Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 133 of 187
Found at i:40296191 original size:20 final size:18
Alignment explanation
Indices: 40296154--40296192 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
40296144 TGATTGAAAT
*
40296154 TATATTTATATTAAATAA
1 TATATTTAAATTAAATAA
40296172 TATATTATAAATTAAAATAA
1 TATATT-TAAATT-AAATAA
40296192 T
1 T
40296193 TAAAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 5 0.28
20 7 0.39
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TATATTTAAATTAAATAA
Found at i:40298448 original size:158 final size:158
Alignment explanation
Indices: 40298151--40298867 Score: 1214
Period size: 158 Copynumber: 4.5 Consensus size: 158
40298141 TTTATCGATG
40298151 TGGTTTCGTGGTGTAGTTGGTTATCACGTCAGTCTAACACACTGAAGGTCTCCGGTTCGAGTCCG
1 TGGTTTCGTGGTGTAGTTGGTTATCACGTCAGTCTAACACACTGAAGGTCTCCGGTTCGAGTCCG
* *
40298216 GGCGAAGCCATTGCTTCAAACATATTTTTAGTCTTTTTAGTTTCTGCACATTTTAGTTTTTTGAC
66 GGCGAAGCCATTGTTTTAAACATATTTTTAGTC-TTTTAGTTTCTGCACATTTTAGTTTTTTGAC
*
40298281 TAAAA-TAAATGTCAAAA-GCTAGT-GAGC-G
130 TAAAATTAAATGTCAAAAGGC-A-TCGA-CTC
*
40298309 TGGTTTCGTGGTGTAGTTGATTATCACGTCAGTCTAACACACTGAAGGTCTCCGGTTCGAGTCCG
1 TGGTTTCGTGGTGTAGTTGGTTATCACGTCAGTCTAACACACTGAAGGTCTCCGGTTCGAGTCCG
*
40298374 GGCGAAGCCATTGTTTTAAACATGTTTTTAGTCTTTTAGTTTCTGCACATTTTAGTTTTTTGACT
66 GGCGAAGCCATTGTTTTAAACATATTTTTAGTCTTTTAGTTTCTGCACATTTTAGTTTTTTGACT
40298439 AAAATTAAATGTCAAAAGGCATCGACTC
131 AAAATTAAATGTCAAAAGGCATCGACTC
40298467 TGGTTTCGTGGTGTAGTTGGTTATCACGTCAGTCTAACACACTGAAGGTCTCCGGTTCGAGTCCG
1 TGGTTTCGTGGTGTAGTTGGTTATCACGTCAGTCTAACACACTGAAGGTCTCCGGTTCGAGTCCG
40298532 GGCGAAGCCATTGTTTTAAACATATTTTTAGTCTTTTAGTTTCTGCACATTTTAGTTTTTTGACT
66 GGCGAAGCCATTGTTTTAAACATATTTTTAGTCTTTTAGTTTCTGCACATTTTAGTTTTTTGACT
40298597 AAAATTAAATGTCAAAAGGCATCGACTC
131 AAAATTAAATGTCAAAAGGCATCGACTC
*
40298625 TGGTTTCGTGGTGTAGTTGGTTATCACGTCAATCTAACACACTGAAGGTCTCCGGTTCGAGTCC-
1 TGGTTTCGTGGTGTAGTTGGTTATCACGTCAGTCTAACACACTGAAGGTCTCCGGTTCGAGTCCG
* * *
40298689 GGCGAAGCCATT-TCTTTAAACATATTTTTAGTCTTTTAGTGTCTGCACATTTTATTTTTTTGAT
66 GGCGAAGCCATTGT-TTTAAACATATTTTTAGTCTTTTAGTTTCTGCACATTTTAGTTTTTTGAC
* * *
40298753 TAAAGTTAAATGTCAAAA-TCTATTGACTC
130 TAAAATTAAATGTCAAAAGGC-ATCGACTC
40298782 TGGTTTCGTGGTGTAGTTGGTTATCACGTCAGTCTAACACACTGAAGGTCTCCGGTTCGAGTCCG
1 TGGTTTCGTGGTGTAGTTGGTTATCACGTCAGTCTAACACACTGAAGGTCTCCGGTTCGAGTCCG
40298847 GGCGAAGCCATTGCTTTTAAA
66 GGCGAAGCCATTG-TTTTAAA
40298868 TTTATAAAAA
Statistics
Matches: 535, Mismatches: 15, Indels: 17
0.94 0.03 0.03
Matches are distributed among these distances:
156 2 0.00
157 184 0.34
158 340 0.64
159 8 0.01
160 1 0.00
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (158 bp):
TGGTTTCGTGGTGTAGTTGGTTATCACGTCAGTCTAACACACTGAAGGTCTCCGGTTCGAGTCCG
GGCGAAGCCATTGTTTTAAACATATTTTTAGTCTTTTAGTTTCTGCACATTTTAGTTTTTTGACT
AAAATTAAATGTCAAAAGGCATCGACTC
Found at i:40298867 original size:316 final size:317
Alignment explanation
Indices: 40298151--40298867 Score: 1218
Period size: 315 Copynumber: 2.3 Consensus size: 317
40298141 TTTATCGATG
40298151 TGGTTTCGTGGTGTAGTTGGTTATCACGTCAGTCTAACACACTGAAGGTCTCCGGTTCGAGTCCG
1 TGGTTTCGTGGTGTAGTTGGTTATCACGTCAGTCTAACACACTGAAGGTCTCCGGTTCGAGTCCG
*
40298216 GGCGAAGCCATTGC-TTCAAACATATTTTTAGTCTTTTTAGTTTCTGCACATTTTAGTTTTTTGA
66 GGCGAAGCCATTGCTTTTAAACATATTTTTAGTCTTTTTAGTTTCTGCACATTTTAGTTTTTTGA
* *
40298280 CTAAAATAAATGTCAAAAGCTAGTGAGCGTGGTTTCGTGGTGTAGTTGATTATCACGTCAGTCTA
131 CTAAAATAAATGTCAAAAGCTAGTGAGCCTGGTTTCGTGGTGTAGTTGATTATCACGTCAATCTA
*
40298345 ACACACTGAAGGTCTCCGGTTCGAGTCCGGGCGAAGCCATTGTTTTAAACATGTTTTTAGTCTTT
196 ACACACTGAAGGTCTCCGGTTCGAGTCCGGGCGAAGCCATTGTTTTAAACATATTTTTAGTCTTT
*
40298410 TAGTTTCTGCACATTTTAGTTTTTTGACTAAAATTAAATGTCAAAAGGCATCGACTC
261 TAGTGTCTGCACATTTTAGTTTTTTGACTAAAATTAAATGTCAAAAGGCATCGACTC
40298467 TGGTTTCGTGGTGTAGTTGGTTATCACGTCAGTCTAACACACTGAAGGTCTCCGGTTCGAGTCCG
1 TGGTTTCGTGGTGTAGTTGGTTATCACGTCAGTCTAACACACTGAAGGTCTCCGGTTCGAGTCCG
40298532 GGCGAAGCCATTG-TTTTAAACATATTTTTAGTC-TTTTAGTTTCTGCACATTTTAGTTTTTTGA
66 GGCGAAGCCATTGCTTTTAAACATATTTTTAGTCTTTTTAGTTTCTGCACATTTTAGTTTTTTGA
*
40298595 CTAAAATTAAATGTCAAAAGGC-A-TCGA-CTCTGGTTTCGTGGTGTAGTTGGTTATCACGTCAA
131 CTAAAA-TAAATGTCAAAA-GCTAGT-GAGC-CTGGTTTCGTGGTGTAGTTGATTATCACGTCAA
40298657 TCTAACACACTGAAGGTCTCCGGTTCGAGTCC-GGCGAAGCCATT-TCTTTAAACATATTTTTAG
192 TCTAACACACTGAAGGTCTCCGGTTCGAGTCCGGGCGAAGCCATTGT-TTTAAACATATTTTTAG
* * * * *
40298720 TCTTTTAGTGTCTGCACATTTTATTTTTTTGATTAAAGTTAAATGTCAAAA-TCTATTGACTC
256 TCTTTTAGTGTCTGCACATTTTAGTTTTTTGACTAAAATTAAATGTCAAAAGGC-ATCGACTC
40298782 TGGTTTCGTGGTGTAGTTGGTTATCACGTCAGTCTAACACACTGAAGGTCTCCGGTTCGAGTCCG
1 TGGTTTCGTGGTGTAGTTGGTTATCACGTCAGTCTAACACACTGAAGGTCTCCGGTTCGAGTCCG
40298847 GGCGAAGCCATTGCTTTTAAA
66 GGCGAAGCCATTGCTTTTAAA
40298868 TTTATAAAAA
Statistics
Matches: 382, Mismatches: 11, Indels: 16
0.93 0.03 0.04
Matches are distributed among these distances:
314 2 0.01
315 198 0.52
316 180 0.47
317 2 0.01
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (317 bp):
TGGTTTCGTGGTGTAGTTGGTTATCACGTCAGTCTAACACACTGAAGGTCTCCGGTTCGAGTCCG
GGCGAAGCCATTGCTTTTAAACATATTTTTAGTCTTTTTAGTTTCTGCACATTTTAGTTTTTTGA
CTAAAATAAATGTCAAAAGCTAGTGAGCCTGGTTTCGTGGTGTAGTTGATTATCACGTCAATCTA
ACACACTGAAGGTCTCCGGTTCGAGTCCGGGCGAAGCCATTGTTTTAAACATATTTTTAGTCTTT
TAGTGTCTGCACATTTTAGTTTTTTGACTAAAATTAAATGTCAAAAGGCATCGACTC
Found at i:40300805 original size:45 final size:47
Alignment explanation
Indices: 40300752--40300862 Score: 122
Period size: 49 Copynumber: 2.4 Consensus size: 47
40300742 TTCATATAAA
* *
40300752 ACTACACTTCTTTTATTT-TATT-TTAGAATAAGGT-TTTTCAAACTT
1 ACTACACTTCATCTATTTATATTATTAGAATAAGGTGTTTT-AAACTT
* *
40300797 ATTACACTTCATCTATTTGATATTGATTAGAATAAGGTGTTTTAACCTT
1 ACTACACTTCATCTATTT-ATATT-ATTAGAATAAGGTGTTTTAAACTT
40300846 ACTACAC-TCATTCTATT
1 ACTACACTTCA-TCTATT
40300863 AGAATATGGT
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
45 15 0.27
47 4 0.07
48 3 0.05
49 29 0.53
50 4 0.07
ACGTcount: A:0.30, C:0.15, G:0.08, T:0.47
Consensus pattern (47 bp):
ACTACACTTCATCTATTTATATTATTAGAATAAGGTGTTTTAAACTT
Found at i:40306446 original size:14 final size:15
Alignment explanation
Indices: 40306418--40306450 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
40306408 AATGTTTATA
40306418 GATTATGGAATTAGG
1 GATTATGGAATTAGG
40306433 GATTATGG-ATTAGG
1 GATTATGGAATTAGG
40306447 GATT
1 GATT
40306451 CTGATTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.36
Consensus pattern (15 bp):
GATTATGGAATTAGG
Found at i:40306625 original size:70 final size:70
Alignment explanation
Indices: 40306551--40306688 Score: 249
Period size: 70 Copynumber: 2.0 Consensus size: 70
40306541 TTAGGTTAGA
*
40306551 GTTTAGGGTTTAGATTAATTAGTGTATTTTAATTTATATATTAAATAATGTTTAGGGGTTAGGGG
1 GTTTAGGATTTAGATTAATTAGTGTATTTTAATTTATATATTAAATAATGTTTAGGGGTTAGGGG
40306616 TTAAG
66 TTAAG
* *
40306621 GTTTAGGATTTAGATTAATTAGTGTTTTTTAATTTATATATTAAATAATGTTTAGGGGTTAGTGG
1 GTTTAGGATTTAGATTAATTAGTGTATTTTAATTTATATATTAAATAATGTTTAGGGGTTAGGGG
40306686 TTA
66 TTA
40306689 GGGGTTTGGG
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 65 1.00
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.48
Consensus pattern (70 bp):
GTTTAGGATTTAGATTAATTAGTGTATTTTAATTTATATATTAAATAATGTTTAGGGGTTAGGGG
TTAAG
Found at i:40306885 original size:14 final size:15
Alignment explanation
Indices: 40306866--40306895 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
40306856 TAAGGGTTAA
40306866 GGGTTA-GGATTTAG
1 GGGTTAGGGATTTAG
40306880 GGGTTAGGGATTTAG
1 GGGTTAGGGATTTAG
40306895 G
1 G
40306896 ATTTAGTGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.20, C:0.00, G:0.47, T:0.33
Consensus pattern (15 bp):
GGGTTAGGGATTTAG
Found at i:40308560 original size:33 final size:30
Alignment explanation
Indices: 40308518--40308626 Score: 113
Period size: 27 Copynumber: 3.7 Consensus size: 30
40308508 AAGATACGGT
40308518 GGAATCAGCACTTAGCAACCACCAATGAATCGG
1 GGAATCAGCACTTAGCAACC-CCAAT--ATCGG
* *
40308551 GGAATCAGCACTTAGCAGCCCC--T-TGGG
1 GGAATCAGCACTTAGCAACCCCAATATCGG
* *
40308578 GGAATTAGCACTTAGCAACCCC--T-TGGG
1 GGAATCAGCACTTAGCAACCCCAATATCGG
40308605 GGAATCAGCACTTAGCAACCCC
1 GGAATCAGCACTTAGCAACCCC
40308627 CTTTATATTT
Statistics
Matches: 71, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
27 49 0.69
30 1 0.01
32 2 0.03
33 19 0.27
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.17
Consensus pattern (30 bp):
GGAATCAGCACTTAGCAACCCCAATATCGG
Found at i:40308587 original size:27 final size:27
Alignment explanation
Indices: 40308549--40308626 Score: 138
Period size: 27 Copynumber: 2.9 Consensus size: 27
40308539 CCAATGAATC
*
40308549 GGGGAATCAGCACTTAGCAGCCCCTTG
1 GGGGAATCAGCACTTAGCAACCCCTTG
*
40308576 GGGGAATTAGCACTTAGCAACCCCTTG
1 GGGGAATCAGCACTTAGCAACCCCTTG
40308603 GGGGAATCAGCACTTAGCAACCCC
1 GGGGAATCAGCACTTAGCAACCCC
40308627 CTTTATATTT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.26, C:0.29, G:0.27, T:0.18
Consensus pattern (27 bp):
GGGGAATCAGCACTTAGCAACCCCTTG
Found at i:40308703 original size:130 final size:130
Alignment explanation
Indices: 40308467--40308704 Score: 431
Period size: 130 Copynumber: 1.8 Consensus size: 130
40308457 NNNNNNNNNN
*
40308467 CCCTTGGGGGAATCAGTACTTAGCAACCCCCTTCACATTTAAAGATACGGTGGAATCAGCACTTA
1 CCCTTGGGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAGATACGGTGGAATCAGCACTTA
*
40308532 GCAACCACCAATGAATCGGGGAATCAGCACTTAGCAGCCCCTTGGGGGAATTAGCACTTAGCAAC
66 GCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTGGGGGAATTAGCACTTAGCAAC
* *
40308597 CCCTTGGGGGAATCAGCACTTAGCAACCCCCTTTATATTTAAAGATACGGTGGAATCAGCACTTA
1 CCCTTGGGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAGATACGGTGGAATCAGCACTTA
*
40308662 GCAACCACCAATGAGTCGGGGAATCAGCACTTAGCAACCCCTT
66 GCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTT
40308705 CATATTCAAT
Statistics
Matches: 103, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
130 103 1.00
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.21
Consensus pattern (130 bp):
CCCTTGGGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAGATACGGTGGAATCAGCACTTA
GCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTGGGGGAATTAGCACTTAGCAAC
Found at i:40309795 original size:11 final size:12
Alignment explanation
Indices: 40309767--40309800 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
40309757 GCCCAAACGT
40309767 CGAAATTTTTGAA
1 CGAAATTTTT-AA
40309780 CGAAATTTTT-A
1 CGAAATTTTTAA
40309791 CGAAATTTTT
1 CGAAATTTTT
40309801 TTGTGAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.52
13 10 0.48
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.44
Consensus pattern (12 bp):
CGAAATTTTTAA
Found at i:40310214 original size:2 final size:2
Alignment explanation
Indices: 40310198--40310235 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
40310188 TATTTAAGAG
*
40310198 AT AT AT A- AT AG AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
40310236 GATCACTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:40310447 original size:21 final size:21
Alignment explanation
Indices: 40310423--40310467 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
40310413 GGACAGGACC
40310423 AAAATATAAGAAA-AAATAAAA
1 AAAATATAA-AAAGAAATAAAA
40310444 AAAATATAAAAAGGAAATAAAA
1 AAAATATAAAAA-GAAATAAAA
40310466 AA
1 AA
40310468 CTAAAATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 3 0.14
21 9 0.41
22 10 0.45
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.13
Consensus pattern (21 bp):
AAAATATAAAAAGAAATAAAA
Found at i:40310498 original size:21 final size:21
Alignment explanation
Indices: 40310474--40310540 Score: 50
Period size: 20 Copynumber: 3.2 Consensus size: 21
40310464 AAAACTAAAA
40310474 TTTATAATTTTA-TCAAAAACT
1 TTTATAATTTTACT-AAAAACT
* *
40310495 TTTA-AATATTACTTAAAACT
1 TTTATAATTTTACTAAAAACT
* *
40310515 TTAATAATTATTTACTTAAAA-T
1 TTTATAA-T-TTTACTAAAAACT
40310537 TTTA
1 TTTA
40310541 ATGAAACATA
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
20 15 0.41
21 7 0.19
22 5 0.14
23 10 0.27
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.49
Consensus pattern (21 bp):
TTTATAATTTTACTAAAAACT
Found at i:40313212 original size:19 final size:19
Alignment explanation
Indices: 40313185--40313229 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
40313175 TTATATACAG
40313185 TTTTAATATATATATT-AAAA
1 TTTT-ATATATAT-TTGAAAA
40313205 TTTTATATATATTTGAAAA
1 TTTTATATATATTTGAAAA
*
40313224 GTTTAT
1 TTTTAT
40313230 CAATCATATC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 2 0.09
19 17 0.74
20 4 0.17
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.53
Consensus pattern (19 bp):
TTTTATATATATTTGAAAA
Found at i:40313329 original size:12 final size:11
Alignment explanation
Indices: 40313291--40313342 Score: 54
Period size: 12 Copynumber: 4.7 Consensus size: 11
40313281 TACACAACAC
*
40313291 ATAACTTACAT
1 ATAACTTATAT
*
40313302 AATAAC-T-TAC
1 -ATAACTTATAT
40313312 ATAACTTATAT
1 ATAACTTATAT
40313323 ATAAACTTATAT
1 AT-AACTTATAT
40313335 ATAACTTA
1 ATAACTTA
40313343 CNNNNNNNNN
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
9 5 0.15
10 2 0.06
11 11 0.32
12 16 0.47
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.38
Consensus pattern (11 bp):
ATAACTTATAT
Found at i:40313501 original size:16 final size:16
Alignment explanation
Indices: 40313482--40313555 Score: 76
Period size: 16 Copynumber: 4.5 Consensus size: 16
40313472 AGCCTACATG
40313482 ACTTACATAATACACA
1 ACTTACATAATACACA
* *
40313498 ACTTAAATAACTTAAACA
1 ACTTACATAA--TACACA
* *
40313516 ACTTACATAATGCATA
1 ACTTACATAATACACA
* *
40313532 ACTTACATTACACACA
1 ACTTACATAATACACA
40313548 ACTTACAT
1 ACTTACAT
40313556 TACTTACATT
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
16 32 0.70
18 14 0.30
ACGTcount: A:0.47, C:0.23, G:0.01, T:0.28
Consensus pattern (16 bp):
ACTTACATAATACACA
Found at i:40313599 original size:61 final size:62
Alignment explanation
Indices: 40313531--40313654 Score: 148
Period size: 61 Copynumber: 2.0 Consensus size: 62
40313521 CATAATGCAT
** * *
40313531 AACTTACATTACACACAACTTACAT-TACTTACATT-CATAACTTGA-ATA-AAATTTATATATA
1 AACTTACACAACACACAACTTACATATA-TAAC-TTACATAACTT-ATATATAAACTTATATATA
*
40313592 AACTTACACAACACATAACTTACATATATAACTTACATAACTTATATATAAACTTATATATA
1 AACTTACACAACACACAACTTACATATATAACTTACATAACTTATATATAAACTTATATATA
40313654 A
1 A
40313655 CTTTCATAAC
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
60 3 0.06
61 36 0.67
62 15 0.28
ACGTcount: A:0.47, C:0.18, G:0.01, T:0.35
Consensus pattern (62 bp):
AACTTACACAACACACAACTTACATATATAACTTACATAACTTATATATAAACTTATATATA
Found at i:40313623 original size:52 final size:51
Alignment explanation
Indices: 40313543--40313647 Score: 126
Period size: 52 Copynumber: 2.0 Consensus size: 51
40313533 CTTACATTAC
* *
40313543 ACACAACTTACATTACTTACATTCATAACTTGA-ATAAAATTTATATATAAACTT
1 ACACAAC-TACATAACTTACATTCATAACTT-ACAT--AACTTATATATAAACTT
40313597 ACACAAC-ACATAACTTACATAT-ATAACTTACATAACTTATATATAAACTT
1 ACACAACTACATAACTTACAT-TCATAACTTACATAACTTATATATAAACTT
40313647 A
1 A
40313648 TATATAACTT
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
50 17 0.36
51 1 0.02
52 21 0.45
53 1 0.02
54 7 0.15
ACGTcount: A:0.47, C:0.18, G:0.01, T:0.34
Consensus pattern (51 bp):
ACACAACTACATAACTTACATTCATAACTTACATAACTTATATATAAACTT
Found at i:40313624 original size:13 final size:13
Alignment explanation
Indices: 40313606--40313630 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40313596 TACACAACAC
40313606 ATAACTTACATAT
1 ATAACTTACATAT
40313619 ATAACTTACATA
1 ATAACTTACATA
40313631 ACTTATATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (13 bp):
ATAACTTACATAT
Found at i:40313631 original size:9 final size:9
Alignment explanation
Indices: 40313619--40313799 Score: 107
Period size: 9 Copynumber: 20.9 Consensus size: 9
40313609 ACTTACATAT
40313619 ATAACTTAC
1 ATAACTTAC
*
40313628 ATAACTTATAT
1 ATAAC-T-TAC
*
40313639 ATAAACTTATAT
1 AT-AAC-T-TAC
*
40313651 ATAACTTTC
1 ATAACTTAC
40313660 ATAACTTAC
1 ATAACTTAC
*
40313669 -TTA-TT--
1 ATAACTTAC
40313674 ATAACTTAC
1 ATAACTTAC
40313683 ATAA--TAC
1 ATAACTTAC
* *
40313690 ATAGCCTAC
1 ATAACTTAC
*
40313699 ATGACTTAC
1 ATAACTTAC
40313708 ATAA--TAC
1 ATAACTTAC
* *
40313715 ACAACTTAA
1 ATAACTTAC
40313724 ATAACTTAC
1 ATAACTTAC
40313733 ATAA--TAC
1 ATAACTTAC
*
40313740 ATAACTTTC
1 ATAACTTAC
40313749 ATAACTTAC
1 ATAACTTAC
*
40313758 ATTA--TAC
1 ATAACTTAC
* *
40313765 ACAACTTAT
1 ATAACTTAC
40313774 ATAACTTAC
1 ATAACTTAC
40313783 ATAACTTAC
1 ATAACTTAC
*
40313792 ATAGCTTA
1 ATAACTTA
40313800 ACTATACTTA
Statistics
Matches: 133, Mismatches: 24, Indels: 30
0.71 0.13 0.16
Matches are distributed among these distances:
6 2 0.02
7 28 0.21
8 2 0.02
9 81 0.61
10 2 0.02
11 7 0.05
12 11 0.08
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.36
Consensus pattern (9 bp):
ATAACTTAC
Found at i:40313651 original size:10 final size:11
Alignment explanation
Indices: 40313615--40313657 Score: 54
Period size: 12 Copynumber: 4.0 Consensus size: 11
40313605 CATAACTTAC
40313615 ATATATAAC-T
1 ATATATAACTT
*
40313625 -TACATAACTT
1 ATATATAACTT
40313635 ATATATAAACTT
1 ATATAT-AACTT
40313647 ATATATAACTT
1 ATATATAACTT
40313658 TCATAACTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
9 7 0.25
10 1 0.04
11 9 0.32
12 11 0.39
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.42
Consensus pattern (11 bp):
ATATATAACTT
Found at i:40313680 original size:34 final size:31
Alignment explanation
Indices: 40313606--40313681 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 31
40313596 TACACAACAC
40313606 ATAACTTACATATATAACTTACATAACTTATAT
1 ATAACTT--ATATATAACTTACATAACTTATAT
*
40313639 ATAAACTTATATATAACTTTCATAACTTACTTATT
1 AT-AACTTATATATAACTTACATAACTTA--TA-T
40313674 ATAACTTA
1 ATAACTTA
40313682 CATAATACAT
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
32 20 0.53
33 2 0.05
34 13 0.34
35 3 0.08
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.42
Consensus pattern (31 bp):
ATAACTTATATATAACTTACATAACTTATAT
Found at i:40313706 original size:25 final size:25
Alignment explanation
Indices: 40313674--40313786 Score: 145
Period size: 25 Copynumber: 4.5 Consensus size: 25
40313664 CTTACTTATT
* *
40313674 ATAACTTACATAATACATAGCCTAC
1 ATAACTTACATAATACATAACTTAC
* * *
40313699 ATGACTTACATAATACACAACTTAA
1 ATAACTTACATAATACATAACTTAC
*
40313724 ATAACTTACATAATACATAACTTTC
1 ATAACTTACATAATACATAACTTAC
* * *
40313749 ATAACTTACATTATACACAACTTAT
1 ATAACTTACATAATACATAACTTAC
40313774 ATAACTTACATAA
1 ATAACTTACATAA
40313787 CTTACATAGC
Statistics
Matches: 74, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 74 1.00
ACGTcount: A:0.46, C:0.20, G:0.02, T:0.32
Consensus pattern (25 bp):
ATAACTTACATAATACATAACTTAC
Found at i:40313741 original size:50 final size:50
Alignment explanation
Indices: 40313674--40313796 Score: 174
Period size: 50 Copynumber: 2.4 Consensus size: 50
40313664 CTTACTTATT
*
40313674 ATAACTTACATAATACATAGCCTACATGACTTACATAATACACAACTTAA
1 ATAACTTACATAATACATAGCCTACATAACTTACATAATACACAACTTAA
* * * * *
40313724 ATAACTTACATAATACATAACTTTCATAACTTACATTATACACAACTTAT
1 ATAACTTACATAATACATAGCCTACATAACTTACATAATACACAACTTAA
40313774 ATAACTTACATAACTTACATAGC
1 ATAACTTACATAA--TACATAGC
40313797 TTAACTATAC
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
50 57 0.89
52 7 0.11
ACGTcount: A:0.45, C:0.21, G:0.02, T:0.32
Consensus pattern (50 bp):
ATAACTTACATAATACATAGCCTACATAACTTACATAATACACAACTTAA
Found at i:40316619 original size:43 final size:43
Alignment explanation
Indices: 40316562--40316810 Score: 261
Period size: 43 Copynumber: 5.8 Consensus size: 43
40316552 CGTTTTTAAA
* * * * *
40316562 AAAAACGCCACTAAATG-TCATAGTCTTTAGTGGCGTTTGTGGG
1 AAAAGCGCCGCTAAA-GATCATGGTCTTTAGCGGCGTTTGTTGG
*
40316605 AAAAGCGCCGCTAAAGATCATGGTCTTCAGCGGCGTTTGTTGG
1 AAAAGCGCCGCTAAAGATCATGGTCTTTAGCGGCGTTTGTTGG
* * * *
40316648 AAAGGCGCCGCTAACGATCAGGGTCTTTAGCGGTGTTT-TCTGG
1 AAAAGCGCCGCTAAAGATCATGGTCTTTAGCGGCGTTTGT-TGG
* ** *
40316691 AGAAGCGCAACTAAAGATCAGGGTCTTTAGCGGCGTTTGTTGG
1 AAAAGCGCCGCTAAAGATCATGGTCTTTAGCGGCGTTTGTTGG
* * **
40316734 AGAAGCGCCGCTAAAGACCATGACCTTTAGCGGCGTTTG-TGG
1 AAAAGCGCCGCTAAAGATCATGGTCTTTAGCGGCGTTTGTTGG
* * *
40316776 TGAAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGC
1 -AAAAGCGCCGCTAAAGATCATGGTCTTTAGCGGC
40316811 ATTTATTTCT
Statistics
Matches: 172, Mismatches: 30, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
42 5 0.03
43 166 0.97
44 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.31, T:0.26
Consensus pattern (43 bp):
AAAAGCGCCGCTAAAGATCATGGTCTTTAGCGGCGTTTGTTGG
Found at i:40316914 original size:22 final size:22
Alignment explanation
Indices: 40316879--40316921 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
40316869 TTGCGGCGCT
*
40316879 AAAAAGCGCCGCTAAAGGCCTA
1 AAAAAGCGCCGCTAAAAGCCTA
* *
40316901 AAAAAGTGCTGCTAAAAGCCT
1 AAAAAGCGCCGCTAAAAGCCT
40316922 GTTTTGGTGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.42, C:0.23, G:0.21, T:0.14
Consensus pattern (22 bp):
AAAAAGCGCCGCTAAAAGCCTA
Found at i:40324222 original size:17 final size:18
Alignment explanation
Indices: 40324202--40324238 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
40324192 TGAAAATATT
*
40324202 AATTTTCAATTGATT-TA
1 AATTTTCAATGGATTGTA
40324219 AATTTTCAATGGATTGTA
1 AATTTTCAATGGATTGTA
40324237 AA
1 AA
40324239 AGTGATAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.38, C:0.05, G:0.11, T:0.46
Consensus pattern (18 bp):
AATTTTCAATGGATTGTA
Found at i:40326231 original size:2 final size:2
Alignment explanation
Indices: 40326224--40326249 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
40326214 TGCTAATTTA
40326224 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
40326250 GTAAGTTGAT
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:40327052 original size:20 final size:21
Alignment explanation
Indices: 40327017--40327058 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
40327007 AAGTAACTAG
40327017 ATAAATAAAATAGAACAATAA
1 ATAAATAAAATAGAACAATAA
*
40327038 ATAAA-AAATTAGAACAATAA
1 ATAAATAAAATAGAACAATAA
40327058 A
1 A
40327059 GAAGATAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.71, C:0.05, G:0.05, T:0.19
Consensus pattern (21 bp):
ATAAATAAAATAGAACAATAA
Found at i:40330255 original size:24 final size:23
Alignment explanation
Indices: 40330157--40330258 Score: 73
Period size: 24 Copynumber: 4.3 Consensus size: 23
40330147 ACTGTAAAAT
*
40330157 TGAGTGGCTTGTCCACAAC-AATA
1 TGAGTGGCTTGGCCACAACGAA-A
* * *
40330180 TGAGTAGCTT-GCCTACAAAGCTAA
1 TGAGTGGCTTGGCC-ACAACG-AAA
* * * *
40330204 CGAGTGACTTGACCACAACGATAT
1 TGAGTGGCTTGGCCACAACGA-AA
40330228 TGAGTGGCTTGGCCACAACGTAAA
1 TGAGTGGCTTGGCCACAACG-AAA
40330252 TGAGTGG
1 TGAGTGG
40330259 TTTGACCCCA
Statistics
Matches: 58, Mismatches: 15, Indels: 11
0.69 0.18 0.13
Matches are distributed among these distances:
22 2 0.03
23 13 0.22
24 39 0.67
25 4 0.07
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.24
Consensus pattern (23 bp):
TGAGTGGCTTGGCCACAACGAAA
Found at i:40333671 original size:25 final size:25
Alignment explanation
Indices: 40333609--40333663 Score: 69
Period size: 23 Copynumber: 2.2 Consensus size: 25
40333599 TATATATATT
* *
40333609 CTAAAAAAGAAAAAGGAATACCTAAT
1 CTAAAAATG-AAAAGGAATACCTAAC
40333635 CTAAAAATGAAAA-GAA-ACCTAAC
1 CTAAAAATGAAAAGGAATACCTAAC
40333658 CTAAAA
1 CTAAAA
40333664 CTATGAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 12 0.44
24 3 0.11
25 4 0.15
26 8 0.30
ACGTcount: A:0.62, C:0.15, G:0.09, T:0.15
Consensus pattern (25 bp):
CTAAAAATGAAAAGGAATACCTAAC
Found at i:40337245 original size:24 final size:24
Alignment explanation
Indices: 40337218--40337269 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
40337208 CCGAAATAAT
40337218 GGAAAGGTTGAAAAGGATAACAAC
1 GGAAAGGTTGAAAAGGATAACAAC
* * *
40337242 GGAAAGGTTGAAAATGATAGCAAT
1 GGAAAGGTTGAAAAGGATAACAAC
40337266 GGAA
1 GGAA
40337270 TGGCTATTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.48, C:0.06, G:0.31, T:0.15
Consensus pattern (24 bp):
GGAAAGGTTGAAAAGGATAACAAC
Found at i:40341193 original size:26 final size:26
Alignment explanation
Indices: 40341157--40341218 Score: 90
Period size: 26 Copynumber: 2.4 Consensus size: 26
40341147 AATAGATTTT
40341157 GTCAAAATTTTAC-TAGGGGTAAAATC
1 GTCAAAATTTTACTTA-GGGTAAAATC
*
40341183 GTCAAACTTTTACTTAGGGTAAAATC
1 GTCAAAATTTTACTTAGGGTAAAATC
*
40341209 ATCAAAATTT
1 GTCAAAATTT
40341219 GTTGGGGGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
26 30 0.94
27 2 0.06
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.34
Consensus pattern (26 bp):
GTCAAAATTTTACTTAGGGTAAAATC
Found at i:40342939 original size:14 final size:13
Alignment explanation
Indices: 40342920--40342949 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
40342910 CTTGATTAGG
40342920 AATTAATTAATCTT
1 AATTAATTAA-CTT
40342934 AATTAATTAACTT
1 AATTAATTAACTT
40342947 AAT
1 AAT
40342950 CATGACTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (13 bp):
AATTAATTAACTT
Found at i:40350602 original size:20 final size:20
Alignment explanation
Indices: 40350577--40350624 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 20
40350567 TCTTATCACC
40350577 ATGTATTTTGAAAT-TAAAAA
1 ATGTATTTT-AAATGTAAAAA
40350597 ATGTA--TTAAATGTAAAAA
1 ATGTATTTTAAATGTAAAAA
40350615 ATGTGATTTT
1 ATGT-ATTTT
40350625 TTAATAAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
17 4 0.17
18 12 0.50
19 1 0.04
20 5 0.21
21 2 0.08
ACGTcount: A:0.46, C:0.00, G:0.12, T:0.42
Consensus pattern (20 bp):
ATGTATTTTAAATGTAAAAA
Found at i:40350914 original size:21 final size:21
Alignment explanation
Indices: 40350870--40350924 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
40350860 TAGGGAATTT
* **
40350870 GGGGAAAGTAAAATTTTTTTA
1 GGGGAAAGTAAAAGTTTTAAA
40350891 GGGGAAAGTAAAAGTTTTAAA
1 GGGGAAAGTAAAAGTTTTAAA
*
40350912 -GGGAAAATAAAAG
1 GGGGAAAGTAAAAG
40350925 GAAAAAAGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 12 0.40
21 18 0.60
ACGTcount: A:0.47, C:0.00, G:0.27, T:0.25
Consensus pattern (21 bp):
GGGGAAAGTAAAAGTTTTAAA
Found at i:40350915 original size:20 final size:20
Alignment explanation
Indices: 40350871--40350924 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
40350861 AGGGAATTTG
* * *
40350871 GGGAAAGTAAAATTTTTTTAG
1 GGGAAAGTAAAA-GTTTTAAA
40350892 GGGAAAGTAAAAGTTTTAAA
1 GGGAAAGTAAAAGTTTTAAA
*
40350912 GGGAAAATAAAAG
1 GGGAAAGTAAAAG
40350925 GAAAAAAGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.48, C:0.00, G:0.26, T:0.26
Consensus pattern (20 bp):
GGGAAAGTAAAAGTTTTAAA
Found at i:40352516 original size:126 final size:126
Alignment explanation
Indices: 40352273--40352540 Score: 337
Period size: 126 Copynumber: 2.1 Consensus size: 126
40352263 AAGGCCAAAC
* * * *
40352273 AGGAATTACTGTAGAATAAGAGCGCCCATGTGAGAGCTTTTTTTAGTATTTTTGCTGACAGTGCA
1 AGGAACTACTGTAGAATAAGAGCGCCCACGTGAGAGCTTTTTTCAGTAATTTTGCTGACAGTGCA
* * * * * * *
40352338 TCCTGCTTGAAGTGTTTTTGACACTATTTGTTTAGAATCGTCTTCTCGAAATTATTTTTTT
66 TCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAACCATCTTATCAAAATTAATTTTTT
*
40352399 AGGAACTACTGTAGTAA-AAGAGCGTCCACGTG-GAAGCTTTTTTCAGTAATTTTGCTGACAGTG
1 AGGAACTACTGTAG-AATAAGAGCGCCCACGTGAG-AGCTTTTTTCAGTAATTTTGCTGACAGTG
*
40352462 CATCCTGCTTGAAGCGTTTTTGACATTATCTT-TTCAGAACCATCTTATCAAAATTAATTTTTCT
64 CATCCTGCTTGAAGCGTTTTTGACACTAT-TTGTTCAGAACCATCTTATCAAAATTAATTTTT-T
* *
40352526 -GAAACTACCGTAGAA
1 AGGAACTACTGTAGAA
40352541 AAAAAACAAA
Statistics
Matches: 123, Mismatches: 15, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
125 3 0.02
126 115 0.93
127 5 0.04
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.38
Consensus pattern (126 bp):
AGGAACTACTGTAGAATAAGAGCGCCCACGTGAGAGCTTTTTTCAGTAATTTTGCTGACAGTGCA
TCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAACCATCTTATCAAAATTAATTTTTT
Found at i:40352652 original size:34 final size:34
Alignment explanation
Indices: 40352608--40352733 Score: 164
Period size: 34 Copynumber: 3.6 Consensus size: 34
40352598 ATTTTTAAAA
* *
40352608 AAAAAATCTAAACCCTAATTTAATTAATTTTCTT
1 AAAAACTCTAAACCCTAATTTAATTAATTTTATT
*
40352642 AAAAACTCTAAACCCTAATTTAAATAA-TTTATT
1 AAAAACTCTAAACCCTAATTTAATTAATTTTATT
* * *
40352675 AAAAACCCCTAAAGCCTAATTTAATTAATTTTTTT
1 AAAAA-CTCTAAACCCTAATTTAATTAATTTTATT
40352710 AAAAAAACTCTAAACCCTAATTTA
1 --AAAAACTCTAAACCCTAATTTA
40352734 TTTTTTAGAA
Statistics
Matches: 79, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
33 10 0.13
34 44 0.56
35 5 0.06
36 15 0.19
37 5 0.06
ACGTcount: A:0.46, C:0.17, G:0.01, T:0.37
Consensus pattern (34 bp):
AAAAACTCTAAACCCTAATTTAATTAATTTTATT
Found at i:40352797 original size:33 final size:33
Alignment explanation
Indices: 40352758--40352867 Score: 131
Period size: 33 Copynumber: 3.4 Consensus size: 33
40352748 TAAACCATAC
*
40352758 ACCCTAAACCTAAATTATTTTAACAAAATCTTA
1 ACCCTAAACCTAAATTATTTTAACAAAATCCTA
*
40352791 ACCCTAAACCTAAACTATTTTAACAAAATCCT-
1 ACCCTAAACCTAAATTATTTTAACAAAATCCTA
*
40352823 A----AAACCATAAATTATTTTAACAAAACCCTA
1 ACCCTAAACC-TAAATTATTTTAACAAAATCCTA
*
40352853 ACACTAAACCCTAAA
1 ACCCTAAA-CCTAAA
40352868 ACACCTAAAC
Statistics
Matches: 66, Mismatches: 4, Indels: 13
0.80 0.05 0.16
Matches are distributed among these distances:
28 5 0.08
29 20 0.30
30 1 0.02
32 1 0.02
33 30 0.45
34 7 0.11
35 2 0.03
ACGTcount: A:0.48, C:0.25, G:0.00, T:0.27
Consensus pattern (33 bp):
ACCCTAAACCTAAATTATTTTAACAAAATCCTA
Found at i:40354287 original size:99 final size:99
Alignment explanation
Indices: 40354146--40354353 Score: 389
Period size: 99 Copynumber: 2.1 Consensus size: 99
40354136 GCCTCCCAGG
40354146 AACCCTAACCCCTCGACCGAACCCGAGTCGATAGCCCAAGAAGAATCCGAACCCAGAACAGCCAA
1 AACCCTAACCCCTCGACCGAACCCGAGTCGATAGCCCAAGAAGAATCCGAACCCAGAACAGCCAA
40354211 AACCACGATGGGTCCTCCGCCACCTCTTCCCATA
66 AACCACGATGGGTCCTCCGCCACCTCTTCCCATA
* * *
40354245 AACCCTAACCCCTCGACCGAACCCGAGTCGATAGCCCCAGAAGAATCCGAACTCATAACAGCCAA
1 AACCCTAACCCCTCGACCGAACCCGAGTCGATAGCCCAAGAAGAATCCGAACCCAGAACAGCCAA
40354310 AACCACGATGGGTCCTCCGCCACCTCTTCCCATA
66 AACCACGATGGGTCCTCCGCCACCTCTTCCCATA
40354344 AACCCTAACC
1 AACCCTAACC
40354354 TGCAAAATCC
Statistics
Matches: 106, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
99 106 1.00
ACGTcount: A:0.31, C:0.41, G:0.15, T:0.13
Consensus pattern (99 bp):
AACCCTAACCCCTCGACCGAACCCGAGTCGATAGCCCAAGAAGAATCCGAACCCAGAACAGCCAA
AACCACGATGGGTCCTCCGCCACCTCTTCCCATA
Found at i:40365123 original size:20 final size:20
Alignment explanation
Indices: 40365084--40365124 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
40365074 AAAAAATTAA
* *
40365084 TATTCTTTTGGTATTTTTTT
1 TATTCTTTTGGTAATATTTT
*
40365104 TATTCTTTTTGTAATATTTT
1 TATTCTTTTGGTAATATTTT
40365124 T
1 T
40365125 GTAAAAGATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.05, G:0.07, T:0.73
Consensus pattern (20 bp):
TATTCTTTTGGTAATATTTT
Found at i:40367955 original size:2 final size:2
Alignment explanation
Indices: 40367948--40367972 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
40367938 TTGTGAGCTT
40367948 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
40367973 GGGGGGACAG
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:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:40368843 original size:22 final size:24
Alignment explanation
Indices: 40368805--40368855 Score: 88
Period size: 23 Copynumber: 2.2 Consensus size: 24
40368795 AAGTTAAAAA
40368805 TTTAAAAATATTATTTTTA-ATTT
1 TTTAAAAATATTATTTTTACATTT
40368828 TTTAAAAATATT-TTTTTACATTT
1 TTTAAAAATATTATTTTTACATTT
40368851 TTTAA
1 TTTAA
40368856 TTTTTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 6 0.22
23 21 0.78
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (24 bp):
TTTAAAAATATTATTTTTACATTT
Found at i:40370552 original size:2 final size:2
Alignment explanation
Indices: 40370547--40370571 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
40370537 TCAAAACAAT
40370547 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
40370572 TAGATTATGA
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:40372677 original size:22 final size:22
Alignment explanation
Indices: 40372652--40372693 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
40372642 ATAGATATAA
*
40372652 AAATTAAAATATATTTAGATTT
1 AAATTAAAATAAATTTAGATTT
*
40372674 AAATTATAATAAATTTAGAT
1 AAATTAAAATAAATTTAGAT
40372694 AAAATCCAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (22 bp):
AAATTAAAATAAATTTAGATTT
Found at i:40376976 original size:19 final size:19
Alignment explanation
Indices: 40376952--40377009 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 19
40376942 TTCAATTTCT
40376952 CAATTTATTCTTTATAGAA
1 CAATTTATTCTTTATAGAA
40376971 CAA--T-TTC--TATA-AA
1 CAATTTATTCTTTATAGAA
*
40376984 GAATTTATTCTTTATAGAA
1 CAATTTATTCTTTATAGAA
40377003 CAATTTA
1 CAATTTA
40377010 GGAACATGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 12
0.69 0.04 0.27
Matches are distributed among these distances:
13 4 0.13
14 4 0.13
15 1 0.03
16 6 0.19
17 1 0.03
18 4 0.13
19 11 0.35
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.45
Consensus pattern (19 bp):
CAATTTATTCTTTATAGAA
Found at i:40378025 original size:20 final size:19
Alignment explanation
Indices: 40377985--40378025 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
40377975 TTAATTAAAT
**
40377985 AAATTATTAAAAATATTAA
1 AAATTATTAAAAATAAAAA
40378004 AAATATATTAAAAATAAAAA
1 AAAT-TATTAAAAATAAAAA
40378024 AA
1 AA
40378026 TCAACTAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (19 bp):
AAATTATTAAAAATAAAAA
Found at i:40379372 original size:21 final size:21
Alignment explanation
Indices: 40379348--40379388 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
40379338 TGATTAACTA
*
40379348 AAATTATAATAAACTTAAAAT
1 AAATTATAATAAACATAAAAT
*
40379369 AAATTATAATATACATAAAA
1 AAATTATAATAAACATAAAA
40379389 ATTGAAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (21 bp):
AAATTATAATAAACATAAAAT
Found at i:40381328 original size:36 final size:36
Alignment explanation
Indices: 40381288--40381357 Score: 108
Period size: 36 Copynumber: 1.9 Consensus size: 36
40381278 TGTGGAGCTC
40381288 GATGA-TTAGTGTTTG-TTTTAGGTGTTGGTCTTTTTT
1 GATGACTT-GTGTTTGTTTTTAGGTGTTGG-CTTTTTT
40381324 GATGACTTGTGTTTGTTTTTAGGTGTTGGCTTTT
1 GATGACTTGTGTTTGTTTTTAGGTGTTGGCTTTT
40381358 CTATAACTCG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
36 17 0.53
37 15 0.47
ACGTcount: A:0.10, C:0.04, G:0.29, T:0.57
Consensus pattern (36 bp):
GATGACTTGTGTTTGTTTTTAGGTGTTGGCTTTTTT
Found at i:40381726 original size:43 final size:43
Alignment explanation
Indices: 40381673--40381898 Score: 307
Period size: 43 Copynumber: 5.3 Consensus size: 43
40381663 CGGCGCTTAC
*
40381673 CCCACAAACGCCGCTATAGATCATGACCTTTAGCAGCGCTTTT
1 CCCACAAACGCCGCTATAGATCATGACTTTTAGCAGCGCTTTT
40381716 CCCACAAACGCCGCTATAGATCATGACTTTTAGC-G-GCATTTT
1 CCCACAAACGCCGCTATAGATCATGACTTTTAGCAGCGC-TTTT
* * * *
40381758 CCCTA-AAACACTGCTATAGATCATGAGTTTTAGCGGCGCTTTT
1 CCC-ACAAACGCCGCTATAGATCATGACTTTTAGCAGCGCTTTT
* * *
40381801 CCCACAAACGCCGCTAAAGGTCATGACTTTTAACAGCGCTTTT
1 CCCACAAACGCCGCTATAGATCATGACTTTTAGCAGCGCTTTT
* *
40381844 -CCACAAACGCTGCTATAGATCATGACTTTTAGCGGCGCTTTT
1 CCCACAAACGCCGCTATAGATCATGACTTTTAGCAGCGCTTTT
*
40381886 TCCACAAACGCCG
1 CCCACAAACGCCG
40381899 TTATTGTTTG
Statistics
Matches: 160, Mismatches: 17, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
41 2 0.01
42 72 0.45
43 84 0.52
44 2 0.01
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.27
Consensus pattern (43 bp):
CCCACAAACGCCGCTATAGATCATGACTTTTAGCAGCGCTTTT
Found at i:40381791 original size:85 final size:85
Alignment explanation
Indices: 40381674--40381898 Score: 312
Period size: 85 Copynumber: 2.6 Consensus size: 85
40381664 GGCGCTTACC
* * * * *
40381674 CCACAAACGCCGCTATAGATCATGACCTTTAGCAGCGCTTTTCCCACAAACGCCGCTATAGATCA
1 CCACAAACACTGCTATAGATCATGACTTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGATCA
*
40381739 TGACTTTTAGC-G-GCATTTT
66 TGACTTTTAACAGCGC-TTTT
* *
40381758 CC-CTAAAACACTGCTATAGATCATGAGTTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGGT
1 CCAC--AAACACTGCTATAGATCATGACTTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGAT
40381822 CATGACTTTTAACAGCGCTTTT
64 CATGACTTTTAACAGCGCTTTT
* *
40381844 CCACAAACGCTGCTATAGATCATGACTTTTAGCGGCGCTTTTTCCACAAACGCCG
1 CCACAAACACTGCTATAGATCATGACTTTTAGCGGCGCTTTTCCCACAAACGCCG
40381899 TTATTGTTTG
Statistics
Matches: 125, Mismatches: 11, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
83 1 0.01
84 2 0.02
85 112 0.90
86 7 0.06
87 3 0.02
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.28
Consensus pattern (85 bp):
CCACAAACACTGCTATAGATCATGACTTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGATCA
TGACTTTTAACAGCGCTTTT
Found at i:40384939 original size:28 final size:28
Alignment explanation
Indices: 40384902--40385030 Score: 197
Period size: 28 Copynumber: 4.6 Consensus size: 28
40384892 TGATAATGAG
* *
40384902 ATTAA-CACTAAGTGTGCGAGTTTAATT
1 ATTAAGCACTAAGTGTGCGAGATTGATT
* *
40384929 GTAAAGCACTAAGTGTGCGAGATTGATT
1 ATTAAGCACTAAGTGTGCGAGATTGATT
*
40384957 ATTAAGCACTAAGTGCGCGAGATTGATT
1 ATTAAGCACTAAGTGTGCGAGATTGATT
*
40384985 ATTAAGCACTAAGTGCGCGAGATTGATT
1 ATTAAGCACTAAGTGTGCGAGATTGATT
40385013 ATTAAGCACTAAGTGTGC
1 ATTAAGCACTAAGTGTGC
40385031 AAACTTATTA
Statistics
Matches: 93, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
27 3 0.03
28 90 0.97
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.30
Consensus pattern (28 bp):
ATTAAGCACTAAGTGTGCGAGATTGATT
Found at i:40385830 original size:70 final size:70
Alignment explanation
Indices: 40385756--40386285 Score: 776
Period size: 70 Copynumber: 7.5 Consensus size: 70
40385746 AGATGCTGCC
* * * * *
40385756 CAATTTGCTGTATTTATGCAGCCTAAATTGTTGTATATATGCTATCCAATTTTGATGTAAAAATG
1 CAATTTGGTATATATATGCTGCCTAAATTGTTGTATATATGCTGTCCAATTTTGATGTAAAAATG
40385821 TTGCT
66 TTGCT
40385826 CAATTTGGTATATATATGCTGCCTAAATTGTTGTATATATGCTGTCCAATTTTGATGTAAAAATG
1 CAATTTGGTATATATATGCTGCCTAAATTGTTGTATATATGCTGTCCAATTTTGATGTAAAAATG
40385891 TTGCT
66 TTGCT
*
40385896 CTATTTGGTATATATATGCTGCCTAAATTGTTGTATATATGCTGTCCAATTTTGATGTAAAAATG
1 CAATTTGGTATATATATGCTGCCTAAATTGTTGTATATATGCTGTCCAATTTTGATGTAAAAATG
*
40385961 CTGCT
66 TTGCT
* *
40385966 CAATTTGTTATATATATGCTGCCTAAATTGTTGTATATATGCTGTCCAGTTTTGATGTAAAAATG
1 CAATTTGGTATATATATGCTGCCTAAATTGTTGTATATATGCTGTCCAATTTTGATGTAAAAATG
40386031 TTGCT
66 TTGCT
*
40386036 CAATTTGTTATATATATGCTGCCTAAATTGTTGTATATATGCTGTCCAATTTTGATGTAAAAATG
1 CAATTTGGTATATATATGCTGCCTAAATTGTTGTATATATGCTGTCCAATTTTGATGTAAAAATG
*
40386101 TTGTT
66 TTGCT
* * *
40386106 CAATTTGGTATATATATGCTGCCCAATTTGTTGTATATATGCTGTCCAATTTTTGGTGTAAAAAT
1 CAATTTGGTATATATATGCTGCCTAAATTGTTGTATATATGCTGTCCAA-TTTTGATGTAAAAAT
*
40386171 GCTGCT
65 GTTGCT
* * * * *
40386177 CAATTTTGTTGTATATATGCTGCCCAAATTGTTGTATATATGCTGTCCAAATTTTGGTGTGAAAA
1 CAA-TTTGGTATATATATGCTGCCTAAATTGTTGTATATATGCTGTCC-AATTTTGATGTAAAAA
*
40386242 TGCTG-T
64 TGTTGCT
* * * *
40386248 CTAGTTTGGTATATAAATGTTGTCC-AAATTGATGTATA
1 C-AATTTGGTATATATATGCTG-CCTAAATTGTTGTATA
40386286 AGGGCTGTCC
Statistics
Matches: 426, Mismatches: 29, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
70 313 0.73
71 49 0.12
72 62 0.15
73 2 0.00
ACGTcount: A:0.28, C:0.12, G:0.17, T:0.43
Consensus pattern (70 bp):
CAATTTGGTATATATATGCTGCCTAAATTGTTGTATATATGCTGTCCAATTTTGATGTAAAAATG
TTGCT
Found at i:40385913 original size:47 final size:45
Alignment explanation
Indices: 40385853--40386200 Score: 180
Period size: 47 Copynumber: 7.4 Consensus size: 45
40385843 GCTGCCTAAA
* * *
40385853 TTGTTGTATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTCTAT
1 TTGTTATATATATGCTG-CCAA-TTTGATGTAAAAATGCTGCTCAAT
* * * * *
40385900 TTGGTATATATATGCTGCCTAAATTGTTGTATATATGCTG-TCCAATT
1 TTGTTATATATATGCTGCC-AATTTGATGTAAAAATGCTGCT-CAA-T
* * * * * * * * *
40385947 TTGATGTAAAAATGCTGCTCAATTTGTTATATATATGCTGC-CTAAA
1 TTGTTATATATATGCTGC-CAATTTGATGTAAAAATGCTGCTC-AAT
* * *
40385993 TTGTTGTATATATGCTGTCCAGTTTTGATGTAAAAATGTTGCTCAAT
1 TTGTTATATATATGCTG-CCA-ATTTGATGTAAAAATGCTGCTCAAT
* * * *
40386040 TTGTTATATATATGCTGCCTAAATTGTTGTATATATGCTG-TCCAATT
1 TTGTTATATATATGCTGCC-AATTTGATGTAAAAATGCTGCT-CAA-T
* * * * * * * * * * *
40386087 TTGATGTAAAAATGTTGTTCAATTTGGTATATATATGCTGCCCAAT
1 TTGTTATATATATGCTG-CCAATTTGATGTAAAAATGCTGCTCAAT
* *
40386133 TTGTTGTATATATGCTGTCCAATTTTTGGTGTAAAAATGCTGCTCAATT
1 TTGTTATATATATGCTG-CCAA--TTTGATGTAAAAATGCTGCTCAA-T
*
40386182 TTGTTGTATATATGCTGCC
1 TTGTTATATATATGCTGCC
40386201 CAAATTGTTG
Statistics
Matches: 233, Mismatches: 51, Indels: 33
0.74 0.16 0.10
Matches are distributed among these distances:
45 2 0.01
46 70 0.30
47 119 0.51
48 24 0.10
49 18 0.08
ACGTcount: A:0.26, C:0.12, G:0.17, T:0.44
Consensus pattern (45 bp):
TTGTTATATATATGCTGCCAATTTGATGTAAAAATGCTGCTCAAT
Found at i:40386247 original size:25 final size:25
Alignment explanation
Indices: 40385787--40386298 Score: 136
Period size: 23 Copynumber: 21.8 Consensus size: 25
40385777 CCTAAATTGT
* * *
40385787 TGTATATATGCTATCC-AATTTTGA
1 TGTATAAATGCTGTCCAAATTTTGG
* *
40385811 TGTAAAAATGTTG-CTC-AA-TTTGG
1 TGTATAAATGCTGTC-CAAATTTTGG
* * *
40385834 TATATATATGCTG-CCTAAA--TTGT
1 TGTATAAATGCTGTCC-AAATTTTGG
* *
40385857 TGTATATATGCTGTCC-AATTTTGA
1 TGTATAAATGCTGTCCAAATTTTGG
* * *
40385881 TGTAAAAATGTTG-CTC-TA-TTTGG
1 TGTATAAATGCTGTC-CAAATTTTGG
* * *
40385904 TATATATATGCTG-CCTAAA--TTGT
1 TGTATAAATGCTGTCC-AAATTTTGG
* *
40385927 TGTATATATGCTGTCC-AATTTTGA
1 TGTATAAATGCTGTCCAAATTTTGG
* *
40385951 TGTAAAAATGCTG-CTC-AA-TTTGT
1 TGTATAAATGCTGTC-CAAATTTTGG
* * *
40385974 TATATATATGCTG-CCTAAA--TTGT
1 TGTATAAATGCTGTCC-AAATTTTGG
* * *
40385997 TGTATATATGCTGTCC-AGTTTTGA
1 TGTATAAATGCTGTCCAAATTTTGG
* * *
40386021 TGTAAAAATGTTG-CTC-AA-TTTGT
1 TGTATAAATGCTGTC-CAAATTTTGG
* * *
40386044 TATATATATGCTG-CCTAAA--TTGT
1 TGTATAAATGCTGTCC-AAATTTTGG
* *
40386067 TGTATATATGCTGTCC-AATTTTGA
1 TGTATAAATGCTGTCCAAATTTTGG
* * *
40386091 TGTAAAAATGTTGTTC-AA-TTTGG
1 TGTATAAATGCTGTCCAAATTTTGG
* * * *
40386114 TATATATATGCTG-CCCAA-TTTGT
1 TGTATAAATGCTGTCCAAATTTTGG
* *
40386137 TGTATATATGCTGTCCAATTTTTGG
1 TGTATAAATGCTGTCCAAATTTTGG
* *
40386162 TGTAAAAATGCTG-CTC-AATTTTGT
1 TGTATAAATGCTGTC-CAAATTTTGG
* * *
40386186 TGTATATATGCTGCCCAAA--TTGT
1 TGTATAAATGCTGTCCAAATTTTGG
*
40386209 TGTATATATGCTGTCCAAATTTTGG
1 TGTATAAATGCTGTCCAAATTTTGG
* *
40386234 TGTGA-AAATGCTGT-C-TAGTTTGG
1 TGT-ATAAATGCTGTCCAAATTTTGG
* * *
40386257 TATATAAATGTTGTCCAAA--TTGA
1 TGTATAAATGCTGTCCAAATTTTGG
**
40386280 TGTATAAGGGCTGTCCAAA
1 TGTATAAATGCTGTCCAAA
40386299 CAGGGTAGAT
Statistics
Matches: 373, Mismatches: 79, Indels: 73
0.71 0.15 0.14
Matches are distributed among these distances:
22 13 0.03
23 210 0.56
24 115 0.31
25 34 0.09
26 1 0.00
ACGTcount: A:0.28, C:0.12, G:0.18, T:0.43
Consensus pattern (25 bp):
TGTATAAATGCTGTCCAAATTTTGG
Found at i:40390831 original size:9 final size:9
Alignment explanation
Indices: 40390819--40391204 Score: 244
Period size: 9 Copynumber: 43.2 Consensus size: 9
40390809 TATGTTTATG
40390819 TATGTAAGT
1 TATGTAAGT
40390828 TATGT-A-T
1 TATGTAAGT
40390835 TATGTAAGT
1 TATGTAAGT
*
40390844 AATGTAAGT
1 TATGTAAGT
*
40390853 TGTGT-A-T
1 TATGTAAGT
40390860 TATGTAAGT
1 TATGTAAGT
40390869 TATGTAAGT
1 TATGTAAGT
*
40390878 TGTGTAAGT
1 TATGTAAGT
*
40390887 TCTGT-A-T
1 TATGTAAGT
*
40390894 GATGTAAGT
1 TATGTAAGT
40390903 TATGTAAGT
1 TATGTAAGT
*
40390912 TGTG-AA-T
1 TATGTAAGT
* *
40390919 AATGTAATT
1 TATGTAAGT
*
40390928 TATGTAATT
1 TATGTAAGT
**
40390937 TGGGT-A-T
1 TATGTAAGT
*
40390944 TATGGAAGT
1 TATGTAAGT
40390953 TATGTAAGT
1 TATGTAAGT
*
40390962 AATGT-A-T
1 TATGTAAGT
40390969 TATGTAAGTT
1 TATGTAAG-T
40390979 TATGTAAGT
1 TATGTAAGT
40390988 TATGTAAGT
1 TATGTAAGT
40390997 TATGTAAGT
1 TATGTAAGT
*
40391006 TATGTAAAT
1 TATGTAAGT
*
40391015 TATATAAGTT
1 TATGTAAG-T
* *
40391025 TATGAAATT
1 TATGTAAGT
* *
40391034 TGATCTTTAAAT
1 T-A--TGTAAGT
40391046 TATGTAAGT
1 TATGTAAGT
*
40391055 TATGTAAAT
1 TATGTAAGT
40391064 TATGTAAGT
1 TATGTAAGT
* * *
40391073 TAAGAAATT
1 TATGTAAGT
* *
40391082 TGATCTTTAAAT
1 T-A--TGTAAGT
*
40391094 TATGTAACT
1 TATGTAAGT
*
40391103 CT-TGTAACT
1 -TATGTAAGT
40391112 TATGTAAGT
1 TATGTAAGT
*
40391121 TATGTAAAT
1 TATGTAAGT
*
40391130 TATGTTAGT
1 TATGTAAGT
* *
40391139 TATGAAATT
1 TATGTAAGT
* *
40391148 TGATCTTTAAAT
1 T-A--TGTAAGT
40391160 TATGTAAGT
1 TATGTAAGT
40391169 TATGT-A-T
1 TATGTAAGT
*
40391176 TATGTAAAT
1 TATGTAAGT
*
40391185 TATGTAAAT
1 TATGTAAGT
40391194 TATGTAAGT
1 TATGTAAGT
40391203 TA
1 TA
40391205 AAATATTTGA
Statistics
Matches: 294, Mismatches: 56, Indels: 54
0.73 0.14 0.13
Matches are distributed among these distances:
7 32 0.11
8 17 0.06
9 209 0.71
10 19 0.06
11 3 0.01
12 14 0.05
ACGTcount: A:0.34, C:0.02, G:0.18, T:0.46
Consensus pattern (9 bp):
TATGTAAGT
Found at i:40390849 original size:25 final size:26
Alignment explanation
Indices: 40390820--40391023 Score: 142
Period size: 25 Copynumber: 8.0 Consensus size: 26
40390810 ATGTTTATGT
40390820 ATGTAAGTTATGT-ATTATGTAAGTA
1 ATGTAAGTTATGTAATTATGTAAGTA
* *
40390845 ATGTAAGTTGTGT-ATTATGTAAGTT
1 ATGTAAGTTATGTAATTATGTAAGTA
* * *
40390870 ATGTAAGTTGTGTAAGTTCTGT-A-TG
1 ATGTAAGTTATGTAA-TTATGTAAGTA
*
40390895 ATGTAAGTTATGTAAGT-TGTGAA-TA
1 ATGTAAGTTATGTAATTATGT-AAGTA
* *
40390920 ATGTAATTTATGTAATT-TGGGT-A-TT
1 ATGTAAGTTATGTAATTAT--GTAAGTA
* * *
40390945 ATGGAAGTTATGTAAGTAATGT-A-TT
1 ATGTAAGTTATGTAA-TTATGTAAGTA
*
40390970 ATGTAAGTTTATGTAAGTTATGTAAGTT
1 ATGTAAG-TTATGTAA-TTATGTAAGTA
*
40390998 ATGTAAGTTATGTAAATTATATAAGT
1 ATGTAAGTTATGT-AATTATGTAAGT
40391024 TTATGAAATT
Statistics
Matches: 151, Mismatches: 16, Indels: 22
0.80 0.08 0.12
Matches are distributed among these distances:
23 3 0.02
24 1 0.01
25 95 0.63
26 17 0.11
27 24 0.16
28 11 0.07
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.45
Consensus pattern (26 bp):
ATGTAAGTTATGTAATTATGTAAGTA
Found at i:40390933 original size:34 final size:34
Alignment explanation
Indices: 40390827--40391024 Score: 143
Period size: 34 Copynumber: 5.6 Consensus size: 34
40390817 TGTATGTAAG
** **
40390827 TTATGT-A-TTATGTAAGTAATGTAAGTTGTGTA
1 TTATGTAAGTTATGTAAGTTGTGTAAGTAATGTA
**
40390859 TTATGTAAGTTATGTAAGTTGTGTAAGTTCTGTA
1 TTATGTAAGTTATGTAAGTTGTGTAAGTAATGTA
*
40390893 TGATGTAAGTTATGTAAGTTGTG-AA-TAATGTAA
1 TTATGTAAGTTATGTAAGTTGTGTAAGTAATGT-A
* *
40390926 TTTATGTAATTTGGGTATTATGGAAGTTATGTAAGTAATGTA
1 -TTATGTAA-----G--TTATGTAAGTTGTGTAAGTAATGTA
* *
40390968 TTATGTAAGTTTATGTAAGTTATGTAAGTTATGTAA
1 TTATGTAAG-TTATGTAAGTTGTGTAAGTAATGT-A
* *
40391004 GTTATGTAAATTATATAAGTT
1 -TTATGTAAGTTATGTAAGTT
40391025 TATGAAATTT
Statistics
Matches: 137, Mismatches: 14, Indels: 26
0.77 0.08 0.15
Matches are distributed among these distances:
32 10 0.07
33 4 0.03
34 51 0.37
35 22 0.16
36 12 0.09
37 8 0.06
39 1 0.01
41 20 0.15
42 3 0.02
43 6 0.04
ACGTcount: A:0.32, C:0.01, G:0.22, T:0.45
Consensus pattern (34 bp):
TTATGTAAGTTATGTAAGTTGTGTAAGTAATGTA
Found at i:40391032 original size:18 final size:18
Alignment explanation
Indices: 40390819--40391259 Score: 250
Period size: 18 Copynumber: 26.6 Consensus size: 18
40390809 TATGTTTATG
*
40390819 TATGTAAGTTATGT-A-T
1 TATGTAAATTATGTAAGT
* *
40390835 TATGTAAGTAATGTAAGT
1 TATGTAAATTATGTAAGT
*
40390853 TGTGT--ATTATGTAAGT
1 TATGTAAATTATGTAAGT
* *
40390869 TATGTAAGTTGTGTAAGT
1 TATGTAAATTATGTAAGT
* *
40390887 TCTGT--ATGATGTAAGT
1 TATGTAAATTATGTAAGT
* *
40390903 TATGTAAGTTGTG-AA-T
1 TATGTAAATTATGTAAGT
* *
40390919 AATGTAATTTATGTAA-T
1 TATGTAAATTATGTAAGT
*** *
40390936 T-TGGGTATTATGGAAGT
1 TATGTAAATTATGTAAGT
* *
40390953 TATGTAAGTAATGT-A-T
1 TATGTAAATTATGTAAGT
*
40390969 TATGTAAGTTTATGTAAGT
1 TATGTAA-ATTATGTAAGT
*
40390988 TATGTAAGTTATGTAAGT
1 TATGTAAATTATGTAAGT
*
40391006 TATGTAAATTATATAAGTT
1 TATGTAAATTATGTAAG-T
40391025 TATG-AAATT-TG--A-T
1 TATGTAAATTATGTAAGT
40391038 CT-T-TAAATTATGTAAGT
1 -TATGTAAATTATGTAAGT
40391055 TATGTAAATTATGTAAGT
1 TATGTAAATTATGTAAGT
*
40391073 TAAG-AAATT-TG--A-T
1 TATGTAAATTATGTAAGT
*
40391086 CT-T-TAAATTATGTAACT
1 -TATGTAAATTATGTAAGT
*
40391103 CT-TGTAACTTATGTAAGT
1 -TATGTAAATTATGTAAGT
*
40391121 TATGTAAATTATGTTAGT
1 TATGTAAATTATGTAAGT
40391139 TATG-AAATT-TG--A-T
1 TATGTAAATTATGTAAGT
40391152 CT-T-TAAATTATGTAAGT
1 -TATGTAAATTATGTAAGT
*
40391169 TATGT--ATTATGTAAAT
1 TATGTAAATTATGTAAGT
40391185 TATGTAAATTATGTAAGT
1 TATGTAAATTATGTAAGT
* *
40391203 TA---AAA-TATTTGATGT
1 TATGTAAATTATGT-AAGT
40391218 T-TG--AATTATGTAAGT
1 TATGTAAATTATGTAAGT
*
40391233 TATATAAATTATGTAAGT
1 TATGTAAATTATGTAAGT
40391251 TATG-AAATT
1 TATGTAAATT
40391260 TTATCTTTAA
Statistics
Matches: 329, Mismatches: 50, Indels: 91
0.70 0.11 0.19
Matches are distributed among these distances:
13 20 0.06
14 15 0.05
15 14 0.04
16 95 0.29
17 39 0.12
18 133 0.40
19 13 0.04
ACGTcount: A:0.35, C:0.02, G:0.18, T:0.46
Consensus pattern (18 bp):
TATGTAAATTATGTAAGT
Found at i:40391099 original size:48 final size:48
Alignment explanation
Indices: 40390996--40391122 Score: 193
Period size: 48 Copynumber: 2.6 Consensus size: 48
40390986 GTTATGTAAG
* *
40390996 TTATGTAAGTTATGTAAATTATATAAGTTTATGAAATTTGATCTTTAAA
1 TTATGTAAGTTATGTAAATTATGTAAG-TTAAGAAATTTGATCTTTAAA
40391045 TTATGTAAGTTATGTAAATTATGTAAGTTAAGAAATTTGATCTTTAAA
1 TTATGTAAGTTATGTAAATTATGTAAGTTAAGAAATTTGATCTTTAAA
* *
40391093 TTATGTAACTCT-TGTAACTTATGTAAGTTA
1 TTATGTAAGT-TATGTAAATTATGTAAGTTA
40391123 TGTAAATTAT
Statistics
Matches: 73, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
48 46 0.63
49 27 0.37
ACGTcount: A:0.37, C:0.04, G:0.13, T:0.46
Consensus pattern (48 bp):
TTATGTAAGTTATGTAAATTATGTAAGTTAAGAAATTTGATCTTTAAA
Found at i:40391127 original size:66 final size:66
Alignment explanation
Indices: 40391041--40391259 Score: 313
Period size: 66 Copynumber: 3.4 Consensus size: 66
40391031 ATTTGATCTT
*
40391041 TAAATTATGTAAGTTATGTAAATTATGTAAGTTAAGAAATTTGATCTTTAAATTATGTAACTCT-
1 TAAATTATGTAAGTTATGTAAATTATGTAAGTTAAGAAATTTGATCTTTAAATTATGTAAGT-TA
40391105 TG
65 TG
* * *
40391107 TAACTTATGTAAGTTATGTAAATTATGTTAGTTATGAAATTTGATCTTTAAATTATGTAAGTTAT
1 TAAATTATGTAAGTTATGTAAATTATGTAAGTTAAGAAATTTGATCTTTAAATTATGTAAGTTAT
40391172 G
66 G
* * *
40391173 T--ATTATGTAAATTATGTAAATTATGTAAGTTAA-AATATTTGATGTTTGAATTATGTAAGTTA
1 TAAATTATGTAAGTTATGTAAATTATGTAAGTTAAGAA-ATTTGATCTTTAAATTATGTAAGTTA
*
40391235 TA
65 TG
40391237 TAAATTATGTAAGTTATG-AAATT
1 TAAATTATGTAAGTTATGTAAATT
40391260 TTATCTTTAA
Statistics
Matches: 137, Mismatches: 12, Indels: 9
0.87 0.08 0.06
Matches are distributed among these distances:
63 2 0.01
64 54 0.39
65 6 0.04
66 75 0.55
ACGTcount: A:0.38, C:0.02, G:0.14, T:0.46
Consensus pattern (66 bp):
TAAATTATGTAAGTTATGTAAATTATGTAAGTTAAGAAATTTGATCTTTAAATTATGTAAGTTAT
G
Found at i:40391206 original size:48 final size:48
Alignment explanation
Indices: 40391111--40391252 Score: 139
Period size: 48 Copynumber: 3.0 Consensus size: 48
40391101 CTCTTGTAAC
* **
40391111 TTATGTAAGTTATGTAAATTATGTTAGTTATG-AAATT-TG-ATCTTTAAA
1 TTATGTAAGTTATGT--ATTATGTAAGTTATGTAAATTATGTA-AGTTAAA
*
40391159 TTATGTAAGTTATGTATTATGTAAATTATGTAAATTATGTAAGTTAAA
1 TTATGTAAGTTATGTATTATGTAAGTTATGTAAATTATGTAAGTTAAA
* * * * *
40391207 ATATTTGATGTT-TGAATTATGTAAGTTATATAAATTATGTAAGTTA
1 TTATGT-AAGTTATGTATTATGTAAGTTATGTAAATTATGTAAGTTA
40391253 TGAAATTTTA
Statistics
Matches: 80, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
46 13 0.16
47 5 0.06
48 57 0.71
49 5 0.06
ACGTcount: A:0.37, C:0.01, G:0.15, T:0.47
Consensus pattern (48 bp):
TTATGTAAGTTATGTATTATGTAAGTTATGTAAATTATGTAAGTTAAA
Found at i:40391273 original size:48 final size:48
Alignment explanation
Indices: 40391174--40391281 Score: 148
Period size: 48 Copynumber: 2.2 Consensus size: 48
40391164 TAAGTTATGT
* * * *
40391174 ATTATGTAAATTATGTAAATTATGTAAGTTAAAATATTTGATGTTTGA
1 ATTATGTAAGTTATATAAATTATGTAAGTTAAAATATTTGATCTTTAA
40391222 ATTATGTAAGTTATATAAATTATGTAAGTTATGAAAT-TTT-ATCTTTAA
1 ATTATGTAAGTTATATAAATTATGTAAGTTA--AAATATTTGATCTTTAA
40391270 ATTATGTAAGTT
1 ATTATGTAAGTT
40391282 GTGTATTAAG
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
48 47 0.87
49 3 0.06
50 4 0.07
ACGTcount: A:0.39, C:0.01, G:0.13, T:0.47
Consensus pattern (48 bp):
ATTATGTAAGTTATATAAATTATGTAAGTTAAAATATTTGATCTTTAA
Found at i:40391418 original size:30 final size:31
Alignment explanation
Indices: 40391384--40391442 Score: 102
Period size: 30 Copynumber: 1.9 Consensus size: 31
40391374 GTATTATATT
*
40391384 TAAATTATGTAATTTATG-AAATTTGAACCA
1 TAAATTATGTAAGTTATGTAAATTTGAACCA
40391414 TAAATTATGTAAGTTATGTAAATTTGAAC
1 TAAATTATGTAAGTTATGTAAATTTGAAC
40391443 TTTAAAATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 17 0.63
31 10 0.37
ACGTcount: A:0.42, C:0.05, G:0.12, T:0.41
Consensus pattern (31 bp):
TAAATTATGTAAGTTATGTAAATTTGAACCA
Found at i:40396629 original size:45 final size:45
Alignment explanation
Indices: 40396565--40396655 Score: 155
Period size: 45 Copynumber: 2.0 Consensus size: 45
40396555 ATAGTTTTGA
* *
40396565 ACCCTGATTTATTTGGTGGCATATTATTGACAGATTGTACACTAG
1 ACCCTGATCTAGTTGGTGGCATATTATTGACAGATTGTACACTAG
*
40396610 ACCCTGATCTAGTTGGTGGCATATTGTTGACAGATTGTACACTAG
1 ACCCTGATCTAGTTGGTGGCATATTATTGACAGATTGTACACTAG
40396655 A
1 A
40396656 AACAGTTCTT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.35
Consensus pattern (45 bp):
ACCCTGATCTAGTTGGTGGCATATTATTGACAGATTGTACACTAG
Found at i:40398338 original size:23 final size:23
Alignment explanation
Indices: 40398294--40398338 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
40398284 ACCTCAGTTT
* *
40398294 GGAATTTGGGGAAATGATATTGG
1 GGAAGTTGGGGAAAGGATATTGG
40398317 GGAAGTTGGGGAAAAGGA-ATTG
1 GGAAGTTGGGG-AAAGGATATTG
40398339 CGAAATTGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.33, C:0.00, G:0.42, T:0.24
Consensus pattern (23 bp):
GGAAGTTGGGGAAAGGATATTGG
Found at i:40398832 original size:21 final size:22
Alignment explanation
Indices: 40398808--40398854 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
40398798 AGCTAAACCC
* *
40398808 TAAACA-TTAAACTCTAAAATA
1 TAAACATTTAAACCCTAAAACA
40398829 TAAA-ATTTAAACCCTAAAACA
1 TAAACATTTAAACCCTAAAACA
40398850 TAAAC
1 TAAAC
40398855 CCCTATCCCT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.57, C:0.17, G:0.00, T:0.26
Consensus pattern (22 bp):
TAAACATTTAAACCCTAAAACA
Found at i:40398897 original size:7 final size:7
Alignment explanation
Indices: 40398877--40398939 Score: 56
Period size: 7 Copynumber: 9.1 Consensus size: 7
40398867 GACCATAATC
*
40398877 CCCTAAC
1 CCCTAAA
40398884 CCCTAAA
1 CCCTAAA
40398891 CCCTAAA
1 CCCTAAA
* *
40398898 CACTTAA
1 CCCTAAA
*
40398905 CCATAAA
1 CCCTAAA
* *
40398912 -CATACA
1 CCCTAAA
40398918 CCCTAAA
1 CCCTAAA
*
40398925 CCATAAA
1 CCCTAAA
40398932 CCCTAAA
1 CCCTAAA
40398939 C
1 C
40398940 TCTTAAAACT
Statistics
Matches: 44, Mismatches: 11, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
6 5 0.11
7 39 0.89
ACGTcount: A:0.44, C:0.40, G:0.00, T:0.16
Consensus pattern (7 bp):
CCCTAAA
Found at i:40399063 original size:8 final size:7
Alignment explanation
Indices: 40399025--40399162 Score: 64
Period size: 7 Copynumber: 18.9 Consensus size: 7
40399015 ATCCAATAAC
*
40399025 CCCTAGA
1 CCCTAAA
*
40399032 CCCTAAG
1 CCCTAAA
*
40399039 CTCTAAA
1 CCCTAAA
40399046 CCCTAAA
1 CCCTAAA
40399053 CCCTAAAA
1 CCCT-AAA
40399061 CCCTTAAA
1 CCC-TAAA
** *
40399069 CTTTTATA
1 C-CCTAAA
* *
40399077 CCATATA
1 CCCTAAA
*
40399084 CCTTAAA
1 CCCTAAA
40399091 CCCTAAA
1 CCCTAAA
40399098 CCCTTAAA
1 CCC-TAAA
40399106 CCCGT-AA
1 CCC-TAAA
*
40399113 CCTTAAA
1 CCCTAAA
*
40399120 CCACTAAC
1 CC-CTAAA
*
40399128 CCCTAGA
1 CCCTAAA
*
40399135 CTCT-AA
1 CCCTAAA
*
40399141 GCCTATAA
1 CCCTA-AA
40399149 CCCCTAAA
1 -CCCTAAA
40399157 CCCTAA
1 CCCTAA
40399163 GCTCTCACCC
Statistics
Matches: 98, Mismatches: 24, Indels: 18
0.70 0.17 0.13
Matches are distributed among these distances:
6 4 0.04
7 58 0.59
8 31 0.32
9 5 0.05
ACGTcount: A:0.37, C:0.37, G:0.04, T:0.22
Consensus pattern (7 bp):
CCCTAAA
Found at i:40399241 original size:14 final size:13
Alignment explanation
Indices: 40399197--40399239 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
40399187 TGTAAATTGA
*
40399197 AAACATACACCAT
1 AAACCTACACCAT
*
40399210 AAACACTAAACCAT
1 AAAC-CTACACCAT
40399224 AAACCTACACCAT
1 AAACCTACACCAT
40399237 AAA
1 AAA
40399240 ACGTAAACAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
13 15 0.58
14 11 0.42
ACGTcount: A:0.56, C:0.30, G:0.00, T:0.14
Consensus pattern (13 bp):
AAACCTACACCAT
Found at i:40399352 original size:22 final size:24
Alignment explanation
Indices: 40399327--40399372 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
40399317 TATCAATAAC
40399327 CCTAACC-CTTAAACCAT-AATAG
1 CCTAACCTCTTAAACCATGAATAG
*
40399349 CCTAACCTGTTAAACCATGAATAG
1 CCTAACCTCTTAAACCATGAATAG
40399373 TAACTAAGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 7 0.33
23 9 0.43
24 5 0.24
ACGTcount: A:0.39, C:0.28, G:0.09, T:0.24
Consensus pattern (24 bp):
CCTAACCTCTTAAACCATGAATAG
Found at i:40400123 original size:168 final size:165
Alignment explanation
Indices: 40399830--40400181 Score: 438
Period size: 168 Copynumber: 2.1 Consensus size: 165
40399820 GATTAGTGGT
* * * * **
40399830 GTTTTTTGATAAACGTCGCAAATGCTAGATCTTTACCGGCGTTTCCATATAAACGCCACTAGTGT
1 GTTTTCTGATAAACGCCGCAAATACTAGATCTTTACCGGCGTTTCCATATAAACGCCACTACTAC
* * *
40399895 CACTATAGGTCAAAGTTAAACGACGGCGTTCTGCTTAATTATCTGCGGAGCAATAGTGGCGTTTT
66 CACTATAGATCAAAGTTAAACGACGGCATTCTGCTTAATTATCTGCAGAGCAATAGTGGCGTTTT
** * *
40399960 TATTCT-AGCGCCGCTAATG-TACCGATCTTTAGCGGC
131 T-TGATAAGCGCCGCAAATGCTA--GATCTTTACCGGC
* * **
40399996 GTTTTCTGATAAGCGCCGCAAATACTAGATCTTTACCGGCGTTTTCATATAAACGCTGCTACTAC
1 GTTTTCTGATAAACGCCGCAAATACTAGATCTTTACCGGCGTTTCCATATAAACGCCACTACTAC
* * * *
40400061 CACTAATATTATTAAAGTTAAACGACGGCATTCTGCTTAATTATTTGCAGAGCATTAGTGGCGTT
66 CACT-ATA-GATCAAAGTTAAACGACGGCATTCTGCTTAATTATCTGCAGAGCAATAGTGGCGTT
40400126 TTTTGATAAGCGCCGCAAATGCTAGATCTTTACCGGC
129 TTTTGATAAGCGCCGCAAATGCTAGATCTTTACCGGC
* *
40400163 GTTTTCAGATAAACACCGC
1 GTTTTCTGATAAACGCCGC
40400182 TAGTGCCATT
Statistics
Matches: 158, Mismatches: 24, Indels: 7
0.84 0.13 0.04
Matches are distributed among these distances:
166 59 0.37
167 33 0.21
168 64 0.41
169 2 0.01
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (165 bp):
GTTTTCTGATAAACGCCGCAAATACTAGATCTTTACCGGCGTTTCCATATAAACGCCACTACTAC
CACTATAGATCAAAGTTAAACGACGGCATTCTGCTTAATTATCTGCAGAGCAATAGTGGCGTTTT
TTGATAAGCGCCGCAAATGCTAGATCTTTACCGGC
Found at i:40402869 original size:44 final size:44
Alignment explanation
Indices: 40402806--40402977 Score: 218
Period size: 44 Copynumber: 3.9 Consensus size: 44
40402796 GCTATACACC
* *
40402806 TAAAATGGGTAAGACCATAGCTGAAAGATGTTATGGTATCGGGA
1 TAAAATGAGTAAGACCATAGCTGAAAGATGTTATGGCATCGGGA
*
40402850 TAAAATGAGTAAGACCATAGCTGAAAGATATTATGGCATCGGGA
1 TAAAATGAGTAAGACCATAGCTGAAAGATGTTATGGCATCGGGA
* * * * **
40402894 TAAAATGAGTAAGATCGTAACTGAAAGATGTTATGACATCATGA
1 TAAAATGAGTAAGACCATAGCTGAAAGATGTTATGGCATCGGGA
* * * *
40402938 CTGAAATAAGTAAGACCATGGATGAAAGATGTTATGGCAT
1 -TAAAATGAGTAAGACCATAGCTGAAAGATGTTATGGCAT
40402978 AATGAGAAAG
Statistics
Matches: 109, Mismatches: 18, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
44 78 0.72
45 31 0.28
ACGTcount: A:0.40, C:0.10, G:0.25, T:0.25
Consensus pattern (44 bp):
TAAAATGAGTAAGACCATAGCTGAAAGATGTTATGGCATCGGGA
Found at i:40403158 original size:73 final size:73
Alignment explanation
Indices: 40403063--40403201 Score: 197
Period size: 73 Copynumber: 1.9 Consensus size: 73
40403053 CTACCGGAAC
* * **
40403063 GGTAAACACGGGGTCATATGGTGTAAGACCATAGCTGAAAAATGCTATGACATCATAGTTAATCC
1 GGTAAAAACGGGGTCATATGGTGTAAGACCATAGCTAAAAAAAACTATGACATCATAGTTAATCC
40403128 GTTGTGAT
66 GTTGTGAT
* * * * *
40403136 GGTAAAAATGGGGTTATATGGTGTAAGACCATAGCTAAAAAAAATTATGACATCATATTTAGTCC
1 GGTAAAAACGGGGTCATATGGTGTAAGACCATAGCTAAAAAAAACTATGACATCATAGTTAATCC
40403201 G
66 G
40403202 ATGGGATGTT
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
73 57 1.00
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.28
Consensus pattern (73 bp):
GGTAAAAACGGGGTCATATGGTGTAAGACCATAGCTAAAAAAAACTATGACATCATAGTTAATCC
GTTGTGAT
Found at i:40403242 original size:27 final size:27
Alignment explanation
Indices: 40403210--40403270 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
40403200 CGATGGGATG
*
40403210 TTAAACACGAGATAG-CTCAAGGGGACA
1 TTAAACACGAGATAGTCT-AACGGGACA
40403237 TTAAACACGAGATAGTCTAACGGGACA
1 TTAAACACGAGATAGTCTAACGGGACA
*
40403264 CTAAACA
1 TTAAACA
40403271 TGGGGTAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
27 29 0.94
28 2 0.06
ACGTcount: A:0.43, C:0.20, G:0.21, T:0.16
Consensus pattern (27 bp):
TTAAACACGAGATAGTCTAACGGGACA
Found at i:40406054 original size:26 final size:27
Alignment explanation
Indices: 40406025--40406076 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
40406015 TTTGTTTTTC
*
40406025 TATTTCCCA-AAATAAACTTCTCAATG
1 TATTTCCAATAAATAAACTTCTCAATG
*
40406051 TATTTCCAATTAAATAATCTTCTCAA
1 TATTTCCAA-TAAATAAACTTCTCAA
40406077 CCCAATTCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 8 0.36
28 14 0.64
ACGTcount: A:0.38, C:0.21, G:0.02, T:0.38
Consensus pattern (27 bp):
TATTTCCAATAAATAAACTTCTCAATG
Found at i:40406328 original size:57 final size:57
Alignment explanation
Indices: 40406235--40406415 Score: 227
Period size: 57 Copynumber: 3.1 Consensus size: 57
40406225 TTTTTTAGGT
* * * *
40406235 CATTTTCATTTTCGTTTTGGAGAAAACCACATTCATTTTCAAATGTTTCTACTTCTC
1 CATTTTCATTTTCATTTTGGAGAAAACCATAATCATTTCCAAATGTTTCTACTTCTC
* * * *
40406292 CATTATCATTTTCATTTTGGAGAAAACCATAATCATTTCCAAATGATTCCATTTCTC
1 CATTTTCATTTTCATTTTGGAGAAAACCATAATCATTTCCAAATGTTTCTACTTCTC
* * * *
40406349 CATTTTTATTTTCATTTTGGACAAAACCATAATTATTTCCAAATGATTTCTCATTTCTC
1 CATTTTCATTTTCATTTTGGAGAAAACCATAATCATTTCCAAATG-TTTCT-ACTTCTC
*
40406408 TATTTTCA
1 CATTTTCA
40406416 CTATTTCTAT
Statistics
Matches: 106, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
57 90 0.85
58 3 0.03
59 13 0.12
ACGTcount: A:0.28, C:0.20, G:0.07, T:0.45
Consensus pattern (57 bp):
CATTTTCATTTTCATTTTGGAGAAAACCATAATCATTTCCAAATGTTTCTACTTCTC
Found at i:40409361 original size:14 final size:14
Alignment explanation
Indices: 40409342--40409369 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
40409332 ATGTTTAAGG
40409342 CTTAATTAATCTAA
1 CTTAATTAATCTAA
40409356 CTTAATTAATCTAA
1 CTTAATTAATCTAA
40409370 TCATGATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (14 bp):
CTTAATTAATCTAA
Found at i:40414326 original size:13 final size:12
Alignment explanation
Indices: 40414288--40414319 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
40414278 CCATCAGTAT
40414288 TAATTTTTTATA
1 TAATTTTTTATA
*
40414300 TTATTTTTTATA
1 TAATTTTTTATA
40414312 TAATTTTT
1 TAATTTTT
40414320 AAATATATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (12 bp):
TAATTTTTTATA
Found at i:40414528 original size:30 final size:30
Alignment explanation
Indices: 40414439--40414531 Score: 159
Period size: 30 Copynumber: 3.1 Consensus size: 30
40414429 CTTTAACAAG
*
40414439 CAAATGCCTCTAAAATAATAACAAAATTAG
1 CAAATGCCTCTAAAATAATAACAAAATTAA
*
40414469 CAAATGCATCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
*
40414499 CAAATGCCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
40414529 CAA
1 CAA
40414532 TAAAGTAAGT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 59 1.00
ACGTcount: A:0.57, C:0.15, G:0.04, T:0.24
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:40416223 original size:22 final size:22
Alignment explanation
Indices: 40416198--40416243 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
40416188 GGAGCACCAT
*
40416198 TAAGGGCCTAGGTATAGG-TACC
1 TAAGGCCCTAGGTA-AGGATACC
40416220 TAAGGCCCTAGGTAAGGATACC
1 TAAGGCCCTAGGTAAGGATACC
40416242 TA
1 TA
40416244 GTTCAGGGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 3 0.14
22 19 0.86
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.22
Consensus pattern (22 bp):
TAAGGCCCTAGGTAAGGATACC
Found at i:40416466 original size:13 final size:13
Alignment explanation
Indices: 40416440--40416477 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
40416430 CATGTACATG
40416440 TAAAACTT-CTCA
1 TAAAACTTACTCA
40416452 TAAAACTTACTCA
1 TAAAACTTACTCA
*
40416465 TAAAACGTACTCA
1 TAAAACTTACTCA
40416478 AAATAAACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 8 0.33
13 16 0.67
ACGTcount: A:0.45, C:0.24, G:0.03, T:0.29
Consensus pattern (13 bp):
TAAAACTTACTCA
Found at i:40425458 original size:49 final size:48
Alignment explanation
Indices: 40425380--40425533 Score: 150
Period size: 49 Copynumber: 3.1 Consensus size: 48
40425370 CTTAGGATGA
*
40425380 AAACCATCGTTGTTAGGCCATCC-GTGATGGTAGAATATGCAAATAGTGG
1 AAACCATCGTTGTTAGGCCA-CCAG-GATGGTAGAATATGAAAATAGTGG
* * ** *
40425429 AAACCATCGTTGCTAGGCCACCAAGGATGGTAAAACGTGAAAATAGTGA
1 AAACCATCGTTGTTAGGCCACC-AGGATGGTAGAATATGAAAATAGTGG
* * * * *
40425478 AAACCCATCATT-TTTGAGCCATCAGGATGGTAGGATATGAAAATACTGG
1 AAA-CCATCGTTGTTAG-GCCACCAGGATGGTAGAATATGAAAATAGTGG
40425527 AAACCAT
1 AAACCAT
40425534 TGTTTCTGGG
Statistics
Matches: 85, Mismatches: 16, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
48 6 0.07
49 66 0.78
50 13 0.15
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.23
Consensus pattern (48 bp):
AAACCATCGTTGTTAGGCCACCAGGATGGTAGAATATGAAAATAGTGG
Found at i:40427964 original size:18 final size:18
Alignment explanation
Indices: 40427941--40428001 Score: 68
Period size: 18 Copynumber: 3.4 Consensus size: 18
40427931 CAATTTGGAA
*
40427941 ATTAATACAGTTCGTCAT
1 ATTAATACAGTTCGCCAT
* * *
40427959 ATTAATACAGATCACCAA
1 ATTAATACAGTTCGCCAT
*
40427977 ATTAACACAGTTCGCCAT
1 ATTAATACAGTTCGCCAT
*
40427995 AATAATA
1 ATTAATA
40428002 TAATTCACCA
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.43, C:0.20, G:0.08, T:0.30
Consensus pattern (18 bp):
ATTAATACAGTTCGCCAT
Found at i:40428010 original size:36 final size:36
Alignment explanation
Indices: 40427939--40428019 Score: 101
Period size: 36 Copynumber: 2.2 Consensus size: 36
40427929 TACAATTTGG
* * *
40427939 AAATTAATACAGTTCGTCATATTAATACAGATCACC
1 AAATTAACACAGTTCGCCATAATAATACAGATCACC
*
40427975 AAATTAACACAGTTCGCCATAATAATATA-ATTCACC
1 AAATTAACACAGTTCGCCATAATAATACAGA-TCACC
*
40428011 AAGTTAACA
1 AAATTAACA
40428020 TGGTTCACAA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
35 1 0.03
36 38 0.97
ACGTcount: A:0.44, C:0.20, G:0.07, T:0.28
Consensus pattern (36 bp):
AAATTAACACAGTTCGCCATAATAATACAGATCACC
Found at i:40428037 original size:17 final size:18
Alignment explanation
Indices: 40428015--40428052 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
40428005 TTCACCAAGT
* *
40428015 TAACATGGTTCAC-AATA
1 TAACATAGTACACAAATA
40428032 TAACATAGTACACAAATA
1 TAACATAGTACACAAATA
40428050 TAA
1 TAA
40428053 TTGGCTCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.50, C:0.16, G:0.08, T:0.26
Consensus pattern (18 bp):
TAACATAGTACACAAATA
Found at i:40432911 original size:40 final size:41
Alignment explanation
Indices: 40432845--40432929 Score: 120
Period size: 40 Copynumber: 2.1 Consensus size: 41
40432835 ATTAAACCCT
*
40432845 TAAAAATCAATAATTACAACAATTTATATGA-AATAAATTAA
1 TAAAAATCAACAATTACAACAATTTATAT-ACAATAAATTAA
* *
40432886 TAAAAATTAACAATT-CAATAATTTATATACAATAAATTAA
1 TAAAAATCAACAATTACAACAATTTATATACAATAAATTAA
40432926 TAAA
1 TAAA
40432930 TTAATTGTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
39 1 0.03
40 26 0.65
41 13 0.32
ACGTcount: A:0.59, C:0.07, G:0.01, T:0.33
Consensus pattern (41 bp):
TAAAAATCAACAATTACAACAATTTATATACAATAAATTAA
Found at i:40435176 original size:20 final size:19
Alignment explanation
Indices: 40435143--40435189 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
40435133 CAAATAACCA
40435143 TTTTCCATTACATATATCC
1 TTTTCCATTACATATATCC
* *
40435162 TTTTGCCATTTCATATATTCA
1 TTTT-CCATTACATATA-TCC
40435183 TTTTCCA
1 TTTTCCA
40435190 CCCGATGAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 4 0.17
20 14 0.58
21 6 0.25
ACGTcount: A:0.23, C:0.23, G:0.02, T:0.51
Consensus pattern (19 bp):
TTTTCCATTACATATATCC
Found at i:40438402 original size:18 final size:18
Alignment explanation
Indices: 40438379--40438416 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
40438369 CTAAATGTTT
40438379 TTTCGTAAAATGAGTAAG
1 TTTCGTAAAATGAGTAAG
40438397 TTTCGTAAAATGAGTAAG
1 TTTCGTAAAATGAGTAAG
40438415 TT
1 TT
40438417 CTACGCATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.37, C:0.05, G:0.21, T:0.37
Consensus pattern (18 bp):
TTTCGTAAAATGAGTAAG
Found at i:40441246 original size:41 final size:41
Alignment explanation
Indices: 40441187--40441292 Score: 153
Period size: 41 Copynumber: 2.6 Consensus size: 41
40441177 AATTGGGATA
40441187 TGTAGGGCACACTA-GTATGTGTGAGGCCATGTGGTAGG-TCG
1 TGTAGGGCACAC-AGGTATGTGTGAGGCCATGTGGTAGGCT-G
40441228 TGTAGGGCACACAGGTATGTGTGAGGCCATGTGGTAGGCTG
1 TGTAGGGCACACAGGTATGTGTGAGGCCATGTGGTAGGCTG
* **
40441269 TGTGGGGCACACAGGCGTGTGTGA
1 TGTAGGGCACACAGGTATGTGTGA
40441293 TCACACGAGC
Statistics
Matches: 60, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
40 1 0.02
41 58 0.97
42 1 0.02
ACGTcount: A:0.19, C:0.15, G:0.42, T:0.25
Consensus pattern (41 bp):
TGTAGGGCACACAGGTATGTGTGAGGCCATGTGGTAGGCTG
Found at i:40441263 original size:19 final size:19
Alignment explanation
Indices: 40441201--40441263 Score: 56
Period size: 19 Copynumber: 3.2 Consensus size: 19
40441191 GGGCACACTA
40441201 GTATGTGTGAGGCCATGTG
1 GTATGTGTGAGGCCATGTG
* **
40441220 GTAGGTCGTGTAGGGCACA-CAG
1 GTATGT-GTG-A-GGC-CATGTG
40441242 GTATGTGTGAGGCCATGTG
1 GTATGTGTGAGGCCATGTG
40441261 GTA
1 GTA
40441264 GGCTGTGTGG
Statistics
Matches: 33, Mismatches: 6, Indels: 10
0.67 0.12 0.20
Matches are distributed among these distances:
18 2 0.06
19 12 0.36
20 4 0.12
21 4 0.12
22 9 0.27
23 2 0.06
ACGTcount: A:0.19, C:0.13, G:0.41, T:0.27
Consensus pattern (19 bp):
GTATGTGTGAGGCCATGTG
Found at i:40442162 original size:7 final size:7
Alignment explanation
Indices: 40442147--40442184 Score: 69
Period size: 7 Copynumber: 5.6 Consensus size: 7
40442137 AGTTTTCAGA
40442147 TTTGGTT
1 TTTGGTT
40442154 TTT-GTT
1 TTTGGTT
40442160 TTTGGTT
1 TTTGGTT
40442167 TTTGGTT
1 TTTGGTT
40442174 TTTGGTT
1 TTTGGTT
40442181 TTTG
1 TTTG
40442185 ATCTGTTCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.20
7 24 0.80
ACGTcount: A:0.00, C:0.00, G:0.26, T:0.74
Consensus pattern (7 bp):
TTTGGTT
Found at i:40445731 original size:31 final size:31
Alignment explanation
Indices: 40445667--40445737 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
40445657 ATACATTGCT
* *
40445667 GAATTTGATTTGTATATAGACATACATTGTC
1 GAATTTGATTCGTATATAGACATACATTATC
* * *
40445698 GAATTTGATTCGTATATGGATATATATTATC
1 GAATTTGATTCGTATATAGACATACATTATC
40445729 GAA-TTGATT
1 GAATTTGATT
40445738 TGAACATTGG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
30 6 0.17
31 29 0.83
ACGTcount: A:0.32, C:0.07, G:0.17, T:0.44
Consensus pattern (31 bp):
GAATTTGATTCGTATATAGACATACATTATC
Found at i:40445966 original size:41 final size:43
Alignment explanation
Indices: 40445860--40445976 Score: 148
Period size: 43 Copynumber: 2.8 Consensus size: 43
40445850 GAGCTGTGAT
40445860 TTCGTGTAAGACCATGTCTGGGACATTGGCATCGAAGTGAGGA
1 TTCGTGTAAGACCATGTCTGGGACATTGGCATCGAAGTGAGGA
** * *
40445903 AACGTGTAAGACCATGTCTGGGACATTGGCATCGTA-T-ATGA
1 TTCGTGTAAGACCATGTCTGGGACATTGGCATCGAAGTGAGGA
* * * *
40445944 TTCGTATAAGACCCTGTCTGGGATAGTGGCATC
1 TTCGTGTAAGACCATGTCTGGGACATTGGCATC
40445977 AATATGCGTT
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
41 30 0.47
42 1 0.02
43 33 0.52
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.27
Consensus pattern (43 bp):
TTCGTGTAAGACCATGTCTGGGACATTGGCATCGAAGTGAGGA
Found at i:40449580 original size:12 final size:12
Alignment explanation
Indices: 40449563--40449587 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40449553 CAGAGGCTGT
40449563 TAACAATATTTA
1 TAACAATATTTA
40449575 TAACAATATTTA
1 TAACAATATTTA
40449587 T
1 T
40449588 GTTATAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (12 bp):
TAACAATATTTA
Found at i:40454834 original size:11 final size:11
Alignment explanation
Indices: 40454805--40454878 Score: 53
Period size: 11 Copynumber: 6.6 Consensus size: 11
40454795 AAATAGATAA
*
40454805 ATAATATAAAT
1 ATAATATTAAT
40454816 ATAATATTAAT
1 ATAATATTAAT
*
40454827 ATAATATTCTATT
1 ATAATA-T-TAAT
* *
40454840 ATATTATAAAT
1 ATAATATTAAT
*
40454851 AAAATATATAA-
1 ATAATAT-TAAT
40454862 ATAA-ATTAAT
1 ATAATATTAAT
*
40454872 AAAATAT
1 ATAATAT
40454879 ATAAATAAAT
Statistics
Matches: 48, Mismatches: 10, Indels: 10
0.71 0.15 0.15
Matches are distributed among these distances:
9 3 0.06
10 5 0.10
11 28 0.58
12 4 0.08
13 8 0.17
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (11 bp):
ATAATATTAAT
Found at i:40454860 original size:13 final size:13
Alignment explanation
Indices: 40454844--40454887 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 13
40454834 TCTATTATAT
40454844 TATAAATAAAATA
1 TATAAATAAAATA
40454857 TATAAAT--AA-A
1 TATAAATAAAATA
40454867 T-T-AATAAAATA
1 TATAAATAAAATA
40454878 TATAAATAAA
1 TATAAATAAA
40454888 TTCTAATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 10
0.72 0.00 0.28
Matches are distributed among these distances:
8 3 0.12
9 1 0.04
10 4 0.15
11 4 0.15
12 1 0.04
13 13 0.50
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
TATAAATAAAATA
Found at i:40454874 original size:21 final size:21
Alignment explanation
Indices: 40454848--40454929 Score: 85
Period size: 21 Copynumber: 3.8 Consensus size: 21
40454838 TTATATTATA
40454848 AATAAAATATATAAATAAATT
1 AATAAAATATATAAATAAATT
40454869 AATAAAATATATAAATAAATT
1 AATAAAATATATAAATAAATT
* * *
40454890 -CTAATATATATTAGAATATATAT
1 AATAAAATATA-TA-AATAAAT-T
* *
40454913 AATAGAATAGATAAATA
1 AATAAAATATATAAATA
40454930 TATAATAGAA
Statistics
Matches: 50, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
20 8 0.16
21 23 0.46
22 10 0.20
23 3 0.06
24 6 0.12
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.34
Consensus pattern (21 bp):
AATAAAATATATAAATAAATT
Found at i:40454902 original size:57 final size:58
Alignment explanation
Indices: 40454789--40454898 Score: 147
Period size: 57 Copynumber: 1.9 Consensus size: 58
40454779 GAAATAAATA
*
40454789 AAATAGAAATAGATAAATAATATAAATATAATATTAATATAATATTCTATTATATTAT
1 AAATAGAAATAGATAAATAATATAAATAAAATATTAATATAATATTCTATTATATTAT
* * *
40454847 AAATA-AAATATATAAATAA-ATTAATAAAATATATAA-ATAA-ATTCTAATATAT
1 AAATAGAAATAGATAAATAATATAAATAAAATAT-TAATATAATATTCTATTATAT
40454899 ATTAGAATAT
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
55 11 0.23
56 15 0.32
57 16 0.34
58 5 0.11
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (58 bp):
AAATAGAAATAGATAAATAATATAAATAAAATATTAATATAATATTCTATTATATTAT
Found at i:40461316 original size:3 final size:3
Alignment explanation
Indices: 40461308--40461357 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
40461298 CATTAAATTC
*
40461308 TAT TAT TAT TAT TAT TAC TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
40461356 TA
1 TA
40461358 GAATTCGATT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:40463456 original size:27 final size:27
Alignment explanation
Indices: 40463425--40463482 Score: 116
Period size: 27 Copynumber: 2.1 Consensus size: 27
40463415 GTGGGAAATC
40463425 TAAGAATATATGTATGTATGTTTTCGT
1 TAAGAATATATGTATGTATGTTTTCGT
40463452 TAAGAATATATGTATGTATGTTTTCGT
1 TAAGAATATATGTATGTATGTTTTCGT
40463479 TAAG
1 TAAG
40463483 TTACACACTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.31, C:0.03, G:0.19, T:0.47
Consensus pattern (27 bp):
TAAGAATATATGTATGTATGTTTTCGT
Found at i:40465773 original size:126 final size:126
Alignment explanation
Indices: 40465548--40465801 Score: 499
Period size: 126 Copynumber: 2.0 Consensus size: 126
40465538 TATGAGCAAC
40465548 AAGGCAAATAAAATACCAATAATTGGGTTTCAAATAGTGTTGTCATGGCCGCGATGGTCGGCAGA
1 AAGGCAAATAAAATACCAATAATTGGGTTTCAAATAGTGTTGTCATGGCCGCGATGGTCGGCAGA
*
40465613 CCTCAAAAACAGTCTTTAAGCTTGAAAATCAAGCGTGAAATAGTAGAAATCAATGAAGCTA
66 CCTCAAAAACAGTCTTTAAGCTTGAAAATCAAGCGTGAAATAGTACAAATCAATGAAGCTA
40465674 AAGGCAAATAAAATACCAATAATTGGGTTTCAAATAGTGTTGTCATGGCCGCGATGGTCGGCAGA
1 AAGGCAAATAAAATACCAATAATTGGGTTTCAAATAGTGTTGTCATGGCCGCGATGGTCGGCAGA
40465739 CCTCAAAAACAGTCTTTAAGCTTGAAAATCAAGCGTGAAATAGTACAAATCAATGAAGCTA
66 CCTCAAAAACAGTCTTTAAGCTTGAAAATCAAGCGTGAAATAGTACAAATCAATGAAGCTA
40465800 AA
1 AA
40465802 ATTATGGTTT
Statistics
Matches: 127, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
126 127 1.00
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.24
Consensus pattern (126 bp):
AAGGCAAATAAAATACCAATAATTGGGTTTCAAATAGTGTTGTCATGGCCGCGATGGTCGGCAGA
CCTCAAAAACAGTCTTTAAGCTTGAAAATCAAGCGTGAAATAGTACAAATCAATGAAGCTA
Found at i:40466639 original size:6 final size:6
Alignment explanation
Indices: 40466630--40466819 Score: 141
Period size: 6 Copynumber: 31.7 Consensus size: 6
40466620 ATTTAGGGTT
* * * * * * *
40466630 ATTTCG ATTTCA ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG
1 ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG
* * * * * **
40466678 ATTTTG ATTTCG ATTTCG ATTTTG ATTTTG ATTTCA ATTTTG A-AAC-
1 ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG
** * * * *
40466724 ACTCACTG ATTTTG ATTTTG ATTTTG ATTTCA ATTTCG ATTTCG ATTTCG
1 A-TTTC-G ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG
* * *
40466774 ATTTCG ATTTCG ATTTCG ATTTTG ATTTTG ATTTCG ATTTAG ATTT
1 ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTT
40466820 TGATCTAGGG
Statistics
Matches: 158, Mismatches: 22, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
4 1 0.01
6 155 0.98
7 1 0.01
8 1 0.01
ACGTcount: A:0.21, C:0.09, G:0.14, T:0.56
Consensus pattern (6 bp):
ATTTCG
Found at i:40466650 original size:12 final size:12
Alignment explanation
Indices: 40466630--40466823 Score: 172
Period size: 12 Copynumber: 15.7 Consensus size: 12
40466620 ATTTAGGGTT
* *
40466630 ATTTCGATTTCA
1 ATTTTGATTTCG
*
40466642 ATTTTGATTTTG
1 ATTTTGATTTCG
*
40466654 ATTTTGATTTTG
1 ATTTTGATTTCG
*
40466666 ATTTTGATTTTG
1 ATTTTGATTTCG
40466678 ATTTTGATTTCG
1 ATTTTGATTTCG
* *
40466690 ATTTCGATTTTG
1 ATTTTGATTTCG
*
40466702 ATTTTGATTTCA
1 ATTTTGATTTCG
**
40466714 ATTTTGAAACACTCACTG
1 ATTTTG----A-TTTC-G
*
40466732 ATTTTGATTTTG
1 ATTTTGATTTCG
*
40466744 ATTTTGATTTCA
1 ATTTTGATTTCG
*
40466756 ATTTCGATTTCG
1 ATTTTGATTTCG
*
40466768 ATTTCGATTTCG
1 ATTTTGATTTCG
*
40466780 ATTTCGATTTCG
1 ATTTTGATTTCG
*
40466792 ATTTTGATTTTG
1 ATTTTGATTTCG
* *
40466804 ATTTCGATTTAG
1 ATTTTGATTTCG
40466816 ATTTTGAT
1 ATTTTGAT
40466824 CTAGGGTTAT
Statistics
Matches: 152, Mismatches: 24, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
12 141 0.93
13 1 0.01
14 1 0.01
16 1 0.01
17 2 0.01
18 6 0.04
ACGTcount: A:0.21, C:0.09, G:0.14, T:0.56
Consensus pattern (12 bp):
ATTTTGATTTCG
Found at i:40466656 original size:18 final size:18
Alignment explanation
Indices: 40466630--40466823 Score: 199
Period size: 18 Copynumber: 10.4 Consensus size: 18
40466620 ATTTAGGGTT
* *
40466630 ATTTCGATTTCAATTTTG
1 ATTTTGATTTCGATTTTG
*
40466648 ATTTTGATTTTGATTTTG
1 ATTTTGATTTCGATTTTG
*
40466666 ATTTTGATTTTGATTTTG
1 ATTTTGATTTCGATTTTG
*
40466684 ATTTCGATTTCGATTTTG
1 ATTTTGATTTCGATTTTG
*
40466702 ATTTTGATTTCAATTTTG
1 ATTTTGATTTCGATTTTG
** *
40466720 AAACACTCACTGATTTTGATTTTG
1 ----A-T-TTTGATTTCGATTTTG
* *
40466744 ATTTTGATTTCAATTTCG
1 ATTTTGATTTCGATTTTG
* *
40466762 ATTTCGATTTCGATTTCG
1 ATTTTGATTTCGATTTTG
*
40466780 ATTTCGATTTCGATTTTG
1 ATTTTGATTTCGATTTTG
*
40466798 ATTTTGATTTCGATTTAG
1 ATTTTGATTTCGATTTTG
40466816 ATTTTGAT
1 ATTTTGAT
40466824 CTAGGGTTAT
Statistics
Matches: 149, Mismatches: 21, Indels: 12
0.82 0.12 0.07
Matches are distributed among these distances:
18 133 0.89
19 1 0.01
20 1 0.01
22 1 0.01
23 1 0.01
24 12 0.08
ACGTcount: A:0.21, C:0.09, G:0.14, T:0.56
Consensus pattern (18 bp):
ATTTTGATTTCGATTTTG
Found at i:40467153 original size:59 final size:58
Alignment explanation
Indices: 40467086--40467200 Score: 203
Period size: 59 Copynumber: 2.0 Consensus size: 58
40467076 TTGTATGTTA
40467086 TTGTCTGCCATGTGCATGACAAAAATGGTTGTGTTTGTATTAAATTATTTTTGTATTAG
1 TTGTCTGCCATGTGCATGACAAAAATGGTTGTGTTTGTATTAAATTA-TTTTGTATTAG
* *
40467145 TTGTCTGCCATGTGCATGGCAGAAATGGTTGTGTTTGTATTAAATTATTTTGTATT
1 TTGTCTGCCATGTGCATGACAAAAATGGTTGTGTTTGTATTAAATTATTTTGTATT
40467201 GGTTATTGTC
Statistics
Matches: 54, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
58 9 0.17
59 45 0.83
ACGTcount: A:0.23, C:0.09, G:0.22, T:0.46
Consensus pattern (58 bp):
TTGTCTGCCATGTGCATGACAAAAATGGTTGTGTTTGTATTAAATTATTTTGTATTAG
Found at i:40470647 original size:40 final size:40
Alignment explanation
Indices: 40470592--40470671 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
40470582 CAAGTTTATG
40470592 GAAGGAATATTGGGTTTGATACTTAATCAACCCATATATA
1 GAAGGAATATTGGGTTTGATACTTAATCAACCCATATATA
*
40470632 GAAGGAATATTGGGTTTGATACTTAATCAACCCATGTATA
1 GAAGGAATATTGGGTTTGATACTTAATCAACCCATATATA
40470672 AGATGGGAGG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (40 bp):
GAAGGAATATTGGGTTTGATACTTAATCAACCCATATATA
Found at i:40472069 original size:35 final size:36
Alignment explanation
Indices: 40472013--40472092 Score: 135
Period size: 35 Copynumber: 2.2 Consensus size: 36
40472003 TTAGCCATGT
40472013 ATACTAGCAGCCATGTATAACAACATAAGCAACAAA
1 ATACTAGCAGCCATGTATAACAACATAAGCAACAAA
*
40472049 ATACTAGCAG-CATGTATAACAACATAAGCAACAAT
1 ATACTAGCAGCCATGTATAACAACATAAGCAACAAA
*
40472084 ATACCAGCA
1 ATACTAGCA
40472093 ACAACATTAC
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
35 32 0.76
36 10 0.24
ACGTcount: A:0.49, C:0.23, G:0.11, T:0.17
Consensus pattern (36 bp):
ATACTAGCAGCCATGTATAACAACATAAGCAACAAA
Found at i:40474704 original size:5 final size:5
Alignment explanation
Indices: 40474694--40474718 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
40474684 ATAAATGAAA
40474694 AGAGG AGAGG AGAGG AGAGG AGAGG
1 AGAGG AGAGG AGAGG AGAGG AGAGG
40474719 GAGAAAACTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.60, T:0.00
Consensus pattern (5 bp):
AGAGG
Found at i:40494376 original size:22 final size:21
Alignment explanation
Indices: 40494326--40494394 Score: 61
Period size: 22 Copynumber: 3.1 Consensus size: 21
40494316 ACTTAATATT
* *
40494326 TAAGTAAATAT-ATATAATAA
1 TAAGTAAATATAATAAAAAAA
40494346 TAAAGTAAATATAATAAAACAAA
1 T-AAGTAAATATAATAAAA-AAA
40494369 TAAGTAAATGA-AATAAAGAAAGA
1 TAAGTAAAT-ATAATAAA-AAA-A
40494392 TAA
1 TAA
40494395 AAGCAAAATC
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
20 1 0.02
21 10 0.24
22 21 0.51
23 9 0.22
ACGTcount: A:0.65, C:0.01, G:0.09, T:0.25
Consensus pattern (21 bp):
TAAGTAAATATAATAAAAAAA
Found at i:40497440 original size:20 final size:21
Alignment explanation
Indices: 40497400--40497441 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
40497390 CTATTTTTTA
40497400 TTATATTTTATAATATATTTG
1 TTATATTTTATAATATATTTG
*
40497421 TTATATTTTA-AATTTATTTG
1 TTATATTTTATAATATATTTG
40497441 T
1 T
40497442 AGAGTTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (21 bp):
TTATATTTTATAATATATTTG
Found at i:40499451 original size:25 final size:25
Alignment explanation
Indices: 40499413--40499503 Score: 78
Period size: 25 Copynumber: 3.6 Consensus size: 25
40499403 TTATGCGACA
**
40499413 GGAAGCTCCGGAGAGCCATTAATCG
1 GGAAGCTCATGAGAGCCATTAATCG
* *
40499438 GGAAGCTCATGAGAGCCA-AATATCA
1 GGAAGCTCATGAGAGCCATTA-ATCG
*
40499463 GGAAGCTCGTGAGAGCCATATAAT-G
1 GGAAGCTCATGAGAGCCAT-TAATCG
* * *
40499488 AGATGCTCATAAGAGC
1 GGAAGCTCATGAGAGC
40499504 TAAATAACGG
Statistics
Matches: 52, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
24 1 0.02
25 48 0.92
26 2 0.04
27 1 0.02
ACGTcount: A:0.34, C:0.20, G:0.29, T:0.18
Consensus pattern (25 bp):
GGAAGCTCATGAGAGCCATTAATCG
Found at i:40499496 original size:50 final size:50
Alignment explanation
Indices: 40499411--40499509 Score: 130
Period size: 50 Copynumber: 2.0 Consensus size: 50
40499401 ACTTATGCGA
* *
40499411 CAGGAAGCTCCGGAGAGCCATTAATCGGGAAGCTCATGAGAGCCAAATAT
1 CAGGAAGCTCCGGAGAGCCATTAATCGAGAAGCTCATAAGAGCCAAATAT
* *
40499461 CAGGAAGCT-CGTGAGAGCCATATAAT-GAGATGCTCATAAGAGCTAAATA
1 CAGGAAGCTCCG-GAGAGCCAT-TAATCGAGAAGCTCATAAGAGCCAAATA
40499510 ACGGGATGCT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
49 2 0.05
50 37 0.86
51 4 0.09
ACGTcount: A:0.36, C:0.19, G:0.26, T:0.18
Consensus pattern (50 bp):
CAGGAAGCTCCGGAGAGCCATTAATCGAGAAGCTCATAAGAGCCAAATAT
Found at i:40499869 original size:21 final size:21
Alignment explanation
Indices: 40499845--40499886 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
40499835 TGAATTTAGC
* *
40499845 TCAATTTAATACAATTCATAT
1 TCAATTCAATACAATACATAT
*
40499866 TCAATTCAATCCAATACATAT
1 TCAATTCAATACAATACATAT
40499887 CTTTGGCAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.43, C:0.19, G:0.00, T:0.38
Consensus pattern (21 bp):
TCAATTCAATACAATACATAT
Found at i:40506646 original size:25 final size:25
Alignment explanation
Indices: 40506531--40506707 Score: 141
Period size: 25 Copynumber: 7.2 Consensus size: 25
40506521 AAACTATTTC
40506531 GAGCCATATAAT-GGGAAGCTCATGA
1 GAGCCAT-TAATCGGGAAGCTCATGA
* *
40506556 GAG--TTGTAATCGGGAAGCTCATGC
1 GAGCCAT-TAATCGGGAAGCTCATGA
* **
40506580 GAGCCAAT-ATCGGGAAGCTCCGGA
1 GAGCCATTAATCGGGAAGCTCATGA
* * *
40506604 GAGCCATTAAACGAGAAGCTCGTGA
1 GAGCCATTAATCGGGAAGCTCATGA
* *
40506629 GAGCCATTAATCGGGAAGATCGTGA
1 GAGCCATTAATCGGGAAGCTCATGA
* *
40506654 GAGCCA-AATATCGGAAAGCTCATGA
1 GAGCCATTA-ATCGGGAAGCTCATGA
* * *
40506679 GAGCCATATAA-CGAGATGCTCATAA
1 GAGCCAT-TAATCGGGAAGCTCATGA
40506704 GAGC
1 GAGC
40506708 TAAATAATAG
Statistics
Matches: 120, Mismatches: 25, Indels: 14
0.75 0.16 0.09
Matches are distributed among these distances:
23 5 0.04
24 36 0.30
25 77 0.64
26 1 0.01
27 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.29, T:0.18
Consensus pattern (25 bp):
GAGCCATTAATCGGGAAGCTCATGA
Found at i:40506682 original size:75 final size:74
Alignment explanation
Indices: 40506531--40506699 Score: 191
Period size: 75 Copynumber: 2.3 Consensus size: 74
40506521 AAACTATTTC
* * * * * * *
40506531 GAGCCATATAATGGGAAGCTCATGAGAG--TTGTAATCGGGAAGCTCATGCGAGCCAATATCGGG
1 GAGCCATATAACGAGAAGCTCGTGAGAGCCAT-TAATCGGGAAGATCATGAGAGCCAATATCGGA
*
40506594 AAGCTCCGGA
65 AAGCTCAGGA
*
40506604 GAGCCAT-TAAACGAGAAGCTCGTGAGAGCCATTAATCGGGAAGATCGTGAGAGCCAAATATCGG
1 GAGCCATAT-AACGAGAAGCTCGTGAGAGCCATTAATCGGGAAGATCATGAGAGCC-AATATCGG
*
40506668 AAAGCTCATGA
64 AAAGCTCAGGA
*
40506679 GAGCCATATAACGAGATGCTC
1 GAGCCATATAACGAGAAGCTC
40506700 ATAAGAGCTA
Statistics
Matches: 80, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
72 1 0.01
73 23 0.29
74 20 0.25
75 35 0.44
76 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.29, T:0.18
Consensus pattern (74 bp):
GAGCCATATAACGAGAAGCTCGTGAGAGCCATTAATCGGGAAGATCATGAGAGCCAATATCGGAA
AGCTCAGGA
Found at i:40508475 original size:15 final size:15
Alignment explanation
Indices: 40508457--40508488 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
40508447 ATGTCATAAT
40508457 TTTAATGGAATGTGA
1 TTTAATGGAATGTGA
*
40508472 TTTAATTGAATGTGA
1 TTTAATGGAATGTGA
40508487 TT
1 TT
40508489 ATTGGAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (15 bp):
TTTAATGGAATGTGA
Found at i:40508724 original size:26 final size:27
Alignment explanation
Indices: 40508675--40508746 Score: 69
Period size: 28 Copynumber: 2.7 Consensus size: 27
40508665 AAATTATTAG
* *
40508675 TAATAAAATTTTAATTAAGTA-TTTAA
1 TAATAATATTTTAATTGAGTATTTTAA
40508701 TAATAATATTTTAATTGA-TAATTTTTAA
1 TAATAATATTTTAATTGAGT-A-TTTTAA
*
40508729 -AATTATTATTTTAATTGA
1 TAA-TAATATTTTAATTGA
40508747 AAATAAAATT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
25 1 0.03
26 17 0.44
27 2 0.05
28 19 0.49
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.51
Consensus pattern (27 bp):
TAATAATATTTTAATTGAGTATTTTAA
Done.