Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr12
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: 39383930
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.32
Warning! 780790 characters in sequence are not A, C, G, or T
File 18 of 126
Found at i:5198885 original size:75 final size:75
Alignment explanation
Indices: 5198762--5198912 Score: 302
Period size: 75 Copynumber: 2.0 Consensus size: 75
5198752 TCAACAAACC
5198762 AGCAATAAGAGAATTGAATCTTCAAAATCTGTGCGGTATATGAAATATCACAGATGTTGAAGGAC
1 AGCAATAAGAGAATTGAATCTTCAAAATCTGTGCGGTATATGAAATATCACAGATGTTGAAGGAC
5198827 TATTATGCAA
66 TATTATGCAA
5198837 AGCAATAAGAGAATTGAATCTTCAAAATCTGTGCGGTATATGAAATATCACAGATGTTGAAGGAC
1 AGCAATAAGAGAATTGAATCTTCAAAATCTGTGCGGTATATGAAATATCACAGATGTTGAAGGAC
5198902 TATTATGCAA
66 TATTATGCAA
5198912 A
1 A
5198913 TAAAATTTGG
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 76 1.00
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (75 bp):
AGCAATAAGAGAATTGAATCTTCAAAATCTGTGCGGTATATGAAATATCACAGATGTTGAAGGAC
TATTATGCAA
Found at i:5205456 original size:4 final size:4
Alignment explanation
Indices: 5205447--5205481 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
5205437 GTGTTGGCTT
5205447 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
5205482 AAATTAGTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:5205868 original size:6 final size:6
Alignment explanation
Indices: 5205857--5205885 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
5205847 ATGGTGTACC
5205857 TACATA TACATA TACATA TACATA TACAT
1 TACATA TACATA TACATA TACATA TACAT
5205886 GATCATGATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.34
Consensus pattern (6 bp):
TACATA
Found at i:5206671 original size:24 final size:24
Alignment explanation
Indices: 5206641--5206688 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
5206631 TTATGATTAA
*
5206641 TATTTTTT-TTATAATGGGTTGAAT
1 TATTTTTTGTTAT-ATGGGTAGAAT
5206665 TATTTTTTGTTATATGGGTAGAAT
1 TATTTTTTGTTATATGGGTAGAAT
5206689 ATAAAGATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.25, C:0.00, G:0.19, T:0.56
Consensus pattern (24 bp):
TATTTTTTGTTATATGGGTAGAAT
Found at i:5208405 original size:11 final size:11
Alignment explanation
Indices: 5208389--5208414 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
5208379 TATTTTTTAA
5208389 TTTTAAAATAC
1 TTTTAAAATAC
5208400 TTTTAAAATAC
1 TTTTAAAATAC
5208411 TTTT
1 TTTT
5208415 TTTAAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:5208483 original size:39 final size:39
Alignment explanation
Indices: 5208373--5208506 Score: 157
Period size: 39 Copynumber: 3.4 Consensus size: 39
5208363 AATATTTTTA
* *
5208373 TTTTTTT-ATTTTTTAATTTTAAAATACTTTTAAAATAC
1 TTTTTTTAATTTTTTAATTTTAAAATAATTTTTAAATAC
* **
5208411 TTTTTTTAAATTTTTTAAATTTT-AATTTTTTTTTAAATAC
1 TTTTTTT-AATTTTTT-AATTTTAAAATAATTTTTAAATAC
* *
5208451 TTTTTTTAATTTTTTAATTTTAAAATAATTTTTTAAT-T
1 TTTTTTTAATTTTTTAATTTTAAAATAATTTTTAAATAC
5208489 TTTGTTTTAATTTTTTAA
1 TTT-TTTTAATTTTTTAA
5208507 ATATATTTTT
Statistics
Matches: 82, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
38 16 0.20
39 33 0.40
40 27 0.33
41 6 0.07
ACGTcount: A:0.31, C:0.02, G:0.01, T:0.66
Consensus pattern (39 bp):
TTTTTTTAATTTTTTAATTTTAAAATAATTTTTAAATAC
Found at i:5210787 original size:30 final size:31
Alignment explanation
Indices: 5210751--5210817 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
5210741 ATTTTTCGAT
*
5210751 AATTTT-ATTTCAC-CCTTAAATAATTTTAAA
1 AATTTTAATTTCACTCCTCAAA-AATTTTAAA
* *
5210781 AATTTTAATTTGACTCCTCAAAAATTTTGAA
1 AATTTTAATTTCACTCCTCAAAAATTTTAAA
5210812 AATTTT
1 AATTTT
5210818 TATTAATTCT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 6 0.19
31 20 0.62
32 6 0.19
ACGTcount: A:0.39, C:0.12, G:0.03, T:0.46
Consensus pattern (31 bp):
AATTTTAATTTCACTCCTCAAAAATTTTAAA
Found at i:5210883 original size:30 final size:29
Alignment explanation
Indices: 5210764--5210875 Score: 98
Period size: 31 Copynumber: 3.7 Consensus size: 29
5210754 TTTATTTCAC
* *
5210764 CCTTAAATAATTTTAAAAATTTTAATTTGACT
1 CCTTAAAT-ATTTTGAAAATTTTAA-TT-AAT
* * *
5210796 CCTCAAAAATTTTGAAAATTTTTATTAAT
1 CCTTAAATATTTTGAAAATTTTAATTAAT
* * *
5210825 TCTTAAATTTTTTAAAAATATTTAATTAAT
1 CCTTAAATATTTTGAAAAT-TTTAATTAAT
*
5210855 CCTATCAATATTTTGAAAATT
1 CCT-TAAATATTTTGAAAATT
5210876 CTCATTAAAT
Statistics
Matches: 63, Mismatches: 15, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
29 16 0.25
30 14 0.22
31 27 0.43
32 6 0.10
ACGTcount: A:0.41, C:0.09, G:0.03, T:0.47
Consensus pattern (29 bp):
CCTTAAATATTTTGAAAATTTTAATTAAT
Found at i:5212651 original size:19 final size:20
Alignment explanation
Indices: 5212615--5212653 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
5212605 AGTAAATAAA
**
5212615 AAAATATTTTAAGTATATTT
1 AAAATATTTTAAAAATATTT
5212635 AAAAT-TTTTAAAAATATTT
1 AAAATATTTTAAAAATATTT
5212654 TTATTACTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
AAAATATTTTAAAAATATTT
Found at i:5219836 original size:34 final size:34
Alignment explanation
Indices: 5219793--5219860 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
5219783 CCTTAAACTT
5219793 ATCTTGCAGACATGTTATAGGTAAATGTATTATG
1 ATCTTGCAGACATGTTATAGGTAAATGTATTATG
5219827 ATCTTGCAGACATGTTATAGGTAAATGTATTATG
1 ATCTTGCAGACATGTTATAGGTAAATGTATTATG
5219861 GAGGTTTTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.38
Consensus pattern (34 bp):
ATCTTGCAGACATGTTATAGGTAAATGTATTATG
Found at i:5220945 original size:31 final size:31
Alignment explanation
Indices: 5220910--5220970 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
5220900 ATCCAACGAC
*
5220910 TTAAATAAAAATTTTCGAATAATTTAATGAT
1 TTAAATAAAAATTTTCAAATAATTTAATGAT
* *
5220941 TTAAATTAAAATTTTTAAATAATTTAATGA
1 TTAAATAAAAATTTTCAAATAATTTAATGA
5220971 CTATTTTGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (31 bp):
TTAAATAAAAATTTTCAAATAATTTAATGAT
Found at i:5221860 original size:37 final size:37
Alignment explanation
Indices: 5221819--5221892 Score: 87
Period size: 37 Copynumber: 2.0 Consensus size: 37
5221809 AAAGTTTATA
* * *
5221819 CCTTCTATTAAAT-TGGTTCTAATTTAACAAATTTAGC
1 CCTTCTATT-AATCTGATTCCAATCTAACAAATTTAGC
* *
5221856 CCTTCTGTTAATCTGATTCCAATCTAATAAATTTAGC
1 CCTTCTATTAATCTGATTCCAATCTAACAAATTTAGC
5221893 TGCAGCAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
36 3 0.10
37 28 0.90
ACGTcount: A:0.31, C:0.19, G:0.08, T:0.42
Consensus pattern (37 bp):
CCTTCTATTAATCTGATTCCAATCTAACAAATTTAGC
Found at i:5223163 original size:182 final size:182
Alignment explanation
Indices: 5222823--5223294 Score: 721
Period size: 182 Copynumber: 2.6 Consensus size: 182
5222813 GTATACATTT
* **
5222823 GAGTTACGCTACAATGGTTAGATGATCATGCCATGTAACTTGGTTTGTCAACTTTATGAGTTGAG
1 GAGTTAAGCTACAATGACTAGATGATCATGCCATGTAACTTGGTTTGTCAACTTTATGAGTTGAG
* * * * * **
5222888 CTTAATTAAA-TGATGTAGCATTAGTTTAAAATATAATGTAACGTGTTATATTCACTTGAATAGT
66 C-AAATAAAACAG-TGTGGCATTAGTTTAAAATATAATGTAACGCGCCATATTCACTTGAATAGT
*
5222952 TGCATGTAATCAGTGAATGGAGTATGAATCAAGTCAGGTCAAATGTAACTACTC
129 TGCATATAATCAGTGAATGGAGTATGAATCAAGTCAGGTCAAATGTAACTACTC
* *
5223006 GAGTTAAGCTACAATGACCAGATGATCATGCCATATAACTTGGTTTGTCAACTTTATGAGTTGAG
1 GAGTTAAGCTACAATGACTAGATGATCATGCCATGTAACTTGGTTTGTCAACTTTATGAGTTGAG
*
5223071 CAAATAAAACAGTGTGGCATTAGTTTAAAATATAATGTAACGCGCCATATTTACTTGAATAGTTG
66 CAAATAAAACAGTGTGGCATTAGTTTAAAATATAATGTAACGCGCCATATTCACTTGAATAGTTG
* * ** *
5223136 TATATAATCAGTGAATGGGGTATGAATCGGGTCGGGTCAAATGTAACTACTC
131 CATATAATCAGTGAATGGAGTATGAATCAAGTCAGGTCAAATGTAACTACTC
*
5223188 GAGTTAAGCTACAATGACTAGATGATCATGCCATGTAACTTGGCTTGTCAACTTTATGAGTTGAG
1 GAGTTAAGCTACAATGACTAGATGATCATGCCATGTAACTTGGTTTGTCAACTTTATGAGTTGAG
* *
5223253 CAAATAAAACAATTTGGCATTAGTTTAAAATATAATGTAACG
66 CAAATAAAACAGTGTGGCATTAGTTTAAAATATAATGTAACG
5223295 TGTCTTATTC
Statistics
Matches: 264, Mismatches: 24, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
182 202 0.77
183 62 0.23
ACGTcount: A:0.34, C:0.13, G:0.20, T:0.33
Consensus pattern (182 bp):
GAGTTAAGCTACAATGACTAGATGATCATGCCATGTAACTTGGTTTGTCAACTTTATGAGTTGAG
CAAATAAAACAGTGTGGCATTAGTTTAAAATATAATGTAACGCGCCATATTCACTTGAATAGTTG
CATATAATCAGTGAATGGAGTATGAATCAAGTCAGGTCAAATGTAACTACTC
Found at i:5223535 original size:207 final size:203
Alignment explanation
Indices: 5223123--5223653 Score: 643
Period size: 207 Copynumber: 2.6 Consensus size: 203
5223113 CGCCATATTT
* * * * * * *
5223123 ACTTGAATAGTTGTATATAATCAGTGAATGGGGTATGAATCGGGTCGGGTCAAATGTAACTACTC
1 ACTTGAATAGTTGCATATAATCGGTGAATGGGGTATGAATCTGGTCGGATTAAATGTAACAATTC
** * *
5223188 GAGTTAAGCTACAATGACTAGATGATCATGCCATGTAACTTGGCTTGTCAACTTTATGAGTTGAG
66 GAGTTAAGCTACAATGGTTAGATGATCATGCCATGTAACTTGGTTTGTTAACTTTATGAGTTGAG
* * * * *
5223253 CAAATAAAACAATTTGGCATTAGTTTAAAATATAATGTAACGTGTCTTATTCACTCGGCCCACTA
131 CAAATAAAACAATGTGGCATTAGTTTAAAATATAATGTAACGTGTCATATTCACTAGACACACTA
5223318 GAGTTTTA
196 GAGTTTTA
* **
5223326 ACTTGAATAGTTGCATGTAATCGGTGAATGGGGTATGAGATCTGGTTAGATTAAATGTAACAATT
1 ACTTGAATAGTTGCATATAATCGGTGAATGGGGTATGA-ATCTGGTCGGATTAAATGTAACAATT
* *
5223391 CGAGTTAATAAGCTACAATGGTTAGATGATCATACCATGTAACTGGGTTTGTTAACTTTATGAGT
65 CGAG-T--TAAGCTACAATGGTTAGATGATCATGCCATGTAACTTGGTTTGTTAACTTTATGAGT
* ** ** * ** *
5223456 TGAGCTTAATTTAATGATGTGGTATTTTTTTAAAATATAATGTAACGTGTCATATTCATTAGACA
127 TGAGC-AAATAAAACAATGTGGCATTAGTTTAAAATATAATGTAACGTGTCATATTCACTAGACA
5223521 CACTAGAG-TTTA
191 CACTAGAGTTTTA
* *
5223533 ACTTGAATAGTTGCATATAACCGGTGAATGGGGTATGATAT-TGGGTCGGATTAAATGTAACGAT
1 ACTTGAATAGTTGCATATAATCGGTGAATGGGGTATGA-ATCT-GGTCGGATTAAATGTAACAAT
* * * * *
5223597 TCGGGTTAAGCTAGAATGGTGAGATGATCCTGTCATGTAAACTTGGTTTGTTAACTT
64 TCGAGTTAAGCTACAATGGTTAGATGATCATGCCATGT-AACTTGGTTTGTTAACTT
5223654 GTTTCACCTT
Statistics
Matches: 278, Mismatches: 43, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
203 35 0.13
204 50 0.18
205 18 0.06
206 2 0.01
207 120 0.43
208 53 0.19
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.35
Consensus pattern (203 bp):
ACTTGAATAGTTGCATATAATCGGTGAATGGGGTATGAATCTGGTCGGATTAAATGTAACAATTC
GAGTTAAGCTACAATGGTTAGATGATCATGCCATGTAACTTGGTTTGTTAACTTTATGAGTTGAG
CAAATAAAACAATGTGGCATTAGTTTAAAATATAATGTAACGTGTCATATTCACTAGACACACTA
GAGTTTTA
Found at i:5227619 original size:52 final size:48
Alignment explanation
Indices: 5227600--5227802 Score: 265
Period size: 46 Copynumber: 4.3 Consensus size: 48
5227590 TGACAAGTGG
* *
5227600 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
5227646 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGA
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC-A---A
* *
5227698 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
** *
5227744 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
5227790 AAAGTGATAAGTG
1 AAAGTGATAAGTG
5227803 GCTACACTTA
Statistics
Matches: 144, Mismatches: 7, Indels: 12
0.88 0.04 0.07
Matches are distributed among these distances:
46 100 0.69
52 44 0.31
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (48 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
Found at i:5227654 original size:98 final size:98
Alignment explanation
Indices: 5227534--5227802 Score: 457
Period size: 98 Copynumber: 2.7 Consensus size: 98
5227524 TTTGAGTACT
*
5227534 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
5227599 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
**
5227632 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
5227697 AAAAGTGATAAGTGATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
* *
5227730 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGAC-AAGT
*
5227795 GATAAGTG
65 GAAAAGTG
5227803 GCTACACTTA
Statistics
Matches: 160, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
98 149 0.93
99 11 0.07
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.28
Consensus pattern (98 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
Found at i:5227810 original size:37 final size:37
Alignment explanation
Indices: 5227766--5227911 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
5227756 GATAGCTTTA
*
5227766 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
5227803 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
5227840 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
5227877 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
5227912 ATCATACGTA
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 11 0.11
36 4 0.04
37 89 0.86
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:5230172 original size:168 final size:168
Alignment explanation
Indices: 5229877--5230214 Score: 405
Period size: 168 Copynumber: 2.0 Consensus size: 168
5229867 CAAAATGGGT
* * * *
5229877 TTTTGATCTCAGGTAATTTAAAACTCTTATTTACGTAATGGTGTAATTTTGAGTTTCACTGGAAA
1 TTTTGATCTCAGATAATTTAAAACTCTTATTTACGTAATGGTGTAAGTCTGAATTTCACTGGAAA
* * *
5229942 CTTTAATTTGTTATAACTTGATCCTCTTAATTTGCAAAAATTGGAAATTTGATCCTGTTTTTGGC
66 CTTTAATTTGTTATAACTTCATCCTCTTAATTTACAAAAATTGAAAATTTGATCCTGTTTTTGGC
* * ** *
5230007 GCATACATGCACTTGAACAGTTGGTTTTTGCTAATTTG
131 GAATACATGAACTTGAACAGTTAATTTGTGCTAATTTG
* * *
5230045 TTTTGATCTCCGATAGTTTAAAACTCTTATTTAC-TCAATGGTGTAAGTCTGAATTTCATTGGAA
1 TTTTGATCTCAGATAATTTAAAACTCTTATTTACGT-AATGGTGTAAGTCTGAATTTCACTGGAA
* * * *
5230109 GCTTTACTTTGTTA-GACTTCCATCCTCTTATTTTACAAAAATTGAAAATTT-AGT-CTGGTTTT
65 ACTTTAATTTGTTATAACTT-CATCCTCTTAATTTACAAAAATTGAAAATTTGA-TCCT-GTTTT
* * **
5230171 TGGTGAATATATGAACTTGAATTGTTAATTTGTGCTAATTTG
127 TGGCGAATACATGAACTTGAACAGTTAATTTGTGCTAATTTG
5230213 TT
1 TT
5230215 GCATATAAAA
Statistics
Matches: 143, Mismatches: 23, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
167 8 0.06
168 135 0.94
ACGTcount: A:0.27, C:0.13, G:0.16, T:0.44
Consensus pattern (168 bp):
TTTTGATCTCAGATAATTTAAAACTCTTATTTACGTAATGGTGTAAGTCTGAATTTCACTGGAAA
CTTTAATTTGTTATAACTTCATCCTCTTAATTTACAAAAATTGAAAATTTGATCCTGTTTTTGGC
GAATACATGAACTTGAACAGTTAATTTGTGCTAATTTG
Found at i:5230808 original size:85 final size:85
Alignment explanation
Indices: 5230516--5230847 Score: 389
Period size: 86 Copynumber: 3.9 Consensus size: 85
5230506 TCCTTCTACT
* * * * * ** *
5230516 TTATAAAAGTTGAAAATTTGGTCTGGTTGTTGGTGAATGCACGAACTTGAACTGTTGATTTTTTC
1 TTATAAAA-TTGAAAATTTAGTCTGATTGTTGGTAAATACATGAACTTGAACCATTGATTTTTGC
*
5230581 TAATTTGTTGCACATAAGTTG
65 TAATTTGTTGCATATAAGTTG
* * *
5230602 TTATAAAAATTGAAAATTTAGTCTGGTTGTTGGTAAATGCATGAACTTGAACCATTTATTTTTGC
1 TTAT-AAAATTGAAAATTTAGTCTGATTGTTGGTAAATACATGAACTTGAACCATTGATTTTTGC
5230667 TAATTTGTTGCATATAAGTTG
65 TAATTTGTTGCATATAAGTTG
* *
5230688 TTATAAATATTGAAAAATTAGTCTGATTTTTGGTAAATACATGAACTTGAACCATTGATTTTTG-
1 TTATAAA-ATTGAAAATTTAGTCTGATTGTTGGTAAATACATGAACTTGAACCATTGATTTTTGC
* *
5230752 TAATTTGTTGCATATAAATCG
65 TAATTTGTTGCATATAAGTTG
* * * * * * *
5230773 TTATAGAAATTGAAGATTTAGCCTTATTGTCGGTAAATATATGAACCATGAA-TAGTTGATTTTT
1 TTATA-AAATTGAAAATTTAGTCTGATTGTTGGTAAATACATGAA-CTTGAACCA-TTGATTTTT
5230837 GCTAATTTGTT
63 GCTAATTTGTT
5230848 TCACATTAAC
Statistics
Matches: 216, Mismatches: 24, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
85 58 0.27
86 145 0.67
87 13 0.06
ACGTcount: A:0.31, C:0.08, G:0.18, T:0.42
Consensus pattern (85 bp):
TTATAAAATTGAAAATTTAGTCTGATTGTTGGTAAATACATGAACTTGAACCATTGATTTTTGCT
AATTTGTTGCATATAAGTTG
Found at i:5230912 original size:40 final size:40
Alignment explanation
Indices: 5230868--5230952 Score: 109
Period size: 40 Copynumber: 2.1 Consensus size: 40
5230858 TGTTGTAAGA
* * * *
5230868 TTGATTTTTGTTAATTTCTTGCATA-TAAATTATTGAAATG
1 TTGATTTTTGATAATTCCTTACATATTAAA-TACTGAAATG
*
5230908 TTGATTTTTGATAATTCCTTACATATTAAATACTGAAGTG
1 TTGATTTTTGATAATTCCTTACATATTAAATACTGAAATG
5230948 TTGAT
1 TTGAT
5230953 ATTCAAGCTA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
40 35 0.90
41 4 0.10
ACGTcount: A:0.31, C:0.07, G:0.13, T:0.49
Consensus pattern (40 bp):
TTGATTTTTGATAATTCCTTACATATTAAATACTGAAATG
Found at i:5231428 original size:28 final size:29
Alignment explanation
Indices: 5231381--5231451 Score: 74
Period size: 29 Copynumber: 2.5 Consensus size: 29
5231371 ATTGGAAAAT
* * * *
5231381 GGACT-ATTTGATTCTTTTTATAGGATAG
1 GGACTAATTTGATCCATTTAATAGGAGAG
*
5231409 GGACTGAA-TTGATCCATTTAATAGTAGAG
1 GGACT-AATTTGATCCATTTAATAGGAGAG
5231438 GGACTAATTTGATC
1 GGACTAATTTGATC
5231452 ATGTCCCTAC
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
28 7 0.20
29 27 0.77
30 1 0.03
ACGTcount: A:0.30, C:0.10, G:0.23, T:0.38
Consensus pattern (29 bp):
GGACTAATTTGATCCATTTAATAGGAGAG
Found at i:5233553 original size:28 final size:29
Alignment explanation
Indices: 5233506--5233576 Score: 74
Period size: 29 Copynumber: 2.5 Consensus size: 29
5233496 ATTGGAAAAT
* * * *
5233506 GGACT-ATTTGATTCTTTTTATAGGATAG
1 GGACTAATTTGATCCATTTAATAGGAGAG
*
5233534 GGACTGAA-TTGATCCATTTAATAGTAGAG
1 GGACT-AATTTGATCCATTTAATAGGAGAG
5233563 GGACTAATTTGATC
1 GGACTAATTTGATC
5233577 ATGTCCCTAC
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
28 7 0.20
29 27 0.77
30 1 0.03
ACGTcount: A:0.30, C:0.10, G:0.23, T:0.38
Consensus pattern (29 bp):
GGACTAATTTGATCCATTTAATAGGAGAG
Found at i:5246574 original size:22 final size:22
Alignment explanation
Indices: 5246549--5246591 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
5246539 TAATAAAAAG
5246549 AATATCTACAAAATATTCCTAA
1 AATATCTACAAAATATTCCTAA
* *
5246571 AATATTTACAGAATATTCCTA
1 AATATCTACAAAATATTCCTA
5246592 CACTCCCCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.47, C:0.16, G:0.02, T:0.35
Consensus pattern (22 bp):
AATATCTACAAAATATTCCTAA
Found at i:5250306 original size:22 final size:22
Alignment explanation
Indices: 5250281--5250325 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
5250271 TTTAATAAAA
5250281 AAAATATCTACAAAATATTCCT
1 AAAATATCTACAAAATATTCCT
* *
5250303 AAAATATTTACAGAATATTCCT
1 AAAATATCTACAAAATATTCCT
5250325 A
1 A
5250326 CAGTAAACGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.49, C:0.16, G:0.02, T:0.33
Consensus pattern (22 bp):
AAAATATCTACAAAATATTCCT
Found at i:5259627 original size:8 final size:8
Alignment explanation
Indices: 5259614--5259669 Score: 53
Period size: 8 Copynumber: 6.8 Consensus size: 8
5259604 TTTTTTTAAG
5259614 TATATTAT
1 TATATTAT
5259622 TATATTAT
1 TATATTAT
5259630 TATATTGTAAAT
1 TATA-T-T--AT
*
5259642 TATATTAA
1 TATATTAT
5259650 T-TA-TAT
1 TATATTAT
5259656 TATATTAT
1 TATATTAT
5259664 TATATT
1 TATATT
5259670 TCAAATAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
6 3 0.08
7 4 0.10
8 23 0.57
9 1 0.03
10 2 0.05
11 1 0.03
12 6 0.15
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (8 bp):
TATATTAT
Found at i:5271205 original size:14 final size:14
Alignment explanation
Indices: 5271164--5271213 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
5271154 CTTTGAATCT
5271164 CTTCTTTT-TATTTC
1 CTTCTTTTCT-TTTC
5271178 CTTCATTTTC-TTTC
1 CTTC-TTTTCTTTTC
5271192 CTTCTTTTCTTTT-
1 CTTCTTTTCTTTTC
5271205 CTT-TTTTCT
1 CTTCTTTTCT
5271214 CTTATTTTCC
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
12 6 0.18
13 8 0.24
14 15 0.45
15 4 0.12
ACGTcount: A:0.04, C:0.24, G:0.00, T:0.72
Consensus pattern (14 bp):
CTTCTTTTCTTTTC
Found at i:5272029 original size:192 final size:194
Alignment explanation
Indices: 5271645--5272030 Score: 453
Period size: 192 Copynumber: 2.0 Consensus size: 194
5271635 GCCGCTTTAG
* *** *
5271645 TTAAATGGTAAAATTTTGATTTTAGTCCCTTCCAAATACAATAATTTAATGTAACCCTTTTCTTG
1 TTAAATGATAAAATTGCAATTTCAGTCCCTTCCAAATACAATAATTTAATGTAACCCTTTTCTTG
* *
5271710 CCTCATTGTTAGATGAAAAGTGGCCTTTCTCAAAAGTTGAAAATTTCGATTTAAACCATTTTAAT
66 CCTCATTGTTAGATGAAAAGT---CTTTCTCAAAAGATGAAAATTTCAATTTAAACCATTTTAAT
* * *
5271775 ACAAAATTTGTAGATTTGGTTGGCCAGAAAATTTGGGTACCCGAAAACCAAGAATTTTCTCCTTT
128 ACAAAATTTGTAGATTTGGTTGGCCACAAAAATGGGGTACCCGAAAACCAAGAATTTTCTCCTTT
5271840 GA
193 GA
** * *
5271842 TTAAATGATAAAATTGCAATTTCAGTCCCTTTTAAATATAATAATTTAATGTAA-CCTTTTTTTG
1 TTAAATGATAAAATTGCAATTTCAGTCCCTTCCAAATACAATAATTTAATGTAACCCTTTTCTTG
* * * *
5271906 CCTCCTTGTTA-AGTGAAAA-T-TATTCTCCAAAA-ATGAGATTTTCAATTTAAGCCATTTTAAT
66 CCTCATTGTTAGA-TGAAAAGTCT-TTCT-CAAAAGATGAAAATTTCAATTTAAACCATTTTAAT
* * * *
5271967 ACAAAATTTTTAGCTCTT-GTTGGCTACAAAAATGGGGTA-CCGAAAAACCTAGAATTTTCTCCT
128 ACAAAATTTGTAGAT-TTGGTTGGCCACAAAAATGGGGTACCCG-AAAACCAAGAATTTTCTCCT
5272030 T
191 T
5272031 CCCGCATAGC
Statistics
Matches: 162, Mismatches: 22, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
191 4 0.02
192 78 0.48
193 7 0.04
195 2 0.01
196 25 0.15
197 46 0.28
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.38
Consensus pattern (194 bp):
TTAAATGATAAAATTGCAATTTCAGTCCCTTCCAAATACAATAATTTAATGTAACCCTTTTCTTG
CCTCATTGTTAGATGAAAAGTCTTTCTCAAAAGATGAAAATTTCAATTTAAACCATTTTAATACA
AAATTTGTAGATTTGGTTGGCCACAAAAATGGGGTACCCGAAAACCAAGAATTTTCTCCTTTGA
Found at i:5273214 original size:30 final size:29
Alignment explanation
Indices: 5273178--5273288 Score: 84
Period size: 30 Copynumber: 3.8 Consensus size: 29
5273168 AAGCCTCCTA
5273178 AAATTTTTGAAAATTTTAATTAAGACTTGT
1 AAATTTTTGAAAATTTTAATTAAGACTT-T
* * * *
5273208 AAATTTTAG-AAATTCTT-ATTTAGCCCTTC
1 AAATTTTTGAAAATT-TTAATTAAG-ACTTT
* ** *
5273237 AAATTTTTAAAAAAATTAATTAA-ACCCTT
1 AAATTTTTGAAAATTTTAATTAAGA-CTTT
5273266 AAAGTTTTTGAAAATTTTAATTA
1 AAA-TTTTTGAAAATTTTAATTA
5273289 GATCCCTAAA
Statistics
Matches: 60, Mismatches: 15, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
29 24 0.40
30 36 0.60
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.44
Consensus pattern (29 bp):
AAATTTTTGAAAATTTTAATTAAGACTTT
Found at i:5273299 original size:30 final size:32
Alignment explanation
Indices: 5273252--5273314 Score: 78
Period size: 30 Copynumber: 2.0 Consensus size: 32
5273242 TTTAAAAAAA
5273252 TTAATTAAACCCTTAAAG-TT-TTTGAAAATT
1 TTAATTAAACCCTTAAAGCTTATTTGAAAATT
*
5273282 TTAATTAGATCCC-TAAAGCTTAATTTGAAAATT
1 TTAATTA-AACCCTTAAAGCTT-ATTTGAAAATT
5273315 GCAGGTTGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
30 12 0.43
31 6 0.21
33 10 0.36
ACGTcount: A:0.40, C:0.11, G:0.08, T:0.41
Consensus pattern (32 bp):
TTAATTAAACCCTTAAAGCTTATTTGAAAATT
Found at i:5284800 original size:30 final size:30
Alignment explanation
Indices: 5284757--5284822 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
5284747 TAAGGATTGT
*
5284757 ATCAAATTAGTCTCTATATTATTAAAAAAG
1 ATCAAATTAGTCTCTATACTATTAAAAAAG
* * *
5284787 ATCAATTTTGTCTCTGTACTATTAAAAATA-
1 ATCAAATTAGTCTCTATACTATTAAAAA-AG
5284817 ATCAAA
1 ATCAAA
5284823 AAAGTCTAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
30 29 0.97
31 1 0.03
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38
Consensus pattern (30 bp):
ATCAAATTAGTCTCTATACTATTAAAAAAG
Found at i:5293767 original size:12 final size:12
Alignment explanation
Indices: 5293723--5293769 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 12
5293713 AAATTAATAC
5293723 ATAA-TAAATTT
1 ATAATTAAATTT
* *
5293734 ATACTTTAATTT
1 ATAATTAAATTT
**
5293746 ATAAAAAAATTT
1 ATAATTAAATTT
5293758 ATAATTAAATTT
1 ATAATTAAATTT
5293770 TGATGCTGCT
Statistics
Matches: 27, Mismatches: 8, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
11 3 0.11
12 24 0.89
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (12 bp):
ATAATTAAATTT
Found at i:5296961 original size:68 final size:67
Alignment explanation
Indices: 5296803--5297133 Score: 236
Period size: 69 Copynumber: 5.0 Consensus size: 67
5296793 ATTTTAATCC
* * * *
5296803 TTGACTAGAAAATACGCTCATAACTAACTT-TTCCACTATTTTTATTAAAAAGTTAATTTTAATA
1 TTGACTAGGAAATACTCTCATAACTCACTTCTT-CACTATTTTCATT-AAAA-TTAATTTTAAT-
*
5296867 GT-ACA
62 CTCACA
* * *
5296872 TCGACTA-GAGAATATTAC-CATAACTCACTTCTTTACTATTTTCATTGAAAATTAATTTTAATC
1 TTGACTAGGA-AATACT-CTCATAACTCACTTCTTCACTATTTTCATT-AAAATTAATTTTAATC
*
5296935 TCATA
63 TCACA
* * * * * *
5296940 TTGACTAGGAAATACTCCCATAATTTACTTCTTCACTA-----A--AAAGTTAATTTTGATCCCA
1 TTGACTAGGAAATACTCTCATAACTCACTTCTTCACTATTTTCATTAAAATTAATTTTAATCTCA
*
5296998 TA
66 CA
* * * * * * *
5297000 TTGACTA-GAGAATACTCTTATAGCCCACTTCTTCATTATTTTTAATAAAATATTAGTTTTAATC
1 TTGACTAGGA-AATACTCTCATAACTCACTTCTTCACTA-TTTTCATTAAA-ATTAATTTTAATC
*
5297064 CCACA
63 TCACA
* * *
5297069 TTGACTAGCAAATACTATCATAATTCACTTCTTCACTATTTTCATTAAACATTAATTTTAATCTC
1 TTGACTAGGAAATACTCTCATAACTCACTTCTTCACTATTTTCATTAAA-ATTAATTTTAATCTC
5297134 TTAAATTTAG
Statistics
Matches: 204, Mismatches: 41, Indels: 35
0.73 0.15 0.12
Matches are distributed among these distances:
59 2 0.01
60 46 0.23
63 1 0.00
66 1 0.00
67 2 0.01
68 67 0.33
69 81 0.40
70 4 0.02
ACGTcount: A:0.35, C:0.18, G:0.06, T:0.40
Consensus pattern (67 bp):
TTGACTAGGAAATACTCTCATAACTCACTTCTTCACTATTTTCATTAAAATTAATTTTAATCTCA
CA
Found at i:5299549 original size:10 final size:10
Alignment explanation
Indices: 5299534--5299559 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
5299524 AATTTTGCCA
5299534 TTATATTAGC
1 TTATATTAGC
5299544 TTATATTAGC
1 TTATATTAGC
5299554 TTATAT
1 TTATAT
5299560 CTTTATGGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.54
Consensus pattern (10 bp):
TTATATTAGC
Found at i:5305023 original size:10 final size:9
Alignment explanation
Indices: 5305003--5305044 Score: 57
Period size: 10 Copynumber: 4.3 Consensus size: 9
5304993 GTGTAAATGT
5305003 AAAAATGAAA
1 AAAAAT-AAA
5305013 AAAATATAAA
1 AAAA-ATAAA
5305023 AAAAATAATA
1 AAAAATAA-A
5305033 AAAAATAAA
1 AAAAATAAA
5305042 AAA
1 AAA
5305045 TTGTGGGGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
9 8 0.27
10 20 0.67
11 2 0.07
ACGTcount: A:0.83, C:0.00, G:0.02, T:0.14
Consensus pattern (9 bp):
AAAAATAAA
Found at i:5305035 original size:19 final size:20
Alignment explanation
Indices: 5305003--5305044 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
5304993 GTGTAAATGT
*
5305003 AAAAATGAAAAAAATATAAA
1 AAAAATGAAAAAAAAATAAA
*
5305023 AAAAAT-AATAAAAAATAAA
1 AAAAATGAAAAAAAAATAAA
5305042 AAA
1 AAA
5305045 TTGTGGGGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.83, C:0.00, G:0.02, T:0.14
Consensus pattern (20 bp):
AAAAATGAAAAAAAAATAAA
Found at i:5305980 original size:14 final size:15
Alignment explanation
Indices: 5305959--5306002 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 15
5305949 TTTTTAAATA
5305959 TATAATTTTTTATTT
1 TATAATTTTTTATTT
* *
5305974 TAT-ATTTATTA-AT
1 TATAATTTTTTATTT
5305987 TATAATTTTTTATTT
1 TATAATTTTTTATTT
5306002 T
1 T
5306003 GCTAAATTTC
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
13 4 0.17
14 14 0.61
15 5 0.22
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TATAATTTTTTATTT
Found at i:5307764 original size:17 final size:16
Alignment explanation
Indices: 5307738--5307783 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
5307728 TAAAGGTGCA
*
5307738 ATTAAAAAATAAATTGT
1 ATTAATAAATAAATT-T
*
5307755 ATTAATAAATATATTT
1 ATTAATAAATAAATTT
*
5307771 TTTAATAAATAAA
1 ATTAATAAATAAA
5307784 AGTACAAGGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
16 12 0.48
17 13 0.52
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (16 bp):
ATTAATAAATAAATTT
Found at i:5308239 original size:25 final size:26
Alignment explanation
Indices: 5308185--5308243 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
5308175 ATAAAAAAAA
*
5308185 TATTAAAAAGTAATAAAAAAATTCTT
1 TATTAAAAAGTAATAAAAAAATTCTG
* *
5308211 TATTAAAAA-TAATTAAATATATT-TG
1 TATTAAAAAGTAA-TAAAAAAATTCTG
5308236 TATTAAAA
1 TATTAAAA
5308244 CGTTCAGTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
25 12 0.41
26 17 0.59
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (26 bp):
TATTAAAAAGTAATAAAAAAATTCTG
Found at i:5316102 original size:18 final size:18
Alignment explanation
Indices: 5316075--5316110 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
5316065 GAAAATATCA
* *
5316075 CAAAATAAAACAAAAATC
1 CAAAACAAAAAAAAAATC
5316093 CAAAACAAAAAAAAAATC
1 CAAAACAAAAAAAAAATC
5316111 AAATTACAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.75, C:0.17, G:0.00, T:0.08
Consensus pattern (18 bp):
CAAAACAAAAAAAAAATC
Found at i:5338643 original size:61 final size:61
Alignment explanation
Indices: 5338573--5338701 Score: 258
Period size: 61 Copynumber: 2.1 Consensus size: 61
5338563 ATTTTGCTAC
5338573 TATTTTAGAGTCATTTGCTTGCTAAGTTGCTATTATCTTAGTGTTATTTAAGTATAACATT
1 TATTTTAGAGTCATTTGCTTGCTAAGTTGCTATTATCTTAGTGTTATTTAAGTATAACATT
5338634 TATTTTAGAGTCATTTGCTTGCTAAGTTGCTATTATCTTAGTGTTATTTAAGTATAACATT
1 TATTTTAGAGTCATTTGCTTGCTAAGTTGCTATTATCTTAGTGTTATTTAAGTATAACATT
5338695 TATTTTA
1 TATTTTA
5338702 ATTTTTTAGT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 68 1.00
ACGTcount: A:0.26, C:0.09, G:0.14, T:0.50
Consensus pattern (61 bp):
TATTTTAGAGTCATTTGCTTGCTAAGTTGCTATTATCTTAGTGTTATTTAAGTATAACATT
Found at i:5340215 original size:19 final size:19
Alignment explanation
Indices: 5340191--5340233 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
5340181 TCTTTTTAAC
5340191 TAGTGATTATAT-ACATACA
1 TAGTGATTATATGA-ATACA
5340210 TAGTGATTATATGAATACA
1 TAGTGATTATATGAATACA
5340229 TAGTG
1 TAGTG
5340234 GCTAATATGC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 22 0.96
20 1 0.04
ACGTcount: A:0.40, C:0.07, G:0.16, T:0.37
Consensus pattern (19 bp):
TAGTGATTATATGAATACA
Found at i:5365139 original size:7 final size:7
Alignment explanation
Indices: 5365127--5365158 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
5365117 TTTAGTGGAC
5365127 GGTTTAG
1 GGTTTAG
5365134 GGTTTAG
1 GGTTTAG
5365141 GGTTTAG
1 GGTTTAG
5365148 GGTTTAG
1 GGTTTAG
5365155 GGTT
1 GGTT
5365159 AATGTCATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.12, C:0.00, G:0.44, T:0.44
Consensus pattern (7 bp):
GGTTTAG
Found at i:5365521 original size:25 final size:25
Alignment explanation
Indices: 5365492--5365542 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
5365482 TTTTAAAATG
5365492 ATGGTTTAAAAACTTAGGAATGGAA
1 ATGGTTTAAAAACTTAGGAATGGAA
5365517 ATGGTTTAAAAACTTAGGAATGGAA
1 ATGGTTTAAAAACTTAGGAATGGAA
5365542 A
1 A
5365543 AAGGATTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.45, C:0.04, G:0.24, T:0.27
Consensus pattern (25 bp):
ATGGTTTAAAAACTTAGGAATGGAA
Found at i:5365551 original size:26 final size:25
Alignment explanation
Indices: 5365497--5365552 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
5365487 AAATGATGGT
* *
5365497 TTAAAAACTTAGGAATGGAAATGGT
1 TTAAAAACTTAGGAATGGAAAAGGA
5365522 TTAAAAACTTAGGAATGGAAAAAGGA
1 TTAAAAACTTAGGAATGG-AAAAGGA
5365548 TTAAA
1 TTAAA
5365553 TTGTGAAACT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
25 18 0.64
26 10 0.36
ACGTcount: A:0.50, C:0.04, G:0.21, T:0.25
Consensus pattern (25 bp):
TTAAAAACTTAGGAATGGAAAAGGA
Found at i:5368355 original size:7 final size:7
Alignment explanation
Indices: 5368343--5368372 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
5368333 CAACAATTAT
5368343 TCCACCA
1 TCCACCA
5368350 TCCACCA
1 TCCACCA
5368357 TCCACCA
1 TCCACCA
5368364 TCCACCA
1 TCCACCA
5368371 TC
1 TC
5368373 TCTTATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.27, C:0.57, G:0.00, T:0.17
Consensus pattern (7 bp):
TCCACCA
Found at i:5389391 original size:21 final size:22
Alignment explanation
Indices: 5389367--5389407 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
5389357 GTCTAGAGGT
* *
5389367 GGTGTTGCGACATC-AGAGCTG
1 GGTGTTACAACATCAAGAGCTG
5389388 GGTGTTACAACATCAAGAGC
1 GGTGTTACAACATCAAGAGC
5389408 AATCCATTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.27, C:0.20, G:0.32, T:0.22
Consensus pattern (22 bp):
GGTGTTACAACATCAAGAGCTG
Found at i:5393436 original size:30 final size:32
Alignment explanation
Indices: 5393400--5393460 Score: 81
Period size: 30 Copynumber: 1.9 Consensus size: 32
5393390 TATCCATTGC
*
5393400 TTCTCTTCCATAT-AGAA-GTTAGATTTTTGT
1 TTCTCTTCCATATGAAAAGGTTAGATTTTTGT
*
5393430 TTCTCTTTCATATGGAAAAGGTTAGATTTTT
1 TTCTCTTCCATAT-GAAAAGGTTAGATTTTT
5393461 ACTTTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 12 0.46
32 3 0.12
33 11 0.42
ACGTcount: A:0.25, C:0.11, G:0.15, T:0.49
Consensus pattern (32 bp):
TTCTCTTCCATATGAAAAGGTTAGATTTTTGT
Found at i:5396898 original size:29 final size:29
Alignment explanation
Indices: 5396856--5396913 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
5396846 GCAGCGGTAC
5396856 AATAGTTCTCGAATAGTGTTACGCCAAGT
1 AATAGTTCTCGAATAGTGTTACGCCAAGT
*
5396885 AATAGTTCTTGAATAGTGTTACGCCAAGT
1 AATAGTTCTCGAATAGTGTTACGCCAAGT
5396914 TGAGTTGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.33
Consensus pattern (29 bp):
AATAGTTCTCGAATAGTGTTACGCCAAGT
Found at i:5401849 original size:6 final size:6
Alignment explanation
Indices: 5401838--5401875 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
5401828 GCAGAGCAGG
5401838 TGCCCC TGCCCC T---CC TGCCCC TGCCCC TGCCCC TGCCC
1 TGCCCC TGCCCC TGCCCC TGCCCC TGCCCC TGCCCC TGCCC
5401876 TTTACTCTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
3 3 0.10
6 26 0.90
ACGTcount: A:0.00, C:0.66, G:0.16, T:0.18
Consensus pattern (6 bp):
TGCCCC
Found at i:5401965 original size:14 final size:14
Alignment explanation
Indices: 5401943--5401979 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
5401933 ATGCTACCCC
5401943 TTCTCTCTTTATCT
1 TTCTCTCTTTATCT
* *
5401957 TTTTCTCTTTTTCT
1 TTCTCTCTTTATCT
5401971 TTCTCTCTT
1 TTCTCTCTT
5401980 GCTTTCCTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.03, C:0.27, G:0.00, T:0.70
Consensus pattern (14 bp):
TTCTCTCTTTATCT
Found at i:5420569 original size:28 final size:28
Alignment explanation
Indices: 5420529--5420585 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
5420519 TGTCCAAGCC
5420529 ACATGTGTATATGTTATAGATGCAAACT
1 ACATGTGTATATGTTATAGATGCAAACT
5420557 ACATGTGTATATGTTATAGATGCAAACT
1 ACATGTGTATATGTTATAGATGCAAACT
5420585 A
1 A
5420586 GTCCTAGCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.35
Consensus pattern (28 bp):
ACATGTGTATATGTTATAGATGCAAACT
Found at i:5424678 original size:21 final size:21
Alignment explanation
Indices: 5424652--5424710 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
5424642 AAGTGATTTA
5424652 ACTTATTTTTTATCTCACGCT
1 ACTTATTTTTTATCTCACGCT
5424673 ACTTA--TTTT-T-T-A-GCT
1 ACTTATTTTTTATCTCACGCT
5424688 ACTTATTTTTTATCTCACGCT
1 ACTTATTTTTTATCTCACGCT
5424709 AC
1 AC
5424711 AATATCATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
15 8 0.25
16 1 0.03
17 5 0.16
18 2 0.06
19 5 0.16
20 1 0.03
21 10 0.31
ACGTcount: A:0.20, C:0.22, G:0.05, T:0.53
Consensus pattern (21 bp):
ACTTATTTTTTATCTCACGCT
Found at i:5424690 original size:15 final size:15
Alignment explanation
Indices: 5424670--5424699 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5424660 TTTATCTCAC
5424670 GCTACTTATTTTTTA
1 GCTACTTATTTTTTA
5424685 GCTACTTATTTTTTA
1 GCTACTTATTTTTTA
5424700 TCTCACGCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.13, G:0.07, T:0.60
Consensus pattern (15 bp):
GCTACTTATTTTTTA
Found at i:5428054 original size:32 final size:32
Alignment explanation
Indices: 5428018--5428079 Score: 124
Period size: 32 Copynumber: 1.9 Consensus size: 32
5428008 TTAGCTACCA
5428018 AAAGGTTAACATTTTGCAAATGAATGGTGGCT
1 AAAGGTTAACATTTTGCAAATGAATGGTGGCT
5428050 AAAGGTTAACATTTTGCAAATGAATGGTGG
1 AAAGGTTAACATTTTGCAAATGAATGGTGG
5428080 TGATTATAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.08, G:0.26, T:0.31
Consensus pattern (32 bp):
AAAGGTTAACATTTTGCAAATGAATGGTGGCT
Found at i:5428198 original size:28 final size:27
Alignment explanation
Indices: 5428115--5428206 Score: 82
Period size: 28 Copynumber: 3.4 Consensus size: 27
5428105 ACCAAAAGGA
* * *
5428115 TATGACTTTTCTGAACAATATTTAGTGT
1 TATGACCTTTCTAAACAATACTTAGT-T
* * * *
5428143 TTTGACCTTT-TCAA-AATAC-CACTT
1 TATGACCTTTCTAAACAATACTTAGTT
5428167 TATGACCTTTCTAAACAATACTTAGTAT
1 TATGACCTTTCTAAACAATACTTAGT-T
5428195 TATGACCTTTCT
1 TATGACCTTTCT
5428207 GAAATGACAC
Statistics
Matches: 50, Mismatches: 10, Indels: 8
0.74 0.15 0.12
Matches are distributed among these distances:
24 10 0.20
25 5 0.10
26 9 0.18
27 5 0.10
28 21 0.42
ACGTcount: A:0.29, C:0.18, G:0.09, T:0.43
Consensus pattern (27 bp):
TATGACCTTTCTAAACAATACTTAGTT
Found at i:5429159 original size:3 final size:3
Alignment explanation
Indices: 5429151--5429180 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
5429141 CATTGCTTAT
5429151 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
5429181 CCCTCTCCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:5440763 original size:22 final size:23
Alignment explanation
Indices: 5440710--5440765 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
5440700 TTAAATTAAA
* * *
5440710 ATTAAAATTAAAATTATTTTTTT
1 ATTAAAATTAAAACTATATTGTT
*
5440733 AATAAAATTAAAACTA-ATTGTT
1 ATTAAAATTAAAACTATATTGTT
5440755 ATTAAAATTAA
1 ATTAAAATTAA
5440766 TTGTTAGTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATTAAAATTAAAACTATATTGTT
Found at i:5440778 original size:16 final size:16
Alignment explanation
Indices: 5440741--5440780 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
5440731 TTAATAAAAT
* *
5440741 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
5440757 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
5440773 TAAAATTA
1 TAAAATTA
5440781 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:5440849 original size:9 final size:9
Alignment explanation
Indices: 5440837--5440864 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
5440827 TTTATCAAAT
5440837 TATTAATTG
1 TATTAATTG
5440846 TATTAATTG
1 TATTAATTG
5440855 TATTAATTG
1 TATTAATTG
5440864 T
1 T
5440865 TGTAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:5441001 original size:22 final size:24
Alignment explanation
Indices: 5440961--5441004 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
5440951 AAATAAACTT
5440961 AAAATAAAAAACTATTATATTTTA
1 AAAATAAAAAACTATTATATTTTA
5440985 AAAATAAAAAA-TA-TATATTT
1 AAAATAAAAAACTATTATATTT
5441005 AATATTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 2 0.10
24 11 0.55
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
AAAATAAAAAACTATTATATTTTA
Found at i:5442221 original size:25 final size:25
Alignment explanation
Indices: 5442180--5442236 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
5442170 ACAATCCATG
** * *
5442180 TAAATCATGTATTTCATGTAACTTT
1 TAAATCATGTAAATCATATAACATT
5442205 TAAATCATGTAAATCATATAACATT
1 TAAATCATGTAAATCATATAACATT
*
5442230 TATATCA
1 TAAATCA
5442237 ATTCTTTCCT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.42
Consensus pattern (25 bp):
TAAATCATGTAAATCATATAACATT
Found at i:5442505 original size:26 final size:23
Alignment explanation
Indices: 5442497--5442565 Score: 104
Period size: 23 Copynumber: 3.0 Consensus size: 23
5442487 CCGAGCTAAT
5442497 AAACGGTAAGCTCTATCGAGCTG
1 AAACGGTAAGCTCTATCGAGCTG
* *
5442520 AAACGGTAAGCTCCATAGAGCTG
1 AAACGGTAAGCTCTATCGAGCTG
5442543 AAACGGTAAGCTC-ATACGAGCTG
1 AAACGGTAAGCTCTAT-CGAGCTG
5442566 TGGTGAGTCC
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
22 2 0.05
23 40 0.95
ACGTcount: A:0.33, C:0.22, G:0.26, T:0.19
Consensus pattern (23 bp):
AAACGGTAAGCTCTATCGAGCTG
Found at i:5446365 original size:28 final size:28
Alignment explanation
Indices: 5446318--5446393 Score: 98
Period size: 28 Copynumber: 2.7 Consensus size: 28
5446308 GCTAACATTA
* * *
5446318 CTCACATAAGCTGGCTTTTAAGGATTTG
1 CTCACACAAGCTGACATTTAAGGATTTG
* *
5446346 TTCATACAAGCTGACATTTAAGGATTTG
1 CTCACACAAGCTGACATTTAAGGATTTG
*
5446374 CTCACACAAGTTGACATTTA
1 CTCACACAAGCTGACATTTA
5446394 TGAATTGATG
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.34
Consensus pattern (28 bp):
CTCACACAAGCTGACATTTAAGGATTTG
Found at i:5449101 original size:15 final size:15
Alignment explanation
Indices: 5449081--5449112 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
5449071 CATTAAACTA
5449081 TTAATAAGTTTAAGT
1 TTAATAAGTTTAAGT
5449096 TTAATAAGTTTAAGT
1 TTAATAAGTTTAAGT
5449111 TT
1 TT
5449113 TGGTCACTTA
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:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (15 bp):
TTAATAAGTTTAAGT
Found at i:5449164 original size:30 final size:30
Alignment explanation
Indices: 5449130--5449196 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 30
5449120 TTAACTTTAA
*
5449130 AAAGTTACAAA-ATAGTTACTGAACTATTTG
1 AAAGTTACAAATA-AGTCACTGAACTATTTG
* **
5449160 AAAGTTTTCATTTAAGTCACTGAACTATTTG
1 AAAG-TTACAAATAAGTCACTGAACTATTTG
5449191 AAAGTT
1 AAAGTT
5449197 TTTATTTAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
30 6 0.19
31 24 0.77
32 1 0.03
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.37
Consensus pattern (30 bp):
AAAGTTACAAATAAGTCACTGAACTATTTG
Found at i:5449183 original size:31 final size:31
Alignment explanation
Indices: 5449147--5449209 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
5449137 CAAAATAGTT
5449147 ACTGAACTATTTGAAAGTTTTCATTTAAGTC
1 ACTGAACTATTTGAAAGTTTTCATTTAAGTC
*
5449178 ACTGAACTATTTGAAAGTTTTTATTTAAGTC
1 ACTGAACTATTTGAAAGTTTTCATTTAAGTC
5449209 A
1 A
5449210 TTGGTTTGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.33, C:0.11, G:0.13, T:0.43
Consensus pattern (31 bp):
ACTGAACTATTTGAAAGTTTTCATTTAAGTC
Found at i:5449348 original size:36 final size:36
Alignment explanation
Indices: 5449301--5449374 Score: 139
Period size: 36 Copynumber: 2.1 Consensus size: 36
5449291 GATCAATACT
5449301 CATTAATGAGTAGAAGAACATACCTTAGAATAAAGC
1 CATTAATGAGTAGAAGAACATACCTTAGAATAAAGC
*
5449337 CATTAATGAGTAGAAGAACATACCTTAGAATCAAGC
1 CATTAATGAGTAGAAGAACATACCTTAGAATAAAGC
5449373 CA
1 CA
5449375 ATGTGACAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.46, C:0.16, G:0.16, T:0.22
Consensus pattern (36 bp):
CATTAATGAGTAGAAGAACATACCTTAGAATAAAGC
Found at i:5453764 original size:11 final size:11
Alignment explanation
Indices: 5453748--5453772 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5453738 TTAGAGAATT
5453748 TAGCCTATAAA
1 TAGCCTATAAA
5453759 TAGCCTATAAA
1 TAGCCTATAAA
5453770 TAG
1 TAG
5453773 GTTCTTTGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.28
Consensus pattern (11 bp):
TAGCCTATAAA
Found at i:5459147 original size:88 final size:88
Alignment explanation
Indices: 5458998--5459173 Score: 307
Period size: 88 Copynumber: 2.0 Consensus size: 88
5458988 ACCAGTCCAC
** *
5458998 TGCCTGCAGCTATATAGTGATCCCTTTCCTACGATTTCCATTCATTCTGCTTATTATTATCTAAA
1 TGCCTGCAGCTATATAGCAATCCCTTTCCTACGATTTCCATTCATTCTACTTATTATTATCTAAA
5459063 CTCTAGATTACAAGTGATGCATA
66 CTCTAGATTACAAGTGATGCATA
* *
5459086 TGCCTGCAGCTATATGGCAATCCCTTTCCTATGATTTCCATTCATTCTACTTATTATTATCTAAA
1 TGCCTGCAGCTATATAGCAATCCCTTTCCTACGATTTCCATTCATTCTACTTATTATTATCTAAA
5459151 CTCTAGATTACAAGTGATGCATA
66 CTCTAGATTACAAGTGATGCATA
5459174 CTAATTGTTG
Statistics
Matches: 83, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
88 83 1.00
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.39
Consensus pattern (88 bp):
TGCCTGCAGCTATATAGCAATCCCTTTCCTACGATTTCCATTCATTCTACTTATTATTATCTAAA
CTCTAGATTACAAGTGATGCATA
Found at i:5462182 original size:2 final size:2
Alignment explanation
Indices: 5462175--5462202 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5462165 TATGTCTGCT
5462175 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
5462203 AGGGAGAGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:5462211 original size:2 final size:2
Alignment explanation
Indices: 5462206--5462230 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5462196 GTGTGTGAGG
5462206 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
5462231 CAGGTTTTCT
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:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5477547 original size:74 final size:75
Alignment explanation
Indices: 5477449--5477590 Score: 225
Period size: 74 Copynumber: 1.9 Consensus size: 75
5477439 TAAAAATTAT
* *
5477449 AAATATTGGTCAGTTAATTTTACTATTATACCAA-AAAAAAATCACATCAACATGATTTAACTTA
1 AAATATTGGTCAGTTAATTTTACTATTATACCAAGAAAAAAATCACATCAACATAATTTAACATA
5477513 TAAAATAAGC
66 TAAAATAAGC
* *
5477523 AAATATTGG-CAGGTTAATTTTACTATTATACCAAGAAAAAAATTACGTCAACATAATTTAACAT
1 AAATATTGGTCA-GTTAATTTTACTATTATACCAAGAAAAAAATCACATCAACATAATTTAACAT
5477587 ATAA
65 ATAA
5477591 GTGACTCGAT
Statistics
Matches: 62, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
73 2 0.03
74 31 0.50
75 29 0.47
ACGTcount: A:0.47, C:0.13, G:0.08, T:0.32
Consensus pattern (75 bp):
AAATATTGGTCAGTTAATTTTACTATTATACCAAGAAAAAAATCACATCAACATAATTTAACATA
TAAAATAAGC
Found at i:5492255 original size:5 final size:5
Alignment explanation
Indices: 5492245--5492271 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
5492235 AGCACTGCCT
5492245 AACCC AACCC AACCC AACCC AACCC AA
1 AACCC AACCC AACCC AACCC AACCC AA
5492272 AGTTAGGTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.44, C:0.56, G:0.00, T:0.00
Consensus pattern (5 bp):
AACCC
Found at i:5492687 original size:59 final size:59
Alignment explanation
Indices: 5492620--5492737 Score: 236
Period size: 59 Copynumber: 2.0 Consensus size: 59
5492610 CAACATAAGA
5492620 ATGGTGTCATGTGATAACATAACATTCAGAAGCAGACACTATTTGATAATTTGAATTTT
1 ATGGTGTCATGTGATAACATAACATTCAGAAGCAGACACTATTTGATAATTTGAATTTT
5492679 ATGGTGTCATGTGATAACATAACATTCAGAAGCAGACACTATTTGATAATTTGAATTTT
1 ATGGTGTCATGTGATAACATAACATTCAGAAGCAGACACTATTTGATAATTTGAATTTT
5492738 GGCCCACTTT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.36
Consensus pattern (59 bp):
ATGGTGTCATGTGATAACATAACATTCAGAAGCAGACACTATTTGATAATTTGAATTTT
Found at i:5496503 original size:27 final size:26
Alignment explanation
Indices: 5496460--5496510 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 26
5496450 AGAAAAACAA
5496460 AGAGAAGAAGAAGAAAAGAGAATTTG
1 AGAGAAGAAGAAGAAAAGAGAATTTG
5496486 AGAGAGAGAAG-AGAAAAAGAGAATT
1 AGAGA-AGAAGAAG-AAAAGAGAATT
5496511 CTAAAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.59, C:0.00, G:0.31, T:0.10
Consensus pattern (26 bp):
AGAGAAGAAGAAGAAAAGAGAATTTG
Found at i:5499021 original size:3 final size:3
Alignment explanation
Indices: 5499013--5499037 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
5499003 TATATGAGGA
5499013 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
5499038 GATTTATTTG
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5499684 original size:14 final size:14
Alignment explanation
Indices: 5499658--5499701 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
5499648 TAAGGTTTGG
5499658 TTAATTAAATTTTAA
1 TTAATT-AATTTTAA
*
5499673 TTAATTAATTTTGA
1 TTAATTAATTTTAA
*
5499687 TTAATTAAGTTTAA
1 TTAATTAATTTTAA
5499701 T
1 T
5499702 CCAAGTATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 20 0.77
15 6 0.23
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (14 bp):
TTAATTAATTTTAA
Found at i:5501433 original size:41 final size:42
Alignment explanation
Indices: 5501388--5501562 Score: 121
Period size: 41 Copynumber: 4.3 Consensus size: 42
5501378 GATTCACTGG
**
5501388 CACTTTA-CCTGATAGGCTTATAGTTTAATTCAGTTCACCGA
1 CACTTTAGCCTGATAGGCTTATAGCCTAATTCAGTTCACCGA
* * * *
5501429 CAC-TTAGCCTGTTAGGCTTGTAGCCTGATTCAGTTCACCGG
1 CACTTTAGCCTGATAGGCTTATAGCCTAATTCAGTTCACCGA
* * * * * *
5501470 CAC-TTAGCCTGCTAGACGTATAGTCC-GATTCAATTCACCGG
1 CACTTTAGCCTGATAGGCTTATAG-CCTAATTCAGTTCACCGA
* * * * * *
5501511 CA-TTTAGCCTGCTAGACGTATAGTCC-GATTCAATTCACCGG
1 CACTTTAGCCTGATAGGCTTATAG-CCTAATTCAGTTCACCGA
5501552 CAC-TTAGCCTG
1 CACTTTAGCCTG
5501563 CTAGACGTAT
Statistics
Matches: 119, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
40 3 0.03
41 114 0.96
42 2 0.02
ACGTcount: A:0.23, C:0.27, G:0.19, T:0.31
Consensus pattern (42 bp):
CACTTTAGCCTGATAGGCTTATAGCCTAATTCAGTTCACCGA
Found at i:5501589 original size:41 final size:41
Alignment explanation
Indices: 5501415--5501576 Score: 236
Period size: 41 Copynumber: 4.0 Consensus size: 41
5501405 TTATAGTTTA
* * * * * *
5501415 ATTCAGTTCACCGACACTTAGCCTGTTAGGCTTGTAG-CCTG
1 ATTCAATTCACCGGCACTTAGCCTGCTAGACGTATAGTCC-G
*
5501456 ATTCAGTTCACCGGCACTTAGCCTGCTAGACGTATAGTCCG
1 ATTCAATTCACCGGCACTTAGCCTGCTAGACGTATAGTCCG
*
5501497 ATTCAATTCACCGGCATTTAGCCTGCTAGACGTATAGTCCG
1 ATTCAATTCACCGGCACTTAGCCTGCTAGACGTATAGTCCG
5501538 ATTCAATTCACCGGCACTTAGCCTGCTAGACGTATAGTC
1 ATTCAATTCACCGGCACTTAGCCTGCTAGACGTATAGTC
5501577 TGAATAATTT
Statistics
Matches: 112, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
41 110 0.98
42 2 0.02
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (41 bp):
ATTCAATTCACCGGCACTTAGCCTGCTAGACGTATAGTCCG
Found at i:5514339 original size:29 final size:29
Alignment explanation
Indices: 5514307--5514369 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
5514297 ATAATGTATA
*
5514307 ATAAACATTAAATAAA-AAATTAAAAATTT
1 ATAAACA-TAAATAAATAAACTAAAAATTT
* * *
5514336 ATAAACATATATAAATGAACTAAAATTTT
1 ATAAACATAAATAAATAAACTAAAAATTT
5514365 ATAAA
1 ATAAA
5514370 GTTGTAATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 7 0.24
29 22 0.76
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.32
Consensus pattern (29 bp):
ATAAACATAAATAAATAAACTAAAAATTT
Found at i:5517443 original size:81 final size:81
Alignment explanation
Indices: 5517334--5517758 Score: 554
Period size: 81 Copynumber: 5.2 Consensus size: 81
5517324 CTTCGACATA
* * ** * * *
5517334 TATTCATTCAAGGATTAAAAGAAGCATTACAAACTAGTATCATACAAGACGGGATTGTTAATGTT
1 TATTCATCCAAGGGTTAAAAGATCCATTACAAACTAGTATCATACAGGACAGGATTCTTAATGTT
5517399 TTTGACATATAACTAG
66 TTTGACATATAACTAG
* * * * *
5517415 CATTCATCCGAGGGTTAAAAGATCCATTACGAGCTAGTATCATACAGGTCAGGATTCTTAATGTT
1 TATTCATCCAAGGGTTAAAAGATCCATTACAAACTAGTATCATACAGGACAGGATTCTTAATGTT
*
5517480 TTTCGACATATAACTTG
66 TTT-GACATATAACTAG
*
5517497 TATTCATCCAAGGGTTAAAAGATCCATTACAAAATAGTATCATACAGGTA-AGGATTCTTAATG-
1 TATTCATCCAAGGGTTAAAAGATCCATTACAAACTAGTATCATACAGG-ACAGGATTCTTAATGT
* * *
5517560 ATTTCATCGTATAACTCA-
65 TTTTGA-CATATAACT-AG
*
5517578 TATTCATCCAAGGGTTAAAAGATCCATTACAAACTAGTATCATACAGGACATGATTCTTAATGTT
1 TATTCATCCAAGGGTTAAAAGATCCATTACAAACTAGTATCATACAGGACAGGATTCTTAATGTT
** *
5517643 TTCAACGTATAACTCA-
66 TTTGACATATAACT-AG
* *
5517659 TATTCATCGAA-GGTTAAAAGATCCATTACAAACTAGTATCATACAGGACAGGATTCTTAATGCT
1 TATTCATCCAAGGGTTAAAAGATCCATTACAAACTAGTATCATACAGGACAGGATTCTTAATGTT
*
5517723 TTTGACATATAACTCG
66 TTTGACATATAACTAG
5517739 TATTCATCCAAGGGTTAAAA
1 TATTCATCCAAGGGTTAAAA
5517759 AAGTTACCTT
Statistics
Matches: 300, Mismatches: 36, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
80 74 0.25
81 155 0.52
82 71 0.24
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.32
Consensus pattern (81 bp):
TATTCATCCAAGGGTTAAAAGATCCATTACAAACTAGTATCATACAGGACAGGATTCTTAATGTT
TTTGACATATAACTAG
Found at i:5517575 original size:163 final size:162
Alignment explanation
Indices: 5517333--5517758 Score: 572
Period size: 163 Copynumber: 2.6 Consensus size: 162
5517323 TCTTCGACAT
* * ** * * * *
5517333 ATATTCATTCAAGGATTAAAAGAAGCATTACAAACTAGTATCATACAAGACGGGATTGTTAATGT
1 ATATTCATCCAAGGGTTAAAAGATCCATTACAAACTAGTATCATACAGGACAGGATTCTTAATGC
* * * *
5517398 TTTTGACATATAACTAGCATTCATCCGAGGGTTAAAAGATCCATTACGAGCTAGTATCATACAGG
66 TTTTGACATATAACTAGTATTCATCCAAGGGTTAAAAGATCCATTACAAACTAGTATCATACAGG
* * *
5517463 TCAGGATTCTTAATGTTTTTCGACATATAACTT
131 ACAGGATTCTTAATG-TTTTCAACATATAACTC
* *
5517496 GTATTCATCCAAGGGTTAAAAGATCCATTACAAAATAGTATCATACAGGTA-AGGATTCTTAATG
1 ATATTCATCCAAGGGTTAAAAGATCCATTACAAACTAGTATCATACAGG-ACAGGATTCTTAATG
* * *
5517560 -ATTTCATCGTATAACTCA-TATTCATCCAAGGGTTAAAAGATCCATTACAAACTAGTATCATAC
65 CTTTTGA-CATATAACT-AGTATTCATCCAAGGGTTAAAAGATCCATTACAAACTAGTATCATAC
* *
5517623 AGGACATGATTCTTAATGTTTTCAACGTATAACTC
128 AGGACAGGATTCTTAATGTTTTCAACATATAACTC
*
5517658 ATATTCATCGAA-GGTTAAAAGATCCATTACAAACTAGTATCATACAGGACAGGATTCTTAATGC
1 ATATTCATCCAAGGGTTAAAAGATCCATTACAAACTAGTATCATACAGGACAGGATTCTTAATGC
*
5517722 TTTTGACATATAACTCGTATTCATCCAAGGGTTAAAA
66 TTTTGACATATAACTAGTATTCATCCAAGGGTTAAAA
5517759 AAGTTACCTT
Statistics
Matches: 229, Mismatches: 28, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
160 1 0.00
161 76 0.33
162 32 0.14
163 118 0.52
164 2 0.01
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (162 bp):
ATATTCATCCAAGGGTTAAAAGATCCATTACAAACTAGTATCATACAGGACAGGATTCTTAATGC
TTTTGACATATAACTAGTATTCATCCAAGGGTTAAAAGATCCATTACAAACTAGTATCATACAGG
ACAGGATTCTTAATGTTTTCAACATATAACTC
Found at i:5526332 original size:4 final size:4
Alignment explanation
Indices: 5526323--5526351 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
5526313 CTTATAATTT
5526323 ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
5526352 ATTTAGTCGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:5527500 original size:6 final size:6
Alignment explanation
Indices: 5527489--5527513 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
5527479 TGAAATTAAC
5527489 CATGCT CATGCT CATGCT CATGCT C
1 CATGCT CATGCT CATGCT CATGCT C
5527514 CTGAACCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.36, G:0.16, T:0.32
Consensus pattern (6 bp):
CATGCT
Found at i:5530063 original size:4 final size:4
Alignment explanation
Indices: 5530054--5530086 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
5530044 GATTTACAGG
5530054 TACA TACA TACA TACA TACA TACA TACA TACA T
1 TACA TACA TACA TACA TACA TACA TACA TACA T
5530087 TTTGTTTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.27
Consensus pattern (4 bp):
TACA
Found at i:5535275 original size:12 final size:12
Alignment explanation
Indices: 5535260--5535310 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
5535250 ATTAGTTTAA
*
5535260 TATTTTAATTAT
1 TATTTTCATTAT
*
5535272 TATTATCATTAT
1 TATTTTCATTAT
* *
5535284 TATTGTT-ACTAC
1 TATT-TTCATTAT
5535296 TATTTTCATTAT
1 TATTTTCATTAT
5535308 TAT
1 TAT
5535311 CAATATTTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
11 2 0.07
12 27 0.90
13 1 0.03
ACGTcount: A:0.29, C:0.08, G:0.02, T:0.61
Consensus pattern (12 bp):
TATTTTCATTAT
Found at i:5535330 original size:33 final size:32
Alignment explanation
Indices: 5535269--5535340 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 32
5535259 ATATTTTAAT
* ** *
5535269 TATTATTATCATTATTATTGTTACTACTATTT
1 TATTATTATCAATATTATTACTACTACTATTA
* *
5535301 TCATTATTATCAATATTTTTACTATTACTATTA
1 T-ATTATTATCAATATTATTACTACTACTATTA
5535334 TATTATT
1 TATTATT
5535341 CGTTTGTATA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
32 7 0.21
33 26 0.79
ACGTcount: A:0.31, C:0.10, G:0.01, T:0.58
Consensus pattern (32 bp):
TATTATTATCAATATTATTACTACTACTATTA
Found at i:5546289 original size:45 final size:45
Alignment explanation
Indices: 5546217--5546302 Score: 127
Period size: 45 Copynumber: 1.9 Consensus size: 45
5546207 CTTGGTAGAT
* * *
5546217 TCAGTACATAGTAACCACCTTATTAATCAATGATGTCCGGTGGAA
1 TCAGCACATAGCAACCACCTTACTAATCAATGATGTCCGGTGGAA
* *
5546262 TCAGCACATAGCAACTACCTTACTAATCAATGATGTTCGGT
1 TCAGCACATAGCAACCACCTTACTAATCAATGATGTCCGGT
5546303 TCACATAGTA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (45 bp):
TCAGCACATAGCAACCACCTTACTAATCAATGATGTCCGGTGGAA
Found at i:5546363 original size:51 final size:50
Alignment explanation
Indices: 5546299--5546494 Score: 187
Period size: 51 Copynumber: 3.9 Consensus size: 50
5546289 CAATGATGTT
* * *
5546299 CGGTTCACATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCA-TACCATC
* * * ** * *
5546350 CGATACACGTAGTATCCTGCACATAGTACTATACACGTGATTGAAACTATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGA-CCATACCATC
* ** * * ** *
5546401 CGGTACGCAAAGTAGCCTACACATAGTACTACACATGCAACC-TATCATTC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATACCA-TC
*
5546451 CGGTACACGTAGTAGCCTGCACATAGCACTACACACGTGACCAT
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAT
5546495 CATTTTCACT
Statistics
Matches: 109, Mismatches: 33, Indels: 6
0.74 0.22 0.04
Matches are distributed among these distances:
49 2 0.02
50 36 0.33
51 70 0.64
52 1 0.01
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.23
Consensus pattern (50 bp):
CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATACCATC
Found at i:5551350 original size:34 final size:36
Alignment explanation
Indices: 5551311--5551383 Score: 96
Period size: 36 Copynumber: 2.1 Consensus size: 36
5551301 TTATTCTAAA
5551311 TTTTTTATAACATTTAA-AA-TTTGTCTATACTTTT
1 TTTTTTATAACATTTAATAATTTTGTCTATACTTTT
** * *
5551345 TTTTTTATAATTTTTAATAATTTTTTCTATAGTTTT
1 TTTTTTATAACATTTAATAATTTTGTCTATACTTTT
5551381 TTT
1 TTT
5551384 ATAAATTTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
34 15 0.45
35 2 0.06
36 16 0.48
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.66
Consensus pattern (36 bp):
TTTTTTATAACATTTAATAATTTTGTCTATACTTTT
Found at i:5551370 original size:12 final size:11
Alignment explanation
Indices: 5551344--5551392 Score: 55
Period size: 12 Copynumber: 4.4 Consensus size: 11
5551334 TCTATACTTT
5551344 TTTTTTTATAA
1 TTTTTTTATAA
*
5551355 -TTTTTAATAA
1 TTTTTTTATAA
*
5551365 TTTTTTCTATAG
1 TTTTTT-TATAA
5551377 TTTTTTTATAAA
1 TTTTTTTAT-AA
5551389 TTTT
1 TTTT
5551393 GTAATATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
10 9 0.29
11 8 0.26
12 14 0.45
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (11 bp):
TTTTTTTATAA
Found at i:5551479 original size:9 final size:9
Alignment explanation
Indices: 5551428--5551486 Score: 50
Period size: 9 Copynumber: 6.4 Consensus size: 9
5551418 ACATTTAAAT
5551428 ATTTTCTATA
1 ATTTT-TATA
5551438 ATTTTTTATA
1 A-TTTTTATA
5551448 ATTATTTATA
1 ATT-TTTATA
* *
5551458 A-ATTTCT-
1 ATTTTTATA
*
5551465 ATTTTTATG
1 ATTTTTATA
5551474 ATTTTTATA
1 ATTTTTATA
5551483 ATTT
1 ATTT
5551487 ATATTTTTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
7 1 0.03
8 8 0.20
9 14 0.35
10 13 0.32
11 4 0.10
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.64
Consensus pattern (9 bp):
ATTTTTATA
Found at i:5551491 original size:24 final size:26
Alignment explanation
Indices: 5551440--5551501 Score: 83
Period size: 24 Copynumber: 2.5 Consensus size: 26
5551430 TTTCTATAAT
*
5551440 TTTTTATAATTATTTATAAATTTCTA
1 TTTTTATAATTATTTATAAATTTATA
*
5551466 TTTTTATGATT-TTTAT-AATTTATA
1 TTTTTATAATTATTTATAAATTTATA
*
5551490 TTTTTAAAATTA
1 TTTTTATAATTA
5551502 GATTTTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
24 16 0.52
25 5 0.16
26 10 0.32
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (26 bp):
TTTTTATAATTATTTATAAATTTATA
Found at i:5551492 original size:15 final size:16
Alignment explanation
Indices: 5551468--5551508 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 16
5551458 AATTTCTATT
*
5551468 TTTATGATTTTTATAA
1 TTTATGATTTTTAAAA
5551484 TTTAT-ATTTTTAAAA
1 TTTATGATTTTTAAAA
5551499 -TTA-GATTTTT
1 TTTATGATTTTT
5551509 TTTAAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 9 0.39
15 9 0.39
16 5 0.22
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (16 bp):
TTTATGATTTTTAAAA
Found at i:5553244 original size:21 final size:21
Alignment explanation
Indices: 5553218--5553409 Score: 102
Period size: 21 Copynumber: 9.1 Consensus size: 21
5553208 CCGAAGGCTG
*
5553218 AACAGAAGCTCATGAGAGCTA
1 AACAGAAGCTCATAAGAGCTA
* * * * *
5553239 AACAGAAACCCATAAGGGTTG
1 AACAGAAGCTCATAAGAGCTA
* *
5553260 AACAGGAGCTCGTAAGAGCTA
1 AACAGAAGCTCATAAGAGCTA
* * *
5553281 AAC-GAAAACTCATATGAGTTGA
1 AACAG-AAGCTCATAAGAGCT-A
*
5553303 AACAGAAGCTCATAAGAGCTG
1 AACAGAAGCTCATAAGAGCTA
** * * * *
5553324 AATGGAAACTCATAATAGTTG
1 AACAGAAGCTCATAAGAGCTA
*
5553345 AACAGAAGCTCA-ATAGAGCTG
1 AACAGAAGCTCATA-AGAGCTA
* * *
5553366 AACAAAAACTCATATGAG-TCA
1 AACAGAAGCTCATAAGAGCT-A
* * *
5553387 AATAGAAGCTCGTGAGAGCTA
1 AACAGAAGCTCATAAGAGCTA
5553408 AA
1 AA
5553410 TGGAAAGTAA
Statistics
Matches: 122, Mismatches: 42, Indels: 14
0.69 0.24 0.08
Matches are distributed among these distances:
20 3 0.02
21 100 0.82
22 18 0.15
23 1 0.01
ACGTcount: A:0.44, C:0.17, G:0.22, T:0.18
Consensus pattern (21 bp):
AACAGAAGCTCATAAGAGCTA
Found at i:5553264 original size:42 final size:42
Alignment explanation
Indices: 5553216--5553409 Score: 185
Period size: 42 Copynumber: 4.6 Consensus size: 42
5553206 GCCCGAAGGC
* * *
5553216 TGAACAGAAGCTCATGAGAGCTAAACAGAAACCCATAAGGGT
1 TGAACAGAAGCTCATAAGAGCTAAACAGAAACTCATAAGAGT
* * *
5553258 TGAACAGGAGCTCGTAAGAGCTAAAC-GAAAACTCATATGAGT
1 TGAACAGAAGCTCATAAGAGCTAAACAG-AAACTCATAAGAGT
* ** *
5553300 TGAAACAGAAGCTCATAAGAGCTGAATGGAAACTCATAATAGT
1 TG-AACAGAAGCTCATAAGAGCTAAACAGAAACTCATAAGAGT
* * *
5553343 TGAACAGAAGCTCA-ATAGAGCTGAACAAAAACTCATATGAGT
1 TGAACAGAAGCTCATA-AGAGCTAAACAGAAACTCATAAGAGT
** * * *
5553385 CAAATAGAAGCTCGTGAGAGCTAAA
1 TGAACAGAAGCTCATAAGAGCTAAA
5553410 TGGAAAGTAA
Statistics
Matches: 124, Mismatches: 23, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
41 2 0.02
42 87 0.70
43 34 0.27
44 1 0.01
ACGTcount: A:0.43, C:0.16, G:0.22, T:0.18
Consensus pattern (42 bp):
TGAACAGAAGCTCATAAGAGCTAAACAGAAACTCATAAGAGT
Found at i:5553363 original size:85 final size:84
Alignment explanation
Indices: 5553218--5553415 Score: 245
Period size: 85 Copynumber: 2.3 Consensus size: 84
5553208 CCGAAGGCTG
** * * *
5553218 AACAGAAGCTCATGAGAGCTAAACAGAAACCCATAAGGGTTGAACAGGAGCTCGTAAGAGCTAAA
1 AACAGAAGCTCATGAGAGCTAAATGGAAACCCATAAGAGTTGAACAGAAGCTCATAAGAGCTAAA
* *
5553283 CGAAAACTCATATGAGTTGA
66 CAAAAACTCATATGAG-TCA
* * * * *
5553303 AACAGAAGCTCATAAGAGCTGAATGGAAACTCATAATAGTTGAACAGAAGCTCA-ATAGAGCTGA
1 AACAGAAGCTCATGAGAGCTAAATGGAAACCCATAAGAGTTGAACAGAAGCTCATA-AGAGCTAA
5553367 ACAAAAACTCATATGAGTCA
65 ACAAAAACTCATATGAGTCA
* *
5553387 AATAGAAGCTCGTGAGAGCTAAATGGAAA
1 AACAGAAGCTCATGAGAGCTAAATGGAAA
5553416 GTAAACACGA
Statistics
Matches: 96, Mismatches: 16, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
84 28 0.29
85 68 0.71
ACGTcount: A:0.44, C:0.16, G:0.22, T:0.18
Consensus pattern (84 bp):
AACAGAAGCTCATGAGAGCTAAATGGAAACCCATAAGAGTTGAACAGAAGCTCATAAGAGCTAAA
CAAAAACTCATATGAGTCA
Found at i:5558526 original size:82 final size:80
Alignment explanation
Indices: 5558362--5558950 Score: 968
Period size: 82 Copynumber: 7.3 Consensus size: 80
5558352 TAAGTTCGTA
*
5558362 TTTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCATGCGACCCGAGGCTCAACTCACTTCTCG
1 TTTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCGT-CGACCCGAGGCTCAACTCACTTCTCG
5558427 CAATATGAGTTGATTT
65 CAATATGAGTTGATTT
* *
5558443 TTTTCGAAAAACAGAGATTTAAAAGAAATACCTCAGCGT-GACCCGAGGCTCAACTCATTTCTCG
1 TTTT-GAAAAACAGAAATTTAAAAGAAATACCTCAGCGTCGACCCGAGGCTCAACTCACTTCTCG
*
5558507 CATTATGAGTTGATTT
65 CAATATGAGTTGATTT
5558523 TTTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCG
1 TTTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCGT-CGACCCGAGGCTCAACTCACTTCTCG
5558588 CAATATGAGTTGATTT
65 CAATATGAGTTGATTT
* *
5558604 TTTTCGAAAAACAGAGATTTAAAAGAAATACCTCAGCGT-GACCCGAGGCTCAACTCATTTCTCG
1 TTTT-GAAAAACAGAAATTTAAAAGAAATACCTCAGCGTCGACCCGAGGCTCAACTCACTTCTCG
*
5558668 CATTATGAGTTGATTT
65 CAATATGAGTTGATTT
5558684 TTTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCG
1 TTTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCGT-CGACCCGAGGCTCAACTCACTTCTCG
*
5558749 CAAAATGAGTTGATTTT
65 CAATATGAGTTGA-TTT
5558766 TTTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCG
1 TTTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCGT-CGACCCGAGGCTCAACTCACTTCTCG
*
5558831 CAAAATGAGTTGATTTT
65 CAATATGAGTTGA-TTT
5558848 TTTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCG
1 TTTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCGT-CGACCCGAGGCTCAACTCACTTCTCG
5558913 CAATATGAGTTGA-TT
65 CAATATGAGTTGATTT
* * *
5558928 TATTGAAAAATAGAAATTGAAAA
1 TTTTGAAAAACAGAAATTTAAAA
5558951 ATATTTCTTA
Statistics
Matches: 483, Mismatches: 18, Indels: 15
0.94 0.03 0.03
Matches are distributed among these distances:
79 66 0.14
80 108 0.22
81 82 0.17
82 227 0.47
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (80 bp):
TTTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCGTCGACCCGAGGCTCAACTCACTTCTCGC
AATATGAGTTGATTT
Found at i:5558627 original size:161 final size:161
Alignment explanation
Indices: 5558362--5558928 Score: 1044
Period size: 161 Copynumber: 3.5 Consensus size: 161
5558352 TAAGTTCGTA
*
5558362 TTTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCATGCGACCCGAGGCTCAACTCACTTCTCG
1 TTTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCG
5558427 CAATATGAGTTGATTTTTTTCGAAAAACAGAGATTTAAAAGAAATACCTCAGCGTGACCCGAGGC
66 CAATATGAGTTGATTTTTTTCGAAAAACAGAGATTTAAAAGAAATACCTCAGCGTGACCCGAGGC
5558492 TCAACTCATTTCTCGCATTATGAGTTGATTT
131 TCAACTCATTTCTCGCATTATGAGTTGATTT
5558523 TTTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCG
1 TTTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCG
5558588 CAATATGAGTTGATTTTTTTCGAAAAACAGAGATTTAAAAGAAATACCTCAGCGTGACCCGAGGC
66 CAATATGAGTTGATTTTTTTCGAAAAACAGAGATTTAAAAGAAATACCTCAGCGTGACCCGAGGC
5558653 TCAACTCATTTCTCGCATTATGAGTTGATTT
131 TCAACTCATTTCTCGCATTATGAGTTGATTT
5558684 TTTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCG
1 TTTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCG
* * *
5558749 CAAAATGAGTTGATTTTTTTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAG
66 CAATATGAGTTGATTTTTTTCGAAAAACAGAGATTTAAAAGAAATACCTCAGCGT--GACCCGAG
* **
5558814 GCTCAACTCACTTCTCGCAAAATGAGTTGATTTT
129 GCTCAACTCATTTCTCGCATTATGAGTTGA-TTT
5558848 TTTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCG
1 TTTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCG
5558913 CAATATGAGTTGATTT
66 CAATATGAGTTGATTT
5558929 ATTGAAAAAT
Statistics
Matches: 395, Mismatches: 8, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
161 277 0.70
163 35 0.09
164 83 0.21
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (161 bp):
TTTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCG
CAATATGAGTTGATTTTTTTCGAAAAACAGAGATTTAAAAGAAATACCTCAGCGTGACCCGAGGC
TCAACTCATTTCTCGCATTATGAGTTGATTT
Found at i:5558794 original size:243 final size:239
Alignment explanation
Indices: 5558362--5558950 Score: 973
Period size: 243 Copynumber: 2.4 Consensus size: 239
5558352 TAAGTTCGTA
*
5558362 TTTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCATGCGACCCGAGGCTCAACTCACTTCTCG
1 TTTTGAAAAACAGAAATTTAAAAGAAATACCTCAGC--GTGACCCGAGGCTCAACTCACTTCTCG
*
5558427 CAATATGAGTTGATTTTTTTCGAAAAACAGAGATTTAAAAGAAATACCTCAGCGTGACCCGAGGC
64 CAATATGAGTTGATTTTTTT-GAAAAACAGAAATTTAAAAGAAATACCTCAGCGTGACCCGAGGC
* **
5558492 TCAACTCATTTCTCGCATTATGAGTTGATTTTTTTGAAAAACAGAAATTTAAAAGAAATACCTCA
128 TCAACTCACTTCTCGCAAAATGAGTTGATTTTTTTGAAAAACAGAAATTTAAAAGAAATACCTCA
*
5558557 GCGTGCGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTT
193 GCGTGCGACCCGAGGCTCAACTCACTTCTCGCAAAATGAGTTGATTT
* *
5558604 TTTTCGAAAAACAGAGATTTAAAAGAAATACCTCAGCGTGACCCGAGGCTCAACTCATTTCTCGC
1 TTTT-GAAAAACAGAAATTTAAAAGAAATACCTCAGCGTGACCCGAGGCTCAACTCACTTCTCGC
*
5558669 ATTATGAGTTGATTTTTTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGC
65 AATATGAGTTGATTTTTTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCGT--GACCCGAGGC
5558734 TCAACTCACTTCTCGCAAAATGAGTTGATTTTTTTTGAAAAACAGAAATTTAAAAGAAATACCTC
128 TCAACTCACTTCTCGCAAAATGAGTTGA-TTTTTTTGAAAAACAGAAATTTAAAAGAAATACCTC
5558799 AGCGTGCGACCCGAGGCTCAACTCACTTCTCGCAAAATGAGTTGATTTT
192 AGCGTGCGACCCGAGGCTCAACTCACTTCTCGCAAAATGAGTTGA-TTT
5558848 TTTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCG
1 TTTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCGT--GACCCGAGGCTCAACTCACTTCTCG
* * *
5558913 CAATATGAGTTGA-TTTATTGAAAAATAGAAATTGAAAA
64 CAATATGAGTTGATTTTTTTGAAAAACAGAAATTTAAAA
5558951 ATATTTCTTA
Statistics
Matches: 325, Mismatches: 15, Indels: 12
0.92 0.04 0.03
Matches are distributed among these distances:
240 33 0.10
241 44 0.14
242 39 0.12
243 144 0.44
244 29 0.09
245 36 0.11
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (239 bp):
TTTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCGTGACCCGAGGCTCAACTCACTTCTCGCA
ATATGAGTTGATTTTTTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCGTGACCCGAGGCTCA
ACTCACTTCTCGCAAAATGAGTTGATTTTTTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCG
TGCGACCCGAGGCTCAACTCACTTCTCGCAAAATGAGTTGATTT
Found at i:5565988 original size:17 final size:16
Alignment explanation
Indices: 5565962--5566013 Score: 52
Period size: 17 Copynumber: 3.2 Consensus size: 16
5565952 ACTTTTTTTT
*
5565962 AAACACGAATTTTTAA
1 AAACAAGAATTTTTAA
*
5565978 AATACAAGAA-TTTTAG
1 AA-ACAAGAATTTTTAA
*
5565994 AAACATGAATTTTTTAA
1 AAACAAGAA-TTTTTAA
5566011 AAA
1 AAA
5566014 AATATGAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
15 6 0.21
16 9 0.31
17 14 0.48
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.33
Consensus pattern (16 bp):
AAACAAGAATTTTTAA
Found at i:5566068 original size:17 final size:16
Alignment explanation
Indices: 5566019--5566071 Score: 52
Period size: 19 Copynumber: 3.1 Consensus size: 16
5566009 AAAAAAATAT
5566019 GAAAATTTTGAAACAC
1 GAAAATTTTGAAACAC
**
5566035 GAGATTTTTTTTGAAACAC
1 GA-A--AATTTTGAAACAC
5566054 GAAAATTTATGAAACAC
1 GAAAATTT-TGAAACAC
5566071 G
1 G
5566072 GTTTTCTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
16 5 0.17
17 10 0.34
18 1 0.03
19 13 0.45
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.30
Consensus pattern (16 bp):
GAAAATTTTGAAACAC
Found at i:5566558 original size:14 final size:14
Alignment explanation
Indices: 5566539--5566613 Score: 61
Period size: 14 Copynumber: 5.6 Consensus size: 14
5566529 GAATTGAACC
*
5566539 TCTTTTTTCTTTTT
1 TCTTTTCTCTTTTT
5566553 TCTTTTCTCTTTTT
1 TCTTTTCTCTTTTT
**
5566567 T-TCCTC-CTTTTT
1 TCTTTTCTCTTTTT
*
5566579 TC-CTTCTCTTTTTCT
1 TCTTTTCTC-TTTT-T
5566594 TCTTTT-TCTTTTT
1 TCTTTTCTCTTTTT
5566607 T-TTTTCT
1 TCTTTTCT
5566614 GCTGGGCTGG
Statistics
Matches: 50, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
12 14 0.28
13 7 0.14
14 22 0.44
15 5 0.10
16 2 0.04
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (14 bp):
TCTTTTCTCTTTTT
Found at i:5566754 original size:17 final size:17
Alignment explanation
Indices: 5566734--5566776 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
5566724 GGCTTGCTTC
5566734 TTTTCTGTTT-TTTTTGT
1 TTTTCT-TTTGTTTTTGT
*
5566751 TTTTGTTTTGTTTTTGT
1 TTTTCTTTTGTTTTTGT
*
5566768 TTTTGTTTT
1 TTTTCTTTT
5566777 TTGGGCTGCT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.00, C:0.02, G:0.14, T:0.84
Consensus pattern (17 bp):
TTTTCTTTTGTTTTTGT
Found at i:5566755 original size:6 final size:6
Alignment explanation
Indices: 5566744--5566777 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
5566734 TTTTCTGTTT
5566744 TTTTTG TTTTTG -TTTTG TTTTTG TTTTTG TTTTT
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTT
5566778 TGGGCTGCTG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (6 bp):
TTTTTG
Found at i:5566759 original size:11 final size:11
Alignment explanation
Indices: 5566741--5566777 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
5566731 TTCTTTTCTG
5566741 TTTT-TTTTGT
1 TTTTGTTTTGT
5566751 TTTTGTTTTGT
1 TTTTGTTTTGT
5566762 TTTTGTTTTTGT
1 TTTTG-TTTTGT
5566774 TTTT
1 TTTT
5566778 TGGGCTGCTG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 4 0.16
11 11 0.44
12 10 0.40
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (11 bp):
TTTTGTTTTGT
Found at i:5566868 original size:22 final size:22
Alignment explanation
Indices: 5566841--5566884 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
5566831 TGTTATAATA
*
5566841 TTTTTTATTATTTCTTTTTCTT
1 TTTTTTATTATTTCTTCTTCTT
* *
5566863 TTTTTTCTTTTTTCTTCTTCTT
1 TTTTTTATTATTTCTTCTTCTT
5566885 CTTCTTCTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.82
Consensus pattern (22 bp):
TTTTTTATTATTTCTTCTTCTT
Found at i:5566880 original size:3 final size:3
Alignment explanation
Indices: 5566852--5566906 Score: 69
Period size: 3 Copynumber: 19.0 Consensus size: 3
5566842 TTTTTATTAT
* * *
5566852 TTC TTT TTC TTT TTT TTC TT- TT- TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
5566898 TTC TTC TTC
1 TTC TTC TTC
5566907 AAAACCCTAG
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
2 4 0.09
3 43 0.91
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (3 bp):
TTC
Found at i:5567285 original size:29 final size:29
Alignment explanation
Indices: 5567250--5567378 Score: 102
Period size: 29 Copynumber: 4.4 Consensus size: 29
5567240 TTTTGGGGCT
*
5567250 AAAATGTAATTTTGAGAAAA-TTTA-GGGTA
1 AAAATGTAATTTT-A-AAAAGGTTATGGGTA
*
5567279 AAAATGTAATTTTAAAAAGGTTATGGGTT
1 AAAATGTAATTTTAAAAAGGTTATGGGTA
* * *
5567308 AAAATGTAA-TTTCAAAAGGTTTAGGGGTC
1 AAAATGTAATTTTAAAAAGG-TTATGGGTA
* * * * * *
5567337 AATATATAATTTCAAAAAGTTTAGGGGTC
1 AAAATGTAATTTTAAAAAGGTTATGGGTA
*
5567366 AAAATGTATTTTT
1 AAAATGTAATTTT
5567379 TTATTTTTTG
Statistics
Matches: 82, Mismatches: 14, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
27 4 0.05
28 13 0.16
29 58 0.71
30 7 0.09
ACGTcount: A:0.41, C:0.03, G:0.19, T:0.36
Consensus pattern (29 bp):
AAAATGTAATTTTAAAAAGGTTATGGGTA
Found at i:5567394 original size:16 final size:16
Alignment explanation
Indices: 5567373--5567403 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5567363 GTCAAAATGT
*
5567373 ATTTTTTTATTTTTTG
1 ATTTTTTAATTTTTTG
5567389 ATTTTTTAATTTTTT
1 ATTTTTTAATTTTTT
5567404 TTGAAGATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.81
Consensus pattern (16 bp):
ATTTTTTAATTTTTTG
Found at i:5570406 original size:18 final size:17
Alignment explanation
Indices: 5570383--5570420 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
5570373 AATCGAAATT
5570383 TATTTTATAATAATATAA
1 TATTTTATAATAAT-TAA
*
5570401 TATTTTGTAATAATTAA
1 TATTTTATAATAATTAA
5570418 TAT
1 TAT
5570421 CATATATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
TATTTTATAATAATTAA
Found at i:5570778 original size:20 final size:19
Alignment explanation
Indices: 5570736--5570775 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
5570726 TTATTAAAAT
5570736 ATAAATTATATAAATTATTA
1 ATAAATTATAT-AATTATTA
5570756 ATAAATTATCAT-ATTATTA
1 ATAAATTAT-ATAATTATTA
5570775 A
1 A
5570776 ATATAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.42
20 9 0.47
21 2 0.11
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (19 bp):
ATAAATTATATAATTATTA
Found at i:5570791 original size:22 final size:22
Alignment explanation
Indices: 5570726--5570791 Score: 66
Period size: 22 Copynumber: 3.0 Consensus size: 22
5570716 GCTAAATAAC
*
5570726 TTATTAAAATATAAATTATATAAA
1 TTATT-AAATATAAATTAT-TATA
*
5570750 TTATT--A-ATAAATTATCATA
1 TTATTAAATATAAATTATTATA
*
5570769 TTATTAAATATAAATAATTATA
1 TTATTAAATATAAATTATTATA
5570791 T
1 T
5570792 AAGTATTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
19 7 0.20
20 9 0.26
21 2 0.06
22 12 0.34
24 5 0.14
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
TTATTAAATATAAATTATTATA
Found at i:5581889 original size:22 final size:20
Alignment explanation
Indices: 5581856--5581915 Score: 59
Period size: 22 Copynumber: 2.9 Consensus size: 20
5581846 AAAATTCTAA
5581856 AAAATTTA-TAAAAATGTATT
1 AAAATTTATTAAAAAT-TATT
* *
5581876 AAAATTCTATTAAAAAATCATG
1 AAAATT-TATT-AAAAATTATT
5581898 AAAATTTTATTAAAAATT
1 AAAA-TTTATTAAAAATT
5581916 TTATTAAAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
20 6 0.18
21 8 0.24
22 11 0.33
23 8 0.24
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.38
Consensus pattern (20 bp):
AAAATTTATTAAAAATTATT
Found at i:5581915 original size:12 final size:12
Alignment explanation
Indices: 5581853--5581924 Score: 55
Period size: 12 Copynumber: 6.4 Consensus size: 12
5581843 TAAAAAATTC
*
5581853 TAAAAAATTTA-
1 TAAAAATTTTAT
*
5581864 TAAAAA-TGTAT
1 TAAAAATTTTAT
*
5581875 T-AAAATTCTAT
1 TAAAAATTTTAT
* *
5581886 TAAAAA-ATCA-
1 TAAAAATTTTAT
*
5581896 TGAAAATTTTAT
1 TAAAAATTTTAT
5581908 TAAAAATTTTAT
1 TAAAAATTTTAT
5581920 TAAAA
1 TAAAA
5581925 CTATTGACAT
Statistics
Matches: 47, Mismatches: 9, Indels: 9
0.72 0.14 0.14
Matches are distributed among these distances:
10 12 0.26
11 15 0.32
12 20 0.43
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.39
Consensus pattern (12 bp):
TAAAAATTTTAT
Found at i:5581924 original size:11 final size:11
Alignment explanation
Indices: 5581872--5581924 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
5581862 TATAAAAATG
*
5581872 TATTAAAATTC
1 TATTAAAATTT
**
5581883 TATTAAAAAAT
1 TATTAAAATTT
* *
5581894 CATGAAAATTT
1 TATTAAAATTT
5581905 TATTAAAAATTT
1 TATT-AAAATTT
5581917 TATTAAAA
1 TATTAAAA
5581925 CTATTGACAT
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
11 21 0.66
12 11 0.34
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.42
Consensus pattern (11 bp):
TATTAAAATTT
Found at i:5582389 original size:20 final size:19
Alignment explanation
Indices: 5582364--5582434 Score: 60
Period size: 20 Copynumber: 3.8 Consensus size: 19
5582354 CCAGTTCAAG
5582364 TTTTTATGATTTATTTATAA
1 TTTTTAT-ATTTATTTATAA
*
5582384 TTTTTATAAATTTATAT-TAA
1 TTTTTAT--ATTTATTTATAA
* *
5582404 TTTTAATATTTA-TTACAA
1 TTTTTATATTTATTTATAA
5582422 TTTTT-TA-TTATTT
1 TTTTTATATTTATTT
5582435 TTTAAAGAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
16 3 0.07
17 5 0.12
18 11 0.26
20 16 0.38
21 7 0.17
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.65
Consensus pattern (19 bp):
TTTTTATATTTATTTATAA
Found at i:5584393 original size:46 final size:46
Alignment explanation
Indices: 5584334--5584425 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
5584324 GGAAATTATC
5584334 CTCCACCTAAAATAAAGAAGTAATTTTCTATGTTTGAATCGGAAGA
1 CTCCACCTAAAATAAAGAAGTAATTTTCTATGTTTGAATCGGAAGA
5584380 CTCCACCTAAAATAAAGAAGTAATTTTCTATGTTTGAATCGGAAGA
1 CTCCACCTAAAATAAAGAAGTAATTTTCTATGTTTGAATCGGAAGA
5584426 GAATCTTAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.30
Consensus pattern (46 bp):
CTCCACCTAAAATAAAGAAGTAATTTTCTATGTTTGAATCGGAAGA
Found at i:5587095 original size:29 final size:29
Alignment explanation
Indices: 5587062--5587118 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
5587052 AAATAAATAA
* *
5587062 ATAAA-AAGAAAGAAAGATAGAAATGAAAC
1 ATAAAGAA-AAAGAAAGAAAGAAAAGAAAC
5587091 ATAAAGAAAAAGAAAGAAAGAAAAGAAA
1 ATAAAGAAAAAGAAAGAAAGAAAAGAAA
5587119 AGAAAGGAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 23 0.92
30 2 0.08
ACGTcount: A:0.74, C:0.02, G:0.18, T:0.07
Consensus pattern (29 bp):
ATAAAGAAAAAGAAAGAAAGAAAAGAAAC
Found at i:5587584 original size:5 final size:5
Alignment explanation
Indices: 5587574--5587607 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
5587564 GCAATATAAA
*
5587574 ATTGT ATTGT ATTGT ATTGT ATTTT ATTGT ATTG
1 ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTG
5587608 ATGAATTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.21, C:0.00, G:0.18, T:0.62
Consensus pattern (5 bp):
ATTGT
Done.