Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D10
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: 65706892
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869813 characters in sequence are not A, C, G, or T
File 179 of 218
Found at i:53769093 original size:22 final size:21
Alignment explanation
Indices: 53769052--53769093 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
53769042 TTTTCCACTC
*
53769052 TTTCTTTTTCTTCTCTTTCAA
1 TTTCTTTTCCTTCTCTTTCAA
*
53769073 TTTCTTGTTCCTTTTCTTTCA
1 TTTCTT-TTCCTTCTCTTTCA
53769094 TCTTTCTTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.07, C:0.24, G:0.02, T:0.67
Consensus pattern (21 bp):
TTTCTTTTCCTTCTCTTTCAA
Found at i:53775309 original size:15 final size:15
Alignment explanation
Indices: 53775289--53775319 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
53775279 AGGGTTTCTG
53775289 ACTGTAATTTGGGCC
1 ACTGTAATTTGGGCC
*
53775304 ACTGTAGTTTGGGCC
1 ACTGTAATTTGGGCC
53775319 A
1 A
53775320 TTGTTATTGT
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:0.19, C:0.19, G:0.29, T:0.32
Consensus pattern (15 bp):
ACTGTAATTTGGGCC
Found at i:53777704 original size:25 final size:24
Alignment explanation
Indices: 53777670--53777733 Score: 69
Period size: 25 Copynumber: 2.7 Consensus size: 24
53777660 TTATTACTGT
*
53777670 TATTT-TATTATATATTACTATTA
1 TATTTATATTATATATTACTATCA
* * *
53777693 TTTTTAGTATTATAGATTGCTATCA
1 TATTTA-TATTATATATTACTATCA
53777718 TATTTAT-TTATATATT
1 TATTTATATTATATATT
53777734 CATTTATTCT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
23 12 0.36
24 1 0.03
25 20 0.61
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.59
Consensus pattern (24 bp):
TATTTATATTATATATTACTATCA
Found at i:53777838 original size:27 final size:27
Alignment explanation
Indices: 53777771--53777838 Score: 68
Period size: 25 Copynumber: 2.6 Consensus size: 27
53777761 ATTTTACTAC
53777771 ATATTATTTTAAAATTACTTTTATATA
1 ATATTATTTTAAAATTACTTTTATATA
* * ** *
53777798 GTTTTA-TTCCAAATT-GTTTTATATA
1 ATATTATTTTAAAATTACTTTTATATA
53777823 ATAATTATTTTAAAAT
1 AT-ATTATTTTAAAAT
53777839 CATCCTATAC
Statistics
Matches: 30, Mismatches: 9, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
25 10 0.33
26 10 0.33
27 10 0.33
ACGTcount: A:0.38, C:0.04, G:0.03, T:0.54
Consensus pattern (27 bp):
ATATTATTTTAAAATTACTTTTATATA
Found at i:53793539 original size:25 final size:25
Alignment explanation
Indices: 53793511--53793562 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
53793501 TCATTTTCTA
53793511 ATATTATTAGATTATTCTATAAAGT
1 ATATTATTAGATTATTCTATAAAGT
53793536 ATATTATTAGATTATTCTATAAAGT
1 ATATTATTAGATTATTCTATAAAGT
53793561 AT
1 AT
53793563 TGCTGCATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (25 bp):
ATATTATTAGATTATTCTATAAAGT
Found at i:53803248 original size:23 final size:24
Alignment explanation
Indices: 53803222--53803291 Score: 72
Period size: 23 Copynumber: 3.0 Consensus size: 24
53803212 TAATTCAAAA
53803222 AATATATA-ATATTTAAATAATTT
1 AATATATATATATTTAAATAATTT
* *
53803245 AATATA-ATATATATAAATTAATCT
1 AATATATATATATTTAAA-TAATTT
* * *
53803269 AATTTTTATATACTTAAATAATT
1 AATATATATATATTTAAATAATT
53803292 GATTAAGGGT
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
22 1 0.03
23 14 0.38
24 13 0.35
25 9 0.24
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (24 bp):
AATATATATATATTTAAATAATTT
Found at i:53811697 original size:31 final size:30
Alignment explanation
Indices: 53811603--53811700 Score: 94
Period size: 31 Copynumber: 3.3 Consensus size: 30
53811593 TAAAATTTAG
* * * *
53811603 ATACCAAATTAAGAAAAAGTACCAAATTCAT
1 ATACCAAATTAAGAAAAA-AAACAAAATCAA
* * *
53811634 ATACCAAATT-A-AACAAAAA-AAACTTAA
1 ATACCAAATTAAGAAAAAAAACAAAATCAA
53811661 ATACCAAATTAAGAAAAAAAATCAAAATCAA
1 ATACCAAATTAAGAAAAAAAA-CAAAATCAA
53811692 ATACCAAAT
1 ATACCAAAT
53811701 ATTATATTAA
Statistics
Matches: 54, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
27 15 0.28
28 2 0.04
29 11 0.20
30 1 0.02
31 25 0.46
ACGTcount: A:0.62, C:0.15, G:0.03, T:0.19
Consensus pattern (30 bp):
ATACCAAATTAAGAAAAAAAACAAAATCAA
Found at i:53813472 original size:34 final size:35
Alignment explanation
Indices: 53813428--53813494 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
53813418 CAGTAAAATA
* * *
53813428 TTTTCCGTAAAATGA-TTTCTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGACTTACAGGAAAATATTTTAC
*
53813462 TTTTCTGTAAAATGACTTACAGGAAAATATTTT
1 TTTTCCGTAAAATGACTTACAGGAAAATATTTT
53813495 CTGGTGTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 14 0.50
35 14 0.50
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.43
Consensus pattern (35 bp):
TTTTCCGTAAAATGACTTACAGGAAAATATTTTAC
Found at i:53813481 original size:20 final size:20
Alignment explanation
Indices: 53813443--53813481 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
53813433 CGTAAAATGA
**
53813443 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGACTTACT
*
53813463 TTTCTGTAAAATGACTTAC
1 TTTCTGGAAAATGACTTAC
53813482 AGGAAAATAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.46
Consensus pattern (20 bp):
TTTCTGGAAAATGACTTACT
Found at i:53817812 original size:19 final size:19
Alignment explanation
Indices: 53817777--53817819 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
53817767 CATTAATGAC
53817777 AATGTTATTAATAATATATT
1 AATGTTATTAATAATATA-T
*
53817797 AATGTTA-TATTAATATAT
1 AATGTTATTAATAATATAT
53817815 AATGT
1 AATGT
53817820 GAATGAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.27
19 9 0.41
20 7 0.32
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (19 bp):
AATGTTATTAATAATATAT
Found at i:53817876 original size:100 final size:100
Alignment explanation
Indices: 53817703--53817886 Score: 368
Period size: 100 Copynumber: 1.8 Consensus size: 100
53817693 ATGAGATAAA
53817703 ATATTAATATATAATGTGAATGAATTTAACCTAAAGAGATTAAGGATATCCTATGAGGGTAACAC
1 ATATTAATATATAATGTGAATGAATTTAACCTAAAGAGATTAAGGATATCCTATGAGGGTAACAC
53817768 ATTAATGACAATGTTATTAATAATATATTAATGTT
66 ATTAATGACAATGTTATTAATAATATATTAATGTT
53817803 ATATTAATATATAATGTGAATGAATTTAACCTAAAGAGATTAAGGATATCCTATGAGGGTAACAC
1 ATATTAATATATAATGTGAATGAATTTAACCTAAAGAGATTAAGGATATCCTATGAGGGTAACAC
53817868 ATTAATGACAATGTTATTA
66 ATTAATGACAATGTTATTA
53817887 GACAAATATA
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
100 84 1.00
ACGTcount: A:0.43, C:0.08, G:0.15, T:0.35
Consensus pattern (100 bp):
ATATTAATATATAATGTGAATGAATTTAACCTAAAGAGATTAAGGATATCCTATGAGGGTAACAC
ATTAATGACAATGTTATTAATAATATATTAATGTT
Found at i:53820295 original size:15 final size:16
Alignment explanation
Indices: 53820265--53820296 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
53820255 ATCATTTAAT
53820265 AATAAAATATTAATTA
1 AATAAAATATTAATTA
53820281 AATAAAATA-TAATTA
1 AATAAAATATTAATTA
53820296 A
1 A
53820297 TTAATTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
AATAAAATATTAATTA
Found at i:53820645 original size:10 final size:11
Alignment explanation
Indices: 53820625--53820661 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
53820615 TGATCATTTT
53820625 AAAAGAAAAGA
1 AAAAGAAAAGA
*
53820636 AAAAG-TAAGA
1 AAAAGAAAAGA
53820646 AAAAGAAAAGA
1 AAAAGAAAAGA
53820657 AAAAG
1 AAAAG
53820662 GGAAGTTTCG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
10 9 0.39
11 14 0.61
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (11 bp):
AAAAGAAAAGA
Found at i:53835431 original size:3 final size:3
Alignment explanation
Indices: 53835423--53835447 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
53835413 AGTGTATTTT
53835423 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
53835448 GTATAGTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:53837429 original size:11 final size:11
Alignment explanation
Indices: 53837413--53837437 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
53837403 ATCCACATTA
53837413 TTAAAAAATAT
1 TTAAAAAATAT
53837424 TTAAAAAATAT
1 TTAAAAAATAT
53837435 TTA
1 TTA
53837438 TTTGTTCAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
TTAAAAAATAT
Found at i:53845130 original size:4 final size:4
Alignment explanation
Indices: 53845121--53845180 Score: 86
Period size: 4 Copynumber: 14.8 Consensus size: 4
53845111 ATATATGTGA
*
53845121 ATGT ATGT ATGA AT-T CAGTGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT -A-TGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
53845170 ATGT ATGT ATG
1 ATGT ATGT ATG
53845181 CTGCCCTTAC
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
4 48 0.94
5 2 0.04
6 1 0.02
ACGTcount: A:0.27, C:0.02, G:0.25, T:0.47
Consensus pattern (4 bp):
ATGT
Found at i:53855166 original size:32 final size:32
Alignment explanation
Indices: 53855121--53855184 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 32
53855111 TTAAACAGGC
*
53855121 TAAGTTATCAAATTAAATTAATTC-ATTTATAA
1 TAAGTTATCAAATTAAAGTAA-TCAATTTATAA
* * *
53855153 TAAGTTGTTAAATTCAAGTAATCAATTTATAA
1 TAAGTTATCAAATTAAAGTAATCAATTTATAA
53855185 GTTTATGATG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 2 0.07
32 25 0.93
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.42
Consensus pattern (32 bp):
TAAGTTATCAAATTAAAGTAATCAATTTATAA
Found at i:53856501 original size:9 final size:9
Alignment explanation
Indices: 53856416--53856610 Score: 101
Period size: 9 Copynumber: 20.7 Consensus size: 9
53856406 GACATGTGAC
*
53856416 AAATCATAA
1 AAATTATAA
53856425 AAATTTATAA
1 AAA-TTATAA
53856435 TAAA-T-TAA
1 -AAATTATAA
*
53856443 AAA-TATTA
1 AAATTATAA
53856451 AAATTGATAA
1 AAATT-ATAA
*
53856461 AAAATATAA
1 AAATTATAA
**
53856470 AAAACATAA
1 AAATTATAA
**
53856479 AAGCGTATAA
1 AA-ATTATAA
53856489 AAATTATAA
1 AAATTATAA
*
53856498 AAATTCTAA
1 AAATTATAA
53856507 TAAATTAT-A
1 -AAATTATAA
*
53856516 AAATTTTATA
1 AAATTATA-A
53856526 AAATTAATAA
1 AAATT-ATAA
*
53856536 AACATATTTAA
1 AA-AT-TATAA
*
53856547 AATTTTATAA
1 AA-ATTATAA
* *
53856557 TGACTTATAA
1 -AAATTATAA
*
53856567 AAAATATAA
1 AAATTATAA
*
53856576 AAATTTCTAA
1 AAA-TTATAA
53856586 CAAATTATAA
1 -AAATTATAA
*
53856596 CAATTATAA
1 AAATTATAA
53856605 AAATTA
1 AAATTA
53856611 AAATTTATAT
Statistics
Matches: 143, Mismatches: 28, Indels: 30
0.71 0.14 0.15
Matches are distributed among these distances:
7 4 0.03
8 14 0.10
9 55 0.38
10 52 0.36
11 17 0.12
12 1 0.01
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (9 bp):
AAATTATAA
Found at i:53856579 original size:30 final size:30
Alignment explanation
Indices: 53856510--53856581 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 30
53856500 ATTCTAATAA
*
53856510 ATTATAAAATTTTATAAAATTAATAAAACAT
1 ATTA-AAAATTTTATAAAATTAATAAAAAAT
* *
53856541 ATTTAAAATTTTATAATGACTT-ATAAAAAAT
1 ATTAAAAATTTTATAA--AATTAATAAAAAAT
53856572 A-TAAAAATTT
1 ATTAAAAATTT
53856582 CTAACAAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
30 20 0.57
31 12 0.34
32 3 0.09
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (30 bp):
ATTAAAAATTTTATAAAATTAATAAAAAAT
Found at i:53857312 original size:30 final size:28
Alignment explanation
Indices: 53857276--53857455 Score: 130
Period size: 30 Copynumber: 6.0 Consensus size: 28
53857266 ATTGTGATTA
53857276 TTTATAATTTATTAGAATTTTTTATAAGTT
1 TTTATAATTT-TTAGAATTTTTTATAA-TT
** * *
53857306 TTTATAAAATTTATAAGTTTTTATGAATT
1 TTTATAATTTTTAGAATTTTTTAT-AATT
* * *
53857335 TTTATAATTTTTATAATTTTTTTAGAAAGT
1 TTTATAATTTTTAGAA-TTTTTTA-TAATT
*
53857365 TTTA-AATATTTTA-AATATGTTTTATATTAT
1 TTTATAAT-TTTTAGAAT-T-TTTTATAAT-T
* *
53857395 TTTATAATATATTAGAATTTTTTTATAATA
1 TTTATAAT-TTTTAGAA-TTTTTTATAATT
*
53857425 TTTATTAGTTTTTATGAATTTTTTATAATT
1 TTTA-TAATTTTTA-GAATTTTTTATAATT
53857455 T
1 T
53857456 ATAAGTTTAT
Statistics
Matches: 120, Mismatches: 18, Indels: 24
0.74 0.11 0.15
Matches are distributed among these distances:
28 1 0.01
29 35 0.29
30 58 0.48
31 22 0.18
32 3 0.03
33 1 0.01
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (28 bp):
TTTATAATTTTTAGAATTTTTTATAATT
Found at i:53857320 original size:19 final size:19
Alignment explanation
Indices: 53857296--53857350 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
53857286 ATTAGAATTT
53857296 TTTATAAGTTTTTATAAAA
1 TTTATAAGTTTTTATAAAA
**
53857315 TTTATAAGTTTTTATGAATT
1 TTTATAAGTTTTTAT-AAAA
53857335 TTTATAA-TTTTTATAA
1 TTTATAAGTTTTTATAA
53857351 TTTTTTTAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
18 2 0.06
19 22 0.67
20 9 0.27
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.58
Consensus pattern (19 bp):
TTTATAAGTTTTTATAAAA
Found at i:53857336 original size:29 final size:29
Alignment explanation
Indices: 53857294--53857356 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
53857284 TTATTAGAAT
53857294 TTTTTATAAGTTTTTATAAAATTTATAAG
1 TTTTTATAAGTTTTTATAAAATTTATAAG
** *
53857323 TTTTTATGAA-TTTTTATAATTTTTATAAT
1 TTTTTAT-AAGTTTTTATAAAATTTATAAG
53857352 TTTTT
1 TTTTT
53857357 TAGAAAGTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 28 0.93
30 2 0.07
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (29 bp):
TTTTTATAAGTTTTTATAAAATTTATAAG
Found at i:53857449 original size:11 final size:10
Alignment explanation
Indices: 53857276--53857455 Score: 104
Period size: 10 Copynumber: 18.0 Consensus size: 10
53857266 ATTGTGATTA
53857276 TTTATAATTT
1 TTTATAATTT
* *
53857286 ATTAGAATTT
1 TTTATAATTT
*
53857296 TTTATAAGTT
1 TTTATAATTT
**
53857306 TTTATAA-AA
1 TTTATAATTT
*
53857315 TTTATAAGTT
1 TTTATAATTT
53857325 TTTATGAA-TT
1 TTTAT-AATTT
53857335 TTTATAA-TT
1 TTTATAATTT
53857344 TTTATAATTTT
1 TTTATAA-TTT
* **
53857355 TTTAGAAAGT
1 TTTATAATTT
*
53857365 TTTA-AATAT
1 TTTATAATTT
53857374 TTTA-AATATGT
1 TTTATAAT-T-T
53857385 TTTAT-ATTAT
1 TTTATAATT-T
*
53857395 TTTATAATAT
1 TTTATAATTT
* *
53857405 ATTAGAATTTT
1 TTTATAA-TTT
*
53857416 TTTATAA-TA
1 TTTATAATTT
* *
53857425 TTTATTAGTT
1 TTTATAATTT
53857435 TTTATGAATTT
1 TTTAT-AATTT
53857446 TTTATAATTT
1 TTTATAATTT
53857456 ATAAGTTTAT
Statistics
Matches: 132, Mismatches: 27, Indels: 22
0.73 0.15 0.12
Matches are distributed among these distances:
9 35 0.27
10 63 0.48
11 34 0.26
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (10 bp):
TTTATAATTT
Found at i:53857475 original size:28 final size:30
Alignment explanation
Indices: 53857414--53857475 Score: 74
Period size: 28 Copynumber: 2.1 Consensus size: 30
53857404 TATTAGAATT
* * * *
53857414 TTTTTATAATATTTATTAGTTTTTATGAAT
1 TTTTTATAATATTTATAAGTTTATATAAAA
53857444 TTTTTAT-A-ATTTATAAGTTTATATAAAA
1 TTTTTATAATATTTATAAGTTTATATAAAA
53857472 TTTT
1 TTTT
53857476 GATATTTGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 20 0.71
29 1 0.04
30 7 0.25
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (30 bp):
TTTTTATAATATTTATAAGTTTATATAAAA
Found at i:53857705 original size:13 final size:12
Alignment explanation
Indices: 53857685--53857721 Score: 56
Period size: 13 Copynumber: 3.0 Consensus size: 12
53857675 CCCATAAAGC
53857685 TAAATAAAAATA
1 TAAATAAAAATA
53857697 TACAATAAAAATA
1 TA-AATAAAAATA
*
53857710 TAAATATAAATA
1 TAAATAAAAATA
53857722 CACTCTTACT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.48
13 12 0.52
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (12 bp):
TAAATAAAAATA
Found at i:53857714 original size:19 final size:18
Alignment explanation
Indices: 53857686--53857721 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
53857676 CCATAAAGCT
53857686 AAATAAAAATATACAATAA
1 AAATAAAAATATA-AATAA
*
53857705 AAATATAAATATAAATA
1 AAATAAAAATATAAATA
53857722 CACTCTTACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (18 bp):
AAATAAAAATATAAATAA
Found at i:53861120 original size:11 final size:11
Alignment explanation
Indices: 53861106--53861130 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
53861096 GTTGAAGGAG
53861106 GATTATAAAAT
1 GATTATAAAAT
53861117 GATTATAAAAT
1 GATTATAAAAT
53861128 GAT
1 GAT
53861131 CCTAAATACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.12, T:0.36
Consensus pattern (11 bp):
GATTATAAAAT
Found at i:53862083 original size:19 final size:19
Alignment explanation
Indices: 53862045--53862083 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
53862035 AATTGTGATT
*
53862045 TTTTTAAATAATTTTATAA
1 TTTTTAAATAATTGTATAA
53862064 TTTTTAAATTAATTGT-TAA
1 TTTTTAAA-TAATTGTATAA
53862083 T
1 T
53862084 GTGACATACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (19 bp):
TTTTTAAATAATTGTATAA
Found at i:53867865 original size:40 final size:40
Alignment explanation
Indices: 53867792--53867887 Score: 122
Period size: 40 Copynumber: 2.4 Consensus size: 40
53867782 TACCGGCCTA
*
53867792 AAGCCTGCTAGGGCACTAAGCCCGACAATTACACCGGTACG
1 AAGCCTGCTA-GGCACTAAGCCCGACAATTACACCGGCACG
* * * *
53867833 AAGCCTGCTTGGCATTAAGCCCGATAGA-TACACTGGCACG
1 AAGCCTGCTAGGCACTAAGCCCGACA-ATTACACCGGCACG
53867873 AAGCCTGCTAGGCAC
1 AAGCCTGCTAGGCAC
53867888 AAGGCTTAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
40 37 0.79
41 10 0.21
ACGTcount: A:0.28, C:0.30, G:0.25, T:0.17
Consensus pattern (40 bp):
AAGCCTGCTAGGCACTAAGCCCGACAATTACACCGGCACG
Found at i:53869028 original size:36 final size:35
Alignment explanation
Indices: 53868988--53869080 Score: 98
Period size: 36 Copynumber: 2.5 Consensus size: 35
53868978 TATATGTGTG
* *
53868988 GAATTGAAATGAATAT-TGACTTGAAAATGGAAAAGT
1 GAATTGAATTGAAT-TGTGA-TTGAAAATGAAAAAGT
*
53869024 GAATTTTGAATTGAATTGTGATTGAAAGTGAAAAAGT
1 GAA--TTGAATTGAATTGTGATTGAAAATGAAAAAGT
*
53869061 GAAATTGAATTGAAATGTGA
1 G-AATTGAATTGAATTGTGA
53869081 ATTTGGAGAC
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
36 18 0.37
37 16 0.33
38 15 0.31
ACGTcount: A:0.44, C:0.01, G:0.24, T:0.31
Consensus pattern (35 bp):
GAATTGAATTGAATTGTGATTGAAAATGAAAAAGT
Found at i:53870687 original size:14 final size:14
Alignment explanation
Indices: 53870660--53870693 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
53870650 AAACTGCAGT
*
53870660 AATGATAAAGGTAC
1 AATGACAAAGGTAC
*
53870674 AATGACAAATGTAC
1 AATGACAAAGGTAC
53870688 AATGAC
1 AATGAC
53870694 TATTGAGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.18, T:0.21
Consensus pattern (14 bp):
AATGACAAAGGTAC
Found at i:53872658 original size:64 final size:63
Alignment explanation
Indices: 53872523--53872673 Score: 221
Period size: 64 Copynumber: 2.4 Consensus size: 63
53872513 ATAACACACC
* * * * *
53872523 ACGTTGTGACCAAGCCACTCAATATCGCAGTCAAGCTGTACGTTGTGGTCAAGCCACTCAATA
1 ACGTTGTGGCCAAGCCACTCAATATCACAGGCAAACTGTACGTTATGGTCAAGCCACTCAATA
* *
53872586 ACATTGTGGCCAAGCCACTCAATATCACAGGCAAACTGTATCGTTATTGTCAAGCCACTCAATA
1 ACGTTGTGGCCAAGCCACTCAATATCACAGGCAAACTGTA-CGTTATGGTCAAGCCACTCAATA
*
53872650 GCGTTGTGGCCAAGCCACTCAATA
1 ACGTTGTGGCCAAGCCACTCAATA
53872674 GCGTTGTGGC
Statistics
Matches: 78, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
63 35 0.45
64 43 0.55
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (63 bp):
ACGTTGTGGCCAAGCCACTCAATATCACAGGCAAACTGTACGTTATGGTCAAGCCACTCAATA
Found at i:53872663 original size:24 final size:24
Alignment explanation
Indices: 53872636--53872694 Score: 118
Period size: 24 Copynumber: 2.5 Consensus size: 24
53872626 TCGTTATTGT
53872636 CAAGCCACTCAATAGCGTTGTGGC
1 CAAGCCACTCAATAGCGTTGTGGC
53872660 CAAGCCACTCAATAGCGTTGTGGC
1 CAAGCCACTCAATAGCGTTGTGGC
53872684 CAAGCCACTCA
1 CAAGCCACTCA
53872695 TTATTGCAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.27, C:0.32, G:0.22, T:0.19
Consensus pattern (24 bp):
CAAGCCACTCAATAGCGTTGTGGC
Found at i:53872833 original size:42 final size:42
Alignment explanation
Indices: 53872784--53872889 Score: 133
Period size: 42 Copynumber: 2.5 Consensus size: 42
53872774 TATTTTCAGT
* *
53872784 GACATGCTTAACATGTAAAT-TGAATTTATAATCAACATAGTC
1 GACATGCTTAACATGCAAATCAGAA-TTATAATCAACATAGTC
* * * *
53872826 GGCATGCTTAACATGCGAATCAGAATTATAATTAATATAGTC
1 GACATGCTTAACATGCAAATCAGAATTATAATCAACATAGTC
*
53872868 GACATGCTTAACATGCGAATCA
1 GACATGCTTAACATGCAAATCA
53872890 TATCTCAATT
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
42 53 0.95
43 3 0.05
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.30
Consensus pattern (42 bp):
GACATGCTTAACATGCAAATCAGAATTATAATCAACATAGTC
Found at i:53875410 original size:16 final size:17
Alignment explanation
Indices: 53875391--53875427 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
53875381 ATAAACATTT
*
53875391 AAAACCTTAA-AAACCA
1 AAAACCCTAACAAACCA
53875407 AAAACCCTAACAAACCA
1 AAAACCCTAACAAACCA
53875424 AAAA
1 AAAA
53875428 ATTGTAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.65, C:0.27, G:0.00, T:0.08
Consensus pattern (17 bp):
AAAACCCTAACAAACCA
Found at i:53880136 original size:15 final size:15
Alignment explanation
Indices: 53880116--53880170 Score: 60
Period size: 15 Copynumber: 3.8 Consensus size: 15
53880106 CCTTTTTTTA
53880116 TTTTAATTTTAAAAT
1 TTTTAATTTTAAAAT
* *
53880131 TTTTAATTTTTATAT
1 TTTTAATTTTAAAAT
**
53880146 TTCAAATTTTAAAA-
1 TTTTAATTTTAAAAT
53880160 -TTTAATTTTAA
1 TTTTAATTTTAA
53880171 TTATTAGTAT
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
13 9 0.28
15 23 0.72
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (15 bp):
TTTTAATTTTAAAAT
Found at i:53880139 original size:21 final size:21
Alignment explanation
Indices: 53880109--53880170 Score: 70
Period size: 22 Copynumber: 2.9 Consensus size: 21
53880099 CCTCCTCCCT
*
53880109 TTTTTTATTTTAATTTTAAAA
1 TTTTTAATTTTAATTTTAAAA
* *
53880130 TTTTTAATTTTTATATTTCAAA
1 TTTTTAATTTTAAT-TTTAAAA
* *
53880152 TTTTAAAATTTAATTTTAA
1 TTTTTAATTTTAATTTTAA
53880171 TTATTAGTAT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
21 16 0.48
22 17 0.52
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTTTAATTTTAATTTTAAAA
Found at i:53880880 original size:24 final size:24
Alignment explanation
Indices: 53880870--53880915 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
53880860 ATTTATTAGT
53880870 ATAATATATTTAGCATTGATTAAC
1 ATAATATATTTAGCATTGATTAAC
53880894 ATAATATATTT-GACATTGATTA
1 ATAATATATTTAG-CATTGATTA
53880916 GAATTAGGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.43
Consensus pattern (24 bp):
ATAATATATTTAGCATTGATTAAC
Found at i:53885349 original size:24 final size:24
Alignment explanation
Indices: 53885292--53885343 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
53885282 TTTCTAGAAA
* * *
53885292 ATTTAGTACTTATTAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
53885316 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATTAGCATAATAT
53885340 ATTT
1 ATTT
53885344 GACATTGATT
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:0.37, C:0.06, G:0.08, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:53885354 original size:24 final size:24
Alignment explanation
Indices: 53885303--53885355 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
53885293 TTTAGTACTT
* *
53885303 ATTAGTATAATATATTTAGCATTT
1 ATTAGCATAATATATTTAGCATTG
53885327 ATTAGCATAATATATTT-GACATTG
1 ATTAGCATAATATATTTAG-CATTG
53885351 ATTAG
1 ATTAG
53885356 AATTAGGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 1 0.04
24 25 0.96
ACGTcount: A:0.38, C:0.06, G:0.11, T:0.45
Consensus pattern (24 bp):
ATTAGCATAATATATTTAGCATTG
Found at i:53887665 original size:2 final size:2
Alignment explanation
Indices: 53887658--53887694 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
53887648 ACTCAATTAC
53887658 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
53887695 AAACTTCAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:53888691 original size:45 final size:45
Alignment explanation
Indices: 53888642--53888731 Score: 144
Period size: 45 Copynumber: 2.0 Consensus size: 45
53888632 TTTGATCGAA
*
53888642 GATGACAACGAGGATGATAGATTGAAGAAGAAGATCAAGAAAGAG
1 GATGACAACGAGGAGGATAGATTGAAGAAGAAGATCAAGAAAGAG
** *
53888687 GATGATGACGAGGAGGATAGATTGAAGAAGAAGATCAAGATAGAG
1 GATGACAACGAGGAGGATAGATTGAAGAAGAAGATCAAGAAAGAG
53888732 AACATTTAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.47, C:0.06, G:0.33, T:0.14
Consensus pattern (45 bp):
GATGACAACGAGGAGGATAGATTGAAGAAGAAGATCAAGAAAGAG
Found at i:53892252 original size:23 final size:21
Alignment explanation
Indices: 53892232--53892296 Score: 67
Period size: 25 Copynumber: 2.8 Consensus size: 21
53892222 TCTATTTACC
53892232 TTTTTTATATATATTATTTTA
1 TTTTTTATATATATTATTTTA
*
53892253 TTTTATTATATACTGTTATTTTTA
1 TTTT-TTATATA-TATTA-TTTTA
53892277 TTCTTTTTATCATATATTAT
1 -T-TTTTTAT-ATATATTAT
53892297 ATCTAATTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
21 4 0.11
22 7 0.19
23 4 0.11
24 6 0.17
25 9 0.25
26 6 0.17
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.68
Consensus pattern (21 bp):
TTTTTTATATATATTATTTTA
Found at i:53892650 original size:14 final size:14
Alignment explanation
Indices: 53892633--53892661 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
53892623 ACAATTTTTT
53892633 TATACATATATATA
1 TATACATATATATA
53892647 TATACATATATATA
1 TATACATATATATA
53892661 T
1 T
53892662 TACTTTTGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (14 bp):
TATACATATATATA
Found at i:53894463 original size:15 final size:15
Alignment explanation
Indices: 53894440--53894473 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
53894430 TGAACTGCAT
53894440 TGTTCTGCTCTGTTC
1 TGTTCTGCTCTGTTC
* *
53894455 TGTTTTGCTTTGTTC
1 TGTTCTGCTCTGTTC
53894470 TGTT
1 TGTT
53894474 GTATTACATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.00, C:0.18, G:0.21, T:0.62
Consensus pattern (15 bp):
TGTTCTGCTCTGTTC
Found at i:53897100 original size:41 final size:41
Alignment explanation
Indices: 53897050--53897359 Score: 485
Period size: 41 Copynumber: 7.6 Consensus size: 41
53897040 TTAAACAGGT
* * * * *
53897050 TCACTGGCACTTAGCTTGTTAGGCTTAAAGCCTGATTTAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
* * * *
53897091 TCATCGGCACTTAGCCTGCTAGGCTTATAGCCTAATCCAGT
1 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
*
53897132 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAAA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
*
53897173 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAAA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
*
53897214 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGT
1 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
*
53897255 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGT
1 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
* *
53897296 TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTTAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
53897337 TCACCGGCACTTAGCCTGCTAGG
1 TCACCGGCACTTAGCCTGCTAGG
53897360 TTTTAAAACC
Statistics
Matches: 250, Mismatches: 19, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 250 1.00
ACGTcount: A:0.22, C:0.28, G:0.21, T:0.29
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
Found at i:53899621 original size:38 final size:38
Alignment explanation
Indices: 53899579--53899666 Score: 158
Period size: 38 Copynumber: 2.3 Consensus size: 38
53899569 CTCCGTCCAA
*
53899579 CCCTACACTTCATGTGGGGATATAATCAACCCACATAT
1 CCCTACACTCCATGTGGGGATATAATCAACCCACATAT
53899617 CCCTACACTCCATGTGGGGATATAATCAACCCACATAT
1 CCCTACACTCCATGTGGGGATATAATCAACCCACATAT
*
53899655 CCTTACACTCCA
1 CCCTACACTCCA
53899667 AGTAGTACCG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
38 48 1.00
ACGTcount: A:0.31, C:0.33, G:0.11, T:0.25
Consensus pattern (38 bp):
CCCTACACTCCATGTGGGGATATAATCAACCCACATAT
Found at i:53905758 original size:79 final size:79
Alignment explanation
Indices: 53905627--53905783 Score: 305
Period size: 79 Copynumber: 2.0 Consensus size: 79
53905617 GATAACCCTT
*
53905627 CGTTTAACTATTGTTAAGACGAGAACATTGAATTCACCAGTCCGAGCCTCCCCCTATGCCCATAT
1 CGTTTAAATATTGTTAAGACGAGAACATTGAATTCACCAGTCCGAGCCTCCCCCTATGCCCATAT
53905692 CGCAGAGAAAAAAC
66 CGCAGAGAAAAAAC
53905706 CGTTTAAATATTGTTAAGACGAGAACATTGAATTCACCAGTCCGAGCCTCCCCCTATGCCCATAT
1 CGTTTAAATATTGTTAAGACGAGAACATTGAATTCACCAGTCCGAGCCTCCCCCTATGCCCATAT
53905771 CGCAGAGAAAAAA
66 CGCAGAGAAAAAA
53905784 AATTACCACT
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 77 1.00
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.23
Consensus pattern (79 bp):
CGTTTAAATATTGTTAAGACGAGAACATTGAATTCACCAGTCCGAGCCTCCCCCTATGCCCATAT
CGCAGAGAAAAAAC
Found at i:53907947 original size:5 final size:5
Alignment explanation
Indices: 53907939--53907972 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
53907929 TATATTTTGT
53907939 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
53907973 AAGGAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTC
Found at i:53909434 original size:45 final size:45
Alignment explanation
Indices: 53909336--53909434 Score: 128
Period size: 45 Copynumber: 2.2 Consensus size: 45
53909326 AACCAATTTT
* *
53909336 GATTGA-AGATGATGACAAGGATGATAGATTGAAGAAGAAGATCAA
1 GATTGAGA-ATGATGACAAGGAGGATAAATTGAAGAAGAAGATCAA
** * *
53909381 GAAAGAGAATGATGACGAGTAGGATAAATTGAAGAAGAAGATCAA
1 GATTGAGAATGATGACAAGGAGGATAAATTGAAGAAGAAGATCAA
53909426 GATTGAGAA
1 GATTGAGAA
53909435 CATTTAAATA
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
45 44 0.98
46 1 0.02
ACGTcount: A:0.48, C:0.04, G:0.29, T:0.18
Consensus pattern (45 bp):
GATTGAGAATGATGACAAGGAGGATAAATTGAAGAAGAAGATCAA
Found at i:53913021 original size:19 final size:19
Alignment explanation
Indices: 53912994--53913031 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
53912984 ATTTAGTATT
*
53912994 TAATTGTAATCTAAAATGA
1 TAATCGTAATCTAAAATGA
53913013 TAATCGTAATCTAAAATGA
1 TAATCGTAATCTAAAATGA
53913032 CAATTACTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.47, C:0.08, G:0.11, T:0.34
Consensus pattern (19 bp):
TAATCGTAATCTAAAATGA
Found at i:53914852 original size:23 final size:23
Alignment explanation
Indices: 53914826--53914869 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
53914816 CATTGCATCG
*
53914826 AAGTGCCACTTTTATTTGCACCA
1 AAGTGCCACTTTCATTTGCACCA
53914849 AAGTGCCACTTTCATTTGCAC
1 AAGTGCCACTTTCATTTGCAC
53914870 GCATAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.25, C:0.27, G:0.14, T:0.34
Consensus pattern (23 bp):
AAGTGCCACTTTCATTTGCACCA
Found at i:53916754 original size:19 final size:20
Alignment explanation
Indices: 53916731--53916774 Score: 51
Period size: 18 Copynumber: 2.4 Consensus size: 20
53916721 ATGATAATCG
53916731 TAATTTAAATAT-TAAAATAA
1 TAATTTAAATATATAAAA-AA
53916751 -AA-TT-AATATATAAAAAA
1 TAATTTAAATATATAAAAAA
53916768 TAATTTA
1 TAATTTA
53916775 GCATTTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 8
0.71 0.00 0.29
Matches are distributed among these distances:
17 7 0.35
18 9 0.45
19 4 0.20
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
TAATTTAAATATATAAAAAA
Found at i:53916807 original size:19 final size:19
Alignment explanation
Indices: 53916780--53916817 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
53916770 ATTTAGCATT
*
53916780 TAATTGTAATCTAAAATGA
1 TAATCGTAATCTAAAATGA
53916799 TAATCGTAATCTAAAATGA
1 TAATCGTAATCTAAAATGA
53916818 CAATTACTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.47, C:0.08, G:0.11, T:0.34
Consensus pattern (19 bp):
TAATCGTAATCTAAAATGA
Found at i:53920630 original size:91 final size:90
Alignment explanation
Indices: 53920472--53920650 Score: 270
Period size: 91 Copynumber: 2.0 Consensus size: 90
53920462 ACACTCCTGC
* * *
53920472 TTGTGGATGAACCACAAGTGTTGTAAGTTAATATGCTACCAGTAATTGTGAATACACAACGGGTT
1 TTGTGGATAAACCACAAGTGTTGTAAGTTAATACGCTACCAGTAATTGTGAATACACAACGGATT
* *
53920537 TGCAGATAAAAGTTGCCATTAAATG
66 TGCAGATAAAAGTTACCAGTAAATG
* *
53920562 TTGTGGATAAACCACAATTGTTTGTAGGTTAATACGCTACCAGTAATTGTGAATACACAATC-GA
1 TTGTGGATAAACCACAAGTG-TTGTAAGTTAATACGCTACCAGTAATTGTGAATACACAA-CGGA
53920626 TTTGCAGATAAAAGTTACCAGTAAA
64 TTTGCAGATAAAAGTTACCAGTAAA
53920651 ACTTTTAGAT
Statistics
Matches: 80, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
90 18 0.22
91 61 0.76
92 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (90 bp):
TTGTGGATAAACCACAAGTGTTGTAAGTTAATACGCTACCAGTAATTGTGAATACACAACGGATT
TGCAGATAAAAGTTACCAGTAAATG
Found at i:53925721 original size:29 final size:27
Alignment explanation
Indices: 53925689--53925742 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 27
53925679 TTCTTTTTAC
*
53925689 TGTTAAACTGAAGTTTTTATAAATTGGTA
1 TGTTAAACT-AAG-GTTTATAAATTGGTA
*
53925718 TGTTAAACTAAGGTTTCTAAATTGG
1 TGTTAAACTAAGGTTTATAAATTGG
53925743 CTTGGTGGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 11 0.48
28 3 0.13
29 9 0.39
ACGTcount: A:0.33, C:0.06, G:0.19, T:0.43
Consensus pattern (27 bp):
TGTTAAACTAAGGTTTATAAATTGGTA
Found at i:53948516 original size:27 final size:27
Alignment explanation
Indices: 53948486--53948555 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
53948476 AATAATCAAT
*
53948486 TCAATATCCAACAATGTTAAAACATA-A
1 TCAATATCCAACAAT-TCAAAACATATA
* *
53948513 TCAATATCTAACAAATTCAAGACATATA
1 TCAATATCCAAC-AATTCAAAACATATA
*
53948541 TCAAAATCCAACAAT
1 TCAATATCCAACAAT
53948556 CTAAAATTTC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
27 22 0.61
28 14 0.39
ACGTcount: A:0.51, C:0.20, G:0.03, T:0.26
Consensus pattern (27 bp):
TCAATATCCAACAATTCAAAACATATA
Found at i:53951435 original size:8 final size:8
Alignment explanation
Indices: 53951422--53951454 Score: 66
Period size: 8 Copynumber: 4.1 Consensus size: 8
53951412 CCATTACCAG
53951422 GAACAACA
1 GAACAACA
53951430 GAACAACA
1 GAACAACA
53951438 GAACAACA
1 GAACAACA
53951446 GAACAACA
1 GAACAACA
53951454 G
1 G
53951455 GAACGGCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.61, C:0.24, G:0.15, T:0.00
Consensus pattern (8 bp):
GAACAACA
Found at i:53952282 original size:24 final size:24
Alignment explanation
Indices: 53952255--53952327 Score: 103
Period size: 24 Copynumber: 3.0 Consensus size: 24
53952245 TGCAATCGAT
* *
53952255 AGGGTGAATAGAAGAGCTGTGGAA
1 AGGGTGAAGAGAGGAGCTGTGGAA
*
53952279 AGGGTGAAGAGAGGA-ATAGTGGAA
1 AGGGTGAAGAGAGGAGCT-GTGGAA
53952303 AGGGTGAAGAGAGGAGCTGTGGAA
1 AGGGTGAAGAGAGGAGCTGTGGAA
53952327 A
1 A
53952328 ATGTCTTACC
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
23 1 0.02
24 41 0.95
25 1 0.02
ACGTcount: A:0.38, C:0.03, G:0.45, T:0.14
Consensus pattern (24 bp):
AGGGTGAAGAGAGGAGCTGTGGAA
Found at i:53955419 original size:21 final size:21
Alignment explanation
Indices: 53955394--53955461 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 21
53955384 TGAGCTTTAG
* *
53955394 TTAACTCATATGAGTTTCAAT
1 TTAACTCTTCTGAGTTTCAAT
*
53955415 TTAACCCTTCT-AGGTTTCAAT
1 TTAACTCTTCTGA-GTTTCAAT
* *
53955436 TCAACTCTTCTGAGCTTCAAT
1 TTAACTCTTCTGAGTTTCAAT
53955457 TTAAC
1 TTAAC
53955462 CCTTATGGGT
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
20 1 0.03
21 36 0.95
22 1 0.03
ACGTcount: A:0.28, C:0.22, G:0.09, T:0.41
Consensus pattern (21 bp):
TTAACTCTTCTGAGTTTCAAT
Found at i:53955473 original size:42 final size:41
Alignment explanation
Indices: 53955396--53955516 Score: 125
Period size: 42 Copynumber: 2.9 Consensus size: 41
53955386 AGCTTTAGTT
* * * *
53955396 AACTCATATGAGTTTCAATTTAACCCTTCTAGGTTTCAATTC
1 AACTCCTATGAGCTTCAATTTAACCCTTATGGGTTTC-ATTC
* *
53955438 AACTCTTCTGAGCTTCAATTTAACCCTTATGGGTTTTCATTC
1 AACTCCTATGAGCTTCAATTTAACCCTTATGGG-TTTCATTC
* ** * *
53955480 AGCTCCTATGAGCTTCTCTTCAACCCTTACGGGTTTC
1 AACTCCTATGAGCTTCAATTTAACCCTTATGGGTTTC
53955517 TGTTTAGCAC
Statistics
Matches: 66, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
41 4 0.06
42 58 0.88
43 4 0.06
ACGTcount: A:0.22, C:0.26, G:0.12, T:0.40
Consensus pattern (41 bp):
AACTCCTATGAGCTTCAATTTAACCCTTATGGGTTTCATTC
Found at i:53959465 original size:26 final size:26
Alignment explanation
Indices: 53959436--53959506 Score: 88
Period size: 26 Copynumber: 2.7 Consensus size: 26
53959426 TACATTCTGA
*
53959436 CCCACAGCTTGTGTGAGCAGGCCCAT
1 CCCACAGCTCGTGTGAGCAGGCCCAT
* * *
53959462 CCCACAACTCATGTGAACAGGCCCAT
1 CCCACAGCTCGTGTGAGCAGGCCCAT
**
53959488 TTCACAGCTCGTGTGAGCA
1 CCCACAGCTCGTGTGAGCA
53959507 ATGATGTAAA
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.24, C:0.34, G:0.23, T:0.20
Consensus pattern (26 bp):
CCCACAGCTCGTGTGAGCAGGCCCAT
Found at i:53961013 original size:26 final size:23
Alignment explanation
Indices: 53960961--53961006 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
53960951 ACAGTGGGAG
53960961 TCATTCCAACAACAGCTCTGAAC
1 TCATTCCAACAACAGCTCTGAAC
* *
53960984 TCATTCCAGCAACGGCTCTGAAC
1 TCATTCCAACAACAGCTCTGAAC
53961007 ATTTCATCCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.30, C:0.35, G:0.13, T:0.22
Consensus pattern (23 bp):
TCATTCCAACAACAGCTCTGAAC
Found at i:53967949 original size:91 final size:91
Alignment explanation
Indices: 53967794--53968001 Score: 301
Period size: 91 Copynumber: 2.3 Consensus size: 91
53967784 GACAGATTCT
* ** * * *
53967794 CTACAAACACTGGTGGTTTATCCACAAGTTTTACTGGTAGCTTTTATCTGCAAACCCTTTGTGTA
1 CTACAAACACTTGTGGTTTATCCACAACATTTAATGGCAGCTTTTATCTGCAAACCCATTGTGTA
*
53967859 TTCACAACTACTGGTAGCATATTAAC
66 TTCACAACTACTAGTAGCATATTAAC
* *
53967885 CTACAAACAATTGTGGTTTATCCACAACATTTAATGGCAGCTTTTATCTGTAAACCCATTGTGTA
1 CTACAAACACTTGTGGTTTATCCACAACATTTAATGGCAGCTTTTATCTGCAAACCCATTGTGTA
* *
53967950 TTCACAATTACTAGTAGCGTATTAAC
66 TTCACAACTACTAGTAGCATATTAAC
*
53967976 CTAC-AACACTTGTGGTTCATCCACAA
1 CTACAAACACTTGTGGTTTATCCACAA
53968002 GCAGGAGTGT
Statistics
Matches: 104, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
90 20 0.19
91 84 0.81
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.34
Consensus pattern (91 bp):
CTACAAACACTTGTGGTTTATCCACAACATTTAATGGCAGCTTTTATCTGCAAACCCATTGTGTA
TTCACAACTACTAGTAGCATATTAAC
Found at i:53969727 original size:45 final size:45
Alignment explanation
Indices: 53969678--53969767 Score: 144
Period size: 45 Copynumber: 2.0 Consensus size: 45
53969668 TTTGATCGAA
*
53969678 GATGACAACGAGGATGATAGATTGAAGAAGAAGATCAAGAAAGAG
1 GATGACAACGAGGAGGATAGATTGAAGAAGAAGATCAAGAAAGAG
** *
53969723 GATGATGACGAGGAGGATAGATTGAAGAAGAAGATCAAGATAGAG
1 GATGACAACGAGGAGGATAGATTGAAGAAGAAGATCAAGAAAGAG
53969768 AACATTTAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.47, C:0.06, G:0.33, T:0.14
Consensus pattern (45 bp):
GATGACAACGAGGAGGATAGATTGAAGAAGAAGATCAAGAAAGAG
Found at i:53973347 original size:23 final size:21
Alignment explanation
Indices: 53973327--53973391 Score: 67
Period size: 25 Copynumber: 2.8 Consensus size: 21
53973317 TCTATTTACC
53973327 TTTTTTATATATATTATTTTA
1 TTTTTTATATATATTATTTTA
*
53973348 TTTTATTATATACTGTTATTTTTA
1 TTTT-TTATATA-TATTA-TTTTA
53973372 TTCTTTTTATCATATATTAT
1 -T-TTTTTAT-ATATATTAT
53973392 ATCTAATTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
21 4 0.11
22 7 0.19
23 4 0.11
24 6 0.17
25 9 0.25
26 6 0.17
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.68
Consensus pattern (21 bp):
TTTTTTATATATATTATTTTA
Found at i:53979635 original size:45 final size:44
Alignment explanation
Indices: 53979585--53979677 Score: 152
Period size: 44 Copynumber: 2.1 Consensus size: 44
53979575 GGTTCGCTGT
53979585 AATGGAATAGAGGCGTAATAGTAATTCAAT-TGTTTGGTTGAATGG
1 AATGGAATAGAGGCGTAATAGT-ATTC-ATGTGTTTGGTTGAATGG
*
53979630 AATGGAATAGAGGCGTAATAGTATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAGAGGCGTAATAGTATTCATGTGTTTGGTTGAATGG
53979674 AATG
1 AATG
53979678 ATGTTGTAAT
Statistics
Matches: 46, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
43 1 0.02
44 23 0.50
45 22 0.48
ACGTcount: A:0.31, C:0.04, G:0.30, T:0.34
Consensus pattern (44 bp):
AATGGAATAGAGGCGTAATAGTATTCATGTGTTTGGTTGAATGG
Found at i:53979954 original size:120 final size:119
Alignment explanation
Indices: 53979817--53980175 Score: 621
Period size: 120 Copynumber: 3.0 Consensus size: 119
53979807 TTAATCATAT
* *
53979817 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTTATAAAATTCTTAATATG
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATAT-
*
53979882 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATAGTATAAAATATAA
65 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
53979937 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATA-T
* *
53980002 AAATATTCTTAAATGAATTTGCTAAAATCATAATATATAATACTATAAAATATAA
65 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
* *
53980057 TCTAAAATAATAATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATA
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATA
*
53980122 ATTATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAA-ATAA
66 AATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
53980175 T
1 T
53980176 ATATAATCTA
Statistics
Matches: 228, Mismatches: 10, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
118 5 0.02
119 48 0.21
120 174 0.76
121 1 0.00
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (119 bp):
TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATA
AATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
Found at i:53980165 original size:21 final size:21
Alignment explanation
Indices: 53980150--53980211 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
53980140 TACTAAAATC
53980150 ATAATATATAATACTATAAAA
1 ATAATATATAATACTATAAAA
**
53980171 ATAATATATAAT-CTACT--TT
1 ATAATATATAATACTA-TAAAA
*
53980190 ATAATGTATAATACTATAAAA
1 ATAATATATAATACTATAAAA
53980211 A
1 A
53980212 ACTTGAAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 8
0.71 0.11 0.18
Matches are distributed among these distances:
19 12 0.38
20 6 0.19
21 14 0.44
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.37
Consensus pattern (21 bp):
ATAATATATAATACTATAAAA
Found at i:53990244 original size:24 final size:24
Alignment explanation
Indices: 53990217--53990269 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
53990207 ATCTTCATTT
53990217 AAGGACAACGAACTCTTTCAAATC
1 AAGGACAACGAACTCTTTCAAATC
*
53990241 AAGGACAACGAACTCTTTCAACTC
1 AAGGACAACGAACTCTTTCAAATC
53990265 AAGGA
1 AAGGA
53990270 TCCCAACTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.42, C:0.25, G:0.15, T:0.19
Consensus pattern (24 bp):
AAGGACAACGAACTCTTTCAAATC
Found at i:53990278 original size:14 final size:14
Alignment explanation
Indices: 53990259--53990287 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
53990249 CGAACTCTTT
53990259 CAACTCAAGGATCC
1 CAACTCAAGGATCC
53990273 CAACTCAAGGATCC
1 CAACTCAAGGATCC
53990287 C
1 C
53990288 GACTAATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.38, G:0.14, T:0.14
Consensus pattern (14 bp):
CAACTCAAGGATCC
Found at i:53997664 original size:18 final size:17
Alignment explanation
Indices: 53997613--53997664 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 17
53997603 TCTTTCTAGT
53997613 TTATTTTTATTTATTAAA
1 TTATTTTTATTT-TTAAA
*
53997631 TTGTTTTTA--TTT-AA
1 TTATTTTTATTTTTAAA
53997645 TTAATTTTTATTTTTAAA
1 TT-ATTTTTATTTTTAAA
53997663 TT
1 TT
53997665 TATTATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 4 0.14
15 8 0.29
16 1 0.04
17 3 0.11
18 12 0.43
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (17 bp):
TTATTTTTATTTTTAAA
Found at i:53997670 original size:15 final size:14
Alignment explanation
Indices: 53997615--53997674 Score: 50
Period size: 15 Copynumber: 3.9 Consensus size: 14
53997605 TTTCTAGTTT
53997615 ATTTTTATTTATTAA
1 ATTTTTATTT-TTAA
53997630 ATTGTTT-TTATTTAATTA
1 ATT-TTTATT-TTT-A--A
53997648 ATTTTTATTTTTAA
1 ATTTTTATTTTTAA
53997662 ATTTATTATTTTT
1 ATTT-TTATTTTT
53997675 CATTATCTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
14 5 0.13
15 15 0.39
16 6 0.16
17 6 0.16
18 6 0.16
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (14 bp):
ATTTTTATTTTTAA
Found at i:53999887 original size:13 final size:13
Alignment explanation
Indices: 53999869--53999894 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
53999859 AAAGAGATTT
53999869 GTTTTCTAGTAAA
1 GTTTTCTAGTAAA
53999882 GTTTTCTAGTAAA
1 GTTTTCTAGTAAA
53999895 AAATTTGAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (13 bp):
GTTTTCTAGTAAA
Found at i:53999965 original size:19 final size:20
Alignment explanation
Indices: 53999928--53999967 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
53999918 TCTTTTCACA
* *
53999928 TTCATTTCATGCATTTGCAT
1 TTCATTACATGCATATGCAT
53999948 TTCATTACAT-CATATGCAT
1 TTCATTACATGCATATGCAT
53999967 T
1 T
53999968 AAACACAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.25, C:0.20, G:0.07, T:0.47
Consensus pattern (20 bp):
TTCATTACATGCATATGCAT
Found at i:54000009 original size:23 final size:23
Alignment explanation
Indices: 53999982--54000028 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
53999972 ACAGTTAAAG
53999982 GATCCTAATTAACTAAAATCATT
1 GATCCTAATTAACTAAAATCATT
54000005 GATCCTAATTAACTAAAATCATT
1 GATCCTAATTAACTAAAATCATT
54000028 G
1 G
54000029 CTCAGTTAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.43, C:0.17, G:0.06, T:0.34
Consensus pattern (23 bp):
GATCCTAATTAACTAAAATCATT
Found at i:54004793 original size:19 final size:19
Alignment explanation
Indices: 54004766--54004808 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
54004756 TTATATAATT
*
54004766 TTTAGTTTGGGCAGTTGAA
1 TTTAATTTGGGCAGTTGAA
54004785 TTTAATTTGGGCAGTTGAA
1 TTTAATTTGGGCAGTTGAA
54004804 TTTAA
1 TTTAA
54004809 CATTAGTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.26, C:0.05, G:0.26, T:0.44
Consensus pattern (19 bp):
TTTAATTTGGGCAGTTGAA
Found at i:54006159 original size:23 final size:23
Alignment explanation
Indices: 54006124--54006167 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
54006114 AGGCAAACCT
*
54006124 AAAACCTACATAAACT-CAATCC
1 AAAACATACATAAACTACAATCC
54006146 AAAACATACCATAAACTACAAT
1 AAAACATA-CATAAACTACAAT
54006168 TCACCATTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 8 0.42
24 4 0.21
ACGTcount: A:0.55, C:0.27, G:0.00, T:0.18
Consensus pattern (23 bp):
AAAACATACATAAACTACAATCC
Found at i:54013361 original size:25 final size:25
Alignment explanation
Indices: 54013283--54013363 Score: 81
Period size: 25 Copynumber: 3.2 Consensus size: 25
54013273 TTCTCGATTA
*
54013283 TGGCTCTCATGAGCTTCCTGTTATT
1 TGGCTCACATGAGCTTCCTGTTATT
* * * * **
54013308 TAGCCCAGATAAGCTTCCTGTTACA
1 TGGCTCACATGAGCTTCCTGTTATT
* *
54013333 TGGCTGACATGAGCTTCCCGTTATT
1 TGGCTCACATGAGCTTCCTGTTATT
54013358 TGGCTC
1 TGGCTC
54013364 GAGAGCGTGC
Statistics
Matches: 40, Mismatches: 16, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.17, C:0.26, G:0.21, T:0.36
Consensus pattern (25 bp):
TGGCTCACATGAGCTTCCTGTTATT
Found at i:54018030 original size:22 final size:22
Alignment explanation
Indices: 54018002--54018054 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
54017992 AAACTTCCGT
54018002 AGCATGTCATGCATATATT-GG-A
1 AGCATGTCAT--ATATATTAGGTA
54018024 AGCATGTCATATATATTAGGTA
1 AGCATGTCATATATATTAGGTA
*
54018046 AGAATGTCA
1 AGCATGTCA
54018055 CTACAACTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 7 0.25
21 2 0.07
22 19 0.68
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.32
Consensus pattern (22 bp):
AGCATGTCATATATATTAGGTA
Found at i:54036124 original size:29 final size:28
Alignment explanation
Indices: 54036092--54036153 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 28
54036082 TATCACGAAA
* *
54036092 ATAAAAG-CCCAAATAAAATCATAAAGTCC
1 ATAAAAGTCCAAAATAAAAT-AT-AAGCCC
54036121 ATAAAAGTTCCAAAATAAAATATAAGCCC
1 ATAAAAG-TCCAAAATAAAATATAAGCCC
54036150 ATAA
1 ATAA
54036154 TCATGAAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 16 0.55
30 2 0.07
31 11 0.38
ACGTcount: A:0.56, C:0.18, G:0.06, T:0.19
Consensus pattern (28 bp):
ATAAAAGTCCAAAATAAAATATAAGCCC
Found at i:54046870 original size:14 final size:15
Alignment explanation
Indices: 54046845--54046880 Score: 56
Period size: 14 Copynumber: 2.4 Consensus size: 15
54046835 GTTTGGTGTA
54046845 TTTGTGTTGTTTTTC
1 TTTGTGTTGTTTTTC
54046860 TTTGT-TTGTTTTTC
1 TTTGTGTTGTTTTTC
54046874 TTATGTG
1 TT-TGTG
54046881 CAGTGAGTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 11 0.58
15 8 0.42
ACGTcount: A:0.03, C:0.06, G:0.19, T:0.72
Consensus pattern (15 bp):
TTTGTGTTGTTTTTC
Found at i:54049499 original size:34 final size:34
Alignment explanation
Indices: 54049453--54049540 Score: 101
Period size: 34 Copynumber: 2.6 Consensus size: 34
54049443 CCGTACTATG
* *
54049453 ATGGGCTAAGGCCCTAATACT-TACTGATACTGAA
1 ATGGGCTTAGGCCCTAA-ACTATACTGATAATGAA
*
54049487 ATGGGCTTAGG-CCTAAACTAATACTGATAATTAA
1 ATGGGCTTAGGCCCTAAACT-ATACTGATAATGAA
*
54049521 AAGGGCTTAGGCCC-AAACTA
1 ATGGGCTTAGGCCCTAAACTA
54049541 AGATTATTTG
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
32 3 0.06
33 6 0.13
34 36 0.77
35 2 0.04
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.25
Consensus pattern (34 bp):
ATGGGCTTAGGCCCTAAACTATACTGATAATGAA
Found at i:54052706 original size:41 final size:41
Alignment explanation
Indices: 54052651--54052851 Score: 285
Period size: 41 Copynumber: 4.9 Consensus size: 41
54052641 GAAGGCTTAT
* * *
54052651 TGCCAGTGAGACAATTCAGACTCTATGTCTAGCAGGCTGGA
1 TGCCGGTGAAACAATTCAGACTTTATGTCTAGCAGGCTGGA
* *
54052692 TGCCGGTGAAACAATTCAGACTCTATGTCTAGAAGGCTGGA
1 TGCCGGTGAAACAATTCAGACTTTATGTCTAGCAGGCTGGA
* * *
54052733 TGCTGGTGAAACAATTCAGACTTTATGTCCAGCAGGCTTGA
1 TGCCGGTGAAACAATTCAGACTTTATGTCTAGCAGGCTGGA
*
54052774 TGCCGGTGAAACAATTCAGACTTTATGTCTAGCAGGCTTGA
1 TGCCGGTGAAACAATTCAGACTTTATGTCTAGCAGGCTGGA
** * *
54052815 TGCTAGTGAAACATTTCAGACTTTAAGTCTAGCAGGC
1 TGCCGGTGAAACAATTCAGACTTTATGTCTAGCAGGC
54052852 CAAAAGCCGG
Statistics
Matches: 146, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 146 1.00
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (41 bp):
TGCCGGTGAAACAATTCAGACTTTATGTCTAGCAGGCTGGA
Found at i:54061728 original size:19 final size:19
Alignment explanation
Indices: 54061701--54061738 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
54061691 ATTTAGTATT
* *
54061701 TAATTGTAATCTAAAATGA
1 TAATCGTAATCCAAAATGA
54061720 TAATCGTAATCCAAAATGA
1 TAATCGTAATCCAAAATGA
54061739 CAATTACTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.32
Consensus pattern (19 bp):
TAATCGTAATCCAAAATGA
Found at i:54065591 original size:91 final size:90
Alignment explanation
Indices: 54065433--54065611 Score: 261
Period size: 91 Copynumber: 2.0 Consensus size: 90
54065423 ACACTCCTGC
* * *
54065433 TTGTGGATGAACCACAAGTGTTGTAAGTTAATATGCTACCAGTAATTGTGAACACACAACGGGTT
1 TTGTGGATAAACCACAAGTGTTGTAAGTTAATACGCTACCAGTAATTGTGAACACACAACGGATT
* *
54065498 TGCAGATAAAAGTTGCCATTAAATG
66 TGCAGATAAAAGTTACCAGTAAATG
* * *
54065523 TTGTGGATAAACCACAATTGTTTGTAGGTTAATACGCTACCAGTAATTGTGAATACACAATC-GA
1 TTGTGGATAAACCACAAGTG-TTGTAAGTTAATACGCTACCAGTAATTGTGAACACACAA-CGGA
54065587 TTTGCAGATAAAAGTTACCAGTAAA
64 TTTGCAGATAAAAGTTACCAGTAAA
54065612 ACTTTTAGAT
Statistics
Matches: 79, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
90 18 0.23
91 60 0.76
92 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.30
Consensus pattern (90 bp):
TTGTGGATAAACCACAAGTGTTGTAAGTTAATACGCTACCAGTAATTGTGAACACACAACGGATT
TGCAGATAAAAGTTACCAGTAAATG
Found at i:54069505 original size:2 final size:2
Alignment explanation
Indices: 54069498--54069522 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
54069488 TTCAAGATAA
54069498 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
54069523 TGTATATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:54072032 original size:27 final size:27
Alignment explanation
Indices: 54071797--54072020 Score: 258
Period size: 27 Copynumber: 8.4 Consensus size: 27
54071787 CCCTAAAATA
54071797 GGTAAAAT-ATCTGAAATACCCCCATAG
1 GGTAAAATGA-CTGAAATACCCCCATAG
* * * *
54071824 AAG-AAAATAATTGAAATA-CCTCATAG
1 -GGTAAAATGACTGAAATACCCCCATAG
* *
54071850 GGTAAAATAACCGAAATACCCCCATAG
1 GGTAAAATGACTGAAATACCCCCATAG
* * * *
54071877 GATAAATTGACCGAAATACCACCATAG
1 GGTAAAATGACTGAAATACCCCCATAG
** *
54071904 GGTAAAATGACCAAAATA-CCCCTTAG
1 GGTAAAATGACTGAAATACCCCCATAG
* *
54071930 GGTAAAATAACTGAAATACCCCTATAG
1 GGTAAAATGACTGAAATACCCCCATAG
54071957 GGTAAAATGACTGAAATACCCCCATAG
1 GGTAAAATGACTGAAATACCCCCATAG
*
54071984 GGTAAAATAACTGAAATACCCCCATAG
1 GGTAAAATGACTGAAATACCCCCATAG
54072011 GGTAAAATGA
1 GGTAAAATGA
54072021 TTATTATACC
Statistics
Matches: 167, Mismatches: 25, Indels: 9
0.83 0.12 0.04
Matches are distributed among these distances:
25 1 0.01
26 41 0.25
27 123 0.74
28 2 0.01
ACGTcount: A:0.45, C:0.20, G:0.16, T:0.20
Consensus pattern (27 bp):
GGTAAAATGACTGAAATACCCCCATAG
Found at i:54072032 original size:54 final size:54
Alignment explanation
Indices: 54071809--54072020 Score: 277
Period size: 53 Copynumber: 4.0 Consensus size: 54
54071799 TAAAATATCT
* * * *
54071809 GAAATACCCCCATAGAAG-AAAATAATTGAAATA-CCTCATAGGGTAAAATAACC
1 GAAATACCCCCATAG-GGTAAAATAACTGAAATACCCCCATAGGGTAAAATGACC
* * * * *
54071862 GAAATACCCCCATAGGATAAATTGACCGAAATACCACCATAGGGTAAAATGACC
1 GAAATACCCCCATAGGGTAAAATAACTGAAATACCCCCATAGGGTAAAATGACC
* * * *
54071916 AAAATA-CCCCTTAGGGTAAAATAACTGAAATACCCCTATAGGGTAAAATGACT
1 GAAATACCCCCATAGGGTAAAATAACTGAAATACCCCCATAGGGTAAAATGACC
54071969 GAAATACCCCCATAGGGTAAAATAACTGAAATACCCCCATAGGGTAAAATGA
1 GAAATACCCCCATAGGGTAAAATAACTGAAATACCCCCATAGGGTAAAATGA
54072021 TTATTATACC
Statistics
Matches: 135, Mismatches: 21, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
53 70 0.52
54 65 0.48
ACGTcount: A:0.45, C:0.21, G:0.16, T:0.19
Consensus pattern (54 bp):
GAAATACCCCCATAGGGTAAAATAACTGAAATACCCCCATAGGGTAAAATGACC
Found at i:54072049 original size:80 final size:79
Alignment explanation
Indices: 54071807--54072018 Score: 259
Period size: 80 Copynumber: 2.6 Consensus size: 79
54071797 GGTAAAATAT
* * * *
54071807 CTGAAATACCCCCATAGAAG-AAAATAATTGAAATACCTCATAGGGTAAAATAACCGAAATACCC
1 CTGAAATACCCCCATAG-GGTAAAATAACTGAAATACCCCATAGGGTAAAATAACTGAAATA-CC
54071871 CCATA-GGATAAATTGA
64 CCATAGGGATAAA-TGA
* * * ** *
54071887 CCGAAATACCACCATAGGGTAAAATGACCAAAATACCCCTTAGGGTAAAATAACTGAAATACCCC
1 CTGAAATACCCCCATAGGGTAAAATAACTGAAATACCCCATAGGGTAAAATAACTGAAATACCCC
54071952 TATAGGG-TAAAATGA
66 -ATAGGGAT-AAATGA
54071967 CTGAAATACCCCCATAGGGTAAAATAACTGAAATACCCCCATAGGGTAAAAT
1 CTGAAATACCCCCATAGGGTAAAATAACTGAAATA-CCCCATAGGGTAAAAT
54072019 GATTATTATA
Statistics
Matches: 111, Mismatches: 16, Indels: 9
0.82 0.12 0.07
Matches are distributed among these distances:
79 5 0.05
80 86 0.77
81 20 0.18
ACGTcount: A:0.44, C:0.21, G:0.15, T:0.19
Consensus pattern (79 bp):
CTGAAATACCCCCATAGGGTAAAATAACTGAAATACCCCATAGGGTAAAATAACTGAAATACCCC
ATAGGGATAAATGA
Found at i:54074838 original size:2 final size:2
Alignment explanation
Indices: 54074831--54074865 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
54074821 TTCAAGATAA
*
54074831 AC AC AC AC AC AC AC AC AC AC AT AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
54074866 TATGTATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.46, G:0.00, T:0.03
Consensus pattern (2 bp):
AC
Found at i:54080156 original size:10 final size:11
Alignment explanation
Indices: 54080132--54080164 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
54080122 TAAAAAGTGC
54080132 AGAGAAAACTA
1 AGAGAAAACTA
*
54080143 AGAGAAACCT-
1 AGAGAAAACTA
54080153 AGAGAAAACTA
1 AGAGAAAACTA
54080164 A
1 A
54080165 ACCTAAAGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.61, C:0.12, G:0.18, T:0.09
Consensus pattern (11 bp):
AGAGAAAACTA
Found at i:54088974 original size:16 final size:16
Alignment explanation
Indices: 54088944--54088985 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
54088934 GATATTTATA
*
54088944 TTTTATTTTTATTAAAT
1 TTTTATTATTATT-AAT
54088961 TTTTATTATT-TTAAT
1 TTTTATTATTATTAAT
54088976 TTTTAATTAT
1 TTTT-ATTAT
54088986 CATGGAACTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 7 0.30
16 7 0.30
17 9 0.39
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTATTATTATTAAT
Found at i:54091030 original size:21 final size:21
Alignment explanation
Indices: 54090997--54091056 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
54090987 AACGTTTGAC
54090997 TTTTACAAT-TTATAATTA-TA
1 TTTTA-AATATTATAATTATTA
*
54091017 TTGTTAATTATTATAATTAATTA
1 TT-TTAAATATTATAATT-ATTA
54091040 TTTTAAATATT-TAATTA
1 TTTTAAATATTATAATTA
54091057 AATAATTAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
20 5 0.15
21 16 0.47
22 9 0.26
23 4 0.12
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (21 bp):
TTTTAAATATTATAATTATTA
Found at i:54091068 original size:17 final size:19
Alignment explanation
Indices: 54091048--54091082 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
54091038 TATTTTAAAT
54091048 ATTTAATT-AAA-TAATTA
1 ATTTAATTCAAATTAATTA
54091065 ATTTAATTCAAATTAATT
1 ATTTAATTCAAATTAATT
54091083 CTCCTACACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 3 0.19
19 5 0.31
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTTAATTCAAATTAATTA
Found at i:54100112 original size:21 final size:21
Alignment explanation
Indices: 54100088--54100140 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
54100078 CATTGTTTCT
*
54100088 AATCTCACCGCTAAAGTATCC
1 AATCTCACCGCTAAAGTAACC
* *
54100109 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTAAAGTAACC
54100130 AATCTCACCGC
1 AATCTCACCGC
54100141 CACCGCTGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.32, C:0.36, G:0.09, T:0.23
Consensus pattern (21 bp):
AATCTCACCGCTAAAGTAACC
Found at i:54103540 original size:22 final size:24
Alignment explanation
Indices: 54103512--54103555 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
54103502 TAATTTCTAA
*
54103512 AAACAAA-TTTT-CTTTTTATTTC
1 AAACAAACTTTTAATTTTTATTTC
54103534 AAACAAACTTTTAATTTTTATT
1 AAACAAACTTTTAATTTTTATT
54103556 ATGATTTCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 4 0.21
24 8 0.42
ACGTcount: A:0.36, C:0.11, G:0.00, T:0.52
Consensus pattern (24 bp):
AAACAAACTTTTAATTTTTATTTC
Found at i:54107071 original size:25 final size:24
Alignment explanation
Indices: 54107033--54107090 Score: 71
Period size: 25 Copynumber: 2.4 Consensus size: 24
54107023 ATGTTCAAGC
* *
54107033 GAGCTATATTAGGAAGCTCAAAAA
1 GAGCTACATCAGGAAGCTCAAAAA
* *
54107057 GAGCATACATCAGGACGCTCATAAA
1 GAGC-TACATCAGGAAGCTCAAAAA
54107082 GAGCTACAT
1 GAGCTACAT
54107091 TTGTGTCTGC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 9 0.31
25 20 0.69
ACGTcount: A:0.41, C:0.19, G:0.21, T:0.19
Consensus pattern (24 bp):
GAGCTACATCAGGAAGCTCAAAAA
Found at i:54109368 original size:29 final size:30
Alignment explanation
Indices: 54109322--54109379 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
54109312 ATGTTGGTTG
*
54109322 TGATTTTGATTTTTGCTGTTAATGGTGTTC
1 TGATTTGGATTTTTGCTGTTAATGGTGTTC
*
54109352 TGATTTGGA-TTTTGCTGTTAATGTTGTT
1 TGATTTGGATTTTTGCTGTTAATGGTGTT
54109380 AATGGTTGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 18 0.69
30 8 0.31
ACGTcount: A:0.14, C:0.05, G:0.24, T:0.57
Consensus pattern (30 bp):
TGATTTGGATTTTTGCTGTTAATGGTGTTC
Found at i:54110643 original size:13 final size:13
Alignment explanation
Indices: 54110625--54110755 Score: 126
Period size: 13 Copynumber: 10.2 Consensus size: 13
54110615 ATTTTTAATG
54110625 TAATATACTGTTT
1 TAATATACTGTTT
*
54110638 TAATATACTGTTA
1 TAATATACTGTTT
*
54110651 TAA-A-A-T-TTG
1 TAATATACTGTTT
54110660 TAATATACTGTTT
1 TAATATACTGTTT
*
54110673 TAATATACTATTAT
1 TAATATACTGTT-T
* *
54110687 AAATATACTTTTT
1 TAATATACTGTTT
*
54110700 TAATATATTGTTT
1 TAATATACTGTTT
* *
54110713 TAATATACTATTA
1 TAATATACTGTTT
*
54110726 TAATTATATTGTTT
1 TAA-TATACTGTTT
*
54110740 TAATATAATGTTT
1 TAATATACTGTTT
54110753 TAA
1 TAA
54110756 CTTTTAACTT
Statistics
Matches: 96, Mismatches: 16, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
9 5 0.05
10 2 0.02
11 2 0.02
12 2 0.02
13 64 0.67
14 21 0.22
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.53
Consensus pattern (13 bp):
TAATATACTGTTT
Found at i:54110715 original size:40 final size:39
Alignment explanation
Indices: 54110625--54110755 Score: 171
Period size: 40 Copynumber: 3.4 Consensus size: 39
54110615 ATTTTTAATG
* *
54110625 TAATATACTGTTTTAATATACTGTTAT-AA-A-A-TTTG
1 TAATATACTGTTTTAATATACTATTATAAATATATTTTT
54110660 TAATATACTGTTTTAATATACTATTATAAATATACTTTTT
1 TAATATACTGTTTTAATATACTATTATAAATATA-TTTTT
* *
54110700 TAATATATTGTTTTAATATACTATTATAATTATATTGTTT
1 TAATATACTGTTTTAATATACTATTATAAATATATT-TTT
*
54110740 TAATATAATGTTTTAA
1 TAATATACTGTTTTAA
54110756 CTTTTAACTT
Statistics
Matches: 85, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
35 26 0.31
36 2 0.02
37 1 0.01
38 1 0.01
39 2 0.02
40 53 0.62
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.53
Consensus pattern (39 bp):
TAATATACTGTTTTAATATACTATTATAAATATATTTTT
Found at i:54110741 original size:27 final size:26
Alignment explanation
Indices: 54110625--54110746 Score: 108
Period size: 27 Copynumber: 4.8 Consensus size: 26
54110615 ATTTTTAATG
* *
54110625 TAATATACTGTTTTAATATACTGTTA
1 TAATATATTGTTTTAATATACTATTA
* * *
54110651 TAA-A-A-T-TTGTAATATACTGTTT
1 TAATATATTGTTTTAATATACTATTA
* * * * *
54110673 TAATATACTATTATAAATATACTTTTT
1 TAATATATTGTT-TTAATATACTATTA
54110700 TAATATATTGTTTTAATATACTATTA
1 TAATATATTGTTTTAATATACTATTA
54110726 TAATTATATTGTTTTAATATA
1 TAA-TATATTGTTTTAATATA
54110747 ATGTTTTAAC
Statistics
Matches: 80, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
22 17 0.21
23 2 0.03
24 2 0.03
25 2 0.03
26 19 0.24
27 38 0.47
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.52
Consensus pattern (26 bp):
TAATATATTGTTTTAATATACTATTA
Found at i:54110811 original size:15 final size:15
Alignment explanation
Indices: 54110791--54110824 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
54110781 AAATATACAT
54110791 TTAATTTGTAACACA
1 TTAATTTGTAACACA
54110806 TTAATTTGTAACACA
1 TTAATTTGTAACACA
54110821 TTAA
1 TTAA
54110825 ATTTTAGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.41, C:0.12, G:0.06, T:0.41
Consensus pattern (15 bp):
TTAATTTGTAACACA
Found at i:54110849 original size:14 final size:14
Alignment explanation
Indices: 54110827--54110862 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
54110817 CACATTAAAT
*
54110827 TTTAGTTTCTATAC
1 TTTATTTTCTATAC
54110841 TTTATTTTCTATAC
1 TTTATTTTCTATAC
54110855 TTTATTTT
1 TTTATTTT
54110863 TTAACATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.19, C:0.11, G:0.03, T:0.67
Consensus pattern (14 bp):
TTTATTTTCTATAC
Found at i:54110985 original size:328 final size:327
Alignment explanation
Indices: 54110514--54111137 Score: 1122
Period size: 328 Copynumber: 1.9 Consensus size: 327
54110504 ATGATTAAAA
*
54110514 TTTAGTTTCTATACTTTATTTTTAACATAAATTGGTGCTTATATTTTTATAATGTTATTAACTAA
1 TTTAGTTTCTATACTTTATTTTTAACATAAAATGGTGCTTATATTTTTATAATGTTATTAACTAA
*
54110579 ATAATTAATATTGTTAATTTTTTGATTAAAACAATAATTTTTAATGTAATATACTGTTTTAATAT
66 ATAATTAATATTGTTAATTTTTTGATTAAAACAATAATTTTTAATGTAATATACTATTTTAATAT
*
54110644 ACTGTTATAAAATTTGTAATATACTGTTTTAATATACTATTATAAATATACTTTTTTAATATATT
131 ACTGTTATAAAATTTATAATATACTGTTTTAATATACTATTATAAATATACTTTTTTAATATATT
* * * * *
54110709 GTTTTAATATACTATTATAATTATATTGTTTTAATATAATGTTTTAACTTTTAACTTTTAGTATA
196 GTTTTAATATACTATTATAATTATATTGTTTTAATATAATATTTTAAATTTTAAATTTGAATATA
54110774 CCGTTATAAATATACATTTAATTTGTAACACATTAATTTGTAACACATTAAATTTTAGTTTCTAT
261 CCGTTATAAATATACATTTAATTTGTAACACATTAATTTGTAACACATTAAATTTTAGTTTCTAT
54110839 AC
326 AC
*
54110841 TTTATTTTCTATACTTTATTTTTTAACATAAAATGGTGCTTATATTTTTATAATGTTATTAACTA
1 TTTAGTTTCTATACTTTA-TTTTTAACATAAAATGGTGCTTATATTTTTATAATGTTATTAACTA
54110906 AATAATTAATATTGTTAATTTTTTGATTAAAACAATAATTTTTAATGTAATATACTATTTTAATA
65 AATAATTAATATTGTTAATTTTTTGATTAAAACAATAATTTTTAATGTAATATACTATTTTAATA
* *
54110971 TACTGTTTTAAAATTTATAATATATTGTTTTAATATACTATTATAAATATACTTTTTTAATATAT
130 TACTGTTATAAAATTTATAATATACTGTTTTAATATACTATTATAAATATACTTTTTTAATATAT
*
54111036 TGTTTTAATATACTGTTATAATTATATTGTTTTAATATAATATTTTAAATTTTAAATTTGAATAT
195 TGTTTTAATATACTATTATAATTATATTGTTTTAATATAATATTTTAAATTTTAAATTTGAATAT
*
54111101 ACTGTTATAAATATACATTTAATTTGTAACACATTAA
260 ACCGTTATAAATATACATTTAATTTGTAACACATTAA
54111138 ATGTTGATGT
Statistics
Matches: 283, Mismatches: 13, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
327 17 0.06
328 266 0.94
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.51
Consensus pattern (327 bp):
TTTAGTTTCTATACTTTATTTTTAACATAAAATGGTGCTTATATTTTTATAATGTTATTAACTAA
ATAATTAATATTGTTAATTTTTTGATTAAAACAATAATTTTTAATGTAATATACTATTTTAATAT
ACTGTTATAAAATTTATAATATACTGTTTTAATATACTATTATAAATATACTTTTTTAATATATT
GTTTTAATATACTATTATAATTATATTGTTTTAATATAATATTTTAAATTTTAAATTTGAATATA
CCGTTATAAATATACATTTAATTTGTAACACATTAATTTGTAACACATTAAATTTTAGTTTCTAT
AC
Found at i:54111043 original size:40 final size:40
Alignment explanation
Indices: 54110988--54111083 Score: 140
Period size: 40 Copynumber: 2.4 Consensus size: 40
54110978 TTAAAATTTA
54110988 TAATATATTGTTTTAATATACTATTATAAATATACTT-TTT
1 TAATATATTGTTTTAATATACTATTATAAATATA-TTGTTT
* *
54111028 TAATATATTGTTTTAATATACTGTTATAATTATATTGTTT
1 TAATATATTGTTTTAATATACTATTATAAATATATTGTTT
* *
54111068 TAATATAATATTTTAA
1 TAATATATTGTTTTAA
54111084 ATTTTAAATT
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
39 2 0.04
40 49 0.96
ACGTcount: A:0.38, C:0.03, G:0.04, T:0.55
Consensus pattern (40 bp):
TAATATATTGTTTTAATATACTATTATAAATATATTGTTT
Found at i:54111069 original size:27 final size:26
Alignment explanation
Indices: 54110953--54111074 Score: 99
Period size: 27 Copynumber: 4.8 Consensus size: 26
54110943 ATTTTTAATG
* * *
54110953 TAATATACTATTTTAATATACTGTTT
1 TAATATATTGTTTTAATATACTGTTA
* * *
54110979 TAA-A-A-T-TTATAATATATTGTTT
1 TAATATATTGTTTTAATATACTGTTA
* * * * *
54111001 TAATATACTATTATAAATATACTTTTT
1 TAATATATTGTT-TTAATATACTGTTA
54111028 TAATATATTGTTTTAATATACTGTTA
1 TAATATATTGTTTTAATATACTGTTA
54111054 TAATTATATTGTTTTAATATA
1 TAA-TATATTGTTTTAATATA
54111075 ATATTTTAAA
Statistics
Matches: 79, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
22 17 0.22
23 2 0.03
24 2 0.03
25 2 0.03
26 19 0.24
27 37 0.47
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (26 bp):
TAATATATTGTTTTAATATACTGTTA
Found at i:54111083 original size:13 final size:13
Alignment explanation
Indices: 54110953--54111074 Score: 117
Period size: 13 Copynumber: 9.5 Consensus size: 13
54110943 ATTTTTAATG
*
54110953 TAATATACTATTT
1 TAATATACTGTTT
54110966 TAATATACTGTTT
1 TAATATACTGTTT
*
54110979 TAA-A-A-T-TTA
1 TAATATACTGTTT
*
54110988 TAATATATTGTTT
1 TAATATACTGTTT
*
54111001 TAATATACTATTAT
1 TAATATACTGTT-T
* *
54111015 AAATATACTTTTT
1 TAATATACTGTTT
*
54111028 TAATATATTGTTT
1 TAATATACTGTTT
*
54111041 TAATATACTGTTA
1 TAATATACTGTTT
*
54111054 TAATTATATTGTTT
1 TAA-TATACTGTTT
54111068 TAATATA
1 TAATATA
54111075 ATATTTTAAA
Statistics
Matches: 89, Mismatches: 14, Indels: 12
0.77 0.12 0.10
Matches are distributed among these distances:
9 5 0.06
10 2 0.02
11 2 0.02
12 2 0.02
13 56 0.63
14 22 0.25
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (13 bp):
TAATATACTGTTT
Found at i:54113551 original size:9 final size:9
Alignment explanation
Indices: 54113537--54113582 Score: 65
Period size: 9 Copynumber: 5.1 Consensus size: 9
54113527 GGTTGCAAAA
54113537 AGGACGATG
1 AGGACGATG
54113546 AGGACGATG
1 AGGACGATG
*
54113555 ACGACGATG
1 AGGACGATG
*
54113564 ACGACGATG
1 AGGACGATG
*
54113573 AGGATGATG
1 AGGACGATG
54113582 A
1 A
54113583 TGTTTCTTCG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 34 1.00
ACGTcount: A:0.35, C:0.13, G:0.39, T:0.13
Consensus pattern (9 bp):
AGGACGATG
Found at i:54113991 original size:19 final size:19
Alignment explanation
Indices: 54113967--54114038 Score: 65
Period size: 19 Copynumber: 3.6 Consensus size: 19
54113957 AATATTTAAA
54113967 TTGACAGTTTTGGTATTAT
1 TTGACAGTTTTGGTATTAT
*
54113986 TTGACAGTTTTTTTGCAGT-TTTT
1 TTGACAG---TTTTG--GTATTAT
*
54114009 TTTACAGTTTTGGTATTAT
1 TTGACAGTTTTGGTATTAT
*
54114028 TTAACAGTTTT
1 TTGACAGTTTT
54114039 TTTGGTATTA
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
18 2 0.05
19 20 0.47
20 5 0.12
22 5 0.12
23 9 0.21
24 2 0.05
ACGTcount: A:0.19, C:0.07, G:0.17, T:0.57
Consensus pattern (19 bp):
TTGACAGTTTTGGTATTAT
Found at i:54114006 original size:11 final size:12
Alignment explanation
Indices: 54113985--54114019 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
54113975 TTTGGTATTA
54113985 TTTGACAGTTTT
1 TTTGACAGTTTT
54113997 TTTG-CAGTTTT
1 TTTGACAGTTTT
*
54114008 TTTTACAGTTTT
1 TTTGACAGTTTT
54114020 GGTATTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.14, C:0.09, G:0.14, T:0.63
Consensus pattern (12 bp):
TTTGACAGTTTT
Found at i:54114044 original size:22 final size:22
Alignment explanation
Indices: 54113974--54114048 Score: 77
Period size: 22 Copynumber: 3.5 Consensus size: 22
54113964 AAATTGACAG
*
54113974 TTTTGGTATTATTTGACAGTTT
1 TTTTGGTATTATTTAACAGTTT
* *
54113996 TTTTGCAGT-TTTTTTTACAG---
1 TTTTG--GTATTATTTAACAGTTT
54114016 TTTTGGTATTATTTAACAGTTT
1 TTTTGGTATTATTTAACAGTTT
54114038 TTTTGGTATTA
1 TTTTGGTATTA
54114049 CTTGTATAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
18 2 0.05
19 9 0.21
20 5 0.12
22 16 0.37
23 9 0.21
24 2 0.05
ACGTcount: A:0.19, C:0.05, G:0.16, T:0.60
Consensus pattern (22 bp):
TTTTGGTATTATTTAACAGTTT
Found at i:54115429 original size:21 final size:21
Alignment explanation
Indices: 54115405--54115553 Score: 99
Period size: 21 Copynumber: 7.0 Consensus size: 21
54115395 ACCAAAAACA
*
54115405 TACAATTAAATGATAAAAAAG
1 TACAACTAAATGATAAAAAAG
*
54115426 TACAACTAAAAAGA-AAAAAAG
1 TACAACT-AAATGATAAAAAAG
*
54115447 TTACAACTAAATGAT-TAAAAG
1 -TACAACTAAATGATAAAAAAG
* * *
54115468 TACAAGTAAA-AACAAAAAAAG
1 TACAACTAAATGA-TAAAAAAG
54115489 TTACAACTAAATGACTAAAAAAG
1 -TACAACTAAATGA-TAAAAAAG
* * * *
54115512 TATAAATAAA-AACAAAAAAG
1 TACAACTAAATGATAAAAAAG
* *
54115532 TTATAACTAAATGTTGAAAAAA
1 -TACAACTAAATGAT-AAAAAA
54115554 AATGCAACTC
Statistics
Matches: 99, Mismatches: 19, Indels: 18
0.73 0.14 0.13
Matches are distributed among these distances:
19 1 0.01
20 16 0.16
21 38 0.38
22 29 0.29
23 15 0.15
ACGTcount: A:0.63, C:0.08, G:0.09, T:0.20
Consensus pattern (21 bp):
TACAACTAAATGATAAAAAAG
Found at i:54115444 original size:42 final size:42
Alignment explanation
Indices: 54115345--54115553 Score: 189
Period size: 42 Copynumber: 4.9 Consensus size: 42
54115335 CATCGAAACT
54115345 ACTAAAAACAAAAAATAAGATACAACTAAA--ATAATAATAA--ACA
1 ACTAAAAAC-AAAAA-AAG-TACAACTAAATGATAA-AA-AAGTACA
* *
54115388 ACTAAAAACCAAAAACA-TACAATTAAATGATAAAAAAGTACA
1 ACTAAAAA-CAAAAAAAGTACAACTAAATGATAAAAAAGTACA
* *
54115430 ACTAAAAAGAAAAAAAGTTACAACTAAATGAT-TAAAAGTACA
1 ACTAAAAACAAAAAAAG-TACAACTAAATGATAAAAAAGTACA
* *
54115472 AGTAAAAACAAAAAAAGTTACAACTAAATGACTAAAAAAGTATA
1 ACTAAAAACAAAAAAAG-TACAACTAAATGA-TAAAAAAGTACA
* * *
54115516 AATAAAAAC-AAAAAAGTTATAACTAAATGTTGAAAAAA
1 ACTAAAAACAAAAAAAG-TACAACTAAATGAT-AAAAAA
54115554 AATGCAACTC
Statistics
Matches: 143, Mismatches: 13, Indels: 20
0.81 0.07 0.11
Matches are distributed among these distances:
40 11 0.08
41 8 0.06
42 55 0.38
43 52 0.36
44 17 0.12
ACGTcount: A:0.65, C:0.10, G:0.07, T:0.18
Consensus pattern (42 bp):
ACTAAAAACAAAAAAAGTACAACTAAATGATAAAAAAGTACA
Found at i:54123852 original size:24 final size:24
Alignment explanation
Indices: 54123825--54123873 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
54123815 TGAAACCTAC
54123825 ATTGTAGTTAAAAAAATTGTTACA
1 ATTGTAGTTAAAAAAATTGTTACA
54123849 ATTGTAGTTAAAAAAATTGTTACA
1 ATTGTAGTTAAAAAAATTGTTACA
54123873 A
1 A
54123874 GTGACCTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.47, C:0.04, G:0.12, T:0.37
Consensus pattern (24 bp):
ATTGTAGTTAAAAAAATTGTTACA
Found at i:54123883 original size:23 final size:24
Alignment explanation
Indices: 54123833--54123884 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
54123823 ACATTGTAGT
* **
54123833 TAAAAAAATTGTTACAATTGTAGT
1 TAAAAAAATTGTTACAAGTGTACC
54123857 TAAAAAAATTGTTACAAGTG-ACC
1 TAAAAAAATTGTTACAAGTGTACC
54123880 TAAAA
1 TAAAA
54123885 GAGGGTATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 6 0.24
24 19 0.76
ACGTcount: A:0.50, C:0.08, G:0.12, T:0.31
Consensus pattern (24 bp):
TAAAAAAATTGTTACAAGTGTACC
Found at i:54125812 original size:29 final size:27
Alignment explanation
Indices: 54125774--54125827 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 27
54125764 CTTTTGAATT
*
54125774 AATAAATTCTTTTTGAGTTTTCTTTTTTC
1 AATAAATTC-TCTTGAG-TTTCTTTTTTC
*
54125803 AATAATTTCTCTTGAGTTTCTTTTT
1 AATAAATTCTCTTGAGTTTCTTTTT
54125828 GAAGACTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 9 0.39
28 6 0.26
29 8 0.35
ACGTcount: A:0.20, C:0.11, G:0.07, T:0.61
Consensus pattern (27 bp):
AATAAATTCTCTTGAGTTTCTTTTTTC
Found at i:54128250 original size:3 final size:3
Alignment explanation
Indices: 54128244--54128291 Score: 53
Period size: 3 Copynumber: 16.3 Consensus size: 3
54128234 AAGAAAAAAA
* * * *
54128244 AAG AAG AGG AGG A-G AAG AAG AAG GAG AAG AAG AAG AAG AAG GAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
54128291 A
1 A
54128292 GGAAAAATGG
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:54132342 original size:6 final size:6
Alignment explanation
Indices: 54132327--54132391 Score: 69
Period size: 6 Copynumber: 10.8 Consensus size: 6
54132317 AACCAAACTG
* * * * *
54132327 AAATCA AAATCT AAATCT AAATCT AAATCT AAGTCG AGATCA AAAT-T
1 AAATCT AAATCT AAATCT AAATCT AAATCT AAATCT AAATCT AAATCT
54132374 GAAATCT AAATCT AAATC
1 -AAATCT AAATCT AAATC
54132392 AGAATCAGTG
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
6 48 0.98
7 1 0.02
ACGTcount: A:0.51, C:0.15, G:0.06, T:0.28
Consensus pattern (6 bp):
AAATCT
Found at i:54132417 original size:6 final size:6
Alignment explanation
Indices: 54132408--54132474 Score: 80
Period size: 6 Copynumber: 11.2 Consensus size: 6
54132398 AGTGAGTGTT
* * * *
54132408 TCAAAA TCAAAA TCGAAA TCAAAA TCAAAA TCAGAA TCAGAA TCGAAA
1 TCAAAA TCAAAA TCAAAA TCAAAA TCAAAA TCAAAA TCAAAA TCAAAA
**
54132456 TCAAAA TTGAAA TCAAAA T
1 TCAAAA TCAAAA TCAAAA T
54132475 AACCCTAAAT
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 51 1.00
ACGTcount: A:0.58, C:0.15, G:0.07, T:0.19
Consensus pattern (6 bp):
TCAAAA
Done.