Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D02
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: 67659327
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 461372 characters in sequence are not A, C, G, or T
File 170 of 216
Found at i:53548031 original size:16 final size:16
Alignment explanation
Indices: 53548010--53548042 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
53548000 TAGCATAAAT
53548010 AACAGT-CTTCTGAGAC
1 AACAGTCCTT-TGAGAC
53548026 AACAGTCCTTTGAGAC
1 AACAGTCCTTTGAGAC
53548042 A
1 A
53548043 TTTCTGCCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24
Consensus pattern (16 bp):
AACAGTCCTTTGAGAC
Found at i:53576264 original size:27 final size:26
Alignment explanation
Indices: 53576197--53576264 Score: 84
Period size: 26 Copynumber: 2.5 Consensus size: 26
53576187 AATAAACACC
*
53576197 AAAAATTTATTTTAAAAATAAAAAAAT
1 AAAAATATATTTT-AAAATAAAAAAAT
*
53576224 AAAAA-AGTATTTTAAAATTAAAAAAT
1 AAAAATA-TATTTTAAAATAAAAAAAT
53576250 AAAAATATATATTTA
1 AAAAATATAT-TTTA
53576265 TTATATATTC
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
26 20 0.56
27 16 0.44
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (26 bp):
AAAAATATATTTTAAAATAAAAAAAT
Found at i:53596390 original size:6 final size:6
Alignment explanation
Indices: 53596375--53596416 Score: 59
Period size: 6 Copynumber: 7.0 Consensus size: 6
53596365 GTATTGTTCA
*
53596375 CTTTTT -TTTTT CTTTTT CTTTTCT CTTTTT CTTCTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTT-T CTTTTT CTTTTT CTTTTT
53596417 TTCCCACTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 5 0.16
6 21 0.66
7 6 0.19
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (6 bp):
CTTTTT
Found at i:53596391 original size:11 final size:11
Alignment explanation
Indices: 53596375--53596419 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
53596365 GTATTGTTCA
53596375 CTTTTTTTTTT
1 CTTTTTTTTTT
*
53596386 CTTTTTCTTTT
1 CTTTTTTTTTT
* *
53596397 CTCTTTTTCTT
1 CTTTTTTTTTT
*
53596408 CTTCTTTTTTT
1 CTTTTTTTTTT
53596419 C
1 C
53596420 CCACTATATA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (11 bp):
CTTTTTTTTTT
Found at i:53596401 original size:13 final size:13
Alignment explanation
Indices: 53596375--53596419 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
53596365 GTATTGTTCA
53596375 CTTTTT-TTTT-T
1 CTTTTTCTTTTCT
53596386 CTTTTTCTTTTCT
1 CTTTTTCTTTTCT
53596399 CTTTTTCTTCTTCT
1 CTTTTTCTT-TTCT
*
53596413 TTTTTTC
1 CTTTTTC
53596420 CCACTATATA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 6 0.20
12 4 0.13
13 10 0.33
14 10 0.33
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (13 bp):
CTTTTTCTTTTCT
Found at i:53601032 original size:24 final size:24
Alignment explanation
Indices: 53601004--53601054 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
53600994 TTCTAGAAGT
* * *
53601004 TTTAGTATTTATGAGTATAATATA
1 TTTAGCATTTATAAGCATAATATA
53601028 TTTAGCATTTATAAGCATAATATA
1 TTTAGCATTTATAAGCATAATATA
53601052 TTT
1 TTT
53601055 GACTTTGATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.49
Consensus pattern (24 bp):
TTTAGCATTTATAAGCATAATATA
Found at i:53605399 original size:24 final size:24
Alignment explanation
Indices: 53605334--53605387 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
53605324 TATTTCTAGA
* * *
53605334 ATATTTAGTATTTATGAGTATAAT
1 ATATTTAGCATTTATTAGCATAAT
53605358 ATATTTAGCATTTATTAGCATAAT
1 ATATTTAGCATTTATTAGCATAAT
53605382 ATATTT
1 ATATTT
53605388 GACTTTGATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.50
Consensus pattern (24 bp):
ATATTTAGCATTTATTAGCATAAT
Found at i:53606667 original size:47 final size:48
Alignment explanation
Indices: 53606614--53606711 Score: 189
Period size: 47 Copynumber: 2.1 Consensus size: 48
53606604 ATGTGTAAAC
53606614 TTGCCACTATATTTTAGTTGGAAGTTAAAATTTGGTAAACTACA-CAA
1 TTGCCACTATATTTTAGTTGGAAGTTAAAATTTGGTAAACTACACCAA
53606661 TTGCCACTATATTTTAGTTGGAAGTTAAAATTTGGTAAACTACACCAA
1 TTGCCACTATATTTTAGTTGGAAGTTAAAATTTGGTAAACTACACCAA
53606709 TTG
1 TTG
53606712 TCCCTAAACT
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
47 44 0.88
48 6 0.12
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (48 bp):
TTGCCACTATATTTTAGTTGGAAGTTAAAATTTGGTAAACTACACCAA
Found at i:53607301 original size:20 final size:20
Alignment explanation
Indices: 53607276--53607313 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
53607266 TTATAATTAA
53607276 AAGTTAAAACCCTAAAATGT
1 AAGTTAAAACCCTAAAATGT
*
53607296 AAGTTAAACCCCTAAAAT
1 AAGTTAAAACCCTAAAAT
53607314 ATAAAACCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.18, G:0.08, T:0.24
Consensus pattern (20 bp):
AAGTTAAAACCCTAAAATGT
Found at i:53607349 original size:14 final size:13
Alignment explanation
Indices: 53607299--53607381 Score: 53
Period size: 14 Copynumber: 5.9 Consensus size: 13
53607289 AAAATGTAAG
*
53607299 TTAAACCCCTAAAA
1 TTAAA-CCCTAAAC
*
53607313 TATAAAACCTAAAC
1 T-TAAACCCTAAAC
53607327 -TAGAGACCCTAAATC
1 TTA-A-ACCCTAAA-C
53607342 TTAAACCC-AAGAC
1 TTAAACCCTAA-AC
53607355 TCTAAACCCTTAAAC
1 T-TAAACCC-TAAAC
*
53607370 TCAAACCCTAAA
1 TTAAACCCTAAA
53607382 TATGATAGTT
Statistics
Matches: 56, Mismatches: 4, Indels: 19
0.71 0.05 0.24
Matches are distributed among these distances:
12 2 0.04
13 9 0.16
14 32 0.57
15 9 0.16
16 4 0.07
ACGTcount: A:0.47, C:0.29, G:0.04, T:0.20
Consensus pattern (13 bp):
TTAAACCCTAAAC
Found at i:53607354 original size:21 final size:21
Alignment explanation
Indices: 53607330--53607382 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
53607320 CCTAAACTAG
53607330 AGACCCTAAATCTTAAACCCA
1 AGACCCTAAATCTTAAACCCA
* * *
53607351 AGACTCTAAACCCTTAAACTCA
1 AGACCCTAAA-TCTTAAACCCA
53607373 A-ACCCTAAAT
1 AGACCCTAAAT
53607383 ATGATAGTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 16 0.62
22 10 0.38
ACGTcount: A:0.43, C:0.32, G:0.04, T:0.21
Consensus pattern (21 bp):
AGACCCTAAATCTTAAACCCA
Found at i:53607953 original size:16 final size:15
Alignment explanation
Indices: 53607921--53607964 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 15
53607911 AGATTACAAA
* *
53607921 ATTAAATCTTATCAG
1 ATTAAATCTTCTAAG
53607936 ATTATAATCTTCTAAG
1 ATTA-AATCTTCTAAG
*
53607952 ATTAATTCTTCTA
1 ATTAAATCTTCTA
53607965 TTTACCAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.36, C:0.14, G:0.05, T:0.45
Consensus pattern (15 bp):
ATTAAATCTTCTAAG
Found at i:53608310 original size:4 final size:4
Alignment explanation
Indices: 53608301--53608326 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
53608291 ACAACAAAGC
53608301 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
53608327 GAAGTAAGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:53610446 original size:26 final size:27
Alignment explanation
Indices: 53610398--53610450 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
53610388 ATTTAATATT
*
53610398 TTAATTTAATACTTAAAAAATAATAAA
1 TTAATATAATACTTAAAAAATAATAAA
*
53610425 TTAATATAATA-TTAAATAATAATAAA
1 TTAATATAATACTTAAAAAATAATAAA
53610451 AGCAAGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 14 0.58
27 10 0.42
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (27 bp):
TTAATATAATACTTAAAAAATAATAAA
Found at i:53617693 original size:28 final size:27
Alignment explanation
Indices: 53617636--53617690 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
53617626 GAAAATATTA
53617636 TGTACTTTTTTTTCCTTCACTAGAATT
1 TGTACTTTTTTTTCCTTCACTAGAATT
53617663 TGTACTTTTTTTTCCTTCACTAGAATT
1 TGTACTTTTTTTTCCTTCACTAGAATT
53617690 T
1 T
53617691 TGTCCCACAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.18, C:0.18, G:0.07, T:0.56
Consensus pattern (27 bp):
TGTACTTTTTTTTCCTTCACTAGAATT
Found at i:53621233 original size:39 final size:37
Alignment explanation
Indices: 53621166--53621258 Score: 98
Period size: 39 Copynumber: 2.5 Consensus size: 37
53621156 ACCAGAATGG
* *
53621166 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAGTTGA
1 CACCCAGTGCCTCATCGGAAAGTCCGAAG-AA-AGTTGA
* *
53621205 CACCCAGTGTCTCATCGGCAAAG-CCGAAGAAAGTTGG
1 CACCCAGTGCCTCATCGG-AAAGTCCGAAGAAAGTTGA
* *
53621242 TACCCAGTACCTCATCG
1 CACCCAGTGCCTCATCG
53621259 AATCTATCCG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
37 19 0.41
38 2 0.04
39 22 0.48
40 3 0.07
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (37 bp):
CACCCAGTGCCTCATCGGAAAGTCCGAAGAAAGTTGA
Found at i:53621620 original size:3 final size:3
Alignment explanation
Indices: 53621612--53621650 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
53621602 ATTCCCACTC
* *
53621612 ATA ATA ATA ATA ATA ATA CTA ATA ATA ATA ATA CTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
53621651 TTATACTTAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:53621636 original size:15 final size:15
Alignment explanation
Indices: 53621616--53621650 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
53621606 CCACTCATAA
53621616 TAATAATAATAATAC
1 TAATAATAATAATAC
53621631 TAATAATAATAATAC
1 TAATAATAATAATAC
53621646 TAATA
1 TAATA
53621651 TTATACTTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (15 bp):
TAATAATAATAATAC
Found at i:53622322 original size:11 final size:11
Alignment explanation
Indices: 53622306--53622331 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
53622296 CTTTTTCTTC
53622306 TTTCTCCCCTG
1 TTTCTCCCCTG
53622317 TTTCTCCCCTG
1 TTTCTCCCCTG
53622328 TTTC
1 TTTC
53622332 GTCTCTTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.42, G:0.08, T:0.50
Consensus pattern (11 bp):
TTTCTCCCCTG
Found at i:53622713 original size:21 final size:21
Alignment explanation
Indices: 53622689--53622731 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
53622679 AATAATAACT
53622689 AATAACTAATAATAAATAATA
1 AATAACTAATAATAAATAATA
* * * *
53622710 AATATCTTATACTAATTAATA
1 AATAACTAATAATAAATAATA
53622731 A
1 A
53622732 GCAAATTAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.35
Consensus pattern (21 bp):
AATAACTAATAATAAATAATA
Found at i:53627800 original size:21 final size:21
Alignment explanation
Indices: 53627758--53627800 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
53627748 TTCAGTATAC
*
53627758 ATTCTTTCATCAGTATCATTT
1 ATTCTTTCATCAGCATCATTT
*
53627779 ATTCTTTCTTCAGACATC-TTT
1 ATTCTTTCATCAG-CATCATTT
53627800 A
1 A
53627801 ATCTATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.23, C:0.21, G:0.05, T:0.51
Consensus pattern (21 bp):
ATTCTTTCATCAGCATCATTT
Found at i:53628908 original size:39 final size:37
Alignment explanation
Indices: 53628841--53628933 Score: 98
Period size: 39 Copynumber: 2.5 Consensus size: 37
53628831 ACCAGAATGG
* *
53628841 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAGTTGA
1 CACCCAGTGCCTCATCGGAAAGTCCGAAG-AA-AGTTGA
* *
53628880 CACCCAGTGTCTCATCGGCAAAG-CCGAAGAAAGTTGG
1 CACCCAGTGCCTCATCGG-AAAGTCCGAAGAAAGTTGA
* *
53628917 TACCCAGTACCTCATCG
1 CACCCAGTGCCTCATCG
53628934 AATCTATCCG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
37 19 0.41
38 2 0.04
39 22 0.48
40 3 0.07
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (37 bp):
CACCCAGTGCCTCATCGGAAAGTCCGAAGAAAGTTGA
Found at i:53630004 original size:11 final size:11
Alignment explanation
Indices: 53629988--53630013 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
53629978 CTTTTTCTTC
53629988 TTTCTCCCCTG
1 TTTCTCCCCTG
53629999 TTTCTCCCCTG
1 TTTCTCCCCTG
53630010 TTTC
1 TTTC
53630014 GTCTCTTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.42, G:0.08, T:0.50
Consensus pattern (11 bp):
TTTCTCCCCTG
Found at i:53630395 original size:21 final size:21
Alignment explanation
Indices: 53630371--53630413 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
53630361 AATAATAACT
53630371 AATAACTAATAATAAATAATA
1 AATAACTAATAATAAATAATA
* * * *
53630392 AATATCTTATACTAATTAATA
1 AATAACTAATAATAAATAATA
53630413 A
1 A
53630414 GCAAATTAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.35
Consensus pattern (21 bp):
AATAACTAATAATAAATAATA
Found at i:53632268 original size:25 final size:25
Alignment explanation
Indices: 53632240--53632433 Score: 133
Period size: 25 Copynumber: 7.8 Consensus size: 25
53632230 TAGCTCGCAA
* * *
53632240 GAGCGTCCCGTTATTTAGCTCTTAT
1 GAGCTTCCCGTTATTTGGCTCTCAT
* * * *
53632265 GAGCATCCCATTATATGGCTCTCAC
1 GAGCTTCCCGTTATTTGGCTCTCAT
* *
53632290 GAGCTTCTCGATATTTGGCTCTCAT
1 GAGCTTCCCGTTATTTGGCTCTCAT
* **
53632315 GAGCTTCCCGATTA-ATGGCTCTTTT
1 GAGCTTCCCG-TTATTTGGCTCTCAT
* *
53632340 AAGCTTCCCGTT-TATGGCTCGT-AT
1 GAGCTTCCCGTTATTTGGCTC-TCAT
* * * *
53632364 GAGCTTTCCGATATTTGGCTCGCAA
1 GAGCTTCCCGTTATTTGGCTCTCAT
*** *
53632389 GAGCTTCCCGTTATACAGCTCACAT
1 GAGCTTCCCGTTATTTGGCTCTCAT
* *
53632414 GAGCTTCCCTTTATATGGCT
1 GAGCTTCCCGTTATTTGGCT
53632434 TGGAAGAGCT
Statistics
Matches: 129, Mismatches: 35, Indels: 10
0.74 0.20 0.06
Matches are distributed among these distances:
24 19 0.15
25 108 0.84
26 2 0.02
ACGTcount: A:0.19, C:0.26, G:0.20, T:0.36
Consensus pattern (25 bp):
GAGCTTCCCGTTATTTGGCTCTCAT
Found at i:53632433 original size:50 final size:50
Alignment explanation
Indices: 53632232--53632443 Score: 164
Period size: 50 Copynumber: 4.3 Consensus size: 50
53632222 ACACACCATA
* * * *
53632232 GCTCGCAAGAGCGTCCCGTTATTTAGCTCTTATGAGCATCCCATTATATG
1 GCTCGCAAGAGCTTCCCGTTATATAGCTCTCATGAGCTTCCCATTATATG
* * * * * *
53632282 GCTCTCACGAGCTTCTCGATATTTGGCTCTCATGAGCTTCCCGATTA-ATG
1 GCTCGCAAGAGCTTCCCGTTATATAGCTCTCATGAGCTTCCC-ATTATATG
*** * * *
53632332 GCTCTTTTA-AGCTTCCCGTT-TATGGCTCGT-ATGAGCTTTCCGA-TATTTG
1 GCTC-GCAAGAGCTTCCCGTTATATAGCTC-TCATGAGC-TTCCCATTATATG
* * *
53632381 GCTCGCAAGAGCTTCCCGTTATACAGCTCACATGAGCTTCCCTTTATATG
1 GCTCGCAAGAGCTTCCCGTTATATAGCTCTCATGAGCTTCCCATTATATG
* *
53632431 GCTTGGAAGAGCT
1 GCTCGCAAGAGCT
53632444 CCCCATTTAC
Statistics
Matches: 126, Mismatches: 27, Indels: 18
0.74 0.16 0.11
Matches are distributed among these distances:
48 3 0.02
49 35 0.28
50 83 0.66
51 5 0.04
ACGTcount: A:0.19, C:0.26, G:0.21, T:0.34
Consensus pattern (50 bp):
GCTCGCAAGAGCTTCCCGTTATATAGCTCTCATGAGCTTCCCATTATATG
Found at i:53633838 original size:18 final size:17
Alignment explanation
Indices: 53633724--53633907 Score: 87
Period size: 17 Copynumber: 10.6 Consensus size: 17
53633714 AAGTTTTTTG
*
53633724 TTTTGAAAACGCGAGAA-
1 TTTTGAAAACACGA-AAT
*
53633741 TTTTG-AAACACAATAATT
1 TTTTGAAAACACGA-AA-T
*
53633759 TTTTGAGAACACGGAAAT
1 TTTTGAAAACAC-GAAAT
*
53633777 TTTTG-AAATACGAGAAT
1 TTTTGAAAACACGA-AAT
* *
53633794 TTTAG-AAACACAAAAAT
1 TTTTGAAAACAC-GAAAT
*
53633811 TTCT-AAAACACGAACAT
1 TTTTGAAAACACGAA-AT
*
53633828 TTTTGAAAACACGAGAT
1 TTTTGAAAACACGAAAT
** *
53633845 TTTTTTAAACAC-AATTTTT
1 TTTTGAAAACACGAA---AT
*
53633864 TTTTAAAAAACACGGAAAT
1 TTTT-GAAAACAC-GAAAT
*
53633883 TTTTG-AAACACGAAGT
1 TTTTGAAAACACGAAAT
53633899 TTTT-AAAAC
1 TTTTGAAAAC
53633908 GTACAGTATT
Statistics
Matches: 127, Mismatches: 24, Indels: 33
0.69 0.13 0.18
Matches are distributed among these distances:
16 25 0.20
17 55 0.43
18 21 0.17
19 17 0.13
20 7 0.06
22 2 0.02
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (17 bp):
TTTTGAAAACACGAAAT
Found at i:53634689 original size:8 final size:8
Alignment explanation
Indices: 53634672--53634728 Score: 51
Period size: 8 Copynumber: 7.0 Consensus size: 8
53634662 GCTGTTTTTA
*
53634672 TTTTTATT
1 TTTTTCTT
53634680 TTTTTCTT
1 TTTTTCTT
* *
53634688 TTTCTCTC
1 TTTTTCTT
*
53634696 CTTTTCTT
1 TTTTTCTT
*
53634704 TTTTCCTT
1 TTTTTCTT
53634712 TTTCTTCTT
1 TTT-TTCTT
*
53634721 CTTTTCTT
1 TTTTTCTT
53634729 AACTTTCTCT
Statistics
Matches: 38, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
8 32 0.84
9 6 0.16
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTTCTT
Found at i:53634706 original size:25 final size:24
Alignment explanation
Indices: 53634673--53634750 Score: 77
Period size: 24 Copynumber: 3.1 Consensus size: 24
53634663 CTGTTTTTAT
*
53634673 TTTTATTTTTTTCTTTTTCTCTCC
1 TTTTCTTTTTTTCTTTTTCTCTCC
* *
53634697 TTTTCTTTTTTCCTTTTTCTTCTTC
1 TTTTCTTTTTTTCTTTTTC-TCTCC
*
53634722 TTTTCTTAACTTTCTCTTTTTCT-TCC
1 TTTTCTT---TTTTTCTTTTTCTCTCC
53634748 TTT
1 TTT
53634751 CAAACCCTAG
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
24 17 0.39
25 11 0.25
26 5 0.11
27 1 0.02
28 10 0.23
ACGTcount: A:0.04, C:0.23, G:0.00, T:0.73
Consensus pattern (24 bp):
TTTTCTTTTTTTCTTTTTCTCTCC
Found at i:53634887 original size:18 final size:16
Alignment explanation
Indices: 53634854--53634926 Score: 55
Period size: 14 Copynumber: 4.7 Consensus size: 16
53634844 TTCCTCATTT
*
53634854 TCTTCTTTTTCTTTTC
1 TCTTCTTTTTCCTTTC
53634870 TCTTCTTTTTTCCCTTTC
1 TCTTC-TTTTT-CCTTTC
* *
53634888 TC-TC-CTTCCCTTTC
1 TCTTCTTTTTCCTTTC
*
53634902 -C-TCTTTTTTCTTTC
1 TCTTCTTTTTCCTTTC
*
53634916 TCTTCTATTTC
1 TCTTCTTTTTC
53634927 GGTAACCCCC
Statistics
Matches: 44, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
13 3 0.07
14 13 0.30
15 3 0.07
16 11 0.25
17 7 0.16
18 7 0.16
ACGTcount: A:0.01, C:0.33, G:0.00, T:0.66
Consensus pattern (16 bp):
TCTTCTTTTTCCTTTC
Found at i:53635497 original size:30 final size:30
Alignment explanation
Indices: 53635434--53635588 Score: 114
Period size: 30 Copynumber: 5.2 Consensus size: 30
53635424 TTCTGGGGCA
* *** * *
53635434 AAAATGTAATTTCAAGAAAAACATGGGGCC
1 AAAATGTAATTTTAAGAAAGTTAAGGGGTC
* *
53635464 AAAATGTAATTTTTAGAAATTTAAGGGGTC
1 AAAATGTAATTTTAAGAAAGTTAAGGGGTC
* *
53635494 AAAATGAAATTTTAAGAAAGTTAAAGGGTC
1 AAAATGTAATTTTAAGAAAGTTAAGGGGTC
* * * * *
53635524 AAAGTGTAAATATAGGAAAGTTTA-GGGTCC
1 AAAATGTAATTTTAAGAAAGTTAAGGGGT-C
* * * *
53635554 AAAATATAATTTAAAGAAAATTTAGGGGTC
1 AAAATGTAATTTTAAGAAAGTTAAGGGGTC
*
53635584 TAAAT
1 AAAAT
53635589 ATGATTTATA
Statistics
Matches: 98, Mismatches: 25, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
29 4 0.04
30 90 0.92
31 4 0.04
ACGTcount: A:0.46, C:0.06, G:0.20, T:0.28
Consensus pattern (30 bp):
AAAATGTAATTTTAAGAAAGTTAAGGGGTC
Found at i:53635809 original size:5 final size:5
Alignment explanation
Indices: 53635799--53635824 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
53635789 AAATATATAT
53635799 ATAAA ATAAA ATAAA ATAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA A
53635825 ACACGAAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
ATAAA
Found at i:53642334 original size:28 final size:28
Alignment explanation
Indices: 53642302--53642367 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 28
53642292 AACCAAAAAA
53642302 GGCCGTTTTTTCAA-AATTTACCGAAATG
1 GGCCGTTTTTT-AATAATTTACCGAAATG
* *
53642330 GGCCGGTTTTTTAATTATTTACCGGAATG
1 GGCC-GTTTTTTAATAATTTACCGAAATG
*
53642359 GGCCATTTT
1 GGCCGTTTT
53642368 CCGCGAAATC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 10 0.30
29 23 0.70
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.39
Consensus pattern (28 bp):
GGCCGTTTTTTAATAATTTACCGAAATG
Found at i:53644680 original size:24 final size:24
Alignment explanation
Indices: 53644642--53644690 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
53644632 TGCCTTTGTA
**
53644642 AGTAGTTGTAGATATGGGAATTCT
1 AGTAGTTGTAGATATGAAAATTCT
53644666 AGTAGTTGT-GTATATGAAAATTCT
1 AGTAGTTGTAG-ATATGAAAATTCT
53644690 A
1 A
53644691 CTGTTCAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 21 0.95
ACGTcount: A:0.33, C:0.04, G:0.24, T:0.39
Consensus pattern (24 bp):
AGTAGTTGTAGATATGAAAATTCT
Found at i:53648007 original size:58 final size:58
Alignment explanation
Indices: 53647917--53648033 Score: 225
Period size: 58 Copynumber: 2.0 Consensus size: 58
53647907 TATAAAACAC
*
53647917 TGTTATGAAGTTTATTTTAAAGATGCATCTAGGTTTTGTATTACTTTTCAATGCTTCA
1 TGTTATGAAGTTCATTTTAAAGATGCATCTAGGTTTTGTATTACTTTTCAATGCTTCA
53647975 TGTTATGAAGTTCATTTTAAAGATGCATCTAGGTTTTGTATTACTTTTCAATGCTTCA
1 TGTTATGAAGTTCATTTTAAAGATGCATCTAGGTTTTGTATTACTTTTCAATGCTTCA
53648033 T
1 T
53648034 TAATGAATGT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.26, C:0.11, G:0.15, T:0.48
Consensus pattern (58 bp):
TGTTATGAAGTTCATTTTAAAGATGCATCTAGGTTTTGTATTACTTTTCAATGCTTCA
Found at i:53653903 original size:22 final size:21
Alignment explanation
Indices: 53653878--53653942 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
53653868 CATGCATGAT
53653878 ACAGACACAAAGTAAACATCTC
1 ACAG-CACAAAGTAAACATCTC
*
53653900 ACAGC-CTAAA--CAAC-TCTC
1 ACAGCAC-AAAGTAAACATCTC
*
53653918 -TAGCACAAAGTAAACATCTC
1 ACAGCACAAAGTAAACATCTC
53653938 ACAGC
1 ACAGC
53653943 CTAAACAACT
Statistics
Matches: 33, Mismatches: 4, Indels: 13
0.66 0.08 0.26
Matches are distributed among these distances:
17 6 0.18
18 5 0.15
19 6 0.18
20 5 0.15
21 7 0.21
22 4 0.12
ACGTcount: A:0.45, C:0.31, G:0.09, T:0.15
Consensus pattern (21 bp):
ACAGCACAAAGTAAACATCTC
Found at i:53653934 original size:38 final size:38
Alignment explanation
Indices: 53653883--53653959 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
53653873 ATGATACAGA
53653883 CACAAAGTAAACATCTCACAGCCTAAACAACTCTCTAG
1 CACAAAGTAAACATCTCACAGCCTAAACAACTCTCTAG
53653921 CACAAAGTAAACATCTCACAGCCTAAACAACTCTCTAG
1 CACAAAGTAAACATCTCACAGCCTAAACAACTCTCTAG
53653959 C
1 C
53653960 GTAGTCCTTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.42, C:0.32, G:0.08, T:0.18
Consensus pattern (38 bp):
CACAAAGTAAACATCTCACAGCCTAAACAACTCTCTAG
Found at i:53657906 original size:42 final size:43
Alignment explanation
Indices: 53657845--53658195 Score: 435
Period size: 43 Copynumber: 8.2 Consensus size: 43
53657835 CTAACTTTTT
*
53657845 GCGGCGCTTACAGAAAAAAACGCCGCTAAAGGTCATGTTCTTTA
1 GCGGCGCTTA-AGAAAAAAACGCCGCTAAAGATCATGTTCTTTA
* * *
53657889 GCGGC-ATTTAGAAAAAAACGCCGCTAAATATCATGTTCTTTA
1 GCGGCGCTTAAGAAAAAAACGCCGCTAAAGATCATGTTCTTTA
** * *
53657931 GCGGCGCTTGTGCAAAAAACACCGCTAAAGATCATGTTCTTTA
1 GCGGCGCTTAAGAAAAAAACGCCGCTAAAGATCATGTTCTTTA
53657974 GCGGCGC-TAAGAAAAAAA-GCCGCTAAAGATCATGTTCTTTA
1 GCGGCGCTTAAGAAAAAAACGCCGCTAAAGATCATGTTCTTTA
* *
53658015 GCGGCGC-TAAGAAAAAAACGCCACTAAAGATCGTGTTCTTTA
1 GCGGCGCTTAAGAAAAAAACGCCGCTAAAGATCATGTTCTTTA
** * *
53658057 GCGGCGCTTGGGAAAAAAACACCGCTAAAGATCGTGTTCTTTA
1 GCGGCGCTTAAGAAAAAAACGCCGCTAAAGATCATGTTCTTTA
**
53658100 GCGGCGCTTGGGAAAAAAACGCCGCTAAAGATCATGTTCTTTA
1 GCGGCGCTTAAGAAAAAAACGCCGCTAAAGATCATGTTCTTTA
* *** * *
53658143 GCGGCGCTTTATCTACAAACGCCGCTAAA-AGT-AGTGTGCTTTA
1 GCGGCGCTTAAGAAAAAAACGCCGCTAAAGA-TCA-TGTTCTTTA
53658186 GCGGCGCTTA
1 GCGGCGCTTA
53658196 TTTCAGAAAC
Statistics
Matches: 272, Mismatches: 30, Indels: 11
0.87 0.10 0.04
Matches are distributed among these distances:
41 40 0.15
42 74 0.27
43 153 0.56
44 5 0.02
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.24
Consensus pattern (43 bp):
GCGGCGCTTAAGAAAAAAACGCCGCTAAAGATCATGTTCTTTA
Found at i:53658001 original size:126 final size:128
Alignment explanation
Indices: 53657845--53658147 Score: 475
Period size: 126 Copynumber: 2.4 Consensus size: 128
53657835 CTAACTTTTT
* * *
53657845 GCGGCGCTTACAGAAAAAAACGCCGCTAAAGGTCATGTTCTTTAGCGGCATTTAGAAAAAAACGC
1 GCGGCGCTTA-AGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCACTAAGAAAAAAACGC
* * * *
53657910 CGCTAAATATCATGTTCTTTAGCGGCGCTTGTGCAAAAAACACCGCTAAAGATCATGTTCTTTA
65 CACTAAAGATCATGTTCTTTAGCGGCGCTTGGGAAAAAAACACCGCTAAAGATCATGTTCTTTA
*
53657974 GCGGCGC-TAAGAAAAAAA-GCCGCTAAAGATCATGTTCTTTAGCGGCGCTAAGAAAAAAACGCC
1 GCGGCGCTTAAGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCACTAAGAAAAAAACGCC
* *
53658037 ACTAAAGATCGTGTTCTTTAGCGGCGCTTGGGAAAAAAACACCGCTAAAGATCGTGTTCTTTA
66 ACTAAAGATCATGTTCTTTAGCGGCGCTTGGGAAAAAAACACCGCTAAAGATCATGTTCTTTA
**
53658100 GCGGCGCTTGGGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGC
1 GCGGCGCTTAAGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGC
53658148 GCTTTATCTA
Statistics
Matches: 160, Mismatches: 12, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
126 105 0.66
127 18 0.11
128 30 0.19
129 7 0.04
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.23
Consensus pattern (128 bp):
GCGGCGCTTAAGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCACTAAGAAAAAAACGCC
ACTAAAGATCATGTTCTTTAGCGGCGCTTGGGAAAAAAACACCGCTAAAGATCATGTTCTTTA
Found at i:53658655 original size:21 final size:21
Alignment explanation
Indices: 53658631--53658708 Score: 93
Period size: 21 Copynumber: 3.7 Consensus size: 21
53658621 TTTGAACCTT
53658631 TGCTTCTCTCGCTGCGGCATC
1 TGCTTCTCTCGCTGCGGCATC
53658652 TGCTTCTCTCGCTGCGGCATC
1 TGCTTCTCTCGCTGCGGCATC
* * * * *
53658673 TACTTCTCTTGTTGCAGCCTC
1 TGCTTCTCTCGCTGCGGCATC
* *
53658694 TGCTTCCCTTGCTGC
1 TGCTTCTCTCGCTGC
53658709 CGCCTCTGTT
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.05, C:0.37, G:0.21, T:0.37
Consensus pattern (21 bp):
TGCTTCTCTCGCTGCGGCATC
Found at i:53664241 original size:9 final size:9
Alignment explanation
Indices: 53664227--53664561 Score: 102
Period size: 9 Copynumber: 37.8 Consensus size: 9
53664217 TTTTTATGTA
53664227 TTATGTAAG
1 TTATGTAAG
*
53664236 TTATGTAAC
1 TTATGTAAG
*
53664245 TTACGTAAG
1 TTATGTAAG
** *
53664254 TTA-CCAAA
1 TTATGTAAG
*
53664262 TTAATGTATG
1 TT-ATGTAAG
*
53664272 CTATGTAAG
1 TTATGTAAG
53664281 -T-TGTAAG
1 TTATGTAAG
*
53664288 TTAT-TATG
1 TTATGTAAG
53664296 TATTATGTAAG
1 --TTATGTAAG
53664307 TTATGT-A-
1 TTATGTAAG
*
53664314 TTATGTAGG
1 TTATGTAAG
53664323 TTATGTAAG
1 TTATGTAAG
*
53664332 TTGTGTAAG
1 TTATGTAAG
* *
53664341 ATATTTAAG
1 TTATGTAAG
53664350 TTATGTAAG
1 TTATGTAAG
* *
53664359 TTTTG-CA-
1 TTATGTAAG
53664366 TTATGTAAG
1 TTATGTAAG
*
53664375 TTATGTATG
1 TTATGTAAG
*
53664384 CTATGT-A-
1 TTATGTAAG
*
53664391 TAATGTAAG
1 TTATGTAAG
* *
53664400 TTGT-TATG
1 TTATGTAAG
53664408 TATAATGTAAG
1 T-T-ATGTAAG
53664419 TTAATATGTAAG
1 -T--TATGTAAG
*
53664431 TAATGT-A-
1 TTATGTAAG
53664438 TTATGTAAG
1 TTATGTAAG
* *
53664447 TTTATATAAAAATT
1 -TTATGT---AA-G
*
53664461 TTATATAAG
1 TTATGTAAG
53664470 TTATGT-A-
1 TTATGTAAG
53664477 TTATGTAAGG
1 TTATGTAA-G
* *
53664487 TAACATATAAG
1 T--TATGTAAG
53664498 TTTATGTAAG
1 -TTATGTAAG
53664508 TTATG--A-
1 TTATGTAAG
53664514 --ATGTAAG
1 TTATGTAAG
53664521 TTATGT-A-
1 TTATGTAAG
53664528 TTATGTAAG
1 TTATGTAAG
* *
53664537 TTATTTAAA
1 TTATGTAAG
*
53664546 TTATTTAAG
1 TTATGTAAG
*
53664555 TTGTGTA
1 TTATGTA
53664562 TTATATAACT
Statistics
Matches: 237, Mismatches: 51, Indels: 76
0.65 0.14 0.21
Matches are distributed among these distances:
4 3 0.01
6 1 0.00
7 38 0.16
8 23 0.10
9 119 0.50
10 21 0.09
11 8 0.03
12 14 0.06
13 10 0.04
ACGTcount: A:0.34, C:0.02, G:0.18, T:0.45
Consensus pattern (9 bp):
TTATGTAAG
Found at i:53664241 original size:16 final size:16
Alignment explanation
Indices: 53664220--53664565 Score: 119
Period size: 16 Copynumber: 20.7 Consensus size: 16
53664210 TGATATATTT
53664220 TTATGTATTATGTAAG
1 TTATGTATTATGTAAG
*
53664236 TTATGTAACTTACGTAAG
1 TTATGT-A-TTATGTAAG
*** *
53664254 TTACCAAATTAATGTATG
1 TTA-TGTATT-ATGTAAG
* *
53664272 CTATGTAAGT-TGTAAG
1 TTATGT-ATTATGTAAG
53664288 TTATTATGTATTATGTAAG
1 -T--TATGTATTATGTAAG
*
53664307 TTATGTATTATGTAGG
1 TTATGTATTATGTAAG
*
53664323 TTATGTAAGTTGTGTAAG
1 TTATGT-A-TTATGTAAG
* *
53664341 ATATTTAAGTTATGTAAG
1 TTATGT-A-TTATGTAAG
* *
53664359 TTTTGCATTATGTAAG
1 TTATGTATTATGTAAG
53664375 TTATGTATGCTATGT-A-
1 TTATGTAT--TATGTAAG
* *
53664391 TAATGTA--A-GT-TG
1 TTATGTATTATGTAAG
*
53664403 TTATGTATAATGTAAG
1 TTATGTATTATGTAAG
53664419 TTA---A-TATGTAAG
1 TTATGTATTATGTAAG
*
53664431 TAATGTATTATGTAAG
1 TTATGTATTATGTAAG
* *
53664447 TTTATATAAAAATTTTATATAAG
1 -TTATGT----A--TTATGTAAG
53664470 TTATGTATTATGTAAGG
1 TTATGTATTATGTAA-G
53664487 TAACATATAAGT-TTATGTAAG
1 T----TAT--GTATTATGTAAG
53664508 TTATG-A--ATGTAAG
1 TTATGTATTATGTAAG
53664521 TTATGTATTATGTAAG
1 TTATGTATTATGTAAG
* *
53664537 TTATTTAAATTATTTAAG
1 TTATGT--ATTATGTAAG
*
53664555 TTGTGTATTAT
1 TTATGTATTAT
53664566 ATAACTCATG
Statistics
Matches: 247, Mismatches: 41, Indels: 84
0.66 0.11 0.23
Matches are distributed among these distances:
11 2 0.01
12 16 0.06
13 13 0.05
14 2 0.01
15 4 0.02
16 88 0.36
17 15 0.06
18 67 0.27
19 11 0.04
21 6 0.02
22 13 0.05
23 10 0.04
ACGTcount: A:0.34, C:0.02, G:0.18, T:0.46
Consensus pattern (16 bp):
TTATGTATTATGTAAG
Found at i:53664297 original size:19 final size:19
Alignment explanation
Indices: 53664273--53664310 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
53664263 TAATGTATGC
53664273 TATGTAAGT-TGTAAGTTAT
1 TATGT-AGTATGTAAGTTAT
*
53664292 TATGTATTATGTAAGTTAT
1 TATGTAGTATGTAAGTTAT
53664311 GTATTATGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 2 0.12
19 15 0.88
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (19 bp):
TATGTAGTATGTAAGTTAT
Found at i:53664332 original size:25 final size:24
Alignment explanation
Indices: 53664292--53664397 Score: 88
Period size: 25 Copynumber: 4.2 Consensus size: 24
53664282 TGTAAGTTAT
53664292 TATGTA-TTATGTAAGTTATGTAT
1 TATGTAGTTATGTAAGTTATGTAT
* *
53664315 TATGTAGGTTATGTAAGTTGTGTAAGA
1 TATGTA-GTTATGTAAGTTATGT-A-T
* * *
53664342 TATTTAAGTTATGTAAGTTTTGCAT
1 TATGT-AGTTATGTAAGTTATGTAT
* *
53664367 TATGTAAGTTATGTATGCTATGTAT
1 TATGT-AGTTATGTAAGTTATGTAT
*
53664392 AATGTA
1 TATGTA
53664398 AGTTGTTATG
Statistics
Matches: 66, Mismatches: 12, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
23 6 0.09
24 1 0.02
25 38 0.58
26 2 0.03
27 18 0.27
28 1 0.02
ACGTcount: A:0.30, C:0.02, G:0.21, T:0.47
Consensus pattern (24 bp):
TATGTAGTTATGTAAGTTATGTAT
Found at i:53664426 original size:19 final size:19
Alignment explanation
Indices: 53664385--53664428 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
53664375 TTATGTATGC
**
53664385 TATGTATAATGTAAGTTGT
1 TATGTATAATGTAAGTTAA
53664404 TATGTATAATGTAAGTTAA
1 TATGTATAATGTAAGTTAA
53664423 TATGTA
1 TATGTA
53664429 AGTAATGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.45
Consensus pattern (19 bp):
TATGTATAATGTAAGTTAA
Found at i:53664519 original size:13 final size:15
Alignment explanation
Indices: 53664500--53664540 Score: 59
Period size: 13 Copynumber: 2.8 Consensus size: 15
53664490 CATATAAGTT
53664500 TATGTAAGTTATG-A
1 TATGTAAGTTATGTA
53664514 -ATGTAAGTTATGTA
1 TATGTAAGTTATGTA
53664528 TTATGTAAGTTAT
1 -TATGTAAGTTAT
53664541 TTAAATTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 12 0.50
14 1 0.04
16 11 0.46
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.46
Consensus pattern (15 bp):
TATGTAAGTTATGTA
Found at i:53666077 original size:19 final size:19
Alignment explanation
Indices: 53666053--53666094 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
53666043 AAATTGAATT
*
53666053 TTCTGTTTTCATTTGTATC
1 TTCTGTTTTCATTTGCATC
53666072 TTCTGTTTTCATTTGCATC
1 TTCTGTTTTCATTTGCATC
53666091 TTCT
1 TTCT
53666095 AATTTCTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.10, C:0.19, G:0.10, T:0.62
Consensus pattern (19 bp):
TTCTGTTTTCATTTGCATC
Found at i:53666100 original size:19 final size:19
Alignment explanation
Indices: 53666059--53666100 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
53666049 AATTTTCTGT
* **
53666059 TTTCATTTGTATCTTCTGT
1 TTTCATTTGCATCTTCTAA
53666078 TTTCATTTGCATCTTCTAA
1 TTTCATTTGCATCTTCTAA
53666097 TTTC
1 TTTC
53666101 TAATTTCATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.14, C:0.19, G:0.07, T:0.60
Consensus pattern (19 bp):
TTTCATTTGCATCTTCTAA
Found at i:53667917 original size:7 final size:7
Alignment explanation
Indices: 53667905--53667949 Score: 63
Period size: 7 Copynumber: 6.1 Consensus size: 7
53667895 CTTAATTGAC
53667905 ACCCTAA
1 ACCCTAA
53667912 ACCCTAA
1 ACCCTAA
53667919 ATCCCTAA
1 A-CCCTAA
53667927 ACCCTAA
1 ACCCTAA
53667934 ATCCCTAA
1 A-CCCTAA
*
53667942 CCCCTAA
1 ACCCTAA
53667949 A
1 A
53667950 TCTCATAACC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
7 21 0.62
8 13 0.38
ACGTcount: A:0.40, C:0.42, G:0.00, T:0.18
Consensus pattern (7 bp):
ACCCTAA
Found at i:53667926 original size:15 final size:15
Alignment explanation
Indices: 53667906--53668036 Score: 101
Period size: 15 Copynumber: 8.9 Consensus size: 15
53667896 TTAATTGACA
53667906 CCCTAAACCCTAAAT
1 CCCTAAACCCTAAAT
53667921 CCCTAAACCCTAAAT
1 CCCTAAACCCTAAAT
*
53667936 CCCTAACCCCTAAAT
1 CCCTAAACCCTAAAT
* *
53667951 CTCATAACCCCTAAAT
1 C-CCTAAACCCTAAAT
* * *
53667967 TCCT-AACCTTTAA-
1 CCCTAAACCCTAAAT
*
53667980 CTCCTAACCCCTAAAT
1 C-CCTAAACCCTAAAT
* *
53667996 TCCTAACCCCT-AA-
1 CCCTAAACCCTAAAT
* *
53668009 CCCTTAAACCTTATAT
1 CCC-TAAACCCTAAAT
53668025 CCC-AAACCCTAA
1 CCCTAAACCCTAA
53668037 TAATCATATA
Statistics
Matches: 91, Mismatches: 18, Indels: 15
0.73 0.15 0.12
Matches are distributed among these distances:
13 2 0.02
14 24 0.26
15 49 0.54
16 16 0.18
ACGTcount: A:0.35, C:0.40, G:0.00, T:0.24
Consensus pattern (15 bp):
CCCTAAACCCTAAAT
Found at i:53667997 original size:29 final size:30
Alignment explanation
Indices: 53667911--53668004 Score: 120
Period size: 29 Copynumber: 3.2 Consensus size: 30
53667901 TGACACCCTA
* *
53667911 AACCCTAAATC-CCTAAACCCTAAATCCCT
1 AACCCTAAATCTCCTAACCCCTAAATTCCT
*
53667940 AACCCCTAAATCTCATAACCCCTAAATTCCT
1 AA-CCCTAAATCTCCTAACCCCTAAATTCCT
* *
53667971 AACCTTTAA-CTCCTAACCCCTAAATTCCT
1 AACCCTAAATCTCCTAACCCCTAAATTCCT
53668000 AACCC
1 AACCC
53668005 CTAACCCTTA
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
29 25 0.45
30 14 0.25
31 17 0.30
ACGTcount: A:0.35, C:0.40, G:0.00, T:0.24
Consensus pattern (30 bp):
AACCCTAAATCTCCTAACCCCTAAATTCCT
Found at i:53668834 original size:40 final size:39
Alignment explanation
Indices: 53668790--53668984 Score: 149
Period size: 41 Copynumber: 4.8 Consensus size: 39
53668780 ATGTTTTTTT
53668790 GCGGCGCTTCAACAAAAACGCCGCTAAAACCTTAACATTA
1 GCGGCGCTTCAA-AAAAACGCCGCTAAAACCTTAACATTA
* * *
53668830 GCGGCGTTTATCATAAAAAACGCCGCTAAAAATCTTAACTTTA
1 GCGGCG-CT-TCA-AAAAAACGCCGCT-AAAACCTTAACATTA
* * * * * *
53668873 GCGTCGCTTACATAAAAACGCCGGCTAAGACC-AAATATTC
1 GCGGCGCTT-CAAAAAAACGCC-GCTAAAACCTTAACATTA
* * *
53668913 GCGGCGCTTCAAAGAAATCGCCACTAAATACCTTAACTTTA
1 GCGGCGCTTCAAA-AAAACGCCGCTAAA-ACCTTAACATTA
* * * *
53668954 GCGGCGGTTGATTAAAAACGCCACTAAAACC
1 GCGGCGCTTCA-AAAAAACGCCGCTAAAACC
53668985 CCCGACCATT
Statistics
Matches: 120, Mismatches: 25, Indels: 20
0.73 0.15 0.12
Matches are distributed among these distances:
39 7 0.06
40 31 0.26
41 41 0.34
42 22 0.18
43 19 0.16
ACGTcount: A:0.36, C:0.26, G:0.16, T:0.22
Consensus pattern (39 bp):
GCGGCGCTTCAAAAAAACGCCGCTAAAACCTTAACATTA
Found at i:53672580 original size:18 final size:18
Alignment explanation
Indices: 53672523--53672581 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
53672513 AAGGTAAAGG
*
53672523 TTTCTAACTCTCTTTTGC
1 TTTCTAACTCTCTTTTTC
* * * *
53672541 TCTCAAACTC-CTTTAATG
1 TTTCTAACTCTCTTT-TTC
53672559 TTTCTAACTCTCTTTTTC
1 TTTCTAACTCTCTTTTTC
53672577 TTTCT
1 TTTCT
53672582 GTAATGAGTT
Statistics
Matches: 30, Mismatches: 9, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
17 4 0.13
18 22 0.73
19 4 0.13
ACGTcount: A:0.15, C:0.27, G:0.03, T:0.54
Consensus pattern (18 bp):
TTTCTAACTCTCTTTTTC
Found at i:53673182 original size:117 final size:119
Alignment explanation
Indices: 53672965--53673188 Score: 271
Period size: 118 Copynumber: 1.9 Consensus size: 119
53672955 GAAACAATTT
*
53672965 TTGGATTAGGCTTAAGAATTGATAACTGTTGTTTGTTGATAAGGTGCCTTGGCTTATATAGATGG
1 TTGGATTAGGCTTAAGAAATGATAACTGTTGTTTGTTGATAAGGTGCCTTGGCTTATATAGATGG
** * *
53673030 ATTTATATATCCAGTTGTAGAGTAATTAAGTGG-AAATTATGTGTTTTGTGTTG
66 ATGGAGATATCCAATTGTAGAGTAATTAAGTGGAAAATTATGTGTTTTGTGTTG
*
53673083 TTGG-TTAGGCTTAAGAAATGATAACTGTTGTTTGTTGAT-AGTGTTG-CTT-GCTTTAATATGG
1 TTGGATTAGGCTTAAGAAATGATAACTGTTGTTTGTTGATAAG-G-TGCCTTGGC-TT-ATATAG
* * ** *
53673144 ATGGATGGGGCTATTGAATTGTAGTGTAATTAAG-GGAAAATTATG
62 ATGGATGGAGATATCCAATTGTAGAGTAATTAAGTGGAAAATTATG
53673189 CATGTATGTC
Statistics
Matches: 90, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
116 4 0.04
117 42 0.47
118 44 0.49
ACGTcount: A:0.27, C:0.05, G:0.27, T:0.41
Consensus pattern (119 bp):
TTGGATTAGGCTTAAGAAATGATAACTGTTGTTTGTTGATAAGGTGCCTTGGCTTATATAGATGG
ATGGAGATATCCAATTGTAGAGTAATTAAGTGGAAAATTATGTGTTTTGTGTTG
Found at i:53674387 original size:37 final size:37
Alignment explanation
Indices: 53674344--53674432 Score: 160
Period size: 37 Copynumber: 2.4 Consensus size: 37
53674334 ATCATAAATA
*
53674344 AATAAACTAATCAATGTTCAAACTTTGAACATGCTTT
1 AATAAACTAATCAATGTTAAAACTTTGAACATGCTTT
*
53674381 AGTAAACTAATCAATGTTAAAACTTTGAACATGCTTT
1 AATAAACTAATCAATGTTAAAACTTTGAACATGCTTT
53674418 AATAAACTAATCAAT
1 AATAAACTAATCAAT
53674433 ATATTTATAC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 49 1.00
ACGTcount: A:0.44, C:0.15, G:0.08, T:0.34
Consensus pattern (37 bp):
AATAAACTAATCAATGTTAAAACTTTGAACATGCTTT
Found at i:53677809 original size:91 final size:91
Alignment explanation
Indices: 53677662--53677869 Score: 335
Period size: 91 Copynumber: 2.3 Consensus size: 91
53677652 TTGATTTTAG
* *
53677662 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTAT
* * *
53677727 ATTTAACATTAATTATTTTAAATTGTA
65 ATGTAACAATAATTATTTTAAATTATA
*
53677754 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
*
53677819 TGTAATAATAATTATTTTAAATTATA
66 TGTAACAATAATTATTTTAAATTATA
*
53677845 CAAATTCATATAAGAAAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
53677870 GTTATAATTA
Statistics
Matches: 108, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
91 92 0.85
92 16 0.15
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
TGTAACAATAATTATTTTAAATTATA
Found at i:53677838 original size:26 final size:28
Alignment explanation
Indices: 53677784--53677844 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
53677774 TATTATCAAG
* *
53677784 AATTTTATGAAATTATATATTATTATTA
1 AATTATATGAAATAATATATTATTATTA
*
53677812 AATTATATGTAATAATA-ATTATT-TTA
1 AATTATATGAAATAATATATTATTATTA
53677838 AATTATA
1 AATTATA
53677845 CAAATTCATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (28 bp):
AATTATATGAAATAATATATTATTATTA
Found at i:53677844 original size:44 final size:43
Alignment explanation
Indices: 53677702--53677844 Score: 112
Period size: 44 Copynumber: 3.2 Consensus size: 43
53677692 GAATTTTATG
* * *
53677702 AAATTATATATCATTATTAAATTATATTTAACATTAATTATTTT
1 AAATTATATATTATTATTAAATTATA-TTAATAATAATTATTTT
* ** * *
53677746 AAATTGTATAAATTCATATAAGAAAATT-TATT-ATCAAGAATT-TTATG
1 AAA-T-TATATATT-AT-T-ATTAAATTATATTAAT-AATAATTATT-TT
53677793 AAATTATATATTATTATTAAATTATATGTAATAATAATTATTTT
1 AAATTATATATTATTATTAAATTATAT-TAATAATAATTATTTT
53677837 AAATTATA
1 AAATTATA
53677845 CAAATTCATA
Statistics
Matches: 75, Mismatches: 13, Indels: 22
0.68 0.12 0.20
Matches are distributed among these distances:
42 6 0.08
43 4 0.05
44 21 0.28
45 12 0.16
46 10 0.13
47 13 0.17
48 3 0.04
49 6 0.08
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (43 bp):
AAATTATATATTATTATTAAATTATATTAATAATAATTATTTT
Found at i:53678013 original size:120 final size:120
Alignment explanation
Indices: 53677885--53678302 Score: 714
Period size: 120 Copynumber: 3.5 Consensus size: 120
53677875 AATTATTTTA
* *
53677885 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTATCTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT-AAATTATCTTT
*
53677949 TATAGTATCTTATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
65 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
53678005 AATTTTATTAAATTATATATTTTAATTAAAATATATTTGATAATAATTATGTTAAATTATCTTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATCTTTT
53678070 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* * *
53678125 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTAT-ATTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATCTTTT
*
53678189 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
53678244 AATTTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAAT
1 AA-TTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATG-TTAAAT
53678303 ATGATTAAAC
Statistics
Matches: 285, Mismatches: 10, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
119 59 0.21
120 219 0.77
121 7 0.02
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATCTTTT
ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:53678034 original size:18 final size:17
Alignment explanation
Indices: 53678006--53678040 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
53677996 ATTATTAAGA
*
53678006 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
53678023 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
53678041 TTGATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:53678165 original size:15 final size:15
Alignment explanation
Indices: 53678130--53678181 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
53678120 TTAAGAATTT
*
53678130 TATTAAATTAT-ATA
1 TATTTAATTATAATA
53678144 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
53678158 TATTTAATAATAAT-
1 TATTTAATTATAATA
53678172 TATGTTAATT
1 TAT-TTAATT
53678182 TATATTTATA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:53678280 original size:16 final size:16
Alignment explanation
Indices: 53678259--53678300 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
53678249 TTATTAAATT
*
53678259 ATATATTTTAATTATA
1 ATATATTTTAATAATA
53678275 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
53678290 AT-TATGTTTAA
1 ATATAT-TTTAA
53678301 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:53678285 original size:15 final size:15
Alignment explanation
Indices: 53678250--53678291 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
53678240 TAAGAATTTT
*
53678250 TATTAAATTAT-ATA
1 TATTTAATTATAATA
53678264 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
53678278 TATTTAATAATAAT
1 TATTTAATTATAAT
53678292 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:53678483 original size:5 final size:5
Alignment explanation
Indices: 53678473--53678498 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
53678463 TGAGCATTCG
53678473 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
53678499 AATTTTTGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:53678570 original size:5 final size:5
Alignment explanation
Indices: 53678562--53678613 Score: 52
Period size: 5 Copynumber: 10.2 Consensus size: 5
53678552 TGAAGTTTTC
* * *
53678562 TCGAA TCGAG TCGAG T-GAGA TGGAA TTCGAA TCGAA TCGAA TCGAA TCGAA
1 TCGAA TCGAA TCGAA TCGA-A TCGAA T-CGAA TCGAA TCGAA TCGAA TCGAA
53678613 T
1 T
53678614 ATATTTGTTC
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
4 2 0.05
5 33 0.80
6 6 0.15
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.23
Consensus pattern (5 bp):
TCGAA
Found at i:53678613 original size:26 final size:26
Alignment explanation
Indices: 53678562--53678613 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
53678552 TGAAGTTTTC
* * *
53678562 TCGAATCGAGTCGAGTGAGATGGAAT
1 TCGAATCGAATCGAATGAGATCGAAT
53678588 TCGAATCGAATCGAATCGA-ATCGAAT
1 TCGAATCGAATCGAAT-GAGATCGAAT
53678614 ATATTTGTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 20 0.91
27 2 0.09
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.23
Consensus pattern (26 bp):
TCGAATCGAATCGAATGAGATCGAAT
Found at i:53679169 original size:17 final size:17
Alignment explanation
Indices: 53679119--53679176 Score: 64
Period size: 16 Copynumber: 3.2 Consensus size: 17
53679109 GGGTGAGAAG
53679119 TAAAAGTTTAGGGGAAAAA
1 TAAAAGTTTA-GGG-AAAA
*
53679138 TAAAAAGTTTTGGG-AAA
1 T-AAAAGTTTAGGGAAAA
53679155 TAAAAGTTTGAGGGAAAA
1 TAAAAGTTT-AGGGAAAA
53679173 TAAA
1 TAAA
53679177 TAGGGGGGAG
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
16 8 0.24
17 7 0.21
18 7 0.21
19 4 0.12
20 8 0.24
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (17 bp):
TAAAAGTTTAGGGAAAA
Found at i:53679548 original size:9 final size:9
Alignment explanation
Indices: 53679534--53679570 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
53679524 TATAGTTTGA
53679534 TATTCGAAT
1 TATTCGAAT
53679543 TATTCGAAT
1 TATTCGAAT
*
53679552 TATTCGAGT
1 TATTCGAAT
53679561 TATTCGAAT
1 TATTCGAAT
53679570 T
1 T
53679571 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:53679644 original size:9 final size:9
Alignment explanation
Indices: 53679623--53679673 Score: 66
Period size: 9 Copynumber: 5.7 Consensus size: 9
53679613 TCGAGTTTAT
*
53679623 TCGAATAAC
1 TCGATTAAC
*
53679632 TCGATTAAA
1 TCGATTAAC
*
53679641 TCGAATAAC
1 TCGATTAAC
53679650 TCGATTAAC
1 TCGATTAAC
*
53679659 TCGAATAAC
1 TCGATTAAC
53679668 TCGATT
1 TCGATT
53679674 CGTTTAACTC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 35 1.00
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.29
Consensus pattern (9 bp):
TCGATTAAC
Found at i:53679646 original size:18 final size:18
Alignment explanation
Indices: 53679623--53679673 Score: 93
Period size: 18 Copynumber: 2.8 Consensus size: 18
53679613 TCGAGTTTAT
53679623 TCGAATAACTCGATTAAA
1 TCGAATAACTCGATTAAA
*
53679641 TCGAATAACTCGATTAAC
1 TCGAATAACTCGATTAAA
53679659 TCGAATAACTCGATT
1 TCGAATAACTCGATT
53679674 CGTTTAACTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.29
Consensus pattern (18 bp):
TCGAATAACTCGATTAAA
Found at i:53679830 original size:16 final size:16
Alignment explanation
Indices: 53679805--53679842 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
53679795 TTGATTTGCT
53679805 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
*
53679821 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
*
53679837 AATACA
1 ATTACA
53679843 GCGAACCAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.29, C:0.34, G:0.03, T:0.34
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:53680974 original size:13 final size:14
Alignment explanation
Indices: 53680944--53680979 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
53680934 AATCTCAAAC
53680944 CCTAAAC-TG-ATA
1 CCTAAACTTGAATA
53680956 CCTAAACTTGAAT-
1 CCTAAACTTGAATA
53680969 CCTAAACTTGA
1 CCTAAACTTGA
53680980 GATTTGGGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.32
13 13 0.59
14 2 0.09
ACGTcount: A:0.39, C:0.25, G:0.08, T:0.28
Consensus pattern (14 bp):
CCTAAACTTGAATA
Found at i:53683021 original size:24 final size:23
Alignment explanation
Indices: 53682993--53683039 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 23
53682983 CTCTTCTGGG
53682993 TTTGCTTTTGTCTTCTATCTTGTT
1 TTTGCTTTTGTCTTCT-TCTTGTT
*
53683017 TTTGCTTTTTTCTTCTTCTTGTT
1 TTTGCTTTTGTCTTCTTCTTGTT
53683040 ATGTTATCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.02, C:0.17, G:0.11, T:0.70
Consensus pattern (23 bp):
TTTGCTTTTGTCTTCTTCTTGTT
Found at i:53692123 original size:24 final size:24
Alignment explanation
Indices: 53692096--53692152 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
53692086 CCTGTCTAGG
53692096 TTATTTATTTTTATGTATTAATTT
1 TTATTTATTTTTATGTATTAATTT
* *
53692120 TTATTTCA-TTTTATTTATTTATTT
1 TTATTT-ATTTTTATGTATTAATTT
*
53692144 AT-TTTATTT
1 TTATTTATTT
53692153 ACTCATTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 1 0.04
23 5 0.18
24 21 0.75
25 1 0.04
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.74
Consensus pattern (24 bp):
TTATTTATTTTTATGTATTAATTT
Found at i:53692149 original size:9 final size:9
Alignment explanation
Indices: 53692118--53692153 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
53692108 ATGTATTAAT
53692118 TTTTATTTCA
1 TTTTATTT-A
53692128 TTTTATTTA
1 TTTTATTTA
53692137 -TTTATTTA
1 TTTTATTTA
53692145 TTTTATTTA
1 TTTTATTTA
53692154 CTCATTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 8 0.32
9 9 0.36
10 8 0.32
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (9 bp):
TTTTATTTA
Found at i:53694965 original size:28 final size:28
Alignment explanation
Indices: 53694933--53694988 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
53694923 CAGTGCGAGT
53694933 TTGTATACAAGGGAGATAATTACAAAAA
1 TTGTATACAAGGGAGATAATTACAAAAA
53694961 TTGTATACAAGGGAGATAATTACAAAAA
1 TTGTATACAAGGGAGATAATTACAAAAA
53694989 GAAAGTTTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.50, C:0.07, G:0.18, T:0.25
Consensus pattern (28 bp):
TTGTATACAAGGGAGATAATTACAAAAA
Found at i:53706289 original size:30 final size:30
Alignment explanation
Indices: 53706250--53706310 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
53706240 GACCATATGA
53706250 TTGCAAAATCCCAAATAGAAAAGGAGCATG
1 TTGCAAAATCCCAAATAGAAAAGGAGCATG
* *
53706280 TTGCCAAATCCCGAATAGAAAAGGAGCATG
1 TTGCAAAATCCCAAATAGAAAAGGAGCATG
53706310 T
1 T
53706311 ACAAGTTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.43, C:0.18, G:0.21, T:0.18
Consensus pattern (30 bp):
TTGCAAAATCCCAAATAGAAAAGGAGCATG
Found at i:53709816 original size:44 final size:44
Alignment explanation
Indices: 53709728--53710533 Score: 529
Period size: 44 Copynumber: 17.6 Consensus size: 44
53709718 CATTATGGCG
* * * * *
53709728 AATCTTATCTTCCTGAAGTTGCAGTAGAGCAGGTTGAAGTTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATACA
* * *
53709772 AGTCTTATCTCCCTAAAGTTGCAGTGGAACAGATTAAAGCTACAAATTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG------A-TACA
** * * * * * * *
53709823 AATCTTATCTTTCTGAAGTTGTAATGGGGTAGATTGAAGTTATA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATACA
* * * ** * *
53709867 GATCTTATCTCCCTGAAATTACAGTGGATTAGATCAGAGATAGCA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATA-CA
* * * *
53709912 AATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAGCTATA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATACA
* * * * * * *
53709956 AACCTTATCTCCTTGAAGTTGTAGTGAAGTAGGTTAAAAATAAACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGAT--ACA
* * * *
53710002 AATCTTATCTCCCTGAAATTGTAGTGGAGTAGATTGAAGACAAGCTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT----A-AAGATACA
** * **
53710051 AATCTTATCTCTTTGAAGTTGCAGTGGAGCATATTAAAGCCACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATACA
** *
53710095 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCATA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATACA
* * * * **
53710139 AATTTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAATATAGTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATA-CA
* * * * * * *
53710184 AATCTTATCTCTCTGAAATTGTAGTAGAGTAGATTGAAGCA-ATA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-ATACA
* * *
53710228 AATTTTATCTCCCTGAAGTTGCAGTGAAGCAGATTGAAGATA-A
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATACA
* *
53710271 TGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACC
1 --AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATACA
* * * *
53710317 AATCTTATTTCTCTGAAGTTGCAGTGGAACATATTAAAGCTACAAGTTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-----A--TACA
* * *
53710368 AA-CATTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAATATACG
1 AATC-TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATACA
* * * * * *
53710412 AATTTTATTTCCCTGAAGTTGTAGTGAAACAGATTAAGGTACAAGTTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-T----TA-AAGATACA
* * * * * *
53710462 AATCTTATCTCCCTAAAGTTACAATGGAGCAGATTGAAGATGCG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATACA
*
53710506 AATCTTATTTCCCTGAAGTTGCAGTGGA
1 AATCTTATCTCCCTGAAGTTGCAGTGGA
53710534 ACGGATCTTA
Statistics
Matches: 588, Mismatches: 138, Indels: 72
0.74 0.17 0.09
Matches are distributed among these distances:
43 2 0.00
44 305 0.52
45 109 0.19
46 34 0.06
49 36 0.06
50 32 0.05
51 70 0.12
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATACA
Found at i:53709963 original size:89 final size:88
Alignment explanation
Indices: 53709820--53710533 Score: 414
Period size: 89 Copynumber: 7.9 Consensus size: 88
53709810 GCTACAAATT
** * * * * * * * * *
53709820 ACAAATCTTATCTTTCTGAAGTTGTAATGGGGTAGATTGAAGTTATAGATCTTATCTCCCTGAAA
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTATAAATCTTATCTCCTTGAAG
* **
53709885 TTACAGTGGATTAGATCAGAGATA
66 TTGCAGTGGAGCAGAT-AGAGATA
* * * *
53709909 GCAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAGCTATAAACCTTATCTCCTTGAAG
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTATAAATCTTATCTCCTTGAAG
* * * * * *
53709974 TTGTAGTGAAGTAGGTTAAAAATAA
66 TTGCAGTGGAGCA-GATAGAGAT-A
* * * * *
53709999 ACAAATCTTATCTCCCTGAAATTGTAGTGGAGTAGATTGAAGACAAGCTACAAATCTTATCTCTT
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT----A-AAGCTATAAATCTTATCTCCT
* * **
53710064 TGAAGTTGCAGTGGAGCATATTAAAG-CC
61 TGAAGTTGCAGTGGAGCAGA-TAGAGATA
* *
53710092 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCATAAATTTTATCTCCTTGAAG
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTATAAATCTTATCTCCTTGAAG
*
53710157 TTGCAGTGGAGCAGATTGA-ATA
66 TTGCAGTGGAGCAGATAGAGATA
** * * * * * * * * *
53710179 TAGTGAATCTTATCTCTCTGAAATTGTAGTAGAGTAGATTGAAGCAATAAATTTTATCTCCCTGA
1 -A-CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTATAAATCTTATCTCCTTGA
* *
53710244 AGTTGCAGTGAAGCAGATTGAAGATA
64 AGTTGCAGTGGAGCAGATAG-AGATA
** * * ** *
53710270 ATGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACCAATCTTAT-TTCTCTGAA
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTATAAATCTTATCTCCT-TGAA
* * * *
53710334 GTTGCAGTGGAACATATTAAAGCTACAAGTT
65 GTTGCAGTGGAGCAGA-T--AG--A-GA-TA
* * * *
53710365 ACAAA-CATTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAA--TATACGAATTTTATTTCCCTG
1 ACAAATC-TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTATA--AATCTTATCTCCTTG
* * * * *
53710427 AAGTTGTAGTGAAACAGATTAAGGTACAAGTT
63 AAGTTGCAGTGGAGCAGA-T-A-G-A-GA-TA
* * * * * *** * *
53710459 ACAAATCTTATCTCCCTAAAGTTACAATGGAGCAGATTGAAGATGCGAATCTTATTTCCCTGAAG
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTATAAATCTTATCTCCTTGAAG
53710524 TTGCAGTGGA
66 TTGCAGTGGA
53710534 ACGGATCTTA
Statistics
Matches: 495, Mismatches: 102, Indels: 51
0.76 0.16 0.08
Matches are distributed among these distances:
87 2 0.00
88 39 0.08
89 198 0.40
90 38 0.08
91 3 0.01
92 1 0.00
93 38 0.08
94 72 0.15
95 101 0.20
96 3 0.01
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (88 bp):
ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTATAAATCTTATCTCCTTGAAG
TTGCAGTGGAGCAGATAGAGATA
Found at i:53710127 original size:183 final size:177
Alignment explanation
Indices: 53709728--53710307 Score: 525
Period size: 184 Copynumber: 3.2 Consensus size: 177
53709718 CATTATGGCG
* * * * ** * ** * *
53709728 AATCTTATCTTCCTGAAGTTGCAGTAGAGCAGGTTGAAGTTACAAGTCTTATCTCCCTAAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCATAAACCTTATCTCCTTGAAGTTG
* ** * * * *
53709793 CAGTGGAA-CAGATTAAAGCTACAAATTACAAATCTTATCTTTCTGAAGTTGTAATGGGGTAGAT
66 CAGT-GAAGCAGATT--A---A-AAATAACAAATCTTATCTCCCTGAAATTGTAGTAGAGTAGAT
** * * * * ** * * *
53709857 TGAAGTTATAGATCTTATCTCCCTGAAATTACAGTGGATTAGATCAGAGATAGCA
124 TGAAGCAATAAATCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTAAAGACA-CA
* * *
53709912 AATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAGCTATAAACCTTATCTCCTTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCATAAACCTTATCTCCTTGAAGTTG
* * * *
53709977 TAGTGAAGTAGGTTAAAAATAAACAAATCTTATCTCCCTGAAATTGTAGTGGAGTAGATTGAAGA
66 CAGTGAAGCAGATTAAAAAT-AACAAATCTTATCTCCCTGAAATTGTAGTAGAGTAGATTGAAG-
** * * *
53710042 CAAGCTACAAATCTTATCTCTTTGAAGTTGCAGTGGAGCATATTAAAGCCACA
129 CAA--T--AAATCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTAAAGACACA
**
53710095 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCATAAATTTTATCTCCTTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCATAAACCTTATCTCCTTGAAGTTG
* * * *** *
53710160 CAGTGGAGCAGATTGAATATAGTGAATCTTATCTCTCTGAAATTGTAGTAGAGTAGATTGAAGCA
66 CAGTGAAGCAGATTAAAAATAACAAATCTTATCTCCCTGAAATTGTAGTAGAGTAGATTGAAGCA
* * *
53710225 ATAAATTTTATCTCCCTGAAGTTGCAGTGAAGCAGATTGAAGATA-A
131 ATAAATCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTAAAGACACA
53710271 TGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT
1 --AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT
53710308 GAAGATACCA
Statistics
Matches: 330, Mismatches: 57, Indels: 24
0.80 0.14 0.06
Matches are distributed among these distances:
176 1 0.00
177 35 0.11
178 39 0.12
179 39 0.12
180 1 0.00
181 3 0.01
182 40 0.12
183 79 0.24
184 93 0.28
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (177 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCATAAACCTTATCTCCTTGAAGTTG
CAGTGAAGCAGATTAAAAATAACAAATCTTATCTCCCTGAAATTGTAGTAGAGTAGATTGAAGCA
ATAAATCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTAAAGACACA
Found at i:53710150 original size:272 final size:268
Alignment explanation
Indices: 53709728--53710405 Score: 707
Period size: 272 Copynumber: 2.5 Consensus size: 268
53709718 CATTATGGCG
* * * * * * * *
53709728 AATCTTATCTTCCTGAAGTTGCAGTAGAGCAGGTTGAAGTTACAAGTCTTATCTCCCTAAAGTTG
1 AATCTTATCTCCCTGAAATTGCAGTGGAGCAGATTGAAGATACAAATCTTATCTCTCTGAAGTTG
* ** * * *
53709793 CAGTGGAACAGATTAAAGCTACAAATTACAAATCTTATCTTTCTGAAGTTGTAATGGGGTAGATT
66 CAGTGGAACATATTAAAGC-AC--A--ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATT
* ** * **
53709858 GAAGTTATAGATCTTATCTCCCTGAAATTACAGTGGATTAGATCAG-AGATAGCAAATCTTATCT
126 AAAGCCATAAATCTTATCTCCCTGAAATTACAGTGGAGCAGAT-AGAAGATAGCAAATCTTATCT
* * * * *
53709922 CTCTGAAGTTGCAGTAGAGCAGATTAAAGCTATAAACCTTATCTCCTTGAAGTTGTAGTGAAGTA
190 CTCTGAAATTGCAGTAGAGCAGATTAAAGCAATAAACCTTATCTCCCTGAAGTTGCAGTGAAGCA
*
53709987 GGTTAAAAATAAACA
255 GATTAAAAAT-AACA
* * *
53710002 AATCTTATCTCCCTGAAATTGTAGTGGAGTAGATTGAAGACAAGCTACAAATCTTATCTCTTTGA
1 AATCTTATCTCCCTGAAATTGCAGTGGAGCAGATTGAAG---A--TACAAATCTTATCTCTCTGA
* *
53710067 AGTTGCAGTGGAGCATATTAAAGC-C-ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT
61 AGTTGCAGTGGAACATATTAAAGCACAACAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATT
* * * * * * **
53710130 AAAGCCATAAATTTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAATATAGTGAATCTTATCTC
126 AAAGCCATAAATCTTATCTCCCTGAAATTACAGTGGAGCAGATAGAAGATAGCAAATCTTATCTC
* * * **
53710195 TCTGAAATTGTAGTAGAGTAGATTGAAGCAATAAATTTTATCTCCCTGAAGTTGCAGTGAAGCAG
191 TCTGAAATTGCAGTAGAGCAGATTAAAGCAATAAACCTTATCTCCCTGAAGTTGCAGTGAAGCAG
* * **
53710260 ATTGAAGATAATG
256 ATTAAAAATAACA
* * *
53710273 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACCAATCTTATTTCTCTGAAGTTG
1 AATCTTATCTCCCTGAAATTGCAGTGGAGCAGATTGAAGATACAAATCTTATCTCTCTGAAGTTG
53710338 CAGTGGAACATATTAAAGCTACAAGTTACAAA-CATTATCTCCCTGAAGTTGCAGTGGAGTAGAT
66 CAGTGGAACATATTAAAGC-AC-A---ACAAATC-TTATCTCCCTGAAGTTGCAGTGGAGTAGAT
53710402 TAAA
125 TAAA
53710406 TATACGAATT
Statistics
Matches: 334, Mismatches: 56, Indels: 29
0.80 0.13 0.07
Matches are distributed among these distances:
266 40 0.12
268 2 0.01
271 39 0.12
272 143 0.43
273 38 0.11
274 33 0.10
277 1 0.00
279 38 0.11
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.31
Consensus pattern (268 bp):
AATCTTATCTCCCTGAAATTGCAGTGGAGCAGATTGAAGATACAAATCTTATCTCTCTGAAGTTG
CAGTGGAACATATTAAAGCACAACAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGC
CATAAATCTTATCTCCCTGAAATTACAGTGGAGCAGATAGAAGATAGCAAATCTTATCTCTCTGA
AATTGCAGTAGAGCAGATTAAAGCAATAAACCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTAA
AAATAACA
Found at i:53710242 original size:133 final size:133
Alignment explanation
Indices: 53709728--53710446 Score: 535
Period size: 139 Copynumber: 5.3 Consensus size: 133
53709718 CATTATGGCG
* * * * * * * *
53709728 AATCTTATCTTCCTGAAGTTGCAGTAGAGCAGGTTGAAGTTA-CAAGTCTTATCTCCCTAAAGTT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGTAAATCTTATCTCTCTGAAGTT
* * ** * * ** *
53709792 GCAGTGGAACAGATTAAAGCTACAAATTACAAATCTTATCTTTCTGAAGTTGTAATGGGGTAGAT
66 GCAGTAGAGCAGATTAAAG---C-AA-T--AAATCTTATCTCCCTGAAGTTGCAGTGAAGCAGAT
* **
53709857 TGAAGTTATA
124 TAAAGAAATA
* * * ** * *
53709867 GATCTTATCTCCCTGAAATTACAGTGGATTAGA-TCAGAGATAGCAAATCTTATCTCTCTGAAGT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGA-AGATAGTAAATCTTATCTCTCTGAAGT
* * * * * *
53709931 TGCAGTAGAGCAGATTAAAGCTATAAACCTTATCTCCTTGAAGTTGTAGTGAAGTAGGTTAAAAA
65 TGCAGTAGAGCAGATTAAAGCAATAAATCTTATCTCCCTGAAGTTGCAGTGAAGCAGATT--AAA
* *
53709996 TAAACA
128 GAAATA
* * * * *
53710002 AATCTTATCTCCCTGAAATTGTAGTGGAGTAGATTGAAGACAAGCTACAAATCTTATCTCTTTGA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGA-TAG-T--AAATCTTATCTCTCTGA
* * * * *
53710067 AGTTGCAGTGGAGCATATTAAAGCCACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAA
62 AGTTGCAGTAGAGCAGATTAAAGCAATAAATCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTAA
**
53710132 AGCCATA
127 AGAAATA
* * * * *
53710139 AATTTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAATATAGTGAATCTTATCTCTCTGAAATT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGTAAATCTTATCTCTCTGAAGTT
* * * * *
53710204 GTAGTAGAGTAGATTGAAGCAATAAATTTTATCTCCCTGAAGTTGCAGTGAAGCAGATTGAAGAT
66 GCAGTAGAGCAGATTAAAGCAATAAATCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTAAAGA-
*
53710269 AATG
130 AATA
** *
53710273 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA-CCAATCTTATTTCTCTGAAGTT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGTAAATCTTATCTCTCTGAAGTT
* * * * * *
53710337 GCAGTGGAACATATTAAAGCTACAAGTTACAAACATTATCTCCCTGAAGTTGCAGTGGAGTAGAT
66 GCAGTAGAGCAGATTAAAG---CAA--TA-AATC-TTATCTCCCTGAAGTTGCAGTGAAGCAGAT
* * **
53710402 TAAATATACG
124 TAAAGAAATA
* * * * *
53710412 AATTTTATTTCCCTGAAGTTGTAGTGAAACAGATT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT
53710447 AAGGTACAAG
Statistics
Matches: 463, Mismatches: 100, Indels: 34
0.78 0.17 0.06
Matches are distributed among these distances:
133 130 0.28
134 41 0.09
135 38 0.08
136 10 0.02
137 40 0.09
138 4 0.01
139 132 0.29
140 68 0.15
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (133 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGTAAATCTTATCTCTCTGAAGTT
GCAGTAGAGCAGATTAAAGCAATAAATCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTAAAGAA
ATA
Found at i:53710616 original size:44 final size:44
Alignment explanation
Indices: 53710551--53710651 Score: 139
Period size: 44 Copynumber: 2.3 Consensus size: 44
53710541 TTATCTCCTT
* *
53710551 AAAGTTGTAGTGGAGCAGATTGAAGCAACAAACCCTATACCTCT
1 AAAGTTGCAGTGGAGCAGATTGAAGCAACAAACCCTATACCTCA
* ** * *
53710595 GAAGTTGCAGTGGAGTGGATTGAAGCAACAAATCTTATACCTCA
1 AAAGTTGCAGTGGAGCAGATTGAAGCAACAAACCCTATACCTCA
53710639 AAAGTTGCAGTGG
1 AAAGTTGCAGTGG
53710652 GTTAGAATGA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 49 1.00
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.24
Consensus pattern (44 bp):
AAAGTTGCAGTGGAGCAGATTGAAGCAACAAACCCTATACCTCA
Found at i:53712095 original size:9 final size:9
Alignment explanation
Indices: 53712072--53712107 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
53712062 ATGTATTACT
53712072 TTTTATTTCA
1 TTTTATTT-A
53712082 TTTTATTTA
1 TTTTATTTA
53712091 TTTTATTTA
1 TTTTATTTA
53712100 -TTTATTTA
1 TTTTATTTA
53712108 CTAATTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 8 0.31
9 10 0.38
10 8 0.31
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (9 bp):
TTTTATTTA
Found at i:53712109 original size:38 final size:39
Alignment explanation
Indices: 53712050--53712129 Score: 92
Period size: 38 Copynumber: 2.1 Consensus size: 39
53712040 CCTGTCTAGG
* **
53712050 TTATTTATTTTTATGTATTACTTTTTATTT-CATTTTAT
1 TTATTTATATTTATGTATTACTAATTATTTCCATTTTAT
* *
53712088 TTATTT-TATTTATTTATTTACTAATTATTTCCTTTTTAT
1 TTATTTATATTTATGTA-TTACTAATTATTTCCATTTTAT
53712127 TTA
1 TTA
53712130 AAAATGGTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
37 8 0.23
38 17 0.49
39 10 0.29
ACGTcount: A:0.23, C:0.06, G:0.01, T:0.70
Consensus pattern (39 bp):
TTATTTATATTTATGTATTACTAATTATTTCCATTTTAT
Found at i:53724911 original size:36 final size:36
Alignment explanation
Indices: 53724837--53724911 Score: 84
Period size: 36 Copynumber: 2.1 Consensus size: 36
53724827 TTTAATCATT
*
53724837 TTAATATTAAATTAATAAAATACTATTAATTAAGTA
1 TTAATATTAAATTAATAAAATACTATTAAATAAGTA
*
53724873 TTAA-ATTAAATTTAATATTAA-ACTATTAAAATAA-TA
1 TTAATATTAAA-TTAATA-AAATACTATT-AAATAAGTA
53724909 TTA
1 TTA
53724912 TTTTTATAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
35 6 0.18
36 21 0.62
37 7 0.21
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (36 bp):
TTAATATTAAATTAATAAAATACTATTAAATAAGTA
Found at i:53731816 original size:21 final size:20
Alignment explanation
Indices: 53731792--53731830 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
53731782 CAGAAACAAT
*
53731792 TATACAAATTAAATGCTAACA
1 TATAAAAATTAAAT-CTAACA
*
53731813 TATAAAAATTGAATCTAA
1 TATAAAAATTAAATCTAA
53731831 TCATGGCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.54, C:0.10, G:0.05, T:0.31
Consensus pattern (20 bp):
TATAAAAATTAAATCTAACA
Found at i:53734498 original size:15 final size:15
Alignment explanation
Indices: 53734451--53734500 Score: 57
Period size: 15 Copynumber: 3.2 Consensus size: 15
53734441 CAATTCAAAT
*
53734451 AATCAATATATATTC
1 AATCAATATAAATTC
53734466 AAT-ATATATACCAATTC
1 AATCA-ATATA--AATTC
53734483 AATCAATATAAATTC
1 AATCAATATAAATTC
53734498 AAT
1 AAT
53734501 AAATTTATCA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
14 1 0.03
15 16 0.53
17 12 0.40
18 1 0.03
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (15 bp):
AATCAATATAAATTC
Found at i:53735209 original size:14 final size:14
Alignment explanation
Indices: 53735190--53735217 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
53735180 TTCTTTCTCC
53735190 TTTTCTTTCTTTTT
1 TTTTCTTTCTTTTT
53735204 TTTTCTTTCTTTTT
1 TTTTCTTTCTTTTT
53735218 CCCTTCTGTT
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:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTTCTTTCTTTTT
Found at i:53735375 original size:5 final size:5
Alignment explanation
Indices: 53735272--53735355 Score: 168
Period size: 5 Copynumber: 16.8 Consensus size: 5
53735262 TTTGTTTTAT
53735272 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
53735322 TATAA TATAA TATAA TATAA TATAA TATAA TATA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATA
53735356 TATTAACTTA
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 79 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TATAA
Found at i:53735375 original size:20 final size:20
Alignment explanation
Indices: 53735284--53735386 Score: 101
Period size: 20 Copynumber: 5.2 Consensus size: 20
53735274 TAATATAATA
53735284 TAATATAATATA-ATATAA-T
1 TAATATAATATATAT-TAACT
53735303 ATAATATAATATA-ATATAA-T
1 -TAATATAATATATAT-TAACT
53735323 ATAATATAATATA-ATATAA-T
1 -TAATATAATATATAT-TAACT
53735343 ATAATATAATATATATTAACT
1 -TAATATAATATATATTAACT
*
53735364 TAATATAGTATATATTAACT
1 TAATATAATATATATTAACT
53735384 TAA
1 TAA
53735387 AGTTTTATGA
Statistics
Matches: 80, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
20 77 0.96
21 3 0.04
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (20 bp):
TAATATAATATATATTAACT
Found at i:53741582 original size:25 final size:25
Alignment explanation
Indices: 53741554--53741603 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
53741544 ACCAAGCATG
53741554 CTATAATACCCTCTAATTTGTTATT
1 CTATAATACCCTCTAATTTGTTATT
*
53741579 CTATAATGCCCTCTAATTTGTTATT
1 CTATAATACCCTCTAATTTGTTATT
53741604 GAATACTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.26, C:0.20, G:0.06, T:0.48
Consensus pattern (25 bp):
CTATAATACCCTCTAATTTGTTATT
Found at i:53742438 original size:18 final size:19
Alignment explanation
Indices: 53742396--53742440 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
53742386 TCAAGATCTT
*
53742396 AAATTAATGTGGTCTAAAG
1 AAATTAATGTGGTCCAAAG
53742415 AAATTAATGTGGTCCAAA-
1 AAATTAATGTGGTCCAAAG
53742433 AAATTAAT
1 AAATTAAT
53742441 TAGTACATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 8 0.32
19 17 0.68
ACGTcount: A:0.47, C:0.07, G:0.16, T:0.31
Consensus pattern (19 bp):
AAATTAATGTGGTCCAAAG
Found at i:53745866 original size:11 final size:11
Alignment explanation
Indices: 53745850--53745901 Score: 61
Period size: 11 Copynumber: 4.7 Consensus size: 11
53745840 TTATATCTTT
53745850 AATAATAATAC
1 AATAATAATAC
53745861 AATAATAATAC
1 AATAATAATAC
* **
53745872 TTATAAT-ATTT
1 -AATAATAATAC
53745883 AATAATAATAC
1 AATAATAATAC
53745894 AATAATAA
1 AATAATAA
53745902 AAAATGTTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
10 5 0.15
11 23 0.70
12 5 0.15
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.35
Consensus pattern (11 bp):
AATAATAATAC
Found at i:53745889 original size:33 final size:32
Alignment explanation
Indices: 53745829--53745901 Score: 128
Period size: 33 Copynumber: 2.2 Consensus size: 32
53745819 TATGTTGAAT
*
53745829 AATAATAATACTTATATCTTTAATAATAATAC
1 AATAATAATACTTATATATTTAATAATAATAC
53745861 AATAATAATACTTATAATATTTAATAATAATAC
1 AATAATAATACTTAT-ATATTTAATAATAATAC
53745894 AATAATAA
1 AATAATAA
53745902 AAAATGTTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
32 15 0.38
33 24 0.62
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (32 bp):
AATAATAATACTTATATATTTAATAATAATAC
Found at i:53747492 original size:18 final size:18
Alignment explanation
Indices: 53747438--53747495 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
53747428 CCTAAAGCTC
*
53747438 TCATGCATTCTTCTCCCT
1 TCATCCATTCTTCTCCCT
* *** *
53747456 TCATCCAGTAAGCTTCCT
1 TCATCCATTCTTCTCCCT
53747474 TCATCCATTCTTCTCCCT
1 TCATCCATTCTTCTCCCT
53747492 TCAT
1 TCAT
53747496 TCCTTCAAAT
Statistics
Matches: 29, Mismatches: 11, Indels: 0
0.73 0.28 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.16, C:0.38, G:0.05, T:0.41
Consensus pattern (18 bp):
TCATCCATTCTTCTCCCT
Found at i:53748218 original size:12 final size:12
Alignment explanation
Indices: 53748201--53748226 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
53748191 CGTTTGTGTA
53748201 TTCGATATAATG
1 TTCGATATAATG
53748213 TTCGATATAATG
1 TTCGATATAATG
53748225 TT
1 TT
53748227 TTCTGGAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (12 bp):
TTCGATATAATG
Found at i:53749624 original size:13 final size:13
Alignment explanation
Indices: 53749606--53749633 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
53749596 CTTGTACAAG
53749606 TAAACTTCATAAA
1 TAAACTTCATAAA
53749619 TAAACTTCATAAA
1 TAAACTTCATAAA
53749632 TA
1 TA
53749634 GAGAAAGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (13 bp):
TAAACTTCATAAA
Found at i:53750092 original size:20 final size:20
Alignment explanation
Indices: 53750067--53750106 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
53750057 AATATTTTTC
*
53750067 AGTAAATCATTTTACAGAAA
1 AGTAAAGCATTTTACAGAAA
*
53750087 AGTAAAGCATTTTCCAGAAA
1 AGTAAAGCATTTTACAGAAA
53750107 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.28
Consensus pattern (20 bp):
AGTAAAGCATTTTACAGAAA
Found at i:53751888 original size:11 final size:11
Alignment explanation
Indices: 53751872--53751897 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
53751862 TATATATGTA
53751872 AATATAATAAT
1 AATATAATAAT
53751883 AATATAATAAT
1 AATATAATAAT
53751894 AATA
1 AATA
53751898 ACAAATAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
AATATAATAAT
Found at i:53754910 original size:55 final size:57
Alignment explanation
Indices: 53754806--53754912 Score: 130
Period size: 55 Copynumber: 1.9 Consensus size: 57
53754796 AATCTATTAT
* * * * * *
53754806 TATTTTTATTATTTATTTTTAACATAAATATGATTTTATTTATTATTTAATATTCAA
1 TATTTTTAATATATATTATTAACATAAATATGAATATATTAATTATTTAATATTCAA
53754863 TATTTTTAATATATATTATT-A-ATAAATATGAATATATATAATT-TTTAATA
1 TATTTTTAATATATATTATTAACATAAATATGAATATAT-TAATTATTTAATA
53754913 ATTTATTATT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
55 21 0.49
56 5 0.12
57 17 0.40
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (57 bp):
TATTTTTAATATATATTATTAACATAAATATGAATATATTAATTATTTAATATTCAA
Found at i:53755216 original size:40 final size:40
Alignment explanation
Indices: 53755163--53755238 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
53755153 GACGAACCAG
* *
53755163 CAAATCGCGTCCACATCAGAGC-ACTTTGCTGACGTGACAA
1 CAAATCACGTCCACATAAGAGCGA-TTTGCTGACGTGACAA
* *
53755203 CAAATCACGTCCACGTAAGCGCGATTTGCTGACGTG
1 CAAATCACGTCCACATAAGAGCGATTTGCTGACGTG
53755239 TAGCGCGCTC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 30 0.97
41 1 0.03
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (40 bp):
CAAATCACGTCCACATAAGAGCGATTTGCTGACGTGACAA
Found at i:53755434 original size:11 final size:12
Alignment explanation
Indices: 53755371--53755435 Score: 77
Period size: 11 Copynumber: 5.8 Consensus size: 12
53755361 AACTAATCCT
53755371 CTCTCAAATTTC
1 CTCTCAAATTTC
53755383 CTCTC-AATTTC
1 CTCTCAAATTTC
*
53755394 CTCTC-AATTTG
1 CTCTCAAATTTC
53755405 CTCTCAAA-TTC
1 CTCTCAAATTTC
53755416 CT-TCCAAATTT-
1 CTCT-CAAATTTC
53755427 CTCTCAAAT
1 CTCTCAAAT
53755436 CCATATTTAA
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
10 1 0.02
11 36 0.77
12 10 0.21
ACGTcount: A:0.25, C:0.32, G:0.02, T:0.42
Consensus pattern (12 bp):
CTCTCAAATTTC
Found at i:53755505 original size:51 final size:50
Alignment explanation
Indices: 53755399--53755494 Score: 122
Period size: 51 Copynumber: 1.9 Consensus size: 50
53755389 ATTTCCTCTC
*
53755399 AATTTGCTCTCAAATTCCTTCCAAATTTCTCTCAAATCCATATTTAATCTT
1 AATTTGCTCTCAAATTCCTTCCAAATTTCTCTCAAATCCATATTTAA-CAT
* * * *
53755450 AATTTGCTCTCAAGTTCC-TCTTAAATTTCTCTTAAATCCCTATTT
1 AATTTGCTCTCAAATTCCTTC-CAAATTTCTCTCAAATCCATATTT
53755495 TTAAATAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
50 2 0.05
51 38 0.95
ACGTcount: A:0.27, C:0.25, G:0.03, T:0.45
Consensus pattern (50 bp):
AATTTGCTCTCAAATTCCTTCCAAATTTCTCTCAAATCCATATTTAACAT
Found at i:53757832 original size:21 final size:21
Alignment explanation
Indices: 53757828--53758084 Score: 257
Period size: 21 Copynumber: 12.0 Consensus size: 21
53757818 CTAAAAACCC
*
53757828 AAACCCTAACCCTTAACTTTA
1 AAACCCTAACCCTTAACTTAA
* *
53757849 AAATCCTAACCCTTAAATTAA
1 AAACCCTAACCCTTAACTTAA
* **
53757870 AACCCCTAAACTTTTAACTTAA
1 AAACCCT-AACCCTTAACTTAA
*
53757892 AAACCCTAAACCCTAAACATT--
1 AAACCCT-AACCCTTAAC-TTAA
*
53757913 AAACCCTAAACCCTTAACCTAA
1 AAACCCT-AACCCTTAACTTAA
* *
53757935 AAACCCTAAACACTTAACCTAA
1 AAACCCT-AACCCTTAACTTAA
*
53757957 AAACCTTAACCCTTAACTTAA
1 AAACCCTAACCCTTAACTTAA
* * *
53757978 AGACCCTAACCTTTAAATTAA
1 AAACCCTAACCCTTAACTTAA
* *
53757999 AAACCCTAAACCTTTAACTTTA
1 AAACCCT-AACCCTTAACTTAA
* * * *
53758021 AAATCGTAACCCTTAAATAAA
1 AAACCCTAACCCTTAACTTAA
*
53758042 AAACCCTAACACTTAACTTAA
1 AAACCCTAACCCTTAACTTAA
53758063 AAACCCTAACCCTTAACTTAA
1 AAACCCTAACCCTTAACTTAA
53758084 A
1 A
53758085 TATAATTTGA
Statistics
Matches: 194, Mismatches: 37, Indels: 10
0.80 0.15 0.04
Matches are distributed among these distances:
20 1 0.01
21 122 0.63
22 69 0.36
23 2 0.01
ACGTcount: A:0.45, C:0.29, G:0.01, T:0.25
Consensus pattern (21 bp):
AAACCCTAACCCTTAACTTAA
Found at i:53757900 original size:43 final size:42
Alignment explanation
Indices: 53757828--53758084 Score: 259
Period size: 43 Copynumber: 6.0 Consensus size: 42
53757818 CTAAAAACCC
* *
53757828 AAACCCT-AACCCTTAACTTTAAAATCCTAACCCTTAAATTA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAAATTA
** *
53757869 AAACCCCTAAACTTTTAACTTAAAAACCCTAAACCCTAAACATT-
1 AAA-CCCTAAACCCTTAACTTAAAAACCCT-AACCCTTAA-ATTA
* * **
53757913 AAACCCTAAACCCTTAACCTAAAAACCCTAAACACTTAACCTA
1 AAACCCTAAACCCTTAACTTAAAAACCCT-AACCCTTAAATTA
* * * *
53757956 AAAACCTTAACCCTTAACTTAAAGACCCTAACCTTTAAATTAA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAAATT-A
* * * * *
53757999 AAACCCTAAACCTTTAACTTTAAAATCGTAACCCTTAAATAAA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAAAT-TA
* *
53758042 AAACCCT-AACACTTAACTTAAAAACCCTAACCCTTAACTTA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAAATTA
53758083 AA
1 AA
53758085 TATAATTTGA
Statistics
Matches: 173, Mismatches: 36, Indels: 14
0.78 0.16 0.06
Matches are distributed among these distances:
41 6 0.03
42 39 0.23
43 114 0.66
44 11 0.06
45 3 0.02
ACGTcount: A:0.45, C:0.29, G:0.01, T:0.25
Consensus pattern (42 bp):
AAACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAAATTA
Found at i:53757902 original size:7 final size:7
Alignment explanation
Indices: 53757892--53757945 Score: 56
Period size: 7 Copynumber: 7.6 Consensus size: 7
53757882 TTTAACTTAA
53757892 AAACCCT
1 AAACCCT
53757899 AAACCCT
1 AAACCCT
**
53757906 AAACATT
1 AAACCCT
53757913 AAACCCT
1 AAACCCT
53757920 AAACCCT
1 AAACCCT
*
53757927 TAA-CCT
1 AAACCCT
53757933 AAAAACCCT
1 --AAACCCT
53757942 AAAC
1 AAAC
53757946 ACTTAACCTA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
6 3 0.08
7 30 0.79
8 2 0.05
9 3 0.08
ACGTcount: A:0.48, C:0.35, G:0.00, T:0.17
Consensus pattern (7 bp):
AAACCCT
Found at i:53757921 original size:64 final size:64
Alignment explanation
Indices: 53757828--53758084 Score: 261
Period size: 64 Copynumber: 4.0 Consensus size: 64
53757818 CTAAAAACCC
* * * * **
53757828 AAACCCTAACCCTTAACTTTAAAATCCTAACCCTTAAATTAAAACCCCTAAACTTTTAACTTAA
1 AAACCCTAACCCTAAACATTAAAACCCTAACCCTTAAATTAAAAACCCTAAACCCTTAACTTAA
** * *
53757892 AAACCCTAAACCCTAAACATT-AAACCCTAAACCCTTAACCTAAAAACCCTAAACACTTAACCTA
1 AAACCCT-AACCCTAAACATTAAAACCCT-AACCCTTAAATTAAAAACCCTAAACCCTTAACTTA
53757956 A
64 A
* * * * *
53757957 AAACCTTAACCCTTAAC-TTAAAGACCCTAACCTTTAAATTAAAAACCCTAAACCTTTAACTTTA
1 AAACCCTAACCCTAAACATTAAA-ACCCTAACCCTTAAATTAAAAACCCTAAACCCTTAACTTAA
* * * * * *
53758021 AAATCGTAACCCTTAA-ATAAAAAACCCTAACACTTAACTTAAAAACCCT-AACCCTTAACTTAA
1 AAACCCTAACCCTAAACAT-TAAAACCCTAACCCTTAAATTAAAAACCCTAAACCCTTAACTTAA
53758084 A
1 A
53758085 TATAATTTGA
Statistics
Matches: 161, Mismatches: 26, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
63 15 0.09
64 91 0.57
65 55 0.34
ACGTcount: A:0.45, C:0.29, G:0.01, T:0.25
Consensus pattern (64 bp):
AAACCCTAACCCTAAACATTAAAACCCTAACCCTTAAATTAAAAACCCTAAACCCTTAACTTAA
Found at i:53757939 original size:36 final size:36
Alignment explanation
Indices: 53757899--53757967 Score: 97
Period size: 36 Copynumber: 1.9 Consensus size: 36
53757889 TAAAAACCCT
*
53757899 AAACCCTAAACA-TTAAACCCT-AAACCCTTAACCTAA
1 AAACCCTAAACACTT-AA-CCTAAAAACCTTAACCTAA
53757935 AAACCCTAAACACTTAACCTAAAAACCTTAACC
1 AAACCCTAAACACTTAACCTAAAAACCTTAACC
53757968 CTTAACTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
35 3 0.10
36 25 0.83
37 2 0.07
ACGTcount: A:0.48, C:0.33, G:0.00, T:0.19
Consensus pattern (36 bp):
AAACCCTAAACACTTAACCTAAAAACCTTAACCTAA
Found at i:53760460 original size:45 final size:46
Alignment explanation
Indices: 53760314--53760502 Score: 202
Period size: 45 Copynumber: 4.0 Consensus size: 46
53760304 GATAATAACA
* * * *
53760314 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA--TCCTC-T--CGG
* *
53760365 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA--TC-C-TCTCGG
* *
53760415 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGATCCTCTCGG
*
53760460 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGATCCTCTC
53760503 ATGATCTGTA
Statistics
Matches: 121, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
45 46 0.38
46 1 0.01
47 1 0.01
50 35 0.29
51 34 0.28
52 2 0.02
53 2 0.02
ACGTcount: A:0.20, C:0.31, G:0.25, T:0.25
Consensus pattern (46 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGATCCTCTCGG
Found at i:53760495 original size:95 final size:98
Alignment explanation
Indices: 53760314--53760504 Score: 298
Period size: 95 Copynumber: 1.9 Consensus size: 98
53760304 GATAATAACA
* *
53760314 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATGT
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA--TCCTCGT-ACGGTGCCCATGCCATGT
*
53760379 CCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
63 CCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
*
53760415 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTC-T-CGGTGCCCATGCCATGTCCC
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATCCTCGTACGGTGCCCATGCCATGTCCC
53760477 AGACATGGTCTTACAGGGGACCTCTCAT
66 AGACATGGTCTTACAGGGGACCTCTCAT
53760505 GATCTGTAAT
Statistics
Matches: 86, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
95 46 0.53
97 1 0.01
98 3 0.03
101 36 0.42
ACGTcount: A:0.20, C:0.30, G:0.25, T:0.25
Consensus pattern (98 bp):
TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATCCTCGTACGGTGCCCATGCCATGTCCC
AGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:53760700 original size:13 final size:13
Alignment explanation
Indices: 53760679--53760710 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
53760669 GCTTGGATCA
*
53760679 TCATCAAATAAAT
1 TCATAAAATAAAT
53760692 TCATAAAATAAAT
1 TCATAAAATAAAT
53760705 TCATAA
1 TCATAA
53760711 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:53760957 original size:30 final size:30
Alignment explanation
Indices: 53760922--53760979 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
53760912 CCTCGACTCT
*
53760922 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
53760952 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
53760980 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:53768052 original size:50 final size:50
Alignment explanation
Indices: 53767928--53768176 Score: 284
Period size: 50 Copynumber: 4.8 Consensus size: 50
53767918 GATAATAACA
* * ** * *
53767928 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
53767979 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
53768029 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
53768079 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
53768134 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
53768177 TTACCCAAAT
Statistics
Matches: 170, Mismatches: 21, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
49 1 0.01
50 92 0.54
51 33 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:53768106 original size:100 final size:104
Alignment explanation
Indices: 53767927--53768176 Score: 357
Period size: 100 Copynumber: 2.4 Consensus size: 104
53767917 TGATAATAAC
**
53767927 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
53767992 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
53768029 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
53768092 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
53768134 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
53768177 TTACCCAAAT
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 50 0.38
101 36 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:53768292 original size:13 final size:13
Alignment explanation
Indices: 53768271--53768302 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
53768261 GCTTGGATCA
*
53768271 TCATCAAATAAAT
1 TCATAAAATAAAT
53768284 TCATAAAATAAAT
1 TCATAAAATAAAT
53768297 TCATAA
1 TCATAA
53768303 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:53768549 original size:30 final size:30
Alignment explanation
Indices: 53768514--53768571 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
53768504 CCTCGACTCT
*
53768514 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
53768544 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
53768572 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:53771904 original size:125 final size:125
Alignment explanation
Indices: 53771642--53772197 Score: 828
Period size: 125 Copynumber: 4.4 Consensus size: 125
53771632 CCCAAACATG
*
53771642 CTACTGTAGCAAAAGTGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
* * * * * *
53771707 TAGAAGCG-ATTTTATACTATTTGCTCAGAAACGTCAAGTCAAAATTATTTTTCCAGTAC
66 TTGAAGCGTTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGAC
* *
53771766 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCA-AATAGCATCCTT
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAA-AGCATCCTG
* * * *
53771830 CTTGCAGCGTTTTTTATACTATTTGCTCAGAAACATCAACTCGAAATTATTTTTTCAGGAC
65 CTTGAAGCGTTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGAC
*
53771891 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGT
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
*
53771956 TTGAAGCGTTTTTTAAACTATTTACTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGAC
66 TTGAAGCGTTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTT-TTCCAGGAC
* * * *
53772017 CAACTGTGGCAAAAGTGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
* * *
53772082 TTCAAGCGTTGTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGTAC
66 TTGAAGCGTTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGAC
* * * * * *
53772142 CTACTGTAGCAAAAACGCGTACACGTGGGCGCGACTTCAAAAATCCTTCTGATAAA
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAA
53772198 TCATACTGTT
Statistics
Matches: 390, Mismatches: 38, Indels: 7
0.90 0.09 0.02
Matches are distributed among these distances:
123 2 0.01
124 65 0.17
125 205 0.53
126 118 0.30
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (125 bp):
CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
TTGAAGCGTTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGAC
Found at i:53772109 original size:251 final size:249
Alignment explanation
Indices: 53771642--53772208 Score: 850
Period size: 251 Copynumber: 2.3 Consensus size: 249
53771632 CCCAAACATG
* *
53771642 CTACTGTAGCAAAAGTGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGT
* * * * * *
53771707 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAGTCAAAATTATTTTTCCAGTACCTACTG
66 TTGAAGCGATTTTAAACTATTTACTCAGAAACGTCAACTCAAAATTATTTTTCCAGGACCAACTG
*
53771772 TAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTTCTTGCAG
131 TAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGCTTGCAG
* * *
53771837 CGTTTTTTATACTATTTGCTCAGAAACATCAACTCGAAATTATTTTTTCAGGAC
196 CGTTGTTTAAACTATTTGCTCAGAAACATCAACTCGAAATTATTTTTCCAGGAC
53771891 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGT
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGT
* *
53771956 TTGAAGCGTTTTTTAAACTATTTACTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGACCAAC
66 TTGAAGCG-ATTTTAAACTATTTACTCAGAAACGTCAACTCAAAATTATTT-TTCCAGGACCAAC
* *
53772021 TGTGGCAAAAGTGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAA-AGCATCCTGCTT-
129 TGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCA-AATAGCATCCTGCTTG
* *
53772084 CAAGCGTTGTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGTAC
193 C-AGCGTTGTTTAAACTATTTGCTCAGAAACATCAACTCGAAATTATTTTTCCAGGAC
* * * * * * * *
53772142 CTACTGTAGCAAAAACGCGTACACGTGGGCGCGACTTCAAAAATCCTTCTGATAAATCATACTGT
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGT
53772207 TT
66 TT
53772209 TGATTTTATC
Statistics
Matches: 288, Mismatches: 26, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
249 70 0.24
250 38 0.13
251 178 0.62
252 2 0.01
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (249 bp):
CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGT
TTGAAGCGATTTTAAACTATTTACTCAGAAACGTCAACTCAAAATTATTTTTCCAGGACCAACTG
TAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGCTTGCAG
CGTTGTTTAAACTATTTGCTCAGAAACATCAACTCGAAATTATTTTTCCAGGAC
Found at i:53772344 original size:8 final size:9
Alignment explanation
Indices: 53772324--53772360 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
53772314 TTTTTTCTCC
*
53772324 AAAACCCTA
1 AAAATCCTA
53772333 AAAATCCTA
1 AAAATCCTA
*
53772342 AAAACCCTA
1 AAAATCCTA
53772351 AAAATCCTA
1 AAAATCCTA
53772360 A
1 A
53772361 CGTGAGAAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.57, C:0.27, G:0.00, T:0.16
Consensus pattern (9 bp):
AAAATCCTA
Done.