Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A07
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: 92880876
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2857347 characters in sequence are not A, C, G, or T
File 128 of 290
Found at i:40125161 original size:11 final size:11
Alignment explanation
Indices: 40125132--40125168 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
40125122 TTAATATTTT
*
40125132 ATTATAAAATA
1 ATTATTAAATA
40125143 A-T-TTAAATA
1 ATTATTAAATA
40125152 ATTATTAAATA
1 ATTATTAAATA
40125163 ATTATT
1 ATTATT
40125169 TTCTCCAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
9 7 0.30
10 2 0.09
11 14 0.61
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
ATTATTAAATA
Found at i:40125350 original size:10 final size:10
Alignment explanation
Indices: 40125331--40125367 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
40125321 AGAAATTATA
40125331 AAATTA-TTT
1 AAATTATTTT
40125340 AAATTATTTT
1 AAATTATTTT
40125350 AAATATATTTT
1 AAAT-TATTTT
40125361 AAATTAT
1 AAATTAT
40125368 ATTATTGTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
9 6 0.23
10 10 0.38
11 10 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (10 bp):
AAATTATTTT
Found at i:40125370 original size:12 final size:11
Alignment explanation
Indices: 40125337--40125370 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
40125327 TATAAAATTA
40125337 TTTAAAT-TAT
1 TTTAAATATAT
40125347 TTTAAATATAT
1 TTTAAATATAT
40125358 TTTAAATTATAT
1 TTTAAA-TATAT
40125370 T
1 T
40125371 ATTGTGATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 7 0.32
11 9 0.41
12 6 0.27
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTAAATATAT
Found at i:40125577 original size:25 final size:25
Alignment explanation
Indices: 40125549--40125599 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
40125539 AAAATATTAA
*
40125549 AGTAAATCTTTTAAAATAATTAGAT
1 AGTAAATCTTTTAAAAGAATTAGAT
40125574 AGTAAATCTTTTAAAAGAATTAGAT
1 AGTAAATCTTTTAAAAGAATTAGAT
40125599 A
1 A
40125600 AAGTTTCCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.49, C:0.04, G:0.10, T:0.37
Consensus pattern (25 bp):
AGTAAATCTTTTAAAAGAATTAGAT
Found at i:40127726 original size:22 final size:21
Alignment explanation
Indices: 40127672--40127759 Score: 92
Period size: 20 Copynumber: 4.2 Consensus size: 21
40127662 CACACGACCA
40127672 TGTG-AGGAAGCACAAGCCCG
1 TGTGAAGGAAGCACAAGCCCG
40127692 TGT-AAGGAAGCACAAGCCCG
1 TGTGAAGGAAGCACAAGCCCG
* * *
40127712 TGTGAAAGGAGGCACACGGCCG
1 TGTG-AAGGAAGCACAAGCCCG
* *
40127734 TGTG-AGGATGACACACGCCCG
1 TGTGAAGGAAG-CACAAGCCCG
40127755 TGTGA
1 TGTGA
40127760 CCGAGTGACA
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
20 27 0.47
21 13 0.22
22 18 0.31
ACGTcount: A:0.28, C:0.24, G:0.35, T:0.12
Consensus pattern (21 bp):
TGTGAAGGAAGCACAAGCCCG
Found at i:40134635 original size:40 final size:40
Alignment explanation
Indices: 40134580--40134762 Score: 291
Period size: 40 Copynumber: 4.6 Consensus size: 40
40134570 CGGATGATAA
40134580 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAT
* *
40134620 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAT
40134660 CC-GGCTAAG-CCCGAAGGCATTTGTGCGAGTTACCAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAT
* *
40134698 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAA-
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCA-AAT
*
40134738 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
40134763 AGTGAGTAGC
Statistics
Matches: 132, Mismatches: 8, Indels: 6
0.90 0.05 0.04
Matches are distributed among these distances:
38 29 0.22
39 14 0.11
40 87 0.66
41 2 0.02
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.23
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAT
Found at i:40134720 original size:78 final size:80
Alignment explanation
Indices: 40134576--40134762 Score: 317
Period size: 78 Copynumber: 2.4 Consensus size: 80
40134566 TATTCGGATG
40134576 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAATCCGGGCTAAGTCCCGAAGGCA
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAATCCGGGCTAAGTCCCGAAGGCA
*
40134641 TTTGTGCGAGTTACT
66 TTGGTGCGAGTTACT
*
40134656 A-ATTCC-GGCTAAG-CCCGAAGGCATTTGTGCGAGTTACCAAATCCGGGCTAAGTCCCGAAGGC
1 ATA-ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAATCCGGGCTAAGTCCCGAAGGC
40134718 ATTGGTGCGAGTTACT
65 ATTGGTGCGAGTTACT
*
40134734 ATAACCGGGCTATGTCCCGAAGGCATTTG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTG
40134763 AGTGAGTAGC
Statistics
Matches: 99, Mismatches: 4, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
78 67 0.68
79 15 0.15
80 17 0.17
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.24
Consensus pattern (80 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAATCCGGGCTAAGTCCCGAAGGCA
TTGGTGCGAGTTACT
Found at i:40136430 original size:19 final size:20
Alignment explanation
Indices: 40136386--40136433 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
40136376 ACAAATTATT
*
40136386 TATAAATTTTAATTTAAATA
1 TATAAATTATAATTTAAATA
*
40136406 TATAAATTATATTTTAAATA
1 TATAAATTATAATTTAAATA
40136426 T-TAAATTA
1 TATAAATTA
40136434 CATTACAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 7 0.27
20 19 0.73
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TATAAATTATAATTTAAATA
Found at i:40136531 original size:17 final size:18
Alignment explanation
Indices: 40136506--40136543 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
40136496 AAGAAATAAA
*
40136506 ATAATTATA-CATTTAAT
1 ATAAATATAGCATTTAAT
40136523 ATAAATATATGCATTTAAT
1 ATAAATATA-GCATTTAAT
40136542 AT
1 AT
40136544 TTATAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 8 0.44
19 10 0.56
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (18 bp):
ATAAATATAGCATTTAAT
Found at i:40139657 original size:24 final size:25
Alignment explanation
Indices: 40139630--40139690 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 25
40139620 TTTAGTTATA
*
40139630 AATATTTATTATTATTT-TGATAAT
1 AATATTTATTATAATTTGTGATAAT
*
40139654 AATATATTAATATAATTTGTGATAAT
1 AATAT-TTATTATAATTTGTGATAAT
*
40139680 AAAATTATATT
1 AATATT-TATT
40139691 TTTAATATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
24 5 0.17
25 11 0.37
26 14 0.47
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (25 bp):
AATATTTATTATAATTTGTGATAAT
Found at i:40139689 original size:23 final size:25
Alignment explanation
Indices: 40139630--40139681 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
40139620 TTTAGTTATA
* *
40139630 AATAT-TTATTATTATTTTGATAAT
1 AATATATTAATATAATTTTGATAAT
40139654 AATATATTAATATAATTTGTGATAAT
1 AATATATTAATATAATTT-TGATAAT
40139680 AA
1 AA
40139682 AATTATATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 5 0.21
25 10 0.42
26 9 0.38
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (25 bp):
AATATATTAATATAATTTTGATAAT
Found at i:40139706 original size:21 final size:22
Alignment explanation
Indices: 40139653--40139706 Score: 53
Period size: 20 Copynumber: 2.6 Consensus size: 22
40139643 ATTTTGATAA
40139653 TAATATAT-TAA-TATAATTTG
1 TAATATATATAATTATAATTTG
* * *
40139673 TGATA-ATAAAATTAT-ATTTT
1 TAATATATATAATTATAATTTG
40139693 TAATATATATAATT
1 TAATATATATAATT
40139707 TATGTAACTT
Statistics
Matches: 26, Mismatches: 5, Indels: 5
0.72 0.14 0.14
Matches are distributed among these distances:
19 2 0.08
20 14 0.54
21 10 0.38
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (22 bp):
TAATATATATAATTATAATTTG
Found at i:40144195 original size:25 final size:27
Alignment explanation
Indices: 40144158--40144210 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
40144148 TCAAACATGC
40144158 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
40144184 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
40144210 A
1 A
40144211 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:40145771 original size:26 final size:26
Alignment explanation
Indices: 40145695--40145778 Score: 132
Period size: 26 Copynumber: 3.2 Consensus size: 26
40145685 CATGAAATTC
* *
40145695 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCTA
*
40145721 TTATCATGGAACATTTATCTAACCTA
1 TTATCATGGAACATTTACCTAACCTA
*
40145747 TTATCATGGAACATTTACCTAACCTT
1 TTATCATGGAACATTTACCTAACCTA
40145773 TTATCA
1 TTATCA
40145779 ATTTGTATCA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 53 1.00
ACGTcount: A:0.35, C:0.23, G:0.06, T:0.37
Consensus pattern (26 bp):
TTATCATGGAACATTTACCTAACCTA
Found at i:40148563 original size:177 final size:176
Alignment explanation
Indices: 40147937--40148573 Score: 771
Period size: 177 Copynumber: 3.6 Consensus size: 176
40147927 CACTATAACT
* * * * * * * *
40147937 TCAGGGAGACAAGGC-TGGTGACTTAAATTTGCTCTATTGCCGATACGTGGAGATAAGATTTGCT
1 TCAGAGAGATAAGGCTTGGTGGCTTAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCGCC
* * * * * * * * *
40148001 ATCTTCGACCTGCTCCACAATTGCTTAAGGAGACAAGATCCTCAATCTTTAGTTTGCTTCCTTGC
66 ATCTTCGATCTGCTCCACAACT-ATTAGGGAGATAAGATCTTCAATCTTCAGTCTGCTTCCTTAC
*
40148066 TACCTCAGGAAGATAAGAC-CAATTTCTTCAACCTGCTCTCTTGCTACC
130 TACCTCAAGAAGATAAGACTCAA--TCTTCAACCTGCTCTCTTGCTACC
* * * ** *
40148114 TCAGAGAAATAAGGC-TAGTAGCAAAAATCTGCTCCATTGCCGATACATGGAGATAAAATTCGCC
1 TCAGAGAGATAAGGCTTGGTGGCTTAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCGCC
* ** *
40148178 ATCTTCGATCTGTTTTGCTGCAACT-TTAGGGAGATAATATCTTCAATCTTCAGTCTGCTTCCTT
66 ATCTTCGATCTG--CT-CCACAACTATTAGGGAGATAAGATCTTCAATCTTCAGTCTGCTTCCTT
*
40148242 ACTACCTCAAGAAGATAAGACTCAATCTTCAACATGCTCTCTTGCTACC
128 ACTACCTCAAGAAGATAAGACTCAATCTTCAACCTGCTCTCTTGCTACC
**
40148291 TCAGAGAGATAAGGCTTGGTGGCTTAAATCTATTCCATTGCCGATACATGGAGATAAGATTCGCC
1 TCAGAGAGATAAGGCTTGGTGGCTTAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCGCC
* * *
40148356 -TCTCCCGATCTGCTCCACTACTACTTAGGGAGATAAGATCTTTAATCTTCAGTCTGCTTCCTTA
66 ATCT-TCGATCTGCTCCACAACTA-TTAGGGAGATAAGATCTTCAATCTTCAGTCTGCTTCCTTA
* *
40148420 CTACTTTAAGAAGATAAGACTCAATCTTCAACCTGCTCTCTTGCTACC
129 CTACCTCAAGAAGATAAGACTCAATCTTCAACCTGCTCTCTTGCTACC
* * *
40148468 TCAGAGAGATAGGGCTTGGTGGCTTAAATCTGCTCCATTGCCGATACATGGAGGTAAGATTCACC
1 TCAGAGAGATAAGGCTTGGTGGCTTAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCGCC
* * * *
40148533 ATCTTCGATCTGTTCCGCCACTGATTAGGGAGAGAAGATCT
66 ATCTTCGATCTGCTCCACAACT-ATTAGGGAGATAAGATCT
40148574 GACTTCACCA
Statistics
Matches: 394, Mismatches: 56, Indels: 20
0.84 0.12 0.04
Matches are distributed among these distances:
175 5 0.01
176 1 0.00
177 274 0.70
178 105 0.27
179 4 0.01
180 5 0.01
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (176 bp):
TCAGAGAGATAAGGCTTGGTGGCTTAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCGCC
ATCTTCGATCTGCTCCACAACTATTAGGGAGATAAGATCTTCAATCTTCAGTCTGCTTCCTTACT
ACCTCAAGAAGATAAGACTCAATCTTCAACCTGCTCTCTTGCTACC
Found at i:40173148 original size:42 final size:42
Alignment explanation
Indices: 40173084--40173165 Score: 130
Period size: 43 Copynumber: 2.0 Consensus size: 42
40173074 ATACCAAATT
40173084 AATTTATTTAAACATACATTCATC-AAACAGCCCCTAGTACG
1 AATTTATTTAAACATACATTCATCAAAACAGCCCCTAGTACG
* *
40173125 AATTTATTTAATGCATACATTCATCAAAATAGCCCCTAGTA
1 AATTTATTTAA-ACATACATTCATCAAAACAGCCCCTAGTA
40173166 AGAACTTTGG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
41 11 0.30
42 12 0.32
43 14 0.38
ACGTcount: A:0.39, C:0.22, G:0.07, T:0.32
Consensus pattern (42 bp):
AATTTATTTAAACATACATTCATCAAAACAGCCCCTAGTACG
Found at i:40187548 original size:48 final size:48
Alignment explanation
Indices: 40187492--40187725 Score: 182
Period size: 48 Copynumber: 4.9 Consensus size: 48
40187482 ATGTGAGTAT
*
40187492 TGAGATCCCGTGTAAGACCATATTTGGGATATGGTATTGGCATCAAGA
1 TGAGATCCCGTGTAAGACCATATCTGGGATATGGTATTGGCATCAAGA
* * *** *** * *
40187540 TGAGATCCCGTGTAAGACCGTATCTAGGATATAACACCAGCATCGATA
1 TGAGATCCCGTGTAAGACCATATCTGGGATATGGTATTGGCATCAAGA
* ** * * * *
40187588 TGAGATCCCGTATAAGACCATGCCTGGGACATGGCATTAGCATCATTG-
1 TGAGATCCCGTGTAAGACCATATCTGGGATATGGTATTGGCATCA-AGA
* * * * * *
40187636 TGAGATCCCATGTAAGATCATATCTGGGATATGGTATTGGTACCGATA
1 TGAGATCCCGTGTAAGACCATATCTGGGATATGGTATTGGCATCAAGA
* * * * * *
40187684 TCAGGTCCCGTCTAAGACCATGTCTGGGACATGGTATCGGCA
1 TGAGATCCCGTGTAAGACCATATCTGGGATATGGTATTGGCA
40187726 CCGTTATGAA
Statistics
Matches: 138, Mismatches: 46, Indels: 4
0.73 0.24 0.02
Matches are distributed among these distances:
48 138 1.00
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.26
Consensus pattern (48 bp):
TGAGATCCCGTGTAAGACCATATCTGGGATATGGTATTGGCATCAAGA
Found at i:40187640 original size:96 final size:96
Alignment explanation
Indices: 40187492--40187667 Score: 228
Period size: 96 Copynumber: 1.8 Consensus size: 96
40187482 ATGTGAGTAT
* ** * * * *
40187492 TGAGATCCCGTGTAAGACCATATTTGGGATATGGTATTGGCATCAAGATGAGATCCCGTGTAAGA
1 TGAGATCCCGTATAAGACCATACCTGGGACATGGCATTAGCATCAAGATGAGATCCCATGTAAGA
*
40187557 CCGTATCTAGGATATAACACCAGCATCGATA
66 CCATATCTAGGATATAACACCAGCATCGATA
* *
40187588 TGAGATCCCGTATAAGACCATGCCTGGGACATGGCATTAGCATCATTG-TGAGATCCCATGTAAG
1 TGAGATCCCGTATAAGACCATACCTGGGACATGGCATTAGCATCA-AGATGAGATCCCATGTAAG
* *
40187652 ATCATATCTGGGATAT
65 ACCATATCTAGGATAT
40187668 GGTATTGGTA
Statistics
Matches: 67, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
96 66 0.99
97 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (96 bp):
TGAGATCCCGTATAAGACCATACCTGGGACATGGCATTAGCATCAAGATGAGATCCCATGTAAGA
CCATATCTAGGATATAACACCAGCATCGATA
Found at i:40192225 original size:47 final size:47
Alignment explanation
Indices: 40192167--40192297 Score: 138
Period size: 47 Copynumber: 2.8 Consensus size: 47
40192157 GTACGAATAA
* * **
40192167 TACCTTAATTTGGCTACGAGCCATGATATAGGTATTTTGAGA-AGAGG
1 TACCTTGATTTGGCTACGAGCCATGGTATAGGTATTTCAAGATA-AGG
* ** * * * *
40192214 TACCTTGATTTGGTTGTGGGCCATGGTATAGGTACTCCAAGATAAGT
1 TACCTTGATTTGGCTACGAGCCATGGTATAGGTATTTCAAGATAAGG
*
40192261 TACCTTGATTTGGCTACAAGCCATGGTATAGGTATTT
1 TACCTTGATTTGGCTACGAGCCATGGTATAGGTATTT
40192298 ATCGATTATG
Statistics
Matches: 65, Mismatches: 18, Indels: 2
0.76 0.21 0.02
Matches are distributed among these distances:
47 64 0.98
48 1 0.02
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.34
Consensus pattern (47 bp):
TACCTTGATTTGGCTACGAGCCATGGTATAGGTATTTCAAGATAAGG
Found at i:40193296 original size:28 final size:28
Alignment explanation
Indices: 40193264--40193321 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
40193254 TACCCTACAG
** *
40193264 GTTTGACACGGCCTGGATACACGGGCGT
1 GTTTGACACAACCTGGACACACGGGCGT
40193292 GTTTGACACAACCTGGACACACGGGCGT
1 GTTTGACACAACCTGGACACACGGGCGT
40193320 GT
1 GT
40193322 GACTGACCGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.33, T:0.21
Consensus pattern (28 bp):
GTTTGACACAACCTGGACACACGGGCGT
Found at i:40195193 original size:15 final size:14
Alignment explanation
Indices: 40195175--40195204 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
40195165 TTAATAGCAT
40195175 TTATGTTAACTTACA
1 TTATGTTAA-TTACA
40195190 TTATGTTAATTACA
1 TTATGTTAATTACA
40195204 T
1 T
40195205 ATTAAAGGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (14 bp):
TTATGTTAATTACA
Found at i:40196396 original size:20 final size:20
Alignment explanation
Indices: 40196349--40196401 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
40196339 TCTTCTAACC
*
40196349 AAAATAAAAAATATATCTAA
1 AAAATAAAAAATATATATAA
* *
40196369 AAACTAAAAAGTATA-ATAA
1 AAAATAAAAAATATATATAA
*
40196388 ATAAATAAATAATA
1 A-AAATAAAAAATA
40196402 AAAAATTTAC
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
19 4 0.15
20 22 0.85
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.25
Consensus pattern (20 bp):
AAAATAAAAAATATATATAA
Found at i:40197445 original size:21 final size:21
Alignment explanation
Indices: 40197419--40197460 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
40197409 TAGTACAGAC
40197419 GATTTTGAATGAAGCACACAA
1 GATTTTGAATGAAGCACACAA
40197440 GATTTTGAATGAAGCACACAA
1 GATTTTGAATGAAGCACACAA
40197461 TGGTAACATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.19, T:0.24
Consensus pattern (21 bp):
GATTTTGAATGAAGCACACAA
Found at i:40208794 original size:13 final size:13
Alignment explanation
Indices: 40208770--40208794 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40208760 TACAAAAAGG
40208770 TTTTACTAAAATA
1 TTTTACTAAAATA
40208783 TTTTACTAAAAT
1 TTTTACTAAAAT
40208795 TGTGGTTTAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (13 bp):
TTTTACTAAAATA
Found at i:40211844 original size:105 final size:105
Alignment explanation
Indices: 40211725--40211932 Score: 416
Period size: 105 Copynumber: 2.0 Consensus size: 105
40211715 TCACTTTAAA
40211725 AAAAAAACTTAATGCTATAATAAGCCTTGAAGTCTAAAAAAATCAATTAAGTCCCTTCGAATCTT
1 AAAAAAACTTAATGCTATAATAAGCCTTGAAGTCTAAAAAAATCAATTAAGTCCCTTCGAATCTT
40211790 TTGTATCAAGTTGAGCCTTTCAATTCACAAAATTCATTTT
66 TTGTATCAAGTTGAGCCTTTCAATTCACAAAATTCATTTT
40211830 AAAAAAACTTAATGCTATAATAAGCCTTGAAGTCTAAAAAAATCAATTAAGTCCCTTCGAATCTT
1 AAAAAAACTTAATGCTATAATAAGCCTTGAAGTCTAAAAAAATCAATTAAGTCCCTTCGAATCTT
40211895 TTGTATCAAGTTGAGCCTTTCAATTCACAAAATTCATT
66 TTGTATCAAGTTGAGCCTTTCAATTCACAAAATTCATT
40211933 AATTAAGTCC
Statistics
Matches: 103, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
105 103 1.00
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.34
Consensus pattern (105 bp):
AAAAAAACTTAATGCTATAATAAGCCTTGAAGTCTAAAAAAATCAATTAAGTCCCTTCGAATCTT
TTGTATCAAGTTGAGCCTTTCAATTCACAAAATTCATTTT
Found at i:40213519 original size:89 final size:89
Alignment explanation
Indices: 40213413--40213589 Score: 295
Period size: 89 Copynumber: 2.0 Consensus size: 89
40213403 AGTACTAAAC
40213413 AAATAGTGATGTTAACATATATAATAACGC-AAATATG-TAGGAATCATATCTCTTACAACAAAA
1 AAATAGTGATGTTAACATATATAATAAC-CTAAATATGTTA-GAATCATATCTCTTACAACAAAA
*
40213476 AGCAACAAAGAAAAAGACAGAAAGAT
64 AACAACAAAGAAAAAGACAGAAAGAT
*
40213502 AAATAGTGATGTTAACATATATAATAACCTAAATATGTTAGAATTATATCTCTTACAACAAAAAA
1 AAATAGTGATGTTAACATATATAATAACCTAAATATGTTAGAATCATATCTCTTACAACAAAAAA
*
40213567 CAATAAAGAAAAAGACAGAAAGA
66 CAACAAAGAAAAAGACAGAAAGA
40213590 AAGAAACAAT
Statistics
Matches: 83, Mismatches: 3, Indels: 4
0.92 0.03 0.04
Matches are distributed among these distances:
88 1 0.01
89 80 0.96
90 2 0.02
ACGTcount: A:0.54, C:0.11, G:0.12, T:0.23
Consensus pattern (89 bp):
AAATAGTGATGTTAACATATATAATAACCTAAATATGTTAGAATCATATCTCTTACAACAAAAAA
CAACAAAGAAAAAGACAGAAAGAT
Found at i:40214179 original size:3 final size:3
Alignment explanation
Indices: 40214171--40214199 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
40214161 GTGATTCAAT
40214171 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
40214200 GTGTTCATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:40215297 original size:16 final size:17
Alignment explanation
Indices: 40215258--40215297 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
40215248 AATTAAAATG
40215258 TAATTTTATCATTATAA
1 TAATTTTATCATTATAA
40215275 TAA-TTTAT-ATT-TATA
1 TAATTTTATCATTATA-A
40215290 TAATTTTA
1 TAATTTTA
40215298 AGAAGGATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 2 0.10
15 7 0.33
16 9 0.43
17 3 0.14
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (17 bp):
TAATTTTATCATTATAA
Found at i:40216748 original size:15 final size:14
Alignment explanation
Indices: 40216719--40216747 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
40216709 ATTATTAAGT
40216719 TAAATAAAAATATA
1 TAAATAAAAATATA
40216733 TAAATAAAAAT-TA
1 TAAATAAAAATATA
40216746 TA
1 TA
40216748 TGTCATAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
TAAATAAAAATATA
Found at i:40221713 original size:28 final size:27
Alignment explanation
Indices: 40221680--40221739 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 27
40221670 TTAATAATTA
40221680 ATTTTTAAAATTTAAAAATTATAAAAACT
1 ATTTTTAAAA-TT-AAAATTATAAAAACT
* *
40221709 ATTTTTTAAAATTAAAATTATTAAAATT
1 A-TTTTTAAAATTAAAATTATAAAAACT
40221737 ATT
1 ATT
40221740 AAAAAATTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 2 0.07
28 14 0.50
29 3 0.11
30 9 0.32
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (27 bp):
ATTTTTAAAATTAAAATTATAAAAACT
Found at i:40221733 original size:9 final size:9
Alignment explanation
Indices: 40221719--40221743 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
40221709 ATTTTTTAAA
40221719 ATTAAAATT
1 ATTAAAATT
40221728 ATTAAAATT
1 ATTAAAATT
40221737 ATTAAAA
1 ATTAAAA
40221744 AATTAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (9 bp):
ATTAAAATT
Found at i:40221754 original size:36 final size:35
Alignment explanation
Indices: 40221684--40221754 Score: 81
Period size: 36 Copynumber: 2.0 Consensus size: 35
40221674 TAATTAATTT
**
40221684 TTAAAATTTAAAAATTATAAAAACTATTTTTTAAAA
1 TTAAAATTTAAAAATTATAAAAAC-ATTAATTAAAA
*
40221720 TTAAAATTATTAAAATTATTAAAAA-ATTAATTAAA
1 TTAAAATT-TAAAAATTA-TAAAAACATTAATTAAA
40221755 TGTTACGTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
36 16 0.53
37 8 0.27
38 6 0.20
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (35 bp):
TTAAAATTTAAAAATTATAAAAACATTAATTAAAA
Found at i:40227459 original size:16 final size:17
Alignment explanation
Indices: 40227433--40227467 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
40227423 TAGAATTGGG
*
40227433 TTGAGAAAATTATTTAA
1 TTGAGAAAATTAATTAA
40227450 TTGA-AAAATTAATTAA
1 TTGAGAAAATTAATTAA
40227466 TT
1 TT
40227468 TAATAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (17 bp):
TTGAGAAAATTAATTAA
Found at i:40228566 original size:30 final size:31
Alignment explanation
Indices: 40228532--40228633 Score: 104
Period size: 30 Copynumber: 3.4 Consensus size: 31
40228522 TTAAAAATAA
*
40228532 AAATTGCATTTTGACCCCTAAACTTTTC-CT
1 AAATTTCATTTTGACCCCTAAACTTTTCTCT
* * * *
40228562 AAATTTTATTTTGACCCTTAAA-ATTTCTTT
1 AAATTTCATTTTGACCCCTAAACTTTTCTCT
* *
40228592 AAATTTCACTTAGACCCCTAAAC-TTTCAT-T
1 AAATTTCATTTTGACCCCTAAACTTTTC-TCT
40228622 AAATTTCATTTT
1 AAATTTCATTTT
40228634 AATCCTAAAT
Statistics
Matches: 58, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
29 4 0.07
30 53 0.91
31 1 0.02
ACGTcount: A:0.30, C:0.21, G:0.04, T:0.45
Consensus pattern (31 bp):
AAATTTCATTTTGACCCCTAAACTTTTCTCT
Found at i:40229009 original size:3 final size:3
Alignment explanation
Indices: 40229003--40229037 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
40228993 TAGGAGGAGG
40229003 AGA AGA AGA AGA AGA AGA AGA AGAA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AG-A AGA AGA AGA A
40229038 AGAAAAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:40229222 original size:29 final size:28
Alignment explanation
Indices: 40229174--40229238 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 28
40229164 ACACAAAAAA
*
40229174 AAAACAAATCAGCCCAAAAAAAACCAAAG-C
1 AAAA-AAAGCAGCCCAAAAAAAA--AAAGCC
*
40229204 AAAAAAAGCAGCCCAAAAAGAAAAAGCC
1 AAAAAAAGCAGCCCAAAAAAAAAAAGCC
40229232 AAAAAAA
1 AAAAAAA
40229239 AAACAAAACC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 4 0.12
28 8 0.25
29 16 0.50
30 4 0.12
ACGTcount: A:0.68, C:0.22, G:0.09, T:0.02
Consensus pattern (28 bp):
AAAAAAAGCAGCCCAAAAAAAAAAAGCC
Found at i:40229372 original size:15 final size:13
Alignment explanation
Indices: 40229351--40229460 Score: 86
Period size: 13 Copynumber: 8.4 Consensus size: 13
40229341 GCAGGCCAGG
40229351 AAAAAAAGAGAGAA
1 AAAAAAAGA-AGAA
40229365 AGAAAAAAGAA-AA
1 A-AAAAAAGAAGAA
*
40229378 AAAGAAAGAAGAA
1 AAAAAAAGAAGAA
*
40229391 AGAAGAAAGAAGAA
1 A-AAAAAAGAAGAA
*
40229405 AAAAAGAA-AAGAG
1 AAAAA-AAGAAGAA
40229418 AAAAAAAG--GAA
1 AAAAAAAGAAGAA
* *
40229429 AAAAGGAAAAAAG-G
1 AAAA--AAAGAAGAA
40229443 AAAAAAAGAAGAA
1 AAAAAAAGAAGAA
40229456 AAAAA
1 AAAAA
40229461 GAAAAAAAAA
Statistics
Matches: 78, Mismatches: 8, Indels: 21
0.73 0.07 0.20
Matches are distributed among these distances:
11 6 0.08
12 16 0.21
13 26 0.33
14 21 0.27
15 9 0.12
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
AAAAAAAGAAGAA
Found at i:40229378 original size:8 final size:8
Alignment explanation
Indices: 40229350--40229468 Score: 98
Period size: 8 Copynumber: 14.0 Consensus size: 8
40229340 AGCAGGCCAG
40229350 GAAAAAAA
1 GAAAAAAA
* *
40229358 GAGAGAAA
1 GAAAAAAA
40229366 G-AAAAAA
1 GAAAAAAA
40229373 GAAAAAAA
1 GAAAAAAA
40229381 GAAAGAAGAAA
1 G-AA-AA-AAA
40229392 GAAGAAAGAA
1 GAA-AAA-AA
40229402 GAAAAAAA
1 GAAAAAAA
*
40229410 G-AAAAGA
1 GAAAAAAA
40229417 GAAAAAAA
1 GAAAAAAA
*
40229425 GGAAAAAAG
1 -GAAAAAAA
40229434 GAAAAAAGGA
1 GAAAAAA--A
*
40229444 AAAAAAGAA
1 GAAAAA-AA
40229453 GAAAAAAA
1 GAAAAAAA
40229461 GAAAAAAA
1 GAAAAAAA
40229469 AAGAGTTTCA
Statistics
Matches: 91, Mismatches: 10, Indels: 20
0.75 0.08 0.17
Matches are distributed among these distances:
7 11 0.12
8 39 0.43
9 19 0.21
10 17 0.19
11 5 0.05
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (8 bp):
GAAAAAAA
Found at i:40229398 original size:14 final size:14
Alignment explanation
Indices: 40229355--40229405 Score: 70
Period size: 14 Copynumber: 3.7 Consensus size: 14
40229345 GCCAGGAAAA
*
40229355 AAAGAGAGAAAGAAA
1 AAAGA-AGAAAGAAG
40229370 AAAGAA-AAA-AAG
1 AAAGAAGAAAGAAG
40229382 AAAGAAGAAAGAAG
1 AAAGAAGAAAGAAG
40229396 AAAGAAGAAA
1 AAAGAAGAAA
40229406 AAAAGAAAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
12 8 0.24
13 6 0.18
14 14 0.42
15 5 0.15
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (14 bp):
AAAGAAGAAAGAAG
Found at i:40229420 original size:44 final size:42
Alignment explanation
Indices: 40229363--40229468 Score: 124
Period size: 44 Copynumber: 2.4 Consensus size: 42
40229353 AAAAAGAGAG
*
40229363 AAAGAAAAAAGAAAAAAA-GAAAGAAGAAAGAAGAAAGAAGAAAA
1 AAAGAAAAAAGAAAAAAAGGAAAAAAGAAA-AA-AAAGAA-AAAA
* * *
40229407 AAAGAAAAGAGAAAAAAAGGAAAAAAGGAAAAAAGGAAAAAA
1 AAAGAAAAAAGAAAAAAAGGAAAAAAGAAAAAAAAGAAAAAA
40229449 AGAAGAAAAAAAGAAAAAAA
1 A-AAG-AAAAAAGAAAAAAA
40229469 AAGAGTTTCA
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
42 5 0.09
43 8 0.15
44 32 0.59
45 9 0.17
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (42 bp):
AAAGAAAAAAGAAAAAAAGGAAAAAAGAAAAAAAAGAAAAAA
Found at i:40229871 original size:19 final size:18
Alignment explanation
Indices: 40229830--40229874 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
40229820 AATTTCTATT
40229830 TTTCAAAATTTTTCGTGC
1 TTTCAAAATTTTTCGTGC
*
40229848 CTTCAAAATTTTTCTCGTG-
1 TTTCAAAA-TTTT-TCGTGC
40229867 TTTCAAAA
1 TTTCAAAA
40229875 AAAATATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 7 0.30
19 11 0.48
20 5 0.22
ACGTcount: A:0.27, C:0.18, G:0.09, T:0.47
Consensus pattern (18 bp):
TTTCAAAATTTTTCGTGC
Found at i:40230054 original size:19 final size:21
Alignment explanation
Indices: 40230014--40230055 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
40230004 AATTTTGTGT
*
40230014 AAAAAAATCCAGTGTTTTCAA
1 AAAAAAATCCAGTGTTTCCAA
40230035 AAAAAAATCCA-T-TTTCCAA
1 AAAAAAATCCAGTGTTTCCAA
40230054 AA
1 AA
40230056 TTTTTAGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 8 0.40
20 1 0.05
21 11 0.55
ACGTcount: A:0.52, C:0.17, G:0.05, T:0.26
Consensus pattern (21 bp):
AAAAAAATCCAGTGTTTCCAA
Found at i:40230093 original size:17 final size:17
Alignment explanation
Indices: 40230047--40230212 Score: 126
Period size: 17 Copynumber: 9.5 Consensus size: 17
40230037 AAAAATCCAT
*
40230047 TTTCCAAAATTTTTAGTG
1 TTTCAAAAATTTTT-GTG
40230065 TCTTCTAAAAATTTTTGTG
1 T-TTC-AAAAATTTTTGTG
*
40230084 TTTCAAAAATTTTCGT-
1 TTTCAAAAATTTTTGTG
*
40230100 TTTCAAAAA-TTTCGTG
1 TTTCAAAAATTTTTGTG
*
40230116 TTTCAAAAATTTTCGTG
1 TTTCAAAAATTTTTGTG
*
40230133 TTTTC-AAAATTTTTCGTA
1 -TTTCAAAAATTTTT-GTG
*
40230151 TTTCAAAAATCCTCTTGT-
1 TTTCAAAAAT--TTTTGTG
**
40230169 TTTCAAAAATTTCGGTG
1 TTTCAAAAATTTTTGTG
**
40230186 TTTTGAAAATTTTCATGT-
1 TTTCAAAAATTTT--TGTG
40230204 TTTCAAAAA
1 TTTCAAAAA
40230213 AAAAATCTCG
Statistics
Matches: 122, Mismatches: 14, Indels: 24
0.76 0.09 0.15
Matches are distributed among these distances:
15 6 0.05
16 21 0.17
17 40 0.33
18 32 0.26
19 11 0.09
20 12 0.10
ACGTcount: A:0.30, C:0.12, G:0.10, T:0.48
Consensus pattern (17 bp):
TTTCAAAAATTTTTGTG
Found at i:40230139 original size:18 final size:18
Alignment explanation
Indices: 40230046--40230212 Score: 152
Period size: 18 Copynumber: 9.6 Consensus size: 18
40230036 AAAAAATCCA
* *
40230046 TTTTCCAAAATTTTTAGTG
1 TTTT-CAAAAATTTTCGTG
* *
40230065 TCTTCTAAAAATTTTTGTG
1 TTTTC-AAAAATTTTCGTG
40230084 -TTTCAAAAATTTTC--G
1 TTTTCAAAAATTTTCGTG
40230099 TTTTCAAAAA-TTTCGTG
1 TTTTCAAAAATTTTCGTG
40230116 -TTTCAAAAATTTTCGTG
1 TTTTCAAAAATTTTCGTG
*
40230133 TTTTCAAAATTTTTCGT-
1 TTTTCAAAAATTTTCGTG
* ** *
40230150 ATTTCAAAAATCCTCTTG
1 TTTTCAAAAATTTTCGTG
40230168 TTTTCAAAAA-TTTCGGTG
1 TTTTCAAAAATTTTC-GTG
* *
40230186 TTTT-GAAAATTTTCATG
1 TTTTCAAAAATTTTCGTG
40230203 TTTTCAAAAA
1 TTTTCAAAAA
40230213 AAAAATCTCG
Statistics
Matches: 120, Mismatches: 18, Indels: 21
0.75 0.11 0.13
Matches are distributed among these distances:
15 5 0.04
16 18 0.15
17 41 0.34
18 42 0.35
19 14 0.12
ACGTcount: A:0.30, C:0.12, G:0.10, T:0.49
Consensus pattern (18 bp):
TTTTCAAAAATTTTCGTG
Found at i:40230155 original size:35 final size:33
Alignment explanation
Indices: 40230071--40230212 Score: 160
Period size: 35 Copynumber: 4.2 Consensus size: 33
40230061 AGTGTCTTCT
*
40230071 AAAAATTTTTGTGTTTCAAAAATTTTC-GTTTTC
1 AAAAA-TTTCGTGTTTCAAAAATTTTCTGTTTTC
40230104 AAAAATTTCGTGTTTCAAAAATTTTCGTGTTTTC
1 AAAAATTTCGTGTTTCAAAAATTTTC-TGTTTTC
* * **
40230138 AAAATTTTTCGTATTTCAAAAATCCTCTTGTTTTC
1 AAAA-ATTTCGTGTTTCAAAAATTTTC-TGTTTTC
**
40230173 AAAAATTTCGGTGTTTTGAAAATTTTCATGTTTTC
1 AAAAATTTC-GTGTTTCAAAAATTTTC-TGTTTTC
40230208 AAAAA
1 AAAAA
40230213 AAAAATCTCG
Statistics
Matches: 92, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
32 20 0.22
33 5 0.05
34 14 0.15
35 53 0.58
ACGTcount: A:0.32, C:0.11, G:0.10, T:0.47
Consensus pattern (33 bp):
AAAAATTTCGTGTTTCAAAAATTTTCTGTTTTC
Found at i:40230227 original size:39 final size:37
Alignment explanation
Indices: 40230173--40230301 Score: 95
Period size: 36 Copynumber: 3.4 Consensus size: 37
40230163 TCTTGTTTTC
*
40230173 AAAAATTTCGGTGTTTTGAAAATTTTCATGTTTTCAAAAA
1 AAAAATCTC-GTGTTTT-AAAATTTTC-TGTTTTCAAAAA
* *
40230213 AAAAATCTCGTGTTTCATAAATTTT-GGTTTT-AAAAA
1 AAAAATCTCGTGTTTTA-AAATTTTCTGTTTTCAAAAA
* * * *
40230249 AAATAT-T-ATGTCTTAAAATTCTCGTGTTTTCAAAACA
1 AAAAATCTCGTGTTTTAAAATTTTC-TGTTTTCAAAA-A
*
40230286 AGAAATTCTCGTGTTT
1 A-AAAATCTCGTGTTT
40230302 CAATCGGATC
Statistics
Matches: 68, Mismatches: 13, Indels: 16
0.70 0.13 0.16
Matches are distributed among these distances:
33 6 0.09
34 5 0.07
35 6 0.09
36 14 0.21
37 7 0.10
38 4 0.06
39 14 0.21
40 12 0.18
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.42
Consensus pattern (37 bp):
AAAAATCTCGTGTTTTAAAATTTTCTGTTTTCAAAAA
Found at i:40242195 original size:122 final size:119
Alignment explanation
Indices: 40241977--40242202 Score: 285
Period size: 121 Copynumber: 1.9 Consensus size: 119
40241967 AATTTTTAAA
** * **
40241977 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTAGTTTATG
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCCGAGGTATTTTA-TAAATG
** *
40242042 TTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTC
65 TTTTAAATCAACTCATATTGCGAGAAGTGAGTTAAGCCTTTTAATTTTTGTTTTC
**
40242097 AAAATCAACTCATATTGCGAGAAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTT-TAAAT-
1 AAAATCAACTCATATTGCGAG-AAATGAGTTGAGCCTCAAGACACGCCGAGGTATTTTATAAATG
*
40242160 TTTTAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT
65 TTTT----AAATCAACTCATATTGCGAGAAGTGAGTTAAGCCT
40242203 CGGGGCACGC
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
118 4 0.04
119 3 0.03
120 21 0.23
121 31 0.34
122 31 0.34
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.33
Consensus pattern (119 bp):
AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCCGAGGTATTTTATAAATGT
TTTAAATCAACTCATATTGCGAGAAGTGAGTTAAGCCTTTTAATTTTTGTTTTC
Found at i:40242356 original size:191 final size:191
Alignment explanation
Indices: 40241909--40242711 Score: 1427
Period size: 190 Copynumber: 4.2 Consensus size: 191
40241899 CTTTCCAAGG
40241909 AAAATCAACTCATA-TGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
40241973 TAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGGCACGCCGAGGTA-TTTTAGT
66 TAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGT
40242037 TTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTG-TTTTC
131 TTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
40242097 AAAATCAACTCATATTGCGAGAAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTT
1 AAAATCAACTCATATTGCGAG-AAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTT
*
40242162 TTAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAG
65 TTAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAG
40242227 TTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTG-TTTTC
130 TTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
40242288 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
* *
40242353 TTAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTC-GGGCACGCCGAGGTATGTTTTAG
66 TAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGGCACGCCGAGGTAT-TTTTAG
* *
40242417 TTTATGTTTTAAATTGACTTATGTTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
130 TTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
40242479 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
*
40242544 AAAAAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGGCACGCCGAGGTATTTT
66 ----TAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGGCACGCCGAGGTATTTT
40242609 TAGTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
127 TAGTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
* **
40242674 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTC
1 -AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTC
40242712 GGCTCACATG
Statistics
Matches: 592, Mismatches: 12, Indels: 14
0.96 0.02 0.02
Matches are distributed among these distances:
188 14 0.02
189 22 0.04
190 244 0.41
191 158 0.27
195 104 0.18
196 50 0.08
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.35
Consensus pattern (191 bp):
AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
TAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGT
TTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
Found at i:40242384 original size:121 final size:121
Alignment explanation
Indices: 40242167--40242392 Score: 303
Period size: 121 Copynumber: 1.9 Consensus size: 121
40242157 AATTTTTAAA
* ** * *
40242167 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTAT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAATTTAT
** ** *
40242232 GTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTC
66 GTTAAAAATCAACTCATATTGCGAGAAGTGAGTTAAGCCTTTTAATTTTTGTTTTC
**
40242288 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTT-
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCCGAGGTATTTTT-AATTTA
*
40242352 T-TTAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT
65 TGTT-AAAAATCAACTCATATTGCGAGAAGTGAGTTAAGCCT
40242393 CGGGCACGCC
Statistics
Matches: 90, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
120 2 0.02
121 84 0.93
122 4 0.04
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.34
Consensus pattern (121 bp):
AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAATTTAT
GTTAAAAATCAACTCATATTGCGAGAAGTGAGTTAAGCCTTTTAATTTTTGTTTTC
Found at i:40242751 original size:16 final size:17
Alignment explanation
Indices: 40242730--40242763 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
40242720 TGCTGAGGTA
*
40242730 TTTTCAATTTATG-TTT
1 TTTTCAATCTATGCTTT
40242746 TTTTCAATCTATGCTTT
1 TTTTCAATCTATGCTTT
40242763 T
1 T
40242764 CAAAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.18, C:0.12, G:0.06, T:0.65
Consensus pattern (17 bp):
TTTTCAATCTATGCTTT
Found at i:40242927 original size:85 final size:88
Alignment explanation
Indices: 40242669--40242927 Score: 300
Period size: 91 Copynumber: 2.9 Consensus size: 88
40242659 TAATTTTTGT
*
40242669 TTTTCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTC-GGCTCACATGCTGAGGTATTT
1 TTTTC-AAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGC-CACACGCTGAGGTATTT
*
40242733 TCAATTTATGTTTTTTTCAA-TCTATGC
64 TCAATTTCTG-TTTTTT-AATTCTA-GC
* *
40242760 TTTTCAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAAGG---CACGCTGAGGTATTT
1 TTTTC-AAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTC-AGGCCACACGCTGAGGTATTT
* **
40242822 TCAGTTTCTGCTTTACTAATTCTA-C
64 TCAATTTCTG-TTTTTTAATTCTAGC
* *
40242847 TTTTC-AAATCAACTCATATTGCAAGAGGTGAGTTGAGTCTCAGGCCACACGCTGAGGTCTTTTC
1 TTTTCAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGCCACACGCTGAGGTATTTTC
*
40242911 AAATTCTG-TTTTTAATT
66 AATTTCTGTTTTTTAATT
40242928 TCTGTTTTTT
Statistics
Matches: 146, Mismatches: 16, Indels: 18
0.81 0.09 0.10
Matches are distributed among these distances:
84 3 0.02
85 40 0.27
87 28 0.19
88 2 0.01
89 30 0.21
91 41 0.28
93 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (88 bp):
TTTTCAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGCCACACGCTGAGGTATTTTC
AATTTCTGTTTTTTAATTCTAGC
Found at i:40242930 original size:13 final size:13
Alignment explanation
Indices: 40242914--40242947 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 13
40242904 TCTTTTCAAA
40242914 TTCTGTTTTTAAT
1 TTCTGTTTTTAAT
40242927 TTCTGTTTTTTTAAT
1 TTCTG--TTTTTAAT
40242942 TTCTGT
1 TTCTGT
40242948 GTTTCAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 6 0.32
15 13 0.68
ACGTcount: A:0.12, C:0.09, G:0.09, T:0.71
Consensus pattern (13 bp):
TTCTGTTTTTAAT
Found at i:40242939 original size:15 final size:15
Alignment explanation
Indices: 40242919--40242947 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
40242909 TCAAATTCTG
40242919 TTTTTAATTTCTGTT
1 TTTTTAATTTCTGTT
40242934 TTTTTAATTTCTGT
1 TTTTTAATTTCTGT
40242948 GTTTCAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.07, G:0.07, T:0.72
Consensus pattern (15 bp):
TTTTTAATTTCTGTT
Found at i:40243112 original size:54 final size:55
Alignment explanation
Indices: 40243024--40243239 Score: 297
Period size: 54 Copynumber: 4.1 Consensus size: 55
40243014 TCAATTTCTA
* *
40243024 CTTTTCAATTTCTGTTTTTCAAAAATCAATTCATATTGCGAGAGGTGAGTTGAGC
1 CTTTTCAATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
*
40243079 CTTTT-AATTTCTATTTTTCAAAAACCAACTCATATTGCGAGAGGTGAGTTGAGC
1 CTTTTCAATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
40243133 C--TT---TTTCTATTTTTCAAAAAATCAACTC--ATTGCGAGAGGTGAGTTGAGC
1 CTTTTCAATTTCTATTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
* * *
40243182 CTTTTGCAAATTCT-GTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGC
1 CTTTT-CAATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
40243237 CTT
1 CTT
40243240 GGCTCACGTG
Statistics
Matches: 145, Mismatches: 7, Indels: 18
0.85 0.04 0.11
Matches are distributed among these distances:
49 22 0.15
50 12 0.08
51 13 0.09
52 2 0.01
53 12 0.08
54 52 0.36
55 32 0.22
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.38
Consensus pattern (55 bp):
CTTTTCAATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
Found at i:40243212 original size:104 final size:103
Alignment explanation
Indices: 40243032--40243239 Score: 312
Period size: 104 Copynumber: 2.0 Consensus size: 103
40243022 TACTTTTCAA
* * * *
40243032 TTTCTGTTTTTCAAAAATCAATTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTCTATTTTT
1 TTTCTATTTTTCAAAAATCAACTCA-ATTGCGAGAGGTGAGTTGAGCCTTTTAAATTCTAGTTTT
*
40243097 CAAAAACCAACTCATATTGCGAGAGGTGAGTTGAGCCTT
65 CAAAAACCAACTCATATTGCGAGAAGTGAGTTGAGCCTT
40243136 TTTCTATTTTTCAAAAAATCAACTC-ATTGCGAGAGGTGAGTTGAGCCTTTTGCAAATTCT-GTT
1 TTTCTATTTTTC-AAAAATCAACTCAATTGCGAGAGGTGAGTTGAGCCTTTT--AAATTCTAGTT
*
40243199 TTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTT
63 TTCAAAAACCAACTCATATTGCGAGAAGTGAGTTGAGCCTT
40243240 GGCTCACGTG
Statistics
Matches: 95, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
103 26 0.27
104 52 0.55
105 17 0.18
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (103 bp):
TTTCTATTTTTCAAAAATCAACTCAATTGCGAGAGGTGAGTTGAGCCTTTTAAATTCTAGTTTTC
AAAAACCAACTCATATTGCGAGAAGTGAGTTGAGCCTT
Found at i:40243505 original size:14 final size:15
Alignment explanation
Indices: 40243480--40243514 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
40243470 TTTAATTTTC
40243480 AAAATTTCAAAAAAA
1 AAAATTTCAAAAAAA
*
40243495 AAAATTT-AAAAATA
1 AAAATTTCAAAAAAA
40243509 AAAATT
1 AAAATT
40243515 GCATTTTGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (15 bp):
AAAATTTCAAAAAAA
Found at i:40243573 original size:30 final size:30
Alignment explanation
Indices: 40243510--40243611 Score: 125
Period size: 30 Copynumber: 3.4 Consensus size: 30
40243500 TTAAAAATAA
* *
40243510 AAATTGCATTTTGACCCCTAAACTTT-TCCT
1 AAATTTCATTTTGACCCCTAAACTTTCT-TT
*
40243540 AAATTTCATTTTGACCCTTAAACTTTCTTT
1 AAATTTCATTTTGACCCCTAAACTTTCTTT
* ** *
40243570 AAATTTCACTTAAACCCCTAAACTTTCATT
1 AAATTTCATTTTGACCCCTAAACTTTCTTT
40243600 AAATTTCATTTT
1 AAATTTCATTTT
40243612 AATCCTAAAT
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
30 60 0.98
31 1 0.02
ACGTcount: A:0.30, C:0.23, G:0.03, T:0.44
Consensus pattern (30 bp):
AAATTTCATTTTGACCCCTAAACTTTCTTT
Found at i:40243893 original size:10 final size:10
Alignment explanation
Indices: 40243874--40243923 Score: 59
Period size: 10 Copynumber: 5.2 Consensus size: 10
40243864 TTTTTCGAAG
*
40243874 GAAAAAAGAA
1 GAAAAGAGAA
40243884 GAAAAGAGAA
1 GAAAAGAGAA
40243894 GAAAAGAGAA
1 GAAAAGAGAA
* *
40243904 -AGAGGAGAA
1 GAAAAGAGAA
40243913 GAAAAGA-AA
1 GAAAAGAGAA
40243922 GA
1 GA
40243924 GTACCGGCGT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
9 11 0.32
10 23 0.68
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (10 bp):
GAAAAGAGAA
Found at i:40243924 original size:17 final size:19
Alignment explanation
Indices: 40243877--40243919 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
40243867 TTCGAAGGAA
40243877 AAAAGAAGAAA-A-GAGAAG
1 AAAAG-AGAAAGAGGAGAAG
40243895 AAAAGAGAAAGAGGAGAAG
1 AAAAGAGAAAGAGGAGAAG
40243914 AAAAGA
1 AAAAGA
40243920 AAGAGTACCG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 5 0.22
18 6 0.26
19 12 0.52
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (19 bp):
AAAAGAGAAAGAGGAGAAG
Found at i:40243995 original size:3 final size:3
Alignment explanation
Indices: 40243989--40244029 Score: 73
Period size: 3 Copynumber: 13.3 Consensus size: 3
40243979 GTGTAGGAGG
40243989 AGA AGA AGA AGA AGA AGA AGA AGA AGAA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AG-A AGA AGA AGA AGA A
40244030 AGAAAAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:40244214 original size:31 final size:33
Alignment explanation
Indices: 40244148--40244222 Score: 91
Period size: 31 Copynumber: 2.3 Consensus size: 33
40244138 AATTAATTAA
*
40244148 AAAAAAACAACACAAAAAAAAAACAAATCAGCCC
1 AAAAAAA-AACACAAAAAAAAAACAAAGCAGCCC
**
40244182 AAAAAAAAAC-CAAAGCAAAAA-AAAGCAGCCC
1 AAAAAAAAACACAAAAAAAAAACAAAGCAGCCC
40244213 AAAAAGAAAA
1 AAAAA-AAAA
40244223 GGCCCAAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
31 14 0.38
32 13 0.35
33 3 0.08
34 7 0.19
ACGTcount: A:0.72, C:0.20, G:0.07, T:0.01
Consensus pattern (33 bp):
AAAAAAAAACACAAAAAAAAAACAAAGCAGCCC
Found at i:40244244 original size:27 final size:24
Alignment explanation
Indices: 40244214--40244264 Score: 57
Period size: 25 Copynumber: 2.0 Consensus size: 24
40244204 AAGCAGCCCA
40244214 AAAAGAAAAGGCCCAAAAAAGAAGAAG
1 AAAA-AAAA-GCCCAAAAAA-AAGAAG
* *
40244241 AAAAAACAGCCCAGAAAAAAGAAG
1 AAAAAAAAGCCCAAAAAAAAGAAG
40244265 CAGCCCACCA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 6 0.27
25 9 0.41
26 3 0.14
27 4 0.18
ACGTcount: A:0.67, C:0.14, G:0.20, T:0.00
Consensus pattern (24 bp):
AAAAAAAAGCCCAAAAAAAAGAAG
Found at i:40244335 original size:15 final size:15
Alignment explanation
Indices: 40244315--40244412 Score: 110
Period size: 15 Copynumber: 6.5 Consensus size: 15
40244305 CAGGCCAGGA
* *
40244315 AAAAAAGAGAGAAAG
1 AAAAAAGAAAAAAAG
40244330 AAAAAAGAAAAAAAG
1 AAAAAAGAAAAAAAG
*
40244345 AAAGAAGAAAAAAAG
1 AAAAAAGAAAAAAAG
*
40244360 AAAAGAGAAAAAAAGG
1 AAAAAAGAAAAAAA-G
*
40244376 AAAAAAGGAAAAAAG
1 AAAAAAGAAAAAAAG
*
40244391 AAGAAAA-AAAGAAA-
1 AA-AAAAGAAAAAAAG
40244405 AAAAAAGA
1 AAAAAAGA
40244413 GTTTCAATTC
Statistics
Matches: 71, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
13 4 0.06
14 3 0.04
15 47 0.66
16 17 0.24
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (15 bp):
AAAAAAGAAAAAAAG
Found at i:40244343 original size:23 final size:23
Alignment explanation
Indices: 40244313--40244412 Score: 102
Period size: 22 Copynumber: 4.4 Consensus size: 23
40244303 AGCAGGCCAG
*
40244313 GAAAAAAAGAGAGAAAGAAAAAA
1 GAAAAAAAGAAAGAAAGAAAAAA
40244336 GAAAAAAAGAAAG-AAGAAAAAA
1 GAAAAAAAGAAAGAAAGAAAAAA
* *
40244358 -AGAAAAGAGAAAAAAAGGAAAAAA
1 GA-AAAAAAGAAAGAAA-GAAAAAA
*
40244382 GGAAAAAAG-AAGAAA-AAAAGAA
1 GAAAAAAAGAAAGAAAGAAAA-AA
40244404 -AAAAAAAGA
1 GAAAAAAAGA
40244413 GTTTCAATTC
Statistics
Matches: 64, Mismatches: 7, Indels: 13
0.76 0.08 0.15
Matches are distributed among these distances:
21 12 0.19
22 20 0.31
23 19 0.30
24 13 0.20
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (23 bp):
GAAAAAAAGAAAGAAAGAAAAAA
Found at i:40244370 original size:27 final size:26
Alignment explanation
Indices: 40244313--40244408 Score: 94
Period size: 26 Copynumber: 3.7 Consensus size: 26
40244303 AGCAGGCCAG
40244313 GAAAAAAAGAGAGAAAGAAAA-AAGAAAA
1 GAAAAAAAGA-AGAAA-AAAAGAA-AAAA
* *
40244341 -AAAGAAAGAAGAAAAAAAGAAAAGA
1 GAAAAAAAGAAGAAAAAAAGAAAAAA
*
40244366 GAAAAAAAG--GAAAAAAGGAAAAAA
1 GAAAAAAAGAAGAAAAAAAGAAAAAA
40244390 GAAGAAAAA-AAGAAAAAAA
1 GAA-AAAAAGAAGAAAAAAA
40244409 AAGAGTTTCA
Statistics
Matches: 57, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
24 16 0.28
25 12 0.21
26 21 0.37
27 8 0.14
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (26 bp):
GAAAAAAAGAAGAAAAAAAGAAAAAA
Found at i:40244407 original size:8 final size:8
Alignment explanation
Indices: 40244313--40244408 Score: 99
Period size: 8 Copynumber: 12.0 Consensus size: 8
40244303 AGCAGGCCAG
40244313 GAAAAAAA
1 GAAAAAAA
* *
40244321 GAGAGAAA
1 GAAAAAAA
40244329 G-AAAAAA
1 GAAAAAAA
40244336 GAAAAAAA
1 GAAAAAAA
*
40244344 G-AAAGAA
1 GAAAAAAA
40244351 GAAAAAAA
1 GAAAAAAA
*
40244359 G-AAAAGA
1 GAAAAAAA
40244366 GAAAAAAA
1 GAAAAAAA
*
40244374 GGAAAAAAG
1 -GAAAAAAA
40244383 GAAAAAAGAA
1 G-AAAAA-AA
40244393 GAAAAAAA
1 GAAAAAAA
40244401 GAAAAAAA
1 GAAAAAAA
40244409 AAGAGTTTCA
Statistics
Matches: 72, Mismatches: 10, Indels: 12
0.77 0.11 0.13
Matches are distributed among these distances:
7 17 0.24
8 36 0.50
9 17 0.24
10 2 0.03
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (8 bp):
GAAAAAAA
Found at i:40244809 original size:19 final size:18
Alignment explanation
Indices: 40244768--40244812 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
40244758 AAATTTCTAT
40244768 TTTCAAAATTTTTCGTGC
1 TTTCAAAATTTTTCGTGC
*
40244786 CTTCAAAATTTTTCTCGTG-
1 TTTCAAAA-TTTT-TCGTGC
40244805 TTTCAAAA
1 TTTCAAAA
40244813 AAAATATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 7 0.30
19 11 0.48
20 5 0.22
ACGTcount: A:0.27, C:0.18, G:0.09, T:0.47
Consensus pattern (18 bp):
TTTCAAAATTTTTCGTGC
Found at i:40245064 original size:18 final size:17
Alignment explanation
Indices: 40244990--40245151 Score: 150
Period size: 17 Copynumber: 9.4 Consensus size: 17
40244980 ATCCATTTTC
* *
40244990 CAAAATTTTTAGTGTCTT
1 CAAAAATTTTCGTGT-TT
*
40245008 CTAAAAATTTTTGTGTTT
1 C-AAAAATTTTCGTGTTT
40245026 CAAAAATTTTCGT-TTT
1 CAAAAATTTTCGTGTTT
*
40245042 CAAAAATTTCCGTGTTT
1 CAAAAATTTTCGTGTTT
40245059 CAAAAATTTTCGTGTTTT
1 CAAAAATTTTCGTG-TTT
* *
40245077 CAAAATTTTTCGTATTT
1 CAAAAATTTTCGTGTTT
** *
40245094 CAAAAATCCTCTTGTTTT
1 CAAAAATTTTCGTG-TTT
40245112 C-AAAA-TTTCGGTGTTT
1 CAAAAATTTTC-GTGTTT
**
40245128 TGAAAATTTTCGTGTTTT
1 CAAAAATTTTCGTG-TTT
40245146 CAAAAA
1 CAAAAA
40245152 AAAATCTCGT
Statistics
Matches: 118, Mismatches: 18, Indels: 16
0.78 0.12 0.11
Matches are distributed among these distances:
16 20 0.17
17 52 0.44
18 34 0.29
19 12 0.10
ACGTcount: A:0.30, C:0.12, G:0.10, T:0.48
Consensus pattern (17 bp):
CAAAAATTTTCGTGTTT
Found at i:40245095 original size:35 final size:35
Alignment explanation
Indices: 40245011--40245150 Score: 164
Period size: 35 Copynumber: 4.1 Consensus size: 35
40245001 GTGTCTTCTA
40245011 AAAATTTTT-GTGTTTCAAAAATTTTC--GTTTTC
1 AAAATTTTTCGTGTTTCAAAAATTTTCGTGTTTTC
* *
40245043 AAAAATTTCCGTGTTTCAAAAATTTTCGTGTTTTC
1 AAAATTTTTCGTGTTTCAAAAATTTTCGTGTTTTC
* ** *
40245078 AAAATTTTTCGTATTTCAAAAATCCTCTTGTTTTC
1 AAAATTTTTCGTGTTTCAAAAATTTTCGTGTTTTC
**
40245113 AAAA--TTTCGGTGTTTTGAAAATTTTCGTGTTTTC
1 AAAATTTTTC-GTGTTTCAAAAATTTTCGTGTTTTC
40245147 AAAA
1 AAAA
40245151 AAAAATCTCG
Statistics
Matches: 90, Mismatches: 14, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
32 7 0.08
33 21 0.23
34 23 0.26
35 39 0.43
ACGTcount: A:0.29, C:0.12, G:0.11, T:0.48
Consensus pattern (35 bp):
AAAATTTTTCGTGTTTCAAAAATTTTCGTGTTTTC
Found at i:40245117 original size:52 final size:50
Alignment explanation
Indices: 40245001--40245151 Score: 148
Period size: 52 Copynumber: 2.9 Consensus size: 50
40244991 AAAATTTTTA
* *
40245001 GTGTCTTCTAAAAATTTTTGTG-TTTCAAAAATTTTCGTTTTCAAAAATTTCC
1 GTGT-TTC-AAAAATTTTCGTGTTTTC-AAAATTTTCGTTTTCAAAAATCTCC
40245053 GTGTTTCAAAAATTTTCGTGTTTTCAAAATTTTTCGTATTTCAAAAATC-CTC
1 GTGTTTCAAAAATTTTCGTGTTTTCAAAA-TTTTCGT-TTTCAAAAATCTC-C
* *
40245105 TTGTTTTC-AAAA-TTTCGGTGTTTTGAAAATTTTCGTGTTTTCAAAAA
1 GTG-TTTCAAAAATTTTC-GTGTTTTCAAAATTTTC--GTTTTCAAAAA
40245152 AAAATCTCGT
Statistics
Matches: 87, Mismatches: 4, Indels: 16
0.81 0.04 0.15
Matches are distributed among these distances:
50 16 0.18
51 24 0.28
52 41 0.47
53 6 0.07
ACGTcount: A:0.28, C:0.13, G:0.11, T:0.48
Consensus pattern (50 bp):
GTGTTTCAAAAATTTTCGTGTTTTCAAAATTTTCGTTTTCAAAAATCTCC
Found at i:40249596 original size:9 final size:10
Alignment explanation
Indices: 40249580--40249751 Score: 55
Period size: 9 Copynumber: 18.2 Consensus size: 10
40249570 TAAACTTATT
40249580 AAATTATAAA
1 AAATTATAAA
40249590 AAA-TATAAA
1 AAATTATAAA
40249599 AAATTAT-AA
1 AAATTATAAA
* * *
40249608 AAGTAATAAG
1 AAATTATAAA
* **
40249618 AACTTATTTA
1 AAATTATAAA
**
40249628 AAA-TATTTA
1 AAATTATAAA
40249637 AAATTA-AATA
1 AAATTATAA-A
* *
40249647 AAAGTAT-TA
1 AAATTATAAA
*
40249656 GAATTATTAAA
1 AAATTA-TAAA
40249667 AAA--ATAAA
1 AAATTATAAA
*
40249675 AAATTGT-AA
1 AAATTATAAA
*
40249684 AAACTATAAA
1 AAATTATAAA
* *
40249694 ATA-TATTAA
1 AAATTATAAA
*
40249703 AAA-TAT-TA
1 AAATTATAAA
*
40249711 AAATTGATATA
1 AAATT-ATAAA
*
40249722 AATTTAT-AA
1 AAATTATAAA
40249731 AAATT-TAAA
1 AAATTATAAA
*
40249740 AAATCATAAA
1 AAATTATAAA
40249750 AA
1 AA
40249752 CTTGAACCGG
Statistics
Matches: 119, Mismatches: 28, Indels: 30
0.67 0.16 0.17
Matches are distributed among these distances:
8 12 0.10
9 60 0.50
10 38 0.32
11 9 0.08
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (10 bp):
AAATTATAAA
Found at i:40249602 original size:19 final size:19
Alignment explanation
Indices: 40249580--40249751 Score: 81
Period size: 19 Copynumber: 9.1 Consensus size: 19
40249570 TAAACTTATT
40249580 AAATTATAAAAAATATAAA
1 AAATTATAAAAAATATAAA
* *
40249599 AAATTAT-AAAAGTAATAAG
1 AAATTATAAAAAAT-ATAAA
* ** **
40249618 AACTTATTTAAAATATTTA
1 AAATTATAAAAAATATAAA
*
40249637 AAATTA-AATAAAAGTAT-TA
1 AAATTATAA-AAAA-TATAAA
*
40249656 GAATTATTAAAAAA-ATAAA
1 AAATTA-TAAAAAATATAAA
* *
40249675 AAATTGTAAAAACTATAAA
1 AAATTATAAAAAATATAAA
* * *
40249694 ATA-TATTAAAAATAT-TA
1 AAATTATAAAAAATATAAA
* *
40249711 AAATTGAT-ATAAATTTATAA
1 AAATT-ATAAAAAATATA-AA
40249731 AAATT-TAAAAAATCATAAA
1 AAATTATAAAAAAT-ATAAA
40249750 AA
1 AA
40249752 CTTGAACCGG
Statistics
Matches: 112, Mismatches: 27, Indels: 28
0.67 0.16 0.17
Matches are distributed among these distances:
17 3 0.03
18 30 0.27
19 58 0.52
20 19 0.17
21 2 0.02
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (19 bp):
AAATTATAAAAAATATAAA
Found at i:40249631 original size:38 final size:36
Alignment explanation
Indices: 40249581--40249713 Score: 124
Period size: 38 Copynumber: 3.6 Consensus size: 36
40249571 AAACTTATTA
*
40249581 AATTATAAAAAATATAAAAAATTATAAAAGTAATAAG
1 AATTATTAAAAATATAAAAAATTATAAAAGT-ATAAG
* ** *
40249618 AACTTATTTAAAATATTTAAAATTAAATAAAAGTATTAG
1 AA-TTATTAAAAATATAAAAAATT--ATAAAAGTATAAG
* * *
40249657 AATTATTAAAAAAATAAAAAATTGTAAAAACTATAA-
1 AATTATTAAAAATATAAAAAATTAT-AAAAGTATAAG
*
40249693 AATATATTAAAAATATTAAAA
1 AAT-TATTAAAAATATAAAAA
40249714 TTGATATAAA
Statistics
Matches: 77, Mismatches: 14, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
36 4 0.05
37 25 0.32
38 34 0.44
39 6 0.08
40 8 0.10
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.32
Consensus pattern (36 bp):
AATTATTAAAAATATAAAAAATTATAAAAGTATAAG
Found at i:40249713 original size:8 final size:9
Alignment explanation
Indices: 40249488--40249713 Score: 67
Period size: 9 Copynumber: 24.6 Consensus size: 9
40249478 TATTTTCTCA
40249488 TAAAAATGAT
1 TAAAAAT-AT
40249498 TACAAAA-A-
1 TA-AAAATAT
40249506 TAAAAA-AT
1 TAAAAATAT
*
40249514 TATAAAATCT
1 TA-AAAATAT
*
40249524 GAAACAATAT
1 TAAA-AATAT
*
40249534 TAGAAATAT
1 TAAAAATAT
*
40249543 TAAAAA-CT
1 TAAAAATAT
*
40249551 TAAAAA-AA
1 TAAAAATAT
*
40249559 TAAAATTGAT
1 TAAAAAT-AT
**
40249569 ATAAACTTAT
1 -TAAAAATAT
*
40249579 T-AAATTAT
1 TAAAAATAT
*
40249587 AAAAAATA-
1 TAAAAATAT
40249595 TAAAAA-AT
1 TAAAAATAT
*
40249603 TATAAAAGTAA
1 TA-AAAA-TAT
*
40249614 TAAGAACTTAT
1 TAA-AA-ATAT
*
40249625 TTAAAATATT
1 TAAAAATA-T
* *
40249635 TAAAATTAAA
1 TAAAAAT-AT
*
40249645 TAAAAGTAT
1 TAAAAATAT
* *
40249654 TAGAATTAT
1 TAAAAATAT
*
40249663 TAAAAAAAT
1 TAAAAATAT
*
40249672 AAAAAAT-T
1 TAAAAATAT
40249680 GTAAAAACTA-
1 -TAAAAA-TAT
40249690 TAAAATATAT
1 TAAAA-ATAT
40249700 TAAAAATAT
1 TAAAAATAT
40249709 TAAAA
1 TAAAA
40249714 TTGATATAAA
Statistics
Matches: 160, Mismatches: 34, Indels: 45
0.67 0.14 0.19
Matches are distributed among these distances:
7 6 0.04
8 30 0.19
9 69 0.43
10 35 0.22
11 20 0.12
ACGTcount: A:0.62, C:0.03, G:0.04, T:0.31
Consensus pattern (9 bp):
TAAAAATAT
Found at i:40249741 original size:28 final size:27
Alignment explanation
Indices: 40249673--40249750 Score: 70
Period size: 28 Copynumber: 2.8 Consensus size: 27
40249663 TAAAAAAATA
40249673 AAAAATTGTAAAAACTATAAAATATATT
1 AAAAATT-TAAAAACTATAAAATATATT
* *
40249701 AAAAATATT-AAAATTGATATAAATTTA-T
1 AAAAAT-TTAAAAACT-ATA-AAATATATT
*
40249729 AAAAATTTAAAAAATCATAAAA
1 AAAAATTTAAAAACT-ATAAAA
40249751 ACTTGAACCG
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
27 10 0.24
28 25 0.60
29 7 0.17
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.32
Consensus pattern (27 bp):
AAAAATTTAAAAACTATAAAATATATT
Found at i:40250305 original size:29 final size:28
Alignment explanation
Indices: 40250241--40250315 Score: 71
Period size: 29 Copynumber: 2.6 Consensus size: 28
40250231 TAGAATTTTT
* *
40250241 ATATTTTTATAGTATTTAAAAGTTTTTAC
1 ATATTTTTATAAT-TTTAAAAGTTTATAC
*
40250270 ATGTTTTTATAATTTTAATAAGTTTATATC
1 ATATTTTTATAATTTTAA-AAGTTTATA-C
* *
40250300 A-ATTTTAATATTTTTA
1 ATATTTTTATAATTTTA
40250316 TAATTTTTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
28 5 0.13
29 31 0.82
30 2 0.05
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.57
Consensus pattern (28 bp):
ATATTTTTATAATTTTAAAAGTTTATAC
Found at i:40259105 original size:5 final size:5
Alignment explanation
Indices: 40259095--40259132 Score: 76
Period size: 5 Copynumber: 7.6 Consensus size: 5
40259085 GGTTTTGTGA
40259095 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
40259133 GAATACACAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:40263562 original size:5 final size:5
Alignment explanation
Indices: 40263552--40263583 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
40263542 CTATTTGTGA
40263552 AAAAT AAAAT AAAAT AAAAT -AAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
40263584 GAACACACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:40263577 original size:9 final size:9
Alignment explanation
Indices: 40263553--40263583 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
40263543 TATTTGTGAA
40263553 AAATAAAAT
1 AAATAAAAT
40263562 AAAATAAAAT
1 -AAATAAAAT
40263572 AAATAAAAT
1 AAATAAAAT
40263581 AAA
1 AAA
40263584 GAACACACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAATAAAAT
Found at i:40264750 original size:51 final size:51
Alignment explanation
Indices: 40264681--40264779 Score: 198
Period size: 51 Copynumber: 1.9 Consensus size: 51
40264671 GGATTAAAGT
40264681 CTTGGTTACGTACTACTGGAAAAATATATATGTACTTTCTCCTAATTAAGC
1 CTTGGTTACGTACTACTGGAAAAATATATATGTACTTTCTCCTAATTAAGC
40264732 CTTGGTTACGTACTACTGGAAAAATATATATGTACTTTCTCCTAATTA
1 CTTGGTTACGTACTACTGGAAAAATATATATGTACTTTCTCCTAATTA
40264780 CATTTGCATT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.38
Consensus pattern (51 bp):
CTTGGTTACGTACTACTGGAAAAATATATATGTACTTTCTCCTAATTAAGC
Found at i:40269206 original size:36 final size:36
Alignment explanation
Indices: 40269138--40269206 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 36
40269128 TGAATAATTT
* * *
40269138 TAAAATAGATAATATATATACATATATATAAAAGTG
1 TAAAATAAATAATATATATACATAAACATAAAAGTG
* *
40269174 TAAAATAAATAATATATATATATAAACCTAAAA
1 TAAAATAAATAATATATATACATAAACATAAAA
40269207 TAAATAATAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 28 1.00
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.32
Consensus pattern (36 bp):
TAAAATAAATAATATATATACATAAACATAAAAGTG
Found at i:40269328 original size:23 final size:24
Alignment explanation
Indices: 40269283--40269328 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
40269273 GTAATAAAAT
40269283 AATAATACATAAAAACAAGTTTAA
1 AATAATACATAAAAACAAGTTTAA
* *
40269307 AATAATATAT-AAAGCAAGTTTA
1 AATAATACATAAAAACAAGTTTA
40269329 GAGTAAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.59, C:0.07, G:0.07, T:0.28
Consensus pattern (24 bp):
AATAATACATAAAAACAAGTTTAA
Found at i:40269522 original size:26 final size:25
Alignment explanation
Indices: 40269493--40269560 Score: 75
Period size: 25 Copynumber: 2.7 Consensus size: 25
40269483 CTTTAAAGTA
** *
40269493 AATAATATATAAAAAGTTTTAACATG
1 AATAATATATAAAAA-ACTTAAAATG
*
40269519 AATAAAATATAAAAAACTTAAAATG
1 AATAATATATAAAAAACTTAAAATG
40269544 AATAATA-ATAATAAAAC
1 AATAATATATAA-AAAAC
40269561 AAATATTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
24 4 0.11
25 18 0.50
26 14 0.39
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.28
Consensus pattern (25 bp):
AATAATATATAAAAAACTTAAAATG
Found at i:40269539 original size:25 final size:26
Alignment explanation
Indices: 40269449--40269559 Score: 73
Period size: 26 Copynumber: 4.1 Consensus size: 26
40269439 AAAATAATGT
* * *
40269449 AAAAG-CTTAAAATAAATAATATGTGGA
1 AAAAGACTTAAAATGAATAAAATAT--A
* * *
40269476 AAAAGAACTTTAAAGTAAATAATATATA
1 AAAAG-AC-TTAAAATGAATAAAATATA
** *
40269504 AAAAGTTTTAACATGAATAAAATATA
1 AAAAGACTTAAAATGAATAAAATATA
40269530 AAAA-ACTTAAAATGAATAATAATAATA
1 AAAAGACTTAAAATGAATAA-AAT-ATA
40269557 AAA
1 AAA
40269560 CAAATATTTT
Statistics
Matches: 68, Mismatches: 11, Indels: 10
0.76 0.12 0.11
Matches are distributed among these distances:
25 12 0.18
26 22 0.32
27 11 0.16
28 6 0.09
29 1 0.01
30 16 0.24
ACGTcount: A:0.61, C:0.04, G:0.08, T:0.27
Consensus pattern (26 bp):
AAAAGACTTAAAATGAATAAAATATA
Found at i:40270380 original size:24 final size:25
Alignment explanation
Indices: 40270353--40270419 Score: 68
Period size: 24 Copynumber: 2.7 Consensus size: 25
40270343 AATCGATTTA
*
40270353 AAATACAAATAAGAAAAAAGA-AAG
1 AAATACAAAAAAGAAAAAAGAGAAG
40270377 AAAT-CGAAAAAAGGAAAAAAAGAGAAG
1 AAATAC-AAAAAA-G-AAAAAAGAGAAG
*
40270404 AAA-ACAAAGAAGAAAA
1 AAATACAAAAAAGAAAA
40270420 TCGAAAATCA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
23 1 0.03
24 13 0.36
25 2 0.06
26 13 0.36
27 7 0.19
ACGTcount: A:0.75, C:0.04, G:0.16, T:0.04
Consensus pattern (25 bp):
AAATACAAAAAAGAAAAAAGAGAAG
Found at i:40276448 original size:17 final size:17
Alignment explanation
Indices: 40276426--40276459 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
40276416 CAAGGGACAA
40276426 TTTCTACATACTTGGTC
1 TTTCTACATACTTGGTC
40276443 TTTCTACATACTTGGTC
1 TTTCTACATACTTGGTC
40276460 AACTAACACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.24, G:0.12, T:0.47
Consensus pattern (17 bp):
TTTCTACATACTTGGTC
Found at i:40280158 original size:38 final size:36
Alignment explanation
Indices: 40280083--40280172 Score: 103
Period size: 38 Copynumber: 2.4 Consensus size: 36
40280073 TTACAAATAT
40280083 AATATTATTTTAATATATTTAATATTAAAATAAATTA
1 AATATTATTTTAATATATTT-ATATTAAAATAAATTA
**
40280120 AATACTTATTTTAATAGTATTT-TATTAATTTAATATTA
1 AATA-TTATTTTAATA-TATTTATATTAAAATAA-ATTA
*
40280158 AAT-TTAATTTAATAT
1 AATATTATTTTAATAT
40280173 TTATCTTGAT
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
35 1 0.02
36 10 0.21
37 13 0.28
38 18 0.38
39 5 0.11
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (36 bp):
AATATTATTTTAATATATTTATATTAAAATAAATTA
Found at i:40280158 original size:48 final size:48
Alignment explanation
Indices: 40280082--40280208 Score: 146
Period size: 49 Copynumber: 2.6 Consensus size: 48
40280072 ATTACAAATA
* * *
40280082 TAATATTATTTTAATATATTTAATATTAAAATAAATTAAATACTTATTT
1 TAATAGTATTTTATTA-ATTTAATATTAAAATAAATTAAATACTTATCT
* * * *
40280131 TAATAGTATTTTATTAATTTAATATTAAATTTAATTTAATATTTATCT
1 TAATAGTATTTTATTAATTTAATATTAAAATAAATTAAATACTTATCT
* * *
40280179 TGATAAGTATTATATTGATTTAATATTAAA
1 TAAT-AGTATTTTATTAATTTAATATTAAA
40280209 GTGATTAAGA
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
48 30 0.45
49 37 0.55
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (48 bp):
TAATAGTATTTTATTAATTTAATATTAAAATAAATTAAATACTTATCT
Found at i:40297932 original size:43 final size:45
Alignment explanation
Indices: 40297884--40297986 Score: 104
Period size: 43 Copynumber: 2.3 Consensus size: 45
40297874 AAGTTGACGC
* * *
40297884 CCCAGACGTGGTCTTACATGCT-ATCACATAT-T-GATGCCAATGT
1 CCCAGACGTGGTCTTACACG-TAACCACATATATCGATGCCAACGT
* * *
40297927 CCCAGACATGATTTTACACGTAACCACATATATCGATGCCAACGT
1 CCCAGACGTGGTCTTACACGTAACCACATATATCGATGCCAACGT
* *
40297972 CCTAGATGTGGTCTT
1 CCCAGACGTGGTCTT
40297987 CCACCAGAAC
Statistics
Matches: 46, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
42 1 0.02
43 24 0.52
44 1 0.02
45 20 0.43
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.29
Consensus pattern (45 bp):
CCCAGACGTGGTCTTACACGTAACCACATATATCGATGCCAACGT
Found at i:40304514 original size:50 final size:50
Alignment explanation
Indices: 40304397--40304641 Score: 165
Period size: 50 Copynumber: 4.9 Consensus size: 50
40304387 TTGTGAGAAA
* * *** *
40304397 ACATGTGTAGTACTATGTGCTGGCTACTATGTGTTTAAGATGATTTTAGGTC
1 ACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGAT-A-GTTAGGTC
* *
40304449 ACGTGTG-ACGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGGTC
1 ACATGTGTA-GTACTAAGTGCAGGCTACTATGTGTACCAGATAGTTAGGTC
* * * * * *
40304499 GCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGACAACTTCA-ATC
1 ACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGA-TAGTT-AGGTC
* * * * * ***
40304550 ACGTATGTAGTACTAAGTGCAAGCTACTACGTGTA-CAGA-ATTTTTTTTC
1 ACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATA-GTTAGGTC
* * * * *
40304599 GCATATCTAGTACTAAGTGTAGGCTACTATGCGTACCAGATAG
1 ACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAG
40304642 CTTTTGTTAC
Statistics
Matches: 151, Mismatches: 34, Indels: 18
0.74 0.17 0.09
Matches are distributed among these distances:
48 1 0.01
49 32 0.21
50 47 0.31
51 38 0.25
52 33 0.22
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.31
Consensus pattern (50 bp):
ACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGTTAGGTC
Found at i:40304859 original size:16 final size:15
Alignment explanation
Indices: 40304838--40304867 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
40304828 GAATGGAGTA
40304838 AGTGAAATTATGTAAG
1 AGTGAAATT-TGTAAG
40304854 AGTGAAATTTGTAA
1 AGTGAAATTTGTAA
40304868 TAAAACAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.43, C:0.00, G:0.23, T:0.33
Consensus pattern (15 bp):
AGTGAAATTTGTAAG
Found at i:40308529 original size:46 final size:46
Alignment explanation
Indices: 40308438--40308616 Score: 161
Period size: 46 Copynumber: 3.8 Consensus size: 46
40308428 GCCATATTAT
* * *
40308438 GAGAGCCAGTGTAAGACCGTGTCTGGGACATGGCATCGGCATTGAGAC
1 GAGAGCTAGTGAAAGA-CATGTCTGGGACAT-GCATCGGCATTGAGAC
* *
40308486 GAGAGCTAGTGAAAGACATGTCTGGGACATGCATCGGCCTTGAGAT
1 GAGAGCTAGTGAAAGACATGTCTGGGACATGCATCGGCATTGAGAC
* * *
40308532 GTA-AGCTAGTGTAAAG-TATGTCTGGGACATGCATCGGC-TACGAGAT
1 G-AGAGCTAGTG-AAAGACATGTCTGGGACATGCATCGGCAT-TGAGAC
* * *
40308578 GTG-TC-AGTGTAAGACCATGTCTGGGACATGGCATCGGCA
1 GAGAGCTAGTGAAAGA-CATGTCTGGGACAT-GCATCGGCA
40308617 CAGATATGTG
Statistics
Matches: 112, Mismatches: 11, Indels: 17
0.80 0.08 0.12
Matches are distributed among these distances:
43 3 0.03
44 4 0.04
45 15 0.13
46 58 0.52
47 18 0.16
48 14 0.12
ACGTcount: A:0.26, C:0.18, G:0.33, T:0.22
Consensus pattern (46 bp):
GAGAGCTAGTGAAAGACATGTCTGGGACATGCATCGGCATTGAGAC
Found at i:40308704 original size:49 final size:50
Alignment explanation
Indices: 40308437--40308756 Score: 157
Period size: 46 Copynumber: 6.7 Consensus size: 50
40308427 AGCCATATTA
* * * ** *
40308437 TGAGAGCCAGTGTAAGACCGTGTCTGGGACATGGCATCGGCATTGAGA--
1 TGAGAGTCAGTGTAAGACCATGTATGGGACATGGCATCGGCACAGATATG
* * * * *
40308485 CGAGAG-CTAGTGAAAGA-CATGTCTGGGACAT-GCATCGGC-CTTGAGATG
1 TGAGAGTC-AGTGTAAGACCATGTATGGGACATGGCATCGGCAC-AGATATG
** * *
40308533 T-A-AG-CTAGTGTAA-AGTATGTCTGGGACAT-GCATCGGCTAC-GAGATG
1 TGAGAGTC-AGTGTAAGACCATGTATGGGACATGGCATCGGC-ACAGATATG
*
40308579 T----GTCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGATATG
1 TGAGAGTCAGTGTAAGACCATGTATGGGACATGGCATCGGCACAGATATG
* * * *
40308625 TGAGAG-CTAGTGTATGACCATATATGGGACATGACATCGGC-CTCGAT-T-
1 TGAGAGTC-AGTGTAAGACCATGTATGGGACATGGCATCGGCAC-AGATATG
* * * **
40308673 TCGATAGTCAGTGTAAGACCATGTTTAGGACATGGCATC-G-ACTTA-ATG
1 T-GAGAGTCAGTGTAAGACCATGTATGGGACATGGCATCGGCACAGATATG
* *
40308721 -GATGAGTCAGTGTAAGAGCATGTTTGGGACATGGCA
1 TGA-GAGTCAGTGTAAGACCATGTATGGGACATGGCA
40308757 CCAACATTAT
Statistics
Matches: 223, Mismatches: 26, Indels: 47
0.75 0.09 0.16
Matches are distributed among these distances:
44 8 0.04
45 18 0.08
46 67 0.30
47 47 0.21
48 17 0.08
49 32 0.14
50 34 0.15
ACGTcount: A:0.27, C:0.17, G:0.31, T:0.25
Consensus pattern (50 bp):
TGAGAGTCAGTGTAAGACCATGTATGGGACATGGCATCGGCACAGATATG
Found at i:40311560 original size:40 final size:40
Alignment explanation
Indices: 40311486--40311707 Score: 376
Period size: 40 Copynumber: 5.6 Consensus size: 40
40311476 AACCCAAGTA
* *
40311486 CCTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAA-TAGCACAAATG
* *
40311525 CCTTCGGGTCTTAGCCCGGATATAGTCAATAGCACAAAAG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
*
40311565 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
40311605 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
40311645 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
40311685 CCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
40311708 CATTCGAATA
Statistics
Matches: 173, Mismatches: 8, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
39 12 0.07
40 158 0.91
41 3 0.02
ACGTcount: A:0.28, C:0.26, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
Found at i:40319770 original size:40 final size:40
Alignment explanation
Indices: 40319694--40319877 Score: 291
Period size: 40 Copynumber: 4.6 Consensus size: 40
40319684 CAAACCCAAG
* *
40319694 TGCCTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAA
1 TGCCTTCGGGACTTAGCCCGGATATAGTCAA-TAGCACAAA
*
40319733 TGCCTTCGGGTCTTAGCCCGGATATAGTCAATAGCACAAA
1 TGCCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAA
* *
40319773 AGCCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAA
1 TGCCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAA
*
40319813 TGCCTTTGGGACTTAGCCCGGATATAGTCAATAGCACAAA
1 TGCCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAA
40319853 TGCCTTCGGGACTTAGCCCGGATAT
1 TGCCTTCGGGACTTAGCCCGGATAT
40319878 CATTCGAATA
Statistics
Matches: 133, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
39 14 0.11
40 116 0.87
41 3 0.02
ACGTcount: A:0.27, C:0.26, G:0.23, T:0.24
Consensus pattern (40 bp):
TGCCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAA
Found at i:40324234 original size:6 final size:6
Alignment explanation
Indices: 40324215--40324248 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
40324205 AATTGAAAAG
*
40324215 AAAATA AAAGTA AAAATA AAAATA AAAATA AAAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAA
40324249 GATAGGAGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:40325701 original size:28 final size:27
Alignment explanation
Indices: 40325658--40325710 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
40325648 TAAAACTAGT
*
40325658 ATATAGAAAATCCTAAAACAATATTCAA
1 ATATAGAAAATACTAAAACAA-ATTCAA
*
40325686 ATATAGAAAATACTAAAGCAAATTC
1 ATATAGAAAATACTAAAACAAATTC
40325711 CTAACTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 4 0.17
28 19 0.83
ACGTcount: A:0.57, C:0.13, G:0.06, T:0.25
Consensus pattern (27 bp):
ATATAGAAAATACTAAAACAAATTCAA
Found at i:40335072 original size:40 final size:40
Alignment explanation
Indices: 40334991--40335211 Score: 322
Period size: 40 Copynumber: 5.6 Consensus size: 40
40334981 AAACCAAGTA
** * * *
40334991 CCTTCGGGGTTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGTTATAG-TAACTCGCACAATTG
40335030 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAATTG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAATTG
* *
40335070 CCTTCGGGACTTGGCCCGGTTATAGTAACTCGCACAATTA
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAATTG
*
40335110 CCTTCGGGACTTGGCCCGGTTATAGTAACTCGCACAATTG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAATTG
* *
40335150 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAATTG
40335190 CCTTCGGG-CTTAGCCCGGTTAT
1 CCTTCGGGACTTAGCCCGGTTAT
40335212 CAATCGAATA
Statistics
Matches: 168, Mismatches: 12, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
39 26 0.15
40 142 0.85
ACGTcount: A:0.21, C:0.28, G:0.24, T:0.27
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAATTG
Found at i:40344802 original size:27 final size:27
Alignment explanation
Indices: 40344779--40345156 Score: 422
Period size: 27 Copynumber: 14.0 Consensus size: 27
40344769 CAAAATTATT
*
40344779 GAAATACCCCTGTAAGGTAGAATTACC
1 GAAATACCCCTGTAGGGTAGAATTACC
* * *
40344806 GAAGTACCCCTGTAGGGTAAAATTACT
1 GAAATACCCCTGTAGGGTAGAATTACC
* **
40344833 GAAATACCCCTGTAAGGTAGAATTATT
1 GAAATACCCCTGTAGGGTAGAATTACC
* * *
40344860 GAAATACCCCTATATGGTAGAATTACT
1 GAAATACCCCTGTAGGGTAGAATTACC
* * *
40344887 AAAATACCCCTGTAGGATAGAATTATC
1 GAAATACCCCTGTAGGGTAGAATTACC
* *
40344914 GAAATATCCCTGTAAGGTAGAATTACC
1 GAAATACCCCTGTAGGGTAGAATTACC
* *
40344941 GAAATACCCTTGTAGGGTAGAATTATC
1 GAAATACCCCTGTAGGGTAGAATTACC
* *
40344968 GAGATACCCCTGTAGGGTAGAATTATC
1 GAAATACCCCTGTAGGGTAGAATTACC
* * *
40344995 AAAATACCCTTGTAGGGTAGAATTATC
1 GAAATACCCCTGTAGGGTAGAATTACC
* *
40345022 GAAATACCCCTGTAGGGTTGAATTACT
1 GAAATACCCCTGTAGGGTAGAATTACC
*
40345049 GAAATACCCCTATAGGGTAGAATTACC
1 GAAATACCCCTGTAGGGTAGAATTACC
*
40345076 GAAATA-CCCTCGTAGGGTAGGAA-TACT
1 GAAATACCCCT-GTAGGGTA-GAATTACC
**
40345103 GAAATACCCCTGTAGTATAGAATTACC
1 GAAATACCCCTGTAGGGTAGAATTACC
* *
40345130 GAGAA-A-CCCTCGTGGGGTAAAATTACC
1 GA-AATACCCCT-GTAGGGTAGAATTACC
40345157 ATTTTACCCC
Statistics
Matches: 297, Mismatches: 48, Indels: 12
0.83 0.13 0.03
Matches are distributed among these distances:
26 11 0.04
27 277 0.93
28 9 0.03
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (27 bp):
GAAATACCCCTGTAGGGTAGAATTACC
Found at i:40345591 original size:19 final size:19
Alignment explanation
Indices: 40345569--40345626 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 19
40345559 TTCTGATTTT
40345569 TGATTCTGTTACCTGATAC
1 TGATTCTGTTACCTGATAC
*
40345588 TGATTCTG--A--T--T-T
1 TGATTCTGTTACCTGATAC
40345600 TGATTCTGTTACCTGATAC
1 TGATTCTGTTACCTGATAC
40345619 TGATTCTG
1 TGATTCTG
40345627 ATTTTGATTC
Statistics
Matches: 30, Mismatches: 2, Indels: 14
0.65 0.04 0.30
Matches are distributed among these distances:
12 8 0.27
13 1 0.03
14 1 0.03
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 16 0.53
ACGTcount: A:0.19, C:0.17, G:0.17, T:0.47
Consensus pattern (19 bp):
TGATTCTGTTACCTGATAC
Found at i:40345596 original size:6 final size:6
Alignment explanation
Indices: 40345558--40345708 Score: 87
Period size: 6 Copynumber: 24.3 Consensus size: 6
40345548 TTGCATTCAC
* * *
40345558 ATTCTG ATTTTTG ATTCTG -TTACCTG ATACTG ATTCTG ATTTTG ATTCTG
1 ATTCTG A-TTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG
* * * *
40345608 -TTACCTG ATACTG ATTCTG ATTTTG ATTCTG -TTACCTG ATACTG ATTCCG
1 ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG
* * *
40345658 ATTCTG ATTCTG -TCACCTA ATTCTG ATTCTA ATTCTG ATTCT- AGTTCTG
1 ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG A-TTCTG
40345707 AT
1 AT
40345709 AATGTTTCTT
Statistics
Matches: 110, Mismatches: 20, Indels: 30
0.69 0.12 0.19
Matches are distributed among these distances:
5 8 0.07
6 81 0.74
7 17 0.15
8 4 0.04
ACGTcount: A:0.20, C:0.18, G:0.15, T:0.48
Consensus pattern (6 bp):
ATTCTG
Found at i:40345604 original size:31 final size:31
Alignment explanation
Indices: 40345558--40345699 Score: 212
Period size: 31 Copynumber: 4.5 Consensus size: 31
40345548 TTGCATTCAC
40345558 ATTCTGATTTTTGATTCTGTTACCTGATACTG
1 ATTCTGA-TTTTGATTCTGTTACCTGATACTG
40345590 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
40345621 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
* * * * *
40345652 ATTCCGATTCTGATTCTGTCACCTAATTCTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
* *
40345683 ATTCTAATTCTGATTCT
1 ATTCTGATTTTGATTCT
40345700 AGTTCTGATA
Statistics
Matches: 103, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
31 96 0.93
32 7 0.07
ACGTcount: A:0.20, C:0.18, G:0.14, T:0.48
Consensus pattern (31 bp):
ATTCTGATTTTGATTCTGTTACCTGATACTG
Found at i:40348418 original size:47 final size:47
Alignment explanation
Indices: 40348204--40348562 Score: 245
Period size: 47 Copynumber: 7.6 Consensus size: 47
40348194 GTTTCAATGC
* *
40348204 CATGTCCCAGACATGGTCTTACACTGGCTATCTTCATAGAGGCGGATG
1 CATGTCCCAGACAT-GTCTTACACTGGCTATCTTCATCGAGGCCGATG
* * * * *
40348252 CCATGTCCCAGACATGGTTTTACACTAGC--TCTT-ATATGTACATGCTGATG
1 -CATGTCCCAGACAT-GTCTTACACTGGCTATCTTCAT-CG---AGGCCGATG
* * * *
40348302 CATGTCCCAAACATGTCTTACACTAGC-A-CTACCCTC-A-GCCGATG
1 CATGTCCCAGACATGTCTTACACTGGCTATCT-TCATCGAGGCCGATG
* *
40348346 CATGTCCCAAACACGTCTTACACTGGCTATCTTCATCGAGGCCGATG
1 CATGTCCCAGACATGTCTTACACTGGCTATCTTCATCGAGGCCGATG
* * ** * * *
40348393 CATGTCCCAGACATGTTTTATACTGGCGCTCATC-TCTATGCCGATG
1 CATGTCCCAGACATGTCTTACACTGGCTATCTTCATCGAGGCCGATG
* * *
40348439 CCATGTCCCAGACATGGTCTTACACTGGCTAT-TATAAT-GTGGCTGATG
1 -CATGTCCCAGACAT-GTCTTACACTGGCTATCT-TCATCGAGGCCGATG
* ** * * **
40348487 CATGTCCCAGACATGTCTTACACTAGCCCTCGTC-TCAATACCGATG
1 CATGTCCCAGACATGTCTTACACTGGCTATCTTCATCGAGGCCGATG
*
40348533 CCATGTCCCAAACATGGTCTTACACTGGCT
1 -CATGTCCCAGACAT-GTCTTACACTGGCT
40348563 CTCACATAAC
Statistics
Matches: 244, Mismatches: 47, Indels: 39
0.74 0.14 0.12
Matches are distributed among these distances:
44 31 0.13
45 6 0.02
46 34 0.14
47 80 0.33
48 45 0.18
49 40 0.16
50 8 0.03
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.28
Consensus pattern (47 bp):
CATGTCCCAGACATGTCTTACACTGGCTATCTTCATCGAGGCCGATG
Found at i:40348487 original size:141 final size:140
Alignment explanation
Indices: 40348204--40348558 Score: 353
Period size: 141 Copynumber: 2.5 Consensus size: 140
40348194 GTTTCAATGC
* *
40348204 CATGTCCCAGACATGGTCTTACACTGGCTATCTTCATAGAGGCGGATGCCATGTCCCAGACATGG
1 CATGTCCCAGACA-CGTCTTACACTGGCTATCTTCATAGAGGCCGATGCCATGTCCCAGACATGG
* * * *
40348269 TTTTACACTAGCTCTTATATGTACATGCTGATGCATGTCCCAAACATGTCTTACACTAGCACTAC
65 TTTTACACTAGCGCTCATATCTA-ATGCCGATGCATGTCCCAAACATGTCTTACACTAGCACTAC
**
40348334 CCTCAGCCGATG
129 AATCAGCCGATG
* *
40348346 CATGTCCCAAACACGTCTTACACTGGCTATCTTCATCGAGGCCGATG-CATGTCCCAGACAT-GT
1 CATGTCCCAGACACGTCTTACACTGGCTATCTTCATAGAGGCCGATGCCATGTCCCAGACATGGT
* * * * * *
40348409 TTTATACTGGCGCTCATCTCT-ATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTATTA
66 TTTACACTAGCGCTCATATCTAATGCCGATG-CATGTCCCAAACAT-GTCTTACACTAGC-ACTA
* ** *
40348473 TAATGTGGCTGATG
128 CAAT-CAGCCGATG
* * ** * *
40348487 CATGTCCCAGACATGTCTTACACTAGCCCTCGTCTCA-ATA--CCGATGCCATGTCCCAAACATG
1 CATGTCCCAGACACGTCTTACACTGGCTATC-T-TCATAGAGGCCGATGCCATGTCCCAGACATG
*
40348549 GTCTTACACT
64 GTTTTACACT
40348559 GGCTCTCACA
Statistics
Matches: 175, Mismatches: 30, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
137 8 0.05
138 13 0.07
139 29 0.17
140 24 0.14
141 76 0.43
142 22 0.13
143 3 0.02
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (140 bp):
CATGTCCCAGACACGTCTTACACTGGCTATCTTCATAGAGGCCGATGCCATGTCCCAGACATGGT
TTTACACTAGCGCTCATATCTAATGCCGATGCATGTCCCAAACATGTCTTACACTAGCACTACAA
TCAGCCGATG
Found at i:40348492 original size:94 final size:93
Alignment explanation
Indices: 40348204--40348562 Score: 345
Period size: 94 Copynumber: 3.8 Consensus size: 93
40348194 GTTTCAATGC
* * ** * * *
40348204 CATGTCCCAGACATGGTCTTACACTGGCTA-TCTTCATAGAGGCGGATGCCATGTCCCAGACATG
1 CATGTCCCAGACAT-GTCTTACACTAGC-ACTCATC-TCTATGCCGATGCCATGTCCCAAACATG
* * * *
40348268 GTTTTACACTAGCTCTTATATGTACATGCTGATG
63 GTCTTACACTGGCTATTATATGT---GGCTGATG
* * *
40348302 CATGTCCCAAACATGTCTTACACTAGCACT-A-CCCTCA-GCCGATG-CATGTCCCAAACA-CGT
1 CATGTCCCAGACATGTCTTACACTAGCACTCATCTCT-ATGCCGATGCCATGTCCCAAACATGGT
* *
40348362 CTTACACTGGCTATCT-TCATCGAGGCCGATG
65 CTTACACTGGCTAT-TAT-AT-GTGGCTGATG
* * * * *
40348393 CATGTCCCAGACATGTTTTATACTGGCGCTCATCTCTATGCCGATGCCATGTCCCAGACATGGTC
1 CATGTCCCAGACATGTCTTACACTAGCACTCATCTCTATGCCGATGCCATGTCCCAAACATGGTC
40348458 TTACACTGGCTATTATAATGTGGCTGATG
66 TTACACTGGCTATTAT-ATGTGGCTGATG
* * * *
40348487 CATGTCCCAGACATGTCTTACACTAGCCCTCGTCTCAATACCGATGCCATGTCCCAAACATGGTC
1 CATGTCCCAGACATGTCTTACACTAGCACTCATCTCTATGCCGATGCCATGTCCCAAACATGGTC
40348552 TTACACTGGCT
66 TTACACTGGCT
40348563 CTCACATAAC
Statistics
Matches: 216, Mismatches: 34, Indels: 26
0.78 0.12 0.09
Matches are distributed among these distances:
91 31 0.14
92 16 0.07
93 25 0.12
94 96 0.44
95 21 0.10
96 1 0.00
97 13 0.06
98 13 0.06
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.28
Consensus pattern (93 bp):
CATGTCCCAGACATGTCTTACACTAGCACTCATCTCTATGCCGATGCCATGTCCCAAACATGGTC
TTACACTGGCTATTATATGTGGCTGATG
Found at i:40350474 original size:28 final size:28
Alignment explanation
Indices: 40350443--40350507 Score: 112
Period size: 28 Copynumber: 2.3 Consensus size: 28
40350433 AGGGGGAGTC
40350443 AAGCCCAAATTCGAAACAAGCATGTTGA
1 AAGCCCAAATTCGAAACAAGCATGTTGA
*
40350471 AAGCCCAAATTCGGAACAAGCATGTTGA
1 AAGCCCAAATTCGAAACAAGCATGTTGA
*
40350499 ATGCCCAAA
1 AAGCCCAAA
40350508 AATCTCTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.42, C:0.23, G:0.18, T:0.17
Consensus pattern (28 bp):
AAGCCCAAATTCGAAACAAGCATGTTGA
Found at i:40381814 original size:27 final size:27
Alignment explanation
Indices: 40381784--40381844 Score: 90
Period size: 26 Copynumber: 2.3 Consensus size: 27
40381774 TTTACAAAAC
40381784 TACCCCTAAGTATG-AAAATTACCATTA
1 TACCCCTAAG-ATGCAAAATTACCATTA
*
40381811 TACCCCT-AGGTGCAAAATTACCATTA
1 TACCCCTAAGATGCAAAATTACCATTA
40381837 TACCCCTA
1 TACCCCTA
40381845 GGGTTAATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
25 2 0.06
26 22 0.71
27 7 0.23
ACGTcount: A:0.36, C:0.28, G:0.08, T:0.28
Consensus pattern (27 bp):
TACCCCTAAGATGCAAAATTACCATTA
Found at i:40381995 original size:28 final size:26
Alignment explanation
Indices: 40381952--40382060 Score: 110
Period size: 27 Copynumber: 4.0 Consensus size: 26
40381942 GGAAGTGTTT
40381952 TGGTGGCTATGCCACAAATATCTATTTC
1 TGGTGGCTATGCCAC-AATATCT-TTTC
* *
40381980 TGGTGGCTATGGCACAAATATCTGTTC
1 TGGTGGCTATGCCAC-AATATCTTTTC
* *
40382007 TAGTGGCTCTGCCACAATATCTTTATC
1 TGGTGGCTATGCCACAATATCTTT-TC
* * * *
40382034 TGGTGACTCTGTCACAATATCTGTTC
1 TGGTGGCTATGCCACAATATCTTTTC
40382060 T
1 T
40382061 AGCAGCCATG
Statistics
Matches: 70, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
26 11 0.16
27 37 0.53
28 22 0.31
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (26 bp):
TGGTGGCTATGCCACAATATCTTTTC
Found at i:40382038 original size:54 final size:54
Alignment explanation
Indices: 40381954--40382062 Score: 150
Period size: 54 Copynumber: 2.0 Consensus size: 54
40381944 AAGTGTTTTG
*
40381954 GTGGCTATGCCACAAATATCTATTTCTGGTGGCTATGGCACAAATATCTGTTCTA
1 GTGGCTATGCCACAAATATCTATTTCTGGTGACTATGGCAC-AATATCTGTTCTA
* * *
40382009 GTGGCTCTGCCAC-AATATCT-TTATCTGGTGACTCTGTCACAATATCTGTTCTA
1 GTGGCTATGCCACAAATATCTATT-TCTGGTGACTATGGCACAATATCTGTTCTA
40382062 G
1 G
40382063 CAGCCATGCT
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
53 16 0.33
54 21 0.43
55 12 0.24
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36
Consensus pattern (54 bp):
GTGGCTATGCCACAAATATCTATTTCTGGTGACTATGGCACAATATCTGTTCTA
Found at i:40390800 original size:34 final size:34
Alignment explanation
Indices: 40390762--40390830 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
40390752 TTCACTCAGA
40390762 TAAAATCATCATTCATACTTGCATACAAACTATC
1 TAAAATCATCATTCATACTTGCATACAAACTATC
40390796 TAAAATCATCATTCATACTTGCATACAAACTATC
1 TAAAATCATCATTCATACTTGCATACAAACTATC
40390830 T
1 T
40390831 CATTAACAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.41, C:0.23, G:0.03, T:0.33
Consensus pattern (34 bp):
TAAAATCATCATTCATACTTGCATACAAACTATC
Found at i:40401234 original size:34 final size:34
Alignment explanation
Indices: 40401191--40401260 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
40401181 AATTTTCAAA
*
40401191 AGAATGACCTTCCCCATGATACACACAGGAAACT
1 AGAATGACCTTCCCCACGATACACACAGGAAACT
40401225 AGAATGACCTTCCCCACGATACACACAGGAAACT
1 AGAATGACCTTCCCCACGATACACACAGGAAACT
40401259 AG
1 AG
40401261 TTCAAACGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.39, C:0.30, G:0.16, T:0.16
Consensus pattern (34 bp):
AGAATGACCTTCCCCACGATACACACAGGAAACT
Found at i:40406604 original size:17 final size:17
Alignment explanation
Indices: 40406584--40406634 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
40406574 TTTAAATTTT
*
40406584 AAAAATTTTAAAAATTCA
1 AAAAATATTAAAAATT-A
40406602 AAAAA-ATTAAAACATTA
1 AAAAATATTAAAA-ATTA
*
40406619 AAAAATATAAAAAATT
1 AAAAATATTAAAAATT
40406635 TAATATTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
17 15 0.52
18 14 0.48
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (17 bp):
AAAAATATTAAAAATTA
Found at i:40406613 original size:8 final size:8
Alignment explanation
Indices: 40406582--40406634 Score: 52
Period size: 8 Copynumber: 6.2 Consensus size: 8
40406572 TTTTTAAATT
*
40406582 TTAAAAAT
1 TTAAAAAA
*
40406590 TTTAAAAA
1 TTAAAAAA
40406598 TTCAAAAAAA
1 TT--AAAAAA
*
40406608 TTAAAACA
1 TTAAAAAA
40406616 TTAAAAAA
1 TTAAAAAA
40406624 TATAAAAAA
1 T-TAAAAAA
40406633 TT
1 TT
40406635 TAATATTGTA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
8 22 0.59
9 8 0.22
10 7 0.19
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (8 bp):
TTAAAAAA
Found at i:40406637 original size:18 final size:18
Alignment explanation
Indices: 40406577--40406637 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
40406567 TTAATTTTTT
* * *
40406577 AAATTTTAAAAATTTTAA
1 AAATTTAAAAAATATAAA
*
40406595 AAATTCAAAAAA-ATTAAA
1 AAATTTAAAAAATA-TAAA
*
40406613 ACA-TTAAAAAATATAAA
1 AAATTTAAAAAATATAAA
40406630 AAATTTAA
1 AAATTTAA
40406638 TATTGTAATT
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
17 13 0.39
18 20 0.61
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (18 bp):
AAATTTAAAAAATATAAA
Found at i:40407680 original size:16 final size:17
Alignment explanation
Indices: 40407647--40407680 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
40407637 GTAATTAATA
*
40407647 AAATATTGTAAAATTAT
1 AAATATTGTAAAACTAT
40407664 AAATATT-TAAAACTAT
1 AAATATTGTAAAACTAT
40407680 A
1 A
40407681 CAAATCTAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (17 bp):
AAATATTGTAAAACTAT
Found at i:40408141 original size:33 final size:33
Alignment explanation
Indices: 40408104--40408170 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
40408094 TTGGTGAAAG
40408104 TTCAATTAATAAATGATGAATACGTATATCATT
1 TTCAATTAATAAATGATGAATACGTATATCATT
40408137 TTCAATTAATAAATGATGAATACGTATATCATT
1 TTCAATTAATAAATGATGAATACGTATATCATT
40408170 T
1 T
40408171 GGTGTCAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40
Consensus pattern (33 bp):
TTCAATTAATAAATGATGAATACGTATATCATT
Found at i:40415273 original size:17 final size:16
Alignment explanation
Indices: 40415234--40415273 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
40415224 AACATAGTCC
40415234 AATATATATATAAAGA
1 AATATATATATAAAGA
*
40415250 AATTATATATATACAGA
1 AA-TATATATATAAAGA
40415267 ACATATA
1 A-ATATA
40415274 ACGGAATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 2 0.10
17 18 0.86
18 1 0.05
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.33
Consensus pattern (16 bp):
AATATATATATAAAGA
Found at i:40419992 original size:28 final size:26
Alignment explanation
Indices: 40419961--40420022 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
40419951 TTACTTGAAT
* *
40419961 ACCCCTATGTATGGAAAATTACTATTAC
1 ACCCCTA-G-ATGCAAAATTACCATTAC
* *
40419989 ACCCCTAGGTGCAAAATTACCATTAT
1 ACCCCTAGATGCAAAATTACCATTAC
40420015 ACCCCTAG
1 ACCCCTAG
40420023 GGTTACTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 22 0.73
27 1 0.03
28 7 0.23
ACGTcount: A:0.34, C:0.27, G:0.11, T:0.27
Consensus pattern (26 bp):
ACCCCTAGATGCAAAATTACCATTAC
Found at i:40420169 original size:27 final size:26
Alignment explanation
Indices: 40420130--40420237 Score: 117
Period size: 27 Copynumber: 4.0 Consensus size: 26
40420120 AAGCGTCCTG
* *
40420130 GTGGCTATGCCACAATTATCTGATCTA
1 GTGGCTCTGCCAC-ATTATCTGTTCTA
* *
40420157 TTGGCTCTGCCACATATATCTGTTCTG
1 GTGGCTCTGCCACAT-TATCTGTTCTA
* *
40420184 GTGGCTCTGCCATGATTATCTGTTCTG
1 GTGGCTCTGCCA-CATTATCTGTTCTA
* *
40420211 GTGACTCTGTCACATTATCTGTTCTA
1 GTGGCTCTGCCACATTATCTGTTCTA
40420237 G
1 G
40420238 CAGCCATGCT
Statistics
Matches: 69, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
26 15 0.22
27 52 0.75
28 2 0.03
ACGTcount: A:0.18, C:0.23, G:0.20, T:0.39
Consensus pattern (26 bp):
GTGGCTCTGCCACATTATCTGTTCTA
Found at i:40420219 original size:54 final size:53
Alignment explanation
Indices: 40420127--40420235 Score: 137
Period size: 54 Copynumber: 2.0 Consensus size: 53
40420117 AGGAAGCGTC
* *
40420127 CTGGTGGCTATGCCACAATTATCTGATCTATTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTAGTGACTCTGCCACAT-TATCTGTT
* ** * * *
40420181 CTGGTGGCTCTGCCATGATTATCTGTTCTGGTGACTCTGTCACATTATCTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTAGTGACTCTGCCACATTATCTGTT
40420234 CT
1 CT
40420236 AGCAGCCATG
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
53 10 0.21
54 37 0.79
ACGTcount: A:0.17, C:0.24, G:0.20, T:0.39
Consensus pattern (53 bp):
CTGGTGGCTATGCCACAATTATCTGATCTAGTGACTCTGCCACATTATCTGTT
Done.