Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold412
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: 4645160
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 19 of 32
Found at i:2526412 original size:21 final size:21
Alignment explanation
Indices: 2526383--2526424 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2526373 TACATTAAAT
2526383 ATAAATTTTTAA-AATAAATAA
1 ATAAATTTTTAACAA-AAATAA
*
2526404 ATAATTTTTTAACAAAAATAA
1 ATAAATTTTTAACAAAAATAA
2526425 TTATATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (21 bp):
ATAAATTTTTAACAAAAATAA
Found at i:2526751 original size:18 final size:18
Alignment explanation
Indices: 2526717--2526766 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
2526707 GGTAGTTTAA
2526717 ATTTATTAT-TTAA-ATAT
1 ATTT-TTATATTAATATAT
2526734 ATTTTTATATTAATATAT
1 ATTTTTATATTAATATAT
2526752 ATTTTTATAATTAAT
1 ATTTTTAT-ATTAAT
2526767 TTTAAATAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.13
17 8 0.27
18 12 0.40
19 6 0.20
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTTTTATATTAATATAT
Found at i:2526830 original size:20 final size:20
Alignment explanation
Indices: 2526797--2526836 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2526787 TATAAATAAT
2526797 AATTTAAAAAATTA-ATTTA
1 AATTTAAAAAATTATATTTA
*
2526816 AATTATAAAATATTATATTTA
1 AATT-TAAAAAATTATATTTA
2526837 GAAAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 9 0.50
21 5 0.28
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
AATTTAAAAAATTATATTTA
Found at i:2526846 original size:32 final size:33
Alignment explanation
Indices: 2526783--2526848 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 33
2526773 TAAATTTTTT
2526783 ATTATATAAATAATAATTTAAAAAATTAATTTAA
1 ATTATATAAATAATAATTTAAAAAA-TAATTTAA
* *
2526817 ATTATA-AAATATTATATTTAGAAAA-AATTTAA
1 ATTATATAAATAATA-ATTTAAAAAATAATTTAA
2526849 TAGGCTCTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
32 7 0.24
33 7 0.24
34 15 0.52
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (33 bp):
ATTATATAAATAATAATTTAAAAAATAATTTAA
Found at i:2527185 original size:22 final size:22
Alignment explanation
Indices: 2527160--2527201 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2527150 TTAAAAAGTG
2527160 TAAAA-AATTAAAAATATATATT
1 TAAAATAA-TAAAAATATATATT
*
2527182 TAAAATAATAAAAATTTATA
1 TAAAATAATAAAAATATATA
2527202 AATATAATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
TAAAATAATAAAAATATATATT
Found at i:2527428 original size:21 final size:20
Alignment explanation
Indices: 2527380--2527424 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
2527370 TCAATTTGAT
2527380 TTAAAAT-A-ATATTTTTAG
1 TTAAAATAATATATTTTTAG
*
2527398 TTAAAATAATATATTTTTAT
1 TTAAAATAATATATTTTTAG
2527418 TTAAAAT
1 TTAAAAT
2527425 TAATTATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 7 0.29
19 1 0.04
20 16 0.67
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
TTAAAATAATATATTTTTAG
Found at i:2527495 original size:20 final size:19
Alignment explanation
Indices: 2527466--2527503 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
2527456 TATTTTTTAA
2527466 AAAATAATAAATAATAATTT
1 AAAATAATAAATAA-AATTT
*
2527486 AAAATTATAAATAAAATT
1 AAAATAATAAATAAAATT
2527504 AAATTTTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAATAATAAATAAAATTT
Found at i:2527557 original size:18 final size:18
Alignment explanation
Indices: 2527480--2527575 Score: 56
Period size: 17 Copynumber: 5.4 Consensus size: 18
2527470 TAATAAATAA
* *
2527480 TAATTTAAAATTATAA-A
1 TAATTTTAAATTATAATT
** *
2527497 TAAAATTAAATTTTAACTT
1 TAATTTTAAATTATAA-TT
* * *
2527516 AAATTTTAAATTTTAAAAT
1 TAATTTTAAATTAT-AATT
2527535 T-ATTTTAAATTATAATT
1 TAATTTTAAATTATAATT
*
2527552 TAATTTATAAA-TAT-TTT
1 TAATTT-TAAATTATAATT
2527569 TAATTTT
1 TAATTTT
2527576 TAATATTTAA
Statistics
Matches: 61, Mismatches: 13, Indels: 11
0.72 0.15 0.13
Matches are distributed among these distances:
16 1 0.02
17 24 0.39
18 18 0.30
19 16 0.26
20 2 0.03
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (18 bp):
TAATTTTAAATTATAATT
Found at i:2527570 original size:17 final size:16
Alignment explanation
Indices: 2527536--2527583 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 16
2527526 TTTTAAAATT
*
2527536 ATTTTAAATTATAATTTA
1 ATTTTAAA-TAT-TTTTA
2527554 ATTTATAAATATTTTTA
1 ATTT-TAAATATTTTTA
*
2527571 ATTTTTAATATTT
1 ATTTTAAATATTT
2527584 AAAATTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 8 0.30
17 8 0.30
18 7 0.26
19 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
ATTTTAAATATTTTTA
Found at i:2527582 original size:16 final size:16
Alignment explanation
Indices: 2527550--2527593 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
2527540 TAAATTATAA
*
2527550 TTTAATTTATAAATATT
1 TTTAATTT-TTAATATT
2527567 TTTAATTTTTAATATT
1 TTTAATTTTTAATATT
**
2527583 TAAAATTTTTA
1 TTTAATTTTTA
2527594 TTAATTTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 16 0.67
17 8 0.33
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTAATTTTTAATATT
Found at i:2527586 original size:24 final size:24
Alignment explanation
Indices: 2527544--2527607 Score: 71
Period size: 24 Copynumber: 2.7 Consensus size: 24
2527534 TTATTTTAAA
*
2527544 TTATAATTTAAT-TTATAAATATTT
1 TTATTATTTAATATTATAAA-ATTT
2527568 TTAATT-TTTAATATT-TAAAATTT
1 TT-ATTATTTAATATTATAAAATTT
2527591 TTATTAATTTAATATTA
1 TTATT-ATTTAATATTA
2527608 CAATTTCGAG
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
22 3 0.09
23 6 0.18
24 21 0.62
25 4 0.12
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
TTATTATTTAATATTATAAAATTT
Found at i:2527777 original size:19 final size:19
Alignment explanation
Indices: 2527753--2527797 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
2527743 ATTACATTAT
2527753 TTATTTAAATTT-TGTAAAA
1 TTATTT-AATTTATGTAAAA
*
2527772 TTATTTGATTTAATGTAAAA
1 TTATTTAATTT-ATGTAAAA
2527792 TTATTT
1 TTATTT
2527798 TTTTAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 4 0.17
19 6 0.26
20 13 0.57
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.56
Consensus pattern (19 bp):
TTATTTAATTTATGTAAAA
Found at i:2528644 original size:26 final size:27
Alignment explanation
Indices: 2528586--2528663 Score: 67
Period size: 27 Copynumber: 3.0 Consensus size: 27
2528576 AAATATGTTT
* *
2528586 TATTAAAATATT-AAATAT--AGAATA
1 TATTATAATATTAAAATATGAAAAATA
* *
2528610 TATTTTAAT-TTAAAATATTAAGAAATA
1 TATTATAATATTAAAATATGAA-AAATA
*
2528637 -ATTATAATATTAATATATGAAAAATA
1 TATTATAATATTAAAATATGAAAAATA
2528663 T
1 T
2528664 TCAGGTTATT
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
23 2 0.05
24 13 0.31
26 13 0.31
27 14 0.33
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (27 bp):
TATTATAATATTAAAATATGAAAAATA
Found at i:2528706 original size:22 final size:21
Alignment explanation
Indices: 2528670--2528733 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 21
2528660 ATATTCAGGT
*
2528670 TATTAAAAT-AGTAATATTGTTA
1 TATTAAAATCA-TAA-ATTATTA
2528692 TATTAAAATCAT-AATTATTA
1 TATTAAAATCATAAATTATTA
*
2528712 TCATTAAAATCAT-ATTTATTA
1 T-ATTAAAATCATAAATTATTA
2528733 T
1 T
2528734 TAAAATAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
20 7 0.18
21 20 0.53
22 10 0.26
23 1 0.03
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (21 bp):
TATTAAAATCATAAATTATTA
Found at i:2528719 original size:21 final size:20
Alignment explanation
Indices: 2528689--2528733 Score: 72
Period size: 21 Copynumber: 2.2 Consensus size: 20
2528679 AGTAATATTG
2528689 TTATATTAAAATCATAATTA
1 TTATATTAAAATCATAATTA
*
2528709 TTATCATTAAAATCATATTTA
1 TTAT-ATTAAAATCATAATTA
2528730 TTAT
1 TTAT
2528734 TAAAATAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (20 bp):
TTATATTAAAATCATAATTA
Found at i:2535288 original size:19 final size:18
Alignment explanation
Indices: 2535248--2535291 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
2535238 GATTTTATTT
*
2535248 TTTAATTTTTAATTTACC
1 TTTAATTTTTAATTTACA
2535266 TTTAATTCTTTAATTT-CTA
1 TTTAATT-TTTAATTTAC-A
2535285 TTTAATT
1 TTTAATT
2535292 AACTTATTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.27, C:0.09, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTAATTTTTAATTTACA
Found at i:2537043 original size:2 final size:2
Alignment explanation
Indices: 2537036--2537083 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
2537026 ATTACATTGT
2537036 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2537078 TA TA TA
1 TA TA TA
2537084 GTAAAGAAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2538116 original size:70 final size:70
Alignment explanation
Indices: 2538033--2538175 Score: 234
Period size: 70 Copynumber: 2.0 Consensus size: 70
2538023 ATGTTTTGAG
* *
2538033 TTTACTACTTTCATTTTGAGGAAATATTTTAAGGCTTAAA-AGTCTTTAATCTCAAACTCCCTAC
1 TTTACTACCTTCATTTAGAGGAAATATTTTAAGGCTTAAAGA-TCTTTAATCTCAAACTCCCTAC
2538097 TTAGAA
65 TTAGAA
* *
2538103 TTTACTACCTTCATTTAGAGGAAATATTTTAAGGCTTAAAGATCTTTGATCTCAAATTCCCTACT
1 TTTACTACCTTCATTTAGAGGAAATATTTTAAGGCTTAAAGATCTTTAATCTCAAACTCCCTACT
2538168 TAGAA
66 TAGAA
2538173 TTT
1 TTT
2538176 TCTTCAATCT
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
70 67 0.99
71 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.10, T:0.41
Consensus pattern (70 bp):
TTTACTACCTTCATTTAGAGGAAATATTTTAAGGCTTAAAGATCTTTAATCTCAAACTCCCTACT
TAGAA
Found at i:2540935 original size:43 final size:43
Alignment explanation
Indices: 2540887--2540972 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
2540877 TTTATGTAAT
2540887 CCAATAAAATGGAAAAACATAAAGGTTTTAATAAAATAATTTC
1 CCAATAAAATGGAAAAACATAAAGGTTTTAATAAAATAATTTC
2540930 CCAATAAAATGGAAAAACATAAAGGTTTTAATAAAATAATTTC
1 CCAATAAAATGGAAAAACATAAAGGTTTTAATAAAATAATTTC
2540973 TAAATTTTTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.53, C:0.09, G:0.09, T:0.28
Consensus pattern (43 bp):
CCAATAAAATGGAAAAACATAAAGGTTTTAATAAAATAATTTC
Found at i:2542630 original size:268 final size:266
Alignment explanation
Indices: 2542156--2542655 Score: 621
Period size: 268 Copynumber: 1.9 Consensus size: 266
2542146 GTGTTGCCAA
* ** *
2542156 TGCTAAAACAGGAAAATTTTCAGATTTGGCTATCCTAGTCATGTATTGAGGTCTTGGACAGTGAA
1 TGCTAAAACAGGAAAATTTTCAGATTTGGCTATCCTAGTCATGTATTGAGATCTTAAACAGTAAA
* ** *
2542221 TGTTCATCATTTGAAGGTCTATGGTAGTGGAGTAACGGACGCATTTGACATCCTAGAAAGTAGGC
66 TGTTCATCATTTGAAGGTCGATGGTAGTGGAGTAACGGACGCATTCAAAATCCTAGAAAGTAGGC
* ** *
2542286 AATAAACGATGCGTTATTTATAACATTTGATTAACAACATAAATGCTCACAACAAGTCCTTTCAA
131 AATAAACGATGCATTATCCATAACATTTGATTAACAACATAAATGCTCACAACAAGACCTTTCAA
2542351 CAAACACTTTAAGACAAAAAATTTTT-GGTTAAAAAATAATTCTTCAAGTTAAAAATCATAGTGC
196 CAAACACTTTAAGACAAAAAATTTTTCGGTTAAAAAATAATTCTTCAAGTTAAAAATCATAGTGC
2542415 TACTAG
261 TACTAG
* * ** * * *
2542421 TGCTAAAACAGAGAGATTTTTTGGATTTTGCTATCTTAGTCATGTATTGAGATTTTAAACATGTA
1 TGCTAAAACAG-GAAAATTTTCAGATTTGGCTATCCTAGTCATGTATTGAGATCTTAAACA-GTA
* * * * *
2542486 AAT-TTCTGTCATTTGAAGGTCGATGGTGGTGGAGTAATGGACGCATTCAAAATCTTGGAGAA-T
64 AATGTTC-ATCATTTGAAGGTCGATGGTAGTGGAGTAACGGACGCATTCAAAATCCTAGA-AAGT
* * * * *
2542549 AGGCTAATGAATGATTCATTATCCATACCATTTGATTAACAACATTAAA-GCTCTCAACAAGACC
127 AGGC-AATAAACGATGCATTATCCATAACATTTGATTAACAACA-TAAATGCTCACAACAAGACC
* ** *
2542613 TTTGAACAAACACTTTAAGACAAAATCTTTTTCGGTTATAAAA
190 TTTCAACAAACACTTTAAGACAAAAAATTTTTCGGTTAAAAAA
2542656 CAAGCTAGAA
Statistics
Matches: 195, Mismatches: 33, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
265 11 0.06
266 42 0.22
267 53 0.27
268 76 0.39
269 13 0.07
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (266 bp):
TGCTAAAACAGGAAAATTTTCAGATTTGGCTATCCTAGTCATGTATTGAGATCTTAAACAGTAAA
TGTTCATCATTTGAAGGTCGATGGTAGTGGAGTAACGGACGCATTCAAAATCCTAGAAAGTAGGC
AATAAACGATGCATTATCCATAACATTTGATTAACAACATAAATGCTCACAACAAGACCTTTCAA
CAAACACTTTAAGACAAAAAATTTTTCGGTTAAAAAATAATTCTTCAAGTTAAAAATCATAGTGC
TACTAG
Found at i:2546600 original size:29 final size:30
Alignment explanation
Indices: 2546522--2546604 Score: 82
Period size: 29 Copynumber: 2.7 Consensus size: 30
2546512 ATTTGAAATG
*
2546522 ATATTTTTTAATTAATATAATATATTTTATTT
1 ATATTTTTTAA-TAAAATAA-ATATTTTATTT
*
2546554 ATATTTAATT-ATAAAAATAAA-ATTTTA-TT
1 ATATTT-TTTAAT-AAAATAAATATTTTATTT
2546583 AGTATTTTTTAATAAAATAAAT
1 A-TATTTTTTAATAAAATAAAT
2546605 TATAATTTAA
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
29 13 0.30
30 13 0.30
31 2 0.05
32 13 0.30
33 2 0.05
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (30 bp):
ATATTTTTTAATAAAATAAATATTTTATTT
Found at i:2546681 original size:23 final size:23
Alignment explanation
Indices: 2546655--2546702 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
2546645 GATGAGTCTA
**
2546655 AACTTAAAATTTTTAAAAAATTT
1 AACTTAAAATTTAAAAAAAATTT
2546678 AACTTAAAATTTAAAAAAAATTT
1 AACTTAAAATTTAAAAAAAATTT
2546701 AA
1 AA
2546703 TCTCTAGTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (23 bp):
AACTTAAAATTTAAAAAAAATTT
Found at i:2547386 original size:36 final size:36
Alignment explanation
Indices: 2547337--2547425 Score: 124
Period size: 36 Copynumber: 2.5 Consensus size: 36
2547327 AGAAGGAGGC
* * *
2547337 GGAGAAGCAGGAGTAGGTCGCCACGTCGAGATCGGA
1 GGAGGAGCAGGAGTAGGTCGCCACGTAGAGAGCGGA
*
2547373 GGAGGAGCGGGAGTAGGTCGCCACGTAGAGAGCGGA
1 GGAGGAGCAGGAGTAGGTCGCCACGTAGAGAGCGGA
* *
2547409 GAAGGAGTAGGAGTAGG
1 GGAGGAGCAGGAGTAGG
2547426 AGTAGGTCGC
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.28, C:0.15, G:0.47, T:0.10
Consensus pattern (36 bp):
GGAGGAGCAGGAGTAGGTCGCCACGTAGAGAGCGGA
Found at i:2552171 original size:19 final size:18
Alignment explanation
Indices: 2552134--2552168 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2552124 AATTATAAAT
2552134 ATTAAAAATTAAATTTTA
1 ATTAAAAATTAAATTTTA
*
2552152 ATTAAAAATTTAATTTT
1 ATTAAAAATTAAATTTT
2552169 TAAAAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATTAAAAATTAAATTTTA
Found at i:2552318 original size:20 final size:22
Alignment explanation
Indices: 2552295--2552341 Score: 66
Period size: 20 Copynumber: 2.3 Consensus size: 22
2552285 TATTTAAAAA
2552295 TATATATTAA-A-ATTTATTTT
1 TATATATTAATATATTTATTTT
2552315 TATA-A-TAATATATTTATTTT
1 TATATATTAATATATTTATTTT
2552335 TATATAT
1 TATATAT
2552342 AAATTTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
18 3 0.13
19 2 0.09
20 17 0.74
21 1 0.04
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TATATATTAATATATTTATTTT
Found at i:2553433 original size:8 final size:8
Alignment explanation
Indices: 2553420--2553470 Score: 50
Period size: 8 Copynumber: 6.0 Consensus size: 8
2553410 TTTAATATTT
2553420 AATTTTTA
1 AATTTTTA
2553428 AA-TTTTA
1 AATTTTTA
2553435 AATTTTTA
1 AATTTTTA
2553443 AATATTATTAA
1 AAT-TT-TT-A
*
2553454 AACTTTTA
1 AATTTTTA
2553462 AATATTTTA
1 AAT-TTTTA
2553471 TTTTTTAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
7 7 0.19
8 13 0.36
9 9 0.25
10 4 0.11
11 3 0.08
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (8 bp):
AATTTTTA
Found at i:2553520 original size:23 final size:23
Alignment explanation
Indices: 2553493--2553538 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
2553483 AAATTATTAA
2553493 TATTA-ACAAAAAATAACATATTT
1 TATTATACAAAAAATAA-ATATTT
**
2553516 TATTATTTAAAAAATAAATATTT
1 TATTATACAAAAAATAAATATTT
2553539 ATAAAATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.41
Consensus pattern (23 bp):
TATTATACAAAAAATAAATATTT
Found at i:2553826 original size:15 final size:15
Alignment explanation
Indices: 2553808--2553853 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
2553798 AAAAAATTTT
*
2553808 AAAATAATATAATAA
1 AAAATTATATAATAA
*
2553823 AAAATTATAT-TTATA
1 AAAATTATATAATA-A
2553838 AAAATTATATAA-AA
1 AAAATTATATAATAA
2553852 AA
1 AA
2553854 TTAAAATTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
14 5 0.19
15 21 0.81
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AAAATTATATAATAA
Found at i:2554448 original size:2 final size:2
Alignment explanation
Indices: 2554441--2554478 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2554431 CATTTCAAGG
2554441 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2554479 TTGTTCTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2557209 original size:50 final size:51
Alignment explanation
Indices: 2557116--2557215 Score: 193
Period size: 50 Copynumber: 2.0 Consensus size: 51
2557106 TTTTTGCTTA
2557116 ATATATATATATATATATATATTTAATAAAGAAGGTTATAACTTAAGAATT
1 ATATATATATATATATATATATTTAATAAAGAAGGTTATAACTTAAGAATT
2557167 ATATATATATATATATATAT-TTTAATAAAGAAGGTTATAACTTAAGAAT
1 ATATATATATATATATATATATTTAATAAAGAAGGTTATAACTTAAGAAT
2557216 AGACGAGGAG
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
50 29 0.59
51 20 0.41
ACGTcount: A:0.49, C:0.02, G:0.08, T:0.41
Consensus pattern (51 bp):
ATATATATATATATATATATATTTAATAAAGAAGGTTATAACTTAAGAATT
Found at i:2557670 original size:9 final size:11
Alignment explanation
Indices: 2557637--2557691 Score: 67
Period size: 11 Copynumber: 4.9 Consensus size: 11
2557627 GAATTAACAC
*
2557637 ATAACATAAAA
1 ATAATATAAAA
2557648 ATAATATAAAA
1 ATAATATAAAA
2557659 ATAAT-TAAAA
1 ATAATATAAAA
*
2557669 TATGATATAAAAA
1 -ATAATAT-AAAA
2557682 ATAATATAAA
1 ATAATATAAA
2557692 TACGTCATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
10 5 0.13
11 22 0.58
12 7 0.18
13 4 0.11
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (11 bp):
ATAATATAAAA
Found at i:2557948 original size:17 final size:17
Alignment explanation
Indices: 2557917--2557950 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2557907 ATAAATTATG
* *
2557917 TAAAATATGAGATGAAT
1 TAAAATATAACATGAAT
2557934 TAAAATATAACATGAAT
1 TAAAATATAACATGAAT
2557951 GCGATAAGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.56, C:0.03, G:0.12, T:0.29
Consensus pattern (17 bp):
TAAAATATAACATGAAT
Found at i:2558242 original size:32 final size:31
Alignment explanation
Indices: 2558189--2558253 Score: 87
Period size: 32 Copynumber: 2.1 Consensus size: 31
2558179 AACATGACAC
2558189 AAATAAATATAAAAATAT-AAAAATATATATA
1 AAATAAATATAAAAATATAAAAAAT-TATATA
* *
2558220 AAATAAATTATTAATATATAAAAAATTATATA
1 AAATAAA-TATAAAAATATAAAAAATTATATA
2558252 AA
1 AA
2558254 TTTATAACAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
31 7 0.23
32 17 0.57
33 6 0.20
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (31 bp):
AAATAAATATAAAAATATAAAAAATTATATA
Found at i:2568135 original size:15 final size:15
Alignment explanation
Indices: 2568115--2568148 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
2568105 ACGAATCGAA
2568115 TTGAACTGATTAATT
1 TTGAACTGATTAATT
2568130 TTGAACTGATTAATT
1 TTGAACTGATTAATT
2568145 TTGA
1 TTGA
2568149 TTTGGCTAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.32, C:0.06, G:0.15, T:0.47
Consensus pattern (15 bp):
TTGAACTGATTAATT
Found at i:2568226 original size:18 final size:18
Alignment explanation
Indices: 2568187--2568222 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
2568177 TTCAATTTTG
*
2568187 ATTTGATTTGTTTTTCAA
1 ATTTGATTTGCTTTTCAA
2568205 ATTT-ATTTGCTTTTCAA
1 ATTTGATTTGCTTTTCAA
2568222 A
1 A
2568223 ATTTTATAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.25, C:0.08, G:0.08, T:0.58
Consensus pattern (18 bp):
ATTTGATTTGCTTTTCAA
Found at i:2568316 original size:26 final size:27
Alignment explanation
Indices: 2568264--2568316 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 27
2568254 TTTTTTATTG
*** *
2568264 AAATATTGATAATTTTTTTATTTTTTA
1 AAATATTGATAATTTTGAAATTATTTA
2568291 AAATATTGAT-ATTTTGAAATTATTTA
1 AAATATTGATAATTTTGAAATTATTTA
2568317 TGAAAATATG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
26 12 0.55
27 10 0.45
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.57
Consensus pattern (27 bp):
AAATATTGATAATTTTGAAATTATTTA
Found at i:2568914 original size:31 final size:30
Alignment explanation
Indices: 2568853--2568916 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
2568843 TTTTTATGTA
*
2568853 AATATGTAAAAATATTTTTTAATTAACTTTT
1 AATAAGTAAAAATATTTTTTAATT-ACTTTT
*
2568884 AATAAGTAAACATATTTTATTATATT-CTTTT
1 AATAAGTAAAAATATTTT-TTA-ATTACTTTT
2568915 AA
1 AA
2568917 AATGCACATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
31 23 0.79
32 3 0.10
33 3 0.10
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (30 bp):
AATAAGTAAAAATATTTTTTAATTACTTTT
Found at i:2568996 original size:25 final size:22
Alignment explanation
Indices: 2568968--2569024 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 22
2568958 TTAACAATTG
2568968 ATAAAATAATATAATAATAATTATT
1 ATAAAA-AATAT-ATAATAA-TATT
*
2568993 AT-AAAAATATATAATTATATT
1 ATAAAAAATATATAATAATATT
2569014 AT-AAAAATATA
1 ATAAAAAATATA
2569025 GATTTTATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 15 0.48
22 6 0.19
23 5 0.16
24 3 0.10
25 2 0.06
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
ATAAAAAATATATAATAATATT
Found at i:2569015 original size:21 final size:22
Alignment explanation
Indices: 2568975--2569024 Score: 75
Period size: 21 Copynumber: 2.3 Consensus size: 22
2568965 TTGATAAAAT
2568975 AATATAATAATAATTATTATAAA
1 AATAT-ATAATAATTATTATAAA
*
2568998 AATATATAATTA-TATTATAAA
1 AATATATAATAATTATTATAAA
2569019 AATATA
1 AATATA
2569025 GATTTTATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 15 0.58
22 6 0.23
23 5 0.19
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
AATATATAATAATTATTATAAA
Found at i:2570193 original size:14 final size:12
Alignment explanation
Indices: 2570140--2570223 Score: 55
Period size: 14 Copynumber: 6.4 Consensus size: 12
2570130 TATGATTTAT
2570140 ATATAAAT-ATA
1 ATATAAATAATA
*
2570151 ATAAAAAATAATTA
1 AT-ATAAATAA-TA
*
2570165 ATATATATATTATA
1 ATATA-A-ATAATA
2570179 ATATAAGATAAATA
1 ATATAA-AT-AATA
2570193 ATAATAAAT-ATA
1 AT-ATAAATAATA
2570205 ATATAAATATATGA
1 ATATAAATA-AT-A
2570219 ATATA
1 ATATA
2570224 TTAAAATTTA
Statistics
Matches: 58, Mismatches: 5, Indels: 17
0.73 0.06 0.21
Matches are distributed among these distances:
11 8 0.14
12 10 0.17
13 8 0.14
14 25 0.43
15 7 0.12
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (12 bp):
ATATAAATAATA
Found at i:2570197 original size:35 final size:32
Alignment explanation
Indices: 2570137--2570215 Score: 99
Period size: 35 Copynumber: 2.4 Consensus size: 32
2570127 ACATATGATT
*
2570137 TATATATAAATAT-AATAAAAAATAATTAATA
1 TATATATAAATATAAATAAAAAATAATAAATA
*
2570168 TATATATTATAATATAAGATAAATAATAATAAATA
1 TATATA-TA-AATATAA-ATAAAAAATAATAAATA
2570203 TA-ATATAAATATA
1 TATATATAAATATA
2570216 TGAATATATT
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
31 6 0.14
32 8 0.19
33 7 0.17
34 4 0.10
35 17 0.40
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (32 bp):
TATATATAAATATAAATAAAAAATAATAAATA
Found at i:2572349 original size:13 final size:13
Alignment explanation
Indices: 2572331--2572356 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2572321 AACTCTTCCA
2572331 ATAGCTTTCCAAT
1 ATAGCTTTCCAAT
2572344 ATAGCTTTCCAAT
1 ATAGCTTTCCAAT
2572357 GAATTATACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (13 bp):
ATAGCTTTCCAAT
Found at i:2577484 original size:18 final size:17
Alignment explanation
Indices: 2577451--2577486 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
2577441 TATTCATTAT
*
2577451 ATTTTAAATTTTTAAAA
1 ATTTTAAATATTTAAAA
2577468 ATTTTAATATATTTAAAA
1 ATTTTAA-ATATTTAAAA
2577486 A
1 A
2577487 ATATTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTTAAATATTTAAAA
Found at i:2578100 original size:9 final size:9
Alignment explanation
Indices: 2578088--2578120 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
2578078 GAGAAGGATC
2578088 GGAGAAAAT
1 GGAGAAAAT
2578097 GGAGAAAAT
1 GGAGAAAAT
2578106 GGAGAAAAT
1 GGAGAAAAT
*
2578115 GAAGAA
1 GGAGAA
2578121 GAGACTGACC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.58, C:0.00, G:0.33, T:0.09
Consensus pattern (9 bp):
GGAGAAAAT
Found at i:2579522 original size:3 final size:3
Alignment explanation
Indices: 2579516--2579543 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2579506 ATAATAATAA
2579516 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2579544 GCTTGGAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2581683 original size:79 final size:81
Alignment explanation
Indices: 2581551--2581700 Score: 241
Period size: 79 Copynumber: 1.9 Consensus size: 81
2581541 ATATCTATAT
*
2581551 CTATATAATATATATAAAATACAATATTTTGACATAAATACTAATGTTTATTATAGGTTTTTTTT
1 CTATATAATATATATAAAATACAATATTTTGACATAAATACTAACGTTTATTATAGGTTTTTTTT
2581616 -AAAAACTTTTTCATA
66 CAAAAACTTTTTCATA
* * * *
2581631 CTATATAATATGTATAAAATATACT-TTTTGACATAAATACTAACGTTTATTATGGGTTTTTTTT
1 CTATATAATATATATAAAATACAATATTTTGACATAAATACTAACGTTTATTATAGGTTTTTTTT
2581695 CAAAAA
66 CAAAAA
2581701 ACATTTCATA
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
79 37 0.58
80 27 0.42
ACGTcount: A:0.40, C:0.08, G:0.07, T:0.45
Consensus pattern (81 bp):
CTATATAATATATATAAAATACAATATTTTGACATAAATACTAACGTTTATTATAGGTTTTTTTT
CAAAAACTTTTTCATA
Found at i:2581708 original size:80 final size:80
Alignment explanation
Indices: 2581551--2581718 Score: 234
Period size: 79 Copynumber: 2.1 Consensus size: 80
2581541 ATATCTATAT
*
2581551 CTATATAATATATATAAAATACAATATTTTGACATAAATACTAATGTTTATTATAGGTTTTTTTT
1 CTATATAATATATATAAAATACAATATTTTGACATAAATACTAACGTTTATTATAGGTTTTTTTT
*
2581616 AAAAACTTTTTCATA
66 AAAAACTATTTCATA
* * * *
2581631 CTATATAATATGTATAAAATATACT-TTTTGACATAAATACTAACGTTTATTATGGGTTTTTTTT
1 CTATATAATATATATAAAATACAATATTTTGACATAAATACTAACGTTTATTATAGGTTTTTTTT
2581695 CAAAAAAC-ATTTCATA
66 --AAAAACTATTTCATA
2581711 -TATTATAA
1 CTA-TATAA
2581719 AAATAATTCA
Statistics
Matches: 79, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
79 39 0.49
80 34 0.43
81 6 0.08
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.45
Consensus pattern (80 bp):
CTATATAATATATATAAAATACAATATTTTGACATAAATACTAACGTTTATTATAGGTTTTTTTT
AAAAACTATTTCATA
Found at i:2583137 original size:484 final size:482
Alignment explanation
Indices: 2582255--2583539 Score: 1969
Period size: 484 Copynumber: 2.7 Consensus size: 482
2582245 ATTATGGGTT
* *
2582255 TTTTTTTTTCAAAATTTTGTTCATATATTATAAAAATAATTCATTTAATTCAATGTATAATATTA
1 TTTTTTTTTC-AAATTTTTTTTATATATTATAAAAATAATTCATTTAATTCAATGTATAATATTA
*
2582320 ATTTGACCAATTAATTTTATCTCA--T-T-TTTCTTCATTGTGTGTAATATAATATATTAATTTT
65 ATTTGACCAATTAATTTTATCTCATTTATCTTTATTCATTGTGTGTAATATAATATATTAATTTT
* * * *
2582381 ATTTTAGCCAT-ATTTATTGAATTTAATATAATATATTAATTTCATTC--TCTTTCTTAATTACG
130 ATCTCAGCC-TCATTTATTGAATTTAATATAATATATTAATTTTATTCATTCTTT-TGAATTACG
2582443 TTTTAATTCTTTTTAGTAGAATTTGAATGGTTTAATTACTAAAAATATAATAATAAAA--ATTAT
193 TTTTAATTCTTTTTAGTAGAATTTGAATGGTTTAATTACTAAAAATATAATAATAAAATTATTAT
*
2582506 -TA-TAATATTTTCTCATTCATTGAATTTAAATTTAATATAATATATTAATTTTATTTATTGTG-
258 CAATTAATATTTTCTCATTCATTGAATTTAAATTTAATATAATATATTAATTTTATTTATTGTGT
*
2582568 TTTTTTAATTTCTTTTCAACTTTTTTAATAGAATTTAAATAGTTAAATTACTAATATATTAATTT
323 TTTTTTAATTTCTTTTCAACTTTTTTAATAGAATTTAAAAAGTTAAATTACTAATATATTAATTT
* * *
2582633 TATCTCTATCTTATTCATTAAATTTAATATAATATATTAATTCTACTCATTGCTTGTTGAATTTT
388 TATCTCTATCTTATTCATTAAATTTAATATAATAAATTAACTCCACTCATTGCTTGTTGAATTTT
*
2582698 GTTTTAATTCTTTTTCATAGAATTGGTGA-
453 GTTTTAATTCTTTTTCATAGAATTGATGAG
* * * *
2582727 TTTTTTTTTCAAATTTTTTTTAAATACTATAACAATAATTCATTTAATTTAATGTATAATATTAA
1 TTTTTTTTTCAAATTTTTTTTATATATTATAAAAATAATTCATTTAATTCAATGTATAATATTAA
2582792 TTTGACCAATTAATTTTATCTCATTTATCTTTATTCATTGTGTGTAATATAATATATTAATTTTA
66 TTTGACCAATTAATTTTATCTCATTTATCTTTATTCATTGTGTGTAATATAATATATTAATTTTA
* *
2582857 TCTCAGCCTCATTCATTGAATTTAATATGATATATTAATTTTATTCATTGCTTTTGAATTACGTT
131 TCTCAGCCTCATTTATTGAATTTAATATAATATATTAATTTTATTCATT-CTTTTGAATTACGTT
*
2582922 TTAATTCTTTTTAATAGAATTTGAATGGTTTAATTACTAAAAATATAATAATAAAATTATTATCA
195 TTAATTCTTTTTAGTAGAATTTGAATGGTTTAATTACTAAAAATATAATAATAAAATTATTATCA
* *
2582987 ATTAATATTTTCTCATTCATGGAATTTAAATTTAATATAATATATTAGTTTTATTTATTGTGTTT
260 ATTAATATTTTCTCATTCATTGAATTTAAATTTAATATAATATATTAATTTTATTTATTGTGTTT
2583052 TTTTAAATTTCGTTTT-AACTTTTTGTAATAGAATTTAAAAAGTTAAATTACTAATATATTAATT
325 TTTT-AATTTC-TTTTCAACTTTTT-TAATAGAATTTAAAAAGTTAAATTACTAATATATTAATT
* * *
2583116 TTATCTC-AGTCTTATTCATTAAATTTGATATAATAAATTAACTCCATTCATTGCTTTTTGAATT
387 TTATCTCTA-TCTTATTCATTAAATTTAATATAATAAATTAACTCCACTCATTGCTTGTTGAATT
*
2583180 TTGTTTTAATTCTTTTTCATAGAATTTATGAG
451 TTGTTTTAATTCTTTTTCATAGAATTGATGAG
* *
2583212 TTTTTTTTTC-AA-TTTTTTTATATATTATAAAAATAATTCATTGAATTCAATGTATCATATTAA
1 TTTTTTTTTCAAATTTTTTTTATATATTATAAAAATAATTCATTTAATTCAATGTATAATATTAA
* * *
2583275 TTTAATCAATTAATTTTATCTCATTTATCTTTATTCATTGTGTGTAATATAATATAATAATTTTA
66 TTTGACCAATTAATTTTATCTCATTTATCTTTATTCATTGTGTGTAATATAATATATTAATTTTA
* * *
2583340 TCTCAACCTCATTTATTGAATTTAATATAATATATTAATTTTATTTATTATTTTTTGAAATTACG
131 TCTCAGCCTCATTTATTGAATTTAATATAATATATTAATTTTATTCA-T-TCTTTTG-AATTACG
* * *
2583405 TTTTAATTATTTTTAGTAAAATTTGAATGGTTTAATTATTAAAAATATAATAATAAAAATTATTA
193 TTTTAATTCTTTTTAGTAGAATTTGAATGGTTTAATTACTAAAAATATAATAAT-AAAATTATTA
* * *
2583470 TCAATTAATATTTT-T-ATTCATTAAATTTAAATTTAATATAATATATTAATTTTATTCATTATG
257 TCAATTAATATTTTCTCATTCATTGAATTTAAATTTAATATAATATATTAATTTTATTTATTGTG
2583533 TTTTTTT
322 TTTTTTT
2583540 TTTAATTTTC
Statistics
Matches: 742, Mismatches: 49, Indels: 32
0.90 0.06 0.04
Matches are distributed among these distances:
471 72 0.10
472 10 0.01
473 1 0.00
474 2 0.00
475 74 0.10
477 66 0.09
478 4 0.01
479 5 0.01
480 1 0.00
481 58 0.08
482 6 0.01
483 165 0.22
484 185 0.25
485 69 0.09
486 24 0.03
ACGTcount: A:0.35, C:0.07, G:0.06, T:0.52
Consensus pattern (482 bp):
TTTTTTTTTCAAATTTTTTTTATATATTATAAAAATAATTCATTTAATTCAATGTATAATATTAA
TTTGACCAATTAATTTTATCTCATTTATCTTTATTCATTGTGTGTAATATAATATATTAATTTTA
TCTCAGCCTCATTTATTGAATTTAATATAATATATTAATTTTATTCATTCTTTTGAATTACGTTT
TAATTCTTTTTAGTAGAATTTGAATGGTTTAATTACTAAAAATATAATAATAAAATTATTATCAA
TTAATATTTTCTCATTCATTGAATTTAAATTTAATATAATATATTAATTTTATTTATTGTGTTTT
TTTAATTTCTTTTCAACTTTTTTAATAGAATTTAAAAAGTTAAATTACTAATATATTAATTTTAT
CTCTATCTTATTCATTAAATTTAATATAATAAATTAACTCCACTCATTGCTTGTTGAATTTTGTT
TTAATTCTTTTTCATAGAATTGATGAG
Found at i:2584166 original size:13 final size:13
Alignment explanation
Indices: 2584148--2584172 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2584138 CATAAAGTGT
2584148 TGTATCGATACAA
1 TGTATCGATACAA
2584161 TGTATCGATACA
1 TGTATCGATACA
2584173 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2584192 original size:32 final size:33
Alignment explanation
Indices: 2584128--2584193 Score: 107
Period size: 32 Copynumber: 2.0 Consensus size: 33
2584118 TTCAACGATT
2584128 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
* *
2584161 TGTATCGATACAT-AAGTTTTGTATCGGTACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
2584193 T
1 T
2584194 TTAAGCTACT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.58
33 13 0.42
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.36
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:2584253 original size:13 final size:13
Alignment explanation
Indices: 2584235--2584260 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2584225 ATTACTCAAA
2584235 TGTATCGATACAT
1 TGTATCGATACAT
2584248 TGTATCGATACAT
1 TGTATCGATACAT
2584261 GCAGGCAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2584326 original size:52 final size:52
Alignment explanation
Indices: 2584248--2584372 Score: 232
Period size: 52 Copynumber: 2.4 Consensus size: 52
2584238 ATCGATACAT
*
2584248 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
2584300 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
2584352 TGTATCGATACATGCAGGCAA
1 TGTATCGATACATGCAGGCAA
2584373 CTTTTCATAT
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:2591489 original size:98 final size:98
Alignment explanation
Indices: 2591303--2591526 Score: 267
Period size: 98 Copynumber: 2.3 Consensus size: 98
2591293 ATGTTAAAGA
*
2591303 TGCCAATATGCTGATTCAAGGCCAACGATATCGAACTTAAAGATGAAAGTGCCAATGTACTGATT
1 TGCCAATATACTGATTCAAGGCCAACGATATCGAACTTAAAGATGAAAGTGCCAATGTACTGATT
*
2591368 CAAGGCCAACGATATCGGACTTAAAGATGAACG
66 CAAGGCCAACGACATCGGACTTAAAGATGAACG
* * * **
2591401 TGCCAATGTACTGATTCAAGGCCAGCGATATC-AGACTTAAAGATGAACGTGCCAATGTGTTGAT
1 TGCCAATATACTGATTCAAGGCCAACGATATCGA-ACTTAAAGATGAAAGTGCCAATGTACTGAT
** * * *
2591465 TCAAGGCCAGTGACATTGGGCTTAAAAATG---G
65 TCAAGGCCAACGACATCGGACTTAAAGATGAACG
* * * *
2591496 TGCCAATATGCTAATTTAAGGCCAACAATAT
1 TGCCAATATACTGATTCAAGGCCAACGATAT
2591527 TGGACTCAAA
Statistics
Matches: 107, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
95 26 0.24
97 1 0.01
98 80 0.75
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.25
Consensus pattern (98 bp):
TGCCAATATACTGATTCAAGGCCAACGATATCGAACTTAAAGATGAAAGTGCCAATGTACTGATT
CAAGGCCAACGACATCGGACTTAAAGATGAACG
Found at i:2591490 original size:49 final size:49
Alignment explanation
Indices: 2591303--2591474 Score: 263
Period size: 49 Copynumber: 3.5 Consensus size: 49
2591293 ATGTTAAAGA
* * * * *
2591303 TGCCAATATGCTGATTCAAGGCCAACGATATCGAACTTAAAGATGAAAG
1 TGCCAATGTACTGATTCAAGGCCAGCGATATCGGACTTAAAGATGAACG
*
2591352 TGCCAATGTACTGATTCAAGGCCAACGATATCGGACTTAAAGATGAACG
1 TGCCAATGTACTGATTCAAGGCCAGCGATATCGGACTTAAAGATGAACG
*
2591401 TGCCAATGTACTGATTCAAGGCCAGCGATATCAGACTTAAAGATGAACG
1 TGCCAATGTACTGATTCAAGGCCAGCGATATCGGACTTAAAGATGAACG
**
2591450 TGCCAATGTGTTGATTCAAGGCCAG
1 TGCCAATGTACTGATTCAAGGCCAG
2591475 TGACATTGGG
Statistics
Matches: 115, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 115 1.00
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.23
Consensus pattern (49 bp):
TGCCAATGTACTGATTCAAGGCCAGCGATATCGGACTTAAAGATGAACG
Found at i:2591517 original size:46 final size:45
Alignment explanation
Indices: 2591298--2591577 Score: 177
Period size: 49 Copynumber: 6.0 Consensus size: 45
2591288 AAGGAATGTT
* ** * *
2591298 AAAGATGCCAATATGCTGATTCAAGGCCAACGATATCGAACTTAAA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGTGATATTGGACTT-AA
* * * ** *
2591344 GATGAAAGTGCCAATGTACTGATTCAAGGCCAACGATATCGGACTTAAA
1 -A--AAGGTGCCAATATGCTGATTCAAGGCCAGTGATATTGGACTT-AA
* * * * **
2591393 GATGAACGTGCCAATGTACTGATTCAAGGCCAGCGATATCAGACTTAAA
1 -A--AAGGTGCCAATATGCTGATTCAAGGCCAGTGATATTGGACTT-AA
* * * * *
2591442 GATGAACGTGCCAATGTGTTGATTCAAGGCCAGTGACATTGGGCTTAA
1 -A--AAGGTGCCAATATGCTGATTCAAGGCCAGTGATATTGGACTTAA
* * *** *
2591490 AAATGGTGCCAATATGCTAATTTAAGGCCAACAATATTGGAC-T-C
1 AAA-GGTGCCAATATGCTGATTCAAGGCCAGTGATATTGGACTTAA
2591534 AAAGGTGCCAATATGCTGATTCAAGGCCAGTGATATTGGACTTA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGTGATATTGGACTTA
2591578 GAAGAAGATG
Statistics
Matches: 197, Mismatches: 31, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
43 33 0.17
44 4 0.02
45 3 0.02
46 28 0.14
47 2 0.01
48 2 0.01
49 125 0.63
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.25
Consensus pattern (45 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGTGATATTGGACTTAA
Found at i:2591644 original size:29 final size:29
Alignment explanation
Indices: 2591599--2591895 Score: 304
Period size: 29 Copynumber: 10.3 Consensus size: 29
2591589 CACCAACTTG
*
2591599 TGTGGGC-TTTTGAAAGGATGCTACTGACT
1 TGTGGGCTTTTTG-AAGGATGCCACTGACT
*
2591628 TGTGGGCTTTTTGAAGGTTGCCACTGACT
1 TGTGGGCTTTTTGAAGGATGCCACTGACT
** * *
2591657 TGTGGGCTTTGAGAATG-TGCCACTAACT
1 TGTGGGCTTTTTGAAGGATGCCACTGACT
*
2591685 TGTGGGC-TTTTGAAAAGATGCCACTGACT
1 TGTGGGCTTTTTG-AAGGATGCCACTGACT
*
2591714 TGTGGGCTTTTTGAAGGTTGCCACTGACT
1 TGTGGGCTTTTTGAAGGATGCCACTGACT
** ** *
2591743 TGTGGGCTTTGAGAA-GATGTTACTAACT
1 TGTGGGCTTTTTGAAGGATGCCACTGACT
*
2591771 TGTGGGC-TTTTGAAAAGATGCCACTGACT
1 TGTGGGCTTTTTG-AAGGATGCCACTGACT
* * *
2591800 TGTAGGCTTTTTAAAGGTTGCCACTGACT
1 TGTGGGCTTTTTGAAGGATGCCACTGACT
* *
2591829 TGT-GGATTTTCAGAA-GATGCCACTGACT
1 TGTGGGCTTTT-TGAAGGATGCCACTGACT
* *
2591857 TGTGGGC-TTTTGAAAAGATGCCATTGACT
1 TGTGGGCTTTTTG-AAGGATGCCACTGACT
2591886 TGTGGGCTTT
1 TGTGGGCTTT
2591896 GAAAAGTGAG
Statistics
Matches: 222, Mismatches: 34, Indels: 23
0.80 0.12 0.08
Matches are distributed among these distances:
27 7 0.03
28 64 0.29
29 135 0.61
30 16 0.07
ACGTcount: A:0.21, C:0.16, G:0.29, T:0.35
Consensus pattern (29 bp):
TGTGGGCTTTTTGAAGGATGCCACTGACT
Found at i:2591689 original size:57 final size:58
Alignment explanation
Indices: 2591599--2591897 Score: 319
Period size: 57 Copynumber: 5.2 Consensus size: 58
2591589 CACCAACTTG
* * *
2591599 TGTGGGCTTTTGA-AAGGATGCTACTGACTTGTGGGCTTTTTGAAGGTTGCCACTGACT
1 TGTGGGC-TTTGAGAAGGATGCCACTGACTTGTGGGCTTTTTGAAAGATGCCACTGACT
* *
2591657 TGTGGGCTTTGAGAATG-TGCCACTAACTTGTGGGC-TTTTGAAAAGATGCCACTGACT
1 TGTGGGCTTTGAGAAGGATGCCACTGACTTGTGGGCTTTTTG-AAAGATGCCACTGACT
** * ** *
2591714 TGTGGGCTTTTTGAAGGTTGCCACTGACTTGTGGGC--TTTGAGAAGATGTTACTAACT
1 TGTGGGCTTTGAGAAGGATGCCACTGACTTGTGGGCTTTTTGA-AAGATGCCACTGACT
* * *
2591771 TGTGGGCTTTTGA-AAAGATGCCACTGACTTGTAGGCTTTTT-AAAGGTTGCCACTGACT
1 TGTGGGC-TTTGAGAAGGATGCCACTGACTTGTGGGCTTTTTGAAA-GATGCCACTGACT
** * *
2591829 TGTGGATTTTCAGAA-GATGCCACTGACTTGTGGGC-TTTTGAAAAGATGCCATTGACT
1 TGTGGGCTTTGAGAAGGATGCCACTGACTTGTGGGCTTTTTG-AAAGATGCCACTGACT
2591886 TGTGGGCTTTGA
1 TGTGGGCTTTGA
2591898 AAAGTGAGGA
Statistics
Matches: 200, Mismatches: 30, Indels: 23
0.79 0.12 0.09
Matches are distributed among these distances:
56 10 0.05
57 137 0.69
58 50 0.25
59 3 0.01
ACGTcount: A:0.21, C:0.16, G:0.29, T:0.35
Consensus pattern (58 bp):
TGTGGGCTTTGAGAAGGATGCCACTGACTTGTGGGCTTTTTGAAAGATGCCACTGACT
Found at i:2591733 original size:86 final size:86
Alignment explanation
Indices: 2591580--2591895 Score: 490
Period size: 86 Copynumber: 3.7 Consensus size: 86
2591570 TGGACTTAGA
* * *
2591580 AGAAGATGCCACCAACTTGTGTGGGCTTTTGAAAGGATGCTACTGACTTGTGGGCTTTTTGAAGG
1 AGAAGATGCCACTAAC-T-TGTGGGCTTTTGAAAAGATGCCACTGACTTGTGGGCTTTTTGAAGG
2591645 TTGCCACTGACTTGTGGGCTTTG
64 TTGCCACTGACTTGTGGGCTTTG
2591668 AGAATG-TGCCACTAACTTGTGGGCTTTTGAAAAGATGCCACTGACTTGTGGGCTTTTTGAAGGT
1 AGAA-GATGCCACTAACTTGTGGGCTTTTGAAAAGATGCCACTGACTTGTGGGCTTTTTGAAGGT
2591732 TGCCACTGACTTGTGGGCTTTG
65 TGCCACTGACTTGTGGGCTTTG
** * *
2591754 AGAAGATGTTACTAACTTGTGGGCTTTTGAAAAGATGCCACTGACTTGTAGGCTTTTTAAAGGTT
1 AGAAGATGCCACTAACTTGTGGGCTTTTGAAAAGATGCCACTGACTTGTGGGCTTTTTGAAGGTT
** *
2591819 GCCACTGACTTGTGGATTTTC
66 GCCACTGACTTGTGGGCTTTG
* *
2591840 AGAAGATGCCACTGACTTGTGGGCTTTTGAAAAGATGCCATTGACTTGTGGGCTTT
1 AGAAGATGCCACTAACTTGTGGGCTTTTGAAAAGATGCCACTGACTTGTGGGCTTT
2591896 GAAAAGTGAG
Statistics
Matches: 211, Mismatches: 15, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
85 1 0.00
86 195 0.92
87 1 0.00
88 13 0.06
89 1 0.00
ACGTcount: A:0.22, C:0.16, G:0.28, T:0.34
Consensus pattern (86 bp):
AGAAGATGCCACTAACTTGTGGGCTTTTGAAAAGATGCCACTGACTTGTGGGCTTTTTGAAGGTT
GCCACTGACTTGTGGGCTTTG
Found at i:2613089 original size:18 final size:18
Alignment explanation
Indices: 2613068--2613126 Score: 50
Period size: 18 Copynumber: 3.2 Consensus size: 18
2613058 TTTTTATAAT
2613068 AAATTAATTTAATATATA
1 AAATTAATTTAATATATA
* *
2613086 AAATT-CTTT-ATAAATTAA
1 AAATTAATTTAATATA-T-A
2613104 AAATTAATTATATATATATA
1 AAATTAATT-TA-ATATATA
2613124 AAA
1 AAA
2613127 ATATTAACCA
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
16 4 0.13
17 4 0.13
18 11 0.35
19 2 0.06
20 5 0.16
21 1 0.03
22 4 0.13
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (18 bp):
AAATTAATTTAATATATA
Found at i:2614893 original size:12 final size:12
Alignment explanation
Indices: 2614871--2614902 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
2614861 TAGTGCAGTT
2614871 TAAAA-AATTTA
1 TAAAATAATTTA
2614882 TAAAATAATTTA
1 TAAAATAATTTA
2614894 TAAAATAAT
1 TAAAATAAT
2614903 AATTCAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.25
12 15 0.75
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
TAAAATAATTTA
Found at i:2615251 original size:20 final size:21
Alignment explanation
Indices: 2615204--2615272 Score: 77
Period size: 22 Copynumber: 3.2 Consensus size: 21
2615194 TTTAGCTAGC
* *
2615204 TTATTTTTTAATTATATAATA
1 TTATTTTATATTTATATAATA
2615225 TTAATTTTATATTTATAT-ATA
1 TT-ATTTTATATTTATATAATA
*
2615246 TTATTTAATAAATTTATATAATA
1 TTATTT--TATATTTATATAATA
2615269 TTAT
1 TTAT
2615273 ACTGTAACAT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
20 4 0.10
21 7 0.17
22 23 0.56
23 7 0.17
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TTATTTTATATTTATATAATA
Found at i:2615712 original size:18 final size:18
Alignment explanation
Indices: 2615686--2615734 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
2615676 TTGAAGGTAT
* *
2615686 TAAAAAATATTTTTTTAA
1 TAAATAATAATTTTTTAA
2615704 TAAATAATAATTTTTTAA
1 TAAATAATAATTTTTTAA
2615722 -AAATTAA-AATTTT
1 TAAA-TAATAATTTT
2615735 AACAATAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 9 0.32
18 19 0.68
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TAAATAATAATTTTTTAA
Found at i:2615828 original size:17 final size:17
Alignment explanation
Indices: 2615801--2615835 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2615791 AGATATTTAA
2615801 AAATAATTTTTAATATTT
1 AAATAATTTTTAAT-TTT
2615819 AAAT-ATTTTTAATTTT
1 AAATAATTTTTAATTTT
2615835 A
1 A
2615836 TTTTATTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 9 0.53
18 4 0.24
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
AAATAATTTTTAATTTT
Found at i:2615979 original size:18 final size:19
Alignment explanation
Indices: 2615957--2616008 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 19
2615947 GTGTTTTTAA
2615957 AAAATAAGTAATTTTTGTT
1 AAAATAAGTAATTTTTGTT
* *
2615976 -AAAT-A-TGATTTTTTTT
1 AAAATAAGTAATTTTTGTT
2615992 AATAATAAGTAATTTTT
1 AA-AATAAGTAATTTTT
2616009 TATAATATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 7
0.72 0.08 0.19
Matches are distributed among these distances:
16 9 0.35
17 2 0.08
18 7 0.27
19 1 0.04
20 7 0.27
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (19 bp):
AAAATAAGTAATTTTTGTT
Found at i:2616006 original size:20 final size:20
Alignment explanation
Indices: 2615959--2616015 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
2615949 GTTTTTAAAA
*
2615959 AATAAGTAATTTTTGTT-A-
1 AATAAGTAATTTTTTTTAAT
*
2615977 AAT-A-TGATTTTTTTTAAT
1 AATAAGTAATTTTTTTTAAT
*
2615995 AATAAGTAATTTTTTATAAT
1 AATAAGTAATTTTTTTTAAT
2616015 A
1 A
2616016 TTTATGTATA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
16 9 0.29
17 2 0.06
18 6 0.19
19 1 0.03
20 13 0.42
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (20 bp):
AATAAGTAATTTTTTTTAAT
Found at i:2616072 original size:13 final size:12
Alignment explanation
Indices: 2616048--2616081 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
2616038 AAAAACCAAA
2616048 TATTTTTTATTT
1 TATTTTTTATTT
2616060 TATTTTGTTATTT
1 TATTTT-TTATTT
2616073 TAATTTTTT
1 T-ATTTTTT
2616082 TTAGGAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 6 0.30
13 9 0.45
14 5 0.25
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (12 bp):
TATTTTTTATTT
Found at i:2616329 original size:63 final size:62
Alignment explanation
Indices: 2616270--2616404 Score: 170
Period size: 63 Copynumber: 2.1 Consensus size: 62
2616260 ATAATTAATT
*
2616270 TAATTTTTTTAAAA-ATTACATTCTTATA-TTTTTT-ATTTAAATAAATATTAATTACAATTAAA
1 TAATATTTTTAAAATATTAC--T-TTATACTTTTTTAATTTAAATAAATATTAATTACAATTAAA
*
2616332 TAATATTTTTAAAATATTACTTTATACTTTTTTAAATTTAAATAAATATT-ATGTATAATTAAA
1 TAATATTTTTAAAATATTACTTTATACTTTTTT-AATTTAAATAAATATTAAT-TACAATTAAA
2616395 TAATTATTTT
1 TAA-TATTTT
2616405 CACCTATATT
Statistics
Matches: 65, Mismatches: 2, Indels: 10
0.84 0.03 0.13
Matches are distributed among these distances:
60 5 0.08
61 7 0.11
62 15 0.23
63 32 0.49
64 6 0.09
ACGTcount: A:0.43, C:0.04, G:0.01, T:0.53
Consensus pattern (62 bp):
TAATATTTTTAAAATATTACTTTATACTTTTTTAATTTAAATAAATATTAATTACAATTAAA
Found at i:2616350 original size:21 final size:21
Alignment explanation
Indices: 2616326--2616381 Score: 51
Period size: 21 Copynumber: 2.6 Consensus size: 21
2616316 ATTAATTACA
2616326 ATTAAATAATATTTTTAAAAT
1 ATTAAATAATATTTTTAAAAT
** * *
2616347 ATTACTTTATACTTTTTTAAAT
1 ATTAAATAATA-TTTTTAAAAT
2616369 -TTAAATAAATATT
1 ATTAAAT-AATATT
2616382 ATGTATAATT
Statistics
Matches: 26, Mismatches: 7, Indels: 4
0.70 0.19 0.11
Matches are distributed among these distances:
21 14 0.54
22 12 0.46
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.52
Consensus pattern (21 bp):
ATTAAATAATATTTTTAAAAT
Found at i:2616594 original size:58 final size:58
Alignment explanation
Indices: 2616516--2616628 Score: 172
Period size: 58 Copynumber: 1.9 Consensus size: 58
2616506 ATGTCTGCGT
* * * *
2616516 CTAAAACAGTTGACTAACTGTATACGGTAATAAAAAAATTAGGGCTAATATATTATCC
1 CTAAAACAATTAACCAACTGTATACAGTAATAAAAAAATTAGGGCTAATATATTATCC
* *
2616574 CTAAAACAATTAACCAACTGTATACAGTAATACAAAAATTAGGGTTAATATATTA
1 CTAAAACAATTAACCAACTGTATACAGTAATAAAAAAATTAGGGCTAATATATTA
2616629 ATTATTTTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
58 49 1.00
ACGTcount: A:0.46, C:0.13, G:0.12, T:0.29
Consensus pattern (58 bp):
CTAAAACAATTAACCAACTGTATACAGTAATAAAAAAATTAGGGCTAATATATTATCC
Found at i:2616810 original size:15 final size:14
Alignment explanation
Indices: 2616753--2616822 Score: 65
Period size: 14 Copynumber: 5.1 Consensus size: 14
2616743 AAAATAATAA
* *
2616753 AATATGATTTTATT
1 AATATTATTTTTTT
*
2616767 AATATTATGTTTTT
1 AATATTATTTTTTT
*
2616781 AA-ATTATTTTTAT
1 AATATTATTTTTTT
2616794 -AT-TTATTTTTTT
1 AATATTATTTTTTT
*
2616806 AATATAAATTTTTTT
1 AATAT-TATTTTTTT
2616821 AA
1 AA
2616823 ATGATGATAT
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
12 10 0.22
13 11 0.24
14 14 0.31
15 10 0.22
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (14 bp):
AATATTATTTTTTT
Found at i:2616942 original size:12 final size:13
Alignment explanation
Indices: 2616896--2616944 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 13
2616886 ATTAATATTA
2616896 TTAATTTAAATA-
1 TTAATTTAAATAT
*
2616908 -AAATTTAAATAT
1 TTAATTTAAATAT
*
2616920 TTAATTATAAATTT
1 TTAATT-TAAATAT
2616934 TTAA-TTAAATA
1 TTAATTTAAATA
2616945 CAAAAATATA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
11 10 0.33
12 5 0.17
13 5 0.17
14 10 0.33
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
TTAATTTAAATAT
Found at i:2618194 original size:6 final size:6
Alignment explanation
Indices: 2618185--2618212 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
2618175 AGATACGTAT
2618185 CTACTC CTACTC CTACTC CTACTC CTAC
1 CTACTC CTACTC CTACTC CTACTC CTAC
2618213 AAGGCTTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.50, G:0.00, T:0.32
Consensus pattern (6 bp):
CTACTC
Found at i:2622915 original size:17 final size:17
Alignment explanation
Indices: 2622893--2622927 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
2622883 TAGGCTCTAA
2622893 ACAGAAACCTTTTAGAT
1 ACAGAAACCTTTTAGAT
2622910 ACAGAAACCTTTTAGAT
1 ACAGAAACCTTTTAGAT
2622927 A
1 A
2622928 GAATAATACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.29
Consensus pattern (17 bp):
ACAGAAACCTTTTAGAT
Found at i:2625543 original size:26 final size:26
Alignment explanation
Indices: 2625513--2625562 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
2625503 GTCATAGTCC
2625513 CTTTTGATCTGTGCGTAATCATTTAT
1 CTTTTGATCTGTGCGTAATCATTTAT
2625539 CTTTTGATCTGTGCGTAATCATTT
1 CTTTTGATCTGTGCGTAATCATTT
2625563 GTGTGCTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.18, C:0.16, G:0.16, T:0.50
Consensus pattern (26 bp):
CTTTTGATCTGTGCGTAATCATTTAT
Found at i:2628289 original size:21 final size:21
Alignment explanation
Indices: 2628263--2628303 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
2628253 TGAAGTATCT
2628263 ATGTCCGATACATATTCGAAC
1 ATGTCCGATACATATTCGAAC
2628284 ATGTCCGATACATATTCGAA
1 ATGTCCGATACATATTCGAA
2628304 TATAAATACG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (21 bp):
ATGTCCGATACATATTCGAAC
Found at i:2632134 original size:14 final size:15
Alignment explanation
Indices: 2632117--2632145 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2632107 AAAAACACTT
2632117 AAAAATT-TTTTAAA
1 AAAAATTATTTTAAA
2632131 AAAAATTATTTTAAA
1 AAAAATTATTTTAAA
2632146 TTATAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AAAAATTATTTTAAA
Found at i:2632618 original size:4 final size:4
Alignment explanation
Indices: 2632609--2632633 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2632599 CTTGGTGGCC
2632609 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
2632634 TATGGTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:2632826 original size:2 final size:2
Alignment explanation
Indices: 2632819--2632848 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2632809 ATAATACTTA
2632819 AT 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 AT
2632849 TCAAAGAGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2633215 original size:2 final size:2
Alignment explanation
Indices: 2633171--2633197 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2633161 AAGAGAGCTT
2633171 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 T
2633198 TTTTATGAAG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2634405 original size:18 final size:19
Alignment explanation
Indices: 2634382--2634420 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
2634372 ACTTTTTCTA
2634382 AATTAAAA-TTTCAAAAAT
1 AATTAAAATTTTCAAAAAT
*
2634400 AATTAAAATTTTTAAAAAT
1 AATTAAAATTTTCAAAAAT
2634419 AA
1 AA
2634421 AATATTTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (19 bp):
AATTAAAATTTTCAAAAAT
Found at i:2637439 original size:29 final size:29
Alignment explanation
Indices: 2637391--2637452 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
2637381 CTAAATTATT
*
2637391 TTTTTCTTCTATCTATTTTTCTT-CCTTTG
1 TTTTTCTTCTA-CTATTTTTATTCCCTTTG
2637420 TTTTTCTTCT-CATATCTTTTATTCCCTTTG
1 TTTTTCTTCTAC-TAT-TTTTATTCCCTTTG
2637450 TTT
1 TTT
2637453 AAGTCAGTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
27 1 0.03
28 3 0.10
29 16 0.55
30 9 0.31
ACGTcount: A:0.08, C:0.21, G:0.03, T:0.68
Consensus pattern (29 bp):
TTTTTCTTCTACTATTTTTATTCCCTTTG
Found at i:2637764 original size:2 final size:2
Alignment explanation
Indices: 2637757--2637799 Score: 61
Period size: 2 Copynumber: 21.5 Consensus size: 2
2637747 ATCAATTACA
*
2637757 AT AT AT AT AT AT AT AT -T CAT AT AT AT AT AT AT AT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT
2637799 A
1 A
2637800 GTTTTACTAC
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
1 1 0.03
2 35 0.95
3 1 0.03
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2637839 original size:2 final size:2
Alignment explanation
Indices: 2637832--2637863 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2637822 ACTCTAAATA
*
2637832 AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2637864 TACATAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2638174 original size:16 final size:16
Alignment explanation
Indices: 2638149--2638185 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
2638139 TTTTAAATGA
2638149 TATTTAAAAT-ATTTT
1 TATTTAAAATCATTTT
2638164 TATTGTAAAATCATTTT
1 TATT-TAAAATCATTTT
2638181 TATTT
1 TATTT
2638186 TTTAATTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 4 0.20
16 7 0.35
17 9 0.45
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (16 bp):
TATTTAAAATCATTTT
Found at i:2649614 original size:30 final size:30
Alignment explanation
Indices: 2649504--2649606 Score: 102
Period size: 30 Copynumber: 3.4 Consensus size: 30
2649494 TTAATTTAAA
* * *
2649504 TCTCTTAAATT-AAGAACTAATGCACCATTAT
1 TCTCTTAAATTAAAG-ATTAATGCATCACT-T
*
2649535 TCT-TTAAATTAAAGATTAATGCATCACTA
1 TCTCTTAAATTAAAGATTAATGCATCACTT
* * * *
2649564 TCCCTTAGATTAAAGATTAGTACATCACTT
1 TCTCTTAAATTAAAGATTAATGCATCACTT
2649594 TCTCTTAAATTAA
1 TCTCTTAAATTAA
2649607 GAATTAGTGC
Statistics
Matches: 59, Mismatches: 11, Indels: 5
0.79 0.15 0.07
Matches are distributed among these distances:
29 2 0.03
30 51 0.86
31 6 0.10
ACGTcount: A:0.38, C:0.17, G:0.07, T:0.38
Consensus pattern (30 bp):
TCTCTTAAATTAAAGATTAATGCATCACTT
Found at i:2650893 original size:3 final size:3
Alignment explanation
Indices: 2650885--2650909 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2650875 ACAAAATTGG
2650885 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
2650910 TGCTGCTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2661863 original size:13 final size:13
Alignment explanation
Indices: 2661847--2661872 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2661837 AAGGAAGTGA
2661847 AATATTATTTACT
1 AATATTATTTACT
2661860 AATATTATTTACT
1 AATATTATTTACT
2661873 TTCCTTTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (13 bp):
AATATTATTTACT
Found at i:2662361 original size:22 final size:22
Alignment explanation
Indices: 2662336--2662377 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
2662326 AATTTTTATT
2662336 TAAAT-TTAATTATAAAAATATA
1 TAAATATTAA-TATAAAAATATA
2662358 TAAATATTAATATAAAAATA
1 TAAATATTAATATAAAAATA
2662378 ATTTTTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAATATTAATATAAAAATATA
Found at i:2662986 original size:22 final size:24
Alignment explanation
Indices: 2662943--2662987 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
2662933 TTTATTATAT
2662943 TAAATAAATAAATAACTTTAAAAC
1 TAAATAAATAAATAACTTTAAAAC
*
2662967 TAAA-AAATAATTAA-TTTAAAA
1 TAAATAAATAAATAACTTTAAAA
2662988 TATTTTAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 7 0.35
23 9 0.45
24 4 0.20
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.31
Consensus pattern (24 bp):
TAAATAAATAAATAACTTTAAAAC
Found at i:2663690 original size:23 final size:23
Alignment explanation
Indices: 2663660--2663709 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
2663650 TTATCGAGCC
2663660 TTAAATGCAACAAAACTGTCAAT
1 TTAAATGCAACAAAACTGTCAAT
*** *
2663683 TTAAATGCAGTTAAATTGTCAAT
1 TTAAATGCAACAAAACTGTCAAT
2663706 TTAA
1 TTAA
2663710 TAGAATTACC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.34
Consensus pattern (23 bp):
TTAAATGCAACAAAACTGTCAAT
Found at i:2665844 original size:16 final size:18
Alignment explanation
Indices: 2665823--2665857 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2665813 TTATATCAAT
2665823 TATACA-TA-TAAATATA
1 TATACATTACTAAATATA
2665839 TATACATTACTAAATATA
1 TATACATTACTAAATATA
2665857 T
1 T
2665858 TAAAATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 2 0.12
18 9 0.53
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (18 bp):
TATACATTACTAAATATA
Found at i:2667611 original size:61 final size:62
Alignment explanation
Indices: 2667539--2667662 Score: 160
Period size: 62 Copynumber: 2.0 Consensus size: 62
2667529 TATTATTACA
* ** * ** * *
2667539 ATTTATGTTATATAGTTCAATGGGTAT-TATGGATTATGTTTCTACGATTGACATGTGGTGG
1 ATTTATATTATATAGTTCAATGACTATAAACAGATTATGTATCTACAATTGACATGTGGTGG
*
2667600 ATTTATATTATATAGTTCAATGACTATAAACATATTATGTATCTACAATTGACATGTGGTGG
1 ATTTATATTATATAGTTCAATGACTATAAACAGATTATGTATCTACAATTGACATGTGGTGG
2667662 A
1 A
2667663 AGTAGGAATT
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
61 24 0.45
62 29 0.55
ACGTcount: A:0.31, C:0.08, G:0.19, T:0.42
Consensus pattern (62 bp):
ATTTATATTATATAGTTCAATGACTATAAACAGATTATGTATCTACAATTGACATGTGGTGG
Found at i:2667686 original size:2 final size:2
Alignment explanation
Indices: 2667679--2667795 Score: 189
Period size: 2 Copynumber: 58.5 Consensus size: 2
2667669 AATTCTTGCA
*
2667679 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
2667721 AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
2667763 AT AT AT AT AT AT GT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2667796 ATTGTATTAG
Statistics
Matches: 105, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 105 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2670594 original size:29 final size:29
Alignment explanation
Indices: 2670552--2670642 Score: 173
Period size: 29 Copynumber: 3.1 Consensus size: 29
2670542 CGCGATTGGG
2670552 GATTTCTATGGCATGATGGGAAGTGTGTT
1 GATTTCTATGGCATGATGGGAAGTGTGTT
2670581 GATTTCTATGGCATGATGGGAAGTGTGTT
1 GATTTCTATGGCATGATGGGAAGTGTGTT
*
2670610 GATTTCTATGGCATGATGGAAAGTGTGTT
1 GATTTCTATGGCATGATGGGAAGTGTGTT
2670639 GATT
1 GATT
2670643 AAAAGGGGAA
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 61 1.00
ACGTcount: A:0.22, C:0.07, G:0.33, T:0.38
Consensus pattern (29 bp):
GATTTCTATGGCATGATGGGAAGTGTGTT
Found at i:2673708 original size:52 final size:52
Alignment explanation
Indices: 2673623--2673747 Score: 232
Period size: 52 Copynumber: 2.4 Consensus size: 52
2673613 ATATGAAAAG
* *
2673623 TTGCTTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
2673675 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
2673727 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
2673748 AAGATCAATG
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
Found at i:2673758 original size:52 final size:52
Alignment explanation
Indices: 2673623--2673767 Score: 202
Period size: 52 Copynumber: 2.8 Consensus size: 52
2673613 ATATGAAAAG
* *** *
2673623 TTGCTTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATAAGATAATGTATCGATACATCTGGGCAAAT
***
2673675 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATAAGATAATGTATCGATACATCTGGGCAAAT
2673727 TTGCCTGCATGTATCGATACA-AAGATCAATGTATCGATACA
1 TTGCCTGCATGTATCGATACATAAGAT-AATGTATCGATACA
2673768 ATGTATCGAT
Statistics
Matches: 87, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
51 2 0.02
52 85 0.98
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATAAGATAATGTATCGATACATCTGGGCAAAT
Found at i:2673771 original size:13 final size:13
Alignment explanation
Indices: 2673753--2673780 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2673743 ATACAAAGAT
2673753 CAATGTATCGATA
1 CAATGTATCGATA
2673766 CAATGTATCGATA
1 CAATGTATCGATA
2673779 CA
1 CA
2673781 TTTGAGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:2673848 original size:20 final size:20
Alignment explanation
Indices: 2673819--2673876 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
2673809 ACAGTAGCTT
2673819 AAAT-TGTATCGATACAAAA
1 AAATATGTATCGATACAAAA
*
2673838 AAATATGTATCGATACAACA
1 AAATATGTATCGATACAAAA
***
2673858 CTTTATGTATCGATACAAA
1 AAATATGTATCGATACAAA
2673877 TCGTTGAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
19 4 0.12
20 29 0.88
ACGTcount: A:0.47, C:0.14, G:0.10, T:0.29
Consensus pattern (20 bp):
AAATATGTATCGATACAAAA
Found at i:2674545 original size:187 final size:184
Alignment explanation
Indices: 2674203--2674569 Score: 592
Period size: 185 Copynumber: 2.0 Consensus size: 184
2674193 CCTTTACAAT
* * *
2674203 TAATAATAGTGATCATTTAGAATTCCTTGCACTCCAAAATAGAAATAAAATGATTAACTTCAAAC
1 TAATAATAATGATCATTTAGAATTCCTTGCACTCCAAAATAAAAATAAAATGATTAACTTAAAAC
* **
2674268 AATTCCCCAAATACCAATTTACATCATCAAGCTTAAACTTTTTTTTTTCAAGTTATACCAACTTG
66 AATTCCCCAAACACCAATTTACATCATCAAGCTTAAACTTTTTTTTTTCAAACTATACCAACTTG
*
2674333 ATCAGATAACCTCTTAACACATCAAAATATTAGCTCAACACAAATTACCTGGCAC
131 ATCAAATAACCTCTTAACACATCAAAATATTAGCTCAACACAAA-TACCTGGCAC
2674388 TAATAATAATGATCATTTAGAATTCCTTGCACTCCAAAATAAAAATAAAATGATTAA-TCTAAAA
1 TAATAATAATGATCATTTAGAATTCCTTGCACTCCAAAATAAAAATAAAATGATTAACT-TAAAA
* * *
2674452 CAATTCTCGAAACACCAATTTACATCATCAAGCTTAAACTTTTTTTTTTTCAAAACTATACCAAT
65 CAATTCCCCAAACACCAATTTACATCATCAAGCTTAAAC-TTTTTTTTTTC-AAACTATACCAAC
*
2674517 TTGATCAAATAACCTTTTAACACATCAAAATATTAGCTCAACACAAATACCTG
128 TTGATCAAATAACCTCTTAACACATCAAAATATTAGCTCAACACAAATACCTG
2674570 ATTGAAACTC
Statistics
Matches: 168, Mismatches: 11, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
184 1 0.01
185 95 0.57
186 17 0.10
187 55 0.33
ACGTcount: A:0.42, C:0.20, G:0.06, T:0.32
Consensus pattern (184 bp):
TAATAATAATGATCATTTAGAATTCCTTGCACTCCAAAATAAAAATAAAATGATTAACTTAAAAC
AATTCCCCAAACACCAATTTACATCATCAAGCTTAAACTTTTTTTTTTCAAACTATACCAACTTG
ATCAAATAACCTCTTAACACATCAAAATATTAGCTCAACACAAATACCTGGCAC
Found at i:2676039 original size:38 final size:36
Alignment explanation
Indices: 2675988--2676103 Score: 106
Period size: 38 Copynumber: 3.1 Consensus size: 36
2675978 GGTTAGAACG
* *
2675988 AAATCCATCATTCTCAACCAATAACACAGTTCGAAACA
1 AAATCCAT-ATTCTTAACCAATAGCACAGTT-GAAACA
* * * **
2676026 AAATCCACTATTCTTAATCGATAGGATTGCTTGAAACA
1 AAATCCA-TATTCTTAACCAATAGCACAG-TTGAAACA
* *
2676064 AAATCCATATTTTTAACCAATAGCACAATTTGAAACA
1 AAATCCATATTCTTAACCAATAGCAC-AGTTGAAACA
2676101 AAA
1 AAA
2676104 ATCACTATTC
Statistics
Matches: 61, Mismatches: 14, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
37 25 0.41
38 33 0.54
39 3 0.05
ACGTcount: A:0.44, C:0.22, G:0.08, T:0.27
Consensus pattern (36 bp):
AAATCCATATTCTTAACCAATAGCACAGTTGAAACA
Found at i:2676137 original size:75 final size:76
Alignment explanation
Indices: 2675988--2676140 Score: 179
Period size: 75 Copynumber: 2.0 Consensus size: 76
2675978 GGTTAGAACG
* * *
2675988 AAATCCATCATTCTCAACCAATAACACAGTTCGAAACAAAATCCACTATTCTTAATCGATAGGAT
1 AAATCCATCATTCTCAACCAATAACACAATTCGAAACAAAATCCACTATTCTAAACCGATAGGAT
*
2676053 TGCTTGAAACA
66 TGATTGAAACA
* * * *
2676064 AAATCCAT-ATTTTTAACCAATAGCACAATTTGAAACAAAAAT-CACTATTCTAAACCGAT-GGC
1 AAATCCATCATTCTCAACCAATAACACAATTCGAAAC-AAAATCCACTATTCTAAACCGATAGG-
2676126 A-TGATTCGAAACA
64 ATTGATT-GAAACA
2676139 AA
1 AA
2676141 GACTACTATT
Statistics
Matches: 66, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
74 6 0.09
75 47 0.71
76 13 0.20
ACGTcount: A:0.43, C:0.22, G:0.09, T:0.26
Consensus pattern (76 bp):
AAATCCATCATTCTCAACCAATAACACAATTCGAAACAAAATCCACTATTCTAAACCGATAGGAT
TGATTGAAACA
Found at i:2679611 original size:26 final size:24
Alignment explanation
Indices: 2679587--2679631 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
2679577 AATTATATAT
2679587 TATA-TAT-TAATTTTATATTTTTA
1 TATATTATGTAATTTT-TATTTTTA
2679610 TATATTATGTAATTTTTATTTT
1 TATATTATGTAATTTTTATTTT
2679632 ATTAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 4 0.20
24 9 0.45
25 7 0.35
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (24 bp):
TATATTATGTAATTTTTATTTTTA
Found at i:2684043 original size:2 final size:2
Alignment explanation
Indices: 2684036--2684074 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
2684026 TGAACAAGAC
2684036 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2684075 TTTTTGTTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2690489 original size:19 final size:19
Alignment explanation
Indices: 2690465--2690523 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 19
2690455 ATTTAAAAAT
2690465 AATATATAAATTAATTTTA
1 AATATATAAATTAATTTTA
* * ** *
2690484 AATATATTATTTAAAATAA
1 AATATATAAATTAATTTTA
* *
2690503 AATAAATAAATTTATTTTA
1 AATATATAAATTAATTTTA
2690522 AA
1 AA
2690524 ATTTATTATA
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
AATATATAAATTAATTTTA
Found at i:2690542 original size:39 final size:38
Alignment explanation
Indices: 2690455--2690532 Score: 104
Period size: 38 Copynumber: 2.1 Consensus size: 38
2690445 TTTTAAATCG
* *
2690455 ATTTAAAA-ATAATATATAAATTAATTTTAAATATATT
1 ATTTAAAATAAAATAAATAAATTAATTTTAAATATATT
* *
2690492 ATTTAAAATAAAATAAATAAATTTATTTTAAAATTTATT
1 ATTTAAAATAAAATAAATAAATTAATTTT-AAATATATT
2690531 AT
1 AT
2690533 AACTAATAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 8 0.23
38 17 0.49
39 10 0.29
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (38 bp):
ATTTAAAATAAAATAAATAAATTAATTTTAAATATATT
Found at i:2690745 original size:18 final size:18
Alignment explanation
Indices: 2690718--2690753 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
2690708 ATACATCATT
2690718 TAAAAATTAAATA-AAAA
1 TAAAAATTAAATATAAAA
2690735 TAAAAATTTAAATATAAAA
1 TAAAAA-TTAAATATAAAA
2690754 AATCTAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 7 0.41
19 4 0.24
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (18 bp):
TAAAAATTAAATATAAAA
Found at i:2691127 original size:19 final size:18
Alignment explanation
Indices: 2691095--2691138 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 18
2691085 AAATTAATAT
*
2691095 TAAAATATATAATTTAAAAA
1 TAAAA-ATAAAATTT-AAAA
2691115 TAAAAATAAAATTTAAAA
1 TAAAAATAAAATTTAAAA
2691133 TAAAAA
1 TAAAAA
2691139 ATACAAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 10 0.43
19 8 0.35
20 5 0.22
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (18 bp):
TAAAAATAAAATTTAAAA
Found at i:2691139 original size:19 final size:19
Alignment explanation
Indices: 2691095--2691141 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
2691085 AAATTAATAT
* *
2691095 TAAAATATATAATTTAAAA
1 TAAAAAATAAAATTTAAAA
2691114 -ATAAAAATAAAATTTAAAA
1 TA-AAAAATAAAATTTAAAA
2691133 TAAAAAATA
1 TAAAAAATA
2691142 CAAAATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 1 0.04
19 22 0.92
20 1 0.04
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
TAAAAAATAAAATTTAAAA
Found at i:2691341 original size:14 final size:15
Alignment explanation
Indices: 2691322--2691355 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
2691312 TATCACATAA
2691322 ATTTAAATTA-AATT
1 ATTTAAATTATAATT
*
2691336 ATTTAAATTATTATT
1 ATTTAAATTATAATT
2691351 ATTTA
1 ATTTA
2691356 TTTAAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
ATTTAAATTATAATT
Found at i:2691371 original size:19 final size:18
Alignment explanation
Indices: 2691333--2691384 Score: 54
Period size: 19 Copynumber: 2.9 Consensus size: 18
2691323 TTTAAATTAA
*
2691333 ATTATTTAAAT-TATTATT
1 ATTATTTAAATAT-TTTTT
2691351 ATTTATTTAAATATTTTTT
1 A-TTATTTAAATATTTTTT
*
2691370 ATAATTTAAA-ATTTT
1 ATTATTTAAATATTTT
2691385 ATGTAATTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
17 5 0.17
18 9 0.30
19 15 0.50
20 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
ATTATTTAAATATTTTTT
Found at i:2691391 original size:17 final size:18
Alignment explanation
Indices: 2691336--2691396 Score: 56
Period size: 17 Copynumber: 3.4 Consensus size: 18
2691326 AAATTAAATT
*
2691336 ATTTAAATTATTATTAT-TT
1 ATTTAAA-TATT-TTATATA
*
2691355 ATTTAAATATTTTTTATA
1 ATTTAAATATTTTATATA
*
2691373 ATTTAAA-ATTTTATGTA
1 ATTTAAATATTTTATATA
2691390 A-TTAAAT
1 ATTTAAAT
2691397 TCGAAGTTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
16 5 0.14
17 12 0.33
18 12 0.33
19 7 0.19
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (18 bp):
ATTTAAATATTTTATATA
Found at i:2692363 original size:52 final size:49
Alignment explanation
Indices: 2692267--2692377 Score: 116
Period size: 52 Copynumber: 2.2 Consensus size: 49
2692257 TCTAATACTT
* * * * **
2692267 TAAATATATAAAAAATAACATGTATATAATATTAAAAATTAATTA-AAA
1 TAAATATAAAAAAAATAACATGAATATAAAAATAAAAAAAAATTATAAA
2692315 TAAAATATAAAAATAAATATGACATGAATATAAAAATAAAAAAAAATTATAAA
1 T-AAATATAAAAA-AAATA--ACATGAATATAAAAATAAAAAAAAATTATAAA
*
2692368 TATATATAAA
1 TAAATATAAA
2692378 TTTATAATAT
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
48 1 0.02
49 10 0.20
50 5 0.10
52 31 0.61
53 4 0.08
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.30
Consensus pattern (49 bp):
TAAATATAAAAAAAATAACATGAATATAAAAATAAAAAAAAATTATAAA
Found at i:2692439 original size:23 final size:23
Alignment explanation
Indices: 2692389--2692431 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
2692379 TTATAATATT
*
2692389 TTAAGTAATAAAAATTATAAACA
1 TTAAATAATAAAAATTATAAACA
*
2692412 ATAAATAATAAAAA-TATAAA
1 TTAAATAATAAAAATTATAAA
2692432 TACTTAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (23 bp):
TTAAATAATAAAAATTATAAACA
Found at i:2693610 original size:12 final size:12
Alignment explanation
Indices: 2693593--2693635 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
2693583 ATAATTAGTG
2693593 TATATAAATTTA
1 TATATAAATTTA
2693605 TATATAAATTTA
1 TATATAAATTTA
*
2693617 TA-AT-AATTAAA
1 TATATAAATT-TA
2693628 TATATAAA
1 TATATAAA
2693636 AAAATAATAC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
10 4 0.15
11 5 0.19
12 16 0.59
13 2 0.07
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TATATAAATTTA
Found at i:2694249 original size:23 final size:23
Alignment explanation
Indices: 2694201--2694250 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
2694191 CAACATAAAT
*
2694201 AAAAATAATTAAAATACAACATA
1 AAAAATAATTAAAATACAACACA
**
2694224 AAAAATAA-TATAAATATGACACA
1 AAAAATAATTA-AAATACAACACA
2694247 AAAA
1 AAAA
2694251 CATGAACTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 2 0.09
23 21 0.91
ACGTcount: A:0.70, C:0.08, G:0.02, T:0.20
Consensus pattern (23 bp):
AAAAATAATTAAAATACAACACA
Found at i:2694507 original size:15 final size:15
Alignment explanation
Indices: 2694487--2694515 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2694477 TATATAATAT
2694487 TTTTTCTTTTTTTTA
1 TTTTTCTTTTTTTTA
2694502 TTTTTCTTTTTTTT
1 TTTTTCTTTTTTTT
2694516 CCTCCTTCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.03, C:0.07, G:0.00, T:0.90
Consensus pattern (15 bp):
TTTTTCTTTTTTTTA
Found at i:2695583 original size:44 final size:44
Alignment explanation
Indices: 2695496--2695584 Score: 108
Period size: 44 Copynumber: 2.0 Consensus size: 44
2695486 TCCCATCTTG
* ** * *
2695496 AGAAAATTCAGGGGTGAGACTTCAGTCTTCAGGAATGGCTTATC
1 AGAAAATTCAAGAATGAGACTTCAGTCTTCAGGAACGGATTATC
*
2695540 AGAAAATTCAAGAATGAGAGTTCAGTCTTCAAGG-ACGGATTATC
1 AGAAAATTCAAGAATGAGACTTCAGTCTTC-AGGAACGGATTATC
2695584 A
1 A
2695585 TATTTTTGGT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
44 35 0.92
45 3 0.08
ACGTcount: A:0.35, C:0.15, G:0.25, T:0.26
Consensus pattern (44 bp):
AGAAAATTCAAGAATGAGACTTCAGTCTTCAGGAACGGATTATC
Found at i:2696192 original size:5 final size:6
Alignment explanation
Indices: 2696177--2696202 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2696167 TATGTGAGAA
2696177 AAAAAT AAAAAT AAAAAT AAAAAT AA
1 AAAAAT AAAAAT AAAAAT AAAAAT AA
2696203 GGTCGTGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:2698258 original size:24 final size:24
Alignment explanation
Indices: 2698231--2698276 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
2698221 AGAATAAAAA
*
2698231 TTTAAATACTAAATTAATAATTTT
1 TTTAAATACTAAATTAAAAATTTT
2698255 TTTAAATACTAAATTAAAAATT
1 TTTAAATACTAAATTAAAAATT
2698277 AAACTAAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (24 bp):
TTTAAATACTAAATTAAAAATTTT
Found at i:2698284 original size:24 final size:24
Alignment explanation
Indices: 2698233--2698284 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
2698223 AATAAAAATT
* ****
2698233 TAAATACTAAATTAATAATTTTTT
1 TAAATACTAAATTAAAAATTAAAC
2698257 TAAATACTAAATTAAAAATTAAAC
1 TAAATACTAAATTAAAAATTAAAC
2698281 TAAA
1 TAAA
2698285 GTATAGAGAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (24 bp):
TAAATACTAAATTAAAAATTAAAC
Done.