATAACGGGGTCGGAGTATCCCC-AATTATGAAAAAATCAA
* * *
170581 TATTTTAGACATAAAGCCGGGGTTGGAGTATCCCCTCGGAAATAATAGGGTTGGAGTATCCCCGA
1 TATTTTAGAAATAAAACCAGGGTTGGAGTATCCCCTCGGAAATAATAGGGTTGGAGTATCCCCGA
* ***
170646 TGAAATAACGGGGTTGGAGTATCCCCAATTATG-AAAAATTGG
66 TGAAATAACGGGGTCGGAGTATCCCCAATTATGAAAAAATCAA
* *
170688 TATTTTGGAAATAAAATC-GGAGTTGGAGTATCCCC
1 TATTTTAGAAATAAAACCAGG-GTTGGAGTATCCCC
170723 GATTGCGGTA
Statistics
Matches: 123, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
106 2 0.02
107 34 0.28
108 80 0.65
109 7 0.06
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.26
Consensus pattern (108 bp):
TATTTTAGAAATAAAACCAGGGTTGGAGTATCCCCTCGGAAATAATAGGGTTGGAGTATCCCCGA
TGAAATAACGGGGTCGGAGTATCCCCAATTATGAAAAAATCAA
Found at i:170640 original size:28 final size:28
Alignment explanation
Indices: 170600--170671 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
170590 CATAAAGCCG
** *
170600 GGGTTGGAGTATCCCCTCGGAAATAATA
1 GGGTTGGAGTATCCCCGAGGAAATAACA
* *
170628 GGGTTGGAGTATCCCCGATGAAATAACG
1 GGGTTGGAGTATCCCCGAGGAAATAACA
170656 GGGTTGGAGTATCCCC
1 GGGTTGGAGTATCCCC
170672 AATTATGAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.24
Consensus pattern (28 bp):
GGGTTGGAGTATCCCCGAGGAAATAACA
Found at i:170736 original size:51 final size:51
Alignment explanation
Indices: 170658--170826 Score: 205
Period size: 51 Copynumber: 3.3 Consensus size: 51
170648 AAATAACGGG
* * * *
170658 GTTGGAGTATCCCCAATTATGAAAAATTGGTATTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTAAGAAAAATTGATGTTTTGGAAATAAAATCGGA
** ** * *
170709 GTTGGAGTATCCCCGATTGCGGTAAATTGATGCTTTAGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTAAGAAAAATTGATGTTTTGGAAATAAAATCGGA
** *
170760 GTTGGAGTATCCCCGATTAAGAAAAATTGATGTTTTGGAAATGGAACCGG-
1 GTTGGAGTATCCCCGATTAAGAAAAATTGATGTTTTGGAAATAAAATCGGA
170810 GATTGGAGTATCCCCGA
1 G-TTGGAGTATCCCCGA
170827 GATGAAAAAT
Statistics
Matches: 99, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
50 1 0.01
51 98 0.99
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTAAGAAAAATTGATGTTTTGGAAATAAAATCGGA
Found at i:174889 original size:19 final size:18
Alignment explanation
Indices: 174865--174962 Score: 90
Period size: 19 Copynumber: 5.8 Consensus size: 18
174855 TAGCTTAAAT
174865 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
174884 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
174897 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
174916 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
174929 TGTATCGATACAATACTTTA
1 TGTATCGATACAA-AC-TTA
174949 TGTATCGATACAAA
1 TGTATCGATACAAA
174963 TCGTTGAAAT
Statistics
Matches: 66, Mismatches: 0, Indels: 26
0.72 0.00 0.28
Matches are distributed among these distances:
13 22 0.33
14 2 0.03
16 4 0.06
18 1 0.02
19 24 0.36
20 13 0.20
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:174902 original size:13 final size:13
Alignment explanation
Indices: 174884--174940 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
174874 ACAAAACTTA
174884 TGTATCGATACAT
1 TGTATCGATACAT
174897 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
174915 ATGTATCGATACAT
1 -TGTATCGATACAT
174929 TGTATCGATACA
1 TGTATCGATACA
174941 ATACTTTATG
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:174904 original size:32 final size:32
Alignment explanation
Indices: 174863--174960 Score: 169
Period size: 32 Copynumber: 3.0 Consensus size: 32
174853 AGTAGCTTAA
174863 ATTGTATCGATACAAAACTTATGTATCGATAC
1 ATTGTATCGATACAAAACTTATGTATCGATAC
*
174895 ATTGTATCGATACAACACTTATGTATCGATAC
1 ATTGTATCGATACAAAACTTATGTATCGATAC
*
174927 ATTGTATCGATACAATACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAC-TTATGTATCGATAC
174960 A
1 A
174961 AATCGTTGAA
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
32 48 0.76
33 15 0.24
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (32 bp):
ATTGTATCGATACAAAACTTATGTATCGATAC
Found at i:176728 original size:20 final size:20
Alignment explanation
Indices: 176703--176755 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 20
176693 AAAATACCTG
* * *
176703 AATGTATCGATATATTGTAA
1 AATGTATCGATACAATGCAA
176723 AATGTA-CGATACAATGCAA
1 AATGTATCGATACAATGCAA
176742 AATGTATCGATACA
1 AATGTATCGATACA
176756 TCTGGGTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.30
Consensus pattern (20 bp):
AATGTATCGATACAATGCAA
Found at i:177242 original size:23 final size:23
Alignment explanation
Indices: 177172--177292 Score: 83
Period size: 21 Copynumber: 5.3 Consensus size: 23
177162 AAAAGTATTT
* *
177172 AATA-TTTTAAATTTAAAT-TTA
1 AATATTTTTATATTTAAATAATA
*
177193 AATATTTTTTAATATTTTTAAA-CATA
1 AATA-TTTTT-ATA--TTTAAATAATA
*
177219 AATATTTTTATATTTTAATAAT-
1 AATATTTTTATATTTAAATAATA
* * * *
177241 AAT-TATTAATATTAAAAAAAT-
1 AATATTTTTATATTTAAATAATA
177262 AATATTTTTATTATTTAAATAATA
1 AATATTTTTA-TATTTAAATAATA
177286 AATATTT
1 AATATTT
177293 ATAAAATATT
Statistics
Matches: 77, Mismatches: 13, Indels: 17
0.72 0.12 0.16
Matches are distributed among these distances:
21 20 0.26
22 12 0.16
23 16 0.21
24 12 0.16
25 5 0.06
26 12 0.16
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (23 bp):
AATATTTTTATATTTAAATAATA
Found at i:177289 original size:24 final size:24
Alignment explanation
Indices: 177182--177292 Score: 74
Period size: 23 Copynumber: 4.8 Consensus size: 24
177172 AATATTTTAA
*
177182 ATTTAAAT-TTAAATATTTTTTAATAT
1 ATTTAAATAATAAATA-TTTTT-AT-T
* *
177208 TTTTAAA-CATAAATATTTTTA-T
1 ATTTAAATAATAAATATTTTTATT
* * *
177230 ATTTTAATAAT--A-ATTATTAAT
1 ATTTAAATAATAAATATTTTTATT
* *
177251 ATTAAAAAAAT-AATATTTTTATT
1 ATTTAAATAATAAATATTTTTATT
177274 ATTTAAATAATAAATATTT
1 ATTTAAATAATAAATATTT
177293 ATAAAATATT
Statistics
Matches: 66, Mismatches: 13, Indels: 14
0.71 0.14 0.15
Matches are distributed among these distances:
20 6 0.09
21 10 0.15
22 7 0.11
23 18 0.27
24 8 0.12
25 5 0.08
26 12 0.18
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (24 bp):
ATTTAAATAATAAATATTTTTATT
Found at i:179428 original size:8 final size:9
Alignment explanation
Indices: 179401--179426 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
179391 ATTTAGGGTG
179401 AATATTTTT
1 AATATTTTT
179410 AATATTTTT
1 AATATTTTT
179419 AATATTTT
1 AATATTTT
179427 AAAAATTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
AATATTTTT
Found at i:179453 original size:26 final size:25
Alignment explanation
Indices: 179424--179483 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
179414 TTTTTAATAT
* **
179424 TTTAAAAATTAATTAAAATTTAAAAA
1 TTTAAAAATT-ATAAAAATAAAAAAA
*
179450 TTTAAAAAATATAAAAATAAAAAAA
1 TTTAAAAATTATAAAAATAAAAAAA
*
179475 TTTTAAAAT
1 TTTAAAAAT
179484 CATTGTAAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
25 19 0.68
26 9 0.32
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (25 bp):
TTTAAAAATTATAAAAATAAAAAAA
Found at i:179458 original size:17 final size:16
Alignment explanation
Indices: 179424--179483 Score: 66
Period size: 16 Copynumber: 3.6 Consensus size: 16
179414 TTTTTAATAT
179424 TTTAAAAATTAATTAAAA
1 TTTAAAAATTAA--AAAA
179442 TTTAAAAATTTAAAAAA
1 TTTAAAAA-TTAAAAAA
* *
179459 TATAAAAATAAAAAAA
1 TTTAAAAATTAAAAAA
*
179475 TTTTAAAAT
1 TTTAAAAAT
179484 CATTGTAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
16 14 0.38
17 11 0.30
18 8 0.22
19 4 0.11
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
TTTAAAAATTAAAAAA
Found at i:180432 original size:22 final size:19
Alignment explanation
Indices: 180373--180422 Score: 55
Period size: 22 Copynumber: 2.5 Consensus size: 19
180363 TGATCTTATA
*
180373 ATATAATTTAATTAATAAT
1 ATATAATTTAATTAAAAAT
*
180392 TTATAATTTAACAGTTAAAAAT
1 ATATAATTT-A-A-TTAAAAAT
180414 ATATAATTT
1 ATATAATTT
180423 GATATTTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 8 0.32
20 1 0.04
21 1 0.04
22 15 0.60
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (19 bp):
ATATAATTTAATTAAAAAT
Found at i:184958 original size:2 final size:2
Alignment explanation
Indices: 184951--184985 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
184941 TCGAAGGCAT
184951 TA TA TA TA 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 TA TA TA TA T
184986 TCTAAAAAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:188524 original size:26 final size:26
Alignment explanation
Indices: 188495--188550 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
188485 ATAGAGATAG
* * *
188495 GATTGATAAAGTTTAACTTTATTTAA
1 GATTAATAAAGTTCAACTTTATCTAA
188521 GATTAATAAAGTTCAACTTTATCTAA
1 GATTAATAAAGTTCAACTTTATCTAA
188547 GATT
1 GATT
188551 CTAGATTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.39, C:0.07, G:0.11, T:0.43
Consensus pattern (26 bp):
GATTAATAAAGTTCAACTTTATCTAA
Found at i:195501 original size:13 final size:14
Alignment explanation
Indices: 195485--195514 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
195475 TAAATATTAA
195485 AAACAAA-TTTTGT
1 AAACAAATTTTTGT
195498 AAACAAATTTTTGT
1 AAACAAATTTTTGT
195512 AAA
1 AAA
195515 TAATCATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.37
Consensus pattern (14 bp):
AAACAAATTTTTGT
Found at i:196019 original size:97 final size:97
Alignment explanation
Indices: 195768--196008 Score: 378
Period size: 97 Copynumber: 2.5 Consensus size: 97
195758 ATTGAAAAAT
* ** *
195768 GGGGTTGGAGTATCCCCTCGGAGGAATAAAGTTGAAGTATCCCCGATGATGACAATTTAAGCGAG
1 GGGGTTGGAGTATCCCCTCGAAGGAATAGGGTTGAAGTATCCCCGATGATGACAATTTAAGCAAG
*
195833 AATAAGATTTAAACTTTGATGAGTTTAAAAGC
66 AATAAGATTTAAACTTTAATGAGTTTAAAAGC
* * *
195865 GGGGTTGGAGTATCCTCTC-AGAGGAATAGGGTT-AGAGTATCCCTGATGATGACAATTTAAGTA
1 GGGGTTGGAGTATCCCCTCGA-AGGAATAGGGTTGA-AGTATCCCCGATGATGACAATTTAAGCA
195928 AGAATAAGATTTAAACTTTAATGAGTTTAAAAGC
64 AGAATAAGATTTAAACTTTAATGAGTTTAAAAGC
195962 GGGGTTGGAGTATCCCCTCGAAGGAATAGGGTTGAAGTATCCCCGAT
1 GGGGTTGGAGTATCCCCTCGAAGGAATAGGGTTGAAGTATCCCCGAT
196009 AAATAAAATT
Statistics
Matches: 130, Mismatches: 10, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
96 1 0.01
97 127 0.98
98 2 0.02
ACGTcount: A:0.32, C:0.13, G:0.27, T:0.27
Consensus pattern (97 bp):
GGGGTTGGAGTATCCCCTCGAAGGAATAGGGTTGAAGTATCCCCGATGATGACAATTTAAGCAAG
AATAAGATTTAAACTTTAATGAGTTTAAAAGC
Found at i:198193 original size:79 final size:79
Alignment explanation
Indices: 198105--198316 Score: 288
Period size: 76 Copynumber: 2.7 Consensus size: 79
198095 TTAGAAATCA
198105 CGGGGTTGGAGTATCCCCTCGAGAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTAATAT
1 CGGGGTTGGAGTATCCCCTCGAGAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTAATAT
198170 TTTAGAAACAAAAC
66 TTTAGAAACAAAAC
* * * * *
198184 CGGGGTTGGAGTATCCCCTCGAAAATAACAGGATTGGAGTATCCCCG---ATGAAAAATTGATGT
1 CGGGGTTGGAGTATCCCCTCGAGAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTAATAT
*
198246 TTTAGAAATAAAAC
66 TTTAGAAACAAAAC
* * * * *
198260 TGGGGTTGGAGTGTCCCCTCG-GAAATAACGAGGTTGGAGTATCCCTGATTGTGAAAA
1 CGGGGTTGGAGTATCCCCTCGAG-AATAACGGGGTTGGAGTATCCCCGATTATGAAAA
198317 GTCAGTGTTT
Statistics
Matches: 115, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
76 65 0.57
79 50 0.43
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.25
Consensus pattern (79 bp):
CGGGGTTGGAGTATCCCCTCGAGAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTAATAT
TTTAGAAACAAAAC
Found at i:199082 original size:9 final size:11
Alignment explanation
Indices: 199060--199088 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
199050 TCTTTGAGGG
199060 AAAAATATCAA
1 AAAAATATCAA
199071 AAAAAT-TCAA
1 AAAAATATCAA
199081 AAAAATAT
1 AAAAATAT
199089 TTTCAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.21
Consensus pattern (11 bp):
AAAAATATCAA
Found at i:200763 original size:20 final size:19
Alignment explanation
Indices: 200738--200831 Score: 107
Period size: 20 Copynumber: 4.7 Consensus size: 19
200728 AATGCCTGAG
200738 TGTATCGATACATTGTAAAA
1 TGTATCGATACATTG-AAAA
* *
200758 TGTATCGATACAATGAGCAA
1 TGTATCGATACATTGA-AAA
* *
200778 TGTATCGATAGAATGCAAAA
1 TGTATCGATACATTG-AAAA
*
200798 TGTATCGATACATTAAATAA
1 TGTATCGATACATTGAA-AA
200818 TGTATCGATACATT
1 TGTATCGATACATT
200832 TCTTGGCAGT
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
19 3 0.05
20 60 0.94
21 1 0.02
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (19 bp):
TGTATCGATACATTGAAAA
Found at i:200798 original size:40 final size:40
Alignment explanation
Indices: 200738--200829 Score: 121
Period size: 40 Copynumber: 2.3 Consensus size: 40
200728 AATGCCTGAG
* * * *
200738 TGTATCGATACATTGTAAAATGTATCGATACAATGAGCAA
1 TGTATCGATACAATGCAAAATGTATCGATACAATAAACAA
* * *
200778 TGTATCGATAGAATGCAAAATGTATCGATACATTAAATAA
1 TGTATCGATACAATGCAAAATGTATCGATACAATAAACAA
200818 TGTATCGATACA
1 TGTATCGATACA
200830 TTTCTTGGCA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.30
Consensus pattern (40 bp):
TGTATCGATACAATGCAAAATGTATCGATACAATAAACAA
Found at i:201698 original size:45 final size:42
Alignment explanation
Indices: 201570--201707 Score: 143
Period size: 42 Copynumber: 3.2 Consensus size: 42
201560 ACATCTCCTT
* * * * **
201570 TTTGAGGACAAAGGAAAAAGGGAAACAAAATACGTCCTGCTC
1 TTTGAGGACAAAAGAAAAAGGAAAAGAAAGTGTGTCCTGCTC
* *
201612 TTTAAGGACAAAAGAAAAAGGAAAATAAAGTGTGTCCTGCTC
1 TTTGAGGACAAAAGAAAAAGGAAAAGAAAGTGTGTCCTGCTC
*
201654 TTTGAGGACAAAAGAGAAAA-GAAGGGAAGGAAGTGTGTCCTGCTC
1 TTTGAGGACAAAAGA-AAAAGGAA---AAGAAAGTGTGTCCTGCTC
*
201699 TTCGAGGAC
1 TTTGAGGAC
201708 TGAAAAGTGC
Statistics
Matches: 81, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
42 52 0.64
43 4 0.05
45 25 0.31
ACGTcount: A:0.41, C:0.14, G:0.27, T:0.19
Consensus pattern (42 bp):
TTTGAGGACAAAAGAAAAAGGAAAAGAAAGTGTGTCCTGCTC
Found at i:201792 original size:61 final size:61
Alignment explanation
Indices: 201690--202601 Score: 1030
Period size: 61 Copynumber: 15.4 Consensus size: 61
201680 AAGGAAGTGT
* * *
201690 GTCCTGCTCTTCGAGGACTGAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAGAC
1 GTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAGGC
* * * * * *
201751 GCCCTGCCCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAGAAGGC
1 GTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAGGC
* *
201812 ATCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT-AAAAGGAGAAGGC
1 GTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAA-GAAAAGGC
* * * *
201873 ATCCTGCTCTTTGAGGACTG-AAGGTGCCACCAGCTTGTGTGGGCTTTAAAAAGAAAAGGC
1 GTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAGGC
* * * *
201933 ATCCTGCCCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAAAAGAAAA--C
1 GTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTG--AAAAGAAAAGGC
* ** *
201994 ATCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTCAGCTTT-AAAAGGAGAAGGC
1 GTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAA-GAAAAGGC
* * * *
202055 GTCCTGCTCTTTGAGGACTG-AAGGTGCCACCAGCTTGTGTGGGCTTTAAAAAAAAAAGGC
1 GTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAGGC
* * *
202115 GTCCTGCCCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAAAAGAAAA--C
1 GTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTG--AAAAGAAAAGGC
* *
202176 ATCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT-AAAAGGAAAAGAC
1 GTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAA-GAAAAGGC
* * *
202237 GTCTTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGC
1 GTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAGGC
* * *
202298 ATCCTCCTCTTTGAGGATTGGAAAA-TGCCACCAACTTGTGTGGGCTTT-----G-AAAGGC
1 GTCCTGCTCTTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAGGC
*
202353 GTCCTGCTCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTT------AAAAGGT
1 GTCCTGCTCTTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAGGC
* * * * * *
202408 GTCATGCTCTTTGAAGACTGAAAAATGCCACTAGCTTATGTGGGCTTT-----G-AAAGGC
1 GTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAGGC
* *
202463 GTCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-----G-AAAGGC
1 GTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAGGC
* * * * *
202518 TTCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTGTATGGGCTTTGAAAGGAAAAGGC
1 GTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAGGC
202579 GTCCTGCTCTTTGAGGACTGAAA
1 GTCCTGCTCTTTGAGGACTGAAA
202602 GTGAAAGGAG
Statistics
Matches: 752, Mismatches: 73, Indels: 52
0.86 0.08 0.06
Matches are distributed among these distances:
54 5 0.01
55 190 0.25
56 1 0.00
58 8 0.01
59 9 0.01
60 104 0.14
61 409 0.54
62 9 0.01
63 17 0.02
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (61 bp):
GTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAGGC
Found at i:201927 original size:182 final size:182
Alignment explanation
Indices: 201690--202601 Score: 1187
Period size: 182 Copynumber: 5.1 Consensus size: 182
201680 AAGGAAGTGT
* * * * * *
201690 GTCCTGCTCTTCGAGGACTGAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAGACGCCC
1 GTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAGCTTGTGTGGGCTTTAAAAAGAAAAGGCGTCC
201755 TGCCCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAGAAGGCATCCTGCT
66 TGCCCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGA-AAGGCATCCTGCT
201820 CTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGC
130 CTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGC
* * *
201873 ATCCTGCTCTTTGAGGACTG-AAGGTGCCACCAGCTTGTGTGGGCTTTAAAAAGAAAAGGCATCC
1 GTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAGCTTGTGTGGGCTTTAAAAAGAAAAGGCGTCC
*
201937 TGCCCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAAAAGAAA-ACATCCTGC
66 TGCCCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTT--AAAAAGAAAGGCATCCTGC
**
202001 TCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTCAGCTTTAAAAGGAGAAGGC
129 TCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGC
* *
202055 GTCCTGCTCTTTGAGGACTG-AAGGTGCCACCAGCTTGTGTGGGCTTTAAAAAAAAAAGGCGTCC
1 GTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAGCTTGTGTGGGCTTTAAAAAGAAAAGGCGTCC
*
202119 TGCCCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAAAAGAAA-ACATCCTGC
66 TGCCCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTT--AAAAAGAAAGGCATCCTGC
* *
202183 TCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGAC
129 TCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGC
* * * * * *
202237 GTCTTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCC
1 GTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAGCTTGTGTGGGCTTTAAAAAGAAAAGGCGTCC
* ** *
202302 T-CCTCTTTGAGGATTGGAAAATGCCACCAACTTGTGTGGGCTTT-----GAAAGGCGTCCTGCT
66 TGCC-CTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAGGCATCCTGCT
*
202361 CTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTT---A--A-AAGGT
130 CTTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGC
* * * * *
202408 GTCATGCTCTTTGAAGACTGAAAAATGCCACTAGCTTATGTGGGCTTT-----G-AAAGGCGTCC
1 GTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAGCTTGTGTGGGCTTTAAAAAGAAAAGGCGTCC
* * * * *
202467 TACTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-----GAAAGGCTTCCTACTC
66 TGCCCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAGGCATCCTGCTC
* * * *
202527 TTTGAGGACTGAAAGGTGCCACCAACTTGTATGGGCTTTGAAAGGAAAAGGC
131 TTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGC
202579 GTCCTGCTCTTTGAGGACTGAAA
1 GTCCTGCTCTTTGAGGACTGAAA
202602 GTGAAAGGAG
Statistics
Matches: 662, Mismatches: 53, Indels: 40
0.88 0.07 0.05
Matches are distributed among these distances:
164 4 0.01
165 91 0.14
166 2 0.00
168 1 0.00
170 1 0.00
171 71 0.11
172 1 0.00
174 1 0.00
176 4 0.01
177 42 0.06
178 5 0.01
182 337 0.51
183 95 0.14
184 7 0.01
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (182 bp):
GTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAGCTTGTGTGGGCTTTAAAAAGAAAAGGCGTCC
TGCCCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAGGCATCCTGCTC
TTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGC
Found at i:202141 original size:243 final size:243
Alignment explanation
Indices: 201691--202598 Score: 1124
Period size: 243 Copynumber: 3.8 Consensus size: 243
201681 AGGAAGTGTG
* * *
201691 TCCTGCTCTTCGAGGACTGAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAGACGCCCT
1 TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAGACGTCCT
* * *
201756 GCCCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAGAAGGCATCCTGCTC
66 GCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT-AAAAGAGAAGGCATCCTGCTC
* *
201821 TTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCATCCTGCTCTTTG
130 TTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTTG
*
201886 AGGACT-GAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAAGAAAAGGCA
195 AGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGCA
* * * *
201934 TCCTGCCCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAAA-AGAAA-ACATC
1 TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTG-AAAAGA-AAAGACGTC
** *
201997 CTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTCAGCTTTAAAAGGAGAAGGCGTCCTGC
64 CTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAA-GAGAAGGCATCCTGC
* * ** *
202062 TCTTTGAGGACTG-AAGGTGCCACCAGCTTGTGTGGGCTTTAAAAAAAAAAGGCGTCCTGCCCTT
128 TCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTT
202126 TGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAAAAGAAAA--CA
193 TGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTT--AAAAAGAAAAGGCA
*
202177 TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT-AAAAGGAAAAGACGTCT
1 TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAA-GAAAAGACGTCC
* * * *
202241 TGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTCCT
65 TGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT-AAAAGAGAAGGCATCCTGCT
*
202306 CTTTGAGGATTGGAAAA-TGCCACCAACTTGTGTGGGCTTT-----G-AAAGGCGTCCTGCTCTT
129 CTTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTT
**
202364 TGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-AAAAG----GTG--
193 TGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAG-GCA
* * * * * *
202409 TCATGCTCTTTGAAGACTGAAAAATGCCACTAGCTTATGTGGGCTTTG-AAAG----G-CGTCCT
1 TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAGACGTCCT
* * * *
202468 ACTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT----GA-AAGGCTTCCTACTCT
66 GCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAGAAGGCATCCTGCTCT
* * *
202528 TTGAGGACTGAAAGGTGCCACCAACTTGTATGGGCTTTGAAAGGAAAAGGCGTCCTGCTCTTTGA
131 TTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTTGA
202593 GGACTG
196 GGACTG
202599 AAAGTGAAAG
Statistics
Matches: 586, Mismatches: 56, Indels: 63
0.83 0.08 0.09
Matches are distributed among these distances:
219 4 0.01
220 42 0.07
221 2 0.00
225 1 0.00
226 71 0.12
227 1 0.00
231 1 0.00
232 44 0.08
235 5 0.01
238 51 0.09
241 4 0.01
242 59 0.10
243 255 0.44
244 34 0.06
245 12 0.02
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (243 bp):
TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAGACGTCCT
GCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAGAAGGCATCCTGCTCT
TTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTTGA
GGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGCA
Found at i:202485 original size:26 final size:26
Alignment explanation
Indices: 202455--202542 Score: 72
Period size: 26 Copynumber: 3.3 Consensus size: 26
202445 ATGTGGGCTT
202455 TGAAAGGCGTCCTACTCTTTGAGGAC
1 TGAAAGGCGTCCTACTCTTTGAGGAC
* * * *
202481 TGAAAGGTG-CC-ACCAACTTGTGTGGGC
1 TGAAAGGCGTCCTA-C-TCTT-TGAGGAC
*
202508 TTTGAAAGGCTTCCTACTCTTTGAGGAC
1 --TGAAAGGCGTCCTACTCTTTGAGGAC
202536 TGAAAGG
1 TGAAAGG
202543 TGCCACCAAC
Statistics
Matches: 46, Mismatches: 9, Indels: 14
0.67 0.13 0.20
Matches are distributed among these distances:
24 1 0.02
25 3 0.07
26 18 0.39
27 5 0.11
28 5 0.11
29 10 0.22
30 3 0.07
31 1 0.02
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.27
Consensus pattern (26 bp):
TGAAAGGCGTCCTACTCTTTGAGGAC
Found at i:203598 original size:1 final size:1
Alignment explanation
Indices: 203578--203670 Score: 69
Period size: 1 Copynumber: 93.0 Consensus size: 1
203568 CTTTTCTCTC
* * * * * * * * * *
203578 TTTTTTCTTTGTTTTGTTTTTTTTTGTTTTTTGTTTTTGTTTTTTGTTTCTTTTTTGTTTTTGTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * *
203643 TTTGTTTTTTGTTTTTTTTATTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
203671 CAGAAGATAA
Statistics
Matches: 66, Mismatches: 26, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 66 1.00
ACGTcount: A:0.01, C:0.02, G:0.11, T:0.86
Consensus pattern (1 bp):
T
Found at i:203599 original size:7 final size:7
Alignment explanation
Indices: 203585--203659 Score: 82
Period size: 7 Copynumber: 10.4 Consensus size: 7
203575 CTCTTTTTTC
203585 TTTGTTT
1 TTTGTTT
*
203592 TGTTTTTT
1 T-TTGTTT
203600 TTTGTTT
1 TTTGTTT
203607 TTTG-TT
1 TTTGTTT
203613 TTTGTTT
1 TTTGTTT
203620 TTTGTTT
1 TTTGTTT
203627 CTTT-TTT
1 -TTTGTTT
*
203634 GTTTTTGTT
1 -TTTGT-TT
203643 TTTGTTT
1 TTTGTTT
203650 TTTGTTT
1 TTTGTTT
203657 TTT
1 TTT
203660 TTATTTTTTT
Statistics
Matches: 59, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
6 6 0.10
7 37 0.63
8 14 0.24
9 2 0.03
ACGTcount: A:0.00, C:0.01, G:0.13, T:0.85
Consensus pattern (7 bp):
TTTGTTT
Found at i:203625 original size:30 final size:30
Alignment explanation
Indices: 203589--203670 Score: 130
Period size: 30 Copynumber: 2.7 Consensus size: 30
203579 TTTTTCTTTG
203589 TTTTGTTTTTTTTTGTTTTTTGTTTTTGTT
1 TTTTGTTTTTTTTTGTTTTTTGTTTTTGTT
203619 TTTTGTTTCTTTTTTG-TTTTTGTTTTTGTT
1 TTTTGTTT-TTTTTTGTTTTTTGTTTTTGTT
*
203649 TTTTGTTTTTTTTATTTTTTTT
1 TTTTGTTTTTTTT-TGTTTTTT
203671 CAGAAGATAA
Statistics
Matches: 48, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
29 5 0.10
30 31 0.65
31 12 0.25
ACGTcount: A:0.01, C:0.01, G:0.11, T:0.87
Consensus pattern (30 bp):
TTTTGTTTTTTTTTGTTTTTTGTTTTTGTT
Found at i:203667 original size:6 final size:6
Alignment explanation
Indices: 203585--203658 Score: 84
Period size: 6 Copynumber: 12.5 Consensus size: 6
203575 CTCTTTTTTC
*
203585 TTTG-T TTTG-T TTT-TT TTTGTTT TTTGTT TTTGTTT TTTGTT TCT-TT
1 TTTGTT TTTGTT TTTGTT TTTG-TT TTTGTT TTTG-TT TTTGTT TTTGTT
203631 TTTGTT TTTGTT TTTGTTT TTTGTT TTT
1 TTTGTT TTTGTT TTTG-TT TTTGTT TTT
203659 TTTATTTTTT
Statistics
Matches: 61, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
5 16 0.26
6 27 0.44
7 18 0.30
ACGTcount: A:0.00, C:0.01, G:0.14, T:0.85
Consensus pattern (6 bp):
TTTGTT
Found at i:216198 original size:79 final size:79
Alignment explanation
Indices: 216067--216239 Score: 240
Period size: 79 Copynumber: 2.2 Consensus size: 79
216057 GATAATAACA
*
216067 GGGTTGGAGTATCCCCTCGAGAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTT
1 GGGTTGGAGTATCCCCTCGAGAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATCGATGTTT
216132 TAGAAATAAAACTG
66 TAGAAATAAAACTG
* * * *
216146 GGGTTGGAGTGTCCCTTCG-GAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAGTCGGTGTT
1 GGGTTGGAGTATCCCCTCGAG-AATAACGGGGTTGGAGTATCCCCGATTATGAAAAATCGATGTT
* * *
216210 TTGGAAATAAAATTA
65 TTAGAAATAAAACTG
* *
216225 GAGTTGGAATATCCC
1 GGGTTGGAGTATCCC
216240 TGATTGTGGA
Statistics
Matches: 82, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
78 1 0.01
79 81 0.99
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.28
Consensus pattern (79 bp):
GGGTTGGAGTATCCCCTCGAGAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATCGATGTTT
TAGAAATAAAACTG
Found at i:216282 original size:51 final size:51
Alignment explanation
Indices: 216172--216291 Score: 134
Period size: 51 Copynumber: 2.4 Consensus size: 51
216162 TCGGAAATAA
* * *
216172 CGGGGTTGGAGTATCCCCGATTATGAAAAGTCGGTGTTTTGGAAATAAAAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAGTCGGTATTTTAGAAATAAAAC
** * * * * *
216223 TAGAGTTGGAATATCCCTGATTGTGGAAAA-TTGGTATTTTAGAAATAAAAC
1 CGGGGTTGGAGTATCCCCGATTAT-GAAAAGTCGGTATTTTAGAAATAAAAC
216274 CGGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
216292 TCGGAAATAA
Statistics
Matches: 53, Mismatches: 15, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
51 48 0.91
52 5 0.09
ACGTcount: A:0.30, C:0.12, G:0.28, T:0.30
Consensus pattern (51 bp):
CGGGGTTGGAGTATCCCCGATTATGAAAAGTCGGTATTTTAGAAATAAAAC
Found at i:218690 original size:20 final size:20
Alignment explanation
Indices: 218665--218773 Score: 117
Period size: 20 Copynumber: 5.8 Consensus size: 20
218655 AAAATGCCTG
*
218665 AATGTATCGATACATTATAA
1 AATGTATCGATACATTGTAA
*
218685 AATGTATCAATACATTGTAA
1 AATGTATCGATACATTGTAA
* *
218705 AATGTATCGATACAATGCAA
1 AATGTATCGATACATTGTAA
218725 AATGTATCGATAC-------
1 AATGTATCGATACATTGTAA
218738 AATGTATCGATACATTG-AA
1 AATGTATCGATACATTGTAA
218757 TAATGTATCGATACATT
1 -AATGTATCGATACATT
218774 TCCCTGACAG
Statistics
Matches: 77, Mismatches: 5, Indels: 14
0.80 0.05 0.15
Matches are distributed among these distances:
13 13 0.17
20 64 0.83
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACATTGTAA
Found at i:218743 original size:13 final size:13
Alignment explanation
Indices: 218725--218751 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
218715 TACAATGCAA
218725 AATGTATCGATAC
1 AATGTATCGATAC
218738 AATGTATCGATAC
1 AATGTATCGATAC
218751 A
1 A
218752 TTGAATAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:218747 original size:33 final size:33
Alignment explanation
Indices: 218705--218771 Score: 109
Period size: 33 Copynumber: 2.0 Consensus size: 33
218695 TACATTGTAA
218705 AATGTATCGATACAATGCAA-AATGTATCGATAC
1 AATGTATCGATACAATG-AATAATGTATCGATAC
*
218738 AATGTATCGATACATTGAATAATGTATCGATAC
1 AATGTATCGATACAATGAATAATGTATCGATAC
218771 A
1 A
218772 TTTCCCTGAC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 2 0.06
33 30 0.94
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.30
Consensus pattern (33 bp):
AATGTATCGATACAATGAATAATGTATCGATAC
Found at i:219547 original size:16 final size:16
Alignment explanation
Indices: 219528--219559 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
219518 ATTTCATTTG
219528 TTTTTTCTTTCTTCTTT
1 TTTTTTCTTT-TTCTTT
219545 TTTTTTCTTTTTCTT
1 TTTTTTCTTTTTCTT
219560 GCTTTCTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTTTCTTTTTCTTT
Found at i:219551 original size:13 final size:14
Alignment explanation
Indices: 219528--219570 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
219518 ATTTCATTTG
219528 TTTTTTCTTTCTTC
1 TTTTTTCTTTCTTC
219542 TTTTTT-TTTCTT-
1 TTTTTTCTTTCTTC
*
219554 TTTCTTGCTTTCTTC
1 TTT-TTTCTTTCTTC
219569 TT
1 TT
219571 CATCTTCTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
12 3 0.12
13 8 0.32
14 12 0.48
15 2 0.08
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (14 bp):
TTTTTTCTTTCTTC
Found at i:219586 original size:17 final size:16
Alignment explanation
Indices: 219531--219587 Score: 50
Period size: 17 Copynumber: 3.6 Consensus size: 16
219521 TCATTTGTTT
219531 TTTCTTTCTTCT-TT-
1 TTTCTTTCTTCTCTTC
*
219545 TTT-TTTCTTTTTCTTGC
1 TTTCTTTC-TTCTCTT-C
219562 TTTC-TTCTTCATCTTC
1 TTTCTTTCTTC-TCTTC
219578 TTTCTTTCTT
1 TTTCTTTCTT
219588 ACCTATAACC
Statistics
Matches: 34, Mismatches: 2, Indels: 11
0.72 0.04 0.23
Matches are distributed among these distances:
13 4 0.12
14 6 0.18
15 2 0.06
16 7 0.21
17 15 0.44
ACGTcount: A:0.02, C:0.23, G:0.02, T:0.74
Consensus pattern (16 bp):
TTTCTTTCTTCTCTTC
Found at i:220952 original size:30 final size:31
Alignment explanation
Indices: 220918--220982 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 31
220908 GGGCTTTTAA
* *
220918 AAAAAAGGTGCCATTAACTTGTGT-GCTTTG
1 AAAAAAGGTACCAATAACTTGTGTAGCTTTG
* *
220948 AAAAAAGTTACCAATGACTTGTGTAGGCTTTG
1 AAAAAAGGTACCAATAACTTGTGTA-GCTTTG
220980 AAA
1 AAA
220983 GGGTATGCCA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 20 0.69
32 9 0.31
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.31
Consensus pattern (31 bp):
AAAAAAGGTACCAATAACTTGTGTAGCTTTG
Found at i:221027 original size:28 final size:28
Alignment explanation
Indices: 220962--221887 Score: 1077
Period size: 28 Copynumber: 33.0 Consensus size: 28
220952 AAGTTACCAA
* *
220962 TGACTTGTGTAGGCTTTGAAAGGGTATGCCAT
1 TGACTTGTG--GGCTTTGAAA-TG-ATGCCAC
* *
220994 TGACTTGTAGGTTTTGAAATGATGCCAC
1 TGACTTGTGGGCTTTGAAATGATGCCAC
* *
221022 TAACTTGTGGGCTTTGAAACGATGCCAC
1 TGACTTGTGGGCTTTGAAATGATGCCAC
*
221050 TGACTTGTAGGCTTTGAAATGATGCCAC
1 TGACTTGTGGGCTTTGAAATGATGCCAC
* *
221078 TAACTTGTGGGCTTTAAAAT-AGTGCCAC
1 TGACTTGTGGGCTTTGAAATGA-TGCCAC
* ** *
221106 TGCCTTACGGGCTTTGAAATGATGCCAT
1 TGACTTGTGGGCTTTGAAATGATGCCAC
* *
221134 TGACTTGTGGGCTTTGAAATGGTGTCA-
1 TGACTTGTGGGCTTTGAAATGATGCCAC
*
221161 TGACTTGTGGGCTTTAAAATGATGCCAC
1 TGACTTGTGGGCTTTGAAATGATGCCAC
221189 TGACTTGTGGGCTTTGAAATGATGCCAC
1 TGACTTGTGGGCTTTGAAATGATGCCAC
* *
221217 TGACTTGTAGGCTTTGAAATGATGCTAC
1 TGACTTGTGGGCTTTGAAATGATGCCAC
* * *
221245 TAACTTGTGGGCTTTGAAATAATGCCCC
1 TGACTTGTGGGCTTTGAAATGATGCCAC
*
221273 TGACTTGTGGGCTTTGAAATAATGCC-C
1 TGACTTGTGGGCTTTGAAATGATGCCAC
221300 TTGACTTGTGGGCTTTGAAATGATGCCAC
1 -TGACTTGTGGGCTTTGAAATGATGCCAC
*
221329 TGACTTGTGGGCTTTGAAATGATGCCAT
1 TGACTTGTGGGCTTTGAAATGATGCCAC
*
221357 TGACTTGTGGGCTTTGAAATGATACCAC
1 TGACTTGTGGGCTTTGAAATGATGCCAC
* * *
221385 TGACTTGTGAGCTTTGAAAGGATGTCAC
1 TGACTTGTGGGCTTTGAAATGATGCCAC
* * * *
221413 TAACTTATAGGCTTTGAAAGGATGCCAC
1 TGACTTGTGGGCTTTGAAATGATGCCAC
* * * *
221441 TAACTTATAGGCTTTGAAAGGATGCCAC
1 TGACTTGTGGGCTTTGAAATGATGCCAC
* * *
221469 TAACTTATGGGCTTTGAAAGGATGCCAC
1 TGACTTGTGGGCTTTGAAATGATGCCAC
* *
221497 TAACTTGTGGGCTTTGAAAAGATGCCAC
1 TGACTTGTGGGCTTTGAAATGATGCCAC
*
221525 TAACTTGTGGGCTTTGAAATGATGCCAC
1 TGACTTGTGGGCTTTGAAATGATGCCAC
*
221553 TGACTTGTGGGCTTTGAAAGGATGCCAC
1 TGACTTGTGGGCTTTGAAATGATGCCAC
* * * *
221581 TAACTTGTGGGCTTTAAAAGGATGCCAA
1 TGACTTGTGGGCTTTGAAATGATGCCAC
* * *
221609 TAACTTGTGGGCTTTGAAAGGATGTCAC
1 TGACTTGTGGGCTTTGAAATGATGCCAC
* *
221637 TAACTT-TGGGCTTTGAAAGGATGCCAC
1 TGACTTGTGGGCTTTGAAATGATGCCAC
* *
221664 TAACTTGTGGGCTTTGAAAAGATGCCAC
1 TGACTTGTGGGCTTTGAAATGATGCCAC
* *
221692 TAACTTGTGGGCTTTGAAAAGATGCCAC
1 TGACTTGTGGGCTTTGAAATGATGCCAC
*
221720 TGACTTGTGGGCTTTGAAATGACGCCAC
1 TGACTTGTGGGCTTTGAAATGATGCCAC
*
221748 TGACTTGTGGGCTTTGAAATGACGCCAC
1 TGACTTGTGGGCTTTGAAATGATGCCAC
* * * *
221776 TAACTTGTGAGCTTTAAAAGGATGCCAC
1 TGACTTGTGGGCTTTGAAATGATGCCAC
* * * *
221804 TGACTTGTGGACTTTAAAAGGGTGCCAC
1 TGACTTGTGGGCTTTGAAATGATGCCAC
* * * * * * *
221832 GGAGTTATGGACTTTCAAAGGGTGCCAC
1 TGACTTGTGGGCTTTGAAATGATGCCAC
* * * * *
221860 AGAGTTGTGGACTTTAAAAAGATGCCAC
1 TGACTTGTGGGCTTTGAAATGATGCCAC
221888 GGAGTTATGG
Statistics
Matches: 803, Mismatches: 85, Indels: 16
0.89 0.09 0.02
Matches are distributed among these distances:
27 52 0.06
28 731 0.91
29 3 0.00
30 9 0.01
32 8 0.01
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (28 bp):
TGACTTGTGGGCTTTGAAATGATGCCAC
Found at i:221831 original size:56 final size:56
Alignment explanation
Indices: 220962--222144 Score: 1064
Period size: 56 Copynumber: 21.2 Consensus size: 56
220952 AAGTTACCAA
* * * *
220962 TGACTTGTGTAGGCTTTGAAAGGGTATGCCATTGACTTGTAGGTTTTGAAATGATGCCAC
1 TGACTTGTG--GGCTTTGAAA-GG-ATGCCACTGACTTGTGGGCTTTGAAAGGATGCCAC
* * * *
221022 TAACTTGTGGGCTTTGAAACGATGCCACTGACTTGTAGGCTTTGAAATGATGCCAC
1 TGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCAC
* ** * ** * *
221078 TAACTTGTGGGCTTT-AAAATAGTGCCACTGCCTTACGGGCTTTGAAATGATGCCAT
1 TGACTTGTGGGCTTTGAAAGGA-TGCCACTGACTTGTGGGCTTTGAAAGGATGCCAC
* * *
221134 TGACTTGTGGGCTTTGAAATGG-TGTCA-TGACTTGTGGGCTTTAAAATGATGCCAC
1 TGACTTGTGGGCTTTGAAA-GGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCAC
* * * *
221189 TGACTTGTGGGCTTTGAAATGATGCCACTGACTTGTAGGCTTTGAAATGATGCTAC
1 TGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCAC
* ** * **
221245 TAACTTGTGGGCTTTGAAATAATGCCCCTGACTTGTGGGCTTTGAAATAATGCC-C
1 TGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCAC
* * *
221300 TTGACTTGTGGGCTTTGAAATGATGCCACTGACTTGTGGGCTTTGAAATGATGCCAT
1 -TGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCAC
* * * *
221357 TGACTTGTGGGCTTTGAAATGATACCACTGACTTGTGAGCTTTGAAAGGATGTCAC
1 TGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCAC
* * * * * *
221413 TAACTTATAGGCTTTGAAAGGATGCCACTAACTTATAGGCTTTGAAAGGATGCCAC
1 TGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCAC
* * * *
221469 TAACTTATGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAAGATGCCAC
1 TGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCAC
* *
221525 TAACTTGTGGGCTTTGAAATGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCAC
1 TGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCAC
* * * * *
221581 TAACTTGTGGGCTTTAAAAGGATGCCAATAACTTGTGGGCTTTGAAAGGATGTCAC
1 TGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCAC
* * *
221637 TAACTT-TGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAAGATGCCAC
1 TGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCAC
* * * *
221692 TAACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAATGACGCCAC
1 TGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCAC
* * * * *
221748 TGACTTGTGGGCTTTGAAATGACGCCACTAACTTGTGAGCTTTAAAAGGATGCCAC
1 TGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCAC
* * * * * * * * *
221804 TGACTTGTGGACTTTAAAAGGGTGCCACGGAGTTATGGACTTTCAAAGGGTGCCAC
1 TGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCAC
* * * * * * * * * *
221860 AGAGTTGTGGACTTTAAAAAGATGCCACGGAGTTATGGACTTTAAAAAGGA-GCCAC
1 TGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTT-GAAAGGATGCCAC
* * * * * * * * * *
221916 AGAGTTATGGAC-TTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGATGTCA-
1 TGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCAC
* * * * * *
221970 TGGAGTTGTGGAC-TT-AAAGGGATGCCA-TGGAGTTGTGGACTTTAAAAGGATACCAC
1 T-GACTTGTGGGCTTTGAAA-GGATGCCACT-GACTTGTGGGCTTTGAAAGGATGCCAC
* * * ** * * * * * *
222026 GGAGTTGTGGACTTAAAAAGGATGCCACGGAGTTATGGAC-TTAAAAAGATGCCAC
1 TGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCAC
* * * * * * * *
222081 GGAGTTGTGGAC-TTAAAAGGATGCTAC-GAAGTTGTGGAC-TTAAAAGGATGCCAC
1 TGACTTGTGGGCTTTGAAAGGATGCCACTG-ACTTGTGGGCTTTGAAAGGATGCCAC
* *
222135 GGAGTTGTGG
1 TGACTTGTGG
222145 ATGCCACGGA
Statistics
Matches: 987, Mismatches: 118, Indels: 42
0.86 0.10 0.04
Matches are distributed among these distances:
53 1 0.00
54 57 0.06
55 213 0.22
56 686 0.70
57 12 0.01
58 10 0.01
60 8 0.01
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (56 bp):
TGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCAC
Found at i:221859 original size:84 final size:84
Alignment explanation
Indices: 220920--222145 Score: 1018
Period size: 84 Copynumber: 14.6 Consensus size: 84
220910 GCTTTTAAAA
* * * * * * *
220920 AAAAGG-TGCCATTAACTTGTGTGCTTTGAAAAAAGTTACCAATGACTTGTGTAGGCTTTGAAAG
1 AAAAGGATGCCACTAACTTGTGGGCTTTG--AAAGGATGCCACTGACTTGTG--GACTTTGAAA-
* * *
220984 GGTATGCCATTGACTTGTAGGTTTT
61 GG-ATGCCACTGACTTGTGGGCTTT
* * * *
221009 GAAATGATGCCACTAACTTGTGGGCTTTGAAACGATGCCACTGACTTGTAGG-CTTTGAAATGAT
1 AAAAGGATGCCACTAACTTGTGGGCTTTGAAAGGATGCCACTGACTTGT-GGACTTTGAAAGGAT
*
221073 GCCACTAACTTGTGGGCTTT
65 GCCACTGACTTGTGGGCTTT
* ** ** * * *
221093 AAAA-TAGTGCCACTGCCTTACGGGCTTTGAAATGATGCCATTGACTTGTGGGCTTTGAAATGG-
1 AAAAGGA-TGCCACTAACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGACTTTGAAA-GGA
*
221156 TGTCA-TGACTTGTGGGCTTT
64 TGCCACTGACTTGTGGGCTTT
* * * *
221176 AAAATGATGCCACTGACTTGTGGGCTTTGAAATGATGCCACTGACTTGTAGG-CTTTGAAATGAT
1 AAAAGGATGCCACTAACTTGTGGGCTTTGAAAGGATGCCACTGACTTGT-GGACTTTGAAAGGAT
* *
221240 GCTACTAACTTGTGGGCTTT
65 GCCACTGACTTGTGGGCTTT
* ** * * ** * *
221260 GAAATAATGCCCCTGACTTGTGGGCTTTGAAATAATGCC-CTTGACTTGTGGGCTTTGAAATGAT
1 AAAAGGATGCCACTAACTTGTGGGCTTTGAAAGGATGCCAC-TGACTTGTGGACTTTGAAAGGAT
221324 GCCACTGACTTGTGGGCTTT
65 GCCACTGACTTGTGGGCTTT
* * * * * *
221344 GAAATGATGCCATTGACTTGTGGGCTTTGAAATGATACCACTGACTTGT-GAGCTTTGAAAGGAT
1 AAAAGGATGCCACTAACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGA-CTTTGAAAGGAT
* * * *
221408 GTCACTAACTTATAGGCTTT
65 GCCACTGACTTGTGGGCTTT
* * * * * *
221428 GAAAGGATGCCACTAACTTATAGGCTTTGAAAGGATGCCACTAACTTATGGGCTTTGAAAGGATG
1 AAAAGGATGCCACTAACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGACTTTGAAAGGATG
*
221493 CCACTAACTTGTGGGCTTT
66 CCACTGACTTGTGGGCTTT
* *
221512 GAAAA-GATGCCACTAACTTGTGGGCTTTGAAATGATGCCACTGACTTGTGGGCTTTGAAAGGAT
1 -AAAAGGATGCCACTAACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGACTTTGAAAGGAT
*
221576 GCCACTAACTTGTGGGCTTT
65 GCCACTGACTTGTGGGCTTT
* * * *
221596 AAAAGGATGCCAATAACTTGTGGGCTTTGAAAGGATGTCACTAACTT-TGGGCTTTGAAAGGATG
1 AAAAGGATGCCACTAACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGACTTTGAAAGGATG
*
221660 CCACTAACTTGTGGGCTTT
66 CCACTGACTTGTGGGCTTT
* * * *
221679 GAAAA-GATGCCACTAACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAATGAC
1 -AAAAGGATGCCACTAACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGACTTTGAAAGGAT
221743 GCCACTGACTTGTGGGCTTT
65 GCCACTGACTTGTGGGCTTT
* * * * * * *
221763 GAAATGACGCCACTAACTTGTGAGCTTTAAAAGGATGCCACTGACTTGTGGACTTTAAAAGGGTG
1 AAAAGGATGCCACTAACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGACTTTGAAAGGATG
* * * *
221828 CCACGGAGTTATGGACTTT
66 CCACTGACTTGTGGGCTTT
* * * * * * * * * *
221847 CAAAGGGTGCCAC-AGAGTTGTGGACTTTAAAAAGATGCCACGGAGTTATGGACTTTAAAAAGGA
1 AAAAGGATGCCACTA-ACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGACTTT-GAAAGGA
* * * *
221911 -GCCACAGAGTTATGGAC-TT
64 TGCCACTGACTTGTGGGCTTT
** * * * * *
221930 AAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGATGTCA-TGGAGTTGTGGAC-TT-AAAGGGA
1 AAAAGGATGCCACTAACTTGTGGGCTTTGAAAGGATGCCACT-GACTTGTGGACTTTGAAA-GGA
* *
221992 TGCCA-TGGAGTTGTGGACTTT
64 TGCCACT-GACTTGTGGGCTTT
* ** * * ** * * * * *
222013 AAAAGGATACCACGGAGTTGTGGACTTAAAAAGGATGCCACGGAGTTATGGAC-TTAAAAAGATG
1 AAAAGGATGCCACTAACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGACTTTGAAAGGATG
* * *
222077 CCACGGAGTTGTGGAC-TT
66 CCACTGACTTGTGGGCTTT
* * * * * * *
222095 AAAAGGATGCTACGAAGTTGTGGAC-TTAAAAGGATGCCACGGAGTTGTGGA
1 AAAAGGATGCCACTAACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGA
222146 TGCCACGGAG
Statistics
Matches: 979, Mismatches: 128, Indels: 68
0.83 0.11 0.06
Matches are distributed among these distances:
80 3 0.00
81 27 0.03
82 41 0.04
83 271 0.28
84 574 0.59
85 13 0.01
86 8 0.01
87 1 0.00
88 16 0.02
89 5 0.01
90 20 0.02
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.29
Consensus pattern (84 bp):
AAAAGGATGCCACTAACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGACTTTGAAAGGATG
CCACTGACTTGTGGGCTTT
Found at i:221892 original size:28 final size:28
Alignment explanation
Indices: 221014--222145 Score: 672
Period size: 28 Copynumber: 40.7 Consensus size: 28
221004 GTTTTGAAAT
* * * * *
221014 GATGCCACTAACTTGTGGGCTTTGAAAC
1 GATGCCACTGAGTTGTGGACTTTAAAAG
* * *
221042 GATGCCACTGACTTGTAGG-CTTTGAAAT
1 GATGCCACTGAGTTGT-GGACTTTAAAAG
* * *
221070 GATGCCACTAACTTGTGGGCTTTAAAA-
1 GATGCCACTGAGTTGTGGACTTTAAAAG
* ** ** * * *
221097 TAGTGCCACTGCCTTACGGGCTTTGAAAT
1 GA-TGCCACTGAGTTGTGGACTTTAAAAG
* * * *
221126 GATGCCATTGACTTGTGGGCTTTGAAATG
1 GATGCCACTGAGTTGTGGACTTT-AAAAG
* * * *
221155 G-TGTCA-TGACTTGTGGGCTTTAAAAT
1 GATGCCACTGAGTTGTGGACTTTAAAAG
* * * *
221181 GATGCCACTGACTTGTGGGCTTTGAAAT
1 GATGCCACTGAGTTGTGGACTTTAAAAG
* * *
221209 GATGCCACTGACTTGTAGG-CTTTGAAAT
1 GATGCCACTGAGTTGT-GGACTTTAAAAG
* * * * * *
221237 GATGCTACTAACTTGTGGGCTTTGAAAT
1 GATGCCACTGAGTTGTGGACTTTAAAAG
* * * * * *
221265 AATGCCCCTGACTTGTGGGCTTTGAAAT
1 GATGCCACTGAGTTGTGGACTTTAAAAG
* * * * *
221293 AATGCC-CTTGACTTGTGGGCTTTGAAAT
1 GATGCCAC-TGAGTTGTGGACTTTAAAAG
* * * *
221321 GATGCCACTGACTTGTGGGCTTTGAAAT
1 GATGCCACTGAGTTGTGGACTTTAAAAG
* * * * *
221349 GATGCCATTGACTTGTGGGCTTTGAAAT
1 GATGCCACTGAGTTGTGGACTTTAAAAG
* * *
221377 GATACCACTGACTTGT-GAGCTTTGAAAG
1 GATGCCACTGAGTTGTGGA-CTTTAAAAG
* * * * *
221405 GATGTCACTAACTTATAGG-CTTTGAAAG
1 GATGCCACTGAGTTGT-GGACTTTAAAAG
* * * *
221433 GATGCCACTAACTTATAGG-CTTTGAAAG
1 GATGCCACTGAGTTGT-GGACTTTAAAAG
* * * * *
221461 GATGCCACTAACTTATGGGCTTTGAAAG
1 GATGCCACTGAGTTGTGGACTTTAAAAG
* * *
221489 GATGCCACTAACTTGTGGGCTTTGAAAA-
1 GATGCCACTGAGTTGTGGACTTT-AAAAG
* * * * *
221517 GATGCCACTAACTTGTGGGCTTTGAAAT
1 GATGCCACTGAGTTGTGGACTTTAAAAG
* * *
221545 GATGCCACTGACTTGTGGGCTTTGAAAG
1 GATGCCACTGAGTTGTGGACTTTAAAAG
* * *
221573 GATGCCACTAACTTGTGGGCTTTAAAAG
1 GATGCCACTGAGTTGTGGACTTTAAAAG
* * * * *
221601 GATGCCAATAACTTGTGGGCTTTGAAAG
1 GATGCCACTGAGTTGTGGACTTTAAAAG
* * * * *
221629 GATGTCACTAACTT-TGGGCTTTGAAAG
1 GATGCCACTGAGTTGTGGACTTTAAAAG
* * *
221656 GATGCCACTAACTTGTGGGCTTTGAAAA-
1 GATGCCACTGAGTTGTGGACTTT-AAAAG
* * *
221684 GATGCCACTAACTTGTGGGCTTTGAAAA-
1 GATGCCACTGAGTTGTGGACTTT-AAAAG
* * * *
221712 GATGCCACTGACTTGTGGGCTTTGAAAT
1 GATGCCACTGAGTTGTGGACTTTAAAAG
* * * * *
221740 GACGCCACTGACTTGTGGGCTTTGAAAT
1 GATGCCACTGAGTTGTGGACTTTAAAAG
* * *
221768 GACGCCACTAACTTGT-GAGCTTTAAAAG
1 GATGCCACTGAGTTGTGGA-CTTTAAAAG
*
221796 GATGCCACTGACTTGTGGACTTTAAAAG
1 GATGCCACTGAGTTGTGGACTTTAAAAG
* * * *
221824 GGTGCCACGGAGTTATGGACTTTCAAAG
1 GATGCCACTGAGTTGTGGACTTTAAAAG
* * *
221852 GGTGCCACAGAGTTGTGGACTTTAAAAA
1 GATGCCACTGAGTTGTGGACTTTAAAAG
* *
221880 GATGCCACGGAGTTATGGACTTTAAAAAG
1 GATGCCACTGAGTTGTGGACTTT-AAAAG
* *
221909 GA-GCCACAGAGTTATGGAC-TTAAAAG
1 GATGCCACTGAGTTGTGGACTTTAAAAG
*
221935 GATGCCACGGAGTTGTGGACTTTAAAAG
1 GATGCCACTGAGTTGTGGACTTTAAAAG
* *
221963 GATGTCA-TGGAGTTGTGGAC-TTAAAGG
1 GATGCCACT-GAGTTGTGGACTTTAAAAG
221990 GATGCCA-TGGAGTTGTGGACTTTAAAAG
1 GATGCCACT-GAGTTGTGGACTTTAAAAG
* * *
222018 GATACCACGGAGTTGTGGACTTAAAAAG
1 GATGCCACTGAGTTGTGGACTTTAAAAG
* * *
222046 GATGCCACGGAGTTATGGAC-TTAAAAA
1 GATGCCACTGAGTTGTGGACTTTAAAAG
*
222073 GATGCCACGGAGTTGTGGAC-TTAAAAG
1 GATGCCACTGAGTTGTGGACTTTAAAAG
*
222100 GATGCTAC-GAAGTTGTGGAC-TTAAAAG
1 GATGCCACTG-AGTTGTGGACTTTAAAAG
*
222127 GATGCCACGGAGTTGTGGA
1 GATGCCACTGAGTTGTGGA
222146 TGCCACGGAG
Statistics
Matches: 980, Mismatches: 94, Indels: 61
0.86 0.08 0.05
Matches are distributed among these distances:
26 12 0.01
27 173 0.18
28 771 0.79
29 23 0.02
30 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (28 bp):
GATGCCACTGAGTTGTGGACTTTAAAAG
Found at i:221957 original size:55 final size:55
Alignment explanation
Indices: 221485--222410 Score: 753
Period size: 55 Copynumber: 17.1 Consensus size: 55
221475 ATGGGCTTTG
** * * ** * * *
221485 AAAGGATGCCACTAACTTGTGGGCTTTGAAAA-GATGCCACTAACTTGTGGGCTTTG
1 AAAGGATGCCACGGAGTTGTGGACTTT-AAAAGGATGCCACGGAGTTGTGGAC-TTA
* * * * * ** * *
221541 AAATGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTA
1 AAAGGATGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGAC-TTA
*** * * * * ** * * *
221597 AAAGGATGCCAATAACTTGTGGGCTTTGAAAGGATGTCACTAACTT-TGGGCTTTG
1 AAAGGATGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGAC-TTA
** * * ** * *
221652 AAAGGATGCCACTAACTTGTGGGCTTTGAAAA-GATGCCACTAACTTGTGGGCTTTGA
1 AAAGGATGCCACGGAGTTGTGGACTTT-AAAAGGATGCCACGGAGTTGTGGAC-TT-A
* * * * * * * * * *
221709 AAA-GATGCCACTGACTTGTGGGCTTTGAAATGACGCCACTGACTTGTGGGCTTTG
1 AAAGGATGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGAC-TTA
* * ** * * *
221764 AAATGACGCCACTAACTTGT-GAGCTTTAAAAGGATGCCACTGACTTGTGGACTTTA
1 AAAGGATGCCACGGAGTTGTGGA-CTTTAAAAGGATGCCACGGAGTTGTGGAC-TTA
* * * * *
221820 AAAGGGTGCCACGGAGTTATGGACTTTCAAAGGGTGCCACAGAGTTGTGGACTTTA
1 AAAGGATGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGAC-TTA
* * * *
221876 AAAAGATGCCACGGAGTTATGGACTTTAAAAAGGA-GCCACAGAGTTATGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTT-AAAAGGATGCCACGGAGTTGTGGACTTA
* *
221931 AAAGGATGCCACGGAGTTGTGGACTTTAAAAGGATGTCATGGAGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTA
* * *
221986 AAGGGATGCCATGGAGTTGTGGACTTTAAAAGGATACCACGGAGTTGTGGACTTAA
1 AAAGGATGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTT-A
* *
222042 AAAGGATGCCACGGAGTTATGGAC-TTAAAAAGATGCCACGGAGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTA
* *
222096 AAAGGATGCTACGAAGTTGTGGAC-TTAAAAGGATGCCACGGAG-T-T-G---T-
1 AAAGGATGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTA
* *
222143 ---GGATGCCACGGAGTTGTGGAC-TTAAAAAGATGCCACGAAGTTGTGGACTTTA
1 AAAGGATGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGAC-TTA
*
222195 AAAGGATACCACGGAGTTGTGGAC-TTAAAAGGATGCCACGGAGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTA
*
222249 AAAGGATGCCACGGAG-T-T-G----T----GGATGCCATGGAGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTA
* * * *
222293 AAAAGATGCCATGAAGGTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTA
* * *
222348 AAAGGATGCCACGGAGTTGTGGACTTTAAAAGAATGCCACGGAGTTATGAACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTA
222403 AAAGGATG
1 AAAGGATG
222411 GAGTTGTAGA
Statistics
Matches: 755, Mismatches: 82, Indels: 67
0.84 0.09 0.07
Matches are distributed among these distances:
44 72 0.10
45 2 0.00
46 2 0.00
47 2 0.00
48 2 0.00
51 4 0.01
52 2 0.00
53 2 0.00
54 65 0.09
55 301 0.40
56 291 0.39
57 10 0.01
ACGTcount: A:0.30, C:0.15, G:0.29, T:0.26
Consensus pattern (55 bp):
AAAGGATGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTA
Found at i:222148 original size:17 final size:17
Alignment explanation
Indices: 222126--222162 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
222116 GGACTTAAAA
222126 GGATGCCACGGAGTTGT
1 GGATGCCACGGAGTTGT
222143 GGATGCCACGGAGTTGT
1 GGATGCCACGGAGTTGT
222160 GGA
1 GGA
222163 CTTAAAAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.19, C:0.16, G:0.43, T:0.22
Consensus pattern (17 bp):
GGATGCCACGGAGTTGT
Found at i:222184 original size:27 final size:27
Alignment explanation
Indices: 222143--222271 Score: 222
Period size: 27 Copynumber: 4.7 Consensus size: 27
222133 ACGGAGTTGT
222143 GGATGCCACGGAGTTGTGGACTTAAAA
1 GGATGCCACGGAGTTGTGGACTTAAAA
* *
222170 AGATGCCACGAAGTTGTGGACTTTAAAA
1 GGATGCCACGGAGTTGTGGAC-TTAAAA
*
222198 GGATACCACGGAGTTGTGGACTTAAAA
1 GGATGCCACGGAGTTGTGGACTTAAAA
222225 GGATGCCACGGAGTTGTGGACTTAAAA
1 GGATGCCACGGAGTTGTGGACTTAAAA
222252 GGATGCCACGGAGTTGTGGA
1 GGATGCCACGGAGTTGTGGA
222272 TGCCATGGAG
Statistics
Matches: 95, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
27 71 0.75
28 24 0.25
ACGTcount: A:0.30, C:0.15, G:0.33, T:0.22
Consensus pattern (27 bp):
GGATGCCACGGAGTTGTGGACTTAAAA
Found at i:222247 original size:126 final size:126
Alignment explanation
Indices: 222017--222393 Score: 630
Period size: 126 Copynumber: 3.0 Consensus size: 126
222007 GACTTTAAAA
* * * *
222017 GGATACCACGGAGTTGTGGACTTAAAAAGGATGCCACGGAGTTATGGAC-TTAAAAAGATGCCAC
1 GGATGCCACGGAGTTGTGGACTTAAAAA-GATGCCACGAAGTTGTGGACTTTAAAAGGATGCCAC
* *
222081 GGAGTTGTGGACTTAAAAGGATGCTACGAAGTTGTGGACTTAAAAGGATGCCACGGAGTTGT
65 GGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGT
*
222143 GGATGCCACGGAGTTGTGGACTTAAAAAGATGCCACGAAGTTGTGGACTTTAAAAGGATACCACG
1 GGATGCCACGGAGTTGTGGACTTAAAAAGATGCCACGAAGTTGTGGACTTTAAAAGGATGCCACG
222208 GAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGT
66 GAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGT
* * *
222269 GGATGCCATGGAGTTGTGGACTTAAAAAGATGCCATGAAGGTGTGGACTTTAAAAGGATGCCACG
1 GGATGCCACGGAGTTGTGGACTTAAAAAGATGCCACGAAGTTGTGGACTTTAAAAGGATGCCACG
*
222334 GAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGAATGCCACGGAGTT
66 GAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGAC-TTAAAAGGATGCCACGGAGTT
222394 ATGAACTTAA
Statistics
Matches: 237, Mismatches: 12, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
125 18 0.08
126 199 0.84
127 20 0.08
ACGTcount: A:0.31, C:0.14, G:0.32, T:0.23
Consensus pattern (126 bp):
GGATGCCACGGAGTTGTGGACTTAAAAAGATGCCACGAAGTTGTGGACTTTAAAAGGATGCCACG
GAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGT
Found at i:222274 original size:17 final size:17
Alignment explanation
Indices: 222252--222288 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
222242 GGACTTAAAA
222252 GGATGCCACGGAGTTGT
1 GGATGCCACGGAGTTGT
*
222269 GGATGCCATGGAGTTGT
1 GGATGCCACGGAGTTGT
222286 GGA
1 GGA
222289 CTTAAAAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.19, C:0.14, G:0.43, T:0.24
Consensus pattern (17 bp):
GGATGCCACGGAGTTGT
Found at i:222274 original size:99 final size:98
Alignment explanation
Indices: 222073--222370 Score: 366
Period size: 99 Copynumber: 3.0 Consensus size: 98
222063 GACTTAAAAA
*
222073 GATGCCACGGAGTTGTGGACTTAAAAGGATGCTACGAAGTTGTGGACTTAAAAGGATGCCACGGA
1 GATGCCACGGAGTTGTGGACTTAAAAGGATGCCACGAAGTTGTGGACTTAAAAGGATGCCACGGA
*** * **** * ***
222138 GTTGTGGA-TGCCACGGA-GTTGTGGACTTAAAAA
66 GTTGTGGACTTAAAAGGATGCCACGGAGTT--GTG
* * *
222171 GATGCCACGAAGTTGTGGACTTTAAAAGGATACCACGGAGTTGTGGACTTAAAAGGATGCCACGG
1 GATGCCACGGAGTTGTGGAC-TTAAAAGGATGCCACGAAGTTGTGGACTTAAAAGGATGCCACGG
222236 AGTTGTGGACTTAAAAGGATGCCACGGAGTTGTG
65 AGTTGTGGACTTAAAAGGATGCCACGGAGTTGTG
* * * *
222270 GATGCCATGGAGTTGTGGACTTAAAAAGATGCCATGAAGGTGTGGACTTTAAAAGGATGCCACGG
1 GATGCCACGGAGTTGTGGACTTAAAAGGATGCCACGAAGTTGTGGAC-TTAAAAGGATGCCACGG
222335 AGTTGTGGACTTAAAAGGATGCCACGGAGTTGTG
65 AGTTGTGGACTTAAAAGGATGCCACGGAGTTGTG
222369 GA
1 GA
222371 CTTTAAAAGA
Statistics
Matches: 173, Mismatches: 23, Indels: 7
0.85 0.11 0.03
Matches are distributed among these distances:
98 41 0.24
99 121 0.70
100 5 0.03
101 6 0.03
ACGTcount: A:0.30, C:0.14, G:0.33, T:0.23
Consensus pattern (98 bp):
GATGCCACGGAGTTGTGGACTTAAAAGGATGCCACGAAGTTGTGGACTTAAAAGGATGCCACGGA
GTTGTGGACTTAAAAGGATGCCACGGAGTTGTG
Found at i:222288 original size:44 final size:44
Alignment explanation
Indices: 222225--222370 Score: 157
Period size: 44 Copynumber: 3.1 Consensus size: 44
222215 GGACTTAAAA
222225 GGATGCCACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGT
1 GGATGCCACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGT
* * * *
222269 GGATGCCATGGAGTTGTGGACTTAAAAAGATGCCATGAAGGTGTGGACTTT
1 GGATGCCACGGAGTTGTGGACTTAAAAGGATGCCACGGA-GT-T-G----T
222320 AAAAGGATGCCACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGT
1 ----GGATGCCACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGT
222368 GGA
1 GGA
222371 CTTTAAAAGA
Statistics
Matches: 83, Mismatches: 8, Indels: 22
0.73 0.07 0.19
Matches are distributed among these distances:
44 38 0.46
45 2 0.02
46 1 0.01
47 1 0.01
48 1 0.01
51 1 0.01
52 1 0.01
53 1 0.01
54 2 0.02
55 35 0.42
ACGTcount: A:0.28, C:0.14, G:0.35, T:0.23
Consensus pattern (44 bp):
GGATGCCACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGT
Found at i:222330 original size:28 final size:27
Alignment explanation
Indices: 222269--222410 Score: 194
Period size: 27 Copynumber: 5.2 Consensus size: 27
222259 ACGGAGTTGT
*
222269 GGATGCCATGGAGTTGTGGACTTAAAA
1 GGATGCCACGGAGTTGTGGACTTAAAA
* * * *
222296 AGATGCCATGAAGGTGTGGACTTTAAAA
1 GGATGCCACGGAGTTGTGGAC-TTAAAA
222324 GGATGCCACGGAGTTGTGGACTTAAAA
1 GGATGCCACGGAGTTGTGGACTTAAAA
222351 GGATGCCACGGAGTTGTGGACTTTAAAA
1 GGATGCCACGGAGTTGTGGAC-TTAAAA
* * *
222379 GAATGCCACGGAGTTATGAACTTAAAA
1 GGATGCCACGGAGTTGTGGACTTAAAA
222406 GGATG
1 GGATG
222411 GAGTTGTAGA
Statistics
Matches: 102, Mismatches: 11, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
27 55 0.54
28 47 0.46
ACGTcount: A:0.32, C:0.13, G:0.31, T:0.24
Consensus pattern (27 bp):
GGATGCCACGGAGTTGTGGACTTAAAA
Found at i:223813 original size:22 final size:22
Alignment explanation
Indices: 223788--223836 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
223778 CTTTTGCATT
* *
223788 TTTTTCTTTCCATTTTTTC-TGC
1 TTTTTCTTTCAACTTTTTCGT-C
*
223810 TTTTGCTTTCAACTTTTTCGTC
1 TTTTTCTTTCAACTTTTTCGTC
223832 TTTTT
1 TTTTT
223837 GAAGGGAACT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 21 0.95
23 1 0.05
ACGTcount: A:0.06, C:0.20, G:0.06, T:0.67
Consensus pattern (22 bp):
TTTTTCTTTCAACTTTTTCGTC
Found at i:228785 original size:97 final size:96
Alignment explanation
Indices: 228529--228774 Score: 402
Period size: 97 Copynumber: 2.5 Consensus size: 96
228519 ATTTTAATGA
* * *
228529 AAAACGGGGTTGGAGTATCCTCTCGGAGGTATAGGGTTGGAGTATTCCCGATGATGACAATTTAA
1 AAAACCGGGTTGGAGTATCCCCTCGGAGGAATAGGGTTGGAGTATTCCCGATGATGACAATTTAA
228594 GCGAGAATAAGATTTAAACTTTGATAAGTTT
66 GCGAGAATAAGATTTAAACTTTGATAAGTTT
* * *
228625 AAAAGCGGAGTTGGAGTATCCCCTTGGAGGAATAGGGTTGGAGTATCCCCGATGATGACAATTTA
1 AAAACCGG-GTTGGAGTATCCCCTCGGAGGAATAGGGTTGGAGTATTCCCGATGATGACAATTTA
*
228690 AGCGAGAATAAGATTTAAACTTTGATGAGTTT
65 AGCGAGAATAAGATTTAAACTTTGATAAGTTT
*
228722 AAAACCAGGGTTGGAGTATCCCCTCGGATGAATAGGGTTGGAGTATTCCCGAT
1 AAAACC-GGGTTGGAGTATCCCCTCGGAGGAATAGGGTTGGAGTATTCCCGAT
228775 AAATAAAATT
Statistics
Matches: 137, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
96 6 0.04
97 129 0.94
98 2 0.01
ACGTcount: A:0.30, C:0.13, G:0.28, T:0.28
Consensus pattern (96 bp):
AAAACCGGGTTGGAGTATCCCCTCGGAGGAATAGGGTTGGAGTATTCCCGATGATGACAATTTAA
GCGAGAATAAGATTTAAACTTTGATAAGTTT
Found at i:231791 original size:3 final size:3
Alignment explanation
Indices: 231783--231820 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
231773 AGTTAAAACT
231783 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
231821 TACATGATGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:241578 original size:21 final size:20
Alignment explanation
Indices: 241534--241605 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
241524 AAAACTCAAA
* *
241534 ATGTATCGATACAATGAA--
1 ATGTATCGATACATTCAAGC
241552 ATGTATCGATACATTTCAAGC
1 ATGTATCGATACA-TTCAAGC
* ***
241573 ATGTATCAATACATTCACTT
1 ATGTATCGATACATTCAAGC
241593 ATGTATCGATACA
1 ATGTATCGATACA
241606 ATTTTTCTAA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
18 13 0.30
19 3 0.07
20 16 0.36
21 12 0.27
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACATTCAAGC
Found at i:247409 original size:20 final size:22
Alignment explanation
Indices: 247366--247418 Score: 67
Period size: 20 Copynumber: 2.5 Consensus size: 22
247356 CAATGACTTA
*
247366 TATCGATAC-TTTCACATAATG
1 TATCGATACATTGCACATAATG
247387 TATCGATACATTGCA-AT-ATG
1 TATCGATACATTGCACATAATG
*
247407 TATCTATACATT
1 TATCGATACATT
247419 CTCATGTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 14 0.48
21 11 0.38
22 4 0.14
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (22 bp):
TATCGATACATTGCACATAATG
Found at i:247513 original size:20 final size:20
Alignment explanation
Indices: 247475--247515 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
247465 GTCAACCATA
*
247475 TGTATCGATACAAAGAGTAT
1 TGTATCGATACAAACAGTAT
**
247495 TGTATCGATACTTACAGTAT
1 TGTATCGATACAAACAGTAT
247515 T
1 T
247516 TATACTTAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (20 bp):
TGTATCGATACAAACAGTAT
Found at i:252640 original size:3 final size:3
Alignment explanation
Indices: 252632--252662 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
252622 CAACCTCTTG
252632 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
252663 CTTGAAGTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:258993 original size:20 final size:20
Alignment explanation
Indices: 258965--259039 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
258955 TTTTACCCAT
258965 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
258985 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
259005 ATGTATCAATATATTCTTCA
1 ATGTATCGATACATTTTTCA
259025 ATGTATCGATACATT
1 ATGTATCGATACATT
259040 CTGTCTTTTT
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:265598 original size:3 final size:3
Alignment explanation
Indices: 265590--265635 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
265580 GCTGTTTTTC
*
265590 ATT ATT ATT ATT ATT ATT ATC ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
265636 GATTTTATGA
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:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:266527 original size:14 final size:15
Alignment explanation
Indices: 266508--266540 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
266498 AATCAATGTA
266508 TTTTGATATATC-AT
1 TTTTGATATATCAAT
*
266522 TTTTGATTTATCAAT
1 TTTTGATATATCAAT
266537 TTTT
1 TTTT
266541 TTAAAATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.24, C:0.06, G:0.06, T:0.64
Consensus pattern (15 bp):
TTTTGATATATCAAT
Found at i:267291 original size:23 final size:24
Alignment explanation
Indices: 267254--267310 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 24
267244 AAAAAAAGAT
*
267254 AAAAAGATAAA-GGAAACGAGA-G
1 AAAAAGAAAAAGGGAAACGAGAGG
**
267276 AAAAAGAAAAAGGGAAGGGAGAGG
1 AAAAAGAAAAAGGGAAACGAGAGG
267300 AAAAA-AAAAAG
1 AAAAAGAAAAAG
267311 AAAGGGAAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
22 10 0.33
23 14 0.47
24 6 0.20
ACGTcount: A:0.67, C:0.02, G:0.30, T:0.02
Consensus pattern (24 bp):
AAAAAGAAAAAGGGAAACGAGAGG
Found at i:267306 original size:27 final size:27
Alignment explanation
Indices: 267276--267330 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
267266 GAAACGAGAG
* * *
267276 AAAAAGAA-AAAGGGAAGGGAGAGGAA
1 AAAAAAAAGAAAGGGAAGAGAAAGGAA
267302 AAAAAAAAGAAAGGGAAGAGAAAGGAA
1 AAAAAAAAGAAAGGGAAGAGAAAGGAA
267329 AA
1 AA
267331 GGGGAAAGGC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 7 0.28
27 18 0.72
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (27 bp):
AAAAAAAAGAAAGGGAAGAGAAAGGAA
Found at i:267710 original size:27 final size:26
Alignment explanation
Indices: 267655--267706 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
267645 AACCCTCAAT
267655 TTTCCCTTCCTGCCCTTCTCTCTTCC
1 TTTCCCTTCCTGCCCTTCTCTCTTCC
*
267681 TTTCCCTTCCCTTCCCTTCTCT-TTCC
1 TTTCCCTT-CCTGCCCTTCTCTCTTCC
267707 CTTTTTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 12 0.50
27 12 0.50
ACGTcount: A:0.00, C:0.50, G:0.02, T:0.48
Consensus pattern (26 bp):
TTTCCCTTCCTGCCCTTCTCTCTTCC
Found at i:267820 original size:28 final size:31
Alignment explanation
Indices: 267765--267826 Score: 85
Period size: 28 Copynumber: 2.1 Consensus size: 31
267755 TTTTTCAAAT
*
267765 TTTTTATTTTTTTATTAATTTTAATTATATA
1 TTTTTATTTTTTGATTAATTTTAATTATATA
*
267796 TTTTTA-TTTTTGA-TAA-TTTATTTATATA
1 TTTTTATTTTTTGATTAATTTTAATTATATA
267824 TTT
1 TTT
267827 AAATTTAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 14 0.48
29 3 0.10
30 6 0.21
31 6 0.21
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (31 bp):
TTTTTATTTTTTGATTAATTTTAATTATATA
Found at i:267926 original size:18 final size:17
Alignment explanation
Indices: 267906--267968 Score: 56
Period size: 18 Copynumber: 3.6 Consensus size: 17
267896 AAATTTAAAA
* *
267906 TATATTTTTTATATTTTA
1 TATATTTTATA-ATTTTT
*
267924 TATACTTTTAAAATTTTT
1 TATA-TTTTATAATTTTT
*
267942 TATAATTTTATAAATTTT
1 TAT-ATTTTATAATTTTT
267960 TAT-TTTTAT
1 TATATTTTAT
267969 TTTTTGAATT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
16 6 0.16
18 26 0.68
19 6 0.16
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (17 bp):
TATATTTTATAATTTTT
Found at i:267944 original size:20 final size:19
Alignment explanation
Indices: 267918--267960 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
267908 TATTTTTTAT
* *
267918 ATTTTATATACTTTTA-AA
1 ATTTTTTATAATTTTATAA
267936 ATTTTTTATAATTTTATAA
1 ATTTTTTATAATTTTATAA
267955 ATTTTT
1 ATTTTT
267961 ATTTTTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (19 bp):
ATTTTTTATAATTTTATAA
Found at i:269202 original size:21 final size:23
Alignment explanation
Indices: 269177--269225 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
269167 GAACCCCTCT
269177 CATAT-CT-TAGAAGAAATTTCA
1 CATATACTCTAGAAGAAATTTCA
* *
269198 CATATATTCTAGAAGAAATTTTA
1 CATATACTCTAGAAGAAATTTCA
269221 CATAT
1 CATAT
269226 TATTTTAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 5 0.21
22 1 0.04
23 18 0.75
ACGTcount: A:0.43, C:0.12, G:0.08, T:0.37
Consensus pattern (23 bp):
CATATACTCTAGAAGAAATTTCA
Found at i:273708 original size:33 final size:33
Alignment explanation
Indices: 273671--273737 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
273661 TTCAACGATT
273671 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
273704 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
273737 T
1 T
273738 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:273709 original size:13 final size:13
Alignment explanation
Indices: 273691--273715 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
273681 CATAAAATGT
273691 TGTATCGATACAA
1 TGTATCGATACAA
273704 TGTATCGATACA
1 TGTATCGATACA
273716 TATTTTTTTG
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):
TGTATCGATACAA
Found at i:273796 original size:13 final size:13
Alignment explanation
Indices: 273778--273802 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
273768 ATTACTCAAA
273778 TGTATCGATACAT
1 TGTATCGATACAT
273791 TGTATCGATACA
1 TGTATCGATACA
273803 CTGATCTTTG
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:273904 original size:52 final size:52
Alignment explanation
Indices: 273811--273934 Score: 214
Period size: 52 Copynumber: 2.4 Consensus size: 52
273801 CACTGATCTT
*
273811 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
273862 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
273914 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
273935 CTTTTCATAT
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
51 19 0.28
52 50 0.72
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:278088 original size:10 final size:10
Alignment explanation
Indices: 278073--278099 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
278063 TGCTAACTAA
278073 GTTTTTGTTT
1 GTTTTTGTTT
278083 GTTTTTGTTT
1 GTTTTTGTTT
278093 GTTTTTG
1 GTTTTTG
278100 CTTGATACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (10 bp):
GTTTTTGTTT
Found at i:284100 original size:21 final size:20
Alignment explanation
Indices: 284056--284127 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
284046 AAAACTCAAA
* *
284056 ATGTATCGATACAATGAA--
1 ATGTATCGATACATTCAAGC
284074 ATGTATCGATACATTTCAAGC
1 ATGTATCGATACA-TTCAAGC
* ***
284095 ATGTATCAATACATTCACTT
1 ATGTATCGATACATTCAAGC
284115 ATGTATCGATACA
1 ATGTATCGATACA
284128 ATTTTTCTAA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
18 13 0.30
19 3 0.07
20 16 0.36
21 12 0.27
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACATTCAAGC
Found at i:289931 original size:20 final size:22
Alignment explanation
Indices: 289888--289940 Score: 67
Period size: 20 Copynumber: 2.5 Consensus size: 22
289878 CAATGACTTA
*
289888 TATCGATAC-TTTCACATAATG
1 TATCGATACATTGCACATAATG
289909 TATCGATACATTGCA-AT-ATG
1 TATCGATACATTGCACATAATG
*
289929 TATCTATACATT
1 TATCGATACATT
289941 CTCATGTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 14 0.48
21 11 0.38
22 4 0.14
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (22 bp):
TATCGATACATTGCACATAATG
Found at i:290035 original size:20 final size:20
Alignment explanation
Indices: 289997--290037 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
289987 GTCAACCATA
*
289997 TGTATCGATACAAAGAGTAT
1 TGTATCGATACAAACAGTAT
**
290017 TGTATCGATACTTACAGTAT
1 TGTATCGATACAAACAGTAT
290037 T
1 T
290038 TATACTTAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (20 bp):
TGTATCGATACAAACAGTAT
Found at i:295162 original size:3 final size:3
Alignment explanation
Indices: 295154--295184 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
295144 CAACCTCTTG
295154 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
295185 CTTGAAGTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:301514 original size:20 final size:20
Alignment explanation
Indices: 301486--301560 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 20
301476 TTTTACCCAT
301486 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
301506 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
301526 ATGTATCAATATATTCTTCA
1 ATGTATCGATACATTTTTCA
*
301546 ATGTATAGATACATT
1 ATGTATCGATACATT
301561 CTGTCTTTTT
Statistics
Matches: 41, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:311160 original size:13 final size:13
Alignment explanation
Indices: 311142--311166 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
311132 CATAAAAAGT
311142 TGTATCGATACAA
1 TGTATCGATACAA
311155 TGTATCGATACA
1 TGTATCGATACA
311167 TATTTTTTTG
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):
TGTATCGATACAA
Found at i:311164 original size:33 final size:33
Alignment explanation
Indices: 311122--311191 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
311112 TTCAACGATT
311122 TGTATCGATACATAAAAAGTTGTATCGATACAA
1 TGTATCGATACATAAAAAGTTGTATCGATACAA
*****
311155 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAAAGTTGTATCGATACAA
311188 TGTA
1 TGTA
311192 AGCTACTGCC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39
Consensus pattern (33 bp):
TGTATCGATACATAAAAAGTTGTATCGATACAA
Found at i:311251 original size:13 final size:13
Alignment explanation
Indices: 311233--311257 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
311223 ATTACTCACA
311233 TGTATCGATACAT
1 TGTATCGATACAT
311246 TGTATCGATACA
1 TGTATCGATACA
311258 CTGATCTTTG
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:311322 original size:52 final size:52
Alignment explanation
Indices: 311266--311394 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
311256 CACTGATCTT
*
311266 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
311318 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
311370 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
311395 TCATATTTCG
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 75 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:320989 original size:20 final size:20
Alignment explanation
Indices: 320961--321034 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 20
320951 TTTTACCCAT
320961 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
320981 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
321001 ATGTATCAATATATTCTTCA
1 ATGTATCGATACATTTTTCA
321021 ATGTATCGATACAT
1 ATGTATCGATACAT
321035 GCTGTCTTTT
Statistics
Matches: 41, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:327592 original size:3 final size:3
Alignment explanation
Indices: 327584--327632 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
327574 GCTGTTTTTC
*
327584 ATT ATT ATT ATT ATT ATT ATC ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
327632 A
1 A
327633 GATTTTAGAT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:329249 original size:7 final size:8
Alignment explanation
Indices: 329230--329256 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
329220 AAAATCTGAA
329230 AAAAAGAT
1 AAAAAGAT
329238 AAAAAGAT
1 AAAAAGAT
329246 AAAAAGAT
1 AAAAAGAT
329254 AAA
1 AAA
329257 GGAAACGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (8 bp):
AAAAAGAT
Found at i:329283 original size:23 final size:24
Alignment explanation
Indices: 329246--329302 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 24
329236 ATAAAAAGAT
*
329246 AAAAAGATAAA-GGAAACGAGA-G
1 AAAAAGAAAAAGGGAAACGAGAGG
**
329268 AAAAAGAAAAAGGGAAGGGAGAGG
1 AAAAAGAAAAAGGGAAACGAGAGG
329292 AAAAA-AAAAAG
1 AAAAAGAAAAAG
329303 AAAGGGAAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
22 10 0.33
23 14 0.47
24 6 0.20
ACGTcount: A:0.67, C:0.02, G:0.30, T:0.02
Consensus pattern (24 bp):
AAAAAGAAAAAGGGAAACGAGAGG
Found at i:329298 original size:27 final size:27
Alignment explanation
Indices: 329268--329322 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
329258 GAAACGAGAG
* * *
329268 AAAAAGAA-AAAGGGAAGGGAGAGGAA
1 AAAAAAAAGAAAGGGAAGAGAAAGGAA
329294 AAAAAAAAGAAAGGGAAGAGAAAGGAA
1 AAAAAAAAGAAAGGGAAGAGAAAGGAA
329321 AA
1 AA
329323 GGGGAAAGGC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 7 0.28
27 18 0.72
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (27 bp):
AAAAAAAAGAAAGGGAAGAGAAAGGAA
Found at i:329702 original size:27 final size:26
Alignment explanation
Indices: 329647--329698 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
329637 AACCCTCAAT
329647 TTTCCCTTCCTGCCCTTCTCTCTTCC
1 TTTCCCTTCCTGCCCTTCTCTCTTCC
*
329673 TTTCCCTTCCCTTCCCTTCTCT-TTCC
1 TTTCCCTT-CCTGCCCTTCTCTCTTCC
329699 CTTTTTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 12 0.50
27 12 0.50
ACGTcount: A:0.00, C:0.50, G:0.02, T:0.48
Consensus pattern (26 bp):
TTTCCCTTCCTGCCCTTCTCTCTTCC
Found at i:329812 original size:28 final size:31
Alignment explanation
Indices: 329757--329818 Score: 85
Period size: 28 Copynumber: 2.1 Consensus size: 31
329747 TTTTTCAAAT
*
329757 TTTTTATTTTTTTATTAATTTTAATTATATA
1 TTTTTATTTTTTGATTAATTTTAATTATATA
*
329788 TTTTTA-TTTTTGA-TAA-TTTATTTATATA
1 TTTTTATTTTTTGATTAATTTTAATTATATA
329816 TTT
1 TTT
329819 AAATTTAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 14 0.48
29 3 0.10
30 6 0.21
31 6 0.21
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (31 bp):
TTTTTATTTTTTGATTAATTTTAATTATATA
Found at i:329917 original size:18 final size:17
Alignment explanation
Indices: 329897--329959 Score: 56
Period size: 18 Copynumber: 3.6 Consensus size: 17
329887 AAATTTAAAA
* *
329897 TATATTTTTTATATTTTA
1 TATATTTTATA-ATTTTT
*
329915 TATACTTTTAAAATTTTT
1 TATA-TTTTATAATTTTT
*
329933 TATAATTTTATAAATTTT
1 TAT-ATTTTATAATTTTT
329951 TAT-TTTTAT
1 TATATTTTAT
329960 TTTTTGAATT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
16 6 0.16
18 26 0.68
19 6 0.16
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (17 bp):
TATATTTTATAATTTTT
Found at i:329935 original size:20 final size:19
Alignment explanation
Indices: 329909--329951 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
329899 TATTTTTTAT
* *
329909 ATTTTATATACTTTTA-AA
1 ATTTTTTATAATTTTATAA
329927 ATTTTTTATAATTTTATAA
1 ATTTTTTATAATTTTATAA
329946 ATTTTT
1 ATTTTT
329952 ATTTTTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (19 bp):
ATTTTTTATAATTTTATAA
Found at i:331193 original size:21 final size:23
Alignment explanation
Indices: 331168--331216 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
331158 GAACCCCTCT
331168 CATAT-CT-TAGAAGAAATTTCA
1 CATATACTCTAGAAGAAATTTCA
* *
331189 CATATATTCTAGAAGAAATTTTA
1 CATATACTCTAGAAGAAATTTCA
331212 CATAT
1 CATAT
331217 TATTTTAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 5 0.21
22 1 0.04
23 18 0.75
ACGTcount: A:0.43, C:0.12, G:0.08, T:0.37
Consensus pattern (23 bp):
CATATACTCTAGAAGAAATTTCA
Found at i:335633 original size:52 final size:52
Alignment explanation
Indices: 335548--335672 Score: 223
Period size: 52 Copynumber: 2.4 Consensus size: 52
335538 ATATGAAAAG
*
335548 TTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
* *
335600 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGTAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
335652 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
335673 AAGATCAGTG
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
Found at i:335685 original size:52 final size:51
Alignment explanation
Indices: 335548--335692 Score: 211
Period size: 52 Copynumber: 2.8 Consensus size: 51
335538 ATATGAAAAG
335548 TTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* * *
335600 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGTAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
335652 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
335693 ATGTATCGAT
Statistics
Matches: 85, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
51 2 0.02
52 83 0.98
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:335699 original size:13 final size:13
Alignment explanation
Indices: 335681--335705 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
335671 CAAAGATCAG
335681 TGTATCGATACAA
1 TGTATCGATACAA
335694 TGTATCGATACA
1 TGTATCGATACA
335706 TTTGAGTAAT
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):
TGTATCGATACAA
Found at i:335869 original size:20 final size:19
Alignment explanation
Indices: 335750--335909 Score: 98
Period size: 13 Copynumber: 9.6 Consensus size: 19
335740 GCTTAAATTA
*
335750 TATCGATACAAAACTTATG
1 TATCGATACAACACTTATG
335769 TATCGAT---ACA--T-TG
1 TATCGATACAACACTTATG
*
335782 TATCGATACAAAACTTATG
1 TATCGATACAACACTTATG
* *
335801 TATTGAT---ACA--T-TC
1 TATCGATACAACACTTATG
335814 TATCGATACAACACTTATG
1 TATCGATACAACACTTATG
335833 TATCGAT---ACA--T-TG
1 TATCGATACAACACTTATG
335846 TATCGATACAACACTTTATG
1 TATCGATACAACAC-TTATG
335866 TATCGAT---ACA--T-TG
1 TATCGATACAACACTTATG
335879 TATCGATACAACACTTTATG
1 TATCGATACAACAC-TTATG
335899 TATCGATACAA
1 TATCGATACAA
335910 ATCGTTGAAA
Statistics
Matches: 108, Mismatches: 7, Indels: 51
0.65 0.04 0.31
Matches are distributed among these distances:
13 34 0.31
14 4 0.04
16 18 0.17
17 3 0.03
18 2 0.02
19 25 0.23
20 22 0.20
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.35
Consensus pattern (19 bp):
TATCGATACAACACTTATG
Found at i:335870 original size:33 final size:32
Alignment explanation
Indices: 335750--335908 Score: 264
Period size: 32 Copynumber: 4.9 Consensus size: 32
335740 GCTTAAATTA
*
335750 TATCGATACAAAACTTATGTATCGATACATTG
1 TATCGATACAACACTTATGTATCGATACATTG
* * *
335782 TATCGATACAAAACTTATGTATTGATACATTC
1 TATCGATACAACACTTATGTATCGATACATTG
335814 TATCGATACAACACTTATGTATCGATACATTG
1 TATCGATACAACACTTATGTATCGATACATTG
335846 TATCGATACAACACTTTATGTATCGATACATTG
1 TATCGATACAACAC-TTATGTATCGATACATTG
335879 TATCGATACAACACTTTATGTATCGATACA
1 TATCGATACAACAC-TTATGTATCGATACA
335909 AATCGTTGAA
Statistics
Matches: 121, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
32 73 0.60
33 48 0.40
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35
Consensus pattern (32 bp):
TATCGATACAACACTTATGTATCGATACATTG
Found at i:336857 original size:55 final size:52
Alignment explanation
Indices: 336757--337278 Score: 431
Period size: 49 Copynumber: 10.9 Consensus size: 52
336747 GAAAAGTGAT
* * * * *
336757 AAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGAGAA
1 AAAGATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATG-G-A
* * *
336811 AAATGATGTCAATGTGCTGATTCAAGGCCAGCTATATTGAACTTAAAGATGGA
1 AAA-GATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
* *
336864 AAAGGTGCCAATATGCTGATTCAAGGTCAGCTATATTGGACTT-AA-A--G-
1 AAAGATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
* *
336911 ---G-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA---A
1 AAAGATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
* * *
336956 GAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-AA-A--G-
1 AAAGATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
* *
337003 ---G-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G-
1 AAAGATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
* *
337049 -AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-AA-A--G-
1 AAAGATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
* *
337095 ---G-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G-
1 AAAGATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
*
337141 -AAGATGCTAATATGCTGATTCAAGGCCAG-TGATATTGGAC-T-----T--A
1 AAAGATGCCAATATGCTGATTCAAGGCCAGCT-ATATTGGACTTAAAGATGGA
* * * *
337184 AAAG-TGCCAATGTGCTGATTCAAGGCCGGCTACATTGGATTTAAAGAT-G-
1 AAAGATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
337233 -AAGATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
1 AAAGATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
337279 GAAGATGCCA
Statistics
Matches: 395, Mismatches: 40, Indels: 71
0.78 0.08 0.14
Matches are distributed among these distances:
43 135 0.34
44 14 0.04
45 3 0.01
46 3 0.01
47 2 0.01
48 13 0.03
49 140 0.35
50 1 0.00
51 2 0.01
52 35 0.09
53 4 0.01
54 4 0.01
55 39 0.10
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.26
Consensus pattern (52 bp):
AAAGATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
Found at i:336925 original size:43 final size:43
Alignment explanation
Indices: 336864--337279 Score: 465
Period size: 43 Copynumber: 9.1 Consensus size: 43
336854 TAAAGATGGA
*
336864 AAAGGTGCCAATATGCTGATTCAAGGTCAGCTATATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* *
336907 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
*
336950 AAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1 -----A-AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* *
336999 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
*
337042 AAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1 ----A--AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* *
337091 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
*
337134 AAAGATGAAGATGCTAATATGCTGATTCAAGGCCAG-TGATATTGGACTT
1 -AA-A-G--G-TGCCAATATGCTGATTCAAGGCCAGCT-ATATTGGACTT
* * * * *
337183 AAAAGTGCCAATGTGCTGATTCAAGGCCGGCTACATTGGATTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
337226 AAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
1 -AA-A-G--G-TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
337275 AAAGG
1 AAAGG
337280 AAGATGCCAC
Statistics
Matches: 318, Mismatches: 29, Indels: 51
0.80 0.07 0.13
Matches are distributed among these distances:
43 149 0.47
44 8 0.03
45 3 0.01
46 2 0.01
47 3 0.01
48 8 0.03
49 145 0.46
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.26
Consensus pattern (43 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
Found at i:336996 original size:92 final size:92
Alignment explanation
Indices: 336820--337279 Score: 776
Period size: 92 Copynumber: 5.0 Consensus size: 92
336810 AAAATGATGT
* *
336820 CAATGTGCTGATTCAAGGCCAGCTATATTGAACTTAAAGATGGAAAAGGTGCCAATATGCTGATT
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGCCAATATGCTGATT
* *
336885 CAAGGTCAGCTATATTGGACTTAAAGGTGC
63 CAAGGCCAGCGATATTGGACTTAAAGGTGC
*
336915 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAA
336980 GGCCAGCGATATTGGACTTAAAGGTGC
66 GGCCAGCGATATTGGACTTAAAGGTGC
337007 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAA
337072 GGCCAGCGATATTGGACTTAAAGGTGC
66 GGCCAGCGATATTGGACTTAAAGGTGC
* *
337099 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCTAATATGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAA
* *
337164 GGCCAGTGATATTGGACTTAAAAGTGC
66 GGCCAGCGATATTGGACTTAAAGGTGC
* * *
337191 CAATGTGCTGATTCAAGGCCGGCTACATTGGATTTAAAGATGAAGATGCCAATATGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAA
*
337256 GGCCAGCTATATTGGACTTAAAGG
66 GGCCAGCGATATTGGACTTAAAGG
337280 AAGATGCCAC
Statistics
Matches: 349, Mismatches: 16, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
92 310 0.89
94 1 0.00
95 38 0.11
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (92 bp):
CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAA
GGCCAGCGATATTGGACTTAAAGGTGC
Found at i:337355 original size:32 final size:32
Alignment explanation
Indices: 337284--337380 Score: 140
Period size: 32 Copynumber: 3.0 Consensus size: 32
337274 TAAAGGAAGA
* * *
337284 TGCCACCAACTTGTGTGGGCTTTTGAAGAAGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAG-GGGT
*
337317 TGCCACCGACTTATGTGGGCTTTAGAAGGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGGGGT
*
337349 TGCCACCGACTTGTGTGGGCTTTAGAAAGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGGGGT
337381 GAAAGATGCC
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
32 33 0.57
33 25 0.43
ACGTcount: A:0.20, C:0.19, G:0.33, T:0.29
Consensus pattern (32 bp):
TGCCACCGACTTGTGTGGGCTTTAGAAGGGGT
Found at i:337424 original size:33 final size:33
Alignment explanation
Indices: 337382--337513 Score: 135
Period size: 36 Copynumber: 3.9 Consensus size: 33
337372 AGAAAGGGTG
* *
337382 AAAGATGCCACGAAGTTGTGGAC-TTAAAAAGA
1 AAAGGTGCCACGGAGTTGTGGACTTTAAAAAGA
* *
337414 ACAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGGAA
1 A-AAGGTGCCACGGAGTTGTGGACTTTAAAA-AG-A
* *
337450 AAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAG-
1 AAAG-GTGCCACGGAGTTGTGGACTTTAAAAAGA
*
337483 -AAGGTGCCACGGAGTCGTGGACTTTAGAAAA
1 AAAGGTGCCACGGAGTTGTGGACTTTA-AAAA
337514 TATGCCACCG
Statistics
Matches: 85, Mismatches: 9, Indels: 12
0.80 0.08 0.11
Matches are distributed among these distances:
31 20 0.24
32 8 0.09
33 19 0.22
34 6 0.07
35 5 0.06
36 27 0.32
ACGTcount: A:0.34, C:0.14, G:0.33, T:0.20
Consensus pattern (33 bp):
AAAGGTGCCACGGAGTTGTGGACTTTAAAAAGA
Found at i:337441 original size:69 final size:68
Alignment explanation
Indices: 337362--337512 Score: 191
Period size: 69 Copynumber: 2.2 Consensus size: 68
337352 CACCGACTTG
**
337362 TGTGGGCTTTAGAAAGGGTGAAAGA-TGCCACGAAGTTGTGGAC-TTAAAAAGAACAAGGTGCCA
1 TGTGGGCTTTAGAAAGGGAAAAAGAGTGCCACGAAGTTGTGGACTTTAAAAAG---AAGGTGCCA
337425 CGGAGT
63 CGGAGT
* * *
337431 TGTGGGCTTTA-AAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGG
1 TGTGGGCTTTAGAAAGGGAAAAAGAGTGCCACGAAGTTGTGGACTTTAAAAAGAAGGTGCCACGG
337495 AGT
66 AGT
* *
337498 CGTGGACTTTAGAAA
1 TGTGGGCTTTAGAAA
337513 ATATGCCACC
Statistics
Matches: 72, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
67 24 0.33
68 14 0.19
69 27 0.38
70 7 0.10
ACGTcount: A:0.32, C:0.13, G:0.34, T:0.21
Consensus pattern (68 bp):
TGTGGGCTTTAGAAAGGGAAAAAGAGTGCCACGAAGTTGTGGACTTTAAAAAGAAGGTGCCACGG
AGT
Found at i:337466 original size:36 final size:36
Alignment explanation
Indices: 337362--337482 Score: 142
Period size: 36 Copynumber: 3.4 Consensus size: 36
337352 CACCGACTTG
** *
337362 TGTGGGCTTTAGAAAGGGTGAAAGA-TGCCACGAAGT
1 TGTGGGCTTTA-AAAGGGAAAAAGAGTGCCACGGAGT
* * *
337398 TGTGGAC-TTAAAA-AGAACAAG-GTGCCACGGAGT
1 TGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGT
337431 TGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGT
337467 TGTGGGCTTTGAAAAG
1 TGTGGGCTTT-AAAAG
337483 AAGGTGCCAC
Statistics
Matches: 71, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
33 20 0.28
34 9 0.13
35 9 0.13
36 28 0.39
37 5 0.07
ACGTcount: A:0.32, C:0.12, G:0.35, T:0.21
Consensus pattern (36 bp):
TGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGT
Found at i:337623 original size:34 final size:35
Alignment explanation
Indices: 337568--337659 Score: 116
Period size: 35 Copynumber: 2.7 Consensus size: 35
337558 GTGGGCTTTG
* * *
337568 AAAAGGGTGCCACT-GACTTGTGGGCTTA-AAAGGA
1 AAAAGAGTGCCA-TGGAGTTGTGGGCTTACAAAAGA
* *
337602 AAAAGAGTGCTATGGAGTTGTGAGCTTACAAAAGA
1 AAAAGAGTGCCATGGAGTTGTGGGCTTACAAAAGA
337637 AAAAGAGTGCCATGGAGTTGTGG
1 AAAAGAGTGCCATGGAGTTGTGG
337660 ACTTTGGAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
33 1 0.02
34 22 0.45
35 26 0.53
ACGTcount: A:0.35, C:0.11, G:0.33, T:0.22
Consensus pattern (35 bp):
AAAAGAGTGCCATGGAGTTGTGGGCTTACAAAAGA
Found at i:337675 original size:157 final size:152
Alignment explanation
Indices: 337418--337784 Score: 520
Period size: 156 Copynumber: 2.4 Consensus size: 152
337408 AAAAGAACAA
* * **
337418 GGTGCCACGGAGTTGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAG
1 GGTGCCACTGACTTGTGGGC-TTAAAA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTACAAAAG
337483 AAGGTGCCACGGAGTCGTGGACTTTAGAAAATATGCCACCGACTTGTGGGCTTCGGAAAAGGGTG
64 AAGGTGCCACGGAGTCGTGGACTTTAGAAAATATGCCACCGACTTGTGGGCTT-GG-AAAGGGTG
*
337548 CCACTAATTTGTGGGC-TTTGAAAAG
127 CCACTAACTTGTGGGCTTTTGAAAAG
* * *
337573 GGTGCCACTGACTTGTGGGCTTAAAAGGAAAAAGAGTGCTATGGAGTTGTGAGCTTACAAAAGAA
1 GGTGCCACTGACTTGTGGGCTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTACAAAAG--
* * * * *
337638 AAAGAGTGCCATGGAGTTGTGGACTTTGGAAAATATGCCACCGACTTGTGGGCTTTGAAAGGTTG
64 -AAG-GTGCCACGGAGTCGTGGACTTTAGAAAATATGCCACCGACTTGTGGGCTTGGAAAGGGTG
*
337703 CCACTGACTTGTGGGCTTTTGAAAAG
127 CCACTAACTTGTGGGCTTTTGAAAAG
*
337729 GGTGCCACTAACTTGTGGGCTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
1 GGTGCCACTGACTTGTGGGCTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
337785 TGAAAAAGAT
Statistics
Matches: 189, Mismatches: 18, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
153 32 0.17
154 6 0.03
155 39 0.21
156 65 0.34
157 47 0.25
ACGTcount: A:0.28, C:0.15, G:0.33, T:0.25
Consensus pattern (152 bp):
GGTGCCACTGACTTGTGGGCTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTACAAAAGAA
GGTGCCACGGAGTCGTGGACTTTAGAAAATATGCCACCGACTTGTGGGCTTGGAAAGGGTGCCAC
TAACTTGTGGGCTTTTGAAAAG
Done.