Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032252.1 Gossypioides kirkii chromosome KI_10
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: 47257441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3600 characters in sequence are not A, C, G, or T
File 76 of 163
Found at i:20056340 original size:20 final size:20
Alignment explanation
Indices: 20056315--20056363 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
20056305 GGAAAGTGAT
20056315 ATTCTTTTTAAAAGAATAAA
1 ATTCTTTTTAAAAGAATAAA
** *
20056335 ATTCTTTTGGAAAGAATATA
1 ATTCTTTTTAAAAGAATAAA
20056355 ATTCTTTTT
1 ATTCTTTTT
20056364 CATTACTTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.39, C:0.06, G:0.08, T:0.47
Consensus pattern (20 bp):
ATTCTTTTTAAAAGAATAAA
Found at i:20058474 original size:29 final size:29
Alignment explanation
Indices: 20058397--20058458 Score: 106
Period size: 29 Copynumber: 2.1 Consensus size: 29
20058387 TAATTTTATT
* *
20058397 ATAATAAAATTAATAAGTAAATACATATA
1 ATAATAAAATTAATAAATAAATACACATA
20058426 ATAATAAAATTAATAAATAAATACACATA
1 ATAATAAAATTAATAAATAAATACACATA
20058455 ATAA
1 ATAA
20058459 ATCAATTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.29
Consensus pattern (29 bp):
ATAATAAAATTAATAAATAAATACACATA
Found at i:20063743 original size:18 final size:18
Alignment explanation
Indices: 20063720--20063755 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
20063710 ATCATAAAAT
20063720 ATTTAAATATATAGTTTA
1 ATTTAAATATATAGTTTA
* *
20063738 ATTTAAATGTATATTTTA
1 ATTTAAATATATAGTTTA
20063756 TTTTTGATGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (18 bp):
ATTTAAATATATAGTTTA
Found at i:20066131 original size:68 final size:68
Alignment explanation
Indices: 20066043--20066254 Score: 284
Period size: 68 Copynumber: 3.1 Consensus size: 68
20066033 TAATCCAAAT
* * * *
20066043 ATGGTCTTATCATCAGAATGCCATAGCCTAGCTATGGTCTTACATAAATACACTACCGTGGTCTA
1 ATGGTCTTATCATCAGAATGCCATAGCCTAGCTATGGTCTTACATATATACACTGCCATGGTCCA
20066108 ACC
66 ACC
* * * *
20066111 ATGGTCTTATCATCAAAATGCCATAGCCCAGCTATGGTCTTACCTATATGCACTGCCATGGTCCA
1 ATGGTCTTATCATCAGAATGCCATAGCCTAGCTATGGTCTTACATATATACACTGCCATGGTCCA
20066176 ACC
66 ACC
* ** * *
20066179 ATGGTCTTATCATCAGAATGTCATAG-CTGAATTATGGTCTTACATATATA-AATGCCCTGGTCC
1 ATGGTCTTATCATCAGAATGCCATAGCCT-AGCTATGGTCTTACATATATACACTGCCATGGTCC
20066242 AACC
65 AACC
20066246 ATGGTCTTA
1 ATGGTCTTA
20066255 CATTTGAATG
Statistics
Matches: 126, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
67 25 0.20
68 101 0.80
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.31
Consensus pattern (68 bp):
ATGGTCTTATCATCAGAATGCCATAGCCTAGCTATGGTCTTACATATATACACTGCCATGGTCCA
ACC
Found at i:20068075 original size:18 final size:18
Alignment explanation
Indices: 20068040--20068075 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
20068030 ATTATATAAT
*
20068040 ATTTAAATATATAGTTTA
1 ATTTAAATAAATAGTTTA
*
20068058 ATTTAAATAAATATTTTA
1 ATTTAAATAAATAGTTTA
20068076 TTTTTGGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
ATTTAAATAAATAGTTTA
Found at i:20073524 original size:22 final size:22
Alignment explanation
Indices: 20073492--20073544 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 22
20073482 TTATTTCTTC
* *
20073492 ATTTA-TTATAA-AAATGATAT
1 ATTTATTTATAAGAAAGGATAA
20073512 ATTTATGTTATAAGAAAGGATAA
1 ATTTAT-TTATAAGAAAGGATAA
20073535 ATTTATTTAT
1 ATTTATTTAT
20073545 TTATTTATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 5 0.18
22 10 0.36
23 13 0.46
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (22 bp):
ATTTATTTATAAGAAAGGATAA
Found at i:20073544 original size:4 final size:4
Alignment explanation
Indices: 20073535--20073559 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
20073525 GAAAGGATAA
20073535 ATTT ATTT ATTT ATTT ATTT ATTT A
1 ATTT ATTT ATTT ATTT ATTT ATTT A
20073560 AAAATATGAT
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:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (4 bp):
ATTT
Found at i:20073826 original size:22 final size:23
Alignment explanation
Indices: 20073798--20073849 Score: 79
Period size: 22 Copynumber: 2.3 Consensus size: 23
20073788 ATTCCATGTA
*
20073798 AAACAAGCAAATAATTTAACT-T
1 AAACAAGCAAATAACTTAACTAT
20073820 AAACAAGCAAATAACTTAACTAAT
1 AAACAAGCAAATAACTTAACT-AT
20073844 AAACAA
1 AAACAA
20073850 TAAGTAATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 20 0.74
24 7 0.26
ACGTcount: A:0.60, C:0.15, G:0.04, T:0.21
Consensus pattern (23 bp):
AAACAAGCAAATAACTTAACTAT
Found at i:20074393 original size:3 final size:3
Alignment explanation
Indices: 20074387--20074422 Score: 63
Period size: 3 Copynumber: 11.7 Consensus size: 3
20074377 TATTTTATTT
20074387 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATAA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA AT
20074423 TAAAAAAAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:20095647 original size:16 final size:17
Alignment explanation
Indices: 20095626--20095658 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
20095616 AATCTCAACC
*
20095626 CATGATCACACA-ATAA
1 CATGATAACACATATAA
20095642 CATGATAACACATATAA
1 CATGATAACACATATAA
20095659 ATTAGTCTCG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.52, C:0.21, G:0.06, T:0.21
Consensus pattern (17 bp):
CATGATAACACATATAA
Found at i:20097502 original size:39 final size:39
Alignment explanation
Indices: 20097447--20097668 Score: 275
Period size: 39 Copynumber: 5.7 Consensus size: 39
20097437 ATAACCTGGT
* * * * *
20097447 AGTGTTTACAGCGTCACTACTACTTCAGTATAGCTTTGC
1 AGTGTTTACAGTGTCACTGCCAATTCAGTATAGCATTGC
*
20097486 AGTGTTTACAGTGTCACCT-CCAATTCAGTATAGCATTGT
1 AGTGTTTACAGTGTCA-CTGCCAATTCAGTATAGCATTGC
* *
20097525 AGTGTTTACAGTGTCACTGCCAATTCAGTAAAGCATTGT
1 AGTGTTTACAGTGTCACTGCCAATTCAGTATAGCATTGC
* *
20097564 AGTGCTTATAGTGTCACTGCCAATTCAGTATAGCATTGC
1 AGTGTTTACAGTGTCACTGCCAATTCAGTATAGCATTGC
* * * * *
20097603 AGTGTTTACAATGTCACTGCCAGTTTAGTATAGTATTTC
1 AGTGTTTACAGTGTCACTGCCAATTCAGTATAGCATTGC
* *
20097642 AGTGTTTATAGTGTCACTGCCAGTTCA
1 AGTGTTTACAGTGTCACTGCCAATTCA
20097669 TGTTCAGATT
Statistics
Matches: 161, Mismatches: 20, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
38 2 0.01
39 157 0.98
40 2 0.01
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.36
Consensus pattern (39 bp):
AGTGTTTACAGTGTCACTGCCAATTCAGTATAGCATTGC
Found at i:20099661 original size:12 final size:13
Alignment explanation
Indices: 20099640--20099682 Score: 52
Period size: 12 Copynumber: 3.3 Consensus size: 13
20099630 GTCTATATGT
20099640 AAAATGTAAAATA
1 AAAATGTAAAATA
*
20099653 AAAAT-TAAATTA
1 AAAATGTAAAATA
*
20099665 GAAATGTAAAATGA
1 AAAATGTAAAAT-A
20099679 AAAA
1 AAAA
20099683 CTAATTTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
12 10 0.42
13 10 0.42
14 4 0.17
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.23
Consensus pattern (13 bp):
AAAATGTAAAATA
Found at i:20103189 original size:17 final size:15
Alignment explanation
Indices: 20103163--20103205 Score: 59
Period size: 17 Copynumber: 2.7 Consensus size: 15
20103153 TCATTTACAA
20103163 TTTATATTTTAGTAC
1 TTTATATTTTAGTAC
*
20103178 TTATATTATTTTAGTTC
1 TT-TA-TATTTTAGTAC
20103195 TTTATATTTTA
1 TTTATATTTTA
20103206 CTTTGTTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 9 0.36
16 4 0.16
17 12 0.48
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.65
Consensus pattern (15 bp):
TTTATATTTTAGTAC
Found at i:20103884 original size:13 final size:12
Alignment explanation
Indices: 20103866--20103899 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
20103856 TTCATTAGAC
20103866 TTTAGTTTTTAGT
1 TTTAGTTTTTA-T
20103879 TTTAGTTTTTAT
1 TTTAGTTTTTAT
20103891 TTTATGTTT
1 TTTA-GTTT
20103900 CGAAACGAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 5 0.25
13 15 0.75
ACGTcount: A:0.15, C:0.00, G:0.12, T:0.74
Consensus pattern (12 bp):
TTTAGTTTTTAT
Found at i:20108791 original size:21 final size:23
Alignment explanation
Indices: 20108738--20108785 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
20108728 AAAGAAGAGA
* *
20108738 AAAAT-AGTGAAAATACAAAAAG
1 AAAATGAGTAAAAACACAAAAAG
20108760 AAAATGAGTAAAAACACAAAAAG
1 AAAATGAGTAAAAACACAAAAAG
20108783 AAA
1 AAA
20108786 GAGTAAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.71, C:0.06, G:0.12, T:0.10
Consensus pattern (23 bp):
AAAATGAGTAAAAACACAAAAAG
Found at i:20112401 original size:17 final size:16
Alignment explanation
Indices: 20112379--20112414 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
20112369 GCCCAAGGAT
*
20112379 AAAATAAACCAAAATAA
1 AAAATAAA-CAAAACAA
20112396 AAAATAAACAAAACAA
1 AAAATAAACAAAACAA
20112412 AAA
1 AAA
20112415 TCCATTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.81, C:0.11, G:0.00, T:0.08
Consensus pattern (16 bp):
AAAATAAACAAAACAA
Found at i:20113996 original size:20 final size:18
Alignment explanation
Indices: 20113971--20114017 Score: 62
Period size: 16 Copynumber: 2.6 Consensus size: 18
20113961 TTTAAAATTC
20113971 CCTTTTATTTTTATTTAAAT
1 CCTTTTATTTTT-TTT-AAT
20113991 CCTTTTA--TTTTTTAAT
1 CCTTTTATTTTTTTTAAT
20114007 CCTTTTATTTT
1 CCTTTTATTTT
20114018 ATGTGTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 10 0.40
17 3 0.12
18 5 0.20
20 7 0.28
ACGTcount: A:0.19, C:0.13, G:0.00, T:0.68
Consensus pattern (18 bp):
CCTTTTATTTTTTTTAAT
Found at i:20118063 original size:27 final size:28
Alignment explanation
Indices: 20118032--20118093 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 28
20118022 ACTTAATTCA
* *
20118032 TTTATTCTCATTCAATTTGA-AAAATAT
1 TTTATTCTCATTCAAATTGACAAAACAT
**
20118059 TTTATTCTTGTTCAAATTGACAAAACAT
1 TTTATTCTCATTCAAATTGACAAAACAT
*
20118087 TCTATTC
1 TTTATTC
20118094 ATTCATAATC
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 17 0.59
28 12 0.41
ACGTcount: A:0.34, C:0.15, G:0.05, T:0.47
Consensus pattern (28 bp):
TTTATTCTCATTCAAATTGACAAAACAT
Found at i:20119608 original size:24 final size:26
Alignment explanation
Indices: 20119572--20119645 Score: 89
Period size: 26 Copynumber: 2.9 Consensus size: 26
20119562 GAAAGAAAAG
*
20119572 AAAGAGAAAAAGAAAAAAT-AATAAT-
1 AAAG-GAAAAAGAAAAAATAAAAAATA
20119597 AAAGGAAAAAGAAAAAATAAAAAATA
1 AAAGGAAAAAGAAAAAATAAAAAATA
* * *
20119623 AAAGGAAATATAAAAAAGAAAAA
1 AAAGGAAAAAGAAAAAATAAAAA
20119646 GGAGAGGTCG
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
24 14 0.33
25 9 0.21
26 20 0.47
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.09
Consensus pattern (26 bp):
AAAGGAAAAAGAAAAAATAAAAAATA
Found at i:20119625 original size:19 final size:19
Alignment explanation
Indices: 20119579--20119644 Score: 60
Period size: 19 Copynumber: 3.2 Consensus size: 19
20119569 AAGAAAGAGA
20119579 AAAAGAAAAAATAATAATAAAGG
1 AAAAGAAAAAAT-A-AA-AAA-G
*
20119602 AAAAAGAAAAAATAAAAAAT
1 -AAAAGAAAAAATAAAAAAG
* *
20119622 AAAAGGAAATATAAAAAAG
1 AAAAGAAAAAATAAAAAAG
20119641 AAAA
1 AAAA
20119645 AGGAGAGGTC
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
19 20 0.53
21 3 0.08
22 2 0.05
23 1 0.03
24 12 0.32
ACGTcount: A:0.79, C:0.00, G:0.11, T:0.11
Consensus pattern (19 bp):
AAAAGAAAAAATAAAAAAG
Found at i:20119644 original size:25 final size:25
Alignment explanation
Indices: 20119556--20119645 Score: 83
Period size: 26 Copynumber: 3.5 Consensus size: 25
20119546 AATTTCACCC
*
20119556 AAAAAAGAAAGAAAAGAAAGAGAAAAAG
1 AAAAAAGAAA-AATA-AAAG-GAAAAAG
* *
20119584 AAAAAATAATAAT-AAAGGAAAAAG
1 AAAAAAGAAAAATAAAAGGAAAAAG
* * *
20119608 AAAAAATAAAAAATAAAAGGAAATAT
1 AAAAAA-GAAAAATAAAAGGAAAAAG
20119634 AAAAAAGAAAAA
1 AAAAAAGAAAAA
20119646 GGAGAGGTCG
Statistics
Matches: 52, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
24 13 0.25
25 14 0.27
26 15 0.29
27 2 0.04
28 8 0.15
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.08
Consensus pattern (25 bp):
AAAAAAGAAAAATAAAAGGAAAAAG
Found at i:20119645 original size:20 final size:20
Alignment explanation
Indices: 20119587--20119648 Score: 63
Period size: 19 Copynumber: 3.0 Consensus size: 20
20119577 GAAAAAGAAA
* *
20119587 AAATAATAATAAAGGAAAAAGA
1 AAAT-ATAA-AAAAGAAAAAGG
* *
20119609 AAAAATAAAAAA-TAAAAGG
1 AAATATAAAAAAGAAAAAGG
20119628 AAATATAAAAAAGAAAAAGG
1 AAATATAAAAAAGAAAAAGG
20119648 A
1 A
20119649 GAGGTCGAGG
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
19 16 0.48
20 10 0.30
21 4 0.12
22 3 0.09
ACGTcount: A:0.76, C:0.00, G:0.13, T:0.11
Consensus pattern (20 bp):
AAATATAAAAAAGAAAAAGG
Found at i:20120783 original size:45 final size:45
Alignment explanation
Indices: 20120719--20121121 Score: 581
Period size: 45 Copynumber: 8.9 Consensus size: 45
20120709 CACCGTTCAG
*
20120719 TCTTTTACCCCTAGTCAAGAGGGGCAGACTGAAGCCACCATCCAA
1 TCTTTTACCCCTAGTCAAGAGGGGCAGATTGAAGCCACCATCCAA
*
20120764 TCTTTTACCCCTAGTCAAGAGGGGCAGATTGAAGCCACCGTCCAA
1 TCTTTTACCCCTAGTCAAGAGGGGCAGATTGAAGCCACCATCCAA
*
20120809 TCTTTTACCCCTAGTCAAGAGGGGCAGATTGAAGCCAACATCCAA
1 TCTTTTACCCCTAGTCAAGAGGGGCAGATTGAAGCCACCATCCAA
* * *
20120854 TCTTTTACCCCTAGTCAAGAAGGGCGGATTGAAGACACCATCCAA
1 TCTTTTACCCCTAGTCAAGAGGGGCAGATTGAAGCCACCATCCAA
* *
20120899 TCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGACACCATCCAA
1 TCTTTTACCCCTAGTCAAGAGGGGCAGATTGAAGCCACCATCCAA
20120944 TCTTTTACCCCTAGTCAAGAGGGGCAGATTGAAGCCACCATCCAA
1 TCTTTTACCCCTAGTCAAGAGGGGCAGATTGAAGCCACCATCCAA
* ** * *
20120989 TCTTTTACCCTTAACCAAGAGGGGCAAATTGAAGCCATCATCCAA
1 TCTTTTACCCCTAGTCAAGAGGGGCAGATTGAAGCCACCATCCAA
* * ** * **
20121034 TCTTTTACCCTTAATCAAGAATGGCAGATTGAAGCAACTGTCCAA
1 TCTTTTACCCCTAGTCAAGAGGGGCAGATTGAAGCCACCATCCAA
* * * *
20121079 TCTTTTACCCCTAAATCAGGAGGGGCAGATTAAAGCTACCATC
1 TCTTTTACCCCT-AGTCAAGAGGGGCAGATTGAAGCCACCATC
20121122 TCATAGAAGC
Statistics
Matches: 323, Mismatches: 34, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
45 300 0.93
46 23 0.07
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.23
Consensus pattern (45 bp):
TCTTTTACCCCTAGTCAAGAGGGGCAGATTGAAGCCACCATCCAA
Found at i:20121576 original size:17 final size:17
Alignment explanation
Indices: 20121544--20121588 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
20121534 TATTCGGCCT
*
20121544 AATAAACAAAATAAAAAA
1 AATAAA-AATATAAAAAA
* *
20121562 AATAATAATATAAAAAT
1 AATAAAAATATAAAAAA
20121579 AATAAAAATA
1 AATAAAAATA
20121589 AATAATTCCC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 18 0.78
18 5 0.22
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (17 bp):
AATAAAAATATAAAAAA
Found at i:20121642 original size:7 final size:7
Alignment explanation
Indices: 20121625--20121653 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
20121615 GTCCATTAAT
20121625 AATCC-A
1 AATCCAA
20121631 AATCCAA
1 AATCCAA
20121638 AATCCAA
1 AATCCAA
20121645 AATCCAA
1 AATCCAA
20121652 AA
1 AA
20121654 AAAAATTACA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.23
7 17 0.77
ACGTcount: A:0.59, C:0.28, G:0.00, T:0.14
Consensus pattern (7 bp):
AATCCAA
Found at i:20123074 original size:20 final size:21
Alignment explanation
Indices: 20123049--20123087 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
20123039 AAATCATGCA
*
20123049 TTTTTTTATCTTTT-TTTTCC
1 TTTTTTTATATTTTGTTTTCC
20123069 TTTTTTTATATTTTGTTTT
1 TTTTTTTATATTTTGTTTT
20123088 ATTACACACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.08, C:0.08, G:0.03, T:0.82
Consensus pattern (21 bp):
TTTTTTTATATTTTGTTTTCC
Found at i:20123595 original size:108 final size:109
Alignment explanation
Indices: 20123393--20123596 Score: 288
Period size: 108 Copynumber: 1.9 Consensus size: 109
20123383 GCTATTTTAT
* * *
20123393 TTAGGAAATTCAAGAAATTATGTCCTAACGTGTTGGGTGGTTTTTTTCCTTTGAACCTAAATAAC
1 TTAGGAAACTCAAGAAATTATGCCCTAACGTGTTGGGTGGTATTTTTCCTTTGAACCTAAATAAC
*
20123458 TGAGTATCCTATTTAAAATCGATGAATGTTCGATGTTCTGTTAC
66 TGAATATCCTATTTAAAATCGATGAATGTTCGATGTTCTGTTAC
* * * *
20123502 TTAGGGAACTCAAGAAATTGTGCCCTAATGTGTTGGGT-ATGATTTTTCC-TTGAACCTAAATAA
1 TTAGGAAACTCAAGAAATTATGCCCTAACGTGTTGGGTGGT-ATTTTTCCTTTGAACCTAAATAA
*
20123565 TTGAATATCCTATTTAAAATCGAT-AGATGTTC
65 CTGAATATCCTATTTAAAATCGATGA-ATGTTC
20123597 TTTATTTTCG
Statistics
Matches: 84, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
107 1 0.01
108 43 0.51
109 40 0.48
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.38
Consensus pattern (109 bp):
TTAGGAAACTCAAGAAATTATGCCCTAACGTGTTGGGTGGTATTTTTCCTTTGAACCTAAATAAC
TGAATATCCTATTTAAAATCGATGAATGTTCGATGTTCTGTTAC
Found at i:20135177 original size:24 final size:24
Alignment explanation
Indices: 20135149--20135197 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
20135139 CAGGAAGAAT
*
20135149 TGGTGGCTTCGTCCATAACCTACA
1 TGGTGGCTTCGTCCACAACCTACA
*
20135173 TGGTGGCTTTGTCCACAACCTACA
1 TGGTGGCTTCGTCCACAACCTACA
20135197 T
1 T
20135198 TGCAACAACC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.20, C:0.29, G:0.20, T:0.31
Consensus pattern (24 bp):
TGGTGGCTTCGTCCACAACCTACA
Found at i:20136079 original size:12 final size:12
Alignment explanation
Indices: 20136059--20136094 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
20136049 AGTTTGACCA
*
20136059 GACCTGTTGACT
1 GACCCGTTGACT
20136071 GACCCGTTGACT
1 GACCCGTTGACT
*
20136083 GAACCGTTGACT
1 GACCCGTTGACT
20136095 TTGACCAGGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.19, C:0.28, G:0.25, T:0.28
Consensus pattern (12 bp):
GACCCGTTGACT
Found at i:20136112 original size:19 final size:20
Alignment explanation
Indices: 20136087--20136154 Score: 70
Period size: 19 Copynumber: 3.5 Consensus size: 20
20136077 TTGACTGAAC
20136087 CGTTGACTTTGACCA-GGCAT
1 CGTTGACTTTGACCATGG-AT
* *
20136107 -GTTGACTTTAACCATTGAT
1 CGTTGACTTTGACCATGGAT
* *
20136126 CGTTGACTTTGA-CTTTGAT
1 CGTTGACTTTGACCATGGAT
20136145 CGTTGACTTT
1 CGTTGACTTT
20136155 TTTTGACCAA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
19 31 0.74
20 11 0.26
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.41
Consensus pattern (20 bp):
CGTTGACTTTGACCATGGAT
Found at i:20139581 original size:15 final size:16
Alignment explanation
Indices: 20139549--20139581 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
20139539 TATTCATACA
*
20139549 TTGCATTTAGGTTAAT
1 TTGCATTTAGGATAAT
20139565 TTGCATTTA-GATAAT
1 TTGCATTTAGGATAAT
20139580 TT
1 TT
20139582 AGTTTAAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.27, C:0.06, G:0.15, T:0.52
Consensus pattern (16 bp):
TTGCATTTAGGATAAT
Found at i:20154452 original size:21 final size:21
Alignment explanation
Indices: 20154426--20154469 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
20154416 TATGCTTGAT
20154426 ATTTATTAATATCAAAAGATC
1 ATTTATTAATATCAAAAGATC
20154447 ATTTATTAATATCAAAAGATC
1 ATTTATTAATATCAAAAGATC
20154468 AT
1 AT
20154470 CTAAAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.48, C:0.09, G:0.05, T:0.39
Consensus pattern (21 bp):
ATTTATTAATATCAAAAGATC
Found at i:20158273 original size:16 final size:16
Alignment explanation
Indices: 20158252--20158282 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20158242 GAATTAATTT
*
20158252 TGAATTCGTTTGTGAA
1 TGAATTCATTTGTGAA
20158268 TGAATTCATTTGTGA
1 TGAATTCATTTGTGA
20158283 CGTTCATTGT
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:0.26, C:0.06, G:0.23, T:0.45
Consensus pattern (16 bp):
TGAATTCATTTGTGAA
Found at i:20159471 original size:17 final size:17
Alignment explanation
Indices: 20159454--20159486 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
20159444 ATAATATTAT
20159454 TTTAATAT-ATTTAATA
1 TTTAATATAATTTAATA
*
20159470 TTTAATTTAATTTAATA
1 TTTAATATAATTTAATA
20159487 ATTATCTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTAATATAATTTAATA
Found at i:20159540 original size:62 final size:59
Alignment explanation
Indices: 20159447--20159578 Score: 178
Period size: 62 Copynumber: 2.2 Consensus size: 59
20159437 TCCAAAAATA
* *
20159447 ATATT-ATTTTAATATATTTAATATTTAATTTAATTTAATAATTATCTTGTAGATAAATATT
1 ATATTAATTTAAAAATATTTAATATTTAATTTAATTTAATAATTATC-T-T-GATAAATATT
* *
20159508 CTATTAATTTAAAAATATTTAAT-TTTAAATTTAATTTAATATTTATCTTGATAAATATT
1 ATATTAATTTAAAAATATTTAATATTT-AATTTAATTTAATAATTATCTTGATAAATATT
20159567 ATATTAATTTAA
1 ATATTAATTTAA
20159579 TATTAAACTG
Statistics
Matches: 64, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
59 21 0.33
60 1 0.02
61 8 0.12
62 34 0.53
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (59 bp):
ATATTAATTTAAAAATATTTAATATTTAATTTAATTTAATAATTATCTTGATAAATATT
Found at i:20159551 original size:12 final size:13
Alignment explanation
Indices: 20159521--20159552 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
20159511 TTAATTTAAA
20159521 AATATTTAATTTT
1 AATATTTAATTTT
20159534 AA-ATTTAA-TTT
1 AATATTTAATTTT
20159545 AATATTTA
1 AATATTTA
20159553 TCTTGATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 11 0.61
13 2 0.11
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
AATATTTAATTTT
Found at i:20165779 original size:13 final size:13
Alignment explanation
Indices: 20165761--20165785 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20165751 TGAAATTTAG
20165761 TTTAGATTAATAA
1 TTTAGATTAATAA
20165774 TTTAGATTAATA
1 TTTAGATTAATA
20165786 TCTCTTATAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TTTAGATTAATAA
Found at i:20167579 original size:74 final size:74
Alignment explanation
Indices: 20167456--20167597 Score: 257
Period size: 74 Copynumber: 1.9 Consensus size: 74
20167446 AATGAAAGTA
*
20167456 AACAGCCATCATTCATCATTCATAAATGAATGTGTTGATTCATTCAAAAACTCTTGAATGAAACA
1 AACAGCCATCATTCATCATTCATAAATGAATGTGTTAATTCATTCAAAAACTCTTGAATGAAACA
20167521 TTGAATGTG
66 TTGAATGTG
* *
20167530 AACAGCCATCATTCATCATTCATAAATGAATGTTTTAATTCATTTAAAAACTCTTGAATGAAACA
1 AACAGCCATCATTCATCATTCATAAATGAATGTGTTAATTCATTCAAAAACTCTTGAATGAAACA
20167595 TTG
66 TTG
20167598 TATCCCTCCA
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
74 65 1.00
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (74 bp):
AACAGCCATCATTCATCATTCATAAATGAATGTGTTAATTCATTCAAAAACTCTTGAATGAAACA
TTGAATGTG
Found at i:20169451 original size:52 final size:52
Alignment explanation
Indices: 20169373--20169476 Score: 199
Period size: 52 Copynumber: 2.0 Consensus size: 52
20169363 TGTAGGATGT
*
20169373 TTAATGTCTTGTTAACTCTGAAATGTCCCATAAGTCCTCTACTATGGGCTTC
1 TTAATGTCTTGTTAACTCCGAAATGTCCCATAAGTCCTCTACTATGGGCTTC
20169425 TTAATGTCTTGTTAACTCCGAAATGTCCCATAAGTCCTCTACTATGGGCTTC
1 TTAATGTCTTGTTAACTCCGAAATGTCCCATAAGTCCTCTACTATGGGCTTC
20169477 CTTTACTAGG
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.23, C:0.24, G:0.15, T:0.38
Consensus pattern (52 bp):
TTAATGTCTTGTTAACTCCGAAATGTCCCATAAGTCCTCTACTATGGGCTTC
Found at i:20181011 original size:20 final size:21
Alignment explanation
Indices: 20180988--20181034 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
20180978 TACTTATATC
* *
20180988 GGTAGAA-CTGAAGTTGTATA
1 GGTAGAATCTGAAGTTCTACA
*
20181008 GGTA-AATGTGAAGTTCTACA
1 GGTAGAATCTGAAGTTCTACA
20181028 GGTAGAA
1 GGTAGAA
20181035 GTCCCAGGGT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 2 0.09
20 18 0.82
21 2 0.09
ACGTcount: A:0.36, C:0.06, G:0.30, T:0.28
Consensus pattern (21 bp):
GGTAGAATCTGAAGTTCTACA
Found at i:20182200 original size:11 final size:11
Alignment explanation
Indices: 20182167--20182200 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
20182157 TAAATTTTAT
20182167 TTAAAAT-ATA
1 TTAAAATAATA
*
20182177 TAAAAATAATA
1 TTAAAATAATA
20182188 TTAAAATAATA
1 TTAAAATAATA
20182199 TT
1 TT
20182201 TATTATTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 6 0.29
11 15 0.71
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
TTAAAATAATA
Found at i:20184053 original size:712 final size:714
Alignment explanation
Indices: 20182205--20184060 Score: 2703
Period size: 719 Copynumber: 2.6 Consensus size: 714
20182195 AATATTTATT
* ** * *
20182205 ATTTTAATATTTTAATAACTAAGACCCGATTATGGGTAACTCCAACTCAACCCGAATCTTT-TAT
1 ATTTTAATATTTTAATAACTAAAACCCGATTATGGGTAAGACCAACTCAATCAGAATCTTTATAT
* * * * *
20182269 ATAATATAGATAAATCTAAAAGAATGAAATTCAAAATAATCCATATATTACATTAATCCTAAGTA
66 ACAATATAAATAAATCT-AAAGAATGAAATTCAAAATAATCTATATATTAAATTAATCCTAAATA
* * *
20182334 GTTAAATATAAATGACCATAACCCAAAATAAATTTATCCGAAAAATTTAATCCTCAAATATAAAA
130 GTTAAATATGAATGACCATAACCCAAAACAAATTTATCCGAAAAATTCAATCCTCAAATATAAAA
* * * *
20182399 TGACTCGATTTCAAAATCATCGATCCCAAAGCGGACATAAATTAAAAATGACTTGAATACAAAAT
195 TGACTCGAATT-AAAATCATCGATCTCAAAACGGACATAAATTAAAAATGACTCGAATACAAAAT
* * *
20182464 TGAAATCGTATTAATCCGATCTAAATTGATCCATGTAAGAACAACTCGATCTACCAAAAGAGATT
259 TGAAATCTTATTAATCCGATCTAAATTGATCCATGTAAGATCAACTCGATCTACCGAAAGAGATT
*
20182529 TGAAGCTAATAACAATCTATACGGAATTAAAATAAAAAATAATTTAAATTGTGAGTAAAAGTAAT
324 TGAAACTAATAACAATCTATACGGAATTAAAATAAAAAATAATTTAAATTGTGAGTAAAAGTAAT
* *
20182594 AATGTTAAATGCACTTC-AATTGTTTATCATAGCATTGTTATTTTTCTTAAGTTGGTATCGAATT
389 AATATTAAATGCAC-TCAAATTGTTTATCATAGCATTATTATTTTTCTTAAGTTGGTATCGAATT
* * * *
20182658 GACTTATGATATTAACTCAATTGATAATATTATCAATAAAATTATGACATACCCATGATGTGAGT
453 GACTTATGATATTAACTAAATTGACAATATTACCAATAAAATTATGACATACCCATGATGTAAGT
20182723 GAAAATAATTATATATATTTATTAAGAATTCACTTAACAACCAAATGTTATATTAATTGAAATGA
518 GAAAATAATTATATATATTTATTAAGAATTCACTTAACAACCAAATGTTATATTAATTGAAATGA
** * * * *
20182788 CAAAATTGTAAGAGTATATGTTTGGTGTTTCGGGTTCAACCTATTGTAAGCATGGATTCTTTTTT
583 CAAAATTAAAAGAGTATATGTTCGGTGTTTCGGGTTCAACCCATAGTAAGCATGAATTCTTTTTT
* *
20182853 CTAGATTTTATTTTAAAAAATAAAAATATTCTTAAATTAACATTTATTACTTTATTAAAATAAGA
648 CTACATTTTATTTAAAAAAATAAAAATATTCTTAAATTAACATTTATTACTTTATTAAAATAAGA
20182918 GC
713 GC
* *
20182920 ATTTTAATATTTTAATAACTAAAACCCTATTATGGGTAAGACCAACTCAATCAGAATCTTTATGT
1 ATTTTAATATTTTAATAACTAAAACCCGATTATGGGTAAGACCAACTCAATCAGAATCTTTATAT
* * * *
20182985 ACAATATAAATAAAT-TGAAAATAATGAAATTCAAAATAAAATAATTCATATATTAATTTAATTC
66 ACAATATAAATAAATCT--AAAGAATGAAATTCAAAAT--AAT--CT-ATATATTAAATTAATCC
*
20183049 TAAATAGTTAAATATGAATGA-C-TAACCCAAAACAAATTTATCTGAAAAATTCAATCCTCAAAT
124 TAAATAGTTAAATATGAATGACCATAACCCAAAACAAATTTATCCGAAAAATTCAATCCTCAAAT
** ** * *
20183112 ATAAAATGACTCGAATCCAAATCATTTAT-TGCAAAACGGACATAAAATAAAAAATGACTCAAAT
189 ATAAAATGACTCGAATTAAAATCATCGATCT-CAAAACGGACAT-AAATTAAAAATGACTCGAAT
* * * *
20183176 ACGAAATTGAAATCTTATTAATCTGATCTAAATCGATCCATGTAAGATCAACTCGATCTACCGGA
252 ACAAAATTGAAATCTTATTAATCCGATCTAAATTGATCCATGTAAGATCAACTCGATCTACCGAA
*
20183241 AGAGATTTGAAACTAATAACAATCTATACGGAATTAAAATTAAAAATAATTTAAATTGTGAGTAA
317 AGAGATTTGAAACTAATAACAATCTATACGGAATTAAAATAAAAAATAATTTAAATTGTGAGTAA
** *
20183306 AAGTAATAATATTAAATGCACTCAAATTGTTTATCATATTATTATTATTTTTCTTGAGTTGGTAT
382 AAGTAATAATATTAAATGCACTCAAATTGTTTATCATAGCATTATTATTTTTCTTAAGTTGGTAT
* * **
20183371 C-AAGTTGACTTATGATATTAACTAAATTGACAATATTACCAATAAGATTATTACATACTTACT-
447 CGAA-TTGACTTATGATATTAACTAAATTGACAATATTACCAATAAAATTATGACATACCCA-TG
* *
20183434 ATGTAAGTGAAAATAATTATATATATTTATTAAGAATTCACTTAACAACCAAATTTTATATTAGT
510 ATGTAAGTGAAAATAATTATATATATTTATTAAGAATTCACTTAACAACCAAATGTTATATTAAT
*
20183499 TGAAATGACAAAATTAAAAGAGTATATGTTCGGTGTTTTGGGTTCAACCCATAGTAAGCATGAAT
575 TGAAATGACAAAATTAAAAGAGTATATGTTCGGTGTTTCGGGTTCAACCCATAGTAAGCATGAAT
* *
20183564 T-TTTTTT-TACATTTTATTTAAAAAAGAT-AAAATACTT-TTAAATTAATATTTATTACTTTGT
640 TCTTTTTTCTACATTTTATTTAAAAAA-ATAAAAATA-TTCTTAAATTAACATTTATTACTTTAT
*
20183625 TAAAATGAGAGC
703 TAAAATAAGAGC
* *
20183637 ATTTTAATATTATAATAACTAAAACCCGATTATCGGTAAGACCAACTCAATCAGAATCTTTATAT
1 ATTTTAATATTTTAATAACTAAAACCCGATTATGGGTAAGACCAACTCAATCAGAATCTTTATAT
20183702 ACAATATAAATAAATCT-AAGAATGAAATTCAAAATAATCTATATATTAAATTAATCCTAAATAG
66 ACAATATAAATAAATCTAAAGAATGAAATTCAAAATAATCTATATATTAAATTAATCCTAAATAG
* * * * *
20183766 TTAACTATGAAGGACCATAACCTAAAACAAATTTATCCAAAAAATTCAATCTTCAAATATAAAAT
131 TTAAATATGAATGACCATAACCCAAAACAAATTTATCCGAAAAATTCAATCCTCAAATATAAAAT
* *
20183831 GATTCGAATATAAAATCATCGATCTCAAAACGGACATAAATTAAAAACGACTCGAATACAAAATT
196 GACTCGAAT-TAAAATCATCGATCTCAAAACGGACATAAATTAAAAATGACTCGAATACAAAATT
* *
20183896 GAAATCTTATTAATCCGATCTAAATTGATTCATGTAAGATCAACTCGATCTATCGAAAGAGATTT
260 GAAATCTTATTAATCCGATCTAAATTGATCCATGTAAGATCAACTCGATCTACCGAAAGAGATTT
* ** * * *
20183961 GAAACTAATAACAATATATACATAATTAAAATAAAAAATAATTTAAATTGTAAGTAAAAATTATA
325 GAAACTAATAACAATCTATACGGAATTAAAATAAAAAATAATTTAAATTGTGAGTAAAAGTAATA
* *
20184026 ATATTAAATACACTCAAATTATTTATCATAGCATT
390 ATATTAAATGCACTCAAATTGTTTATCATAGCATT
20184061 TTTTTGAGTT
Statistics
Matches: 1017, Mismatches: 105, Indels: 41
0.87 0.09 0.04
Matches are distributed among these distances:
710 34 0.03
711 2 0.00
712 225 0.22
713 24 0.02
714 1 0.00
715 73 0.07
716 34 0.03
717 131 0.13
718 38 0.04
719 420 0.41
720 2 0.00
721 33 0.03
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.34
Consensus pattern (714 bp):
ATTTTAATATTTTAATAACTAAAACCCGATTATGGGTAAGACCAACTCAATCAGAATCTTTATAT
ACAATATAAATAAATCTAAAGAATGAAATTCAAAATAATCTATATATTAAATTAATCCTAAATAG
TTAAATATGAATGACCATAACCCAAAACAAATTTATCCGAAAAATTCAATCCTCAAATATAAAAT
GACTCGAATTAAAATCATCGATCTCAAAACGGACATAAATTAAAAATGACTCGAATACAAAATTG
AAATCTTATTAATCCGATCTAAATTGATCCATGTAAGATCAACTCGATCTACCGAAAGAGATTTG
AAACTAATAACAATCTATACGGAATTAAAATAAAAAATAATTTAAATTGTGAGTAAAAGTAATAA
TATTAAATGCACTCAAATTGTTTATCATAGCATTATTATTTTTCTTAAGTTGGTATCGAATTGAC
TTATGATATTAACTAAATTGACAATATTACCAATAAAATTATGACATACCCATGATGTAAGTGAA
AATAATTATATATATTTATTAAGAATTCACTTAACAACCAAATGTTATATTAATTGAAATGACAA
AATTAAAAGAGTATATGTTCGGTGTTTCGGGTTCAACCCATAGTAAGCATGAATTCTTTTTTCTA
CATTTTATTTAAAAAAATAAAAATATTCTTAAATTAACATTTATTACTTTATTAAAATAAGAGC
Found at i:20184675 original size:8 final size:7
Alignment explanation
Indices: 20184655--20184688 Score: 59
Period size: 7 Copynumber: 4.7 Consensus size: 7
20184645 GCACACATTT
20184655 AGAAAAA
1 AGAAAAA
20184662 AGAAAAA
1 AGAAAAA
20184669 AGAAAAAA
1 AG-AAAAA
20184677 AGAAAAA
1 AGAAAAA
20184684 AGAAA
1 AGAAA
20184689 TAGTAAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 19 0.73
8 7 0.27
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (7 bp):
AGAAAAA
Found at i:20184677 original size:15 final size:15
Alignment explanation
Indices: 20184657--20184688 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
20184647 ACACATTTAG
20184657 AAAAAAGAAAAAAGA
1 AAAAAAGAAAAAAGA
20184672 AAAAAAGAAAAAAGA
1 AAAAAAGAAAAAAGA
20184687 AA
1 AA
20184689 TAGTAAATTA
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:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (15 bp):
AAAAAAGAAAAAAGA
Found at i:20189514 original size:21 final size:21
Alignment explanation
Indices: 20189490--20189530 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
20189480 AAATGCAATA
20189490 GGAAAAA-AAGTAAAGAGAAGG
1 GGAAAAACAAGTAAA-AGAAGG
*
20189511 GGAAAAACAATTAAAAGAAG
1 GGAAAAACAAGTAAAAGAAG
20189531 AATAAATGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.63, C:0.02, G:0.27, T:0.07
Consensus pattern (21 bp):
GGAAAAACAAGTAAAAGAAGG
Found at i:20194394 original size:15 final size:14
Alignment explanation
Indices: 20194367--20194393 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
20194357 GGTTAAAGTA
20194367 AAATATTAAAAAAT
1 AAATATTAAAAAAT
20194381 AAATATTAAAAAA
1 AAATATTAAAAAA
20194394 AAGAGATGTA
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:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
AAATATTAAAAAAT
Found at i:20201196 original size:23 final size:25
Alignment explanation
Indices: 20201143--20201201 Score: 68
Period size: 26 Copynumber: 2.4 Consensus size: 25
20201133 TTAATGTAAT
*
20201143 TAATATTATAATTATATAAATTTAAA
1 TAATATTTTAATTATATAAA-TTAAA
*
20201169 AAATATTTTAATTATA-AAA-TAAA
1 TAATATTTTAATTATATAAATTAAA
*
20201192 TAATAATTTA
1 TAATATTTTA
20201202 TATGTATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
23 12 0.41
25 3 0.10
26 14 0.48
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
TAATATTTTAATTATATAAATTAAA
Found at i:20203277 original size:22 final size:22
Alignment explanation
Indices: 20203209--20203287 Score: 70
Period size: 26 Copynumber: 3.5 Consensus size: 22
20203199 TGTGGACAAG
*
20203209 CCACCACATAGATGCCGATAAA
1 CCACCACATAAATGCCGATAAA
* **
20203231 CGACCACATAACACATTGTGGATAAA
1 CCACCACAT-A-A-A-TGCCGATAAA
20203257 CCACCACATAAATGCCGAT-AA
1 CCACCACATAAATGCCGATAAA
*
20203278 CAACCACATA
1 CCACCACATA
20203288 GTCGTATCAT
Statistics
Matches: 45, Mismatches: 8, Indels: 9
0.73 0.13 0.15
Matches are distributed among these distances:
21 11 0.24
22 13 0.29
23 2 0.04
24 1 0.02
25 2 0.04
26 16 0.36
ACGTcount: A:0.43, C:0.30, G:0.11, T:0.15
Consensus pattern (22 bp):
CCACCACATAAATGCCGATAAA
Found at i:20203301 original size:48 final size:48
Alignment explanation
Indices: 20203209--20203315 Score: 126
Period size: 48 Copynumber: 2.2 Consensus size: 48
20203199 TGTGGACAAG
* * **
20203209 CCACCACATAGATGCCGATAAACGACCACATAACACATTGTGGATAAA
1 CCACCACATAAATGCCGATAAACAACCACATAACACATCATGGATAAA
* **
20203257 CCACCACATAAATGCCGAT-AACAACCACATAGTCGTATCATGGATAAA
1 CCACCACATAAATGCCGATAAACAACCACATA-ACACATCATGGATAAA
*
20203305 CCACTACATAA
1 CCACCACATAA
20203316 TTGCAGTTAA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
47 11 0.22
48 39 0.78
ACGTcount: A:0.42, C:0.28, G:0.12, T:0.18
Consensus pattern (48 bp):
CCACCACATAAATGCCGATAAACAACCACATAACACATCATGGATAAA
Found at i:20206921 original size:28 final size:26
Alignment explanation
Indices: 20206876--20206935 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 26
20206866 GACTTACCCC
*
20206876 GTGTTTACTTTCTCAGCGAACTTCATCT
1 GTGTTTACTGTCTCAGCGAA-TT-ATCT
20206904 GTGTTTACTGTC-CAAGCGAATTATCT
1 GTGTTTACTGTCTC-AGCGAATTATCT
*
20206930 CTGTTT
1 GTGTTT
20206936 TATGTTTACT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 9 0.31
27 3 0.10
28 17 0.59
ACGTcount: A:0.18, C:0.22, G:0.17, T:0.43
Consensus pattern (26 bp):
GTGTTTACTGTCTCAGCGAATTATCT
Found at i:20206947 original size:33 final size:33
Alignment explanation
Indices: 20206905--20206999 Score: 104
Period size: 33 Copynumber: 2.9 Consensus size: 33
20206895 ACTTCATCTG
*
20206905 TGTTTACTGTCCAAGCGAATTATCTCTGTTTTA
1 TGTTTACTGTCCAAGCGAATTATCTCTGTTCTA
* *
20206938 TGTTTACTGTCCCAGCGGACTT-TCTCTGTTCTA
1 TGTTTACTGTCCAAGC-GAATTATCTCTGTTCTA
* * *
20206971 TGTTTATTGTCTCAA-CGGACTATCTCTGT
1 TGTTTACTGTC-CAAGCGAATTATCTCTGT
20207000 GGATGCTATA
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
32 2 0.04
33 43 0.84
34 6 0.12
ACGTcount: A:0.17, C:0.22, G:0.17, T:0.44
Consensus pattern (33 bp):
TGTTTACTGTCCAAGCGAATTATCTCTGTTCTA
Found at i:20208478 original size:32 final size:32
Alignment explanation
Indices: 20208437--20208500 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
20208427 CTTAGTCAAA
20208437 ATTTGTCCAAATTAGCTAAGGTAAGGTAGGTT
1 ATTTGTCCAAATTAGCTAAGGTAAGGTAGGTT
20208469 ATTTGTCCAAATTAGCTAAGGTAAGGTAGGTT
1 ATTTGTCCAAATTAGCTAAGGTAAGGTAGGTT
20208501 TTCTTTGATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.31, C:0.09, G:0.25, T:0.34
Consensus pattern (32 bp):
ATTTGTCCAAATTAGCTAAGGTAAGGTAGGTT
Found at i:20215503 original size:50 final size:50
Alignment explanation
Indices: 20215449--20215554 Score: 124
Period size: 50 Copynumber: 2.1 Consensus size: 50
20215439 TGAAGTTGCA
* * * *
20215449 ACATCAAGCTATTGTTTCCATAGTCGCGA-ACTTCCCTTACTAAAGTCGTG
1 ACATCAAGCTACTGTCTCCATAGTCACGATA-TTCCCTTACTAAAGTCATG
* * * *
20215499 ACATCAAGCTGCTGTCTCCATAGTTACGATATTCCCTTGCTGAAGTCATG
1 ACATCAAGCTACTGTCTCCATAGTCACGATATTCCCTTACTAAAGTCATG
20215549 ACATCA
1 ACATCA
20215555 TGATATTGCT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
50 46 0.98
51 1 0.02
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.31
Consensus pattern (50 bp):
ACATCAAGCTACTGTCTCCATAGTCACGATATTCCCTTACTAAAGTCATG
Found at i:20218016 original size:29 final size:30
Alignment explanation
Indices: 20217937--20218278 Score: 338
Period size: 30 Copynumber: 11.5 Consensus size: 30
20217927 GAAGTTCTCG
* * * * *
20217937 AACTTTCCCAAAATCATATTTTGACCCTTA
1 AACTTTTCCAAAATTACATTTTAACCCTCA
* * *
20217967 AACTTTTCCAAAATTATATTTTGACCCTCG
1 AACTTTTCCAAAATTACATTTTAACCCTCA
20217997 AAC-TTTCCAAAATTACATTTTAACCCTCA
1 AACTTTTCCAAAATTACATTTTAACCCTCA
*
20218026 AACTTTTCCAAAATTACATTTTAAACCT-A
1 AACTTTTCCAAAATTACATTTTAACCCTCA
*
20218055 AACTTCTT-TAAAATTACATTTTAACCC-CA
1 AACTT-TTCCAAAATTACATTTTAACCCTCA
20218084 AACTTTTCCAAAATTACATTTTAACCC-CTA
1 AACTTTTCCAAAATTACATTTTAACCCTC-A
* * *
20218114 AACTTCTCTAAAATTGCATTTTAACCCTCA
1 AACTTTTCCAAAATTACATTTTAACCCTCA
** * * *
20218144 AACTTAGCTAAAATTACATTTTGACCCTTA
1 AACTTTTCCAAAATTACATTTTAACCCTCA
* * *
20218174 AACTTTTCTAAAATAACATTTTGACTCCT-A
1 AACTTTTCCAAAATTACATTTTAAC-CCTCA
* * *
20218204 AACTTTTCTAAAATAACAATTTAACCC-CA
1 AACTTTTCCAAAATTACATTTTAACCCTCA
* * * *
20218233 AAATTTTCTAAAATTACATTTTGACCCTTA
1 AACTTTTCCAAAATTACATTTTAACCCTCA
* *
20218263 AACATCTCCAAAATTA
1 AACTTTTCCAAAATTA
20218279 TGATTTTCCC
Statistics
Matches: 270, Mismatches: 33, Indels: 18
0.84 0.10 0.06
Matches are distributed among these distances:
28 2 0.01
29 100 0.37
30 164 0.61
31 4 0.01
ACGTcount: A:0.37, C:0.23, G:0.02, T:0.37
Consensus pattern (30 bp):
AACTTTTCCAAAATTACATTTTAACCCTCA
Found at i:20218029 original size:59 final size:59
Alignment explanation
Indices: 20217954--20218278 Score: 345
Period size: 59 Copynumber: 5.5 Consensus size: 59
20217944 CCAAAATCAT
* * * * * *
20217954 ATTTTGACCCTTAAACTTTTCCAAAATTATATTTTGACCCTCGAACTTTCCAAAATTAC
1 ATTTTAACCCTCAAACTTTTCCAAAATTACATTTTAACCCTCAAACTTTCTAAAATTAC
* *
20218013 ATTTTAACCCTCAAACTTTTCCAAAATTACATTTTAAACCT-AAACTTCTTTAAAATTAC
1 ATTTTAACCCTCAAACTTTTCCAAAATTACATTTTAACCCTCAAACTT-TCTAAAATTAC
*
20218072 ATTTTAACCC-CAAACTTTTCCAAAATTACATTTTAACCC-CTAAACTTCTCTAAAATTGC
1 ATTTTAACCCTCAAACTTTTCCAAAATTACATTTTAACCCTC-AAACTT-TCTAAAATTAC
** * * * *
20218131 ATTTTAACCCTCAAACTTAGCTAAAATTACATTTTGACCCTTAAACTTTTCTAAAATAAC
1 ATTTTAACCCTCAAACTTTTCCAAAATTACATTTTAACCCTCAAAC-TTTCTAAAATTAC
* * * * *
20218191 ATTTTGACTCCT-AAACTTTTCTAAAATAACAATTTAACCC-CAAAATTTTCTAAAATTAC
1 ATTTTAAC-CCTCAAACTTTTCCAAAATTACATTTTAACCCTC-AAACTTTCTAAAATTAC
* * * *
20218250 ATTTTGACCCTTAAACATCTCCAAAATTA
1 ATTTTAACCCTCAAACTTTTCCAAAATTA
20218279 TGATTTTCCC
Statistics
Matches: 226, Mismatches: 31, Indels: 18
0.82 0.11 0.07
Matches are distributed among these distances:
58 36 0.16
59 114 0.50
60 71 0.31
61 5 0.02
ACGTcount: A:0.37, C:0.23, G:0.02, T:0.37
Consensus pattern (59 bp):
ATTTTAACCCTCAAACTTTTCCAAAATTACATTTTAACCCTCAAACTTTCTAAAATTAC
Found at i:20218314 original size:29 final size:29
Alignment explanation
Indices: 20218242--20218342 Score: 107
Period size: 29 Copynumber: 3.5 Consensus size: 29
20218232 AAAATTTTCT
* *
20218242 AAAATTA-CATTTTGACCCTTAAACATCTCC
1 AAAATTACCATTTT-TCCCTTAAACATC-CA
** *
20218272 AAAATTATGA-TTTTCCCTTGAACATCCA
1 AAAATTACCATTTTTCCCTTAAACATCCA
**
20218300 AAAATTACCATTTTTCCCCCAAACATCCA
1 AAAATTACCATTTTTCCCTTAAACATCCA
20218329 AAAATTACCATTTT
1 AAAATTACCATTTT
20218343 ACCCCAAAAT
Statistics
Matches: 60, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
28 9 0.15
29 40 0.67
30 10 0.17
31 1 0.02
ACGTcount: A:0.38, C:0.26, G:0.03, T:0.34
Consensus pattern (29 bp):
AAAATTACCATTTTTCCCTTAAACATCCA
Found at i:20218368 original size:28 final size:29
Alignment explanation
Indices: 20218292--20218370 Score: 106
Period size: 29 Copynumber: 2.8 Consensus size: 29
20218282 TTTTCCCTTG
* *
20218292 AACATCCAAAAATTACCATTTTTCCCCCA
1 AACATCCAAAAATTACCATTTTACCCCAA
20218321 AACATCCAAAAATTACCATTTTACCCCAA
1 AACATCCAAAAATTACCATTTTACCCCAA
** *
20218350 AATTTCCAAAAATCA-CATTTT
1 AACATCCAAAAATTACCATTTT
20218371 CAACCTTAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
28 6 0.13
29 39 0.87
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (29 bp):
AACATCCAAAAATTACCATTTTACCCCAA
Found at i:20224929 original size:3 final size:3
Alignment explanation
Indices: 20224921--20224950 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
20224911 TTATGATATT
20224921 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
20224951 AGGGATGACC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:20227533 original size:39 final size:39
Alignment explanation
Indices: 20227485--20228042 Score: 274
Period size: 39 Copynumber: 14.4 Consensus size: 39
20227475 ATATCAGCCA
* * *
20227485 ATCTCTTACCCCGAGCCTAGGGTAGATTGTAGCCATTCG
1 ATCTTTTACCCCGAGCCTGGGGTAGATTGCAGCCATTCG
* * ** * * ** *
20227524 ATCTTTTACCTCGAGCCTGAGACAGATTACCA-TCAGCCA
1 ATCTTTTACCCCGAGCCTGGGGTAGATT-GCAGCCATTCG
* * * ** *
20227563 ATCTCTTA-CCCGAGCCTGGGGAAAATTATAGCCATTGG
1 ATCTTTTACCCCGAGCCTGGGGTAGATTGCAGCCATTCG
* *
20227601 ATCTTTTACCCCGAG-CTTGGGTAGATTGCAGCCATCCG
1 ATCTTTTACCCCGAGCCTGGGGTAGATTGCAGCCATTCG
* *
20227639 ATCTTTTACCCTGAGCCTGGGGTAGA-T-CA-CCATTAGCCA
1 ATCTTTTACCCCGAGCCTGGGGTAGATTGCAGCCATT---CG
* * * *
20227678 ATCTCTTACCCCGAGCCTGAGGCAGATTGTAGCCATTCG
1 ATCTTTTACCCCGAGCCTGGGGTAGATTGCAGCCATTCG
* * *
20227717 ATCTTTTACTCTGAGCCTAGGGTAGA-T-CA-CCA-TCAG
1 ATCTTTTACCCCGAGCCTGGGGTAGATTGCAGCCATTC-G
* *
20227753 CCAATCTCTTACCCCGAGCCTGGGGCAGATTGCAGCCATTCG
1 ---ATCTTTTACCCCGAGCCTGGGGTAGATTGCAGCCATTCG
* * * * * *
20227795 ATCTTTTATCCTGAGCTTGGGGCAGA-T-CA-CCATCAACCA
1 ATCTTTTACCCCGAGCCTGGGGTAGATTGCAGCCAT---TCG
* * * * *
20227834 ATCTCTTACCTCGAGCCTGGAGTAGATTGTAGTCA-TCTG
1 ATCTTTTACCCCGAGCCTGGGGTAGATTGCAGCCATTC-G
* *
20227873 ATCTTTTACCCCAAGCCTGGGGTAGA-T-CA-CCATTAGCTA
1 ATCTTTTACCCCGAGCCTGGGGTAGATTGCAGCCATT--C-G
* * *
20227912 ATCTTTTACCCCGCA-ACAGGGGTAGATTGCAGCCATTCA
1 ATCTTTTACCCCG-AGCCTGGGGTAGATTGCAGCCATTCG
* * * * *
20227951 ATCTTTTACCCCGATCATGGGGCAGA-T-CATCGCCAATCA
1 ATCTTTTACCCCGAGCCTGGGGTAGATTGCA--GCCATTCG
* * * * * * *
20227990 ATCTCTTACCCCGCGACAGGGGCAGATTGCAACCATCCG
1 ATCTTTTACCCCGAGCCTGGGGTAGATTGCAGCCATTCG
*
20228029 ATCTTTTATCCCGA
1 ATCTTTTACCCCGA
20228043 TTATGGGGCA
Statistics
Matches: 382, Mismatches: 100, Indels: 74
0.69 0.18 0.13
Matches are distributed among these distances:
35 2 0.01
36 14 0.04
37 10 0.03
38 60 0.16
39 262 0.69
40 8 0.02
41 8 0.02
42 16 0.04
43 2 0.01
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (39 bp):
ATCTTTTACCCCGAGCCTGGGGTAGATTGCAGCCATTCG
Found at i:20227610 original size:38 final size:38
Alignment explanation
Indices: 20227515--20227660 Score: 100
Period size: 38 Copynumber: 3.8 Consensus size: 38
20227505 GGTAGATTGT
* * *
20227515 AGCCATTCGATCTTTTACCTCGAGCCT-GAGACAGATTACC
1 AGCCATCCGATCTTTTACC-CGAGCCTGGGGA-AAATTA-C
* * * * *
20227555 A-TCAGCCAATCTCTTACCCGAGCCTGGGGAAAATTAT
1 AGCCATCCGATCTTTTACCCGAGCCTGGGGAAAATTAC
** * * * *
20227592 AGCCATTGGATCTTTTACCCCGAG-CTTGGGTAGATTGC
1 AGCCATCCGATCTTTTA-CCCGAGCCTGGGGAAAATTAC
20227630 AGCCATCCGATCTTTTACCCTGAGCCTGGGG
1 AGCCATCCGATCTTTTACCC-GAGCCTGGGG
20227661 TAGATCACCA
Statistics
Matches: 79, Mismatches: 22, Indels: 11
0.71 0.20 0.10
Matches are distributed among these distances:
37 4 0.05
38 48 0.61
39 26 0.33
40 1 0.01
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.27
Consensus pattern (38 bp):
AGCCATCCGATCTTTTACCCGAGCCTGGGGAAAATTAC
Found at i:20227655 original size:115 final size:117
Alignment explanation
Indices: 20227485--20227743 Score: 344
Period size: 115 Copynumber: 2.2 Consensus size: 117
20227475 ATATCAGCCA
* * *
20227485 ATCTCTTACCCCGAGCCTAGGGTAGATTGTAGCCATTCGATCTTTTACCTCGAGCCTGAGACAGA
1 ATCTTTTACCCCGAGCCTAGGGTAGATTGCAGCCATCCGATCTTTTACCTCGAGCCTGAGACAGA
* * *
20227550 TTACCATCAGCCAATCTCTTA-CCCGAGCCTGGGGAAAATTATAGCCATTGG
66 TCACCATCAGCCAATCTCTTACCCCGAGCCTGAGGAAAATTATAGCCATTCG
* * **
20227601 ATCTTTTACCCCGAG-CTTGGGTAGATTGCAGCCATCCGATCTTTTACC-CTGAGCCTGGGGTAG
1 ATCTTTTACCCCGAGCCTAGGGTAGATTGCAGCCATCCGATCTTTTACCTC-GAGCCTGAGACAG
* * * *
20227664 ATCACCATTAGCCAATCTCTTACCCCGAGCCTGAGGCAGATTGTAGCCATTCG
65 ATCACCATCAGCCAATCTCTTACCCCGAGCCTGAGGAAAATTATAGCCATTCG
* *
20227717 ATCTTTTACTCTGAGCCTAGGGTAGAT
1 ATCTTTTACCCCGAGCCTAGGGTAGAT
20227744 CACCATCAGC
Statistics
Matches: 123, Mismatches: 17, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
114 1 0.01
115 60 0.49
116 52 0.42
117 10 0.08
ACGTcount: A:0.23, C:0.27, G:0.22, T:0.28
Consensus pattern (117 bp):
ATCTTTTACCCCGAGCCTAGGGTAGATTGCAGCCATCCGATCTTTTACCTCGAGCCTGAGACAGA
TCACCATCAGCCAATCTCTTACCCCGAGCCTGAGGAAAATTATAGCCATTCG
Found at i:20227723 original size:78 final size:77
Alignment explanation
Indices: 20227601--20228036 Score: 451
Period size: 78 Copynumber: 5.6 Consensus size: 77
20227591 TAGCCATTGG
* * *
20227601 ATCTTTTACCCCGAGCTTGGGTAGATTGCAGCCATCCGATCTTTTACCCTGAGCCTGGGGTAGAT
1 ATCTCTTACCCCGAGCCTGGGTAGATTGCAGCCATTCGATCTTTTACCCTGAGCCTGGGGTAGAT
*
20227666 CACCATTAGCCA
66 CACCATCAGCCA
* * * *
20227678 ATCTCTTACCCCGAGCCTGAGGCAGATTGTAGCCATTCGATCTTTTACTCTGAGCCTAGGGTAGA
1 ATCTCTTACCCCGAGCCTG-GGTAGATTGCAGCCATTCGATCTTTTACCCTGAGCCTGGGGTAGA
20227743 TCACCATCAGCCA
65 TCACCATCAGCCA
* * * *
20227756 ATCTCTTACCCCGAGCCTGGGGCAGATTGCAGCCATTCGATCTTTTATCCTGAGCTTGGGGCAGA
1 ATCTCTTACCCCGAGCCT-GGGTAGATTGCAGCCATTCGATCTTTTACCCTGAGCCTGGGGTAGA
*
20227821 TCACCATCAACCA
65 TCACCATCAGCCA
* * * **
20227834 ATCTCTTACCTCGAGCCTGGAGTAGATTGTAGTCA-TCTGATCTTTTACCCCAAGCCTGGGGTAG
1 ATCTCTTACCCCGAGCCTGG-GTAGATTGCAGCCATTC-GATCTTTTACCCTGAGCCTGGGGTAG
* *
20227898 ATCACCATTAGCTA
64 ATCACCATCAGCCA
* * ** * * * * *
20227912 ATCTTTTACCCCGCAACAGGGGTAGATTGCAGCCATTCAATCTTTTACCCCGATCATGGGGCAGA
1 ATCTCTTACCCCG-AGCCTGGGTAGATTGCAGCCATTCGATCTTTTACCCTGAGCCTGGGGTAGA
* ** **
20227977 TCATCGCCAATCA
65 TCACCATCAGCCA
* ** * * *
20227990 ATCTCTTACCCCGCGACAGGGGCAGATTGCAACCATCCGATCTTTTA
1 ATCTCTTACCCCGAG-CCTGGGTAGATTGCAGCCATTCGATCTTTTA
20228037 TCCCGATTAT
Statistics
Matches: 299, Mismatches: 53, Indels: 13
0.82 0.15 0.04
Matches are distributed among these distances:
77 21 0.07
78 271 0.91
79 7 0.02
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (77 bp):
ATCTCTTACCCCGAGCCTGGGTAGATTGCAGCCATTCGATCTTTTACCCTGAGCCTGGGGTAGAT
CACCATCAGCCA
Found at i:20227810 original size:156 final size:155
Alignment explanation
Indices: 20227601--20228036 Score: 507
Period size: 156 Copynumber: 2.8 Consensus size: 155
20227591 TAGCCATTGG
* * *
20227601 ATCTTTTACCCCGAGCTTGGGTAGATTGCAGCCATCCGATCTTTTACCCTGAGCCTGGGGTAGAT
1 ATCTTTTACCCCGAGCTGGGGTAGATTGCAGCCATTCGATCTTTTACCCTGAGCCTGGGGCAGAT
* * * *
20227666 CACCATTAGCCAATCTCTTACCCCGAGCCT-GAGGCAGATTGTAGCCAT-TCGATCTTTTACTCT
66 CACCATCAACCAATCTCTTACCCCGAGCCTGGA-GCAGATTGTAGCCATCT-GATCTTTTACCCC
*
20227729 GAGCCTAGGGTAGATCACCATCAGCCA
129 AAGCCTAGGGTAGATCACCATCAGCCA
* * * *
20227756 ATCTCTTACCCCGAGCCTGGGGCAGATTGCAGCCATTCGATCTTTTATCCTGAGCTTGGGGCAGA
1 ATCTTTTACCCCGAG-CTGGGGTAGATTGCAGCCATTCGATCTTTTACCCTGAGCCTGGGGCAGA
* * *
20227821 TCACCATCAACCAATCTCTTACCTCGAGCCTGGAGTAGATTGTAGTCATCTGATCTTTTACCCCA
65 TCACCATCAACCAATCTCTTACCCCGAGCCTGGAGCAGATTGTAGCCATCTGATCTTTTACCCCA
* * *
20227886 AGCCTGGGGTAGATCACCATTAGCTA
130 AGCCTAGGGTAGATCACCATCAGCCA
* * * * * *
20227912 ATCTTTTACCCCGCAACAGGGGTAGATTGCAGCCATTCAATCTTTTACCCCGATCATGGGGCAGA
1 ATCTTTTACCCCG-AGCTGGGGTAGATTGCAGCCATTCGATCTTTTACCCTGAGCCTGGGGCAGA
* ** * * * * * * * *
20227977 TCATCGCCAATCAATCTCTTACCCCGCGACAGGGGCAGATTGCAACCATCCGATCTTTTA
65 TCACCATCAACCAATCTCTTACCCCGAGCCTGGAGCAGATTGTAGCCATCTGATCTTTTA
20228037 TCCCGATTAT
Statistics
Matches: 236, Mismatches: 41, Indels: 7
0.83 0.14 0.02
Matches are distributed among these distances:
155 14 0.06
156 218 0.92
157 4 0.02
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (155 bp):
ATCTTTTACCCCGAGCTGGGGTAGATTGCAGCCATTCGATCTTTTACCCTGAGCCTGGGGCAGAT
CACCATCAACCAATCTCTTACCCCGAGCCTGGAGCAGATTGTAGCCATCTGATCTTTTACCCCAA
GCCTAGGGTAGATCACCATCAGCCA
Found at i:20228042 original size:78 final size:77
Alignment explanation
Indices: 20227619--20228130 Score: 320
Period size: 78 Copynumber: 6.6 Consensus size: 77
20227609 CCCCGAGCTT
* * * *
20227619 GGGTAGATTGCAGCCATCCGATCTTTTACCCTGAGCCTGGGGTAGATCA--CCATTAGCCAATCT
1 GGGTAGATTGCAGCCATCCGATCTTTTACCCCGATCATGGGGCAGATCACGCCA--A-CCAATCT
* * *
20227682 CTTACCCCGAGCCTG
63 CTTACCCCGCGACAG
* * * * * * * * * * *
20227697 AGGCAGATTGTAGCCATTCGATCTTTTACTCTGAGCCTAGGGTAGATCAC-CATCAGCCAATCTC
1 GGGTAGATTGCAGCCATCCGATCTTTTACCCCGATCATGGGGCAGATCACGC--CAACCAATCTC
* * *
20227761 TTACCCCGAGCCTG
64 TTACCCCGCGACAG
* * * * * *
20227775 GGGCAGATTGCAGCCATTCGATCTTTTATCCTGAGCTTGGGGCAGATCAC-CATCAACCAATCTC
1 GGGTAGATTGCAGCCATCCGATCTTTTACCCCGATCATGGGGCAGATCACGC--CAACCAATCTC
* * * *
20227839 TTACCTCGAGCCTG
64 TTACCCCGCGACAG
* * * * * * * * *
20227853 GAGTAGATTGTAGTCATCTGATCTTTTACCCCAAGCCTGGGGTAGATCA--CCATTAGCTAATCT
1 GGGTAGATTGCAGCCATCCGATCTTTTACCCCGATCATGGGGCAGATCACGCCA--A-CCAATCT
* *
20227916 TTTACCCCGCAACAG
63 CTTACCCCGCGACAG
* * *
20227931 GGGTAGATTGCAGCCATTCAATCTTTTACCCCGATCATGGGGCAGATCATCGCCAATCAATCTCT
1 GGGTAGATTGCAGCCATCCGATCTTTTACCCCGATCATGGGGCAGATCA-CGCCAACCAATCTCT
20227996 TACCCCGCGACAG
65 TACCCCGCGACAG
* * * * * *
20228009 GGGCAGATTGCAACCATCCGATCTTTTATCCCGATTATGGGGCAGATCACAGCCACCCGATCTCT
1 GGGTAGATTGCAGCCATCCGATCTTTTACCCCGATCATGGGGCAGATCAC-GCCAACCAATCTCT
*
20228074 TA--CCTCGACCATG
65 TACCCCGCGA-CA-G
** * * * *
20228087 GGGTAGATCACAACCATCCAATCTCTTACCTCGATCATGGGGCA
1 GGGTAGATTGCAGCCATCCGATCTTTTACCCCGATCATGGGGCA
20228131 AATTGTAGTT
Statistics
Matches: 356, Mismatches: 66, Indels: 24
0.80 0.15 0.05
Matches are distributed among these distances:
75 2 0.01
76 5 0.01
77 5 0.01
78 337 0.95
79 2 0.01
81 5 0.01
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.26
Consensus pattern (77 bp):
GGGTAGATTGCAGCCATCCGATCTTTTACCCCGATCATGGGGCAGATCACGCCAACCAATCTCTT
ACCCCGCGACAG
Found at i:20228051 original size:39 final size:39
Alignment explanation
Indices: 20227951--20228130 Score: 154
Period size: 39 Copynumber: 4.6 Consensus size: 39
20227941 CAGCCATTCA
* * * *
20227951 ATCTTTTACCCCGATCATGGGGCAGATCATC-GCCAAT-CA
1 ATCTCTTACCTCGATCATGGGGCAGATCA-CAACC-ATCCG
* **
20227990 ATCTCTTACCCCGCGA-CA-GGGGCAGATTGCAACCATCCG
1 ATCTCTTA--CCTCGATCATGGGGCAGATCACAACCATCCG
* * * *
20228029 ATCTTTTATCC-CGATTATGGGGCAGATCACAGCCACCCG
1 ATCTCTTA-CCTCGATCATGGGGCAGATCACAACCATCCG
* * *
20228068 ATCTCTTACCTCGACCATGGGGTAGATCACAACCATCCA
1 ATCTCTTACCTCGATCATGGGGCAGATCACAACCATCCG
20228107 ATCTCTTACCTCGATCATGGGGCA
1 ATCTCTTACCTCGATCATGGGGCA
20228131 AATTGTAGTT
Statistics
Matches: 112, Mismatches: 22, Indels: 14
0.76 0.15 0.09
Matches are distributed among these distances:
37 3 0.03
38 8 0.07
39 94 0.84
40 2 0.02
41 5 0.04
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.24
Consensus pattern (39 bp):
ATCTCTTACCTCGATCATGGGGCAGATCACAACCATCCG
Found at i:20228654 original size:113 final size:113
Alignment explanation
Indices: 20228452--20228673 Score: 356
Period size: 113 Copynumber: 2.0 Consensus size: 113
20228442 AAGTGATGCA
*
20228452 GTCATCTTTCTGATGAGATACAGAGAAGTACACCAAATCAATGAAACAAAGCTCAAAAAGAGCGA
1 GTCATCTTCCTGATGAGATACAGAGAAGTACACCAAATCAATGAAACAAAGCTCAAAAAGAGCGA
*
20228517 AACTTCAAACCCCAGCTTTCTGATGAGATACTGAGAAGCAGGTCAAAG
66 AACTTCAAACCCCAACTTTCTGATGAGATACTGAGAAGCAGGTCAAAG
* ***
20228565 GTCATCTTCCTGATGAGATACAGAGAAGTATACCAAATCAATGAAACAAAGCTCAATGTGAGCGA
1 GTCATCTTCCTGATGAGATACAGAGAAGTACACCAAATCAATGAAACAAAGCTCAAAAAGAGCGA
**
20228630 AACTTTGAACCCCAAC-TTCTTGATGAGATACTGAGAAGCAGGTC
66 AACTTCAAACCCCAACTTTC-TGATGAGATACTGAGAAGCAGGTC
20228674 GAAGCAATAA
Statistics
Matches: 100, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
112 3 0.03
113 97 0.97
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.21
Consensus pattern (113 bp):
GTCATCTTCCTGATGAGATACAGAGAAGTACACCAAATCAATGAAACAAAGCTCAAAAAGAGCGA
AACTTCAAACCCCAACTTTCTGATGAGATACTGAGAAGCAGGTCAAAG
Found at i:20230721 original size:30 final size:30
Alignment explanation
Indices: 20230669--20230764 Score: 133
Period size: 30 Copynumber: 3.2 Consensus size: 30
20230659 AAAACTTTCA
*
20230669 AAAATTACATTTTAA-TCCTAAACTTCTTT
1 AAAATTACATTTTAACCCCTAAACTTCTTT
20230698 AAAATTACATTTTAACCCCTAAACTT-TTCT
1 AAAATTACATTTTAACCCCTAAACTTCTT-T
* * *
20230728 AAAATTGCATTTTAACCCCCAAACTTCTCT
1 AAAATTACATTTTAACCCCTAAACTTCTTT
20230758 AAAATTA
1 AAAATTA
20230765 TGATTTTGCC
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
29 17 0.29
30 41 0.69
31 1 0.02
ACGTcount: A:0.39, C:0.22, G:0.01, T:0.39
Consensus pattern (30 bp):
AAAATTACATTTTAACCCCTAAACTTCTTT
Found at i:20230781 original size:30 final size:30
Alignment explanation
Indices: 20230660--20230771 Score: 99
Period size: 30 Copynumber: 3.8 Consensus size: 30
20230650 TTGATCGCCA
* * * *
20230660 AAACTT-TCAAAAATTA-CATTTTAATCCT
1 AAACTTCTCTAAAATTATGATTTTAACCCC
* *
20230688 AAACTTCTTTAAAATTA-CATTTTAACCCC
1 AAACTTCTCTAAAATTATGATTTTAACCCC
*
20230717 TAAACTTTTCTAAAA-T-TGCATTTTAACCCCC
1 -AAACTTCTCTAAAATTATG-ATTTTAA-CCCC
20230748 AAACTTCTCTAAAATTATGATTTT
1 AAACTTCTCTAAAATTATGATTTT
20230772 GCCCTCAAAC
Statistics
Matches: 69, Mismatches: 8, Indels: 11
0.78 0.09 0.12
Matches are distributed among these distances:
28 6 0.09
29 19 0.28
30 32 0.46
31 10 0.14
32 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.02, T:0.40
Consensus pattern (30 bp):
AAACTTCTCTAAAATTATGATTTTAACCCC
Found at i:20230800 original size:28 final size:29
Alignment explanation
Indices: 20230769--20230828 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
20230759 AAATTATGAT
*
20230769 TTTG-CCCTCAAACATCTAAAAATTACCA
1 TTTGTCCCTCAAACATCCAAAAATTACCA
*
20230797 TTTGTCCCTCGAACATCCAAAAATTACCA
1 TTTGTCCCTCAAACATCCAAAAATTACCA
20230826 TTT
1 TTT
20230829 TGTTCCCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 4 0.14
29 25 0.86
ACGTcount: A:0.35, C:0.28, G:0.05, T:0.32
Consensus pattern (29 bp):
TTTGTCCCTCAAACATCCAAAAATTACCA
Found at i:20230915 original size:28 final size:27
Alignment explanation
Indices: 20230864--20230919 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
20230854 TTTTCAACCT
*
20230864 CAAATTTTCCAAAAGTGCGATTTTAAC
1 CAAATTTTCCAAAAGTGCAATTTTAAC
* *
20230891 CAAATTTTCCAAAAATTTCAATTTTAAC
1 CAAATTTTCC-AAAAGTGCAATTTTAAC
20230919 C
1 C
20230920 CCTAAATTCC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 10 0.40
28 15 0.60
ACGTcount: A:0.39, C:0.20, G:0.05, T:0.36
Consensus pattern (27 bp):
CAAATTTTCCAAAAGTGCAATTTTAAC
Found at i:20236535 original size:17 final size:17
Alignment explanation
Indices: 20236513--20236551 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
20236503 CTCCACCTTG
* *
20236513 ACAAGAATTCTCTACGA
1 ACAAGAACTCTCAACGA
20236530 ACAAGAACTCTCAACGA
1 ACAAGAACTCTCAACGA
*
20236547 GCAAG
1 ACAAG
20236552 TTCTCCACCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.44, C:0.26, G:0.15, T:0.15
Consensus pattern (17 bp):
ACAAGAACTCTCAACGA
Found at i:20249104 original size:43 final size:43
Alignment explanation
Indices: 20249008--20249258 Score: 348
Period size: 43 Copynumber: 5.9 Consensus size: 43
20248998 TCTTTACACG
* * **
20249008 TAATCTCATGCTC-ATCCTGAGTCACAAGTCTT-CTTTAAAACA
1 TAATCTCATGCTCTTTCC-GAGTCACGAGTCTTCCTTTTTAACA
*
20249050 TAATCTCATGCTCTTTCCGAGTCACGAGTCTTCCTTTTAAACA
1 TAATCTCATGCTCTTTCCGAGTCACGAGTCTTCCTTTTTAACA
**
20249093 TAATCTCATGCTCTTTCTAAGTCACGAGTCTTCCTTTTTAACA
1 TAATCTCATGCTCTTTCCGAGTCACGAGTCTTCCTTTTTAACA
* *
20249136 TAATCTCATGCTTTTTTCGAGTCACGAGTCTTCCTTTTTAACA
1 TAATCTCATGCTCTTTCCGAGTCACGAGTCTTCCTTTTTAACA
20249179 TAATCTCATGCTCATTT-CGAGTCACGAGTCTTCCTTTTTAACA
1 TAATCTCATGCTC-TTTCCGAGTCACGAGTCTTCCTTTTTAACA
* *
20249222 TAATCTCATGCTC-TTCTCGAGACATGAGTCTTCCTTT
1 TAATCTCATGCTCTTTC-CGAGTCACGAGTCTTCCTTT
20249259 AATATACCCT
Statistics
Matches: 191, Mismatches: 13, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
41 2 0.01
42 26 0.14
43 160 0.84
44 3 0.02
ACGTcount: A:0.24, C:0.26, G:0.11, T:0.39
Consensus pattern (43 bp):
TAATCTCATGCTCTTTCCGAGTCACGAGTCTTCCTTTTTAACA
Found at i:20250114 original size:13 final size:13
Alignment explanation
Indices: 20250068--20250122 Score: 60
Period size: 13 Copynumber: 4.3 Consensus size: 13
20250058 CCTAGTTGTT
20250068 AACCC-AAACCC-
1 AACCCTAAACCCA
* *
20250079 AACACTTAACCCA
1 AACCCTAAACCCA
*
20250092 AACCTTTAAACCCA
1 AACC-CTAAACCCA
20250106 AACCCTAAACCCA
1 AACCCTAAACCCA
20250119 AACC
1 AACC
20250123 AAACACCCAA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
11 4 0.11
12 5 0.14
13 15 0.43
14 11 0.31
ACGTcount: A:0.45, C:0.44, G:0.00, T:0.11
Consensus pattern (13 bp):
AACCCTAAACCCA
Found at i:20250358 original size:14 final size:14
Alignment explanation
Indices: 20250336--20250367 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
20250326 TTTAGAGGTT
*
20250336 TAATTTGGGAAATC
1 TAATGTGGGAAATC
20250350 TAATGTGGGAAATC
1 TAATGTGGGAAATC
20250364 TAAT
1 TAAT
20250368 ATATATTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.38, C:0.06, G:0.22, T:0.34
Consensus pattern (14 bp):
TAATGTGGGAAATC
Found at i:20250427 original size:6 final size:6
Alignment explanation
Indices: 20250416--20250446 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
20250406 TGTAATATCA
*
20250416 TGAGAT TGAGAT TGAGAG TGAGAT TGAGAT T
1 TGAGAT TGAGAT TGAGAT TGAGAT TGAGAT T
20250447 AAAACTGAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.32, C:0.00, G:0.35, T:0.32
Consensus pattern (6 bp):
TGAGAT
Found at i:20250455 original size:18 final size:18
Alignment explanation
Indices: 20250416--20250457 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
20250406 TGTAATATCA
* * *
20250416 TGAGATTGAGATTGAGAG
1 TGAGATTGAGATTAAAAC
20250434 TGAGATTGAGATTAAAAC
1 TGAGATTGAGATTAAAAC
20250452 TGAGAT
1 TGAGAT
20250458 ATACATGTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.38, C:0.02, G:0.31, T:0.29
Consensus pattern (18 bp):
TGAGATTGAGATTAAAAC
Found at i:20260224 original size:2 final size:2
Alignment explanation
Indices: 20260217--20260241 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20260207 ATTACCATTA
20260217 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
20260242 AGAAGTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20266701 original size:19 final size:19
Alignment explanation
Indices: 20266677--20266717 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
20266667 AACTAAATTA
*
20266677 ACAAAA-AAGAAATGCTATG
1 ACAAAATAA-AAATGCAATG
20266696 ACAAAATAAAAATGCAATG
1 ACAAAATAAAAATGCAATG
20266715 ACA
1 ACA
20266718 GTAAAATGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 18 0.90
20 2 0.10
ACGTcount: A:0.61, C:0.12, G:0.12, T:0.15
Consensus pattern (19 bp):
ACAAAATAAAAATGCAATG
Found at i:20274425 original size:19 final size:19
Alignment explanation
Indices: 20274401--20274437 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
20274391 ACTGAGATAG
20274401 TACAGATTAGATCCTTCTT
1 TACAGATTAGATCCTTCTT
20274420 TACAGATTAGATCCTTCT
1 TACAGATTAGATCCTTCT
20274438 CATGTGATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.22, G:0.11, T:0.41
Consensus pattern (19 bp):
TACAGATTAGATCCTTCTT
Found at i:20278066 original size:15 final size:15
Alignment explanation
Indices: 20278051--20278080 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
20278041 CTCTGACGAT
20278051 GATATCTATGAAGATG
1 GATAT-TATGAAGATG
20278067 GATATTATGAAGAT
1 GATATTATGAAGAT
20278081 TAGGAGATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.40, C:0.03, G:0.23, T:0.33
Consensus pattern (15 bp):
GATATTATGAAGATG
Found at i:20298974 original size:55 final size:55
Alignment explanation
Indices: 20298903--20299031 Score: 186
Period size: 55 Copynumber: 2.3 Consensus size: 55
20298893 AGATTGAATT
* * ** *
20298903 GATTGTTATGCTGGAATATTGCTTCTTTTGAATCGATTGTTTTTATGTTTAAATC
1 GATTGTCATGTTGGAATACCGCTTCTTTTGAATCGATTGTTTTTATATTTAAATC
20298958 GATTGTCATGTTGGAATACCGCTTCTTTTGAATCGATTGTTTTTATATTTAAATC
1 GATTGTCATGTTGGAATACCGCTTCTTTTGAATCGATTGTTTTTATATTTAAATC
* * *
20299013 AATTGTCATATTGAAATAC
1 GATTGTCATGTTGGAATAC
20299032 TTTTATGCAG
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
55 66 1.00
ACGTcount: A:0.26, C:0.11, G:0.16, T:0.47
Consensus pattern (55 bp):
GATTGTCATGTTGGAATACCGCTTCTTTTGAATCGATTGTTTTTATATTTAAATC
Found at i:20299812 original size:18 final size:18
Alignment explanation
Indices: 20299789--20299835 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
20299779 ATGGTAAAAT
20299789 AATAAAATACATGAATAA
1 AATAAAATACATGAATAA
* * *
20299807 AATAAATTAAATGAATAC
1 AATAAAATACATGAATAA
*
20299825 AATTAAATACA
1 AATAAAATACA
20299836 ATTAATAACA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.64, C:0.06, G:0.04, T:0.26
Consensus pattern (18 bp):
AATAAAATACATGAATAA
Found at i:20300954 original size:4 final size:4
Alignment explanation
Indices: 20300947--20301003 Score: 66
Period size: 4 Copynumber: 14.8 Consensus size: 4
20300937 TAACAACAAG
* *
20300947 ATAA ATAA ACAA A-AA ATAA ATAA A-AA ATAA ATAA AT-A CTAAA ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA AT-AA ATAA
20300993 ATAA ATAA ATA
1 ATAA ATAA ATA
20301004 TAAACAATAA
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
3 8 0.17
4 36 0.78
5 2 0.04
ACGTcount: A:0.75, C:0.04, G:0.00, T:0.21
Consensus pattern (4 bp):
ATAA
Found at i:20300978 original size:11 final size:11
Alignment explanation
Indices: 20300949--20301014 Score: 69
Period size: 11 Copynumber: 5.6 Consensus size: 11
20300939 ACAACAAGAT
*
20300949 AAATAAACAAA
1 AAATAAATAAA
20300960 AAATAAATAAA
1 AAATAAATAAA
20300971 AAATAAATAAA
1 AAATAAATAAA
* *
20300982 TACTAAAATAAA
1 AAAT-AAATAAA
20300994 TAAATAAATATAA
1 -AAATAAATA-AA
20301007 ACAATAAA
1 A-AATAAA
20301015 AATAATTAGG
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
11 23 0.50
12 13 0.28
13 10 0.22
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.20
Consensus pattern (11 bp):
AAATAAATAAA
Found at i:20300981 original size:30 final size:29
Alignment explanation
Indices: 20300929--20301001 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 29
20300919 AAATGACATG
* *
20300929 AAAATAAATAACAACAAGATAAATA-AACAA
1 AAAATAAATAA-AAAAAAATAAATACAA-AA
20300959 AAAATAAATAAAAAATAAATAAATACTAAAA
1 AAAATAAATAAAAAA-AAATAAATAC-AAAA
*
20300990 TAAATAAATAAA
1 AAAATAAATAAA
20301002 TATAAACAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
29 3 0.08
30 19 0.51
31 13 0.35
32 2 0.05
ACGTcount: A:0.75, C:0.05, G:0.01, T:0.18
Consensus pattern (29 bp):
AAAATAAATAAAAAAAAATAAATACAAAA
Found at i:20300991 original size:16 final size:15
Alignment explanation
Indices: 20300947--20301001 Score: 76
Period size: 15 Copynumber: 3.6 Consensus size: 15
20300937 TAACAACAAG
20300947 ATAAATAAACAAA-AA
1 ATAAATAAA-AAATAA
20300962 ATAAATAAAAAATAA
1 ATAAATAAAAAATAA
*
20300977 ATAAATACTAAAATAA
1 ATAAATA-AAAAATAA
20300993 ATAAATAAA
1 ATAAATAAA
20301002 TATAAACAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
14 3 0.08
15 19 0.53
16 14 0.39
ACGTcount: A:0.76, C:0.04, G:0.00, T:0.20
Consensus pattern (15 bp):
ATAAATAAAAAATAA
Found at i:20301016 original size:27 final size:26
Alignment explanation
Indices: 20300951--20301019 Score: 74
Period size: 27 Copynumber: 2.7 Consensus size: 26
20300941 AACAAGATAA
20300951 ATAAAC-A-AAAAATAAATAAAAAAT
1 ATAAACAATAAAAATAAATAAAAAAT
20300975 A-AATA-AATACTAAAATAAATAAATAAAT
1 ATAA-ACAATA--AAAATAAATAAA-AAAT
20301003 ATAAACAATAAAAATAA
1 ATAAACAATAAAAATAA
20301020 TTAGGATTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 13
0.74 0.00 0.26
Matches are distributed among these distances:
23 2 0.05
24 3 0.08
25 1 0.03
27 19 0.51
28 6 0.16
29 6 0.16
ACGTcount: A:0.75, C:0.04, G:0.00, T:0.20
Consensus pattern (26 bp):
ATAAACAATAAAAATAAATAAAAAAT
Found at i:20301368 original size:23 final size:25
Alignment explanation
Indices: 20301323--20301371 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
20301313 GAATTTTCTA
*
20301323 TGAATGTATGTCTAAAAATAATCTC
1 TGAATGTATGTATAAAAATAATCTC
20301348 TGAATGT-TGTATAAAAA-AATCTC
1 TGAATGTATGTATAAAAATAATCTC
20301371 T
1 T
20301372 AAATCTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 7 0.30
24 9 0.39
25 7 0.30
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (25 bp):
TGAATGTATGTATAAAAATAATCTC
Found at i:20302136 original size:45 final size:45
Alignment explanation
Indices: 20301947--20302537 Score: 644
Period size: 45 Copynumber: 12.9 Consensus size: 45
20301937 GCTTTCTATA
* * * *
20301947 GCTTCAATTTGCCCCTCTGGATTTAGGGGTATAAGATTGGATGTGGTA
1 GCTTCAATCTGCCCCTTTGGA-TTAGGGGTAAAAGATTGGA--TGGTG
* * * * * *
20301995 GCTTAAATCTGCCCCTCTAGATTTAAGGGTATAAGATTGGATGTGGTA
1 GCTTCAATCTGCCCCTTTGGA-TTAGGGGTAAAAGATTGGA--TGGTG
* * *
20302043 GCTTCAATCTGTCCATTTGGATTTATGGGGTAAAAGATTGGATAGTG
1 GCTTCAATCTGCCCCTTTGGA-TTA-GGGGTAAAAGATTGGATGGTG
** *
20302090 GCTTCAATCTATCCCTTTGGATTAAGGGTAAAAGATTGGATGGTG
1 GCTTCAATCTGCCCCTTTGGATTAGGGGTAAAAGATTGGATGGTG
* * * *
20302135 GCTTAAATCTACCCCTTTGGATTAGGAGTAAAAGATTGGATGGAG
1 GCTTCAATCTGCCCCTTTGGATTAGGGGTAAAAGATTGGATGGTG
* * * **
20302180 ACTTCAATTTGTCCCTTTGGATTAGGGGTAAAAGATTGGATGACG
1 GCTTCAATCTGCCCCTTTGGATTAGGGGTAAAAGATTGGATGGTG
*
20302225 GCTTCAATCTGCCCCTTTAGATTAGGGGTAAAAGATTGGATGGTG
1 GCTTCAATCTGCCCCTTTGGATTAGGGGTAAAAGATTGGATGGTG
* * * *
20302270 GTTTCAATCTGCCCCTCTAGATTAGGGGTGAAAGATTGGATGGTG
1 GCTTCAATCTGCCCCTTTGGATTAGGGGTAAAAGATTGGATGGTG
* * *
20302315 GCTTTAATCTG-TCCTTCTGGATTAGGGGTAAAAGATTGGATTTTGTG
1 GCTTCAATCTGCCCCTT-TGGATTAGGGGTAAAAGATTGGA--TGGTG
* * * *
20302362 ACTTCAATCTGCCCTTTTAGATTAGGGGTAAAAGACTGGATGGTG
1 GCTTCAATCTGCCCCTTTGGATTAGGGGTAAAAGATTGGATGGTG
* * * *
20302407 GCTTCAATCTGCCCCTCTAGATTAGGGGTAAAAGACTAGATGGTG
1 GCTTCAATCTGCCCCTTTGGATTAGGGGTAAAAGATTGGATGGTG
* * * * *
20302452 GCTTCAATCTGCCTCTCTGGATTAAGGGTAAATGACTGGATGGTG
1 GCTTCAATCTGCCCCTTTGGATTAGGGGTAAAAGATTGGATGGTG
* *
20302497 GCTTCAATTTGCCCCTCTGGATTAGGGGTAAAAGATTGGAT
1 GCTTCAATCTGCCCCTTTGGATTAGGGGTAAAAGATTGGAT
20302538 TTGGTGATGT
Statistics
Matches: 471, Mismatches: 67, Indels: 13
0.85 0.12 0.02
Matches are distributed among these distances:
44 3 0.01
45 328 0.70
46 3 0.01
47 56 0.12
48 67 0.14
49 14 0.03
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.33
Consensus pattern (45 bp):
GCTTCAATCTGCCCCTTTGGATTAGGGGTAAAAGATTGGATGGTG
Found at i:20302451 original size:182 final size:180
Alignment explanation
Indices: 20301947--20302544 Score: 691
Period size: 182 Copynumber: 3.3 Consensus size: 180
20301937 GCTTTCTATA
* * * * * *
20301947 GCTTCAATTTGCCCCTCTGGATTTAGGGGTATAAGATTGGATGTGGT-AGCTTAAATCTGCCCCT
1 GCTTAAATCTGCCCTTCTGGA-TTAGGGGTAAAAGATTGGATTTGGTGA-CTTCAATCTG-CCCT
* * * * * * *
20302011 CTAGATTTAAGGGTATAAGATTGGATGTGGTAGCTTCAATCTGTCCATTTGGATTTATGGGGTAA
63 TTAGA-TTAGGGGTAAAAGATTGGA--TGGTGGCTTCAATCTGCCCCTTTAGA-TTA-GGGGTAA
* ** *
20302076 AAGATTGGATAGTGGCTTCAATCTATCCCTTTGGATTAAGGGTAAAAGATTGGATGGTG
123 AAGATTGGATGGTGGCTTCAATCTGCCCCTCTGGATTAAGGGT-AAAGATTGGATGGTG
* * * *
20302135 GCTTAAATCTACCCCTT-TGGATTAGGAGTAAAAGATTGGA--TGGAGACTTCAATTTGTCCCTT
1 GCTTAAATCT-GCCCTTCTGGATTAGGGGTAAAAGATTGGATTTGGTGACTTCAATCTG-CCCTT
* **
20302197 TGGATTAGGGGTAAAAGATTGGATGACGGCTTCAATCTGCCCCTTTAGATTAGGGGTAAAAGATT
64 TAGATTAGGGGTAAAAGATTGGATGGTGGCTTCAATCTGCCCCTTTAGATTAGGGGTAAAAGATT
* * *
20302262 GGATGGTGGTTTCAATCTGCCCCTCTAGATTAGGGGTGAAAGATTGGATGGTG
129 GGATGGTGGCTTCAATCTGCCCCTCTGGATTAAGGGT-AAAGATTGGATGGTG
* * *
20302315 GCTTTAATCTGTCCTTCTGGATTAGGGGTAAAAGATTGGATTTTGTGACTTCAATCTGCCCTTTT
1 GCTTAAATCTGCCCTTCTGGATTAGGGGTAAAAGATTGGATTTGGTGACTTCAATCTGCCC-TTT
* * * *
20302380 AGATTAGGGGTAAAAGACTGGATGGTGGCTTCAATCTGCCCCTCTAGATTAGGGGTAAAAGACTA
65 AGATTAGGGGTAAAAGATTGGATGGTGGCTTCAATCTGCCCCTTTAGATTAGGGGTAAAAGATTG
* *
20302445 GATGGTGGCTTCAATCTGCCTCTCTGGATTAAGGGTAAATGACTGGATGGTG
130 GATGGTGGCTTCAATCTGCCCCTCTGGATTAAGGGTAAA-GATTGGATGGTG
* * *
20302497 GCTTCAATTTGCCCCTCTGGATTAGGGGTAAAAGATTGGATTTGGTGA
1 GCTTAAATCTGCCCTTCTGGATTAGGGGTAAAAGATTGGATTTGGTGA
20302545 TGTAACTTCA
Statistics
Matches: 351, Mismatches: 52, Indels: 20
0.83 0.12 0.05
Matches are distributed among these distances:
179 4 0.01
180 89 0.25
181 9 0.03
182 180 0.51
184 17 0.05
185 18 0.05
186 1 0.00
187 17 0.05
188 12 0.03
189 4 0.01
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.33
Consensus pattern (180 bp):
GCTTAAATCTGCCCTTCTGGATTAGGGGTAAAAGATTGGATTTGGTGACTTCAATCTGCCCTTTA
GATTAGGGGTAAAAGATTGGATGGTGGCTTCAATCTGCCCCTTTAGATTAGGGGTAAAAGATTGG
ATGGTGGCTTCAATCTGCCCCTCTGGATTAAGGGTAAAGATTGGATGGTG
Found at i:20302583 original size:50 final size:50
Alignment explanation
Indices: 20302529--20302684 Score: 136
Period size: 50 Copynumber: 3.1 Consensus size: 50
20302519 TAGGGGTAAA
* * *
20302529 AGATTGGATTTGGTGATGTAACTTCACTCCATTTCACTGTAACTTTATGG
1 AGATTGGATTTGGTGATGTAACTTCACTCCATTACACTGTAACTTCAAGG
* * ** * * ** * *
20302579 AGATTGAGATCTGCT-ACTGTAGTTTTAATCCGCTACACTGCAACTTCAAGA
1 AGATTG-GATTTGGTGA-TGTAACTTCACTCCATTACACTGTAACTTCAAGG
* *
20302630 AGATAGGATTTGGTG-TGGTAACTTCACTCCATTCCACTGTAACTTCAAGG
1 AGATTGGATTTGGTGAT-GTAACTTCACTCCATTACACTGTAACTTCAAGG
20302680 AGATT
1 AGATT
20302685 AAGGTCCGTT
Statistics
Matches: 76, Mismatches: 26, Indels: 8
0.69 0.24 0.07
Matches are distributed among these distances:
49 1 0.01
50 41 0.54
51 34 0.45
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.35
Consensus pattern (50 bp):
AGATTGGATTTGGTGATGTAACTTCACTCCATTACACTGTAACTTCAAGG
Found at i:20302703 original size:101 final size:101
Alignment explanation
Indices: 20302528--20302774 Score: 331
Period size: 101 Copynumber: 2.5 Consensus size: 101
20302518 TTAGGGGTAA
* * * * * *
20302528 AAGATTGGATTTGGTGAT-GTAACTTCACTCCATTTCACTGTAACTTTATGGAGATTGAGATCTG
1 AAGATAGGATTTGGTG-TGGTAACTTCACTCCATTCCACTGTAACTTCAAGGAGATTAAGATCCG
20302592 CTACTGTAGTTTTAATCCGCTACACTGCAACTTCAAG
65 CTACTGTAGTTTTAATCCGCTACACTGCAACTTCAAG
* *
20302629 AAGATAGGATTTGGTGTGGTAACTTCACTCCATTCCACTGTAACTTCAAGGAGATTAAGGTCCGT
1 AAGATAGGATTTGGTGTGGTAACTTCACTCCATTCCACTGTAACTTCAAGGAGATTAAGATCCGC
* * *
20302694 TACTGTAGTTTTAATCCGCTTCACTGCAACTTTAGG
66 TACTGTAGTTTTAATCCGCTACACTGCAACTTCAAG
* * *
20302730 AATATAGGATTTGGTGTGG---CTTCACTCCGTTCCACTGCAACTTCA
1 AAGATAGGATTTGGTGTGGTAACTTCACTCCATTCCACTGTAACTTCA
20302775 GTGGGTGTTG
Statistics
Matches: 131, Mismatches: 14, Indels: 5
0.87 0.09 0.03
Matches are distributed among these distances:
98 24 0.18
100 1 0.01
101 106 0.81
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (101 bp):
AAGATAGGATTTGGTGTGGTAACTTCACTCCATTCCACTGTAACTTCAAGGAGATTAAGATCCGC
TACTGTAGTTTTAATCCGCTACACTGCAACTTCAAG
Found at i:20306177 original size:32 final size:32
Alignment explanation
Indices: 20306136--20306199 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
20306126 TCTTTATGAG
20306136 GTAGGATCTGTTTCTCATATTACTCAACCATC
1 GTAGGATCTGTTTCTCATATTACTCAACCATC
*
20306168 GTAGGATCTGTTTCTCATCTTACTCAACCATC
1 GTAGGATCTGTTTCTCATATTACTCAACCATC
20306200 CGCTGTAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.23, C:0.27, G:0.12, T:0.38
Consensus pattern (32 bp):
GTAGGATCTGTTTCTCATATTACTCAACCATC
Found at i:20306836 original size:14 final size:15
Alignment explanation
Indices: 20306789--20306838 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 15
20306779 ATGTGAGGAA
*
20306789 TTTTATT-TTTATTT
1 TTTTATTATGTATTT
* *
20306803 TATTTATTATTTATTA
1 T-TTTATTATGTATTT
20306819 TTTT-TTATGTATTT
1 TTTTATTATGTATTT
20306833 TTTTAT
1 TTTTAT
20306839 GAAATTTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
14 13 0.43
15 10 0.33
16 7 0.23
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (15 bp):
TTTTATTATGTATTT
Found at i:20309384 original size:73 final size:73
Alignment explanation
Indices: 20309301--20309447 Score: 294
Period size: 73 Copynumber: 2.0 Consensus size: 73
20309291 CCATTATAGG
20309301 CTCATACGGACTAGTTTGATTTAGGGGGATACATTTCCCATATGTTTGCATGAAAGTGAAAACCT
1 CTCATACGGACTAGTTTGATTTAGGGGGATACATTTCCCATATGTTTGCATGAAAGTGAAAACCT
20309366 CACGAAAA
66 CACGAAAA
20309374 CTCATACGGACTAGTTTGATTTAGGGGGATACATTTCCCATATGTTTGCATGAAAGTGAAAACCT
1 CTCATACGGACTAGTTTGATTTAGGGGGATACATTTCCCATATGTTTGCATGAAAGTGAAAACCT
20309439 CACGAAAA
66 CACGAAAA
20309447 C
1 C
20309448 ATTGGTACGA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 74 1.00
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (73 bp):
CTCATACGGACTAGTTTGATTTAGGGGGATACATTTCCCATATGTTTGCATGAAAGTGAAAACCT
CACGAAAA
Found at i:20309618 original size:20 final size:21
Alignment explanation
Indices: 20309589--20309629 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
20309579 CTATCCTCCA
20309589 ACGCAAGTCC-TTTTTCTGAC
1 ACGCAAGTCCGTTTTTCTGAC
* *
20309609 ACGCATGTCCGTTTTTTTGAC
1 ACGCAAGTCCGTTTTTCTGAC
20309630 GCATTGAGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.17, C:0.27, G:0.17, T:0.39
Consensus pattern (21 bp):
ACGCAAGTCCGTTTTTCTGAC
Found at i:20313815 original size:83 final size:83
Alignment explanation
Indices: 20313676--20313842 Score: 334
Period size: 83 Copynumber: 2.0 Consensus size: 83
20313666 CAACTACCTC
20313676 GATACTCAATCACACAACCTCACAACATGTCTTTCAAAACCTGAATCACACGTTTGGATTGATCG
1 GATACTCAATCACACAACCTCACAACATGTCTTTCAAAACCTGAATCACACGTTTGGATTGATCG
20313741 TCAGTATGCGAATGGTAA
66 TCAGTATGCGAATGGTAA
20313759 GATACTCAATCACACAACCTCACAACATGTCTTTCAAAACCTGAATCACACGTTTGGATTGATCG
1 GATACTCAATCACACAACCTCACAACATGTCTTTCAAAACCTGAATCACACGTTTGGATTGATCG
20313824 TCAGTATGCGAATGGTAA
66 TCAGTATGCGAATGGTAA
20313842 G
1 G
20313843 TAGTACTGAA
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 84 1.00
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (83 bp):
GATACTCAATCACACAACCTCACAACATGTCTTTCAAAACCTGAATCACACGTTTGGATTGATCG
TCAGTATGCGAATGGTAA
Found at i:20318425 original size:18 final size:18
Alignment explanation
Indices: 20318402--20318449 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
20318392 CATGTAAAGT
20318402 AACCACAAAGCATGATAC
1 AACCACAAAGCATGATAC
20318420 AACCACAAAGCATGATAC
1 AACCACAAAGCATGATAC
20318438 AACCAC-AAGCAT
1 AACCACAAAGCAT
20318450 AATGCAATGC
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 6 0.20
18 24 0.80
ACGTcount: A:0.50, C:0.29, G:0.10, T:0.10
Consensus pattern (18 bp):
AACCACAAAGCATGATAC
Found at i:20335499 original size:20 final size:20
Alignment explanation
Indices: 20335464--20335555 Score: 71
Period size: 20 Copynumber: 4.6 Consensus size: 20
20335454 ATTCTAAAAT
* *
20335464 CAAGTTAAAATGATTTTAAA
1 CAAGTCAAAATAATTTTAAA
* *
20335484 CATGTCAAAATAA-TTTGAA
1 CAAGTCAAAATAATTTTAAA
*
20335503 CTAAGTCAAAATCATTTT-AA
1 C-AAGTCAAAATAATTTTAAA
** **
20335523 CACTTCAAAATGTTTTTCAAA
1 CAAGTCAAAATAATTTT-AAA
20335544 CAAGTCAAAATA
1 CAAGTCAAAATA
20335556 GCTCCAGGCC
Statistics
Matches: 55, Mismatches: 13, Indels: 7
0.73 0.17 0.09
Matches are distributed among these distances:
19 18 0.33
20 23 0.42
21 14 0.25
ACGTcount: A:0.47, C:0.13, G:0.08, T:0.33
Consensus pattern (20 bp):
CAAGTCAAAATAATTTTAAA
Found at i:20355795 original size:20 final size:20
Alignment explanation
Indices: 20355752--20355805 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 20
20355742 ATACCGATTT
* ** *
20355752 AAAATTATCGATACTTTTAT
1 AAAAATATCGATACTCGTAA
20355772 AAAAATATCGATACTCGTAA
1 AAAAATATCGATACTCGTAA
* *
20355792 AAAAGTATTGATAC
1 AAAAATATCGATAC
20355806 CACAAGCCTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.46, C:0.11, G:0.09, T:0.33
Consensus pattern (20 bp):
AAAAATATCGATACTCGTAA
Found at i:20358023 original size:20 final size:20
Alignment explanation
Indices: 20357994--20358079 Score: 68
Period size: 20 Copynumber: 4.3 Consensus size: 20
20357984 AAATCAGTTT
* *
20357994 AAAATGATTTTAAACATGTC
1 AAAATAATTTTAAACAAGTC
* *
20358014 AAAATAATTTGAAATAAGTC
1 AAAATAATTTTAAACAAGTC
* **
20358034 AAAATCATTTT-AACACTTC
1 AAAATAATTTTAAACAAGTC
*
20358053 AAAAT-GTTTTCCAAACAAGTC
1 AAAATAATTTT--AAACAAGTC
20358074 AAAATA
1 AAAATA
20358080 GCTCCAAGCC
Statistics
Matches: 50, Mismatches: 12, Indels: 6
0.74 0.18 0.09
Matches are distributed among these distances:
18 4 0.08
19 10 0.20
20 25 0.50
21 11 0.22
ACGTcount: A:0.49, C:0.13, G:0.07, T:0.31
Consensus pattern (20 bp):
AAAATAATTTTAAACAAGTC
Found at i:20362505 original size:17 final size:17
Alignment explanation
Indices: 20362466--20362511 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
20362456 ATATATATGA
**
20362466 AAATGCAATGACAATGT
1 AAATGCAATGACAATAC
* *
20362483 AGATGCAGTGACAATAC
1 AAATGCAATGACAATAC
20362500 AAATGCAATGAC
1 AAATGCAATGAC
20362512 GTTAATAATG
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.46, C:0.15, G:0.20, T:0.20
Consensus pattern (17 bp):
AAATGCAATGACAATAC
Found at i:20369583 original size:21 final size:22
Alignment explanation
Indices: 20369536--20369589 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
20369526 TAGTACAGAT
*
20369536 TTCTACCGATACAAGTGGCAGC
1 TTCTACCGATACAAGTGACAGC
* *
20369558 -GCTACCGATACAAGTGAC-TC
1 TTCTACCGATACAAGTGACAGC
20369578 TTCTACCGATAC
1 TTCTACCGATAC
20369590 TAGAAACTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 1 0.04
21 26 0.96
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.24
Consensus pattern (22 bp):
TTCTACCGATACAAGTGACAGC
Found at i:20369598 original size:21 final size:21
Alignment explanation
Indices: 20369559--20369599 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
20369549 AGTGGCAGCG
**
20369559 CTACCGATACAAGTGACTCTT
1 CTACCGATACAAGAAACTCTT
*
20369580 CTACCGATACTAGAAACTCT
1 CTACCGATACAAGAAACTCT
20369600 AGAGAGCTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.32, C:0.29, G:0.12, T:0.27
Consensus pattern (21 bp):
CTACCGATACAAGAAACTCTT
Found at i:20369675 original size:18 final size:17
Alignment explanation
Indices: 20369643--20369676 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
20369633 CGATACAAGT
20369643 ACACAAACTACCGATAA
1 ACACAAACTACCGATAA
*
20369660 ACACATAACTATCGATA
1 ACACA-AACTACCGATA
20369677 CTTGCAATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.50, C:0.26, G:0.06, T:0.18
Consensus pattern (17 bp):
ACACAAACTACCGATAA
Found at i:20370298 original size:19 final size:19
Alignment explanation
Indices: 20370274--20370382 Score: 139
Period size: 19 Copynumber: 5.8 Consensus size: 19
20370264 TGTGATCCAA
*
20370274 TATTGCTCTTATGAGCCAG
1 TATTGCTCTTACGAGCCAG
* *
20370293 TATTGCTCTTACAAGCCAA
1 TATTGCTCTTACGAGCCAG
*
20370312 TATTGCTCTTATGAGCCAG
1 TATTGCTCTTACGAGCCAG
*
20370331 TATTGCTC-AACGAGCCAG
1 TATTGCTCTTACGAGCCAG
* * *
20370349 TATTACTCTTACGAACTAG
1 TATTGCTCTTACGAGCCAG
20370368 TATTGCTCTTACGAG
1 TATTGCTCTTACGAG
20370383 TAAGTTTTTA
Statistics
Matches: 75, Mismatches: 14, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
18 15 0.20
19 60 0.80
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.34
Consensus pattern (19 bp):
TATTGCTCTTACGAGCCAG
Found at i:20370716 original size:25 final size:26
Alignment explanation
Indices: 20370686--20370743 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
20370676 TTTTAGGTAA
*
20370686 ATTTTTAGAAGTACCCCTATACTTTC
1 ATTTTTAAAAGTACCCCTATACTTTC
*
20370712 ATTTTTAAAAGTACCCTTATACTTTC
1 ATTTTTAAAAGTACCCCTATACTTTC
20370738 ATTTTT
1 ATTTTT
20370744 TATTCAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.28, C:0.19, G:0.05, T:0.48
Consensus pattern (26 bp):
ATTTTTAAAAGTACCCCTATACTTTC
Found at i:20372351 original size:20 final size:20
Alignment explanation
Indices: 20372315--20372364 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
20372305 ATTAGCATGA
20372315 TTTATATTAAGTGTAAATAG-G
1 TTTA-ATTAAGTGTAAA-AGTG
20372336 TTTAATTAAGAT-TAAAAGTG
1 TTTAATTAAG-TGTAAAAGTG
*
20372356 ATTAATTAA
1 TTTAATTAA
20372365 ATCTTAATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 2 0.08
20 19 0.73
21 5 0.19
ACGTcount: A:0.44, C:0.00, G:0.14, T:0.42
Consensus pattern (20 bp):
TTTAATTAAGTGTAAAAGTG
Found at i:20378786 original size:26 final size:26
Alignment explanation
Indices: 20378757--20378810 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
20378747 TAACTTGATT
*
20378757 AATCATATTAAATAATTCAAAATTTA
1 AATCAGATTAAATAATTCAAAATTTA
*
20378783 AATCCGATTAAATAATTCAAAATTTA
1 AATCAGATTAAATAATTCAAAATTTA
20378809 AA
1 AA
20378811 CTTTTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.54, C:0.09, G:0.02, T:0.35
Consensus pattern (26 bp):
AATCAGATTAAATAATTCAAAATTTA
Found at i:20381833 original size:16 final size:17
Alignment explanation
Indices: 20381801--20381833 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
20381791 TAATTATATA
20381801 TAATAAATATATCAAAT
1 TAATAAATATATCAAAT
*
20381818 TAATAATTAT-TCAAAT
1 TAATAAATATATCAAAT
20381834 CTATAAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (17 bp):
TAATAAATATATCAAAT
Found at i:20390839 original size:95 final size:95
Alignment explanation
Indices: 20390676--20390861 Score: 232
Period size: 95 Copynumber: 2.0 Consensus size: 95
20390666 TGTGAATCGA
* * * *
20390676 ACATTAACCATTACACGGTGCTGCTTACACAAGTTGTGAAGAATCCGCAACACATGCAGAATCTT
1 ACATTAACCATTACACGATGCTGCTCACACAAGCTATGAAGAATCCGCAACACATGCAGAATCTT
* *
20390741 AGCCAT-TGATAAGGTGTCTAGTAAGTCTTG
66 AGCCATCAG-TAAGGTATCTAGTAAGTCTTG
* * * * * *
20390771 ACATTAACCATTACACGATGTTGCTCACACGAGCTATGATGAATCTGCAATATATGCAGAA-CTT
1 ACATTAACCATTACACGATGCTGCTCACACAAGCTATGAAGAATCCGCAACACATGCAGAATC-T
20390835 TAGCCATCAGTAAGGTATCTAGTAAGT
65 TAGCCATCAGTAAGGTATCTAGTAAGT
20390862 TGAAACATTA
Statistics
Matches: 77, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
94 1 0.01
95 75 0.97
96 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (95 bp):
ACATTAACCATTACACGATGCTGCTCACACAAGCTATGAAGAATCCGCAACACATGCAGAATCTT
AGCCATCAGTAAGGTATCTAGTAAGTCTTG
Found at i:20390870 original size:95 final size:95
Alignment explanation
Indices: 20390674--20390888 Score: 224
Period size: 95 Copynumber: 2.3 Consensus size: 95
20390664 GCTGTGAATC
* * * *
20390674 GAACATTAACCATTACACGGTGCTGCTTACACAAGTTGTGAAGAATCCGCAACACATGCAGAATC
1 GAACATTAACCATTACACGATGCTGCTCACACAAGCTATGAAGAATCCGCAACACATGCAGAATC
* *
20390739 TTAGCCATTGATAAGGTGTCTAGTAAGTCTT
66 TTAGCCATAGATAAGGTATCTAGTAAG-CTT
* * * * * *
20390770 G-ACATTAACCATTACACGATGTTGCTCACACGAGCTATGATGAATCTGCAATATATGCAGAA-C
1 GAACATTAACCATTACACGATGCTGCTCACACAAGCTATGAAGAATCCGCAACACATGCAGAATC
20390833 TTTAGCCATCAG-TAAGGTATCTAGTAAG-TT
66 -TTAGCCAT-AGATAAGGTATCTAGTAAGCTT
**
20390863 GAAACATT-ATTAGTTACACGATGCTG
1 G-AACATTAACCA-TTACACGATGCTG
20390889 TGAAAAATCC
Statistics
Matches: 99, Mismatches: 15, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
93 3 0.03
94 3 0.03
95 91 0.92
96 2 0.02
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (95 bp):
GAACATTAACCATTACACGATGCTGCTCACACAAGCTATGAAGAATCCGCAACACATGCAGAATC
TTAGCCATAGATAAGGTATCTAGTAAGCTT
Found at i:20394762 original size:8 final size:8
Alignment explanation
Indices: 20394749--20394780 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
20394739 AAGTCCATTA
20394749 TATTATTT
1 TATTATTT
20394757 TATTATTT
1 TATTATTT
20394765 TATTATTT
1 TATTATTT
20394773 TATT-TTT
1 TATTATTT
20394780 T
1 T
20394781 GAAGTTATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 4 0.17
8 20 0.83
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (8 bp):
TATTATTT
Found at i:20396244 original size:40 final size:37
Alignment explanation
Indices: 20396207--20396301 Score: 118
Period size: 37 Copynumber: 2.5 Consensus size: 37
20396197 ATTTTTAATG
*
20396207 ACTTAAAATATATCTATTTATGTTGCAATTGAGTTTAACT
1 ACTTAAAATA-A-CTA-TGATGTTGCAATTGAGTTTAACT
* *
20396247 ACTTAAGATAAGTATGATGTTGCAATTGAGTTTAACT
1 ACTTAAAATAACTATGATGTTGCAATTGAGTTTAACT
* *
20396284 ACTTAAGATAAGTATGAT
1 ACTTAAAATAACTATGAT
20396302 ATGAGTCAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
37 40 0.77
38 2 0.04
39 1 0.02
40 9 0.17
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.40
Consensus pattern (37 bp):
ACTTAAAATAACTATGATGTTGCAATTGAGTTTAACT
Found at i:20396273 original size:37 final size:37
Alignment explanation
Indices: 20396226--20396301 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
20396216 ATATCTATTT
20396226 ATGTTGCAATTGAGTTTAACTACTTAAGATAAGTATG
1 ATGTTGCAATTGAGTTTAACTACTTAAGATAAGTATG
20396263 ATGTTGCAATTGAGTTTAACTACTTAAGATAAGTATG
1 ATGTTGCAATTGAGTTTAACTACTTAAGATAAGTATG
20396300 AT
1 AT
20396302 ATGAGTCAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.36, C:0.08, G:0.18, T:0.38
Consensus pattern (37 bp):
ATGTTGCAATTGAGTTTAACTACTTAAGATAAGTATG
Found at i:20396574 original size:24 final size:24
Alignment explanation
Indices: 20396547--20396690 Score: 72
Period size: 24 Copynumber: 5.7 Consensus size: 24
20396537 GATGAATTTC
* *
20396547 TAAACGTGTGCAAGCTGGCGAGCG
1 TAAACGTATGCAAGCTGACGAGCG
**
20396571 TAAACGCATATATATAAGCTGACGAGCG
1 TAAACG----TATGCAAGCTGACGAGCG
* * * * *
20396599 TAAATGTGTGCAAGATGGCGAGCA
1 TAAACGTATGCAAGCTGACGAGCG
** *
20396623 TAAACGCATATATATTGCTGACGAGCG
1 TAAACG--TATGCA-AGCTGACGAGCG
* * * *
20396650 TAAACGTGTGCAAGTTGACAAGTG
1 TAAACGTATGCAAGCTGACGAGCG
*
20396674 TAAACGTATGAAAGCTG
1 TAAACGTATGCAAGCTG
20396691 GTGAGTGTAA
Statistics
Matches: 84, Mismatches: 29, Indels: 14
0.66 0.23 0.11
Matches are distributed among these distances:
24 45 0.54
25 3 0.04
26 3 0.04
27 14 0.17
28 19 0.23
ACGTcount: A:0.34, C:0.16, G:0.28, T:0.22
Consensus pattern (24 bp):
TAAACGTATGCAAGCTGACGAGCG
Found at i:20396679 original size:51 final size:52
Alignment explanation
Indices: 20396547--20396663 Score: 191
Period size: 52 Copynumber: 2.3 Consensus size: 52
20396537 GATGAATTTC
*
20396547 TAAACGTGTGCAAGCTGGCGAGCGTAAACGCATATATATAAGCTGACGAGCG
1 TAAACGTGTGCAAGATGGCGAGCGTAAACGCATATATATAAGCTGACGAGCG
* * *
20396599 TAAATGTGTGCAAGATGGCGAGCATAAACGCATATATAT-TGCTGACGAGCG
1 TAAACGTGTGCAAGATGGCGAGCGTAAACGCATATATATAAGCTGACGAGCG
20396650 TAAACGTGTGCAAG
1 TAAACGTGTGCAAG
20396664 TTGACAAGTG
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
51 24 0.40
52 36 0.60
ACGTcount: A:0.33, C:0.17, G:0.28, T:0.21
Consensus pattern (52 bp):
TAAACGTGTGCAAGATGGCGAGCGTAAACGCATATATATAAGCTGACGAGCG
Found at i:20397040 original size:30 final size:30
Alignment explanation
Indices: 20397006--20397064 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
20396996 TAGGAAGGAA
20397006 ATGTAAGTATAACATATAATGAATCTTTAT
1 ATGTAAGTATAACATATAATGAATCTTTAT
* * *
20397036 ATGTAAGTGTAAGATTTAATGAATCTTTA
1 ATGTAAGTATAACATATAATGAATCTTTA
20397065 CATGAAAGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.41, C:0.05, G:0.14, T:0.41
Consensus pattern (30 bp):
ATGTAAGTATAACATATAATGAATCTTTAT
Found at i:20397873 original size:103 final size:103
Alignment explanation
Indices: 20397689--20397898 Score: 357
Period size: 103 Copynumber: 2.0 Consensus size: 103
20397679 CAAAGATGTC
20397689 ACTGCAAGAACCTGTCCTGAAGGATCAATGCATGAAGGTGTCCAAAGTTGTCGCTGCAAAATAGG
1 ACTGCAAGAACCTGTCCTGAAGGATCAATGCATGAAGGTGTCCAAAGTTGTCGCTGCAAAATAGG
*
20397754 ATCCAAATTTGTGCCCAGAACTGTCGCTGCACCTGACA
66 ATCCAAATTTGCGCCCAGAACTGTCGCTGCACCTGACA
* * * * * *
20397792 ACTGCAGGAACCTGTCTTGAAGGATCAGTGCATGAAGGTGTTCAGAGTTGTTGCTGCAAAATAGG
1 ACTGCAAGAACCTGTCCTGAAGGATCAATGCATGAAGGTGTCCAAAGTTGTCGCTGCAAAATAGG
20397857 ATCCAAATTTGCGCCCAGAACTGTCGCTGCACCTGACA
66 ATCCAAATTTGCGCCCAGAACTGTCGCTGCACCTGACA
20397895 ACTG
1 ACTG
20397899 TCTGATGAAC
Statistics
Matches: 100, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
103 100 1.00
ACGTcount: A:0.29, C:0.23, G:0.25, T:0.23
Consensus pattern (103 bp):
ACTGCAAGAACCTGTCCTGAAGGATCAATGCATGAAGGTGTCCAAAGTTGTCGCTGCAAAATAGG
ATCCAAATTTGCGCCCAGAACTGTCGCTGCACCTGACA
Found at i:20405477 original size:23 final size:23
Alignment explanation
Indices: 20405448--20405493 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
20405438 CGATGTACTA
20405448 GATGATCTAATTGAGGAAGAATT
1 GATGATCTAATTGAGGAAGAATT
*
20405471 GATGATCTAATTGTGGAAGAATT
1 GATGATCTAATTGAGGAAGAATT
20405494 AAATAATCGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.37, C:0.04, G:0.26, T:0.33
Consensus pattern (23 bp):
GATGATCTAATTGAGGAAGAATT
Done.