Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 103066607
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: 103066607
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 238 characters in sequence are not A, C, G, or T
File 4 of 345
Found at i:1210379 original size:21 final size:22
Alignment explanation
Indices: 1210339--1210381 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1210329 AAATTAATAG
*
1210339 TACATATTTAAAATTTTATAAA
1 TACATATTTAAAATTCTATAAA
*
1210361 TACATA-TTAAAGTTCTATAAA
1 TACATATTTAAAATTCTATAAA
1210382 AATTATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (22 bp):
TACATATTTAAAATTCTATAAA
Found at i:1211336 original size:17 final size:18
Alignment explanation
Indices: 1211307--1211340 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
1211297 GAATTAATGC
1211307 AATAATATTTTAATTAAA
1 AATAATATTTTAATTAAA
1211325 AATAAT-TTTTAATTAA
1 AATAATATTTTAATTAA
1211341 TTAACCTAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AATAATATTTTAATTAAA
Found at i:1212067 original size:28 final size:29
Alignment explanation
Indices: 1212009--1212071 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 29
1211999 TTTATGATTT
* *
1212009 TTTTTATATCTTTTATAAGTTAATATCAA
1 TTTTAATATCTTTTATAAGTTAATATAAA
*
1212038 TTTTAATAT-TTTTATAA-TTATTTATAAA
1 TTTTAATATCTTTTATAAGTTA-ATATAAA
1212066 TTTTAA
1 TTTTAA
1212072 GAATTCTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
27 3 0.10
28 19 0.63
29 8 0.27
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.59
Consensus pattern (29 bp):
TTTTAATATCTTTTATAAGTTAATATAAA
Found at i:1212129 original size:9 final size:9
Alignment explanation
Indices: 1212128--1212302 Score: 99
Period size: 9 Copynumber: 19.0 Consensus size: 9
1212118 TTTATAATTT
*
1212128 TTTTTGTAA
1 TTTTTATAA
*
1212137 TTTATTAGAA
1 TTT-TTATAA
1212147 TTTATTAT-A
1 TTT-TTATAA
* *
1212156 TATTATATAG
1 T-TTTTATAA
1212166 T-TTTATAA
1 TTTTTATAA
*
1212174 TATTTATAA
1 TTTTTATAA
*
1212183 GTTTTTATAT
1 -TTTTTATAA
1212193 TTTTTATAA
1 TTTTTATAA
* *
1212202 TTTTAAAAA
1 TTTTTATAA
1212211 TTTTATATTAA
1 TTTT-TA-TAA
*
1212222 TTTTAATAA
1 TTTTTATAA
*
1212231 TTTTAATAA
1 TTTTTATAA
1212240 -TTTT-TAA
1 TTTTTATAA
*
1212247 TTTATA-AA
1 TTTTTATAA
* *
1212255 TCTTTTTTGA
1 T-TTTTATAA
*
1212265 TCTTTTATAT
1 T-TTTTATAA
*
1212275 TTTTTATGA
1 TTTTTATAA
1212284 TTTTTAATAA
1 TTTTT-ATAA
1212294 TTTTTATAA
1 TTTTTATAA
1212303 AAAAATATTA
Statistics
Matches: 128, Mismatches: 26, Indels: 24
0.72 0.15 0.13
Matches are distributed among these distances:
7 3 0.02
8 15 0.12
9 64 0.50
10 40 0.31
11 6 0.05
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.61
Consensus pattern (9 bp):
TTTTTATAA
Found at i:1212188 original size:19 final size:19
Alignment explanation
Indices: 1212147--1212205 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
1212137 TTTATTAGAA
*
1212147 TTTATTATATATTATATAG-T
1 TTTATAATAT-TTATA-AGTT
1212167 TTTATAATATTTATAAGTT
1 TTTATAATATTTATAAGTT
* *
1212186 TTTATATTTTTTATAA-TT
1 TTTATAATATTTATAAGTT
1212204 TT
1 TT
1212206 AAAAATTTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
18 6 0.17
19 20 0.57
20 9 0.26
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.64
Consensus pattern (19 bp):
TTTATAATATTTATAAGTT
Found at i:1212190 original size:29 final size:27
Alignment explanation
Indices: 1212114--1212245 Score: 79
Period size: 29 Copynumber: 4.6 Consensus size: 27
1212104 AAGTTCTTAT
* *
1212114 TAATTTTATAATTTTTTTTGTAA-TTTA
1 TAATTTTATAA-TTTTTATATAATTTTA
* * * *
1212141 TTAGAATTTATTATATATTATATAGTTTTA
1 -TA-ATTTTATAAT-TTTTATATAATTTTA
* *
1212171 TAATATTTATAAGTTTT-TATATTTTTTA
1 TAAT-TTTATAATTTTTATATA-ATTTTA
* *
1212199 TAATTTTAAAAATTTTATATTAATTTTAA
1 TAATTTTATAATTTTTATA-TAATTTT-A
1212228 TAATTTTAATAATTTTTA
1 TAATTTT-ATAATTTTTA
1212246 ATTTATAAAT
Statistics
Matches: 79, Mismatches: 16, Indels: 16
0.71 0.14 0.14
Matches are distributed among these distances:
27 14 0.18
28 22 0.28
29 31 0.39
30 12 0.15
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (27 bp):
TAATTTTATAATTTTTATATAATTTTA
Found at i:1212224 original size:20 final size:18
Alignment explanation
Indices: 1212193--1212243 Score: 66
Period size: 20 Copynumber: 2.7 Consensus size: 18
1212183 GTTTTTATAT
*
1212193 TTTTTATAATTTTAAAAA
1 TTTTAATAATTTTAAAAA
*
1212211 TTTTATATTAATTTTAATAA
1 TTTTA-A-TAATTTTAAAAA
1212231 TTTTAATAATTTT
1 TTTTAATAATTTT
1212244 TAATTTATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 11 0.38
19 2 0.07
20 16 0.55
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTTAATAATTTTAAAAA
Found at i:1212297 original size:19 final size:17
Alignment explanation
Indices: 1212166--1212301 Score: 78
Period size: 19 Copynumber: 7.4 Consensus size: 17
1212156 TATTATATAG
*
1212166 TTTTATAATATTTATAAGT
1 TTTTAT-ATTTTTATAA-T
1212185 TTTTATATTTTTTATAAT
1 TTTTATA-TTTTTATAAT
* *
1212203 TTTAAAAATTTTATATTAAT
1 TTT-TATATTTT-TA-TAAT
* *
1212223 TTTAATAATTTTAATAAT
1 TTTTAT-ATTTTTATAAT
*
1212241 TTTTA-ATTTATA-AAT
1 TTTTATATTTTTATAAT
* *
1212256 CTTTTTTGATCTTTTATATT
1 -TTTTAT-AT-TTTTATAAT
1212276 TTTTATGATTTTTAATAAT
1 TTTTAT-ATTTTT-ATAAT
1212295 TTTTATA
1 TTTTATA
1212302 AAAAAATATT
Statistics
Matches: 93, Mismatches: 13, Indels: 23
0.72 0.10 0.18
Matches are distributed among these distances:
15 3 0.03
16 9 0.10
18 24 0.26
19 43 0.46
20 14 0.15
ACGTcount: A:0.34, C:0.01, G:0.02, T:0.62
Consensus pattern (17 bp):
TTTTATATTTTTATAAT
Found at i:1213332 original size:3 final size:3
Alignment explanation
Indices: 1213324--1213364 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
1213314 TACCTACACA
1213324 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1213365 GGTAAATATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1214542 original size:14 final size:15
Alignment explanation
Indices: 1214512--1214550 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
1214502 TATAAATCAG
*
1214512 TATATAATAACTATT
1 TATATAATAAATATT
1214527 TATATAA-AAATATT
1 TATATAATAAATATT
*
1214541 TAAATAATAA
1 TATATAATAA
1214551 TTATATCTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (15 bp):
TATATAATAAATATT
Found at i:1215105 original size:65 final size:65
Alignment explanation
Indices: 1215034--1215164 Score: 262
Period size: 65 Copynumber: 2.0 Consensus size: 65
1215024 TTTATAGTAG
1215034 GTTTTTTTAGGCAAATGGGGTTTCAAAGTAAAGAATCAAGCTTACAAGCCGAGAATACAGTGGAT
1 GTTTTTTTAGGCAAATGGGGTTTCAAAGTAAAGAATCAAGCTTACAAGCCGAGAATACAGTGGAT
1215099 GTTTTTTTAGGCAAATGGGGTTTCAAAGTAAAGAATCAAGCTTACAAGCCGAGAATACAGTGGAT
1 GTTTTTTTAGGCAAATGGGGTTTCAAAGTAAAGAATCAAGCTTACAAGCCGAGAATACAGTGGAT
1215164 G
1 G
1215165 ATGATGATGA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 66 1.00
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.27
Consensus pattern (65 bp):
GTTTTTTTAGGCAAATGGGGTTTCAAAGTAAAGAATCAAGCTTACAAGCCGAGAATACAGTGGAT
Found at i:1215169 original size:3 final size:3
Alignment explanation
Indices: 1215161--1215206 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
1215151 GAATACAGTG
1215161 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
1215207 TAATGGAGGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.35, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:1215525 original size:18 final size:18
Alignment explanation
Indices: 1215502--1215536 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1215492 AATTCCTTCG
1215502 GCCACCAAACTATTACGT
1 GCCACCAAACTATTACGT
1215520 GCCACCAAACTATTACG
1 GCCACCAAACTATTACG
1215537 CGAATATTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.34, G:0.11, T:0.20
Consensus pattern (18 bp):
GCCACCAAACTATTACGT
Found at i:1217908 original size:13 final size:13
Alignment explanation
Indices: 1217890--1217916 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1217880 ACACCTAGGC
1217890 ATGCTCTCTTGTA
1 ATGCTCTCTTGTA
1217903 ATGCTCTCTTGTA
1 ATGCTCTCTTGTA
1217916 A
1 A
1217917 GGCAATAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.19, C:0.22, G:0.15, T:0.44
Consensus pattern (13 bp):
ATGCTCTCTTGTA
Found at i:1221240 original size:24 final size:24
Alignment explanation
Indices: 1221213--1221263 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
1221203 AAATTAGTAT
*
1221213 TTATATATTAAATTAAAGAGTAAA
1 TTATATATTAAATTAAAGAATAAA
*
1221237 TTATATATTAAATTGAAGAATAAA
1 TTATATATTAAATTAAAGAATAAA
1221261 TTA
1 TTA
1221264 ATTTTTTCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (24 bp):
TTATATATTAAATTAAAGAATAAA
Found at i:1227563 original size:18 final size:18
Alignment explanation
Indices: 1227542--1227577 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1227532 TTCAATTAAT
*
1227542 TTTAGTTTTATTTATTTA
1 TTTAGTTTTATTAATTTA
1227560 TTTAGTTTTATTAATTTA
1 TTTAGTTTTATTAATTTA
1227578 AAACAATGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (18 bp):
TTTAGTTTTATTAATTTA
Found at i:1229612 original size:20 final size:21
Alignment explanation
Indices: 1229587--1229629 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
1229577 ATTGCTAGGC
* *
1229587 AAAAAAAATAAAG-GTAAAGA
1 AAAAAAAACAAAGAATAAAGA
1229607 AAAAAAAACAAAGAATAAAGA
1 AAAAAAAACAAAGAATAAAGA
1229628 AA
1 AA
1229630 GAAAGCATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.79, C:0.02, G:0.12, T:0.07
Consensus pattern (21 bp):
AAAAAAAACAAAGAATAAAGA
Found at i:1231730 original size:20 final size:19
Alignment explanation
Indices: 1231689--1231727 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1231679 TTATTATTCT
*
1231689 ATTTATTTATTTTTAAATA
1 ATTTATTTATTTTTAAAAA
1231708 ATTTAATTT-TTTTTAAAAA
1 ATTT-ATTTATTTTTAAAAA
1231727 A
1 A
1231728 ATTAAAACTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
ATTTATTTATTTTTAAAAA
Found at i:1231732 original size:19 final size:20
Alignment explanation
Indices: 1231693--1231732 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
1231683 TATTCTATTT
* *
1231693 ATTTATTTTTAAATAATTTA
1 ATTTATTTTTAAAAAAATTA
1231713 ATTT-TTTTTAAAAAAATTA
1 ATTTATTTTTAAAAAAATTA
1231732 A
1 A
1231733 AACTGTTCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
ATTTATTTTTAAAAAAATTA
Found at i:1246693 original size:29 final size:30
Alignment explanation
Indices: 1246655--1246730 Score: 86
Period size: 29 Copynumber: 2.6 Consensus size: 30
1246645 TTTTTTGAAA
*
1246655 ATTT-AAAATTTAGTCCTTGTAC-TTTAAT
1 ATTTCAAAATTTAGTCCTTCTACTTTTAAT
* *
1246683 -TTTCAAAAATTTAGTCATTCTACTTTTCAT
1 ATTTC-AAAATTTAGTCCTTCTACTTTTAAT
1246713 ATTTCAAAATTTAAGTCC
1 ATTTCAAAATTT-AGTCC
1246731 AAATGTCAAC
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
27 3 0.08
29 16 0.41
30 12 0.31
31 8 0.21
ACGTcount: A:0.33, C:0.14, G:0.05, T:0.47
Consensus pattern (30 bp):
ATTTCAAAATTTAGTCCTTCTACTTTTAAT
Found at i:1247721 original size:25 final size:25
Alignment explanation
Indices: 1247693--1247748 Score: 105
Period size: 24 Copynumber: 2.3 Consensus size: 25
1247683 GATATTTCTA
1247693 TTTAAAAAATAAAAATTTTATATTT
1 TTTAAAAAATAAAAATTTTATATTT
1247718 TTT-AAAAATAAAAATTTTATATTT
1 TTTAAAAAATAAAAATTTTATATTT
1247742 TTTAAAA
1 TTTAAAA
1247749 GATTAGTGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
24 24 0.80
25 6 0.20
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
TTTAAAAAATAAAAATTTTATATTT
Found at i:1248863 original size:3 final size:3
Alignment explanation
Indices: 1248841--1248907 Score: 111
Period size: 3 Copynumber: 23.0 Consensus size: 3
1248831 AATCTTAAAT
*
1248841 TAA T-A TAA AAA TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1248887 TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
1248908 AGTAATAAAG
Statistics
Matches: 60, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
2 4 0.07
3 56 0.93
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:1249109 original size:29 final size:29
Alignment explanation
Indices: 1249059--1249128 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 29
1249049 TTGTGTTAAT
*
1249059 AATTTATG-A-AAATTTGATC-AAATTAA
1 AATTTATGTATAAATTTGATCAAAATCAA
*
1249085 ATTTTTATGTATAAATTT-ATACAAAATCAA
1 A-ATTTATGTATAAATTTGAT-CAAAATCAA
1249115 AATTTATGTATAAA
1 AATTTATGTATAAA
1249129 ATTACACATT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
26 1 0.03
27 6 0.17
28 3 0.08
29 19 0.53
30 7 0.19
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.41
Consensus pattern (29 bp):
AATTTATGTATAAATTTGATCAAAATCAA
Found at i:1249413 original size:13 final size:13
Alignment explanation
Indices: 1249386--1249421 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
1249376 AGTCTGTGAG
1249386 TTTAATTTAATTAA
1 TTTAATTT-ATTAA
1249400 TTTAATTTATTAA
1 TTTAATTTATTAA
*
1249413 TTTTATTTA
1 TTTAATTTA
1249422 GTCCGATCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 13 0.62
14 8 0.38
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTAATTTATTAA
Found at i:1250534 original size:27 final size:26
Alignment explanation
Indices: 1250480--1250532 Score: 83
Period size: 24 Copynumber: 2.1 Consensus size: 26
1250470 GATAATTGTG
1250480 TAAATACTTTAAAAAATAATAATAAA
1 TAAATACTTTAAAAAATAATAATAAA
*
1250506 TAAATA-TTTTAAAAAT-ATAATAAA
1 TAAATACTTTAAAAAATAATAATAAA
1250530 TAA
1 TAA
1250533 TAGAGTTGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 11 0.42
25 9 0.35
26 6 0.23
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (26 bp):
TAAATACTTTAAAAAATAATAATAAA
Found at i:1256606 original size:22 final size:20
Alignment explanation
Indices: 1256566--1256622 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
1256556 AATAGAATTG
1256566 AAATATTAAATAATTTATTT
1 AAATATTAAATAATTTATTT
*
1256586 AAATATTCAATTATATTTA-TT
1 AAATATT-AAATA-ATTTATTT
1256607 --ATATT-AATAATTTATT
1 AAATATTAAATAATTTATT
1256623 ATATGACTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
16 5 0.16
17 4 0.12
19 5 0.16
20 7 0.22
21 6 0.19
22 5 0.16
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (20 bp):
AAATATTAAATAATTTATTT
Found at i:1256621 original size:16 final size:17
Alignment explanation
Indices: 1256568--1256626 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 17
1256558 TAGAATTGAA
1256568 ATATTAAATAATTTATTT
1 ATATTAAATAATTTA-TT
*
1256586 AAATATTCAATTATATTTATT
1 --ATATT-AAATA-ATTTATT
1256607 ATATT-AATAATTTATT
1 ATATTAAATAATTTATT
1256623 ATAT
1 ATAT
1256627 GACTAAATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
16 11 0.31
17 3 0.09
19 5 0.14
20 5 0.14
21 6 0.17
22 5 0.14
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (17 bp):
ATATTAAATAATTTATT
Found at i:1258099 original size:16 final size:17
Alignment explanation
Indices: 1258072--1258104 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1258062 GCGTAATTAC
*
1258072 GAAATATAAATATAAAT
1 GAAATATAAATAAAAAT
1258089 GAAAT-TAAATAAAAAT
1 GAAATATAAATAAAAAT
1258105 AAAACTCCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (17 bp):
GAAATATAAATAAAAAT
Found at i:1270482 original size:115 final size:115
Alignment explanation
Indices: 1270263--1270471 Score: 262
Period size: 115 Copynumber: 1.8 Consensus size: 115
1270253 TCACACATGG
* * * *
1270263 ATAGATTTAATGTTAATAAAGTAGTGCCAACTAATGGCATGCAGCTACTAATCAAATAAATTGCG
1 ATAGATTTAATGTTAATAAAGTAGTGCCAAATAATGGCATACAACTACTAATCAAATAAATTACG
* ***
1270328 AGCATCAAAAAATAATTGTAGATTTTGATATTCGAAAAATTCACATATAA
66 AGCATCAAAAAATAATTGTAAATTCACATATTCGAAAAATTCACATATAA
* * *
1270378 ATAGATTTAATGTTAATAAAGTAGTG-CAATATAATGGGATACAACTATTAATCAAATAAGTTAC
1 ATAGATTTAATGTTAATAAAGTAGTGCCAA-ATAATGGCATACAACTACTAATCAAATAAATTAC
* *
1270442 GAGGA-CAAAAAA-AATTATTAAATTCACATA
65 GAGCATCAAAAAATAATT-GTAAATTCACATA
1270472 ATTTTAAAAA
Statistics
Matches: 79, Mismatches: 13, Indels: 5
0.81 0.13 0.05
Matches are distributed among these distances:
113 4 0.05
114 18 0.23
115 57 0.72
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.30
Consensus pattern (115 bp):
ATAGATTTAATGTTAATAAAGTAGTGCCAAATAATGGCATACAACTACTAATCAAATAAATTACG
AGCATCAAAAAATAATTGTAAATTCACATATTCGAAAAATTCACATATAA
Found at i:1276128 original size:22 final size:23
Alignment explanation
Indices: 1276069--1276119 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
1276059 CATAACAGCC
1276069 AAGTAACTTAAATAAAAAATTTT
1 AAGTAACTTAAATAAAAAATTTT
1276092 AAGTAACTTAAATAAAAAATTTT
1 AAGTAACTTAAATAAAAAATTTT
1276115 AAGTA
1 AAGTA
1276120 GTTGAATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.57, C:0.04, G:0.06, T:0.33
Consensus pattern (23 bp):
AAGTAACTTAAATAAAAAATTTT
Found at i:1288020 original size:44 final size:44
Alignment explanation
Indices: 1287934--1288021 Score: 158
Period size: 45 Copynumber: 2.0 Consensus size: 44
1287924 TCTAATTCAA
*
1287934 TCAACTTGATTGGTTCAATTGCTATACAACAAGAATTAAAAAAG
1 TCAACTTGATTGGTTCAATTACTATACAACAAGAATTAAAAAAG
1287978 TCAACTTGATTGGTTCAAATTACTATACAACAAGAATTAAAAAA
1 TCAACTTGATTGGTTC-AATTACTATACAACAAGAATTAAAAAA
1288022 ATAATTAAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
44 16 0.38
45 26 0.62
ACGTcount: A:0.45, C:0.14, G:0.11, T:0.30
Consensus pattern (44 bp):
TCAACTTGATTGGTTCAATTACTATACAACAAGAATTAAAAAAG
Found at i:1290454 original size:27 final size:26
Alignment explanation
Indices: 1290424--1290485 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
1290414 AGATAATTAA
1290424 AATAAAATCCTAAAT-TTAAATAATCCT
1 AATAAAAT-CTAAATATT-AATAATCCT
* * *
1290451 AATAATTATCTTAATATTAATTATCCT
1 AATAA-AATCTAAATATTAATAATCCT
1290478 AATAAAAT
1 AATAAAAT
1290486 AAAATAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
26 2 0.07
27 23 0.79
28 4 0.14
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (26 bp):
AATAAAATCTAAATATTAATAATCCT
Found at i:1291075 original size:12 final size:12
Alignment explanation
Indices: 1291052--1291086 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
1291042 TTTATTAGTA
1291052 CTTATT-TTTTT
1 CTTATTCTTTTT
*
1291063 CTTCTTCTTTTT
1 CTTATTCTTTTT
1291075 CTTATTCTTTTT
1 CTTATTCTTTTT
1291087 TTGATTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 5 0.24
12 16 0.76
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.77
Consensus pattern (12 bp):
CTTATTCTTTTT
Found at i:1291365 original size:118 final size:118
Alignment explanation
Indices: 1291227--1291439 Score: 345
Period size: 118 Copynumber: 1.8 Consensus size: 118
1291217 ATTTACCCAA
1291227 CACGTCACACAACCTCTTGACACAAAGTAGAATGACAACCCAAGCACCCTACCCCGGTTACTAAG
1 CACGTCACACAACCTCTTGACACAAAGTAGAATGACAACCCAAGCACCCTACCCCGGTTACTAAG
* *
1291292 TCAGTCACGATTTGAGCCATACTCATAACCTCGGCTAGCGGAGTTTTACTTGT
66 TCAGTCACGATCTAAGCCATACTCATAACCTCGGCTAGCGGAGTTTTACTTGT
* * * * *
1291345 CACGTCACACAACCTTTTGACGCGAAGTAGAATGACAACCCAAGCACCCTACCCTGGTTACTCAG
1 CACGTCACACAACCTCTTGACACAAAGTAGAATGACAACCCAAGCACCCTACCCCGGTTACTAAG
**
1291410 TCAGTCACGATCTAAGCTGTACTCATAACC
66 TCAGTCACGATCTAAGCCATACTCATAACC
1291440 ATGAAAAGCT
Statistics
Matches: 86, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
118 86 1.00
ACGTcount: A:0.30, C:0.31, G:0.16, T:0.22
Consensus pattern (118 bp):
CACGTCACACAACCTCTTGACACAAAGTAGAATGACAACCCAAGCACCCTACCCCGGTTACTAAG
TCAGTCACGATCTAAGCCATACTCATAACCTCGGCTAGCGGAGTTTTACTTGT
Found at i:1292269 original size:42 final size:42
Alignment explanation
Indices: 1292218--1292321 Score: 156
Period size: 42 Copynumber: 2.5 Consensus size: 42
1292208 GGGGATTTTA
* *
1292218 GGGCTGGAATATG-ACTGTTTGGCTGTAGAGATATGGCATTCT
1 GGGCTGGAATA-GAACTGTTTGGCAGCAGAGATATGGCATTCT
* *
1292260 GGGCTGGAATAGAACTGTTTGGCAGCAGTGATATGGCATTTT
1 GGGCTGGAATAGAACTGTTTGGCAGCAGAGATATGGCATTCT
1292302 GGGCTGGAATAGAACTGTTT
1 GGGCTGGAATAGAACTGTTT
1292322 CGTACCATGG
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
41 1 0.02
42 56 0.98
ACGTcount: A:0.23, C:0.12, G:0.34, T:0.32
Consensus pattern (42 bp):
GGGCTGGAATAGAACTGTTTGGCAGCAGAGATATGGCATTCT
Found at i:1292446 original size:10 final size:9
Alignment explanation
Indices: 1292434--1292503 Score: 68
Period size: 10 Copynumber: 7.1 Consensus size: 9
1292424 ATATTTAACT
1292434 AAAATAAAA
1 AAAATAAAA
1292443 TAAAATAATAA
1 -AAAATAA-AA
*
1292454 ATAATAAAA
1 AAAATAAAA
1292463 GAAAATAAAGA
1 -AAAATAAA-A
1292474 AAAATAATAA
1 AAAATAA-AA
*
1292484 ATAATAAATA
1 AAAATAAA-A
1292494 AAAATAAAA
1 AAAATAAAA
1292503 A
1 A
1292504 GAAAGATTGG
Statistics
Matches: 51, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
9 5 0.10
10 42 0.82
11 4 0.08
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.19
Consensus pattern (9 bp):
AAAATAAAA
Found at i:1292461 original size:20 final size:19
Alignment explanation
Indices: 1292439--1292502 Score: 64
Period size: 17 Copynumber: 3.5 Consensus size: 19
1292429 TAACTAAAAT
1292439 AAAATAAAATAATAAATAA
1 AAAATAAAATAATAAATAA
*
1292458 TAAAAGAAAATAA-AGAA-AA
1 -AAAATAAAATAATA-AATAA
*
1292477 ATAAT-AAATAATAAAT-A
1 AAAATAAAATAATAAATAA
1292494 AAAATAAAA
1 AAAATAAAA
1292503 AGAAAGATTG
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
17 13 0.36
18 7 0.19
19 3 0.08
20 13 0.36
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (19 bp):
AAAATAAAATAATAAATAA
Found at i:1292468 original size:30 final size:29
Alignment explanation
Indices: 1292434--1292503 Score: 106
Period size: 30 Copynumber: 2.3 Consensus size: 29
1292424 ATATTTAACT
1292434 AAAATAAAATAAAATAATAAATAATAAA-A
1 AAAATAAAA-AAAATAATAAATAATAAATA
1292463 GAAAATAAAGAAAAATAATAAATAATAAATA
1 -AAAATAAA-AAAAATAATAAATAATAAATA
1292494 AAAATAAAAA
1 AAAATAAAAA
1292504 GAAAGATTGG
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
29 2 0.05
30 34 0.89
31 2 0.05
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.19
Consensus pattern (29 bp):
AAAATAAAAAAAATAATAAATAATAAATA
Found at i:1296188 original size:27 final size:26
Alignment explanation
Indices: 1296158--1296217 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 26
1296148 AGATAATTAA
1296158 AATAAAATCTTAA-ATTTGAATAATCCT
1 AATAAAATCTTAATA-TT-AATAATCCT
* *
1296185 AATAATTATCTTAATATTAATTATCCT
1 AATAA-AATCTTAATATTAATAATCCT
1296212 AATAAA
1 AATAAA
1296218 TAAAATAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
27 18 0.64
28 9 0.32
29 1 0.04
ACGTcount: A:0.48, C:0.10, G:0.02, T:0.40
Consensus pattern (26 bp):
AATAAAATCTTAATATTAATAATCCT
Found at i:1296748 original size:33 final size:33
Alignment explanation
Indices: 1296688--1296777 Score: 107
Period size: 33 Copynumber: 2.7 Consensus size: 33
1296678 ATATCTAAAC
*
1296688 AATAACAATAAAATAGT-AGTAATACAATA-GTAA
1 AATAACAATAAAATAGTGAG-AAAACAATATG-AA
1296721 AACTATA-AA-AAAATAGTGAGAAAACAATATGAA
1 AA-TA-ACAATAAAATAGTGAGAAAACAATATGAA
1296754 AATAACAATAAAATAGTGAGAAAA
1 AATAACAATAAAATAGTGAGAAAA
1296778 TAACATAATA
Statistics
Matches: 50, Mismatches: 1, Indels: 12
0.79 0.02 0.19
Matches are distributed among these distances:
31 1 0.02
32 4 0.08
33 37 0.74
34 7 0.14
35 1 0.02
ACGTcount: A:0.63, C:0.06, G:0.11, T:0.20
Consensus pattern (33 bp):
AATAACAATAAAATAGTGAGAAAACAATATGAA
Found at i:1297007 original size:33 final size:34
Alignment explanation
Indices: 1296951--1297031 Score: 87
Period size: 33 Copynumber: 2.4 Consensus size: 34
1296941 ATAAATAATA
* *
1296951 ACAATAAAATAGT-AGCAACATAATAATAAAACT-
1 ACAACAAAATAGTGAGCAACATAATAA-AAAAATG
* *
1296984 ATAACAAAATAGTGAGGAA-ATAATAAAAAAATG
1 ACAACAAAATAGTGAGCAACATAATAAAAAAATG
*
1297017 ACAATAAAATAGTGA
1 ACAACAAAATAGTGA
1297032 AAAAATAACA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
32 5 0.12
33 31 0.77
34 4 0.10
ACGTcount: A:0.62, C:0.07, G:0.11, T:0.20
Consensus pattern (34 bp):
ACAACAAAATAGTGAGCAACATAATAAAAAAATG
Found at i:1297023 original size:259 final size:260
Alignment explanation
Indices: 1296551--1297066 Score: 854
Period size: 259 Copynumber: 2.0 Consensus size: 260
1296541 AAAATAAAAA
*
1296551 TTTCCTAACAAATTGAAAATAAATTTTTAAAAATGCGTATACTTAAATAACATTAAGATAAGTAC
1 TTTCCTAACAAATTAAAAATAAATTTTTAAAAATGCGTATACTTAAATAACATTAAGATAAGTAC
*
1296616 AACTTAACAAGCAAATGTCTCGAAAATAGTAACAAAATTAATGATAAAATAAGAGTTATGCAATA
66 AACTTAACAAGCAAATGTCTCGAAAATAGTAACAAAATTAATGATAAAATAAGAGTTATACAATA
* * * *
1296681 TCTAAACAATAACAATAAAATAGTAGTAATACAATAGTAAAACTATAAAAAAATAGTGAGAAAAC
131 TATAAACAATAACAATAAAATAGTAGCAACACAATAATAAAACTATAAAAAAATAGTGAGAAAAC
** * * *
1296746 AATATGAAAATAACAATAAAATAGTGAGAAAATAACATAATAGGCCCGGATCATTTTCTAAATAT
196 AATAAAAAAATAACAATAAAATAGTGAAAAAATAACATAATAGACCCGAATCATTTTCTAAATAT
1296811 TTTCC-AACAAATTAAAAATAAATTTTTAAAAATGCGTATACTTAAATAACATTAAGATAAGTAC
1 TTTCCTAACAAATTAAAAATAAATTTTTAAAAATGCGTATACTTAAATAACATTAAGATAAGTAC
*
1296875 AACTTAACAAGCAAATGTCTCTAAAATAGTAACAAAATTAATGATAAAATAAGAGTTATACAATA
66 AACTTAACAAGCAAATGTCTCGAAAATAGTAACAAAATTAATGATAAAATAAGAGTTATACAATA
* * * * *
1296940 TATAAATAATAACAATAAAATAGTAGCAACATAATAATAAAACTATAACAAAATAGTGAGGAAAT
131 TATAAACAATAACAATAAAATAGTAGCAACACAATAATAAAACTATAAAAAAATAGTGAGAAAAC
* *
1297005 AATAAAAAAATGACAATAAAATAGTGAAAAAATAACATAATAGACCCGAATCATTTTTTAAA
196 AATAAAAAAATAACAATAAAATAGTGAAAAAATAACATAATAGACCCGAATCATTTTCTAAA
1297067 CATACTTTTT
Statistics
Matches: 237, Mismatches: 19, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
259 232 0.98
260 5 0.02
ACGTcount: A:0.54, C:0.10, G:0.09, T:0.27
Consensus pattern (260 bp):
TTTCCTAACAAATTAAAAATAAATTTTTAAAAATGCGTATACTTAAATAACATTAAGATAAGTAC
AACTTAACAAGCAAATGTCTCGAAAATAGTAACAAAATTAATGATAAAATAAGAGTTATACAATA
TATAAACAATAACAATAAAATAGTAGCAACACAATAATAAAACTATAAAAAAATAGTGAGAAAAC
AATAAAAAAATAACAATAAAATAGTGAAAAAATAACATAATAGACCCGAATCATTTTCTAAATAT
Found at i:1297099 original size:12 final size:12
Alignment explanation
Indices: 1297075--1297109 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
1297065 AACATACTTT
1297075 TTTATTATTTAAA
1 TTTATT-TTTAAA
1297088 TTTATTTTTAAA
1 TTTATTTTTAAA
1297100 TTTATATTTT
1 TTTAT-TTTT
1297110 TACCCGAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTATTTTTAAA
Found at i:1302363 original size:2 final size:2
Alignment explanation
Indices: 1302356--1302388 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1302346 ACTTAGTGGT
*
1302356 TA TA TA TA TA TA TC 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 T
1302389 TAATTTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1312082 original size:14 final size:14
Alignment explanation
Indices: 1312063--1312089 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1312053 ATATAGCACT
1312063 TGGATGGATGGATA
1 TGGATGGATGGATA
1312077 TGGATGGATGGAT
1 TGGATGGATGGAT
1312090 TCATGCATGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.00, G:0.44, T:0.30
Consensus pattern (14 bp):
TGGATGGATGGATA
Found at i:1312362 original size:15 final size:16
Alignment explanation
Indices: 1312341--1312372 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1312331 GAAAATATAG
1312341 AAAAAAAATAGGGATT
1 AAAAAAAATAGGGATT
1312357 AAAAAAAATAGGGATT
1 AAAAAAAATAGGGATT
1312373 TTTTATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.19, T:0.19
Consensus pattern (16 bp):
AAAAAAAATAGGGATT
Found at i:1313422 original size:41 final size:41
Alignment explanation
Indices: 1313377--1313497 Score: 174
Period size: 41 Copynumber: 3.0 Consensus size: 41
1313367 TCCAAACGGC
*
1313377 GCTATAGATCGAGGTTTTAGCGGCGCTTCTGGAAAAACGCA
1 GCTATAGGTCGAGGTTTTAGCGGCGCTTCTGGAAAAACGCA
* *
1313418 GCTATAGGTCGAGGTTTTAGTGGCGCTTCTGGAAAAATGCCA
1 GCTATAGGTCGAGGTTTTAGCGGCGCTTCTGGAAAAACG-CA
* *
1313460 -CTATAGGTCGAGCTTTTAGCGGCGCTT-TTGAAAAACGC
1 GCTATAGGTCGAGGTTTTAGCGGCGCTTCTGGAAAAACGC
1313498 CGCAAAAAAT
Statistics
Matches: 72, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
39 1 0.01
40 8 0.11
41 61 0.85
42 2 0.03
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (41 bp):
GCTATAGGTCGAGGTTTTAGCGGCGCTTCTGGAAAAACGCA
Found at i:1315258 original size:46 final size:46
Alignment explanation
Indices: 1315077--1315258 Score: 231
Period size: 46 Copynumber: 4.0 Consensus size: 46
1315067 TTTGACATGA
* * * * * * * *
1315077 TGCCATAGTGTCTTTGAACTATGGTGTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
*** *
1315123 TGCCATGGTATCTTTCAACCATGGTCTTGTTCATTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
1315169 TCCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1315215 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1315259 AGAGCACACT
Statistics
Matches: 120, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
45 4 0.03
46 116 0.97
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.40
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:1317970 original size:3 final size:3
Alignment explanation
Indices: 1317962--1317996 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1317952 ATTGGTGACA
1317962 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1317997 ATGTTAAAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1319793 original size:24 final size:24
Alignment explanation
Indices: 1319761--1319807 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
1319751 AACCATGTTG
1319761 GTTAATTATTACGAGCTTTGTAGT
1 GTTAATTATTACGAGCTTTGTAGT
* *
1319785 GTTAATTATTACTAGTTTTGTAG
1 GTTAATTATTACGAGCTTTGTAG
1319808 CTTCTATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.26, C:0.06, G:0.19, T:0.49
Consensus pattern (24 bp):
GTTAATTATTACGAGCTTTGTAGT
Found at i:1319974 original size:24 final size:22
Alignment explanation
Indices: 1319947--1319990 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
1319937 AATTTCAAAA
1319947 ATAAAACATAATATAATATTTATC
1 ATAAAA-ATAA-ATAATATTTATC
*
1319971 ATAAAAATAAATATTATTTA
1 ATAAAAATAAATAATATTTA
1319991 ATAAAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 4 0.21
24 6 0.32
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.39
Consensus pattern (22 bp):
ATAAAAATAAATAATATTTATC
Found at i:1320234 original size:43 final size:43
Alignment explanation
Indices: 1320034--1320243 Score: 303
Period size: 43 Copynumber: 4.9 Consensus size: 43
1320024 TGTTTTCAAA
* * * *
1320034 AAAAGTGCCGCTAAAGGTTATGATTTTTAGCGGCGTTTGCGGG
1 AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGCGGG
*
1320077 AAAAGCGTCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGCGGG
1 AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGCGGG
*
1320120 AAAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGCGGG
1 AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGCGGG
* * *
1320163 AAAAGCGCCGCTAAAGGTCTTGGTCTTTAGTGGCGTTTGCGGA
1 AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGCGGG
* ** *
1320206 AAAAGCGCCGCTAAAGGTCAAGACCTTTAGCAGCGTTT
1 AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTT
1320244 TTTTTTAAAT
Statistics
Matches: 152, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 152 1.00
ACGTcount: A:0.23, C:0.19, G:0.32, T:0.26
Consensus pattern (43 bp):
AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGCGGG
Found at i:1323002 original size:19 final size:18
Alignment explanation
Indices: 1322953--1323003 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
1322943 ATTGTTTAGA
* *
1322953 TATTGTATAACTATTGTTT
1 TATTGTATAA-TTTTGTTC
1322972 TATTGT-TAATTTTGTTAC
1 TATTGTATAATTTTGTT-C
1322990 TATTGTATAATTTT
1 TATTGTATAATTTT
1323004 TTAATTTGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 6 0.21
18 9 0.32
19 13 0.46
ACGTcount: A:0.25, C:0.04, G:0.10, T:0.61
Consensus pattern (18 bp):
TATTGTATAATTTTGTTC
Found at i:1326116 original size:3 final size:3
Alignment explanation
Indices: 1326108--1326143 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
1326098 CCACTCAGTA
1326108 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1326144 ATGTGAATCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1328573 original size:96 final size:96
Alignment explanation
Indices: 1328401--1328582 Score: 258
Period size: 96 Copynumber: 1.9 Consensus size: 96
1328391 AACTGTAGCA
** * *
1328401 ACAATAATAATATAAACCGAATTAATACTCAATCATCATACTCATAAATTTTTAATTTTATAAAA
1 ACAATAATAATATAAACCGAACAAATACACAACCATCATACTCATAAATTTTTAATTTTATAAAA
1328466 TATGACAACTTTGGGTGGCTATTGGCTAATC
66 TATGACAACTTTGGGTGGCTATTGGCTAATC
* * *
1328497 ACAATAATAATATAAACTGAACAAATACACAACCATCAT-CTTCATAATTTTTTAGTTTTATAAA
1 ACAATAATAATATAAACCGAACAAATACACAACCATCATAC-TCATAAATTTTTAATTTTATAAA
* * *
1328561 ATTTGGCTACTTTGGGTGGCTA
65 ATATGACAACTTTGGGTGGCTA
1328583 ATCTGATTTG
Statistics
Matches: 75, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
95 1 0.01
96 74 0.99
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.36
Consensus pattern (96 bp):
ACAATAATAATATAAACCGAACAAATACACAACCATCATACTCATAAATTTTTAATTTTATAAAA
TATGACAACTTTGGGTGGCTATTGGCTAATC
Found at i:1336571 original size:32 final size:32
Alignment explanation
Indices: 1336526--1336591 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
1336516 ATTATTGAGC
*
1336526 TTCACAACTTTTTCTAATTTGGTATTTAGATT
1 TTCACAACATTTTCTAATTTGGTATTTAGATT
1336558 TTCACAACATTTTCTAATTTGGTATTTAGATT
1 TTCACAACATTTTCTAATTTGGTATTTAGATT
1336590 TT
1 TT
1336592 TTAACGCATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.26, C:0.12, G:0.09, T:0.53
Consensus pattern (32 bp):
TTCACAACATTTTCTAATTTGGTATTTAGATT
Found at i:1339682 original size:8 final size:8
Alignment explanation
Indices: 1339668--1339697 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
1339658 GTAGGAACCT
1339668 GAAAAAAA
1 GAAAAAAA
1339676 -AAAAAAA
1 GAAAAAAA
1339683 GAAAAAAA
1 GAAAAAAA
1339691 GAAAAAA
1 GAAAAAA
1339698 CCCAAAGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (8 bp):
GAAAAAAA
Found at i:1339688 original size:15 final size:16
Alignment explanation
Indices: 1339668--1339697 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1339658 GTAGGAACCT
1339668 GAAAAAAA-AAAAAAA
1 GAAAAAAAGAAAAAAA
1339683 GAAAAAAAGAAAAAA
1 GAAAAAAAGAAAAAA
1339698 CCCAAAGTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (16 bp):
GAAAAAAAGAAAAAAA
Found at i:1342127 original size:29 final size:30
Alignment explanation
Indices: 1342076--1342147 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
1342066 TAGGGACTAG
* * * *
1342076 ATCAAATTAGTCCTTCTATTATT-AAATGA
1 ATCAAATTAGTCCCTATACTATTAAAAAGA
*
1342105 ATCAATTTAGTCCCTATACTATTAAAAAGA
1 ATCAAATTAGTCCCTATACTATTAAAAAGA
*
1342135 ATCAAATAAGTCC
1 ATCAAATTAGTCC
1342148 AAATTGTAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
29 19 0.54
30 16 0.46
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.35
Consensus pattern (30 bp):
ATCAAATTAGTCCCTATACTATTAAAAAGA
Found at i:1344504 original size:28 final size:30
Alignment explanation
Indices: 1344455--1344517 Score: 78
Period size: 29 Copynumber: 2.1 Consensus size: 30
1344445 ACAAGCTATT
1344455 AAAATTATGAAATTAT-ATTTTTACTATTATA
1 AAAATTAT-AAATTATAATTTTTAC-ATTATA
*
1344486 AAAATTAT-AATT-TAATTTTTACATTCTA
1 AAAATTATAAATTATAATTTTTACATTATA
1344514 AAAA
1 AAAA
1344518 AATTTTCTAG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
28 10 0.33
29 12 0.40
31 8 0.27
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.46
Consensus pattern (30 bp):
AAAATTATAAATTATAATTTTTACATTATA
Found at i:1344518 original size:29 final size:31
Alignment explanation
Indices: 1344455--1344517 Score: 87
Period size: 28 Copynumber: 2.1 Consensus size: 31
1344445 ACAAGCTATT
1344455 AAAATTATGAAATTATATTTTTACTATTATA
1 AAAATTATGAAATTATATTTTTACTATTATA
* *
1344486 AAAATTAT-AATTTA-ATTTTTAC-ATTCTA
1 AAAATTATGAAATTATATTTTTACTATTATA
1344514 AAAA
1 AAAA
1344518 AATTTTCTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 9 0.30
29 8 0.27
30 5 0.17
31 8 0.27
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.46
Consensus pattern (31 bp):
AAAATTATGAAATTATATTTTTACTATTATA
Found at i:1344521 original size:30 final size:31
Alignment explanation
Indices: 1344455--1344521 Score: 77
Period size: 30 Copynumber: 2.2 Consensus size: 31
1344445 ACAAGCTATT
*
1344455 AAAATTATGAAATTATATTTTTACTATTATA
1 AAAATTATGAAATTATATTTTTACTATTAAA
*
1344486 AAAATTAT-AATTTA-ATTTTTAC-ATTCTAAA
1 AAAATTATGAAATTATATTTTTACTA-T-TAAA
1344516 AAAATT
1 AAAATT
1344522 TTCTAGTTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 1 0.03
29 9 0.28
30 14 0.44
31 8 0.25
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.46
Consensus pattern (31 bp):
AAAATTATGAAATTATATTTTTACTATTAAA
Found at i:1351656 original size:21 final size:21
Alignment explanation
Indices: 1351632--1351693 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
1351622 CATAGCATTC
1351632 TATTAAATATAAAATTATATT
1 TATTAAATATAAAATTATATT
* *
1351653 TATTAACT-TGAAAATTAT-TA
1 TATTAAATAT-AAAATTATATT
* * *
1351673 TATTTAATATATACTTATATT
1 TATTAAATATAAAATTATATT
1351694 AATAAAAATT
Statistics
Matches: 31, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
20 14 0.45
21 17 0.55
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (21 bp):
TATTAAATATAAAATTATATT
Found at i:1360703 original size:2 final size:2
Alignment explanation
Indices: 1360692--1360730 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
1360682 CTTTCATACG
*
1360692 CT CT -T CT CT CT CT CT CT CT CT CT CT CT CT CT CT CC CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1360731 TTTTGCAGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1360831 original size:12 final size:12
Alignment explanation
Indices: 1360811--1360843 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
1360801 AGGATGAAAG
*
1360811 TTCAACTTCAGT
1 TTCAGCTTCAGT
1360823 TTCAGCTTCAGT
1 TTCAGCTTCAGT
1360835 TTCAGCTTC
1 TTCAGCTTC
1360844 TTTAACAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.18, C:0.27, G:0.12, T:0.42
Consensus pattern (12 bp):
TTCAGCTTCAGT
Found at i:1364723 original size:24 final size:23
Alignment explanation
Indices: 1364683--1364730 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
1364673 ACTTAATTTT
* *
1364683 TTTTTTTAAATTAAGGGTTTTAA
1 TTTTTTAAAATTAAGGGGTTTAA
*
1364706 TTTTTTAAAATTTTAGGGGTTTAA
1 TTTTTTAAAA-TTAAGGGGTTTAA
1364730 T
1 T
1364731 AAAATTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.29, C:0.00, G:0.15, T:0.56
Consensus pattern (23 bp):
TTTTTTAAAATTAAGGGGTTTAA
Found at i:1364737 original size:29 final size:28
Alignment explanation
Indices: 1364704--1364758 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
1364694 TAAGGGTTTT
* *
1364704 AATTTTTTAAAATTTTAGGGGTTTAATAA
1 AATTTTTTAAAA-ATTACGGGTTTAATAA
1364733 AATTTTTTAAAAATTACGGGTTTAAT
1 AATTTTTTAAAAATTACGGGTTTAAT
1364759 TAATTATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 12 0.50
29 12 0.50
ACGTcount: A:0.38, C:0.02, G:0.13, T:0.47
Consensus pattern (28 bp):
AATTTTTTAAAAATTACGGGTTTAATAA
Found at i:1365362 original size:2 final size:2
Alignment explanation
Indices: 1365355--1365380 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1365345 GGAACCAAAA
1365355 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
1365381 TTTAAGAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1373189 original size:21 final size:21
Alignment explanation
Indices: 1373146--1373198 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
1373136 TTTAAGTAAT
1373146 AACAACAAAATGACTGCAAAAC
1 AACAACAAAATGACT-CAAAAC
*
1373168 AACATCAAAATGACAT-AAAAC
1 AACAACAAAATGAC-TCAAAAC
*
1373189 AATAACAAAA
1 AACAACAAAA
1373199 CAATAGTGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 13 0.48
22 13 0.48
23 1 0.04
ACGTcount: A:0.64, C:0.19, G:0.06, T:0.11
Consensus pattern (21 bp):
AACAACAAAATGACTCAAAAC
Found at i:1375952 original size:29 final size:29
Alignment explanation
Indices: 1375918--1375973 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
1375908 ATAGAGATTT
*
1375918 GATTAAATCAATCTTTCTATTATTAAATG
1 GATTAAATCAATCTTTATATTATTAAATG
* * *
1375947 GATTAATTTAATTTTTATATTATTAAA
1 GATTAAATCAATCTTTATATTATTAAA
1375974 AAGAATTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.50
Consensus pattern (29 bp):
GATTAAATCAATCTTTATATTATTAAATG
Found at i:1381148 original size:59 final size:60
Alignment explanation
Indices: 1381056--1381182 Score: 220
Period size: 61 Copynumber: 2.1 Consensus size: 60
1381046 ATCACTACTA
1381056 AACTTAAAAATAACATAAAGCCTTAACAACC-ATACCTTATTCTCTTGAAACCAAACTTT
1 AACTTAAAAATAACATAAAGCCTTAACAACCAATACCTTATTCTCTTGAAACCAAACTTT
* *
1381115 AACTTAAAAATAACATAAAGCCTTAATATCCATATACCTTATTCTCTTGAAACCAAACTTT
1 AACTTAAAAATAACATAAAGCCTTAACAACCA-ATACCTTATTCTCTTGAAACCAAACTTT
1381176 AACTTAA
1 AACTTAA
1381183 CTTTCTCTCT
Statistics
Matches: 64, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
59 29 0.45
61 35 0.55
ACGTcount: A:0.44, C:0.22, G:0.03, T:0.31
Consensus pattern (60 bp):
AACTTAAAAATAACATAAAGCCTTAACAACCAATACCTTATTCTCTTGAAACCAAACTTT
Found at i:1381445 original size:11 final size:11
Alignment explanation
Indices: 1381428--1381484 Score: 53
Period size: 11 Copynumber: 5.1 Consensus size: 11
1381418 TTATATACTA
1381428 AATAAAATAAT
1 AATAAAATAAT
*
1381439 GATAAAATAAT
1 AATAAAATAAT
*
1381450 AATAAAAGTTA-
1 AATAAAA-TAAT
*
1381461 AATCAAAATATT
1 AAT-AAAATAAT
*
1381473 AATAAACTAAT
1 AATAAAATAAT
1381484 A
1 A
1381485 TTTATTTATT
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
11 27 0.75
12 9 0.25
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.28
Consensus pattern (11 bp):
AATAAAATAAT
Found at i:1385654 original size:29 final size:29
Alignment explanation
Indices: 1385621--1385677 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
1385611 CAAACAATGT
*
1385621 GCATATGACGCAAACCAAAGTCAAACCAA
1 GCATATGACGCAAACCAAACTCAAACCAA
* *
1385650 GCATATGACGTAAACCACACTCAAACCA
1 GCATATGACGCAAACCAAACTCAAACCA
1385678 CATGTTAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.46, C:0.30, G:0.12, T:0.12
Consensus pattern (29 bp):
GCATATGACGCAAACCAAACTCAAACCAA
Found at i:1385820 original size:30 final size:31
Alignment explanation
Indices: 1385786--1385844 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
1385776 TATTTTTTAA
1385786 ATTTTTAAAAAATAAAATAAAT-ATAAAATT
1 ATTTTTAAAAAATAAAATAAATCATAAAATT
* * *
1385816 ATTTTTAGAAATTAAAATATATCATAAAA
1 ATTTTTAAAAAATAAAATAAATCATAAAA
1385845 ATTAAAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 19 0.76
31 6 0.24
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (31 bp):
ATTTTTAAAAAATAAAATAAATCATAAAATT
Found at i:1386195 original size:20 final size:19
Alignment explanation
Indices: 1386165--1386202 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1386155 AATTAAACAT
1386165 AAATAATAAATAAATTTTA
1 AAATAATAAATAAATTTTA
*
1386184 AAATACATAAATGAATTTT
1 AAATA-ATAAATAAATTTT
1386203 TTTAATTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.37
Consensus pattern (19 bp):
AAATAATAAATAAATTTTA
Found at i:1396030 original size:47 final size:47
Alignment explanation
Indices: 1395921--1396031 Score: 154
Period size: 47 Copynumber: 2.4 Consensus size: 47
1395911 CCGGGATAAG
*
1395921 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACATTATAGTA
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
* * *
1395968 CACAAAGTACTTCATCGGAACAAATCCGGAACTTTAACAGTAGTCG-A
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTA-TAGTA
1396015 CACATAGTG-TCTCATCG
1 CACATAGTGCT-TCATCG
1396032 ACTCAATGTC
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
46 1 0.02
47 53 0.95
48 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.25
Consensus pattern (47 bp):
CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
Found at i:1402178 original size:19 final size:20
Alignment explanation
Indices: 1402138--1402183 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
1402128 CGGGAAATGA
*
1402138 TTTCTGGAAAATGATTTAAT
1 TTTCTGGAAAATGATTAAAT
1402158 TTTCTGGAAAA-G-TTAATAT
1 TTTCTGGAAAATGATTAA-AT
1402177 TTTCTGG
1 TTTCTGG
1402184 TGTTTGGATG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 3 0.12
19 10 0.42
20 11 0.46
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.46
Consensus pattern (20 bp):
TTTCTGGAAAATGATTAAAT
Found at i:1402653 original size:19 final size:19
Alignment explanation
Indices: 1402629--1402665 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1402619 TATTATTAAT
*
1402629 ATATTTATAATTGTAATAA
1 ATATTTATAATTGAAATAA
*
1402648 ATATTTATTATTGAAATA
1 ATATTTATAATTGAAATA
1402666 TTAATATTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (19 bp):
ATATTTATAATTGAAATAA
Found at i:1402731 original size:16 final size:16
Alignment explanation
Indices: 1402700--1402736 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
1402690 ATGTGAATAA
1402700 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
1402716 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
1402732 TATTA
1 TATTA
1402737 AAATAAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:1402787 original size:22 final size:22
Alignment explanation
Indices: 1402747--1402802 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
1402737 AAATAAATTG
*
1402747 AAATATTAAA-TA-ATTTATTA
1 AAATAATAAATTATATTTATTA
1402767 AAATAATAAATTATATTTATTA
1 AAATAATAAATTATATTTATTA
* * *
1402789 CATTAATAATTTAT
1 AAATAATAAATTAT
1402803 TATATGACTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 9 0.30
21 2 0.07
22 19 0.63
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (22 bp):
AAATAATAAATTATATTTATTA
Found at i:1407002 original size:53 final size:52
Alignment explanation
Indices: 1406922--1407023 Score: 168
Period size: 53 Copynumber: 1.9 Consensus size: 52
1406912 GTTCTTTTAC
* *
1406922 TTTAACTAATTAGTTTGAACTAATACAACTTTATATTTTGAAAATTGAACACG
1 TTTAACTAATTAGTTCGAACTAATACAACCTTATA-TTTGAAAATTGAACACG
*
1406975 TTTAACTAGTTAGTTCGAACTAATACAACCTTATATTTGAAAATTGAAC
1 TTTAACTAATTAGTTCGAACTAATACAACCTTATATTTGAAAATTGAAC
1407024 TAATACAACC
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
52 14 0.30
53 32 0.70
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.38
Consensus pattern (52 bp):
TTTAACTAATTAGTTCGAACTAATACAACCTTATATTTGAAAATTGAACACG
Found at i:1408675 original size:9 final size:9
Alignment explanation
Indices: 1408661--1408689 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
1408651 AGTCTCCCTC
1408661 TTTTTCTTT
1 TTTTTCTTT
1408670 TTTTTCTTT
1 TTTTTCTTT
1408679 TTTTT-TTT
1 TTTTTCTTT
1408687 TTT
1 TTT
1408690 ATATTTTAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 6 0.30
9 14 0.70
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:1408689 original size:15 final size:15
Alignment explanation
Indices: 1408659--1408688 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1408649 TTAGTCTCCC
1408659 TCTTTTTCTTTTTTT
1 TCTTTTTCTTTTTTT
1408674 TCTTTTT-TTTTTTT
1 TCTTTTTCTTTTTTT
1408688 T
1 T
1408689 TATATTTTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (15 bp):
TCTTTTTCTTTTTTT
Found at i:1421923 original size:30 final size:29
Alignment explanation
Indices: 1421874--1421940 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 29
1421864 TTTTTCTCTC
*
1421874 AATTAAAAAATAGATAAATTAATCCTTAT
1 AATTAAAAAATAGATAAATTAATCATTAT
1421903 AATTAAACTAAATA-ATAAATTAATCATTAT
1 AATTAAA--AAATAGATAAATTAATCATTAT
1421933 -ATTAAAAA
1 AATTAAAAA
1421941 TTTCACTCGT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
27 2 0.06
29 13 0.37
30 15 0.43
31 5 0.14
ACGTcount: A:0.58, C:0.06, G:0.01, T:0.34
Consensus pattern (29 bp):
AATTAAAAAATAGATAAATTAATCATTAT
Found at i:1425925 original size:20 final size:22
Alignment explanation
Indices: 1425900--1425940 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
1425890 TTTGCGGCGG
*
1425900 GTTTTTTTCTT-TTTG-GGAAT
1 GTTTTTTCCTTGTTTGAGGAAT
1425920 GTTTTTTCCTTGTTTGAGGAA
1 GTTTTTTCCTTGTTTGAGGAA
1425941 ATAGCTAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
21 4 0.22
22 4 0.22
ACGTcount: A:0.12, C:0.07, G:0.22, T:0.59
Consensus pattern (22 bp):
GTTTTTTCCTTGTTTGAGGAAT
Found at i:1427199 original size:23 final size:24
Alignment explanation
Indices: 1427173--1427218 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
1427163 GATTTAAAAA
* *
1427173 ATTTCAAA-CAAACCTTATCCATT
1 ATTTAAAACCAAAACTTATCCATT
*
1427196 ATTTAAAACCAAAATTTATCCAT
1 ATTTAAAACCAAAACTTATCCAT
1427219 AACTTTAATC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.43, C:0.22, G:0.00, T:0.35
Consensus pattern (24 bp):
ATTTAAAACCAAAACTTATCCATT
Found at i:1438807 original size:13 final size:13
Alignment explanation
Indices: 1438789--1438813 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1438779 GAAGTTATGA
1438789 CGTATATATACAT
1 CGTATATATACAT
1438802 CGTATATATACA
1 CGTATATATACA
1438814 CATTAATCTT
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:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (13 bp):
CGTATATATACAT
Found at i:1441911 original size:16 final size:17
Alignment explanation
Indices: 1441866--1441921 Score: 64
Period size: 16 Copynumber: 3.4 Consensus size: 17
1441856 AGCCAGTTAA
1441866 ATAAAATTTAAATACA-
1 ATAAAATTTAAATACAT
*
1441882 A-AAAATTATAAATAAAT
1 ATAAAATT-TAAATACAT
1441899 ATAAAATTT-AATACAT
1 ATAAAATTTAAATACAT
1441915 AATAAAA
1 -ATAAAA
1441922 AAATGACAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
15 6 0.18
16 14 0.41
17 8 0.24
18 6 0.18
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (17 bp):
ATAAAATTTAAATACAT
Found at i:1443859 original size:22 final size:22
Alignment explanation
Indices: 1443831--1443873 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
1443821 AAATTTTGGG
1443831 ATTTATATGAA-AATTTTAATTA
1 ATTTATAT-AATAATTTTAATTA
1443853 ATTTATATAATTAATTTTAAT
1 ATTTATATAA-TAATTTTAAT
1443874 CAGTTTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 2 0.11
22 8 0.42
23 9 0.47
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
ATTTATATAATAATTTTAATTA
Found at i:1449093 original size:71 final size:72
Alignment explanation
Indices: 1448976--1449194 Score: 350
Period size: 72 Copynumber: 3.1 Consensus size: 72
1448966 TGGCTTTCAT
1448976 TCTTCGGGTTCTACATTGGGTAATGGGCTCTTCGGAAGCAGTAGCAGCTCTTACCCTAGTCTGAA
1 TCTTCGGGTTCTACATTGGGTAATGGGCTCTTCGGAAGCAGTAGCAGCTCTTACCCTAGTCTGAA
1449041 TAGCAGC
66 TAGCAGC
* * * * * * *
1449048 TCTTCGGGTTCTATAGTGGTTAAT-GGCTCTTTGGAAGCAGTAGCAGGTCTCACCCTAGTCTCAA
1 TCTTCGGGTTCTACATTGGGTAATGGGCTCTTCGGAAGCAGTAGCAGCTCTTACCCTAGTCTGAA
1449112 TAGCAGC
66 TAGCAGC
*
1449119 TCTTCGGGTGCTACATTGGGTAATGGGCTCTTCGGAAGCAGTAGCAGCTCTTACCCTAGTCTGAA
1 TCTTCGGGTTCTACATTGGGTAATGGGCTCTTCGGAAGCAGTAGCAGCTCTTACCCTAGTCTGAA
*
1449184 TAACAGC
66 TAGCAGC
1449191 TCTT
1 TCTT
1449195 ACCCTACCCT
Statistics
Matches: 130, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
71 63 0.48
72 67 0.52
ACGTcount: A:0.21, C:0.23, G:0.26, T:0.30
Consensus pattern (72 bp):
TCTTCGGGTTCTACATTGGGTAATGGGCTCTTCGGAAGCAGTAGCAGCTCTTACCCTAGTCTGAA
TAGCAGC
Found at i:1449206 original size:24 final size:24
Alignment explanation
Indices: 1449163--1449208 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1449153 GAAGCAGTAG
**
1449163 CAGCTCTTACCCTAGTCTGAATAA
1 CAGCTCTTACCCTACCCTGAATAA
1449187 CAGCTCTTACCCTACCCTGAAT
1 CAGCTCTTACCCTACCCTGAAT
1449209 CCTGGTTACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.26, C:0.35, G:0.11, T:0.28
Consensus pattern (24 bp):
CAGCTCTTACCCTACCCTGAATAA
Found at i:1450210 original size:6 final size:6
Alignment explanation
Indices: 1450195--1450258 Score: 74
Period size: 6 Copynumber: 10.7 Consensus size: 6
1450185 GACTGCCCCA
* * * *
1450195 GCTCCT GCTCCC GCTCCC GCTCCC GCTCCC GCTCCT GCTCCA GCTCCT
1 GCTCCC GCTCCC GCTCCC GCTCCC GCTCCC GCTCCC GCTCCC GCTCCC
* *
1450243 GCTCCT GCTCCA GCTC
1 GCTCCC GCTCCC GCTC
1450259 TGGCTGTATA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.03, C:0.56, G:0.17, T:0.23
Consensus pattern (6 bp):
GCTCCC
Found at i:1450222 original size:18 final size:18
Alignment explanation
Indices: 1450195--1450258 Score: 92
Period size: 18 Copynumber: 3.6 Consensus size: 18
1450185 GACTGCCCCA
* *
1450195 GCTCCTGCTCCCGCTCCC
1 GCTCCAGCTCCCGCTCCT
*
1450213 GCTCCCGCTCCCGCTCCT
1 GCTCCAGCTCCCGCTCCT
*
1450231 GCTCCAGCTCCTGCTCCT
1 GCTCCAGCTCCCGCTCCT
1450249 GCTCCAGCTC
1 GCTCCAGCTC
1450259 TGGCTGTATA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 42 1.00
ACGTcount: A:0.03, C:0.56, G:0.17, T:0.23
Consensus pattern (18 bp):
GCTCCAGCTCCCGCTCCT
Found at i:1451431 original size:19 final size:20
Alignment explanation
Indices: 1451393--1451431 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
1451383 CAATTATAGA
* *
1451393 TTTTAAGAAATTTTTTTATT
1 TTTTAAGAAATATTTATATT
1451413 TTTTAA-AAATATTTATATT
1 TTTTAAGAAATATTTATATT
1451432 AATTCCGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (20 bp):
TTTTAAGAAATATTTATATT
Found at i:1452145 original size:18 final size:18
Alignment explanation
Indices: 1452112--1452147 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
1452102 AATACAATTG
1452112 TATGGTAATAATAATATA
1 TATGGTAATAATAATATA
1452130 TATGTGTAATAA-AATATA
1 TATG-GTAATAATAATATA
1452148 CATACATTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (18 bp):
TATGGTAATAATAATATA
Found at i:1452210 original size:11 final size:12
Alignment explanation
Indices: 1452192--1452229 Score: 51
Period size: 11 Copynumber: 3.1 Consensus size: 12
1452182 ATTTAAGTAA
1452192 ATATATTATATT
1 ATATATTATATT
1452204 A-ATATTATATT
1 ATATATTATATT
1452215 ATTATATTATTATT
1 A-TATATTA-TATT
1452229 A
1 A
1452230 GAATTAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 11 0.48
12 1 0.04
13 6 0.26
14 5 0.22
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
ATATATTATATT
Found at i:1452258 original size:18 final size:18
Alignment explanation
Indices: 1452235--1452275 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
1452225 TATTAGAATT
* *
1452235 AAACAAAAAAATTAAAGG
1 AAACAAAAAAATGAAAAG
*
1452253 AAACAAAAGAATGAAAAG
1 AAACAAAAAAATGAAAAG
1452271 AAACA
1 AAACA
1452276 TAATAGCCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.73, C:0.07, G:0.12, T:0.07
Consensus pattern (18 bp):
AAACAAAAAAATGAAAAG
Found at i:1453029 original size:27 final size:27
Alignment explanation
Indices: 1452997--1453048 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
1452987 GTATGTGTAT
*
1452997 GATTGAAA-AGTTTATTGAATTGGAATG
1 GATTGAAATAGTATATTG-ATTGGAATG
*
1453024 GATTGAAATTGTATATTGATTGGAA
1 GATTGAAATAGTATATTGATTGGAA
1453049 ATTGAATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 15 0.68
28 7 0.32
ACGTcount: A:0.37, C:0.00, G:0.25, T:0.38
Consensus pattern (27 bp):
GATTGAAATAGTATATTGATTGGAATG
Found at i:1464106 original size:2 final size:2
Alignment explanation
Indices: 1464099--1464123 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1464089 AAGTCAATGG
1464099 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 T
1464124 TTTAAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1468520 original size:10 final size:10
Alignment explanation
Indices: 1468507--1468531 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1468497 TTCTGTTTCT
1468507 TTTTTTTATA
1 TTTTTTTATA
1468517 TTTTTTTATA
1 TTTTTTTATA
1468527 TTTTT
1 TTTTT
1468532 ATAAAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTTTTATA
Found at i:1470490 original size:3 final size:3
Alignment explanation
Indices: 1470482--1470511 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
1470472 AAGTGGCTGT
*
1470482 TGA TGA TGA TGA TGA TGA TGC TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
1470512 CAGCAAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:1474690 original size:2 final size:2
Alignment explanation
Indices: 1474685--1474716 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1474675 AATAACCATA
1474685 AT 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 AT
1474717 TAATCCACTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1477808 original size:11 final size:12
Alignment explanation
Indices: 1477788--1477813 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1477778 TGGCAAACTA
1477788 TTTTCTTTTTTT
1 TTTTCTTTTTTT
1477800 TTTTCTTTTTTT
1 TTTTCTTTTTTT
1477812 TT
1 TT
1477814 ACTAATAAAT
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:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (12 bp):
TTTTCTTTTTTT
Found at i:1486233 original size:14 final size:12
Alignment explanation
Indices: 1486203--1486232 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1486193 TAAGTCCTAG
*
1486203 TTATTTTTGTGT
1 TTATATTTGTGT
1486215 TTATATTTGTGT
1 TTATATTTGTGT
1486227 TTATAT
1 TTATAT
1486233 AATTTTTTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.13, T:0.70
Consensus pattern (12 bp):
TTATATTTGTGT
Found at i:1486691 original size:15 final size:16
Alignment explanation
Indices: 1486671--1486702 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1486661 TCTTGAAATT
1486671 GGAAAAA-AAAAAAAA
1 GGAAAAAGAAAAAAAA
1486686 GGAAAAAGAAAAAAAA
1 GGAAAAAGAAAAAAAA
1486702 G
1 G
1486703 AAAGTCTTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (16 bp):
GGAAAAAGAAAAAAAA
Found at i:1489937 original size:16 final size:15
Alignment explanation
Indices: 1489911--1489948 Score: 67
Period size: 16 Copynumber: 2.5 Consensus size: 15
1489901 AACATTATTA
1489911 TATAAATAAAATAAT
1 TATAAATAAAATAAT
1489926 TATAATATAAAATAAT
1 TATAA-ATAAAATAAT
1489942 TATAAAT
1 TATAAAT
1489949 CCAAAACACA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TATAAATAAAATAAT
Found at i:1493079 original size:33 final size:33
Alignment explanation
Indices: 1493008--1493077 Score: 90
Period size: 33 Copynumber: 2.2 Consensus size: 33
1492998 TGTTCAAAAG
*
1493008 TTTTTATTTAAATTATTGAACTAGTTAAAGTTT
1 TTTTTATTTAAAGTATTGAACTAGTTAAAGTTT
* *
1493041 TTTTTATTTAAGGTATTGAA-TTGTT-AAGTTT
1 TTTTTATTTAAAGTATTGAACTAGTTAAAGTTT
1493072 ATTTTT
1 -TTTTT
1493078 TAAAAATAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
31 6 0.18
32 9 0.27
33 18 0.55
ACGTcount: A:0.29, C:0.01, G:0.11, T:0.59
Consensus pattern (33 bp):
TTTTTATTTAAAGTATTGAACTAGTTAAAGTTT
Found at i:1494112 original size:16 final size:17
Alignment explanation
Indices: 1494091--1494123 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1494081 CGAATTTTCA
*
1494091 ATTATAATA-TATTTTT
1 ATTATAAAATTATTTTT
1494107 ATTATAAAATTATTTTT
1 ATTATAAAATTATTTTT
1494124 CACTTTTCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTATAAAATTATTTTT
Found at i:1497594 original size:16 final size:15
Alignment explanation
Indices: 1497569--1497619 Score: 59
Period size: 16 Copynumber: 3.4 Consensus size: 15
1497559 CAATTTTATC
*
1497569 ATTTTA-AATTTAAA
1 ATTTTATAAATTAAA
1497583 ATTTTATAAATTATAA
1 ATTTTATAAATTA-AA
* *
1497599 AGTGTATAAATTAAA
1 ATTTTATAAATTAAA
1497614 ATTTTA
1 ATTTTA
1497620 CCATTTTAAG
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
14 6 0.20
15 11 0.37
16 13 0.43
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (15 bp):
ATTTTATAAATTAAA
Found at i:1506642 original size:3 final size:3
Alignment explanation
Indices: 1506634--1506670 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
1506624 ACCAACTCCA
*
1506634 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAA CAG C
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG C
1506671 TTAGTGGTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.35, C:0.35, G:0.30, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:1508431 original size:2 final size:2
Alignment explanation
Indices: 1508424--1508448 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1508414 AAAAGTTAAA
1508424 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 A
1508449 ACCATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1512559 original size:13 final size:13
Alignment explanation
Indices: 1512531--1512569 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
1512521 TTTTTTATTT
* *
1512531 CAAAATATTAAAC
1 CAAAAAATTTAAC
*
1512544 CAACAAATTTAAC
1 CAAAAAATTTAAC
1512557 CAAAAAATTTAAC
1 CAAAAAATTTAAC
1512570 AGAGTTAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.59, C:0.18, G:0.00, T:0.23
Consensus pattern (13 bp):
CAAAAAATTTAAC
Found at i:1516443 original size:2 final size:2
Alignment explanation
Indices: 1516436--1516463 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1516426 GGGTAGAATC
1516436 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
1516464 TTGTATTTTG
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:1518597 original size:14 final size:14
Alignment explanation
Indices: 1518578--1518604 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1518568 ATTTACTCTT
1518578 TGAATTAATTTACA
1 TGAATTAATTTACA
1518592 TGAATTAATTTAC
1 TGAATTAATTTAC
1518605 CCATTTTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (14 bp):
TGAATTAATTTACA
Found at i:1519518 original size:29 final size:30
Alignment explanation
Indices: 1519453--1519521 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 30
1519443 TTTAATAATT
* * *
1519453 TATATTTTTATAATTTTTTAAAAATTAAAT
1 TATAATTTTATAATTTTTTAAAAATCAAAG
* * *
1519483 TAAAATTTTATCA-TTTTTAAACATCAAAG
1 TATAATTTTATAATTTTTTAAAAATCAAAG
1519512 TATAATTTTA
1 TATAATTTTA
1519522 GGGAAAAATG
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
29 22 0.69
30 10 0.31
ACGTcount: A:0.43, C:0.04, G:0.01, T:0.51
Consensus pattern (30 bp):
TATAATTTTATAATTTTTTAAAAATCAAAG
Found at i:1526047 original size:16 final size:17
Alignment explanation
Indices: 1526001--1526053 Score: 63
Period size: 16 Copynumber: 3.1 Consensus size: 17
1525991 GTTGAACTGG
*
1526001 ATTTTATATTCTTTTAAT
1 ATTTTATAAT-TTTTAAT
*
1526019 ATCTTTTTAATTTTTAAT
1 AT-TTTATAATTTTTAAT
1526037 -TTTTATAATTTTTAAT
1 ATTTTATAATTTTTAAT
1526053 A
1 A
1526054 AGTTATTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
16 14 0.47
17 1 0.03
18 9 0.30
19 6 0.20
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (17 bp):
ATTTTATAATTTTTAAT
Found at i:1530459 original size:45 final size:45
Alignment explanation
Indices: 1530390--1530478 Score: 142
Period size: 45 Copynumber: 2.0 Consensus size: 45
1530380 AATGTTGTTG
* * * *
1530390 ACTGTGGCCATTATTCTATCAGAGTACTGTTTGATGGTCTCTGAA
1 ACTGTGGCCATTATCCTATAAGAGTACTGCTTGATGATCTCTGAA
1530435 ACTGTGGCCATTATCCTATAAGAGTACTGCTTGATGATCTCTGA
1 ACTGTGGCCATTATCCTATAAGAGTACTGCTTGATGATCTCTGA
1530479 CTCCCTTATC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (45 bp):
ACTGTGGCCATTATCCTATAAGAGTACTGCTTGATGATCTCTGAA
Found at i:1532976 original size:40 final size:40
Alignment explanation
Indices: 1532921--1533003 Score: 123
Period size: 40 Copynumber: 2.0 Consensus size: 40
1532911 AAAATTCTAA
* *
1532921 AATAAAATATTTATTATATTTAT-TTGTGTTTTTTAAATAT
1 AATAAAACATTTATTATATTTATGTAGTGTTTTTT-AATAT
1532961 AATAAAACATTTATTATATTTATGGTAGTGTTTTTTAATAT
1 AATAAAACATTTATTATATTTAT-GTAGTGTTTTTTAATAT
1533002 AA
1 AA
1533004 ATATTTTTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
40 22 0.56
41 7 0.18
42 10 0.26
ACGTcount: A:0.39, C:0.01, G:0.07, T:0.53
Consensus pattern (40 bp):
AATAAAACATTTATTATATTTATGTAGTGTTTTTTAATAT
Found at i:1533557 original size:22 final size:22
Alignment explanation
Indices: 1533532--1533575 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1533522 CTTTTTAAGC
* *
1533532 ATTTTTTTATTTTCTTTTTTTT
1 ATTTCTTTATTTCCTTTTTTTT
1533554 ATTTCTTTATTTCCTTTTTTTT
1 ATTTCTTTATTTCCTTTTTTTT
1533576 TAATGTTTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.82
Consensus pattern (22 bp):
ATTTCTTTATTTCCTTTTTTTT
Found at i:1535374 original size:35 final size:35
Alignment explanation
Indices: 1535347--1535474 Score: 166
Period size: 35 Copynumber: 3.5 Consensus size: 35
1535337 CATGGCAAAG
*
1535347 TGTGAAATGTAGGTATGGTATCATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
*
1535382 TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
1 TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
*
1535417 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGT
1 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGC
**
1535457 TAAGAAATGTAGGTATGG
1 TGTGAAATGTAGGTATGG
1535475 CATTTCCCAT
Statistics
Matches: 82, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
35 51 0.62
38 3 0.04
40 28 0.34
ACGTcount: A:0.31, C:0.09, G:0.26, T:0.34
Consensus pattern (35 bp):
TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
Done.