Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D13
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: 64892201
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 23 of 221
Found at i:6463829 original size:26 final size:28
Alignment explanation
Indices: 6463779--6463833 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
6463769 ATACTTATAT
6463779 TATATTTAAATTAAATAATATATGAAAA
1 TATATTTAAATTAAATAATATATGAAAA
* *
6463807 TATA-TTATATTAAATCATA-ATGAAAA
1 TATATTTAAATTAAATAATATATGAAAA
6463833 T
1 T
6463834 CATTACATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 8 0.32
27 13 0.52
28 4 0.16
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.40
Consensus pattern (28 bp):
TATATTTAAATTAAATAATATATGAAAA
Found at i:6464720 original size:16 final size:16
Alignment explanation
Indices: 6464699--6464736 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
6464689 TTAAAATAAT
* *
6464699 TTTAAAATAATTTAAC
1 TTTAAAATAATCTAAA
6464715 TTT-AAATAATCTAAA
1 TTTAAAATAATCTAAA
6464730 TTTAAAA
1 TTTAAAA
6464737 CGATTAGAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (16 bp):
TTTAAAATAATCTAAA
Found at i:6469752 original size:18 final size:18
Alignment explanation
Indices: 6469716--6469749 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
6469706 GTATAAATAC
6469716 GTATATATAAAATATAAG
1 GTATATATAAAATATAAG
6469734 GTATATA-AAAATATAA
1 GTATATATAAAATATAA
6469750 AGGATAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.59, C:0.00, G:0.09, T:0.32
Consensus pattern (18 bp):
GTATATATAAAATATAAG
Found at i:6471487 original size:44 final size:42
Alignment explanation
Indices: 6471437--6471586 Score: 117
Period size: 44 Copynumber: 3.4 Consensus size: 42
6471427 TCCACACCAT
6471437 TGCAACTTCAAGGAGATAGGATTGGTTACTTCTGTCTGCTCCAC
1 TGCAACTTCAAGGAGATAGGATTGGTTA-TT-TGTCTGCTCCAC
* ** ** *
6471481 TGCAACTTC-A-GAGAAATGAGATCTGCGGTT-TTAATCCACTCCAT
1 TGCAACTTCAAGGAGATA-G-GAT-T--GGTTATTTGTCTGCTCCAC
* *
6471525 TGCAACTTCAAGGAGATAGGATTGATTAGTTTTGTCTGCTCTAC
1 TGCAACTTCAAGGAGATAGGATTGGTTA--TTTGTCTGCTCCAC
*
6471569 TGCAACTTCAGGGAGATA
1 TGCAACTTCAAGGAGATA
6471587 AGACTTGTAT
Statistics
Matches: 81, Mismatches: 15, Indels: 20
0.70 0.13 0.17
Matches are distributed among these distances:
41 3 0.04
42 5 0.06
43 3 0.04
44 56 0.69
45 5 0.06
46 5 0.06
47 4 0.05
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (42 bp):
TGCAACTTCAAGGAGATAGGATTGGTTATTTGTCTGCTCCAC
Found at i:6471518 original size:88 final size:86
Alignment explanation
Indices: 6471385--6471579 Score: 291
Period size: 88 Copynumber: 2.2 Consensus size: 86
6471375 CTTGATGCGA
* * *
6471385 TCTGCTCTACTGCAACTCCAGAGAGATGATCTGCAGTTTTGATCCACACCATTGCAACTTCAAGG
1 TCTGCTCTACTGCAACTTCAGAGAAATGATCTGCAGTTTTAATCCACACCATTGCAACTTCAAGG
*
6471450 AGATAGGATTGGTTACTTCTG
66 AGATAGGATTGATTACTTCTG
* * *
6471471 TCTGCTCCACTGCAACTTCAGAGAAATGAGATCTGCGGTTTTAATCCACTCCATTGCAACTTCAA
1 TCTGCTCTACTGCAACTTCAGAGAAAT--GATCTGCAGTTTTAATCCACACCATTGCAACTTCAA
* *
6471536 GGAGATAGGATTGATTAGTTTTG
64 GGAGATAGGATTGATTACTTCTG
6471559 TCTGCTCTACTGCAACTTCAG
1 TCTGCTCTACTGCAACTTCAG
6471580 GGAGATAAGA
Statistics
Matches: 97, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
86 24 0.25
88 73 0.75
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (86 bp):
TCTGCTCTACTGCAACTTCAGAGAAATGATCTGCAGTTTTAATCCACACCATTGCAACTTCAAGG
AGATAGGATTGATTACTTCTG
Found at i:6471878 original size:50 final size:50
Alignment explanation
Indices: 6471816--6472575 Score: 361
Period size: 50 Copynumber: 15.2 Consensus size: 50
6471806 GATCTGTAAT
* *
6471816 CTTCAATTTGTTCAATTGCAATGTTGGGGAAACTAGATCCGCCGTCGTAG
1 CTTCAATCTGTTCAATTGCAATGTTAGGGAAACTAGATCCGCCGTCGTAG
* ** * ** * * *
6471866 CTTCAATCTGTTCCACCGCACTGCCAGGG-AAGTAAGATCCGCCGTTGTGG
1 CTTCAATCTGTTCAATTGCAATGTTAGGGAAACT-AGATCCGCCGTCGTAG
* * * *
6471916 CTTCAATCTTTTTTAATTGCAATATTAGGGAAACCAGATCCGCCGTCGTAG
1 CTTCAATC-TGTTCAATTGCAATGTTAGGGAAACTAGATCCGCCGTCGTAG
* * * * * * *
6471967 CTTCAATCTGTTCCATTGCACTGCTAAGG-AAGTAAGATCTGCCGTTGTAG
1 CTTCAATCTGTTCAATTGCAATGTTAGGGAAACT-AGATCCGCCGTCGTAG
* * * * *
6472017 CTTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAG
1 CTTCAATCTGTTCAATTGCAATGTTAGGGAAACTAGATCCGCCGTCGTAG
* * * * * * *
6472067 CTTCAATCTGTTCCATTGCACTGCTAAGG-AAGTAAGATCCGCCGTTGTGG
1 CTTCAATCTGTTCAATTGCAATGTTAGGGAAACT-AGATCCGCCGTCGTAG
* * * * *
6472117 CTTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAG
1 CTTCAATCTGTTCAATTGCAATGTTAGGGAAACTAGATCCGCCGTCGTAG
* *** * * * * * *
6472167 CTTCAATCTATTCCGCTGTACTGCTAAGG-AAGTAAGATCCGCCG-CTGTGG
1 CTTCAATCTGTTCAATTGCAATGTTAGGGAAACT-AGATCCGCCGTC-GTAG
* * * * * * *
6472217 CTTCAATCTTTTTAATTGCAATATCATGGAAACCAGATCTGCCGTCGTAG
1 CTTCAATCTGTTCAATTGCAATGTTAGGGAAACTAGATCCGCCGTCGTAG
* ** * * * * * * * *
6472267 CTTCAATCTATTTC-GCTGTACTGCTAAGG-AAGTAAGATCCGCTGTTGTGG
1 CTTCAATCT-GTTCAATTGCAATGTTAGGGAAACT-AGATCCGCCGTCGTAG
* * * * * * *
6472317 CTTCAATATCTTTAATTGCAATATCAGGGAAACCAGATCCGCTGTCGTAG
1 CTTCAATCTGTTCAATTGCAATGTTAGGGAAACTAGATCCGCCGTCGTAG
* *** * ** * * * *
6472367 CTTCAATCTATTCCGCTGTAATACTAAGG-AAGTAAGATCCGCCGTTGTGG
1 CTTCAATCTGTTCAATTGCAATGTTAGGGAAACT-AGATCCGCCGTCGTAG
* * * * * * *
6472417 CTTCAATCTTTTTAATTGAAATATCAGGGAAACCAGATCTGCCGTCGTAG
1 CTTCAATCTGTTCAATTGCAATGTTAGGGAAACTAGATCCGCCGTCGTAG
* *** * * * * * * *
6472467 CTTCAATCTATTCCGCTGTACTGCTAAGG-AAGTAAGATCCACCGTTGT-G
1 CTTCAATCTGTTCAATTGCAATGTTAGGGAAACT-AGATCCGCCGTCGTAG
* * * * * * *
6472516 ACTTCAATCTCTTTAATTGCAATATCAGGGAAACCAGACCCGCTGTCGTAG
1 -CTTCAATCTGTTCAATTGCAATGTTAGGGAAACTAGATCCGCCGTCGTAG
6472567 CTTCAATCT
1 CTTCAATCT
6472576 ATTCCGCTGT
Statistics
Matches: 497, Mismatches: 192, Indels: 42
0.68 0.26 0.06
Matches are distributed among these distances:
49 19 0.04
50 425 0.86
51 51 0.10
52 2 0.00
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (50 bp):
CTTCAATCTGTTCAATTGCAATGTTAGGGAAACTAGATCCGCCGTCGTAG
Found at i:6472082 original size:100 final size:100
Alignment explanation
Indices: 6471816--6472634 Score: 1262
Period size: 100 Copynumber: 8.2 Consensus size: 100
6471806 GATCTGTAAT
* * ** * *
6471816 CTTCAAT-TTGTTCAATTGCAATGTTGGGGAAACTAGATCCGCCGTCGTAGCTTCAATCTGTTCC
1 CTTCAATCTT-TTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTATTCC
* * * * *
6471880 ACCGCACTGCCAGGGAAGTAAGATCCGCCGTTGTGG
65 GCTGTACTGCTAAGGAAGTAAGATCCGCCGTTGTGG
* *
6471916 CTTCAATCTTTTTTAATTGCAATATTAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCC
1 CTTCAATC-TTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTATTCC
** * * *
6471981 ATTGCACTGCTAAGGAAGTAAGATCTGCCGTTGTAG
65 GCTGTACTGCTAAGGAAGTAAGATCCGCCGTTGTGG
* *
6472017 CTTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCA
1 CTTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTATTCCG
* *
6472082 TTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGG
66 CTGTACTGCTAAGGAAGTAAGATCCGCCGTTGTGG
6472117 CTTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTATTCCG
1 CTTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTATTCCG
*
6472182 CTGTACTGCTAAGGAAGTAAGATCCGCCGCTGTGG
66 CTGTACTGCTAAGGAAGTAAGATCCGCCGTTGTGG
* * *
6472217 CTTCAATCTTTTTAATTGCAATATCATGGAAACCAGATCTGCCGTCGTAGCTTCAATCTATTTCG
1 CTTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTATTCCG
*
6472282 CTGTACTGCTAAGGAAGTAAGATCCGCTGTTGTGG
66 CTGTACTGCTAAGGAAGTAAGATCCGCCGTTGTGG
* * *
6472317 CTTCAATATCTTTAATTGCAATATCAGGGAAACCAGATCCGCTGTCGTAGCTTCAATCTATTCCG
1 CTTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTATTCCG
* *
6472382 CTGTAATACTAAGGAAGTAAGATCCGCCGTTGTGG
66 CTGTACTGCTAAGGAAGTAAGATCCGCCGTTGTGG
* *
6472417 CTTCAATCTTTTTAATTGAAATATCAGGGAAACCAGATCTGCCGTCGTAGCTTCAATCTATTCCG
1 CTTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTATTCCG
* *
6472482 CTGTACTGCTAAGGAAGTAAGATCCACCGTTGTGA
66 CTGTACTGCTAAGGAAGTAAGATCCGCCGTTGTGG
* * *
6472517 CTTCAATCTCTTTAATTGCAATATCAGGGAAACCAGACCCGCTGTCGTAGCTTCAATCTATTCCG
1 CTTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTATTCCG
6472582 CTGTACTGCTAAGGAAGTAAGATCCGCCGTTGTGG
66 CTGTACTGCTAAGGAAGTAAGATCCGCCGTTGTGG
6472617 CTTCAATCTTTTTAATTG
1 CTTCAATCTTTTTAATTG
6472635 TAACCCGCTC
Statistics
Matches: 668, Mismatches: 49, Indels: 4
0.93 0.07 0.01
Matches are distributed among these distances:
100 578 0.87
101 88 0.13
102 2 0.00
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (100 bp):
CTTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTATTCCG
CTGTACTGCTAAGGAAGTAAGATCCGCCGTTGTGG
Found at i:6477169 original size:19 final size:18
Alignment explanation
Indices: 6477147--6477186 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
6477137 AAAAAGTATA
6477147 AAAAATATAGAAAAAACTT
1 AAAAATATA-AAAAAACTT
*
6477166 AAAAATATAAAAAACCTT
1 AAAAATATAAAAAAACTT
6477184 AAA
1 AAA
6477187 CCATAAACCC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.70, C:0.07, G:0.03, T:0.20
Consensus pattern (18 bp):
AAAAATATAAAAAAACTT
Found at i:6477178 original size:9 final size:9
Alignment explanation
Indices: 6477127--6477179 Score: 54
Period size: 9 Copynumber: 5.7 Consensus size: 9
6477117 TTTACAAGTC
6477127 AAAAAAGTAT
1 AAAAAA-TAT
*
6477137 AAAAAGTAT
1 AAAAAATAT
6477146 AAAAAATAT
1 AAAAAATAT
6477155 AGAAAAA-ACT
1 A-AAAAATA-T
*
6477165 TAAAAATAT
1 AAAAAATAT
6477174 AAAAAA
1 AAAAAA
6477180 CCTTAAACCA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
9 24 0.67
10 12 0.33
ACGTcount: A:0.74, C:0.02, G:0.06, T:0.19
Consensus pattern (9 bp):
AAAAAATAT
Found at i:6477179 original size:17 final size:19
Alignment explanation
Indices: 6477147--6477186 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
6477137 AAAAAGTATA
6477147 AAAAATATAGAAAAAA-CTT
1 AAAAATATA-AAAAAACCTT
6477166 AAAAATAT-AAAAAACCTT
1 AAAAATATAAAAAAACCTT
6477184 AAA
1 AAA
6477187 CCATAAACCC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 6 0.30
18 6 0.30
19 8 0.40
ACGTcount: A:0.70, C:0.07, G:0.03, T:0.20
Consensus pattern (19 bp):
AAAAATATAAAAAAACCTT
Found at i:6480102 original size:16 final size:16
Alignment explanation
Indices: 6480052--6480104 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
6480042 TTTCTTCAAC
*
6480052 TTAAACTTAAAATTGAT
1 TTAAATTTAAAA-TGAT
* * **
6480069 TTGAATTCAAAACAAT
1 TTAAATTTAAAATGAT
6480085 TTAAATTTAAAATGAT
1 TTAAATTTAAAATGAT
6480101 TTAA
1 TTAA
6480105 TTCTAAATAA
Statistics
Matches: 27, Mismatches: 9, Indels: 1
0.73 0.24 0.03
Matches are distributed among these distances:
16 18 0.67
17 9 0.33
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.40
Consensus pattern (16 bp):
TTAAATTTAAAATGAT
Found at i:6481579 original size:26 final size:26
Alignment explanation
Indices: 6481550--6481602 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
6481540 AGCCACAATT
6481550 TGAGGTTAAACTAA-CTCAAATTATTC
1 TGAGGTTAAACTAACCT-AAATTATTC
* *
6481576 TGAGGTTAAATTGACCTAAATTATTC
1 TGAGGTTAAACTAACCTAAATTATTC
6481602 T
1 T
6481603 TTGAGAAGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 22 0.92
27 2 0.08
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (26 bp):
TGAGGTTAAACTAACCTAAATTATTC
Found at i:6485933 original size:14 final size:14
Alignment explanation
Indices: 6485898--6485942 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
6485888 AAAAATCCTG
*
6485898 AACCTTGAA-CTCA
1 AACCTTGAACCTTA
*
6485911 AACCATGAACCTTA
1 AACCTTGAACCTTA
*
6485925 AACCTTGAACCCTA
1 AACCTTGAACCTTA
6485939 AACC
1 AACC
6485943 CTAAAGTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
13 8 0.30
14 19 0.70
ACGTcount: A:0.40, C:0.33, G:0.07, T:0.20
Consensus pattern (14 bp):
AACCTTGAACCTTA
Found at i:6485968 original size:14 final size:14
Alignment explanation
Indices: 6485949--6485978 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
6485939 AACCCTAAAG
*
6485949 TTTAAGGTTTAAGA
1 TTTAAGGTTCAAGA
6485963 TTTAAGGTTCAAGA
1 TTTAAGGTTCAAGA
6485977 TT
1 TT
6485979 CGGTTTTGGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.03, G:0.20, T:0.43
Consensus pattern (14 bp):
TTTAAGGTTCAAGA
Found at i:6486447 original size:27 final size:28
Alignment explanation
Indices: 6486416--6486469 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
6486406 ACCCTAAAAG
6486416 CATAACAATAAACCATAAA-CTAGAACC
1 CATAACAATAAACCATAAATCTAGAACC
* * *
6486443 CATAACACTAAATCTTAAATCTAGAAC
1 CATAACAATAAACCATAAATCTAGAAC
6486470 TTGAACCACA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 16 0.70
28 7 0.30
ACGTcount: A:0.52, C:0.24, G:0.04, T:0.20
Consensus pattern (28 bp):
CATAACAATAAACCATAAATCTAGAACC
Found at i:6486495 original size:19 final size:19
Alignment explanation
Indices: 6486471--6486507 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
6486461 ATCTAGAACT
6486471 TGAACCACA-AACCCTAAAC
1 TGAACC-CATAACCCTAAAC
6486490 TGAACCCATAACCCTAAA
1 TGAACCCATAACCCTAAA
6486508 TCATAAGACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 2 0.12
19 15 0.88
ACGTcount: A:0.46, C:0.35, G:0.05, T:0.14
Consensus pattern (19 bp):
TGAACCCATAACCCTAAAC
Found at i:6486548 original size:28 final size:28
Alignment explanation
Indices: 6486495--6486563 Score: 72
Period size: 28 Copynumber: 2.5 Consensus size: 28
6486485 TAAACTGAAC
*
6486495 CCAT-AACCCTAAATCATAAGACTAAAA
1 CCATAAACCCTAAATAATAAGACTAAAA
* *
6486522 TC-TCAAACCCTAAATAATTAA-ATTAAAA
1 CCAT-AAACCCTAAATAA-TAAGACTAAAA
6486550 CCATAAACCCTAAA
1 CCATAAACCCTAAA
6486564 CTTAAACACA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
26 1 0.03
27 1 0.03
28 28 0.82
29 4 0.12
ACGTcount: A:0.52, C:0.25, G:0.01, T:0.22
Consensus pattern (28 bp):
CCATAAACCCTAAATAATAAGACTAAAA
Found at i:6487015 original size:21 final size:21
Alignment explanation
Indices: 6486971--6487015 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
6486961 TAATAACCAT
* * * *
6486971 AAATCCTAAACCTTAAATCTA
1 AAATCCCAAACCATAAACCCA
6486992 AAATCCCAAACCATAAACCCA
1 AAATCCCAAACCATAAACCCA
6487013 AAA
1 AAA
6487016 CCTAGAAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.53, C:0.29, G:0.00, T:0.18
Consensus pattern (21 bp):
AAATCCCAAACCATAAACCCA
Found at i:6487224 original size:7 final size:7
Alignment explanation
Indices: 6487214--6487239 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
6487204 CCTTGAATTC
6487214 TAAACAT
1 TAAACAT
6487221 TAAACAT
1 TAAACAT
6487228 TAAACAT
1 TAAACAT
6487235 TAAAC
1 TAAAC
6487240 CATGAACTTT
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):
TAAACAT
Found at i:6487286 original size:28 final size:27
Alignment explanation
Indices: 6487265--6487328 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 27
6487255 TAAAATCTCG
6487265 AACCCTAAATCTAAAACATAAAACCTAA
1 AACCCTAAA-CTAAAACATAAAACCTAA
* *
6487293 AACTCTAAACTTAAACATAAAA-CTATA
1 AACCCTAAACTAAAACATAAAACCTA-A
*
6487320 AACCATAAA
1 AACCCTAAA
6487329 TTTAGAATCA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
26 3 0.10
27 20 0.65
28 8 0.26
ACGTcount: A:0.58, C:0.22, G:0.00, T:0.20
Consensus pattern (27 bp):
AACCCTAAACTAAAACATAAAACCTAA
Found at i:6487308 original size:20 final size:20
Alignment explanation
Indices: 6487285--6487322 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
6487275 CTAAAACATA
* *
6487285 AAACCTAAAACTCTAAACTT
1 AAACATAAAACTATAAACTT
6487305 AAACATAAAACTATAAAC
1 AAACATAAAACTATAAAC
6487323 CATAAATTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.58, C:0.21, G:0.00, T:0.21
Consensus pattern (20 bp):
AAACATAAAACTATAAACTT
Found at i:6487483 original size:7 final size:7
Alignment explanation
Indices: 6487401--6487494 Score: 52
Period size: 7 Copynumber: 13.6 Consensus size: 7
6487391 CCTAAACACT
*
6487401 TAAACCC
1 TAAACCA
*
6487408 TAAA-CT
1 TAAACCA
*
6487414 TAAACAA
1 TAAACCA
*
6487421 TAAACAA
1 TAAACCA
6487428 TAAACCA
1 TAAACCA
6487435 TAAAACC-
1 T-AAACCA
*
6487442 TCAATCACA
1 T-AAAC-CA
6487451 T-AACCA
1 TAAACCA
* *
6487457 TCAACCC
1 TAAACCA
6487464 TAAACC-
1 TAAACCA
6487470 TAAACCA
1 TAAACCA
6487477 TAAACCA
1 TAAACCA
* *
6487484 TTAACCT
1 TAAACCA
6487491 TAAA
1 TAAA
6487495 TCTAAAATCA
Statistics
Matches: 69, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
6 14 0.20
7 48 0.70
8 6 0.09
9 1 0.01
ACGTcount: A:0.52, C:0.29, G:0.00, T:0.19
Consensus pattern (7 bp):
TAAACCA
Found at i:6487489 original size:20 final size:20
Alignment explanation
Indices: 6487452--6487490 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
6487442 TCAATCACAT
* *
6487452 AACCATCAACCCTAAACCTA
1 AACCATAAACCATAAACCTA
*
6487472 AACCATAAACCATTAACCT
1 AACCATAAACCATAAACCT
6487491 TAAATCTAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.46, C:0.36, G:0.00, T:0.18
Consensus pattern (20 bp):
AACCATAAACCATAAACCTA
Found at i:6487504 original size:56 final size:55
Alignment explanation
Indices: 6487403--6487512 Score: 132
Period size: 56 Copynumber: 2.0 Consensus size: 55
6487393 TAAACACTTA
* *
6487403 AACCCTAAACTTAAACAATAAACAATAAACCATAAAACCTCAATCACATAACCATC
1 AACCCTAAACCTAAACAATAAACAATAAACCATAAAACCTAAATCACA-AACCATC
* * * * *
6487459 AACCCTAAACCTAAACCATAAACCATTAACC-TTAAATCTAAAATCACAAACCAT
1 AACCCTAAACCTAAACAATAAACAATAAACCATAAAACCT-AAATCACAAACCAT
6487513 GGACCATAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
55 12 0.26
56 34 0.74
ACGTcount: A:0.52, C:0.29, G:0.00, T:0.19
Consensus pattern (55 bp):
AACCCTAAACCTAAACAATAAACAATAAACCATAAAACCTAAATCACAAACCATC
Found at i:6487639 original size:14 final size:14
Alignment explanation
Indices: 6487622--6487668 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
6487612 CCTTAAACAA
*
6487622 TAAACTATAAAATC
1 TAAACTATAAAACC
*
6487636 TAAACTCTAAAACC
1 TAAACTATAAAACC
*
6487650 TAAAACT-TAAACCC
1 T-AAACTATAAAACC
6487664 TAAAC
1 TAAAC
6487669 CTTTAAATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
13 4 0.14
14 20 0.69
15 5 0.17
ACGTcount: A:0.53, C:0.23, G:0.00, T:0.23
Consensus pattern (14 bp):
TAAACTATAAAACC
Found at i:6487738 original size:28 final size:28
Alignment explanation
Indices: 6487707--6487793 Score: 79
Period size: 28 Copynumber: 3.1 Consensus size: 28
6487697 TCTCAAACCA
*
6487707 TAAACCATAAACATAAAAGCCT-AATCAC
1 TAAACCATAAACATAAAACCCTAAAT-AC
* * * * *
6487735 TAAACCTTAAAGACACAACCCTAAATAT
1 TAAACCATAAACATAAAACCCTAAATAC
*
6487763 TAAACCATAAACACT-AAACCCTAAATCC
1 TAAACCATAAACA-TAAAACCCTAAATAC
6487791 TAA
1 TAA
6487794 GCCCAAACCT
Statistics
Matches: 45, Mismatches: 12, Indels: 4
0.74 0.20 0.07
Matches are distributed among these distances:
28 42 0.93
29 3 0.07
ACGTcount: A:0.52, C:0.26, G:0.02, T:0.20
Consensus pattern (28 bp):
TAAACCATAAACATAAAACCCTAAATAC
Found at i:6487768 original size:14 final size:14
Alignment explanation
Indices: 6487733--6487793 Score: 52
Period size: 14 Copynumber: 4.4 Consensus size: 14
6487723 AAGCCTAATC
* *
6487733 ACTAAACCTTAAAG
1 ACTAAACCCTAAAT
6487747 AC-ACAACCCTAAAT
1 ACTA-AACCCTAAAT
* * *
6487761 ATTAAACCATAAAC
1 ACTAAACCCTAAAT
6487775 ACTAAACCCTAAAT
1 ACTAAACCCTAAAT
*
6487789 CCTAA
1 ACTAA
6487794 GCCCAAACCT
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
13 1 0.03
14 34 0.94
15 1 0.03
ACGTcount: A:0.51, C:0.28, G:0.02, T:0.20
Consensus pattern (14 bp):
ACTAAACCCTAAAT
Found at i:6487852 original size:6 final size:7
Alignment explanation
Indices: 6487763--6487857 Score: 54
Period size: 7 Copynumber: 13.7 Consensus size: 7
6487753 CCCTAAATAT
*
6487763 TAAACCA
1 TAAACCC
*
6487770 TAAACAC
1 TAAACCC
6487777 TAAACCC
1 TAAACCC
*
6487784 TAAATCC
1 TAAACCC
*
6487791 TAAGCCC
1 TAAACCC
*
6487798 -AAACCT
1 TAAACCC
*
6487804 TAAACTC
1 TAAACCC
6487811 -AAACCC
1 TAAACCC
*
6487817 -ATCACCC
1 TA-AACCC
6487824 TAAACCCC
1 TAAA-CCC
* *
6487832 TTTAACCA
1 -TAAACCC
6487840 TAAACCC
1 TAAACCC
6487847 -AAACCC
1 TAAACCC
6487853 TAAAC
1 TAAAC
6487858 TAGTAAACCA
Statistics
Matches: 65, Mismatches: 17, Indels: 12
0.69 0.18 0.13
Matches are distributed among these distances:
6 16 0.25
7 40 0.62
8 6 0.09
9 3 0.05
ACGTcount: A:0.44, C:0.38, G:0.01, T:0.17
Consensus pattern (7 bp):
TAAACCC
Found at i:6492752 original size:164 final size:164
Alignment explanation
Indices: 6492481--6492783 Score: 588
Period size: 164 Copynumber: 1.8 Consensus size: 164
6492471 ACATAAAGGG
*
6492481 GAATCTCCATTAAGATCAAAGATCTCCTTTTAATTTCTTTCGAAGTTTTATTGAGTTTCTTTGTA
1 GAATCTCCATTAAGATCAAAGATCTCCTTTTAATTTCTTTCGAAGTTTTATTGAGTTTCTTTATA
*
6492546 TATTGTGGTTATTTTGATTTTGAGATATTTCTATTCAGGATTATGAACTAAATTCCCTAGATACC
66 TATTGTGGTTATTTTGACTTTGAGATATTTCTATTCAGGATTATGAACTAAATTCCCTAGATACC
6492611 TAGGGAAGAACACCATCGGAATCAACTCGAAAGC
131 TAGGGAAGAACACCATCGGAATCAACTCGAAAGC
6492645 GAATCTCCATTAAGATCAAAGATCTCCTTTTAATTTCTTTCGAAGTTTTATTGAGTTTCTTTATA
1 GAATCTCCATTAAGATCAAAGATCTCCTTTTAATTTCTTTCGAAGTTTTATTGAGTTTCTTTATA
6492710 TATTGTGGTTATTTTGACTTTGAGATATTTCTATTCAGGATTATGAACTAAATTCCCTAGATACC
66 TATTGTGGTTATTTTGACTTTGAGATATTTCTATTCAGGATTATGAACTAAATTCCCTAGATACC
6492775 TAGGGAAGA
131 TAGGGAAGA
6492784 TGAAATCTAT
Statistics
Matches: 137, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
164 137 1.00
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.40
Consensus pattern (164 bp):
GAATCTCCATTAAGATCAAAGATCTCCTTTTAATTTCTTTCGAAGTTTTATTGAGTTTCTTTATA
TATTGTGGTTATTTTGACTTTGAGATATTTCTATTCAGGATTATGAACTAAATTCCCTAGATACC
TAGGGAAGAACACCATCGGAATCAACTCGAAAGC
Found at i:6501983 original size:25 final size:25
Alignment explanation
Indices: 6501936--6502007 Score: 62
Period size: 23 Copynumber: 3.0 Consensus size: 25
6501926 ACATACCGCA
* *
6501936 GCTCTTTATGAGCGTTCC-AATATAAG
1 GCTCGTTATGAGC-TTCCTGATAT-AG
6501962 GCTC-TTATGAGCTTCCTGATAT-G
1 GCTCGTTATGAGCTTCCTGATATAG
* *
6501985 GCTCGCT-TGAACTTCCTGATATA
1 GCTCGTTATGAGCTTCCTGATATA
6502008 TAACTATCCG
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
23 19 0.47
24 5 0.12
25 12 0.30
26 4 0.10
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.36
Consensus pattern (25 bp):
GCTCGTTATGAGCTTCCTGATATAG
Found at i:6506919 original size:7 final size:7
Alignment explanation
Indices: 6506907--6506932 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
6506897 GGACTATTTA
6506907 ATTTTGG
1 ATTTTGG
6506914 ATTTTGG
1 ATTTTGG
6506921 ATTTTGG
1 ATTTTGG
6506928 ATTTT
1 ATTTT
6506933 ATAACTGTTT
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:0.15, C:0.00, G:0.23, T:0.62
Consensus pattern (7 bp):
ATTTTGG
Found at i:6508669 original size:20 final size:20
Alignment explanation
Indices: 6508644--6508682 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
6508634 TAAATTTCAA
*
6508644 ATATAAATTATTCATTAATT
1 ATATAAATTACTCATTAATT
6508664 ATATAAATTACTCATTAAT
1 ATATAAATTACTCATTAAT
6508683 AAGCTCAACA
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:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (20 bp):
ATATAAATTACTCATTAATT
Found at i:6510197 original size:159 final size:159
Alignment explanation
Indices: 6509908--6510527 Score: 981
Period size: 159 Copynumber: 3.9 Consensus size: 159
6509898 AACGAGAACG
* * *
6509908 TGGTGGAGAAAAGAAAGGAATAGAAGGAATTACAGTTGGGATTATGGGGACTGAGGGAATGCTTG
1 TGGTGGAGAAAAGAAAGGAATAGAGGGAATTGCAGTTGGGATTGTGGGGACTGAGGGAATGCTTG
* * * *
6509973 GCACAGGGGGCAGTGTGCCCCTTGGTCCACTTGGAAATATGGTAGAAAGTGGAGGAAGTGCCCCA
66 GCAGAGGGGGCAGTGTGGCCCTTGGTCCACTTGGAAATATGGTAGGAAGTGGAGGAAGCGCCCCA
*
6510038 GGGTTTGGGAGATTAGGGAAAGATGGCAA
131 GGCTTTGGGAGATTAGGGAAAGATGGCAA
* *
6510067 TGGTGGAGAAGAGAAAGGAATAGAGGGAATTGCAGTTGGGATTGTGGGGACTAAGGGAATGCTTG
1 TGGTGGAGAAAAGAAAGGAATAGAGGGAATTGCAGTTGGGATTGTGGGGACTGAGGGAATGCTTG
6510132 GCAGAGGGGGCAGTGTGGCCCTTGGTCCACTTGGAAATATGGTAGGAAGTGGAGGAAGCGCCCCA
66 GCAGAGGGGGCAGTGTGGCCCTTGGTCCACTTGGAAATATGGTAGGAAGTGGAGGAAGCGCCCCA
*
6510197 GGATTTGGGAGATTAGGGAAAGATGGCAA
131 GGCTTTGGGAGATTAGGGAAAGATGGCAA
* *
6510226 TGGTGGA-AAAGAGAAAGGAATCGAGGGAATTGCAGTTGGGATTGTGGGGATTGAGGGAATGCTT
1 TGGTGGAGAAA-AGAAAGGAATAGAGGGAATTGCAGTTGGGATTGTGGGGACTGAGGGAATGCTT
* * *
6510290 GGCAGAGGGGGCAGTGTGGCCTTTGGTCCACTTGGAAATATGGTAGGAAGTGGAGGTAGTGCCCC
65 GGCAGAGGGGGCAGTGTGGCCCTTGGTCCACTTGGAAATATGGTAGGAAGTGGAGGAAGCGCCCC
*
6510355 AGGCTTTGGGAGATTAGGGAAAGATGGAAA
130 AGGCTTTGGGAGATTAGGGAAAGATGGCAA
* * **
6510385 TGGTGGAGAAAATAAATTAGCAATAGAGGGAATTGCAGTTGGGATTCCGGGGACTGAGGGAATGC
1 TGGTGGAGAAAA-GAA--AGGAATAGAGGGAATTGCAGTTGGGATTGTGGGGACTGAGGGAATGC
* *
6510450 TCGGCAGAGGGGGCAGTGTGGCCTTTGGTCCACTTGGAAATATGGTAGGAAGTGGAGGAAGCGCC
63 TTGGCAGAGGGGGCAGTGTGGCCCTTGGTCCACTTGGAAATATGGTAGGAAGTGGAGGAAGCGCC
*
6510515 CCAAGCTTTGGGA
128 CCAGGCTTTGGGA
6510528 ATGAGGGTAT
Statistics
Matches: 427, Mismatches: 29, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
158 2 0.00
159 304 0.71
160 5 0.01
162 116 0.27
ACGTcount: A:0.28, C:0.11, G:0.40, T:0.21
Consensus pattern (159 bp):
TGGTGGAGAAAAGAAAGGAATAGAGGGAATTGCAGTTGGGATTGTGGGGACTGAGGGAATGCTTG
GCAGAGGGGGCAGTGTGGCCCTTGGTCCACTTGGAAATATGGTAGGAAGTGGAGGAAGCGCCCCA
GGCTTTGGGAGATTAGGGAAAGATGGCAA
Found at i:6511937 original size:2 final size:2
Alignment explanation
Indices: 6511930--6511956 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6511920 TGTTGTCTTT
6511930 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
6511957 TTTTCCTCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6512181 original size:17 final size:17
Alignment explanation
Indices: 6512149--6512182 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
6512139 ATTTCCCCTT
* *
6512149 AATCCCAATCCTACAAA
1 AATCCCAATACAACAAA
6512166 AATCCCAATACAACAAA
1 AATCCCAATACAACAAA
6512183 CCTCAAAAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.32, G:0.00, T:0.15
Consensus pattern (17 bp):
AATCCCAATACAACAAA
Found at i:6513220 original size:10 final size:11
Alignment explanation
Indices: 6513195--6513220 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
6513185 TTTCAAAGGA
6513195 AAAAAATAAAT
1 AAAAAATAAAT
6513206 AAAAAATAAAT
1 AAAAAATAAAT
6513217 AAAA
1 AAAA
6513221 GGTTTTTAAA
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:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAAAATAAAT
Found at i:6516581 original size:109 final size:111
Alignment explanation
Indices: 6516449--6516651 Score: 311
Period size: 109 Copynumber: 1.8 Consensus size: 111
6516439 TTTTTTATGT
6516449 TTTTCTTTGCTTAAGAATATATTGAACCTTTTGACGCGAAGAGAAATGACAACCAATCACCCCAC
1 TTTTCTTTGCTTAAGAATATATTGAACCTTTTGACGCGAAGAGAAATGACAACCAATCACCCCAC
** *
6516514 CCTGGTTACTCAGCCCAACATACTCCTAATTTATTATATTTATATA
66 CCCAGTTAATCAGCCCAACATACTCCTAATTTATTATATTTATATA
* * *
6516560 TTTT-TTT-CTTAAGAATATATTGAACCTTTTGACGCGAGGAGAGATGACAACCAATCACCCTAC
1 TTTTCTTTGCTTAAGAATATATTGAACCTTTTGACGCGAAGAGAAATGACAACCAATCACCCCAC
* * *
6516623 CCCAGTTAATTAGCCCAACGTATTCCTAA
66 CCCAGTTAATCAGCCCAACATACTCCTAA
6516652 AATTTTTTTG
Statistics
Matches: 83, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
109 76 0.92
110 3 0.04
111 4 0.05
ACGTcount: A:0.32, C:0.24, G:0.12, T:0.32
Consensus pattern (111 bp):
TTTTCTTTGCTTAAGAATATATTGAACCTTTTGACGCGAAGAGAAATGACAACCAATCACCCCAC
CCCAGTTAATCAGCCCAACATACTCCTAATTTATTATATTTATATA
Found at i:6517641 original size:19 final size:19
Alignment explanation
Indices: 6517617--6517663 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
6517607 TAGAAGAAAG
6517617 GGTGTTTGGCTATAAGGTA
1 GGTGTTTGGCTATAAGGTA
*
6517636 GGTGTTTGGCTATAGGGTA
1 GGTGTTTGGCTATAAGGTA
6517655 GGTGTTTGG
1 GGTGTTTGG
6517664 ATGCATATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.15, C:0.04, G:0.43, T:0.38
Consensus pattern (19 bp):
GGTGTTTGGCTATAAGGTA
Found at i:6517839 original size:20 final size:19
Alignment explanation
Indices: 6517814--6517854 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
6517804 TTAATATCCA
*
6517814 AATAAAATAAAGTAATAAAT
1 AATAAAATAAAATAA-AAAT
6517834 AATAAAATAAAATAAAAAT
1 AATAAAATAAAATAAAAAT
6517853 AA
1 AA
6517855 AGAAAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (19 bp):
AATAAAATAAAATAAAAAT
Found at i:6517855 original size:16 final size:16
Alignment explanation
Indices: 6517813--6517868 Score: 60
Period size: 16 Copynumber: 3.2 Consensus size: 16
6517803 ATTAATATCC
6517813 AAATAAAATAAAGTAATAA
1 AAATAAAAT-AA--AATAA
6517832 ATAATAAAATAAAATAA
1 A-AATAAAATAAAATAA
6517849 AAATAAAGA-AAAATAA
1 AAATAAA-ATAAAATAA
6517865 AAAT
1 AAAT
6517869 TGGGTTGCCT
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
16 17 0.49
17 7 0.20
19 3 0.09
20 8 0.23
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.20
Consensus pattern (16 bp):
AAATAAAATAAAATAA
Found at i:6517860 original size:20 final size:21
Alignment explanation
Indices: 6517817--6517866 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
6517807 ATATCCAAAT
* *
6517817 AAAATAAAGTAATAAATAA-T
1 AAAATAAAATAATAAATAAGA
6517837 AAAATAAAATAA-AAATAAAGA
1 AAAATAAAATAATAAAT-AAGA
6517858 AAAATAAAA
1 AAAATAAAA
6517867 ATTGGGTTGC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 4 0.15
20 13 0.50
21 9 0.35
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (21 bp):
AAAATAAAATAATAAATAAGA
Found at i:6523770 original size:10 final size:9
Alignment explanation
Indices: 6523732--6523892 Score: 62
Period size: 9 Copynumber: 17.2 Consensus size: 9
6523722 TGTGACAGAG
*
6523732 AAATGATAA
1 AAATTATAA
*
6523741 AAA-AATAA
1 AAATTATAA
*
6523749 AAATCAATAA
1 AAAT-TATAA
*
6523759 AAGTTATAA
1 AAATTATAA
6523768 AAATTATAA
1 AAATTATAA
* *
6523777 AAATTGT-T
1 AAATTATAA
*
6523785 AAATTTTAATA
1 AAATTAT-A-A
6523796 AAATTATAA
1 AAATTATAA
*
6523805 AAA-TATTTA
1 AAATTA-TAA
*
6523814 AAATTAGAAAA
1 AAATT--ATAA
6523825 AAATTATAA
1 AAATTATAA
*
6523834 AACTCGTA-AA
1 AAAT--TATAA
*
6523844 AAAATATAA
1 AAATTATAA
* *
6523853 AAACTGTAA
1 AAATTATAA
*
6523862 AATTTTATAA
1 AA-ATTATAA
6523872 AAAGTGTA-AA
1 AAA-T-TATAA
6523882 AAATTATAA
1 AAATTATAA
6523891 AA
1 AA
6523893 TATATAGAAA
Statistics
Matches: 114, Mismatches: 22, Indels: 32
0.68 0.13 0.19
Matches are distributed among these distances:
8 19 0.17
9 52 0.46
10 26 0.23
11 16 0.14
12 1 0.01
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (9 bp):
AAATTATAA
Found at i:6523787 original size:19 final size:19
Alignment explanation
Indices: 6523765--6523892 Score: 66
Period size: 19 Copynumber: 6.7 Consensus size: 19
6523755 ATAAAAGTTA
6523765 TAAAAATTATAAAAATTGT
1 TAAAAATTATAAAAATTGT
** *
6523784 TAAATTTTA-ATAAAATT-A
1 TAAAAATTATA-AAAATTGT
* *
6523802 TAAAAA-TATTTAAAATTAGA
1 TAAAAATTA-TAAAAATT-GT
* * *
6523822 AAAAAATTATAAAACTCGT
1 TAAAAATTATAAAAATTGT
* * *
6523841 AAAAAAATATAAAAACTG-
1 TAAAAATTATAAAAATTGT
* *
6523859 TAAAATTTTATAAAAAGTGT
1 TAAAA-ATTATAAAAATTGT
*
6523879 AAAAAATTATAAAA
1 TAAAAATTATAAAA
6523893 TATATAGAAA
Statistics
Matches: 80, Mismatches: 21, Indels: 16
0.68 0.18 0.14
Matches are distributed among these distances:
17 2 0.03
18 15 0.19
19 46 0.57
20 15 0.19
21 2 0.03
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (19 bp):
TAAAAATTATAAAAATTGT
Found at i:6523797 original size:29 final size:29
Alignment explanation
Indices: 6523764--6523835 Score: 87
Period size: 28 Copynumber: 2.5 Consensus size: 29
6523754 AATAAAAGTT
*
6523764 ATAAAAATTATAAAAAT-TGTTAAATTTTA-
1 ATAAAAATTATAAAAATAT-TTAAA-ATTAG
6523793 AT-AAAATTATAAAAATATTTAAAATTAG
1 ATAAAAATTATAAAAATATTTAAAATTAG
*
6523821 AAAAAAATTATAAAA
1 ATAAAAATTATAAAA
6523836 CTCGTAAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
27 3 0.08
28 20 0.53
29 15 0.39
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (29 bp):
ATAAAAATTATAAAAATATTTAAAATTAG
Found at i:6523826 original size:20 final size:21
Alignment explanation
Indices: 6523803--6523863 Score: 67
Period size: 20 Copynumber: 3.1 Consensus size: 21
6523793 ATAAAATTAT
* *
6523803 AAAAATATTTAAAATTAG-AA
1 AAAAATATATAAAACTAGTAA
*
6523823 AAAAAT-TATAAAACTCGTAA
1 AAAAATATATAAAACTAGTAA
6523843 AAAAATATA-AAAACT-GTAA
1 AAAAATATATAAAACTAGTAA
6523862 AA
1 AA
6523864 TTTTATAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
19 14 0.39
20 20 0.56
21 2 0.06
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.25
Consensus pattern (21 bp):
AAAAATATATAAAACTAGTAA
Found at i:6523843 original size:28 final size:28
Alignment explanation
Indices: 6523766--6523844 Score: 86
Period size: 29 Copynumber: 2.8 Consensus size: 28
6523756 TAAAAGTTAT
* **
6523766 AAAAATTATAAAAATTGTTAAATTTTAA
1 AAAAATTATAAAAATTGTAAAATTAGAA
* *
6523794 TAAAATTATAAAAATATTTAAAATTAGAA
1 AAAAATTATAAAAAT-TGTAAAATTAGAA
* *
6523823 AAAAATTATAAAACTCGTAAAA
1 AAAAATTATAAAAATTGTAAAA
6523845 AAATATAAAA
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
28 19 0.46
29 22 0.54
ACGTcount: A:0.61, C:0.03, G:0.04, T:0.33
Consensus pattern (28 bp):
AAAAATTATAAAAATTGTAAAATTAGAA
Found at i:6524228 original size:31 final size:31
Alignment explanation
Indices: 6524184--6524252 Score: 104
Period size: 31 Copynumber: 2.3 Consensus size: 31
6524174 TTTGTTATGA
*
6524184 TTTTTA-TAAAATTTTATAATTTTTAATAAT
1 TTTTTATTAAAATTTAATAATTTTTAATAAT
* *
6524214 TTTTTATTAAAATTTAATAATTTTTTATATT
1 TTTTTATTAAAATTTAATAATTTTTAATAAT
6524245 TTTTTATT
1 TTTTTATT
6524253 TTTTATAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
30 6 0.17
31 29 0.83
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (31 bp):
TTTTTATTAAAATTTAATAATTTTTAATAAT
Found at i:6524250 original size:21 final size:21
Alignment explanation
Indices: 6524195--6524265 Score: 66
Period size: 21 Copynumber: 3.7 Consensus size: 21
6524185 TTTTATAAAA
6524195 TTTTATA-ATTTTTAATAATT
1 TTTTATATATTTTTAATAATT
**
6524215 TTTTAT-TAAAATTTAATAATT
1 TTTTATAT-ATTTTTAATAATT
6524236 TTTTATAT-TTTTT--T-ATT
1 TTTTATATATTTTTAATAATT
6524253 TTTTATA-ATTTTT
1 TTTTATATATTTTT
6524266 TTCCACATGC
Statistics
Matches: 43, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
17 15 0.35
18 1 0.02
20 9 0.21
21 17 0.40
22 1 0.02
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (21 bp):
TTTTATATATTTTTAATAATT
Found at i:6524253 original size:17 final size:18
Alignment explanation
Indices: 6524233--6524267 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
6524223 AAATTTAATA
6524233 ATTTTTTAT-ATTTTTTT
1 ATTTTTTATAATTTTTTT
6524250 ATTTTTTATAATTTTTTT
1 ATTTTTTATAATTTTTTT
6524268 CCACATGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (18 bp):
ATTTTTTATAATTTTTTT
Found at i:6526560 original size:5 final size:5
Alignment explanation
Indices: 6526501--6526544 Score: 88
Period size: 5 Copynumber: 8.8 Consensus size: 5
6526491 AATATGAAAA
6526501 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAA
6526545 ATTATAAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 39 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:6540242 original size:20 final size:20
Alignment explanation
Indices: 6540213--6540254 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
6540203 CACGTATCCT
*
6540213 AATTTTATTTGATTCTAATC
1 AATTTGATTTGATTCTAATC
*
6540233 AATTTGATTTGATTTTAATC
1 AATTTGATTTGATTCTAATC
6540253 AA
1 AA
6540255 ATAGATTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.52
Consensus pattern (20 bp):
AATTTGATTTGATTCTAATC
Found at i:6540261 original size:20 final size:20
Alignment explanation
Indices: 6540219--6540262 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
6540209 TCCTAATTTT
* *
6540219 ATTTGATTCTAATCAATTTG
1 ATTTGATTCTAATCAAATAG
*
6540239 ATTTGATTTTAATCAAATAG
1 ATTTGATTCTAATCAAATAG
6540259 ATTT
1 ATTT
6540263 AATTACTCCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.07, G:0.09, T:0.50
Consensus pattern (20 bp):
ATTTGATTCTAATCAAATAG
Found at i:6540739 original size:22 final size:22
Alignment explanation
Indices: 6540714--6540755 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
6540704 AATTTATATT
*
6540714 TTATTTTTATATAAATATTTGC
1 TTATTTATATATAAATATTTGC
* *
6540736 TTATTTATATTTATATATTT
1 TTATTTATATATAAATATTT
6540756 TGTTCGCTAA
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:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (22 bp):
TTATTTATATATAAATATTTGC
Found at i:6541011 original size:87 final size:87
Alignment explanation
Indices: 6540879--6541442 Score: 681
Period size: 87 Copynumber: 6.5 Consensus size: 87
6540869 TTGAAAATAA
* ** * * *
6540879 ATATTAAAATTAAATAAAATCTGTTTCGGCATTTATTCTCGCCGTTCAACAGATTTTATTTCATA
1 ATATTAAAATTAAATAAAATCTATTTCGGGTTTTATTCCCGCCGTTCAACAGATTTTATTCCATT
6540944 TTTTATTTTGTTTCCAAACAAG
66 TTTTATTTTGTTTCCAAACAAG
* * *
6540966 -TATTAAAATTAAATAAAACTCTATTTCGAGATTTATTCCCCCCGTTCAACAGATTTTATTCCAT
1 ATATTAAAATTAAATAAAA-TCTATTTCGGGTTTTATTCCCGCCGTTCAACAGATTTTATTCCA-
* **
6541030 TTTTTTCTTTTGTTTCCAAATGAG
64 TTTTTTATTTTGTTTCCAAACAAG
* * * * * *
6541054 -TATTAAACTAAAATAAAATCTATTTCGGGGTTTATTCCTGTCGTTCAACAGATTTTATTCTATT
1 ATATTAAAATTAAATAAAATCTATTTCGGGTTTTATTCCCGCCGTTCAACAGATTTTATTCCA-T
6541118 TTTTTATTTTGTTTCCAAACAAG
65 TTTTTATTTTGTTTCCAAACAAG
*
6541141 -TATTAAAATTAAATAAAATCTATTTTGGGTTTTATTCCCGCCGTTCAACAGATTTTATTCCATT
1 ATATTAAAATTAAATAAAATCTATTTCGGGTTTTATTCCCGCCGTTCAACAGATTTTATTCCATT
*
6541205 TTTTATTTTGTTGT-CAAACGAG
66 TTTTATTTTGTT-TCCAAACAAG
* * * * * * *
6541227 AAATTAAAATTAAATAAAATCTGTTTTGGGTTTTATTCTCGCCGTTAAATAGACTTTATTCCATT
1 ATATTAAAATTAAATAAAATCTATTTCGGGTTTTATTCCCGCCGTTCAACAGATTTTATTCCATT
*
6541292 TTTTATTTTGTTGCCAAA-AGAG
66 TTTTATTTTGTTTCCAAACA-AG
* * * * * * *
6541314 AAATTAAAATTAAATAAAATATGTTTCAGGTTTTATTCTCGCTGTTCAATAGATTTTATTCCATT
1 ATATTAAAATTAAATAAAATCTATTTCGGGTTTTATTCCCGCCGTTCAACAGATTTTATTCCATT
* *
6541379 TTTTATTTT-TTGCCAAACGAG
66 TTTTATTTTGTTTCCAAACAAG
* * *
6541400 AAATTAAAATTAAATAAAATTTGTTTCGGGTTTTATTCCCGCC
1 ATATTAAAATTAAATAAAATCTATTTCGGGTTTTATTCCCGCC
6541443 TTTATTCCAT
Statistics
Matches: 422, Mismatches: 48, Indels: 15
0.87 0.10 0.03
Matches are distributed among these distances:
86 88 0.21
87 298 0.71
88 36 0.09
ACGTcount: A:0.31, C:0.14, G:0.10, T:0.44
Consensus pattern (87 bp):
ATATTAAAATTAAATAAAATCTATTTCGGGTTTTATTCCCGCCGTTCAACAGATTTTATTCCATT
TTTTATTTTGTTTCCAAACAAG
Found at i:6541351 original size:261 final size:257
Alignment explanation
Indices: 6540879--6541551 Score: 757
Period size: 261 Copynumber: 2.6 Consensus size: 257
6540869 TTGAAAATAA
** * *
6540879 ATATTAAAATTAAATAAAATCTGTTTCGGCATTTATTCTCGCCGTTCAACAGATTTTATTTCATA
1 ATATTAAAATTAAATAAAATCTGTTTCGGGTTTTATTC-CGCCGTTCAACAGATTTTATTCCATT
* * * * * * *
6540944 TTTTATTTTGTTTCCAAACAAG-TATTAAAATTAAATAAAACTCTATTTCGAGATTTATTCCCCC
65 TTTTATTTTGTTT-CAAACGAGAAATTAAAATTAAATAAAA-TCTGTTTTGGGATTTATTCTCGC
* * * * * * * *
6541008 CGTTCAACAGATTTTATTCCATTTTTTTCTTTTGTTTCCAAATGAGTATTAAACTAAAATAAAAT
128 CGTTAAATAGAATTTATTCCA-TTTTTTATTTTGTTGCCAAAAGAGAATTAAAATAAAATAAAAT
* * * *
6541073 CTATTTCGGGGTTTATTC-CTG-TCGTTCAACAGATTTTATTCTATTTTTTTATTTTGTTTCCAA
192 ATATTTCAGGGTTTATTCTC-GCT-GTTCAACAGATTTTATTCCA-TTTTTTATTTT-TTGCCAA
6541136 ACAAG
253 ACAAG
* *
6541141 -TATTAAAATTAAATAAAATCTATTTTGGGTTTTATTCCCGCCGTTCAACAGATTTTATTCCATT
1 ATATTAAAATTAAATAAAATCTGTTTCGGGTTTTATT-CCGCCGTTCAACAGATTTTATTCCATT
*
6541205 TTTTATTTTGTTGTCAAACGAGAAATTAAAATTAAATAAAATCTGTTTTGGGTTTTATTCTCGCC
65 TTTTATTTTGTT-TCAAACGAGAAATTAAAATTAAATAAAATCTGTTTTGGGATTTATTCTCGCC
* *
6541270 GTTAAATAGACTTTATTCCATTTTTTATTTTGTTGCCAAAAGAGAAATTAAAATTAAATAAAATA
129 GTTAAATAGAATTTATTCCATTTTTTATTTTGTTGCCAAAAGAG-AATTAAAATAAAATAAAATA
* * * *
6541335 TGTTTCAGGTTTTATTCTCGCTGTTCAATAGATTTTATTCCATTTTTTATTTTTTGCCAAACGAG
193 TATTTCAGGGTTTATTCTCGCTGTTCAACAGATTTTATTCCATTTTTTATTTTTTGCCAAACAAG
* *
6541400 AAATTAAAATTAAATAAAATTTGTTTCGGGTTTTATT-C-CCG--C--C----TTTATTCCATTT
1 ATATTAAAATTAAATAAAATCTGTTTCGGGTTTTATTCCGCCGTTCAACAGATTTTATTCCA-TT
* * *
6541455 TTTTATTTT-TTTCTAAACGAGAAATTTAAATTAAATAAAATCTGTTCTGGGATTTAATCTCGCC
65 TTTTATTTTGTTTC-AAACGAGAAATTAAAATTAAATAAAATCTGTTTTGGGATTTATTCTCGCC
* * *
6541519 GTTTAATAGAATTTATT-CAATTTTAATTTTGTT
129 GTTAAATAGAATTTATTCCATTTTTTATTTTGTT
6541552 TCTAAATTAG
Statistics
Matches: 359, Mismatches: 43, Indels: 32
0.83 0.10 0.07
Matches are distributed among these distances:
248 16 0.04
249 72 0.20
250 11 0.03
253 1 0.00
255 1 0.00
257 3 0.01
258 1 0.00
259 10 0.03
260 64 0.18
261 159 0.44
262 21 0.06
ACGTcount: A:0.31, C:0.13, G:0.10, T:0.45
Consensus pattern (257 bp):
ATATTAAAATTAAATAAAATCTGTTTCGGGTTTTATTCCGCCGTTCAACAGATTTTATTCCATTT
TTTATTTTGTTTCAAACGAGAAATTAAAATTAAATAAAATCTGTTTTGGGATTTATTCTCGCCGT
TAAATAGAATTTATTCCATTTTTTATTTTGTTGCCAAAAGAGAATTAAAATAAAATAAAATATAT
TTCAGGGTTTATTCTCGCTGTTCAACAGATTTTATTCCATTTTTTATTTTTTGCCAAACAAG
Found at i:6549556 original size:23 final size:24
Alignment explanation
Indices: 6549505--6549557 Score: 67
Period size: 22 Copynumber: 2.3 Consensus size: 24
6549495 TATTATGCTG
*
6549505 AATATGTTAAAAATATTTTAATTAT
1 AATAT-TTAAAAAAATTTTAATTAT
6549530 --TATTTAAAAAAATTTT-ATTAT
1 AATATTTAAAAAAATTTTAATTAT
6549551 AATATTT
1 AATATTT
6549558 GAATTGATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
21 5 0.20
22 12 0.48
23 8 0.32
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (24 bp):
AATATTTAAAAAAATTTTAATTAT
Found at i:6554311 original size:25 final size:26
Alignment explanation
Indices: 6554278--6554337 Score: 95
Period size: 27 Copynumber: 2.3 Consensus size: 26
6554268 CCCAGCCCAT
*
6554278 TTTTAAAAT-AAACATAAAAAAATTA
1 TTTTAAAATAAAAAATAAAAAAATTA
6554303 TTTTAAAATAAAAAAATAAAAAAATTA
1 TTTTAAAAT-AAAAAATAAAAAAATTA
6554330 TTTTAAAA
1 TTTTAAAA
6554338 GTACTTTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 9 0.28
27 23 0.72
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (26 bp):
TTTTAAAATAAAAAATAAAAAAATTA
Found at i:6555834 original size:24 final size:23
Alignment explanation
Indices: 6555790--6555835 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
6555780 AAAATAATTG
* **
6555790 GAAAAGAAATCTAAAGCCTAAAA
1 GAAAAGAAAACTAAAAACTAAAA
6555813 GAAAAGAAAAACTAAAAACTAAA
1 GAAAAG-AAAACTAAAAACTAAA
6555836 TTATAGGGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.67, C:0.11, G:0.11, T:0.11
Consensus pattern (23 bp):
GAAAAGAAAACTAAAAACTAAAA
Found at i:6557057 original size:19 final size:19
Alignment explanation
Indices: 6557035--6557076 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
6557025 TAGCAATATT
**
6557035 TTTTTTATGTTAAAAGTGC
1 TTTTTTATACTAAAAGTGC
6557054 -TTTTTATACTAAAAGTGC
1 TTTTTTATACTAAAAGTGC
6557072 TTTTT
1 TTTTT
6557077 AGAAGTGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.26, C:0.07, G:0.12, T:0.55
Consensus pattern (19 bp):
TTTTTTATACTAAAAGTGC
Found at i:6563188 original size:20 final size:20
Alignment explanation
Indices: 6563163--6563200 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
6563153 CAAATTTCTA
6563163 AAATTAAAAACATATGAATT
1 AAATTAAAAACATATGAATT
* *
6563183 AAATTATAAATATATGAA
1 AAATTAAAAACATATGAA
6563201 AAGTTTACCT
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:0.61, C:0.03, G:0.05, T:0.32
Consensus pattern (20 bp):
AAATTAAAAACATATGAATT
Found at i:6570883 original size:10 final size:11
Alignment explanation
Indices: 6570868--6570896 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
6570858 TCCAAAGGTG
6570868 TGAATTGAAT-
1 TGAATTGAATA
6570878 TGAATTGAATA
1 TGAATTGAATA
6570889 TGAATTGA
1 TGAATTGA
6570897 TATTTAATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.41, C:0.00, G:0.21, T:0.38
Consensus pattern (11 bp):
TGAATTGAATA
Found at i:6571518 original size:73 final size:74
Alignment explanation
Indices: 6571433--6571590 Score: 203
Period size: 73 Copynumber: 2.1 Consensus size: 74
6571423 AACTTATCGA
* * * * **
6571433 TTAATGGCTCTCCTGAGCTTCCCGATAC-TGGCTCACTTAAACCTTCCCGTTA-TTGGCTCGTAT
1 TTAATGGCTCTCCGGAGCTTCCCGATACATGGCTCACAT-AACCTTCCCATTACATGGCTCACAT
6571496 GAGCTTCCCG
65 GAGCTTCCCG
* *
6571506 TTAATGGCTCTCCGGAGCTTCCCGTTACATGGCTCACATAAGCTTCCCATTACATGGCTCACATG
1 TTAATGGCTCTCCGGAGCTTCCCGATACATGGCTCACATAACCTTCCCATTACATGGCTCACATG
*
6571571 AGCTTCCTG
66 AGCTTCCCG
6571580 TTATATGGCTC
1 TTA-ATGGCTC
6571591 GAAAGAGGGC
Statistics
Matches: 73, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
73 37 0.51
74 29 0.40
75 7 0.10
ACGTcount: A:0.18, C:0.30, G:0.19, T:0.32
Consensus pattern (74 bp):
TTAATGGCTCTCCGGAGCTTCCCGATACATGGCTCACATAACCTTCCCATTACATGGCTCACATG
AGCTTCCCG
Found at i:6571549 original size:25 final size:25
Alignment explanation
Indices: 6571436--6571590 Score: 136
Period size: 25 Copynumber: 6.3 Consensus size: 25
6571426 TTATCGATTA
* * *
6571436 ATGGCTCTCCTGAGCTTCCCGATAC
1 ATGGCTCACATGAGCTTCCCGTTAC
* * *
6571461 -TGGCTCACTTAAACCTTCCCGTTA-
1 ATGGCTCACAT-GAGCTTCCCGTTAC
* **
6571485 TTGGCTCGTATGAGCTTCCCGTTA-
1 ATGGCTCACATGAGCTTCCCGTTAC
* **
6571509 ATGGCTCTCCGGAGCTTCCCGTTAC
1 ATGGCTCACATGAGCTTCCCGTTAC
* *
6571534 ATGGCTCACATAAGCTTCCCATTAC
1 ATGGCTCACATGAGCTTCCCGTTAC
* *
6571559 ATGGCTCACATGAGCTTCCTGTTAT
1 ATGGCTCACATGAGCTTCCCGTTAC
6571584 ATGGCTC
1 ATGGCTC
6571591 GAAAGAGGGC
Statistics
Matches: 103, Mismatches: 24, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
24 38 0.37
25 65 0.63
ACGTcount: A:0.18, C:0.31, G:0.19, T:0.32
Consensus pattern (25 bp):
ATGGCTCACATGAGCTTCCCGTTAC
Found at i:6574360 original size:20 final size:21
Alignment explanation
Indices: 6574320--6574360 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
6574310 TTTTAAATAA
6574320 TTATTTCAAATTATTTATTAT
1 TTATTTCAAATTATTTATTAT
* *
6574341 TTATTTTAAA-TATTTTTTAT
1 TTATTTCAAATTATTTATTAT
6574361 GTGAAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (21 bp):
TTATTTCAAATTATTTATTAT
Found at i:6581350 original size:42 final size:43
Alignment explanation
Indices: 6581252--6581398 Score: 129
Period size: 43 Copynumber: 3.4 Consensus size: 43
6581242 AGCTCGTGCA
* * * * *
6581252 ATGCCAATGTCCCAGAC-GTGGTTTTACATGT-ATTCAAATAACG
1 ATGCCAATGTCCCAAACAG-GGTCTTACACGTAAATCATAT-ACG
* * *
6581295 ATGCCACTGTCCCAGATAGGGTCTTACACG-AAATCATATACG
1 ATGCCAATGTCCCAAACAGGGTCTTACACGTAAATCATATACG
* * * *
6581337 ATGCTAATGTCCCAAACATGGTCTTACACGTAAATCTTAAATCG
1 ATGCCAATGTCCCAAACAGGGTCTTACACGTAAATCATATA-CG
*
6581381 ATGCCAACGTCCCAAACA
1 ATGCCAATGTCCCAAACA
6581399 TGATCTTATA
Statistics
Matches: 85, Mismatches: 15, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
42 28 0.33
43 38 0.45
44 19 0.22
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (43 bp):
ATGCCAATGTCCCAAACAGGGTCTTACACGTAAATCATATACG
Found at i:6581393 original size:44 final size:42
Alignment explanation
Indices: 6581291--6581416 Score: 128
Period size: 44 Copynumber: 3.0 Consensus size: 42
6581281 GTATTCAAAT
* * *
6581291 AACGATGCC-ACTGTCCCAGATAGGGTCTTACACGAAATCATA
1 AACGATGCCAAC-GTCCCAAACATGGTCTTACACGAAATCATA
* * * *
6581333 TACGATGCTAATGTCCCAAACATGGTCTTACACGTAAATCTTA
1 AACGATGCCAACGTCCCAAACATGGTCTTACACG-AAATCATA
* * *
6581376 AATCGATGCCAACGTCCCAAACATGATCTTATACGATATCA
1 AA-CGATGCCAACGTCCCAAACATGGTCTTACACGAAATCA
6581417 CGTATCGAAA
Statistics
Matches: 67, Mismatches: 14, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
42 26 0.39
43 13 0.19
44 28 0.42
ACGTcount: A:0.34, C:0.25, G:0.15, T:0.25
Consensus pattern (42 bp):
AACGATGCCAACGTCCCAAACATGGTCTTACACGAAATCATA
Found at i:6583345 original size:14 final size:14
Alignment explanation
Indices: 6583326--6583352 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
6583316 AGTCATTTTT
6583326 TATTTTTATTTTAA
1 TATTTTTATTTTAA
6583340 TATTTTTATTTTA
1 TATTTTTATTTTA
6583353 TTTAATTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TATTTTTATTTTAA
Found at i:6584320 original size:9 final size:9
Alignment explanation
Indices: 6584226--6584319 Score: 152
Period size: 9 Copynumber: 10.4 Consensus size: 9
6584216 GTAGTGATTC
*
6584226 AATTTGGTT
1 AATTCGGTT
6584235 AATTCGGTT
1 AATTCGGTT
6584244 AATTCGGTT
1 AATTCGGTT
*
6584253 AATTCGGGT
1 AATTCGGTT
6584262 AATTCGGTT
1 AATTCGGTT
6584271 AATTCGGTT
1 AATTCGGTT
*
6584280 AATTCGGGT
1 AATTCGGTT
6584289 AATTCGGTT
1 AATTCGGTT
6584298 AATTCGGTT
1 AATTCGGTT
*
6584307 AATTTGGTT
1 AATTCGGTT
6584316 AATT
1 AATT
6584320 TTTAACCAAA
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 79 1.00
ACGTcount: A:0.23, C:0.09, G:0.23, T:0.45
Consensus pattern (9 bp):
AATTCGGTT
Found at i:6594888 original size:21 final size:22
Alignment explanation
Indices: 6594853--6594893 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
6594843 ATTTGATTTT
6594853 TTTCTTTTATGTTCT-TTTAAC
1 TTTCTTTTATGTTCTCTTTAAC
* *
6594874 TTTCTTTTTTTTTCTCTTTA
1 TTTCTTTTATGTTCTCTTTA
6594894 TTTTTCGTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.10, C:0.15, G:0.02, T:0.73
Consensus pattern (22 bp):
TTTCTTTTATGTTCTCTTTAAC
Found at i:6601623 original size:21 final size:22
Alignment explanation
Indices: 6601597--6601637 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
6601587 ATTATAAGTG
6601597 AAAAATA-ATCTCA-TTAAAAGA
1 AAAAATAGATC-CATTTAAAAGA
6601618 AAAAATAGATCCATTTAAAA
1 AAAAATAGATCCATTTAAAA
6601638 TATGTATCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.61, C:0.10, G:0.05, T:0.24
Consensus pattern (22 bp):
AAAAATAGATCCATTTAAAAGA
Found at i:6602455 original size:16 final size:17
Alignment explanation
Indices: 6602436--6602480 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
6602426 ATTCTTATTT
*
6602436 AGAATAATTGTTGTT-A
1 AGAATAACTGTTGTTCA
*
6602452 AGAACAACTGTTGTTCGA
1 AGAATAACTGTTGTTC-A
6602470 AGAATAACTGT
1 AGAATAACTGT
6602481 CCAGAATAGC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 13 0.54
18 11 0.46
ACGTcount: A:0.38, C:0.09, G:0.20, T:0.33
Consensus pattern (17 bp):
AGAATAACTGTTGTTCA
Found at i:6606356 original size:3 final size:3
Alignment explanation
Indices: 6606348--6606384 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
6606338 TAATATCTCC
6606348 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
6606385 GTTTTTTTAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:6609108 original size:29 final size:29
Alignment explanation
Indices: 6609042--6609109 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
6609032 AGCTATACCG
* *
6609042 CTAGAACTCCAATATTTGCGGCTAAACAA
1 CTAGAACTCCAATATTTACGGATAAACAA
* * *
6609071 CCA-AGACTCCCATATTTACGGATAAACCA
1 CTAGA-ACTCCAATATTTACGGATAAACAA
6609100 CTAGAACTCC
1 CTAGAACTCC
6609110 TCTGTCACCA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
28 1 0.03
29 29 0.94
30 1 0.03
ACGTcount: A:0.37, C:0.29, G:0.12, T:0.22
Consensus pattern (29 bp):
CTAGAACTCCAATATTTACGGATAAACAA
Found at i:6622742 original size:3 final size:3
Alignment explanation
Indices: 6622734--6622775 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
6622724 TAAATAAGTA
* * *
6622734 AAT AAT AAT ATT AAT AAT -AG AAT AAT AAT AAT ATT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
6622776 GAATAGCAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
2 1 0.03
3 31 0.97
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:6622744 original size:20 final size:20
Alignment explanation
Indices: 6622721--6622780 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 20
6622711 CTAAAAAAAG
6622721 ATATAAATAAGTA-AATAATA
1 ATATAAATAA-TAGAATAATA
*
6622741 ATATTAATAATAGAATAATA
1 ATATAAATAATAGAATAATA
6622761 ATAATATTAATAATAGAATA
1 AT-ATA--AATAATAGAATA
6622781 GCAAATAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
19 2 0.06
20 18 0.53
21 2 0.06
23 12 0.35
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (20 bp):
ATATAAATAATAGAATAATA
Found at i:6622760 original size:23 final size:23
Alignment explanation
Indices: 6622734--6622780 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
6622724 TAAATAAGTA
6622734 AATAATAATATTAATAATAGAAT
1 AATAATAATATTAATAATAGAAT
6622757 AATAATAATATTAATAATAGAAT
1 AATAATAATATTAATAATAGAAT
6622780 A
1 A
6622781 GCAAATAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (23 bp):
AATAATAATATTAATAATAGAAT
Found at i:6626615 original size:24 final size:24
Alignment explanation
Indices: 6626551--6626616 Score: 62
Period size: 24 Copynumber: 2.8 Consensus size: 24
6626541 AGAATATGTG
*
6626551 CATATATATAT-TATGAAATATAAA
1 CATATATATATGTATG-TATATAAA
* * * * *
6626575 AATATATGTAAGAATGTATATATA
1 CATATATATATGTATGTATATAAA
6626599 CATATATATATGTATGTA
1 CATATATATATGTATGTA
6626617 AATTAAAATA
Statistics
Matches: 31, Mismatches: 10, Indels: 2
0.72 0.23 0.05
Matches are distributed among these distances:
24 28 0.90
25 3 0.10
ACGTcount: A:0.48, C:0.03, G:0.09, T:0.39
Consensus pattern (24 bp):
CATATATATATGTATGTATATAAA
Found at i:6626627 original size:24 final size:24
Alignment explanation
Indices: 6626552--6626627 Score: 59
Period size: 24 Copynumber: 3.2 Consensus size: 24
6626542 GAATATGTGC
6626552 ATATATATAT-TATG-AAATATAAAA
1 ATATATATATGTATGTAAAT-T-AAA
* * * * *
6626576 ATATATGTAAGAATGTATA-TATAC
1 ATATATATATGTATGTAAATTA-AA
6626600 ATATATATATGTATGTAAATTAAA
1 ATATATATATGTATGTAAATTAAA
6626624 ATAT
1 ATAT
6626628 GTACCTATGT
Statistics
Matches: 38, Mismatches: 10, Indels: 8
0.68 0.18 0.14
Matches are distributed among these distances:
23 1 0.03
24 30 0.79
25 5 0.13
26 2 0.05
ACGTcount: A:0.51, C:0.01, G:0.08, T:0.39
Consensus pattern (24 bp):
ATATATATATGTATGTAAATTAAA
Found at i:6627164 original size:3 final size:3
Alignment explanation
Indices: 6627151--6627182 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
6627141 AATACGTGGC
*
6627151 AAT ATT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
6627183 GAGTACATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:6627802 original size:18 final size:19
Alignment explanation
Indices: 6627779--6627814 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
6627769 AAAAGGTATG
*
6627779 AAACAA-AGATGAAAAAAA
1 AAACAATAGAAGAAAAAAA
6627797 AAACAATAGAAGAAAAAA
1 AAACAATAGAAGAAAAAA
6627815 TCGAAGTGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.78, C:0.06, G:0.11, T:0.06
Consensus pattern (19 bp):
AAACAATAGAAGAAAAAAA
Found at i:6636490 original size:147 final size:147
Alignment explanation
Indices: 6636223--6636490 Score: 428
Period size: 147 Copynumber: 1.8 Consensus size: 147
6636213 GAACGAGAAC
* * *
6636223 ATGGTGGAGAAAAGAAAGGAATAGGGGGAATTGCAGTTGGGATTGTAGGGACTTAAGGAATGCTT
1 ATGGTGGAGAAAAGAAAGGAATAGGGGGAATTGCAGTTGGGATTATAGGGACTGAAGGAAAGCTT
* * *
6636288 GGTAGAGGGGGCAGTCCTCTTGGCAATGTGGTAGGAAGTGGAGGAAGCGCCCCAGGGTTTGGGAG
66 GGCAGAAGGGACAGTCCTCTTGGCAATGTGGTAGGAAGTGGAGGAAGCGCCCCAGGGTTTGGGAG
6636353 ATTAGGGAAAGATGGCA
131 ATTAGGGAAAGATGGCA
* * * * *
6636370 ATGGTGGAGAAGAGAAAGGAATAGGGGGAATTGTAGTTGGGATTATGGGGACTGAGGGAAAGTTT
1 ATGGTGGAGAAAAGAAAGGAATAGGGGGAATTGCAGTTGGGATTATAGGGACTGAAGGAAAGCTT
*
6636435 GGCAGAAGGGACAGTCCTGTTGGCAATGTGGTAGGAAGTGGAGGAAGCGCCCCAGG
66 GGCAGAAGGGACAGTCCTCTTGGCAATGTGGTAGGAAGTGGAGGAAGCGCCCCAGG
6636491 CCATGGGAAT
Statistics
Matches: 109, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
147 109 1.00
ACGTcount: A:0.29, C:0.09, G:0.42, T:0.20
Consensus pattern (147 bp):
ATGGTGGAGAAAAGAAAGGAATAGGGGGAATTGCAGTTGGGATTATAGGGACTGAAGGAAAGCTT
GGCAGAAGGGACAGTCCTCTTGGCAATGTGGTAGGAAGTGGAGGAAGCGCCCCAGGGTTTGGGAG
ATTAGGGAAAGATGGCA
Found at i:6642674 original size:20 final size:21
Alignment explanation
Indices: 6642628--6642674 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
6642618 TTGTTGGAAA
6642628 ATAATTATTGAGTGATGAATG
1 ATAATTATTGAGTGATGAATG
*
6642649 AAAATTATTGAGTGAT-AATG
1 ATAATTATTGAGTGATGAATG
6642669 ATAATT
1 ATAATT
6642675 GCATCTCTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 9 0.38
21 15 0.62
ACGTcount: A:0.43, C:0.00, G:0.19, T:0.38
Consensus pattern (21 bp):
ATAATTATTGAGTGATGAATG
Found at i:6657676 original size:28 final size:30
Alignment explanation
Indices: 6657610--6657670 Score: 79
Period size: 32 Copynumber: 2.0 Consensus size: 30
6657600 GCACAAGAAG
*
6657610 ACATACATATTCGAACAACTTGCAAAACAT
1 ACATACATATTCGAACAACTTACAAAACAT
6657640 ATGCATACATATTC-AACCAACTTACAAAACA
1 A--CATACATATTCGAA-CAACTTACAAAACA
6657671 AATACAACAC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 1 0.04
31 2 0.07
32 24 0.89
ACGTcount: A:0.48, C:0.25, G:0.05, T:0.23
Consensus pattern (30 bp):
ACATACATATTCGAACAACTTACAAAACAT
Found at i:6658893 original size:40 final size:40
Alignment explanation
Indices: 6658844--6658922 Score: 140
Period size: 40 Copynumber: 2.0 Consensus size: 40
6658834 GCGCTTGGAT
*
6658844 AAAAAACGCCGCTAAAAATCGAGCATTAGCGTCGCTTTAC
1 AAAAAACGCCGCTAAAAATCGAGCATTAGCGGCGCTTTAC
*
6658884 AAAAAACGCCGCTAAAGATCGAGCATTAGCGGCGCTTTA
1 AAAAAACGCCGCTAAAAATCGAGCATTAGCGGCGCTTTA
6658923 AGGAAAGCAC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.19
Consensus pattern (40 bp):
AAAAAACGCCGCTAAAAATCGAGCATTAGCGGCGCTTTAC
Found at i:6658936 original size:40 final size:40
Alignment explanation
Indices: 6658844--6658942 Score: 128
Period size: 40 Copynumber: 2.5 Consensus size: 40
6658834 GCGCTTGGAT
* *
6658844 AAAAAACGCCGCTAAAAATCGAGCATTAGCGTCGCTTTAC
1 AAAAAACACCGCTAAAAATCGAGCATTAGCGGCGCTTTAC
* *
6658884 AAAAAACGCCGCTAAAGATCGAGCATTAGCGGCGCTTTA-
1 AAAAAACACCGCTAAAAATCGAGCATTAGCGGCGCTTTAC
* *
6658923 AGGAAAGCACCGCTAAAAAT
1 A-AAAAACACCGCTAAAAAT
6658943 ACCTTAAAGC
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
39 1 0.02
40 51 0.98
ACGTcount: A:0.39, C:0.23, G:0.20, T:0.17
Consensus pattern (40 bp):
AAAAAACACCGCTAAAAATCGAGCATTAGCGGCGCTTTAC
Found at i:6659095 original size:41 final size:41
Alignment explanation
Indices: 6659038--6659180 Score: 241
Period size: 41 Copynumber: 3.5 Consensus size: 41
6659028 TGACCTTTCG
* *
6659038 GGGCTTTAGCGGCGTTTTTAGAGAAGCGCCGCTAATGCTCC
1 GGGCTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCA
6659079 GGGCTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCA
1 GGGCTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCA
* *
6659120 GGGCTTTAGCGGCGATTTTGGAAAAGCGCCGCTAATGCTCA
1 GGGCTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCA
*
6659161 GTGCTTTAGCGGCGTTTTTG
1 GGGCTTTAGCGGCGTTTTTG
6659181 AAAAGTGCCG
Statistics
Matches: 96, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 96 1.00
ACGTcount: A:0.17, C:0.22, G:0.33, T:0.29
Consensus pattern (41 bp):
GGGCTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCA
Found at i:6659620 original size:14 final size:15
Alignment explanation
Indices: 6659593--6659621 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
6659583 AGGTTTATAT
6659593 ATTATGGAATTAGGG
1 ATTATGGAATTAGGG
6659608 ATTATGG-ATTAGGG
1 ATTATGGAATTAGGG
6659622 GTTCTGGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.31, C:0.00, G:0.34, T:0.34
Consensus pattern (15 bp):
ATTATGGAATTAGGG
Found at i:6659879 original size:22 final size:22
Alignment explanation
Indices: 6659836--6659887 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
6659826 ATATTAAATA
*
6659836 AGGTTTAGGGGTTAGTAGTTAG
1 AGGTTAAGGGGTTAGTAGTTAG
*
6659858 GGGTTAAGGGGTTAG-AGCTTAG
1 AGGTTAAGGGGTTAGTAG-TTAG
6659880 AGGTTAAG
1 AGGTTAAG
6659888 AGTTAGTGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 2 0.08
22 24 0.92
ACGTcount: A:0.25, C:0.02, G:0.42, T:0.31
Consensus pattern (22 bp):
AGGTTAAGGGGTTAGTAGTTAG
Found at i:6667609 original size:27 final size:26
Alignment explanation
Indices: 6667579--6667635 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
6667569 AATTTCGAGG
*
6667579 TTTACGATTTT-TAATTTTTATTAATT
1 TTTACG-TTTTCTAACTTTTATTAATT
* *
6667605 ATTTATGTTTTCTCACTTTTATTAATT
1 -TTTACGTTTTCTAACTTTTATTAATT
6667632 TTTA
1 TTTA
6667636 TTTTTATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 8 0.31
27 18 0.69
ACGTcount: A:0.25, C:0.07, G:0.04, T:0.65
Consensus pattern (26 bp):
TTTACGTTTTCTAACTTTTATTAATT
Found at i:6667931 original size:43 final size:43
Alignment explanation
Indices: 6667818--6668049 Score: 231
Period size: 43 Copynumber: 5.4 Consensus size: 43
6667808 TTTGCATGAT
* * * *
6667818 ATGTT-TTTAGCGGCGTTT-TTACGAGAAGTGTCGCTAAAGGT-
1 ATGTTCTTTAGCGGCGTTTGTGAC-AAAAGCGCCGCTAAAGGTC
* * * *
6667859 TTGTTCTATAGCGGCGTTTGTGATAAAAAGCGCCGCTAAAGTTC
1 ATGTTCTTTAGCGGCGTTTGTGA-CAAAAGCGCCGCTAAAGGTC
6667903 ATGTTCTTTAGCGGCGTTTGTGACAAAAGCGCCGCTAAAGGTC
1 ATGTTCTTTAGCGGCGTTTGTGACAAAAGCGCCGCTAAAGGTC
* * **
6667946 ATGGTCTTTAGCGGCATTTGTGGGAAAAGCGCCGCTAAAGGTC
1 ATGTTCTTTAGCGGCGTTTGTGACAAAAGCGCCGCTAAAGGTC
* * * *
6667989 ATGGTCTATAGCGGCATTTGTTTGA-AAAA-CGTCGCTAAAGGTC
1 ATGTTCTTTAGCGGCGTTTG--TGACAAAAGCGCCGCTAAAGGTC
* *
6668032 ATGATCTTTAGCAGCGTT
1 ATGTTCTTTAGCGGCGTT
6668050 CGTGGTCTAT
Statistics
Matches: 162, Mismatches: 23, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
41 4 0.02
42 12 0.07
43 119 0.73
44 25 0.15
45 2 0.01
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (43 bp):
ATGTTCTTTAGCGGCGTTTGTGACAAAAGCGCCGCTAAAGGTC
Found at i:6668755 original size:41 final size:41
Alignment explanation
Indices: 6668709--6668915 Score: 254
Period size: 41 Copynumber: 5.0 Consensus size: 41
6668699 CAGCGTTTAC
* *
6668709 AGAAAAAACGCTGCTAAAGGTCATGTTCTTTAGCGACGCTT
1 AGAAAAAACGCTGCTAAAGATCATGTTCTTTAGCGGCGCTT
* * * * *
6668750 CGAAAAAACGCCGCTAAAGGTCATGTTCTTTAGCGGGGCTA
1 AGAAAAAACGCTGCTAAAGATCATGTTCTTTAGCGGCGCTT
* *
6668791 AAAAAAAGACG-TCACTAAAGATCATGTTCTTTAGCGGCGCTT
1 AGAAAAA-ACGCT-GCTAAAGATCATGTTCTTTAGCGGCGCTT
*
6668833 AAAGAAAAACGCTGCTAAAGATCATGTTCTTTAGCGGCGCTT
1 AGA-AAAAACGCTGCTAAAGATCATGTTCTTTAGCGGCGCTT
* * * *
6668875 GGTAAAAACGCCGCTAGAGATCATGTTCTTTAGCGGCGCTT
1 AGAAAAAACGCTGCTAAAGATCATGTTCTTTAGCGGCGCTT
6668916 TCTTTACAAA
Statistics
Matches: 144, Mismatches: 18, Indels: 8
0.85 0.11 0.05
Matches are distributed among these distances:
41 77 0.53
42 62 0.43
43 5 0.03
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (41 bp):
AGAAAAAACGCTGCTAAAGATCATGTTCTTTAGCGGCGCTT
Found at i:6668819 original size:83 final size:83
Alignment explanation
Indices: 6668711--6668915 Score: 250
Period size: 83 Copynumber: 2.5 Consensus size: 83
6668701 GCGTTTACAG
** * * ** *
6668711 AAAAAACGCTGCTAAAGGTCATGTTCTTTAGCGACGCTTCGA-AAAAACGCCGCTAAAGGTCATG
1 AAAAAACGCCACTAAAGATCATGTTCTTTAGCGGCGCTTAAAGAAAAACGCCGCTAAAGATCATG
*
6668775 TTCTTTAGCGGGGCTAAA
66 TTCTTTAGCGGCGCTAAA
* *
6668793 AAAAAGACGTCACTAAAGATCATGTTCTTTAGCGGCGCTTAAAGAAAAACGCTGCTAAAGATCAT
1 AAAAA-ACGCCACTAAAGATCATGTTCTTTAGCGGCGCTTAAAGAAAAACGCCGCTAAAGATCAT
***
6668858 GTTCTTTAGCGGCGCTTGG
65 GTTCTTTAGCGGCGCTAAA
* * *
6668877 TAAAAACGCCGCTAGAGATCATGTTCTTTAGCGGCGCTT
1 AAAAAACGCCACTAAAGATCATGTTCTTTAGCGGCGCTT
6668916 TCTTTACAAA
Statistics
Matches: 104, Mismatches: 17, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
82 5 0.05
83 61 0.59
84 38 0.37
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (83 bp):
AAAAAACGCCACTAAAGATCATGTTCTTTAGCGGCGCTTAAAGAAAAACGCCGCTAAAGATCATG
TTCTTTAGCGGCGCTAAA
Found at i:6674927 original size:7 final size:7
Alignment explanation
Indices: 6674917--6674960 Score: 70
Period size: 7 Copynumber: 6.0 Consensus size: 7
6674907 TGATATATTT
6674917 TTATGTA
1 TTATGTA
6674924 TTATGTAA
1 TTATGT-A
6674932 GTTATGTA
1 -TTATGTA
6674940 TTATGTA
1 TTATGTA
6674947 TTATGTA
1 TTATGTA
6674954 TTATGTA
1 TTATGTA
6674961 AGTAATGTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
7 27 0.77
8 2 0.06
9 6 0.17
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (7 bp):
TTATGTA
Found at i:6674931 original size:34 final size:30
Alignment explanation
Indices: 6674890--6675327 Score: 126
Period size: 34 Copynumber: 13.7 Consensus size: 30
6674880 CATAAATGAG
* *
6674890 TTATGTAAGTTATGATATGATATATTTTTATGTA
1 TTATGTAAGTTATG-TAT--TAT-GTATTATGTA
6674924 TTATGTAAGTTATGTATTATGTATTATGTA
1 TTATGTAAGTTATGTATTATGTATTATGTA
*
6674954 TTATGTAAGTAATGTAAGTTATGTA--A-GTA
1 TTATGTAAGTTATGT-A-TTATGTATTATGTA
* *
6674983 --ATGTAAGTAATGTATTATGTAAGTTGTGTA
1 TTATGTAAGTTATGTATTATGT-A-TTATGTA
*
6675013 TAATAT-TAA-TTATGTA--A-G--TTGTGTA
1 T--TATGTAAGTTATGTATTATGTATTATGTA
* * * *
6675038 TAATGTAAGTTAAGAAGGTTATATATTATGTAA
1 TTATGTAAGTTATGTA--TTATGTATTATGT-A
6675071 GTTATGTAAGTTATGTA--A-GTAAGTTATGTAA
1 -TTATGTAAGTTATGTATTATGT-A-TTATGT-A
* *
6675102 GTTATGTAAGTTATGCAAGTTATTTAATTTATGTAA
1 -TTATGTAAGTTATG-TA-TTATGT-A-TTATGT-A
**
6675138 GTTATGTAAGTTATGTAGGCAATGTATTATGTAAA
1 -TTATGTAAGTTATGTA--TTATGTATTATGT--A
* *
6675173 TAATGTAAGTTA-GGAGGGTTATGTATTATGTAA
1 TTATGTAAGTTATGTA---TTATGTATTATGT-A
* *
6675206 GTTATTTAAGTTATGTAAGTTATGTAAGTTATTTAA
1 -TTATGTAAGTTATGT-A-TTATGT-A-TTATGT-A
6675242 TTTATGTAAGTTATGTA--A-G--TTATGTAA
1 -TTATGTAAGTTATGTATTATGTATTATGT-A
*
6675269 GTTATGTAAGTTATTTAATTTATGTAAGTTATGTAA
1 -TTATGTAAGTTATGT-A-TTATGT-A-TTATGT-A
*
6675305 GTTATGTAGGTTATGTATTATGT
1 -TTATGTAAGTTATGTATTATGT
6675328 TAGTTATTAT
Statistics
Matches: 322, Mismatches: 36, Indels: 92
0.72 0.08 0.20
Matches are distributed among these distances:
23 2 0.01
24 3 0.01
25 19 0.06
26 2 0.01
27 34 0.11
28 1 0.00
29 6 0.02
30 29 0.09
31 29 0.09
32 21 0.07
33 11 0.03
34 82 0.25
35 9 0.03
36 74 0.23
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.46
Consensus pattern (30 bp):
TTATGTAAGTTATGTATTATGTATTATGTA
Found at i:6674938 original size:9 final size:9
Alignment explanation
Indices: 6674924--6675334 Score: 365
Period size: 9 Copynumber: 48.4 Consensus size: 9
6674914 TTTTTATGTA
6674924 TTATGTAAG
1 TTATGTAAG
6674933 TTATGT-A-
1 TTATGTAAG
6674940 TTATGT-A-
1 TTATGTAAG
6674947 TTATGT-A-
1 TTATGTAAG
6674954 TTATGTAAG
1 TTATGTAAG
*
6674963 TAATGTAAG
1 TTATGTAAG
6674972 TTATGTAAG
1 TTATGTAAG
*
6674981 TAATGTAAG
1 TTATGTAAG
*
6674990 TAATGT-A-
1 TTATGTAAG
6674997 TTATGTAAG
1 TTATGTAAG
*
6675006 TTGTGTATA-
1 TTATGTA-AG
*
6675015 ATAT-TAA-
1 TTATGTAAG
6675022 TTATGTAAG
1 TTATGTAAG
*
6675031 TTGTGT-A-
1 TTATGTAAG
*
6675038 TAATGTAAG
1 TTATGTAAG
*
6675047 TTAAG-AAGG
1 TTATGTAA-G
*
6675056 TTATAT-A-
1 TTATGTAAG
6675063 TTATGTAAG
1 TTATGTAAG
6675072 TTATGTAAG
1 TTATGTAAG
6675081 TTATGT-A-
1 TTATGTAAG
6675088 --A-GTAAG
1 TTATGTAAG
6675094 TTATGTAAG
1 TTATGTAAG
6675103 TTATGTAAG
1 TTATGTAAG
*
6675112 TTATGCAAG
1 TTATGTAAG
* *
6675121 TTATTTAAT
1 TTATGTAAG
6675130 TTATGTAAG
1 TTATGTAAG
6675139 TTATGTAAG
1 TTATGTAAG
*
6675148 TTATGTAGG
1 TTATGTAAG
**
6675157 CAATGT-A-
1 TTATGTAAG
*
6675164 TTATGTAAA
1 TTATGTAAG
*
6675173 TAATGTAAG
1 TTATGTAAG
* *
6675182 TTA-GGAGGG
1 TTATGTA-AG
6675191 TTATGT-A-
1 TTATGTAAG
6675198 TTATGTAAG
1 TTATGTAAG
*
6675207 TTATTTAAG
1 TTATGTAAG
6675216 TTATGTAAG
1 TTATGTAAG
6675225 TTATGTAAG
1 TTATGTAAG
* *
6675234 TTATTTAAT
1 TTATGTAAG
6675243 TTATGTAAG
1 TTATGTAAG
6675252 TTATGTAAG
1 TTATGTAAG
6675261 TTATGTAAG
1 TTATGTAAG
6675270 TTATGTAAG
1 TTATGTAAG
* *
6675279 TTATTTAAT
1 TTATGTAAG
6675288 TTATGTAAG
1 TTATGTAAG
6675297 TTATGTAAG
1 TTATGTAAG
*
6675306 TTATGTAGG
1 TTATGTAAG
6675315 TTATGT-A-
1 TTATGTAAG
*
6675322 TTATGTTAG
1 TTATGTAAG
6675331 TTAT
1 TTAT
6675335 TATGTTATTA
Statistics
Matches: 329, Mismatches: 47, Indels: 52
0.77 0.11 0.12
Matches are distributed among these distances:
4 2 0.01
5 2 0.01
7 54 0.16
8 21 0.06
9 248 0.75
10 2 0.01
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.46
Consensus pattern (9 bp):
TTATGTAAG
Found at i:6675094 original size:13 final size:13
Alignment explanation
Indices: 6675076--6675103 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
6675066 TGTAAGTTAT
6675076 GTAAGTTATGTAA
1 GTAAGTTATGTAA
6675089 GTAAGTTATGTAA
1 GTAAGTTATGTAA
6675102 GT
1 GT
6675104 TATGTAAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.25, T:0.39
Consensus pattern (13 bp):
GTAAGTTATGTAA
Found at i:6675095 original size:22 final size:22
Alignment explanation
Indices: 6675071--6675112 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
6675061 TATTATGTAA
6675071 GTTATGTAAGTTATGTAAGTAA
1 GTTATGTAAGTTATGTAAGTAA
6675093 GTTATGTAAGTTATGTAAGT
1 GTTATGTAAGTTATGTAAGT
6675113 TATGCAAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.24, T:0.43
Consensus pattern (22 bp):
GTTATGTAAGTTATGTAAGTAA
Found at i:6677018 original size:40 final size:40
Alignment explanation
Indices: 6676943--6677023 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 40
6676933 TTGGGGATTT
*
6676943 GGGGAAATAAAATCGAGGAAATTAGGGGAAAAGGAATTGG
1 GGGGAAATAAAATCGAGGAAATTAGGGGAAAAGGAAATGG
* * * * * *
6676983 GGGGAAATGAAATCGGGGAAGTTGGGGGGATAGGAAATGG
1 GGGGAAATAAAATCGAGGAAATTAGGGGAAAAGGAAATGG
6677023 G
1 G
6677024 AAATTAGGGA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.38, C:0.02, G:0.44, T:0.15
Consensus pattern (40 bp):
GGGGAAATAAAATCGAGGAAATTAGGGGAAAAGGAAATGG
Found at i:6677387 original size:115 final size:115
Alignment explanation
Indices: 6677171--6677620 Score: 405
Period size: 115 Copynumber: 3.9 Consensus size: 115
6677161 TCCCATATAG
* * * * *
6677171 AAAACGACAACGTTTAGCAAACACTTAAAACATATTTGCGGCGTTTATAATAAAGACGCCACTAA
1 AAAACGACAACGTTTAGCAAACACTAAAAACATAATTGCGGCATTT-TTATAAAAACGCCACTAA
* * ** * *
6677236 AACATATCCTTTACCGGTGTTTTAGTACAAACGCCACTAAAATCGTAGATA
65 CACATAACCTTTTGCGGCGTTTTAGTAAAAACGCCACTAAAATCGTAGATA
* * * * *
6677287 AAAATGACAACGTTTAGCGAACACTTATAACATAATTGCGGCATTTTTATAAAAACGCCACTACC
1 AAAACGACAACGTTTAGCAAACACTAAAAACATAATTGCGGCATTTTTATAAAAACGCCACTAAC
* * *
6677352 ACATAACCTTTTGCGGTGTTTTTGTAAAAATGCCACTAATAAT-GTAGATA
66 ACATAACCTTTTGCGGCGTTTTAGTAAAAACGCCACTAA-AATCGTAGATA
* * * *** * *
6677402 AAAACGACAACGTTTA-CAAAAGACTAATAACATAATTGCGGC-GTTACCTGAAAATGCCACTAA
1 AAAACGACAACGTTTAGC-AAACACTAAAAACATAATTGCGGCATTTTTATAAAAACGCCACTAA
* * * *
6677465 CACAT--CATTTTGCGGCGTTTTGGCAAAAACGCCACTGAAAA-CCTAGATA
65 CACATAACCTTTTGCGGCGTTTTAGTAAAAACGCCACT-AAAATCGTAGATA
* * * * * * *
6677514 AAAATGACAACGTTT-GAAAAAGACAAAAAACATAATTGCGGCATTTTTTGTAGAAACACCACT-
1 AAAACGACAACGTTTAG-CAAACACTAAAAACATAATTGCGGCA-TTTTTATAAAAACGCCACTA
* *
6677577 A-ATATAACTCGTTTTGCGGCATTTTAGTAAAAACGCCACTAAAA
64 ACACATAAC-C-TTTTGCGGCGTTTTAGTAAAAACGCCACTAAAA
6677621 AATCAGACTA
Statistics
Matches: 273, Mismatches: 49, Indels: 25
0.79 0.14 0.07
Matches are distributed among these distances:
112 73 0.27
113 3 0.01
114 32 0.12
115 95 0.35
116 70 0.26
ACGTcount: A:0.40, C:0.20, G:0.14, T:0.26
Consensus pattern (115 bp):
AAAACGACAACGTTTAGCAAACACTAAAAACATAATTGCGGCATTTTTATAAAAACGCCACTAAC
ACATAACCTTTTGCGGCGTTTTAGTAAAAACGCCACTAAAATCGTAGATA
Found at i:6677965 original size:14 final size:14
Alignment explanation
Indices: 6677879--6678096 Score: 77
Period size: 14 Copynumber: 15.5 Consensus size: 14
6677869 TTTAACCTCT
*
6677879 TAAACCCTAAACAA
1 TAAACCCTAAACCA
* *
6677893 TAAACACTAGACCA
1 TAAACCCTAAACCA
*
6677907 TAAA-CCTACACCA
1 TAAACCCTAAACCA
* * *
6677920 TAAATCGTAAACAA
1 TAAACCCTAAACCA
* *
6677934 TAAACTCTTAA-CA
1 TAAACCCTAAACCA
* *
6677947 CTAAACCATAAACCT
1 -TAAACCCTAAACCA
** * *
6677962 TAAACTTTATACCC
1 TAAACCCTAAACCA
* *
6677976 TAAACACCCTAAGCTA
1 T-AA-ACCCTAAACCA
6677992 TAAACCCT-AA--A
1 TAAACCCTAAACCA
* * *
6678003 TTAACCTTAAAATCA
1 TAAACCCT-AAACCA
* * **
6678018 TAAATCATAAATTA
1 TAAACCCTAAACCA
*
6678032 TAAACCCTAAAATCA
1 TAAACCCT-AAACCA
* * *
6678047 TAAATCTTAAACCT
1 TAAACCCTAAACCA
*
6678061 TAAACCCTAAACCC
1 TAAACCCTAAACCA
*
6678075 TTAACCCTAAACCAA
1 TAAACCCTAAACC-A
6678090 TAAACCC
1 TAAACCC
6678097 CATGAACCCC
Statistics
Matches: 146, Mismatches: 47, Indels: 21
0.68 0.22 0.10
Matches are distributed among these distances:
11 7 0.05
13 15 0.10
14 90 0.62
15 28 0.19
16 6 0.04
ACGTcount: A:0.48, C:0.28, G:0.01, T:0.23
Consensus pattern (14 bp):
TAAACCCTAAACCA
Found at i:6678044 original size:22 final size:22
Alignment explanation
Indices: 6678019--6678064 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
6678009 TTAAAATCAT
6678019 AAATCATAAAT-TATAAACCCTA
1 AAATCATAAATCT-TAAACCCTA
*
6678041 AAATCATAAATCTTAAACCTTA
1 AAATCATAAATCTTAAACCCTA
6678063 AA
1 AA
6678065 CCCTAAACCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 21 0.95
23 1 0.05
ACGTcount: A:0.54, C:0.17, G:0.00, T:0.28
Consensus pattern (22 bp):
AAATCATAAATCTTAAACCCTA
Found at i:6678046 original size:29 final size:29
Alignment explanation
Indices: 6678005--6678071 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
6677995 ACCCTAAATT
* *
6678005 AACCTTAAAATCATAAATCATAAA-TTATA
1 AACCCTAAAATCATAAATCATAAACCT-TA
*
6678034 AACCCTAAAATCATAAATCTTAAACCTTA
1 AACCCTAAAATCATAAATCATAAACCTTA
6678063 AACCCTAAA
1 AACCCTAAA
6678072 CCCTTAACCC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 33 0.97
30 1 0.03
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.27
Consensus pattern (29 bp):
AACCCTAAAATCATAAATCATAAACCTTA
Found at i:6678077 original size:22 final size:22
Alignment explanation
Indices: 6678068--6678133 Score: 62
Period size: 24 Copynumber: 2.9 Consensus size: 22
6678058 CCTTAAACCC
6678068 TAAACCCTTAACCCTAAACCAA
1 TAAACCCTTAACCCTAAACCAA
* *
6678090 TAAACCCCATGAACCCCT-AACCTA
1 TAAA-CCC-TTAA-CCCTAAACCAA
*
6678114 TAAACCCTTAAACCCAAAAC
1 TAAACCCTT-AACCCTAAAC
6678134 TCTAAGCCAC
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
22 8 0.23
23 11 0.31
24 12 0.34
25 4 0.11
ACGTcount: A:0.44, C:0.38, G:0.02, T:0.17
Consensus pattern (22 bp):
TAAACCCTTAACCCTAAACCAA
Found at i:6678318 original size:21 final size:22
Alignment explanation
Indices: 6678288--6678342 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
6678278 ATAAATCCTA
*
6678288 AAACCCTAAACTA-TAAA-AATT
1 AAACCTTAAA-TACTAAACAATT
*
6678309 AAACCTTAAATACTAAACACTT
1 AAACCTTAAATACTAAACAATT
*
6678331 AAACCTAAAATA
1 AAACCTTAAATA
6678343 AATTTATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.07
21 13 0.45
22 14 0.48
ACGTcount: A:0.56, C:0.20, G:0.00, T:0.24
Consensus pattern (22 bp):
AAACCTTAAATACTAAACAATT
Found at i:6685880 original size:20 final size:21
Alignment explanation
Indices: 6685843--6685885 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 21
6685833 TATGCAGCAG
6685843 ATAAACCAAAGGGGGTATTTCA
1 ATAAACCAAA-GGGGTATTTCA
6685865 ATAAACCAAA-GGGTATTTCA
1 ATAAACCAAAGGGGTATTTCA
6685885 A
1 A
6685886 GGAGTAGAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 11 0.52
22 10 0.48
ACGTcount: A:0.44, C:0.14, G:0.19, T:0.23
Consensus pattern (21 bp):
ATAAACCAAAGGGGTATTTCA
Found at i:6691091 original size:194 final size:196
Alignment explanation
Indices: 6690757--6691151 Score: 643
Period size: 194 Copynumber: 2.0 Consensus size: 196
6690747 AATTCTTTAG
* *
6690757 TTCAGGGAGACAACCTAGAATAATAATTTTTGAAAAACAACTTATCATGCTTGACTCTCTCGTGT
1 TTCAGGGAGACAACCTAAAATAATAATTTCTGAAAAACAACTTATCATGCTTGACTCTCTCGTGT
* * * *
6690822 CTTAAAATATTAATCACACAATGCACAAATATCCATAAATTATTCCCAAAATAGAATCACTAAAA
66 CTTAAAATATTAATCACACAATGCACAAACATCCACAAATTATTCACAAAACAGAATCACTAAAA
* * *
6690887 ACTCTAAATTAAAAAAATAACTTTAATGATAGGTGTGAGAAAATCACTT-AA-ACACGAACAATA
131 ACTCTAAATTAAAAAAAAAACTTCAATGATAGGTGTGAGAAAATCACTTAAACACACAAACAATA
6690950 A
196 A
*
6690951 TTCATGGAGAC-ACCTAAAATAATAATTTCTGAAAAACAACTTATCATGCTTGACTCTCTCGTGT
1 TTCAGGGAGACAACCTAAAATAATAATTTCTGAAAAACAACTTATCATGCTTGACTCTCTCGTGT
* *
6691015 CTTAAAAATATTAATTACACAATGCACAAACATCCACAAATTATTCACAAAACAGAATCACTTAA
66 CTT-AAAATATTAATCACACAATGCACAAACATCCACAAATTATTCACAAAACAGAATCACTAAA
*
6691080 AACTCTAAATTAAAAAAAAAACTTCAATGATAGGTGTGAGAAAATTACTTAAACACACAAACAAT
130 AACTCTAAATTAAAAAAAAAACTTCAATGATAGGTGTGAGAAAATCACTTAAACACACAAACAAT
6691145 AA
195 AA
6691147 TTCAG
1 TTCAG
6691152 AGATTTCATC
Statistics
Matches: 184, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
193 54 0.29
194 112 0.61
195 2 0.01
196 16 0.09
ACGTcount: A:0.46, C:0.18, G:0.09, T:0.27
Consensus pattern (196 bp):
TTCAGGGAGACAACCTAAAATAATAATTTCTGAAAAACAACTTATCATGCTTGACTCTCTCGTGT
CTTAAAATATTAATCACACAATGCACAAACATCCACAAATTATTCACAAAACAGAATCACTAAAA
ACTCTAAATTAAAAAAAAAACTTCAATGATAGGTGTGAGAAAATCACTTAAACACACAAACAATA
A
Found at i:6692073 original size:12 final size:12
Alignment explanation
Indices: 6692058--6692112 Score: 53
Period size: 13 Copynumber: 4.7 Consensus size: 12
6692048 CATGTGGACC
*
6692058 AATTTTTTTTCC
1 AATTTTTTTTCA
*
6692070 AA-TTTTTTTAA
1 AATTTTTTTTCA
6692081 ATATTTTTTTTCA
1 A-ATTTTTTTTCA
6692094 AATTATTTTTT--
1 AATT-TTTTTTCA
6692105 AATTTTTT
1 AATTTTTT
6692113 AGGTAATAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
10 4 0.11
11 12 0.32
12 6 0.16
13 15 0.41
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.69
Consensus pattern (12 bp):
AATTTTTTTTCA
Found at i:6692090 original size:15 final size:15
Alignment explanation
Indices: 6692072--6692104 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
6692062 TTTTTTCCAA
6692072 TTTTTTT-AAA-TAT
1 TTTTTTTCAAATTAT
6692085 TTTTTTTCAAATTAT
1 TTTTTTTCAAATTAT
6692100 TTTTT
1 TTTTT
6692105 AATTTTTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.39
14 3 0.17
15 8 0.44
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTTTTTCAAATTAT
Found at i:6692091 original size:24 final size:25
Alignment explanation
Indices: 6692059--6692112 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 25
6692049 ATGTGGACCA
*
6692059 ATTTTTTTTCCAATT-TTTTTAAAT
1 ATTTTTTTTCAAATTATTTTTAAAT
*
6692083 ATTTTTTTTCAAATTATTTTTTAAT
1 ATTTTTTTTCAAATTATTTTTAAAT
6692108 -TTTTT
1 ATTTTT
6692113 AGGTAATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 19 0.70
25 8 0.30
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70
Consensus pattern (25 bp):
ATTTTTTTTCAAATTATTTTTAAAT
Found at i:6692953 original size:14 final size:14
Alignment explanation
Indices: 6692934--6692964 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
6692924 TGATTGCTTT
*
6692934 TAATCTAAATTTAC
1 TAATCTAAATTAAC
6692948 TAATCTAAATTAAC
1 TAATCTAAATTAAC
6692962 TAA
1 TAA
6692965 GAACACAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.39
Consensus pattern (14 bp):
TAATCTAAATTAAC
Found at i:6700563 original size:12 final size:12
Alignment explanation
Indices: 6700540--6700577 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
6700530 TAAGTCTAAG
*
6700540 AAAATAACAATA
1 AAAATAAAAATA
*
6700552 AACATAAAAATA
1 AAAATAAAAATA
6700564 AAAAT-AAAATA
1 AAAATAAAAATA
6700575 AAA
1 AAA
6700578 CAAATGGACT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
11 9 0.39
12 14 0.61
ACGTcount: A:0.79, C:0.05, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAATAAAAATA
Found at i:6700563 original size:18 final size:17
Alignment explanation
Indices: 6700540--6700577 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
6700530 TAAGTCTAAG
*
6700540 AAAATAACAATAAACATA
1 AAAATAAAAATAAA-ATA
6700558 AAAATAAAAATAAAATA
1 AAAATAAAAATAAAATA
6700575 AAA
1 AAA
6700578 CAAATGGACT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.79, C:0.05, G:0.00, T:0.16
Consensus pattern (17 bp):
AAAATAAAAATAAAATA
Found at i:6710230 original size:23 final size:21
Alignment explanation
Indices: 6710205--6710245 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
6710195 AAATAGCGTT
* *
6710205 GTGTGTCTATTTCACACGCCC
1 GTGTGGCTAATTCACACGCCC
6710226 GTGTGGCTAATTCACACGCC
1 GTGTGGCTAATTCACACGCC
6710246 TATGTATGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.32, G:0.22, T:0.29
Consensus pattern (21 bp):
GTGTGGCTAATTCACACGCCC
Found at i:6710921 original size:16 final size:17
Alignment explanation
Indices: 6710889--6710921 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
6710879 ATTCACATGA
6710889 ACCAAAATCATTTCAAG
1 ACCAAAATCATTTCAAG
6710906 ACCAAAATCA-TTCAAG
1 ACCAAAATCATTTCAAG
6710922 TATAGCAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.48, C:0.24, G:0.06, T:0.21
Consensus pattern (17 bp):
ACCAAAATCATTTCAAG
Found at i:6715554 original size:147 final size:147
Alignment explanation
Indices: 6715287--6715556 Score: 409
Period size: 147 Copynumber: 1.8 Consensus size: 147
6715277 TAGAATGAGA
* *
6715287 AAATGGTGGAGAAAAGAAAGGAATAGAGGGAACTGCAGTTGGGATTGTAGGGACTGAAGGAATGC
1 AAATGGTGGAGAAAAGAAAGGAATAGAGGGAAATACAGTTGGGATTGTAGGGACTGAAGGAATGC
* * *
6715352 TTTGTAGAGGGGGAAGTCCTCTTGGCAATGTGGTAGGAAGTGGAGGAAACACCCCAGGGTTTGGG
66 TTGGCAGAGGGGGAAGTCCTCTTCGCAATGTGGTAGGAAGTGGAGGAAACACCCCAGGGTTTGGG
6715417 AAATTAGGGAAATATAG
131 AAATTAGGGAAATATAG
* * *
6715434 AAATGGTGGA-AAAGAGAAAGGAAT-TAGGGAAATCACAGTTGGGATTGTGGGGACTGAGGGAAT
1 AAATGGTGGAGAAA-AGAAAGGAATAGAGGGAAAT-ACAGTTGGGATTGTAGGGACTGAAGGAAT
* * *
6715497 GCTTGGCAGAGGGGGCAGTCCTGTTCGCAATGTGGTAGGAAGTGGAGGAAACGCCCCAGG
64 GCTTGGCAGAGGGGGAAGTCCTCTTCGCAATGTGGTAGGAAGTGGAGGAAACACCCCAGG
6715557 CCATAGGAAT
Statistics
Matches: 110, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
146 10 0.09
147 100 0.91
ACGTcount: A:0.32, C:0.10, G:0.39, T:0.19
Consensus pattern (147 bp):
AAATGGTGGAGAAAAGAAAGGAATAGAGGGAAATACAGTTGGGATTGTAGGGACTGAAGGAATGC
TTGGCAGAGGGGGAAGTCCTCTTCGCAATGTGGTAGGAAGTGGAGGAAACACCCCAGGGTTTGGG
AAATTAGGGAAATATAG
Found at i:6716003 original size:24 final size:24
Alignment explanation
Indices: 6715975--6716026 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
6715965 TTAGTAAGTC
* *
6715975 AAATAAACTATGCTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
6715999 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
6716023 AAAT
1 AAAT
6716027 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:6722106 original size:23 final size:22
Alignment explanation
Indices: 6721965--6722106 Score: 72
Period size: 23 Copynumber: 6.0 Consensus size: 22
6721955 TTTTTCTTTT
* * *
6721965 AAAATAATGCTTAATAAATATGA
1 AAAATAATACATAATAAAT-TTA
*
6721988 AATGATAATACATAATAAATTTA
1 AA-AATAATACATAATAAATTTA
* *
6722011 AAAATAAATATATAATAAATCTA
1 AAAAT-AATACATAATAAATTTA
*
6722034 AGCTAATAATACATAA-AAATTTA
1 A--AAATAATACATAATAAATTTA
*** *
6722057 TGATGTTAATA-ATATATTGTAATTTA
1 --AAAATAATACATA-A-T-AAATTTA
6722083 AAAATAATACATAATGAAATTTA
1 AAAATAATACATAAT-AAATTTA
6722106 A
1 A
6722107 CGTTAATAAA
Statistics
Matches: 91, Mismatches: 17, Indels: 22
0.70 0.13 0.17
Matches are distributed among these distances:
22 5 0.05
23 44 0.48
24 29 0.32
25 7 0.08
26 6 0.07
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.35
Consensus pattern (22 bp):
AAAATAATACATAATAAATTTA
Found at i:6722225 original size:20 final size:20
Alignment explanation
Indices: 6722184--6722232 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
6722174 ATATATATAT
*
6722184 ATATAAAT-AGATAAATAAA
1 ATATAAATAACATAAATAAA
* *
6722203 ATATAAATAACATAATTACA
1 ATATAAATAACATAAATAAA
*
6722223 ATATCAATAA
1 ATATAAATAA
6722233 GGCTAGTGGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.63, C:0.06, G:0.02, T:0.29
Consensus pattern (20 bp):
ATATAAATAACATAAATAAA
Found at i:6728848 original size:17 final size:16
Alignment explanation
Indices: 6728812--6728881 Score: 63
Period size: 17 Copynumber: 4.2 Consensus size: 16
6728802 AGGCAACCCA
*
6728812 ATTTTTATTTTTATTATT
1 ATTTTTA-TTTTACT-TT
*
6728830 ATTTTTTTCTTTACTTT
1 ATTTTTAT-TTTACTTT
*
6728847 ATTTATTATTTTATTTT
1 ATTT-TTATTTTACTTT
6728864 A-TTTTATTTTAC-TT
1 ATTTTTATTTTACTTT
6728878 ATTT
1 ATTT
6728882 GGATATTAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
14 3 0.07
15 10 0.23
16 2 0.05
17 15 0.34
18 14 0.32
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (16 bp):
ATTTTTATTTTACTTT
Found at i:6728860 original size:5 final size:5
Alignment explanation
Indices: 6728814--6728874 Score: 50
Period size: 5 Copynumber: 11.0 Consensus size: 5
6728804 GCAACCCAAT
* *
6728814 TTTTA TTTTTA TTATTA TTTTTT TCTTTA CTTTA TTTATTA TTTTA TTTTA
1 TTTTA -TTTTA TT-TTA -TTTTA T-TTTA TTTTA -TT-TTA TTTTA TTTTA
6728865 TTTTA TTTTA
1 TTTTA TTTTA
6728875 CTTATTTGGA
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
5 25 0.54
6 16 0.35
7 5 0.11
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTTA
Done.