Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D02
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 70731513
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1900000 characters in sequence are not A, C, G, or T
File 43 of 222
Found at i:12771458 original size:81 final size:84
Alignment explanation
Indices: 12771352--12771503 Score: 186
Period size: 81 Copynumber: 1.8 Consensus size: 84
12771342 CACCTATCAT
* * ** **
12771352 CCATCAATTCCTTTGAATCAGAATCATTCATAATTTCACCCTCA-T-CTTT-CAAACAAACCACA
1 CCATCAATTCCTTTCAACCAGAATCACCCATAAGGTCACCCTCATTACTTTCCAAACAAACCACA
*
12771414 GTATCATCATTCGCATTGC
66 CTATCATCATTCGCATTGC
* *
12771433 CCATCAATTCC-TTCAAGCCAGAATCACCCATAAGGTCACCCTGATTATTTTCCAAACAAACCAC
1 CCATCAATTCCTTTCAA-CCAGAATCACCCATAAGGTCACCCTCATTACTTTCCAAACAAACCAC
12771497 ACTATCA
65 ACTATCA
12771504 CCGCACATAT
Statistics
Matches: 58, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
80 4 0.07
81 32 0.55
82 1 0.02
83 3 0.05
84 18 0.31
ACGTcount: A:0.34, C:0.32, G:0.07, T:0.28
Consensus pattern (84 bp):
CCATCAATTCCTTTCAACCAGAATCACCCATAAGGTCACCCTCATTACTTTCCAAACAAACCACA
CTATCATCATTCGCATTGC
Found at i:12785692 original size:18 final size:18
Alignment explanation
Indices: 12785669--12785706 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
12785659 GATAGTGAGT
12785669 CATGTCATGACGTCAAAC
1 CATGTCATGACGTCAAAC
12785687 CATGTCATGACGTCAAAC
1 CATGTCATGACGTCAAAC
12785705 CA
1 CA
12785707 CTTGACATCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.34, C:0.29, G:0.16, T:0.21
Consensus pattern (18 bp):
CATGTCATGACGTCAAAC
Found at i:12792094 original size:15 final size:16
Alignment explanation
Indices: 12792074--12792103 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
12792064 ATTGTATTAT
12792074 TTAATTGTT-TAATAG
1 TTAATTGTTGTAATAG
12792089 TTAATTGTTGTAATA
1 TTAATTGTTGTAATA
12792104 CAATAATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.53
Consensus pattern (16 bp):
TTAATTGTTGTAATAG
Found at i:12799830 original size:39 final size:39
Alignment explanation
Indices: 12799749--12799868 Score: 111
Period size: 39 Copynumber: 2.9 Consensus size: 39
12799739 ATTTGCCGGC
* * * *
12799749 TTACTGA-TCAGGCAC-TTATGTGCCGACTACTGTTACTG
1 TTACTGATTC-GGCACTTTGTGTGTCGAATACTGTTACTA
12799787 TTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACTA
1 TTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACTA
12799826 TTACTG-TTACCGACTCGACACTTTGTGTGTCGAATACTGTTAC
1 TTACTGATT--CG----G-CACTTTGTGTGTCGAATACTGTTAC
12799869 CGTTACTGTT
Statistics
Matches: 69, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
38 14 0.20
39 27 0.39
40 2 0.03
44 1 0.01
45 25 0.36
ACGTcount: A:0.21, C:0.22, G:0.20, T:0.38
Consensus pattern (39 bp):
TTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACTA
Found at i:12799848 original size:45 final size:45
Alignment explanation
Indices: 12799776--12799925 Score: 194
Period size: 45 Copynumber: 3.3 Consensus size: 45
12799766 ATGTGCCGAC
* *
12799776 TACTGTTACTGTTACTGATTCGGCACTTTGTGTGTCGAATACTGT
1 TACTGTTACTGTTACAGATTCGACACTTTGTGTGTCGAATACTGT
* * *
12799821 TACTATTACTGTTACCGACTCGACACTTTGTGTGTCGAATACTGT
1 TACTGTTACTGTTACAGATTCGACACTTTGTGTGTCGAATACTGT
* * * *
12799866 TACCGTTACTGTTACAGGTTC-AGCACTTTGTATGTTGAATACTGT
1 TACTGTTACTGTTACAGATTCGA-CACTTTGTGTGTCGAATACTGT
*
12799911 TACTGTTACCGTTAC
1 TACTGTTACTGTTAC
12799926 TGCTACCGTT
Statistics
Matches: 91, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
44 1 0.01
45 90 0.99
ACGTcount: A:0.21, C:0.20, G:0.19, T:0.40
Consensus pattern (45 bp):
TACTGTTACTGTTACAGATTCGACACTTTGTGTGTCGAATACTGT
Found at i:12799916 original size:6 final size:6
Alignment explanation
Indices: 12799905--12799953 Score: 53
Period size: 6 Copynumber: 7.8 Consensus size: 6
12799895 GTATGTTGAA
* * *
12799905 TACTGT TACTGT TACCGT TACTGC TACCGT TACTGAT TACTGT TCACTG
1 TACTGT TACTGT TACTGT TACTGT TACTGT TACTG-T TACTGT T-ACTG
12799954 GTGTGTTTGG
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
6 25 0.71
7 10 0.29
ACGTcount: A:0.18, C:0.24, G:0.16, T:0.41
Consensus pattern (6 bp):
TACTGT
Found at i:12800573 original size:9 final size:9
Alignment explanation
Indices: 12800556--12800589 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
12800546 GTGAAATGAT
12800556 TTGGTTGAA
1 TTGGTTGAA
*
12800565 TTTGTTGAA
1 TTGGTTGAA
12800574 TTGGTTGAA
1 TTGGTTGAA
12800583 TTGGTTG
1 TTGGTTG
12800590 TGATTTGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.32, T:0.50
Consensus pattern (9 bp):
TTGGTTGAA
Found at i:12801513 original size:42 final size:42
Alignment explanation
Indices: 12801409--12801571 Score: 181
Period size: 43 Copynumber: 3.8 Consensus size: 42
12801399 CAAAAATATC
*
12801409 ATACAATGCCAACGTCCCAGACATGGTCTTACATGTAATCAA
1 ATACAATGCCAACGTCCCAGACATGGTCTTACACGTAATCAA
* * * *
12801451 ATAACGATGTC-ACTGTCCCAGAC-CGAGTCTTACACGTAATCAT
1 AT-ACAATGCCAAC-GTCCCAGACATG-GTCTTACACGTAATCAA
* *
12801494 ATACGATGCCAATGTCCCAGACATGGTCTTACACGTAAATCGCAA
1 ATACAATGCCAACGTCCCAGACATGGTCTTACACGT-AAT--CAA
12801539 AT-CAATGCCAACGTCCCAGACA-GGTCTTACACG
1 ATACAATGCCAACGTCCCAGACATGGTCTTACACG
12801572 ATATCACATA
Statistics
Matches: 102, Mismatches: 11, Indels: 15
0.80 0.09 0.12
Matches are distributed among these distances:
42 32 0.31
43 48 0.47
44 18 0.18
45 4 0.04
ACGTcount: A:0.33, C:0.28, G:0.17, T:0.23
Consensus pattern (42 bp):
ATACAATGCCAACGTCCCAGACATGGTCTTACACGTAATCAA
Found at i:12801566 original size:85 final size:84
Alignment explanation
Indices: 12801409--12801571 Score: 206
Period size: 85 Copynumber: 1.9 Consensus size: 84
12801399 CAAAAATATC
* * *
12801409 ATACAATGCCAACGTCCCAGACATGGTCTTACATGTAATCAAATAACGATGTCACTGTCCCAGAC
1 ATACAATGCCAACGTCCCAGACATGGTCTTACACGTAATCAAAT-ACAATGCCACTGTCCCAGAC
*
12801474 CGAGTCTTACACGTAATCAT
65 AGAGTCTTACACGTAATCAT
* *
12801494 ATACGATGCCAATGTCCCAGACATGGTCTTACACGTAAATCGCAAAT-CAATGCCAAC-GTCCCA
1 ATACAATGCCAACGTCCCAGACATGGTCTTACACGT-AAT--CAAATACAATGCC-ACTGTCCCA
12801557 GACAG-GTCTTACACG
62 GACAGAGTCTTACACG
12801572 ATATCACATA
Statistics
Matches: 68, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
85 43 0.63
86 18 0.26
87 2 0.03
88 5 0.07
ACGTcount: A:0.33, C:0.28, G:0.17, T:0.23
Consensus pattern (84 bp):
ATACAATGCCAACGTCCCAGACATGGTCTTACACGTAATCAAATACAATGCCACTGTCCCAGACA
GAGTCTTACACGTAATCAT
Found at i:12808106 original size:2 final size:2
Alignment explanation
Indices: 12808099--12808135 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
12808089 CTTAACTATA
12808099 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
12808136 AAGTATGTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:12820226 original size:26 final size:27
Alignment explanation
Indices: 12820197--12820255 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 27
12820187 AACCTTAAAG
12820197 TAAAC-TTGTTTTCTCATTTTAATACC
1 TAAACTTTGTTTTCTCATTTTAATACC
* *
12820223 TAAACTTTTTTTTTTCTCATTTTGATACC
1 TAAAC--TTTGTTTTCTCATTTTAATACC
12820252 TAAA
1 TAAA
12820256 GTACTATTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 5 0.18
29 23 0.82
ACGTcount: A:0.27, C:0.17, G:0.03, T:0.53
Consensus pattern (27 bp):
TAAACTTTGTTTTCTCATTTTAATACC
Found at i:12820640 original size:19 final size:19
Alignment explanation
Indices: 12820618--12820677 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 19
12820608 ATAAAAAATA
*
12820618 AAAATAAATAAAATTTATT
1 AAAATAATTAAAATTTATT
* *
12820637 AAAAT-ATTAAATTTTAATA
1 AAAATAATTAAAATTT-ATT
*
12820656 AAAATATTTAAAATTTATT
1 AAAATAATTAAAATTTATT
12820675 AAA
1 AAA
12820678 TATTAGAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
18 8 0.24
19 17 0.52
20 8 0.24
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
AAAATAATTAAAATTTATT
Found at i:12820652 original size:18 final size:18
Alignment explanation
Indices: 12820626--12820682 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
12820616 TAAAAATAAA
12820626 TAAAATTTATTAAAATAT
1 TAAAATTTATTAAAATAT
* *
12820644 TAAATTTTAATAAAAATATT
1 TAAAATTT-ATTAAAATA-T
12820664 TAAAATTTATT-AAATAT
1 TAAAATTTATTAAAATAT
12820681 TA
1 TA
12820683 GAAAAAATCA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
17 3 0.09
18 12 0.36
19 10 0.30
20 8 0.24
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TAAAATTTATTAAAATAT
Found at i:12820706 original size:19 final size:19
Alignment explanation
Indices: 12820684--12820757 Score: 69
Period size: 19 Copynumber: 3.7 Consensus size: 19
12820674 TAAATATTAG
*
12820684 AAAAAATCATAAAAATCAT
1 AAAAAATTATAAAAATCAT
*
12820703 AAAAAAAATTATAAAAAAT-TT
1 --AAAAAATTAT-AAAAATCAT
* *
12820724 TAAAATTTAATAAAAATCAT
1 AAAAAATT-ATAAAAATCAT
12820744 AAAAAATTATAAAA
1 AAAAAATTATAAAA
12820758 TGCAACAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
19 18 0.42
20 9 0.21
21 10 0.23
22 6 0.14
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (19 bp):
AAAAAATTATAAAAATCAT
Found at i:12820707 original size:10 final size:10
Alignment explanation
Indices: 12820684--12820757 Score: 53
Period size: 10 Copynumber: 7.4 Consensus size: 10
12820674 TAAATATTAG
12820684 AAAAAATCAT
1 AAAAAATCAT
12820694 -AAAAATCAT
1 AAAAAATCAT
*
12820703 AAAAAAAATTAT
1 --AAAAAATCAT
**
12820715 AAAAAATTTT
1 AAAAAATCAT
** *
12820725 AAAATTTAAT
1 AAAAAATCAT
12820735 -AAAAATCAT
1 AAAAAATCAT
*
12820744 AAAAAATTAT
1 AAAAAATCAT
12820754 AAAA
1 AAAA
12820758 TGCAACAAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 8
0.74 0.15 0.12
Matches are distributed among these distances:
9 15 0.30
10 27 0.54
12 8 0.16
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (10 bp):
AAAAAATCAT
Found at i:12820718 original size:9 final size:9
Alignment explanation
Indices: 12820600--12820757 Score: 52
Period size: 10 Copynumber: 16.4 Consensus size: 9
12820590 ACATGTGGCA
12820600 AAAAGATTAT
1 AAAA-ATTAT
12820610 AAAAA--AT
1 AAAAATTAT
*
12820617 AAAAATAAAT
1 AAAAAT-TAT
*
12820627 AAAATTTAT
1 AAAAATTAT
*
12820636 TAAAA-TATT
1 AAAAATTA-T
**
12820645 AAATTTTAAT
1 AAAAATT-AT
*
12820655 AAAAATATTT
1 AAAAAT-TAT
*
12820665 AAAATTTATT
1 AAAAATTA-T
* *
12820675 AAATATTAGA
1 AAAAATTA-T
*
12820685 AAAAATCAT
1 AAAAATTAT
*
12820694 AAAAATCATAAA
1 AAAAAT--T-AT
12820706 AAAAATTAT
1 AAAAATTAT
*
12820715 AAAAAATTTT
1 -AAAAATTAT
*
12820725 AAAATTTAAT
1 AAAAATT-AT
*
12820735 AAAAATCAT
1 AAAAATTAT
12820744 AAAAAATTAT
1 -AAAAATTAT
12820754 AAAA
1 AAAA
12820758 TGCAACAAAA
Statistics
Matches: 106, Mismatches: 28, Indels: 29
0.65 0.17 0.18
Matches are distributed among these distances:
7 7 0.07
8 2 0.02
9 29 0.27
10 59 0.56
11 2 0.02
12 7 0.07
ACGTcount: A:0.65, C:0.02, G:0.01, T:0.32
Consensus pattern (9 bp):
AAAAATTAT
Found at i:12820739 original size:29 final size:30
Alignment explanation
Indices: 12820655--12820758 Score: 97
Period size: 29 Copynumber: 3.5 Consensus size: 30
12820645 AAATTTTAAT
* * *
12820655 AAAAATATTTAAAATTTATTAAATATTAGA
1 AAAAATATTTAAAATTTAATAAAAATTATA
* * *
12820685 AAAAATCA-TAAAAATCATAAAAAAAATTATA
1 AAAAAT-ATTTAAAAT-TTAATAAAAATTATA
*
12820716 AAAAAT-TTTAAAATTTAATAAAAATCATA
1 AAAAATATTTAAAATTTAATAAAAATTATA
*
12820745 AAAAAT-TATAAAAT
1 AAAAATATTTAAAAT
12820759 GCAACAAAAG
Statistics
Matches: 60, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
29 25 0.42
30 18 0.30
31 17 0.28
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32
Consensus pattern (30 bp):
AAAAATATTTAAAATTTAATAAAAATTATA
Found at i:12820767 original size:29 final size:29
Alignment explanation
Indices: 12820706--12820767 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
12820696 AAATCATAAA
* * ** *
12820706 AAAAATTATAAAAAATTTTAAAATTTAAT
1 AAAAATCATAAAAAATTATAAAATGCAAC
12820735 AAAAATCATAAAAAATTATAAAATGCAAC
1 AAAAATCATAAAAAATTATAAAATGCAAC
12820764 AAAA
1 AAAA
12820768 GCCCTTTTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (29 bp):
AAAAATCATAAAAAATTATAAAATGCAAC
Found at i:12820962 original size:20 final size:19
Alignment explanation
Indices: 12820925--12820972 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
12820915 ATTTTATATG
12820925 AATTTTAT-ATTTCTTTAC
1 AATTTTATAATTTCTTTAC
12820943 ATATTTTATAATTT-TCTTAC
1 A-ATTTTATAATTTCT-TTAC
*
12820963 AACTTTATAA
1 AATTTTATAA
12820973 AATTTTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 1 0.04
19 16 0.62
20 9 0.35
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.56
Consensus pattern (19 bp):
AATTTTATAATTTCTTTAC
Found at i:12821047 original size:20 final size:19
Alignment explanation
Indices: 12821004--12821065 Score: 79
Period size: 19 Copynumber: 3.2 Consensus size: 19
12820994 TTTCTATATG
12821004 TTTTATAAAATTTTACGAT
1 TTTTATAAAATTTTACGAT
*
12821023 TTTTATAAAATTTTACAGTT
1 TTTTATAAAATTTTAC-GAT
**
12821043 TTTTATAATTTTTTTACGAT
1 TTTTATAA-AATTTTACGAT
12821063 TTT
1 TTT
12821066 GTAATTTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
19 16 0.43
20 15 0.41
21 6 0.16
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.60
Consensus pattern (19 bp):
TTTTATAAAATTTTACGAT
Found at i:12821416 original size:13 final size:13
Alignment explanation
Indices: 12821398--12821422 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12821388 ATAACAAATA
12821398 TAAAAATATATAT
1 TAAAAATATATAT
12821411 TAAAAATATATA
1 TAAAAATATATA
12821423 AAATAGAAGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TAAAAATATATAT
Found at i:12823356 original size:7 final size:7
Alignment explanation
Indices: 12823344--12823371 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
12823334 AGACATAATA
12823344 GTGAAAT
1 GTGAAAT
12823351 GTGAAAT
1 GTGAAAT
12823358 GTGAAAT
1 GTGAAAT
12823365 GTGAAAT
1 GTGAAAT
12823372 TAAATTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.29, T:0.29
Consensus pattern (7 bp):
GTGAAAT
Found at i:12827581 original size:12 final size:12
Alignment explanation
Indices: 12827564--12827588 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12827554 GTAAAAGTGC
12827564 ATATTTTATTAA
1 ATATTTTATTAA
12827576 ATATTTTATTAA
1 ATATTTTATTAA
12827588 A
1 A
12827589 ATTAGTGAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATATTTTATTAA
Found at i:12828790 original size:22 final size:22
Alignment explanation
Indices: 12828742--12828783 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
12828732 AATATAATAG
12828742 CAAAATGACAACAAAGCAACAT
1 CAAAATGACAACAAAGCAACAT
*
12828764 CAAAATGACAATAAA-CAACA
1 CAAAATGACAACAAAGCAACA
12828784 GTGAAAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.62, C:0.21, G:0.07, T:0.10
Consensus pattern (22 bp):
CAAAATGACAACAAAGCAACAT
Found at i:12829727 original size:12 final size:12
Alignment explanation
Indices: 12829710--12829735 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
12829700 CAAAACAGGC
12829710 TTTTAGCGGCGT
1 TTTTAGCGGCGT
12829722 TTTTAGCGGCGT
1 TTTTAGCGGCGT
12829734 TT
1 TT
12829736 AGACAAAAAA
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:0.08, C:0.15, G:0.31, T:0.46
Consensus pattern (12 bp):
TTTTAGCGGCGT
Found at i:12829794 original size:40 final size:38
Alignment explanation
Indices: 12829742--12829861 Score: 127
Period size: 40 Copynumber: 3.1 Consensus size: 38
12829732 GTTTAGACAA
* *
12829742 AAAACG-CACTAAAAATCAAGCTTTAGCGGCGCTTTTAT
1 AAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTT-T
** *
12829780 AAAACCGCCGCTAAAGGTCGAGCATTAGCGGCGCTTTTT
1 AAAA-CGCCGCTAAAAATCAAGCATTAGCGGCGCTTTTT
* *
12829819 GGAAAACGCCGCTAAAAAT-AAGCATTAACGGCGTTTTTT
1 --AAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTTT
12829858 AAAA
1 AAAA
12829862 AGCGTCGCAA
Statistics
Matches: 68, Mismatches: 10, Indels: 9
0.78 0.11 0.10
Matches are distributed among these distances:
37 4 0.06
38 4 0.06
39 20 0.29
40 36 0.53
41 4 0.06
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.24
Consensus pattern (38 bp):
AAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTTT
Found at i:12830001 original size:41 final size:41
Alignment explanation
Indices: 12829914--12830028 Score: 155
Period size: 41 Copynumber: 2.8 Consensus size: 41
12829904 TTTTTGGGGG
12829914 CTTTAGCGGCGTTTTT-ATGAAAGCGCCGCTAATGCTCGAGC
1 CTTTAGCGGCGTTTTTGA-GAAAGCGCCGCTAATGCTCGAGC
* * *
12829955 TTTTAGTGGCTTTTTTGAGAAAGCGCCGCTAATGCTCCG-GC
1 CTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCT-CGAGC
12829996 CTTTAGCGGCGTTTTTGA-AAATGCGCCGCTAAT
1 CTTTAGCGGCGTTTTTGAGAAA-GCGCCGCTAAT
12830029 AATAATAAAA
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
40 3 0.05
41 59 0.91
42 3 0.05
ACGTcount: A:0.19, C:0.23, G:0.26, T:0.32
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCGAGC
Found at i:12830893 original size:33 final size:33
Alignment explanation
Indices: 12830847--12830919 Score: 103
Period size: 33 Copynumber: 2.2 Consensus size: 33
12830837 ATTAAATAAT
* * *
12830847 GTTTAGGGGTTAAGGGTTCAGGG-CTGGGTTAGG
1 GTTTAGGGATTAAGGATCCAGGGTC-GGGTTAGG
12830880 GTTTAGGGATTAAGGATCCAGGGTCGGGTTAGG
1 GTTTAGGGATTAAGGATCCAGGGTCGGGTTAGG
12830913 GTTTAGG
1 GTTTAGG
12830920 ATTTAGATTA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
33 35 0.97
34 1 0.03
ACGTcount: A:0.18, C:0.07, G:0.45, T:0.30
Consensus pattern (33 bp):
GTTTAGGGATTAAGGATCCAGGGTCGGGTTAGG
Found at i:12835927 original size:24 final size:25
Alignment explanation
Indices: 12835900--12835946 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
12835890 TTGATAAATT
12835900 TTATGTGT-GGTG-TTTAATTTTTTG
1 TTAT-TGTCGGTGTTTTAATTTTTTG
*
12835924 TTATTGTCTGTGTTTTAATTTTT
1 TTATTGTCGGTGTTTTAATTTTT
12835947 CATATGTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 3 0.15
24 7 0.35
25 10 0.50
ACGTcount: A:0.13, C:0.02, G:0.19, T:0.66
Consensus pattern (25 bp):
TTATTGTCGGTGTTTTAATTTTTTG
Found at i:12836406 original size:43 final size:43
Alignment explanation
Indices: 12836359--12836475 Score: 198
Period size: 43 Copynumber: 2.7 Consensus size: 43
12836349 CACGATCTAC
*
12836359 AGCGGCGTTTGTGGGTAAAGCGCCGCTAAAGGTCTTGGTCTTT
1 AGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTCTTT
* *
12836402 AGCGGCGTTTGTGGGAAAAGCGCCTCTAAAGGTCTTGGTTTTT
1 AGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTCTTT
*
12836445 AGCGGCGTTTATGGGAAAAGCGCCGCTAAAG
1 AGCGGCGTTTGTGGGAAAAGCGCCGCTAAAG
12836476 TTAGCGACGC
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 69 1.00
ACGTcount: A:0.21, C:0.18, G:0.34, T:0.27
Consensus pattern (43 bp):
AGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTCTTT
Found at i:12837719 original size:20 final size:20
Alignment explanation
Indices: 12837694--12837733 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
12837684 ATATATTAAT
*
12837694 TATATACAAAACTT-AAAATA
1 TATATA-AAAAATTCAAAATA
12837714 TATATAAAAAATTCAAAATA
1 TATATAAAAAATTCAAAATA
12837734 AAAGTTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.30
Consensus pattern (20 bp):
TATATAAAAAATTCAAAATA
Found at i:12838294 original size:27 final size:27
Alignment explanation
Indices: 12838252--12838305 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
12838242 TTGCACTCCA
**
12838252 AAATAGATAATGTTTATTAACTTTGTT
1 AAATAGATAAAATTTATTAACTTTGTT
12838279 AAATAGATAAAATTTATTAACTTTGTT
1 AAATAGATAAAATTTATTAACTTTGTT
12838306 GATGTGATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.41, C:0.04, G:0.09, T:0.46
Consensus pattern (27 bp):
AAATAGATAAAATTTATTAACTTTGTT
Found at i:12841974 original size:20 final size:21
Alignment explanation
Indices: 12841936--12841975 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
12841926 GAAAATATTA
*
12841936 ATAATAACGATAAATAATAAT
1 ATAATAACGATAAACAATAAT
12841957 ATAATAAC-ATAAACAATAA
1 ATAATAACGATAAACAATAA
12841976 ACAATTTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.65, C:0.07, G:0.03, T:0.25
Consensus pattern (21 bp):
ATAATAACGATAAACAATAAT
Found at i:12842189 original size:3 final size:3
Alignment explanation
Indices: 12842181--12842226 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
12842171 AAAAGGGAAC
12842181 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
12842227 CAGAAAACAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:12843833 original size:44 final size:44
Alignment explanation
Indices: 12843783--12843979 Score: 209
Period size: 44 Copynumber: 4.4 Consensus size: 44
12843773 TATCTACAGT
* *
12843783 CTGCTCCACTACAACTTCAAGGAGATAAGACTTGTTATTTCAAC
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTTATTTCAAC
*
12843827 CTGCTCCACTACAACTTCAGGGAGATAAGACTTGTTATTTCAAC
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTTATTTCAAC
* * ** * *** * *
12843871 CTG-TCCCATTGCAACTTCAGGGGGATAAGGTTTATGGCTTCCAT
1 CTGCT-CCACTGCAACTTCAGGGAGATAAGACTTGTTATTTCAAC
* *
12843915 CTGCTCCGCTGCAACTTCAGGGAGATAAGA-TTGATTTATTTTTAAC
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTG--TTA-TTTCAAC
12843961 CTGCTCCACTGCAACTTCA
1 CTGCTCCACTGCAACTTCA
12843980 ATGAGGTCAG
Statistics
Matches: 124, Mismatches: 24, Indels: 8
0.79 0.15 0.05
Matches are distributed among these distances:
43 3 0.02
44 98 0.79
45 2 0.02
46 21 0.17
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (44 bp):
CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTTATTTCAAC
Found at i:12844007 original size:90 final size:87
Alignment explanation
Indices: 12843783--12844009 Score: 212
Period size: 88 Copynumber: 2.6 Consensus size: 87
12843773 TATCTACAGT
* * * *
12843783 CTGCTCCACTACAACTTCAAGGAGATAAGACTTGTTAT-TTCAACCTGCTCCACTACAACTTCAG
1 CTGCTCCACTGCAACTTCAAGGAGGTAAG-GTTG-TATCTTCAATCTGCTCCACTACAACTTCAG
12843847 GGAGATAAGACTTGTTATTTCAAC
64 GGAGATAAGACTTGTTATTTCAAC
* * * * *
12843871 CTG-TCCCATTGCAACTTC-AGGGGGATAAGGTT-TATGGCTTCCATCTGCTCCGCTGCAACTTC
1 CTGCT-CCACTGCAACTTCAAGGAGG-TAAGGTTGTAT--CTTCAATCTGCTCCACTACAACTTC
*
12843933 AGGGAGATAAGA-TTGATTTATTTTTAAC
62 AGGGAGATAAGACTTG--TTA-TTTCAAC
* * *
12843961 CTGCTCCACTGCAACTTCAATGAGGTCAGGTTGGTATCTTCGATCTGCT
1 CTGCTCCACTGCAACTTCAAGGAGGTAAGGTT-GTATCTTCAATCTGCT
12844010 TTGCTGCCAA
Statistics
Matches: 112, Mismatches: 15, Indels: 22
0.75 0.10 0.15
Matches are distributed among these distances:
85 3 0.03
87 10 0.09
88 50 0.45
89 3 0.03
90 38 0.34
91 5 0.04
92 3 0.03
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (87 bp):
CTGCTCCACTGCAACTTCAAGGAGGTAAGGTTGTATCTTCAATCTGCTCCACTACAACTTCAGGG
AGATAAGACTTGTTATTTCAAC
Found at i:12844248 original size:89 final size:89
Alignment explanation
Indices: 12843982--12844253 Score: 364
Period size: 89 Copynumber: 3.1 Consensus size: 89
12843972 CAACTTCAAT
* * * ** * * *
12843982 GAGGTCAGGTTGGTATCTTCGATCTGCTTTGCTGCCAATATAGGAAGACAAGATCTACTATCTTC
1 GAGGTCAGGCTGGTGTCTTCGATCTGCTTCGCTGCCGGTACAGGAAGACAAGATCTGCTATCTTT
* *
12844047 AGTCTGTTCCGCTACAAACTCAAG
66 AGTCTGTTCCGCTGCAAACTCAGG
12844071 GAGGTCAGGCTGGTGTCTTCGATCTGCTTCGCTGCCGGTACAGGAAGACAAGATCTGCTATCTTT
1 GAGGTCAGGCTGGTGTCTTCGATCTGCTTCGCTGCCGGTACAGGAAGACAAGATCTGCTATCTTT
*
12844136 AGTCTGTTCTGCTGCAAACTCAGG
66 AGTCTGTTCCGCTGCAAACTCAGG
* * *
12844160 GAGGTCAGGCTGATGTCTTCGATCTGCTTCGCTGCTGGTACAGGAAGACAAGATCTGCTATTTTT
1 GAGGTCAGGCTGGTGTCTTCGATCTGCTTCGCTGCCGGTACAGGAAGACAAGATCTGCTATCTTT
* ** * **
12844225 AATCTACTCCGCTGTAATTTCAGG
66 AGTCTGTTCCGCTGCAAACTCAGG
12844249 GAGGT
1 GAGGT
12844254 AAAAATTGAT
Statistics
Matches: 162, Mismatches: 21, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
89 162 1.00
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (89 bp):
GAGGTCAGGCTGGTGTCTTCGATCTGCTTCGCTGCCGGTACAGGAAGACAAGATCTGCTATCTTT
AGTCTGTTCCGCTGCAAACTCAGG
Found at i:12845253 original size:51 final size:51
Alignment explanation
Indices: 12845146--12845462 Score: 458
Period size: 51 Copynumber: 6.3 Consensus size: 51
12845136 CTTGCGTATG
** *
12845146 ATCACTTATCACTTGTCCCTGATCAGATAAGTGTAGCT-AAGCTACCACTT
1 ATCACTTGCCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACCACTT
* ** *
12845196 ATCACTTGCCATTTACCACTGATCAGGTAAGTGTAGCTGAAGCTACCACTT
1 ATCACTTGCCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACCACTT
* * *
12845247 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTGAAACTATCACTT
1 ATCACTTGCCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACCACTT
* *
12845298 ATCACTTGCCACTTGCCACTGATCAGATAAGTGTAGCTGAAGCTATCACTT
1 ATCACTTGCCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACCACTT
* *
12845349 ATCACTTGCCACTTGTCACTAATCAGATAAGTGTAGCTGAAGCTATCACTT
1 ATCACTTGCCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACCACTT
* *
12845400 ATCACTTGCCATTTGTCACTGATTAGATAAGTGTAGCTG-AGCTACCACTT
1 ATCACTTGCCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACCACTT
* *
12845450 ATCGCTTGTCACT
1 ATCACTTGCCACT
12845463 GATCAGAAGT
Statistics
Matches: 240, Mismatches: 26, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
50 51 0.21
51 189 0.79
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.32
Consensus pattern (51 bp):
ATCACTTGCCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACCACTT
Found at i:12848567 original size:14 final size:14
Alignment explanation
Indices: 12848548--12848579 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
12848538 TTGCCTCTCA
12848548 TTTTTCTTTTTCAT
1 TTTTTCTTTTTCAT
*
12848562 TTTTTCTTTTTCCT
1 TTTTTCTTTTTCAT
12848576 TTTT
1 TTTT
12848580 ATGAAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTTCTTTTTCAT
Found at i:12853098 original size:16 final size:16
Alignment explanation
Indices: 12853077--12853127 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 16
12853067 AAGAAAGAGC
12853077 AAATACGCTAGTAAAT
1 AAATACGCTAGTAAAT
*
12853093 AAATACGTTAGTAAAT
1 AAATACGCTAGTAAAT
* * *
12853109 AAACATGCGAGTAAAT
1 AAATACGCTAGTAAAT
12853125 AAA
1 AAA
12853128 ATACTAGAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.53, C:0.10, G:0.14, T:0.24
Consensus pattern (16 bp):
AAATACGCTAGTAAAT
Found at i:12854024 original size:19 final size:18
Alignment explanation
Indices: 12853991--12854029 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
12853981 GCAATTTAGA
*
12853991 AACGAAAATATTAATAAT
1 AACGAAAATAATAATAAT
12854009 AACGATAAATAATAATAAT
1 AACGA-AAATAATAATAAT
12854028 AA
1 AA
12854030 TAACAATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.26
Consensus pattern (18 bp):
AACGAAAATAATAATAAT
Found at i:12854027 original size:22 final size:22
Alignment explanation
Indices: 12853997--12854045 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
12853987 TAGAAACGAA
* * *
12853997 AATATTAATAATAACGATAAAT
1 AATAATAATAATAACAATAAAC
12854019 AATAATAATAATAACAATAAAC
1 AATAATAATAATAACAATAAAC
12854041 AATAA
1 AATAA
12854046 ACAATAAACA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.65, C:0.06, G:0.02, T:0.27
Consensus pattern (22 bp):
AATAATAATAATAACAATAAAC
Found at i:12854041 original size:7 final size:7
Alignment explanation
Indices: 12854031--12854057 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
12854021 TAATAATAAT
12854031 AACAATA
1 AACAATA
12854038 AACAATA
1 AACAATA
12854045 AACAATA
1 AACAATA
12854052 AACAAT
1 AACAAT
12854058 TTAAGGCTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.70, C:0.15, G:0.00, T:0.15
Consensus pattern (7 bp):
AACAATA
Found at i:12854265 original size:3 final size:3
Alignment explanation
Indices: 12854257--12854287 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
12854247 AAAAGGGAAC
12854257 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
12854288 CAGAAACACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:12861336 original size:22 final size:21
Alignment explanation
Indices: 12861311--12861366 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
12861301 AATGAAATTA
12861311 TCGAGACTTAAACGATGTTGTC
1 TCGAGACTTAAACGAT-TTGTC
* ** *
12861333 TCGATACTTGTACGGTTTGTC
1 TCGAGACTTAAACGATTTGTC
*
12861354 TCGAGACCTAAAC
1 TCGAGACTTAAAC
12861367 TAATGTAATG
Statistics
Matches: 26, Mismatches: 8, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
21 14 0.54
22 12 0.46
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.32
Consensus pattern (21 bp):
TCGAGACTTAAACGATTTGTC
Found at i:12862284 original size:28 final size:28
Alignment explanation
Indices: 12862252--12862330 Score: 95
Period size: 28 Copynumber: 2.8 Consensus size: 28
12862242 GAATCATTGC
* * *
12862252 AATATAGCACACATTAAATGTTGAGTCA
1 AATATAACACACATTAAACGTTGAATCA
*
12862280 AATATAACACACATTAACCGTTGAATCA
1 AATATAACACACATTAAACGTTGAATCA
** *
12862308 AATATAACATGCATTAAGCGTTG
1 AATATAACACACATTAAACGTTG
12862331 GATCTCCCAT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.43, C:0.16, G:0.13, T:0.28
Consensus pattern (28 bp):
AATATAACACACATTAAACGTTGAATCA
Found at i:12863531 original size:5 final size:5
Alignment explanation
Indices: 12863521--12863549 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
12863511 ACAACCGATC
12863521 TAATT TAATT TAATT TAATT TAATT TAAT
1 TAATT TAATT TAATT TAATT TAATT TAAT
12863550 AATTCAACCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TAATT
Found at i:12863728 original size:4 final size:4
Alignment explanation
Indices: 12863719--12863745 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
12863709 TCTTCCTCAA
12863719 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
12863746 GCATGACATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:12867358 original size:19 final size:20
Alignment explanation
Indices: 12867325--12867369 Score: 67
Period size: 19 Copynumber: 2.3 Consensus size: 20
12867315 CCATATTGCC
12867325 CAAAAAAATAGATGGCGCAAA
1 CAAAAAAATA-ATGGCGCAAA
12867346 CAAAAAAAT-ATGGCGCAAA
1 CAAAAAAATAATGGCGCAAA
12867365 -AAAAA
1 CAAAAA
12867370 CTCTACCGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.21
19 10 0.42
21 9 0.38
ACGTcount: A:0.62, C:0.13, G:0.16, T:0.09
Consensus pattern (20 bp):
CAAAAAAATAATGGCGCAAA
Found at i:12869130 original size:88 final size:88
Alignment explanation
Indices: 12868978--12869379 Score: 606
Period size: 88 Copynumber: 4.6 Consensus size: 88
12868968 GTGAAGATAA
* * *
12868978 CAGATCTTGCCTTCCTACACCGACAGCGAAGCAGATTGAAGACACCAACCTTGTCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAACCTTGCCTCCCTGGGTT
*
12869043 GTAGCGGAGCAGGTTAAAAATAG
66 GCAGCGGAGCAGGTTAAAAATAG
* * * * *
12869066 CAAATCTTGCCTTCCTGCACCGACAGCGAAGTAGATCGAAGATACTAGCCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAACCTTGCCTCCCTGGGTT
12869131 GCAGCGGAGCAGGTTAAAAATAG
66 GCAGCGGAGCAGGTTAAAAATAG
* * * *
12869154 CAGATCTTGCCTTCCTACACCGACAGCGAAGCAGATTGAAGACACTAGCCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAACCTTGCCTCCCTGGGTT
* **
12869219 GTAGCAAAGCAGGTTAAAAATAG
66 GCAGCGGAGCAGGTTAAAAATAG
*
12869242 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAACCTTGCTTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAACCTTGCCTCCCTGGGTT
12869307 GCAGCGGAGCAGGTTAAAAATAG
66 GCAGCGGAGCAGGTTAAAAATAG
* * * * *
12869330 CAGATCTTACCTTCCTGCACCTACAACGAAGCAGATCGATGACCCCAACC
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAACC
12869380 CTATCTCCCT
Statistics
Matches: 284, Mismatches: 30, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
88 284 1.00
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.21
Consensus pattern (88 bp):
CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAACCTTGCCTCCCTGGGTT
GCAGCGGAGCAGGTTAAAAATAG
Found at i:12869163 original size:44 final size:44
Alignment explanation
Indices: 12869027--12869346 Score: 155
Period size: 44 Copynumber: 7.3 Consensus size: 44
12869017 AGACACCAAC
* * * *
12869027 CTTGTCTCCCTGGGTTGTAGCGGAGCAGGTTAAAAATAGCAAAT
1 CTTGCCTCCCTGGGTTGCAGCGAAGCAGGTTAAAAATAGCAGAT
* **** * * ** * *
12869071 CTTGCCTTCCTGCACCGACAGCGAAGTAGATCGAAGATA-CTAG-C
1 CTTGCCTCCCTGGGTTG-CAGCGAAGCAGGTTAAAAATAGC-AGAT
*
12869115 CTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTAAAAATAGCAGAT
1 CTTGCCTCCCTGGGTTGCAGCGAAGCAGGTTAAAAATAGCAGAT
* ***** * * * * *
12869159 CTTGCCTTCCTACACCGACAGCGAAGCAGATTGAAGACA-CTAG-C
1 CTTGCCTCCCTGGGTTG-CAGCGAAGCAGGTTAAAAATAGC-AGAT
* *
12869203 CTTGCCTCCCTGGGTTGTAGCAAAGCAGGTTAAAAATAGCAGAT
1 CTTGCCTCCCTGGGTTGCAGCGAAGCAGGTTAAAAATAGCAGAT
* **** * ** * * * *
12869247 CTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCA-AC
1 CTTGCCTCCCTGGGTTG-CAGCGAAGCAGGTTAAAAATAGCAGAT
* *
12869291 CTTGCTTCCCTGGGTTGCAGCGGAGCAGGTTAAAAATAGCAGAT
1 CTTGCCTCCCTGGGTTGCAGCGAAGCAGGTTAAAAATAGCAGAT
* *
12869335 CTTACCTTCCTG
1 CTTGCCTCCCTG
12869347 CACCTACAAC
Statistics
Matches: 183, Mismatches: 83, Indels: 20
0.64 0.29 0.07
Matches are distributed among these distances:
43 51 0.28
44 83 0.45
45 49 0.27
ACGTcount: A:0.27, C:0.26, G:0.24, T:0.23
Consensus pattern (44 bp):
CTTGCCTCCCTGGGTTGCAGCGAAGCAGGTTAAAAATAGCAGAT
Found at i:12869879 original size:44 final size:44
Alignment explanation
Indices: 12869820--12869941 Score: 140
Period size: 44 Copynumber: 2.8 Consensus size: 44
12869810 AAAGATGGTG
* *
12869820 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCA-A
1 AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAACCACA
* * *
12869863 TAATCCTATCTTCCTGAAGTTGCAATGGAGCGGATTAAAACCACA
1 -AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAACCACA
* * *
12869908 GATCTTATC-TCTCTGAAGTTGCAGTAGAGTAGAT
1 AATCTTATCTTC-CTGAAGTTGCAGTGGAGCAGAT
12869942 CACATCGAGT
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
43 2 0.03
44 62 0.95
45 1 0.02
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (44 bp):
AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAACCACA
Found at i:12870423 original size:21 final size:21
Alignment explanation
Indices: 12870383--12870454 Score: 87
Period size: 19 Copynumber: 3.4 Consensus size: 21
12870373 AAGGATACGT
12870383 AATCTTAGATATGA--TATGC
1 AATCTTAGATATGATTTATGC
12870402 AATCTTAGATATGATTTATGC
1 AATCTTAGATATGATTTATGC
*
12870423 AATCTTAGAAGATATGATTT-TGT
1 AATCTT---AGATATGATTTATGC
12870446 AATCTTAGA
1 AATCTTAGA
12870455 GATTTAATTT
Statistics
Matches: 47, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
19 14 0.30
20 3 0.06
21 11 0.23
23 8 0.17
24 11 0.23
ACGTcount: A:0.36, C:0.08, G:0.15, T:0.40
Consensus pattern (21 bp):
AATCTTAGATATGATTTATGC
Found at i:12870453 original size:23 final size:24
Alignment explanation
Indices: 12870389--12870454 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 24
12870379 ACGTAATCTT
12870389 AGATATGA--TATGCAATCTT---
1 AGATATGATTTATGCAATCTTAGA
12870408 AGATATGATTTATGCAATCTTAGA
1 AGATATGATTTATGCAATCTTAGA
*
12870432 AGATATGATTT-TGTAATCTTAGA
1 AGATATGATTTATGCAATCTTAGA
12870455 GATTTAATTT
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
19 8 0.20
21 11 0.27
23 11 0.27
24 11 0.27
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.39
Consensus pattern (24 bp):
AGATATGATTTATGCAATCTTAGA
Found at i:12870784 original size:20 final size:20
Alignment explanation
Indices: 12870728--12870787 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 20
12870718 CTTTTTTTAT
* *
12870728 TTATTATTTATTTTTATTAAAT
1 TTATTA-TTATTGTTATT-AAG
*
12870750 TTGATT-TTCTTGTTATTAAG
1 TT-ATTATTATTGTTATTAAG
12870770 TTATTATTATTGTTATTA
1 TTATTATTATTGTTATTA
12870788 TTACCAATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
19 3 0.09
20 15 0.47
21 9 0.28
22 2 0.06
23 3 0.09
ACGTcount: A:0.27, C:0.02, G:0.07, T:0.65
Consensus pattern (20 bp):
TTATTATTATTGTTATTAAG
Found at i:12870965 original size:17 final size:17
Alignment explanation
Indices: 12870934--12870977 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
12870924 CATAACTTTT
*
12870934 ATATACA-TATATATAC
1 ATATACATTTTATATAC
*
12870950 ATTTACATTTTATATAC
1 ATATACATTTTATATAC
12870967 ATATACATTTT
1 ATATACATTTT
12870978 TTATTTCCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 6 0.25
17 18 0.75
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.48
Consensus pattern (17 bp):
ATATACATTTTATATAC
Found at i:12871082 original size:24 final size:24
Alignment explanation
Indices: 12871055--12871101 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
12871045 ATACGTATGT
12871055 TTTTTTATAT-TATTCTTCATAAAA
1 TTTTTTATATATATTCTTC-TAAAA
*
12871079 TTTTTTATATATATTTTTCTAAA
1 TTTTTTATATATATTCTTCTAAA
12871102 TTAATTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (24 bp):
TTTTTTATATATATTCTTCTAAAA
Found at i:12871414 original size:23 final size:21
Alignment explanation
Indices: 12871346--12871414 Score: 56
Period size: 23 Copynumber: 3.2 Consensus size: 21
12871336 GTTATTGATT
12871346 TATT-TTTATTTATT-TATT-
1 TATTGTTTATTTATTCTATTG
12871364 TATTTGTTTATATTATTTCTA-TG
1 TA-TTGTTTAT-TTA-TTCTATTG
12871387 CTATTGTTGTATTTATTACTATTG
1 -TATTGTT-TATTTATT-CTATTG
12871411 TATT
1 TATT
12871415 TGTTATCACG
Statistics
Matches: 41, Mismatches: 0, Indels: 15
0.73 0.00 0.27
Matches are distributed among these distances:
18 2 0.05
19 2 0.05
20 5 0.12
21 3 0.07
22 5 0.12
23 17 0.41
24 7 0.17
ACGTcount: A:0.22, C:0.04, G:0.07, T:0.67
Consensus pattern (21 bp):
TATTGTTTATTTATTCTATTG
Found at i:12872765 original size:17 final size:16
Alignment explanation
Indices: 12872724--12872765 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
12872714 AAATATATCA
12872724 TTTAAAA-ATAATTTT
1 TTTAAAATATAATTTT
**
12872739 TTTATGATATGAATTTT
1 TTTAAAATAT-AATTTT
12872756 TTTAAAATAT
1 TTTAAAATAT
12872766 TACACAACAA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
15 5 0.24
16 2 0.10
17 14 0.67
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (16 bp):
TTTAAAATATAATTTT
Found at i:12877477 original size:14 final size:14
Alignment explanation
Indices: 12877456--12877489 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
12877446 TGGTATGGGT
12877456 TTAT-GGGTTTTGG
1 TTATAGGGTTTTGG
12877469 TTATAGGGTTTTGG
1 TTATAGGGTTTTGG
12877483 TTATAGG
1 TTATAGG
12877490 CAAATAATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (14 bp):
TTATAGGGTTTTGG
Found at i:12883585 original size:6 final size:6
Alignment explanation
Indices: 12883574--12883599 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
12883564 TTTATCATTT
12883574 TAATCA TAATCA TAATCA TAATCA TA
1 TAATCA TAATCA TAATCA TAATCA TA
12883600 TTTTATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (6 bp):
TAATCA
Found at i:12887869 original size:26 final size:26
Alignment explanation
Indices: 12887806--12887889 Score: 89
Period size: 26 Copynumber: 3.2 Consensus size: 26
12887796 ATATTGAAAT
*
12887806 AATTTTCTCAAAATTTTATCGAGGGTA
1 AATTTT-TCAAAATTTTATCGGGGGTA
* ***
12887833 AAATCGCCAAAATTTTATCGGGGGTA
1 AATTTTTCAAAATTTTATCGGGGGTA
*
12887859 AATTTTTCAAAAATTTTA-CTGGGGTA
1 AATTTTTC-AAAATTTTATCGGGGGTA
12887885 AATTT
1 AATTT
12887890 GCGATAAGAA
Statistics
Matches: 46, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
26 34 0.74
27 12 0.26
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.38
Consensus pattern (26 bp):
AATTTTTCAAAATTTTATCGGGGGTA
Found at i:12900062 original size:2 final size:2
Alignment explanation
Indices: 12900057--12900086 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
12900047 TATATATATA
12900057 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
12900087 AGTGATAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:12920535 original size:18 final size:18
Alignment explanation
Indices: 12920512--12920546 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12920502 TGTCTCTTCT
*
12920512 ACCTTTTCCCCTTCCTCG
1 ACCTTTGCCCCTTCCTCG
*
12920530 ACCTTTGCCTCTTCCTC
1 ACCTTTGCCCCTTCCTC
12920547 TGAAAGAATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.06, C:0.49, G:0.06, T:0.40
Consensus pattern (18 bp):
ACCTTTGCCCCTTCCTCG
Found at i:12924730 original size:50 final size:54
Alignment explanation
Indices: 12924668--12924806 Score: 169
Period size: 50 Copynumber: 2.6 Consensus size: 54
12924658 TGATCATAAC
* *
12924668 ATGCCAAAGCCATGTCCTAGACATGGTCTTACGGGGGACCT-C-TCATCTC-GG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACAGGGGACCTCCATCATCTCAGG
* * *
12924719 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCGCATGATCTCAAGG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACAGGGGACCTC-CATCATCTC-AGG
* *
12924774 ATGCCAATGCCATGTCCCAAACATGGTCTTACA
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACA
12924807 TGAGATCTCT
Statistics
Matches: 75, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
50 36 0.48
52 1 0.01
53 6 0.08
55 2 0.03
56 30 0.40
ACGTcount: A:0.24, C:0.30, G:0.22, T:0.23
Consensus pattern (54 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACAGGGGACCTCCATCATCTCAGG
Found at i:12925189 original size:30 final size:30
Alignment explanation
Indices: 12925155--12925212 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
12925145 CCTCGAATCT
*
12925155 AACTTTGGCAAAATTACAATTTTGCCCCTA
1 AACTTTGACAAAATTACAATTTTGCCCCTA
* * *
12925185 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTGACAAAATTACAATTTTGCCCC
12925213 ATGGCTCGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (30 bp):
AACTTTGACAAAATTACAATTTTGCCCCTA
Found at i:12941470 original size:103 final size:98
Alignment explanation
Indices: 12941259--12941458 Score: 215
Period size: 103 Copynumber: 2.0 Consensus size: 98
12941249 TTATAGGCCA
** * *
12941259 AAAAGTATCGATACCTTTTTGGCCCAGTATCGATAATTTTTGAATTATCGATACCATTAAAAGCG
1 AAAAGTATCGATACCTTTTTGGCAAAGTATCGATAATTTTTGAAATATCGATACCATTAAAAACG
* *
12941324 ATACCAAAATAACATTCTCTTTTTGAAAAACCC
66 ATACCAAAATAACATTCTCTTTCTAAAAAACCC
* * *
12941357 AATTAAGTATCGATACC-TTTTGGTAAAGTATCGAT-ATTTTCTTAAATATCGATATCCCGTCTT
1 AA--AAGTATCGATACCTTTTTGGCAAAGTATCGATAATTTT-TGAAATATCGATA--CC--ATT
* *
12941420 AAAAACGATACCAAAATAACATTTTGTTTCTAACAAAAC
59 AAAAACGATACCAAAATAACATTCTCTTTCTAA-AAAAC
12941459 TTACAAAGTA
Statistics
Matches: 83, Mismatches: 11, Indels: 10
0.80 0.11 0.10
Matches are distributed among these distances:
98 7 0.08
99 26 0.31
100 13 0.16
101 2 0.02
103 30 0.36
104 5 0.06
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34
Consensus pattern (98 bp):
AAAAGTATCGATACCTTTTTGGCAAAGTATCGATAATTTTTGAAATATCGATACCATTAAAAACG
ATACCAAAATAACATTCTCTTTCTAAAAAACCC
Found at i:12944862 original size:6 final size:6
Alignment explanation
Indices: 12944842--12944902 Score: 104
Period size: 6 Copynumber: 9.8 Consensus size: 6
12944832 TTAAACTAAG
12944842 TAAAAA TAAATAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA
1 TAAAAA T-AA-AAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA
12944892 TAAAAA TAAAA
1 TAAAAA TAAAA
12944903 CTTTACAACT
Statistics
Matches: 53, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
6 45 0.85
7 4 0.08
8 4 0.08
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (6 bp):
TAAAAA
Found at i:12947857 original size:15 final size:13
Alignment explanation
Indices: 12947831--12947882 Score: 61
Period size: 12 Copynumber: 3.8 Consensus size: 13
12947821 GAATATTTAC
12947831 ATAAAAATTAAACTA
1 ATAAAAA-TAAA-TA
12947846 AGTAAAAATAAATA
1 A-TAAAAATAAATA
*
12947860 AAAAAAATAAA-A
1 ATAAAAATAAATA
12947872 ATAAAAATAAA
1 ATAAAAATAAA
12947883 ACTTTACAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
12 11 0.32
13 9 0.26
14 3 0.09
15 5 0.15
16 6 0.18
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (13 bp):
ATAAAAATAAATA
Found at i:12947862 original size:9 final size:10
Alignment explanation
Indices: 12947848--12947876 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
12947838 TTAAACTAAG
12947848 TAAAAATAAA
1 TAAAAATAAA
12947858 TAAAAA-AAA
1 TAAAAATAAA
12947867 TAAAAATAAA
1 TAAAAATAAA
12947877 AATAAAACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (10 bp):
TAAAAATAAA
Found at i:12947871 original size:6 final size:6
Alignment explanation
Indices: 12947848--12947883 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
12947838 TTAAACTAAG
*
12947848 TAAAAA TAAATAA AAAAAA TAAAAA TAAAAA TAAAA
1 TAAAAA TAAA-AA TAAAAA TAAAAA TAAAAA TAAAA
12947884 CTTTACAACT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
6 22 0.81
7 5 0.19
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
TAAAAA
Found at i:12948536 original size:45 final size:44
Alignment explanation
Indices: 12948486--12948590 Score: 112
Period size: 45 Copynumber: 2.4 Consensus size: 44
12948476 GAATGAACAG
* *
12948486 AAAATGAGAAATGAGAAACATTG-AGAAATGATTAT-GGTTTTCTCC
1 AAAATGAGAAATGAGAAACATTGCA-AAATGAATATAGG-TTTC-CA
*
12948531 AAAATGGAGAAATGA-AATCATTGCAAAATGAATATAGGTTTCCA
1 AAAAT-GAGAAATGAGAAACATTGCAAAATGAATATAGGTTTCCA
12948575 AAAATG-GAAATG-GAAA
1 AAAATGAGAAATGAGAAA
12948591 TAGAAATGGA
Statistics
Matches: 52, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
42 8 0.15
43 1 0.02
44 6 0.12
45 25 0.48
46 12 0.23
ACGTcount: A:0.48, C:0.08, G:0.20, T:0.25
Consensus pattern (44 bp):
AAAATGAGAAATGAGAAACATTGCAAAATGAATATAGGTTTCCA
Found at i:12948587 original size:6 final size:6
Alignment explanation
Indices: 12948576--12948639 Score: 119
Period size: 6 Copynumber: 10.7 Consensus size: 6
12948566 AGGTTTCCAA
*
12948576 AAATGG AAATGG AAATAG AAATGG AAATGG AAATGG AAATGG AAATGG
1 AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG
12948624 AAATGG AAATGG AAAT
1 AAATGG AAATGG AAAT
12948640 AAAAAAGAAA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 56 1.00
ACGTcount: A:0.53, C:0.00, G:0.30, T:0.17
Consensus pattern (6 bp):
AAATGG
Found at i:12948651 original size:18 final size:18
Alignment explanation
Indices: 12948575--12948656 Score: 76
Period size: 18 Copynumber: 4.6 Consensus size: 18
12948565 TAGGTTTCCA
*
12948575 AAAATGGAAATGGAAATAG
1 AAAATGGAAAT-GAAAAAG
* *
12948594 -AAATGGAAATGGAAATG
1 AAAATGGAAATGAAAAAG
* * *
12948611 GAAATGGAAATGGAAATG
1 AAAATGGAAATGAAAAAG
* *
12948629 GAAATGGAAATAAAAAAG
1 AAAATGGAAATGAAAAAG
12948647 AAAATGGAAA
1 AAAATGGAAA
12948657 CTTGCAATCT
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
17 4 0.07
18 51 0.93
ACGTcount: A:0.59, C:0.00, G:0.27, T:0.15
Consensus pattern (18 bp):
AAAATGGAAATGAAAAAG
Found at i:12948830 original size:26 final size:26
Alignment explanation
Indices: 12948801--12948860 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
12948791 TTTTTTCAAA
*
12948801 ATTTTATTAAGGCTAGAATCGTAAAT
1 ATTTTATTAAGGCTAAAATCGTAAAT
* * * * *
12948827 ATTTTACTAGGGGTAAAATTGTCAAT
1 ATTTTATTAAGGCTAAAATCGTAAAT
12948853 ATTTTATT
1 ATTTTATT
12948861 GGGATAAAAT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.43
Consensus pattern (26 bp):
ATTTTATTAAGGCTAAAATCGTAAAT
Found at i:12952629 original size:80 final size:80
Alignment explanation
Indices: 12952496--12952657 Score: 324
Period size: 80 Copynumber: 2.0 Consensus size: 80
12952486 CATAAACGGA
12952496 TCTAGGATCTATTCTACTTAGTTCATGTTCGATGTAGTGTCAGTTTTGTCAGTCATATCTATGTC
1 TCTAGGATCTATTCTACTTAGTTCATGTTCGATGTAGTGTCAGTTTTGTCAGTCATATCTATGTC
12952561 TTTATCTTTTAGGAT
66 TTTATCTTTTAGGAT
12952576 TCTAGGATCTATTCTACTTAGTTCATGTTCGATGTAGTGTCAGTTTTGTCAGTCATATCTATGTC
1 TCTAGGATCTATTCTACTTAGTTCATGTTCGATGTAGTGTCAGTTTTGTCAGTCATATCTATGTC
12952641 TTTATCTTTTAGGAT
66 TTTATCTTTTAGGAT
12952656 TC
1 TC
12952658 ATTTGCTTTG
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 82 1.00
ACGTcount: A:0.20, C:0.15, G:0.17, T:0.48
Consensus pattern (80 bp):
TCTAGGATCTATTCTACTTAGTTCATGTTCGATGTAGTGTCAGTTTTGTCAGTCATATCTATGTC
TTTATCTTTTAGGAT
Found at i:12956956 original size:51 final size:53
Alignment explanation
Indices: 12956875--12956989 Score: 155
Period size: 51 Copynumber: 2.2 Consensus size: 53
12956865 ATTTCTGAGT
* *
12956875 CATTTTCA-TTTAGGAGAAAACCACATTCATTTCCAAATGATT-CCACTTCTC
1 CATTTTTATTTTAGGAGAAAACCACAATCATTTCCAAATGATTCCCACTTCTC
* * * *
12956926 CATTTTTATTTTA-GAGAAAACCATAATCATTTCCAAATGTTTCCCATTTCTT
1 CATTTTTATTTTAGGAGAAAACCACAATCATTTCCAAATGATTCCCACTTCTC
12956978 CATTTTTATTTT
1 CATTTTTATTTT
12956990 CATTTTCGAG
Statistics
Matches: 56, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
51 33 0.59
52 23 0.41
ACGTcount: A:0.30, C:0.21, G:0.06, T:0.43
Consensus pattern (53 bp):
CATTTTTATTTTAGGAGAAAACCACAATCATTTCCAAATGATTCCCACTTCTC
Found at i:12960538 original size:25 final size:25
Alignment explanation
Indices: 12960462--12960543 Score: 89
Period size: 25 Copynumber: 3.3 Consensus size: 25
12960452 CAGCTCATGA
*
12960462 GAGCATATCGATTTATAGCTCGTGA-
1 GAGCATATCGATTCATAGCTCGT-AT
**
12960487 GAGCATATCGA-TCA-ACGACTCAAAT
1 GAGCATATCGATTCATA-G-CTCGTAT
12960512 GAGCATATCGATTCATAGCTCGTAT
1 GAGCATATCGATTCATAGCTCGTAT
12960537 GAGCATA
1 GAGCATA
12960544 CTCGTATATG
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
23 1 0.02
24 4 0.09
25 37 0.79
26 4 0.09
27 1 0.02
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.27
Consensus pattern (25 bp):
GAGCATATCGATTCATAGCTCGTAT
Found at i:12966457 original size:25 final size:26
Alignment explanation
Indices: 12966432--12966514 Score: 100
Period size: 25 Copynumber: 3.3 Consensus size: 26
12966422 CACCTCGTGA
* *
12966432 GAGCATACCAATTTATAGCTCATGA-
1 GAGCATACCGATTTACAGCTCATGAT
* *
12966457 GAGCATACCGATCTACAGCTCA-AAT
1 GAGCATACCGATTTACAGCTCATGAT
*
12966482 GAGCATACCGATTCACAGCTCAT-AT
1 GAGCATACCGATTTACAGCTCATGAT
12966507 GAGCATAC
1 GAGCATAC
12966515 TTGTACATGA
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
24 1 0.02
25 49 0.98
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.23
Consensus pattern (26 bp):
GAGCATACCGATTTACAGCTCATGAT
Found at i:12977083 original size:2 final size:2
Alignment explanation
Indices: 12977076--12977104 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12977066 CAATAATAAA
12977076 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
12977105 TATATATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:12980461 original size:2 final size:2
Alignment explanation
Indices: 12980454--12980488 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
12980444 ATCAACATCA
12980454 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
12980489 TATATAATCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:12984269 original size:19 final size:21
Alignment explanation
Indices: 12984242--12984280 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
12984232 ATTTAATTTA
12984242 ATTTAATTTAAT-TAAAAATT
1 ATTTAATTTAATCTAAAAATT
*
12984262 ATTT-ATTTTATCTAAAAAT
1 ATTTAATTTAATCTAAAAAT
12984281 ACAAAACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (21 bp):
ATTTAATTTAATCTAAAAATT
Found at i:12993464 original size:64 final size:64
Alignment explanation
Indices: 12993327--12993502 Score: 167
Period size: 64 Copynumber: 2.8 Consensus size: 64
12993317 GTGCAGGGTT
* * * * *
12993327 CACACGGGTAAGACACACGGGCATGTG-CCAGGCCGTGTAACTCTCTGTGTTAGGATTTGTAGC
1 CACACGGGCAAGACACACGGGCGTGTGTCCAGGCCGTGTAACTCTCTGAGTTAGGATTTGGAGA
* ** * * * *
12993390 CATATAGGCAAAACACACGGGCGTGTGTCCAGGCTGTGTAACTCAT-TGAGTTCGTATTTGGAGA
1 CACACGGGCAAGACACACGGGCGTGTGTCCAGGCCGTGTAACTC-TCTGAGTTAGGATTTGGAGA
* * * * * *
12993454 CACACGGGCAAGAGACAAGGGCGTGTGTTCAAGCCATGTAACTCACTGA
1 CACACGGGCAAGACACACGGGCGTGTGTCCAGGCCGTGTAACTCTCTGA
12993503 CTTCAGATTT
Statistics
Matches: 87, Mismatches: 23, Indels: 5
0.76 0.20 0.04
Matches are distributed among these distances:
63 21 0.24
64 65 0.75
65 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.29, T:0.23
Consensus pattern (64 bp):
CACACGGGCAAGACACACGGGCGTGTGTCCAGGCCGTGTAACTCTCTGAGTTAGGATTTGGAGA
Found at i:12994122 original size:60 final size:60
Alignment explanation
Indices: 12994024--12994146 Score: 165
Period size: 60 Copynumber: 2.0 Consensus size: 60
12994014 TCTGTATCTA
* * *
12994024 TACCGTATGACATATACATCTGATCGTATTTCTGTTATATGTGAATTTGTACTAATATGC
1 TACCATATGACATATACATCTGATCGTATTTCTGTTATACGTGAATCTGTACTAATATGC
* * * * * *
12994084 TACCATATGACATGTGCATCTGATCGTATTTGTGTTATACGTGCATCTGTATTAATCTGC
1 TACCATATGACATATACATCTGATCGTATTTCTGTTATACGTGAATCTGTACTAATATGC
12994144 TAC
1 TAC
12994147 GTATAAGCAC
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 54 1.00
ACGTcount: A:0.26, C:0.17, G:0.16, T:0.41
Consensus pattern (60 bp):
TACCATATGACATATACATCTGATCGTATTTCTGTTATACGTGAATCTGTACTAATATGC
Found at i:12998190 original size:2 final size:2
Alignment explanation
Indices: 12998183--12998209 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12998173 AACGAAATAA
12998183 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
12998210 TAAAAGAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:13001773 original size:21 final size:21
Alignment explanation
Indices: 13001747--13001788 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
13001737 CAATGAATTA
*
13001747 ACTTTTCTTGTTTTGATTTTG
1 ACTTTTCTTGTTTCGATTTTG
13001768 ACTTTTCTTGTTTCGATTTTG
1 ACTTTTCTTGTTTCGATTTTG
13001789 TTGATCACCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.10, C:0.12, G:0.14, T:0.64
Consensus pattern (21 bp):
ACTTTTCTTGTTTCGATTTTG
Found at i:13004627 original size:44 final size:44
Alignment explanation
Indices: 13004564--13004653 Score: 162
Period size: 44 Copynumber: 2.0 Consensus size: 44
13004554 TAAAATCATA
*
13004564 AGATATGCTTGTTATATGTGATGAATTTCAGTATAATAGCAAAG
1 AGATATGCTTGTTATATGTGATGAATTTCAGTATAATAGAAAAG
*
13004608 AGATATGCTTGTTATATGTGATGAATTTCAGTGTAATAGAAAAG
1 AGATATGCTTGTTATATGTGATGAATTTCAGTATAATAGAAAAG
13004652 AG
1 AG
13004654 CATACTTAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.37, C:0.06, G:0.22, T:0.36
Consensus pattern (44 bp):
AGATATGCTTGTTATATGTGATGAATTTCAGTATAATAGAAAAG
Found at i:13010797 original size:21 final size:21
Alignment explanation
Indices: 13010771--13010822 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
13010761 TCATATAGTT
13010771 GAAGAAGCTACCTG-GAAACAA
1 GAAGAAGCTACCTGAG-AACAA
*
13010792 GAAGAAGCTACCTGAGAACCA
1 GAAGAAGCTACCTGAGAACAA
13010813 GAAGAAGCTA
1 GAAGAAGCTA
13010823 TGAAAGTGCA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 28 0.97
22 1 0.03
ACGTcount: A:0.46, C:0.19, G:0.25, T:0.10
Consensus pattern (21 bp):
GAAGAAGCTACCTGAGAACAA
Found at i:13012081 original size:41 final size:41
Alignment explanation
Indices: 13012033--13012182 Score: 191
Period size: 41 Copynumber: 3.7 Consensus size: 41
13012023 ATTGGGTGTT
13012033 ATTCAGGCTTTGTGCCTAGCAGGCTTAATGTCGGTGTATTG
1 ATTCAGGCTTTGTGCCTAGCAGGCTTAATGTCGGTGTATTG
* * *
13012074 ATTCAGGCTTTGTGCCTAGCAGGCTTAGTGCCAGTGTATTG
1 ATTCAGGCTTTGTGCCTAGCAGGCTTAATGTCGGTGTATTG
* * * *
13012115 ATTCAGGCTTTGTGCCTAGGAGACTT-A-GT-GCTAGTGTT-
1 ATTCAGGCTTTGTGCCTAGCAGGCTTAATGTCGGT-GTATTG
*
13012153 ATTCAGGCTTAGTGCCTAGCAGGCTTAATG
1 ATTCAGGCTTTGTGCCTAGCAGGCTTAATG
13012183 CCAGCGTTAC
Statistics
Matches: 93, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
38 24 0.26
39 6 0.06
40 1 0.01
41 62 0.67
ACGTcount: A:0.19, C:0.18, G:0.29, T:0.35
Consensus pattern (41 bp):
ATTCAGGCTTTGTGCCTAGCAGGCTTAATGTCGGTGTATTG
Found at i:13012168 original size:38 final size:38
Alignment explanation
Indices: 13012028--13012238 Score: 244
Period size: 38 Copynumber: 5.4 Consensus size: 38
13012018 TTCAAATTGG
*
13012028 GTGTTATTCAGGCTTTGTGCCTAGCAGGCTTAATGTCGGT-
1 GTGTTATTCAGGCTTTGTGCCTAGCAGGCTT-A-GT-GCTA
* *
13012068 GTATTGATTCAGGCTTTGTGCCTAGCAGGCTTAGTGCCA
1 GTGTT-ATTCAGGCTTTGTGCCTAGCAGGCTTAGTGCTA
* *
13012107 GTGTATTGATTCAGGCTTTGTGCCTAGGAGACTTAGTGCTA
1 GTG--TT-ATTCAGGCTTTGTGCCTAGCAGGCTTAGTGCTA
* * *
13012148 GTGTTATTCAGGCTTAGTGCCTAGCAGGCTTAATGCCA
1 GTGTTATTCAGGCTTTGTGCCTAGCAGGCTTAGTGCTA
* * * *
13012186 GCGTTACTCAGGCTTTGTGCCTAGGAGACTTAGTGCTA
1 GTGTTATTCAGGCTTTGTGCCTAGCAGGCTTAGTGCTA
13012224 GTGTTATTCAGGCTT
1 GTGTTATTCAGGCTT
13012239 AATGCTAGCG
Statistics
Matches: 146, Mismatches: 21, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
38 73 0.50
39 6 0.04
40 5 0.03
41 62 0.42
ACGTcount: A:0.18, C:0.18, G:0.28, T:0.35
Consensus pattern (38 bp):
GTGTTATTCAGGCTTTGTGCCTAGCAGGCTTAGTGCTA
Found at i:13012224 original size:76 final size:76
Alignment explanation
Indices: 13012030--13012247 Score: 278
Period size: 76 Copynumber: 2.8 Consensus size: 76
13012020 CAAATTGGGT
* * * * *
13012030 GTTATTCAGGCTTTGTGCCTAGCAGGCTTAATGTCGGT-GTATTGATTCAGGCTTTGTGCCTAGC
1 GTTATTCAGGCTTTGTGCCTAGGAGACTT-A-GT-GCTAGTGTT-ATTCAGGCTTAGTGCCTAGC
* *
13012094 AGGCTTAGTGCCAGT
62 AGGCTTAATGCCAGC
13012109 GTATTGATTCAGGCTTTGTGCCTAGGAGACTTAGTGCTAGTGTTATTCAGGCTTAGTGCCTAGCA
1 G--TT-ATTCAGGCTTTGTGCCTAGGAGACTTAGTGCTAGTGTTATTCAGGCTTAGTGCCTAGCA
13012174 GGCTTAATGCCAGC
63 GGCTTAATGCCAGC
* *
13012188 GTTACTCAGGCTTTGTGCCTAGGAGACTTAGTGCTAGTGTTATTCAGGCTTAATG-CTAGC
1 GTTATTCAGGCTTTGTGCCTAGGAGACTTAGTGCTAGTGTTATTCAGGCTTAGTGCCTAGC
13012248 GTTACTCAGG
Statistics
Matches: 126, Mismatches: 9, Indels: 12
0.86 0.06 0.08
Matches are distributed among these distances:
75 5 0.04
76 50 0.40
77 2 0.02
79 36 0.29
80 6 0.05
81 3 0.02
82 24 0.19
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.34
Consensus pattern (76 bp):
GTTATTCAGGCTTTGTGCCTAGGAGACTTAGTGCTAGTGTTATTCAGGCTTAGTGCCTAGCAGGC
TTAATGCCAGC
Found at i:13012244 original size:22 final size:22
Alignment explanation
Indices: 13012214--13012262 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
13012204 GCCTAGGAGA
* * *
13012214 CTTAGTGCTAGTGTTATTCAGG
1 CTTAATGCTAGCGTTACTCAGG
13012236 CTTAATGCTAGCGTTACTCAGG
1 CTTAATGCTAGCGTTACTCAGG
13012258 CTTAA
1 CTTAA
13012263 AGCCTAGTAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.37
Consensus pattern (22 bp):
CTTAATGCTAGCGTTACTCAGG
Found at i:13018048 original size:114 final size:113
Alignment explanation
Indices: 13017598--13018038 Score: 458
Period size: 114 Copynumber: 3.8 Consensus size: 113
13017588 AAAATAAGCA
* * * *
13017598 TTAGCGGCGTTTTTGAGAAAGCGCCGC-AAAAAACCTAAGCCCAACGACGT-CGTTTCCCGAGCT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCAAACGAC-TCCATTTTCTGAGCT
* * * * *
13017661 TTCAGGGATTTAGCGGCGTTTCTAAGAAAGCACCGCTAATGCTCAGGGCT
65 TTCGGGGATTTAGCGGCGTTTTTAAG-AAGCGCTGCTAATGCTCAGGGAT
* *
13017711 TTAGCGGCGTTTTCAGGAAGTGTTTTTGGGAAAGCGCCGCAAAAAAACCTAAGCCAAACGACGCC
1 TTAGC-G-G----C-------GTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCAAACGACTCC
* * * *
13017776 GTTTTCTAATCTTTCGGGGGTTTAGCGGCGTTTTTAAGGAAGCG-TCGCTAATGCTCAGGGAT
53 ATTTTCTGAGCTTTCGGGGATTTAGCGGCGTTTTTAA-GAAGCGCT-GCTAATGCTCAGGGAT
* * *
13017838 TTAGCGGCGTTTTTGATAAAGCGCTGCAAAAAAACCTAAGCCCAACGA-TGCCATTTTCTGAGCT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCAAACGACT-CCATTTTCTGAGCT
* * *
13017902 TTCAGGGATTTAGCGGCATTTTTAAGGAAGCGCTGCTAATGCTCAGGGCT
65 TTCGGGGATTTAGCGGCGTTTTTAA-GAAGCGCTGCTAATGCTCAGGGAT
* * *
13017952 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACTTAAGCCTAACGACTCCATTTTTTGAGCTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCAAACGACTCCATTTTCTGAGCTT
*
13018017 TCGGGGATTTAGCGGTGTTTTT
66 TCGGGGATTTAGCGGCGTTTTT
13018039 GGAAAAGCGC
Statistics
Matches: 275, Mismatches: 33, Indels: 39
0.79 0.10 0.11
Matches are distributed among these distances:
113 5 0.02
114 169 0.61
115 3 0.01
119 1 0.00
121 1 0.00
125 1 0.00
126 19 0.07
127 75 0.27
128 1 0.00
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.28
Consensus pattern (113 bp):
TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCAAACGACTCCATTTTCTGAGCTT
TCGGGGATTTAGCGGCGTTTTTAAGAAGCGCTGCTAATGCTCAGGGAT
Found at i:13018320 original size:15 final size:15
Alignment explanation
Indices: 13018302--13018332 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
13018292 TACACTTTAA
13018302 GGTTTAGGGAGTATG
1 GGTTTAGGGAGTATG
*
13018317 GGTTTAGGGATTATG
1 GGTTTAGGGAGTATG
13018332 G
1 G
13018333 ATTAGGGGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.45, T:0.35
Consensus pattern (15 bp):
GGTTTAGGGAGTATG
Found at i:13018590 original size:15 final size:15
Alignment explanation
Indices: 13018570--13018616 Score: 62
Period size: 14 Copynumber: 3.3 Consensus size: 15
13018560 TATTTTCAGG
*
13018570 TTTAGGGAGTATGGA
1 TTTAGGGATTATGGA
13018585 TTTAGGGATTAT-GA
1 TTTAGGGATTATGGA
*
13018599 ATTAGGGATTATGG-
1 TTTAGGGATTATGGA
13018613 TTTA
1 TTTA
13018617 AGGGTTGGGA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 16 0.57
15 12 0.43
ACGTcount: A:0.28, C:0.00, G:0.32, T:0.40
Consensus pattern (15 bp):
TTTAGGGATTATGGA
Found at i:13018637 original size:21 final size:22
Alignment explanation
Indices: 13018600--13018652 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
13018590 GGATTATGAA
*
13018600 TTAGGGA-TTATGGTTTAAGGG
1 TTAGGGATTTAAGGTTTAAGGG
*
13018621 TT-GGGATTTAAGGTTTAGGGG
1 TTAGGGATTTAAGGTTTAAGGG
*
13018642 TTAGGGGTTTA
1 TTAGGGATTTA
13018653 GGGGTTAGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 4 0.15
21 16 0.59
22 7 0.26
ACGTcount: A:0.21, C:0.00, G:0.40, T:0.40
Consensus pattern (22 bp):
TTAGGGATTTAAGGTTTAAGGG
Found at i:13018645 original size:7 final size:7
Alignment explanation
Indices: 13018635--13018673 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
13018625 GATTTAAGGT
13018635 TTAGGGG
1 TTAGGGG
13018642 TTAGGGG
1 TTAGGGG
13018649 TTTAGGGG
1 -TTAGGGG
**
13018657 TTAGATG
1 TTAGGGG
13018664 TTAGGGG
1 TTAGGGG
13018671 TTA
1 TTA
13018674 AGATTAGTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 20 0.74
8 7 0.26
ACGTcount: A:0.18, C:0.00, G:0.46, T:0.36
Consensus pattern (7 bp):
TTAGGGG
Found at i:13018652 original size:15 final size:15
Alignment explanation
Indices: 13018631--13018673 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
13018621 TTGGGATTTA
13018631 AGGTTTAGGGGTTAG
1 AGGTTTAGGGGTTAG
*
13018646 GGGTTTAGGGGTTAG
1 AGGTTTAGGGGTTAG
*
13018661 ATG-TTAGGGGTTA
1 AGGTTTAGGGGTTA
13018674 AGATTAGTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.19, C:0.00, G:0.47, T:0.35
Consensus pattern (15 bp):
AGGTTTAGGGGTTAG
Found at i:13018660 original size:22 final size:22
Alignment explanation
Indices: 13018618--13018672 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
13018608 TATGGTTTAA
* *
13018618 GGGTT-GGGATTTAAGGTTTAG
1 GGGTTAGGGGTTTAAGGGTTAG
*
13018639 GGGTTAGGGGTTTAGGGGTTAG
1 GGGTTAGGGGTTTAAGGGTTAG
**
13018661 ATGTTAGGGGTT
1 GGGTTAGGGGTT
13018673 AAGATTAGTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 5 0.18
22 23 0.82
ACGTcount: A:0.16, C:0.00, G:0.47, T:0.36
Consensus pattern (22 bp):
GGGTTAGGGGTTTAAGGGTTAG
Found at i:13019434 original size:19 final size:19
Alignment explanation
Indices: 13019410--13019446 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
13019400 AAAAACGCCG
13019410 TAAAAAATAAATCAATTTA
1 TAAAAAATAAATCAATTTA
*
13019429 TAAAAAATAAATTAATTT
1 TAAAAAATAAATCAATTT
13019447 TTAGAATAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAAAAATAAATCAATTTA
Found at i:13019645 original size:279 final size:276
Alignment explanation
Indices: 13019268--13020319 Score: 1469
Period size: 279 Copynumber: 3.8 Consensus size: 276
13019258 ATTTTATAAA
* * * * * **
13019268 AAATCAATTTATAAAAAATAAAATAAAAAATTTTGGCATAGCAAAATGGCGTCGTTTTGTTTTAA
1 AAATCAATTTATAAAAAAT-AAAT--TAATTTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAA
13019333 ATGAAAAAAATTTTGCGGCGTTTTATGAAAAGCGCCGCTAAAGGTAGGCAATAGCGGCGTTTGTT
63 ATGAAAAAAA-TTTGCGGCGTTTTATGAAAAGCGCCGCTAAAGGTAGGCAATAGCGGCGTTTGTT
*
13019398 ATAAAAACGCCGTAAAAAATAAATCAATTTATAAAAAATAAATTAATTTTTAGAATAGCAAAACG
127 ATAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAATAAATTAATTTTTAGAATAGCAAAACG
*
13019463 GCGTCGTTTTGTTCAAAATGAAAAAATTTTGTGGCGCTTTAAAGTTAGGCAATAGCGGCGTTTGT
192 GCGTCGTTTTGTTCAAAATGAAAAAATTTTGTAGCGCTTTAAAGTTAGGCAATAGCGGCGTTTGT
13019528 TATAAAAACGCCGCAAAAAAT
257 TATAAAAACGCCGC-AAAAAT
* *
13019549 AAATCAATTTATAAAAAATAAATTAATTTTTAGAATAGGAAAACAGCGTCGTTTTGTTCAAAATG
1 AAATCAATTTATAAAAAATAAATTAATTTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATG
13019614 AAAAAGAAATTTGCGGCGTTTTATGAAAAGCGCCGCTAAAGGTAGGCAATAGCGGCGTTTGTTAT
66 -AAAA-AAATTTGCGGCGTTTTATGAAAAGCGCCGCTAAAGGTAGGCAATAGCGGCGTTTGTTAT
*
13019679 AAAAACGCCGCAAAAAATAAATTAATTTATAAAAAATAAATTAATTTTTAGAATAGCAAAACGGC
129 AAAAACGCCGCAAAAAATAAATCAATTTATAAAAAATAAATTAATTTTTAGAATAGCAAAACGGC
** *
13019744 GTCGTTTTGTTCAAAATGAAAAAATTTTGCTTAAAGCGCCGCTAAAGGTAGGCAATAGCGGCGTT
194 GTCGTTTTGTTCAAAATGAAAAAATTTTG--T--AGCG-CTTTAAAGTTAGGCAATAGCGGCGTT
* *
13019809 TATTATAAAAACGCCGTAAAAAT
254 TGTTATAAAAACGCCGCAAAAAT
* * *
13019832 AAATCAATTTATAAAAAATAGATTAATTTTTAGAATAGCAAGACGGCATCGTTTTGTTCAAAATG
1 AAATCAATTTATAAAAAATAAATTAATTTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATG
*
13019897 AAAAAATTTTGCGGCGCTTTTATGAAAAGCGCCGCTAAAGGTAGGCAATAGCGGCGTTTGTTATA
66 AAAAAAATTTGCGGCG-TTTTATGAAAAGCGCCGCTAAAGGTAGGCAATAGCGGCGTTTGTTATA
*
13019962 AAAACGCCGCAAAAAATAAATCAATTTAT-AAAAATAAATTAATTTTTAGAATAGCAAAATGGCG
130 AAAACGCCGCAAAAAATAAATCAATTTATAAAAAATAAATTAATTTTTAGAATAGCAAAACGGCG
*
13020026 TCGTTTTGTTCAAAATGAAAAAATTTTGCAGCGCTTTCATAAAGCGCCGCTAAAGGTAGGCAATA
195 TCGTTTTGTTCAAAATGAAAAAATTTTGTAGCGC-TT--TAAA-----G-T-----TAGGCAATA
13020091 GCGGCGTTTGTTATAAAAACGCCGCAAAAA-
246 GCGGCGTTTGTTATAAAAACGCCGCAAAAAT
*
13020121 AAATCAATTTATAAAAAATAAATTAATTTTTAGAATAGCAAAACGGCGTCTTTTTGTTCAAAATG
1 AAATCAATTTATAAAAAATAAATTAATTTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATG
*
13020186 AAAAAAATTTGCGGCG--CT-T------------T---GGTAGGCAATAGCGGCGTTTGTTATAA
66 AAAAAAATTTGCGGCGTTTTATGAAAAGCGCCGCTAAAGGTAGGCAATAGCGGCGTTTGTTATAA
* * *
13020233 AAACGCCGAAAAAAATAAATTAATTTATAAAAAATAAATTAATTTTTAGAATAACAAAACGGCGT
131 AAACGCCGCAAAAAATAAATCAATTTATAAAAAATAAATTAATTTTTAGAATAGCAAAACGGCGT
13020298 CGTTTTGTTCAAAATGAAAAAA
196 CGTTTTGTTCAAAATGAAAAAA
13020320 ATAAAGCGCC
Statistics
Matches: 707, Mismatches: 41, Indels: 56
0.88 0.05 0.07
Matches are distributed among these distances:
270 53 0.07
271 56 0.08
273 1 0.00
276 1 0.00
277 4 0.01
278 33 0.05
279 156 0.22
280 7 0.01
281 93 0.13
282 80 0.11
283 69 0.10
284 39 0.06
285 1 0.00
286 1 0.00
289 76 0.11
290 37 0.05
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (276 bp):
AAATCAATTTATAAAAAATAAATTAATTTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATG
AAAAAAATTTGCGGCGTTTTATGAAAAGCGCCGCTAAAGGTAGGCAATAGCGGCGTTTGTTATAA
AAACGCCGCAAAAAATAAATCAATTTATAAAAAATAAATTAATTTTTAGAATAGCAAAACGGCGT
CGTTTTGTTCAAAATGAAAAAATTTTGTAGCGCTTTAAAGTTAGGCAATAGCGGCGTTTGTTATA
AAAACGCCGCAAAAAT
Found at i:13019962 original size:146 final size:145
Alignment explanation
Indices: 13019502--13020205 Score: 1121
Period size: 146 Copynumber: 4.9 Consensus size: 145
13019492 TGTGGCGCTT
*
13019502 TAAAGTTAGGCAATAGCGGCGTTTGTTATAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAA
1 TAAAGGTAGGCAATAGCGGCGTTTGTTATAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAA
* * *
13019567 TAAATTAATTTTTAGAATAGGAAAACAGCGTCGTTTTGTTCAAAATGAAAAAGAAATTTGCGGCG
66 TAAATTAATTTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATG-AAAA-AATTTTGCGGCG
13019632 -TTTTATGAAAAGCGCCGC
129 CTTTTAT--AAAGCGCCGC
*
13019650 TAAAGGTAGGCAATAGCGGCGTTTGTTATAAAAACGCCGCAAAAAATAAATTAATTTATAAAAAA
1 TAAAGGTAGGCAATAGCGGCGTTTGTTATAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAA
13019715 TAAATTAATTTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAATTTT-----GC-
66 TAAATTAATTTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAATTTTGCGGCGCT
13019774 --T-TAAAGCGCCGC
131 TTTATAAAGCGCCGC
* *
13019786 TAAAGGTAGGCAATAGCGGCGTTTATTATAAAAACGCCG-TAAAAATAAATCAATTTATAAAAAA
1 TAAAGGTAGGCAATAGCGGCGTTTGTTATAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAA
* * *
13019850 TAGATTAATTTTTAGAATAGCAAGACGGCATCGTTTTGTTCAAAATGAAAAAATTTTGCGGCGCT
66 TAAATTAATTTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAATTTTGCGGCGCT
13019915 TTTATGAAAAGCGCCGC
131 TTTAT--AAAGCGCCGC
13019932 TAAAGGTAGGCAATAGCGGCGTTTGTTATAAAAACGCCGCAAAAAATAAATCAATTTAT-AAAAA
1 TAAAGGTAGGCAATAGCGGCGTTTGTTATAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAA
* *
13019996 TAAATTAATTTTTAGAATAGCAAAATGGCGTCGTTTTGTTCAAAATGAAAAAATTTTGCAGCGCT
66 TAAATTAATTTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAATTTTGCGGCGCT
*
13020061 TTCATAAAGCGCCGC
131 TTTATAAAGCGCCGC
13020076 TAAAGGTAGGCAATAGCGGCGTTTGTTATAAAAACGCCGC-AAAAA-AAATCAATTTATAAAAAA
1 TAAAGGTAGGCAATAGCGGCGTTTGTTATAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAA
* *
13020139 TAAATTAATTTTTAGAATAGCAAAACGGCGTCTTTTTGTTCAAAATGAAAAAAATTTGCGGCGCT
66 TAAATTAATTTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAATTTTGCGGCGCT
13020204 TT
131 TT
13020206 GGTAGGCAAT
Statistics
Matches: 519, Mismatches: 23, Indels: 33
0.90 0.04 0.06
Matches are distributed among these distances:
135 77 0.15
136 48 0.09
138 1 0.00
139 1 0.00
140 2 0.00
141 1 0.00
142 12 0.02
143 74 0.14
144 51 0.10
146 122 0.24
147 22 0.04
148 108 0.21
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.29
Consensus pattern (145 bp):
TAAAGGTAGGCAATAGCGGCGTTTGTTATAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAA
TAAATTAATTTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAATTTTGCGGCGCT
TTTATAAAGCGCCGC
Found at i:13020216 original size:126 final size:128
Alignment explanation
Indices: 13020080--13020321 Score: 434
Period size: 128 Copynumber: 1.9 Consensus size: 128
13020070 CGCCGCTAAA
*
13020080 GGTAGGCAATAGCGGCGTTTGTTATAAAAACGCCG-CAAAAA-AAATCAATTTATAAAAAATAAA
1 GGTAGGCAATAGCGGCGTTTGTTATAAAAACGCCGAAAAAAATAAATCAATTTATAAAAAATAAA
* *
13020143 TTAATTTTTAGAATAGCAAAACGGCGTCTTTTTGTTCAAAATGAAAAAAATTTGCGGCGCTTT
66 TTAATTTTTAGAATAACAAAACGGCGTCGTTTTGTTCAAAATGAAAAAAATTTGCGGCGCTTT
*
13020206 GGTAGGCAATAGCGGCGTTTGTTATAAAAACGCCGAAAAAAATAAATTAATTTATAAAAAATAAA
1 GGTAGGCAATAGCGGCGTTTGTTATAAAAACGCCGAAAAAAATAAATCAATTTATAAAAAATAAA
13020271 TTAATTTTTAGAATAACAAAACGGCGTCGTTTTGTTCAAAATGAAAAAAAT
66 TTAATTTTTAGAATAACAAAACGGCGTCGTTTTGTTCAAAATGAAAAAAAT
13020322 AAAGCGCCGC
Statistics
Matches: 110, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
126 35 0.32
127 5 0.05
128 70 0.64
ACGTcount: A:0.43, C:0.11, G:0.17, T:0.29
Consensus pattern (128 bp):
GGTAGGCAATAGCGGCGTTTGTTATAAAAACGCCGAAAAAAATAAATCAATTTATAAAAAATAAA
TTAATTTTTAGAATAACAAAACGGCGTCGTTTTGTTCAAAATGAAAAAAATTTGCGGCGCTTT
Found at i:13025149 original size:20 final size:19
Alignment explanation
Indices: 13025105--13025151 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
13025095 AAAAATAAAA
13025105 TAAAATAAAATATTTATCAT
1 TAAAATAAAATATTTA-CAT
*
13025125 AAAAATAAATATTATTTA-AT
1 TAAAATAAA-A-TATTTACAT
13025145 TAAAATA
1 TAAAATA
13025152 TATTTTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 16 0.70
21 1 0.04
22 6 0.26
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAAATAAAATATTTACAT
Found at i:13025281 original size:43 final size:42
Alignment explanation
Indices: 13025213--13025528 Score: 353
Period size: 43 Copynumber: 7.4 Consensus size: 42
13025203 AAAGGTTTAT
* * * * *
13025213 TCTTTAGTGGCATTTGTGATAAAAGCGCCGCTAAAGTTCATGT
1 TCTTTAGCGGCGTTTGTG-GAAAAGCGCCGCTAAAGGTCATGG
* * *
13025256 TTTTTAGCGGCGTTTATAGAAAAAGCGCCGCTAAAGGTCATGG
1 TCTTTAGCGGCGTTTGT-GGAAAAGCGCCGCTAAAGGTCATGG
13025299 TCTTTAGCGGCGTTTGTGTGAAAAGCGCCGCTAAAGGTCATGG
1 TCTTTAGCGGCGTTTGTG-GAAAAGCGCCGCTAAAGGTCATGG
*
13025342 TCTTTAGCGGCGTTTGTGTGAAAAGCGCCGCTAAAGGTCAGGG
1 TCTTTAGCGGCGTTTGTG-GAAAAGCGCCGCTAAAGGTCATGG
** * * *
13025385 TCTACAGCGGCGTTTGTGGGAGAAGCGCCGCTAAATGTCAGGG
1 TCTTTAGCGGCGTTTGT-GGAAAAGCGCCGCTAAAGGTCATGG
* * * * * *
13025428 TCTATAGCGACGTTTTTTGGATAAGCGCCACTAAAGGTCATGA
1 TCTTTAGCGGCG-TTTGTGGAAAAGCGCCGCTAAAGGTCATGG
* * * *
13025471 TCTTTAGCGGCGTTTCTTGAAATGCGCCGCTAAAGGTCATGA
1 TCTTTAGCGGCGTTTGTGGAAAAGCGCCGCTAAAGGTCATGG
13025513 TCTTTTAGCGGCGTTT
1 TC-TTTAGCGGCGTTT
13025529 ATTTCTGAAA
Statistics
Matches: 238, Mismatches: 30, Indels: 10
0.86 0.11 0.04
Matches are distributed among these distances:
42 28 0.12
43 204 0.86
44 6 0.03
ACGTcount: A:0.23, C:0.19, G:0.29, T:0.29
Consensus pattern (42 bp):
TCTTTAGCGGCGTTTGTGGAAAAGCGCCGCTAAAGGTCATGG
Found at i:13027372 original size:55 final size:58
Alignment explanation
Indices: 13027266--13027396 Score: 178
Period size: 55 Copynumber: 2.3 Consensus size: 58
13027256 TTAATATGAA
* * * *
13027266 AATAATTATATTGAGAATGTTATTAAATTATATATTATTTTTATTAAATTATATTTAAT
1 AATAATTATATT-AAAATATGATTAAATTATATATTATTATTATTAAATTATATTTAAT
13027325 AATAATTATATTAAAATATGATTAAA-T-TAT-TTATTATTATTAAATTATATTTAAT
1 AATAATTATATTAAAATATGATTAAATTATATATTATTATTATTAAATTATATTTAAT
**
13027380 AATAATCCTATTAAAAT
1 AATAATTATATTAAAAT
13027397 TTAATAACAA
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
55 39 0.59
56 3 0.05
57 1 0.02
58 11 0.17
59 12 0.18
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.50
Consensus pattern (58 bp):
AATAATTATATTAAAATATGATTAAATTATATATTATTATTATTAAATTATATTTAAT
Found at i:13029145 original size:39 final size:40
Alignment explanation
Indices: 13029102--13029184 Score: 100
Period size: 40 Copynumber: 2.1 Consensus size: 40
13029092 GCCCGGCCCG
13029102 AATATATAAT-AAATA--TTTTTTTTATTTTTTTAATTTTAA
1 AATAT-TAATAAAATACTTTTTTTTTA-TTTTTTAATTTTAA
** *
13029141 AATATTTTTAAAATACTTTTTTTTTATTTTTTATTTTTAA
1 AATATTAATAAAATACTTTTTTTTTATTTTTTAATTTTAA
13029181 AATA
1 AATA
13029185 AATTTTTGGT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
38 2 0.05
39 10 0.26
40 17 0.45
41 9 0.24
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (40 bp):
AATATTAATAAAATACTTTTTTTTTATTTTTTAATTTTAA
Found at i:13030019 original size:20 final size:21
Alignment explanation
Indices: 13029994--13030035 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
13029984 TTGTAAATTA
13029994 ATTTAATT-TTT-TGATTTATT
1 ATTTAATTGTTTATGA-TTATT
13030014 ATTTAATTGTTTATGATTATT
1 ATTTAATTGTTTATGATTATT
13030035 A
1 A
13030036 ATTGAGTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 8 0.40
21 9 0.45
22 3 0.15
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (21 bp):
ATTTAATTGTTTATGATTATT
Found at i:13038213 original size:13 final size:13
Alignment explanation
Indices: 13038195--13038233 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
13038185 AGATAAATTG
13038195 AACATCTTTTTGT
1 AACATCTTTTTGT
*
13038208 AACATC-TTTAGTT
1 AACATCTTTTTG-T
13038221 AACATCTTTTTGT
1 AACATCTTTTTGT
13038234 TGATATTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 4 0.18
13 14 0.64
14 4 0.18
ACGTcount: A:0.26, C:0.15, G:0.08, T:0.51
Consensus pattern (13 bp):
AACATCTTTTTGT
Found at i:13041334 original size:21 final size:21
Alignment explanation
Indices: 13041310--13041350 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
13041300 TGGCTTAAAA
*
13041310 GCATGGTCGTG-AGGCTACTTT
1 GCATGCTCGTGTA-GCTACTTT
13041331 GCATGCTCGTGTAGCTACTT
1 GCATGCTCGTGTAGCTACTT
13041351 CACACACCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.15, C:0.22, G:0.29, T:0.34
Consensus pattern (21 bp):
GCATGCTCGTGTAGCTACTTT
Found at i:13045712 original size:12 final size:12
Alignment explanation
Indices: 13045692--13045724 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
13045682 TTTACACTAC
13045692 ATTTATTTTGAT
1 ATTTATTTTGAT
*
13045704 ATTTGTTTTGAT
1 ATTTATTTTGAT
13045716 -TTTATTTTG
1 ATTTATTTTG
13045725 CAACTATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.18, C:0.00, G:0.12, T:0.70
Consensus pattern (12 bp):
ATTTATTTTGAT
Found at i:13050871 original size:41 final size:40
Alignment explanation
Indices: 13050805--13051122 Score: 216
Period size: 41 Copynumber: 7.8 Consensus size: 40
13050795 ATTTTTAAAC
* *
13050805 CTTTAGCGGCGTTTTTA-CTTTAGCGCCGCTAATTCTCCGAT
1 CTTTAGCGGCGTTTTTATC-TGAGCGCCGCTAATTCT-TGAT
* * **
13050846 CTTTAGCGGCATTTTTATCTGAGCGCCACTAATGT-TCTGGC
1 CTTTAGCGGCGTTTTTATCTGAGCGCCGCTAAT-TCT-TGAT
* * * *
13050887 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGTAT
1 CTTTAGCGGCGTTTTTATCTGAGCGCCGCTAATTCTTG-AT
* * * * * * *
13050928 CATTAGTGGCGTTATTGTCTGAGTGCCACTAATTCTTTGTT
1 CTTTAGCGGCGTTTTTATCTGAGCGCCGCTAATTC-TTGAT
* * *
13050969 CTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGTTCGTG-T
1 CTTTAGCGGCGTTTTTATCTGAGCGCCGCT-AA-TTCTTGAT
* * * * **
13051010 TTTTAGTGGCGTTTTTATCTGAGCGCCACTAATACTCTGGC
1 CTTTAGCGGCGTTTTTATCTGAGCGCCGCTAATTCT-TGAT
* * * *
13051051 CTTTAGCGGCGTTTTATATGTAAGCGCCGCTAATGC-T-AC
1 CTTTAGCGGCGTTTT-TATCTGAGCGCCGCTAATTCTTGAT
*
13051090 CTTTAGCGGCGTTTTT-TCCGAAGCGCCGCTAAT
1 CTTTAGCGGCGTTTTTATCTG-AGCGCCGCTAAT
13051123 AGTAACAAAA
Statistics
Matches: 217, Mismatches: 49, Indels: 25
0.75 0.17 0.09
Matches are distributed among these distances:
37 1 0.00
38 13 0.06
39 18 0.08
40 6 0.03
41 152 0.70
42 24 0.11
43 3 0.01
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.38
Consensus pattern (40 bp):
CTTTAGCGGCGTTTTTATCTGAGCGCCGCTAATTCTTGAT
Found at i:13050949 original size:82 final size:80
Alignment explanation
Indices: 13050804--13051087 Score: 318
Period size: 82 Copynumber: 3.5 Consensus size: 80
13050794 GATTTTTAAA
* * * * *
13050804 CCTTTAGCGGCGTTTTTACTTTAGCGCCGCTAATTCTCCG-ATCTTTAGCGGCATTTTTATCTGA
1 CCTTTAGCGGCGTTTTTTC-TAAGCGCCGCTAATGCT-CGTATCTTTAGTGGCGTTTTTATCTGA
13050868 GCGCCACTAATGTTCTGG
64 GCGCCACTAAT-TTCTGG
* * *
13050886 CCTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGTATCATTAGTGGCGTTATTGTCTGAG
1 CCTTTAGCGGCGTTTTT-TCTAAGCGCCGCTAATGCTCGTATCTTTAGTGGCGTTTTTATCTGAG
* * *
13050951 TGCCACTAATTCTTTGT
65 CGCCACTAATT-TCTGG
* * * * *
13050968 TCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGTTCGTGTTTTTAGTGGCGTTTTTATCTGAG
1 CCTTTAGCGGCG-TTTTTTCTAAGCGCCGCTAATGCTCGTATCTTTAGTGGCGTTTTTATCTGAG
*
13051033 CGCCACTAATACTCTGG
65 CGCCACTAAT-TTCTGG
*
13051050 CCTTTAGCGGCGTTTTATATGTAAGCGCCGCTAATGCT
1 CCTTTAGCGGCGTTTT-T-TCTAAGCGCCGCTAATGCT
13051088 ACCTTTAGCG
Statistics
Matches: 168, Mismatches: 27, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
81 7 0.04
82 139 0.83
83 22 0.13
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.38
Consensus pattern (80 bp):
CCTTTAGCGGCGTTTTTTCTAAGCGCCGCTAATGCTCGTATCTTTAGTGGCGTTTTTATCTGAGC
GCCACTAATTTCTGG
Found at i:13051660 original size:15 final size:15
Alignment explanation
Indices: 13051639--13051676 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
13051629 TTTAAGGTTA
13051639 ATTTAGGGGTTGGAG
1 ATTTAGGGGTTGGAG
* *
13051654 GTTTAGGGGTTTGAG
1 ATTTAGGGGTTGGAG
13051669 ATTTAGGG
1 ATTTAGGG
13051677 TTTCAACGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.18, C:0.00, G:0.45, T:0.37
Consensus pattern (15 bp):
ATTTAGGGGTTGGAG
Found at i:13051679 original size:14 final size:14
Alignment explanation
Indices: 13051612--13051679 Score: 52
Period size: 15 Copynumber: 4.9 Consensus size: 14
13051602 GACTGGGTAT
*
13051612 AGATTTAAGGTTTG
1 AGATTTAGGGTTTG
* *
13051626 GGATTTAAGG-TT-
1 AGATTTAGGGTTTG
*
13051638 A-ATTTAGGGGTTGG
1 AGATTTA-GGGTTTG
*
13051652 AGGTTTAGGGGTTTG
1 AGATTTA-GGGTTTG
13051667 AGATTTAGGGTTT
1 AGATTTAGGGTTT
13051680 CAACGGTCAT
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
11 5 0.12
12 2 0.05
13 3 0.07
14 16 0.37
15 17 0.40
ACGTcount: A:0.22, C:0.00, G:0.37, T:0.41
Consensus pattern (14 bp):
AGATTTAGGGTTTG
Found at i:13053426 original size:8 final size:10
Alignment explanation
Indices: 13053404--13053440 Score: 65
Period size: 10 Copynumber: 3.7 Consensus size: 10
13053394 TATTTTTACT
13053404 TATATATGGA
1 TATATATGGA
*
13053414 TATATATGAA
1 TATATATGGA
13053424 TATATATGGA
1 TATATATGGA
13053434 TATATAT
1 TATATAT
13053441 ATAGTTATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (10 bp):
TATATATGGA
Found at i:13055996 original size:13 final size:13
Alignment explanation
Indices: 13055978--13056002 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13055968 AGACATAATA
13055978 CATAACTTACATT
1 CATAACTTACATT
13055991 CATAACTTACAT
1 CATAACTTACAT
13056003 AAACTTATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.00, T:0.36
Consensus pattern (13 bp):
CATAACTTACATT
Found at i:13056110 original size:34 final size:34
Alignment explanation
Indices: 13056067--13056226 Score: 216
Period size: 34 Copynumber: 4.7 Consensus size: 34
13056057 GGGTGATGTG
13056067 ATATTATACATAAATTACATAACTTAATTAATTA
1 ATATTATACATAAATTACATAACTTAATTAATTA
13056101 ATATTATACATAAATTACATAACTTAATTAATTA
1 ATATTATACATAAATTACATAACTTAATTAATTA
* * *
13056135 ATATTATACATAACTTACATTAA--TATTATACATAA
1 ATATTATACATAAATTACA-TAACTTAAT-TA-ATTA
* * *
13056170 ATATTATAAATAAATTACATAACTCAGTTAATTA
1 ATATTATACATAAATTACATAACTTAATTAATTA
*
13056204 ATATTATACATAACTTACATAAC
1 ATATTATACATAAATTACATAAC
13056227 ATTTTAACAA
Statistics
Matches: 111, Mismatches: 10, Indels: 10
0.85 0.08 0.08
Matches are distributed among these distances:
33 3 0.03
34 81 0.73
35 25 0.23
36 2 0.02
ACGTcount: A:0.49, C:0.11, G:0.01, T:0.39
Consensus pattern (34 bp):
ATATTATACATAAATTACATAACTTAATTAATTA
Found at i:13056172 original size:13 final size:13
Alignment explanation
Indices: 13056150--13056184 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
13056140 ATACATAACT
*
13056150 TACATTAATATTA
1 TACATAAATATTA
13056163 TACATAAATATTA
1 TACATAAATATTA
*
13056176 TAAATAAAT
1 TACATAAAT
13056185 TACATAACTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (13 bp):
TACATAAATATTA
Found at i:13056181 original size:22 final size:22
Alignment explanation
Indices: 13056116--13056218 Score: 84
Period size: 22 Copynumber: 4.4 Consensus size: 22
13056106 ATACATAAAT
13056116 TACATAACTTAATTAATTAATATTA
1 TACATAAC-T-ATT-ATTAATATTA
*
13056141 TACATAACT-TACATTAATATTA
1 TACATAACTAT-TATTAATATTA
* * *
13056163 TACATAAATATTATAAATA-AA
1 TACATAACTATTATTAATATTA
13056184 TTACATAACTCAGTTAATTAATATTA
1 -TACATAACT-A-TT-ATTAATATTA
13056210 TACATAACT
1 TACATAACT
13056219 TACATAACAT
Statistics
Matches: 63, Mismatches: 8, Indels: 14
0.74 0.09 0.16
Matches are distributed among these distances:
21 1 0.02
22 33 0.52
23 2 0.03
24 3 0.05
25 23 0.37
26 1 0.02
ACGTcount: A:0.49, C:0.11, G:0.01, T:0.40
Consensus pattern (22 bp):
TACATAACTATTATTAATATTA
Done.