Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D07
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: 58101237
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1550000 characters in sequence are not A, C, G, or T
File 141 of 199
Found at i:41241211 original size:40 final size:40
Alignment explanation
Indices: 41241029--41241251 Score: 234
Period size: 40 Copynumber: 5.6 Consensus size: 40
41241019 TCCTCGTTCA
* * * * *
41241029 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
41241068 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
41241108 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
41241148 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* ** * * * * * *
41241188 AAGGCCTTC-GGATCTTAGTCCGGATATATTCATTAGCACC
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAACTCGCACG
* *
41241228 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
41241252 CAGCATTCAA
Statistics
Matches: 159, Mismatches: 22, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
39 37 0.23
40 119 0.75
41 3 0.02
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:41252693 original size:1 final size:1
Alignment explanation
Indices: 41252689--41252713 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
41252679 AATTGAATAC
41252689 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
41252714 TTGCATACGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:41253764 original size:20 final size:20
Alignment explanation
Indices: 41253734--41253779 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 20
41253724 AATCTTGAAT
41253734 GAAATTGAGAGAAGAAA-AAAA
1 GAAA-TGAGAGAA-AAAGAAAA
41253755 GAAATGAGAGAAAAAGAAAA
1 GAAATGAGAGAAAAAGAAAA
41253775 GAAAT
1 GAAAT
41253780 AAAATAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.12
20 17 0.71
21 4 0.17
ACGTcount: A:0.67, C:0.00, G:0.24, T:0.09
Consensus pattern (20 bp):
GAAATGAGAGAAAAAGAAAA
Found at i:41253788 original size:20 final size:20
Alignment explanation
Indices: 41253751--41253791 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
41253741 AGAGAAGAAA
* *
41253751 AAAAGAAATGAGAGAAAAAG
1 AAAAGAAATAAAAGAAAAAG
*
41253771 AAAAGAAATAAAATAAAAAG
1 AAAAGAAATAAAAGAAAAAG
41253791 A
1 A
41253792 TGAAAATGAG
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:0.76, C:0.00, G:0.17, T:0.07
Consensus pattern (20 bp):
AAAAGAAATAAAAGAAAAAG
Found at i:41258484 original size:10 final size:10
Alignment explanation
Indices: 41258469--41258506 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
41258459 GCTCGTTTCC
*
41258469 AGCTCACTCG
1 AGCTCAATCG
41258479 AGCTCAAGTC-
1 AGCTCAA-TCG
41258489 AGCTCAATCG
1 AGCTCAATCG
41258499 AGCTCAAT
1 AGCTCAAT
41258507 TTAGCTACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (10 bp):
AGCTCAATCG
Found at i:41258493 original size:20 final size:20
Alignment explanation
Indices: 41258468--41258505 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
41258458 AGCTCGTTTC
*
41258468 CAGCTCACTCGAGCTCAAGT
1 CAGCTCAATCGAGCTCAAGT
41258488 CAGCTCAATCGAGCTCAA
1 CAGCTCAATCGAGCTCAA
41258506 TTTAGCTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.34, G:0.18, T:0.18
Consensus pattern (20 bp):
CAGCTCAATCGAGCTCAAGT
Found at i:41258512 original size:20 final size:20
Alignment explanation
Indices: 41258469--41258529 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
41258459 GCTCGTTTCC
* * *
41258469 AGCTCACTCGAGCTCAAGTC
1 AGCTCAATCGAGCTCAATTT
41258489 AGCTCAATCGAGCTCAATTT
1 AGCTCAATCGAGCTCAATTT
41258509 AGCTACAATTC-AGCTC-ATTT
1 AGCT-CAA-TCGAGCTCAATTT
41258529 A
1 A
41258530 TTTTATTGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 26 0.72
21 8 0.22
22 2 0.06
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (20 bp):
AGCTCAATCGAGCTCAATTT
Found at i:41258523 original size:11 final size:10
Alignment explanation
Indices: 41258479--41258525 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
41258469 AGCTCACTCG
*
41258479 AGCTCAAGTC
1 AGCTCAATTC
41258489 AGCTCAA-TC
1 AGCTCAATTC
*
41258498 GAGCTCAATTT
1 -AGCTCAATTC
41258509 AGCTACAATTC
1 AGCT-CAATTC
41258520 AGCTCA
1 AGCTCA
41258526 TTTATTTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 2 0.06
10 20 0.62
11 10 0.31
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.26
Consensus pattern (10 bp):
AGCTCAATTC
Found at i:41259920 original size:13 final size:13
Alignment explanation
Indices: 41259904--41259981 Score: 61
Period size: 12 Copynumber: 5.7 Consensus size: 13
41259894 CAAAAAAAAT
41259904 AAAAAAAAATTCG
1 AAAAAAAAATTCG
*
41259917 AAAAAAAAAATTGATTG
1 -AAAAAAAAA-T--TCG
41259934 AAAAAAAAATTC-
1 AAAAAAAAATTCG
*
41259946 AAAAAAAAAGT-G
1 AAAAAAAAATTCG
*
41259958 AAAAAAAAAATCG
1 AAAAAAAAATTCG
41259971 AGCAAAAAAAA
1 A--AAAAAAAA
41259982 AAAAAGGTGA
Statistics
Matches: 53, Mismatches: 4, Indels: 13
0.76 0.06 0.19
Matches are distributed among these distances:
12 20 0.38
13 3 0.06
14 9 0.17
15 10 0.19
16 9 0.17
17 2 0.04
ACGTcount: A:0.73, C:0.05, G:0.09, T:0.13
Consensus pattern (13 bp):
AAAAAAAAATTCG
Found at i:41259921 original size:14 final size:14
Alignment explanation
Indices: 41259904--41259982 Score: 69
Period size: 13 Copynumber: 5.6 Consensus size: 14
41259894 CAAAAAAAAT
41259904 AAAAAAAAATTCGA
1 AAAAAAAAATTCGA
41259918 AAAAAAAAATT-GA
1 AAAAAAAAATTCGA
41259931 TTGAAAAAAAAATTC--
1 ---AAAAAAAAATTCGA
*
41259946 AAAAAAAAAGT-GA
1 AAAAAAAAATTCGA
41259959 AAAAAAAAA-TCGA
1 AAAAAAAAATTCGA
41259972 GCAAAAAAAAA
1 --AAAAAAAAA
41259983 AAAAGGTGAC
Statistics
Matches: 55, Mismatches: 1, Indels: 17
0.75 0.01 0.23
Matches are distributed among these distances:
12 11 0.20
13 13 0.24
14 11 0.20
15 9 0.16
16 11 0.20
ACGTcount: A:0.73, C:0.05, G:0.09, T:0.13
Consensus pattern (14 bp):
AAAAAAAAATTCGA
Found at i:41259979 original size:41 final size:40
Alignment explanation
Indices: 41259895--41259983 Score: 110
Period size: 41 Copynumber: 2.2 Consensus size: 40
41259885 TTGGAGTAAC
* *
41259895 AAAAAAAATAAAAAAAAATTCGAAAAAAAAAATTGATTG-AA
1 AAAAAAAATAAAAAAAAAGTCGAAAAAAAAAATCGA--GCAA
*
41259936 AAAAAAATTCAAAAAAAAAGT-GAAAAAAAAAATCGAGCAA
1 AAAAAAAAT-AAAAAAAAAGTCGAAAAAAAAAATCGAGCAA
41259976 AAAAAAAA
1 AAAAAAAA
41259984 AAAGGTGACC
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
39 1 0.02
40 9 0.21
41 22 0.52
42 10 0.24
ACGTcount: A:0.75, C:0.04, G:0.08, T:0.12
Consensus pattern (40 bp):
AAAAAAAATAAAAAAAAAGTCGAAAAAAAAAATCGAGCAA
Found at i:41260013 original size:34 final size:32
Alignment explanation
Indices: 41259946--41260015 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
41259936 AAAAAAATTC
*
41259946 AAAAAAAAAGTGAAAAAAAAAATCGAGCAAAA
1 AAAAAAAAAGTGAAAAAAAAAATCAAGCAAAA
* **
41259978 AAAAAAAAAGGTGACCAAAAAAAATCAAGTTAAA
1 AAAAAAAAA-GTGA-AAAAAAAAATCAAGCAAAA
41260012 AAAA
1 AAAA
41260016 GTGAAAAGTC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 9 0.28
33 4 0.12
34 19 0.59
ACGTcount: A:0.73, C:0.07, G:0.11, T:0.09
Consensus pattern (32 bp):
AAAAAAAAAGTGAAAAAAAAAATCAAGCAAAA
Found at i:41260993 original size:18 final size:18
Alignment explanation
Indices: 41260955--41260996 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
41260945 AAATCGAAAG
* **
41260955 AAAAGAAAAAGAGATTGA
1 AAAAGAAAAAGAAATCCA
41260973 AAAAGAAAAAGAAATCCA
1 AAAAGAAAAAGAAATCCA
41260991 AAAAGA
1 AAAAGA
41260997 GAGTGAGGTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.71, C:0.05, G:0.17, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAATCCA
Found at i:41261061 original size:33 final size:34
Alignment explanation
Indices: 41261024--41261088 Score: 80
Period size: 33 Copynumber: 1.9 Consensus size: 34
41261014 AAAGTGAAAA
*
41261024 TGAGA-GAGGAAATGAAA-AGAGAAAAAGAGAAGT
1 TGAGATGA-GAAAAGAAACAGAGAAAAAGAGAAGT
*
41261057 TGAGATTAGAAAAGAAACGAGAGAAAAAGAGA
1 TGAGATGAGAAAAGAAAC-AGAGAAAAAGAGA
41261089 TAAACGAACC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 13 0.48
34 1 0.04
35 13 0.48
ACGTcount: A:0.58, C:0.02, G:0.31, T:0.09
Consensus pattern (34 bp):
TGAGATGAGAAAAGAAACAGAGAAAAAGAGAAGT
Found at i:41262709 original size:10 final size:10
Alignment explanation
Indices: 41262694--41262731 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
41262684 GCTCGTTTCC
*
41262694 AGCTCACTCG
1 AGCTCAATCG
41262704 AGCTCAAGTC-
1 AGCTCAA-TCG
41262714 AGCTCAATCG
1 AGCTCAATCG
41262724 AGCTCAAT
1 AGCTCAAT
41262732 TTAGCTACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (10 bp):
AGCTCAATCG
Found at i:41262718 original size:20 final size:20
Alignment explanation
Indices: 41262693--41262730 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
41262683 AGCTCGTTTC
*
41262693 CAGCTCACTCGAGCTCAAGT
1 CAGCTCAATCGAGCTCAAGT
41262713 CAGCTCAATCGAGCTCAA
1 CAGCTCAATCGAGCTCAA
41262731 TTTAGCTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.34, G:0.18, T:0.18
Consensus pattern (20 bp):
CAGCTCAATCGAGCTCAAGT
Found at i:41262737 original size:20 final size:20
Alignment explanation
Indices: 41262694--41262754 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
41262684 GCTCGTTTCC
* * *
41262694 AGCTCACTCGAGCTCAAGTC
1 AGCTCAATCGAGCTCAATTT
41262714 AGCTCAATCGAGCTCAATTT
1 AGCTCAATCGAGCTCAATTT
41262734 AGCTACAATTC-AGCTC-ATTT
1 AGCT-CAA-TCGAGCTCAATTT
41262754 A
1 A
41262755 TTTTATTGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 26 0.72
21 8 0.22
22 2 0.06
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (20 bp):
AGCTCAATCGAGCTCAATTT
Found at i:41262748 original size:11 final size:10
Alignment explanation
Indices: 41262704--41262750 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
41262694 AGCTCACTCG
*
41262704 AGCTCAAGTC
1 AGCTCAATTC
41262714 AGCTCAA-TC
1 AGCTCAATTC
*
41262723 GAGCTCAATTT
1 -AGCTCAATTC
41262734 AGCTACAATTC
1 AGCT-CAATTC
41262745 AGCTCA
1 AGCTCA
41262751 TTTATTTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 2 0.06
10 20 0.62
11 10 0.31
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.26
Consensus pattern (10 bp):
AGCTCAATTC
Found at i:41264360 original size:18 final size:20
Alignment explanation
Indices: 41264316--41264365 Score: 68
Period size: 18 Copynumber: 2.5 Consensus size: 20
41264306 CTCGTATCAA
41264316 TCTCTTTTTGCTATTTTTCAT
1 TCTCTTTTT-CTATTTTTCAT
*
41264337 TCTCTTTTTCT-TTTTTGAT
1 TCTCTTTTTCTATTTTTCAT
41264356 T-TCTTTTTCT
1 TCTCTTTTTCT
41264366 GTCTTTCTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 9 0.32
19 8 0.29
20 2 0.07
21 9 0.32
ACGTcount: A:0.06, C:0.18, G:0.04, T:0.72
Consensus pattern (20 bp):
TCTCTTTTTCTATTTTTCAT
Found at i:41269812 original size:30 final size:30
Alignment explanation
Indices: 41269778--41269874 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
41269768 AGCTCACTCC
41269778 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
41269808 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
41269838 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
41269868 TAGCTCA
1 TAGCTCA
41269875 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:41272190 original size:11 final size:10
Alignment explanation
Indices: 41272165--41272225 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
41272155 ACCAATAAAA
41272165 TAAA-TGAGC
1 TAAATTGAGC
*
41272174 TGAATTGTAGC
1 TAAATTG-AGC
41272185 TAAATTGAGC
1 TAAATTGAGC
**
41272195 TCGATTGAGC
1 TAAATTGAGC
41272205 TGAAA-TGAGC
1 T-AAATTGAGC
*
41272215 TCAATTGAGC
1 TAAATTGAGC
41272225 T
1 T
41272226 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:41272226 original size:20 final size:20
Alignment explanation
Indices: 41272166--41272226 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
41272156 CCAATAAAAT
*
41272166 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
41272186 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
41272207 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
41272227 GTCGGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:41274390 original size:20 final size:20
Alignment explanation
Indices: 41274367--41274420 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
41274357 AGTTTTTCCC
*
41274367 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
41274387 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
41274407 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
41274421 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:41274402 original size:30 final size:30
Alignment explanation
Indices: 41274367--41274440 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
41274357 AGTTTTTCCC
41274367 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
41274397 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
41274427 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
41274441 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:41274430 original size:20 final size:20
Alignment explanation
Indices: 41274367--41274431 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
41274357 AGTTTTTCCC
* * * *
41274367 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
41274387 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
41274406 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
41274427 AGCTC
1 AGCTC
41274432 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:41276049 original size:13 final size:13
Alignment explanation
Indices: 41276031--41276103 Score: 76
Period size: 13 Copynumber: 5.5 Consensus size: 13
41276021 TTGGAGTAAC
41276031 AAAAAAAA-TCAA
1 AAAAAAAATTCAA
*
41276043 AAAAAAAATTCGA
1 AAAAAAAATTCAA
* *
41276056 AAAAAAAATTGATTG
1 AAAAAAAATTCA--A
41276071 AAAAAAAATTCAA
1 AAAAAAAATTCAA
* *
41276084 AAAAAAAAGTGAA
1 AAAAAAAATTCAA
41276097 AAAAAAA
1 AAAAAAA
41276104 TCGAGCAAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
12 8 0.16
13 31 0.62
15 11 0.22
ACGTcount: A:0.75, C:0.04, G:0.07, T:0.14
Consensus pattern (13 bp):
AAAAAAAATTCAA
Found at i:41276102 original size:28 final size:28
Alignment explanation
Indices: 41276041--41276103 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
41276031 AAAAAAAATC
* * *
41276041 AAAAAAAAAATTCGAAAAAAAAATTGAT
1 AAAAAAAAAATTCAAAAAAAAAAGTGAA
**
41276069 TGAAAAAAAATTCAAAAAAAAAAGTGAA
1 AAAAAAAAAATTCAAAAAAAAAAGTGAA
41276097 AAAAAAA
1 AAAAAAA
41276104 TCGAGCAAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.75, C:0.03, G:0.08, T:0.14
Consensus pattern (28 bp):
AAAAAAAAAATTCAAAAAAAAAAGTGAA
Found at i:41276112 original size:28 final size:28
Alignment explanation
Indices: 41276081--41276154 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 28
41276071 AAAAAAAATT
*
41276081 CAAAAAAAAAAGTGAAAAAAAAATCGAG
1 CAAAAAAAAAAGTGAAAAAAAAATCAAG
* *
41276109 CAAAAAAAAAGGTGACCAAAAAAATCAAG
1 CAAAAAAAAAAGTGA-AAAAAAAATCAAG
**
41276138 -TTAAAAAAAAGTGAAAA
1 CAAAAAAAAAAGTGAAAA
41276155 GTCTTGCGAG
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
27 2 0.05
28 25 0.66
29 11 0.29
ACGTcount: A:0.69, C:0.08, G:0.14, T:0.09
Consensus pattern (28 bp):
CAAAAAAAAAAGTGAAAAAAAAATCAAG
Found at i:41276115 original size:40 final size:40
Alignment explanation
Indices: 41276031--41276118 Score: 117
Period size: 41 Copynumber: 2.2 Consensus size: 40
41276021 TTGGAGTAAC
* *
41276031 AAAAAAAATCAAAAAAAAAATTCGAAAAAAAAATTGATTG-A
1 AAAAAAAATCAAAAAAAAAAGTCGAAAAAAAAATCGA--GCA
*
41276072 AAAAAAATTCAAAAAAAAAAGT-GAAAAAAAAATCGAGCA
1 AAAAAAAATCAAAAAAAAAAGTCGAAAAAAAAATCGAGCA
41276111 AAAAAAAA
1 AAAAAAAA
41276119 GGTGACCAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
38 1 0.02
39 8 0.19
40 13 0.31
41 20 0.48
ACGTcount: A:0.74, C:0.06, G:0.08, T:0.12
Consensus pattern (40 bp):
AAAAAAAATCAAAAAAAAAAGTCGAAAAAAAAATCGAGCA
Found at i:41276129 original size:29 final size:28
Alignment explanation
Indices: 41276081--41276154 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 28
41276071 AAAAAAAATT
* *
41276081 CAAAAAAAAAAGTGAAAAAAAAATCGAG
1 CAAAAAAAAAGGTGAAAAAAAAATCAAG
*
41276109 CAAAAAAAAAGGTGACCAAAAAAATCAAG
1 CAAAAAAAAAGGTGA-AAAAAAAATCAAG
**
41276138 TTAAAAAAAA-GTGAAAA
1 CAAAAAAAAAGGTGAAAA
41276155 GTCTTGCGAG
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
27 2 0.05
28 18 0.46
29 19 0.49
ACGTcount: A:0.69, C:0.08, G:0.14, T:0.09
Consensus pattern (28 bp):
CAAAAAAAAAGGTGAAAAAAAAATCAAG
Found at i:41277076 original size:15 final size:16
Alignment explanation
Indices: 41277056--41277087 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
41277046 AGAAAATGAA
41277056 AAAGAAAAAGAA-ATG
1 AAAGAAAAAGAAGATG
41277071 AAAGAAAAAGAAGATG
1 AAAGAAAAAGAAGATG
41277087 A
1 A
41277088 GTGTGAGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (16 bp):
AAAGAAAAAGAAGATG
Found at i:41277202 original size:17 final size:18
Alignment explanation
Indices: 41277170--41277203 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41277160 AAAAGAGAGT
*
41277170 GAGATTGAAGGAAGAAAC
1 GAGAGTGAAGGAAGAAAC
41277188 GAGAGTGAA-GAAGAAA
1 GAGAGTGAAGGAAGAAA
41277204 GGAGTGTTGT
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:0.53, C:0.03, G:0.35, T:0.09
Consensus pattern (18 bp):
GAGAGTGAAGGAAGAAAC
Found at i:41278492 original size:20 final size:20
Alignment explanation
Indices: 41278469--41278522 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
41278459 AGTTTTTCCC
*
41278469 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
41278489 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
41278509 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
41278523 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:41278504 original size:30 final size:30
Alignment explanation
Indices: 41278469--41278542 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
41278459 AGTTTTTCCC
41278469 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
41278499 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
41278529 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
41278543 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:41278532 original size:20 final size:20
Alignment explanation
Indices: 41278469--41278533 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
41278459 AGTTTTTCCC
* * * *
41278469 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
41278489 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
41278508 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
41278529 AGCTC
1 AGCTC
41278534 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:41280087 original size:21 final size:21
Alignment explanation
Indices: 41280058--41280113 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
41280048 CAAGCTATCT
*
41280058 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
41280079 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
41280100 TTCATTTTCTTTTT
1 TTCATTTTCTTTTT
41280114 CTCTCACTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (21 bp):
TTCATTTTCTTTTTTCCTTTC
Found at i:41280106 original size:14 final size:14
Alignment explanation
Indices: 41280057--41280113 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
41280047 TCAAGCTATC
41280057 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
41280070 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
41280084 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
41280098 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
41280112 TT
1 TT
41280114 CTCTCACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.17
14 26 0.72
15 4 0.11
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTCAATTTTCTTT
Found at i:41280141 original size:18 final size:18
Alignment explanation
Indices: 41280120--41280178 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 18
41280110 TTTTCTCTCA
41280120 CTTTTTCGATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
* *
41280138 CTTTTGCAATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
* *
41280156 CTTCTTCGTTTTCTTTTT
1 CTTTTTCGATTTCTTTTT
*
41280174 GTTTT
1 CTTTT
41280179 CTTTCAATTT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.05, C:0.17, G:0.07, T:0.71
Consensus pattern (18 bp):
CTTTTTCGATTTCTTTTT
Found at i:41280195 original size:6 final size:6
Alignment explanation
Indices: 41280075--41280182 Score: 65
Period size: 6 Copynumber: 17.7 Consensus size: 6
41280065 TCTTTTTTCG
* * * **
41280075 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * ** * *
41280126 CGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTCTT CGTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
41280174 -GTTTT CTTT
1 CTTTTT CTTT
41280183 CAATTTCTTT
Statistics
Matches: 72, Mismatches: 27, Indels: 6
0.69 0.26 0.06
Matches are distributed among these distances:
5 4 0.06
6 56 0.78
7 9 0.12
8 3 0.04
ACGTcount: A:0.06, C:0.19, G:0.04, T:0.70
Consensus pattern (6 bp):
CTTTTT
Found at i:41281267 original size:11 final size:11
Alignment explanation
Indices: 41281253--41281287 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
41281243 TTTTTTTTCC
*
41281253 TTTTTTTCG-A
1 TTTTTTTTGAA
41281263 TTTTTTTTGAA
1 TTTTTTTTGAA
41281274 TTTTTTTTGAA
1 TTTTTTTTGAA
41281285 TTT
1 TTT
41281288 CTTCTCTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 8 0.35
11 15 0.65
ACGTcount: A:0.14, C:0.03, G:0.09, T:0.74
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:41282421 original size:20 final size:20
Alignment explanation
Indices: 41282375--41282421 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
41282365 AGCTCGTTTC
*
41282375 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
41282395 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
41282415 CAGCTCA
1 CAGCTCA
41282422 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:41283031 original size:20 final size:20
Alignment explanation
Indices: 41283008--41283061 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
41282998 AGTTTTTCCC
*
41283008 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
41283028 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
41283048 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
41283062 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:41283043 original size:30 final size:30
Alignment explanation
Indices: 41283008--41283081 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
41282998 AGTTTTTCCC
41283008 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
41283038 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
41283068 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
41283082 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:41283071 original size:20 final size:20
Alignment explanation
Indices: 41283008--41283072 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
41282998 AGTTTTTCCC
* * * *
41283008 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
41283028 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
41283047 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
41283068 AGCTC
1 AGCTC
41283073 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:41285627 original size:14 final size:13
Alignment explanation
Indices: 41285604--41285642 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
41285594 CACATTGTAG
41285604 TGAAAAAAGAAAA
1 TGAAAAAAGAAAA
41285617 TGAAGAAAAGAAAA
1 TGAA-AAAAGAAAA
41285631 TTG-AAAAAGAAA
1 -TGAAAAAAGAAA
41285643 TTGAGATTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 12 0.50
14 10 0.42
15 2 0.08
ACGTcount: A:0.72, C:0.00, G:0.18, T:0.10
Consensus pattern (13 bp):
TGAAAAAAGAAAA
Found at i:41285651 original size:18 final size:18
Alignment explanation
Indices: 41285630--41285664 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
41285620 AGAAAAGAAA
41285630 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
41285648 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
41285665 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:41287384 original size:20 final size:20
Alignment explanation
Indices: 41287338--41287384 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
41287328 AGCTCGTTTC
*
41287338 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
41287358 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
41287378 CAGCTCA
1 CAGCTCA
41287385 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:41287994 original size:20 final size:20
Alignment explanation
Indices: 41287971--41288024 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
41287961 AGTTTTTCCC
*
41287971 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
41287991 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
41288011 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
41288025 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:41288006 original size:30 final size:30
Alignment explanation
Indices: 41287971--41288044 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
41287961 AGTTTTTCCC
41287971 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
41288001 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
41288031 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
41288045 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:41288034 original size:20 final size:20
Alignment explanation
Indices: 41287971--41288035 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
41287961 AGTTTTTCCC
* * * *
41287971 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
41287991 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
41288010 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
41288031 AGCTC
1 AGCTC
41288036 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:41292663 original size:24 final size:25
Alignment explanation
Indices: 41292636--41292689 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 25
41292626 ATGAGTGATA
*
41292636 AAAAAAGAGA-GAGTGATTCAAAA-G
1 AAAAAAGAAACGAGTGA-TCAAAATG
*
41292660 -AAAAAGAAACGAGTGATGAAAATG
1 AAAAAAGAAACGAGTGATCAAAATG
41292684 AAAAAA
1 AAAAAA
41292690 AGAATTTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 13 0.52
24 7 0.28
25 5 0.20
ACGTcount: A:0.63, C:0.04, G:0.22, T:0.11
Consensus pattern (25 bp):
AAAAAAGAAACGAGTGATCAAAATG
Found at i:41299659 original size:20 final size:20
Alignment explanation
Indices: 41299636--41299682 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
41299626 GGGTTAAGAT
*
41299636 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
41299656 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
41299676 TGAGCTG
1 TGAGCTG
41299683 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:41301221 original size:20 final size:19
Alignment explanation
Indices: 41301198--41301262 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
41301188 AAGCTCAAAC
41301198 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
41301218 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
41301238 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
41301258 GAGCT
1 GAGCT
41301263 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:41301779 original size:21 final size:22
Alignment explanation
Indices: 41301750--41301792 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
41301740 TTTGGTATTT
41301750 GGGAATTGGTA-GAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
41301771 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
41301793 TGGTTCAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.35, C:0.02, G:0.37, T:0.26
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:41305273 original size:23 final size:22
Alignment explanation
Indices: 41305221--41305273 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
41305211 TTCCACGTCT
*
41305221 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
41305243 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
41305266 TTTCTTTT
1 TTTCTTTT
41305274 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:41306933 original size:20 final size:19
Alignment explanation
Indices: 41306910--41306974 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
41306900 AAGCTCAAAC
41306910 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
41306930 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
41306950 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
41306970 GAGCT
1 GAGCT
41306975 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:41315021 original size:20 final size:20
Alignment explanation
Indices: 41314975--41315021 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
41314965 AGCTTGTTTC
*
41314975 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
41314995 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
41315015 CAGCTCA
1 CAGCTCA
41315022 ATCTTAACCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:41316583 original size:24 final size:23
Alignment explanation
Indices: 41316533--41316587 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
41316523 AAACGAAATT
** *
41316533 CAAAAAAAAAAAAAAGAAGTGAG
1 CAAAAAAAAAAAAAAGAAAAGAA
*
41316556 CAAAAAAAAAGTAAAAGAAAAGAA
1 CAAAAAAAAA-AAAAAGAAAAGAA
41316580 CAAAAAAA
1 CAAAAAAA
41316588 GTGAAAAGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
23 10 0.37
24 17 0.63
ACGTcount: A:0.78, C:0.05, G:0.13, T:0.04
Consensus pattern (23 bp):
CAAAAAAAAAAAAAAGAAAAGAA
Found at i:41317693 original size:48 final size:47
Alignment explanation
Indices: 41317614--41317719 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
41317604 GAGTGTCATG
*
41317614 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
41317662 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
41317710 GAAAAAGAAA
1 GAAAAAGAAA
41317720 GAAAAGACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.59, C:0.02, G:0.25, T:0.14
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATC
Found at i:41319436 original size:20 final size:20
Alignment explanation
Indices: 41319391--41319436 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
41319381 GCTTGTTTCT
*
41319391 AGCTCACTCGAGCTCAAGTC
1 AGCTCACTCAAGCTCAAGTC
* * *
41319411 AACTCATTCAAGCTCAATTC
1 AGCTCACTCAAGCTCAAGTC
41319431 AGCTCA
1 AGCTCA
41319437 ATCTTAACCT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.30, C:0.33, G:0.13, T:0.24
Consensus pattern (20 bp):
AGCTCACTCAAGCTCAAGTC
Found at i:41321003 original size:25 final size:24
Alignment explanation
Indices: 41320951--41321008 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 24
41320941 ACGAAATTCA
** *
41320951 AAAAAAGAAAAGAAAAGAAGTGAGC
1 AAAAAA-AAAAGAAAAGAAAAGAAC
41320976 AAAAAAAAAAGTAAAAGAAAAGAAC
1 AAAAAAAAAAG-AAAAGAAAAGAAC
41321001 AAAAAAAA
1 AAAAAAAA
41321009 GTGAAAAGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 5 0.17
25 24 0.83
ACGTcount: A:0.78, C:0.03, G:0.16, T:0.03
Consensus pattern (24 bp):
AAAAAAAAAAGAAAAGAAAAGAAC
Found at i:41327057 original size:20 final size:20
Alignment explanation
Indices: 41327011--41327048 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
41327001 AGCTCGTTTC
*
41327011 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
*
41327031 CAACTCACTCAAGCTCAA
1 CAGCTCACTCAAGCTCAA
41327049 TTTAGCTCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.37, G:0.13, T:0.18
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:41328694 original size:30 final size:30
Alignment explanation
Indices: 41328638--41328694 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
41328628 TGGGCTCAAA
* **
41328638 TCAAGAAAATCAAGATTCACTTTCTTGTTT
1 TCAAGAAAATCAAGAATCACAATCTTGTTT
41328668 TCAAGAAAATCAAGAAATCA-AATCTTG
1 TCAAGAAAATCAAG-AATCACAATCTTG
41328695 GCCCAATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
30 19 0.83
31 4 0.17
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.32
Consensus pattern (30 bp):
TCAAGAAAATCAAGAATCACAATCTTGTTT
Found at i:41329181 original size:327 final size:327
Alignment explanation
Indices: 41328587--41329239 Score: 1236
Period size: 327 Copynumber: 2.0 Consensus size: 327
41328577 TTTTGAGGAA
*
41328587 GATACGAGTCACAAAGGCCCAACCCAAGCTTAAGAAGGTGATGGGCTCAAATCAAGAAAATCAAG
1 GATACGAGTCACAAAGGCCCAACCCAAGCTTAAGAAGGTGATGGGCTAAAATCAAGAAAATCAAG
*
41328652 ATTCACTTTCTTGTTTTCAAGAAAATCAAGAAATCAAATCTTGGCCCAATTTTGCTGTTCGGAGT
66 ATTCACTTTCTTGTTTTCAAGAAAATCAAGAAATCAAATCTTGGCCCAATTTTGCTGTTCGGAGC
41328717 GATTTCAAGAATCAAGAAAATCAAGATTTCAAATCTTGGAAATCTTGGTCCAAGAAACTGAATCT
131 GATTTCAAGAATCAAGAAAATCAAGATTTCAAATCTTGGAAATCTTGGTCCAAGAAACTGAATCT
*
41328782 TGCAGCCAAAGCGCGTTGGATCTCCATTACGAGCGTCAACGACCCAATTTCGGTAGGAGATGGAT
196 TGCAGCCAAAGCGCATTGGATCTCCATTACGAGCGTCAACGACCCAATTTCGGTAGGAGATGGAT
*
41328847 CACAAGCCCAAATTCTTAAAGGTGAGGCCCAATAAGCAAATTCCCAGCCCAATCAAGAAATCCAT
261 CACAAGCCCAAATTCTTAAAGGCGAGGCCCAATAAGCAAATTCCCAGCCCAATCAAGAAATCCAT
41328912 AT
326 AT
41328914 GATACGAGTCACAAAGGCCCAACCCAAGCTTAAGAAGGTGATGGGCTAAAATCAAGAAAATCAAG
1 GATACGAGTCACAAAGGCCCAACCCAAGCTTAAGAAGGTGATGGGCTAAAATCAAGAAAATCAAG
*
41328979 ATTCACTTTCTTGTTTTCAAGAAAATCAAGAAATCGAATCTTGGCCCAATTTTGCTGTTCGGAGC
66 ATTCACTTTCTTGTTTTCAAGAAAATCAAGAAATCAAATCTTGGCCCAATTTTGCTGTTCGGAGC
41329044 GATTTCAAGAATCAAGAAAATCAAGATTTCAAATCTTGGAAATCTTGGTCCAAGAAA-TCGAATC
131 GATTTCAAGAATCAAGAAAATCAAGATTTCAAATCTTGGAAATCTTGGTCCAAGAAACT-GAATC
*
41329108 TTGCAGCCAAAGCGCATTGGATCTCCATTACGAGCGTCAACGACCTAATTTCGGTAGGAGATGGA
195 TTGCAGCCAAAGCGCATTGGATCTCCATTACGAGCGTCAACGACCCAATTTCGGTAGGAGATGGA
41329173 TCACAAGCCCAAATTCTTAAAGGCGAGGCCCAATAAGCAAATTCCCAGCCCAATCAAGAAATCCA
260 TCACAAGCCCAAATTCTTAAAGGCGAGGCCCAATAAGCAAATTCCCAGCCCAATCAAGAAATCCA
41329238 TA
325 TA
41329240 CATATTTAGT
Statistics
Matches: 319, Mismatches: 6, Indels: 2
0.98 0.02 0.01
Matches are distributed among these distances:
326 1 0.00
327 318 1.00
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.23
Consensus pattern (327 bp):
GATACGAGTCACAAAGGCCCAACCCAAGCTTAAGAAGGTGATGGGCTAAAATCAAGAAAATCAAG
ATTCACTTTCTTGTTTTCAAGAAAATCAAGAAATCAAATCTTGGCCCAATTTTGCTGTTCGGAGC
GATTTCAAGAATCAAGAAAATCAAGATTTCAAATCTTGGAAATCTTGGTCCAAGAAACTGAATCT
TGCAGCCAAAGCGCATTGGATCTCCATTACGAGCGTCAACGACCCAATTTCGGTAGGAGATGGAT
CACAAGCCCAAATTCTTAAAGGCGAGGCCCAATAAGCAAATTCCCAGCCCAATCAAGAAATCCAT
AT
Found at i:41329550 original size:20 final size:20
Alignment explanation
Indices: 41329504--41329550 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
41329494 AGCTCGTTTC
*
41329504 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
41329524 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
41329544 CAGCTCA
1 CAGCTCA
41329551 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:41332561 original size:10 final size:11
Alignment explanation
Indices: 41332539--41332563 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
41332529 AAAAAAATCG
41332539 AAATTCAAAAA
1 AAATTCAAAAA
41332550 AAATTCAAAAA
1 AAATTCAAAAA
41332561 AAA
1 AAA
41332564 AGTGAAAAAA
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:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (11 bp):
AAATTCAAAAA
Found at i:41332588 original size:29 final size:29
Alignment explanation
Indices: 41332556--41332616 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
41332546 AAAAAAATTC
**
41332556 AAAAAAAAAGTGAAAAAAA-TCGAGCAAAA
1 AAAAAAAAAGAAAAAAAAAGT-GAGCAAAA
*
41332585 AAAAAGAAAGAAAAAAAAAGTGAGCAAAA
1 AAAAAAAAAGAAAAAAAAAGTGAGCAAAA
41332614 AAA
1 AAA
41332617 TCAAGTTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 27 0.96
30 1 0.04
ACGTcount: A:0.75, C:0.05, G:0.15, T:0.05
Consensus pattern (29 bp):
AAAAAAAAAGAAAAAAAAAGTGAGCAAAA
Found at i:41335462 original size:20 final size:20
Alignment explanation
Indices: 41335437--41335480 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
41335427 TCGTTTCCAG
*
41335437 CTCACTCGAGCTCAAGTCAA
1 CTCACTCAAGCTCAAGTCAA
*
41335457 CTCACTCAAGCTCAATTCAA
1 CTCACTCAAGCTCAAGTCAA
41335477 CTCA
1 CTCA
41335481 ATCTTAACCC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.32, C:0.36, G:0.09, T:0.23
Consensus pattern (20 bp):
CTCACTCAAGCTCAAGTCAA
Found at i:41350788 original size:33 final size:33
Alignment explanation
Indices: 41350750--41350812 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
41350740 GATTACTCAC
41350750 TTCACTCG-TTTCTTTT-ATAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
41350783 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
41350813 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.25, G:0.06, T:0.56
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:41350858 original size:14 final size:15
Alignment explanation
Indices: 41350829--41350866 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
41350819 TTTTTTCGCT
41350829 TTTTC-TTT-TTCAA
1 TTTTCTTTTCTTCAA
41350842 TTTTCTTTTCTTC-A
1 TTTTCTTTTCTTCAA
41350856 TTTTCTTTTCT
1 TTTTCTTTTCT
41350867 CTCACTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 5 0.22
14 15 0.65
15 3 0.13
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTCTTTTCTTCAA
Found at i:41350892 original size:18 final size:18
Alignment explanation
Indices: 41350871--41350922 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
41350861 TTTTCTCTCA
41350871 CTTTTTCGATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
***
41350889 CTTTTGAAATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
*
41350907 CTTTTTCGTTTTCTTT
1 CTTTTTCGATTTCTTT
41350923 CAATTTCTTT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.08, C:0.15, G:0.06, T:0.71
Consensus pattern (18 bp):
CTTTTTCGATTTCTTTTT
Found at i:41350935 original size:6 final size:6
Alignment explanation
Indices: 41350827--41350922 Score: 50
Period size: 6 Copynumber: 15.7 Consensus size: 6
41350817 TCTTTTTTCG
* * * **
41350827 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT C-TTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * *** *
41350877 CGATTT CTTTTT CTTTTG AAATTT CTTTTT CTTTTT CGTTTT CTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTT
41350923 CAATTTCTTT
Statistics
Matches: 63, Mismatches: 24, Indels: 6
0.68 0.26 0.06
Matches are distributed among these distances:
5 5 0.08
6 46 0.73
7 9 0.14
8 3 0.05
ACGTcount: A:0.08, C:0.19, G:0.03, T:0.70
Consensus pattern (6 bp):
CTTTTT
Found at i:41350943 original size:22 final size:22
Alignment explanation
Indices: 41350904--41350945 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
41350894 GAAATTTCTT
** *
41350904 TTTCTTTTTCGTTTTCTTTCAA
1 TTTCTTTTTCAATCTCTTTCAA
41350926 TTTCTTTTTCAATCTCTTTC
1 TTTCTTTTTCAATCTCTTTC
41350946 TCCTTTTCTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.10, C:0.21, G:0.02, T:0.67
Consensus pattern (22 bp):
TTTCTTTTTCAATCTCTTTCAA
Found at i:41351983 original size:19 final size:18
Alignment explanation
Indices: 41351937--41351986 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
41351927 AGACTTTTCA
* *
41351937 CTTTTTTTTTTGTTCTTT
1 CTTTTTTTTTTGCTCCTT
*
41351955 TTTTTCTTTTTTGCTCACTT
1 CTTTT-TTTTTTGCTC-CTT
41351975 CTTTTTTTTTTG
1 CTTTTTTTTTTG
41351987 AATTTCGATT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 4 0.15
19 16 0.62
20 6 0.23
ACGTcount: A:0.02, C:0.14, G:0.06, T:0.78
Consensus pattern (18 bp):
CTTTTTTTTTTGCTCCTT
Found at i:41365538 original size:13 final size:13
Alignment explanation
Indices: 41365520--41365544 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41365510 TGGTCATCAT
41365520 GGTGTGAACACAA
1 GGTGTGAACACAA
41365533 GGTGTGAACACA
1 GGTGTGAACACA
41365545 TGATCAATAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:41366063 original size:10 final size:10
Alignment explanation
Indices: 41366050--41366087 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
41366040 TTGTAGCTAA
41366050 ATTGAGCTCG
1 ATTGAGCTCG
41366060 ATTGAGCT-G
1 ATTGAGCTCG
41366069 ACTTGAGCTCG
1 A-TTGAGCTCG
*
41366080 AGTGAGCT
1 ATTGAGCT
41366088 GGAAACGAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (10 bp):
ATTGAGCTCG
Found at i:41366067 original size:20 final size:20
Alignment explanation
Indices: 41366027--41366087 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
41366017 ACCAATAAAA
41366027 TAAA-TGAGCT-GAATTGTAGC
1 TAAATTGAGCTCG-ATTG-AGC
41366047 TAAATTGAGCTCGATTGAGC
1 TAAATTGAGCTCGATTGAGC
* * *
41366067 TGACTTGAGCTCGAGTGAGC
1 TAAATTGAGCTCGATTGAGC
41366087 T
1 T
41366088 GGAAACGAGC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 25 0.69
21 10 0.28
22 1 0.03
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (20 bp):
TAAATTGAGCTCGATTGAGC
Found at i:41366088 original size:20 final size:20
Alignment explanation
Indices: 41366051--41366088 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
41366041 TGTAGCTAAA
*
41366051 TTGAGCTCGATTGAGCTGAC
1 TTGAGCTCGAGTGAGCTGAC
41366071 TTGAGCTCGAGTGAGCTG
1 TTGAGCTCGAGTGAGCTG
41366089 GAAACGAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.34, T:0.29
Consensus pattern (20 bp):
TTGAGCTCGAGTGAGCTGAC
Found at i:41367422 original size:21 final size:22
Alignment explanation
Indices: 41367392--41367433 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
41367382 AAAGAAGAGG
41367392 AAATTCGAAAAAAAAATCGAAA
1 AAATTCGAAAAAAAAATCGAAA
*
41367414 AAATT-GAAAAAAAATTCGAA
1 AAATTCGAAAAAAAAATCGAA
41367434 GTATTAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.67, C:0.07, G:0.10, T:0.17
Consensus pattern (22 bp):
AAATTCGAAAAAAAAATCGAAA
Found at i:41370870 original size:56 final size:55
Alignment explanation
Indices: 41370754--41370871 Score: 150
Period size: 55 Copynumber: 2.1 Consensus size: 55
41370744 TGCATGCTTT
* * * * *
41370754 CATT-AATGCCGTCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCC
1 CATTAAATGCCGTCCATACATGGTGAACATCTCATTCAATTCATGTTTTGCTGCA
*
41370808 CTTTAAATGCCGTTCCATACATGG-GAACATCTCATTCAATTCATGTCTTTGCTGCA
1 CATTAAATGCCG-TCCATACATGGTGAACATCTCATTCAATTCATGT-TTTGCTGCA
41370864 CATTAAAT
1 CATTAAAT
41370872 CAGCAAGCAG
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
54 3 0.06
55 27 0.50
56 24 0.44
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.38
Consensus pattern (55 bp):
CATTAAATGCCGTCCATACATGGTGAACATCTCATTCAATTCATGTTTTGCTGCA
Found at i:41371521 original size:20 final size:20
Alignment explanation
Indices: 41371496--41371550 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
41371486 ACGAGTTAAA
* *
41371496 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTCGAATGAGCTAAC
*
41371516 TTGAGCACGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
41371536 TTGAGCTCGAATGAG
1 TTGAGCTCGAATGAG
41371551 TTGAACCACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:41382445 original size:15 final size:15
Alignment explanation
Indices: 41382425--41382473 Score: 57
Period size: 17 Copynumber: 3.3 Consensus size: 15
41382415 AAAAAATAAG
41382425 AAAATTTCGAAAAAA
1 AAAATTTCGAAAAAA
*
41382440 AAAATTGATTGAAAAAA
1 AAAATT--TCGAAAAAA
41382457 AAAA-TTC-AAAAAA
1 AAAATTTCGAAAAAA
41382470 AAAA
1 AAAA
41382474 GTGAAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
13 10 0.33
14 1 0.03
15 6 0.20
16 1 0.03
17 12 0.40
ACGTcount: A:0.71, C:0.04, G:0.06, T:0.18
Consensus pattern (15 bp):
AAAATTTCGAAAAAA
Found at i:41382467 original size:13 final size:13
Alignment explanation
Indices: 41382451--41382484 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
41382441 AAATTGATTG
*
41382451 AAAAAAAAAATTC
1 AAAAAAAAAAGTC
*
41382464 AAAAAAAAAAGTG
1 AAAAAAAAAAGTC
41382477 AAAAAAAA
1 AAAAAAAA
41382485 TCGAGCAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.82, C:0.03, G:0.06, T:0.09
Consensus pattern (13 bp):
AAAAAAAAAAGTC
Found at i:41382496 original size:16 final size:16
Alignment explanation
Indices: 41382477--41382519 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
41382467 AAAAAAAGTG
*
41382477 AAAAAAAATCGAGCAA
1 AAAAAAAATCGACCAA
41382493 AAAAAAAAGGT-GACCAA
1 AAAAAAAA--TCGACCAA
41382510 AAAAAAAATC
1 AAAAAAAATC
41382520 AAGTTAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
15 1 0.04
16 8 0.35
17 13 0.57
18 1 0.04
ACGTcount: A:0.70, C:0.12, G:0.12, T:0.07
Consensus pattern (16 bp):
AAAAAAAATCGACCAA
Found at i:41383597 original size:17 final size:18
Alignment explanation
Indices: 41383565--41383598 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41383555 AAAAGAGAGT
*
41383565 GAGATTGAAGGAAGAAAC
1 GAGAGTGAAGGAAGAAAC
41383583 GAGAGTGAA-GAAGAAA
1 GAGAGTGAAGGAAGAAA
41383599 GGAGTGTTGT
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:0.53, C:0.03, G:0.35, T:0.09
Consensus pattern (18 bp):
GAGAGTGAAGGAAGAAAC
Found at i:41387971 original size:16 final size:17
Alignment explanation
Indices: 41387950--41387987 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
41387940 CTTCTTCTTC
41387950 TTTTTTCAC-AAATTTT
1 TTTTTTCACGAAATTTT
41387966 TTTTTTCACGAAATTTT
1 TTTTTTCACGAAATTTT
41387983 TTTTT
1 TTTTT
41387988 CAACTTGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.21, C:0.11, G:0.03, T:0.66
Consensus pattern (17 bp):
TTTTTTCACGAAATTTT
Found at i:41388043 original size:12 final size:12
Alignment explanation
Indices: 41388026--41388064 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
41388016 AAAGGAAACC
41388026 AATTTTTTTTTG
1 AATTTTTTTTTG
*
41388038 AATTTTTTTTTCA
1 AATTTTTTTTT-G
*
41388051 AATATTTTTTTG
1 AATTTTTTTTTG
41388063 AA
1 AA
41388065 GAAACTACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
12 13 0.57
13 10 0.43
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.67
Consensus pattern (12 bp):
AATTTTTTTTTG
Found at i:41397141 original size:12 final size:11
Alignment explanation
Indices: 41397086--41397138 Score: 79
Period size: 11 Copynumber: 4.7 Consensus size: 11
41397076 TAGTTTCTCG
* *
41397086 AAAAAAACTTG
1 AAAAAAAATTC
41397097 AAAAGAAAATTC
1 AAAA-AAAATTC
41397109 AAAAAAAATTC
1 AAAAAAAATTC
41397120 AAAAAAAATTC
1 AAAAAAAATTC
41397131 AAAAAAAA
1 AAAAAAAA
41397139 ATTTTTGGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
11 30 0.77
12 9 0.23
ACGTcount: A:0.74, C:0.08, G:0.04, T:0.15
Consensus pattern (11 bp):
AAAAAAAATTC
Found at i:41397204 original size:14 final size:14
Alignment explanation
Indices: 41397180--41397230 Score: 86
Period size: 14 Copynumber: 3.7 Consensus size: 14
41397170 GGATATCAAG
41397180 TTGTG-AAAAAAAA
1 TTGTGAAAAAAAAA
*
41397193 TTTTGAAAAAAAAA
1 TTGTGAAAAAAAAA
41397207 TTGTGAAAAAAAAA
1 TTGTGAAAAAAAAA
41397221 TTGTGAAAAA
1 TTGTGAAAAA
41397231 TAAAGGAGAG
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
13 4 0.11
14 31 0.89
ACGTcount: A:0.61, C:0.00, G:0.14, T:0.25
Consensus pattern (14 bp):
TTGTGAAAAAAAAA
Found at i:41401819 original size:30 final size:30
Alignment explanation
Indices: 41401763--41401819 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
41401753 TGGGCTCAAA
* **
41401763 TCAAGAAAATCAAGATTCACTTTCTTGTTT
1 TCAAGAAAATCAAGAATCACAATCTTGTTT
41401793 TCAAGAAAATCAAGAAATCA-AATCTTG
1 TCAAGAAAATCAAG-AATCACAATCTTG
41401820 GCCCAATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
30 19 0.83
31 4 0.17
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.32
Consensus pattern (30 bp):
TCAAGAAAATCAAGAATCACAATCTTGTTT
Found at i:41402306 original size:327 final size:327
Alignment explanation
Indices: 41401712--41403672 Score: 3688
Period size: 327 Copynumber: 6.0 Consensus size: 327
41401702 TTTTGAGGAA
41401712 GATACGAGTCACAAAGGCCCAACCCAAGCTTAAGAAGGTGATGGGCTCAAATCAAGAAAATCAAG
1 GATACGAGTCACAAAGGCCCAACCCAAGCTTAAGAAGGTGATGGGCTCAAATCAAGAAAATCAAG
* * *
41401777 ATTCACTTTCTTGTTTTCAAGAAAATCAAGAAATCAAATCTTGGCCCAATTTTACTGTTCGGAGT
66 ATTCACTTTCTTGTTTTCAAGAAAATCAAGAAATCGAATCTTGGCCCAATTTTGCTGTTCGGAGC
*
41401842 GATTTCAAGAATCAAGAAAATCAAGATTTCAAATCTTCGAAATCTTGGTCCAAGAAACCGAATCT
131 GATTTCAAGAATCAAGAAAATCAAGATTTCAAATCTTGGAAATCTTGGTCCAAGAAACCGAATCT
* *
41401907 TGCAACCAAAGCGCGTTGGATCCCCATTACGAGCGTCAACGACCCAATTTCGGTAGGAGATGGAT
196 TGCAGCCAAAGCGCGTTGGATCTCCATTACGAGCGTCAACGACCCAATTTCGGTAGGAGATGGAT
41401972 CACAAGCCCAAATTCTTAAAGGCGAGGCCCAATAAGCAAATTCCCAGCCCAATCAAGAAATCCAT
261 CACAAGCCCAAATTCTTAAAGGCGAGGCCCAATAAGCAAATTCCCAGCCCAATCAAGAAATCCAT
41402037 AT
326 AT
41402039 GATACGAGTCACAAAGGCCCAACCCAAGCTTAAGAAGGTGATGGGCTCAAATCAAGAAAATCAAG
1 GATACGAGTCACAAAGGCCCAACCCAAGCTTAAGAAGGTGATGGGCTCAAATCAAGAAAATCAAG
41402104 ATTCACTTTCTTGTTTTCAAGAAAATCAAGAAATCGAATCTTGGCCCAATTTTGCTGTTCGGAGC
66 ATTCACTTTCTTGTTTTCAAGAAAATCAAGAAATCGAATCTTGGCCCAATTTTGCTGTTCGGAGC
*
41402169 GATTTCAAGAATCAAGAAAATCAAGATTTCAAATCTTGGAAATCTGGGTCCAAGAAACCGAATCT
131 GATTTCAAGAATCAAGAAAATCAAGATTTCAAATCTTGGAAATCTTGGTCCAAGAAACCGAATCT
*
41402234 TGCATCCAAAGCGCGTTGGATCTCCATTACGAGCGTCAACGACCCAATTTCGGTAGGAGATGGAT
196 TGCAGCCAAAGCGCGTTGGATCTCCATTACGAGCGTCAACGACCCAATTTCGGTAGGAGATGGAT
*
41402299 CACAAGCCCAAATTCTTAAAGGCGAGGCCCAATAAGCAAATTCCCAGCCCAATAAAGAAATCCAT
261 CACAAGCCCAAATTCTTAAAGGCGAGGCCCAATAAGCAAATTCCCAGCCCAATCAAGAAATCCAT
41402364 AT
326 AT
41402366 GATACGAGTCACAAAGGCCCAACCCAAGCTTAAGAAGGTGATGGGCTCAAATCAAGAAAATCAAG
1 GATACGAGTCACAAAGGCCCAACCCAAGCTTAAGAAGGTGATGGGCTCAAATCAAGAAAATCAAG
41402431 ATTCACTTTCTTGTTTTCAAGAAAATCAAGAAATCGAATCTTGGCCCAATTTTGCTGTTCGGAGC
66 ATTCACTTTCTTGTTTTCAAGAAAATCAAGAAATCGAATCTTGGCCCAATTTTGCTGTTCGGAGC
*
41402496 GATTTCAAGAATCAAGAAAATCAAGATTTCAAATCTTGGAAATCTTGGTCCAAGAAACTGAATCT
131 GATTTCAAGAATCAAGAAAATCAAGATTTCAAATCTTGGAAATCTTGGTCCAAGAAACCGAATCT
*
41402561 TGCAGCCAAAGCGTGTTGGATCTCCATTACGAGCGTCAACGACCCAATTTCGGTAGGAGATGGAT
196 TGCAGCCAAAGCGCGTTGGATCTCCATTACGAGCGTCAACGACCCAATTTCGGTAGGAGATGGAT
41402626 CACAAGCCCAAATTCTTAAAGGCGAGGCCCAATAAGCAAATTCCCAGCCCAATCAAGAAATCCAT
261 CACAAGCCCAAATTCTTAAAGGCGAGGCCCAATAAGCAAATTCCCAGCCCAATCAAGAAATCCAT
41402691 AT
326 AT
*
41402693 GATACGAGTCACAAAGGCCCAACCCAAGCTTAAGAAGGTGATGGGCTCAAATCAGGAAAATCAAG
1 GATACGAGTCACAAAGGCCCAACCCAAGCTTAAGAAGGTGATGGGCTCAAATCAAGAAAATCAAG
* * *
41402758 ATTCACTTTCTTGTTTTCAAGAAAATCAAGAAATCGAATCTTGGCGCAATTTTGATATTCGGAGC
66 ATTCACTTTCTTGTTTTCAAGAAAATCAAGAAATCGAATCTTGGCCCAATTTTGCTGTTCGGAGC
* *
41402823 AATTTCAAGAATCAAGAAAATCAAGATTTCAAATCTTGGAAATCTTGGTCCAAGAAACCAAATCT
131 GATTTCAAGAATCAAGAAAATCAAGATTTCAAATCTTGGAAATCTTGGTCCAAGAAACCGAATCT
* *
41402888 TGTAGCCAAAGCGTGTTGGATCTCCATTACGAGCGTCAACGACCCAATTTCGGTAGGAGATGGAT
196 TGCAGCCAAAGCGCGTTGGATCTCCATTACGAGCGTCAACGACCCAATTTCGGTAGGAGATGGAT
41402953 CACAAGCCCAAATTCTTAAAGGCGAGGCCCAATAAGCAAATTCCCAGCCCAATCAAGAAATCCAT
261 CACAAGCCCAAATTCTTAAAGGCGAGGCCCAATAAGCAAATTCCCAGCCCAATCAAGAAATCCAT
41403018 AT
326 AT
*
41403020 GATACGAGTCACAAAGGCCCAACCCAAGCTTAAGTAGGTGATGGGCTCAAATCAAGAAAATCAAG
1 GATACGAGTCACAAAGGCCCAACCCAAGCTTAAGAAGGTGATGGGCTCAAATCAAGAAAATCAAG
41403085 ATTCACTTTCTTGTTTTCAAGAAAATCAAGAAATCGAATCTTGGCCCAATTTTGCTGTTCGGAGC
66 ATTCACTTTCTTGTTTTCAAGAAAATCAAGAAATCGAATCTTGGCCCAATTTTGCTGTTCGGAGC
*
41403150 GATTTCAAGAATCAAGAAAATCAAGATTTCAAATCTTGGAAATCTTGGTCCAAGAAACTGAATCT
131 GATTTCAAGAATCAAGAAAATCAAGATTTCAAATCTTGGAAATCTTGGTCCAAGAAACCGAATCT
41403215 TGCAGCCAAAGCGCGTTGGATCTCCATTACGAGCGTCAACGACCCAATTTCGGTAGGAGATGGAT
196 TGCAGCCAAAGCGCGTTGGATCTCCATTACGAGCGTCAACGACCCAATTTCGGTAGGAGATGGAT
41403280 CACAAGCCCAAATTCTTAAAGGCGAGGCCCAATAAGCAAATTCCCAGCCCAATCAAGAAATCCAT
261 CACAAGCCCAAATTCTTAAAGGCGAGGCCCAATAAGCAAATTCCCAGCCCAATCAAGAAATCCAT
41403345 AT
326 AT
*
41403347 GATACGAGTCACAAAGGCCCAACCCAAGCTTAAGAAGGTGATGGGCTCAAATCAAGAAAATCAAT
1 GATACGAGTCACAAAGGCCCAACCCAAGCTTAAGAAGGTGATGGGCTCAAATCAAGAAAATCAAG
*
41403412 ATTCACTTTCTTGTTTTCAAGAAAATCAAGAAATCGAATCTTGGCCCAATTTTGCTATTCGGAGC
66 ATTCACTTTCTTGTTTTCAAGAAAATCAAGAAATCGAATCTTGGCCCAATTTTGCTGTTCGGAGC
* * *
41403477 GATTTCAAGAATCAAGAAAATCAAGATTTCAAATCTTGGAAACCTTTGTCCAAGAAACTGAATCT
131 GATTTCAAGAATCAAGAAAATCAAGATTTCAAATCTTGGAAATCTTGGTCCAAGAAACCGAATCT
41403542 TGCAGCCAAAGCGCGTTGGATCTCCATTACGAGCGTCAACGACCCAATTTCGGTAGGAGATGGAT
196 TGCAGCCAAAGCGCGTTGGATCTCCATTACGAGCGTCAACGACCCAATTTCGGTAGGAGATGGAT
41403607 CACAAGCCCAAATTCTTAAAGGCGAGGCCCAATAAGCAAATTCCCAGCCCAATCAAGAAATCCAT
261 CACAAGCCCAAATTCTTAAAGGCGAGGCCCAATAAGCAAATTCCCAGCCCAATCAAGAAATCCAT
41403672 A
326 A
41403673 CATATTTAGT
Statistics
Matches: 1598, Mismatches: 36, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
327 1598 1.00
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.23
Consensus pattern (327 bp):
GATACGAGTCACAAAGGCCCAACCCAAGCTTAAGAAGGTGATGGGCTCAAATCAAGAAAATCAAG
ATTCACTTTCTTGTTTTCAAGAAAATCAAGAAATCGAATCTTGGCCCAATTTTGCTGTTCGGAGC
GATTTCAAGAATCAAGAAAATCAAGATTTCAAATCTTGGAAATCTTGGTCCAAGAAACCGAATCT
TGCAGCCAAAGCGCGTTGGATCTCCATTACGAGCGTCAACGACCCAATTTCGGTAGGAGATGGAT
CACAAGCCCAAATTCTTAAAGGCGAGGCCCAATAAGCAAATTCCCAGCCCAATCAAGAAATCCAT
AT
Found at i:41407971 original size:20 final size:19
Alignment explanation
Indices: 41407948--41408012 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
41407938 AAGCTCAAAC
41407948 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
41407968 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
41407988 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
41408008 GAGCT
1 GAGCT
41408013 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:41409300 original size:17 final size:18
Alignment explanation
Indices: 41409278--41409311 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41409268 ACAACACTCC
*
41409278 TTTCTT-CTTCACTCTCG
1 TTTCTTCCTTCAATCTCG
41409295 TTTCTTCCTTCAATCTC
1 TTTCTTCCTTCAATCTC
41409312 ACTCTCTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.09, C:0.35, G:0.03, T:0.53
Consensus pattern (18 bp):
TTTCTTCCTTCAATCTCG
Found at i:41409419 original size:15 final size:16
Alignment explanation
Indices: 41409394--41409425 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
41409384 TATCTCACAC
41409394 TCATCTTCTTTTTCTT
1 TCATCTTCTTTTTCTT
41409410 TCAT-TTCTTTTTCTT
1 TCATCTTCTTTTTCTT
41409425 T
1 T
41409426 TTCATTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (16 bp):
TCATCTTCTTTTTCTT
Found at i:41410403 original size:16 final size:16
Alignment explanation
Indices: 41410365--41410406 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
41410355 TTTTTAACTT
*
41410365 GATTTTTTTTTTGGTC
1 GATTTTTTTTTTGCTC
*
41410381 -ACCTTTTTTTTTGCTC
1 GA-TTTTTTTTTTGCTC
41410397 GATTTTTTTT
1 GATTTTTTTT
41410407 CACCTTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 4
0.75 0.11 0.14
Matches are distributed among these distances:
15 1 0.05
16 19 0.90
17 1 0.05
ACGTcount: A:0.07, C:0.12, G:0.12, T:0.69
Consensus pattern (16 bp):
GATTTTTTTTTTGCTC
Found at i:41410429 original size:27 final size:27
Alignment explanation
Indices: 41410363--41410430 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 27
41410353 TTTTTTTAAC
41410363 TTGATTTTTTTTTTGGTCACCTTTTTTT
1 TTGATTTTTTTTTT-GTCACCTTTTTTT
* **
41410391 TTGCTCGATTTTTTT-TCACCTTTTTTT
1 TTGAT-TTTTTTTTTGTCACCTTTTTTT
*
41410418 TTGAATTTTTTTT
1 TTGATTTTTTTTT
41410431 CAATCAATTT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
26 6 0.19
27 15 0.47
28 4 0.12
29 7 0.22
ACGTcount: A:0.09, C:0.12, G:0.09, T:0.71
Consensus pattern (27 bp):
TTGATTTTTTTTTTGTCACCTTTTTTT
Found at i:41411258 original size:20 final size:19
Alignment explanation
Indices: 41411235--41411299 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
41411225 AAGCTCAAAC
41411235 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
41411255 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
41411275 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
41411295 GAGCT
1 GAGCT
41411300 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:41415431 original size:4 final size:4
Alignment explanation
Indices: 41415422--41415453 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
41415412 TTAAACTAAG
41415422 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
41415454 AATAAAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:41416858 original size:23 final size:22
Alignment explanation
Indices: 41416806--41416858 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
41416796 TCCACGTCTT
*
41416806 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
41416828 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
41416851 TTTCTTTT
1 TTTCTTTT
41416859 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:41421382 original size:13 final size:14
Alignment explanation
Indices: 41421312--41421383 Score: 57
Period size: 12 Copynumber: 5.4 Consensus size: 14
41421302 CAAAAAAATC
41421312 GAAAAAAAA-AAG-
1 GAAAAAAAAGAAGT
*
41421324 AAAAAAAAAGAAGT
1 GAAAAAAAAGAAGT
41421338 GACAAAAAAATCG-AGT
1 GA-AAAAAAA--GAAGT
*
41421354 TAAAAAAAAGAA--
1 GAAAAAAAAGAAGT
41421366 GAAAAAAAA-AAGT
1 GAAAAAAAAGAAGT
41421379 GAAAA
1 GAAAA
41421384 GTCTTGCGAG
Statistics
Matches: 48, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
11 2 0.04
12 16 0.33
13 9 0.19
14 2 0.04
15 14 0.29
16 4 0.08
17 1 0.02
ACGTcount: A:0.75, C:0.03, G:0.15, T:0.07
Consensus pattern (14 bp):
GAAAAAAAAGAAGT
Found at i:41421395 original size:41 final size:40
Alignment explanation
Indices: 41421302--41421380 Score: 117
Period size: 41 Copynumber: 2.0 Consensus size: 40
41421292 AAAAAAATTT
* *
41421302 CAAAAAAATCGA--AAAAAAAAAGAAAAAAAAAGAAGTGA
1 CAAAAAAATCGAGTTAAAAAAAAGAAAAAAAAAAAAGTGA
41421340 CAAAAAAATCGAGTTAAAAAAAAGAAGAAAAAAAAAAGTGA
1 CAAAAAAATCGAGTTAAAAAAAAGAA-AAAAAAAAAAGTGA
41421381 AAAGTCTTGC
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
38 12 0.33
40 11 0.31
41 13 0.36
ACGTcount: A:0.73, C:0.05, G:0.14, T:0.08
Consensus pattern (40 bp):
CAAAAAAATCGAGTTAAAAAAAAGAAAAAAAAAAAAGTGA
Found at i:41422429 original size:6 final size:6
Alignment explanation
Indices: 41422397--41422504 Score: 67
Period size: 6 Copynumber: 17.7 Consensus size: 6
41422387 AAAGAAATTG
* * ** *
41422397 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
* ** * * *
41422444 AAAGAA ATCA-AA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA A-AAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
41422495 AAAGAA AAAG
1 AAAGAA AAAG
41422505 CGAAAAAAGA
Statistics
Matches: 75, Mismatches: 22, Indels: 11
0.69 0.20 0.10
Matches are distributed among these distances:
5 4 0.05
6 59 0.79
7 8 0.11
8 4 0.05
ACGTcount: A:0.72, C:0.04, G:0.18, T:0.06
Consensus pattern (6 bp):
AAAGAA
Found at i:41422484 original size:14 final size:13
Alignment explanation
Indices: 41422465--41422502 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
41422455 AAAAGTGAGA
41422465 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
41422477 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
41422492 GAAAAAGAAAA
1 GAAAAAGAAAA
41422503 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:41422539 original size:12 final size:12
Alignment explanation
Indices: 41422508--41422539 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
41422498 GAAAAAGCGA
*
41422508 AAAAAGAATTTG
1 AAAAAGAGTTTG
41422520 AAAAAGAGTTTG
1 AAAAAGAGTTTG
41422532 AAAAAGAG
1 AAAAAGAG
41422540 AAGAGTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.22, T:0.19
Consensus pattern (12 bp):
AAAAAGAGTTTG
Found at i:41427319 original size:327 final size:327
Alignment explanation
Indices: 41426725--41427704 Score: 1852
Period size: 327 Copynumber: 3.0 Consensus size: 327
41426715 TTTTGAGGAA
*
41426725 GATACGAGTCACAAAGGCCCAACCCAAGCTTAAGAAGGTGATGGGCTCAAATTAAGAAAATCAAG
1 GATACGAGTCACAAAGGCCCAACCCAAGCTTAAGAAGGTGATGGGCTCAAATCAAGAAAATCAAG
*
41426790 ATTCACTTTCTTGTTTTCAAGAAAATCAAGAAATCAAATCTTGGCCCAATTTTGCTGTTCGGAGT
66 ATTCACTTTCTTGTTTTCAAGAAAATCAAGAAATCAAATCTTGGCCCAATTTTGCTGTTCGGAGC
* *
41426855 GTTTTCAAGAATCAGGAAAATCAAGATTTCAAATCTTGGAAATCTTGGTCCAAGAAACCGAATCT
131 GATTTCAAGAATCAAGAAAATCAAGATTTCAAATCTTGGAAATCTTGGTCCAAGAAACCGAATCT
* *
41426920 TGCAGCCAAAGCGCGTTGGATCTCTATTACGAGCGTCAATGACCCAATTTCGGTAGGAGATGGAT
196 TGCAGCCAAAGCGCGTTGGATCTCCATTACGAGCGTCAACGACCCAATTTCGGTAGGAGATGGAT
* *
41426985 CACAAGCCCAAATTCTTAAAGGCGAGGCCCAATAAGCAAATTCCTAGCCTAATCAAGAAATCCAT
261 CACAAGCCCAAATTCTTAAAGGCGAGGCCCAATAAGCAAATTCCCAGCCCAATCAAGAAATCCAT
41427050 AT
326 AT
41427052 GATACGAGTCACAAAGGCCCAACCCAAGCTTAAGAAGGTGATGGGCTCAAATCAAGAAAATCAAG
1 GATACGAGTCACAAAGGCCCAACCCAAGCTTAAGAAGGTGATGGGCTCAAATCAAGAAAATCAAG
*
41427117 ATTCACTTTCTTGTTTTCAAGAAAATCAAGAAATCTAATCTTGGCCCAATTTTGCTGTTCGGAGC
66 ATTCACTTTCTTGTTTTCAAGAAAATCAAGAAATCAAATCTTGGCCCAATTTTGCTGTTCGGAGC
41427182 GATTTCAAGAATCAAGAAAATCAAGATTTCAAATCTTGGAAATCTTGGTCCAAGAAACCGAATCT
131 GATTTCAAGAATCAAGAAAATCAAGATTTCAAATCTTGGAAATCTTGGTCCAAGAAACCGAATCT
41427247 TGCAGCCAAAGCGCGTTGGATCTCCATTACGAGCGTCAACGACCCAATTTCGGTAGGAGATGGAT
196 TGCAGCCAAAGCGCGTTGGATCTCCATTACGAGCGTCAACGACCCAATTTCGGTAGGAGATGGAT
41427312 CACAAGCCCAAATTCTTAAAGGCGAGGCCCAATAAGCAAATTCCCAGCCCAATCAAGAAATCCAT
261 CACAAGCCCAAATTCTTAAAGGCGAGGCCCAATAAGCAAATTCCCAGCCCAATCAAGAAATCCAT
41427377 AT
326 AT
41427379 GATACGAGTCACAAAGGCCCAACCCAAGCTTAAGAAGGTGATGGGCTCAAATCAAGAAAATCAAG
1 GATACGAGTCACAAAGGCCCAACCCAAGCTTAAGAAGGTGATGGGCTCAAATCAAGAAAATCAAG
* *
41427444 ATTCACTTTCTTGTTTTCAAGAAAATCAAGAAATCGAATCTTGGCCCAATTTTGCTGTTTGGAGC
66 ATTCACTTTCTTGTTTTCAAGAAAATCAAGAAATCAAATCTTGGCCCAATTTTGCTGTTCGGAGC
*
41427509 GATTTCAAGAATCAAGAAAATCAAGATTTCAAATCTTGGAAATCTTGGTCCAAGAAACTGAATCT
131 GATTTCAAGAATCAAGAAAATCAAGATTTCAAATCTTGGAAATCTTGGTCCAAGAAACCGAATCT
41427574 TGCAGCCAAAGCGCGTTGGATCTCCATTACGAGCGTCAACGACCCAATTTCGGTAGGAGATGGAT
196 TGCAGCCAAAGCGCGTTGGATCTCCATTACGAGCGTCAACGACCCAATTTCGGTAGGAGATGGAT
41427639 CACAAGCCCAAATTCTTAAAGGCGAGGCCCAATAAGCAAATTCCCAGCCCAATCAAGAAATCCAT
261 CACAAGCCCAAATTCTTAAAGGCGAGGCCCAATAAGCAAATTCCCAGCCCAATCAAGAAATCCAT
41427704 A
326 A
41427705 CATATTTAGT
Statistics
Matches: 641, Mismatches: 12, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
327 641 1.00
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (327 bp):
GATACGAGTCACAAAGGCCCAACCCAAGCTTAAGAAGGTGATGGGCTCAAATCAAGAAAATCAAG
ATTCACTTTCTTGTTTTCAAGAAAATCAAGAAATCAAATCTTGGCCCAATTTTGCTGTTCGGAGC
GATTTCAAGAATCAAGAAAATCAAGATTTCAAATCTTGGAAATCTTGGTCCAAGAAACCGAATCT
TGCAGCCAAAGCGCGTTGGATCTCCATTACGAGCGTCAACGACCCAATTTCGGTAGGAGATGGAT
CACAAGCCCAAATTCTTAAAGGCGAGGCCCAATAAGCAAATTCCCAGCCCAATCAAGAAATCCAT
AT
Found at i:41436405 original size:975 final size:973
Alignment explanation
Indices: 41434507--41436446 Score: 3343
Period size: 975 Copynumber: 2.0 Consensus size: 973
41434497 ATCAAGAAAT
41434507 CCATACATATTTAGTTGAAAATCAGGCCAAAATGTCAAAGGGCCCAATTTGTAAACATTTTAGTT
1 CCATACATATTTAGTTGAAAATCAGGCCAAAATGTCAAAGGGCCCAATTTGTAAACATTTTAGTT
* *
41434572 GTTTAAGTTAATTTTTAAGTTTTAGGAATATCACATGTTAAATTCGGCCCAAAACAGCCCAATAG
66 GTTTAAGTTAATTTTTAAGTTTTAGAAATATCACATGTTAAATTCAGCCCAAAACAGCCCAATAG
* *
41434637 GATGCATGGCTGAATTTTCCTTTGTTTTTTTCATTAAGTTTAAATTTTTTAAGTTTTCTAATTAG
131 GATGCATGGCCGAATTTTCCTTTGTTTTTTTAATTAAGTTTAAATTTTTTAAGTTTTCTAATTAG
41434702 ATTAGGATTTGTTGGAGGCCTATATAAGCATTGGCCAGCCACCCTTTGTAAACATCTTATTATTA
196 ATTAGGATTTGTTGGAGGCCTATATAAGCATTGGCCAGCCACCCTTTGTAAACATCTTATTATTA
41434767 TTTTTCTATCAAATTTCAGATTTGTTGAGTGCAGAATTTTATTTGGGGTTTTCTCCAAGAATTCT
261 TTTTTCTATCAAATTTCAGATTTGTTGAGTGCAGAATTTTATTTGGGGTTTTCTCCAAGAATTCT
41434832 CTCTTGAGTTTTCTTTAGAAGTTGTTTTAACAATCTTTTGATTGTGGGAGCCATCTTCAACCTTC
326 CTCTTGAGTTTTCTTTAGAAGTTGTTTTAACAATCTTTTGATTGTGGGAGCCATCTTCAACCTTC
41434897 TTCTTGCCATCGATATTCTTTGAAGGGGAGATTAGAGCCGTTTGAAGAGATTTGTGAAATCTTTC
391 TTCTTGCCATCGATATTCTTTGAAGGGGAGATTAGAGCCGTTTGAAGAGATTTGTGAAATCTTTC
41434962 GAGATTTCAAGGATCTTTAGGACTTATCCTTTAATTCTTGCTGTTTTCGATTTCTTTCTTTACTT
456 GAGATTTCAAGGATCTTTAGGACTTATCCTTTAATTCTTGCTGTTTTCGATTTCTTTCTTTACTT
* *
41435027 TTCTTTGCTTATACTTGTGCCAATTTGTCATCTAATATTTTGTTGTTCTTGTTTGTTTTCCAGCA
521 TTCTTTGCTTATACTTGTGCCAATTTCTCATCTAATATTTTGCTGTTCTTGTTTGTTTTCCAGCA
41435092 TTGATTAAACTCAAGATCTCATCGTTTAAGTTGTTCTCCTATTGGCAGCACCCATTCGAACCCAA
586 TTGATTAAACTCAAGATCTCATCGTTTAAGTTGTTCTCCTATTGGCAGCACCCATTCGAACCCAA
*
41435157 AAATCCCCAATTCCTAGGGTTTGGCCGATTGGATTTCTTTCAATTTGGGAATCAATTGATTGTTG
651 AAATCCCCAATTCCTAGGGTTTGGCCGATTGGATTTCTTTCAATTTGGGAATCAATTGATTGCTG
* *
41435222 GAAATTAGGCATTCTTGGCCGAATCAATCCCTTGGCAGATTCGCATCCTTTCCATACTTTCAATT
716 GAAATTAGGCATTCTTGGCCGAATCAATCCCTTGCCAGATTCGCATCCTTTCCATACTTCCAATT
*
41435287 CCATTTGATTCGCTTATTCTATTTCTTTATTTCTTGCTGCTCTTTTAATTGAATTTGGGGAATTT
781 CCATTTGATTCGCTTATTCTATTTCTTTATTTCTTGCTGCTCCTTTAATTGAATTTGGGGAATTT
* * * * * ** * *
41435352 CAATTCAATTCTGATTTGTTTTTAATCTTGTTCTTTGTTTCGATTTTAGATCTGATTCGTCCAGA
846 AAATTCAAATATGATTCGTGTTTAATCTTAATCTTTGTTTCGATTTCAGATATGATTCGTCCAGA
*
41435417 GCTTTCATAGGAGTTTCTCGTGACTTGGTAACTCGATCTTGGTCCGCGCGCAACCTCATATTA
911 GCTTTCATAGGAGTTTCTCGTGACTTGGCAACTCGATCTTGGTCCGCGCGCAACCTCATATTA
*
41435480 CCATACATATTTAGTTGAAAATCAGGCCAAAATGTCAAAGGGCCTAATTTGTAAACATTTTAGTT
1 CCATACATATTTAGTTGAAAATCAGGCCAAAATGTCAAAGGGCCCAATTTGTAAACATTTTAGTT
*
41435545 GTTTAAGTTAATTTTTAAGTTTTAGAAATATCACATGTTAAATTTAGCCCAAAACAGCCCAATAG
66 GTTTAAGTTAATTTTTAAGTTTTAGAAATATCACATGTTAAATTCAGCCCAAAACAGCCCAATAG
41435610 GATGCATGGCCGAATTTTCCTTTGTTTTTTTTAATTAAGTTTAAATTTTTTAAGTTTTCTAATTA
131 GATGCATGGCCGAATTTTCCTTTG-TTTTTTTAATTAAGTTTAAATTTTTTAAGTTTTCTAATTA
41435675 GATTAGGATTTGTTGGAGGCCTATATAAGCATTGGCCAGCCACCCTTTGTAAACATCTTATTATT
195 GATTAGGATTTGTTGGAGGCCTATATAAGCATTGGCCAGCCACCCTTTGTAAACATCTTATTATT
* * *
41435740 ATTTTTTCTATCAAATTTTAGATTTGTTGAGTGCAGAATTTTCTTTGGGGTTTTCTCTAAGAATT
260 A-TTTTTCTATCAAATTTCAGATTTGTTGAGTGCAGAATTTTATTTGGGGTTTTCTCCAAGAATT
41435805 CTCTCTTGAGTTTTCTTTAGAAGTTGTTTTAACAATCTTTTGATTGTGGGAGCCATCTTCAACCT
324 CTCTCTTGAGTTTTCTTTAGAAGTTGTTTTAACAATCTTTTGATTGTGGGAGCCATCTTCAACCT
* *
41435870 TCTTCTTGCCATTGATATTCTTTGGAGGGGAGATTAGAGCCGTTTGAAGAGATTTGTGAAATCTT
389 TCTTCTTGCCATCGATATTCTTTGAAGGGGAGATTAGAGCCGTTTGAAGAGATTTGTGAAATCTT
* *
41435935 TCGGGATTTCAAGGATCTTTAGGACTTATCCTTTAATTCTTGTTGTTTTCGATTTCTTTCTTTAC
454 TCGAGATTTCAAGGATCTTTAGGACTTATCCTTTAATTCTTGCTGTTTTCGATTTCTTTCTTTAC
*
41436000 TTTTCTTTGCTTATACTTGTGCCGATTTCTCATCTAATATTTTGCTGTTCTTGTTTGTTTTCCAG
519 TTTTCTTTGCTTATACTTGTGCCAATTTCTCATCTAATATTTTGCTGTTCTTGTTTGTTTTCCAG
* *
41436065 CATTGATTAAACTCAAGATTTCATCGTTTAAGTTGTTCTCCTATTGGCAGCACCCATTCGACCCC
584 CATTGATTAAACTCAAGATCTCATCGTTTAAGTTGTTCTCCTATTGGCAGCACCCATTCGAACCC
41436130 AAAAATCCCCAATTCCTAGGGTTTGGCCGATTGGATTTCTTTCAATTTGGGAATCAATTGATTGC
649 AAAAATCCCCAATTCCTAGGGTTTGGCCGATTGGATTTCTTTCAATTTGGGAATCAATTGATTGC
* *** *
41436195 TGGAAATTGGGCATTCTTGGCCGAATCAATTTGTTGACCA-ATTCGCAAT-CTTTCTATACTTCC
714 TGGAAATTAGGCATTCTTGGCCGAATCAATCCCTTG-CCAGATTCGC-ATCCTTTCCATACTTCC
* * * *
41436258 AATTTCGTTTGATTC-ATCTATTCTATTTCTTTGTTTCTTGCTGCTCCTTTAATTGAATTTGGGG
777 AATTCCATTTGATTCGCT-TATTCTATTTCTTTATTTCTTGCTGCTCCTTTAATTGAATTTGGGG
*
41436322 -ATTTAAATTCAAATATGATTCG-GTTTAATCTTAATCTTTGTTTTTGGATTTCAGATATG-TTC
841 AATTTAAATTCAAATATGATTCGTGTTTAATCTTAATCTTTG--TTTCGATTTCAGATATGATTC
* * * * *
41436384 GTCTAGGATCTTTCGTAGGAGTTTCTCGTGACTTGGCAACTTGATCTTGGTCCGCGCGTAACC
904 GTCCA-GAGCTTTCATAGGAGTTTCTCGTGACTTGGCAACTCGATCTTGGTCCGCGCGCAACC
41436447 CCGTATCAGA
Statistics
Matches: 912, Mismatches: 47, Indels: 14
0.94 0.05 0.01
Matches are distributed among these distances:
973 164 0.18
974 131 0.14
975 613 0.67
976 4 0.00
ACGTcount: A:0.24, C:0.17, G:0.17, T:0.42
Consensus pattern (973 bp):
CCATACATATTTAGTTGAAAATCAGGCCAAAATGTCAAAGGGCCCAATTTGTAAACATTTTAGTT
GTTTAAGTTAATTTTTAAGTTTTAGAAATATCACATGTTAAATTCAGCCCAAAACAGCCCAATAG
GATGCATGGCCGAATTTTCCTTTGTTTTTTTAATTAAGTTTAAATTTTTTAAGTTTTCTAATTAG
ATTAGGATTTGTTGGAGGCCTATATAAGCATTGGCCAGCCACCCTTTGTAAACATCTTATTATTA
TTTTTCTATCAAATTTCAGATTTGTTGAGTGCAGAATTTTATTTGGGGTTTTCTCCAAGAATTCT
CTCTTGAGTTTTCTTTAGAAGTTGTTTTAACAATCTTTTGATTGTGGGAGCCATCTTCAACCTTC
TTCTTGCCATCGATATTCTTTGAAGGGGAGATTAGAGCCGTTTGAAGAGATTTGTGAAATCTTTC
GAGATTTCAAGGATCTTTAGGACTTATCCTTTAATTCTTGCTGTTTTCGATTTCTTTCTTTACTT
TTCTTTGCTTATACTTGTGCCAATTTCTCATCTAATATTTTGCTGTTCTTGTTTGTTTTCCAGCA
TTGATTAAACTCAAGATCTCATCGTTTAAGTTGTTCTCCTATTGGCAGCACCCATTCGAACCCAA
AAATCCCCAATTCCTAGGGTTTGGCCGATTGGATTTCTTTCAATTTGGGAATCAATTGATTGCTG
GAAATTAGGCATTCTTGGCCGAATCAATCCCTTGCCAGATTCGCATCCTTTCCATACTTCCAATT
CCATTTGATTCGCTTATTCTATTTCTTTATTTCTTGCTGCTCCTTTAATTGAATTTGGGGAATTT
AAATTCAAATATGATTCGTGTTTAATCTTAATCTTTGTTTCGATTTCAGATATGATTCGTCCAGA
GCTTTCATAGGAGTTTCTCGTGACTTGGCAACTCGATCTTGGTCCGCGCGCAACCTCATATTA
Found at i:41438614 original size:13 final size:13
Alignment explanation
Indices: 41438596--41438626 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
41438586 TTGTAGATTC
41438596 AAAAAAATCGAAA
1 AAAAAAATCGAAA
*
41438609 AAAAAAATTGAAA
1 AAAAAAATCGAAA
41438622 AAAAA
1 AAAAA
41438627 TTTGAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.81, C:0.03, G:0.06, T:0.10
Consensus pattern (13 bp):
AAAAAAATCGAAA
Found at i:41438635 original size:13 final size:12
Alignment explanation
Indices: 41438596--41438638 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
41438586 TTGTAGATTC
*
41438596 AAAAAAATCGAAA
1 AAAAAAATTG-AA
41438609 AAAAAAATTGAA
1 AAAAAAATTGAA
*
41438621 AAAAAATTTGAA
1 AAAAAAATTGAA
41438633 AAAAAA
1 AAAAAA
41438639 TTGCATACGG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
12 19 0.68
13 9 0.32
ACGTcount: A:0.77, C:0.02, G:0.07, T:0.14
Consensus pattern (12 bp):
AAAAAAATTGAA
Found at i:41445209 original size:9 final size:9
Alignment explanation
Indices: 41445197--41445224 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
41445187 CCAAGATTTC
41445197 AAATCTTGG
1 AAATCTTGG
41445206 AAATCTTGG
1 AAATCTTGG
41445215 AAATCTTGG
1 AAATCTTGG
41445224 A
1 A
41445225 TTACAAGCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.32
Consensus pattern (9 bp):
AAATCTTGG
Found at i:41447593 original size:12 final size:12
Alignment explanation
Indices: 41447575--41447633 Score: 84
Period size: 13 Copynumber: 4.8 Consensus size: 12
41447565 AAGAAATTCA
41447575 GAAAAAAAAATT
1 GAAAAAAAAATT
*
41447587 CAAAAAAAAAATT
1 -GAAAAAAAAATT
41447600 G-AAAAAAAATT
1 GAAAAAAAAATT
41447611 GAAAAAAAAATT
1 GAAAAAAAAATT
41447623 GAAAAGAAAAA
1 GAAAA-AAAAA
41447634 AAAAATCGCA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.26
12 15 0.36
13 16 0.38
ACGTcount: A:0.76, C:0.02, G:0.08, T:0.14
Consensus pattern (12 bp):
GAAAAAAAAATT
Found at i:41447604 original size:10 final size:11
Alignment explanation
Indices: 41447590--41447632 Score: 68
Period size: 11 Copynumber: 3.7 Consensus size: 11
41447580 AAAAATTCAA
41447590 AAAAAAAATTG
1 AAAAAAAATTG
41447601 AAAAAAAATTG
1 AAAAAAAATTG
41447612 AAAAAAAAATTG
1 -AAAAAAAATTG
41447624 AAAAGAAAA
1 AAAA-AAAA
41447633 AAAAAATCGC
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
11 15 0.50
12 15 0.50
ACGTcount: A:0.77, C:0.00, G:0.09, T:0.14
Consensus pattern (11 bp):
AAAAAAAATTG
Found at i:41447604 original size:23 final size:23
Alignment explanation
Indices: 41447577--41447632 Score: 85
Period size: 23 Copynumber: 2.3 Consensus size: 23
41447567 GAAATTCAGA
41447577 AAAAAAAATTCAAAAAAAAAATTG
1 AAAAAAAATT-AAAAAAAAAATTG
*
41447601 AAAAAAAATTGAAAAAAAAATTG
1 AAAAAAAATTAAAAAAAAAATTG
41447624 AAAAGAAAA
1 AAAA-AAAA
41447633 AAAAAATCGC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 16 0.53
24 14 0.47
ACGTcount: A:0.77, C:0.02, G:0.07, T:0.14
Consensus pattern (23 bp):
AAAAAAAATTAAAAAAAAAATTG
Found at i:41448723 original size:18 final size:18
Alignment explanation
Indices: 41448685--41448726 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
41448675 AAATCGAAAG
* **
41448685 AAAAGAAAAAGAGATTGA
1 AAAAGAAAAAGAAATCCA
41448703 AAAAGAAAAAGAAATCCA
1 AAAAGAAAAAGAAATCCA
41448721 AAAAGA
1 AAAAGA
41448727 GAGTGAGGTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.71, C:0.05, G:0.17, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAATCCA
Found at i:41451991 original size:13 final size:13
Alignment explanation
Indices: 41451973--41452040 Score: 86
Period size: 13 Copynumber: 5.2 Consensus size: 13
41451963 AAAGGAGAAG
41451973 AAATTCAAAAAAA
1 AAATTCAAAAAAA
41451986 AAATTCAAAAAAA
1 AAATTCAAAAAAA
41451999 AAA-TCGAAAAAAA
1 AAATTC-AAAAAAA
*
41452012 AAATT-GAAAAAA
1 AAATTCAAAAAAA
*
41452024 AAATTGAAAAGAAA
1 AAATTCAAAA-AAA
41452038 AAA
1 AAA
41452041 AATCGCATAT
Statistics
Matches: 49, Mismatches: 2, Indels: 7
0.84 0.03 0.12
Matches are distributed among these distances:
12 13 0.27
13 29 0.59
14 7 0.14
ACGTcount: A:0.76, C:0.04, G:0.06, T:0.13
Consensus pattern (13 bp):
AAATTCAAAAAAA
Found at i:41451997 original size:12 final size:12
Alignment explanation
Indices: 41451973--41452039 Score: 71
Period size: 12 Copynumber: 5.2 Consensus size: 12
41451963 AAAGGAGAAG
41451973 AAATTCAAAAAAA
1 AAATTC-AAAAAA
41451986 AAATTCAAAAAA
1 AAATTCAAAAAA
*
41451998 AAAATCGAAAAAAA
1 AAATTC--AAAAAA
*
41452012 AAATTGAAAAAA
1 AAATTCAAAAAA
*
41452024 AAATTGAAAAGAA
1 AAATTCAAAA-AA
41452037 AAA
1 AAA
41452040 AAATCGCATA
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
12 27 0.56
13 11 0.23
14 10 0.21
ACGTcount: A:0.76, C:0.04, G:0.06, T:0.13
Consensus pattern (12 bp):
AAATTCAAAAAA
Found at i:41453097 original size:21 final size:22
Alignment explanation
Indices: 41453073--41453121 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
41453063 AGTACGAGCG
41453073 AGAAAAAGAAATCG-AAAGAAA
1 AGAAAAAGAAATCGAAAAGAAA
* *
41453094 AGAAAAAGAGATTGAAAAAGAAA
1 AGAAAAAGAAATCG-AAAAGAAA
41453117 AGAAA
1 AGAAA
41453122 TCCAAAAGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 12 0.50
23 12 0.50
ACGTcount: A:0.71, C:0.02, G:0.20, T:0.06
Consensus pattern (22 bp):
AGAAAAAGAAATCGAAAAGAAA
Found at i:41461479 original size:29 final size:29
Alignment explanation
Indices: 41461442--41461514 Score: 119
Period size: 29 Copynumber: 2.5 Consensus size: 29
41461432 TTAGATATTA
* *
41461442 TTAAATATGTCCTAATTAGTTTAGGTGTT
1 TTAAATATGTCCTAATTAGTTCAAGTGTT
*
41461471 TTAATTATGTCCTAATTAGTTCAAGTGTT
1 TTAAATATGTCCTAATTAGTTCAAGTGTT
41461500 TTAAATATGTCCTAA
1 TTAAATATGTCCTAA
41461515 ACTAATACAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.30, C:0.10, G:0.14, T:0.47
Consensus pattern (29 bp):
TTAAATATGTCCTAATTAGTTCAAGTGTT
Found at i:41467884 original size:20 final size:19
Alignment explanation
Indices: 41467861--41467925 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
41467851 AAGCTCAAAC
41467861 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
41467881 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
41467901 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
41467921 GAGCT
1 GAGCT
41467926 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:41469213 original size:17 final size:18
Alignment explanation
Indices: 41469191--41469224 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41469181 ACAACACTCC
*
41469191 TTTCTT-CTTCACTCTCG
1 TTTCTTCCTTCAATCTCG
41469208 TTTCTTCCTTCAATCTC
1 TTTCTTCCTTCAATCTC
41469225 ACTCTCTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.09, C:0.35, G:0.03, T:0.53
Consensus pattern (18 bp):
TTTCTTCCTTCAATCTCG
Found at i:41469332 original size:15 final size:16
Alignment explanation
Indices: 41469307--41469338 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
41469297 TATCTCACAC
41469307 TCATCTTCTTTTTCTT
1 TCATCTTCTTTTTCTT
41469323 TCAT-TTCTTTTTCTT
1 TCATCTTCTTTTTCTT
41469338 T
1 T
41469339 TTCATTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (16 bp):
TCATCTTCTTTTTCTT
Done.