Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold317
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: 948703
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 33011 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:385018 original size:16 final size:17
Alignment explanation
Indices: 384999--385032 Score: 52
Period size: 16 Copynumber: 2.0 Consensus size: 17
384989 AATGCCTTAG
384999 TTTTAATA-ATTATTAA
1 TTTTAATACATTATTAA
385015 TTTTAATATCATTATTAA
1 TTTTAATA-CATTATTAA
385033 GTAGTTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
18 8 0.50
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTTAATACATTATTAA
Found at i:394640 original size:43 final size:43
Alignment explanation
Indices: 394532--394646 Score: 158
Period size: 43 Copynumber: 2.7 Consensus size: 43
394522 GGCTCGTACA
* * * *
394532 ATGCCAACGTCCCAGACGTGGTCTCACATGTAATCACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAAACACAAATCG
* * *
394575 ATGCCAATGTCCAAGACATGGTCTTACACGTAAACACAAATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAAACACAAATCG
*
394618 ATGCCAACGTCCCAGGCGTGGTCTTACAC
1 ATGCCAACGTCCCAGACGTGGTCTTACAC
394647 AAAAATACAT
Statistics
Matches: 61, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 61 1.00
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.22
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGTAAACACAAATCG
Found at i:394661 original size:43 final size:43
Alignment explanation
Indices: 394532--394661 Score: 138
Period size: 43 Copynumber: 3.0 Consensus size: 43
394522 GGCTCGTACA
**
394532 ATGCCAACGTCCCAGACGTGGTC-T-CACATGTAATCACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACA-AAAAT-ACATATCG
* * * ** * *
394575 ATGCCAATGTCCAAGACATGGTCTTACACGTAAACACAAATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACAAAAATACATATCG
*
394618 ATGCCAACGTCCCAGGCGTGGTCTTACACAAAAATACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACAAAAATACATATCG
394661 A
1 A
394662 AAATCCTATG
Statistics
Matches: 69, Mismatches: 16, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
43 63 0.91
44 3 0.04
45 3 0.04
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.22
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACAAAAATACATATCG
Found at i:401369 original size:26 final size:26
Alignment explanation
Indices: 401297--401369 Score: 83
Period size: 26 Copynumber: 2.8 Consensus size: 26
401287 TTTTATCCCT
* *
401297 ATTTTACCCCCAGTAAAATTCTAACG
1 ATTTTACCCCTAGTAAAATTTTAACG
* * * *
401323 ATTTTACCCTTGGTAAAATTTTGATG
1 ATTTTACCCCTAGTAAAATTTTAACG
*
401349 ATTTTTCCCCTAGTAAAATTT
1 ATTTTACCCCTAGTAAAATTT
401370 CGAGAAAATA
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.30, C:0.19, G:0.10, T:0.41
Consensus pattern (26 bp):
ATTTTACCCCTAGTAAAATTTTAACG
Found at i:401532 original size:6 final size:6
Alignment explanation
Indices: 401518--401569 Score: 68
Period size: 6 Copynumber: 8.7 Consensus size: 6
401508 CAAATGAGTT
* * * *
401518 ATTTAC ATTTTC ATTTTC ATTTTC ATTTCC ATTTCC ATTTCC ATTTCC
1 ATTTCC ATTTCC ATTTCC ATTTCC ATTTCC ATTTCC ATTTCC ATTTCC
401566 ATTT
1 ATTT
401570 TTGGAAACCT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.19, C:0.23, G:0.00, T:0.58
Consensus pattern (6 bp):
ATTTCC
Found at i:417260 original size:14 final size:15
Alignment explanation
Indices: 417236--417270 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
417226 AGCTATCAGA
417236 ATTTATAAAACAGTT
1 ATTTATAAAACAGTT
*
417251 ATTT-TAAAACATTT
1 ATTTATAAAACAGTT
417265 ATTTAT
1 ATTTAT
417271 CTTAGAAGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.49
Consensus pattern (15 bp):
ATTTATAAAACAGTT
Found at i:430094 original size:18 final size:19
Alignment explanation
Indices: 430079--430118 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
430069 ATTTTTCTTT
430079 ATTTTATGTGTTTTCTTGC
1 ATTTTATGTGTTTTCTTGC
*
430098 ATTTTATGTGCTTTCTTGC
1 ATTTTATGTGTTTTCTTGC
430117 AT
1 AT
430119 GAACTTTCGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.12, C:0.12, G:0.15, T:0.60
Consensus pattern (19 bp):
ATTTTATGTGTTTTCTTGC
Found at i:433854 original size:15 final size:15
Alignment explanation
Indices: 433834--433864 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
433824 AAAACAACAT
433834 AACTCTTGACCTTTC
1 AACTCTTGACCTTTC
433849 AACTCTTGACCTTTC
1 AACTCTTGACCTTTC
433864 A
1 A
433865 CTTACATAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.23, C:0.32, G:0.06, T:0.39
Consensus pattern (15 bp):
AACTCTTGACCTTTC
Found at i:438201 original size:9 final size:9
Alignment explanation
Indices: 438189--438214 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
438179 AAAAATTAAC
438189 AAAACATTT
1 AAAACATTT
438198 AAAACATTT
1 AAAACATTT
438207 AAAACATT
1 AAAACATT
438215 ATACAAAAAA
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:0.58, C:0.12, G:0.00, T:0.31
Consensus pattern (9 bp):
AAAACATTT
Found at i:438447 original size:20 final size:20
Alignment explanation
Indices: 438424--438462 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
438414 ATACTATTAC
438424 TGTTCACGACATGACCCCAT
1 TGTTCACGACATGACCCCAT
* *
438444 TGTTCATGACTTGACCCCA
1 TGTTCACGACATGACCCCA
438463 CTATTCCTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.33, G:0.15, T:0.28
Consensus pattern (20 bp):
TGTTCACGACATGACCCCAT
Found at i:438709 original size:9 final size:9
Alignment explanation
Indices: 438695--438720 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
438685 TTTTGGTTAA
438695 AAATTAACC
1 AAATTAACC
438704 AAATTAACC
1 AAATTAACC
438713 AAATTAAC
1 AAATTAAC
438721 TGAATTACCC
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:0.58, C:0.19, G:0.00, T:0.23
Consensus pattern (9 bp):
AAATTAACC
Found at i:438789 original size:37 final size:37
Alignment explanation
Indices: 438743--438817 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
438733 ATTACCCGAA
*
438743 TTGAATCACTACATAATTAAAAATATTACATAAGTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
*
438780 TTGAATCACTACATAATTAAAAACATTATATAAGTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
438817 T
1 T
438818 GAAATTAACA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.45, C:0.13, G:0.05, T:0.36
Consensus pattern (37 bp):
TTGAATCACTACATAATTAAAAACATTACATAAGTCT
Found at i:438831 original size:37 final size:37
Alignment explanation
Indices: 438743--438834 Score: 116
Period size: 37 Copynumber: 2.5 Consensus size: 37
438733 ATTACCCGAA
* *
438743 TTGAATCACTACATAATTAAAAATATTACATAAGTCT
1 TTGAATAACTACATAATTAAAAACATTACATAAGTCT
* *
438780 TTGAATCACTACATAATTAAAAACATTATATAAGTC-
1 TTGAATAACTACATAATTAAAAACATTACATAAGTCT
438816 TTGAAATTAAC-ACATAATT
1 TTG-AA-TAACTACATAATT
438835 GAAATGTAAG
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
36 3 0.06
37 44 0.88
38 3 0.06
ACGTcount: A:0.47, C:0.13, G:0.05, T:0.35
Consensus pattern (37 bp):
TTGAATAACTACATAATTAAAAACATTACATAAGTCT
Found at i:438927 original size:9 final size:9
Alignment explanation
Indices: 438915--438940 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
438905 AAAAATTAAC
438915 AAAACATTT
1 AAAACATTT
438924 AAAACATTT
1 AAAACATTT
438933 AAAACATT
1 AAAACATT
438941 ATACAAAAAA
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:0.58, C:0.12, G:0.00, T:0.31
Consensus pattern (9 bp):
AAAACATTT
Found at i:439173 original size:20 final size:20
Alignment explanation
Indices: 439150--439188 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
439140 ATACTATTAC
439150 TGTTCACGACATGACCCCAT
1 TGTTCACGACATGACCCCAT
* *
439170 TGTTCATGACTTGACCCCA
1 TGTTCACGACATGACCCCA
439189 CTATTCCTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.33, G:0.15, T:0.28
Consensus pattern (20 bp):
TGTTCACGACATGACCCCAT
Found at i:439435 original size:9 final size:9
Alignment explanation
Indices: 439421--439446 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
439411 TTTTGGTTAA
439421 AAATTAACC
1 AAATTAACC
439430 AAATTAACC
1 AAATTAACC
439439 AAATTAAC
1 AAATTAAC
439447 TGAATTACCC
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:0.58, C:0.19, G:0.00, T:0.23
Consensus pattern (9 bp):
AAATTAACC
Found at i:439515 original size:37 final size:37
Alignment explanation
Indices: 439469--439543 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
439459 ATTACCCGAA
*
439469 TTGAATCACTACATAATTAAAAATATTACATAAGTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
* *
439506 TTGAATCACTACATAATTAAAAACATTATATAATTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
439543 T
1 T
439544 AAAATTAACA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.45, C:0.13, G:0.04, T:0.37
Consensus pattern (37 bp):
TTGAATCACTACATAATTAAAAACATTACATAAGTCT
Found at i:439551 original size:726 final size:726
Alignment explanation
Indices: 438154--439606 Score: 2870
Period size: 726 Copynumber: 2.0 Consensus size: 726
438144 TTAATTTTAA
438154 TTATGTATTATATTTATTTTTATATAAAAATTAACAAAACATTTAAAACATTTAAAACATTATAC
1 TTATGTATTATATTTATTTTTATATAAAAATTAACAAAACATTTAAAACATTTAAAACATTATAC
438219 AAAAAAAAAATTGAACCTACTGAATCTTAGCTCATTTGACATTAGCATTGTTACCAGTGCAGAAG
66 AAAAAAAAAATTGAACCTACTGAATCTTAGCTCATTTGACATTAGCATTGTTACCAGTGCAGAAG
438284 GACACAAGTTCGAATGCGATAAAGCACATAATCCTCTTATTTGAGAAGGGGTTATGGTAGTTCTA
131 GACACAAGTTCGAATGCGATAAAGCACATAATCCTCTTATTTGAGAAGGGGTTATGGTAGTTCTA
438349 GGTATTGTATCTGTTGAGTAATTTTATCTCGTATCATATTAATGAGAATATTCGAATATTTATAC
196 GGTATTGTATCTGTTGAGTAATTTTATCTCGTATCATATTAATGAGAATATTCGAATATTTATAC
438414 ATACTATTACTGTTCACGACATGACCCCATTGTTCATGACTTGACCCCACTATTCCTAAGACTGA
261 ATACTATTACTGTTCACGACATGACCCCATTGTTCATGACTTGACCCCACTATTCCTAAGACTGA
438479 CATTTTGAACAGACTTCAGGCATGCTGGATACTAGGGGTGTGCATTCGGTTAACCGACCCGAAAT
326 CATTTTGAACAGACTTCAGGCATGCTGGATACTAGGGGTGTGCATTCGGTTAACCGACCCGAAAT
438544 AGCTATAACCGAATTAACTGACCTTCCAAAATTTTTGACCGTTAACCGAACCGAATTTTTTAAAA
391 AGCTATAACCGAATTAACTGACCTTCCAAAATTTTTGACCGTTAACCGAACCGAATTTTTTAAAA
438609 AAAATTAACAGAACCGAAATTTTTTCGGTTAATTAGGTCAGTTAACCGAATTAACCGAAAATTGT
456 AAAATTAACAGAACCGAAATTTTTTCGGTTAATTAGGTCAGTTAACCGAATTAACCGAAAATTGT
438674 ATGATTTTTATTTTTGGTTAAAAATTAACCAAATTAACCAAATTAACTGAATTACCCGAATTACC
521 ATGATTTTTATTTTTGGTTAAAAATTAACCAAATTAACCAAATTAACTGAATTACCCGAATTACC
438739 CGAATTGAATCACTACATAATTAAAAATATTACATAAGTCTTTGAATCACTACATAATTAAAAAC
586 CGAATTGAATCACTACATAATTAAAAATATTACATAAGTCTTTGAATCACTACATAATTAAAAAC
* *
438804 ATTATATAAGTCTTGAAATTAACACATAATTGAAATGTAAGTCTTTAATATTCTCCATTTGTATC
651 ATTATATAAGTCTTAAAATTAACACATAATTGAAATGTAAGTCTTTAATATTCTCCATTTATATC
438869 CATTTCTTCTC
716 CATTTCTTCTC
438880 TTATGTATTATATTTATTTTTATATAAAAATTAACAAAACATTTAAAACATTTAAAACATTATAC
1 TTATGTATTATATTTATTTTTATATAAAAATTAACAAAACATTTAAAACATTTAAAACATTATAC
438945 AAAAAAAAAATTGAACCTACTGAATCTTAGCTCATTTGACATTAGCATTGTTACCAGTGCAGAAG
66 AAAAAAAAAATTGAACCTACTGAATCTTAGCTCATTTGACATTAGCATTGTTACCAGTGCAGAAG
439010 GACACAAGTTCGAATGCGATAAAGCACATAATCCTCTTATTTGAGAAGGGGTTATGGTAGTTCTA
131 GACACAAGTTCGAATGCGATAAAGCACATAATCCTCTTATTTGAGAAGGGGTTATGGTAGTTCTA
439075 GGTATTGTATCTGTTGAGTAATTTTATCTCGTATCATATTAATGAGAATATTCGAATATTTATAC
196 GGTATTGTATCTGTTGAGTAATTTTATCTCGTATCATATTAATGAGAATATTCGAATATTTATAC
439140 ATACTATTACTGTTCACGACATGACCCCATTGTTCATGACTTGACCCCACTATTCCTAAGACTGA
261 ATACTATTACTGTTCACGACATGACCCCATTGTTCATGACTTGACCCCACTATTCCTAAGACTGA
439205 CATTTTGAACAGACTTCAGGCATGCTGGATACTAGGGGTGTGCATTCGGTTAACCGACCCGAAAT
326 CATTTTGAACAGACTTCAGGCATGCTGGATACTAGGGGTGTGCATTCGGTTAACCGACCCGAAAT
439270 AGCTATAACCGAATTAACTGACCTTCCAAAATTTTTGACCGTTAACCGAACCGAATTTTTTAAAA
391 AGCTATAACCGAATTAACTGACCTTCCAAAATTTTTGACCGTTAACCGAACCGAATTTTTTAAAA
439335 AAAATTAACAGAACCGAAATTTTTTCGGTTAATTAGGTCAGTTAACCGAATTAACCGAAAATTGT
456 AAAATTAACAGAACCGAAATTTTTTCGGTTAATTAGGTCAGTTAACCGAATTAACCGAAAATTGT
439400 ATGATTTTTATTTTTGGTTAAAAATTAACCAAATTAACCAAATTAACTGAATTACCCGAATTACC
521 ATGATTTTTATTTTTGGTTAAAAATTAACCAAATTAACCAAATTAACTGAATTACCCGAATTACC
439465 CGAATTGAATCACTACATAATTAAAAATATTACATAAGTCTTTGAATCACTACATAATTAAAAAC
586 CGAATTGAATCACTACATAATTAAAAATATTACATAAGTCTTTGAATCACTACATAATTAAAAAC
* *
439530 ATTATATAATTCTTAAAATTAACACATAGTTGAAATGTAAGTCTTTAATATTCTCCATTTATATC
651 ATTATATAAGTCTTAAAATTAACACATAATTGAAATGTAAGTCTTTAATATTCTCCATTTATATC
439595 CATTTCTTCTC
716 CATTTCTTCTC
439606 T
1 T
439607 CCAAAAAATC
Statistics
Matches: 723, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
726 723 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.34
Consensus pattern (726 bp):
TTATGTATTATATTTATTTTTATATAAAAATTAACAAAACATTTAAAACATTTAAAACATTATAC
AAAAAAAAAATTGAACCTACTGAATCTTAGCTCATTTGACATTAGCATTGTTACCAGTGCAGAAG
GACACAAGTTCGAATGCGATAAAGCACATAATCCTCTTATTTGAGAAGGGGTTATGGTAGTTCTA
GGTATTGTATCTGTTGAGTAATTTTATCTCGTATCATATTAATGAGAATATTCGAATATTTATAC
ATACTATTACTGTTCACGACATGACCCCATTGTTCATGACTTGACCCCACTATTCCTAAGACTGA
CATTTTGAACAGACTTCAGGCATGCTGGATACTAGGGGTGTGCATTCGGTTAACCGACCCGAAAT
AGCTATAACCGAATTAACTGACCTTCCAAAATTTTTGACCGTTAACCGAACCGAATTTTTTAAAA
AAAATTAACAGAACCGAAATTTTTTCGGTTAATTAGGTCAGTTAACCGAATTAACCGAAAATTGT
ATGATTTTTATTTTTGGTTAAAAATTAACCAAATTAACCAAATTAACTGAATTACCCGAATTACC
CGAATTGAATCACTACATAATTAAAAATATTACATAAGTCTTTGAATCACTACATAATTAAAAAC
ATTATATAAGTCTTAAAATTAACACATAATTGAAATGTAAGTCTTTAATATTCTCCATTTATATC
CATTTCTTCTC
Found at i:439557 original size:37 final size:37
Alignment explanation
Indices: 439476--439557 Score: 94
Period size: 37 Copynumber: 2.2 Consensus size: 37
439466 GAATTGAATC
* ** *
439476 ACTACATAATTAAAAATATTACATAAGTCTTTGAATC
1 ACTACATAATTAAAAACATTACATAAGTCTTAAAATA
* *
439513 ACTACATAATTAAAAACATTATATAATTCTTAAAATTA
1 ACTACATAATTAAAAACATTACATAAGTCTTAAAA-TA
439551 AC-ACATA
1 ACTACATA
439558 GTTGAAATGT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
37 35 0.92
38 3 0.08
ACGTcount: A:0.50, C:0.13, G:0.02, T:0.34
Consensus pattern (37 bp):
ACTACATAATTAAAAACATTACATAAGTCTTAAAATA
Found at i:439754 original size:12 final size:12
Alignment explanation
Indices: 439739--439764 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
439729 AGTTTTATTG
439739 GGTTGGGTAATT
1 GGTTGGGTAATT
439751 GGTTGGGTAATT
1 GGTTGGGTAATT
439763 GG
1 GG
439765 GTAGACTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.00, G:0.46, T:0.38
Consensus pattern (12 bp):
GGTTGGGTAATT
Found at i:439812 original size:13 final size:13
Alignment explanation
Indices: 439786--439822 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
439776 TTTTAGTTTT
439786 ATTGGGTT-GGTA
1 ATTGGGTTGGGTA
439798 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
439811 ATTGGGTTGGGT
1 ATTGGGTTGGGT
439823 TTGATAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 8 0.33
13 16 0.67
ACGTcount: A:0.14, C:0.00, G:0.46, T:0.41
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:442338 original size:21 final size:20
Alignment explanation
Indices: 442300--442338 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
442290 TTTAACTCAA
442300 TAAAAAATTAAAATTATTTT
1 TAAAAAATTAAAATTATTTT
442320 TAAAATAA-TAAATATTATT
1 TAAAA-AATTAAA-ATTATT
442339 ATAAAAGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TAAAAAATTAAAATTATTTT
Found at i:442343 original size:20 final size:20
Alignment explanation
Indices: 442299--442344 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
442289 ATTTAACTCA
442299 ATAAAAAATTAAAATTATTT
1 ATAAAAAATTAAAATTATTT
*
442319 TTAAAATAA-TAAATATTA-TT
1 ATAAAA-AATTAAA-ATTATTT
442339 ATAAAA
1 ATAAAA
442345 GTATGTTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
ATAAAAAATTAAAATTATTT
Found at i:442989 original size:4 final size:4
Alignment explanation
Indices: 442980--443032 Score: 106
Period size: 4 Copynumber: 13.2 Consensus size: 4
442970 CAGTAATTTA
442980 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
443028 TATG T
1 TATG T
443033 TGCATCAGGT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 49 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:447466 original size:52 final size:53
Alignment explanation
Indices: 447403--447512 Score: 204
Period size: 52 Copynumber: 2.1 Consensus size: 53
447393 CAAATGTCTC
*
447403 TAAAGTAGTAGAAAAATTAACAATACAACAAGAGTTATACAATATCCAAACAA
1 TAAACTAGTAGAAAAATTAACAATACAACAAGAGTTATACAATATCCAAACAA
447456 -AAACTAGTAGAAAAATTAACAATACAACAAGAGTTATACAATATCCAAACAA
1 TAAACTAGTAGAAAAATTAACAATACAACAAGAGTTATACAATATCCAAACAA
447508 TAAAC
1 TAAAC
447513 AAAAATAATA
Statistics
Matches: 55, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
52 51 0.93
53 4 0.07
ACGTcount: A:0.57, C:0.15, G:0.08, T:0.20
Consensus pattern (53 bp):
TAAACTAGTAGAAAAATTAACAATACAACAAGAGTTATACAATATCCAAACAA
Found at i:447573 original size:33 final size:33
Alignment explanation
Indices: 447531--447598 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 33
447521 TAATAGCAAT
* **
447531 ATAATAGTGAAGTGATAATGAAATGACAACAAA
1 ATAATAGTGAAATGATAATGAAACAACAACAAA
* *
447564 ATAATAGTGAAATGATAGTTAAACAACAACAAA
1 ATAATAGTGAAATGATAATGAAACAACAACAAA
447597 AT
1 AT
447599 GGTAGTGAGA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.56, C:0.07, G:0.15, T:0.22
Consensus pattern (33 bp):
ATAATAGTGAAATGATAATGAAACAACAACAAA
Found at i:447598 original size:22 final size:22
Alignment explanation
Indices: 447573--447619 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
447563 AATAATAGTG
* *
447573 AAATGATAGTTAAACAACAACA
1 AAATGATAGTGAAACAACAAAA
* *
447595 AAATGGTAGTGAGACAACAAAA
1 AAATGATAGTGAAACAACAAAA
447617 AAA
1 AAA
447620 CATGGCAACA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.60, C:0.11, G:0.15, T:0.15
Consensus pattern (22 bp):
AAATGATAGTGAAACAACAAAA
Found at i:450526 original size:5 final size:5
Alignment explanation
Indices: 450516--450556 Score: 64
Period size: 5 Copynumber: 8.2 Consensus size: 5
450506 AAAGTATCCT
* *
450516 AAAAG AAAAG AAAAG AAAAC AAAAG AAAAG AAAAG TAAAG A
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG A
450557 CCCCTTAGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.02
Consensus pattern (5 bp):
AAAAG
Found at i:482801 original size:21 final size:21
Alignment explanation
Indices: 482762--482805 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
482752 TAAATATTAG
**
482762 ATTAAATTTAATATTAAATCTT
1 ATTAAATTTAATAGAAAAT-TT
482784 ATTAAA-TTAATAGAAAATTT
1 ATTAAATTTAATAGAAAATTT
482804 AT
1 AT
482806 CTACAAGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.20
21 10 0.50
22 6 0.30
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (21 bp):
ATTAAATTTAATAGAAAATTT
Found at i:482832 original size:62 final size:59
Alignment explanation
Indices: 482725--482924 Score: 186
Period size: 62 Copynumber: 3.2 Consensus size: 59
482715 TCACTCTAAA
* * *
482725 ATTAAATTAATATAATATTTATCAAGATAAATATTAGATTAAATTTAATATTAAATCTT
1 ATTAAATTAATAGAAAATTTATCAAGATAAATATTAAATTAAATTTAATATTAAATCTT
* * *
482784 ATTAAATTAATAGAAAATTTATCTACAAGATAAATATTAAATTCAATTTAATATTAATATAATC
1 ATTAAATTAATAGAAAATTTA--T-CAAGATAAATATTAAATTAAATTTAATATTAA-AT-CTT
* * * *
482848 ACTTTAATATTAAATTAATAAAATACTATTAAGATAAATATTAAATTAAATCTAATATTAAATC-
1 A--TTAA-ATT-AA-T-AGAAAAT-TTATCAAGATAAATATTAAATTAAATTTAATATTAAATCT
482912 T
59 T
*
482913 ATTAAAATAATA
1 ATTAAATTAATA
482925 CTACTTTTAG
Statistics
Matches: 115, Mismatches: 14, Indels: 24
0.75 0.09 0.16
Matches are distributed among these distances:
59 20 0.17
60 1 0.01
61 3 0.03
62 32 0.28
63 6 0.05
64 2 0.02
65 1 0.01
66 4 0.03
67 5 0.04
68 31 0.27
69 2 0.02
70 6 0.05
71 2 0.02
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.41
Consensus pattern (59 bp):
ATTAAATTAATAGAAAATTTATCAAGATAAATATTAAATTAAATTTAATATTAAATCTT
Found at i:490340 original size:19 final size:19
Alignment explanation
Indices: 490302--490341 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
490292 TTTGTTTCTC
*
490302 AAAATAAATATTATTTATT
1 AAAATAAATATTATTAATT
490321 AAAATAAAT-TTAATTAATT
1 AAAATAAATATT-ATTAATT
490340 AA
1 AA
490342 TTTTCTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 2 0.11
19 17 0.89
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AAAATAAATATTATTAATT
Found at i:490352 original size:16 final size:16
Alignment explanation
Indices: 490331--490361 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
490321 AAAATAAATT
*
490331 TAATTAATTAATTTTC
1 TAATTAAATAATTTTC
490347 TAATTAAATAATTTT
1 TAATTAAATAATTTT
490362 TTCAATCCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (16 bp):
TAATTAAATAATTTTC
Found at i:491770 original size:25 final size:27
Alignment explanation
Indices: 491742--491793 Score: 90
Period size: 26 Copynumber: 2.0 Consensus size: 27
491732 TTCTTATCCC
491742 GATTTTA-CCCTAGTAAAA-TTATGAA
1 GATTTTACCCCTAGTAAAATTTATGAA
491767 GATTTTACCCCTAGTAAAATTTATGAA
1 GATTTTACCCCTAGTAAAATTTATGAA
491794 AAAATATGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 7 0.28
26 11 0.44
27 7 0.28
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.37
Consensus pattern (27 bp):
GATTTTACCCCTAGTAAAATTTATGAA
Found at i:495227 original size:20 final size:21
Alignment explanation
Indices: 495182--495228 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
495172 ATTAAATACT
*
495182 ATAAAAATTATTAACACAATA
1 ATAAAAATTATGAACACAATA
* *
495203 A-AAAAATTCTGAACA-AGTA
1 ATAAAAATTATGAACACAATA
495222 ATAAAAA
1 ATAAAAA
495229 CTAAAATCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 4 0.18
20 17 0.77
21 1 0.05
ACGTcount: A:0.64, C:0.09, G:0.04, T:0.23
Consensus pattern (21 bp):
ATAAAAATTATGAACACAATA
Found at i:506165 original size:31 final size:31
Alignment explanation
Indices: 506125--506194 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 31
506115 TTCAAACGTG
506125 TATAATTGAATCAAAATAAAAGTTTCATATA
1 TATAATTGAATCAAAATAAAAGTTTCATATA
* * * * *
506156 TATATTTGAATTATAATTAAAGTTTCATATG
1 TATAATTGAATCAAAATAAAAGTTTCATATA
506187 TATAATTG
1 TATAATTG
506195 TACCAAATCA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.43
Consensus pattern (31 bp):
TATAATTGAATCAAAATAAAAGTTTCATATA
Found at i:507587 original size:58 final size:58
Alignment explanation
Indices: 507458--507613 Score: 181
Period size: 58 Copynumber: 2.7 Consensus size: 58
507448 TTACATTTTG
* * * *
507458 AACTTGACAAGTT-TTCTCACATTGGAGCTTAAACTTTCTTTTATCCAAGTTAGGCTCTA
1 AACTTGGCAA-TTGTTCTCACATTGGGGCCTAAACTTT-TTTTATCCAAATTAGGCTCTA
* * *
507517 AACTTGGCAATTGTTCTCAAATTGGGGCCTAAACTTTTTTTATCCAAATTAGTC-CGTG
1 AACTTGGCAATTGTTCTCACATTGGGGCCTAAACTTTTTTTATCCAAATTAGGCTC-TA
* **
507575 AACTTGGTAATTGTTCTCACATTAAGGCCTAAACTTTTT
1 AACTTGGCAATTGTTCTCACATTGGGGCCTAAACTTTTT
507614 CCTTTTTTTT
Statistics
Matches: 84, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
57 1 0.01
58 53 0.63
59 30 0.36
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (58 bp):
AACTTGGCAATTGTTCTCACATTGGGGCCTAAACTTTTTTTATCCAAATTAGGCTCTA
Found at i:507781 original size:31 final size:31
Alignment explanation
Indices: 507722--507782 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
507712 GCAAACCCTA
* *
507722 AAGTTCAAGCCCCAATGTAAGAATAATTGCT
1 AAGTTCAAGCCCCAATATAAGAACAATTGCT
* **
507753 AAGTTCATGCCCCAATATGGGAACAATTGC
1 AAGTTCAAGCCCCAATATAAGAACAATTGC
507783 CAAAATCAAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25
Consensus pattern (31 bp):
AAGTTCAAGCCCCAATATAAGAACAATTGCT
Found at i:515007 original size:18 final size:19
Alignment explanation
Indices: 514986--515023 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
514976 AAAAATATCG
*
514986 TTAAACATA-TTAAAAAAA
1 TTAAACACATTTAAAAAAA
515004 TTAAACACATTTAAAAAAA
1 TTAAACACATTTAAAAAAA
515023 T
1 T
515024 AAATTACCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (19 bp):
TTAAACACATTTAAAAAAA
Found at i:516904 original size:20 final size:20
Alignment explanation
Indices: 516875--516923 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
516865 CATGTGCTCC
516875 AGCC-GTGTGGAGGTCTACA
1 AGCCTGTGTGGAGGTCTACA
*
516894 CA-CCTGTGTGGTGGTCTACA
1 -AGCCTGTGTGGAGGTCTACA
516914 AGCCTGTGTG
1 AGCCTGTGTG
516924 CAAGCTGCAC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 3 0.12
20 23 0.88
ACGTcount: A:0.16, C:0.22, G:0.35, T:0.27
Consensus pattern (20 bp):
AGCCTGTGTGGAGGTCTACA
Found at i:517780 original size:17 final size:17
Alignment explanation
Indices: 517754--517786 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
517744 TAATTAACCT
517754 TTAAAACAAAACTAAAC
1 TTAAAACAAAACTAAAC
*
517771 TTAAACCAAAACTAAA
1 TTAAAACAAAACTAAA
517787 ATAACACACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.64, C:0.18, G:0.00, T:0.18
Consensus pattern (17 bp):
TTAAAACAAAACTAAAC
Found at i:518046 original size:181 final size:181
Alignment explanation
Indices: 517742--518100 Score: 583
Period size: 181 Copynumber: 2.0 Consensus size: 181
517732 AAAGTAAATA
517742 AATAATTAACCTTTAAAACAAAACTAAACTTAAACCAAAACTAAAATAACACACATAAGGACTCA
1 AATAATTAACCTTTAAAACAAAACTAAACTTAAACCAAAACTAAAATAACACACATAAGGACTCA
* * * ** *
517807 AACCCGAGACCTAATGATAGACTAACACTCATTCAACCACCGAACCAGTAGGCTCATTCTAAAAC
66 AACCCAAGACCCAATGATAGACGAACACTCATTCAACCACCGAACCAACAGACTCATTCTAAAAC
* * *
517872 TAAATTGCAAAAATAATTTCAACTGCTCGACCTAGTCATTGACACTAACTT
131 TAAATTGCAAAAATAAATTCAACTACTCGACCTACTCATTGACACTAACTT
* * *
517923 AATAATTAATCTTTAAAACAAAACTAGACTTCAACCAAAACTAAAATAACACACATAAGGACTCA
1 AATAATTAACCTTTAAAACAAAACTAAACTTAAACCAAAACTAAAATAACACACATAAGGACTCA
* *
517988 AACCCAAGACCCAATGATAGACGAACACTCATTCAACCACTGAACCAACAGACTCATTCTAATAC
66 AACCCAAGACCCAATGATAGACGAACACTCATTCAACCACCGAACCAACAGACTCATTCTAAAAC
*
518053 TAAATTGCAAAAATAAATTCAACTACTCGACCTACTCATTGACCCTAA
131 TAAATTGCAAAAATAAATTCAACTACTCGACCTACTCATTGACACTAA
518101 TACAAACCTC
Statistics
Matches: 163, Mismatches: 15, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
181 163 1.00
ACGTcount: A:0.45, C:0.25, G:0.08, T:0.22
Consensus pattern (181 bp):
AATAATTAACCTTTAAAACAAAACTAAACTTAAACCAAAACTAAAATAACACACATAAGGACTCA
AACCCAAGACCCAATGATAGACGAACACTCATTCAACCACCGAACCAACAGACTCATTCTAAAAC
TAAATTGCAAAAATAAATTCAACTACTCGACCTACTCATTGACACTAACTT
Found at i:521025 original size:8 final size:8
Alignment explanation
Indices: 521012--521043 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
521002 TTATAGGGCA
521012 ATAATATT
1 ATAATATT
521020 ATAATATT
1 ATAATATT
521028 ATAATATT
1 ATAATATT
521036 ATAATATT
1 ATAATATT
521044 GAATACCAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
ATAATATT
Found at i:535708 original size:20 final size:19
Alignment explanation
Indices: 535670--535709 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
535660 AATTTTGATA
* *
535670 TATTTTAATTGTTTCAATT
1 TATTTTAATAGTATCAATT
535689 TATTTTGAATAGTATCAATT
1 TATTTT-AATAGTATCAATT
535709 T
1 T
535710 GTATCGATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.30, C:0.05, G:0.07, T:0.57
Consensus pattern (19 bp):
TATTTTAATAGTATCAATT
Found at i:535916 original size:19 final size:19
Alignment explanation
Indices: 535892--536002 Score: 186
Period size: 19 Copynumber: 5.8 Consensus size: 19
535882 AATTTTTGAG
535892 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
535911 GATATGCAATCCTAGATAT
1 GATATGCAATCTTAGATAT
535930 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
535949 GATATGCAATCTCAGATAT
1 GATATGCAATCTTAGATAT
**
535968 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
535987 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
536003 GTTTTGTAAT
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 84 1.00
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:549768 original size:44 final size:44
Alignment explanation
Indices: 549697--549901 Score: 137
Period size: 44 Copynumber: 4.7 Consensus size: 44
549687 ACAGTGGAAT
* * * *
549697 AGATTAAAGATTTCAGATCTTATCTCCCTAAGCAGTACTAGAGC
1 AGATTGAAGATTGCAGATTTTACCTCCCTAAGCAGTACTAGAGC
* ** * *
549741 AGATTGAAGATTGCGGATTTTACCTCCCT--GTGGTTACAGTGGAGT
1 AGATTGAAGATTGCAGATTTTACCTCCCTAAGCAG-TAC--TAGAGC
* * * * * * * * * * **
549786 ACATTGAAGCTAGTA-ATTCTACTTCCCTAGGCAATAGTGGAAT
1 AGATTGAAGATTGCAGATTTTACCTCCCTAAGCAGTACTAGAGC
* * *
549829 AGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTACTAGAGC
1 AGATTGAAGATTGCAGATTTTACCTCCCTAAGCAGTACTAGAGC
*
549873 AGATTGAAGATTGCGGATTTTACCTCCCT
1 AGATTGAAGATTGCAGATTTTACCTCCCT
549902 GTGGTTACAG
Statistics
Matches: 115, Mismatches: 40, Indels: 12
0.69 0.24 0.07
Matches are distributed among these distances:
42 2 0.02
43 18 0.16
44 78 0.68
45 16 0.14
46 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.31
Consensus pattern (44 bp):
AGATTGAAGATTGCAGATTTTACCTCCCTAAGCAGTACTAGAGC
Found at i:549825 original size:132 final size:131
Alignment explanation
Indices: 549579--549989 Score: 621
Period size: 132 Copynumber: 3.1 Consensus size: 131
549569 NNNNNNNNNN
* * * *
549579 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTT
1 AGATCTTATCTCCCTAAGCAGTACTAGAGCAGATTGAAGATTGCGGATTTTACCTCCCTGTGGTT
* * * * *
549644 ATAGTGGAGTACATTGAAGCCAATAATTCTACTTCTCTGAGCAACAGTGGAATAGATTAAAGATT
66 ACAGTGGAGTACATTGAAGCTAGTAATTCTACTTCCCTG-GCAACAGTGGAATAGATTGAAGATT
549709 TC
130 TC
549711 AGATCTTATCTCCCTAAGCAGTACTAGAGCAGATTGAAGATTGCGGATTTTACCTCCCTGTGGTT
1 AGATCTTATCTCCCTAAGCAGTACTAGAGCAGATTGAAGATTGCGGATTTTACCTCCCTGTGGTT
*
549776 ACAGTGGAGTACATTGAAGCTAGTAATTCTACTTCCCTAGGCAATAGTGGAATAGATTGAAGATT
66 ACAGTGGAGTACATTGAAGCTAGTAATTCTACTTCCCT-GGCAACAGTGGAATAGATTGAAGATT
549841 TC
130 TC
549843 AGATCTTATCTCCCTAAGCAGTACTAGAGCAGATTGAAGATTGCGGATTTTACCTCCCTGTGGTT
1 AGATCTTATCTCCCTAAGCAGTACTAGAGCAGATTGAAGATTGCGGATTTTACCTCCCTGTGGTT
* * *
549908 ACAGTGGAGTACATTGAAG-TCAGTAATCCTA-TCTCCCTGGTCAGCAGTGGAATAGGTTGAAGA
66 ACAGTGGAGTACATTGAAGCT-AGTAATTCTACT-TCCCTGG-CAACAGTGGAATAGATTGAAGA
*
549971 TTGTA
128 TT-TC
549976 AG-TCTTATCTCCCT
1 AGATCTTATCTCCCT
549990 GCAGTTGCAG
Statistics
Matches: 259, Mismatches: 15, Indels: 10
0.91 0.05 0.04
Matches are distributed among these distances:
131 4 0.02
132 251 0.97
133 4 0.02
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (131 bp):
AGATCTTATCTCCCTAAGCAGTACTAGAGCAGATTGAAGATTGCGGATTTTACCTCCCTGTGGTT
ACAGTGGAGTACATTGAAGCTAGTAATTCTACTTCCCTGGCAACAGTGGAATAGATTGAAGATTT
C
Found at i:550206 original size:19 final size:19
Alignment explanation
Indices: 550182--550292 Score: 177
Period size: 19 Copynumber: 5.8 Consensus size: 19
550172 AATTTTTGAG
*
550182 GATATGCAATATTAGATAT
1 GATATGCAATCTTAGATAT
*
550201 GATATGCAATCCTAGATAT
1 GATATGCAATCTTAGATAT
550220 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
550239 GATATGCAATCTCAGATAT
1 GATATGCAATCTTAGATAT
**
550258 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
550277 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
550293 ATATATGATT
Statistics
Matches: 83, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 83 1.00
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:557450 original size:23 final size:23
Alignment explanation
Indices: 557424--557472 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
557414 GAATTTCCTC
*
557424 AAGGTACCCACGAAGAACAGCAG
1 AAGGTACCCACGAAAAACAGCAG
*
557447 AAGGTACCCACGAAAAACAGTAG
1 AAGGTACCCACGAAAAACAGCAG
557470 AAG
1 AAG
557473 AACGAAGTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.47, C:0.22, G:0.24, T:0.06
Consensus pattern (23 bp):
AAGGTACCCACGAAAAACAGCAG
Found at i:564846 original size:41 final size:41
Alignment explanation
Indices: 564786--564873 Score: 131
Period size: 41 Copynumber: 2.1 Consensus size: 41
564776 GAAATTGACT
* *
564786 TGTAAATGGTTGGATAATATGGTGGTATACACCGTGGAAGG
1 TGTAAATGGTTGGACAATATGGTGGTACACACCGTGGAAGG
* **
564827 TGTAAATGGTTGGACAATATGGTGGTACATATTGTGGAAGG
1 TGTAAATGGTTGGACAATATGGTGGTACACACCGTGGAAGG
564868 TGTAAA
1 TGTAAA
564874 GAGTGATTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.31, C:0.06, G:0.33, T:0.31
Consensus pattern (41 bp):
TGTAAATGGTTGGACAATATGGTGGTACACACCGTGGAAGG
Found at i:569248 original size:15 final size:15
Alignment explanation
Indices: 569210--569249 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
569200 CTGACGTGTG
569210 TTTTAGTTTT-AGAC
1 TTTTAGTTTTAAGAC
*
569224 TTTTAGTTTTAAGAT
1 TTTTAGTTTTAAGAC
*
569239 TTTTATTTTTA
1 TTTTAGTTTTA
569250 TTTATTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 10 0.43
15 13 0.57
ACGTcount: A:0.23, C:0.03, G:0.10, T:0.65
Consensus pattern (15 bp):
TTTTAGTTTTAAGAC
Found at i:572259 original size:25 final size:24
Alignment explanation
Indices: 572202--572261 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 24
572192 GTACATGTAG
* *
572202 GCTCATACGAGTGATAAATGGTAA
1 GCTCATACGAGTGACAAATGATAA
*
572226 GCTCCTACGAGTTG-CAAATCGATAA
1 GCTCATACGAG-TGACAAAT-GATAA
572251 GCTCATACGAG
1 GCTCATACGAG
572262 CTGTGGTGAG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 14 0.47
25 16 0.53
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.23
Consensus pattern (24 bp):
GCTCATACGAGTGACAAATGATAA
Found at i:582686 original size:2 final size:2
Alignment explanation
Indices: 582679--582703 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
582669 TCGGACAGAT
582679 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
582704 AACCTATGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:590428 original size:19 final size:18
Alignment explanation
Indices: 590400--590435 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
590390 AAATAAATTA
590400 ATTTTCAAAAATTCAAAAT
1 ATTTTC-AAAATTCAAAAT
*
590419 ATTTTGAAAATTCAAAA
1 ATTTTCAAAATTCAAAA
590436 AATTATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.53, C:0.08, G:0.03, T:0.36
Consensus pattern (18 bp):
ATTTTCAAAATTCAAAAT
Found at i:590486 original size:20 final size:19
Alignment explanation
Indices: 590432--590513 Score: 62
Period size: 19 Copynumber: 4.3 Consensus size: 19
590422 TTGAAAATTC
*
590432 AAAAAATTAT-ATATCTTTT
1 AAAAAATTATAATA-ATTTT
*
590451 AAACAATTATAATAATTTT
1 AAAAAATTATAATAATTTT
* *
590470 AAAAAATTCTAAATAATATAT
1 AAAAAATTAT-AATAAT-TTT
*
590491 AAATAAAGT-TAA-AATTTT
1 AAA-AAATTATAATAATTTT
590509 AAAAA
1 AAAAA
590514 TGTCCTAAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 10
0.75 0.10 0.14
Matches are distributed among these distances:
17 2 0.04
18 5 0.10
19 24 0.46
20 11 0.21
21 6 0.12
22 4 0.08
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.38
Consensus pattern (19 bp):
AAAAAATTATAATAATTTT
Found at i:595772 original size:15 final size:15
Alignment explanation
Indices: 595752--595783 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
595742 AAGAATTAAA
595752 GTGAATTGTCAAATT
1 GTGAATTGTCAAATT
595767 GTGAATTGTCAAATT
1 GTGAATTGTCAAATT
595782 GT
1 GT
595784 ACTTGTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.31, C:0.06, G:0.22, T:0.41
Consensus pattern (15 bp):
GTGAATTGTCAAATT
Found at i:597750 original size:20 final size:21
Alignment explanation
Indices: 597725--597763 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
597715 TATTGATGTT
*
597725 AAATTGAAT-TGCTATTATGA
1 AAATTGAATGTGATATTATGA
597745 AAATTGAATGTGATATTAT
1 AAATTGAATGTGATATTAT
597764 ATATGAAACG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.41, C:0.03, G:0.15, T:0.41
Consensus pattern (21 bp):
AAATTGAATGTGATATTATGA
Found at i:601710 original size:104 final size:105
Alignment explanation
Indices: 601592--601798 Score: 258
Period size: 104 Copynumber: 2.0 Consensus size: 105
601582 GCCGATATGG
** * ** *
601592 CTCACACGGCCTGGACACATTCCCATGTCCTTACCCATGTGGTTTTAAAG-CATAAACAGAGAGT
1 CTCACACGGCCTGGACACACGCCCATGTCCTCACCCATGTGGTCCT-AAGTCACAAACAGAGAGT
* *
601656 TACACGGCC-AGGACACACGGCCGTGTCC-TTGCCCGTGTAA
65 TACACAGCCTA-GACACACGACCGTGTCCTTTGCCCGTGTAA
* ** * *
601696 CTCACACGGCCTGGACACACGCCCATGTGCTCGTCCGTGTGGTCCTAAGTCACAAACAGTGAGTT
1 CTCACACGGCCTGGACACACGCCCATGTCCTCACCCATGTGGTCCTAAGTCACAAACAGAGAGTT
601761 ACACAGCCTAGACACACGACCGTGTCCTTTGCCCGTGT
66 ACACAGCCTAGACACACGACCGTGTCCTTTGCCCGTGT
601799 GAACCCTACA
Statistics
Matches: 87, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
103 3 0.03
104 73 0.84
105 11 0.13
ACGTcount: A:0.23, C:0.32, G:0.23, T:0.22
Consensus pattern (105 bp):
CTCACACGGCCTGGACACACGCCCATGTCCTCACCCATGTGGTCCTAAGTCACAAACAGAGAGTT
ACACAGCCTAGACACACGACCGTGTCCTTTGCCCGTGTAA
Found at i:606992 original size:13 final size:13
Alignment explanation
Indices: 606974--607000 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
606964 TTAATTTATA
606974 TGTGTGAAAATTT
1 TGTGTGAAAATTT
606987 TGTGTGAAAATTT
1 TGTGTGAAAATTT
607000 T
1 T
607001 ACCGTTTGTG
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:0.30, C:0.00, G:0.22, T:0.48
Consensus pattern (13 bp):
TGTGTGAAAATTT
Found at i:610718 original size:129 final size:129
Alignment explanation
Indices: 610488--610742 Score: 474
Period size: 129 Copynumber: 2.0 Consensus size: 129
610478 AATTACCTGG
*
610488 TATTTCTTTCAATCTAAATTTCGGAAGAAATACACTAGTTAGATATTTATTGATCAAAAGCGAAA
1 TATTTCTTTCAATCTAAATTTCGGAAGAAATACACTAGTTAGAGATTTATTGATCAAAAGCGAAA
610553 AGAGTTTATTGAGCTTAAATAGGGTCGTATGTCCGTAACGGAATACGAGGGAGAATTTGTTCGA
66 AGAGTTTATTGAGCTTAAATAGGGTCGTATGTCCGTAACGGAATACGAGGGAGAATTTGTTCGA
*
610617 TATTTCTTTCAATCTAAATTTCGGAAGAAATGCACTAGTTAGAGATTTATTGATCAAAAGCGAAA
1 TATTTCTTTCAATCTAAATTTCGGAAGAAATACACTAGTTAGAGATTTATTGATCAAAAGCGAAA
* *
610682 AGAGTTTCTTGAGCTTAAATAGGGTCGTATGTCCGTAACGGAATACGAGTGAGAATTTGTT
66 AGAGTTTATTGAGCTTAAATAGGGTCGTATGTCCGTAACGGAATACGAGGGAGAATTTGTT
610743 GGATTGAGCC
Statistics
Matches: 122, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
129 122 1.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (129 bp):
TATTTCTTTCAATCTAAATTTCGGAAGAAATACACTAGTTAGAGATTTATTGATCAAAAGCGAAA
AGAGTTTATTGAGCTTAAATAGGGTCGTATGTCCGTAACGGAATACGAGGGAGAATTTGTTCGA
Found at i:627421 original size:21 final size:20
Alignment explanation
Indices: 627394--627451 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
627384 TATGTTATTA
627394 AACATTTATTACTATTTATC
1 AACATTTATTACTATTTATC
*
627414 AACAATTTATTA-TATTT-TT
1 AAC-ATTTATTACTATTTATC
* *
627433 ATCATATATTACTATTTAT
1 AACATTTATTACTATTTAT
627452 AATTATTTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
18 7 0.22
19 8 0.25
20 9 0.28
21 8 0.25
ACGTcount: A:0.36, C:0.10, G:0.00, T:0.53
Consensus pattern (20 bp):
AACATTTATTACTATTTATC
Found at i:629323 original size:119 final size:119
Alignment explanation
Indices: 629112--629354 Score: 468
Period size: 119 Copynumber: 2.0 Consensus size: 119
629102 AGGAAAAAGA
629112 CTTATTTTCTGTTGACCTGTAAATCATTTTCCATTGACCAAACTGTTTTCTGTGAAACAAACACA
1 CTTATTTTCTGTTGACCTGTAAATCATTTTCCATTGACCAAACTGTTTTCTGTGAAACAAACACA
629177 GAAAAATGCAGAAAATATTTTCCGTAAAACATTTTACATGTAAACAAACAGACC
66 GAAAAATGCAGAAAATATTTTCCGTAAAACATTTTACATGTAAACAAACAGACC
629231 CTTATTTTCTGTTGACCTGTAAATCATTTTCCATTGACCAAACTGTTTTCTGTGAAACAAACACA
1 CTTATTTTCTGTTGACCTGTAAATCATTTTCCATTGACCAAACTGTTTTCTGTGAAACAAACACA
* *
629296 GGAAAATGCAGAAAATATTTTCCGTAAAACCTTTTACATGTAAACAAACAGACC
66 GAAAAATGCAGAAAATATTTTCCGTAAAACATTTTACATGTAAACAAACAGACC
629350 CTTAT
1 CTTAT
629355 ATTAAAAAAC
Statistics
Matches: 122, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
119 122 1.00
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.33
Consensus pattern (119 bp):
CTTATTTTCTGTTGACCTGTAAATCATTTTCCATTGACCAAACTGTTTTCTGTGAAACAAACACA
GAAAAATGCAGAAAATATTTTCCGTAAAACATTTTACATGTAAACAAACAGACC
Found at i:630098 original size:3 final size:3
Alignment explanation
Indices: 630090--630117 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
630080 NNNTTGAAGC
630090 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
630118 TTATTATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:630122 original size:3 final size:3
Alignment explanation
Indices: 630116--630161 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
630106 ATAATAATAA
630116 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
630162 GTCTAATGCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:636927 original size:24 final size:24
Alignment explanation
Indices: 636885--636936 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
636875 AATCAAATTA
** *
636885 AAATATATTATGTTAATAAATGCT
1 AAATATATTATACTAATAAATACT
*
636909 AAATATATTATACTCATAAATACT
1 AAATATATTATACTAATAAATACT
636933 AAAT
1 AAAT
636937 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.38
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:641306 original size:24 final size:24
Alignment explanation
Indices: 641279--641330 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
641269 AATTAAAGTC
**
641279 AAATATATTATGTTAATAAATACT
1 AAATATATTATACTAATAAATACT
*
641303 AAATATATTATACTCATAAATACT
1 AAATATATTATACTAATAAATACT
641327 AAAT
1 AAAT
641331 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.52, C:0.08, G:0.02, T:0.38
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:650241 original size:132 final size:132
Alignment explanation
Indices: 650004--650284 Score: 456
Period size: 132 Copynumber: 2.1 Consensus size: 132
649994 NNNNNNNNNN
* *
650004 CTTAGGGAGATAAGATCTGAAATCTTCAATCTACTCCACTGTTGCCTAAGGAAGTAGAATTACTA
1 CTTAGGGAGATAAGATCTGAAATCTTCAATCTACTCCAATGTTGCCCAAGGAAGTAGAATTACTA
* ** *
650069 GCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGTCATCTTCGATTTGCCCCACTAC
66 GCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCACCATCTTCGATCTGCCCCACTAC
*
650134 TT
131 TG
*
650136 CTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCAATGTTGCCC-AGAGAAGTAGAATTACT
1 CTTAGGGAGATAAGATCTGAAATCTTCAATCTACTCCAATGTTGCCCAAG-GAAGTAGAATTACT
* *
650200 GGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCACCATCTTCGATCTGCTCCACTA
65 AGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCACCATCTTCGATCTGCCCCACTA
650265 CTG
130 CTG
650268 CTTAGGGAGATAAGATC
1 CTTAGGGAGATAAGATC
650285 GGTTTTAACC
Statistics
Matches: 138, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
131 2 0.01
132 136 0.99
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (132 bp):
CTTAGGGAGATAAGATCTGAAATCTTCAATCTACTCCAATGTTGCCCAAGGAAGTAGAATTACTA
GCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCACCATCTTCGATCTGCCCCACTAC
TG
Found at i:650350 original size:44 final size:43
Alignment explanation
Indices: 650297--650583 Score: 173
Period size: 44 Copynumber: 6.7 Consensus size: 43
650287 TTTTAACCCA
*
650297 CTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTG
1 CTCC-CTGCAACTTCAGGGAGATAAGATTATTGGCTTTAATCTG
* * * **
650341 CTCACCTGCAACTTCAGAGAGATAAGA-T-TCGCCATCTTGGGTCTG
1 CTC-CCTGCAACTTCAGGGAGATAAGATTATTGGC-T-TT-AATCTG
* * ** *
650386 CCTCACTGCAACTTCA-GGAGGATAAGACTTGTTTAC-TT-AGCTG
1 -CTCCCTGCAACTTCAGGGA-GATAAGA-TTATTGGCTTTAATCTG
* ** * * *
650429 CTCCACTTGCAACTTCAAGGAGATAAGACCA---GATGTGATCTG
1 CTCC-C-TGCAACTTCAGGGAGATAAGATTATTGGCTTTAATCTG
* * * *
650471 CTCTCTGCAACTTCAGAGAGATAAG---ATCGGCTTTAATCCG
1 CTCCCTGCAACTTCAGGGAGATAAGATTATTGGCTTTAATCTG
* * *
650511 CTCCACTGCAACTTCAGAGAGATAGGATCATTGGCTTTAATCTG
1 CTCC-CTGCAACTTCAGGGAGATAAGATTATTGGCTTTAATCTG
650555 CTCCACTGCAACTTCAGGGAGATAAGATT
1 CTCC-CTGCAACTTCAGGGAGATAAGATT
650584 TGCCATCTTC
Statistics
Matches: 187, Mismatches: 35, Indels: 42
0.71 0.13 0.16
Matches are distributed among these distances:
37 1 0.01
40 28 0.15
41 22 0.12
42 13 0.07
43 6 0.03
44 83 0.44
45 28 0.15
46 3 0.02
47 1 0.01
48 2 0.01
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (43 bp):
CTCCCTGCAACTTCAGGGAGATAAGATTATTGGCTTTAATCTG
Found at i:650679 original size:50 final size:50
Alignment explanation
Indices: 650622--650794 Score: 139
Period size: 50 Copynumber: 3.5 Consensus size: 50
650612 GTCGAGGACG
* *
650622 AGATTCGCCGTCGTAGCTTCAATCTGATCCACTGCACTGCCAAAGAAATA
1 AGATTCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCCAGAGAAATA
* * ** * * ** * * ** * *
650672 AGATTCGCCATTGCGGTTTCAATCTTTTTAATTGCAATGTTAGGGAAACA
1 AGATTCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCCAGAGAAATA
* ** *
650722 AGATTCGTCGTCGTAGCTTCAATCTGTTCCACTATACTGCCAGAGAAGTA
1 AGATTCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCCAGAGAAATA
* * *
650772 AGATTCACCGTCGTGGTTTCAAT
1 AGATTCGCCGTCGTAGCTTCAAT
650795 GTGCTTCACT
Statistics
Matches: 85, Mismatches: 38, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
50 85 1.00
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.31
Consensus pattern (50 bp):
AGATTCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCCAGAGAAATA
Found at i:654727 original size:126 final size:127
Alignment explanation
Indices: 654493--654748 Score: 453
Period size: 126 Copynumber: 2.0 Consensus size: 127
654483 CGTCTCATCG
*
654493 AAATAAGGAATAGCAGGATTAACAAAGTTGGCCGCGGTGTTAGAACCTGATCCTACTTGGAGATT
1 AAATAAGGAATAGCAGGATTAACAAAGTTGGCCGCGGGGTTAGAACCTGATCCTACTTGGAGATT
654558 CAATAGCGTTGCAGCGTCACCCGGAGGATTAATGGTAACAGAGGACCTACGC-GTATATCTC
66 CAATAGCGTTGCAGCGTCACCCGGAGGATTAATGGTAACAGAGGACCTACGCAGTATATCTC
* *
654619 AAATCAGGGATAGCAGGATTAACAAAGTTGGCTC-CGGGGTTAGAACCTGATCCTACTTGGAGAT
1 AAATAAGGAATAGCAGGATTAACAAAGTTGGC-CGCGGGGTTAGAACCTGATCCTACTTGGAGAT
654683 TCAATAGCGTTGCAGCGTCACCCGGAGGATTAATGGTAACAGAGGACCTACGCGAGTATATCTC
65 TCAATAGCGTTGCAGCGTCACCCGGAGGATTAATGGTAACAGAGGACCTACGC-AGTATATCTC
654747 AA
1 AA
654749 CTTGTTGGGG
Statistics
Matches: 124, Mismatches: 3, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
126 112 0.90
127 1 0.01
128 11 0.09
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.23
Consensus pattern (127 bp):
AAATAAGGAATAGCAGGATTAACAAAGTTGGCCGCGGGGTTAGAACCTGATCCTACTTGGAGATT
CAATAGCGTTGCAGCGTCACCCGGAGGATTAATGGTAACAGAGGACCTACGCAGTATATCTC
Found at i:657664 original size:19 final size:19
Alignment explanation
Indices: 657640--657712 Score: 128
Period size: 19 Copynumber: 3.8 Consensus size: 19
657630 AATCATATAT
657640 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
657659 TCTAAGATTGTATATCATA
1 TCTAAGATTGCATATCATA
*
657678 TCTAGGATTGCATATCATA
1 TCTAAGATTGCATATCATA
657697 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
657713 CTCAAAAATT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 50 1.00
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:661652 original size:22 final size:22
Alignment explanation
Indices: 661603--661656 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
661593 GTGGGAGGGA
*
661603 GTAAAAGTATTGGGGGAAAAGT
1 GTAAAAGTATTGGGGGAAAAAT
**
661625 AAAAAAGT-TTGGGGGTAAAAAT
1 GTAAAAGTATTGGGGG-AAAAAT
661647 GTAAAA-TATT
1 GTAAAAGTATT
661657 ATAGTTTGGT
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
21 8 0.32
22 17 0.68
ACGTcount: A:0.46, C:0.00, G:0.28, T:0.26
Consensus pattern (22 bp):
GTAAAAGTATTGGGGGAAAAAT
Found at i:676710 original size:3 final size:3
Alignment explanation
Indices: 676702--676734 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
676692 TGGTTTTTCA
676702 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
676735 CATGTTAAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:679307 original size:38 final size:38
Alignment explanation
Indices: 679265--679361 Score: 158
Period size: 38 Copynumber: 2.6 Consensus size: 38
679255 TTTTCTAGCA
*
679265 TAGTGGTTTGTCATGGGATGTGTTCCTAGTTTTAAGGG
1 TAGTGGTTTGTCATGGGATGTGTCCCTAGTTTTAAGGG
*
679303 TAGTGGCTTGTCATGGGATGTGTCCCTAGTTTTAAGGG
1 TAGTGGTTTGTCATGGGATGTGTCCCTAGTTTTAAGGG
* *
679341 TAGTGGTTTGCCATGAGATGT
1 TAGTGGTTTGTCATGGGATGT
679362 AAGCTTATAT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 54 1.00
ACGTcount: A:0.16, C:0.10, G:0.34, T:0.39
Consensus pattern (38 bp):
TAGTGGTTTGTCATGGGATGTGTCCCTAGTTTTAAGGG
Found at i:700842 original size:29 final size:29
Alignment explanation
Indices: 700800--701023 Score: 254
Period size: 29 Copynumber: 7.7 Consensus size: 29
700790 GTATCGATGC
* *
700800 CCATTGAACATGAAAAGGGATGGTGACGA
1 CCATCGAATATGAAAAGGGATGGTGACGA
*
700829 CCATCGAATATGAAAAGGGTTGGTGACGA
1 CCATCGAATATGAAAAGGGATGGTGACGA
* ** *
700858 CCATTGAATATGAAAAGGGATGGTTTCAA
1 CCATCGAATATGAAAAGGGATGGTGACGA
*
700887 CCATCGAAGATGAAAAGGGATGGTGACGA
1 CCATCGAATATGAAAAGGGATGGTGACGA
* * * **
700916 CCATCGCATATAAAAAGGGATTGTTTCGA
1 CCATCGAATATGAAAAGGGATGGTGACGA
*
700945 CCATC-AGATATGAAAAGAGATGGTGACGA
1 CCATCGA-ATATGAAAAGGGATGGTGACGA
* * *
700974 CCATCAAATATGAAAAGGGATGGCT-TCAA
1 CCATCGAATATGAAAAGGGATGG-TGACGA
*
701003 CCATCGAATATGACAAGGGAT
1 CCATCGAATATGAAAAGGGAT
701024 TCATATATGG
Statistics
Matches: 162, Mismatches: 30, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
29 160 0.99
30 2 0.01
ACGTcount: A:0.38, C:0.15, G:0.27, T:0.21
Consensus pattern (29 bp):
CCATCGAATATGAAAAGGGATGGTGACGA
Found at i:700890 original size:58 final size:58
Alignment explanation
Indices: 700800--701023 Score: 288
Period size: 58 Copynumber: 3.9 Consensus size: 58
700790 GTATCGATGC
* * ** * *
700800 CCATTGAACATGAAAAGGGATGGTGACGACCATCGAATATGAAAAGGGTTGGTGACGA
1 CCATCGAATATGAAAAGGGATGGTTTCAACCATCGAATATGAAAAGGGATGGTGACGA
* *
700858 CCATTGAATATGAAAAGGGATGGTTTCAACCATCGAAGATGAAAAGGGATGGTGACGA
1 CCATCGAATATGAAAAGGGATGGTTTCAACCATCGAATATGAAAAGGGATGGTGACGA
* * * * *
700916 CCATCGCATATAAAAAGGGATTGTTTCGACCATC-AGATATGAAAAGAGATGGTGACGA
1 CCATCGAATATGAAAAGGGATGGTTTCAACCATCGA-ATATGAAAAGGGATGGTGACGA
* * *
700974 CCATCAAATATGAAAAGGGATGGCTTCAACCATCGAATATGACAAGGGAT
1 CCATCGAATATGAAAAGGGATGGTTTCAACCATCGAATATGAAAAGGGAT
701024 TCATATATGG
Statistics
Matches: 143, Mismatches: 21, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
57 1 0.01
58 141 0.99
59 1 0.01
ACGTcount: A:0.38, C:0.15, G:0.27, T:0.21
Consensus pattern (58 bp):
CCATCGAATATGAAAAGGGATGGTTTCAACCATCGAATATGAAAAGGGATGGTGACGA
Found at i:704255 original size:98 final size:99
Alignment explanation
Indices: 704105--704301 Score: 387
Period size: 98 Copynumber: 2.0 Consensus size: 99
704095 AGTTTACAGA
704105 GAACTAAAAATGGGGAAAGAATGTGAAGCAGTTAAGTATTTTTTTTAGATAAAAAATAAAAGTAA
1 GAACTAAAAATGGGGAAAGAATGTGAAGCAGTTAAGTATTTTTTTTAGATAAAAAATAAAAGTAA
704170 TAAATAAATGTTTTAAAAAT-AAACAAATTTAAG
66 TAAATAAATGTTTTAAAAATAAAACAAATTTAAG
704203 GAACTAAAAATGGGGAAAGAATGTGAAGCAGTTAAGTATTTTTTTTAGATAAAAAATAAAAGTAA
1 GAACTAAAAATGGGGAAAGAATGTGAAGCAGTTAAGTATTTTTTTTAGATAAAAAATAAAAGTAA
704268 TAAATAAATGTTTTAAAAATAAAACAAATTTAAG
66 TAAATAAATGTTTTAAAAATAAAACAAATTTAAG
704302 ATAAAGAACA
Statistics
Matches: 98, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
98 85 0.87
99 13 0.13
ACGTcount: A:0.52, C:0.03, G:0.15, T:0.29
Consensus pattern (99 bp):
GAACTAAAAATGGGGAAAGAATGTGAAGCAGTTAAGTATTTTTTTTAGATAAAAAATAAAAGTAA
TAAATAAATGTTTTAAAAATAAAACAAATTTAAG
Found at i:707770 original size:11 final size:11
Alignment explanation
Indices: 707754--707790 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
707744 AAGAGAGAAT
*
707754 GATGCTTGATG
1 GATGCTTGAGG
707765 GATGCTTGAGG
1 GATGCTTGAGG
*
707776 GATGATTGAGG
1 GATGCTTGAGG
707787 GATG
1 GATG
707791 AGAGGGTCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.22, C:0.05, G:0.43, T:0.30
Consensus pattern (11 bp):
GATGCTTGAGG
Found at i:720601 original size:41 final size:41
Alignment explanation
Indices: 720541--720629 Score: 119
Period size: 41 Copynumber: 2.2 Consensus size: 41
720531 AATATTGTTT
*
720541 AATTGCACATACGTGCCCCTG-TTAGTACTTCAATACCCCTG
1 AATTGCACATACGTACCCCTGTTTA-TACTTCAATACCCCTG
** *
720582 AATTGCACATACGTACCCCTGTTTATACTTCGGTACCGCTG
1 AATTGCACATACGTACCCCTGTTTATACTTCAATACCCCTG
720623 AA-TGCAC
1 AATTGCAC
720630 TTTTGTACCA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
40 5 0.12
41 35 0.81
42 3 0.07
ACGTcount: A:0.25, C:0.30, G:0.16, T:0.29
Consensus pattern (41 bp):
AATTGCACATACGTACCCCTGTTTATACTTCAATACCCCTG
Found at i:728054 original size:20 final size:20
Alignment explanation
Indices: 728029--728070 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
728019 AACTTGTTGA
728029 AAGCAAAGACTACATCCAAC
1 AAGCAAAGACTACATCCAAC
728049 AAGCAAAGACTACATCCAAC
1 AAGCAAAGACTACATCCAAC
728069 AA
1 AA
728071 TTCTTTCTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.52, C:0.29, G:0.10, T:0.10
Consensus pattern (20 bp):
AAGCAAAGACTACATCCAAC
Found at i:736830 original size:21 final size:18
Alignment explanation
Indices: 736816--736852 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
736806 TATACGACTC
736816 TTCATCACCAGTATACAT
1 TTCATCACCAGTATACAT
*
736834 TTCATCATCAGTAT-CAT
1 TTCATCACCAGTATACAT
736851 TT
1 TT
736853 ATTCTTTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.30, C:0.24, G:0.05, T:0.41
Consensus pattern (18 bp):
TTCATCACCAGTATACAT
Found at i:738656 original size:11 final size:12
Alignment explanation
Indices: 738642--738673 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
738632 TTAGTTTCTC
738642 CTTT-TTCTTTT
1 CTTTCTTCTTTT
738653 CTTTCTTC-TTT
1 CTTTCTTCTTTT
738664 CTTTCTTCTT
1 CTTTCTTCTT
738674 ATTTTCGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 15 0.79
12 4 0.21
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (12 bp):
CTTTCTTCTTTT
Found at i:740752 original size:13 final size:13
Alignment explanation
Indices: 740734--740761 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
740724 TTTTATATGC
740734 TTTTATTTTATTT
1 TTTTATTTTATTT
740747 TTTTATTTTATTT
1 TTTTATTTTATTT
740760 TT
1 TT
740762 ACTTTTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTATTTTATTT
Found at i:745762 original size:18 final size:18
Alignment explanation
Indices: 745739--745785 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
745729 AGAAATATAG
745739 GCCCACATGCCCGTGTGA
1 GCCCACATGCCCGTGTGA
*
745757 GCCCACATGCTCGTGTGA
1 GCCCACATGCCCGTGTGA
*
745775 -CCCACACGCCC
1 GCCCACATGCCC
745786 AAATTAGCCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 9 0.35
18 17 0.65
ACGTcount: A:0.17, C:0.45, G:0.23, T:0.15
Consensus pattern (18 bp):
GCCCACATGCCCGTGTGA
Found at i:748423 original size:28 final size:28
Alignment explanation
Indices: 748391--748474 Score: 168
Period size: 28 Copynumber: 3.0 Consensus size: 28
748381 TAACATTCAA
748391 AGTTAGAATAATATAATCTTATTAGAAG
1 AGTTAGAATAATATAATCTTATTAGAAG
748419 AGTTAGAATAATATAATCTTATTAGAAG
1 AGTTAGAATAATATAATCTTATTAGAAG
748447 AGTTAGAATAATATAATCTTATTAGAAG
1 AGTTAGAATAATATAATCTTATTAGAAG
748475 TTAGTTACCA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 56 1.00
ACGTcount: A:0.46, C:0.04, G:0.14, T:0.36
Consensus pattern (28 bp):
AGTTAGAATAATATAATCTTATTAGAAG
Found at i:749568 original size:42 final size:42
Alignment explanation
Indices: 749509--749626 Score: 146
Period size: 42 Copynumber: 2.8 Consensus size: 42
749499 GGTACAATAC
* * *
749509 CACACGGCCAAGGACACAGGCGTGTGCCCAAGCTGTGTGAGT
1 CACACGGGCAGGGACACAGGCGTGTGCCCAAGCCGTGTGAGT
* * *
749551 CACACGGGCAGGGACACAAGCGTATGCCCAGGCCGTGTGAGT
1 CACACGGGCAGGGACACAGGCGTGTGCCCAAGCCGTGTGAGT
** * *
749593 CACACAAGCAGGGATACGGGCGTGTGCCCAAGCC
1 CACACGGGCAGGGACACAGGCGTGTGCCCAAGCC
749627 ATGTAACTCA
Statistics
Matches: 63, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.25, C:0.30, G:0.34, T:0.12
Consensus pattern (42 bp):
CACACGGGCAGGGACACAGGCGTGTGCCCAAGCCGTGTGAGT
Found at i:751928 original size:14 final size:14
Alignment explanation
Indices: 751909--751935 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
751899 CTTATAATTT
751909 AATTTAATTTTTTC
1 AATTTAATTTTTTC
751923 AATTTAATTTTTT
1 AATTTAATTTTTT
751936 TTGTTTTAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.67
Consensus pattern (14 bp):
AATTTAATTTTTTC
Found at i:754641 original size:3 final size:3
Alignment explanation
Indices: 754633--754669 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
754623 TCGACCTTTA
* *
754633 TAT TAT TAT TAT TAT TAT TAT TAT CAT TTT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
754670 TACTCATTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:755163 original size:4 final size:4
Alignment explanation
Indices: 755154--755178 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
755144 GTTCATCTCT
755154 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
755179 GTTTTATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:758092 original size:19 final size:18
Alignment explanation
Indices: 758054--758092 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
758044 TGTGCTTTCG
*
758054 AAAAGCACTTTTAGTTTA
1 AAAAGCACTTTTACTTTA
758072 AAAAGCACTTTTGACTTTA
1 AAAAGCACTTTT-ACTTTA
758091 AA
1 AA
758093 GTTGTGCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.36
Consensus pattern (18 bp):
AAAAGCACTTTTACTTTA
Found at i:761076 original size:26 final size:25
Alignment explanation
Indices: 760991--761079 Score: 76
Period size: 24 Copynumber: 3.6 Consensus size: 25
760981 CTTTCGAGCT
***
760991 ATAA-CGGGAAGCTCATCTGAGCC-
1 ATAATCGGGAAGCTCAAGAGAGCCA
*
761014 ATAATCGGGAAGCTCAAGCGAGCCA
1 ATAATCGGGAAGCTCAAGAGAGCCA
** * *
761039 AT-ATCGAAAAGCTCCAGAGAGTCA
1 ATAATCGGGAAGCTCAAGAGAGCCA
761063 ATTAATCGGGAAGCTCA
1 A-TAATCGGGAAGCTCA
761080 TAAATAAGCC
Statistics
Matches: 51, Mismatches: 11, Indels: 5
0.76 0.16 0.07
Matches are distributed among these distances:
23 4 0.08
24 34 0.67
25 3 0.06
26 10 0.20
ACGTcount: A:0.36, C:0.22, G:0.25, T:0.17
Consensus pattern (25 bp):
ATAATCGGGAAGCTCAAGAGAGCCA
Found at i:762222 original size:68 final size:68
Alignment explanation
Indices: 762150--762278 Score: 233
Period size: 68 Copynumber: 1.9 Consensus size: 68
762140 AATTTAATCA
*
762150 TTTTCTTTATTTAATTTTCCATTGGTGACTAATCATACTTATCTACTAACT-CTTCTTAATGTTA
1 TTTTCTTTATTTAATTTTCCATTGATGACTAATCATACTTATCTACTAACTCCTT-TTAATGTTA
762214 ATAT
65 ATAT
762218 TTTTCTTTATTTAATTTTCCATTGATGACTAATCATACTTATCTACTAACTCCTTTTAATG
1 TTTTCTTTATTTAATTTTCCATTGATGACTAATCATACTTATCTACTAACTCCTTTTAATG
762279 GTCTATTTGC
Statistics
Matches: 59, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
68 56 0.95
69 3 0.05
ACGTcount: A:0.26, C:0.17, G:0.05, T:0.51
Consensus pattern (68 bp):
TTTTCTTTATTTAATTTTCCATTGATGACTAATCATACTTATCTACTAACTCCTTTTAATGTTAA
TAT
Found at i:767913 original size:28 final size:26
Alignment explanation
Indices: 767857--767922 Score: 71
Period size: 28 Copynumber: 2.5 Consensus size: 26
767847 GCGAGTCAAT
*
767857 ATCGGGAAGCTCTAGAGAGCCAATTA
1 ATCGGGAAGCTCTAAAGAGCCAATTA
*
767883 ATCGGGAAGCTCATAAATGAGCC-TTTAA
1 ATCGGGAAGCTC-TAAA-GAGCCAATT-A
*
767911 ATCAGGAAGCTC
1 ATCGGGAAGCTC
767923 CGAAAAGTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
26 12 0.35
27 5 0.15
28 17 0.50
ACGTcount: A:0.35, C:0.20, G:0.24, T:0.21
Consensus pattern (26 bp):
ATCGGGAAGCTCTAAAGAGCCAATTA
Found at i:770765 original size:10 final size:10
Alignment explanation
Indices: 770752--770781 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
770742 AAATATTAAC
*
770752 AATAAGTTAT
1 AATAATTTAT
770762 AATAATTTAT
1 AATAATTTAT
770772 AATAATTTAT
1 AATAATTTAT
770782 TTTTATATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (10 bp):
AATAATTTAT
Found at i:771756 original size:109 final size:109
Alignment explanation
Indices: 771565--771858 Score: 507
Period size: 109 Copynumber: 2.7 Consensus size: 109
771555 NNNNNNNNNN
* *
771565 AATCGACACCCAACACCTTAGGGCATGTTTTCTCGAATTTTCAAACGCAAAACATTGCCTTATTT
1 AATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTT
771630 TAAAATTTTTAAAAGGATATTAAGCCCTTTGGTTGAACGAGAAA
66 TAAAATTTTTAAAAGGATATTAAGCCCTTTGGTTGAACGAGAAA
*
771674 AATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAAAGCAAAACATTGCCTTATTT
1 AATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTT
771739 TAAAATTTTTAAAAGGATATTAAGCCCTTTGGTTGAACGAGAAA
66 TAAAATTTTTAAAAGGATATTAAGCCCTTTGGTTGAACGAGAAA
* * * *
771783 AATCGACACCCAGCACCTTAGGGCGTGTTTTCTCGAATTTCCAAACGCTAAATATTGCCTTAATT
1 AATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTT
*
771848 TGAAATATTTT
66 TAAAAT-TTTT
771859 CCTTTTTGAA
Statistics
Matches: 175, Mismatches: 9, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
109 171 0.98
110 4 0.02
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.32
Consensus pattern (109 bp):
AATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTT
TAAAATTTTTAAAAGGATATTAAGCCCTTTGGTTGAACGAGAAA
Found at i:772508 original size:3 final size:3
Alignment explanation
Indices: 772500--772591 Score: 91
Period size: 3 Copynumber: 31.0 Consensus size: 3
772490 AGGCTACTAT
* *
772500 ATA ATA ATA ATA AT- ATG ATA AGTA ACA ATA AT- ATAA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA AT-A ATA ATA ATA
* * * *
772545 AAA ATG ATA AAA ATA ATA ATA ACA A-A ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
772592 TTACAGAAAA
Statistics
Matches: 74, Mismatches: 10, Indels: 10
0.79 0.11 0.11
Matches are distributed among these distances:
2 6 0.08
3 63 0.85
4 5 0.07
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:773273 original size:5 final size:5
Alignment explanation
Indices: 773265--773301 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
773255 TTTCTTAAGG
773265 AAATA AAATCA AAATA AAATA AAA-A AAATA AAA-A AAA
1 AAATA AAAT-A AAATA AAATA AAATA AAATA AAATA AAA
773302 AACTTTGCGA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
4 8 0.27
5 17 0.57
6 5 0.17
ACGTcount: A:0.84, C:0.03, G:0.00, T:0.14
Consensus pattern (5 bp):
AAATA
Found at i:778546 original size:21 final size:22
Alignment explanation
Indices: 778512--778552 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
778502 ATGGTTAGAC
*
778512 AAATCAGAGGTCAAGGAACAGG
1 AAATCAGAGGTCAAGAAACAGG
778534 AAATCAG-GGTCAAGAAACA
1 AAATCAGAGGTCAAGAAACA
778553 ATATTGGCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.49, C:0.15, G:0.27, T:0.10
Consensus pattern (22 bp):
AAATCAGAGGTCAAGAAACAGG
Found at i:797852 original size:54 final size:54
Alignment explanation
Indices: 797770--797878 Score: 191
Period size: 54 Copynumber: 2.0 Consensus size: 54
797760 ATGGGGGGTA
797770 TCGGCACCGCCTGACACTGTTCATTTTATATTATTCTAGTCATTATTTTTGAAG
1 TCGGCACCGCCTGACACTGTTCATTTTATATTATTCTAGTCATTATTTTTGAAG
* * *
797824 TCGGCACTGCCTGACACTGTTCTTTTTATATTATTCTCGTCATTATTTTTGAAG
1 TCGGCACCGCCTGACACTGTTCATTTTATATTATTCTAGTCATTATTTTTGAAG
797878 T
1 T
797879 TGTGTCATTC
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.20, C:0.20, G:0.15, T:0.45
Consensus pattern (54 bp):
TCGGCACCGCCTGACACTGTTCATTTTATATTATTCTAGTCATTATTTTTGAAG
Found at i:798530 original size:21 final size:21
Alignment explanation
Indices: 798500--798561 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
798490 TCCTCCCTTT
*
798500 TTTTTTATTTTTATTTTAAAA
1 TTTTTAATTTTTATTTTAAAA
*
798521 TTTTTAATTTTTATATTTCAAA
1 TTTTTAATTTTTAT-TTTAAAA
* * *
798543 TTTTAAAATTTAATTTTAA
1 TTTTTAATTTTTATTTTAA
798562 TTATTAGTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 17 0.50
22 17 0.50
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTTTAATTTTTATTTTAAAA
Found at i:798921 original size:37 final size:37
Alignment explanation
Indices: 798880--798987 Score: 157
Period size: 35 Copynumber: 3.0 Consensus size: 37
798870 TTTTGGGATG
*
798880 GGCCCAGGCCTAAGAAGCGGGCTGAAATTTTTTTCTA
1 GGCCCGGGCCTAAGAAGCGGGCTGAAATTTTTTTCTA
* * *
798917 GGCCCGGGCCTAAAAAGCGGGATGAAA-TTTTTT-TG
1 GGCCCGGGCCTAAGAAGCGGGCTGAAATTTTTTTCTA
*
798952 GGCCCGGGCCTAAGAAGCGAGCTGAAATTTTTTTCT
1 GGCCCGGGCCTAAGAAGCGGGCTGAAATTTTTTTCT
798988 GAACCCGGAC
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
35 25 0.40
36 12 0.19
37 25 0.40
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (37 bp):
GGCCCGGGCCTAAGAAGCGGGCTGAAATTTTTTTCTA
Found at i:798995 original size:37 final size:37
Alignment explanation
Indices: 798881--798995 Score: 146
Period size: 37 Copynumber: 3.2 Consensus size: 37
798871 TTTGGGATGG
*
798881 GCCCAGGCCTAAGAAGCGGGCTGAAATTTTTTTCT-A
1 GCCCGGGCCTAAGAAGCGGGCTGAAATTTTTTTCTGA
* * *
798917 GGCCCGGGCCTAAAAAGCGGGATGAAA-TTTTTT-TGG
1 -GCCCGGGCCTAAGAAGCGGGCTGAAATTTTTTTCTGA
*
798953 GCCCGGGCCTAAGAAGCGAGCTGAAATTTTTTTCTGA
1 GCCCGGGCCTAAGAAGCGGGCTGAAATTTTTTTCTGA
*
798990 ACCCGG
1 GCCCGG
798996 ACCGGCCCGG
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
35 24 0.36
36 12 0.18
37 30 0.45
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.25
Consensus pattern (37 bp):
GCCCGGGCCTAAGAAGCGGGCTGAAATTTTTTTCTGA
Found at i:804500 original size:18 final size:18
Alignment explanation
Indices: 804477--804511 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
804467 GTAAATGAAT
804477 TTAAAATTAAAAAAATAA
1 TTAAAATTAAAAAAATAA
804495 TTAAAATTAAAAAAATA
1 TTAAAATTAAAAAAATA
804512 TTTAGAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
TTAAAATTAAAAAAATAA
Found at i:804573 original size:10 final size:9
Alignment explanation
Indices: 804539--804564 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
804529 GCTTACTCAC
804539 AATTAAAAA
1 AATTAAAAA
804548 AATTAAAAA
1 AATTAAAAA
804557 AATTAAAA
1 AATTAAAA
804565 CAAGTTAAAC
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:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (9 bp):
AATTAAAAA
Found at i:805030 original size:130 final size:131
Alignment explanation
Indices: 804793--805043 Score: 414
Period size: 130 Copynumber: 1.9 Consensus size: 131
804783 TCAAAATTTT
*
804793 AGGGATTTTTGGGTTATGGGATTGCTGATTTTAGCAAATTTCAGGTTTAGGGTTCATTTATAACT
1 AGGGATTTTTGGGTTATGGGATTGCTGATTTTAGCAAATTTCAGGTTTAGGGTTCATTTATAACA
* * *
804858 TCTTTTCTCTTGGCTCTTTTGCAGTGAAGATTGGTGAGGGTTCATGCTCCAAATCACAGATTCGT
66 TCTTTTCTCTTGGCTCTTTTACAGTGAAGATTGGTAAAGGTTCATGCTCCAAATCACAGATTCGT
804923 A
131 A
* * *
804924 AGGGATTTTTGGGTTATGGGATTGTTGGTTTTAG-GAATTTCAGGTTTAGGGTTCATTTATAACA
1 AGGGATTTTTGGGTTATGGGATTGCTGATTTTAGCAAATTTCAGGTTTAGGGTTCATTTATAACA
* *
804988 TCTTTTCTCTTGGCTCTTTTATAGTGAAGATTGGTAAAGGTTCATGCTCGAAATCA
66 TCTTTTCTCTTGGCTCTTTTACAGTGAAGATTGGTAAAGGTTCATGCTCCAAATCA
805044 GAAAGAAGAA
Statistics
Matches: 111, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
130 79 0.71
131 32 0.29
ACGTcount: A:0.22, C:0.12, G:0.25, T:0.41
Consensus pattern (131 bp):
AGGGATTTTTGGGTTATGGGATTGCTGATTTTAGCAAATTTCAGGTTTAGGGTTCATTTATAACA
TCTTTTCTCTTGGCTCTTTTACAGTGAAGATTGGTAAAGGTTCATGCTCCAAATCACAGATTCGT
A
Found at i:805716 original size:15 final size:15
Alignment explanation
Indices: 805696--805725 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
805686 ATGTCTTGGG
*
805696 GAAAATTAAGTAAAT
1 GAAAATTAAATAAAT
805711 GAAAATTAAATAAAT
1 GAAAATTAAATAAAT
805726 TATCTGTCTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.10, T:0.27
Consensus pattern (15 bp):
GAAAATTAAATAAAT
Found at i:807522 original size:24 final size:24
Alignment explanation
Indices: 807482--807597 Score: 76
Period size: 24 Copynumber: 4.8 Consensus size: 24
807472 GACTCACCAC
* *
807482 AGCTCTCAAGAGCATCCCGTTATT
1 AGCTCTCATGAGTATCCCGTTATT
*
807506 AGCTCTCATGAGTATCCCATTATT
1 AGCTCTCATGAGTATCCCGTTATT
* *
807530 -GACTCTCTTGAGCTA-CCCGATATAT
1 AG-CTCTCATGAG-TATCCCGTTAT-T
* * * * *
807555 GGCTCTTACGAGCT-TTCCGTTAAT
1 AGCTCTCATGAG-TATCCCGTTATT
*
807579 AGCTCTTATGAGTATCCCG
1 AGCTCTCATGAGTATCCCG
807598 ATTCAGTTGT
Statistics
Matches: 71, Mismatches: 15, Indels: 12
0.72 0.15 0.12
Matches are distributed among these distances:
23 2 0.03
24 51 0.72
25 17 0.24
26 1 0.01
ACGTcount: A:0.22, C:0.27, G:0.17, T:0.34
Consensus pattern (24 bp):
AGCTCTCATGAGTATCCCGTTATT
Found at i:807679 original size:25 final size:25
Alignment explanation
Indices: 807645--807724 Score: 81
Period size: 25 Copynumber: 3.1 Consensus size: 25
807635 CAAATCTTAT
*
807645 GAGCGTTTCGA-TAATTGGCTCTCTA
1 GAGCTTTTCGATTAA-TGGCTCTCTA
* *
807670 GAGCTTTTCGATTAAAGGCTCTTTCA
1 GAGCTTTTCGATTAATGGCTCTCT-A
* *
807696 TGAGCTTCTCGATTAATGGCTCTCCA
1 -GAGCTTTTCGATTAATGGCTCTCTA
807722 GAG
1 GAG
807725 TTACCCGATA
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
25 20 0.44
26 5 0.11
27 20 0.44
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.35
Consensus pattern (25 bp):
GAGCTTTTCGATTAATGGCTCTCTA
Found at i:807848 original size:25 final size:25
Alignment explanation
Indices: 807749--807853 Score: 99
Period size: 25 Copynumber: 4.2 Consensus size: 25
807739 TTCATATAAA
* **
807749 CTTCCCGAT-TATGGCTCTTATGAG
1 CTTCCCGTTATATGGCTCACATGAG
*
807773 CTTCCCGTTACATGGCTCACATGAG
1 CTTCCCGTTATATGGCTCACATGAG
* *
807798 CTTCCAGTTATATGGCTCGA-AAGAG
1 CTTCCCGTTATATGGCTC-ACATGAG
*
807823 CTACCCGTTTATAT-GCTCACATGAG
1 CTTCCCG-TTATATGGCTCACATGAG
807848 CATTCC
1 C-TTCC
807854 TGAATATGAA
Statistics
Matches: 65, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
24 9 0.14
25 46 0.71
26 10 0.15
ACGTcount: A:0.22, C:0.28, G:0.19, T:0.31
Consensus pattern (25 bp):
CTTCCCGTTATATGGCTCACATGAG
Found at i:815087 original size:24 final size:24
Alignment explanation
Indices: 815060--815156 Score: 81
Period size: 24 Copynumber: 4.0 Consensus size: 24
815050 TAGTGTCGCA
*
815060 TTATTAGCTCTCATGAGCATCCCG
1 TTATTGGCTCTCATGAGCATCCCG
* *
815084 TTATTGGCTCTCTTAAGC-TACCCG
1 TTATTGGCTCTCATGAGCAT-CCCG
* * *
815108 ATATATGGCTCTCACGAGCTTCCCG
1 TTAT-TGGCTCTCATGAGCATCCCG
* *
815133 TTAATT-GATCTTATGAGCATCCCG
1 TT-ATTGGCTCTCATGAGCATCCCG
815157 ATTTGGTTGT
Statistics
Matches: 57, Mismatches: 12, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
23 1 0.02
24 36 0.63
25 17 0.30
26 3 0.05
ACGTcount: A:0.21, C:0.28, G:0.18, T:0.34
Consensus pattern (24 bp):
TTATTGGCTCTCATGAGCATCCCG
Found at i:823342 original size:159 final size:159
Alignment explanation
Indices: 823064--823483 Score: 436
Period size: 159 Copynumber: 2.6 Consensus size: 159
823054 AACAAAAGAT
* * * * * *
823064 CATGCATTCAACCTAACACAACGGGAACACAGGTATATCGTAAACAC-ATTTTCATTATTAATTC
1 CATGCATTTAACCTAACACAACTGGATCACAGGTATATCGTAAACACTATTTT-AATGTCAATTC
* * * * * ** *
823128 CAAAATATTAAAATCTAATTT-AGGTTCTCAATTTTTTTTGTTTTAGTCTGGTACGAGTGCA-AG
65 CAAAATATT-TAATCTAATTTGGGGTCCTCAATTTTTTTGGTCTTAGTCTAATACGAGTACACA-
* * *
823191 AACTAGAAGCCCAAAAAATAACAACATAACAC
128 AACTAGAAGCCAAAAAAAGAACAACAGAACAC
* * * * *
823223 TATGCATTTAACCTAATACAACTGGATCATAGGTATATCGTATACACTATTTTAATGTCAATTCA
1 CATGCATTTAACCTAACACAACTGGATCACAGGTATATCGTAAACACTATTTTAATGTCAATTCC
** * *
823288 AAAATATTCTAATCTAATTTGGGGTCCT-GGTTTTTTTGGTCTTGGTCTAATACGAGTATACAAA
66 AAAATATT-TAATCTAATTTGGGGTCCTCAATTTTTTTGGTCTTAGTCTAATACGAGTACACAAA
823352 CTAGAAGCCAAAAAAAGAACAACAGAACAC
130 CTAGAAGCCAAAAAAAGAACAACAGAACAC
* * * * * * * *
823382 CATGCATTTAGCCTAACACAATTGGATCACCGATATATCATAAAAACTTTTTTAATGTCAACTCC
1 CATGCATTTAACCTAACACAACTGGATCACAGGTATATCGTAAACACTATTTTAATGTCAATTCC
* *
823447 AAATTATTTAAATCTAATTTGGGGTTCT-AATTTTTTT
66 AAAATATTT-AATCTAATTTGGGGTCCTCAATTTTTTT
823484 TCTCAGTCTG
Statistics
Matches: 213, Mismatches: 44, Indels: 8
0.80 0.17 0.03
Matches are distributed among these distances:
158 1 0.00
159 201 0.94
160 11 0.05
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.33
Consensus pattern (159 bp):
CATGCATTTAACCTAACACAACTGGATCACAGGTATATCGTAAACACTATTTTAATGTCAATTCC
AAAATATTTAATCTAATTTGGGGTCCTCAATTTTTTTGGTCTTAGTCTAATACGAGTACACAAAC
TAGAAGCCAAAAAAAGAACAACAGAACAC
Found at i:823741 original size:84 final size:84
Alignment explanation
Indices: 823600--823806 Score: 310
Period size: 84 Copynumber: 2.5 Consensus size: 84
823590 TTGAGATGGT
* ** *
823600 TAACATATTTTGTTTGTTTTTTTTGAAATGATTTGTTGAAATAGTTGGTTAACATCTTACTGCTA
1 TAACATATTTTGTTTTTTTTTTTTGAAATGATTTGTTGAAATAGTTGGCAAACATCTTACTACTA
823665 TAGGATAATTTTGTTAGCA
66 TAGGATAATTTTGTTAGCA
*
823684 TAACATATTTTGTTTTTTTTTTTTGAAATGATTTGTTGAAATGGTTGGCAAACATCTTACTACTA
1 TAACATATTTTGTTTTTTTTTTTTGAAATGATTTGTTGAAATAGTTGGCAAACATCTTACTACTA
* *
823749 TAGGATCATTTTGTTAGTA
66 TAGGATAATTTTGTTAGCA
* * *
823768 TAACATATTTTG--TTTGTTTTTTGAAATGCTTTATTGAAA
1 TAACATATTTTGTTTTTTTTTTTTGAAATGATTTGTTGAAA
823807 GATGTATACC
Statistics
Matches: 113, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
82 24 0.21
84 89 0.79
ACGTcount: A:0.28, C:0.07, G:0.15, T:0.50
Consensus pattern (84 bp):
TAACATATTTTGTTTTTTTTTTTTGAAATGATTTGTTGAAATAGTTGGCAAACATCTTACTACTA
TAGGATAATTTTGTTAGCA
Found at i:824066 original size:14 final size:14
Alignment explanation
Indices: 824047--824076 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
824037 TTATAGAGAG
*
824047 TAGTTTTAATCTAA
1 TAGTTTTAATCCAA
824061 TAGTTTTAATCCAA
1 TAGTTTTAATCCAA
824075 TA
1 TA
824077 AAAATCAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.10, G:0.07, T:0.47
Consensus pattern (14 bp):
TAGTTTTAATCCAA
Found at i:836497 original size:161 final size:160
Alignment explanation
Indices: 836322--836626 Score: 400
Period size: 161 Copynumber: 1.9 Consensus size: 160
836312 CGAATAAGGA
*
836322 TGGAAATCAAGTTTGAAAAACTGTTGTCCAAATCAAGGACT-ATGA-TTACAAAAGTCATTAAAT
1 TGGAAATCAAGTTTGAAAAACTGTTGTCCAAATCAAAGACTGA-GATTTA-AAAAGTCATTAAAT
* * * **
836385 TAGGTAATTCAAATAAGAAAGAATTCTTATTTGAAGCAT-CGTAAAAAAGCTTCTTCCTCTTAAA
64 TAAGTAATTCAAATAAGAAAGAATCCTTATTTGAAGCATAC-TAAAAAAGCTTC-TCCCCCAAAA
836449 AGTTTAATTGATCAATTACAGAGGGTAATTAGGG
127 AGTTTAATTGATCAATTACAGAGGGTAATTAGGG
* * * *
836483 TGGAAATCAAGTTTGAAAAATTGTTGTCCAAATCAAAGACTGAGATTTAGAAATTCGTTAAATTA
1 TGGAAATCAAGTTTGAAAAACTGTTGTCCAAATCAAAGACTGAGATTTAAAAAGTCATTAAATTA
* * * * * *
836548 AGTAATTCATATAAGGAATAATCCTTATTTTAAGCTTACTAGAAAAGCTTCTCCCCCAAAAAGTT
66 AGTAATTCAAATAAGAAAGAATCCTTATTTGAAGCATACTAAAAAAGCTTCTCCCCCAAAAAGTT
*
836613 TAATTGGTCAATTA
131 TAATTGATCAATTA
836627 GATAGATGAT
Statistics
Matches: 124, Mismatches: 17, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
160 24 0.19
161 95 0.77
162 5 0.04
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.32
Consensus pattern (160 bp):
TGGAAATCAAGTTTGAAAAACTGTTGTCCAAATCAAAGACTGAGATTTAAAAAGTCATTAAATTA
AGTAATTCAAATAAGAAAGAATCCTTATTTGAAGCATACTAAAAAAGCTTCTCCCCCAAAAAGTT
TAATTGATCAATTACAGAGGGTAATTAGGG
Found at i:839452 original size:31 final size:31
Alignment explanation
Indices: 839417--839478 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
839407 AGGCAACTTA
839417 CAAGAGTAATTGAATCCTAATAAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAACTCTTT
*
839448 CAAGAGTAATTGAATCTTAATAAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAACTCTTT
839479 AAAATTATCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.34
Consensus pattern (31 bp):
CAAGAGTAATTGAATCCTAATAAAACTCTTT
Found at i:858882 original size:19 final size:19
Alignment explanation
Indices: 858847--858901 Score: 51
Period size: 19 Copynumber: 3.0 Consensus size: 19
858837 CTTTACTTTA
* *
858847 TATT-ATAATAATATAATT
1 TATTAATAATCATTTAATT
858865 TATTAATAATCATTTAATT
1 TATTAATAATCATTTAATT
* * *
858884 AATAAAT-ATCTTTTAATT
1 TATTAATAATCATTTAATT
858902 ATAACACAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
18 14 0.45
19 17 0.55
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (19 bp):
TATTAATAATCATTTAATT
Found at i:858992 original size:20 final size:21
Alignment explanation
Indices: 858967--859008 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
858957 ATTTGGCACC
* *
858967 ATTTAATTTATTTAT-TTTAT
1 ATTTAATTAATTAATATTTAT
858987 ATTTAATTAATTAATATTTAT
1 ATTTAATTAATTAATATTTAT
859008 A
1 A
859009 AATATCNNNN
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
ATTTAATTAATTAATATTTAT
Found at i:862275 original size:31 final size:32
Alignment explanation
Indices: 862238--862314 Score: 93
Period size: 34 Copynumber: 2.3 Consensus size: 32
862228 AATATTATAT
**
862238 TTAATTTAATACTTATCTTGATAA-TATTTGA
1 TTAATTTAATACTTATCTTGATAAGTATTACA
*
862269 TTAATTTAATTCTATTTATCTTGATAAGTATTACA
1 TTAATTTAA---TACTTATCTTGATAAGTATTACA
862304 TTAATTTAATA
1 TTAATTTAATA
862315 TTAAAGTTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
31 9 0.23
32 2 0.05
34 14 0.36
35 14 0.36
ACGTcount: A:0.36, C:0.06, G:0.05, T:0.52
Consensus pattern (32 bp):
TTAATTTAATACTTATCTTGATAAGTATTACA
Found at i:862580 original size:11 final size:11
Alignment explanation
Indices: 862564--862593 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
862554 TTATAGGCAC
862564 AAGAAGTATAA
1 AAGAAGTATAA
862575 AAGAAGTATAA
1 AAGAAGTATAA
862586 AAGAAGTA
1 AAGAAGTA
862594 GAGATCTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.63, C:0.00, G:0.20, T:0.17
Consensus pattern (11 bp):
AAGAAGTATAA
Found at i:869926 original size:16 final size:14
Alignment explanation
Indices: 869892--869937 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 14
869882 AGCGAAAAAT
869892 AAAAAATAAACACACA
1 AAAAAATAAA-A-ACA
869908 AAATAACATAAAAACA
1 AAA-AA-ATAAAAACA
869924 AAAAAATAAAAACA
1 AAAAAATAAAAACA
869938 CATAAAACTA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
14 9 0.32
15 2 0.07
16 9 0.32
17 3 0.11
18 5 0.18
ACGTcount: A:0.78, C:0.13, G:0.00, T:0.09
Consensus pattern (14 bp):
AAAAAATAAAAACA
Found at i:872749 original size:26 final size:25
Alignment explanation
Indices: 872697--872754 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
872687 TACTCTTAGC
*
872697 AAAATTTTGACGATTTTTCCGTGGT
1 AAAATTTTGACGATTTTTCCCTGGT
* *
872722 AAAATTTTGATGATTTTTCCCCTTGT
1 AAAATTTTGACGATTTTT-CCCTGGT
872748 AAAATTT
1 AAAATTT
872755 CGAGAAATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 17 0.59
26 12 0.41
ACGTcount: A:0.28, C:0.12, G:0.14, T:0.47
Consensus pattern (25 bp):
AAAATTTTGACGATTTTTCCCTGGT
Done.