Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D12
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: 58873029
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 639818 characters in sequence are not A, C, G, or T
File 10 of 196
Found at i:2901927 original size:21 final size:20
Alignment explanation
Indices: 2901885--2901923 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2901875 TTTTATCTAT
2901885 AAACATTTACAAGTCATTTA
1 AAACATTTACAAGTCATTTA
*
2901905 AAACACTTTAGAA-TCATTT
1 AAACA-TTTACAAGTCATTT
2901924 TAAATTGAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.44, C:0.15, G:0.05, T:0.36
Consensus pattern (20 bp):
AAACATTTACAAGTCATTTA
Found at i:2905528 original size:20 final size:21
Alignment explanation
Indices: 2905473--2905529 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
2905463 TAGGGGACCA
2905473 TTAACTTAAGTAAAA-TAAGGT
1 TTAA-TTAAGTAAAATTAAGGT
*
2905494 TTAATTAA-TTAAATTAAGG-
1 TTAATTAAGTAAAATTAAGGT
*
2905513 TTAATTAAGCAAAATTA
1 TTAATTAAGTAAAATTA
2905530 TAATTTAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 12 0.39
20 15 0.48
21 4 0.13
ACGTcount: A:0.49, C:0.04, G:0.11, T:0.37
Consensus pattern (21 bp):
TTAATTAAGTAAAATTAAGGT
Found at i:2906608 original size:20 final size:19
Alignment explanation
Indices: 2906583--2906634 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
2906573 TATGTTCCAG
* *
2906583 TATGCACTTCGTGTGCTAGA
1 TATGCACTTTGTGTGCCA-A
*
2906603 TATGCA-TTTATGTGCCAA
1 TATGCACTTTGTGTGCCAA
2906621 TATGCACTTTGTGT
1 TATGCACTTTGTGT
2906635 ACCAGGTATG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 7 0.26
19 14 0.52
20 6 0.22
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.40
Consensus pattern (19 bp):
TATGCACTTTGTGTGCCAA
Found at i:2908559 original size:20 final size:20
Alignment explanation
Indices: 2908534--2908573 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2908524 CGTAAAATGA
*
2908534 TTTCTGAAAAATGTTTTACT
1 TTTCTGAAAAATGATTTACT
*
2908554 TTTCTGTAAAATGATTTACT
1 TTTCTGAAAAATGATTTACT
2908574 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (20 bp):
TTTCTGAAAAATGATTTACT
Found at i:2909321 original size:21 final size:21
Alignment explanation
Indices: 2909282--2909322 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2909272 CTAATTAATT
2909282 TAAAATTTTATGATGTAAAAA
1 TAAAATTTTATGATGTAAAAA
*
2909303 TAAATATTTTAT-ATTTAAAA
1 TAAA-ATTTTATGATGTAAAA
2909323 TAGTGGAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (21 bp):
TAAAATTTTATGATGTAAAAA
Found at i:2910227 original size:19 final size:18
Alignment explanation
Indices: 2910203--2910255 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
2910193 GAAAAACAAG
2910203 TAAAAAAAACCTAAAAAAA
1 TAAAAAAAACC-AAAAAAA
* *
2910222 TAAAAACAACCACAAAAA
1 TAAAAAAAACCAAAAAAA
**
2910240 TAACTAAAA-CAAAAAA
1 TAAAAAAAACCAAAAAA
2910256 CTAAGCAGTA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
17 6 0.21
18 12 0.43
19 10 0.36
ACGTcount: A:0.75, C:0.15, G:0.00, T:0.09
Consensus pattern (18 bp):
TAAAAAAAACCAAAAAAA
Found at i:2910238 original size:18 final size:19
Alignment explanation
Indices: 2910203--2910242 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
2910193 GAAAAACAAG
2910203 TAAAAAAAACCTAAAAAAA
1 TAAAAAAAACCTAAAAAAA
* *
2910222 TAAAAACAACC-ACAAAAA
1 TAAAAAAAACCTAAAAAAA
2910240 TAA
1 TAA
2910243 CTAAAACAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.75, C:0.15, G:0.00, T:0.10
Consensus pattern (19 bp):
TAAAAAAAACCTAAAAAAA
Found at i:2919817 original size:12 final size:12
Alignment explanation
Indices: 2919800--2919832 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
2919790 CGGCTCGTCA
2919800 ATATTATTTTTT
1 ATATTATTTTTT
2919812 ATATTA-TTTTT
1 ATATTATTTTTT
*
2919823 ATATAATTTT
1 ATATTATTTT
2919833 AAAATATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
ATATTATTTTTT
Found at i:2919988 original size:30 final size:30
Alignment explanation
Indices: 2919954--2920018 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
2919944 CAACTTAACA
2919954 AACAAAT-ACCTCTAAAATAATAACAAAATT
1 AACAAATGA-CTCTAAAATAATAACAAAATT
*
2919984 AACAAATGACTTTAAAATAATAACAAAATT
1 AACAAATGACTCTAAAATAATAACAAAATT
2920014 AACAA
1 AACAA
2920019 TAAAATAAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
30 32 0.97
31 1 0.03
ACGTcount: A:0.62, C:0.14, G:0.02, T:0.23
Consensus pattern (30 bp):
AACAAATGACTCTAAAATAATAACAAAATT
Found at i:2920323 original size:20 final size:20
Alignment explanation
Indices: 2920298--2920338 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
2920288 TGCAACTTTG
2920298 AAAATT-TTTAATGTTTCCAA
1 AAAATTCTTTAA-GTTTCCAA
*
2920318 AAAATTCTTTGAGTTTCCAA
1 AAAATTCTTTAAGTTTCCAA
2920338 A
1 A
2920339 TTAGTCCCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.41
Consensus pattern (20 bp):
AAAATTCTTTAAGTTTCCAA
Found at i:2920873 original size:21 final size:20
Alignment explanation
Indices: 2920845--2920912 Score: 50
Period size: 23 Copynumber: 3.2 Consensus size: 20
2920835 CACAACTTTT
2920845 TTAA-CTAATAATTCT-AAA
1 TTAATCTAATAATTCTAAAA
* *
2920863 TTAAATTCTAAATATTTTTAAAA
1 TT-AA-TCT-AATAATTCTAAAA
2920886 TTAATCTAATAATATACTAAAAA
1 TTAATCTAATAAT-T-CT-AAAA
2920909 TTAA
1 TTAA
2920913 AGGGCATTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 11
0.72 0.08 0.21
Matches are distributed among these distances:
18 2 0.05
19 2 0.05
20 5 0.13
21 6 0.16
22 10 0.26
23 13 0.34
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.41
Consensus pattern (20 bp):
TTAATCTAATAATTCTAAAA
Found at i:2936086 original size:24 final size:23
Alignment explanation
Indices: 2936053--2936110 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 23
2936043 AGTTGAAAAG
2936053 TATAA-AATAAAATAAATAATGATA
1 TATAATAATAAAAT-AAT-ATGATA
*
2936077 -ATAATAATAAAATGATATGATA
1 TATAATAATAAAATAATATGATA
2936099 TATATATAATAA
1 TATA-ATAATAA
2936111 TGCTTGATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
22 6 0.20
23 9 0.30
24 15 0.50
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (23 bp):
TATAATAATAAAATAATATGATA
Found at i:2936461 original size:49 final size:49
Alignment explanation
Indices: 2936381--2936489 Score: 186
Period size: 49 Copynumber: 2.2 Consensus size: 49
2936371 CTTACTTTGA
2936381 GAATGTGAAA--GTGTATATATGTGATAAGGCCTAATGGCCGATGTGAT
1 GAATGTGAAAGTGTGTATATATGTGATAAGGCCTAATGGCCGATGTGAT
*
2936428 GAATGTGAAAGTGTGTATATATGTGATAGGGCCTAATGGCCGATGTGAT
1 GAATGTGAAAGTGTGTATATATGTGATAAGGCCTAATGGCCGATGTGAT
2936477 GAATGTGATAAGT
1 GAATGTGA-AAGT
2936490 CCCGAAGGGC
Statistics
Matches: 58, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
47 10 0.17
49 44 0.76
50 4 0.07
ACGTcount: A:0.31, C:0.07, G:0.31, T:0.30
Consensus pattern (49 bp):
GAATGTGAAAGTGTGTATATATGTGATAAGGCCTAATGGCCGATGTGAT
Found at i:2936663 original size:37 final size:37
Alignment explanation
Indices: 2936607--2936685 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
2936597 TCGAGCTCTA
* * *
2936607 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
2936644 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
2936681 AAGAC
1 AAGAC
2936686 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:2940414 original size:40 final size:40
Alignment explanation
Indices: 2940366--2940504 Score: 135
Period size: 40 Copynumber: 3.5 Consensus size: 40
2940356 AACACACCAG
* *
2940366 TTTGCACCCGGTGCCTCATCGGATAATTC-GAAATAATAA
1 TTTGCACCCAGTGCCTCATCGGATAATTCTGAAGTAATAA
* * *
2940405 TTTGACACCCAGTGTCTCATCGGCTAA-ACTGAAGT-A-AA
1 TTTG-CACCCAGTGCCTCATCGGATAATTCTGAAGTAATAA
* **
2940443 TTAGCACCCAGTGCCTCATCAAAT-ATATCTGAAGTAATAA
1 TTTGCACCCAGTGCCTCATCGGATAAT-TCTGAAGTAATAA
*
2940483 TTTGACACCCAGTGTCTCATCG
1 TTTG-CACCCAGTGCCTCATCG
2940505 ACTCGAAGTC
Statistics
Matches: 79, Mismatches: 14, Indels: 12
0.75 0.13 0.11
Matches are distributed among these distances:
36 1 0.01
37 16 0.20
38 12 0.15
39 7 0.09
40 28 0.35
41 15 0.19
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (40 bp):
TTTGCACCCAGTGCCTCATCGGATAATTCTGAAGTAATAA
Found at i:2940454 original size:37 final size:41
Alignment explanation
Indices: 2940399--2940505 Score: 123
Period size: 37 Copynumber: 2.7 Consensus size: 41
2940389 TAATTCGAAA
* **
2940399 TAATAATTTGACACCCAGTGTCTCATCGGCTA-AACTGAAG
1 TAATAATTAGACACCCAGTGTCTCATCGAATATAACTGAAG
* * *
2940439 T-A-AATTAG-CACCCAGTGCCTCATCAAATATATCTGAAG
1 TAATAATTAGACACCCAGTGTCTCATCGAATATAACTGAAG
*
2940477 TAATAATTTGACACCCAGTGTCTCATCGA
1 TAATAATTAGACACCCAGTGTCTCATCGA
2940506 CTCGAAGTCG
Statistics
Matches: 54, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
37 17 0.31
38 13 0.24
39 2 0.04
40 6 0.11
41 16 0.30
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (41 bp):
TAATAATTAGACACCCAGTGTCTCATCGAATATAACTGAAG
Found at i:2941660 original size:16 final size:16
Alignment explanation
Indices: 2941639--2941671 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2941629 TAATTTCTCC
*
2941639 TTTCTTTCTTTCTCTT
1 TTTCTTTCTTTCCCTT
2941655 TTTCTTTCTTTCCCTT
1 TTTCTTTCTTTCCCTT
2941671 T
1 T
2941672 CTGTTTTCGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTCTTTCTTTCCCTT
Found at i:2956555 original size:29 final size:29
Alignment explanation
Indices: 2956522--2956617 Score: 106
Period size: 29 Copynumber: 3.2 Consensus size: 29
2956512 CAATTACAAA
2956522 TAAAATTATTTTATATTAATTATTGCAAT
1 TAAAATTATTTTATATTAATTATTGCAAT
* * *
2956551 TAAAATATAATATT-TA-CAATTATTTACAAT
1 TAAAAT-T-ATTTTATATTAATTA-TTGCAAT
2956581 ATAAAAATTATTTTATATTAATTATTGCAAT
1 -T-AAAATTATTTTATATTAATTATTGCAAT
2956612 TAAAAT
1 TAAAAT
2956618 ATAATATTTA
Statistics
Matches: 54, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
29 16 0.30
30 14 0.26
31 14 0.26
32 10 0.19
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (29 bp):
TAAAATTATTTTATATTAATTATTGCAAT
Found at i:2956602 original size:61 final size:59
Alignment explanation
Indices: 2956515--2956627 Score: 208
Period size: 61 Copynumber: 1.9 Consensus size: 59
2956505 TTACTTACAA
2956515 TTACAAATAAAATTATTTTATATTAATTATTGCAATTAAAATATAATATTTACAATTAT
1 TTACAAATAAAATTATTTTATATTAATTATTGCAATTAAAATATAATATTTACAATTAT
2956574 TTACAATATAAAAATTATTTTATATTAATTATTGCAATTAAAATATAATATTTA
1 TTACAA-AT-AAAATTATTTTATATTAATTATTGCAATTAAAATATAATATTTA
2956628 AAAAATTAAT
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
59 6 0.12
60 2 0.04
61 44 0.85
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (59 bp):
TTACAAATAAAATTATTTTATATTAATTATTGCAATTAAAATATAATATTTACAATTAT
Found at i:2964840 original size:16 final size:16
Alignment explanation
Indices: 2964816--2964868 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
2964806 TAGCCAAAAT
*
2964816 ATTATTTATTTAATCA
1 ATTAATTATTTAATCA
*
2964832 ATTAATTATTTAATTA
1 ATTAATTATTTAATCA
* *
2964848 AATAATTTTTTCAATCCA
1 ATTAATTATTT-AAT-CA
2964866 ATT
1 ATT
2964869 CTAATTTTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
16 23 0.79
17 3 0.10
18 3 0.10
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTAATTATTTAATCA
Found at i:2968510 original size:90 final size:89
Alignment explanation
Indices: 2968329--2968553 Score: 337
Period size: 90 Copynumber: 2.5 Consensus size: 89
2968319 TATGTAGCAT
* * * * *
2968329 CACCAAGGTGGTCATGCTAAAGAGAATGGTTCCACCAAAAT-AAAAT-AAAAATCATTTTTATGG
1 CACCAAAGTGGTCACGCCAAAGAGAATGGCTCCACCAAAATAAAAATAAAAAATAATTTTTATGG
2968392 TGGTCACACCATTCTCAATGGCAC
66 TGGTCACACCATTCTCAATGGCAC
2968416 CACCAAAGTGGTCACGCCAAAGAGAATGGCTCCACCAAAATAAAAATAAAAAATTAATTTTTATG
1 CACCAAAGTGGTCACGCCAAAGAGAATGGCTCCACCAAAATAAAAATAAAAAA-TAATTTTTATG
*
2968481 GTGGTCACGCCATTCTCAATGGCAC
65 GTGGTCACACCATTCTCAATGGCAC
* * * *
2968506 CACCAAAGTGGTCACGTCAAAGTGAATGACTCCACTAAAATAAAAATA
1 CACCAAAGTGGTCACGCCAAAGAGAATGGCTCCACCAAAATAAAAATA
2968554 TTTTATTATT
Statistics
Matches: 125, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
87 37 0.30
88 5 0.04
89 5 0.04
90 78 0.62
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.23
Consensus pattern (89 bp):
CACCAAAGTGGTCACGCCAAAGAGAATGGCTCCACCAAAATAAAAATAAAAAATAATTTTTATGG
TGGTCACACCATTCTCAATGGCAC
Found at i:2970771 original size:11 final size:11
Alignment explanation
Indices: 2970757--2970787 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
2970747 TGTTTTTGCA
2970757 TGTTATTTTCT
1 TGTTATTTTCT
*
2970768 TGTTGTTTTCT
1 TGTTATTTTCT
2970779 TGTTATTTT
1 TGTTATTTT
2970788 ACTACTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.06, C:0.06, G:0.13, T:0.74
Consensus pattern (11 bp):
TGTTATTTTCT
Found at i:2970796 original size:11 final size:11
Alignment explanation
Indices: 2970781--2970821 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
2970771 TGTTTTCTTG
2970781 TTATTTTACTA
1 TTATTTTACTA
*
2970792 CTATTTTACTA
1 TTATTTTACTA
*
2970803 TTATGTTACTA
1 TTATTTTACTA
2970814 TTATTTTA
1 TTATTTTA
2970822 TTGTTATTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.27, C:0.10, G:0.02, T:0.61
Consensus pattern (11 bp):
TTATTTTACTA
Found at i:2970798 original size:22 final size:22
Alignment explanation
Indices: 2970773--2970829 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
2970763 TTTCTTGTTG
2970773 TTTTCTTGTTATTTTACTACTA
1 TTTTCTTGTTATTTTACTACTA
* * *
2970795 TTTTAC-TATTATGTTACTATTA
1 TTTT-CTTGTTATTTTACTACTA
*
2970817 TTTTATTGTTATT
1 TTTTCTTGTTATT
2970830 GTTTGTATAT
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
22 26 0.96
23 1 0.04
ACGTcount: A:0.21, C:0.09, G:0.05, T:0.65
Consensus pattern (22 bp):
TTTTCTTGTTATTTTACTACTA
Found at i:2970828 original size:11 final size:11
Alignment explanation
Indices: 2970757--2970829 Score: 51
Period size: 11 Copynumber: 6.6 Consensus size: 11
2970747 TGTTTTTGCA
2970757 TGTTATTTT-C
1 TGTTATTTTAC
*
2970767 TTGTTGTTTT-C
1 -TGTTATTTTAC
2970778 TTGTTATTTTAC
1 -TGTTATTTTAC
**
2970790 TACTATTTTAC
1 TGTTATTTTAC
* *
2970801 TATTATGTTAC
1 TGTTATTTTAC
* *
2970812 TATTATTTTAT
1 TGTTATTTTAC
2970823 TGTTATT
1 TGTTATT
2970830 GTTTGTATAT
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
11 51 0.98
12 1 0.02
ACGTcount: A:0.18, C:0.08, G:0.08, T:0.66
Consensus pattern (11 bp):
TGTTATTTTAC
Found at i:2970895 original size:30 final size:30
Alignment explanation
Indices: 2970861--2970920 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
2970851 TATTTTATTA
2970861 TTAATTTTGTTATTATTTTAAAGGCATTTG
1 TTAATTTTGTTATTATTTTAAAGGCATTTG
*
2970891 TTAATTTTGTTATTATTTTAGAGGCATTTG
1 TTAATTTTGTTATTATTTTAAAGGCATTTG
2970921 CTTGTTAAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.25, C:0.03, G:0.15, T:0.57
Consensus pattern (30 bp):
TTAATTTTGTTATTATTTTAAAGGCATTTG
Found at i:2971056 original size:11 final size:11
Alignment explanation
Indices: 2971042--2971067 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2971032 TATATATGTT
2971042 TAAAAATAATA
1 TAAAAATAATA
2971053 TAAAAATAATA
1 TAAAAATAATA
2971064 TAAA
1 TAAA
2971068 TAATTAATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
TAAAAATAATA
Found at i:2979043 original size:31 final size:29
Alignment explanation
Indices: 2978972--2979043 Score: 71
Period size: 28 Copynumber: 2.5 Consensus size: 29
2978962 TTTGTTTATA
*
2978972 CTTAT-TATGTAAATTTTATATATATATG
1 CTTATATATGTATATTTTATATATATATG
*
2979000 CTT-CATAT-TATATTATTAT-TATATAATTG
1 CTTATATATGTATATT-TTATATATAT-A-TG
2979029 CTTATATATGTATAT
1 CTTATATATGTATAT
2979044 AGGTATATGT
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
27 10 0.29
28 11 0.31
29 5 0.14
30 4 0.11
31 5 0.14
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.54
Consensus pattern (29 bp):
CTTATATATGTATATTTTATATATATATG
Found at i:2991852 original size:44 final size:44
Alignment explanation
Indices: 2991711--2992008 Score: 195
Period size: 44 Copynumber: 6.9 Consensus size: 44
2991701 ATTATACAGG
* * * *
2991711 TCTTATCTCCCTGAGATTACAGGGGAACAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGAA-GT-AGA
* * ** *
2991757 TCTTATCTCCTTGAGGTTACAGCGGAGCAGATTGAAGCCAG-AGA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAG-AAGTAGA
2991801 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAGTA-A
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGA-AGTAGA
* * ** * *
2991845 TCCTATCTCCTTGAGATTACAATGGAGCGGAT--TA-AAG--GA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGAAGTAGA
* ** * * **
2991884 TCTTATCTCTCTGA-AGTTACAGTAGAGAAGATCACATCAG--G-
1 TCTTATCTCCCTGAGA-TTACAGCGGAGCAGATCAAAGAAGTAGA
* * * * * *
2991925 TCTTATTTCCCTAAGATTACAGTGGAACAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGAA-GT-AGA
*
2991971 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGA
2992009 CACTATCCTA
Statistics
Matches: 192, Mismatches: 46, Indels: 28
0.72 0.17 0.11
Matches are distributed among these distances:
38 1 0.01
39 24 0.12
40 2 0.01
41 29 0.15
42 5 0.03
44 66 0.34
45 2 0.01
46 62 0.32
47 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.26
Consensus pattern (44 bp):
TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGAAGTAGA
Found at i:2992105 original size:174 final size:170
Alignment explanation
Indices: 2991798--2992130 Score: 474
Period size: 174 Copynumber: 1.9 Consensus size: 170
2991788 TTGAAGCCAG
* * **
2991798 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAGTAATCCTATCTCCTTGAGATT
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACACTAATCCTATCTCCTAAAGATT
* *
2991863 ACAATGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGTCT
66 ACAATGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGAAGATCACATCAAGTCT
2991928 TATTTCCCT-AAGATTACAGTGGAACAGACCAAAGAATTTC
131 TATTTCCCTGAAGA-TACAGTGGAACAGACCAAAGAATTTC
*
2991968 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACT-ATCCTATCTCCCTAAAG-T
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACACTAATCCTATCT-CCTAAAGAT
* * * *
2992031 TACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAGGTTACAGCAGAGTAGATCGCATC
65 TACAATGGAGCGGA-T----TAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGAAGATCACATC
*
2992096 AAGTCTTATTTCCCTGAAGATGCAGTGGAACAGAC
125 AAGTCTTATTTCCCTGAAGATACAGTGGAACAGAC
2992131 TGAAAACAAG
Statistics
Matches: 144, Mismatches: 12, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
169 23 0.16
170 48 0.33
174 69 0.48
175 4 0.03
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.27
Consensus pattern (170 bp):
AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACACTAATCCTATCTCCTAAAGATT
ACAATGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGAAGATCACATCAAGTCT
TATTTCCCTGAAGATACAGTGGAACAGACCAAAGAATTTC
Found at i:2994171 original size:19 final size:22
Alignment explanation
Indices: 2994144--2994198 Score: 73
Period size: 20 Copynumber: 2.7 Consensus size: 22
2994134 TTTTTATTGT
2994144 TTATTATTTTGC-TTGT-ATCA
1 TTATTATTTTGCATTGTCATCA
*
2994164 TT-TTA-TTTACATTGTCATCA
1 TTATTATTTTGCATTGTCATCA
2994184 TTATTATTTTGCATT
1 TTATTATTTTGCATT
2994199 CATTTTTACT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
18 4 0.14
19 7 0.24
20 8 0.28
21 3 0.10
22 7 0.24
ACGTcount: A:0.22, C:0.11, G:0.07, T:0.60
Consensus pattern (22 bp):
TTATTATTTTGCATTGTCATCA
Found at i:2995911 original size:16 final size:16
Alignment explanation
Indices: 2995887--2995922 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
2995877 TAGATTATGG
* *
2995887 ATTTTAAAATGTTAGT
1 ATTTCAAAATATTAGT
2995903 ATTTCAAAATATTAGT
1 ATTTCAAAATATTAGT
2995919 ATTT
1 ATTT
2995923 GTGATTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.39, C:0.03, G:0.08, T:0.50
Consensus pattern (16 bp):
ATTTCAAAATATTAGT
Found at i:3001375 original size:8 final size:8
Alignment explanation
Indices: 3001362--3001389 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
3001352 TTATTGATTA
3001362 ATAAAATT
1 ATAAAATT
3001370 ATAAAATT
1 ATAAAATT
3001378 ATAAAATT
1 ATAAAATT
3001386 ATAA
1 ATAA
3001390 TCTATAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
ATAAAATT
Found at i:3001685 original size:16 final size:16
Alignment explanation
Indices: 3001666--3001698 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3001656 ATATATATTA
3001666 TTAAATTATTATA-AAT
1 TTAAATT-TTATACAAT
3001682 TTAAATTTTATACAAT
1 TTAAATTTTATACAAT
3001698 T
1 T
3001699 AACAAAATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (16 bp):
TTAAATTTTATACAAT
Found at i:3005603 original size:13 final size:13
Alignment explanation
Indices: 3005585--3005635 Score: 66
Period size: 13 Copynumber: 3.9 Consensus size: 13
3005575 AGTTCTTTAT
*
3005585 TGCTTTTGAGAAG
1 TGCTTTTCAGAAG
*
3005598 TGCTTTTCAGAAC
1 TGCTTTTCAGAAG
*
3005611 TGCTTTTCAGAGG
1 TGCTTTTCAGAAG
*
3005624 TGCTTTTGAGAA
1 TGCTTTTCAGAA
3005636 ATTTGAGTGT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.22, C:0.14, G:0.25, T:0.39
Consensus pattern (13 bp):
TGCTTTTCAGAAG
Found at i:3005616 original size:26 final size:26
Alignment explanation
Indices: 3005585--3005635 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
3005575 AGTTCTTTAT
*
3005585 TGCTTTTGAGAAGTGCTTTTCAGAAC
1 TGCTTTTCAGAAGTGCTTTTCAGAAC
* *
3005611 TGCTTTTCAGAGGTGCTTTTGAGAA
1 TGCTTTTCAGAAGTGCTTTTCAGAA
3005636 ATTTGAGTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.22, C:0.14, G:0.25, T:0.39
Consensus pattern (26 bp):
TGCTTTTCAGAAGTGCTTTTCAGAAC
Found at i:3006272 original size:22 final size:22
Alignment explanation
Indices: 3006219--3006262 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
3006209 AAGCATATGA
* *
3006219 AAATGATTTGGTTATATTCAAT
1 AAATAATTTGGTTATATACAAT
3006241 AAATAATTTGGTTA-ATACAAT
1 AAATAATTTGGTTATATACAAT
3006262 A
1 A
3006263 CTTACATTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.43, C:0.05, G:0.11, T:0.41
Consensus pattern (22 bp):
AAATAATTTGGTTATATACAAT
Found at i:3012895 original size:20 final size:20
Alignment explanation
Indices: 3012851--3012896 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
3012841 ATCTATATTG
*
3012851 AAGTATCAATACCTTTCCTA
1 AAGTATCAATACCTTTACTA
*
3012871 TAGTATCAATA-CTTTGACTA
1 AAGTATCAATACCTTT-ACTA
3012891 AAGTAT
1 AAGTAT
3012897 TGATACCTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (20 bp):
AAGTATCAATACCTTTACTA
Found at i:3017714 original size:12 final size:13
Alignment explanation
Indices: 3017694--3017732 Score: 64
Period size: 12 Copynumber: 3.2 Consensus size: 13
3017684 TATTTTCTGA
3017694 AATTAAATATAAT
1 AATTAAATATAAT
3017707 AATT-AATATAA-
1 AATTAAATATAAT
3017718 AATTAAATATAAT
1 AATTAAATATAAT
3017731 AA
1 AA
3017733 ATTGGACCGT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 4 0.17
12 14 0.58
13 6 0.25
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AATTAAATATAAT
Found at i:3018083 original size:52 final size:52
Alignment explanation
Indices: 3018019--3018122 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
3018009 GGAATCGTGC
3018019 AACTTATCCCGGCGAAACACCGCTTATGTTAAGTTTAGATGGACGGTGGTGT
1 AACTTATCCCGGCGAAACACCGCTTATGTTAAGTTTAGATGGACGGTGGTGT
3018071 AACTTATCCCGGCGAAACACCGCTTATGTTAAGTTTAGATGGACGGTGGTGT
1 AACTTATCCCGGCGAAACACCGCTTATGTTAAGTTTAGATGGACGGTGGTGT
3018123 GGAAACAATT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (52 bp):
AACTTATCCCGGCGAAACACCGCTTATGTTAAGTTTAGATGGACGGTGGTGT
Found at i:3026454 original size:229 final size:229
Alignment explanation
Indices: 3026048--3026510 Score: 917
Period size: 229 Copynumber: 2.0 Consensus size: 229
3026038 TAGGCTCTTA
*
3026048 ACATATTTGGTCACCCTGGGGATCATGTCAAGCTTTCTATGACGTTGCTTTTGCAGCATGATAAT
1 ACATTTTTGGTCACCCTGGGGATCATGTCAAGCTTTCTATGACGTTGCTTTTGCAGCATGATAAT
3026113 AGAAGAGGGGTGCAACGAGAGTTAGATCAGTTGTGGCCTTCCTTTCATAAAATGGTTGGGTGTAA
66 AGAAGAGGGGTGCAACGAGAGTTAGATCAGTTGTGGCCTTCCTTTCATAAAATGGTTGGGTGTAA
3026178 ATATAAAGCTGTGTCTCTATATAGGTAGGAGAGATTGGAAGTCTAAAAAATGTTTACCGTTAATA
131 ATATAAAGCTGTGTCTCTATATAGGTAGGAGAGATTGGAAGTCTAAAAAATGTTTACCGTTAATA
3026243 AAAATTTAATTGTTAGATTTAGATATTTCAAGTT
196 AAAATTTAATTGTTAGATTTAGATATTTCAAGTT
3026277 ACATTTTTGGTCACCCTGGGGATCATGTCAAGCTTTCTATGACGTTGCTTTTGCAGCATGATAAT
1 ACATTTTTGGTCACCCTGGGGATCATGTCAAGCTTTCTATGACGTTGCTTTTGCAGCATGATAAT
3026342 AGAAGAGGGGTGCAACGAGAGTTAGATCAGTTGTGGCCTTCCTTTCATAAAATGGTTGGGTGTAA
66 AGAAGAGGGGTGCAACGAGAGTTAGATCAGTTGTGGCCTTCCTTTCATAAAATGGTTGGGTGTAA
3026407 ATATAAAGCTGTGTCTCTATATAGGTAGGAGAGATTGGAAGTCTAAAAAATGTTTACCGTTAATA
131 ATATAAAGCTGTGTCTCTATATAGGTAGGAGAGATTGGAAGTCTAAAAAATGTTTACCGTTAATA
3026472 AAAATTTAATTGTTAGATTTAGATATTTCAAGTT
196 AAAATTTAATTGTTAGATTTAGATATTTCAAGTT
3026506 ACATT
1 ACATT
3026511 GATCTTTTAA
Statistics
Matches: 233, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
229 233 1.00
ACGTcount: A:0.30, C:0.12, G:0.23, T:0.34
Consensus pattern (229 bp):
ACATTTTTGGTCACCCTGGGGATCATGTCAAGCTTTCTATGACGTTGCTTTTGCAGCATGATAAT
AGAAGAGGGGTGCAACGAGAGTTAGATCAGTTGTGGCCTTCCTTTCATAAAATGGTTGGGTGTAA
ATATAAAGCTGTGTCTCTATATAGGTAGGAGAGATTGGAAGTCTAAAAAATGTTTACCGTTAATA
AAAATTTAATTGTTAGATTTAGATATTTCAAGTT
Found at i:3034576 original size:55 final size:54
Alignment explanation
Indices: 3034495--3034598 Score: 147
Period size: 55 Copynumber: 1.9 Consensus size: 54
3034485 TATTAAATTA
* * *
3034495 TAAATTATTATTTTTGTTAAATTATATTTGATAATAAT-TATATTAAAATATGAT
1 TAAATTATTATTATTATTAAATTATATTTAATAATAATCT-TATTAAAATATGAT
*
3034549 TAAATTATTTATTATTATTGAATTATATTTAATAATAATCTTATTAAAAT
1 TAAATTA-TTATTATTATTAAATTATATTTAATAATAATCTTATTAAAAT
3034599 TTAATAATAA
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
54 7 0.16
55 36 0.82
56 1 0.02
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (54 bp):
TAAATTATTATTATTATTAAATTATATTTAATAATAATCTTATTAAAATATGAT
Found at i:3039808 original size:41 final size:41
Alignment explanation
Indices: 3039751--3039948 Score: 297
Period size: 41 Copynumber: 4.8 Consensus size: 41
3039741 TTATATAAAA
* * * *
3039751 CACCGGCATAAAGCCTGCTAGGCACAAAGTCCGATACATTT
1 CACCGGCACAGAGCCTGCTAGGCATAAAGCCCGATACATTT
* *
3039792 CACCGGCACAGAGCCTGCTAGGCATAAAGCCTGTTACATTT
1 CACCGGCACAGAGCCTGCTAGGCATAAAGCCCGATACATTT
* *
3039833 CACCGGCACAGAGCTTGCTAGGCATAAAGCCCAATACATTT
1 CACCGGCACAGAGCCTGCTAGGCATAAAGCCCGATACATTT
*
3039874 CACTGGCACAGAGCCTGCTAGGCATAAAGCCCGATACATTT
1 CACCGGCACAGAGCCTGCTAGGCATAAAGCCCGATACATTT
* *
3039915 CACCGGTACAGAGCCTGCTAGGCATAAAACCCGA
1 CACCGGCACAGAGCCTGCTAGGCATAAAGCCCGA
3039949 ACTTACAAAG
Statistics
Matches: 141, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 141 1.00
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.19
Consensus pattern (41 bp):
CACCGGCACAGAGCCTGCTAGGCATAAAGCCCGATACATTT
Found at i:3040149 original size:47 final size:47
Alignment explanation
Indices: 3040093--3040422 Score: 196
Period size: 47 Copynumber: 6.6 Consensus size: 47
3040083 ACATTCGGTC
* *
3040093 ATAGTTTAATTCATTTCTCTGCATAACAATTACATATACATTCAACT
1 ATAGATTAATTCATTTCTATGCATAACAATTACATATACATTCAACT
* * * * * *
3040140 ATAAATTAATTCATTTCAATGTATAACAAATATATATATATATACATTCGACC
1 ATAGATTAATTCATTTCTATGCATAAC----A-AT-TACATATACATTCAACT
* * * *
3040193 ATAGTTTAATTTATTTCTTTGCATAACAATTACATATACATTCAGCT
1 ATAGATTAATTCATTTCTATGCATAACAATTACATATACATTCAACT
* * * *
3040240 ATAGATTAATTAATTTCAATGTATAACAAATATATATATACATTCGGCCATAACCT
1 ATAGATTAATTCATTTCTATGCATAAC-AAT-TACATATACATT----C--AA-CT
* * * * ** *
3040296 AT-GTAATTTCAAATAATTTATTTCAATGCATAACAAATATATATACATTCGGCC
1 ATAG--A--T----TAATTCATTTCTATGCATAACAATTACATATACATTCAACT
* * *
3040350 ATAGTTTAATTCATTTCTCTGCATAACAATTACATATACATTCAGCT
1 ATAGATTAATTCATTTCTATGCATAACAATTACATATACATTCAACT
3040397 ATAGATTAATTCATTT-TCATGCATAA
1 ATAGATTAATTCATTTCT-ATGCATAA
3040423 AAAATATATT
Statistics
Matches: 217, Mismatches: 41, Indels: 50
0.70 0.13 0.16
Matches are distributed among these distances:
46 1 0.00
47 113 0.52
48 5 0.02
49 12 0.06
51 2 0.01
52 2 0.01
53 36 0.17
54 3 0.01
55 3 0.01
56 4 0.02
57 2 0.01
59 1 0.00
61 12 0.06
62 2 0.01
63 19 0.09
ACGTcount: A:0.39, C:0.15, G:0.06, T:0.39
Consensus pattern (47 bp):
ATAGATTAATTCATTTCTATGCATAACAATTACATATACATTCAACT
Found at i:3040196 original size:100 final size:100
Alignment explanation
Indices: 3040073--3040279 Score: 351
Period size: 100 Copynumber: 2.1 Consensus size: 100
3040063 CAATACATAA
**
3040073 ATATATATATACATTCGGTCATAGTTTAATTCATTTCTCTGCATAACAATTACATATACATTCAA
1 ATATATATATACATTCGACCATAGTTTAATTCATTTCTCTGCATAACAATTACATATACATTCAA
*
3040138 CTATAAATTAATTCATTTCAATGTATAACAAATAT
66 CTATAAATTAATTAATTTCAATGTATAACAAATAT
* * *
3040173 ATATATATATACATTCGACCATAGTTTAATTTATTTCTTTGCATAACAATTACATATACATTCAG
1 ATATATATATACATTCGACCATAGTTTAATTCATTTCTCTGCATAACAATTACATATACATTCAA
*
3040238 CTATAGATTAATTAATTTCAATGTATAACAAATAT
66 CTATAAATTAATTAATTTCAATGTATAACAAATAT
3040273 ATATATA
1 ATATATA
3040280 CATTCGGCCA
Statistics
Matches: 100, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
100 100 1.00
ACGTcount: A:0.41, C:0.14, G:0.05, T:0.41
Consensus pattern (100 bp):
ATATATATATACATTCGACCATAGTTTAATTCATTTCTCTGCATAACAATTACATATACATTCAA
CTATAAATTAATTAATTTCAATGTATAACAAATAT
Found at i:3054381 original size:17 final size:17
Alignment explanation
Indices: 3054361--3054397 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
3054351 ACTTATACAC
*
3054361 ATTTAGTACAATTTCTA
1 ATTTAGCACAATTTCTA
*
3054378 ATTTAGCATAATTTCTA
1 ATTTAGCACAATTTCTA
3054395 ATT
1 ATT
3054398 AGCCCATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.35, C:0.11, G:0.05, T:0.49
Consensus pattern (17 bp):
ATTTAGCACAATTTCTA
Found at i:3059582 original size:27 final size:27
Alignment explanation
Indices: 3059552--3059618 Score: 125
Period size: 27 Copynumber: 2.5 Consensus size: 27
3059542 CCTATCAGGT
3059552 AGGCGCCAATGAAGGTGCCTCATAGAG
1 AGGCGCCAATGAAGGTGCCTCATAGAG
*
3059579 AGGCGCCAATGAAGGTGCCTTATAGAG
1 AGGCGCCAATGAAGGTGCCTCATAGAG
3059606 AGGCGCCAATGAA
1 AGGCGCCAATGAA
3059619 ATTTATGTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.31, C:0.21, G:0.33, T:0.15
Consensus pattern (27 bp):
AGGCGCCAATGAAGGTGCCTCATAGAG
Found at i:3060061 original size:6 final size:6
Alignment explanation
Indices: 3060005--3060045 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
3059995 CGTCTCATTT
*
3060005 ATGATA ATGATA ATGATA ATGATA ATGATA ATGACA ATGAT
1 ATGATA ATGATA ATGATA ATGATA ATGATA ATGATA ATGAT
3060046 GTGGATGATG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.49, C:0.02, G:0.17, T:0.32
Consensus pattern (6 bp):
ATGATA
Found at i:3061415 original size:91 final size:91
Alignment explanation
Indices: 3061249--3061515 Score: 299
Period size: 91 Copynumber: 2.9 Consensus size: 91
3061239 AAAAGCTCTA
* * * *
3061249 AAACTTTTTCAAAAAAAAGTAATTAA-GCCACTGCTTTTTTTTTTTTACACTCAATTGGGTACTT
1 AAACTTTTTC-AAAAAAAGCAATTAAGGCC-CTAC--TTTTTTTTTTGCACTCAATTGGATACTT
* * *
3061313 GAACTTTCAAAATGCATAAAAAATACCCTT
62 GAACTGTCAAAATGCATAAAAAAGACCCTC
* * * *
3061343 AAACTTTTTCAAATAAAGCAATTAAGGCCCTACTTTTTTTTTTGCACTTAATTAGATAATTGAAC
1 AAACTTTTTCAAAAAAAGCAATTAAGGCCCTACTTTTTTTTTTGCACTCAATTGGATACTTGAAC
*
3061408 TGTCAAAATGCATAAAAAAGGCCCTC
66 TGTCAAAATGCATAAAAAAGACCCTC
* * * * * *
3061434 AAAC--TTTAAAAAAAAACAATTAAGTCACTA-ATTTTTTTTTGCACTCAATTGGATACTTGAAT
1 AAACTTTTTCAAAAAAAGCAATTAAGGCCCTACTTTTTTTTTTGCACTCAATTGGATACTTGAAC
*
3061496 TGCCAAAATGCATAAAAAAG
66 TGTCAAAATGCATAAAAAAG
3061516 GCCAAAGGTG
Statistics
Matches: 149, Mismatches: 23, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
88 46 0.31
89 21 0.14
91 53 0.36
93 16 0.11
94 13 0.09
ACGTcount: A:0.40, C:0.16, G:0.10, T:0.34
Consensus pattern (91 bp):
AAACTTTTTCAAAAAAAGCAATTAAGGCCCTACTTTTTTTTTTGCACTCAATTGGATACTTGAAC
TGTCAAAATGCATAAAAAAGACCCTC
Found at i:3061876 original size:9 final size:9
Alignment explanation
Indices: 3061862--3062072 Score: 63
Period size: 10 Copynumber: 22.0 Consensus size: 9
3061852 ATTTGGTACG
3061862 ATAATTTTT
1 ATAATTTTT
3061871 ATAATTTTTT
1 ATAA-TTTTT
*
3061881 ATGAA-TCTT
1 AT-AATTTTT
*
3061890 ATATTTCTTT
1 ATAATT-TTT
*
3061900 ACAATTTTTT
1 ATAA-TTTTT
3061910 ATAATTTTCT
1 ATAATTTT-T
***
3061920 -TACGGCTTT
1 ATA-ATTTTT
*
3061929 ATAAAATTTT
1 AT-AATTTTT
3061939 ATAAATTTTTTT
1 AT-AA--TTTTT
* *
3061951 CTATATTTCT
1 ATA-ATTTTT
3061961 ATATATT-TT
1 ATA-ATTTTT
3061970 ATAATATTTT
1 ATAAT-TTTT
*
3061980 ATGATTTTT
1 ATAATTTTT
*
3061989 ATAAAATTTT
1 AT-AATTTTT
*
3061999 AAATATTTTT
1 ATA-ATTTTT
3062009 AT-ATTTTT
1 ATAATTTTT
* *
3062017 ATTAAAATTTA
1 A-T-AATTTTT
3062028 ATAATTTTT
1 ATAATTTTT
*
3062037 ATAATCTTT
1 ATAATTTTT
*
3062046 ATTGATTTTT
1 A-TAATTTTT
*
3062056 AT-TTTTTT
1 ATAATTTTT
*
3062064 ATCATTTTT
1 ATAATTTTT
3062073 TACCACATGT
Statistics
Matches: 149, Mismatches: 32, Indels: 42
0.67 0.14 0.19
Matches are distributed among these distances:
8 17 0.11
9 50 0.34
10 65 0.44
11 11 0.07
12 6 0.04
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (9 bp):
ATAATTTTT
Found at i:3061988 original size:19 final size:19
Alignment explanation
Indices: 3061953--3062015 Score: 69
Period size: 19 Copynumber: 3.4 Consensus size: 19
3061943 ATTTTTTTCT
3061953 ATATTTCTATATATTTTATA
1 ATATTT-TATATATTTTATA
3061973 ATATTTTATGAT-TTTTATA
1 ATATTTTAT-ATATTTTATA
* *
3061992 AAATTTTAAATATTTT-T-
1 ATATTTTATATATTTTATA
3062009 ATATTTT
1 ATATTTT
3062016 TATTAAAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
17 6 0.16
18 3 0.08
19 21 0.55
20 8 0.21
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (19 bp):
ATATTTTATATATTTTATA
Found at i:3062003 original size:28 final size:30
Alignment explanation
Indices: 3061926--3062036 Score: 101
Period size: 29 Copynumber: 3.8 Consensus size: 30
3061916 TTCTTACGGC
*
3061926 TTTA-TAAAATTTTATAAATTTTTTTCTATATT
1 TTTATTAAAATTTTAT-AA-TATTTT-TATATT
* *
3061958 TCTA-T-ATATTTTATAATA-TTTTATGATT
1 TTTATTAAAATTTTATAATATTTTTAT-ATT
3061986 TTTA-TAAAATTTTA-AATATTTTTATATT
1 TTTATTAAAATTTTATAATATTTTTATATT
*
3062014 TTTATTAAAATTTAATAAT-TTTT
1 TTTATTAAAATTTTATAATATTTT
3062037 ATAATCTTTA
Statistics
Matches: 68, Mismatches: 6, Indels: 13
0.78 0.07 0.15
Matches are distributed among these distances:
27 3 0.04
28 21 0.31
29 27 0.40
30 5 0.07
31 8 0.12
32 4 0.06
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.61
Consensus pattern (30 bp):
TTTATTAAAATTTTATAATATTTTTATATT
Found at i:3062037 original size:28 final size:29
Alignment explanation
Indices: 3061983--3062048 Score: 84
Period size: 28 Copynumber: 2.3 Consensus size: 29
3061973 ATATTTTATG
3061983 ATTTTTA-TAAAATTTTAA-ATATTTTTAT-
1 ATTTTTATTAAAA-TTTAATA-ATTTTTATA
3062011 ATTTTTATTAAAATTTAATAATTTTTATA
1 ATTTTTATTAAAATTTAATAATTTTTATA
*
3062040 ATCTTTATT
1 ATTTTTATT
3062049 GATTTTTATT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
28 20 0.59
29 14 0.41
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (29 bp):
ATTTTTATTAAAATTTAATAATTTTTATA
Found at i:3062048 original size:29 final size:29
Alignment explanation
Indices: 3061965--3062048 Score: 86
Period size: 29 Copynumber: 2.9 Consensus size: 29
3061955 ATTTCTATAT
*
3061965 ATTTTATAATA-TTTTATGATTTTTA-TAAA
1 ATTTTA-AATATTTTTAT-ATCTTTATTAAA
*
3061994 ATTTTAAATATTTTTATATTTTTATTAAA
1 ATTTTAAATATTTTTATATCTTTATTAAA
3062023 A-TTT-AATAATTTTTATAATCTTTATT
1 ATTTTAAAT-ATTTTTAT-ATCTTTATT
3062049 GATTTTTATT
Statistics
Matches: 50, Mismatches: 1, Indels: 8
0.85 0.02 0.14
Matches are distributed among these distances:
27 3 0.06
28 22 0.44
29 25 0.50
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (29 bp):
ATTTTAAATATTTTTATATCTTTATTAAA
Found at i:3064529 original size:19 final size:19
Alignment explanation
Indices: 3064506--3064655 Score: 93
Period size: 19 Copynumber: 7.8 Consensus size: 19
3064496 TAATGTGATG
* * *
3064506 CCAAAATCTTTAACGGATG
1 CCAAAATCTCTAACAGATA
* *
3064525 TCAAAATCTCTAACAAATA
1 CCAAAATCTCTAACAGATA
* * * *
3064544 TCAAAATTTTTAACTGATA
1 CCAAAATCTCTAACAGATA
*
3064563 CCAAAATCTCTAACCAAATA
1 CCAAAATCTCTAA-CAGATA
* * **
3064583 CTAAAGTCTCTAATTGATA
1 CCAAAATCTCTAACAGATA
**
3064602 CCAAAATCTCTAATGGATA
1 CCAAAATCTCTAACAGATA
* * *
3064621 CCAAAATTTGTAACCAAATA
1 CCAAAATCTCTAA-CAGATA
**
3064641 CCGCAATCTCTAACA
1 CCAAAATCTCTAACA
3064656 AAAATCTCTA
Statistics
Matches: 98, Mismatches: 31, Indels: 4
0.74 0.23 0.03
Matches are distributed among these distances:
19 71 0.72
20 27 0.28
ACGTcount: A:0.43, C:0.22, G:0.07, T:0.28
Consensus pattern (19 bp):
CCAAAATCTCTAACAGATA
Found at i:3064568 original size:38 final size:38
Alignment explanation
Indices: 3064507--3064614 Score: 128
Period size: 39 Copynumber: 2.8 Consensus size: 38
3064497 AATGTGATGC
* **
3064507 CAAAATCTTTAACGGATGTCAAAATCTCTAA-CAAATA
1 CAAAATCTTTAACTGATACCAAAATCTCTAACCAAATA
*
3064544 TCAAAATTTTTAACTGATACCAAAATCTCTAACCAAATA
1 -CAAAATCTTTAACTGATACCAAAATCTCTAACCAAATA
* * *
3064583 CTAAAGTCTCTAATTGATACCAAAATCTCTAA
1 C-AAAATCTTTAACTGATACCAAAATCTCTAA
3064615 TGGATACCAA
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
38 28 0.47
39 32 0.53
ACGTcount: A:0.44, C:0.20, G:0.06, T:0.30
Consensus pattern (38 bp):
CAAAATCTTTAACTGATACCAAAATCTCTAACCAAATA
Found at i:3081053 original size:37 final size:37
Alignment explanation
Indices: 3080980--3081053 Score: 89
Period size: 37 Copynumber: 2.0 Consensus size: 37
3080970 TATCTCCCTG
*
3080980 AAGTTGCAGTGGAGCAGACTAAGCAAAGCAAGTCTTA
1 AAGTTGCAGTGGAGCAGACTAAGCAAAGCAAATCTTA
**
3081017 AAGTTGCAGT-GAGGCAGACTGAAG-ATGGCAAATCTTA
1 AAGTTGCAGTGGA-GCAGACT-AAGCAAAGCAAATCTTA
3081054 TCTCCCTGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
36 2 0.06
37 27 0.84
38 3 0.09
ACGTcount: A:0.36, C:0.15, G:0.28, T:0.20
Consensus pattern (37 bp):
AAGTTGCAGTGGAGCAGACTAAGCAAAGCAAATCTTA
Found at i:3081107 original size:44 final size:44
Alignment explanation
Indices: 3081047--3081328 Score: 213
Period size: 44 Copynumber: 6.5 Consensus size: 44
3081037 GAAGATGGCA
*
3081047 AATCTTATCTCCCTGAAGTTGCGGTGGAGCAGATTAAAGCCGAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGAT
* * ** * *
3081091 AATCCTATCTCCCTGAAGTTACAGTGGAGTGGATTAAAACC-TT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGAT
* * * * *** *
3081134 AGATCTTATCTCTCTGAAGATGCAG-AGAGTAGATCGTA-TC--T
1 A-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGAT
* * * *
3081175 AGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACT-AAGCAAAGCA-
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGC--CG-AT
* * *
3081220 AATCTTATCTCCCTGAAGTTGCAGCGGAACAGATTAAAGCCGAC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGAT
* * *
3081264 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTATAA-CC-AC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTA-AAGCCGAT
*
3081307 AGATCTTATCTCTCTGAAGTTG
1 A-ATCTTATCTCCCTGAAGTTG
3081329 TAGTAGAGTA
Statistics
Matches: 188, Mismatches: 38, Indels: 24
0.75 0.15 0.10
Matches are distributed among these distances:
40 21 0.11
41 9 0.05
42 1 0.01
43 14 0.07
44 107 0.57
45 32 0.17
46 4 0.02
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGAT
Found at i:3081280 original size:129 final size:128
Alignment explanation
Indices: 3081049--3081287 Score: 277
Period size: 129 Copynumber: 1.9 Consensus size: 128
3081039 AGATGGCAAA
* * *
3081049 TCTTATCTCCCTGAAGTTGCGGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTACA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGCAGATAATCCTATCTCCCTGAAGTTACA
* *** * * * *
3081114 GTGGAGTGGATTAAAACCTTAGATCTTATCTCTCTGAAGATGCAGAGAGTAGATCGTATCTAG
66 GCGGAACAGATTAAAACCTGAAATCCTATCTCCCTGAAGATGCAGAGAGTAGATCGTATCTAG
* *
3081177 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGACT-AAGCAAAGCA-AATCTTATCTCCCTGAAGTT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGC--AG-ATAATCCTATCTCCCTGAAGTT
* * *
3081240 GCAGCGGAACAGATTAAAGCC-GACAATCCTATCTCCCTGAAGTTGCAG
63 ACAGCGGAACAGATTAAAACCTGA-AATCCTATCTCCCTGAAGATGCAG
3081288 TGGAGCGGAT
Statistics
Matches: 91, Mismatches: 16, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
127 4 0.04
128 31 0.34
129 55 0.60
130 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.28
Consensus pattern (128 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGCAGATAATCCTATCTCCCTGAAGTTACA
GCGGAACAGATTAAAACCTGAAATCCTATCTCCCTGAAGATGCAGAGAGTAGATCGTATCTAG
Found at i:3081313 original size:173 final size:175
Alignment explanation
Indices: 3081017--3081471 Score: 573
Period size: 173 Copynumber: 2.6 Consensus size: 175
3081007 GCAAGTCTTA
* * ** * *
3081017 AAGTTGCAGT-GAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGCGGTGGAGCAGAT
1 AAGTTGCAGTGGA-GTAGACTCAAGAAAGCAAATCTTATCTCCCTGAAGTTGCAGTGGAACAGAT
* * **
3081081 TAAAGCCGATAATCCTATCTCCCTGAAGTTACAGTGGAGTGGATTAAAACCTTAGATCTTATCTC
65 TAAAGCCGACAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACCACAGATCTTATCTC
** *
3081146 TCTGAAGATGCAG-AGAGTAGATCGTATCTAGTCTT-ATCTCCCTG
130 TCTGAAGATGCAGTAGAGTAGATCACATCGAGTCTTAATCTCCCTG
*
3081190 AAGTTGCAGTGGAGTAGACT-AAGCAAAGCAAATCTTATCTCCCTGAAGTTGCAGCGGAACAGAT
1 AAGTTGCAGTGGAGTAGACTCAAG-AAAGCAAATCTTATCTCCCTGAAGTTGCAGTGGAACAGAT
* *
3081254 TAAAGCCGACAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTATAACCACAGATCTTATCTC
65 TAAAGCCGACAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACCACAGATCTTATCTC
* * *
3081319 TCTGAAGTTGTAGTAGAGTAGATCACATCGGGTCTTAATCTCCCTG
130 TCTGAAGATGCAGTAGAGTAGATCACATCGAGTCTTAATCTCCCTG
* * * * *
3081365 AAGTTGCAGTGGAGTAGACTCAAGAAAGCAAGT-TTATC-CCCTTGAAATTGCTGTGGGACAGAC
1 AAGTTGCAGTGGAGTAGACTCAAGAAAGCAAATCTTATCTCCC-TGAAGTTGCAGTGGAACAGAT
** * *
3081428 TAAA-CATACCAATCCTATCTCCCCGACGTTGCAGTGGAGTGGAT
65 TAAAGCCGA-CAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGAT
3081472 CGAGACACCA
Statistics
Matches: 246, Mismatches: 29, Indels: 13
0.85 0.10 0.05
Matches are distributed among these distances:
172 3 0.01
173 126 0.51
174 77 0.31
175 37 0.15
176 3 0.01
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (175 bp):
AAGTTGCAGTGGAGTAGACTCAAGAAAGCAAATCTTATCTCCCTGAAGTTGCAGTGGAACAGATT
AAAGCCGACAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACCACAGATCTTATCTCT
CTGAAGATGCAGTAGAGTAGATCACATCGAGTCTTAATCTCCCTG
Found at i:3083613 original size:98 final size:98
Alignment explanation
Indices: 3083499--3083695 Score: 351
Period size: 98 Copynumber: 2.0 Consensus size: 98
3083489 TTAAAAATTA
*
3083499 TAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAATT-GTGCCCTAACGTATTGGGTGTGATTT
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGG-ATTCGTGCCCTAACGTATTGGGTGTGATTT
*
3083563 CTTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
65 CTTAAATCTTGGATAAGTGGATATTCTTTTAAAG
*
3083597 TAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGATTCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGATTCGTGCCCTAACGTATTGGGTGTGATTTC
3083662 TTAAATCTTGGATAAGTGGATATTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATATTCTTTTAAAG
3083695 T
1 T
3083696 TTTATTGTAC
Statistics
Matches: 95, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
97 3 0.03
98 92 0.97
ACGTcount: A:0.28, C:0.10, G:0.24, T:0.38
Consensus pattern (98 bp):
TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGATTCGTGCCCTAACGTATTGGGTGTGATTTC
TTAAATCTTGGATAAGTGGATATTCTTTTAAAG
Found at i:3085868 original size:18 final size:18
Alignment explanation
Indices: 3085845--3085880 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3085835 TCATTGTTTG
3085845 TAACATTGGAATCGTTCT
1 TAACATTGGAATCGTTCT
*
3085863 TAACATTGGAATTGTTCT
1 TAACATTGGAATCGTTCT
3085881 AGTATTACTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.42
Consensus pattern (18 bp):
TAACATTGGAATCGTTCT
Found at i:3102917 original size:21 final size:19
Alignment explanation
Indices: 3102878--3102920 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
3102868 GTATGTAATT
3102878 TATATGAAATTAAATTAAA
1 TATATGAAATTAAATTAAA
3102897 TATAT-AATATTATAATGTAAA
1 TATATGAA-ATTA-AAT-TAAA
3102918 TAT
1 TAT
3102921 TAAAGTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
18 2 0.10
19 9 0.43
20 3 0.14
21 7 0.33
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (19 bp):
TATATGAAATTAAATTAAA
Found at i:3108601 original size:27 final size:27
Alignment explanation
Indices: 3108563--3108618 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
3108553 GCTTCATGGA
*
3108563 TATCAATAGGTACAGTAGCAGATAAAC
1 TATCAATAGGTACAATAGCAGATAAAC
* * *
3108590 TATCAGTAGGTACAATATCAGATGAAC
1 TATCAATAGGTACAATAGCAGATAAAC
3108617 TA
1 TA
3108619 GTTACCCTGG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.43, C:0.14, G:0.18, T:0.25
Consensus pattern (27 bp):
TATCAATAGGTACAATAGCAGATAAAC
Found at i:3111856 original size:6 final size:6
Alignment explanation
Indices: 3111845--3111872 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
3111835 TGTAGACCAA
3111845 TTTATT TTTATT TTTATT TTTATT TTTA
1 TTTATT TTTATT TTTATT TTTATT TTTA
3111873 AAGTTTTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTATT
Found at i:3117379 original size:31 final size:31
Alignment explanation
Indices: 3117341--3117401 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
3117331 CCTTCCATCA
* *
3117341 TTGCGATAGCTGCCTTGTACTCTAGTGATCC
1 TTGCGATAGCTGCCTCGTACTCCAGTGATCC
3117372 TTGCGATAGCTGCCTCGTACTCCAGTGATC
1 TTGCGATAGCTGCCTCGTACTCCAGTGATC
3117402 AATTTGCTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.16, C:0.28, G:0.23, T:0.33
Consensus pattern (31 bp):
TTGCGATAGCTGCCTCGTACTCCAGTGATCC
Found at i:3126450 original size:51 final size:50
Alignment explanation
Indices: 3126334--3126547 Score: 304
Period size: 51 Copynumber: 4.2 Consensus size: 50
3126324 CTTACGTATG
3126334 ATCACTTATCACTTGTC-CTTGATCAGATAAGTGTAGCTAAGCTACCACTT
1 ATCACTTATCACTTGTCAC-TGATCAGATAAGTGTAGCTAAGCTACCACTT
* * * * *
3126384 ATCACTTGTCGCTTGTCACTGATTAGATAAGTGTAGATAATGCTACCAATT
1 ATCACTTATCACTTGTCACTGATCAGATAAGTGTAGCTAA-GCTACCACTT
* *
3126435 ATGACTTATCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTATCACTT
1 ATCACTTATCACTTGTCACTGATCAGATAAGTGTAGCT-AAGCTACCACTT
* *
3126486 ATCACTTGTCACTTGTCACTAATCAGATAAGTGTAGCTAAAGCTACCACTT
1 ATCACTTATCACTTGTCACTGATCAGATAAGTGTAGCT-AAGCTACCACTT
3126537 ATCACTTATCA
1 ATCACTTATCA
3126548 GAAGTACTTA
Statistics
Matches: 143, Mismatches: 18, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
50 34 0.24
51 107 0.75
52 2 0.01
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (50 bp):
ATCACTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAGCTACCACTT
Found at i:3132177 original size:44 final size:44
Alignment explanation
Indices: 3132114--3132422 Score: 300
Period size: 44 Copynumber: 6.6 Consensus size: 44
3132104 TTTGAGTACT
*
3132114 TCTGATCAGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
3132158 TCTGATCAGTGACACGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAGTG--AC-----AAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
3132209 TCTGATCAGTGACAAGTGATAAGTGATAAGTGGTAGC-TTAGCTACTCTTA
1 TCTGATCAGTGAC-------AAGTGATAAGTGGTAGCTTTAGCTACACTTA
* * *
3132259 TCTGATCAGTGACAAGTGGCAAGTGATAAGTGATAGCGTCAGCTACACTTA
1 TCTGATCAGTG---A----CAAGTGATAAGTGGTAGCTTTAGCTACACTTA
3132310 TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
** * *
3132354 TCTGATCAGTGACAAGTGGCAAGTGATAAG-TGGTAGC-ACACTTA
1 TCTGATCAGTGACAAGTGATAAGTGGT-AGCT-TTAGCTACACTTA
*
3132398 TCTGATCAGGGACAAGTGATAAGTG
1 TCTGATCAGTGACAAGTGATAAGTG
3132423 ATCATACGTA
Statistics
Matches: 231, Mismatches: 15, Indels: 38
0.81 0.05 0.13
Matches are distributed among these distances:
44 94 0.41
45 6 0.03
46 1 0.00
48 1 0.00
49 2 0.01
50 39 0.17
51 86 0.37
53 1 0.00
57 1 0.00
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.29
Consensus pattern (44 bp):
TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
Found at i:3132198 original size:51 final size:51
Alignment explanation
Indices: 3132121--3132424 Score: 413
Period size: 51 Copynumber: 6.3 Consensus size: 51
3132111 ACTTCTGATC
3132121 AGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
*
3132172 CGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
*
3132223 AGTGATAAGTGATAAGTGGTAGC-TTAGCTACTCTTATCTGATCAGTGACA
1 AGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
** * * *
3132273 AGTGGCAAGTGATAAGTGATAGCGTCAGCTACACTTATCTGATCAGTGAC-
1 AGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
3132323 ------AAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
** *
3132368 AGTGGCAAGTGATAAGT-G--G---TAGC-ACACTTATCTGATCAGGGACA
1 AGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
3132412 AGTGATAAGTGAT
1 AGTGATAAGTGAT
3132425 CATACGTAAG
Statistics
Matches: 231, Mismatches: 14, Indels: 23
0.86 0.05 0.09
Matches are distributed among these distances:
44 72 0.31
45 4 0.02
48 1 0.00
50 47 0.20
51 107 0.46
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (51 bp):
AGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
Found at i:3132876 original size:30 final size:30
Alignment explanation
Indices: 3132842--3132998 Score: 112
Period size: 29 Copynumber: 5.3 Consensus size: 30
3132832 TTATTTTTGT
*
3132842 ATTTTGACCCCTAAAATTTTCTAAAATTGC
1 ATTTTGACCCCTAAAATTTTCTAAAATTAC
* *
3132872 ATTTTAACCCCT-AAACTTTCTAAAAATTAC
1 ATTTTGACCCCTAAAATTTTCT-AAAATTAC
*
3132902 ATTTCT-ACCCCTAAAATTTT-TTAAATTAC
1 ATTT-TGACCCCTAAAATTTTCTAAAATTAC
* * ** *
3132931 ATTTGGGCCATTAAAA-TATCTATAAATTAC
1 ATTTTGACCCCTAAAATTTTCTA-AAATTAC
* * *
3132961 A-TTTGGCCCC--ATATTTTCCTAAAATTGC
1 ATTTTGACCCCTAAAATTTT-CTAAAATTAC
*
3132989 ATTTTTACCC
1 ATTTTGACCC
3132999 TAGAAACTTT
Statistics
Matches: 99, Mismatches: 19, Indels: 19
0.72 0.14 0.14
Matches are distributed among these distances:
27 2 0.02
28 11 0.11
29 42 0.42
30 37 0.37
31 7 0.07
ACGTcount: A:0.34, C:0.21, G:0.05, T:0.40
Consensus pattern (30 bp):
ATTTTGACCCCTAAAATTTTCTAAAATTAC
Found at i:3133392 original size:14 final size:13
Alignment explanation
Indices: 3133358--3133395 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
3133348 AACAACAAGC
3133358 AAAAGAGAAA-AA
1 AAAAGAGAAAGAA
*
3133370 AAAAGAGAAAGAG
1 AAAAGAGAAAGAA
3133383 AAAAGAAGAAAGA
1 AAAAG-AGAAAGA
3133396 TGGGGGAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.43
13 6 0.26
14 7 0.30
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (13 bp):
AAAAGAGAAAGAA
Found at i:3133504 original size:4 final size:4
Alignment explanation
Indices: 3133495--3133568 Score: 71
Period size: 4 Copynumber: 18.0 Consensus size: 4
3133485 GGCTGATCGG
*
3133495 GAAA GAAA GAAA AAAGA GAAA GAACA GAGAA GAAA GAAA GAAA GAAA -AAGA
1 GAAA GAAA GAAA GAA-A GAAA GAA-A GA-AA GAAA GAAA GAAA GAAA GAA-A
* *
3133546 GAAA -ACA GAAA GAAG GAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA
3133569 AAAAAGGGAG
Statistics
Matches: 58, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
3 4 0.07
4 42 0.72
5 11 0.19
6 1 0.02
ACGTcount: A:0.72, C:0.03, G:0.26, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:3133530 original size:31 final size:30
Alignment explanation
Indices: 3133495--3133574 Score: 108
Period size: 31 Copynumber: 2.6 Consensus size: 30
3133485 GGCTGATCGG
*
3133495 GAAAGAAAGAAAAAAGAGA-AAGAACAGAGAA
1 GAAAGAAAGAAAAAAAAGAGAA-AACAGA-AA
3133526 GAAAGAAAGAAAGAAAAAGAGAAAACAGAAA
1 GAAAGAAAGAAA-AAAAAGAGAAAACAGAAA
*
3133557 GAAGGAAAGAAAAAAAAG
1 GAAAGAAAGAAAAAAAAG
3133575 GGAGATAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
30 6 0.13
31 25 0.56
32 12 0.27
33 2 0.04
ACGTcount: A:0.72, C:0.03, G:0.25, T:0.00
Consensus pattern (30 bp):
GAAAGAAAGAAAAAAAAGAGAAAACAGAAA
Found at i:3133546 original size:23 final size:23
Alignment explanation
Indices: 3133496--3133564 Score: 72
Period size: 23 Copynumber: 3.0 Consensus size: 23
3133486 GCTGATCGGG
*
3133496 AAAGA-AAGAAAAAAGAGAAAG-A
1 AAAGAGAAGAAAGAA-AGAAAGAA
*
3133518 ACAGAGAAGAAAGAAAGAAAGAA
1 AAAGAGAAGAAAGAAAGAAAGAA
*
3133541 AAAGAGAA-AACAGAAAGAAGGAA
1 AAAGAGAAGAA-AGAAAGAAAGAA
3133564 A
1 A
3133565 GAAAAAAAAG
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
22 12 0.30
23 28 0.70
ACGTcount: A:0.72, C:0.03, G:0.25, T:0.00
Consensus pattern (23 bp):
AAAGAGAAGAAAGAAAGAAAGAA
Found at i:3134034 original size:10 final size:9
Alignment explanation
Indices: 3133996--3134038 Score: 52
Period size: 9 Copynumber: 4.7 Consensus size: 9
3133986 TTTTTAAGTA
3133996 TTTTTATTT
1 TTTTTATTT
*
3134005 TGTATTTA-TG
1 T-T-TTTATTT
3134015 TTTTTATTT
1 TTTTTATTT
3134024 TTTTTATTT
1 TTTTTATTT
3134033 TTTTTA
1 TTTTTA
3134039 AATTCGAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
8 4 0.14
9 18 0.62
10 3 0.10
11 4 0.14
ACGTcount: A:0.14, C:0.00, G:0.05, T:0.81
Consensus pattern (9 bp):
TTTTTATTT
Found at i:3134348 original size:18 final size:18
Alignment explanation
Indices: 3134320--3134405 Score: 81
Period size: 18 Copynumber: 4.8 Consensus size: 18
3134310 TCTTAAAAAA
3134320 TCGTG-TTTCAAAAATTT
1 TCGTGTTTTCAAAAATTT
3134337 TCGTGTTTTCAAAAAAATTT
1 TCGTGTTTTC--AAAAATTT
* *
3134357 CCCGTGTTTT-AAAAATTC
1 -TCGTGTTTTCAAAAATTT
*
3134375 TCGTATTTT--AAAATTT
1 TCGTGTTTTCAAAAATTT
*
3134391 TCTTGTTTTCAAAAA
1 TCGTGTTTTCAAAAA
3134406 AAATGATTTC
Statistics
Matches: 56, Mismatches: 7, Indels: 11
0.76 0.09 0.15
Matches are distributed among these distances:
16 13 0.23
17 12 0.21
18 15 0.27
20 8 0.14
21 8 0.14
ACGTcount: A:0.31, C:0.13, G:0.09, T:0.47
Consensus pattern (18 bp):
TCGTGTTTTCAAAAATTT
Found at i:3134362 original size:21 final size:19
Alignment explanation
Indices: 3134329--3134371 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
3134319 ATCGTGTTTC
*
3134329 AAAAATTTTCGTGTTTTCAA
1 AAAAATTTCCGTGTTTT-AA
3134349 AAAAATTTCCCGTGTTTTAA
1 AAAAATTT-CCGTGTTTTAA
3134369 AAA
1 AAA
3134372 TTCTCGTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.40
Consensus pattern (19 bp):
AAAAATTTCCGTGTTTTAA
Found at i:3134399 original size:16 final size:17
Alignment explanation
Indices: 3134320--3134405 Score: 66
Period size: 17 Copynumber: 4.8 Consensus size: 17
3134310 TCTTAAAAAA
* *
3134320 TCGTGTTTCAAAAATTT
1 TCGTGTTTTAAAAATTC
3134337 TCGTGTTTTCAAAAAAATTTC
1 TCGTGTTTT---AAAAA-TTC
*
3134358 CCGTGTTTTAAAAATTC
1 TCGTGTTTTAAAAATTC
* *
3134375 TCGTATTTT-AAAATTT
1 TCGTGTTTTAAAAATTC
*
3134391 TCTTGTTTTCAAAAA
1 TCGTGTTTT-AAAAA
3134406 AAATGATTTC
Statistics
Matches: 55, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
16 13 0.24
17 18 0.33
18 9 0.16
20 5 0.09
21 10 0.18
ACGTcount: A:0.31, C:0.13, G:0.09, T:0.47
Consensus pattern (17 bp):
TCGTGTTTTAAAAATTC
Found at i:3134468 original size:38 final size:38
Alignment explanation
Indices: 3134367--3134486 Score: 118
Period size: 38 Copynumber: 3.1 Consensus size: 38
3134357 CCCGTGTTTT
*
3134367 AAAAATTCTCGTATTT-TAAAATTTTCTTGTTTTCAAAA
1 AAAAATTCTCGTATTTCAAAAATTTTCTTGTTTT-AAAA
* ** *
3134405 AAAATGATT-TCCGTGTTTCCTAAATTTTTTTGTTTTAAAA
1 AAAA--ATTCT-CGTATTTCAAAAATTTTCTTGTTTTAAAA
* * *
3134445 AAAAATTCTCGTCTTTCAAAAATTTTCGTGTTTTCAAA
1 AAAAATTCTCGTATTTCAAAAATTTTCTTGTTTTAAAA
3134483 AAAA
1 AAAA
3134487 TTGACCGTGT
Statistics
Matches: 67, Mismatches: 10, Indels: 10
0.77 0.11 0.11
Matches are distributed among these distances:
38 34 0.51
39 2 0.03
40 17 0.25
41 14 0.21
ACGTcount: A:0.36, C:0.12, G:0.07, T:0.45
Consensus pattern (38 bp):
AAAAATTCTCGTATTTCAAAAATTTTCTTGTTTTAAAA
Found at i:3134479 original size:18 final size:17
Alignment explanation
Indices: 3134445--3134484 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
3134435 TGTTTTAAAA
3134445 AAAAATTCTCGTCTTTC
1 AAAAATTCTCGTCTTTC
* *
3134462 AAAAATTTTCGTGTTTTC
1 AAAAATTCTCGT-CTTTC
3134480 AAAAA
1 AAAAA
3134485 AATTGACCGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.38, C:0.15, G:0.07, T:0.40
Consensus pattern (17 bp):
AAAAATTCTCGTCTTTC
Found at i:3134500 original size:38 final size:38
Alignment explanation
Indices: 3134384--3134525 Score: 128
Period size: 38 Copynumber: 3.7 Consensus size: 38
3134374 CTCGTATTTT
* * *
3134384 AAAATTTTCTTGTTTTCAAAAAAAATGATTTCCGTGTTTCC
1 AAAATTTTCGTGTTTTCAAAAAAATTGA---CCGTGTTTCA
* ** * *
3134425 TAAATTTTTTTGTTTTAAAAAAAAATT--CTCGTCTTTCA
1 AAAATTTTCGTGTTTT-CAAAAAAATTGAC-CGTGTTTCA
3134463 AAAATTTTCGTGTTTTCAAAAAAATTGACCGTGTTTCA
1 AAAATTTTCGTGTTTTCAAAAAAATTGACCGTGTTTCA
* *
3134501 TAAATTTTCGAG-TTTCAAAAAAATT
1 AAAATTTTCGTGTTTTCAAAAAAATT
3134526 CTCGTGTTTC
Statistics
Matches: 84, Mismatches: 13, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
37 23 0.27
38 38 0.45
39 1 0.01
41 14 0.17
42 8 0.10
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (38 bp):
AAAATTTTCGTGTTTTCAAAAAAATTGACCGTGTTTCA
Found at i:3134589 original size:16 final size:17
Alignment explanation
Indices: 3134568--3134681 Score: 61
Period size: 20 Copynumber: 6.3 Consensus size: 17
3134558 TTTCAAAAAC
*
3134568 AAATTTT-GTGTTTTAA
1 AAATTTTCGTGTTTCAA
3134584 AAATTTTCGTGTTTCAAAA
1 AAATTTTCGTGTTTC--AA
**
3134603 AGAAAATTCGTGTTTTCAAAA
1 A-AATTTTCGTG-TTTC--AA
* *
3134624 AAAATCTCGTGTTTC-A
1 AAATTTTCGTGTTTCAA
*
3134640 AAATTTTCGTGTTTTTAAAA
1 AAATTTTCGTG--TTT-CAA
* *
3134660 AAAATTTCGTGTTTCTA
1 AAATTTTCGTGTTTCAA
3134677 AAATT
1 AAATT
3134682 CTTGTATTTA
Statistics
Matches: 77, Mismatches: 12, Indels: 17
0.73 0.11 0.16
Matches are distributed among these distances:
16 17 0.22
17 11 0.14
18 6 0.08
19 7 0.09
20 27 0.35
21 9 0.12
ACGTcount: A:0.36, C:0.09, G:0.11, T:0.44
Consensus pattern (17 bp):
AAATTTTCGTGTTTCAA
Found at i:3134590 original size:38 final size:38
Alignment explanation
Indices: 3134545--3134624 Score: 99
Period size: 37 Copynumber: 2.1 Consensus size: 38
3134535 CGTTTTTATC
* * *
3134545 AAAATTTTTATGTTTTCAAAAACAAATTTTGTGTTTT-A
1 AAAATTTTCATG-TTTCAAAAACAAAATTCGTGTTTTCA
* *
3134583 AAAATTTTCGTGTTTCAAAAAGAAAATTCGTGTTTTCA
1 AAAATTTTCATGTTTCAAAAACAAAATTCGTGTTTTCA
3134621 AAAA
1 AAAA
3134625 AAATCTCGTG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
37 21 0.58
38 15 0.42
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.42
Consensus pattern (38 bp):
AAAATTTTCATGTTTCAAAAACAAAATTCGTGTTTTCA
Found at i:3134616 original size:37 final size:38
Alignment explanation
Indices: 3134558--3134642 Score: 100
Period size: 37 Copynumber: 2.2 Consensus size: 38
3134548 ATTTTTATGT
* * * *
3134558 TTTCAAAAACAAATTTTGTGTTTT-AAAAATTTTCGTG
1 TTTCAAAAACAAAATTCGTGTTTTAAAAAAATCTCGTG
*
3134595 TTTCAAAAAGAAAATTCGTGTTTTCAAAAAAAATCTCGTG
1 TTTCAAAAACAAAATTCGTGTTTT--AAAAAAATCTCGTG
3134635 TTTCAAAA
1 TTTCAAAA
3134643 TTTTCGTGTT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
37 21 0.52
40 19 0.47
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.39
Consensus pattern (38 bp):
TTTCAAAAACAAAATTCGTGTTTTAAAAAAATCTCGTG
Found at i:3134644 original size:56 final size:58
Alignment explanation
Indices: 3134555--3134673 Score: 163
Period size: 56 Copynumber: 2.1 Consensus size: 58
3134545 AAAATTTTTA
* *
3134555 TGTTTTCAAAAACAAATTTTGTGTTTTAAAAATTTTCGTG-TTTCAAAAAGAAAATTCG
1 TGTTTTCAAAAACAAATCTCGTGTTTTAAAAATTTTCGTGTTTTCAAAAA-AAAATTCG
* * *
3134613 TGTTTTCAAAAA-AAATCTCGTG-TTTCAAAATTTTCGTGTTTTTAAAAAAAATTTCG
1 TGTTTTCAAAAACAAATCTCGTGTTTTAAAAATTTTCGTGTTTTCAAAAAAAAATTCG
3134669 TGTTT
1 TGTTT
3134674 CTAAAATTCT
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
56 27 0.49
57 16 0.29
58 12 0.22
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.44
Consensus pattern (58 bp):
TGTTTTCAAAAACAAATCTCGTGTTTTAAAAATTTTCGTGTTTTCAAAAAAAAATTCG
Found at i:3134680 original size:37 final size:37
Alignment explanation
Indices: 3134609--3134715 Score: 130
Period size: 36 Copynumber: 2.9 Consensus size: 37
3134599 AAAAAGAAAA
* *
3134609 TTCGTGTTTTCAAAAAAAATCTCGTGTTTCAAAATT-
1 TTCGTGTTTTAAAAAAAAATTTCGTGTTTCAAAATTC
*
3134645 TTCGTGTTTTTAAAAAAAATTTCGTGTTTCTAAAATTC
1 TTCGTGTTTTAAAAAAAAATTTCGTGTTTC-AAAATTC
* *
3134683 TT-GT-ATTTAAAAAAAAAATTCGTGTTTTCAAAA
1 TTCGTGTTTTAAAAAAAAATTTCGTG-TTTCAAAA
3134716 AAAAGAAAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
36 49 0.78
37 12 0.19
38 2 0.03
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.43
Consensus pattern (37 bp):
TTCGTGTTTTAAAAAAAAATTTCGTGTTTCAAAATTC
Found at i:3134700 original size:21 final size:20
Alignment explanation
Indices: 3134676--3134719 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
3134666 TCGTGTTTCT
*
3134676 AAAATTCTTGTATTTAAAAAA
1 AAAATTCGTGT-TTTAAAAAA
3134697 AAAATTCGTGTTTTCAAAAAA
1 AAAATTCGTGTTTT-AAAAAA
3134718 AA
1 AA
3134720 GAAAAAGTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 3 0.14
21 18 0.86
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.34
Consensus pattern (20 bp):
AAAATTCGTGTTTTAAAAAA
Found at i:3140087 original size:1 final size:1
Alignment explanation
Indices: 3140081--3140149 Score: 57
Period size: 1 Copynumber: 69.0 Consensus size: 1
3140071 TATTATGCCT
* ** * * * * * *
3140081 AAAAAAACAAAAAAAAACCAAAAAAAAACAAACAAAAAAAACAAAAAAAACAAAAAAGAAAAAGA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3140146 AAAA
1 AAAA
3140150 TCAAGATGAA
Statistics
Matches: 52, Mismatches: 16, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 52 1.00
ACGTcount: A:0.87, C:0.10, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:3140095 original size:9 final size:9
Alignment explanation
Indices: 3140081--3140137 Score: 73
Period size: 9 Copynumber: 6.6 Consensus size: 9
3140071 TATTATGCCT
3140081 AAAAAAACA
1 AAAAAAACA
3140090 AAAAAAA-A
1 AAAAAAACA
**
3140098 CCAAAAA-A
1 AAAAAAACA
*
3140106 AAACAAACA
1 AAAAAAACA
3140115 AAAAAAACA
1 AAAAAAACA
3140124 AAAAAAACA
1 AAAAAAACA
3140133 AAAAA
1 AAAAA
3140138 GAAAAAGAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
8 11 0.27
9 30 0.73
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (9 bp):
AAAAAAACA
Found at i:3140096 original size:10 final size:10
Alignment explanation
Indices: 3140081--3140137 Score: 78
Period size: 11 Copynumber: 5.4 Consensus size: 10
3140071 TATTATGCCT
3140081 AAAAAAACAA
1 AAAAAAACAA
3140091 AAAAAAACCAA
1 AAAAAAA-CAA
3140102 AAAAAAACAA
1 AAAAAAACAA
*
3140112 ACAAAAAAAACA
1 A-AAAAAACA-A
3140124 AAAAAAACAA
1 AAAAAAACAA
3140134 AAAA
1 AAAA
3140138 GAAAAAGAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
10 16 0.38
11 24 0.57
12 2 0.05
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:3140108 original size:14 final size:13
Alignment explanation
Indices: 3140081--3140149 Score: 63
Period size: 13 Copynumber: 5.4 Consensus size: 13
3140071 TATTATGCCT
3140081 AAAAAAAC--AAA
1 AAAAAAACAAAAA
*
3140092 AAAAAACCAAAAA
1 AAAAAAACAAAAA
3140105 AAAACAAACAAAAA
1 AAAA-AAACAAAAA
*
3140119 AAACAAA-AAAAA
1 AAAAAAACAAAAA
* *
3140131 CAAAAAAGAAAAA
1 AAAAAAACAAAAA
3140144 GAAAAA
1 -AAAAA
3140150 TCAAGATGAA
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
11 7 0.15
12 10 0.21
13 15 0.32
14 15 0.32
ACGTcount: A:0.87, C:0.10, G:0.03, T:0.00
Consensus pattern (13 bp):
AAAAAAACAAAAA
Found at i:3140117 original size:22 final size:21
Alignment explanation
Indices: 3140081--3140149 Score: 86
Period size: 22 Copynumber: 3.2 Consensus size: 21
3140071 TATTATGCCT
*
3140081 AAAAAAAC-AAAAAAAAACCAA
1 AAAAAAACAAAAAAAAAAAC-A
3140102 AAAAAAACAAACAAAAAAAACA
1 AAAAAAACAAA-AAAAAAAACA
*
3140124 AAAAAAACAAAAAAGAAAAAGA
1 AAAAAAACAAAAAA-AAAAACA
3140146 AAAA
1 AAAA
3140150 TCAAGATGAA
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
21 11 0.26
22 24 0.56
23 8 0.19
ACGTcount: A:0.87, C:0.10, G:0.03, T:0.00
Consensus pattern (21 bp):
AAAAAAACAAAAAAAAAAACA
Found at i:3141181 original size:74 final size:74
Alignment explanation
Indices: 3141032--3142358 Score: 1376
Period size: 77 Copynumber: 17.5 Consensus size: 74
3141022 TTTTCCAAAT
* *
3141032 ATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGTTGAGGTATTTTTAATTTCGGTT
1 ATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAATTTCTGTT
*
3141097 TTTTTTAAA
66 TTTTTAAAA
*
3141106 ATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAATTTATGTC
1 ATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAATTTCTGT-
3141170 TTTTTTAAAA
65 TTTTTTAAAA
* *
3141180 ATCAACTCATAATAC-AGAGGTGGGTTGAGCCTCGGGTCACGCTGAGGTTTTTTTAATTTCTGTC
1 ATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAATTTCTGT-
3141244 TTTTTT-AAA
65 TTTTTTAAAA
*
3141253 ATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAATTTCGGTT
1 ATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAATTTCTGTT
**
3141318 TTTTTTTAA
66 TTTTTAAAA
* *
3141327 ATCAACTCATAATA-TAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAATTTATGTC
1 ATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAATTTCTG--
3141391 TTTTTTTAAAA
64 TTTTTTTAAAA
** * *
3141402 ATCAACTCATAATAC-AGATATGAGTTGAGCCTCGGGTCACGCTGAGGCATTTTTAATTTATGTC
1 ATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAATTTCTGT-
*
3141466 TTTTTAAAAAAA
65 TTTTT--TAAAA
* *
3141478 ATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCACGCTGAGATATTTTTAATTTATGTC
1 ATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAATTTCTGT-
3141542 TTTTTTAAAAA
65 TTTTTT-AAAA
*
3141553 ATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAATTTATGTC
1 ATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAATTTCTGT-
*
3141617 TTTTTT-TAA
65 TTTTTTAAAA
*
3141626 ATCAACTCATAATATGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAATTTCTGTT
1 ATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAATTTCTGTT
3141691 TTTTTCAAAA
66 TTTTT-AAAA
* *
3141701 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTTTTAATTT-T
1 ATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTA---TTTTTAATTTCT
*
3141765 GTTTTTCATAAAAAAAA
63 GTTTTT--T---TAAAA
* * * ** * *
3141782 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGACCATGCCGAGGTATTTCTTTTAAATTTC
1 ATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTA--T-TTTT-AATTTC
* *
3141847 TG-TTTCTCAAAA
62 TGTTTTTTTAAAA
* * * * * *
3141859 ATCAACTCATATTGCGAGAGGTGGGTTGAGCCTC-GGACAATGCCGAGGTATTTCTTTTAAATTT
1 ATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTC-ACGCTGAGGTA--T-TTTT-AATTT
**
3141923 CTGTTTTTCAAAAA
61 CTGTTTTTTTAAAA
* * ** * *
3141937 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACCATGCCGAGGTATTTCTTTTAAATTTC
1 ATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTA--T-TTTT-AATTTC
*
3142002 TG-TTTTTCAAAA
62 TGTTTTTTTAAAA
* * ** *
3142014 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACCATGCTGAGGTATTTCTTTTAAATTTC
1 ATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTA--T-TTTT-AATTTC
*
3142079 TG-TTTTTCAAAA
62 TGTTTTTTTAAAA
* * * * * * ** * *
3142091 ATCAACTTATATTGCTAGAGATGAGTTGAGCCTTGGACCATGCCGAGGTATTTCTTTTAAATTTC
1 ATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTA--T-TTTT-AATTTC
*
3142156 TG-TTTTTCAAAA
62 TGTTTTTTTAAAA
* * * *
3142168 ATCAACTCATATTGCGAGAGGTGAGTTTAGCCTCGGGTCACGCCGAGGTATTTTTCAA-TTCT-T
1 ATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTT-AATTTCTGT
*
3142231 GTTTTTCAAAA
65 -TTTTTTAAAA
* * * * *
3142242 ATCAACTCATACTGCGAGGGGTGAGTTGAGCCTCGGGTCGCATGCCGAGGTATTCTTTTCAAATT
1 ATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGT--CACGCTGAGGTA-T-TTTT--AATT
*
3142307 T-TG-TTTTTCAAAA
60 TCTGTTTTTTTAAAA
* * * *
3142320 ATCAACTCATATTGCAAGAGGTGAGTTGAGCCTTGGGTC
1 ATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTC
3142359 GCACGCCGAG
Statistics
Matches: 1140, Mismatches: 77, Indels: 70
0.89 0.06 0.05
Matches are distributed among these distances:
73 141 0.12
74 255 0.22
75 190 0.17
76 83 0.07
77 270 0.24
78 126 0.11
79 6 0.01
80 6 0.01
81 53 0.05
82 8 0.01
83 2 0.00
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.36
Consensus pattern (74 bp):
ATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAATTTCTGTT
TTTTTAAAA
Found at i:3142630 original size:29 final size:28
Alignment explanation
Indices: 3142560--3142649 Score: 99
Period size: 29 Copynumber: 3.1 Consensus size: 28
3142550 TTTTTTGCAT
* *
3142560 TTTGACCCCTAAACTTTTCAAAATCACA
1 TTTGACCCCTAAACTTTTCTAAATTACA
*
3142588 TTTCTACCCCTAAACTTTTCTAAATTACA
1 TTT-GACCCCTAAACTTTTCTAAATTACA
* * *
3142617 TTTGAGCCCTTAAAATTTCTATAAATTACA
1 TTTGA-CCCCTAAACTTT-TCTAAATTACA
3142647 TTT
1 TTT
3142650 TGGCACCATA
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
28 4 0.08
29 35 0.67
30 13 0.25
ACGTcount: A:0.33, C:0.23, G:0.03, T:0.40
Consensus pattern (28 bp):
TTTGACCCCTAAACTTTTCTAAATTACA
Found at i:3143165 original size:4 final size:4
Alignment explanation
Indices: 3143156--3143226 Score: 60
Period size: 4 Copynumber: 17.8 Consensus size: 4
3143146 GGCTGATCGG
*
3143156 GAAA GAAA GAAA AAAGA GAAA GAAAA GAGAA GAAA GAAA G--A GAAA GAGAA
1 GAAA GAAA GAAA GAA-A GAAA G-AAA GA-AA GAAA GAAA GAAA GAAA GA-AA
*
3143206 -AAA GAAA GAAA -ACA GAAA GAA
1 GAAA GAAA GAAA GAAA GAAA GAA
3143227 GAAGGAAGAA
Statistics
Matches: 55, Mismatches: 4, Indels: 16
0.73 0.05 0.21
Matches are distributed among these distances:
2 2 0.04
3 4 0.07
4 36 0.65
5 13 0.24
ACGTcount: A:0.73, C:0.01, G:0.25, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:3143177 original size:13 final size:13
Alignment explanation
Indices: 3143159--3143217 Score: 72
Period size: 13 Copynumber: 4.8 Consensus size: 13
3143149 TGATCGGGAA
3143159 AGAAAGAAAAAAG
1 AGAAAGAAAAAAG
3143172 AGAAAG--AAAAG
1 AGAAAGAAAAAAG
3143183 AG-AAGAAAGAAAG
1 AGAAAGAAA-AAAG
*
3143196 AGAAAGAGAAAA-
1 AGAAAGAAAAAAG
3143208 AGAAAGAAAA
1 AGAAAGAAAA
3143218 CAGAAAGAAG
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
10 3 0.08
11 7 0.17
12 10 0.25
13 15 0.38
14 5 0.12
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (13 bp):
AGAAAGAAAAAAG
Found at i:3143193 original size:18 final size:17
Alignment explanation
Indices: 3143156--3143229 Score: 87
Period size: 18 Copynumber: 4.2 Consensus size: 17
3143146 GGCTGATCGG
*
3143156 GAAAG-AAAGAAAAAAGA
1 GAAAGAAAAGAGAAAA-A
3143173 GAAAGAAAAGAGAAGAAA
1 GAAAGAAAAGAGAA-AAA
3143191 GAAAGAGAAAGAGAAAAA
1 GAAAGA-AAAGAGAAAAA
*
3143209 GAAAGAAAACAGAAAGAA
1 GAAAGAAAAGAGAAA-AA
3143227 GAA
1 GAA
3143230 GGAAGAAAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
17 13 0.25
18 28 0.55
19 10 0.20
ACGTcount: A:0.73, C:0.01, G:0.26, T:0.00
Consensus pattern (17 bp):
GAAAGAAAAGAGAAAAA
Found at i:3143201 original size:6 final size:6
Alignment explanation
Indices: 3143168--3143225 Score: 66
Period size: 6 Copynumber: 9.8 Consensus size: 6
3143158 AAGAAAGAAA
* *
3143168 AAAGAG AAAGA- AAAGAG AAGAAAG AAAGAG AAAGAG AAAAAG AAAGA-
1 AAAGAG AAAGAG AAAGAG AA-AGAG AAAGAG AAAGAG AAAGAG AAAGAG
*
3143215 AAACAG AAAGA
1 AAAGAG AAAGA
3143226 AGAAGGAAGA
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
5 9 0.21
6 29 0.67
7 5 0.12
ACGTcount: A:0.72, C:0.02, G:0.26, T:0.00
Consensus pattern (6 bp):
AAAGAG
Found at i:3143702 original size:10 final size:9
Alignment explanation
Indices: 3143659--3143700 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
3143649 TTTTTAAGTA
3143659 TTTTTATTT
1 TTTTTATTT
*
3143668 TGTATTTA-TG
1 T-T-TTTATTT
3143678 TTTTTATTT
1 TTTTTATTT
3143687 TTTTTATTT
1 TTTTTATTT
3143696 TTTTT
1 TTTTT
3143701 TAAATTCGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
8 4 0.14
9 17 0.61
10 3 0.11
11 4 0.14
ACGTcount: A:0.12, C:0.00, G:0.05, T:0.83
Consensus pattern (9 bp):
TTTTTATTT
Found at i:3144027 original size:21 final size:20
Alignment explanation
Indices: 3143993--3144035 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
3143983 ATCGTGTTTC
*
3143993 AAAAATTTTCGTGTTTTCAA
1 AAAAATTTCCGTGTTTTCAA
3144013 AAAAATTTCCAGTGTTTTCAA
1 AAAAATTTCC-GTGTTTTCAA
3144034 AA
1 AA
3144036 TTCTCGTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.40
Consensus pattern (20 bp):
AAAAATTTCCGTGTTTTCAA
Found at i:3144073 original size:37 final size:38
Alignment explanation
Indices: 3144032--3144195 Score: 169
Period size: 37 Copynumber: 4.3 Consensus size: 38
3144022 CAGTGTTTTC
* *
3144032 AAAATTCTCGTATTTCA-AAATTTTCTTGTTTTCAGAAA
1 AAAATTCTCGTGTTTCATAAATTTTCGTGTTTTCA-AAA
* *
3144070 AAATGATT-TCCGTGTTTCATAAATTTTTGTG-TTTAAAAA
1 AAA--ATTCT-CGTGTTTCATAAATTTTCGTGTTTTCAAAA
* * *
3144109 AAAATTATCGTCTTTCAAAAATTTTCGTGTTTTC-AAA
1 AAAATTCTCGTGTTTCATAAATTTTCGTGTTTTCAAAA
3144146 AAAATTGAC-CGTGTTTCATAAATTTTCGTG-TTTCAAAA
1 AAAATT--CTCGTGTTTCATAAATTTTCGTGTTTTCAAAA
3144184 AAAATTCTCGTG
1 AAAATTCTCGTG
3144196 CTTCGTTTTT
Statistics
Matches: 105, Mismatches: 11, Indels: 21
0.77 0.08 0.15
Matches are distributed among these distances:
36 1 0.01
37 38 0.36
38 35 0.33
39 7 0.07
40 15 0.14
41 9 0.09
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.43
Consensus pattern (38 bp):
AAAATTCTCGTGTTTCATAAATTTTCGTGTTTTCAAAA
Found at i:3144147 original size:38 final size:37
Alignment explanation
Indices: 3144032--3144306 Score: 164
Period size: 37 Copynumber: 7.0 Consensus size: 37
3144022 CAGTGTTTTC
* * *
3144032 AAAATTCTCGTATTTC-AAAATTTTCTTGTTTTCAGAAA
1 AAAATTATCGTGTTTCAAAAATTTTCGTG-TTTCA-AAA
* * *
3144070 AAATGATT-TCCGTGTTTCATAAATTTTTGTGTTTAAAAA
1 AAA--ATTAT-CGTGTTTCAAAAATTTTCGTGTTTCAAAA
*
3144109 AAAATTATCGTCTTTCAAAAATTTTCGTGTTTTC-AAA
1 AAAATTATCGTGTTTCAAAAATTTTCGTG-TTTCAAAA
* *
3144146 AAAATTGACCGTGTTTCATAAATTTTCGTGTTTCAAAA
1 AAAATT-ATCGTGTTTCAAAAATTTTCGTGTTTCAAAA
* * **
3144184 AAAATTCTCGTGCTTCGTTTTTATCAAAATTTTTATGTTTTCAAAA
1 AAAATTATC--G--T-G-TTTCA--AAAATTTTCGTG-TTTCAAAA
* *
3144230 ACAAATT-TTGTGTTTTAAAAATTTTCGTGTTTCAAAA
1 A-AAATTATCGTGTTTCAAAAATTTTCGTGTTTCAAAA
* * *
3144267 AGAAAAT-TCGTGTTTTCAAAAAAAATCTCGTGTTTCAAAA
1 A-AAATTATCGTG-TTTC--AAAAATTTTCGTGTTTCAAAA
3144307 TTTTCGTGTT
Statistics
Matches: 189, Mismatches: 27, Indels: 40
0.74 0.11 0.16
Matches are distributed among these distances:
37 52 0.28
38 49 0.26
39 8 0.04
40 38 0.20
41 11 0.06
42 2 0.01
43 4 0.02
44 1 0.01
45 9 0.05
46 10 0.05
47 5 0.03
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.43
Consensus pattern (37 bp):
AAAATTATCGTGTTTCAAAAATTTTCGTGTTTCAAAA
Found at i:3144165 original size:75 final size:75
Alignment explanation
Indices: 3144032--3144194 Score: 231
Period size: 75 Copynumber: 2.1 Consensus size: 75
3144022 CAGTGTTTTC
*
3144032 AAAATTCTCGTATTTCAAAATTTTCTTGTTTTCAGAAAAAATGATTTCCGTGTTTCATAAATTTT
1 AAAATTCTCGTATTTCAAAATTTTCGTGTTTTCAGAAAAAATGA--TCCGTGTTTCATAAATTTT
*
3144097 TGTGTTTAAAAA
64 CGTGTTTAAAAA
* *
3144109 AAAATTATCGTCTTTCAAAAATTTTCGTGTTTTCA-AAAAAATTGA-CCGTGTTTCATAAATTTT
1 AAAATTCTCGTATTTC-AAAATTTTCGTGTTTTCAGAAAAAA-TGATCCGTGTTTCATAAATTTT
*
3144172 CGTGTTTCAAAA
64 CGTGTTTAAAAA
3144184 AAAATTCTCGT
1 AAAATTCTCGT
3144195 GCTTCGTTTT
Statistics
Matches: 78, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
75 38 0.49
77 20 0.26
78 20 0.26
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.43
Consensus pattern (75 bp):
AAAATTCTCGTATTTCAAAATTTTCGTGTTTTCAGAAAAAATGATCCGTGTTTCATAAATTTTCG
TGTTTAAAAA
Found at i:3144253 original size:16 final size:17
Alignment explanation
Indices: 3144232--3144378 Score: 66
Period size: 20 Copynumber: 8.2 Consensus size: 17
3144222 TTTCAAAAAC
*
3144232 AAATTTT-GTGTTTTAA
1 AAATTTTCGTGTTTCAA
3144248 AAATTTTCGTGTTTCAAAA
1 AAATTTTCGTGTTTC--AA
**
3144267 AGAAAATTCGTGTTTTCAAAA
1 A-AATTTTCGTG-TTTC--AA
* *
3144288 AAAATCTCGTGTTTC-A
1 AAATTTTCGTGTTTCAA
*
3144304 AAATTTTCGTGTTTTTAAAA
1 AAATTTTCGTG--TTT-CAA
* *
3144324 AAAATTTCGTGTTTCTA
1 AAATTTTCGTGTTTCAA
* *
3144341 AAATTCTT-GTATTTAAA
1 AAATT-TTCGTGTTTCAA
**
3144358 AAAAATTCGTGTTTTCAA
1 AAATTTTCGTG-TTTCAA
3144376 AAA
1 AAA
3144379 AAAAAGTTGT
Statistics
Matches: 100, Mismatches: 19, Indels: 22
0.71 0.13 0.16
Matches are distributed among these distances:
16 19 0.19
17 22 0.22
18 16 0.16
19 7 0.07
20 27 0.27
21 9 0.09
ACGTcount: A:0.37, C:0.09, G:0.11, T:0.43
Consensus pattern (17 bp):
AAATTTTCGTGTTTCAA
Found at i:3144263 original size:37 final size:37
Alignment explanation
Indices: 3144222--3144306 Score: 66
Period size: 40 Copynumber: 2.2 Consensus size: 37
3144212 ATTTTTATGT
* *
3144222 TTTCAAAAACAAATT-TTGTGTTTTAAAAATTTTCGTG
1 TTTCAAAAA-AAATTATCGTGTTTCAAAAATTTTCGTG
* * *
3144259 TTTCAAAAAGAAAAT-TCGTGTTTTCAAAAAAAATCTCGTG
1 TTTCAAAAA-AAATTATCGTG-TTTC--AAAAATTTTCGTG
3144299 TTTCAAAA
1 TTTCAAAA
3144307 TTTTCGTGTT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
37 17 0.44
38 3 0.08
40 19 0.49
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.39
Consensus pattern (37 bp):
TTTCAAAAAAAATTATCGTGTTTCAAAAATTTTCGTG
Found at i:3144309 original size:56 final size:58
Alignment explanation
Indices: 3144219--3144337 Score: 163
Period size: 56 Copynumber: 2.1 Consensus size: 58
3144209 AAAATTTTTA
* *
3144219 TGTTTTCAAAAACAAATTTTGTGTTTTAAAAATTTTCGTG-TTTCAAAAAGAAAATTCG
1 TGTTTTCAAAAACAAATCTCGTGTTTTAAAAATTTTCGTGTTTTCAAAAA-AAAATTCG
* * *
3144277 TGTTTTCAAAAA-AAATCTCGTG-TTTCAAAATTTTCGTGTTTTTAAAAAAAATTTCG
1 TGTTTTCAAAAACAAATCTCGTGTTTTAAAAATTTTCGTGTTTTCAAAAAAAAATTCG
3144333 TGTTT
1 TGTTT
3144338 CTAAAATTCT
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
56 27 0.49
57 16 0.29
58 12 0.22
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.44
Consensus pattern (58 bp):
TGTTTTCAAAAACAAATCTCGTGTTTTAAAAATTTTCGTGTTTTCAAAAAAAAATTCG
Found at i:3144324 original size:36 final size:33
Alignment explanation
Indices: 3144269--3144377 Score: 137
Period size: 36 Copynumber: 3.1 Consensus size: 33
3144259 TTTCAAAAAG
*
3144269 AAAATTCGTGTTTTCAAAAAAAATCTCGTGTTTC
1 AAAATTCGTGTTTTTAAAAAAAAT-TCGTGTTTC
3144303 AAAATTTTCGTGTTTTTAAAAAAAATTTCGTGTTTC
1 AAAA--TTCGTGTTTTTAAAAAAAA-TTCGTGTTTC
* *
3144339 TAAAATTCTTGTATTTAAAAAAAATTCGTGTTTTC
1 -AAAATTCGTGTTTTTAAAAAAAATTCGTG-TTTC
3144374 AAAA
1 AAAA
3144378 AAAAAAGTTG
Statistics
Matches: 67, Mismatches: 3, Indels: 10
0.84 0.04 0.12
Matches are distributed among these distances:
34 14 0.21
35 21 0.31
36 27 0.40
37 5 0.07
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.42
Consensus pattern (33 bp):
AAAATTCGTGTTTTTAAAAAAAATTCGTGTTTC
Found at i:3145472 original size:131 final size:132
Alignment explanation
Indices: 3145310--3145567 Score: 473
Period size: 131 Copynumber: 2.0 Consensus size: 132
3145300 ATATAAAAAC
* *
3145310 ATAATTAAATATTTAAATTAACTTTTAATCCAGTGCGATTTTTAGTTGATAAAAACATTAACCCA
1 ATAATTAAATATTTAAATTAAATTTTAATCCAGTGCAATTTTTAGTTGATAAAAACATTAACCCA
*
3145375 CGTTAGACTATATGATTATATAAGTATATTTATGGTAACACTTCTTAATTAC-ATTTTTTTTGAA
66 CGTTAGACTATATGATTATATAAGTATATATATGGTAACACTTCTTAATTACAATTTTTTTTGAA
3145439 TT
131 TT
3145441 ATAATTAAATATTTAAATTAAATTTTAATCCAGTGCAATTTTTAGTTGATAAAAACATTAACCCA
1 ATAATTAAATATTTAAATTAAATTTTAATCCAGTGCAATTTTTAGTTGATAAAAACATTAACCCA
*
3145506 CGTTAGACTATATGGTTATATAAGTATATATATGGTAACACTTCTTAATTACAATTTTTTTT
66 CGTTAGACTATATGATTATATAAGTATATATATGGTAACACTTCTTAATTACAATTTTTTTT
3145568 TTTGAATTAT
Statistics
Matches: 122, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
131 113 0.93
132 9 0.07
ACGTcount: A:0.38, C:0.10, G:0.09, T:0.43
Consensus pattern (132 bp):
ATAATTAAATATTTAAATTAAATTTTAATCCAGTGCAATTTTTAGTTGATAAAAACATTAACCCA
CGTTAGACTATATGATTATATAAGTATATATATGGTAACACTTCTTAATTACAATTTTTTTTGAA
TT
Found at i:3152407 original size:35 final size:35
Alignment explanation
Indices: 3152318--3152388 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
3152308 GTTTACAATT
*
3152318 ATATTGATACACTATTAATATTTATCAATTTTTAC
1 ATATGGATACACTATTAATATTTATCAATTTTTAC
3152353 ATATGGATACACTATTAATATTTATCAATTTTTAC
1 ATATGGATACACTATTAATATTTATCAATTTTTAC
3152388 A
1 A
3152389 AGGTTAATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.38, C:0.11, G:0.04, T:0.46
Consensus pattern (35 bp):
ATATGGATACACTATTAATATTTATCAATTTTTAC
Found at i:3155562 original size:18 final size:20
Alignment explanation
Indices: 3155532--3155568 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
3155522 TAAAGTATTT
3155532 AATTTATAGCATAA-ATAAC
1 AATTTATAGCATAATATAAC
3155551 AATTTA-AGCATAATATAA
1 AATTTATAGCATAATATAA
3155569 GGAACAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.54, C:0.08, G:0.05, T:0.32
Consensus pattern (20 bp):
AATTTATAGCATAATATAAC
Found at i:3160805 original size:26 final size:25
Alignment explanation
Indices: 3160776--3160824 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 25
3160766 GTGTTCCATC
3160776 TCTTTT-TTACTTATTATGTATTGTGT
1 TCTTTTATTA-TTATTAT-TATTGTGT
3160802 TCTTTTATTATTATTATTATTGT
1 TCTTTTATTATTATTATTATTGT
3160825 TCTTCTTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 6 0.27
26 13 0.59
27 3 0.14
ACGTcount: A:0.18, C:0.06, G:0.08, T:0.67
Consensus pattern (25 bp):
TCTTTTATTATTATTATTATTGTGT
Found at i:3160815 original size:23 final size:24
Alignment explanation
Indices: 3160780--3160828 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
3160770 TCCATCTCTT
3160780 TTTTACTTATTATGTATT-GTGTTC
1 TTTTACTTATTAT-TATTAGTGTTC
*
3160804 TTTTA-TTATTATTATTATTGTTC
1 TTTTACTTATTATTATTAGTGTTC
3160827 TT
1 TT
3160829 CTTGTTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 4 0.17
23 14 0.61
24 5 0.22
ACGTcount: A:0.18, C:0.06, G:0.08, T:0.67
Consensus pattern (24 bp):
TTTTACTTATTATTATTAGTGTTC
Found at i:3160830 original size:26 final size:26
Alignment explanation
Indices: 3160776--3160831 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
3160766 GTGTTCCATC
*
3160776 TCTTTTTTACTTATTATGTATTGTGT
1 TCTTTTTTACTTATTATGTATTGTCT
3160802 TCTTTTATTA-TTATTAT-TATTGTTCT
1 TCTTTT-TTACTTATTATGTATTG-TCT
3160828 TCTT
1 TCTT
3160832 GTTAAAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
25 5 0.19
26 19 0.70
27 3 0.11
ACGTcount: A:0.16, C:0.09, G:0.07, T:0.68
Consensus pattern (26 bp):
TCTTTTTTACTTATTATGTATTGTCT
Found at i:3167069 original size:23 final size:23
Alignment explanation
Indices: 3167017--3167069 Score: 54
Period size: 22 Copynumber: 2.2 Consensus size: 23
3167007 CTTCAATTAG
*
3167017 TATTTATCAAAAATAATTTTTAATT
1 TATTTAT--AAAATAATTTTGAATT
*
3167042 TATTTATAAAAT-ATTTTGATTT
1 TATTTATAAAATAATTTTGAATT
3167064 TGATTT
1 T-ATTT
3167070 TGATTTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
22 9 0.36
23 9 0.36
25 7 0.28
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.57
Consensus pattern (23 bp):
TATTTATAAAATAATTTTGAATT
Found at i:3171255 original size:45 final size:45
Alignment explanation
Indices: 3171175--3171294 Score: 120
Period size: 45 Copynumber: 2.7 Consensus size: 45
3171165 GCAGATTTTT
* * * * *
3171175 ATATG-CGAACTCATATATGCT-AACTCGTAGAAGAAAATTCATAG
1 ATATGACGAACTCATACATG-TGAATTCATAGTAGAAAATTCATAA
*
3171219 ATGTGGA-GAACTCATACATGTGAATTCATAGTAGAAAATTCATAA
1 ATAT-GACGAACTCATACATGTGAATTCATAGTAGAAAATTCATAA
* **
3171264 ATATGACGGACTCATACATGTGGGTTCATAG
1 ATATGACGAACTCATACATGTGAATTCATAG
3171295 ACATAGTGAA
Statistics
Matches: 62, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
44 6 0.10
45 56 0.90
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.28
Consensus pattern (45 bp):
ATATGACGAACTCATACATGTGAATTCATAGTAGAAAATTCATAA
Found at i:3171407 original size:31 final size:31
Alignment explanation
Indices: 3171256--3171413 Score: 140
Period size: 31 Copynumber: 5.1 Consensus size: 31
3171246 ATAGTAGAAA
* *
3171256 ATTCATAAATAT-GACGGACTCATACATGTGG
1 ATTCATAGATATGGA-GAACTCATACATGTGG
* * * * * ****
3171287 GTTCATAGACATAGTGAACTTATACATACAA
1 ATTCATAGATATGGAGAACTCATACATGTGG
* * *
3171318 ATTCATAGATATGGCGAACTCATACAAGCGG
1 ATTCATAGATATGGAGAACTCATACATGTGG
* *
3171349 ATTCATAGATATAGCA-AACTCATACATGTTG
1 ATTCATAGATAT-GGAGAACTCATACATGTGG
3171380 ATTCATAGATATGGAGAACTCATACATGTGG
1 ATTCATAGATATGGAGAACTCATACATGTGG
3171411 ATT
1 ATT
3171414 GTGTCACGGA
Statistics
Matches: 98, Mismatches: 26, Indels: 6
0.75 0.20 0.05
Matches are distributed among these distances:
30 2 0.02
31 94 0.96
32 2 0.02
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (31 bp):
ATTCATAGATATGGAGAACTCATACATGTGG
Found at i:3171413 original size:62 final size:62
Alignment explanation
Indices: 3171254--3171413 Score: 178
Period size: 62 Copynumber: 2.6 Consensus size: 62
3171244 TCATAGTAGA
* * * ** *
3171254 AAATTCATAAATAT-GACGGACTCATACATGTGGGTTCATAGACATAGTGAACTTATACATAC
1 AAATTCATAGATATGGA-GAACTCATACATGTGGATTCATAGACATAGCAAACTCATACATAC
* * * * **
3171316 AAATTCATAGATATGGCGAACTCATACAAGCGGATTCATAGATATAGCAAACTCATACATGT
1 AAATTCATAGATATGGAGAACTCATACATGTGGATTCATAGACATAGCAAACTCATACATAC
**
3171378 TGATTCATAGATATGGAGAACTCATACATGTGGATT
1 AAATTCATAGATATGGAGAACTCATACATGTGGATT
3171414 GTGTCACGGA
Statistics
Matches: 80, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
62 79 0.99
63 1 0.01
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (62 bp):
AAATTCATAGATATGGAGAACTCATACATGTGGATTCATAGACATAGCAAACTCATACATAC
Found at i:3172029 original size:54 final size:54
Alignment explanation
Indices: 3171947--3172056 Score: 220
Period size: 54 Copynumber: 2.0 Consensus size: 54
3171937 TTATTACCTC
3171947 CTAGCCTCTAATTAACTGATTGATTGGTTGATACTTGCTTATTTCCTTATCTCA
1 CTAGCCTCTAATTAACTGATTGATTGGTTGATACTTGCTTATTTCCTTATCTCA
3172001 CTAGCCTCTAATTAACTGATTGATTGGTTGATACTTGCTTATTTCCTTATCTCA
1 CTAGCCTCTAATTAACTGATTGATTGGTTGATACTTGCTTATTTCCTTATCTCA
3172055 CT
1 CT
3172057 TTCTCAACCA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.22, C:0.21, G:0.13, T:0.45
Consensus pattern (54 bp):
CTAGCCTCTAATTAACTGATTGATTGGTTGATACTTGCTTATTTCCTTATCTCA
Found at i:3177828 original size:29 final size:30
Alignment explanation
Indices: 3177787--3177845 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
3177777 GAATCGGATC
3177787 AAATCAAAATTTCATGTATAAAATTACACA
1 AAATCAAAATTTCATGTATAAAATTACACA
* *
3177817 AAATC-AAATTTCATGTATATAATTGCACA
1 AAATCAAAATTTCATGTATAAAATTACACA
3177846 GTAAACGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 22 0.81
30 5 0.19
ACGTcount: A:0.49, C:0.14, G:0.05, T:0.32
Consensus pattern (30 bp):
AAATCAAAATTTCATGTATAAAATTACACA
Found at i:3178074 original size:17 final size:17
Alignment explanation
Indices: 3178048--3178081 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3178038 AGACATAACT
*
3178048 AAAGTTTTAAAATTAAA
1 AAAGTATTAAAATTAAA
3178065 AAAGTATTAAAATTAAA
1 AAAGTATTAAAATTAAA
3178082 TGATCAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (17 bp):
AAAGTATTAAAATTAAA
Done.