Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168037.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_29, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 14313602
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 50000 characters in sequence are not A, C, G, or T
File 54 of 74
Found at i:10772452 original size:31 final size:31
Alignment explanation
Indices: 10772407--10772476 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
10772397 TTAAACCCTT
* * *
10772407 AACCATAAATCTAAC-CTTAAACCTTAACATA
1 AACCCTAAACCTAACTC-TAAACCCTAACATA
* *
10772438 TACCCTAAACCTAACTCTAAACCCTAACTTA
1 AACCCTAAACCTAACTCTAAACCCTAACATA
10772469 AACCCTAA
1 AACCCTAA
10772477 GCTCAAATCA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
31 31 0.97
32 1 0.03
ACGTcount: A:0.44, C:0.31, G:0.00, T:0.24
Consensus pattern (31 bp):
AACCCTAAACCTAACTCTAAACCCTAACATA
Found at i:10772473 original size:12 final size:13
Alignment explanation
Indices: 10772442--10772476 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
10772432 AACATATACC
10772442 CTAAA-CCTAACT
1 CTAAACCCTAACT
10772454 CTAAACCCTAACT
1 CTAAACCCTAACT
10772467 -TAAACCCTAA
1 CTAAACCCTAA
10772477 GCTCAAATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 15 0.68
13 7 0.32
ACGTcount: A:0.43, C:0.34, G:0.00, T:0.23
Consensus pattern (13 bp):
CTAAACCCTAACT
Found at i:10772476 original size:19 final size:20
Alignment explanation
Indices: 10772345--10772464 Score: 63
Period size: 19 Copynumber: 6.1 Consensus size: 20
10772335 TACCTAACCA
*
10772345 AAACCCTAA-GCTAAACCCT
1 AAACCCTAACTCTAAACCCT
* * *
10772364 -AACCCTAACCCTAACCTAGCCA
1 AAACCCTAACTCTAA---ACCCT
10772386 AAACCCTAAACT-TAAACCCT
1 AAACCCT-AACTCTAAACCCT
* * * *
10772406 TAACCATAAATCT-AACCTT
1 AAACCCTAACTCTAAACCCT
* * *
10772425 AAACCTTAAC-ATATACCCT
1 AAACCCTAACTCTAAACCCT
10772444 AAA-CCTAACTCTAAACCCT
1 AAACCCTAACTCTAAACCCT
10772463 AA
1 AA
10772465 CTTAAACCCT
Statistics
Matches: 73, Mismatches: 19, Indels: 18
0.66 0.17 0.16
Matches are distributed among these distances:
18 14 0.19
19 35 0.48
20 9 0.12
22 3 0.04
23 9 0.12
24 3 0.04
ACGTcount: A:0.42, C:0.35, G:0.02, T:0.21
Consensus pattern (20 bp):
AAACCCTAACTCTAAACCCT
Found at i:10775562 original size:18 final size:18
Alignment explanation
Indices: 10775494--10775562 Score: 54
Period size: 18 Copynumber: 3.8 Consensus size: 18
10775484 AATATTAAGA
10775494 AATTATT-AAA-AATATT
1 AATTATTAAAATAATATT
*
10775510 CATATTATGAAAATAATATT
1 -A-ATTATTAAAATAATATT
* **
10775530 -ATTATATTATTTAATATT
1 AATTAT-TAAAATAATATT
10775548 AATTATTAAAATAAT
1 AATTATTAAAATAAT
10775563 CAAAATATTA
Statistics
Matches: 39, Mismatches: 8, Indels: 9
0.70 0.14 0.16
Matches are distributed among these distances:
17 6 0.15
18 19 0.49
19 8 0.21
20 6 0.15
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (18 bp):
AATTATTAAAATAATATT
Found at i:10775664 original size:30 final size:28
Alignment explanation
Indices: 10775629--10775685 Score: 78
Period size: 30 Copynumber: 2.0 Consensus size: 28
10775619 TGAAATATTA
**
10775629 AAAATATTTATTTTTAATAATATACAAAAT
1 AAAATATTTATAATTAA-AATAT-CAAAAT
10775659 AAAATATTTATAATTAAAATATCAAAA
1 AAAATATTTATAATTAAAATATCAAAA
10775686 AATTAATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 5 0.20
29 5 0.20
30 15 0.60
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.39
Consensus pattern (28 bp):
AAAATATTTATAATTAAAATATCAAAAT
Found at i:10775751 original size:25 final size:25
Alignment explanation
Indices: 10775704--10775751 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
10775694 TTAATATTTT
*
10775704 AATATTTTAATTAAAATTAAATACA
1 AATATTTTAATTAAAATAAAATACA
*
10775729 AATATTTT-ATTAATATAATAATA
1 AATATTTTAATTAAAATAA-AATA
10775752 TTTTAGGTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (25 bp):
AATATTTTAATTAAAATAAAATACA
Found at i:10776062 original size:22 final size:22
Alignment explanation
Indices: 10776037--10776080 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
10776027 ATTTAATCTC
*
10776037 ATTTTTTATTAATTAATAAATT
1 ATTTTTTATTAATCAATAAATT
*
10776059 ATTTTTTATTAATCAATCAATT
1 ATTTTTTATTAATCAATAAATT
10776081 TTTATTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.57
Consensus pattern (22 bp):
ATTTTTTATTAATCAATAAATT
Found at i:10776071 original size:18 final size:18
Alignment explanation
Indices: 10776048--10776094 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
10776038 TTTTTTATTA
* *
10776048 ATTAATAAATTATTTTTT
1 ATTAATAAATCAATTTTT
*
10776066 ATTAATCAATCAATTTTT
1 ATTAATAAATCAATTTTT
10776084 ATTAAATAAAT
1 ATT-AATAAAT
10776095 ACTAAAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 18 0.75
19 6 0.25
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTAATAAATCAATTTTT
Found at i:10778274 original size:159 final size:158
Alignment explanation
Indices: 10778033--10778392 Score: 402
Period size: 159 Copynumber: 2.3 Consensus size: 158
10778023 ATGCAATGAC
* * * * * * *
10778033 TTTGTAAAAAATGAAAACTAATATGTTTTTTTCTTTGTGATTCTAGTTATGTATTGTAATTGTTA
1 TTTGTAAAAGATGAAAACTATTGTGTATTTTACTTTATGATTCTAGTTATGTATTATAATTGTTA
* * * ** *
10778098 GTGAACTACTTTTATAGTAATTTAAA-TCATAAATTTTGTAGGAAATTCTTTGTTAAACTAGATA
66 GTGAACTACTTTTATAGTAATTCAAAGT-ATAAAATTTATAAAAAATTCTTTATTAAACTAGATA
* *
10778162 GTATATTACATGTATCATG-ATGAGATCACA
130 ATATATTACATGTAT--TGAATGAGATAACA
* * *
10778192 TTTGTAAAAGATGAAAACTATTGTGTATTTTACTTTATGATTCTTGTTGTGTATTATGATTGTT-
1 TTTGTAAAAGATGAAAACTATTGTGTATTTTACTTTATGATTCTAGTTATGTATTATAATTGTTA
*
10778256 GATGAAGTACTTTTATAGTAATTCAAAGTATAAAATTTATAAAAAATTCTTTATTAAACTAGATA
66 G-TGAACTACTTTTATAGTAATTCAAAGTATAAAATTTATAAAAAATTCTTTATTAAACTAGATA
* *
10778321 ATATATTGCATTTATTGCAATGAGATAACA
130 ATATATTACATGTATTG-AATGAGATAACA
** * * * * *
10778351 TTTGTGGAAGGTGAAAATTATTGTATATGTTGCTTTATGATT
1 TTTGTAAAAGATGAAAACTATTGTGTATTTTACTTTATGATT
10778393 ATGATTGCGT
Statistics
Matches: 169, Mismatches: 28, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
157 2 0.01
158 1 0.01
159 165 0.98
160 1 0.01
ACGTcount: A:0.35, C:0.06, G:0.15, T:0.44
Consensus pattern (158 bp):
TTTGTAAAAGATGAAAACTATTGTGTATTTTACTTTATGATTCTAGTTATGTATTATAATTGTTA
GTGAACTACTTTTATAGTAATTCAAAGTATAAAATTTATAAAAAATTCTTTATTAAACTAGATAA
TATATTACATGTATTGAATGAGATAACA
Found at i:10778405 original size:159 final size:157
Alignment explanation
Indices: 10778091--10778438 Score: 379
Period size: 159 Copynumber: 2.2 Consensus size: 157
10778081 ATGTATTGTA
* * * ** *
10778091 ATTGTT-AGTGAACTACTTTTATAGTAATTTAAA-TCATAAATTTTGTAGGAAATTCTTTGTTAA
1 ATTGTTGA-TGAACTACTTTTATAGTAATTCAAAGTCATAAAATTTATAAAAAATTCTTTATTAA
* * *
10778154 ACTAGATAGTATATTACATGTATCATGATGAGATCACATTTGTAAAAGATGAAAACTATTGTGTA
65 ACTAGATAATATATTACATGTATCA-GATGAGATAACATTTGTAAAAGATGAAAACTATTGTATA
* * *
10778219 TTTTACTTTATGATTCTTGTTGTGTATTATG
129 TGTTACTTTATGATTCATGTTGCGTA-T-TG
*
10778250 ATTGTTGATGAAGTACTTTTATAGTAATTCAAAGT-ATAAAATTTATAAAAAATTCTTTATTAAA
1 ATTGTTGATGAACTACTTTTATAGTAATTCAAAGTCATAAAATTTATAAAAAATTCTTTATTAAA
* * ** * *
10778314 CTAGATAATATATTGCATTTATTGCA-ATGAGATAACATTTGTGGAAGGTGAAAATTATTGTATA
66 CTAGATAATATATTACATGTA-T-CAGATGAGATAACATTTGTAAAAGATGAAAACTATTGTATA
*
10778378 TGTTGCTTTATGATT-ATGATTGCGTATTG
129 TGTTACTTTATGATTCATG-TTGCGTATTG
* *
10778407 --T-TTGACGAACTATTTTTATAGTAATTCAAAGT
1 ATTGTTGATGAACTACTTTTATAGTAATTCAAAGT
10778439 TTACAAATAG
Statistics
Matches: 161, Mismatches: 23, Indels: 15
0.81 0.12 0.08
Matches are distributed among these distances:
154 28 0.17
155 1 0.01
157 2 0.01
158 3 0.02
159 122 0.76
160 3 0.02
161 2 0.01
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.43
Consensus pattern (157 bp):
ATTGTTGATGAACTACTTTTATAGTAATTCAAAGTCATAAAATTTATAAAAAATTCTTTATTAAA
CTAGATAATATATTACATGTATCAGATGAGATAACATTTGTAAAAGATGAAAACTATTGTATATG
TTACTTTATGATTCATGTTGCGTATTG
Found at i:10778658 original size:17 final size:17
Alignment explanation
Indices: 10778634--10778718 Score: 59
Period size: 17 Copynumber: 4.9 Consensus size: 17
10778624 TAACTATTCA
10778634 AATATTAAAAATTATTT
1 AATATTAAAAATTATTT
*
10778651 ATTATT-AAAATTA-TT
1 AATATTAAAAATTATTT
* *
10778666 AATATTCAAGAA-TAATT
1 AATATT-AAAAATTATTT
* *
10778683 ATATTTTAATAATAATATTT
1 A-ATATTAA-AA-ATTATTT
10778703 AATATTAAAATATTAT
1 AATATTAAAA-ATTAT
10778719 AGTAATATAA
Statistics
Matches: 53, Mismatches: 8, Indels: 13
0.72 0.11 0.18
Matches are distributed among these distances:
15 7 0.13
16 9 0.17
17 13 0.25
18 12 0.23
19 7 0.13
20 5 0.09
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (17 bp):
AATATTAAAAATTATTT
Found at i:10778857 original size:15 final size:16
Alignment explanation
Indices: 10778837--10778876 Score: 64
Period size: 17 Copynumber: 2.5 Consensus size: 16
10778827 AAATAGTAGC
10778837 ATTTAT-TATTAAAAT
1 ATTTATATATTAAAAT
10778852 ATTTATACTATTAAAAT
1 ATTTATA-TATTAAAAT
10778869 ATTTATAT
1 ATTTATAT
10778877 TTTATATTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.26
16 1 0.04
17 16 0.70
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTTATATATTAAAAT
Found at i:10778865 original size:17 final size:17
Alignment explanation
Indices: 10778843--10778875 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
10778833 TAGCATTTAT
10778843 TATTAAAATATTTATAC
1 TATTAAAATATTTATAC
10778860 TATTAAAATATTTATA
1 TATTAAAATATTTATA
10778876 TTTTATATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (17 bp):
TATTAAAATATTTATAC
Found at i:10779468 original size:152 final size:149
Alignment explanation
Indices: 10779178--10779468 Score: 361
Period size: 152 Copynumber: 1.9 Consensus size: 149
10779168 TATACAAAAT
* * * *
10779178 AAAAATATTTATAATTGAAATAGTGAAAGATTTTTAATGTTAATATTTTAATTTTTAATTAAAAT
1 AAAAATATTTAAAATTAAAATAGTGAAAGACTTTTAATATTAATATTTTAATTTTTAATTAAAAT
* *
10779243 TAAATAAAATATTTTTATTAATATAATAGAATATTAAGTCAAATCAAATCAAATTTGAGCTTAAA
66 TAAATAAAATATTTTTATTAATAAAATAGAATATTAAGTCAAATCAAATCAAATTTGAACTTAAA
* *
10779308 ATATTATGTTAAAACTAAA
131 AAAATATGTTAAAACTAAA
* *
10779327 AAAAATATTTAAAATTAAAATA-TTATAAGACTTTTAATATTAATATTTTAATATTTTAATTAGA
1 AAAAATATTTAAAATTAAAATAGTGA-AAGACTTTTAATATTAATATTTTAAT-TTTTAATTAAA
* * ** *** *
10779391 ATTATATAAAAATATTATTTATTAATAAAATA-ATATTTTGGGTCGGGTCAAATTAAATTTGAAC
64 ATTAAAT-AAAATATT-TTTATTAATAAAATAGA-ATATTAAGTCAAATCAAATCAAATTTGAAC
10779455 TTAAAAAAATATGT
126 TTAAAAAAATATGT
10779469 ACAAGGTTAG
Statistics
Matches: 119, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
148 2 0.02
149 44 0.37
150 16 0.13
151 9 0.08
152 48 0.40
ACGTcount: A:0.48, C:0.03, G:0.07, T:0.42
Consensus pattern (149 bp):
AAAAATATTTAAAATTAAAATAGTGAAAGACTTTTAATATTAATATTTTAATTTTTAATTAAAAT
TAAATAAAATATTTTTATTAATAAAATAGAATATTAAGTCAAATCAAATCAAATTTGAACTTAAA
AAAATATGTTAAAACTAAA
Found at i:10783369 original size:88 final size:89
Alignment explanation
Indices: 10783273--10783451 Score: 333
Period size: 90 Copynumber: 2.0 Consensus size: 89
10783263 TTAATTATTT
10783273 ATATATTTTTAAAATTAATAAATTAGATTAAATGTTATTCTA-TTATTCCATTCAAACAACATTC
1 ATATATTTTTAAAATTAATAAATTAGATTAAATGTTATTCTATTTATTCCATTCAAACAACATTC
10783337 ACCATAAAAATAATTATGTAAGGA
66 ACCATAAAAATAATTATGTAAGGA
*
10783361 ATATATTTTTAAAATTAATAAATTAGATTAAATGTTATTCTATTTTATTCCATTCAAACGACATT
1 ATATATTTTTAAAATTAATAAATTAGATTAAATGTTATTCTA-TTTATTCCATTCAAACAACATT
10783426 CACCATAAAAATAATTATGTAAGGA
65 CACCATAAAAATAATTATGTAAGGA
10783451 A
1 A
10783452 ACACAATTTT
Statistics
Matches: 88, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
88 42 0.48
90 46 0.52
ACGTcount: A:0.45, C:0.10, G:0.06, T:0.39
Consensus pattern (89 bp):
ATATATTTTTAAAATTAATAAATTAGATTAAATGTTATTCTATTTATTCCATTCAAACAACATTC
ACCATAAAAATAATTATGTAAGGA
Found at i:10792423 original size:32 final size:32
Alignment explanation
Indices: 10792382--10792461 Score: 133
Period size: 32 Copynumber: 2.5 Consensus size: 32
10792372 CTTATCAAAA
**
10792382 TAATGAAATAAAATTTAATTGCATGAAAAACT
1 TAATGAAATAAAATTTAATTGCAAAAAAAACT
*
10792414 TAATGAAATAAAATTTAATTGTAAAAAAAACT
1 TAATGAAATAAAATTTAATTGCAAAAAAAACT
10792446 TAATGAAATAAAATTT
1 TAATGAAATAAAATTT
10792462 TCTAAATACC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.56, C:0.04, G:0.07, T:0.33
Consensus pattern (32 bp):
TAATGAAATAAAATTTAATTGCAAAAAAAACT
Found at i:10792448 original size:17 final size:16
Alignment explanation
Indices: 10792407--10792458 Score: 54
Period size: 15 Copynumber: 3.2 Consensus size: 16
10792397 TAATTGCATG
10792407 AAAAACTTAA-TGAAA
1 AAAAACTTAATTGAAA
* *
10792422 TAAAATTTAATTGTAAA
1 AAAAACTTAATTG-AAA
10792439 AAAAACTTAA-TGAAA
1 AAAAACTTAATTGAAA
10792454 TAAAA
1 -AAAA
10792459 TTTTCTAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
15 11 0.37
16 8 0.27
17 11 0.37
ACGTcount: A:0.63, C:0.04, G:0.06, T:0.27
Consensus pattern (16 bp):
AAAAACTTAATTGAAA
Found at i:10792688 original size:19 final size:19
Alignment explanation
Indices: 10792649--10792702 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
10792639 TTTTGATTAA
*
10792649 TTTTAGGGTTTAAGG-TAG
1 TTTTAGGGTTCAAGGTTAG
10792667 -TTTAGGGGTTCAAGGTTAG
1 TTTTA-GGGTTCAAGGTTAG
10792686 TTTTAGGGTTCAAGGTT
1 TTTTAGGGTTCAAGGTT
10792703 GATTTAAGGT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
17 4 0.12
18 9 0.28
19 15 0.47
20 4 0.12
ACGTcount: A:0.20, C:0.04, G:0.33, T:0.43
Consensus pattern (19 bp):
TTTTAGGGTTCAAGGTTAG
Found at i:10794441 original size:144 final size:139
Alignment explanation
Indices: 10794231--10794619 Score: 358
Period size: 144 Copynumber: 2.7 Consensus size: 139
10794221 AGGAACAACC
* * * *
10794231 AAATTACAAAATTACCCTTAAAGGCATTGTGGTAATTTCACCCTTTTAGATGTGCAATCAATGTT
1 AAATTACAAAA-TACCC-TAAAGGCATTTTGATAATTTCA-CCTTTTTG-TGTGCAATCAAGGTT
10794296 TTCAATGCATCAAAATTCATGGAATAATATTAAAACA-AGATCTAGAGCTTTTTTCA-AAAAACT
62 TTCAATGCATCAAAATTCATGGAATAATATTAAAACATA-ATCTAGAGC--TTTTCACAAAAACT
*
10794359 -GACCTCAAGAAGATA
124 CAACCTCAAGAAGATA
10794374 AAATTACGAAAATACCTCTAAAGAGCATTTTGATAATTTCACCATTTTTGTGGTGCAATCAAGGT
1 AAATTAC-AAAATACC-CTAAAG-GCATTTTGATAATTTCACC-TTTTTGT-GTGCAATCAAGGT
* * * *** * * * *
10794439 TTTTAGTGCATCAAAGTTCATGGAATGGCATTAAAACATAATTTGGAGCTTTTCACGAAAAGTCA
61 TTTCAATGCATCAAAATTCATGGAATAATATTAAAACATAATCTAGAGCTTTTCACAAAAACTCA
* * *
10794504 ACCTTAAGAAGGTC
126 ACCTCAAGAAGATA
* * * **
10794518 AAATTATAAAAATAACCCTAAAGGGCATTTT-AGTAATGTCAACTTTTCTAAAGTGCAATCAAGG
1 AAATTA-CAAAAT-ACCCTAAA-GGCATTTTGA-TAATTTCACCTTTT-T-GTGTGCAATCAAGG
*
10794582 TTTTCAATGTA-C-AAATTCATGGAATAATATTAAAACAT
60 TTTTCAATGCATCAAAATTCATGGAATAATATTAAAACAT
10794620 TATCAGGAGT
Statistics
Matches: 202, Mismatches: 30, Indels: 29
0.77 0.11 0.11
Matches are distributed among these distances:
142 28 0.14
143 30 0.15
144 139 0.69
145 5 0.02
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.32
Consensus pattern (139 bp):
AAATTACAAAATACCCTAAAGGCATTTTGATAATTTCACCTTTTTGTGTGCAATCAAGGTTTTCA
ATGCATCAAAATTCATGGAATAATATTAAAACATAATCTAGAGCTTTTCACAAAAACTCAACCTC
AAGAAGATA
Found at i:10794672 original size:142 final size:140
Alignment explanation
Indices: 10794282--10794696 Score: 358
Period size: 144 Copynumber: 2.9 Consensus size: 140
10794272 CCTTTTAGAT
*
10794282 GTGCAATCAATGTTTTCAATGCATCAAAATTCATGGAATAATATTAAAACA-AGATCTA-GAGCT
1 GTGCAATCAAGGTTTTCAATGCATC-AAATTCATGGAATAATATTAAAACATA-ATC-AGGAGC-
* * * *
10794345 TTTTTCA-AAAAACTGACCTCAAGAAGATAAAATTACGAAAATACCTCTAAAGAGCATTTT-GAT
62 -TTTTCAGAAAAATTGACCTAAAGAAG-TAAAATTATGAAAATACC-CTAAAGGGCATTTTAG-T
* * ***
10794408 AATTTCACCATTTTTGTG
123 AATGTCAACATTTTTAAA
* * *** **
10794426 GTGCAATCAAGGTTTTTAGTGCATCAAAGTTCATGGAATGGCATTAAAACATAATTTGGAGCTTT
1 GTGCAATCAAGGTTTTCAATGCATCAAA-TTCATGGAATAATATTAAAACATAATCAGGAGCTTT
* ** * * *
10794491 TCACGAAAAGTCAACCTTAAGAAGGTCAAATTATAAAAATAACCCTAAAGGGCATTTTAGTAATG
65 TCA-GAAAAATTGACCTAAAGAA-GTAAAATTATGAAAAT-ACCCTAAAGGGCATTTTAGTAATG
10794556 TCAAC-TTTTCTAAA
127 TCAACATTTT-TAAA
* *
10794570 GTGCAATCAAGGTTTTCAATGTA-CAAATTCATGGAATAATATTAAAACATTATCAGGAG-TGTT
1 GTGCAATCAAGGTTTTCAATGCATCAAATTCATGGAATAATATTAAAACATAATCAGGAGCT-TT
* * * * *
10794633 TCATGAAAAATTGACCTAAAAAATGTTAAAGTATGAAAATACCCTTAAATGGCATTCTAGTAAT
65 TCA-GAAAAATTGACCTAAAGAA-GTAAAATTATGAAAATACCC-TAAAGGGCATTTTAGTAAT
10794697 TTACTCTTAT
Statistics
Matches: 217, Mismatches: 43, Indels: 24
0.76 0.15 0.08
Matches are distributed among these distances:
141 5 0.02
142 81 0.37
143 11 0.05
144 114 0.53
145 6 0.03
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (140 bp):
GTGCAATCAAGGTTTTCAATGCATCAAATTCATGGAATAATATTAAAACATAATCAGGAGCTTTT
CAGAAAAATTGACCTAAAGAAGTAAAATTATGAAAATACCCTAAAGGGCATTTTAGTAATGTCAA
CATTTTTAAA
Found at i:10795462 original size:3 final size:3
Alignment explanation
Indices: 10795454--10795491 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
10795444 TTTATTAGTG
10795454 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
10795492 TTCTGGTTCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:10799964 original size:19 final size:19
Alignment explanation
Indices: 10799936--10799983 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
10799926 CATATGTAAG
* *
10799936 TTTTTCTTTTTCCATTTCA
1 TTTTTATTTTTCAATTTCA
*
10799955 TTTTTATTTTTTAATTTCA
1 TTTTTATTTTTCAATTTCA
*
10799974 TTTTGATTTT
1 TTTTTATTTT
10799984 ATTTTATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.15, C:0.10, G:0.02, T:0.73
Consensus pattern (19 bp):
TTTTTATTTTTCAATTTCA
Found at i:10800953 original size:28 final size:27
Alignment explanation
Indices: 10800895--10800963 Score: 66
Period size: 28 Copynumber: 2.4 Consensus size: 27
10800885 TATGAAAAAA
*** *
10800895 TTTCAAGAATTTTGTAAATAGTGAATTT
1 TTTCAA-AATTTTGTAAATAAAAAATAT
10800923 TTTCAAAATTTTGTTAAATAAAAAATAT
1 TTTCAAAATTTTG-TAAATAAAAAATAT
10800951 TTTCTATAAATTT
1 TTTC-A-AAATTT
10800964 CGCTAAAGTG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
27 7 0.21
28 20 0.59
29 1 0.03
30 6 0.18
ACGTcount: A:0.41, C:0.04, G:0.07, T:0.48
Consensus pattern (27 bp):
TTTCAAAATTTTGTAAATAAAAAATAT
Found at i:10807193 original size:23 final size:24
Alignment explanation
Indices: 10807167--10807213 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
10807157 AAGTTTTAAG
* *
10807167 TTTTTTAAA-ATAAATATTCATAA
1 TTTTTTAAAGAAAAATACTCATAA
10807190 TTTTTTAAAGAAAAATACTCATAA
1 TTTTTTAAAGAAAAATACTCATAA
10807214 GTTGAATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (24 bp):
TTTTTTAAAGAAAAATACTCATAA
Found at i:10815172 original size:16 final size:16
Alignment explanation
Indices: 10815115--10815172 Score: 52
Period size: 15 Copynumber: 3.8 Consensus size: 16
10815105 ATGTAAATTT
10815115 TAAAATTT--TTAATA
1 TAAAATTTAATTAATA
*
10815129 TAACATTTTAATT-ATA
1 TAA-AATTTAATTAATA
10815145 -AAAATATTAATTAATA
1 TAAAAT-TTAATTAATA
*
10815161 TAATATTTAATT
1 TAAAATTTAATT
10815173 TTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 5 0.14
15 12 0.34
16 12 0.34
17 6 0.17
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (16 bp):
TAAAATTTAATTAATA
Found at i:10815184 original size:31 final size:32
Alignment explanation
Indices: 10815123--10815187 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 32
10815113 TTTAAAATTT
10815123 TTAATATAACATTTTAATTATAAAAATATTAA
1 TTAATATAACATTTTAATTATAAAAATATTAA
* * * *
10815155 TTAATATAATA-TTTAATTTTAATATTATTAA
1 TTAATATAACATTTTAATTATAAAAATATTAA
10815186 TT
1 TT
10815188 TTAAATGATA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 19 0.66
32 10 0.34
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (32 bp):
TTAATATAACATTTTAATTATAAAAATATTAA
Found at i:10815185 original size:15 final size:15
Alignment explanation
Indices: 10815147--10815191 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
10815137 TAATTATAAA
*
10815147 AATATTAATTAA-TAT
1 AATATT-ATTAATTTT
10815162 AATA-T-TTAATTTT
1 AATATTATTAATTTT
10815175 AATATTATTAATTTT
1 AATATTATTAATTTT
10815190 AA
1 AA
10815192 ATGATAACAC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
12 4 0.15
13 6 0.23
14 2 0.08
15 14 0.54
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
AATATTATTAATTTT
Found at i:10815284 original size:29 final size:30
Alignment explanation
Indices: 10815251--10815316 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 30
10815241 TATATTCATT
* *
10815251 ATTCAAATATTACTTTAAAAATTTTTTA-A
1 ATTCAAATATTACATTAAAAATTTTCTATA
* * * *
10815280 ATTCAGATGTTACATTCAATATTTTCTATA
1 ATTCAAATATTACATTAAAAATTTTCTATA
10815310 ATTCAAA
1 ATTCAAA
10815317 AATAATTTGT
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
29 22 0.76
30 7 0.24
ACGTcount: A:0.41, C:0.11, G:0.03, T:0.45
Consensus pattern (30 bp):
ATTCAAATATTACATTAAAAATTTTCTATA
Found at i:10818592 original size:3 final size:3
Alignment explanation
Indices: 10818586--10818612 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
10818576 ACAAAAAAAA
10818586 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
10818613 CTCTCACACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:10819776 original size:3 final size:3
Alignment explanation
Indices: 10819768--10819829 Score: 54
Period size: 3 Copynumber: 19.3 Consensus size: 3
10819758 AGCTTTCTCC
* *
10819768 TCT TCT TCT TGCT TCT TTT TC- TCT TCT TCT TGCT TCCT TTT TGCT TCT
1 TCT TCT TCT T-CT TCT TCT TCT TCT TCT TCT T-CT T-CT TCT T-CT TCT
10819816 TCT TCT TGCT TCT T
1 TCT TCT T-CT TCT T
10819830 TCTCTCCTCT
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
2 2 0.04
3 33 0.67
4 14 0.29
ACGTcount: A:0.00, C:0.29, G:0.06, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:10819793 original size:21 final size:21
Alignment explanation
Indices: 10819767--10819835 Score: 102
Period size: 21 Copynumber: 3.1 Consensus size: 21
10819757 TAGCTTTCTC
10819767 CTCTTCTTCTTGCTTCTTTTT
1 CTCTTCTTCTTGCTTCTTTTT
10819788 CTCTTCTTCTTGCTTCCTTTTT
1 CTCTTCTTCTTGCTT-CTTTTT
*
10819810 GCTTCTTCTTCTTGCTTCTTTCT
1 -C-TCTTCTTCTTGCTTCTTTTT
10819833 CTC
1 CTC
10819836 CTCTAGCTCC
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
21 17 0.39
22 7 0.16
23 6 0.14
24 14 0.32
ACGTcount: A:0.00, C:0.32, G:0.06, T:0.62
Consensus pattern (21 bp):
CTCTTCTTCTTGCTTCTTTTT
Found at i:10824889 original size:15 final size:16
Alignment explanation
Indices: 10824871--10824907 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
10824861 GTGATAAAAT
*
10824871 AAATAAACA-ATATAA
1 AAATAAAAACATATAA
10824886 AAATAAAAACATATAA
1 AAATAAAAACATATAA
10824902 AAATAA
1 AAATAA
10824908 TATTTTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.19
Consensus pattern (16 bp):
AAATAAAAACATATAA
Found at i:10827833 original size:15 final size:14
Alignment explanation
Indices: 10827813--10827864 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 14
10827803 GTTTGGATTG
10827813 AAGGAAGAGGAAAGA
1 AAGGAA-AGGAAAGA
*
10827828 AAGGAAAGTAAAGTA
1 AAGGAAAGGAAAG-A
* *
10827843 AAGTAAAGGAATATA
1 AAGGAAAGGAA-AGA
10827858 AAGGAAA
1 AAGGAAA
10827865 CAAAACCCCT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
14 6 0.20
15 23 0.77
16 1 0.03
ACGTcount: A:0.62, C:0.00, G:0.29, T:0.10
Consensus pattern (14 bp):
AAGGAAAGGAAAGA
Found at i:10827845 original size:10 final size:10
Alignment explanation
Indices: 10827820--10827864 Score: 58
Period size: 10 Copynumber: 4.6 Consensus size: 10
10827810 TTGAAGGAAG
10827820 AGGAAAG-AA
1 AGGAAAGTAA
10827829 AGGAAAGTAA
1 AGGAAAGTAA
*
10827839 AGTAAAGTAA
1 AGGAAAGTAA
10827849 AGGAATA-TAA
1 AGGAA-AGTAA
10827859 AGGAAA
1 AGGAAA
10827865 CAAAACCCCT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
9 8 0.25
10 23 0.72
11 1 0.03
ACGTcount: A:0.62, C:0.00, G:0.27, T:0.11
Consensus pattern (10 bp):
AGGAAAGTAA
Found at i:10829549 original size:21 final size:21
Alignment explanation
Indices: 10829523--10829564 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
10829513 GTTTTACATG
10829523 GCTAGAAGCTCTTTGAGTCTA
1 GCTAGAAGCTCTTTGAGTCTA
10829544 GCTAGAAGCTCTTTGAGTCTA
1 GCTAGAAGCTCTTTGAGTCTA
10829565 CTTTCTAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (21 bp):
GCTAGAAGCTCTTTGAGTCTA
Found at i:10830601 original size:136 final size:136
Alignment explanation
Indices: 10830357--10830626 Score: 452
Period size: 136 Copynumber: 2.0 Consensus size: 136
10830347 AATTTATGGA
* *
10830357 ATTGAGAGGTTACTACTTAGCCTATAAAGTAGAGTATAAGGTTTCTATCTTAAGCCTTTGTGAGA
1 ATTGAAAGGCTACTACTTAGCCTATAAAGTAGAGTATAAGGTTTCTATCTTAAGCCTTTGTGAGA
* * *
10830422 AAAAGATAGGGTTCTAATTTCAATTCAAGTATAGTGGATTGAATCTTTGGTGTGGATAACCAAGA
66 AAAAGATAGGGTTCTAATTTCAATTCAAGTATAGTGGATTGAATCCTTAGTGTGGAGAACCAAGA
10830487 GAGAGG
131 GAGAGG
*
10830493 ATTGAAAGGCTACTATTTAGCCTA-AAATGTAGAGTATAAGGTTTCTATCTTAAGCCTTTGTGAG
1 ATTGAAAGGCTACTACTTAGCCTATAAA-GTAGAGTATAAGGTTTCTATCTTAAGCCTTTGTGAG
* *
10830557 AAAAAGATAGGGTTGTAATTTCAATTTAAGTATAGTGGATTGAATCCTTAGTGTGGAGAACCAAG
65 AAAAAGATAGGGTTCTAATTTCAATTCAAGTATAGTGGATTGAATCCTTAGTGTGGAGAACCAAG
10830622 AGAGA
130 AGAGA
10830627 AGATGTAGGT
Statistics
Matches: 125, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
135 3 0.02
136 122 0.98
ACGTcount: A:0.34, C:0.10, G:0.24, T:0.32
Consensus pattern (136 bp):
ATTGAAAGGCTACTACTTAGCCTATAAAGTAGAGTATAAGGTTTCTATCTTAAGCCTTTGTGAGA
AAAAGATAGGGTTCTAATTTCAATTCAAGTATAGTGGATTGAATCCTTAGTGTGGAGAACCAAGA
GAGAGG
Found at i:10834753 original size:19 final size:19
Alignment explanation
Indices: 10834725--10834761 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
10834715 TTAATCGACA
*
10834725 TTTAGTTTGAAGTTTTGGG
1 TTTAGATTGAAGTTTTGGG
*
10834744 TTTAGATTGAATTTTTGG
1 TTTAGATTGAAGTTTTGG
10834762 ACTTAAAAGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.27, T:0.54
Consensus pattern (19 bp):
TTTAGATTGAAGTTTTGGG
Found at i:10835308 original size:15 final size:15
Alignment explanation
Indices: 10835286--10835324 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
10835276 ATTTATTTGA
*
10835286 TAATTTTTTTTTATT
1 TAATTTTTTTTTAAT
*
10835301 TTA-TTTTTTTTAAT
1 TAATTTTTTTTTAAT
10835315 TAATTTTTTT
1 TAATTTTTTT
10835325 AAAAAATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (15 bp):
TAATTTTTTTTTAAT
Found at i:10838177 original size:20 final size:20
Alignment explanation
Indices: 10838152--10838189 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
10838142 TGTGCAAAAA
10838152 AAAAAAAACAAAAAAAAGGC
1 AAAAAAAACAAAAAAAAGGC
* *
10838172 AAAAAAAAGAGAAAAAAG
1 AAAAAAAACAAAAAAAAG
10838190 AAAGACCTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.82, C:0.05, G:0.13, T:0.00
Consensus pattern (20 bp):
AAAAAAAACAAAAAAAAGGC
Found at i:10838180 original size:11 final size:11
Alignment explanation
Indices: 10838150--10838188 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
10838140 GATGTGCAAA
*
10838150 AAAAAAAAAAC
1 AAAAAAAAGAC
*
10838161 AAAAAAAAGGC
1 AAAAAAAAGAC
*
10838172 AAAAAAAAGAG
1 AAAAAAAAGAC
10838183 AAAAAA
1 AAAAAA
10838189 GAAAGACCTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.85, C:0.05, G:0.10, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAC
Found at i:10842262 original size:13 final size:13
Alignment explanation
Indices: 10842244--10842269 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
10842234 CAACGCAGAA
10842244 AAAATGTATTATG
1 AAAATGTATTATG
10842257 AAAATGTATTATG
1 AAAATGTATTATG
10842270 GCATCTATTA
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:0.46, C:0.00, G:0.15, T:0.38
Consensus pattern (13 bp):
AAAATGTATTATG
Found at i:10848735 original size:22 final size:23
Alignment explanation
Indices: 10848710--10848758 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
10848700 TAATTAAAAA
10848710 AAAAAACCAAAAAAAC-CAAA-CT
1 AAAAAACC-AAAAAACTCAAACCT
10848732 AAAAAACCAAAAAACTCAAACCT
1 AAAAAACCAAAAAACTCAAACCT
10848755 AAAA
1 AAAA
10848759 GAGATCTGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 7 0.28
22 12 0.48
23 6 0.24
ACGTcount: A:0.71, C:0.22, G:0.00, T:0.06
Consensus pattern (23 bp):
AAAAAACCAAAAAACTCAAACCT
Found at i:10848872 original size:25 final size:25
Alignment explanation
Indices: 10848835--10848883 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
10848825 CGAAGCTCTA
10848835 AAAACACTACCTTCTTTGTTGTTGC
1 AAAACACTACCTTCTTTGTTGTTGC
* * *
10848860 AAAACATTGCCTTTTTTGTTGTTG
1 AAAACACTACCTTCTTTGTTGTTG
10848884 TAGATAAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.22, C:0.18, G:0.14, T:0.45
Consensus pattern (25 bp):
AAAACACTACCTTCTTTGTTGTTGC
Found at i:10857588 original size:22 final size:23
Alignment explanation
Indices: 10857563--10857611 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
10857553 AATTAAAAAA
10857563 AAAAAACCAAAAAAAC-CAAA-CT
1 AAAAAACC-AAAAAACTCAAACCT
10857585 AAAAAACCAAAAAACTCAAACCT
1 AAAAAACCAAAAAACTCAAACCT
10857608 AAAA
1 AAAA
10857612 GAGATCTGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 7 0.28
22 12 0.48
23 6 0.24
ACGTcount: A:0.71, C:0.22, G:0.00, T:0.06
Consensus pattern (23 bp):
AAAAAACCAAAAAACTCAAACCT
Found at i:10857726 original size:25 final size:25
Alignment explanation
Indices: 10857689--10857737 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
10857679 CGAAGCTCTA
10857689 AAAACACTACCTTCTTTGTTGTTGC
1 AAAACACTACCTTCTTTGTTGTTGC
* * *
10857714 AAAACATTGCCTTTTTTGTTGTTG
1 AAAACACTACCTTCTTTGTTGTTG
10857738 TAGATAAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.22, C:0.18, G:0.14, T:0.45
Consensus pattern (25 bp):
AAAACACTACCTTCTTTGTTGTTGC
Found at i:10859277 original size:3 final size:3
Alignment explanation
Indices: 10859269--10859297 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
10859259 ACAGTAAGTA
10859269 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
10859298 AAGAAAATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:10866564 original size:16 final size:16
Alignment explanation
Indices: 10866543--10866578 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
10866533 AGGTAAATAC
10866543 CAAAATTACAA-AGTCA
1 CAAAATTACAATA-TCA
10866559 CAAAATTACAATATCA
1 CAAAATTACAATATCA
10866575 CAAA
1 CAAA
10866579 TTGAACTGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 18 0.95
17 1 0.05
ACGTcount: A:0.58, C:0.19, G:0.03, T:0.19
Consensus pattern (16 bp):
CAAAATTACAATATCA
Found at i:10870926 original size:10 final size:10
Alignment explanation
Indices: 10870903--10870945 Score: 54
Period size: 9 Copynumber: 4.5 Consensus size: 10
10870893 ACTTTAGAAG
10870903 AAAAAATTTT
1 AAAAAATTTT
10870913 -AAAAATTTT
1 AAAAAATTTT
*
10870922 AAAAAATATT
1 AAAAAATTTT
*
10870932 AATAAA-TTT
1 AAAAAATTTT
10870941 AAAAA
1 AAAAA
10870946 CAAAAAGAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
9 15 0.54
10 13 0.46
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (10 bp):
AAAAAATTTT
Found at i:10870927 original size:19 final size:19
Alignment explanation
Indices: 10870903--10870945 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
10870893 ACTTTAGAAG
*
10870903 AAAAAATTTTAA-AAATTTT
1 AAAAAATATTAATAAA-TTT
10870922 AAAAAATATTAATAAATTT
1 AAAAAATATTAATAAATTT
10870941 AAAAA
1 AAAAA
10870946 CAAAAAGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 19 0.86
20 3 0.14
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAAAATATTAATAAATTT
Found at i:10871127 original size:15 final size:15
Alignment explanation
Indices: 10871117--10871147 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
10871107 TGAAAAAATC
10871117 AAAATCAAAAATAAA
1 AAAATCAAAAATAAA
*
10871132 AAAATCAAAAACAAA
1 AAAATCAAAAATAAA
10871147 A
1 A
10871148 TCTTTAAACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.81, C:0.10, G:0.00, T:0.10
Consensus pattern (15 bp):
AAAATCAAAAATAAA
Found at i:10871135 original size:21 final size:22
Alignment explanation
Indices: 10871100--10871147 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
10871090 ATTGAAAAGG
*
10871100 AAAAATATGAAAAAATCAAAATC
1 AAAAATA-GAAAAAATCAAAAAC
10871123 AAAAATA-AAAAAATCAAAAAC
1 AAAAATAGAAAAAATCAAAAAC
10871144 AAAA
1 AAAA
10871148 TCTTTAAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 17 0.71
23 7 0.29
ACGTcount: A:0.77, C:0.08, G:0.02, T:0.12
Consensus pattern (22 bp):
AAAAATAGAAAAAATCAAAAAC
Found at i:10871337 original size:11 final size:11
Alignment explanation
Indices: 10871321--10871352 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
10871311 CAATATGTAG
10871321 TATTTAAAAAA
1 TATTTAAAAAA
10871332 TATTT--AAAA
1 TATTTAAAAAA
10871341 TATTTAAAAAA
1 TATTTAAAAAA
10871352 T
1 T
10871353 TGAAAAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
9 9 0.47
11 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
TATTTAAAAAA
Found at i:10872108 original size:27 final size:26
Alignment explanation
Indices: 10872078--10872133 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 26
10872068 TTTTTTTGGA
* * *
10872078 TTTTTGGAAATTGTTTGAATTTTTTAT
1 TTTTTGAAAATTATTT-AATTTTTAAT
10872105 TTTTTGAAAATTATTTAATTTTTAAT
1 TTTTTGAAAATTATTTAATTTTTAAT
10872131 TTT
1 TTT
10872134 AATTTTTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 12 0.46
27 14 0.54
ACGTcount: A:0.27, C:0.00, G:0.09, T:0.64
Consensus pattern (26 bp):
TTTTTGAAAATTATTTAATTTTTAAT
Found at i:10872774 original size:34 final size:34
Alignment explanation
Indices: 10872731--10872796 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
10872721 CTTTGAACTA
*
10872731 TAATAAAATATTCAATATAATACAAATAATTTTT
1 TAATAAAATATTCAATATAATACAAAAAATTTTT
* * **
10872765 TAATGAAATATTTAATATGTTACAAAAAATTT
1 TAATAAAATATTCAATATAATACAAAAAATTT
10872797 AAGAATCTCT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.41
Consensus pattern (34 bp):
TAATAAAATATTCAATATAATACAAAAAATTTTT
Found at i:10877537 original size:24 final size:25
Alignment explanation
Indices: 10877490--10877543 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 25
10877480 ACAACTTTTG
10877490 AAAGGTAAATAAAACTATTCTAAA-
1 AAAGGTAAATAAAACTATTCTAAAT
*
10877514 AAAGGTAAATAAAACTCCTT-TAAAT
1 AAAGGTAAATAAAACT-ATTCTAAAT
10877539 AAAGG
1 AAAGG
10877544 CATAGTAACT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 20 0.74
25 7 0.26
ACGTcount: A:0.56, C:0.09, G:0.11, T:0.24
Consensus pattern (25 bp):
AAAGGTAAATAAAACTATTCTAAAT
Found at i:10877554 original size:68 final size:67
Alignment explanation
Indices: 10877445--10877581 Score: 177
Period size: 68 Copynumber: 2.0 Consensus size: 67
10877435 AATAACTTTT
* *
10877445 AAAAAGTAAATAAAACTTCTCTAAACAAAAGCACAACAACTTTTGAAAGGTAAATAAAACTAT-T
1 AAAAAGTAAATAAAACTCCTCTAAACAAAAGCACAACAACTTTTGAAAAGTAAATAAAACT-TCT
10877509 CTA
65 CTA
* * * * **
10877512 AAAAAGGTAAATAAAACTCCTTTAAATAAAGGCATAGTAACTTTTGAAAAGTAAATAAAACTTCT
1 AAAAA-GTAAATAAAACTCCTCTAAACAAAAGCACAACAACTTTTGAAAAGTAAATAAAACTTCT
10877577 CTA
65 CTA
10877580 AA
1 AA
10877582 CAGAGGCACG
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
67 6 0.10
68 54 0.90
ACGTcount: A:0.53, C:0.13, G:0.09, T:0.26
Consensus pattern (67 bp):
AAAAAGTAAATAAAACTCCTCTAAACAAAAGCACAACAACTTTTGAAAAGTAAATAAAACTTCTC
TA
Found at i:10877624 original size:112 final size:113
Alignment explanation
Indices: 10877416--10877630 Score: 279
Period size: 112 Copynumber: 1.9 Consensus size: 113
10877406 TAACTTTAGG
*
10877416 CTCCTCTAAATAGAGGCACAATAACTTTTAAAAAGTAAATAAAACTTCTCTAAACAAAAGCACAA
1 CTCCTCTAAATAAAGGCACAATAACTTTTAAAAAGTAAATAAAACTTCTCTAAACAAAAGCACAA
* ** *
10877481 CAACTTTTGAAAGGTAAATAAAACTATTCTAAA-AAAGGTAAATAAAA
66 CAACTTTTAAAAAATAAATAAAACTACTCTAAACAAAGGTAAATAAAA
* * * * * * *
10877528 CTCCTTTAAATAAAGGCATAGTAACTTTTGAAAAGTAAATAAAACTTCTCTAAACAGAGGCACGA
1 CTCCTCTAAATAAAGGCACAATAACTTTTAAAAAGTAAATAAAACTTCTCTAAACAAAAGCACAA
* * * *
10877593 TAATTTTTAAAAAATAAATAAAATTCCTCTAAACAAAG
66 CAACTTTTAAAAAATAAATAAAACTACTCTAAACAAAG
10877631 ACACGACAAC
Statistics
Matches: 86, Mismatches: 16, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
112 82 0.95
113 4 0.05
ACGTcount: A:0.50, C:0.15, G:0.09, T:0.26
Consensus pattern (113 bp):
CTCCTCTAAATAAAGGCACAATAACTTTTAAAAAGTAAATAAAACTTCTCTAAACAAAAGCACAA
CAACTTTTAAAAAATAAATAAAACTACTCTAAACAAAGGTAAATAAAA
Found at i:10877758 original size:132 final size:133
Alignment explanation
Indices: 10877513--10877766 Score: 334
Period size: 132 Copynumber: 1.9 Consensus size: 133
10877503 ACTATTCTAA
* * *
10877513 AAAAGGTAAATAAAACTCCTTTAAATAAAGGCATAGTAACTTTTGAAAAGTAAATAAAACTTCTC
1 AAAAGGTAAATAAAACTCCTTTAAATAAAAGCATAGCAACTTTTGAAAAGTAAATAAAACTCCTC
* * * *
10877578 TAAACAGAGGCACGATAATTTTTAAAAAATAAATAAAATTCCTCTAAACAAAGACACGACAACTT
66 TAAACAAAGGCACAATAACTTTTAAAAAATAAATAAAACTCCTCTAAACAAAGACACGACAACTT
10877643 TTG
131 TTG
* *
10877646 AAAA-GTAAATAAAACT-CTTCTAAATAAAAGCATTA-CAATTTTTGAAAGGTAAATAAAACTCC
1 AAAAGGTAAATAAAACTCCTT-TAAATAAAAGCA-TAGCAACTTTTGAAAAGTAAATAAAACTCC
* * ** * *
10877708 TTTAAACAAAGGCACAATAACTTTTGAAAGGTAAATAAAACTCTTTTAAACAAAGACAC
64 TCTAAACAAAGGCACAATAACTTTTAAAAAATAAATAAAACTCCTCTAAACAAAGACAC
10877767 AATAATTTAT
Statistics
Matches: 104, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
131 3 0.03
132 95 0.91
133 6 0.06
ACGTcount: A:0.50, C:0.14, G:0.10, T:0.26
Consensus pattern (133 bp):
AAAAGGTAAATAAAACTCCTTTAAATAAAAGCATAGCAACTTTTGAAAAGTAAATAAAACTCCTC
TAAACAAAGGCACAATAACTTTTAAAAAATAAATAAAACTCCTCTAAACAAAGACACGACAACTT
TTG
Found at i:10877768 original size:44 final size:44
Alignment explanation
Indices: 10877513--10877771 Score: 250
Period size: 44 Copynumber: 5.9 Consensus size: 44
10877503 ACTATTCTAA
* * * * *
10877513 AAAAGGTAAATAAAACTCCTTTAAATAAAGGCATAGTAACTTTTG
1 AAAA-GTAAATAAAACTCCTCTAAACAAAGACACAATAACTTTTG
* * * * * *
10877558 AAAAGTAAATAAAACTTCTCTAAACAGAGGCACGATAATTTTTA
1 AAAAGTAAATAAAACTCCTCTAAACAAAGACACAATAACTTTTG
* * * *
10877602 AAAAATAAATAAAATTCCTCTAAACAAAGACACGACAACTTTTG
1 AAAAGTAAATAAAACTCCTCTAAACAAAGACACAATAACTTTTG
* * ** * *
10877646 AAAAGTAAATAAAACTCTTCTAAATAAA-AGCATTACAATTTTTG
1 AAAAGTAAATAAAACTCCTCTAAACAAAGA-CACAATAACTTTTG
* * *
10877690 AAAGGTAAATAAAACTCCTTTAAACAAAGGCACAATAACTTTTG
1 AAAAGTAAATAAAACTCCTCTAAACAAAGACACAATAACTTTTG
* * *
10877734 AAAGGTAAATAAAACTCTTTTAAACAAAGACACAATAA
1 AAAAGTAAATAAAACTCCTCTAAACAAAGACACAATAA
10877772 TTTATCATAA
Statistics
Matches: 177, Mismatches: 35, Indels: 5
0.82 0.16 0.02
Matches are distributed among these distances:
43 1 0.01
44 172 0.97
45 4 0.02
ACGTcount: A:0.50, C:0.14, G:0.10, T:0.26
Consensus pattern (44 bp):
AAAAGTAAATAAAACTCCTCTAAACAAAGACACAATAACTTTTG
Found at i:10877774 original size:88 final size:88
Alignment explanation
Indices: 10877513--10877774 Score: 312
Period size: 88 Copynumber: 3.0 Consensus size: 88
10877503 ACTATTCTAA
* * *
10877513 AAAAGGTAAATAAAACTCCTTTAAATAAAGGCATAGTAACTTTTGAAAAGTAAATAAAACT-TCT
1 AAAAGGTAAATAAAACTCCTTTAAACAAAGGCACAATAACTTTTGAAAAGTAAATAAAACTCT-T
* * *
10877577 CTAAACAGAGGCACGATAATTTTT
65 CTAAACAAAGACACAATAATTTTT
** * * * * *
10877601 AAAAAATAAATAAAATTCCTCTAAACAAAGACACGACAACTTTTGAAAAGTAAATAAAACTCTTC
1 AAAAGGTAAATAAAACTCCTTTAAACAAAGGCACAATAACTTTTGAAAAGTAAATAAAACTCTTC
* ** *
10877666 TAAATAAA-AGCATTACAATTTTT
66 TAAACAAAGA-CACAATAATTTTT
* * *
10877689 GAAAGGTAAATAAAACTCCTTTAAACAAAGGCACAATAACTTTTGAAAGGTAAATAAAACTCTTT
1 AAAAGGTAAATAAAACTCCTTTAAACAAAGGCACAATAACTTTTGAAAAGTAAATAAAACTCTTC
10877754 TAAACAAAGACACAATAATTT
66 TAAACAAAGACACAATAATTT
10877775 ATCATAAAAT
Statistics
Matches: 141, Mismatches: 30, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
88 139 0.99
89 2 0.01
ACGTcount: A:0.50, C:0.14, G:0.10, T:0.27
Consensus pattern (88 bp):
AAAAGGTAAATAAAACTCCTTTAAACAAAGGCACAATAACTTTTGAAAAGTAAATAAAACTCTTC
TAAACAAAGACACAATAATTTTT
Found at i:10878755 original size:14 final size:14
Alignment explanation
Indices: 10878730--10878770 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
10878720 TCTCCTTTCT
*
10878730 TTTTTCTTTTTTT-
1 TTTTTGTTTTTTTA
*
10878743 TTGTTGTTTTTTTA
1 TTTTTGTTTTTTTA
10878757 TTTTTGTTTTTTTA
1 TTTTTGTTTTTTTA
10878771 GGCAAAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.05, C:0.02, G:0.07, T:0.85
Consensus pattern (14 bp):
TTTTTGTTTTTTTA
Found at i:10878762 original size:17 final size:15
Alignment explanation
Indices: 10878730--10878769 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
10878720 TCTCCTTTCT
10878730 TTTTTCTTTTTTTTTG
1 TTTTT-TTTTTTTTTG
10878746 TTGTTTTTTTATTTTTG
1 TT-TTTTTTT-TTTTTG
10878763 TTTTTTT
1 TTTTTTT
10878770 AGGCAAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 11 0.50
17 11 0.50
ACGTcount: A:0.03, C:0.03, G:0.07, T:0.88
Consensus pattern (15 bp):
TTTTTTTTTTTTTTG
Found at i:10883751 original size:5 final size:5
Alignment explanation
Indices: 10883741--10883770 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
10883731 TAATGAATAA
10883741 TTTCC TTTCC TTTCC TTTCC TTTCC TTTCC
1 TTTCC TTTCC TTTCC TTTCC TTTCC TTTCC
10883771 ACTCCTTAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (5 bp):
TTTCC
Found at i:10883776 original size:15 final size:15
Alignment explanation
Indices: 10883743--10883777 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
10883733 ATGAATAATT
**
10883743 TCCTTTCCTTTCCTT
1 TCCTTTCCTTTCCAC
10883758 TCCTTTCCTTTCCAC
1 TCCTTTCCTTTCCAC
10883773 TCCTT
1 TCCTT
10883778 AACCAAACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.03, C:0.43, G:0.00, T:0.54
Consensus pattern (15 bp):
TCCTTTCCTTTCCAC
Found at i:10896979 original size:25 final size:25
Alignment explanation
Indices: 10896899--10896985 Score: 93
Period size: 28 Copynumber: 3.3 Consensus size: 25
10896889 TTTCAGTCTG
10896899 GGCCCATTTTGGTCCAAGCCCAATTATA
1 GGCCCATTTTGGT-CAAGCCCAA--ATA
** * *
10896927 CACCCATTTTGGTCTGAGCCCAATTA
1 GGCCCATTTTGGTC-AAGCCCAAATA
*
10896953 GGCCCATTTTGGTCAAGCCCAACTA
1 GGCCCATTTTGGTCAAGCCCAAATA
10896978 GGCCCATT
1 GGCCCATT
10896986 ATAGCTCATT
Statistics
Matches: 50, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
25 17 0.34
26 14 0.28
27 1 0.02
28 18 0.36
ACGTcount: A:0.23, C:0.31, G:0.18, T:0.28
Consensus pattern (25 bp):
GGCCCATTTTGGTCAAGCCCAAATA
Found at i:10897036 original size:3 final size:3
Alignment explanation
Indices: 10897030--10897088 Score: 73
Period size: 3 Copynumber: 19.7 Consensus size: 3
10897020 GTTGTTGTTG
* * * * *
10897030 TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TTA TCA TCA TCA TCA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
10897078 TTA TTA TTA TT
1 TTA TTA TTA TT
10897089 TTTTTTATTT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:10897110 original size:20 final size:20
Alignment explanation
Indices: 10897081--10897125 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
10897071 ATCATTATTA
*
10897081 TTATTATTTTTTTTATTTTT
1 TTATTATTTTGTTTATTTTT
* *
10897101 TTATTTTTTTGTTTCTTTTT
1 TTATTATTTTGTTTATTTTT
*
10897121 CTATT
1 TTATT
10897126 CAATCTGCAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.11, C:0.04, G:0.02, T:0.82
Consensus pattern (20 bp):
TTATTATTTTGTTTATTTTT
Found at i:10897533 original size:21 final size:20
Alignment explanation
Indices: 10897504--10897553 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 20
10897494 GAATTATCTG
* *
10897504 GGATTTTTTCATGATTTTTTT
1 GGATTTTTTCA-AACTTTTTT
10897525 GGAATTTTTTCAAACTTTTTT
1 GG-ATTTTTTCAAACTTTTTT
10897546 GGATTTTT
1 GGATTTTT
10897554 CTGGGTTTGG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 6 0.23
21 11 0.42
22 9 0.35
ACGTcount: A:0.18, C:0.06, G:0.14, T:0.62
Consensus pattern (20 bp):
GGATTTTTTCAAACTTTTTT
Found at i:10898097 original size:15 final size:14
Alignment explanation
Indices: 10898070--10898096 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
10898060 GAGAAATATG
10898070 TTTCAAAAAAAAAT
1 TTTCAAAAAAAAAT
10898084 TTTCAAAAAAAAA
1 TTTCAAAAAAAAA
10898097 AGAATTCTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (14 bp):
TTTCAAAAAAAAAT
Found at i:10898876 original size:23 final size:23
Alignment explanation
Indices: 10898837--10898880 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
10898827 ATTCTAGGTG
*
10898837 TGGGTTTTGGTTATTGGGATTCT
1 TGGGTTTTGGATATTGGGATTCT
10898860 TGGGTTTTGGA-ATTTGGGATT
1 TGGGTTTTGGATA-TTGGGATT
10898881 TGGGATTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 1 0.05
23 18 0.95
ACGTcount: A:0.11, C:0.02, G:0.36, T:0.50
Consensus pattern (23 bp):
TGGGTTTTGGATATTGGGATTCT
Found at i:10898935 original size:20 final size:20
Alignment explanation
Indices: 10898910--10898961 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
10898900 ATTTGATGGG
*
10898910 AAGTTTATGGGTTTAGATTT
1 AAGTTTATGGGATTAGATTT
*
10898930 AAGTTTATGGGATTAGGTTT
1 AAGTTTATGGGATTAGATTT
* *
10898950 AGGTTTTTGGGA
1 AAGTTTATGGGA
10898962 GTTTTCGGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.46
Consensus pattern (20 bp):
AAGTTTATGGGATTAGATTT
Found at i:10899412 original size:5 final size:5
Alignment explanation
Indices: 10899397--10899466 Score: 56
Period size: 5 Copynumber: 13.8 Consensus size: 5
10899387 GATTTTCCTT
* *
10899397 TTTTCA TTTTA TTTTA TTTTTA GTTTA TTTTA TTTTA TTTT- TCAGTT-
1 TTTT-A TTTTA TTTTA -TTTTA TTTTA TTTTA TTTTA TTTTA T--TTTA
*
10899444 TTTTA TTTTA -TTGA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTT
10899467 TAAATTTTAT
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
4 6 0.11
5 35 0.66
6 12 0.23
ACGTcount: A:0.17, C:0.03, G:0.04, T:0.76
Consensus pattern (5 bp):
TTTTA
Found at i:10899428 original size:21 final size:21
Alignment explanation
Indices: 10899402--10899455 Score: 85
Period size: 21 Copynumber: 2.6 Consensus size: 21
10899392 TCCTTTTTTC
10899402 ATTTTATTTTATTTTT-AGTTT
1 ATTTTATTTTATTTTTCAG-TT
10899423 ATTTTATTTTATTTTTCAGTT
1 ATTTTATTTTATTTTTCAGTT
10899444 -TTTTATTTTATT
1 ATTTTATTTTATT
10899456 GATTTTATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
20 12 0.38
21 18 0.56
22 2 0.06
ACGTcount: A:0.19, C:0.02, G:0.04, T:0.76
Consensus pattern (21 bp):
ATTTTATTTTATTTTTCAGTT
Found at i:10899474 original size:29 final size:30
Alignment explanation
Indices: 10899413--10899482 Score: 88
Period size: 29 Copynumber: 2.3 Consensus size: 30
10899403 TTTTATTTTA
* * * *
10899413 TTTTTAGTTTATTTTATTTTATTTTTCAGT
1 TTTTTATTTTATTTGATTTTATTTTTAAAT
10899443 TTTTTATTTTA-TTGATTTTATTTTTAAAT
1 TTTTTATTTTATTTGATTTTATTTTTAAAT
10899472 TTTATTATTTT
1 TTT-TTATTTT
10899483 TTAAAAATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 18 0.51
30 17 0.49
ACGTcount: A:0.20, C:0.01, G:0.04, T:0.74
Consensus pattern (30 bp):
TTTTTATTTTATTTGATTTTATTTTTAAAT
Found at i:10899483 original size:22 final size:23
Alignment explanation
Indices: 10899431--10899483 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 23
10899421 TTATTTTATT
*
10899431 TTATTTTTCAGTTTTTTATTTTA
1 TTATTTTTCAGTTTTTAATTTTA
10899454 TTGA-TTTT-A-TTTTTAAATTTTA
1 TT-ATTTTTCAGTTTTT-AATTTTA
10899476 TTATTTTT
1 TTATTTTT
10899484 TAAAAATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 6 0.23
22 13 0.50
23 6 0.23
24 1 0.04
ACGTcount: A:0.21, C:0.02, G:0.04, T:0.74
Consensus pattern (23 bp):
TTATTTTTCAGTTTTTAATTTTA
Found at i:10899598 original size:31 final size:31
Alignment explanation
Indices: 10899555--10899617 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
10899545 AAATCTTTTT
** *
10899555 AGATAAATAAAAAAAGGGAAAAAAGGATAAA
1 AGATAAATAAAAAAAAAGAAAAAAGGAAAAA
10899586 AGATCAAA-AAAAAAAAAGAAAAAAGGAAAAA
1 AGAT-AAATAAAAAAAAAGAAAAAAGGAAAAA
10899617 A
1 A
10899618 ATTTTCACAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 25 0.89
32 3 0.11
ACGTcount: A:0.76, C:0.02, G:0.16, T:0.06
Consensus pattern (31 bp):
AGATAAATAAAAAAAAAGAAAAAAGGAAAAA
Found at i:10899879 original size:37 final size:37
Alignment explanation
Indices: 10899828--10899916 Score: 169
Period size: 37 Copynumber: 2.4 Consensus size: 37
10899818 AAAATCTCAT
*
10899828 CAAACTATTAGGAGATTTGTTTCAAAGTAAGTCCTAC
1 CAAACTATTGGGAGATTTGTTTCAAAGTAAGTCCTAC
10899865 CAAACTATTGGGAGATTTGTTTCAAAGTAAGTCCTAC
1 CAAACTATTGGGAGATTTGTTTCAAAGTAAGTCCTAC
10899902 CAAACTATTGGGAGA
1 CAAACTATTGGGAGA
10899917 CTTTATTGAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 51 1.00
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (37 bp):
CAAACTATTGGGAGATTTGTTTCAAAGTAAGTCCTAC
Found at i:10907126 original size:22 final size:20
Alignment explanation
Indices: 10907092--10907133 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
10907082 TTTGTTTTCA
10907092 ATTTTCAAATTTATTGATTTT
1 ATTTTCAAATTTATT-ATTTT
*
10907113 ATTTTTAAATTTTATTATTTT
1 ATTTTCAAA-TTTATTATTTT
10907134 GTAAAATTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (20 bp):
ATTTTCAAATTTATTATTTT
Found at i:10911913 original size:103 final size:103
Alignment explanation
Indices: 10911752--10911943 Score: 242
Period size: 103 Copynumber: 1.9 Consensus size: 103
10911742 GTTTTAACTT
* * * * ** *
10911752 TTTTCAACAACTATAAAATTTGGTTATAAAAACTCTTACGTCATTATATGATTGTGGTTATATAA
1 TTTTCAAAAACTATAAAAGTTGGTTATAAAAACTCTTAAGTAACAATATGATTGTGGTTACATAA
* *
10911817 TATATTTCGTAACGATTAAATGTCGTTTGTCAAAATAC
66 CATATTTCGTAACCATTAAATGTCGTTTGTCAAAATAC
* * *
10911855 TTTTCAAAAACTATAAAAGTTGGTTATAAAAATTGTTAAGTAACAATATTACTT-TGGTTACATA
1 TTTTCAAAAACTATAAAAGTTGGTTATAAAAACTCTTAAGTAACAATATGA-TTGTGGTTACATA
* *
10911919 ACATATTTTGTAACCATTGAATGTC
65 ACATATTTCGTAACCATTAAATGTC
10911944 ATTATTTTAA
Statistics
Matches: 74, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
103 72 0.97
104 2 0.03
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.40
Consensus pattern (103 bp):
TTTTCAAAAACTATAAAAGTTGGTTATAAAAACTCTTAAGTAACAATATGATTGTGGTTACATAA
CATATTTCGTAACCATTAAATGTCGTTTGTCAAAATAC
Found at i:10912095 original size:100 final size:102
Alignment explanation
Indices: 10911895--10912113 Score: 253
Period size: 100 Copynumber: 2.1 Consensus size: 102
10911885 AATTGTTAAG
* * * *
10911895 TAACAATATTACTTTGGTTACATAACATATTTTGTAACCATTGAATGTCATTATTTTAATTTTAT
1 TAACAATATTATTTTGGCTACATAACATATTTCGTAACCATTGAATGTC--TATTTTAATTTTAC
* * * *
10911960 TTTAGCAACCTTAAATTTTGGTTAAAAAAATCTTTTTCA
64 TTTAGAAACCATAAAATTTGGTTAAAAAAACCTTTTTCA
* ** *
10911999 TAACAATATTATTTTGGCTACATAAGATATTTCGTAATGATT-AATGTC-ATTTTAGTTTTACTT
1 TAACAATATTATTTTGGCTACATAACATATTTCGTAACCATTGAATGTCTATTTTAATTTTACTT
* * *
10912062 TAGAAACCATAAAATTTGGTTACAAAAGCCTTTTTCG
66 TAGAAACCATAAAATTTGGTTAAAAAAACCTTTTTCA
* *
10912099 TAACACTATTGTTTT
1 TAACAATATTATTTT
10912114 CATTGCTTTA
Statistics
Matches: 98, Mismatches: 17, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
100 56 0.57
103 6 0.06
104 36 0.37
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.45
Consensus pattern (102 bp):
TAACAATATTATTTTGGCTACATAACATATTTCGTAACCATTGAATGTCTATTTTAATTTTACTT
TAGAAACCATAAAATTTGGTTAAAAAAACCTTTTTCA
Found at i:10913272 original size:19 final size:19
Alignment explanation
Indices: 10913250--10913308 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 19
10913240 TACCACCAAA
10913250 AACATATGCTGCCAACAAG
1 AACATATGCTGCCAACAAG
* ** * *
10913269 AACAAATAATGCCAAGAAC
1 AACATATGCTGCCAACAAG
* *
10913288 AACGTGTGCTGCCAACAAG
1 AACATATGCTGCCAACAAG
10913307 AA
1 AA
10913309 TGTGTGTGCA
Statistics
Matches: 28, Mismatches: 12, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.46, C:0.24, G:0.17, T:0.14
Consensus pattern (19 bp):
AACATATGCTGCCAACAAG
Found at i:10925380 original size:58 final size:58
Alignment explanation
Indices: 10925287--10925684 Score: 494
Period size: 58 Copynumber: 6.8 Consensus size: 58
10925277 GATAAAAAGA
* * *
10925287 TTTAAAAAATATTTTTTTAAAGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAAATT
1 TTTAAAAAATA--TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAATT
* *
10925347 TTTTAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAATT
1 TTTAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAATT
*
10925404 TTTAAAAAAATGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAATT
1 TTT-AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAATT
* * **
10925463 TCTAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTTTGAAAATAAGTTTTT
1 TTTAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAA--AATT
* * **
10925523 TTTGAAAAAATATTTTTGAGGAAAAGTTGAAACTATCAATTTTTCTTGAAAATAAGCTT
1 TTT-AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAATT
** * * * * *
10925582 TCAAAAAAAAAAATCTTTGAGGAAAAGTTGAAAGTATTAATTTTCCTCGAAATTAAAATT
1 T--TTAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAATT
* * *
10925642 TCTAAAAAATA-TTTTGAGAAAAAGTTGAAAGTGTCAATTTTCC
1 TTTAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCC
10925685 CTGTACAAAA
Statistics
Matches: 294, Mismatches: 37, Indels: 17
0.84 0.11 0.05
Matches are distributed among these distances:
57 36 0.12
58 139 0.47
59 10 0.03
60 61 0.21
61 48 0.16
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (58 bp):
TTTAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAATT
Found at i:10929670 original size:19 final size:19
Alignment explanation
Indices: 10929619--10929716 Score: 83
Period size: 19 Copynumber: 5.1 Consensus size: 19
10929609 AACAATGGAT
10929619 GAAAAATAAGAAAAAAAAAGA
1 GAAAAA-AAGAAAAAAAAA-A
**
10929640 TGATGAAAA-AAAAAAAAAA
1 -GAAAAAAAGAAAAAAAAAA
* *
10929659 -AAAAAAAGAAAAAATAGA
1 GAAAAAAAGAAAAAAAAAA
* *
10929677 GGAAAAAAGAAAAAAAAAT
1 GAAAAAAAGAAAAAAAAAA
* *
10929696 GAGAAAATGAAAAAAAAAA
1 GAAAAAAAGAAAAAAAAAA
10929715 GA
1 GA
10929717 TAGTCAAATT
Statistics
Matches: 60, Mismatches: 14, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
17 5 0.08
18 8 0.13
19 32 0.53
20 9 0.15
21 2 0.03
22 4 0.07
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.06
Consensus pattern (19 bp):
GAAAAAAAGAAAAAAAAAA
Found at i:10929715 original size:30 final size:30
Alignment explanation
Indices: 10929642--10929716 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
10929632 AAAAAAGATG
*
10929642 ATGAAAAAAAAAAAAAAAAAAAAAGAAAAA
1 ATGAAAAAAAAAAGAAAAAAAAAAGAAAAA
** * *
10929672 AT-AGAGGAAAAAAGAAAAAAAAATGAGAAA
1 ATGA-AAAAAAAAAGAAAAAAAAAAGAAAAA
10929702 ATGAAAAAAAAAAGA
1 ATGAAAAAAAAAAGA
10929717 TAGTCAAATT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
29 1 0.03
30 34 0.94
31 1 0.03
ACGTcount: A:0.81, C:0.00, G:0.13, T:0.05
Consensus pattern (30 bp):
ATGAAAAAAAAAAGAAAAAAAAAAGAAAAA
Found at i:10930473 original size:63 final size:63
Alignment explanation
Indices: 10930400--10930527 Score: 202
Period size: 63 Copynumber: 2.0 Consensus size: 63
10930390 GACGAAACTG
* ** * *
10930400 GTATTGAGAAGCTTATGAATGATGACCAAGTGACAGATGATGAAATTTTTTTTGAGATGGCTA
1 GTATTGAGAAGCTTATGAACGATGACCAAGTGACAGAACATGAAATTTATTTTGAAATGGCTA
*
10930463 GTATTGAGAAGCTTATGAACGATGACCAAGTGACAGAACATGAAATTTATTTTGAAATGGTTA
1 GTATTGAGAAGCTTATGAACGATGACCAAGTGACAGAACATGAAATTTATTTTGAAATGGCTA
10930526 GT
1 GT
10930528 GCTGATAAGC
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
63 59 1.00
ACGTcount: A:0.35, C:0.09, G:0.24, T:0.32
Consensus pattern (63 bp):
GTATTGAGAAGCTTATGAACGATGACCAAGTGACAGAACATGAAATTTATTTTGAAATGGCTA
Found at i:10930847 original size:24 final size:24
Alignment explanation
Indices: 10930797--10930850 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
10930787 ATTTGATGAA
*
10930797 TTAAACTCTTACGAAGTTTGAGTTC
1 TTAAACTCTTACGAAG-CTGAGTTC
10930822 TTAAACTTCTTACGAA-CTGAGTTC
1 TTAAAC-TCTTACGAAGCTGAGTTC
10930846 TTAAA
1 TTAAA
10930851 AATTCTCATC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 12 0.44
25 6 0.22
26 9 0.33
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39
Consensus pattern (24 bp):
TTAAACTCTTACGAAGCTGAGTTC
Found at i:10931063 original size:40 final size:42
Alignment explanation
Indices: 10930982--10931076 Score: 108
Period size: 42 Copynumber: 2.3 Consensus size: 42
10930972 GATTGTGAAT
*
10930982 GAGTAATTTATTTTCCAAAGTTGGGGTTACCTCTATCTAGAG
1 GAGTAATTTATTTTCCAAAATTGGGGTTACCTCTATCTAGAG
* * *
10931024 GAGTAATTTACTTTT-CAAAATTGTGG-T-CCTCTGTTTAGAG
1 GAGTAATTTA-TTTTCCAAAATTGGGGTTACCTCTATCTAGAG
*
10931064 GAG-CATTTATTTT
1 GAGTAATTTATTTT
10931077 TGAAGTCATG
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
38 4 0.09
39 5 0.11
40 14 0.30
41 1 0.02
42 19 0.40
43 4 0.09
ACGTcount: A:0.25, C:0.13, G:0.20, T:0.42
Consensus pattern (42 bp):
GAGTAATTTATTTTCCAAAATTGGGGTTACCTCTATCTAGAG
Found at i:10931198 original size:45 final size:44
Alignment explanation
Indices: 10931105--10931305 Score: 216
Period size: 42 Copynumber: 4.6 Consensus size: 44
10931095 GCTTAAAGAA
*
10931105 TTTATTTA-TTTTCCAAAGTCGTTGAGCC-CTTGTTTAGATGAG-
1 TTTATTTATTTTTCCAAAGTCGTTGAGCCTC-TGCTTAGATGAGC
* * *
10931147 -TAATTTATTTTTTCAAAGTCGTTGAGCCTCTACTTAGATGAGCC
1 TTTATTTATTTTTCCAAAGTCGTTGAGCCTCTGCTTAGATGAG-C
* *
10931191 TTTATTTATTTTTCCAAAGTCGTTGAGCCTCTGTTTAGAGGAGC
1 TTTATTTATTTTTCCAAAGTCGTTGAGCCTCTGCTTAGATGAGC
* * *
10931235 --AATTTATTTTTCCAAAATCGTTGAGCCTCTGCTTAGAAGAGCC
1 TTTATTTATTTTTCCAAAGTCGTTGAGCCTCTGCTTAGATGAG-C
* * *
10931278 TTTGTTTATTTTTTTCAAAGTTGTTGAG
1 TTTATTTA-TTTTTCCAAAGTCGTTGAG
10931306 TTTCTGTCGT
Statistics
Matches: 132, Mismatches: 18, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
41 6 0.05
42 66 0.50
43 2 0.02
44 1 0.01
45 41 0.31
46 16 0.12
ACGTcount: A:0.23, C:0.15, G:0.18, T:0.44
Consensus pattern (44 bp):
TTTATTTATTTTTCCAAAGTCGTTGAGCCTCTGCTTAGATGAGC
Found at i:10931211 original size:87 final size:87
Alignment explanation
Indices: 10931105--10931305 Score: 289
Period size: 87 Copynumber: 2.3 Consensus size: 87
10931095 GCTTAAAGAA
* * * *
10931105 TTTATTTA-TTTTCCAAAGTCGTTGAGCC-CTTGTTTAGATGAGTAATTTATTTTTTCAAAGTCG
1 TTTATTTATTTTTCCAAAGTCGTTGAGCCTC-TGTTTAGAGGAGCAATTTATTTTTCCAAAATCG
*
10931168 TTGAGCCTCTACTTAGATGAGCC
65 TTGAGCCTCTACTTAGAAGAGCC
10931191 TTTATTTATTTTTCCAAAGTCGTTGAGCCTCTGTTTAGAGGAGCAATTTATTTTTCCAAAATCGT
1 TTTATTTATTTTTCCAAAGTCGTTGAGCCTCTGTTTAGAGGAGCAATTTATTTTTCCAAAATCGT
*
10931256 TGAGCCTCTGCTTAGAAGAGCC
66 TGAGCCTCTACTTAGAAGAGCC
* * *
10931278 TTTGTTTATTTTTTTCAAAGTTGTTGAG
1 TTTATTTA-TTTTTCCAAAGTCGTTGAG
10931306 TTTCTGTCGT
Statistics
Matches: 103, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
86 8 0.08
87 77 0.75
88 18 0.17
ACGTcount: A:0.23, C:0.15, G:0.18, T:0.44
Consensus pattern (87 bp):
TTTATTTATTTTTCCAAAGTCGTTGAGCCTCTGTTTAGAGGAGCAATTTATTTTTCCAAAATCGT
TGAGCCTCTACTTAGAAGAGCC
Found at i:10931483 original size:12 final size:12
Alignment explanation
Indices: 10931468--10931499 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
10931458 AAAAGAAAAC
10931468 AAAAAAAAGCAA
1 AAAAAAAAGCAA
*
10931480 AAAAAAAGGCAA
1 AAAAAAAAGCAA
10931492 AAAAAAAA
1 AAAAAAAA
10931500 TCCAGTTGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.84, C:0.06, G:0.09, T:0.00
Consensus pattern (12 bp):
AAAAAAAAGCAA
Found at i:10933585 original size:117 final size:114
Alignment explanation
Indices: 10933398--10933831 Score: 552
Period size: 117 Copynumber: 3.7 Consensus size: 114
10933388 TTTTTTTAAA
* * *
10933398 GAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAAATTTTTAAAAAATATTTTTGAGGAAAAGT
1 GAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT-AAGTTTCTAAAAAATATTTTTGAGGAAAAGT
*
10933463 TGAAAGTATCAATTTTCCTTGAAAATAAGTTTCTAAAAAGCATTTTTGAG
65 TGAAAGTATCAATTTTCCTTGAAAATAAGTTTCTAAAAAGAATTTTTGAG
* * *
10933513 TAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGTTTTTTTTGAAAAATATTTTTGAGGAAAA
1 GAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAG---TTTCTAAAAAATATTTTTGAGGAAAA
*
10933578 GTTGAAAGTATCAATTTTCTTTGAAAATAAGTTTTTCTAAAAA-ATATTTTTGAG
63 GTTGAAAGTATCAATTTTCCTTGAAAATAAG--TTTCTAAAAAGA-ATTTTTGAG
* * *
10933632 GAAAAGTTAAAAGTATCAATTTTCCTTGAAAATAAGCTTTCAAAAAAATTATCTTTGAGGAAAAG
1 GAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAG-TTTCTAAAAAA-TATTTTTGAGGAAAAG
* * *
10933697 TTGAAAATATCAATTTTCCTTAAAAATAAGTTT-TCAAAATTGAATTTTTGAG
64 TTGAAAGTATCAATTTTCCTTGAAAATAAGTTTCT-AAAA-AGAATTTTTGAG
* * *
10933749 GAAAAGTTGAAAGTATTAATTTTTTCCTCGAAATTAAAGTTTCTAAAAAATA-TTTTG-GGAAAA
1 GAAAAGTTGAAAGTATCAA--TTTTCCTTGAAAAT-AAGTTTCTAAAAAATATTTTTGAGG-AAA
10933812 AGTTGAAAGTATCAATTTTC
62 AGTTGAAAGTATCAATTTTC
10933832 TTTAATGTTA
Statistics
Matches: 281, Mismatches: 24, Indels: 26
0.85 0.07 0.08
Matches are distributed among these distances:
114 2 0.01
115 32 0.11
116 9 0.03
117 115 0.41
118 45 0.16
119 75 0.27
120 3 0.01
ACGTcount: A:0.42, C:0.07, G:0.13, T:0.38
Consensus pattern (114 bp):
GAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGTTTCTAAAAAATATTTTTGAGGAAAAGTT
GAAAGTATCAATTTTCCTTGAAAATAAGTTTCTAAAAAGAATTTTTGAG
Found at i:10933645 original size:59 final size:58
Alignment explanation
Indices: 10933379--10933831 Score: 560
Period size: 59 Copynumber: 7.7 Consensus size: 58
10933369 TAAAAAGATT
* * * *
10933379 TAAAAAATATTTTTTTAAAGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAAATTTT-
1 TAAAAAATA--TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT-AAGTTTTC
10933439 TAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAG-TTTC
1 TAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGTTTTC
** * *
10933496 TAAAAAGCATTTTTGAGTAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGTTTTTTT
1 TAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAG--TTTTC
* *
10933556 TGAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTTTGAAAATAAGTTTTTC
1 TAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAG-TTTTC
* *
10933615 TAAAAAATATTTTTGAGGAAAAGTTAAAAGTATCAATTTTCCTTGAAAATAAGCTTTC
1 TAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGTTTTC
* * * *
10933673 AAAAAAATTATCTTTGAGGAAAAGTTGAAAATATCAATTTTCCTTAAAAATAAGTTTTC
1 TAAAAAA-TATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGTTTTC
* * * *
10933732 --AAAATTGAATTTTTGAGGAAAAGTTGAAAGTATTAATTTTTTCCTCGAAATTAAAG-TTTC
1 TAAAAAAT--ATTTTTGAGGAAAAGTTGAAAGTATCAA--TTTTCCTTGAAAAT-AAGTTTTC
10933792 TAAAAAATA-TTTTG-GGAAAAAGTTGAAAGTATCAATTTTC
1 TAAAAAATATTTTTGAGG-AAAAGTTGAAAGTATCAATTTTC
10933832 TTTAATGTTA
Statistics
Matches: 347, Mismatches: 33, Indels: 29
0.85 0.08 0.07
Matches are distributed among these distances:
56 4 0.01
57 61 0.18
58 75 0.22
59 123 0.35
60 76 0.22
61 3 0.01
62 5 0.01
ACGTcount: A:0.42, C:0.06, G:0.13, T:0.39
Consensus pattern (58 bp):
TAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGTTTTC
Found at i:10933654 original size:176 final size:173
Alignment explanation
Indices: 10933398--10933831 Score: 576
Period size: 176 Copynumber: 2.5 Consensus size: 173
10933388 TTTTTTTAAA
*
10933398 GAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAAATTTT-TAAAAAATATTTTTGAGGAAAAG
1 GAAAAGTTGAAAGTATCAATTTTT-TTGAAAAT-AAGTTTTCTAAAAAATATTTTTGAGGAAAAG
* * *
10933462 TTGAAAGTATCAATTTTCCTTGAAAATAAG-TTTC-TAAAAAGCATTTTTGAGTAAAAGTTGAAA
64 TTGAAAGTATCAATTTTCCTTGAAAATAAGCTTTCAAAAAAAGCATCTTTGAGGAAAAGTTGAAA
* * *
10933525 GTATCAATTTTCCTTGAAAATAAGTTTTTTTTGAAAAAT-ATTTTTGAG
129 ATATCAATTTTCCTTAAAAATAAG----TTTTCAAAAATAATTTTTGAG
10933573 GAAAAGTTGAAAGTATCAATTTTCTTTGAAAATAAGTTTTTCTAAAAAATATTTTTGAGGAAAAG
1 GAAAAGTTGAAAGTATCAATTTT-TTTGAAAATAAG-TTTTCTAAAAAATATTTTTGAGGAAAAG
* **
10933638 TTAAAAGTATCAATTTTCCTTGAAAATAAGCTTTCAAAAAAATTATCTTTGAGGAAAAGTTGAAA
64 TTGAAAGTATCAATTTTCCTTGAAAATAAGCTTTCAAAAAAAGCATCTTTGAGGAAAAGTTGAAA
*
10933703 ATATCAATTTTCCTTAAAAATAAGTTTTCAAAATTGAATTTTTGAG
129 ATATCAATTTTCCTTAAAAATAAGTTTTCAAAAAT-AATTTTTGAG
* *
10933749 GAAAAGTTGAAAGTATTAATTTTTTCCTCGAAATTAAAG-TTTCTAAAAAATA-TTTTG-GGAAA
1 GAAAAGTTGAAAGTATCAATTTTTT--T-GAAAAT-AAGTTTTCTAAAAAATATTTTTGAGG-AA
10933811 AAGTTGAAAGTATCAATTTTC
61 AAGTTGAAAGTATCAATTTTC
10933832 TTTAATGTTA
Statistics
Matches: 233, Mismatches: 14, Indels: 23
0.86 0.05 0.09
Matches are distributed among these distances:
174 11 0.05
175 39 0.17
176 111 0.48
177 18 0.08
178 51 0.22
179 3 0.01
ACGTcount: A:0.42, C:0.07, G:0.13, T:0.38
Consensus pattern (173 bp):
GAAAAGTTGAAAGTATCAATTTTTTTGAAAATAAGTTTTCTAAAAAATATTTTTGAGGAAAAGTT
GAAAGTATCAATTTTCCTTGAAAATAAGCTTTCAAAAAAAGCATCTTTGAGGAAAAGTTGAAAAT
ATCAATTTTCCTTAAAAATAAGTTTTCAAAAATAATTTTTGAG
Found at i:10935798 original size:62 final size:60
Alignment explanation
Indices: 10935624--10935801 Score: 155
Period size: 62 Copynumber: 2.9 Consensus size: 60
10935614 GAACATGAAG
* * *
10935624 GAACATTCTGACTTGAGAGGACCT-ATCCTAGGATCAATCTTTTATATTGAAAAATAAGGGAG
1 GAACATTCTGACTTGAGAGGA--TAATCCTAGGAT-GATCTTTTACATTGAAAAATAAGGGAA
* * * * *
10935686 GAACATTCTGACTTTG-GGGGATAGATCCTGGGAATGATCCTCTACCTTGAAAAAT-AGGGAAA
1 GAACATTCTGAC-TTGAGAGGATA-ATCCTAGG-ATGATCTTTTACATTGAAAAATAAGGG-AA
* * *
10935748 GAGCATTCTGACTTGAGAGGATTAATCTTAGGATGGATCTTTTAGATTGAAAAA
1 GAACATTCTGACTTGAGAGGA-TAATCCTAGGAT-GATCTTTTACATTGAAAAA
10935802 CATGGGATGA
Statistics
Matches: 92, Mismatches: 16, Indels: 16
0.74 0.13 0.13
Matches are distributed among these distances:
60 1 0.01
61 9 0.10
62 75 0.82
63 7 0.08
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (60 bp):
GAACATTCTGACTTGAGAGGATAATCCTAGGATGATCTTTTACATTGAAAAATAAGGGAA
Found at i:10937166 original size:132 final size:130
Alignment explanation
Indices: 10937027--10937379 Score: 331
Period size: 131 Copynumber: 2.7 Consensus size: 130
10937017 TTCATTATAC
* * * * * *
10937027 TTTTTTTATCGTTATAAATATGATAAATATTTTCATATCATCTTTTTTTGTCCTTGTA-AACATA
1 TTTTTTTATCGTTATAAATATGATAAA-ATTTTCATAACA-ATTTTATT-TCATTGTATAAAACA
* *
10937091 TTAAAAAAATAAATTAAGCAATGACGATGAA-AAATTGTAGGAAAAT-AAA-TAATTTTTTGCAA
63 TTAAAAAAATAAATTAAGCAATGAC-ATGAATAAATTGT-GGAAAATAAAACAAAATTTTTGCAA
10937153 CAATTA
126 CAA-TA
* * * *
10937159 TTTTTTTATCATTATAAATATGGTTAGAATTTTCGTAACAATTTTATTTCATTGTATAAAACATT
1 TTTTTTTATCGTTATAAATAT-GATAAAATTTTCATAACAATTTTATTTCATTGTATAAAACATT
* * * * *
10937224 AAAAAAATAAATTAAGGAATGACATTAATAAATTGTTGCAAATAAAACAAAATTTTTGTAACAAT
65 AAAAAAATAAATTAAGCAATGACATGAATAAATTGTGGAAAATAAAACAAAATTTTTGCAACAAT
10937289 A
130 A
** * * * * * * *
10937290 AGTTTTTATCGTTACAAATATGATAGAAGTATTCCTAACAACATTTT-TTTTATTCTATAAAATA
1 TTTTTTTATCGTTATAAATATGATA-AAATTTTCATAAC-A-ATTTTATTTCATTGTATAAAACA
*
10937354 TTAAAAAAAT-ATTTAAGCAATGACAT
63 TTAAAAAAATAAATTAAGCAATGACAT
10937380 TTAAAAATGA
Statistics
Matches: 182, Mismatches: 31, Indels: 17
0.79 0.13 0.07
Matches are distributed among these distances:
130 19 0.10
131 86 0.47
132 68 0.37
133 9 0.05
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.40
Consensus pattern (130 bp):
TTTTTTTATCGTTATAAATATGATAAAATTTTCATAACAATTTTATTTCATTGTATAAAACATTA
AAAAAATAAATTAAGCAATGACATGAATAAATTGTGGAAAATAAAACAAAATTTTTGCAACAATA
Found at i:10939027 original size:24 final size:25
Alignment explanation
Indices: 10938981--10939034 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
10938971 TCTTCTATTG
**
10938981 TTTTCATTTTTTTGTTTCATTTTCC
1 TTTTCATTTTTTTCATTCATTTTCC
*
10939006 TTTTCA-TTTTTTCATTCTTTTTCC
1 TTTTCATTTTTTTCATTCATTTTCC
*
10939030 ATTTC
1 TTTTC
10939035 TTGCCATACA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
24 19 0.76
25 6 0.24
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (25 bp):
TTTTCATTTTTTTCATTCATTTTCC
Found at i:10943565 original size:42 final size:42
Alignment explanation
Indices: 10943493--10943636 Score: 109
Period size: 42 Copynumber: 3.4 Consensus size: 42
10943483 TCATAGGAGT
* * * *
10943493 CTTTCAAAATTTTAGAGTGGTTGA-GCCTTTGTTTAGAAAAGC
1 CTTTCAAATTTTTAAAGTCGTT-ATGACTTTGTTTAGAAAAGC
* *
10943535 CTTTCAAATTTTTAAAGTCCGTTATG-CTTTGTTCA-AATGAGC
1 CTTTCAAATTTTTAAAGT-CGTTATGACTTTGTTTAGAA-AAGC
* * * * *
10943577 CTCTT-AAAATTTTAAAGTTGTTATGACTTTATTTAGAGAAGT
1 CT-TTCAAATTTTTAAAGTCGTTATGACTTTGTTTAGAAAAGC
10943619 C-TTCTAAATTTTTAAAGT
1 CTTTC-AAATTTTTAAAGT
10943637 TGTTGTGCTC
Statistics
Matches: 81, Mismatches: 13, Indels: 16
0.74 0.12 0.15
Matches are distributed among these distances:
40 2 0.02
41 8 0.10
42 64 0.79
43 7 0.09
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.43
Consensus pattern (42 bp):
CTTTCAAATTTTTAAAGTCGTTATGACTTTGTTTAGAAAAGC
Found at i:10943567 original size:84 final size:84
Alignment explanation
Indices: 10943459--10943636 Score: 193
Period size: 84 Copynumber: 2.1 Consensus size: 84
10943449 TGGTTGTGAT
* * * * *
10943459 TTTTTAAAGTTGTCATGCCTTTGTTCATAGGAGTCT-TTCAAAATTTTAGAGTGGTTGA-GCCTT
1 TTTTTAAAGTCGTCATGCCTTTGTTCAAAGGAGCCTCTT-AAAATTTTAAAGTGGTT-ATGACTT
*
10943522 TGTTTAGAAAAGCCTT-TCAAA
64 TATTTAGAAAAGCCTTCT-AAA
* * *
10943543 TTTTTAAAGTCCGTTATG-CTTTGTTCAAATGAGCCTCTTAAAATTTTAAAGTTGTTATGACTTT
1 TTTTTAAAGT-CGTCATGCCTTTGTTCAAAGGAGCCTCTTAAAATTTTAAAGTGGTTATGACTTT
* *
10943607 ATTTAGAGAAGTCTTCTAAA
65 ATTTAGAAAAGCCTTCTAAA
10943627 TTTTTAAAGT
1 TTTTTAAAGT
10943637 TGTTGTGCTC
Statistics
Matches: 79, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
83 1 0.01
84 70 0.89
85 8 0.10
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.44
Consensus pattern (84 bp):
TTTTTAAAGTCGTCATGCCTTTGTTCAAAGGAGCCTCTTAAAATTTTAAAGTGGTTATGACTTTA
TTTAGAAAAGCCTTCTAAA
Found at i:10944158 original size:4 final size:4
Alignment explanation
Indices: 10944149--10944207 Score: 63
Period size: 4 Copynumber: 15.5 Consensus size: 4
10944139 TATTATTTTC
*
10944149 TCTT TCTT TCTT T-TT T-TT TATT T-TCT TCTT T-TT TCTT TCTT TCTT
1 TCTT TCTT TCTT TCTT TCTT TCTT TCT-T TCTT TCTT TCTT TCTT TCTT
*
10944194 TCTT TCTT TTTT TC
1 TCTT TCTT TCTT TC
10944208 CCCAAAGTCC
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
3 10 0.20
4 38 0.78
5 1 0.02
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.80
Consensus pattern (4 bp):
TCTT
Found at i:10944160 original size:25 final size:25
Alignment explanation
Indices: 10944132--10944186 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
10944122 ATTATTATTA
10944132 TCTTTATTATTATTTTC-TCTTTCTT
1 TCTTTATTATTATTTTCTTCTTT-TT
* *
10944157 TCTTTTTTTTTATTTTCTTCTTTTT
1 TCTTTATTATTATTTTCTTCTTTTT
10944182 TCTTT
1 TCTTT
10944187 CTTTCTTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 22 0.81
26 5 0.19
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (25 bp):
TCTTTATTATTATTTTCTTCTTTTT
Found at i:10945254 original size:21 final size:21
Alignment explanation
Indices: 10945221--10945278 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
10945211 TGTTACTTAA
* * *
10945221 TTTTTAATATATTTTTATTA-
1 TTTTTATTTTATTTTTATGAT
*
10945241 TTTTTATTTCTATTTTTGTGAT
1 TTTTTATTT-TATTTTTATGAT
10945263 TTTTTATTTTATTTTT
1 TTTTTATTTTATTTTT
10945279 GTGTGAACTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 7 0.22
21 16 0.50
22 9 0.28
ACGTcount: A:0.19, C:0.02, G:0.03, T:0.76
Consensus pattern (21 bp):
TTTTTATTTTATTTTTATGAT
Found at i:10945284 original size:23 final size:22
Alignment explanation
Indices: 10945241--10945281 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
10945231 ATTTTTATTA
10945241 TTTTTATTTCTATTTTTGTGAT
1 TTTTTATTTCTATTTTTGTGAT
10945263 TTTTTATTT-TATTTTTGTG
1 TTTTTATTTCTATTTTTGTG
10945282 TGAACTTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.12, C:0.02, G:0.10, T:0.76
Consensus pattern (22 bp):
TTTTTATTTCTATTTTTGTGAT
Found at i:10945661 original size:142 final size:141
Alignment explanation
Indices: 10945469--10945723 Score: 327
Period size: 141 Copynumber: 1.8 Consensus size: 141
10945459 AAATGTTATG
*** *
10945469 GAAAAAGTTGAAATATCAAAATTTTCTTAAAACAAAATTTTGGTAATATTTAGGAAAAAATTGAA
1 GAAAAAGTTGAAATATCAAAATTTTCTTAAAACAAAATTTTAAAAATATTTA-GAAAAAATTAAA
* *
10945534 ACATAAATTTTTCTTAAATTCTTTAAGAATAGA-AATAAAATAAAATAAAAATTAAATGAAGATT
65 ACATAAATTTTTCCTAAATTCTTTAA-AATAAATAATAAAATAAAATAAAAATTAAATGAAGATT
10945598 TGAAAAATGCTAA
129 TGAAAAATGCTAA
* * * *
10945611 GAAAAATGTTG-AATATC-AAATTTTCCTTAGAATAAATTTTTAAAAATATTTAGAAAATATTAA
1 GAAAAA-GTTGAAATATCAAAATTTT-CTTAAAACAAAATTTTAAAAATATTTAGAAAAAATTAA
* * * *
10945674 AATATCAATTTTTCCTAAATTCTTTGAAATAAATAATAAAATAAATTAAA
64 AACATAAATTTTTCCTAAATTCTTTAAAATAAATAATAAAATAAAATAAA
10945724 TTATGAAAAA
Statistics
Matches: 96, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
140 5 0.05
141 54 0.56
142 33 0.34
143 4 0.04
ACGTcount: A:0.52, C:0.05, G:0.08, T:0.35
Consensus pattern (141 bp):
GAAAAAGTTGAAATATCAAAATTTTCTTAAAACAAAATTTTAAAAATATTTAGAAAAAATTAAAA
CATAAATTTTTCCTAAATTCTTTAAAATAAATAATAAAATAAAATAAAAATTAAATGAAGATTTG
AAAAATGCTAA
Found at i:10955850 original size:2 final size:2
Alignment explanation
Indices: 10955843--10955872 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
10955833 TTTGGTCAAT
*
10955843 TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10955873 AATAGAGTGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:10957305 original size:15 final size:15
Alignment explanation
Indices: 10957282--10957324 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
10957272 GATTGACAGG
10957282 TTTTTTTCTTTT-TT
1 TTTTTTTCTTTTCTT
10957296 TTTTTCTTCTTTTCTT
1 TTTTT-TTCTTTTCTT
* *
10957312 TTATTTTCCTTTC
1 TTTTTTTCTTTTC
10957325 CCTTATTTCC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 5 0.20
15 14 0.56
16 6 0.24
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTTTTTCTTTTCTT
Found at i:10962521 original size:2 final size:2
Alignment explanation
Indices: 10962514--10962548 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
10962504 TCAAGGAAAG
*
10962514 AT AT AT AT AT TT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
10962549 CTTAATAGTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:10965088 original size:10 final size:10
Alignment explanation
Indices: 10965069--10965127 Score: 52
Period size: 10 Copynumber: 6.1 Consensus size: 10
10965059 TGCTGTTATC
10965069 AATTTAAATA
1 AATTTAAATA
*
10965079 AATTTGAAT-
1 AATTTAAATA
*
10965088 ATTTTAAATA
1 AATTTAAATA
*
10965098 GATTTAAAT-
1 AATTTAAATA
10965107 AATATTAAAT-
1 AAT-TTAAATA
*
10965117 AAGTTAAATA
1 AATTTAAATA
10965127 A
1 A
10965128 TCATGTATCC
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
9 15 0.38
10 24 0.62
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (10 bp):
AATTTAAATA
Found at i:10965095 original size:19 final size:20
Alignment explanation
Indices: 10965071--10965128 Score: 66
Period size: 19 Copynumber: 3.0 Consensus size: 20
10965061 CTGTTATCAA
*
10965071 TTTAAATAAATTTGAAT-AT
1 TTTAAATAAATTTAAATAAT
*
10965090 TTTAAATAGATTTAAATAAT
1 TTTAAATAAATTTAAATAAT
* *
10965110 ATTAAAT-AAGTTAAATAAT
1 TTTAAATAAATTTAAATAAT
10965129 CATGTATCCT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
19 25 0.76
20 8 0.24
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (20 bp):
TTTAAATAAATTTAAATAAT
Found at i:10965117 original size:29 final size:29
Alignment explanation
Indices: 10965070--10965126 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
10965060 GCTGTTATCA
* **
10965070 ATTTAAATAAATTTGAATATTTTAAATAG
1 ATTTAAATAAATTTAAATAAGTTAAATAG
10965099 ATTTAAAT-AATATTAAATAAGTTAAATA
1 ATTTAAATAAAT-TTAAATAAGTTAAATA
10965127 ATCATGTATC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 3 0.12
29 21 0.88
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (29 bp):
ATTTAAATAAATTTAAATAAGTTAAATAG
Found at i:10965196 original size:31 final size:30
Alignment explanation
Indices: 10965161--10965219 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 30
10965151 TAAATTAATA
10965161 TTTAAATA-TTTGTTATTATTTAATGATTTAG
1 TTTAAA-AGTTTGTTA-TATTTAATGATTTAG
* *
10965192 TTTAAAAGTTTTTTATATTTAATTATTT
1 TTTAAAAGTTTGTTATATTTAATGATTT
10965220 TAATAAGATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 13 0.52
31 12 0.48
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (30 bp):
TTTAAAAGTTTGTTATATTTAATGATTTAG
Found at i:10965313 original size:44 final size:44
Alignment explanation
Indices: 10965230--10965316 Score: 140
Period size: 44 Copynumber: 2.0 Consensus size: 44
10965220 TAATAAGATA
*
10965230 TATTATAATTATTTATTATTATCCTATATGTCATCCAAAGAAAC
1 TATTATAATTATTTATTATTATCCTATATATCATCCAAAGAAAC
*
10965274 TATTATAATTATTTATTATTATCCTATGA-ATCATTCAAAGAAA
1 TATTATAATTATTTATTATTATCCTAT-ATATCATCCAAAGAAA
10965317 TTATCCATCT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
44 39 0.98
45 1 0.03
ACGTcount: A:0.40, C:0.11, G:0.05, T:0.44
Consensus pattern (44 bp):
TATTATAATTATTTATTATTATCCTATATATCATCCAAAGAAAC
Found at i:10967783 original size:2 final size:2
Alignment explanation
Indices: 10967776--10967802 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
10967766 ATATACAAAT
10967776 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
10967803 TATATGTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:10975057 original size:25 final size:27
Alignment explanation
Indices: 10974997--10975062 Score: 82
Period size: 25 Copynumber: 2.5 Consensus size: 27
10974987 ACCTTTTTTA
*
10974997 AAATTCAAAAATTACAAAATAAAAATT
1 AAATTCAAAAAATACAAAATAAAAATT
**
10975024 ATTTTCAAAAAATA-AAAATAAAAA-T
1 AAATTCAAAAAATACAAAATAAAAATT
*
10975049 AAATACAAAAAATA
1 AAATTCAAAAAATA
10975063 TTTTCCATAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
25 12 0.36
26 10 0.30
27 11 0.33
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.24
Consensus pattern (27 bp):
AAATTCAAAAAATACAAAATAAAAATT
Found at i:10979709 original size:143 final size:143
Alignment explanation
Indices: 10979505--10979768 Score: 339
Period size: 143 Copynumber: 1.8 Consensus size: 143
10979495 AAAAAGAGTA
* * * * *
10979505 AAATTACAAAAACACCTTTTAAGGGTACTTTCACAATTTGACCTTGTTATGGTTGACTTTTTGTG
1 AAATTACAAAAACACATTTTAAGGGCACTTTCACAATTTGACCTTGTTAAGATTGACTTTTTATG
* * * *
10979570 AAATATTTTAGATCATATTTGGATATTATTTGATGAACTCTGATGCATTAAAAATCCCTATTGCA
66 AAACATTTTAGATCATATTTAGATATTACTTCATGAACTCTGATGCATTAAAAATCCCTATTGCA
10979635 CTTCGAAAGGGTT
131 CTTCGAAAGGGTT
* * * * * * * *
10979648 AAATTACTAAAATACATTTTAGGGGCATTTTCATAATTTGATCTTTTTAAGATTGATTTTTTATG
1 AAATTACAAAAACACATTTTAAGGGCACTTTCACAATTTGACCTTGTTAAGATTGACTTTTTATG
* * * *
10979713 AAACATTTTAGATCATGTTTAGATATTGCTTCATGAATTTTGATGCATTAAAAATC
66 AAACATTTTAGATCATATTTAGATATTACTTCATGAACTCTGATGCATTAAAAATC
10979769 TTGATTTTAC
Statistics
Matches: 100, Mismatches: 21, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
143 100 1.00
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.42
Consensus pattern (143 bp):
AAATTACAAAAACACATTTTAAGGGCACTTTCACAATTTGACCTTGTTAAGATTGACTTTTTATG
AAACATTTTAGATCATATTTAGATATTACTTCATGAACTCTGATGCATTAAAAATCCCTATTGCA
CTTCGAAAGGGTT
Found at i:10981925 original size:18 final size:18
Alignment explanation
Indices: 10981904--10981944 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
10981894 AACCCTAAAT
* *
10981904 CTAACCTTAACCTAAACC
1 CTAAACTTAAACTAAACC
10981922 CTAAACTTAAACTAAACC
1 CTAAACTTAAACTAAACC
10981940 CTAAA
1 CTAAA
10981945 TTTGACCTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.46, C:0.32, G:0.00, T:0.22
Consensus pattern (18 bp):
CTAAACTTAAACTAAACC
Found at i:10981939 original size:24 final size:24
Alignment explanation
Indices: 10981887--10981944 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
10981877 TTAAACCTTA
*
10981887 AAACCTAAACCCTAAATCTAACCT
1 AAACCTAAACCCTAAATCTAAACT
*
10981911 TAACCTAAACCCTAAA-CTTAAACT
1 AAACCTAAACCCTAAATC-TAAACT
10981935 AAACCCTAAA
1 AAA-CCTAAA
10981945 TTTGACCTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
23 1 0.03
24 22 0.76
25 6 0.21
ACGTcount: A:0.48, C:0.31, G:0.00, T:0.21
Consensus pattern (24 bp):
AAACCTAAACCCTAAATCTAAACT
Found at i:10981954 original size:24 final size:22
Alignment explanation
Indices: 10981881--10981958 Score: 65
Period size: 24 Copynumber: 3.5 Consensus size: 22
10981871 CAATTTTTAA
10981881 ACCTTAAAACCTAAACCCTAAATCT
1 ACCTT-AAA-CTAAACCCTAAAT-T
*
10981906 AACCTTAACCTAAACCCT-AA--
1 -ACCTTAAACTAAACCCTAAATT
10981926 A-CTTAAACTAAACCCTAAATTT
1 ACCTTAAACTAAACCCTAAA-TT
10981948 GACCTTAAACT
1 -ACCTTAAACT
10981959 TTAAATTATC
Statistics
Matches: 44, Mismatches: 2, Indels: 14
0.73 0.03 0.23
Matches are distributed among these distances:
18 14 0.32
19 3 0.07
23 3 0.07
24 17 0.39
25 2 0.05
26 5 0.11
ACGTcount: A:0.44, C:0.29, G:0.01, T:0.26
Consensus pattern (22 bp):
ACCTTAAACTAAACCCTAAATT
Found at i:10986289 original size:16 final size:16
Alignment explanation
Indices: 10986252--10986290 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
10986242 TAATAATAAT
* *
10986252 AAATAAATATATATAA
1 AAATAAATATAAAAAA
*
10986268 ATATAAATATAAAAAA
1 AAATAAATATAAAAAA
10986284 AAATAAA
1 AAATAAA
10986291 AAAAAAACTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
AAATAAATATAAAAAA
Found at i:10986578 original size:22 final size:19
Alignment explanation
Indices: 10986550--10986592 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
10986540 AGACCACTTC
* *
10986550 TTTTTCTCTCTCTCTTCTCT
1 TTTTTTTCTCTCCCTT-TCT
10986570 TTTTTTTCTCTCCCTTTCT
1 TTTTTTTCTCTCCCTTTCT
10986589 TTTT
1 TTTT
10986593 AAACAATCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTTTTTCTCTCCCTTTCT
Found at i:10994672 original size:88 final size:88
Alignment explanation
Indices: 10994523--10994698 Score: 307
Period size: 88 Copynumber: 2.0 Consensus size: 88
10994513 CATATCACTC
*
10994523 CAAGAACGAATGCGGGTTCTATCCAATTAGACATACCACTTGACAGTAGAGCCTATAAGGCTATC
1 CAAGAACGAATGCGGGTTCTATCCAACTAGACATACCACTTGACAGTAGAGCCTATAAGGCTATC
10994588 TTGAAAAACATGCATTAGTAATT
66 TTGAAAAACATGCATTAGTAATT
* * * *
10994611 CAAGAACGAATGCGGGTTCTGTCCAACTGGACATACCACTTGGCAGTAGAGCCTGTAAGGCTATC
1 CAAGAACGAATGCGGGTTCTATCCAACTAGACATACCACTTGACAGTAGAGCCTATAAGGCTATC
10994676 TTGAAAAACATGCATTAGTAATT
66 TTGAAAAACATGCATTAGTAATT
10994699 TTTCATTATG
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:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (88 bp):
CAAGAACGAATGCGGGTTCTATCCAACTAGACATACCACTTGACAGTAGAGCCTATAAGGCTATC
TTGAAAAACATGCATTAGTAATT
Done.