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 55 of 144
Found at i:10900619 original size:14 final size:14
Alignment explanation
Indices: 10900600--10900631 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
10900590 ATTAGTATAT
10900600 AAATTAAAATAAAG
1 AAATTAAAATAAAG
10900614 AAATTAAAATAAAG
1 AAATTAAAATAAAG
10900628 AAAT
1 AAAT
10900632 AAAGGCATAT
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:0.72, C:0.00, G:0.06, T:0.22
Consensus pattern (14 bp):
AAATTAAAATAAAG
Found at i:10905054 original size:13 final size:13
Alignment explanation
Indices: 10905027--10905061 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
10905017 TCTCGTATCG
10905027 AAACTGAAAAATAA
1 AAACT-AAAAATAA
*
10905041 AAACTAAAACTAA
1 AAACTAAAAATAA
10905054 AAACTAAA
1 AAACTAAA
10905062 GTCTAAAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 15 0.75
14 5 0.25
ACGTcount: A:0.71, C:0.11, G:0.03, T:0.14
Consensus pattern (13 bp):
AAACTAAAAATAA
Found at i:10918754 original size:18 final size:18
Alignment explanation
Indices: 10918731--10918767 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
10918721 TTTGTGATCA
10918731 AAATTGAAACTGAAAGTG
1 AAATTGAAACTGAAAGTG
* *
10918749 AAATTGGAATTGAAAGTG
1 AAATTGAAACTGAAAGTG
10918767 A
1 A
10918768 TATGAATTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.03, G:0.24, T:0.24
Consensus pattern (18 bp):
AAATTGAAACTGAAAGTG
Found at i:10930212 original size:22 final size:22
Alignment explanation
Indices: 10930187--10930229 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
10930177 GTCACTTGAA
10930187 AAAGA-AAAAAAATGAAAAAAAG
1 AAAGAGAAAAAAA-GAAAAAAAG
*
10930209 AAAGAGAAAAGAAGAAAAAAA
1 AAAGAGAAAAAAAGAAAAAAA
10930230 AGAATTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.02
Consensus pattern (22 bp):
AAAGAGAAAAAAAGAAAAAAAG
Found at i:10943523 original size:23 final size:22
Alignment explanation
Indices: 10943493--10943661 Score: 144
Period size: 23 Copynumber: 7.4 Consensus size: 22
10943483 ACACTAGCGC
* * *
10943493 GCTCTCTGTTTAGCACGTCTCGT
1 GCTCTCTGATTAGCAC-TTTTGT
10943516 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTTT-TGT
10943539 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTTT-TGT
*
10943562 GCTCTCTGATTAGTACTTTGTGT
1 GCTCTCTGATTAGCACTTT-TGT
* * *
10943585 ACTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGATTAGCACT-TTTGT
*
10943608 GCTCTCTG-TTGCCCAGCACTTATGT
1 GCTCTCTGATT----AGCACTTTTGT
* *
10943633 GCTCTCTG-TTAGTACTTTGGT
1 GCTCTCTGATTAGCACTTTTGT
*
10943654 ACTCTCTG
1 GCTCTCTG
10943662 CTTGTTCCGT
Statistics
Matches: 126, Mismatches: 14, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
21 15 0.12
22 4 0.03
23 86 0.68
24 1 0.01
25 14 0.11
26 6 0.05
ACGTcount: A:0.12, C:0.24, G:0.21, T:0.43
Consensus pattern (22 bp):
GCTCTCTGATTAGCACTTTTGT
Found at i:10943564 original size:46 final size:45
Alignment explanation
Indices: 10943514--10943661 Score: 167
Period size: 46 Copynumber: 3.2 Consensus size: 45
10943504 AGCACGTCTC
10943514 GTGCTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGCACTTTGT
1 GTGCTCTCTGATTAGCACTTTGTGTGCTCTCTG-TTAGCACTTTGT
* * *
10943560 GTGCTCTCTGATTAGTACTTTGTGTACTCTCTGTTTAGCACTGTGT
1 GTGCTCTCTGATTAGCACTTTGTGTGCTCTCTG-TTAGCACTTTGT
* *
10943606 GTGCTCTCTG-TTGCCCAGCAC-TTATGTGCTCTCTGTTAGTACTTTG-
1 GTGCTCTCTGATT----AGCACTTTGTGTGCTCTCTGTTAGCACTTTGT
*
10943652 GTACTCTCTG
1 GTGCTCTCTG
10943662 CTTGTTCCGT
Statistics
Matches: 88, Mismatches: 10, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
45 2 0.02
46 61 0.69
47 9 0.10
48 12 0.14
49 4 0.05
ACGTcount: A:0.12, C:0.23, G:0.22, T:0.43
Consensus pattern (45 bp):
GTGCTCTCTGATTAGCACTTTGTGTGCTCTCTGTTAGCACTTTGT
Found at i:10943607 original size:69 final size:66
Alignment explanation
Indices: 10943517--10943661 Score: 193
Period size: 69 Copynumber: 2.1 Consensus size: 66
10943507 ACGTCTCGTG
* *
10943517 CTCTCTGATTAGCACTTTGTGTGCTCTCTGATT-AGCACTTTGTGTGCTCTCTGATTAGTACTTT
1 CTCTCTGATTAGCACTGTGTGTGCTCTCTG-TTCAGCAC-TTATGTGCTCTCTG-TTAGTACTTT
10943581 GTGTA
63 G-GTA
*
10943586 CTCTCTGTTTAGCACTGTGTGTGCTCTCTGTTGCCCAGCACTTATGTGCTCTCTGTTAGTACTTT
1 CTCTCTGATTAGCACTGTGTGTGCTCTCTGTT---CAGCACTTATGTGCTCTCTGTTAGTACTTT
10943651 GGTA
63 GGTA
10943655 CTCTCTG
1 CTCTCTG
10943662 CTTGTTCCGT
Statistics
Matches: 69, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
68 2 0.03
69 38 0.55
70 11 0.16
71 13 0.19
72 5 0.07
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.43
Consensus pattern (66 bp):
CTCTCTGATTAGCACTGTGTGTGCTCTCTGTTCAGCACTTATGTGCTCTCTGTTAGTACTTTGGT
A
Found at i:10950884 original size:23 final size:22
Alignment explanation
Indices: 10950854--10951022 Score: 144
Period size: 23 Copynumber: 7.4 Consensus size: 22
10950844 ACACTAGCGC
* * *
10950854 GCTCTCTGTTTAGCACGTCTCGT
1 GCTCTCTGATTAGCAC-TTTTGT
10950877 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTTT-TGT
10950900 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTTT-TGT
*
10950923 GCTCTCTGATTAGTACTTTGTGT
1 GCTCTCTGATTAGCACTTT-TGT
* * *
10950946 ACTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGATTAGCACT-TTTGT
*
10950969 GCTCTCTG-TTGCCCAGCACTTATGT
1 GCTCTCTGATT----AGCACTTTTGT
* *
10950994 GCTCTCTG-TTAGTACTTTGGT
1 GCTCTCTGATTAGCACTTTTGT
*
10951015 ACTCTCTG
1 GCTCTCTG
10951023 CTTGTTCCGT
Statistics
Matches: 126, Mismatches: 14, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
21 15 0.12
22 4 0.03
23 86 0.68
24 1 0.01
25 14 0.11
26 6 0.05
ACGTcount: A:0.12, C:0.24, G:0.21, T:0.43
Consensus pattern (22 bp):
GCTCTCTGATTAGCACTTTTGT
Found at i:10950925 original size:46 final size:45
Alignment explanation
Indices: 10950875--10951022 Score: 167
Period size: 46 Copynumber: 3.2 Consensus size: 45
10950865 AGCACGTCTC
10950875 GTGCTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGCACTTTGT
1 GTGCTCTCTGATTAGCACTTTGTGTGCTCTCTG-TTAGCACTTTGT
* * *
10950921 GTGCTCTCTGATTAGTACTTTGTGTACTCTCTGTTTAGCACTGTGT
1 GTGCTCTCTGATTAGCACTTTGTGTGCTCTCTG-TTAGCACTTTGT
* *
10950967 GTGCTCTCTG-TTGCCCAGCAC-TTATGTGCTCTCTGTTAGTACTTTG-
1 GTGCTCTCTGATT----AGCACTTTGTGTGCTCTCTGTTAGCACTTTGT
*
10951013 GTACTCTCTG
1 GTGCTCTCTG
10951023 CTTGTTCCGT
Statistics
Matches: 88, Mismatches: 10, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
45 2 0.02
46 61 0.69
47 9 0.10
48 12 0.14
49 4 0.05
ACGTcount: A:0.12, C:0.23, G:0.22, T:0.43
Consensus pattern (45 bp):
GTGCTCTCTGATTAGCACTTTGTGTGCTCTCTGTTAGCACTTTGT
Found at i:10950968 original size:69 final size:66
Alignment explanation
Indices: 10950878--10951022 Score: 193
Period size: 69 Copynumber: 2.1 Consensus size: 66
10950868 ACGTCTCGTG
* *
10950878 CTCTCTGATTAGCACTTTGTGTGCTCTCTGATT-AGCACTTTGTGTGCTCTCTGATTAGTACTTT
1 CTCTCTGATTAGCACTGTGTGTGCTCTCTG-TTCAGCAC-TTATGTGCTCTCTG-TTAGTACTTT
10950942 GTGTA
63 G-GTA
*
10950947 CTCTCTGTTTAGCACTGTGTGTGCTCTCTGTTGCCCAGCACTTATGTGCTCTCTGTTAGTACTTT
1 CTCTCTGATTAGCACTGTGTGTGCTCTCTGTT---CAGCACTTATGTGCTCTCTGTTAGTACTTT
10951012 GGTA
63 GGTA
10951016 CTCTCTG
1 CTCTCTG
10951023 CTTGTTCCGT
Statistics
Matches: 69, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
68 2 0.03
69 38 0.55
70 11 0.16
71 13 0.19
72 5 0.07
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.43
Consensus pattern (66 bp):
CTCTCTGATTAGCACTGTGTGTGCTCTCTGTTCAGCACTTATGTGCTCTCTGTTAGTACTTTGGT
A
Found at i:10953470 original size:211 final size:211
Alignment explanation
Indices: 10953106--10953534 Score: 858
Period size: 211 Copynumber: 2.0 Consensus size: 211
10953096 GCCTGAAAAG
10953106 AAAACCAAGAAGCCCGATACCCACACCCAAGAAAACACCAATCACATGTAGCAATGCAAGAACAC
1 AAAACCAAGAAGCCCGATACCCACACCCAAGAAAACACCAATCACATGTAGCAATGCAAGAACAC
10953171 CTAAAAAACATTAAGGAAATGAAAAAACCAAGAAAATAGCTAAAAAGTATTTTCTACAAAGAGTA
66 CTAAAAAACATTAAGGAAATGAAAAAACCAAGAAAATAGCTAAAAAGTATTTTCTACAAAGAGTA
10953236 AATGATTTTTAAGAACATATAAACCAAACAAAAAAGAAAAAAATGGAAATATTAAAATCTAACTT
131 AATGATTTTTAAGAACATATAAACCAAACAAAAAAGAAAAAAATGGAAATATTAAAATCTAACTT
10953301 CACGCCGTGAAACTCA
196 CACGCCGTGAAACTCA
10953317 AAAACCAAGAAGCCCGATACCCACACCCAAGAAAACACCAATCACATGTAGCAATGCAAGAACAC
1 AAAACCAAGAAGCCCGATACCCACACCCAAGAAAACACCAATCACATGTAGCAATGCAAGAACAC
10953382 CTAAAAAACATTAAGGAAATGAAAAAACCAAGAAAATAGCTAAAAAGTATTTTCTACAAAGAGTA
66 CTAAAAAACATTAAGGAAATGAAAAAACCAAGAAAATAGCTAAAAAGTATTTTCTACAAAGAGTA
10953447 AATGATTTTTAAGAACATATAAACCAAACAAAAAAGAAAAAAATGGAAATATTAAAATCTAACTT
131 AATGATTTTTAAGAACATATAAACCAAACAAAAAAGAAAAAAATGGAAATATTAAAATCTAACTT
10953512 CACGCCGTGAAACTCA
196 CACGCCGTGAAACTCA
10953528 AAAACCA
1 AAAACCA
10953535 TGTAGTATAC
Statistics
Matches: 218, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
211 218 1.00
ACGTcount: A:0.53, C:0.19, G:0.11, T:0.17
Consensus pattern (211 bp):
AAAACCAAGAAGCCCGATACCCACACCCAAGAAAACACCAATCACATGTAGCAATGCAAGAACAC
CTAAAAAACATTAAGGAAATGAAAAAACCAAGAAAATAGCTAAAAAGTATTTTCTACAAAGAGTA
AATGATTTTTAAGAACATATAAACCAAACAAAAAAGAAAAAAATGGAAATATTAAAATCTAACTT
CACGCCGTGAAACTCA
Found at i:10966169 original size:147 final size:146
Alignment explanation
Indices: 10965900--10966192 Score: 505
Period size: 147 Copynumber: 2.0 Consensus size: 146
10965890 TGGGAAAGGA
10965900 AGAGAATGAAACAAACACTAGGCCTGACAACCCTAGAAAGGCATTTAGGTGGGAATGACCCAAAA
1 AGAGAATGAAACAAACACTAGGCCTGACAACCCTAGAAAGGCATTTAGGTGGGAATGACCCAAAA
* * *
10965965 TTGGTATTGCCTATTCATGAAAACTTTTTCCCCAAACTAATTTAGATTGAGACATCTAGCGATAA
66 TTGGAATTGCCTATTCATGAAAACCTTTTCCCCAAACCAATTTAGATTGAGACATCTAGCGATAA
10966030 GTAGTCTCTATCGACT
131 GTAGTCTCTATCGACT
*
10966046 AGAGAATGAAACAAACACTAGGCCTGACAACCCTAGAAAGTCATTTAGGTGGGAATGAACCCAAA
1 AGAGAATGAAACAAACACTAGGCCTGACAACCCTAGAAAGGCATTTAGGTGGGAATG-ACCCAAA
* * * *
10966111 ATTGGAATTGCCTATTCGTGAAAACCTTTTCCCCAGACCGATTTAGATTGTGACATCTAGCGATA
65 ATTGGAATTGCCTATTCATGAAAACCTTTTCCCCAAACCAATTTAGATTGAGACATCTAGCGATA
10966176 AGTAGTCTCTATCGACT
130 AGTAGTCTCTATCGACT
10966193 TGCTATGCTG
Statistics
Matches: 138, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
146 56 0.41
147 82 0.59
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (146 bp):
AGAGAATGAAACAAACACTAGGCCTGACAACCCTAGAAAGGCATTTAGGTGGGAATGACCCAAAA
TTGGAATTGCCTATTCATGAAAACCTTTTCCCCAAACCAATTTAGATTGAGACATCTAGCGATAA
GTAGTCTCTATCGACT
Found at i:10967991 original size:38 final size:39
Alignment explanation
Indices: 10967896--10967991 Score: 119
Period size: 38 Copynumber: 2.5 Consensus size: 39
10967886 TCTGTAGCGA
** *
10967896 CAATTCTGGGCAT-GCTCATGCAGTGACAATTTTGGGCG
1 CAATTCTGAACATAGCTCATGCAGTGACAATTCTGGGCG
*
10967934 CAATTCTGAACATCG-TCATGCAGTGACAATTCTGGGCG
1 CAATTCTGAACATAGCTCATGCAGTGACAATTCTGGGCG
10967972 CAATTCT-AA-ATAGACTCATG
1 CAATTCTGAACATAG-CTCATG
10967992 TAGGGACATT
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
36 3 0.06
37 2 0.04
38 45 0.88
39 1 0.02
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Consensus pattern (39 bp):
CAATTCTGAACATAGCTCATGCAGTGACAATTCTGGGCG
Found at i:10975581 original size:23 final size:23
Alignment explanation
Indices: 10975555--10975675 Score: 156
Period size: 23 Copynumber: 5.2 Consensus size: 23
10975545 ACACTAGCGC
10975555 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
10975578 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGATTAGCACTGTGT-GT
10975601 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG--ATTAGCACTGTGTGT
*
10975626 GCTCTCCGATTAGCACT-TCGTGT
1 GCTCTCTGATTAGCACTGT-GTGT
*
10975649 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
10975672 GCTC
1 GCTC
10975676 AGTACTTTGT
Statistics
Matches: 86, Mismatches: 6, Indels: 12
0.83 0.06 0.12
Matches are distributed among these distances:
22 4 0.05
23 62 0.72
24 1 0.01
25 16 0.19
26 3 0.03
ACGTcount: A:0.12, C:0.26, G:0.23, T:0.40
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:10975624 original size:48 final size:46
Alignment explanation
Indices: 10975555--10975675 Score: 172
Period size: 48 Copynumber: 2.6 Consensus size: 46
10975545 ACACTAGCGC
* *
10975555 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACGTC-TCGT
1 GCTCTCTGATTAGCACTGTGTGTGCTCTCCGATTAGCACGTCGT-GT
*
10975601 GCTCTCTGTTATTAGCACTGTGTGTGCTCTCCGATTAGCACTTCGTGT
1 GCTCTCTG--ATTAGCACTGTGTGTGCTCTCCGATTAGCACGTCGTGT
*
10975649 GCTCTCTGATTAGCACTTTGTGTGCTC
1 GCTCTCTGATTAGCACTGTGTGTGCTC
10975676 AGTACTTTGT
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
46 26 0.38
48 41 0.60
49 1 0.01
ACGTcount: A:0.12, C:0.26, G:0.23, T:0.40
Consensus pattern (46 bp):
GCTCTCTGATTAGCACTGTGTGTGCTCTCCGATTAGCACGTCGTGT
Found at i:10975706 original size:23 final size:23
Alignment explanation
Indices: 10975679--10975743 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 23
10975669 TGTGCTCAGT
*
10975679 ACTTTGTGTACTTTCTGTTTAGC
1 ACTTTGTGTACTCTCTGTTTAGC
* * *
10975702 ACTTTGTGTGCTCTCTGTTCAGT
1 ACTTTGTGTACTCTCTGTTTAGC
*
10975725 ACTTCG-GTACTCTCTGTTT
1 ACTTTGTGTACTCTCTGTTT
10975744 GTTCCGTTTA
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
22 11 0.31
23 24 0.69
ACGTcount: A:0.11, C:0.22, G:0.18, T:0.49
Consensus pattern (23 bp):
ACTTTGTGTACTCTCTGTTTAGC
Found at i:10978449 original size:14 final size:15
Alignment explanation
Indices: 10978422--10978450 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
10978412 ATATTTTATT
10978422 TAAAATTCATTCAAA
1 TAAAATTCATTCAAA
10978437 TAAAATT-ATTCAAA
1 TAAAATTCATTCAAA
10978451 ATCAAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.34
Consensus pattern (15 bp):
TAAAATTCATTCAAA
Found at i:10979939 original size:30 final size:31
Alignment explanation
Indices: 10979876--10979941 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 31
10979866 AAAAACCCTA
* *
10979876 AAGTTCAAGCCCCCAATGTGGAATAATTATC
1 AAGTTCAAGCCCCCAACGTGGAACAATTATC
* *
10979907 AAGTTCAAG-CCCTAACGTGGAACAATTGTC
1 AAGTTCAAGCCCCCAACGTGGAACAATTATC
10979937 AAGTT
1 AAGTT
10979942 TAGGACCTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 22 0.71
31 9 0.29
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (31 bp):
AAGTTCAAGCCCCCAACGTGGAACAATTATC
Found at i:10979951 original size:30 final size:30
Alignment explanation
Indices: 10979893--10979957 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
10979883 AGCCCCCAAT
* *
10979893 GTGGAATAATTATCAAGTTCAAGCCCTAAC
1 GTGGAACAATTATCAAGTTCAAGACCTAAC
* * *
10979923 GTGGAACAATTGTCAAGTTTAGGACCTAAC
1 GTGGAACAATTATCAAGTTCAAGACCTAAC
*
10979953 TTGGA
1 GTGGA
10979958 CCAAAAAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.28
Consensus pattern (30 bp):
GTGGAACAATTATCAAGTTCAAGACCTAAC
Found at i:10990362 original size:21 final size:21
Alignment explanation
Indices: 10990338--10990377 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
10990328 AACAAGCTAA
10990338 CAAATCTCCCTAGAACTTAGT
1 CAAATCTCCCTAGAACTTAGT
* *
10990359 CAAATCTCTCTAGGACTTA
1 CAAATCTCCCTAGAACTTA
10990378 AGTCTTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.33, C:0.28, G:0.10, T:0.30
Consensus pattern (21 bp):
CAAATCTCCCTAGAACTTAGT
Found at i:10997416 original size:18 final size:17
Alignment explanation
Indices: 10997373--10997416 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
10997363 ATGCTTAGTT
*
10997373 ATTTATTTATTTATTTA
1 ATTTATTTAATTATTTA
*
10997390 ATTTAATTTAATTGTTTAA
1 ATTT-ATTTAATTATTT-A
10997409 ATTTATTT
1 ATTTATTT
10997417 TTCACGTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 4 0.17
18 14 0.61
19 5 0.22
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (17 bp):
ATTTATTTAATTATTTA
Found at i:10998217 original size:42 final size:42
Alignment explanation
Indices: 10998134--10998217 Score: 98
Period size: 41 Copynumber: 2.0 Consensus size: 42
10998124 AACATCAAAT
* * * *
10998134 TAAATATTTAAATTTTTTTTTAATTTTTTTAAAGTTATATTA
1 TAAACATTTAAATTTTATTTTAATTTTTTGAAAATTATATTA
* *
10998176 TAAACATTT-AATTTTATTTTCATTTTTTGAGAAATTTTATTA
1 TAAACATTTAAATTTTATTTTAATTTTTTGA-AAATTATATTA
10998218 ATTTATTTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
41 18 0.51
42 17 0.49
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.60
Consensus pattern (42 bp):
TAAACATTTAAATTTTATTTTAATTTTTTGAAAATTATATTA
Found at i:11000408 original size:16 final size:16
Alignment explanation
Indices: 11000369--11000409 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
11000359 ATAATAAAAA
11000369 TATAATTTTATTATTT
1 TATAATTTTATTATTT
11000385 TA-ATATTTTA-TATCTT
1 TATA-ATTTTATTAT-TT
11000401 TATAATTTT
1 TATAATTTT
11000410 TAAAAGATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 4 0.18
16 17 0.77
17 1 0.05
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (16 bp):
TATAATTTTATTATTT
Found at i:11000827 original size:12 final size:13
Alignment explanation
Indices: 11000795--11000828 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
11000785 TTTATACACT
11000795 TTATTA-TTATCA
1 TTATTATTTATCA
11000807 TTATTATTTAT-A
1 TTATTATTTATCA
11000819 TTATTATTTA
1 TTATTATTTA
11000829 AAATTTTGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 17 0.81
13 4 0.19
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (13 bp):
TTATTATTTATCA
Found at i:11005537 original size:13 final size:13
Alignment explanation
Indices: 11005519--11005581 Score: 67
Period size: 13 Copynumber: 4.8 Consensus size: 13
11005509 AGTTCTTAAA
11005519 AAATTTAAATATC
1 AAATTTAAATATC
11005532 AAATTTAAATATC
1 AAATTTAAATATC
* * *
11005545 GAATTAAAAAAATC
1 AAATT-TAAATATC
11005559 AAATTTAAATA-C
1 AAATTTAAATATC
11005571 TAAA-TTAAATA
1 -AAATTTAAATA
11005582 AAAAAAAATT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
12 8 0.19
13 24 0.57
14 10 0.24
ACGTcount: A:0.59, C:0.06, G:0.02, T:0.33
Consensus pattern (13 bp):
AAATTTAAATATC
Found at i:11005564 original size:27 final size:27
Alignment explanation
Indices: 11005529--11005612 Score: 107
Period size: 27 Copynumber: 3.1 Consensus size: 27
11005519 AAATTTAAAT
*
11005529 ATCAAATTTAAATATCGAATTAAAAAA
1 ATCAAATTTAAATATCAAATTAAAAAA
11005556 ATCAAATTTAAATA-CTAAATTAAATAAA
1 ATCAAATTTAAATATC-AAATTAAA-AAA
** *
11005584 AAAAAATTTAAACATCAAATTAAAAAA
1 ATCAAATTTAAATATCAAATTAAAAAA
11005611 AT
1 AT
11005613 ATCAAATTCA
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
26 1 0.02
27 25 0.51
28 22 0.45
29 1 0.02
ACGTcount: A:0.63, C:0.07, G:0.01, T:0.29
Consensus pattern (27 bp):
ATCAAATTTAAATATCAAATTAAAAAA
Found at i:11008418 original size:13 final size:13
Alignment explanation
Indices: 11008384--11008427 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
11008374 GTTGACTCGA
11008384 TTTGACCGTTGACCC
1 TTTGACCGTTGA--C
*
11008399 ATTGACCGTTGAC
1 TTTGACCGTTGAC
*
11008412 TTTGACCATTGAC
1 TTTGACCGTTGAC
11008425 TTT
1 TTT
11008428 TTTTGAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
13 15 0.58
15 11 0.42
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (13 bp):
TTTGACCGTTGAC
Found at i:11015531 original size:7 final size:7
Alignment explanation
Indices: 11015519--11015623 Score: 95
Period size: 7 Copynumber: 15.0 Consensus size: 7
11015509 CGACTAGACT
11015519 CGTTGAC
1 CGTTGAC
11015526 CGTTGAC
1 CGTTGAC
* *
11015533 CATTGAT
1 CGTTGAC
11015540 CGTTGAC
1 CGTTGAC
11015547 CGTTGAC
1 CGTTGAC
*
11015554 ACGTTGGC
1 -CGTTGAC
*
11015562 CATTGAC
1 CGTTGAC
11015569 CGTTGAC
1 CGTTGAC
11015576 CGTTGAC
1 CGTTGAC
**
11015583 TATTGAC
1 CGTTGAC
*
11015590 CGTTAAC
1 CGTTGAC
*
11015597 CTTTGAC
1 CGTTGAC
*
11015604 AGTTGA-
1 CGTTGAC
*
11015610 CTTTGAC
1 CGTTGAC
*
11015617 CATTGAC
1 CGTTGAC
11015624 TTTTTTGAGA
Statistics
Matches: 76, Mismatches: 20, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
6 4 0.05
7 66 0.87
8 6 0.08
ACGTcount: A:0.20, C:0.25, G:0.23, T:0.32
Consensus pattern (7 bp):
CGTTGAC
Found at i:11015564 original size:29 final size:28
Alignment explanation
Indices: 11015519--11015623 Score: 113
Period size: 28 Copynumber: 3.8 Consensus size: 28
11015509 CGACTAGACT
*
11015519 CGTTGACCGTTGACCATTGATCGTTGAC
1 CGTTGACCGTTGACCATTGACCGTTGAC
*
11015547 CGTTGACACGTTGGCCATTGACCGTTGAC
1 CGTTGAC-CGTTGACCATTGACCGTTGAC
** * * *
11015576 CGTTGACTATTGACCGTTAACCTTTGAC
1 CGTTGACCGTTGACCATTGACCGTTGAC
* *
11015604 AGTTGA-CTTTGACCATTGAC
1 CGTTGACCGTTGACCATTGAC
11015624 TTTTTTGAGA
Statistics
Matches: 63, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
27 10 0.16
28 27 0.43
29 26 0.41
ACGTcount: A:0.20, C:0.25, G:0.23, T:0.32
Consensus pattern (28 bp):
CGTTGACCGTTGACCATTGACCGTTGAC
Found at i:11017153 original size:17 final size:19
Alignment explanation
Indices: 11017107--11017155 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 19
11017097 AATATTTTAT
11017107 TAATTTAATATTAAAAGGA
1 TAATTTAATATTAAAAGGA
* *
11017126 TTATCTTAATATT-AAA-TA
1 TAAT-TTAATATTAAAAGGA
11017144 TAATTTAATATT
1 TAATTTAATATT
11017156 TATCTTGTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 8 0.31
18 4 0.15
19 6 0.23
20 8 0.31
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (19 bp):
TAATTTAATATTAAAAGGA
Found at i:11017201 original size:59 final size:56
Alignment explanation
Indices: 11017131--11017242 Score: 161
Period size: 59 Copynumber: 1.9 Consensus size: 56
11017121 AAGGATTATC
* *
11017131 TTAATATTAAATATAATTTAATATTTATCTTGTAAATAAATATTCTATTAATTTAAGAT
1 TTAATATTAAATATAATCTAATATTTATCTTG---ATAAATATTATATTAATTTAAGAT
* *
11017190 TTAATATTAAATTTAATCTAATATTTATCTTGATAAGTATTATATTAATTTAA
1 TTAATATTAAATATAATCTAATATTTATCTTGATAAATATTATATTAATTTAA
11017243 TATTAAAGTA
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
56 19 0.39
59 30 0.61
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.50
Consensus pattern (56 bp):
TTAATATTAAATATAATCTAATATTTATCTTGATAAATATTATATTAATTTAAGAT
Found at i:11018052 original size:23 final size:23
Alignment explanation
Indices: 11018022--11018068 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
11018012 TCAATGGGAC
11018022 AAAACCTCGTTTAAGGGAAAAAG
1 AAAACCTCGTTTAAGGGAAAAAG
11018045 AAAACCTCGTTTAAGGGAAAAAG
1 AAAACCTCGTTTAAGGGAAAAAG
11018068 A
1 A
11018069 GTATAATGCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.49, C:0.13, G:0.21, T:0.17
Consensus pattern (23 bp):
AAAACCTCGTTTAAGGGAAAAAG
Found at i:11022204 original size:17 final size:18
Alignment explanation
Indices: 11022171--11022204 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
11022161 TTTTAAAAGC
*
11022171 ACTTTTGACATTAAAAAT
1 ACTTTTGACAGTAAAAAT
11022189 ACTTTTGA-AGTAAAAA
1 ACTTTTGACAGTAAAAA
11022205 AAATGTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.47, C:0.09, G:0.09, T:0.35
Consensus pattern (18 bp):
ACTTTTGACAGTAAAAAT
Found at i:11022617 original size:26 final size:26
Alignment explanation
Indices: 11022577--11022637 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 26
11022567 TAAACAAAAA
* *
11022577 TTTTCAAAAGTATTTCTTAAAATCACT
1 TTTTCAAAAGCATTTCTTAAAAGCA-T
*
11022604 TTTTCAAAA-CATTTTTTAAAAGCAT
1 TTTTCAAAAGCATTTCTTAAAAGCAT
11022629 TTTTCAAAA
1 TTTTCAAAA
11022638 ACAATACTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
25 10 0.32
26 12 0.39
27 9 0.29
ACGTcount: A:0.39, C:0.13, G:0.03, T:0.44
Consensus pattern (26 bp):
TTTTCAAAAGCATTTCTTAAAAGCAT
Found at i:11022629 original size:13 final size:13
Alignment explanation
Indices: 11022577--11022637 Score: 63
Period size: 13 Copynumber: 4.7 Consensus size: 13
11022567 TAAACAAAAA
*
11022577 TTTTCAAAAGTAT
1 TTTTCAAAAGCAT
*
11022590 TTCTT-AAAATCACT
1 TT-TTCAAAAGCA-T
11022604 TTTTCAAAA-CAT
1 TTTTCAAAAGCAT
*
11022616 TTTTTAAAAGCAT
1 TTTTCAAAAGCAT
11022629 TTTTCAAAA
1 TTTTCAAAA
11022638 ACAATACTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
12 9 0.22
13 22 0.55
14 9 0.22
ACGTcount: A:0.39, C:0.13, G:0.03, T:0.44
Consensus pattern (13 bp):
TTTTCAAAAGCAT
Found at i:11023668 original size:9 final size:9
Alignment explanation
Indices: 11023652--11023682 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
11023642 GGTTTACCCC
11023652 ACAATTAAA
1 ACAATTAAA
*
11023661 ATAATTAAA
1 ACAATTAAA
11023670 ACAATTAAA
1 ACAATTAAA
11023679 ACAA
1 ACAA
11023683 CTTTAACATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.68, C:0.10, G:0.00, T:0.23
Consensus pattern (9 bp):
ACAATTAAA
Found at i:11024429 original size:12 final size:12
Alignment explanation
Indices: 11024412--11024476 Score: 57
Period size: 12 Copynumber: 5.5 Consensus size: 12
11024402 GACTTAATTA
11024412 GTATGTGTAAAT
1 GTATGTGTAAAT
*
11024424 GTATGTTTCATAAT
1 GTATGTGT-A-AAT
11024438 -TAATGTGTAAAT
1 GT-ATGTGTAAAT
*
11024450 G--TG-GAAAAT
1 GTATGTGTAAAT
11024459 GTATGTGTAAAT
1 GTATGTGTAAAT
11024471 GTATGT
1 GTATGT
11024477 TTTATAATTA
Statistics
Matches: 42, Mismatches: 4, Indels: 14
0.70 0.07 0.23
Matches are distributed among these distances:
9 6 0.14
10 2 0.05
11 2 0.05
12 21 0.50
13 3 0.07
14 8 0.19
ACGTcount: A:0.34, C:0.02, G:0.23, T:0.42
Consensus pattern (12 bp):
GTATGTGTAAAT
Found at i:11025523 original size:24 final size:24
Alignment explanation
Indices: 11025491--11025559 Score: 93
Period size: 24 Copynumber: 2.9 Consensus size: 24
11025481 AATATTATGT
11025491 TGATGGTAATAAAGGTGGTGAGGG
1 TGATGGTAATAAAGGTGGTGAGGG
* *
11025515 TGATGGTAATAAAGGTGGTGATGT
1 TGATGGTAATAAAGGTGGTGAGGG
* **
11025539 TGAGGGTGTTAAAGGTGGTGA
1 TGATGGTAATAAAGGTGGTGA
11025560 TTGTGAGGGT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.28, C:0.00, G:0.43, T:0.29
Consensus pattern (24 bp):
TGATGGTAATAAAGGTGGTGAGGG
Found at i:11025560 original size:24 final size:23
Alignment explanation
Indices: 11025500--11025758 Score: 129
Period size: 24 Copynumber: 11.0 Consensus size: 23
11025490 TTGATGGTAA
* * * *
11025500 TAAAGGTGGTGAGGGTGATGGTAA
1 TAAAGGTGGTGATGTTGAGGGT-G
11025524 TAAAGGTGGTGATGTTGAGGGTG
1 TAAAGGTGGTGATGTTGAGGGTG
11025547 TTAAAGGTGGTGAT-TGTGAGGGTG
1 -TAAAGGTGGTGATGT-TGAGGGTG
* * * **
11025571 --AGGGTGGTGAGGTTGTTGGCAG
1 TAAAGGTGGTGATGTTG-AGGGTG
11025593 TAAAGGTGGTGATGTTGAGGGTG
1 TAAAGGTGGTGATGTTGAGGGTG
*
11025616 TTAAAGGTAGTGAT-TGTGAGGGTGAGGG
1 -TAAAGGTGGTGATGT-TGAGGGT----G
* * * * **
11025644 TGAGGGTGGTGAGGTTGTTGGCAG
1 TAAAGGTGGTGATGTTG-AGGGTG
*
11025668 TAAAGGTGGTGA-GGTGAGGGTG
1 TAAAGGTGGTGATGTTGAGGGTG
* * * **
11025690 --AGGGTGGTGAGGTTGTTGGCAG
1 TAAAGGTGGTGATGTTG-AGGGTG
11025712 TAAAGGTGGTGATGTTGAGGGTG
1 TAAAGGTGGTGATGTTGAGGGTG
*
11025735 TTAAAGGTAGTGAT-TGTGAGGGTG
1 -TAAAGGTGGTGATGT-TGAGGGTG
11025759 AGGGTGAGGG
Statistics
Matches: 176, Mismatches: 39, Indels: 40
0.69 0.15 0.16
Matches are distributed among these distances:
20 9 0.05
21 14 0.08
22 10 0.06
23 12 0.07
24 116 0.66
27 11 0.06
28 4 0.02
ACGTcount: A:0.21, C:0.01, G:0.49, T:0.29
Consensus pattern (23 bp):
TAAAGGTGGTGATGTTGAGGGTG
Found at i:11025615 original size:69 final size:72
Alignment explanation
Indices: 11025504--11025689 Score: 263
Period size: 69 Copynumber: 2.6 Consensus size: 72
11025494 TGGTAATAAA
* * * * *
11025504 GGTGGTGAGGGTGATGGTAATAAAGGTGGTGATGTTGAGGGTGTTAAAGGTGGTGA-T-T-GTGA
1 GGTGGTGAGGTTGTTGGCAGTAAAGGTGGTGATGTTGAGGGTGTTAAAGGTAGTGATTGTGGTGA
11025566 GGGTGAG
66 GGGTGAG
11025573 GGTGGTGAGGTTGTTGGCAGTAAAGGTGGTGATGTTGAGGGTGTTAAAGGTAGTGATTGTGAGGG
1 GGTGGTGAGGTTGTTGGCAGTAAAGGTGGTGATGTTGAGGGTGTTAAAGGTAGTGATTGT---GG
11025638 TGAGGGTGAG
63 TGAGGGTGAG
*
11025648 GGTGGTGAGGTTGTTGGCAGTAAAGGTGGTGA-GGTGAGGGTG
1 GGTGGTGAGGTTGTTGGCAGTAAAGGTGGTGATGTTGAGGGTG
11025690 AGGGTGGTGA
Statistics
Matches: 105, Mismatches: 6, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
69 51 0.49
70 1 0.01
71 1 0.01
74 9 0.09
75 43 0.41
ACGTcount: A:0.20, C:0.01, G:0.51, T:0.28
Consensus pattern (72 bp):
GGTGGTGAGGTTGTTGGCAGTAAAGGTGGTGATGTTGAGGGTGTTAAAGGTAGTGATTGTGGTGA
GGGTGAG
Found at i:11025690 original size:44 final size:45
Alignment explanation
Indices: 11025631--11025734 Score: 183
Period size: 44 Copynumber: 2.3 Consensus size: 45
11025621 GGTAGTGATT
11025631 GTGAGGGTGAGGGTGAGGGTGGTGAGGTTGTTGGCAGTAAAGGTG
1 GTGAGGGTGAGGGTGAGGGTGGTGAGGTTGTTGGCAGTAAAGGTG
11025676 GTGA-GGTGAGGGTGAGGGTGGTGAGGTTGTTGGCAGTAAAGGTG
1 GTGAGGGTGAGGGTGAGGGTGGTGAGGTTGTTGGCAGTAAAGGTG
* *
11025720 GTGATGTTGAGGGTG
1 GTGAGGGTGAGGGTG
11025735 TTAAAGGTAG
Statistics
Matches: 57, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
44 44 0.77
45 13 0.23
ACGTcount: A:0.17, C:0.02, G:0.55, T:0.26
Consensus pattern (45 bp):
GTGAGGGTGAGGGTGAGGGTGGTGAGGTTGTTGGCAGTAAAGGTG
Found at i:11025700 original size:119 final size:119
Alignment explanation
Indices: 11025548--11025800 Score: 488
Period size: 119 Copynumber: 2.1 Consensus size: 119
11025538 TTGAGGGTGT
*
11025548 TAAAGGTGGTGATTGTGAGGGTGAGGGTGGTGAGGTTGTTGGCAGTAAAGGTGGTGATGTTGAGG
1 TAAAGGTGGTGA-GGTGAGGGTGAGGGTGGTGAGGTTGTTGGCAGTAAAGGTGGTGATGTTGAGG
11025613 GTGTTAAAGGTAGTGATTGTGAGGGTGAGGGTGAGGGTGGTGAGGTTGTTGGCAG
65 GTGTTAAAGGTAGTGATTGTGAGGGTGAGGGTGAGGGTGGTGAGGTTGTTGGCAG
11025668 TAAAGGTGGTGAGGTGAGGGTGAGGGTGGTGAGGTTGTTGGCAGTAAAGGTGGTGATGTTGAGGG
1 TAAAGGTGGTGAGGTGAGGGTGAGGGTGGTGAGGTTGTTGGCAGTAAAGGTGGTGATGTTGAGGG
11025733 TGTTAAAGGTAGTGATTGTGAGGGTGAGGGTGAGGGTGGTGAGGTTGTTGGCAG
66 TGTTAAAGGTAGTGATTGTGAGGGTGAGGGTGAGGGTGGTGAGGTTGTTGGCAG
11025787 TAAAGGTGGTGAGG
1 TAAAGGTGGTGAGG
11025801 GTTTAGATGC
Statistics
Matches: 132, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
119 120 0.91
120 12 0.09
ACGTcount: A:0.20, C:0.02, G:0.51, T:0.28
Consensus pattern (119 bp):
TAAAGGTGGTGAGGTGAGGGTGAGGGTGGTGAGGTTGTTGGCAGTAAAGGTGGTGATGTTGAGGG
TGTTAAAGGTAGTGATTGTGAGGGTGAGGGTGAGGGTGGTGAGGTTGTTGGCAG
Found at i:11025849 original size:30 final size:30
Alignment explanation
Indices: 11025795--11025862 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
11025785 AGTAAAGGTG
*
11025795 GTGAGGGTTTAGATGCTAGTAGTAAGGGCA
1 GTGAGGGTTTAGATGCTAGCAGTAAGGGCA
* **
11025825 GTGAGGGTTTAGATG-TTGACAGTAAGGGTG
1 GTGAGGGTTTAGATGCTAG-CAGTAAGGGCA
11025855 GTGAGGGT
1 GTGAGGGT
11025863 GATGAAGGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 2 0.06
30 31 0.94
ACGTcount: A:0.24, C:0.04, G:0.44, T:0.28
Consensus pattern (30 bp):
GTGAGGGTTTAGATGCTAGCAGTAAGGGCA
Found at i:11025863 original size:9 final size:9
Alignment explanation
Indices: 11025849--11025898 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
11025839 GTTGACAGTA
11025849 AGGGTGGTG
1 AGGGTGGTG
*
11025858 AGGGTGATG
1 AGGGTGGTG
*
11025867 AAGGTGGTG
1 AGGGTGGTG
11025876 AGGGTAAGG-G
1 AGGGT--GGTG
11025886 A-GGTGGTG
1 AGGGTGGTG
11025894 AGGGT
1 AGGGT
11025899 TTGGATGATG
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
7 2 0.06
8 2 0.06
9 25 0.76
10 2 0.06
11 2 0.06
ACGTcount: A:0.20, C:0.00, G:0.60, T:0.20
Consensus pattern (9 bp):
AGGGTGGTG
Found at i:11025874 original size:18 final size:18
Alignment explanation
Indices: 11025851--11025898 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
11025841 TGACAGTAAG
* *
11025851 GGTGGTGAGGGTGATGAA
1 GGTGGTGAGGGTAAGGAA
*
11025869 GGTGGTGAGGGTAAGGGA
1 GGTGGTGAGGGTAAGGAA
11025887 GGTGGTGAGGGT
1 GGTGGTGAGGGT
11025899 TTGGATGATG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.19, C:0.00, G:0.60, T:0.21
Consensus pattern (18 bp):
GGTGGTGAGGGTAAGGAA
Found at i:11026616 original size:398 final size:398
Alignment explanation
Indices: 11025880--11026677 Score: 1569
Period size: 398 Copynumber: 2.0 Consensus size: 398
11025870 GTGGTGAGGG
11025880 TAAGGGAGGTGGTGAGGGTTTGGATGATGGCAGTAATGGTGGTGAGGGTGAGGGAGGTGGTAAGG
1 TAAGGGAGGTGGTGAGGGTTTGGATGATGGCAGTAATGGTGGTGAGGGTGAGGGAGGTGGTAAGG
11025945 GTTCAGGTAAGGGTGCTGTTAATGAAGGTGTTGAGGGTCAGGGTAAGGTTGATGTTGCTATTAGT
66 GTTCAGGTAAGGGTGCTGTTAATGAAGGTGTTGAGGGTCAGGGTAAGGTTGATGTTGCTATTAGT
*
11026010 GATGGAGGTGGTGATGATTATGAAGAGCTTCAAGATGATATTTACTTATCAGATGGTGATGATGA
131 AATGGAGGTGGTGATGATTATGAAGAGCTTCAAGATGATATTTACTTATCAGATGGTGATGATGA
11026075 TGAGGAGCTTCAAGAAGCTAGGCAAAAGGTGAGGGAGTGGAGGGGAAAACCAATGGGAAAGGTAA
196 TGAGGAGCTTCAAGAAGCTAGGCAAAAGGTGAGGGAGTGGAGGGGAAAACCAATGGGAAAGGTAA
*
11026140 AGAAACAGTGCTTGATGAGATTGAAAGTGAAAGCACTGGAGAGCAGTTTGAGGCTGATGTCCCTG
261 AGAAACAGTGCTTGATGAGACTGAAAGTGAAAGCACTGGAGAGCAGTTTGAGGCTGATGTCCCTG
11026205 AAGAAGTCGAGGCTGAAGGACTAAATTATAGTGTTGGTAGGGAAGAAGATGGAAATGAGATTGAA
326 AAGAAGTCGAGGCTGAAGGACTAAATTATAGTGTTGGTAGGGAAGAAGATGGAAATGAGATTGAA
11026270 TATTTTGA
391 TATTTTGA
11026278 TAAGGGAGGTGGTGAGGGTTTGGATGATGGCAGTAATGGTGGTGAGGGTGAGGGAGGTGGTAAGG
1 TAAGGGAGGTGGTGAGGGTTTGGATGATGGCAGTAATGGTGGTGAGGGTGAGGGAGGTGGTAAGG
*
11026343 GTTCAGGTAAGGGTGCTGTTAGTGAAGGTGTTGAGGGTCAGGGTAAGGTTGATGTTGCTATTAGT
66 GTTCAGGTAAGGGTGCTGTTAATGAAGGTGTTGAGGGTCAGGGTAAGGTTGATGTTGCTATTAGT
11026408 AATGGAGGTGGTGATGATTATGAAGAGCTTCAAGATGATATTTACTTATCAGATGGTGATGATGA
131 AATGGAGGTGGTGATGATTATGAAGAGCTTCAAGATGATATTTACTTATCAGATGGTGATGATGA
11026473 TGAGGAGCTTCAAGAAGCTAGGCAAAAGGTGAGGGAGTGGAGGGGAAAACCAATGGGAAAGGTAA
196 TGAGGAGCTTCAAGAAGCTAGGCAAAAGGTGAGGGAGTGGAGGGGAAAACCAATGGGAAAGGTAA
11026538 AGAAACAGTGCTTGATGAGACTGAAAGTGAAAGCACTGGAGAGCAGTTTGAGGCTGATGTCCCTG
261 AGAAACAGTGCTTGATGAGACTGAAAGTGAAAGCACTGGAGAGCAGTTTGAGGCTGATGTCCCTG
11026603 AAGAAGTCGAGGCTGAAGGACTAAATTATAGTGTTGGTAGGGAAGAAGATGGAAATGAGATTGAA
326 AAGAAGTCGAGGCTGAAGGACTAAATTATAGTGTTGGTAGGGAAGAAGATGGAAATGAGATTGAA
11026668 TATTTTGA
391 TATTTTGA
11026676 TA
1 TA
11026678 GTGATAATCA
Statistics
Matches: 397, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
398 397 1.00
ACGTcount: A:0.30, C:0.07, G:0.38, T:0.25
Consensus pattern (398 bp):
TAAGGGAGGTGGTGAGGGTTTGGATGATGGCAGTAATGGTGGTGAGGGTGAGGGAGGTGGTAAGG
GTTCAGGTAAGGGTGCTGTTAATGAAGGTGTTGAGGGTCAGGGTAAGGTTGATGTTGCTATTAGT
AATGGAGGTGGTGATGATTATGAAGAGCTTCAAGATGATATTTACTTATCAGATGGTGATGATGA
TGAGGAGCTTCAAGAAGCTAGGCAAAAGGTGAGGGAGTGGAGGGGAAAACCAATGGGAAAGGTAA
AGAAACAGTGCTTGATGAGACTGAAAGTGAAAGCACTGGAGAGCAGTTTGAGGCTGATGTCCCTG
AAGAAGTCGAGGCTGAAGGACTAAATTATAGTGTTGGTAGGGAAGAAGATGGAAATGAGATTGAA
TATTTTGA
Found at i:11031834 original size:30 final size:30
Alignment explanation
Indices: 11031792--11031947 Score: 100
Period size: 31 Copynumber: 5.2 Consensus size: 30
11031782 GTTTGGGGGT
11031792 AAAATGGTAATTTTTGGTGAAATAGAGGTCA
1 AAAATGGTAATTTTTGGTGAAATAGAGGT-A
*
11031823 AAAATGG-AA-TTTT-G-GAAAGTTTAGGGGT-
1 AAAATGGTAATTTTTGGTGAAA---TAGAGGTA
**
11031851 AAAATGGTAATTTTTGGTGAAACCGAGGTTA
1 AAAATGGTAATTTTTGGTGAAATAGAGG-TA
11031882 AAAATGG-AA-TTTT-G-GAAAGTTTACG-GGT-
1 AAAATGGTAATTTTTGGTGAAA---TA-GAGGTA
* *
11031910 AAAATGGTAATTTTTGGTGAAATCGGGGTTA
1 AAAATGGTAATTTTTGGTGAAATAGAGG-TA
11031941 AAAATGG
1 AAAATGG
11031948 GATTTTGGAA
Statistics
Matches: 98, Mismatches: 7, Indels: 40
0.68 0.05 0.28
Matches are distributed among these distances:
27 8 0.08
28 17 0.17
29 19 0.19
30 22 0.22
31 24 0.24
32 8 0.08
ACGTcount: A:0.37, C:0.03, G:0.28, T:0.32
Consensus pattern (30 bp):
AAAATGGTAATTTTTGGTGAAATAGAGGTA
Found at i:11031837 original size:59 final size:59
Alignment explanation
Indices: 11031730--11031985 Score: 401
Period size: 59 Copynumber: 4.4 Consensus size: 59
11031720 TTTGACTTTC
* * *
11031730 GGGGTAAAAATGG-AA-TTTTGGTAAAATCG-GGTTAAAAATGGGATTTTGGAAAGTTTG
1 GGGGT-AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTA
* *
11031787 GGGGTAAAATGGTAATTTTTGGTGAAATAGAGGTCAAAAATGGAATTTTGGAAAGTTTA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTA
*
11031846 GGGGTAAAATGGTAATTTTTGGTGAAACCGAGGTTAAAAATGGAATTTTGGAAAGTTTA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTA
* * *
11031905 CGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTTA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTA
11031964 GGGGTAAAATGGTAATTTTTGG
1 GGGGTAAAATGGTAATTTTTGG
11031986 ACAGTTCAAG
Statistics
Matches: 183, Mismatches: 13, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
56 7 0.04
57 7 0.04
58 12 0.07
59 157 0.86
ACGTcount: A:0.34, C:0.02, G:0.30, T:0.33
Consensus pattern (59 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTA
Found at i:11031968 original size:30 final size:30
Alignment explanation
Indices: 11031730--11031991 Score: 125
Period size: 28 Copynumber: 8.9 Consensus size: 30
11031720 TTTGACTTTC
*
11031730 GGGG-TAAAAATGGAATTTTGGTAAA--AT-
1 GGGGTTAAAAATGGAATTTTGG-AAAGTTTA
* *
11031757 CGGGTTAAAAATGGGATTTTGGAAAGTTT-
1 GGGGTTAAAAATGGAATTTTGGAAAGTTTA
*
11031786 GGGGGT-AAAATGGTAATTTTTGGTGAAA---TA
1 GGGGTTAAAAATGG-AA-TTTT-G-GAAAGTTTA
* *
11031816 GAGGTCAAAAATGGAATTTTGGAAAGTTTA
1 GGGGTTAAAAATGGAATTTTGGAAAGTTTA
**
11031846 GGGG-T-AAAATGGTAATTTTTGGTGAAA---CC
1 GGGGTTAAAAATGG-AA-TTTT-G-GAAAGTTTA
*
11031875 GAGGTTAAAAATGGAATTTTGGAAAGTTTA
1 GGGGTTAAAAATGGAATTTTGGAAAGTTTA
* *
11031905 CGGG-T-AAAATGGTAATTTTTGGTGAAA---TC
1 GGGGTTAAAAATGG-AA-TTTT-G-GAAAGTTTA
*
11031934 GGGGTTAAAAATGGGATTTTGGAAAGTTTA
1 GGGGTTAAAAATGGAATTTTGGAAAGTTTA
*
11031964 GGGG-T-AAAATGGTAATTTTTGGACAGTT
1 GGGGTTAAAAATGG-AA-TTTTGGAAAGTT
11031992 CAAGGACCTA
Statistics
Matches: 179, Mismatches: 24, Indels: 61
0.68 0.09 0.23
Matches are distributed among these distances:
27 18 0.10
28 47 0.26
29 33 0.18
30 45 0.25
31 24 0.13
32 12 0.07
ACGTcount: A:0.34, C:0.03, G:0.30, T:0.33
Consensus pattern (30 bp):
GGGGTTAAAAATGGAATTTTGGAAAGTTTA
Found at i:11033964 original size:17 final size:17
Alignment explanation
Indices: 11033944--11033988 Score: 65
Period size: 16 Copynumber: 2.7 Consensus size: 17
11033934 TTTCAAATGT
11033944 ATTTAAATTTAAAACAA
1 ATTTAAATTTAAAACAA
*
11033961 ATTTAAATTT-AAATAA
1 ATTTAAATTTAAAACAA
*
11033977 ATTTAAAATTAA
1 ATTTAAATTTAA
11033989 TTTCAAACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (17 bp):
ATTTAAATTTAAAACAA
Found at i:11033985 original size:23 final size:24
Alignment explanation
Indices: 11033959--11034008 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
11033949 AATTTAAAAC
11033959 AAATTTAAATTT-AAA-TAAATTTA
1 AAATTT-AATTTCAAACTAAATTTA
*
11033982 AAA-TTAATTTCAAACTTAATTTA
1 AAATTTAATTTCAAACTAAATTTA
11034005 AAAT
1 AAAT
11034009 CTAAGTTGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
21 5 0.22
22 5 0.22
23 13 0.57
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (24 bp):
AAATTTAATTTCAAACTAAATTTA
Found at i:11033990 original size:27 final size:28
Alignment explanation
Indices: 11033947--11034000 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
11033937 CAAATGTATT
*
11033947 TAAATTTAAAACAAATTT-AAATTTAAA
1 TAAATTTAAAACAAATTTCAAACTTAAA
**
11033974 TAAATTTAAAATTAATTTCAAACTTAA
1 TAAATTTAAAACAAATTTCAAACTTAA
11034001 TTTAAAATCT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 16 0.70
28 7 0.30
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.39
Consensus pattern (28 bp):
TAAATTTAAAACAAATTTCAAACTTAAA
Found at i:11034002 original size:12 final size:11
Alignment explanation
Indices: 11033966--11034008 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
11033956 AACAAATTTA
*
11033966 AATTT-AAATA
1 AATTTAAAATT
11033976 AATTTAAAATT
1 AATTTAAAATT
*
11033987 AATTTCAAACTT
1 AATTT-AAAATT
11033999 AATTTAAAAT
1 AATTTAAAAT
11034009 CTAAGTTGGG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
10 5 0.18
11 13 0.46
12 10 0.36
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (11 bp):
AATTTAAAATT
Found at i:11036869 original size:14 final size:15
Alignment explanation
Indices: 11036850--11036880 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
11036840 TTTCACTTTA
11036850 TTTTATTTTTA-GCT
1 TTTTATTTTTATGCT
11036864 TTTTATTTTTATGCT
1 TTTTATTTTTATGCT
11036879 TT
1 TT
11036881 CAATTACACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.13, C:0.06, G:0.06, T:0.74
Consensus pattern (15 bp):
TTTTATTTTTATGCT
Found at i:11041609 original size:6 final size:6
Alignment explanation
Indices: 11041600--11041636 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
11041590 TTTTGAATTT
*
11041600 ATTTAA ATTTAA ATTT-A TTTTAA ATTTAA ATTTAA AT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT
11041637 CAAATTATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 4 0.14
6 24 0.86
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
ATTTAA
Found at i:11041614 original size:23 final size:23
Alignment explanation
Indices: 11041588--11041636 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 23
11041578 TTTATGTTTT
11041588 AATTTTGAATTT-ATTTAAATTTA
1 AATTTT-AATTTAATTTAAATTTA
*
11041611 AA-TTTATTTTAAATTTAAATTTA
1 AATTTTAATTT-AATTTAAATTTA
11041634 AAT
1 AAT
11041637 CAAATTATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
21 4 0.18
22 3 0.14
23 15 0.68
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (23 bp):
AATTTTAATTTAATTTAAATTTA
Found at i:11041621 original size:17 final size:17
Alignment explanation
Indices: 11041584--11041633 Score: 75
Period size: 17 Copynumber: 3.0 Consensus size: 17
11041574 GACTTTTATG
* *
11041584 TTTTAATTTTGAATTTA
1 TTTTAAATTTAAATTTA
11041601 -TTTAAATTTAAATTTA
1 TTTTAAATTTAAATTTA
11041617 TTTTAAATTTAAATTTA
1 TTTTAAATTTAAATTTA
11041634 AATCAAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 14 0.47
17 16 0.53
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (17 bp):
TTTTAAATTTAAATTTA
Found at i:11041641 original size:17 final size:17
Alignment explanation
Indices: 11041604--11041642 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
11041594 GAATTTATTT
** *
11041604 AAATTTAAATTTATTTT
1 AAATTTAAATTTAAATC
11041621 AAATTTAAATTTAAATC
1 AAATTTAAATTTAAATC
11041638 AAATT
1 AAATT
11041643 ATGAAAATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (17 bp):
AAATTTAAATTTAAATC
Found at i:11041908 original size:26 final size:26
Alignment explanation
Indices: 11041879--11041929 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
11041869 ATAGGAGTTC
11041879 GCCACA-TCAGCAGCCAACTTGCTCCT
1 GCCACAGTCAGCAGCCAAC-TGCTCCT
* *
11041905 GCCACAGTCGGCTGCCAACTGCTCC
1 GCCACAGTCAGCAGCCAACTGCTCC
11041930 AACCGCCACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 12 0.55
27 10 0.45
ACGTcount: A:0.20, C:0.43, G:0.20, T:0.18
Consensus pattern (26 bp):
GCCACAGTCAGCAGCCAACTGCTCCT
Found at i:11042498 original size:15 final size:15
Alignment explanation
Indices: 11042470--11042510 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
11042460 ATGCTAATAA
*
11042470 TAATAAATATATTATT
1 TAATAAA-ATATTAAT
*
11042486 TATTAAAATATTAAT
1 TAATAAAATATTAAT
11042501 TAATAAAATA
1 TAATAAAATA
11042511 AAAAAGGGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 16 0.73
16 6 0.27
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TAATAAAATATTAAT
Found at i:11043652 original size:30 final size:30
Alignment explanation
Indices: 11043619--11043811 Score: 273
Period size: 30 Copynumber: 6.4 Consensus size: 30
11043609 AAACTGCCCA
* *
11043619 AAAATTATATTTTGATCCTAAAAC-TTTCT
1 AAAATTACATTTTGACCCTAAAACTTTTCT
*
11043648 AAAAATTACATTTT-AGCCCCAAAACTTTTCT
1 -AAAATTACATTTTGA-CCCTAAAACTTTTCT
11043679 AAAATTACATTTTGACCCTAAAACTTTTCT
1 AAAATTACATTTTGACCCTAAAACTTTTCT
11043709 AAAATTACATTTTGACCCTAAAACTTTTCT
1 AAAATTACATTTTGACCCTAAAACTTTTCT
*
11043739 AAAATTACATTTTGACCCTAAAACTTTACT
1 AAAATTACATTTTGACCCTAAAACTTTTCT
* * * *
11043769 AATATTACATTTTGATCCAAAAACTTTTCC
1 AAAATTACATTTTGACCCTAAAACTTTTCT
*
11043799 AATATTACATTTT
1 AAAATTACATTTT
11043812 TTACCCCGAT
Statistics
Matches: 150, Mismatches: 10, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
29 1 0.01
30 143 0.95
31 6 0.04
ACGTcount: A:0.38, C:0.19, G:0.03, T:0.40
Consensus pattern (30 bp):
AAAATTACATTTTGACCCTAAAACTTTTCT
Found at i:11044039 original size:15 final size:16
Alignment explanation
Indices: 11044012--11044057 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 16
11044002 ATTTATTTGC
*
11044012 ATCTGCATCTTATATT
1 ATCTGCATATTATATT
*
11044028 TTC-GCATATTAT-TT
1 ATCTGCATATTATATT
*
11044042 ATCTGCTTATTATATT
1 ATCTGCATATTATATT
11044058 GCTTCGTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
14 4 0.17
15 16 0.67
16 4 0.17
ACGTcount: A:0.24, C:0.15, G:0.07, T:0.54
Consensus pattern (16 bp):
ATCTGCATATTATATT
Found at i:11051676 original size:25 final size:28
Alignment explanation
Indices: 11051625--11051676 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
11051615 TTTCAATTCC
*
11051625 AAATAAATTATTTGCTTGTAACACATAA
1 AAATAAATCATTTGCTTGTAACACATAA
11051653 AAATAAATCA-TT-CTTG-AACACATA
1 AAATAAATCATTTGCTTGTAACACATA
11051677 CACCCATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 8 0.35
26 4 0.17
27 2 0.09
28 9 0.39
ACGTcount: A:0.48, C:0.13, G:0.06, T:0.33
Consensus pattern (28 bp):
AAATAAATCATTTGCTTGTAACACATAA
Found at i:11056228 original size:38 final size:39
Alignment explanation
Indices: 11056174--11058303 Score: 1089
Period size: 38 Copynumber: 55.2 Consensus size: 39
11056164 ATTTCCTATC
*
11056174 CTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTAT
1 CTCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTTTAT
** ** *
11056213 CT-TTGAAATTGAAGTAAGAGCAAGAT-A-ATTTC-CTAT
1 CTCTTGAAATTGAAGT-AGAGCTGGATAACAAGTCTTTAT
*
11056249 CCTCTTGAAATTGAAGTAGAGCTGGATAGCAAGTCTTTAT
1 -CTCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTTTAT
* * * *
11056289 CTCTCTGAAATTGAAGTAAGAGCAAGACGGAGCACCAACATCATTTCCTAT
1 CTCT-TGAAATTGAAGT-AGAGC----TGGA-TAACAA-GTC--TT--TAT
*
11056340 CCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTAT
1 -CTCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTTTAT
** ** *
11056380 CTC-TGAAATTGAAGTAAGAGCAAGAT-A-ATTTC-CTAT
1 CTCTTGAAATTGAAGT-AGAGCTGGATAACAAGTCTTTAT
* *
11056416 CCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTAT
1 -CTCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTTTAT
** *** *
11056456 CTC-TGAAATTGAAGTAAGAGCAAGAT--CTTTTC-CTAT
1 CTCTTGAAATTGAAGT-AGAGCTGGATAACAAGTCTTTAT
* *
11056492 CCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTAT
1 -CTCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTTTAT
** ** *
11056532 CTC-TGAAATTGAAGTAAGAGCAAGAT--CATTTC-CTAT
1 CTCTTGAAATTGAAGT-AGAGCTGGATAACAAGTCTTTAT
*
11056568 CCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTAT
1 -CTCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTTTAT
** *** *
11056608 CTC-TGAAATTGAAGTAAGAGCAAGAT--CTTTTC-CTAT
1 CTCTTGAAATTGAAGT-AGAGCTGGATAACAAGTCTTTAT
* * *
11056644 CCTCTTAAAATTGAAGTAAAGCTGGATATCAAGTCTTTAT
1 -CTCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTTTAT
** ** *
11056684 CTC-TGAAATTGAAGTAAGAGCAAGAT--CATTTC-CTAT
1 CTCTTGAAATTGAAGT-AGAGCTGGATAACAAGTCTTTAT
* *
11056720 CCTCTTGAAATTGAAGTAGAGTTGGATAACATGTCTTTAT
1 -CTCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTTTAT
** ** *
11056760 CTC-TGAAATTGAAGTAAGAGCAAGAT--CATTTC-CTAT
1 CTCTTGAAATTGAAGT-AGAGCTGGATAACAAGTCTTTAT
* * *
11056796 CCTCTTGAAATTGAAGTAAAGTTGGATATCAAGTCTTTAT
1 -CTCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTTTAT
** ** *
11056836 CT-TTGAAATTGAAGTAAGAGCAAGAT--CATTTC-CTAT
1 CTCTTGAAATTGAAGT-AGAGCTGGATAACAAGTCTTTAT
* *
11056872 CCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTAT
1 -CTCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTTTAT
** ** *
11056912 CTC-TGAAATTGAAGTAAGAGCAAGAT--CATTTC-CTAT
1 CTCTTGAAATTGAAGT-AGAGCTGGATAACAAGTCTTTAT
* *
11056948 CCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTAT
1 -CTCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTTTAT
** ** *
11056988 CTC-TGAAATTGAAGTAAGAGCAAGAT--CATTTC-CTAT
1 CTCTTGAAATTGAAGT-AGAGCTGGATAACAAGTCTTTAT
*
11057024 CCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTAT
1 -CTCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTTTAT
** ** *
11057064 CTC-TGAAATTGAAGTAAGAGCAAGAT-A-ATTTC-CTAT
1 CTCTTGAAATTGAAGT-AGAGCTGGATAACAAGTCTTTAT
*
11057100 CCTCTTGAAATTGAAGTAGAGCTGGATATCAAGTCTTTAT
1 -CTCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTTTAT
** ** *
11057140 CT-TTGAAATTGAAGTAAGAGCAAGAT--CATTTC-CTAT
1 CTCTTGAAATTGAAGT-AGAGCTGGATAACAAGTCTTTAT
*
11057176 CCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTAT
1 -CTCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTTTAT
** ** *
11057216 CTC-TGAAATTGAAGTAAGAGCAAGAT--CATTTC-CTAT
1 CTCTTGAAATTGAAGT-AGAGCTGGATAACAAGTCTTTAT
* *
11057252 CCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTAT
1 -CTCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTTTAT
** *** *
11057292 CTC-TGAAATTGAAGTAAGAGCAAGAT--CTTTTC-CTAT
1 CTCTTGAAATTGAAGT-AGAGCTGGATAACAAGTCTTTAT
* *
11057328 CCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTAT
1 -CTCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTTTAT
** ** *
11057368 CTC-TGAAATTGAAGTAAGAGCAAGAT--CATTTC-CTAT
1 CTCTTGAAATTGAAGT-AGAGCTGGATAACAAGTCTTTAT
*
11057404 CCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTAT
1 -CTCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTTTAT
** *** *
11057444 CTC-TGAAATTGAAGTAAGAGCAAGAT--CTTTTC-CTAT
1 CTCTTGAAATTGAAGT-AGAGCTGGATAACAAGTCTTTAT
* *
11057480 CCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTAT
1 -CTCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTTTAT
** ** *
11057520 CTC-TGAAATTGAAGTAAGAGCAAGAT--CATTTC-CTAT
1 CTCTTGAAATTGAAGT-AGAGCTGGATAACAAGTCTTTAT
*
11057556 CCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTAT
1 -CTCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTTTAT
** *** *
11057596 CTC-TGAAATTGAAGTAAGAGCAAGAT--CTTTTC-CTAT
1 CTCTTGAAATTGAAGT-AGAGCTGGATAACAAGTCTTTAT
* *
11057632 CCTCTTGAAATTGAAGTA-AACTTGGATATCAAGTCTTTAT
1 -CTCTTGAAATTGAAGTAGAGC-TGGATAACAAGTCTTTAT
** ** *
11057672 CTC-TGAAATTGAAGTAAGAGCAAGAT--CATTTC-CTAT
1 CTCTTGAAATTGAAGT-AGAGCTGGATAACAAGTCTTTAT
*
11057708 CCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTAT
1 -CTCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTTTAT
** *** *
11057748 CTC-TGAAATTGAAGTAAGAGCAAGAT--CTTTTC-CTAT
1 CTCTTGAAATTGAAGT-AGAGCTGGATAACAAGTCTTTAT
* *
11057784 CCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTAT
1 -CTCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTTTAT
** ** *
11057824 CTC-TGAAATTGAAGTAAGAGCAAGAT--CATTTC-CTAT
1 CTCTTGAAATTGAAGT-AGAGCTGGATAACAAGTCTTTAT
* *
11057860 CCTCTTGAAATTGAAGTAGAGTTGGATAACATGTCTTTAT
1 -CTCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTTTAT
** ** *
11057900 CTC-TGAAATTGAAGTAAGAGCAAGAT--CATTTC-CTAT
1 CTCTTGAAATTGAAGT-AGAGCTGGATAACAAGTCTTTAT
* * *
11057936 CCTCTTGAAATTGAAGTAAAGTTGGATATCAAGTCTTTAT
1 -CTCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTTTAT
** ** *
11057976 CTC-TGAAATTGAAGTAAGAGCAAGAT--CATTTC-CTAT
1 CTCTTGAAATTGAAGT-AGAGCTGGATAACAAGTCTTTAT
* * *
11058012 CCTCTTGAAATTGAAATAAAGCTGGATATCAAGTCTTTAT
1 -CTCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTTTAT
* * * * *
11058052 CTCTCTGAAATTGATGTAAGAGCAAGACAGAGCATCAACATCATTTCCTAT
1 CTCT-TGAAATTGAAGT-AGAGC-TG---GA-TAACAA-GTC--TT--TAT
** * * *
11058103 CCTCTTGATGTTGAAGTAGAGTTGAATAACAGGTCTTTAT
1 -CTCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTTTAT
** * ** *
11058143 CTC-TGAAATTGAAGTAAGAGCAAGAT--TATTTC-CTAT
1 CTCTTGAAATTGAAGT-AGAGCTGGATAACAAGTCTTTAT
* *
11058179 CCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTAT
1 -CTCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTTTAT
* **
11058219 CTC-TAAAATTGAAGTAAGAGCAAGAT--C-A-TCTCTTAT
1 CTCTTGAAATTGAAGT-AGAGCTGGATAACAAGTCT-TTAT
* * * *
11058255 CCTCCTGAAATTGAAGTAGAGCCGGATATCAAGACTTTAT
1 -CTCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTTTAT
11058295 CTCTCTGAA
1 CTCT-TGAA
11058304 GCTATAGTAG
Statistics
Matches: 1568, Mismatches: 342, Indels: 361
0.69 0.15 0.16
Matches are distributed among these distances:
35 3 0.00
36 79 0.05
37 334 0.21
38 602 0.38
39 342 0.22
40 111 0.07
41 11 0.01
42 5 0.00
44 4 0.00
45 12 0.01
46 13 0.01
47 4 0.00
49 5 0.00
50 8 0.01
51 27 0.02
52 8 0.01
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Consensus pattern (39 bp):
CTCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTTTAT
Found at i:11056457 original size:76 final size:76
Alignment explanation
Indices: 11056328--11058298 Score: 3117
Period size: 76 Copynumber: 25.7 Consensus size: 76
11056318 GAGCACCAAC
* * *
11056328 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
11056393 GTAAGAGCAAG
66 GTAAGAGCAAG
*
11056404 ATAATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
11056469 GTAAGAGCAAG
66 GTAAGAGCAAG
*
11056480 ATCTTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
11056545 GTAAGAGCAAG
66 GTAAGAGCAAG
* * *
11056556 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
11056621 GTAAGAGCAAG
66 GTAAGAGCAAG
* *
11056632 ATCTTTTCCTATCCTCTTAAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
11056697 GTAAGAGCAAG
66 GTAAGAGCAAG
* * * *
11056708 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACATGTCTTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
11056773 GTAAGAGCAAG
66 GTAAGAGCAAG
* *
11056784 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATATCAAGTCTTTATCTTTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
11056849 GTAAGAGCAAG
66 GTAAGAGCAAG
11056860 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
11056925 GTAAGAGCAAG
66 GTAAGAGCAAG
11056936 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
11057001 GTAAGAGCAAG
66 GTAAGAGCAAG
* * *
11057012 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
11057077 GTAAGAGCAAG
66 GTAAGAGCAAG
* * *
11057088 ATAATTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATATCAAGTCTTTATCTTTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
11057153 GTAAGAGCAAG
66 GTAAGAGCAAG
* * *
11057164 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
11057229 GTAAGAGCAAG
66 GTAAGAGCAAG
11057240 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
11057305 GTAAGAGCAAG
66 GTAAGAGCAAG
*
11057316 ATCTTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
11057381 GTAAGAGCAAG
66 GTAAGAGCAAG
* * *
11057392 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
11057457 GTAAGAGCAAG
66 GTAAGAGCAAG
*
11057468 ATCTTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
11057533 GTAAGAGCAAG
66 GTAAGAGCAAG
* * *
11057544 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
11057609 GTAAGAGCAAG
66 GTAAGAGCAAG
*
11057620 ATCTTTTCCTATCCTCTTGAAATTGAAGTAAA-CTTGGATATCAAGTCTTTATCTCTGAAATTGA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGC-TGGATATCAAGTCTTTATCTCTGAAATTGA
11057684 AGTAAGAGCAAG
65 AGTAAGAGCAAG
* * *
11057696 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
11057761 GTAAGAGCAAG
66 GTAAGAGCAAG
*
11057772 ATCTTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
11057837 GTAAGAGCAAG
66 GTAAGAGCAAG
* * * *
11057848 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACATGTCTTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
11057913 GTAAGAGCAAG
66 GTAAGAGCAAG
*
11057924 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATATCAAGTCTTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
11057989 GTAAGAGCAAG
66 GTAAGAGCAAG
*
11058000 ATCATTTCCTATCCTCTTGAAATTGAAATAAAGCTGGATATCAAGTCTTTATCTCTCTGAAATTG
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTA--TCTCTGAAATTG
*
11058065 ATGTAAGAGCAAG
64 AAGTAAGAGCAAG
** * **** * * * * *
11058078 A-CAGAGCATCAACATCATTTCCT-ATCCTCTTGATGTTGAAG-TAGAGTTGAATAACAG-GTCT
1 ATC--A-TTTC--C-T-A--TCCTCTTGAAATTGAAG-TAAAGCT-G-GAT--ATCA-AGTCT-T
*
11058139 T-TATCTCTGAAATTGAAGTAAGAGCAAG
50 TATCT--CTGAAATTGAAGTAAGAGCAAG
* *
11058167 ATTATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTAAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
11058232 GTAAGAGCAAG
66 GTAAGAGCAAG
* * * * * *
11058243 ATCATCTCTTATCCTCCTGAAATTGAAGTAGAGCCGGATATCAAGACTTTATCTCT
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCT
11058299 CTGAAGCTAT
Statistics
Matches: 1754, Mismatches: 114, Indels: 54
0.91 0.06 0.03
Matches are distributed among these distances:
76 1639 0.93
77 5 0.00
78 31 0.02
79 1 0.00
80 4 0.00
81 9 0.01
82 8 0.00
83 2 0.00
84 2 0.00
85 7 0.00
86 9 0.01
87 6 0.00
88 1 0.00
89 26 0.01
90 4 0.00
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (76 bp):
ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
GTAAGAGCAAG
Found at i:11058284 original size:243 final size:243
Alignment explanation
Indices: 11057848--11058303 Score: 786
Period size: 243 Copynumber: 1.9 Consensus size: 243
11057838 TAAGAGCAAG
* *
11057848 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACATGTCTTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGAATAACAGGTCTTTATCTCTGAAATTGAA
*
11057913 GTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATATCAAGTCTTTATCT
66 GTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCT
* * * *
11057978 CTGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAATAAAGCTGGATATCA
131 CTAAAATTGAAGTAAGAGCAAGATCATCTCCTATCCTCCTGAAATTGAAATAAAGCCGGATATCA
*
11058043 AGTCTTTATCTCTCTGAAATTGATGTAAGAGCAAGACAGAGCATCAAC
196 AGACTTTATCTCTCTGAAATTGATGTAAGAGCAAGACAGAGCATCAAC
**
11058091 ATCATTTCCTATCCTCTTGATGTTGAAGTAGAGTTGAATAACAGGTCTTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGAATAACAGGTCTTTATCTCTGAAATTGAA
*
11058156 GTAAGAGCAAGATTATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCT
66 GTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCT
* * *
11058221 CTAAAATTGAAGTAAGAGCAAGATCATCTCTTATCCTCCTGAAATTGAAGTAGAGCCGGATATCA
131 CTAAAATTGAAGTAAGAGCAAGATCATCTCCTATCCTCCTGAAATTGAAATAAAGCCGGATATCA
11058286 AGACTTTATCTCTCTGAA
196 AGACTTTATCTCTCTGAA
11058304 GCTATAGTAG
Statistics
Matches: 199, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
243 199 1.00
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Consensus pattern (243 bp):
ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGAATAACAGGTCTTTATCTCTGAAATTGAA
GTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCT
CTAAAATTGAAGTAAGAGCAAGATCATCTCCTATCCTCCTGAAATTGAAATAAAGCCGGATATCA
AGACTTTATCTCTCTGAAATTGATGTAAGAGCAAGACAGAGCATCAAC
Found at i:11058600 original size:6 final size:6
Alignment explanation
Indices: 11058591--11058627 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
11058581 TTTTGAATTT
*
11058591 ATTTAA ATTTAA ATTT-A TTTTAA ATTTAA ATTTAA AT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT
11058628 CAAATTATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 4 0.14
6 24 0.86
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
ATTTAA
Found at i:11058605 original size:23 final size:23
Alignment explanation
Indices: 11058579--11058627 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 23
11058569 TTTATGTTTT
11058579 AATTTTGAATTT-ATTTAAATTTA
1 AATTTT-AATTTAATTTAAATTTA
*
11058602 AA-TTTATTTTAAATTTAAATTTA
1 AATTTTAATTT-AATTTAAATTTA
11058625 AAT
1 AAT
11058628 CAAATTATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
21 4 0.18
22 3 0.14
23 15 0.68
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (23 bp):
AATTTTAATTTAATTTAAATTTA
Found at i:11058612 original size:17 final size:17
Alignment explanation
Indices: 11058575--11058624 Score: 75
Period size: 17 Copynumber: 3.0 Consensus size: 17
11058565 GACTTTTATG
* *
11058575 TTTTAATTTTGAATTTA
1 TTTTAAATTTAAATTTA
11058592 -TTTAAATTTAAATTTA
1 TTTTAAATTTAAATTTA
11058608 TTTTAAATTTAAATTTA
1 TTTTAAATTTAAATTTA
11058625 AATCAAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 14 0.47
17 16 0.53
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (17 bp):
TTTTAAATTTAAATTTA
Found at i:11058632 original size:17 final size:17
Alignment explanation
Indices: 11058595--11058633 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
11058585 GAATTTATTT
** *
11058595 AAATTTAAATTTATTTT
1 AAATTTAAATTTAAATC
11058612 AAATTTAAATTTAAATC
1 AAATTTAAATTTAAATC
11058629 AAATT
1 AAATT
11058634 ATGAAAATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (17 bp):
AAATTTAAATTTAAATC
Found at i:11059489 original size:15 final size:15
Alignment explanation
Indices: 11059461--11059501 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
11059451 ATGCTAATAA
*
11059461 TAATAAATATATTATT
1 TAATAAA-ATATTAAT
*
11059477 TATTAAAATATTAAT
1 TAATAAAATATTAAT
11059492 TAATAAAATA
1 TAATAAAATA
11059502 AAAAAAGGGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 16 0.73
16 6 0.27
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TAATAAAATATTAAT
Found at i:11060839 original size:30 final size:30
Alignment explanation
Indices: 11060611--11060841 Score: 256
Period size: 30 Copynumber: 7.7 Consensus size: 30
11060601 AAACTGCCCA
* * *
11060611 AAAATTATATTTTGA-CCTCAAAA-ATTTCTA
1 AAAATTACATTTTGACCCT-AAAACTTTTC-C
* *
11060641 AAAATTACATTTT-ATCCCCAAAACTTTTCT
1 AAAATTACATTTTGA-CCCTAAAACTTTTCC
* *
11060671 AAAATTACATTTTGA-TCTCAAAAC-TTTCTA
1 AAAATTACATTTTGACCCT-AAAACTTTTC-C
11060701 AAAATTACATTTTGACCCTAAAACTTTTCC
1 AAAATTACATTTTGACCCTAAAACTTTTCC
*
11060731 AAAATTACATTTTGACCCCAAAACTTTTCC
1 AAAATTACATTTTGACCCTAAAACTTTTCC
* * * *
11060761 AATATTATATTTTAACCCTAAAAGTTTTCC
1 AAAATTACATTTTGACCCTAAAACTTTTCC
* *
11060791 AAAACTACATTTTAACCCTAAAACTTTTCC
1 AAAATTACATTTTGACCCTAAAACTTTTCC
11060821 AAAATTACATTTTGACCCTAA
1 AAAATTACATTTTGACCCTAA
11060842 TTTTGCCAAA
Statistics
Matches: 172, Mismatches: 21, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
29 6 0.03
30 153 0.89
31 13 0.08
ACGTcount: A:0.39, C:0.21, G:0.03, T:0.38
Consensus pattern (30 bp):
AAAATTACATTTTGACCCTAAAACTTTTCC
Found at i:11060862 original size:60 final size:59
Alignment explanation
Indices: 11060641--11060864 Score: 231
Period size: 60 Copynumber: 3.7 Consensus size: 59
11060631 AAAATTTCTA
* * * * * *
11060641 AAAATTACATTTT-ATCCCCAAAACTTTTCTAAAATTACATTTTGATCTCAAAAC-TTTCTA
1 AAAATTACATTTTGA--CCCTAAACTTTTCCAAAATTACATTTTAACCCCAAAACTTTTC-C
*
11060701 AAAATTACATTTTGACCCTAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCC
1 AAAATTACATTTTGACCCT-AAACTTTTCCAAAATTACATTTTAACCCCAAAACTTTTCC
* * * * * *
11060761 AATATTATATTTTAACCCTAAAAGTTTTCCAAAACTACATTTTAACCCTAAAACTTTTCC
1 AAAATTACATTTTGACCCT-AAACTTTTCCAAAATTACATTTTAACCCCAAAACTTTTCC
11060821 AAAATTACATTTTGACCCT-AA-TTTTGCCAAAATTTATCATTTTA
1 AAAATTACATTTTGACCCTAAACTTTT-CCAAAA-TTA-CATTTTA
11060865 TCTCCCCGAA
Statistics
Matches: 142, Mismatches: 16, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
57 4 0.03
58 8 0.06
59 5 0.04
60 120 0.85
61 5 0.04
ACGTcount: A:0.38, C:0.21, G:0.03, T:0.39
Consensus pattern (59 bp):
AAAATTACATTTTGACCCTAAACTTTTCCAAAATTACATTTTAACCCCAAAACTTTTCC
Found at i:11061029 original size:15 final size:16
Alignment explanation
Indices: 11061002--11061047 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 16
11060992 ATTTATTTGC
*
11061002 ATCTGCATCTTATATT
1 ATCTGCATATTATATT
*
11061018 TTC-GCATATTAT-TT
1 ATCTGCATATTATATT
*
11061032 ATCTGCTTATTATATT
1 ATCTGCATATTATATT
11061048 GCGTCGTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
14 4 0.17
15 16 0.67
16 4 0.17
ACGTcount: A:0.24, C:0.15, G:0.07, T:0.54
Consensus pattern (16 bp):
ATCTGCATATTATATT
Found at i:11061045 original size:30 final size:30
Alignment explanation
Indices: 11060987--11061047 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
11060977 CTCACCAATA
*
11060987 TTCGCATTTATTTGCATCTGCATCTTATATT
1 TTCGCATTTATTT-CATCTGCATATTATATT
*
11061018 TTCGCATATTATTT-ATCTGCTTATTATATT
1 TTCGCAT-TTATTTCATCTGCATATTATATT
11061048 GCGTCGTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 14 0.52
31 7 0.26
32 6 0.22
ACGTcount: A:0.21, C:0.16, G:0.08, T:0.54
Consensus pattern (30 bp):
TTCGCATTTATTTCATCTGCATATTATATT
Found at i:11070236 original size:21 final size:21
Alignment explanation
Indices: 11070210--11070262 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
11070200 GAGTTTGTTG
11070210 TATCGGTAGAAGTAATAATTA
1 TATCGGTAGAAGTAATAATTA
* * * *
11070231 TATCGGTAGTAGTCATACTTG
1 TATCGGTAGAAGTAATAATTA
*
11070252 TATCGTTAGAA
1 TATCGGTAGAA
11070263 CCATCCCAAC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.34, C:0.09, G:0.21, T:0.36
Consensus pattern (21 bp):
TATCGGTAGAAGTAATAATTA
Found at i:11071500 original size:24 final size:24
Alignment explanation
Indices: 11071468--11071515 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
11071458 AATCTGATAG
11071468 GATAGAGCTGGTATGTCGAAACTA
1 GATAGAGCTGGTATGTCGAAACTA
11071492 GATAGAGCTGGTATGTCGAAACTA
1 GATAGAGCTGGTATGTCGAAACTA
11071516 TCTGCTGGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.12, G:0.29, T:0.25
Consensus pattern (24 bp):
GATAGAGCTGGTATGTCGAAACTA
Found at i:11076165 original size:37 final size:37
Alignment explanation
Indices: 11076090--11076165 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 37
11076080 TCTAAGAATA
*
11076090 CAGGCTATGTGCCTAGTAGGCTTTGCGTCGGTGTATT
1 CAGGCTATGTGCCTAGTAGGCTTTGCGTCGGTGCATT
11076127 CAGGCTATGTG-CTGAGTAGGC-TT-CGTGCTGGTGCATT
1 CAGGCTATGTGCCT-AGTAGGCTTTGCGT-C-GGTGCATT
11076164 CA
1 CA
11076166 AGAATGAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
35 3 0.09
36 5 0.14
37 27 0.77
ACGTcount: A:0.14, C:0.20, G:0.33, T:0.33
Consensus pattern (37 bp):
CAGGCTATGTGCCTAGTAGGCTTTGCGTCGGTGCATT
Found at i:11078180 original size:20 final size:18
Alignment explanation
Indices: 11078152--11078199 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 18
11078142 TCACGTCAAC
*
11078152 AAATGATTTTAAAATTATTA
1 AAATTATTTTAAAA-TA-TA
11078172 AAATTATTTTTTAAAATATA
1 AAATTA--TTTTAAAATATA
11078192 AAATTATT
1 AAATTATT
11078200 AACATCATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
18 2 0.08
20 13 0.52
21 2 0.08
22 8 0.32
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (18 bp):
AAATTATTTTAAAATATA
Found at i:11089899 original size:17 final size:17
Alignment explanation
Indices: 11089849--11089911 Score: 63
Period size: 17 Copynumber: 3.6 Consensus size: 17
11089839 CAGTAAATTA
*
11089849 CAATGACAAATGGAAATG
1 CAATGAC-AATGAAAATG
*
11089867 CAATGACAATGCAAATG
1 CAATGACAATGAAAATG
* * *
11089884 CAGTGACAATTAAAATA
1 CAATGACAATGAAAATG
*
11089901 TAATGACAATG
1 CAATGACAATG
11089912 GTAATGCTTA
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
17 30 0.81
18 7 0.19
ACGTcount: A:0.49, C:0.13, G:0.17, T:0.21
Consensus pattern (17 bp):
CAATGACAATGAAAATG
Found at i:11124891 original size:32 final size:32
Alignment explanation
Indices: 11124845--11124905 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
11124835 CCCGGGAAAG
11124845 TATTCTTTTCTTTCTATTATATTAGTATTTTC
1 TATTCTTTTCTTTCTATTATATTAGTATTTTC
* *
11124877 TATTCTATTT-TTTCTCTTCTATTAGTATT
1 TATTCT-TTTCTTTCTATTATATTAGTATT
11124906 AGTTAGTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
32 23 0.88
33 3 0.12
ACGTcount: A:0.18, C:0.13, G:0.03, T:0.66
Consensus pattern (32 bp):
TATTCTTTTCTTTCTATTATATTAGTATTTTC
Found at i:11128403 original size:21 final size:21
Alignment explanation
Indices: 11128379--11128418 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
11128369 AGTGTTATCT
11128379 AATTCATTTTGATC-TAATTAA
1 AATTCA-TTTGATCTTAATTAA
*
11128400 AATTTATTTGATCTTAATT
1 AATTCATTTGATCTTAATT
11128419 TCACAAGTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.35, C:0.07, G:0.05, T:0.53
Consensus pattern (21 bp):
AATTCATTTGATCTTAATTAA
Found at i:11129416 original size:19 final size:18
Alignment explanation
Indices: 11129381--11129417 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
11129371 ATTAAACCTT
11129381 TAATTAATCAAAATTAAC
1 TAATTAATCAAAATTAAC
*
11129399 TAATTAATACATAATTAAC
1 TAATTAAT-CAAAATTAAC
11129418 ATTATAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.35
Consensus pattern (18 bp):
TAATTAATCAAAATTAAC
Found at i:11133683 original size:21 final size:21
Alignment explanation
Indices: 11133657--11133713 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
11133647 CTTAAGAGGC
11133657 GGATATCGCGATACCCAAAGA
1 GGATATCGCGATACCCAAAGA
*
11133678 GGATATCGCGATGCCCAAAGA
1 GGATATCGCGATACCCAAAGA
* *
11133699 GGATATTGTGATACC
1 GGATATCGCGATACC
11133714 ACTGAAGGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.33, C:0.21, G:0.26, T:0.19
Consensus pattern (21 bp):
GGATATCGCGATACCCAAAGA
Found at i:11140379 original size:196 final size:195
Alignment explanation
Indices: 11140036--11140467 Score: 612
Period size: 196 Copynumber: 2.2 Consensus size: 195
11140026 ACACGATCGT
* * * *
11140036 TGAGGTACCGCATATGTTGCGAGTCCTTGACAACTCTATTAGTAGCATCATGAGTCAAGAAAATG
1 TGAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCTGTGAGTAGCATCATGAGTCAAGAAAATG
* * *
11140101 AGAAATGAATCAAAGAATGGATTATAGGCCCTATGATGGTTGAGATTTATGCATAAGTGCATATT
66 AGAAATGAATCAAAGAATGAATTATAGGCCCTACGATGGCTGAGATTTATGCATAAGTGCATATT
* * * *
11140166 CTCGACAGCTCGTGTGAGCAGCATCGTTAGGGAACAGTTATATGCACAGATACCGTATCGATGGC
131 CTCGACAACTCGTGTGAGCAACATCGTTAGGGAACAATTATATGCACAGATACCATATCGATGGC
* * * **
11140231 TGAGGTACCACATATGTTGTGAGTCCTCGACAGCTCGTGTGAGTAGCATCGTGAGTCGGGAAAAT
1 TGAGGTACCGCATATGTTGCGAGTCCTCGACAGCTC-TGTGAGTAGCATCATGAGTCAAGAAAAT
* *
11140296 GAGAAATGAATCCAAGAATGAATTATAGGCCTTACGATGGCTGAGATTTATGCATAAGTGCATAT
65 GAGAAATGAATCAAAGAATGAATTATAGGCCCTACGATGGCTGAGATTTATGCATAAGTGCATAT
* *
11140361 TCTCGACAACTTGTGTGAGCAACATCGTTAGGGAACAATTATATGCACAGATATCATATCGATGG
130 TCTCGACAACTCGTGTGAGCAACATCGTTAGGGAACAATTATATGCACAGATACCATATCGATGG
*
11140426 T
195 C
* * * * *
11140427 TGGGGTACCGTATATTTTGCAAGTCCTCGATAGCTCATGTG
1 TGAGGTACCGCATATGTTGCGAGTCCTCGACAGCTC-TGTG
11140468 GTATCATGTA
Statistics
Matches: 207, Mismatches: 29, Indels: 1
0.87 0.12 0.00
Matches are distributed among these distances:
195 32 0.15
196 175 0.85
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (195 bp):
TGAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCTGTGAGTAGCATCATGAGTCAAGAAAATG
AGAAATGAATCAAAGAATGAATTATAGGCCCTACGATGGCTGAGATTTATGCATAAGTGCATATT
CTCGACAACTCGTGTGAGCAACATCGTTAGGGAACAATTATATGCACAGATACCATATCGATGGC
Found at i:11163650 original size:24 final size:24
Alignment explanation
Indices: 11163617--11163663 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
11163607 GTTAAGAGTA
*
11163617 AAAATTGTCAGTGCAAATATAATAT
1 AAAATTGTCAGAGCAAAT-TAATAT
11163642 AAAA-TGTCAGAGCAAATTAATA
1 AAAATTGTCAGAGCAAATTAATA
11163664 AAATATGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.24
24 12 0.57
25 4 0.19
ACGTcount: A:0.51, C:0.09, G:0.13, T:0.28
Consensus pattern (24 bp):
AAAATTGTCAGAGCAAATTAATAT
Found at i:11166309 original size:18 final size:19
Alignment explanation
Indices: 11166277--11166320 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 19
11166267 AGTCAAATTC
*
11166277 TTCTTCTTCTCCTTTCTCT
1 TTCTTCTTCTCCTTTCTCG
11166296 TTCTTCTTCT-CTTTCTCG
1 TTCTTCTTCTCCTTTCTCG
11166314 TTCTTCT
1 TTCTTCT
11166321 CTTGCTTCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.00, C:0.34, G:0.02, T:0.64
Consensus pattern (19 bp):
TTCTTCTTCTCCTTTCTCG
Found at i:11173707 original size:24 final size:24
Alignment explanation
Indices: 11173674--11173720 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
11173664 GTTAAGAGTA
*
11173674 AAAATTGTCAGTGCAAATATAATAT
1 AAAATTGTCAGAGCAAAT-TAATAT
11173699 AAAA-TGTCAGAGCAAATTAATA
1 AAAATTGTCAGAGCAAATTAATA
11173721 AAAGATGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.24
24 12 0.57
25 4 0.19
ACGTcount: A:0.51, C:0.09, G:0.13, T:0.28
Consensus pattern (24 bp):
AAAATTGTCAGAGCAAATTAATAT
Found at i:11175227 original size:25 final size:25
Alignment explanation
Indices: 11175159--11175236 Score: 95
Period size: 25 Copynumber: 3.2 Consensus size: 25
11175149 GTGATATACA
* *
11175159 CTTATATATGTTAATATGATACATG
1 CTTATATGTGTTAATATGATAAATG
* *
11175184 CTT-TAGGTGTTAATGTGATAAATG
1 CTTATATGTGTTAATATGATAAATG
**
11175208 CTTATATGTGTTAATATGATTTATG
1 CTTATATGTGTTAATATGATAAATG
11175233 CTTA
1 CTTA
11175237 AAAGTTAATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
24 20 0.45
25 24 0.55
ACGTcount: A:0.31, C:0.06, G:0.17, T:0.46
Consensus pattern (25 bp):
CTTATATGTGTTAATATGATAAATG
Found at i:11175254 original size:23 final size:23
Alignment explanation
Indices: 11175228--11175316 Score: 106
Period size: 23 Copynumber: 3.9 Consensus size: 23
11175218 TTAATATGAT
*
11175228 TTATGCTTAAAAGTTAATGCGAG
1 TTATGCTTAAAAGTTAATGCGAC
* * *
11175251 TTATGCTTAAAATTTAATGTGAT
1 TTATGCTTAAAAGTTAATGCGAC
* *
11175274 TTATGCTTGAAAGTTAAAGCGAC
1 TTATGCTTAAAAGTTAATGCGAC
**
11175297 TTATGCTTAAGTGTTAATGC
1 TTATGCTTAAAAGTTAATGC
11175317 AATTAATGTG
Statistics
Matches: 54, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 54 1.00
ACGTcount: A:0.33, C:0.09, G:0.19, T:0.39
Consensus pattern (23 bp):
TTATGCTTAAAAGTTAATGCGAC
Found at i:11175314 original size:46 final size:46
Alignment explanation
Indices: 11175205--11175315 Score: 143
Period size: 46 Copynumber: 2.4 Consensus size: 46
11175195 AATGTGATAA
* * *
11175205 ATGCTTATATGTGTTAATATGATTTATGCTTAAAAGTTAATGCGAGTT
1 ATGCTTA-A-GTGTTAATGTGATTTATGCTTAAAAGTTAAAGCGACTT
* *
11175253 ATGCTTAAAAT-TTAATGTGATTTATGCTTGAAAGTTAAAGCGACTT
1 ATGCTT-AAGTGTTAATGTGATTTATGCTTAAAAGTTAAAGCGACTT
11175299 ATGCTTAAGTGTTAATG
1 ATGCTTAAGTGTTAATG
11175316 CAATTAATGT
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
45 3 0.05
46 43 0.78
47 1 0.02
48 7 0.13
49 1 0.02
ACGTcount: A:0.32, C:0.07, G:0.19, T:0.41
Consensus pattern (46 bp):
ATGCTTAAGTGTTAATGTGATTTATGCTTAAAAGTTAAAGCGACTT
Found at i:11175750 original size:24 final size:24
Alignment explanation
Indices: 11175705--11175751 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
11175695 GGACTATTGT
*
11175705 TGAGATATTTTGCTGCTTATATTA
1 TGAGATATTTTGCTGCTGATATTA
*
11175729 TGAGATA-TTTGTTGCATGATATT
1 TGAGATATTTTGCTGC-TGATATT
11175752 TGGAACTTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.26, C:0.06, G:0.19, T:0.49
Consensus pattern (24 bp):
TGAGATATTTTGCTGCTGATATTA
Found at i:11177291 original size:158 final size:158
Alignment explanation
Indices: 11177008--11177340 Score: 490
Period size: 158 Copynumber: 2.1 Consensus size: 158
11176998 GTAACCATAT
* * *
11177008 ATGCTCACACGAGCTGTGAAATGGGTCTGCTCACACGAGCTGTGGGTCAAGATGTAAGGCTACAC
1 ATGCTCACACGAGCTGTGAAATGGGCCTACTCACACGAGCTATGGGTCAAGATGTAAGGCTACAC
* *
11177073 AATGCTACTCACACAAGCTGTGGAGAATTCGTAATAAATGTCGGACCTCAACCATTGGTAGGACA
66 AATGCTACTCACACAAGCTGTGGAGAATTCGTAACAAATGTCGGACCTCAACCATCGGTAGGACA
11177138 TCTAAGACTAGCACCCATATAACCTGTA
131 TCTAAGACTAGCACCCATATAACCTGTA
* * **
11177166 ATGCTCACACGAGCTGTGAAATGGGCCTACTCTCACGAGCTATGGGTCAAGATGTTAGGCTAGGC
1 ATGCTCACACGAGCTGTGAAATGGGCCTACTCACACGAGCTATGGGTCAAGATGTAAGGCTACAC
* * * * *
11177231 GATGCTGCTCACACGAA-CTGTGGAGCATTCGTAACCAATG-CAGGACCTCAGCCATCGGTAGGA
66 AATGCTACTCACAC-AAGCTGTGGAGAATTCGTAACAAATGTC-GGACCTCAACCATCGGTAGGA
*
11177294 CATCTAAGACTAGCACCCATATAACTTGTA
129 CATCTAAGACTAGCACCCATATAACCTGTA
*
11177324 ATGCTCACAAGAGCTGT
1 ATGCTCACACGAGCTGT
11177341 AACTGTAACA
Statistics
Matches: 157, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
157 1 0.01
158 154 0.98
159 2 0.01
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.23
Consensus pattern (158 bp):
ATGCTCACACGAGCTGTGAAATGGGCCTACTCACACGAGCTATGGGTCAAGATGTAAGGCTACAC
AATGCTACTCACACAAGCTGTGGAGAATTCGTAACAAATGTCGGACCTCAACCATCGGTAGGACA
TCTAAGACTAGCACCCATATAACCTGTA
Found at i:11178950 original size:17 final size:18
Alignment explanation
Indices: 11178928--11178965 Score: 69
Period size: 17 Copynumber: 2.2 Consensus size: 18
11178918 AGGCAATAAC
11178928 AGATGGAAAG-AAGAAGA
1 AGATGGAAAGAAAGAAGA
11178945 AGATGGAAAGAAAGAAGA
1 AGATGGAAAGAAAGAAGA
11178963 AGA
1 AGA
11178966 AAAAACTGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.61, C:0.00, G:0.34, T:0.05
Consensus pattern (18 bp):
AGATGGAAAGAAAGAAGA
Found at i:11185119 original size:23 final size:23
Alignment explanation
Indices: 11185085--11185209 Score: 112
Period size: 23 Copynumber: 5.3 Consensus size: 23
11185075 TGCCGGGCAA
11185085 CAGAGAGCACACACAGTGCTAAAT
1 CAGAGAGCACACACAGTGCT-AAT
* *
11185109 -AGAGAGTACACA-AGGTACTAAT
1 CAGAGAGCACACACA-GTGCTAAT
* * * *
11185131 CAGAGAGTAGAAAAAGTGCTAAT
1 CAGAGAGCACACACAGTGCTAAT
11185154 CAGAGAGCACACACAGTGCTAAT
1 CAGAGAGCACACACAGTGCTAAT
* *
11185177 AACAGAGAGCACGAGAC-GTGCTAAA
1 --CAGAGAGCAC-ACACAGTGCTAAT
11185202 CAGAGAGC
1 CAGAGAGC
11185210 GCGCTAGTGT
Statistics
Matches: 84, Mismatches: 11, Indels: 13
0.78 0.10 0.12
Matches are distributed among these distances:
22 4 0.05
23 59 0.70
24 1 0.01
25 17 0.20
26 3 0.04
ACGTcount: A:0.43, C:0.19, G:0.25, T:0.13
Consensus pattern (23 bp):
CAGAGAGCACACACAGTGCTAAT
Found at i:11203435 original size:7 final size:7
Alignment explanation
Indices: 11203423--11203555 Score: 95
Period size: 7 Copynumber: 19.0 Consensus size: 7
11203413 CGAACCCGAC
11203423 CCGTTGA
1 CCGTTGA
11203430 CCGTTGA
1 CCGTTGA
* *
11203437 TCATTGA
1 CCGTTGA
* * *
11203444 TCATTAA
1 CCGTTGA
11203451 CCGTTGA
1 CCGTTGA
*
11203458 CAGTTGA
1 CCGTTGA
11203465 CCGTTGA
1 CCGTTGA
*
11203472 CCGTTAA
1 CCGTTGA
11203479 CCGTTGA
1 CCGTTGA
*
11203486 CAGTTGA
1 CCGTTGA
**
11203493 TAGTTGA
1 CCGTTGA
*
11203500 CCGTTGT
1 CCGTTGA
*
11203507 TCGTTGA
1 CCGTTGA
**
11203514 TAGTTGA
1 CCGTTGA
*
11203521 CCATTGA
1 CCGTTGA
*
11203528 CTGTTGA
1 CCGTTGA
**
11203535 CAATTGA
1 CCGTTGA
*
11203542 TCGTTGA
1 CCGTTGA
11203549 CCGTTGA
1 CCGTTGA
11203556 TTGTTGACTT
Statistics
Matches: 97, Mismatches: 29, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
7 97 1.00
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.35
Consensus pattern (7 bp):
CCGTTGA
Found at i:11203541 original size:28 final size:26
Alignment explanation
Indices: 11203510--11203583 Score: 78
Period size: 28 Copynumber: 2.8 Consensus size: 26
11203500 CCGTTGTTCG
11203510 TTGATAGTTGACCATTGACTGTTGAC
1 TTGATAGTTGACCATTGACTGTTGAC
* * *
11203536 AATTGATCGTTGACCGTTGATTGTTGAC
1 --TTGATAGTTGACCATTGACTGTTGAC
*
11203564 TT-TTAGGTTGACCATTGACT
1 TTGATA-GTTGACCATTGACT
11203584 TTTTTTGAGA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
25 1 0.03
26 14 0.37
28 23 0.61
ACGTcount: A:0.22, C:0.15, G:0.23, T:0.41
Consensus pattern (26 bp):
TTGATAGTTGACCATTGACTGTTGAC
Found at i:11203562 original size:21 final size:21
Alignment explanation
Indices: 11203453--11203563 Score: 105
Period size: 21 Copynumber: 5.3 Consensus size: 21
11203443 ATCATTAACC
* **
11203453 GTTGACAGTTGACCGTTGACC
1 GTTGACCGTTGACCGTTGATA
* *
11203474 GTTAACCGTTGACAGTTGATA
1 GTTGACCGTTGACCGTTGATA
**
11203495 GTTGACCGTTGTTCGTTGATA
1 GTTGACCGTTGACCGTTGATA
* * *
11203516 GTTGACCATTGACTGTTGACA
1 GTTGACCGTTGACCGTTGATA
* * *
11203537 ATTGATCGTTGACCGTTGATT
1 GTTGACCGTTGACCGTTGATA
11203558 GTTGAC
1 GTTGAC
11203564 TTTTAGGTTG
Statistics
Matches: 68, Mismatches: 22, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 68 1.00
ACGTcount: A:0.21, C:0.17, G:0.26, T:0.36
Consensus pattern (21 bp):
GTTGACCGTTGACCGTTGATA
Found at i:11208502 original size:19 final size:19
Alignment explanation
Indices: 11208460--11208502 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
11208450 GATTCATGCT
* *
11208460 ATTTTTGAATTTTTTTATA
1 ATTTTTGAATATTTTTAAA
*
11208479 TTTTTTGAATATTTTTAAA
1 ATTTTTGAATATTTTTAAA
11208498 ATTTT
1 ATTTT
11208503 AAAATTATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (19 bp):
ATTTTTGAATATTTTTAAA
Found at i:11209750 original size:17 final size:17
Alignment explanation
Indices: 11209728--11209775 Score: 66
Period size: 15 Copynumber: 3.0 Consensus size: 17
11209718 ATAATGAAAA
11209728 TAATTTTTATTATTTTC
1 TAATTTTTATTATTTTC
11209745 TAATTTTTATT-TTTT-
1 TAATTTTTATTATTTTC
*
11209760 AAATTTTT-TTATTTTC
1 TAATTTTTATTATTTTC
11209776 ATTTTTCTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 2 0.07
15 11 0.39
16 4 0.14
17 11 0.39
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.73
Consensus pattern (17 bp):
TAATTTTTATTATTTTC
Found at i:11209779 original size:14 final size:15
Alignment explanation
Indices: 11209730--11209781 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
11209720 AATGAAAATA
11209730 ATTTTTATTATTTTC
1 ATTTTTATTATTTTC
*
11209745 TAATTTTTATT-TTTTAA
1 --ATTTTTATTATTTT-C
11209762 ATTTTT-TTATTTTC
1 ATTTTTATTATTTTC
11209776 ATTTTT
1 ATTTTT
11209782 CTTACGTGTG
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
14 8 0.26
15 10 0.32
16 4 0.13
17 9 0.29
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (15 bp):
ATTTTTATTATTTTC
Found at i:11213751 original size:22 final size:21
Alignment explanation
Indices: 11213726--11213776 Score: 50
Period size: 22 Copynumber: 2.4 Consensus size: 21
11213716 TTTTAGTAAA
*
11213726 ATAAAAAAAATTATTTATAGAT
1 ATAAAAAAAATTATTAATA-AT
* **
11213748 ATAATAAATCTTATTAATAAT
1 ATAAAAAAAATTATTAATAAT
11213769 A-AAAAAAA
1 ATAAAAAAA
11213777 TTGAAAAGAC
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 5 0.22
21 3 0.13
22 15 0.65
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (21 bp):
ATAAAAAAAATTATTAATAAT
Found at i:11218305 original size:23 final size:23
Alignment explanation
Indices: 11218275--11218359 Score: 100
Period size: 23 Copynumber: 3.7 Consensus size: 23
11218265 AATATCACGG
11218275 AATACGCCACAAAGGCTTTACCA
1 AATACGCCACAAAGGCTTTACCA
* **
11218298 AATACGCCACAAAAGCCATA-CA
1 AATACGCCACAAAGGCTTTACCA
* *
11218320 GAACATGCCACAAAGGCTTTACCA
1 -AATACGCCACAAAGGCTTTACCA
*
11218344 ATTACGCCACAAAGGC
1 AATACGCCACAAAGGC
11218360 GTCATAGCGA
Statistics
Matches: 49, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
22 2 0.04
23 45 0.92
24 2 0.04
ACGTcount: A:0.41, C:0.31, G:0.14, T:0.14
Consensus pattern (23 bp):
AATACGCCACAAAGGCTTTACCA
Found at i:11229735 original size:59 final size:58
Alignment explanation
Indices: 11229670--11229816 Score: 174
Period size: 58 Copynumber: 2.5 Consensus size: 58
11229660 ATATATTATA
* *
11229670 ATTTTTACT-AATTCATATTTTAATAATAATTATATTAAAAATATTATTAAATT-ATATATT
1 ATTTTTACTAAATT-ATA-TTTAATAATAATTATATT-AAAATATAATTAAATTAAT-TAAT
* * *
11229730 A-TTTTATGTAAATTGTATTTAATAATAATTATGTTAAAATATAATTAAATTAATTAAT
1 ATTTTTA-CTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATTAATTAAT
*
11229788 ATTTTTATTAAATTATATTTAATAATAAT
1 ATTTTTACTAAATTATATTTAATAATAAT
11229817 CATTAAAATT
Statistics
Matches: 76, Mismatches: 7, Indels: 10
0.82 0.08 0.11
Matches are distributed among these distances:
58 39 0.51
59 29 0.38
60 4 0.05
61 4 0.05
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (58 bp):
ATTTTTACTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATTAATTAAT
Found at i:11230021 original size:16 final size:16
Alignment explanation
Indices: 11229995--11230038 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
11229985 GATTACAGTC
* *
11229995 CTATTCCATTACAGCT
1 CTATTCTATTACACCT
* *
11230011 CTTTTCTATTATACCT
1 CTATTCTATTACACCT
11230027 CTATTCTATTAC
1 CTATTCTATTAC
11230039 GGCGAACCAA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.23, C:0.27, G:0.02, T:0.48
Consensus pattern (16 bp):
CTATTCTATTACACCT
Found at i:11234031 original size:19 final size:20
Alignment explanation
Indices: 11234007--11234047 Score: 75
Period size: 19 Copynumber: 2.1 Consensus size: 20
11233997 CTCTAATTTT
11234007 TAGATAGATTATAA-ATAAA
1 TAGATAGATTATAATATAAA
11234026 TAGATAGATTATAATATAAA
1 TAGATAGATTATAATATAAA
11234046 TA
1 TA
11234048 TATTATAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.56, C:0.00, G:0.10, T:0.34
Consensus pattern (20 bp):
TAGATAGATTATAATATAAA
Found at i:11245145 original size:18 final size:19
Alignment explanation
Indices: 11245117--11245155 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
11245107 CTTCTCTTTC
**
11245117 TTTTATAAAATTTATATAA
1 TTTTATAAAATAAATATAA
11245136 TTTT-TAAAATAAATATAA
1 TTTTATAAAATAAATATAA
11245154 TT
1 TT
11245156 AAATATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TTTTATAAAATAAATATAA
Found at i:11259747 original size:3 final size:3
Alignment explanation
Indices: 11259739--11259779 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
11259729 TACATCTCAA
11259739 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
11259780 ATAGAATATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:11260793 original size:7 final size:7
Alignment explanation
Indices: 11260782--11260854 Score: 96
Period size: 7 Copynumber: 10.7 Consensus size: 7
11260772 TTTCAAAAAA
*
11260782 GTCAACA
1 GTCAACG
11260789 GTCAACG
1 GTCAACG
*
11260796 GTCAA-A
1 GTCAACG
11260802 GTCAACG
1 GTCAACG
11260809 GTCAACG
1 GTCAACG
*
11260816 GTCAACC
1 GTCAACG
*
11260823 GTCAA-A
1 GTCAACG
11260829 GTCAACG
1 GTCAACG
11260836 GTCAACG
1 GTCAACG
11260843 GTCAACG
1 GTCAACG
11260850 GTCAA
1 GTCAA
11260855 TCAACACCGA
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
6 10 0.17
7 48 0.83
ACGTcount: A:0.34, C:0.27, G:0.23, T:0.15
Consensus pattern (7 bp):
GTCAACG
Found at i:11260804 original size:20 final size:21
Alignment explanation
Indices: 11260781--11260854 Score: 98
Period size: 20 Copynumber: 3.6 Consensus size: 21
11260771 TTTTCAAAAA
11260781 AGTCAACAGTCAACGGTCAA-
1 AGTCAACAGTCAACGGTCAAC
*
11260801 AGTCAACGGTCAACGGTCAAC
1 AGTCAACAGTCAACGGTCAAC
*
11260822 CGTCAA-AGTCAACGGTCAAC
1 AGTCAACAGTCAACGGTCAAC
* *
11260842 GGTCAACGGTCAA
1 AGTCAACAGTCAA
11260855 TCAACACCGA
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
20 37 0.79
21 10 0.21
ACGTcount: A:0.35, C:0.27, G:0.23, T:0.15
Consensus pattern (21 bp):
AGTCAACAGTCAACGGTCAAC
Found at i:11260814 original size:27 final size:27
Alignment explanation
Indices: 11260782--11260854 Score: 128
Period size: 27 Copynumber: 2.7 Consensus size: 27
11260772 TTTCAAAAAA
*
11260782 GTCAACAGTCAACGGTCAAAGTCAACG
1 GTCAACGGTCAACGGTCAAAGTCAACG
*
11260809 GTCAACGGTCAACCGTCAAAGTCAACG
1 GTCAACGGTCAACGGTCAAAGTCAACG
11260836 GTCAACGGTCAACGGTCAA
1 GTCAACGGTCAACGGTCAA
11260855 TCAACACCGA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.34, C:0.27, G:0.23, T:0.15
Consensus pattern (27 bp):
GTCAACGGTCAACGGTCAAAGTCAACG
Found at i:11260868 original size:21 final size:21
Alignment explanation
Indices: 11260844--11260891 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
11260834 CGGTCAACGG
11260844 TCAACGGTCAATCAACACCGA
1 TCAACGGTCAATCAACACCGA
** * *
11260865 TCAACGGTCGGTCAACATCGG
1 TCAACGGTCAATCAACACCGA
11260886 TCAACG
1 TCAACG
11260892 TCGGTCAATG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.31, C:0.31, G:0.21, T:0.17
Consensus pattern (21 bp):
TCAACGGTCAATCAACACCGA
Found at i:11260959 original size:20 final size:20
Alignment explanation
Indices: 11260934--11260975 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
11260924 CTTGGTTCAA
*
11260934 TTGGTTTGGTTCAAAAGGGT
1 TTGGTTAGGTTCAAAAGGGT
* *
11260954 TTGGTTAGGTTTAAATGGGT
1 TTGGTTAGGTTCAAAAGGGT
11260974 TT
1 TT
11260976 TGGGCTTGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.19, C:0.02, G:0.33, T:0.45
Consensus pattern (20 bp):
TTGGTTAGGTTCAAAAGGGT
Found at i:11262422 original size:21 final size:21
Alignment explanation
Indices: 11262377--11262422 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
11262367 TTCTGGTGTT
* *
11262377 TTTTTGCTATTTTGGTTGCTA
1 TTTTTACTATTTTGGTTACTA
11262398 TTTTTACTATTTTGG-TACTA
1 TTTTTACTATTTTGGTTACTA
*
11262418 CTTTT
1 TTTTT
11262423 GCTGTTGTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.13, C:0.11, G:0.13, T:0.63
Consensus pattern (21 bp):
TTTTTACTATTTTGGTTACTA
Found at i:11262505 original size:20 final size:20
Alignment explanation
Indices: 11262482--11262520 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
11262472 TATTTGGGTG
* *
11262482 TTATTTTTTATGCGTTTTTA
1 TTATTGTTTATCCGTTTTTA
*
11262502 TTATTGTTTCTCCGTTTTT
1 TTATTGTTTATCCGTTTTT
11262521 TTAATATTAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.10, C:0.10, G:0.10, T:0.69
Consensus pattern (20 bp):
TTATTGTTTATCCGTTTTTA
Found at i:11265386 original size:36 final size:36
Alignment explanation
Indices: 11265313--11265434 Score: 163
Period size: 36 Copynumber: 3.4 Consensus size: 36
11265303 TTTACCACAT
* * *
11265313 CGAGACATAAGCAATCACATAAACCTTACGCTTTAAC
1 CGAGACATAAGCAATCAAAT-AGCCTTACGCTCTAAC
* **
11265350 CGAGACGTAAGCAATCAAATAGTTTTACGCTCTAAC
1 CGAGACATAAGCAATCAAATAGCCTTACGCTCTAAC
*
11265386 CGAGACATAAGCAATCACATAGCCTTACGCTCTAAC
1 CGAGACATAAGCAATCAAATAGCCTTACGCTCTAAC
*
11265422 CGAGACTTAAGCA
1 CGAGACATAAGCA
11265435 TTCCATAGCT
Statistics
Matches: 74, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
36 56 0.76
37 18 0.24
ACGTcount: A:0.38, C:0.26, G:0.15, T:0.21
Consensus pattern (36 bp):
CGAGACATAAGCAATCAAATAGCCTTACGCTCTAAC
Found at i:11265505 original size:56 final size:56
Alignment explanation
Indices: 11265402--11265509 Score: 146
Period size: 56 Copynumber: 1.9 Consensus size: 56
11265392 ATAAGCAATC
* * * * *
11265402 ACATAGCCTTACGCTCTAACCGAGACTTAAGCATTCCATAGCTCTACCCGAGTTGT
1 ACATAGCCTTACGATCTAACCAAGACGTAAGCAATCCATAGCACTACCCGAGTTGT
*
11265458 ACATAGCCTTACGATCTAACCAAGACGTAAGCAGATCGA-AGCACTACCCGAG
1 ACATAGCCTTACGATCTAACCAAGACGTAAGCA-ATCCATAGCACTACCCGAG
11265510 CTATATCAGA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
56 42 0.93
57 3 0.07
ACGTcount: A:0.31, C:0.30, G:0.18, T:0.21
Consensus pattern (56 bp):
ACATAGCCTTACGATCTAACCAAGACGTAAGCAATCCATAGCACTACCCGAGTTGT
Found at i:11272918 original size:16 final size:16
Alignment explanation
Indices: 11272897--11272944 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
11272887 GAAATATTTT
*
11272897 AATATAATTATTATTA
1 AATATAATTATTATAA
*
11272913 AATATAATTTAATATAA
1 AATATAA-TTATTATAA
11272930 AAT-TAATTA-TATAA
1 AATATAATTATTATAA
11272944 A
1 A
11272945 GAAGGTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 6 0.21
15 3 0.10
16 10 0.34
17 10 0.34
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AATATAATTATTATAA
Found at i:11273005 original size:21 final size:21
Alignment explanation
Indices: 11272976--11273076 Score: 55
Period size: 21 Copynumber: 4.9 Consensus size: 21
11272966 TTTTATTTTT
*
11272976 ATTAAATTATATTTAATAATA
1 ATTATATTATATTTAATAATA
* * * *
11272997 ATTATATTAAAGTATGATTA-A
1 ATTATATTATA-TTTAATAATA
* * ** *
11273018 ATTAT-TTAT-TATCATTTTT
1 ATTATATTATATTTAATAATA
* *
11273037 ATTAAATTATATTTAATAATT
1 ATTATATTATATTTAATAATA
*
11273058 ATCATATTATATTTAATAA
1 ATTATATTATATTTAATAA
11273077 CAATAATTAT
Statistics
Matches: 60, Mismatches: 16, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
18 6 0.10
19 4 0.07
20 7 0.12
21 38 0.63
22 5 0.08
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (21 bp):
ATTATATTATATTTAATAATA
Found at i:11273035 original size:61 final size:61
Alignment explanation
Indices: 11272952--11273066 Score: 176
Period size: 61 Copynumber: 1.9 Consensus size: 61
11272942 AAAGAAGGTT
* * * *
11272952 ATTAAGTTATATATTTTTATTTTTATTAAATTATATTTAATAATAATTATATTAAAGTATG
1 ATTAAATTATATATTATCATTTTTATTAAATTATATTTAATAATAATCATATTAAAGTATG
* *
11273013 ATTAAATTATTTATTATCATTTTTATTAAATTATATTTAATAATTATCATATTA
1 ATTAAATTATATATTATCATTTTTATTAAATTATATTTAATAATAATCATATTA
11273067 TATTTAATAA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.55
Consensus pattern (61 bp):
ATTAAATTATATATTATCATTTTTATTAAATTATATTTAATAATAATCATATTAAAGTATG
Done.