Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 145 of 204
Found at i:43711391 original size:46 final size:47
Alignment explanation
Indices: 43711307--43711404 Score: 121
Period size: 46 Copynumber: 2.1 Consensus size: 47
43711297 AAATTTGATC
* *
43711307 TGATCATATTTTATTTTTTAAATTTGTTTGTATATTTTTT-TAAATT
1 TGATAATATTTTATTTTTTAAATTTATTTGTATATTTTTTCTAAATT
** *
43711353 TGATAATATTTTATTATTTTGTATTTATTTGT-TTTTTTTTCTAAATT
1 TGATAATATTTTATT-TTTTAAATTTATTTGTATATTTTTTCTAAATT
43711400 T-ATAA
1 TGATAA
43711405 CTGTGTAATT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
46 25 0.56
47 20 0.44
ACGTcount: A:0.27, C:0.02, G:0.06, T:0.65
Consensus pattern (47 bp):
TGATAATATTTTATTTTTTAAATTTATTTGTATATTTTTTCTAAATT
Found at i:43712564 original size:21 final size:20
Alignment explanation
Indices: 43712535--43712578 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
43712525 GTTAAAAACG
43712535 AAAAATTAAAGTTAAAGTTA
1 AAAAATTAAAGTTAAAGTTA
**
43712555 AAAAATTTAAAGTTTTAGTTA
1 AAAAA-TTAAAGTTAAAGTTA
43712576 AAA
1 AAA
43712579 TTTTTTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.57, C:0.00, G:0.09, T:0.34
Consensus pattern (20 bp):
AAAAATTAAAGTTAAAGTTA
Found at i:43718570 original size:109 final size:104
Alignment explanation
Indices: 43718407--43718707 Score: 306
Period size: 108 Copynumber: 2.8 Consensus size: 104
43718397 TTCATTTCAG
*
43718407 AAAAAAAGAAGATTGAAATTAAAAAAAAAAGTGATGGGATTGGACGGTCCTAGAGAAGTGGGGCT
1 AAAAAAAGAAGATTGAAATTAAAAAAAAAAGTGATGGGATTGGACGGGCCTAGAGAAGT-GGGCT
*
43718472 TGTTAGGTTGTTGGCCAACACCAGGCTTGGGT-TTT-TA-A
65 CGTTAGGTTGTTGGCCAACACCAGGC-TGGGTATTTATATA
*
43718510 AAAAAAAGAGAGATTGAAATTAAAAAAAAAGTAAAGGTGATGGGATTGGACGGGCTTAGAGAAGT
1 AAAAAAAGA-AGATTGAAATT--AAAAAAA--AAA-GTGATGGGATTGGACGGGCCTAGAGAAGT
** *
43718575 GGGCTCGTTAGGTTGTTGGCTGACACTAGGCTGGGTATTTATATA
60 GGGCTCGTTAGGTTGTTGGCCAACACCAGGCTGGGTATTTATATA
* * * * * * *
43718620 AAAAAAAGAAATATTGAAA-AAATAAGAACAAAATGTGATGGAATTGAACGAGCCTAAAGAAGCG
1 AAAAAAAG-AAGATTGAAATTAA-AA-AA-AAAA-GTGATGGGATTGGACGGGCCTAGAGAAGTG
* *
43718684 AGAC-CGTCAGGTTGTTGGCCAACA
61 -GGCTCGTTAGGTTGTTGGCCAACA
43718708 TTAGAGAAGT
Statistics
Matches: 165, Mismatches: 19, Indels: 23
0.80 0.09 0.11
Matches are distributed among these distances:
103 9 0.05
104 11 0.07
106 7 0.04
107 7 0.04
108 79 0.48
109 33 0.20
110 18 0.11
111 1 0.01
ACGTcount: A:0.40, C:0.10, G:0.28, T:0.23
Consensus pattern (104 bp):
AAAAAAAGAAGATTGAAATTAAAAAAAAAAGTGATGGGATTGGACGGGCCTAGAGAAGTGGGCTC
GTTAGGTTGTTGGCCAACACCAGGCTGGGTATTTATATA
Found at i:43722333 original size:19 final size:19
Alignment explanation
Indices: 43722311--43722364 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
43722301 TTGAAGTCCT
43722311 CCAACCCCATTTTACTCCC
1 CCAACCCCATTTTACTCCC
43722330 CCAACCCCATTTTACTCCC
1 CCAACCCCATTTTACTCCC
*
43722349 CCAACCCCACTTTACT
1 CCAACCCCATTTTACT
43722365 GTTTATTTCA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.22, C:0.52, G:0.00, T:0.26
Consensus pattern (19 bp):
CCAACCCCATTTTACTCCC
Found at i:43726530 original size:33 final size:33
Alignment explanation
Indices: 43726493--43726562 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
43726483 AATCTATCTA
*
43726493 AAAAGAAAAGAAAAAACTTAACCTAAAAAAATG
1 AAAAGAAAAGAAAAAACCTAACCTAAAAAAATG
* **
43726526 AAAAGAAAAGAAAAACCCTAACCTAAAACTATG
1 AAAAGAAAAGAAAAAACCTAACCTAAAAAAATG
43726559 AAAA
1 AAAA
43726563 CCTTAGGAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.67, C:0.13, G:0.09, T:0.11
Consensus pattern (33 bp):
AAAAGAAAAGAAAAAACCTAACCTAAAAAAATG
Found at i:43727626 original size:46 final size:46
Alignment explanation
Indices: 43727559--43727694 Score: 245
Period size: 46 Copynumber: 3.0 Consensus size: 46
43727549 ATGCTATAAT
*
43727559 TCAGTATGGTTTTCTTCACTGAAATACCATACCTACATTCCACAAC
1 TCAGTATGGTTTTCTTTACTGAAATACCATACCTACATTCCACAAC
* *
43727605 TCAGTATGGTTTTCTTTACTGAAATACCATACTTACGTTCCACAAC
1 TCAGTATGGTTTTCTTTACTGAAATACCATACCTACATTCCACAAC
43727651 TCAGTATGGTTTTCTTTACTGAAATACCATACCTACATTCCACA
1 TCAGTATGGTTTTCTTTACTGAAATACCATACCTACATTCCACA
43727695 CTTTGCCATG
Statistics
Matches: 85, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 85 1.00
ACGTcount: A:0.29, C:0.26, G:0.10, T:0.35
Consensus pattern (46 bp):
TCAGTATGGTTTTCTTTACTGAAATACCATACCTACATTCCACAAC
Found at i:43731664 original size:140 final size:137
Alignment explanation
Indices: 43731443--43731867 Score: 634
Period size: 138 Copynumber: 3.1 Consensus size: 137
43731433 AGAGAACAAA
*
43731443 AATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTACATATTTTACTGAATTTAT
1 AATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACTGAATTTAT
* * * *
43731508 TAGTATAAACAGTTATATTAATTAATTTTGGTCAAAAATATAAAATAAATGAAAAATTAATATTT
66 TAATATAAACAGTTATATTAATTAATTTCGGTC-AAAATATAAAAGAAATG-GAAATTAATATTT
*
43731573 CTTTGAAAAG
129 -TTTGGAAAG
* *
43731583 AATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTGTATATTTTACCGAATTTAT
1 AATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACTGAATTTAT
* * * *
43731648 TAATATAAACTGTTATATTAATTAATTTCGATCAAAATAGAAAAGATATGGAAATTAATATTATT
66 TAATATAAACAGTTATATTAATTAATTTCGGTCAAAATATAAAAGAAATGGAAATTAATATT-TT
43731713 TTGGAAAG
130 TTGGAAAG
* *
43731721 AATATAATTAACATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTGCTGAATTTAT
1 AATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACTGAATTTAT
* * * *
43731786 TAATATAAACAGTTATATTAATTAATGTCAGTCAAAATATAAAAGACATGGGAATTAATATTTTT
66 TAATATAAACAGTTATATTAATTAATTTCGGTCAAAATATAAAAGAAATGGAAATTAATA-TTTT
*
43731851 TTGGAAAT
130 TTGGAAAG
43731859 AATATAATT
1 AATATAATT
43731868 CATTTTTCTA
Statistics
Matches: 259, Mismatches: 24, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
138 151 0.58
139 17 0.07
140 91 0.35
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.41
Consensus pattern (137 bp):
AATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACTGAATTTAT
TAATATAAACAGTTATATTAATTAATTTCGGTCAAAATATAAAAGAAATGGAAATTAATATTTTT
TGGAAAG
Found at i:43733583 original size:13 final size:13
Alignment explanation
Indices: 43733565--43733589 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43733555 TCGAACGCCA
43733565 GAGTTAAACTCAT
1 GAGTTAAACTCAT
43733578 GAGTTAAACTCA
1 GAGTTAAACTCA
43733590 ATATTCTCAG
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:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (13 bp):
GAGTTAAACTCAT
Found at i:43736587 original size:51 final size:51
Alignment explanation
Indices: 43736506--43736607 Score: 186
Period size: 51 Copynumber: 2.0 Consensus size: 51
43736496 GTAGCATGTG
* *
43736506 AAACTAGTGGTAAAGTTATGGAGGGTATTATTGTGCTATGATGGGATATGA
1 AAACTAGTGGTAAAGTTATGGAAGGCATTATTGTGCTATGATGGGATATGA
43736557 AAACTAGTGGTAAAGTTATGGAAGGCATTATTGTGCTATGATGGGATATGA
1 AAACTAGTGGTAAAGTTATGGAAGGCATTATTGTGCTATGATGGGATATGA
43736608 CTAGCCTATA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.32, C:0.05, G:0.30, T:0.32
Consensus pattern (51 bp):
AAACTAGTGGTAAAGTTATGGAAGGCATTATTGTGCTATGATGGGATATGA
Found at i:43737445 original size:30 final size:30
Alignment explanation
Indices: 43737406--43737466 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
43737396 TCTCCTTTAC
*
43737406 ATAATAAACAAACTTACTTTTATGACTCAT
1 ATAACAAACAAACTTACTTTTATGACTCAT
43737436 ATAACAAACAAACTTACTTTTATGACTCAT
1 ATAACAAACAAACTTACTTTTATGACTCAT
43737466 A
1 A
43737467 CAAATAGTGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.44, C:0.18, G:0.03, T:0.34
Consensus pattern (30 bp):
ATAACAAACAAACTTACTTTTATGACTCAT
Found at i:43743948 original size:43 final size:43
Alignment explanation
Indices: 43743879--43744007 Score: 143
Period size: 43 Copynumber: 3.0 Consensus size: 43
43743869 AACTAATACA
** * * * *
43743879 ATGCCAACATCCCAGACGTGGCCTTACATGTAATCACAGATCG
1 ATGCCAATGTCCCAGACGTGGTCTTACACGTAAACACAAATCG
** * *
43743922 ATGCCGCTGTCCCAGACAG-GGTCTTACACATAAACACAAATTG
1 ATGCCAATGTCCCAGAC-GTGGTCTTACACGTAAACACAAATCG
*
43743965 ATGCCAATGTCCCAGACGTGGTCTTACACGTAAACACATATCG
1 ATGCCAATGTCCCAGACGTGGTCTTACACGTAAACACAAATCG
43744008 GAAATCCTAT
Statistics
Matches: 69, Mismatches: 15, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
42 1 0.01
43 67 0.97
44 1 0.01
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.22
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACGTGGTCTTACACGTAAACACAAATCG
Found at i:43747193 original size:14 final size:14
Alignment explanation
Indices: 43747171--43747200 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
43747161 AGGAAATAAC
*
43747171 ATAATAAAAAGAAA
1 ATAAGAAAAAGAAA
43747185 ATAAGAAAAAGAAA
1 ATAAGAAAAAGAAA
43747199 AT
1 AT
43747201 TGTGCCAAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (14 bp):
ATAAGAAAAAGAAA
Found at i:43752886 original size:26 final size:26
Alignment explanation
Indices: 43752856--43752908 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
43752846 TTTAATAATC
*
43752856 ATTATTTTAT-TTTAAATAATACAAAA
1 ATTATTTT-TCTTTAAATAATAAAAAA
*
43752882 ATTATTTTTCTTTAATTAATAAAAAA
1 ATTATTTTTCTTTAAATAATAAAAAA
43752908 A
1 A
43752909 CTTTCTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 1 0.04
26 23 0.96
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (26 bp):
ATTATTTTTCTTTAAATAATAAAAAA
Found at i:43768065 original size:41 final size:41
Alignment explanation
Indices: 43768019--43768149 Score: 165
Period size: 41 Copynumber: 3.2 Consensus size: 41
43768009 TCATGTGCTA
* *
43768019 CTAATGCTCAGATTTTTAGGGGCGTTTTTGAAAAAGCGCCG
1 CTAATGCTCAGATCTTTAGCGGCGTTTTTGAAAAAGCGCCG
* * *
43768060 CTAATGCTCAGATCTTTAGCGGCGATTTTGGAAAAGCCCCG
1 CTAATGCTCAGATCTTTAGCGGCGTTTTTGAAAAAGCGCCG
** * * *
43768101 CTAATGCTC-GGGCTTTAGCAGCGTTTTTTAAGAAGCGCCG
1 CTAATGCTCAGATCTTTAGCGGCGTTTTTGAAAAAGCGCCG
43768141 CTAATGCTC
1 CTAATGCTC
43768150 GAGGATTTAA
Statistics
Matches: 77, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
40 32 0.42
41 45 0.58
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.30
Consensus pattern (41 bp):
CTAATGCTCAGATCTTTAGCGGCGTTTTTGAAAAAGCGCCG
Found at i:43768142 original size:40 final size:39
Alignment explanation
Indices: 43768040--43768152 Score: 136
Period size: 40 Copynumber: 2.8 Consensus size: 39
43768030 ATTTTTAGGG
* *
43768040 GCGTTTTTGAAAAAGCGCCGCTAATGCTCAGATCTTTAGCG
1 GCGTTTTTG-AAAAGCGCCGCTAATGCTC-GAGCTTTAGCA
* * *
43768081 GCGATTTTGGAAAAGCCCCGCTAATGCTCGGGCTTTAGCA
1 GCG-TTTTTGAAAAGCGCCGCTAATGCTCGAGCTTTAGCA
*
43768121 GCGTTTTTTAAGAAGCGCCGCTAATGCTCGAG
1 GCGTTTTTGAA-AAGCGCCGCTAATGCTCGAG
43768153 GATTTAACAT
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
39 6 0.10
40 29 0.48
41 21 0.34
42 5 0.08
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.27
Consensus pattern (39 bp):
GCGTTTTTGAAAAGCGCCGCTAATGCTCGAGCTTTAGCA
Found at i:43768590 original size:14 final size:15
Alignment explanation
Indices: 43768564--43768594 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
43768554 GGTTTATAGG
43768564 TTATGGAATTAGGGA
1 TTATGGAATTAGGGA
43768579 TTATGG-ATTAGGGA
1 TTATGGAATTAGGGA
43768593 TT
1 TT
43768595 CTGATTTAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.29, C:0.00, G:0.32, T:0.39
Consensus pattern (15 bp):
TTATGGAATTAGGGA
Found at i:43773613 original size:43 final size:43
Alignment explanation
Indices: 43773517--43773613 Score: 124
Period size: 43 Copynumber: 2.3 Consensus size: 43
43773507 GTTATGTTTT
* * *
43773517 TAGCGGCGTTTTTGCGAGAAGCGCCGCTAAAGGTCGTGGTCTA
1 TAGCAGCGTTTGTGCGAAAAGCGCCGCTAAAGGTCGTGGTCTA
* * *
43773560 TTG-TGACGTTTGTGGGAAAAGCGCCGCTAAAGGTCGTGGTCTA
1 TAGCAG-CGTTTGTGCGAAAAGCGCCGCTAAAGGTCGTGGTCTA
43773603 TAGCAGCGTTT
1 TAGCAGCGTTT
43773614 TTTGTGGCGC
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
42 1 0.02
43 43 0.96
44 1 0.02
ACGTcount: A:0.20, C:0.19, G:0.34, T:0.28
Consensus pattern (43 bp):
TAGCAGCGTTTGTGCGAAAAGCGCCGCTAAAGGTCGTGGTCTA
Found at i:43776068 original size:3 final size:3
Alignment explanation
Indices: 43776062--43776092 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
43776052 TTAAAAAAAA
43776062 AAG AAG AAG AAG AAG AAG AAG AAG AAAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG -AAG AAG
43776093 CCAGAAAGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:43781451 original size:22 final size:22
Alignment explanation
Indices: 43781426--43781525 Score: 164
Period size: 22 Copynumber: 4.5 Consensus size: 22
43781416 TTTCACAAAC
43781426 AAATTCTCTCAATTTCCTTCAA
1 AAATTCTCTCAATTTCCTTCAA
* *
43781448 AAATTCTTTCAATTCCCTTCAA
1 AAATTCTCTCAATTTCCTTCAA
*
43781470 AAATTCTCTCAATTTCCTTCCA
1 AAATTCTCTCAATTTCCTTCAA
*
43781492 AAATTCTCTCAATTTCCTTCCA
1 AAATTCTCTCAATTTCCTTCAA
43781514 AAATTCTCTCAA
1 AAATTCTCTCAA
43781526 ACTCTCAAAT
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 73 1.00
ACGTcount: A:0.31, C:0.29, G:0.00, T:0.40
Consensus pattern (22 bp):
AAATTCTCTCAATTTCCTTCAA
Found at i:43781533 original size:30 final size:30
Alignment explanation
Indices: 43781497--43781555 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
43781487 TTCCAAAATT
* *
43781497 CTCTCAATTTCCTTCCAAAATTCTCTCAAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAAA
43781527 CTCTCAAATTCCTTCCAAAATCCTCTCAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAA
43781556 TTTCCTTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.31, C:0.36, G:0.00, T:0.34
Consensus pattern (30 bp):
CTCTCAAATTCCTTCCAAAATCCTCTCAAA
Found at i:43781541 original size:52 final size:51
Alignment explanation
Indices: 43781475--43781577 Score: 161
Period size: 52 Copynumber: 2.0 Consensus size: 51
43781465 TTCAAAAATT
* * * *
43781475 CTCTCAATTTCCTTCCAAAATTCTCTCAATTTCCTTCCAAAATTCTCTCAAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAATTTCCTTCAAAAAATCTC-CAAA
43781527 CTCTCAAATTCCTTCCAAAATCCTCTCAATTTCCTTCAAAAAATCTCCAAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAATTTCCTTCAAAAAATCTCCAAA
43781578 TCCACATTAA
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
51 4 0.09
52 43 0.91
ACGTcount: A:0.32, C:0.33, G:0.00, T:0.35
Consensus pattern (51 bp):
CTCTCAAATTCCTTCCAAAATCCTCTCAATTTCCTTCAAAAAATCTCCAAA
Found at i:43781566 original size:21 final size:22
Alignment explanation
Indices: 43781527--43781568 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
43781517 TTCTCTCAAA
43781527 CTCTCAAATTCCTTCCAAAATC
1 CTCTCAAATTCCTTCCAAAATC
* *
43781549 CTCTCAATTTCCTTCAAAAA
1 CTCTCAAATTCCTTCCAAAA
43781569 ATCTCCAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (22 bp):
CTCTCAAATTCCTTCCAAAATC
Found at i:43781795 original size:14 final size:15
Alignment explanation
Indices: 43781766--43781799 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
43781756 ATATTTTATA
43781766 TTTTATTTAAGATAT
1 TTTTATTTAAGATAT
*
43781781 TTTTATTTATG-TAT
1 TTTTATTTAAGATAT
43781795 TTTTA
1 TTTTA
43781800 GATATTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (15 bp):
TTTTATTTAAGATAT
Found at i:43781821 original size:24 final size:23
Alignment explanation
Indices: 43781764--43781821 Score: 55
Period size: 24 Copynumber: 2.3 Consensus size: 23
43781754 TTATATTTTA
*
43781764 TATTTTATTTAAGATATTTTTATT
1 TATTTT-TTTAAGATATTTTTAAT
43781788 TATGTATTTTT-AGATATTTATTAAAT
1 TAT-T-TTTTTAAGATATTT-TT-AAT
43781814 TATTTTTT
1 TATTTTTT
43781822 GTTATAAAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
24 15 0.52
25 7 0.24
26 7 0.24
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (23 bp):
TATTTTTTTAAGATATTTTTAAT
Found at i:43783977 original size:23 final size:23
Alignment explanation
Indices: 43783951--43784595 Score: 520
Period size: 23 Copynumber: 27.3 Consensus size: 23
43783941 AAAACCCTAA
*
43783951 CCTAACTTAATTTAATTAAAAAC
1 CCTAACCTAATTTAATTAAAAAC
*
43783974 CCTAACCTAATTTAATTAAAATCCTAA
1 CCTAACCTAATTTAATTAAAA----AC
*
43784001 CCTAACTTAATTTAATTAAAAAC
1 CCTAACCTAATTTAATTAAAAAC
* *
43784024 CCTAACCTAATTGAATTAAAACCCAAA
1 CCTAACCTAATTTAATT-AAA---AAC
*
43784051 CCTAACCTAACTTAATTAAAAAC
1 CCTAACCTAATTTAATTAAAAAC
*
43784074 CCTAACCTAATTGAATT--AAA-
1 CCTAACCTAATTTAATTAAAAAC
43784094 ---AACCTAATTTAATTAAAAAC
1 CCTAACCTAATTTAATTAAAAAC
*
43784114 CCTAACCTAACTTAATGT-AAAAC
1 CCTAACCTAATTTAAT-TAAAAAC
*
43784137 CCTAACCTAACTTAACTT-AAAA-
1 CCTAACCTAATTTAA-TTAAAAAC
*
43784159 CCTAACTTAATTTAATTAAAAATCC
1 CCTAACCTAATTTAATTAAAAA--C
*
43784184 TAACCTAACTTAATTTAATTAAAAAC
1 ---CCTAACCTAATTTAATTAAAAAC
* * *
43784210 CCTAAGCTAACTGT-ATTTAAAAC
1 CCTAACCTAA-TTTAATTAAAAAC
* *
43784233 CCTACCCTAACTTAATTAAAAAC
1 CCTAACCTAATTTAATTAAAAAC
*
43784256 CCTAACCTAACTTAATTTAATTAAAAGC
1 CCTAA-C---C-TAATTTAATTAAAAAC
43784284 CCTAACCTAATTTAATTAAAAAC
1 CCTAACCTAATTTAATTAAAAAC
43784307 CCTAACCTAACTTAATTTAATTAAAAAC
1 CCTAA-C---C-TAATTTAATTAAAAAC
* * *
43784335 CCTAAGCTAACTTAATTTAAAAC
1 CCTAACCTAATTTAATTAAAAAC
* *
43784358 CCTACCCTAACTTAATTAAAAAC
1 CCTAACCTAATTTAATTAAAAAC
*
43784381 CCTAACCTAACTTAATGT-AAAAC
1 CCTAACCTAATTTAAT-TAAAAAC
*
43784404 CCTAACCTAATTGAATT--AAA-
1 CCTAACCTAATTTAATTAAAAAC
43784424 ---AACCTAATTTAATTAAAAAC
1 CCTAACCTAATTTAATTAAAAAC
*
43784444 CCTAACCTAACTTAATGT-AAAAC
1 CCTAACCTAATTTAAT-TAAAAAC
43784467 CCTAACCTAACTTAATTTAATTAAAAAC
1 CCTAA-C---C-TAATTTAATTAAAAAC
* *
43784495 CCTAACCGAACTTAATTTAAAAAAC
1 CCTAACCTAATTTAA-TT-AAAAAC
* * *
43784520 CCTAAGCTAA-CTATATTTAAAAC
1 CCTAACCTAATTTA-ATTAAAAAC
* *
43784543 CCTACCCTAACTTAATTAAAAAC
1 CCTAACCTAATTTAATTAAAAAC
*
43784566 CCTAACCTAACTTAATGT-AAAAC
1 CCTAACCTAATTTAAT-TAAAAAC
43784589 CCTAACC
1 CCTAACC
43784596 CTAAGCTAAT
Statistics
Matches: 516, Mismatches: 52, Indels: 108
0.76 0.08 0.16
Matches are distributed among these distances:
17 26 0.05
19 6 0.01
21 8 0.02
22 19 0.04
23 290 0.56
24 24 0.05
25 15 0.03
26 4 0.01
27 44 0.09
28 80 0.16
ACGTcount: A:0.46, C:0.23, G:0.02, T:0.29
Consensus pattern (23 bp):
CCTAACCTAATTTAATTAAAAAC
Found at i:43784079 original size:18 final size:18
Alignment explanation
Indices: 43784056--43784119 Score: 67
Period size: 18 Copynumber: 3.3 Consensus size: 18
43784046 CCAAACCTAA
43784056 CCTAACTTAATTAAAAAC
1 CCTAACTTAATTAAAAAC
43784074 CCTAACCTAATTGAATTAAAAA-
1 CCTAA-C---TT-AATTAAAAAC
*
43784096 CCTAATTTAATTAAAAAC
1 CCTAACTTAATTAAAAAC
43784114 CCTAAC
1 CCTAAC
43784120 CTAACTTAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
17 9 0.24
18 12 0.32
19 1 0.03
22 7 0.18
23 9 0.24
ACGTcount: A:0.48, C:0.22, G:0.02, T:0.28
Consensus pattern (18 bp):
CCTAACTTAATTAAAAAC
Found at i:43784099 original size:17 final size:17
Alignment explanation
Indices: 43784077--43784114 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
43784067 TAAAAACCCT
43784077 AACCTAATTGAATTAAA
1 AACCTAATTGAATTAAA
*
43784094 AACCTAATTTAATTAAA
1 AACCTAATTGAATTAAA
43784111 AACC
1 AACC
43784115 CTAACCTAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.53, C:0.16, G:0.03, T:0.29
Consensus pattern (17 bp):
AACCTAATTGAATTAAA
Found at i:43784162 original size:17 final size:17
Alignment explanation
Indices: 43784140--43784173 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
43784130 GTAAAACCCT
43784140 AACCTAACTTAACTTAA
1 AACCTAACTTAACTTAA
*
43784157 AACCTAACTTAATTTAA
1 AACCTAACTTAACTTAA
43784174 TTAAAAATCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (17 bp):
AACCTAACTTAACTTAA
Found at i:43784382 original size:18 final size:18
Alignment explanation
Indices: 43784361--43784449 Score: 63
Period size: 18 Copynumber: 4.4 Consensus size: 18
43784351 TTAAAACCCT
43784361 ACCCTAACTTAATTAAAA
1 ACCCTAACTTAATTAAAA
*
43784379 ACCCTAACCTAACTTAATGTAAA
1 ACCCTAACTTAA-TT-A---AAA
43784402 ACCCTAACCTAATTGAATTAAAA
1 ACCCTAA-C---TT-AATTAAAA
*
43784425 A-CCTAATTTAATTAAAA
1 ACCCTAACTTAATTAAAA
43784442 ACCCTAAC
1 ACCCTAAC
43784450 CTAACTTAAT
Statistics
Matches: 56, Mismatches: 4, Indels: 22
0.68 0.05 0.27
Matches are distributed among these distances:
17 9 0.16
18 18 0.32
19 2 0.04
20 1 0.02
22 5 0.09
23 14 0.25
24 1 0.02
26 1 0.02
27 3 0.05
28 2 0.04
ACGTcount: A:0.47, C:0.24, G:0.02, T:0.27
Consensus pattern (18 bp):
ACCCTAACTTAATTAAAA
Found at i:43784429 original size:17 final size:17
Alignment explanation
Indices: 43784407--43784444 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
43784397 GTAAAACCCT
43784407 AACCTAATTGAATTAAA
1 AACCTAATTGAATTAAA
*
43784424 AACCTAATTTAATTAAA
1 AACCTAATTGAATTAAA
43784441 AACC
1 AACC
43784445 CTAACCTAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.53, C:0.16, G:0.03, T:0.29
Consensus pattern (17 bp):
AACCTAATTGAATTAAA
Found at i:43787320 original size:125 final size:125
Alignment explanation
Indices: 43787096--43787377 Score: 372
Period size: 125 Copynumber: 2.3 Consensus size: 125
43787086 CCACGAGGGC
*
43787096 GCGATTTGACACTATTTGCTCAGAAACGTCAAAAAAAAAATATTTCCTACATGACCAACTGTAGC
1 GCGATTTGACACTATTTGCTCAGAAACGTCAAAAAAAAAATATTTCCTACATGACCAACTGTACC
* * * **
43787161 GAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTACCCAATATAGCATCCTTGTATCA
66 GAAATCGCGTCCACGAGGCCACGATTTCACAATTTCTACCCAA-ATAGCATCCTAGTAGAA
* * * *
43787222 GCGATTTTATACTATTTGCTCAGAAAACGTC-AAAAAAAATTATTTCTTACATGACC-ACTGTAC
1 GCGATTTGACACTATTTGCTCAG-AAACGTCAAAAAAAAAATATTTCCTACATGACCAACTGTAC
* * *
43787285 CGAAATCGCGTCCACGAGGCCACGATTTCGCAATTTCTTCTCAAATAGCATCCTAGTAGAA
65 CGAAATCGCGTCCACGAGGCCACGATTTCACAATTTCTACCCAAATAGCATCCTAGTAGAA
** *
43787346 GCGATTTCCCACTATTTGAC-CAGATACGTCAA
1 GCGATTTGACACTATTTG-CTCAGAAACGTCAA
43787378 CTCGAAAATT
Statistics
Matches: 136, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
123 6 0.04
124 33 0.24
125 46 0.34
126 44 0.32
127 7 0.05
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.28
Consensus pattern (125 bp):
GCGATTTGACACTATTTGCTCAGAAACGTCAAAAAAAAAATATTTCCTACATGACCAACTGTACC
GAAATCGCGTCCACGAGGCCACGATTTCACAATTTCTACCCAAATAGCATCCTAGTAGAA
Found at i:43796667 original size:16 final size:16
Alignment explanation
Indices: 43796646--43796692 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
43796636 TTATTAAATT
43796646 ATATATTTTAATTATA
1 ATATATTTTAATTATA
*
43796662 ATATA-TTTAATAATA
1 ATATATTTTAATTATA
*
43796677 AT-TATGTTAAATTATA
1 ATATAT-TTTAATTATA
43796693 TTTTATAGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 2 0.08
15 11 0.42
16 13 0.50
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (16 bp):
ATATATTTTAATTATA
Found at i:43796684 original size:110 final size:111
Alignment explanation
Indices: 43796551--43796810 Score: 407
Period size: 120 Copynumber: 2.3 Consensus size: 111
43796541 TGCTTCCTAG
43796551 TAAT-TATTTAATAATAATTATG-TTAAATAGTATCATATATTATGATTTGAGTAAATTCATATA
1 TAATATATTTAATAATAATTATGATTAAATAGTATCATATATTATGATTTGAGTAAATTCATATA
43796614 AGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTA
66 AGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTA
43796660 TAATATATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAA
1 TAATATATTTAATAATAATTATG----ATTA-A----ATAGTATCATATATTATGATTTGAGTAA
*
43796725 ATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTTTAATTA
57 ATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTA
*
43796780 TAATATATTTAATAATAATTATGTTTAAATA
1 TAATATATTTAATAATAATTATGATTAAATA
43796811 TGATTAAATT
Statistics
Matches: 138, Mismatches: 2, Indels: 20
0.86 0.01 0.12
Matches are distributed among these distances:
109 4 0.03
110 18 0.13
111 3 0.02
115 4 0.03
116 4 0.03
120 105 0.76
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (111 bp):
TAATATATTTAATAATAATTATGATTAAATAGTATCATATATTATGATTTGAGTAAATTCATATA
AGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTA
Found at i:43796770 original size:61 final size:61
Alignment explanation
Indices: 43796585--43796772 Score: 192
Period size: 61 Copynumber: 3.1 Consensus size: 61
43796575 AAATAGTATC
*
43796585 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
* * * * * * * *
43796646 ATATATTTTAATTAT-AATATATTTA-ATAATAAT-TATG-TTAAATT-A-TATTTTA-TAGTAT
1 ATATATTATGATT-TGAGTAAATTCATATAAGAATAT-TGATT--ATTAAGAATTTTATTA-AAT
*
43796704 C
61 T
43796705 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
43796766 ATATATT
1 ATATATT
43796773 TTAATTATAA
Statistics
Matches: 96, Mismatches: 19, Indels: 24
0.69 0.14 0.17
Matches are distributed among these distances:
58 3 0.03
59 32 0.33
60 19 0.20
61 39 0.41
62 3 0.03
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (61 bp):
ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
Found at i:43796779 original size:120 final size:121
Alignment explanation
Indices: 43796577--43796809 Score: 450
Period size: 120 Copynumber: 1.9 Consensus size: 121
43796567 ATTATGTTAA
43796577 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTA
1 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTA
43796642 AATTATATATTTTAATTATAATATATTTAATAATAATTATG-TTAAATTATATTTT
66 AATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAATTATATTTT
*
43796697 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTA
1 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTA
43796762 AATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAAT
66 AATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAAT
43796810 ATGATTAAAT
Statistics
Matches: 111, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
120 105 0.95
121 6 0.05
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.48
Consensus pattern (121 bp):
ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTA
AATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAATTATATTTT
Found at i:43796787 original size:16 final size:16
Alignment explanation
Indices: 43796766--43796807 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
43796756 TTATTAAATT
*
43796766 ATATATTTTAATTATA
1 ATATATTTTAATAATA
43796782 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
43796797 AT-TATGTTTAA
1 ATATAT-TTTAA
43796808 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:43796792 original size:15 final size:15
Alignment explanation
Indices: 43796757--43796798 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
43796747 TTAAGAATTT
*
43796757 TATTAAATTAT-ATA
1 TATTTAATTATAATA
43796771 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
43796785 TATTTAATAATAAT
1 TATTTAATTATAAT
43796799 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:43797041 original size:16 final size:16
Alignment explanation
Indices: 43797022--43797075 Score: 81
Period size: 16 Copynumber: 3.4 Consensus size: 16
43797012 TTGATTTGCT
* *
43797022 ATTACACTTCTATTCT
1 ATTACACCTCTATTCC
43797038 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
*
43797054 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
43797070 ATTACA
1 ATTACA
43797076 GCGAACCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.26, C:0.31, G:0.02, T:0.41
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:43797135 original size:29 final size:29
Alignment explanation
Indices: 43797103--43797166 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 29
43797093 TAAATGTTTA
*
43797103 AAAAAACAATGGAA-CCTCATAAAATAATT
1 AAAAAACAAT-GAAGCCTCACAAAATAATT
* *
43797132 -AAAAACAATTAAGTCCTCACAACATAATT
1 AAAAAACAATGAAG-CCTCACAAAATAATT
43797161 AAAAAA
1 AAAAAA
43797167 AATTAATTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
27 2 0.07
28 9 0.31
29 13 0.45
30 5 0.17
ACGTcount: A:0.59, C:0.16, G:0.05, T:0.20
Consensus pattern (29 bp):
AAAAAACAATGAAGCCTCACAAAATAATT
Found at i:43797170 original size:29 final size:29
Alignment explanation
Indices: 43797117--43797172 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
43797107 AACAATGGAA
* *
43797117 CCTCATAAAATAATTAAAAACAATTAAGT
1 CCTCACAAAATAATTAAAAAAAATTAAGT
*
43797146 CCTCACAACATAATTAAAAAAAATTAA
1 CCTCACAAAATAATTAAAAAAAATTAA
43797173 TTAATCCCAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.57, C:0.16, G:0.02, T:0.25
Consensus pattern (29 bp):
CCTCACAAAATAATTAAAAAAAATTAAGT
Found at i:43799074 original size:16 final size:16
Alignment explanation
Indices: 43799049--43799081 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
43799039 AAATGCACTC
43799049 TCTTTCTTTTTCTTTT
1 TCTTTCTTTTTCTTTT
*
43799065 TCTTTTTTTTTCTTTT
1 TCTTTCTTTTTCTTTT
43799081 T
1 T
43799082 TACTTTCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (16 bp):
TCTTTCTTTTTCTTTT
Found at i:43806351 original size:5 final size:5
Alignment explanation
Indices: 43806341--43806365 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
43806331 ACTAAATTGT
43806341 AAATA AAATA AAATA AAATA AAATA
1 AAATA AAATA AAATA AAATA AAATA
43806366 TGAAACTGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAATA
Found at i:43808832 original size:26 final size:26
Alignment explanation
Indices: 43808758--43808834 Score: 72
Period size: 26 Copynumber: 3.1 Consensus size: 26
43808748 ATCCGGTACG
43808758 CATAGTAGCCTGCACATAGTACTACA
1 CATAGTAGCCTGCACATAGTACTACA
* ** *
43808784 CAT-G-CGACCT--ACATTCTAGTACA
1 CATAGTAG-CCTGCACATAGTACTACA
*
43808807 CGTAGTAGCCTGCACATAGTACTACA
1 CATAGTAGCCTGCACATAGTACTACA
43808833 CA
1 CA
43808835 CGTGACCATC
Statistics
Matches: 36, Mismatches: 10, Indels: 10
0.64 0.18 0.18
Matches are distributed among these distances:
23 12 0.33
24 5 0.14
25 5 0.14
26 14 0.39
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.23
Consensus pattern (26 bp):
CATAGTAGCCTGCACATAGTACTACA
Found at i:43808863 original size:100 final size:102
Alignment explanation
Indices: 43808651--43808839 Score: 240
Period size: 100 Copynumber: 1.9 Consensus size: 102
43808641 AATGATACCA
* * * *
43808651 GTTCACATAGTAGCCTGCAGATAGTACTACACATGTGGCCATCACTATCCAATACATGTAGGACC
1 GTTCACATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTATCCAATACACGTAGGACC
* *
43808716 CTGCACATAGTACTTCACACGTGATCGAAGCTATCCG
66 CTGCACATAGTACTACACACGTGATCCAAGCTATCCG
* * * * * *
43808753 GTACGCATAGTAGCCTGCACATAGTACTACACATGCGACC-T-AC-ATTCTAGTACACGTAGTAG
1 GTTCACATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTA-TCCAATACACGTAGGAC
43808815 CCTGCACATAGTACTACACACGTGA
65 CCTGCACATAGTACTACACACGTGA
43808840 CCATCACTTT
Statistics
Matches: 75, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
99 1 0.01
100 38 0.51
101 1 0.01
102 35 0.47
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.24
Consensus pattern (102 bp):
GTTCACATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTATCCAATACACGTAGGACC
CTGCACATAGTACTACACACGTGATCCAAGCTATCCG
Found at i:43817396 original size:96 final size:96
Alignment explanation
Indices: 43817223--43817424 Score: 309
Period size: 96 Copynumber: 2.1 Consensus size: 96
43817213 TAAAGCAATG
* * *
43817223 AGGAGTGTTGAGAATGTGCCTTAGACTTGCTAAATAATAGGTGTAGACCAAGTATTTAAGGATTT
1 AGGA-TGTGGAGAATGTGCCTTAGACTAGCCAAATAATAGGTGTAGACCAAGTATTTAAGGATTT
*
43817288 GTTCATTTGTGGCATGATTTTAGGAGTAAGTT
65 GTTCATTTGTGGCATGATTTTAGGAATAAGTT
*
43817320 AGGATGTGGAGAATGTGCCTTAGACTAGCCAAATAATAGGTGTAGACCAAGTATTTAGGGAATTT
1 AGGATGTGGAGAATGTGCCTTAGACTAGCCAAATAATAGGTGTAGACCAAGTATTTAAGG-ATTT
*
43817385 -TT-AGTTTGTGGCATGATTTTATGAATAAGTT
65 GTTCA-TTTGTGGCATGATTTTAGGAATAAGTT
43817416 AGGATGTGG
1 AGGATGTGG
43817425 TTAGATATCA
Statistics
Matches: 97, Mismatches: 6, Indels: 5
0.90 0.06 0.05
Matches are distributed among these distances:
95 1 0.01
96 88 0.91
97 8 0.08
ACGTcount: A:0.30, C:0.08, G:0.28, T:0.35
Consensus pattern (96 bp):
AGGATGTGGAGAATGTGCCTTAGACTAGCCAAATAATAGGTGTAGACCAAGTATTTAAGGATTTG
TTCATTTGTGGCATGATTTTAGGAATAAGTT
Found at i:43817940 original size:101 final size:101
Alignment explanation
Indices: 43817815--43818024 Score: 262
Period size: 101 Copynumber: 2.1 Consensus size: 101
43817805 AAATTATTTG
* * * * * * * * *
43817815 GTTAAGTAGAAATATGAGATATAAATGAAACAT-TTTAATTCAATGTTAAAAGAAAA-AACCCTA
1 GTTAAATAGAAAAATGAAAAATAAATCAAACATCATAAATTCAATGTTAAAACAAAATAA--CAA
43817878 ATACCTTAACTAATTACTAAATAGATAGTAATCAATCA
64 ATACCTTAACTAATTACTAAATAGATAGTAATCAATCA
*** *
43817916 GTTAAATAGAAAAATGAAAAATAAATCAAACATCATAAATTGGTTGTTAAAACAAAATTACAAAT
1 GTTAAATAGAAAAATGAAAAATAAATCAAACATCATAAATTCAATGTTAAAACAAAATAACAAAT
*
43817981 ACCTTAACTAATTACTAAATAGATAGTAATCAATCG
66 ACCTTAACTAATTACTAAATAGATAGTAATCAATCA
43818017 GTTAAATA
1 GTTAAATA
43818025 AATTACAAAT
Statistics
Matches: 93, Mismatches: 14, Indels: 4
0.84 0.13 0.04
Matches are distributed among these distances:
101 75 0.81
102 17 0.18
103 1 0.01
ACGTcount: A:0.51, C:0.10, G:0.10, T:0.29
Consensus pattern (101 bp):
GTTAAATAGAAAAATGAAAAATAAATCAAACATCATAAATTCAATGTTAAAACAAAATAACAAAT
ACCTTAACTAATTACTAAATAGATAGTAATCAATCA
Found at i:43819140 original size:27 final size:27
Alignment explanation
Indices: 43819096--43819175 Score: 81
Period size: 27 Copynumber: 3.0 Consensus size: 27
43819086 ACAACCAGTG
*
43819096 TAGTCCATC-GGAATAGTAAACACGAGA
1 TAGTCTATCAGGAA-AGTAAACACGAGA
* *
43819123 TAGTCTATCAGGAAAGTAAACACGTGG
1 TAGTCTATCAGGAAAGTAAACACGAGA
* * * *
43819150 TAGTTTGTCATGACAGTAAACACGAG
1 TAGTCTATCAGGAAAGTAAACACGAG
43819176 GATTACGAGA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
27 40 0.91
28 4 0.09
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.23
Consensus pattern (27 bp):
TAGTCTATCAGGAAAGTAAACACGAGA
Found at i:43824205 original size:38 final size:34
Alignment explanation
Indices: 43824163--43824235 Score: 92
Period size: 38 Copynumber: 2.0 Consensus size: 34
43824153 AAATAGATAA
43824163 AAAATTTAAAAATTATTTTTTTATTAAATAAAAACATT
1 AAAATTTAAAAATTA-TTTTTTA--AAATAAAAA-ATT
**
43824201 AAAATTTAAATTTTATTTTTTAAAATAAAAAATT
1 AAAATTTAAAAATTATTTTTTAAAATAAAAAATT
43824235 A
1 A
43824236 TGAAAAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
34 4 0.12
35 9 0.27
37 7 0.21
38 13 0.39
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.45
Consensus pattern (34 bp):
AAAATTTAAAAATTATTTTTTAAAATAAAAAATT
Found at i:43825269 original size:18 final size:19
Alignment explanation
Indices: 43825248--43825289 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
43825238 ATAACATTGA
43825248 ATTTTTAAAAT-TTTTTTT
1 ATTTTTAAAATCTTTTTTT
43825266 ATTTTTAAAATCTTTTTTT
1 ATTTTTAAAATCTTTTTTT
43825285 ATTTT
1 ATTTT
43825290 ATGAATTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.71
Consensus pattern (19 bp):
ATTTTTAAAATCTTTTTTT
Found at i:43835024 original size:84 final size:84
Alignment explanation
Indices: 43834868--43835025 Score: 192
Period size: 84 Copynumber: 1.9 Consensus size: 84
43834858 GGAGCAGCGT
* * * * **
43834868 TAGCGACATTTTTCCCATAAACGCCACGAAAGGTAAAGAAGTAGCGATGTTTTTCCCTAAACATT
1 TAGCGACATTTTTCCCATAAACGCCACAAAAGGTAAAGAAGTAGCGACGTTTATCCATAAACACC
*
43834933 GCTAAAGGTATAACAACAA
66 GCAAAAGGTATAACAACAA
* * * **
43834952 TAGCGGCATTTTTCCCATAAACGCCATAAAAGGTAAAGCAA-TAGCGACGTTTATGCATAAATGC
1 TAGCGACATTTTTCCCATAAACGCCACAAAAGGTAAAG-AAGTAGCGACGTTTATCCATAAACAC
43835016 CGCAAAAGGT
65 CGCAAAAGGT
43835026 TAAAAATGAT
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
84 59 0.97
85 2 0.03
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.24
Consensus pattern (84 bp):
TAGCGACATTTTTCCCATAAACGCCACAAAAGGTAAAGAAGTAGCGACGTTTATCCATAAACACC
GCAAAAGGTATAACAACAA
Found at i:43835209 original size:25 final size:25
Alignment explanation
Indices: 43835170--43835228 Score: 82
Period size: 25 Copynumber: 2.3 Consensus size: 25
43835160 TATTCCCCCA
*
43835170 AATTGTTTTCTCCAAATCCCTAACTT
1 AATT-TTTTCCCCAAATCCCTAACTT
* *
43835196 AGTTTTTTCCCCAAATCCCTATCTT
1 AATTTTTTCCCCAAATCCCTAACTT
43835221 AATTTTTT
1 AATTTTTT
43835229 TTCTTTCCCA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 26 0.90
26 3 0.10
ACGTcount: A:0.24, C:0.25, G:0.03, T:0.47
Consensus pattern (25 bp):
AATTTTTTCCCCAAATCCCTAACTT
Found at i:43840979 original size:19 final size:19
Alignment explanation
Indices: 43840951--43840989 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
43840941 CTAATACCAA
*
43840951 GGCTTTAAAGGCTTTTCAT
1 GGCTTCAAAGGCTTTTCAT
43840970 GGCTTCAAAGGCTTTTCAT
1 GGCTTCAAAGGCTTTTCAT
43840989 G
1 G
43840990 TCATCAAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.38
Consensus pattern (19 bp):
GGCTTCAAAGGCTTTTCAT
Found at i:43840996 original size:19 final size:19
Alignment explanation
Indices: 43840957--43840998 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
43840947 CCAAGGCTTT
*
43840957 AAAGGCTTTTCATGGCTTC
1 AAAGGCTTTTCATGGCATC
*
43840976 AAAGGCTTTTCATGTCATC
1 AAAGGCTTTTCATGGCATC
43840995 AAAG
1 AAAG
43840999 ACAGCCGAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (19 bp):
AAAGGCTTTTCATGGCATC
Found at i:43845484 original size:21 final size:20
Alignment explanation
Indices: 43845459--43845505 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
43845449 AAAGCGGAGA
*
43845459 CAGCAGCGAGGGAAGCAGAGG
1 CAGCAGCAAGGG-AGCAGAGG
* *
43845480 TAGCAGTAAGGGAGCAGAGG
1 CAGCAGCAAGGGAGCAGAGG
43845500 CAGCAG
1 CAGCAG
43845506 AGGTATTAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.34, C:0.17, G:0.45, T:0.04
Consensus pattern (20 bp):
CAGCAGCAAGGGAGCAGAGG
Found at i:43845497 original size:20 final size:21
Alignment explanation
Indices: 43845467--43845505 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
43845457 GACAGCAGCG
*
43845467 AGGGAAGCAGAGGTAGCAGTA
1 AGGGAAGCAGAGGCAGCAGTA
43845488 AGGG-AGCAGAGGCAGCAG
1 AGGGAAGCAGAGGCAGCAG
43845506 AGGTATTAAG
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:0.36, C:0.13, G:0.46, T:0.05
Consensus pattern (21 bp):
AGGGAAGCAGAGGCAGCAGTA
Found at i:43854939 original size:31 final size:31
Alignment explanation
Indices: 43854903--43855014 Score: 101
Period size: 31 Copynumber: 3.8 Consensus size: 31
43854893 AAATCTCAAA
*
43854903 ATTATACATTAACTCTGATTTAATGTGTATT
1 ATTATACACTAACTCTGATTTAATGTGTATT
* * * **
43854934 ATTATACACTAA----GA-TAAATCT-CAAA
1 ATTATACACTAACTCTGATTTAATGTGTATT
*
43854959 ATTATACATTAACTCTGATTTAATGTGTATT
1 ATTATACACTAACTCTGATTTAATGTGTATT
* *
43854990 ATTATACACTAACTTTAATTTAATG
1 ATTATACACTAACTCTGATTTAATG
43855015 CAATTATATA
Statistics
Matches: 60, Mismatches: 15, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
25 12 0.20
26 5 0.08
27 2 0.03
29 2 0.03
30 5 0.08
31 34 0.57
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.43
Consensus pattern (31 bp):
ATTATACACTAACTCTGATTTAATGTGTATT
Found at i:43854952 original size:56 final size:56
Alignment explanation
Indices: 43854889--43855001 Score: 226
Period size: 56 Copynumber: 2.0 Consensus size: 56
43854879 TTTATATTAG
43854889 AGATAAATCTCAAAATTATACATTAACTCTGATTTAATGTGTATTATTATACACTA
1 AGATAAATCTCAAAATTATACATTAACTCTGATTTAATGTGTATTATTATACACTA
43854945 AGATAAATCTCAAAATTATACATTAACTCTGATTTAATGTGTATTATTATACACTA
1 AGATAAATCTCAAAATTATACATTAACTCTGATTTAATGTGTATTATTATACACTA
43855001 A
1 A
43855002 CTTTAATTTA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.39
Consensus pattern (56 bp):
AGATAAATCTCAAAATTATACATTAACTCTGATTTAATGTGTATTATTATACACTA
Found at i:43857557 original size:14 final size:13
Alignment explanation
Indices: 43857535--43857568 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
43857525 TTGAGCCTTA
*
43857535 AGTTTTTTTTTTT
1 AGTTTTTTTCTTT
43857548 AGTGTTTTTTCTTT
1 AGT-TTTTTTCTTT
43857562 AGTTTTT
1 AGTTTTT
43857569 CTCATGGCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.09, C:0.03, G:0.12, T:0.76
Consensus pattern (13 bp):
AGTTTTTTTCTTT
Found at i:43859695 original size:112 final size:112
Alignment explanation
Indices: 43859498--43859716 Score: 429
Period size: 112 Copynumber: 2.0 Consensus size: 112
43859488 TGGTAGAGAG
43859498 GAAGCACAAACATATAGTTGATACTGGTATGACTTTAAAGGCTCAATCTAGTATGCCTATGCATC
1 GAAGCACAAACATATAGTTGATACTGGTATGACTTTAAAGGCTCAATCTAGTATGCCTATGCATC
43859563 TTTGGACACATGCCTTCATCAGTGTTGTCTATCTCATTAACACTGAT
66 TTTGGACACATGCCTTCATCAGTGTTGTCTATCTCATTAACACTGAT
43859610 GAAGCACAAACATATAGTTGATACTGGTATGACTTTAAAGGCTCAATCTAGTATGCCTATGCATC
1 GAAGCACAAACATATAGTTGATACTGGTATGACTTTAAAGGCTCAATCTAGTATGCCTATGCATC
*
43859675 TTTGGACACGTGCCTTCATCAGTGTTGTCTATCTCATTAACA
66 TTTGGACACATGCCTTCATCAGTGTTGTCTATCTCATTAACA
43859717 GGCTTCCCAC
Statistics
Matches: 106, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
112 106 1.00
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (112 bp):
GAAGCACAAACATATAGTTGATACTGGTATGACTTTAAAGGCTCAATCTAGTATGCCTATGCATC
TTTGGACACATGCCTTCATCAGTGTTGTCTATCTCATTAACACTGAT
Found at i:43860905 original size:15 final size:17
Alignment explanation
Indices: 43860887--43860918 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
43860877 TATGAAAGAG
43860887 AACA-TTTAGA-AACAA
1 AACAGTTTAGACAACAA
43860902 AACAGTTTAGACAACAA
1 AACAGTTTAGACAACAA
43860919 CAGTTGTGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.27
16 6 0.40
17 5 0.33
ACGTcount: A:0.56, C:0.16, G:0.09, T:0.19
Consensus pattern (17 bp):
AACAGTTTAGACAACAA
Found at i:43862675 original size:50 final size:52
Alignment explanation
Indices: 43862600--43862734 Score: 141
Period size: 56 Copynumber: 2.6 Consensus size: 52
43862590 TAATGTAACA
** * *
43862600 TCCCAGACATGGTCTTACCGGGGACCTCTCATCTC-TG-TGCCAACT-CCATG
1 TCCCAGACATGGTCTTACATGGGACCTCTAATCGCATGATGCCAA-TGCCATG
*
43862650 TCCCAGACATGGTCTTACATAGGACCTTTCATAATCGCAATGATGCCAATGCCATG
1 TCCCAGACATGGTCTTACATGGGACC--TC-TAATCGC-ATGATGCCAATGCCATG
* *
43862706 TCCCAAACATGGTCTTACATGGGATCTCT
1 TCCCAGACATGGTCTTACATGGGACCTCT
43862735 TTACCCAAAT
Statistics
Matches: 70, Mismatches: 8, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
50 23 0.33
52 2 0.03
53 6 0.09
54 2 0.03
55 3 0.04
56 34 0.49
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (52 bp):
TCCCAGACATGGTCTTACATGGGACCTCTAATCGCATGATGCCAATGCCATG
Found at i:43867357 original size:15 final size:16
Alignment explanation
Indices: 43867328--43867361 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
43867318 TTTCTTTAGG
43867328 TTTTGTTCTGATTGTT
1 TTTTGTTCTGATTGTT
*
43867344 TTTTGTTTTG-TTGTT
1 TTTTGTTCTGATTGTT
43867359 TTT
1 TTT
43867362 ATTTTTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.03, C:0.03, G:0.18, T:0.76
Consensus pattern (16 bp):
TTTTGTTCTGATTGTT
Found at i:43867979 original size:9 final size:9
Alignment explanation
Indices: 43867965--43867995 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
43867955 GTTAAATGAA
43867965 TCGAGTTAT
1 TCGAGTTAT
*
43867974 TCGAGTTAA
1 TCGAGTTAT
43867983 TCGAGTTAT
1 TCGAGTTAT
43867992 TCGA
1 TCGA
43867996 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:43868197 original size:30 final size:30
Alignment explanation
Indices: 43868135--43868197 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
43868125 ACTTTTACCT
* * *
43868135 CAAAACTTTTACTCCTTCTCACTTTCCCCC
1 CAAAACTTTTACTCCTCCTCACCTCCCCCC
*
43868165 CAAAACTTTTACTCC-CCTCCCCTCCCCTCC
1 CAAAACTTTTACTCCTCCTCACCTCCCC-CC
43868195 CAA
1 CAA
43868198 CCCCCCAATC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 8 0.29
30 20 0.71
ACGTcount: A:0.21, C:0.49, G:0.00, T:0.30
Consensus pattern (30 bp):
CAAAACTTTTACTCCTCCTCACCTCCCCCC
Found at i:43872267 original size:81 final size:81
Alignment explanation
Indices: 43872132--43872301 Score: 313
Period size: 81 Copynumber: 2.1 Consensus size: 81
43872122 GAAATTAAAA
*
43872132 CCAAAGAAGGGTGCAGAGCTGAAGCCCATGAATGATATTTTTGGTGACAATTTAAATATAATAAA
1 CCAAAGAAGGATGCAGAGCTGAAGCCCATGAATGATATTTTTGGTGACAATTTAAATATAATAAA
*
43872197 GGACACTGAACCGAAG
66 AGACACTGAACCGAAG
43872213 CCAAAGAAGGATGCAGAGCTGAAGCCCATGAATGATATTTTTGGTGACAATTTAAATATAATAAA
1 CCAAAGAAGGATGCAGAGCTGAAGCCCATGAATGATATTTTTGGTGACAATTTAAATATAATAAA
*
43872278 AGACACTGAACTGAAG
66 AGACACTGAACCGAAG
43872294 CCAAAGAA
1 CCAAAGAA
43872302 TAATTCTTTC
Statistics
Matches: 86, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
81 86 1.00
ACGTcount: A:0.42, C:0.15, G:0.22, T:0.22
Consensus pattern (81 bp):
CCAAAGAAGGATGCAGAGCTGAAGCCCATGAATGATATTTTTGGTGACAATTTAAATATAATAAA
AGACACTGAACCGAAG
Found at i:43875131 original size:3 final size:3
Alignment explanation
Indices: 43875123--43875148 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
43875113 GATCTATTAC
43875123 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
43875149 GCTTCCCTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:43882176 original size:64 final size:64
Alignment explanation
Indices: 43882098--43882221 Score: 160
Period size: 64 Copynumber: 1.9 Consensus size: 64
43882088 ATCCCAATCA
* * * * *
43882098 GTATTAATCATGCATGTGTTGTGGATATACTGTAACTCTTTGTGAGCGTCCT-ATTATATGATCG
1 GTATTAATCATGCATGTATTGCGGACATACCGTAACTCTTTATGAGCGTCCTGA-TATATGATCG
* * *
43882162 GTATTGATCCTGCATGTATTGCGGACATACCGTAGCTCTTTATGAGCGTCCTGATATATG
1 GTATTAATCATGCATGTATTGCGGACATACCGTAACTCTTTATGAGCGTCCTGATATATG
43882222 GCTTTTCATG
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
64 50 0.98
65 1 0.02
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.38
Consensus pattern (64 bp):
GTATTAATCATGCATGTATTGCGGACATACCGTAACTCTTTATGAGCGTCCTGATATATGATCG
Found at i:43882408 original size:25 final size:25
Alignment explanation
Indices: 43882370--43882418 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
43882360 TATATCCCGG
43882370 ATAAGCTTCTTGTTACATGGCTCAC
1 ATAAGCTTCTTGTTACATGGCTCAC
*
43882395 ATAAGCTT-TCTGTTATATGGCTCA
1 ATAAGCTTCT-TGTTACATGGCTCA
43882419 AGAGAATCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 1 0.05
25 21 0.95
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.39
Consensus pattern (25 bp):
ATAAGCTTCTTGTTACATGGCTCAC
Found at i:43891844 original size:24 final size:24
Alignment explanation
Indices: 43891816--43891867 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
43891806 TTCAATTAGT
43891816 AAATATA-TATTTAAAAAATTATAA
1 AAATATATTATTTAAAAAATT-TAA
* *
43891840 AAATATATTATTTTATAAATTTAA
1 AAATATATTATTTAAAAAATTTAA
43891864 AAAT
1 AAAT
43891868 TAAACTAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 14 0.56
25 11 0.44
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
AAATATATTATTTAAAAAATTTAA
Found at i:43901209 original size:16 final size:16
Alignment explanation
Indices: 43901179--43901233 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
43901169 AAGAGAATGG
43901179 AAAAAAAAGAAAAAGAA
1 AAAAAAAAG-AAAAGAA
* **
43901196 AAAAAAAAGGAAAGTT
1 AAAAAAAAGAAAAGAA
* *
43901212 AAAAAACATAAAAGAA
1 AAAAAAAAGAAAAGAA
43901228 AAAAAA
1 AAAAAA
43901234 CTAAATTGCT
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
16 21 0.70
17 9 0.30
ACGTcount: A:0.82, C:0.02, G:0.11, T:0.05
Consensus pattern (16 bp):
AAAAAAAAGAAAAGAA
Found at i:43904460 original size:19 final size:19
Alignment explanation
Indices: 43904436--43904474 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
43904426 TAAGGTTAGT
43904436 TATTATTTGTATGTAATTA
1 TATTATTTGTATGTAATTA
43904455 TATTATTTGTATGTAATTA
1 TATTATTTGTATGTAATTA
43904474 T
1 T
43904475 TATTTGAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.59
Consensus pattern (19 bp):
TATTATTTGTATGTAATTA
Found at i:43904477 original size:17 final size:18
Alignment explanation
Indices: 43904435--43904480 Score: 76
Period size: 19 Copynumber: 2.6 Consensus size: 18
43904425 ATAAGGTTAG
43904435 TTATTATTTGTATGTAAT
1 TTATTATTTGTATGTAAT
43904453 TATATTATTTGTATGTAA-
1 T-TATTATTTGTATGTAAT
43904471 TTATTATTTG
1 TTATTATTTG
43904481 AATCTTTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.33
18 2 0.07
19 16 0.59
ACGTcount: A:0.28, C:0.00, G:0.11, T:0.61
Consensus pattern (18 bp):
TTATTATTTGTATGTAAT
Found at i:43904634 original size:93 final size:93
Alignment explanation
Indices: 43904475--43904656 Score: 312
Period size: 93 Copynumber: 2.0 Consensus size: 93
43904465 ATGTAATTAT
**
43904475 TATTTGAATCTTTTAAGCAAATAAGAATGCAATTTAATAAGAATGTAAAACTCGAAGATAGAAAA
1 TATTTGAATCTCGTAAGCAAATAAGAATGCAATTTAATAAGAATGTAAAACTCGAAGATAGAAAA
*
43904540 CAAAAGATTAGTGCAAATATAGCTCCCA
66 CAAAAGATTAGTGCAAAAATAGCTCCCA
*
43904568 TATTTGAATCTCGTCAGCAAATAAGAATGCAATTTAATAAGAATGTAAAACTCGAAGATA-AGAA
1 TATTTGAATCTCGTAAGCAAATAAGAATGCAATTTAATAAGAATGTAAAACTCGAAGATAGA-AA
43904632 ACAAAAGATTAGTGCAAAAATAGCT
65 ACAAAAGATTAGTGCAAAAATAGCT
43904657 TGACGTTGTG
Statistics
Matches: 84, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
92 1 0.01
93 83 0.99
ACGTcount: A:0.48, C:0.12, G:0.15, T:0.26
Consensus pattern (93 bp):
TATTTGAATCTCGTAAGCAAATAAGAATGCAATTTAATAAGAATGTAAAACTCGAAGATAGAAAA
CAAAAGATTAGTGCAAAAATAGCTCCCA
Found at i:43904759 original size:17 final size:16
Alignment explanation
Indices: 43904732--43904768 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
43904722 ATTTACCGAG
*
43904732 ATGAAACTTGAAGATA
1 ATGAAACTTGAAGACA
43904748 ATGAAGACTTGAAGACA
1 ATGAA-ACTTGAAGACA
43904765 ATGA
1 ATGA
43904769 CCACACTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.49, C:0.08, G:0.22, T:0.22
Consensus pattern (16 bp):
ATGAAACTTGAAGACA
Found at i:43916866 original size:1 final size:1
Alignment explanation
Indices: 43916860--43916884 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
43916850 ATCTGAATAT
43916860 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
43916885 TCAGATACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:43919343 original size:2 final size:2
Alignment explanation
Indices: 43919336--43919380 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
43919326 TGGTTTTTAA
43919336 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
43919378 AT A
1 AT A
43919381 GGGAGAAATC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:43920353 original size:25 final size:27
Alignment explanation
Indices: 43920322--43920389 Score: 79
Period size: 25 Copynumber: 2.6 Consensus size: 27
43920312 AAAATTGGTA
43920322 AGACATTTTCCATTCT-TCTCTAAGCAG
1 AGACATTTTCCATTCTCT-TCTAAGCAG
**
43920349 -G-CATTTTCTGTTCTCTTCTAAGCAG
1 AGACATTTTCCATTCTCTTCTAAGCAG
43920374 CAGACATTTTCCATTC
1 -AGACATTTTCCATTC
43920390 CTCAAAGCTT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
25 20 0.61
26 2 0.06
27 1 0.03
28 10 0.30
ACGTcount: A:0.22, C:0.26, G:0.12, T:0.40
Consensus pattern (27 bp):
AGACATTTTCCATTCTCTTCTAAGCAG
Found at i:43922805 original size:15 final size:15
Alignment explanation
Indices: 43922761--43922809 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
43922751 CAGAACCGAT
43922761 TTTTTCATT-TTTCA
1 TTTTTCATTCTTTCA
** *
43922775 ACTTTCAATGCTTTCA
1 TTTTTC-ATTCTTTCA
43922791 TTTTTCATTCTTTCA
1 TTTTTCATTCTTTCA
43922806 TTTT
1 TTTT
43922810 AAGTGGTACT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
14 4 0.15
15 14 0.52
16 9 0.33
ACGTcount: A:0.16, C:0.18, G:0.02, T:0.63
Consensus pattern (15 bp):
TTTTTCATTCTTTCA
Found at i:43925469 original size:71 final size:72
Alignment explanation
Indices: 43925350--43925492 Score: 261
Period size: 71 Copynumber: 2.0 Consensus size: 72
43925340 TTGATACATT
*
43925350 TATGTGGTGTAATATTATGCACTTGGACAATGTTCTTACTATGTGGTGTACCATTAATTATGTAT
1 TATGTGGTGTAATATTATGCACTTAGACAATGTTCTTACTATGTGGTGTACCATTAATTATGTAT
43925415 TTGGATA
66 TTGGATA
*
43925422 TATGTGGTGTAATATTATGCAC-TAGACAATGTTGTTACTATGTGGTGTACCATTAATTATGTAT
1 TATGTGGTGTAATATTATGCACTTAGACAATGTTCTTACTATGTGGTGTACCATTAATTATGTAT
43925486 TTGGATA
66 TTGGATA
43925493 ATAATATTAT
Statistics
Matches: 69, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
71 47 0.68
72 22 0.32
ACGTcount: A:0.27, C:0.09, G:0.21, T:0.43
Consensus pattern (72 bp):
TATGTGGTGTAATATTATGCACTTAGACAATGTTCTTACTATGTGGTGTACCATTAATTATGTAT
TTGGATA
Found at i:43925706 original size:14 final size:14
Alignment explanation
Indices: 43925687--43925716 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
43925677 TTTATTAATA
43925687 TATATTAATAAATG
1 TATATTAATAAATG
*
43925701 TATATTAATATATG
1 TATATTAATAAATG
43925715 TA
1 TA
43925717 AAAACAACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (14 bp):
TATATTAATAAATG
Found at i:43925768 original size:32 final size:33
Alignment explanation
Indices: 43925732--43925816 Score: 93
Period size: 32 Copynumber: 2.6 Consensus size: 33
43925722 AACTTTTCCG
* * *
43925732 GAAAATATTTT-CAGGAAATCTGCCAAACAGCA
1 GAAAATATTTTACAGCAAATCTACCAAACACCA
* *
43925764 GAAAATATTTTACA-CAGATTTACCAAACACCA
1 GAAAATATTTTACAGCAAATCTACCAAACACCA
* *
43925796 GAAAATATTTTCCAGTAAATC
1 GAAAATATTTTACAGCAAATC
43925817 ATTTTACAGA
Statistics
Matches: 42, Mismatches: 9, Indels: 3
0.78 0.17 0.06
Matches are distributed among these distances:
32 37 0.88
33 5 0.12
ACGTcount: A:0.45, C:0.19, G:0.11, T:0.26
Consensus pattern (33 bp):
GAAAATATTTTACAGCAAATCTACCAAACACCA
Found at i:43925815 original size:14 final size:15
Alignment explanation
Indices: 43925793--43925869 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
43925783 TTACCAAACA
43925793 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
43925807 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
43925822 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
43925842 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
43925856 ACGGAAAAT-ATTTT
1 CCAGAAAATCATTTT
43925870 AGTGCCAAAC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 21 0.42
15 15 0.30
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:43925834 original size:20 final size:20
Alignment explanation
Indices: 43925809--43925848 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
43925799 AATATTTTCC
*
43925809 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
43925829 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
43925849 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:43925854 original size:34 final size:35
Alignment explanation
Indices: 43925797--43925863 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
43925787 CAAACACCAG
*
43925797 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
43925832 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
43925864 TATTTTAGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:43926502 original size:2 final size:2
Alignment explanation
Indices: 43926495--43926526 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
43926485 TCAAATGCAT
43926495 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
43926527 CAACTTATGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:43928970 original size:1 final size:1
Alignment explanation
Indices: 43928964--43928988 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
43928954 TACTGTAATG
43928964 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
43928989 GTAAAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:43936463 original size:9 final size:9
Alignment explanation
Indices: 43936451--43936485 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
43936441 CGGTTGAATC
43936451 AAATTTTTA
1 AAATTTTTA
43936460 AAATTTTTA
1 AAATTTTTA
*
43936469 AAATTGTTA
1 AAATTTTTA
*
43936478 ATATTTTT
1 AAATTTTT
43936486 TTAATTAGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (9 bp):
AAATTTTTA
Found at i:43941064 original size:54 final size:54
Alignment explanation
Indices: 43940979--43941089 Score: 177
Period size: 54 Copynumber: 2.1 Consensus size: 54
43940969 TCTCTTGGTC
* * **
43940979 TATGACAATGTATAAATTATAGATTTGTAATAAAAATTATGTAATTTAGTTAAA
1 TATGACAATGTATAAATAATAGATTTATAATAAAAAGGATGTAATTTAGTTAAA
*
43941033 TATGACCATGTATAAATAATAGATTTATAATAAAAAGGATGTAATTTAGTTAAA
1 TATGACAATGTATAAATAATAGATTTATAATAAAAAGGATGTAATTTAGTTAAA
43941087 TAT
1 TAT
43941090 TTAATAGGTT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.47, C:0.03, G:0.12, T:0.39
Consensus pattern (54 bp):
TATGACAATGTATAAATAATAGATTTATAATAAAAAGGATGTAATTTAGTTAAA
Found at i:43945185 original size:41 final size:42
Alignment explanation
Indices: 43945118--43945222 Score: 151
Period size: 41 Copynumber: 2.5 Consensus size: 42
43945108 TGGTCCCAGC
* *
43945118 TTGGACGTTTC-CAAGGGATGGAGCGTCACTCGGTCGATTTTG
1 TTGGA-GTTTCGCAAGGGCTCGAGCGTCACTCGGTCGATTTTG
43945160 TTGGAGTTTCGCAAGGGCTCG-GCGTCACTCGGTCGATTTTG
1 TTGGAGTTTCGCAAGGGCTCGAGCGTCACTCGGTCGATTTTG
* *
43945201 TTGGACTTTTGCAAGGGCTCGA
1 TTGGAGTTTCGCAAGGGCTCGA
43945223 ATGTCGAGCG
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
41 44 0.77
42 13 0.23
ACGTcount: A:0.15, C:0.20, G:0.33, T:0.31
Consensus pattern (42 bp):
TTGGAGTTTCGCAAGGGCTCGAGCGTCACTCGGTCGATTTTG
Found at i:43945839 original size:2 final size:2
Alignment explanation
Indices: 43945834--43945858 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
43945824 GTATATAAAT
43945834 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
43945859 TTGACGACTA
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:43951725 original size:22 final size:22
Alignment explanation
Indices: 43951669--43951766 Score: 80
Period size: 22 Copynumber: 4.5 Consensus size: 22
43951659 AGTGTTTGGG
43951669 TGGCATTCT-A-TTAGCCTTTA
1 TGGCATTCTGATTTAGCCTTTA
*
43951689 TGG-AGTACTCTGATTTTGCCTTTA
1 TGGCA-T--TCTGATTTAGCCTTTA
*
43951713 TGGCATTCTGATTTAGCCTTTG
1 TGGCATTCTGATTTAGCCTTTA
* *
43951735 TGGCATATTCTG--TTAGACTTTG
1 TGGC--ATTCTGATTTAGCCTTTA
43951757 TGGCATTCTG
1 TGGCATTCTG
43951767 TAGCTTTTGT
Statistics
Matches: 66, Mismatches: 4, Indels: 16
0.77 0.05 0.19
Matches are distributed among these distances:
19 1 0.02
20 10 0.15
22 34 0.52
23 1 0.02
24 19 0.29
25 1 0.02
ACGTcount: A:0.16, C:0.17, G:0.21, T:0.45
Consensus pattern (22 bp):
TGGCATTCTGATTTAGCCTTTA
Found at i:43951777 original size:19 final size:19
Alignment explanation
Indices: 43951708--43951781 Score: 69
Period size: 22 Copynumber: 3.6 Consensus size: 19
43951698 CTGATTTTGC
*
43951708 CTTTATGGCATTCTGATTTAG
1 CTTTGTGGCATTCTG--TTAG
43951729 CCTTTGTGGCATATTCTGTTAG
1 -CTTTGTGGC--ATTCTGTTAG
43951751 ACTTTGTGGCATTCTG-TAG
1 -CTTTGTGGCATTCTGTTAG
43951770 CTTTTGTGGCAT
1 C-TTTGTGGCAT
43951782 ATTTTGTATG
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
18 1 0.02
19 13 0.28
20 6 0.13
22 21 0.45
24 6 0.13
ACGTcount: A:0.15, C:0.16, G:0.23, T:0.46
Consensus pattern (19 bp):
CTTTGTGGCATTCTGTTAG
Found at i:43952296 original size:28 final size:28
Alignment explanation
Indices: 43952256--43952315 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 28
43952246 AATTTGATTT
*
43952256 AGTAAGATCAATATAGGTAT-TCGCCAAA
1 AGTAAGACCAATATAGGTATCT-GCCAAA
*
43952284 AGTAAGACCAATATGGGTATCTGCCAAA
1 AGTAAGACCAATATAGGTATCTGCCAAA
43952312 AGTA
1 AGTA
43952316 TGAACAGTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 28 0.97
29 1 0.03
ACGTcount: A:0.42, C:0.15, G:0.20, T:0.23
Consensus pattern (28 bp):
AGTAAGACCAATATAGGTATCTGCCAAA
Found at i:43970210 original size:33 final size:33
Alignment explanation
Indices: 43970173--43970248 Score: 143
Period size: 33 Copynumber: 2.3 Consensus size: 33
43970163 ATGAAACAAA
43970173 AGAAAATATTTTACACAAATTCATCCAAACACC
1 AGAAAATATTTTACACAAATTCATCCAAACACC
*
43970206 AGAAAATATTTTACACAGATTCATCCAAACACC
1 AGAAAATATTTTACACAAATTCATCCAAACACC
43970239 AGAAAATATT
1 AGAAAATATT
43970249 AGCTTTTCCA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.49, C:0.21, G:0.05, T:0.25
Consensus pattern (33 bp):
AGAAAATATTTTACACAAATTCATCCAAACACC
Found at i:43972065 original size:15 final size:14
Alignment explanation
Indices: 43972047--43972080 Score: 59
Period size: 15 Copynumber: 2.4 Consensus size: 14
43972037 GGCATTAGCA
43972047 GTTTAGGGATTATG
1 GTTTAGGGATTATG
43972061 TGTTTAGGGATTATG
1 -GTTTAGGGATTATG
43972076 GTTTA
1 GTTTA
43972081 TTGTTTAGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.21, C:0.00, G:0.32, T:0.47
Consensus pattern (14 bp):
GTTTAGGGATTATG
Found at i:43972130 original size:50 final size:49
Alignment explanation
Indices: 43972075--43972229 Score: 152
Period size: 50 Copynumber: 3.1 Consensus size: 49
43972065 TAGGGATTAT
* *
43972075 GGTTTATTGTTTAGTGTTTAAGGGTTGGGGTTTAAGGGTTAGGGGTTTAA
1 GGTTTATAGTTTA-TGTTTAAGGGTTAGGGTTTAAGGGTTAGGGGTTTAA
* * * * *
43972125 GGTTTATAGTTTATGTTTTATGATTCAGGGTTTAAGGGATAAGGG-TTAGA
1 GGTTTATAGTTTATGTTTAAGGGTT-AGGGTTTAAGGGTTAGGGGTTTA-A
** * * *
43972175 GGTTTAGGGATTATAGTTTATGGGTTATGGTTTAAGGGTT-GGGGTTTAA
1 GGTTTATAGTTTAT-GTTTAAGGGTTAGGGTTTAAGGGTTAGGGGTTTAA
43972224 GGTTTA
1 GGTTTA
43972230 GGTGTTAGGG
Statistics
Matches: 84, Mismatches: 17, Indels: 9
0.76 0.15 0.08
Matches are distributed among these distances:
49 22 0.26
50 55 0.65
51 7 0.08
ACGTcount: A:0.21, C:0.01, G:0.35, T:0.43
Consensus pattern (49 bp):
GGTTTATAGTTTATGTTTAAGGGTTAGGGTTTAAGGGTTAGGGGTTTAA
Found at i:43972137 original size:57 final size:56
Alignment explanation
Indices: 43972062--43972243 Score: 190
Period size: 57 Copynumber: 3.2 Consensus size: 56
43972052 GGGATTATGT
*
43972062 GTTTAGGGATTATGGTTTATTGTTTAGTGTTTAAGGGTTGGGGTTTAAGGGTTAGGG
1 GTTTAGGGATTATAGTTTATTGTTTA-TGTTTAAGGGTTGGGGTTTAAGGGTTAGGG
* * * * * * *
43972119 GTTTAAGGTTTATAGTTTA-TGTTTTATGATTCAGGGTTTAAGGG-ATAAGGGTTAGAG
1 GTTTAGGGATTATAGTTTATTG-TTTATGTTTAAGGG-TT-GGGGTTTAAGGGTTAGGG
* * * *
43972176 GTTTAGGGATTATAGTTTATGGGTTATGGTTTAAGGGTTGGGGTTTAAGGTTTAGGT
1 GTTTAGGGATTATAGTTTATTGTTTAT-GTTTAAGGGTTGGGGTTTAAGGGTTAGGG
43972233 G-TTAGGGATTA
1 GTTTAGGGATTA
43972244 AGGGTTAAGG
Statistics
Matches: 100, Mismatches: 19, Indels: 13
0.76 0.14 0.10
Matches are distributed among these distances:
56 23 0.23
57 66 0.66
58 11 0.11
ACGTcount: A:0.21, C:0.01, G:0.35, T:0.43
Consensus pattern (56 bp):
GTTTAGGGATTATAGTTTATTGTTTATGTTTAAGGGTTGGGGTTTAAGGGTTAGGG
Found at i:43972266 original size:8 final size:7
Alignment explanation
Indices: 43972047--43972272 Score: 70
Period size: 7 Copynumber: 31.7 Consensus size: 7
43972037 GGCATTAGCA
43972047 GTTTAGG
1 GTTTAGG
* *
43972054 GATTATGT
1 GTTTA-GG
43972062 GTTTAGG
1 GTTTAGG
* *
43972069 GATTATG
1 GTTTAGG
**
43972076 GTTTATT
1 GTTTAGG
*
43972083 GTTTAGT
1 GTTTAGG
43972090 GTTTAAGG
1 GTTT-AGG
*
43972098 G-TTGGG
1 GTTTAGG
43972104 GTTTAAGG
1 GTTT-AGG
43972112 G-TTAGGG
1 GTTTA-GG
*
43972119 GTTTAAG
1 GTTTAGG
**
43972126 GTTTATA
1 GTTTAGG
*
43972133 GTTTATG
1 GTTTAGG
* *
43972140 TTTTATG
1 GTTTAGG
* *
43972147 ATTCAGG
1 GTTTAGG
43972154 GTTTAAGG
1 GTTT-AGG
* *
43972162 GATAAGG
1 GTTTAGG
43972169 G-TTAGAG
1 GTTTAG-G
43972176 GTTTAGG
1 GTTTAGG
* **
43972183 GATTATA
1 GTTTAGG
43972190 GTTTATGG
1 GTTTA-GG
*
43972198 G-TTATG
1 GTTTAGG
43972204 GTTTAAGG
1 GTTT-AGG
*
43972212 G-TTGGG
1 GTTTAGG
*
43972218 GTTTAAG
1 GTTTAGG
43972225 GTTTA-G
1 GTTTAGG
43972231 GTGTTAGG
1 GT-TTAGG
*
43972239 GATTAAGG
1 G-TTTAGG
*
43972247 GTTAAGG
1 GTTTAGG
43972254 G-TTAGAG
1 GTTTAG-G
43972261 GTTTAGG
1 GTTTAGG
43972268 GTTTA
1 GTTTA
43972273 TAATTTATAT
Statistics
Matches: 163, Mismatches: 38, Indels: 36
0.69 0.16 0.15
Matches are distributed among these distances:
6 18 0.11
7 106 0.65
8 38 0.23
9 1 0.01
ACGTcount: A:0.22, C:0.00, G:0.36, T:0.42
Consensus pattern (7 bp):
GTTTAGG
Found at i:43972347 original size:21 final size:22
Alignment explanation
Indices: 43972323--43972374 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 22
43972313 TAGAGGTTTA
*
43972323 GGGATTATGGTTTAAGAGTT-G
1 GGGATTAAGGTTTAAGAGTTAG
*
43972344 GGGATTAAGGTTTAAGTGTTAG
1 GGGATTAAGGTTTAAGAGTTAG
43972366 GGG-TTAAGG
1 GGGATTAAGG
43972375 GTTATGGGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 24 0.86
22 4 0.14
ACGTcount: A:0.25, C:0.00, G:0.40, T:0.35
Consensus pattern (22 bp):
GGGATTAAGGTTTAAGAGTTAG
Found at i:43972510 original size:15 final size:15
Alignment explanation
Indices: 43972465--43972513 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
43972455 GTTTAAAGGA
43972465 TAGGGTTTATGGTTT
1 TAGGGTTTATGGTTT
**
43972480 TAGGGGCTA--GTGTT
1 TAGGGTTTATGGT-TT
43972494 TAGGGTTTATGGTTT
1 TAGGGTTTATGGTTT
43972509 TAGGG
1 TAGGG
43972514 ATAATGGTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
13 2 0.07
14 9 0.33
15 14 0.52
16 2 0.07
ACGTcount: A:0.14, C:0.02, G:0.39, T:0.45
Consensus pattern (15 bp):
TAGGGTTTATGGTTT
Found at i:43972961 original size:124 final size:125
Alignment explanation
Indices: 43972817--43973057 Score: 378
Period size: 124 Copynumber: 1.9 Consensus size: 125
43972807 AATGGCACCG
* * * *
43972817 TTTCTCTTCAGGAATATAATTTTTAGTGGCGTTTT-TTGTAAAACGCCGCAAATGTTATGCAATT
1 TTTCACTTCAGGAACATAATTTTTAATGGCATTTTGTT-TAAAACGCCGCAAATGTTATGCAATT
* *
43972881 ACTGGC-TTTTTTATAAAACGCCGCAAATATTGAAATTTCAATTTGACTTAAACGGTGCCA
65 ACTGGCGTTTATTATAAAACGCCACAAATATTGAAATTTCAATTTGACTTAAACGGTGCCA
*
43972941 TTTCACTTCAGGAACATAATTTTTAATGGCATTTTGTTTAAAACGCTGCAAATGTTATGCAATTA
1 TTTCACTTCAGGAACATAATTTTTAATGGCATTTTGTTTAAAACGCCGCAAATGTTATGCAATTA
* *
43973006 GTGGCGTTTATTGTAAAACGCCACAAATATTGAAATTTCAATTTGACTTAAA
66 CTGGCGTTTATTATAAAACGCCACAAATATTGAAATTTCAATTTGACTTAAA
43973058 AGGAGTCGTG
Statistics
Matches: 106, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
124 61 0.58
125 45 0.42
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (125 bp):
TTTCACTTCAGGAACATAATTTTTAATGGCATTTTGTTTAAAACGCCGCAAATGTTATGCAATTA
CTGGCGTTTATTATAAAACGCCACAAATATTGAAATTTCAATTTGACTTAAACGGTGCCA
Found at i:43975858 original size:43 final size:43
Alignment explanation
Indices: 43975811--43975992 Score: 197
Period size: 43 Copynumber: 4.2 Consensus size: 43
43975801 AGAACATGAC
* * *
43975811 CTTTAGCAGTGTTTATGACAAAAGCGTCGCTAAAGGTCATGTT
1 CTTTAGCAGCGTTTGTGAGAAAAGCGTCGCTAAAGGTCATGTT
*
43975854 CTTTAGCAGCATTTGTGAGAAAAGCGTCGCTAAAGGTCATGTT
1 CTTTAGCAGCGTTTGTGAGAAAAGCGTCGCTAAAGGTCATGTT
* * * *
43975897 -TTTAGCATCGTTTCTGATAAAAACGCCG-CTGCTAAAGGTAATGTT
1 CTTTAGCAGCGTTTGTGA-GAAAA-G-CGTC-GCTAAAGGTCATGTT
* * ** *
43975942 CTTCAGCGGCGTTTGTGAGAAAAATGCCGCTAAAGGTCATGTT
1 CTTTAGCAGCGTTTGTGAGAAAAGCGTCGCTAAAGGTCATGTT
43975985 CTTTAGCA
1 CTTTAGCA
43975993 AGCGCCGCTA
Statistics
Matches: 114, Mismatches: 19, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
42 14 0.12
43 64 0.56
44 3 0.03
45 20 0.18
46 13 0.11
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (43 bp):
CTTTAGCAGCGTTTGTGAGAAAAGCGTCGCTAAAGGTCATGTT
Found at i:43978321 original size:24 final size:26
Alignment explanation
Indices: 43978280--43978331 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 26
43978270 GATAATGTAA
43978280 TTTATATATATATATGTA-AT-TATT
1 TTTATATATATATATGTATATATATT
* *
43978304 TTTATCTATATATGTGTATATATATT
1 TTTATATATATATATGTATATATATT
43978330 TT
1 TT
43978332 GTTTTTCTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 16 0.67
25 2 0.08
26 6 0.25
ACGTcount: A:0.33, C:0.02, G:0.06, T:0.60
Consensus pattern (26 bp):
TTTATATATATATATGTATATATATT
Found at i:43978435 original size:3 final size:3
Alignment explanation
Indices: 43978427--43978460 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
43978417 ACTTATTTAT
43978427 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
43978461 ATATATATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:43978654 original size:20 final size:18
Alignment explanation
Indices: 43978619--43978655 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
43978609 GTACCTTTTA
43978619 TTCTTTATTTTTTATTAG
1 TTCTTTATTTTTTATTAG
43978637 TTCTTTCATTTGTTTATTA
1 TTCTTT-ATTT-TTTATTA
43978656 ATTTGTGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 4 0.24
20 7 0.41
ACGTcount: A:0.16, C:0.08, G:0.05, T:0.70
Consensus pattern (18 bp):
TTCTTTATTTTTTATTAG
Found at i:43991057 original size:216 final size:217
Alignment explanation
Indices: 43990602--43991146 Score: 783
Period size: 216 Copynumber: 2.5 Consensus size: 217
43990592 AAAGCCAATG
* * * * * * *
43990602 ATCCTATCTCTCTGAAGTTGCAATGGAGTGGATTAACACCACATATCTTATCTCTCTGAAGTTGT
1 ATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACCACAGATCTTATTTCTCTGAAATTGC
* *
43990667 AGAGAGCAGATCGCATCTAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAGCAAGCAAGT
66 AGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTACAGTGGAGCAGACTAAGCAAGCAAGT
* *
43990732 CCTATCTCCCTAAAGTTGCAGTGAAGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGTA
131 CCTATCTCCCTAAAGTTGCAGTGAAGCAGACTGAAGATGGCAAACCTTATCTCCCTGAAGTTGCA
*
43990797 GTGGAGCAGATTAAAGCTGATA
196 GTGGAGCAGATTAAAGCGGATA
* **
43990819 ATCCTATCTCCCTGAAGTTGCAGTAGAGTGGATTAAAACCTTAGATCTTATTTCTCTGAAATTGC
1 ATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACCACAGATCTTATTTCTCTGAAATTGC
* * *
43990884 AGAGAGCAGATCACATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGT
66 AGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTACAGTGGAGCAGACTAAGCAAGCAAGT
* * **
43990949 CTTATC-CCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCAAACCTTATCTCCCTGAAGTTGCA
131 CCTATCTCCCTAAAGTTGCAGTGAAGCAGACTGAAGATGGCAAACCTTATCTCCCTGAAGTTGCA
*
43991013 GTGGAGCAGGTTAAAGCGGATA
196 GTGGAGCAGATTAAAGCGGATA
* * * *
43991035 GTCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATATTATCTT-TCT-AAAGTT
1 ATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACCACAGATCTTAT-TTCTCTGAAA-TT
*
43991098 GCAGAGAGCAGATCGCATCTAGTCTTATCTCCCGGACA-TTACAGTGGAG
64 GCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGA-AGTTACAGTGGAG
43991147 TAAACTGCAG
Statistics
Matches: 292, Mismatches: 33, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
215 3 0.01
216 166 0.57
217 123 0.42
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.28
Consensus pattern (217 bp):
ATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACCACAGATCTTATTTCTCTGAAATTGC
AGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTACAGTGGAGCAGACTAAGCAAGCAAGT
CCTATCTCCCTAAAGTTGCAGTGAAGCAGACTGAAGATGGCAAACCTTATCTCCCTGAAGTTGCA
GTGGAGCAGATTAAAGCGGATA
Found at i:43991087 original size:44 final size:44
Alignment explanation
Indices: 43990601--43991110 Score: 262
Period size: 44 Copynumber: 11.8 Consensus size: 44
43990591 GAAAGCCAAT
* * * ** * *
43990601 GATCCTATCTCTCTGAAGTTGCAATGGAGTGGATTAACACCACA
1 GATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCACA
* * * * *** *
43990645 TATCTTATCTCTCTGAAGTTGTAG-AGAGCAGA-TCGCATC-TA
1 GATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCACA
* *
43990686 -ATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAGCAAGCA-A
1 GATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAA--AATCACA
* * * * * **
43990730 G-TCCTATCTCCCTAAAGTTGCAGTGAAGCAGACTGAAGATGGCA
1 GATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAAAATCACA
* * * * *
43990774 AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGCTGATA
1 GATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA-ATCACA
* * ** * **
43990819 -ATCCTATCTCCCTGAAGTTGCAGTAGAGTGGATTAAAACCTTA
1 GATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCACA
* * * * * * *
43990862 GATCTTATTTCTCTGAAATTGCAG-AGAGCAGA-TCACATC-TA
1 GATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCACA
* *
43990903 G-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA-A
1 GATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAA--AATCACA
* * * **
43990947 G-TCTTATC-CCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCA
1 GATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAAAATCACA
* * * * *
43990990 AACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTT-AAAGCGGATA
1 GATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATC--ACA
* *
43991035 G-TCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACA
1 GATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCACA
* ** * *
43991078 GATATTATCTTTCTAAAGTTGCAG-AGAGCAGAT
1 GATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
43991111 CGCATCTAGT
Statistics
Matches: 348, Mismatches: 94, Indels: 49
0.71 0.19 0.10
Matches are distributed among these distances:
40 39 0.11
41 18 0.05
42 12 0.03
43 49 0.14
44 171 0.49
45 59 0.17
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.28
Consensus pattern (44 bp):
GATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCACA
Found at i:43998803 original size:20 final size:19
Alignment explanation
Indices: 43998774--43998817 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
43998764 GTTCATAGAC
*
43998774 TTTTTAAAATTATAGTTATTA
1 TTTTTAAAATTA-AG-AATTA
43998795 TTTTT-AAATTAAGAATTA
1 TTTTTAAAATTAAGAATTA
43998813 TTTTT
1 TTTTT
43998818 TGAAATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 9 0.41
19 2 0.09
20 6 0.27
21 5 0.23
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (19 bp):
TTTTTAAAATTAAGAATTA
Found at i:44005881 original size:12 final size:12
Alignment explanation
Indices: 44005864--44005888 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
44005854 AATTTTGTAA
44005864 TAATTGGACTCT
1 TAATTGGACTCT
44005876 TAATTGGACTCT
1 TAATTGGACTCT
44005888 T
1 T
44005889 CGAACTCTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.44
Consensus pattern (12 bp):
TAATTGGACTCT
Found at i:44007493 original size:24 final size:23
Alignment explanation
Indices: 44007449--44007494 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
44007439 ATTATTAATT
* **
44007449 TTAATTTATAATTTTGTTTTTAA
1 TTAATTTATAATTATAATTTTAA
44007472 TTAATATTATAATTATAATTTTA
1 TTAAT-TTATAATTATAATTTTA
44007495 TACAAATCTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (23 bp):
TTAATTTATAATTATAATTTTAA
Found at i:44008377 original size:16 final size:16
Alignment explanation
Indices: 44008358--44008402 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
44008348 TAGTAATTTT
44008358 AATGTTAAAGGACTAA
1 AATGTTAAAGGACTAA
44008374 AATGTTAAAGTGA-TAA
1 AATGTTAAAG-GACTAA
*
44008390 AA-GTTCAAGGACT
1 AATGTTAAAGGACT
44008403 TAATGTAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 2 0.08
15 7 0.27
16 15 0.58
17 2 0.08
ACGTcount: A:0.47, C:0.07, G:0.20, T:0.27
Consensus pattern (16 bp):
AATGTTAAAGGACTAA
Found at i:44010124 original size:65 final size:66
Alignment explanation
Indices: 44009999--44010129 Score: 228
Period size: 66 Copynumber: 2.0 Consensus size: 66
44009989 TCCTCTTTGA
* *
44009999 AGGGATTTTTTCATGTTAAATTTGTGTGTTCAATTTCTCAATTTCTTCCGCTATTTTTTACTTGT
1 AGGGATTTTTTCACGTTAAATTTGTGTGTTCAATTTCTCAATTTCTTCCGCTATATTTTACTTGT
44010064 T
66 T
*
44010065 AGGGATTTTTTCACGTTAAATTTGTGTGTTCAATTTCTCAA-TTCTTTCGCTATATTTTACTTGT
1 AGGGATTTTTTCACGTTAAATTTGTGTGTTCAATTTCTCAATTTCTTCCGCTATATTTTACTTGT
44010129 T
66 T
44010130 GCTTAATCAG
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
65 22 0.35
66 40 0.65
ACGTcount: A:0.19, C:0.14, G:0.14, T:0.53
Consensus pattern (66 bp):
AGGGATTTTTTCACGTTAAATTTGTGTGTTCAATTTCTCAATTTCTTCCGCTATATTTTACTTGT
T
Found at i:44012435 original size:3 final size:3
Alignment explanation
Indices: 44012427--44012475 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
44012417 TTTAACCTTG
44012427 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
44012475 T
1 T
44012476 TACTCATTTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:44019075 original size:24 final size:24
Alignment explanation
Indices: 44019024--44019075 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
44019014 TTCGTAGGTC
* *
44019024 AAATAAATTATGCTAATAAATGCA
1 AAATAAATTATACTAATAAATACA
* *
44019048 AAATATATTATACTAATAAATACT
1 AAATAAATTATACTAATAAATACA
44019072 AAAT
1 AAAT
44019076 CTTCTAAAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.56, C:0.08, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACA
Found at i:44021012 original size:2 final size:2
Alignment explanation
Indices: 44021005--44021030 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
44020995 TTGCAGGTGG
44021005 GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT
44021031 ACATCAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:44023957 original size:18 final size:18
Alignment explanation
Indices: 44023936--44023979 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
44023926 TACCACCATT
*
44023936 ATTGTCGTTGCCACTGCC
1 ATTGTCATTGCCACTGCC
* *
44023954 ATTGCCATTGCCATTGCC
1 ATTGTCATTGCCACTGCC
44023972 ATTGTCAT
1 ATTGTCAT
44023980 CATCTTCCTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.16, C:0.30, G:0.18, T:0.36
Consensus pattern (18 bp):
ATTGTCATTGCCACTGCC
Found at i:44023959 original size:6 final size:6
Alignment explanation
Indices: 44023943--44023975 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
44023933 ATTATTGTCG
*
44023943 TTGCCA CTGCCA TTGCCA TTGCCA TTGCCA TTG
1 TTGCCA TTGCCA TTGCCA TTGCCA TTGCCA TTG
44023976 TCATCATCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.15, C:0.33, G:0.18, T:0.33
Consensus pattern (6 bp):
TTGCCA
Found at i:44030722 original size:35 final size:36
Alignment explanation
Indices: 44030682--44030753 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 36
44030672 TCTAGGATCA
44030682 CATATC-TCAAAAGATCACCTTCCATAATTGCCAAG
1 CATATCTTCAAAAGATCACCTTCCATAATTGCCAAG
* * * * *
44030717 CATATCTTTAGAAGATCACTTTCCTTATTTGCCAAG
1 CATATCTTCAAAAGATCACCTTCCATAATTGCCAAG
44030753 C
1 C
44030754 TCCGAAGATG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
35 6 0.19
36 25 0.81
ACGTcount: A:0.32, C:0.26, G:0.10, T:0.32
Consensus pattern (36 bp):
CATATCTTCAAAAGATCACCTTCCATAATTGCCAAG
Found at i:44033768 original size:26 final size:26
Alignment explanation
Indices: 44033732--44033790 Score: 100
Period size: 26 Copynumber: 2.3 Consensus size: 26
44033722 TTAAGTGTTT
44033732 TGAAACTGATACATGCTATGATATTC
1 TGAAACTGATACATGCTATGATATTC
* *
44033758 TGAAACTGATATATGTTATGATATTC
1 TGAAACTGATACATGCTATGATATTC
44033784 TGAAACT
1 TGAAACT
44033791 ACTGTAGGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (26 bp):
TGAAACTGATACATGCTATGATATTC
Found at i:44042105 original size:11 final size:11
Alignment explanation
Indices: 44042089--44042144 Score: 67
Period size: 11 Copynumber: 4.7 Consensus size: 11
44042079 ATCGAAGTTT
44042089 AAAAAAATTCAAA
1 AAAAAAATTC--A
44042102 AAAAAAATTCA
1 AAAAAAATTCA
44042113 AAAAAAATTCA
1 AAAAAAATTCA
*
44042124 AAAAAAAGTGACA
1 AAAAAAA-T-TCA
44042137 AAAAAAAT
1 AAAAAAAT
44042145 CGAGCAACAA
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
11 19 0.47
12 2 0.05
13 19 0.47
ACGTcount: A:0.75, C:0.07, G:0.04, T:0.14
Consensus pattern (11 bp):
AAAAAAATTCA
Done.