Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167882.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_15, whole genome shotgun sequence
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: 22478863
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 61000 characters in sequence are not A, C, G, or T
File 30 of 106
Found at i:5568083 original size:12 final size:12
Alignment explanation
Indices: 5568066--5568096 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
5568056 AACTTGCTAT
5568066 TTTTGAAGAAAA
1 TTTTGAAGAAAA
5568078 TTTTGAAGAAAA
1 TTTTGAAGAAAA
*
5568090 TATTGAA
1 TTTTGAA
5568097 TGTTGATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.16, T:0.35
Consensus pattern (12 bp):
TTTTGAAGAAAA
Found at i:5569558 original size:585 final size:585
Alignment explanation
Indices: 5568448--5569620 Score: 2132
Period size: 585 Copynumber: 2.0 Consensus size: 585
5568438 GATTTGGAGG
*
5568448 CTTATGTGGCGTGATAACTTGGAAATTTTATCCATACTTGGAGAGTTCCAAATAGCCCTTAGTTT
1 CTTATGTGGCGTGATAACTTGGAAATTCTATCCATACTTGGAGAGTTCCAAATAGCCCTTAGTTT
**
5568513 TCCTAGTTTAAGAAGGTTTTCCCACTTTGATTTGGAAATCCCAATTTGACTTAGAATTCTTACAT
66 GACTAGTTTAAGAAGGTTTTCCCACTTTGATTTGGAAATCCCAATTTGACTTAGAATTCTTACAT
*
5568578 TGACTAGAAAGAGCACTTGGCTATCCTTCTTAGAGTTATTTTTCCTAAGTTGACTAGCAAATCTT
131 TGACTAGAAAGAGCACTTAGCTATCCTTCTTAGAGTTATTTTTCCTAAGTTGACTAGCAAATCTT
*
5568643 AGTTACCAAGGCAATTATAAAAAAATAGGCAGTACATGAGGAGAAAACAACTCAAAATTTTATTT
196 AGTTACCAAGGCAATTATAAAAAAATAGGCAATACATGAGGAGAAAACAACTCAAAATTTTATTT
* *
5568708 CTCTCTTCTGTAATAACTTTTTAACTAGGAGCATAAGTCTAAGAGCTAAGAAATTGATTTGAGAC
261 CTCTCTTCTGCAATAACTTTTTAACTAGGAGCATAAGTCTAAGAGCTAAGAAATTGATTTAAGAC
* * *
5568773 CAATTGATTTTAAGATTTAAGCCTAATTCAAGAAAGGCCTAAGAACTGCTAAAGCTTAGTCCAAG
326 CAATTGATTTCAAGATTTAAGCCTAATTCAAGAAAGGCCTAAGAACTGCTAAAACCTAGTCCAAG
* *
5568838 TTGGAGTTCTTATTCAAGGCGGTTGCCAATGGTTTAAAGGTAATTACAAAAAAAGCCCTAGCCAT
391 TTGGAGTTCTTATTCAAGGAGGTTGCCAATGGTTTAAAAGTAATTACAAAAAAAGCCCTAGCCAT
5568903 CATCTACCTATCATTTCTAACTTTAGGATTCTTTGTAGTCATGTTCTATAAATAGCTAGCTTAGG
456 CATCTACCTATCATTTCTAACTTTAGGATTCTTTGTAGTCATGTTCTATAAATAGCTAGCTTAGG
5568968 TATTAGGAAAAGTCATGGTTGGGATGACAGACCAATATTTAGTTTATTAGCCTTGTTCTTGTTTT
521 TATTAGGAAAAGTCATGGTTGGGATGACAGACCAATATTTAGTTTATTAGCCTTGTTCTTGTTTT
*
5569033 CTTATGTGGTGTGATAACTTGGAAATTCTATCCATACTTGGAGAGTTCCAAATAGCCCTTAGTTT
1 CTTATGTGGCGTGATAACTTGGAAATTCTATCCATACTTGGAGAGTTCCAAATAGCCCTTAGTTT
5569098 GACTAGTTTAAGAAGGTTTTCCCACTTTGATTTGGAAATCCCAATTTGACTTAGAATTCTTACAT
66 GACTAGTTTAAGAAGGTTTTCCCACTTTGATTTGGAAATCCCAATTTGACTTAGAATTCTTACAT
5569163 TGACTAGAAAGAGCACTTAGCTATCCTTCTTAGAGTTATTTTTCCTAAGTTGACTAGCAAATCTT
131 TGACTAGAAAGAGCACTTAGCTATCCTTCTTAGAGTTATTTTTCCTAAGTTGACTAGCAAATCTT
* *
5569228 AGTTACCAAGGTAATTATAAAAAAA-AGGGTAATACATGAGGAGAAAACAACTCAAAATTTTATT
196 AGTTACCAAGGCAATTATAAAAAAATA-GGCAATACATGAGGAGAAAACAACTCAAAATTTTATT
5569292 TCTCTCTTCTGCAATAACTTTTTAACTAGGAGCATAAGTCTAAGAGCTAAGAAATTGATTTAAGA
260 TCTCTCTTCTGCAATAACTTTTTAACTAGGAGCATAAGTCTAAGAGCTAAGAAATTGATTTAAGA
5569357 CCAATTGATTTCAAGATTTAAGCCTAATTCAAGAAAGGCCTAAGAACTGCTAAAACCTAGTCCAA
325 CCAATTGATTTCAAGATTTAAGCCTAATTCAAGAAAGGCCTAAGAACTGCTAAAACCTAGTCCAA
* * *
5569422 GTTGGAGTTCTTATTCAAGGAGTTTGCCAATGGTTTAAAAGTAGTTACAAAGAAAGCCCTAGCCA
390 GTTGGAGTTCTTATTCAAGGAGGTTGCCAATGGTTTAAAAGTAATTACAAAAAAAGCCCTAGCCA
* * *
5569487 TCATCTACCTATCATTTCTAACTTTAGGATTCTTTGTATTCGTGTTCTATAAATAGTTAGCTTAG
455 TCATCTACCTATCATTTCTAACTTTAGGATTCTTTGTAGTCATGTTCTATAAATAGCTAGCTTAG
*
5569552 GTATTAGGAAAAGTCATGGTTGGGATGACAGACCAATCTTTAGTTTATTAGCCTTGTTCTTGTTT
520 GTATTAGGAAAAGTCATGGTTGGGATGACAGACCAATATTTAGTTTATTAGCCTTGTTCTTGTTT
5569617 T
585 T
5569618 CTT
1 CTT
5569621 TTAAGTTTTA
Statistics
Matches: 565, Mismatches: 22, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
584 1 0.00
585 564 1.00
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (585 bp):
CTTATGTGGCGTGATAACTTGGAAATTCTATCCATACTTGGAGAGTTCCAAATAGCCCTTAGTTT
GACTAGTTTAAGAAGGTTTTCCCACTTTGATTTGGAAATCCCAATTTGACTTAGAATTCTTACAT
TGACTAGAAAGAGCACTTAGCTATCCTTCTTAGAGTTATTTTTCCTAAGTTGACTAGCAAATCTT
AGTTACCAAGGCAATTATAAAAAAATAGGCAATACATGAGGAGAAAACAACTCAAAATTTTATTT
CTCTCTTCTGCAATAACTTTTTAACTAGGAGCATAAGTCTAAGAGCTAAGAAATTGATTTAAGAC
CAATTGATTTCAAGATTTAAGCCTAATTCAAGAAAGGCCTAAGAACTGCTAAAACCTAGTCCAAG
TTGGAGTTCTTATTCAAGGAGGTTGCCAATGGTTTAAAAGTAATTACAAAAAAAGCCCTAGCCAT
CATCTACCTATCATTTCTAACTTTAGGATTCTTTGTAGTCATGTTCTATAAATAGCTAGCTTAGG
TATTAGGAAAAGTCATGGTTGGGATGACAGACCAATATTTAGTTTATTAGCCTTGTTCTTGTTTT
Found at i:5572317 original size:92 final size:91
Alignment explanation
Indices: 5572146--5572317 Score: 202
Period size: 92 Copynumber: 1.9 Consensus size: 91
5572136 AATAAGAAAT
* * * *
5572146 AAAAATTTTTATCCGACGATAAAATTCAAAGGTATTCCGAGTAGTGATACATATGAAATCTCTAG
1 AAAAAATTTTATCCGACGATAAAATTCAAAGGTATTCCGAGTAATGATACATACGAAATCCCTAG
* * *
5572211 GTGATAAGATTTTTTTAAATATTAAA
66 GTAAGAAGAATTTTTTAAATATTAAA
* * * * *
5572237 AAAAAATTTTATCCGAGGATGAGATTCTAAAGGTATTTCGAGTAATGATACTTTACGAAATCCCT
1 AAAAAATTTTATCCGACGATAAAATTC-AAAGGTATTCCGAGTAATGATAC-ATACGAAATCCCT
*
5572302 TGGTAAGAA-AATTTTT
64 AGGTAAGAAGAATTTTT
5572318 CTTAAGTATT
Statistics
Matches: 66, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
91 23 0.35
92 27 0.41
93 16 0.24
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (91 bp):
AAAAAATTTTATCCGACGATAAAATTCAAAGGTATTCCGAGTAATGATACATACGAAATCCCTAG
GTAAGAAGAATTTTTTAAATATTAAA
Found at i:5572408 original size:18 final size:19
Alignment explanation
Indices: 5572385--5572420 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
5572375 TCTCTTCTCT
5572385 TTAATAAAAT-AATAAAAA
1 TTAATAAAATCAATAAAAA
5572403 TTAATAAAATCAATAAAA
1 TTAATAAAATCAATAAAA
5572421 TTTCTAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (19 bp):
TTAATAAAATCAATAAAAA
Found at i:5572411 original size:9 final size:9
Alignment explanation
Indices: 5572385--5572422 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
5572375 TCTCTTCTCT
5572385 TTAATAAAA
1 TTAATAAAA
5572394 -TAATAAAAA
1 TTAAT-AAAA
5572403 TTAATAAAA
1 TTAATAAAA
*
5572412 TCAATAAAA
1 TTAATAAAA
5572421 TT
1 TT
5572423 TCTAAAAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
8 4 0.16
9 17 0.68
10 4 0.16
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (9 bp):
TTAATAAAA
Found at i:5573626 original size:5 final size:5
Alignment explanation
Indices: 5573616--5573665 Score: 50
Period size: 5 Copynumber: 10.2 Consensus size: 5
5573606 GTGTAAGAAT
* * *
5573616 ACAAA ACAAA ACAAA ACAAA ATAAA A-AATC TCAAA ACAAA ACAAA A-AAA
1 ACAAA ACAAA ACAAA ACAAA ACAAA ACAA-A ACAAA ACAAA ACAAA ACAAA
5573665 A
1 A
5573666 GAGCTTTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
4 6 0.16
5 30 0.79
6 2 0.05
ACGTcount: A:0.78, C:0.16, G:0.00, T:0.06
Consensus pattern (5 bp):
ACAAA
Found at i:5580569 original size:27 final size:27
Alignment explanation
Indices: 5580531--5580586 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
5580521 CTTAAGAAAG
*
5580531 ATAAAAAAATGAAAATGTGTATCGATT
1 ATAAAAAAATGAAAATGTGTACCGATT
* *
5580558 ATAAAAAAATGAGAATGTGTGCCGATT
1 ATAAAAAAATGAAAATGTGTACCGATT
5580585 AT
1 AT
5580587 CAAGACTCGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.48, C:0.05, G:0.18, T:0.29
Consensus pattern (27 bp):
ATAAAAAAATGAAAATGTGTACCGATT
Found at i:5583514 original size:23 final size:20
Alignment explanation
Indices: 5583474--5583525 Score: 61
Period size: 23 Copynumber: 2.5 Consensus size: 20
5583464 ATATTTTACT
5583474 TAAAAAAAAC-AAAAAAAAG
1 TAAAAAAAACAAAAAAAAAG
5583493 ATAAAAAAAAGCAAAAACAAAAAG
1 -TAAAAAAAA-C-AAAA-AAAAAG
5583517 TAAAAAAAA
1 TAAAAAAAA
5583526 AATGACATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
20 9 0.32
21 1 0.04
23 12 0.43
24 6 0.21
ACGTcount: A:0.83, C:0.06, G:0.06, T:0.06
Consensus pattern (20 bp):
TAAAAAAAACAAAAAAAAAG
Found at i:5583526 original size:24 final size:20
Alignment explanation
Indices: 5583474--5583525 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
5583464 ATATTTTACT
*
5583474 TAAAAAAAACAAAAAAAAGA
1 TAAAAAAAACAAAAAAAAAA
5583494 TAAAAAAAAGCAAAAACAAAAA
1 TAAAAAAAA-CAAAAA-AAAAA
5583516 GTAAAAAAAA
1 -TAAAAAAAA
5583526 AATGACATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 9 0.32
21 6 0.21
22 4 0.14
23 9 0.32
ACGTcount: A:0.83, C:0.06, G:0.06, T:0.06
Consensus pattern (20 bp):
TAAAAAAAACAAAAAAAAAA
Found at i:5584518 original size:48 final size:48
Alignment explanation
Indices: 5584341--5584764 Score: 444
Period size: 48 Copynumber: 8.8 Consensus size: 48
5584331 CAGATAAGAT
*
5584341 TTTTAAAGTTGTTGAGCCT-TAGCTTAGAGGAG-CTTTTCCCAAGATGAA
1 TTTTAAAGTTGTTGAGCCTCT-GCTTAGAGGAGCCTTTT-TCAAGATGAA
* * * * *
5584389 TCTTTAAAGTTGTTGAGCCTCGGCTTGGAAGAGTCTTTTCCAAGATGAA
1 T-TTTAAAGTTGTTGAGCCTCTGCTTAGAGGAGCCTTTTTCAAGATGAA
* * *
5584438 TGTTTAAAGTTATTGAGCCTCTGCTTATAGGAGCCTTTTTCAAGATAAA
1 T-TTTAAAGTTGTTGAGCCTCTGCTTAGAGGAGCCTTTTTCAAGATGAA
* * * * * *
5584487 TTTTAAAATTGTTGAGCATTTTCTTAAAGGAGCCTTTTCCAAGATGAA
1 TTTTAAAGTTGTTGAGCCTCTGCTTAGAGGAGCCTTTTTCAAGATGAA
* ** * * *
5584535 TTTTAAAGTTGTTGAGTCTCTGCTTAGATAAGCTTTTTTTAAGATAAA
1 TTTTAAAGTTGTTGAGCCTCTGCTTAGAGGAGCCTTTTTCAAGATGAA
* * * *
5584583 TTTTAAAATTGCTGAGCCTCTACTTAGAGAAGCC-TTTTCGAAGATGAA
1 TTTTAAAGTTGTTGAGCCTCTGCTTAGAGGAGCCTTTTTC-AAGATGAA
* ** *
5584631 TTTTAAAGTTGTTAAGCCAT-TATTTAGAGGAGCTTTTTTCAAGATGAA
1 TTTTAAAGTTGTTGAGCC-TCTGCTTAGAGGAGCCTTTTTCAAGATGAA
* * * *
5584679 TTTTAAAGTTGTTAAACCTCTGCTTAGATGAGCTTTTTTCAAGATGAA
1 TTTTAAAGTTGTTGAGCCTCTGCTTAGAGGAGCCTTTTTCAAGATGAA
* *
5584727 TTTTAAAGTTATTGAGCCTCTGATTAGAGGAG-CTTTTT
1 TTTTAAAGTTGTTGAGCCTCTGCTTAGAGGAGCCTTTTT
5584765 AAATTTCTAT
Statistics
Matches: 313, Mismatches: 56, Indels: 15
0.82 0.15 0.04
Matches are distributed among these distances:
47 10 0.03
48 214 0.68
49 84 0.27
50 5 0.02
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.39
Consensus pattern (48 bp):
TTTTAAAGTTGTTGAGCCTCTGCTTAGAGGAGCCTTTTTCAAGATGAA
Found at i:5584627 original size:144 final size:143
Alignment explanation
Indices: 5584332--5584764 Score: 507
Period size: 144 Copynumber: 3.0 Consensus size: 143
5584322 TTTCAAGAAC
* *
5584332 AGATAAGATTTTTAAAGTTGTTGAGCCTTAGCTTAGAGGAG-CTTTTCCCAAGATGAATCTTTAA
1 AGATAA-A-TTTTAAAGTTGTTGAGCATTATCTTAGAGGAGCCTTTT-CCAAGATGAAT-TTTAA
* * *
5584396 AGTTGTTGAGCCTCGGCTTGGA-AGAG-TCTTTTCCAAGATGAATGTTTAAAGTTATTGAGCCTC
62 AGTTGTTGAGCCTCTGCTTAGATA-AGCT-TTTTTCAAGATGAAT-TTTAAAGTTATTGAGCCTC
* *
5584459 TGCTTATAGGAGCCTTTTTCA
124 TACTTAGAGGAGCC-TTTTCA
* * *
5584480 AGATAAATTTTAAAATTGTTGAGCATTTTCTTAAAGGAGCCTTTTCCAAGATGAATTTTAAAGTT
1 AGATAAATTTTAAAGTTGTTGAGCATTATCTTAGAGGAGCCTTTTCCAAGATGAATTTTAAAGTT
* * * * **
5584545 GTTGAGTCTCTGCTTAGATAAGCTTTTTTTAAGATAAATTTTAAAATTGCTGAGCCTCTACTTAG
66 GTTGAGCCTCTGCTTAGATAAGCTTTTTTCAAGATGAATTTTAAAGTTATTGAGCCTCTACTTAG
*
5584610 AGAAGCCTTTTCGA
131 AGGAGCCTTTTC-A
* * * *
5584624 AGATGAATTTTAAAGTTGTTAAGCCATTAT-TTAGAGGAGCTTTTTTCAAGATGAATTTTAAAGT
1 AGATAAATTTTAAAGTTGTTGAG-CATTATCTTAGAGGAGCCTTTTCCAAGATGAATTTTAAAGT
* * *
5584688 TGTTAAACCTCTGCTTAGATGAGCTTTTTTCAAGATGAATTTTAAAGTTATTGAGCCTCTGA-TT
65 TGTTGAGCCTCTGCTTAGATAAGCTTTTTTCAAGATGAATTTTAAAGTTATTGAGCCTCT-ACTT
*
5584752 AGAGGAGCTTTTT
129 AGAGGAGCCTTTT
5584765 AAATTTCTAT
Statistics
Matches: 244, Mismatches: 35, Indels: 16
0.83 0.12 0.05
Matches are distributed among these distances:
143 5 0.02
144 143 0.59
145 44 0.18
146 40 0.16
147 6 0.02
148 6 0.02
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.39
Consensus pattern (143 bp):
AGATAAATTTTAAAGTTGTTGAGCATTATCTTAGAGGAGCCTTTTCCAAGATGAATTTTAAAGTT
GTTGAGCCTCTGCTTAGATAAGCTTTTTTCAAGATGAATTTTAAAGTTATTGAGCCTCTACTTAG
AGGAGCCTTTTCA
Found at i:5587255 original size:17 final size:17
Alignment explanation
Indices: 5587233--5587268 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
5587223 TATATTTATG
5587233 AAAATGCATATAAAAAT
1 AAAATGCATATAAAAAT
5587250 AAAATGCATATAAAAAT
1 AAAATGCATATAAAAAT
5587267 AA
1 AA
5587269 TAGCTCAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.67, C:0.06, G:0.06, T:0.22
Consensus pattern (17 bp):
AAAATGCATATAAAAAT
Found at i:5591288 original size:21 final size:21
Alignment explanation
Indices: 5591264--5591321 Score: 98
Period size: 21 Copynumber: 2.7 Consensus size: 21
5591254 AAAATTTTAA
5591264 GCCTGCAAAATAAAACAACAT
1 GCCTGCAAAATAAAACAACAT
5591285 GCCTGCAAAATAAAACAACAT
1 GCCTGCAAAATAAAACAACAT
*
5591306 ACCTGCAAAAGTAAAA
1 GCCTGCAAAA-TAAAA
5591322 GTAAAAGCCA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
21 30 0.86
22 5 0.14
ACGTcount: A:0.53, C:0.22, G:0.10, T:0.14
Consensus pattern (21 bp):
GCCTGCAAAATAAAACAACAT
Found at i:5591897 original size:39 final size:39
Alignment explanation
Indices: 5591832--5591908 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
5591822 GATGAGGTAT
*
5591832 GGAGGATTAGGTGTGGTGGGGCGTTGGG-GGGAAGGTGG
1 GGAGGATTAGGTGTGGTGGGACGTTGGGAGGGAAGGTGG
* *
5591870 GGAGTGATTGGGTGTGGTGGGATGTTGGGAGGGAAGGTG
1 GGAG-GATTAGGTGTGGTGGGACGTTGGGAGGGAAGGTG
5591909 AAGAGGGATT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
38 4 0.12
39 21 0.62
40 9 0.26
ACGTcount: A:0.14, C:0.01, G:0.61, T:0.23
Consensus pattern (39 bp):
GGAGGATTAGGTGTGGTGGGACGTTGGGAGGGAAGGTGG
Found at i:5591919 original size:40 final size:39
Alignment explanation
Indices: 5591835--5591919 Score: 107
Period size: 39 Copynumber: 2.2 Consensus size: 39
5591825 GAGGTATGGA
* * **
5591835 GGATTAGGTGTGGTGGGGCGTTGGGGGGAAGGTGGGGAG
1 GGATTGGGTGTGGTGGGACGTTGGGGGGAAGGTGAAGAG
* *
5591874 TGATTGGGTGTGGTGGGATGTTGGGAGGGAAGGTGAAGAG
1 GGATTGGGTGTGGTGGGACGTTGGG-GGGAAGGTGAAGAG
5591914 GGATTG
1 GGATTG
5591920 ATGGGGATGG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
39 21 0.55
40 17 0.45
ACGTcount: A:0.16, C:0.01, G:0.59, T:0.24
Consensus pattern (39 bp):
GGATTGGGTGTGGTGGGACGTTGGGGGGAAGGTGAAGAG
Found at i:5591956 original size:15 final size:15
Alignment explanation
Indices: 5591936--5591967 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
5591926 ATGGGGAGGT
5591936 ATTGGGTGTGGTGGG
1 ATTGGGTGTGGTGGG
5591951 ATTGGGTGTGGTGGG
1 ATTGGGTGTGGTGGG
5591966 AT
1 AT
5591968 GTTGGGGGGG
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:0.09, C:0.00, G:0.56, T:0.34
Consensus pattern (15 bp):
ATTGGGTGTGGTGGG
Found at i:5591962 original size:75 final size:76
Alignment explanation
Indices: 5591875--5592024 Score: 248
Period size: 77 Copynumber: 2.0 Consensus size: 76
5591865 GGTGGGGAGT
*
5591875 GATTGGGTGTGGTGGGATGTT-GGGAGGGAAGGTGAAGAGGGATTGATGGGGATGGGGAGGTATT
1 GATTGGGTGTGGTGGGATGTTGGGGAGGGAAGGTGAAGAGGGATTGATGGGGATGGGGAGGGATT
5591939 GGGTGTGGTGG
66 GGGTGTGGTGG
* * *
5591950 GATTGGGTGTGGTGGGATGTTGGGGGGGGGAAGGTGGAGAGGGATTGATGGGGGTGGGGAGGGAT
1 GATTGGGTGTGGTGGGATGTT-GGGGAGGGAAGGTGAAGAGGGATTGATGGGGATGGGGAGGGAT
5592015 TGGGTGTGGT
65 TGGGTGTGGT
5592025 AGGGTGTTTG
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
75 21 0.30
77 48 0.70
ACGTcount: A:0.15, C:0.00, G:0.60, T:0.25
Consensus pattern (76 bp):
GATTGGGTGTGGTGGGATGTTGGGGAGGGAAGGTGAAGAGGGATTGATGGGGATGGGGAGGGATT
GGGTGTGGTGG
Found at i:5592259 original size:19 final size:18
Alignment explanation
Indices: 5592231--5592266 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
5592221 GATTGTGTTA
*
5592231 TATATTAATTTATAATTTG
1 TATATGAATTT-TAATTTG
5592250 TATATGAATTTTAATTT
1 TATATGAATTTTAATTT
5592267 TTTTGTTGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (18 bp):
TATATGAATTTTAATTTG
Found at i:5596348 original size:18 final size:18
Alignment explanation
Indices: 5596325--5596449 Score: 105
Period size: 18 Copynumber: 6.9 Consensus size: 18
5596315 ATGGTTATTA
5596325 TCCACCTCAAATGTATCC
1 TCCACCTCAAATGTATCC
* *
5596343 TCCACCTCCTCAAATATATCT
1 TCCA---CCTCAAATGTATCC
*
5596364 TCCACCTCAAATGTATCAG
1 TCCACCTCAAATGTATC-C
* * *
5596383 T-TACCACAAATGTACCC
1 TCCACCTCAAATGTATCC
* *
5596400 TCCACCACAAATGTATCA
1 TCCACCTCAAATGTATCC
*
5596418 TCCA---CAAATATATCC
1 TCCACCTCAAATGTATCC
5596433 TCCACCTCAAATGTATC
1 TCCACCTCAAATGTATC
5596450 AAGAACAAAG
Statistics
Matches: 85, Mismatches: 14, Indels: 16
0.74 0.12 0.14
Matches are distributed among these distances:
15 13 0.15
17 1 0.01
18 54 0.64
19 1 0.01
21 16 0.19
ACGTcount: A:0.33, C:0.35, G:0.05, T:0.27
Consensus pattern (18 bp):
TCCACCTCAAATGTATCC
Found at i:5596355 original size:21 final size:21
Alignment explanation
Indices: 5596329--5596371 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
5596319 TTATTATCCA
*
5596329 CCTCAAATGTATCCTCCACCT
1 CCTCAAATATATCCTCCACCT
*
5596350 CCTCAAATATATCTTCCACCT
1 CCTCAAATATATCCTCCACCT
5596371 C
1 C
5596372 AAATGTATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.42, G:0.02, T:0.30
Consensus pattern (21 bp):
CCTCAAATATATCCTCCACCT
Found at i:5596422 original size:15 final size:15
Alignment explanation
Indices: 5596404--5596437 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
5596394 GTACCCTCCA
*
5596404 CCACAAATGTATCAT
1 CCACAAATATATCAT
*
5596419 CCACAAATATATCCT
1 CCACAAATATATCAT
5596434 CCAC
1 CCAC
5596438 CTCAAATGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.35, G:0.03, T:0.24
Consensus pattern (15 bp):
CCACAAATATATCAT
Found at i:5596435 original size:33 final size:35
Alignment explanation
Indices: 5596353--5596450 Score: 137
Period size: 33 Copynumber: 2.8 Consensus size: 35
5596343 TCCACCTCCT
*
5596353 CAAATATATCTTCCACCTCAAATGTATCAGTTACCA
1 CAAATATATCCTCCACCTCAAATGTATCAG-TACCA
* * *
5596389 CAAATGTACCCTCCACCACAAATGTATCA-T-CCA
1 CAAATATATCCTCCACCTCAAATGTATCAGTACCA
5596422 CAAATATATCCTCCACCTCAAATGTATCA
1 CAAATATATCCTCCACCTCAAATGTATCA
5596451 AGAACAAAGG
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
33 29 0.53
34 1 0.02
36 25 0.45
ACGTcount: A:0.37, C:0.32, G:0.05, T:0.27
Consensus pattern (35 bp):
CAAATATATCCTCCACCTCAAATGTATCAGTACCA
Found at i:5600330 original size:40 final size:40
Alignment explanation
Indices: 5600275--5600354 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
5600265 ACCTTGACCA
5600275 AGAAAATAAAAGCTATAGAAACCTAACAAACTATTGCCCT
1 AGAAAATAAAAGCTATAGAAACCTAACAAACTATTGCCCT
5600315 AGAAAATAAAAGCTATAGAAACCTAACAAACTATTGCCCT
1 AGAAAATAAAAGCTATAGAAACCTAACAAACTATTGCCCT
5600355 TGTCCAAGCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.50, C:0.20, G:0.10, T:0.20
Consensus pattern (40 bp):
AGAAAATAAAAGCTATAGAAACCTAACAAACTATTGCCCT
Found at i:5609028 original size:3 final size:3
Alignment explanation
Indices: 5609020--5609079 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
5609010 TTTTGTTCAG
5609020 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
5609068 TAT TAT TAT TAT
1 TAT TAT TAT TAT
5609080 AATTTCCTTT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:5609107 original size:12 final size:12
Alignment explanation
Indices: 5609087--5609125 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
5609077 TATAATTTCC
5609087 TTTTT-TTTCTT
1 TTTTTCTTTCTT
5609098 TTTTTCTTTCTT
1 TTTTTCTTTCTT
5609110 TTTTTCTTT-TT
1 TTTTTCTTTCTT
5609121 TTTTT
1 TTTTT
5609126 GATATGTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 12 0.44
12 15 0.56
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (12 bp):
TTTTTCTTTCTT
Found at i:5609289 original size:23 final size:22
Alignment explanation
Indices: 5609261--5609324 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 22
5609251 CAGATTGGTT
*
5609261 AAAAATCAGGGATTTGAATATAA
1 AAAAATCAGGGATTTGAAT-CAA
** * *
5609284 AAAAATTTGAGATTTGAATCCA
1 AAAAATCAGGGATTTGAATCAA
5609306 AAAAATCTA-GGATTTGAAT
1 AAAAATC-AGGGATTTGAAT
5609325 TTCAGAAAGC
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
22 16 0.50
23 16 0.50
ACGTcount: A:0.48, C:0.06, G:0.16, T:0.30
Consensus pattern (22 bp):
AAAAATCAGGGATTTGAATCAA
Found at i:5610230 original size:21 final size:20
Alignment explanation
Indices: 5610195--5610249 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 20
5610185 ATTAAAATTT
5610195 TAATGAATAAGAATAAAGAAATA
1 TAATGAA-AA-AATAAAGAAA-A
*
5610218 TAATGAAAAAATAAATAAAA
1 TAATGAAAAAATAAAGAAAA
*
5610238 T-ATGATAAAATA
1 TAATGAAAAAATA
5610250 GAAATAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 10 0.33
20 2 0.07
21 9 0.30
22 2 0.07
23 7 0.23
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.24
Consensus pattern (20 bp):
TAATGAAAAAATAAAGAAAA
Found at i:5615546 original size:5 final size:5
Alignment explanation
Indices: 5615533--5615569 Score: 56
Period size: 5 Copynumber: 7.4 Consensus size: 5
5615523 ACATGTAAAT
* *
5615533 AAAGG AAAGC AAAGG AAAGG AAAGG AAAAG AAAGG AA
1 AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG AA
5615570 TGTTTTTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.65, C:0.03, G:0.32, T:0.00
Consensus pattern (5 bp):
AAAGG
Found at i:5619558 original size:85 final size:86
Alignment explanation
Indices: 5619414--5619584 Score: 254
Period size: 85 Copynumber: 2.0 Consensus size: 86
5619404 GAATTTACTG
* * * *
5619414 AGCTTGAAAATTAACTATTACAGTAGTGGAATAAAGGCATGCAAATAAAATATTCATAAAGAAAT
1 AGCTTGAAAAATAACTACTACAGTAGTAGAATAAAGGCAGGCAAATAAAATATTCATAAAGAAAT
5619479 AGA-GGATTATCAGATCATCA
66 AGAGGGATTATCAGATCATCA
* * *
5619499 AGCTTGAAAAATAACTACTGCAGTAGTAGAATAAAGGTAGGCAAATAAAATATTTATAAAGAAAT
1 AGCTTGAAAAATAACTACTACAGTAGTAGAATAAAGGCAGGCAAATAAAATATTCATAAAGAAAT
* *
5619564 AGAGGGCTTCTCAGATCATCA
66 AGAGGGATTATCAGATCATCA
5619585 GACCATAGTC
Statistics
Matches: 76, Mismatches: 9, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
85 61 0.80
86 15 0.20
ACGTcount: A:0.46, C:0.11, G:0.18, T:0.25
Consensus pattern (86 bp):
AGCTTGAAAAATAACTACTACAGTAGTAGAATAAAGGCAGGCAAATAAAATATTCATAAAGAAAT
AGAGGGATTATCAGATCATCA
Found at i:5632484 original size:27 final size:27
Alignment explanation
Indices: 5632444--5632498 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
5632434 AAAGTAGAGA
* * * *
5632444 AAATTGAAGGGGATCCATGTGAAGATG
1 AAATTAAAGAGGATCCAAGTGAAAATG
*
5632471 AAATTAAAGAGGATTCAAGTGAAAATG
1 AAATTAAAGAGGATCCAAGTGAAAATG
5632498 A
1 A
5632499 GCTTGAGAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.45, C:0.05, G:0.27, T:0.22
Consensus pattern (27 bp):
AAATTAAAGAGGATCCAAGTGAAAATG
Found at i:5641739 original size:23 final size:23
Alignment explanation
Indices: 5641709--5641754 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
5641699 AAATGAATAA
5641709 ATAATTAATTATTAAAGGCATTT
1 ATAATTAATTATTAAAGGCATTT
5641732 ATAATTAATTATTAAAGGCATTT
1 ATAATTAATTATTAAAGGCATTT
5641755 CTGTGGAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.43
Consensus pattern (23 bp):
ATAATTAATTATTAAAGGCATTT
Found at i:5642916 original size:355 final size:352
Alignment explanation
Indices: 5641981--5643166 Score: 1517
Period size: 355 Copynumber: 3.3 Consensus size: 352
5641971 AGTTTATAAC
* * * *
5641981 AAATTATTGAAGGCGTTGTTATTTGCAACCATCTTTACTAATTATCTACAAACTATGATAGAAAT
1 AAATTATTGAAGGCATTGTTATCTGCAACCACCTTTACTAATTATCTACAAACTGTGATAG-AAT
*
5642046 TATCAAAGGCGTCTTTCTTGGATATACACTTTCAATAACCGTGTTAAAATTTGTGT-A-GTAGTA
65 TATCAAAGGCGTCTTTCTTGGATATACACCTTCAATAACCGTGTTAAAATTTGTGTGACG--GTA
* * * * *
5642109 TATAGAAGGCATTTTACAATAGAAAACACATTTAATAATTCCTAAAATGTTTAGTGAAAAAATTT
128 TATAAAAGGCATTTTACAATAGAAGACACCTTTAATAATTCCTAAAATTTTTAGTGGAAAAATTT
** *
5642174 TGAAGGCGTC---TATTAACAAATGCCTTCAGTAATGGATTACTACATTTAAAGGTATATTGAAG
193 TGAAGGCGTCTGTTATTAACAAACACCTTCAGTAATGGATTACTAAATTTAAAGGTATATTGAAG
* * * * *
5642236 GCACTTGTCTGACTAAACGCCTTCTATAACCATTGTGGTATATTGAAGGCATTTCATAATAAAAG
258 GCACTT-TTTGAATAAAAGCCTTCTATAACCATCGTGGTATATTAAAGGCATTTCATAATAAAAG
* * *
5642301 ACACCTTTAATAATTCAAAAATTTTTTTTAAG
322 A-TCCTTTAATAATCCAAAAAATTTTTTTAAG
* * *
5642333 AAAATTATTGAAGGCATTATTATCTGCAACCACCTTCACTTATTATCTACAAACTGTGATAGGAA
1 -AAATTATTGAAGGCATTGTTATCTGCAACCACCTTTACTAATTATCTACAAACTGTGATA-GAA
* * * *
5642398 TTATCAAAGGCTTCTTTCTTGGATATACGCCTTCAATAACCTTGTTAAAATTTGTGTAACGGTAT
64 TTATCAAAGGCGTCTTTCTTGGATATACACCTTCAATAACCGTGTTAAAATTTGTGTGACGGTAT
* *
5642463 ATAAAAGGCATTTTACAGTAAAAGACACCTTTAATAATTCCTAAAATTTTTAGTGGAAAAATTTT
129 ATAAAAGGCATTTTACAATAGAAGACACCTTTAATAATTCCTAAAATTTTTAGTGGAAAAATTTT
* * *
5642528 GAAGGCATTTGTTATTAACAAACACTTTCAGTAATGGATTACTAAATTTAAAGGTATATTGAAGG
194 GAAGGCGTCTGTTATTAACAAACACCTTCAGTAATGGATTACTAAATTTAAAGGTATATTGAA-G
* ** *
5642593 TGC-CTTTTTGAATAAAAGCCTTTTATAACCATCGTGGTATATTAAAGGTGTTTTATAATAAAAG
258 -GCACTTTTTGAATAAAAGCCTTCTATAACCATCGTGGTATATTAAAGGCATTTCATAATAAAAG
*
5642657 ATCCTTTGATAATCCAAAAAATATTTTTTAAAG
322 ATCCTTTAATAATCCAAAAAAT-TTTTTT-AAG
** * *
5642690 AAATTATTGAAGGTGTTGTTATCTGCAACCGCCTTTACTAATTATCTACAAACTGTGATAGGATT
1 AAATTATTGAAGGCATTGTTATCTGCAACCACCTTTACTAATTATCTACAAACTGTGATAGAATT
* * * *
5642755 ATTAAAGGCATCTTTCTTGGATATACACCTTCAATAACCATGTTAAAATTTGTGTGACGGTATTT
66 ATCAAAGGCGTCTTTCTTGGATATACACCTTCAATAACCGTGTTAAAATTTGTGTGACGGTATAT
* ** * *
5642820 AAAAGGTATTTTACAATAGAAGATGCCTTTAATAAAT-CTCAAAATTTTTAATGGAAAAATTTTG
131 AAAAGGCATTTTACAATAGAAGACACCTTTAATAATTCCT-AAAATTTTTAGTGGAAAAATTTTG
* *
5642884 AAAGCGTCTGTTATTAACAAACACCTTCAGTAATGGATTACTAAGTTTAAAGGTATATTGAAGGC
195 AAGGCGTCTGTTATTAACAAACACCTTCAGTAATGGATTACTAAATTTAAAGGTATATTGAAGGC
* * *
5642949 ACTTTTTCGAATAAATGCCTTCCATAACCATCATGGTATATTAAAGGCATTTCATAATAAAAGAT
260 ACTTTTT-GAATAAAAGCCTTCTATAACCATCGTGGTATATTAAAGGCATTTCATAATAAAAGAT
* * *
5643014 GCCTTTAATAATCTAAAAAACCTTTTTTAGG
324 -CCTTTAATAATCCAAAAAA-TTTTTTTAAG
** ** *
5643045 AAATTATTGAAGGCATTGTTATCTGTTA-CTGCTTTCACTAATTATCTACAAATTGTGATACGAA
1 AAATTATTGAAGGCATTGTTATCTGCAACCACCTTT-ACTAATTATCTACAAACTGTGATA-GAA
* * * ** *
5643109 TTATTAAATGCGTCTTTCTTGGATATA-AGCCTTTAATAATTGTATTAAAATTTGTGTG
64 TTATCAAAGGCGTCTTTCTTGGATATACA-CCTTCAATAACCGTGTTAAAATTTGTGTG
5643167 GCGATATGTT
Statistics
Matches: 727, Mismatches: 88, Indels: 33
0.86 0.10 0.04
Matches are distributed among these distances:
353 179 0.25
354 16 0.02
355 292 0.40
356 231 0.32
357 7 0.01
358 2 0.00
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Consensus pattern (352 bp):
AAATTATTGAAGGCATTGTTATCTGCAACCACCTTTACTAATTATCTACAAACTGTGATAGAATT
ATCAAAGGCGTCTTTCTTGGATATACACCTTCAATAACCGTGTTAAAATTTGTGTGACGGTATAT
AAAAGGCATTTTACAATAGAAGACACCTTTAATAATTCCTAAAATTTTTAGTGGAAAAATTTTGA
AGGCGTCTGTTATTAACAAACACCTTCAGTAATGGATTACTAAATTTAAAGGTATATTGAAGGCA
CTTTTTGAATAAAAGCCTTCTATAACCATCGTGGTATATTAAAGGCATTTCATAATAAAAGATCC
TTTAATAATCCAAAAAATTTTTTTAAG
Found at i:5647726 original size:13 final size:13
Alignment explanation
Indices: 5647708--5647733 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5647698 CTAGGTTTAG
5647708 ACTACCCCATTAA
1 ACTACCCCATTAA
5647721 ACTACCCCATTAA
1 ACTACCCCATTAA
5647734 TTGATTATGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.23
Consensus pattern (13 bp):
ACTACCCCATTAA
Found at i:5652158 original size:55 final size:55
Alignment explanation
Indices: 5652099--5652234 Score: 173
Period size: 55 Copynumber: 2.5 Consensus size: 55
5652089 TAGCATCCAT
* *
5652099 CAGTATAGACTTGTATTTTTTAATTTTCTTACCTATACCGATGGTTAGAGACTAA
1 CAGTATAGACTTGTATGTTTTAATTTTCTTACCTATACCGATGGTTAAAGACTAA
* * * * * **
5652154 CAGTATAGAATTGTATGCTTTAATTTTCTTACCTTTATCGATGGTTAAAGATTGT
1 CAGTATAGACTTGTATGTTTTAATTTTCTTACCTATACCGATGGTTAAAGACTAA
* *
5652209 CAATATAGACTTATATGTTTTAATTT
1 CAGTATAGACTTGTATGTTTTAATTT
5652235 ATTTTATTAT
Statistics
Matches: 68, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
55 68 1.00
ACGTcount: A:0.29, C:0.12, G:0.14, T:0.45
Consensus pattern (55 bp):
CAGTATAGACTTGTATGTTTTAATTTTCTTACCTATACCGATGGTTAAAGACTAA
Found at i:5652924 original size:68 final size:68
Alignment explanation
Indices: 5652852--5652978 Score: 175
Period size: 68 Copynumber: 1.9 Consensus size: 68
5652842 ATATAAGGTA
* * * *
5652852 AAAAGGTAATCCATCCATTCATATACCAGTGAAA-TAGTTTTATAAACATCTTATTCATTGATAT
1 AAAAGGTAAT-CATCCATTCATATACCAATAAAAGTAATTTTATAAACATCCTATTCATTGATAT
5652916 ATAC
65 ATAC
* **
5652920 AAAAGGTAATCATCCATTTATATATGAATAAAAGTAATTTTATAAACATCCTATTCATT
1 AAAAGGTAATCATCCATTCATATACCAATAAAAGTAATTTTATAAACATCCTATTCATT
5652979 AGTGTAATGC
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
67 18 0.35
68 33 0.65
ACGTcount: A:0.42, C:0.14, G:0.08, T:0.36
Consensus pattern (68 bp):
AAAAGGTAATCATCCATTCATATACCAATAAAAGTAATTTTATAAACATCCTATTCATTGATATA
TAC
Found at i:5659750 original size:21 final size:21
Alignment explanation
Indices: 5659724--5659763 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5659714 TTTTTAGCCA
* *
5659724 AAAAACTCCTTGAATAATCAT
1 AAAAACACCTGGAATAATCAT
5659745 AAAAACACCTGGAATAATC
1 AAAAACACCTGGAATAATC
5659764 TCTAGATAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.20, G:0.07, T:0.23
Consensus pattern (21 bp):
AAAAACACCTGGAATAATCAT
Found at i:5659985 original size:64 final size:62
Alignment explanation
Indices: 5659816--5659983 Score: 167
Period size: 64 Copynumber: 2.7 Consensus size: 62
5659806 ATTTAAGGTA
* ** * *
5659816 TTTTCTACCAAAAATGTCTTCAATAATCCCCTCCATTTTTTAGGCAGGGATTAATTAAGACG
1 TTTTATACCAAAAATACCTTTAATAATCCCCTCCATTTTTTAGGAAGGGATTAATTAAGACG
** * ** * *
5659878 TTTTAGCCCAAAAAATACCTTTAATAATCCCTTTAGATTTTTTATGAATGGA-TAATTGAAGACA
1 TTTTATACC-AAAAATACCTTTAATAATCCC-CTCCATTTTTTAGGAAGGGATTAATT-AAGAC-
*
5659942 T
62 G
*
5659943 TTTTTTACCAAAAATACCTTTAATAATCCCCTCCATTTTTT
1 TTTTATACCAAAAATACCTTTAATAATCCCCTCCATTTTTT
5659984 TAGATGGAAT
Statistics
Matches: 83, Mismatches: 19, Indels: 7
0.76 0.17 0.06
Matches are distributed among these distances:
62 6 0.07
63 31 0.37
64 40 0.48
65 6 0.07
ACGTcount: A:0.33, C:0.19, G:0.09, T:0.39
Consensus pattern (62 bp):
TTTTATACCAAAAATACCTTTAATAATCCCCTCCATTTTTTAGGAAGGGATTAATTAAGACG
Found at i:5671259 original size:10 final size:10
Alignment explanation
Indices: 5671244--5671276 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
5671234 GCAAGAAAAG
5671244 AAATATATAA
1 AAATATATAA
*
5671254 AAATATGTAA
1 AAATATATAA
5671264 AAATATA-AA
1 AAATATATAA
5671273 AAAT
1 AAAT
5671277 CATTTTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 6 0.29
10 15 0.71
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (10 bp):
AAATATATAA
Found at i:5678219 original size:45 final size:44
Alignment explanation
Indices: 5678118--5678221 Score: 109
Period size: 45 Copynumber: 2.3 Consensus size: 44
5678108 GTGCATGGTG
* * * * *
5678118 TGGGCATATGCCTTGACCATTATCGGCACAAGTTGGCCTTGAGTA
1 TGGGCAT-TGCCTCGACCATCATCAGCACAAGCTAGCCTTGAGTA
* * *
5678163 TTGACATTTGCCTCGACCATCATCAGCACAAGCTAGCCTTTAGTA
1 TGGGCA-TTGCCTCGACCATCATCAGCACAAGCTAGCCTTGAGTA
5678208 TGGGCACTTGCCTC
1 TGGGCA-TTGCCTC
5678222 AACAACTATC
Statistics
Matches: 47, Mismatches: 11, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
45 46 0.98
46 1 0.02
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.29
Consensus pattern (44 bp):
TGGGCATTGCCTCGACCATCATCAGCACAAGCTAGCCTTGAGTA
Found at i:5678354 original size:45 final size:46
Alignment explanation
Indices: 5678312--5678412 Score: 105
Period size: 46 Copynumber: 2.2 Consensus size: 46
5678302 CAGTTGCCCT
* * *
5678312 AAACACCATCGATACATGTTA-GCCCTTGCTATGGGCATTTGCCTC
1 AAACACCATCGATAAATGCTAGGCCCTTGCTACGGGCATTTGCCTC
* * * **
5678357 AAAGACCATTGGTAAATGCTAGGCCCTTGCTACGGGCACATGCCTC
1 AAACACCATCGATAAATGCTAGGCCCTTGCTACGGGCATTTGCCTC
* *
5678403 GACCACCATC
1 AAACACCATC
5678413 AGCACCCGCA
Statistics
Matches: 43, Mismatches: 12, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
45 16 0.37
46 27 0.63
ACGTcount: A:0.26, C:0.31, G:0.20, T:0.24
Consensus pattern (46 bp):
AAACACCATCGATAAATGCTAGGCCCTTGCTACGGGCATTTGCCTC
Found at i:5691372 original size:20 final size:20
Alignment explanation
Indices: 5691343--5691383 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
5691333 GAAAGCCAAA
5691343 CCAAAGGCCTTAATAAGTGC
1 CCAAAGGCCTTAATAAGTGC
* * *
5691363 CCAAATGCCTTGATGAGTGC
1 CCAAAGGCCTTAATAAGTGC
5691383 C
1 C
5691384 TATCTTTAGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.27, G:0.22, T:0.22
Consensus pattern (20 bp):
CCAAAGGCCTTAATAAGTGC
Found at i:5698413 original size:42 final size:43
Alignment explanation
Indices: 5698359--5698495 Score: 154
Period size: 43 Copynumber: 3.2 Consensus size: 43
5698349 AGGATTCTAT
*
5698359 TTTAAAGTTGTTTAGCCTCTGTACAGAAG-AGCTCATTTTTTA
1 TTTAAAGTTGTTTAGCCTCTGTATAGAAGAAGCTCATTTTTTA
* * * *
5698401 TTTAAAGTTGTTTAGTCTTTGTATA-AAGGAAGCCCATTTCTTA
1 TTTAAAGTTGTTTAGCCTCTGTATAGAA-GAAGCTCATTTTTTA
* * * *
5698444 TTTAAAGTTGTTTATCCTCTATATAG-CGAAGCTCATTTCTTAA
1 TTTAAAGTTGTTTAGCCTCTGTATAGAAGAAGCTCATTT-TTTA
5698487 TTTAAAGTT
1 TTTAAAGTT
5698496 TCTTAATTTA
Statistics
Matches: 78, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
41 2 0.03
42 33 0.42
43 43 0.55
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.45
Consensus pattern (43 bp):
TTTAAAGTTGTTTAGCCTCTGTATAGAAGAAGCTCATTTTTTA
Found at i:5698445 original size:43 final size:43
Alignment explanation
Indices: 5698359--5698495 Score: 156
Period size: 42 Copynumber: 3.2 Consensus size: 43
5698349 AGGATTCTAT
* * *
5698359 TTTAAAGTTGTTTAGCCTCTGTACAGAA-G-AGCTCATTTTTTA
1 TTTAAAGTTGTTTAGTCTCTGTATA-AAGGAAGCTCATTTCTTA
* *
5698401 TTTAAAGTTGTTTAGTCTTTGTATAAAGGAAGCCCATTTCTTA
1 TTTAAAGTTGTTTAGTCTCTGTATAAAGGAAGCTCATTTCTTA
* *
5698444 TTTAAAGTTGTTTA-TC-CTCTATATAGCGAAGCTCATTTCTTAA
1 TTTAAAGTTGTTTAGTCTCTGTATAAAG-GAAGCTCATTTCTT-A
5698487 TTTAAAGTT
1 TTTAAAGTT
5698496 TCTTAATTTA
Statistics
Matches: 82, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
41 9 0.11
42 38 0.46
43 35 0.43
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.45
Consensus pattern (43 bp):
TTTAAAGTTGTTTAGTCTCTGTATAAAGGAAGCTCATTTCTTA
Found at i:5698499 original size:15 final size:15
Alignment explanation
Indices: 5698479--5698510 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
5698469 GCGAAGCTCA
5698479 TTTCTTAATTTAAAG
1 TTTCTTAATTTAAAG
5698494 TTTCTTAATTTAAAG
1 TTTCTTAATTTAAAG
5698509 TT
1 TT
5698511 GTTTAGCCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.56
Consensus pattern (15 bp):
TTTCTTAATTTAAAG
Found at i:5698544 original size:35 final size:35
Alignment explanation
Indices: 5698498--5698566 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
5698488 TTAAAGTTTC
5698498 TTAATTTAAAGTTG-TTTAGCCTCTGTACAGAGGAT
1 TTAATTTAAAGTTGTTTTA-CCTCTGTACAGAGGAT
*
5698533 TTAATTTAAAGTTGTTTTACCTCTGTATAGAGGA
1 TTAATTTAAAGTTGTTTTACCTCTGTACAGAGGA
5698567 GTCCACTTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
35 28 0.88
36 4 0.12
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.42
Consensus pattern (35 bp):
TTAATTTAAAGTTGTTTTACCTCTGTACAGAGGAT
Found at i:5699889 original size:9 final size:9
Alignment explanation
Indices: 5699875--5699909 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
5699865 AACTTAGGTA
5699875 ATTTATTTT
1 ATTTATTTT
*
5699884 ATTTATTCT
1 ATTTATTTT
*
5699893 ACTTATTTT
1 ATTTATTTT
5699902 ATTTATTT
1 ATTTATTT
5699910 ATTCCCTTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (9 bp):
ATTTATTTT
Found at i:5703260 original size:4 final size:4
Alignment explanation
Indices: 5703253--5703300 Score: 51
Period size: 4 Copynumber: 11.8 Consensus size: 4
5703243 TATATATATA
* * * *
5703253 TATG TATG TATG TACG TATG TATG TCTT TATG TATAA TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TAT-G TATG TATG TAT
5703301 ATTATGAGCC
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
4 32 0.91
5 3 0.09
ACGTcount: A:0.27, C:0.04, G:0.19, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:5703885 original size:3 final size:3
Alignment explanation
Indices: 5703877--5703901 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
5703867 TAACTTTTAT
5703877 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
5703902 ATTTTTCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5705311 original size:3 final size:3
Alignment explanation
Indices: 5705303--5705328 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
5705293 AATGAATGCA
5705303 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
5705329 ATAAATAAAT
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:5720558 original size:19 final size:19
Alignment explanation
Indices: 5720534--5720574 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
5720524 GGTTTTGGGG
*
5720534 TTTCACTTAAAGTTTAGGA
1 TTTCACATAAAGTTTAGGA
**
5720553 TTTCACATAGGGTTTAGGA
1 TTTCACATAAAGTTTAGGA
5720572 TTT
1 TTT
5720575 TACCTAGGGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.27, C:0.10, G:0.20, T:0.44
Consensus pattern (19 bp):
TTTCACATAAAGTTTAGGA
Found at i:5720582 original size:19 final size:19
Alignment explanation
Indices: 5720545--5720610 Score: 78
Period size: 19 Copynumber: 3.4 Consensus size: 19
5720535 TTCACTTAAA
5720545 GTTTAGGATTTCACATAGG
1 GTTTAGGATTTCACATAGG
* *
5720564 GTTTAGGATTTTACCTAGG
1 GTTTAGGATTTCACATAGG
*
5720583 GTTTAGGGTTTACACATAAGG
1 GTTTAGGATTT-CACAT-AGG
*
5720604 ATTTAGG
1 GTTTAGG
5720611 GTTTACCTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
19 27 0.69
20 3 0.08
21 9 0.23
ACGTcount: A:0.26, C:0.09, G:0.27, T:0.38
Consensus pattern (19 bp):
GTTTAGGATTTCACATAGG
Found at i:5720599 original size:39 final size:39
Alignment explanation
Indices: 5720545--5720626 Score: 105
Period size: 40 Copynumber: 2.1 Consensus size: 39
5720535 TTCACTTAAA
* *
5720545 GTTTAGGATTTCACAT-AGGGTTTAGGATTTTACCT-AGG
1 GTTTAGGATTTCACATAAGGATTTAGG-GTTTACCTAAGG
*
5720583 GTTTAGGGTTTACACATAAGGATTTAGGGTTTACCTAAGG
1 GTTTAGGATTT-CACATAAGGATTTAGGGTTTACCTAAGG
5720623 GTTT
1 GTTT
5720627 GTTTTAGGGT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
38 10 0.26
39 12 0.32
40 16 0.42
ACGTcount: A:0.24, C:0.10, G:0.27, T:0.39
Consensus pattern (39 bp):
GTTTAGGATTTCACATAAGGATTTAGGGTTTACCTAAGG
Found at i:5720677 original size:33 final size:33
Alignment explanation
Indices: 5720634--5720720 Score: 106
Period size: 33 Copynumber: 2.6 Consensus size: 33
5720624 TTTGTTTTAG
5720634 GGTTTACATTTTAGGGTTTCAAGTTTTCACCT-A
1 GGTTT-CATTTTAGGGTTTCAAGTTTTCACCTAA
* **
5720667 GTGTTTCATTTTAGAGTTTCGGGTTTTCACCTAA
1 G-GTTTCATTTTAGGGTTTCAAGTTTTCACCTAA
*
5720701 GG-TTCATTTTAAGGTTTCAA
1 GGTTTCATTTTAGGGTTTCAA
5720721 AAATTTATGA
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
32 14 0.31
33 25 0.56
34 6 0.13
ACGTcount: A:0.21, C:0.14, G:0.20, T:0.46
Consensus pattern (33 bp):
GGTTTCATTTTAGGGTTTCAAGTTTTCACCTAA
Found at i:5722958 original size:16 final size:17
Alignment explanation
Indices: 5722932--5722966 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
5722922 TTATTAATTT
5722932 TTAATTAATTTTGTTAA
1 TTAATTAATTTTGTTAA
*
5722949 TTAA-TAATTTTTTTAA
1 TTAATTAATTTTGTTAA
5722965 TT
1 TT
5722967 CTAAACTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (17 bp):
TTAATTAATTTTGTTAA
Found at i:5722988 original size:7 final size:7
Alignment explanation
Indices: 5722958--5723009 Score: 50
Period size: 7 Copynumber: 7.3 Consensus size: 7
5722948 ATTAATAATT
*
5722958 TTTTTAA
1 TTTTAAA
*
5722965 TTCTAAA
1 TTTTAAA
*
5722972 CTTTTCAA
1 -TTTTAAA
5722980 TTTTAAA
1 TTTTAAA
5722987 TTTTAAA
1 TTTTAAA
*
5722994 ATTTAAA
1 TTTTAAA
*
5723001 ATTTAAA
1 TTTTAAA
5723008 TT
1 TT
5723010 GAAAATTTAT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
7 32 0.86
8 5 0.14
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (7 bp):
TTTTAAA
Found at i:5723025 original size:20 final size:21
Alignment explanation
Indices: 5722978--5723025 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
5722968 TAAACTTTTC
*
5722978 AATTTTAAATTTTAAAATTTA
1 AATTTTAAATTTGAAAATTTA
*
5722999 AAATTTAAA-TTGAAAATTTA
1 AATTTTAAATTTGAAAATTTA
*
5723019 TATTTTA
1 AATTTTA
5723026 TATACTTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (21 bp):
AATTTTAAATTTGAAAATTTA
Found at i:5723034 original size:9 final size:9
Alignment explanation
Indices: 5723017--5723049 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
5723007 ATTGAAAATT
*
5723017 TATATTTTA
1 TATACTTTA
5723026 TATACTTTA
1 TATACTTTA
5723035 TATA-TTTA
1 TATACTTTA
5723043 TATACTT
1 TATACTT
5723050 ATTATTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (9 bp):
TATACTTTA
Found at i:5723044 original size:8 final size:8
Alignment explanation
Indices: 5723014--5723055 Score: 52
Period size: 8 Copynumber: 5.4 Consensus size: 8
5723004 TAAATTGAAA
5723014 ATTTATAT
1 ATTTATAT
5723022 -TTTATAT
1 ATTTATAT
5723029 ACTTTATAT
1 A-TTTATAT
5723038 ATTTATAT
1 ATTTATAT
*
5723046 ACTTAT-T
1 ATTTATAT
5723053 ATT
1 ATT
5723056 ATTATTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
7 10 0.33
8 12 0.40
9 8 0.27
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (8 bp):
ATTTATAT
Found at i:5723044 original size:17 final size:16
Alignment explanation
Indices: 5723015--5723049 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
5723005 AAATTGAAAA
5723015 TTTATATTTTATATAC
1 TTTATATTTTATATAC
5723031 TTTATATATTTATATAC
1 TTTATAT-TTTATATAC
5723048 TT
1 TT
5723050 ATTATTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (16 bp):
TTTATATTTTATATAC
Found at i:5723056 original size:3 final size:3
Alignment explanation
Indices: 5723048--5723093 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
5723038 ATTTATATAC
5723048 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
5723094 GACCATTAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:5725336 original size:23 final size:24
Alignment explanation
Indices: 5725310--5725358 Score: 91
Period size: 23 Copynumber: 2.1 Consensus size: 24
5725300 GATACAATCA
5725310 AATCAATATGGCATAAG-AAATAT
1 AATCAATATGGCATAAGAAAATAT
5725333 AATCAATATGGCATAAGAAAATAT
1 AATCAATATGGCATAAGAAAATAT
5725357 AA
1 AA
5725359 AGACTACTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 17 0.68
24 8 0.32
ACGTcount: A:0.55, C:0.08, G:0.12, T:0.24
Consensus pattern (24 bp):
AATCAATATGGCATAAGAAAATAT
Found at i:5728613 original size:20 final size:20
Alignment explanation
Indices: 5728584--5728633 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
5728574 ACATAAAACT
*
5728584 TTAAACAACTTGAT-TAAAAA
1 TTAAAGAACTTG-TCTAAAAA
*
5728604 TTAAAGAACTTGTCTTAAAA
1 TTAAAGAACTTGTCTAAAAA
5728624 TTAAAGAACT
1 TTAAAGAACT
5728634 CAAAATTAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 1 0.04
20 26 0.96
ACGTcount: A:0.50, C:0.10, G:0.08, T:0.32
Consensus pattern (20 bp):
TTAAAGAACTTGTCTAAAAA
Found at i:5733259 original size:18 final size:19
Alignment explanation
Indices: 5733236--5733279 Score: 81
Period size: 18 Copynumber: 2.4 Consensus size: 19
5733226 CAAAAAAACC
5733236 TAATGCAGTAAAATAATAA
1 TAATGCAGTAAAATAATAA
5733255 T-ATGCAGTAAAATAATAA
1 TAATGCAGTAAAATAATAA
5733273 TAATGCA
1 TAATGCA
5733280 ATAGCCCTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 18 0.75
19 6 0.25
ACGTcount: A:0.55, C:0.07, G:0.11, T:0.27
Consensus pattern (19 bp):
TAATGCAGTAAAATAATAA
Found at i:5733992 original size:20 final size:20
Alignment explanation
Indices: 5733967--5734016 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
5733957 CATAAAAACT
*
5733967 TTAAAGAACTTGAGTAAAAA
1 TTAAAGAACTTGACTAAAAA
* *
5733987 TTAAAGAACTTGTCTTAAAA
1 TTAAAGAACTTGACTAAAAA
5734007 TTAAAGAACT
1 TTAAAGAACT
5734017 CAAAATTAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.50, C:0.08, G:0.12, T:0.30
Consensus pattern (20 bp):
TTAAAGAACTTGACTAAAAA
Found at i:5736371 original size:87 final size:87
Alignment explanation
Indices: 5736225--5736399 Score: 296
Period size: 87 Copynumber: 2.0 Consensus size: 87
5736215 CATACCTTAA
* *
5736225 ACACAAATCTGCCACTAGATTTGTGTATAGCAAAGAAACCTATTAAAGATGTCTAAATGAATTTC
1 ACACAAATCTGCCACTAGATTTGTGTATAGCAAAAAAACCTATTAAAGATGTCTAAATGAACTTC
* *
5736290 ATTTTAGCACCTCAACAAATTT
66 ATTTCAACACCTCAACAAATTT
*
5736312 ACACAAATCTGCCACTAGATTTGTTTATAGCAAAAAAACCTATTAAAGATGTCTAAATGAACTTC
1 ACACAAATCTGCCACTAGATTTGTGTATAGCAAAAAAACCTATTAAAGATGTCTAAATGAACTTC
*
5736377 ATTTCAACACCTTAACAAATTT
66 ATTTCAACACCTCAACAAATTT
5736399 A
1 A
5736400 ATCATTAACA
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 82 1.00
ACGTcount: A:0.41, C:0.19, G:0.10, T:0.31
Consensus pattern (87 bp):
ACACAAATCTGCCACTAGATTTGTGTATAGCAAAAAAACCTATTAAAGATGTCTAAATGAACTTC
ATTTCAACACCTCAACAAATTT
Found at i:5736508 original size:18 final size:18
Alignment explanation
Indices: 5736485--5736520 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
5736475 AAATCTATAG
5736485 TTAACACAAATATATTAA
1 TTAACACAAATATATTAA
5736503 TTAACACAAATATATTAA
1 TTAACACAAATATATTAA
5736521 ATTGACTAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (18 bp):
TTAACACAAATATATTAA
Found at i:5742166 original size:31 final size:34
Alignment explanation
Indices: 5742133--5742195 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 34
5742123 AATTGTTCAA
5742133 TTTT-AAGTACCATAACCTTTAGTTA-AAGAAAT
1 TTTTCAAGTACCATAACCTTTAGTTAGAAGAAAT
* *
5742165 TTTTCAAGTACCATAGCCTTTGGTTAGAAGA
1 TTTTCAAGTACCATAACCTTTAGTTAGAAGA
5742196 TTTTTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 4 0.15
33 19 0.70
34 4 0.15
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (34 bp):
TTTTCAAGTACCATAACCTTTAGTTAGAAGAAAT
Found at i:5742884 original size:145 final size:145
Alignment explanation
Indices: 5742688--5743024 Score: 347
Period size: 145 Copynumber: 2.3 Consensus size: 145
5742678 GGTTTTTTTG
* ** * * * * *
5742688 AGCTCAAATTTTCATGAAAAATTCCAGATCATAATTTCATAACATGTCATGACTTTTGGTGCATT
1 AGCTCAAATTTCCATGAAACTTTTCAGATCTTAATTTCATAATATTTCATGACTTTTGATGCATT
* * **
5742753 T-ATAATCACAGCCGT-ACCTCGAAATGTGTAAAATTACCAAAATACCCCTATAAAGGTA-TTTT
66 TGA-AATCACAGCAGTGACC-CAAAAAATGTAAAATTACCAAAATACCCCTATAAAGGTAGTTTT
* *
5742815 CGTAATTTGCCCTTCCCA
129 -GTAATTTGACATTCCCA
* * * *
5742833 AGTTCAAATTTCCATGAAACTTTTTAGATCTTAATTTCATAATATTTCATGATTTTTTATGCATT
1 AGCTCAAATTTCCATGAAACTTTTCAGATCTTAATTTCATAATATTTCATGACTTTTGATGCATT
* * ** * *
5742898 TGAAATCATAGCAGTGTCCCAAAAAATGTGGAATTACCAAAATACCCTTATAAGGGTAGTTTTGT
66 TGAAATCACAGCAGTGACCCAAAAAATGTAAAATTACCAAAATACCCCTATAAAGGTAGTTTTGT
*
5742963 AATTTGACATTCTCA
131 AATTTGACATTCCCA
** * * * *
5742978 AGCTCGGATTTTCATGAAACTTTTCATATCTCAATTTTATAATATTT
1 AGCTCAAATTTCCATGAAACTTTTCAGATCTTAATTTCATAATATTT
5743025 TTATGATTTT
Statistics
Matches: 156, Mismatches: 33, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
145 149 0.96
146 7 0.04
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.38
Consensus pattern (145 bp):
AGCTCAAATTTCCATGAAACTTTTCAGATCTTAATTTCATAATATTTCATGACTTTTGATGCATT
TGAAATCACAGCAGTGACCCAAAAAATGTAAAATTACCAAAATACCCCTATAAAGGTAGTTTTGT
AATTTGACATTCCCA
Found at i:5744331 original size:3 final size:3
Alignment explanation
Indices: 5744323--5744362 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
5744313 TTATGGAAAA
5744323 AAT AAT AAT AAT AAT AAT AA- AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
5744363 ATCGATCAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:5744346 original size:20 final size:20
Alignment explanation
Indices: 5744321--5744363 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
5744311 GTTTATGGAA
5744321 AAAATAATAATAATAATAAT
1 AAAATAATAATAATAATAAT
5744341 AAAATAATAATAATAATAAT
1 AAAATAATAATAATAATAAT
5744361 AAA
1 AAA
5744364 TCGATCAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (20 bp):
AAAATAATAATAATAATAAT
Found at i:5744348 original size:17 final size:17
Alignment explanation
Indices: 5744326--5744359 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
5744316 TGGAAAAAAT
5744326 AATAATAATAATAATAA
1 AATAATAATAATAATAA
5744343 AATAATAATAATAATAA
1 AATAATAATAATAATAA
5744360 TAAATCGATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AATAATAATAATAATAA
Found at i:5751063 original size:2 final size:2
Alignment explanation
Indices: 5751056--5751089 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5751046 TGGTGATTAC
5751056 TA 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 TA
5751090 AAACCTCATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5752112 original size:17 final size:15
Alignment explanation
Indices: 5752088--5752128 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
5752078 AAACATAAAT
5752088 AAAT-AAAAAAAGAG
1 AAATGAAAAAAAGAG
5752102 AAGA-GAAAAAAAGAG
1 AA-ATGAAAAAAAGAG
5752117 AAATGAAAAAAA
1 AAATGAAAAAAA
5752129 ATAGTTATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 3 0.12
15 21 0.88
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (15 bp):
AAATGAAAAAAAGAG
Found at i:5752625 original size:11 final size:12
Alignment explanation
Indices: 5752609--5752641 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
5752599 AAAGGAAAGG
5752609 AAAAAA-AAATA
1 AAAAAAGAAATA
5752620 AAAAAAGAAA-A
1 AAAAAAGAAATA
5752631 AAAAAAGAAAT
1 AAAAAAGAAAT
5752642 GAATTAGTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 17 0.85
12 3 0.15
ACGTcount: A:0.88, C:0.00, G:0.06, T:0.06
Consensus pattern (12 bp):
AAAAAAGAAATA
Found at i:5753840 original size:22 final size:23
Alignment explanation
Indices: 5753815--5753858 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
5753805 TGAAAATTGG
5753815 TTGAG-CATTTTT-GTACAAGATA
1 TTGAGACATTTTTAGTA-AAGATA
5753837 TTGAGATCATTTTTAGTAAAGA
1 TTGAGA-CATTTTTAGTAAAGA
5753859 GTGAACCTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 5 0.26
24 11 0.58
25 3 0.16
ACGTcount: A:0.34, C:0.07, G:0.18, T:0.41
Consensus pattern (23 bp):
TTGAGACATTTTTAGTAAAGATA
Found at i:5754039 original size:38 final size:39
Alignment explanation
Indices: 5753946--5754114 Score: 137
Period size: 41 Copynumber: 4.3 Consensus size: 39
5753936 CTGCATAAAA
*
5753946 AAAAAAAAAGACATTTGTATCATTCACATCTACATCAAC
1 AAAAAAAAAGACATTTGCATCATTCACATCTACATCAAC
** * * * *
5753985 AACAAAAAATTCACATTTGCATCCTTTACATCTATAT-TAC
1 AA-AAAAAA-AGACATTTGCATCATTCACATCTACATCAAC
* * *
5754025 AAAAAAAAAGACATTTGCATCATTCAAATCTGCATCAAT
1 AAAAAAAAAGACATTTGCATCATTCACATCTACATCAAC
*** * *
5754064 AAAAAGACATTCACATTTGCGTCACTT-GCATCTACATC-AC
1 AAAAA-A-AAAGACATTTGCATCA-TTCACATCTACATCAAC
5754104 AAAAAAAAAGA
1 AAAAAAAAAGA
5754115 AATAAAAAAT
Statistics
Matches: 97, Mismatches: 27, Indels: 13
0.71 0.20 0.09
Matches are distributed among these distances:
38 22 0.23
39 15 0.15
40 17 0.18
41 41 0.42
42 2 0.02
ACGTcount: A:0.46, C:0.21, G:0.07, T:0.27
Consensus pattern (39 bp):
AAAAAAAAAGACATTTGCATCATTCACATCTACATCAAC
Found at i:5754040 original size:79 final size:79
Alignment explanation
Indices: 5753946--5754114 Score: 225
Period size: 79 Copynumber: 2.1 Consensus size: 79
5753936 CTGCATAAAA
* *
5753946 AAAAAAAAAGACATTTGTATCATTCACATCTACATCAACAACAAA-AAATTCACATTTGCATC-C
1 AAAAAAAAAGACATTTGCATCATTCAAATCTACATCAACAA-AAAGAAATTCACATTTGCATCAC
* *
5754009 TTTACATCTATATTAC
65 -TTACATCTACATCAC
* * * *
5754025 AAAAAAAAAGACATTTGCATCATTCAAATCTGCATCAATAAAAAGACATTCACATTTGCGTCACT
1 AAAAAAAAAGACATTTGCATCATTCAAATCTACATCAACAAAAAGAAATTCACATTTGCATCACT
*
5754090 TGCATCTACATCAC
66 TACATCTACATCAC
5754104 AAAAAAAAAGA
1 AAAAAAAAAGA
5754115 AATAAAAAAT
Statistics
Matches: 79, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
78 3 0.04
79 75 0.95
80 1 0.01
ACGTcount: A:0.46, C:0.21, G:0.07, T:0.27
Consensus pattern (79 bp):
AAAAAAAAAGACATTTGCATCATTCAAATCTACATCAACAAAAAGAAATTCACATTTGCATCACT
TACATCTACATCAC
Found at i:5754342 original size:32 final size:32
Alignment explanation
Indices: 5754297--5754358 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
5754287 CTTGCATGTG
* *
5754297 CATCATGAGAAAGACATTTGCATTCGCATCTA
1 CATCATAAAAAAGACATTTGCATTCGCATCTA
* *
5754329 CATCATAAAAAAGATATTTGCATTTGCATC
1 CATCATAAAAAAGACATTTGCATTCGCATC
5754359 GCTTGCATCT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (32 bp):
CATCATAAAAAAGACATTTGCATTCGCATCTA
Found at i:5754548 original size:18 final size:18
Alignment explanation
Indices: 5754525--5754568 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
5754515 TTGCATCAAA
5754525 CATTCACATTGACATTTG
1 CATTCACATTGACATTTG
5754543 CATTCACATTGACATTTG
1 CATTCACATTGACATTTG
*
5754561 GATTCACA
1 CATTCACA
5754569 CCAATTGATG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.36
Consensus pattern (18 bp):
CATTCACATTGACATTTG
Found at i:5754648 original size:16 final size:17
Alignment explanation
Indices: 5754627--5754658 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
5754617 CATAAATATT
5754627 AAAAAAAAAGA-AAAAG
1 AAAAAAAAAGAGAAAAG
5754643 AAAAAAAAAGAGAAAA
1 AAAAAAAAAGAGAAAA
5754659 AAAGAACAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAGAGAAAAG
Found at i:5754650 original size:10 final size:10
Alignment explanation
Indices: 5754627--5754664 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
5754617 CATAAATATT
5754627 AAAAAA-AAA
1 AAAAAAGAAA
*
5754636 GAAAAAGAAA
1 AAAAAAGAAA
*
5754646 AAAAAAGAGA
1 AAAAAAGAAA
5754656 AAAAAAGAA
1 AAAAAAGAA
5754665 CAAGATTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
9 5 0.21
10 19 0.79
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:5755112 original size:22 final size:22
Alignment explanation
Indices: 5755080--5755133 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
5755070 TTGAGATTTT
* *
5755080 TAAGACTTCCAAGCATAATCTC
1 TAAGACCTCCAAGCACAATCTC
*
5755102 TAAGACCTCCAAGCACAATTTC
1 TAAGACCTCCAAGCACAATCTC
*
5755124 CAAGACCTCC
1 TAAGACCTCC
5755134 GGGCAAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.35, C:0.33, G:0.09, T:0.22
Consensus pattern (22 bp):
TAAGACCTCCAAGCACAATCTC
Found at i:5757350 original size:3 final size:3
Alignment explanation
Indices: 5757342--5757409 Score: 127
Period size: 3 Copynumber: 22.7 Consensus size: 3
5757332 TCTATGCCAA
5757342 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
5757390 AAT AAT AAT AAT AAA AAT AA
1 AAT AAT AAT AAT AAT AAT AA
5757410 ATAAATAAAT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:5757549 original size:11 final size:10
Alignment explanation
Indices: 5757522--5757570 Score: 50
Period size: 11 Copynumber: 5.0 Consensus size: 10
5757512 AGAATTATCA
5757522 AATAATAAA-
1 AATAATAAAT
5757531 AAT-A-AAAT
1 AATAATAAAT
5757539 AATAACTAAAT
1 AATAA-TAAAT
*
5757550 AATAAATAACT
1 AAT-AATAAAT
5757561 AATAATAAAT
1 AATAATAAAT
5757571 TTTAATGGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
7 3 0.09
8 4 0.12
9 4 0.12
10 6 0.18
11 14 0.42
12 2 0.06
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (10 bp):
AATAATAAAT
Found at i:5757569 original size:14 final size:14
Alignment explanation
Indices: 5757522--5757570 Score: 61
Period size: 14 Copynumber: 3.7 Consensus size: 14
5757512 AGAATTATCA
5757522 AATAATAAA-AA-T
1 AATAATAAATAACT
5757534 AA-AAT-AATAACT
1 AATAATAAATAACT
5757546 AAATAATAAATAACT
1 -AATAATAAATAACT
5757561 AATAATAAAT
1 AATAATAAAT
5757571 TTTAATGGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
10 2 0.06
11 5 0.16
12 3 0.09
13 2 0.06
14 13 0.41
15 7 0.22
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (14 bp):
AATAATAAATAACT
Found at i:5759548 original size:3 final size:3
Alignment explanation
Indices: 5759540--5759578 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
5759530 GTCATTTTAA
5759540 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5759579 TCTTTCTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:5760426 original size:5 final size:5
Alignment explanation
Indices: 5760413--5760466 Score: 54
Period size: 5 Copynumber: 10.0 Consensus size: 5
5760403 TCTTATCTCT
* *
5760413 TTTTT TTTTA TTTTGA TTTTA TTTCTT TTTTA TTTTA TTTTA TTAATTA
1 TTTTA TTTTA TTTT-A TTTTA TTT-TA TTTTA TTTTA TTTTA TT--TTA
5760462 TTTTA
1 TTTTA
5760467 AAATTAAAGA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
5 28 0.67
6 9 0.21
7 5 0.12
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:5760432 original size:11 final size:10
Alignment explanation
Indices: 5760413--5760466 Score: 54
Period size: 11 Copynumber: 5.0 Consensus size: 10
5760403 TCTTATCTCT
*
5760413 TTTTTTTTTA
1 TTTTATTTTA
5760423 TTTTGATTTTA
1 TTTT-ATTTTA
*
5760434 TTTCTTTTTTA
1 TTT-TATTTTA
5760445 TTTTATTTTA
1 TTTTATTTTA
5760455 TTAATTATTTTA
1 TT--TTATTTTA
5760467 AAATTAAAGA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
10 12 0.32
11 16 0.43
12 9 0.24
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.78
Consensus pattern (10 bp):
TTTTATTTTA
Found at i:5760441 original size:21 final size:21
Alignment explanation
Indices: 5760416--5760456 Score: 73
Period size: 22 Copynumber: 1.9 Consensus size: 21
5760406 TATCTCTTTT
5760416 TTTTTTATTTTGATTTTATTTC
1 TTTTTTATTTT-ATTTTATTTC
5760438 TTTTTTATTTTATTTTATT
1 TTTTTTATTTTATTTTATT
5760457 AATTATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.15, C:0.02, G:0.02, T:0.80
Consensus pattern (21 bp):
TTTTTTATTTTATTTTATTTC
Found at i:5760934 original size:3 final size:3
Alignment explanation
Indices: 5760928--5760972 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
5760918 AATGGATGGA
*
5760928 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAA AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5760973 TAAATAAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:5761850 original size:64 final size:64
Alignment explanation
Indices: 5761771--5761918 Score: 224
Period size: 64 Copynumber: 2.3 Consensus size: 64
5761761 AGAAGCCCAT
* * * * *
5761771 AGGTTAACTTAGAAGAAGAAATGCTAATGGCACAAAATTCGTATCCCATGCTTTGAGTTTTGAA
1 AGGTGAACTTAGAAGAAGAAATGCTAATCGCAAAAAATTCGCATCCCATGCTTTGAGCTTTGAA
* *
5761835 AGGTGAACTTAGAAGAAGAAATGCTAATCGCAAAAAATTGGCATCGCATGCTTTGAGCTTTGAA
1 AGGTGAACTTAGAAGAAGAAATGCTAATCGCAAAAAATTCGCATCCCATGCTTTGAGCTTTGAA
*
5761899 AGGTGAACTTAAAAGAAGAA
1 AGGTGAACTTAGAAGAAGAA
5761919 GAAGAAGCCT
Statistics
Matches: 76, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
64 76 1.00
ACGTcount: A:0.39, C:0.13, G:0.22, T:0.26
Consensus pattern (64 bp):
AGGTGAACTTAGAAGAAGAAATGCTAATCGCAAAAAATTCGCATCCCATGCTTTGAGCTTTGAA
Found at i:5762921 original size:79 final size:79
Alignment explanation
Indices: 5762790--5763004 Score: 261
Period size: 79 Copynumber: 2.7 Consensus size: 79
5762780 CACCCAAAGC
** * * * *
5762790 AATTAATTTATCTCATCCCCATCCAGGTACAATACTTTTTATTATAATTTTATAATTTTCCGATC
1 AATTAATGAATCTCATCTCCATCCAGCTACAATACTTTTTATTATAATTTTATAATTTTACAATC
* *
5762855 GA-GATAATTTTAAG
66 -ACAATAATTTTAAA
**
5762869 AATTAATGAATCTCATCTCCATCCAATTACAATACTTTTTATTATAATTTTATAATTTTACAATC
1 AATTAATGAATCTCATCTCCATCCAGCTACAATACTTTTTATTATAATTTTATAATTTTACAATC
5762934 ACAATAATTTTAAA
66 ACAATAATTTTAAA
* * ** * * *
5762948 AATTAACGAATCTCATCTTCATCTTGCTACAATATTTTTTATTATACTTTTAAAATT
1 AATTAATGAATCTCATCTCCATCCAGCTACAATACTTTTTATTATAATTTTATAATT
5763005 ATATAAGAGT
Statistics
Matches: 117, Mismatches: 18, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
78 1 0.01
79 116 0.99
ACGTcount: A:0.36, C:0.16, G:0.04, T:0.44
Consensus pattern (79 bp):
AATTAATGAATCTCATCTCCATCCAGCTACAATACTTTTTATTATAATTTTATAATTTTACAATC
ACAATAATTTTAAA
Found at i:5764336 original size:13 final size:12
Alignment explanation
Indices: 5764314--5764343 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
5764304 CATTCCTAGG
5764314 TTTTTTTTTATT
1 TTTTTTTTTATT
5764326 TTTTTTATTTATT
1 TTTTTT-TTTATT
5764339 TTTTT
1 TTTTT
5764344 ATTATTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (12 bp):
TTTTTTTTTATT
Found at i:5764342 original size:21 final size:21
Alignment explanation
Indices: 5764316--5764359 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
5764306 TTCCTAGGTT
* *
5764316 TTTTTTTATTTTTTTTATTTA
1 TTTTTTTATTATTATTATTTA
5764337 TTTTTTTATTATTATTATTTA
1 TTTTTTTATTATTATTATTTA
5764358 TT
1 TT
5764360 GATTAGATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (21 bp):
TTTTTTTATTATTATTATTTA
Found at i:5764394 original size:5 final size:5
Alignment explanation
Indices: 5764384--5764436 Score: 63
Period size: 5 Copynumber: 10.0 Consensus size: 5
5764374 TGTTTAATAC
5764384 ATTTT ATTTT ATTTT -TCTTT ATTTT CATTTT CATTTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT AT-TTT ATTTT -ATTTT -A-TTTT ATTTT ATTTT
5764432 ATTTT
1 ATTTT
5764437 CTTTAAATAA
Statistics
Matches: 44, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
4 1 0.02
5 30 0.68
6 9 0.20
7 4 0.09
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (5 bp):
ATTTT
Found at i:5764522 original size:58 final size:58
Alignment explanation
Indices: 5764454--5764669 Score: 276
Period size: 58 Copynumber: 3.7 Consensus size: 58
5764444 TAAAATTCAA
*
5764454 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTCAAAATAAGCTTTCT
1 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAGCTTTCT
* * * *
5764512 AAAAAATATTTTTGAGAAAAAATTGAAAGTATCAATTTTCCTTGAAAATAAGCTTTCT
1 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAGCTTTCT
* *
5764570 AAAAAGATATATTTTTG-GGAAAAAGTTGAAAGTATCAA-TTGTCTTTAAAAATAGGCTTTC-
1 -AAAA-A-ATATTTTTGAGG-AAAAGTTGAAAGTATCAATTTTTC-TTAAAAATAAGCTTTCT
* * *
5764630 AAAATAGATTTTTGAGGAAAAGTTGAAAATATCAATTTTT
1 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTT
5764670 TATGTACAAA
Statistics
Matches: 137, Mismatches: 14, Indels: 14
0.83 0.08 0.08
Matches are distributed among these distances:
57 25 0.18
58 59 0.43
59 8 0.06
60 5 0.04
61 40 0.29
ACGTcount: A:0.43, C:0.07, G:0.13, T:0.37
Consensus pattern (58 bp):
AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAGCTTTCT
Found at i:5768661 original size:31 final size:30
Alignment explanation
Indices: 5768619--5768704 Score: 84
Period size: 31 Copynumber: 2.8 Consensus size: 30
5768609 AATGGATAAG
* *
5768619 AGATGAGAAAAAAAGAAAAAAAAATGATGAA
1 AGATGAAAAAAAAAGAAAAAAAAATGA-AAA
* ***
5768650 AGATGAAAAAAAAAGGGAAAATGGATGAAAA
1 AGATGAAAAAAAAA-GAAAAAAAAATGAAAA
5768681 AGA-GAGAAAAAAAAGAAAAAAAAA
1 AGATGA-AAAAAAAAGAAAAAAAAA
5768705 AGAGAAAAAA
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
30 8 0.19
31 26 0.60
32 9 0.21
ACGTcount: A:0.72, C:0.00, G:0.21, T:0.07
Consensus pattern (30 bp):
AGATGAAAAAAAAAGAAAAAAAAATGAAAA
Found at i:5768695 original size:13 final size:12
Alignment explanation
Indices: 5768677--5768717 Score: 66
Period size: 11 Copynumber: 3.4 Consensus size: 12
5768667 AAAATGGATG
5768677 AAAAAGAGAGAAA
1 AAAAAGAGA-AAA
5768690 AAAAAGA-AAAA
1 AAAAAGAGAAAA
5768701 AAAAAGAGAAAA
1 AAAAAGAGAAAA
5768713 AAAAA
1 AAAAA
5768718 ATATATGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
11 10 0.37
12 10 0.37
13 7 0.26
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAAAGAGAAAA
Found at i:5768718 original size:13 final size:13
Alignment explanation
Indices: 5768677--5768718 Score: 61
Period size: 12 Copynumber: 3.4 Consensus size: 13
5768667 AAAATGGATG
*
5768677 AAAAAGAG-AGAA
1 AAAAAGAGAAAAA
5768689 AAAAA-AGAAAAA
1 AAAAAGAGAAAAA
5768701 AAAAAGAGAAAAA
1 AAAAAGAGAAAAA
5768714 AAAAA
1 AAAAA
5768719 TATATGAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 2 0.07
12 13 0.48
13 12 0.44
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (13 bp):
AAAAAGAGAAAAA
Found at i:5770654 original size:45 final size:43
Alignment explanation
Indices: 5770460--5770672 Score: 215
Period size: 42 Copynumber: 5.0 Consensus size: 43
5770450 TCAATGAGCC
*
5770460 ATTT-ATTTTCAAAGTCATTGAGCCTCTGATTAGAGGAGC--C
1 ATTTAATTTTCAAAGTCATTGAGCCTCTGATTAGAGGAGCTTT
** * *
5770500 ATTT-ATTTTCCAAAAGTTGTTGAGCCTTTGTTTAGAGGAGCTTT
1 ATTTAATTTT-C-AAAGTCATTGAGCCTCTGATTAGAGGAGCTTT
* *
5770544 ATTTAA-TTTAAAAGTCATTGAGCCTCT-ATTTAGAGGAGCTGT
1 ATTTAATTTTCAAAGTCATTGAGCCTCTGA-TTAGAGGAGCTTT
*
5770586 ATTTAA-TTTCAAAATCATTGAGCCTCTGATTAGAGGAGCTTT
1 ATTTAATTTTCAAAGTCATTGAGCCTCTGATTAGAGGAGCTTT
* * * * *
5770628 GTTTATATTTTTCAAAGTAATTGAGCCTTTGCTTAGAAGAGCTTT
1 ATTTA-A-TTTTCAAAGTCATTGAGCCTCTGATTAGAGGAGCTTT
5770673 GATCAGAATT
Statistics
Matches: 143, Mismatches: 20, Indels: 15
0.80 0.11 0.08
Matches are distributed among these distances:
40 9 0.06
41 1 0.01
42 92 0.64
43 2 0.01
44 7 0.05
45 32 0.22
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.40
Consensus pattern (43 bp):
ATTTAATTTTCAAAGTCATTGAGCCTCTGATTAGAGGAGCTTT
Found at i:5770867 original size:4 final size:4
Alignment explanation
Indices: 5770858--5771084 Score: 100
Period size: 4 Copynumber: 55.8 Consensus size: 4
5770848 TTCAATTTGT
* *
5770858 TTTA TTTA TTTA TTTA TTTTA TTTA -TTA TGTA TTT- TTGTA TTT- TGTA
1 TTTA TTTA TTTA TTTA -TTTA TTTA TTTA TTTA TTTA TT-TA TTTA TTTA
*
5770905 TTTTA TTTA TTTA -TTA TTTA TTTA TCTA -TTA TTACTA TTTA TTACTA
1 -TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT--TA TTTA TT--TA
* * * *
5770952 TATA TTT- TTTA TATT- TTTA -TT- TTTA TCTA TTTA TATA TAT- TTTA
1 TTTA TTTA TTTA T-TTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* ** * * *
5770996 TATTA -TTA TTTA TCTA TTTA CATA TTATCA TTTA TCTA TGAATA TATA
1 T-TTA TTTA TTTA TTTA TTTA TTTA TT-T-A TTTA TTTA T--TTA TTTA
*
5771044 TATA TTTA TTTA TTTA TTTA -TTA TTTTA TTTTA TTTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA -TTTA -TTTA -TTTA TTT
5771085 TCTTGGTTGA
Statistics
Matches: 176, Mismatches: 21, Indels: 52
0.71 0.08 0.21
Matches are distributed among these distances:
3 29 0.16
4 105 0.60
5 29 0.16
6 13 0.07
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (4 bp):
TTTA
Found at i:5770970 original size:25 final size:26
Alignment explanation
Indices: 5770942--5771000 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 26
5770932 ATTATTACTA
*
5770942 TTTATTACTATATATTT-TTTATATT
1 TTTATTACTATATATTTATATATATT
** *
5770967 TTTATTTTTATCTATTTATATATATT
1 TTTATTACTATATATTTATATATATT
5770993 TTATATTA
1 TT-TATTA
5771001 TTATTTATCT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
25 14 0.52
26 9 0.33
27 4 0.15
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (26 bp):
TTTATTACTATATATTTATATATATT
Found at i:5770972 original size:35 final size:33
Alignment explanation
Indices: 5770908--5771015 Score: 96
Period size: 35 Copynumber: 3.2 Consensus size: 33
5770898 TTTTGTATTT
5770908 TATTTATTTAT-TAT-TTATT-TATCTATTATTAC
1 TATTTATTTATATATATT-TTATAT-TATTATTAC
* * **
5770940 TATTTATTACTATATATTTTTTATATTTTTATTTT
1 TATTTATT--TATATATATTTTATATTATTATTAC
*
5770975 TATCTATTTATATATATTTTATATTATTATTTATC
1 TATTTATTTATATATATTTTATATTATTA-TTA-C
5771010 TATTTA
1 TATTTA
5771016 CATATTATCA
Statistics
Matches: 60, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
32 8 0.13
33 19 0.32
34 5 0.08
35 23 0.38
36 5 0.08
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.67
Consensus pattern (33 bp):
TATTTATTTATATATATTTTATATTATTATTAC
Found at i:5771008 original size:31 final size:29
Alignment explanation
Indices: 5770858--5771082 Score: 116
Period size: 28 Copynumber: 7.8 Consensus size: 29
5770848 TTCAATTTGT
5770858 TTTATTTATTTAT-TTATTTTAT-TTATTA
1 TTTA-TTATTTATATTATTTTATATTATTA
* * * *
5770886 TGTATT-TTTGTATT-TTGTATTTTATTTA
1 TTTATTATTTATATTATTTTATATTA-TTA
* *
5770914 TTTATTATTTAT-TTA-TCTATTATTACTA
1 TTTATTATTTATATTATTTTA-TATTATTA
* *
5770942 TTTATTACTATATATT-TTTTATATTTTTA
1 TTTATTA-TTTATATTATTTTATATTATTA
5770971 TTTTTATCTATTTATATATATTTTATATTATTA
1 --TTTAT-TATTTATAT-TATTTTATATTATTA
* *
5771004 TTTATCTATTTACA-TATTATCAT-TTATCTA
1 TTTAT-TATTTATATTATT-TTATATTAT-TA
* * *
5771034 -TGAATATATATA-TA-TTTAT-TTATTTA
1 TTTATTATTTATATTATTTTATATTA-TTA
*
5771060 TTTATTATTTTATTTTATTTTAT
1 TTTATTA-TTTATATTATTTTAT
5771083 TTTCTTGGTT
Statistics
Matches: 151, Mismatches: 25, Indels: 40
0.70 0.12 0.19
Matches are distributed among these distances:
26 17 0.11
27 13 0.09
28 37 0.25
29 30 0.20
30 15 0.10
31 24 0.16
32 3 0.02
33 12 0.08
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.67
Consensus pattern (29 bp):
TTTATTATTTATATTATTTTATATTATTA
Found at i:5771023 original size:22 final size:21
Alignment explanation
Indices: 5770989--5771069 Score: 78
Period size: 22 Copynumber: 3.9 Consensus size: 21
5770979 TATTTATATA
*
5770989 TATTTTATATTATTATTTATC
1 TATTTAATATTATTATTTATC
*
5771010 TATTTACATATTATCATTTATC
1 TATTTA-ATATTATTATTTATC
* *
5771032 TA-TGAATATATATATATTTATT
1 TATTTAATAT-TAT-TATTTATC
5771054 TATTT-AT-TTATTATTT
1 TATTTAATATTATTATTT
5771070 TATTTTATTT
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
19 5 0.10
20 7 0.14
21 11 0.22
22 26 0.52
23 1 0.02
ACGTcount: A:0.32, C:0.05, G:0.01, T:0.62
Consensus pattern (21 bp):
TATTTAATATTATTATTTATC
Found at i:5771895 original size:12 final size:10
Alignment explanation
Indices: 5771878--5771920 Score: 52
Period size: 9 Copynumber: 4.1 Consensus size: 10
5771868 TTTTTTTTTC
5771878 ATTTATTTATTT
1 ATTTA-TTA-TT
5771890 ATTTATTATT
1 ATTTATTATT
5771900 A-TTATTATT
1 ATTTATTATT
5771909 ATTTATTGATT
1 ATTTATT-ATT
5771920 A
1 A
5771921 GATTAGAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
9 9 0.31
10 8 0.28
11 7 0.24
12 5 0.17
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (10 bp):
ATTTATTATT
Found at i:5771925 original size:19 final size:19
Alignment explanation
Indices: 5771888--5771925 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
5771878 ATTTATTTAT
*
5771888 TTATTTATTATTATTATTA
1 TTATTTATTATTATGATTA
5771907 TTATTTATTGATTA-GATTA
1 TTATTTATT-ATTATGATTA
5771926 GAATTGTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (19 bp):
TTATTTATTATTATGATTA
Found at i:5771950 original size:5 final size:5
Alignment explanation
Indices: 5771940--5772002 Score: 74
Period size: 5 Copynumber: 12.0 Consensus size: 5
5771930 TGTTTAATAC
*
5771940 ATTTT ATTTT ATTTT -TCTTT ATTTTT AATTTC ATTTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT AT-TTT A-TTTT -ATTTT A-TTTT ATTTT ATTTT
5771988 ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT
5772003 CTTTAAGTAA
Statistics
Matches: 51, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
4 1 0.02
5 38 0.75
6 10 0.20
7 2 0.04
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (5 bp):
ATTTT
Found at i:5772088 original size:59 final size:59
Alignment explanation
Indices: 5772019--5772232 Score: 272
Period size: 58 Copynumber: 3.7 Consensus size: 59
5772009 GTAAAATTCA
* *
5772019 AAAAAAATATTTTTGAGGAAATGTTGAAAACATCAATTTTCCTTGAAAATAAGTTTTTC
1 AAAAAAATATTTTTGAGGAAAAGTTGAAAGCATCAATTTTCCTTGAAAATAAGTTTTTC
* *
5772078 AAAAAAATATTTTTGAGGAAAAGTTGAAAGCATCAATTTTCTTTGAAAATAAG-CTTTC
1 AAAAAAATATTTTTGAGGAAAAGTTGAAAGCATCAATTTTCCTTGAAAATAAGTTTTTC
* * * *
5772136 TAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGTTTTT-
1 AAAAAAATATTTTTGAGGAAAAGTTGAAAGCATCAATTTTCCTTGAAAATAAGTTTTTC
**** * * *
5772194 AAAAGTGGATTTTTG-GGGAAAGTTGAAAGTATTAATTTT
1 AAAAAAATATTTTTGAGGAAAAGTTGAAAGCATCAATTTT
5772233 TTCTGTACAA
Statistics
Matches: 136, Mismatches: 18, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
57 21 0.15
58 62 0.46
59 53 0.39
ACGTcount: A:0.42, C:0.06, G:0.14, T:0.37
Consensus pattern (59 bp):
AAAAAAATATTTTTGAGGAAAAGTTGAAAGCATCAATTTTCCTTGAAAATAAGTTTTTC
Found at i:5772236 original size:117 final size:117
Alignment explanation
Indices: 5772020--5772232 Score: 304
Period size: 117 Copynumber: 1.8 Consensus size: 117
5772010 TAAAATTCAA
* * *
5772020 AAAAAATATTTTTGAGGAAATGTTGAAAACATCAATTTTCCTTGAAAATAAGTTTTTCAAAAAAA
1 AAAAAATATTTTTGAGAAAAAGTTGAAAACATCAATTTTCCTTAAAAATAAGTTTTTCAAAAAAA
*
5772085 TATTTTTGAGGAAAAGTTGAAAGCATCAATTTTCTTTGAAAATAAGCTTTCT
66 GATTTTTGAGGAAAAGTTGAAAGCATCAATTTTCTTTGAAAATAAGCTTTCT
** ***
5772137 AAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGTTTTT-AAAAGTG
1 AAAAAATATTTTTGAGAAAAAGTTGAAAACATCAATTTTCCTTAAAAATAAGTTTTTCAAAAAAA
* * *
5772201 GATTTTTG-GGGAAAGTTGAAAGTATTAATTTT
66 GATTTTTGAGGAAAAGTTGAAAGCATCAATTTT
5772233 TTCTGTACAA
Statistics
Matches: 84, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
115 21 0.25
116 11 0.13
117 52 0.62
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.38
Consensus pattern (117 bp):
AAAAAATATTTTTGAGAAAAAGTTGAAAACATCAATTTTCCTTAAAAATAAGTTTTTCAAAAAAA
GATTTTTGAGGAAAAGTTGAAAGCATCAATTTTCTTTGAAAATAAGCTTTCT
Found at i:5772700 original size:30 final size:30
Alignment explanation
Indices: 5772659--5772719 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
5772649 AATGTCTAGC
*
5772659 GATAGATCCCCGGATATATACGTTATGACA
1 GATAAATCCCCGGATATATACGTTATGACA
5772689 GATAAATCCCCGGATATATACGTTATGACA
1 GATAAATCCCCGGATATATACGTTATGACA
5772719 G
1 G
5772720 GTTTCTGCAT
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:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (30 bp):
GATAAATCCCCGGATATATACGTTATGACA
Found at i:5773477 original size:129 final size:131
Alignment explanation
Indices: 5773268--5773532 Score: 446
Period size: 129 Copynumber: 2.0 Consensus size: 131
5773258 TCCCTGCAGT
*
5773268 CTTCATGCCGCTCTCTACCATTCCTTGTTTTTTTTTTGTTTTTTTTTAATCCTTTTTTTTGCCTA
1 CTTCATGCCGCTCTCTACCATTCCTTGTTTTTTTGTTGTTTTTTTTTAATCCTTTTTTTTGCCTA
* * *
5773333 GTTTTTCCGACCACGTTTTTAAGCCATGCCGTGCCTTTCAG-TTTTTTAACAGTTACCTTCTTCC
66 GTTTTTCCGACCACGTTTTCAAGCAATGCCATGCCTTTCAGTTTTTTTAACAGTTACCTTCTT-C
5773397 CC
130 CC
*
5773399 CTTCATGCCGCTCTCTACCATTCCTTGTTTTTTTGTT-TTTTTTTTT-CTCCTTTTTTTTGCCTA
1 CTTCATGCCGCTCTCTACCATTCCTTGTTTTTTTGTTGTTTTTTTTTAATCCTTTTTTTTGCCTA
*
5773462 GTTTTTCCGACCACGTTTTCAAGCAATGCCATGCCTTTCAGTTTTTTTAACAGTTTCCTTCTTCC
66 GTTTTTCCGACCACGTTTTCAAGCAATGCCATGCCTTTCAGTTTTTTTAACAGTTACCTTCTTCC
5773527 C
131 C
5773528 CTTCA
1 CTTCA
5773533 CGTGTTGCAT
Statistics
Matches: 127, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
129 62 0.49
130 29 0.23
131 36 0.28
ACGTcount: A:0.12, C:0.27, G:0.10, T:0.51
Consensus pattern (131 bp):
CTTCATGCCGCTCTCTACCATTCCTTGTTTTTTTGTTGTTTTTTTTTAATCCTTTTTTTTGCCTA
GTTTTTCCGACCACGTTTTCAAGCAATGCCATGCCTTTCAGTTTTTTTAACAGTTACCTTCTTCC
C
Found at i:5774339 original size:22 final size:22
Alignment explanation
Indices: 5774307--5774367 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 22
5774297 TTGGGCATGC
*
5774307 TGCCAGCTAATCTGGGCTT-TCG
1 TGCCAACTAATCTGGGCTTAT-G
* *
5774329 TGCCAATTAATTCTAGGCTTATG
1 TGCCAACTAA-TCTGGGCTTATG
*
5774352 TGCCAACTAAACTGGG
1 TGCCAACTAATCTGGG
5774368 TTTAAATTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
22 12 0.39
23 18 0.58
24 1 0.03
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (22 bp):
TGCCAACTAATCTGGGCTTATG
Found at i:5774546 original size:67 final size:61
Alignment explanation
Indices: 5774466--5774622 Score: 145
Period size: 67 Copynumber: 2.4 Consensus size: 61
5774456 CTAAATCGAA
* * * * *
5774466 CTTAAAATTTCATTGTGTGCCAGATAATTTGAGTTTAATTTTTGTCATGAGTGCTAGATAAACTA
1 CTTAAAA-TTCATTG-GTGCCAGATAACTAGACTTGAATATTT-TCATGA--GC-AGATAAACTA
5774531 GG
60 GG
* *
5774533 CTTAAAACTTCATTAGGTGCCAAATAAACTAGACTTGAATATTTTCTTGAGCAGATAAACTAGG
1 CTTAAAA-TTCATT-GGTGCCAGAT-AACTAGACTTGAATATTTTCATGAGCAGATAAACTAGG
5774597 CTT-AAATATCATTGAGTGCCAGATAA
1 CTTAAAAT-TCATTG-GTGCCAGATAA
5774623 AATGAGCTTA
Statistics
Matches: 77, Mismatches: 9, Indels: 13
0.78 0.09 0.13
Matches are distributed among these distances:
62 4 0.05
63 16 0.21
64 15 0.19
65 2 0.03
67 26 0.34
68 14 0.18
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.35
Consensus pattern (61 bp):
CTTAAAATTCATTGGTGCCAGATAACTAGACTTGAATATTTTCATGAGCAGATAAACTAGG
Found at i:5774895 original size:22 final size:22
Alignment explanation
Indices: 5774870--5774948 Score: 88
Period size: 22 Copynumber: 3.6 Consensus size: 22
5774860 ACTTTTTCAA
* *
5774870 CTAATTTGGGCTTATATGCCAG
1 CTAATTTAGGCTTATGTGCCAG
* *
5774892 CTAA-ATAGGCATATGTGCCAG
1 CTAATTTAGGCTTATGTGCCAG
* *
5774913 CTAATCTAGGCTTATGTGCCCG
1 CTAATTTAGGCTTATGTGCCAG
*
5774935 TTAATTTAGGCTTA
1 CTAATTTAGGCTTA
5774949 AATCCTAGGT
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
21 17 0.36
22 30 0.64
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (22 bp):
CTAATTTAGGCTTATGTGCCAG
Found at i:5775052 original size:32 final size:32
Alignment explanation
Indices: 5775007--5775160 Score: 105
Period size: 32 Copynumber: 4.8 Consensus size: 32
5774997 TTAAAACTTG
* *
5775007 GATGCTAACTAAACTAGGCTTAAATTTTGATT
1 GATGCCAACTAAACTAGGCTTAAATTTTCATT
* * *
5775039 GATGCCAATTAAACTGGGCTTAGAA-TGTCATT
1 GATGCCAACTAAACTAGGCTTA-AATTTTCATT
* * * *
5775071 GGTGCCAGA-TAATCTAAGCTTAAATCTTCATT
1 GATGCCA-ACTAAACTAGGCTTAAATTTTCATT
* * * *
5775103 GGTGCCAACTAAACTGGGTTTAAATCTTTTATT
1 GATGCCAACTAAACTAGGCTTAAAT-TTTCATT
* * * *
5775136 GGGTGCTAGCTAAACTGGGCTTAAA
1 -GATGCCAACTAAACTAGGCTTAAA
5775161 ACTGTATTGG
Statistics
Matches: 96, Mismatches: 20, Indels: 10
0.76 0.16 0.08
Matches are distributed among these distances:
31 3 0.03
32 64 0.67
33 8 0.08
34 21 0.22
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.34
Consensus pattern (32 bp):
GATGCCAACTAAACTAGGCTTAAATTTTCATT
Found at i:5775149 original size:34 final size:33
Alignment explanation
Indices: 5775088--5775325 Score: 148
Period size: 34 Copynumber: 7.2 Consensus size: 33
5775078 GATAATCTAA
* * *
5775088 GCTTAAATCTTCATT-GGTGCCAACTAAACTGG
1 GCTTAAATCTTTATTGGGTGCTAGCTAAACTGG
*
5775120 GTTTAAATCTTTTATTGGGTGCTAGCTAAACTGG
1 GCTTAAATC-TTTATTGGGTGCTAGCTAAACTGG
* * *
5775154 GCTTAAAACTGTATTGGGTG-TCAGCTAAACTTG
1 GCTTAAATCTTTATTGGGTGCT-AGCTAAACTGG
* * * *
5775187 GCTTAAATCTTT-TCATGAGTGCTGGATAAACTGA
1 GCTTAAATCTTTAT--TGGGTGCTAGCTAAACTGG
** * *
5775221 GCTTAAAT-TTCT-TTGGGTTATAGAT-AACTGT
1 GCTTAAATCTT-TATTGGGTGCTAGCTAAACTGG
* * * * * *
5775252 GCTTAAAACTTCATT-AGTGCCAGCTAAATTAG
1 GCTTAAATCTTTATTGGGTGCTAGCTAAACTGG
* * * *
5775284 GCTTAAATATTTTATTGGGTACTAGATAAACTAG
1 GCTTAAAT-CTTTATTGGGTGCTAGCTAAACTGG
5775318 GCTTAAAT
1 GCTTAAAT
5775326 TTTCATGGGG
Statistics
Matches: 156, Mismatches: 38, Indels: 22
0.72 0.18 0.10
Matches are distributed among these distances:
31 17 0.11
32 32 0.21
33 42 0.27
34 64 0.41
35 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.37
Consensus pattern (33 bp):
GCTTAAATCTTTATTGGGTGCTAGCTAAACTGG
Found at i:5775169 original size:33 final size:34
Alignment explanation
Indices: 5775111--5775193 Score: 107
Period size: 33 Copynumber: 2.5 Consensus size: 34
5775101 TTGGTGCCAA
* * *
5775111 CTAAACTGGGTTTAAATCTTTTATTGGGTG-CTAG
1 CTAAACTGGGCTTAAAACTTGTATTGGGTGTC-AG
5775145 CTAAACTGGGCTTAAAAC-TGTATTGGGTGTCAG
1 CTAAACTGGGCTTAAAACTTGTATTGGGTGTCAG
*
5775178 CTAAACTTGGCTTAAA
1 CTAAACTGGGCTTAAA
5775194 TCTTTTCATG
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
33 27 0.61
34 17 0.39
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.35
Consensus pattern (34 bp):
CTAAACTGGGCTTAAAACTTGTATTGGGTGTCAG
Found at i:5775312 original size:97 final size:98
Alignment explanation
Indices: 5775148--5775327 Score: 226
Period size: 97 Copynumber: 1.8 Consensus size: 98
5775138 GTGCTAGCTA
* * * * *
5775148 AACTGGGCTTAAAACTGTATTGGGTGTCAGCTAAACTTGGCTTAAATCTTTTCATGAGTGCTGGA
1 AACTGGGCTTAAAACTGTATTGAGTGCCAGCTAAACTTGGCTTAAATATTTTCATGAGTACTAGA
5775213 TAAACT-GAGCTTAAATTTCTTTGGGTTATAGAT
66 TAAACTAG-GCTTAAATTTCTTTGGGTTATAGAT
* *
5775246 AACTGTGCTTAAAACT-TCATT-AGTGCCAGCTAAA-TTAGGCTTAAATATTTT-ATTGGGTACT
1 AACTGGGCTTAAAACTGT-ATTGAGTGCCAGCTAAACTT-GGCTTAAATATTTTCA-TGAGTACT
5775307 AGATAAACTAGGCTTAAATTT
63 AGATAAACTAGGCTTAAATTT
5775328 TCATGGGGCC
Statistics
Matches: 71, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
96 3 0.04
97 49 0.69
98 19 0.27
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (98 bp):
AACTGGGCTTAAAACTGTATTGAGTGCCAGCTAAACTTGGCTTAAATATTTTCATGAGTACTAGA
TAAACTAGGCTTAAATTTCTTTGGGTTATAGAT
Found at i:5776299 original size:4 final size:4
Alignment explanation
Indices: 5776276--5776372 Score: 54
Period size: 4 Copynumber: 23.0 Consensus size: 4
5776266 CACCTAGTCA
* * * * *
5776276 TTTC TTTTC TTCTT TTTC TTTC TTTC TTTC TTTG TTTT TTTT TTTC ATTC
1 TTTC -TTTC TT-TC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
* *
5776326 TTTC ATTTT TTTC TTT- TTGTCC TTAC TTT- TTTC TTTTGC TTTC TTTC
1 TTTC -TTTC TTTC TTTC TT-T-C TTTC TTTC TTTC -TTT-C TTTC TTTC
5776373 ACTGATTGGA
Statistics
Matches: 73, Mismatches: 11, Indels: 17
0.72 0.11 0.17
Matches are distributed among these distances:
3 5 0.07
4 49 0.67
5 16 0.22
6 3 0.04
ACGTcount: A:0.03, C:0.19, G:0.03, T:0.75
Consensus pattern (4 bp):
TTTC
Done.