Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr5
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: 43060996
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2186021 characters in sequence are not A, C, G, or T
File 9 of 128
Found at i:2689671 original size:159 final size:156
Alignment explanation
Indices: 2689252--2689658 Score: 417
Period size: 159 Copynumber: 2.5 Consensus size: 156
2689242 ATTTAATATT
* * * * *
2689252 ATAAATACGAGATAAATTTTAAAATTATATATAAATTTAAATTTAATGTGTAATTCGATACATAA
1 ATAAATACGAG-TAAATTTTAAAATAATAAATAAATATAAATTTAATATGTAATTC-ATAAATAA
* * ** * *
2689317 ACTTTGATTTTATGTAATCATACATGAAATTCTAATTGTGGTTCAAAGATATATGTAAAATTTTA
64 AC-ATGATTCTATCCAATAATACATGAAA-ACTAATTGTGGTTCAAAGATATATGTAAAATTTTA
2689382 ATTTTGATTTAATTATATATATTTTAAGAA
127 ATTTTGATTTAATTATATATATTTTAAGAA
* * * * *
2689412 ATAAATACGAGTAAATTTTAAAATTATATATAAATTTAAATTTAATGTGTAATTCGATACATAAA
1 ATAAATACGAGTAAATTTTAAAATAATAAATAAATATAAATTTAATATGTAATTC-ATAAATAAA
* * ** *
2689477 CTTTGATTTTATGTAATCATACATGAAAATCTAATTGTGGTTCAAAGATATATGTAAAATTTTAA
65 C-ATGATTCTATCCAATAATACATGAAAA-CTAATTGTGGTTCAAAGATATATGTAAAATTTTAA
2689542 TTTTGATTTAATTATATATATTTTAAGAA
128 TTTTGATTTAATTATATATATTTTAAGAA
* ***
2689571 ATAAATAC-ATTAAATTATTTTTATAATAAATAAATATAATTATTCGT-ATATGTAATAT-ATAA
1 ATAAATACGAGTAAATT-TTAAAATAATAAATAAATATAA--ATT--TAATATGTAAT-TCATAA
2689633 ATTTAAA-ATGATTCTATACCAATAAT
60 A--TAAACATGATTCTAT-CCAATAAT
2689659 TATGTTAATA
Statistics
Matches: 222, Mismatches: 15, Indels: 18
0.87 0.06 0.07
Matches are distributed among these distances:
158 7 0.03
159 170 0.77
160 11 0.05
161 15 0.07
162 13 0.06
163 6 0.03
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.43
Consensus pattern (156 bp):
ATAAATACGAGTAAATTTTAAAATAATAAATAAATATAAATTTAATATGTAATTCATAAATAAAC
ATGATTCTATCCAATAATACATGAAAACTAATTGTGGTTCAAAGATATATGTAAAATTTTAATTT
TGATTTAATTATATATATTTTAAGAA
Found at i:2692836 original size:25 final size:25
Alignment explanation
Indices: 2692786--2692836 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
2692776 TATTTTAAGA
* **
2692786 AATAAATACATTAAATTATTTTTAT
1 AATAAATAAATTAAATTATTCGTAT
2692811 AATAAATAAA-TATAATTATTCGTAT
1 AATAAATAAATTA-AATTATTCGTAT
2692836 A
1 A
2692837 TGTAATATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 2 0.09
25 20 0.91
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (25 bp):
AATAAATAAATTAAATTATTCGTAT
Found at i:2704856 original size:13 final size:14
Alignment explanation
Indices: 2704818--2704858 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
2704808 ATTGTGGTAG
*
2704818 GATTCTCTATATCT
1 GATTCTGTATATCT
*
2704832 -ATTCTGTTTATCT
1 GATTCTGTATATCT
2704845 GATTCTG-ATATCT
1 GATTCTGTATATCT
2704858 G
1 G
2704859 TATATGTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
13 17 0.74
14 6 0.26
ACGTcount: A:0.20, C:0.17, G:0.12, T:0.51
Consensus pattern (14 bp):
GATTCTGTATATCT
Found at i:2710635 original size:57 final size:57
Alignment explanation
Indices: 2710559--2710667 Score: 157
Period size: 57 Copynumber: 1.9 Consensus size: 57
2710549 GATCCTATAC
* *
2710559 TGATATAGCCCTCCTGAAGAAAATGTGTGAAAA-AGATCTAGCCTGGACGGGTGATCT
1 TGATATAGCCCTCCCGAAGAAAATGTG-GAAAATAGATCTAGCCCGGACGGGTGATCT
* * *
2710616 TGATATAGCCCTCCCGAAGAATATGTGGAAAATGGATTTAGCCCGGACGGGT
1 TGATATAGCCCTCCCGAAGAAAATGTGGAAAATAGATCTAGCCCGGACGGGT
2710668 AATCCGAATT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
56 5 0.11
57 41 0.89
ACGTcount: A:0.30, C:0.18, G:0.28, T:0.24
Consensus pattern (57 bp):
TGATATAGCCCTCCCGAAGAAAATGTGGAAAATAGATCTAGCCCGGACGGGTGATCT
Found at i:2710814 original size:54 final size:54
Alignment explanation
Indices: 2710741--2710877 Score: 247
Period size: 54 Copynumber: 2.5 Consensus size: 54
2710731 TTGTCATTGT
* *
2710741 AGGGGATTTAGCCTAGACTGGTAATCCCGACAATATTCTATGAGTTTATATTAC
1 AGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATATTAC
2710795 AGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATATTAC
1 AGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATATTAC
*
2710849 AGGGGATTTAGCATGGACTGGTAATCCCG
1 AGGGGATTTAGCCTGGACTGGTAATCCCG
2710878 CTGTAAGAAA
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 80 1.00
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.31
Consensus pattern (54 bp):
AGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATATTAC
Found at i:2710963 original size:67 final size:67
Alignment explanation
Indices: 2710851--2710979 Score: 231
Period size: 67 Copynumber: 1.9 Consensus size: 67
2710841 TATATTACAG
* *
2710851 GGGATTTAGCATGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCGGGAGTGTGCTCTCTTGC
1 GGGATTTAGCATGGACTGGTAATCCCACTGTAAGAAATGACGTTCGCGGGAGTGTGCTCTCTTGC
2710916 AA
66 AA
*
2710918 GGGATTTAGCCTGGACTGGTAATCCCACTGTAAGAAATGACGTTCGCGGGAGTGTGCTCTCT
1 GGGATTTAGCATGGACTGGTAATCCCACTGTAAGAAATGACGTTCGCGGGAGTGTGCTCTCT
2710980 AAATTGGAAA
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
67 59 1.00
ACGTcount: A:0.22, C:0.19, G:0.32, T:0.27
Consensus pattern (67 bp):
GGGATTTAGCATGGACTGGTAATCCCACTGTAAGAAATGACGTTCGCGGGAGTGTGCTCTCTTGC
AA
Found at i:2712200 original size:11 final size:11
Alignment explanation
Indices: 2712181--2712211 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
2712171 AAAACAACTC
*
2712181 TTTTTGCTCGA
1 TTTTGGCTCGA
2712192 TTTTGGCTCGA
1 TTTTGGCTCGA
2712203 TTTTGGCTC
1 TTTTGGCTC
2712212 CTTTCACTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.06, C:0.19, G:0.23, T:0.52
Consensus pattern (11 bp):
TTTTGGCTCGA
Found at i:2719731 original size:21 final size:21
Alignment explanation
Indices: 2719707--2719876 Score: 108
Period size: 21 Copynumber: 8.1 Consensus size: 21
2719697 CAGAAACCCG
*
2719707 TAAGGGTTGAACTGAAGCTCG
1 TAAGGGTTGAACTGAAGCTCA
* * * * *
2719728 TAAGAGCTGAACGGAAACCCA
1 TAAGGGTTGAACTGAAGCTCA
*
2719749 TAAGGGTTAAACTGAAGCTCA
1 TAAGGGTTGAACTGAAGCTCA
* * * * * *
2719770 AAAGAGCTGAACGGAAACCCA
1 TAAGGGTTGAACTGAAGCTCA
*
2719791 TAAGGGTTAAACTGAAGCTCA
1 TAAGGGTTGAACTGAAGCTCA
* * * * * *
2719812 AAAGAGCTGAACGGAAACCCA
1 TAAGGGTTGAACTGAAGCTCA
* * *
2719833 TAAGGGTTAAACGGAAACTCA
1 TAAGGGTTGAACTGAAGCTCA
* *
2719854 TATGAGTT-AACTGAAGCTCA
1 TAAGGGTTGAACTGAAGCTCA
2719874 TAA
1 TAA
2719877 TAGCTAAACA
Statistics
Matches: 106, Mismatches: 43, Indels: 1
0.71 0.29 0.01
Matches are distributed among these distances:
20 12 0.11
21 94 0.89
ACGTcount: A:0.41, C:0.18, G:0.24, T:0.18
Consensus pattern (21 bp):
TAAGGGTTGAACTGAAGCTCA
Found at i:2719746 original size:42 final size:42
Alignment explanation
Indices: 2719699--2719853 Score: 256
Period size: 42 Copynumber: 3.7 Consensus size: 42
2719689 ATTCTAAACA
* * **
2719699 GAAACCCGTAAGGGTTGAACTGAAGCTCGTAAGAGCTGAACG
1 GAAACCCATAAGGGTTAAACTGAAGCTCAAAAGAGCTGAACG
2719741 GAAACCCATAAGGGTTAAACTGAAGCTCAAAAGAGCTGAACG
1 GAAACCCATAAGGGTTAAACTGAAGCTCAAAAGAGCTGAACG
2719783 GAAACCCATAAGGGTTAAACTGAAGCTCAAAAGAGCTGAACG
1 GAAACCCATAAGGGTTAAACTGAAGCTCAAAAGAGCTGAACG
* *
2719825 GAAACCCATAAGGGTTAAACGGAAACTCA
1 GAAACCCATAAGGGTTAAACTGAAGCTCA
2719854 TATGAGTTAA
Statistics
Matches: 107, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 107 1.00
ACGTcount: A:0.41, C:0.19, G:0.25, T:0.15
Consensus pattern (42 bp):
GAAACCCATAAGGGTTAAACTGAAGCTCAAAAGAGCTGAACG
Found at i:2725058 original size:25 final size:26
Alignment explanation
Indices: 2725024--2725085 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 26
2725014 AAGTAAAAGC
*
2725024 ATTAAAAATAATAT-AATAAA-ATAAT
1 ATTAATAATAATATAAATAAAGA-AAT
2725049 ATTAATAATAA-ATAAATAAAGAAAT
1 ATTAATAATAATATAAATAAAGAAAT
*
2725074 AATAATAA-AATA
1 ATTAATAATAATA
2725086 GGAAAATGGG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 4 0.12
25 27 0.84
26 1 0.03
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (26 bp):
ATTAATAATAATATAAATAAAGAAAT
Found at i:2725061 original size:16 final size:13
Alignment explanation
Indices: 2725028--2725085 Score: 59
Period size: 13 Copynumber: 4.5 Consensus size: 13
2725018 AAAAGCATTA
2725028 AAAATAATATAAT
1 AAAATAATATAAT
2725041 AAAATAATATTAAT
1 AAAATAATA-TAAT
*
2725055 AATA-AATA-AAT
1 AAAATAATATAAT
2725066 AAAGA-AATAATAAT
1 AAA-ATAAT-ATAAT
2725080 AAAATA
1 AAAATA
2725086 GGAAAATGGG
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
11 5 0.13
12 4 0.11
13 15 0.39
14 14 0.37
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.28
Consensus pattern (13 bp):
AAAATAATATAAT
Found at i:2728758 original size:13 final size:13
Alignment explanation
Indices: 2728725--2728765 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
2728715 AACCTGCCAG
*
2728725 AAACAAATAAAAGA
1 AAACAAA-AATAGA
2728739 AAA-AAAAATAGA
1 AAACAAAAATAGA
2728751 AAACAAAAATA-A
1 AAACAAAAATAGA
2728763 AAA
1 AAA
2728766 AATAAAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
12 12 0.48
13 10 0.40
14 3 0.12
ACGTcount: A:0.83, C:0.05, G:0.05, T:0.07
Consensus pattern (13 bp):
AAACAAAAATAGA
Found at i:2728766 original size:21 final size:20
Alignment explanation
Indices: 2728740--2728778 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
2728730 AATAAAAGAA
2728740 AAAAAAATAGAAAACAAAAAT
1 AAAAAAATA-AAAACAAAAAT
*
2728761 AAAAAAATAAAAATAAAA
1 AAAAAAATAAAAACAAAA
2728779 TGCAATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.85, C:0.03, G:0.03, T:0.10
Consensus pattern (20 bp):
AAAAAAATAAAAACAAAAAT
Found at i:2729880 original size:22 final size:23
Alignment explanation
Indices: 2729850--2729899 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
2729840 GCACCTTTTG
*
2729850 AGGGCTTAT-GTATATG-TGCAAA
1 AGGGATTATAGTATATGTTG-AAA
2729872 AGGGATTATAGGTATATGTTGAAA
1 AGGGATTATA-GTATATGTTGAAA
2729896 AGGG
1 AGGG
2729900 TGAGAAAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 8 0.33
24 14 0.58
25 2 0.08
ACGTcount: A:0.34, C:0.04, G:0.32, T:0.30
Consensus pattern (23 bp):
AGGGATTATAGTATATGTTGAAA
Found at i:2739650 original size:15 final size:14
Alignment explanation
Indices: 2739608--2739654 Score: 60
Period size: 14 Copynumber: 3.3 Consensus size: 14
2739598 GTTTATTAAA
*
2739608 ATAAAAAAATAAATT
1 ATAAAATAA-AAATT
2739623 -TAAAATAAAAATT
1 ATAAAATAAAAATT
2739636 ATAAAATATAAAATT
1 ATAAAATA-AAAATT
2739651 ATAA
1 ATAA
2739655 TATTAAATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 5 0.17
14 14 0.48
15 10 0.34
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
ATAAAATAAAAATT
Found at i:2739666 original size:15 final size:15
Alignment explanation
Indices: 2739618--2739654 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
2739608 ATAAAAAAAT
2739618 AAATT-TAAAATA-A
1 AAATTATAAAATATA
2739631 AAATTATAAAATATA
1 AAATTATAAAATATA
2739646 AAATTATAA
1 AAATTATAA
2739655 TATTAAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 5 0.23
14 7 0.32
15 10 0.45
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
AAATTATAAAATATA
Found at i:2740709 original size:25 final size:25
Alignment explanation
Indices: 2740680--2740784 Score: 126
Period size: 25 Copynumber: 4.3 Consensus size: 25
2740670 ACCTAAGCGC
2740680 GCTCTCTGATTAATAGCACGTCAGT
1 GCTCTCTGATTAATAGCACGTCAGT
* ** *
2740705 GCTCTCTGATTATTAATATGTCAGT
1 GCTCTCTGATTAATAGCACGTCAGT
2740730 GCTCTCTGATTAATAGCACGTCAGT
1 GCTCTCTGATTAATAGCACGTCAGT
* *
2740755 GCTATCTG--T-ATAGCACTTCAGT
1 GCTCTCTGATTAATAGCACGTCAGT
*
2740777 ACTCTCTG
1 GCTCTCTG
2740785 TTCATTAGTG
Statistics
Matches: 68, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
22 18 0.26
23 1 0.01
25 49 0.72
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.36
Consensus pattern (25 bp):
GCTCTCTGATTAATAGCACGTCAGT
Found at i:2740785 original size:22 final size:22
Alignment explanation
Indices: 2740742--2740785 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2740732 TCTCTGATTA
*
2740742 ATAGCACGTCAGTGCTATCTGT
1 ATAGCACGTCAGTACTATCTGT
* *
2740764 ATAGCACTTCAGTACTCTCTGT
1 ATAGCACGTCAGTACTATCTGT
2740786 TCATTAGTGC
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:0.23, C:0.25, G:0.18, T:0.34
Consensus pattern (22 bp):
ATAGCACGTCAGTACTATCTGT
Found at i:2741678 original size:23 final size:23
Alignment explanation
Indices: 2741652--2741704 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
2741642 TAAATCATAT
2741652 AATATATTTTTA-AAAAGTTCAAA
1 AATATATTTTTATAAAA-TTCAAA
* *
2741675 AATATTTTTTTATAAAATTCTAA
1 AATATATTTTTATAAAATTCAAA
2741698 AATATAT
1 AATATAT
2741705 AATTATTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 22 0.85
24 4 0.15
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (23 bp):
AATATATTTTTATAAAATTCAAA
Found at i:2743551 original size:85 final size:85
Alignment explanation
Indices: 2743451--2743623 Score: 328
Period size: 85 Copynumber: 2.0 Consensus size: 85
2743441 AATATCGATA
2743451 ATGCATAAATATGTTATTTTAAAATCTTAACTAAGATAAACGATAATTAAAAATCAGTTAAAAAA
1 ATGCATAAATATGTTATTTTAAAATCTTAACTAAGATAAACGATAATTAAAAATCAGTTAAAAAA
2743516 CAACAAATATTATTATAAGT
66 CAACAAATATTATTATAAGT
* *
2743536 ATGCATAAATATGTTATTTTAAAATCTTAACTAAGATAAATGATAATTAGAAATCAGTTAAAAAA
1 ATGCATAAATATGTTATTTTAAAATCTTAACTAAGATAAACGATAATTAAAAATCAGTTAAAAAA
2743601 CAACAAATATTATTATAAGT
66 CAACAAATATTATTATAAGT
2743621 ATG
1 ATG
2743624 TTTTTATCTT
Statistics
Matches: 86, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
85 86 1.00
ACGTcount: A:0.51, C:0.08, G:0.08, T:0.34
Consensus pattern (85 bp):
ATGCATAAATATGTTATTTTAAAATCTTAACTAAGATAAACGATAATTAAAAATCAGTTAAAAAA
CAACAAATATTATTATAAGT
Found at i:2743900 original size:28 final size:30
Alignment explanation
Indices: 2743867--2743928 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 30
2743857 AGATTTATTT
2743867 AAAATAAAAATATTAAAT-TT-AAAT-TAAA
1 AAAAT-AAAATATTAAATATTCAAATATAAA
* *
2743895 AAAATATAATGTTAAATATTCAAATATAAA
1 AAAATAAAATATTAAATATTCAAATATAAA
2743925 AAAA
1 AAAA
2743929 CTTTTGACTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 10 0.34
28 7 0.24
29 4 0.14
30 8 0.28
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (30 bp):
AAAATAAAATATTAAATATTCAAATATAAA
Found at i:2744231 original size:21 final size:22
Alignment explanation
Indices: 2744173--2744245 Score: 62
Period size: 21 Copynumber: 3.4 Consensus size: 22
2744163 NNNNNNNTTT
2744173 TATTT-TTTTCTAGTTTTTATATA
1 TATTTATTTTC-A-TTTTTATATA
* **
2744196 TATATATTTGAATTTTT-TATA
1 TATTTATTTTCATTTTTATATA
*
2744217 TATTTATTTTCATTTTCATAT-
1 TATTTATTTTCATTTTTATATA
*
2744238 TTTTTATT
1 TATTTATT
2744246 GTGCATATGT
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
21 24 0.60
22 8 0.20
23 5 0.12
24 3 0.08
ACGTcount: A:0.25, C:0.04, G:0.03, T:0.68
Consensus pattern (22 bp):
TATTTATTTTCATTTTTATATA
Found at i:2744430 original size:9 final size:10
Alignment explanation
Indices: 2744394--2744422 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
2744384 ATTTATCCAA
2744394 AAAATTATTT
1 AAAATTATTT
2744404 AAAATTATTT
1 AAAATTATTT
2744414 AAAATTATT
1 AAAATTATT
2744423 AACATTATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (10 bp):
AAAATTATTT
Found at i:2745340 original size:18 final size:17
Alignment explanation
Indices: 2745297--2745342 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
2745287 ACATGACAAC
* *
2745297 AAAAATTAAAAAAATTT
1 AAAAATTTAAAAAATGT
*
2745314 AAAATTTTAAAAAATGT
1 AAAAATTTAAAAAATGT
2745331 AAAGAATTTAAA
1 AAA-AATTTAAA
2745343 TTTTTATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 17 0.71
18 7 0.29
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.30
Consensus pattern (17 bp):
AAAAATTTAAAAAATGT
Found at i:2747715 original size:58 final size:58
Alignment explanation
Indices: 2747631--2747761 Score: 199
Period size: 58 Copynumber: 2.3 Consensus size: 58
2747621 CAAATCAAGT
* * * *
2747631 AAAGTTGAACATCACGAGATTCTTGATTCAAATAGAAGATGATAGACCTGATTCAAGC
1 AAAGTTGAATATCACAAGATTCTTGATTCAAACAGAAGATGATAGACCTGATTCAAAC
* * *
2747689 AGAGTTGAATATCACAAGATTCTTGATTCAAGCAGAAGATGATAGACCTGATTTAAAC
1 AAAGTTGAATATCACAAGATTCTTGATTCAAACAGAAGATGATAGACCTGATTCAAAC
2747747 AAAGTTGAATATCAC
1 AAAGTTGAATATCAC
2747762 GGGATTACTA
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
58 65 1.00
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (58 bp):
AAAGTTGAATATCACAAGATTCTTGATTCAAACAGAAGATGATAGACCTGATTCAAAC
Found at i:2748664 original size:16 final size:16
Alignment explanation
Indices: 2748627--2748666 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
2748617 TTGATAAAAT
* *
2748627 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
2748643 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
2748659 TAAAATTA
1 TAAAATTA
2748667 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:2748773 original size:18 final size:18
Alignment explanation
Indices: 2748730--2748774 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
2748720 ATTAGTTTAC
*
2748730 ATTTTTGCATTATCAAAT
1 ATTTTTGTATTATCAAAT
2748748 ATTTTTGTATTATCAAAT
1 ATTTTTGTATTATCAAAT
2748766 ATTTTTGTA
1 ATTTTTGTA
2748775 AACAAATAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.31, C:0.07, G:0.07, T:0.56
Consensus pattern (18 bp):
ATTTTTGTATTATCAAAT
Found at i:2748782 original size:16 final size:17
Alignment explanation
Indices: 2748743--2748782 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
2748733 TTTGCATTAT
*
2748743 CAAATATTTTTGTATTAT
1 CAAATATTTTTGTA-TAA
2748761 CAAATATTTTTGTA-AA
1 CAAATATTTTTGTATAA
2748777 CAAATA
1 CAAATA
2748783 AGTTTATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 7 0.33
18 14 0.67
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.45
Consensus pattern (17 bp):
CAAATATTTTTGTATAA
Found at i:2748916 original size:16 final size:16
Alignment explanation
Indices: 2748895--2748928 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
2748885 TATATATTTT
2748895 AAACATAAAAAACTTA
1 AAACATAAAAAACTTA
2748911 AAACATAAAAAACTTA
1 AAACATAAAAAACTTA
2748927 AA
1 AA
2748929 CTAGTATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.71, C:0.12, G:0.00, T:0.18
Consensus pattern (16 bp):
AAACATAAAAAACTTA
Found at i:2749289 original size:16 final size:16
Alignment explanation
Indices: 2749268--2749301 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
2749258 TATATATTTT
2749268 AAACATAAAAAACTTA
1 AAACATAAAAAACTTA
2749284 AAACATAAAAAACTTA
1 AAACATAAAAAACTTA
2749300 AA
1 AA
2749302 CTAGTATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.71, C:0.12, G:0.00, T:0.18
Consensus pattern (16 bp):
AAACATAAAAAACTTA
Found at i:2758450 original size:3 final size:3
Alignment explanation
Indices: 2758442--2758466 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2758432 AGAAAAAGTG
2758442 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
2758467 AACTAATAGA
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):
ATA
Found at i:2761926 original size:23 final size:24
Alignment explanation
Indices: 2761896--2761941 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 24
2761886 TAGTGTTATT
2761896 TAAGTATACAT-ATTTTTTAAAAA
1 TAAGTATACATAATTTTTTAAAAA
2761919 TAAGTATACATAATTTTTTAAAA
1 TAAGTATACATAATTTTTTAAAA
2761942 TTTATTTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.43
Consensus pattern (24 bp):
TAAGTATACATAATTTTTTAAAAA
Found at i:2762033 original size:13 final size:12
Alignment explanation
Indices: 2762003--2762040 Score: 53
Period size: 11 Copynumber: 3.3 Consensus size: 12
2761993 TATGTATTAT
*
2762003 ATATATTTAAAA
1 ATATATATAAAA
2762015 AT-TATATAAAA
1 ATATATATAAAA
2762026 ATA-ATATAAAA
1 ATATATATAAAA
2762037 ATAT
1 ATAT
2762041 TAATATGGGC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
11 21 0.91
12 2 0.09
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
ATATATATAAAA
Found at i:2768001 original size:17 final size:17
Alignment explanation
Indices: 2767976--2768009 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2767966 ATGTAAGTTT
*
2767976 AAATTTGAACTTGTATG
1 AAATATGAACTTGTATG
2767993 AAATATGAACTTGTATG
1 AAATATGAACTTGTATG
2768010 GAACCTCTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.18, T:0.38
Consensus pattern (17 bp):
AAATATGAACTTGTATG
Found at i:2772486 original size:19 final size:19
Alignment explanation
Indices: 2772445--2772493 Score: 73
Period size: 18 Copynumber: 2.6 Consensus size: 19
2772435 TTTGTATTAT
2772445 TATTTTTATATAATTCTAA
1 TATTTTTATATAATTCTAA
* *
2772464 -ATTTTTATATTATTTTAA
1 TATTTTTATATAATTCTAA
2772482 TATTTTTATATA
1 TATTTTTATATA
2772494 TTAATTCTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 16 0.62
19 10 0.38
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (19 bp):
TATTTTTATATAATTCTAA
Found at i:2773195 original size:54 final size:54
Alignment explanation
Indices: 2773137--2773250 Score: 124
Period size: 54 Copynumber: 2.1 Consensus size: 54
2773127 GAGTCCTAGC
* ** *
2773137 CCGTGTCCTCA-CCCGTGTAACTCAT-TGAGGTGCCCCACACGTCCGTGTGTCAAG
1 CCGTGTCCT-AGCCCGTGTAACTC-TCTGAGGTGCCACACACACCCGTGTGCCAAG
* ** *
2773191 CCGTGTGCTAGGTCGTGTAACTCTCTGAGTTGCCACACACACCCGTGTGCCAAG
1 CCGTGTCCTAGCCCGTGTAACTCTCTGAGGTGCCACACACACCCGTGTGCCAAG
2773245 CCGTGT
1 CCGTGT
2773251 AACTCACTGA
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
53 2 0.04
54 48 0.96
ACGTcount: A:0.17, C:0.33, G:0.25, T:0.25
Consensus pattern (54 bp):
CCGTGTCCTAGCCCGTGTAACTCTCTGAGGTGCCACACACACCCGTGTGCCAAG
Found at i:2783569 original size:54 final size:54
Alignment explanation
Indices: 2783511--2783624 Score: 124
Period size: 54 Copynumber: 2.1 Consensus size: 54
2783501 GAGTCCTAGC
* ** *
2783511 CCGTGTCCTCA-CCCGTGTAACTCAT-TGAGGTGCCCCACACGTCCGTGTGTCAAG
1 CCGTGTCCT-AGCCCGTGTAACTC-TCTGAGGTGCCACACACACCCGTGTGCCAAG
* ** *
2783565 CCGTGTGCTAGGTCGTGTAACTCTCTGAGTTGCCACACACACCCGTGTGCCAAG
1 CCGTGTCCTAGCCCGTGTAACTCTCTGAGGTGCCACACACACCCGTGTGCCAAG
2783619 CCGTGT
1 CCGTGT
2783625 AACTCACTGA
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
53 2 0.04
54 48 0.96
ACGTcount: A:0.17, C:0.33, G:0.25, T:0.25
Consensus pattern (54 bp):
CCGTGTCCTAGCCCGTGTAACTCTCTGAGGTGCCACACACACCCGTGTGCCAAG
Found at i:2788810 original size:61 final size:61
Alignment explanation
Indices: 2788736--2788864 Score: 240
Period size: 61 Copynumber: 2.1 Consensus size: 61
2788726 AGTATTTTAG
*
2788736 ATCGATATGATAGAGATATTAGATTGATTCAAAAATTTACATGCATGGCAATTACAATTAT
1 ATCGATATGATAGAGATATTAAATTGATTCAAAAATTTACATGCATGGCAATTACAATTAT
*
2788797 ATCGATATGATAGAGATATTAAATTGATTCAAAAATTTATATGCATGGCAATTACAATTAT
1 ATCGATATGATAGAGATATTAAATTGATTCAAAAATTTACATGCATGGCAATTACAATTAT
2788858 ATCGATA
1 ATCGATA
2788865 AATTCAACGC
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 66 1.00
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.35
Consensus pattern (61 bp):
ATCGATATGATAGAGATATTAAATTGATTCAAAAATTTACATGCATGGCAATTACAATTAT
Found at i:2794848 original size:19 final size:19
Alignment explanation
Indices: 2794824--2794874 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
2794814 ATATTAAAAT
2794824 ATAATTTTTTTAATTTTTA
1 ATAATTTTTTTAATTTTTA
*
2794843 ATAATTTTTATT-TTTTTTA
1 ATAATTTTT-TTAATTTTTA
*
2794862 AAAATATTTTTTA
1 ATAAT-TTTTTTA
2794875 CAATTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 21 0.78
20 6 0.22
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
ATAATTTTTTTAATTTTTA
Found at i:2795551 original size:18 final size:18
Alignment explanation
Indices: 2795530--2795567 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
2795520 TATTCTTTAA
2795530 CTTTCTTTTT-TTCTTCTT
1 CTTTCTTTTTATTC-TCTT
*
2795548 CTTTTTTTTTATTCTCTT
1 CTTTCTTTTTATTCTCTT
2795566 CT
1 CT
2795568 GCTTCTCCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (18 bp):
CTTTCTTTTTATTCTCTT
Found at i:2796510 original size:42 final size:42
Alignment explanation
Indices: 2796464--2796579 Score: 135
Period size: 42 Copynumber: 2.8 Consensus size: 42
2796454 GGCGTGCTTC
* *
2796464 CACTGTCGTTTCAGTGAAAATGCATCCTACAAGACGCATTTT
1 CACTGTCGTTTCAGTGAAAACGCATCCTACAAGACACATTTT
** *
2796506 CACTGTCGTGCCAGTGAAAACGCATCCTACAAGGCACATTTT
1 CACTGTCGTTTCAGTGAAAACGCATCCTACAAGACACATTTT
* * * *
2796548 TACTGTC-TTGTCAGTGACAACACGTCCTACAA
1 CACTGTCGTT-TCAGTGAAAACGCATCCTACAA
2796580 TGTATGTTTT
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
41 1 0.02
42 61 0.98
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.28
Consensus pattern (42 bp):
CACTGTCGTTTCAGTGAAAACGCATCCTACAAGACACATTTT
Found at i:2796978 original size:13 final size:14
Alignment explanation
Indices: 2796960--2796993 Score: 52
Period size: 13 Copynumber: 2.4 Consensus size: 14
2796950 AGTTTTTTCA
2796960 TTTTTAATT-AATC
1 TTTTTAATTAAATC
2796973 TTTTTAATTAAATC
1 TTTTTAATTAAATC
2796987 TCTTTTA
1 T-TTTTA
2796994 TTTATAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 9 0.47
14 5 0.26
15 5 0.26
ACGTcount: A:0.29, C:0.09, G:0.00, T:0.62
Consensus pattern (14 bp):
TTTTTAATTAAATC
Found at i:2801791 original size:23 final size:23
Alignment explanation
Indices: 2801746--2801791 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
2801736 TTTTTACAAT
** *
2801746 GGTTTTGCCTGCTTTTATGGCAC
1 GGTTTTGCCTGCTTCCATAGCAC
*
2801769 GGTTTTGTCTGCTTCCATAGCAC
1 GGTTTTGCCTGCTTCCATAGCAC
2801792 AGTAGTTTGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.11, C:0.24, G:0.24, T:0.41
Consensus pattern (23 bp):
GGTTTTGCCTGCTTCCATAGCAC
Found at i:2802975 original size:90 final size:84
Alignment explanation
Indices: 2802774--2803017 Score: 244
Period size: 90 Copynumber: 2.8 Consensus size: 84
2802764 CTTAAGGGTG
* *
2802774 TAAAAAA-ACCCTCAAACTTAAAAAAAAAAACAATTAAG-TCCTATTTTTTTCACTTAATTGAGT
1 TAAAAAAGACCCTCAAACTT-AAAAAAAAAACAATTAAGCCCCTATTTTTTGCACTTAATTGAGT
***
2802837 ACTTGAACTTTTAAAATGCA
65 ACTTGAACTACCAAAATGCA
* * ** * *
2802857 TCAAAAAGACCCTCAAAATTTTTCAAAAAAAGCAATTAAGCCCCTACTCATTTTTCGCACTTAGT
1 TAAAAAAGACCCTC-AAA-CTTAAAAAAAAAACAATTAAGCCCCTA-T--TTTTT-GCACTTA-A
2802922 TTG-GTACTTGAACTACCAAAATGCA
59 TTGAGTACTTGAACTACCAAAATGCA
* ** *
2802947 TAAAAAAGATCCTCAAACTTAAAAAAAAAACAATTAAGCCTTTTTTTTTTTGCAC-TAATTGAGT
1 TAAAAAAGACCCTCAAACTTAAAAAAAAAACAATTAAGCC-CCTATTTTTTGCACTTAATTGAGT
2803011 ACTTGAA
65 ACTTGAA
2803018 TGCATCAAAA
Statistics
Matches: 129, Mismatches: 21, Indels: 21
0.75 0.12 0.12
Matches are distributed among these distances:
83 9 0.07
84 17 0.13
85 22 0.17
86 11 0.09
87 1 0.01
88 20 0.16
89 9 0.07
90 37 0.29
91 3 0.02
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.32
Consensus pattern (84 bp):
TAAAAAAGACCCTCAAACTTAAAAAAAAAACAATTAAGCCCCTATTTTTTGCACTTAATTGAGTA
CTTGAACTACCAAAATGCA
Found at i:2805224 original size:19 final size:19
Alignment explanation
Indices: 2805202--2805255 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
2805192 TTACAAAAAG
*
2805202 AATTCAAAATGATTT-TTAA
1 AATTCAAAAT-ATTTATAAA
2805221 AATTCAAAATATTTATAAA
1 AATTCAAAATATTTATAAA
*
2805240 AATTCCAAA-ATTTATA
1 AATTCAAAATATTTATA
2805256 TTTTTAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
18 11 0.34
19 21 0.66
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (19 bp):
AATTCAAAATATTTATAAA
Found at i:2805281 original size:20 final size:20
Alignment explanation
Indices: 2805256--2805294 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
2805246 AAAATTTATA
2805256 TTTTTAAAAAAATTATAAAT
1 TTTTTAAAAAAATTATAAAT
2805276 TTTTTAAAAAAATTATAAA
1 TTTTTAAAAAAATTATAAA
2805295 GAATATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TTTTTAAAAAAATTATAAAT
Found at i:2805403 original size:3 final size:3
Alignment explanation
Indices: 2805395--2805422 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2805385 TACTAAAATA
2805395 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
2805423 GCTTTGGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:2808145 original size:32 final size:32
Alignment explanation
Indices: 2808104--2808196 Score: 168
Period size: 32 Copynumber: 2.9 Consensus size: 32
2808094 TGTCAATCAT
2808104 TTCAATATCCAACAAGCTTAAAACATAATAAA
1 TTCAATATCCAACAAGCTTAAAACATAATAAA
*
2808136 TTCAATATCCAACAAGCTTAAAATATAATAAA
1 TTCAATATCCAACAAGCTTAAAACATAATAAA
*
2808168 TTCAATATCTAACAAGCTTAAAACATAAT
1 TTCAATATCCAACAAGCTTAAAACATAAT
2808197 CAATATCTAA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 58 1.00
ACGTcount: A:0.52, C:0.17, G:0.03, T:0.28
Consensus pattern (32 bp):
TTCAATATCCAACAAGCTTAAAACATAATAAA
Found at i:2808203 original size:27 final size:29
Alignment explanation
Indices: 2808104--2808209 Score: 117
Period size: 32 Copynumber: 3.5 Consensus size: 29
2808094 TGTCAATCAT
2808104 TTCAATATCCAACAAGCTTAAAACATAATAAA
1 TTCAATATCCAACAAGCTTAAAAC---ATAAA
*
2808136 TTCAATATCCAACAAGCTTAAAATATAATAAA
1 TTCAATATCCAACAAGCTT-AAA-A-CATAAA
*
2808168 TTCAATATCTAACAAGCTTAAAACAT-AA
1 TTCAATATCCAACAAGCTTAAAACATAAA
*
2808196 -TCAATATCTAACAA
1 TTCAATATCCAACAA
2808210 ATTCAAGAAA
Statistics
Matches: 68, Mismatches: 3, Indels: 11
0.83 0.04 0.13
Matches are distributed among these distances:
27 14 0.21
28 2 0.03
29 2 0.03
30 1 0.01
31 3 0.04
32 42 0.62
33 3 0.04
34 1 0.01
ACGTcount: A:0.52, C:0.18, G:0.03, T:0.27
Consensus pattern (29 bp):
TTCAATATCCAACAAGCTTAAAACATAAA
Found at i:2811951 original size:43 final size:42
Alignment explanation
Indices: 2811881--2812002 Score: 149
Period size: 42 Copynumber: 2.9 Consensus size: 42
2811871 AAAAAGCTCG
* *
2811881 TACGATGCCAAC-GTCCCAAAC-GTGGTCTTACATGTAATCAAA
1 TACGATGCC-ACTGTCCCAGACAG-GGTCTTACACGTAATCAAA
*
2811923 TAACGATGCCACTGTCCCAGACAGGGTCTTACACGTAATCATA
1 T-ACGATGCCACTGTCCCAGACAGGGTCTTACACGTAATCAAA
* * *
2811966 TACGATGCCAATGTCCCAGACATGGTCTGACACGTAA
1 TACGATGCCACTGTCCCAGACAGGGTCTTACACGTAA
2812003 ATCACATATC
Statistics
Matches: 71, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
42 36 0.51
43 34 0.48
44 1 0.01
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.23
Consensus pattern (42 bp):
TACGATGCCACTGTCCCAGACAGGGTCTTACACGTAATCAAA
Found at i:2811984 original size:42 final size:42
Alignment explanation
Indices: 2811881--2812002 Score: 156
Period size: 43 Copynumber: 2.9 Consensus size: 42
2811871 AAAAAGCTCG
* * *
2811881 TACGATGCCAACGTCCCAAAC-GTGGTCTTACATGTAATCAAA
1 TACGATGCCAATGTCCCAGACAG-GGTCTTACACGTAATCAAA
* *
2811923 TAACGATGCCACTGTCCCAGACAGGGTCTTACACGTAATCATA
1 T-ACGATGCCAATGTCCCAGACAGGGTCTTACACGTAATCAAA
* *
2811966 TACGATGCCAATGTCCCAGACATGGTCTGACACGTAA
1 TACGATGCCAATGTCCCAGACAGGGTCTTACACGTAA
2812003 ATCACATATC
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
42 34 0.49
43 35 0.50
44 1 0.01
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.23
Consensus pattern (42 bp):
TACGATGCCAATGTCCCAGACAGGGTCTTACACGTAATCAAA
Found at i:2825168 original size:18 final size:20
Alignment explanation
Indices: 2825145--2825182 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2825135 ACTATCTCCA
2825145 GGATCA-AGT-TGCAAGAAG
1 GGATCACAGTATGCAAGAAG
*
2825163 GGATCACAGTATGGAAGAAG
1 GGATCACAGTATGCAAGAAG
2825183 CTGTGGTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 3 0.18
20 8 0.47
ACGTcount: A:0.39, C:0.11, G:0.34, T:0.16
Consensus pattern (20 bp):
GGATCACAGTATGCAAGAAG
Found at i:2825467 original size:20 final size:20
Alignment explanation
Indices: 2825434--2825473 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2825424 TTCATCTCAT
*
2825434 GCATCGCATCATATGCATTA
1 GCATCACATCATATGCATTA
* *
2825454 GCATCACATTATATGGATTA
1 GCATCACATCATATGCATTA
2825474 TAGACCTTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.33
Consensus pattern (20 bp):
GCATCACATCATATGCATTA
Found at i:2835204 original size:44 final size:44
Alignment explanation
Indices: 2835155--2836599 Score: 1513
Period size: 44 Copynumber: 32.6 Consensus size: 44
2835145 TACTGGTGGC
* *
2835155 GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTACTGGCGT
1 GAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCGT
* * *** * *
2835199 GAAGTAGATCAAAGATACCAGATCTTGTCTTCCCATACTGGTGGC
1 GAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGG-CGT
* * * *
2835244 GAAGTAGATCGAAGAAAATAGATCTTGTTTTCATGTACTGCCGT
1 GAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCGT
* * * *
2835288 GAAATAGATCAAAG-AAACAGATCTTGTCTTC-TCATACTGGTGGC
1 GAAGTAGATCAAAGAAAACAGATCTTGTCTTCAT-GTACTGG-CGT
* *
2835332 GAAGTAGATCGAAGAAAACAAATCTTGTCTTCATGTACTGGCGT
1 GAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCGT
* * *** * *
2835376 GAAGTAGATCAAAGATACCAGATCTTGTCTTCCCATACTGGTGGC
1 GAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGG-CGT
** * *
2835421 GAAGTAGATTGAAGAAAACGGATCTTGTCTTCATGTGCTGGCGT
1 GAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCGT
*** * * *
2835465 GAAGTAGATCAAAG-AAACAGATCTTGTCTTCCCATATTGGTGGA
1 GAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGG-CGT
*
2835509 GAAATAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCGT
1 GAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCGT
* * * *** * *
2835553 AAAGTAGATCAAAGATATCAGATCTTGTCTTCCCATACTGGTGGC
1 GAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGG-CGT
*
2835598 GAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGGCGT
1 GAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCGT
* * *** *
2835642 GAAATAGATCAAAGAAAATAGATCTTGTCTTCCCATACTGGTG-
1 GAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCGT
2835685 GCAAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCGT
1 G--AAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCGT
* * *** * *
2835731 GAAGTAGATCAAA-AATAGCAGATCTTGCCTTCCCATACTGGTGGC
1 GAAGTAGATCAAAGAA-AACAGATCTTGTCTTCATGTACTGG-CGT
*
2835776 GAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGGCGT
1 GAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCGT
* * *** * *
2835820 GAAGTAGATAAAAGAAAACAGATCTTGCCTTCCCATACTGGTGGC
1 GAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGG-CGT
* * *
2835865 GAAGCAGATCGAAGAAAACAGATCTTGTCTTCATGTATTGGCGT
1 GAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCGT
* *
2835909 GAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTATTGGCGT
1 GAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCGT
* *
2835953 GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTACTGGCGT
1 GAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCGT
* * *** * *
2835997 GAAGTAGATCAAAGATACCAGATCTTGTCTTCCCATACTGGTGGC
1 GAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGG-CGT
*
2836042 GAAGTAGATCGAAGAAAAC-GAATCTTGTCTTCATGTACTGGCGT
1 GAAGTAGATCAAAGAAAACAG-ATCTTGTCTTCATGTACTGGCGT
* *** * *
2836086 GAAGTAGAT-AAAAAAAACAGATCTTGTCTTCCCATACTGGTGGC
1 GAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGG-CGT
* *
2836130 GAAGTAGATCGAAGAAAACGGATCTTGTCTTCATGTACTGGCGT
1 GAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCGT
*** * *
2836174 GAAGTAGATCAAAGAAAACAGATCTTGTCTTCCCATACTGGTGGC
1 GAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGG-CGT
*** * *
2836219 GAAGTAGATCAAAGAAAACAGATCTTGTCTTCCCATACTGGTGGC
1 GAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGG-CGT
2836264 GAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCGT
1 GAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCGT
* * * * * * *** * *
2836308 -AAATAGATCAAAGATAGCAAATATTGCCTTCCCATACTGGTGGC
1 GAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGG-CGT
*
2836352 GAAGCAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCGT
1 GAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCGT
* ** *** *
2836396 GAAGTAGATCAAAGAAAACAAATCTTACCTTCCCATACTGGTG-
1 GAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCGT
* * *
2836439 GCAAAGCAGATCGAAGAAAACAGATCTTGTCTTCATGTATTGGCGT
1 G--AAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCGT
* *
2836485 GAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTATTGGCGT
1 GAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCGT
* *
2836529 GAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTATTGGCGT
1 GAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCGT
*
2836573 GAAGTAGATCGAAGAAAACAGATCTTG
1 GAAGTAGATCAAAGAAAACAGATCTTG
2836600 GCAAATCAAA
Statistics
Matches: 1152, Mismatches: 222, Indels: 54
0.81 0.16 0.04
Matches are distributed among these distances:
42 1 0.00
43 99 0.09
44 594 0.52
45 453 0.39
46 5 0.00
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (44 bp):
GAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCGT
Found at i:2835279 original size:89 final size:89
Alignment explanation
Indices: 2835121--2836599 Score: 1942
Period size: 89 Copynumber: 16.7 Consensus size: 89
2835111 GAACAGGTTG
* *
2835121 AAAG-AAACAGATCTTGCCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCT
1 AAAGAAAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCT
2835185 TCATGTACTGGCGTGAAGTAGATC
66 TCATGTACTGGCGTGAAGTAGATC
* * * *
2835209 AAAGATACCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAATAGATCTTGTTT
1 AAAGAAAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCT
* *
2835274 TCATGTACTGCCGTGAAATAGATC
66 TCATGTACTGGCGTGAAGTAGATC
* *
2835298 AAAG-AAACAGATCTTGTCTTCTCATACTGGTGGCGAAGTAGATCGAAGAAAACAAATCTTGTCT
1 AAAGAAAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCT
2835362 TCATGTACTGGCGTGAAGTAGATC
66 TCATGTACTGGCGTGAAGTAGATC
* * * *
2835386 AAAGATACCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATTGAAGAAAACGGATCTTGTCT
1 AAAGAAAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCT
*
2835451 TCATGTGCTGGCGTGAAGTAGATC
66 TCATGTACTGGCGTGAAGTAGATC
* * * *
2835475 AAAG-AAACAGATCTTGTCTTCCCATATTGGTGGAGAAATAGATCAAAGAAAACAGATCTTGTCT
1 AAAGAAAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCT
*
2835539 TCATGTACTGGCGTAAAGTAGATC
66 TCATGTACTGGCGTGAAGTAGATC
* *
2835563 AAAGATATCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCT
1 AAAGAAAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCT
*
2835628 TCATGTACTGGCGTGAAATAGATC
66 TCATGTACTGGCGTGAAGTAGATC
* * *
2835652 AAAGAAAATAGATCTTGTCTTCCCATACTGGTGGCAAAGTAGATCAAAGAAAACAGATCTTGTCT
1 AAAGAAAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCT
2835717 TCATGTACTGGCGTGAAGTAGATC
66 TCATGTACTGGCGTGAAGTAGATC
* *
2835741 AAA-AATAGCAGATCTTGCCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTC
1 AAAGAA-AACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTC
*
2835805 TTCATGTACTGGCGTGAAGTAGATA
65 TTCATGTACTGGCGTGAAGTAGATC
* *
2835830 AAAGAAAACAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCGAAGAAAACAGATCTTGTCT
1 AAAGAAAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCT
*
2835895 TCATGTATTGGCGTGAAGTAGATC
66 TCATGTACTGGCGTGAAGTAGATC
* *** * * * *
2835919 GAAGAAAACAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGAAAGCAGATCTTGTCT
1 AAAGAAAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCT
2835983 TCATGTACTGGCGTGAAGTAGATC
66 TCATGTACTGGCGTGAAGTAGATC
* *
2836007 AAAGATACCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAAC-GAATCTTGTC
1 AAAGAAAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAG-ATCTTGTC
2836071 TTCATGTACTGGCGTGAAGTAGAT-
65 TTCATGTACTGGCGTGAAGTAGATC
* *
2836095 AAAAAAAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACGGATCTTGTCT
1 AAAGAAAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCT
2836160 TCATGTACTGGCGTGAAGTAGATC
66 TCATGTACTGGCGTGAAGTAGATC
*
2836184 AAAGAAAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGAAAACAGATCTTGTCT
1 AAAGAAAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCT
*** * *
2836249 TCCCATACTGGTGGCGAAGTAGATC
66 TCATGTACTGG-CGTGAAGTAGATC
* ** * * * * * * *
2836274 AAAGAAAACAGATCTTGTCTT--CAT-GTACTGGCGTAAATAGATCAAAGATAGCAAATATTGCC
1 AAAGAAAACAGATCTTGTCTTCCCATACTGGTGGCG-AAGTAGATCGAAGAAAACAGATCTTGTC
*** * * *
2836336 TTCCCATACTGGTGGCGAAGCAGATC
65 TTCATGTACTGG-CGTGAAGTAGATC
*** * * * * **
2836362 AAAGAAAACAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATCAAAGAAAACAAATCTTACCT
1 AAAGAAAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCT
*** * *
2836426 TCCCATACTGGTG-GCAAAGCAGATC
66 TCATGTACTGGCGTG--AAGTAGATC
* *** * * *
2836451 GAAGAAAACAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGAAAACAGATCTTGTCT
1 AAAGAAAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCT
*
2836515 TCATGTATTGGCGTGAAGTAGATC
66 TCATGTACTGGCGTGAAGTAGATC
* *** * * *
2836539 GAAGAAAACAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGAAAACAGATCTTG
1 AAAGAAAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTG
2836600 GCAAATCAAA
Statistics
Matches: 1250, Mismatches: 124, Indels: 34
0.89 0.09 0.02
Matches are distributed among these distances:
87 7 0.01
88 465 0.37
89 739 0.59
90 38 0.03
91 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.27
Consensus pattern (89 bp):
AAAGAAAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCT
TCATGTACTGGCGTGAAGTAGATC
Found at i:2835417 original size:177 final size:178
Alignment explanation
Indices: 2835121--2836599 Score: 1942
Period size: 177 Copynumber: 8.3 Consensus size: 178
2835111 GAACAGGTTG
* *
2835121 AAAG-AAACAGATCTTGCCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCT
1 AAAGAAAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCT
* *
2835185 TCATGTACTGGCGTGAAGTAGATCAAAGATACCAGATCTTGTCTTCCCATACTGGTGGCGAAGTA
66 TCATGTACTGGCGTGAAGTAGATCAAAGAAAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTA
* * * *
2835250 GATCGAAGAAAATAGATCTTGTTTTCATGTACTGCCGTGAAATAGATC
131 GATCGAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATC
* *
2835298 AAAG-AAACAGATCTTGTCTTCTCATACTGGTGGCGAAGTAGATCGAAGAAAACAAATCTTGTCT
1 AAAGAAAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCT
* *
2835362 TCATGTACTGGCGTGAAGTAGATCAAAGATACCAGATCTTGTCTTCCCATACTGGTGGCGAAGTA
66 TCATGTACTGGCGTGAAGTAGATCAAAGAAAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTA
* * *
2835427 GATTGAAGAAAACGGATCTTGTCTTCATGTGCTGGCGTGAAGTAGATC
131 GATCGAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATC
* * * *
2835475 AAAG-AAACAGATCTTGTCTTCCCATATTGGTGGAGAAATAGATCAAAGAAAACAGATCTTGTCT
1 AAAGAAAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCT
* * *
2835539 TCATGTACTGGCGTAAAGTAGATCAAAGATATCAGATCTTGTCTTCCCATACTGGTGGCGAAGTA
66 TCATGTACTGGCGTGAAGTAGATCAAAGAAAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTA
*
2835604 GATCGAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAATAGATC
131 GATCGAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATC
* * *
2835652 AAAGAAAATAGATCTTGTCTTCCCATACTGGTGGCAAAGTAGATCAAAGAAAACAGATCTTGTCT
1 AAAGAAAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCT
* *
2835717 TCATGTACTGGCGTGAAGTAGATCAAA-AATAGCAGATCTTGCCTTCCCATACTGGTGGCGAAGT
66 TCATGTACTGGCGTGAAGTAGATCAAAGAA-AACAGATCTTGTCTTCCCATACTGGTGGCGAAGT
*
2835781 AGATCGAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATA
130 AGATCGAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATC
* *
2835830 AAAGAAAACAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCGAAGAAAACAGATCTTGTCT
1 AAAGAAAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCT
* * *** * * *
2835895 TCATGTATTGGCGTGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTATTGG-CGTGAAGTA
66 TCATGTACTGGCGTGAAGTAGATCAAAGAAAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTA
*
2835959 GATCGAAGAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATC
131 GATCGAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATC
* *
2836007 AAAGATACCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAAC-GAATCTTGTC
1 AAAGAAAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAG-ATCTTGTC
*
2836071 TTCATGTACTGGCGTGAAGTAGAT-AAAAAAAACAGATCTTGTCTTCCCATACTGGTGGCGAAGT
65 TTCATGTACTGGCGTGAAGTAGATCAAAGAAAACAGATCTTGTCTTCCCATACTGGTGGCGAAGT
*
2836135 AGATCGAAGAAAACGGATCTTGTCTTCATGTACTGGCGTGAAGTAGATC
130 AGATCGAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATC
*
2836184 AAAGAAAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGAAAACAGATCTTGTCT
1 AAAGAAAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCT
*** * * * ** *
2836249 TCCCATACTGGTGGCGAAGTAGATCAAAGAAAACAGATCTTGTCTT--CAT-GTACTGGCGTAAA
66 TCATGTACTGG-CGTGAAGTAGATCAAAGAAAACAGATCTTGTCTTCCCATACTGGTGGCG-AAG
* * * * * * *** * * *
2836311 TAGATCAAAGATAGCAAATATTGCCTTCCCATACTGGTGGCGAAGCAGATC
129 TAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATC
*** * * * * **
2836362 AAAGAAAACAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATCAAAGAAAACAAATCTTACCT
1 AAAGAAAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCT
*** * * * *** * * *
2836426 TCCCATACTGGTG-GCAAAGCAGATCGAAGAAAACAGATCTTGTCTTCATGTATTGG-CGTGAAG
66 TCATGTACTGGCGTG--AAGTAGATCAAAGAAAACAGATCTTGTCTTCCCATACTGGTGGCGAAG
*
2836489 TAGATCGAAGAAAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATC
129 TAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATC
* *** * * *
2836539 GAAGAAAACAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGAAAACAGATCTTG
1 AAAGAAAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTG
2836600 GCAAATCAAA
Statistics
Matches: 1158, Mismatches: 129, Indels: 30
0.88 0.10 0.02
Matches are distributed among these distances:
175 1 0.00
176 33 0.03
177 756 0.65
178 342 0.30
179 25 0.02
180 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.27
Consensus pattern (178 bp):
AAAGAAAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCT
TCATGTACTGGCGTGAAGTAGATCAAAGAAAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTA
GATCGAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATC
Found at i:2837320 original size:10 final size:11
Alignment explanation
Indices: 2837300--2837324 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2837290 AGTTTCGGAC
2837300 TTTCTTTTTTT
1 TTTCTTTTTTT
2837311 TTTCTTTTTTT
1 TTTCTTTTTTT
2837322 TTT
1 TTT
2837325 TCTGCTTATT
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:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTCTTTTTTT
Found at i:2843007 original size:13 final size:14
Alignment explanation
Indices: 2842983--2843011 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
2842973 TATAAATATA
2842983 AATAATTATATAAT
1 AATAATTATATAAT
2842997 AATAA-TATATAAT
1 AATAATTATATAAT
2843010 AA
1 AA
2843012 GACAAATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AATAATTATATAAT
Found at i:2843115 original size:48 final size:48
Alignment explanation
Indices: 2843063--2843162 Score: 116
Period size: 49 Copynumber: 2.1 Consensus size: 48
2843053 ATATAGTTAT
* * * *
2843063 AAATATATAAAA-TAAAAAATAATACAA-AACTAATTAATATATTAATA-C
1 AAATAAATAAAAGGAAAAAATAAAACAATAA-TAAATAATA-A-TAATATC
2843111 AAATAAATAAAAGGAAAAAATAAAACAATAATAAATAATAATAATATC
1 AAATAAATAAAAGGAAAAAATAAAACAATAATAAATAATAATAATATC
2843159 AAAT
1 AAAT
2843163 TATTAGTTTA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
47 5 0.11
48 17 0.38
49 21 0.47
50 2 0.04
ACGTcount: A:0.68, C:0.05, G:0.02, T:0.25
Consensus pattern (48 bp):
AAATAAATAAAAGGAAAAAATAAAACAATAATAAATAATAATAATATC
Found at i:2849334 original size:20 final size:21
Alignment explanation
Indices: 2849309--2849357 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
2849299 GTTTAGAAAT
*
2849309 AAAAAATA-AATAAAAATTTC
1 AAAAAATACAATAAAAATTTA
* *
2849329 AAAAAATACATTAAAAGTTTA
1 AAAAAATACAATAAAAATTTA
2849350 AAAAAATA
1 AAAAAATA
2849358 TTGCTTCATC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 8 0.32
21 17 0.68
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.24
Consensus pattern (21 bp):
AAAAAATACAATAAAAATTTA
Found at i:2851997 original size:45 final size:44
Alignment explanation
Indices: 2851831--2851997 Score: 120
Period size: 45 Copynumber: 3.8 Consensus size: 44
2851821 TTCAAACGAG
* * * ** ** * *
2851831 TAAGACCATAGCTGAAAGATGTTATAACATCAAAATAAAATAAG
1 TAAGACCATAGCTGAAAGACGCTATAGCATCATGAGGAAATGAC
* * * *
2851875 TAAAACCATAGCTGAAAGACACTATAGCATCATGACGGAAGTGAG
1 TAAGACCATAGCTGAAAGACGCTATAGCATCATGA-GGAAATGAC
* * * * *
2851920 TAAGACCATGGCTGAAAGATGCTATGGTATCATG-GTAAATAGGAC
1 TAAGACCATAGCTGAAAGACGCTATAGCATCATGAGGAAAT--GAC
* *
2851965 TATGACCATAGCTAAAAGACGCTATAGCATCAT
1 TAAGACCATAGCTGAAAGACGCTATAGCATCAT
2851998 TTGACAGTTA
Statistics
Matches: 94, Mismatches: 26, Indels: 5
0.75 0.21 0.04
Matches are distributed among these distances:
43 4 0.04
44 28 0.30
45 62 0.66
ACGTcount: A:0.43, C:0.16, G:0.20, T:0.22
Consensus pattern (44 bp):
TAAGACCATAGCTGAAAGACGCTATAGCATCATGAGGAAATGAC
Found at i:2856874 original size:13 final size:13
Alignment explanation
Indices: 2856852--2856881 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2856842 ATTGGTACCA
*
2856852 CAAATTATATCAT
1 CAAATCATATCAT
2856865 CAAATCATATCAT
1 CAAATCATATCAT
2856878 CAAA
1 CAAA
2856882 GTATCATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (13 bp):
CAAATCATATCAT
Found at i:2857660 original size:40 final size:38
Alignment explanation
Indices: 2857611--2857742 Score: 99
Period size: 40 Copynumber: 3.4 Consensus size: 38
2857601 AACACACCAG
*
2857611 TTTGGCACCCAGTGCTTCATCGGATAATTCGAAGTAATAA
1 TTTGACACCCAGTGCTTCATCGGATAA-TCGAAGT-ATAA
* *
2857651 TTTGACACCCAGTG-TCTCATCGGCTAAACCGAAGTA-AA
1 TTTGACACCCAGTGCT-TCATCGGAT-AATCGAAGTATAA
* * * * *
2857689 -TTGGCACACAGTGCCTCATCGAATTAATCTGAAGTCGTAA
1 TTTGACACCCAGTGCTTCATCGGA-TAATC-GAAGT-ATAA
*
2857729 ATTGACACCCAGTG
1 TTTGACACCCAGTG
2857743 TCACATCGAC
Statistics
Matches: 72, Mismatches: 12, Indels: 15
0.73 0.12 0.15
Matches are distributed among these distances:
37 20 0.28
38 8 0.11
39 2 0.03
40 29 0.40
41 13 0.18
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (38 bp):
TTTGACACCCAGTGCTTCATCGGATAATCGAAGTATAA
Found at i:2857915 original size:19 final size:16
Alignment explanation
Indices: 2857873--2857932 Score: 52
Period size: 17 Copynumber: 3.6 Consensus size: 16
2857863 TATTCATTTC
2857873 AATTCAA-ATAATCAATA
1 AATTCAATATAAT--ATA
*
2857890 TATTCAATATATATATA
1 AATTCAATATA-ATATA
2857907 CCAATTCAAT-TAATATA
1 --AATTCAATATAATATA
2857924 AATTCAATA
1 AATTCAATA
2857933 AATTCATCAC
Statistics
Matches: 36, Mismatches: 2, Indels: 11
0.73 0.04 0.22
Matches are distributed among these distances:
15 8 0.22
17 14 0.39
18 5 0.14
19 9 0.25
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.37
Consensus pattern (16 bp):
AATTCAATATAATATA
Found at i:2858190 original size:19 final size:19
Alignment explanation
Indices: 2858166--2858221 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
2858156 CCCTAGTTTC
*
2858166 TCCTTTCTCATTCTTTCTT
1 TCCTTTCTCTTTCTTTCTT
*
2858185 TCCTTTTTCTTTCTCTT-TT
1 TCCTTTCTCTTTCT-TTCTT
2858204 TCC-TTCTCTTTCGTTTCT
1 TCCTTTCTCTTTC-TTTCT
2858222 ATCTTTGTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
18 10 0.32
19 19 0.61
20 2 0.06
ACGTcount: A:0.02, C:0.30, G:0.02, T:0.66
Consensus pattern (19 bp):
TCCTTTCTCTTTCTTTCTT
Found at i:2858204 original size:12 final size:12
Alignment explanation
Indices: 2858168--2858214 Score: 60
Period size: 12 Copynumber: 3.8 Consensus size: 12
2858158 CTAGTTTCTC
2858168 CTTTCTCATTCTTT
1 CTTTCTC-TT-TTT
2858182 CTTTC-CTTTTT
1 CTTTCTCTTTTT
2858193 CTTTCTCTTTTT
1 CTTTCTCTTTTT
*
2858205 CCTTCTCTTT
1 CTTTCTCTTT
2858215 CGTTTCTATC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
11 8 0.26
12 17 0.55
13 1 0.03
14 5 0.16
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.68
Consensus pattern (12 bp):
CTTTCTCTTTTT
Found at i:2858267 original size:5 final size:5
Alignment explanation
Indices: 2858257--2858294 Score: 69
Period size: 5 Copynumber: 7.8 Consensus size: 5
2858247 TTTGTTTTAT
2858257 TATAA TATAA TATAA TATAA TATAA TATAA TAT-A TATA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATA
2858295 CTTAATTCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 4 0.12
5 28 0.88
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
TATAA
Found at i:2858324 original size:10 final size:10
Alignment explanation
Indices: 2858254--2858326 Score: 53
Period size: 10 Copynumber: 7.3 Consensus size: 10
2858244 TTATTTGTTT
2858254 TATTATAATA
1 TATTATAATA
*
2858264 TAATATAATA
1 TATTATAATA
*
2858274 TAATATAATA
1 TATTATAATA
*
2858284 TAATAT-ATA
1 TATTATAATA
*
2858293 TACT-TAAT-
1 TATTATAATA
*
2858301 TCTTAAGGTAATA
1 TATT-A--TAATA
2858314 TATTATAATA
1 TATTATAATA
2858324 TAT
1 TAT
2858327 ATTTTAACTT
Statistics
Matches: 52, Mismatches: 5, Indels: 12
0.75 0.07 0.17
Matches are distributed among these distances:
8 3 0.06
9 8 0.15
10 33 0.63
12 5 0.10
13 3 0.06
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.45
Consensus pattern (10 bp):
TATTATAATA
Found at i:2865461 original size:26 final size:26
Alignment explanation
Indices: 2865428--2865490 Score: 92
Period size: 26 Copynumber: 2.4 Consensus size: 26
2865418 ATTACCCTAG
2865428 TAAAATTTTGAC-AGTTTTACCCCCAA
1 TAAAATTTTGACGA-TTTTACCCCCAA
* *
2865454 TCAAATTTTGACGATTTTACCCTCAA
1 TAAAATTTTGACGATTTTACCCCCAA
2865480 TAAAATTTTGA
1 TAAAATTTTGA
2865491 GAAAATTCAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
26 32 0.97
27 1 0.03
ACGTcount: A:0.35, C:0.19, G:0.08, T:0.38
Consensus pattern (26 bp):
TAAAATTTTGACGATTTTACCCCCAA
Found at i:2866257 original size:16 final size:16
Alignment explanation
Indices: 2866236--2866271 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
2866226 TTTGGTTCGC
2866236 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
2866252 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
2866268 TGTA
1 TGTA
2866272 ATAGCTAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.36, T:0.39
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:2866336 original size:44 final size:45
Alignment explanation
Indices: 2866252--2866342 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
2866242 GGATTAGAGG
* * *
2866252 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
2866297 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
2866341 TG
1 TG
2866343 GAAAAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:2876890 original size:2 final size:2
Alignment explanation
Indices: 2876883--2876919 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2876873 ATGTTGTCGT
2876883 GA GA GA GA GA GA 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 GA GA GA GA GA GA G
2876920 TTCTTGTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2878686 original size:17 final size:17
Alignment explanation
Indices: 2878664--2878727 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 17
2878654 AATCTTAGAG
2878664 TTCTAATTGTATACAGC
1 TTCTAATTGTATACAGC
* *
2878681 TTCTAATTGTGTTTTAGAG-
1 TTCTAA-T-TG-TATACAGC
*
2878700 TTCTAATTGTATACAAC
1 TTCTAATTGTATACAGC
*
2878717 TTTTAATTGTA
1 TTCTAATTGTA
2878728 GCCTTTGATG
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
16 4 0.11
17 18 0.49
18 2 0.05
19 8 0.22
20 5 0.14
ACGTcount: A:0.28, C:0.11, G:0.12, T:0.48
Consensus pattern (17 bp):
TTCTAATTGTATACAGC
Found at i:2878705 original size:36 final size:36
Alignment explanation
Indices: 2878658--2878726 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 36
2878648 TTATGTAATC
*
2878658 TTAGAGTTCTAATTGTATACAGCTTCTAATTGTGTT
1 TTAGAGTTCTAATTGTATACAACTTCTAATTGTGTT
*
2878694 TTAGAGTTCTAATTGTATACAACTTTTAATTGT
1 TTAGAGTTCTAATTGTATACAACTTCTAATTGT
2878727 AGCCTTTGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.28, C:0.10, G:0.14, T:0.48
Consensus pattern (36 bp):
TTAGAGTTCTAATTGTATACAACTTCTAATTGTGTT
Found at i:2879006 original size:48 final size:48
Alignment explanation
Indices: 2878931--2879025 Score: 163
Period size: 48 Copynumber: 2.0 Consensus size: 48
2878921 TGAGGGAATT
2878931 CTGTTGAATCCTTTATCATTGCAAGTTAGGCCAACTTAGGCGTTTTTG
1 CTGTTGAATCCTTTATCATTGCAAGTTAGGCCAACTTAGGCGTTTTTG
* **
2878979 CTGTTGAATCCTTTATCATTGCGAGTTAGGCTGACTTAGGCGTTTTT
1 CTGTTGAATCCTTTATCATTGCAAGTTAGGCCAACTTAGGCGTTTTT
2879026 AAGCAAAGAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.19, C:0.18, G:0.22, T:0.41
Consensus pattern (48 bp):
CTGTTGAATCCTTTATCATTGCAAGTTAGGCCAACTTAGGCGTTTTTG
Found at i:2880026 original size:3 final size:3
Alignment explanation
Indices: 2880018--2880059 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
2880008 CTCATTTCCT
2880018 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
2880060 ATTGCTTTGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:2897159 original size:27 final size:27
Alignment explanation
Indices: 2897121--2897194 Score: 114
Period size: 27 Copynumber: 2.7 Consensus size: 27
2897111 TAGTATTGGC
2897121 GCCTATCTGGGAGGCGCCAATGGTGGT
1 GCCTATCTGGGAGGCGCCAATGGTGGT
*
2897148 GCCTACCTGGGAGGCGCCAATGGTGGT
1 GCCTATCTGGGAGGCGCCAATGGTGGT
*
2897175 GCC-ATTCTGAGAGGCGCCAA
1 GCCTA-TCTGGGAGGCGCCAA
2897195 ATGGGCCGGC
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
26 1 0.02
27 42 0.98
ACGTcount: A:0.18, C:0.26, G:0.38, T:0.19
Consensus pattern (27 bp):
GCCTATCTGGGAGGCGCCAATGGTGGT
Found at i:2897433 original size:19 final size:19
Alignment explanation
Indices: 2897411--2897448 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2897401 AATTTAATTT
*
2897411 ATTAGTAATAAATTACTAA
1 ATTACTAATAAATTACTAA
*
2897430 ATTACTAATAAGTTACTAA
1 ATTACTAATAAATTACTAA
2897449 TAAATTTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.50, C:0.08, G:0.05, T:0.37
Consensus pattern (19 bp):
ATTACTAATAAATTACTAA
Found at i:2897599 original size:22 final size:26
Alignment explanation
Indices: 2897544--2897608 Score: 93
Period size: 22 Copynumber: 2.6 Consensus size: 26
2897534 ATATACCGAC
2897544 ATTACAATATTCATACAAAATTATAAT
1 ATTACAATATTCATACAAAA-TATAAT
2897571 ATTACAATATTCATAC-AAA-A-AA-
1 ATTACAATATTCATACAAAATATAAT
2897593 ATTACAATATTCATAC
1 ATTACAATATTCATAC
2897609 NNNNNNNNNN
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
22 16 0.42
23 2 0.05
24 1 0.03
26 3 0.08
27 16 0.42
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (26 bp):
ATTACAATATTCATACAAAATATAAT
Found at i:2908105 original size:23 final size:24
Alignment explanation
Indices: 2908065--2908112 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 24
2908055 AAATAATAAA
2908065 ATTTTTTTAATAAAATATAATTTTAT
1 ATTTTTTTAAT--AATATAATTTTAT
*
2908091 ATTTTTTTAAT-ATATATTTTTA
1 ATTTTTTTAATAATATAATTTTA
2908113 AAAAATATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 10 0.48
26 11 0.52
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
ATTTTTTTAATAATATAATTTTAT
Found at i:2908349 original size:14 final size:14
Alignment explanation
Indices: 2908342--2908386 Score: 67
Period size: 14 Copynumber: 3.3 Consensus size: 14
2908332 GAGAGAAAGG
2908342 AGAAG-AGAAGGAGA
1 AGAAGAAGAA-GAGA
2908356 AGAAGAAGAAGAGA
1 AGAAGAAGAAGAGA
2908370 AGAAGAAGAAGA-A
1 AGAAGAAGAAGAGA
2908383 AGAA
1 AGAA
2908387 AGAAAAAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
13 5 0.17
14 21 0.70
15 4 0.13
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (14 bp):
AGAAGAAGAAGAGA
Found at i:2908354 original size:11 final size:11
Alignment explanation
Indices: 2908342--2908378 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
2908332 GAGAGAAAGG
*
2908342 AGAAGAGAAGG
1 AGAAGAGAAGA
2908353 AG-A-AGAAGA
1 AGAAGAGAAGA
2908362 AGAAGAGAAGA
1 AGAAGAGAAGA
2908373 AGAAGA
1 AGAAGA
2908379 AGAAAGAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
9 7 0.30
10 2 0.09
11 14 0.61
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (11 bp):
AGAAGAGAAGA
Found at i:2908361 original size:3 final size:3
Alignment explanation
Indices: 2908342--2908382 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
2908332 GAGAGAAAGG
*
2908342 AGA AG- AGA AGG AGA AGA AGA AGA AG- AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
2908383 AGAAAGAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 4 0.12
3 30 0.88
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:2908389 original size:14 final size:15
Alignment explanation
Indices: 2908330--2908390 Score: 58
Period size: 14 Copynumber: 4.1 Consensus size: 15
2908320 AGAAAAAAAA
2908330 AAGAGAGAAAG-G-AG
1 AAGA-AGAAAGAGAAG
*
2908344 AAG-AGAAGGAGAAG
1 AAGAAGAAAGAGAAG
2908358 AAGAAGAAGAGAAGAAG
1 AAGAAGAA-AG-AGAAG
2908375 AAGAAGAAAGA-AAG
1 AAGAAGAAAGAGAAG
2908389 AA
1 AA
2908391 AAAAGGTAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
12 5 0.12
13 1 0.03
14 13 0.32
15 5 0.12
16 3 0.08
17 13 0.32
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (15 bp):
AAGAAGAAAGAGAAG
Found at i:2908390 original size:17 final size:17
Alignment explanation
Indices: 2908342--2908386 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
2908332 GAGAGAAAGG
2908342 AGAAG-AGAAG-G-AGA
1 AGAAGAAGAAGAGAAGA
2908356 AGAAGAAGAAGAGAAGA
1 AGAAGAAGAAGAGAAGA
2908373 AGAAGAAGAA-AGAA
1 AGAAGAAGAAGAGAA
2908387 AGAAAAAAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 5 0.18
15 5 0.18
16 5 0.18
17 13 0.46
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (17 bp):
AGAAGAAGAAGAGAAGA
Found at i:2908475 original size:12 final size:12
Alignment explanation
Indices: 2908458--2908483 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2908448 TTTGTGAATT
2908458 TTTTAGAAGATA
1 TTTTAGAAGATA
2908470 TTTTAGAAGATA
1 TTTTAGAAGATA
2908482 TT
1 TT
2908484 GTGAATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (12 bp):
TTTTAGAAGATA
Found at i:2908578 original size:21 final size:21
Alignment explanation
Indices: 2908552--2908597 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
2908542 TGGATTAGAA
2908552 TTTTGTATGAATATTCTAATT
1 TTTTGTATGAATATTCTAATT
*
2908573 TTTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTCTAATT
2908594 TTTT
1 TTTT
2908598 NNNNNNNNNN
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.26, C:0.02, G:0.11, T:0.61
Consensus pattern (21 bp):
TTTTGTATGAATATTCTAATT
Found at i:2910029 original size:22 final size:23
Alignment explanation
Indices: 2910004--2910057 Score: 76
Period size: 22 Copynumber: 2.4 Consensus size: 23
2909994 ATACCTTATT
*
2910004 TTTTTCTTCT-TTTCCTTCCTTC
1 TTTTTCTTCTGCTTCCTTCCTTC
2910026 -TTTTCTTCTGCTTCCTTCCTTC
1 TTTTTCTTCTGCTTCCTTCCTTC
2910048 TTATTTCTTC
1 TT-TTTCTTC
2910058 CGTTTCTGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 9 0.32
22 11 0.39
23 1 0.04
24 7 0.25
ACGTcount: A:0.02, C:0.31, G:0.02, T:0.65
Consensus pattern (23 bp):
TTTTTCTTCTGCTTCCTTCCTTC
Found at i:2910029 original size:24 final size:22
Alignment explanation
Indices: 2909997--2910057 Score: 61
Period size: 24 Copynumber: 2.7 Consensus size: 22
2909987 AACCAAAATA
*
2909997 CCTTATTTTTTTCTTCTTTTCCTT
1 CCTTCTTTTTTTCTTC--TTCCTT
* *
2910021 CCTTCTTTTCTTCTGCTTCCTT
1 CCTTCTTTTTTTCTTCTTCCTT
*
2910043 CCTTC-TTATTTCTTC
1 CCTTCTTTTTTTCTTC
2910058 CGTTTCTGTA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
21 7 0.23
22 11 0.35
24 13 0.42
ACGTcount: A:0.03, C:0.31, G:0.02, T:0.64
Consensus pattern (22 bp):
CCTTCTTTTTTTCTTCTTCCTT
Found at i:2910159 original size:27 final size:27
Alignment explanation
Indices: 2910118--2910208 Score: 121
Period size: 27 Copynumber: 3.4 Consensus size: 27
2910108 ATCAGAGCAT
2910118 TGGCGCCTCTCAGTATGGCACCAATAA
1 TGGCGCCTCTCAGTATGGCACCAATAA
*
2910145 TGGCGCCTCTTAGTATGGCACCAATAA
1 TGGCGCCTCTCAGTATGGCACCAATAA
* ** *
2910172 TGGCGCCTCCCAG-ATAGGCACCACCAT
1 TGGCGCCTCTCAGTAT-GGCACCAATAA
2910199 TGGCGCCTCT
1 TGGCGCCTCT
2910209 GAGATAGGCG
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
26 2 0.04
27 54 0.96
ACGTcount: A:0.22, C:0.33, G:0.23, T:0.22
Consensus pattern (27 bp):
TGGCGCCTCTCAGTATGGCACCAATAA
Found at i:2910223 original size:54 final size:54
Alignment explanation
Indices: 2910118--2910224 Score: 128
Period size: 54 Copynumber: 2.0 Consensus size: 54
2910108 ATCAGAGCAT
* * *
2910118 TGGCGCCTCTCAGTATGGCACCAATAATGGCGCCTCTTAGTATGGCACCAATAA
1 TGGCGCCTCCCAGTATGGCACCAACAATGGCGCCTCTGAGTATGGCACCAATAA
* * *
2910172 TGGCGCCTCCCAG-ATAGGCACCACCATTGGCGCCTCTGAG-ATAGGCGCCAATA
1 TGGCGCCTCCCAGTAT-GGCACCAACAATGGCGCCTCTGAGTAT-GGCACCAATA
2910225 CTATGTATTA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
53 4 0.09
54 41 0.91
ACGTcount: A:0.24, C:0.31, G:0.24, T:0.21
Consensus pattern (54 bp):
TGGCGCCTCCCAGTATGGCACCAACAATGGCGCCTCTGAGTATGGCACCAATAA
Found at i:2917565 original size:6 final size:6
Alignment explanation
Indices: 2917554--2917600 Score: 76
Period size: 6 Copynumber: 7.8 Consensus size: 6
2917544 GCATCATGCA
* *
2917554 CCAGAG CCAGAG CCAGAG CCAGAG CCAGAG CCAGTG CCAGAG ACAGA
1 CCAGAG CCAGAG CCAGAG CCAGAG CCAGAG CCAGAG CCAGAG CCAGA
2917601 ACTACATTCT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.34, C:0.32, G:0.32, T:0.02
Consensus pattern (6 bp):
CCAGAG
Found at i:2917985 original size:27 final size:28
Alignment explanation
Indices: 2917921--2917989 Score: 124
Period size: 28 Copynumber: 2.5 Consensus size: 28
2917911 ACCTCATATT
2917921 TAATGGTTTTTTTATGTAAATAAAATTA
1 TAATGGTTTTTTTATGTAAATAAAATTA
2917949 TAATGGTTTTTTTATGTAAATAAAATTA
1 TAATGGTTTTTTTATGTAAATAAAATTA
2917977 TAAT--TTTTTTTAT
1 TAATGGTTTTTTTAT
2917990 TTTGCAATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
26 9 0.22
28 32 0.78
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (28 bp):
TAATGGTTTTTTTATGTAAATAAAATTA
Found at i:2918794 original size:35 final size:37
Alignment explanation
Indices: 2918754--2918823 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
2918744 TACGTATGAT
2918754 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTCCCTGATCAGATAAGTGTAGC
* *
2918789 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 CACTTATCACTTTGTTCCCTGATCAGATAAGTGTA
2918824 AGGGTAGCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 10 0.32
36 3 0.10
37 18 0.58
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTTCCCTGATCAGATAAGTGTAGC
Found at i:2918880 original size:46 final size:45
Alignment explanation
Indices: 2918822--2918912 Score: 137
Period size: 46 Copynumber: 2.0 Consensus size: 45
2918812 CAGATAAGTG
* *
2918822 TAAGGGTAGCTAAGGCTACCACTTACCGCTTTGTCACTTGATCAGA
1 TAAGGGTAGCTAAGGCTACCACTTACCACTTTGCCAC-TGATCAGA
* *
2918868 TAAGTGTAGCTAAGGCTACCACTTATCACTTTGCCACTGATCAGA
1 TAAGGGTAGCTAAGGCTACCACTTACCACTTTGCCACTGATCAGA
2918913 AGTACTCAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 8 0.20
46 33 0.80
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (45 bp):
TAAGGGTAGCTAAGGCTACCACTTACCACTTTGCCACTGATCAGA
Found at i:2920311 original size:11 final size:11
Alignment explanation
Indices: 2920295--2920319 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2920285 AATTAATACT
2920295 TTACCTAGACA
1 TTACCTAGACA
2920306 TTACCTAGACA
1 TTACCTAGACA
2920317 TTA
1 TTA
2920320 TAAGTTGTTT
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:0.36, C:0.24, G:0.08, T:0.32
Consensus pattern (11 bp):
TTACCTAGACA
Found at i:2932308 original size:15 final size:15
Alignment explanation
Indices: 2932288--2932337 Score: 77
Period size: 15 Copynumber: 3.4 Consensus size: 15
2932278 TAATCCTTAA
2932288 TAATTAT-CTCAATAT
1 TAATTATCCT-AATAT
2932303 TAATTATCCTAATAT
1 TAATTATCCTAATAT
2932318 TAATTATCCTAATA-
1 TAATTATCCTAATAT
2932332 TAATTA
1 TAATTA
2932338 AAATAGAGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
14 6 0.18
15 26 0.76
16 2 0.06
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.46
Consensus pattern (15 bp):
TAATTATCCTAATAT
Found at i:2932737 original size:13 final size:13
Alignment explanation
Indices: 2932719--2932744 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2932709 TTTGTTTCAG
2932719 ATTTTTTAGAGAT
1 ATTTTTTAGAGAT
2932732 ATTTTTTAGAGAT
1 ATTTTTTAGAGAT
2932745 TATGATTATG
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:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (13 bp):
ATTTTTTAGAGAT
Found at i:2937981 original size:30 final size:29
Alignment explanation
Indices: 2937932--2937991 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 29
2937922 ATCGTTGCCA
*
2937932 CAACTAATTATCCTCAACGATAAATTCAT
1 CAACCAATTATCCTCAACGATAAATTCAT
*
2937961 CAACCAATTATCTTTCAACGATAAATTCAT
1 CAACCAATTATC-CTCAACGATAAATTCAT
2937991 C
1 C
2937992 CCTTGCGTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
29 11 0.39
30 17 0.61
ACGTcount: A:0.40, C:0.25, G:0.03, T:0.32
Consensus pattern (29 bp):
CAACCAATTATCCTCAACGATAAATTCAT
Found at i:2945312 original size:44 final size:44
Alignment explanation
Indices: 2945217--2945312 Score: 122
Period size: 44 Copynumber: 2.2 Consensus size: 44
2945207 CTGCCATTTT
2945217 GGCTTGCACCCACTCAAACTTGCATTTAGATCGTCCGCCACTCC
1 GGCTTGCACCCACTCAAACTTGCATTTAGATCGTCCGCCACTCC
* * * ** *
2945261 AGTTTGCACCCATTCAAGTTTGCATTTAGA-CTGTCCGCCACTTC
1 GGCTTGCACCCACTCAAACTTGCATTTAGATC-GTCCGCCACTCC
2945305 GGCTTGCA
1 GGCTTGCA
2945313 ATTTGATAGG
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
43 1 0.02
44 42 0.98
ACGTcount: A:0.20, C:0.33, G:0.18, T:0.29
Consensus pattern (44 bp):
GGCTTGCACCCACTCAAACTTGCATTTAGATCGTCCGCCACTCC
Found at i:2945524 original size:18 final size:18
Alignment explanation
Indices: 2945488--2945527 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2945478 ACTATACAGG
**
2945488 GCTCGCACCTTTTGATGA
1 GCTCGCACCACTTGATGA
*
2945506 GCTCGCACCACTTGCTGA
1 GCTCGCACCACTTGATGA
2945524 GCTC
1 GCTC
2945528 ATAGCTCGCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.15, C:0.35, G:0.23, T:0.28
Consensus pattern (18 bp):
GCTCGCACCACTTGATGA
Found at i:2945551 original size:25 final size:25
Alignment explanation
Indices: 2945505--2945552 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
2945495 CCTTTTGATG
* *
2945505 AGCTCGCACCACTTGCTGAGCTCAT
1 AGCTCGCACCACTCGCTAAGCTCAT
**
2945530 AGCTCGCACTTCTCGCTAAGCTC
1 AGCTCGCACCACTCGCTAAGCTC
2945553 GCAGCTTTGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.19, C:0.38, G:0.19, T:0.25
Consensus pattern (25 bp):
AGCTCGCACCACTCGCTAAGCTCAT
Found at i:2945600 original size:26 final size:26
Alignment explanation
Indices: 2945567--2945617 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
2945557 CTTTGACATC
2945567 TTGCTGAGCTTGCAACTTGCACATTT
1 TTGCTGAGCTTGCAACTTGCACATTT
* *
2945593 TTGCTGAGGTTGCAGCTTGCACATT
1 TTGCTGAGCTTGCAACTTGCACATT
2945618 GGAAAGCTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.18, C:0.22, G:0.24, T:0.37
Consensus pattern (26 bp):
TTGCTGAGCTTGCAACTTGCACATTT
Found at i:2948419 original size:31 final size:31
Alignment explanation
Indices: 2948340--2948419 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 31
2948330 TTCATATATG
* *
2948340 AACTTTAA-TTTGATGCAATTATACACATGA
1 AACTTTAATTTTGATTCAAATATACACATGA
* * * * *
2948370 AACTTTGATTGTGGTTCAAATGTATACATGA
1 AACTTTAATTTTGATTCAAATATACACATGA
2948401 AACTTTAATTTTGATTCAA
1 AACTTTAATTTTGATTCAA
2948420 TTAAATGCAC
Statistics
Matches: 39, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
30 7 0.18
31 32 0.82
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.40
Consensus pattern (31 bp):
AACTTTAATTTTGATTCAAATATACACATGA
Found at i:2948666 original size:13 final size:13
Alignment explanation
Indices: 2948648--2948672 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2948638 ATAACATCTA
2948648 AACAATTTTATAC
1 AACAATTTTATAC
2948661 AACAATTTTATA
1 AACAATTTTATA
2948673 GTATTAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (13 bp):
AACAATTTTATAC
Found at i:2955387 original size:16 final size:18
Alignment explanation
Indices: 2955366--2955398 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
2955356 TTTAATAAGT
2955366 TAATTT-ATA-ATAATTA
1 TAATTTCATATATAATTA
2955382 TAATTTCATATATAATT
1 TAATTTCATATATAATT
2955399 TTAGGATGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 3 0.20
18 6 0.40
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (18 bp):
TAATTTCATATATAATTA
Found at i:2955521 original size:27 final size:27
Alignment explanation
Indices: 2955491--2955543 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
2955481 AAGACAATTT
2955491 ATTGCTTTGTAAGATGTAAAAGGAAAC
1 ATTGCTTTGTAAGATGTAAAAGGAAAC
2955518 ATTGCTTTGTAAGATGTAAAAGGAAA
1 ATTGCTTTGTAAGATGTAAAAGGAAA
2955544 TACATATGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.42, C:0.06, G:0.23, T:0.30
Consensus pattern (27 bp):
ATTGCTTTGTAAGATGTAAAAGGAAAC
Found at i:2963861 original size:29 final size:29
Alignment explanation
Indices: 2963829--2963887 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
2963819 CTACTAAGAC
2963829 ACTCAGGTTTTTCATATCATTCCTCAAAG
1 ACTCAGGTTTTTCATATCATTCCTCAAAG
2963858 ACTCAGGTTTTTCATATCATTCCTCAAAG
1 ACTCAGGTTTTTCATATCATTCCTCAAAG
2963887 A
1 A
2963888 ATATTAATAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.37
Consensus pattern (29 bp):
ACTCAGGTTTTTCATATCATTCCTCAAAG
Found at i:2965786 original size:12 final size:11
Alignment explanation
Indices: 2965758--2965787 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
2965748 TTTATTTTTT
2965758 TATTTTTAAAA
1 TATTTTTAAAA
2965769 TATTTTTAAAA
1 TATTTTTAAAA
2965780 TACTTTTT
1 TA-TTTTT
2965788 TATTTATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (11 bp):
TATTTTTAAAA
Found at i:2972782 original size:8 final size:8
Alignment explanation
Indices: 2972769--2972793 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
2972759 TTCAGTTCAA
2972769 TTTCACTT
1 TTTCACTT
2972777 TTTCACTT
1 TTTCACTT
2972785 TTTCACTT
1 TTTCACTT
2972793 T
1 T
2972794 CAAATCACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.24, G:0.00, T:0.64
Consensus pattern (8 bp):
TTTCACTT
Found at i:2972813 original size:45 final size:46
Alignment explanation
Indices: 2972748--2972834 Score: 115
Period size: 45 Copynumber: 1.9 Consensus size: 46
2972738 ATAGGGTCTC
* * * *
2972748 CAAATTCACATTTCAGTTC-AATTTCACTTTTTCACTTTTTCACTTT
1 CAAATTCACAATTCAATTCAAAATTCACTTTTCCA-TTTTTCACTTT
2972794 CAAA-TCACAATTCAATTCAAAATTCACTTTTCCATTTTTCA
1 CAAATTCACAATTCAATTCAAAATTCACTTTTCCATTTTTCA
2972835 AGTCAATATT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
45 19 0.53
46 17 0.47
ACGTcount: A:0.30, C:0.24, G:0.01, T:0.45
Consensus pattern (46 bp):
CAAATTCACAATTCAATTCAAAATTCACTTTTCCATTTTTCACTTT
Found at i:2972846 original size:39 final size:38
Alignment explanation
Indices: 2972778--2972852 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 38
2972768 ATTTCACTTT
*
2972778 TTCACTTTTTCACTTTCAAATCACAATTCAATTCAAAA
1 TTCACTTTTCCACTTTCAAATCACAATTCAATTCAAAA
* *
2972816 TTCACTTTTCCATTTTTCAAGTCA-ATATTCAATTCAA
1 TTCACTTTTCCA-CTTTCAAATCACA-ATTCAATTCAA
2972853 TGCCAAACAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
38 12 0.38
39 20 0.62
ACGTcount: A:0.33, C:0.23, G:0.01, T:0.43
Consensus pattern (38 bp):
TTCACTTTTCCACTTTCAAATCACAATTCAATTCAAAA
Found at i:2976830 original size:18 final size:18
Alignment explanation
Indices: 2976807--2976846 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
2976797 CAGATCGATG
2976807 AGAATTGCAACCTAGATC
1 AGAATTGCAACCTAGATC
2976825 AGAATTGCAACCTAGATC
1 AGAATTGCAACCTAGATC
2976843 AGAA
1 AGAA
2976847 GGTAAAGGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.42, C:0.20, G:0.17, T:0.20
Consensus pattern (18 bp):
AGAATTGCAACCTAGATC
Found at i:2982749 original size:27 final size:26
Alignment explanation
Indices: 2982704--2982754 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
2982694 AACATCGGAT
*
2982704 GGCTTGGGGGTAAGGCGAGTAAGGTA
1 GGCTTGGGGGTAAGACGAGTAAGGTA
*
2982730 GGCTTGGAGGGTGAGACGAGTAAGG
1 GGCTTGG-GGGTAAGACGAGTAAGG
2982755 AAGAATCTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.24, C:0.08, G:0.51, T:0.18
Consensus pattern (26 bp):
GGCTTGGGGGTAAGACGAGTAAGGTA
Found at i:2984522 original size:23 final size:23
Alignment explanation
Indices: 2984496--2984616 Score: 99
Period size: 23 Copynumber: 5.3 Consensus size: 23
2984486 AATTTTATGG
2984496 ATTTGTTTGGCTAAATTGTAGGC
1 ATTTGTTTGGCTAAATTGTAGGC
* *
2984519 ATTTGTCTT-TC-ACAATTTTATGG-
1 ATTTGT-TTGGCTA-AATTGTA-GGC
*
2984542 ATTTGTTTGGCTAATTTGTAGGC
1 ATTTGTTTGGCTAAATTGTAGGC
* * *
2984565 ATTTGTCTT--CCATAATTTTAGGG
1 ATTTGT-TTGGCTA-AATTGTAGGC
*
2984588 ATTTGTTTGGCTAAATTGTGGGC
1 ATTTGTTTGGCTAAATTGTAGGC
2984611 ATTTGT
1 ATTTGT
2984617 CTTCCACAAT
Statistics
Matches: 75, Mismatches: 13, Indels: 20
0.69 0.12 0.19
Matches are distributed among these distances:
22 9 0.12
23 57 0.76
24 9 0.12
ACGTcount: A:0.20, C:0.10, G:0.22, T:0.48
Consensus pattern (23 bp):
ATTTGTTTGGCTAAATTGTAGGC
Found at i:2984546 original size:46 final size:46
Alignment explanation
Indices: 2984483--2984641 Score: 264
Period size: 46 Copynumber: 3.5 Consensus size: 46
2984473 AGTTACCTTT
*
2984483 CACAATTTTATGGATTTGTTTGGCTAAATTGTAGGCATTTGTCTTT
1 CACAATTTTATGGATTTGTTTGGCTAAATTGTAGGCATTTGTCTTC
*
2984529 CACAATTTTATGGATTTGTTTGGCTAATTTGTAGGCATTTGTCTTC
1 CACAATTTTATGGATTTGTTTGGCTAAATTGTAGGCATTTGTCTTC
* * *
2984575 CATAATTTTAGGGATTTGTTTGGCTAAATTGTGGGCATTTGTCTTC
1 CACAATTTTATGGATTTGTTTGGCTAAATTGTAGGCATTTGTCTTC
*
2984621 CACAATTTTAAGGATTTGTTT
1 CACAATTTTATGGATTTGTTT
2984642 CTATTTTATT
Statistics
Matches: 105, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 105 1.00
ACGTcount: A:0.21, C:0.11, G:0.20, T:0.47
Consensus pattern (46 bp):
CACAATTTTATGGATTTGTTTGGCTAAATTGTAGGCATTTGTCTTC
Found at i:2984637 original size:23 final size:23
Alignment explanation
Indices: 2984519--2984639 Score: 65
Period size: 23 Copynumber: 5.3 Consensus size: 23
2984509 AATTGTAGGC
* *
2984519 ATTTGTCTTTCACAATTTTATGG
1 ATTTGTCTTCCACAATTTTAAGG
* *
2984542 ATTTGT-TTGGC-TAATTTGT-AGG
1 ATTTGTCTT-CCACAATTT-TAAGG
* *
2984564 CATTTGTCTTCCATAATTTTAGGG
1 -ATTTGTCTTCCACAATTTTAAGG
* * *
2984588 ATTTGT-TTGGCTA-AATTGT-GGG
1 ATTTGTCTT--CCACAATTTTAAGG
2984610 CATTTGTCTTCCACAATTTTAAGG
1 -ATTTGTCTTCCACAATTTTAAGG
2984634 ATTTGT
1 ATTTGT
2984640 TTCTATTTTA
Statistics
Matches: 76, Mismatches: 10, Indels: 24
0.69 0.09 0.22
Matches are distributed among these distances:
22 16 0.21
23 44 0.58
24 16 0.21
ACGTcount: A:0.21, C:0.12, G:0.20, T:0.48
Consensus pattern (23 bp):
ATTTGTCTTCCACAATTTTAAGG
Found at i:2987221 original size:6 final size:6
Alignment explanation
Indices: 2987210--2987254 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
2987200 ATTCCCACTC
* * * *
2987210 ATAATA ATAATA ATACTA ATAATA ATATTA ATACTA ATATTA ATA
1 ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATA
2987255 CTTACCTCAC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (6 bp):
ATAATA
Found at i:2987233 original size:18 final size:18
Alignment explanation
Indices: 2987210--2987254 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
2987200 ATTCCCACTC
2987210 ATAATAATAATAATACTA
1 ATAATAATAATAATACTA
*
2987228 ATAATAATATTAATACTA
1 ATAATAATAATAATACTA
*
2987246 ATATTAATA
1 ATAATAATA
2987255 CTTACCTCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (18 bp):
ATAATAATAATAATACTA
Found at i:2987256 original size:12 final size:12
Alignment explanation
Indices: 2987214--2987254 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
2987204 CCACTCATAA
*
2987214 TAATAATAATAC
1 TAATAATAATAT
2987226 TAATAATAATAT
1 TAATAATAATAT
*
2987238 TAATACTAATAT
1 TAATAATAATAT
2987250 TAATA
1 TAATA
2987255 CTTACCTCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (12 bp):
TAATAATAATAT
Done.