Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032251.1 Gossypioides kirkii chromosome KI_09
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: 38743931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2800 characters in sequence are not A, C, G, or T
File 136 of 144
Found at i:34861093 original size:26 final size:26
Alignment explanation
Indices: 34861036--34861093 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
34861026 GTAAATTTTT
* * *
34861036 GAAGAAGGAAAGGAAACAAAAGTTTT
1 GAAGAAGAAAAGGAAACAAAAGGTTA
*
34861062 GAAGAAGAAAAGGAAACAGAAGGTTA
1 GAAGAAGAAAAGGAAACAAAAGGTTA
*
34861088 GCAGAA
1 GAAGAA
34861094 AATTTTAACT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.55, C:0.05, G:0.29, T:0.10
Consensus pattern (26 bp):
GAAGAAGAAAAGGAAACAAAAGGTTA
Found at i:34863894 original size:28 final size:28
Alignment explanation
Indices: 34863841--34863898 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
34863831 CATTTTTCTG
*
34863841 TTGGAATTAATTAAATTTATGATTGAAT
1 TTGGAATTAATTAAATTTATAATTGAAT
**
34863869 TTGGAATTAATTCTATTTA-AATTTGAAT
1 TTGGAATTAATTAAATTTATAA-TTGAAT
34863897 TT
1 TT
34863899 ATTTAATAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 1 0.04
28 25 0.96
ACGTcount: A:0.36, C:0.02, G:0.12, T:0.50
Consensus pattern (28 bp):
TTGGAATTAATTAAATTTATAATTGAAT
Found at i:34863939 original size:26 final size:26
Alignment explanation
Indices: 34863890--34863939 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
34863880 TCTATTTAAA
* *
34863890 TTTGAATTTATTTAATAGTTTTTATG
1 TTTGAATTAATTTAATAGTGTTTATG
34863916 TTTGAATTAATTTAATTAG-GTTTA
1 TTTGAATTAATTTAA-TAGTGTTTA
34863940 GCAAATGACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 18 0.86
27 3 0.14
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (26 bp):
TTTGAATTAATTTAATAGTGTTTATG
Found at i:34864016 original size:6 final size:6
Alignment explanation
Indices: 34864005--34864039 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
34863995 ATATTTGCAT
34864005 ACATAA ACATAA ACATAA ACATAA ACATAA ACATA
1 ACATAA ACATAA ACATAA ACATAA ACATAA ACATA
34864040 TTTAATGGCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.66, C:0.17, G:0.00, T:0.17
Consensus pattern (6 bp):
ACATAA
Found at i:34864484 original size:6 final size:6
Alignment explanation
Indices: 34864472--34864514 Score: 77
Period size: 6 Copynumber: 7.2 Consensus size: 6
34864462 CTGCGACTGC
*
34864472 GGCTCA GGTTCA GGCTCA GGCTCA GGCTCA GGCTCA GGCTCA G
1 GGCTCA GGCTCA GGCTCA GGCTCA GGCTCA GGCTCA GGCTCA G
34864515 CCGGCTGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.16, C:0.30, G:0.35, T:0.19
Consensus pattern (6 bp):
GGCTCA
Found at i:34866270 original size:25 final size:26
Alignment explanation
Indices: 34866216--34866271 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 26
34866206 TAAAATTTTA
*
34866216 ATTTTCGAAATTTATATTAAAAAATT
1 ATTTTCGAAATTTATATTAAAAAATC
34866242 ATTTT-GAAA-TT-TATTAAAATATATC
1 ATTTTCGAAATTTATATTAAAA-A-ATC
34866267 ATTTT
1 ATTTT
34866272 TTTATAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 8 0.30
24 3 0.11
25 11 0.41
26 5 0.19
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.50
Consensus pattern (26 bp):
ATTTTCGAAATTTATATTAAAAAATC
Found at i:34866482 original size:17 final size:16
Alignment explanation
Indices: 34866450--34866481 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
34866440 TTTTTTTAAA
34866450 AAAATATTTAATATAT
1 AAAATATTTAATATAT
34866466 AAAATATTTAA-ATAT
1 AAAATATTTAATATAT
34866481 A
1 A
34866482 TCAATTGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AAAATATTTAATATAT
Found at i:34867902 original size:30 final size:31
Alignment explanation
Indices: 34867867--34867948 Score: 98
Period size: 30 Copynumber: 2.7 Consensus size: 31
34867857 GTTACATTTA
34867867 ACAAAACAGTCACTCAACTT-T-GAAAATGTG
1 ACAAAACAGTCACTCAACTTATCGAAAA-GTG
* *
34867897 ACAAAACAGTCACTAAAGTTATCGAAAAGTG
1 ACAAAACAGTCACTCAACTTATCGAAAAGTG
* *
34867928 ACAGAACAGT-ACTCTACTTAT
1 ACAAAACAGTCACTCAACTTAT
34867949 TATTCATTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
30 26 0.59
31 13 0.30
32 5 0.11
ACGTcount: A:0.44, C:0.20, G:0.13, T:0.23
Consensus pattern (31 bp):
ACAAAACAGTCACTCAACTTATCGAAAAGTG
Found at i:34870161 original size:69 final size:66
Alignment explanation
Indices: 34870072--34870219 Score: 199
Period size: 69 Copynumber: 2.2 Consensus size: 66
34870062 ACGTCTCGTG
* *
34870072 CTCTCTGATTAGCACTGTGTGTGCTCTCTGATT-AGCACTTTGTGTGCTCTCTGATTAGTACTTT
1 CTCTCTGTTTAGCACTGTGTGTGCTCTCTG-TTCAGCAC-TTATGTGCTCTCTG-TTAGTACTTT
*
34870136 GTGTA
63 G-ATA
34870141 CTCTCTGTTTAGCACTGTGTGTGCTCTCTGTTGCCCAGCACTTATGTGCTCTCTGTTAGTACTTT
1 CTCTCTGTTTAGCACTGTGTGTGCTCTCTGTT---CAGCACTTATGTGCTCTCTGTTAGTACTTT
34870206 GATA
63 GATA
34870210 CTCTCTGTTT
1 CTCTCTGTTT
34870220 GTTCCGTATA
Statistics
Matches: 72, Mismatches: 3, Indels: 8
0.87 0.04 0.10
Matches are distributed among these distances:
68 2 0.03
69 41 0.57
70 11 0.15
71 13 0.18
72 5 0.07
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.44
Consensus pattern (66 bp):
CTCTCTGTTTAGCACTGTGTGTGCTCTCTGTTCAGCACTTATGTGCTCTCTGTTAGTACTTTGAT
A
Found at i:34870172 original size:23 final size:23
Alignment explanation
Indices: 34870050--34870170 Score: 163
Period size: 23 Copynumber: 5.3 Consensus size: 23
34870040 ACTAGCGCGT
* *
34870050 TCTCTGTTTAGCAC-GTCTCGTGC
1 TCTCTGATTAGCACTGTGT-GTGC
34870073 TCTCTGATTAGCACTGTGTGTGC
1 TCTCTGATTAGCACTGTGTGTGC
*
34870096 TCTCTGATTAGCACTTTGTGTGC
1 TCTCTGATTAGCACTGTGTGTGC
* * *
34870119 TCTCTGATTAGTACTTTGTGTAC
1 TCTCTGATTAGCACTGTGTGTGC
*
34870142 TCTCTGTTTAGCACTGTGTGTGC
1 TCTCTGATTAGCACTGTGTGTGC
34870165 TCTCTG
1 TCTCTG
34870171 TTGCCCAGCA
Statistics
Matches: 88, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
23 85 0.97
24 3 0.03
ACGTcount: A:0.12, C:0.23, G:0.22, T:0.43
Consensus pattern (23 bp):
TCTCTGATTAGCACTGTGTGTGC
Found at i:34871120 original size:30 final size:31
Alignment explanation
Indices: 34871050--34871121 Score: 83
Period size: 31 Copynumber: 2.4 Consensus size: 31
34871040 AAGCCAATAG
* * * *
34871050 GACTGTTTTGTCACTTTTTGATAATTTTAGT
1 GACTGTTTTGTCACATTTTCATAAGTTGAGT
*
34871081 GATTGTTTTGTCACATTTTCA-AAGTTGAGT
1 GACTGTTTTGTCACATTTTCATAAGTTGAGT
*
34871111 GGCTGTTTTGT
1 GACTGTTTTGT
34871122 TAAATGTAAC
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
30 16 0.47
31 18 0.53
ACGTcount: A:0.18, C:0.10, G:0.21, T:0.51
Consensus pattern (31 bp):
GACTGTTTTGTCACATTTTCATAAGTTGAGT
Found at i:34874750 original size:61 final size:60
Alignment explanation
Indices: 34874667--34874971 Score: 250
Period size: 61 Copynumber: 5.1 Consensus size: 60
34874657 AAAAAATACA
* * * *
34874667 TTTTTGGGTGTTGGCCATCAAATGGCCGACATCCCTTTTTATCGAGAAAAAAATTTCAAAT
1 TTTTTTGGTGTTGGTCATTAAATGGCCGACACCCCTTTTT-TCGAGAAAAAAATTTCAAAT
* * * * *
34874728 TTTTTTGGTATTGATCATCAAATTGCCGACACCCCCTTTTTTCAAGAAAAAAAATTT-AAAT
1 TTTTTTGGTGTTGGTCATTAAATGGCCGACA-CCCCTTTTTTCGAG-AAAAAAATTTCAAAT
* * * * *
34874789 TTTTTTGATGTTGGCCATTAAATGGTCGACACCCCATATTTT----AAAAAAATTGC--A-
1 TTTTTTGGTGTTGGTCATTAAATGGCCGACACCCC-TTTTTTCGAGAAAAAAATTTCAAAT
* * ** *
34874843 TTTTTGGGTGTTGGTTATTGCATGGCCGACA-CCCTTTTTCTCGAGAAAAAAAATTTTAAAT
1 TTTTTTGGTGTTGGTCATTAAATGGCCGACACCCCTTTTT-TCGAG-AAAAAAATTTCAAAT
* ** * * *
34874904 TTTTTTGGTGTTGGTTATTGCATGGCCGACACCCCCTTTTCTCGGATAAAAAAATTACAAAT
1 TTTTTTGGTGTTGGTCATTAAATGGCCGACA-CCCCTTTTTTC-GAGAAAAAAATTTCAAAT
34874966 TTTTTT
1 TTTTTT
34874972 TGTATTGGCC
Statistics
Matches: 197, Mismatches: 31, Indels: 31
0.76 0.12 0.12
Matches are distributed among these distances:
52 4 0.02
53 4 0.02
54 24 0.12
55 1 0.01
56 9 0.05
58 9 0.05
60 5 0.03
61 93 0.47
62 39 0.20
63 9 0.05
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38
Consensus pattern (60 bp):
TTTTTTGGTGTTGGTCATTAAATGGCCGACACCCCTTTTTTCGAGAAAAAAATTTCAAAT
Found at i:34877766 original size:23 final size:23
Alignment explanation
Indices: 34877738--34877819 Score: 85
Period size: 23 Copynumber: 3.6 Consensus size: 23
34877728 ACACTAGTGC
*
34877738 GCTCTCTGTTTAGCACATCT-CGT
1 GCTCTCTGATTAGCAC-TCTACGT
* *
34877761 GCTCTCTGATTAGCACTTTATGT
1 GCTCTCTGATTAGCACTCTACGT
* **
34877784 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTCTACGT
*
34877807 GCTTTCTGATTAG
1 GCTCTCTGATTAG
34877820 TACTTTATGC
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
22 2 0.04
23 51 0.96
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.43
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTCTACGT
Found at i:34877809 original size:46 final size:45
Alignment explanation
Indices: 34877759--34877906 Score: 142
Period size: 46 Copynumber: 3.2 Consensus size: 45
34877749 AGCACATCTC
34877759 GTGCTCTCTGATTAGCACTTTATGTGCTCTCTGATTAGCACTTTGT
1 GTGCTCTCTGATTAGCACTTTATGTGCTCTCTG-TTAGCACTTTGT
* * ** *
34877805 GTGCTTTCTGATTAGTACTTTATGCACTCTTTGTTTAGCA-TTGTGT
1 GTGCTCTCTGATTAGCACTTTATGTGCTCTCTG-TTAGCACTT-TGT
*
34877851 GTGCTCTCTG-TTGCCCAGCAC-TTATGTGCTCTCTGTTAGTACTTTG-
1 GTGCTCTCTGATT----AGCACTTTATGTGCTCTCTGTTAGCACTTTGT
*
34877897 GTACTCTCTG
1 GTGCTCTCTG
34877907 TTTGTTCCGT
Statistics
Matches: 83, Mismatches: 13, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
45 4 0.05
46 55 0.66
47 7 0.08
48 13 0.16
49 4 0.05
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.45
Consensus pattern (45 bp):
GTGCTCTCTGATTAGCACTTTATGTGCTCTCTGTTAGCACTTTGT
Found at i:34877824 original size:23 final size:23
Alignment explanation
Indices: 34877759--34877895 Score: 120
Period size: 23 Copynumber: 5.9 Consensus size: 23
34877749 AGCACATCTC
34877759 GTGCTCTCTGATTAGCACTTTAT
1 GTGCTCTCTGATTAGCACTTTAT
*
34877782 GTGCTCTCTGATTAGCACTTTGT
1 GTGCTCTCTGATTAGCACTTTAT
* *
34877805 GTGCTTTCTGATTAGTACTTTAT
1 GTGCTCTCTGATTAGCACTTTAT
** * * *
34877828 GCACTCTTTGTTTAGCA-TTGTGT
1 GTGCTCTCTGATTAGCACTT-TAT
34877851 GTGCTCTCTG-TTGCCCAGCAC-TTAT
1 GTGCTCTCTGATT----AGCACTTTAT
*
34877876 GTGCTCTCTG-TTAGTACTTT
1 GTGCTCTCTGATTAGCACTTT
34877896 GGTACTCTCT
Statistics
Matches: 91, Mismatches: 16, Indels: 15
0.75 0.13 0.12
Matches are distributed among these distances:
21 4 0.04
22 6 0.07
23 62 0.68
25 14 0.15
26 5 0.05
ACGTcount: A:0.14, C:0.21, G:0.20, T:0.45
Consensus pattern (23 bp):
GTGCTCTCTGATTAGCACTTTAT
Found at i:34879062 original size:57 final size:56
Alignment explanation
Indices: 34878902--34879208 Score: 234
Period size: 56 Copynumber: 5.3 Consensus size: 56
34878892 CCAACACAAA
** * *
34878902 AAAAAATTGAATTTTTTCTCGAGAAAAGGGGGTGTCGGCCATTTGATGATCAACACC
1 AAAAAATACAATTTTTTTTCGAGAAAAGGGGGTGTCGGCCATTTGATG-GCAACACC
*
34878959 AAAAAAATTTGA-AATTTTTTTCTC-AGGAAAAGGGGGTGTCGACCATTTGATGGCAAACACC
1 -AAAAAA--T-ACAATTTTTTT-TCGA-GAAAAGGGGGTGTCGGCCATTTGATGGC-AACACC
* *
34879020 CAAAAATACAATTTTTTTTCGAGAAAAGGGGGTGTCGGCCATTTGATGGCAACACT
1 AAAAAATACAATTTTTTTTCGAGAAAAGGGGGTGTCGGCCATTTGATGGCAACACC
** * **
34879076 AAAAAATTTTGAATTTTTTTTCTCA-AAAAGGGGGTGTC-G--ATTATGCAATAACCAACACC
1 AAAAAA--TACAATTTTTTTTC-GAGAAAAGGGGGTGTCGGCCATT-TG--AT-GGCAACACC
* * ** * *
34879135 CAAAAAT-CTAATTTTTTTT-GAGAAAAGAGGGTGTCGATCATTTGATGGTCAATACA
1 AAAAAATAC-AATTTTTTTTCGAGAAAAGGGGGTGTCGGCCATTTGATGG-CAACACC
*
34879191 AAAAAATTCAATTTTTTT
1 AAAAAATACAATTTTTTT
34879209 CAAATTCTTG
Statistics
Matches: 203, Mismatches: 24, Indels: 46
0.74 0.09 0.17
Matches are distributed among these distances:
55 4 0.02
56 46 0.23
57 43 0.21
58 46 0.23
59 15 0.07
60 16 0.08
61 33 0.16
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (56 bp):
AAAAAATACAATTTTTTTTCGAGAAAAGGGGGTGTCGGCCATTTGATGGCAACACC
Found at i:34879113 original size:58 final size:58
Alignment explanation
Indices: 34878901--34879114 Score: 258
Period size: 61 Copynumber: 3.7 Consensus size: 58
34878891 GCCAACACAA
* *
34878901 AAAAAAATTGAA--TTTTTTCTCGAGAAAAGGGGGTGTCGGCCATTTGATGATCAACACC
1 AAAAAATTTGAATTTTTTTTCTC-AGAAAAGGGGGTGTCGGCCATTTGATG-GCAACACC
* *
34878959 AAAAAAATTTGAAATTTTTTTCTCAGGAAAAGGGGGTGTCGACCATTTGATGGCAAACACC
1 -AAAAAATTTGAATTTTTTTTCTCA-GAAAAGGGGGTGTCGGCCATTTGATGGC-AACACC
* ** * *
34879020 CAAAAA-TACAATTTTTTTTC-GAGAAAAGGGGGTGTCGGCCATTTGATGGCAACACT
1 AAAAAATTTGAATTTTTTTTCTCAGAAAAGGGGGTGTCGGCCATTTGATGGCAACACC
34879076 AAAAAATTTTGAATTTTTTTTCTCA-AAAAGGGGGTGTCG
1 AAAAAA-TTTGAATTTTTTTTCTCAGAAAAGGGGGTGTCG
34879115 ATTATGCAAT
Statistics
Matches: 134, Mismatches: 14, Indels: 15
0.82 0.09 0.09
Matches are distributed among these distances:
56 10 0.07
57 27 0.20
58 27 0.20
59 23 0.17
60 7 0.05
61 40 0.30
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.30
Consensus pattern (58 bp):
AAAAAATTTGAATTTTTTTTCTCAGAAAAGGGGGTGTCGGCCATTTGATGGCAACACC
Found at i:34879153 original size:115 final size:116
Alignment explanation
Indices: 34878903--34879198 Score: 359
Period size: 115 Copynumber: 2.5 Consensus size: 116
34878893 CAACACAAAA
* *
34878903 AAAAAT-TGAATTTTTTCTCGAGAAAAGGGGGTGTCGGCCATTTGATGATCAACACCAAAAAAA-
1 AAAAATCT-AATTTTTTTTCGAGAAAAGGGGGTGTCGGCCATTTGATG-GCAACA-CAAAAAAAT
*** **
34878966 TTTGAAATTTTTTTCTCAGGAAAAGGGGGTGTCGACCATTTGATGGCAAACACCC
63 TTTGAAATTTTTTTCTCA-GAAAAGGGGGTGTCGACCATGCAATAACAAACACCC
*
34879021 AAAAATAC-AATTTTTTTTCGAGAAAAGGGGGTGTCGGCCATTTGATGGCAACACTAAAAAATTT
1 AAAAAT-CTAATTTTTTTTCGAGAAAAGGGGGTGTCGGCCATTTGATGGCAACACAAAAAAATTT
* ** *
34879085 TGAATTTTTTTTCTCA-AAAAGGGGGTGTCGATTATGCAATAACCAACACCC
65 TGAAATTTTTTTCTCAGAAAAGGGGGTGTCGACCATGCAATAACAAACACCC
* ** *
34879136 AAAAATCTAATTTTTTTT-GAGAAAAGAGGGTGTCGATCATTTGATGGTCAATACAAAAAAATT
1 AAAAATCTAATTTTTTTTCGAGAAAAGGGGGTGTCGGCCATTTGATGG-CAACACAAAAAAATT
34879199 CAATTTTTTT
Statistics
Matches: 156, Mismatches: 17, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
114 27 0.17
115 56 0.36
116 7 0.04
117 22 0.14
118 44 0.28
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (116 bp):
AAAAATCTAATTTTTTTTCGAGAAAAGGGGGTGTCGGCCATTTGATGGCAACACAAAAAAATTTT
GAAATTTTTTTCTCAGAAAAGGGGGTGTCGACCATGCAATAACAAACACCC
Found at i:34879446 original size:31 final size:31
Alignment explanation
Indices: 34879384--34879447 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
34879374 GTATATTTTT
* * **
34879384 AAATTTGAGTTATTTTTATAAATAATTAAAA
1 AAATTTAAGTTATTTTAATAAATAACCAAAA
*
34879415 AAATTTAAGTTATTTTAATAAATTACCAAAA
1 AAATTTAAGTTATTTTAATAAATAACCAAAA
34879446 AA
1 AA
34879448 CTGAATTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.52, C:0.03, G:0.05, T:0.41
Consensus pattern (31 bp):
AAATTTAAGTTATTTTAATAAATAACCAAAA
Found at i:34879740 original size:110 final size:110
Alignment explanation
Indices: 34879547--34879775 Score: 343
Period size: 110 Copynumber: 2.1 Consensus size: 110
34879537 CACGGCACAC
* * * * *
34879547 CATTATTGCTCAGAATTTCGAAGCTTTTGCCGCTGCAAAAGGGTATTGCCGCTACCATAGTTGCA
1 CATTATTGCACAGAATTTCGAAGCTTTTGCAGCCGCAAAAGGGGATTGCCGCTACCATAATTGCA
* *
34879612 AGCAATGGTGTCGTATTACTATTGTTTTAAGTGCACGTGTCATAA
66 AGCAATGGTGGCGTATTACTATTGTTTTAAGTGCACGTGGCATAA
*
34879657 CATTATTGCACAGAATTTGGAAAG-TTTTGCAGCCGCAAAAGGGGATTGCCGCTACCATAATTGC
1 CATTATTGCACAGAATTTCG-AAGCTTTTGCAGCCGCAAAAGGGGATTGCCGCTACCATAATTGC
* * *
34879721 AGGCAATTGTGGCGTATTACTATTGTTTTAAGTGCACGTGGCATAC
65 AAGCAATGGTGGCGTATTACTATTGTTTTAAGTGCACGTGGCATAA
34879767 CATTATTGC
1 CATTATTGC
34879776 TCAAAGTTAT
Statistics
Matches: 107, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
110 104 0.97
111 3 0.03
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (110 bp):
CATTATTGCACAGAATTTCGAAGCTTTTGCAGCCGCAAAAGGGGATTGCCGCTACCATAATTGCA
AGCAATGGTGGCGTATTACTATTGTTTTAAGTGCACGTGGCATAA
Found at i:34882087 original size:29 final size:26
Alignment explanation
Indices: 34882016--34882087 Score: 67
Period size: 29 Copynumber: 2.7 Consensus size: 26
34882006 AATTTTAATC
*
34882016 AAATTCAAATTTT-T-AAAAAAAATT
1 AAATTTAAATTTTATAAAAAAAAATT
* *
34882040 AGATTTAAATTTAATTAAAAATAAAGATT
1 AAATTTAAATTTTA-TAAAAA-AAA-ATT
34882069 AAATTTAAAATTTTATAAA
1 AAATTT-AAATTTTATAAA
34882088 TATCAAAACC
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
24 10 0.27
26 1 0.03
27 4 0.11
28 3 0.08
29 12 0.32
30 7 0.19
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (26 bp):
AAATTTAAATTTTATAAAAAAAAATT
Found at i:34886442 original size:17 final size:19
Alignment explanation
Indices: 34886411--34886445 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
34886401 ATATATATAT
34886411 TAAAAATAGATATCATTAA
1 TAAAAATAGATATCATTAA
34886430 TAAAAATA-A-ATCATTA
1 TAAAAATAGATATCATTA
34886446 CCATACATCC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 1 0.06
19 8 0.50
ACGTcount: A:0.60, C:0.06, G:0.03, T:0.31
Consensus pattern (19 bp):
TAAAAATAGATATCATTAA
Found at i:34901988 original size:3 final size:3
Alignment explanation
Indices: 34901980--34902004 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
34901970 ACGTCTTCTA
34901980 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
34902005 TAATTTCCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:34908703 original size:32 final size:32
Alignment explanation
Indices: 34908665--34908731 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
34908655 TTTAGTTCAT
34908665 ATTTTTTTT-TCTAAAAAATTAGTTTATTTAGAA
1 ATTTTTTTTATCTAAAAAA-T-GTTTATTTAGAA
* *
34908698 ATTTTTTTTATCTCAAAAATGTTTTTTTAGAA
1 ATTTTTTTTATCTAAAAAATGTTTATTTAGAA
34908730 AT
1 AT
34908732 AATACTAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
32 13 0.42
33 10 0.32
34 8 0.26
ACGTcount: A:0.34, C:0.04, G:0.06, T:0.55
Consensus pattern (32 bp):
ATTTTTTTTATCTAAAAAATGTTTATTTAGAA
Found at i:34911517 original size:193 final size:193
Alignment explanation
Indices: 34911184--34911579 Score: 785
Period size: 193 Copynumber: 2.1 Consensus size: 193
34911174 ATGAAATGTG
34911184 AAAT-TATTGATTAATTTAACTCAAATGTAAGATTCAAGTATTTGATTGACGGAATGAAATATTT
1 AAATATATTGATTAATTTAACTCAAATGTAAGATTCAAGTATTTGATTGACGGAATGAAATATTT
34911248 TATCCAATCGTCTTTGTTATGAAATATTATTTTAACACACTTTAATATTTTTTTAATCTTAATTT
66 TATCCAATCGTCTTTGTTATGAAATATTATTTTAACACACTTTAATATTTTTTTAATCTTAATTT
34911313 CAATAAAATTAATATAAATTATTACAATTCATACTTTTTATTACAATTTATATATTAATAAGT
131 CAATAAAATTAATATAAATTATTACAATTCATACTTTTTATTACAATTTATATATTAATAAGT
34911376 AAATATATTGATTAATTTAACTCAAATGTAAGATTCAAGTATTTGATTGACGGAATGAAATATTT
1 AAATATATTGATTAATTTAACTCAAATGTAAGATTCAAGTATTTGATTGACGGAATGAAATATTT
34911441 TATCCAATCGTCTTTGTTATGAAATATTATTTTAACACACTTTAATATTTTTTTAATCTTAATTT
66 TATCCAATCGTCTTTGTTATGAAATATTATTTTAACACACTTTAATATTTTTTTAATCTTAATTT
34911506 CAATAAAATTAATATAAATTATTACAATTCATACTTTTTATTACAATTTATATATTAATAAGT
131 CAATAAAATTAATATAAATTATTACAATTCATACTTTTTATTACAATTTATATATTAATAAGT
34911569 AAATATATTGA
1 AAATATATTGA
34911580 GTTGAAATAA
Statistics
Matches: 203, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
192 4 0.02
193 199 0.98
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.45
Consensus pattern (193 bp):
AAATATATTGATTAATTTAACTCAAATGTAAGATTCAAGTATTTGATTGACGGAATGAAATATTT
TATCCAATCGTCTTTGTTATGAAATATTATTTTAACACACTTTAATATTTTTTTAATCTTAATTT
CAATAAAATTAATATAAATTATTACAATTCATACTTTTTATTACAATTTATATATTAATAAGT
Found at i:34915579 original size:12 final size:12
Alignment explanation
Indices: 34915562--34915599 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
34915552 TTCTAATCAT
*
34915562 GGGTCGGGGTTG
1 GGGTCGGGGTCG
34915574 GGGTCGGGGTCG
1 GGGTCGGGGTCG
*
34915586 GGGTCGGGTTCG
1 GGGTCGGGGTCG
34915598 GG
1 GG
34915600 TTGGATCGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.00, C:0.13, G:0.66, T:0.21
Consensus pattern (12 bp):
GGGTCGGGGTCG
Found at i:34915585 original size:18 final size:18
Alignment explanation
Indices: 34915562--34915599 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
34915552 TTCTAATCAT
*
34915562 GGGTCGGGGTTGGGGTCG
1 GGGTCGGGGTCGGGGTCG
*
34915580 GGGTCGGGGTCGGGTTCG
1 GGGTCGGGGTCGGGGTCG
34915598 GG
1 GG
34915600 TTGGATCGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.00, C:0.13, G:0.66, T:0.21
Consensus pattern (18 bp):
GGGTCGGGGTCGGGGTCG
Found at i:34931700 original size:195 final size:197
Alignment explanation
Indices: 34931266--34931711 Score: 555
Period size: 195 Copynumber: 2.3 Consensus size: 197
34931256 CGCGACGGCT
* * *
34931266 GAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGCGAGCAACATCGTGAGTCTGGAAATGA
1 GAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTGAG-CTCG-AA-GA
* * * *
34931331 GGAAAGAAATATGTATCCTAAATGGATTACAGGCCCTACGATGGCTGAGATTTATGCATAAGTGC
63 -GAAAGAAATATGAATCCTAAATGGACTACAGGCCCTACGATGGCTGAGATCTATACATAAGTGC
* * * *
34931396 ATATTCTCGACAGCTCGTGTGAGCAGCATCGTTAGGGAACAGTTATATGCACAGATATCGTATCG
127 ATACTCTCGACAGCTCGTGTGAGCAGCATCGTTAGGGAACAGTTATATACACAGATACCATATCG
*
34931461 ATGGTT
192 ATGGTA
*
34931467 GAGGTACCGCATATGTTGCGAGTCCTCGACAACTCGTGTGAGCAGCATCGTGA-CTCG-A-A-AA
1 GAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTGAGCTCGAAGAGAA
* * * *
34931528 AGAGATATGAATCCTAAATGGACTACAGGCCCTACGATGGTTGAGA-CTATAC-TTATTGCATAC
66 AGAAATATGAATCCTAAATGGACTACAGGCCCTACGATGGCTGAGATCTATACATAAGTGCATAC
* * *
34931591 TCTTGACAGCTCGTGTGAGCAGCATCGTTAGGGAACAATTTATAGTACAGACAGGTACCATATCG
131 TCTCGACAGCTCGTGTGAGCAGCATCGTTAGGGAAC-AGTTATA-TAC--ACAGATACCATATCG
34931656 ATGGCTA
192 ATGG-TA
* * *
34931663 G-GGTACCGCATACGTTGCGAGTCCTCAACAGCTCGTGTAAGCAGCATCG
1 GAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCG
34931712 AGTACTGGTA
Statistics
Matches: 216, Mismatches: 24, Indels: 16
0.84 0.09 0.06
Matches are distributed among these distances:
191 43 0.20
192 10 0.05
193 46 0.21
195 61 0.28
196 2 0.01
197 1 0.00
199 3 0.01
201 50 0.23
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (197 bp):
GAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTGAGCTCGAAGAGAA
AGAAATATGAATCCTAAATGGACTACAGGCCCTACGATGGCTGAGATCTATACATAAGTGCATAC
TCTCGACAGCTCGTGTGAGCAGCATCGTTAGGGAACAGTTATATACACAGATACCATATCGATGG
TA
Found at i:34932493 original size:21 final size:21
Alignment explanation
Indices: 34932467--34932515 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
34932457 GTTTTTAGTA
34932467 TCGGTAGAAG-CATTA-TATGTT
1 TCGGTAGAAGTCA-TACT-TGTT
34932488 TCGGTAGAAGTCATACTTGTT
1 TCGGTAGAAGTCATACTTGTT
34932509 TCGGTAG
1 TCGGTAG
34932516 TATTGTCTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
21 23 0.88
22 3 0.12
ACGTcount: A:0.24, C:0.12, G:0.27, T:0.37
Consensus pattern (21 bp):
TCGGTAGAAGTCATACTTGTT
Found at i:34937686 original size:13 final size:12
Alignment explanation
Indices: 34937651--34937689 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
34937641 TTTATAAATA
34937651 TAAATAA-ATTT
1 TAAATAATATTT
34937662 TAAATAATATTT
1 TAAATAATATTT
*
34937674 TAAACTCATATTT
1 TAAA-TAATATTT
34937687 TAA
1 TAA
34937690 GTTGGATCGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 7 0.28
12 8 0.32
13 10 0.40
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (12 bp):
TAAATAATATTT
Found at i:34938446 original size:25 final size:24
Alignment explanation
Indices: 34938403--34938461 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 24
34938393 CATTTATTAT
* *
34938403 AATAAAAAAAATTATAATTATAAA
1 AATAAAACAAATTAAAATTATAAA
*
34938427 ATATTAAACAAATTAAAATTATAAA
1 A-ATAAAACAAATTAAAATTATAAA
34938452 AATAAAACAA
1 AATAAAACAA
34938462 CTCAAACATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 9 0.30
25 21 0.70
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.27
Consensus pattern (24 bp):
AATAAAACAAATTAAAATTATAAA
Found at i:34939646 original size:29 final size:30
Alignment explanation
Indices: 34939602--34939672 Score: 99
Period size: 29 Copynumber: 2.4 Consensus size: 30
34939592 ACAAAATACT
*
34939602 AACATAAGTGATTAAAATGTAACATT-TCA
1 AACATAAGTGACTAAAATGTAACATTATCA
*
34939631 AACATAAGTGACTAAAATGTAACCTTAATCA
1 AACATAAGTGACTAAAATGTAACATT-ATCA
*
34939662 AACAAAAGTGA
1 AACATAAGTGA
34939673 TTATTTTTGT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 24 0.65
31 13 0.35
ACGTcount: A:0.51, C:0.13, G:0.11, T:0.25
Consensus pattern (30 bp):
AACATAAGTGACTAAAATGTAACATTATCA
Found at i:34949441 original size:20 final size:20
Alignment explanation
Indices: 34949405--34949444 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
34949395 GGAGGATATC
34949405 TATATTAAGATTATATTAAA
1 TATATTAAGATTATATTAAA
*
34949425 TATATATAA-ATTCTATTAAA
1 TATAT-TAAGATTATATTAAA
34949445 AAGATGGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (20 bp):
TATATTAAGATTATATTAAA
Found at i:34975599 original size:31 final size:30
Alignment explanation
Indices: 34975561--34975658 Score: 91
Period size: 31 Copynumber: 3.3 Consensus size: 30
34975551 TTAATATAAC
34975561 ATTTGGTACGTGAACTTGACATTTTTTACTA
1 ATTTGGTAC-TGAACTTGACATTTTTTACTA
* *
34975592 ATTTGGTATCT-AA-TT---TTTTTTTACCCA
1 ATTTGGTA-CTGAACTTGACATTTTTTA-CTA
34975619 ATTTGGTACCTGAACTTGACATTTTTT-CTTA
1 ATTTGGTA-CTGAACTTGACATTTTTTAC-TA
34975650 ATTTGGTAC
1 ATTTGGTAC
34975659 CTATATTTCT
Statistics
Matches: 54, Mismatches: 5, Indels: 17
0.71 0.07 0.22
Matches are distributed among these distances:
26 7 0.13
27 12 0.22
28 2 0.04
29 4 0.07
30 4 0.07
31 18 0.33
32 7 0.13
ACGTcount: A:0.23, C:0.14, G:0.13, T:0.49
Consensus pattern (30 bp):
ATTTGGTACTGAACTTGACATTTTTTACTA
Found at i:34975763 original size:59 final size:58
Alignment explanation
Indices: 34975561--34975753 Score: 251
Period size: 59 Copynumber: 3.3 Consensus size: 58
34975551 TTAATATAAC
* * * * **
34975561 ATTTGGTACGTGAACTTGACATTTTTTACTAATTTGGTATCTAATTTTTTTTTACCCA
1 ATTTGGTACCTGAACTTGACACTTTTTCCTAATTTGGTACCTAATTTTTTTGGACCCA
* * *
34975619 ATTTGGTACCTGAACTTGACATTTTTTCTTAATTTGGTACCTATATTTCTTTGGACCCA
1 ATTTGGTACCTGAACTTGACACTTTTTCCTAATTTGGTACCTA-ATTTTTTTGGACCCA
* *
34975678 AATTGGTACCTGAACTTGACACTTTTTCCTAATTTGGTACCTCAACTTTTTTTGGACCTA
1 ATTTGGTACCTGAACTTGACACTTTTTCCTAATTTGGTACCT-AA-TTTTTTTGGACCCA
*
34975738 ATTTGGTACATGAACT
1 ATTTGGTACCTGAACT
34975754 CGGTATTTTT
Statistics
Matches: 118, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
58 39 0.33
59 52 0.44
60 27 0.23
ACGTcount: A:0.24, C:0.18, G:0.13, T:0.45
Consensus pattern (58 bp):
ATTTGGTACCTGAACTTGACACTTTTTCCTAATTTGGTACCTAATTTTTTTGGACCCA
Found at i:34976256 original size:20 final size:20
Alignment explanation
Indices: 34976231--34976268 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
34976221 CACAATATAC
*
34976231 ATAAAATATAAGGACTAATA
1 ATAAAATATAAGCACTAATA
*
34976251 ATAAAATTTAAGCACTAA
1 ATAAAATATAAGCACTAA
34976269 ATTCTTTTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.58, C:0.08, G:0.08, T:0.26
Consensus pattern (20 bp):
ATAAAATATAAGCACTAATA
Found at i:34978657 original size:22 final size:23
Alignment explanation
Indices: 34978614--34978658 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
34978604 CAAGTTATTG
**
34978614 AAAAAAACTATTCAAATTAAAAAC
1 AAAAAAAC-ATTCAAAAAAAAAAC
34978638 AAAAAAA-ATTCAAAAAAAAAA
1 AAAAAAACATTCAAAAAAAAAA
34978659 TCCCATATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 12 0.63
24 7 0.37
ACGTcount: A:0.76, C:0.09, G:0.00, T:0.16
Consensus pattern (23 bp):
AAAAAAACATTCAAAAAAAAAAC
Found at i:34996522 original size:18 final size:19
Alignment explanation
Indices: 34996501--34996539 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
34996491 TTTAATAAAA
*
34996501 TTTATTATT-AGTAATATT
1 TTTATTATTAAGTAACATT
*
34996519 TTTATTTTTAAGTAACATT
1 TTTATTATTAAGTAACATT
34996538 TT
1 TT
34996540 AAATATTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.62
Consensus pattern (19 bp):
TTTATTATTAAGTAACATT
Found at i:34996528 original size:34 final size:35
Alignment explanation
Indices: 34996466--34996538 Score: 89
Period size: 33 Copynumber: 2.1 Consensus size: 35
34996456 TTAATTATAT
34996466 ATTTAATTATATAGTAATTTATTATTTTAA-TAAA
1 ATTTAATTATATAGTAATTTATTATTTTAAGTAAA
* *
34996500 ATTT-ATTAT-TAGTAATATTTTTATTTTTAAGTAAC
1 ATTTAATTATATAGTAAT-TTATTA-TTTTAAGTAAA
34996535 ATTT
1 ATTT
34996539 TAAATATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
32 7 0.21
33 10 0.29
34 10 0.29
35 7 0.21
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.56
Consensus pattern (35 bp):
ATTTAATTATATAGTAATTTATTATTTTAAGTAAA
Found at i:35016183 original size:20 final size:21
Alignment explanation
Indices: 35016145--35016195 Score: 95
Period size: 20 Copynumber: 2.5 Consensus size: 21
35016135 CAAATGATTT
35016145 TAAAATTATTTTTTAAAAATA
1 TAAAATTATTTTTTAAAAATA
35016166 TAAAATTATTTTTT-AAAATA
1 TAAAATTATTTTTTAAAAATA
35016186 TAAAATTATT
1 TAAAATTATT
35016196 AAAATATCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 16 0.53
21 14 0.47
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TAAAATTATTTTTTAAAAATA
Found at i:35016237 original size:14 final size:15
Alignment explanation
Indices: 35016218--35016248 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
35016208 TTCTCTTCCC
35016218 CTCCTTCCCC-TCTT
1 CTCCTTCCCCTTCTT
35016232 CTCCTTCCCCTTCTT
1 CTCCTTCCCCTTCTT
35016247 CT
1 CT
35016249 TATTTTCCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.00, C:0.55, G:0.00, T:0.45
Consensus pattern (15 bp):
CTCCTTCCCCTTCTT
Found at i:35016389 original size:15 final size:15
Alignment explanation
Indices: 35016369--35016402 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
35016359 TTCCCCTTCC
*
35016369 CCTTCTTCTTATTTT
1 CCTTCTTCTTATTTA
*
35016384 CCTTCTTTTTATTTA
1 CCTTCTTCTTATTTA
35016399 CCTT
1 CCTT
35016403 TTTTGGATAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.09, C:0.26, G:0.00, T:0.65
Consensus pattern (15 bp):
CCTTCTTCTTATTTA
Found at i:35017161 original size:69 final size:66
Alignment explanation
Indices: 35017039--35017186 Score: 174
Period size: 69 Copynumber: 2.2 Consensus size: 66
35017029 TATACGGAAC
* *
35017039 AAACAGAAAGTACCAAAGTACTAACAGAGAGCACATAAGTGCTGGGCAACAGAGAGCAC-ACACA
1 AAACAGAGAGTACCAAAGTACTAACAGAGAGCACACAAGTGCT--G-AACAGAGAGCACGACAC-
35017103 ATGCT
62 ATGCT
*
35017108 AAACAGAGAGTACACAAAGTACTAATCAGAGAGCACACACAGTGCT-AATCAGAGAGCACGAGAC
1 AAACAGAGAGTAC-CAAAGTACTAA-CAGAGAGCACACA-AGTGCTGAA-CAGAGAGCACGACAC
*
35017172 GTGCT
62 ATGCT
35017177 AAACAGAGAG
1 AAACAGAGAG
35017187 CACGCTAGTG
Statistics
Matches: 70, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
68 2 0.03
69 36 0.51
70 14 0.20
71 12 0.17
72 6 0.09
ACGTcount: A:0.45, C:0.21, G:0.23, T:0.11
Consensus pattern (66 bp):
AAACAGAGAGTACCAAAGTACTAACAGAGAGCACACAAGTGCTGAACAGAGAGCACGACACATGC
T
Found at i:35017190 original size:23 final size:23
Alignment explanation
Indices: 35017086--35017189 Score: 129
Period size: 23 Copynumber: 4.5 Consensus size: 23
35017076 AGTGCTGGGC
*
35017086 AACAGAGAGCACACACAATGCTA
1 AACAGAGAGCACACACAGTGCTA
* * *
35017109 AACAGAGAGTACACAAAGTACTA
1 AACAGAGAGCACACACAGTGCTA
*
35017132 ATCAGAGAGCACACACAGTGCTA
1 AACAGAGAGCACACACAGTGCTA
* *
35017155 ATCAGAGAGCACGAGAC-GTGCTA
1 AACAGAGAGCAC-ACACAGTGCTA
35017178 AACAGAGAGCAC
1 AACAGAGAGCAC
35017190 GCTAGTGTTC
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
23 67 0.96
24 3 0.04
ACGTcount: A:0.44, C:0.23, G:0.22, T:0.11
Consensus pattern (23 bp):
AACAGAGAGCACACACAGTGCTA
Found at i:35018935 original size:15 final size:16
Alignment explanation
Indices: 35018895--35018936 Score: 50
Period size: 19 Copynumber: 2.5 Consensus size: 16
35018885 TTTCCAACAA
35018895 AGCCATGGGTATTATG
1 AGCCATGGGTATTATG
35018911 AACAGCCATGGGTATTATG
1 ---AGCCATGGGTATTATG
35018930 -GCCATGG
1 AGCCATGG
35018937 TTTTGATTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 7 0.30
19 16 0.70
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.26
Consensus pattern (16 bp):
AGCCATGGGTATTATG
Found at i:35019380 original size:25 final size:25
Alignment explanation
Indices: 35019352--35019402 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
35019342 CAGACAAAAA
35019352 AACCCAAAAGAACAAGATGATGATG
1 AACCCAAAAGAACAAGATGATGATG
* *
35019377 AACCCAGAAGAACAGGATGATGATG
1 AACCCAAAAGAACAAGATGATGATG
35019402 A
1 A
35019403 TGATTAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.49, C:0.16, G:0.24, T:0.12
Consensus pattern (25 bp):
AACCCAAAAGAACAAGATGATGATG
Found at i:35019435 original size:8 final size:9
Alignment explanation
Indices: 35019418--35019515 Score: 53
Period size: 9 Copynumber: 10.2 Consensus size: 9
35019408 AAAATATTAA
35019418 AATAATTTT
1 AATAATTTT
35019427 AATAA-TTT
1 AATAATTTT
35019435 -AT-ATTTT
1 AATAATTTT
35019442 AAAAAATAATTTT
1 ---A-ATAATTTT
35019455 AAATTAATTTT
1 -AA-TAATTTT
35019466 AAAATAATTTT
1 --AATAATTTT
35019477 AATAA-TTT
1 AATAATTTT
*
35019485 -ATATTTTT
1 AATAATTTT
35019493 AAAAATAATTTT
1 ---AATAATTTT
35019505 AATAATTTT
1 AATAATTTT
35019514 AA
1 AA
35019516 AATCATTTGC
Statistics
Matches: 73, Mismatches: 2, Indels: 28
0.71 0.02 0.27
Matches are distributed among these distances:
6 1 0.01
7 8 0.11
8 9 0.12
9 21 0.29
10 1 0.01
11 16 0.22
12 12 0.16
13 5 0.07
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (9 bp):
AATAATTTT
Found at i:35019452 original size:28 final size:27
Alignment explanation
Indices: 35019416--35019512 Score: 141
Period size: 28 Copynumber: 3.7 Consensus size: 27
35019406 TTAAAATATT
35019416 AAAATAATTTTAATAATTTATATTTTAA
1 AAAATAATTTTAATAATTTATATTTT-A
35019444 AAAATAATTTT-A-AA-TTA-ATTTT-
1 AAAATAATTTTAATAATTTATATTTTA
35019466 AAAATAATTTTAATAATTTATATTTTTA
1 AAAATAATTTTAATAATTTATA-TTTTA
35019494 AAAATAATTTTAATAATTT
1 AAAATAATTTTAATAATTT
35019513 TAAAATCATT
Statistics
Matches: 63, Mismatches: 0, Indels: 12
0.84 0.00 0.16
Matches are distributed among these distances:
22 11 0.17
23 1 0.02
24 7 0.11
25 6 0.10
26 3 0.05
27 5 0.08
28 30 0.48
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
AAAATAATTTTAATAATTTATATTTTA
Found at i:35019464 original size:11 final size:11
Alignment explanation
Indices: 35019414--35019523 Score: 80
Period size: 11 Copynumber: 9.1 Consensus size: 11
35019404 GATTAAAATA
35019414 TTAAAATAATT
1 TTAAAATAATT
35019425 TTAATAATTTATATT
1 TTAA-AA--TA-ATT
35019440 TTAAAAAATAATT
1 TT--AAAATAATT
*
35019453 TTAAATTAATT
1 TTAAAATAATT
35019464 TTAAAATAATT
1 TTAAAATAATT
35019475 TTAATAATTTATATTT
1 TTAA-AA--TA-A-TT
35019491 TTAAAAATAATT
1 TT-AAAATAATT
35019503 TT--AATAATT
1 TTAAAATAATT
*
35019512 TTAAAATCATT
1 TTAAAATAATT
35019523 T
1 T
35019524 GCTGACGTAG
Statistics
Matches: 82, Mismatches: 3, Indels: 28
0.73 0.03 0.25
Matches are distributed among these distances:
9 9 0.11
11 33 0.40
12 8 0.10
13 6 0.07
14 8 0.10
15 6 0.07
16 8 0.10
17 4 0.05
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (11 bp):
TTAAAATAATT
Found at i:35019478 original size:50 final size:48
Alignment explanation
Indices: 35019406--35019523 Score: 184
Period size: 50 Copynumber: 2.4 Consensus size: 48
35019396 ATGATGATGA
*
35019406 TTAA-AATATTAAAATAATTTTAATAATTTATATTTTAAAAAATAATT
1 TTAATAATTTTAAAATAATTTTAATAATTTATATTTTAAAAAATAATT
*
35019453 TTAAATTAATTTTAAAATAATTTTAATAATTTATATTTTTAAAAATAATT
1 TT-AA-TAATTTTAAAATAATTTTAATAATTTATATTTTAAAAAATAATT
*
35019503 TTAATAATTTTAAAATCATTT
1 TTAATAATTTTAAAATAATTT
35019524 GCTGACGTAG
Statistics
Matches: 65, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
47 2 0.03
48 18 0.28
49 2 0.03
50 43 0.66
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (48 bp):
TTAATAATTTTAAAATAATTTTAATAATTTATATTTTAAAAAATAATT
Found at i:35019893 original size:22 final size:23
Alignment explanation
Indices: 35019868--35019913 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
35019858 TTAAAGTTCC
*
35019868 TTTATATATATTATT-TTAATAT
1 TTTATATATATAATTATTAATAT
*
35019890 TTTATATTTATAATTATTAATAT
1 TTTATATATATAATTATTAATAT
35019913 T
1 T
35019914 ATTAAAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (23 bp):
TTTATATATATAATTATTAATAT
Found at i:35028215 original size:30 final size:29
Alignment explanation
Indices: 35028132--35028215 Score: 71
Period size: 30 Copynumber: 2.8 Consensus size: 29
35028122 TCTCAAAACT
**
35028132 ATAAACTTTGATTTAAT-ATGTAATCCTATAC
1 ATAAACTTTGATTTAATCA---AATTTTATAC
** *
35028163 ATAAACTTTGATTTTTTGAAATTTTATAC
1 ATAAACTTTGATTTAATCAAATTTTATAC
*
35028192 ATAAAATTTTGATTTAATCAAATT
1 AT-AAACTTTGATTTAATCAAATT
35028216 CTCACAAATT
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
29 10 0.23
30 17 0.40
31 15 0.35
32 1 0.02
ACGTcount: A:0.39, C:0.08, G:0.06, T:0.46
Consensus pattern (29 bp):
ATAAACTTTGATTTAATCAAATTTTATAC
Found at i:35035768 original size:20 final size:20
Alignment explanation
Indices: 35035743--35035822 Score: 70
Period size: 21 Copynumber: 3.5 Consensus size: 20
35035733 CAAATAATTT
35035743 TAAAATTATTTTTTAAAATA
1 TAAAATTATTTTTTAAAATA
35035763 TAAAATTATTTAAATTATTTAAAAATTA
1 TAAAATTA--T---TT-TTT-AAAA-TA
35035791 TTAAAATTATTTTTTAAAATAA
1 -TAAAATTATTTTTTAAAAT-A
35035813 TAAAATTATT
1 TAAAATTATT
35035823 AAATAATTTT
Statistics
Matches: 50, Mismatches: 0, Indels: 19
0.72 0.00 0.28
Matches are distributed among these distances:
20 8 0.16
21 11 0.22
22 6 0.12
23 3 0.06
24 2 0.04
25 2 0.04
26 3 0.06
27 5 0.10
28 2 0.04
29 8 0.16
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TAAAATTATTTTTTAAAATA
Found at i:35035779 original size:29 final size:29
Alignment explanation
Indices: 35035745--35035832 Score: 79
Period size: 29 Copynumber: 3.3 Consensus size: 29
35035735 AATAATTTTA
35035745 AAATTATTTTTTAAAATATAAAATTATTT
1 AAATTATTTTTTAAAATATAAAATTATTT
*
35035774 AAATTA----TT----TA-AAAATTATTA
1 AAATTATTTTTTAAAATATAAAATTATTT
35035794 AAATTATTTTTTAAAATAATAAAATTA-TT
1 AAATTATTTTTTAAAAT-ATAAAATTATTT
*
35035823 AAATAATTTT
1 AAATTATTTT
35035833 AATTTACAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 20
0.67 0.04 0.29
Matches are distributed among these distances:
20 15 0.33
21 2 0.04
24 2 0.04
25 2 0.04
28 1 0.02
29 17 0.37
30 7 0.15
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (29 bp):
AAATTATTTTTTAAAATATAAAATTATTT
Found at i:35035834 original size:50 final size:48
Alignment explanation
Indices: 35035738--35035831 Score: 154
Period size: 49 Copynumber: 1.9 Consensus size: 48
35035728 GTCAACAAAT
*
35035738 AATTTTAAAATTATTTTTTAAAATATAAAATTATTTAAATTATTTAAA
1 AATTTTAAAATTATTTTTTAAAATATAAAATTATTTAAATAATTTAAA
35035786 AATTATTAAAATTATTTTTTAAAATAATAAAATTA-TTAAATAATTT
1 AATT-TTAAAATTATTTTTTAAAAT-ATAAAATTATTTAAATAATTT
35035832 TAATTTACAA
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
48 4 0.09
49 30 0.70
50 9 0.21
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (48 bp):
AATTTTAAAATTATTTTTTAAAATATAAAATTATTTAAATAATTTAAA
Found at i:35036824 original size:18 final size:19
Alignment explanation
Indices: 35036774--35036837 Score: 66
Period size: 20 Copynumber: 3.5 Consensus size: 19
35036764 AAAATTATTT
*
35036774 AATAATTTTATTATTTCAAA
1 AATAATTTTA-TATTTTAAA
35036794 AATAA---TA-ATTTT-AA
1 AATAATTTTATATTTTAAA
35036808 AATAATTTTATATTTTAAAA
1 AATAATTTTATATTTT-AAA
35036828 AATAATTTTA
1 AATAATTTTA
35036838 AAATCATTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
14 7 0.19
15 4 0.11
17 4 0.11
18 5 0.14
20 17 0.46
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (19 bp):
AATAATTTTATATTTTAAA
Found at i:35036835 original size:31 final size:34
Alignment explanation
Indices: 35036774--35036846 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 34
35036764 AAAATTATTT
35036774 AATAATTTTATTATTTCAAAAATAATAATTTTAA
1 AATAATTTTATTATTTCAAAAATAATAATTTTAA
*
35036808 AATAATTTTA-TATTT-TAAAA-AATAATTTTAA
1 AATAATTTTATTATTTCAAAAATAATAATTTTAA
*
35036839 AATCATTT
1 AATAATTT
35036847 ATTGATGTGA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
31 18 0.49
32 4 0.11
33 5 0.14
34 10 0.27
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (34 bp):
AATAATTTTATTATTTCAAAAATAATAATTTTAA
Found at i:35040409 original size:14 final size:14
Alignment explanation
Indices: 35040392--35040435 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
35040382 TTTTCATATT
35040392 AAAATTTATCTTAA
1 AAAATTTATCTTAA
* *
35040406 AAAATATAT-TCAA
1 AAAATTTATCTTAA
35040419 AAAATTTATCTTAA
1 AAAATTTATCTTAA
35040433 AAA
1 AAA
35040436 TTATAACATT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
13 11 0.44
14 14 0.56
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (14 bp):
AAAATTTATCTTAA
Found at i:35045288 original size:13 final size:13
Alignment explanation
Indices: 35045270--35045296 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
35045260 ATTATTGAAG
35045270 TGTGGTGTGCTAC
1 TGTGGTGTGCTAC
35045283 TGTGGTGTGCTAC
1 TGTGGTGTGCTAC
35045296 T
1 T
35045297 CATACATCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.15, G:0.37, T:0.41
Consensus pattern (13 bp):
TGTGGTGTGCTAC
Found at i:35048623 original size:37 final size:37
Alignment explanation
Indices: 35048581--35048651 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
35048571 TTTGATTTTG
*
35048581 AATAATTTTGTGAGCGAAATAGAATAAATTAAAACGA
1 AATAATTTTGTGAGCAAAATAGAATAAATTAAAACGA
*
35048618 AATAATTTTGTGAGTAAAATAGAATAAATTAAAA
1 AATAATTTTGTGAGCAAAATAGAATAAATTAAAA
35048652 ATTCTAATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.54, C:0.03, G:0.14, T:0.30
Consensus pattern (37 bp):
AATAATTTTGTGAGCAAAATAGAATAAATTAAAACGA
Found at i:35048896 original size:13 final size:13
Alignment explanation
Indices: 35048856--35048912 Score: 53
Period size: 14 Copynumber: 4.3 Consensus size: 13
35048846 GTTGAATTGT
*
35048856 AAATATCGAATTTC
1 AAAT-TCGAATTTA
*
35048870 AAATTCAAATTTTA
1 AAATTCGAA-TTTA
*
35048884 AAATTTGAATTT-
1 AAATTCGAATTTA
*
35048896 AAACTCGAATTTA
1 AAATTCGAATTTA
35048909 AAAT
1 AAAT
35048913 CCAAATTCAC
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
12 10 0.29
13 10 0.29
14 14 0.41
ACGTcount: A:0.47, C:0.09, G:0.05, T:0.39
Consensus pattern (13 bp):
AAATTCGAATTTA
Found at i:35051708 original size:8 final size:8
Alignment explanation
Indices: 35051697--35051728 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
35051687 TGTTTTTTTT
35051697 TTTTTTAA
1 TTTTTTAA
35051705 TTTTTTAA
1 TTTTTTAA
35051713 TTTTTTAA
1 TTTTTTAA
35051721 TTTTTTAA
1 TTTTTTAA
35051729 ATGAATGTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (8 bp):
TTTTTTAA
Found at i:35067988 original size:21 final size:21
Alignment explanation
Indices: 35067963--35068037 Score: 73
Period size: 21 Copynumber: 3.4 Consensus size: 21
35067953 ACAGACAAAC
35067963 AAAAGAAAACTGAATATTATT
1 AAAAGAAAACTGAATATTATT
*
35067984 AAAAGAAAGA-TGAAAAAGATTAAATT
1 AAAAGAAA-ACTG---AATATT--ATT
35068010 AAAA-AAAACTGAATATTATT
1 AAAAGAAAACTGAATATTATT
35068030 AAAAGAAA
1 AAAAGAAA
35068038 GATGAAAAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 16
0.71 0.03 0.26
Matches are distributed among these distances:
20 7 0.16
21 13 0.30
22 6 0.14
24 6 0.14
25 5 0.11
26 7 0.16
ACGTcount: A:0.64, C:0.03, G:0.11, T:0.23
Consensus pattern (21 bp):
AAAAGAAAACTGAATATTATT
Found at i:35067992 original size:25 final size:25
Alignment explanation
Indices: 35067964--35068039 Score: 70
Period size: 25 Copynumber: 3.2 Consensus size: 25
35067954 CAGACAAACA
35067964 AAAGAAAACTGAATATTATTAAAAG
1 AAAGAAAACTGAATATTATTAAAAG
* ** **
35067989 AAAG---A-TGAAAAAGATTAAATT
1 AAAGAAAACTGAATATTATTAAAAG
*
35068010 AAAAAAAACTGAATATTATTAAAAG
1 AAAGAAAACTGAATATTATTAAAAG
35068035 AAAGA
1 AAAGA
35068040 TGAAAAATAT
Statistics
Matches: 35, Mismatches: 12, Indels: 8
0.64 0.22 0.15
Matches are distributed among these distances:
21 14 0.40
22 1 0.03
24 1 0.03
25 19 0.54
ACGTcount: A:0.63, C:0.03, G:0.12, T:0.22
Consensus pattern (25 bp):
AAAGAAAACTGAATATTATTAAAAG
Found at i:35068021 original size:46 final size:46
Alignment explanation
Indices: 35067963--35068063 Score: 184
Period size: 46 Copynumber: 2.2 Consensus size: 46
35067953 ACAGACAAAC
35067963 AAAAGAAAACTGAATATTATTAAAAGAAAGATGAAAAAGATTAAATT
1 AAAA-AAAACTGAATATTATTAAAAGAAAGATGAAAAAGATTAAATT
*
35068010 AAAAAAAACTGAATATTATTAAAAGAAAGATGAAAAATATTAAATT
1 AAAAAAAACTGAATATTATTAAAAGAAAGATGAAAAAGATTAAATT
35068056 AAAAAAAA
1 AAAAAAAA
35068064 ACTGCGTAAA
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
46 49 0.92
47 4 0.08
ACGTcount: A:0.65, C:0.02, G:0.10, T:0.23
Consensus pattern (46 bp):
AAAAAAAACTGAATATTATTAAAAGAAAGATGAAAAAGATTAAATT
Found at i:35068050 original size:21 final size:22
Alignment explanation
Indices: 35067963--35068053 Score: 71
Period size: 21 Copynumber: 4.1 Consensus size: 22
35067953 ACAGACAAAC
* *
35067963 AAAAGAAA-ACTGAATATTATT
1 AAAAGAAAGACTGAAAAATATT
*
35067984 AAAAGAAAGA-TGAAAAAGATT
1 AAAAGAAAGACTGAAAAATATT
* * * *
35068005 AAATTAAAAAAAACTGAATATTATT
1 -AA--AAGAAAGACTGAAAAATATT
35068030 AAAAGAAAGA-TGAAAAATATT
1 AAAAGAAAGACTGAAAAATATT
35068051 AAA
1 AAA
35068054 TTAAAAAAAA
Statistics
Matches: 53, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
21 28 0.53
22 9 0.17
24 8 0.15
25 8 0.15
ACGTcount: A:0.64, C:0.02, G:0.11, T:0.23
Consensus pattern (22 bp):
AAAAGAAAGACTGAAAAATATT
Found at i:35091510 original size:22 final size:22
Alignment explanation
Indices: 35091476--35091519 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
35091466 CAAAAGGTTA
35091476 TAAAATTGTCA-TTAAATTATT
1 TAAAATTGTCATTTAAATTATT
* *
35091497 TAAAAGTTTTCATTTAAGTTATT
1 TAAAA-TTGTCATTTAAATTATT
35091520 GACTGTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 5 0.26
22 5 0.26
23 9 0.47
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.50
Consensus pattern (22 bp):
TAAAATTGTCATTTAAATTATT
Found at i:35111641 original size:92 final size:93
Alignment explanation
Indices: 35111483--35111669 Score: 286
Period size: 92 Copynumber: 2.0 Consensus size: 93
35111473 TTCTTTTTTG
35111483 TTCAATCAATCATTTAATAAAAAAAATTAACATAAAAATACTAAATTCAATCAATCATATTTAAT
1 TTCAATCAATCATTTAATAAAAAAAATTAACATAAAAATACTAAATTCAATCAATCATATTTAAT
*
35111548 AAAGTTACCTAAATTAATTTATTATTTA
66 AAAATTACCTAAATTAATTTATTATTTA
* * * * * *
35111576 TTCAATCAATCATTTAA-GAAAAAATTTACCTTACAAATATTAAATTCAATCAATCATATTTAAT
1 TTCAATCAATCATTTAATAAAAAAAATTAACATAAAAATACTAAATTCAATCAATCATATTTAAT
**
35111640 AAAATTGTCTAAATTAATTTATTATTTA
66 AAAATTACCTAAATTAATTTATTATTTA
35111668 TT
1 TT
35111670 AAATATGATT
Statistics
Matches: 85, Mismatches: 9, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
92 68 0.80
93 17 0.20
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.40
Consensus pattern (93 bp):
TTCAATCAATCATTTAATAAAAAAAATTAACATAAAAATACTAAATTCAATCAATCATATTTAAT
AAAATTACCTAAATTAATTTATTATTTA
Found at i:35113452 original size:18 final size:18
Alignment explanation
Indices: 35113414--35113454 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
35113404 ATTAATCAAC
* *
35113414 CGATTAACCGAATTCGAT
1 CGATTAACCAAATTAGAT
*
35113432 CGATTAACCAAATTAGTT
1 CGATTAACCAAATTAGAT
35113450 CGATT
1 CGATT
35113455 TTATCCGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.32
Consensus pattern (18 bp):
CGATTAACCAAATTAGAT
Found at i:35130942 original size:3 final size:3
Alignment explanation
Indices: 35130934--35130958 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
35130924 GTTTAACAAG
35130934 GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA G
35130959 GGTTTATTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:35137950 original size:22 final size:22
Alignment explanation
Indices: 35137921--35137962 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
35137911 AATCTCTATA
35137921 CTTTAATTTTATTT-TTTTAGT
1 CTTTAATTTTATTTATTTTAGT
*
35137942 CTTTGAATTTTTTTTATTTTA
1 CTTT-AATTTTATTTATTTTA
35137963 AAATTTTAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 9 0.50
23 5 0.28
ACGTcount: A:0.19, C:0.05, G:0.05, T:0.71
Consensus pattern (22 bp):
CTTTAATTTTATTTATTTTAGT
Found at i:35142692 original size:23 final size:24
Alignment explanation
Indices: 35142646--35142694 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
35142636 TGACCAAATT
* *
35142646 AAAATATAAGTATTAATTCACCAAA
1 AAAATATAAATATTAAAT-ACCAAA
35142671 AAAATATAAATATTAAAT-CCAAA
1 AAAATATAAATATTAAATACCAAA
35142694 A
1 A
35142695 TTTACGTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 6 0.27
25 16 0.73
ACGTcount: A:0.61, C:0.10, G:0.02, T:0.27
Consensus pattern (24 bp):
AAAATATAAATATTAAATACCAAA
Found at i:35143050 original size:14 final size:14
Alignment explanation
Indices: 35143031--35143062 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
35143021 ATTCTCCTAC
35143031 TCTTTATATTTATT
1 TCTTTATATTTATT
35143045 TCTTTATATTTATT
1 TCTTTATATTTATT
35143059 TCTT
1 TCTT
35143063 CTTCAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.19, C:0.09, G:0.00, T:0.72
Consensus pattern (14 bp):
TCTTTATATTTATT
Found at i:35148297 original size:41 final size:41
Alignment explanation
Indices: 35148230--35148467 Score: 271
Period size: 41 Copynumber: 5.8 Consensus size: 41
35148220 TCTACATAAA
* *
35148230 CGCCGCAAAAGGT-AGGGCAATAGCGGCGCTTATGGGAAAG
1 CGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAG
* * * **
35148270 CGCCGCTACAGGTTAGAGCAATTGCGGCGCTTATCAGAAAG
1 CGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAG
* * * *
35148311 TGCCGCTAAAGGTCAGAGCAATAGTGACGCTTATGGGAAGG
1 CGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAG
*
35148352 CGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGTGAAAG
1 CGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAG
* * * **
35148393 CGCCGCTGAAGGTCAAAGCAATAGCGGTGCTTATGGGCCAG
1 CGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAG
* * * * *
35148434 CGCTGCTAAAGATCAGAGCACTAACGACGCTTAT
1 CGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTAT
35148468 TTGAAAAACG
Statistics
Matches: 163, Mismatches: 34, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
40 11 0.07
41 152 0.93
ACGTcount: A:0.29, C:0.22, G:0.32, T:0.18
Consensus pattern (41 bp):
CGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAG
Found at i:35149902 original size:41 final size:41
Alignment explanation
Indices: 35149845--35150007 Score: 184
Period size: 41 Copynumber: 3.9 Consensus size: 41
35149835 TTAATTTTAG
35149845 CGACGTTTGTGGGAAAAGCGCCGCTAAAGATCATGTTATTT
1 CGACGTTTGTGGGAAAAGCGCCGCTAAAGATCATGTTATTT
* * *
35149886 CGACGTTTGTGAGAAAAGCGCCGTTAAAGATCATGTTTTTT
1 CGACGTTTGTGGGAAAAGCGCCGCTAAAGATCATGTTATTT
* * * *
35149927 AGCAGCATTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTTT
1 CG-A-CGTTTGTGGGAAAAGCGCCGCTAAAGATCATGTTATTT
* * * *
35149970 AGCGGCGTTTAT-GGATAAGCACCGCTAAAGATCATGTT
1 --CGACGTTTGTGGGAAAAGCGCCGCTAAAGATCATGTT
35150008 CTATAACGAT
Statistics
Matches: 102, Mismatches: 16, Indels: 7
0.82 0.13 0.06
Matches are distributed among these distances:
41 39 0.38
42 24 0.24
43 38 0.37
45 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.29
Consensus pattern (41 bp):
CGACGTTTGTGGGAAAAGCGCCGCTAAAGATCATGTTATTT
Found at i:35149949 original size:43 final size:43
Alignment explanation
Indices: 35149840--35150007 Score: 200
Period size: 43 Copynumber: 4.0 Consensus size: 43
35149830 ATTTATTAAT
35149840 TTTAGC-GACGTTTGTGGGAAAAGCGCCGCTAAAGATCATGTTA
1 TTTAGCAG-CGTTTGTGGGAAAAGCGCCGCTAAAGATCATGTTA
* * * *
35149883 TTTCG-A-CGTTTGTGAGAAAAGCGCCGTTAAAGATCATGTTT
1 TTTAGCAGCGTTTGTGGGAAAAGCGCCGCTAAAGATCATGTTA
* * *
35149924 TTTAGCAGCATTTGTGGGAAAAGCGCCGCTAAAGACCATGTTC
1 TTTAGCAGCGTTTGTGGGAAAAGCGCCGCTAAAGATCATGTTA
* * * *
35149967 TTTAGCGGCGTTTAT-GGATAAGCACCGCTAAAGATCATGTT
1 TTTAGCAGCGTTTGTGGGAAAAGCGCCGCTAAAGATCATGTT
35150008 CTATAACGAT
Statistics
Matches: 106, Mismatches: 16, Indels: 7
0.82 0.12 0.05
Matches are distributed among these distances:
41 36 0.34
42 24 0.23
43 46 0.43
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (43 bp):
TTTAGCAGCGTTTGTGGGAAAAGCGCCGCTAAAGATCATGTTA
Found at i:35149965 original size:84 final size:84
Alignment explanation
Indices: 35149850--35150007 Score: 228
Period size: 84 Copynumber: 1.9 Consensus size: 84
35149840 TTTAGCGACG
* * * *
35149850 TTTGTGGGAAAAGCGCCGCTAAAGATCATGTTATTT-CGACGTTTGTGAGAAAAGCGCCGTTAAA
1 TTTGTGGGAAAAGCGCCGCTAAAGACCATGTTATTTACGACGTTTATG-GAAAAGCACCGCTAAA
35149914 GATCATGTTTTTTAGCAGCA
65 GATCATGTTTTTTAGCAGCA
* * *
35149934 TTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTATGGATAAGCACCGCTAAA
1 TTTGTGGGAAAAGCGCCGCTAAAGACCATGTTATTTA-CGACGTTTATGGAAAAGCACCGCTAAA
35149999 GATCATGTT
65 GATCATGTT
35150008 CTATAACGAT
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
84 34 0.52
85 22 0.34
86 9 0.14
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (84 bp):
TTTGTGGGAAAAGCGCCGCTAAAGACCATGTTATTTACGACGTTTATGGAAAAGCACCGCTAAAG
ATCATGTTTTTTAGCAGCA
Found at i:35150089 original size:21 final size:20
Alignment explanation
Indices: 35150051--35150089 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
35150041 ATTTTTAGTG
* *
35150051 GCATTTTTTACGGTGCTTTT
1 GCATGTTTTACGGCGCTTTT
35150071 GCATGTTTTAGCGGCGCTT
1 GCATGTTTTA-CGGCGCTT
35150090 ATAAGCGCCG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.10, C:0.18, G:0.26, T:0.46
Consensus pattern (20 bp):
GCATGTTTTACGGCGCTTTT
Found at i:35152600 original size:2 final size:2
Alignment explanation
Indices: 35152593--35152642 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
35152583 CTCAACACGC
35152593 AT AT 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 AT AT
35152635 AT AT AT AT
1 AT AT AT AT
35152643 TGGAATAAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35156835 original size:6 final size:7
Alignment explanation
Indices: 35156819--35156887 Score: 52
Period size: 7 Copynumber: 9.3 Consensus size: 7
35156809 TTGTTTAATG
35156819 AAAATTA
1 AAAATTA
35156826 AAAATTA
1 AAAATTA
35156833 AAAATTTTA
1 AAAA--TTA
*
35156842 AAAATACA
1 AAAAT-TA
35156850 AAAATTA
1 AAAATTA
35156857 AAAA-TA
1 AAAATTA
35156863 ACCAAA-TA
1 A--AAATTA
*
35156871 AAAGTATA
1 AAAAT-TA
35156879 AAAATTA
1 AAAATTA
35156886 AA
1 AA
35156888 TCTATAACTT
Statistics
Matches: 51, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
6 5 0.10
7 21 0.41
8 18 0.35
9 7 0.14
ACGTcount: A:0.70, C:0.04, G:0.01, T:0.25
Consensus pattern (7 bp):
AAAATTA
Found at i:35156857 original size:15 final size:14
Alignment explanation
Indices: 35156819--35156887 Score: 59
Period size: 15 Copynumber: 4.6 Consensus size: 14
35156809 TTGTTTAATG
35156819 AAAATTAAAAATTAA
1 AAAATTAAAAA-TAA
*
35156834 AAATTTTAAAAATACA
1 AAA-ATTAAAAATA-A
35156850 AAAATTAAAAATAA
1 AAAATTAAAAATAA
* *
35156864 CCAAA-TAAAAGTATA
1 -AAAATTAAAAATA-A
35156879 AAAATTAAA
1 AAAATTAAA
35156888 TCTATAACTT
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
14 11 0.25
15 22 0.50
16 11 0.25
ACGTcount: A:0.70, C:0.04, G:0.01, T:0.25
Consensus pattern (14 bp):
AAAATTAAAAATAA
Found at i:35157730 original size:27 final size:25
Alignment explanation
Indices: 35157699--35157752 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
35157689 AAAAATATCA
*
35157699 TTTATTATTTAATAAAATTAATATTTT
1 TTTATAATTTAAT-AAA-TAATATTTT
* *
35157726 TTTATAATTTTATGAATAATATTTT
1 TTTATAATTTAATAAATAATATTTT
35157751 TT
1 TT
35157753 GTTGAAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 11 0.46
26 2 0.08
27 11 0.46
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (25 bp):
TTTATAATTTAATAAATAATATTTT
Found at i:35165810 original size:14 final size:13
Alignment explanation
Indices: 35165776--35165806 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
35165766 TTAAACCAAA
35165776 CTTTTT-AAAATT
1 CTTTTTCAAAATT
35165788 CTTTTTCAAAATT
1 CTTTTTCAAAATT
35165801 CTTTTT
1 CTTTTT
35165807 TCAACACACT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.26, C:0.13, G:0.00, T:0.61
Consensus pattern (13 bp):
CTTTTTCAAAATT
Found at i:35165830 original size:13 final size:13
Alignment explanation
Indices: 35165775--35165830 Score: 51
Period size: 13 Copynumber: 4.3 Consensus size: 13
35165765 CTTAAACCAA
35165775 ACTTTTT-AAAAT
1 ACTTTTTCAAAAT
*
35165787 TCTTTTTCAAAAT
1 ACTTTTTCAAAAT
* * *
35165800 TCTTTTTTCAACAC
1 AC-TTTTTCAAAAT
*
35165814 ACTTTTTAAAAAT
1 ACTTTTTCAAAAT
35165827 ACTT
1 ACTT
35165831 CTCAAAAGTA
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
12 6 0.17
13 19 0.54
14 10 0.29
ACGTcount: A:0.34, C:0.16, G:0.00, T:0.50
Consensus pattern (13 bp):
ACTTTTTCAAAAT
Found at i:35167656 original size:33 final size:31
Alignment explanation
Indices: 35167605--35167669 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 31
35167595 AATAATAGTA
*
35167605 AATATTATTTTATATAAATTATTTTTAATTATT
1 AATAATATTTTATATAAATT-TTTTT-ATTATT
* *
35167638 AATAATATTTTTTTTAAATTTTTTTATTATT
1 AATAATATTTTATATAAATTTTTTTATTATT
35167669 A
1 A
35167670 TTTATTAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 7 0.24
32 5 0.17
33 17 0.59
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (31 bp):
AATAATATTTTATATAAATTTTTTTATTATT
Found at i:35176111 original size:21 final size:21
Alignment explanation
Indices: 35176087--35176131 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
35176077 AAATTAATTT
35176087 AATAACTATTAAAATAATAAA
1 AATAACTATTAAAATAATAAA
** * *
35176108 AATATTTTTTATAATAATAAA
1 AATAACTATTAAAATAATAAA
35176129 AAT
1 AAT
35176132 TATAATTTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (21 bp):
AATAACTATTAAAATAATAAA
Found at i:35191786 original size:31 final size:32
Alignment explanation
Indices: 35191720--35191789 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 32
35191710 ATTTTTTAAA
35191720 ATGTATACAGTTGAATCAAAACCAAAAGTTTT
1 ATGTATACAGTTGAATCAAAACCAAAAGTTTT
* *
35191752 ATGTATACA-TTCGAATCACAATCAAAA-TTTT
1 ATGTATACAGTT-GAATCAAAACCAAAAGTTTT
35191783 ATGTATA
1 ATGTATA
35191790 TAATTATGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
31 13 0.37
32 22 0.63
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.34
Consensus pattern (32 bp):
ATGTATACAGTTGAATCAAAACCAAAAGTTTT
Found at i:35202273 original size:25 final size:25
Alignment explanation
Indices: 35202258--35202311 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
35202248 TATATATGTC
35202258 GATTTTTTTATCAATTAGTTAAATA
1 GATTTTTTTATCAATTAGTTAAATA
35202283 GATTTTTTTATCAATTAGTTAAATA
1 GATTTTTTTATCAATTAGTTAAATA
35202308 GATT
1 GATT
35202312 GCTTTTTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.35, C:0.04, G:0.09, T:0.52
Consensus pattern (25 bp):
GATTTTTTTATCAATTAGTTAAATA
Found at i:35205060 original size:29 final size:29
Alignment explanation
Indices: 35205011--35205078 Score: 102
Period size: 28 Copynumber: 2.3 Consensus size: 29
35205001 TGATAAATAT
*
35205011 AAAATTATAATTTAATTTTTTTAAAATGATA
1 AAAATT-TAATTTAATTTTTTTAAAAT-AAA
35205042 AAAATTTAATTTAA-TTTTTTAAAATAAA
1 AAAATTTAATTTAATTTTTTTAAAATAAA
35205070 AAAATTTAA
1 AAAATTTAA
35205079 ATATTTAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
28 11 0.31
29 11 0.31
30 8 0.22
31 6 0.17
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (29 bp):
AAAATTTAATTTAATTTTTTTAAAATAAA
Found at i:35205095 original size:22 final size:23
Alignment explanation
Indices: 35205049--35205097 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
35205039 ATAAAAATTT
* *
35205049 AATTTAATTTTTTAAAATAAAAA
1 AATTTAAATATTTAAAATAAAAA
*
35205072 AATTTAAATATTT-AAATAATAA
1 AATTTAAATATTTAAAATAAAAA
35205094 AATT
1 AATT
35205098 ATATTTTTAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 12 0.52
23 11 0.48
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
AATTTAAATATTTAAAATAAAAA
Found at i:35217398 original size:117 final size:116
Alignment explanation
Indices: 35217269--35217628 Score: 580
Period size: 117 Copynumber: 3.1 Consensus size: 116
35217259 GCGTAAGTAT
** * *
35217269 TTTTATTTTTATTATTATAATATATGATCTCCCCACTACAATAATTAAATCAGACAGATAGTATT
1 TTTTATTTTTATTATTATAATATATGATCTCGTCACTACAATAATTAAACCAGACAAATAGTATT
* *
35217334 AATGGCCTAGATATTAATATATTGAATTCTAGTAGTTTCACGAGAAATTAG
66 AATGGCTTAGATACTAATATATTGAATTCTAGTAGTTTCACGAGAAATTAG
35217385 TTTTATTTTTTATTATTATAATATATGATCTCGTCACTACAATAATTAAACCAGACAAATAGTAT
1 TTTTA-TTTTTATTATTATAATATATGATCTCGTCACTACAATAATTAAACCAGACAAATAGTAT
* * *
35217450 TAATGGCTTTGATACTAATATATTGAATTGTAGTAGTTTCACGAGAAATTAA
65 TAATGGCTTAGATACTAATATATTGAATTCTAGTAGTTTCACGAGAAATTAG
35217502 TTTTATTTTT-TTATTATAATATATGATCTCGTCACTACAATAATTAAACCAGACAAATAGTATT
1 TTTTATTTTTATTATTATAATATATGATCTCGTCACTACAATAATTAAACCAGACAAATAGTATT
* * *
35217566 AATGGCTTGGATACTAATATATTGAATTTTAGTAGTTTCACGGGAAATT-G
66 AATGGCTTAGATACTAATATATTGAATTCTAGTAGTTTCACGAGAAATTAG
*
35217616 TTTTTTTTTTATT
1 TTTTATTTTTATT
35217629 TTTTATTTTT
Statistics
Matches: 228, Mismatches: 14, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
114 9 0.04
115 102 0.45
116 10 0.04
117 107 0.47
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (116 bp):
TTTTATTTTTATTATTATAATATATGATCTCGTCACTACAATAATTAAACCAGACAAATAGTATT
AATGGCTTAGATACTAATATATTGAATTCTAGTAGTTTCACGAGAAATTAG
Found at i:35251198 original size:3 final size:3
Alignment explanation
Indices: 35251190--35251218 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
35251180 TTTAGCGTGC
35251190 TAT TAT TAT TAT TAT TAT TAT T-T TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
35251219 CCCAAGCAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:35251346 original size:19 final size:19
Alignment explanation
Indices: 35251319--35251375 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
35251309 GGCGAAGGAA
35251319 AAAAAAAGAAAAGAAAGAT
1 AAAAAAAGAAAAGAAAGAT
* *
35251338 AAAATAAGAAAAGAAAGAG
1 AAAAAAAGAAAAGAAAGAT
*
35251357 AAAGAAAGAGAAAAAAAAG
1 AAA-AAA-AGAAAAGAAAG
35251376 TACGTCTATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 20 0.62
20 2 0.06
21 10 0.31
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (19 bp):
AAAAAAAGAAAAGAAAGAT
Found at i:35251369 original size:10 final size:9
Alignment explanation
Indices: 35251318--35251365 Score: 53
Period size: 9 Copynumber: 5.1 Consensus size: 9
35251308 TGGCGAAGGA
*
35251318 AAAAAAAAG
1 AAAAGAAAG
35251327 AAAAGAAAG
1 AAAAGAAAG
35251336 ATAAA-ATAAG
1 A-AAAGA-AAG
35251346 AAAAGAAAG
1 AAAAGAAAG
35251355 AGAAAGAAAG
1 A-AAAGAAAG
35251365 A
1 A
35251366 GAAAAAAAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
9 17 0.50
10 17 0.50
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (9 bp):
AAAAGAAAG
Found at i:35251680 original size:29 final size:30
Alignment explanation
Indices: 35251629--35251687 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 30
35251619 TTAAAATTAT
**
35251629 ACATGAATTTTAGTTTAATGTATAATTTTAG
1 ACATGAATTTTAAATT-ATGTATAATTTTAG
*
35251660 ACATGAATTTTAAATT-TGTATATTTTTA
1 ACATGAATTTTAAATTATGTATAATTTTA
35251688 TATATAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 11 0.44
31 14 0.56
ACGTcount: A:0.36, C:0.03, G:0.10, T:0.51
Consensus pattern (30 bp):
ACATGAATTTTAAATTATGTATAATTTTAG
Found at i:35251796 original size:25 final size:25
Alignment explanation
Indices: 35251762--35251809 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
35251752 TTTTATGTTT
*
35251762 ATATAGAAAT-AATTGTATTTATTCA
1 ATATAAAAATAAATT-TATTTATTCA
35251787 ATATAAAAATAAATTTATTTATT
1 ATATAAAAATAAATTTATTTATT
35251810 TATTTCTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 17 0.81
26 4 0.19
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (25 bp):
ATATAAAAATAAATTTATTTATTCA
Found at i:35251866 original size:31 final size:29
Alignment explanation
Indices: 35251822--35251880 Score: 73
Period size: 31 Copynumber: 2.0 Consensus size: 29
35251812 TTTCTTCAAA
*
35251822 TATATATGATTAAATCAAAATTAAAATTT
1 TATATATGATTAAACCAAAATTAAAATTT
* *
35251851 TATATATGCATTTAAACCACAATTTAAATT
1 TATATATG-A-TTAAACCAAAATTAAAATT
35251881 ACACATTGCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 8 0.32
30 1 0.04
31 16 0.64
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.41
Consensus pattern (29 bp):
TATATATGATTAAACCAAAATTAAAATTT
Found at i:35252155 original size:33 final size:32
Alignment explanation
Indices: 35252118--35252182 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 32
35252108 AAACTAGAAC
*
35252118 TAAAAAAAAAACAAATT-AAATTCTTACAATTTA
1 TAAAAAAAAAA-AAATTCAAATTCATA-AATTTA
* *
35252151 TAAAATAAATAAAATTCAAATTCATAAATTTA
1 TAAAAAAAAAAAAATTCAAATTCATAAATTTA
35252183 CGTTTCCCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
32 11 0.39
33 17 0.61
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (32 bp):
TAAAAAAAAAAAAATTCAAATTCATAAATTTA
Found at i:35254412 original size:52 final size:51
Alignment explanation
Indices: 35254349--35254450 Score: 143
Period size: 52 Copynumber: 2.0 Consensus size: 51
35254339 CTTCCCCTTA
* * * *
35254349 CTTATCTTACATCAGTTGTTTTGAAACACACAACATT-TTGCAAAGCTAAAGC
1 CTTATCCTACATCACTTGTTTCGAAACACA-AA-ATTCCTGCAAAGCTAAAGC
35254401 CTTATCCTACATCACTTGTTTCGAAACACAAAATTCCTGCAAAGCTAAAG
1 CTTATCCTACATCACTTGTTTCGAAACACAAAATTCCTGCAAAGCTAAAG
35254451 TATGCATTAG
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
50 3 0.07
51 15 0.33
52 27 0.60
ACGTcount: A:0.35, C:0.24, G:0.11, T:0.30
Consensus pattern (51 bp):
CTTATCCTACATCACTTGTTTCGAAACACAAAATTCCTGCAAAGCTAAAGC
Found at i:35256084 original size:21 final size:20
Alignment explanation
Indices: 35256048--35256089 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
35256038 AAAAAGTATA
* *
35256048 AAAAATAACATTAAAATAAC
1 AAAAATAACATCAAAACAAC
35256068 AAAAATAACAATCAAAACAAC
1 AAAAATAAC-ATCAAAACAAC
35256089 A
1 A
35256090 GCAAAAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.71, C:0.14, G:0.00, T:0.14
Consensus pattern (20 bp):
AAAAATAACATCAAAACAAC
Found at i:35256096 original size:12 final size:12
Alignment explanation
Indices: 35256065--35256166 Score: 57
Period size: 12 Copynumber: 8.6 Consensus size: 12
35256055 ACATTAAAAT
*
35256065 AACAAAAATAAC
1 AACAAAAACAAC
35256077 AATC-AAAACAAC
1 AA-CAAAAACAAC
* * *
35256089 AGCAAAAATAAT
1 AACAAAAACAAC
* *
35256101 AGC-AAGACAAC
1 AACAAAAACAAC
*
35256112 AACAAAAACAAG
1 AACAAAAACAAC
*
35256124 AACAAAAATAAC
1 AACAAAAACAAC
* * *
35256136 AATAAAGACAGC
1 AACAAAAACAAC
*
35256148 -ACCAAAACAAC
1 AACAAAAACAAC
35256159 AACCAAAA
1 AA-CAAAA
35256167 TAATAAAAAA
Statistics
Matches: 64, Mismatches: 21, Indels: 9
0.68 0.22 0.10
Matches are distributed among these distances:
11 15 0.23
12 44 0.69
13 5 0.08
ACGTcount: A:0.68, C:0.21, G:0.06, T:0.06
Consensus pattern (12 bp):
AACAAAAACAAC
Found at i:35256185 original size:22 final size:22
Alignment explanation
Indices: 35256160--35256238 Score: 83
Period size: 22 Copynumber: 3.6 Consensus size: 22
35256150 CAAAACAACA
*
35256160 ACCAAAATAATAAAAAAATAGC
1 ACCAAAACAATAAAAAAATAGC
35256182 ACCAAAACAGCA-AAAAACAATA--
1 ACCAAAACA--ATAAAAA-AATAGC
* *
35256204 ATCAAAACAGTAAAAAAATAGC
1 ACCAAAACAATAAAAAAATAGC
35256226 ACCAAAACAATAA
1 ACCAAAACAATAA
35256239 TATAATTTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
20 4 0.09
21 5 0.11
22 27 0.59
23 5 0.11
24 5 0.11
ACGTcount: A:0.67, C:0.18, G:0.05, T:0.10
Consensus pattern (22 bp):
ACCAAAACAATAAAAAAATAGC
Found at i:35256188 original size:34 final size:35
Alignment explanation
Indices: 35256116--35256204 Score: 99
Period size: 35 Copynumber: 2.5 Consensus size: 35
35256106 GACAACAACA
* *
35256116 AAAACAAGAACAAAAATAACAATAAAGACAGCACC
1 AAAACAACAACAAAAATAACAATAAAAACAGCACC
* * *
35256151 AAAACAACAACCAAAATAATAA-AAAAATAGCACC
1 AAAACAACAACAAAAATAACAATAAAAACAGCACC
* *
35256185 AAAACAGCAAAAAACAATAA
1 AAAACAACAACAAA-AATAA
35256205 TCAAAACAGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
34 21 0.47
35 24 0.53
ACGTcount: A:0.69, C:0.19, G:0.06, T:0.07
Consensus pattern (35 bp):
AAAACAACAACAAAAATAACAATAAAAACAGCACC
Found at i:35256199 original size:44 final size:44
Alignment explanation
Indices: 35256107--35256234 Score: 139
Period size: 44 Copynumber: 2.8 Consensus size: 44
35256097 TAATAGCAAG
* * * ** *
35256107 ACAACAACAAAAACAAGAACAAAAATAACAATAAAGACAGCACCAAA
1 ACAACAACCAAAACAATAA-AAAAATAGCACCAAA-ACAGCA-AAAA
*
35256154 ACAACAACCAAAATAATAAAAAAATAGCACCAAAACAGCAAAAA
1 ACAACAACCAAAACAATAAAAAAATAGCACCAAAACAGCAAAAA
* * *
35256198 ACAATAATCAAAACAGTAAAAAAATAGCACCAAAACA
1 ACAACAACCAAAACAATAAAAAAATAGCACCAAAACA
35256235 ATAATATAAT
Statistics
Matches: 70, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
44 36 0.51
45 6 0.09
46 12 0.17
47 16 0.23
ACGTcount: A:0.67, C:0.20, G:0.05, T:0.07
Consensus pattern (44 bp):
ACAACAACCAAAACAATAAAAAAATAGCACCAAAACAGCAAAAA
Found at i:35256753 original size:18 final size:18
Alignment explanation
Indices: 35256710--35256750 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
35256700 ATGTTCTATA
35256710 TAAAAATTATAAAAAAAC
1 TAAAAATTATAAAAAAAC
* *
35256728 TTAAAATTATTAAAAAA-
1 TAAAAATTATAAAAAAAC
35256745 TAAAAA
1 TAAAAA
35256751 ATTCTATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (18 bp):
TAAAAATTATAAAAAAAC
Found at i:35257433 original size:222 final size:222
Alignment explanation
Indices: 35257047--35257495 Score: 853
Period size: 222 Copynumber: 2.0 Consensus size: 222
35257037 AGACAAACAA
*
35257047 AAGTGACTATTTTGATAACCTATCCATATATATTATGATTAACAAGGTAATTAAGCTATAAATCA
1 AAGTGACTATTTTGATAACCTATCCATATATATTAGGATTAACAAGGTAATTAAGCTATAAATCA
* *
35257112 CTAACCTAATGGCATTAACATAGAATTTGAAATGGTTTAATTGTTAATATAACTTTTGTTTAATT
66 CTAACCAAATGGCATTAACATAGAATTTGAAATGGTTTAATTGTTAATATAACTTTTGTTTAATC
35257177 GTTTATTTGTCATTTAAGGAACTTATCAATTTTAAAACCACTTTCCTTTCACTTTAGTCCCTAAT
131 GTTTATTTGTCATTTAAGGAACTTATCAATTTTAAAACCACTTTCCTTTCACTTTAGTCCCTAAT
35257242 CAATTTAGTTTTTGTACTGAACCTAAC
196 CAATTTAGTTTTTGTACTGAACCTAAC
*
35257269 AAGTGACTATTTTGATAGCCTATCCATATATATTAGGATTAACAAGGTAATTAAGCTATAAATCA
1 AAGTGACTATTTTGATAACCTATCCATATATATTAGGATTAACAAGGTAATTAAGCTATAAATCA
35257334 CTAACCAAATGGCATTAACATAGAATTTGAAATGGTTTAATTGTTAATATAACTTTTGTTTAATC
66 CTAACCAAATGGCATTAACATAGAATTTGAAATGGTTTAATTGTTAATATAACTTTTGTTTAATC
35257399 GTTTATTTGTCATTTAAGGAACTTATCAATTTTAAAACCACTTTCCTTTCACTTTAGTCCCTAAT
131 GTTTATTTGTCATTTAAGGAACTTATCAATTTTAAAACCACTTTCCTTTCACTTTAGTCCCTAAT
*
35257464 CAATTTAGTTTTTGTATTGAACCTAAC
196 CAATTTAGTTTTTGTACTGAACCTAAC
35257491 AAGTG
1 AAGTG
35257496 GTTTCAATGG
Statistics
Matches: 222, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
222 222 1.00
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.40
Consensus pattern (222 bp):
AAGTGACTATTTTGATAACCTATCCATATATATTAGGATTAACAAGGTAATTAAGCTATAAATCA
CTAACCAAATGGCATTAACATAGAATTTGAAATGGTTTAATTGTTAATATAACTTTTGTTTAATC
GTTTATTTGTCATTTAAGGAACTTATCAATTTTAAAACCACTTTCCTTTCACTTTAGTCCCTAAT
CAATTTAGTTTTTGTACTGAACCTAAC
Found at i:35265859 original size:2 final size:2
Alignment explanation
Indices: 35265852--35265913 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
35265842 ACAATTTGCA
35265852 AT AT 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 AT AT
35265894 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
35265914 CAACTCATTA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35280796 original size:28 final size:31
Alignment explanation
Indices: 35280765--35280825 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 31
35280755 TTTTTTTTCG
35280765 TTTTT-AATAAATGACCCAATAT-TTT-TAC
1 TTTTTGAATAAATGACCCAATATGTTTCTAC
** *
35280793 TTTTTGTGTAAATGGCCCAATATGTTTCTAC
1 TTTTTGAATAAATGACCCAATATGTTTCTAC
35280824 TT
1 TT
35280826 ATTCTTCTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 5 0.19
29 14 0.52
30 3 0.11
31 5 0.19
ACGTcount: A:0.28, C:0.15, G:0.10, T:0.48
Consensus pattern (31 bp):
TTTTTGAATAAATGACCCAATATGTTTCTAC
Found at i:35281718 original size:30 final size:31
Alignment explanation
Indices: 35281659--35281723 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
35281649 TGGGTGTTTG
* * *
35281659 ATTTTTTGAAAGTTAGTATGATTGATTTGTT
1 ATTTTTTGAAAGTTAGAATGACTGATTTGTC
*
35281690 ATTTTTTGAAAGTT-GAATGACTGTTTTGTC
1 ATTTTTTGAAAGTTAGAATGACTGATTTGTC
35281720 ATTT
1 ATTT
35281724 ACCCTTATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 16 0.53
31 14 0.47
ACGTcount: A:0.25, C:0.03, G:0.18, T:0.54
Consensus pattern (31 bp):
ATTTTTTGAAAGTTAGAATGACTGATTTGTC
Found at i:35283893 original size:6 final size:6
Alignment explanation
Indices: 35283884--35283909 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
35283874 GGGTTGATTC
35283884 TTGGTT TTGGTT TTGGTT TTGGTT TT
1 TTGGTT TTGGTT TTGGTT TTGGTT TT
35283910 CCATTTCCCT
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:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (6 bp):
TTGGTT
Found at i:35291429 original size:1 final size:1
Alignment explanation
Indices: 35291425--35291449 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
35291415 TTATTTTTTT
35291425 GGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGG
35291450 AAGGGGAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:35294808 original size:18 final size:18
Alignment explanation
Indices: 35294785--35294823 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
35294775 TACTTTTACT
* *
35294785 AATTTAAAATTTTAAAAA
1 AATTTAAAAATTAAAAAA
35294803 AATTTAAAAATTAAAAAA
1 AATTTAAAAATTAAAAAA
35294821 AAT
1 AAT
35294824 CATTTTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AATTTAAAAATTAAAAAA
Found at i:35296922 original size:124 final size:124
Alignment explanation
Indices: 35296702--35297076 Score: 750
Period size: 124 Copynumber: 3.0 Consensus size: 124
35296692 AAATCAAATA
35296702 CAAATATCAAACTTCTCTCACATTACACAAAACATTCATTTTTTATTAAAAACAAATTCAAGTAA
1 CAAATATCAAACTTCTCTCACATTACACAAAACATTCATTTTTTATTAAAAACAAATTCAAGTAA
35296767 TTTTAAACACTTTAGAATCATTTTTAATCAAGTTCTAGGTGTTTGGGGATGATTGAGAC
66 TTTTAAACACTTTAGAATCATTTTTAATCAAGTTCTAGGTGTTTGGGGATGATTGAGAC
35296826 CAAATATCAAACTTCTCTCACATTACACAAAACATTCATTTTTTATTAAAAACAAATTCAAGTAA
1 CAAATATCAAACTTCTCTCACATTACACAAAACATTCATTTTTTATTAAAAACAAATTCAAGTAA
35296891 TTTTAAACACTTTAGAATCATTTTTAATCAAGTTCTAGGTGTTTGGGGATGATTGAGAC
66 TTTTAAACACTTTAGAATCATTTTTAATCAAGTTCTAGGTGTTTGGGGATGATTGAGAC
35296950 CAAATATCAAACTTCTCTCACATTACACAAAACATTCATTTTTTATTAAAAACAAATTCAAGTAA
1 CAAATATCAAACTTCTCTCACATTACACAAAACATTCATTTTTTATTAAAAACAAATTCAAGTAA
35297015 TTTTAAACACTTTAGAATCATTTTTAATCAAGTTCTAGGTGTTTGGGGATGATTGAGAC
66 TTTTAAACACTTTAGAATCATTTTTAATCAAGTTCTAGGTGTTTGGGGATGATTGAGAC
35297074 CAA
1 CAA
35297077 GTTCGGTCTC
Statistics
Matches: 251, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
124 251 1.00
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.36
Consensus pattern (124 bp):
CAAATATCAAACTTCTCTCACATTACACAAAACATTCATTTTTTATTAAAAACAAATTCAAGTAA
TTTTAAACACTTTAGAATCATTTTTAATCAAGTTCTAGGTGTTTGGGGATGATTGAGAC
Found at i:35301620 original size:88 final size:86
Alignment explanation
Indices: 35301459--35301672 Score: 225
Period size: 88 Copynumber: 2.4 Consensus size: 86
35301449 CCAAATTCAG
* ** *
35301459 TATACTCCTAATATGCCATCAATATACCAA-TTCCATAAACATTAGCCATTAAATTAAAGACATT
1 TATACACCTAATATG-CATCAATATACCAATTTCCATAAACACAAGCCATCAAATTAAAGACATT
*
35301523 TTCCCATCATGATCGAATAGTCAA
65 TT--CATCATGACCGAATAGTCAA
* *
35301547 TTTACACCTAATATGACATCAATATACCAATTTCCCATAAACACAAGCCATCAAATTCAAGACAT
1 TATACACCTAATATG-CATCAATATACCAATTT-CCATAAACACAAGCCATCAAATTAAAGACAT
* * *
35301612 TTAT-ATCATGGCCTAATATTCAA
64 TT-TCATCATGACCGAATAGTCAA
* * *
35301635 TATACAACAAATATGCTATCAATACACCAATTTTCCAT
1 TATACACCTAATATGC-ATCAATATACCAA-TTTCCAT
35301673 TTCTGTCATT
Statistics
Matches: 106, Mismatches: 15, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
87 1 0.01
88 70 0.66
89 5 0.05
90 29 0.27
91 1 0.01
ACGTcount: A:0.41, C:0.23, G:0.06, T:0.30
Consensus pattern (86 bp):
TATACACCTAATATGCATCAATATACCAATTTCCATAAACACAAGCCATCAAATTAAAGACATTT
TCATCATGACCGAATAGTCAA
Found at i:35307408 original size:105 final size:105
Alignment explanation
Indices: 35307274--35307494 Score: 311
Period size: 110 Copynumber: 2.1 Consensus size: 105
35307264 GTGTGAATAT
35307274 GTTGCTTTAATTTGTTGTGTGCCTG-TTTTTTTTCTAGAGATGCATG-TTATTGTTTGAAGCTAA
1 GTTGCTTTAATTTGTTGTGTGCCTGTTTTTTTTTCTAGAGAT--ATGATTATTGTTTGAAGCTAA
**
35307337 ATGTGCTGATGTTTATTCCAGACCTACATGGGAAATATATTG
64 ATGTGCTGATGTTTATTCCAGACCTACACAGGAAATATATTG
* * *
35307379 GTTGCTTTAATTTGTTGTGTGGCTGTTTTTTTTTTTTTCTAGGGATATGTATTGTTGTTTGAAGC
1 GTTGCTTTAATTTGTTGTGTGCCTG----TTTTTTTTTCTAGAGATATG-ATTATTGTTTGAAGC
35307444 TAAATGTGCTGATGTTTATTCCAGACCTACACAGGAAATATATTG
61 TAAATGTGCTGATGTTTATTCCAGACCTACACAGGAAATATATTG
*
35307489 ATTGCT
1 GTTGCT
35307495 GTAAATCCTT
Statistics
Matches: 103, Mismatches: 6, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
105 24 0.23
108 3 0.03
110 76 0.74
ACGTcount: A:0.21, C:0.11, G:0.22, T:0.46
Consensus pattern (105 bp):
GTTGCTTTAATTTGTTGTGTGCCTGTTTTTTTTTCTAGAGATATGATTATTGTTTGAAGCTAAAT
GTGCTGATGTTTATTCCAGACCTACACAGGAAATATATTG
Found at i:35314600 original size:66 final size:66
Alignment explanation
Indices: 35314494--35314872 Score: 548
Period size: 66 Copynumber: 5.7 Consensus size: 66
35314484 CAGGTTGACC
* * *
35314494 TTGAGGAAT-CAAAAAAGCAGGAAAGTGCAAGGTTTGAATCTACTATACAAAAGATGCAACTTGA
1 TTGAGGAATCCAAAAAA-CAGGAAAGTGAAAGGTTTGAATCTACTTTGCAAAAGATGCAACTTGA
35314558 GT
65 GT
* * * * *
35314560 TTGAGGAATCGAAGAAAA-AGGAAAGTGCAAGGTTTGAATCTATTTTGCAAAAGAAGGAACTTGA
1 TTGAGGAATCCAA-AAAACAGGAAAGTGAAAGGTTTGAATCTACTTTGCAAAAGATGCAACTTGA
35314624 GT
65 GT
*
35314626 TTGAGGAATCCAAAAAACAGGAAAGTGAAAGGTTTGAATCTACTTTGCACAAGATGCAACTTGAG
1 TTGAGGAATCCAAAAAACAGGAAAGTGAAAGGTTTGAATCTACTTTGCAAAAGATGCAACTTGAG
35314691 T
66 T
* * * *
35314692 TTGAGGAATCGAAAAAAAAGGAAAGTGAAAGGTTTGAATCTACTTTCCACAAGATGCAACTTGAG
1 TTGAGGAATCCAAAAAACAGGAAAGTGAAAGGTTTGAATCTACTTTGCAAAAGATGCAACTTGAG
35314757 T
66 T
***
35314758 TTGAGGAATCCAAAAAACAGGAAAGTGAAAGGTTTGAATCTACCACGCAAAAGATGCAACTTGAG
1 TTGAGGAATCCAAAAAACAGGAAAGTGAAAGGTTTGAATCTACTTTGCAAAAGATGCAACTTGAG
35314823 T
66 T
* *
35314824 TTGAGGAATCCAAAAAACAAGAAAGAGCAAA-GTTTGAATCTACTTTGCA
1 TTGAGGAATCCAAAAAACAGGAAAGTG-AAAGGTTTGAATCTACTTTGCA
35314873 CAGAAAGGAA
Statistics
Matches: 282, Mismatches: 27, Indels: 8
0.89 0.09 0.03
Matches are distributed among these distances:
65 4 0.01
66 269 0.95
67 5 0.02
68 4 0.01
ACGTcount: A:0.42, C:0.12, G:0.23, T:0.23
Consensus pattern (66 bp):
TTGAGGAATCCAAAAAACAGGAAAGTGAAAGGTTTGAATCTACTTTGCAAAAGATGCAACTTGAG
T
Found at i:35315017 original size:66 final size:66
Alignment explanation
Indices: 35314935--35315071 Score: 186
Period size: 66 Copynumber: 2.1 Consensus size: 66
35314925 CGTGAGTTTG
*
35314935 AGGAATCCAAACAACAGGAAAAAGAAACACTAGAATCTACTTTGCATAAGAAGGAACTTGAATTT
1 AGGAATCCAAACAACAGGAAAAAGAAACACTAGAATCTACTTTGCACAAGAAGGAACTTGAATTT
35315000 C
66 C
* * * * * * *
35315001 AGGAATCCAGAA-AACAGGAAAGAGCAACATTTGAATCTACTTTGTACAAGAAGGATCTTGAGTT
1 AGGAATCCA-AACAACAGGAAAAAGAAACACTAGAATCTACTTTGCACAAGAAGGAACTTGAATT
35315065 TC
65 TC
35315067 AGGAA
1 AGGAA
35315072 CTGCAAGTTG
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
66 60 0.97
67 2 0.03
ACGTcount: A:0.44, C:0.15, G:0.20, T:0.21
Consensus pattern (66 bp):
AGGAATCCAAACAACAGGAAAAAGAAACACTAGAATCTACTTTGCACAAGAAGGAACTTGAATTT
C
Found at i:35315043 original size:174 final size:174
Alignment explanation
Indices: 35314745--35315113 Score: 463
Period size: 174 Copynumber: 2.1 Consensus size: 174
35314735 TTTCCACAAG
** *** *
35314745 ATGCAACTTGAGTTTGAGGAATCCAAAAAACAGGAAAGTGAAAGGTTTGAATCTACCACGCAAAA
1 ATGCAACTTGAGTTTGAGGAATCCAAAAAACAGGAAAAAGAAACACTAGAATCTACCACGCAAAA
* * *
35314810 GATGCAACTTGAGTTTGAGGAATCCAAAAAACAAGAAAGAGCAAAGTTTGAATCTACTTTGCAC-
66 GAAGCAACTTGAATTTCAGGAATCCAAAAAACAAGAAAGAGCAAAGTTTGAATCTACTTTGCACA
* *
35314874 AGAAAGGAACTTCAGTTTCAGCAACTGCAATTTGAGTTGCAGACA
131 AG-AAGGAACTTCAGTTTCAGCAACTGCAAGTTGAGTTGCAGAAA
* * * *** *
35314919 CTGCAACGTGAGTTTGAGGAATCCAAACAACAGGAAAAAGAAACACTAGAATCTACTTTGCATAA
1 ATGCAACTTGAGTTTGAGGAATCCAAAAAACAGGAAAAAGAAACACTAGAATCTACCACGCAAAA
* * * *
35314984 GAAGGAACTTGAATTTCAGGAATCCAGAAAACAGGAAAGAGCAACA-TTTGAATCTACTTTGTAC
66 GAAGCAACTTGAATTTCAGGAATCCAAAAAACAAGAAAGAGCAA-AGTTTGAATCTACTTTGCAC
* * * *
35315048 AAGAAGGATCTTGAGTTTCAGGAACTGCAAGTTGAGTTTCAGAAA
130 AAGAAGGAACTTCAGTTTCAGCAACTGCAAGTTGAGTTGCAGAAA
*
35315093 ATGCAACTTGAGCTTGAGGAA
1 ATGCAACTTGAGTTTGAGGAA
35315114 ACAAAAGAGT
Statistics
Matches: 164, Mismatches: 29, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
174 161 0.98
175 3 0.02
ACGTcount: A:0.40, C:0.16, G:0.22, T:0.23
Consensus pattern (174 bp):
ATGCAACTTGAGTTTGAGGAATCCAAAAAACAGGAAAAAGAAACACTAGAATCTACCACGCAAAA
GAAGCAACTTGAATTTCAGGAATCCAAAAAACAAGAAAGAGCAAAGTTTGAATCTACTTTGCACA
AGAAGGAACTTCAGTTTCAGCAACTGCAAGTTGAGTTGCAGAAA
Found at i:35315084 original size:21 final size:21
Alignment explanation
Indices: 35315057--35315114 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
35315047 CAAGAAGGAT
*
35315057 CTTGAGTTTCAGGAACTGCAA
1 CTTGAGTTTCAGGAAATGCAA
* *
35315078 GTTGAGTTTCAGAAAATGCAA
1 CTTGAGTTTCAGGAAATGCAA
* *
35315099 CTTGAGCTTGAGGAAA
1 CTTGAGTTTCAGGAAA
35315115 CAAAAGAGTT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.28
Consensus pattern (21 bp):
CTTGAGTTTCAGGAAATGCAA
Found at i:35315902 original size:33 final size:33
Alignment explanation
Indices: 35315860--35315982 Score: 210
Period size: 33 Copynumber: 3.7 Consensus size: 33
35315850 GTTGTTGACA
35315860 ATGAATCAATGAATAAACCTACTGTTATTGAAG
1 ATGAATCAATGAATAAACCTACTGTTATTGAAG
*
35315893 ATGAATCAATGAATAAACCTAATGTTATTGAAG
1 ATGAATCAATGAATAAACCTACTGTTATTGAAG
* *
35315926 ACGAATCAATGAATAAACCTACCGTTATTGAAG
1 ATGAATCAATGAATAAACCTACTGTTATTGAAG
*
35315959 ATGAATCAATAAATAAACCTACTG
1 ATGAATCAATGAATAAACCTACTG
35315983 CTGAAAACAA
Statistics
Matches: 83, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 83 1.00
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.28
Consensus pattern (33 bp):
ATGAATCAATGAATAAACCTACTGTTATTGAAG
Done.