Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr2
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: 61750188
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1877335 characters in sequence are not A, C, G, or T
File 43 of 186
Found at i:12798885 original size:21 final size:21
Alignment explanation
Indices: 12798859--12798899 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
12798849 ATCTGCTCAA
* *
12798859 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
12798880 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
12798900 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:12803930 original size:31 final size:31
Alignment explanation
Indices: 12803895--12803954 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 31
12803885 CAATCCAGTG
12803895 ACTTAAAT-AAAAGTTTTCA-AATAGTTTAGCT
1 ACTTAAATGAAAA-TTTT-AGAATAGTTTAGCT
12803926 ACTTAAATGAAAATTTTAGAATAGTTTAG
1 ACTTAAATGAAAATTTTAGAATAGTTTAG
12803955 TGACAATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
30 1 0.04
31 22 0.81
32 4 0.15
ACGTcount: A:0.43, C:0.07, G:0.12, T:0.38
Consensus pattern (31 bp):
ACTTAAATGAAAATTTTAGAATAGTTTAGCT
Found at i:12807349 original size:144 final size:143
Alignment explanation
Indices: 12807089--12807373 Score: 489
Period size: 144 Copynumber: 2.0 Consensus size: 143
12807079 TTTGTTTACC
*
12807089 AACATTATAAATTTTCACGTGAATGGTCATTAGCAATCCCTTTGGAATGAGGTTCTTCCGCCAAA
1 AACATTACAAATTTTCACGTGAATGGTCATTAGCAATCCCTTTGGAATGAGGTTCTTCCGCCAAA
* *
12807154 GATTAAAGAATTTTTATAAAGATTATTATGTGGTTTTGTGGATTGTATTAGTCAATTTTTAACTC
66 GATTAAAGAATTTTTATAAAGATTATTATGTGGTTTTATGCATTGTATTAGTCAATTTTTAA-TC
12807219 ATGGGGTGAATACT
130 ATGGGGTGAATACT
* * *
12807233 AACATTACAGATTTTCATGTGAATGGTCATTAGCAATCCCTTTGGAATGAGGTTTTTCCGCCAAA
1 AACATTACAAATTTTCACGTGAATGGTCATTAGCAATCCCTTTGGAATGAGGTTCTTCCGCCAAA
* *
12807298 GATTAAAGAATTTTTATAGAGATTATTATGTGGTTTTATGCATTGTATTAGTCAATTTTTGATCA
66 GATTAAAGAATTTTTATAAAGATTATTATGTGGTTTTATGCATTGTATTAGTCAATTTTTAATCA
12807363 TGGGGTGAATA
131 TGGGGTGAATA
12807374 TTGACCCTTA
Statistics
Matches: 133, Mismatches: 8, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
143 14 0.11
144 119 0.89
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.39
Consensus pattern (143 bp):
AACATTACAAATTTTCACGTGAATGGTCATTAGCAATCCCTTTGGAATGAGGTTCTTCCGCCAAA
GATTAAAGAATTTTTATAAAGATTATTATGTGGTTTTATGCATTGTATTAGTCAATTTTTAATCA
TGGGGTGAATACT
Found at i:12808274 original size:25 final size:25
Alignment explanation
Indices: 12808237--12808286 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
12808227 GTGGGGAGTT
*
12808237 AGGATTTGGGTGTATTAGGTAAGTC
1 AGGACTTGGGTGTATTAGGTAAGTC
*
12808262 AGGACTTGTGTGTATTAGGTAAGTC
1 AGGACTTGGGTGTATTAGGTAAGTC
12808287 TTATGGCTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.24, C:0.06, G:0.34, T:0.36
Consensus pattern (25 bp):
AGGACTTGGGTGTATTAGGTAAGTC
Found at i:12809119 original size:29 final size:29
Alignment explanation
Indices: 12809086--12809141 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
12809076 TTTGGTCTTT
*
12809086 ATATTTGTATAATGTTATTAATTAGTTTA
1 ATATTTGTATAATGTAATTAATTAGTTTA
* *
12809115 ATATTTTTGTAATGTAATTAATTAGTT
1 ATATTTGTATAATGTAATTAATTAGTT
12809142 AAACTAGTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.55
Consensus pattern (29 bp):
ATATTTGTATAATGTAATTAATTAGTTTA
Found at i:12810289 original size:29 final size:30
Alignment explanation
Indices: 12810255--12810313 Score: 102
Period size: 29 Copynumber: 2.0 Consensus size: 30
12810245 CTTGGTTTGA
12810255 TGTGTAATTTTATACA-AAAATTTTGATTT
1 TGTGTAATTTTATACATAAAATTTTGATTT
*
12810284 TGTGTAATTTTATATATAAAATTTTGATTT
1 TGTGTAATTTTATACATAAAATTTTGATTT
12810314 GATTTTATTC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 15 0.54
30 13 0.46
ACGTcount: A:0.34, C:0.02, G:0.10, T:0.54
Consensus pattern (30 bp):
TGTGTAATTTTATACATAAAATTTTGATTT
Found at i:12816530 original size:42 final size:42
Alignment explanation
Indices: 12816479--12816572 Score: 134
Period size: 42 Copynumber: 2.2 Consensus size: 42
12816469 AAGGCCTGAG
* *
12816479 ACACGGGTGTGTCTAGAGCCGTGTGAGGCACACGGCCTGTTC
1 ACACGGGTGTGTCTAGAACCGAGTGAGGCACACGGCCTGTTC
* * * *
12816521 ACATGGGTGTGTTTGGAATCGAGTGAGGCACACGGCCTGTTC
1 ACACGGGTGTGTCTAGAACCGAGTGAGGCACACGGCCTGTTC
12816563 ACACGGGTGT
1 ACACGGGTGT
12816573 TTGACCCCTG
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.18, C:0.22, G:0.36, T:0.23
Consensus pattern (42 bp):
ACACGGGTGTGTCTAGAACCGAGTGAGGCACACGGCCTGTTC
Found at i:12818731 original size:5 final size:5
Alignment explanation
Indices: 12818721--12818747 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
12818711 GTTATCTAAA
12818721 TTATT TTATT TTATT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TT
12818748 TCTCTCTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:12819757 original size:16 final size:16
Alignment explanation
Indices: 12819736--12819768 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
12819726 CATATGAGAA
12819736 GGAAGTTTTTTGTATG
1 GGAAGTTTTTTGTATG
12819752 GGAAGTTTTTTGTATG
1 GGAAGTTTTTTGTATG
12819768 G
1 G
12819769 CGATCATCGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.00, G:0.33, T:0.48
Consensus pattern (16 bp):
GGAAGTTTTTTGTATG
Found at i:12823331 original size:12 final size:12
Alignment explanation
Indices: 12823314--12823353 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
12823304 GCTAATGGGA
*
12823314 ATATATCAATAT
1 ATATATAAATAT
12823326 ATATATAAATAT
1 ATATATAAATAT
*
12823338 ATATATAAATAC
1 ATATATAAATAT
12823350 ATAT
1 ATAT
12823354 GAAAGTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (12 bp):
ATATATAAATAT
Found at i:12825320 original size:79 final size:81
Alignment explanation
Indices: 12825205--12825368 Score: 226
Period size: 79 Copynumber: 2.0 Consensus size: 81
12825195 TTTTTATCAT
* * * * *
12825205 TTTTGGGGGGAAAATTATAATTTTACCATTATTAATTTAAAATTTTATAAATTATAAAAG-GCTT
1 TTTTGGGGGGAAAACTACAATTTTACCATAACTAATTTAAAATTTTATAAATTATAAAAGATC-T
*
12825269 AAATTAAAAATTTATTA
65 AAATTAAAAATTTACTA
*
12825286 TTTT-GGGGG-AAACTACAATTTTACCATAACTAATTTAAAATTTTATAGATTATAAAAGATCTA
1 TTTTGGGGGGAAAACTACAATTTTACCATAACTAATTTAAAATTTTATAAATTATAAAAGATCTA
*
12825349 AATTGAAAATTTACTA
66 AATTAAAAATTTACTA
12825365 TTTT
1 TTTT
12825369 AAAGGAGATG
Statistics
Matches: 74, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
79 64 0.86
80 6 0.08
81 4 0.05
ACGTcount: A:0.42, C:0.06, G:0.10, T:0.42
Consensus pattern (81 bp):
TTTTGGGGGGAAAACTACAATTTTACCATAACTAATTTAAAATTTTATAAATTATAAAAGATCTA
AATTAAAAATTTACTA
Found at i:12828262 original size:31 final size:29
Alignment explanation
Indices: 12828217--12828311 Score: 97
Period size: 31 Copynumber: 3.2 Consensus size: 29
12828207 TTCTTTAAAT
* *
12828217 ATGTATAATTGAATCAAAATTAAAGTTTC
1 ATGTATAATTGAATCAAAATCAAAGGTTC
12828246 ATGTATATATTTGAATCAAAATCAAAGGTTC
1 ATGTATA-A-TTGAATCAAAATCAAAGGTTC
*
12828277 ATATGTATAATT-ACA-CCAAATCAAA-GTTC
1 --ATGTATAATTGA-ATCAAAATCAAAGGTTC
12828306 ATGTAT
1 ATGTAT
12828312 GATTTTGAGA
Statistics
Matches: 58, Mismatches: 3, Indels: 12
0.79 0.04 0.16
Matches are distributed among these distances:
27 6 0.10
29 11 0.19
30 11 0.19
31 22 0.38
32 1 0.02
33 7 0.12
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.36
Consensus pattern (29 bp):
ATGTATAATTGAATCAAAATCAAAGGTTC
Found at i:12830784 original size:18 final size:21
Alignment explanation
Indices: 12830748--12830791 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
12830738 AAAATTATAA
12830748 AAAAAATTATAATATATT-AT
1 AAAAAATTATAATATATTAAT
*
12830768 AAAAAATTATCA-A-ATTAAT
1 AAAAAATTATAATATATTAAT
12830787 AAAAA
1 AAAAA
12830792 CATATTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 3 0.14
19 8 0.36
20 11 0.50
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (21 bp):
AAAAAATTATAATATATTAAT
Found at i:12835874 original size:9 final size:9
Alignment explanation
Indices: 12835782--12835874 Score: 71
Period size: 10 Copynumber: 9.8 Consensus size: 9
12835772 ATTCATAACA
12835782 ATAAAAATAT
1 ATAAAAAT-T
*
12835792 ATTAAAATT
1 ATAAAAATT
*
12835801 CTTAAAAACTT
1 -ATAAAAA-TT
*
12835812 ATAAAAATC
1 ATAAAAATT
12835821 ATATAAAATT
1 ATA-AAAATT
*
12835831 AT-TAAATT
1 ATAAAAATT
*
12835839 AAAAAAATT
1 ATAAAAATT
*
12835848 AATATAAACTT
1 -ATA-AAAATT
12835859 ATAAAAATT
1 ATAAAAATT
12835868 ATAAAAA
1 ATAAAAA
12835875 AACATAAAAA
Statistics
Matches: 65, Mismatches: 12, Indels: 13
0.72 0.13 0.14
Matches are distributed among these distances:
8 6 0.09
9 22 0.34
10 30 0.46
11 7 0.11
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (9 bp):
ATAAAAATT
Found at i:12836313 original size:9 final size:9
Alignment explanation
Indices: 12836301--12836502 Score: 58
Period size: 9 Copynumber: 21.4 Consensus size: 9
12836291 TTTTATGTTT
12836301 TTTTAATAA
1 TTTTAATAA
*
12836310 TTTTTATAA
1 TTTTAATAA
*
12836319 GTTTATATCAA
1 TTTTA-AT-AA
12836330 TTTTAAT--
1 TTTTAATAA
*
12836337 TTTTTATAA
1 TTTTAATAA
*
12836346 GTTTTTAAGAA
1 --TTTTAATAA
12836357 TTTTAATACA
1 TTTTAATA-A
*
12836367 TTTTTATAAAA
1 -TTTTA-ATAA
*
12836378 TTTTAAATATG
1 TTTT-AATA-A
*
12836389 TTTTATTAA
1 TTTTAATAA
12836398 TTTT-ATAAA
1 TTTTAAT-AA
12836407 TTTT-ATAAA
1 TTTTAAT-AA
*
12836416 ATTT-ATAA
1 TTTTAATAA
** *
12836424 GTTTTTTTCA
1 -TTTTAATAA
*
12836434 TTTTATTATA
1 TTTTAATA-A
12836444 TTTTAATAA
1 TTTTAATAA
*
12836453 GTTTATATAA
1 TTTTA-ATAA
* * *
12836463 GTTTATTAT
1 TTTTAATAA
*
12836472 TTTTAAAATA
1 TTTTAATA-A
12836482 TATTTAAT--
1 T-TTTAATAA
12836490 TTTTAATAA
1 TTTTAATAA
12836499 TTTT
1 TTTT
12836503 TATACTTTTT
Statistics
Matches: 144, Mismatches: 29, Indels: 40
0.68 0.14 0.19
Matches are distributed among these distances:
7 12 0.08
8 4 0.03
9 63 0.44
10 34 0.24
11 29 0.20
12 2 0.01
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.58
Consensus pattern (9 bp):
TTTTAATAA
Found at i:12836348 original size:27 final size:28
Alignment explanation
Indices: 12836301--12836375 Score: 89
Period size: 27 Copynumber: 2.6 Consensus size: 28
12836291 TTTTATGTTT
*
12836301 TTTTAATAATTTTTATAAGTTTATATCAA
1 TTTTAAT-ATTTTTATAAGTTTATAACAA
* *
12836330 TTTTAAT-TTTTTATAAGTTTTTAAGAA
1 TTTTAATATTTTTATAAGTTTATAACAA
12836357 TTTTAATACATTTTTATAA
1 TTTTAAT--ATTTTTATAA
12836376 AATTTTAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
27 24 0.60
29 7 0.17
30 9 0.22
ACGTcount: A:0.36, C:0.03, G:0.04, T:0.57
Consensus pattern (28 bp):
TTTTAATATTTTTATAAGTTTATAACAA
Found at i:12836412 original size:18 final size:18
Alignment explanation
Indices: 12836389--12836480 Score: 69
Period size: 18 Copynumber: 5.1 Consensus size: 18
12836379 TTTAAATATG
12836389 TTTTATTAATTTTATAAA
1 TTTTATTAATTTTATAAA
* * *
12836407 TTTTATAAAATTTATAAG
1 TTTTATTAATTTTATAAA
* * *
12836425 TTTTTTTCATTTTATTATA
1 TTTTATTAATTTTA-TAAA
* *
12836444 TTTTAATAAGTTTATATAA
1 TTTTATTAATTTTATA-AA
* *
12836463 GTTTATTATTTTTA-AAA
1 TTTTATTAATTTTATAAA
12836480 T
1 T
12836481 ATATTTAATT
Statistics
Matches: 53, Mismatches: 19, Indels: 5
0.69 0.25 0.06
Matches are distributed among these distances:
17 2 0.04
18 28 0.53
19 23 0.43
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.60
Consensus pattern (18 bp):
TTTTATTAATTTTATAAA
Found at i:12837566 original size:14 final size:15
Alignment explanation
Indices: 12837547--12837584 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
12837537 AAGTAAAAAA
12837547 ATAATATAAA-TTTT
1 ATAATATAAACTTTT
12837561 ATAATATATAACTTTT
1 ATAATATA-AACTTTT
12837577 ATAA-ATAA
1 ATAATATAA
12837585 TGTTTTATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 9 0.41
15 5 0.23
16 8 0.36
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (15 bp):
ATAATATAAACTTTT
Found at i:12837569 original size:16 final size:16
Alignment explanation
Indices: 12837550--12837580 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12837540 TAAAAAAATA
12837550 ATATAAATTTTATAAT
1 ATATAAATTTTATAAT
*
12837566 ATATAACTTTTATAA
1 ATATAAATTTTATAA
12837581 ATAATGTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (16 bp):
ATATAAATTTTATAAT
Found at i:12850798 original size:4 final size:4
Alignment explanation
Indices: 12850784--12850815 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
12850774 CTATTACCAT
12850784 AAAC AAAAC AAAC AAAC AAAC AAAC AAAC AAA
1 AAAC -AAAC AAAC AAAC AAAC AAAC AAAC AAA
12850816 TCGAATCTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:12857764 original size:30 final size:30
Alignment explanation
Indices: 12857725--12857785 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
12857715 ACTAACAAAG
*
12857725 TGTATGATATATCATCAAATTCTACATTTT
1 TGTAGGATATATCATCAAATTCTACATTTT
12857755 TGTAGGATATATCATCAAATTCTACATTTT
1 TGTAGGATATATCATCAAATTCTACATTTT
12857785 T
1 T
12857786 TGTTTTGAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (30 bp):
TGTAGGATATATCATCAAATTCTACATTTT
Found at i:12858796 original size:39 final size:39
Alignment explanation
Indices: 12858744--12858821 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
12858734 TTGCTCATCA
12858744 AAACCCAAAGTACTAAGCTGTACTTTTTTAGTTTTTTTC
1 AAACCCAAAGTACTAAGCTGTACTTTTTTAGTTTTTTTC
*
12858783 AAACCCAAAGTACTAAGCTTTACTTTTTTAGTTTTTTTC
1 AAACCCAAAGTACTAAGCTGTACTTTTTTAGTTTTTTTC
12858822 TTAGTGACCA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.28, C:0.18, G:0.09, T:0.45
Consensus pattern (39 bp):
AAACCCAAAGTACTAAGCTGTACTTTTTTAGTTTTTTTC
Found at i:12859649 original size:23 final size:24
Alignment explanation
Indices: 12859623--12859673 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
12859613 TTATGGTTTT
12859623 AAGGCAAAA-AAAAAAGA-AAAAAA
1 AAGG-AAAATAAAAAAGAGAAAAAA
**
12859646 AAGGAAAATAGTAAAGAGAAAAAA
1 AAGGAAAATAAAAAAGAGAAAAAA
12859670 AAGG
1 AAGG
12859674 GTTTCTAGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 4 0.17
23 10 0.42
24 10 0.42
ACGTcount: A:0.75, C:0.02, G:0.20, T:0.04
Consensus pattern (24 bp):
AAGGAAAATAAAAAAGAGAAAAAA
Found at i:12864170 original size:5 final size:5
Alignment explanation
Indices: 12864160--12864232 Score: 132
Period size: 5 Copynumber: 15.0 Consensus size: 5
12864150 AATAATTAAG
12864160 TATAT TATA- T-TAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
12864208 TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT
12864233 GAAANNNNNN
Statistics
Matches: 66, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
3 2 0.03
4 2 0.03
5 62 0.94
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:12864862 original size:12 final size:12
Alignment explanation
Indices: 12864845--12864869 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12864835 GCCGACTACT
12864845 GTTACTGTTACC
1 GTTACTGTTACC
12864857 GTTACTGTTACC
1 GTTACTGTTACC
12864869 G
1 G
12864870 ATTCGACACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.20, T:0.40
Consensus pattern (12 bp):
GTTACTGTTACC
Found at i:12864900 original size:45 final size:45
Alignment explanation
Indices: 12864847--12864953 Score: 162
Period size: 45 Copynumber: 2.4 Consensus size: 45
12864837 CGACTACTGT
*
12864847 TACTGTTACCGTTACTGTTACCGATTC-GACACTTTGTGTGTCGAA
1 TACTGTTACCGTTACTGTTACAGATTCAG-CACTTTGTGTGTCGAA
* *
12864892 TATTGTTACCGTTACTGTTACAGATTCAGCACTTTGTGTGTTGAA
1 TACTGTTACCGTTACTGTTACAGATTCAGCACTTTGTGTGTCGAA
*
12864937 TACTGTTACTGTTACTG
1 TACTGTTACCGTTACTG
12864954 CTACTGCTAC
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
45 55 0.98
46 1 0.02
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.41
Consensus pattern (45 bp):
TACTGTTACCGTTACTGTTACAGATTCAGCACTTTGTGTGTCGAA
Found at i:12864948 original size:6 final size:6
Alignment explanation
Indices: 12864937--12864978 Score: 57
Period size: 6 Copynumber: 6.8 Consensus size: 6
12864927 GTGTGTTGAA
* *
12864937 TACTGT TACTGT TACTGC TACTGC TACTGT TACTGAT TACTG
1 TACTGT TACTGT TACTGT TACTGT TACTGT TACTG-T TACTG
12864979 ATTAGGTACT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
6 27 0.82
7 6 0.18
ACGTcount: A:0.19, C:0.21, G:0.17, T:0.43
Consensus pattern (6 bp):
TACTGT
Found at i:12869860 original size:30 final size:30
Alignment explanation
Indices: 12869821--12869882 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
12869811 TGTATGAGTA
* *
12869821 TGGGTAAAATTCAGCCTAACATGGGTATAT
1 TGGGGAAAATTCAGCCCAACATGGGTATAT
*
12869851 TGGGGAAAATTCGGCCCAACATGGGTATAT
1 TGGGGAAAATTCAGCCCAACATGGGTATAT
12869881 TG
1 TG
12869883 AAATTATGGG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (30 bp):
TGGGGAAAATTCAGCCCAACATGGGTATAT
Found at i:12869907 original size:38 final size:38
Alignment explanation
Indices: 12869851--12869925 Score: 132
Period size: 38 Copynumber: 2.0 Consensus size: 38
12869841 ATGGGTATAT
12869851 TGGGGAAAATTCGGCCCAACATGGGTATATTGAAATTA
1 TGGGGAAAATTCGGCCCAACATGGGTATATTGAAATTA
* *
12869889 TGGGTAAAATTTGGCCCAACATGGGTATATTGAAATT
1 TGGGGAAAATTCGGCCCAACATGGGTATATTGAAATT
12869926 TTGCATATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.29
Consensus pattern (38 bp):
TGGGGAAAATTCGGCCCAACATGGGTATATTGAAATTA
Found at i:12870603 original size:56 final size:56
Alignment explanation
Indices: 12870533--12870732 Score: 310
Period size: 56 Copynumber: 3.6 Consensus size: 56
12870523 ACCTGGAAGT
*
12870533 ATATGCGATTCCGATATATGTGTACGAGTAAGACCACGTTTTATACGTTGGCATCG
1 ATATGCGACTCCGATATATGTGTACGAGTAAGACCACGTTTTATACGTTGGCATCG
* *
12870589 ATTTGCGACTCCGATATATGTGTGCGAGTAAGACCACGTTTTATACGTTGGCATCG
1 ATATGCGACTCCGATATATGTGTACGAGTAAGACCACGTTTTATACGTTGGCATCG
* *
12870645 ATATGTGACTCCGATATATGTGTGCGAGTAAGACCACGTTTTATACGTTGGCATCG
1 ATATGCGACTCCGATATATGTGTACGAGTAAGACCACGTTTTATACGTTGGCATCG
* * ** *
12870701 ATATGTGATTCCGATATGCGTTTACGAGTAAG
1 ATATGCGACTCCGATATATGTGTACGAGTAAG
12870733 GCCCTATCTG
Statistics
Matches: 134, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 134 1.00
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (56 bp):
ATATGCGACTCCGATATATGTGTACGAGTAAGACCACGTTTTATACGTTGGCATCG
Found at i:12874829 original size:14 final size:14
Alignment explanation
Indices: 12874812--12874847 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
12874802 ATAAATATAT
* *
12874812 AATATAAATACAAA
1 AATAAAAATAAAAA
12874826 AATAAAAATAAAAA
1 AATAAAAATAAAAA
12874840 AATAAAAA
1 AATAAAAA
12874848 AGAGAGCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.17
Consensus pattern (14 bp):
AATAAAAATAAAAA
Found at i:12875445 original size:3 final size:3
Alignment explanation
Indices: 12875437--12875483 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
12875427 TTATTCTACT
12875437 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
12875484 GTGTGTTGTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:12875631 original size:18 final size:17
Alignment explanation
Indices: 12875595--12875634 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
12875585 TTATGTTATA
*
12875595 TATATATATTTATACAT
1 TATATATATTTAAACAT
*
12875612 TATATATACTTTAAATAT
1 TATATATA-TTTAAACAT
12875630 TATAT
1 TATAT
12875635 CTTATATACT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATATATTTAAACAT
Found at i:12875771 original size:20 final size:20
Alignment explanation
Indices: 12875748--12875796 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
12875738 TTAATACTAC
***
12875748 ATTATATATATATTTTTTAT
1 ATTATATATATATTTCAAAT
**
12875768 ATTATGCATATATTTCAAAT
1 ATTATATATATATTTCAAAT
12875788 ATTATATAT
1 ATTATATAT
12875797 TAAGTATTTC
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.55
Consensus pattern (20 bp):
ATTATATATATATTTCAAAT
Found at i:12875913 original size:15 final size:15
Alignment explanation
Indices: 12875893--12875942 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
12875883 ATTGCTAATG
12875893 TATATG-TATATATCA
1 TATATGTTATATAT-A
*
12875908 TATATGTTTTATATA
1 TATATGTTATATATA
* *
12875923 TATATATTATGTATA
1 TATATGTTATATATA
12875938 TATAT
1 TATAT
12875943 TTTCAATATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
15 24 0.80
16 6 0.20
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.54
Consensus pattern (15 bp):
TATATGTTATATATA
Found at i:12875932 original size:13 final size:13
Alignment explanation
Indices: 12875893--12875943 Score: 52
Period size: 13 Copynumber: 4.1 Consensus size: 13
12875883 ATTGCTAATG
*
12875893 TATATGTATATAT
1 TATATATATATAT
* *
12875906 CATATATGT-T-T
1 TATATATATATAT
12875917 TATATATATATAT
1 TATATATATATAT
*
12875930 TATGTATATATAT
1 TATATATATATAT
12875943 T
1 T
12875944 TTCAATATTA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
11 8 0.27
12 2 0.07
13 20 0.67
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.55
Consensus pattern (13 bp):
TATATATATATAT
Found at i:12875951 original size:24 final size:26
Alignment explanation
Indices: 12875922--12876031 Score: 74
Period size: 26 Copynumber: 4.5 Consensus size: 26
12875912 TGTTTTATAT
12875922 ATATA-TATTATGTATATATATTTTC
1 ATATACTATTATGTATATATATTTTC
*
12875947 A-ATATTATTA-GT-TATAT-TTTT-
1 ATATACTATTATGTATATATATTTTC
* * * * *
12875968 ATATACTATTCTATGTACATATTTCC
1 ATATACTATTATGTATATATATTTTC
*
12875994 ATAT-CATCTTATGTATATATATTCTT-
1 ATATAC-TATTATGTATATATATT-TTC
*
12876020 AAATACTATTAT
1 ATATACTATTAT
12876032 ATGTATATGT
Statistics
Matches: 63, Mismatches: 13, Indels: 17
0.68 0.14 0.18
Matches are distributed among these distances:
21 1 0.02
22 11 0.17
23 6 0.10
24 9 0.14
25 10 0.16
26 24 0.38
27 2 0.03
ACGTcount: A:0.35, C:0.09, G:0.04, T:0.53
Consensus pattern (26 bp):
ATATACTATTATGTATATATATTTTC
Found at i:12877103 original size:27 final size:28
Alignment explanation
Indices: 12877073--12877131 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 28
12877063 TAATGATAAA
*
12877073 AATTTAA-ATAATATTTATCTTAATGAT
1 AATTTAACATAATATTTATATTAATGAT
*
12877100 AA-TTAACATAATATTTATATTTATGAT
1 AATTTAACATAATATTTATATTAATGAT
12877127 AATTT
1 AATTT
12877132 TATATATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 4 0.14
27 22 0.79
28 2 0.07
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.49
Consensus pattern (28 bp):
AATTTAACATAATATTTATATTAATGAT
Found at i:12877195 original size:20 final size:20
Alignment explanation
Indices: 12877172--12877209 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
12877162 TTACGTAAAA
12877172 TTTTCAAAATTTATTTAACC
1 TTTTCAAAATTTATTTAACC
*
12877192 TTTTCAAATTTTATTTAA
1 TTTTCAAAATTTATTTAA
12877210 ATGTGTTAAA
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:0.34, C:0.11, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTTCAAAATTTATTTAACC
Found at i:12877850 original size:19 final size:19
Alignment explanation
Indices: 12877828--12877867 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
12877818 TTTTAATAAT
12877828 AAAATAGGAATTTTTTT-AA
1 AAAATA-GAATTTTTTTGAA
*
12877847 AAAATAGATTTTTTTTGAA
1 AAAATAGAATTTTTTTGAA
12877866 AA
1 AA
12877868 CACTTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.47, C:0.00, G:0.10, T:0.42
Consensus pattern (19 bp):
AAAATAGAATTTTTTTGAA
Found at i:12878046 original size:13 final size:13
Alignment explanation
Indices: 12878028--12878057 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
12878018 ATATAATTAT
12878028 TTTAAAATTTAAA
1 TTTAAAATTTAAA
*
12878041 TTTAAAATTTATA
1 TTTAAAATTTAAA
12878054 TTTA
1 TTTA
12878058 TCAAATACTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TTTAAAATTTAAA
Found at i:12879092 original size:24 final size:24
Alignment explanation
Indices: 12879065--12879116 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
12879055 TTAGTAAGTC
*
12879065 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
12879089 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
12879113 AAAT
1 AAAT
12879117 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:12880322 original size:19 final size:20
Alignment explanation
Indices: 12880286--12880333 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
12880276 ATATGTAATT
*
12880286 TTTTTAATTTTTATAAAT-A
1 TTTTAAATTTTTATAAATAA
12880305 TTTTAAATTTTTGA-AAATAA
1 TTTTAAATTTTT-ATAAATAA
*
12880325 TTTTGAATT
1 TTTTAAATT
12880334 ATTTTGTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (20 bp):
TTTTAAATTTTTATAAATAA
Found at i:12880819 original size:21 final size:22
Alignment explanation
Indices: 12880767--12880821 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
12880757 AAAAAATTTA
* *
12880767 AAATATTATTTTGTTAAATAAT
1 AAATATTATATTGTTAAACAAT
* **
12880789 AATTGGTATATT-TTAAACAAT
1 AAATATTATATTGTTAAACAAT
12880810 AAATATTATATT
1 AAATATTATATT
12880822 CATTGAAATT
Statistics
Matches: 25, Mismatches: 8, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
21 17 0.68
22 8 0.32
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.47
Consensus pattern (22 bp):
AAATATTATATTGTTAAACAAT
Found at i:12881278 original size:29 final size:31
Alignment explanation
Indices: 12881222--12881281 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 31
12881212 AACCTGAAAT
* *
12881222 TTGAAATCTAAAAAGTAGAAGGACTAAATTC
1 TTGAAATCTAAAAAGTACAAAGACTAAATTC
*
12881253 TTGAAAT-TAAAAA-TACAAAGATTAAATTC
1 TTGAAATCTAAAAAGTACAAAGACTAAATTC
12881282 CTAATTTGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 13 0.50
30 6 0.23
31 7 0.27
ACGTcount: A:0.52, C:0.08, G:0.12, T:0.28
Consensus pattern (31 bp):
TTGAAATCTAAAAAGTACAAAGACTAAATTC
Found at i:12881346 original size:18 final size:17
Alignment explanation
Indices: 12881314--12881347 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
12881304 ACCTATGGCA
12881314 TATTTTAGCATTTTTTG
1 TATTTTAGCATTTTTTG
*
12881331 TATTTATAGTATTTTTT
1 TATTT-TAGCATTTTTT
12881348 TAAAAAGTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.21, C:0.03, G:0.09, T:0.68
Consensus pattern (17 bp):
TATTTTAGCATTTTTTG
Found at i:12882473 original size:11 final size:10
Alignment explanation
Indices: 12882436--12882478 Score: 54
Period size: 11 Copynumber: 4.3 Consensus size: 10
12882426 TTTCTAAAAT
12882436 TTTATATTTA
1 TTTATATTTA
12882446 TTTGA-ATTT-
1 TTT-ATATTTA
12882455 TTTATATTTA
1 TTTATATTTA
12882465 TTATATATTTA
1 TT-TATATTTA
12882476 TTT
1 TTT
12882479 CAATTTTAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
8 1 0.03
9 7 0.24
10 10 0.34
11 11 0.38
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (10 bp):
TTTATATTTA
Found at i:12886022 original size:15 final size:15
Alignment explanation
Indices: 12885999--12886029 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
12885989 CAAATATTAG
*
12885999 CATCTTCTTCTTCTT
1 CATCATCTTCTTCTT
12886014 CATCATCTTCTTCTT
1 CATCATCTTCTTCTT
12886029 C
1 C
12886030 GGCTGTTGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.10, C:0.35, G:0.00, T:0.55
Consensus pattern (15 bp):
CATCATCTTCTTCTT
Found at i:12890044 original size:4 final size:4
Alignment explanation
Indices: 12890035--12890066 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
12890025 TTTTTCTACA
12890035 TATG TATG TATG TATG TATG TAATG TATG TAT
1 TATG TATG TATG TATG TATG T-ATG TATG TAT
12890067 TAGTTTACCA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.28, C:0.00, G:0.22, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:12907866 original size:25 final size:25
Alignment explanation
Indices: 12907837--12907931 Score: 154
Period size: 25 Copynumber: 3.8 Consensus size: 25
12907827 CTGTACATGT
*
12907837 ATGCTCACATGAGCTGTAAATCAGA
1 ATGCTCACATGAGCTGTGAATCAGA
12907862 ATGCTCACATGAGCTGTGAATCAGA
1 ATGCTCACATGAGCTGTGAATCAGA
* *
12907887 ATGCTCACACGAGCTGTGAATTAGA
1 ATGCTCACATGAGCTGTGAATCAGA
*
12907912 ATGCTTACATGAGCTGTGAA
1 ATGCTCACATGAGCTGTGAA
12907932 AATGGGTCTG
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 65 1.00
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (25 bp):
ATGCTCACATGAGCTGTGAATCAGA
Found at i:12907952 original size:27 final size:25
Alignment explanation
Indices: 12907837--12907955 Score: 121
Period size: 25 Copynumber: 4.7 Consensus size: 25
12907827 CTGTACATGT
* * *
12907837 ATGCTCACATGAGCTGTAAATCAGA
1 ATGCTCACACGAGCTGTGAATGAGA
* *
12907862 ATGCTCACATGAGCTGTGAATCAGA
1 ATGCTCACACGAGCTGTGAATGAGA
*
12907887 ATGCTCACACGAGCTGTGAATTAGA
1 ATGCTCACACGAGCTGTGAATGAGA
* * * *
12907912 ATGCTTACATGAGCTGTGAAAATGGGT
1 ATGCTCACACGAGCTGTG--AATGAGA
*
12907939 CTGCTCACACGAGCTGT
1 ATGCTCACACGAGCTGT
12907956 AGGTCGAAAC
Statistics
Matches: 81, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
25 63 0.78
27 18 0.22
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.25
Consensus pattern (25 bp):
ATGCTCACACGAGCTGTGAATGAGA
Found at i:12928571 original size:29 final size:29
Alignment explanation
Indices: 12928525--12928583 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
12928515 AAATTGAATC
*
12928525 AAATCAAAACGTTATATATAAAATTGCACA
1 AAATCAAAAC-TTATATATAAAATTACACA
*
12928555 AAATCAAAA-TTCATATATAACATTACACA
1 AAATCAAAACTT-ATATATAAAATTACACA
12928584 TTGAACAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 2 0.08
29 15 0.58
30 9 0.35
ACGTcount: A:0.54, C:0.15, G:0.03, T:0.27
Consensus pattern (29 bp):
AAATCAAAACTTATATATAAAATTACACA
Found at i:12933237 original size:24 final size:22
Alignment explanation
Indices: 12933182--12933240 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 22
12933172 TATACATAAT
12933182 ATATATA-ATAAATATTGAAAA
1 ATATATACATAAATATTGAAAA
*
12933203 ATGTATGTACATAACATATATGAAAA
1 A--TATATACATAA-ATAT-TGAAAA
12933229 ATATATACATAA
1 ATATATACATAA
12933241 TAATATTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
21 1 0.03
23 5 0.16
24 14 0.45
25 4 0.13
26 7 0.23
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.32
Consensus pattern (22 bp):
ATATATACATAAATATTGAAAA
Found at i:12933243 original size:27 final size:24
Alignment explanation
Indices: 12933179--12933300 Score: 72
Period size: 26 Copynumber: 4.8 Consensus size: 24
12933169 ATATATACAT
12933179 AATATAT-ATAATAAATATTGAAA
1 AATATATAATAATAAATATTGAAA
* *
12933202 AATGTAT-GTACATAACATATATGAAA
1 AATATATAATA-ATAA-ATAT-TGAAA
*
12933228 AATATATACATAAT-AATATTTAAA
1 AATATATA-ATAATAAATATTGAAA
* *
12933252 AA-AAATAATAAGTGATAATAGTGAAAA
1 AATATATAATAA-T-A-AATATTG-AAA
12933279 TAATAGGTATAATAATAAATAT
1 -AATA--TATAATAATAAATAT
12933301 AATGATGTAT
Statistics
Matches: 75, Mismatches: 10, Indels: 23
0.69 0.09 0.21
Matches are distributed among these distances:
22 4 0.05
23 13 0.17
24 10 0.13
25 8 0.11
26 17 0.23
27 5 0.07
28 8 0.11
29 2 0.03
30 1 0.01
31 7 0.09
ACGTcount: A:0.57, C:0.02, G:0.08, T:0.32
Consensus pattern (24 bp):
AATATATAATAATAAATATTGAAA
Found at i:12933755 original size:3 final size:3
Alignment explanation
Indices: 12933728--12933808 Score: 50
Period size: 3 Copynumber: 28.3 Consensus size: 3
12933718 AGCTAGAACA
* * *
12933728 AAT ACT AAT AAT AGT AAA AACT AAT AAT -AT AAT -AT AAT -AT AA-
1 AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT
*
12933770 AAT AA- AGAT AA- AGA- AAT AAT AGT AAT AAT AAT AAT AAT A
1 AAT AAT A-AT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT A
12933809 GAAAAGATTG
Statistics
Matches: 61, Mismatches: 8, Indels: 18
0.70 0.09 0.21
Matches are distributed among these distances:
2 11 0.18
3 47 0.77
4 3 0.05
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:12933806 original size:26 final size:25
Alignment explanation
Indices: 12933734--12933812 Score: 74
Period size: 26 Copynumber: 3.1 Consensus size: 25
12933724 AACAAATACT
*
12933734 AATAATAGTAAAAACTAATAATATA-A
1 AATAATAGT-AAAA-TAATAATAAAGA
*
12933760 TATAATA-TAAAATAA-AGATAAAGA
1 AATAATAGTAAAATAATA-ATAAAGA
12933784 AATAATAGTAATAATAATAATAATAGA
1 AATAATAGTAA-AATAATAATAA-AGA
12933811 AA
1 AA
12933813 AGATTGGTAC
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
22 1 0.02
23 7 0.16
24 11 0.25
25 4 0.09
26 15 0.34
27 6 0.14
ACGTcount: A:0.66, C:0.01, G:0.06, T:0.27
Consensus pattern (25 bp):
AATAATAGTAAAATAATAATAAAGA
Found at i:12935689 original size:14 final size:14
Alignment explanation
Indices: 12935645--12935680 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
12935635 ATTCTTTAAA
*
12935645 AAAAACAGACATT-
1 AAAAACAGAAATTG
12935658 AAAAACAGAAATTG
1 AAAAACAGAAATTG
12935672 AAAAACAGA
1 AAAAACAGA
12935681 TTTTGAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.67, C:0.11, G:0.11, T:0.11
Consensus pattern (14 bp):
AAAAACAGAAATTG
Found at i:12935917 original size:76 final size:76
Alignment explanation
Indices: 12935708--12935909 Score: 298
Period size: 76 Copynumber: 2.7 Consensus size: 76
12935698 CATGTAACGA
* *
12935708 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAATAGAAACTAAAAATACCTCA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAAAACATAAACTAAAAATACCTCA
* *
12935773 GCGTGTGACCCG
65 ACGTATGACCCG
* *
12935785 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTAAAAAACATCAACTAAAAATACCTCAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACATAAACTAAAAATACCTCAA
12935850 CGTATGACCCG
66 CGTATGACCCG
* ** *
12935861 AGGCTCAGCTCACCTCTAACAATATGAATTGA-TTTTTGAAAAACATAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACATAAA
12935910 TTGAAAAAAA
Statistics
Matches: 113, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
75 15 0.13
76 66 0.58
77 32 0.28
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (76 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACATAAACTAAAAATACCTCAA
CGTATGACCCG
Found at i:12935972 original size:87 final size:87
Alignment explanation
Indices: 12935838--12936091 Score: 350
Period size: 89 Copynumber: 2.9 Consensus size: 87
12935828 ACATCAACTA
* * * *
12935838 AAAATACCTCAACGTATGACCC-GAGGCTCAGCTCACCTCTA-ACAATATGAATTGATTTTTGAA
1 AAAATACCTCAGCG--TG-CCCTGAGGCTCAACTCACCTC-ACGCAATATGAGTTGATTTTTGAA
*
12935901 AAACATAAATTGAAAAAAAGACATTG
62 AAACAGAAATTGAAAAAAAGACATTG
12935927 AAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCACGCAATATGAGTTGATTTTTTTGAAAA
1 AAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCACGCAATATGAGTTGA--TTTTTGAAAA
* **
12935992 GCAGAAATTGAAAAGCAGACATTG
64 ACAGAAATTGAAAAAAAGACATTG
* *
12936016 AAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAAC
1 AAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCACGCAATATGAGTTGATTTTTGAAAAAC
12936081 AGAAATTGAAA
66 AGAAATTGAAA
12936092 TTACCTCAGC
Statistics
Matches: 150, Mismatches: 11, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
86 4 0.03
87 51 0.34
89 95 0.63
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.25
Consensus pattern (87 bp):
AAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCACGCAATATGAGTTGATTTTTGAAAAAC
AGAAATTGAAAAAAAGACATTG
Found at i:12936004 original size:14 final size:14
Alignment explanation
Indices: 12935985--12936019 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
12935975 GTTGATTTTT
12935985 TTGAAAAGCAGAAA
1 TTGAAAAGCAGAAA
*
12935999 TTGAAAAGCAGACA
1 TTGAAAAGCAGAAA
12936013 TTGAAAA
1 TTGAAAA
12936020 TACCTCAGCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.54, C:0.09, G:0.20, T:0.17
Consensus pattern (14 bp):
TTGAAAAGCAGAAA
Found at i:12936132 original size:73 final size:72
Alignment explanation
Indices: 12935999--12936158 Score: 248
Period size: 73 Copynumber: 2.2 Consensus size: 72
12935989 AAAGCAGAAA
*
12935999 TTGAAAAGCAGACATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAA-CAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGA
12936064 GTTGATTT
65 GTTGATTT
* * * *
12936072 TTGACAAACAGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCACCTCTTGCAATATGA
1 TTGA-AAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGA
12936137 GTTGATTT
65 GTTGATTT
*
12936145 TTGAAAATAGAAAT
1 TTGAAAACAGAAAT
12936159 AAACATCAAA
Statistics
Matches: 80, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
72 9 0.11
73 68 0.85
74 3 0.04
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.29
Consensus pattern (72 bp):
TTGAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAG
TTGATTT
Found at i:12945820 original size:50 final size:51
Alignment explanation
Indices: 12945766--12945864 Score: 130
Period size: 51 Copynumber: 2.0 Consensus size: 51
12945756 TTTTTATTTC
12945766 ATATT-GTTTCAAATTTTTT-TATTTTTAATTAAGATTTATAATTAATAAAT
1 ATATTAGTTTCAAATTTTTTAT-TTTTTAATTAAGATTTATAATTAATAAAT
* * ** *
12945816 ATATTATTTTCAAATTTTTTATTTTTTAATTCATCTTTTTAATTAATAA
1 ATATTAGTTTCAAATTTTTTATTTTTTAATTAAGATTTATAATTAATAA
12945865 CTTTTTTATT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
50 5 0.12
51 36 0.86
52 1 0.02
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (51 bp):
ATATTAGTTTCAAATTTTTTATTTTTTAATTAAGATTTATAATTAATAAAT
Found at i:12946428 original size:31 final size:34
Alignment explanation
Indices: 12946383--12946454 Score: 96
Period size: 35 Copynumber: 2.2 Consensus size: 34
12946373 CATCATTGGA
*
12946383 TATTATTATAGG-A-TATTA-TAAAATACATTGT
1 TATTATCATAGGAATTATTAGTAAAATACATTGT
*
12946414 TATTATCATTGGATATTATTAGTAAAATACATTGT
1 TATTATCATAGGA-ATTATTAGTAAAATACATTGT
12946449 TATTAT
1 TATTAT
12946455 AAAAACATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
31 10 0.29
33 1 0.03
34 5 0.14
35 19 0.54
ACGTcount: A:0.39, C:0.04, G:0.10, T:0.47
Consensus pattern (34 bp):
TATTATCATAGGAATTATTAGTAAAATACATTGT
Found at i:12946468 original size:17 final size:18
Alignment explanation
Indices: 12946396--12946471 Score: 68
Period size: 17 Copynumber: 4.3 Consensus size: 18
12946386 TATTATAGGA
12946396 TATTATAAAATACATTGT
1 TATTATAAAATACATTGT
* * ** *
12946414 TATTAT-CATTGGA-TAT
1 TATTATAAAATACATTGT
12946430 TATTAGTAAAATACATTGT
1 TATTA-TAAAATACATTGT
*
12946449 TATTATAAAA-ACATTTT
1 TATTATAAAATACATTGT
12946466 TATTAT
1 TATTAT
12946472 TTATTATAGT
Statistics
Matches: 44, Mismatches: 11, Indels: 7
0.71 0.18 0.11
Matches are distributed among these distances:
16 7 0.16
17 16 0.36
18 14 0.32
19 7 0.16
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.47
Consensus pattern (18 bp):
TATTATAAAATACATTGT
Found at i:12951565 original size:19 final size:19
Alignment explanation
Indices: 12951527--12951565 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
12951517 TCATACTACA
**
12951527 AAATATTTATTATTGTAAT
1 AAATATTTATTATTAAAAT
12951546 AAATATTTATTATTAAAAT
1 AAATATTTATTATTAAAAT
12951565 A
1 A
12951566 TTAATATTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (19 bp):
AAATATTTATTATTAAAAT
Found at i:12957382 original size:20 final size:20
Alignment explanation
Indices: 12957359--12957412 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 20
12957349 TAAATCTATT
12957359 TTAAATTTTATAA-TTATAAA
1 TTAAATTTTATAATTTA-AAA
*
12957379 TTAAATTATAGTAATTTAAAA
1 TTAAATTTTA-TAATTTAAAA
*
12957400 TT-AATTTAATAAT
1 TTAAATTTTATAAT
12957413 ATGATAGAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 4 0.14
20 14 0.48
21 8 0.28
22 3 0.10
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
TTAAATTTTATAATTTAAAA
Found at i:12957400 original size:21 final size:20
Alignment explanation
Indices: 12957359--12957412 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 20
12957349 TAAATCTATT
*
12957359 TTAAATTTTATAATTATAAA
1 TTAAATTATATAATTATAAA
12957379 TTAAATTATAGTAATT-TAAAA
1 TTAAATTATA-TAATTAT-AAA
*
12957400 TTAATTTA-ATAAT
1 TTAAATTATATAAT
12957413 ATGATAGAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
19 4 0.13
20 11 0.37
21 15 0.50
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
TTAAATTATATAATTATAAA
Found at i:12966671 original size:22 final size:22
Alignment explanation
Indices: 12966610--12966678 Score: 61
Period size: 22 Copynumber: 3.1 Consensus size: 22
12966600 ATGAAAAAAA
* * *
12966610 CTATTTTTTTAATATTATTTT-
1 CTATTATTTTACTACTATTTTG
*
12966631 CTTATTATTTT-CTCTCTATTTTG
1 C-TATTATTTTACT-ACTATTTTG
*
12966654 CTATTATTTTACTACTATATTG
1 CTATTATTTTACTACTATTTTG
12966676 CTA
1 CTA
12966679 CGATTTTATT
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
21 2 0.05
22 33 0.87
23 3 0.08
ACGTcount: A:0.22, C:0.13, G:0.03, T:0.62
Consensus pattern (22 bp):
CTATTATTTTACTACTATTTTG
Found at i:12966939 original size:12 final size:12
Alignment explanation
Indices: 12966909--12966941 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
12966899 TATATATTTT
12966909 AAAATT-ATATA
1 AAAATTAATATA
12966920 AAAA-TAATATA
1 AAAATTAATATA
12966931 AAAATTAATAT
1 AAAATTAATAT
12966942 GGGTGGGCCG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 13 0.65
12 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:12970401 original size:96 final size:99
Alignment explanation
Indices: 12970276--12970481 Score: 262
Period size: 96 Copynumber: 2.1 Consensus size: 99
12970266 GTTTTTAAAT
* * * ** *
12970276 TTTAGGG-TTTTAAGGAAAAAAATTAAATAAATTAGGGTTTAGTGTTTGTTAATTAAATTAATTA
1 TTTAGGGTTTTTAAGGAAAAAAATAAAATAAATTAGGATTTAGGGTTACTTAAGTAAATTAATTA
*
12970340 CT-AA-TTTT-AAAAAATTAGATTATGG-TTTAGTG
66 -TAAATTTTTAAAAAAATTAGATTA-GGATTTAGGG
* *
12970372 TTTATGGTTTTTAAGG-AAAAAATAAAATAAATTAGGATTTAGGGTTACTTGAGTAAATTAATTA
1 TTTAGGGTTTTTAAGGAAAAAAATAAAATAAATTAGGATTTAGGGTTACTTAAGTAAATTAATTA
12970436 TAAATTTTTAAAAAAATTAGATTAGGATTTTAGGG
66 TAAATTTTTAAAAAAATTAGATTAGGA-TTTAGGG
12970471 TTTAGGGTTTT
1 TTTAGGGTTTT
12970482 AGGGTATTTA
Statistics
Matches: 94, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
95 1 0.01
96 49 0.52
97 14 0.15
98 14 0.15
99 16 0.17
ACGTcount: A:0.39, C:0.01, G:0.17, T:0.42
Consensus pattern (99 bp):
TTTAGGGTTTTTAAGGAAAAAAATAAAATAAATTAGGATTTAGGGTTACTTAAGTAAATTAATTA
TAAATTTTTAAAAAAATTAGATTAGGATTTAGGG
Found at i:12970481 original size:15 final size:15
Alignment explanation
Indices: 12970457--12970486 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12970447 AAAAATTAGA
12970457 TTAGGATTTTAGGGT
1 TTAGGATTTTAGGGT
*
12970472 TTAGGGTTTTAGGGT
1 TTAGGATTTTAGGGT
12970487 ATTTAAGAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.00, G:0.37, T:0.47
Consensus pattern (15 bp):
TTAGGATTTTAGGGT
Found at i:12970926 original size:126 final size:126
Alignment explanation
Indices: 12970562--12971091 Score: 819
Period size: 126 Copynumber: 4.2 Consensus size: 126
12970552 AAAAGCTTCT
* * * * *
12970562 ACGTGGATGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAAATTTGAGAAGACGTGTCTGCGCAA
1 ACGTGGACGCTCTTTTGCTACAGTGGTCTCTAAAAAAATAATTTTGAGAAGACGTGTCTGCACAA
* * *
12970627 ATAGTGTCAAAAACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTAAAAGAAGCTCCA
66 ATAATGTCAAAAACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAGAAGCTCCC
* * * * **
12970688 ACGTGGACGCTCTTTTGCTACAGTAGTATCT-GAAAAATAATTTTGAGAAGACGTGACTGTGCAA
1 ACGTGGACGCTCTTTTGCTACAGTGGTCTCTAAAAAAATAATTTTGAGAAGACGTGTCTGCACAA
* * *
12970752 ATAGTGTAAAAAATGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAGAAGCTCCC
66 ATAATGTCAAAAACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAGAAGCTCCC
* *
12970813 ACGTGGACGCTCTTTTGCTACAGTGGTCTTTAAAAAAATAATTTTGAGAAGACGTGTCTGCATAA
1 ACGTGGACGCTCTTTTGCTACAGTGGTCTCTAAAAAAATAATTTTGAGAAGACGTGTCTGCACAA
* * *
12970878 ATAATGTCAAAAACGCTTCAAGCAGGATGCATTTTCAGCAAAATTACTGGAAGAAGCTCCC
66 ATAATGTCAAAAACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAGAAGCTCCC
* * *
12970939 ACGTGGATGCTCTTTTGCTACAGTGGTCTTTAAAAAAATAATTTTGAGAAGACGTGTCTGCATAA
1 ACGTGGACGCTCTTTTGCTACAGTGGTCTCTAAAAAAATAATTTTGAGAAGACGTGTCTGCACAA
*
12971004 ATAATGTCAAAAACGCTTCAAGCAGGATGCATTTTCAGCAAAAGTACTGAAAGAAGCTCCC
66 ATAATGTCAAAAACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAGAAGCTCCC
12971065 ACGTGGACGCTCTTTTGCTACAGTGGT
1 ACGTGGACGCTCTTTTGCTACAGTGGT
12971092 TTCTGAAATA
Statistics
Matches: 375, Mismatches: 28, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
125 114 0.30
126 261 0.70
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (126 bp):
ACGTGGACGCTCTTTTGCTACAGTGGTCTCTAAAAAAATAATTTTGAGAAGACGTGTCTGCACAA
ATAATGTCAAAAACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAGAAGCTCCC
Found at i:12974278 original size:116 final size:116
Alignment explanation
Indices: 12974103--12974483 Score: 690
Period size: 116 Copynumber: 3.3 Consensus size: 116
12974093 TTTATATTTT
* * *
12974103 ATTACATGAAATAATATAAAAATATTCAAAATATTGCTTTATTTAAAATAATTTTCATTTTATTA
1 ATTACATGAAATAATATAAAAATATTCAAAATGTTGCCTTATTTAAAATAATTTCCATTTTATTA
* * * *
12974168 AAAATGTAAAAGTAAATTATAATTACTTTATTTAAAACAACCTTTTATATT
66 AAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACCTTTTATCTA
*
12974219 ATCACATGAAATAATATAAAAATATTCAAAATGTTGCCTTATTTAAAATAATTTCCATTTTATTA
1 ATTACATGAAATAATATAAAAATATTCAAAATGTTGCCTTATTTAAAATAATTTCCATTTTATTA
12974284 AAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACCTTTTATCTA
66 AAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACCTTTTATCTA
12974335 ATTACATGAAATAATATAAAAATATTCAAAATGTTGCCTTATTTAAAATAATTTCCATTTTATTA
1 ATTACATGAAATAATATAAAAATATTCAAAATGTTGCCTTATTTAAAATAATTTCCATTTTATTA
12974400 AAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACCTTTTATCTA
66 AAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACCTTTTATCTA
12974451 ATTACATGAAATAATATAAAAATATTCAAAATG
1 ATTACATGAAATAATATAAAAATATTCAAAATG
12974484 GTCGTCGACA
Statistics
Matches: 256, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
116 256 1.00
ACGTcount: A:0.48, C:0.09, G:0.04, T:0.40
Consensus pattern (116 bp):
ATTACATGAAATAATATAAAAATATTCAAAATGTTGCCTTATTTAAAATAATTTCCATTTTATTA
AAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACCTTTTATCTA
Found at i:12976658 original size:30 final size:31
Alignment explanation
Indices: 12976624--12976692 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 31
12976614 AAAAATTAAC
*
12976624 GAGAGTTTTGAGAGGAATTTAAGAGAA-ATT
1 GAGAGATTTGAGAGGAATTTAAGAGAATATT
*
12976654 GAGAGATTTGAGAGGAATTTGAGAGAATATT
1 GAGAGATTTGAGAGGAATTTAAGAGAATATT
*
12976685 GAAAGATT
1 GAGAGATT
12976693 GAAGATTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
30 25 0.71
31 10 0.29
ACGTcount: A:0.41, C:0.00, G:0.30, T:0.29
Consensus pattern (31 bp):
GAGAGATTTGAGAGGAATTTAAGAGAATATT
Found at i:12976677 original size:20 final size:19
Alignment explanation
Indices: 12976630--12976679 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
12976620 TAACGAGAGT
12976630 TTTGAGAGGAATTTAAGAGAA
1 TTTGAGA-G-ATTTAAGAGAA
* *
12976651 ATTGAGAGATTTGAGAGGAA
1 TTTGAGAGATTTAAGA-GAA
12976671 TTTGAGAGA
1 TTTGAGAGA
12976680 ATATTGAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 7 0.28
20 12 0.48
21 6 0.24
ACGTcount: A:0.40, C:0.00, G:0.32, T:0.28
Consensus pattern (19 bp):
TTTGAGAGATTTAAGAGAA
Found at i:12976686 original size:11 final size:10
Alignment explanation
Indices: 12976630--12976686 Score: 62
Period size: 11 Copynumber: 5.5 Consensus size: 10
12976620 TAACGAGAGT
12976630 TTTGAGAGGAA
1 TTTGAGA-GAA
*
12976641 TTTAAGAGAA
1 TTTGAGAGAA
*
12976651 ATTGAGAG-A
1 TTTGAGAGAA
12976660 TTTGAGAGGAA
1 TTTGAGA-GAA
12976671 TTTGAGAGAA
1 TTTGAGAGAA
12976681 TATTGA
1 T-TTGA
12976687 AAGATTGAAG
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
9 7 0.18
10 14 0.36
11 18 0.46
ACGTcount: A:0.40, C:0.00, G:0.30, T:0.30
Consensus pattern (10 bp):
TTTGAGAGAA
Found at i:12986922 original size:20 final size:22
Alignment explanation
Indices: 12986892--12986939 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
12986882 GAACATGCTG
*
12986892 TAAATTGAAAG-TTTTTGATAGA
1 TAAA-TGAAAGATTATTGATAGA
12986914 -AAATGAAAGATTATTGATAGA
1 TAAATGAAAGATTATTGATAGA
12986935 TAAAT
1 TAAAT
12986940 CATTTTTACA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 6 0.26
21 13 0.57
22 4 0.17
ACGTcount: A:0.48, C:0.00, G:0.17, T:0.35
Consensus pattern (22 bp):
TAAATGAAAGATTATTGATAGA
Found at i:12987867 original size:33 final size:33
Alignment explanation
Indices: 12987622--12987866 Score: 210
Period size: 33 Copynumber: 7.5 Consensus size: 33
12987612 TACCCAAATG
* ** *
12987622 GTACAACTTGAAAAGGCTATGTACACTTTGTGT
1 GTACCACTTGAAAAGGAAAGGTACACTTTGTGT
* *
12987655 GTA-CACTTGGAAAGGAAAGGTATACTTTGTGT
1 GTACCACTTGAAAAGGAAAGGTACACTTTGTGT
* * * *
12987687 ATAACA-TATGAAAATGAAAGGTATACTTTGTGT
1 GTACCACT-TGAAAAGGAAAGGTACACTTTGTGT
* *
12987720 ATACCA-TATGAAAAGGAAAGGTATACTTTGTGT
1 GTACCACT-TGAAAAGGAAAGGTACACTTTGTGT
* * * *
12987753 ATACCACTTGAAAAGGAAAGGTACACTATATGC
1 GTACCACTTGAAAAGGAAAGGTACACTTTGTGT
** * * *
12987786 GTACC-CTTGAAAAGGTTATGTGCACTTTGAGT
1 GTACCACTTGAAAAGGAAAGGTACACTTTGTGT
* * ** *
12987818 GTACAAATTGAAAAGGGTATGTACACTTTGTGT
1 GTACCACTTGAAAAGGAAAGGTACACTTTGTGT
12987851 GTACCACTTGAAAAGG
1 GTACCACTTGAAAAGG
12987867 GAATGTGCAC
Statistics
Matches: 177, Mismatches: 31, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
32 49 0.28
33 127 0.72
34 1 0.01
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.30
Consensus pattern (33 bp):
GTACCACTTGAAAAGGAAAGGTACACTTTGTGT
Found at i:12987886 original size:33 final size:33
Alignment explanation
Indices: 12987786--12987887 Score: 125
Period size: 33 Copynumber: 3.1 Consensus size: 33
12987776 CACTATATGC
*
12987786 GTACC-CTTGAAAAGGTTATGTGCACTTTGAGT
1 GTACCACTTGAAAAGGGTATGTGCACTTTGAGT
* * * *
12987818 GTACAAATTGAAAAGGGTATGTACACTTTGTGT
1 GTACCACTTGAAAAGGGTATGTGCACTTTGAGT
* * *
12987851 GTACCACTTGAAAAGGGAATGTGCACCTCGAGT
1 GTACCACTTGAAAAGGGTATGTGCACTTTGAGT
12987884 GTAC
1 GTAC
12987888 AATTATAAAA
Statistics
Matches: 57, Mismatches: 12, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
32 4 0.07
33 53 0.93
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.29
Consensus pattern (33 bp):
GTACCACTTGAAAAGGGTATGTGCACTTTGAGT
Found at i:12994359 original size:40 final size:40
Alignment explanation
Indices: 12993643--12994357 Score: 1223
Period size: 40 Copynumber: 17.9 Consensus size: 40
12993633 CGAATACACG
* * * ** *
12993643 TCACTAGCATGATTGCTCTTCGGGACCTAGCCCGAATATA
1 TCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGGTACA
* * ** * * *
12993683 ACACCAGCACGAATGCTCTTCGGGGTTTAGCACGGATATA
1 TCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGGTACA
* * *
12993723 TCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGATACA
1 TCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGGTACA
* *
12993763 TCACTAGCACGAATGCTCTTCGAGACTTAGCCCGGATACA
1 TCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGGTACA
*
12993803 TCAGTAGCACGAATGCTCTTCGGGACTTAGCCCGGGTACA
1 TCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGGTACA
12993843 TCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGGTACA
1 TCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGGTACA
12993883 TCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGGTACA
1 TCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGGTACA
12993923 TCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGGTACA
1 TCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGGTACA
12993963 TCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGGTACA
1 TCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGGTACA
12994003 TCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGGTACA
1 TCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGGTACA
12994043 TCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGGTACA
1 TCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGGTACA
12994083 TCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGGTACA
1 TCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGGTACA
* *
12994123 TCACTAGCACGAATACTCTTCGAGACTTAGCCCGGGTACA
1 TCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGGTACA
12994163 TCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGGTACA
1 TCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGGTACA
*
12994203 TCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATACA
1 TCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGGTACA
12994243 TCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGGTACA
1 TCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGGTACA
*
12994283 TCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATACA
1 TCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGGTACA
12994323 TCACTAGCACGAATGCTCTTCGGGACTTAGCCCGG
1 TCACTAGCACGAATGCTCTTCGGGACTTAGCCCGG
12994358 ATCATCGTCG
Statistics
Matches: 644, Mismatches: 31, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 644 1.00
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.23
Consensus pattern (40 bp):
TCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGGTACA
Found at i:13001977 original size:40 final size:40
Alignment explanation
Indices: 13001892--13001981 Score: 101
Period size: 40 Copynumber: 2.2 Consensus size: 40
13001882 AGTATAAAAT
* * *
13001892 TTTTATAAAAATTATAAGAAAATCATTAAAATTTCTTAAA
1 TTTTATAAAAATTATAAGAAAATAATTAAAATATCATAAA
* * * *
13001932 ATTTATAATAATTATTAGAAATTAATTAAAA-ATCATAGAA
1 TTTTATAAAAATTATAAGAAAATAATTAAAATATCATA-AA
13001972 TTTTATAAAA
1 TTTTATAAAA
13001982 GTAATTTATT
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
39 4 0.10
40 36 0.90
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.40
Consensus pattern (40 bp):
TTTTATAAAAATTATAAGAAAATAATTAAAATATCATAAA
Found at i:13002109 original size:26 final size:27
Alignment explanation
Indices: 13002080--13002138 Score: 111
Period size: 26 Copynumber: 2.2 Consensus size: 27
13002070 AAGAAATTAT
13002080 TTTTTTATAAAATTTCAT-AAAAAATA
1 TTTTTTATAAAATTTCATAAAAAAATA
13002106 TTTTTTATAAAATTTCATAAAAAAATA
1 TTTTTTATAAAATTTCATAAAAAAATA
13002133 TTTTTT
1 TTTTTT
13002139 TTATTTTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 18 0.56
27 14 0.44
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (27 bp):
TTTTTTATAAAATTTCATAAAAAAATA
Found at i:13003019 original size:21 final size:21
Alignment explanation
Indices: 13002994--13003036 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
13002984 ATTAACAAAA
13002994 AAGATAAAATTAAATAGTTAG
1 AAGATAAAATTAAATAGTTAG
13003015 AAGATAAAATTAAATAGTTAG
1 AAGATAAAATTAAATAGTTAG
13003036 A
1 A
13003037 TGATCATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.58, C:0.00, G:0.14, T:0.28
Consensus pattern (21 bp):
AAGATAAAATTAAATAGTTAG
Found at i:13009128 original size:20 final size:20
Alignment explanation
Indices: 13009099--13009143 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
13009089 CTTACATTGA
* *
13009099 CATTTTTAACAA-TTTTATT
1 CATTTGTAACAACTTTGATT
13009118 CCATTTGTAACAACTTTGATT
1 -CATTTGTAACAACTTTGATT
13009139 CATTT
1 CATTT
13009144 AATTTAAGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.29, C:0.16, G:0.04, T:0.51
Consensus pattern (20 bp):
CATTTGTAACAACTTTGATT
Found at i:13009284 original size:5 final size:5
Alignment explanation
Indices: 13009276--13009318 Score: 86
Period size: 5 Copynumber: 8.6 Consensus size: 5
13009266 TAATTTAATT
13009276 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TAT
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TAT
13009319 CTATCTCATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 38 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATTA
Found at i:13020788 original size:26 final size:24
Alignment explanation
Indices: 13020759--13020817 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 24
13020749 GAAATTTATT
13020759 TAAAAGTTATTTTATGATAAAATACA
1 TAAAAGTTATTTTAT--TAAAATACA
*
13020785 T-AAAGAT-TTTTATTAAAATACA
1 TAAAAGTTATTTTATTAAAATACA
*
13020807 TACAAAATTAT
1 TA-AAAGTTAT
13020818 AAAAATATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
22 10 0.37
24 10 0.37
25 6 0.22
26 1 0.04
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.39
Consensus pattern (24 bp):
TAAAAGTTATTTTATTAAAATACA
Found at i:13022219 original size:20 final size:19
Alignment explanation
Indices: 13022173--13022219 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 19
13022163 GTAATTCATG
13022173 TTTAATTGCTGAATGGAGT
1 TTTAATTGCTGAATGGAGT
* *
13022192 TTTGAATTGGTAGAATTGAGT
1 TTT-AATTGCT-GAATGGAGT
13022213 TTTAATT
1 TTTAATT
13022220 TTAAGAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 3 0.12
20 10 0.42
21 11 0.46
ACGTcount: A:0.28, C:0.02, G:0.23, T:0.47
Consensus pattern (19 bp):
TTTAATTGCTGAATGGAGT
Found at i:13026029 original size:29 final size:27
Alignment explanation
Indices: 13025995--13026076 Score: 74
Period size: 29 Copynumber: 2.9 Consensus size: 27
13025985 CGTTGAGGGT
13025995 TAAATTTATTTATTTTTTAGAATTAGGA
1 TAAATTTATTTATTTTTTAGAATTA-GA
* ** * * *
13026023 CTAAATTGATAGAATTTATAAATATTAGA
1 -TAAATTTATTTATTTTTTAGA-ATTAGA
*
13026052 GAAATTTATTTATTTTTTAGAATTA
1 TAAATTTATTTATTTTTTAGAATTA
13026077 AAATCAAATT
Statistics
Matches: 39, Mismatches: 13, Indels: 4
0.70 0.23 0.07
Matches are distributed among these distances:
27 4 0.10
28 14 0.36
29 17 0.44
30 4 0.10
ACGTcount: A:0.40, C:0.01, G:0.10, T:0.49
Consensus pattern (27 bp):
TAAATTTATTTATTTTTTAGAATTAGA
Found at i:13026063 original size:57 final size:57
Alignment explanation
Indices: 13025996--13026111 Score: 182
Period size: 57 Copynumber: 2.0 Consensus size: 57
13025986 GTTGAGGGTT
**
13025996 AAATTTATTTATTTTTTAGAATTAGGA-CTAAATT-GATAGAATTTATAAATATTAGAG
1 AAATTTATTTATTTTTTAGAATTAAAATC-AAATTAG-TAGAATTTATAAATATTAGAG
13026053 AAATTTATTTATTTTTTAGAATTAAAATCAAATTAGTAGAATTTATAAATATTAGAG
1 AAATTTATTTATTTTTTAGAATTAAAATCAAATTAGTAGAATTTATAAATATTAGAG
13026110 AA
1 AA
13026112 TTAAATTTAT
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
57 53 0.96
58 2 0.04
ACGTcount: A:0.45, C:0.02, G:0.10, T:0.43
Consensus pattern (57 bp):
AAATTTATTTATTTTTTAGAATTAAAATCAAATTAGTAGAATTTATAAATATTAGAG
Found at i:13036996 original size:120 final size:121
Alignment explanation
Indices: 13036783--13037010 Score: 440
Period size: 120 Copynumber: 1.9 Consensus size: 121
13036773 ATGCCATTGA
13036783 TTCAATATATCTAATCATTAGCCTTTCTTTGGATATGAAATTAAAAATAGAAAAAATTAAAATCA
1 TTCAATATATCTAATCATTAGCCTTTCTTTGGATATGAAATTAAAAATAGAAAAAATTAAAATCA
*
13036848 GTAATAAAATATGTATTTAGAGTTATAG-CTAGATTTGATCATTGGCTCGAAAGTC
66 GTAATAAAATATGTATTTAGAGTTATAGCCTAGAGTTGATCATTGGCTCGAAAGTC
13036903 TTCAATATATCTAATCATTAGCCTTTCTTTGGATATGAAATTAAAAATAGAAAAAATTAAAATCA
1 TTCAATATATCTAATCATTAGCCTTTCTTTGGATATGAAATTAAAAATAGAAAAAATTAAAATCA
13036968 GTAATAAAATATGTATTTAGAGTTATAGCCTAGAGTTGATCAT
66 GTAATAAAATATGTATTTAGAGTTATAGCCTAGAGTTGATCAT
13037011 GATCAGTAAT
Statistics
Matches: 106, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
120 93 0.88
121 13 0.12
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.36
Consensus pattern (121 bp):
TTCAATATATCTAATCATTAGCCTTTCTTTGGATATGAAATTAAAAATAGAAAAAATTAAAATCA
GTAATAAAATATGTATTTAGAGTTATAGCCTAGAGTTGATCATTGGCTCGAAAGTC
Found at i:13037311 original size:22 final size:22
Alignment explanation
Indices: 13037272--13037330 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
13037262 GTTTTAAGAA
*
13037272 TTGTTTTAGTA-TTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
13037293 TTGTTTTAATATTTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
* *
13037315 GT-TTTTAA-ATATATTT
1 TTGTTTTAATATTTATTT
13037331 GATTTATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.21
21 16 0.47
22 11 0.32
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (22 bp):
TTGTTTTAATATTTATTTTTAT
Found at i:13037347 original size:26 final size:24
Alignment explanation
Indices: 13037301--13037349 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 24
13037291 ATTTGTTTTA
*
13037301 ATATTTATTTTTATGTTTTTAAAT
1 ATATTTATTTTTATATTTTTAAAT
13037325 ATATTTGATTTATTATATTTTTAAA
1 ATATTT-ATTT-TTATATTTTTAAA
13037350 ATTTTTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.27
25 4 0.18
26 12 0.55
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (24 bp):
ATATTTATTTTTATATTTTTAAAT
Found at i:13037360 original size:25 final size:26
Alignment explanation
Indices: 13037304--13037361 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 26
13037294 TGTTTTAATA
*
13037304 TTTATTT-TTATGTTTTTAAATATAT
1 TTTATTTATTATATTTTTAAATATAT
* *
13037329 TTGATTTATTATATTTTTAAA-ATTT
1 TTTATTTATTATATTTTTAAATATAT
13037354 TTTATTTA
1 TTTATTTA
13037362 ATGAAATAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 16 0.57
26 12 0.43
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.67
Consensus pattern (26 bp):
TTTATTTATTATATTTTTAAATATAT
Found at i:13044610 original size:51 final size:51
Alignment explanation
Indices: 13044512--13044610 Score: 112
Period size: 51 Copynumber: 1.9 Consensus size: 51
13044502 TAGAAGACGC
* * * * *
13044512 TGATTGTAAGGAGCCTGCATCATCAAAAGATGAAAAGGATGGGGATGCAAG
1 TGATTGTAAGAAGCCTCCACCATCAAAAGATGAAAAGAATGAGGATGCAAG
*
13044563 TGATTGTAAGAAGCCTCCACCATCAGAAA-ATGGAAAA-AATGATGATGC
1 TGATTGTAAGAAGCCTCCACCATCA-AAAGAT-GAAAAGAATGAGGATGC
13044611 TGATGATGCC
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
51 32 0.80
52 8 0.20
ACGTcount: A:0.39, C:0.14, G:0.26, T:0.20
Consensus pattern (51 bp):
TGATTGTAAGAAGCCTCCACCATCAAAAGATGAAAAGAATGAGGATGCAAG
Found at i:13047085 original size:44 final size:41
Alignment explanation
Indices: 13047021--13047106 Score: 136
Period size: 44 Copynumber: 2.0 Consensus size: 41
13047011 GAATTCTAGT
13047021 AGTTACAGTATGTGAAGTTGAAAGAGGGTGAAAGAGGTGAG
1 AGTTACAGTATGTGAAGTTGAAAGAGGGTGAAAGAGGTGAG
*
13047062 ANNNGTTACAGTATGTGAAGTTGAAAGAGTGTGAAAGAGGTGAG
1 A---GTTACAGTATGTGAAGTTGAAAGAGGGTGAAAGAGGTGAG
13047106 A
1 A
13047107 ATAATAAATA
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
41 1 0.02
44 40 0.98
ACGTcount: A:0.36, C:0.02, G:0.36, T:0.22
Consensus pattern (41 bp):
AGTTACAGTATGTGAAGTTGAAAGAGGGTGAAAGAGGTGAG
Found at i:13050696 original size:17 final size:17
Alignment explanation
Indices: 13050674--13050708 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
13050664 AGTTTCTGCA
13050674 ACTTCTTTCATGTTTCT
1 ACTTCTTTCATGTTTCT
13050691 ACTTCTTTCATGTTTCT
1 ACTTCTTTCATGTTTCT
13050708 A
1 A
13050709 AATAACTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.14, C:0.23, G:0.06, T:0.57
Consensus pattern (17 bp):
ACTTCTTTCATGTTTCT
Found at i:13053482 original size:125 final size:123
Alignment explanation
Indices: 13053300--13053703 Score: 393
Period size: 127 Copynumber: 3.2 Consensus size: 123
13053290 CCCAAACGGT
** * * * * * *
13053300 AAATCGAAACCCAGCA-GATTGGGCACGATTTATCGAATTTTCAAATACGAAACATTGCCTCATT
1 AAATCGAAACCCAGCACGATTGGGCACGATTTCCCAAACTTCCAAACACGAAATATTGCCTCGTT
* *
13053364 TTAATTTGAGAAAACACGTATGAAATTTCAAAAGGATATTCTGTATTTTAGTCAACTGGA
66 TTAATTT-AAAAAACATGTATGAAATTTCAAAAGGATATT-TGTATTTTAGTCAACTGGA
* * *
13053424 AAATTGAAGCCCAGCACAATTGGGCACGATTTCCCAAACTTCCAAACACGAAATATTGCCTCGTT
1 AAATCGAAACCCAGCACGATTGGGCACGATTTCCCAAACTTCCAAACACGAAATATTGCCTCGTT
* * * *
13053489 TT-ATTTTAAGAACATGTGGATGAAATTTCAAAAAAGGATATTTCATATTTTAGTCGAA-TAGA
66 TTAATTTAAAAAACATGT--ATGAAATTTC--AAAAGGATATTT-GTATTTTAGTC-AACTGGA
* * * *** *
13053551 AAATTGAAGCCTAGCACGATTGGGCACGGCCTCCCAAACTTCCAAACACGAAGTATTGCCTCGTT
1 AAATCGAAACCCAGCACGATTGGGCACGATTTCCCAAACTTCCAAACACGAAATATTGCCTCGTT
* ** * * *
13053616 TTAATTTTAAAAAAACATGGACAAAATTTCCAAAGGATATTTTGTATTTTAGCTGAAC-GAA
66 TTAA-TTT-AAAAAACATGTATGAAATTTCAAAAGGATA-TTTGTATTTTAG-TCAACTGGA
*
13053677 AAATCGAAACCCAGCACGATCGGGCAC
1 AAATCGAAACCCAGCACGATTGGGCAC
13053704 AACCCCTCGA
Statistics
Matches: 230, Mismatches: 37, Indels: 24
0.79 0.13 0.08
Matches are distributed among these distances:
123 7 0.03
124 18 0.08
125 51 0.22
126 43 0.19
127 89 0.39
128 11 0.05
129 3 0.01
130 8 0.03
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.28
Consensus pattern (123 bp):
AAATCGAAACCCAGCACGATTGGGCACGATTTCCCAAACTTCCAAACACGAAATATTGCCTCGTT
TTAATTTAAAAAACATGTATGAAATTTCAAAAGGATATTTGTATTTTAGTCAACTGGA
Found at i:13054510 original size:74 final size:76
Alignment explanation
Indices: 13054388--13054536 Score: 266
Period size: 74 Copynumber: 2.0 Consensus size: 76
13054378 AACAAATATA
*
13054388 AAAGAAGGTATTTACAAAAAAAAAAGTGATATGAAAAGAAAAGAAATAATGTATATGGAATAAAG
1 AAAGAAGGTATTTACAAAAAAAAAAGTAATATGAAAAGAAAAGAAATAATGTATATGGAATAAAG
13054453 CTAATTTTATT
66 CTAATTTTATT
*
13054464 AAAGAAGGTATTTAC-AAAAAAAAA-TAATATGAAAAGAAAAGAAATAATGTATATGGAATAGAG
1 AAAGAAGGTATTTACAAAAAAAAAAGTAATATGAAAAGAAAAGAAATAATGTATATGGAATAAAG
13054527 CTAATTTTAT
66 CTAATTTTAT
13054537 CATAAATTAT
Statistics
Matches: 71, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
74 47 0.66
75 9 0.13
76 15 0.21
ACGTcount: A:0.56, C:0.03, G:0.15, T:0.26
Consensus pattern (76 bp):
AAAGAAGGTATTTACAAAAAAAAAAGTAATATGAAAAGAAAAGAAATAATGTATATGGAATAAAG
CTAATTTTATT
Found at i:13055136 original size:21 final size:21
Alignment explanation
Indices: 13055095--13055137 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
13055085 CATTCTGCCA
*
13055095 TTTTTTTAAAAAGACCCTTTT
1 TTTTTTTAAAAAGACCATTTT
*
13055116 TTTTTTTGAAAA-ACTCATTTT
1 TTTTTTTAAAAAGAC-CATTTT
13055137 T
1 T
13055138 CTATTGTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.28, C:0.12, G:0.05, T:0.56
Consensus pattern (21 bp):
TTTTTTTAAAAAGACCATTTT
Found at i:13056224 original size:44 final size:44
Alignment explanation
Indices: 13056088--13056272 Score: 152
Period size: 44 Copynumber: 4.2 Consensus size: 44
13056078 CGATACATGG
*
13056088 AGATAAGATCTGTAATTTTCAGTCTACTTCCTGCAACTTCAGGA
1 AGATAAGATCTGTAATTTTCAGTCTGCTTCCTGCAACTTCAGGA
* * **
13056132 AGATAAGA-CTAGTAA--CTAAGATCTGC-TCCATAGTTGA-TAT-ATGG-
1 AGATAAGATCT-GTAATTTTCAG-TCTGCTTCC-T-G-CAACT-TCA-GGA
13056176 AGATAAGATCTGTAATTTTCAGTCTGCTTCCTGCAACTTCAGGA
1 AGATAAGATCTGTAATTTTCAGTCTGCTTCCTGCAACTTCAGGA
* * * *
13056220 AGATAAGACCTGCT-ATCTTCAGTCTGCTCCACTGCAACTTCAGGG
1 AGATAAGATCTG-TAATTTTCAGTCTGCTTC-CTGCAACTTCAGGA
13056265 AGATAAGA
1 AGATAAGA
13056273 CTTACTATCT
Statistics
Matches: 112, Mismatches: 13, Indels: 31
0.72 0.08 0.20
Matches are distributed among these distances:
42 6 0.05
43 11 0.10
44 55 0.49
45 34 0.30
46 6 0.05
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (44 bp):
AGATAAGATCTGTAATTTTCAGTCTGCTTCCTGCAACTTCAGGA
Found at i:13056506 original size:223 final size:222
Alignment explanation
Indices: 13056237--13056808 Score: 635
Period size: 223 Copynumber: 2.6 Consensus size: 222
13056227 ACCTGCTATC
* * * * * *
13056237 TTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTACTATCTTTAGTTTGCTCTACTACAA
1 TTCAGTCTGCTTC-CTGCAACTTCAGGAAGATAAGACTTGCTATCTTTAGTCTGCTCCACTGCAA
* * *
13056302 CTTCAGAGAGACAAGACTTAGT-ATCTTTAG-TCTGCTCCACT-G-CAACTTCAGGGAGATAAG-
65 CTTCAGGGAGATAAGACTT-GTCA--TTTAGATCTGCTCCA-TAGTCAA-TACAGGGAGATAAGA
* * * * **
13056362 GCTGGT-GGCTGAAATCTGC-TCCATAGTCGA-TACATGG-AGATAGGACTCGCCATTTTTTATC
125 GCT-ATAAGCTGAAATCTGCTTCC-T-G-CAACTACA-GGAAGATAAGACTCGCCATTTTCGATC
*
13056423 TACTCCATAGCCGATACATGGAGATAAGATCTATAATT
185 TACTCCATAGCCGATACATAGAGATAAGATCTATAATT
*
13056461 TTCAGTCTGCTTCCTGCAACTTCAGGAAGATAAGACTTGCTATCTTCAGTCTGCTCCACTGCAAC
1 TTCAGTCTGCTTCCTGCAACTTCAGGAAGATAAGACTTGCTATCTTTAGTCTGCTCCACTGCAAC
* * * *
13056526 TTCAGGGAGATAAGACTTGTCATTTCGATCTGCTCCATAGTCGATACATGGAGATAAGATCTATA
66 TTCAGGGAGATAAGACTTGTCATTTAGATCTGCTCCATAGTCAATACAGGGAGATAAGAGCTAT-
** ** * * *
13056591 AATTTTCAGTCTGCTTCCTGCAACTTCAGGAAGATAAGACTCGCCATTTTCGATCTGCTCCATAG
130 AAGCTGAAATCTGCTTCCTGCAACTACAGGAAGATAAGACTCGCCATTTTCGATCTACTCCATAG
*
13056656 CCGATACATAGAGATAAGATCTGTAATT
195 CCGATACATAGAGATAAGATCTATAATT
13056684 TTCAGTCTGCTTCCTGCAACTTCAGGAAGATAAGACTTGCTAT-TTTCAGTCTGCTCCACTGCAA
1 TTCAGTCTGCTTCCTGCAACTTCAGGAAGATAAGACTTGCTATCTTT-AGTCTGCTCCACTGCAA
* * * *
13056748 CTTCAGGGAGATAAGACTTGACATTTTCGATCTGCTCCATAG-CAGATATATGGAGATAAGA
65 CTTCAGGGAGATAAGACTTGTCA-TTTAGATCTGCTCCATAGTCA-ATACAGGGAGATAAGA
13056809 TCTGTAAATT
Statistics
Matches: 302, Mismatches: 33, Indels: 26
0.84 0.09 0.07
Matches are distributed among these distances:
221 5 0.02
222 31 0.10
223 210 0.70
224 53 0.18
225 3 0.01
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (222 bp):
TTCAGTCTGCTTCCTGCAACTTCAGGAAGATAAGACTTGCTATCTTTAGTCTGCTCCACTGCAAC
TTCAGGGAGATAAGACTTGTCATTTAGATCTGCTCCATAGTCAATACAGGGAGATAAGAGCTATA
AGCTGAAATCTGCTTCCTGCAACTACAGGAAGATAAGACTCGCCATTTTCGATCTACTCCATAGC
CGATACATAGAGATAAGATCTATAATT
Found at i:13056648 original size:134 final size:132
Alignment explanation
Indices: 13056105--13056652 Score: 492
Period size: 134 Copynumber: 4.1 Consensus size: 132
13056095 ATCTGTAATT
* * * * * ** *
13056105 TTCAGTCTACTTC-CTGCAACTTCAGGAAGATAAGACTAGTAACTAAGATCTGCTCCATAGTTGA
1 TTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTCA-TTTGATCTGCTCCATAGTCGA
* *
13056169 TATATGGAGATAAGATCTGTAATTTTCAGTCTGCTTCCTGCAACTTCAGGAAGATAAGAC-CTGC
65 TACATGGAGATAAGATCTATAATTTTCAGTCTGCTTCCTGCAACTTCAGGAAGATAAGACTC-GC
13056233 TATC
129 TATC
* * * *
13056237 TTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTT-ACTATCTTTAGTTTGCT-C-TACTA
1 TTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTC-AT-TTGA-TCTGCTCCATAGT-
* * * * *
13056299 CAACTTCA-GAGAGACAAGA-CT-TAGTATCTTT-AGTCTGCTCCACTGCAACTTCAGGGAGATA
62 CGA-TACATG-GAGATAAGATCTATA--AT-TTTCAGTCTGCTTC-CTGCAACTTCAGGAAGATA
* * **
13056360 AGGCT-GGTGGC
121 AGACTCGCTATC
** * * * * * * * * * *
13056371 TGAAATCTGCTCCA-TAGTCGA-TACATGGAGATAGGACTCGCCATTTTTTATCTACTCCATAGC
1 TTCAGTCTGCTCCACT-G-CAACTTCAGGGAGATAAGACTTGTCA--TTTGATCTGCTCCATAGT
*
13056434 CGATACATGGAGATAAGATCTATAATTTTCAGTCTGCTTCCTGCAACTTCAGGAAGATAAGACTT
62 CGATACATGGAGATAAGATCTATAATTTTCAGTCTGCTTCCTGCAACTTCAGGAAGATAAGACTC
13056499 GCTATC
127 GCTATC
13056505 TTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTCATTTCGATCTGCTCCATAGTCGA
1 TTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTCATTT-GATCTGCTCCATAGTCGA
13056570 TACATGGAGATAAGATCTATAAATTTTCAGTCTGCTTCCTGCAACTTCAGGAAGATAAGACTCGC
65 TACATGGAGATAAGATCTAT-AATTTTCAGTCTGCTTCCTGCAACTTCAGGAAGATAAGACTCGC
* *
13056635 CATT
129 TATC
13056639 TTC-GATCTGCTCCA
1 TTCAG-TCTGCTCCA
13056653 TAGCCGATAC
Statistics
Matches: 328, Mismatches: 59, Indels: 56
0.74 0.13 0.13
Matches are distributed among these distances:
132 20 0.06
133 94 0.29
134 171 0.52
135 38 0.12
136 5 0.02
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (132 bp):
TTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTCATTTGATCTGCTCCATAGTCGAT
ACATGGAGATAAGATCTATAATTTTCAGTCTGCTTCCTGCAACTTCAGGAAGATAAGACTCGCTA
TC
Found at i:13056670 original size:134 final size:134
Alignment explanation
Indices: 13056176--13057166 Score: 668
Period size: 134 Copynumber: 7.4 Consensus size: 134
13056166 TGATATATGG
* * * * *
13056176 AGATAAGA-TCTGTAATTTTCAGTCTGCTTC-CTGCAACTTCAGGAAGATAAGACCTGCTATCTT
1 AGATAAGACT-TGCAATTTTCAGTCTGCTCCACTGCAACTTCAGGAAGATAAGACTTGCCATTTT
* * * *
13056239 C-AGTCTGCTCCACT-G-CAACTTCAGGGAGATAAGA-CT-TACTATCTTT-AGTTTGCTCTACT
65 CGA-TCTGCTCCA-TAGCCGA-TACATGGAGATAAGATCTGTA--AT-TTTCAGTCTGCTC--CT
*
13056298 A-CAACTTCA-GA
122 AGCAACTACAGGA
* * * * *
13056309 GAGACAAGACTTAG-TATCTTT-AGTCTGCTCCACTGCAACTTCAGGGAGATAAGGCTGGTGGC-
1 -AGATAAGACTT-GCAAT-TTTCAGTCTGCTCCACTGCAACTTCAGGAAGATAAGACT--TGCCA
*** * * * * * *
13056371 --TGAAATCTGCTCCATAGTCGATACATGGAGATAGGA-CTCGCCATTTTTTA-TCTACTCCATA
61 TTTTCGATCTGCTCCATAGCCGATACATGGAGATAAGATCT-G-TAATTTTCAGTCTGCTCC-TA
*
13056432 GCCGA-TACATGG-
123 G-CAACTACA-GGA
* * *
13056444 AGATAAGATCTAT--AATTTTCAGTCTGCTTC-CTGCAACTTCAGGAAGATAAGACTTGCTATCT
1 AGATAAGA-CT-TGCAATTTTCAGTCTGCTCCACTGCAACTTCAGGAAGATAAGACTTGCCATTT
* * * *
13056506 TC-AGTCTGCTCCACT-G-CAACTTCAGGGAGATAAGA-CTTGTCA-TTTC-GATCTGCTCCATA
64 TCGA-TCTGCTCCA-TAGCCGA-TACATGGAGATAAGATC-TGTAATTTTCAG-TCTGCTCC-TA
*
13056565 GTCGA-TACATGG-
123 G-CAACTACA-GGA
* * *
13056577 AGATAAGATCTAT-AAATTTTCAGTCTGCTTC-CTGCAACTTCAGGAAGATAAGACTCGCCATTT
1 AGATAAGA-CT-TGCAATTTTCAGTCTGCTCCACTGCAACTTCAGGAAGATAAGACTTGCCATTT
*
13056640 TCGATCTGCTCCATAGCCGATACATAGAGATAAGATCTGTAATTTTCAGTCTGCTTCCT-GCAAC
64 TCGATCTGCTCCATAGCCGATACATGGAGATAAGATCTGTAATTTTCAGTCTGC-TCCTAGCAAC
*
13056704 TTCAGGA
128 TACAGGA
* * *
13056711 AGATAAGACTTGCTATTTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGACATTTTC
1 AGATAAGACTTGCAATTTTCAGTCTGCTCCACTGCAACTTCAGGAAGATAAGACTTGCCATTTTC
* *
13056776 GATCTGCTCCATAGCAGATATATGGAGATAAGATCTGTAAATTTTCAGTCTGCCTCCTA-CAACT
66 GATCTGCTCCATAGCCGATACATGGAGATAAGATCTGT-AATTTTCAGTCTG-CTCCTAGCAACT
*
13056840 TCAGGA
129 ACAGGA
* * * * *
13056846 AGATAAGACTTGCTATCTTCAGTCTGCTCCACTACAACTTCAGGGAGATAAGACTTGTCATTTTC
1 AGATAAGACTTGCAATTTTCAGTCTGCTCCACTGCAACTTCAGGAAGATAAGACTTGCCATTTTC
* * * * *
13056911 GATCTACTCCATAGCCGATACATAGAGATAAGATCTGTAATTTTTAGTTTGCTTCCT-GCAACTT
66 GATCTGCTCCATAGCCGATACATGGAGATAAGATCTGTAATTTTCAGTCTGC-TCCTAGCAACTA
13056975 CAGGA
130 CAGGA
* * * * * *
13056980 AGATAAGACTTGCTAA-----AATCTGCTCTA-TAGCCGA-TACATGG-AGATAAGACTCGTCA-
1 AGATAAGACTTGC-AATTTTCAGTCTGCTCCACT-G-CAACTTCA-GGAAGATAAGACTTGCCAT
* * * *
13057036 TTTCTGATCTGTTCCATAGTCGATACATGGAGATAAGATCTGTAACTTTCAGTCTGCTTCCT-GA
62 TTTC-GATCTGCTCCATAGCCGATACATGGAGATAAGATCTGTAATTTTCAGTCTGC-TCCTAGC
** *
13057100 AACTTTAAGA
125 AACTACAGGA
* * *
13057110 AGATAAGACTTGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTG
1 AGATAAGACTTGCAATTTTCAGTCTGCTCCACTGCAACTTCAGGAAGATAAGACTTG
13057167 TAATCTTCGA
Statistics
Matches: 707, Mismatches: 90, Indels: 120
0.77 0.10 0.13
Matches are distributed among these distances:
129 6 0.01
130 98 0.14
131 6 0.01
132 5 0.01
133 92 0.13
134 313 0.44
135 177 0.25
136 7 0.01
137 3 0.00
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (134 bp):
AGATAAGACTTGCAATTTTCAGTCTGCTCCACTGCAACTTCAGGAAGATAAGACTTGCCATTTTC
GATCTGCTCCATAGCCGATACATGGAGATAAGATCTGTAATTTTCAGTCTGCTCCTAGCAACTAC
AGGA
Found at i:13056900 original size:45 final size:45
Alignment explanation
Indices: 13056174--13056910 Score: 389
Period size: 45 Copynumber: 16.5 Consensus size: 45
13056164 GTTGATATAT
* *
13056174 GGAGATAAGA-TCTG-TAATTTTCAGTCTGCTTC-CTGCAACTTCAG
1 GGAGATAAGACT-TGCT-ATTTTCAGTCTGCTCCACTACAACTTCAG
* * * *
13056218 GAAGATAAGACCTGCTATCTTCAGTCTGCTCCACTGCAACTTCAG
1 GGAGATAAGACTTGCTATTTTCAGTCTGCTCCACTACAACTTCAG
* * *
13056263 GGAGATAAGACTTACTATCTTT-AGTTTGCTCTACTACAACTTCAG
1 GGAGATAAGACTTGCTAT-TTTCAGTCTGCTCCACTACAACTTCAG
* * *
13056308 AGAGACAAGACTTAG-TATCTTT-AGTCTGCTCCACTGCAACTTCAG
1 GGAGATAAGACTT-GCTAT-TTTCAGTCTGCTCCACTACAACTTCAG
* * *** ** * * * *
13056353 GGAGATAAGGC-TGGTGGCTGAAATCTGCTCCA-TAGTCGA-TACAT
1 GGAGATAAGACTTGCTATTTTCAGTCTGCTCCACTA--CAACTTCAG
* * * * * * * *
13056397 GGAGATAGGACTCGCCATTTTTTA-TCTACTCCA-TAGCCGA-TACAT
1 GGAGATAAGACTTGCTA-TTTTCAGTCTGCTCCACTA--CAACTTCAG
* * *
13056442 GGAGATAAGATCTAT--AATTTTCAGTCTGCTTC-CTGCAACTTCAG
1 GGAGATAAGA-CT-TGCTATTTTCAGTCTGCTCCACTACAACTTCAG
* * *
13056486 GAAGATAAGACTTGCTATCTTCAGTCTGCTCCACTGCAACTTCAG
1 GGAGATAAGACTTGCTATTTTCAGTCTGCTCCACTACAACTTCAG
* * *
13056531 GGAGATAAGACTTG-TCA-TTTC-GATCTGCTCCA-TAGTCGA-TACAT
1 GGAGATAAGACTTGCT-ATTTTCAG-TCTGCTCCACTA--CAACTTCAG
** * *
13056575 GGAGATAAGATCTAT-AAATTTTCAGTCTGCTTC-CTGCAACTTCAG
1 GGAGATAAGA-CT-TGCTATTTTCAGTCTGCTCCACTACAACTTCAG
* * * * * *
13056620 GAAGATAAGACTCGCCATTTTC-GATCTGCTCCA-TAGCCGA-TACAT
1 GGAGATAAGACTTGCTATTTTCAG-TCTGCTCCACTA--CAACTTCAG
* * *
13056665 AGAGATAAGA-TCTG-TAATTTTCAGTCTGCTTC-CTGCAACTTCAG
1 GGAGATAAGACT-TGCT-ATTTTCAGTCTGCTCCACTACAACTTCAG
* *
13056709 GAAGATAAGACTTGCTATTTTCAGTCTGCTCCACTGCAACTTCAG
1 GGAGATAAGACTTGCTATTTTCAGTCTGCTCCACTACAACTTCAG
*
13056754 GGAGATAAGACTTGAC-ATTTTC-GATCTGCTCCA-TAGCAGA-TAT-AT
1 GGAGATAAGACTTG-CTATTTTCAG-TCTGCTCCACTA-CA-ACT-TCAG
13056799 GGAGATAAGA-TCTG-TAAATTTTCAGTCTGC-CTC-CTACAACTTCAG
1 GGAGATAAGACT-TGCT--ATTTTCAGTCTGCTC-CACTACAACTTCAG
* *
13056844 GAAGATAAGACTTGCTATCTTCAGTCTGCTCCACTACAACTTCAG
1 GGAGATAAGACTTGCTATTTTCAGTCTGCTCCACTACAACTTCAG
13056889 GGAGATAAGACTTG-TCATTTTC
1 GGAGATAAGACTTGCT-ATTTTC
13056911 GATCTACTCC
Statistics
Matches: 535, Mismatches: 96, Indels: 123
0.71 0.13 0.16
Matches are distributed among these distances:
42 1 0.00
43 12 0.02
44 172 0.32
45 307 0.57
46 41 0.08
47 2 0.00
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (45 bp):
GGAGATAAGACTTGCTATTTTCAGTCTGCTCCACTACAACTTCAG
Found at i:13056972 original size:224 final size:222
Alignment explanation
Indices: 13056399--13057028 Score: 689
Period size: 223 Copynumber: 2.8 Consensus size: 222
13056389 CGATACATGG
* * ** * * *
13056399 AGATAGGACTCGCCATTTTTTATCTACTCCATAGCCGATACATG-GAGATAAGATCTATAATTTT
1 AGATAAGACTCGCCATCTTCGATCTGCTCCATA-CCAATACA-GAGAGATAAGATCTGTAATTTT
* * *
13056463 CAGTCTGCTTCCTGCAACTTCAGGAAGATAAGACTTGCTATCTTCAGTCTGCTCCACTGCAACTT
64 CAGTCTACTTCCTGCAACATCAGGAAGATAAGACTTGCTATTTTCAGTCTGCTCCACTGCAACTT
*
13056528 CAGGGAGATAAGACTTGTCATTTCGATCTGCTCCATAGTCGATACATGGAGATAAGATCTATAAA
129 CAGGGAGATAAGACTTGACATTTCGATCTGCTCCATAGTCGATACATGGAGATAAGATCTATAAA
* *
13056593 TTTTCAGTCTGCTTCCTGCAACTTCAGGA
194 TTTTCAGTCTGCCTCCTACAACTTCAGGA
* * *
13056622 AGATAAGACTCGCCATTTTCGATCTGCTCCATAGCCGATACATAGAGATAAGATCTGTAATTTTC
1 AGATAAGACTCGCCATCTTCGATCTGCTCCATA-CCAATACAGAGAGATAAGATCTGTAATTTTC
* *
13056687 AGTCTGCTTCCTGCAACTTCAGGAAGATAAGACTTGCTATTTTCAGTCTGCTCCACTGCAACTTC
65 AGTCTACTTCCTGCAACATCAGGAAGATAAGACTTGCTATTTTCAGTCTGCTCCACTGCAACTTC
* *
13056752 AGGGAGATAAGACTTGACATTTTCGATCTGCTCCATAG-CAGATATATGGAGATAAGATCTGTAA
130 AGGGAGATAAGACTTGACA-TTTCGATCTGCTCCATAGTC-GATACATGGAGATAAGATCTATAA
13056816 ATTTTCAGTCTGCCTCCTACAACTTCAGGA
193 ATTTTCAGTCTGCCTCCTACAACTTCAGGA
* * * * *
13056846 AGATAAGACTTGCTATCTTC-AGTCTGCTCCACTA-CAACTTCAGGGAGATAAGA-CTTGTCATT
1 AGATAAGACTCGCCATCTTCGA-TCTGCTCCA-TACCAA-TACAGAGAGATAAGATC-TGTAATT
* * *
13056908 TTC-GATCTAC-TCCATAGCCGATACAT-A-G-AGATAAGA-TCTG-TAATTTTTAGTTTGCTTC
62 TTCAG-TCTACTTCC-T-G-C-A-ACATCAGGAAGATAAGACT-TGCT-ATTTTCAGTCTGCTCC
* *** * *
13056966 -CTGCAACTTCAGGAAGATAAGACTTG-C--TAAAATCTGCTCTATAGCCGATACATGGAGATAA
119 ACTGCAACTTCAGGGAGATAAGACTTGACATTTCGATCTGCTCCATAGTCGATACATGGAGATAA
13057027 GA
184 GA
13057029 CTCGTCATTT
Statistics
Matches: 360, Mismatches: 31, Indels: 35
0.85 0.07 0.08
Matches are distributed among these distances:
220 29 0.08
221 1 0.00
223 150 0.42
224 147 0.41
225 26 0.07
226 2 0.01
227 2 0.01
228 3 0.01
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (222 bp):
AGATAAGACTCGCCATCTTCGATCTGCTCCATACCAATACAGAGAGATAAGATCTGTAATTTTCA
GTCTACTTCCTGCAACATCAGGAAGATAAGACTTGCTATTTTCAGTCTGCTCCACTGCAACTTCA
GGGAGATAAGACTTGACATTTCGATCTGCTCCATAGTCGATACATGGAGATAAGATCTATAAATT
TTCAGTCTGCCTCCTACAACTTCAGGA
Found at i:13057052 original size:130 final size:132
Alignment explanation
Indices: 13056596--13057179 Score: 727
Period size: 134 Copynumber: 4.4 Consensus size: 132
13056586 CTATAAATTT
* * *
13056596 TCAGTCTGCTTC-CT-GCAACTTCAGGAAGATAAGACTCGCCATTTTCGATCTGCTCCATAGCCG
1 TCAGTCTGCTCCACTAGCAACTTCAGGGAGATAAGACTCGTCATTTTCGATCTGCTCCATAGCCG
13056659 ATACATAGAGATAAGATCTGTAATTTTCAGTCTGCTTCCTGCAACTTCAGGAAGATAAGACTTGC
66 ATACATAGAGATAAGATCTGTAATTTTCAGTCTGCTTCCTGCAACTTCAGGAAGATAAGACTTGC
13056724 TA
131 TA
* *
13056726 TTTTCAGTCTGCTCCACT-GCAACTTCAGGGAGATAAGACTTGACATTTTCGATCTGCTCCATAG
1 ---TCAGTCTGCTCCACTAGCAACTTCAGGGAGATAAGACTCGTCATTTTCGATCTGCTCCATAG
* * * * *
13056790 CAGATATATGGAGATAAGATCTGTAAATTTTCAGTCTGCCTCCTACAACTTCAGGAAGATAAGAC
63 CCGATACATAGAGATAAGATCTGT-AATTTTCAGTCTGCTTCCTGCAACTTCAGGAAGATAAGAC
13056855 TTGCTA
127 TTGCTA
* *
13056861 TCTTCAGTCTGCTCCACTA-CAACTTCAGGGAGATAAGACTTGTCATTTTCGATCTACTCCATAG
1 ---TCAGTCTGCTCCACTAGCAACTTCAGGGAGATAAGACTCGTCATTTTCGATCTGCTCCATAG
* *
13056925 CCGATACATAGAGATAAGATCTGTAATTTTTAGTTTGCTTCCTGCAACTTCAGGAAGATAAGACT
63 CCGATACATAGAGATAAGATCTGTAATTTTCAGTCTGCTTCCTGCAACTTCAGGAAGATAAGACT
13056990 TGCTA
128 TGCTA
* * * * * * * *
13056995 -AAATCTGCTCTA-TAGCCGA-TACATGGAGATAAGACTCGTCA-TTTCTGATCTGTTCCATAGT
1 TCAGTCTGCTCCACTAG-CAACTTCAGGGAGATAAGACTCGTCATTTTC-GATCTGCTCCATAGC
* * * * *
13057056 CGATACATGGAGATAAGATCTGTAACTTTCAGTCTGCTTCCTGAAACTTTAAGAAGATAAGACTT
64 CGATACATAGAGATAAGATCTGTAATTTTCAGTCTGCTTCCTGCAACTTCAGGAAGATAAGACTT
13057121 GCTA
129 GCTA
* * *
13057125 TCTTCAGTCTGCTCCACT-GCAACTTCAGGGAGATAAGACTTGTAATCTTCGATCT
1 ---TCAGTCTGCTCCACTAGCAACTTCAGGGAGATAAGACTCGTCATTTTCGATCT
13057180 ATTCCGCTGC
Statistics
Matches: 393, Mismatches: 45, Indels: 25
0.85 0.10 0.05
Matches are distributed among these distances:
129 6 0.02
130 102 0.26
131 2 0.01
133 13 0.03
134 141 0.36
135 129 0.33
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (132 bp):
TCAGTCTGCTCCACTAGCAACTTCAGGGAGATAAGACTCGTCATTTTCGATCTGCTCCATAGCCG
ATACATAGAGATAAGATCTGTAATTTTCAGTCTGCTTCCTGCAACTTCAGGAAGATAAGACTTGC
TA
Found at i:13057161 original size:45 final size:44
Alignment explanation
Indices: 13057064--13057205 Score: 130
Period size: 45 Copynumber: 3.2 Consensus size: 44
13057054 GTCGATACAT
* * *
13057064 GGAGATAAGA-TCTGTAA-CTTTCAGTCTGCTTCCTGAAACTTTAA
1 GGAGATAAGACT-TGTAATC-TTCAGTCTGCTCCCTGCAACTTCAA
* *
13057108 GAAGATAAGACTTGCT-ATCTTCAGTCTGCTCCACTGCAACTTCAG
1 GGAGATAAGACTTG-TAATCTTCAGTCTGCTCC-CTGCAACTTCAA
**
13057153 GGAGATAAGACTTGTAATCTTC-GATCTATTCCGCTGCAACTTCAA
1 GGAGATAAGACTTGTAATCTTCAG-TCTGCTCC-CTGCAACTTCAA
*
13057198 GGAAATAA
1 GGAGATAA
13057206 TATCTGCCTT
Statistics
Matches: 81, Mismatches: 11, Indels: 11
0.79 0.11 0.11
Matches are distributed among these distances:
44 26 0.32
45 55 0.68
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.30
Consensus pattern (44 bp):
GGAGATAAGACTTGTAATCTTCAGTCTGCTCCCTGCAACTTCAA
Found at i:13057385 original size:64 final size:64
Alignment explanation
Indices: 13057275--13057401 Score: 193
Period size: 64 Copynumber: 2.0 Consensus size: 64
13057265 TCATGTATCT
* * *
13057275 ATGCTTATGCCAAATAACTAGGATGCTATGATCGAAATAATCCAAGTGTTCCTAGCTAGATGTG
1 ATGCTTATGCCAAATAACTAGGATGCTATGATCAAAATAATCCAAGTGCTCCTAACTAGATGTG
* *
13057339 ATGCTTATGTCAAATAATTAGGATGCTATGATCAAAATGAAT-CAAGTGCTCCTAACTAGATGT
1 ATGCTTATGCCAAATAACTAGGATGCTATGATCAAAAT-AATCCAAGTGCTCCTAACTAGATGT
13057402 ATTATGAATG
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
64 54 0.95
65 3 0.05
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.31
Consensus pattern (64 bp):
ATGCTTATGCCAAATAACTAGGATGCTATGATCAAAATAATCCAAGTGCTCCTAACTAGATGTG
Found at i:13068685 original size:127 final size:123
Alignment explanation
Indices: 13068416--13068735 Score: 381
Period size: 127 Copynumber: 2.6 Consensus size: 123
13068406 TAAATCAAAA
* ** * * * * *
13068416 CCCAGCACGATTGGGCACGATTTATCGAATTTCCAAATC-TGAAACATTGCCTCATTTTAATTTG
1 CCCAGCACGATTGGGCACGACTTCCCAAACTTCCAAA-CATGAAATATTGCCTCGTTTT-ATTTT
** *
13068480 AGAAAACACGTATAAAATTTCAAAAGGATATTCTGTATTTTAGTCGAATGGAAAATTGAAG
64 A-AAAACACGTATAAAATTTCAAAAGGATATTCCATATTTTAGTCGAATAGAAAATTGAAG
13068541 CCCAGCACGATTGGGCACGACTTCCCAAACTTCCAAACATGAAATATTGCCTCGTTTTATTTTAA
1 CCCAGCACGATTGGGCACGACTTCCCAAACTTCCAAACATGAAATATTGCCTCGTTTTATTTTAA
* * * *
13068606 GAACATGTGGATGAAATTTCAAAAAAGGATATTCCATATTTTAGTTGAATAGAAAATTGAAG
66 AAACACGT--ATAAAATTTC--AAAAGGATATTCCATATTTTAGTCGAATAGAAAATTGAAG
* * * * * *
13068668 CCCAACACGATTGGGCACGACCTCCCAAACTTTCAAACACGAAGTATTGCCTCGTTTTAATTTAA
1 CCCAGCACGATTGGGCACGACTTCCCAAACTTCCAAACATGAAATATTGCCTCGTTTTATTTTAA
13068733 AAA
66 AAA
13068736 AAACATGGAC
Statistics
Matches: 168, Mismatches: 22, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
123 7 0.04
124 6 0.04
125 58 0.35
127 97 0.58
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (123 bp):
CCCAGCACGATTGGGCACGACTTCCCAAACTTCCAAACATGAAATATTGCCTCGTTTTATTTTAA
AAACACGTATAAAATTTCAAAAGGATATTCCATATTTTAGTCGAATAGAAAATTGAAG
Found at i:13068831 original size:126 final size:122
Alignment explanation
Indices: 13068456--13068841 Score: 403
Period size: 127 Copynumber: 3.1 Consensus size: 122
13068446 TTCCAAATCT
* * * * *
13068456 GAAACATTGCCTCATTTTAATTTGAGAAAACACGTATAAAATTTCAAAAGGATATTCTGTATTTT
1 GAAATATTGCCTCGTTTTAATTTAAGAAAACATGGATAAAATTTCAAAAGGATATTCTGTATTTT
* * *
13068521 AGTCGAATGGAAAATTGAAGCCCAGCACGATTGGGCACGACTTCCCAAACTTCCAAACAT
66 AGTTGAA-GAAAAATTGAAGCCCAGCACGATTGGGCACGAC--CCCAAACTTCCAAACAC
* * ** * **
13068581 GAAATATTGCCTCGTTTTATTTTAAGAACATGTGGATGAAATTTCAAAAAAGGATATTCCATATT
1 GAAATATTGCCTCGTTTTAATTTAAGAAAACATGGATAAAATTTC--AAAAGGATATTCTGTATT
* * *
13068646 TTAGTTGAATAGAAAATTGAAGCCCAACACGATTGGGCACGACCTCCCAAACTTTCAAACAC
64 TTAGTTGAAGA-AAAATTGAAGCCCAGCACGATTGGGCACGA-C-CCCAAACTTCCAAACAC
* * * * *
13068708 GAAGTATTGCCTCGTTTTAATTTAAAAAAAACATGGACAAAATTTCCAAAGGATATTTTGTATTT
1 GAAATATTGCCTCGTTTTAATTT-AAGAAAACATGGATAAAATTTCAAAAGGATATTCTGTATTT
* * * * * *
13068773 TAATTGAACGAAAAATCGAAACCCAGCACGATCGGGCAGGACCCCTAGAACTCCCAAACAC
65 TAGTTGAA-GAAAAATTGAAGCCCAGCACGATTGGGCACGACCCC-A-AACTTCCAAACAC
13068834 GAAATATT
1 GAAATATT
13068842 TCCTTATGTT
Statistics
Matches: 213, Mismatches: 40, Indels: 15
0.79 0.15 0.06
Matches are distributed among these distances:
124 3 0.01
125 37 0.17
126 65 0.31
127 91 0.43
128 17 0.08
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.27
Consensus pattern (122 bp):
GAAATATTGCCTCGTTTTAATTTAAGAAAACATGGATAAAATTTCAAAAGGATATTCTGTATTTT
AGTTGAAGAAAAATTGAAGCCCAGCACGATTGGGCACGACCCCAAACTTCCAAACAC
Found at i:13069413 original size:41 final size:40
Alignment explanation
Indices: 13069367--13069446 Score: 133
Period size: 41 Copynumber: 2.0 Consensus size: 40
13069357 TTCAAAACAA
*
13069367 TCAAAATATACGGAAAAAAATCTTTAAAAGAAATTATGCAT
1 TCAAAATATACGAAAAAAAATCTTTAAAA-AAATTATGCAT
*
13069408 TCAAAATTTACGAAAAAAAATCTTTAAAAAAATTATGCA
1 TCAAAATATACGAAAAAAAATCTTTAAAAAAATTATGCA
13069447 AAAATAGATT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
40 10 0.27
41 27 0.73
ACGTcount: A:0.55, C:0.10, G:0.07, T:0.28
Consensus pattern (40 bp):
TCAAAATATACGAAAAAAAATCTTTAAAAAAATTATGCAT
Found at i:13072034 original size:12 final size:12
Alignment explanation
Indices: 13072019--13072046 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
13072009 ACAAAGAACA
13072019 AAACAAGCAAAT
1 AAACAAGCAAAT
13072031 AAACAAGCAAAT
1 AAACAAGCAAAT
13072043 AAAC
1 AAAC
13072047 GATTAACAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.68, C:0.18, G:0.07, T:0.07
Consensus pattern (12 bp):
AAACAAGCAAAT
Found at i:13075128 original size:24 final size:24
Alignment explanation
Indices: 13075100--13075147 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
13075090 ATATATTTTA
*
13075100 AAATTTTTATAATTTTT-TAAATAT
1 AAATTTTGA-AATTTTTATAAATAT
13075124 AAATTTTGAAATTTTTATAAATAT
1 AAATTTTGAAATTTTTATAAATAT
13075148 TTTTAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (24 bp):
AAATTTTGAAATTTTTATAAATAT
Found at i:13075136 original size:32 final size:34
Alignment explanation
Indices: 13075089--13075153 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 34
13075079 AACTTTTTTG
*
13075089 TATATATTTTAAAATTTTTAT-AAT-TTTTTAAA
1 TATAAATTTTAAAATTTTTATAAATATTTTTAAA
*
13075121 TATAAATTTTGAAATTTTTATAAATATTTTTAA
1 TATAAATTTTAAAATTTTTATAAATATTTTTAA
13075154 TTTTAAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 19 0.66
33 3 0.10
34 7 0.24
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (34 bp):
TATAAATTTTAAAATTTTTATAAATATTTTTAAA
Found at i:13075144 original size:18 final size:18
Alignment explanation
Indices: 13075062--13075145 Score: 52
Period size: 18 Copynumber: 4.8 Consensus size: 18
13075052 ATTATTTTAG
*
13075062 AAAAATTTTA-AAATTTT
1 AAAATTTTTATAAATTTT
** *
13075079 AACTTTTTTGTATATATTTT
1 AA-AATTTT-TATAAATTTT
*
13075099 AAAATTTTTATAATTTTT
1 AAAATTTTTATAAATTTT
*
13075117 TAAA----TATAAATTTT
1 AAAATTTTTATAAATTTT
*
13075131 GAAATTTTTATAAAT
1 AAAATTTTTATAAAT
13075146 ATTTTTAATT
Statistics
Matches: 49, Mismatches: 11, Indels: 13
0.67 0.15 0.18
Matches are distributed among these distances:
14 12 0.24
17 2 0.04
18 21 0.43
19 6 0.12
20 8 0.16
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (18 bp):
AAAATTTTTATAAATTTT
Found at i:13080178 original size:74 final size:72
Alignment explanation
Indices: 13080003--13080201 Score: 211
Period size: 74 Copynumber: 2.7 Consensus size: 72
13079993 AGCTCTATCG
* * * * * * *
13080003 ATTAAGTGAGAGCAAGTTTGTGAAAGTCAAAGTGTTTAATTTGATTACATCCTTTAAGGGATTTG
1 ATTAAATGAGAGCAAG-TAGTGAAA-TCAAAATGTTTGACTTGATTGCATCCTTTAAGAGATTTG
*
13080068 GCTTTACTA
64 GCTTTACCA
* * * *
13080077 ATTAAATGGGAGAAACTATGTGAAAATCAAAATGTTTGACTTGATTGCATCTTTTAAGAGATTTG
1 ATTAAATGAGAGCAAGTA-GTG-AAATCAAAATGTTTGACTTGATTGCATCCTTTAAGAGATTTG
13080142 GCTTTACCA
64 GCTTTACCA
* *
13080151 ATTGAATGAGAGCAAGTCAGCTGAAATCAAATTG-TTGACTTGATTGCATCC
1 ATTAAATGAGAGCAAGT-AG-TGAAATCAAAATGTTTGACTTGATTGCATCC
13080202 CCTGAGGGAC
Statistics
Matches: 103, Mismatches: 18, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
73 17 0.17
74 80 0.78
75 6 0.06
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.35
Consensus pattern (72 bp):
ATTAAATGAGAGCAAGTAGTGAAATCAAAATGTTTGACTTGATTGCATCCTTTAAGAGATTTGGC
TTTACCA
Found at i:13088312 original size:26 final size:26
Alignment explanation
Indices: 13088275--13088326 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
13088265 TAAGTAAGAT
13088275 AGAGAGGAGATTTTATTGGGCACCAA
1 AGAGAGGAGATTTTATTGGGCACCAA
*
13088301 AGAGAGGGGATTTTATTGGGCACCAA
1 AGAGAGGAGATTTTATTGGGCACCAA
13088327 TTTGATGAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.33, C:0.12, G:0.33, T:0.23
Consensus pattern (26 bp):
AGAGAGGAGATTTTATTGGGCACCAA
Found at i:13091996 original size:15 final size:15
Alignment explanation
Indices: 13091973--13092007 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
13091963 GGTTGCCACA
*
13091973 AATCAAGTGAATCAG
1 AATCTAGTGAATCAG
*
13091988 AATCTAGTGAATTAG
1 AATCTAGTGAATCAG
13092003 AATCT
1 AATCT
13092008 TGCTCCTCGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.43, C:0.11, G:0.17, T:0.29
Consensus pattern (15 bp):
AATCTAGTGAATCAG
Found at i:13099537 original size:6 final size:6
Alignment explanation
Indices: 13099501--13099564 Score: 60
Period size: 6 Copynumber: 10.3 Consensus size: 6
13099491 TTTGAGTCCA
*
13099501 TTTATTT TTTATCT TTTATT TTT-TCGC TTTATT TTTATT TTTATT TTTA-T
1 TTTA-TT TTTAT-T TTTATT TTTAT--T TTTATT TTTATT TTTATT TTTATT
*
13099551 TTTATG TTTATT TT
1 TTTATT TTTATT TT
13099565 AAAGACTTGT
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
5 6 0.12
6 28 0.58
7 13 0.27
8 1 0.02
ACGTcount: A:0.14, C:0.05, G:0.03, T:0.78
Consensus pattern (6 bp):
TTTATT
Found at i:13099547 original size:11 final size:11
Alignment explanation
Indices: 13099528--13099565 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
13099518 ATTTTTTCGC
13099528 TTTATTTTTATT
1 TTTATTTTTA-T
13099540 TTTATTTTTAT
1 TTTATTTTTAT
*
13099551 TTTATGTTTAT
1 TTTATTTTTAT
13099562 TTTA
1 TTTA
13099566 AAGACTTGTC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (11 bp):
TTTATTTTTAT
Done.