Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D12
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: 58873029
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 639818 characters in sequence are not A, C, G, or T
File 132 of 196
Found at i:39444530 original size:21 final size:21
Alignment explanation
Indices: 39444501--39444569 Score: 75
Period size: 21 Copynumber: 3.3 Consensus size: 21
39444491 CAACAACTTA
* * *
39444501 AAGCTGAGGCGGCAGCGAGGG
1 AAGCAGAGGCCGCAGCGAGAG
**
39444522 AAGCAGAGGCTACAGCGAGAG
1 AAGCAGAGGCCGCAGCGAGAG
* *
39444543 AAGCAGATGCCGCAGTGAGAG
1 AAGCAGAGGCCGCAGCGAGAG
39444564 AAGCAG
1 AAGCAG
39444570 CGATAGAAGC
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.33, C:0.19, G:0.42, T:0.06
Consensus pattern (21 bp):
AAGCAGAGGCCGCAGCGAGAG
Found at i:39445053 original size:42 final size:43
Alignment explanation
Indices: 39444991--39445073 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 43
39444981 CAAAACAGTG
39444991 GCGTTTGTGAAACAAGCGCCGCTAAAGAACACTACTTTTAGCA
1 GCGTTTGTGAAACAAGCGCCGCTAAAGAACACTACTTTTAGCA
* * *
39445034 GCGTTTTTG-AACAAGCGCCGCTATAGAACATTACTTTTAG
1 GCGTTTGTGAAACAAGCGCCGCTAAAGAACACTACTTTTAG
39445074 AGGCTTTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
42 29 0.78
43 8 0.22
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (43 bp):
GCGTTTGTGAAACAAGCGCCGCTAAAGAACACTACTTTTAGCA
Found at i:39445094 original size:41 final size:41
Alignment explanation
Indices: 39445004--39445137 Score: 114
Period size: 42 Copynumber: 3.2 Consensus size: 41
39444994 TTTGTGAAAC
* * **
39445004 AAGCGCCGCTAAAGAACACTACTTTTAGCA-GCGTTTTTGAAC-
1 AAGCGCCGCT-AAGAACATTACTTTTAG-AGGCATTTTT-TTCT
39445046 AAGCGCCGCTATAGAACATTACTTTTAGAGGC-TTTTTTTCT
1 AAGCGCCGCTA-AGAACATTACTTTTAGAGGCATTTTTTTCT
* *
39445087 AAGCGCCGCTAACGAACATGA-TCTTTAGCGGCATTTTTTTCTGT
1 AAGCGCCGCTAA-GAACATTACT-TTTAGAGGCATTTTTTTC--T
39445131 AAGCGCC
1 AAGCGCC
39445138 ACAAAAGTTA
Statistics
Matches: 79, Mismatches: 5, Indels: 14
0.81 0.05 0.14
Matches are distributed among these distances:
40 3 0.04
41 33 0.42
42 35 0.44
44 8 0.10
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.31
Consensus pattern (41 bp):
AAGCGCCGCTAAGAACATTACTTTTAGAGGCATTTTTTTCT
Found at i:39445259 original size:22 final size:22
Alignment explanation
Indices: 39445216--39445259 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
39445206 TAGTGGCGTT
* **
39445216 AAAAAGCGCCGCTAAAGGCCTA
1 AAAAAACGCCGCTAAAAACCTA
39445238 AAAAAACGCCGCTAAAAACCTA
1 AAAAAACGCCGCTAAAAACCTA
39445260 TTCTACTGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.48, C:0.27, G:0.16, T:0.09
Consensus pattern (22 bp):
AAAAAACGCCGCTAAAAACCTA
Found at i:39457141 original size:23 final size:23
Alignment explanation
Indices: 39457099--39457148 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
39457089 ACAATTGTCA
**
39457099 AATTTAGACCCTGATATAGAAAC
1 AATTTAGACCCCAATATAGAAAC
* *
39457122 AATTTAGACCCCAATGTAGAAGC
1 AATTTAGACCCCAATATAGAAAC
39457145 AATT
1 AATT
39457149 ATTAAGTTCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.26
Consensus pattern (23 bp):
AATTTAGACCCCAATATAGAAAC
Found at i:39459095 original size:16 final size:18
Alignment explanation
Indices: 39459059--39459095 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
39459049 TTTACCCTTG
*
39459059 TTACAAATATTAATTTAT
1 TTACAAATATAAATTTAT
39459077 TTACAAAT-TAAATTT-T
1 TTACAAATATAAATTTAT
39459093 TTA
1 TTA
39459096 TTGTTTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 4 0.22
17 6 0.33
18 8 0.44
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.51
Consensus pattern (18 bp):
TTACAAATATAAATTTAT
Found at i:39460226 original size:6 final size:6
Alignment explanation
Indices: 39460206--39460248 Score: 52
Period size: 6 Copynumber: 7.0 Consensus size: 6
39460196 TTTACGTCAA
*
39460206 AATTTT AATTAAT AATTAT AAATTA- AATTAT AATTAT AATTAT
1 AATTAT AATT-AT AATTAT -AATTAT AATTAT AATTAT AATTAT
39460249 CACGGTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
5 5 0.15
6 18 0.55
7 10 0.30
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (6 bp):
AATTAT
Found at i:39473389 original size:26 final size:26
Alignment explanation
Indices: 39473348--39473423 Score: 75
Period size: 27 Copynumber: 2.9 Consensus size: 26
39473338 TCTCGTCCCT
39473348 ATTTTA-CTCC-AGTAAAATTTTGACG
1 ATTTTACCTCCGA-TAAAATTTTGACG
*
39473373 ATTTTACCTCCGATAAATTTTTTGACG
1 ATTTTACCTCCGATAAA-ATTTTGACG
* * * *
39473400 GTTTTACTTCTGGTAAAATTTTGA
1 ATTTTACCTCCGATAAAATTTTGA
39473424 GAAAATATGT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
25 6 0.14
26 14 0.33
27 22 0.52
ACGTcount: A:0.28, C:0.14, G:0.13, T:0.45
Consensus pattern (26 bp):
ATTTTACCTCCGATAAAATTTTGACG
Found at i:39474739 original size:15 final size:15
Alignment explanation
Indices: 39474721--39474749 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
39474711 AACAGAAGGG
39474721 AAAAAGAAAGAAAAA
1 AAAAAGAAAGAAAAA
39474736 AAAAAGAAAGAAAA
1 AAAAAGAAAGAAAA
39474750 GGAGAAAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAGAAAAA
Found at i:39478611 original size:25 final size:25
Alignment explanation
Indices: 39478583--39478689 Score: 144
Period size: 25 Copynumber: 4.3 Consensus size: 25
39478573 ACTTTAGCGC
39478583 GCTCTCTGATTATTAGCACGTTAGT
1 GCTCTCTGATTATTAGCACGTTAGT
* *
39478608 GCTCTCTGATTATTAGCACATTGGT
1 GCTCTCTGATTATTAGCACGTTAGT
* * *
39478633 GCTCTCTGACTACTAGCACGTTGGT
1 GCTCTCTGATTATTAGCACGTTAGT
* *
39478658 GCTCTCTGATT-TTAGCGCGTCAGT
1 GCTCTCTGATTATTAGCACGTTAGT
39478682 GCTCTCTG
1 GCTCTCTG
39478690 TTTAGCACAC
Statistics
Matches: 72, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
24 17 0.24
25 55 0.76
ACGTcount: A:0.16, C:0.24, G:0.22, T:0.37
Consensus pattern (25 bp):
GCTCTCTGATTATTAGCACGTTAGT
Found at i:39485721 original size:25 final size:25
Alignment explanation
Indices: 39485693--39485807 Score: 144
Period size: 25 Copynumber: 4.6 Consensus size: 25
39485683 ACTTTAGCGC
39485693 GCTCTCTGATTATTAGCACGTTAGT
1 GCTCTCTGATTATTAGCACGTTAGT
* *
39485718 GCTCTCTGATTATTAGCACATTGGT
1 GCTCTCTGATTATTAGCACGTTAGT
* * *
39485743 GCTCTCTGACTACTAGCACGTTGGT
1 GCTCTCTGATTATTAGCACGTTAGT
* *
39485768 GCTCTCTGATT-TTAGCGCGTCAGT
1 GCTCTCTGATTATTAGCACGTTAGT
39485792 GCTCTCTG-TTCATTAG
1 GCTCTCTGATT-ATTAG
39485808 TGCATACCAA
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
23 2 0.03
24 17 0.22
25 59 0.76
ACGTcount: A:0.17, C:0.23, G:0.22, T:0.38
Consensus pattern (25 bp):
GCTCTCTGATTATTAGCACGTTAGT
Found at i:39492896 original size:29 final size:30
Alignment explanation
Indices: 39492862--39492928 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
39492852 CGTAAATTTG
* *
39492862 AAATTTAGTCTCTGTA-TTTTTAT-TTTTA
1 AAATTTAGTCTCTCTACTTTTTATATTTCA
*
39492890 AGAATTTAGTCTTTCTACTTTTTATATTTCA
1 A-AATTTAGTCTCTCTACTTTTTATATTTCA
39492921 AAATTTAG
1 AAATTTAG
39492929 GTCCAACTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 1 0.03
29 13 0.39
30 14 0.42
31 5 0.15
ACGTcount: A:0.28, C:0.09, G:0.07, T:0.55
Consensus pattern (30 bp):
AAATTTAGTCTCTCTACTTTTTATATTTCA
Found at i:39494204 original size:3 final size:3
Alignment explanation
Indices: 39494196--39494234 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
39494186 TCCATTTGGT
39494196 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
39494235 AGTTTGTGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:39498060 original size:118 final size:109
Alignment explanation
Indices: 39497984--39498287 Score: 321
Period size: 109 Copynumber: 2.8 Consensus size: 109
39497974 ATGAATAATT
* * *
39497984 GGATAAAGTCCAACCATGGCAAATGCACACATGTTAGGATTGAAGACCCACACATCATAGATACA
1 GGATAAAATCCAACCATGGCAAATGCACACATATTAGGATTGAAGACCCACACATCATAAATACA
* * * * * *
39498049 TACGATGAGACTCAAATTTAGGAACCAATAGAGAGCACATTGCA
66 TATGATGAGACTCAAATTTAGGAATCAATACAAAACACATTGAA
* * *
39498093 GGATAAAATCCAACTATGGCAAATGCACACATATTAGGATTGGAGACCCACACATTATAAATACA
1 GGATAAAATCCAACCATGGCAAATGCACACATATTAGGATTGAAGACCCACACATCATAAATACA
* *
39498158 TATGATGGGACTCAAATTTAGGAATCAATACAAAA-A-AAT-AA
66 TATGATGAGACTCAAATTTAGGAATCAATACAAAACACATTGAA
* * ** * * * * * * *
39498199 TTGGATAAAACCCATCCATAACAAATG--TACATATTAAGACTAAAGACTCGCACATCACAAATA
1 --GGATAAAATCCAACCATGGCAAATGCACACATATTAGGATTGAAGACCCACACATCATAAATA
*
39498262 CATATGATAAGACTCAAATTTAGGAA
64 CATATGATGAGACTCAAATTTAGGAA
39498288 CTGGATAAAA
Statistics
Matches: 163, Mismatches: 30, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
106 52 0.32
107 2 0.01
108 21 0.13
109 88 0.54
ACGTcount: A:0.44, C:0.19, G:0.15, T:0.22
Consensus pattern (109 bp):
GGATAAAATCCAACCATGGCAAATGCACACATATTAGGATTGAAGACCCACACATCATAAATACA
TATGATGAGACTCAAATTTAGGAATCAATACAAAACACATTGAA
Found at i:39498175 original size:109 final size:109
Alignment explanation
Indices: 39497984--39498187 Score: 327
Period size: 109 Copynumber: 1.9 Consensus size: 109
39497974 ATGAATAATT
* * *
39497984 GGATAAAGTCCAACCATGGCAAATGCACACATGTTAGGATTGAAGACCCACACATCATAGATACA
1 GGATAAAATCCAACCATGGCAAATGCACACATATTAGGATTGAAGACCCACACATCATAAATACA
39498049 TACGATGAGACTCAAATTTAGGAACCAATAGAGAGCACATTGCA
66 TACGATGAGACTCAAATTTAGGAACCAATAGAGAGCACATTGCA
* * *
39498093 GGATAAAATCCAACTATGGCAAATGCACACATATTAGGATTGGAGACCCACACATTATAAATACA
1 GGATAAAATCCAACCATGGCAAATGCACACATATTAGGATTGAAGACCCACACATCATAAATACA
* * *
39498158 TATGATGGGACTCAAATTTAGGAATCAATA
66 TACGATGAGACTCAAATTTAGGAACCAATA
39498188 CAAAAAAATA
Statistics
Matches: 86, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
109 86 1.00
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (109 bp):
GGATAAAATCCAACCATGGCAAATGCACACATATTAGGATTGAAGACCCACACATCATAAATACA
TACGATGAGACTCAAATTTAGGAACCAATAGAGAGCACATTGCA
Found at i:39500538 original size:4 final size:4
Alignment explanation
Indices: 39500519--39500553 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
39500509 TTCCTTCTAT
* *
39500519 TTTA TCTA TATA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
39500554 CAAGAAGTAG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:39501566 original size:31 final size:31
Alignment explanation
Indices: 39501517--39501575 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
39501507 GAGGGGCTAC
*
39501517 TTAAAATTTTCAAAATTTTCAG-GGATTTAA
1 TTAAAATTTTAAAAATTTTCAGAGGATTTAA
*
39501547 TTAAAATTTTTAAAAATTTTGAGAGGATT
1 TTAAAA-TTTTAAAAATTTTCAGAGGATT
39501576 AAGGAGAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 6 0.24
31 14 0.56
32 5 0.20
ACGTcount: A:0.41, C:0.03, G:0.12, T:0.44
Consensus pattern (31 bp):
TTAAAATTTTAAAAATTTTCAGAGGATTTAA
Found at i:39501660 original size:31 final size:32
Alignment explanation
Indices: 39501580--39501661 Score: 80
Period size: 31 Copynumber: 2.6 Consensus size: 32
39501570 AGGATTAAGG
39501580 AGAATTGTC-AAAATTTTTGAAAGGTCTAATTA
1 AGAATT-TCTAAAATTTTTGAAAGGTCTAATTA
* * * * * *
39501612 AAAATTT-TAGAACTTTTGGAAGG-CTTATTT
1 AGAATTTCTAAAATTTTTGAAAGGTCTAATTA
39501642 AGAATTTCTAAAATTTTTGA
1 AGAATTTCTAAAATTTTTGA
39501662 GGGGGAGTTT
Statistics
Matches: 38, Mismatches: 10, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
30 11 0.29
31 22 0.58
32 5 0.13
ACGTcount: A:0.38, C:0.06, G:0.15, T:0.41
Consensus pattern (32 bp):
AGAATTTCTAAAATTTTTGAAAGGTCTAATTA
Found at i:39502385 original size:6 final size:6
Alignment explanation
Indices: 39502374--39502398 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
39502364 AGGTACATTG
39502374 CTTGCA CTTGCA CTTGCA CTTGCA C
1 CTTGCA CTTGCA CTTGCA CTTGCA C
39502399 GAGTGTGTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.36, G:0.16, T:0.32
Consensus pattern (6 bp):
CTTGCA
Found at i:39504469 original size:78 final size:78
Alignment explanation
Indices: 39504339--39504495 Score: 251
Period size: 78 Copynumber: 2.0 Consensus size: 78
39504329 TTTTAGATTT
* * *
39504339 TTTTTTATGTTTTCATTTTTACGTTAGCCAATCAGTGATAAAAAAATCATAATTAAGTGATCATT
1 TTTTTGATGTTTTCATTTTTACGTTAGCCAATCAGTGATAAAAAAATAATAATTAAGTGACCATT
*
39504404 TTGTAACTTTTCA
66 TTGAAACTTTTCA
* * *
39504417 TTTTTGATGTTTTTATTTTTATGTTAGCCAATTAGTGATAAAAAAATAATAATTAAGTGACCATT
1 TTTTTGATGTTTTCATTTTTACGTTAGCCAATCAGTGATAAAAAAATAATAATTAAGTGACCATT
39504482 TTGAAACTTTTCA
66 TTGAAACTTTTCA
39504495 T
1 T
39504496 AGTTAAGTGA
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
78 72 1.00
ACGTcount: A:0.33, C:0.10, G:0.11, T:0.46
Consensus pattern (78 bp):
TTTTTGATGTTTTCATTTTTACGTTAGCCAATCAGTGATAAAAAAATAATAATTAAGTGACCATT
TTGAAACTTTTCA
Found at i:39504519 original size:58 final size:59
Alignment explanation
Indices: 39504456--39504571 Score: 164
Period size: 58 Copynumber: 2.0 Consensus size: 59
39504446 AATTAGTGAT
* *
39504456 AAAAAAATAATAATTAAGTGACCATTTT-GAAACTTTTCATAGTT-AAGTGATAAAAAAG
1 AAAAAAACAATAATTAAATGACCATTTTAGAAACTTTTCATAGTTGAA-TGATAAAAAAG
* * *
39504514 AAAAAAACCATAATTAAATGACCATTTTATAAATTTTTCATAGTTGAATGATAAAAAA
1 AAAAAAACAATAATTAAATGACCATTTTAGAAACTTTTCATAGTTGAATGATAAAAAA
39504572 ATCATAATTA
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
58 25 0.49
59 24 0.47
60 2 0.04
ACGTcount: A:0.51, C:0.08, G:0.09, T:0.32
Consensus pattern (59 bp):
AAAAAAACAATAATTAAATGACCATTTTAGAAACTTTTCATAGTTGAATGATAAAAAAG
Found at i:39511350 original size:22 final size:21
Alignment explanation
Indices: 39511324--39511391 Score: 82
Period size: 22 Copynumber: 3.1 Consensus size: 21
39511314 TTCACAAACA
39511324 AATTCCTTTCAAATATTCTCTC
1 AATTCCTTTCAAA-ATTCTCTC
* *
39511346 AATTCCCTTGAAAATTTCTCTC
1 AATTCCTTTCAAAA-TTCTCTC
*
39511368 AATTTCCTTCCAAAATTCTCTC
1 AA-TTCCTTTCAAAATTCTCTC
39511390 AA
1 AA
39511392 ACTCTCAAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
21 1 0.03
22 29 0.74
23 9 0.23
ACGTcount: A:0.29, C:0.28, G:0.01, T:0.41
Consensus pattern (21 bp):
AATTCCTTTCAAAATTCTCTC
Found at i:39511397 original size:30 final size:30
Alignment explanation
Indices: 39511363--39511421 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
39511353 TTGAAAATTT
* *
39511363 CTCTCAATTTCCTTCCAAAATTCTCTCAAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAAA
39511393 CTCTCAAATTCCTTCCAAAATCCTCTCAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAA
39511422 TTTCCTTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.31, C:0.36, G:0.00, T:0.34
Consensus pattern (30 bp):
CTCTCAAATTCCTTCCAAAATCCTCTCAAA
Found at i:39511432 original size:21 final size:22
Alignment explanation
Indices: 39511393--39511434 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
39511383 TTCTCTCAAA
39511393 CTCTCAAATTCCTTCCAAAATC
1 CTCTCAAATTCCTTCCAAAATC
* *
39511415 CTCTCAATTTCCTTCAAAAA
1 CTCTCAAATTCCTTCCAAAA
39511435 ATCTCCAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (22 bp):
CTCTCAAATTCCTTCCAAAATC
Found at i:39511514 original size:18 final size:18
Alignment explanation
Indices: 39511491--39511540 Score: 55
Period size: 20 Copynumber: 2.7 Consensus size: 18
39511481 TTTAAGAAAA
* *
39511491 TTTTAAAATTTTTTATTT
1 TTTTAAAATTTTTAAATT
39511509 TTTTAAAATAATTTTAAATT
1 TTTTAAAAT--TTTTAAATT
*
39511529 TTTTAATATTTT
1 TTTTAAAATTTT
39511541 CAACAATGGC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 12 0.44
20 15 0.56
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTTAAAATTTTTAAATT
Found at i:39511527 original size:28 final size:29
Alignment explanation
Indices: 39511476--39511533 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 29
39511466 ATTAAATTTC
39511476 ATTTTTTTAAGAAAATTTTAAAATTTTTT
1 ATTTTTTTAAGAAAATTTTAAAATTTTTT
39511505 ATTTTTTTAA-AATAATTTT-AAATTTTTT
1 ATTTTTTTAAGAA-AATTTTAAAATTTTTT
39511533 A
1 A
39511534 ATATTTTCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 12 0.43
29 16 0.57
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (29 bp):
ATTTTTTTAAGAAAATTTTAAAATTTTTT
Found at i:39511540 original size:28 final size:29
Alignment explanation
Indices: 39511480--39511540 Score: 81
Period size: 28 Copynumber: 2.1 Consensus size: 29
39511470 AATTTCATTT
* *
39511480 TTTTAAGAAAATTTTAAAATTTTTTATTT
1 TTTTAAGAAAATTTTAAAATTTTTTAATA
39511509 TTTTAA-AATAATTTT-AAATTTTTTAATA
1 TTTTAAGAA-AATTTTAAAATTTTTTAATA
39511537 TTTT
1 TTTT
39511541 CAACAATGGC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 17 0.59
29 12 0.41
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (29 bp):
TTTTAAGAAAATTTTAAAATTTTTTAATA
Found at i:39511540 original size:29 final size:29
Alignment explanation
Indices: 39511479--39511540 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 29
39511469 AAATTTCATT
*
39511479 TTTTTAAGAAAATTTTAAAATTTTTTATT
1 TTTTTAAGAAAATTTTAAAATTTTTTATA
39511508 TTTTTAA-AATAATTTT-AAATTTTTTAATA
1 TTTTTAAGAA-AATTTTAAAATTTTTT-ATA
39511537 TTTT
1 TTTT
39511541 CAACAATGGC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 11 0.37
29 19 0.63
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (29 bp):
TTTTTAAGAAAATTTTAAAATTTTTTATA
Found at i:39511686 original size:24 final size:23
Alignment explanation
Indices: 39511624--39511686 Score: 58
Period size: 24 Copynumber: 2.7 Consensus size: 23
39511614 TAAATTTATA
*
39511624 TTTTAAAT-TTTTTTTAAGATAT
1 TTTTATATATTTTTTTAAGATAT
*
39511646 TTTTATTTATGTATTTTT-AGATAT
1 TTTTATATAT-T-TTTTTAAGATAT
39511670 TTATTAATATATTTTTT
1 TT-TT-ATATATTTTTT
39511687 GTTATAAAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
22 6 0.18
23 1 0.03
24 13 0.39
25 8 0.24
26 5 0.15
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.67
Consensus pattern (23 bp):
TTTTATATATTTTTTTAAGATAT
Found at i:39513835 original size:23 final size:24
Alignment explanation
Indices: 39513801--39513875 Score: 91
Period size: 23 Copynumber: 3.2 Consensus size: 24
39513791 ACATTATTTG
*
39513801 ATTAAAATCCCTAACCCT-ACTTA
1 ATTAAAAACCCTAACCCTAACTTA
*
39513824 ATTAAAAACCCTAA-CCTAATTTA
1 ATTAAAAACCCTAACCCTAACTTA
* * *
39513847 ATTAAAAACCCAAACCCAAACATA
1 ATTAAAAACCCTAACCCTAACTTA
39513871 ATTAA
1 ATTAA
39513876 TTAAGTTAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
22 3 0.07
23 30 0.68
24 11 0.25
ACGTcount: A:0.49, C:0.25, G:0.00, T:0.25
Consensus pattern (24 bp):
ATTAAAAACCCTAACCCTAACTTA
Found at i:39513885 original size:33 final size:31
Alignment explanation
Indices: 39513833--39514417 Score: 442
Period size: 33 Copynumber: 19.3 Consensus size: 31
39513823 AATTAAAAAC
*
39513833 CCTAACCTAA-T--TTAATTAAAAACCCAAA
1 CCTAACCTAATTAATTAATTAAAAACCCTAA
* *
39513861 CCCAAACATAATTAATTAAGTTAAAAACCCTAA
1 -CCTAACCTAATTAATTAA-TTAAAAACCCTAA
* * * *
39513894 ACTAACTTAATTTAAATAATTAAAAACCAAAACCCAAA
1 CCTAACCTAA-TTAATTAATT----A--AAAACCCTAA
*
39513932 CCTAACTTAACTTAATTTAAATAATTAAAAACCCTAA
1 CCTAAC----C-TAA-TTAATTAATTAAAAACCCTAA
39513969 CCCTAACCTAA-T--TTAATTAAAAACCCTAA
1 -CCTAACCTAATTAATTAATTAAAAACCCTAA
*
39513998 CCTAACCTAA-T--TTAATT-AAAA-GC---
1 CCTAACCTAATTAATTAATTAAAAACCCTAA
*
39514021 CCTAACCTAA-T--TTAATTAAAAACCCAAA
1 CCTAACCTAATTAATTAATTAAAAACCCTAA
*
39514049 CCCAAACCTAATTAATTAAATTAAAAACCCTAA
1 -CCTAACCTAATTAATT-AATTAAAAACCCTAA
*
39514082 CCTAACTTAATTTAATTAAATTAAAAACCCTAA
1 CCTAACCTAA-TTAATT-AATTAAAAACCCTAA
*
39514115 CCTAACCTAA-T--TTAATTAAAAACCCAAA
1 CCTAACCTAATTAATTAATTAAAAACCCTAA
*
39514143 CCCAAACCTAATTAATTAAATTAAAAACCCTAA
1 -CCTAACCTAATTAATT-AATTAAAAACCCTAA
* *
39514176 CCTAACTTAATTTAAATAATTAAAAACCCTAA
1 CCTAACCTAA-TTAATTAATTAAAAACCCTAA
39514208 CCTAACCTAA-T--TTAATTAAAAA--C---
1 CCTAACCTAATTAATTAATTAAAAACCCTAA
*
39514231 CCTAACCTAA-T--TTAATTAAAAACCCAAA
1 CCTAACCTAATTAATTAATTAAAAACCCTAA
*
39514259 CCCAAACCTAATTAATTAAATTAAAAACCCTAA
1 -CCTAACCTAATTAATT-AATTAAAAACCCTAA
*
39514292 CCTAACTTAATTTAATTAAATTAAAAACCCTAA
1 CCTAACCTAA-TTAATT-AATTAAAAACCCTAA
39514325 CCTAA--T--TTAATTAAATTAAAAACCCTAA
1 CCTAACCTAATTAATT-AATTAAAAACCCTAA
*
39514353 CCTAACCTAA-T--TTAATTAAAAACCCAAA
1 CCTAACCTAATTAATTAATTAAAAACCCTAA
39514381 CCCTAACCTAA-T--TTAATTAAAAACCCTAA
1 -CCTAACCTAATTAATTAATTAAAAACCCTAA
39514410 CCTAACCT
1 CCTAACCT
39514418 TGGTGCATCG
Statistics
Matches: 473, Mismatches: 33, Indels: 101
0.78 0.05 0.17
Matches are distributed among these distances:
23 39 0.08
24 4 0.01
25 2 0.00
26 2 0.00
27 4 0.01
28 90 0.19
29 82 0.17
30 6 0.01
31 4 0.01
32 67 0.14
33 127 0.27
34 1 0.00
36 1 0.00
37 9 0.02
38 20 0.04
39 1 0.00
43 14 0.03
ACGTcount: A:0.49, C:0.23, G:0.00, T:0.28
Consensus pattern (31 bp):
CCTAACCTAATTAATTAATTAAAAACCCTAA
Found at i:39513937 original size:38 final size:38
Alignment explanation
Indices: 39513884--39513986 Score: 109
Period size: 43 Copynumber: 2.6 Consensus size: 38
39513874 AATTAAGTTA
39513884 AAAACCCTAAA-CTAACTTAATTTAAATAATTAAAAACC
1 AAAACCC-AAACCTAACTTAATTTAAATAATTAAAAACC
39513922 AAAACCCAAACCTAACTTAACTTAATTTAAATAATTAAAAACC
1 AAAACCCAAA-C---C-TAACTTAATTTAAATAATTAAAAACC
** * *
39513965 CTAACCCTAACCTAATTTAATT
1 AAAACCCAAACCTAACTTAATT
39513987 AAAAACCCTA
Statistics
Matches: 55, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
37 3 0.05
38 16 0.29
39 1 0.02
42 2 0.04
43 33 0.60
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.28
Consensus pattern (38 bp):
AAAACCCAAACCTAACTTAATTTAAATAATTAAAAACC
Found at i:39513943 original size:43 final size:43
Alignment explanation
Indices: 39513896--39513988 Score: 143
Period size: 43 Copynumber: 2.2 Consensus size: 43
39513886 AACCCTAAAC
39513896 TAACTTAATTTAAATAATTAAAAACCAAAACCCAAACCTAACT
1 TAACTTAATTTAAATAATTAAAAACCAAAACCCAAACCTAACT
** * *
39513939 TAACTTAATTTAAATAATTAAAAACCCTAACCCTAACCTAATT
1 TAACTTAATTTAAATAATTAAAAACCAAAACCCAAACCTAACT
39513982 TAA-TTAA
1 TAACTTAA
39513989 AAACCCTAAC
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
42 4 0.09
43 42 0.91
ACGTcount: A:0.51, C:0.19, G:0.00, T:0.30
Consensus pattern (43 bp):
TAACTTAATTTAAATAATTAAAAACCAAAACCCAAACCTAACT
Found at i:39513994 original size:23 final size:23
Alignment explanation
Indices: 39513967--39514050 Score: 105
Period size: 23 Copynumber: 3.4 Consensus size: 23
39513957 TAAAAACCCT
39513967 AACCCTAACCTAATTTAATTAAA
1 AACCCTAACCTAATTTAATTAAA
39513990 AACCCTAACCTAACCTAATTTAATTAAA
1 AA--C---CCTAACCTAATTTAATTAAA
*
39514018 AGCCCTAACCTAATTTAATTAAA
1 AACCCTAACCTAATTTAATTAAA
*
39514041 AACCCAAACC
1 AACCCTAACC
39514051 CAAACCTAAT
Statistics
Matches: 53, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
23 30 0.57
25 1 0.02
26 1 0.02
28 21 0.40
ACGTcount: A:0.46, C:0.26, G:0.01, T:0.26
Consensus pattern (23 bp):
AACCCTAACCTAATTTAATTAAA
Found at i:39514001 original size:28 final size:28
Alignment explanation
Indices: 39513953--39514417 Score: 455
Period size: 33 Copynumber: 15.9 Consensus size: 28
39513943 TTAATTTAAA
39513953 TAATTAAAAACCCTAACCCTAACCTAATT
1 TAATTAAAAACCCTAA-CCTAACCTAATT
39513982 TAATTAAAAACCCTAACCTAACCTAATT
1 TAATTAAAAACCCTAACCTAACCTAATT
*
39514010 TAATT-AAAA-GC---CCTAACCTAATT
1 TAATTAAAAACCCTAACCTAACCTAATT
* *
39514033 TAATTAAAAACCCAAACCCAAACCTAATTAAT
1 TAATTAAAAACCCTAA-CCTAACCTAA-T--T
*
39514065 TAAATTAAAAACCCTAACCTAACTTAATTTAAT
1 T-AATTAAAAACCCTAACCTAACCTAA--T--T
39514098 TAAATTAAAAACCCTAACCTAACCTAATT
1 T-AATTAAAAACCCTAACCTAACCTAATT
* *
39514127 TAATTAAAAACCCAAACCCAAACCTAATTAAT
1 TAATTAAAAACCCTAA-CCTAACCTAA-T--T
*
39514159 TAAATTAAAAACCCTAACCTAACTTAATTT
1 T-AATTAAAAACCCTAACCTAACCTAA-TT
39514189 AAATAATTAAAAACCCTAACCTAACCTAATT
1 ---TAATTAAAAACCCTAACCTAACCTAATT
39514220 TAATTAAAAA--C---CCTAACCTAATT
1 TAATTAAAAACCCTAACCTAACCTAATT
* *
39514243 TAATTAAAAACCCAAACCCAAACCTAATTAAT
1 TAATTAAAAACCCTAA-CCTAACCTAA-T--T
*
39514275 TAAATTAAAAACCCTAACCTAACTTAATTTAAT
1 T-AATTAAAAACCCTAACCTAACCTAA--T--T
**
39514308 TAAATTAAAAACCCTAACCTAATTTAATT
1 T-AATTAAAAACCCTAACCTAACCTAATT
*
39514337 AAATTAAAAACCCTAACCTAACCTAATT
1 TAATTAAAAACCCTAACCTAACCTAATT
*
39514365 TAATTAAAAACCCAAACCCTAACCTAATT
1 TAATTAAAAACCCTAA-CCTAACCTAATT
39514394 TAATTAAAAACCCTAACCTAACCT
1 TAATTAAAAACCCTAACCTAACCT
39514418 TGGTGCATCG
Statistics
Matches: 381, Mismatches: 24, Indels: 63
0.81 0.05 0.13
Matches are distributed among these distances:
23 39 0.10
24 4 0.01
25 2 0.01
26 2 0.01
27 4 0.01
28 88 0.23
29 73 0.19
30 4 0.01
31 4 0.01
32 56 0.15
33 105 0.28
ACGTcount: A:0.49, C:0.23, G:0.00, T:0.28
Consensus pattern (28 bp):
TAATTAAAAACCCTAACCTAACCTAATT
Found at i:39514218 original size:23 final size:23
Alignment explanation
Indices: 39514192--39514273 Score: 74
Period size: 28 Copynumber: 3.3 Consensus size: 23
39514182 TTAATTTAAA
39514192 TAATTAAAAACCCTAACCTAACC
1 TAATTAAAAACCCTAACCTAACC
**
39514215 TAATTTAATTAAAAACCCTAACCTAATT
1 -----TAATTAAAAACCCTAACCTAACC
* *
39514243 TAATTAAAAACCCAAACCCAAACC
1 TAATTAAAAACCCTAA-CCTAACC
39514267 TAATTAA
1 TAATTAA
39514274 TTAAATTAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
23 15 0.32
24 11 0.23
28 21 0.45
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (23 bp):
TAATTAAAAACCCTAACCTAACC
Found at i:39517990 original size:23 final size:23
Alignment explanation
Indices: 39517947--39517991 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
39517937 AATGAACTTG
*
39517947 TTCGTAAATATTAAATAAACATA
1 TTCGTAAATATTAAACAAACATA
*
39517970 TTCGTAAATATTAAACGAACAT
1 TTCGTAAATATTAAACAAACAT
39517992 GTTGACAAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.49, C:0.11, G:0.07, T:0.33
Consensus pattern (23 bp):
TTCGTAAATATTAAACAAACATA
Found at i:39519308 original size:30 final size:31
Alignment explanation
Indices: 39519269--39519328 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
39519259 TGGGATGGGA
*
39519269 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
39519300 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
39519329 TAAAAAGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:39520167 original size:19 final size:19
Alignment explanation
Indices: 39520124--39520167 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
39520114 GATAGTAATA
* *
39520124 TATAAAAATTAAAAATTGT
1 TATAAAAATTAAAAAGTAT
39520143 TATAAAAATTTAAAAAGTAT
1 TATAAAAA-TTAAAAAGTAT
39520163 T-TAAA
1 TATAAA
39520168 TTTCAAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (19 bp):
TATAAAAATTAAAAAGTAT
Found at i:39520235 original size:23 final size:22
Alignment explanation
Indices: 39520201--39520266 Score: 71
Period size: 23 Copynumber: 2.8 Consensus size: 22
39520191 CTTGAATTTT
39520201 AAATAATTTTTAGAATTTTATAAAA
1 AAAT-ATTTTTA-AATTTT-TAAAA
39520226 AAATA-TTTTAAACTTTTTAAAA
1 AAATATTTTTAAA-TTTTTAAAA
*
39520248 ATATATTTTTATAATTTTT
1 AAATATTTTTA-AATTTTT
39520267 CTTATATATT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
22 11 0.30
23 19 0.51
24 3 0.08
25 4 0.11
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (22 bp):
AAATATTTTTAAATTTTTAAAA
Found at i:39520296 original size:20 final size:22
Alignment explanation
Indices: 39520248--39520300 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
39520238 CTTTTTAAAA
*
39520248 ATATATTTTTATAATTTTTCTT
1 ATATATTTTTACAATTTTTCTT
*
39520270 ATATATTTTTACAATTTTTTTT
1 ATATATTTTTACAATTTTTCTT
39520292 ATAT-TTTTT
1 ATATATTTTT
39520301 CAAGTAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 5 0.17
22 24 0.83
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (22 bp):
ATATATTTTTACAATTTTTCTT
Found at i:39521817 original size:17 final size:19
Alignment explanation
Indices: 39521788--39521822 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
39521778 GGCATAGTTT
39521788 AAAATGAAAAGTT-TAAAG
1 AAAATGAAAAGTTATAAAG
39521806 AAAATG-AAAGTTATAAA
1 AAAATGAAAAGTTATAAA
39521823 AATCTTGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.63, C:0.00, G:0.14, T:0.23
Consensus pattern (19 bp):
AAAATGAAAAGTTATAAAG
Found at i:39522392 original size:18 final size:18
Alignment explanation
Indices: 39522366--39522402 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
39522356 CGCCTTCTTC
39522366 TCCCCTTTCCCTTCCCCT
1 TCCCCTTTCCCTTCCCCT
*
39522384 TCCCTTTTCCCTTCCCCT
1 TCCCCTTTCCCTTCCCCT
39522402 T
1 T
39522403 GGGTTGCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (18 bp):
TCCCCTTTCCCTTCCCCT
Found at i:39522521 original size:25 final size:25
Alignment explanation
Indices: 39522462--39522511 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
39522452 CAGGTAAGGC
39522462 TCCTTCTTCTTCTTCCGTTCTTCAT
1 TCCTTCTTCTTCTTCCGTTCTTCAT
* * *
39522487 TCCTTTTTCTTCTTCTGTTTTTCAT
1 TCCTTCTTCTTCTTCCGTTCTTCAT
39522512 ATTCTCTTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.04, C:0.30, G:0.04, T:0.62
Consensus pattern (25 bp):
TCCTTCTTCTTCTTCCGTTCTTCAT
Found at i:39522715 original size:11 final size:11
Alignment explanation
Indices: 39522699--39522724 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
39522689 TTGCTGGATG
39522699 ATATTTTGGTT
1 ATATTTTGGTT
39522710 ATATTTTGGTT
1 ATATTTTGGTT
39522721 ATAT
1 ATAT
39522725 ACAGATGGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.15, T:0.62
Consensus pattern (11 bp):
ATATTTTGGTT
Found at i:39525048 original size:22 final size:20
Alignment explanation
Indices: 39525005--39525043 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
39524995 TAATTTAAAA
39525005 TATAAAAATTTATTAATATG
1 TATAAAAATTTATTAATATG
*
39525025 TATATAAATTTATTAATAT
1 TATAAAAATTTATTAATAT
39525044 ATGTAAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
TATAAAAATTTATTAATATG
Found at i:39525180 original size:20 final size:20
Alignment explanation
Indices: 39525142--39525181 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
39525132 AATAATTTCC
* *
39525142 AGTAAATCATTTTATAGAAA
1 AGTAAAACATTTTACAGAAA
*
39525162 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
39525182 TCATTTTACG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:39528295 original size:29 final size:29
Alignment explanation
Indices: 39528258--39528343 Score: 91
Period size: 29 Copynumber: 2.9 Consensus size: 29
39528248 ATCAGAAAGT
* *
39528258 CAAACCTTTCAAAGTGCTCCAATAAGGGC
1 CAAACCTTTCAAAGTGCTCAAATAAGAGC
* * *
39528287 CAAAACTTTGAGAGTGCTCAAATAAGAGC
1 CAAACCTTTCAAAGTGCTCAAATAAGAGC
* *
39528316 CAAACCTTTTTGAAATTGCTCAAATAAG
1 CAAACC--TTTCAAAGTGCTCAAATAAG
39528344 GGCTTCTCAA
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
29 29 0.62
31 18 0.38
ACGTcount: A:0.38, C:0.21, G:0.16, T:0.24
Consensus pattern (29 bp):
CAAACCTTTCAAAGTGCTCAAATAAGAGC
Found at i:39530864 original size:15 final size:15
Alignment explanation
Indices: 39530846--39530899 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
39530836 AGAAAAACTA
*
39530846 TATTTTTCATCTTTC
1 TATTTTTCATCCTTC
*
39530861 TATTTTTCTACCCTTC
1 TATTTTTC-ATCCTTC
*
39530877 AATTTTTCATCCTTC
1 TATTTTTCATCCTTC
*
39530892 TAATTTTC
1 TATTTTTC
39530900 TTTTCACTCT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
15 20 0.62
16 12 0.38
ACGTcount: A:0.17, C:0.24, G:0.00, T:0.59
Consensus pattern (15 bp):
TATTTTTCATCCTTC
Found at i:39530881 original size:16 final size:16
Alignment explanation
Indices: 39530847--39530898 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
39530837 GAAAAACTAT
* *
39530847 ATTTTTCATCTTTCT-
1 ATTTTTCACCCTTCTA
39530862 ATTTTTCTACCCTTC-A
1 ATTTTTC-ACCCTTCTA
*
39530878 ATTTTTCATCCTTCTA
1 ATTTTTCACCCTTCTA
39530894 ATTTT
1 ATTTT
39530899 CTTTTCACTC
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
15 13 0.42
16 18 0.58
ACGTcount: A:0.17, C:0.23, G:0.00, T:0.60
Consensus pattern (16 bp):
ATTTTTCACCCTTCTA
Found at i:39531001 original size:2 final size:2
Alignment explanation
Indices: 39530988--39531025 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
39530978 CATTTGTAAA
* *
39530988 AT AT AT AC AT AT AT AT AT AT AT AT AT AT CT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
39531026 CTCAACTAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:39532381 original size:11 final size:11
Alignment explanation
Indices: 39532365--39532396 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
39532355 ATTTCTTTAA
39532365 TTTTTATGAAT
1 TTTTTATGAAT
39532376 TTTTTAT-AAT
1 TTTTTATGAAT
39532386 TTTTT-TGAAT
1 TTTTTATGAAT
39532396 T
1 T
39532397 ACGATTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
9 1 0.05
10 12 0.60
11 7 0.35
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (11 bp):
TTTTTATGAAT
Found at i:39537858 original size:43 final size:43
Alignment explanation
Indices: 39537797--39537890 Score: 161
Period size: 43 Copynumber: 2.2 Consensus size: 43
39537787 GATGTGGCCA
39537797 ACATATTATCATACATGTAATGTCATGTCATCTTATTATTTCC
1 ACATATTATCATACATGTAATGTCATGTCATCTTATTATTTCC
* * *
39537840 ACATATTATCATATATGTAATGTCGTGTCATCTTGTTATTTCC
1 ACATATTATCATACATGTAATGTCATGTCATCTTATTATTTCC
39537883 ACATATTA
1 ACATATTA
39537891 CTCACTAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 48 1.00
ACGTcount: A:0.30, C:0.17, G:0.09, T:0.45
Consensus pattern (43 bp):
ACATATTATCATACATGTAATGTCATGTCATCTTATTATTTCC
Found at i:39538743 original size:23 final size:23
Alignment explanation
Indices: 39538713--39538758 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
39538703 TACAACTTTT
39538713 GTAAAAAGCAAGACAGAATTTAA
1 GTAAAAAGCAAGACAGAATTTAA
*
39538736 GTAAAAAGCAGGACAGAATTTAA
1 GTAAAAAGCAAGACAGAATTTAA
39538759 CATTTACAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.54, C:0.09, G:0.20, T:0.17
Consensus pattern (23 bp):
GTAAAAAGCAAGACAGAATTTAA
Found at i:39542009 original size:29 final size:30
Alignment explanation
Indices: 39541950--39542009 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
39541940 CTATATATAT
* * **
39541950 TTAGTTTAAGATTTAATTAAGTTAATTTAA
1 TTAGTTTAAGACTTAATTAAATTAAACTAA
39541980 TTAGTTTAAG-CTTAATTAAATTAAACTAA
1 TTAGTTTAAGACTTAATTAAATTAAACTAA
39542009 T
1 T
39542010 CATACATGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (30 bp):
TTAGTTTAAGACTTAATTAAATTAAACTAA
Found at i:39545435 original size:16 final size:16
Alignment explanation
Indices: 39545414--39545447 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
39545404 TCAATGTTAC
39545414 TTGAAATGAAAACCAA
1 TTGAAATGAAAACCAA
* *
39545430 TTGAAATGCAAATCAA
1 TTGAAATGAAAACCAA
39545446 TT
1 TT
39545448 CAAAATTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.12, G:0.12, T:0.26
Consensus pattern (16 bp):
TTGAAATGAAAACCAA
Found at i:39545945 original size:13 final size:13
Alignment explanation
Indices: 39545927--39545952 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
39545917 ATATGAATAA
39545927 GTTGAAACAAAAT
1 GTTGAAACAAAAT
39545940 GTTGAAACAAAAT
1 GTTGAAACAAAAT
39545953 TATTGCATCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.15, T:0.23
Consensus pattern (13 bp):
GTTGAAACAAAAT
Found at i:39550939 original size:9 final size:9
Alignment explanation
Indices: 39550925--39551013 Score: 99
Period size: 9 Copynumber: 9.8 Consensus size: 9
39550915 TTTGGTTAAA
39550925 AATTACCCG
1 AATTACCCG
*
39550934 AATTACCCC
1 AATTACCCG
39550943 AATTACCCG
1 AATTACCCG
39550952 AATTACCCG
1 AATTACCCG
*
39550961 AATTAACCG
1 AATTACCCG
**
39550970 AATTAATCG
1 AATTACCCG
*
39550979 AATTAACCG
1 AATTACCCG
39550988 AATTA-CCG
1 AATTACCCG
*
39550996 AAAAATACCCG
1 --AATTACCCG
39551007 AATTACC
1 AATTACC
39551014 TGATTTTTTT
Statistics
Matches: 70, Mismatches: 7, Indels: 6
0.84 0.08 0.07
Matches are distributed among these distances:
8 3 0.04
9 60 0.86
10 4 0.06
11 3 0.04
ACGTcount: A:0.40, C:0.28, G:0.09, T:0.22
Consensus pattern (9 bp):
AATTACCCG
Found at i:39551178 original size:13 final size:13
Alignment explanation
Indices: 39551160--39551189 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
39551150 TTTTAGTTTT
39551160 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
39551173 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
39551186 ATTG
1 ATTG
39551190 AGTTTGGGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.43, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:39552794 original size:30 final size:30
Alignment explanation
Indices: 39552748--39552871 Score: 203
Period size: 30 Copynumber: 4.1 Consensus size: 30
39552738 TTTTATTATG
*
39552748 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
39552779 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
39552809 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* * *
39552839 CTATTATTTGATACCCATATCTTTGATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
39552869 CCA
1 CCA
39552872 TAAATATTGA
Statistics
Matches: 88, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
30 81 0.92
31 7 0.08
ACGTcount: A:0.26, C:0.24, G:0.06, T:0.44
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:39552803 original size:15 final size:15
Alignment explanation
Indices: 39552758--39552865 Score: 78
Period size: 15 Copynumber: 7.2 Consensus size: 15
39552748 CCAATATCTC
39552758 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
39552773 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
39552788 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
39552803 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
39552818 GATACCCATATCTTT
1 GATACCCATATCTTT
** * *
39552833 GACTTTCTAT-TATTT
1 GA-TACCCATATCTTT
39552848 GATACCCATATCTTT
1 GATACCCATATCTTT
39552863 GAT
1 GAT
39552866 TTTCCATAAA
Statistics
Matches: 67, Mismatches: 20, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
14 12 0.18
15 43 0.64
16 12 0.18
ACGTcount: A:0.26, C:0.22, G:0.07, T:0.44
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:39558766 original size:29 final size:29
Alignment explanation
Indices: 39558696--39558775 Score: 92
Period size: 31 Copynumber: 2.7 Consensus size: 29
39558686 TTTACAATTG
* *
39558696 TTGAAAATTGTAATTAGATCTTCTAAAGGAT
1 TTGAAAATTTTAATTAGA-CCTCTAAA-GAT
39558727 TTGAAAATTTTAATTAGACCTCTAAA-AT
1 TTGAAAATTTTAATTAGACCTCTAAAGAT
*
39558755 TATGAAAATTTTCATTA-ACCT
1 T-TGAAAATTTTAATTAGACCT
39558776 TCTCCCCATA
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
28 7 0.16
29 14 0.31
30 7 0.16
31 17 0.38
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (29 bp):
TTGAAAATTTTAATTAGACCTCTAAAGAT
Found at i:39566349 original size:18 final size:18
Alignment explanation
Indices: 39566323--39566357 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
39566313 ATATGTTTAT
*
39566323 TATATATATATTATAAAA
1 TATAAATATATTATAAAA
*
39566341 TATAAATATATTTTAAA
1 TATAAATATATTATAAA
39566358 TAATTTAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TATAAATATATTATAAAA
Found at i:39572879 original size:20 final size:20
Alignment explanation
Indices: 39572846--39572886 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
39572836 TAGATATTTG
** *
39572846 TTTTATTACCATTTTATATA
1 TTTTATTAAAATTTTAAATA
39572866 TTTTATTAAAATTTTAAATA
1 TTTTATTAAAATTTTAAATA
39572886 T
1 T
39572887 AAAAAGCTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTTATTAAAATTTTAAATA
Found at i:39573009 original size:20 final size:21
Alignment explanation
Indices: 39572984--39573025 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
39572974 ATTCATCTCA
39572984 TATTTTAATTG-ATTT-ATTAT
1 TATTTT-ATTGAATTTCATTAT
39573004 TATTTTATTGAATTTCATTAT
1 TATTTTATTGAATTTCATTAT
39573025 T
1 T
39573026 CAAGTTTCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 4 0.20
20 10 0.50
21 6 0.30
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.64
Consensus pattern (21 bp):
TATTTTATTGAATTTCATTAT
Found at i:39574111 original size:43 final size:42
Alignment explanation
Indices: 39574052--39574331 Score: 269
Period size: 43 Copynumber: 6.5 Consensus size: 42
39574042 GTGGAGAAAT
* *
39574052 GCTGCTATAGAACATGACCTTTAGTGGCGCTTATCCCAGAAAC
1 GCTGCTATAGAACATGACCTTTAGCGGCGCTT-TCCCACAAAC
* *
39574095 GCTGCTATAGATCATGACCTTTAGCGGCACTTTTCCCACAAAC
1 GCTGCTATAGAACATGACCTTTAGCGGCGC-TTTCCCACAAAC
*
39574138 -CTTGCTATAGAACATGACCTTTAGCGGCGCTTTCCCTACAATC
1 GC-TGCTATAGAACATGACCTTTAGCGGCGCTTTCCC-ACAAAC
* * * * *
39574181 GCTGCTATAGAATATGACCTTTTGCAGCACTTTCCCACAAAT
1 GCTGCTATAGAACATGACCTTTAGCGGCGCTTTCCCACAAAC
* * ** *
39574223 GCCGCTATAGAGCATGACCTTTAATGGCGCTTTCCCTACAAAT
1 GCTGCTATAGAACATGACCTTTAGCGGCGCTTTCCC-ACAAAC
* * * * * *
39574266 GCCGCTAAAGAACATGACTTTTAGTGGCACTTTTTACCACAAAAC
1 GCTGCTATAGAACATGACCTTTAGCGGCGC--TTTCCCAC-AAAC
*
39574311 -C-GCTAAAGAACATGACCTTTA
1 GCTGCTATAGAACATGACCTTTA
39574332 ATGGTGCTTT
Statistics
Matches: 200, Mismatches: 29, Indels: 16
0.82 0.12 0.07
Matches are distributed among these distances:
42 39 0.19
43 147 0.74
44 6 0.03
45 8 0.04
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.28
Consensus pattern (42 bp):
GCTGCTATAGAACATGACCTTTAGCGGCGCTTTCCCACAAAC
Found at i:39574154 original size:86 final size:84
Alignment explanation
Indices: 39574055--39574341 Score: 328
Period size: 86 Copynumber: 3.4 Consensus size: 84
39574045 GAGAAATGCT
* *
39574055 GCTATAGAACATGACCTTTAGTGGCGCTTATCCC-AGAAACGCTGCTATAGATCATGACCTTTAG
1 GCTATAGAACATGACCTTTAATGGCGCTT-TCCCTACAAACGCTGCTATAGATCATGACCTTTAG
39574119 CGGCACTTTTCCCACAAACC
65 CGGCACTTTTCCCACAAACC
** *
39574139 TTGCTATAGAACATGACCTTTAGCGGCGCTTTCCCTACAATCGCTGCTATAGAAT-ATGACCTTT
1 --GCTATAGAACATGACCTTTAATGGCGCTTTCCCTACAAACGCTGCTATAG-ATCATGACCTTT
* *
39574203 TGCAGCAC-TTTCCCACAAATGCC
63 AGCGGCACTTTTCCCACAAA--CC
* * * * * * *
39574226 GCTATAGAGCATGACCTTTAATGGCGCTTTCCCTACAAATGCCGCTAAAGAACATGACTTTTAGT
1 GCTATAGAACATGACCTTTAATGGCGCTTTCCCTACAAACGCTGCTATAGATCATGACCTTTAGC
*
39574291 GGCACTTTTTACCACAAAACC
66 GGCAC-TTTTCCCAC-AAACC
* *
39574312 GCTAAAGAACATGACCTTTAATGGTGCTTT
1 GCTATAGAACATGACCTTTAATGGCGCTTT
39574342 TCCGAAAACG
Statistics
Matches: 172, Mismatches: 21, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
84 1 0.01
85 71 0.41
86 86 0.50
87 11 0.06
88 3 0.02
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.29
Consensus pattern (84 bp):
GCTATAGAACATGACCTTTAATGGCGCTTTCCCTACAAACGCTGCTATAGATCATGACCTTTAGC
GGCACTTTTCCCACAAACC
Found at i:39580407 original size:9 final size:9
Alignment explanation
Indices: 39580393--39580453 Score: 56
Period size: 9 Copynumber: 7.0 Consensus size: 9
39580383 TAAGTATAAT
39580393 TAAGTTATG
1 TAAGTTATG
39580402 TAAGTTATGG
1 TAAGTTAT-G
* * *
39580412 TATGATATA
1 TAAGTTATG
*
39580421 T-ATTTATG
1 TAAGTTATG
39580429 T-A-TTATG
1 TAAGTTATG
39580436 TAAGTTATG
1 TAAGTTATG
39580445 TAAGTTATG
1 TAAGTTATG
39580454 ATCCAAAGTT
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
7 6 0.14
8 6 0.14
9 23 0.55
10 7 0.17
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.48
Consensus pattern (9 bp):
TAAGTTATG
Found at i:39580523 original size:13 final size:13
Alignment explanation
Indices: 39580505--39580530 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
39580495 TGATTATCAT
39580505 CTTTAAATTTTAA
1 CTTTAAATTTTAA
39580518 CTTTAAATTTTAA
1 CTTTAAATTTTAA
39580531 TAATTATATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (13 bp):
CTTTAAATTTTAA
Found at i:39581063 original size:8 final size:9
Alignment explanation
Indices: 39581042--39581071 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
39581032 TTTAAGTTTA
39581042 AAAAATTTT
1 AAAAATTTT
39581051 AAAAATTTT
1 AAAAATTTT
39581060 AAAAATTTT
1 AAAAATTTT
39581069 AAA
1 AAA
39581072 TATTAAAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (9 bp):
AAAAATTTT
Found at i:39581539 original size:39 final size:39
Alignment explanation
Indices: 39581480--39581559 Score: 124
Period size: 39 Copynumber: 2.1 Consensus size: 39
39581470 ATTCAGCCAA
* *
39581480 ATAGTTTAAACATTCAGCCAAATAGTTTGCAAACAGCAT
1 ATAGGTTAAACATTCAGCCAAACAGTTTGCAAACAGCAT
* *
39581519 ATAGGTTAAACATTTAGCCAAACAGTTTGCAAACATCAT
1 ATAGGTTAAACATTCAGCCAAACAGTTTGCAAACAGCAT
39581558 AT
1 AT
39581560 GACAATGAAG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.29
Consensus pattern (39 bp):
ATAGGTTAAACATTCAGCCAAACAGTTTGCAAACAGCAT
Found at i:39583609 original size:14 final size:15
Alignment explanation
Indices: 39583585--39583619 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
39583575 TATATATATT
39583585 ACCATATAAATACTA
1 ACCATATAAATACTA
39583600 ACCATA-AAATACTA
1 ACCATATAAATACTA
39583614 ATCCAT
1 A-CCAT
39583620 GATTAAAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (15 bp):
ACCATATAAATACTA
Found at i:39584316 original size:41 final size:41
Alignment explanation
Indices: 39584285--39584566 Score: 361
Period size: 41 Copynumber: 6.9 Consensus size: 41
39584275 CTATATAAAA
* * * * * *
39584285 CACCGGCATAAAGCCTGCTAGGCACAAAGCCCG-ATTCATTT
1 CACCGGCATCAAGCCTGCTAGGCATAAAGCCTGAAAT-AATC
* * * * *
39584326 CACCGGCA-CAAAGCCTGCTAGACATAAAGTCGGAATTAATT
1 CACCGGCATC-AAGCCTGCTAGGCATAAAGCCTGAAATAATC
* * * *
39584367 CACCGGCATCAAGCCTGCTAGACATAAAGTCTAAAATAATT
1 CACCGGCATCAAGCCTGCTAGGCATAAAGCCTGAAATAATC
*
39584408 CACCGGCATCAAGCCTGCTAGGCATTAAGCCTGAAATAATC
1 CACCGGCATCAAGCCTGCTAGGCATAAAGCCTGAAATAATC
*
39584449 CACCGGCATCAAGCCTGCTAGGCATTAAGCCTGAAATAATC
1 CACCGGCATCAAGCCTGCTAGGCATAAAGCCTGAAATAATC
*
39584490 CACCGGCATCAAGCCTGCTAGGCATTAAGCCTGAAATAATC
1 CACCGGCATCAAGCCTGCTAGGCATAAAGCCTGAAATAATC
*
39584531 CACCGGCATCAAGCCTGCTAGGCATTAAGCCTGAAA
1 CACCGGCATCAAGCCTGCTAGGCATAAAGCCTGAAA
39584567 ATCTCATATA
Statistics
Matches: 224, Mismatches: 14, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
41 220 0.98
42 4 0.02
ACGTcount: A:0.33, C:0.28, G:0.19, T:0.20
Consensus pattern (41 bp):
CACCGGCATCAAGCCTGCTAGGCATAAAGCCTGAAATAATC
Found at i:39584799 original size:64 final size:63
Alignment explanation
Indices: 39584681--39584861 Score: 262
Period size: 64 Copynumber: 2.9 Consensus size: 63
39584671 GCAAACAAAC
*
39584681 ATTCGAACCACATATGT-AT-AATTTACA-ACATTAAAATTCAGCTCAAAGAA-TTTGTAACCTA
1 ATTCGAACCACATATGTAATAAAATT-CATACATT-AAATTCAGCTC-AAGAACTTTGTAACCTA
39584742 T
63 T
39584743 ATTCGAACCACATATGTAAGTAAAATTCATACATTAAATTCAGCTCAAGAACTTTGTAACCTAT
1 ATTCGAACCACATATGTAA-TAAAATTCATACATTAAATTCAGCTCAAGAACTTTGTAACCTAT
* *
39584807 ATTTGAACCACATATGTATATAAAATTCATACATTAAATACAGCTCAAGAACTTT
1 ATTCGAACCACATATGTA-ATAAAATTCATACATTAAATTCAGCTCAAGAACTTT
39584862 AAATATATAT
Statistics
Matches: 110, Mismatches: 3, Indels: 10
0.89 0.02 0.08
Matches are distributed among these distances:
62 17 0.15
63 6 0.05
64 77 0.70
65 10 0.09
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.32
Consensus pattern (63 bp):
ATTCGAACCACATATGTAATAAAATTCATACATTAAATTCAGCTCAAGAACTTTGTAACCTAT
Found at i:39590573 original size:14 final size:15
Alignment explanation
Indices: 39590549--39590583 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
39590539 TATATATATT
39590549 ACCATATAAATACTA
1 ACCATATAAATACTA
39590564 ACCATA-AAATACTA
1 ACCATATAAATACTA
39590578 ATCCAT
1 A-CCAT
39590584 GATTAAAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (15 bp):
ACCATATAAATACTA
Found at i:39591282 original size:41 final size:39
Alignment explanation
Indices: 39591240--39591488 Score: 205
Period size: 41 Copynumber: 6.1 Consensus size: 39
39591230 AACATAGAGC
* * *
39591240 CCTATATAAAACACCGGCATAAAGCCTGCTAGGCACAAAG
1 CCTA-ATAATACACCGGCATCAAGCCTGCTAGGCATAAAG
* * * * *
39591280 CCCGATTCATTTCACCGGCA-CAAAGCCTGCTAGACATAAAG
1 -CCTAAT-AATACACCGGCATC-AAGCCTGCTAGGCATAAAG
** * *
39591321 TCAGAATTAATTCACCGGCATCAAGCCTGCTAGACATAAAG
1 -CCTAA-TAATACACCGGCATCAAGCCTGCTAGGCATAAAG
* *
39591362 TCTAA-AATAATCACCGGCATCAAGCCTGCTAGGCATTAAG
1 CCTAATAAT-A-CACCGGCATCAAGCCTGCTAGGCATAAAG
* * *
39591402 CCTGAAATAATCCACTGGCATCAAGCCTGCTAGGCATTAAG
1 CCT--AATAATACACCGGCATCAAGCCTGCTAGGCATAAAG
* *
39591443 CCTGAAATAATCCACCGGCATCAAGCCTGCTAGGCATTAAG
1 CCT--AATAATACACCGGCATCAAGCCTGCTAGGCATAAAG
39591484 CCTAA
1 CCTAA
39591489 AAATCTCATA
Statistics
Matches: 177, Mismatches: 22, Indels: 20
0.81 0.10 0.09
Matches are distributed among these distances:
38 3 0.02
39 2 0.01
40 32 0.18
41 133 0.75
42 4 0.02
43 3 0.02
ACGTcount: A:0.35, C:0.28, G:0.18, T:0.20
Consensus pattern (39 bp):
CCTAATAATACACCGGCATCAAGCCTGCTAGGCATAAAG
Found at i:39591422 original size:81 final size:81
Alignment explanation
Indices: 39591291--39591493 Score: 268
Period size: 81 Copynumber: 2.5 Consensus size: 81
39591281 CCGATTCATT
* * * * * *
39591291 TCACCGGCA-CAAAGCCTGCTAGACATAAAGTCAGAATTAATTCACCGGCATCAAGCCTGCTAGA
1 TCACCGGCATC-AAGCCTGCTAGGCATTAAGCCTGAAATAATCCACCGGCATCAAGCCTGCTAGA
*
39591355 CATAAAGTCTAAAATAA
65 CATAAAGCCTAAAATAA
* *
39591372 TCACCGGCATCAAGCCTGCTAGGCATTAAGCCTGAAATAATCCACTGGCATCAAGCCTGCTAGGC
1 TCACCGGCATCAAGCCTGCTAGGCATTAAGCCTGAAATAATCCACCGGCATCAAGCCTGCTAGAC
* *
39591437 ATTAAGCCTGAAATAA
66 ATAAAGCCTAAAATAA
39591453 TCCACCGGCATCAAGCCTGCTAGGCATTAAGCCT-AAA-AATC
1 T-CACCGGCATCAAGCCTGCTAGGCATTAAGCCTGAAATAATC
39591494 TCATATACAA
Statistics
Matches: 109, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
80 4 0.04
81 72 0.66
82 33 0.30
ACGTcount: A:0.35, C:0.27, G:0.18, T:0.20
Consensus pattern (81 bp):
TCACCGGCATCAAGCCTGCTAGGCATTAAGCCTGAAATAATCCACCGGCATCAAGCCTGCTAGAC
ATAAAGCCTAAAATAA
Found at i:39591723 original size:64 final size:62
Alignment explanation
Indices: 39591605--39591784 Score: 258
Period size: 64 Copynumber: 2.9 Consensus size: 62
39591595 GCAAACAAAC
*
39591605 ATTCGAACCACATATGTAT-AATTTACA-ACATTAAAATTCAGCTCAAAGAA-TTTGTAACCTAT
1 ATTCGAACCACATATGTATAAAATT-CATACATT-AAATTCAGCTC-AAGAACTTTGTAACCTAT
39591667 ATTCGAACCACATATGTAAGTAAAATTCATACATTAAATTCAGCTCAAGAACTTTGTAACCTAT
1 ATTCGAACCACATATGT-A-TAAAATTCATACATTAAATTCAGCTCAAGAACTTTGTAACCTAT
* *
39591731 ATTTGAACCACATATGTATATAAATTCATACATTAAATACAGCTCAAGAACTTT
1 ATTCGAACCACATATGTATA-AAATTCATACATTAAATTCAGCTCAAGAACTTT
39591785 AAATATATAT
Statistics
Matches: 109, Mismatches: 3, Indels: 11
0.89 0.02 0.09
Matches are distributed among these distances:
62 19 0.17
63 39 0.36
64 42 0.39
65 9 0.08
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.32
Consensus pattern (62 bp):
ATTCGAACCACATATGTATAAAATTCATACATTAAATTCAGCTCAAGAACTTTGTAACCTAT
Found at i:39593308 original size:29 final size:29
Alignment explanation
Indices: 39593270--39593328 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
39593260 CCAAATCTCC
*
39593270 AAATTTTTATATTTTCCAATTTAAATGCA
1 AAATTTTTATATTTTCCAAGTTAAATGCA
39593299 AAATTTTTATATTTTCCAAGTTAAATGCA
1 AAATTTTTATATTTTCCAAGTTAAATGCA
39593328 A
1 A
39593329 GTACCGAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.39, C:0.10, G:0.05, T:0.46
Consensus pattern (29 bp):
AAATTTTTATATTTTCCAAGTTAAATGCA
Found at i:39594673 original size:41 final size:41
Alignment explanation
Indices: 39594616--39594734 Score: 132
Period size: 41 Copynumber: 2.9 Consensus size: 41
39594606 CGACTTTTAA
39594616 AAATGCCGCTAATGCTTGACTTTTTGTGGCATTTTTCTCAT
1 AAATGCCGCTAATGCTTGACTTTTTGTGGCATTTTTCTCAT
* * *
39594657 AAATGCCGCTATTGCTTGA-TCGTTTGTGGCGTTTTTCTCAT
1 AAATGCCGCTAATGCTTGACT-TTTTGTGGCATTTTTCTCAT
** * * * * *
39594698 AAGCGCCGCTACTGCTTTACCTATTGCGGCATTTTTC
1 AAATGCCGCTAATGCTTGACTTTTTGTGGCATTTTTC
39594735 CATTAGCGCC
Statistics
Matches: 64, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
40 1 0.02
41 63 0.98
ACGTcount: A:0.17, C:0.23, G:0.19, T:0.41
Consensus pattern (41 bp):
AAATGCCGCTAATGCTTGACTTTTTGTGGCATTTTTCTCAT
Found at i:39596295 original size:24 final size:24
Alignment explanation
Indices: 39596276--39596325 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
39596266 AGATTTAGTA
*
39596276 TTTATGAGTATAATATATTTAACT
1 TTTATGAGCATAATATATTTAACT
* *
39596300 TTTATTAGCATAATATATTTGACT
1 TTTATGAGCATAATATATTTAACT
39596324 TT
1 TT
39596326 GATTAGAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.34, C:0.06, G:0.08, T:0.52
Consensus pattern (24 bp):
TTTATGAGCATAATATATTTAACT
Found at i:39596330 original size:24 final size:24
Alignment explanation
Indices: 39596285--39596331 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
39596275 ATTTATGAGT
*
39596285 ATAATATATTTAACTTTTATTAGC
1 ATAATATATTTAACTTTGATTAGC
*
39596309 ATAATATATTTGACTTTGATTAG
1 ATAATATATTTAACTTTGATTAG
39596332 AATTAGGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.36, C:0.06, G:0.09, T:0.49
Consensus pattern (24 bp):
ATAATATATTTAACTTTGATTAGC
Found at i:39604720 original size:39 final size:39
Alignment explanation
Indices: 39604663--39604738 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 39
39604653 TGTGGATACA
* *
39604663 AAGCGCGCTTACGAGGACGCGATTTGTTGCCACGTAGGC
1 AAGCGCGCTGACGAGGACGCGATTTATTGCCACGTAGGC
* * *
39604702 AAGCGTGCTGACGTGGACGCGTTTTATTGCCACGTAG
1 AAGCGCGCTGACGAGGACGCGATTTATTGCCACGTAG
39604739 CGCGCCCCTG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.20, C:0.24, G:0.33, T:0.24
Consensus pattern (39 bp):
AAGCGCGCTGACGAGGACGCGATTTATTGCCACGTAGGC
Found at i:39605184 original size:126 final size:125
Alignment explanation
Indices: 39604950--39605219 Score: 461
Period size: 126 Copynumber: 2.2 Consensus size: 125
39604940 GATAAAATCA
*
39604950 AAGCAGGATGCTTTATCAGAAGAATTTCTAAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATCAGAAGAATTTCTAAAATCACGCCCACGTGGACGCGCTTTTGCTACAGT
*
39605015 AGGTCCTGAAAAAATAATTTCGAGTTGACGTTTCAGAGAAAATAGTATAAAAAA-ACGCTTC
66 AGGTCCTAAAAAAATAATTTCGAGTTGACGTTTCAGAGAAAATAGTATAAAAAATA--CTTC
*
39605076 AAGCAGGATGCTTTATCAGAAGAATTTCTAAAATCACGCCTACGTGGACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATCAGAAGAATTTCTAAAATCACGCCCACGTGGACGCGCTTTTGCTACAGT
* * *
39605141 AGGTCTTAAAAAAATAATTTCGAGTTGACGTTTCTGAGTAAATAGTATAAAAAATACTTC
66 AGGTCCTAAAAAAATAATTTCGAGTTGACGTTTCAGAGAAAATAGTATAAAAAATACTTC
39605201 AAGCAGGATGCTTTATCAG
1 AAGCAGGATGCTTTATCAG
39605220 GATGCTTCAA
Statistics
Matches: 137, Mismatches: 6, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
125 23 0.17
126 113 0.82
127 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (125 bp):
AAGCAGGATGCTTTATCAGAAGAATTTCTAAAATCACGCCCACGTGGACGCGCTTTTGCTACAGT
AGGTCCTAAAAAAATAATTTCGAGTTGACGTTTCAGAGAAAATAGTATAAAAAATACTTC
Found at i:39605222 original size:13 final size:13
Alignment explanation
Indices: 39605202--39605242 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
39605192 AAATACTTCA
39605202 AGCAGGATGCTTT
1 AGCAGGATGCTTT
* *
39605215 ATCAGGATGCTTCA
1 AGCAGGATGCTT-T
39605229 AGCAGGATGCTTT
1 AGCAGGATGCTTT
39605242 A
1 A
39605243 AGTTAAGGGT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (13 bp):
AGCAGGATGCTTT
Found at i:39605236 original size:14 final size:14
Alignment explanation
Indices: 39605197--39605240 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
39605187 ATAAAAAATA
39605197 CTTCAAGCAGGATG
1 CTTCAAGCAGGATG
* *
39605211 CTT-TATCAGGATG
1 CTTCAAGCAGGATG
39605224 CTTCAAGCAGGATG
1 CTTCAAGCAGGATG
39605238 CTT
1 CTT
39605241 TAAGTTAAGG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
13 11 0.44
14 14 0.56
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (14 bp):
CTTCAAGCAGGATG
Found at i:39605280 original size:22 final size:21
Alignment explanation
Indices: 39605239--39605323 Score: 161
Period size: 21 Copynumber: 4.0 Consensus size: 21
39605229 AGCAGGATGC
39605239 TTTAAGTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
39605260 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
39605282 TTTAAGTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
39605303 TTTAAGTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
39605324 AGGGTTTTTT
Statistics
Matches: 63, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
21 42 0.67
22 21 0.33
ACGTcount: A:0.24, C:0.00, G:0.33, T:0.44
Consensus pattern (21 bp):
TTTAAGTTAAGGGTTAGGGTT
Found at i:39605300 original size:43 final size:42
Alignment explanation
Indices: 39605239--39605323 Score: 161
Period size: 43 Copynumber: 2.0 Consensus size: 42
39605229 AGCAGGATGC
39605239 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGG-TTAGGGTT
39605282 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTT
39605324 AGGGTTTTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 8 0.19
43 34 0.81
ACGTcount: A:0.24, C:0.00, G:0.33, T:0.44
Consensus pattern (42 bp):
TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTT
Found at i:39605361 original size:12 final size:12
Alignment explanation
Indices: 39605344--39605368 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39605334 AGGGTTTGTC
39605344 AATTAAATTATA
1 AATTAAATTATA
39605356 AATTAAATTATA
1 AATTAAATTATA
39605368 A
1 A
39605369 TTTATAAATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AATTAAATTATA
Found at i:39605906 original size:18 final size:18
Alignment explanation
Indices: 39605880--39605922 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
39605870 GACTCGAAAA
* * *
39605880 AGGAAACATATAAGGGTT
1 AGGATACATAAAAGGGCT
39605898 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
39605916 AGGATAC
1 AGGATAC
39605923 GCACCTGGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.28, T:0.19
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:39606579 original size:7 final size:7
Alignment explanation
Indices: 39606569--39606594 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
39606559 TTATATACAT
39606569 AATACTA
1 AATACTA
39606576 AATACTA
1 AATACTA
39606583 AATACTA
1 AATACTA
39606590 AATAC
1 AATAC
39606595 CAATCGACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
AATACTA
Found at i:39607822 original size:22 final size:22
Alignment explanation
Indices: 39607797--39607859 Score: 69
Period size: 22 Copynumber: 2.8 Consensus size: 22
39607787 AAATATGGAT
39607797 TTGAGAGAAATTTG-GAAGGAAA
1 TTGAGAGAAATTTGAG-AGGAAA
39607819 TTGAGAGCAAA-TTGAGAGGAAA
1 TTGAGAG-AAATTTGAGAGGAAA
39607841 TTGAGA-AAATAATTGAGAG
1 TTGAGAGAAAT--TTGAGAG
39607860 AGGATTAGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
20 3 0.08
22 22 0.61
23 11 0.31
ACGTcount: A:0.46, C:0.02, G:0.30, T:0.22
Consensus pattern (22 bp):
TTGAGAGAAATTTGAGAGGAAA
Found at i:39609258 original size:10 final size:9
Alignment explanation
Indices: 39609238--39609279 Score: 59
Period size: 10 Copynumber: 4.6 Consensus size: 9
39609228 ACTACTATTC
39609238 TTTTTACTT
1 TTTTTACTT
39609247 TTTTTAC-T
1 TTTTTACTT
39609255 TTTTTACTGT
1 TTTTTACT-T
39609265 TTTTTACTAT
1 TTTTTACT-T
39609275 TTTTT
1 TTTTT
39609280 TGTTGCTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
8 8 0.27
9 7 0.23
10 15 0.50
ACGTcount: A:0.12, C:0.10, G:0.02, T:0.76
Consensus pattern (9 bp):
TTTTTACTT
Found at i:39609283 original size:18 final size:18
Alignment explanation
Indices: 39609238--39609278 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
39609228 ACTACTATTC
39609238 TTTTTACT-TTTTTTACT
1 TTTTTACTGTTTTTTACT
39609255 TTTTTACTGTTTTTTACT
1 TTTTTACTGTTTTTTACT
39609273 ATTTTT
1 -TTTTT
39609279 TTGTTGCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 8 0.36
18 9 0.41
19 5 0.23
ACGTcount: A:0.12, C:0.10, G:0.02, T:0.76
Consensus pattern (18 bp):
TTTTTACTGTTTTTTACT
Found at i:39610562 original size:11 final size:11
Alignment explanation
Indices: 39610546--39610570 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
39610536 CACTGACATG
39610546 AAAATATTATT
1 AAAATATTATT
39610557 AAAATATTATT
1 AAAATATTATT
39610568 AAA
1 AAA
39610571 TAATTGAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
AAAATATTATT
Found at i:39612641 original size:19 final size:20
Alignment explanation
Indices: 39612604--39612641 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
39612594 ATTTAAATAA
**
39612604 TTAATTATTATTTTGATATT
1 TTAATTATTATTTACATATT
39612624 TTAATTA-TATTTACATAT
1 TTAATTATTATTTACATAT
39612642 ATGCAAATGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 9 0.56
20 7 0.44
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.61
Consensus pattern (20 bp):
TTAATTATTATTTACATATT
Found at i:39613192 original size:40 final size:40
Alignment explanation
Indices: 39613132--39613343 Score: 148
Period size: 35 Copynumber: 5.6 Consensus size: 40
39613122 AATCATCGTT
* *
39613132 GGTTCATCCAACTAGAGCTGGGCTCACTATTTATATCATC
1 GGTTTATCCGACTAGAGCTGGGCTCACTATTTATATCATC
* * *
39613172 GGTTTATCTGACTAGTGCTGGG-TGCA--A-ATAT-TGC-T-
1 GGTTTATCCGACTAGAGCTGGGCT-CACTATTTATAT-CATC
* *
39613207 AGTTTATCCAACTAGAGCTGGGCTCACTATTTATATCATC
1 GGTTTATCCGACTAGAGCTGGGCTCACTATTTATATCATC
* *
39613247 GGTTTATCCGACTAGTA-CTGGG-TGCA--A---ATATCGTT
1 GGTTTATCCGACTAG-AGCTGGGCT-CACTATTTATATCATC
* * * *
39613282 GGTTTATCCAACCAGAGCTGGGCTCACTAATTAT-TCGTC
1 GGTTTATCCGACTAGAGCTGGGCTCACTATTTATATCATC
* *
39613321 GGTATATCCGACTAGCGCTGGGC
1 GGTTTATCCGACTAGAGCTGGGC
39613344 GCAACTTCCG
Statistics
Matches: 133, Mismatches: 21, Indels: 37
0.70 0.11 0.19
Matches are distributed among these distances:
34 1 0.01
35 46 0.35
36 4 0.03
37 6 0.05
38 6 0.05
39 27 0.20
40 42 0.32
41 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.33
Consensus pattern (40 bp):
GGTTTATCCGACTAGAGCTGGGCTCACTATTTATATCATC
Found at i:39613219 original size:75 final size:75
Alignment explanation
Indices: 39613095--39613347 Score: 330
Period size: 75 Copynumber: 3.4 Consensus size: 75
39613085 ATTGATATTG
* * * * * *
39613095 TCGGTTCATCCGACTAGCGCTGGGCGC-AATCATCGTTGGTTCATCCAACTAGAGCTGGGCTCAC
1 TCGGTTTATCCGACTAGTGCTGGGTGCAAAT-ATCGCTAGTTTATCCAACTAGAGCTGGGCTCAC
39613159 TATTTATATCA
65 TATTTATATCA
* *
39613170 TCGGTTTATCTGACTAGTGCTGGGTGCAAATATTGCTAGTTTATCCAACTAGAGCTGGGCTCACT
1 TCGGTTTATCCGACTAGTGCTGGGTGCAAATATCGCTAGTTTATCCAACTAGAGCTGGGCTCACT
39613235 ATTTATATCA
66 ATTTATATCA
* * * *
39613245 TCGGTTTATCCGACTAGTACTGGGTGCAAATATCGTTGGTTTATCCAACCAGAGCTGGGCTCACT
1 TCGGTTTATCCGACTAGTGCTGGGTGCAAATATCGCTAGTTTATCCAACTAGAGCTGGGCTCACT
* *
39613310 AATTAT-TCG
66 ATTTATATCA
* * *
39613319 TCGGTATATCCGACTAGCGCTGGGCGCAA
1 TCGGTTTATCCGACTAGTGCTGGGTGCAA
39613348 CTTCCGTCAG
Statistics
Matches: 157, Mismatches: 20, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
74 27 0.17
75 127 0.81
76 3 0.02
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (75 bp):
TCGGTTTATCCGACTAGTGCTGGGTGCAAATATCGCTAGTTTATCCAACTAGAGCTGGGCTCACT
ATTTATATCA
Found at i:39613303 original size:35 final size:35
Alignment explanation
Indices: 39613097--39613303 Score: 107
Period size: 35 Copynumber: 5.6 Consensus size: 35
39613087 TGATATTGTC
* * * *
39613097 GGTTCATCCGACTAGCGCTGGGCGC-AATCATCGTT
1 GGTTTATCCAACTAGAGCTGGGTGCAAAT-ATCGTT
* * *
39613132 GGTTCATCCAACTAGAGCTGGGCT-CACTATTTATATCATC
1 GGTTTATCCAACTAGAGCTGGG-TGCA--A---ATATCGTT
** * * *
39613172 GGTTTATCTGACTAGTGCTGGGTGCAAATATTGCT
1 GGTTTATCCAACTAGAGCTGGGTGCAAATATCGTT
* * *
39613207 AGTTTATCCAACTAGAGCTGGGCT-CACTATTTATATCATC
1 GGTTTATCCAACTAGAGCTGGG-TGCA--A---ATATCGTT
*
39613247 GGTTTATCCGACTAGTA-CTGGGTGCAAATATCGTT
1 GGTTTATCCAACTAG-AGCTGGGTGCAAATATCGTT
*
39613282 GGTTTATCCAACCAGAGCTGGG
1 GGTTTATCCAACTAGAGCTGGG
39613304 CTCACTAATT
Statistics
Matches: 128, Mismatches: 27, Indels: 34
0.68 0.14 0.18
Matches are distributed among these distances:
34 1 0.01
35 69 0.54
36 1 0.01
37 1 0.01
38 3 0.02
39 2 0.02
40 48 0.38
41 3 0.02
ACGTcount: A:0.23, C:0.22, G:0.24, T:0.32
Consensus pattern (35 bp):
GGTTTATCCAACTAGAGCTGGGTGCAAATATCGTT
Found at i:39622768 original size:22 final size:22
Alignment explanation
Indices: 39622736--39622783 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
39622726 TAATATTATT
39622736 TTTATTATTTAAAT-ATAAAATA
1 TTTATTATTTAAATCAT-AAATA
* *
39622758 TTTATTTTTTATATCATAAATA
1 TTTATTATTTAAATCATAAATA
39622780 TTTA
1 TTTA
39622784 AAATAACAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 21 0.91
23 2 0.09
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (22 bp):
TTTATTATTTAAATCATAAATA
Found at i:39628906 original size:18 final size:19
Alignment explanation
Indices: 39628885--39628926 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 19
39628875 TTCTTAATTT
39628885 TTTTATAATTATTAAGGA-
1 TTTTATAATTATTAAGGAG
* *
39628903 TTTTA-AGTTATTTAGGAG
1 TTTTATAATTATTAAGGAG
39628921 TTTTAT
1 TTTTAT
39628927 GTTAACAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (19 bp):
TTTTATAATTATTAAGGAG
Found at i:39628919 original size:17 final size:18
Alignment explanation
Indices: 39628893--39628930 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
39628883 TTTTTTATAA
39628893 TTATTAAGGA-TTTTAAG
1 TTATTAAGGAGTTTTAAG
* *
39628910 TTATTTAGGAGTTTTATG
1 TTATTAAGGAGTTTTAAG
39628928 TTA
1 TTA
39628931 ACAAGAAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.29, C:0.00, G:0.18, T:0.53
Consensus pattern (18 bp):
TTATTAAGGAGTTTTAAG
Found at i:39629360 original size:17 final size:18
Alignment explanation
Indices: 39629340--39629376 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
39629330 ATTATTCTAA
*
39629340 TATTTTATTTA-TTATTT
1 TATTTTAGTTATTTATTT
39629357 TATTTTAGTTATTTATTT
1 TATTTTAGTTATTTATTT
39629375 TA
1 TA
39629377 ATTGTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (18 bp):
TATTTTAGTTATTTATTT
Found at i:39629363 original size:13 final size:13
Alignment explanation
Indices: 39629340--39629388 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
39629330 ATTATTCTAA
39629340 TATTTTA-TTTAT
1 TATTTTATTTTAT
39629352 TATTTTATTTTAGT
1 TATTTTATTTTA-T
39629366 TA-TTTATTTTAAT
1 TATTTTATTTT-AT
*
39629379 TGTTTTATTT
1 TATTTTATTT
39629389 GACTTGGATT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
12 7 0.22
13 14 0.44
14 11 0.34
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.73
Consensus pattern (13 bp):
TATTTTATTTTAT
Found at i:39634511 original size:47 final size:46
Alignment explanation
Indices: 39634460--39634550 Score: 110
Period size: 46 Copynumber: 2.0 Consensus size: 46
39634450 TTCTGGAAGT
* *
39634460 TTGGCTACAATTATAGTGGCCCGACCGCACATATCTGTTCTAGTAAC
1 TTGGCTACAA-TATAGTGGCCCGACCACACATATCTGATCTAGTAAC
* * ** *
39634507 TTGGCTGCAATATGGTGGCTTGACCACATATATCTGATCTAGTA
1 TTGGCTACAATATAGTGGCCCGACCACACATATCTGATCTAGTA
39634551 GTTTAACTGC
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
46 28 0.76
47 9 0.24
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (46 bp):
TTGGCTACAATATAGTGGCCCGACCACACATATCTGATCTAGTAAC
Found at i:39646094 original size:21 final size:21
Alignment explanation
Indices: 39646068--39646137 Score: 86
Period size: 21 Copynumber: 3.3 Consensus size: 21
39646058 TGTAACTCGG
*
39646068 TCACACGGGCGTGTGCCTCTT
1 TCACACGGGTGTGTGCCTCTT
* *
39646089 TCACACGGGTGTGTGCTTCGT
1 TCACACGGGTGTGTGCCTCTT
* *
39646110 TCATATGGGTGTGTGCCTCTT
1 TCACACGGGTGTGTGCCTCTT
*
39646131 TTACACG
1 TCACACG
39646138 TCCATGTCGA
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.11, C:0.26, G:0.29, T:0.34
Consensus pattern (21 bp):
TCACACGGGTGTGTGCCTCTT
Found at i:39656985 original size:30 final size:32
Alignment explanation
Indices: 39656949--39657010 Score: 101
Period size: 30 Copynumber: 2.0 Consensus size: 32
39656939 ATAAATTATA
*
39656949 AAAAATATTAATTAA-ATTAAAAAA-TGAAAT
1 AAAAATATTAAATAATATTAAAAAAGTGAAAT
39656979 AAAAATATTAAATAATATTAAAAAAGTGAAAT
1 AAAAATATTAAATAATATTAAAAAAGTGAAAT
39657011 TAACCCTTAC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 14 0.48
31 9 0.31
32 6 0.21
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (32 bp):
AAAAATATTAAATAATATTAAAAAAGTGAAAT
Found at i:39658657 original size:31 final size:31
Alignment explanation
Indices: 39658619--39658682 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
39658609 CGATCCTTTT
39658619 TGATGAGGTGTGATCGGATCACCTCGAAAAG
1 TGATGAGGTGTGATCGGATCACCTCGAAAAG
39658650 TGATGAGGTGTGATCGGATCACCTCGAAAAG
1 TGATGAGGTGTGATCGGATCACCTCGAAAAG
39658681 TG
1 TG
39658683 GTTGTTTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.28, C:0.16, G:0.33, T:0.23
Consensus pattern (31 bp):
TGATGAGGTGTGATCGGATCACCTCGAAAAG
Found at i:39659193 original size:40 final size:37
Alignment explanation
Indices: 39659149--39659264 Score: 153
Period size: 39 Copynumber: 3.0 Consensus size: 37
39659139 AATAAATATA
* *
39659149 TTTATTTTTTTAACTTTAAAATATTTTTTACATACTTTTT
1 TTTATTTTTTTAATTTTAAAATATTTTTT---TAATTTTT
39659189 TTTATTTTTTTAATTTTAAAAT-TTTTTTTAATTTTT
1 TTTATTTTTTTAATTTTAAAATATTTTTTTAATTTTT
*
39659225 TTAATTTTTTTAATTTTTAAAATACTTTTTTTAATTTTT
1 TTTATTTTTTTAA-TTTTAAAATA-TTTTTTTAATTTTT
39659264 T
1 T
39659265 AAAAATTTTA
Statistics
Matches: 70, Mismatches: 3, Indels: 7
0.88 0.04 0.09
Matches are distributed among these distances:
36 19 0.27
37 9 0.13
39 21 0.30
40 21 0.30
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (37 bp):
TTTATTTTTTTAATTTTAAAATATTTTTTTAATTTTT
Found at i:39659198 original size:9 final size:9
Alignment explanation
Indices: 39659184--39659242 Score: 75
Period size: 9 Copynumber: 6.6 Consensus size: 9
39659174 TTTTACATAC
*
39659184 TTTTTTTTA
1 TTTTTTTAA
39659193 TTTTTTTAA
1 TTTTTTTAA
**
39659202 -TTTTAAAA
1 TTTTTTTAA
39659210 TTTTTTTTAA
1 -TTTTTTTAA
39659220 TTTTTTTAA
1 TTTTTTTAA
39659229 TTTTTTTAA
1 TTTTTTTAA
39659238 TTTTT
1 TTTTT
39659243 AAAATACTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
8 6 0.14
9 31 0.72
10 6 0.14
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTTTTTAA
Found at i:39659214 original size:18 final size:19
Alignment explanation
Indices: 39659193--39659273 Score: 94
Period size: 18 Copynumber: 4.2 Consensus size: 19
39659183 CTTTTTTTTA
39659193 TTTTTTTAA-TTTTAAAAT
1 TTTTTTTAATTTTTAAAAT
**
39659211 TTTTTTTAATTTTTTTAA-
1 TTTTTTTAATTTTTAAAAT
39659229 TTTTTTTAATTTTTAAAAT
1 TTTTTTTAATTTTTAAAAT
39659248 ACTTTTTTTAATTTTTTAAAAAT
1 --TTTTTTTAA-TTTTT-AAAAT
39659271 TTT
1 TTT
39659274 AAAATAAAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
18 25 0.47
19 6 0.11
21 12 0.23
22 5 0.09
23 5 0.09
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTTTTTAATTTTTAAAAT
Found at i:39659264 original size:31 final size:30
Alignment explanation
Indices: 39659220--39659279 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
39659210 TTTTTTTTAA
** *
39659220 TTTTTTTAATTTTTTTAATTTTTAAAATAC
1 TTTTTTTAATTTTTAAAAATTTTAAAATAC
39659250 TTTTTTTAATTTTTTAAAAATTTTAAAATA
1 TTTTTTTAA-TTTTTAAAAATTTTAAAATA
39659280 AAAATGGGCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 9 0.35
31 17 0.65
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (30 bp):
TTTTTTTAATTTTTAAAAATTTTAAAATAC
Found at i:39660091 original size:9 final size:9
Alignment explanation
Indices: 39660079--39660107 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
39660069 GTATATAGAT
39660079 TATAAAATA
1 TATAAAATA
39660088 TATAAAATA
1 TATAAAATA
39660097 TATAAAATA
1 TATAAAATA
39660106 TA
1 TA
39660108 AGTATATACG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (9 bp):
TATAAAATA
Found at i:39660446 original size:3 final size:3
Alignment explanation
Indices: 39660432--39660473 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
39660422 CAAATAAAAC
* *
39660432 TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
39660474 ATGCTAATAC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:39663424 original size:22 final size:22
Alignment explanation
Indices: 39663399--39663619 Score: 273
Period size: 22 Copynumber: 10.0 Consensus size: 22
39663389 CCAACATTCA
* *
39663399 GACAACATTTAATTAACATTTG
1 GACAACATTTAATCAACAATTG
39663421 GACAACATTTAATCAACAATTG
1 GACAACATTTAATCAACAATTG
* * *
39663443 GACAGCATTAAATTAAC-ATGTG
1 GACAACATTTAATCAACAAT-TG
*
39663465 GACAGCATTTAATCAACAATTG
1 GACAACATTTAATCAACAATTG
* * *
39663487 GACAACATTAAATCAATATTTG
1 GACAACATTTAATCAACAATTG
39663509 GACAACATTTAATCAACAATTG
1 GACAACATTTAATCAACAATTG
* * *
39663531 GACATCATTAAATCAACATTTG
1 GACAACATTTAATCAACAATTG
*
39663553 GACAGCATTTAATCAACAATTG
1 GACAACATTTAATCAACAATTG
* * * *
39663575 GACAGCATTCAATCAATATTTG
1 GACAACATTTAATCAACAATTG
39663597 GACAACATTTAATCAACAATTG
1 GACAACATTTAATCAACAATTG
39663619 G
1 G
39663620 CACTAAACCA
Statistics
Matches: 170, Mismatches: 27, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
21 2 0.01
22 166 0.98
23 2 0.01
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.29
Consensus pattern (22 bp):
GACAACATTTAATCAACAATTG
Found at i:39663457 original size:44 final size:44
Alignment explanation
Indices: 39663399--39663619 Score: 334
Period size: 44 Copynumber: 5.0 Consensus size: 44
39663389 CCAACATTCA
* *
39663399 GACAACATTTAATTAACATTTGGACAACATTTAATCAACAATTG
1 GACAACATTAAATCAACATTTGGACAACATTTAATCAACAATTG
* * * *
39663443 GACAGCATTAAATTAACATGTGGACAGCATTTAATCAACAATTG
1 GACAACATTAAATCAACATTTGGACAACATTTAATCAACAATTG
*
39663487 GACAACATTAAATCAATATTTGGACAACATTTAATCAACAATTG
1 GACAACATTAAATCAACATTTGGACAACATTTAATCAACAATTG
* *
39663531 GACATCATTAAATCAACATTTGGACAGCATTTAATCAACAATTG
1 GACAACATTAAATCAACATTTGGACAACATTTAATCAACAATTG
* * *
39663575 GACAGCATTCAATCAATATTTGGACAACATTTAATCAACAATTG
1 GACAACATTAAATCAACATTTGGACAACATTTAATCAACAATTG
39663619 G
1 G
39663620 CACTAAACCA
Statistics
Matches: 161, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 161 1.00
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.29
Consensus pattern (44 bp):
GACAACATTAAATCAACATTTGGACAACATTTAATCAACAATTG
Found at i:39663493 original size:88 final size:88
Alignment explanation
Indices: 39663399--39663619 Score: 370
Period size: 88 Copynumber: 2.5 Consensus size: 88
39663389 CCAACATTCA
* * * *
39663399 GACAACATTTAATTAACATTTGGACAACATTTAATCAACAATTGGACAGCATTAAATTAACATGT
1 GACAACATTAAATCAATATTTGGACAACATTTAATCAACAATTGGACAGCATTAAATCAACATGT
39663464 GGACAGCATTTAATCAACAATTG
66 GGACAGCATTTAATCAACAATTG
* *
39663487 GACAACATTAAATCAATATTTGGACAACATTTAATCAACAATTGGACATCATTAAATCAACATTT
1 GACAACATTAAATCAATATTTGGACAACATTTAATCAACAATTGGACAGCATTAAATCAACATGT
39663552 GGACAGCATTTAATCAACAATTG
66 GGACAGCATTTAATCAACAATTG
* *
39663575 GACAGCATTCAATCAATATTTGGACAACATTTAATCAACAATTGG
1 GACAACATTAAATCAATATTTGGACAACATTTAATCAACAATTGG
39663620 CACTAAACCA
Statistics
Matches: 125, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
88 125 1.00
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.29
Consensus pattern (88 bp):
GACAACATTAAATCAATATTTGGACAACATTTAATCAACAATTGGACAGCATTAAATCAACATGT
GGACAGCATTTAATCAACAATTG
Found at i:39663769 original size:42 final size:40
Alignment explanation
Indices: 39663722--39663835 Score: 111
Period size: 42 Copynumber: 2.8 Consensus size: 40
39663712 CGCTATTGAC
39663722 AACGCCGCTAAAGGTCATGTTCTTTAGCGGTGCTACGAAAAA
1 AACGCCGCTAAAGGTCATGTTCTTTAGCGGT-CTAC-AAAAA
* * * * * ** *
39663764 AACGCCGCTAAAAGTCAGGGTCTTTAGCTGCGTTTTCCTACA
1 AACGCCGCTAAAGGTCATGTTCTTTAGC-G-GTCTACAAAAA
*
39663806 AACGCCGCTAAAGGTCATGTTCTCTAGCGG
1 AACGCCGCTAAAGGTCATGTTCTTTAGCGG
39663836 CGCTTTTTCA
Statistics
Matches: 58, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
40 1 0.02
41 1 0.02
42 51 0.88
43 3 0.05
44 2 0.03
ACGTcount: A:0.26, C:0.25, G:0.24, T:0.25
Consensus pattern (40 bp):
AACGCCGCTAAAGGTCATGTTCTTTAGCGGTCTACAAAAA
Found at i:39663858 original size:43 final size:43
Alignment explanation
Indices: 39663722--39663984 Score: 257
Period size: 43 Copynumber: 6.2 Consensus size: 43
39663712 CGCTATTGAC
* **** *
39663722 AACGCCGCTAAAGGTCATGTTCTTTAGCGGTGC-TACGAAAAA
1 AACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTTCAACA
* * * * * *
39663764 AACGCCGCTAAAAGTCAGGGTCTTTAGCTGCG-TTTTCCTACA
1 AACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTTCAACA
*
39663806 AACGCCGCTAAAGGTCATGTTCTCTAGCGGCGCTTTTTCAACA
1 AACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTTCAACA
** * *
39663849 AACGCCGCTAAAGAACATGTTCCTTAGCGGCGCTTTTTCCACA
1 AACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTTCAACA
* * **
39663892 AACGCCGCTAAAGATCATGTTCTTTAACGGCG-TTTCTTCCGCA
1 AACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTT-TTCAACA
* *
39663935 AACGCCACTAAAGGTCATGTTCTTTTAGCGGC-ATTTTT-ACACA
1 AACGCCGCTAAAGGTCATGTTC-TTTAGCGGCGCTTTTTCA-ACA
39663978 AACGCCG
1 AACGCCG
39663985 TTATTTCTTT
Statistics
Matches: 182, Mismatches: 33, Indels: 11
0.81 0.15 0.05
Matches are distributed among these distances:
42 60 0.33
43 111 0.61
44 11 0.06
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.27
Consensus pattern (43 bp):
AACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTTCAACA
Found at i:39664446 original size:21 final size:21
Alignment explanation
Indices: 39664422--39664472 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
39664412 TTCTTTTGAA
* *
39664422 CCTCTGCTTCTCTTGCTGCAG
1 CCTCTGCTTCCCTCGCTGCAG
*
39664443 CCTCTGCTTCCCTCGCTGCCG
1 CCTCTGCTTCCCTCGCTGCAG
*
39664464 CCTATGCTT
1 CCTCTGCTT
39664473 TAAGTTGTAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.04, C:0.43, G:0.18, T:0.35
Consensus pattern (21 bp):
CCTCTGCTTCCCTCGCTGCAG
Done.