Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr6
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: 26303135
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.30
Warning! 1968672 characters in sequence are not A, C, G, or T
File 19 of 66
Found at i:6383294 original size:2 final size:2
Alignment explanation
Indices: 6383287--6383311 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6383277 TTGAACTCCA
6383287 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
6383312 CACACTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6392758 original size:33 final size:33
Alignment explanation
Indices: 6392721--6392800 Score: 92
Period size: 33 Copynumber: 2.5 Consensus size: 33
6392711 GTTAACATAT
* *
6392721 CATAATTAATGATGATATGACATGCTGATTTAA
1 CATAATTAATGATGATATGACATACTAATTTAA
* * * *
6392754 CATAATTGATGATAATGTGACATACTAATTTGA
1 CATAATTAATGATGATATGACATACTAATTTAA
6392787 CATAA-TAAT-ATGAT
1 CATAATTAATGATGAT
6392801 CATATTGTAT
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
31 4 0.10
32 3 0.08
33 32 0.82
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (33 bp):
CATAATTAATGATGATATGACATACTAATTTAA
Found at i:6395570 original size:80 final size:79
Alignment explanation
Indices: 6395430--6395579 Score: 185
Period size: 80 Copynumber: 1.9 Consensus size: 79
6395420 TTCTCCTAAA
* * ** *
6395430 ATAATTTAAAGATAATATTTAAATTGGATCAATTAAAATTTAAGTATTAGTTATGCAATTTATCT
1 ATAACTTAAAGATAATATTTAAATTGGACCAATTAAAATTTAACAATTAGTCATGCAATTTATCT
*
6395495 CTAAATAAATCAAG
66 ATAAATAAATCAAG
* * * *
6395509 ATAACTTAAAGATAATATTTAATTTTTGACCAATTAAAATTTACCAATTTGTCAT-CTAATTTAT
1 ATAACTTAAAGATAATATTTAA-ATTGGACCAATTAAAATTTAACAATTAGTCATGC-AATTTAT
6395573 CTATAAA
64 CTATAAA
6395580 AATCATGATA
Statistics
Matches: 59, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
79 22 0.37
80 37 0.63
ACGTcount: A:0.44, C:0.09, G:0.07, T:0.41
Consensus pattern (79 bp):
ATAACTTAAAGATAATATTTAAATTGGACCAATTAAAATTTAACAATTAGTCATGCAATTTATCT
ATAAATAAATCAAG
Found at i:6396078 original size:76 final size:76
Alignment explanation
Indices: 6395988--6396140 Score: 256
Period size: 76 Copynumber: 2.0 Consensus size: 76
6395978 AGATCAAGTC
6395988 CAAGTTCATACCCTT-AAAGATGAAGCACAAAGAAATTAATCAAAGAAATTCTAGAA-ATTATAG
1 CAAGTTCATACCCTTGAAA-ATGAAGCACAAAGAAATTAATCAAAGAAATTCTA-AAGATTATAG
6396051 ACCCACACCAAAT
64 ACCCACACCAAAT
*
6396064 CAAGTTCATACCCTTGAAAATGAAGCACAAAGAAATTAATCAAAGAAATTCTAAAGATTGTAGAC
1 CAAGTTCATACCCTTGAAAATGAAGCACAAAGAAATTAATCAAAGAAATTCTAAAGATTATAGAC
*
6396129 TCACACCAAAT
66 CCACACCAAAT
6396140 C
1 C
6396141 TTTGTAATTT
Statistics
Matches: 73, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
75 2 0.03
76 68 0.93
77 3 0.04
ACGTcount: A:0.48, C:0.20, G:0.11, T:0.22
Consensus pattern (76 bp):
CAAGTTCATACCCTTGAAAATGAAGCACAAAGAAATTAATCAAAGAAATTCTAAAGATTATAGAC
CCACACCAAAT
Found at i:6398329 original size:22 final size:22
Alignment explanation
Indices: 6398299--6398343 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
6398289 GGGAACATTC
*
6398299 TACCTTAAATGTATCGATACAT
1 TACCCTAAATGTATCGATACAT
*
6398321 TACCCTAAATGTGTCGATACAT
1 TACCCTAAATGTATCGATACAT
6398343 T
1 T
6398344 CATTCAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.36
Consensus pattern (22 bp):
TACCCTAAATGTATCGATACAT
Found at i:6399850 original size:2 final size:2
Alignment explanation
Indices: 6399843--6399871 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6399833 GTGTTTAATG
6399843 TA 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 TA T
6399872 GTATTTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6399919 original size:2 final size:2
Alignment explanation
Indices: 6399912--6399940 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6399902 AGTTATTANG
6399912 TA 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 TA T
6399941 GATTTTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6399956 original size:67 final size:66
Alignment explanation
Indices: 6399842--6399974 Score: 225
Period size: 69 Copynumber: 2.0 Consensus size: 66
6399832 TGTGTTTAAT
6399842 GTATATATATATATATATATATATATATATGTATTTTATTTATTCTATACCACTCATTGTAGTTA
1 GTATATATATATATATATATATATATATATGTATTTTATTTATTCTATACCACTCATTG-AG-TA
6399907 TTA
64 TTA
6399910 NGTATATATATATATATATATATATATATATG-ATTTTATTTA-TCTATACCACTCATTGAGTAT
1 -GTATATATATATATATATATATATATATATGTATTTTATTTATTCTATACCACTCATTGAGTAT
6399973 TA
65 TA
6399975 TGGTACTTAC
Statistics
Matches: 64, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
65 5 0.08
66 2 0.03
67 16 0.25
68 10 0.16
69 31 0.48
ACGTcount: A:0.36, C:0.08, G:0.06, T:0.50
Consensus pattern (66 bp):
GTATATATATATATATATATATATATATATGTATTTTATTTATTCTATACCACTCATTGAGTATT
A
Found at i:6403857 original size:36 final size:36
Alignment explanation
Indices: 6403767--6403867 Score: 112
Period size: 36 Copynumber: 2.8 Consensus size: 36
6403757 ACTATCAGCT
* * * *
6403767 TGCCTTTTCAATAGGATCAAATGTAATCTTTACAACA
1 TGCC-TTTCAACAGGATCAAGTGTAACCTTCACAACA
* * *
6403804 TGCCTTTTAACAAGATCAGGTGTAACCTTCACAACA
1 TGCCTTTCAACAGGATCAAGTGTAACCTTCACAACA
* *
6403840 TGCCTTTCACCAGGATCAAGCGTAACCT
1 TGCCTTTCAACAGGATCAAGTGTAACCT
6403868 CCATTAAGAC
Statistics
Matches: 52, Mismatches: 12, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
36 48 0.92
37 4 0.08
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.30
Consensus pattern (36 bp):
TGCCTTTCAACAGGATCAAGTGTAACCTTCACAACA
Found at i:6404813 original size:26 final size:26
Alignment explanation
Indices: 6404784--6404846 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 26
6404774 CATGTTGAGT
*
6404784 ATTTTAGTTTAAGTTATTTTAGTTTA
1 ATTTTAGTTTAAGTTATTTTAATTTA
* *
6404810 ATTTTA-TGTTAATTTGTTTTAATTTA
1 ATTTTAGT-TTAAGTTATTTTAATTTA
* *
6404836 CTTTAAGTTTA
1 ATTTTAGTTTA
6404847 GTCATTGCTT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
25 1 0.03
26 28 0.93
27 1 0.03
ACGTcount: A:0.27, C:0.02, G:0.10, T:0.62
Consensus pattern (26 bp):
ATTTTAGTTTAAGTTATTTTAATTTA
Found at i:6404815 original size:21 final size:21
Alignment explanation
Indices: 6404791--6404834 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
6404781 AGTATTTTAG
*
6404791 TTTAAGTTATTTTAG-TTTAAT
1 TTTAAGTTAATTT-GTTTTAAT
*
6404812 TTTATGTTAATTTGTTTTAAT
1 TTTAAGTTAATTTGTTTTAAT
6404833 TT
1 TT
6404835 ACTTTAAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.25, C:0.00, G:0.09, T:0.66
Consensus pattern (21 bp):
TTTAAGTTAATTTGTTTTAAT
Found at i:6406840 original size:41 final size:41
Alignment explanation
Indices: 6406783--6406878 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
6406773 CTTTTCAAGA
6406783 AGCAAGCATAACCTTTACACAAACACTGCCTTGTCGAGACG
1 AGCAAGCATAACCTTTACACAAACACTGCCTTGTCGAGACG
*
6406824 AGCAAGCATAACCTTTACACAAGCACTGCCTTGTCGAGACG
1 AGCAAGCATAACCTTTACACAAACACTGCCTTGTCGAGACG
6406865 AGCAAGCATAACCT
1 AGCAAGCATAACCT
6406879 CATTGTCAGT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.34, C:0.29, G:0.18, T:0.19
Consensus pattern (41 bp):
AGCAAGCATAACCTTTACACAAACACTGCCTTGTCGAGACG
Found at i:6408023 original size:15 final size:16
Alignment explanation
Indices: 6408003--6408045 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
6407993 ACATAAAATT
*
6408003 AAAATAACTCACT-TA
1 AAAATAACTAACTATA
*
6408018 AAAATAAACTAATTATA
1 AAAAT-AACTAACTATA
6408035 AAAATAACTAA
1 AAAATAACTAA
6408046 AAATAAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 5 0.21
16 12 0.50
17 7 0.29
ACGTcount: A:0.63, C:0.12, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAATAACTAACTATA
Found at i:6408689 original size:5 final size:5
Alignment explanation
Indices: 6408679--6408706 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
6408669 ACACACTTTA
6408679 TTTCT TTTCT TTTCT TTTCT TTTCT TTT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTT
6408707 TTTCAACCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTCT
Found at i:6411663 original size:10 final size:9
Alignment explanation
Indices: 6411650--6411674 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
6411640 TTTTTTGAAA
6411650 TTTTTTTCT
1 TTTTTTTCT
6411659 TTTTTTTCT
1 TTTTTTTCT
6411668 TTTTTTT
1 TTTTTTT
6411675 AGTTGTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:6418661 original size:26 final size:26
Alignment explanation
Indices: 6418632--6418688 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
6418622 AAAGAATAAC
* *
6418632 ATAAAATTATAATAAATC-ACTTAAAA
1 ATAAAATAATAATAAAGCAAC-TAAAA
* *
6418658 ATAAACTAATTATAAAGCAACTAAAA
1 ATAAAATAATAATAAAGCAACTAAAA
6418684 ATAAA
1 ATAAA
6418689 TAAATTATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 24 0.92
27 2 0.08
ACGTcount: A:0.63, C:0.09, G:0.02, T:0.26
Consensus pattern (26 bp):
ATAAAATAATAATAAAGCAACTAAAA
Found at i:6418891 original size:28 final size:28
Alignment explanation
Indices: 6418793--6418921 Score: 100
Period size: 30 Copynumber: 4.4 Consensus size: 28
6418783 TTGCCTAAAG
** * *
6418793 GTATAACCAATACTACATTTTTCAGAAGAG
1 GTATAACCTTTACTAC-TTTTTCA-AGGAA
6418823 GTATAACCTATT-CTACTTTTTCCAACGG-A
1 GTATAACCT-TTACTACTTTTT-CAA-GGAA
6418852 GCTATAACCTTTACTACTTTTTCAAGGAA
1 G-TATAACCTTTACTACTTTTTCAAGGAA
* * *
6418881 GTATAACCTTTAGCACTACCTTTTCAATGAG
1 GTATAACCTTT---ACTACTTTTTCAAGGAA
6418912 GTATAACCTT
1 GTATAACCTT
6418922 CAGCACAACC
Statistics
Matches: 83, Mismatches: 7, Indels: 17
0.78 0.07 0.16
Matches are distributed among these distances:
28 12 0.14
29 14 0.17
30 32 0.39
31 25 0.30
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.36
Consensus pattern (28 bp):
GTATAACCTTTACTACTTTTTCAAGGAA
Found at i:6418905 original size:31 final size:31
Alignment explanation
Indices: 6418864--6418961 Score: 119
Period size: 31 Copynumber: 3.2 Consensus size: 31
6418854 TATAACCTTT
*
6418864 ACTACTTTTTCAAGGAAGTATAACCTTTAGC
1 ACTACCTTTTCAAGGAAGTATAACCTTTAGC
* * *
6418895 ACTACCTTTTCAATGAGGTATAACCTTCAGC
1 ACTACCTTTTCAAGGAAGTATAACCTTTAGC
* *
6418926 ACAACCTTTTCAAGG-AGTTGTAACCTTTA-C
1 ACTACCTTTTCAAGGAAG-TATAACCTTTAGC
6418956 ACTACC
1 ACTACC
6418962 ATTTACTGGA
Statistics
Matches: 56, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
30 7 0.12
31 49 0.88
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.33
Consensus pattern (31 bp):
ACTACCTTTTCAAGGAAGTATAACCTTTAGC
Found at i:6420427 original size:20 final size:20
Alignment explanation
Indices: 6420402--6420439 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
6420392 TTCAAGCAAC
*
6420402 ATAATCACACAAAGAAAGTT
1 ATAATCACAAAAAGAAAGTT
6420422 ATAATCACAAAAAGAAAG
1 ATAATCACAAAAAGAAAG
6420440 ATTGGCCAAA
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:0.61, C:0.13, G:0.11, T:0.16
Consensus pattern (20 bp):
ATAATCACAAAAAGAAAGTT
Found at i:6422204 original size:19 final size:17
Alignment explanation
Indices: 6422166--6422204 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 17
6422156 TGTCATAACT
6422166 AAAATAATAATAATTAA
1 AAAATAATAATAATTAA
6422183 AAAATATATAAATATATTAA
1 AAAATA-AT-AATA-ATTAA
6422203 AA
1 AA
6422205 TCCATAAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 2 0.11
19 4 0.21
20 7 0.37
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
AAAATAATAATAATTAA
Found at i:6423185 original size:12 final size:12
Alignment explanation
Indices: 6423168--6423196 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
6423158 TTTTTCATTT
6423168 ATAAAAAAATTA
1 ATAAAAAAATTA
6423180 AT-AAAAAATTA
1 ATAAAAAAATTA
6423191 ATAAAA
1 ATAAAA
6423197 TTATATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
ATAAAAAAATTA
Found at i:6423196 original size:10 final size:11
Alignment explanation
Indices: 6423171--6423196 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
6423161 TTCATTTATA
6423171 AAAAAATTAAT
1 AAAAAATTAAT
6423182 AAAAAATTAAT
1 AAAAAATTAAT
6423193 AAAA
1 AAAA
6423197 TTATATAATA
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:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (11 bp):
AAAAAATTAAT
Found at i:6425489 original size:9 final size:9
Alignment explanation
Indices: 6425475--6425499 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
6425465 ATATATCTAC
6425475 AAAATAAAT
1 AAAATAAAT
6425484 AAAATAAAT
1 AAAATAAAT
6425493 AAAATAA
1 AAAATAA
6425500 GACTGATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (9 bp):
AAAATAAAT
Found at i:6428379 original size:38 final size:37
Alignment explanation
Indices: 6428337--6428444 Score: 128
Period size: 38 Copynumber: 2.9 Consensus size: 37
6428327 TTGAATTGTG
*
6428337 CTATGATAAAGAGCACCTTCCAAGGATCAACAATTATA
1 CTATGA-AAAGAGCACCTTCCAAAGATCAACAATTATA
* * *
6428375 CTATGAGAAAAAGCACCCTT-CAATGATCAACAATTGTA
1 CTATGA-AAAGAGCA-CCTTCCAAAGATCAACAATTATA
* *
6428413 CTATGACAAGAACACCTTCCAAAGATCAACAA
1 CTATGAAAAGAGCACCTTCCAAAGATCAACAA
6428445 GTATGCACTC
Statistics
Matches: 60, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
36 4 0.07
37 17 0.28
38 35 0.58
39 4 0.07
ACGTcount: A:0.44, C:0.23, G:0.12, T:0.21
Consensus pattern (37 bp):
CTATGAAAAGAGCACCTTCCAAAGATCAACAATTATA
Found at i:6431906 original size:53 final size:53
Alignment explanation
Indices: 6431848--6432007 Score: 212
Period size: 53 Copynumber: 3.0 Consensus size: 53
6431838 CATAATTCGA
* * *
6431848 ATTGAACTTGAATTGCAAATCCGTCAAGGCATACTAGGATTATAAGATGTCTT
1 ATTGAACTTGAATTGCAAATCCGACAAGGCATACTAGAATTTTAAGATGTCTT
* * *
6431901 ATTGAACTTGAATTGCAAATCCGCCAAGGTATACTAGAATTTTAAGATGTCCT
1 ATTGAACTTGAATTGCAAATCCGACAAGGCATACTAGAATTTTAAGATGTCTT
* * * * * *
6431954 ATTGAACTTGAATTACAAACCCAACAAGGCATATTAGTATTTTAAGATATCTT
1 ATTGAACTTGAATTGCAAATCCGACAAGGCATACTAGAATTTTAAGATGTCTT
6432007 A
1 A
6432008 AGAAAAAAAT
Statistics
Matches: 93, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
53 93 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.33
Consensus pattern (53 bp):
ATTGAACTTGAATTGCAAATCCGACAAGGCATACTAGAATTTTAAGATGTCTT
Found at i:6432291 original size:15 final size:17
Alignment explanation
Indices: 6432258--6432295 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
6432248 TAAGGACATC
6432258 ATTAA-TATAACATATA
1 ATTAATTATAACATATA
6432274 ATTAATTATAA-A-ATA
1 ATTAATTATAACATATA
6432289 ATTAATT
1 ATTAATT
6432296 TATTAGCTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 10 0.48
16 6 0.29
17 5 0.24
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
ATTAATTATAACATATA
Found at i:6432926 original size:57 final size:57
Alignment explanation
Indices: 6432823--6432930 Score: 162
Period size: 57 Copynumber: 1.9 Consensus size: 57
6432813 TTGAAGACTT
* * *
6432823 AAAAGCTCAAGTCCAGATCATGTTCAAGATCAAGTCTAAGCCTAGACCCTTACAAAA
1 AAAAGCTCAAGTCCAAATCATGTTCAAGATCAAGTCCAAACCTAGACCCTTACAAAA
* **
6432880 AAAATCTCAAGTCCAAATCATGTTCAAGATCAAGTCCAAATTTAGACCCTT
1 AAAAGCTCAAGTCCAAATCATGTTCAAGATCAAGTCCAAACCTAGACCCTT
6432931 GAAGATGAAG
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
57 45 1.00
ACGTcount: A:0.40, C:0.24, G:0.12, T:0.24
Consensus pattern (57 bp):
AAAAGCTCAAGTCCAAATCATGTTCAAGATCAAGTCCAAACCTAGACCCTTACAAAA
Found at i:6433585 original size:18 final size:18
Alignment explanation
Indices: 6433559--6433606 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
6433549 AAAAATTTTT
6433559 TTTTATTTAAAATTTAAAA
1 TTTT-TTTAAAATTTAAAA
*
6433578 TTTTTTTAAAAATTTTAAA
1 TTTTTTT-AAAATTTAAAA
6433597 -TTTTTTAAAA
1 TTTTTTTAAAA
6433607 AATTTTAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
17 4 0.15
18 9 0.33
19 14 0.52
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTTTTTAAAATTTAAAA
Found at i:6433607 original size:18 final size:19
Alignment explanation
Indices: 6433567--6433616 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
6433557 TTTTTTATTT
* *
6433567 AAAATTTAAAATTTTTTTA
1 AAAATTTTAAATTTTTTAA
6433586 AAAATTTTAAATTTTTTAA
1 AAAATTTTAAATTTTTTAA
6433605 AAAATTTTAAAT
1 AAAATTTTAAAT
6433617 AAGTTTTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
AAAATTTTAAATTTTTTAA
Found at i:6433960 original size:30 final size:29
Alignment explanation
Indices: 6433919--6433994 Score: 84
Period size: 27 Copynumber: 2.7 Consensus size: 29
6433909 AACTATTAAT
* **
6433919 TATAAAGATTTATTTGATTTAAAATAAAAA
1 TATAAAAATTTATTT-AAATAAAATAAAAA
* *
6433949 TATAAAAATTTAATTAAATATAATAAAAA
1 TATAAAAATTTATTTAAATAAAATAAAAA
6433978 -AT-AAAATTTATTTAAAT
1 TATAAAAATTTATTTAAAT
6433995 TTTTAAATAA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
27 14 0.35
28 2 0.05
29 11 0.28
30 13 0.32
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (29 bp):
TATAAAAATTTATTTAAATAAAATAAAAA
Found at i:6433992 original size:27 final size:29
Alignment explanation
Indices: 6433941--6433994 Score: 85
Period size: 27 Copynumber: 1.9 Consensus size: 29
6433931 TTTGATTTAA
6433941 AATAAAAATATAAAAATTTAATTAAATAT
1 AATAAAAATATAAAAATTTAATTAAATAT
*
6433970 AATAAAAA-AT-AAAATTTATTTAAAT
1 AATAAAAATATAAAAATTTAATTAAAT
6433995 TTTTAAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 14 0.58
28 2 0.08
29 8 0.33
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (29 bp):
AATAAAAATATAAAAATTTAATTAAATAT
Found at i:6454745 original size:81 final size:82
Alignment explanation
Indices: 6454604--6454757 Score: 247
Period size: 81 Copynumber: 1.9 Consensus size: 82
6454594 GTCACTTGGC
* *
6454604 CATTAGCAATTTTTTCTTCTTTTGTCTTGAATATTTGCTCAACACGCTTTTGAAACTTCTTTGGT
1 CATTAGCAATTTTTTCTTCGTTTGTCTTGAATATTTGCTCAACACACTTTTGAAACTTCTTTGGT
6454669 GAAGACTAAGACGGGCT
66 GAAGACTAAGACGGGCT
* **
6454686 CATTGGCAATTTTTTCTT-GTTTGTCTTTTATATTTGCTCAACACACTTTTGAAACTTCTTTGGT
1 CATTAGCAATTTTTTCTTCGTTTGTCTTGAATATTTGCTCAACACACTTTTGAAACTTCTTTGGT
*
6454750 GAGGACTA
66 GAAGACTA
6454758 GGACCGTTAC
Statistics
Matches: 66, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
81 49 0.74
82 17 0.26
ACGTcount: A:0.22, C:0.18, G:0.16, T:0.44
Consensus pattern (82 bp):
CATTAGCAATTTTTTCTTCGTTTGTCTTGAATATTTGCTCAACACACTTTTGAAACTTCTTTGGT
GAAGACTAAGACGGGCT
Found at i:6456678 original size:20 final size:20
Alignment explanation
Indices: 6456632--6456679 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
6456622 ATGTTGAAAT
* *
6456632 TTGTGAATGAATGGTAAAAA
1 TTGTGAATCAATAGTAAAAA
**
6456652 TCATGAATCAATAGTAAAAA
1 TTGTGAATCAATAGTAAAAA
6456672 TTGTGAAT
1 TTGTGAAT
6456680 GCTATGTCCA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.46, C:0.04, G:0.19, T:0.31
Consensus pattern (20 bp):
TTGTGAATCAATAGTAAAAA
Found at i:6473246 original size:45 final size:45
Alignment explanation
Indices: 6473174--6473287 Score: 140
Period size: 45 Copynumber: 2.4 Consensus size: 45
6473164 AAAATATTTA
* *
6473174 AATATTATTTAATGTATTAATATTATTTAACTATAATAAATATTATAAAG
1 AATATTATTT-A-GTATTATTA-T-TTTAA-TATAATAAATATAATAAAG
*
6473224 AATATTATTT-GATATTATTATTTTAATATAATAAATGTAATAAAG
1 AATATTATTTAG-TATTATTATTTTAATATAATAAATATAATAAAG
6473269 AATATTATTTAGTATTATT
1 AATATTATTTAGTATTATT
6473288 TAAATTTAAT
Statistics
Matches: 59, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
45 34 0.58
46 6 0.10
47 2 0.03
48 7 0.12
50 10 0.17
ACGTcount: A:0.46, C:0.01, G:0.05, T:0.48
Consensus pattern (45 bp):
AATATTATTTAGTATTATTATTTTAATATAATAAATATAATAAAG
Found at i:6476231 original size:15 final size:14
Alignment explanation
Indices: 6476211--6476242 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
6476201 TTAATGATAA
6476211 TTATTTATTTATCTT
1 TTATTTATTTAT-TT
6476226 TTATTTATTTATTT
1 TTATTTATTTATTT
6476240 TTA
1 TTA
6476243 AACTTGAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (14 bp):
TTATTTATTTATTT
Found at i:6476320 original size:2 final size:2
Alignment explanation
Indices: 6476313--6476357 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
6476303 AAATGATAAT
* *
6476313 TA TA TA TA CA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6476355 TA T
1 TA T
6476358 TGTTAACAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:6476523 original size:2 final size:2
Alignment explanation
Indices: 6476516--6476571 Score: 80
Period size: 2 Copynumber: 28.5 Consensus size: 2
6476506 AAATGATAAT
*
6476516 TA TA TA TA -A TA TA T- TA CTT TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
6476557 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
6476572 TGGTTACAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
1 2 0.04
2 46 0.94
3 1 0.02
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6482908 original size:19 final size:19
Alignment explanation
Indices: 6482884--6482921 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
6482874 CTGCCAAACC
*
6482884 CTCAAATTATACTCCAATA
1 CTCAAATCATACTCCAATA
6482903 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
6482922 AGTCAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:6493214 original size:2 final size:2
Alignment explanation
Indices: 6493207--6493236 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
6493197 ATTCATGATC
6493207 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6493237 AAGAAACATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6495726 original size:13 final size:13
Alignment explanation
Indices: 6495708--6495732 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6495698 GGAAAATGAG
6495708 ATTTTATAAAATA
1 ATTTTATAAAATA
6495721 ATTTTATAAAAT
1 ATTTTATAAAAT
6495733 TTTTGAAAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTTTATAAAATA
Found at i:6512684 original size:21 final size:20
Alignment explanation
Indices: 6512656--6512694 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
6512646 GAGCATTCTG
6512656 TTGAAAATGTATCGATACAT
1 TTGAAAATGTATCGATACAT
6512676 TTGACAAATGTATCGATAC
1 TTGA-AAATGTATCGATAC
6512695 TTGTGAGGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.33
Consensus pattern (20 bp):
TTGAAAATGTATCGATACAT
Found at i:6528476 original size:13 final size:13
Alignment explanation
Indices: 6528458--6528482 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6528448 AGAGAAATTG
6528458 TGATTTTATAAAA
1 TGATTTTATAAAA
6528471 TGATTTTATAAA
1 TGATTTTATAAA
6528483 TTTTCTGAAA
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:6530728 original size:29 final size:29
Alignment explanation
Indices: 6530682--6530800 Score: 141
Period size: 29 Copynumber: 4.1 Consensus size: 29
6530672 GAGCTAATAA
*
6530682 AGAAG-AGTTGTACATGAATAGGTACAAG
1 AGAAGAAGTTATACATGAATAGGTACAAG
*
6530710 AGAAGAAGTTATACGTGAATAGGTACAAG
1 AGAAGAAGTTATACATGAATAGGTACAAG
* * * *
6530739 AGAATAAGTTGTACATAAATAGGTATAAG
1 AGAAGAAGTTATACATGAATAGGTACAAG
* * * *
6530768 AGAAGAAGCTATACATGAACAAGTACGAG
1 AGAAGAAGTTATACATGAATAGGTACAAG
6530797 AGAA
1 AGAA
6530801 CATGGTAAAA
Statistics
Matches: 75, Mismatches: 15, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
28 5 0.07
29 70 0.93
ACGTcount: A:0.47, C:0.08, G:0.25, T:0.20
Consensus pattern (29 bp):
AGAAGAAGTTATACATGAATAGGTACAAG
Found at i:6530781 original size:58 final size:58
Alignment explanation
Indices: 6530687--6530800 Score: 165
Period size: 58 Copynumber: 2.0 Consensus size: 58
6530677 AATAAAGAAG
* * * * *
6530687 AGTTGTACATGAATAGGTACAAGAGAAGAAGTTATACGTGAATAGGTACAAGAGAATA
1 AGTTGTACATAAATAGGTACAAGAGAAGAAGCTATACATGAACAAGTACAAGAGAATA
* *
6530745 AGTTGTACATAAATAGGTATAAGAGAAGAAGCTATACATGAACAAGTACGAGAGAA
1 AGTTGTACATAAATAGGTACAAGAGAAGAAGCTATACATGAACAAGTACAAGAGAA
6530801 CATGGTAAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
58 49 1.00
ACGTcount: A:0.46, C:0.08, G:0.25, T:0.21
Consensus pattern (58 bp):
AGTTGTACATAAATAGGTACAAGAGAAGAAGCTATACATGAACAAGTACAAGAGAATA
Found at i:6531029 original size:18 final size:18
Alignment explanation
Indices: 6530987--6531029 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
6530977 ATTCTGCGCA
* *
6530987 AAGTAATTGTTCTACTTG
1 AAGTAATTGTTCCACATG
* *
6531005 TATTAATTGTTCCACATG
1 AAGTAATTGTTCCACATG
6531023 AAGTAAT
1 AAGTAAT
6531030 GCTCCATTTA
Statistics
Matches: 19, Mismatches: 6, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.42
Consensus pattern (18 bp):
AAGTAATTGTTCCACATG
Found at i:6531796 original size:2 final size:2
Alignment explanation
Indices: 6531791--6531837 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
6531781 TTTTTTTATG
6531791 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6531833 TA TA T
1 TA TA T
6531838 GTATGTATGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6538822 original size:15 final size:14
Alignment explanation
Indices: 6538787--6538824 Score: 53
Period size: 12 Copynumber: 2.8 Consensus size: 14
6538777 CTAACACTGT
6538787 AAACTTTAAAAAAA
1 AAACTTTAAAAAAA
6538801 AAA--TTAAAACAAA
1 AAACTTTAAAA-AAA
6538814 AAACTTTAAAA
1 AAACTTTAAAA
6538825 TCATGCTCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 6 0.29
13 6 0.29
14 3 0.14
15 6 0.29
ACGTcount: A:0.71, C:0.08, G:0.00, T:0.21
Consensus pattern (14 bp):
AAACTTTAAAAAAA
Found at i:6543234 original size:13 final size:13
Alignment explanation
Indices: 6543216--6543240 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6543206 GGAAAATGAG
6543216 ATTTTATAAAATA
1 ATTTTATAAAATA
6543229 ATTTTATAAAAT
1 ATTTTATAAAAT
6543241 TTTTGTAAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTTTATAAAATA
Found at i:6545300 original size:17 final size:17
Alignment explanation
Indices: 6545270--6545302 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
6545260 TTCTTGATAA
6545270 AATAAAACTCCTTATTG
1 AATAAAACTCCTTATTG
6545287 AATAATAACT-CTTATT
1 AATAA-AACTCCTTATT
6545303 TTATTATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.39
Consensus pattern (17 bp):
AATAAAACTCCTTATTG
Found at i:6545497 original size:28 final size:28
Alignment explanation
Indices: 6545466--6545617 Score: 146
Period size: 28 Copynumber: 5.3 Consensus size: 28
6545456 TAAGACAAAA
*
6545466 AAATAT-TTTATCTTGTCTAAATTGAGAC
1 AAATATGTTT-TCTTGTCTAAATTAAGAC
*
6545494 AAATATGTTTTCTTGACTAAATTAAGAC
1 AAATATGTTTTCTTGTCTAAATTAAGAC
* *
6545522 AAAAAATAT-TTTTCTTGTCTTAAGTTAAGGC
1 ---AAATATGTTTTCTTGTC-TAAATTAAGAC
* * *
6545553 AAACATATTTTCTTATCTAAATTAAGATC
1 AAATATGTTTTCTTGTCTAAATTAAGA-C
* *
6545582 GAACATGTTTTCTTGTCTAAATTAAGAC
1 AAATATGTTTTCTTGTCTAAATTAAGAC
*
6545610 AAACATGT
1 AAATATGT
6545618 CAAAGCTGTC
Statistics
Matches: 104, Mismatches: 13, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
28 43 0.41
29 37 0.36
30 9 0.09
31 15 0.14
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.40
Consensus pattern (28 bp):
AAATATGTTTTCTTGTCTAAATTAAGAC
Found at i:6545564 original size:59 final size:60
Alignment explanation
Indices: 6545455--6545615 Score: 174
Period size: 59 Copynumber: 2.8 Consensus size: 60
6545445 TTATTTGTAG
* * *
6545455 TTAAGACAAAAAAATATTTTATCTTGTCTAAATTGAGACAAATATGTTTTCTTGA-CTAAA
1 TTAAGACAAAAAAATATTTTATCTTGTCTAAATTAAGACAAACATATTTTCTT-ATCTAAA
* *
6545515 TTAAGAC-AAAAAATATTTT-TCTTGTCTTAAGTTAAGGCAAACATATTTTCTTATCTAAA
1 TTAAGACAAAAAAATATTTTATCTTGTC-TAAATTAAGACAAACATATTTTCTTATCTAAA
* * *
6545574 TTAAGATC--GAACAT-GTTT-TCTTGTCTAAATTAAGACAAACAT
1 TTAAGA-CAAAAAAATATTTTATCTTGTCTAAATTAAGACAAACAT
6545616 GTCAAAGCTG
Statistics
Matches: 88, Mismatches: 10, Indels: 9
0.82 0.09 0.08
Matches are distributed among these distances:
57 15 0.17
58 18 0.20
59 47 0.53
60 8 0.09
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.39
Consensus pattern (60 bp):
TTAAGACAAAAAAATATTTTATCTTGTCTAAATTAAGACAAACATATTTTCTTATCTAAA
Found at i:6547937 original size:229 final size:230
Alignment explanation
Indices: 6547518--6547977 Score: 796
Period size: 229 Copynumber: 2.0 Consensus size: 230
6547508 TTTTTGATCA
* *
6547518 TCTTCTAGGGCGAACTGGGTAAAATGGTAAACATGAAAGTTGTAGATTTTTCTCTAACCTTTCCA
1 TCTTCCAGGCCGAACTGGGTAAAATGGTAAACATGAAAGTTGTAGATTTTTCTCTAACCTTTCCA
*
6547583 ATTATCTAAGAATCATCTCTTTTGGAGTTTTGTAGAGAGAGTTAAGATTGAAATACCAGAACATG
66 ATTATCTAAGAATCATCTCTTTTAGAGTTTTGTAGAGAGAGTTAAGATTGAAATACCAGAACATG
* * ** * *
6547648 TGTAGTGAAAGTTTGCACCTCAAAATTCTTTTCCTTCTTCCATTAAAAGTTTTTCTTCAATAAAC
131 TGCAGTGAAAGTTTGCACCTCAAAATTCCTCACCTTCTTCCATTAAAAGTCTTCCTTCAATAAAC
*
6547713 ATCTATAAAAGCACAAATAATTCAATAACAACCTG
196 ATCTACAAAAGCACAAATAATTCAATAACAACCTG
* * *
6547748 TCTTCCAGGCCGAACTGGGTAGAATGGTAAACATGAAAGTTGTAGATTTTT-TCTTAGCTTTCCA
1 TCTTCCAGGCCGAACTGGGTAAAATGGTAAACATGAAAGTTGTAGATTTTTCTCTAACCTTTCCA
6547812 ATTATCTAAGAATCATCTCTTTTAGAGTTTTGTAGAGAGAGTTAAGATTGAAATACCAGAACATG
66 ATTATCTAAGAATCATCTCTTTTAGAGTTTTGTAGAGAGAGTTAAGATTGAAATACCAGAACATG
6547877 TGCAGTGAAAGTTTGCACCTCAAAATTCCTCACCTTCTTCCATTAAAAGTCTTCCTTCAATAAAC
131 TGCAGTGAAAGTTTGCACCTCAAAATTCCTCACCTTCTTCCATTAAAAGTCTTCCTTCAATAAAC
6547942 ATCTACAAAAGCACAAATAATTCAATAACAACCTG
196 ATCTACAAAAGCACAAATAATTCAATAACAACCTG
6547977 T
1 T
6547978 TTTAAGCACA
Statistics
Matches: 217, Mismatches: 13, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
229 169 0.78
230 48 0.22
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (230 bp):
TCTTCCAGGCCGAACTGGGTAAAATGGTAAACATGAAAGTTGTAGATTTTTCTCTAACCTTTCCA
ATTATCTAAGAATCATCTCTTTTAGAGTTTTGTAGAGAGAGTTAAGATTGAAATACCAGAACATG
TGCAGTGAAAGTTTGCACCTCAAAATTCCTCACCTTCTTCCATTAAAAGTCTTCCTTCAATAAAC
ATCTACAAAAGCACAAATAATTCAATAACAACCTG
Found at i:6550540 original size:27 final size:28
Alignment explanation
Indices: 6550505--6550596 Score: 127
Period size: 27 Copynumber: 3.4 Consensus size: 28
6550495 ATCTTTTCAC
6550505 TATTCATCTACTTTTGGTGGGTT-AAAG
1 TATTCATCTACTTTTGGTGGGTTAAAAG
* *
6550532 TA-TCTATCTACTTTTAGTGGATTAAAAG
1 TATTC-ATCTACTTTTGGTGGGTTAAAAG
*
6550560 TATTCATCTACTTTTGGTGGG-TAAAAT
1 TATTCATCTACTTTTGGTGGGTTAAAAG
6550587 TATTCATCTA
1 TATTCATCTA
6550597 TTTGTTACTA
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
26 2 0.04
27 33 0.58
28 20 0.35
29 2 0.04
ACGTcount: A:0.27, C:0.12, G:0.16, T:0.45
Consensus pattern (28 bp):
TATTCATCTACTTTTGGTGGGTTAAAAG
Found at i:6550786 original size:46 final size:45
Alignment explanation
Indices: 6550687--6550773 Score: 104
Period size: 46 Copynumber: 1.9 Consensus size: 45
6550677 AAAACAAATT
* *
6550687 TATATATACTGAGCATAATCATATTTGAAATTCAAAACAAAAAAA
1 TATATATACTGAGCATAATCATATTTAAAAATCAAAACAAAAAAA
* * *
6550732 AATCATATATTGAGTA-AATCATATTTTAAAAATCAAAACAAA
1 TAT-ATATACTGAGCATAATCATA-TTTAAAAATCAAAACAAA
6550774 GAGACTATAT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
45 9 0.26
46 26 0.74
ACGTcount: A:0.54, C:0.10, G:0.06, T:0.30
Consensus pattern (45 bp):
TATATATACTGAGCATAATCATATTTAAAAATCAAAACAAAAAAA
Found at i:6551838 original size:2 final size:2
Alignment explanation
Indices: 6551831--6551959 Score: 148
Period size: 2 Copynumber: 68.0 Consensus size: 2
6551821 TTTAACATTT
6551831 TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
6551872 -A TA T- TA T- TA TA TNA CA T- TA AA CA T- TA -A TA TA TA TA TA
1 TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
6551909 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA -A TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6551950 TA TA TA TA TA
1 TA TA TA TA TA
6551960 ATTGGATTCG
Statistics
Matches: 109, Mismatches: 9, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
1 8 0.07
2 100 0.92
3 1 0.01
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:6552073 original size:119 final size:119
Alignment explanation
Indices: 6551950--6552181 Score: 358
Period size: 119 Copynumber: 1.9 Consensus size: 119
6551940 ATAAATAATT
* * *
6551950 TATATATATAATTGGATTCGAATTTAAGGTATCCTAAGAGTGATACTCGAGCTTGAGTTGAGTAT
1 TATATATATAATTGGATTCGAATTTAAGGTATCCTAAGAGTGATACTCAAACTTGAGTCGAGTA-
* ** *
6552015 TAAA-AGCTTTACTCGAATCCGCCCCATAACTGAATATAGGGTACTCAATATATA
65 TAAATAGCCTTACTCGAATCCGCCCCATAACCCAATATAGGGAACTCAATATATA
* *
6552069 TATATATATAATTGGATTTGGATTTAAGGTATCCTAAGAGTGATACTCAAACTTGAGTCGAGTAT
1 TATATATATAATTGGATTCGAATTTAAGGTATCCTAAGAGTGATACTCAAACTTGAGTCGAGTAT
*
6552134 AAATAGCCTTACTCGAATCTGCCCCATAACCCAATATAGGGAACTCAA
66 AAATAGCCTTACTCGAATCCGCCCCATAACCCAATATAGGGAACTCAA
6552182 GCCCTATATT
Statistics
Matches: 102, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
118 4 0.04
119 98 0.96
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.31
Consensus pattern (119 bp):
TATATATATAATTGGATTCGAATTTAAGGTATCCTAAGAGTGATACTCAAACTTGAGTCGAGTAT
AAATAGCCTTACTCGAATCCGCCCCATAACCCAATATAGGGAACTCAATATATA
Found at i:6555936 original size:23 final size:23
Alignment explanation
Indices: 6555905--6555948 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
6555895 ATGAAATATT
6555905 ACTTAAAAGAACAAATAAAGATA
1 ACTTAAAAGAACAAATAAAGATA
* *
6555928 ACTTGAAAGAACAACTAAAGA
1 ACTTAAAAGAACAAATAAAGA
6555949 AAGAGAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.61, C:0.11, G:0.11, T:0.16
Consensus pattern (23 bp):
ACTTAAAAGAACAAATAAAGATA
Found at i:6562482 original size:2 final size:2
Alignment explanation
Indices: 6562475--6562507 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
6562465 ATATTCACAT
6562475 TA TA TA 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 TA TA TA T
6562508 TAATAGTATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6564527 original size:22 final size:21
Alignment explanation
Indices: 6564487--6564536 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
6564477 GTTCAATAGT
6564487 TATAAAAATTAAATTTAAAAAA
1 TATAAAAATTAAATTT-AAAAA
*
6564509 TATAAAAA-TATATTATAAAAA
1 TATAAAAATTAAATT-TAAAAA
6564530 T-TAAAAA
1 TATAAAAA
6564537 CTTTTGGAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 6 0.23
21 11 0.42
22 9 0.35
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (21 bp):
TATAAAAATTAAATTTAAAAA
Found at i:6565217 original size:16 final size:18
Alignment explanation
Indices: 6565188--6565221 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
6565178 CATCCTTTAG
6565188 TTTTATATTATAAATTAA
1 TTTTATATTATAAATTAA
6565206 TTTTAT-TT-TAAATTAA
1 TTTTATATTATAAATTAA
6565222 ATTACTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 2 0.12
18 6 0.38
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TTTTATATTATAAATTAA
Found at i:6572549 original size:109 final size:110
Alignment explanation
Indices: 6572344--6572559 Score: 265
Period size: 109 Copynumber: 2.0 Consensus size: 110
6572334 TGTAACAAAG
**
6572344 TGATTCATGCCTTGGCATGTAACATCAGTAAGAAAGAAGGAAGCTTTGGTATGTAATATTCGGTG
1 TGATTCATGCCTTGGCATGTAACATCAGTAAGAAAGAAGGAAGCTTTGGTATGTAATATTCAATG
* * * * * * *
6572409 CTAACATTTGGCATGTAAAGCATCGATCTTAGCGTGTAACATTCA
66 CTAACATCTGACACGTAAAACATCGACCTTAGCATATAACATTCA
* ** * *
6572454 TGATTCATGCTTTGGTGTGTAACATCAGT-AGGAAGAAGGAAGCTTTGGTGTGTAATA-TCTAAT
1 TGATTCATGCCTTGGCATGTAACATCAGTAAGAAAGAAGGAAGCTTTGGTATGTAATATTC-AAT
* *
6572517 GCTAACATCTGACACGTAAAACTTTGACCTTAGCATATAACAT
65 GCTAACATCTGACACGTAAAACATCGACCTTAGCATATAACAT
6572560 CTGATGTTGA
Statistics
Matches: 89, Mismatches: 16, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
108 2 0.02
109 61 0.69
110 26 0.29
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.31
Consensus pattern (110 bp):
TGATTCATGCCTTGGCATGTAACATCAGTAAGAAAGAAGGAAGCTTTGGTATGTAATATTCAATG
CTAACATCTGACACGTAAAACATCGACCTTAGCATATAACATTCA
Found at i:6575482 original size:21 final size:23
Alignment explanation
Indices: 6575458--6575519 Score: 60
Period size: 24 Copynumber: 2.7 Consensus size: 23
6575448 TTTTTTTGTC
6575458 ATTTTTTATTATTTA-ATTAT-T
1 ATTTTTTATTATTTATATTATAT
6575479 ATTTTCATT-TTATTTCATATTATCAT
1 ATTTT--TTATTATTT-ATATTAT-AT
6575505 ATTTTTTATT-TTTAT
1 ATTTTTTATTATTTAT
6575520 TCTCCTATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
21 5 0.15
22 6 0.18
23 5 0.15
24 10 0.29
25 2 0.06
26 6 0.18
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (23 bp):
ATTTTTTATTATTTATATTATAT
Found at i:6576973 original size:43 final size:43
Alignment explanation
Indices: 6576912--6577001 Score: 135
Period size: 43 Copynumber: 2.1 Consensus size: 43
6576902 GATTTCTCAC
* *
6576912 CCTCACGCCGGCGAACTCCTCTTGGCCATCAATTTACAGGTGG
1 CCTCACGCCGGCGAACTCCTCTTGGCCACCAATCTACAGGTGG
* * *
6576955 CCTCACGTCGGCGAACTCCTCTTTGCCACCGATCTACAGGTGG
1 CCTCACGCCGGCGAACTCCTCTTGGCCACCAATCTACAGGTGG
6576998 CCTC
1 CCTC
6577002 GCAGGTTCCC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.17, C:0.38, G:0.22, T:0.23
Consensus pattern (43 bp):
CCTCACGCCGGCGAACTCCTCTTGGCCACCAATCTACAGGTGG
Found at i:6578214 original size:101 final size:100
Alignment explanation
Indices: 6578100--6578298 Score: 357
Period size: 101 Copynumber: 2.0 Consensus size: 100
6578090 AAAGTTTTTC
6578100 ATAAAAAAATTAAAAAAATGAAAATAAAACTTATGGGGGAGTTGAGATAATAGAAATGTTCACAT
1 ATAAAAAAATTAAAAAAATGAAAATAAAACTTATGGGGGAGTTGAGATAATAGAAATGTTCACAT
6578165 GTGAAGTA-ATAGTATATATATATATA-ATATATAAA
66 GTGAA-TATATA-TATATATATATATATATATATAAA
6578200 NATAAAAAAATTAAAAAAATGAAAATAAAACTTATGGGGGAGTTGAGATAATAGAAATGTTCACA
1 -ATAAAAAAATTAAAAAAATGAAAATAAAACTTATGGGGGAGTTGAGATAATAGAAATGTTCACA
6578265 TGTGAATATATATATATATATATATATATATATA
65 TGTGAATATATATATATATATATATATATATATA
6578299 TAGAAAGTTG
Statistics
Matches: 96, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
100 16 0.17
101 80 0.83
ACGTcount: A:0.52, C:0.03, G:0.14, T:0.30
Consensus pattern (100 bp):
ATAAAAAAATTAAAAAAATGAAAATAAAACTTATGGGGGAGTTGAGATAATAGAAATGTTCACAT
GTGAATATATATATATATATATATATATATATAAA
Found at i:6578277 original size:2 final size:2
Alignment explanation
Indices: 6578270--6578300 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
6578260 TCACATGTGA
6578270 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6578301 GAAAGTTGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6578687 original size:25 final size:24
Alignment explanation
Indices: 6578659--6578788 Score: 73
Period size: 25 Copynumber: 5.3 Consensus size: 24
6578649 TGTTCCCCAG
6578659 GGAGCACTGGATCAATGCTCCCTAT
1 GGAGCAC-GGATCAATGCTCCCTAT
** * * **
6578684 GGAGCACCCATCTATGCTCTCTGG
1 GGAGCACGGATCAATGCTCCCTAT
* *
6578708 GGAGCACGGAAACAGTGCTCCCTAT
1 GGAGCACGG-ATCAATGCTCCCTAT
** * * * *
6578733 GGAGCACCCATCTAGGCTCCCCAG
1 GGAGCACGGATCAATGCTCCCTAT
* *
6578757 GGAGCACGAGAACAGTGCTCCCTA-
1 GGAGCACG-GATCAATGCTCCCTAT
6578781 GAGAGCAC
1 G-GAGCAC
6578789 CCACAATGGG
Statistics
Matches: 73, Mismatches: 29, Indels: 6
0.68 0.27 0.06
Matches are distributed among these distances:
24 35 0.48
25 38 0.52
ACGTcount: A:0.25, C:0.32, G:0.27, T:0.17
Consensus pattern (24 bp):
GGAGCACGGATCAATGCTCCCTAT
Found at i:6578711 original size:49 final size:48
Alignment explanation
Indices: 6578652--6578791 Score: 183
Period size: 49 Copynumber: 2.9 Consensus size: 48
6578642 AGATTGATGT
* * *
6578652 TCCCCAGGGAGCACTGGATCAATGCTCCCTATGGAGCACCCATCTATGC
1 TCCCCAGGGAGCAC-GGAACAGTGCTCCCTATGGAGCACCCATCTAGGC
* **
6578701 TCTCTGGGGAGCACGGAAACAGTGCTCCCTATGGAGCACCCATCTAGGC
1 TCCCCAGGGAGCACGG-AACAGTGCTCCCTATGGAGCACCCATCTAGGC
6578750 TCCCCAGGGAGCACGAGAACAGTGCTCCCTA-GAGAGCACCCA
1 TCCCCAGGGAGCACG-GAACAGTGCTCCCTATG-GAGCACCCA
6578792 CAATGGGTGT
Statistics
Matches: 79, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
48 3 0.04
49 75 0.95
50 1 0.01
ACGTcount: A:0.24, C:0.34, G:0.26, T:0.16
Consensus pattern (48 bp):
TCCCCAGGGAGCACGGAACAGTGCTCCCTATGGAGCACCCATCTAGGC
Found at i:6597786 original size:3 final size:3
Alignment explanation
Indices: 6597773--6597814 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
6597763 ATCGCAGCTT
* * *
6597773 TTA TCA TTA TTA TTA TTA TCA TTA TTA TTA CTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
6597815 CCATGAACTC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:6597793 original size:15 final size:15
Alignment explanation
Indices: 6597773--6597814 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
6597763 ATCGCAGCTT
6597773 TTATCATTATTATTA
1 TTATCATTATTATTA
6597788 TTATCATTATTATTA
1 TTATCATTATTATTA
* *
6597803 CTATTATTATTA
1 TTATCATTATTA
6597815 CCATGAACTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (15 bp):
TTATCATTATTATTA
Found at i:6598029 original size:2 final size:2
Alignment explanation
Indices: 6598022--6598059 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
6598012 TTTTTGACTG
6598022 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6598060 GTTATGGTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6600415 original size:44 final size:44
Alignment explanation
Indices: 6600347--6600438 Score: 141
Period size: 44 Copynumber: 2.1 Consensus size: 44
6600337 AGAACTAATT
* *
6600347 CTAAGGCTTTGCTAATGGGTTATAGTAG-TCAACACATGGCCCTG
1 CTAACGCTTTGCTAATGGGTTATAGTAGTTC-ACACATGGCCCTA
*
6600391 CTAACGCTTTGCTAATGGGTTATAGTAGTTCGCACATGGCCCTA
1 CTAACGCTTTGCTAATGGGTTATAGTAGTTCACACATGGCCCTA
6600435 CTAA
1 CTAA
6600439 TGAGTTACAA
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
44 42 0.95
45 2 0.05
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (44 bp):
CTAACGCTTTGCTAATGGGTTATAGTAGTTCACACATGGCCCTA
Found at i:6601717 original size:20 final size:22
Alignment explanation
Indices: 6601662--6601718 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 22
6601652 ATATCTAATC
* *
6601662 TCCAGCAACTCTTCTT-CATTTT
1 TCCAGCAGC-CTTCTTCCAATTT
6601684 TCCAGCAGCC-TCTTCCAATTT
1 TCCAGCAGCCTTCTTCCAATTT
6601705 T-CAGCA-CCTTCTTC
1 TCCAGCAGCCTTCTTC
6601719 ATCTTCCATG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
19 2 0.06
20 14 0.45
21 7 0.23
22 8 0.26
ACGTcount: A:0.18, C:0.37, G:0.07, T:0.39
Consensus pattern (22 bp):
TCCAGCAGCCTTCTTCCAATTT
Found at i:6602970 original size:2 final size:2
Alignment explanation
Indices: 6602965--6603076 Score: 138
Period size: 2 Copynumber: 56.0 Consensus size: 2
6602955 TATCATGTTG
6602965 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
6603007 AT AT GT A- AT AT AT NT AT AT AT AT AT AT AT AT AA AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
6603048 GT AT AT GT AA AT AT AT GAT -T AT AT GAT AT
1 AT AT AT AT AT AT AT AT -AT AT AT AT -AT AT
6603077 GTATTGATAA
Statistics
Matches: 94, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
1 2 0.02
2 88 0.94
3 4 0.04
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.47
Consensus pattern (2 bp):
AT
Found at i:6603247 original size:38 final size:39
Alignment explanation
Indices: 6603183--6603285 Score: 113
Period size: 39 Copynumber: 2.6 Consensus size: 39
6603173 TGATATTGCC
* * **
6603183 TGTGCGCGATGTGGGGGGGACGCACACGATG-GT-ATTTGA
1 TGTGCACGATGT-GGGGGGATGCACACGATGAGTCAACT-A
*
6603222 TGTGCACGATGTGGGGGGATGCACACGATGACTTCAACTA
1 TGTGCACGATGTGGGGGGATGCACACGATGA-GTCAACTA
6603262 TGTGCACGATGT-GGGGGATGCACA
1 TGTGCACGATGTGGGGGGATGCACA
6603286 TGAGCTGGGT
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
38 17 0.30
39 23 0.41
40 14 0.25
41 2 0.04
ACGTcount: A:0.21, C:0.17, G:0.39, T:0.22
Consensus pattern (39 bp):
TGTGCACGATGTGGGGGGATGCACACGATGAGTCAACTA
Found at i:6613944 original size:2 final size:2
Alignment explanation
Indices: 6613937--6613966 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
6613927 ATGCACATAA
6613937 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6613967 CGTATCAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6614779 original size:27 final size:27
Alignment explanation
Indices: 6614729--6614783 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
6614719 TTTACTTCAA
**
6614729 ATGTATCGATACATTGGGACAATGTAT
1 ATGTATCGATACATTAAGACAATGTAT
* *
6614756 ATGTATTGATACATTAAGATAATGTAT
1 ATGTATCGATACATTAAGACAATGTAT
6614783 A
1 A
6614784 GATACATGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.38, C:0.07, G:0.18, T:0.36
Consensus pattern (27 bp):
ATGTATCGATACATTAAGACAATGTAT
Found at i:6618372 original size:20 final size:20
Alignment explanation
Indices: 6618285--6618374 Score: 73
Period size: 20 Copynumber: 4.7 Consensus size: 20
6618275 ATGTTATTAT
* * *
6618285 TATTTTTGTTTTATTATAAT
1 TATTTTTATTTAATTATAAA
6618305 TATTTTTA--TAATTATAAA
1 TATTTTTATTTAATTATAAA
** *
6618323 T-TTTAAATTTAAATAATAAA
1 TATTTTTATTT-AATTATAAA
*
6618343 -A-TTATATTTAATTATAAA
1 TATTTTTATTTAATTATAAA
6618361 TATTTTTATTTAAT
1 TATTTTTATTTAAT
6618375 CGTGTTAAAC
Statistics
Matches: 55, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
17 4 0.07
18 17 0.31
19 9 0.16
20 25 0.45
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (20 bp):
TATTTTTATTTAATTATAAA
Found at i:6624207 original size:28 final size:28
Alignment explanation
Indices: 6624176--6624231 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
6624166 TTAATCATGA
*
6624176 AATTTTTTATTTATTATGAAA-AAATTTT
1 AATTTTTTATTTATT-TAAAACAAATTTT
6624204 AATTTTTTATTTATTTAAAACAAATTTT
1 AATTTTTTATTTATTTAAAACAAATTTT
6624232 TGAGAAGAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 4 0.15
28 22 0.85
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (28 bp):
AATTTTTTATTTATTTAAAACAAATTTT
Found at i:6626973 original size:19 final size:19
Alignment explanation
Indices: 6626928--6626973 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
6626918 AAGAAGAATG
*
6626928 AAATGAAAAATACGCAGCGG
1 AAATG-AAAATACGCAGCGA
*
6626948 AAA-GAAAATACGCAGTGA
1 AAATGAAAATACGCAGCGA
6626966 AAATGAAA
1 AAATGAAA
6626974 GAAGGCTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 15 0.65
19 5 0.22
20 3 0.13
ACGTcount: A:0.57, C:0.11, G:0.22, T:0.11
Consensus pattern (19 bp):
AAATGAAAATACGCAGCGA
Found at i:6627812 original size:291 final size:290
Alignment explanation
Indices: 6627287--6627869 Score: 1042
Period size: 291 Copynumber: 2.0 Consensus size: 290
6627277 ACAAAGGAGG
*
6627287 AAGTTTTTTAACTACACTTTGTGCTAGCAAATAGGACAACAATTGCCCTTTCCTTCTTTTTCACA
1 AAGTTTTTTAACTACACTTTGTGCTAGCAAATAGGACAACAATTACCCTTTCCTTCTTTTTCACA
6627352 ATCTTAGCTGAATCTTTCTCGAAAATTGCTTCATAAGCAAATTTCTCTTTCACACAAAGGGAGTG
66 ATCTTAGCTGAATCTTTCTCGAAAATTGCTTCATAAGCAAATTTCTCTTTCACACAAAGGGAGTG
* *
6627417 GTGGCAAAGAAAAAAAAACGTTTTTCTTTTTCTGACAAAAACTAGGTTTTCTTCAATTGTGAAAA
131 GTGGCAAAGAAAAAAAAACGTTTCTATTTTTCTGACAAAAACTAGGTTTTCTTCAATTGTGAAAA
6627482 ACTCTAATATGAAAAATAATTAAAAGGTGACTTATATAGTTAAGTTAAAATAACTTCAACTTTGC
196 ACTCTAATATGAAAAATAATTAAAAGGTGACTTATATAGTTAAGTTAAAATAACTTCAACTTTGC
6627547 AATTAAGCCCTCAATATTATAAAACATTAT
261 AATTAAGCCCTCAATATTATAAAACATTAT
* *
6627577 ANAGTTTTTTAACTACACTTTGTGCTAGCAAATAGGACAACAATTATCCTTTTCTTCTTTTTCAC
1 A-AGTTTTTTAACTACACTTTGTGCTAGCAAATAGGACAACAATTACCCTTTCCTTCTTTTTCAC
*
6627642 AATCTTAGCTGAATCTTTCTCGAAAATTGCTTCATAAGCAATTTTCTCTTTCACACAAAGGGAGT
65 AATCTTAGCTGAATCTTTCTCGAAAATTGCTTCATAAGCAAATTTCTCTTTCACACAAAGGGAGT
* *
6627707 GGTGGCAAAG-AAAGAAAACGTTTCTATTTTTCTGACAAAAAACTATGTTTTCTTCAATTGTGAA
130 GGTGGCAAAGAAAAAAAAACGTTTCTATTTTTCTGAC-AAAAACTAGGTTTTCTTCAATTGTGAA
* *
6627771 AAACTCTAATATGAAAAATAATTAAAAGGTGACTTATATAGTTAGGTTAAAATAACTTCAATTTT
194 AAACTCTAATATGAAAAATAATTAAAAGGTGACTTATATAGTTAAGTTAAAATAACTTCAACTTT
*
6627836 GCAATTAAGCCCTCAATATTATAACACATTAT
259 GCAATTAAGCCCTCAATATTATAAAACATTAT
6627868 AA
1 AA
6627870 TATTGGACCC
Statistics
Matches: 280, Mismatches: 11, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
290 25 0.09
291 255 0.91
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.35
Consensus pattern (290 bp):
AAGTTTTTTAACTACACTTTGTGCTAGCAAATAGGACAACAATTACCCTTTCCTTCTTTTTCACA
ATCTTAGCTGAATCTTTCTCGAAAATTGCTTCATAAGCAAATTTCTCTTTCACACAAAGGGAGTG
GTGGCAAAGAAAAAAAAACGTTTCTATTTTTCTGACAAAAACTAGGTTTTCTTCAATTGTGAAAA
ACTCTAATATGAAAAATAATTAAAAGGTGACTTATATAGTTAAGTTAAAATAACTTCAACTTTGC
AATTAAGCCCTCAATATTATAAAACATTAT
Found at i:6631709 original size:58 final size:57
Alignment explanation
Indices: 6631620--6631739 Score: 213
Period size: 58 Copynumber: 2.1 Consensus size: 57
6631610 AGGGTCTCAT
*
6631620 CTTTGCATGCATAACATTTATTAAATTGCATAAAATAAATCTATCACATGCATACTA
1 CTTTGCATGCATAACATTTATTAAATTGCATAAAATAAATCTATCACATGCAAACTA
*
6631677 CTTTGCATTGCATAGCATTTATTAAATTGCATAAAATAAATCTATCACATGCAAACTA
1 CTTTGCA-TGCATAACATTTATTAAATTGCATAAAATAAATCTATCACATGCAAACTA
6631735 CTTTG
1 CTTTG
6631740 GATGATTATG
Statistics
Matches: 60, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
57 7 0.12
58 53 0.88
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.36
Consensus pattern (57 bp):
CTTTGCATGCATAACATTTATTAAATTGCATAAAATAAATCTATCACATGCAAACTA
Found at i:6642171 original size:14 final size:15
Alignment explanation
Indices: 6642154--6642184 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
6642144 ACAAATAAAA
6642154 AGATAA-AAAGAGTT
1 AGATAAGAAAGAGTT
6642168 AGATAAGAAAGAGTT
1 AGATAAGAAAGAGTT
6642183 AG
1 AG
6642185 TGAATATACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.55, C:0.00, G:0.26, T:0.19
Consensus pattern (15 bp):
AGATAAGAAAGAGTT
Found at i:6642806 original size:27 final size:26
Alignment explanation
Indices: 6642755--6642808 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 26
6642745 GAAAGAAATT
*
6642755 TCTTCTAGTAATGATTTTTACACTTA
1 TCTTCTAGTAATGATCTTTACACTTA
*
6642781 TCTTGTAGATAATGATCCTTTA-ACTTA
1 TCTTCTAG-TAATGAT-CTTTACACTTA
6642808 T
1 T
6642809 GCTGATAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 7 0.29
27 13 0.54
28 4 0.17
ACGTcount: A:0.28, C:0.15, G:0.09, T:0.48
Consensus pattern (26 bp):
TCTTCTAGTAATGATCTTTACACTTA
Found at i:6643773 original size:39 final size:39
Alignment explanation
Indices: 6643691--6643830 Score: 119
Period size: 39 Copynumber: 3.7 Consensus size: 39
6643681 TCAACTCAAC
* * *
6643691 TCATGTGCACTCCCACACTACACAT-AGC-TA-AT-ATCC
1 TCATGTGCACTACCACACCACACATGA-CATATATCATCA
* * * * *
6643727 TTATGTGCACTATCACACCATACATGCCATATGTCATCA
1 TCATGTGCACTACCACACCACACATGACATATATCATCA
* *
6643766 TCATGTGCTCTCCCACACCACACATGACATATATCATCA
1 TCATGTGCACTACCACACCACACATGACATATATCATCA
* *
6643805 TCATGTGCTCT-CACACACCGCACATG
1 TCATGTGCACTAC-CACACCACACATG
6643831 GCATTTATGC
Statistics
Matches: 83, Mismatches: 16, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
36 21 0.25
37 2 0.02
38 2 0.02
39 58 0.70
ACGTcount: A:0.29, C:0.34, G:0.10, T:0.26
Consensus pattern (39 bp):
TCATGTGCACTACCACACCACACATGACATATATCATCA
Found at i:6644969 original size:4 final size:4
Alignment explanation
Indices: 6644960--6644997 Score: 51
Period size: 4 Copynumber: 9.5 Consensus size: 4
6644950 TTCCTTTTTC
*
6644960 CTTT CTTT CTTT CTTT CCTTT C-TT CTTT CTTC CTTT CT
1 CTTT CTTT CTTT CTTT -CTTT CTTT CTTT CTTT CTTT CT
6644998 CTGTTCTAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
3 3 0.10
4 23 0.77
5 4 0.13
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (4 bp):
CTTT
Found at i:6644987 original size:24 final size:25
Alignment explanation
Indices: 6644944--6644999 Score: 80
Period size: 24 Copynumber: 2.3 Consensus size: 25
6644934 CCTCTGAACT
*
6644944 TTTCTCTTCCTTTTTCCTTTCTTTC
1 TTTCTCTTCCTTTTTCCTTTCTTCC
6644969 TTTCT-TTCCTTTCTT-CTTTCTTCC
1 TTTCTCTTCCTTT-TTCCTTTCTTCC
6644993 TTTCTCT
1 TTTCTCT
6645000 GTTCTAGGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 20 0.71
25 8 0.29
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (25 bp):
TTTCTCTTCCTTTTTCCTTTCTTCC
Found at i:6645004 original size:15 final size:15
Alignment explanation
Indices: 6644948--6644997 Score: 66
Period size: 15 Copynumber: 3.2 Consensus size: 15
6644938 TGAACTTTTC
6644948 TCTTCCTTT-TTCCTT
1 TCTT-CTTTCTTCCTT
6644963 TCTTTCTTTCTTTCCTT
1 TC-TTCTTTC-TTCCTT
6644980 TCTTCTTTCTTCCTT
1 TCTTCTTTCTTCCTT
6644995 TCT
1 TCT
6644998 CTGTTCTAGG
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
15 15 0.47
16 9 0.28
17 8 0.25
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (15 bp):
TCTTCTTTCTTCCTT
Found at i:6648435 original size:17 final size:17
Alignment explanation
Indices: 6648410--6648442 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
6648400 GTATTCTTCA
6648410 AATTGGGGTTTTTTTTT
1 AATTGGGGTTTTTTTTT
*
6648427 AATTTGGGTTTTTTTT
1 AATTGGGGTTTTTTTT
6648443 CATATTTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.12, C:0.00, G:0.21, T:0.67
Consensus pattern (17 bp):
AATTGGGGTTTTTTTTT
Found at i:6648449 original size:18 final size:17
Alignment explanation
Indices: 6648410--6648449 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
6648400 GTATTCTTCA
* *
6648410 AATTGGGGTTTTTTTTT
1 AATTTGGGTTTTTTTTC
6648427 AATTTGGGTTTTTTTTC
1 AATTTGGGTTTTTTTTC
6648444 ATATTT
1 A-ATTT
6648450 ATATTTTTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.15, C:0.03, G:0.17, T:0.65
Consensus pattern (17 bp):
AATTTGGGTTTTTTTTC
Found at i:6655109 original size:8 final size:8
Alignment explanation
Indices: 6655096--6655120 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
6655086 ACCATTTAAC
6655096 ATCAATGA
1 ATCAATGA
6655104 ATCAATGA
1 ATCAATGA
6655112 ATCAATGA
1 ATCAATGA
6655120 A
1 A
6655121 ATAAAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.12, G:0.12, T:0.24
Consensus pattern (8 bp):
ATCAATGA
Found at i:6657859 original size:65 final size:64
Alignment explanation
Indices: 6657755--6657883 Score: 249
Period size: 65 Copynumber: 2.0 Consensus size: 64
6657745 ATTTTTTTGA
6657755 AAAAAAAAATGAGCTGGCCCAACCCAGCCCATGGGCTAACAAGTAGTGCGCTGAGTTAGGGATT
1 AAAAAAAAATGAGCTGGCCCAACCCAGCCCATGGGCTAACAAGTAGTGCGCTGAGTTAGGGATT
6657819 NAAAAAAAAATGAGCTGGCCCAACCCAGCCCATGGGCTAACAAGTAGTGCGCTGAGTTAGGGATT
1 -AAAAAAAAATGAGCTGGCCCAACCCAGCCCATGGGCTAACAAGTAGTGCGCTGAGTTAGGGATT
6657884 TCACAGCCCA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 64 1.00
ACGTcount: A:0.34, C:0.22, G:0.26, T:0.17
Consensus pattern (64 bp):
AAAAAAAAATGAGCTGGCCCAACCCAGCCCATGGGCTAACAAGTAGTGCGCTGAGTTAGGGATT
Found at i:6663354 original size:15 final size:15
Alignment explanation
Indices: 6663334--6663362 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
6663324 GATTTCTACC
6663334 TTTCCTATGCCTTTA
1 TTTCCTATGCCTTTA
6663349 TTTCCTATGCCTTT
1 TTTCCTATGCCTTT
6663363 GTTTTCATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.28, G:0.07, T:0.55
Consensus pattern (15 bp):
TTTCCTATGCCTTTA
Found at i:6681674 original size:18 final size:19
Alignment explanation
Indices: 6681636--6681674 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
6681626 CTATCTATGG
*
6681636 TATTTTAATTGCTGTTTGA
1 TATTTTAACTGCTGTTTGA
6681655 TATTTTAACTGCTG-TTGA
1 TATTTTAACTGCTGTTTGA
6681673 TA
1 TA
6681675 AAAATCTGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.23, C:0.08, G:0.15, T:0.54
Consensus pattern (19 bp):
TATTTTAACTGCTGTTTGA
Found at i:6681952 original size:2 final size:2
Alignment explanation
Indices: 6681905--6681939 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
6681895 ATGCCTGCAC
*
6681905 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6681940 CTTTGAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:6682492 original size:62 final size:62
Alignment explanation
Indices: 6682395--6682531 Score: 247
Period size: 62 Copynumber: 2.2 Consensus size: 62
6682385 AAGGAATGAG
*
6682395 TTAGTCGACTAAGTGCACACTGCCAGAACTGCCAGAAACTGGAAACAGAAGATAGAGACGAC
1 TTAGTCGACTAAGTGCACACTGCCAGAACTGCCAGAAACTGGAAACAGAAGATAGAAACGAC
* *
6682457 TTAGTCGACTAAGTGCATACTGCCAGAACTGCCAGAAACTGGAAACAGAAGATAGAAATGAC
1 TTAGTCGACTAAGTGCACACTGCCAGAACTGCCAGAAACTGGAAACAGAAGATAGAAACGAC
6682519 TTAGTCGACTAAG
1 TTAGTCGACTAAG
6682532 ATATCAGTTA
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
62 72 1.00
ACGTcount: A:0.39, C:0.20, G:0.23, T:0.18
Consensus pattern (62 bp):
TTAGTCGACTAAGTGCACACTGCCAGAACTGCCAGAAACTGGAAACAGAAGATAGAAACGAC
Found at i:6683339 original size:16 final size:16
Alignment explanation
Indices: 6683316--6683354 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
6683306 AAATTACTAG
6683316 TTTAAATTATGAA-AT
1 TTTAAATTATGAATAT
*
6683331 TTATAAATTATTAATAT
1 TT-TAAATTATGAATAT
6683348 TTTAAAT
1 TTTAAAT
6683355 GAATTATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 2 0.10
16 15 0.71
17 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (16 bp):
TTTAAATTATGAATAT
Found at i:6683390 original size:36 final size:34
Alignment explanation
Indices: 6683345--6683450 Score: 112
Period size: 36 Copynumber: 3.1 Consensus size: 34
6683335 AAATTATTAA
* *
6683345 TATTTTAAATGAATTATAAAATATTATTAATAATT
1 TATTATAAATG-ATTATAAAATATTATTAATAAAT
* *
6683380 TCATTATAAATGATTAAAAAATTATTATTCATAAAT
1 T-ATTATAAATGATTATAAAA-TATTATTAATAAAT
*
6683416 TATTA-AAAT-ATT-T-AAATTTTATTAATAAAT
1 TATTATAAATGATTATAAAATATTATTAATAAAT
6683446 TATTA
1 TATTA
6683451 ATGTTTTAAT
Statistics
Matches: 62, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
30 17 0.27
31 3 0.05
33 3 0.05
34 4 0.06
35 13 0.21
36 22 0.35
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (34 bp):
TATTATAAATGATTATAAAATATTATTAATAAAT
Found at i:6683427 original size:22 final size:22
Alignment explanation
Indices: 6683367--6683427 Score: 54
Period size: 25 Copynumber: 2.6 Consensus size: 22
6683357 ATTATAAAAT
6683367 ATTATTAATAAT-TTCATTATAA
1 ATTATTAA-AATATTCATTATAA
*
6683389 ATGATTAAAAAATTATT-ATTCATAA
1 ATTATT--AAAA-TATTCATT-ATAA
6683414 ATTATTAAAATATT
1 ATTATTAAAATATT
6683428 TAAATTTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
22 9 0.28
23 6 0.19
24 6 0.19
25 11 0.34
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (22 bp):
ATTATTAAAATATTCATTATAA
Found at i:6683448 original size:11 final size:11
Alignment explanation
Indices: 6683333--6683452 Score: 55
Period size: 11 Copynumber: 11.2 Consensus size: 11
6683323 TATGAAATTT
6683333 ATAAATTATTA
1 ATAAATTATTA
6683344 AT--ATT-TTAA
1 ATAAATTATT-A
*
6683353 ATGAATTA-TA
1 ATAAATTATTA
6683363 A-AATATTATTA
1 ATAA-ATTATTA
*
6683374 ATAATTTCATT-
1 ATAAATT-ATTA
*
6683385 ATAAATGATTA
1 ATAAATTATTA
*
6683396 AAAAATTATTA
1 ATAAATTATTA
6683407 TTCATAAATTATT-
1 ---ATAAATTATTA
6683420 A-AAA-TATT-
1 ATAAATTATTA
6683428 -TAAATTTTATTA
1 ATAAA--TTATTA
6683440 ATAAATTATTA
1 ATAAATTATTA
6683451 AT
1 AT
6683453 GTTTTAATTA
Statistics
Matches: 84, Mismatches: 7, Indels: 36
0.66 0.06 0.28
Matches are distributed among these distances:
8 9 0.11
9 10 0.12
10 10 0.12
11 37 0.44
12 5 0.06
13 4 0.05
14 9 0.11
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (11 bp):
ATAAATTATTA
Found at i:6683473 original size:23 final size:23
Alignment explanation
Indices: 6683432--6683481 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 23
6683422 AATATTTAAA
6683432 TTTT-ATTAATAAATTATTA-AT
1 TTTTAATTAATAAATTATTATAT
6683453 GTTTTAATTAA-AAATTAATTATAT
1 -TTTTAATTAATAAATT-ATTATAT
6683477 TTTTA
1 TTTTA
6683482 GATAAATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 9 0.36
23 14 0.56
24 2 0.08
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (23 bp):
TTTTAATTAATAAATTATTATAT
Found at i:6683479 original size:22 final size:22
Alignment explanation
Indices: 6683333--6683491 Score: 68
Period size: 22 Copynumber: 7.4 Consensus size: 22
6683323 TATGAAATTT
6683333 ATAAATTATTAATATTTTA--A
1 ATAAATTATTAATATTTTATTA
* * *
6683353 ATGAATTA-TAAAATATTATTA
1 ATAAATTATTAATATTTTATTA
* ** *
6683374 ATAATTTCATT-ATAAATGATTA
1 ATAAATT-ATTAATATTTTATTA
* * **
6683396 AAAAATTATTATTCA-TAAATTA
1 ATAAATTATTAAT-ATTTTATTA
* *
6683418 TTAAAATATTTAA-ATTTTATTA
1 ATAAATTA-TTAATATTTTATTA
*
6683440 ATAAATTATTAATGTTTTAATTA
1 ATAAATTATTAATATTTT-ATTA
6683463 A-AAATTAATT-ATA-TTT-TTA
1 ATAAATT-ATTAATATTTTATTA
6683482 GATAAATTAT
1 -ATAAATTAT
6683492 AAAAAAATTA
Statistics
Matches: 102, Mismatches: 24, Indels: 26
0.67 0.16 0.17
Matches are distributed among these distances:
19 11 0.11
20 10 0.10
21 22 0.22
22 46 0.45
23 13 0.13
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (22 bp):
ATAAATTATTAATATTTTATTA
Found at i:6683537 original size:24 final size:24
Alignment explanation
Indices: 6683510--6683562 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
6683500 TAATGTTTGT
6683510 ATTAT-AAAGAAAAAATTATTAAAA
1 ATTATGAAA-AAAAAATTATTAAAA
* **
6683534 ATTATGTAAAAATTATTATTAAAA
1 ATTATGAAAAAAAAATTATTAAAA
6683558 ATTAT
1 ATTAT
6683563 TTATATTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 23 0.92
25 2 0.08
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (24 bp):
ATTATGAAAAAAAAATTATTAAAA
Found at i:6683563 original size:10 final size:10
Alignment explanation
Indices: 6683520--6683551 Score: 55
Period size: 10 Copynumber: 3.1 Consensus size: 10
6683510 ATTATAAAGA
6683520 AAAAATTATT
1 AAAAATTATT
6683530 AAAAATTATGT
1 AAAAATTAT-T
6683541 AAAAATTATT
1 AAAAATTATT
6683551 A
1 A
6683552 TTAAAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 11 0.52
11 10 0.48
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (10 bp):
AAAAATTATT
Found at i:6683566 original size:14 final size:14
Alignment explanation
Indices: 6683534--6683563 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
6683524 ATTATTAAAA
6683534 ATTATGTAAAAATT
1 ATTATGTAAAAATT
6683548 ATTAT-TAAAAATT
1 ATTATGTAAAAATT
6683561 ATT
1 ATT
6683564 TATATTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (14 bp):
ATTATGTAAAAATT
Found at i:6683581 original size:22 final size:22
Alignment explanation
Indices: 6683551--6683600 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
6683541 AAAAATTATT
* *
6683551 ATTAAAAATTATTTATATTTTA
1 ATTATAAATTATTAATATTTTA
6683573 ATTATAAATTATTAATATTTTA
1 ATTATAAATTATTAATATTTTA
*
6683595 AATATA
1 ATTATA
6683601 TTTTAAAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
ATTATAAATTATTAATATTTTA
Found at i:6686518 original size:2 final size:2
Alignment explanation
Indices: 6686511--6686559 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
6686501 AACATATCAT
6686511 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6686553 TA TA TA T
1 TA TA TA T
6686560 TTGTGCATAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6700971 original size:29 final size:29
Alignment explanation
Indices: 6700939--6701000 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
6700929 CGCACTTGTT
* *
6700939 GTTAAACCCCATGCCTACCTATATTGTCA
1 GTTAAACACCATGCCTACATATATTGTCA
* * *
6700968 GTTACACACTATGCCTATATATATTGTCA
1 GTTAAACACCATGCCTACATATATTGTCA
6700997 GTTA
1 GTTA
6701001 CATGCCATGC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.35
Consensus pattern (29 bp):
GTTAAACACCATGCCTACATATATTGTCA
Found at i:6701010 original size:29 final size:29
Alignment explanation
Indices: 6700947--6701011 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
6700937 TTGTTAAACC
*
6700947 CCATGCCTACCTATATTGTCAGTTACACA
1 CCATGCCTACATATATTGTCAGTTACACA
* * **
6700976 CTATGCCTATATATATTGTCAGTTACATG
1 CCATGCCTACATATATTGTCAGTTACACA
6701005 CCATGCC
1 CCATGCC
6701012 GGTACTAAGT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.26, C:0.28, G:0.12, T:0.34
Consensus pattern (29 bp):
CCATGCCTACATATATTGTCAGTTACACA
Found at i:6704004 original size:80 final size:80
Alignment explanation
Indices: 6703916--6704162 Score: 329
Period size: 80 Copynumber: 3.1 Consensus size: 80
6703906 ATAACATTTC
* * **
6703916 CATAAATCA-TCATCATACTTAGCCCATGGTGTATATGACTATCTCAGCACATACATCTCATGAC
1 CATAAATCACTTA-CATGCTTAGCCCATAATGTATATGACTATCTCAGCACATACATCTCATGAC
6703980 ATACATTTTATAACCT
65 ATACATTTTATAACCT
*
6703996 CATAAATCACTTACATGCTTAGCCCATAATGTATATGACTATCTCAGCACATACATCTCATGGCA
1 CATAAATCACTTACATGCTTAGCCCATAATGTATATGACTATCTCAGCACATACATCTCATGACA
*
6704061 TACATTTCATAACCT
66 TACATTTTATAACCT
* * * * *
6704076 CATAAATCACTTACATGCTTAGCCCATAATGTACATGA-TATACTTAACACATATATCGCATGGA
1 CATAAATCACTTACATGCTTAGCCCATAATGTATATGACTAT-CTCAGCACATACATCTCAT-GA
* *
6704140 -ATACATGTTATAATCT
64 CATACATTTTATAACCT
6704156 CATAAAT
1 CATAAAT
6704163 GGAACTCTTG
Statistics
Matches: 149, Mismatches: 15, Indels: 6
0.88 0.09 0.04
Matches are distributed among these distances:
79 3 0.02
80 143 0.96
81 3 0.02
ACGTcount: A:0.36, C:0.23, G:0.09, T:0.32
Consensus pattern (80 bp):
CATAAATCACTTACATGCTTAGCCCATAATGTATATGACTATCTCAGCACATACATCTCATGACA
TACATTTTATAACCT
Found at i:6706257 original size:14 final size:16
Alignment explanation
Indices: 6706236--6706276 Score: 54
Period size: 14 Copynumber: 2.8 Consensus size: 16
6706226 ATCTCACAAA
6706236 AAAGATCTCTCAAT-G
1 AAAGATCTCTCAATAG
6706251 AAA-ATCTCT--ATAG
1 AAAGATCTCTCAATAG
6706264 AAAGATCTCTCAA
1 AAAGATCTCTCAA
6706277 CATAACTTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
12 2 0.09
13 4 0.18
14 12 0.55
15 3 0.14
16 1 0.05
ACGTcount: A:0.44, C:0.20, G:0.10, T:0.27
Consensus pattern (16 bp):
AAAGATCTCTCAATAG
Found at i:6706545 original size:31 final size:31
Alignment explanation
Indices: 6706507--6706612 Score: 108
Period size: 31 Copynumber: 3.5 Consensus size: 31
6706497 GTGGGCATGT
6706507 AACAATTGCCTACTAAAGG-ATGGCATGTAGC
1 AACAATTGCCTACT-AAGGCATGGCATGTAGC
* *
6706538 AACAATTGCCTACTAAGGCATGGCGTGTAGT
1 AACAATTGCCTACTAAGGCATGGCATGTAGC
* * ** * *
6706569 AATAATTGCCTAAT-ACCCATGGCAGGTAAC
1 AACAATTGCCTACTAAGGCATGGCATGTAGC
*
6706599 AACAAATGCCTACT
1 AACAATTGCCTACT
6706613 GTTAGTGTAA
Statistics
Matches: 61, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
30 25 0.41
31 36 0.59
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.24
Consensus pattern (31 bp):
AACAATTGCCTACTAAGGCATGGCATGTAGC
Found at i:6707556 original size:6 final size:6
Alignment explanation
Indices: 6707545--6707569 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
6707535 GCTCATGATC
6707545 TATAAA TATAAA TATAAA TATAAA T
1 TATAAA TATAAA TATAAA TATAAA T
6707570 TCTTAGTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (6 bp):
TATAAA
Found at i:6708327 original size:31 final size:31
Alignment explanation
Indices: 6708292--6708426 Score: 149
Period size: 31 Copynumber: 4.5 Consensus size: 31
6708282 CACAGTAGAT
*
6708292 AGGCATGGTGTGTAGCAACAATTGCTTACTA
1 AGGCATGGTGTGTAGCAACAATTGCCTACTA
6708323 AGGCATGGTGTGTAGCAACAATTGCCTAC-A
1 AGGCATGGTGTGTAGCAACAATTGCCTACTA
* *
6708353 AGGCATGGTGTGTAACAACACATT--ATA-T-
1 AGGCATGGTGTGTAGCAACA-ATTGCCTACTA
* *
6708381 AGGCAT--CGTGTAGCAATAATTGCCTACTA
1 AGGCATGGTGTGTAGCAACAATTGCCTACTA
**
6708410 AGGCATGGCATGTAGCA
1 AGGCATGGTGTGTAGCA
6708427 CCAACTTTTC
Statistics
Matches: 88, Mismatches: 8, Indels: 16
0.79 0.07 0.14
Matches are distributed among these distances:
25 3 0.03
26 9 0.10
27 2 0.02
28 7 0.08
29 8 0.09
30 20 0.23
31 39 0.44
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (31 bp):
AGGCATGGTGTGTAGCAACAATTGCCTACTA
Found at i:6708424 original size:87 final size:89
Alignment explanation
Indices: 6708274--6708458 Score: 230
Period size: 87 Copynumber: 2.1 Consensus size: 89
6708264 ACCCATGGCA
* * **
6708274 TGTAACAACACAGTAGATAGGCATGGTGTGTAGCAACAATTGCTTACTAAGGCATGGTGTGTAGC
1 TGTAACAACACAGTAGATAGGCAT-GCGTGTAGCAACAATTGCCTACTAAGGCATGGCATGTAGC
*
6708339 AACAA-TTGCCTACAAGGCATGGTG
65 AACAACTTGCCTACAAGGAATGGTG
* * *
6708363 TGTAACAACACATTATATAGGCAT-CGTGTAGCAATAATTGCCTACTAAGGCATGGCATGTAGCA
1 TGTAACAACACAGTAGATAGGCATGCGTGTAGCAACAATTGCCTACTAAGGCATGGCATGTAGCA
* ** **
6708427 CCAACTTTTCTTTAAGGAATGGTG
66 ACAACTTGCCTACAAGGAATGGTG
6708451 TGTAACAA
1 TGTAACAA
6708459 TTATTCTTTT
Statistics
Matches: 82, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
87 38 0.46
88 22 0.27
89 22 0.27
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.27
Consensus pattern (89 bp):
TGTAACAACACAGTAGATAGGCATGCGTGTAGCAACAATTGCCTACTAAGGCATGGCATGTAGCA
ACAACTTGCCTACAAGGAATGGTG
Found at i:6713432 original size:26 final size:25
Alignment explanation
Indices: 6713403--6713452 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
6713393 AATCAATTTA
* *
6713403 TCAAAAACTTGCTACATGCCATGTTC
1 TCAAAAAC-TCCTACACGCCATGTTC
*
6713429 TCAAAATCTCCTACACGCCATGTT
1 TCAAAAACTCCTACACGCCATGTT
6713453 GAAAAAAAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.30, C:0.30, G:0.10, T:0.30
Consensus pattern (25 bp):
TCAAAAACTCCTACACGCCATGTTC
Found at i:6713861 original size:25 final size:25
Alignment explanation
Indices: 6713814--6713888 Score: 69
Period size: 25 Copynumber: 2.9 Consensus size: 25
6713804 TATCTACGAG
** *
6713814 TTGTTACACACCATGTTCTAAAATT
1 TTGTTACACACCATGTTGAAAAATA
* *
6713839 TTTTTACACTCCATGTTGAAAAAAATA
1 TTGTTACACACCATGTTG--AAAAATA
**
6713866 TTGTTACAGGCCATGTTGAAAAA
1 TTGTTACACACCATGTTGAAAAA
6713889 AAAAAGTTAT
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
25 20 0.50
27 20 0.50
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (25 bp):
TTGTTACACACCATGTTGAAAAATA
Found at i:6713901 original size:29 final size:28
Alignment explanation
Indices: 6713842--6713919 Score: 86
Period size: 29 Copynumber: 2.8 Consensus size: 28
6713832 TAAAATTTTT
* * *
6713842 TTACACTCCATGTTG-AAAAAAATATTG
1 TTACACACCATGTTGAAAAAAAAAATTA
**
6713869 TTACAGGCCATGTTGAAAAAAAAAAGTTA
1 TTACACACCATGTTGAAAAAAAAAA-TTA
*
6713898 TTACACACCATGTTCAAAAAAA
1 TTACACACCATGTTGAAAAAAA
6713920 TTTTGCTACA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
27 13 0.31
28 8 0.19
29 21 0.50
ACGTcount: A:0.46, C:0.15, G:0.12, T:0.27
Consensus pattern (28 bp):
TTACACACCATGTTGAAAAAAAAAATTA
Found at i:6713999 original size:27 final size:27
Alignment explanation
Indices: 6713818--6714013 Score: 123
Period size: 27 Copynumber: 7.3 Consensus size: 27
6713808 TACGAGTTGT
* **
6713818 TACACACCATGTTC--TAAAATTTTTT
1 TACACACCATGTTCAAAAAAATTTTAC
* * * **
6713843 TACACTCCATGTTGAAAAAAATATTGT
1 TACACACCATGTTCAAAAAAATTTTAC
** * ** *
6713870 TACAGGCCATGTTGAAAAAAAAAAGTTAT
1 TACACACCATGTT--CAAAAAAATTTTAC
*
6713899 TACACACCATGTTCAAAAAAATTTTGC
1 TACACACCATGTTCAAAAAAATTTTAC
* * *
6713926 TACACGCTATGTTC--AAAAATTTTTC
1 TACACACCATGTTCAAAAAAATTTTAC
*
6713951 TACACACCATGTAT-AAACAAATTTTAC
1 TACACACCATGT-TCAAAAAAATTTTAC
* * *
6713978 TGCACACCATGTTCAAAAAAATATTAA
1 TACACACCATGTTCAAAAAAATTTTAC
*
6714005 GACACACCA
1 TACACACCA
6714014 CGTACAAATA
Statistics
Matches: 132, Mismatches: 31, Indels: 14
0.75 0.18 0.08
Matches are distributed among these distances:
25 32 0.24
26 2 0.02
27 77 0.58
29 21 0.16
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.31
Consensus pattern (27 bp):
TACACACCATGTTCAAAAAAATTTTAC
Found at i:6717316 original size:144 final size:143
Alignment explanation
Indices: 6717053--6717330 Score: 382
Period size: 144 Copynumber: 1.9 Consensus size: 143
6717043 GAGAAATTGG
* * * ** *
6717053 GAGCATCTAATTGTCTAAAAGGGTTTTAAAGGCTATTTTGTCAAGTCATGGTAAATTTTGAGTAA
1 GAGCATCTAATTGTCTAAAAGAGTTTCAAAGGCTATTTAGTCAAGTCATGACAAATTTTAAGTAA
* * *
6717118 AAATAGTTAACTTTATATTCAAGGCTATTTTTGAAATGGGCTTATAAGGGTGGCTATTTCTCACA
66 AAAGAGTTAACTTTATATTCAAGGCTATTTTTGAAATAGACTTATAAGGGTGGCTA-TTCTCACA
6717183 ATTTGCTCAATCAT
130 ATTTGCTCAATCAT
*
6717197 GAGCATCTAATTTGTCTAAAAGAGTTTCAAGGGGC-ATTTAGTCAAGTCATGACAAA-TTTAAGT
1 GAGCATCTAA-TTGTCTAAAAGAGTTTCAA-AGGCTATTTAGTCAAGTCATGACAAATTTTAAGT
* * *
6717260 AAAAACGA-TTAACTTTATATTCAAGGCTATTTTTGAAATAGACTTATGAGGTTGGCTATTCTTA
64 AAAAA-GAGTTAACTTTATATTCAAGGCTATTTTTGAAATAGACTTATAAGGGTGGCTATTCTCA
6717324 CAATTTG
128 CAATTTG
6717331 GTCATGCAAA
Statistics
Matches: 118, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
143 12 0.10
144 67 0.57
145 36 0.31
146 3 0.03
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (143 bp):
GAGCATCTAATTGTCTAAAAGAGTTTCAAAGGCTATTTAGTCAAGTCATGACAAATTTTAAGTAA
AAAGAGTTAACTTTATATTCAAGGCTATTTTTGAAATAGACTTATAAGGGTGGCTATTCTCACAA
TTTGCTCAATCAT
Found at i:6722392 original size:30 final size:30
Alignment explanation
Indices: 6722323--6722388 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
6722313 ATTATTAGTC
* * *
6722323 ATAAAGGCTTATTTGGCTCAAAAGATAAGT
1 ATAATGGCTTATTTGACTCAAAAGATAAAT
6722353 ATAATGGCTTATTTGACTC-AAA-ATAAAT
1 ATAATGGCTTATTTGACTCAAAAGATAAAT
6722381 ATATATGG
1 ATA-ATGG
6722389 GCTTGATTGA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 8 0.25
29 7 0.22
30 17 0.53
ACGTcount: A:0.41, C:0.09, G:0.17, T:0.33
Consensus pattern (30 bp):
ATAATGGCTTATTTGACTCAAAAGATAAAT
Done.