Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr6
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: 47432654
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2298022 characters in sequence are not A, C, G, or T
File 101 of 136
Found at i:33968619 original size:35 final size:36
Alignment explanation
Indices: 33968545--33968622 Score: 88
Period size: 35 Copynumber: 2.2 Consensus size: 36
33968535 TGACATATAA
*
33968545 TTTTATTTTATTCTTGTATTTCAAATATTCAATTCC
1 TTTTATTTTATTCTTGTAATTCAAATATTCAATTCC
* ** *
33968581 TTTTATTTTATT-TTTTAATT-AACATATTGGATTTC
1 TTTTATTTTATTCTTGTAATTCAA-ATATTCAATTCC
33968616 TTTTATT
1 TTTTATT
33968623 GGATTTTTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
34 2 0.06
35 22 0.61
36 12 0.33
ACGTcount: A:0.24, C:0.09, G:0.04, T:0.63
Consensus pattern (36 bp):
TTTTATTTTATTCTTGTAATTCAAATATTCAATTCC
Found at i:33969772 original size:3 final size:3
Alignment explanation
Indices: 33969764--33969788 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
33969754 ACACCCACAA
33969764 CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT C
33969789 ATCGGCAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:33974736 original size:24 final size:24
Alignment explanation
Indices: 33974691--33974743 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
33974681 TGAGTTGTTT
* *
33974691 TATTTTATGATATTATTCTTTTAA
1 TATTTTATAATATAATTCTTTTAA
33974715 TATTTTATAATTATAATT-TTTTAA
1 TATTTTATAA-TATAATTCTTTTAA
*
33974739 CATTT
1 TATTT
33974744 AGAATAGTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 19 0.76
25 6 0.24
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (24 bp):
TATTTTATAATATAATTCTTTTAA
Found at i:33975106 original size:24 final size:23
Alignment explanation
Indices: 33975079--33975144 Score: 78
Period size: 24 Copynumber: 2.7 Consensus size: 23
33975069 ATCATTATTC
* *
33975079 TAAATATTCAAAAATTTATAATTA
1 TAAAAATT-AAAAATTTAAAATTA
*
33975103 TAAAACATTAAAAATATAAAATTA
1 TAAAA-ATTAAAAATTTAAAATTA
33975127 TAAAAATTAAACAATTTA
1 TAAAAATTAAA-AATTTA
33975145 GTCATTTTGA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
23 6 0.17
24 27 0.75
25 3 0.08
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.35
Consensus pattern (23 bp):
TAAAAATTAAAAATTTAAAATTA
Found at i:33975215 original size:29 final size:29
Alignment explanation
Indices: 33975159--33975215 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
33975149 TTTTGATTAA
* * *
33975159 ATAAAATAAAATTATAAAAACTTTAAAAT
1 ATAAAATAAAACTATAAAAACATAAAAAT
33975188 ATAAATATAAAACTA-AAAAACATAAAAA
1 ATAAA-ATAAAACTATAAAAACATAAAAA
33975216 GAAATTAAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (29 bp):
ATAAAATAAAACTATAAAAACATAAAAAT
Found at i:33978442 original size:66 final size:66
Alignment explanation
Indices: 33978366--33978811 Score: 296
Period size: 66 Copynumber: 6.8 Consensus size: 66
33978356 AACAGGTAAA
* *
33978366 GCTTCTGAGTATACAGATTATGCTGCCCAGAAAGCTAAGGACGCAAAGGACACCACAGCAAAAAA
1 GCTTCTGAGTATACAGATTATGCAGCCCAGAAAGCTAAGGACGCAAAGGACACCACAGCACAAAA
33978431 G
66 G
* * * ** ** * * ***
33978432 GCTTCCGAGTATACAGACTATGCAGCACAGCAAA-CTAAGGGTGCAAAGGATGCTACAACGGGGA
1 GCTTCTGAGTATACAGATTATGCAGCCCAG-AAAGCTAAGGACGCAAAGGACACCACAGC-ACAA
33978496 AA-
64 AAG
** * * * * * * *
33978498 GCGACTGAATATA-AGGATTATACAGCCGAGAAAGCCAAGGAGGC-AAGAGATACCACAGCCCAA
1 GCTTCTGAGTATACA-GATTATGCAGCCCAGAAAGCTAAGGACGCAAAG-GACACCACAGCACAA
33978561 AAG
64 AAG
* * * *
33978564 GCTTCTGAGTATACAGATTATGCTGCCCAGAAAGCTAAGGACGCAAAAGACACCACTGCACAGAA
1 GCTTCTGAGTATACAGATTATGCAGCCCAGAAAGCTAAGGACGCAAAGGACACCACAGCACAAAA
33978629 G
66 G
* ** * * * ** * ***
33978630 GCTTCCGAGTATACAGGCTATGCAGCACAGAAAACTAAGGATGCAAAGGATGCTACAATG-GGGA
1 GCTTCTGAGTATACAGATTATGCAGCCCAGAAAGCTAAGGACGCAAAGGACACCAC-A-GCACAA
33978694 AA-
64 AAG
** * * * * * * * * *
33978696 GCGACTGAATATA-AGGATTATACAGCCCACAAAGCCAAGGAGGC-AAGAGATACTACATCCCAA
1 GCTTCTGAGTATACA-GATTATGCAGCCCAGAAAGCTAAGGACGCAAAG-GACACCACAGCACAA
33978759 AAG
64 AAG
* *
33978762 GCTTCTGAGTATACAGATTATGCAGCACAGAAAGCTAAGGATGCAAAGGA
1 GCTTCTGAGTATACAGATTATGCAGCCCAGAAAGCTAAGGACGCAAAGGA
33978812 TGCTGCAATT
Statistics
Matches: 280, Mismatches: 84, Indels: 32
0.71 0.21 0.08
Matches are distributed among these distances:
65 18 0.06
66 246 0.88
67 15 0.05
68 1 0.00
ACGTcount: A:0.39, C:0.21, G:0.25, T:0.15
Consensus pattern (66 bp):
GCTTCTGAGTATACAGATTATGCAGCCCAGAAAGCTAAGGACGCAAAGGACACCACAGCACAAAA
G
Found at i:33978704 original size:198 final size:198
Alignment explanation
Indices: 33978366--33978808 Score: 751
Period size: 198 Copynumber: 2.2 Consensus size: 198
33978356 AACAGGTAAA
*
33978366 GCTTCTGAGTATACAGATTATGCTGCCCAGAAAGCTAAGGACGCAAAGGACACCACAGCAAAAAA
1 GCTTCTGAGTATACAGATTATGCTGCCCAGAAAGCTAAGGACGCAAAAGACACCACAGCAAAAAA
* *
33978431 GGCTTCCGAGTATACAGACTATGCAGCACAGCAAACTAAGGGTGCAAAGGATGCTACAACGGGGA
66 GGCTTCCGAGTATACAGACTATGCAGCACAGAAAACTAAGGATGCAAAGGATGCTACAACGGGGA
* *
33978496 AAGCGACTGAATATAAGGATTATACAGCCGAGAAAGCCAAGGAGGCAAGAGATACCACAGCCCAA
131 AAGCGACTGAATATAAGGATTATACAGCCCACAAAGCCAAGGAGGCAAGAGATACCACAGCCCAA
33978561 AAG
196 AAG
* * *
33978564 GCTTCTGAGTATACAGATTATGCTGCCCAGAAAGCTAAGGACGCAAAAGACACCACTGCACAGAA
1 GCTTCTGAGTATACAGATTATGCTGCCCAGAAAGCTAAGGACGCAAAAGACACCACAGCAAAAAA
* *
33978629 GGCTTCCGAGTATACAGGCTATGCAGCACAGAAAACTAAGGATGCAAAGGATGCTACAATGGGGA
66 GGCTTCCGAGTATACAGACTATGCAGCACAGAAAACTAAGGATGCAAAGGATGCTACAACGGGGA
* *
33978694 AAGCGACTGAATATAAGGATTATACAGCCCACAAAGCCAAGGAGGCAAGAGATACTACATCCCAA
131 AAGCGACTGAATATAAGGATTATACAGCCCACAAAGCCAAGGAGGCAAGAGATACCACAGCCCAA
33978759 AAG
196 AAG
* * *
33978762 GCTTCTGAGTATACAGATTATGCAGCACAGAAAGCTAAGGATGCAAA
1 GCTTCTGAGTATACAGATTATGCTGCCCAGAAAGCTAAGGACGCAAA
33978809 GGATGCTGCA
Statistics
Matches: 230, Mismatches: 15, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
198 230 1.00
ACGTcount: A:0.39, C:0.21, G:0.24, T:0.15
Consensus pattern (198 bp):
GCTTCTGAGTATACAGATTATGCTGCCCAGAAAGCTAAGGACGCAAAAGACACCACAGCAAAAAA
GGCTTCCGAGTATACAGACTATGCAGCACAGAAAACTAAGGATGCAAAGGATGCTACAACGGGGA
AAGCGACTGAATATAAGGATTATACAGCCCACAAAGCCAAGGAGGCAAGAGATACCACAGCCCAA
AAG
Found at i:33978852 original size:66 final size:67
Alignment explanation
Indices: 33978639--33978878 Score: 215
Period size: 66 Copynumber: 3.6 Consensus size: 67
33978629 GGCTTCCGAG
* * * *
33978639 TATACAGG-CTATGCAGCACAGAAAACTAAGGATGCAAAGGATGCTACAATGGGGAAAGCGACTG
1 TATACAGGACTATGCAGCACAGAAAGCCAAGGATGCAAAGGATGCTACAATCGGAAAAGCGACTG
33978703 AA
66 AA
* * * * * * ** **
33978705 TATA-AGGATTATACAGCCCACAAAGCCAAGGAGGC-AAGAGATACTAC-ATCCCAAAAGGCTTC
1 TATACAGGACTATGCAGCACAGAAAGCCAAGGATGCAAAG-GATGCTACAATCGGAAAA-GCGAC
*
33978767 TGAG
64 TGAA
* * * *
33978771 TATACA-GATTATGCAGCACAGAAAGCTAAGGATGCAAAGGATGCTGCAATTGGAAAAGCGACTG
1 TATACAGGACTATGCAGCACAGAAAGCCAAGGATGCAAAGGATGCTACAATCGGAAAAGCGACTG
33978835 AA
66 AA
**
33978837 TATA-AGGACTATGCAGCTGAGAAAGCCAAGGGA-GCAAAGGAT
1 TATACAGGACTATGCAGCACAGAAAGCCAA-GGATGCAAAGGAT
33978879 ACGGCAGCGC
Statistics
Matches: 134, Mismatches: 32, Indels: 16
0.74 0.18 0.09
Matches are distributed among these distances:
65 12 0.09
66 109 0.81
67 13 0.10
ACGTcount: A:0.40, C:0.17, G:0.26, T:0.16
Consensus pattern (67 bp):
TATACAGGACTATGCAGCACAGAAAGCCAAGGATGCAAAGGATGCTACAATCGGAAAAGCGACTG
AA
Found at i:33978876 original size:198 final size:198
Alignment explanation
Indices: 33978366--33978878 Score: 631
Period size: 198 Copynumber: 2.6 Consensus size: 198
33978356 AACAGGTAAA
* * * * * * *
33978366 GCTTCTGAGTATACAGATTATGCTGCCCAGAAAGCTAAGGACGCAAAGGACACCACAGCAAAAAA
1 GCTTCTGAGTATACAGATTATGCAGCACAGAAAGCTAAGGACGCAAAAGACACAACTGCACAGAA
** * * * * *
33978431 GGCTTCCGAGTATACAGACTATGCAGCACAGCAAACTAAGGGTGCAAAGGATGCTACAACGGGGA
66 GGCGACCGAATATACAGGCTATGCAGCACAGAAAACCAAGGGAGCAAAGGATGCTACAACGGGGA
* *
33978496 AAGCGACTGAATATAAGGATTATACAGCCGAGAAAGCCAAGGAGGCAAGAGATACCACAGCCCAA
131 AAGCGACTGAATATAAGGATTATACAGCCCACAAAGCCAAGGAGGCAAGAGATACCACAGCCCAA
33978561 AAG
196 AAG
* * *
33978564 GCTTCTGAGTATACAGATTATGCTGCCCAGAAAGCTAAGGACGCAAAAGACACCACTGCACAGAA
1 GCTTCTGAGTATACAGATTATGCAGCACAGAAAGCTAAGGACGCAAAAGACACAACTGCACAGAA
** * * *
33978629 GGCTTCCGAGTATACAGGCTATGCAGCACAGAAAACTAA-GGATGCAAAGGATGCTACAATGGGG
66 GGCGACCGAATATACAGGCTATGCAGCACAGAAAACCAAGGGA-GCAAAGGATGCTACAACGGGG
* *
33978693 AAAGCGACTGAATATAAGGATTATACAGCCCACAAAGCCAAGGAGGCAAGAGATACTACATCCCA
130 AAAGCGACTGAATATAAGGATTATACAGCCCACAAAGCCAAGGAGGCAAGAGATACCACAGCCCA
33978758 AAAG
195 AAAG
* * * * *
33978762 GCTTCTGAGTATACAGATTATGCAGCACAGAAAGCTAAGGATGCAAAGGATGCTGCAATTGGA-A
1 GCTTCTGAGTATACAGATTATGCAGCACAGAAAGCTAAGGACGCAAAAGA--C-ACAACTGCACA
* ** *
33978826 -AA-GCGACTGAATATA-AGGACTATGCAGCTGAGAAAGCCAAGGGAGCAAAGGAT
63 GAAGGCGACCGAATATACAGG-CTATGCAGCACAGAAAACCAAGGGAGCAAAGGAT
33978879 ACGGCAGCGC
Statistics
Matches: 281, Mismatches: 28, Indels: 12
0.88 0.09 0.04
Matches are distributed among these distances:
197 5 0.02
198 264 0.94
199 5 0.02
200 2 0.01
201 5 0.02
ACGTcount: A:0.39, C:0.20, G:0.25, T:0.15
Consensus pattern (198 bp):
GCTTCTGAGTATACAGATTATGCAGCACAGAAAGCTAAGGACGCAAAAGACACAACTGCACAGAA
GGCGACCGAATATACAGGCTATGCAGCACAGAAAACCAAGGGAGCAAAGGATGCTACAACGGGGA
AAGCGACTGAATATAAGGATTATACAGCCCACAAAGCCAAGGAGGCAAGAGATACCACAGCCCAA
AAG
Found at i:33978986 original size:132 final size:130
Alignment explanation
Indices: 33978624--33979009 Score: 443
Period size: 132 Copynumber: 2.9 Consensus size: 130
33978614 CACCACTGCA
* *
33978624 CAGAAGGCTTCCGAGTATACAGGCTATGCAGCACAGAAAACTAAGGATGCAAAGGATGCTACAAT
1 CAGAAGGCTTCCGAGTATACAGACTATGCAGCACAGAAAGCTAAGGATGCAAAGGATGCTACAAT
* * * ** * *
33978689 GGGGAAAGCGACTGAATATAAGGATTATACAGCCCACAAAGCCAA-GGAGGCAAGAGATACTACA
66 -GGAAAAGCGACTGAATATAAGGACTATGCAGCTGAAAAAGCCAAGGGA-GCAAG-GATACGACA
*
33978753 TCC
128 GCC
* * * *
33978756 CAAAAGGCTTCTGAGTATACAGATTATGCAGCACAGAAAGCTAAGGATGCAAAGGATGCTGCAAT
1 CAGAAGGCTTCCGAGTATACAGACTATGCAGCACAGAAAGCTAAGGATGCAAAGGATGCTACAA-
* *
33978821 TGGAAAAGCGACTGAATATAAGGACTATGCAGCTGAGAAAGCCAAGGGAGCAAAGGATACGGCAG
65 TGGAAAAGCGACTGAATATAAGGACTATGCAGCTGAAAAAGCCAAGGGAGC-AAGGATACGACAG
*
33978886 CG
129 CC
* * * * *
33978888 CAGAAGGCTTCCGAGT-TGACAGACTACGCAGCGCAGAAAGCTAAGGAAGCAAAAGATACTACAA
1 CAGAAGGCTTCCGAGTAT-ACAGACTATGCAGCACAGAAAGCTAAGGATGCAAAGGATGCTACAA
* * * * *
33978952 TGGAAAAAGCGACCGAGTATAAAGACTATGCAGCTGAAAAAGCGAAGGAAGCGAAGGA
65 TGG-AAAAGCGACTGAATATAAGGACTATGCAGCTGAAAAAGCCAAGGGAGC-AAGGA
33979010 CGTGACAGCT
Statistics
Matches: 217, Mismatches: 32, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
131 4 0.02
132 206 0.95
133 7 0.03
ACGTcount: A:0.40, C:0.18, G:0.27, T:0.14
Consensus pattern (130 bp):
CAGAAGGCTTCCGAGTATACAGACTATGCAGCACAGAAAGCTAAGGATGCAAAGGATGCTACAAT
GGAAAAGCGACTGAATATAAGGACTATGCAGCTGAAAAAGCCAAGGGAGCAAGGATACGACAGCC
Found at i:33992766 original size:2 final size:2
Alignment explanation
Indices: 33992759--33992785 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
33992749 ACATTTCTTT
33992759 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
33992786 TCTTTGCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:33998926 original size:15 final size:14
Alignment explanation
Indices: 33998908--33998947 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
33998898 TATTTTGTTT
33998908 TTTTTTTGAAATTTG
1 TTTTTTT-AAATTTG
*
33998923 TTTTTTTAAATTTT
1 TTTTTTTAAATTTG
33998937 TTATTTTTAAA
1 TT-TTTTTAAA
33998948 ATTATTACTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.35
15 15 0.65
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (14 bp):
TTTTTTTAAATTTG
Found at i:33998926 original size:16 final size:14
Alignment explanation
Indices: 33998905--33998947 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
33998895 GGTTATTTTG
*
33998905 TTTTTTTTTTGAAA
1 TTTTTTTTTTTAAA
*
33998919 TTTGTTTTTTTAAA
1 TTTTTTTTTTTAAA
33998933 TTTTTTATTTTTAAA
1 TTTTTT-TTTTTAAA
33998948 ATTATTACTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
14 17 0.68
15 8 0.32
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (14 bp):
TTTTTTTTTTTAAA
Found at i:34005427 original size:15 final size:15
Alignment explanation
Indices: 34005409--34005461 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
34005399 AGAAGAGGAT
*
34005409 GACGATGAAGATGAG
1 GACGATGAAGAAGAG
* *
34005424 GACGATGAGGACGAG
1 GACGATGAAGAAGAG
* * *
34005439 GATGATGACGAAGAC
1 GACGATGAAGAAGAG
34005454 GACGATGA
1 GACGATGA
34005462 TGAGGCAGTG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.38, C:0.11, G:0.40, T:0.11
Consensus pattern (15 bp):
GACGATGAAGAAGAG
Found at i:34005442 original size:21 final size:21
Alignment explanation
Indices: 34005409--34005466 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 21
34005399 AGAAGAGGAT
* * *
34005409 GACGATGAAGATGAGGACGAT
1 GACGACGAGGATGAGGACGAA
* *
34005430 GAGGACGAGGATGATGACGAA
1 GACGACGAGGATGAGGACGAA
*
34005451 GACGACGATGATGAGG
1 GACGACGAGGATGAGG
34005467 CAGTGGATGG
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.36, C:0.10, G:0.41, T:0.12
Consensus pattern (21 bp):
GACGACGAGGATGAGGACGAA
Found at i:34006302 original size:30 final size:30
Alignment explanation
Indices: 34006268--34006327 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
34006258 TAAAAAGGTC
34006268 GGTCCAAAATCTAGAAAAGGGATAAAATGA
1 GGTCCAAAATCTAGAAAAGGGATAAAATGA
34006298 GGTCCAAAATCTAGAAAAGGGATAAAATGA
1 GGTCCAAAATCTAGAAAAGGGATAAAATGA
34006328 AGTTAGTTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.50, C:0.10, G:0.23, T:0.17
Consensus pattern (30 bp):
GGTCCAAAATCTAGAAAAGGGATAAAATGA
Found at i:34009492 original size:44 final size:45
Alignment explanation
Indices: 34009429--34009517 Score: 119
Period size: 44 Copynumber: 2.0 Consensus size: 45
34009419 ACCTCTATTC
*
34009429 CATTCAACCAAACACAAGAA-TATC-ATTACGCATCTATTCCATTA
1 CATTCAACCAAACAAAAGAATTA-CGATTACGCATCTATTCCATTA
* *
34009473 CATTCAACTAAACAAAAGAATTACGTATTACGCCTCTATTCCATT
1 CATTCAACCAAACAAAAGAATTACG-ATTACGCATCTATTCCATT
34009518 CTGTAAGATT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
44 19 0.49
45 2 0.05
46 18 0.46
ACGTcount: A:0.39, C:0.26, G:0.06, T:0.29
Consensus pattern (45 bp):
CATTCAACCAAACAAAAGAATTACGATTACGCATCTATTCCATTA
Found at i:34012756 original size:62 final size:62
Alignment explanation
Indices: 34012659--34012781 Score: 237
Period size: 62 Copynumber: 2.0 Consensus size: 62
34012649 TTGGTAAAGG
34012659 CCACTACATTACAATGATAAAAACATTATTCACAATAGAATCATTAGGATGAATAAATACCA
1 CCACTACATTACAATGATAAAAACATTATTCACAATAGAATCATTAGGATGAATAAATACCA
*
34012721 CCACTACCTTACAATGATAAAAACATTATTCACAATAGAATCATTAGGATGAATAAATACC
1 CCACTACATTACAATGATAAAAACATTATTCACAATAGAATCATTAGGATGAATAAATACC
34012782 GCAGAGGAAG
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 60 1.00
ACGTcount: A:0.47, C:0.19, G:0.08, T:0.26
Consensus pattern (62 bp):
CCACTACATTACAATGATAAAAACATTATTCACAATAGAATCATTAGGATGAATAAATACCA
Found at i:34022819 original size:180 final size:177
Alignment explanation
Indices: 34022396--34022839 Score: 658
Period size: 180 Copynumber: 2.5 Consensus size: 177
34022386 ACGAGATTCA
* * * *
34022396 AAAATAATTTCACAATTATAAATCCACCATATGTACATTACGATAAAACAAATCACAATATAAAT
1 AAAATAATGTGACAATTATAAATCCACCATATGTATATTACTATAAAACAAAT-AC-ATATAAAT
* *
34022461 AATAGTGATGCTAAATTAAGTTCCTCATATTGCAATAATGTAATTTGAAATTAATTTATTATAAA
64 AATAATGATGCTAAATTAAGTTCCTCATATTGCAATAATGTAATTTGAAATTAAATTATTATAAA
34022526 AAATAACACATTACGATTTATTTTCAATGTCCCTACTTACCATTAATAT
129 AAATAACACATTACGATTTATTTTCAATGTCCCTACTTACCATTAATAT
34022575 AAAATAATGTGACAATTATAAATCCACCATATGTATATTACTATAAAACAAATCACAATATAAAT
1 AAAATAATGTGACAATTATAAATCCACCATATGTATATTACTATAAAACAAAT-AC-ATATAAAT
*
34022640 AATAATGATGCTAAATTAAGTCTCCTCATATTGCAATAATGTAATTTGAAATTAAATTATTATTA
64 AATAATGATGCTAAATTAAGT-TCCTCATATTGCAATAATGTAATTTGAAATTAAATTATTATAA
* * *
34022705 ATAGTAACACATTGCGATTTATTTTCAATGTCCCTACTTTCCTACCATTAATAT
128 AAAATAACACATTACGATTTATTTTCAATGTCCCTAC--T--TACCATTAATAT
* **
34022759 AAAATAATGTGACAATTATAAATCCACCTTACCTATATTACTATAAAACAAAT-C-TATAAATAA
1 AAAATAATGTGACAATTATAAATCCACCATATGTATATTACTATAAAACAAATACATATAAATAA
*
34022822 TAATTATGCTAAAATTAA
66 TAATGATGCT-AAATTAA
34022840 ATTATTAATA
Statistics
Matches: 245, Mismatches: 14, Indels: 10
0.91 0.05 0.04
Matches are distributed among these distances:
179 81 0.33
180 93 0.38
181 7 0.03
182 2 0.01
184 62 0.25
ACGTcount: A:0.44, C:0.14, G:0.06, T:0.35
Consensus pattern (177 bp):
AAAATAATGTGACAATTATAAATCCACCATATGTATATTACTATAAAACAAATACATATAAATAA
TAATGATGCTAAATTAAGTTCCTCATATTGCAATAATGTAATTTGAAATTAAATTATTATAAAAA
ATAACACATTACGATTTATTTTCAATGTCCCTACTTACCATTAATAT
Found at i:34026592 original size:2 final size:2
Alignment explanation
Indices: 34026585--34026626 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
34026575 TTTTATTATG
* *
34026585 TA TA TA TA TA TA TG TA TA TA -A GA -A TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
34026625 TA
1 TA
34026627 AAAACGAGAG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (2 bp):
TA
Found at i:34028365 original size:107 final size:106
Alignment explanation
Indices: 34028178--34028386 Score: 321
Period size: 107 Copynumber: 2.0 Consensus size: 106
34028168 TTCCTAAATA
*
34028178 AGGCAATATTTCGCGTTTGGAAAATTCGAGAAAACGTGCCCTAACGTACTGGGTTTCGATTTCTC
1 AGGCAATATTTCGCGTTTGGAAAATTCGAGAAAACGTGCCCTAACGTACTGGGTTTCGATGTCTC
* *
34028243 GTTCGACCAAATAGCCAAATATCCTTTTTAAACTTTCAAAACG
66 GTCCGACCAAATAGCCAAATATCC-TCTTAAA-TTTCAAAACG
* * * *
34028286 AGGCAATGTTTTGCGTTTGG-AAATTCGAGAGAACGTGCCCTAACGTGCTGGGTTTCGATGTCTC
1 AGGCAATATTTCGCGTTTGGAAAATTCGAGAAAACGTGCCCTAACGTACTGGGTTTCGATGTCTC
*
34028350 GTCCGACTAAATAGCCAAATATCCTCTTAAATTTCAA
66 GTCCGACCAAATAGCCAAATATCCTCTTAAATTTCAA
34028387 TCCATGTCAT
Statistics
Matches: 93, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
105 6 0.06
106 6 0.06
107 63 0.68
108 18 0.19
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.31
Consensus pattern (106 bp):
AGGCAATATTTCGCGTTTGGAAAATTCGAGAAAACGTGCCCTAACGTACTGGGTTTCGATGTCTC
GTCCGACCAAATAGCCAAATATCCTCTTAAATTTCAAAACG
Found at i:34029497 original size:37 final size:38
Alignment explanation
Indices: 34029408--34029500 Score: 102
Period size: 37 Copynumber: 2.4 Consensus size: 38
34029398 CTACAAGATA
* *
34029408 AATATTAAATTTATTAAGATAATTACTTTAATATTAAATT
1 AATATTAAA-CTATTAAGATAAGTAC-TTAATATTAAATT
*
34029448 AATA-AAATACTATTAAGATAAGTA-TTAA-ATTAAATTT
1 AATATTAA-ACTATTAAGATAAGTACTTAATATTAAA-TT
34029485 AATATTAAACTATTAA
1 AATATTAAACTATTAA
34029501 AATATTATTA
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
36 6 0.13
37 18 0.39
38 2 0.04
39 15 0.33
40 5 0.11
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (38 bp):
AATATTAAACTATTAAGATAAGTACTTAATATTAAATT
Found at i:34031771 original size:13 final size:15
Alignment explanation
Indices: 34031733--34031780 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 15
34031723 AACTTTATTC
* *
34031733 TTAACAAATATTTTA
1 TTAATAAATATTTAA
34031748 TT--TAAATATTTAA
1 TTAATAAATATTTAA
34031761 -TAATAAA-ATTTAA
1 TTAATAAATATTTAA
34031774 TTAATAA
1 TTAATAA
34031781 TTTTTACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
12 1 0.04
13 15 0.54
14 10 0.36
15 2 0.07
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (15 bp):
TTAATAAATATTTAA
Found at i:34036881 original size:17 final size:18
Alignment explanation
Indices: 34036859--34036893 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
34036849 TATATACTAT
*
34036859 AATATTTA-ATTAATTAA
1 AATATTTAGAATAATTAA
34036876 AATATTTAGAATAATTAA
1 AATATTTAGAATAATTAA
34036894 GATTAATGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (18 bp):
AATATTTAGAATAATTAA
Found at i:34037088 original size:210 final size:211
Alignment explanation
Indices: 34036851--34037273 Score: 839
Period size: 210 Copynumber: 2.0 Consensus size: 211
34036841 CTAGTTTATA
34036851 TATACTATAATATTTAATTAATTAAAATATTTAGAATAATTAAGATTAATGTTTTAAAAATTAAC
1 TATACTATAATATTTAATTAATTAAAATATTTAGAATAATTAAGATTAATGTTTTAAAAATTAAC
34036916 CCAAAAAAAAGTCATTTGGAAGAGAAAAAAAAAGAAATACTATATTAAATAAACTATCTTACTTT
66 CCAAAAAAAAGTCATTTGGAAGAGAAAAAAAAAGAAATACTATATTAAATAAACTATCTTACTTT
34036981 TTATACCTTAGTATCAATAATTGCAATAATAATTACATTTTTAGTAACCGTATTCTTTAAAAATT
131 TTATACCTTAGTATCAATAATTGCAATAATAATTACATTTTTAGTAACCGTATTCTTTAAAAATT
34037046 ATGTTTTATTGAAGGG
196 ATGTTTTATTGAAGGG
34037062 TATACTATAA-ATTTAATTAATTAAAATATTTAGAATAATTAAGATTAATGTTTTAAAAATTAAC
1 TATACTATAATATTTAATTAATTAAAATATTTAGAATAATTAAGATTAATGTTTTAAAAATTAAC
34037126 CCAAAAAAAAGTCATTTGGAAGAGAAAAAAAAAGAAATACTATATTAAATAAACTATCTTACTTT
66 CCAAAAAAAAGTCATTTGGAAGAGAAAAAAAAAGAAATACTATATTAAATAAACTATCTTACTTT
34037191 TTATACCTTAGTATCAATAATTGCAATAATAATTACATTTTTAGTAACCGTATTCTTTAAAAATT
131 TTATACCTTAGTATCAATAATTGCAATAATAATTACATTTTTAGTAACCGTATTCTTTAAAAATT
34037256 ATGTTTTATTGAAGGG
196 ATGTTTTATTGAAGGG
34037272 TA
1 TA
34037274 AGTTATATGG
Statistics
Matches: 212, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
210 202 0.95
211 10 0.05
ACGTcount: A:0.46, C:0.08, G:0.09, T:0.38
Consensus pattern (211 bp):
TATACTATAATATTTAATTAATTAAAATATTTAGAATAATTAAGATTAATGTTTTAAAAATTAAC
CCAAAAAAAAGTCATTTGGAAGAGAAAAAAAAAGAAATACTATATTAAATAAACTATCTTACTTT
TTATACCTTAGTATCAATAATTGCAATAATAATTACATTTTTAGTAACCGTATTCTTTAAAAATT
ATGTTTTATTGAAGGG
Found at i:34041159 original size:29 final size:29
Alignment explanation
Indices: 34041126--34041196 Score: 94
Period size: 28 Copynumber: 2.5 Consensus size: 29
34041116 AATTGACATT
34041126 TAAACTATTTTTTTTTCA-AAGTTAGTACC
1 TAAACTATTTTTTTTTCACAAGTT-GTACC
*
34041155 TAAAC-ATTTTTTTATCACAAGTTGTACC
1 TAAACTATTTTTTTTTCACAAGTTGTACC
*
34041183 TAAA-TAATTTTTTT
1 TAAACTATTTTTTTT
34041197 GTTACTCAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
28 27 0.73
29 10 0.27
ACGTcount: A:0.32, C:0.13, G:0.06, T:0.49
Consensus pattern (29 bp):
TAAACTATTTTTTTTTCACAAGTTGTACC
Found at i:34041337 original size:17 final size:17
Alignment explanation
Indices: 34041291--34041340 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
34041281 ATATTTTAAA
*
34041291 TTTTT-TTCTTTTACAT
1 TTTTTCTTCTTTTATAT
34041307 TATTTATC-TCTTTTATAT
1 T-TTT-TCTTCTTTTATAT
34041325 TTTTTCTTCTTTTATA
1 TTTTTCTTCTTTTATA
34041341 ATCTCTGAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
16 3 0.10
17 15 0.52
18 11 0.38
ACGTcount: A:0.16, C:0.12, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTTTCTTCTTTTATAT
Found at i:34043136 original size:21 final size:21
Alignment explanation
Indices: 34043111--34043232 Score: 84
Period size: 21 Copynumber: 5.8 Consensus size: 21
34043101 TGAGCTTCAG
*
34043111 TTAACTCATATGAGTTTTCGT
1 TTAACTCTTATGAGTTTTCGT
* * *
34043132 TTAACTCTAATGGGTTTCCGT
1 TTAACTCTTATGAGTTTTCGT
* * *
34043153 TTAGCTCTTTTGAG-CTTCAGT
1 TTAACTCTTATGAGTTTTC-GT
* *
34043174 TTAACCCTTATGGGTTTTCGT
1 TTAACTCTTATGAGTTTTCGT
* * * *
34043195 TCAGCTCTTATGAGCTTCCGT
1 TTAACTCTTATGAGTTTTCGT
* * *
34043216 TCAACCCTTATGGGTTT
1 TTAACTCTTATGAGTTT
34043233 CTGTTTAGCA
Statistics
Matches: 74, Mismatches: 25, Indels: 4
0.72 0.24 0.04
Matches are distributed among these distances:
20 2 0.03
21 69 0.93
22 3 0.04
ACGTcount: A:0.17, C:0.20, G:0.18, T:0.44
Consensus pattern (21 bp):
TTAACTCTTATGAGTTTTCGT
Found at i:34043189 original size:42 final size:42
Alignment explanation
Indices: 34043130--34043254 Score: 160
Period size: 42 Copynumber: 3.0 Consensus size: 42
34043120 ATGAGTTTTC
* * *
34043130 GTTTAACTCTAATGGGTTTCCGTTTAGCTCTTTTGAGCTTCA
1 GTTTAACCCTTATGGGTTTCCGTTTAGCTCTTATGAGCTTCA
* * *
34043172 GTTTAACCCTTATGGGTTTTCGTTCAGCTCTTATGAGCTTCC
1 GTTTAACCCTTATGGGTTTCCGTTTAGCTCTTATGAGCTTCA
* * * *
34043214 GTTCAACCCTTATGGGTTTCTGTTTAGCACTTATGTGCTTC
1 GTTTAACCCTTATGGGTTTCCGTTTAGCTCTTATGAGCTTC
34043255 TGTGCAGCCT
Statistics
Matches: 71, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.15, C:0.22, G:0.19, T:0.44
Consensus pattern (42 bp):
GTTTAACCCTTATGGGTTTCCGTTTAGCTCTTATGAGCTTCA
Found at i:34043216 original size:63 final size:62
Alignment explanation
Indices: 34043089--34043216 Score: 157
Period size: 63 Copynumber: 2.0 Consensus size: 62
34043079 TTTACTTTCT
* * * *
34043089 GTTTAGCTCTCATGAGCTTCAGTTAACTCATATGAGTTTTCGTTTAACTCTAATGGGTTTCC
1 GTTTAGCTCTCATGAGCTTCAGTTAACCCATATGAGTTTTCGTTCAACTCTAATGAGCTTCC
** * * * *
34043151 GTTTAGCTCTTTTGAGCTTCAGTTTAACCCTTATGGGTTTTCGTTCAGCTCTTATGAGCTTCC
1 GTTTAGCTCTCATGAGCTTCAG-TTAACCCATATGAGTTTTCGTTCAACTCTAATGAGCTTCC
34043214 GTT
1 GTT
34043217 CAACCCTTAT
Statistics
Matches: 55, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
62 20 0.36
63 35 0.64
ACGTcount: A:0.17, C:0.20, G:0.19, T:0.44
Consensus pattern (62 bp):
GTTTAGCTCTCATGAGCTTCAGTTAACCCATATGAGTTTTCGTTCAACTCTAATGAGCTTCC
Found at i:34043246 original size:21 final size:21
Alignment explanation
Indices: 34043141--34043257 Score: 65
Period size: 21 Copynumber: 5.6 Consensus size: 21
34043131 TTTAACTCTA
* * *
34043141 ATGGGTTTCCGTTTAGCTCTT
1 ATGGGCTTCTGTTTAGCCCTT
* * * *
34043162 TTGAGCTTCAGTTTAACCCTT
1 ATGGGCTTCTGTTTAGCCCTT
* * *
34043183 ATGGG-TTTTCGTTCAGCTCTT
1 ATGGGCTTCT-GTTTAGCCCTT
* * * *
34043204 ATGAGCTTCCGTTCAACCCTT
1 ATGGGCTTCTGTTTAGCCCTT
* *
34043225 ATGGGTTTCTGTTTAGCACTT
1 ATGGGCTTCTGTTTAGCCCTT
*
34043246 ATGTGCTTCTGT
1 ATGGGCTTCTGT
34043258 GCAGCCTTCG
Statistics
Matches: 68, Mismatches: 26, Indels: 4
0.69 0.27 0.04
Matches are distributed among these distances:
20 2 0.03
21 64 0.94
22 2 0.03
ACGTcount: A:0.14, C:0.21, G:0.21, T:0.44
Consensus pattern (21 bp):
ATGGGCTTCTGTTTAGCCCTT
Found at i:34043512 original size:10 final size:10
Alignment explanation
Indices: 34043497--34043528 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
34043487 AGCCAACGAA
34043497 TTTATTAAGC
1 TTTATTAAGC
34043507 TTTATTAAGC
1 TTTATTAAGC
*
34043517 TTCATTAAGC
1 TTTATTAAGC
34043527 TT
1 TT
34043529 ACTTGTGTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.28, C:0.12, G:0.09, T:0.50
Consensus pattern (10 bp):
TTTATTAAGC
Found at i:34045683 original size:6 final size:6
Alignment explanation
Indices: 34045672--34045697 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
34045662 ATTTTGGTTC
34045672 TTTATT TTTATT TTTATT TTTATT TT
1 TTTATT TTTATT TTTATT TTTATT TT
34045698 CTGATTTTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTATT
Found at i:34046942 original size:24 final size:24
Alignment explanation
Indices: 34046827--34046967 Score: 173
Period size: 25 Copynumber: 6.0 Consensus size: 24
34046817 TAATCTTAGC
*
34046827 CCAAAGTGCTAA-A-CAGAGAGCA
1 CCAACGTGCTAATATCAGAGAGCA
* *
34046849 CAAATGTGCTAA-A-CAGAGAGCA
1 CCAACGTGCTAATATCAGAGAGCA
***
34046871 CTGCCGTGCTAAATATCAGAGAGCA
1 CCAACGTGCT-AATATCAGAGAGCA
34046896 CCAACGTGCTAATAATCAGAGAGCA
1 CCAACGTGCTAAT-ATCAGAGAGCA
34046921 CCAACGTGCTAATATCAGAGAGCA
1 CCAACGTGCTAATATCAGAGAGCA
*
34046945 CCAATGTGCTAATATCAGAGAGC
1 CCAACGTGCTAATATCAGAGAGC
34046968 GCGCTAAAGT
Statistics
Matches: 105, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
22 26 0.25
23 2 0.02
24 37 0.35
25 40 0.38
ACGTcount: A:0.39, C:0.23, G:0.22, T:0.16
Consensus pattern (24 bp):
CCAACGTGCTAATATCAGAGAGCA
Found at i:34051748 original size:16 final size:16
Alignment explanation
Indices: 34051727--34051766 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
34051717 TAATTTGATA
*
34051727 ATTTTACTAACAATTT
1 ATTTTAATAACAATTT
34051743 ATTTTAATAACAA-TT
1 ATTTTAATAACAATTT
34051758 AGTTTTAAT
1 A-TTTTAAT
34051767 TTTATTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 3 0.14
16 19 0.86
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.50
Consensus pattern (16 bp):
ATTTTAATAACAATTT
Found at i:34051800 original size:23 final size:23
Alignment explanation
Indices: 34051743--34051800 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 23
34051733 CTAACAATTT
* * *
34051743 ATTTTAA-TAACAATTAGTTTTA
1 ATTTTAATTAAAAAATAATTTTA
34051765 ATTTT-ATTAAAAAATAATTTTA
1 ATTTTAATTAAAAAATAATTTTA
34051787 ATTTTAATTAAAAA
1 ATTTTAATTAAAAA
34051801 CGGGCCGGCC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 1 0.03
22 22 0.71
23 8 0.26
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (23 bp):
ATTTTAATTAAAAAATAATTTTA
Found at i:34057076 original size:21 final size:22
Alignment explanation
Indices: 34057052--34057097 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
34057042 TAAAATAAAA
*
34057052 AAATTG-AC-TAATAAATCAATT
1 AAATTGAACATAA-AAACCAATT
34057073 AAATTGAACATAAAAACCAATT
1 AAATTGAACATAAAAACCAATT
34057095 AAA
1 AAA
34057098 AAACCAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 6 0.27
22 13 0.59
23 3 0.14
ACGTcount: A:0.59, C:0.11, G:0.04, T:0.26
Consensus pattern (22 bp):
AAATTGAACATAAAAACCAATT
Found at i:34063059 original size:20 final size:22
Alignment explanation
Indices: 34063020--34063059 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
34063010 AACGTATCAA
34063020 AATTTCTATGTATTTCAAGTTT
1 AATTTCTATGTATTTCAAGTTT
*
34063042 AATTTC-ATG-ATTTTAAGT
1 AATTTCTATGTATTTCAAGT
34063060 ACTTATCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 3 0.18
22 6 0.35
ACGTcount: A:0.30, C:0.07, G:0.10, T:0.53
Consensus pattern (22 bp):
AATTTCTATGTATTTCAAGTTT
Found at i:34068297 original size:2 final size:2
Alignment explanation
Indices: 34068290--34068327 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
34068280 CTCTCCAAAG
*
34068290 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34068328 GCGAATAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34069371 original size:29 final size:31
Alignment explanation
Indices: 34069339--34069399 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
34069329 ATCTTATTTT
* * *
34069339 AATTACTCA-ATTTTAAAAAA-TAACAAAAC
1 AATTACTAACATTGTAAAAAAGAAACAAAAC
34069368 AATTACTAACATTGTAAAAAAGAAACAAAAC
1 AATTACTAACATTGTAAAAAAGAAACAAAAC
34069399 A
1 A
34069400 GTTATTAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 8 0.30
30 10 0.37
31 9 0.33
ACGTcount: A:0.61, C:0.13, G:0.03, T:0.23
Consensus pattern (31 bp):
AATTACTAACATTGTAAAAAAGAAACAAAAC
Found at i:34069456 original size:20 final size:20
Alignment explanation
Indices: 34069431--34069468 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
34069421 TTGGTGTCGA
*
34069431 TGATGTGGTAAGTTAACTGC
1 TGATGTGGCAAGTTAACTGC
34069451 TGATGTGGCAAGTTAACT
1 TGATGTGGCAAGTTAACT
34069469 TGCCCACCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.11, G:0.29, T:0.34
Consensus pattern (20 bp):
TGATGTGGCAAGTTAACTGC
Found at i:34075114 original size:39 final size:39
Alignment explanation
Indices: 34075047--34075178 Score: 192
Period size: 39 Copynumber: 3.4 Consensus size: 39
34075037 TATTACACAT
* **
34075047 AAAGAGCAGAAGGCAATTATCCCCTACAATATGAGATAC
1 AAAGAGCAGAATGCAATCGTCCCCTACAATATGAGATAC
* * *
34075086 AAAAAGCAGAATGCAATCGTCCCTTACAATCTGAGATAC
1 AAAGAGCAGAATGCAATCGTCCCCTACAATATGAGATAC
* *
34075125 AAGGAGCAGAATGCAGTCGTCCCCTACAATATGAGATAC
1 AAAGAGCAGAATGCAATCGTCCCCTACAATATGAGATAC
34075164 AAAGAGCAGAATGCA
1 AAAGAGCAGAATGCA
34075179 CTTGTTGTCT
Statistics
Matches: 81, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 81 1.00
ACGTcount: A:0.42, C:0.21, G:0.20, T:0.17
Consensus pattern (39 bp):
AAAGAGCAGAATGCAATCGTCCCCTACAATATGAGATAC
Found at i:34079182 original size:129 final size:129
Alignment explanation
Indices: 34078952--34079208 Score: 442
Period size: 129 Copynumber: 2.0 Consensus size: 129
34078942 AGAAAACCTG
*
34078952 GTCATAACCATGCTGTCATTATTGATCAAAAGGCCCTGCCCCTACCCCAGCCAATTGAACAATCA
1 GTCATAACCATGCTGTCATCATTGATCAAAAGGCCCTGCCCCTACCCCAGCCAATTGAACAATCA
* *
34079017 GATAGGAACTGTCAGCCTGAAGCAAACCAGCAATTACAAGCAAAGTCCTGGGTCAATAACTGTA
66 GATAGGAACTGTCAGCCTGAAGCAAACCAGCAATTACAAGCAAAATCCAGGGTCAATAACTGTA
* * *
34079081 GTCATAACCATGCTGTCATCATTGATCAACAGGCCCTGCCCTTACTCCAGCCAATTGAACAATCA
1 GTCATAACCATGCTGTCATCATTGATCAAAAGGCCCTGCCCCTACCCCAGCCAATTGAACAATCA
* *
34079146 GATAGGAACTGTCAGTCTGAAGCAAACCGGCAATTACAAGCAAAATCCAGGGTCAATAACTGT
66 GATAGGAACTGTCAGCCTGAAGCAAACCAGCAATTACAAGCAAAATCCAGGGTCAATAACTGT
34079209 GACCCTATAA
Statistics
Matches: 120, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
129 120 1.00
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.21
Consensus pattern (129 bp):
GTCATAACCATGCTGTCATCATTGATCAAAAGGCCCTGCCCCTACCCCAGCCAATTGAACAATCA
GATAGGAACTGTCAGCCTGAAGCAAACCAGCAATTACAAGCAAAATCCAGGGTCAATAACTGTA
Found at i:34082898 original size:29 final size:29
Alignment explanation
Indices: 34082845--34082900 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
34082835 AAATTTATTT
**
34082845 ATAATTTTTATACTTTTTTTCATTTTTAA
1 ATAATTTTTATACTTTTTTAAATTTTTAA
34082874 ATAATTTTTATACTTTTTTAAATTTTT
1 ATAATTTTTATACTTTTTTAAATTTTT
34082901 TATATTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (29 bp):
ATAATTTTTATACTTTTTTAAATTTTTAA
Found at i:34084774 original size:15 final size:15
Alignment explanation
Indices: 34084754--34084796 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
34084744 TAATTTGAGT
* *
34084754 TTTTTCAAGTTTAGA
1 TTTTTCAAGTTCAAA
*
34084769 TTTTTCTAGTTCAAA
1 TTTTTCAAGTTCAAA
34084784 TTTTT-AAGTTCAA
1 TTTTTCAAGTTCAA
34084797 TTCAAGTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 7 0.29
15 17 0.71
ACGTcount: A:0.28, C:0.09, G:0.09, T:0.53
Consensus pattern (15 bp):
TTTTTCAAGTTCAAA
Found at i:34088920 original size:21 final size:21
Alignment explanation
Indices: 34088894--34088948 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
34088884 AACAATGGTG
34088894 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGTTACTGTA
*
34088915 GCGGTGAGATTAGTTATTGTA
1 GCGGTGAGATTAGTTACTGTA
*
34088936 GTGGTGAGATTAG
1 GCGGTGAGATTAG
34088949 AAACAATAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.24, C:0.05, G:0.36, T:0.35
Consensus pattern (21 bp):
GCGGTGAGATTAGTTACTGTA
Found at i:34090877 original size:70 final size:71
Alignment explanation
Indices: 34090777--34090916 Score: 246
Period size: 70 Copynumber: 2.0 Consensus size: 71
34090767 TAAAAAATAA
34090777 AGAAACTAAAAAAGGGTTTTCATTAATTTCCCTATAATATTGTTTAATCCAATAAAAAAATTAAA
1 AGAAACTAAAAAAGGGTTTTCATTAATTTCCCTATAATATTGTTTAATCCAATAAAAAAATTAAA
34090842 TTTTAG
66 TTTTAG
* * *
34090848 AGAAACTAAAAAA-GGTTTTCATTATTTTCCCTATAATTTTGTTTAATCCAATAAAAAGATTAAA
1 AGAAACTAAAAAAGGGTTTTCATTAATTTCCCTATAATATTGTTTAATCCAATAAAAAAATTAAA
34090912 TTTTA
66 TTTTA
34090917 ACAAATAAAT
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
70 53 0.80
71 13 0.20
ACGTcount: A:0.44, C:0.10, G:0.08, T:0.39
Consensus pattern (71 bp):
AGAAACTAAAAAAGGGTTTTCATTAATTTCCCTATAATATTGTTTAATCCAATAAAAAAATTAAA
TTTTAG
Found at i:34099432 original size:34 final size:33
Alignment explanation
Indices: 34099387--34099459 Score: 137
Period size: 34 Copynumber: 2.2 Consensus size: 33
34099377 CATCAATCTG
34099387 TGCATAGATCCATGCGTGCACAATCTGTGCTGA
1 TGCATAGATCCATGCGTGCACAATCTGTGCTGA
34099420 TGCATACGATCCATGCGTGCACAATCTGTGCTGA
1 TGCATA-GATCCATGCGTGCACAATCTGTGCTGA
34099454 TGCATA
1 TGCATA
34099460 TGCATTTTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
33 6 0.15
34 33 0.85
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (33 bp):
TGCATAGATCCATGCGTGCACAATCTGTGCTGA
Found at i:34099457 original size:17 final size:17
Alignment explanation
Indices: 34099403--34099457 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
34099393 GATCCATGCG
34099403 TGCACAATCTGTGCTGA
1 TGCACAATCTGTGCTGA
* **
34099420 TGCATACGATCCATGC-G-
1 TGC--ACAATCTGTGCTGA
34099437 TGCACAATCTGTGCTGA
1 TGCACAATCTGTGCTGA
34099454 TGCA
1 TGCA
34099458 TATGCATTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 8
0.67 0.14 0.19
Matches are distributed among these distances:
15 8 0.29
16 1 0.04
17 10 0.36
18 1 0.04
19 8 0.29
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.27
Consensus pattern (17 bp):
TGCACAATCTGTGCTGA
Found at i:34115322 original size:10 final size:10
Alignment explanation
Indices: 34115236--34115329 Score: 68
Period size: 10 Copynumber: 9.3 Consensus size: 10
34115226 AAATTTTATG
34115236 AAAA-TATATA
1 AAAATTATA-A
*
34115246 AAAATTCTAAA
1 AAAATTAT-AA
34115257 AAAATTATAA
1 AAAATTATAA
**
34115267 GAAAAGAATAA
1 -AAAATTATAA
* *
34115278 AAACTTATTA
1 AAAATTATAA
*
34115288 AAAA-TAT-T
1 AAAATTATAA
*
34115296 AAAATTGATAT
1 AAAATT-ATAA
34115307 AAAATTATAA
1 AAAATTATAA
34115317 AAAATTATAA
1 AAAATTATAA
34115327 AAA
1 AAA
34115330 CATGAACTAG
Statistics
Matches: 67, Mismatches: 11, Indels: 12
0.74 0.12 0.13
Matches are distributed among these distances:
8 4 0.06
9 4 0.06
10 33 0.49
11 25 0.37
12 1 0.01
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.29
Consensus pattern (10 bp):
AAAATTATAA
Found at i:34118278 original size:10 final size:10
Alignment explanation
Indices: 34118263--34118385 Score: 61
Period size: 10 Copynumber: 12.1 Consensus size: 10
34118253 CAATTCAAGC
*
34118263 TTTTATGATT
1 TTTTATAATT
34118273 TTTTATAA-T
1 TTTTATAATT
*
34118282 TTTTATAAGT
1 TTTTATAATT
* *
34118292 TTATATAAAT
1 TTTTATAATT
* *
34118302 TTTAAT-ATG
1 TTTTATAATT
*
34118311 TTTAATAATT
1 TTTTATAATT
* *
34118321 GTTAATAATTT
1 TTTTATAA-TT
*
34118332 TTTTATTATT
1 TTTTATAATT
*
34118342 TTTGTAAAATT
1 TTT-TATAATT
**
34118353 TTAAATAATTTT
1 TTTTATAA--TT
34118365 TTTTATAATT
1 TTTTATAATT
* *
34118375 TATTAAAATT
1 TTTTATAATT
34118385 T
1 T
34118386 ATTACATTCA
Statistics
Matches: 86, Mismatches: 21, Indels: 12
0.72 0.18 0.10
Matches are distributed among these distances:
9 16 0.19
10 48 0.56
11 14 0.16
12 8 0.09
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (10 bp):
TTTTATAATT
Found at i:34118360 original size:32 final size:32
Alignment explanation
Indices: 34118324--34118385 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
34118314 AATAATTGTT
* *
34118324 AATAA-TTTTTTTATTATTTTTGTAAAATTTTA
1 AATAATTTTTTTTATAATTTAT-TAAAATTTTA
34118356 AATAATTTTTTTTATAATTTATTAAAATTT
1 AATAATTTTTTTTATAATTTATTAAAATTT
34118386 ATTACATTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 13 0.48
33 14 0.52
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (32 bp):
AATAATTTTTTTTATAATTTATTAAAATTTTA
Found at i:34118432 original size:29 final size:30
Alignment explanation
Indices: 34118395--34118453 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
34118385 TATTACATTC
*
34118395 ATTAGATTTTTGT-AATATTTATAAGTTTTT
1 ATTAGATTTTTATAAAT-TTTATAAGTTTTT
34118425 ATTA-ATTTTTATAAATTTTATAAGTTTTT
1 ATTAGATTTTTATAAATTTTATAAGTTTTT
34118454 TAGCGATCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 20 0.74
30 7 0.26
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (30 bp):
ATTAGATTTTTATAAATTTTATAAGTTTTT
Found at i:34118453 original size:10 final size:9
Alignment explanation
Indices: 34118272--34118453 Score: 55
Period size: 10 Copynumber: 18.6 Consensus size: 9
34118262 CTTTTATGAT
34118272 TTTTTATAA
1 TTTTTATAA
34118281 TTTTTATAA
1 TTTTTATAA
*
34118290 GTTTATATAA
1 -TTTTTATAA
*
34118300 ATTTTA-ATA
1 TTTTTATA-A
*
34118309 TGTTTAATAA
1 T-TTTTATAA
*
34118319 TTGTTAATAA
1 TT-TTTATAA
*
34118329 TTTTTTTATTAT
1 --TTTTTA-TAA
*
34118341 TTTTGTAAAA
1 TTTT-TATAA
*
34118351 TTTTAAATAA
1 TTTT-TATAA
34118361 TTTTTTTTATAA
1 ---TTTTTATAA
*
34118373 TTTATTAAAA
1 TTT-TTATAA
*
34118383 TTTATTA-CA
1 TTT-TTATAA
* *
34118392 TTCATTA-GA
1 TT-TTTATAA
*
34118401 TTTTTGTAA
1 TTTTTATAA
*
34118410 TATTTATAA
1 TTTTTATAA
34118419 GTTTTTATTAA
1 -TTTTTA-TAA
34118430 TTTTTATAA
1 TTTTTATAA
*
34118439 ATTTTATAA
1 TTTTTATAA
34118448 GTTTTT
1 -TTTTT
34118454 TAGCGATCAA
Statistics
Matches: 130, Mismatches: 25, Indels: 35
0.68 0.13 0.18
Matches are distributed among these distances:
8 3 0.02
9 46 0.35
10 60 0.46
11 9 0.07
12 8 0.06
13 4 0.03
ACGTcount: A:0.35, C:0.01, G:0.04, T:0.60
Consensus pattern (9 bp):
TTTTTATAA
Found at i:34124304 original size:27 final size:25
Alignment explanation
Indices: 34124271--34124335 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 25
34124261 TGGCTCTCCG
*
34124271 GAGCTTCCCAATTAAAGGCTCTTTCAT
1 GAGCTTCCCAATTAAAGG-T-TCTCAT
* *
34124298 GAGCTTCCCGATT-ACGGTTCTCAT
1 GAGCTTCCCAATTAAAGGTTCTCAT
*
34124322 GAGCTTCCAAATTA
1 GAGCTTCCCAATTA
34124336 TATGGCTCGG
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
24 16 0.50
25 1 0.03
26 3 0.09
27 12 0.38
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.32
Consensus pattern (25 bp):
GAGCTTCCCAATTAAAGGTTCTCAT
Found at i:34126115 original size:11 final size:10
Alignment explanation
Indices: 34126091--34126123 Score: 50
Period size: 11 Copynumber: 3.3 Consensus size: 10
34126081 ACTTAAGGAT
34126091 AAAATTAATA
1 AAAATTAATA
34126101 AAAATTAATTA
1 AAAATTAA-TA
34126112 AAAATTAA-A
1 AAAATTAATA
34126121 AAA
1 AAA
34126124 GCTTAAAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 4 0.18
10 8 0.36
11 10 0.45
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (10 bp):
AAAATTAATA
Found at i:34129330 original size:20 final size:21
Alignment explanation
Indices: 34129305--34129343 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
34129295 TCCAATCCAT
*
34129305 GGATTATTTAAA-ATTTATTA
1 GGATTATATAAATATTTATTA
34129325 GGATTATATAAATATTTAT
1 GGATTATATAAATATTTAT
34129344 ATTATTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (21 bp):
GGATTATATAAATATTTATTA
Found at i:34133767 original size:14 final size:14
Alignment explanation
Indices: 34133748--34133778 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
34133738 TCAGAAAAAT
34133748 AAATTATTTTCCAA
1 AAATTATTTTCCAA
*
34133762 AAATTATTTTTCAA
1 AAATTATTTTCCAA
34133776 AAA
1 AAA
34133779 CCATTTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (14 bp):
AAATTATTTTCCAA
Found at i:34136035 original size:19 final size:19
Alignment explanation
Indices: 34136013--34136057 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
34136003 TATTTACCTA
34136013 TCATTTTAATATCATCATT
1 TCATTTTAATATCATCATT
34136032 TCATTTTAATATCATCATT
1 TCATTTTAATATCATCATT
34136051 TCATTTT
1 TCATTTT
34136058 TACCCGCTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.29, C:0.16, G:0.00, T:0.56
Consensus pattern (19 bp):
TCATTTTAATATCATCATT
Found at i:34164311 original size:4 final size:4
Alignment explanation
Indices: 34164302--34164327 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
34164292 CCATTTTTGG
34164302 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
34164328 GTGCGTTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:34168243 original size:26 final size:26
Alignment explanation
Indices: 34168212--34168284 Score: 80
Period size: 26 Copynumber: 2.8 Consensus size: 26
34168202 CCCATTATAT
34168212 GGCTCTTCTCGAGCTTCTCGATTAAA
1 GGCTCTTCTCGAGCTTCTCGATTAAA
* * *
34168238 GGCTCTT-TGTGAGCTTCTTGATTAAT
1 GGCTCTTCT-CGAGCTTCTCGATTAAA
34168264 GGCTC-TC-CGGAGCTTCTCGAT
1 GGCTCTTCTC-GAGCTTCTCGAT
34168285 ATGGCTCGCT
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
25 13 0.33
26 26 0.67
ACGTcount: A:0.15, C:0.25, G:0.23, T:0.37
Consensus pattern (26 bp):
GGCTCTTCTCGAGCTTCTCGATTAAA
Found at i:34169491 original size:28 final size:28
Alignment explanation
Indices: 34169438--34169493 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
34169428 ATAGGCAGAG
* *
34169438 ACATGGGCGTGTGTCTTAGCCGTGTGTC
1 ACATGGGCGTGTGTCATAGCCATGTGTC
*
34169466 ACATGGGCGTGTGAT-ATGGCCATGTGTC
1 ACATGGGCGTGTG-TCATAGCCATGTGTC
34169494 CTTTGCATCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 23 0.96
29 1 0.04
ACGTcount: A:0.14, C:0.20, G:0.36, T:0.30
Consensus pattern (28 bp):
ACATGGGCGTGTGTCATAGCCATGTGTC
Found at i:34179808 original size:64 final size:64
Alignment explanation
Indices: 34179700--34179820 Score: 154
Period size: 64 Copynumber: 1.9 Consensus size: 64
34179690 CCATATATCG
* * * * * *
34179700 GGACGCTCATAAAGAGCTGCGGTATGTATGCAATATATAGAGGATCCATACCTATCATACAACA
1 GGACGCTCAGAAAGAGCTGCGGTATGTATACAACACATAGAGGATCAATACCGATCATACAACA
* *
34179764 GGACGCTTAGAAAGAGCTGCGGTATGTCTACAACACAT-GCAGGATCAATACCGATCA
1 GGACGCTCAGAAAGAGCTGCGGTATGTATACAACACATAG-AGGATCAATACCGATCA
34179821 GGATGCTCGC
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
63 1 0.02
64 47 0.98
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.21
Consensus pattern (64 bp):
GGACGCTCAGAAAGAGCTGCGGTATGTATACAACACATAGAGGATCAATACCGATCATACAACA
Found at i:34180204 original size:11 final size:11
Alignment explanation
Indices: 34180188--34180218 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
34180178 TATATAAATG
34180188 AATTTAACATC
1 AATTTAACATC
34180199 AATTTAACATC
1 AATTTAACATC
34180210 AATTTAACA
1 AATTTAACA
34180219 CATTTCATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.35
Consensus pattern (11 bp):
AATTTAACATC
Found at i:34191290 original size:27 final size:28
Alignment explanation
Indices: 34191216--34191290 Score: 64
Period size: 28 Copynumber: 2.7 Consensus size: 28
34191206 TTTAATTATG
*
34191216 TTTTAACTA-TTATTTTTATATATAAAA
1 TTTTAATTATTTATTTTTATATATAAAA
* *** * *
34191243 TTTTAATAATGCCTTTATTATAT-TGATA
1 TTTTAATTATTTATTT-TTATATATAAAA
34191271 TTTTAATTATTTATTTTTAT
1 TTTTAATTATTTATTTTTAT
34191291 CAAATTATAA
Statistics
Matches: 35, Mismatches: 11, Indels: 4
0.70 0.22 0.08
Matches are distributed among these distances:
27 11 0.31
28 18 0.51
29 6 0.17
ACGTcount: A:0.33, C:0.04, G:0.03, T:0.60
Consensus pattern (28 bp):
TTTTAATTATTTATTTTTATATATAAAA
Found at i:34213435 original size:6 final size:6
Alignment explanation
Indices: 34213420--34213448 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
34213410 TATTTTTTAT
34213420 AAAA-A AAAAGA AAAAGA AAAAGA AAAAGA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
34213449 GAAACCCTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.17
6 19 0.83
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:34224716 original size:11 final size:12
Alignment explanation
Indices: 34224688--34224721 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
34224678 GCCCAAACGT
34224688 CGAAATTTTTGAA
1 CGAAATTTTT-AA
34224701 CGAAATTTTT-A
1 CGAAATTTTTAA
34224712 CGAAATTTTT
1 CGAAATTTTT
34224722 CCGTAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.52
13 10 0.48
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.44
Consensus pattern (12 bp):
CGAAATTTTTAA
Found at i:34228010 original size:18 final size:16
Alignment explanation
Indices: 34227989--34228032 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
34227979 TATGTGTTAC
34227989 AAAATTACATTATATATA
1 AAAATTACA-TA-ATATA
*
34228007 AAAATAACATAATATA
1 AAAATTACATAATATA
34228023 AAACATTACA
1 AAA-ATTACA
34228033 AACTTGAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 8 0.35
17 7 0.30
18 8 0.35
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (16 bp):
AAAATTACATAATATA
Found at i:34240473 original size:17 final size:16
Alignment explanation
Indices: 34240453--34240493 Score: 50
Period size: 14 Copynumber: 2.6 Consensus size: 16
34240443 TTTTATCAAA
34240453 ATTAATTAATAAATAAT
1 ATTAATTAATAAA-AAT
34240470 ATTAA--AATAAAAAT
1 ATTAATTAATAAAAAT
34240484 ATTAGATTAA
1 ATTA-ATTAA
34240494 ATTATTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
14 7 0.33
15 7 0.33
17 7 0.33
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (16 bp):
ATTAATTAATAAAAAT
Found at i:34240951 original size:9 final size:9
Alignment explanation
Indices: 34240937--34241069 Score: 50
Period size: 9 Copynumber: 13.8 Consensus size: 9
34240927 TTTTTCTTTA
34240937 ATAAAAATT
1 ATAAAAATT
*
34240946 ATAAAAAAAT
1 AT-AAAAATT
* *
34240956 ATATAAACTA
1 ATA-AAAATT
*
34240966 AAAAAAATT
1 ATAAAAATT
34240975 ATAAAACATT
1 ATAAAA-ATT
*
34240985 ATAAAGATT
1 ATAAAAATT
*
34240994 CATGAAAAAAAT
1 -AT--AAAAATT
**
34241006 ATAAATTTT
1 ATAAAAATT
* **
34241015 ATATATTTT
1 ATAAAAATT
*
34241024 ATAAAAATC
1 ATAAAAATT
*
34241033 ACAAAAACTT
1 ATAAAAA-TT
*
34241043 ATAAAAAAAT
1 AT-AAAAATT
*
34241053 CTAATAAATT
1 ATAA-AAATT
34241063 ATAAAAA
1 ATAAAAA
34241070 GTCATCAAAA
Statistics
Matches: 89, Mismatches: 26, Indels: 18
0.67 0.20 0.14
Matches are distributed among these distances:
9 43 0.48
10 34 0.38
11 7 0.08
12 5 0.06
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.30
Consensus pattern (9 bp):
ATAAAAATT
Found at i:34240985 original size:10 final size:10
Alignment explanation
Indices: 34240939--34240989 Score: 50
Period size: 10 Copynumber: 5.2 Consensus size: 10
34240929 TTTCTTTAAT
34240939 AAAAATTATA
1 AAAAATTATA
*
34240949 AAAAAATAT-
1 AAAAATTATA
* * *
34240958 ATAAACTAAA
1 AAAAATTATA
34240968 AAAAATTATA
1 AAAAATTATA
*
34240978 AAACATTATA
1 AAAAATTATA
34240988 AA
1 AA
34240990 GATTCATGAA
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
9 6 0.19
10 26 0.81
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (10 bp):
AAAAATTATA
Found at i:34241049 original size:20 final size:19
Alignment explanation
Indices: 34241022--34241081 Score: 52
Period size: 19 Copynumber: 3.1 Consensus size: 19
34241012 TTTATATATT
34241022 TTAT-AAAAATCACAAAAA
1 TTATAAAAAATCACAAAAA
*
34241040 CTTATAAAAAAATCTA-ATAAA
1 -TTAT-AAAAAATC-ACAAAAA
*
34241061 TTATAAAAAGTCATCAAAAA
1 TTATAAAAAATCA-CAAAAA
34241081 T
1 T
34241082 AGTTATCAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
18 1 0.03
19 11 0.33
20 9 0.27
21 11 0.33
22 1 0.03
ACGTcount: A:0.62, C:0.10, G:0.02, T:0.27
Consensus pattern (19 bp):
TTATAAAAAATCACAAAAA
Found at i:34241052 original size:21 final size:20
Alignment explanation
Indices: 34241026--34241069 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
34241016 TATATTTTAT
34241026 AAAAATC-ACAAAAACTTATAA
1 AAAAATCTA-AAAAA-TTATAA
*
34241047 AAAAATCTAATAAATTATAA
1 AAAAATCTAAAAAATTATAA
34241067 AAA
1 AAA
34241070 GTCATCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 9 0.43
21 11 0.52
22 1 0.05
ACGTcount: A:0.68, C:0.09, G:0.00, T:0.23
Consensus pattern (20 bp):
AAAAATCTAAAAAATTATAA
Found at i:34241474 original size:12 final size:12
Alignment explanation
Indices: 34241457--34241504 Score: 50
Period size: 11 Copynumber: 4.3 Consensus size: 12
34241447 ATATAAATGC
34241457 TTTTTTATATAA
1 TTTTTTATATAA
34241469 TTTTTTAT-T-A
1 TTTTTTATATAA
* *
34241479 GTTTTTA-ACAA
1 TTTTTTATATAA
34241490 TTTTTT-TATAA
1 TTTTTTATATAA
34241501 TTTT
1 TTTT
34241505 AAGTTGCTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
10 7 0.24
11 14 0.48
12 8 0.28
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (12 bp):
TTTTTTATATAA
Found at i:34245358 original size:49 final size:49
Alignment explanation
Indices: 34245250--34245358 Score: 123
Period size: 49 Copynumber: 2.2 Consensus size: 49
34245240 ATTATTTTCA
* * *
34245250 GGCAACTCGGGGTGACATATTAATCAGATCTAGAAAACCATCATTGTTG
1 GGCAACTCGGGCTGAAAAATTAATCAGATCTAGAAAACCATCATTGTTG
* * *
34245299 GGTAACTCGGGCTGAAAAATTAATTAGAT-TGAGAAAATCATCATTGTCT-
1 GGCAACTCGGGCTGAAAAATTAATCAGATCT-AGAAAACCATCATTGT-TG
*
34245348 GGCAATTCGGG
1 GGCAACTCGGG
34245359 ATGGTAATAT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
48 1 0.02
49 48 0.96
50 1 0.02
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.28
Consensus pattern (49 bp):
GGCAACTCGGGCTGAAAAATTAATCAGATCTAGAAAACCATCATTGTTG
Found at i:34256212 original size:10 final size:10
Alignment explanation
Indices: 34256199--34256223 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
34256189 ATATGGTTTA
34256199 AAATGGCATG
1 AAATGGCATG
34256209 AAATGGCATG
1 AAATGGCATG
34256219 AAATG
1 AAATG
34256224 TTGTAATTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.44, C:0.08, G:0.28, T:0.20
Consensus pattern (10 bp):
AAATGGCATG
Found at i:34259718 original size:19 final size:20
Alignment explanation
Indices: 34259681--34259721 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
34259671 TACAACACAA
34259681 TTCAATTTCATATTAAATAT
1 TTCAATTTCATATTAAATAT
* *
34259701 TTCAATTT-TTATTCAATAT
1 TTCAATTTCATATTAAATAT
34259720 TT
1 TT
34259722 GCCTAAATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.34, C:0.10, G:0.00, T:0.56
Consensus pattern (20 bp):
TTCAATTTCATATTAAATAT
Found at i:34260143 original size:6 final size:6
Alignment explanation
Indices: 34260132--34260160 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
34260122 GGTTCTTCTT
34260132 TCTTTC TCTTTC TCTTTC TCTTTC TCTTT
1 TCTTTC TCTTTC TCTTTC TCTTTC TCTTT
34260161 TTCCTTCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (6 bp):
TCTTTC
Found at i:34260168 original size:18 final size:18
Alignment explanation
Indices: 34260132--34260168 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
34260122 GGTTCTTCTT
*
34260132 TCTTTCTCTTTCTCTTTC
1 TCTTTCTCTTTCTCCTTC
*
34260150 TCTTTCTCTTTTTCCTTC
1 TCTTTCTCTTTCTCCTTC
34260168 T
1 T
34260169 TTCTGTTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (18 bp):
TCTTTCTCTTTCTCCTTC
Found at i:34261540 original size:74 final size:75
Alignment explanation
Indices: 34261441--34261591 Score: 295
Period size: 74 Copynumber: 2.0 Consensus size: 75
34261431 GTCAAAAAAA
34261441 AATCTTAAAACTTATAATTTATTATTTAAAAGTATGTAAAATTAAATTATTATTATTATTATGCA
1 AATCTTAAAACTTATAATTTATTATTTAAAAGTATGTAAAATTAAATTATTATTATTATTATGCA
34261506 AAAAAATTTT
66 AAAAAATTTT
34261516 AATCTTAAAA-TTATAATTTATTATTTAAAAGTATGTAAAATTAAATTATTATTATTATTATGCA
1 AATCTTAAAACTTATAATTTATTATTTAAAAGTATGTAAAATTAAATTATTATTATTATTATGCA
34261580 AAAAAATTTT
66 AAAAAATTTT
34261590 AA
1 AA
34261592 AATGTAATCA
Statistics
Matches: 76, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
74 66 0.87
75 10 0.13
ACGTcount: A:0.48, C:0.03, G:0.04, T:0.45
Consensus pattern (75 bp):
AATCTTAAAACTTATAATTTATTATTTAAAAGTATGTAAAATTAAATTATTATTATTATTATGCA
AAAAAATTTT
Found at i:34261617 original size:74 final size:73
Alignment explanation
Indices: 34261454--34261610 Score: 237
Period size: 74 Copynumber: 2.2 Consensus size: 73
34261444 CTTAAAACTT
* *
34261454 ATAATTTATTATTTAAAAGTATGTAAAATTAAATTATTATTATTATTATGCAAAAAAATTTTAAT
1 ATAATTTATCATTTAAAAGTATGTAAAATTAAATTATTATTATTATTATGCAAAAAAATTTTAAA
* *
34261519 CTTAAAATT
66 ATT-AAATC
*
34261528 ATAATTTATTATTTAAAAGTATGTAAAATTAAATTATTATTATTATTATGCAAAAAAATTTTAAA
1 ATAATTTATCATTTAAAAGTATGTAAAATTAAATTATTATTATTATTATGCAAAAAAATTTTAAA
34261593 ATGT-AATC
66 AT-TAAATC
34261601 A-AATTTATCA
1 ATAATTTATCA
34261611 CATTTAATCC
Statistics
Matches: 78, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
72 8 0.10
73 4 0.05
74 65 0.83
75 1 0.01
ACGTcount: A:0.48, C:0.03, G:0.04, T:0.45
Consensus pattern (73 bp):
ATAATTTATCATTTAAAAGTATGTAAAATTAAATTATTATTATTATTATGCAAAAAAATTTTAAA
ATTAAATC
Found at i:34268833 original size:98 final size:99
Alignment explanation
Indices: 34268663--34268857 Score: 383
Period size: 98 Copynumber: 2.0 Consensus size: 99
34268653 TTATTATCAT
34268663 TAGACTTGTCCAAAAGTTGAGTAGCCCGCCCATCTCAATAGCTCCGGTCTAAATTTAATTTAAAT
1 TAGACTTGTCCAAAAGTTGAGTAGCCCGCCCATCTCAATAGCTCCGGTCTAAATTTAATTTAAAT
34268728 AATAATAAAAATTTAAATTTAATTATAAAATACA
66 AATAATAAAAATTTAAATTTAATTATAAAATACA
34268762 TAGACTTGTCC-AAAGTTGAGTAGCCCGCCCATCTCAATAGCTCCGGTCTAAATTTAATTTAAAT
1 TAGACTTGTCCAAAAGTTGAGTAGCCCGCCCATCTCAATAGCTCCGGTCTAAATTTAATTTAAAT
34268826 AATAATAAAAATTTAAATTTAATTATAAAATA
66 AATAATAAAAATTTAAATTTAATTATAAAATA
34268858 AATAATATTA
Statistics
Matches: 96, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
98 85 0.89
99 11 0.11
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.33
Consensus pattern (99 bp):
TAGACTTGTCCAAAAGTTGAGTAGCCCGCCCATCTCAATAGCTCCGGTCTAAATTTAATTTAAAT
AATAATAAAAATTTAAATTTAATTATAAAATACA
Found at i:34268860 original size:23 final size:24
Alignment explanation
Indices: 34268810--34268860 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
34268800 AGCTCCGGTC
34268810 TAAATTTAATTTAAATAATAATAA
1 TAAATTTAATTTAAATAATAATAA
*
34268834 -AAATTTAAATTT-AATTATAA-AA
1 TAAATTT-AATTTAAATAATAATAA
34268856 TAAAT
1 TAAAT
34268861 AATATTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
22 2 0.08
23 17 0.71
24 5 0.21
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (24 bp):
TAAATTTAATTTAAATAATAATAA
Found at i:34272517 original size:20 final size:18
Alignment explanation
Indices: 34272492--34272540 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 18
34272482 CGAGCATAAA
34272492 TTAAAAAAATAAAAATATTT
1 TTAAAAAAATAAAAA-A-TT
34272512 TTAAAAATAA-AAAAAATT
1 TTAAAAA-AATAAAAAATT
*
34272530 ATAAAAAAATA
1 TTAAAAAAATA
34272541 TAATTTTTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 2 0.08
18 9 0.35
19 1 0.04
20 12 0.46
21 2 0.08
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
TTAAAAAAATAAAAAATT
Found at i:34272534 original size:18 final size:18
Alignment explanation
Indices: 34272489--34272536 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
34272479 TAACGAGCAT
*
34272489 AAATTAAAAAAATAAAAA
1 AAATTATAAAAATAAAAA
* * *
34272507 TATTTTTAAAAATAAAAA
1 AAATTATAAAAATAAAAA
34272525 AAATTATAAAAA
1 AAATTATAAAAA
34272537 AATATAATTT
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (18 bp):
AAATTATAAAAATAAAAA
Found at i:34272536 original size:19 final size:18
Alignment explanation
Indices: 34272489--34272537 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
34272479 TAACGAGCAT
34272489 AAATTA-AAAAAATAAAA
1 AAATTATAAAAAATAAAA
* * *
34272506 ATATTTTTAAAAATAAAAA
1 AAATTATAAAAAAT-AAAA
34272525 AAATTATAAAAAA
1 AAATTATAAAAAA
34272538 ATATAATTTT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
17 4 0.17
18 6 0.25
19 14 0.58
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (18 bp):
AAATTATAAAAAATAAAA
Found at i:34276122 original size:31 final size:29
Alignment explanation
Indices: 34276087--34276144 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
34276077 CAAAACTTTG
34276087 TATTATAGAAACTGGATCAAACTAGTCACGC
1 TATTAT-GAAA-TGGATCAAACTAGTCACGC
* **
34276118 TATTATTAAATGGATCAATTTAGTCAC
1 TATTATGAAATGGATCAAACTAGTCAC
34276145 TATACTATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 15 0.62
30 3 0.12
31 6 0.25
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.33
Consensus pattern (29 bp):
TATTATGAAATGGATCAAACTAGTCACGC
Found at i:34276700 original size:25 final size:24
Alignment explanation
Indices: 34276650--34276700 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
34276640 TACCTAATTT
* *
34276650 TTTATTTTTAATTTAATATTATAA
1 TTTATTTTTAATATAATATTAAAA
34276674 TTTATTTTCTAATATAAT-TCTAAAA
1 TTTATTTT-TAATATAATAT-TAAAA
34276699 TT
1 TT
34276701 CTATATTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 9 0.39
25 14 0.61
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (24 bp):
TTTATTTTTAATATAATATTAAAA
Found at i:34278344 original size:9 final size:9
Alignment explanation
Indices: 34278330--34278396 Score: 82
Period size: 9 Copynumber: 7.4 Consensus size: 9
34278320 TTTGGTTAAA
*
34278330 AATTAACAG
1 AATTAACCG
34278339 AATTAACCG
1 AATTAACCG
*
34278348 AATTACCCG
1 AATTAACCG
34278357 AATTAACCG
1 AATTAACCG
*
34278366 AATTAATCG
1 AATTAACCG
*
34278375 GATT-ACCTG
1 AATTAACC-G
34278384 AATTAACCG
1 AATTAACCG
34278393 AATT
1 AATT
34278397 GAATCACTAT
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
8 2 0.04
9 44 0.90
10 3 0.06
ACGTcount: A:0.42, C:0.19, G:0.12, T:0.27
Consensus pattern (9 bp):
AATTAACCG
Found at i:34278368 original size:27 final size:27
Alignment explanation
Indices: 34278330--34278396 Score: 98
Period size: 27 Copynumber: 2.5 Consensus size: 27
34278320 TTTGGTTAAA
*
34278330 AATTAACAGAATTAACCGAATTACCCG
1 AATTAACCGAATTAACCGAATTACCCG
* * *
34278357 AATTAACCGAATTAATCGGATTACCTG
1 AATTAACCGAATTAACCGAATTACCCG
34278384 AATTAACCGAATT
1 AATTAACCGAATT
34278397 GAATCACTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.42, C:0.19, G:0.12, T:0.27
Consensus pattern (27 bp):
AATTAACCGAATTAACCGAATTACCCG
Found at i:34288187 original size:19 final size:18
Alignment explanation
Indices: 34288123--34288186 Score: 60
Period size: 18 Copynumber: 3.4 Consensus size: 18
34288113 AATTAGAAAT
*
34288123 AAATTTATAATAAATA-AT
1 AAATTTATAA-AAATATAA
34288141 AAATTT-TAAAAATATTATTA
1 AAATTTATAAAAATA-TA--A
34288161 AAATTTAATAAAAATATAA
1 AAATTT-ATAAAAATATAA
34288180 AAATTTA
1 AAATTTA
34288187 AATTTTATTA
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
16 5 0.13
17 3 0.08
18 8 0.21
19 7 0.18
20 6 0.15
21 2 0.05
22 8 0.21
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
AAATTTATAAAAATATAA
Found at i:34288204 original size:45 final size:44
Alignment explanation
Indices: 34288140--34288224 Score: 107
Period size: 45 Copynumber: 1.9 Consensus size: 44
34288130 TAATAAATAA
34288140 TAAATTTTAAAAATATTATTAAAATTTAATAAAAATATAAAAATT
1 TAAATTTTAAAAATATTATTAAAATTTAATAAAAAT-TAAAAATT
** * ** *
34288185 TAAATTTTATTAATTTTATTAATTTTTTATAAAAATTAAA
1 TAAATTTTAAAAATATTATTAAAATTTAATAAAAATTAAA
34288225 TTGGAAAGTT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
44 4 0.12
45 30 0.88
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (44 bp):
TAAATTTTAAAAATATTATTAAAATTTAATAAAAATTAAAAATT
Found at i:34291169 original size:25 final size:23
Alignment explanation
Indices: 34291143--34291235 Score: 118
Period size: 22 Copynumber: 4.0 Consensus size: 23
34291133 CCTTTCTGAT
* *
34291143 TATTAGCACGTTAGTGCTCTCTAAT
1 TATTAGCACATTAGTGCTCTCT--G
34291168 TATTAGCACATTAGTGCTCTCTG
1 TATTAGCACATTAGTGCTCTCTG
*
34291191 T-TTAGCACATTTGTGCTCTCTG
1 TATTAGCACATTAGTGCTCTCTG
*
34291213 TA-TAGCACTTTAGTGCTCTCTG
1 TATTAGCACATTAGTGCTCTCTG
34291235 T
1 T
34291236 TTAATAGTGC
Statistics
Matches: 62, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
22 40 0.65
23 1 0.02
25 21 0.34
ACGTcount: A:0.19, C:0.22, G:0.17, T:0.42
Consensus pattern (23 bp):
TATTAGCACATTAGTGCTCTCTG
Found at i:34294474 original size:20 final size:19
Alignment explanation
Indices: 34294465--34294502 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
34294455 CATAATTTTC
34294465 AAAAATTCAAAATATTTAT
1 AAAAATTCAAAATATTTAT
*
34294484 AAAAATTCCAAA-ATTTAT
1 AAAAATTCAAAATATTTAT
34294502 A
1 A
34294503 TTTTTAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAAATTCAAAATATTTAT
Found at i:34294481 original size:19 final size:20
Alignment explanation
Indices: 34294445--34294497 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
34294435 AAATTACAAA
* *
34294445 AAAAAATCAACATAATTT-T
1 AAAAATTCAAAATAATTTAT
34294464 CAAAAATTCAAAAT-ATTTAT
1 -AAAAATTCAAAATAATTTAT
34294484 AAAAATTCCAAAAT
1 AAAAATT-CAAAAT
34294498 TTATATTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 11 0.38
20 18 0.62
ACGTcount: A:0.58, C:0.11, G:0.00, T:0.30
Consensus pattern (20 bp):
AAAAATTCAAAATAATTTAT
Found at i:34305869 original size:175 final size:174
Alignment explanation
Indices: 34305547--34305901 Score: 597
Period size: 175 Copynumber: 2.0 Consensus size: 174
34305537 CAAAATTGAG
*
34305547 CAAATG-GTGCATCAAGTATTTTAACGAAATTGCGGCAACAAATTCTTGATTGAAGCAAGACACC
1 CAAATGAGTGCATCAAGTATTTTAACGAAATTGCAGCAACAAATTCTTGATTGAAGCAAGACACC
* * *
34305611 AACATATTAGACAGCCAGGGAGAAAACAATCACCTAAATGTTGTTACATTTTCACATGAAATTAC
66 AACATATTAGACAGCCACGGAGAAAACAATCACCCAAATGTTGTTACATCTTCACATGAAATTAC
*
34305676 AGCACACCCAAGAAGGATAGAGAGACCATGGTGATTAGCTCTCA
131 AGCACACCCAAAAAGGATAGAGAGACCATGGTGATTAGCTCTCA
* *
34305720 CAAATGAGTGCATCAAGTATTTTAACGAAATTGTAGCAACAAATTCTTGTTTGAAGCAAGACA-C
1 CAAATGAGTGCATCAAGTATTTTAACGAAATTGCAGCAACAAATTCTTGATTGAAGCAAGACACC
* *
34305784 AAGCATATTTAGAGAGCCACGGTGAAAACAATCACCCAAATGTTGTTACATCTTCACATGAAATT
66 AA-CATA-TTAGACAGCCACGGAGAAAACAATCACCCAAATGTTGTTACATCTTCACATGAAATT
34305849 ACAGCACACCCAAAAAGGATAGAGAGACCATGGTGATTAGCTCTCA
129 ACAGCACACCCAAAAAGGATAGAGAGACCATGGTGATTAGCTCTCA
34305895 CAAATGA
1 CAAATGA
34305902 AGCAAATTGC
Statistics
Matches: 170, Mismatches: 9, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
173 9 0.05
174 57 0.34
175 104 0.61
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.23
Consensus pattern (174 bp):
CAAATGAGTGCATCAAGTATTTTAACGAAATTGCAGCAACAAATTCTTGATTGAAGCAAGACACC
AACATATTAGACAGCCACGGAGAAAACAATCACCCAAATGTTGTTACATCTTCACATGAAATTAC
AGCACACCCAAAAAGGATAGAGAGACCATGGTGATTAGCTCTCA
Found at i:34311590 original size:7 final size:7
Alignment explanation
Indices: 34311580--34311612 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
34311570 AAAATAAAAA
34311580 TAAATTG
1 TAAATTG
34311587 TAAATTG
1 TAAATTG
34311594 TAAATTG
1 TAAATTG
34311601 TAAATTG
1 TAAATTG
34311608 TAAAT
1 TAAAT
34311613 AAAATGAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.42
Consensus pattern (7 bp):
TAAATTG
Found at i:34315647 original size:21 final size:21
Alignment explanation
Indices: 34315600--34315659 Score: 54
Period size: 19 Copynumber: 3.0 Consensus size: 21
34315590 ATTTAATATT
* *
34315600 AATATTAATATA-AATTTTAA
1 AATATTATTATATATTTTTAA
*
34315620 ATTTATTATTATATATTTTTAA
1 A-ATATTATTATATATTTTTAA
*
34315642 AATA-T-TTATGTATTTTTA
1 AATATTATTATATATTTTTA
34315660 TATATTTCTT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
19 12 0.36
20 2 0.06
21 11 0.33
22 8 0.24
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
AATATTATTATATATTTTTAA
Found at i:34320550 original size:97 final size:97
Alignment explanation
Indices: 34320424--34320727 Score: 520
Period size: 97 Copynumber: 3.1 Consensus size: 97
34320414 TACTAAGGTT
34320424 TTTTTTTTTTTCCACAAAGTAAACAAATGACCGTGGAGATATAGATAAAATGGCCATTTTTAGAG
1 TTTTTTTTTTTCCACAAAGTAAACAAATGACCGTGGAGATATAGATAAAATGGCCATTTTTAGAG
*
34320489 TCTTTTCTCAAAATAAATTGCAAAGAAGACGA
66 TCTTTTCTCAAAATAAATTGCAAAGACGACGA
**
34320521 TTTTTTTTTCCCCACAAAGTAAACAAATGACCGTGGAGATATAGATAAAATGGCCATTTTTA-AG
1 TTTTTTTTTTTCCACAAAGTAAACAAATGACCGTGGAGATATAGATAAAATGGCCATTTTTAGAG
34320585 TCTTTTCTCAAAATAAATTGCAAAGACGACGA
66 TCTTTTCTCAAAATAAATTGCAAAGACGACGA
* *
34320617 TGTTTTTTTTTTTTTCCACAAAATAAACAAATGACCGTGGAGATAGAGATAAAATGGCCATTTTT
1 ----TTTTTTTTTTTCCACAAAGTAAACAAATGACCGTGGAGATATAGATAAAATGGCCATTTTT
34320682 AGAGTCTTTTCTCAAAATAAATTGCAAAGACGACGA
62 AGAGTCTTTTCTCAAAATAAATTGCAAAGACGACGA
34320718 TTTTTTTTTT
1 TTTTTTTTTT
34320728 CTAAAGTAAT
Statistics
Matches: 195, Mismatches: 7, Indels: 10
0.92 0.03 0.05
Matches are distributed among these distances:
96 33 0.17
97 70 0.36
100 58 0.30
101 34 0.17
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (97 bp):
TTTTTTTTTTTCCACAAAGTAAACAAATGACCGTGGAGATATAGATAAAATGGCCATTTTTAGAG
TCTTTTCTCAAAATAAATTGCAAAGACGACGA
Found at i:34320679 original size:100 final size:100
Alignment explanation
Indices: 34320422--34320727 Score: 530
Period size: 100 Copynumber: 3.1 Consensus size: 100
34320412 TATACTAAGG
34320422 TTTTTTTTTTTTTCCACAAAGTAAACAAATGACCGTGGAGATATAGATAAAATGGCCATTTTTAG
1 TTTTTTTTTTTTTCCACAAAGTAAACAAATGACCGTGGAGATATAGATAAAATGGCCATTTTTAG
*
34320487 AGTCTTTTCTCAAAATAAATTGCAAAGAAGACGA-
66 AGTCTTTTCTCAAAATAAATTGCAAAGACGACGAT
**
34320521 --TTTTTTTTTCCCCACAAAGTAAACAAATGACCGTGGAGATATAGATAAAATGGCCATTTTTA-
1 TTTTTTTTTTTTTCCACAAAGTAAACAAATGACCGTGGAGATATAGATAAAATGGCCATTTTTAG
34320583 AGTCTTTTCTCAAAATAAATTGCAAAGACGACGAT
66 AGTCTTTTCTCAAAATAAATTGCAAAGACGACGAT
* *
34320618 GTTTTTTTTTTTTTCCACAAAATAAACAAATGACCGTGGAGATAGAGATAAAATGGCCATTTTTA
1 -TTTTTTTTTTTTTCCACAAAGTAAACAAATGACCGTGGAGATATAGATAAAATGGCCATTTTTA
34320683 GAGTCTTTTCTCAAAATAAATTGCAAAGACGACGAT
65 GAGTCTTTTCTCAAAATAAATTGCAAAGACGACGAT
34320719 TTTTTTTTT
1 TTTTTTTTT
34320728 CTAAAGTAAT
Statistics
Matches: 195, Mismatches: 7, Indels: 9
0.92 0.03 0.04
Matches are distributed among these distances:
96 33 0.17
97 60 0.31
100 67 0.34
101 35 0.18
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (100 bp):
TTTTTTTTTTTTTCCACAAAGTAAACAAATGACCGTGGAGATATAGATAAAATGGCCATTTTTAG
AGTCTTTTCTCAAAATAAATTGCAAAGACGACGAT
Found at i:34321742 original size:25 final size:25
Alignment explanation
Indices: 34321690--34321739 Score: 77
Period size: 24 Copynumber: 2.0 Consensus size: 25
34321680 TCTTAAAAGA
34321690 TAATATTATAAATATATATGTTTTT
1 TAATATTATAAATATATATGTTTTT
34321715 TAAT-TTATAAATATA-ATGATTTTT
1 TAATATTATAAATATATATG-TTTTT
34321739 T
1 T
34321740 TAAATATAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 3 0.12
24 17 0.71
25 4 0.17
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (25 bp):
TAATATTATAAATATATATGTTTTT
Found at i:34321747 original size:24 final size:24
Alignment explanation
Indices: 34321690--34321747 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 24
34321680 TCTTAAAAGA
34321690 TAATATTATAAATATATATGTTTTT
1 TAATA-TATAAATATATATGTTTTT
*
34321715 TAATTTATAAATATA-ATGATTTTTT
1 TAATATATAAATATATATG--TTTTT
34321740 TAA-ATATA
1 TAATATATA
34321748 GAATGAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
23 3 0.10
24 14 0.48
25 12 0.41
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (24 bp):
TAATATATAAATATATATGTTTTT
Found at i:34326232 original size:13 final size:13
Alignment explanation
Indices: 34326214--34326256 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
34326204 ATCGAACAAT
34326214 AATAAAATATAAA
1 AATAAAATATAAA
34326227 AATAAAAT-TAATA
1 AATAAAATATAA-A
34326240 AATTATAAATATAAA
1 AA-TA-AAATATAAA
34326255 AA
1 AA
34326257 CTCATTTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 3 0.12
13 11 0.42
14 2 0.08
15 7 0.27
16 3 0.12
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AATAAAATATAAA
Found at i:34326238 original size:22 final size:22
Alignment explanation
Indices: 34326213--34326255 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
34326203 AATCGAACAA
34326213 TAATAAAATATAAAAATAAAAT
1 TAATAAAATATAAAAATAAAAT
* *
34326235 TAATAAATTATAAATATAAAA
1 TAATAAAATATAAAAATAAAA
34326256 ACTCATTTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (22 bp):
TAATAAAATATAAAAATAAAAT
Found at i:34329363 original size:72 final size:73
Alignment explanation
Indices: 34329248--34329393 Score: 285
Period size: 72 Copynumber: 2.0 Consensus size: 73
34329238 AATTTGTGTA
34329248 TTTAAATAATTATAATTAAAAAGTATAAGTTTGAGTACATTTAAACACGTAAGTGTTTGAGAATT
1 TTTAAATAATTATAATTAAAAAGTATAAGTTTGAGTACATTTAAACACGTAAGTGTTTGAGAATT
34329313 ATAGATAT
66 ATAGATAT
34329321 TTTAAATAATT-TAATTAAAAAGTATAAGTTTGAGTACATTTAAACACGTAAGTGTTTGAGAATT
1 TTTAAATAATTATAATTAAAAAGTATAAGTTTGAGTACATTTAAACACGTAAGTGTTTGAGAATT
34329385 ATAGATAT
66 ATAGATAT
34329393 T
1 T
34329394 AGTAAATTGA
Statistics
Matches: 73, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
72 62 0.85
73 11 0.15
ACGTcount: A:0.43, C:0.04, G:0.14, T:0.39
Consensus pattern (73 bp):
TTTAAATAATTATAATTAAAAAGTATAAGTTTGAGTACATTTAAACACGTAAGTGTTTGAGAATT
ATAGATAT
Found at i:34332907 original size:25 final size:25
Alignment explanation
Indices: 34332855--34332907 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
34332845 TTTTCTTTTC
* **
34332855 TTTCCTTTTCTTTTTTGGATTAGGT
1 TTTCCTTTTCTTTTTAGGATTACAT
34332880 TTTCTCTTTTCTTTTTAGGA-TACAT
1 TTTC-CTTTTCTTTTTAGGATTACAT
34332905 TTT
1 TTT
34332908 ATTTTTGCTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 10 0.42
26 14 0.58
ACGTcount: A:0.11, C:0.13, G:0.11, T:0.64
Consensus pattern (25 bp):
TTTCCTTTTCTTTTTAGGATTACAT
Found at i:34334987 original size:58 final size:60
Alignment explanation
Indices: 34334898--34335013 Score: 191
Period size: 58 Copynumber: 2.0 Consensus size: 60
34334888 TTGCATTTTG
*
34334898 ACCCCTAAAATTTTCTAAAATTGCATTTTGACCCCTAAACTTTCTCAAAATTACATTTCA
1 ACCCCTAAAATTTTCTAAAATTACATTTTGACCCCTAAACTTTCTCAAAATTACATTTCA
* *
34334958 ACCCCT-AAATTTT-TTAAATTACATTTTGACCCCTAAACTTTCTCGAAATTACATTT
1 ACCCCTAAAATTTTCTAAAATTACATTTTGACCCCTAAACTTTCTCAAAATTACATTT
34335014 TGACCCATAA
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
58 40 0.75
59 7 0.13
60 6 0.11
ACGTcount: A:0.34, C:0.24, G:0.03, T:0.39
Consensus pattern (60 bp):
ACCCCTAAAATTTTCTAAAATTACATTTTGACCCCTAAACTTTCTCAAAATTACATTTCA
Found at i:34335045 original size:30 final size:30
Alignment explanation
Indices: 34334891--34335038 Score: 194
Period size: 30 Copynumber: 5.0 Consensus size: 30
34334881 TTTTTTTTTG
* *
34334891 CATTTTGACCCCTAAAATTT-TCTAAAATTG
1 CATTTTGACCCCTAAACTTTCTC-AAAATTA
34334921 CATTTTGACCCCTAAACTTTCTCAAAATTA
1 CATTTTGACCCCTAAACTTTCTCAAAATTA
** **
34334951 CATTTCAACCCCTAAA-TTT-TTTAAATTA
1 CATTTTGACCCCTAAACTTTCTCAAAATTA
*
34334979 CATTTTGACCCCTAAACTTTCTCGAAATTA
1 CATTTTGACCCCTAAACTTTCTCAAAATTA
*
34335009 CATTTTGACCCATAAACTTTCTCAAAATTA
1 CATTTTGACCCCTAAACTTTCTCAAAATTA
34335039 TGTTTTGGCC
Statistics
Matches: 103, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
28 21 0.20
29 6 0.06
30 74 0.72
31 2 0.02
ACGTcount: A:0.34, C:0.24, G:0.04, T:0.39
Consensus pattern (30 bp):
CATTTTGACCCCTAAACTTTCTCAAAATTA
Found at i:34335448 original size:22 final size:21
Alignment explanation
Indices: 34335410--34335452 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
34335400 TCGGGTTTCG
*
34335410 AAATTTTTGTGTCTTCAAAAA
1 AAATTTTCGTGTCTTCAAAAA
*
34335431 AAATTTCTCGTGTTTTCAAAAA
1 AAATTT-TCGTGTCTTCAAAAA
34335453 TAAGGTAACG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.37, C:0.12, G:0.09, T:0.42
Consensus pattern (21 bp):
AAATTTTCGTGTCTTCAAAAA
Found at i:34335585 original size:18 final size:18
Alignment explanation
Indices: 34335556--34335630 Score: 109
Period size: 18 Copynumber: 4.3 Consensus size: 18
34335546 TAAAAAATAA
34335556 AAAAATT-TCGTGTTTTC
1 AAAAATTCTCGTGTTTTC
*
34335573 AAAAATTCCCGTG-TTTC
1 AAAAATTCTCGTGTTTTC
* *
34335590 AAAAATTTTCATGTTTTC
1 AAAAATTCTCGTGTTTTC
34335608 AAAAATTCTCGTGTTTTC
1 AAAAATTCTCGTGTTTTC
34335626 AAAAA
1 AAAAA
34335631 AATATTAATT
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
17 21 0.42
18 29 0.58
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (18 bp):
AAAAATTCTCGTGTTTTC
Found at i:34335605 original size:35 final size:36
Alignment explanation
Indices: 34335555--34335631 Score: 120
Period size: 35 Copynumber: 2.2 Consensus size: 36
34335545 ATAAAAAATA
*
34335555 AAAAAATTTCGTGTTTTCAAAAATTCCCGTG-TTTC
1 AAAAAATTTCATGTTTTCAAAAATTCCCGTGTTTTC
* *
34335590 AAAAATTTTCATGTTTTCAAAAATTCTCGTGTTTTC
1 AAAAAATTTCATGTTTTCAAAAATTCCCGTGTTTTC
34335626 AAAAAA
1 AAAAAA
34335632 ATATTAATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
35 28 0.76
36 9 0.24
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.40
Consensus pattern (36 bp):
AAAAAATTTCATGTTTTCAAAAATTCCCGTGTTTTC
Found at i:34341592 original size:27 final size:27
Alignment explanation
Indices: 34341553--34341606 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
34341543 TATGCTTAAA
*
34341553 AAAAACAAGACAATAAAAACA-AAAAAT
1 AAAAACAAGACAA-AAAAAAAGAAAAAT
34341580 AAAAA-AAGCACAAAAAAAAAGAAAAAT
1 AAAAACAAG-ACAAAAAAAAAGAAAAAT
34341607 CAAGATGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 9 0.38
27 15 0.62
ACGTcount: A:0.80, C:0.09, G:0.06, T:0.06
Consensus pattern (27 bp):
AAAAACAAGACAAAAAAAAAGAAAAAT
Found at i:34342578 original size:75 final size:75
Alignment explanation
Indices: 34342471--34343117 Score: 1025
Period size: 75 Copynumber: 8.6 Consensus size: 75
34342461 CACTTTCTGT
34342471 TTTTTTTTAAAATCAACTCATAATACTGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGCATTTTT
1 TTTTTTTTAAAATCAACTCATAATACTGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGCATTTTT
34342536 AATTTATGTC
66 AATTTATGTC
34342546 TTTTTTTTAAAATCAACTCATAATACTGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGCATTTTT
1 TTTTTTTTAAAATCAACTCATAATACTGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGCATTTTT
34342611 AATTTATGTC
66 AATTTATGTC
34342621 TTTTTTTTAAAATCAACTCATAATACTGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGCATTTTT
1 TTTTTTTTAAAATCAACTCATAATACTGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGCATTTTT
34342686 AATTTATGTC
66 AATTTATGTC
34342696 TTTTTTTTAAAATCAACTCATAATACTGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGCATTTTT
1 TTTTTTTTAAAATCAACTCATAATACTGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGCATTTTT
34342761 AATTTATGTC
66 AATTTATGTC
* * * *
34342771 TTTTTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGTCTCGGCTCACGCTGAGGTATTT
1 --TTTTTTTTAAAATCAACTCATAATACTGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGCATTT
34342836 TTAATTTATGTC
64 TTAATTTATGTC
* * * *
34342848 TTTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGTCTCGGCTCACGCTGAGGTATTTTT
1 TTTTTTTTAAAATCAACTCATAATACTGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGCATTTTT
34342913 AATTTATGTC
66 AATTTATGTC
* ** * *
34342923 TTTTTTTTTAAATCAACTCATAATACAAAGGTGAGTTGAGCCTCGGGTCACGCTGATGTATTTTT
1 TTTTTTTTAAAATCAACTCATAATACTGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGCATTTTT
34342988 AATTTATGT-
66 AATTTATGTC
*
34342997 TTTTTTTT-AAATCAACTCATAATACTGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTT
1 TTTTTTTTAAAATCAACTCATAATACTGAGGTGAGTTGAGCCTCGGGT--CACGCTGAGGCATTT
* *
34343061 TAAATTTCTG--
64 TTAATTTATGTC
** * * *
34343071 -TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
1 TTTTTTTTAAAATCAACTCATAATAC-TGAGGTGAGTTGAGCCTCGGG
34343118 NNNNNNNNNN
Statistics
Matches: 547, Mismatches: 19, Indels: 12
0.95 0.03 0.02
Matches are distributed among these distances:
73 42 0.08
74 23 0.04
75 411 0.75
77 71 0.13
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.39
Consensus pattern (75 bp):
TTTTTTTTAAAATCAACTCATAATACTGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGCATTTTT
AATTTATGTC
Found at i:34343052 original size:302 final size:297
Alignment explanation
Indices: 34342470--34343116 Score: 1028
Period size: 302 Copynumber: 2.2 Consensus size: 297
34342460 TCACTTTCTG
* *
34342470 TTTTTTTTTAAAATCAACTCATAATACTGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGCATTTT
1 TTTTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGCTCACGCTGAGGCATTTT
* *
34342535 TAATTTATGTCTTTTTTTTAAAATCAACTCATAATACTGAGGTGAGTTGAGCCTCGGGTCACGCT
66 TAATTTATGTCTTTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGCTCACGCT
**
34342600 GAGGCATTTTTAATTTATGTCTTTTTTTTAAAATCAACTCATAATACTGAGGTGAGTTGAGCCTC
131 GAGGCATTTTTAATTTATGTCTTTTTTTTAAAATCAACTCATAATACAAAGGTGAGTTGAGCCTC
34342665 GGGTCACGCTGAGGCATTTTTAATTTATGTCTTTTTTTTAAAATCAACTCATAATACTGAGGTGA
196 GGGTCACGCTGAGGCATTTTTAATTTATGTCTTTTTTTTAAAATCAACTCATAATACTGAGGTGA
34342730 GTTGAGCCTCGGGTCACGCTGAGGCATTTTTAATTTATGTC
261 GTTGAGCCTCGGGTCACGCTGAGGCA-TTTTAA---ATGTC
* *
34342771 TTTTTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGTCTCGGCTCACGCTGAGGTATTT
1 -TTTTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGCTCACGCTGAGGCATTT
*
34342836 TTAATTTATGTCTTTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGTCTCGGCTCACGC
65 TTAATTTATGTCTTTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGCTCACGC
* *
34342901 TGAGGTATTTTTAATTTATGTCTTTTTTTTTAAATCAACTCATAATACAAAGGTGAGTTGAGCCT
130 TGAGGCATTTTTAATTTATGTCTTTTTTTTAAAATCAACTCATAATACAAAGGTGAGTTGAGCCT
* *
34342966 CGGGTCACGCTGATGTATTTTTAATTTATGT-TTTTTTTT-AAATCAACTCATAATACTGAGGTG
195 CGGGTCACGCTGAGGCATTTTTAATTTATGTCTTTTTTTTAAAATCAACTCATAATACTGAGGTG
* *
34343029 AGTTGAGCCTCGGGTCGCACGCTGAGGTATTTTAAATTTC
260 AGTTGAGCCTCGGGT--CACGCTGAGGCATTTTAAATGTC
* ** * *
34343069 TGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG
1 TTTTTTTTTAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGG
34343117 GNNNNNNNNN
Statistics
Matches: 321, Mismatches: 21, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
297 22 0.07
298 23 0.07
300 39 0.12
301 14 0.04
302 223 0.69
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.39
Consensus pattern (297 bp):
TTTTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGCTCACGCTGAGGCATTTT
TAATTTATGTCTTTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGCTCACGCT
GAGGCATTTTTAATTTATGTCTTTTTTTTAAAATCAACTCATAATACAAAGGTGAGTTGAGCCTC
GGGTCACGCTGAGGCATTTTTAATTTATGTCTTTTTTTTAAAATCAACTCATAATACTGAGGTGA
GTTGAGCCTCGGGTCACGCTGAGGCATTTTAAATGTC
Found at i:34364335 original size:2 final size:2
Alignment explanation
Indices: 34364301--34364326 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
34364291 CTTAGAGCAC
34364301 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
34364327 GCATATATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34379678 original size:27 final size:28
Alignment explanation
Indices: 34379648--34379708 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
34379638 AAGGACTTAA
*
34379648 TTAATTT-TTA-ACTTTTTGATTAATAAC
1 TTAATTTATTACAATTTTTGATTAA-AAC
* *
34379675 TTAATTTATTACAATTTTTTATTAAAGC
1 TTAATTTATTACAATTTTTGATTAAAAC
34379703 TTAATT
1 TTAATT
34379709 AAAATTTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 7 0.24
28 11 0.38
29 11 0.38
ACGTcount: A:0.34, C:0.07, G:0.03, T:0.56
Consensus pattern (28 bp):
TTAATTTATTACAATTTTTGATTAAAAC
Found at i:34382145 original size:22 final size:24
Alignment explanation
Indices: 34382118--34382161 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
34382108 GAAAATTTTA
34382118 AGTTTTAT-ATAA-AAATTAAAAT
1 AGTTTTATCATAACAAATTAAAAT
*
34382140 AGTTTTATCATAACATATTAAA
1 AGTTTTATCATAACAAATTAAA
34382162 TTTATATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 4 0.21
24 7 0.37
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.41
Consensus pattern (24 bp):
AGTTTTATCATAACAAATTAAAAT
Found at i:34386716 original size:25 final size:25
Alignment explanation
Indices: 34386688--34386745 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
34386678 ATTTTTACAT
*
34386688 ATTTATTAAAT-TATTATGTAAATAA
1 ATTTATTAAATATATTATAT-AATAA
*
34386713 ATTTATT-TATATATTATATAATAA
1 ATTTATTAAATATATTATATAATAA
34386737 ATTTCATTA
1 ATTT-ATTA
34386746 TCTTAGTGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
24 11 0.39
25 17 0.61
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (25 bp):
ATTTATTAAATATATTATATAATAA
Found at i:34387355 original size:11 final size:11
Alignment explanation
Indices: 34387335--34387372 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
34387325 GGCCCGGCCC
34387335 ATATTAAATAT
1 ATATTAAATAT
*
34387346 ATATTTAATAT
1 ATATTAAATAT
*
34387357 ATATAAAATAT
1 ATATTAAATAT
34387368 ATATT
1 ATATT
34387373 TGATTAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
ATATTAAATAT
Found at i:34387365 original size:22 final size:22
Alignment explanation
Indices: 34387335--34387407 Score: 74
Period size: 22 Copynumber: 3.1 Consensus size: 22
34387325 GGCCCGGCCC
*
34387335 ATATTAAATATATATTTAATAT
1 ATATAAAATATATATTTAATAT
* *
34387357 ATATAAAATATATATTTGATTAA
1 ATATAAAATATATATTT-AATAT
*
34387380 AAATAAAAATATATATTTTTAATAT
1 ATAT-AAAATATATA--TTTAATAT
34387405 ATA
1 ATA
34387408 ATTCGGGCCG
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
22 16 0.40
23 6 0.15
24 10 0.25
25 5 0.12
26 3 0.08
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.45
Consensus pattern (22 bp):
ATATAAAATATATATTTAATAT
Done.