Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 138 of 168
Found at i:40396200 original size:119 final size:120
Alignment explanation
Indices: 40395898--40396312 Score: 665
Period size: 120 Copynumber: 3.5 Consensus size: 120
40395888 TTATTTTAAA
* * * *
40395898 TTTATTAAATCATATATTTTAATTAAAATATATTTTAATATTAATTAT-TTCAAATTATATTTGA
1 TTTATTAAATTATATATTTTAATTATAATATA-TTTAATAATAATTATGTT-AAATTATATTTTA
*
40395962 TAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAGAAT
64 TAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAAT
* * *
40396019 TTTATTAAATTATATATATTAATTATAATATATTTAATAATAATTATGTTAAATGATCTTTTATA
1 TTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATATTTTATA
* *
40396084 GTATCATATATTATGATTTGAGTAAAATTCATATAAGAATATTAATTATTACGAAT
66 GTATCATATATTATGATTTGAGT-AAATTCATATAAGAATATTGATTATTAAGAAT
*
40396140 TTTA-TAAATTATATA-TTTAATTATAATATATTTAATAATTATTATGTTAAATTATATTTTATA
1 TTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATATTTTATA
*
40396203 GTATCATATATTATGATTTGAGTAAATTCATATAAGAATACTGATTATTAAGAAT
66 GTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAAT
40396258 TTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAAT
1 TTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATG-TTAAAT
40396313 ATGATTAAAT
Statistics
Matches: 271, Mismatches: 18, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
118 33 0.12
119 78 0.29
120 89 0.33
121 71 0.26
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.49
Consensus pattern (120 bp):
TTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATATTTTATA
GTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAAT
Found at i:40396229 original size:38 final size:38
Alignment explanation
Indices: 40396068--40396235 Score: 94
Period size: 38 Copynumber: 4.3 Consensus size: 38
40396058 ATAATTATGT
* *
40396068 TAAATGATCTTTTATAGTATCATATATTATGATTTGAG
1 TAAATTATATTTTATAGTATCATATATTATGATTTGAG
* * * * * *
40396106 TAAAATTCATA--TAAGAATATTA-ATTATTACGAATTTTA-
1 T-AAATT-ATATTTTATAGTATCATA-TATTATG-ATTTGAG
* * * *
40396144 TAAATTATATATTTA-ATTATAATATATTTAATAATTATTATG
1 TAAATTATAT-TTTATAGTATCATATA-TT-ATGATT-TGA-G
40396186 TTAAATTATATTTTATAGTATCATATATTATGATTTGAG
1 -TAAATTATATTTTATAGTATCATATATTATGATTTGAG
40396225 TAAATTCATAT
1 TAAATT-ATAT
40396236 AAGAATACTG
Statistics
Matches: 97, Mismatches: 17, Indels: 31
0.67 0.12 0.21
Matches are distributed among these distances:
36 3 0.03
37 6 0.06
38 28 0.29
39 22 0.23
40 8 0.08
41 5 0.05
42 6 0.06
43 19 0.20
ACGTcount: A:0.41, C:0.04, G:0.07, T:0.48
Consensus pattern (38 bp):
TAAATTATATTTTATAGTATCATATATTATGATTTGAG
Found at i:40396290 original size:16 final size:16
Alignment explanation
Indices: 40396269--40396310 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
40396259 TTATTAAATT
*
40396269 ATATATTTTAATTATA
1 ATATATTTTAATAATA
40396285 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
40396300 AT-TATGTTTAA
1 ATATAT-TTTAA
40396311 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:40396295 original size:15 final size:15
Alignment explanation
Indices: 40396260--40396301 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
40396250 TTAAGAATTT
*
40396260 TATTAAATTAT-ATA
1 TATTTAATTATAATA
40396274 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
40396288 TATTTAATAATAAT
1 TATTTAATTATAAT
40396302 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:40400372 original size:12 final size:12
Alignment explanation
Indices: 40400355--40400387 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
40400345 AGAGCCAGAT
40400355 TCATCTTCATCC
1 TCATCTTCATCC
*
40400367 TCATCTTCGTCC
1 TCATCTTCATCC
40400379 TCATCTTCA
1 TCATCTTCA
40400388 AACTTCTCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.15, C:0.39, G:0.03, T:0.42
Consensus pattern (12 bp):
TCATCTTCATCC
Found at i:40404573 original size:40 final size:40
Alignment explanation
Indices: 40404515--40404605 Score: 121
Period size: 40 Copynumber: 2.3 Consensus size: 40
40404505 CAACCTTTTT
** *
40404515 CAACCTTTTCATTGGATATCTGTTTCGGATATATCCTTTA
1 CAACCTTTTCATTGGATATCCATTTCGGATATACCCTTTA
* *
40404555 CAACCATTTT-ATTTGATATCCATTTCGGATATACCCTTTT
1 CAACC-TTTTCATTGGATATCCATTTCGGATATACCCTTTA
40404595 CAACCTTTTCA
1 CAACCTTTTCA
40404606 AGAATTCAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
39 4 0.09
40 36 0.82
41 4 0.09
ACGTcount: A:0.24, C:0.23, G:0.09, T:0.44
Consensus pattern (40 bp):
CAACCTTTTCATTGGATATCCATTTCGGATATACCCTTTA
Found at i:40405995 original size:8 final size:8
Alignment explanation
Indices: 40405982--40406006 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
40405972 CCACAATTAT
40405982 TCACATAA
1 TCACATAA
40405990 TCACATAA
1 TCACATAA
40405998 TCACATAA
1 TCACATAA
40406006 T
1 T
40406007 TTGCCAAAAT
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:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (8 bp):
TCACATAA
Found at i:40407442 original size:35 final size:35
Alignment explanation
Indices: 40407400--40407519 Score: 116
Period size: 35 Copynumber: 3.3 Consensus size: 35
40407390 GTATTGAATG
*
40407400 TGAGCCCAGCTTTAGTTGGATGAACCAACAATGTT
1 TGAGCCCAGCTCTAGTTGGATGAACCAACAATGTT
* * * *
40407435 TGCGCCCAGCACTAGTTGGAT-ATACCGACAATAATAAAT
1 TGAGCCCAGCTCTAGTTGGATGA-ACCAACAAT-GT---T
* *
40407474 GTGAGCCCAGCTCTAGTTGGATGAACCAATAGTGTT
1 -TGAGCCCAGCTCTAGTTGGATGAACCAACAATGTT
40407510 TGAGCCCAGC
1 TGAGCCCAGC
40407520 GTTAGTCGGA
Statistics
Matches: 67, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
34 1 0.01
35 36 0.54
36 2 0.03
39 2 0.03
40 25 0.37
41 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (35 bp):
TGAGCCCAGCTCTAGTTGGATGAACCAACAATGTT
Found at i:40407494 original size:75 final size:75
Alignment explanation
Indices: 40407366--40407538 Score: 222
Period size: 75 Copynumber: 2.3 Consensus size: 75
40407356 AGATTACGGT
* * * * *
40407366 CAGCGCTAGTCGGATTA-ACCGACAGTATTGAATGTGAGCCCAGCTTTAGTTGGATGAACCAACA
1 CAGCACTAGTCGGA-TAGACCGACAATAATAAATGTGAGCCCAGCTCTAGTTGGATGAACCAACA
*
40407430 ATGTTTGCGCC
65 ATGTTTGAGCC
* * * *
40407441 CAGCACTAGTTGGATATACCGACAATAATAAATGTGAGCCCAGCTCTAGTTGGATGAACCAATAG
1 CAGCACTAGTCGGATAGACCGACAATAATAAATGTGAGCCCAGCTCTAGTTGGATGAACCAACAA
40407506 TGTTTGAGCC
66 TGTTTGAGCC
**
40407516 CAGCGTTAGTCGGATAGACCGAC
1 CAGCACTAGTCGGATAGACCGAC
40407539 GATTGTGTGC
Statistics
Matches: 84, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
74 2 0.02
75 82 0.98
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.24
Consensus pattern (75 bp):
CAGCACTAGTCGGATAGACCGACAATAATAAATGTGAGCCCAGCTCTAGTTGGATGAACCAACAA
TGTTTGAGCC
Found at i:40416076 original size:12 final size:12
Alignment explanation
Indices: 40416059--40416091 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
40416049 AGAGCCAGAT
40416059 TCATCTTCATCC
1 TCATCTTCATCC
*
40416071 TCATCTTCGTCC
1 TCATCTTCATCC
40416083 TCATCTTCA
1 TCATCTTCA
40416092 AACTTCTCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.15, C:0.39, G:0.03, T:0.42
Consensus pattern (12 bp):
TCATCTTCATCC
Found at i:40417405 original size:24 final size:24
Alignment explanation
Indices: 40417352--40417405 Score: 56
Period size: 25 Copynumber: 2.2 Consensus size: 24
40417342 ACTCACATAT
* *
40417352 TAATTAAATAGTTAAAAATATTAT
1 TAATTAAATAGTTAAAAATATGAA
*
40417376 TAAATT-AATATTTAAAAAATATGAA
1 T-AATTAAATAGTT-AAAAATATGAA
40417401 TAATT
1 TAATT
40417406 TTTAAATTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
24 11 0.44
25 14 0.56
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.41
Consensus pattern (24 bp):
TAATTAAATAGTTAAAAATATGAA
Found at i:40419571 original size:80 final size:80
Alignment explanation
Indices: 40419436--40419598 Score: 238
Period size: 80 Copynumber: 2.0 Consensus size: 80
40419426 AAAACTAAAA
* * * * *
40419436 AAAAGTTTAAATTTGACAAATAGACGATCACGTCACAACTTACCTTATCTTTGCGTTACAATGTG
1 AAAAGTTCAAAATTGACAAATAAACGATCACATCACAACTTACCTTATCTCTGCGTTACAATGTG
*
40419501 CATATATGTAAAGCC
66 CATATATGCAAAGCC
* *
40419516 AAAAGTTCAAAATTGACAAATAAAC-AGTCATATCACAACTTACCTTATCTCTGCGTTGCAATGT
1 AAAAGTTCAAAATTGACAAATAAACGA-TCACATCACAACTTACCTTATCTCTGCGTTACAATGT
40419580 GCATATATGCAAAGCC
65 GCATATATGCAAAGCC
40419596 AAA
1 AAA
40419599 GGTGTTCCAA
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
79 1 0.01
80 73 0.99
ACGTcount: A:0.39, C:0.20, G:0.13, T:0.29
Consensus pattern (80 bp):
AAAAGTTCAAAATTGACAAATAAACGATCACATCACAACTTACCTTATCTCTGCGTTACAATGTG
CATATATGCAAAGCC
Found at i:40425381 original size:4 final size:4
Alignment explanation
Indices: 40425372--40425398 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
40425362 TTTGAAACAA
40425372 AAAC AAAC AAAC AAAC AAAC AAAC AAA
1 AAAC AAAC AAAC AAAC AAAC AAAC AAA
40425399 GCATTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:40427857 original size:20 final size:20
Alignment explanation
Indices: 40427832--40427871 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
40427822 CGTAAAATGA
*
40427832 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
40427852 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
40427872 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:40427861 original size:34 final size:35
Alignment explanation
Indices: 40427817--40427883 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
40427807 CAGTAAAATA
*
40427817 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
40427851 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
40427884 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:40427887 original size:14 final size:15
Alignment explanation
Indices: 40427811--40427887 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
40427801 GATAGCCAGT
* *
40427811 AAAAT-ATTTTCCGT
1 AAAATGATTTTCTGG
40427825 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
40427839 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
40427859 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
40427874 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
40427888 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 24 0.48
15 12 0.24
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:40429695 original size:23 final size:23
Alignment explanation
Indices: 40429665--40429709 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
40429655 GCATCCTAAT
40429665 TTTTCCACTTTTGTCAAAGATAG
1 TTTTCCACTTTTGTCAAAGATAG
*
40429688 TTTTCCACTTTTGTTAAAGATA
1 TTTTCCACTTTTGTCAAAGATA
40429710 AGTGGAGTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.27, C:0.16, G:0.11, T:0.47
Consensus pattern (23 bp):
TTTTCCACTTTTGTCAAAGATAG
Found at i:40430748 original size:18 final size:18
Alignment explanation
Indices: 40430703--40430748 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
40430693 CTAAAGGAGT
40430703 TGAGAGTTAGTGGGTTAG
1 TGAGAGTTAGTGGGTTAG
* *
40430721 TGGGATTTAGT-GGTTAG
1 TGAGAGTTAGTGGGTTAG
40430738 TGAGAGGTTAG
1 TGAGA-GTTAG
40430749 GATATATATT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
17 10 0.43
18 13 0.57
ACGTcount: A:0.22, C:0.00, G:0.43, T:0.35
Consensus pattern (18 bp):
TGAGAGTTAGTGGGTTAG
Found at i:40431340 original size:33 final size:32
Alignment explanation
Indices: 40431284--40431376 Score: 105
Period size: 33 Copynumber: 2.8 Consensus size: 32
40431274 ATGATAGTGT
*
40431284 AAGTGTGGCCGTGTGGGCCACACGGGCTAGGCC
1 AAGT-TGGCCGTGTGGGCCACACGGGCAAGGCC
* *
40431317 AAGTTGGGCGTGTTGGCCTACACGGGCAAGGCC
1 AAGTTGGCCGTGTGGGCC-ACACGGGCAAGGCC
* ** *
40431350 AATTTGGATGTGTGGGCCGCACGGGCA
1 AAGTTGGCCGTGTGGGCCACACGGGCA
40431377 TGTGGGCCCA
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
32 20 0.39
33 31 0.61
ACGTcount: A:0.17, C:0.24, G:0.41, T:0.18
Consensus pattern (32 bp):
AAGTTGGCCGTGTGGGCCACACGGGCAAGGCC
Found at i:40436916 original size:11 final size:11
Alignment explanation
Indices: 40436900--40436924 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
40436890 TTTTGTCTCA
40436900 CGCTACAGTAT
1 CGCTACAGTAT
40436911 CGCTACAGTAT
1 CGCTACAGTAT
40436922 CGC
1 CGC
40436925 ATCTCACCGT
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:0.24, C:0.32, G:0.20, T:0.24
Consensus pattern (11 bp):
CGCTACAGTAT
Found at i:40448390 original size:13 final size:13
Alignment explanation
Indices: 40448372--40448430 Score: 64
Period size: 13 Copynumber: 4.5 Consensus size: 13
40448362 CTCAAAATTT
40448372 TCAAAAGCACTTC
1 TCAAAAGCACTTC
* *
40448385 TCAAAAACACTTT
1 TCAAAAGCACTTC
* *
40448398 TCCACAGCACTTC
1 TCAAAAGCACTTC
* *
40448411 TGAAAAGCACTTT
1 TCAAAAGCACTTC
40448424 TCAAAAG
1 TCAAAAG
40448431 TAATGAAGAA
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
13 35 1.00
ACGTcount: A:0.39, C:0.27, G:0.08, T:0.25
Consensus pattern (13 bp):
TCAAAAGCACTTC
Found at i:40448398 original size:26 final size:26
Alignment explanation
Indices: 40448369--40448430 Score: 88
Period size: 26 Copynumber: 2.4 Consensus size: 26
40448359 ACACTCAAAA
40448369 TTTTCAAAAGCACTTCTCAAAAACAC
1 TTTTCAAAAGCACTTCTCAAAAACAC
* * * *
40448395 TTTTCCACAGCACTTCTGAAAAGCAC
1 TTTTCAAAAGCACTTCTCAAAAACAC
40448421 TTTTCAAAAG
1 TTTTCAAAAG
40448431 TAATGAAGAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.37, C:0.26, G:0.08, T:0.29
Consensus pattern (26 bp):
TTTTCAAAAGCACTTCTCAAAAACAC
Found at i:40454724 original size:21 final size:22
Alignment explanation
Indices: 40454682--40454726 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
40454672 AAGAAGGCAA
* **
40454682 TAGATGACTTAAATTATTTAAT
1 TAGATGACATAAATTAAATAAT
40454704 TAGATGA-ATAAATTAAATAAT
1 TAGATGACATAAATTAAATAAT
40454725 TA
1 TA
40454727 AGTCTTAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.49, C:0.02, G:0.09, T:0.40
Consensus pattern (22 bp):
TAGATGACATAAATTAAATAAT
Found at i:40465087 original size:17 final size:17
Alignment explanation
Indices: 40465065--40465102 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
40465055 AATTATAGTA
40465065 CACATGACGACAATAAT
1 CACATGACGACAATAAT
40465082 CACATGACGACAATAAT
1 CACATGACGACAATAAT
40465099 CACA
1 CACA
40465103 CAATGTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.47, C:0.26, G:0.11, T:0.16
Consensus pattern (17 bp):
CACATGACGACAATAAT
Found at i:40465185 original size:17 final size:17
Alignment explanation
Indices: 40465165--40465199 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
40465155 AATAATATGC
40465165 AAAACAATTTAAAGTAA
1 AAAACAATTTAAAGTAA
*
40465182 AAAATAATTTAAAGTAA
1 AAAACAATTTAAAGTAA
40465199 A
1 A
40465200 TAATTTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.66, C:0.03, G:0.06, T:0.26
Consensus pattern (17 bp):
AAAACAATTTAAAGTAA
Found at i:40465332 original size:2 final size:2
Alignment explanation
Indices: 40465325--40465394 Score: 103
Period size: 2 Copynumber: 36.5 Consensus size: 2
40465315 CAGTTTTAAA
40465325 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
40465367 AT A- AT A- AT A- AT A- AT AT AT ACT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT A
40465395 ATTAAGTTAA
Statistics
Matches: 63, Mismatches: 0, Indels: 10
0.86 0.00 0.14
Matches are distributed among these distances:
1 4 0.06
2 57 0.90
3 2 0.03
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:40465525 original size:2 final size:2
Alignment explanation
Indices: 40465518--40465557 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
40465508 NNNNNNNNNN
40465518 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
40465558 ATAAGAATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:40465677 original size:24 final size:23
Alignment explanation
Indices: 40465606--40465687 Score: 65
Period size: 24 Copynumber: 3.4 Consensus size: 23
40465596 AATGAATCAT
* *
40465606 ATAATAAAAAATTTAAATAAATA
1 ATAATAAAAAATTAAAACAAATA
* * * * *
40465629 GTATGTAAAACAGTTTAAAATAAATG
1 ATA-ATAAAA-A-ATTAAAACAAATA
40465655 ATAAATAAAAAATTAAAACAAATA
1 AT-AATAAAAAATTAAAACAAATA
40465679 ATAATAAAA
1 ATAATAAAA
40465688 GAGTTTTTTT
Statistics
Matches: 45, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
23 9 0.20
24 17 0.38
25 2 0.04
26 16 0.36
27 1 0.02
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.27
Consensus pattern (23 bp):
ATAATAAAAAATTAAAACAAATA
Found at i:40465687 original size:49 final size:51
Alignment explanation
Indices: 40465590--40465693 Score: 131
Period size: 50 Copynumber: 2.1 Consensus size: 51
40465580 ACATATAATG
* * * * *
40465590 GTTTAAAATGAATCATATAATAAAAAATTTAAATAAATAGTATGTAAAACA
1 GTTTAAAATAAATCATATAATAAAAAATTAAAACAAATAATATATAAAACA
* *
40465641 GTTTAAAATAAATGATA-AATAAAAAATTAAAACAAATAATA-ATAAAAGA
1 GTTTAAAATAAATCATATAATAAAAAATTAAAACAAATAATATATAAAACA
40465690 GTTT
1 GTTT
40465694 TTTTTAATAA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
49 10 0.22
50 21 0.46
51 15 0.33
ACGTcount: A:0.60, C:0.03, G:0.08, T:0.30
Consensus pattern (51 bp):
GTTTAAAATAAATCATATAATAAAAAATTAAAACAAATAATATATAAAACA
Found at i:40467394 original size:28 final size:28
Alignment explanation
Indices: 40467354--40467479 Score: 182
Period size: 28 Copynumber: 4.5 Consensus size: 28
40467344 TGACTTTCGA
*
40467354 CACTAAGTGTGCGAATTTAATTGTAAAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
40467382 CACTAAGTGTGCGAGTTTAATTGTAAAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
* *
40467410 CACTAAGTGTGCGAGTTTAATGGCAAAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
* * *
40467438 CACTAAATGTGCGAGTTTGATTAGTGAA-
1 CACTAAGTGTGCGAGTTTAATT-GTAAAG
40467466 CACTAAGTGTGCGA
1 CACTAAGTGTGCGA
40467480 ACTTATTAAA
Statistics
Matches: 88, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
28 85 0.97
29 3 0.03
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (28 bp):
CACTAAGTGTGCGAGTTTAATTGTAAAG
Found at i:40468240 original size:23 final size:23
Alignment explanation
Indices: 40468178--40468477 Score: 256
Period size: 23 Copynumber: 12.9 Consensus size: 23
40468168 TCTAAAATTG
* *
40468178 GTATATATATGCTGCCCAATTTT
1 GTATATACATGCTGTCCAATTTT
*
40468201 GGTGA-ATAAATGCTGTCCAATTTT
1 -GT-ATATACATGCTGTCCAATTTT
*
40468225 GTATATACATGCTGTCAAATTTT
1 GTATATACATGCTGTCCAATTTT
* *
40468248 GTGTATA-AGTGCTGTCCAA-ATT
1 GTATATACA-TGCTGTCCAATTTT
* * *
40468270 GCTACATATATGCTGCCCAATTTT
1 G-TATATACATGCTGTCCAATTTT
*
40468294 GGTGA-ATAAATGCTGTCCAATTTT
1 -GT-ATATACATGCTGTCCAATTTT
40468318 GTATATACATGCTGTCCAATTTT
1 GTATATACATGCTGTCCAATTTT
* *
40468341 GTGTATA-AGTGCTGTCCAA-ATT
1 GTATATACA-TGCTGTCCAATTTT
* * *
40468363 GCTACATATATGCTGCCCAATTTT
1 G-TATATACATGCTGTCCAATTTT
*
40468387 GGTGA-ATAAATGCTGTCCAATTTT
1 -GT-ATATACATGCTGTCCAATTTT
*
40468411 GTATATACATGCTGTCAAATTTT
1 GTATATACATGCTGTCCAATTTT
* * *
40468434 GTGTATA-AGTGCTGTCCAAATTG
1 GTATATACA-TGCTGTCCAATTTT
*
40468457 GTATATACATGCTGTTCAATT
1 GTATATACATGCTGTCCAATT
40468478 GCTGATGTAT
Statistics
Matches: 227, Mismatches: 31, Indels: 37
0.77 0.11 0.13
Matches are distributed among these distances:
22 12 0.05
23 148 0.65
24 62 0.27
25 5 0.02
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (23 bp):
GTATATACATGCTGTCCAATTTT
Found at i:40468477 original size:93 final size:93
Alignment explanation
Indices: 40468172--40468470 Score: 544
Period size: 93 Copynumber: 3.2 Consensus size: 93
40468162 TAATGGTCTA
* *
40468172 AAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGC
1 AAATTGCTACATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGC
40468237 TGTCAAATTTTGTGTATAAGTGCTGTCC
66 TGTCAAATTTTGTGTATAAGTGCTGTCC
40468265 AAATTGCTACATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGC
1 AAATTGCTACATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGC
*
40468330 TGTCCAATTTTGTGTATAAGTGCTGTCC
66 TGTCAAATTTTGTGTATAAGTGCTGTCC
40468358 AAATTGCTACATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGC
1 AAATTGCTACATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGC
40468423 TGTCAAATTTTGTGTATAAGTGCTGTCC
66 TGTCAAATTTTGTGTATAAGTGCTGTCC
* * *
40468451 AAATTGGTATATACATGCTG
1 AAATTGCTACATATATGCTG
40468471 TTCAATTGCT
Statistics
Matches: 199, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
93 199 1.00
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.39
Consensus pattern (93 bp):
AAATTGCTACATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGC
TGTCAAATTTTGTGTATAAGTGCTGTCC
Found at i:40471714 original size:19 final size:20
Alignment explanation
Indices: 40471673--40471714 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
40471663 GTTTCTATGT
* *
40471673 CATTGTAATATTTATTATTG
1 CATTGTAATATTTAATATAG
*
40471693 CATTGT-ATATTTAATGTAG
1 CATTGTAATATTTAATATAG
40471712 CAT
1 CAT
40471715 CACATCATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.31, C:0.07, G:0.12, T:0.50
Consensus pattern (20 bp):
CATTGTAATATTTAATATAG
Found at i:40474508 original size:27 final size:27
Alignment explanation
Indices: 40474470--40474529 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
40474460 CGCGCCACAC
* *
40474470 CCCAAAATTTCCAGTGCTCCATTTATG
1 CCCAATATTTCCACTGCTCCATTTATG
40474497 CCCAATATTTCCACTGCTCCATTTATG
1 CCCAATATTTCCACTGCTCCATTTATG
*
40474524 TCCAAT
1 CCCAAT
40474530 TGAAAATTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.25, C:0.32, G:0.08, T:0.35
Consensus pattern (27 bp):
CCCAATATTTCCACTGCTCCATTTATG
Found at i:40487993 original size:13 final size:13
Alignment explanation
Indices: 40487975--40487999 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40487965 TTTTTTTATA
40487975 TTTTTAATTAATC
1 TTTTTAATTAATC
40487988 TTTTTAATTAAT
1 TTTTTAATTAAT
40488000 AACTCTTTTA
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:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTTTAATTAATC
Found at i:40491104 original size:18 final size:18
Alignment explanation
Indices: 40491082--40491134 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
40491072 AAAAAACAAA
40491082 GATATTTGAAATATATTAT
1 GATATTTGAAATA-ATTAT
** *
40491101 -ATA-TAAAAATAATAAT
1 GATATTTGAAATAATTAT
40491117 GATATTTGAAATAATTAT
1 GATATTTGAAATAATTAT
40491135 TTGATTTTAT
Statistics
Matches: 26, Mismatches: 6, Indels: 5
0.70 0.16 0.14
Matches are distributed among these distances:
16 4 0.15
17 9 0.35
18 13 0.50
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.42
Consensus pattern (18 bp):
GATATTTGAAATAATTAT
Found at i:40496755 original size:15 final size:16
Alignment explanation
Indices: 40496737--40496774 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
40496727 AATTTATTAT
*
40496737 TTTTTAATTTT-CATA
1 TTTTTAATTTTAAATA
*
40496752 TTTTTATTTTTAAATA
1 TTTTTAATTTTAAATA
40496768 TTTTTAA
1 TTTTTAA
40496775 AACAGAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTTAATTTTAAATA
Found at i:40497276 original size:22 final size:22
Alignment explanation
Indices: 40497237--40497282 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
40497227 TATAAAGGGC
40497237 AATTATTTTAAAACAATT-ATA
1 AATTATTTTAAAACAATTAATA
* *
40497258 AATTTTTTTAAAAATAATTAATA
1 AATTATTTT-AAAACAATTAATA
40497281 AA
1 AA
40497283 AATTACATCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 8 0.38
22 8 0.38
23 5 0.24
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
AATTATTTTAAAACAATTAATA
Found at i:40497604 original size:20 final size:21
Alignment explanation
Indices: 40497581--40497619 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
40497571 TTTTAATTTG
*
40497581 ATTATATAT-TATTTATAAAA
1 ATTATATATATATATATAAAA
40497601 ATTATATATATATATATAA
1 ATTATATATATATATATAA
40497620 TTTGAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
ATTATATATATATATATAAAA
Found at i:40500263 original size:25 final size:24
Alignment explanation
Indices: 40500221--40500269 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
40500211 ATATCTATAA
* *
40500221 ATATTTTTATATACATTAATTAAAT
1 ATATTTTTAAAAACATTAA-TAAAT
*
40500246 ATATTTTTAAAAATATTAATAAAT
1 ATATTTTTAAAAACATTAATAAAT
40500270 CCAAAATAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (24 bp):
ATATTTTTAAAAACATTAATAAAT
Found at i:40507974 original size:12 final size:12
Alignment explanation
Indices: 40507953--40507988 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
40507943 ACTCAAGCCA
40507953 ATAA-ATAATAT
1 ATAATATAATAT
40507964 ATAATATAATAT
1 ATAATATAATAT
40507976 AT-ATAT-ATAT
1 ATAATATAATAT
40507986 ATA
1 ATA
40507989 TGGTGCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 6 0.26
11 8 0.35
12 9 0.39
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
ATAATATAATAT
Found at i:40511257 original size:22 final size:22
Alignment explanation
Indices: 40511232--40511284 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
40511222 GTTGTTTTGT
* *
40511232 TACTATTTTACTATTATGTTGC
1 TACTATTTTACTATTATATTAC
* *
40511254 TACTATTTCACTATTATATTAT
1 TACTATTTTACTATTATATTAC
40511276 TACTATTTT
1 TACTATTTT
40511285 GTTATTTTTG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.26, C:0.13, G:0.04, T:0.57
Consensus pattern (22 bp):
TACTATTTTACTATTATATTAC
Found at i:40512082 original size:21 final size:22
Alignment explanation
Indices: 40512049--40512090 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
40512039 AAAAACATGG
*
40512049 AAAATAAATGAACTAAATTCTT
1 AAAAGAAATGAACTAAATTCTT
40512071 AAAAGAAA-GAACTAAATTCT
1 AAAAGAAATGAACTAAATTCT
40512091 AAATATACGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.57, C:0.10, G:0.07, T:0.26
Consensus pattern (22 bp):
AAAAGAAATGAACTAAATTCTT
Found at i:40517319 original size:15 final size:15
Alignment explanation
Indices: 40517286--40517335 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
40517276 AGTGTACCAA
40517286 ATATTAT-TCCATCAAT
1 ATATTATAT-CAT-AAT
40517302 ATATTATATCATAAT
1 ATATTATATCATAAT
*
40517317 ATATTTTAT-ATAAT
1 ATATTATATCATAAT
40517331 -TATTA
1 ATATTA
40517336 AATTTAAGGA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
13 4 0.13
14 5 0.16
15 11 0.35
16 10 0.32
17 1 0.03
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (15 bp):
ATATTATATCATAAT
Found at i:40520119 original size:2 final size:2
Alignment explanation
Indices: 40520112--40520137 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
40520102 TCAAATAATC
40520112 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
40520138 TAAAGTACTA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40521165 original size:38 final size:38
Alignment explanation
Indices: 40521123--40521201 Score: 149
Period size: 38 Copynumber: 2.1 Consensus size: 38
40521113 TGTCTCAATC
40521123 TAAATAACCTAAACTGTTATATTAATTAATGAAAGGTA
1 TAAATAACCTAAACTGTTATATTAATTAATGAAAGGTA
*
40521161 TAAATAACCTAAATTGTTATATTAATTAATGAAAGGTA
1 TAAATAACCTAAACTGTTATATTAATTAATGAAAGGTA
40521199 TAA
1 TAA
40521202 TAATTTATTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.48, C:0.06, G:0.10, T:0.35
Consensus pattern (38 bp):
TAAATAACCTAAACTGTTATATTAATTAATGAAAGGTA
Found at i:40521200 original size:19 final size:19
Alignment explanation
Indices: 40521140--40521206 Score: 52
Period size: 19 Copynumber: 3.5 Consensus size: 19
40521130 CCTAAACTGT
40521140 TATATTAATTAATGAAAGG
1 TATATTAATTAATGAAAGG
*
40521159 TATA--AA-TAACCT-AAATTGT
1 TATATTAATTAA--TGAAA--GG
40521178 TATATTAATTAATGAAAGG
1 TATATTAATTAATGAAAGG
*
40521197 TATAATAATT
1 TATATTAATT
40521207 TATTTGACCC
Statistics
Matches: 37, Mismatches: 3, Indels: 16
0.66 0.05 0.29
Matches are distributed among these distances:
16 3 0.08
17 5 0.14
18 1 0.03
19 19 0.51
20 1 0.03
21 5 0.14
22 3 0.08
ACGTcount: A:0.48, C:0.03, G:0.10, T:0.39
Consensus pattern (19 bp):
TATATTAATTAATGAAAGG
Found at i:40529327 original size:20 final size:20
Alignment explanation
Indices: 40529302--40529364 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
40529292 AGTTATTAAA
40529302 GTAAACAAAAACTACAATTT
1 GTAAACAAAAACTACAATTT
* ***
40529322 GTAAACTAAAAATTGA-AAAAA
1 GTAAAC-AAAAACT-ACAATTT
*
40529343 GTAAGCAAAAACTACAATTT
1 GTAAACAAAAACTACAATTT
40529363 GT
1 GT
40529365 TTTCTCCATG
Statistics
Matches: 31, Mismatches: 9, Indels: 6
0.67 0.20 0.13
Matches are distributed among these distances:
19 1 0.03
20 16 0.52
21 13 0.42
22 1 0.03
ACGTcount: A:0.56, C:0.11, G:0.10, T:0.24
Consensus pattern (20 bp):
GTAAACAAAAACTACAATTT
Found at i:40541445 original size:22 final size:20
Alignment explanation
Indices: 40541418--40541458 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
40541408 AATAACTTCC
40541418 AAAAAATAGATTGATTTTCTAA
1 AAAAAATAGA-T-ATTTTCTAA
*
40541440 AAAAAATTGATATTTTCTA
1 AAAAAATAGATATTTTCTA
40541459 GTGTTTGGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 1 0.06
22 9 0.50
ACGTcount: A:0.49, C:0.05, G:0.07, T:0.39
Consensus pattern (20 bp):
AAAAAATAGATATTTTCTAA
Found at i:40541797 original size:23 final size:23
Alignment explanation
Indices: 40541750--40541798 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
40541740 TGATCTAAAC
*
40541750 AAATACTCATATTTATATAATTA
1 AAATACTCATATTTATATAAGTA
*
40541773 AAATATTCATATTT-TATACAGTA
1 AAATACTCATATTTATATA-AGTA
40541796 AAA
1 AAA
40541799 CATTTAGTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 4 0.17
23 19 0.83
ACGTcount: A:0.49, C:0.08, G:0.02, T:0.41
Consensus pattern (23 bp):
AAATACTCATATTTATATAAGTA
Found at i:40541882 original size:23 final size:24
Alignment explanation
Indices: 40541837--40541896 Score: 70
Period size: 23 Copynumber: 2.5 Consensus size: 24
40541827 AATATATATT
*
40541837 TATTATTAAAATATTAATAT-AAA
1 TATTATTAAAATAATAATATAAAA
*
40541860 TATTATT-AAATAATATATTTAAAA
1 TATTATTAAAATAATA-ATATAAAA
40541884 TATTATTTAAAAT
1 TATTA-TTAAAAT
40541897 TTAAAATCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 7 0.23
23 10 0.32
24 8 0.26
25 2 0.06
26 4 0.13
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
TATTATTAAAATAATAATATAAAA
Found at i:40541890 original size:12 final size:12
Alignment explanation
Indices: 40541837--40541896 Score: 63
Period size: 12 Copynumber: 5.1 Consensus size: 12
40541827 AATATATATT
40541837 TATTA-TTAAAA
1 TATTATTTAAAA
*
40541848 TATTA-ATATAAA
1 TATTATTTA-AAA
*
40541860 TATTATTAAATAA
1 TATTATTTAA-AA
40541873 TA-TATTTAAAA
1 TATTATTTAAAA
40541884 TATTATTTAAAA
1 TATTATTTAAAA
40541896 T
1 T
40541897 TTAAAATCAT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
11 11 0.27
12 25 0.61
13 5 0.12
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
TATTATTTAAAA
Found at i:40541918 original size:22 final size:19
Alignment explanation
Indices: 40541876--40541921 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 19
40541866 TAAATAATAT
40541876 ATTTAAAATATTATTTAAA
1 ATTTAAAATATTATTTAAA
40541895 ATTTAAAATCATTACTGTTAAA
1 ATTTAAAAT-ATTA-T-TTAAA
40541917 ATTTA
1 ATTTA
40541922 TTATTAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 9 0.38
20 4 0.17
21 1 0.04
22 10 0.42
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (19 bp):
ATTTAAAATATTATTTAAA
Found at i:40541936 original size:18 final size:19
Alignment explanation
Indices: 40541913--40541952 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
40541903 TCATTACTGT
*
40541913 TAAAATT-TATTATTAAAA
1 TAAAATTGTAATATTAAAA
*
40541931 TAAAATTGTAATATTTAAA
1 TAAAATTGTAATATTAAAA
40541950 TAA
1 TAA
40541953 TTTATTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (19 bp):
TAAAATTGTAATATTAAAA
Found at i:40542039 original size:21 final size:22
Alignment explanation
Indices: 40541999--40542042 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
40541989 ATTTTTAATA
40541999 ATATTAAAAATTATAATATTTT
1 ATATTAAAAATTATAATATTTT
* *
40542021 ATATTAATATTTA-AATATTTT
1 ATATTAAAAATTATAATATTTT
40542042 A
1 A
40542043 AAAAATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
ATATTAAAAATTATAATATTTT
Found at i:40544567 original size:86 final size:84
Alignment explanation
Indices: 40544424--40544583 Score: 216
Period size: 86 Copynumber: 1.9 Consensus size: 84
40544414 ATATCGAACA
* *
40544424 ATGCCAACGTCCCAGACGTGGTCTTACATGCAATCTCATATCGATGCCACTGTCCCAGACAG-GG
1 ATGCCAACGTCCCAGACATGGTCTTACACGCAATCTCATATCGATGCCACTGTCCCAGAC-GTGG
40544488 TCTTACACGAATCAAATACG
65 TCTTACACGAATCAAATACG
* * * *
40544508 ATGCCAATGTCCTAGACATGGTCTTACACGTAATCATATATATCGATGCCA-TCGTCCCAGACGT
1 ATGCCAACGTCCCAGACATGGTCTTACACGCAATC-T-CATATCGATGCCACT-GTCCCAGACGT
40544572 GGTCTTACACGA
63 GGTCTTACACGA
40544584 GAACACATAT
Statistics
Matches: 66, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
84 30 0.45
85 3 0.05
86 33 0.50
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (84 bp):
ATGCCAACGTCCCAGACATGGTCTTACACGCAATCTCATATCGATGCCACTGTCCCAGACGTGGT
CTTACACGAATCAAATACG
Found at i:40545899 original size:23 final size:23
Alignment explanation
Indices: 40545873--40545927 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
40545863 AGCCCATTTA
*
40545873 AGCTTCCTGATAGGCTCTTTGTG
1 AGCTTCCTGATAGGCTCTTTATG
*
40545896 AGCTT-CTCGATATGCTCTTTATG
1 AGCTTCCT-GATAGGCTCTTTATG
*
40545919 AGTTTCCTG
1 AGCTTCCTG
40545928 TTATATGGCT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 2 0.07
23 23 0.85
24 2 0.07
ACGTcount: A:0.15, C:0.22, G:0.22, T:0.42
Consensus pattern (23 bp):
AGCTTCCTGATAGGCTCTTTATG
Found at i:40548055 original size:11 final size:11
Alignment explanation
Indices: 40548041--40548084 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
40548031 AGATAAATAT
40548041 TATTTTATTAA
1 TATTTTATTAA
*
40548052 TATTTTAAATATA
1 TATTTT-ATTA-A
*
40548065 TATTTTATTAT
1 TATTTTATTAA
40548076 TATTTTATT
1 TATTTTATT
40548085 TAGTATTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
11 15 0.54
12 6 0.21
13 7 0.25
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:40548068 original size:24 final size:23
Alignment explanation
Indices: 40548034--40548082 Score: 80
Period size: 24 Copynumber: 2.1 Consensus size: 23
40548024 TTTAATTAGA
40548034 TAAATATTATTTTATTAATATTT
1 TAAATATTATTTTATTAATATTT
*
40548057 TAAATATATATTTTATTATTATTT
1 TAAATAT-TATTTTATTAATATTT
40548081 TA
1 TA
40548083 TTTAGTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 7 0.29
24 17 0.71
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (23 bp):
TAAATATTATTTTATTAATATTT
Found at i:40549460 original size:207 final size:207
Alignment explanation
Indices: 40549105--40549521 Score: 798
Period size: 207 Copynumber: 2.0 Consensus size: 207
40549095 GTAATAGTGG
40549105 AATTATAGATAATGTTACATATAAGCATGTTATATACATTAAGGATGTGGAATGGACAGGAGGAG
1 AATTATAGATAATGTTACATATAAGCATGTTATATACATTAAGGATGTGGAATGGACAGGAGGAG
40549170 GAAAATATATATGAATATTCAACTAGCATGGGTTTACATTAAAAATGGCTAATTTGCATGTTTTA
66 GAAAATATATATGAATATTCAACTAGCATGGGTTTACATTAAAAATGGCTAATTTGCATGTTTTA
*
40549235 GGCTCAGGGACTAAATTGAATAAAAGTAAAACTTTAGGGGTAATTTTGTAAAAATGTCAAAAAAC
131 GGCCCAGGGACTAAATTGAATAAAAGTAAAACTTTAGGGGTAATTTTGTAAAAATGTCAAAAAAC
*
40549300 CAAATTGTAGGA
196 CAAATTGCAGGA
*
40549312 AATTATAGATAATGTTACATATAAGCATGTTATATACATTAAGGATGTGGAATGGCCAGGAGGAG
1 AATTATAGATAATGTTACATATAAGCATGTTATATACATTAAGGATGTGGAATGGACAGGAGGAG
*
40549377 GAAAATATATATGAATATTCAGCTAGCATGGGTTTACATTAAAAATGGCTAATTTGCATGTTTTA
66 GAAAATATATATGAATATTCAACTAGCATGGGTTTACATTAAAAATGGCTAATTTGCATGTTTTA
40549442 GGCCCAGGGACTAAATTGAATAAAAGTAAAACTTTAGGGGTAATTTTGTAAAAATGTCAAAAAAC
131 GGCCCAGGGACTAAATTGAATAAAAGTAAAACTTTAGGGGTAATTTTGTAAAAATGTCAAAAAAC
40549507 CAAATTGCAGGA
196 CAAATTGCAGGA
40549519 AAT
1 AAT
40549522 GAATTTTTTT
Statistics
Matches: 206, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
207 206 1.00
ACGTcount: A:0.41, C:0.09, G:0.20, T:0.30
Consensus pattern (207 bp):
AATTATAGATAATGTTACATATAAGCATGTTATATACATTAAGGATGTGGAATGGACAGGAGGAG
GAAAATATATATGAATATTCAACTAGCATGGGTTTACATTAAAAATGGCTAATTTGCATGTTTTA
GGCCCAGGGACTAAATTGAATAAAAGTAAAACTTTAGGGGTAATTTTGTAAAAATGTCAAAAAAC
CAAATTGCAGGA
Found at i:40551797 original size:105 final size:105
Alignment explanation
Indices: 40551615--40551824 Score: 402
Period size: 105 Copynumber: 2.0 Consensus size: 105
40551605 TGGGTTATTC
40551615 TTGATACGTATAGATTTCATATTTGAAATGAATTAATATGATTAAAGTTTATATGAGCTTACTAA
1 TTGATACGTATAGATTTCATATTTGAAATGAATTAATATGATTAAAGTTTATATGAGCTTACTAA
40551680 GCATTTGTTGCTTACGTAGTTGTTTTCCAGTACTTTTCAG
66 GCATTTGTTGCTTACGTAGTTGTTTTCCAGTACTTTTCAG
40551720 TTGATACGTATAGATTTCATATTTGAAATGAATTAATATGATTAAAGTTTATATGAGCTTACTAA
1 TTGATACGTATAGATTTCATATTTGAAATGAATTAATATGATTAAAGTTTATATGAGCTTACTAA
**
40551785 GCATTTGTTGCTTACGTAGTTGTTTTCCTTTACTTTTCAG
66 GCATTTGTTGCTTACGTAGTTGTTTTCCAGTACTTTTCAG
40551825 ATTATCGAAA
Statistics
Matches: 103, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
105 103 1.00
ACGTcount: A:0.29, C:0.10, G:0.16, T:0.45
Consensus pattern (105 bp):
TTGATACGTATAGATTTCATATTTGAAATGAATTAATATGATTAAAGTTTATATGAGCTTACTAA
GCATTTGTTGCTTACGTAGTTGTTTTCCAGTACTTTTCAG
Found at i:40554201 original size:35 final size:35
Alignment explanation
Indices: 40554145--40554214 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
40554135 TATATATACT
*
40554145 AAATAAAATTAATAAAATAATAAAATATTATTTAA
1 AAATAAAATTAATAAAATAATAAAATAATATTTAA
* * *
40554180 AAATCAAATTAA-AATATTAATAAACTAATATTTAA
1 AAATAAAATTAATAA-AATAATAAAATAATATTTAA
40554215 TTAATTAATC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
34 2 0.07
35 28 0.93
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (35 bp):
AAATAAAATTAATAAAATAATAAAATAATATTTAA
Found at i:40554708 original size:23 final size:23
Alignment explanation
Indices: 40554650--40554700 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
40554640 ACCTATTTTC
* *
40554650 TTACTGTAGTAATTTTCGGGGTA
1 TTACAGTAGTAATTTTCGGGATA
40554673 TTACAGTAGTAATTTTCGGGATA
1 TTACAGTAGTAATTTTCGGGATA
40554696 TTACA
1 TTACA
40554701 ATTATAATCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.27, C:0.10, G:0.22, T:0.41
Consensus pattern (23 bp):
TTACAGTAGTAATTTTCGGGATA
Found at i:40557331 original size:2 final size:2
Alignment explanation
Indices: 40557318--40557370 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
40557308 CAAGCCTTAA
*
40557318 AC AC AC AT AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
40557360 AC AC AC AC AC A
1 AC AC AC AC AC A
40557371 TATATGAGGC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.47, G:0.00, T:0.02
Consensus pattern (2 bp):
AC
Found at i:40559056 original size:140 final size:139
Alignment explanation
Indices: 40558900--40559178 Score: 515
Period size: 139 Copynumber: 2.0 Consensus size: 139
40558890 TGTGAAATTT
40558900 AATTTAATAATATAAATAGTAGATATAAATAAAATTATTACCATTTATGTTTAGTGA-TTTTTTT
1 AATTTAATAATATAAATAGTAGATATAAATAAAATTATTACCATTTATGTTTAGTGATTTTTTTT
*
40558964 TGGATAATTTTGATTTTTTTTATTTGAGAGTAAAGGGTGATAAGTAAAAGTTTAGGGGGAAAATA
66 TGGATAATTTTGA--TTTTTTATTTGAGAGTAAAGGGTGAGAAGTAAAAGTTTAGGGGGAAAATA
40559029 AAAAGTTTTGG
129 AAAAGTTTTGG
*
40559040 AATTTAATAATATAAATAGTAGATATAAATAAAATTATTACTATTTATGTTTAGTGATTTTTTTT
1 AATTTAATAATATAAATAGTAGATATAAATAAAATTATTACCATTTATGTTTAGTGATTTTTTTT
40559105 TGGATAATTTTGATTTTTTATTTGAGAGTAAAGGGTGAGAAGTAAAAGTTTAGGGGGAAAATAAA
66 TGGATAATTTTGATTTTTTATTTGAGAGTAAAGGGTGAGAAGTAAAAGTTTAGGGGGAAAATAAA
40559170 AAGTTTTGG
131 AAGTTTTGG
40559179 GGAATAAAAG
Statistics
Matches: 136, Mismatches: 2, Indels: 3
0.96 0.01 0.02
Matches are distributed among these distances:
139 60 0.44
140 56 0.41
141 20 0.15
ACGTcount: A:0.39, C:0.01, G:0.18, T:0.42
Consensus pattern (139 bp):
AATTTAATAATATAAATAGTAGATATAAATAAAATTATTACCATTTATGTTTAGTGATTTTTTTT
TGGATAATTTTGATTTTTTATTTGAGAGTAAAGGGTGAGAAGTAAAAGTTTAGGGGGAAAATAAA
AAGTTTTGG
Found at i:40559894 original size:31 final size:30
Alignment explanation
Indices: 40559853--40559927 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 30
40559843 TTTTAATTTG
* *
40559853 ATCAAATTTAATCTTAGTATTTTTTGAATTA
1 ATCAATTTTAATCTTA-TACTTTTTGAATTA
*
40559884 ATCAATTTTAATTCTTATACTTTTTGAATTT
1 ATCAATTTTAA-TCTTATACTTTTTGAATTA
* *
40559915 TTAAATTTTAATC
1 ATCAATTTTAATC
40559928 CTAATCTAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
30 2 0.05
31 31 0.82
32 5 0.13
ACGTcount: A:0.33, C:0.08, G:0.04, T:0.55
Consensus pattern (30 bp):
ATCAATTTTAATCTTATACTTTTTGAATTA
Found at i:40563961 original size:19 final size:20
Alignment explanation
Indices: 40563933--40563971 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
40563923 ATATCTAAAT
40563933 TACCACACACACATA-TATA
1 TACCACACACACATACTATA
*
40563952 TACCATACACACATACTATA
1 TACCACACACACATACTATA
40563972 AAACTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.46, C:0.31, G:0.00, T:0.23
Consensus pattern (20 bp):
TACCACACACACATACTATA
Found at i:40567510 original size:3 final size:3
Alignment explanation
Indices: 40567502--40567526 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
40567492 TTTTATATTT
40567502 TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC T
40567527 CTTAAGCTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:40571148 original size:42 final size:42
Alignment explanation
Indices: 40571062--40571162 Score: 105
Period size: 42 Copynumber: 2.4 Consensus size: 42
40571052 GATTTATTCA
* * * * * *
40571062 ATGATGCACTTATGTGTCAGTATAATTGCTTTGGTATATTCG
1 ATGATGCACTTGTGTGCCAATATAATTGCTTTGATACATCCG
*
40571104 ATGATGCACTTGTGTGCCAATATATTTG-TTTCGATACATCCG
1 ATGATGCACTTGTGTGCCAATATAATTGCTTT-GATACATCCG
*
40571146 ATGATGTACTATGTGTG
1 ATGATGCACT-TGTGTG
40571163 TTAGTATAAT
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
41 3 0.06
42 40 0.82
43 6 0.12
ACGTcount: A:0.24, C:0.14, G:0.22, T:0.41
Consensus pattern (42 bp):
ATGATGCACTTGTGTGCCAATATAATTGCTTTGATACATCCG
Found at i:40576448 original size:15 final size:15
Alignment explanation
Indices: 40576428--40576457 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
40576418 GCATTCGATC
40576428 GAATCAAATCGAATT
1 GAATCAAATCGAATT
40576443 GAATCAAATCGAATT
1 GAATCAAATCGAATT
40576458 AAAATTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.27
Consensus pattern (15 bp):
GAATCAAATCGAATT
Found at i:40577465 original size:9 final size:9
Alignment explanation
Indices: 40577451--40577487 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
40577441 CATAGTTTGA
40577451 TATTCGAAT
1 TATTCGAAT
40577460 TATTCGAAT
1 TATTCGAAT
*
40577469 TATTCGAGT
1 TATTCGAAT
40577478 TATTCGAAT
1 TATTCGAAT
40577487 T
1 T
40577488 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:40578692 original size:17 final size:18
Alignment explanation
Indices: 40578665--40578717 Score: 63
Period size: 17 Copynumber: 2.9 Consensus size: 18
40578655 GTCAGTGAGC
*
40578665 AATTTTGGTATCAATAAA
1 AATTATGGTATCAATAAA
*
40578683 AA-TATGGTATCGATAAA
1 AATTATGGTATCAATAAA
40578700 AATTGTATGGTATCAATA
1 AA-T-TATGGTATCAATA
40578718 CGTTTTGTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 15 0.52
18 2 0.07
20 12 0.41
ACGTcount: A:0.43, C:0.06, G:0.15, T:0.36
Consensus pattern (18 bp):
AATTATGGTATCAATAAA
Found at i:40578939 original size:15 final size:16
Alignment explanation
Indices: 40578908--40578941 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
40578898 AATTTCTTTG
40578908 TTCAAAAACAAATTTTA
1 TTCAAAAAC-AATTTTA
40578925 TTCAAAAAC-ATTTTA
1 TTCAAAAACAATTTTA
40578940 TT
1 TT
40578942 TGTTATATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
17 9 0.53
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (16 bp):
TTCAAAAACAATTTTA
Found at i:40578952 original size:23 final size:21
Alignment explanation
Indices: 40578922--40578963 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
40578912 AAAACAAATT
*
40578922 TTATTCAAAAACATTTTATTTG
1 TTATTC-AAAACAATTTATTTG
40578944 TTATATCAAAACAATTTATT
1 TTAT-TCAAAACAATTTATT
40578964 AAATAAAGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.40, C:0.10, G:0.02, T:0.48
Consensus pattern (21 bp):
TTATTCAAAACAATTTATTTG
Found at i:40581841 original size:25 final size:25
Alignment explanation
Indices: 40581780--40581830 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
40581770 AATAACTTCC
40581780 TTATTTTTAAATATTGTTTAATTAT
1 TTATTTTTAAATATTGTTTAATTAT
40581805 TTATTTTTAAATA-T-TTTAA-TAT
1 TTATTTTTAAATATTGTTTAATTAT
40581827 TTAT
1 TTAT
40581831 GATTCTTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 7 0.27
23 5 0.19
24 1 0.04
25 13 0.50
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (25 bp):
TTATTTTTAAATATTGTTTAATTAT
Found at i:40591346 original size:17 final size:16
Alignment explanation
Indices: 40591322--40591365 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
40591312 CAATAGTCAG
40591322 TCCTTCACCAACCTCC
1 TCCTTCACCAACCTCC
**
40591338 TCACTTCACTCCTCCTCC
1 TC-CTTCAC-CAACCTCC
40591356 TCCTTCACCA
1 TCCTTCACCA
40591366 CCCTATCTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 3 0.13
17 12 0.52
18 8 0.35
ACGTcount: A:0.16, C:0.55, G:0.00, T:0.30
Consensus pattern (16 bp):
TCCTTCACCAACCTCC
Found at i:40612846 original size:21 final size:21
Alignment explanation
Indices: 40612820--40612862 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
40612810 TTGTATGTCT
*
40612820 ACAATTACATTCTCGTTAGGC
1 ACAATTACATTCTCCTTAGGC
*
40612841 ACAATTTCATTCTCCTTAGGC
1 ACAATTACATTCTCCTTAGGC
40612862 A
1 A
40612863 AAATATCAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.35
Consensus pattern (21 bp):
ACAATTACATTCTCCTTAGGC
Found at i:40618313 original size:14 final size:13
Alignment explanation
Indices: 40618286--40618311 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40618276 TATGATGTGG
40618286 TGTTTTTAAAAAA
1 TGTTTTTAAAAAA
40618299 TGTTTTTAAAAAA
1 TGTTTTTAAAAAA
40618312 ATTATTACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
TGTTTTTAAAAAA
Found at i:40634939 original size:21 final size:21
Alignment explanation
Indices: 40634921--40634993 Score: 75
Period size: 21 Copynumber: 3.7 Consensus size: 21
40634911 ATATTTAATT
40634921 AATT-TTTT-AAAATTATTAA
1 AATTATTTTAAAAATTATTAA
*
40634940 AATTATTTTAAAAATTATGAA
1 AATTATTTTAAAAATTATTAA
* *
40634961 AATATATTTTTAATATT-TT-A
1 AAT-TATTTTAAAAATTATTAA
40634981 AATT-TTTTAAAAA
1 AATTATTTTAAAAA
40634994 GTGATCAAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
18 7 0.16
19 5 0.11
20 8 0.18
21 14 0.31
22 11 0.24
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (21 bp):
AATTATTTTAAAAATTATTAA
Found at i:40637802 original size:22 final size:22
Alignment explanation
Indices: 40637740--40637805 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
40637730 ATTGTTCAAA
* **
40637740 CATGAGAGCTTAGTACGTGAAA
1 CATGAGAGCTTAGTACGTTAGC
40637762 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
40637784 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
40637806 AAGAATACAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.30, C:0.17, G:0.27, T:0.26
Consensus pattern (22 bp):
CATGAGAGCTTAGTACGTTAGC
Found at i:40638175 original size:31 final size:31
Alignment explanation
Indices: 40638137--40638245 Score: 130
Period size: 31 Copynumber: 3.3 Consensus size: 31
40638127 CCAACCCAAT
40638137 TACCCAATCCAATAAAACTAAAACTAAAGTC
1 TACCCAATCCAATAAAACTAAAACTAAAGTC
40638168 TACCCAATTACCCAACCCAATAAAACTAAAACTAAAGTC
1 TACCCAA-T-------CCAATAAAACTAAAACTAAAGTC
40638207 TACCCAA-CTCAATAAAACTAAAACTAAAGTC
1 TACCCAATC-CAATAAAACTAAAACTAAAGTC
40638238 TACCCAAT
1 TACCCAAT
40638246 TACCAACCCA
Statistics
Matches: 68, Mismatches: 0, Indels: 19
0.78 0.00 0.22
Matches are distributed among these distances:
30 1 0.01
31 36 0.53
32 1 0.01
39 30 0.44
ACGTcount: A:0.50, C:0.28, G:0.03, T:0.19
Consensus pattern (31 bp):
TACCCAATCCAATAAAACTAAAACTAAAGTC
Found at i:40638175 original size:39 final size:38
Alignment explanation
Indices: 40638130--40638277 Score: 202
Period size: 39 Copynumber: 4.0 Consensus size: 38
40638120 ATCCAACCCA
*
40638130 ACCCAATTACCCAATCCAATAAAACTAAAACTAAAGTCT
1 ACCCAATTA-CCAACCCAATAAAACTAAAACTAAAGTCT
40638169 ACCCAATTACCCAACCCAATAAAACTAAAACTAAAGTCT
1 ACCCAATTA-CCAACCCAATAAAACTAAAACTAAAGTCT
*
40638208 A--C-----CCAACTCAATAAAACTAAAACTAAAGTCT
1 ACCCAATTACCAACCCAATAAAACTAAAACTAAAGTCT
*
40638239 ACCCAATTACCAACCCAATAAAAATAAAACTAAAGTCT
1 ACCCAATTACCAACCCAATAAAACTAAAACTAAAGTCT
40638277 A
1 A
40638278 ACTCTTAACT
Statistics
Matches: 98, Mismatches: 4, Indels: 15
0.84 0.03 0.13
Matches are distributed among these distances:
31 29 0.30
33 1 0.01
37 1 0.01
38 28 0.29
39 39 0.40
ACGTcount: A:0.51, C:0.28, G:0.03, T:0.19
Consensus pattern (38 bp):
ACCCAATTACCAACCCAATAAAACTAAAACTAAAGTCT
Found at i:40638220 original size:70 final size:69
Alignment explanation
Indices: 40638137--40638277 Score: 248
Period size: 70 Copynumber: 2.0 Consensus size: 69
40638127 CCAACCCAAT
*
40638137 TACCCAATCCAATAAAACTAAAACTAAAGTCTACCCAATTACCCAACCCAATAAAACTAAAACTA
1 TACCCAATCCAATAAAACTAAAACTAAAGTCTACCCAATTA-CCAACCCAATAAAAATAAAACTA
40638202 AAGTC
65 AAGTC
40638207 TACCCAA-CTCAATAAAACTAAAACTAAAGTCTACCCAATTACCAACCCAATAAAAATAAAACTA
1 TACCCAATC-CAATAAAACTAAAACTAAAGTCTACCCAATTACCAACCCAATAAAAATAAAACTA
40638271 AAGTC
65 AAGTC
40638276 TA
1 TA
40638278 ACTCTTAACT
Statistics
Matches: 69, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
69 30 0.43
70 39 0.57
ACGTcount: A:0.51, C:0.27, G:0.03, T:0.19
Consensus pattern (69 bp):
TACCCAATCCAATAAAACTAAAACTAAAGTCTACCCAATTACCAACCCAATAAAAATAAAACTAA
AGTC
Found at i:40638433 original size:17 final size:17
Alignment explanation
Indices: 40638413--40638475 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
40638403 TAATTTCAAG
40638413 AATTATGTAATGTTTTT
1 AATTATGTAATGTTTTT
* ***
40638430 AATTATGTAGTGATTCAA
1 AATTATGTAATG-TTTTT
*
40638448 AGACTTATGTAATATTTTT
1 A-A-TTATGTAATGTTTTT
40638467 AATTATGTA
1 AATTATGTA
40638476 GTGATTCAAT
Statistics
Matches: 34, Mismatches: 9, Indels: 6
0.69 0.18 0.12
Matches are distributed among these distances:
17 18 0.53
18 4 0.12
19 4 0.12
20 8 0.24
ACGTcount: A:0.35, C:0.03, G:0.13, T:0.49
Consensus pattern (17 bp):
AATTATGTAATGTTTTT
Found at i:40638456 original size:37 final size:37
Alignment explanation
Indices: 40638410--40638484 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
40638400 TGTTAATTTC
*
40638410 AAGAATTATGTAATGTTTTTAATTATGTAGTGATTCA
1 AAGAATTATGTAATATTTTTAATTATGTAGTGATTCA
*
40638447 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
1 AAGAATTATGTAATATTTTTAATTATGTAGTGATTCA
40638484 A
1 A
40638485 TTCGGGTAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.36, C:0.04, G:0.15, T:0.45
Consensus pattern (37 bp):
AAGAATTATGTAATATTTTTAATTATGTAGTGATTCA
Found at i:40638497 original size:9 final size:9
Alignment explanation
Indices: 40638483--40638513 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
40638473 GTAGTGATTC
*
40638483 AATTCGGGT
1 AATTCGGTT
40638492 AATTCGGTT
1 AATTCGGTT
40638501 AATTCGGTT
1 AATTCGGTT
40638510 AATT
1 AATT
40638514 TTTAACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.26, C:0.10, G:0.23, T:0.42
Consensus pattern (9 bp):
AATTCGGTT
Found at i:40638859 original size:12 final size:12
Alignment explanation
Indices: 40638842--40638866 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40638832 AATAGTGCAA
40638842 ATGATAATAAAT
1 ATGATAATAAAT
40638854 ATGATAATAAAT
1 ATGATAATAAAT
40638866 A
1 A
40638867 CAAAAAGAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (12 bp):
ATGATAATAAAT
Found at i:40639736 original size:40 final size:41
Alignment explanation
Indices: 40639677--40639768 Score: 123
Period size: 44 Copynumber: 2.2 Consensus size: 41
40639667 GATTCCCTTC
* *
40639677 CATTTTCTGTCT-GTTTGTTTCTGGTTAATCCGGGTAACTT
1 CATTTTCTGTCTGGCTTGTTTCTAGTTAATCCGGGTAACTT
*
40639717 CATTTTCTGTTTGGCTGTTTGTTTCTAGTTAATCCGGGTAACTT
1 CATTTTCTGTCTGGC---TTGTTTCTAGTTAATCCGGGTAACTT
40639761 CATTTTCT
1 CATTTTCT
40639769 TCTTCTTCTT
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
40 11 0.24
41 1 0.02
44 33 0.73
ACGTcount: A:0.13, C:0.17, G:0.18, T:0.51
Consensus pattern (41 bp):
CATTTTCTGTCTGGCTTGTTTCTAGTTAATCCGGGTAACTT
Found at i:40641016 original size:16 final size:15
Alignment explanation
Indices: 40640997--40641038 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 15
40640987 TTTAATCTCA
40640997 TCTTTTTTTTCTTTTT
1 TCTTTTTTTT-TTTTT
40641013 TCTTTTTTTTTTTTT
1 TCTTTTTTTTTTTTT
40641028 TGCTTTGTTTT
1 T-CTTT-TTTT
40641039 ATTGCAGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.25
16 14 0.58
17 4 0.17
ACGTcount: A:0.00, C:0.10, G:0.05, T:0.86
Consensus pattern (15 bp):
TCTTTTTTTTTTTTT
Found at i:40641020 original size:15 final size:16
Alignment explanation
Indices: 40641000--40641038 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
40640990 AATCTCATCT
40641000 TTTTTTTCTTTTTT-C
1 TTTTTTTCTTTTTTGC
*
40641015 TTTTTTTTTTTTTTGC
1 TTTTTTTCTTTTTTGC
40641031 TTTGTTTT
1 TTT-TTTT
40641039 ATTGCAGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.62
16 4 0.19
17 4 0.19
ACGTcount: A:0.00, C:0.08, G:0.05, T:0.87
Consensus pattern (16 bp):
TTTTTTTCTTTTTTGC
Found at i:40643728 original size:20 final size:20
Alignment explanation
Indices: 40643705--40643767 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
40643695 TGTAATATTC
40643705 CAATTTTACCCTTAATTCTT
1 CAATTTTACCCTTAATTCTT
* * *
40643725 CAATTCT--CC-TGATTTTT
1 CAATTTTACCCTTAATTCTT
*
40643742 CCAATTTTACCCTTATTTCTT
1 -CAATTTTACCCTTAATTCTT
40643763 CAATT
1 CAATT
40643768 CTCCTGATTT
Statistics
Matches: 32, Mismatches: 7, Indels: 8
0.68 0.15 0.17
Matches are distributed among these distances:
17 6 0.19
18 8 0.25
20 13 0.41
21 5 0.16
ACGTcount: A:0.22, C:0.25, G:0.02, T:0.51
Consensus pattern (20 bp):
CAATTTTACCCTTAATTCTT
Found at i:40643753 original size:38 final size:38
Alignment explanation
Indices: 40643702--40643780 Score: 149
Period size: 38 Copynumber: 2.1 Consensus size: 38
40643692 NTTTGTAATA
40643702 TTCCAATTTTACCCTTAATTCTTCAATTCTCCTGATTT
1 TTCCAATTTTACCCTTAATTCTTCAATTCTCCTGATTT
*
40643740 TTCCAATTTTACCCTTATTTCTTCAATTCTCCTGATTT
1 TTCCAATTTTACCCTTAATTCTTCAATTCTCCTGATTT
40643778 TTC
1 TTC
40643781 TCAGCGTATG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.19, C:0.27, G:0.03, T:0.52
Consensus pattern (38 bp):
TTCCAATTTTACCCTTAATTCTTCAATTCTCCTGATTT
Found at i:40643777 original size:18 final size:18
Alignment explanation
Indices: 40643720--40643777 Score: 64
Period size: 18 Copynumber: 3.1 Consensus size: 18
40643710 TTACCCTTAA
40643720 TTCTTCAATTCTCCTGAT
1 TTCTTCAATTCTCCTGAT
* *
40643738 TT-TTCCAATTTTACCCTTAT
1 TTCTT-CAATTCT--CCTGAT
40643758 TTCTTCAATTCTCCTGAT
1 TTCTTCAATTCTCCTGAT
40643776 TT
1 TT
40643778 TTCTCAGCGT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
17 2 0.06
18 15 0.47
20 13 0.41
21 2 0.06
ACGTcount: A:0.17, C:0.26, G:0.03, T:0.53
Consensus pattern (18 bp):
TTCTTCAATTCTCCTGAT
Found at i:40643780 original size:20 final size:20
Alignment explanation
Indices: 40643720--40643781 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
40643710 TTACCCTTAA
40643720 TTCTTCAATTCTCCTGATTT
1 TTCTTCAATTCTCCTGATTT
* *
40643740 TTC--CAATTTTACCCT--TAT
1 TTCTTCAATTCT--CCTGATTT
40643758 TTCTTCAATTCTCCTGATTT
1 TTCTTCAATTCTCCTGATTT
40643778 TTCT
1 TTCT
40643782 CAGCGTATGC
Statistics
Matches: 32, Mismatches: 4, Indels: 12
0.67 0.08 0.25
Matches are distributed among these distances:
18 14 0.44
20 18 0.56
ACGTcount: A:0.16, C:0.26, G:0.03, T:0.55
Consensus pattern (20 bp):
TTCTTCAATTCTCCTGATTT
Found at i:40644324 original size:20 final size:19
Alignment explanation
Indices: 40644290--40644329 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
40644280 AGATGCTTCT
40644290 ATTTATGAATTTGGATTGG
1 ATTTATGAATTTGGATTGG
*
40644309 ATTTATGCAGTTTGGATTGG
1 ATTTATG-AATTTGGATTGG
40644329 A
1 A
40644330 AAATAACTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.25, C:0.03, G:0.28, T:0.45
Consensus pattern (19 bp):
ATTTATGAATTTGGATTGG
Found at i:40645386 original size:22 final size:23
Alignment explanation
Indices: 40645361--40645406 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
40645351 CTTTTTTATA
*
40645361 TATTTT-TAAATTTAAATTATTT
1 TATTTTATAAATTTAAATGATTT
*
40645383 TATTTTATAATTTTAAATGATTT
1 TATTTTATAAATTTAAATGATTT
40645406 T
1 T
40645407 TAGCATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (23 bp):
TATTTTATAAATTTAAATGATTT
Found at i:40647895 original size:62 final size:62
Alignment explanation
Indices: 40647827--40647952 Score: 225
Period size: 62 Copynumber: 2.0 Consensus size: 62
40647817 CCACCAATCC
*
40647827 TTTTTGATAAGGTGTGATCAGATCACCTTGAAAAGTGGTTGTTTTTAATAAACGATTTGATT
1 TTTTTGATAAGGTGTGATCAGATCACCTTGAAAAGTGGTTATTTTTAATAAACGATTTGATT
* *
40647889 TTTTTGATAAGGTGTGATCGGATCACCTTGAAAAGTGGTTATTTTTAATAAATGATTTGATT
1 TTTTTGATAAGGTGTGATCAGATCACCTTGAAAAGTGGTTATTTTTAATAAACGATTTGATT
40647951 TT
1 TT
40647953 ATTAAAACAA
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 61 1.00
ACGTcount: A:0.29, C:0.07, G:0.21, T:0.44
Consensus pattern (62 bp):
TTTTTGATAAGGTGTGATCAGATCACCTTGAAAAGTGGTTATTTTTAATAAACGATTTGATT
Found at i:40654062 original size:2 final size:2
Alignment explanation
Indices: 40654055--40654090 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
40654045 ATAAGCAGCA
40654055 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
40654091 CCAGACATGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40665257 original size:38 final size:39
Alignment explanation
Indices: 40665180--40665268 Score: 94
Period size: 39 Copynumber: 2.3 Consensus size: 39
40665170 ATGATTAAAC
*
40665180 TATACATATATAAATTATTATATATTATAATAGTGCATG-
1 TATA-ATATATAAATTATTATATATTATAATAATGCATGT
* *
40665219 TATAATATATATATTGATT-TAATATTATATTAAT-CATGTT
1 TATAATATATAAATT-ATTAT-ATATTATAATAATGCATG-T
40665259 TATAATATAT
1 TATAATATAT
40665269 GCTAAATATA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
38 15 0.35
39 18 0.42
40 10 0.23
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.48
Consensus pattern (39 bp):
TATAATATATAAATTATTATATATTATAATAATGCATGT
Found at i:40673586 original size:14 final size:14
Alignment explanation
Indices: 40673569--40673658 Score: 65
Period size: 16 Copynumber: 6.1 Consensus size: 14
40673559 AACTTATAAA
*
40673569 ATATTATTTATTTTAT
1 ATATTATATA-TTT-T
*
40673585 ATATTATATATTAT
1 ATATTATATATTTT
40673599 ATATTATATATTATTT
1 ATATTATATA-T-TTT
* *
40673615 ATATGAAATATTTT
1 ATATTATATATTTT
40673629 ATATGCTATATATTTT
1 ATAT--TATATATTTT
* *
40673645 TTATT-TTTATTTT
1 ATATTATATATTTT
40673658 A
1 A
40673659 AAACAATAAA
Statistics
Matches: 60, Mismatches: 10, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
13 7 0.12
14 19 0.32
15 4 0.07
16 30 0.50
ACGTcount: A:0.34, C:0.01, G:0.02, T:0.62
Consensus pattern (14 bp):
ATATTATATATTTT
Found at i:40673591 original size:7 final size:7
Alignment explanation
Indices: 40673581--40673612 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
40673571 ATTATTTATT
40673581 TTATATA
1 TTATATA
40673588 TTATATA
1 TTATATA
40673595 TTATATA
1 TTATATA
40673602 TTATATA
1 TTATATA
40673609 TTAT
1 TTAT
40673613 TTATATGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
TTATATA
Found at i:40673603 original size:23 final size:23
Alignment explanation
Indices: 40673569--40673651 Score: 78
Period size: 23 Copynumber: 3.6 Consensus size: 23
40673559 AACTTATAAA
*
40673569 ATATTATTTATTTTATATATTAT
1 ATATTATATATTTTATATATTAT
*
40673592 ATATTATATATTATATATTATT-T
1 ATATTATATATTTTATA-TATTAT
* * **
40673615 ATATGAAATATTTTATATGCTAT
1 ATATTATATATTTTATATATTAT
* *
40673638 ATATTTTTTATTTT
1 ATATTATATATTTT
40673652 TATTTTAAAA
Statistics
Matches: 47, Mismatches: 11, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
22 2 0.04
23 41 0.87
24 4 0.09
ACGTcount: A:0.35, C:0.01, G:0.02, T:0.61
Consensus pattern (23 bp):
ATATTATATATTTTATATATTAT
Found at i:40676679 original size:16 final size:16
Alignment explanation
Indices: 40676658--40676716 Score: 73
Period size: 16 Copynumber: 3.4 Consensus size: 16
40676648 TTTCCATGTA
40676658 CATGTAACATCTATAC
1 CATGTAACATCTATAC
*
40676674 CATGTAATTCATGTAAATAC
1 CATGTAA--CATCT--ATAC
40676694 CATGTAACATCTATAC
1 CATGTAACATCTATAC
40676710 CATGTAA
1 CATGTAA
40676717 TTCATGTAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
16 18 0.49
18 8 0.22
20 11 0.30
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.32
Consensus pattern (16 bp):
CATGTAACATCTATAC
Found at i:40676695 original size:20 final size:20
Alignment explanation
Indices: 40676670--40676734 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 20
40676660 TGTAACATCT
40676670 ATACCATGTAATTCATGTAA
1 ATACCATGTAATTCATGTAA
*
40676690 ATACCATGTAA--CATCT--
1 ATACCATGTAATTCATGTAA
40676706 ATACCATGTAATTCATGTAA
1 ATACCATGTAATTCATGTAA
40676726 ATA-CATGTA
1 ATACCATGTA
40676735 CTAGTTCATA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
16 11 0.28
18 8 0.21
19 6 0.15
20 14 0.36
ACGTcount: A:0.40, C:0.17, G:0.09, T:0.34
Consensus pattern (20 bp):
ATACCATGTAATTCATGTAA
Found at i:40676699 original size:36 final size:35
Alignment explanation
Indices: 40676656--40676734 Score: 149
Period size: 36 Copynumber: 2.2 Consensus size: 35
40676646 AATTTCCATG
40676656 TACATGTAACATCTATACCATGTAATTCATGTAAA
1 TACATGTAACATCTATACCATGTAATTCATGTAAA
40676691 TACCATGTAACATCTATACCATGTAATTCATGTAAA
1 TA-CATGTAACATCTATACCATGTAATTCATGTAAA
40676727 TACATGTA
1 TACATGTA
40676735 CTAGTTCATA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
35 8 0.19
36 35 0.81
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.34
Consensus pattern (35 bp):
TACATGTAACATCTATACCATGTAATTCATGTAAA
Found at i:40676951 original size:25 final size:25
Alignment explanation
Indices: 40676866--40676953 Score: 70
Period size: 25 Copynumber: 3.6 Consensus size: 25
40676856 GTACATGTAT
*
40676866 GCTCATACGAGCT-ATTAACGGTAA
1 GCTCATACGAGCTGAATAACGGTAA
* * * * ***
40676890 ACTCCTCCGAGTTGAATAATAATAA
1 GCTCATACGAGCTGAATAACGGTAA
* **
40676915 GCTCCTTTGAGCTGAATAACGGTAA
1 GCTCATACGAGCTGAATAACGGTAA
40676940 GCTCATACGAGCTG
1 GCTCATACGAGCTG
40676954 GAATCGGTAA
Statistics
Matches: 45, Mismatches: 18, Indels: 1
0.70 0.28 0.02
Matches are distributed among these distances:
24 9 0.20
25 36 0.80
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (25 bp):
GCTCATACGAGCTGAATAACGGTAA
Found at i:40678986 original size:19 final size:19
Alignment explanation
Indices: 40678964--40679013 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 19
40678954 TCTCAACAAA
40678964 AATTCTAAAAAATCAAAAT
1 AATTCTAAAAAATCAAAAT
* *
40678983 AATTTCCAAAAATTCAAAAT
1 AA-TTCTAAAAAATCAAAAT
* *
40679003 ATTTATAAAAA
1 AATTCTAAAAA
40679014 TTCCAAATTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.30
Consensus pattern (19 bp):
AATTCTAAAAAATCAAAAT
Found at i:40679014 original size:19 final size:19
Alignment explanation
Indices: 40678969--40679027 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
40678959 ACAAAAATTC
* *
40678969 TAAAAAATCAAAATAATTTC
1 TAAAAATTCAAAAT-ATTTA
*
40678989 CAAAAATTCAAAATATTTA
1 TAAAAATTCAAAATATTTA
* *
40679008 TAAAAATTCCAAATTTTTA
1 TAAAAATTCAAAATATTTA
40679027 T
1 T
40679028 TTTTTTAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 21 0.64
20 12 0.36
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.36
Consensus pattern (19 bp):
TAAAAATTCAAAATATTTA
Found at i:40683976 original size:19 final size:20
Alignment explanation
Indices: 40683954--40683994 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
40683944 TTTATATCAA
40683954 TTTATAAATTT-TAAATTTT
1 TTTATAAATTTATAAATTTT
*
40683973 TTTATTAATTTAATAAATTTT
1 TTTATAAATTT-ATAAATTTT
40683994 T
1 T
40683995 AATTGTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 10 0.53
21 9 0.47
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTATAAATTTATAAATTTT
Found at i:40684220 original size:26 final size:26
Alignment explanation
Indices: 40684189--40684240 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
40684179 TCTACATTTA
* *
40684189 AAAATTATAAAAA-CAATTTTTTAAAT
1 AAAATT-TAAAAATCAAATATTTAAAT
40684215 AAAATTTAAAAATCAAATATTTAAAT
1 AAAATTTAAAAATCAAATATTTAAAT
40684241 TCAAATCCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 6 0.26
26 17 0.74
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.37
Consensus pattern (26 bp):
AAAATTTAAAAATCAAATATTTAAAT
Found at i:40684522 original size:15 final size:16
Alignment explanation
Indices: 40684496--40684529 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
40684486 ATTTAAGAGT
*
40684496 TAATATAAATATTTTC
1 TAATATAAATATTTAC
40684512 TAATA-AAATATTTAC
1 TAATATAAATATTTAC
40684527 TAA
1 TAA
40684530 CTCGAATAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (16 bp):
TAATATAAATATTTAC
Found at i:40685193 original size:9 final size:8
Alignment explanation
Indices: 40685148--40685189 Score: 50
Period size: 8 Copynumber: 5.1 Consensus size: 8
40685138 AATTTTAATG
40685148 ATTTTT-A
1 ATTTTTAA
40685155 ATTTTTAA
1 ATTTTTAA
*
40685163 TTTTTTATA
1 ATTTTTA-A
40685172 ACTTTTTAA
1 A-TTTTTAA
40685181 ATTTTTAA
1 ATTTTTAA
40685189 A
1 A
40685190 ATTTAAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
7 6 0.20
8 15 0.50
9 3 0.10
10 6 0.20
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (8 bp):
ATTTTTAA
Found at i:40698400 original size:26 final size:26
Alignment explanation
Indices: 40698371--40698420 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
40698361 AAACTCTAAC
40698371 GCTTCCAATGGAACTGAACTATTATA
1 GCTTCCAATGGAACTGAACTATTATA
*
40698397 GCTTCCAGTGGAACTGAACTATTA
1 GCTTCCAATGGAACTGAACTATTA
40698421 CGATAAGTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (26 bp):
GCTTCCAATGGAACTGAACTATTATA
Found at i:40700007 original size:6 final size:6
Alignment explanation
Indices: 40699993--40700022 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
40699983 GCTTATTGTT
*
40699993 GAGGCG GAGGTG GAGGTG GAGGTG GAGGTG
1 GAGGTG GAGGTG GAGGTG GAGGTG GAGGTG
40700023 AAGTTGTTGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.03, G:0.67, T:0.13
Consensus pattern (6 bp):
GAGGTG
Found at i:40706466 original size:8 final size:8
Alignment explanation
Indices: 40706453--40706481 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
40706443 TTTTAAATAA
40706453 TATTTTAT
1 TATTTTAT
40706461 TATTTTAT
1 TATTTTAT
40706469 TATTTTAT
1 TATTTTAT
40706477 TATTT
1 TATTT
40706482 AGTATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTTTAT
Found at i:40709768 original size:322 final size:322
Alignment explanation
Indices: 40709183--40709827 Score: 1290
Period size: 322 Copynumber: 2.0 Consensus size: 322
40709173 TCAGCATTTG
40709183 TTGCGGACTTTCGTGTTTACTATCTGTTTAGCTCTCATGAGCTTAAGTTCATCCTTCGGGCTTCT
1 TTGCGGACTTTCGTGTTTACTATCTGTTTAGCTCTCATGAGCTTAAGTTCATCCTTCGGGCTTCT
40709248 GAAAATGATGTACTCATATTCGTAAGTCGTTCTTCGATACAGAAAGAAACGGTAAAAGACTTATG
66 GAAAATGATGTACTCATATTCGTAAGTCGTTCTTCGATACAGAAAGAAACGGTAAAAGACTTATG
40709313 TGGTTGAATTGAAAGATTTATAGATTATTATTGGTATTGATCTAAAATAAATGTAACCATTGATA
131 TGGTTGAATTGAAAGATTTATAGATTATTATTGGTATTGATCTAAAATAAATGTAACCATTGATA
40709378 TTTAAATGATATAACGGGTAAAGTTCTGAAGTGAGATAACATGAGTTTGAAATGAACTATTACCG
196 TTTAAATGATATAACGGGTAAAGTTCTGAAGTGAGATAACATGAGTTTGAAATGAACTATTACCG
40709443 GTATGTACGCAAAATTAATGAAAATGATGGTACATGAAATATCGAAATAATAAAATGAATGA
261 GTATGTACGCAAAATTAATGAAAATGATGGTACATGAAATATCGAAATAATAAAATGAATGA
40709505 TTGCGGACTTTCGTGTTTACTATCTGTTTAGCTCTCATGAGCTTAAGTTCATCCTTCGGGCTTCT
1 TTGCGGACTTTCGTGTTTACTATCTGTTTAGCTCTCATGAGCTTAAGTTCATCCTTCGGGCTTCT
40709570 GAAAATGATGTACTCATATTCGTAAGTCGTTCTTCGATACAGAAAGAAACGGTAAAAGACTTATG
66 GAAAATGATGTACTCATATTCGTAAGTCGTTCTTCGATACAGAAAGAAACGGTAAAAGACTTATG
40709635 TGGTTGAATTGAAAGATTTATAGATTATTATTGGTATTGATCTAAAATAAATGTAACCATTGATA
131 TGGTTGAATTGAAAGATTTATAGATTATTATTGGTATTGATCTAAAATAAATGTAACCATTGATA
40709700 TTTAAATGATATAACGGGTAAAGTTCTGAAGTGAGATAACATGAGTTTGAAATGAACTATTACCG
196 TTTAAATGATATAACGGGTAAAGTTCTGAAGTGAGATAACATGAGTTTGAAATGAACTATTACCG
40709765 GTATGTACGCAAAATTAATGAAAATGATGGTACATGAAATATCGAAATAATAAAATGAATGA
261 GTATGTACGCAAAATTAATGAAAATGATGGTACATGAAATATCGAAATAATAAAATGAATGA
40709827 T
1 T
40709828 ATATACCTAT
Statistics
Matches: 323, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
322 323 1.00
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.34
Consensus pattern (322 bp):
TTGCGGACTTTCGTGTTTACTATCTGTTTAGCTCTCATGAGCTTAAGTTCATCCTTCGGGCTTCT
GAAAATGATGTACTCATATTCGTAAGTCGTTCTTCGATACAGAAAGAAACGGTAAAAGACTTATG
TGGTTGAATTGAAAGATTTATAGATTATTATTGGTATTGATCTAAAATAAATGTAACCATTGATA
TTTAAATGATATAACGGGTAAAGTTCTGAAGTGAGATAACATGAGTTTGAAATGAACTATTACCG
GTATGTACGCAAAATTAATGAAAATGATGGTACATGAAATATCGAAATAATAAAATGAATGA
Found at i:40716629 original size:2 final size:2
Alignment explanation
Indices: 40716622--40716652 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
40716612 GAATATGTAC
40716622 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
40716653 AATGTACATC
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:40717046 original size:41 final size:41
Alignment explanation
Indices: 40716997--40717146 Score: 237
Period size: 41 Copynumber: 3.6 Consensus size: 41
40716987 GACTTTAAGT
*
40716997 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTACAAAC
1 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
40717038 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
* **
40717079 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGCTATAAGT
1 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
* *
40717120 CTAGCAGGCTATGTGCCGTTGAATCTG
1 CTAGCAGGCTACGTGCCGGTG-ATCTG
40717147 TTTTAATTAA
Statistics
Matches: 102, Mismatches: 6, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
41 97 0.95
42 5 0.05
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (41 bp):
CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
Found at i:40728174 original size:17 final size:17
Alignment explanation
Indices: 40728152--40728185 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
40728142 AAAATATTTT
40728152 ACTTGTATAATT-AATTA
1 ACTTGT-TAATTGAATTA
40728169 ACTTGTTAATTGAATTA
1 ACTTGTTAATTGAATTA
40728186 GCGTCGGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (17 bp):
ACTTGTTAATTGAATTA
Found at i:40729194 original size:9 final size:9
Alignment explanation
Indices: 40729167--40729203 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
40729157 TGAGTTTTTA
40729167 AATTCGAAT
1 AATTCGAAT
* *
40729176 AACTCAAAT
1 AATTCGAAT
40729185 AATTCGAAT
1 AATTCGAAT
40729194 AATTCGAAT
1 AATTCGAAT
40729203 A
1 A
40729204 TCAAACTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Done.