Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr1
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: 96304692
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2448173 characters in sequence are not A, C, G, or T
File 126 of 313
Found at i:40659941 original size:23 final size:23
Alignment explanation
Indices: 40659915--40659962 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
40659905 CTTCAATCAC
40659915 AACTCATGTTTAACTCAAGCATT
1 AACTCATGTTTAACTCAAGCATT
40659938 AACTCATGTTTAACTCAAGCATT
1 AACTCATGTTTAACTCAAGCATT
40659961 AA
1 AA
40659963 TATGTTGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.38, C:0.21, G:0.08, T:0.33
Consensus pattern (23 bp):
AACTCATGTTTAACTCAAGCATT
Found at i:40667146 original size:15 final size:16
Alignment explanation
Indices: 40667126--40667155 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40667116 ATACTTGTAC
40667126 TGAAAA-TTTTAAATA
1 TGAAAACTTTTAAATA
40667141 TGAAAACTTTTAAAT
1 TGAAAACTTTTAAAT
40667156 TTTTAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.40
Consensus pattern (16 bp):
TGAAAACTTTTAAATA
Found at i:40669941 original size:11 final size:11
Alignment explanation
Indices: 40669925--40669996 Score: 53
Period size: 11 Copynumber: 6.8 Consensus size: 11
40669915 TATTTTTTAA
40669925 TTTTAAAATAC
1 TTTTAAAATAC
40669936 TTTTAAAATAC
1 TTTTAAAATAC
* *
40669947 TTTTTTAAAT-T
1 -TTTTAAAATAC
*
40669958 TTTTTAAAT--
1 TTTTAAAATAC
**
40669967 TTTT-AAATTT
1 TTTTAAAATAC
40669977 TTTTAAAATAC
1 TTTTAAAATAC
*
40669988 TTTTTAAAT
1 TTTTAAAAT
40669997 TTTTTTTAAT
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
8 4 0.08
9 4 0.08
10 13 0.25
11 23 0.44
12 8 0.15
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:40669963 original size:40 final size:40
Alignment explanation
Indices: 40669917--40670020 Score: 163
Period size: 40 Copynumber: 2.6 Consensus size: 40
40669907 TTTATTTTTA
40669917 TTTTTTAATTTTAAAATACTTTTAAAATACTTTTTTAAATT
1 TTTTTTAATTTTAAAATACTTTTAAAATAC-TTTTTAAATT
* * **
40669958 TTTTTAAATTTTTAAATTTTTTTAAAATACTTTTTAAATT
1 TTTTTTAATTTTAAAATACTTTTAAAATACTTTTTAAATT
40669998 TTTTTTAATTTTAAAATACTTTT
1 TTTTTTAATTTTAAAATACTTTT
40670021 TTAATTTTTT
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
40 29 0.53
41 26 0.47
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.62
Consensus pattern (40 bp):
TTTTTTAATTTTAAAATACTTTTAAAATACTTTTTAAATT
Found at i:40669994 original size:30 final size:30
Alignment explanation
Indices: 40669957--40670038 Score: 98
Period size: 30 Copynumber: 2.7 Consensus size: 30
40669947 TTTTTTAAAT
40669957 TTTTTTAAATTTTTAAATTTTTTTAAAATAC
1 TTTTTTAAATTTTT-AATTTTTTTAAAATAC
40669988 -TTTTTAAATTTTT--TTTAATTTTAAAATAC
1 TTTTTTAAATTTTTAATTT--TTTTAAAATAC
*
40670017 TTTTTTAATTTTTTTAATTTTT
1 TTTTTTAA-ATTTTTAATTTTT
40670039 AAAACAAATT
Statistics
Matches: 44, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
27 3 0.07
29 11 0.25
30 20 0.45
31 7 0.16
33 3 0.07
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (30 bp):
TTTTTTAAATTTTTAATTTTTTTAAAATAC
Found at i:40670009 original size:29 final size:29
Alignment explanation
Indices: 40669958--40670042 Score: 111
Period size: 29 Copynumber: 2.9 Consensus size: 29
40669948 TTTTTAAATT
*
40669958 TTTTTAAA-TTTTTAAATTTTTTTAAAATAC
1 TTTTTAAATTTTTTTAA--TTTTTAAAATAC
40669988 TTTTTAAATTTTTTTTAA-TTTTAAAATAC
1 TTTTTAAA-TTTTTTTAATTTTTAAAATAC
*
40670017 TTTTTTAATTTTTTTAATTTTTAAAA
1 TTTTTAAATTTTTTTAATTTTTAAAA
40670043 CAAATTGTTG
Statistics
Matches: 50, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
28 9 0.18
29 26 0.52
30 8 0.16
32 7 0.14
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (29 bp):
TTTTTAAATTTTTTTAATTTTTAAAATAC
Found at i:40670021 original size:41 final size:42
Alignment explanation
Indices: 40669917--40670021 Score: 162
Period size: 41 Copynumber: 2.6 Consensus size: 42
40669907 TTTATTTTTA
40669917 TTTTTTAATTTTAAAATAC-TTTTAAAATACTTTTTTAAATT
1 TTTTTTAATTTTAAAATACTTTTTAAAATACTTTTTTAAATT
* * *
40669958 TTTTTAAATTTTTAAAT-TTTTTTAAAATAC-TTTTTAAATT
1 TTTTTTAATTTTAAAATACTTTTTAAAATACTTTTTTAAATT
40669998 TTTTTTAATTTTAAAATACTTTTT
1 TTTTTTAATTTTAAAATACTTTTT
40670022 TAATTTTTTT
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
40 25 0.45
41 31 0.55
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (42 bp):
TTTTTTAATTTTAAAATACTTTTTAAAATACTTTTTTAAATT
Found at i:40674224 original size:39 final size:37
Alignment explanation
Indices: 40674157--40674249 Score: 98
Period size: 39 Copynumber: 2.5 Consensus size: 37
40674147 ACCAGAATGG
* *
40674157 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAGTTGA
1 CACCCAGTGCCTCATCGGAAAGTCCGAAG-AA-AGTTGA
* *
40674196 CACCCAGTGTCTCATCGGCAAAG-CCGAAGAAAGTTGG
1 CACCCAGTGCCTCATCGG-AAAGTCCGAAGAAAGTTGA
* *
40674233 TACCCAGTACCTCATCG
1 CACCCAGTGCCTCATCG
40674250 AATCTATCCG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
37 19 0.41
38 2 0.04
39 22 0.48
40 3 0.07
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (37 bp):
CACCCAGTGCCTCATCGGAAAGTCCGAAGAAAGTTGA
Found at i:40675314 original size:11 final size:11
Alignment explanation
Indices: 40675300--40675325 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
40675290 CTTTTTCTTC
40675300 TTTCTCCCCTG
1 TTTCTCCCCTG
40675311 TTTCTCCCCTG
1 TTTCTCCCCTG
40675322 TTTC
1 TTTC
40675326 GTCTCTTCTA
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:0.00, C:0.42, G:0.08, T:0.50
Consensus pattern (11 bp):
TTTCTCCCCTG
Found at i:40675707 original size:21 final size:21
Alignment explanation
Indices: 40675683--40675725 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
40675673 AATAATAACT
40675683 AATAACTAATAATAAATAATA
1 AATAACTAATAATAAATAATA
* * * *
40675704 AATATCTTATACTAATTAATA
1 AATAACTAATAATAAATAATA
40675725 A
1 A
40675726 GCAAATTAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.35
Consensus pattern (21 bp):
AATAACTAATAATAAATAATA
Found at i:40680796 original size:21 final size:21
Alignment explanation
Indices: 40680754--40680796 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
40680744 TTCAGTATAC
*
40680754 ATTCTTTCATCAGTATCATTT
1 ATTCTTTCATCAGCATCATTT
*
40680775 ATTCTTTCTTCAGACATC-TTT
1 ATTCTTTCATCAG-CATCATTT
40680796 A
1 A
40680797 ATCTATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.23, C:0.21, G:0.05, T:0.51
Consensus pattern (21 bp):
ATTCTTTCATCAGCATCATTT
Found at i:40690655 original size:17 final size:16
Alignment explanation
Indices: 40690623--40690656 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
40690613 TTGGCTATTC
*
40690623 TGTTTCTTTCTTCTTT
1 TGTTTCTTTATTCTTT
40690639 TGTTTCTTTTATTCTTT
1 TGTTTC-TTTATTCTTT
40690656 T
1 T
40690657 ATTTTAACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.03, C:0.15, G:0.06, T:0.76
Consensus pattern (16 bp):
TGTTTCTTTATTCTTT
Found at i:40690704 original size:14 final size:14
Alignment explanation
Indices: 40690645--40690695 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
40690635 CTTTTGTTTC
*
40690645 TTTTA-TTCTTTTA
1 TTTTATTTCCTTTA
* *
40690658 TTTTAACTTACTTTA
1 TTTT-ATTTCCTTTA
*
40690673 CTTTATTTCCTTTA
1 TTTTATTTCCTTTA
40690687 TTTTATTTC
1 TTTTATTTC
40690696 TTTTGTTTTC
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
13 4 0.13
14 17 0.57
15 9 0.30
ACGTcount: A:0.18, C:0.14, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTATTTCCTTTA
Found at i:40690864 original size:14 final size:17
Alignment explanation
Indices: 40690845--40690881 Score: 53
Period size: 14 Copynumber: 2.4 Consensus size: 17
40690835 ATTTATTTCT
40690845 TAATATAA-T-ATTT-A
1 TAATATAATTAATTTAA
40690859 TAATATAATTAATTTAA
1 TAATATAATTAATTTAA
40690876 TAATAT
1 TAATAT
40690882 CCTTTATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 8 0.40
15 1 0.05
16 4 0.20
17 7 0.35
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TAATATAATTAATTTAA
Found at i:40694131 original size:30 final size:30
Alignment explanation
Indices: 40694096--40694152 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
40694086 AAATATTATT
* *
40694096 TTATTAATTTAAATCTTTATAATTTTTAAA
1 TTATTAAATCAAATCTTTATAATTTTTAAA
* *
40694126 TTATTAAATCAAATTTTTATCATTTTT
1 TTATTAAATCAAATCTTTATAATTTTT
40694153 GGGAATCAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (30 bp):
TTATTAAATCAAATCTTTATAATTTTTAAA
Found at i:40696389 original size:17 final size:16
Alignment explanation
Indices: 40696366--40696411 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
40696356 AACATTTAAA
40696366 TAAAAATAAATAAAAT
1 TAAAAATAAATAAAAT
*
40696382 TAGTAAAT--ATAAAAT
1 TA-AAAATAAATAAAAT
40696397 TAAAAATAATATAAA
1 TAAAAATAA-ATAAA
40696412 TATTTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 7
0.73 0.06 0.21
Matches are distributed among these distances:
14 4 0.17
15 9 0.38
16 2 0.08
17 9 0.38
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (16 bp):
TAAAAATAAATAAAAT
Found at i:40700662 original size:93 final size:93
Alignment explanation
Indices: 40700552--40700729 Score: 225
Period size: 93 Copynumber: 1.9 Consensus size: 93
40700542 AATTCCCAAC
* * * * *
40700552 TTTCGAGTTTTGATTCATTTTATTATTTCAGGTTCAACT-CTCAACTTGATGATTAATGAGAA-A
1 TTTCGAATTTTGATTCATTTTATCATCTCAGGTTCAAATCCT-AACTTGATAATTAATGA-AAGA
** *
40700615 ATGTTTAGTTATTGTACTTTTCAAATGACA
64 ATGACTAGTTATTATACTTTTCAAATGACA
* * *
40700645 TTTCGAATTTTGATTCATTTTATCATCTCAGTTTCAAATCCTGACTTGATAATTAATTAAAGAAT
1 TTTCGAATTTTGATTCATTTTATCATCTCAGGTTCAAATCCTAACTTGATAATTAATGAAAGAAT
40700710 GACTAGTTATTATACTTTTC
66 GACTAGTTATTATACTTTTC
40700730 GTGTAACACC
Statistics
Matches: 72, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
92 2 0.03
93 68 0.94
94 2 0.03
ACGTcount: A:0.30, C:0.13, G:0.12, T:0.46
Consensus pattern (93 bp):
TTTCGAATTTTGATTCATTTTATCATCTCAGGTTCAAATCCTAACTTGATAATTAATGAAAGAAT
GACTAGTTATTATACTTTTCAAATGACA
Found at i:40701100 original size:12 final size:12
Alignment explanation
Indices: 40701083--40701107 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40701073 CCAAAAATAA
40701083 TTAATGGAAACT
1 TTAATGGAAACT
40701095 TTAATGGAAACT
1 TTAATGGAAACT
40701107 T
1 T
40701108 AAAAAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (12 bp):
TTAATGGAAACT
Found at i:40712003 original size:20 final size:22
Alignment explanation
Indices: 40711959--40712008 Score: 72
Period size: 20 Copynumber: 2.5 Consensus size: 22
40711949 TATAAAAAAG
40711959 GATTTT-TT-AAAAAATTGATT
1 GATTTTCTTAAAAAAATTGATT
40711979 GATTTTCTTAAAAAAATTGA-T
1 GATTTTCTTAAAAAAATTGATT
40712000 -ATTTTCTTA
1 GATTTTCTTA
40712009 TGTTTGAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 15 0.54
21 3 0.11
22 10 0.36
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (22 bp):
GATTTTCTTAAAAAAATTGATT
Found at i:40712071 original size:14 final size:14
Alignment explanation
Indices: 40712052--40712093 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 14
40712042 TGTTTGACAA
40712052 ATTTTTCTAAAATT
1 ATTTTTCTAAAATT
40712066 ATTTTT-TAAAAATT
1 ATTTTTCT-AAAATT
40712080 ATTCTTTCTAAAAT
1 ATT-TTTCTAAAAT
40712094 AAACATAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 1 0.04
14 15 0.60
15 8 0.32
16 1 0.04
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (14 bp):
ATTTTTCTAAAATT
Found at i:40712259 original size:23 final size:23
Alignment explanation
Indices: 40712228--40712295 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
40712218 TATTTAAACC
* *
40712228 AATACTTATATTTATGTAAT-TAA
1 AATATTTATATTT-TATAATATAA
*
40712251 AATATTTATATTTTATACTATAA
1 AATATTTATATTTTATAATATAA
**
40712274 AATATTTATAAATTATAATATA
1 AATATTTATATTTTATAATATA
40712296 GATAGATTAT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
22 4 0.11
23 34 0.89
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (23 bp):
AATATTTATATTTTATAATATAA
Found at i:40712562 original size:33 final size:34
Alignment explanation
Indices: 40712501--40712565 Score: 89
Period size: 33 Copynumber: 1.9 Consensus size: 34
40712491 GTTTAATATT
*
40712501 ATTGAATATTATAATATTACATATTAATATTAAA
1 ATTGAATATTATAATATTACATAATAATATTAAA
*
40712535 ATTGAATATT-TACTATTA-ATTAATAATATTA
1 ATTGAATATTATAATATTACA-TAATAATATTA
40712566 TGTTTTCTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 1 0.04
33 17 0.61
34 10 0.36
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (34 bp):
ATTGAATATTATAATATTACATAATAATATTAAA
Found at i:40719660 original size:11 final size:11
Alignment explanation
Indices: 40719646--40719670 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
40719636 ATAATAACAA
40719646 CAATATAATAG
1 CAATATAATAG
40719657 CAATATAATAG
1 CAATATAATAG
40719668 CAA
1 CAA
40719671 AATGATAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.12, G:0.08, T:0.24
Consensus pattern (11 bp):
CAATATAATAG
Found at i:40726165 original size:24 final size:23
Alignment explanation
Indices: 40726125--40726169 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
40726115 ACGGTTATAT
40726125 TTATTTTTAATGAATTTATAAAA
1 TTATTTTTAATGAATTTATAAAA
**
40726148 TTATTTATTAATTTATTTATAA
1 TTATTT-TTAATGAATTTATAA
40726170 TGTGTCTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (23 bp):
TTATTTTTAATGAATTTATAAAA
Found at i:40733566 original size:23 final size:23
Alignment explanation
Indices: 40733523--40733567 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
40733513 AATTAAAATT
**
40733523 ATAACATAATATTTATTATTATA
1 ATAACATAATATTTAAAATTATA
*
40733546 ATAACTTAATATTTAAAATTAT
1 ATAACATAATATTTAAAATTAT
40733568 TATCTAATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (23 bp):
ATAACATAATATTTAAAATTATA
Found at i:40740546 original size:19 final size:19
Alignment explanation
Indices: 40740522--40740558 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
40740512 CAACTTTCAC
40740522 AAAATACATAAATTAAATT
1 AAAATACATAAATTAAATT
40740541 AAAATACATAAATTAAAT
1 AAAATACATAAATTAAAT
40740559 CTACAACTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (19 bp):
AAAATACATAAATTAAATT
Found at i:40745445 original size:29 final size:30
Alignment explanation
Indices: 40745412--40745471 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
40745402 TATTAATTAT
40745412 TAATTTTAATGAA-TTTTAAAATATTTTTA
1 TAATTTTAATGAATTTTTAAAATATTTTTA
** * *
40745441 TAATTTTTCTGAATTTTTATAATTTTTTTA
1 TAATTTTAATGAATTTTTAAAATATTTTTA
40745471 T
1 T
40745472 GGGAAAATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 11 0.42
30 15 0.58
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (30 bp):
TAATTTTAATGAATTTTTAAAATATTTTTA
Found at i:40745448 original size:9 final size:9
Alignment explanation
Indices: 40745342--40745467 Score: 55
Period size: 9 Copynumber: 13.8 Consensus size: 9
40745332 AATCTTATAA
40745342 AATTTTTAT
1 AATTTTTAT
*
40745351 AATTTATTGAA
1 AATTT-TT-AT
*
40745362 AATTATTA-
1 AATTTTTAT
*
40745370 GATTTATTAT
1 AATTT-TTAT
40745380 -A-TTTTAT
1 AATTTTTAT
*
40745387 AATATTTAT
1 AATTTTTAT
**
40745396 AAGGTTTATT
1 AATTTTTA-T
*
40745406 AA-TTAT-T
1 AATTTTTAT
*
40745413 AATTTTAAT
1 AATTTTTAT
* *
40745422 GAATTTTAAA
1 -AATTTTTAT
40745432 ATATTTTTAT
1 A-ATTTTTAT
*
40745442 AATTTTTCT
1 AATTTTTAT
40745451 GAATTTTTAT
1 -AATTTTTAT
40745461 AATTTTT
1 AATTTTT
40745468 TTATGGGAAA
Statistics
Matches: 89, Mismatches: 16, Indels: 24
0.69 0.12 0.19
Matches are distributed among these distances:
7 7 0.08
8 8 0.09
9 39 0.44
10 30 0.34
11 5 0.06
ACGTcount: A:0.37, C:0.01, G:0.05, T:0.58
Consensus pattern (9 bp):
AATTTTTAT
Found at i:40746315 original size:22 final size:23
Alignment explanation
Indices: 40746290--40746343 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 23
40746280 TAAAAAAACT
*
40746290 AAAAAAAATACATAAATAT-TAA
1 AAAAAAAATACAAAAATATATAA
* **
40746312 AAAATAAATTTAAAAATATATAA
1 AAAAAAAATACAAAAATATATAA
40746335 AAATAAAAA
1 AAA-AAAAA
40746344 ATATTGTTGA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
22 15 0.60
23 6 0.24
24 4 0.16
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (23 bp):
AAAAAAAATACAAAAATATATAA
Found at i:40746426 original size:57 final size:59
Alignment explanation
Indices: 40746317--40746441 Score: 164
Period size: 59 Copynumber: 2.1 Consensus size: 59
40746307 ATTAAAAAAT
* *
40746317 AAATTTAAAAATATATAAAAATAAAAAATATTGTTGACAAGAAATAATAATAATATATA
1 AAATTTAAAAATATATAAAAATAAAAAATATTGTTCACAAAAAATAATAATAATATATA
* * * *
40746376 AAATTTAAAAATATATAAATAA-GAAAAATATTTTTCAAAAAAATATAATAATAA-ATTTA
1 AAATTTAAAAATATATAAA-AATAAAAAATATTGTTCACAAAAA-ATAATAATAATATATA
40746435 AAATTTA
1 AAATTTA
40746442 TATTATATTA
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
59 46 0.79
60 12 0.21
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (59 bp):
AAATTTAAAAATATATAAAAATAAAAAATATTGTTCACAAAAAATAATAATAATATATA
Found at i:40746459 original size:6 final size:6
Alignment explanation
Indices: 40746448--40746476 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
40746438 TTTATATTAT
40746448 ATTAAC ATTAAC ATTAAC ATTAAC ATTAA
1 ATTAAC ATTAAC ATTAAC ATTAAC ATTAA
40746477 ATAAATATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (6 bp):
ATTAAC
Found at i:40750753 original size:18 final size:17
Alignment explanation
Indices: 40750722--40750756 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
40750712 AAGGATGGTT
40750722 AGATGATGAGCCTGAGG
1 AGATGATGAGCCTGAGG
*
40750739 AGATAGATGATCCTGAGG
1 AGAT-GATGAGCCTGAGG
40750757 CAACCAAGCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.31, C:0.11, G:0.37, T:0.20
Consensus pattern (17 bp):
AGATGATGAGCCTGAGG
Found at i:40755306 original size:31 final size:31
Alignment explanation
Indices: 40755266--40755324 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
40755256 CAAGCTCTAA
* * *
40755266 TGTGAGAATAGTTGTCTAGTTCAAGACCCAG
1 TGTGAGAATAATTATCAAGTTCAAGACCCAG
*
40755297 TGTGGGAATAATTATCAAGTTCAAGACC
1 TGTGAGAATAATTATCAAGTTCAAGACC
40755325 TAACTTGAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (31 bp):
TGTGAGAATAATTATCAAGTTCAAGACCCAG
Found at i:40763156 original size:12 final size:12
Alignment explanation
Indices: 40763139--40763164 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
40763129 AAATATATTT
40763139 TTTATAATAAAA
1 TTTATAATAAAA
40763151 TTTATAATAAAA
1 TTTATAATAAAA
40763163 TT
1 TT
40763165 GACATTTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
TTTATAATAAAA
Found at i:40765531 original size:13 final size:13
Alignment explanation
Indices: 40765515--40765539 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40765505 TAAATATATA
40765515 TTTTTTATTTTTC
1 TTTTTTATTTTTC
40765528 TTTTTTATTTTT
1 TTTTTTATTTTT
40765540 AAAATACTTT
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:0.08, C:0.04, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTATTTTTC
Found at i:40765581 original size:19 final size:19
Alignment explanation
Indices: 40765547--40765583 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
40765537 TTTAAAATAC
**
40765547 TTTTAAAATATTTTTTTAT
1 TTTTAAAATAAATTTTTAT
40765566 TTTTAAAATAAATTTTTA
1 TTTTAAAATAAATTTTTA
40765584 ATGTTTATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTAAAATAAATTTTTAT
Found at i:40765590 original size:20 final size:19
Alignment explanation
Indices: 40765548--40765590 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
40765538 TTAAAATACT
* * *
40765548 TTTAAAATATTTTTTTATT
1 TTTAAAATAATTTTTAATG
40765567 TTTAAAATAAATTTTTAATG
1 TTTAAAAT-AATTTTTAATG
40765587 TTTA
1 TTTA
40765591 TTAAAAAATG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
TTTAAAATAATTTTTAATG
Found at i:40771267 original size:29 final size:30
Alignment explanation
Indices: 40771235--40771294 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 30
40771225 TTTAGAATTT
*
40771235 AGAATTT-AATTTTTATATTTTTAT-TTTTA
1 AGAATTTAAAATTTTA-ATTTTTATATTTTA
*
40771264 AGAATTTAAAATTTTACTTTTTATATTTTA
1 AGAATTTAAAATTTTAATTTTTATATTTTA
40771294 A
1 A
40771295 AGTTCAGGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 14 0.52
30 13 0.48
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.60
Consensus pattern (30 bp):
AGAATTTAAAATTTTAATTTTTATATTTTA
Found at i:40772643 original size:29 final size:30
Alignment explanation
Indices: 40772584--40772641 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
40772574 TCCGAGCCTT
*
40772584 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
40772614 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
40772642 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:40772800 original size:27 final size:27
Alignment explanation
Indices: 40772762--40772813 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
40772752 ACTATCGTGA
*
40772762 AAGGGGTTGCTAAGTGCTGATTCCCTC
1 AAGGGGTAGCTAAGTGCTGATTCCCTC
*
40772789 AAGGGGTAGCTAAGTGTTGATTCCC
1 AAGGGGTAGCTAAGTGCTGATTCCC
40772814 CGACTCTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.21, C:0.19, G:0.31, T:0.29
Consensus pattern (27 bp):
AAGGGGTAGCTAAGTGCTGATTCCCTC
Found at i:40774209 original size:9 final size:9
Alignment explanation
Indices: 40774197--40774226 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
40774187 TTGAGGAATA
*
40774197 GGAGGGGGT
1 GGAGGAGGT
40774206 GGAGGAGGT
1 GGAGGAGGT
40774215 GGAGGAGGT
1 GGAGGAGGT
40774224 GGA
1 GGA
40774227 ACATTCAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.70, T:0.10
Consensus pattern (9 bp):
GGAGGAGGT
Found at i:40775791 original size:33 final size:34
Alignment explanation
Indices: 40775745--40775879 Score: 116
Period size: 33 Copynumber: 3.7 Consensus size: 34
40775735 ATAACCGTTA
*
40775745 TCGGTGGATTCAGCACTTAGCAACCACCAGTGAT
1 TCGGTGGAATCAGCACTTAGCAACCACCAGTGAT
40775779 TCGG-GGAATCAGCACTTAGCAACCCCTTTTTACATTCAAG-GAT
1 TCGGTGGAATCAGCACTTAGCAA--CC-----AC---C-AGTGAT
*
40775822 AT-GGTGGAATCATCACTTAGCAACCACCAGTGAT
1 -TCGGTGGAATCAGCACTTAGCAACCACCAGTGAT
40775856 TCGG-GGAATCAGCACTTAGCAACC
1 TCGGTGGAATCAGCACTTAGCAACC
40775880 CCTTTCACAT
Statistics
Matches: 83, Mismatches: 3, Indels: 31
0.71 0.03 0.26
Matches are distributed among these distances:
33 39 0.47
34 10 0.12
35 2 0.02
37 2 0.02
40 2 0.02
42 2 0.02
43 6 0.07
44 20 0.24
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (34 bp):
TCGGTGGAATCAGCACTTAGCAACCACCAGTGAT
Found at i:40775874 original size:77 final size:77
Alignment explanation
Indices: 40775747--40775959 Score: 347
Period size: 76 Copynumber: 2.8 Consensus size: 77
40775737 AACCGTTATC
* * *
40775747 GGTGGATTCAGCACTTAGCAACCACCAGTGATTCGGGGAATCAGCACTTAGCAACCCCTTTTTAC
1 GGTGGAATCAACACTTAGCAACCACCAGTGATTCGGGGAATCAGCACTTAGCAACCCCTTTTCAC
40775812 ATTCAAGGATAT
66 ATTCAAGGATAT
*
40775824 GGTGGAATCATCACTTAGCAACCACCAGTGATTCGGGGAATCAGCACTTAGCAACCCC-TTTCAC
1 GGTGGAATCAACACTTAGCAACCACCAGTGATTCGGGGAATCAGCACTTAGCAACCCCTTTTCAC
40775888 ATTCAAGGATAT
66 ATTCAAGGATAT
** * *
40775900 GGTGGAATCAACACTTAGCAACCACCAAAGAGTCGGGGAATCAGCACTTAGCTACCCCTT
1 GGTGGAATCAACACTTAGCAACCACCAGTGATTCGGGGAATCAGCACTTAGCAACCCCTT
40775960 GAGGGAATCA
Statistics
Matches: 127, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
76 70 0.55
77 57 0.45
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (77 bp):
GGTGGAATCAACACTTAGCAACCACCAGTGATTCGGGGAATCAGCACTTAGCAACCCCTTTTCAC
ATTCAAGGATAT
Found at i:40775948 original size:33 final size:32
Alignment explanation
Indices: 40775903--40776058 Score: 97
Period size: 33 Copynumber: 4.6 Consensus size: 32
40775893 AGGATATGGT
*
40775903 GGAATCAACACTTAGCAACCACCAAAGAGTCGG
1 GGAATCAGCACTTAGCAACCACCAAAGA-TCGG
* **
40775936 GGAATCAGCACTTAGCTACC-CC-TTGA---G
1 GGAATCAGCACTTAGCAACCACCAAAGATCGG
* *
40775963 GGAATCAGCACTTAGCAGCCCCTTTCACATTCAAAGATATGG
1 GGAATCAGCACTTAGCA---AC---CAC---CAAAGAT-CGG
*
40776005 TGGAATCAGCACTTAGCAACCACCAAAAAGTCGG
1 -GGAATCAGCACTTAGCAACCACCAAAGA-TCGG
40776039 GGAATCAGCACTTAGCAACC
1 GGAATCAGCACTTAGCAACC
40776059 CCTTGTTATT
Statistics
Matches: 95, Mismatches: 11, Indels: 34
0.68 0.08 0.24
Matches are distributed among these distances:
27 17 0.18
30 1 0.01
31 2 0.02
32 2 0.02
33 39 0.41
34 8 0.08
35 1 0.01
37 4 0.04
38 2 0.02
40 1 0.01
42 1 0.01
43 17 0.18
ACGTcount: A:0.34, C:0.28, G:0.21, T:0.18
Consensus pattern (32 bp):
GGAATCAGCACTTAGCAACCACCAAAGATCGG
Found at i:40775965 original size:27 final size:27
Alignment explanation
Indices: 40775935--40775986 Score: 88
Period size: 27 Copynumber: 1.9 Consensus size: 27
40775925 CAAAGAGTCG
40775935 GGGAATCAGCACTTAGCTA-CCCCTTGA
1 GGGAATCAGCACTTAGC-AGCCCCTTGA
40775962 GGGAATCAGCACTTAGCAGCCCCTT
1 GGGAATCAGCACTTAGCAGCCCCTT
40775987 TCACATTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 1 0.04
27 23 0.96
ACGTcount: A:0.25, C:0.31, G:0.23, T:0.21
Consensus pattern (27 bp):
GGGAATCAGCACTTAGCAGCCCCTTGA
Found at i:40775977 original size:103 final size:103
Alignment explanation
Indices: 40775859--40776063 Score: 365
Period size: 103 Copynumber: 2.0 Consensus size: 103
40775849 CAGTGATTCG
*
40775859 GGGAATCAGCACTTAGCAACCCCTTTCACATTCAAGGATATGGTGGAATCAACACTTAGCAACCA
1 GGGAATCAGCACTTAGCAACCCCTTTCACATTCAAAGATATGGTGGAATCAACACTTAGCAACCA
* *
40775924 CCAAAGAGTCGGGGAATCAGCACTTAGCTACCCCTTGA
66 CCAAAAAGTCGGGGAATCAGCACTTAGCAACCCCTTGA
* *
40775962 GGGAATCAGCACTTAGCAGCCCCTTTCACATTCAAAGATATGGTGGAATCAGCACTTAGCAACCA
1 GGGAATCAGCACTTAGCAACCCCTTTCACATTCAAAGATATGGTGGAATCAACACTTAGCAACCA
40776027 CCAAAAAGTCGGGGAATCAGCACTTAGCAACCCCTTG
66 CCAAAAAGTCGGGGAATCAGCACTTAGCAACCCCTTG
40776064 TTATTCAATA
Statistics
Matches: 97, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 97 1.00
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.20
Consensus pattern (103 bp):
GGGAATCAGCACTTAGCAACCCCTTTCACATTCAAAGATATGGTGGAATCAACACTTAGCAACCA
CCAAAAAGTCGGGGAATCAGCACTTAGCAACCCCTTGA
Found at i:40778299 original size:20 final size:20
Alignment explanation
Indices: 40778263--40778301 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
40778253 GGATGATAGG
*
40778263 ACATTTTTGTATAATTAAAC
1 ACATTTTTGTACAATTAAAC
40778283 ACATTTTT-TACACATTAAA
1 ACATTTTTGTACA-ATTAAA
40778302 AGAATTGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.41, C:0.13, G:0.03, T:0.44
Consensus pattern (20 bp):
ACATTTTTGTACAATTAAAC
Found at i:40779299 original size:21 final size:19
Alignment explanation
Indices: 40779261--40779323 Score: 67
Period size: 18 Copynumber: 3.2 Consensus size: 19
40779251 TTCGAAATGA
40779261 ATTAAAATAATATAAAATATTAT
1 ATTAAAA-AA-AT-AAATATT-T
40779284 ATTAATAAAAATAAATATTT
1 ATTAA-AAAAATAAATATTT
40779304 -TTAAAAAAAT-AATATTT
1 ATTAAAAAAATAAATATTT
40779321 ATT
1 ATT
40779324 TTTATCAAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
17 7 0.18
18 8 0.21
19 4 0.11
20 1 0.03
21 7 0.18
22 2 0.05
23 7 0.18
24 2 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTAAAAAAATAAATATTT
Found at i:40779313 original size:18 final size:20
Alignment explanation
Indices: 40779275--40779323 Score: 68
Period size: 18 Copynumber: 2.5 Consensus size: 20
40779265 AAATAATATA
40779275 AAATATTATATTAATAAAAAT
1 AAATATT-TATTAATAAAAAT
40779296 AAATATTT-TTAA-AAAAAT
1 AAATATTTATTAATAAAAAT
40779314 -AATATTTATT
1 AAATATTTATT
40779324 TTTATCAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 7 0.26
18 8 0.30
19 4 0.15
20 1 0.04
21 7 0.26
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
AAATATTTATTAATAAAAAT
Found at i:40784973 original size:23 final size:24
Alignment explanation
Indices: 40784947--40785009 Score: 69
Period size: 23 Copynumber: 2.7 Consensus size: 24
40784937 TATTTATATT
40784947 ATTTTTA-ATTTAATATTTAATAA
1 ATTTTTATATTTAATATTTAATAA
* *
40784970 ATTTATATATTCT--TATTTATTAA
1 ATTTTTATATT-TAATATTTAATAA
*
40784993 ATTTTTATATATAATAT
1 ATTTTTATATTTAATAT
40785010 GCCGTCTATA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
22 1 0.03
23 24 0.75
24 6 0.19
25 1 0.03
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.59
Consensus pattern (24 bp):
ATTTTTATATTTAATATTTAATAA
Found at i:40785036 original size:17 final size:17
Alignment explanation
Indices: 40785016--40785076 Score: 63
Period size: 17 Copynumber: 3.7 Consensus size: 17
40785006 ATATGCCGTC
* *
40785016 TATATATATATATTTTG
1 TATATATATAAATTTTA
*
40785033 TATATATTTAAATTTTA
1 TATATATATAAATTTTA
* *
40785050 TATA-CTATAAATTATA
1 TATATATATAAATTTTA
40785066 TA-ATATATAAA
1 TATATATATAAA
40785077 AATAACATAA
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
15 1 0.03
16 17 0.47
17 18 0.50
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (17 bp):
TATATATATAAATTTTA
Found at i:40795946 original size:31 final size:31
Alignment explanation
Indices: 40795904--40795975 Score: 108
Period size: 31 Copynumber: 2.3 Consensus size: 31
40795894 TAGATGTTAA
* **
40795904 AAATTTAACTCTTTTTTAAAAATTGATGATC
1 AAATTTAACTCTTTTTAAAAAATAAATGATC
*
40795935 AAATTTGACTCTTTTTAAAAAATAAATGATC
1 AAATTTAACTCTTTTTAAAAAATAAATGATC
40795966 AAATTTAACT
1 AAATTTAACT
40795976 AAAAAATTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.43, C:0.10, G:0.06, T:0.42
Consensus pattern (31 bp):
AAATTTAACTCTTTTTAAAAAATAAATGATC
Found at i:40803608 original size:152 final size:152
Alignment explanation
Indices: 40803332--40803641 Score: 611
Period size: 152 Copynumber: 2.0 Consensus size: 152
40803322 TTTAGGAAAC
40803332 CCCATTGTTACAAGTCGATCAGATCGGAACATCAGCTTGTCTGATACAGCATCCATCTTCTAGTT
1 CCCATTGTTACAAGTCGATCAGATCGGAACATCAGCTTGTCTGATACAGCATCCATCTTCTAGTT
40803397 GCTTATTCCTAGTACTGTACAATTCCCCGAATCTAATCCGAAATCCGGGAATTCATGTAATTAGG
66 GCTTATTCCTAGTACTGTACAATTCCCCGAATCTAATCCGAAATCCGGGAATTCATGTAATTAGG
40803462 TTTCGAGTTTCAATATCTGCAA
131 TTTCGAGTTTCAATATCTGCAA
40803484 CCCATTGTTACAAGTCGATCAGATCGGAACATCAGCTTGTCTGATACAGCATCCATCTTCTAGTT
1 CCCATTGTTACAAGTCGATCAGATCGGAACATCAGCTTGTCTGATACAGCATCCATCTTCTAGTT
40803549 GCTTATTCCTAGTACTGTACAATTCCCCGAATCTAATCCGAAATCCGGGAATTCATGTAATTAGG
66 GCTTATTCCTAGTACTGTACAATTCCCCGAATCTAATCCGAAATCCGGGAATTCATGTAATTAGG
40803614 TTTCGAGTTTCAATATCTGCAA
131 TTTCGAGTTTCAATATCTGCAA
*
40803636 CTCATT
1 CCCATT
40803642 TCTCTATTCT
Statistics
Matches: 157, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
152 157 1.00
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (152 bp):
CCCATTGTTACAAGTCGATCAGATCGGAACATCAGCTTGTCTGATACAGCATCCATCTTCTAGTT
GCTTATTCCTAGTACTGTACAATTCCCCGAATCTAATCCGAAATCCGGGAATTCATGTAATTAGG
TTTCGAGTTTCAATATCTGCAA
Found at i:40803832 original size:7 final size:7
Alignment explanation
Indices: 40803820--40803846 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
40803810 TTAAATATTT
40803820 ATAAATA
1 ATAAATA
40803827 ATAAATA
1 ATAAATA
40803834 ATAAATA
1 ATAAATA
40803841 ATAAAT
1 ATAAAT
40803847 GTGCATTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (7 bp):
ATAAATA
Found at i:40804907 original size:21 final size:20
Alignment explanation
Indices: 40804883--40804922 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
40804873 GAATTTTTAT
*
40804883 AATTTATAATATTTCTTAAAA
1 AATTTAAAAT-TTTCTTAAAA
*
40804904 AATTTAAAATTTTTTTAAA
1 AATTTAAAATTTTCTTAAA
40804923 TTTATTTCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (20 bp):
AATTTAAAATTTTCTTAAAA
Found at i:40805644 original size:24 final size:24
Alignment explanation
Indices: 40805599--40805645 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
40805589 AACAACCACA
* *
40805599 GCAAGAACAACTACAACTACAACT
1 GCAAGAACAACAACAACGACAACT
* *
40805623 GCAAGAACAAGAAGAACGACAAC
1 GCAAGAACAACAACAACGACAAC
40805646 CCCATTTATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.53, C:0.26, G:0.15, T:0.06
Consensus pattern (24 bp):
GCAAGAACAACAACAACGACAACT
Found at i:40817059 original size:23 final size:23
Alignment explanation
Indices: 40817031--40817078 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
40817021 CTAAATTTAT
40817031 ATAGTACTGTACTGCCTAACAAA
1 ATAGTACTGTACTGCCTAACAAA
40817054 ATAGTACTGTACTGCCTAACAAA
1 ATAGTACTGTACTGCCTAACAAA
40817077 AT
1 AT
40817079 TCCATTCAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.27
Consensus pattern (23 bp):
ATAGTACTGTACTGCCTAACAAA
Found at i:40819446 original size:189 final size:193
Alignment explanation
Indices: 40819110--40819689 Score: 672
Period size: 201 Copynumber: 2.9 Consensus size: 193
40819100 CAACACCGAT
* ** *
40819110 ACAAACAACTAAAGATGCTTATACAAGATGTTACCATTAGCATCTTTCGGTCGTCTTCCCCGAAT
1 ACAAACAACTAAAGATGCTTATACAAGATGTTACCATTA--A---TGCAATC-T-TT-CCCGGAT
* * * *
40819175 T-AAAAACTTGCTTTAAAACGATGTAAGATAGATCACCGGAGAAATTTCTTTTCC-TACAAATAA
58 TAAAAAACTTGCTTTAAAACGATGTATGATCGATCACCGGAGAAATTTCTTTTCCTTTC-ACTAA
* * * ** ** *
40819238 ATCGGAGTTTTCAAGCAACTACTATAAAACTTTATAACATGAGTTTTCGATCCGGAATTGTAT-A
122 ATCAGAGTTTTCGAGCAACTAATATACGACTTTATAACACAAGTTTTCGATCCGGATTTGTATCA
*
40819302 TAGCTAT
187 TAGCTAA
*
40819309 AC-AATAACTAAAGATGCTTATACAAGATGTTACCATT-A-GC-ATCTTTCCCGGATTAAAAAAC
1 ACAAACAACTAAAGATGCTTATACAAGATGTTACCATTAATGCAATCTTTCCCGGATTAAAAAA-
* * **
40819370 CTTGATTTAAAACGATGCATGATCGATCAGTGGAGAAATTTCTTTTCCTTTCACTAAATCAGAGT
65 CTTGCTTTAAAACGATGTATGATCGATCACCGGAGAAATTTCTTTTCCTTTCACTAAATCAGAGT
40819435 TTTCGAGCAACTAATATACGACTTTATAACACAAGTTTTCGATCCGGATTTGT-TCATAGCTAA
130 TTTCGAGCAACTAATATACGACTTTATAACACAAGTTTTCGATCCGGATTTGTATCATAGCTAA
* *
40819498 ACAAACAACTAAAGATGCTTATATAAGATGTTACCATTAACATCTTTCAATCGTCTTCCCCGGAT
1 ACAAACAACTAAAGATGCTTATACAAGATGTTACCATT-A-A---TGCAATC-T-TT-CCCGGAT
* * *
40819563 TAAGAAAACTAGCTTCAAAACGATGTATGATCGATCACCAGAGAAATTTCTTTTCCTTTCACTAA
58 TAA-AAAACTTGCTTTAAAACGATGTATGATCGATCACCGGAGAAATTTCTTTTCCTTTCACTAA
* *
40819628 ATCAGAGTTTTCGAGCAACTAATATACGACTTTATAGCCCAAGTTTTCGATCCGGATTTGTA
122 ATCAGAGTTTTCGAGCAACTAATATACGACTTTATAACACAAGTTTTCGATCCGGATTTGTA
40819690 AATTAGCATC
Statistics
Matches: 330, Mismatches: 33, Indels: 33
0.83 0.08 0.08
Matches are distributed among these distances:
187 7 0.02
188 8 0.02
189 109 0.33
190 37 0.11
191 1 0.00
193 1 0.00
195 1 0.00
197 1 0.00
198 37 0.11
199 3 0.01
200 2 0.01
201 119 0.36
202 4 0.01
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.32
Consensus pattern (193 bp):
ACAAACAACTAAAGATGCTTATACAAGATGTTACCATTAATGCAATCTTTCCCGGATTAAAAAAC
TTGCTTTAAAACGATGTATGATCGATCACCGGAGAAATTTCTTTTCCTTTCACTAAATCAGAGTT
TTCGAGCAACTAATATACGACTTTATAACACAAGTTTTCGATCCGGATTTGTATCATAGCTAA
Found at i:40821154 original size:9 final size:9
Alignment explanation
Indices: 40821135--40821165 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
40821125 TATTGAACAG
40821135 ATTTT-AAT
1 ATTTTAAAT
40821143 ATTTTAAAT
1 ATTTTAAAT
40821152 ATTTTAAAT
1 ATTTTAAAT
40821161 ATTTT
1 ATTTT
40821166 TTTTTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 5 0.23
9 17 0.77
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (9 bp):
ATTTTAAAT
Found at i:40822798 original size:29 final size:29
Alignment explanation
Indices: 40822766--40822821 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
40822756 AAAACCTTTT
40822766 TTTTTCAA-AATTTACCGAAATGAGCCACA
1 TTTTT-AATAATTTACCGAAATGAGCCACA
* * *
40822795 TTTTTAATTATTTACCGGAATGGGCCA
1 TTTTTAATAATTTACCGAAATGAGCCA
40822822 TTTCCGTGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 2 0.09
29 21 0.91
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (29 bp):
TTTTTAATAATTTACCGAAATGAGCCACA
Found at i:40823789 original size:30 final size:29
Alignment explanation
Indices: 40823729--40823790 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 29
40823719 GATTTCGCGG
*
40823729 AAAATGGCCCATTCCGGTAAATAATCAAA
1 AAAATGGCCCATTCCGGTAAATAATAAAA
* **
40823758 AAAATCGGCCCATTTCGGTAAATTTTAAAA
1 AAAAT-GGCCCATTCCGGTAAATAATAAAA
40823788 AAA
1 AAA
40823791 GGGCTTTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 5 0.18
30 23 0.82
ACGTcount: A:0.45, C:0.18, G:0.13, T:0.24
Consensus pattern (29 bp):
AAAATGGCCCATTCCGGTAAATAATAAAA
Found at i:40831829 original size:17 final size:17
Alignment explanation
Indices: 40831804--40831844 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
40831794 ATTGTGTGTG
*
40831804 TGAATTGTTATGTCTAA
1 TGAACTGTTATGTCTAA
*
40831821 TGAACTGTTATTTCTAA
1 TGAACTGTTATGTCTAA
*
40831838 TAAACTG
1 TGAACTG
40831845 ATTTGGTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.32, C:0.10, G:0.15, T:0.44
Consensus pattern (17 bp):
TGAACTGTTATGTCTAA
Found at i:40837086 original size:12 final size:12
Alignment explanation
Indices: 40837069--40837093 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40837059 GCTGTTTGTG
40837069 TTGTTAAATTCA
1 TTGTTAAATTCA
40837081 TTGTTAAATTCA
1 TTGTTAAATTCA
40837093 T
1 T
40837094 CAAAGGAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.52
Consensus pattern (12 bp):
TTGTTAAATTCA
Found at i:40842243 original size:11 final size:11
Alignment explanation
Indices: 40842209--40842245 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
40842199 TTGACAGTAT
40842209 AAATAATTAAA
1 AAATAATTAAA
*
40842220 AAATTA-T-AA
1 AAATAATTAAA
40842229 AAATAATTAAA
1 AAATAATTAAA
40842240 AAATAA
1 AAATAA
40842246 AAATAATAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
9 7 0.32
10 2 0.09
11 13 0.59
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
AAATAATTAAA
Found at i:40842247 original size:17 final size:19
Alignment explanation
Indices: 40842209--40842252 Score: 65
Period size: 17 Copynumber: 2.4 Consensus size: 19
40842199 TTGACAGTAT
40842209 AAATAATTAAAAAATTATAA
1 AAATAATTAAAAAA-TATAA
40842229 AAATAATT-AAAAA-ATAA
1 AAATAATTAAAAAATATAA
40842246 AAATAAT
1 AAATAAT
40842253 AGTATAAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.46
19 5 0.21
20 8 0.33
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (19 bp):
AAATAATTAAAAAATATAA
Found at i:40842253 original size:20 final size:20
Alignment explanation
Indices: 40842209--40842253 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
40842199 TTGACAGTAT
*
40842209 AAATAATTAAAAAATTATAA
1 AAATAATTAAAAAATTAAAA
40842229 AAATAATTAAAAAA-TAAAA
1 AAATAATTAAAAAATTAAAA
40842248 ATAATA
1 A-AATA
40842254 GTATAAAGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (20 bp):
AAATAATTAAAAAATTAAAA
Found at i:40844785 original size:20 final size:22
Alignment explanation
Indices: 40844744--40844786 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
40844734 AAGAAAACTA
*
40844744 TTTATAGTTTTATGTTTCTCTT
1 TTTATAGTTTTATGTCTCTCTT
40844766 TTTATA-TTTTAT-TCTCTCTT
1 TTTATAGTTTTATGTCTCTCTT
40844786 T
1 T
40844787 CTTCACTATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 8 0.40
21 6 0.30
22 6 0.30
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.70
Consensus pattern (22 bp):
TTTATAGTTTTATGTCTCTCTT
Found at i:40867946 original size:24 final size:24
Alignment explanation
Indices: 40867914--40867961 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
40867904 TCTTTATCAC
40867914 ATTATACACCGTCAGAATTAATTG
1 ATTATACACCGTCAGAATTAATTG
*
40867938 ATTATACACCGTTAGAATTAATTG
1 ATTATACACCGTCAGAATTAATTG
40867962 TCTCAATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (24 bp):
ATTATACACCGTCAGAATTAATTG
Found at i:40868451 original size:18 final size:18
Alignment explanation
Indices: 40868430--40868481 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 18
40868420 AACCACCACC
40868430 ACCACTTCCACCACCAGA
1 ACCACTTCCACCACCAGA
** * *
40868448 ACCACCACCACCACCGGT
1 ACCACTTCCACCACCAGA
* *
40868466 TCCACTTCCAGCACCA
1 ACCACTTCCACCACCA
40868482 TATCCACCAC
Statistics
Matches: 25, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.29, C:0.52, G:0.08, T:0.12
Consensus pattern (18 bp):
ACCACTTCCACCACCAGA
Found at i:40868520 original size:6 final size:6
Alignment explanation
Indices: 40868513--40868563 Score: 50
Period size: 6 Copynumber: 8.7 Consensus size: 6
40868503 CCACTCCCAT
* * * * *
40868513 AACCAT AACCAG AACCAG AACCTG AACCAG TACCAG ACCCA- AACCCG
1 AACCAG AACCAG AACCAG AACCAG AACCAG AACCAG AACCAG AACCAG
40868560 AACC
1 AACC
40868564 CGTAACCCCT
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
5 3 0.08
6 33 0.92
ACGTcount: A:0.43, C:0.39, G:0.12, T:0.06
Consensus pattern (6 bp):
AACCAG
Found at i:40872248 original size:26 final size:26
Alignment explanation
Indices: 40872199--40872248 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
40872189 TAAATCAAAT
* **
40872199 ATATATTATAAAATTTTATAAAAACA
1 ATATATTATAAAAATACATAAAAACA
*
40872225 ATATATTATAAAAATACATGAAAA
1 ATATATTATAAAAATACATAAAAA
40872249 TTTTTAAGAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (26 bp):
ATATATTATAAAAATACATAAAAACA
Found at i:40882124 original size:14 final size:14
Alignment explanation
Indices: 40882105--40882131 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40882095 TTGCTACTTT
40882105 TTGAATTTTTATAA
1 TTGAATTTTTATAA
40882119 TTGAATTTTTATA
1 TTGAATTTTTATA
40882132 GTTTTACATT
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:0.33, C:0.00, G:0.07, T:0.59
Consensus pattern (14 bp):
TTGAATTTTTATAA
Found at i:40883817 original size:42 final size:43
Alignment explanation
Indices: 40883757--40883910 Score: 136
Period size: 42 Copynumber: 3.7 Consensus size: 43
40883747 TCAACTCATA
**
40883757 TGAG-TTTCAGTTTAACCCTTCTGGGTTTCAGTTCAGCTATTT
1 TGAGCTTTCAGTTTAACCCTAATGGGTTTCAGTTCAGCTATTT
* * *
40883799 TGAGCTTT-AGTTTTACCCTAATGGGTTTCAGTTTAGCTCTTT
1 TGAGCTTTCAGTTTAACCCTAATGGGTTTCAGTTCAGCTATTT
** * * * * * *
40883841 TGAGC-TTCAAATTAACCTTTATGGGTTTCCGTTTAGCTCTTA
1 TGAGCTTTCAGTTTAACCCTAATGGGTTTCAGTTCAGCTATTT
* * *
40883883 TGAGC-TTCCGTTTAACCCTTACGGGTTT
1 TGAGCTTTCAGTTTAACCCTAATGGGTTT
40883911 TTGCGTAGCA
Statistics
Matches: 93, Mismatches: 17, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
41 2 0.02
42 88 0.95
43 3 0.03
ACGTcount: A:0.18, C:0.19, G:0.19, T:0.44
Consensus pattern (43 bp):
TGAGCTTTCAGTTTAACCCTAATGGGTTTCAGTTCAGCTATTT
Found at i:40883849 original size:21 final size:21
Alignment explanation
Indices: 40883825--40883896 Score: 56
Period size: 21 Copynumber: 3.4 Consensus size: 21
40883815 CCTAATGGGT
40883825 TTCAGTTTAGCTCTTTTGAGC
1 TTCAGTTTAGCTCTTTTGAGC
** * * *
40883846 TTCAAATTAAC-CTTTATGGGT
1 TTCAGTTTAGCTCTTT-TGAGC
* *
40883867 TTCCGTTTAGCTCTTATGAGC
1 TTCAGTTTAGCTCTTTTGAGC
*
40883888 TTCCGTTTA
1 TTCAGTTTA
40883897 ACCCTTACGG
Statistics
Matches: 37, Mismatches: 12, Indels: 4
0.70 0.23 0.08
Matches are distributed among these distances:
20 4 0.11
21 30 0.81
22 3 0.08
ACGTcount: A:0.18, C:0.19, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCAGTTTAGCTCTTTTGAGC
Found at i:40883903 original size:21 final size:21
Alignment explanation
Indices: 40883852--40883903 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
40883842 GAGCTTCAAA
* * *
40883852 TTAACCTTTATGGGTTTCCGT
1 TTAACCCTTATGAGCTTCCGT
* *
40883873 TTAGCTCTTATGAGCTTCCGT
1 TTAACCCTTATGAGCTTCCGT
40883894 TTAACCCTTA
1 TTAACCCTTA
40883904 CGGGTTTTTG
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.17, C:0.23, G:0.15, T:0.44
Consensus pattern (21 bp):
TTAACCCTTATGAGCTTCCGT
Found at i:40888681 original size:109 final size:107
Alignment explanation
Indices: 40888483--40888687 Score: 286
Period size: 109 Copynumber: 1.9 Consensus size: 107
40888473 TGTTATATTA
*
40888483 ATTTTGAGCTATGAAAAGCAAATTTGTTAAGGTTGAACTTTGATTATGAATTTTGAAATGTATTA
1 ATTTTGAGCTATGAAAAGCAAATTTGTTAAGGTTGAACTTTGATTATGAATTTTGAAATGTATAA
* *
40888548 GAAAACACAAATTTCGAAAGCTTAGGAATTTTGAAATTTATG
66 GAAAACACAAATGTCAAAAGCTTAGGAATTTTGAAATTTATG
* * * *
40888590 ATTTTGAGCTCTGAAAAAGCCAAATTTAGTTAAGGTTGAACTTTGATTCTGTA-TTTGAATTGTA
1 ATTTTGAGCTATG-AAAAG-CAAATTT-GTTAAGGTTGAACTTTGATTATGAATTTTGAAATGTA
** *
40888654 TAAGAAAACATGAATGTCAAAATCTTAGGAATTT
63 TAAGAAAACACAAATGTCAAAAGCTTAGGAATTT
40888688 AGGATTTTAT
Statistics
Matches: 85, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
107 12 0.14
108 5 0.06
109 45 0.53
110 23 0.27
ACGTcount: A:0.38, C:0.08, G:0.18, T:0.37
Consensus pattern (107 bp):
ATTTTGAGCTATGAAAAGCAAATTTGTTAAGGTTGAACTTTGATTATGAATTTTGAAATGTATAA
GAAAACACAAATGTCAAAAGCTTAGGAATTTTGAAATTTATG
Found at i:40889036 original size:150 final size:150
Alignment explanation
Indices: 40888588--40889444 Score: 1254
Period size: 150 Copynumber: 5.7 Consensus size: 150
40888578 TTGAAATTTA
* * *
40888588 TGATTTTGAGCTCTGAAAAAGCCAAATTTAGTTAAGGTTGAACTTTGATTCTGTATTTGAATTGT
1 TGATTTTGAGCTATGAAAAAGCCAAA-TTAGTTAAGGTTGAACTTTGATTATGTATTTGAAATGT
* * *
40888653 ATAAGAAAACATGAATGTCAAAATCTTAGGAATTTAGGATTTTATAAGGTATGAGAAGCTAAATT
65 ATAAAAAAACATGAATTTCAAAATCTTAGGAATTTATGATTTTATAAGGTATGAGAAGCTAAATT
*
40888718 TGGATTTTTCATTTGTTATAC
130 TGGATTTTTCATTTGTTATAT
* *
40888739 TGATTTTGAGCT-TGAAAAAGCCAAATTAGTTAAGGTTGAACTTTGACTATGTATTTGAAATATA
1 TGATTTTGAGCTATGAAAAAGCCAAATTAGTTAAGGTTGAACTTTGATTATGTATTTGAAATGTA
40888803 TTAAAAAAAACATGAATTTCAAAATCTTAGGAATTTATGATTTTATAAGGTATGAGAAGCTAAAT
66 -T-AAAAAAACATGAATTTCAAAATCTTAGGAATTTATGATTTTATAAGGTATGAGAAGCTAAAT
* *
40888868 TTGGATATTTCACTTGTTATAT
129 TTGGATTTTTCATTTGTTATAT
* * *
40888890 TGATTTTGAGCT-TGAAAAAGCCAAATTAGTCAAGGTTGAACTTTGACTATGTATTTGAAATATA
1 TGATTTTGAGCTATGAAAAAGCCAAATTAGTTAAGGTTGAACTTTGATTATGTATTTGAAATGTA
*
40888954 TTAAAAAAACATGAATTTCAAAATCTTAGGAATTTATGATTTTATAAGGTATGAGAAGTTAAATT
66 -TAAAAAAACATGAATTTCAAAATCTTAGGAATTTATGATTTTATAAGGTATGAGAAGCTAAATT
* *
40889019 TGGATATTTCACTTGTTATAT
130 TGGATTTTTCATTTGTTATAT
* *
40889040 TGATTTTGAGCT-TGAAAAAGCCAAATTGGTTAAGGTTGAACTTTGATCATGTATTTGAAATGTA
1 TGATTTTGAGCTATGAAAAAGCCAAATTAGTTAAGGTTGAACTTTGATTATGTATTTGAAATGTA
* * * * *
40889104 TAAGAAAACAAGAATTTCAAAATCTTAGGAATTTATGATTTTATAAGCTATGAAAAGCTGAATTT
66 TAAAAAAACATGAATTTCAAAATCTTAGGAATTTATGATTTTATAAGGTATGAGAAGCTAAATTT
* *
40889169 GGATTTTTCATTTCTTTTAT
131 GGATTTTTCATTTGTTATAT
* * **
40889189 TAATTTTGAGCTATGAAAAGGCCAAATTAGTTAAGGTTGAACGCTGATTATGTATTTGAAATGTA
1 TGATTTTGAGCTATGAAAAAGCCAAATTAGTTAAGGTTGAACTTTGATTATGTATTTGAAATGTA
* * * * *
40889254 TTAAGAAAAACATAAATTTCAAAATCTTAAGAATTTATGATTTTATAAGCTATGAAAAGCTGAAT
66 -TAA-AAAAACATGAATTTCAAAATCTTAGGAATTTATGATTTTATAAGGTATGAGAAGCTAAAT
*
40889319 TTGGATTTTTTATTTGTTATAT
129 TTGGATTTTTCATTTGTTATAT
* * * *
40889341 TAACTATGAGCTATG-AAAAGACAAATTAGTTAAGGTTGAACTTTGATTATGTATTTGAAATGTA
1 TGATTTTGAGCTATGAAAAAGCCAAATTAGTTAAGGTTGAACTTTGATTATGTATTTGAAATGTA
* *
40889405 TAGAAAAACATGAATTTCAAAATCTTGGGAATTTATGATT
66 TAAAAAAACATGAATTTCAAAATCTTAGGAATTTATGATT
40889445 ACAAAATGTG
Statistics
Matches: 651, Mismatches: 50, Indels: 12
0.91 0.07 0.02
Matches are distributed among these distances:
149 155 0.24
150 205 0.31
151 203 0.31
152 88 0.14
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.39
Consensus pattern (150 bp):
TGATTTTGAGCTATGAAAAAGCCAAATTAGTTAAGGTTGAACTTTGATTATGTATTTGAAATGTA
TAAAAAAACATGAATTTCAAAATCTTAGGAATTTATGATTTTATAAGGTATGAGAAGCTAAATTT
GGATTTTTCATTTGTTATAT
Found at i:40889265 original size:301 final size:300
Alignment explanation
Indices: 40888590--40889444 Score: 1254
Period size: 301 Copynumber: 2.8 Consensus size: 300
40888580 GAAATTTATG
* *
40888590 ATTTTGAGCTCTGAAAAAGCCAAATTTAGTTAAGGTTGAACTTTGATTCTGTATTTGAATTGTA-
1 ATTTTGAGCT-TGAAAAAGCCAAA-TTAGTTAAGGTTGAACTTTGATTATGTATTTGAAATGTAT
* *
40888654 TAAG-AAAACATGAATGTCAAAATCTTAGGAATTTAGGATTTTATAAGGTATGAGAAGCTAAATT
64 TAAGAAAAACATGAATTTCAAAATCTTAGGAATTTATGATTTTATAAGGTATGAGAAGCTAAATT
*
40888718 TGGATTTTTCATTTGTTATACTGATTTTGAGCTTGAAAAAGCCAAATTAGTTAAGGTTGAACTTT
129 TGGATTTTTCATTTGTTATATTGATTTTGAGCTTGAAAAAGCCAAATTAGTTAAGGTTGAACTTT
* *
40888783 GA-CTATGTATTTGAAATATATTAAAAAAAACATGAATTTCAAAATCTTAGGAATTTATGATTTT
194 GATC-ATGTATTTGAAATGTA-T-AAGAAAACATGAATTTCAAAATCTTAGGAATTTATGATTTT
* * * *
40888847 ATAAGGTATGAGAAGCTAAATTTGGATATTTCACTTGTTATATTG
256 ATAAGCTATGAAAAGCTAAATTTGGATATTTCACTTCTTATATTA
* * *
40888892 ATTTTGAGCTTGAAAAAGCCAAATTAGTCAAGGTTGAACTTTGACTATGTATTTGAAATATATTA
1 ATTTTGAGCTTGAAAAAGCCAAATTAGTTAAGGTTGAACTTTGATTATGTATTTGAAATGTATTA
*
40888957 A-AAAAACATGAATTTCAAAATCTTAGGAATTTATGATTTTATAAGGTATGAGAAGTTAAATTTG
66 AGAAAAACATGAATTTCAAAATCTTAGGAATTTATGATTTTATAAGGTATGAGAAGCTAAATTTG
* * *
40889021 GATATTTCACTTGTTATATTGATTTTGAGCTTGAAAAAGCCAAATTGGTTAAGGTTGAACTTTGA
131 GATTTTTCATTTGTTATATTGATTTTGAGCTTGAAAAAGCCAAATTAGTTAAGGTTGAACTTTGA
*
40889086 TCATGTATTTGAAATGTATAAGAAAACAAGAATTTCAAAATCTTAGGAATTTATGATTTTATAAG
196 TCATGTATTTGAAATGTATAAGAAAACATGAATTTCAAAATCTTAGGAATTTATGATTTTATAAG
* * * *
40889151 CTATGAAAAGCTGAATTTGGATTTTTCATTTCTTTTATTA
261 CTATGAAAAGCTAAATTTGGATATTTCACTTCTTATATTA
* **
40889191 ATTTTGAGCTATGAAAAGGCCAAATTAGTTAAGGTTGAACGCTGATTATGTATTTGAAATGTATT
1 ATTTTGAGCT-TGAAAAAGCCAAATTAGTTAAGGTTGAACTTTGATTATGTATTTGAAATGTATT
* * * * *
40889256 AAGAAAAACATAAATTTCAAAATCTTAAGAATTTATGATTTTATAAGCTATGAAAAGCTGAATTT
65 AAGAAAAACATGAATTTCAAAATCTTAGGAATTTATGATTTTATAAGGTATGAGAAGCTAAATTT
* * * * *
40889321 GGATTTTTTATTTGTTATATTAACTATGAGCTATG-AAAAGACAAATTAGTTAAGGTTGAACTTT
130 GGATTTTTCATTTGTTATATTGATTTTGAGCT-TGAAAAAGCCAAATTAGTTAAGGTTGAACTTT
* *
40889385 GATTATGTATTTGAAATGTAT-AGAAAAACATGAATTTCAAAATCTTGGGAATTTATGATT
194 GATCATGTATTTGAAATGTATAAG-AAAACATGAATTTCAAAATCTTAGGAATTTATGATT
40889445 ACAAAATGTG
Statistics
Matches: 500, Mismatches: 46, Indels: 15
0.89 0.08 0.03
Matches are distributed among these distances:
299 86 0.17
300 87 0.17
301 314 0.63
302 13 0.03
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.39
Consensus pattern (300 bp):
ATTTTGAGCTTGAAAAAGCCAAATTAGTTAAGGTTGAACTTTGATTATGTATTTGAAATGTATTA
AGAAAAACATGAATTTCAAAATCTTAGGAATTTATGATTTTATAAGGTATGAGAAGCTAAATTTG
GATTTTTCATTTGTTATATTGATTTTGAGCTTGAAAAAGCCAAATTAGTTAAGGTTGAACTTTGA
TCATGTATTTGAAATGTATAAGAAAACATGAATTTCAAAATCTTAGGAATTTATGATTTTATAAG
CTATGAAAAGCTAAATTTGGATATTTCACTTCTTATATTA
Found at i:40896138 original size:31 final size:31
Alignment explanation
Indices: 40896100--40896171 Score: 144
Period size: 31 Copynumber: 2.3 Consensus size: 31
40896090 AGTTGTAGTT
40896100 TTTTTGGGGAACTTTTATTTTCACTCTATTC
1 TTTTTGGGGAACTTTTATTTTCACTCTATTC
40896131 TTTTTGGGGAACTTTTATTTTCACTCTATTC
1 TTTTTGGGGAACTTTTATTTTCACTCTATTC
40896162 TTTTTGGGGA
1 TTTTTGGGGA
40896172 TCCCCTGTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.15, C:0.14, G:0.17, T:0.54
Consensus pattern (31 bp):
TTTTTGGGGAACTTTTATTTTCACTCTATTC
Found at i:40917383 original size:16 final size:18
Alignment explanation
Indices: 40917345--40917385 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
40917335 TATTTTAAAT
*
40917345 TATTTTTTAGTTTTGTTA
1 TATTTTCTAGTTTTGTTA
40917363 TATTTTCTAGTTTT-TTA
1 TATTTTCTAGTTTTGTTA
40917380 -ATTTTC
1 TATTTTC
40917386 GTGAAACTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 6 0.27
17 3 0.14
18 13 0.59
ACGTcount: A:0.17, C:0.05, G:0.07, T:0.71
Consensus pattern (18 bp):
TATTTTCTAGTTTTGTTA
Found at i:40921160 original size:20 final size:21
Alignment explanation
Indices: 40921137--40921186 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
40921127 TTGCAAATGC
*
40921137 TTTAAAAATAT-ATCAAAAAT
1 TTTAAAAATATGATAAAAAAT
* *
40921157 TTTAACAATATGTTAAAAAAT
1 TTTAAAAATATGATAAAAAAT
40921178 TTTATAAAA
1 TTTA-AAAA
40921187 ATTTAAAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 10 0.42
21 11 0.46
22 3 0.12
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (21 bp):
TTTAAAAATATGATAAAAAAT
Found at i:40921192 original size:20 final size:21
Alignment explanation
Indices: 40921151--40921194 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
40921141 AAAATATATC
*
40921151 AAAAATTTTAACAATATGTTA
1 AAAAATTTTAACAAAATGTTA
40921172 AAAAATTTTATA-AAAAT-TTA
1 AAAAATTTTA-ACAAAATGTTA
40921192 AAA
1 AAA
40921195 TTTTGGCGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 6 0.29
21 14 0.67
22 1 0.05
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (21 bp):
AAAAATTTTAACAAAATGTTA
Found at i:40923956 original size:22 final size:23
Alignment explanation
Indices: 40923910--40923955 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
40923900 TTTAAAAATT
* *
40923910 AGACTTAATTTTTAAAATTAAAA
1 AGACTAAATTTTTAAAAATAAAA
40923933 AGACTAAATTTTTAAAAATAAAA
1 AGACTAAATTTTTAAAAATAAAA
40923956 GTACAGATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (23 bp):
AGACTAAATTTTTAAAAATAAAA
Found at i:40924094 original size:20 final size:20
Alignment explanation
Indices: 40924057--40924095 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
40924047 AAATTGAAAT
* *
40924057 ATTAAATAATTTATTATATG
1 ATTAAATAATTAAATATATG
*
40924077 ATTAGATAATTAAATATAT
1 ATTAAATAATTAAATATAT
40924096 ATGTTCAATA
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:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (20 bp):
ATTAAATAATTAAATATATG
Found at i:40927426 original size:28 final size:30
Alignment explanation
Indices: 40927386--40927457 Score: 105
Period size: 28 Copynumber: 2.5 Consensus size: 30
40927376 ATAAAAAATA
40927386 ACCAAAATATTATAACT-TTTTT-TTATTT
1 ACCAAAATATTATAACTATTTTTATTATTT
* *
40927414 ACTAAAATATTATAATTATTTTTATTATTT
1 ACCAAAATATTATAACTATTTTTATTATTT
40927444 ACCAAAATA-TATAA
1 ACCAAAATATTATAA
40927458 AAAAACAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
28 15 0.38
29 10 0.26
30 14 0.36
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (30 bp):
ACCAAAATATTATAACTATTTTTATTATTT
Found at i:40927582 original size:4 final size:4
Alignment explanation
Indices: 40927575--40927718 Score: 79
Period size: 4 Copynumber: 35.0 Consensus size: 4
40927565 GAAGGAGAGG
* *
40927575 GAAA GAAA GAAA GAAA GAAA GAAA GGAAA GAAG GAGAG GAAA GAAA G-AA
1 GAAA GAAA GAAA GAAA GAAA GAAA -GAAA GAAA GA-AA GAAA GAAA GAAA
* *
40927624 -AAA GAAG GAAA GAAAA GGAAA GGAGAA GAGAA -AAA GAAAA GGAA G-AA
1 GAAA GAAA GAAA G-AAA -GAAA -GA-AA GA-AA GAAA G-AAA GAAA GAAA
*
40927671 G-AA GAAGA GGAAA GGAAAA GAAA -AAA GAAA G-AA -AAA GAAG GAAA
1 GAAA GAA-A -GAAA -G-AAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
40927715 GAAA
1 GAAA
40927719 AGGAAAGGAG
Statistics
Matches: 117, Mismatches: 7, Indels: 32
0.75 0.04 0.21
Matches are distributed among these distances:
3 19 0.16
4 58 0.50
5 31 0.26
6 9 0.08
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:40927605 original size:13 final size:13
Alignment explanation
Indices: 40927574--40927732 Score: 94
Period size: 14 Copynumber: 11.5 Consensus size: 13
40927564 GGAAGGAGAG
40927574 GGAAAGAAAGAAA
1 GGAAAGAAAGAAA
40927587 -GAAAGAAAGAAA
1 GGAAAGAAAGAAA
* *
40927599 GGAAAGAAGGAGA
1 GGAAAGAAAGAAA
40927612 GGAAAGAAAGAAAA
1 GGAAAGAAAG-AAA
* *
40927626 AGAAGGAAAGAAAA
1 GGAAAGAAAG-AAA
40927640 GGAAAGGAGAAGAGAA
1 GGAAA-GA-AAGA-AA
*
40927656 --AAAGAAAAGGAA
1 GGAAAG-AAAGAAA
*
40927668 GAAGAAGAAGAGGAAA
1 GGA-AAGAA-A-GAAA
40927684 GGAAAAGAAA-AAA
1 GG-AAAGAAAGAAA
*
40927697 -GAAAGAAAAAGAA
1 GGAAAGAAAGA-AA
40927710 GGAAAGAAAAGGAAA
1 GGAAAG-AAA-GAAA
40927725 GGAGAAGA
1 GGA-AAGA
40927733 GAAAAAAAAA
Statistics
Matches: 116, Mismatches: 12, Indels: 34
0.72 0.07 0.21
Matches are distributed among these distances:
11 7 0.06
12 16 0.14
13 28 0.24
14 29 0.25
15 17 0.15
16 18 0.16
17 1 0.01
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (13 bp):
GGAAAGAAAGAAA
Found at i:40927629 original size:6 final size:6
Alignment explanation
Indices: 40927618--40927752 Score: 62
Period size: 6 Copynumber: 22.0 Consensus size: 6
40927608 GAGAGGAAAG
* * * *
40927618 AAAGAA AAAGAA GGAAAG-A AAAGGA AAGGAGA AGAGAA AAAGAA AAGGAA
1 AAAGAA AAAGAA --AAAGAA AAAGAA AAAGA-A AAAGAA AAAGAA AAAGAA
* * * * *
40927668 GAAGAA GAAGAGG AAAGGA AAAGAA AAA-AG AAAGAA AAAGAA GGAAAG-A
1 AAAGAA AAAGA-A AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA --AAAGAA
* * * *
40927717 AAAGGA AAGGAGA AGAGAA AAA-AA AAAGAA GAAGAA
1 AAAGAA AAAGA-A AAAGAA AAAGAA AAAGAA AAAGAA
40927753 GAGGGAAGGA
Statistics
Matches: 97, Mismatches: 21, Indels: 22
0.69 0.15 0.16
Matches are distributed among these distances:
5 17 0.18
6 59 0.61
7 13 0.13
8 8 0.08
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:40927645 original size:5 final size:5
Alignment explanation
Indices: 40927574--40927727 Score: 59
Period size: 5 Copynumber: 32.6 Consensus size: 5
40927564 GGAAGGAGAG
*
40927574 GGAAA -GAAA -GAAA -GAAA -GAAA -GAAA GGAAA -G-AA GGAGA GGAAA
1 GGAAA GGAAA GGAAA GGAAA GGAAA GGAAA GGAAA GGAAA GGAAA GGAAA
* * * *
40927617 -GAAA GAAAA AG-AA GGAAA GAAAA GGAAA GGAGAA GAGAAAAA GAAAA
1 GGAAA GGAAA GGAAA GGAAA GGAAA GGAAA GGA-AA G-G--AAA GGAAA
* * * *
40927664 GG-AA -GAAGA AGAAGA GGAAA GGAAA AGAAA --AAA -GAAA GAAAA AG-AA
1 GGAAA GGAA-A GGAA-A GGAAA GGAAA GGAAA GGAAA GGAAA GGAAA GGAAA
*
40927710 GGAAA GAAAA GGAAA GGA
1 GGAAA GGAAA GGAAA GGA
40927728 GAAGAGAAAA
Statistics
Matches: 116, Mismatches: 18, Indels: 30
0.71 0.11 0.18
Matches are distributed among these distances:
3 6 0.05
4 38 0.33
5 56 0.48
6 11 0.09
7 1 0.01
8 3 0.03
9 1 0.01
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (5 bp):
GGAAA
Found at i:40927749 original size:46 final size:47
Alignment explanation
Indices: 40927585--40927763 Score: 62
Period size: 49 Copynumber: 3.9 Consensus size: 47
40927575 GAAAGAAAGA
*
40927585 AAGAAAGAAAGA-AAGGAAAGAAG--G-AGAGGAAA-G-AAAGAAAAA
1 AAGAAAGAAAAAGAAGGAAAGAAGAAGAAGAGGAAAGGAAAAG-AAAA
* *
40927627 GAAGGAAAGAAAAGGAAAGGAGAAG-AGAA-AA-AGAAAAGGAAGAAGAAGAA
1 -AA-GAAAGAAAAAG-AAGGA-AAGAAGAAGAAGAGGAAAGGAA-AAGAA-AA
* * * * *
40927677 GAGGAAAGGAAAAGAA-AAAAGAAAGAAAAAGAAGGAAA-GAAAAGGAAAG
1 -AAGAAAGAAAAAGAAGGAAAG-AAGAAGAAG-AGGAAAGGAAAA-GAAAA
* *
40927726 GAGAAGAGAAAAA-AA--AAAGAAGAAGAAGAGGGAAGGAA
1 AAGAA-AGAAAAAGAAGGAAAGAAGAAGAAGAGGAAAGGAA
40927764 GGAAGGAAAA
Statistics
Matches: 103, Mismatches: 14, Indels: 35
0.68 0.09 0.23
Matches are distributed among these distances:
43 2 0.02
44 8 0.08
45 5 0.05
46 21 0.20
47 13 0.13
48 13 0.13
49 23 0.22
50 13 0.13
51 5 0.05
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (47 bp):
AAGAAAGAAAAAGAAGGAAAGAAGAAGAAGAGGAAAGGAAAAGAAAA
Found at i:40927766 original size:80 final size:80
Alignment explanation
Indices: 40927614--40927784 Score: 260
Period size: 80 Copynumber: 2.1 Consensus size: 80
40927604 GAAGGAGAGG
*
40927614 AAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAGAAAAGGAAGAAGAAGAAGA
1 AAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAGAAAAAGAAGAAGAAGAAGA
40927679 GGAAAGGAAA-AGAAA
66 GGAAAGGAAAGA-AAA
*
40927694 AAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAA-AAAAAGAAGAAGAAGAGGG
1 AAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAGAAAAAGAAGAAGAAGA-AG
*
40927758 AAGG-AAGGAAGGAAAA
65 -AGGAAAGGAAAGAAAA
40927774 AAAGAAA-AAAA
1 AAAGAAAGAAAA
40927785 GGTAATTTTT
Statistics
Matches: 85, Mismatches: 3, Indels: 7
0.89 0.03 0.07
Matches are distributed among these distances:
79 19 0.22
80 62 0.73
81 4 0.05
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (80 bp):
AAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAGAAAAAGAAGAAGAAGAAGA
GGAAAGGAAAGAAAA
Found at i:40927770 original size:43 final size:46
Alignment explanation
Indices: 40927691--40927784 Score: 106
Period size: 46 Copynumber: 2.1 Consensus size: 46
40927681 AAAGGAAAAG
40927691 AAAAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAA
1 AAAAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGA-AAGAGAAAA
* * *
40927738 AAAAAAG-AAGAAGAAGAGGGAAGGAAGGAAGGAAA--AAA-AGAAAA
1 AAAAAAGAAAGAAAAAGAAGGAAAGAA--AAGGAAAGGAAAGAGAAAA
40927782 AAA
1 AAA
40927785 GGTAATTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
44 9 0.21
45 2 0.05
46 17 0.40
47 7 0.17
48 7 0.17
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (46 bp):
AAAAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAAAGAGAAAA
Found at i:40928541 original size:27 final size:27
Alignment explanation
Indices: 40928511--40928566 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
40928501 AAGAAGGGTG
*
40928511 ATGGAGGGGAATAAAAAAGCGGCACCA
1 ATGGAGAGGAATAAAAAAGCGGCACCA
*
40928538 ATGGAGAGGAATAAAAAGGCGGCACCA
1 ATGGAGAGGAATAAAAAAGCGGCACCA
40928565 AT
1 AT
40928567 ATGTGGCTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.45, C:0.14, G:0.32, T:0.09
Consensus pattern (27 bp):
ATGGAGAGGAATAAAAAAGCGGCACCA
Found at i:40933490 original size:18 final size:18
Alignment explanation
Indices: 40933467--40933511 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
40933457 ATCCCAATGA
40933467 TCGCCACCACATTCTTCT
1 TCGCCACCACATTCTTCT
* *
40933485 TCGCCAGCACTTTCTTCT
1 TCGCCACCACATTCTTCT
*
40933503 TCACCACCA
1 TCGCCACCA
40933512 ACCATATCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.18, C:0.44, G:0.07, T:0.31
Consensus pattern (18 bp):
TCGCCACCACATTCTTCT
Found at i:40934327 original size:3 final size:3
Alignment explanation
Indices: 40934321--40934357 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
40934311 AACAACAGTC
40934321 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
40934358 CTAAAACTAT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:40934433 original size:19 final size:21
Alignment explanation
Indices: 40934409--40934447 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
40934399 CTTAAAACAA
*
40934409 AAAAC-ATTACAA-AATATAC
1 AAAACAATAACAACAATATAC
40934428 AAAACAATAACAACAATATA
1 AAAACAATAACAACAATATA
40934448 ATCAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 6 0.35
21 6 0.35
ACGTcount: A:0.67, C:0.15, G:0.00, T:0.18
Consensus pattern (21 bp):
AAAACAATAACAACAATATAC
Found at i:40939080 original size:17 final size:17
Alignment explanation
Indices: 40939058--40939094 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
40939048 TGTCACTTGA
*
40939058 TGAACAGTCGTATCTTT
1 TGAACAATCGTATCTTT
*
40939075 TGAACAATTGTATCTTT
1 TGAACAATCGTATCTTT
40939092 TGA
1 TGA
40939095 TGAACAGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.27, C:0.14, G:0.16, T:0.43
Consensus pattern (17 bp):
TGAACAATCGTATCTTT
Found at i:40939100 original size:20 final size:19
Alignment explanation
Indices: 40939054--40939100 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
40939044 GTTCTGTCAC
*
40939054 TTGATGAACAGTCGTATCT
1 TTGATGAACAATCGTATCT
*
40939073 TT--TGAACAATTGTATCTT
1 TTGATGAACAATCGTATC-T
40939091 TTGATGAACA
1 TTGATGAACA
40939101 GATTCATTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
17 12 0.52
18 3 0.13
19 2 0.09
20 6 0.26
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.40
Consensus pattern (19 bp):
TTGATGAACAATCGTATCT
Found at i:40941320 original size:22 final size:20
Alignment explanation
Indices: 40941279--40941325 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 20
40941269 TTAGCGAATA
40941279 AATATAAATAAACAAATATT
1 AATATAAATAAACAAATATT
* *
40941299 TATATAAAATAAAATAAATATT
1 AATAT-AAAT-AAACAAATATT
40941321 AATAT
1 AATAT
40941326 TTAAAATATC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 4 0.18
21 4 0.18
22 14 0.64
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (20 bp):
AATATAAATAAACAAATATT
Found at i:40945309 original size:34 final size:34
Alignment explanation
Indices: 40945246--40945310 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
40945236 TTACTTTATC
40945246 TATATAACTAAATAGAGAAGAAAATAATAAAAAA
1 TATATAACTAAATAGAGAAGAAAATAATAAAAAA
*
40945280 TATATAATTGAAATATGA-AAGAAAA-AATAAA
1 TATATAACT-AAATA-GAGAAGAAAATAATAAA
40945311 TTACTACAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
34 14 0.50
35 12 0.43
36 2 0.07
ACGTcount: A:0.66, C:0.02, G:0.09, T:0.23
Consensus pattern (34 bp):
TATATAACTAAATAGAGAAGAAAATAATAAAAAA
Found at i:40950548 original size:20 final size:20
Alignment explanation
Indices: 40950514--40950561 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
40950504 TTGGTAAATT
*
40950514 CATGTGTA-ATAATAATAAA
1 CATGTGTATTTAATAATAAA
40950533 CATGTGTATTTAATAATAAA
1 CATGTGTATTTAATAATAAA
*
40950553 -ATATGTATT
1 CATGTGTATT
40950562 GCTTATTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.46, C:0.04, G:0.10, T:0.40
Consensus pattern (20 bp):
CATGTGTATTTAATAATAAA
Found at i:40950559 original size:19 final size:20
Alignment explanation
Indices: 40950523--40950561 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
40950513 TCATGTGTAA
*
40950523 TAATAATAAACATGTGTATT
1 TAATAATAAACATATGTATT
40950543 TAATAATAAA-ATATGTATT
1 TAATAATAAACATATGTATT
40950562 GCTTATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.41
Consensus pattern (20 bp):
TAATAATAAACATATGTATT
Found at i:40951662 original size:40 final size:40
Alignment explanation
Indices: 40951541--40951680 Score: 169
Period size: 40 Copynumber: 3.5 Consensus size: 40
40951531 AACTTTGAGT
* *
40951541 CGATGAGACACTGGGTGTCAATTTATTACTTCGGATTAATT
1 CGATGAGACACTGGGTGTCAAATTATTACTTCGGATT-ATC
* * * *
40951582 CGATGAGGCACTGGGTG-CTAA-T-TTACTTCGGTTTAGC
1 CGATGAGACACTGGGTGTCAAATTATTACTTCGGATTATC
*
40951619 CGATGAGACACTGGGTGTCAAATTATTACTTCGAATTATC
1 CGATGAGACACTGGGTGTCAAATTATTACTTCGGATTATC
* *
40951659 CGATGAGACACTGCGTGCCAAA
1 CGATGAGACACTGGGTGTCAAA
40951681 CTGGTGTGTT
Statistics
Matches: 83, Mismatches: 13, Indels: 7
0.81 0.13 0.07
Matches are distributed among these distances:
37 17 0.20
38 14 0.17
39 2 0.02
40 34 0.41
41 16 0.19
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (40 bp):
CGATGAGACACTGGGTGTCAAATTATTACTTCGGATTATC
Found at i:40952526 original size:15 final size:15
Alignment explanation
Indices: 40952506--40952536 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
40952496 GATTATTATT
40952506 ATAATAATAGAAGGA
1 ATAATAATAGAAGGA
40952521 ATAATAATAGAAGGA
1 ATAATAATAGAAGGA
40952536 A
1 A
40952537 AAAGTCTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.19, T:0.19
Consensus pattern (15 bp):
ATAATAATAGAAGGA
Found at i:40954850 original size:20 final size:20
Alignment explanation
Indices: 40954812--40954856 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
40954802 TGAATCAATC
* * *
40954812 TAATTCGGTTGGAAGTTGGT
1 TAATTCGATTGGAAATTGGA
*
40954832 TAATTCGATTTGAAATTGGA
1 TAATTCGATTGGAAATTGGA
40954852 TAATT
1 TAATT
40954857 AACTGAATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.04, G:0.24, T:0.42
Consensus pattern (20 bp):
TAATTCGATTGGAAATTGGA
Found at i:40958595 original size:22 final size:22
Alignment explanation
Indices: 40958547--40958595 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
40958537 ATATCCAAAC
40958547 AATAATAACAAAATAGTAACAA
1 AATAATAACAAAATAGTAACAA
* ** * *
40958569 CATAATAGTAAAATGGTAGCAA
1 AATAATAACAAAATAGTAACAA
40958591 AATAA
1 AATAA
40958596 GGAGAAAACA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.61, C:0.08, G:0.10, T:0.20
Consensus pattern (22 bp):
AATAATAACAAAATAGTAACAA
Found at i:40970750 original size:26 final size:26
Alignment explanation
Indices: 40970714--40970767 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
40970704 AAGTCAGAAG
40970714 AATCACAAAGTGAGATTTAAGGTGAC
1 AATCACAAAGTGAGATTTAAGGTGAC
40970740 AATCACAAAGTGAGATTTAAGGTGAC
1 AATCACAAAGTGAGATTTAAGGTGAC
40970766 AA
1 AA
40970768 CATCTCTTGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.44, C:0.11, G:0.22, T:0.22
Consensus pattern (26 bp):
AATCACAAAGTGAGATTTAAGGTGAC
Found at i:40975778 original size:34 final size:33
Alignment explanation
Indices: 40975725--40975793 Score: 111
Period size: 34 Copynumber: 2.1 Consensus size: 33
40975715 CAAGTAAGTA
*
40975725 TTAGTTTTCTCCTTCTGTGATAATGTTTTGTTT
1 TTAGTTTTCACCTTCTGTGATAATGTTTTGTTT
*
40975758 TTAGTTTTTCACCTTTTGTGATAATGTTTTGTTT
1 TTAG-TTTTCACCTTCTGTGATAATGTTTTGTTT
40975792 TT
1 TT
40975794 TAAATGTTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
33 4 0.12
34 29 0.88
ACGTcount: A:0.13, C:0.10, G:0.14, T:0.62
Consensus pattern (33 bp):
TTAGTTTTCACCTTCTGTGATAATGTTTTGTTT
Found at i:40976264 original size:48 final size:48
Alignment explanation
Indices: 40976205--40976301 Score: 185
Period size: 48 Copynumber: 2.0 Consensus size: 48
40976195 GTATAAAATA
*
40976205 TAGTAATTTGGTTGCTATCGCCTGGTGATTCTCATATGAATTACTATC
1 TAGTAAATTGGTTGCTATCGCCTGGTGATTCTCATATGAATTACTATC
40976253 TAGTAAATTGGTTGCTATCGCCTGGTGATTCTCATATGAATTACTATC
1 TAGTAAATTGGTTGCTATCGCCTGGTGATTCTCATATGAATTACTATC
40976301 T
1 T
40976302 GCTGTAGGCA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.24, C:0.16, G:0.19, T:0.41
Consensus pattern (48 bp):
TAGTAAATTGGTTGCTATCGCCTGGTGATTCTCATATGAATTACTATC
Found at i:40977643 original size:19 final size:19
Alignment explanation
Indices: 40977605--40977645 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
40977595 AAGCTGATTA
40977605 TTTTTTGCTACTTGTCCTGC
1 TTTTTTGCTACTTG-CCTGC
40977625 TTTTTTGCATACTTG-CTGC
1 TTTTTTGC-TACTTGCCTGC
40977644 TT
1 TT
40977646 CTAAGCTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.30
20 8 0.40
21 6 0.30
ACGTcount: A:0.07, C:0.22, G:0.15, T:0.56
Consensus pattern (19 bp):
TTTTTTGCTACTTGCCTGC
Found at i:40998047 original size:18 final size:17
Alignment explanation
Indices: 40998020--40998055 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
40998010 AAACACACCC
40998020 CACTTTAAAAATTCAAG
1 CACTTTAAAAATTCAAG
40998037 CACTTTAAAAATTCAAG
1 CACTTTAAAAATTCAAG
40998054 CA
1 CA
40998056 ATAAAATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.47, C:0.19, G:0.06, T:0.28
Consensus pattern (17 bp):
CACTTTAAAAATTCAAG
Found at i:41013304 original size:3 final size:3
Alignment explanation
Indices: 41013296--41013342 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
41013286 TTACTAGTAT
*
41013296 TTA TTA TTA TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
41013343 TGTCTTATTC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:41015919 original size:3 final size:3
Alignment explanation
Indices: 41015913--41015950 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
41015903 AAGAGAAAAA
41015913 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
41015951 AAAATCTGGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:41016294 original size:21 final size:22
Alignment explanation
Indices: 41016252--41016298 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
41016242 CTTTTATGTT
* * *
41016252 AAATTTTTAACTTTTAATAATA
1 AAATATTTAACTTTAAAAAATA
41016274 AAATATTTAA-TTTAAAAAATA
1 AAATATTTAACTTTAAAAAATA
41016295 AAAT
1 AAAT
41016299 CCAAATGATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
AAATATTTAACTTTAAAAAATA
Found at i:41021977 original size:27 final size:27
Alignment explanation
Indices: 41021944--41022004 Score: 122
Period size: 27 Copynumber: 2.3 Consensus size: 27
41021934 CCACCATTTT
41021944 TACTTAAACAAGAAACTAAACTAATCA
1 TACTTAAACAAGAAACTAAACTAATCA
41021971 TACTTAAACAAGAAACTAAACTAATCA
1 TACTTAAACAAGAAACTAAACTAATCA
41021998 TACTTAA
1 TACTTAA
41022005 TATATGTATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.54, C:0.18, G:0.03, T:0.25
Consensus pattern (27 bp):
TACTTAAACAAGAAACTAAACTAATCA
Found at i:41025038 original size:24 final size:24
Alignment explanation
Indices: 41025011--41025062 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
41025001 TTTCTAGAAG
* **
41025011 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATGAACATAATAT
*
41025035 ATTTAGCATTTATTAACATAATAT
1 ATTTAGCATTTATGAACATAATAT
41025059 ATTT
1 ATTT
41025063 GACTTTGATT
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:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATGAACATAATAT
Found at i:41029506 original size:24 final size:24
Alignment explanation
Indices: 41029443--41029494 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
41029433 TTTCTAAAAG
* * *
41029443 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
41029467 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATTAGCATAATAT
41029491 ATTT
1 ATTT
41029495 GACTTTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:41047191 original size:46 final size:46
Alignment explanation
Indices: 41047124--41047254 Score: 217
Period size: 46 Copynumber: 2.8 Consensus size: 46
41047114 AGTGTGGAAC
41047124 GTAGGTATGGTATTTTAGTAAAGAAAACCATACTGAGTTGTGAAAA
1 GTAGGTATGGTATTTTAGTAAAGAAAACCATACTGAGTTGTGAAAA
* *
41047170 GTAGGTATGGTATTTTAGTAAAGAAAATCATACTGAGTTGTGAGAA
1 GTAGGTATGGTATTTTAGTAAAGAAAACCATACTGAGTTGTGAAAA
* * *
41047216 GTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGTT
1 GTAGGTATGGTATTTTAGTAAAGAAAACCATACTGAGTT
41047255 ATAGCATTGC
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 79 1.00
ACGTcount: A:0.36, C:0.07, G:0.26, T:0.31
Consensus pattern (46 bp):
GTAGGTATGGTATTTTAGTAAAGAAAACCATACTGAGTTGTGAAAA
Found at i:41053421 original size:2 final size:2
Alignment explanation
Indices: 41053414--41053439 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
41053404 TCATCATTGC
41053414 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
41053440 GCAAATGCTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:41060358 original size:21 final size:18
Alignment explanation
Indices: 41060319--41060362 Score: 52
Period size: 21 Copynumber: 2.3 Consensus size: 18
41060309 TCCCTAAATT
*
41060319 AATAATAAATAAAATATA
1 AATAATAAATAAAACATA
41060337 AATAATATAATTAAGAACATA
1 AATAATA-AA-TAA-AACATA
41060358 AATAA
1 AATAA
41060363 AATAGTTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 7 0.32
19 2 0.09
20 3 0.14
21 10 0.45
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (18 bp):
AATAATAAATAAAACATA
Done.