Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032246.1 Gossypioides kirkii chromosome KI_03
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: 42061019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2000 characters in sequence are not A, C, G, or T
File 118 of 135
Found at i:35410780 original size:17 final size:16
Alignment explanation
Indices: 35410743--35410779 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
35410733 AATCAAATAG
* *
35410743 AAAAATTGATTAAATT
1 AAAAATCGAATAAATT
35410759 AAAAATCGAATAAATT
1 AAAAATCGAATAAATT
35410775 AAAAA
1 AAAAA
35410780 AATATTCAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.27
Consensus pattern (16 bp):
AAAAATCGAATAAATT
Found at i:35415029 original size:12 final size:12
Alignment explanation
Indices: 35415012--35415036 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35415002 CCAATTTTAC
35415012 AAAAAAAAAAAT
1 AAAAAAAAAAAT
35415024 AAAAAAAAAAAT
1 AAAAAAAAAAAT
35415036 A
1 A
35415037 GTATTTCATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (12 bp):
AAAAAAAAAAAT
Found at i:35415822 original size:21 final size:23
Alignment explanation
Indices: 35415798--35415839 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
35415788 AAGATATAAA
*
35415798 TACTTT-T-AAAATAATATTTGT
1 TACTTTATAAAAAAAATATTTGT
35415819 TACTTTATAAAAAAAATATTT
1 TACTTTATAAAAAAAATATTT
35415840 TTTTAATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 1 0.06
23 11 0.61
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (23 bp):
TACTTTATAAAAAAAATATTTGT
Found at i:35423347 original size:15 final size:15
Alignment explanation
Indices: 35423327--35423376 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 15
35423317 TTATTTTTTA
35423327 TTTTTAAAATATAAT
1 TTTTTAAAATATAAT
*
35423342 TTTTTAATTAATATTTAT
1 TTTTTAA--AATA-TAAT
*
35423360 TTATTAAAATATAAT
1 TTTTTAAAATATAAT
35423375 TT
1 TT
35423377 ATAATATCCA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
15 12 0.41
16 4 0.14
17 4 0.14
18 9 0.31
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTTTAAAATATAAT
Found at i:35430540 original size:41 final size:39
Alignment explanation
Indices: 35430476--35430553 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 39
35430466 CAATTATTCA
*
35430476 TAAAATCTCAATTAATATATTTATTTAAAAA-CTAATTTG
1 TAAAATCTCAATTAAAATATTTA-TTAAAAATCTAATTTG
*
35430515 TAAAATCTATAATTATAAATATTTATTAAAAATCTAATT
1 TAAAATCT-CAATTA-AAATATTTATTAAAAATCTAATT
35430554 AAACGTTGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
39 8 0.24
40 12 0.35
41 14 0.41
ACGTcount: A:0.49, C:0.06, G:0.01, T:0.44
Consensus pattern (39 bp):
TAAAATCTCAATTAAAATATTTATTAAAAATCTAATTTG
Found at i:35432866 original size:23 final size:24
Alignment explanation
Indices: 35432829--35432884 Score: 96
Period size: 23 Copynumber: 2.3 Consensus size: 24
35432819 CAATACTTTA
35432829 AAAAAAAATATTTTTTTTGTGATC
1 AAAAAAAATATTTTTTTTGTGATC
35432853 AAAAAAAATA-TTTTTTTGTGATC
1 AAAAAAAATATTTTTTTTGTGATC
35432876 AAAATAAAA
1 AAAA-AAAA
35432885 GCTAATGACT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
23 17 0.55
24 14 0.45
ACGTcount: A:0.50, C:0.04, G:0.07, T:0.39
Consensus pattern (24 bp):
AAAAAAAATATTTTTTTTGTGATC
Found at i:35446353 original size:16 final size:15
Alignment explanation
Indices: 35446294--35446346 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
35446284 TTATTATTTA
*
35446294 AATAATCTAATAAAAT
1 AATAATATAA-AAAAT
*
35446310 AATTATATGTAAAAAAT
1 AA-TA-ATATAAAAAAT
35446327 AATAATATAAATAAAT
1 AATAATATAAA-AAAT
35446343 AATA
1 AATA
35446347 CATTAAAATC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 6 0.19
16 12 0.38
17 9 0.28
18 5 0.16
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (15 bp):
AATAATATAAAAAAT
Found at i:35446474 original size:9 final size:9
Alignment explanation
Indices: 35446460--35446485 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
35446450 TTATTAAGCA
35446460 AAAAAAAAC
1 AAAAAAAAC
35446469 AAAAAAAAC
1 AAAAAAAAC
35446478 AAAAAAAA
1 AAAAAAAA
35446486 GTTTAAGAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:35454760 original size:24 final size:24
Alignment explanation
Indices: 35454733--35454796 Score: 85
Period size: 24 Copynumber: 2.7 Consensus size: 24
35454723 CTTTTTGAAG
* * *
35454733 ATTTAGTATTTTTTAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
35454757 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATTAGCATAATAT
35454781 ATTT-GACATTTATTAG
1 ATTTAG-CATTTATTAG
35454797 TATATTTGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
23 1 0.03
24 35 0.97
ACGTcount: A:0.34, C:0.05, G:0.09, T:0.52
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:35459265 original size:30 final size:30
Alignment explanation
Indices: 35459231--35459301 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 30
35459221 AAAATTACAT
*
35459231 TTTAATTTTTTAAAAATAATAAAAATTTAA
1 TTTAATTTTTTAAAAATAATAAAAATATAA
* * *
35459261 TTTAATATTTTATAAATTATAAAAATATAA
1 TTTAATTTTTTAAAAATAATAAAAATATAA
*
35459291 ATTATATTTTT
1 TTTA-ATTTTT
35459302 ACTATCCTGC
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
30 29 0.85
31 5 0.15
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (30 bp):
TTTAATTTTTTAAAAATAATAAAAATATAA
Found at i:35462973 original size:202 final size:201
Alignment explanation
Indices: 35462608--35463008 Score: 527
Period size: 201 Copynumber: 2.0 Consensus size: 201
35462598 CTTCATATGC
* * * *
35462608 TTTTTTTTTTTTAATTTGGTTATGCCAACTTTAACTGTTTTGTCACTCATCTGCTCTTCTGATTC
1 TTTTCTTTTTTTAATTTGGTTATGCCAACTGTAACTGTTTTGTCACTCATCTGCTCTTCTCATGC
** * * **
35462673 TGATTGGGATACAAAATTGTAATTTCTGTTCCATAGTCTCCCTCCTTATTCTTCCTCATGCTATC
66 TGAAAGGGATACAAAAATGAAATTTCTGTTCCATAGTCTCCCTCCTTATTCTTCCTCACACTATC
* * * *
35462738 AGTCAAGAACTAGAATTTCTAACTGAATTAGGGAGAACATAACCTGTTTTAACTTCCATTGCTGA
131 AGTCAAGAACTAGAATTTCTAACTGAATTAGGGAGAACACAACCTGTGTTAACTTCCATGGCTAA
35462803 TATTGG
196 TATTGG
* * * * *
35462809 TTTTCTTTTTTT-ATTTTGTTATGCCATCTGTAACTGTTTTGTCATTCTTCTGTTCTTCCTCATG
1 TTTTCTTTTTTTAATTTGGTTATGCCAACTGTAACTGTTTTGTCACTCATCTGCTCTT-CTCATG
* * *
35462873 CTGAAAGGGATACAAAAATGAAATTTCTTTTCCATAGTCTCCTTCCTT-TATCTTCTTCACACTC
65 CTGAAAGGGATACAAAAATGAAATTTCTGTTCCATAGTCTCCCTCCTTAT-TCTTCCTCACACT-
* * * *
35462937 ATCAGTCAAGAACTAGAGTTTCTAACTGATTTAGGGAGAACACAACTTGTGTTAGCTTCCATGGC
128 ATCAGTCAAGAACTAGAATTTCTAACTGAATTAGGGAGAACACAACCTGTGTTAACTTCCATGGC
35463002 TAATATT
193 TAATATT
35463009 TATTTATTAA
Statistics
Matches: 171, Mismatches: 26, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
200 40 0.23
201 67 0.39
202 64 0.37
ACGTcount: A:0.24, C:0.20, G:0.14, T:0.43
Consensus pattern (201 bp):
TTTTCTTTTTTTAATTTGGTTATGCCAACTGTAACTGTTTTGTCACTCATCTGCTCTTCTCATGC
TGAAAGGGATACAAAAATGAAATTTCTGTTCCATAGTCTCCCTCCTTATTCTTCCTCACACTATC
AGTCAAGAACTAGAATTTCTAACTGAATTAGGGAGAACACAACCTGTGTTAACTTCCATGGCTAA
TATTGG
Found at i:35466713 original size:23 final size:24
Alignment explanation
Indices: 35466669--35466713 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
35466659 AATTCAACCT
* *
35466669 AATATATATTTTTCTATTTATTAA
1 AATAAATATTATTCTATTTATTAA
35466693 AATAAATATTATT-TATTTATT
1 AATAAATATTATTCTATTTATT
35466714 TATTTTAGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (24 bp):
AATAAATATTATTCTATTTATTAA
Found at i:35477103 original size:38 final size:38
Alignment explanation
Indices: 35477059--35477135 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 38
35477049 TTTTTTTTAA
* * *
35477059 AATAGCGTATCTTGATTTGGATTTTTGAAAATTTGAAT
1 AATAGCGAATCCTGATTTGGATTTTTGAAAATTTAAAT
35477097 AATAGCGAATCCTGATTTGGATTTTTGAAAATTTAAAT
1 AATAGCGAATCCTGATTTGGATTTTTGAAAATTTAAAT
35477135 A
1 A
35477136 TCTAAAAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (38 bp):
AATAGCGAATCCTGATTTGGATTTTTGAAAATTTAAAT
Found at i:35477661 original size:20 final size:19
Alignment explanation
Indices: 35477638--35477700 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 19
35477628 ATTAATTATT
35477638 TATAAAATTTATTTAGAATA
1 TATAAAATTTATTTA-AATA
35477658 TAT-AAATTATATTTTAAATA
1 TATAAAATT-TA-TTTAAATA
*
35477678 TTTAAATATTTATAATTAAATA
1 TATAAA-ATTTAT--TTAAATA
35477700 T
1 T
35477701 TATTATTTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
19 5 0.14
20 12 0.33
21 8 0.22
22 11 0.31
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (19 bp):
TATAAAATTTATTTAAATA
Found at i:35479473 original size:21 final size:19
Alignment explanation
Indices: 35479449--35479490 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
35479439 TGGTTTGAGT
*
35479449 TTTTAAGAGATATTATATTAA
1 TTTTAAG-GATAATAT-TTAA
35479470 TTTTAAGGATAATATTTAA
1 TTTTAAGGATAATATTTAA
35479489 TT
1 TT
35479491 ACATTAACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
20 7 0.35
21 7 0.35
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (19 bp):
TTTTAAGGATAATATTTAA
Found at i:35479760 original size:110 final size:110
Alignment explanation
Indices: 35479582--35479786 Score: 329
Period size: 110 Copynumber: 1.9 Consensus size: 110
35479572 TATTGTATTA
* * *
35479582 TCGGATTATAATGTAAGAAGATAATTTATATTAGTAGATAACTTAAACAATTCGTAATCTAATCG
1 TCGGATCATAATGTAAAAAGATAATTTATATTAGTAGATAACCTAAACAATTCGTAATCTAATCG
* *
35479647 AAATTGAGTAGATTAGTTGAAAGACTATTAAGTTGCATTACGTTG
66 AAATTGAGTAAATTAATTGAAAGACTATTAAGTTGCATTACGTTG
* * * *
35479692 TCGGATCATAATGTAAAAAGATAATTTATATTATTAGATAGCCTAAACAGTTCGTAATCTAATTG
1 TCGGATCATAATGTAAAAAGATAATTTATATTAGTAGATAACCTAAACAATTCGTAATCTAATCG
35479757 AAATTGAGTAAATTAATTGAAAGACTATTA
66 AAATTGAGTAAATTAATTGAAAGACTATTA
35479787 TGTCGTCTAT
Statistics
Matches: 86, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
110 86 1.00
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.35
Consensus pattern (110 bp):
TCGGATCATAATGTAAAAAGATAATTTATATTAGTAGATAACCTAAACAATTCGTAATCTAATCG
AAATTGAGTAAATTAATTGAAAGACTATTAAGTTGCATTACGTTG
Found at i:35482396 original size:18 final size:19
Alignment explanation
Indices: 35482375--35482421 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
35482365 CTTTTTTAAT
35482375 TTTTATAAATTTTTCATA-
1 TTTTATAAATTTTTCATAG
* * *
35482393 TTTTTTGAATTTTTTATAG
1 TTTTATAAATTTTTCATAG
35482412 TTTTA-AAATT
1 TTTTATAAATT
35482422 ATTTGTTGAT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.64
Consensus pattern (19 bp):
TTTTATAAATTTTTCATAG
Found at i:35482835 original size:91 final size:90
Alignment explanation
Indices: 35482682--35482856 Score: 228
Period size: 91 Copynumber: 1.9 Consensus size: 90
35482672 TTGGTACTTG
* * * ** *
35482682 AACTTAACACTTTTTTTTAATTTGGTATTTAAACTTTTTTTGGTCCAATTTTGTACTAAAACTTG
1 AACTTAACACTTTTTTTTAAGTTGGCACTTAAACTTTTTGGGGTCCAATTTGGTACTAAAACTTG
*
35482747 A-TACTTTTTCTTAATTTGGTGCCTA
66 ACT-CTTTTTCCTAATTTGGTGCCTA
*
35482772 AACTTGACACTTTTTTTTTAAGTTGGCACTTAAACTTTTTGGGGTCCAATTTGGTACCT-AAACT
1 AACTTAACAC-TTTTTTTTAAGTTGGCACTTAAACTTTTTGGGGTCCAATTTGGTA-CTAAAACT
*
35482836 TGACTTTTTTTCCTAATTTGG
64 TGACTCTTTTTCCTAATTTGG
35482857 CACCTAATCC
Statistics
Matches: 73, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
90 9 0.12
91 61 0.84
92 3 0.04
ACGTcount: A:0.24, C:0.15, G:0.13, T:0.49
Consensus pattern (90 bp):
AACTTAACACTTTTTTTTAAGTTGGCACTTAAACTTTTTGGGGTCCAATTTGGTACTAAAACTTG
ACTCTTTTTCCTAATTTGGTGCCTA
Found at i:35483071 original size:33 final size:33
Alignment explanation
Indices: 35483034--35483097 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
35483024 GAATCTAAAA
*
35483034 AAGTTTAGATACCAAATTAGGA-AAAAAAATATC
1 AAGTTCAGATACCAAATT-GGACAAAAAAATATC
*
35483067 AAGTTCAGATACTAAATTGGATCAAAAAAAT
1 AAGTTCAGATACCAAATTGGA-CAAAAAAAT
35483098 TTAAGTATCA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 3 0.11
33 16 0.59
34 8 0.30
ACGTcount: A:0.53, C:0.09, G:0.12, T:0.25
Consensus pattern (33 bp):
AAGTTCAGATACCAAATTGGACAAAAAAATATC
Found at i:35490344 original size:33 final size:33
Alignment explanation
Indices: 35490307--35490377 Score: 142
Period size: 33 Copynumber: 2.2 Consensus size: 33
35490297 CTGGTTCTCT
35490307 TAATTTATTTTAAATTTATTATGGATTTAAATC
1 TAATTTATTTTAAATTTATTATGGATTTAAATC
35490340 TAATTTATTTTAAATTTATTATGGATTTAAATC
1 TAATTTATTTTAAATTTATTATGGATTTAAATC
35490373 TAATT
1 TAATT
35490378 GTGTCTTCGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.37, C:0.03, G:0.06, T:0.55
Consensus pattern (33 bp):
TAATTTATTTTAAATTTATTATGGATTTAAATC
Found at i:35495228 original size:17 final size:17
Alignment explanation
Indices: 35495184--35495229 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
35495174 ATGTATGTCA
*
35495184 AATTTGATATAA--ATT
1 AATTTTATATAATTATT
* *
35495199 AATTTTTTTTAATTATT
1 AATTTTATATAATTATT
35495216 AATTTTATATAATT
1 AATTTTATATAATT
35495230 TTTTTATATT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
15 9 0.38
17 15 0.62
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (17 bp):
AATTTTATATAATTATT
Found at i:35512494 original size:26 final size:25
Alignment explanation
Indices: 35512446--35512495 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
35512436 AAAAGAAAAT
*
35512446 AAATATATTTTATGATTAAATTAAA
1 AAATATATTTTATGATAAAATTAAA
35512471 AAATATTATTTTAT-ATAAATATTAA
1 AAATA-TATTTTATGATAAA-ATTAA
35512496 TTGTTTCTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (25 bp):
AAATATATTTTATGATAAAATTAAA
Found at i:35513115 original size:43 final size:43
Alignment explanation
Indices: 35513054--35513138 Score: 170
Period size: 43 Copynumber: 2.0 Consensus size: 43
35513044 GAAATCAAGG
35513054 AAGTTTTGCTGTGGCGGGGGCATAGTGAAATCTCGAGATGAGT
1 AAGTTTTGCTGTGGCGGGGGCATAGTGAAATCTCGAGATGAGT
35513097 AAGTTTTGCTGTGGCGGGGGCATAGTGAAATCTCGAGATGAG
1 AAGTTTTGCTGTGGCGGGGGCATAGTGAAATCTCGAGATGAG
35513139 GAGTGGATTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.24, C:0.12, G:0.38, T:0.27
Consensus pattern (43 bp):
AAGTTTTGCTGTGGCGGGGGCATAGTGAAATCTCGAGATGAGT
Found at i:35517105 original size:23 final size:23
Alignment explanation
Indices: 35517047--35517105 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
35517037 TATATAATTT
* *
35517047 TTTTAAAATAAAAATATTTAAAA
1 TTTTAAAATAAAAAGATCTAAAA
** *
35517070 TTCAAAAAT-AAAAGATCTCAAA
1 TTTTAAAATAAAAAGATCTAAAA
35517092 TTTTAAAATAAAAA
1 TTTTAAAATAAAAA
35517106 AAATTCTCAA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
22 17 0.61
23 11 0.39
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (23 bp):
TTTTAAAATAAAAAGATCTAAAA
Found at i:35517339 original size:22 final size:23
Alignment explanation
Indices: 35517310--35517355 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
35517300 TGATCAGTTC
*
35517310 AAAAAAA-ATAAATTATTAAAAAT
1 AAAAAAATATATATTA-TAAAAAT
35517333 AAAAAAATATATATTATAAAAAT
1 AAAAAAATATATATTATAAAAAT
35517356 CGGTTCAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (23 bp):
AAAAAAATATATATTATAAAAAT
Found at i:35520807 original size:26 final size:27
Alignment explanation
Indices: 35520760--35520819 Score: 77
Period size: 26 Copynumber: 2.2 Consensus size: 27
35520750 ACACTAACGC
* **
35520760 GCTCTCCGTTATTTTTAGCACGTATTGT
1 GCTCTCCG-TATTATTAGCACGTAAAGT
35520788 GCTCTCCG-ATTATTAGCACGTAAAGT
1 GCTCTCCGTATTATTAGCACGTAAAGT
35520814 GCTCTC
1 GCTCTC
35520820 TATTTAGCAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 21 0.72
28 8 0.28
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.38
Consensus pattern (27 bp):
GCTCTCCGTATTATTAGCACGTAAAGT
Found at i:35520837 original size:22 final size:22
Alignment explanation
Indices: 35520812--35520863 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
35520802 AGCACGTAAA
*
35520812 GTGCTCTCTATTTAGCACATTT
1 GTGCTCTCTATTTAGCACATTG
* *
35520834 GTGCTCTCTGTTTAGCACCTTG
1 GTGCTCTCTATTTAGCACATTG
35520856 GTGCTCTC
1 GTGCTCTC
35520864 CGTTCATTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.12, C:0.27, G:0.19, T:0.42
Consensus pattern (22 bp):
GTGCTCTCTATTTAGCACATTG
Found at i:35524517 original size:4 final size:4
Alignment explanation
Indices: 35524508--35524538 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
35524498 TCGAAATAGA
*
35524508 ATAC ATAC ATAC ATGC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
35524539 TACATATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.48, C:0.23, G:0.03, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:35524549 original size:4 final size:4
Alignment explanation
Indices: 35524536--35524617 Score: 56
Period size: 4 Copynumber: 20.5 Consensus size: 4
35524526 ACATACATAC
* * * * * * *
35524536 ATAT ACAT ATAT ATAT ATGT ATGT ATAT ATAT GTAT ATGT ATGT ATGT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * * * *
35524584 ATAT ATAT GTAT ATGT ATAT GTAT GTAT GTAT AT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT AT
35524618 GTATGAAAAT
Statistics
Matches: 64, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
4 64 1.00
ACGTcount: A:0.37, C:0.01, G:0.13, T:0.49
Consensus pattern (4 bp):
ATAT
Found at i:35524562 original size:10 final size:10
Alignment explanation
Indices: 35524555--35524622 Score: 82
Period size: 10 Copynumber: 6.8 Consensus size: 10
35524545 TATATATATG
*
35524555 TATGTATATA
1 TATGTATGTA
* *
35524565 TATGTATATG
1 TATGTATGTA
35524575 TATGTATGTA
1 TATGTATGTA
*
35524585 TATATATGTA
1 TATGTATGTA
* *
35524595 TATGTATATG
1 TATGTATGTA
35524605 TATGTATGTA
1 TATGTATGTA
35524615 TATGTATG
1 TATGTATG
35524623 AAAATAGTAC
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 49 1.00
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (10 bp):
TATGTATGTA
Found at i:35524568 original size:14 final size:14
Alignment explanation
Indices: 35524542--35524622 Score: 94
Period size: 14 Copynumber: 5.9 Consensus size: 14
35524532 ATACATATAC
*
35524542 ATATATATATATGT
1 ATATATATGTATGT
* *
35524556 ATGTATATATATGT
1 ATATATATGTATGT
*
35524570 ATATGTATGTATGT
1 ATATATATGTATGT
35524584 ATATATATGTA--T
1 ATATATATGTATGT
*
35524596 ATGTATATGTATGT
1 ATATATATGTATGT
*
35524610 ATGTATATGTATG
1 ATATATATGTATG
35524623 AAAATAGTAC
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
12 11 0.19
14 48 0.81
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.49
Consensus pattern (14 bp):
ATATATATGTATGT
Found at i:35524621 original size:20 final size:20
Alignment explanation
Indices: 35524543--35524615 Score: 86
Period size: 20 Copynumber: 4.0 Consensus size: 20
35524533 TACATATACA
* *
35524543 TATATATATATGTATGTATA
1 TATATGTATATGTATGTATG
35524563 TATATGTATATGTATGTATG
1 TATATGTATATGTATGTATG
35524583 TATA--TATATGTA--TATG
1 TATATGTATATGTATGTATG
35524599 TATATG--TATGTATGTAT
1 TATATGTATATGTATGTAT
35524616 ATGTATGAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
16 14 0.30
18 11 0.23
20 22 0.47
ACGTcount: A:0.34, C:0.00, G:0.15, T:0.51
Consensus pattern (20 bp):
TATATGTATATGTATGTATG
Found at i:35530908 original size:27 final size:27
Alignment explanation
Indices: 35530878--35530931 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
35530868 ATTACATCCC
*
35530878 CACAATCTCATTAACAAATTTATTTAT
1 CACAATCTCAATAACAAATTTATTTAT
*
35530905 CACAATCTCAATAAGAAATTTATTTAT
1 CACAATCTCAATAACAAATTTATTTAT
35530932 TTTTACACCG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.43, C:0.17, G:0.02, T:0.39
Consensus pattern (27 bp):
CACAATCTCAATAACAAATTTATTTAT
Found at i:35533921 original size:2 final size:2
Alignment explanation
Indices: 35533914--35533942 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
35533904 ATAGATGTTA
35533914 AT AT AT 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 A
35533943 GTACTTTACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35536184 original size:2 final size:2
Alignment explanation
Indices: 35536177--35536211 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
35536167 AGACTTCGGA
35536177 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
35536212 AGTGACTGAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:35540487 original size:22 final size:21
Alignment explanation
Indices: 35540458--35540529 Score: 92
Period size: 21 Copynumber: 3.4 Consensus size: 21
35540448 ATTTTGGTGA
* *
35540458 TTTTTTTACTATTTTGATTGT
1 TTTTTTTACTGTTTTGATTGC
35540479 TGTTTTTTACTGTTTTGA-TGC
1 T-TTTTTTACTGTTTTGATTGC
*
35540500 TATTTTTTACTGTTTTGGTTGC
1 T-TTTTTTACTGTTTTGATTGC
35540522 TTTTTTTA
1 TTTTTTTA
35540530 AATTATTTTG
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
21 26 0.58
22 19 0.42
ACGTcount: A:0.11, C:0.07, G:0.14, T:0.68
Consensus pattern (21 bp):
TTTTTTTACTGTTTTGATTGC
Found at i:35540630 original size:21 final size:22
Alignment explanation
Indices: 35540593--35540639 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
35540583 TTTTCTGCTA
*
35540593 TTTTGATTGTTAGTTTTGT-TG
1 TTTTGATTGTTAGTTTTATGTG
*
35540614 TTTTGA-TGTTATTTTTTATGTG
1 TTTTGATTGTTA-GTTTTATGTG
35540636 TTTT
1 TTTT
35540640 TACTATTGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 11 0.50
22 6 0.27
ACGTcount: A:0.11, C:0.00, G:0.19, T:0.70
Consensus pattern (22 bp):
TTTTGATTGTTAGTTTTATGTG
Found at i:35546491 original size:192 final size:194
Alignment explanation
Indices: 35546134--35546577 Score: 527
Period size: 191 Copynumber: 2.3 Consensus size: 194
35546124 GAAACCGACG
* * * *
35546134 CGATGGCTGAGGTACCACATATGTTGCGAGCCCTCGATAGCTCA-TGTGAGCAGCATCGTGAGTC
1 CGATGGTTGAGGTACCGCATATGTTGCGAGTCCTCGATAGCT-AGTGTGAGCAACATCGTGAGTC
* * * * * * *
35546198 GGGAAATGAGAAAAGAATCCAATAATGGATTACAGGCCCTACAATGGCTGAGATTTATGCATAAG
65 GGAAAAAGAGAAAAGAATCCAATAATAGATTACAAGCCCTACAATGACCGAGATTTATGCATAAA
* * * * * *
35546263 TGCATATTCTCGACAGCTCGTGTGAGTAGCATCGTTAGGGAATAGTTATATACACAGATACCATA
130 TGCATATTCTCGACAGCTCGTGTGAGCAACATCGTTAGGGAACAGTT-TACAAACAGACACCATA
*
35546328 T
194 C
*
35546329 CGATGGTTGAGGTACCGCATATGTTGCGAGTCCTCGACAGCTAGTGTGAGCAACATCGTGAGTC-
1 CGATGGTTGAGGTACCGCATATGTTGCGAGTCCTCGATAGCTAGTGTGAGCAACATCGTGAGTCG
* * * * * * *
35546393 GAAAAAGAGATATGAATCCTA-AATAGATTATAAGCCTTACGATGACCG-GATTTATGCTTAAAT
66 GAAAAAGAGAAAAGAATCCAATAATAGATTACAAGCCCTACAATGACCGAGATTTATGCATAAAT
* * *
35546456 GCATATTCTCGATAGCTCGTGTGAGCAACATCGTTAGGGGACAGTTTACAAACAGACACCGTAC
131 GCATATTCTCGACAGCTCGTGTGAGCAACATCGTTAGGGAACAGTTTACAAACAGACACCATAC
* * * * * *
35546520 CAATGGTTGGGGTACTGCATACGTTGCGAGTCCTCAATAGCTCGTGTGAGCAACATCG
1 CGATGGTTGAGGTACCGCATATGTTGCGAGTCCTCGATAGCTAGTGTGAGCAACATCG
35546578 GGTGCTGGTA
Statistics
Matches: 212, Mismatches: 36, Indels: 6
0.83 0.14 0.02
Matches are distributed among these distances:
191 64 0.30
192 54 0.25
193 20 0.09
194 17 0.08
195 57 0.27
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (194 bp):
CGATGGTTGAGGTACCGCATATGTTGCGAGTCCTCGATAGCTAGTGTGAGCAACATCGTGAGTCG
GAAAAAGAGAAAAGAATCCAATAATAGATTACAAGCCCTACAATGACCGAGATTTATGCATAAAT
GCATATTCTCGACAGCTCGTGTGAGCAACATCGTTAGGGAACAGTTTACAAACAGACACCATAC
Found at i:35547312 original size:20 final size:21
Alignment explanation
Indices: 35547283--35547331 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
35547273 TTTTTAACAC
* * *
35547283 CGGTAGAAGCATGATTTGT-T
1 CGGTAAAAGCATCACTTGTAT
*
35547303 CGGTAAAAGCTTCACTTGTAT
1 CGGTAAAAGCATCACTTGTAT
35547324 CGGTAAAA
1 CGGTAAAA
35547332 CTGTTATAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 15 0.62
21 9 0.38
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (21 bp):
CGGTAAAAGCATCACTTGTAT
Found at i:35547376 original size:38 final size:38
Alignment explanation
Indices: 35547333--35547406 Score: 121
Period size: 38 Copynumber: 1.9 Consensus size: 38
35547323 TCGGTAAAAC
*
35547333 TGTTATAAGTATCGGTAGAAGTCTGCACTGTTTCCTAT
1 TGTTATAAGTATCGGTAGAAGTCTACACTGTTTCCTAT
* *
35547371 TGTTATAGGTATCGGTAGAAGTCTATACTGTTTCCT
1 TGTTATAAGTATCGGTAGAAGTCTACACTGTTTCCT
35547407 GAATTGTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.23, C:0.15, G:0.22, T:0.41
Consensus pattern (38 bp):
TGTTATAAGTATCGGTAGAAGTCTACACTGTTTCCTAT
Found at i:35550287 original size:28 final size:31
Alignment explanation
Indices: 35550222--35550309 Score: 87
Period size: 28 Copynumber: 2.9 Consensus size: 31
35550212 CCTTTAATTA
*
35550222 ATTTTTAAA-ATTTTTAAAATTTTAAAAAAACT
1 ATTTTTAAATA-TATTAAAA-TTTAAAAAAACT
*
35550254 ATTTTTAAA-A-ATTAAAA-TTATAAAAA-T
1 ATTTTTAAATATATTAAAATTTAAAAAAACT
*
35550281 ATTTTTTAAATATTTTAAAATTTAAAAAA
1 A-TTTTTAAATATATTAAAATTTAAAAAA
35550310 TTAATTAAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
27 2 0.04
28 16 0.33
29 1 0.02
30 12 0.25
31 7 0.15
32 10 0.21
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.45
Consensus pattern (31 bp):
ATTTTTAAATATATTAAAATTTAAAAAAACT
Found at i:35550310 original size:30 final size:30
Alignment explanation
Indices: 35550222--35550310 Score: 89
Period size: 30 Copynumber: 3.0 Consensus size: 30
35550212 CCTTTAATTA
*
35550222 ATTTTTAAAAT-TTTTAAAATTTTAAAAAA-
1 ATTTTTTAAATATTTTAAAA-TTTAAAAAAT
*
35550251 ACTATTTTTAAA-A-ATTAAAA-TTATAAAAAT
1 A-T-TTTTTAAATATTTTAAAATTTA-AAAAAT
35550281 ATTTTTTAAATATTTTAAAATTTAAAAAAT
1 ATTTTTTAAATATTTTAAAATTTAAAAAAT
35550311 TAATTAAATA
Statistics
Matches: 49, Mismatches: 3, Indels: 15
0.73 0.04 0.22
Matches are distributed among these distances:
28 11 0.22
29 8 0.16
30 20 0.41
31 10 0.20
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (30 bp):
ATTTTTTAAATATTTTAAAATTTAAAAAAT
Found at i:35550317 original size:28 final size:30
Alignment explanation
Indices: 35550265--35550322 Score: 84
Period size: 28 Copynumber: 2.0 Consensus size: 30
35550255 TTTTTAAAAA
**
35550265 TTAAAATTATAAAAATATTTTTTAAATATT
1 TTAAAATTATAAAAATATTAATTAAATATT
35550295 TTAAAATT-TAAAAA-ATTAATTAAATATT
1 TTAAAATTATAAAAATATTAATTAAATATT
35550323 AATATGTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 12 0.46
29 6 0.23
30 8 0.31
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (30 bp):
TTAAAATTATAAAAATATTAATTAAATATT
Found at i:35553709 original size:30 final size:31
Alignment explanation
Indices: 35553670--35553741 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 31
35553660 TTTTTCATTG
*
35553670 ATATGTAAATTTTGAT-TTCATTTAATTACT-T
1 ATAT-TAAATTTTAATATTCATTTAATTA-TGT
*
35553701 ATATTAAATTTTAATATTGATTTAATTATGT
1 ATATTAAATTTTAATATTCATTTAATTATGT
*
35553732 ATATGAAATT
1 ATATTAAATT
35553742 ATAAGTTTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
30 11 0.31
31 25 0.69
ACGTcount: A:0.38, C:0.03, G:0.07, T:0.53
Consensus pattern (31 bp):
ATATTAAATTTTAATATTCATTTAATTATGT
Found at i:35557854 original size:43 final size:42
Alignment explanation
Indices: 35557806--35558020 Score: 252
Period size: 43 Copynumber: 5.0 Consensus size: 42
35557796 GGAAAATGCT
* *
35557806 GCTATAGAACATGATCTTTAGCGGCGTTTTTCTCACAAGCGCC
1 GCTATAGAACATGATCTTTAGCGGCATTTTTC-CACAAACGCC
* * * ***
35557849 GCTATAGAACATGATCTTTAGCGGCGCTTTTCCCATAAATATC
1 GCTATAGAACATGATCTTTAGCGGC-ATTTTTCCACAAACGCC
*
35557892 GCTATA-AAGCATGATCTTTAGCGGCATTTTTCCTACAAACACC
1 GCTATAGAA-CATGATCTTTAGCGGCATTTTTCC-ACAAACGCC
* * *
35557935 GCTATAAAACATGGTCTTTAGCGGCTTTTTTACCACAAACGCC
1 GCTATAGAACATGATCTTTAGCGGCATTTTT-CCACAAACGCC
*
35557978 GCTATAGAACATGTTCTTTAGCGGCATTTTTCCCACAAACGCC
1 GCTATAGAACATGATCTTTAGCGGCATTTTT-CCACAAACGCC
35558021 ATTAACATTG
Statistics
Matches: 148, Mismatches: 19, Indels: 10
0.84 0.11 0.06
Matches are distributed among these distances:
42 8 0.05
43 131 0.89
44 9 0.06
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.31
Consensus pattern (42 bp):
GCTATAGAACATGATCTTTAGCGGCATTTTTCCACAAACGCC
Found at i:35558116 original size:15 final size:15
Alignment explanation
Indices: 35558093--35558125 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
35558083 TTTTCCTGTA
35558093 AATTCAAATCTAACC
1 AATTCAAATCTAACC
*
35558108 AATTTAAATCTAACC
1 AATTCAAATCTAACC
35558123 AAT
1 AAT
35558126 AACTTCAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.48, C:0.21, G:0.00, T:0.30
Consensus pattern (15 bp):
AATTCAAATCTAACC
Found at i:35558137 original size:19 final size:16
Alignment explanation
Indices: 35558095--35558139 Score: 56
Period size: 15 Copynumber: 2.7 Consensus size: 16
35558085 TTCCTGTAAA
35558095 TTCAAATCTAACCAAT
1 TTCAAATCTAACCAAT
35558111 TT-AAATCTAACCAAT
1 TTCAAATCTAACCAAT
35558126 AACTTCAAATCTAA
1 ---TTCAAATCTAA
35558140 ATGATACTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 13 0.52
16 2 0.08
18 2 0.08
19 8 0.32
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.31
Consensus pattern (16 bp):
TTCAAATCTAACCAAT
Found at i:35564464 original size:24 final size:24
Alignment explanation
Indices: 35564437--35564484 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
35564427 GGAAAACAGA
35564437 AAGTTTAAATTCATAAAATGCATG
1 AAGTTTAAATTCATAAAATGCATG
35564461 AAGTTTAAATTCATAAAATGCATG
1 AAGTTTAAATTCATAAAATGCATG
35564485 CTGACAAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.33
Consensus pattern (24 bp):
AAGTTTAAATTCATAAAATGCATG
Found at i:35566264 original size:43 final size:42
Alignment explanation
Indices: 35566216--35566302 Score: 102
Period size: 42 Copynumber: 2.0 Consensus size: 42
35566206 CTATTGCTTA
* *
35566216 ACCTTTACTAGTGTTTTTCCCATAAACGCCGCTAATGCTCCTT
1 ACCTTTACTAGCG-CTTTCCCATAAACGCCGCTAATGCTCCTT
** * * *
35566259 ACCTTTTGTGGCGCTTTCCCATAAACGCCGCTATTGCTCTTT
1 ACCTTTACTAGCGCTTTCCCATAAACGCCGCTAATGCTCCTT
35566301 AC
1 AC
35566303 ATTTTGCGGC
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
42 28 0.76
43 9 0.24
ACGTcount: A:0.18, C:0.31, G:0.14, T:0.37
Consensus pattern (42 bp):
ACCTTTACTAGCGCTTTCCCATAAACGCCGCTAATGCTCCTT
Found at i:35566278 original size:42 final size:42
Alignment explanation
Indices: 35566231--35566393 Score: 186
Period size: 42 Copynumber: 3.9 Consensus size: 42
35566221 TACTAGTGTT
* * *
35566231 TTTCCCATAAACGCCGCTAATGCTCCTTACCTTTTGTGGCGC
1 TTTCCCATAAACGCCGCTATTGCTCTTTACCTTTTGCGGCGC
* *
35566273 TTTCCCATAAACGCCGCTATTGCTCTTTACATTTTGCGGCGT
1 TTTCCCATAAACGCCGCTATTGCTCTTTACCTTTTGCGGCGC
* ** * * *
35566315 TTTCCCTTAAGTGCCACTATTGCTCTTTACCTTTTACGACGC
1 TTTCCCATAAACGCCGCTATTGCTCTTTACCTTTTGCGGCGC
* *
35566357 TTTTTCCATAAGCGCCGCTATTG--CTTTACCTTTTGCG
1 -TTTCCCATAAACGCCGCTATTGCTCTTTACCTTTTGCG
35566394 ACGTTATGGG
Statistics
Matches: 102, Mismatches: 18, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
41 13 0.13
42 71 0.70
43 18 0.18
ACGTcount: A:0.16, C:0.30, G:0.15, T:0.39
Consensus pattern (42 bp):
TTTCCCATAAACGCCGCTATTGCTCTTTACCTTTTGCGGCGC
Found at i:35567767 original size:41 final size:40
Alignment explanation
Indices: 35567707--35567851 Score: 112
Period size: 41 Copynumber: 3.5 Consensus size: 40
35567697 CGCTAATGCT
* *
35567707 CTTTGCCTTTTGCGACGTTTTTTCTATAAACGTCGCAATTG
1 CTTTACCTTTTGCGACGTTTTTCCTATAAACG-CGCAATTG
* * ** * *
35567748 CTTTACCTTTTGCGGCGTTTATGGTA-AAACGCCGCTATTTCA
1 CTTTACCTTTTGCGACGTTTTTCCTATAAACG-CGC-AATT-G
* * * * *
35567790 CTTTACCTTTTGCGACATTTTTCCCATAAATGCTACTATTG
1 CTTTACCTTTTGCGACGTTTTTCCTATAAACGC-GCAATTG
*
35567831 CTTTACCTTTTGCGGCGTTTT
1 CTTTACCTTTTGCGACGTTTT
35567852 CGTTCCAAAT
Statistics
Matches: 79, Mismatches: 21, Indels: 8
0.73 0.19 0.07
Matches are distributed among these distances:
40 8 0.10
41 43 0.54
42 23 0.29
43 5 0.06
ACGTcount: A:0.17, C:0.23, G:0.16, T:0.43
Consensus pattern (40 bp):
CTTTACCTTTTGCGACGTTTTTCCTATAAACGCGCAATTG
Found at i:35567801 original size:83 final size:84
Alignment explanation
Indices: 35567665--35567850 Score: 232
Period size: 83 Copynumber: 2.2 Consensus size: 84
35567655 GTTTTTGCAA
* * * * * *
35567665 TTTACCTTTAGCAGCGTTTATGGGAAAAACGCCGCTAATGCTCTTTGCCTTTTGCGACGTTTTTT
1 TTTACCTTTTGCGGCGTTTATGGGAAAAACGCCGCTAATGCACTTTACCTTTTGCGACATTTTTC
* *
35567730 CTATAAACG-TCGCAATTGC
66 CCATAAACGCT-ACAATTGC
* * *
35567749 TTTACCTTTTGCGGCGTTTAT-GGTAAAACGCCGCTATTTCACTTTACCTTTTGCGACATTTTTC
1 TTTACCTTTTGCGGCGTTTATGGGAAAAACGCCGCTAATGCACTTTACCTTTTGCGACATTTTTC
* *
35567813 CCATAAATGCTACTATTGC
66 CCATAAACGCTACAATTGC
35567832 TTTACCTTTTGCGGCGTTT
1 TTTACCTTTTGCGGCGTTT
35567851 TCGTTCCAAA
Statistics
Matches: 88, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
83 68 0.77
84 20 0.23
ACGTcount: A:0.19, C:0.23, G:0.17, T:0.40
Consensus pattern (84 bp):
TTTACCTTTTGCGGCGTTTATGGGAAAAACGCCGCTAATGCACTTTACCTTTTGCGACATTTTTC
CCATAAACGCTACAATTGC
Found at i:35568315 original size:2 final size:2
Alignment explanation
Indices: 35568310--35568350 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
35568300 TAATATTTGC
35568310 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
35568351 TTTTTTTTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:35570910 original size:31 final size:31
Alignment explanation
Indices: 35570874--35570942 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
35570864 ATTAAAAACC
*
35570874 TAGTGACTTAGATAAAAACTTTTCAATAATT
1 TAGTGACTTAAATAAAAACTTTTCAATAATT
* * * *
35570905 TAGTGACTTAAATGAAAATTTTTGAATAGTT
1 TAGTGACTTAAATAAAAACTTTTCAATAATT
*
35570936 CAGTGAC
1 TAGTGAC
35570943 CAAATTGTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.38
Consensus pattern (31 bp):
TAGTGACTTAAATAAAAACTTTTCAATAATT
Found at i:35574363 original size:506 final size:506
Alignment explanation
Indices: 35573577--35575098 Score: 2904
Period size: 506 Copynumber: 3.0 Consensus size: 506
35573567 GGACAAATAT
*
35573577 ATTAAGCTACTATCATATCTAT-TTTTTAATTTATTCAAATCTTTCATTCAATTATTTTTCATGA
1 ATTAAGCTACTATCATATCTATCTTTTTAATTTACTCAAATCTTTCATTCAATTATTTTTCATGA
* *
35573641 TTTGTAAATCTAGGTTTTGGGTTTTCTCATTTTTATTTTAAATGAAAATTTTCACCTCTTTTTTT
66 TTTGTAAATCTAGGTTTTGGGTTTTCTCATTTTTATTTCAAATGAAAATTTTCACCTCTTCTTTT
*
35573706 TAATATTTAACTTTCCTATTTCAGTTTCTGAGAGCTAATTGGAGGGTATAGAAATAAGAAATTAG
131 TAATATTTAACTTTCCTATTTCAGTTTCTGTGAGCTAATTGGAGGGTATAGAAATAAGAAATTAG
35573771 GACAACAAAAGAGAATGTATTTTATTGATTCATAGAAATGTTTACAATGCTTCTTTAAACTCTAT
196 GACAACAAAAGAGAATGTATTTTATTGATTCATAGAAATGTTTACAATGCTTCTTTAAACTCTAT
*
35573836 ATCTATACATATAAGAAGTATACAAGATATAAAACTCTATTTTTAATAAACATTAGAGTCCTAAC
261 ATCTATACACATAAGAAGTATACAAGATATAAAACTCTATTTTTAATAAACATTAGAGTCCTAAC
35573901 GTATATCAAACTTATCTTAATCCCGATGGATATCCACCTAATAATAAAATATTCATAACACCCCC
326 GTATATCAAACTTATCTTAATCCCGATGGATATCCACCTAATAATAAAATATTCATAACACCCCC
35573966 TCTAGTAGATAATGCGCCTCGTTAAAATCTTAATAAGTTAAAAATTCAATGAGAAAAAAAATTTT
391 TCTAGTAGATAATGCGCCTCGTTAAAATCTTAATAAGTTAAAAATTCAATGAGAAAAAAAATTTT
35574031 AGTGAAGAAAAAAGAGTACACATATCTATAATACGTATAACATGCTGCCTC
456 AGTGAAGAAAAAAGAGTACACATATCTATAATACGTATAACATGCTGCCTC
35574082 ATTAAGCTACTATCATATCTATCTTTTTAATTTACTCAAATCTTTCATTCAATTATTTTTCATGA
1 ATTAAGCTACTATCATATCTATCTTTTTAATTTACTCAAATCTTTCATTCAATTATTTTTCATGA
35574147 TTTGTAAATCTAGGTTTTGGGTTTTCTCATTTTTATTTCAAATGAAAATTTTCACCTCTTCTTTT
66 TTTGTAAATCTAGGTTTTGGGTTTTCTCATTTTTATTTCAAATGAAAATTTTCACCTCTTCTTTT
35574212 TAATATTTAACTTTCCTATTTCAGTTTCTGTGAGCTAATTGGAGGGTATAGAAATAAGAAATTAG
131 TAATATTTAACTTTCCTATTTCAGTTTCTGTGAGCTAATTGGAGGGTATAGAAATAAGAAATTAG
35574277 GACAACAAAAGAGAATGTATTTTATTGATTCATAGAAATGTTTACAATGCTTCTTTAAACTCTAT
196 GACAACAAAAGAGAATGTATTTTATTGATTCATAGAAATGTTTACAATGCTTCTTTAAACTCTAT
35574342 ATCTATACACATAAGAAGTATACAAGATATAAAACTCTATTTTTAATAAACATTAGAGTCCTAAC
261 ATCTATACACATAAGAAGTATACAAGATATAAAACTCTATTTTTAATAAACATTAGAGTCCTAAC
*
35574407 GTATATCAAACTTATCTTAATCCCGATGGATATCCACCTAATAATAAAATATTCATAACATCCCC
326 GTATATCAAACTTATCTTAATCCCGATGGATATCCACCTAATAATAAAATATTCATAACACCCCC
35574472 TCTAGTAGATAATGCGCCTCGTTAAAATCTTAATAAGTTAAAAATTCAATGAGAAAAAAAATTTT
391 TCTAGTAGATAATGCGCCTCGTTAAAATCTTAATAAGTTAAAAATTCAATGAGAAAAAAAATTTT
*
35574537 AGTGAAGAAAAAAGAGTACACATATCTATAATACGTATAACATGCTACCTC
456 AGTGAAGAAAAAAGAGTACACATATCTATAATACGTATAACATGCTGCCTC
35574588 ATTAAGCTACTATCATATCTATCTTTTTAATTTACTCAAATCTTTCATTCAATTATTTTTCATGA
1 ATTAAGCTACTATCATATCTATCTTTTTAATTTACTCAAATCTTTCATTCAATTATTTTTCATGA
35574653 TTTGTAAATCTAGGTTTTGGGTTTTCTCATTTTTATTTCAAATGAAAATTTTCACCTCTTCTTTT
66 TTTGTAAATCTAGGTTTTGGGTTTTCTCATTTTTATTTCAAATGAAAATTTTCACCTCTTCTTTT
* *
35574718 TAATATTTAATTTTCCTATTTTAGTTTCTGTGAGCTAATTGGAGGGTATAGAAATAAGAAATTAG
131 TAATATTTAACTTTCCTATTTCAGTTTCTGTGAGCTAATTGGAGGGTATAGAAATAAGAAATTAG
*
35574783 GACAACAAAAGAGAATGTATTTTATTGATTAATAGAAATGTTTACAATGCTTCTTTAAACTCTAT
196 GACAACAAAAGAGAATGTATTTTATTGATTCATAGAAATGTTTACAATGCTTCTTTAAACTCTAT
*
35574848 ATCTATACACATAAGAAGTATACAAGATATAAAACTCTATTTTTAATAAACATTAGAGTCTTAAC
261 ATCTATACACATAAGAAGTATACAAGATATAAAACTCTATTTTTAATAAACATTAGAGTCCTAAC
*
35574913 GTATATCAAACTTATCTTAATCCCGATGGACATCCACCTAATAATAAAATATTCATAACACCCCC
326 GTATATCAAACTTATCTTAATCCCGATGGATATCCACCTAATAATAAAATATTCATAACACCCCC
*
35574978 TCTAGTAGATAATGTGCCTCGTTAAAATCTTAATAAGTTAAAAATTCAATGAG-AAAAAAATTTC
391 TCTAGTAGATAATGCGCCTCGTTAAAATCTTAATAAGTTAAAAATTCAATGAGAAAAAAAATTT-
35575042 TAGTGAAGAAAAAAGAGTACACATATCTATAATACGTATAACATGCTGCCTC
455 TAGTGAAGAAAAAAGAGTACACATATCTATAATACGTATAACATGCTGCCTC
35575094 ATTAA
1 ATTAA
35575099 AATCTTACCG
Statistics
Matches: 1000, Mismatches: 15, Indels: 3
0.98 0.01 0.00
Matches are distributed among these distances:
505 32 0.03
506 968 0.97
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.38
Consensus pattern (506 bp):
ATTAAGCTACTATCATATCTATCTTTTTAATTTACTCAAATCTTTCATTCAATTATTTTTCATGA
TTTGTAAATCTAGGTTTTGGGTTTTCTCATTTTTATTTCAAATGAAAATTTTCACCTCTTCTTTT
TAATATTTAACTTTCCTATTTCAGTTTCTGTGAGCTAATTGGAGGGTATAGAAATAAGAAATTAG
GACAACAAAAGAGAATGTATTTTATTGATTCATAGAAATGTTTACAATGCTTCTTTAAACTCTAT
ATCTATACACATAAGAAGTATACAAGATATAAAACTCTATTTTTAATAAACATTAGAGTCCTAAC
GTATATCAAACTTATCTTAATCCCGATGGATATCCACCTAATAATAAAATATTCATAACACCCCC
TCTAGTAGATAATGCGCCTCGTTAAAATCTTAATAAGTTAAAAATTCAATGAGAAAAAAAATTTT
AGTGAAGAAAAAAGAGTACACATATCTATAATACGTATAACATGCTGCCTC
Found at i:35578402 original size:52 final size:52
Alignment explanation
Indices: 35578321--35578460 Score: 226
Period size: 52 Copynumber: 2.7 Consensus size: 52
35578311 AATGAAAAAG
* * * * *
35578321 GGTCCAATGACTAAGTGTCATCGTAAGTATATGAATCCTTTACGGATTATGA
1 GGTCCGATGGCTATGTGTCATCGTGAGTATATGAATCCTTTACGAATTATGA
35578373 GGTCCGATGGCTATGTGTCATCGTGAGTATATGAATCCTTTACGAATTATGA
1 GGTCCGATGGCTATGTGTCATCGTGAGTATATGAATCCTTTACGAATTATGA
*
35578425 GGTCCGGTGGCTATGTGTCATCGTGAGTATATGAAT
1 GGTCCGATGGCTATGTGTCATCGTGAGTATATGAAT
35578461 GAAATGAGAT
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 82 1.00
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.34
Consensus pattern (52 bp):
GGTCCGATGGCTATGTGTCATCGTGAGTATATGAATCCTTTACGAATTATGA
Found at i:35584589 original size:3 final size:3
Alignment explanation
Indices: 35584581--35584624 Score: 79
Period size: 3 Copynumber: 14.3 Consensus size: 3
35584571 ATTACTAACG
35584581 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA TGAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA -GAA G
35584625 TGAAACAGTG
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 37 0.93
4 3 0.08
ACGTcount: A:0.64, C:0.00, G:0.34, T:0.02
Consensus pattern (3 bp):
GAA
Found at i:35585058 original size:5 final size:5
Alignment explanation
Indices: 35585048--35585077 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
35585038 GGAAAAGAAC
35585048 AAAAG AAAAG AAAAG AAAAG AAAAGG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAA-G AAAA
35585078 TGTAATGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:35586502 original size:3 final size:3
Alignment explanation
Indices: 35586494--35586533 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
35586484 ATTCACAAAT
35586494 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
35586534 TTCATTAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:35587855 original size:16 final size:17
Alignment explanation
Indices: 35587834--35587867 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
35587824 TTTTCTTTAC
*
35587834 ACTTT-AATATAATATT
1 ACTTTAAATAAAATATT
35587850 ACTTTAAATAAAATATT
1 ACTTTAAATAAAATATT
35587867 A
1 A
35587868 AATATTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (17 bp):
ACTTTAAATAAAATATT
Found at i:35589865 original size:166 final size:163
Alignment explanation
Indices: 35589519--35589853 Score: 508
Period size: 166 Copynumber: 2.0 Consensus size: 163
35589509 ACGATGCTCA
*
35589519 TAAAAAAAAGTATACAAAGAACCCAACAAATGGCTCTAGTGGAAAAAAAGATATTGTTCATCCTA
1 TAAAAAAAAGTATATAAAGAACCCAACAAATGGCTCTAGTGGAAAAAAAGATATTGTTCATCCTA
* * *
35589584 GGGATTTCTGGTAGTACCTATGCGTGCAAGATGTGTGTATGTTGTCAAAGAGTTAAGAAAATATG
66 AGGATTTCTGGTAGTACCCATGCGTGCAAGATGTGTGTACGTTGTCAAAGAGTTAAGAAAATATG
* *
35589649 AACAGATACTATCATGTAAGCACAACAATATAT
131 AACAGATACTACCATGTAACCACAACAATATAT
* * *
35589682 TAAAAAAAAGTATATAAAGAACCCAACAAATTGCTCTAGTGGAAAAAAGGATGTTGTTCATCCTA
1 TAAAAAAAAGTATATAAAGAACCCAACAAATGGCTCTAGTGGAAAAAAAGATATTGTTCATCCTA
* * * * *
35589747 AGGATTTTTGGTTCGAGTACCCATGTGTGCAAGGTGTGTGTACGTTGTCAAAGAGTTAATAATAT
66 AGGATTTCTGG-T--AGTACCCATGCGTGCAAGATGTGTGTACGTTGTCAAAGAGTTAAGAAAAT
*
35589812 ATGAACAGATACTACCATGTAACCACACCAATATAT
128 ATGAACAGATACTACCATGTAACCACAACAATATAT
35589848 TAAAAA
1 TAAAAA
35589854 TATATATATA
Statistics
Matches: 154, Mismatches: 15, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
163 70 0.45
164 1 0.01
166 83 0.54
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (163 bp):
TAAAAAAAAGTATATAAAGAACCCAACAAATGGCTCTAGTGGAAAAAAAGATATTGTTCATCCTA
AGGATTTCTGGTAGTACCCATGCGTGCAAGATGTGTGTACGTTGTCAAAGAGTTAAGAAAATATG
AACAGATACTACCATGTAACCACAACAATATAT
Found at i:35591021 original size:12 final size:12
Alignment explanation
Indices: 35591006--35591031 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
35590996 ATACAATTAA
35591006 AAATATTAAAAC
1 AAATATTAAAAC
35591018 AAATATTAAAAC
1 AAATATTAAAAC
35591030 AA
1 AA
35591032 CAAACAAATT
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:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (12 bp):
AAATATTAAAAC
Found at i:35591160 original size:23 final size:24
Alignment explanation
Indices: 35591133--35591201 Score: 79
Period size: 23 Copynumber: 3.0 Consensus size: 24
35591123 AATATCCAAA
35591133 TAATATTAAAAATGACAGTGAAAC
1 TAATATTAAAAATGACAGTGAAAC
* *
35591157 -AATATTAAAAACGATAGTGAAAC
1 TAATATTAAAAATGACAGTGAAAC
** *
35591180 TACGA-TAAAAGTGACAGTGAAA
1 TAATATTAAAAATGACAGTGAAA
35591202 TAACAGGAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
23 35 0.95
24 2 0.05
ACGTcount: A:0.54, C:0.09, G:0.16, T:0.22
Consensus pattern (24 bp):
TAATATTAAAAATGACAGTGAAAC
Found at i:35593228 original size:31 final size:32
Alignment explanation
Indices: 35593192--35593269 Score: 88
Period size: 32 Copynumber: 2.5 Consensus size: 32
35593182 AACAACCCAA
35593192 TGACTTAAAT-AAAAATTTTTGAATAATTAAG
1 TGACTTAAATGAAAAATTTTTGAATAATTAAG
* ** * *
35593223 TGACTTAGATGAAATTTTTTTGAATAGTTCAG
1 TGACTTAAATGAAAAATTTTTGAATAATTAAG
35593255 TGAC-TAATATGAAAA
1 TGACTTAA-ATGAAAA
35593270 CTTACCCATA
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
31 11 0.29
32 27 0.71
ACGTcount: A:0.42, C:0.05, G:0.14, T:0.38
Consensus pattern (32 bp):
TGACTTAAATGAAAAATTTTTGAATAATTAAG
Found at i:35602109 original size:18 final size:17
Alignment explanation
Indices: 35602086--35602121 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
35602076 TGAATTTCTA
*
35602086 TCCAATTTATATCTTAAT
1 TCCAATTTA-ATCCTAAT
35602104 TCCAATTTAATCCTAAT
1 TCCAATTTAATCCTAAT
35602121 T
1 T
35602122 AACTCATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.33, C:0.19, G:0.00, T:0.47
Consensus pattern (17 bp):
TCCAATTTAATCCTAAT
Found at i:35604572 original size:20 final size:21
Alignment explanation
Indices: 35604547--35604585 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
35604537 CTGTTTCACA
35604547 AAGTTTTCTAACTT-TTTCTT
1 AAGTTTTCTAACTTGTTTCTT
35604567 AAGTTTTCTAACTTGTTTC
1 AAGTTTTCTAACTTGTTTC
35604586 AAATCAGTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.21, C:0.15, G:0.08, T:0.56
Consensus pattern (21 bp):
AAGTTTTCTAACTTGTTTCTT
Found at i:35608301 original size:2 final size:2
Alignment explanation
Indices: 35608294--35608321 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
35608284 CTTTAACACA
35608294 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35608322 TTATTTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35622171 original size:19 final size:20
Alignment explanation
Indices: 35622149--35622192 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
35622139 TAAAATTAAA
35622149 TATTTATT-TTAAATATAAT
1 TATTTATTCTTAAATATAAT
*
35622168 TATTT-TTCTTAAATATGAT
1 TATTTATTCTTAAATATAAT
35622187 T-TTTAT
1 TATTTAT
35622193 ATATAAAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (20 bp):
TATTTATTCTTAAATATAAT
Found at i:35622655 original size:20 final size:21
Alignment explanation
Indices: 35622617--35622660 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
35622607 ATATATTCTG
35622617 AAATTATAAAAAGACATTAAA
1 AAATTATAAAAAGACATTAAA
*
35622638 AAATTATAAAAA-ATATTAAA
1 AAATTATAAAAAGACATTAAA
35622658 AAA
1 AAA
35622661 CTTCTTCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.25
Consensus pattern (21 bp):
AAATTATAAAAAGACATTAAA
Found at i:35630354 original size:23 final size:22
Alignment explanation
Indices: 35630328--35630405 Score: 79
Period size: 23 Copynumber: 3.5 Consensus size: 22
35630318 TTCAACTAAA
*
35630328 ATTTTATTTTTATTGATTTATAT
1 ATTTTATTTTTATT-ATTTATAC
* *
35630351 ATTTTAATTTTGTTA--TATAC
1 ATTTTATTTTTATTATTTATAC
*
35630371 ACTTTATTTTTATTAATTTATAC
1 ATTTTATTTTTATT-ATTTATAC
35630394 ATTTTAATTTTT
1 ATTTT-ATTTTT
35630406 GTATTTTAGA
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
20 15 0.34
21 1 0.02
22 1 0.02
23 21 0.48
24 6 0.14
ACGTcount: A:0.28, C:0.04, G:0.03, T:0.65
Consensus pattern (22 bp):
ATTTTATTTTTATTATTTATAC
Found at i:35630413 original size:23 final size:23
Alignment explanation
Indices: 35630344--35630413 Score: 58
Period size: 23 Copynumber: 3.2 Consensus size: 23
35630334 TTTTTATTGA
*
35630344 TTTATATATTTTAA-TTTTG--T
1 TTTATACATTTTAATTTTTGTAT
* * * *
35630364 TATATACACTTT-ATTTTTATTAA
1 TTTATACATTTTAATTTTT-GTAT
35630387 TTTATACATTTTAATTTTTGTAT
1 TTTATACATTTTAATTTTTGTAT
35630410 TTTA
1 TTTA
35630414 GAATTATGGT
Statistics
Matches: 36, Mismatches: 9, Indels: 7
0.69 0.17 0.13
Matches are distributed among these distances:
19 1 0.03
20 13 0.36
23 16 0.44
24 6 0.17
ACGTcount: A:0.29, C:0.04, G:0.03, T:0.64
Consensus pattern (23 bp):
TTTATACATTTTAATTTTTGTAT
Found at i:35641398 original size:58 final size:58
Alignment explanation
Indices: 35641286--35641405 Score: 179
Period size: 58 Copynumber: 2.1 Consensus size: 58
35641276 TCCCATCAAC
* * *
35641286 AAACTAAACTCAAATATTTTTAAACCCAAATATAATTTCATTCTTCAAAAACACTTAT
1 AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTCATTCCTCAAAAACACTCAT
* *
35641344 AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTTATTCCT-AAATTACACTCAT
1 AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTCATTCCTCAAA-AACACTCAT
35641402 AAAC
1 AAAC
35641406 AACTCCTTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
57 3 0.05
58 53 0.95
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.33
Consensus pattern (58 bp):
AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTCATTCCTCAAAAACACTCAT
Found at i:35641660 original size:18 final size:20
Alignment explanation
Indices: 35641629--35641666 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
35641619 TTTATTTGAC
35641629 TTTTGTTATGTTGTT-TTTA
1 TTTTGTTATGTTGTTGTTTA
*
35641648 TTTT-TTATTTTGTTGTTTA
1 TTTTGTTATGTTGTTGTTTA
35641667 GAATGGTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.11, C:0.00, G:0.13, T:0.76
Consensus pattern (20 bp):
TTTTGTTATGTTGTTGTTTA
Found at i:35642718 original size:5 final size:5
Alignment explanation
Indices: 35642708--35642749 Score: 84
Period size: 5 Copynumber: 8.4 Consensus size: 5
35642698 GAAGGGGCAT
35642708 GGAAG GGAAG GGAAG GGAAG GGAAG GGAAG GGAAG GGAAG GG
1 GGAAG GGAAG GGAAG GGAAG GGAAG GGAAG GGAAG GGAAG GG
35642750 GTTTTAGGTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.38, C:0.00, G:0.62, T:0.00
Consensus pattern (5 bp):
GGAAG
Found at i:35645442 original size:59 final size:59
Alignment explanation
Indices: 35645366--35645719 Score: 508
Period size: 59 Copynumber: 6.0 Consensus size: 59
35645356 TGACTTTCGA
** * *
35645366 GGGTAAAAAT-GTAATTTTTGGTGAAATCGGGGTCGAAGATGGGATTTTAGGAAA-TTCAG
1 GGGT-AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTT-GGAAAGTTTAG
35645425 GGGTAAAATGGTAA-TTTTGGTGAAA-CTGGGGTT-AAAATGGGATTTTGGAAAGTTTAG
1 GGGTAAAATGGTAATTTTTGGTGAAATC-GGGGTTAAAAATGGGATTTTGGAAAGTTTAG
* *
35645482 GGGTAAAATGGTAATTTTTGGTGAAAATCGGGGTTAAAAATGAGATTTTGGAAAGTTTGG
1 GGGTAAAATGGTAATTTTTGGTG-AAATCGGGGTTAAAAATGGGATTTTGGAAAGTTTAG
*
35645542 GGGTAAAATGGTAATTTTTGGTGAAAATCGGGGTT-AAAATGGGATTTTGGAAAGTTCAG
1 GGGTAAAATGGTAATTTTTGGTG-AAATCGGGGTTAAAAATGGGATTTTGGAAAGTTTAG
* * *
35645601 AGGTAAAAGGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTTTG
1 GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTTAG
35645660 GGGTAAAATGGTAA-TTTTGGTGAAATTC-GGGTTAAAAATGGGATTTTGGAAAGTTTAG
1 GGGTAAAATGGTAATTTTTGGTGAAA-TCGGGGTTAAAAATGGGATTTTGGAAAGTTTAG
35645718 GG
1 GG
35645720 ACCTATAAAA
Statistics
Matches: 271, Mismatches: 15, Indels: 19
0.89 0.05 0.06
Matches are distributed among these distances:
56 5 0.02
57 31 0.11
58 82 0.30
59 95 0.35
60 58 0.21
ACGTcount: A:0.32, C:0.03, G:0.32, T:0.33
Consensus pattern (59 bp):
GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTTAG
Found at i:35645694 original size:176 final size:176
Alignment explanation
Indices: 35645366--35645715 Score: 541
Period size: 176 Copynumber: 2.0 Consensus size: 176
35645356 TGACTTTCGA
* *
35645366 GGGTAAAAATGTAATTTTTGGTGAAATCGGGGTCGAAGATGGGATTTTAGGAAATTCAGGGGTAA
1 GGGTAAAAATGTAATTTTTGGTGAAATCGGGGTCGAAAATGGGATTTTAGGAAATTCAGAGGTAA
*
35645431 AATGGTAATTTTGGTGAAACTGGGGTTAAAATGGGATTTTGGAAAGTTTAGGGGTAAAATGGTAA
66 AAGGGTAATTTTGGTGAAACTGGGGTTAAAATGGGATTTTGGAAAGTTTAGGGGTAAAATGGTAA
35645496 TTTTTGGTGAAAATCGGGGTTAAAAATGAGATTTTGGAAAGTTTGG
131 TTTTTGGTGAAAATCGGGGTTAAAAATGAGATTTTGGAAAGTTTGG
*
35645542 GGGT-AAAATGGTAATTTTTGGTGAAAATCGGGGT-TAAAATGGGATTTT-GGAAAGTTCAGAGG
1 GGGTAAAAAT-GTAATTTTTGGTG-AAATCGGGGTCGAAAATGGGATTTTAGGAAA-TTCAGAGG
*
35645604 TAAAAGGGTAATTTTTGGTGAAA-TCGGGGTTAAAAATGGGATTTTGGAAAGTTTTGGGGTAAAA
63 TAAAAGGGTAA-TTTTGGTGAAACT-GGGGTT-AAAATGGGATTTTGGAAAGTTTAGGGGTAAAA
* *
35645668 TGGTAA-TTTTGGTGAAATTC-GGGTTAAAAATGGGATTTTGGAAAGTTT
125 TGGTAATTTTTGGTGAAAATCGGGGTTAAAAATGAGATTTTGGAAAGTTT
35645716 AGGGACCTAT
Statistics
Matches: 161, Mismatches: 7, Indels: 12
0.89 0.04 0.07
Matches are distributed among these distances:
175 10 0.06
176 74 0.46
177 40 0.25
178 37 0.23
ACGTcount: A:0.32, C:0.03, G:0.32, T:0.33
Consensus pattern (176 bp):
GGGTAAAAATGTAATTTTTGGTGAAATCGGGGTCGAAAATGGGATTTTAGGAAATTCAGAGGTAA
AAGGGTAATTTTGGTGAAACTGGGGTTAAAATGGGATTTTGGAAAGTTTAGGGGTAAAATGGTAA
TTTTTGGTGAAAATCGGGGTTAAAAATGAGATTTTGGAAAGTTTGG
Found at i:35646755 original size:15 final size:13
Alignment explanation
Indices: 35646730--35646770 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 13
35646720 CTTTCCTTTT
*
35646730 TTATTATTTATTA
1 TTATTATTAATTA
*
35646743 -TAATATTAATTA
1 TTATTATTAATTA
35646755 TTATTATTAA-TA
1 TTATTATTAATTA
35646767 TTAT
1 TTAT
35646771 GAACAAAGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
12 16 0.67
13 8 0.33
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
TTATTATTAATTA
Found at i:35646756 original size:19 final size:19
Alignment explanation
Indices: 35646732--35646769 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
35646722 TTCCTTTTTT
35646732 ATTATTTATTA-TAATATTA
1 ATTA-TTATTATTAATATTA
35646751 ATTATTATTATTAATATTA
1 ATTATTATTATTAATATTA
35646770 TGAACAAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
ATTATTATTATTAATATTA
Found at i:35649283 original size:21 final size:21
Alignment explanation
Indices: 35649257--35649310 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
35649247 AAGCCTATTA
35649257 GGCACAAAGCCTGATAACACC
1 GGCACAAAGCCTGATAACACC
35649278 GGCACAAAGCCTGATAACACC
1 GGCACAAAGCCTGATAACACC
**
35649299 GATACAAAGCCT
1 GGCACAAAGCCT
35649311 ACTAGGCACA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.39, C:0.31, G:0.19, T:0.11
Consensus pattern (21 bp):
GGCACAAAGCCTGATAACACC
Found at i:35650280 original size:19 final size:19
Alignment explanation
Indices: 35650239--35650281 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
35650229 TTATGAGTGT
* *
35650239 AATTTACTCAATAAAATTT
1 AATTTACTAAATAAAATTA
**
35650258 AATTTACTAAATGTAATTA
1 AATTTACTAAATAAAATTA
35650277 AATTT
1 AATTT
35650282 TAAAAATCTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (19 bp):
AATTTACTAAATAAAATTA
Found at i:35660966 original size:18 final size:17
Alignment explanation
Indices: 35660935--35660992 Score: 71
Period size: 18 Copynumber: 3.2 Consensus size: 17
35660925 CAGAAGCTGC
35660935 AAAGAAAAATAAAGGAAAG
1 AAAGAAAAA-AAAGG-AAG
*
35660954 AAAGAAAAGAAAGGGAAG
1 AAAGAAAA-AAAAGGAAG
35660972 AAAGAAAGAAAAAGGAAG
1 AAAGAAA-AAAAAGGAAG
35660990 AAA
1 AAA
35660993 ATTTTCCATC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 21 0.60
19 13 0.37
20 1 0.03
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.02
Consensus pattern (17 bp):
AAAGAAAAAAAAGGAAG
Found at i:35660990 original size:10 final size:10
Alignment explanation
Indices: 35660935--35660993 Score: 50
Period size: 10 Copynumber: 5.8 Consensus size: 10
35660925 CAGAAGCTGC
*
35660935 AAAGAAAAAT
1 AAAGAAAAAG
*
35660945 AAAG-GAAAG
1 AAAGAAAAAG
35660954 AAAG-AAAAG
1 AAAGAAAAAG
35660963 AAAGGGAAGAAAG
1 AAA--GAA-AAAG
35660976 AAAGAAAAAG
1 AAAGAAAAAG
*
35660986 GAAGAAAA
1 AAAGAAAA
35660994 TTTTCCATCA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
9 14 0.34
10 15 0.37
11 4 0.10
12 1 0.02
13 7 0.17
ACGTcount: A:0.73, C:0.00, G:0.25, T:0.02
Consensus pattern (10 bp):
AAAGAAAAAG
Found at i:35661486 original size:18 final size:17
Alignment explanation
Indices: 35661442--35661487 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 17
35661432 ATTTTTTATA
35661442 TTTAGTTTTTATTTTCT
1 TTTAGTTTTTATTTTCT
35661459 TTTA-TATTTTGATTTT-T
1 TTTAGT-TTTT-ATTTTCT
35661476 TTCTAGTTTTTA
1 TT-TAGTTTTTA
35661488 CCTGCCTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
16 1 0.04
17 12 0.48
18 11 0.44
19 1 0.04
ACGTcount: A:0.15, C:0.04, G:0.07, T:0.74
Consensus pattern (17 bp):
TTTAGTTTTTATTTTCT
Found at i:35661521 original size:23 final size:23
Alignment explanation
Indices: 35661493--35661546 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
35661483 TTTTACCTGC
*
35661493 CTTTGTGGCATACTTTTTCTCTG
1 CTTTGTGGCACACTTTTTCTCTG
* *
35661516 -TCTTGTAGCACGCTTTTTCTCTG
1 CT-TTGTGGCACACTTTTTCTCTG
35661539 CTTTGTGG
1 CTTTGTGG
35661547 TACTCTTCTA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
22 1 0.04
23 23 0.92
24 1 0.04
ACGTcount: A:0.07, C:0.22, G:0.20, T:0.50
Consensus pattern (23 bp):
CTTTGTGGCACACTTTTTCTCTG
Found at i:35664721 original size:18 final size:18
Alignment explanation
Indices: 35664698--35664740 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
35664688 TAATAGATTT
35664698 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
* *
35664716 TTAATTGAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
35664734 TTAATTA
1 TTAATTA
35664741 CTGTTTCTCC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:35667709 original size:140 final size:143
Alignment explanation
Indices: 35667441--35667702 Score: 305
Period size: 140 Copynumber: 1.8 Consensus size: 143
35667431 ATCTTTAAAT
* * * * *
35667441 TTTTTCTTTACCACTTCAATCAAACTTTTATTTTGATTTTTTTTTATATATTTTTTAATGTTATT
1 TTTTTCTTTACCACTTCAAGCAAAATTTTATTTTGA-TTATTTTTATACA-TTTTCAATGTTATT
* * * *
35667506 ACACAAATTATTTCACCCACCCTATTTATATATATTTATAATGCCGTTGATTGAATTTGTGTCAC
64 ACACAAATTATTTCACCCACACTATTTATATATATTAATAATACCATTGATTGAATTTGTGTCAC
35667571 AGCATCTGTGCAATC
129 AGCATCTGTGCAATC
* *
35667586 TTTTT-TTTATCACTTCAAGCAAAATTTTATTTTGA-TATTTTTATACA-TTTCAATGTTATTAT
1 TTTTTCTTTACCACTTCAAGCAAAATTTTATTTTGATTATTTTTATACATTTTCAATGTTATTAC
* * * * * * ** *
35667648 ACAAATTGTTTCACCTATATTGTTTGTATATATTAATAATATTATTTATTGAATT
66 ACAAATTATTTCACCCACACTATTTATATATATTAATAATACCATTGATTGAATT
35667703 GATGTCATAA
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
140 55 0.57
142 10 0.10
144 27 0.28
145 5 0.05
ACGTcount: A:0.29, C:0.13, G:0.07, T:0.51
Consensus pattern (143 bp):
TTTTTCTTTACCACTTCAAGCAAAATTTTATTTTGATTATTTTTATACATTTTCAATGTTATTAC
ACAAATTATTTCACCCACACTATTTATATATATTAATAATACCATTGATTGAATTTGTGTCACAG
CATCTGTGCAATC
Found at i:35668618 original size:21 final size:22
Alignment explanation
Indices: 35668592--35668636 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
35668582 AAAAACTAGG
35668592 AAAAAAACAAAATAT-AAAAGA
1 AAAAAAACAAAATATAAAAAGA
**
35668613 AAAAAAACTGAATATAAAAAGA
1 AAAAAAACAAAATATAAAAAGA
35668635 AA
1 AA
35668637 TGGATAGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.78, C:0.04, G:0.07, T:0.11
Consensus pattern (22 bp):
AAAAAAACAAAATATAAAAAGA
Found at i:35670581 original size:22 final size:22
Alignment explanation
Indices: 35670556--35670604 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
35670546 ATTAAATTTT
35670556 AAAATTTAAAATT-TTAAAAATA
1 AAAATTT-AAATTCTTAAAAATA
* *
35670578 AAAAATTGAATTCTTAAAAATA
1 AAAATTTAAATTCTTAAAAATA
35670600 AAAAT
1 AAAAT
35670605 ACTAAAGCTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 4 0.17
22 19 0.83
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (22 bp):
AAAATTTAAATTCTTAAAAATA
Found at i:35675086 original size:31 final size:31
Alignment explanation
Indices: 35675050--35675117 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 31
35675040 CTTTTTTTTT
35675050 TTTGGTGAATAATGTTGTACATC-AACTTT-AA
1 TTTGGTGAAT-ATG-TGTACATCAAACTTTAAA
* * *
35675081 TTTGGTGCATTTGTGTATATCAAACTTTAAA
1 TTTGGTGAATATGTGTACATCAAACTTTAAA
35675112 TTTGGT
1 TTTGGT
35675118 TCATTTTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 7 0.22
30 8 0.25
31 17 0.53
ACGTcount: A:0.28, C:0.09, G:0.18, T:0.46
Consensus pattern (31 bp):
TTTGGTGAATATGTGTACATCAAACTTTAAA
Found at i:35675102 original size:29 final size:31
Alignment explanation
Indices: 35675065--35675123 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
35675055 TGAATAATGT
35675065 TGTACATC-AACTTT-AATTTGGTGCATTTG
1 TGTACATCAAACTTTAAATTTGGTGCATTTG
* *
35675094 TGTATATCAAACTTTAAATTTGGTTCATTT
1 TGTACATCAAACTTTAAATTTGGTGCATTT
35675124 TTTATATGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 7 0.27
30 6 0.23
31 13 0.50
ACGTcount: A:0.27, C:0.12, G:0.14, T:0.47
Consensus pattern (31 bp):
TGTACATCAAACTTTAAATTTGGTGCATTTG
Found at i:35678140 original size:19 final size:20
Alignment explanation
Indices: 35678116--35678172 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 20
35678106 ATTTCTCGTG
35678116 TAATTTTTTAAA-AATTTTA
1 TAATTTTTTAAATAATTTTA
*
35678135 TAATTTTTTTAAATATTTTTA
1 TAA-TTTTTTAAATAATTTTA
* *
35678156 TAA-ATTTTAAATTATTT
1 TAATTTTTTAAATAATTT
35678173 GTGAATGTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 14 0.44
20 9 0.28
21 9 0.28
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TAATTTTTTAAATAATTTTA
Found at i:35678154 original size:21 final size:20
Alignment explanation
Indices: 35678117--35678163 Score: 67
Period size: 21 Copynumber: 2.3 Consensus size: 20
35678107 TTTCTCGTGT
35678117 AATTTTTTAAAAATTTTATA
1 AATTTTTTAAAAATTTTATA
* *
35678137 ATTTTTTTAAATATTTTTATA
1 AATTTTTTAAA-AATTTTATA
35678158 AATTTT
1 AATTTT
35678164 AAATTATTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
AATTTTTTAAAAATTTTATA
Found at i:35678947 original size:40 final size:40
Alignment explanation
Indices: 35678870--35678948 Score: 97
Period size: 39 Copynumber: 2.0 Consensus size: 40
35678860 TATCAAAAAT
* * * * *
35678870 TTTTAATGTATTTTTAATTTATTTGTTGTTTTAATATTTG
1 TTTTAATGTATTTTAAATATATTTGATATATTAATATTTG
35678910 TTTTAATGT-TTTTAAATATATTTGATATATTATATATTT
1 TTTTAATGTATTTTAAATATATTTGATATATTA-ATATTT
35678949 TTTAAATTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
39 18 0.55
40 15 0.45
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.65
Consensus pattern (40 bp):
TTTTAATGTATTTTAAATATATTTGATATATTAATATTTG
Found at i:35683116 original size:12 final size:14
Alignment explanation
Indices: 35683089--35683120 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
35683079 TTGCAAAAAT
35683089 GTTTTTTTTCCTTG
1 GTTTTTTTTCCTTG
35683103 GTTTTTTTT-C-TG
1 GTTTTTTTTCCTTG
35683115 GTTTTT
1 GTTTTT
35683121 GGATGCTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 8 0.44
13 1 0.06
14 9 0.50
ACGTcount: A:0.00, C:0.09, G:0.16, T:0.75
Consensus pattern (14 bp):
GTTTTTTTTCCTTG
Found at i:35696217 original size:43 final size:43
Alignment explanation
Indices: 35696156--35696240 Score: 161
Period size: 43 Copynumber: 2.0 Consensus size: 43
35696146 TGATCCAATA
35696156 TGCAGTAACTAAAATTTGATAGGACAATCATGTATCCTGAATT
1 TGCAGTAACTAAAATTTGATAGGACAATCATGTATCCTGAATT
*
35696199 TGCAGTAACTAAAATTTGATAGGATAATCATGTATCCTGAAT
1 TGCAGTAACTAAAATTTGATAGGACAATCATGTATCCTGAAT
35696241 GATTACGTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (43 bp):
TGCAGTAACTAAAATTTGATAGGACAATCATGTATCCTGAATT
Found at i:35704200 original size:23 final size:22
Alignment explanation
Indices: 35704168--35704210 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
35704158 AAAGTTTTAA
35704168 TAAATGAAAAAAATATTAAATAT
1 TAAATGAAAAAAATA-TAAATAT
* *
35704191 TAAATTAAAAATATATAAAT
1 TAAATGAAAAAAATATAAAT
35704211 GTTTTTAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (22 bp):
TAAATGAAAAAAATATAAATAT
Found at i:35706696 original size:23 final size:23
Alignment explanation
Indices: 35706648--35706699 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
35706638 TTTTTTTAAG
* *
35706648 ATTAAATGTAATTTTATTAATAT
1 ATTAAATATAATTTTATCAATAT
*
35706671 ATTAACATATAATTTTA-CAATTT
1 ATTAA-ATATAATTTTATCAATAT
35706694 ATTAAA
1 ATTAAA
35706700 AAATTAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
22 1 0.04
23 14 0.56
24 10 0.40
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (23 bp):
ATTAAATATAATTTTATCAATAT
Found at i:35706696 original size:31 final size:31
Alignment explanation
Indices: 35706660--35706724 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
35706650 TAAATGTAAT
* *
35706660 TTTATTAATATATTAACA-TATAATTTTACAA
1 TTTATTAAAAAATTAA-ATTATAATTTTACAA
*
35706691 TTTATTAAAAAATTAAATTATAATTTTACTA
1 TTTATTAAAAAATTAAATTATAATTTTACAA
35706722 TTT
1 TTT
35706725 TGGGACAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 1 0.03
31 29 0.97
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.51
Consensus pattern (31 bp):
TTTATTAAAAAATTAAATTATAATTTTACAA
Found at i:35707889 original size:19 final size:19
Alignment explanation
Indices: 35707867--35707906 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
35707857 TCATCCAACA
*
35707867 TCAGAAAATATTAGTT-TTT
1 TCAGAAAA-ATAAGTTATTT
35707886 TCAGAAAAATAAGTTATTT
1 TCAGAAAAATAAGTTATTT
35707905 TC
1 TC
35707907 TAAAAAAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.42
Consensus pattern (19 bp):
TCAGAAAAATAAGTTATTT
Found at i:35713328 original size:25 final size:25
Alignment explanation
Indices: 35713300--35713349 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
35713290 ATTTATCATT
*
35713300 TTAACTCT-AATTCTTAAAAAAAAAA
1 TTAACTCTCAAAT-TTAAAAAAAAAA
*
35713325 TTAACTTTCAAATTTAAAAAAAAAA
1 TTAACTCTCAAATTTAAAAAAAAAA
35713350 CAAACTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 19 0.86
26 3 0.14
ACGTcount: A:0.58, C:0.10, G:0.00, T:0.32
Consensus pattern (25 bp):
TTAACTCTCAAATTTAAAAAAAAAA
Found at i:35718062 original size:18 final size:18
Alignment explanation
Indices: 35717992--35718050 Score: 73
Period size: 18 Copynumber: 3.1 Consensus size: 18
35717982 AGGTGATAAC
* *
35717992 GAAGACGAAGAGGAAGTG
1 GAAGACGAAGAAGAAGAG
35718010 GAAGAGCAGAACGAAGAAGAG
1 GAAGA-C-GAA-GAAGAAGAG
35718031 GAAGACGAAGAAGAAGAG
1 GAAGACGAAGAAGAAGAG
35718049 GA
1 GA
35718051 GGAGGAGGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
18 16 0.44
19 4 0.11
20 4 0.11
21 12 0.33
ACGTcount: A:0.51, C:0.07, G:0.41, T:0.02
Consensus pattern (18 bp):
GAAGACGAAGAAGAAGAG
Found at i:35718556 original size:18 final size:17
Alignment explanation
Indices: 35718529--35718562 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
35718519 GAAAGGAAGC
*
35718529 GAAGAGACACCAAAGAT
1 GAAGAGACACAAAAGAT
35718546 GAAGAAGACACAAAAGA
1 GAAG-AGACACAAAAGA
35718563 GCATTAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.59, C:0.15, G:0.24, T:0.03
Consensus pattern (17 bp):
GAAGAGACACAAAAGAT
Found at i:35719246 original size:15 final size:15
Alignment explanation
Indices: 35719228--35719263 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
35719218 CATACAACAT
35719228 CATATTTCACAATTA
1 CATATTTCACAATTA
35719243 CATATTTCACAATTA
1 CATATTTCACAATTA
*
35719258 CGTATT
1 CATATT
35719264 CCAAAACATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.36, C:0.19, G:0.03, T:0.42
Consensus pattern (15 bp):
CATATTTCACAATTA
Found at i:35722004 original size:27 final size:28
Alignment explanation
Indices: 35721948--35722004 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 28
35721938 CAAGCTTCTC
* *
35721948 AATACTTAACATCTCTACTTTAACCCAT
1 AATACTTAAAATCTCTACTTTAACCAAT
*
35721976 AATA-TTAAAATCT-TATTTTACACCAAT
1 AATACTTAAAATCTCTACTTTA-ACCAAT
35722003 AA
1 AA
35722005 AATCAATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
26 6 0.24
27 15 0.60
28 4 0.16
ACGTcount: A:0.42, C:0.21, G:0.00, T:0.37
Consensus pattern (28 bp):
AATACTTAAAATCTCTACTTTAACCAAT
Found at i:35730692 original size:12 final size:12
Alignment explanation
Indices: 35730633--35730731 Score: 53
Period size: 13 Copynumber: 7.8 Consensus size: 12
35730623 TGATAAAAAC
35730633 TCAATTAA--AA
1 TCAATTAATTAA
*
35730643 TCAAATTAATCAA
1 TC-AATTAATTAA
*
35730656 TCGAATCAATTTAA
1 TC-AATTAA-TTAA
*
35730670 TTCAGTTAATTAA
1 -TCAATTAATTAA
35730683 T-AGATTAATTGATA
1 TCA-ATTAATT-A-A
*
35730697 T-AACTTAGTTAA
1 TCAA-TTAATTAA
35730709 TCAATTAATTAA
1 TCAATTAATTAA
35730721 TCAAATTAATT
1 TC-AATTAATT
35730732 TAGTCGAAAG
Statistics
Matches: 70, Mismatches: 8, Indels: 19
0.72 0.08 0.20
Matches are distributed among these distances:
10 2 0.03
11 7 0.10
12 18 0.26
13 26 0.37
14 15 0.21
15 2 0.03
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.39
Consensus pattern (12 bp):
TCAATTAATTAA
Found at i:35736497 original size:23 final size:24
Alignment explanation
Indices: 35736454--35736500 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
35736444 ACTAATAACA
* *
35736454 ATATTGATATTAAAATTATATTTT
1 ATATTCATATTAAAATAATATTTT
35736478 ATATTCATA-TAAAATAATATTTT
1 ATATTCATATTAAAATAATATTTT
35736501 CACTATGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (24 bp):
ATATTCATATTAAAATAATATTTT
Found at i:35739888 original size:19 final size:19
Alignment explanation
Indices: 35739850--35739901 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
35739840 TGACACCAAT
* *
35739850 TTAATAAAAATCTTAAATA
1 TTAATATAAATATTAAATA
*
35739869 TTAATATAAATATTATATA
1 TTAATATAAATATTAAATA
*
35739888 -T-ATATATATATTAA
1 TTAATATAAATATTAA
35739902 CAAATTTGAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
17 11 0.39
18 1 0.04
19 16 0.57
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
TTAATATAAATATTAAATA
Found at i:35751895 original size:11 final size:11
Alignment explanation
Indices: 35751879--35751925 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
35751869 TAATTAAAAT
35751879 TATTGAATATG
1 TATTGAATATG
*
35751890 TATTGAATTTG
1 TATTGAATATG
*
35751901 ATAATGAATATG
1 -TATTGAATATG
*
35751913 TATTTAA-ATG
1 TATTGAATATG
35751923 TAT
1 TAT
35751926 GTTAGTAATG
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
10 6 0.20
11 15 0.50
12 9 0.30
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.47
Consensus pattern (11 bp):
TATTGAATATG
Found at i:35759750 original size:19 final size:20
Alignment explanation
Indices: 35759713--35759766 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
35759703 TCACCTGTAT
35759713 TATAATATTTT-TTTAAATA
1 TATAATATTTTATTTAAATA
*
35759732 TATACTATTTTATTT-AATA
1 TATAATATTTTATTTAAATA
* *
35759751 TTTAGTAATTTTATTT
1 TATAAT-ATTTTATTT
35759767 TTTTTCTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 18 0.60
20 12 0.40
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (20 bp):
TATAATATTTTATTTAAATA
Found at i:35764515 original size:27 final size:27
Alignment explanation
Indices: 35764471--35764533 Score: 69
Period size: 28 Copynumber: 2.4 Consensus size: 27
35764461 TATTATAGTG
35764471 ATTTTG-CC-CATAATTTTGT-TGTTTT
1 ATTTTGTCCACATAATTTTGTAT-TTTT
*
35764496 ATTTTGTCCACATTATTTTGTAATTTTT
1 ATTTTGTCCACATAATTTTGT-ATTTTT
*
35764524 GTTTTGTCCA
1 ATTTTGTCCA
35764534 TTTTGTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
25 6 0.19
26 2 0.06
27 10 0.31
28 13 0.41
29 1 0.03
ACGTcount: A:0.17, C:0.13, G:0.11, T:0.59
Consensus pattern (27 bp):
ATTTTGTCCACATAATTTTGTATTTTT
Found at i:35766102 original size:22 final size:22
Alignment explanation
Indices: 35766050--35766117 Score: 77
Period size: 22 Copynumber: 3.1 Consensus size: 22
35766040 TAATATAAAA
35766050 TTTAAATTTATTATTATAT-TT
1 TTTAAATTTATTATTATATATT
*** *
35766071 AAAAACATTTATTTTTATATATT
1 TTTAA-ATTTATTATTATATATT
35766094 TTTAAATTTATTATTATA-ATT
1 TTTAAATTTATTATTATATATT
35766115 TTT
1 TTT
35766118 TTAAAAATGT
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
21 8 0.22
22 25 0.68
23 4 0.11
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (22 bp):
TTTAAATTTATTATTATATATT
Found at i:35766125 original size:25 final size:23
Alignment explanation
Indices: 35766053--35766125 Score: 64
Period size: 22 Copynumber: 3.2 Consensus size: 23
35766043 TATAAAATTT
*
35766053 AAATTTATTATTATA--TTTAAA
1 AAATTTATTATTATATTTTTTAA
*
35766074 AACATTTATTTTTATATATTTTT--
1 AA-ATTTATTATTATAT-TTTTTAA
35766097 AAATTTATTATTATAATTTTTTTAA
1 AAATTTATTATTAT-A-TTTTTTAA
35766122 AAAT
1 AAAT
35766126 GTTTATGTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
21 2 0.05
22 23 0.56
23 8 0.20
24 1 0.02
25 7 0.17
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (23 bp):
AAATTTATTATTATATTTTTTAA
Found at i:35768007 original size:26 final size:25
Alignment explanation
Indices: 35767960--35768008 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
35767950 AATTAAAAAA
*
35767960 TAATTAAATTTTATTATTAAATATT
1 TAATTAAATTTTATTATAAAATATT
35767985 TAATTCAAATATTTATTA-AAAATA
1 TAATT-AAAT-TTTATTATAAAATA
35768009 AGGTTTATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 5 0.24
26 9 0.43
27 7 0.33
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (25 bp):
TAATTAAATTTTATTATAAAATATT
Found at i:35770519 original size:10 final size:10
Alignment explanation
Indices: 35770489--35770578 Score: 66
Period size: 10 Copynumber: 9.5 Consensus size: 10
35770479 AAAAAAATTC
35770489 AAATAT-TAA
1 AAATATATAA
*
35770498 AAAT-TAGAAA
1 AAATATA-TAA
35770508 AAATATATAA
1 AAATATATAA
*
35770518 AAAT-TGTAA
1 AAATATATAA
* *
35770527 AATTTTATAA
1 AAATATATAA
*
35770537 AAAT-CATAA
1 AAATATATAA
35770546 AAAT-TAT-A
1 AAATATATAA
*
35770554 AAATATATAG
1 AAATATATAA
*
35770564 AAATATAAAA
1 AAATATATAA
35770574 AAATA
1 AAATA
35770579 AAATTTTGTA
Statistics
Matches: 64, Mismatches: 11, Indels: 11
0.74 0.13 0.13
Matches are distributed among these distances:
8 6 0.09
9 24 0.38
10 32 0.50
11 2 0.03
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (10 bp):
AAATATATAA
Found at i:35770528 original size:19 final size:19
Alignment explanation
Indices: 35770489--35770556 Score: 68
Period size: 19 Copynumber: 3.6 Consensus size: 19
35770479 AAAAAAATTC
*
35770489 AAATAT-TAAAAATTAGAAA
1 AAATATATAAAAATT-GTAA
35770508 AAATATATAAAAATTGTAA
1 AAATATATAAAAATTGTAA
* * **
35770527 AATTTTATAAAAATCATAA
1 AAATATATAAAAATTGTAA
35770546 AAAT-TATAAAA
1 AAATATATAAAA
35770557 TATATAGAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
18 7 0.17
19 27 0.64
20 8 0.19
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (19 bp):
AAATATATAAAAATTGTAA
Found at i:35770529 original size:28 final size:28
Alignment explanation
Indices: 35770493--35770583 Score: 75
Period size: 28 Copynumber: 3.4 Consensus size: 28
35770483 AAATTCAAAT
*
35770493 ATTA-AAAATTAGA-AAAAATATATAAAA
1 ATTATAAAATTAGATAAAAAT-CATAAAA
* **
35770520 ATTGTAAAATTTTATAAAAATCATAAAA
1 ATTATAAAATTAGATAAAAATCATAAAA
* *
35770548 ATTATAAAA-TATATAGAAAT-ATAAAA
1 ATTATAAAATTAGATAAAAATCATAAAA
*
35770574 A-AATAAAATT
1 ATTATAAAATT
35770584 TTGTAAAGTC
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
25 6 0.11
26 8 0.15
27 12 0.23
28 21 0.40
29 6 0.11
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (28 bp):
ATTATAAAATTAGATAAAAATCATAAAA
Found at i:35770552 original size:18 final size:17
Alignment explanation
Indices: 35770506--35770581 Score: 64
Period size: 19 Copynumber: 4.2 Consensus size: 17
35770496 AAAAATTAGA
*
35770506 AAAAATATATAAAAATTGT
1 AAAAAT-TATAAAAA-TAT
*
35770525 AAAATTTTATAAAAATCAT
1 AAAA-ATTATAAAAAT-AT
35770544 AAAAATTATAAAATATAT
1 AAAAATTATAAAA-ATAT
* *
35770562 AGAAA-TATAAAAAAAT
1 AAAAATTATAAAAATAT
35770578 AAAA
1 AAAA
35770582 TTTTGTAAAG
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
16 6 0.12
17 7 0.15
18 15 0.31
19 19 0.40
20 1 0.02
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.29
Consensus pattern (17 bp):
AAAAATTATAAAAATAT
Found at i:35770915 original size:27 final size:28
Alignment explanation
Indices: 35770885--35770937 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 28
35770875 AAAAAATCTA
*
35770885 ATTTTTAATAAATTTTAA-AATTTTTAT
1 ATTTTTAATAAAATTTAATAATTTTTAT
*
35770912 ATTTTTATTAAAATTTAATAATTTTT
1 ATTTTTAATAAAATTTAATAATTTTT
35770938 CTAAAATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 16 0.70
28 7 0.30
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (28 bp):
ATTTTTAATAAAATTTAATAATTTTTAT
Found at i:35770927 original size:39 final size:39
Alignment explanation
Indices: 35770888--35770960 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
35770878 AAATCTAATT
*
35770888 TTTAATAA-ATTT-TAAAATTT-TTATATTTTTATTAAAA
1 TTTAATAATATTTCTAAAATTTATTAT-TTATTATTAAAA
*
35770925 TTTAATAATTTTTCTAAAATTTATTATTTATTATTA
1 TTTAATAATATTTCTAAAATTTATTATTTATTATTA
35770961 TTTGTATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
37 8 0.26
38 3 0.10
39 16 0.52
40 4 0.13
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (39 bp):
TTTAATAATATTTCTAAAATTTATTATTTATTATTAAAA
Found at i:35770935 original size:20 final size:19
Alignment explanation
Indices: 35770899--35770960 Score: 63
Period size: 20 Copynumber: 3.2 Consensus size: 19
35770889 TTAATAAATT
*
35770899 TTAAAATTTTTATATTTTTA
1 TTAAAATTTATA-ATTTTTA
35770919 TTAAAATTTAATAATTTTT-
1 TTAAAATTT-ATAATTTTTA
* *
35770938 CTAAAATTTATTATTTATTA
1 TTAAAATTTATAATTT-TTA
35770958 TTA
1 TTA
35770961 TTTGTATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
18 6 0.17
19 10 0.29
20 17 0.49
21 2 0.06
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
TTAAAATTTATAATTTTTA
Done.