Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032254.1 Gossypioides kirkii chromosome KI_12
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: 43711324
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 132 of 135
Found at i:42640754 original size:12 final size:12
Alignment explanation
Indices: 42640737--42640762 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
42640727 ATACTTTTAT
42640737 ATACATGCATGC
1 ATACATGCATGC
42640749 ATACATGCATGC
1 ATACATGCATGC
42640761 AT
1 AT
42640763 GTATTTATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (12 bp):
ATACATGCATGC
Found at i:42642013 original size:12 final size:11
Alignment explanation
Indices: 42641976--42642012 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
42641966 TTTATAGTTA
42641976 AAAATAATTTT
1 AAAATAATTTT
*
42641987 AAATTAATTTT
1 AAAATAATTTT
*
42641998 AAAATATTTTT
1 AAAATAATTTT
42642009 AAAA
1 AAAA
42642013 AATAATTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
AAAATAATTTT
Found at i:42659214 original size:24 final size:28
Alignment explanation
Indices: 42659178--42659230 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 28
42659168 TGAATTTAAC
42659178 TTTTATTTGTTT-AATT-T-TACTTTTT
1 TTTTATTTGTTTAAATTATATACTTTTT
42659203 TTTTATTT-TTTAAATTATATACTTTTT
1 TTTTATTTGTTTAAATTATATACTTTTT
42659230 T
1 T
42659231 AATTTTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
24 3 0.12
25 12 0.48
26 1 0.04
27 9 0.36
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.74
Consensus pattern (28 bp):
TTTTATTTGTTTAAATTATATACTTTTT
Found at i:42670624 original size:14 final size:14
Alignment explanation
Indices: 42670607--42670637 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
42670597 TGATATACAT
42670607 TATATAATATATGA
1 TATATAATATATGA
*
42670621 TATATACTATATGA
1 TATATAATATATGA
42670635 TAT
1 TAT
42670638 GATATAGCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.45
Consensus pattern (14 bp):
TATATAATATATGA
Found at i:42672301 original size:33 final size:33
Alignment explanation
Indices: 42672258--42672355 Score: 135
Period size: 33 Copynumber: 3.0 Consensus size: 33
42672248 GGAGAAAATT
* * * *
42672258 TTTTTAAGCCTCTTAAAAGTTGATAAAACAAAA
1 TTTTTGAGCCTCTTAAAAGCTGAAAAAAAAAAA
42672291 TTTTTGAGCCTCTTAAAAGCTGAAAAAAAAAAA
1 TTTTTGAGCCTCTTAAAAGCTGAAAAAAAAAAA
*
42672324 TTTTTGGGCCTCTTAGAAA-CTGAAAAAAAAAA
1 TTTTTGAGCCTCTTA-AAAGCTGAAAAAAAAAA
42672356 TTTAAACCCT
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 56 0.95
34 3 0.05
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.30
Consensus pattern (33 bp):
TTTTTGAGCCTCTTAAAAGCTGAAAAAAAAAAA
Found at i:42672518 original size:17 final size:17
Alignment explanation
Indices: 42672496--42672576 Score: 76
Period size: 17 Copynumber: 4.8 Consensus size: 17
42672486 ATTTTTAAAT
*
42672496 TTTAAGTTTAGATTTAG
1 TTTAAGTTTAAATTTAG
*
42672513 TTTAAGTTTAAATTTAT
1 TTTAAGTTTAAATTTAG
*
42672530 TTTGAA-TTTAAA-TTCG
1 TTT-AAGTTTAAATTTAG
* *
42672546 TTCTAAATTTAAATTTAT
1 TT-TAAGTTTAAATTTAG
*
42672564 TTTAAATTTAAAT
1 TTTAAGTTTAAAT
42672577 GTAATTAAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
16 6 0.11
17 42 0.78
18 6 0.11
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.54
Consensus pattern (17 bp):
TTTAAGTTTAAATTTAG
Found at i:42673209 original size:27 final size:27
Alignment explanation
Indices: 42673178--42673233 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
42673168 TACTAAATGC
42673178 TATTAAAT-GCATAATAAATAA-ATATAA
1 TATTAAATAG-ATAATAAATAATA-ATAA
42673205 TATTAAATAGATAATAAATAATAATAA
1 TATTAAATAGATAATAAATAATAATAA
42673232 TA
1 TA
42673234 AAATTGAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
27 25 0.93
28 2 0.07
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.34
Consensus pattern (27 bp):
TATTAAATAGATAATAAATAATAATAA
Found at i:42674316 original size:30 final size:30
Alignment explanation
Indices: 42674260--42674686 Score: 274
Period size: 30 Copynumber: 14.4 Consensus size: 30
42674250 TTGTTTAAAA
*
42674260 AAAATTATATTTTGACCCT-AAACTTCTTC
1 AAAATTACATTTTGACCCTCAAACTTCTTC
* * *
42674289 AAAATTATAATTTGACCCTCGAACTTC-TC
1 AAAATTACATTTTGACCCTCAAACTTCTTC
* * * * *
42674318 AAAAATCACATTTTAACCAT-GAACTTCTTA
1 -AAAATTACATTTTGACCCTCAAACTTCTTC
* *
42674348 AAAATCACATTTTGACCC-CTAAACTT-TCC
1 AAAATTACATTTTGACCCTC-AAACTTCTTC
* *
42674377 AAAAATTACATTTTAACCCTCAAACTTCTTT
1 -AAAATTACATTTTGACCCTCAAACTTCTTC
*
42674408 AAAATTACATTTTGACCC-CAAACATT-TCC
1 AAAATTACATTTTGACCCTCAAAC-TTCTTC
* * *
42674437 AAAATCATATTTTCACCC-CAAACTT-TTCC
1 AAAATTACATTTTGACCCTCAAACTTCTT-C
** * * *
42674466 AAAATTGTATTTTTACCCTCGAA--TATTC
1 AAAATTACATTTTGACCCTCAAACTTCTTC
* * *
42674494 AAAAATTACCATTTTTACCCT-AAAATTTTTC
1 -AAAATTA-CATTTTGACCCTCAAACTTCTTC
* * *
42674525 AAAATTACATTTT-AACCTCGAACTT-TAC
1 AAAATTACATTTTGACCCTCAAACTTCTTC
* * *
42674553 AAAAATTACATTTTAACCTTCGAACTTC-TC
1 -AAAATTACATTTTGACCCTCAAACTTCTTC
* * * **
42674583 AAAATCACATTTTGACCCCTCGATCTTCTGA
1 AAAATTACATTTTGA-CCCTCAAACTTCTTC
* * * * *
42674614 AAAATAACATTTTAACCCTCGACCTT-TCC
1 AAAATTACATTTTGACCCTCAAACTTCTTC
*
42674643 AAAAATTACATTTTGACCCTCAAACTTCTCC
1 -AAAATTACATTTTGACCCTCAAACTTCTTC
42674674 AAAATTACATTTT
1 AAAATTACATTTT
42674687 AACCTCGAAT
Statistics
Matches: 320, Mismatches: 54, Indels: 47
0.76 0.13 0.11
Matches are distributed among these distances:
28 11 0.03
29 133 0.42
30 154 0.48
31 22 0.07
ACGTcount: A:0.36, C:0.24, G:0.04, T:0.36
Consensus pattern (30 bp):
AAAATTACATTTTGACCCTCAAACTTCTTC
Found at i:42674331 original size:59 final size:58
Alignment explanation
Indices: 42674259--42674690 Score: 365
Period size: 59 Copynumber: 7.3 Consensus size: 58
42674249 TTTGTTTAAA
* * * *
42674259 AAAAATTATATTTTGACCCTAAACTTCTTCAAAATTATAATTTGACCCTCGAACTTCTC
1 AAAAATTACATTTTAACCCTAAACTTCTTCAAAATTACATTTTGACCCTCGAACTT-TC
* * * * * *
42674318 AAAAATCACATTTTAACCATGAACTTCTTAAAAATCACATTTTGACCC-CTAAACTTTCC
1 AAAAATTACATTTTAACCCTAAACTTCTTCAAAATTACATTTTGACCCTC-GAACTTT-C
* *
42674377 AAAAATTACATTTTAACCCTCAAACTTCTTTAAAATTACATTTTGACCC-CAAACATTTC
1 AAAAATTACATTTTAACCCT-AAACTTCTTCAAAATTACATTTTGACCCTCGAAC-TTTC
* * * * * ** *
42674436 CAAAATCATATTTTCACCCCAAACTT-TTCCAAAATTGTATTTTTACCCTCGAA-TATTC
1 AAAAATTACATTTTAACCCTAAACTTCTT-CAAAATTACATTTTGACCCTCGAACT-TTC
* * * *
42674494 AAAAATTACCATTTTTACCCTAAAATTTTTCAAAATTACATTTT-AACCTCGAACTTTAC
1 AAAAATTA-CATTTTAACCCTAAACTTCTTCAAAATTACATTTTGACCCTCGAACTTT-C
* * * * *
42674553 AAAAATTACATTTTAACCTTCGAACTTC-TCAAAATCACATTTTGACCCCTCGATCTTCTG
1 AAAAATTACATTTTAACCCT-AAACTTCTTCAAAATTACATTTTGA-CCCTCGAACTT-TC
* * * * *
42674613 AAAAATAACATTTTAACCCTCGACCTT-TCCAAAAATTACATTTTGACCCTCAAACTTCTC
1 AAAAATTACATTTTAACCCT-AAACTTCTTC-AAAATTACATTTTGACCCTCGAACTT-TC
*
42674673 CAAAATTACATTTTAACC
1 AAAAATTACATTTTAACC
42674691 TCGAATTTCT
Statistics
Matches: 303, Mismatches: 53, Indels: 33
0.78 0.14 0.08
Matches are distributed among these distances:
57 3 0.01
58 66 0.22
59 127 0.42
60 92 0.30
61 15 0.05
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.35
Consensus pattern (58 bp):
AAAAATTACATTTTAACCCTAAACTTCTTCAAAATTACATTTTGACCCTCGAACTTTC
Found at i:42674720 original size:29 final size:29
Alignment explanation
Indices: 42674317--42674786 Score: 97
Period size: 30 Copynumber: 15.9 Consensus size: 29
42674307 TCGAACTTCT
* * *
42674317 CAAAAATCACATTTTAACCATGAACTTCTT-
1 CAAAAGTCACATTTTAACC-TCAAATT-TTC
* * * *
42674347 -AAAAATCACATTTTGACCCCTAAACTTTC
1 CAAAAGTCACATTTTAACCTC-AAATTTTC
* *
42674376 CAAAAATTACATTTTAACCCTCAAACTTCTT-
1 CAAAAGTCACATTTTAA-CCTCAAA-TT-TTC
* * * * *
42674407 TAAAA-TTACATTTTGACCCCAAACATTTC
1 CAAAAGTCACATTTTAACCTCAAA-TTTTC
* * *
42674436 CAAAA-TCATATTTTCACCCCAAACTTTTC
1 CAAAAGTCACATTTTAACCTCAAA-TTTTC
* * * *
42674465 CAAAATTGT-A-TTTTTACCCTCGAATATT-
1 CAAAA--GTCACATTTTAACCTCAAATTTTC
* * * * *
42674493 CAAAAATTACCATTTTTACCCTAAAATTTTT
1 CAAAAGTCA-CA-TTTTAACCTCAAATTTTC
* * * *
42674524 CAAAA-TTACATTTTAACCTCGAACTTTA
1 CAAAAGTCACATTTTAACCTCAAATTTTC
* * * *
42674552 CAAAAATTACATTTTAACCTTCGAA-CTTC
1 CAAAAGTCACATTTTAACC-TCAAATTTTC
* * *
42674581 TCAAAA-TCACATTTTGACCCCTC-GATCTTC
1 -CAAAAGTCACATTTT-A-ACCTCAAATTTTC
* * * * **
42674611 TGAAAAATAACATTTTAACCCTCGACCTTTC
1 -CAAAAGTCACATTTTAA-CCTCAAATTTTC
* * * *
42674642 CAAAAATTACATTTTGACCCTCAAACTTCTC
1 CAAAAGTCACATTTT-AACCTCAAA-TTTTC
* *
42674673 CAAAA-TTACATTTTAACCTCGAA-TTTC
1 CAAAAGTCACATTTTAACCTCAAATTTTC
* *
42674700 TAAAAGTCACATTTTCGACCTCAAATTTTC
1 CAAAAGTCACATTTT-AACCTCAAATTTTC
*** *
42674730 CAAAAGTTTGATTTTAATCCCCAAATCTTTC
1 CAAAAGTCACATTTTAA-CCTCAAAT-TTTC
* * *
42674761 AAAAATTTCA-ATTTTGACCTCAAATT
1 CAAAA-GTCACATTTTAACCTCAAATT
42674787 CCTCGAAAAG
Statistics
Matches: 336, Mismatches: 72, Indels: 65
0.71 0.15 0.14
Matches are distributed among these distances:
26 1 0.00
27 8 0.02
28 35 0.10
29 102 0.30
30 136 0.40
31 50 0.15
32 4 0.01
ACGTcount: A:0.36, C:0.24, G:0.04, T:0.36
Consensus pattern (29 bp):
CAAAAGTCACATTTTAACCTCAAATTTTC
Found at i:42674746 original size:58 final size:60
Alignment explanation
Indices: 42674299--42674734 Score: 230
Period size: 59 Copynumber: 7.4 Consensus size: 60
42674289 AAAATTATAA
* * * * * *
42674299 TTTGACCCTCGAACTTCTCAAAAATCACATTTTAACCAT-GA-ACTTCTTAAAAATCACAT
1 TTTGACCCTCAAACTTCTCCAAAATTACATTTTAACCCTCGACATTTC-CAAAAATCACAT
* * ** *
42674358 TTTGACCC-CTAAACTT-TCCAAAAATTACATTTTAACCCTC-AAACTTCTTTAAAATTACAT
1 TTTGACCCTC-AAACTTCTCC-AAAATTACATTTTAACCCTCGACATTTC-CAAAAATCACAT
* * * * * ***
42674418 TTTGACCC-CAAACATT-TCCAAAATCATATTTTCACCC-CAAACTTTTCC-AAAATTGTAT
1 TTTGACCCTCAAAC-TTCTCCAAAATTACATTTTAACCCTC-GACATTTCCAAAAATCACAT
* * * * * * * *
42674476 TTTTACCCTCGAA-TAT-TCAAAAATTACCATTTTTACCCT-AAAATTTTTC-AAAATTACAT
1 TTTGACCCTCAAACT-TCTCCAAAATTA-CATTTTAACCCTCGACA-TTTCCAAAAATCACAT
* * * * *
42674535 TTT-AACCTCGAACTT-TACAAAAATTACATTTTAACCTTCGA-ACTTCTC-AAAATCACAT
1 TTTGACCCTCAAACTTCT-CCAAAATTACATTTTAACCCTCGACATTTC-CAAAAATCACAT
* * ** * * *
42674593 TTTGACCCCTCGATCTTCTGAAAAATAACATTTTAACCCTCGACCTTTCCAAAAATTACAT
1 TTTGA-CCCTCAAACTTCTCCAAAATTACATTTTAACCCTCGACATTTCCAAAAATCACAT
* *
42674654 TTTGACCCTCAAACTTCTCCAAAATTACATTTTAA-CCTCGA-ATTTCTAAAAGTCACAT
1 TTTGACCCTCAAACTTCTCCAAAATTACATTTTAACCCTCGACATTTCCAAAAATCACAT
*
42674712 TTTCGA-CCTCAAA-TTTTCCAAAA
1 TTT-GACCCTCAAACTTCTCCAAAA
42674735 GTTTGATTTT
Statistics
Matches: 304, Mismatches: 51, Indels: 46
0.76 0.13 0.11
Matches are distributed among these distances:
57 12 0.04
58 87 0.29
59 97 0.32
60 90 0.30
61 18 0.06
ACGTcount: A:0.36, C:0.25, G:0.04, T:0.35
Consensus pattern (60 bp):
TTTGACCCTCAAACTTCTCCAAAATTACATTTTAACCCTCGACATTTCCAAAAATCACAT
Found at i:42677423 original size:28 final size:29
Alignment explanation
Indices: 42677374--42677701 Score: 283
Period size: 28 Copynumber: 11.3 Consensus size: 29
42677364 GGAGGTCCTT
* *
42677374 AACTGTCCAAAAATTACGTTTTTACCTCGA
1 AACT-TCCAAAAATTACATTTTTACCCCGA
* *
42677404 AA-TTCCAAAAATTCCATTTTAACCCCGA
1 AACTTCCAAAAATTACATTTTTACCCCGA
* * **
42677432 AACTTTCAAAAATTACATTTTTGCCCTTA
1 AACTTCCAAAAATTACATTTTTACCCCGA
* *
42677461 AACTTTCC-AAATTTGA-ATTTTTAACCTCGA
1 AAC-TTCCAAAAATT-ACATTTTT-ACCCCGA
** **
42677491 AACTTCCAAAAATTATGTTTTGCCCCCG-
1 AACTTCCAAAAATTACATTTTTACCCCGA
* * *
42677519 AACTTTCAAAAATTTCATTTTTGACCCCAA
1 AACTTCCAAAAATTACATTTTT-ACCCCGA
*
42677549 AACTTCCAAAAATTACATTTTTGCCCC-A
1 AACTTCCAAAAATTACATTTTTACCCCGA
** *
42677577 AACTTTTAAAAATTCCATTTTTAACCCCGA
1 AACTTCCAAAAATTACATTTTT-ACCCCGA
* * * *
42677607 AACCTCCAAAAATTATAGTTTT-CCCCTA
1 AACTTCCAAAAATTACATTTTTACCCCGA
* *
42677635 AACTTCCAAAAATTACATTTTAACCCCAA
1 AACTTCCAAAAATTACATTTTTACCCCGA
* *
42677664 AATTTCC-AAAATTACATTTTTACCCCCA
1 AACTTCCAAAAATTACATTTTTACCCCGA
*
42677692 AAATTCCAAA
1 AACTTCCAAA
42677702 CTATCCATTT
Statistics
Matches: 235, Mismatches: 51, Indels: 25
0.76 0.16 0.08
Matches are distributed among these distances:
28 108 0.46
29 69 0.29
30 58 0.25
ACGTcount: A:0.37, C:0.25, G:0.04, T:0.34
Consensus pattern (29 bp):
AACTTCCAAAAATTACATTTTTACCCCGA
Found at i:42677523 original size:58 final size:57
Alignment explanation
Indices: 42677411--42677693 Score: 263
Period size: 58 Copynumber: 4.9 Consensus size: 57
42677401 CGAAATTCCA
* * **
42677411 AAAATTCCA-TTTTAACCCCGAAACTTTCAAAAATTACATTTTTGCCCTTAAACTTTC
1 AAAATTTCATTTTTAACCCCGAAACTTCCAAAAATTA-ATTTTTGCCCCCAAACTTTC
* * * *
42677468 CAAATTTGAATTTTTAACCTCGAAACTTCCAAAAATT-ATGTTTTGCCCCCGAACTTTC
1 AAAATTT-CATTTTTAACCCCGAAACTTCCAAAAATTAAT-TTTTGCCCCCAAACTTTC
* * *
42677526 AAAAATTTCATTTTTGACCCCAAAACTTCCAAAAATTACATTTTTG-CCCCAAACTTTTA
1 -AAAATTTCATTTTTAACCCCGAAACTTCCAAAAATTA-ATTTTTGCCCCCAAAC-TTTC
* * * * *
42677585 AAAATTCCATTTTTAACCCCGAAACCTCCAAAAATTATAGTTTT-CCCCTAAACTTCC
1 AAAATTTCATTTTTAACCCCGAAACTTCCAAAAATTA-ATTTTTGCCCCCAAACTTTC
* * * *
42677642 AAAAATTACA-TTTTAACCCCAAAATTTCC-AAAATTACATTTTTACCCCCAAA
1 -AAAATTTCATTTTTAACCCCGAAACTTCCAAAAATTA-ATTTTTGCCCCCAAA
42677694 ATTCCAAACT
Statistics
Matches: 185, Mismatches: 31, Indels: 20
0.78 0.13 0.08
Matches are distributed among these distances:
56 12 0.06
57 32 0.17
58 101 0.55
59 38 0.21
60 2 0.01
ACGTcount: A:0.36, C:0.25, G:0.04, T:0.34
Consensus pattern (57 bp):
AAAATTTCATTTTTAACCCCGAAACTTCCAAAAATTAATTTTTGCCCCCAAACTTTC
Found at i:42677523 original size:87 final size:86
Alignment explanation
Indices: 42677392--42677689 Score: 234
Period size: 86 Copynumber: 3.4 Consensus size: 86
42677382 AAAAATTACG
*
42677392 TTTTTACCTCGAAATTCCAAAAATTCCATTTTAACCCCGAAACTTTCAAAAATTACATTTTTG-C
1 TTTTTACCTCGAAATTCCAAAAATTACATTTTAACCCCGAAACTTTCAAAAATTACATTTTTGAC
**
42677456 CCTTAAACTTTCCAAATTTGAA
66 CCCAAAAC-TTCCAAATTTGAA
** ** *
42677478 TTTTTAACCTCGAAACTTCCAAAAATTATGTTTTGCCCCCG-AACTTTCAAAAATTTCATTTTTG
1 TTTTT-ACCTCGAAA-TTCCAAAAATTACATTTTAACCCCGAAACTTTCAAAAATTACATTTTTG
*
42677542 ACCCCAAAACTTCCAAAAATT-ACA
64 ACCCCAAAACTTCC-AAATTTGA-A
* * ** * * * * *
42677566 TTTTTGCC-CCAAACTTTTAAAAATTCCATTTTTAACCCCGAAACCTCCAAAAATTATAGTTTT-
1 TTTTTACCTCGAAA-TTCCAAAAATTACA-TTTTAACCCCGAAACTTTCAAAAATTACATTTTTG
* *
42677629 -CCCCTAAACTTCCAAAAATT-ACA
64 ACCCCAAAACTTCC-AAATTTGA-A
* * * *
42677652 TTTTAACCCCAAAATTTCC-AAAATTACATTTTTACCCC
1 TTTTTACCTCGAAA-TTCCAAAAATTACATTTTAACCCC
42677690 CAAAATTCCA
Statistics
Matches: 172, Mismatches: 32, Indels: 17
0.78 0.14 0.08
Matches are distributed among these distances:
85 9 0.05
86 55 0.32
87 53 0.31
88 55 0.32
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.35
Consensus pattern (86 bp):
TTTTTACCTCGAAATTCCAAAAATTACATTTTAACCCCGAAACTTTCAAAAATTACATTTTTGAC
CCCAAAACTTCCAAATTTGAA
Found at i:42677712 original size:28 final size:29
Alignment explanation
Indices: 42677383--42677717 Score: 161
Period size: 29 Copynumber: 11.6 Consensus size: 29
42677373 TAACTGTCCA
* * *
42677383 AAAATTACGTTTTTA-CCTCGAAA-TTCC
1 AAAATTACATTTTTACCCCCAAAATTTCC
* * * * *
42677410 AAAAATTCCATTTTAACCCCGAAACTTTCA
1 -AAAATTACATTTTTACCCCCAAAATTTCC
* ** *
42677440 AAAATTACATTTTTGCCCTTAAACTTTCC
1 AAAATTACATTTTTACCCCCAAAATTTCC
* * * * *
42677469 AAATTTGA-ATTTTTAACCTCGAAACTTCC
1 AAAATT-ACATTTTTACCCCCAAAATTTCC
* * * *
42677498 AAAAATT--ATGTTTTGCCCCCGAACTTTCA
1 -AAAATTACAT-TTTTACCCCCAAAATTTCC
* *
42677527 AAAATTTCATTTTTGA-CCCCAAAACTTCC
1 AAAATTACATTTTT-ACCCCCAAAATTTCC
* * **
42677556 AAAAATTACATTTTT-GCCCCAAACTTTTA
1 -AAAATTACATTTTTACCCCCAAAATTTCC
* * * **
42677585 AAAATTCCATTTTTAACCCCGAAACCTCC
1 AAAATTACATTTTTACCCCCAAAATTTCC
* * * *
42677614 AAAAATTATAGTTTT--CCCCTAAACTTCC
1 -AAAATTACATTTTTACCCCCAAAATTTCC
*
42677642 AAAAATTACA-TTTTAACCCCAAAATTTCC
1 -AAAATTACATTTTTACCCCCAAAATTTCC
42677671 AAAATTACATTTTTACCCCCAAAA-TTCC
1 AAAATTACATTTTTACCCCCAAAATTTCC
* *
42677699 AAACTATCCATTTTTACCC
1 AAAAT-TACATTTTTACCC
42677718 TAACACTTTT
Statistics
Matches: 234, Mismatches: 57, Indels: 31
0.73 0.18 0.10
Matches are distributed among these distances:
27 4 0.02
28 70 0.30
29 125 0.53
30 35 0.15
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.35
Consensus pattern (29 bp):
AAAATTACATTTTTACCCCCAAAATTTCC
Found at i:42677841 original size:59 final size:58
Alignment explanation
Indices: 42677724--42677858 Score: 150
Period size: 58 Copynumber: 2.3 Consensus size: 58
42677714 ACCCTAACAC
* * * **
42677724 TTTT-AAAATTACCATTTTACCCCAAGATGTTCGAAAATTTCATTTTTAATCCTGATT
1 TTTTAAAAATTACCATTTTACCCCAAGATGATCGAAAATGTCATTTTTAACCCAAATT
* *
42677781 TTTCTAAAAATTACCGTTTTACCCTCAA-AT-ATCTAAAATGTCATTTTTAACCGCAAATT
1 TTT-TAAAAATTACCATTTTACCC-CAAGATGATCGAAAATGTCATTTTTAACC-CAAATT
*
42677840 TTTTCAAAATTACCATTTT
1 TTTTAAAAATTACCATTTT
42677859 TGCCCTCGAG
Statistics
Matches: 65, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
57 3 0.05
58 33 0.51
59 26 0.40
60 3 0.05
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.43
Consensus pattern (58 bp):
TTTTAAAAATTACCATTTTACCCCAAGATGATCGAAAATGTCATTTTTAACCCAAATT
Found at i:42677896 original size:28 final size:29
Alignment explanation
Indices: 42677844--42677904 Score: 90
Period size: 28 Copynumber: 2.1 Consensus size: 29
42677834 CAAATTTTTT
*
42677844 CAAAATTACCATTTTTGCCCTCGAG-AGTC
1 CAAAATTACCATTTTTGCCCCCGAGCA-TC
42677873 CAAAATTACCA-TTTTGCCCCCGAGCATC
1 CAAAATTACCATTTTTGCCCCCGAGCATC
42677901 CAAA
1 CAAA
42677905 GTCTTATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 18 0.60
29 12 0.40
ACGTcount: A:0.31, C:0.31, G:0.11, T:0.26
Consensus pattern (29 bp):
CAAAATTACCATTTTTGCCCCCGAGCATC
Found at i:42682732 original size:7 final size:7
Alignment explanation
Indices: 42682710--42682867 Score: 136
Period size: 7 Copynumber: 22.4 Consensus size: 7
42682700 TTCAATGAAT
42682710 AAAAGAA
1 AAAAGAA
42682717 AAGAA-AA
1 AA-AAGAA
42682724 AAAAG-A
1 AAAAGAA
42682730 AAAAGAA
1 AAAAGAA
*
42682737 AACATAAAA
1 AA-A-AGAA
42682746 GAAAAG-A
1 -AAAAGAA
42682753 AAAAG-A
1 AAAAGAA
*
42682759 AGAAGAA
1 AAAAGAA
*
42682766 AAAA-AGG
1 AAAAGA-A
42682773 AAAAGAA
1 AAAAGAA
42682780 AAAAG--
1 AAAAGAA
42682785 AAAAGAA
1 AAAAGAA
42682792 AAAAGAA
1 AAAAGAA
42682799 GAAGAAGAA
1 -AA-AAGAA
42682808 AAAAG-A
1 AAAAGAA
42682814 AAAAG-A
1 AAAAGAA
42682820 AAAAGAA
1 AAAAGAA
42682827 AAAAGAA
1 AAAAGAA
42682834 AAAAGAA
1 AAAAGAA
42682841 AAAAGAAA
1 AAAAG-AA
42682849 AAAGGAGAA
1 AAA--AGAA
42682858 AAAAGAA
1 AAAAGAA
42682865 AAA
1 AAA
42682868 TAAAACGAGA
Statistics
Matches: 128, Mismatches: 6, Indels: 34
0.76 0.04 0.20
Matches are distributed among these distances:
5 5 0.04
6 31 0.24
7 60 0.47
8 14 0.11
9 14 0.11
10 4 0.03
ACGTcount: A:0.81, C:0.01, G:0.18, T:0.01
Consensus pattern (7 bp):
AAAAGAA
Found at i:42682758 original size:43 final size:41
Alignment explanation
Indices: 42682710--42682872 Score: 163
Period size: 43 Copynumber: 3.9 Consensus size: 41
42682700 TTCAATGAAT
42682710 AAAAGAAAAGAAAAAAAAGAAAAAGAAAACATAAAAGAAAAGA
1 AAAAGAAAAGAAAAAAAAGAAAAAGAAAA-ATAAAAGAAAA-A
* * *
42682753 AAAAGAAGAAG-AAAAAAAGGAAAAGAAAAA-AGAA-AAGAA
1 AAAAGAA-AAGAAAAAAAAGAAAAAGAAAAATAAAAGAAAAA
*
42682792 AAAAGAAGAAGAAGAAAAAAGAAAAAGAAAAAGAAAA-AAGAAA
1 AAAAGAA-AAGAA-AAAAAAGAAAAAGAAAAATAAAAGAA-AAA
* *
42682835 AAAGAAAAAAGAAAAAAGGAGAAAAAAGAAAAATAAAA
1 AAA-AGAAAAGAAAAAA-AAG-AAAAAGAAAAATAAAA
42682873 CGAGAGGTCG
Statistics
Matches: 103, Mismatches: 9, Indels: 15
0.81 0.07 0.12
Matches are distributed among these distances:
39 12 0.12
40 4 0.04
41 20 0.19
42 10 0.10
43 36 0.35
44 21 0.20
ACGTcount: A:0.81, C:0.01, G:0.17, T:0.01
Consensus pattern (41 bp):
AAAAGAAAAGAAAAAAAAGAAAAAGAAAAATAAAAGAAAAA
Found at i:42682867 original size:1 final size:1
Alignment explanation
Indices: 42682710--42682851 Score: 50
Period size: 1 Copynumber: 142.0 Consensus size: 1
42682700 TTCAATGAAT
* * * * * * * * * * * **
42682710 AAAAGAAAAGAAAAAAAAGAAAAAGAAAACATAAAAGAAAAGAAAAAGAAGAAGAAAAAAAGGAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * * * * * * * *
42682775 AAGAAAAAAGAAAAGAAAAAAGAAGAAGAAGAAAAAAGAAAAAGAAAAAGAAAAAAGAAAAAAGA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
42682840 AAAAAGAAAAAA
1 AAAAAAAAAAAA
42682852 GGAGAAAAAA
Statistics
Matches: 91, Mismatches: 50, Indels: 0
0.65 0.35 0.00
Matches are distributed among these distances:
1 91 1.00
ACGTcount: A:0.82, C:0.01, G:0.17, T:0.01
Consensus pattern (1 bp):
A
Found at i:42682872 original size:6 final size:6
Alignment explanation
Indices: 42682723--42682850 Score: 104
Period size: 6 Copynumber: 20.8 Consensus size: 6
42682713 AGAAAAGAAA
* *
42682723 AAAAAG AAAAAG AAAACA- TAAAAG -AAAAG AAAAAG AAGAAGAA AAAAAG
1 AAAAAG AAAAAG AAAA-AG AAAAAG AAAAAG AAAAAG AA-AA-AG AAAAAG
* * *
42682772 GAAAAG AAAAA- AGAAAAG -AAAA- AAGAAG AAGAAG AAAAAAG AAAAAG
1 AAAAAG AAAAAG A-AAAAG AAAAAG AAAAAG AAAAAG -AAAAAG AAAAAG
42682819 AAAAAG AAAAAAG AAAAAAG AAAAAAG AAAAA
1 AAAAAG -AAAAAG -AAAAAG -AAAAAG AAAAA
42682851 AGGAGAAAAA
Statistics
Matches: 104, Mismatches: 7, Indels: 22
0.78 0.05 0.17
Matches are distributed among these distances:
5 14 0.13
6 57 0.55
7 30 0.29
8 3 0.03
ACGTcount: A:0.81, C:0.01, G:0.17, T:0.01
Consensus pattern (6 bp):
AAAAAG
Found at i:42682877 original size:21 final size:20
Alignment explanation
Indices: 42682710--42682852 Score: 98
Period size: 23 Copynumber: 7.0 Consensus size: 20
42682700 TTCAATGAAT
* *
42682710 AAAAGAAAAGAAAAAAAAGA
1 AAAAAAAAAGAGAAAAAAGA
* *
42682730 AAAAGAAAACATAAAAGAAAAGA
1 AAAA-AAAA-AGAGAA-AAAAGA
*
42682753 AAAAGAAGAAGA-AAAAAAGGA
1 AAAA-AAAAAGAGAAAAAA-GA
*
42682774 AAAGAAAAA-AG--AAAAGA
1 AAAAAAAAAGAGAAAAAAGA
42682791 AAAAAGAAGAAGAAGAAAAAAGA
1 AAAAA-AA-AAG-AGAAAAAAGA
*
42682814 AAAAGAAAA-AGAAAAAAGA
1 AAAAAAAAAGAGAAAAAAGA
*
42682833 AAAAAGAAAAAAGAAAAAAG
1 AAAAA-AAAAGAGAAAAAAG
42682853 GAGAAAAAAG
Statistics
Matches: 101, Mismatches: 9, Indels: 25
0.75 0.07 0.19
Matches are distributed among these distances:
17 6 0.06
18 6 0.06
19 17 0.17
20 16 0.16
21 23 0.23
22 9 0.09
23 24 0.24
ACGTcount: A:0.81, C:0.01, G:0.17, T:0.01
Consensus pattern (20 bp):
AAAAAAAAAGAGAAAAAAGA
Found at i:42684105 original size:49 final size:49
Alignment explanation
Indices: 42683846--42684111 Score: 223
Period size: 50 Copynumber: 5.3 Consensus size: 49
42683836 TAGTACTAGG
*
42683846 AAGACATGAAGGGAAAGATCTAAGATCGCAACGACGGATCCAGTACCACA
1 AAGACATGAAGGGAAAGATCTAAG-CCGCAACGACGGATCCAGTACCACA
** * * * * * * *
42683896 AAGACACAAAAGGGAAAGGTCTAAGTCGTAATGGCGGA-CCATGTAACTCA
1 AAGACA-TGAAGGGAAAGATCTAAGCCGCAACGACGGATCCA-GTACCACA
* ** * *
42683946 GAAGACAAT-AAGGGAAAGATTTAAGCCGCAACGGTGGATCCAATACCGCAAA
1 -AAGAC-ATGAAGGGAAAGATCTAAGCCGCAACGACGGATCCAGTA-C-CACA
* *
42683998 AAGACA-GAAGGGAAAGATCTAAGCTGCAACGACGGATCCAGTACCACG
1 AAGACATGAAGGGAAAGATCTAAGCCGCAACGACGGATCCAGTACCACA
* * * * * *
42684046 AAGACATGAAGAGAAAGATCTAAGCCGCGACGATGGATCCGGTATCATA
1 AAGACATGAAGGGAAAGATCTAAGCCGCAACGACGGATCCAGTACCACA
**
42684095 AAGATTTGAAGGGAAAG
1 AAGACATGAAGGGAAAG
42684112 GTTTAAGTCG
Statistics
Matches: 170, Mismatches: 37, Indels: 19
0.75 0.16 0.08
Matches are distributed among these distances:
48 8 0.05
49 52 0.31
50 79 0.46
51 28 0.16
52 3 0.02
ACGTcount: A:0.41, C:0.19, G:0.26, T:0.14
Consensus pattern (49 bp):
AAGACATGAAGGGAAAGATCTAAGCCGCAACGACGGATCCAGTACCACA
Found at i:42685049 original size:201 final size:201
Alignment explanation
Indices: 42684492--42685535 Score: 1180
Period size: 201 Copynumber: 5.2 Consensus size: 201
42684482 AAACAACGAG
* * * * *
42684492 GCGGTCATCTTCCTGATGACATACAGAGAAGTATACCAACTCAACACTCAATATGAGCAAACCTT
1 GCGGTCATCTTCCTGATGAGATACAAAGAAGTATACCAACTCAACGCTCAATGTGAGCAAATCTT
** * *
42684557 CGAACCCTAGCTTCCTGATGAGATACTGAGAAATAGGTCGAAGCAAT-AAATGATTAGCTTCCTG
66 CGAACCCTAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAGGGTTAGCTTCCTG
* * * * *
42684621 ATGAGACACTGAGAAGTGGACCAAACTCGTCTTCCTGAGGAGAT-CTAAAGAAGCGAATTAAAAC
131 ATGAGACACAGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATAC-AGAGAAGCGAATTGAAAC
*
42684685 AAATGAT
195 AAGTGAT
* * * * * * * * *
42684692 GCGGTCATCTTCTTGATGAGACACTAAGAAGAAGACTAAATCAAACCCAGGCTCAATGCGAGTAA
1 GCGGTCATCTTCCTGATGAGATACAAAGAAGTATACCAACTC-AA--C--GCTCAATGTGAGCAA
* * * *
42684757 ATCTTCGAACCC-AGCTTCCTGATGAGACACTCAGAAGTAGGTTGAAGCAATAAAAGGGTTAGCT
61 ATCTTCGAACCCTAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAGGGTTAGCT
*
42684821 TCCTGATGAGACACAGAAAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTG
126 TCCTGATGAGACACAGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTG
42684886 AAACAAGTGA-
191 AAACAAGTGAT
* *
42684896 GACGGTCATCTTCCTGATGAGATACAAAGAAGTATACCAACTCAACGCTTAATGCGAGCAAATCT
1 G-CGGTCATCTTCCTGATGAGATACAAAGAAGTATACCAACTCAACGCTCAATGTGAGCAAATCT
* *
42684961 TCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCACGTCGAAGCAATAAAAGGGTTAGCTTCCT
65 TCGAACCCTAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAGGGTTAGCTTCCT
* * * * *
42685026 GATGAGACACAGAGAATTGGACCAAATTCGTTTTCCTGATGAGATAAAGAGAAACGAATTGAAAT
130 GATGAGACACAGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAAC
* *
42685091 AAGCGAG
195 AAGTGAT
* *
42685098 GTGGTCATCTTCCTGATGAGATACAAAGAAGTATACCAACTCAACGCTCGATGTGAGCAAATCTT
1 GCGGTCATCTTCCTGATGAGATACAAAGAAGTATACCAACTCAACGCTCAATGTGAGCAAATCTT
* * * ** * * *
42685163 CGAACCCTAACTTCCTGATGAGACACTTAGAAGCAGACCGAAGCTATAAAATGGTTAGCATCCTG
66 CGAACCCTAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAGGGTTAGCTTCCTG
* * * *
42685228 ATGAGATACTGAGAAGTGGACCAAATTCGTCTTCTTAATGAGATACAGAGAAGCGAATTGAAACA
131 ATGAGACACAGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAACA
*
42685293 AATGAT
196 AGTGAT
* * * * * * * * * * *
42685299 GTGGTCATCTTCTTAACGTGATACTAAGAAGAAGACCAAATCAAACCCACGCACGATGTGAGCAA
1 GCGGTCATCTTCCTGATGAGATACAAAGAAGTATACCAACTC--A---ACGCTCAATGTGAGCAA
* * *
42685364 ATCTTCGAATCCTAGCTTCCTGATGAGATACTAAGAAGCAGGTCGAAGTAAT-AAAGTGGTTAGC
61 ATCTTCGAACCCTAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAG-GGTTAGC
* * * * * * * * *
42685428 TTCCTGATGAGACACAGAGAAGTGAATCAAATCCGTCTTCCTGTTGAAACACAGAGAAGTGGATC
125 TTCCTGATGAGACACAGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATT
* *
42685493 AAAACAAGTGAC
190 GAAACAAGTGAT
* * * *
42685505 GCGATCGTCTTCCTGATCAGATACTAAGAAG
1 GCGGTCATCTTCCTGATGAGATACAAAGAAG
42685536 AAGGCCAAAC
Statistics
Matches: 711, Mismatches: 117, Indels: 26
0.83 0.14 0.03
Matches are distributed among these distances:
200 58 0.08
201 325 0.46
202 2 0.00
203 2 0.00
204 38 0.05
205 135 0.19
206 151 0.21
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.22
Consensus pattern (201 bp):
GCGGTCATCTTCCTGATGAGATACAAAGAAGTATACCAACTCAACGCTCAATGTGAGCAAATCTT
CGAACCCTAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAGGGTTAGCTTCCTG
ATGAGACACAGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAACA
AGTGAT
Found at i:42687931 original size:29 final size:28
Alignment explanation
Indices: 42687695--42687958 Score: 196
Period size: 30 Copynumber: 9.1 Consensus size: 28
42687685 CCCTGGAGGT
* *
42687695 CCCTAAACTATCCAAAAATTACGTTTTTA
1 CCCTAAACT-TCCAAAAATTCCATTTTTA
* *
42687724 CCCCAAAATTCCAAAAATTCCATTTTTGA
1 CCCTAAACTTCCAAAAATTCCATTTTT-A
* * * * *
42687753 TCTCGAAACTTCAAAAAATTTCATTTTTGC
1 -CCCTAAACTTCCAAAAATTCCATTTTT-A
*
42687783 CCCTAAACTTTCC-AAAATTACATTTTTAA
1 CCCTAAAC-TTCCAAAAATTCCATTTTT-A
*
42687812 CCCTGAAACTTCCAAAAATT-AAGTTTTT-
1 CCCT-AAACTTCCAAAAATTCCA-TTTTTA
* *
42687840 CCCTTGAACTTTCAAAAATTCCATTTTTAA
1 CCC-TAAACTTCCAAAAATTCCATTTTT-A
* * * *
42687870 CCCCAAAACCTCCAAAAATTTCATTTTTC
1 -CCCTAAACTTCCAAAAATTCCATTTTTA
*
42687899 CCCTGAACTTCCAAAAATTCCATTTTTGA
1 CCCTAAACTTCCAAAAATTCCATTTTT-A
*
42687928 CCCTAACACTTTC-AAAATTACCA-TTTTA
1 CCCTAA-ACTTCCAAAAATT-CCATTTTTA
42687956 CCC
1 CCC
42687959 CCCGGATGTC
Statistics
Matches: 188, Mismatches: 33, Indels: 29
0.75 0.13 0.12
Matches are distributed among these distances:
28 64 0.34
29 53 0.28
30 68 0.36
31 3 0.02
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.35
Consensus pattern (28 bp):
CCCTAAACTTCCAAAAATTCCATTTTTA
Found at i:42687954 original size:58 final size:57
Alignment explanation
Indices: 42687695--42687944 Score: 245
Period size: 58 Copynumber: 4.3 Consensus size: 57
42687685 CCCTGGAGGT
* * * * *
42687695 CCCTAAACTATCCAAAAATTACGTTTTTACCCC-AAAATTCCAAAAATTCCATTTTTGAT
1 CCCTAAACT-TCCAAAAATTTCATTTTT-CCCCTGAACTTCCAAAAATTCCATTTTT-AA
* * * * *
42687754 CTCGAAACTTCAAAAAATTTCATTTTTGCCCCTAAACTTTCC-AAAATTACATTTTTAA
1 CCCTAAACTTCCAAAAATTTCATTTTT-CCCCTGAAC-TTCCAAAAATTCCATTTTTAA
* * *
42687812 CCCTGAAACTTCCAAAAA-TTAAGTTTTTCCCTTGAACTTTCAAAAATTCCATTTTTAA
1 CCCT-AAACTTCCAAAAATTTCA-TTTTTCCCCTGAACTTCCAAAAATTCCATTTTTAA
* * *
42687870 CCCCAAAACCTCCAAAAATTTCATTTTTCCCCTGAACTTCCAAAAATTCCATTTTTGA
1 -CCCTAAACTTCCAAAAATTTCATTTTTCCCCTGAACTTCCAAAAATTCCATTTTTAA
*
42687928 CCCTAACACTTTCAAAA
1 CCCTAA-ACTTCCAAAA
42687945 TTACCATTTT
Statistics
Matches: 157, Mismatches: 26, Indels: 17
0.79 0.13 0.09
Matches are distributed among these distances:
57 8 0.05
58 99 0.63
59 46 0.29
60 4 0.03
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.35
Consensus pattern (57 bp):
CCCTAAACTTCCAAAAATTTCATTTTTCCCCTGAACTTCCAAAAATTCCATTTTTAA
Found at i:42688104 original size:86 final size:87
Alignment explanation
Indices: 42688001--42688197 Score: 236
Period size: 87 Copynumber: 2.3 Consensus size: 87
42687991 TATTTTTCTA
* * * *
42688001 AAAATT-TCTATTTTACCCTCGAATATCTAAAATGTCATTTTTAA-ACCAAATTTTTCCAAAATT
1 AAAATTATC-ATTTTACCCCCGAACATCCAAAATCTCATTTTTAATACCAAATTTTTCCAAAATT
*
42688064 ACCAGATTTGCCCCCGAAAGTCC
65 ACCAGATTTGCCCCAGAAAGTCC
** * * **
42688087 AAAATTATCATTTTACCCCCGGGCGTCCAAAGTCTCATTTTTAATACCATTTTTTTCCAAAATTA
1 AAAATTATCATTTTACCCCCGAACATCCAAAATCTCATTTTTAATACCAAATTTTTCCAAAATTA
* * *
42688152 CCATATTTTCCCCATAAAGTCC
66 CCAGATTTGCCCCAGAAAGTCC
*
42688174 AAAATTACCATTTTACCCCCGAAC
1 AAAATTATCATTTTACCCCCGAAC
42688198 TTTCAAAAAT
Statistics
Matches: 92, Mismatches: 17, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
86 33 0.36
87 59 0.64
ACGTcount: A:0.33, C:0.26, G:0.07, T:0.35
Consensus pattern (87 bp):
AAAATTATCATTTTACCCCCGAACATCCAAAATCTCATTTTTAATACCAAATTTTTCCAAAATTA
CCAGATTTGCCCCAGAAAGTCC
Found at i:42688178 original size:87 final size:86
Alignment explanation
Indices: 42688035--42688194 Score: 248
Period size: 87 Copynumber: 1.8 Consensus size: 86
42688025 ATCTAAAATG
* *
42688035 TCATTTTTAAACCAAATTTTTCCAAAATTACCAGATTTGCCCCCGAAAGTCCAAAATTATCATTT
1 TCATTTTTAAACCAAATTTTTCCAAAATTACCAGATTTGCCCCAGAAAGTCCAAAATTACCATTT
42688100 TACCCCCGGGCGTCCAAAGTC
66 TACCCCCGGGCGTCCAAAGTC
** * * *
42688121 TCATTTTTAATACCATTTTTTTCCAAAATTACCATATTTTCCCCATAAAGTCCAAAATTACCATT
1 TCATTTTTAA-ACCAAATTTTTCCAAAATTACCAGATTTGCCCCAGAAAGTCCAAAATTACCATT
42688186 TTACCCCCG
65 TTACCCCCG
42688195 AACTTTCAAA
Statistics
Matches: 66, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
86 10 0.15
87 56 0.85
ACGTcount: A:0.31, C:0.28, G:0.07, T:0.34
Consensus pattern (86 bp):
TCATTTTTAAACCAAATTTTTCCAAAATTACCAGATTTGCCCCAGAAAGTCCAAAATTACCATTT
TACCCCCGGGCGTCCAAAGTC
Found at i:42698414 original size:15 final size:15
Alignment explanation
Indices: 42698388--42698426 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
42698378 ATGATATTGG
42698388 AGAAGAAAAAGAAAA
1 AGAAGAAAAAGAAAA
* *
42698403 ATAAGAAGAAGAAAA
1 AGAAGAAAAAGAAAA
42698418 AGAAGAAAA
1 AGAAGAAAA
42698427 GGATGACCGC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.03
Consensus pattern (15 bp):
AGAAGAAAAAGAAAA
Found at i:42700232 original size:39 final size:39
Alignment explanation
Indices: 42700184--42700559 Score: 264
Period size: 39 Copynumber: 9.6 Consensus size: 39
42700174 CAGGCATTCG
* * *
42700184 ATCTTTTACCCCTAGCCTGGGGTAGATCACCATCAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCCA
* * * *
42700223 ATCTCTTACCCCGAGCCT-GGGCAGATTA-CAGACATCCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCA-TCAGCCA
* * *
42700261 ATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAACCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCCA
* * *
42700300 ATCTCTTACCTCGAGCCTGGGGCAGATTGCAGACATCTG---
1 ATCTCTTACCCCGAGCCTGGGGCAGA-T-CA-CCATCAGCCA
* *
42700339 ATCTTTTACCCCGAGCCTGGGGCAGATCACATTATCAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCAC--CATCAGCCA
* * * * *
42700380 ATCTCTTACCCCGAGCTTAGGGCAGATTGCA-GA-CATCCG
1 ATCTCTTACCCCGAGCCTGGGGCAGA-T-CACCATCAGCCA
* * * * *
42700419 ATCTTTTACCCCAAGACTGGAGCATATCACCATCAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCCA
* * ** ** *
42700458 ATCTCTTACCCCGAGCTTAGGGCAGAT-TGCAGTCATTCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCA-TCAGCCA
* * * * *
42700497 ATCTTTTATCCTGAGCCTGGGGTAGATCACCATCAGTCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCCA
* *
42700536 ATCTCTTACCCCGAACCTAGGGCA
1 ATCTCTTACCCCGAGCCTGGGGCA
42700560 TATTGCAACC
Statistics
Matches: 252, Mismatches: 68, Indels: 34
0.71 0.19 0.10
Matches are distributed among these distances:
37 6 0.02
38 37 0.15
39 171 0.68
40 6 0.02
41 25 0.10
42 5 0.02
43 2 0.01
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.25
Consensus pattern (39 bp):
ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCCA
Found at i:42700360 original size:78 final size:78
Alignment explanation
Indices: 42700142--42700566 Score: 534
Period size: 78 Copynumber: 5.4 Consensus size: 78
42700132 GATTGAAGAT
* * * * *
42700142 CCAATCTCTTACCCCGAG-CTTGGTGCAGGTTACAGGCAT-TCGATCTTTTACCCCTAGCCTGGG
1 CCAATCTCTTACCCCGAGCCTAGG-GCAGATTGCAGACATCT-GATCTTTTACCCCGAGCCTGGG
*
42700205 GTAGATCACCATCAG
64 GCAGATCACCATCAG
* * *
42700220 CCAATCTCTTACCCCGAGCCT-GGGCAGATTACAGACATCCGATCTTTTACCCCGAGCTTGGGGC
1 CCAATCTCTTACCCCGAGCCTAGGGCAGATTGCAGACATCTGATCTTTTACCCCGAGCCTGGGGC
*
42700284 AGATCACCATCAA
66 AGATCACCATCAG
* *
42700297 CCAATCTCTTACCTCGAGCCTGGGGCAGATTGCAGACATCTGATCTTTTACCCCGAGCCTGGGGC
1 CCAATCTCTTACCCCGAGCCTAGGGCAGATTGCAGACATCTGATCTTTTACCCCGAGCCTGGGGC
*
42700362 AGATCACATTATCAG
66 AGATCAC--CATCAG
* * * * *
42700377 CCAATCTCTTACCCCGAGCTTAGGGCAGATTGCAGACATCCGATCTTTTACCCCAAGACTGGAGC
1 CCAATCTCTTACCCCGAGCCTAGGGCAGATTGCAGACATCTGATCTTTTACCCCGAGCCTGGGGC
*
42700442 ATATCACCATCAG
66 AGATCACCATCAG
* * * *
42700455 CCAATCTCTTACCCCGAGCTTAGGGCAGATTGCAGTCAT-TCGATCTTTTATCCTGAGCCTGGGG
1 CCAATCTCTTACCCCGAGCCTAGGGCAGATTGCAGACATCT-GATCTTTTACCCCGAGCCTGGGG
*
42700519 TAGATCACCATCAG
65 CAGATCACCATCAG
* * *
42700533 TCAATCTCTTACCCCGAACCTAGGGCATATTGCA
1 CCAATCTCTTACCCCGAGCCTAGGGCAGATTGCA
42700567 ACCATCCAAT
Statistics
Matches: 306, Mismatches: 35, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
77 66 0.22
78 170 0.56
79 2 0.01
80 68 0.22
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.25
Consensus pattern (78 bp):
CCAATCTCTTACCCCGAGCCTAGGGCAGATTGCAGACATCTGATCTTTTACCCCGAGCCTGGGGC
AGATCACCATCAG
Found at i:42700460 original size:158 final size:156
Alignment explanation
Indices: 42700142--42700566 Score: 595
Period size: 158 Copynumber: 2.7 Consensus size: 156
42700132 GATTGAAGAT
* * * * *
42700142 CCAATCTCTTACCCCGAGCTTGGTGCAGGTTACAGGCATTCGATCTTTTACCCCTAGCCTGGGGT
1 CCAATCTCTTACCCCGAGCTTGGGGCAGATTGCAGACATTCGATCTTTTACCCCGAGCCTGGGGT
*
42700207 AGATCACCATCAGCCAATCTCTTACCCCGAGCCT-GGGCAGATTACAGACATCCGATCTTTTACC
66 AGATCACCATCAGCCAATCTCTTACCCCGAGCCTAGGGCAGATTGCAGACATCCGATCTTTTACC
* *
42700271 CCGAGCTTGGGGCAGATCACCATCAA
131 CCAAGCTTGGAGCAGATCACCATCAA
* *
42700297 CCAATCTCTTACCTCGAGCCTGGGGCAGATTGCAGACA-TCTGATCTTTTACCCCGAGCCTGGGG
1 CCAATCTCTTACCCCGAGCTTGGGGCAGATTGCAGACATTC-GATCTTTTACCCCGAGCCTGGGG
* * *
42700361 CAGATCACATTATCAGCCAATCTCTTACCCCGAGCTTAGGGCAGATTGCAGACATCCGATCTTTT
65 TAGATCAC--CATCAGCCAATCTCTTACCCCGAGCCTAGGGCAGATTGCAGACATCCGATCTTTT
* *
42700426 ACCCCAAGAC-TGGAGCATATCACCATCAG
128 ACCCCAAG-CTTGGAGCAGATCACCATCAA
* * * *
42700455 CCAATCTCTTACCCCGAGCTTAGGGCAGATTGCAGTCATTCGATCTTTTATCCTGAGCCTGGGGT
1 CCAATCTCTTACCCCGAGCTTGGGGCAGATTGCAGACATTCGATCTTTTACCCCGAGCCTGGGGT
* * *
42700520 AGATCACCATCAGTCAATCTCTTACCCCGAACCTAGGGCATATTGCA
66 AGATCACCATCAGCCAATCTCTTACCCCGAGCCTAGGGCAGATTGCA
42700567 ACCATCCAAT
Statistics
Matches: 237, Mismatches: 27, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
154 2 0.01
155 61 0.26
156 35 0.15
157 25 0.11
158 111 0.47
159 3 0.01
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.25
Consensus pattern (156 bp):
CCAATCTCTTACCCCGAGCTTGGGGCAGATTGCAGACATTCGATCTTTTACCCCGAGCCTGGGGT
AGATCACCATCAGCCAATCTCTTACCCCGAGCCTAGGGCAGATTGCAGACATCCGATCTTTTACC
CCAAGCTTGGAGCAGATCACCATCAA
Found at i:42701069 original size:17 final size:17
Alignment explanation
Indices: 42701043--42701123 Score: 83
Period size: 17 Copynumber: 4.7 Consensus size: 17
42701033 ATTTTTAAAT
*
42701043 TTTAAGTTTAAATTTAG
1 TTTAAATTTAAATTTAG
*
42701060 TTTAAATTTAAATTTAT
1 TTTAAATTTAAATTTAG
* *
42701077 TTTGAATTTAAA-TTCG
1 TTTAAATTTAAATTTAG
*
42701093 TTCTAAATTTAAATTTAA
1 TT-TAAATTTAAATTTAG
*
42701111 TTAAAAATTTAAA
1 TT-TAAATTTAAA
42701124 AAAAAGAGTC
Statistics
Matches: 52, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
16 4 0.08
17 35 0.67
18 13 0.25
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (17 bp):
TTTAAATTTAAATTTAG
Found at i:42701087 original size:34 final size:34
Alignment explanation
Indices: 42701041--42701109 Score: 97
Period size: 34 Copynumber: 2.0 Consensus size: 34
42701031 CCATTTTTAA
42701041 ATTTTAAGTTTAAATTTAGTT-TAAATTTAAATTT
1 ATTTTAAGTTTAAA-TTAGTTCTAAATTTAAATTT
*
42701075 ATTTTGAA-TTTAAATTCGTTCTAAATTTAAATTT
1 ATTTT-AAGTTTAAATTAGTTCTAAATTTAAATTT
42701109 A
1 A
42701110 ATTAAAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 5 0.16
34 25 0.78
35 2 0.06
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.54
Consensus pattern (34 bp):
ATTTTAAGTTTAAATTAGTTCTAAATTTAAATTT
Found at i:42701110 original size:6 final size:6
Alignment explanation
Indices: 42701036--42701090 Score: 51
Period size: 6 Copynumber: 9.3 Consensus size: 6
42701026 TGGACCCATT
* * * *
42701036 TTTAAA TTTTAAG TTTAAA TTT-AG TTTAAA TTTAAA TTT-AT TTTGAA
1 TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
42701083 TTTAAA TT
1 TTTAAA TT
42701091 CGTTCTAAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
5 8 0.21
6 26 0.67
7 5 0.13
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:42701112 original size:11 final size:12
Alignment explanation
Indices: 42701036--42701090 Score: 51
Period size: 11 Copynumber: 4.7 Consensus size: 12
42701026 TGGACCCATT
*
42701036 TTTAAATTTTAAG
1 TTTAAA-TTTAAA
*
42701049 TTTAAATTT-AG
1 TTTAAATTTAAA
42701060 TTTAAATTTAAA
1 TTTAAATTTAAA
* *
42701072 TTT-ATTTTGAA
1 TTTAAATTTAAA
42701083 TTTAAATT
1 TTTAAATT
42701091 CGTTCTAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
11 20 0.56
12 10 0.28
13 6 0.17
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (12 bp):
TTTAAATTTAAA
Found at i:42702922 original size:30 final size:29
Alignment explanation
Indices: 42702869--42703448 Score: 264
Period size: 30 Copynumber: 19.8 Consensus size: 29
42702859 TTTTGTTTAA
**
42702869 AAAAATTACATTTT-AATCTCAAACTTCAT
1 AAAAATTACATTTTGACCCTCAAACTTC-T
*
42702898 ACAAATTACATTTTGACCCTCAAACTTCT
1 AAAAATTACATTTTGACCCTCAAACTTCT
* * **
42702927 CAAAAAATCACATTTTGACCTTTGAACTTCT
1 --AAAAATTACATTTTGACCCTCAAACTTCT
* * *
42702958 CAAAAATCACATTTTGACCCTTAAACTTTT
1 -AAAAATTACATTTTGACCCTCAAACTTCT
* * *
42702988 CAAAAACTACATTTTAACCC-CTAAACTCCT
1 -AAAAATTACATTTTGACCCTC-AAACTTCT
* *
42703018 CCAAAATTACATTTTGACCC-CTAAACTTTTCC
1 -AAAAATTACATTTTGACCCTC-AAAC--TTCT
* *
42703050 AAAAA-CACATTTT-ACCCT-AAACTTTT
1 AAAAATTACATTTTGACCCTCAAACTTCT
* * * *
42703076 CCAAAATTTCATTTTTACCCTCGAACATTC-
1 -AAAAATTACATTTTGACCCTCAAAC-TTCT
* * *
42703106 AAAAATTACCATTTTGA-CCTC-GAGTTGTT
1 AAAAATTA-CATTTTGACCCTCAAACTT-CT
* * * * **
42703135 CCAATATTACATTCT-AACCTTGAACTTCGT
1 -AAAAATTACATTTTGACCCTCAAACTTC-T
* * *
42703165 AAAAAATACATTTTAACCC-CTTAACTTCT
1 AAAAATTACATTTTGACCCTC-AAACTTCT
*
42703194 CAAAAATCACATTTTGACCCTCAAACTTCT
1 -AAAAATTACATTTTGACCCTCAAACTTCT
* * *
42703224 AAAAATTCACATTTTAACCCTTAAACTTCC
1 AAAAATT-ACATTTTGACCCTCAAACTTCT
* * *
42703254 GAAAATTACATTTT-AACATCAAAC-TC-
1 AAAAATTACATTTTGACCCTCAAACTTCT
* * *
42703280 CAAAATTATATTTTGACCC-CTAAACTTTT
1 AAAAATTACATTTTGACCCTC-AAACTTCT
* * * *
42703309 CCAAAATCACATTTTCACCC-CAAACTTTT
1 -AAAAATTACATTTTGACCCTCAAACTTCT
* * * *
42703338 CCAAAATTACATTTTG-CCCCCGAA-TATCC
1 -AAAAATTACATTTTGACCCTCAAACT-TCT
* * *
42703367 AAAAATTACCATTTT-ACCCTCGAACATCC
1 AAAAATTA-CATTTTGACCCTCAAACTTCT
*
42703396 AAAAATTACCATTTT-ACCCTCAAATTTCT
1 AAAAATTA-CATTTTGACCCTCAAACTTCT
* * * *
42703425 AAAAGTCACATTTTCAACCTCAAA
1 AAAAATTACATTTTGACCCTCAAA
42703449 TTTCCCAAAA
Statistics
Matches: 429, Mismatches: 87, Indels: 70
0.73 0.15 0.12
Matches are distributed among these distances:
26 15 0.03
27 14 0.03
28 37 0.09
29 146 0.34
30 184 0.43
31 31 0.07
32 2 0.00
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.34
Consensus pattern (29 bp):
AAAAATTACATTTTGACCCTCAAACTTCT
Found at i:42703397 original size:115 final size:115
Alignment explanation
Indices: 42702951--42703458 Score: 258
Period size: 118 Copynumber: 4.4 Consensus size: 115
42702941 TTGACCTTTG
* * * * * *
42702951 AACTTCTCAAAAATCACATTTTGACCCTTAAACTTTTCAAAAACT-ACATTTTAACCCCTAAACT
1 AACTTTTCAAAAATCACATTTTCACCC-CAAACTTTTCCAAAATTCACATTTTAACCCCGAAACT
* * ** *
42703015 CCTCCAAAATTACATTTTGACCCCTAAACTTTTCCAAAAA-CA-CATTTTA-CCCTA
65 -C-CAAAAATTACATTTTAACATC-AAAC---TCCAAAAATTACCATTTTACCCCTA
* ** * * * * * * *
42703069 AACTTTTCCAAAATTTCATTTTTACCCTCGAAC-ATTCAAAAATT-ACCATTTTGACCTCGAGTT
1 AACTTTTCAAAAATCACATTTTCACCC-CAAACTTTTCCAAAATTCA-CATTTTAACCCCGA--A
** * * * ** * * *
42703132 GTTCC-AATATTACATTCTAACCTTGAACTTCGTAAAAAATA-CATTTTAACCCCTT
62 ACTCCAAAAATTACATTTTAACATCAAAC-TC-CAAAAATTACCATTTT-ACCCCTA
* * * * **
42703187 AACTTCTCAAAAATCACATTTTGACCCTCAAACTTCT-AAAAATTCACATTTTAACCCTTAAACT
1 AACTTTTCAAAAATCACATTTTCACCC-CAAACTTTTCCAAAATTCACATTTTAACCCCGAAAC-
* *
42703251 TCCGAAAATTACATTTTAACATCAAACTCC-AAAATTA-TATTTTGACCCCTA
64 TCCAAAAATTACATTTTAACATCAAACTCCAAAAATTACCATTTT-ACCCCTA
* **
42703302 AACTTTTCCAAAATCACATTTTCACCCCAAACTTTTCCAAAATT-ACATTTTGCCCCCGAATA-T
1 AACTTTTCAAAAATCACATTTTCACCCCAAACTTTTCCAAAATTCACATTTTAACCCCGAA-ACT
* * *
42703365 CCAAAAATTACCATTTTACCCTCGAACATCCAAAAATTACCATTTTA-CCCTCA
65 CCAAAAATTA-CATTTTAACATCAAAC-TCCAAAAATTACCATTTTACCCCT-A
* * *
42703418 AA--TTTCTAAAAGTCACATTTTCAACCTCAAA-TTTCCCAAAA
1 AACTTTTC-AAAAATCACATTTTC-ACCCCAAACTTTTCCAAAA
42703459 GTTTGATTTT
Statistics
Matches: 303, Mismatches: 67, Indels: 43
0.73 0.16 0.10
Matches are distributed among these distances:
113 10 0.03
114 40 0.13
115 82 0.27
116 28 0.09
117 35 0.12
118 104 0.34
119 3 0.01
120 1 0.00
ACGTcount: A:0.37, C:0.27, G:0.03, T:0.33
Consensus pattern (115 bp):
AACTTTTCAAAAATCACATTTTCACCCCAAACTTTTCCAAAATTCACATTTTAACCCCGAAACTC
CAAAAATTACATTTTAACATCAAACTCCAAAAATTACCATTTTACCCCTA
Found at i:42703428 original size:29 final size:28
Alignment explanation
Indices: 42703194--42703458 Score: 132
Period size: 29 Copynumber: 9.2 Consensus size: 28
42703184 CTTAACTTCT
*
42703194 CAAAAATCACATTTTGACCCTCAAACT-TC
1 CAAAAATTACATTTT-ACCCTCAAA-TATC
* *
42703223 TAAAAATTCACATTTTAACCCTTAAACT-TC
1 CAAAAATT-ACATTTT-ACCCTCAAA-TATC
* * * *
42703253 CGAAAATTACATTTTAACATCAAA-CTC
1 CAAAAATTACATTTTACCCTCAAATATC
* *
42703280 C-AAAATTATATTTTGACCC-CTAAACTTTTC
1 CAAAAATTACATTTT-ACCCTC-AAA--TATC
* *
42703310 C-AAAATCACATTTTCACCC-CAAACTTTTC
1 CAAAAATTACATTTT-ACCCTCAAA--TATC
* * *
42703339 C-AAAATTACATTTTGCCCCCGAATATC
1 CAAAAATTACATTTTACCCTCAAATATC
* *
42703366 CAAAAATTACCATTTTACCCTCGAACATC
1 CAAAAATTA-CATTTTACCCTCAAATATC
*
42703395 CAAAAATTACCATTTTACCCTCAAATTTC
1 CAAAAATTA-CATTTTACCCTCAAATATC
* * * * *
42703424 TAAAAGTCACATTTTCAACCTCAAATTTC
1 CAAAAATTACATTTT-ACCCTCAAATATC
*
42703453 CCAAAA
1 CAAAAA
42703459 GTTTGATTTT
Statistics
Matches: 192, Mismatches: 33, Indels: 22
0.78 0.13 0.09
Matches are distributed among these distances:
26 13 0.07
27 12 0.06
28 22 0.11
29 101 0.53
30 44 0.23
ACGTcount: A:0.38, C:0.28, G:0.03, T:0.32
Consensus pattern (28 bp):
CAAAAATTACATTTTACCCTCAAATATC
Found at i:42704825 original size:17 final size:17
Alignment explanation
Indices: 42704803--42704896 Score: 118
Period size: 17 Copynumber: 5.4 Consensus size: 17
42704793 CTCAACTCAT
42704803 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
42704820 TTTAAATTTATTTCTAAAA
1 TTTAAATTTATTT-T-AAA
* *
42704839 TTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
*
42704856 TTTAAATTTACATTTAAA
1 TTTAAATTTA-TTTTAAA
*
42704874 TTTAAA-TTATTATAAA
1 TTTAAATTTATTTTAAA
42704890 TTTAAAT
1 TTTAAAT
42704897 AAGTAAAAGT
Statistics
Matches: 68, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
16 11 0.16
17 28 0.41
18 14 0.21
19 15 0.22
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.53
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:42704843 original size:36 final size:35
Alignment explanation
Indices: 42704803--42704896 Score: 120
Period size: 36 Copynumber: 2.7 Consensus size: 35
42704793 CTCAACTCAT
*
42704803 TTTAAATTTATTTTAAATTTAAATTTA-TTTCTAAAA
1 TTTAAATTTATTTTAAATTTAAATTTACATT-T-AAA
* *
42704839 TTTAAATTTAATTTAAGTTTAAATTTACATTTAAA
1 TTTAAATTTATTTTAAATTTAAATTTACATTTAAA
*
42704874 TTTAAA-TTATTATAAATTTAAAT
1 TTTAAATTTATTTTAAATTTAAAT
42704897 AAGTAAAAGT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
34 14 0.27
35 9 0.18
36 26 0.51
37 2 0.04
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.53
Consensus pattern (35 bp):
TTTAAATTTATTTTAAATTTAAATTTACATTTAAA
Found at i:42704896 original size:6 final size:6
Alignment explanation
Indices: 42704803--42704881 Score: 83
Period size: 6 Copynumber: 13.3 Consensus size: 6
42704793 CTCAACTCAT
* *
42704803 TTTAAA TTT-AT TTTAAA TTTAAA TTT-AT TTCTAAAA TTTAAA TTT-AA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT-T-AAA TTTAAA TTTAAA
* *
42704850 TTTAAG TTTAAA TTTACA TTTAAA TTTAAA TT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT
42704882 ATTATAAATT
Statistics
Matches: 60, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
5 12 0.20
6 44 0.73
7 1 0.02
8 3 0.05
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:42704980 original size:27 final size:27
Alignment explanation
Indices: 42704901--42704980 Score: 85
Period size: 27 Copynumber: 3.0 Consensus size: 27
42704891 TTAAATAAGT
* *
42704901 AAAAGTCCAAATACAGAATGTCC-ATTT
1 AAAAGTCCAAATACA-AATGCCCAATTA
*
42704928 AAAAGTCCCACATAC-AA-GCCCAAATTA
1 AAAAGT-CCAAATACAAATGCCC-AATTA
42704955 AAAAGTCCAAATACAAATGCCCAATT
1 AAAAGTCCAAATACAAATGCCCAATT
42704981 GGGCCCAAGT
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
25 3 0.07
26 9 0.20
27 21 0.48
28 11 0.25
ACGTcount: A:0.47, C:0.24, G:0.09, T:0.20
Consensus pattern (27 bp):
AAAAGTCCAAATACAAATGCCCAATTA
Found at i:42706821 original size:30 final size:30
Alignment explanation
Indices: 42706783--42707069 Score: 167
Period size: 29 Copynumber: 9.7 Consensus size: 30
42706773 CCCTAGAGGT
*
42706783 CCCT-AAACTTTCTAAAAATTATATTTTGA
1 CCCTCAAACTTTCTAAAAATTACATTTTGA
*
42706812 CACC-CAAACTTTAC-CAAAATTACATTTTTGA
1 C-CCTCAAACTTT-CTAAAAATTACA-TTTTGA
* *
42706843 CCCTAAAAC-TTCTAAAAATTACATTTTTA
1 CCCTCAAACTTTCTAAAAATTACATTTTGA
* *
42706872 CCCAT-AAAC-TTCTAAAAATTCCATTTTTA
1 CCC-TCAAACTTTCTAAAAATTACATTTTGA
*
42706901 ACCTCGAAACTTTC-AAAAATTATCATTTT-A
1 CCCTC-AAACTTTCTAAAAATTA-CATTTTGA
* * * * *
42706931 CCCTTACA-TGTCTAAAATTTTCATTTTTTGA
1 CCCTCAAACTTTCTAAAAATTACA--TTTTGA
*
42706962 CCCTAAAACTTT-TAAAAATTACCATTTT-A
1 CCCTCAAACTTTCTAAAAATTA-CATTTTGA
* * * *
42706991 CCC-CTAAA-TGTCCAAAAACTCCATTTTTGA
1 CCCTC-AAACTTTCTAAAAATTACA-TTTTGA
42707021 CCC-CGAAACTTTC-AAAAATTATCATTTT-A
1 CCCTC-AAACTTTCTAAAAATTA-CATTTTGA
* *
42707050 CCCCCAAAC-TTCCAAAAATT
1 CCCTCAAACTTTCTAAAAATT
42707070 CTGTTTTTGA
Statistics
Matches: 205, Mismatches: 28, Indels: 50
0.72 0.10 0.18
Matches are distributed among these distances:
28 13 0.06
29 75 0.37
30 73 0.36
31 40 0.20
32 4 0.02
ACGTcount: A:0.37, C:0.24, G:0.03, T:0.36
Consensus pattern (30 bp):
CCCTCAAACTTTCTAAAAATTACATTTTGA
Found at i:42706919 original size:59 final size:59
Alignment explanation
Indices: 42706783--42707111 Score: 273
Period size: 59 Copynumber: 5.5 Consensus size: 59
42706773 CCCTAGAGGT
*
42706783 CCCT-AAACTTTCTAAAAATTAT-ATTTTGACACCC-AAACTT-TACCAAAATTACATTTTTGA
1 CCCTAAAACTTTC-AAAAATTATCATTTT-AC-CCCTAAACTTCTA--AAAATTCCATTTTTGA
*
42706843 CCCTAAAAC-TTCTAAAAATTA-CATTTTTACCCATAAACTTCTAAAAATTCCATTTTT-A
1 CCCTAAAACTTTC-AAAAATTATCA-TTTTACCCCTAAACTTCTAAAAATTCCATTTTTGA
* * * * * *
42706901 ACCTCGAAACTTTCAAAAATTATCATTTTACCCTTACA-TGTCTAAAATTTTCATTTTTTGA
1 CCCT-AAAACTTTCAAAAATTATCATTTTACCCCTAAACT-TCTAAAAATTCCA-TTTTTGA
* * * *
42706962 CCCTAAAACTTTTAAAAATTACCATTTTACCCCTAAA-TGTCCAAAAACTCCATTTTTGA
1 CCCTAAAACTTTCAAAAATTATCATTTTACCCCTAAACT-TCTAAAAATTCCATTTTTGA
** * * **
42707021 CCCCGAAACTTTCAAAAATTATCATTTTACCCCCAAACTTCCAAAAATTCTGTTTTTGA
1 CCCTAAAACTTTCAAAAATTATCATTTTACCCCTAAACTTCTAAAAATTCCATTTTTGA
* * ** *
42707080 TCCT-GATTTTTCTAAAAATTATCGTTTTACCC
1 CCCTAAAACTTTC-AAAAATTATCATTTTACCC
42707112 TCGGATGTCT
Statistics
Matches: 224, Mismatches: 32, Indels: 27
0.79 0.11 0.10
Matches are distributed among these distances:
58 10 0.04
59 125 0.56
60 75 0.33
61 14 0.06
ACGTcount: A:0.35, C:0.23, G:0.04, T:0.38
Consensus pattern (59 bp):
CCCTAAAACTTTCAAAAATTATCATTTTACCCCTAAACTTCTAAAAATTCCATTTTTGA
Found at i:42706959 original size:119 final size:119
Alignment explanation
Indices: 42706836--42707052 Score: 348
Period size: 119 Copynumber: 1.8 Consensus size: 119
42706826 CAAAATTACA
* *
42706836 TTTTTGACCCTAAAACTTCTAAAAATTA-CATTTTTACCCATAAACT-TCTAAAAATTCCATTTT
1 TTTTTGACCCTAAAACTTCTAAAAATTACCA-TTTTACCCATAAA-TGTCCAAAAACTCCATTTT
*
42706899 TAACCTCGAAACTTTCAAAAATTATCATTTTACCCTTACATGTCTAAAATTTTCAT
64 TAACCCCGAAACTTTCAAAAATTATCATTTTACCCTTACATGTCTAAAATTTTCAT
* * *
42706955 TTTTTGACCCTAAAACTTTTAAAAATTACCATTTTACCCCTAAATGTCCAAAAACTCCATTTTTG
1 TTTTTGACCCTAAAACTTCTAAAAATTACCATTTTACCCATAAATGTCCAAAAACTCCATTTTTA
42707020 ACCCCGAAACTTTCAAAAATTATCATTTTACCC
66 ACCCCGAAACTTTCAAAAATTATCATTTTACCC
42707053 CCAAACTTCC
Statistics
Matches: 90, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
118 1 0.01
119 87 0.97
120 2 0.02
ACGTcount: A:0.35, C:0.23, G:0.03, T:0.38
Consensus pattern (119 bp):
TTTTTGACCCTAAAACTTCTAAAAATTACCATTTTACCCATAAATGTCCAAAAACTCCATTTTTA
ACCCCGAAACTTTCAAAAATTATCATTTTACCCTTACATGTCTAAAATTTTCAT
Found at i:42707076 original size:28 final size:30
Alignment explanation
Indices: 42706787--42707069 Score: 131
Period size: 30 Copynumber: 9.5 Consensus size: 30
42706777 AGAGGTCCCT
* *
42706787 AAACTTTCTAAAAATTAT-ATTTTGACACCC
1 AAAC-TTCCAAAAATTATCATTTTGACCCCC
**
42706817 AAACTTTACC-AAAATTA-CATTTTTGACCCTA
1 AAAC-TT-CCAAAAATTATCA-TTTTGACCCCC
* * **
42706848 AAACTTCTAAAAATTA-CATTTTTACCCAT
1 AAACTTCCAAAAATTATCATTTTGACCCCC
* * * * *
42706877 AAACTTCTAAAAATT-CCATTTTTAACCTCG
1 AAACTTCCAAAAATTATCA-TTTTGACCCCC
* **
42706907 AAACTTTCAAAAATTATCATTTT-ACCCTT
1 AAACTTCCAAAAATTATCATTTTGACCCCC
* * * **
42706936 ACA-TGT-CTAAAATTTTCATTTTTTGACCCTA
1 AAACT-TCCAAAAATTATCA--TTTTGACCCCC
** * *
42706967 AAACTTTTAAAAATTACCATTTT-ACCCCT
1 AAACTTCCAAAAATTATCATTTTGACCCCC
* * *
42706996 AAA-TGTCCAAAAACT-CCATTTTTGACCCCG
1 AAACT-TCCAAAAATTATCA-TTTTGACCCCC
*
42707026 AAACTTTCAAAAATTATCATTTT-ACCCCC
1 AAACTTCCAAAAATTATCATTTTGACCCCC
42707055 AAACTTCCAAAAATT
1 AAACTTCCAAAAATT
42707070 CTGTTTTTGA
Statistics
Matches: 197, Mismatches: 38, Indels: 37
0.72 0.14 0.14
Matches are distributed among these distances:
28 15 0.08
29 69 0.35
30 78 0.40
31 26 0.13
32 9 0.05
ACGTcount: A:0.38, C:0.23, G:0.03, T:0.36
Consensus pattern (30 bp):
AAACTTCCAAAAATTATCATTTTGACCCCC
Found at i:42707077 original size:119 final size:117
Alignment explanation
Indices: 42706787--42707079 Score: 326
Period size: 119 Copynumber: 2.5 Consensus size: 117
42706777 AGAGGTCCCT
* *
42706787 AAACTTTCTAAAAATTAT-ATTTTGACACCCAAACTTTACCAAAATTAC-ATTTTTGACCCTAAA
1 AAACTTTC-AAAAATTATCATTTT-ACCCCCAAAC-TT-CCAAAATT-CTTTTTTTGACCCTAAA
* * *
42706850 ACTTCTAAAAATTACATTTTTACCCATAAACTTCTAAAAATTCCATTTTTAACCTCG
61 ACTTCTAAAAATTACATTTTTACCCATAAACTTCCAAAAACTCCATTTTTAACCCCG
** * * *
42706907 AAACTTTCAAAAATTATCATTTTACCCTTACA-TGTCTAAAATTTTCATTTTTTGACCCTAAAAC
1 AAACTTTCAAAAATTATCATTTTACCCCCAAACT-TCCAAAA--TTCTTTTTTTGACCCTAAAAC
* * *
42706971 TTTTAAAAATTACCA-TTTTACCCCTAAA-TGTCCAAAAACTCCATTTTTGACCCCG
63 TTCTAAAAATTA-CATTTTTACCCATAAACT-TCCAAAAACTCCATTTTTAACCCCG
*
42707026 AAACTTTCAAAAATTATCATTTTACCCCCAAACTTCCAAAAATTCTGTTTTTGA
1 AAACTTTCAAAAATTATCATTTTACCCCCAAACTTCC-AAAATTCTTTTTTTGA
42707080 TCCTGATTTT
Statistics
Matches: 146, Mismatches: 18, Indels: 20
0.79 0.10 0.11
Matches are distributed among these distances:
117 6 0.04
118 13 0.09
119 107 0.73
120 20 0.14
ACGTcount: A:0.37, C:0.23, G:0.03, T:0.37
Consensus pattern (117 bp):
AAACTTTCAAAAATTATCATTTTACCCCCAAACTTCCAAAATTCTTTTTTTGACCCTAAAACTTC
TAAAAATTACATTTTTACCCATAAACTTCCAAAAACTCCATTTTTAACCCCG
Found at i:42709108 original size:31 final size:31
Alignment explanation
Indices: 42709049--42709120 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
42709039 TTTTGTTAAA
*
42709049 AATCAAA-TTAATTATTTATAAAAGGTTTAG
1 AATCAAATTTAAATATTTATAAAAGGTTTAG
*
42709079 AATCAAATTTAAATATTTTTAGAAA-GTTTAG
1 AATCAAATTTAAATATTTATA-AAAGGTTTAG
* *
42709110 TACCAAATTTA
1 AATCAAATTTA
42709121 GTTAAAATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 7 0.19
31 26 0.72
32 3 0.08
ACGTcount: A:0.46, C:0.06, G:0.08, T:0.40
Consensus pattern (31 bp):
AATCAAATTTAAATATTTATAAAAGGTTTAG
Found at i:42714275 original size:17 final size:17
Alignment explanation
Indices: 42714253--42714286 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
42714243 TAAGTATTAA
42714253 TCCATAGTACCCATCGT
1 TCCATAGTACCCATCGT
42714270 TCCATAGTACCCATCGT
1 TCCATAGTACCCATCGT
42714287 CAAATCATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.35, G:0.12, T:0.29
Consensus pattern (17 bp):
TCCATAGTACCCATCGT
Found at i:42720195 original size:13 final size:13
Alignment explanation
Indices: 42720179--42720234 Score: 51
Period size: 13 Copynumber: 4.3 Consensus size: 13
42720169 TGCTTTTGAG
*
42720179 AAGTGTTTTTAAA
1 AAGTGATTTTAAA
* *
42720192 AAGTGCTTTAAAA
1 AAGTGATTTTAAA
*
42720205 AAGTGATTTTGAA
1 AAGTGATTTTAAA
*
42720218 AAGT-ACTTTTGAA
1 AAGTGA-TTTTAAA
42720231 AAGT
1 AAGT
42720235 TTGGTTTAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
12 1 0.03
13 36 0.97
ACGTcount: A:0.41, C:0.04, G:0.18, T:0.38
Consensus pattern (13 bp):
AAGTGATTTTAAA
Found at i:42720198 original size:26 final size:26
Alignment explanation
Indices: 42720169--42720234 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
42720159 AATTTAGCAT
* *
42720169 TGCTTTTGAGAAGTGTTTTTAAAAAG
1 TGCTTTTGAAAAGTGATTTTAAAAAG
** *
42720195 TGCTTTAAAAAAGTGATTTTGAAAAG
1 TGCTTTTGAAAAGTGATTTTAAAAAG
*
42720221 TACTTTTGAAAAGT
1 TGCTTTTGAAAAGT
42720235 TTGGTTTAAT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.36, C:0.05, G:0.20, T:0.39
Consensus pattern (26 bp):
TGCTTTTGAAAAGTGATTTTAAAAAG
Found at i:42720854 original size:18 final size:19
Alignment explanation
Indices: 42720817--42720854 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
42720807 TTCAGATGAA
* *
42720817 TTTTTTTTGTTTATTCCTT
1 TTTTTTTTCTTTATTACTT
42720836 TTTTTTTTCTTTA-TACTT
1 TTTTTTTTCTTTATTACTT
42720854 T
1 T
42720855 AATCAATTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.08, C:0.11, G:0.03, T:0.79
Consensus pattern (19 bp):
TTTTTTTTCTTTATTACTT
Found at i:42728551 original size:30 final size:28
Alignment explanation
Indices: 42728515--42728812 Score: 182
Period size: 29 Copynumber: 10.2 Consensus size: 28
42728505 GTAAATTGGT
*
42728515 AATTTT-GAGAGTTTCGAGGTCAAAACTGGA
1 AATTTTGGA-AGTTTCG-GGTCAAAAAT-GA
42728545 AATTTTGGAAG-TTCGGGATCAAAAATGA
1 AATTTTGGAAGTTTCGGG-TCAAAAATGA
*
42728573 AATTTTTGGAAG-TTCGGGGGCAAAAATGTA
1 AA-TTTTGGAAGTTTC-GGGTCAAAAATG-A
* *
42728603 ATTTTTAGAAGTTTCGGAGTCAAAAATGGA
1 AATTTTGGAAGTTTCGG-GTCAAAAAT-GA
* *
42728633 ATTTTTGGAAGTTTTGAGGTC-AAAATGTA
1 AATTTTGGAAGTTTCG-GGTCAAAAATG-A
* ** *
42728662 ATTTTTGGAAGTTTTAAGGTTAAAAATAGA
1 AATTTTGGAAG-TTTCGGGTCAAAAAT-GA
* *
42728692 ATTTTTGGAAG-TTCGGGGGCAAAAATGTA
1 AATTTTGGAAGTTTC-GGGTCAAAAATG-A
* *
42728721 ATTTTTGGAAGTTTTAGGGTCAAAAATAGA
1 AATTTTGGAAG-TTTCGGGTCAAAAAT-GA
* *
42728751 ATTTTTGGAAG-TTCAGGG-AAAAAAT-A
1 AATTTTGGAAGTTTC-GGGTCAAAAATGA
* *
42728777 TAATTTTTGGAAGTTTTAGGGTC-AAAATGG
1 -AA-TTTTGGAAG-TTTCGGGTCAAAAATGA
42728807 AATTTT
1 AATTTT
42728813 CAAAAGTTTT
Statistics
Matches: 221, Mismatches: 22, Indels: 52
0.75 0.07 0.18
Matches are distributed among these distances:
26 1 0.00
27 1 0.00
28 31 0.14
29 94 0.43
30 86 0.39
31 8 0.04
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.35
Consensus pattern (28 bp):
AATTTTGGAAGTTTCGGGTCAAAAATGA
Found at i:42728628 original size:59 final size:58
Alignment explanation
Indices: 42728527--42728812 Score: 312
Period size: 59 Copynumber: 4.9 Consensus size: 58
42728517 TTTTGAGAGT
* * * *
42728527 TTCGAGGTCAAAACTGGAAATTTTGGAAG-TTCGGGATCAAAAAT-GAAATTTTTGGAAG
1 TTCGAGGGCAAAAATGTAATTTTTGGAAGTTTCGGG-TCAAAAATAG-AATTTTTGGAAG
* * *
42728585 TTCGGGGGCAAAAATGTAATTTTTAGAAGTTTCGGAGTCAAAAATGGAATTTTTGGAAG
1 TTCGAGGGCAAAAATGTAATTTTTGGAAGTTTCGG-GTCAAAAATAGAATTTTTGGAAG
* * ** *
42728644 TTTTGAGGTC-AAAATGTAATTTTTGGAAGTTTTAAGGTTAAAAATAGAATTTTTGGAAG
1 -TTCGAGGGCAAAAATGTAATTTTTGGAAG-TTTCGGGTCAAAAATAGAATTTTTGGAAG
* *
42728703 TTCGGGGGCAAAAATGTAATTTTTGGAAGTTTTAGGGTCAAAAATAGAATTTTTGGAAG
1 TTCGAGGGCAAAAATGTAATTTTTGGAAG-TTTCGGGTCAAAAATAGAATTTTTGGAAG
* * * *
42728762 TTC-AGGGAAAAAATATAATTTTTGGAAGTTTTAGGGTC-AAAATGGAATTTT
1 TTCGAGGGCAAAAATGTAATTTTTGGAAG-TTTCGGGTCAAAAATAGAATTTT
42728813 CAAAAGTTTT
Statistics
Matches: 199, Mismatches: 23, Indels: 13
0.85 0.10 0.06
Matches are distributed among these distances:
57 12 0.06
58 61 0.31
59 114 0.57
60 12 0.06
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.35
Consensus pattern (58 bp):
TTCGAGGGCAAAAATGTAATTTTTGGAAGTTTCGGGTCAAAAATAGAATTTTTGGAAG
Found at i:42728797 original size:29 final size:29
Alignment explanation
Indices: 42728565--42728885 Score: 258
Period size: 29 Copynumber: 11.0 Consensus size: 29
42728555 GTTCGGGATC
* *** *
42728565 AAAAATGAAATTTTTGGAAGTTCGGGGGC
1 AAAAATGTAATTTTTGGAAGTTTTAGGGT
* *
42728594 AAAAATGTAATTTTTAGAAG-TTTCGGAGT
1 AAAAATGTAATTTTTGGAAGTTTTAGG-GT
*
42728623 CAAAAATGGAATTTTTGGAAGTTTT-GAGGT
1 -AAAAATGTAATTTTTGGAAGTTTTAG-GGT
* *
42728653 CAAAATGTAATTTTTGGAAGTTTTAAGGTT
1 AAAAATGTAATTTTTGGAAGTTTT-AGGGT
*** *
42728683 AAAAATAG-AATTTTTGGAAGTTCGGGGGC
1 AAAAAT-GTAATTTTTGGAAGTTTTAGGGT
42728712 AAAAATGTAATTTTTGGAAGTTTTAGGGT
1 AAAAATGTAATTTTTGGAAGTTTTAGGGT
* *
42728741 CAAAAATAG-AATTTTTGGAAG-TTCAGGGA
1 -AAAAAT-GTAATTTTTGGAAGTTTTAGGGT
*
42728770 AAAAATATAATTTTTGGAAGTTTTAGGGT
1 AAAAATGTAATTTTTGGAAGTTTTAGGGT
* * *** *
42728799 CAAAATGGAATTTTCAAAAGTTTTAAGGT
1 AAAAATGTAATTTTTGGAAGTTTTAGGGT
* * **
42728828 TAAAATGTAATTTTTAAGAAGTTCGAGGGT
1 AAAAATGTAATTTTT-GGAAGTTTTAGGGT
* *
42728858 TAAAATATAATTTTTGGATAG-TTTAGGG
1 AAAAATGTAATTTTTGGA-AGTTTTAGGG
42728886 ACCTCCAGGG
Statistics
Matches: 234, Mismatches: 44, Indels: 28
0.76 0.14 0.09
Matches are distributed among these distances:
28 22 0.09
29 119 0.51
30 86 0.37
31 7 0.03
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.36
Consensus pattern (29 bp):
AAAAATGTAATTTTTGGAAGTTTTAGGGT
Found at i:42748356 original size:2 final size:2
Alignment explanation
Indices: 42748349--42748386 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
42748339 TTGATATTTC
42748349 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42748387 GTTGACTTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42751695 original size:16 final size:17
Alignment explanation
Indices: 42751662--42751696 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
42751652 ATTAAAACAT
42751662 TTTAAAATTTAGGAGTAA
1 TTTAAAATTTA-GAGTAA
42751680 TTTAAAATTT-GAGTAA
1 TTTAAAATTTAGAGTAA
42751696 T
1 T
42751697 AAATGAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
18 10 0.59
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (17 bp):
TTTAAAATTTAGAGTAA
Found at i:42752016 original size:37 final size:37
Alignment explanation
Indices: 42751948--42752020 Score: 94
Period size: 37 Copynumber: 2.0 Consensus size: 37
42751938 AACCCCAGAA
* * *
42751948 TTTTTGAAATTATTCATTAAGGTTTTTAATTTTTTTT
1 TTTTTGAAATTATTAATTAAGGTCTTGAATTTTTTTT
*
42751985 TTTTTGAAATTTTTAATT-AGGCTCTTGAATTTTTTT
1 TTTTTGAAATTATTAATTAAGG-TCTTGAATTTTTTT
42752021 AAAAAATTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 3 0.10
37 28 0.90
ACGTcount: A:0.23, C:0.04, G:0.10, T:0.63
Consensus pattern (37 bp):
TTTTTGAAATTATTAATTAAGGTCTTGAATTTTTTTT
Found at i:42753489 original size:36 final size:36
Alignment explanation
Indices: 42753449--42753518 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 36
42753439 TTTATCTCTA
42753449 TCTTTTCTTT-GTAGAAATCATTACTGTTCATCTTCG
1 TCTTTTCTTTCGTAG-AATCATTACTGTTCATCTTCG
* *
42753485 TCTTTTCTTTGCGTAGAATCATTATTGTTTATCT
1 TCTTTTCTTT-CGTAGAATCATTACTGTTCATCT
42753519 CTATCTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
36 10 0.33
37 16 0.53
38 4 0.13
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (36 bp):
TCTTTTCTTTCGTAGAATCATTACTGTTCATCTTCG
Found at i:42753526 original size:37 final size:36
Alignment explanation
Indices: 42753428--42753527 Score: 123
Period size: 36 Copynumber: 2.8 Consensus size: 36
42753418 TTTGACAAAT
*
42753428 AATCATTACTATTTATCTCTATCTTTTCTTTGTAGA
1 AATCATTACTGTTTATCTCTATCTTTTCTTTGTAGA
* *
42753464 AATCATTACTGTTCATCT-TCGTCTTTTCTTTGCGTAG-
1 AATCATTACTGTTTATCTCT-ATCTTTTCTTT--GTAGA
*
42753501 AATCATTATTGTTTATCTCTATCTTTT
1 AATCATTACTGTTTATCTCTATCTTTT
42753528 TGTCATTCAG
Statistics
Matches: 54, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
35 1 0.02
36 26 0.48
37 22 0.41
38 5 0.09
ACGTcount: A:0.21, C:0.18, G:0.08, T:0.53
Consensus pattern (36 bp):
AATCATTACTGTTTATCTCTATCTTTTCTTTGTAGA
Found at i:42758367 original size:12 final size:12
Alignment explanation
Indices: 42758325--42758383 Score: 50
Period size: 12 Copynumber: 4.9 Consensus size: 12
42758315 TATTTAGATA
*
42758325 AATATTTAATTT
1 AATATTAAATTT
*
42758337 AAT-TTAATATAT
1 AATATTAA-ATTT
* *
42758349 CACATTAAATATT
1 AATATTAAAT-TT
42758362 AA-ATTAAATTT
1 AATATTAAATTT
42758373 AATATTAAATT
1 AATATTAAATT
42758384 CATTAAAACA
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
11 7 0.19
12 24 0.65
13 6 0.16
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.47
Consensus pattern (12 bp):
AATATTAAATTT
Found at i:42762829 original size:6 final size:6
Alignment explanation
Indices: 42762784--42762826 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
42762774 AACGGCAACG
* * *
42762784 GTTGCT GTTGCT GTTGCT GTTGCT GTTGCA GCTGCT GCTGCT G
1 GTTGCT GTTGCT GTTGCT GTTGCT GTTGCT GTTGCT GTTGCT G
42762827 CTGTAACGGT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.02, C:0.21, G:0.35, T:0.42
Consensus pattern (6 bp):
GTTGCT
Found at i:42762891 original size:3 final size:3
Alignment explanation
Indices: 42762883--42762917 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
42762873 GGAGATTGCC
42762883 GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GT
1 GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GT
42762918 GATTGAGGGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.34, T:0.66
Consensus pattern (3 bp):
GTT
Found at i:42772309 original size:24 final size:26
Alignment explanation
Indices: 42772282--42772343 Score: 74
Period size: 28 Copynumber: 2.4 Consensus size: 26
42772272 CTCTATGTGT
*
42772282 TTTTCTTTTTTT-AG-AATTTAGTCC
1 TTTTCTTTTTTTAAGAAATTTAGCCC
42772306 TTTTCTTTTATTTTAAGAAATTTAGCCC
1 TTTTC-TTT-TTTTAAGAAATTTAGCCC
*
42772334 TTTACTTTTT
1 TTTTCTTTTT
42772344 GAATTAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 5 0.16
25 3 0.09
26 6 0.19
27 5 0.16
28 13 0.41
ACGTcount: A:0.19, C:0.13, G:0.06, T:0.61
Consensus pattern (26 bp):
TTTTCTTTTTTTAAGAAATTTAGCCC
Found at i:42774515 original size:52 final size:52
Alignment explanation
Indices: 42774458--42774562 Score: 210
Period size: 52 Copynumber: 2.0 Consensus size: 52
42774448 ATTTTGCAGA
42774458 CTTCTTGTGTAACCTCTTAAGGCCAACTTCAAGAGTGCCATAAGCTGACATC
1 CTTCTTGTGTAACCTCTTAAGGCCAACTTCAAGAGTGCCATAAGCTGACATC
42774510 CTTCTTGTGTAACCTCTTAAGGCCAACTTCAAGAGTGCCATAAGCTGACATC
1 CTTCTTGTGTAACCTCTTAAGGCCAACTTCAAGAGTGCCATAAGCTGACATC
42774562 C
1 C
42774563 ATCACATTTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.27, C:0.28, G:0.17, T:0.29
Consensus pattern (52 bp):
CTTCTTGTGTAACCTCTTAAGGCCAACTTCAAGAGTGCCATAAGCTGACATC
Found at i:42776176 original size:59 final size:58
Alignment explanation
Indices: 42776002--42776178 Score: 169
Period size: 59 Copynumber: 3.0 Consensus size: 58
42775992 AACGTTTAAC
* * * *
42776002 AAGTACCAAA-TCGAACAAAAAAAAATTAGGCT-CCAAATTAAGAAAAATAGTCAAGATT
1 AAGTACCAAATTCGACCCAAAAAAATTTAGG-TACCAAATTAAGAAAAAT-GTCAAGTTT
* * * * * * * *
42776060 AGGTACCAAATTGGACCCCAAAAAGTTTAAGTATCAACTTAAGAAAAACTATCAAGTTT
1 AAGTACCAAATTCGACCCAAAAAAATTTAGGTACCAAATTAAGAAAAA-TGTCAAGTTT
* * *
42776119 AAGTACCAAATTTGACCCAAAAAAATTTAGGTACCAAATTAGGAAAATATGTTAAGTTT
1 AAGTACCAAATTCGACCCAAAAAAATTTAGGTACCAAATTAAGAAAA-ATGTCAAGTTT
42776178 A
1 A
42776179 GATACTAAAT
Statistics
Matches: 93, Mismatches: 22, Indels: 7
0.76 0.18 0.06
Matches are distributed among these distances:
58 10 0.11
59 81 0.87
60 2 0.02
ACGTcount: A:0.49, C:0.14, G:0.13, T:0.24
Consensus pattern (58 bp):
AAGTACCAAATTCGACCCAAAAAAATTTAGGTACCAAATTAAGAAAAATGTCAAGTTT
Found at i:42778099 original size:16 final size:16
Alignment explanation
Indices: 42778078--42778138 Score: 68
Period size: 16 Copynumber: 3.8 Consensus size: 16
42778068 CTCACTTAAC
42778078 TTAAATCCAAAATAAT
1 TTAAATCCAAAATAAT
** **
42778094 TTAAATTTAAAACGAT
1 TTAAATCCAAAATAAT
* *
42778110 TCAAACCCAAAATAAT
1 TTAAATCCAAAATAAT
42778126 TTAAATCCAAAAT
1 TTAAATCCAAAAT
42778139 TACTCAAATT
Statistics
Matches: 33, Mismatches: 12, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.54, C:0.15, G:0.02, T:0.30
Consensus pattern (16 bp):
TTAAATCCAAAATAAT
Found at i:42778146 original size:32 final size:32
Alignment explanation
Indices: 42778084--42778146 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
42778074 TAACTTAAAT
** *
42778084 CCAAAATAATTTAAATTTAAAACGATTCAAAC
1 CCAAAATAATTTAAATCCAAAACGACTCAAAC
**
42778116 CCAAAATAATTTAAATCCAAAATTACTCAAA
1 CCAAAATAATTTAAATCCAAAACGACTCAAA
42778147 TTCGAAATCA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.54, C:0.17, G:0.02, T:0.27
Consensus pattern (32 bp):
CCAAAATAATTTAAATCCAAAACGACTCAAAC
Found at i:42780948 original size:11 final size:11
Alignment explanation
Indices: 42780932--42780957 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
42780922 TAAATCTCAA
42780932 AACTATACATG
1 AACTATACATG
42780943 AACTATACATG
1 AACTATACATG
42780954 AACT
1 AACT
42780958 TTATTCTAAT
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:0.46, C:0.19, G:0.08, T:0.27
Consensus pattern (11 bp):
AACTATACATG
Found at i:42780983 original size:31 final size:29
Alignment explanation
Indices: 42780945--42781025 Score: 83
Period size: 29 Copynumber: 2.7 Consensus size: 29
42780935 TATACATGAA
42780945 CTATACATGAACTTT-ATTCTAATGTGCAATT
1 CTATACATGAACTTTGATT-T--TGTGCAATT
* *
42780976 CTATACATGTACTTTGATTTTGTGCCATT
1 CTATACATGAACTTTGATTTTGTGCAATT
* *
42781005 TTATACATGAAATTTTGATTT
1 CTATACATG-AACTTTGATTT
42781026 GATCAAATTA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
29 16 0.37
30 9 0.21
31 15 0.35
32 3 0.07
ACGTcount: A:0.28, C:0.14, G:0.11, T:0.47
Consensus pattern (29 bp):
CTATACATGAACTTTGATTTTGTGCAATT
Found at i:42781257 original size:29 final size:27
Alignment explanation
Indices: 42781191--42781257 Score: 89
Period size: 31 Copynumber: 2.3 Consensus size: 27
42781181 AAGTTTCATG
42781191 TGTATAATTGCATCAAATTAAAGTTCA
1 TGTATAATTGCATCAAATTAAAGTTCA
*
42781218 TGTATCAAATTGCACATTAAATTAAAGTTCA
1 TGTAT--AATTG--CATCAAATTAAAGTTCA
42781249 TGTATAATT
1 TGTATAATT
42781258 ATGGGATTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
27 5 0.14
29 9 0.26
31 21 0.60
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.39
Consensus pattern (27 bp):
TGTATAATTGCATCAAATTAAAGTTCA
Found at i:42781363 original size:12 final size:12
Alignment explanation
Indices: 42781345--42781374 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
42781335 TGCTAGTAAT
42781345 TAATTTTTT-AA
1 TAATTTTTTAAA
42781356 TAATTTTTTAAA
1 TAATTTTTTAAA
42781368 TAATTTT
1 TAATTTT
42781375 AATTATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.50
12 9 0.50
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
TAATTTTTTAAA
Found at i:42782434 original size:3 final size:3
Alignment explanation
Indices: 42782426--42782453 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
42782416 TCCTAACCCA
42782426 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
42782454 TTATTAACCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:42793571 original size:11 final size:11
Alignment explanation
Indices: 42793557--42793596 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
42793547 ATTTAATTAA
42793557 TTTTTAAAAAT
1 TTTTTAAAAAT
*
42793568 TTTTAAAAATAT
1 TTTTTAAAA-AT
*
42793580 TTTTTAATAAT
1 TTTTTAAAAAT
42793591 TTTTTA
1 TTTTTA
42793597 TACTTTTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 16 0.64
12 9 0.36
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TTTTTAAAAAT
Found at i:42793645 original size:32 final size:32
Alignment explanation
Indices: 42793595--42793661 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 32
42793585 AATAATTTTT
42793595 TATACTTTTTTATAA-TTTTAATAATTTTAAAA
1 TATACTTTTTTATAATTTTTAA-AATTTTAAAA
* *
42793627 TATATTTTTTTA-ATATTTTTAAATTTTTAAAA
1 TATACTTTTTTATA-ATTTTTAAAATTTTAAAA
42793659 TAT
1 TAT
42793662 CAATTCCTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
31 1 0.03
32 24 0.77
33 6 0.19
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (32 bp):
TATACTTTTTTATAATTTTTAAAATTTTAAAA
Found at i:42807017 original size:573 final size:574
Alignment explanation
Indices: 42806320--42807471 Score: 2162
Period size: 573 Copynumber: 2.0 Consensus size: 574
42806310 TTTGGAGTTT
*
42806320 TTTAATTTTGTGTATTTGATTGATGAAATTTAAAAAAAAAAAATTAAATTACTGTATTTAAGCTT
1 TTTAATTTTGTGTATTTGATTGATGAAATTTAAAAAAAAAAAATTAAATTACTGTATTTAAGCTC
*
42806385 GAACTCGATTTTTTAACACGATAATTAAGTTTAAGTTAGAGGAGGTCGGGATTGAATAATATATT
66 GAACTCGAGTTTTTAACACGATAATTAAGTTTAAGTTAGAGGAGGTCGGGATTGAATAATATATT
* *
42806450 TTTTTAAATATCAATACATAATTTTATAATGTATTAATTTATTATTTTATAATTTTTTTAAAGGA
131 TTTTTAAACATCAATACATAATTTTATAATGTATTAATTTATTATTTCATAATTTTTTTAAAGGA
*
42806515 TTAAACATGTACTTTTTTTCATTTTAAGGATCAAAGTGACATTTTATCATAAATTAACTTTTAAT
196 TTAAACATATACTTTTTTTCATTTTAAGGATCAAAGTGACATTTTATCATAAATTAACTTTTAAT
*
42806580 TTAATCATGTATAGAAGATTTAAATAGTGATTTTCCATTTGAGTCTCTTTTCAGATTCATGCGTA
261 TTAATCATGTATAGAAGATTTAAATAGTGATTTTCCATTTGAGTCTCTCTTCAGATTCATGCGTA
* *
42806645 ATCTCGACTTGATAATTACTGAATTAAATTTGAGTTTTTTTAATTGAATTCGAGTAGTTTGTAAA
326 ATCTCGACTTGATAATTACTGAATCAAATTTGAATTTTTTTAATTGAATTCGAGTAGTTTGTAAA
42806710 TATCAATACCCTTAAATAATATTCTTCGATTAGTTTAGTAAGAATGAAATAGGATTTAACTAAAT
391 TATCAATACCCTTAAATAATATTCTTCGATTAGTTTAGTAAGAATGAAATAGGATTTAACTAAAT
42806775 ACATGTAAATTTATTTTTATTTATTTTATATAAATAAAATTTAAGCAAATTATATGCTAATTGAA
456 ACATGTAAATTTATTTTTATTTATTTTATATAAATAAAATTTAAGCAAATTATATGCTAATTGAA
42806840 TCACTATGGTTCTTTAATTAAAATCATGAGTACCAATTTGGAAATCTTCAAAAC
521 TCACTATGGTTCTTTAATTAAAATCATGAGTACCAATTTGGAAATCTTCAAAAC
*
42806894 TTTAATTTTGTGTATTTGATTGATGAAATTT-AAAAAAAAAATTTAAATTACTGTATTTAAGCTC
1 TTTAATTTTGTGTATTTGATTGATGAAATTTAAAAAAAAAAAATTAAATTACTGTATTTAAGCTC
* *
42806958 GAACTCGAGTTTTTAACACGATAGTTAAGTTTAAGTTAGAGGAGGTCGGGATTGAATAATATTTT
66 GAACTCGAGTTTTTAACACGATAATTAAGTTTAAGTTAGAGGAGGTCGGGATTGAATAATATATT
42807023 TTTTTAAACATCAATACATAATTTTATAATGTATTAATTTATTATTTCATAATTTTTTTAAAGGA
131 TTTTTAAACATCAATACATAATTTTATAATGTATTAATTTATTATTTCATAATTTTTTTAAAGGA
* *
42807088 TTAAACATATATTTTTTTTCATTTTAAGGGTCAAAGTGACATTTTATCATAAATTAACTTTTAAT
196 TTAAACATATACTTTTTTTCATTTTAAGGATCAAAGTGACATTTTATCATAAATTAACTTTTAAT
42807153 TTAATCATGTATAGAAGATTTAAATAGTGATTTTCCATTTGAGTCTCTCTTCAGATTCATGCGTA
261 TTAATCATGTATAGAAGATTTAAATAGTGATTTTCCATTTGAGTCTCTCTTCAGATTCATGCGTA
42807218 ATCTCGACTTGATAATTACTGAATCAAATTTGAATTTTTTTAATTGAATTCGAGTAGTTTGTAAA
326 ATCTCGACTTGATAATTACTGAATCAAATTTGAATTTTTTTAATTGAATTCGAGTAGTTTGTAAA
* *
42807283 TATCAGTACCCTTAAATAATATTCTTCGATTAGTTTAGTAAGAATGAAATAGGATTTAACTTAAT
391 TATCAATACCCTTAAATAATATTCTTCGATTAGTTTAGTAAGAATGAAATAGGATTTAACTAAAT
42807348 ACATGTAAATTTATTTTTATTTATTTTATATAAATAAAATTTAAGCAAATTATATGCTAATTGAA
456 ACATGTAAATTTATTTTTATTTATTTTATATAAATAAAATTTAAGCAAATTATATGCTAATTGAA
42807413 TCACTATGGTTCTTTAATTAAAATCATGAGTACCAATTTGGAAATCTTCAAAAC
521 TCACTATGGTTCTTTAATTAAAATCATGAGTACCAATTTGGAAATCTTCAAAAC
42807467 TTTAA
1 TTTAA
42807472 CCATTTTTTA
Statistics
Matches: 563, Mismatches: 15, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
573 532 0.94
574 31 0.06
ACGTcount: A:0.37, C:0.09, G:0.12, T:0.43
Consensus pattern (574 bp):
TTTAATTTTGTGTATTTGATTGATGAAATTTAAAAAAAAAAAATTAAATTACTGTATTTAAGCTC
GAACTCGAGTTTTTAACACGATAATTAAGTTTAAGTTAGAGGAGGTCGGGATTGAATAATATATT
TTTTTAAACATCAATACATAATTTTATAATGTATTAATTTATTATTTCATAATTTTTTTAAAGGA
TTAAACATATACTTTTTTTCATTTTAAGGATCAAAGTGACATTTTATCATAAATTAACTTTTAAT
TTAATCATGTATAGAAGATTTAAATAGTGATTTTCCATTTGAGTCTCTCTTCAGATTCATGCGTA
ATCTCGACTTGATAATTACTGAATCAAATTTGAATTTTTTTAATTGAATTCGAGTAGTTTGTAAA
TATCAATACCCTTAAATAATATTCTTCGATTAGTTTAGTAAGAATGAAATAGGATTTAACTAAAT
ACATGTAAATTTATTTTTATTTATTTTATATAAATAAAATTTAAGCAAATTATATGCTAATTGAA
TCACTATGGTTCTTTAATTAAAATCATGAGTACCAATTTGGAAATCTTCAAAAC
Found at i:42823441 original size:28 final size:28
Alignment explanation
Indices: 42823389--42823442 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 28
42823379 TGATATAGCA
*
42823389 AAAATTGTAACAAATATTATCCTATTTT
1 AAAATTGTAACAAATATTATACTATTTT
42823417 AAAATT-T-ACAAATGATATATACTATT
1 AAAATTGTAACAAAT-AT-TATACTATT
42823443 AGAGTACTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 6 0.26
27 3 0.13
28 14 0.61
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (28 bp):
AAAATTGTAACAAATATTATACTATTTT
Found at i:42828099 original size:31 final size:31
Alignment explanation
Indices: 42828064--42828166 Score: 115
Period size: 31 Copynumber: 3.4 Consensus size: 31
42828054 TCCAAGTTGC
42828064 ACTGCCACAGCCACCTTCTCCACCAGCTCAA
1 ACTGCCACAGCCACCTTCTCCACCAGCTCAA
* * ** *
42828095 ACTGCCACTGCCAGCGGCTCCA--AGTTGC--
1 ACTGCCACAGCCACCTTCTCCACCAGCT-CAA
42828123 ACTGCCACAGCCACCTTCTCCACCAGCTCAA
1 ACTGCCACAGCCACCTTCTCCACCAGCTCAA
*
42828154 ACTGCCACTGCCA
1 ACTGCCACAGCCA
42828167 TGGAACCTGC
Statistics
Matches: 56, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
28 18 0.32
29 4 0.07
30 4 0.07
31 30 0.54
ACGTcount: A:0.23, C:0.46, G:0.15, T:0.17
Consensus pattern (31 bp):
ACTGCCACAGCCACCTTCTCCACCAGCTCAA
Found at i:42828138 original size:59 final size:59
Alignment explanation
Indices: 42828046--42828166 Score: 233
Period size: 59 Copynumber: 2.1 Consensus size: 59
42828036 AGGGTCACCT
42828046 CCAGCAGCTCCAAGTTGCACTGCCACAGCCACCTTCTCCACCAGCTCAAACTGCCACTG
1 CCAGCAGCTCCAAGTTGCACTGCCACAGCCACCTTCTCCACCAGCTCAAACTGCCACTG
*
42828105 CCAGCGGCTCCAAGTTGCACTGCCACAGCCACCTTCTCCACCAGCTCAAACTGCCACTG
1 CCAGCAGCTCCAAGTTGCACTGCCACAGCCACCTTCTCCACCAGCTCAAACTGCCACTG
42828164 CCA
1 CCA
42828167 TGGAACCTGC
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.23, C:0.45, G:0.16, T:0.17
Consensus pattern (59 bp):
CCAGCAGCTCCAAGTTGCACTGCCACAGCCACCTTCTCCACCAGCTCAAACTGCCACTG
Found at i:42828143 original size:28 final size:28
Alignment explanation
Indices: 42828053--42828144 Score: 96
Period size: 28 Copynumber: 3.2 Consensus size: 28
42828043 CCTCCAGCAG
42828053 CTCCAAGTTGCACTGCCACAGCCACCTT
1 CTCCAAGTTGCACTGCCACAGCCACCTT
* * * **
42828081 CTCCACCAGCT-CAAACTGCCACTGCCAGCGG
1 CTCCA--AGTTGC--ACTGCCACAGCCACCTT
42828112 CTCCAAGTTGCACTGCCACAGCCACCTT
1 CTCCAAGTTGCACTGCCACAGCCACCTT
42828140 CTCCA
1 CTCCA
42828145 CCAGCTCAAA
Statistics
Matches: 49, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
28 23 0.47
29 4 0.08
30 4 0.08
31 18 0.37
ACGTcount: A:0.22, C:0.45, G:0.15, T:0.18
Consensus pattern (28 bp):
CTCCAAGTTGCACTGCCACAGCCACCTT
Found at i:42828217 original size:14 final size:14
Alignment explanation
Indices: 42828198--42828224 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
42828188 AGAATTAGAC
42828198 ATACATTAATATCG
1 ATACATTAATATCG
42828212 ATACATTAATATC
1 ATACATTAATATC
42828225 AACTCTTGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.15, G:0.04, T:0.37
Consensus pattern (14 bp):
ATACATTAATATCG
Found at i:42829420 original size:29 final size:29
Alignment explanation
Indices: 42829388--42829589 Score: 92
Period size: 30 Copynumber: 6.9 Consensus size: 29
42829378 ACATTCTGAC
*
42829388 CCCGAACCTTCTAAAATTCTATTTTTAAA
1 CCCGAACCTTCTAAAATTCCATTTTTAAA
** ** * **
42829417 CCCGATTTCACCAAAAATTACCA-TTTTACC
1 CCCGA-ACCTTCTAAAATT-CCATTTTTAAA
*
42829447 CCCGAACCTTCTAAAATTCAATTTTT-AA
1 CCCGAACCTTCTAAAATTCCATTTTTAAA
* ** * *
42829475 CCCCAATTTTACCAAAAATTACCA-TTTT-AC
1 CCCGAACCTT--CTAAAATT-CCATTTTTAAA
*
42829505 CCCTGAACCTTCTAAAATTCTATTTTT-AA
1 CCC-GAACCTTCTAAAATTCCATTTTTAAA
*** * **
42829534 CCTCGATTTTATCAAAAATTACCA-TTTTACC
1 CC-CGAACCT-TCTAAAATT-CCATTTTTAAA
42829565 CCCGAACCTTCTAAAATTCCATTTT
1 CCCGAACCTTCTAAAATTCCATTTT
42829590 AACCTCGATT
Statistics
Matches: 121, Mismatches: 39, Indels: 26
0.65 0.21 0.14
Matches are distributed among these distances:
28 14 0.12
29 45 0.37
30 50 0.41
31 12 0.10
ACGTcount: A:0.33, C:0.28, G:0.03, T:0.36
Consensus pattern (29 bp):
CCCGAACCTTCTAAAATTCCATTTTTAAA
Found at i:42829461 original size:59 final size:58
Alignment explanation
Indices: 42829369--42829681 Score: 411
Period size: 59 Copynumber: 5.4 Consensus size: 58
42829359 CCCAAACAGT
* *
42829369 CCAAAAATTA-CATTCTGA-CCCCGAACCTTCTAAAATTCTATTTTTAAACCCGATTTCA
1 CCAAAAATTACCATT-TTACCCCCGAACCTTCTAAAATTCCATTTTT-AACCCGATTTCA
* * *
42829427 CCAAAAATTACCATTTTACCCCCGAACCTTCTAAAATTCAATTTTTAACCCCAATTTTA
1 CCAAAAATTACCATTTTACCCCCGAACCTTCTAAAATTCCATTTTTAA-CCCGATTTCA
* * *
42829486 CCAAAAATTACCATTTTACCCCTGAACCTTCTAAAATTCTATTTTTAACCTCGATTTTA
1 CCAAAAATTACCATTTTACCCCCGAACCTTCTAAAATTCCATTTTTAACC-CGATTTCA
*
42829545 TCAAAAATTACCATTTTACCCCCGAACCTTCTAAAATTCCA-TTTTAACCTCGATTTCA
1 CCAAAAATTACCATTTTACCCCCGAACCTTCTAAAATTCCATTTTTAACC-CGATTTCA
* * *
42829603 CTAAAAATTACCATTTTACCCCC-AAACTCTCAAAAATTCCATTTTTAACCCTGATTTCA
1 CCAAAAATTACCATTTTACCCCCGAACCT-TCTAAAATTCCATTTTTAACCC-GATTTCA
*
42829662 -CTAAAATTACCATTTTACCC
1 CCAAAAATTACCATTTTACCC
42829682 TCGGGTATCC
Statistics
Matches: 231, Mismatches: 17, Indels: 14
0.88 0.06 0.05
Matches are distributed among these distances:
57 4 0.02
58 83 0.36
59 144 0.62
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.35
Consensus pattern (58 bp):
CCAAAAATTACCATTTTACCCCCGAACCTTCTAAAATTCCATTTTTAACCCGATTTCA
Found at i:42829525 original size:118 final size:114
Alignment explanation
Indices: 42829369--42829681 Score: 430
Period size: 117 Copynumber: 2.7 Consensus size: 114
42829359 CCCAAACAGT
*
42829369 CCAAAAATTA-CATTCTGACCCCGAACCTTCTAAAATTCTATTTTTAAACCCGATTTCACCAAAA
1 CCAAAAATTACCATT-TTACCCCGAACCTTCTAAAATTCTATTTTT-AACCCGATTTCA-CAAAA
*
42829433 ATTACCATTTTACCCCCGAACCTTCTAAAATTCAATTTTTAACCCCAATTTTA
63 ATTACCATTTTACCCCCGAACCTTCTAAAATTCAA-TTTTAACCCCAATTTCA
*
42829486 CCAAAAATTACCATTTTACCCCTGAACCTTCTAAAATTCTATTTTTAACCTCGATTTTATCAAAA
1 CCAAAAATTACCATTTTACCCC-GAACCTTCTAAAATTCTATTTTTAACC-CGATTTCA-CAAAA
* * *
42829551 ATTACCATTTTACCCCCGAACCTTCTAAAATTCCATTTTAACCTCGATTTCA
63 ATTACCATTTTACCCCCGAACCTTCTAAAATTCAATTTTAACCCCAATTTCA
* * * * * *
42829603 CTAAAAATTACCATTTTACCCCCAAACTCTCAAAAATTCCATTTTTAACCCTGATTTCACTAAAA
1 CCAAAAATTACCATTTTACCCCGAACCT-TCTAAAATTCTATTTTTAACCC-GATTTCACAAAAA
42829668 TTACCATTTTACCC
64 TTACCATTTTACCC
42829682 TCGGGTATCC
Statistics
Matches: 177, Mismatches: 14, Indels: 11
0.88 0.07 0.05
Matches are distributed among these distances:
116 24 0.14
117 80 0.45
118 73 0.41
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.35
Consensus pattern (114 bp):
CCAAAAATTACCATTTTACCCCGAACCTTCTAAAATTCTATTTTTAACCCGATTTCACAAAAATT
ACCATTTTACCCCCGAACCTTCTAAAATTCAATTTTAACCCCAATTTCA
Found at i:42829609 original size:29 final size:30
Alignment explanation
Indices: 42829528--42829684 Score: 107
Period size: 29 Copynumber: 5.4 Consensus size: 30
42829518 AAAATTCTAT
*
42829528 TTTTAACCTCGATTTTA-TCAAAAATTACCA
1 TTTTAACCTCGATTTCACT-AAAAATTACCA
* * *
42829558 TTTTACCCCCGAACCTT--CT-AAAATT-CCA
1 TTTTAACCTCG-A-TTTCACTAAAAATTACCA
42829586 TTTTAACCTCGATTTCACTAAAAATTACCA
1 TTTTAACCTCGATTTCACTAAAAATTACCA
* * * ** *
42829616 TTTTACCCCCAAACTCTC-AAAAATT-CCA
1 TTTTAACCTCGATTTCACTAAAAATTACCA
42829644 TTTTTAACC-CTGATTTCACT-AAAATTACCA
1 -TTTTAACCTC-GATTTCACTAAAAATTACCA
*
42829674 TTTTACCCTCG
1 TTTTAACCTCG
42829685 GGTATCCAAA
Statistics
Matches: 97, Mismatches: 18, Indels: 25
0.69 0.13 0.18
Matches are distributed among these distances:
26 2 0.02
27 1 0.01
28 18 0.19
29 44 0.45
30 28 0.29
31 2 0.02
32 2 0.02
ACGTcount: A:0.32, C:0.28, G:0.03, T:0.36
Consensus pattern (30 bp):
TTTTAACCTCGATTTCACTAAAAATTACCA
Found at i:42829711 original size:117 final size:116
Alignment explanation
Indices: 42829371--42829719 Score: 343
Period size: 117 Copynumber: 3.0 Consensus size: 116
42829361 CAAACAGTCC
* * * * *
42829371 AAAAATTA-CATTCTGA-CCCCGAACCTTCTAAAATTCTATTTTTAAACC-CGATTTCACCAAAA
1 AAAAATTACCATT-TTACCCCCAAACCTTCAAAAATTCCATTTTT-AACCTCGATTTCATCAAAA
* * * * * * *
42829433 ATTACCATTTTACCCCCGAACCTTCTAAAATTCAATTTTTAACCCCAATTTTACC
64 ATTACCATTTTACCCCCG-ACCTTCCAAAATTCCA-TTTCAACCTCGATTTCACT
** * * *
42829488 AAAAATTACCATTTTACCCCTGAACCTTCTAAAATTCTATTTTTAACCTCGATTTTATCAAAAAT
1 AAAAATTACCATTTTACCCCCAAACCTTCAAAAATTCCATTTTTAACCTCGATTTCATCAAAAAT
* *
42829553 TACCATTTTACCCCCGAACCTTCTAAAATTCCATTTTAACCTCGATTTCACT
66 TACCATTTTACCCCCG-ACCTTCCAAAATTCCATTTCAACCTCGATTTCACT
*
42829605 AAAAATTACCATTTTACCCCCAAA-CTCTCAAAAATTCCATTTTTAACC-CTGATTTCA-CTAAA
1 AAAAATTACCATTTTACCCCCAAACCT-TCAAAAATTCCATTTTTAACCTC-GATTTCATCAAAA
* ** *
42829667 ATTACCATTTTACCCTCG-GGTATCCAAAAGTTCCGTTTCCAACCTCGATTTCA
64 ATTACCATTTTACCCCCGACCT-TCCAAAA-TTCCATTT-CAACCTCGATTTCA
42829720 TTATTTTTTC
Statistics
Matches: 203, Mismatches: 21, Indels: 16
0.85 0.09 0.07
Matches are distributed among these distances:
114 1 0.00
115 6 0.03
116 31 0.15
117 89 0.44
118 76 0.37
ACGTcount: A:0.33, C:0.28, G:0.04, T:0.35
Consensus pattern (116 bp):
AAAAATTACCATTTTACCCCCAAACCTTCAAAAATTCCATTTTTAACCTCGATTTCATCAAAAAT
TACCATTTTACCCCCGACCTTCCAAAATTCCATTTCAACCTCGATTTCACT
Found at i:42840766 original size:6 final size:6
Alignment explanation
Indices: 42840755--42840802 Score: 62
Period size: 6 Copynumber: 7.8 Consensus size: 6
42840745 TTACACATAA
*
42840755 AAAAAT AAAAAT AAAAAT -AAAAT AAAAAT AAAAAAAT AGAAAT AAAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT --AAAAAT AAAAAT AAAAA
42840803 AATCGGAGAG
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
5 5 0.14
6 26 0.70
8 6 0.16
ACGTcount: A:0.83, C:0.00, G:0.02, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:42840770 original size:14 final size:14
Alignment explanation
Indices: 42840751--42840805 Score: 74
Period size: 14 Copynumber: 3.7 Consensus size: 14
42840741 AATATTACAC
42840751 ATAAAAAAATAAAA
1 ATAAAAAAATAAAA
42840765 ATAAAAATAAAATAAAA
1 AT--AAA-AAAATAAAA
*
42840782 ATAAAAAAATAGAA
1 ATAAAAAAATAAAA
42840796 ATAAAAAAAT
1 ATAAAAAAAT
42840806 CGGAGAGGTC
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
14 20 0.54
15 3 0.08
16 3 0.08
17 11 0.30
ACGTcount: A:0.82, C:0.00, G:0.02, T:0.16
Consensus pattern (14 bp):
ATAAAAAAATAAAA
Found at i:42840776 original size:11 final size:11
Alignment explanation
Indices: 42840755--42840787 Score: 57
Period size: 11 Copynumber: 2.9 Consensus size: 11
42840745 TTACACATAA
42840755 AAAAATAAAAAT
1 AAAAAT-AAAAT
42840767 AAAAATAAAAT
1 AAAAATAAAAT
42840778 AAAAATAAAA
1 AAAAATAAAA
42840788 AAATAGAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.71
12 6 0.29
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:42840780 original size:25 final size:25
Alignment explanation
Indices: 42840751--42840801 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
42840741 AATATTACAC
42840751 ATAAAAA-AATAAAAATAAAAATAAA
1 ATAAAAATAA-AAAAATAAAAATAAA
*
42840776 ATAAAAATAAAAAAATAGAAATAAA
1 ATAAAAATAAAAAAATAAAAATAAA
42840801 A
1 A
42840802 AAATCGGAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 22 0.92
26 2 0.08
ACGTcount: A:0.82, C:0.00, G:0.02, T:0.16
Consensus pattern (25 bp):
ATAAAAATAAAAAAATAAAAATAAA
Found at i:42841941 original size:151 final size:152
Alignment explanation
Indices: 42841663--42842345 Score: 982
Period size: 151 Copynumber: 4.5 Consensus size: 152
42841653 CAGACCGCAC
* * *
42841663 CAAGATCTTTTCCTATCCGCTTGAAATTGAAGTAGAGTTGGACAACACGTCTTTATCTCTGAAAT
1 CAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAAT
* * * * * * *
42841728 TGAAGTAGGAGCAAGATCTTTTCTTGTCCGCTTGAAATTGAAGTA-A-TGTGGATAACACGTCTT
66 TGAAGTAAGAACAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGT-TGGATAACAAGTCTT
*
42841791 TATCTCTGAAATTGAAGTAGGAG
130 TATCTCTGAAATTGAAGTAAGAG
* *
42841814 CAAGATCTTTTCCTGTCCGCTTGAAATTGAAGTAGAG-TGGATAACAAGTCTTTATCTCTGAAAT
1 CAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAAT
42841878 TGAAGTAAGAACAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTT
66 TGAAGTAAGAACAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTT
42841943 ATCTCTGAAATTGAAGTAAGAG
131 ATCTCTGAAATTGAAGTAAGAG
* *
42841965 CAACAT-TGTTTCCTATCCTCTTGAAATTGAAGTAAAG-TGGATAACAAGTCTTTATCTCTGAAA
1 CAAGATCT-TTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAA
* *
42842028 TTGAAGTAAGAACAAGATCATTTCCTGTCCTCTTGAAATTGAAGTAGAGTTGGATAACAAATCTT
65 TTGAAGTAAGAACAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTT
*
42842093 TATCTTTGAAATTGAAGTAAGAG
130 TATCTCTGAAATTGAAGTAAGAG
* *
42842116 CAACAT-TGTTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTTAAA
1 CAAGATCT-TTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAA
* * * * *
42842180 TTGAAGTAAGAGCAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTT
65 TTGAAGTAAGAACAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTT
42842245 TATCTCTGAAATTGAAGTAAGAG
130 TATCTCTGAAATTGAAGTAAGAG
* * * * * **
42842268 CAAGATCATTTCATATCCTCTTGAAATTGAAGTAAAAGTTGGATATCAAGCCTTCGTCCCTCTGA
1 CAAGATCTTTTCCTATCCTCTTGAAATTGAAGT-AGAGTTGGATAACAAGTCTT--TATCTCTGA
42842333 AATTGAAGTAAGA
63 AATTGAAGTAAGA
42842346 GTAAGATGAA
Statistics
Matches: 487, Mismatches: 37, Indels: 12
0.91 0.07 0.02
Matches are distributed among these distances:
150 65 0.13
151 251 0.52
152 135 0.28
153 17 0.03
155 19 0.04
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Consensus pattern (152 bp):
CAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAAT
TGAAGTAAGAACAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTT
ATCTCTGAAATTGAAGTAAGAG
Found at i:42841959 original size:76 final size:76
Alignment explanation
Indices: 42841663--42842352 Score: 987
Period size: 76 Copynumber: 9.1 Consensus size: 76
42841653 CAGACCGCAC
* * *
42841663 CAAGATCTTTTCCTATCCGCTTGAAATTGAAGTAGAGTTGGACAACACGTCTTTATCTCTGAAAT
1 CAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAAT
*
42841728 TGAAGTAGGAG
66 TGAAGTAAGAG
* * * *
42841739 CAAGATCTTTTCTTGTCCGCTTGAAATTGAAGTA-A-TGTGGATAACACGTCTTTATCTCTGAAA
1 CAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAGAGT-TGGATAACAAGTCTTTATCTCTGAAA
*
42841802 TTGAAGTAGGAG
65 TTGAAGTAAGAG
* *
42841814 CAAGATCTTTTCCTGTCCGCTTGAAATTGAAGTAGAG-TGGATAACAAGTCTTTATCTCTGAAAT
1 CAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAAT
*
42841878 TGAAGTAAGAA
66 TGAAGTAAGAG
*
42841889 CAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAAT
1 CAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAAT
42841954 TGAAGTAAGAG
66 TGAAGTAAGAG
* *
42841965 CAACAT-TGTTTCCTATCCTCTTGAAATTGAAGTAAAG-TGGATAACAAGTCTTTATCTCTGAAA
1 CAAGATCT-TTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAA
*
42842028 TTGAAGTAAGAA
65 TTGAAGTAAGAG
* * * *
42842040 CAAGATCATTTCCTGTCCTCTTGAAATTGAAGTAGAGTTGGATAACAAATCTTTATCTTTGAAAT
1 CAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAAT
42842105 TGAAGTAAGAG
66 TGAAGTAAGAG
* *
42842116 CAACAT-TGTTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTTAAA
1 CAAGATCT-TTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAA
42842180 TTGAAGTAAGAG
65 TTGAAGTAAGAG
* * *
42842192 CAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAAT
1 CAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAAT
42842257 TGAAGTAAGAG
66 TGAAGTAAGAG
* * * * * **
42842268 CAAGATCATTTCATATCCTCTTGAAATTGAAGTAAAAGTTGGATATCAAGCCTTCGTCCCTCTGA
1 CAAGATCTTTTCCTATCCTCTTGAAATTGAAGT-AGAGTTGGATAACAAGTCTT--TATCTCTGA
42842333 AATTGAAGTAAGAG
63 AATTGAAGTAAGAG
*
42842347 TAAGAT
1 CAAGAT
42842353 GAAGCACCAA
Statistics
Matches: 562, Mismatches: 40, Indels: 21
0.90 0.06 0.03
Matches are distributed among these distances:
74 1 0.00
75 209 0.37
76 307 0.55
77 19 0.03
79 26 0.05
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (76 bp):
CAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAAT
TGAAGTAAGAG
Found at i:42842264 original size:38 final size:38
Alignment explanation
Indices: 42842213--42842343 Score: 106
Period size: 38 Copynumber: 3.4 Consensus size: 38
42842203 CCTATCCTCT
42842213 TGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTC
1 TGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTC
* * ** *
42842251 TGAAATTGAAGTAAGAGC--AAGATCATTTC-ATATCCTC
1 TGAAATTGAAGTAA-AGCTGGATATCAAGTCTTTAT-CTC
* * **
42842288 TTGAAATTGAAGTAAAAGTTGGATATCAAGCCTTCGTCCCTC
1 -TGAAATTGAAGT-AAAGCTGGATATCAAGTCTT--TATCTC
42842330 TGAAATTGAAGTAA
1 TGAAATTGAAGTAA
42842344 GAGTAAGATG
Statistics
Matches: 70, Mismatches: 14, Indels: 16
0.70 0.14 0.16
Matches are distributed among these distances:
36 3 0.04
37 10 0.14
38 28 0.40
39 5 0.07
40 8 0.11
41 12 0.17
42 3 0.04
43 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (38 bp):
TGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTC
Found at i:42842429 original size:92 final size:92
Alignment explanation
Indices: 42842272--42842485 Score: 346
Period size: 92 Copynumber: 2.3 Consensus size: 92
42842262 TAAGAGCAAG
*
42842272 ATCA-TTTCATATCCTCTTGAAATTGAAGTAAAAGTTGGATATCAAGCCTTCGTCCCTCTGAAAT
1 ATCATTTTCATATCCTCTTGAAATTGAAGT-AAAGCTGGATATCAAGCCTTCGTCCCTCTGAAAT
42842336 TGAAGTAAGAGTAAGATGAAGCACCAAC
65 TGAAGTAAGAGTAAGATGAAGCACCAAC
*
42842364 ATCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAAT-AAGCCTTCGTCCCTCTGAAAT
1 ATCATTTTCATATCCTCTTGAAATTGAAGTAAAGCTGGAT-ATCAAGCCTTCGTCCCTCTGAAAT
*
42842428 TGAAGTAAGAGTAAGATGAGGCACCAAC
65 TGAAGTAAGAGTAAGATGAAGCACCAAC
*
42842456 ATCATTTTCGT-TCCTC-TGAAATTGAAGTAA
1 ATCATTTTCATATCCTCTTGAAATTGAAGTAA
42842486 GAGCAAGACG
Statistics
Matches: 116, Mismatches: 4, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
90 14 0.12
91 5 0.04
92 71 0.61
93 26 0.22
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (92 bp):
ATCATTTTCATATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGCCTTCGTCCCTCTGAAATT
GAAGTAAGAGTAAGATGAAGCACCAAC
Found at i:42842507 original size:50 final size:50
Alignment explanation
Indices: 42842412--42842509 Score: 135
Period size: 50 Copynumber: 2.0 Consensus size: 50
42842402 ATAATAAGCC
* * * *
42842412 TTCGTCCCTCTGAAATTGAAGTAAGAGTAAGATGAGGCACCAACATCATT
1 TTCGTCCCTCTGAAATTGAAGTAAGAGCAAGACGAAGCACAAACATCATT
*
42842462 TTCGTTCCTCTGAAATTGAAGTAAGAGCAAGACGAAGC-CTAAACATCA
1 TTCGTCCCTCTGAAATTGAAGTAAGAGCAAGACGAAGCAC-AAACATCA
42842510 AACCCTACTT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
49 1 0.02
50 41 0.98
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.24
Consensus pattern (50 bp):
TTCGTCCCTCTGAAATTGAAGTAAGAGCAAGACGAAGCACAAACATCATT
Found at i:42842780 original size:17 final size:16
Alignment explanation
Indices: 42842758--42842816 Score: 73
Period size: 17 Copynumber: 3.6 Consensus size: 16
42842748 CATTTGGAAA
42842758 TTAAATTTATTTTAAT
1 TTAAATTTATTTTAAT
*
42842774 TTGAAATTTATTTTAAA
1 TT-AAATTTATTTTAAT
* *
42842791 TTCAATTTGAATTTAAT
1 TTAAATTT-ATTTTAAT
42842808 TTAAATTTA
1 TTAAATTTA
42842817 ATATTATTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
16 8 0.22
17 28 0.78
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (16 bp):
TTAAATTTATTTTAAT
Found at i:42842817 original size:11 final size:11
Alignment explanation
Indices: 42842755--42842818 Score: 67
Period size: 11 Copynumber: 5.8 Consensus size: 11
42842745 AACCATTTGG
*
42842755 AAATTAAATTT
1 AAATTTAATTT
*
42842766 -ATTTTAATTT
1 AAATTTAATTT
*
42842776 GAAATTTATTTT
1 -AAATTTAATTT
*
42842788 AAATTCAATTT
1 AAATTTAATTT
*
42842799 GAATTTAATTT
1 AAATTTAATTT
42842810 AAATTTAAT
1 AAATTTAAT
42842819 ATTATTATAA
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
10 8 0.19
11 26 0.62
12 8 0.19
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (11 bp):
AAATTTAATTT
Found at i:42843842 original size:17 final size:17
Alignment explanation
Indices: 42843820--42843865 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
42843810 AAGAAGATTG
42843820 AAATGAATAA-AAAAGAA
1 AAATGAA-AAGAAAAGAA
42843837 AAATGAAAAGAAAAGAA
1 AAATGAAAAGAAAAGAA
*
42843854 CAAAAGAAAAGA
1 -AAATGAAAAGA
42843866 GAAAAGAAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 2 0.08
17 14 0.54
18 10 0.38
ACGTcount: A:0.76, C:0.02, G:0.15, T:0.07
Consensus pattern (17 bp):
AAATGAAAAGAAAAGAA
Found at i:42843847 original size:12 final size:12
Alignment explanation
Indices: 42843830--42843873 Score: 54
Period size: 12 Copynumber: 3.6 Consensus size: 12
42843820 AAATGAATAA
42843830 AAAAGAAAA-ATG
1 AAAAGAAAAGA-G
*
42843842 AAAAGAAAAGAAC
1 AAAAGAAAAG-AG
42843855 AAAAGAAAAGAG
1 AAAAGAAAAGAG
42843867 AAAAGAA
1 AAAAGAA
42843874 GGAAGAAAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 17 0.61
13 10 0.36
14 1 0.04
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.02
Consensus pattern (12 bp):
AAAAGAAAAGAG
Found at i:42844628 original size:30 final size:29
Alignment explanation
Indices: 42844582--42844752 Score: 120
Period size: 29 Copynumber: 5.8 Consensus size: 29
42844572 CCAAAACCTT
42844582 CTAAAATTCCATTTTTAACCCCGATTTTA
1 CTAAAATTCCATTTTTAACCCCGATTTTA
* **
42844611 CTAAAAATTACCA-TTTTACCCCCGAACCTT-
1 CT-AAAATT-CCATTTTTAACCCCG-ATTTTA
* *
42844641 CTAAAATTCCATTTTTATCCCCGATTTCA
1 CTAAAATTCCATTTTTAACCCCGATTTTA
* **
42844670 TCAAAAATTACCA-TTTT-ACCCCTGAACCTT-
1 -CTAAAATT-CCATTTTTAACCCC-G-ATTTTA
* *
42844700 CTAAAATTCCATTTTTAACCCTGATTTCA
1 CTAAAATTCCATTTTTAACCCCGATTTTA
* *
42844729 CCAAAATTACCA-TTTTGACCCCGA
1 CTAAAATT-CCATTTTTAACCCCGA
42844753 CTATCCAAAA
Statistics
Matches: 109, Mismatches: 20, Indels: 26
0.70 0.13 0.17
Matches are distributed among these distances:
28 10 0.09
29 51 0.47
30 37 0.34
31 11 0.10
ACGTcount: A:0.32, C:0.29, G:0.04, T:0.36
Consensus pattern (29 bp):
CTAAAATTCCATTTTTAACCCCGATTTTA
Found at i:42844723 original size:29 final size:29
Alignment explanation
Indices: 42844576--42844720 Score: 136
Period size: 30 Copynumber: 4.9 Consensus size: 29
42844566 TCTGACCCAA
42844576 AACCTTCTAAAATTCCATTTTTAACCCCG
1 AACCTTCTAAAATTCCATTTTTAACCCCG
** *
42844605 -ATTTTACTAAAAATTACCA-TTTTACCCCCG
1 AACCTT-CT-AAAATT-CCATTTTTAACCCCG
*
42844635 AACCTTCTAAAATTCCATTTTTATCCCCG
1 AACCTTCTAAAATTCCATTTTTAACCCCG
** * *
42844664 ATTTCATCAAAAATTACCA-TTTT-ACCCCTG
1 A-ACCTTCTAAAATT-CCATTTTTAACCCC-G
42844694 AACCTTCTAAAATTCCATTTTTAACCC
1 AACCTTCTAAAATTCCATTTTTAACCC
42844721 TGATTTCACC
Statistics
Matches: 91, Mismatches: 15, Indels: 19
0.73 0.12 0.15
Matches are distributed among these distances:
28 9 0.10
29 36 0.40
30 37 0.41
31 9 0.10
ACGTcount: A:0.32, C:0.29, G:0.03, T:0.37
Consensus pattern (29 bp):
AACCTTCTAAAATTCCATTTTTAACCCCG
Found at i:42844770 original size:58 final size:57
Alignment explanation
Indices: 42844576--42844786 Score: 273
Period size: 59 Copynumber: 3.6 Consensus size: 57
42844566 TCTGACCCAA
*
42844576 AACCTTCTAAAATTCCATTTTTAACCCCGATTTTACTAAAAATTACCATTTTACCCCCG
1 AACCTTCTAAAATTCCATTTTTAACCCCGATTTCAC-AAAAATTACCATTTTA-CCCCG
*
42844635 AACCTTCTAAAATTCCATTTTTATCCCCGATTTCATCAAAAATTACCATTTTACCCCTG
1 AACCTTCTAAAATTCCATTTTTAACCCCGATTTCA-CAAAAATTACCATTTTACCCC-G
* *
42844694 AACCTTCTAAAATTCCATTTTTAACCCTGATTTCACCAAAATTACCATTTTGACCCCG
1 AACCTTCTAAAATTCCATTTTTAACCCCGATTTCACAAAAATTACCATTTT-ACCCCG
* * **
42844752 -A-CTATCCAAAAGTCCCATTTCCAACCCCGATTTCA
1 AACCT-TCTAAAA-TTCCATTTTTAACCCCGATTTCA
42844787 TCATTTTTTC
Statistics
Matches: 137, Mismatches: 10, Indels: 11
0.87 0.06 0.07
Matches are distributed among these distances:
56 2 0.01
57 7 0.05
58 39 0.28
59 88 0.64
60 1 0.01
ACGTcount: A:0.31, C:0.30, G:0.04, T:0.34
Consensus pattern (57 bp):
AACCTTCTAAAATTCCATTTTTAACCCCGATTTCACAAAAATTACCATTTTACCCCG
Found at i:42850675 original size:23 final size:24
Alignment explanation
Indices: 42850649--42850695 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
42850639 AAGCGCTGCA
*
42850649 AAAGAT-AGGGCAATAGCGGCGCT
1 AAAGATCAGGGAAATAGCGGCGCT
* *
42850672 AAAGGTCAGGGAAATAGTGGCGCT
1 AAAGATCAGGGAAATAGCGGCGCT
42850696 TATGAGAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.34, C:0.15, G:0.36, T:0.15
Consensus pattern (24 bp):
AAAGATCAGGGAAATAGCGGCGCT
Found at i:42850734 original size:40 final size:40
Alignment explanation
Indices: 42850684--42850765 Score: 119
Period size: 40 Copynumber: 2.0 Consensus size: 40
42850674 AGGTCAGGGA
*
42850684 AATAGTGGCGCTTATGAGAAAACGCCGCAAAAGGTAAGGC
1 AATAGCGGCGCTTATGAGAAAACGCCGCAAAAGGTAAGGC
* * * *
42850724 AATAGCGGCGCTTATGGGAAAGCGCCGTAAAAGGTACGGC
1 AATAGCGGCGCTTATGAGAAAACGCCGCAAAAGGTAAGGC
42850764 AA
1 AA
42850766 CCGCGGGTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.35, C:0.18, G:0.32, T:0.15
Consensus pattern (40 bp):
AATAGCGGCGCTTATGAGAAAACGCCGCAAAAGGTAAGGC
Found at i:42850852 original size:96 final size:95
Alignment explanation
Indices: 42850684--42850861 Score: 257
Period size: 96 Copynumber: 1.9 Consensus size: 95
42850674 AGGTCAGGGA
* *
42850684 AATAGTGGCGCTTATGAGAAAACGCCGCAAAAGGTAAGGCAATAGCGGCGCTTATGGGAAAGCGC
1 AATAGCGGCGCTTATGAGAAAACGCCGCAAAAGGTAAGGAAATAGCGGCGCTTATGGGAAAGCGC
*
42850749 CGTAAAAGGTACGGCAACCGCGGGTAAGGC
66 CGCAAAAGGTACGGCAACCGCGGGTAAGGC
* * * * * *
42850779 AATAGCGGCGCTTATGGGAAAGCGTCGCTAAAGGTCAGAGAAATAGCGGCGCTTATGGGTAAGCG
1 AATAGCGGCGCTTATGAGAAAACGCCGCAAAAGGTAAG-GAAATAGCGGCGCTTATGGGAAAGCG
*
42850844 CCGCAAAAGGTAGGGCAA
65 CCGCAAAAGGTACGGCAA
42850862 TAGTGACGCT
Statistics
Matches: 72, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
95 32 0.44
96 40 0.56
ACGTcount: A:0.32, C:0.19, G:0.34, T:0.15
Consensus pattern (95 bp):
AATAGCGGCGCTTATGAGAAAACGCCGCAAAAGGTAAGGAAATAGCGGCGCTTATGGGAAAGCGC
CGCAAAAGGTACGGCAACCGCGGGTAAGGC
Found at i:42850875 original size:40 final size:41
Alignment explanation
Indices: 42850776--42850907 Score: 185
Period size: 41 Copynumber: 3.2 Consensus size: 41
42850766 CCGCGGGTAA
*
42850776 GGCAATAGCGGCGCTTATGGGAAAGCGTCGCTAAAGGTCAG
1 GGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGGTCAG
* * * *
42850817 AGAAATAGCGGCGCTTATGGGTAAGCGCCGCAAAAGGT-AG
1 GGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGGTCAG
* * *
42850857 GGCAATAGTGACGCTTATGGGGAAGCGCCGCTAAAGGTCAG
1 GGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGGTCAG
42850898 GGCAATAGCG
1 GGCAATAGCG
42850908 ACTCAATAAT
Statistics
Matches: 78, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
40 34 0.44
41 44 0.56
ACGTcount: A:0.29, C:0.19, G:0.36, T:0.16
Consensus pattern (41 bp):
GGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGGTCAG
Found at i:42851767 original size:20 final size:21
Alignment explanation
Indices: 42851718--42851767 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
42851708 ATTTTCTAAC
* * *
42851718 CCTTGGTTCTCTTTAGTTTCT
1 CCTTTGTTCTCTTCAGATTCT
42851739 CCTTT-TTCTCTTCAGATT-T
1 CCTTTGTTCTCTTCAGATTCT
42851758 CCTTTGTTCT
1 CCTTTGTTCT
42851768 ATTACCCTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 6 0.24
20 15 0.60
21 4 0.16
ACGTcount: A:0.06, C:0.26, G:0.10, T:0.58
Consensus pattern (21 bp):
CCTTTGTTCTCTTCAGATTCT
Found at i:42854892 original size:42 final size:43
Alignment explanation
Indices: 42854832--42855057 Score: 235
Period size: 42 Copynumber: 5.1 Consensus size: 43
42854822 TGTTAATGGT
*
42854832 GTTTGTG-GAAAAGTGCCGCTAAAGAACATG-TCTTTAGCGGC
1 GTTTGTGAGAAAAGCGCCGCTAAAGAACATGTTCTTTAGCGGC
* *
42854873 GTTTGTGAGAAAAGCGCCGCTAAAGAACATG-ACTTTCGCGGC
1 GTTTGTGAGAAAAGCGCCGCTAAAGAACATGTTCTTTAGCGGC
* *
42854915 GTTTGTGAGAAAAGCGCCGCTAAAGACCACGTTCTTTAGCGGC
1 GTTTGTGAGAAAAGCGCCGCTAAAGAACATGTTCTTTAGCGGC
* *
42854958 GTTTTTG-GGAAAGCGCCGCTAAAGAACAGCTAAAGACCATGTTCTTTAGCGGC
1 GTTTGTGAGAAAAGCGCCGCT----AA-AG----A-A-CATGTTCTTTAGCGGC
* * *
42855011 GTTTGTGAGATAAGCGCTGCTAAAGACCATGTTCTTTAGCGGC
1 GTTTGTGAGAAAAGCGCCGCTAAAGAACATGTTCTTTAGCGGC
42855054 GTTT
1 GTTT
42855058 CTCCTCATAA
Statistics
Matches: 155, Mismatches: 16, Indels: 26
0.79 0.08 0.13
Matches are distributed among these distances:
41 7 0.05
42 72 0.46
43 35 0.23
45 1 0.01
46 2 0.01
47 2 0.01
49 2 0.01
50 2 0.01
51 1 0.01
53 21 0.14
54 10 0.06
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (43 bp):
GTTTGTGAGAAAAGCGCCGCTAAAGAACATGTTCTTTAGCGGC
Found at i:42855013 original size:53 final size:54
Alignment explanation
Indices: 42854933--42855036 Score: 165
Period size: 53 Copynumber: 1.9 Consensus size: 54
42854923 GAAAAGCGCC
* *
42854933 GCTAAAGACCACGTTCTTTAGCGGCGTTTTTGGGA-AAGCGCCGCTAAAGAACA
1 GCTAAAGACCACGTTCTTTAGCGGCGTTTGTGAGATAAGCGCCGCTAAAGAACA
* *
42854986 GCTAAAGACCATGTTCTTTAGCGGCGTTTGTGAGATAAGCGCTGCTAAAGA
1 GCTAAAGACCACGTTCTTTAGCGGCGTTTGTGAGATAAGCGCCGCTAAAGA
42855037 CCATGTTCTT
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
53 32 0.70
54 14 0.30
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (54 bp):
GCTAAAGACCACGTTCTTTAGCGGCGTTTGTGAGATAAGCGCCGCTAAAGAACA
Found at i:42857117 original size:16 final size:16
Alignment explanation
Indices: 42857072--42857122 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
42857062 CCCTAAAACG
42857072 ATAAAATTTT-AATTT
1 ATAAAATTTTAAATTT
* *
42857087 A-GATATTTTATAATTT
1 ATAAAATTTTA-AATTT
*
42857103 ATAAAATTTTAAATTA
1 ATAAAATTTTAAATTT
42857119 ATAA
1 ATAA
42857123 TGGTAAAATT
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
14 6 0.21
15 1 0.04
16 14 0.50
17 7 0.25
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (16 bp):
ATAAAATTTTAAATTT
Found at i:42859300 original size:3 final size:3
Alignment explanation
Indices: 42859294--42859342 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
42859284 ACAAAGAGTG
42859294 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
42859342 G
1 G
42859343 GCCTTTGAAC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.35, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:42859824 original size:3 final size:3
Alignment explanation
Indices: 42859818--42859853 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
42859808 ATAATAATAA
* *
42859818 TAG TAG TAG TAG TTG TAG TTG TAG TAG TAG TAG TAG
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
42859854 AAGTTTGGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.33, T:0.39
Consensus pattern (3 bp):
TAG
Found at i:42870146 original size:33 final size:31
Alignment explanation
Indices: 42870109--42870189 Score: 80
Period size: 30 Copynumber: 2.6 Consensus size: 31
42870099 ATGATTATAT
42870109 TTAAATATTTAAAATATAATTTATATATTCTAA
1 TTAAATATTTAAAATATAATTTAT-TATT-TAA
* *
42870142 TTAAAT-TTTATAA-ATAA-TTATTATTTAC
1 TTAAATATTTAAAATATAATTTATTATTTAA
*
42870170 TAGAAATATTTAAAAT-TAAT
1 T-TAAATATTTAAAATATAAT
42870190 ATTTCATATA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
28 3 0.08
29 8 0.20
30 13 0.32
31 4 0.10
32 6 0.15
33 6 0.15
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.48
Consensus pattern (31 bp):
TTAAATATTTAAAATATAATTTATTATTTAA
Found at i:42871503 original size:31 final size:31
Alignment explanation
Indices: 42871465--42871550 Score: 109
Period size: 31 Copynumber: 2.8 Consensus size: 31
42871455 CACTGGATTG
42871465 TTTGAAAGTTTTTATTTAAGTCATCAAACTA
1 TTTGAAAGTTTTTATTTAAGTCATCAAACTA
* * * *
42871496 TTTGAAAGTTTTCATTTAAGTTACCTAACTA
1 TTTGAAAGTTTTTATTTAAGTCATCAAACTA
** *
42871527 TTCAAAAATTTTTATTTAAGTCAT
1 TTTGAAAGTTTTTATTTAAGTCAT
42871551 TTGGCTATTA
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.35, C:0.10, G:0.08, T:0.47
Consensus pattern (31 bp):
TTTGAAAGTTTTTATTTAAGTCATCAAACTA
Found at i:42873997 original size:31 final size:31
Alignment explanation
Indices: 42873954--42874023 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
42873944 AATTTAACAA
* *
42873954 TTTAATGACTTAAAT-AAAAATTTCCGAATAG
1 TTTAGTGACTTAAATGAAAAATTT-CAAATAG
* *
42873985 TTTAGTGACTTAAATGAAAACTTTTAAATAG
1 TTTAGTGACTTAAATGAAAAATTTCAAATAG
42874016 TTTAGTGA
1 TTTAGTGA
42874024 TCATTTTATA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 27 0.79
32 7 0.21
ACGTcount: A:0.41, C:0.07, G:0.13, T:0.39
Consensus pattern (31 bp):
TTTAGTGACTTAAATGAAAAATTTCAAATAG
Found at i:42886365 original size:46 final size:46
Alignment explanation
Indices: 42886277--42886369 Score: 161
Period size: 47 Copynumber: 2.0 Consensus size: 46
42886267 TACATGGACT
*
42886277 AGCTAAATCAAGTCTCATGACTTCAAATCCATAAAAATTTACAAGA
1 AGCTAAATCAAGTCCCATGACTTCAAATCCATAAAAATTTACAAGA
42886323 AGCTAAATCAAGCTCCCATGACTTCAAATCCATAAAAA-TTACAAGA
1 AGCTAAATCAAG-TCCCATGACTTCAAATCCATAAAAATTTACAAGA
42886369 A
1 A
42886370 AAGGGCTTGA
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
46 21 0.47
47 24 0.53
ACGTcount: A:0.46, C:0.22, G:0.09, T:0.24
Consensus pattern (46 bp):
AGCTAAATCAAGTCCCATGACTTCAAATCCATAAAAATTTACAAGA
Found at i:42891390 original size:33 final size:33
Alignment explanation
Indices: 42891298--42891394 Score: 124
Period size: 32 Copynumber: 3.0 Consensus size: 33
42891288 TTGTGTGATA
* * * *
42891298 ATGCGAACCCACCACGTGCGAACTCAAGTAAAG
1 ATGCAAACTCACCACATGCGAACTCATGTAAAG
* * *
42891331 ATGCAAACTCA-CGCATACGAACTCATGTAAGG
1 ATGCAAACTCACCACATGCGAACTCATGTAAAG
42891363 ATGCAAACTCACCACATGCGAACTCATGTAAA
1 ATGCAAACTCACCACATGCGAACTCATGTAAA
42891395 CGAACTATGC
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
32 27 0.51
33 26 0.49
ACGTcount: A:0.38, C:0.28, G:0.18, T:0.16
Consensus pattern (33 bp):
ATGCAAACTCACCACATGCGAACTCATGTAAAG
Found at i:42904877 original size:21 final size:21
Alignment explanation
Indices: 42904853--42904909 Score: 114
Period size: 21 Copynumber: 2.7 Consensus size: 21
42904843 GATTTTGATC
42904853 ATTTGTTCAAAATTTAATTTA
1 ATTTGTTCAAAATTTAATTTA
42904874 ATTTGTTCAAAATTTAATTTA
1 ATTTGTTCAAAATTTAATTTA
42904895 ATTTGTTCAAAATTT
1 ATTTGTTCAAAATTT
42904910 GCTGCAAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.53
Consensus pattern (21 bp):
ATTTGTTCAAAATTTAATTTA
Found at i:42911538 original size:11 final size:11
Alignment explanation
Indices: 42911514--42911552 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
42911504 TCTTTAAATA
42911514 TAAAATT-A-T
1 TAAAATTAATT
42911523 TAAAATTAATT
1 TAAAATTAATT
*
42911534 TAAAAGTAATT
1 TAAAATTAATT
42911545 TAAAATTA
1 TAAAATTA
42911553 TTTTTTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
9 7 0.27
10 1 0.04
11 18 0.69
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (11 bp):
TAAAATTAATT
Done.