Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 146 of 198
Found at i:46456683 original size:22 final size:22
Alignment explanation
Indices: 46456625--46456685 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 22
46456615 AACCTTTACC
* *
46456625 TCCGGCACCAATCCACCTCCGG
1 TCCGCCACCGATCCACCTCCGG
*
46456647 TCCGGCACCGATCCACCTCCGG
1 TCCGCCACCGATCCACCTCCGG
* * *
46456669 TCCTCCACGGCTCCACC
1 TCCGCCACCGATCCACC
46456686 CATTTCCAGA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.15, C:0.52, G:0.18, T:0.15
Consensus pattern (22 bp):
TCCGCCACCGATCCACCTCCGG
Found at i:46459332 original size:22 final size:24
Alignment explanation
Indices: 46459285--46459338 Score: 76
Period size: 22 Copynumber: 2.3 Consensus size: 24
46459275 GGACCTTAGC
46459285 GTGCTCTCTGATTATTAGCACATTA
1 GTGCTCTCT-ATTATTAGCACATTA
*
46459310 GTGCTCTCT-TTA-TAGCACTTTA
1 GTGCTCTCTATTATTAGCACATTA
46459332 GTGCTCT
1 GTGCTCT
46459339 ATGTTCAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 16 0.57
23 3 0.11
25 9 0.32
ACGTcount: A:0.19, C:0.22, G:0.17, T:0.43
Consensus pattern (24 bp):
GTGCTCTCTATTATTAGCACATTA
Found at i:46463864 original size:18 final size:18
Alignment explanation
Indices: 46463841--46463877 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
46463831 AATTGTAGAT
*
46463841 CGATTGACAAAGTCTGCC
1 CGATTGACAAAGTCCGCC
*
46463859 CGATTGACGAAGTCCGCC
1 CGATTGACAAAGTCCGCC
46463877 C
1 C
46463878 ATTTTCTACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.32, G:0.24, T:0.19
Consensus pattern (18 bp):
CGATTGACAAAGTCCGCC
Found at i:46466193 original size:22 final size:22
Alignment explanation
Indices: 46466168--46466229 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
46466158 TATCTGATTA
46466168 TTAGCACATTAGTGCTCTCCGT
1 TTAGCACATTAGTGCTCTCCGT
* *
46466190 TTAGCACATTCGTGCTCTCTGT
1 TTAGCACATTAGTGCTCTCCGT
* * *
46466212 ATAGCACTTTAGTACTCT
1 TTAGCACATTAGTGCTCT
46466230 ATGTTCAATA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.19, C:0.26, G:0.16, T:0.39
Consensus pattern (22 bp):
TTAGCACATTAGTGCTCTCCGT
Found at i:46467211 original size:15 final size:14
Alignment explanation
Indices: 46467186--46467229 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 14
46467176 TCGCCCATAT
46467186 TATTTTTAATTTAA
1 TATTTTTAATTTAA
46467200 TATTTATTAATTTTATA
1 TATTT-TTAA-TTTA-A
*
46467217 TATTTTTTATTTA
1 TATTTTTAATTTA
46467230 TTGATATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 5 0.19
15 8 0.31
16 7 0.27
17 6 0.23
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TATTTTTAATTTAA
Found at i:46467230 original size:15 final size:15
Alignment explanation
Indices: 46467186--46467240 Score: 58
Period size: 17 Copynumber: 3.5 Consensus size: 15
46467176 TCGCCCATAT
46467186 TATTTTTAATTTA-A
1 TATTTTTAATTTATA
46467200 TATTTATTAATTTTATA
1 TATTT-TTAA-TTTATA
*
46467217 TATTTTTTATTTATTGA
1 TATTTTTAATTTA-T-A
46467234 TATTTTT
1 TATTTTT
46467241 TATATAGTCA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
14 5 0.14
15 8 0.23
16 8 0.23
17 14 0.40
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (15 bp):
TATTTTTAATTTATA
Found at i:46469753 original size:27 final size:28
Alignment explanation
Indices: 46469728--46469781 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
46469718 CAGGAACAGC
*
46469728 ACAGTGTGGGCCTTAGCCCAATACAGAA
1 ACAGTGTGGGCCTAAGCCCAATACAGAA
* *
46469756 ATAGTGTGGGCCTAAGCCCGATACAG
1 ACAGTGTGGGCCTAAGCCCAATACAG
46469782 TATTAGTATG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.30, C:0.24, G:0.28, T:0.19
Consensus pattern (28 bp):
ACAGTGTGGGCCTAAGCCCAATACAGAA
Found at i:46470067 original size:32 final size:32
Alignment explanation
Indices: 46469999--46470233 Score: 240
Period size: 32 Copynumber: 7.4 Consensus size: 32
46469989 GAATGATTAC
* * * *
46469999 AAGCCATAAGT-ACAGTAATGTGATTGGCAGA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
** *
46470030 AAGCCATCAGTAGTAGTGATATGATCGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* * *
46470062 TAGCCATCAGTAACGGTAACATGATCGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* *
46470094 AAGCCATCAGTAAGAGTGATATGATCGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* * *
46470126 CAA-CCATCAATAACAGTAAAATGATCAGCACA
1 -AAGCCATCAGTAACAGTAATATGATCGGCACA
* ** **
46470158 CAGCCATTGGTAATGGTAATATGATCGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* * *
46470190 AAGCCATCAGTAACGGTACTATGATCGGCATA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
46470222 AAGCCATCAGTA
1 AAGCCATCAGTA
46470234 GCATCGCAGC
Statistics
Matches: 164, Mismatches: 37, Indels: 5
0.80 0.18 0.02
Matches are distributed among these distances:
31 11 0.07
32 151 0.92
33 2 0.01
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.20
Consensus pattern (32 bp):
AAGCCATCAGTAACAGTAATATGATCGGCACA
Found at i:46470288 original size:26 final size:26
Alignment explanation
Indices: 46470236--46470289 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
46470226 CATCAGTAGC
* *
46470236 ATCGCAGCAAAGCTGCTAGCAAGAGT
1 ATCGCAACAAAGCTGCCAGCAAGAGT
* *
46470262 ATCGCAACAAAGCTGCCAGTAATAGT
1 ATCGCAACAAAGCTGCCAGCAAGAGT
46470288 AT
1 AT
46470290 ATGTGGCCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.19
Consensus pattern (26 bp):
ATCGCAACAAAGCTGCCAGCAAGAGT
Found at i:46470307 original size:27 final size:27
Alignment explanation
Indices: 46470277--46470340 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 27
46470267 AACAAAGCTG
*
46470277 CCAGTAATAGT-ATATGTGGCCA-AGCCA
1 CCAGTAACAGTGAT-TGTGG-CAGAGCCA
*
46470304 CCAGTAGCAGTGATTGTGGCAGAGCCA
1 CCAGTAACAGTGATTGTGGCAGAGCCA
46470331 CCAGT-ACAGT
1 CCAGTAACAGT
46470341 ACTTCCTCCA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
26 6 0.19
27 24 0.75
28 2 0.06
ACGTcount: A:0.30, C:0.23, G:0.27, T:0.20
Consensus pattern (27 bp):
CCAGTAACAGTGATTGTGGCAGAGCCA
Found at i:46470438 original size:24 final size:24
Alignment explanation
Indices: 46470405--46470486 Score: 80
Period size: 24 Copynumber: 3.5 Consensus size: 24
46470395 CCATGCTCAG
*
46470405 AATCAATCATTCAAATCACAGACA
1 AATCAGTCATTCAAATCACAGACA
*
46470429 AATTAGTCATATCAAAT-ACAGACA
1 AATCAGTCAT-TCAAATCACAGACA
*
46470453 AATCAGTCAATT--AACCACAGACA
1 AATCAGTC-ATTCAAATCACAGACA
* *
46470476 AAACAATCATT
1 AATCAGTCATT
46470487 TAACCTCGAG
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
22 5 0.10
23 13 0.27
24 23 0.47
25 8 0.16
ACGTcount: A:0.50, C:0.22, G:0.06, T:0.22
Consensus pattern (24 bp):
AATCAGTCATTCAAATCACAGACA
Found at i:46470476 original size:23 final size:23
Alignment explanation
Indices: 46470421--46470491 Score: 70
Period size: 23 Copynumber: 3.0 Consensus size: 23
46470411 TCATTCAAAT
* * *
46470421 CACAGACAAATTAGTCATATCAAA
1 CACAGACAAATCAGTCA-ATTAAC
*
46470445 TACAGACAAATCAGTCAATTAAC
1 CACAGACAAATCAGTCAATTAAC
* * *
46470468 CACAGACAAAACAATCATTTAAC
1 CACAGACAAATCAGTCAATTAAC
46470491 C
1 C
46470492 TCGAGGGGCA
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
23 24 0.62
24 15 0.38
ACGTcount: A:0.49, C:0.24, G:0.07, T:0.20
Consensus pattern (23 bp):
CACAGACAAATCAGTCAATTAAC
Found at i:46471814 original size:21 final size:21
Alignment explanation
Indices: 46471767--46471814 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
46471757 TGTGTTTAGC
* *
46471767 CACACGACTGTGTGAGAGGCT
1 CACACAACTGTGTCAGAGGCT
*
46471788 CGCACAACTGTGTCAGAGAG-T
1 CACACAACTGTGTCAGAG-GCT
46471809 CACACA
1 CACACA
46471815 GCCGTGTGAG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 21 0.95
22 1 0.05
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.17
Consensus pattern (21 bp):
CACACAACTGTGTCAGAGGCT
Found at i:46472421 original size:28 final size:29
Alignment explanation
Indices: 46472375--46472432 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 29
46472365 ATTTGAAAAC
* *
46472375 TTAATCATATTGCGGAATAGTCAAC-AAT
1 TTAATCATATTGCGAAATAATCAACTAAT
*
46472403 TTAATCATATTGCTAAATAATCAACTAAT
1 TTAATCATATTGCGAAATAATCAACTAAT
46472432 T
1 T
46472433 CATGTCCCAC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 22 0.85
29 4 0.15
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (29 bp):
TTAATCATATTGCGAAATAATCAACTAAT
Found at i:46472729 original size:71 final size:71
Alignment explanation
Indices: 46472626--46472949 Score: 344
Period size: 71 Copynumber: 4.6 Consensus size: 71
46472616 GGTAAAATCG
* * * * *** * * *
46472626 ACAAATAAGTGTGCCTAACACTGGTAGATATAACTGGCAATAATTGCGCCTTGTGTTGGTCGGTA
1 ACAAATAAGTGTGCCCAGCACTGGTCGGTATAACCAACAATAAATGCGCCTTGCGCTGGTCGGTA
46472691 GAACCA
66 GAACCA
* * * * * * * ** *
46472697 AAAAATAAGTGTACTCAGCACTAGTTGGTATAACCGACAAGAAATGTACCTTGCGCTAGTCGGTA
1 ACAAATAAGTGTGCCCAGCACTGGTCGGTATAACCAACAATAAATGCGCCTTGCGCTGGTCGGTA
**
46472762 GAACTG
66 GAACCA
* * * * *
46472768 CCAAATAAGTGTGCCCAGCACTGATTGGTATAACCAACAATAAATGCGCTTTGCACTGGTCGGTA
1 ACAAATAAGTGTGCCCAGCACTGGTCGGTATAACCAACAATAAATGCGCCTTGCGCTGGTCGGTA
46472833 GAATCC-
66 GAA-CCA
* * *
46472839 ATAAATAAGTGTGCCAAGCAATGGTCGGTATAACCAACAATAAATGCGCCTTGCGCTGGTCGGTA
1 ACAAATAAGTGTGCCCAGCACTGGTCGGTATAACCAACAATAAATGCGCCTTGCGCTGGTCGGTA
*
46472904 AAACCA
66 GAACCA
*
46472910 ACAAATAAGTGTGCCCAGCACTGGTCGGTATAACCGACAA
1 ACAAATAAGTGTGCCCAGCACTGGTCGGTATAACCAACAA
46472950 ATAAGTGTTC
Statistics
Matches: 205, Mismatches: 46, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
70 2 0.01
71 202 0.99
72 1 0.00
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (71 bp):
ACAAATAAGTGTGCCCAGCACTGGTCGGTATAACCAACAATAAATGCGCCTTGCGCTGGTCGGTA
GAACCA
Found at i:46472864 original size:36 final size:36
Alignment explanation
Indices: 46472682--46472957 Score: 177
Period size: 36 Copynumber: 7.8 Consensus size: 36
46472672 CGCCTTGTGT
* * *
46472682 TGGTCGGTAGAACCAAAAAATAAGTGTACTC-AGCAC
1 TGGTCGGTATAACCAACAAATAAGTGTGC-CAAGCAC
* * * * ** *
46472718 TAGTTGGTATAACCGACAAGA-AA-TGTACCTTGCGC
1 TGGTCGGTATAACCAACAA-ATAAGTGTGCCAAGCAC
* * *** *
46472753 TAGTCGGTAGAACTGCCAAATAAGTGTGCCCAGCAC
1 TGGTCGGTATAACCAACAAATAAGTGTGCCAAGCAC
* * * * ***
46472789 TGATTGGTATAACCAAC-AATAAATGCGCTTTGCAC
1 TGGTCGGTATAACCAACAAATAAGTGTGCCAAGCAC
* * *
46472824 TGGTCGGTAGAATCC-ATAAATAAGTGTGCCAAGCAA
1 TGGTCGGTATAA-CCAACAAATAAGTGTGCCAAGCAC
* * ** *
46472860 TGGTCGGTATAACCAAC-AATAAATGCGCCTTGCGC
1 TGGTCGGTATAACCAACAAATAAGTGTGCCAAGCAC
* *
46472895 TGGTCGGTAAAACCAACAAATAAGTGTGCCCAGCAC
1 TGGTCGGTATAACCAACAAATAAGTGTGCCAAGCAC
*
46472931 TGGTCGGTATAACCGACAAATAAGTGT
1 TGGTCGGTATAACCAACAAATAAGTGT
46472958 TCATTCATTT
Statistics
Matches: 179, Mismatches: 53, Indels: 16
0.72 0.21 0.06
Matches are distributed among these distances:
34 2 0.01
35 78 0.44
36 98 0.55
37 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.23, T:0.22
Consensus pattern (36 bp):
TGGTCGGTATAACCAACAAATAAGTGTGCCAAGCAC
Found at i:46473732 original size:3 final size:3
Alignment explanation
Indices: 46473708--46473746 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
46473698 CTTTTATCTT
46473708 TTA TTA TT- TTA TT- TTA TT- TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
46473747 ACATATATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 6 0.18
3 27 0.82
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (3 bp):
TTA
Found at i:46473740 original size:9 final size:9
Alignment explanation
Indices: 46473708--46473746 Score: 57
Period size: 8 Copynumber: 4.7 Consensus size: 9
46473698 CTTTTATCTT
46473708 TTATTATT-
1 TTATTATTA
46473716 TTATT-TTA
1 TTATTATTA
46473724 TT-TTATTA
1 TTATTATTA
46473732 TTATTATTA
1 TTATTATTA
46473741 TTATTA
1 TTATTA
46473747 ACATATATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
7 4 0.14
8 12 0.43
9 12 0.43
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (9 bp):
TTATTATTA
Found at i:46488366 original size:40 final size:40
Alignment explanation
Indices: 46488310--46488497 Score: 252
Period size: 40 Copynumber: 4.7 Consensus size: 40
46488300 ATCGAAGTGT
* *
46488310 AAACAAGGGCATGTATGTGCAATCAGGGGTACCGAAATAC
1 AAACAGGGGCACGTATGTGCAATCAGGGGTACCGAAATAC
46488350 AAACAGGGGCACGTATGTGCAATCAGGGGTACC-AAAGTAC
1 AAACAGGGGCACGTATGTGCAATCAGGGGTACCGAAA-TAC
* * * *
46488390 AAACAGGGGCACGTATGTGGAATTAGGGGTACTGAAGTAC
1 AAACAGGGGCACGTATGTGCAATCAGGGGTACCGAAATAC
* * * *
46488430 AAACAGGGGCACGTATATGCAATTAGGGGCACCGAAGTAC
1 AAACAGGGGCACGTATGTGCAATCAGGGGTACCGAAATAC
*
46488470 AAACAGGGGCATGTATGTGCAATTCAGG
1 AAACAGGGGCACGTATGTGCAA-TCAGG
46488498 TATAATTAAC
Statistics
Matches: 132, Mismatches: 13, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
39 3 0.02
40 123 0.93
41 6 0.05
ACGTcount: A:0.35, C:0.17, G:0.31, T:0.18
Consensus pattern (40 bp):
AAACAGGGGCACGTATGTGCAATCAGGGGTACCGAAATAC
Found at i:46488443 original size:80 final size:80
Alignment explanation
Indices: 46488310--46488493 Score: 278
Period size: 80 Copynumber: 2.3 Consensus size: 80
46488300 ATCGAAGTGT
* * *
46488310 AAACAAGGGCATGTATGTGCAATCAGGGGTACCGAAATACAAACAGGGGCACGTATGTGCAATCA
1 AAACAGGGGCATGTATGTGCAATTAGGGGTACCGAAATACAAACAGGGGCACGTATATGCAATCA
*
46488375 GGGGTACCAAAGTAC
66 GGGGCACCAAAGTAC
* * * * *
46488390 AAACAGGGGCACGTATGTGGAATTAGGGGTACTGAAGTACAAACAGGGGCACGTATATGCAATTA
1 AAACAGGGGCATGTATGTGCAATTAGGGGTACCGAAATACAAACAGGGGCACGTATATGCAATCA
*
46488455 GGGGCACCGAAGTAC
66 GGGGCACCAAAGTAC
46488470 AAACAGGGGCATGTATGTGCAATT
1 AAACAGGGGCATGTATGTGCAATT
46488494 CAGGTATAAT
Statistics
Matches: 92, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
80 92 1.00
ACGTcount: A:0.35, C:0.17, G:0.30, T:0.18
Consensus pattern (80 bp):
AAACAGGGGCATGTATGTGCAATTAGGGGTACCGAAATACAAACAGGGGCACGTATATGCAATCA
GGGGCACCAAAGTAC
Found at i:46488479 original size:20 final size:20
Alignment explanation
Indices: 46488333--46488480 Score: 79
Period size: 20 Copynumber: 7.4 Consensus size: 20
46488323 TATGTGCAAT
* *
46488333 CAGGGGTACCGAAATACAAA
1 CAGGGGCACCGAAGTACAAA
* * *
46488353 CAGGGGCA-CGTATGTGCAAT
1 CAGGGGCACCG-AAGTACAAA
* *
46488373 CAGGGGTACCAAAGTACAAA
1 CAGGGGCACCGAAGTACAAA
* ** *
46488393 CAGGGGCA-CGTATGTGGAAT
1 CAGGGGCACCG-AAGTACAAA
* * *
46488413 TAGGGGTACTGAAGTACAAA
1 CAGGGGCACCGAAGTACAAA
* *
46488433 CAGGGGCA-CGTATA-TGCAAT
1 CAGGGGCACCG-A-AGTACAAA
*
46488453 TAGGGGCACCGAAGTACAAA
1 CAGGGGCACCGAAGTACAAA
46488473 CAGGGGCA
1 CAGGGGCA
46488481 TGTATGTGCA
Statistics
Matches: 88, Mismatches: 32, Indels: 16
0.65 0.24 0.12
Matches are distributed among these distances:
19 5 0.06
20 78 0.89
21 5 0.06
ACGTcount: A:0.35, C:0.18, G:0.32, T:0.15
Consensus pattern (20 bp):
CAGGGGCACCGAAGTACAAA
Found at i:46492822 original size:23 final size:23
Alignment explanation
Indices: 46492790--46492876 Score: 84
Period size: 23 Copynumber: 3.7 Consensus size: 23
46492780 ATAGTGCTTA
*
46492790 CTGTTAATCCACTTCGGCGGTGTT
1 CTGTT-ATCCACTTCGGCAGTGTT
* *
46492814 CTGTCATCCACTTCGGTAGTGTT
1 CTGTTATCCACTTCGGCAGTGTT
* * * *
46492837 ATGTTATTCGCTTCGGTAGTGTT
1 CTGTTATCCACTTCGGCAGTGTT
* *
46492860 CTGTTATTCGCTTCGGC
1 CTGTTATCCACTTCGGC
46492877 GATGTTCAGT
Statistics
Matches: 54, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
23 50 0.93
24 4 0.07
ACGTcount: A:0.11, C:0.23, G:0.24, T:0.41
Consensus pattern (23 bp):
CTGTTATCCACTTCGGCAGTGTT
Found at i:46498613 original size:45 final size:45
Alignment explanation
Indices: 46498554--46498706 Score: 234
Period size: 45 Copynumber: 3.4 Consensus size: 45
46498544 CACCAGTATA
* * *
46498554 CAGTAATCAGTAACAGTAACAGTATTCAACACACAAAGTGCTGAAC
1 CAGTAA-CAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT
* *
46498600 CTGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAGT
1 CAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT
* *
46498645 CGGTAACGGTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT
1 CAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT
46498690 CAGTAACAGTAACAGTA
1 CAGTAACAGTAACAGTA
46498707 GTCGGCACAT
Statistics
Matches: 97, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
45 92 0.95
46 5 0.05
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.19
Consensus pattern (45 bp):
CAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT
Found at i:46498730 original size:38 final size:39
Alignment explanation
Indices: 46498558--46498733 Score: 149
Period size: 45 Copynumber: 4.2 Consensus size: 39
46498548 AGTATACAGT
* * *
46498558 AATCAGTAACAGTAACAGTATTCAACACACAAAGTGCTG
1 AATCAGTAACAGTAACAGTAGTCGACACACAAAGTGCCG
*
46498597 AACCTGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCG
1 AA----T--CAGTAACAGTAACAGTAGTCGACACACAAAGTGCCG
* *
46498642 AGTCGGTAACGGTAACAGTAACAGTATTCGACACACAAAGTGCCG
1 AATC----A--GTAACAGTAACAGTAGTCGACACACAAAGTGCCG
* *
46498687 AATCAGTAACAGTAACAGTAGTCGGCACA-TAAGTGCCTG
1 AATCAGTAACAGTAACAGTAGTCGACACACAAAGTGCC-G
46498726 -ATCAGTAA
1 AATCAGTAA
46498734 GCCGGCAAAT
Statistics
Matches: 117, Mismatches: 7, Indels: 27
0.77 0.05 0.18
Matches are distributed among these distances:
38 15 0.13
39 26 0.22
41 2 0.02
43 2 0.02
45 72 0.62
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.19
Consensus pattern (39 bp):
AATCAGTAACAGTAACAGTAGTCGACACACAAAGTGCCG
Found at i:46498994 original size:39 final size:40
Alignment explanation
Indices: 46498908--46498995 Score: 110
Period size: 40 Copynumber: 2.2 Consensus size: 40
46498898 AATTCTTTAC
* *
46498908 TTCAGTAATTTCACAATTCAATGCATTATGCATAACAATA
1 TTCAGTATTTTCACAATTCAATGCATAATGCATAACAATA
*
46498948 TTCAGTATTTTCACAATTCACT-CAGTAAT-CA-AGACAATA
1 TTCAGTATTTTCACAATTCAATGCA-TAATGCATA-ACAATA
46498987 TTCAGTATT
1 TTCAGTATT
46498996 CCATAATTCG
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
38 1 0.02
39 19 0.44
40 23 0.53
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.36
Consensus pattern (40 bp):
TTCAGTATTTTCACAATTCAATGCATAATGCATAACAATA
Found at i:46499729 original size:11 final size:11
Alignment explanation
Indices: 46499715--46499740 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
46499705 CTTTTTCTTC
46499715 TTTCTCCCCTG
1 TTTCTCCCCTG
46499726 TTTCTCCCCTG
1 TTTCTCCCCTG
46499737 TTTC
1 TTTC
46499741 GTCTCTTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.42, G:0.08, T:0.50
Consensus pattern (11 bp):
TTTCTCCCCTG
Found at i:46501751 original size:47 final size:47
Alignment explanation
Indices: 46501678--46501772 Score: 172
Period size: 47 Copynumber: 2.0 Consensus size: 47
46501668 TGTGAGTATG
46501678 ATTAATCTCTTTTAGAGAAGTACCTCTATTAAGAACCTCAAGACAAA
1 ATTAATCTCTTTTAGAGAAGTACCTCTATTAAGAACCTCAAGACAAA
* *
46501725 ATTAATCTCTTTTAGAGAAGTGCCTCTATTAAGAACCTTAAGACAAA
1 ATTAATCTCTTTTAGAGAAGTACCTCTATTAAGAACCTCAAGACAAA
46501772 A
1 A
46501773 CGCACCAATT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.31
Consensus pattern (47 bp):
ATTAATCTCTTTTAGAGAAGTACCTCTATTAAGAACCTCAAGACAAA
Found at i:46507619 original size:17 final size:17
Alignment explanation
Indices: 46507605--46507668 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 17
46507595 CTCCAAAAGT
46507605 ACTTTTGAAAAAAAAAC
1 ACTTTTGAAAAAAAAAC
46507622 ACTTTTG---AAAAAAC
1 ACTTTTGAAAAAAAAAC
*** *
46507636 ACTTTTGACTCCAAAAGC
1 ACTTTTGA-AAAAAAAAC
46507654 ACTTTTGAAAAAAAA
1 ACTTTTGAAAAAAAA
46507669 GCTGTGTTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
14 14 0.37
17 11 0.29
18 13 0.34
ACGTcount: A:0.50, C:0.16, G:0.08, T:0.27
Consensus pattern (17 bp):
ACTTTTGAAAAAAAAAC
Found at i:46507640 original size:31 final size:32
Alignment explanation
Indices: 46507605--46507666 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
46507595 CTCCAAAAGT
46507605 ACTTTTGA-AAAAAAAACACTTTTGAAAAAAC
1 ACTTTTGACAAAAAAAACACTTTTGAAAAAAC
*** *
46507636 ACTTTTGACTCCAAAAGCACTTTTGAAAAAA
1 ACTTTTGACAAAAAAAACACTTTTGAAAAAA
46507667 AAGCTGTGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 8 0.31
32 18 0.69
ACGTcount: A:0.48, C:0.16, G:0.08, T:0.27
Consensus pattern (32 bp):
ACTTTTGACAAAAAAAACACTTTTGAAAAAAC
Found at i:46507651 original size:18 final size:17
Alignment explanation
Indices: 46507581--46507661 Score: 69
Period size: 18 Copynumber: 4.8 Consensus size: 17
46507571 GCATGCTTAA
46507581 AAAAACACTTTTGACTCC
1 AAAAACACTTTTGA-TCC
** ***
46507599 AAAAGTACTTTTGAAAA
1 AAAAACACTTTTGATCC
46507616 AAAAACACTTTTGA---
1 AAAAACACTTTTGATCC
46507630 AAAAACACTTTTGACTCC
1 AAAAACACTTTTGA-TCC
*
46507648 AAAAGCACTTTTGA
1 AAAAACACTTTTGA
46507662 AAAAAAAGCT
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
14 14 0.27
17 12 0.24
18 25 0.49
ACGTcount: A:0.44, C:0.19, G:0.09, T:0.28
Consensus pattern (17 bp):
AAAAACACTTTTGATCC
Found at i:46507669 original size:17 final size:17
Alignment explanation
Indices: 46507599--46507670 Score: 69
Period size: 17 Copynumber: 4.4 Consensus size: 17
46507589 TTTTGACTCC
*
46507599 AAAAGTACTTTTGAAAA
1 AAAAGCACTTTTGAAAA
*
46507616 AAAAACACTTTTG--AA
1 AAAAGCACTTTTGAAAA
***
46507631 AAAA-CACTTTTGACTCC
1 AAAAGCACTTTTGA-AAA
46507648 AAAAGCACTTTTGAAAA
1 AAAAGCACTTTTGAAAA
46507665 AAAAGC
1 AAAAGC
46507671 TGTGTTAAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
14 8 0.18
15 6 0.14
17 21 0.48
18 9 0.20
ACGTcount: A:0.50, C:0.15, G:0.10, T:0.25
Consensus pattern (17 bp):
AAAAGCACTTTTGAAAA
Found at i:46512068 original size:9 final size:8
Alignment explanation
Indices: 46512049--46512100 Score: 58
Period size: 9 Copynumber: 6.8 Consensus size: 8
46512039 TAAAACAATT
46512049 TTTTATA-
1 TTTTATAG
46512056 TTTTATTAG
1 TTTTA-TAG
46512065 TTTTAT-G
1 TTTTATAG
46512072 -TTTATA-
1 TTTTATAG
46512078 TTTTATAG
1 TTTTATAG
46512086 TTTTTATAG
1 -TTTTATAG
46512095 TTTTAT
1 TTTTAT
46512101 TTTATTTAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
6 5 0.13
7 12 0.31
8 9 0.23
9 13 0.33
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (8 bp):
TTTTATAG
Found at i:46512077 original size:22 final size:24
Alignment explanation
Indices: 46512050--46512106 Score: 86
Period size: 22 Copynumber: 2.5 Consensus size: 24
46512040 AAAACAATTT
46512050 TTTATATTTTATTAG-TTTTAT-G
1 TTTATATTTTATTAGTTTTTATAG
46512072 TTTATATTTTA-TAGTTTTTATAG
1 TTTATATTTTATTAGTTTTTATAG
46512095 TTT-TATTTTATT
1 TTTATATTTTATT
46512107 TAATAAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
21 3 0.09
22 24 0.75
23 5 0.16
ACGTcount: A:0.23, C:0.00, G:0.07, T:0.70
Consensus pattern (24 bp):
TTTATATTTTATTAGTTTTTATAG
Found at i:46512098 original size:30 final size:28
Alignment explanation
Indices: 46512049--46512105 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 28
46512039 TAAAACAATT
46512049 TTTTATATTTTATTAGTTTTATGTTTATA
1 TTTTATATTTTATTAGTTTTAT-TTTATA
46512078 TTTTATAGTTTT-TATAGTTTTATTTTAT
1 TTTTATA-TTTTAT-TAGTTTTATTTTAT
46512106 TTAATAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 13 0.50
30 13 0.50
ACGTcount: A:0.23, C:0.00, G:0.07, T:0.70
Consensus pattern (28 bp):
TTTTATATTTTATTAGTTTTATTTTATA
Found at i:46512724 original size:16 final size:15
Alignment explanation
Indices: 46512700--46512750 Score: 52
Period size: 16 Copynumber: 3.4 Consensus size: 15
46512690 TAACAAATTT
*
46512700 TTATTAAATAAATAAA
1 TTATAAAAT-AATAAA
46512716 TTATAAAAT-ATAAA
1 TTATAAAATAATAAA
46512730 -TATAAAACTAATAAA
1 TTATAAAA-TAATAAA
*
46512745 ATATAA
1 TTATAA
46512751 TTTTTTTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
13 7 0.23
14 6 0.19
15 5 0.16
16 13 0.42
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (15 bp):
TTATAAAATAATAAA
Found at i:46512730 original size:22 final size:22
Alignment explanation
Indices: 46512704--46512750 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
46512694 AAATTTTTAT
*
46512704 TAAATA-AATAAATTATAAAATA
1 TAAATATAA-AAATAATAAAATA
*
46512726 TAAATATAAAACTAATAAAATA
1 TAAATATAAAAATAATAAAATA
46512748 TAA
1 TAA
46512751 TTTTTTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 20 0.91
23 2 0.09
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (22 bp):
TAAATATAAAAATAATAAAATA
Found at i:46513044 original size:16 final size:16
Alignment explanation
Indices: 46513023--46513062 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
46513013 TATATATTTT
46513023 TATTTTTAATCAAATA
1 TATTTTTAATCAAATA
* *
46513039 TATTTTTTATTAAATA
1 TATTTTTAATCAAATA
46513055 TATATTTT
1 TAT-TTTT
46513063 TTGGACTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (16 bp):
TATTTTTAATCAAATA
Found at i:46516353 original size:19 final size:18
Alignment explanation
Indices: 46516321--46516367 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 18
46516311 TATTCAACCT
*
46516321 TTCTTTTGAGTTAATAAA
1 TTCTTTTGACTTAATAAA
46516339 TTCTCTTTGACTTAATAAA
1 TTCT-TTTGACTTAATAAA
46516358 TTCTATTTGA
1 TTCT-TTTGA
46516368 GTTTTTCTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 4 0.15
19 22 0.85
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.51
Consensus pattern (18 bp):
TTCTTTTGACTTAATAAA
Found at i:46517388 original size:10 final size:10
Alignment explanation
Indices: 46517373--46517399 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
46517363 GCAATCAGGG
46517373 ATCAAAATGA
1 ATCAAAATGA
46517383 ATCAAAATGA
1 ATCAAAATGA
46517393 ATCAAAA
1 ATCAAAA
46517400 CATAAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.63, C:0.11, G:0.07, T:0.19
Consensus pattern (10 bp):
ATCAAAATGA
Found at i:46518724 original size:25 final size:25
Alignment explanation
Indices: 46518696--46518748 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
46518686 CTAGGCAGAG
*
46518696 AGCCTGACATAAATAACCGGCACGA
1 AGCCTAACATAAATAACCGGCACGA
* * **
46518721 AGCCTAATATAAATCAGTGGCACGA
1 AGCCTAACATAAATAACCGGCACGA
46518746 AGC
1 AGC
46518749 ATGCTAGGCA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.40, C:0.25, G:0.21, T:0.15
Consensus pattern (25 bp):
AGCCTAACATAAATAACCGGCACGA
Found at i:46518771 original size:41 final size:40
Alignment explanation
Indices: 46518721--46518919 Score: 177
Period size: 41 Copynumber: 4.8 Consensus size: 40
46518711 ACCGGCACGA
* *
46518721 AGCCTAATATAAATCAGTGGCACGAAGCATGCTAGGCACAG
1 AGCCTGATATAAATCACTGGCACGAAGC-TGCTAGGCACAG
* * *
46518762 AGCCTAATATAAATCACCGGCACGAAGCTTGCTAGGCACAC
1 AGCCTGATATAAATCACTGGCACGAAGC-TGCTAGGCACAG
* * * * *
46518803 AACTTGATA-CAA-CACATGGGCACGGAGTCTGCTAGGCACAT
1 AGCCTGATATAAATCAC-T-GGCACGAAG-CTGCTAGGCACAG
* * *
46518844 AACCTGATATAAATCACTAGCACGAAGCCTGCTAGGCATAG
1 AGCCTGATATAAATCACTGGCACGAAG-CTGCTAGGCACAG
** *
46518885 AGCCTGATATAAATCACCAGCATGAAGCCTGCTAG
1 AGCCTGATATAAATCACTGGCACGAAG-CTGCTAG
46518920 ACTCAAAGTC
Statistics
Matches: 132, Mismatches: 21, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
39 3 0.02
40 2 0.02
41 120 0.91
42 4 0.03
43 3 0.02
ACGTcount: A:0.35, C:0.25, G:0.22, T:0.19
Consensus pattern (40 bp):
AGCCTGATATAAATCACTGGCACGAAGCTGCTAGGCACAG
Found at i:46529072 original size:32 final size:32
Alignment explanation
Indices: 46529031--46529095 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
46529021 TTTCGTAATA
46529031 ATTAGAAAGTGTAATTGGAGTACTCAAATCAT
1 ATTAGAAAGTGTAATTGGAGTACTCAAATCAT
*
46529063 ATTAGAAAGTGTAATTGGAGTACTCCAATCAT
1 ATTAGAAAGTGTAATTGGAGTACTCAAATCAT
46529095 A
1 A
46529096 CTCAATTTAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.31
Consensus pattern (32 bp):
ATTAGAAAGTGTAATTGGAGTACTCAAATCAT
Found at i:46529554 original size:13 final size:13
Alignment explanation
Indices: 46529536--46529560 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
46529526 TTTTATTTTA
46529536 TTTTTAATTAATG
1 TTTTTAATTAATG
46529549 TTTTTAATTAAT
1 TTTTTAATTAAT
46529561 AAATATATCA
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:0.00, G:0.04, T:0.64
Consensus pattern (13 bp):
TTTTTAATTAATG
Found at i:46530943 original size:20 final size:19
Alignment explanation
Indices: 46530918--46530959 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
46530908 CATACTGATA
* *
46530918 TATATAATATATATTTTTAT
1 TATATAAT-TACATATTTAT
46530938 TATATAATTACATATTTAT
1 TATATAATTACATATTTAT
46530957 TAT
1 TAT
46530960 TTTATTTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (19 bp):
TATATAATTACATATTTAT
Found at i:46531034 original size:97 final size:96
Alignment explanation
Indices: 46530820--46531036 Score: 226
Period size: 97 Copynumber: 2.3 Consensus size: 96
46530810 AATGTTTTTT
* *
46530820 AAAA-ATAAAAT-ATATTTTTATTATATAATTATATAATCATTAATTTATTTATATAAATAAAGG
1 AAAATATAAAATAATATTTTTATTATATAATTACATAATCATTAATTTATTTATATAAATAAAAG
* * * **
46530883 AGTTATTAATTAAAAATACTTTTAACATACT
66 AATTATTAATTAAAAATACATTAAACATAAA
* * * * * *
46530914 GATATATATAATATATATTTTTATTATATAATTACATATTTATTATTTTATTTATATAAATAAAA
1 AAAATATAAAATA-ATATTTTTATTATATAATTACATAATCATTAATTTATTTATATAAATAAAA
* *
46530979 GAATTATTAGTTAAAAATGA-ATTAAAGATAAA
65 GAATTATTAATTAAAAAT-ACATTAAACATAAA
*
46531011 AAAACTCA-AAAATAATATATTTATTA
1 AAAA-T-ATAAAATAATATTTTTATTA
46531037 ATTAAATATA
Statistics
Matches: 98, Mismatches: 19, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
94 2 0.02
95 6 0.06
97 82 0.84
98 7 0.07
99 1 0.01
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.43
Consensus pattern (96 bp):
AAAATATAAAATAATATTTTTATTATATAATTACATAATCATTAATTTATTTATATAAATAAAAG
AATTATTAATTAAAAATACATTAAACATAAA
Found at i:46548687 original size:2 final size:2
Alignment explanation
Indices: 46548680--46548722 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
46548670 GTAATACTAG
46548680 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
46548722 T
1 T
46548723 GGATGAAATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:46551006 original size:24 final size:24
Alignment explanation
Indices: 46550941--46551031 Score: 155
Period size: 24 Copynumber: 3.7 Consensus size: 24
46550931 AGCACTGCCA
46550941 TGCTAAATATCAGAGAGCACCAACG
1 TGCT-AATATCAGAGAGCACCAACG
46550966 TGCTAATAATCAGAGAGCACCAACG
1 TGCTAAT-ATCAGAGAGCACCAACG
*
46550991 TGCTAATATCAGAGAGCACAAACG
1 TGCTAATATCAGAGAGCACCAACG
46551015 TGCTAATATCAGAGAGC
1 TGCTAATATCAGAGAGC
46551032 GCGCTAAAGT
Statistics
Matches: 64, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
24 36 0.56
25 28 0.44
ACGTcount: A:0.40, C:0.22, G:0.21, T:0.18
Consensus pattern (24 bp):
TGCTAATATCAGAGAGCACCAACG
Found at i:46551015 original size:49 final size:50
Alignment explanation
Indices: 46550899--46551031 Score: 161
Period size: 49 Copynumber: 2.8 Consensus size: 50
46550889 TATACGGAAC
* * ***
46550899 AAATA-CAGAGAGCACAAATGTGC---TAAGCAGAGAGCACTGCCATGCT
1 AAATATCAGAGAGCACAAACGTGCTAATAATCAGAGAGCACCAACATGCT
* *
46550945 AAATATCAGAGAGCACCAACGTGCTAATAATCAGAGAGCACCAACGTGCT
1 AAATATCAGAGAGCACAAACGTGCTAATAATCAGAGAGCACCAACATGCT
46550995 -AATATCAGAGAGCACAAACGTGCTAAT-ATCAGAGAGC
1 AAATATCAGAGAGCACAAACGTGCTAATAATCAGAGAGC
46551032 GCGCTAAAGT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
46 5 0.07
47 16 0.21
48 10 0.13
49 26 0.35
50 18 0.24
ACGTcount: A:0.41, C:0.22, G:0.22, T:0.16
Consensus pattern (50 bp):
AAATATCAGAGAGCACAAACGTGCTAATAATCAGAGAGCACCAACATGCT
Found at i:46552472 original size:8 final size:8
Alignment explanation
Indices: 46552459--46552540 Score: 59
Period size: 8 Copynumber: 10.5 Consensus size: 8
46552449 TGTCATATAT
46552459 ATATAATA
1 ATATAATA
46552467 ATATAAT-
1 ATATAATA
46552474 A-AT-ATA
1 ATATAATA
46552480 ATATAAT-
1 ATATAATA
46552487 ATATTAATA
1 ATA-TAATA
46552496 ATA-ATATA
1 ATATA-ATA
*
46552504 ATATAAAA
1 ATATAATA
* *
46552512 ACATAATC
1 ATATAATA
46552520 AT-TACTATA
1 ATATA--ATA
46552529 ATATAATA
1 ATATAATA
46552537 ATAT
1 ATAT
46552541 TTTTTAACAC
Statistics
Matches: 58, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
5 2 0.03
6 3 0.05
7 9 0.16
8 34 0.59
9 8 0.14
10 2 0.03
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.38
Consensus pattern (8 bp):
ATATAATA
Found at i:46552474 original size:5 final size:5
Alignment explanation
Indices: 46552453--46552536 Score: 61
Period size: 5 Copynumber: 16.6 Consensus size: 5
46552443 TTTCTTTGTC
46552453 ATATA TATATA ATA-A TATAATA ATATA ATATA ATAT- AT-TA ATAATA
1 ATATA -ATATA ATATA -AT-ATA ATATA ATATA ATATA ATATA AT-ATA
* *
46552499 ATATA ATATA A-A-A ACATA ATCATTA CTATA ATATA ATA
1 ATATA ATATA ATATA ATATA AT-A-TA ATATA ATATA ATA
46552537 ATATTTTTTA
Statistics
Matches: 65, Mismatches: 3, Indels: 21
0.73 0.03 0.24
Matches are distributed among these distances:
3 3 0.05
4 7 0.11
5 37 0.57
6 14 0.22
7 4 0.06
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (5 bp):
ATATA
Found at i:46552518 original size:24 final size:24
Alignment explanation
Indices: 46552455--46552537 Score: 80
Period size: 24 Copynumber: 3.4 Consensus size: 24
46552445 TCTTTGTCAT
46552455 ATATATATAATAAT-ATAATAATATA
1 ATATA-ATAA-AATAATAATAATATA
* *
46552480 ATATAATATATTAATAATAATATA
1 ATATAATAAAATAATAATAATATA
* *
46552504 ATATAA-AAACATAATCATTACTATA
1 ATATAATAAA-ATAAT-AATAATATA
46552529 ATATAATAA
1 ATATAATAA
46552538 TATTTTTTAA
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
23 4 0.08
24 24 0.50
25 18 0.38
26 2 0.04
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (24 bp):
ATATAATAAAATAATAATAATATA
Found at i:46555096 original size:19 final size:19
Alignment explanation
Indices: 46555072--46555110 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
46555062 CTCCAAATTT
46555072 TTTCTATGTATTATTTGTA
1 TTTCTATGTATTATTTGTA
46555091 TTTCTATGTATTATTTGTA
1 TTTCTATGTATTATTTGTA
46555110 T
1 T
46555111 AGAAATATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.21, C:0.05, G:0.10, T:0.64
Consensus pattern (19 bp):
TTTCTATGTATTATTTGTA
Found at i:46556172 original size:3 final size:3
Alignment explanation
Indices: 46556164--46556189 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
46556154 TCCTTACGTC
46556164 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
46556190 AAACCTAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:46561363 original size:30 final size:30
Alignment explanation
Indices: 46561307--46561364 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
46561297 TCCGAGCTTT
*
46561307 GGGGCAAAAGTGTAATTATGTAAAAGTTTA
1 GGGGCAAAAGTGTAATTATGCAAAAGTTTA
* *
46561337 GGGGCAAAA-TGGTAATTTTGCCAAAGTT
1 GGGGCAAAAGT-GTAATTATGCAAAAGTT
46561365 AGAGTCGAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 1 0.04
30 23 0.96
ACGTcount: A:0.36, C:0.07, G:0.28, T:0.29
Consensus pattern (30 bp):
GGGGCAAAAGTGTAATTATGCAAAAGTTTA
Found at i:46561870 original size:50 final size:50
Alignment explanation
Indices: 46561707--46561863 Score: 197
Period size: 50 Copynumber: 3.0 Consensus size: 50
46561697 TAAAGAAATT
** * *
46561707 CCATGTAAGACCATGTCTGGGACATGGAATTGTCATCATTGAGATTATGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-C--CGAG---ATGAGAGGTC
* * *
46561763 CCATGTAAGATCATGTCTGGGACATGGCGTTGGCCCCTAGATGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTC
46561813 CCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTC
46561863 C
1 C
46561864 ACTGTAATGG
Statistics
Matches: 91, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
50 58 0.64
53 2 0.02
55 1 0.01
56 30 0.33
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.24
Consensus pattern (50 bp):
CCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTC
Found at i:46562972 original size:13 final size:13
Alignment explanation
Indices: 46562954--46562984 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
46562944 TTCCAGCAAC
46562954 TATGAATTTATTT
1 TATGAATTTATTT
46562967 TATGAATTTATTT
1 TATGAATTTATTT
*
46562980 GATGA
1 TATGA
46562985 TGATCTAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (13 bp):
TATGAATTTATTT
Found at i:46563154 original size:50 final size:50
Alignment explanation
Indices: 46563079--46563321 Score: 414
Period size: 50 Copynumber: 4.8 Consensus size: 50
46563069 ATTTGGGTAA
46563079 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
46563129 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
*
46563179 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * *
46563229 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** *
46563279 AGAATATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
46563322 TGTTATTATC
Statistics
Matches: 183, Mismatches: 9, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
50 147 0.80
51 36 0.20
ACGTcount: A:0.27, C:0.22, G:0.30, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:46564753 original size:49 final size:50
Alignment explanation
Indices: 46564637--46564756 Score: 129
Period size: 49 Copynumber: 2.4 Consensus size: 50
46564627 TACATCCACC
* *
46564637 GTAAGACCT-TGTCTGGGACATGGCATGGGCACCTATATGAGAACTCCCAT
1 GTAAGA-CTATGTCTGGGACATGGCATGGGCACCTACAAGAGAACTCCCAT
* * * * * *
46564687 GTAAGACCATATTTGGGATATGGCATTGGCA-GTACAAGA-AACATCCCAT
1 GTAAGACTATGTCTGGGACATGGCATGGGCACCTACAAGAGAAC-TCCCAT
46564736 GTAAGACTATGTCTGGGACAT
1 GTAAGACTATGTCTGGGACAT
46564757 AGCTTTGGCA
Statistics
Matches: 56, Mismatches: 12, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
48 3 0.05
49 29 0.52
50 24 0.43
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (50 bp):
GTAAGACTATGTCTGGGACATGGCATGGGCACCTACAAGAGAACTCCCAT
Found at i:46566457 original size:33 final size:33
Alignment explanation
Indices: 46566420--46566485 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
46566410 ATCACAAGTT
46566420 GGACTAAAGAGAATTTATAATTTGACTTTGTTA
1 GGACTAAAGAGAATTTATAATTTGACTTTGTTA
46566453 GGACTAAAGAGAATTTATAATTTGACTTTGTTA
1 GGACTAAAGAGAATTTATAATTTGACTTTGTTA
46566486 TATCAAAACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.36, C:0.06, G:0.18, T:0.39
Consensus pattern (33 bp):
GGACTAAAGAGAATTTATAATTTGACTTTGTTA
Found at i:46566807 original size:33 final size:33
Alignment explanation
Indices: 46566769--46566847 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
46566759 CTTGTAATAT
46566769 AAAAAAGAAGTATACATTTAAAAAAATAAGGGA
1 AAAAAAGAAGTATACATTTAAAAAAATAAGGGA
46566802 AAAAAAGAAGTATACATTTAAAAAAATAAGGGA
1 AAAAAAGAAGTATACATTTAAAAAAATAAGGGA
*
46566835 GAAAAAGAA-TATA
1 AAAAAAGAAGTATA
46566848 AAAGTTGAGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 4 0.09
33 41 0.91
ACGTcount: A:0.65, C:0.03, G:0.15, T:0.18
Consensus pattern (33 bp):
AAAAAAGAAGTATACATTTAAAAAAATAAGGGA
Found at i:46570830 original size:830 final size:830
Alignment explanation
Indices: 46569232--46570891 Score: 3293
Period size: 830 Copynumber: 2.0 Consensus size: 830
46569222 CCGTGTGGTG
46569232 TCGACTGTGAAGATATTTAGCTTTCACTGTTCATTACTTTTTCGTGTTTTTTGTTATACACCTGG
1 TCGACTGTGAAGATATTTAGCTTTCACTGTTCATTACTTTTTCGTGTTTTTTGTTATACACCTGG
46569297 TTCGATTTTGATGCGTAAACATCCACGAGACTTTCAGAACCTAAATACGATATTTAATATAGTCA
66 TTCGATTTTGATGCGTAAACATCCACGAGACTTTCAGAACCTAAATACGATATTTAATATAGTCA
46569362 ATTCCAAAAACAAGACACCATATTAATCAAGATTTGAACACAATAATCTTATACACCACTACCAA
131 ATTCCAAAAACAAGACACCATATTAATCAAGATTTGAACACAATAATCTTATACACCACTACCAA
46569427 AAACATGTTCGATCGCTTACCGTCAAAAGAACGACAACTACACACCACTTAGACCGTTGGAGGAA
196 AAACATGTTCGATCGCTTACCGTCAAAAGAACGACAACTACACACCACTTAGACCGTTGGAGGAA
*
46569492 CACCCAACCCCTCTCAATCCTTCCCTAAACACAACGGATTAGTTAGTCAACACATAATACAAATT
261 CACCCAACCCCTCTCAATCCTTCCCTAAACACAACGGATTAATTAGTCAACACATAATACAAATT
46569557 TAACAATACCACTTTGCAACCCAAAACCCCTAAACCAAACGAACACCCACAACACGTGATTAGAG
326 TAACAATACCACTTTGCAACCCAAAACCCCTAAACCAAACGAACACCCACAACACGTGATTAGAG
46569622 AACTAACAAGTAGCCTTACCTACCAAGAATGAAGTCGATGAAGCCAAACGAAGGAACAAAATAAA
391 AACTAACAAGTAGCCTTACCTACCAAGAATGAAGTCGATGAAGCCAAACGAAGGAACAAAATAAA
46569687 ACCAAATGAAGAGAAATCCAAGACCAAAAGAGATAAAGAAAAAATATTAAAGAAAAGAACAAAAA
456 ACCAAATGAAGAGAAATCCAAGACCAAAAGAGATAAAGAAAAAATATTAAAGAAAAGAACAAAAA
46569752 TGAGAGATTGAAATTTTCCAATTTCTATACTGGCAATGGTGTAAATAATGAATGAAAAAGAAAAT
521 TGAGAGATTGAAATTTTCCAATTTCTATACTGGCAATGGTGTAAATAATGAATGAAAAAGAAAAT
46569817 AAGGAAAGATGGGAAACGTGGGATTGATGGGAATTTGGGATAAAGAAATAAAAATAAAATAATAA
586 AAGGAAAGATGGGAAACGTGGGATTGATGGGAATTTGGGATAAAGAAATAAAAATAAAATAATAA
46569882 TATATTTTAAACAAAAACCAGTTCCCAACTAACTCAACATTCTAATAACTTATCAGATTTTCCCC
651 TATATTTTAAACAAAAACCAGTTCCCAACTAACTCAACATTCTAATAACTTATCAGATTTTCCCC
46569947 AGACAGGGTTCGATTAGACCTGAATTACCCCATAATCTACTTAAACAAAAATAGAAAAAATATTG
716 AGACAGGGTTCGATTAGACCTGAATTACCCCATAATCTACTTAAACAAAAATAGAAAAAATATTG
46570012 CCAACAAGCTCACATAGGGATTCTAACATAAGACCCAAGGGTAAGCTAAC
781 CCAACAAGCTCACATAGGGATTCTAACATAAGACCCAAGGGTAAGCTAAC
46570062 TCGACTGTGAAGATATTTAGCTTTCACTGTTCATTACTTTTTCGTGTTTTTTGTTATACACCTGG
1 TCGACTGTGAAGATATTTAGCTTTCACTGTTCATTACTTTTTCGTGTTTTTTGTTATACACCTGG
46570127 TTCGATTTTGATGCGTAAACATCCACGAGACTTTCAGAACCTAAATACGATATTTAATATAGTCA
66 TTCGATTTTGATGCGTAAACATCCACGAGACTTTCAGAACCTAAATACGATATTTAATATAGTCA
46570192 ATTCCAAAAACAAGACACCATATTAATCAAGATTTGAACACAATAATCTTATACACCACTACCAA
131 ATTCCAAAAACAAGACACCATATTAATCAAGATTTGAACACAATAATCTTATACACCACTACCAA
*
46570257 AAACGTGTTCGATCGCTTACCGTCAAAAGAACGACAACTACACACCACTTAGACCGTTGGAGGAA
196 AAACATGTTCGATCGCTTACCGTCAAAAGAACGACAACTACACACCACTTAGACCGTTGGAGGAA
46570322 CACCCAACCCCTCTCAATCCTTCCCTAAACACAACGGATTAATTAGTCAACACATAATACAAATT
261 CACCCAACCCCTCTCAATCCTTCCCTAAACACAACGGATTAATTAGTCAACACATAATACAAATT
46570387 TAACAATACCACTTTGCAACCCAAAACCCCTAAACCAAACGAACACCCACAACACGTGATTAGAG
326 TAACAATACCACTTTGCAACCCAAAACCCCTAAACCAAACGAACACCCACAACACGTGATTAGAG
46570452 AACTAACAAGTAGCCTTACCTACCAAGAATGAAGTCGATGAAGCCAAACGAAGGAACAAAATAAA
391 AACTAACAAGTAGCCTTACCTACCAAGAATGAAGTCGATGAAGCCAAACGAAGGAACAAAATAAA
*
46570517 ACCAAATGAAGAGAAATCCAAGACCAAAAGAGATAAAGAAAAAATATTAAAGAAAAGAGCAAAAA
456 ACCAAATGAAGAGAAATCCAAGACCAAAAGAGATAAAGAAAAAATATTAAAGAAAAGAACAAAAA
46570582 TGAGAGATTGAAATTTTCCAATTTCTATACTGGCAATGGTGTAAATAATGAATGAAAAAGAAAAT
521 TGAGAGATTGAAATTTTCCAATTTCTATACTGGCAATGGTGTAAATAATGAATGAAAAAGAAAAT
46570647 AAGGAAAGATGGGAAACGTGGGATTGATGGGAATTTGGGATAAAGAAATAAAAATAAAATAATAA
586 AAGGAAAGATGGGAAACGTGGGATTGATGGGAATTTGGGATAAAGAAATAAAAATAAAATAATAA
46570712 TATATTTTAAACAAAAACCAGTTCCCAACTAACTCAACATTCTAATAACTTATCAGATTTTCCCC
651 TATATTTTAAACAAAAACCAGTTCCCAACTAACTCAACATTCTAATAACTTATCAGATTTTCCCC
46570777 AGACAGGGTTCGATTAGACCTGAATTACCCCATAATCTACTTAAACAAAAATAGAAAAAATATTG
716 AGACAGGGTTCGATTAGACCTGAATTACCCCATAATCTACTTAAACAAAAATAGAAAAAATATTG
46570842 CCAACAAGCTCACATAGGGATTCTAACATAAGACCCAAGGGTAAGCTAAC
781 CCAACAAGCTCACATAGGGATTCTAACATAAGACCCAAGGGTAAGCTAAC
46570892 ACCTTACCAT
Statistics
Matches: 827, Mismatches: 3, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
830 827 1.00
ACGTcount: A:0.42, C:0.20, G:0.14, T:0.24
Consensus pattern (830 bp):
TCGACTGTGAAGATATTTAGCTTTCACTGTTCATTACTTTTTCGTGTTTTTTGTTATACACCTGG
TTCGATTTTGATGCGTAAACATCCACGAGACTTTCAGAACCTAAATACGATATTTAATATAGTCA
ATTCCAAAAACAAGACACCATATTAATCAAGATTTGAACACAATAATCTTATACACCACTACCAA
AAACATGTTCGATCGCTTACCGTCAAAAGAACGACAACTACACACCACTTAGACCGTTGGAGGAA
CACCCAACCCCTCTCAATCCTTCCCTAAACACAACGGATTAATTAGTCAACACATAATACAAATT
TAACAATACCACTTTGCAACCCAAAACCCCTAAACCAAACGAACACCCACAACACGTGATTAGAG
AACTAACAAGTAGCCTTACCTACCAAGAATGAAGTCGATGAAGCCAAACGAAGGAACAAAATAAA
ACCAAATGAAGAGAAATCCAAGACCAAAAGAGATAAAGAAAAAATATTAAAGAAAAGAACAAAAA
TGAGAGATTGAAATTTTCCAATTTCTATACTGGCAATGGTGTAAATAATGAATGAAAAAGAAAAT
AAGGAAAGATGGGAAACGTGGGATTGATGGGAATTTGGGATAAAGAAATAAAAATAAAATAATAA
TATATTTTAAACAAAAACCAGTTCCCAACTAACTCAACATTCTAATAACTTATCAGATTTTCCCC
AGACAGGGTTCGATTAGACCTGAATTACCCCATAATCTACTTAAACAAAAATAGAAAAAATATTG
CCAACAAGCTCACATAGGGATTCTAACATAAGACCCAAGGGTAAGCTAAC
Found at i:46572720 original size:76 final size:76
Alignment explanation
Indices: 46572621--46572799 Score: 216
Period size: 76 Copynumber: 2.4 Consensus size: 76
46572611 TGTGCCCTAT
* * *
46572621 ACTAGTCGGATAAACCGGA-AATGTTTTGCGCCCAGAGCTAGTTGGATAAACCAACGATATCAAA
1 ACTAGTCGGATAAA-CTGACAATGTTTTGCGCCCAGAGCTAGTCGAATAAACCAACGATATCAAA
*
46572685 TGTATGCCCAGC
65 TATATGCCCAGC
* * ** * **
46572697 ACTAGTCGGGTAAACTGACAATGTTTTGTGCTTAGCGCTAGTCGAATAAACTGACGATATCAAAT
1 ACTAGTCGGATAAACTGACAATGTTTTGCGCCCAGAGCTAGTCGAATAAACCAACGATATCAAAT
*
46572762 ATGTGCCCAGC
66 ATATGCCCAGC
* *
46572773 ACTAGTCGAATAAATTGACAATGTTTT
1 ACTAGTCGGATAAACTGACAATGTTTT
46572800 ACATTTCATA
Statistics
Matches: 87, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
75 3 0.03
76 84 0.97
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (76 bp):
ACTAGTCGGATAAACTGACAATGTTTTGCGCCCAGAGCTAGTCGAATAAACCAACGATATCAAAT
ATATGCCCAGC
Found at i:46572778 original size:40 final size:40
Alignment explanation
Indices: 46572674--46572791 Score: 109
Period size: 40 Copynumber: 3.0 Consensus size: 40
46572664 GGATAAACCA
* * **
46572674 ACGATATCAAATGTATGCCCAGCACTAGTCGGGTAAACTG
1 ACGATATCAAATATGTGCCCAGCACTAGTCGAATAAACTG
** * ** *
46572714 AC-A-AT--GTTTTGTGCTTAGCGCTAGTCGAATAAACTG
1 ACGATATCAAATATGTGCCCAGCACTAGTCGAATAAACTG
*
46572750 ACGATATCAAATATGTGCCCAGCACTAGTCGAATAAATTG
1 ACGATATCAAATATGTGCCCAGCACTAGTCGAATAAACTG
46572790 AC
1 AC
46572792 AATGTTTTAC
Statistics
Matches: 58, Mismatches: 16, Indels: 8
0.71 0.20 0.10
Matches are distributed among these distances:
36 24 0.41
37 1 0.02
38 4 0.07
39 1 0.02
40 28 0.48
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.26
Consensus pattern (40 bp):
ACGATATCAAATATGTGCCCAGCACTAGTCGAATAAACTG
Found at i:46579780 original size:17 final size:17
Alignment explanation
Indices: 46579758--46579791 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
46579748 ATTGTTTTTG
46579758 TCACTTAACTTTTGGCT
1 TCACTTAACTTTTGGCT
*
46579775 TCACTTGACTTTTGGCT
1 TCACTTAACTTTTGGCT
46579792 CTTTCTCACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.15, C:0.24, G:0.15, T:0.47
Consensus pattern (17 bp):
TCACTTAACTTTTGGCT
Found at i:46583934 original size:17 final size:17
Alignment explanation
Indices: 46583912--46583972 Score: 86
Period size: 17 Copynumber: 3.5 Consensus size: 17
46583902 AACGTACTTG
46583912 AATAAATAATCAATTTC
1 AATAAATAATCAATTTC
*
46583929 AATAAATAATCAATTTT
1 AATAAATAATCAATTTC
*
46583946 AATAAATAATCACTTATC
1 AATAAATAATCAATT-TC
46583964 AAATAAATA
1 -AATAAATA
46583973 GTTTATTAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
17 30 0.77
18 1 0.03
19 8 0.21
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.34
Consensus pattern (17 bp):
AATAAATAATCAATTTC
Found at i:46586619 original size:45 final size:45
Alignment explanation
Indices: 46586555--46586640 Score: 154
Period size: 45 Copynumber: 1.9 Consensus size: 45
46586545 AGTTTACGAA
46586555 AACTCAATGTGTAATCCCATATAAAGCAAACAGACAAAAAGAAAT
1 AACTCAATGTGTAATCCCATATAAAGCAAACAGACAAAAAGAAAT
* *
46586600 AACTCAGTGTGTAATCCCATATAAAGTAAACAGACAAAAAG
1 AACTCAATGTGTAATCCCATATAAAGCAAACAGACAAAAAG
46586641 CAATCACAGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.51, C:0.17, G:0.13, T:0.19
Consensus pattern (45 bp):
AACTCAATGTGTAATCCCATATAAAGCAAACAGACAAAAAGAAAT
Found at i:46600240 original size:61 final size:59
Alignment explanation
Indices: 46600130--46600245 Score: 160
Period size: 61 Copynumber: 1.9 Consensus size: 59
46600120 ATTACTTTAA
* * * *
46600130 TATTAAATTAATATAATATTTATAAAGATAAAAATTAGATTAAATTTAATATTAAATAT
1 TATTAAAATAATAGAATATTTATAAAGATAAAAATTAAACTAAATTTAATATTAAATAT
* *
46600189 TATTAAAATAATAGAATATTATCTACAAGATAAACATTAAACTAAATTTAATATTAA
1 TATTAAAATAATAGAATATT-TATA-AAGATAAAAATTAAACTAAATTTAATATTAA
46600246 GATAATCACT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
59 18 0.37
60 3 0.06
61 28 0.57
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.39
Consensus pattern (59 bp):
TATTAAAATAATAGAATATTTATAAAGATAAAAATTAAACTAAATTTAATATTAAATAT
Found at i:46613386 original size:18 final size:17
Alignment explanation
Indices: 46613360--46613410 Score: 66
Period size: 18 Copynumber: 2.9 Consensus size: 17
46613350 TTTTGCTTCC
46613360 TTTATTTTTACTTTTAAT
1 TTTATTTTTA-TTTTAAT
* *
46613378 TTTACTTTTATTTTCAT
1 TTTATTTTTATTTTAAT
46613395 TGTTATTTTTATTTTA
1 T-TTATTTTTATTTTA
46613411 GTCTATTGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 7 0.25
18 21 0.75
ACGTcount: A:0.20, C:0.06, G:0.02, T:0.73
Consensus pattern (17 bp):
TTTATTTTTATTTTAAT
Found at i:46613406 original size:6 final size:6
Alignment explanation
Indices: 46613360--46613409 Score: 55
Period size: 6 Copynumber: 8.3 Consensus size: 6
46613350 TTTTGCTTCC
* * * * *
46613360 TTTATT TTTACT TTTAAT TTTACT TTTATT TTCATT GTTATT TTTATT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
46613408 TT
1 TT
46613410 AGTCTATTGT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.18, C:0.06, G:0.02, T:0.74
Consensus pattern (6 bp):
TTTATT
Found at i:46615915 original size:41 final size:41
Alignment explanation
Indices: 46615858--46615967 Score: 168
Period size: 41 Copynumber: 2.7 Consensus size: 41
46615848 CCGAAAATGT
*
46615858 CGCAAAAGGTAAGGCAATAGC-GCCATTTTTCCCATAAACGC
1 CGCAAAAGGTTAGGCAATAGCAG-CATTTTTCCCATAAACGC
** *
46615899 CGCAAAAGGTTAGGCAATAGCAGTGTTTTTTCCATAAACGC
1 CGCAAAAGGTTAGGCAATAGCAGCATTTTTCCCATAAACGC
46615940 CGCAAAAGGTTAGGCAATAGCAGCATTT
1 CGCAAAAGGTTAGGCAATAGCAGCATTT
46615968 GTTACATAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
41 61 0.98
42 1 0.02
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.23
Consensus pattern (41 bp):
CGCAAAAGGTTAGGCAATAGCAGCATTTTTCCCATAAACGC
Found at i:46616971 original size:25 final size:25
Alignment explanation
Indices: 46616942--46616989 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
46616932 TATTAGCTCA
46616942 ATTTTTATTATTTCATTTAACAATT
1 ATTTTTATTATTTCATTTAACAATT
46616967 ATTTTTATTATTTCATTTAACAA
1 ATTTTTATTATTTCATTTAACAA
46616990 AATCCTGTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.58
Consensus pattern (25 bp):
ATTTTTATTATTTCATTTAACAATT
Found at i:46619012 original size:19 final size:19
Alignment explanation
Indices: 46618989--46619040 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
46618979 ATTTAATCCA
*
46618989 ATTTTTATTATT-TATTTTT
1 ATTTTTATT-TTAAATTTTT
* *
46619008 GTTTTGATTTTAAATTTTT
1 ATTTTTATTTTAAATTTTT
46619027 ATTTTTATTTTAAA
1 ATTTTTATTTTAAA
46619041 ATTTAAGATA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
18 2 0.07
19 25 0.93
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (19 bp):
ATTTTTATTTTAAATTTTT
Found at i:46619038 original size:5 final size:6
Alignment explanation
Indices: 46618989--46619037 Score: 53
Period size: 6 Copynumber: 7.8 Consensus size: 6
46618979 ATTTAATCCA
* * *
46618989 ATTTTT ATTATTT ATTTTT GTTTTG ATTTTAA ATTTTT ATTTTT ATTTT
1 ATTTTT ATT-TTT ATTTTT ATTTTT ATTTT-T ATTTTT ATTTTT ATTTT
46619038 AAAATTTAAG
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
6 25 0.69
7 11 0.31
ACGTcount: A:0.20, C:0.00, G:0.04, T:0.76
Consensus pattern (6 bp):
ATTTTT
Found at i:46619379 original size:25 final size:26
Alignment explanation
Indices: 46619346--46619396 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
46619336 TTTCATATAT
*
46619346 ATTATCATAAAAATAAATA-TATTTA
1 ATTACCATAAAAATAAATATTATTTA
*
46619371 ATTACCATAAAGATAAATATTATTTA
1 ATTACCATAAAAATAAATATTATTTA
46619397 TCTATATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 17 0.74
26 6 0.26
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.39
Consensus pattern (26 bp):
ATTACCATAAAAATAAATATTATTTA
Found at i:46626857 original size:12 final size:12
Alignment explanation
Indices: 46626840--46626876 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
46626830 CAATTTCATA
46626840 AGAAGTGCAATC
1 AGAAGTGCAATC
46626852 AGAAGTGCAATC
1 AGAAGTGCAATC
46626864 AGAAGTGCAATC
1 AGAAGTGCAATC
46626876 A
1 A
46626877 TACTAGTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.43, C:0.16, G:0.24, T:0.16
Consensus pattern (12 bp):
AGAAGTGCAATC
Found at i:46627487 original size:20 final size:21
Alignment explanation
Indices: 46627448--46627487 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
46627438 ATGAGAAAGA
*
46627448 TTATATGATAATGTTGTGAGT
1 TTATATGATAAAGTTGTGAGT
*
46627469 TTATTTGATAAAG-TGTGAG
1 TTATATGATAAAGTTGTGAG
46627488 AAAGAAAGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.30, C:0.00, G:0.25, T:0.45
Consensus pattern (21 bp):
TTATATGATAAAGTTGTGAGT
Found at i:46629917 original size:15 final size:16
Alignment explanation
Indices: 46629897--46629933 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
46629887 AACATTATTG
*
46629897 AAAAAATTATTT-TTA
1 AAAAAATTATTTATGA
46629912 AAAAAA-TATTTATGA
1 AAAAAATTATTTATGA
46629927 AAAAAAT
1 AAAAAAT
46629934 CTTGAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (16 bp):
AAAAAATTATTTATGA
Found at i:46633917 original size:6 final size:6
Alignment explanation
Indices: 46633906--46633934 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
46633896 GCGTGCTAAT
46633906 TGAGCC TGAGCC TGAGCC TGAGCC TGAGC
1 TGAGCC TGAGCC TGAGCC TGAGCC TGAGC
46633935 GGCGACGACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.31, G:0.34, T:0.17
Consensus pattern (6 bp):
TGAGCC
Found at i:46657627 original size:30 final size:30
Alignment explanation
Indices: 46657593--46657656 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 30
46657583 TTGGACTTAT
** * *
46657593 TTGATTCTTTTTAATAGTATAGGGACTAAA
1 TTGATTCCATTTAATAATAGAGGGACTAAA
*
46657623 TTGA-TCCATTTAATAATAGAGGGACTAAT
1 TTGATTCCATTTAATAATAGAGGGACTAAA
46657652 TTGAT
1 TTGAT
46657657 CCACACCCTA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
29 24 0.86
30 4 0.14
ACGTcount: A:0.34, C:0.08, G:0.17, T:0.41
Consensus pattern (30 bp):
TTGATTCCATTTAATAATAGAGGGACTAAA
Found at i:46657645 original size:29 final size:29
Alignment explanation
Indices: 46657602--46657659 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
46657592 TTTGATTCTT
* *
46657602 TTTAATAGTATAGGGACTAAATTGATCCA
1 TTTAATAATAGAGGGACTAAATTGATCCA
*
46657631 TTTAATAATAGAGGGACTAATTTGATCCA
1 TTTAATAATAGAGGGACTAAATTGATCCA
46657660 CACCCTATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.34
Consensus pattern (29 bp):
TTTAATAATAGAGGGACTAAATTGATCCA
Found at i:46659358 original size:16 final size:16
Alignment explanation
Indices: 46659310--46659358 Score: 71
Period size: 16 Copynumber: 3.1 Consensus size: 16
46659300 TTCGCTGTAT
46659310 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
* * *
46659326 CGGATTAAAGGCGTAA
1 TGGAATAGAGGCGTAA
46659342 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
46659358 T
1 T
46659359 AGCAAATTAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.37, C:0.08, G:0.35, T:0.20
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:46659609 original size:16 final size:16
Alignment explanation
Indices: 46659572--46659613 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
46659562 TTAATCATAT
*
46659572 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
46659588 TT-AAATATATTATAA
1 TTAAAATATATTATAA
46659603 TTAAAATATAT
1 TTAAAATATAT
46659614 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:46659620 original size:14 final size:15
Alignment explanation
Indices: 46659581--46659622 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
46659571 TTTAAACATA
*
46659581 ATTATTATTAAATAT
1 ATTATAATTAAATAT
46659596 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
46659610 A-TATAATTTAATA
1 ATTATAATTAAATA
46659623 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:46659672 original size:61 final size:61
Alignment explanation
Indices: 46659607--46659794 Score: 199
Period size: 61 Copynumber: 3.1 Consensus size: 61
46659597 TTATAATTAA
46659607 AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
* * * * * * * * * *
46659668 AATATATGATACT-ATAAAA-TATAAATTAA-C-ATAATTATTAT-TAAATATA-TTATAATTAA
1 AATATATAAT-TTAATAAAATTCTTAA-TAATCAAT-ATTCTTATATGAATTTACTCA-AATCAT
*
46659727 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
46659788 AATATAT
1 AATATAT
46659795 GATACTATAA
Statistics
Matches: 96, Mismatches: 21, Indels: 20
0.70 0.15 0.15
Matches are distributed among these distances:
58 3 0.03
59 30 0.31
60 23 0.24
61 37 0.39
62 3 0.03
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.43
Consensus pattern (61 bp):
AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
Found at i:46659740 original size:14 final size:15
Alignment explanation
Indices: 46659691--46659742 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
46659681 ATAAAATATA
46659691 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
46659706 TATTAAATATATTAT
1 AATTAAATATATTAT
46659721 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
46659734 AATTTAATA
1 AATTAAATA
46659743 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:46659788 original size:120 final size:121
Alignment explanation
Indices: 46659575--46659867 Score: 518
Period size: 120 Copynumber: 2.4 Consensus size: 121
46659565 ATCATATTTA
46659575 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
*
46659640 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT-
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATTG
*
46659695 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
*
46659760 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTTG
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATTG
* * *
46659816 AA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
46659868 TAAAATAATT
Statistics
Matches: 166, Mismatches: 6, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
120 164 0.99
121 2 0.01
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.42
Consensus pattern (121 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATTG
Found at i:46659914 original size:101 final size:96
Alignment explanation
Indices: 46659808--46660090 Score: 286
Period size: 91 Copynumber: 3.0 Consensus size: 96
46659798 ACTATAAAAG
* *
46659808 ATAATTTGAAATAATTAATATTAAATATATTTTAATTAA-AATATATGATTTAATAAAATTTAAA
1 ATAATTTAAAATAATTAATATTAAATATAATTTAA-TAATAATATAT-ATTT-ATAAAATTTAAA
*
46659872 ATAAT-TATAACTAATAAATTATCTTATATGAATTTGT
63 AT--TCT-TAA-TAATAAATTATCTTATATGAATTTAT
* * *
46659909 ATAATTTAAAATAATTATTATTACATATAATTTAATAATAATATATATTT-T--CA--TAAAATT
1 ATAATTTAAAATAATTAATATTAAATATAATTTAATAATAATATATATTTATAAAATTTAAAATT
* *
46659969 CTTGATAATAAATTTTCTTATATGAATTTAT
66 CTTAATAATAAATTATCTTATATGAATTTAT
* * * *
46660000 ACAATTTAAAATAATTAATATTAAATATAATTTAATAATGATATATAATT-T--CA--TAAAATT
1 ATAATTTAAAATAATTAATATTAAATATAATTTAATAATAATATATATTTATAAAATTTAAAATT
46660060 CTTAATAATAAAATGT-TCTTATATGAATTTA
66 CTTAATAAT-AAAT-TATCTTATATGAATTTA
46660091 CTAAAATCAA
Statistics
Matches: 164, Mismatches: 14, Indels: 17
0.84 0.07 0.09
Matches are distributed among these distances:
91 87 0.53
92 22 0.13
93 2 0.01
94 6 0.04
96 1 0.01
98 1 0.01
100 7 0.04
101 38 0.23
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (96 bp):
ATAATTTAAAATAATTAATATTAAATATAATTTAATAATAATATATATTTATAAAATTTAAAATT
CTTAATAATAAATTATCTTATATGAATTTAT
Found at i:46659978 original size:91 final size:90
Alignment explanation
Indices: 46659883--46660090 Score: 317
Period size: 91 Copynumber: 2.3 Consensus size: 90
46659873 TAATTATAAC
* * * *
46659883 TAATAAATTATCTTATATGAATTTGTATAATTTAAAATAATTATTATTACATATAATTTAATAAT
1 TAATAAATT-TCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
* *
46659948 AATATATATTTTCATAAAATTCTTGA
65 AATATATAATTTCATAAAATTCTTAA
46659974 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
1 TAATAAA-TTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
*
46660039 GATATATAATTTCATAAAATTCTTAA
65 AATATATAATTTCATAAAATTCTTAA
46660065 TAATAAAATGTTCTTATATGAATTTA
1 TAAT-AAAT-TTCTTATATGAATTTA
46660091 CTAAAATCAA
Statistics
Matches: 107, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
91 86 0.80
92 21 0.20
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.46
Consensus pattern (90 bp):
TAATAAATTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAATA
ATATATAATTTCATAAAATTCTTAA
Found at i:46660050 original size:44 final size:43
Alignment explanation
Indices: 46659908--46660050 Score: 110
Period size: 44 Copynumber: 3.2 Consensus size: 43
46659898 TATGAATTTG
* *
46659908 TATAATTTAAAATAATTATTATTACATATAATTTAATAATAATA
1 TATAATTTAAAATAATTAATATTAAATATAATTTAATAAT-ATA
* ** * * * *
46659952 TATATTTTCATAAAATTCTTGATAATAAAT-T-TTCTTATATGAATTTA
1 TATA-ATT--TAAAATAATTAATATTAAATATAAT-TTA-AT-AATATA
*
46659999 TACAATTTAAAATAATTAATATTAAATATAATTTAATAATGATA
1 TATAATTTAAAATAATTAATATTAAATATAATTTAATAAT-ATA
46660043 TATAATTT
1 TATAATTT
46660051 CATAAAATTC
Statistics
Matches: 72, Mismatches: 18, Indels: 18
0.67 0.17 0.17
Matches are distributed among these distances:
43 3 0.04
44 31 0.43
45 7 0.10
46 7 0.10
47 21 0.29
48 3 0.04
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (43 bp):
TATAATTTAAAATAATTAATATTAAATATAATTTAATAATATA
Found at i:46660065 original size:47 final size:47
Alignment explanation
Indices: 46659933--46660071 Score: 128
Period size: 47 Copynumber: 3.0 Consensus size: 47
46659923 TTATTATTAC
* * *
46659933 ATATAATTTAATAATAATATATATTTTCATAAAATTCTTGATAATAA
1 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
* * * ** *
46659980 AT-T--TTCTTAT-ATGAATTTATACAATT--TAAAATAATTAATATTAA
1 ATATAATT-TAATAATG-ATATATA-ATTTCATAAAATTCTTAATAATAA
46660024 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
1 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
46660071 A
1 A
46660072 ATGTTCTTAT
Statistics
Matches: 68, Mismatches: 15, Indels: 18
0.67 0.15 0.18
Matches are distributed among these distances:
44 20 0.29
45 13 0.19
46 12 0.18
47 23 0.34
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (47 bp):
ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
Found at i:46670383 original size:18 final size:18
Alignment explanation
Indices: 46670360--46670394 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
46670350 AAGTTAATTT
46670360 TTAAAAATATTT-TTTAAA
1 TTAAAAAT-TTTATTTAAA
46670378 TTAAAAATTTTATTTAA
1 TTAAAAATTTTATTTAA
46670395 TATATATTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTAAAAATTTTATTTAAA
Found at i:46672023 original size:32 final size:29
Alignment explanation
Indices: 46671987--46672059 Score: 76
Period size: 32 Copynumber: 2.4 Consensus size: 29
46671977 ATATAACAAG
* *
46671987 TTTAAATATTTATTTTTCAATATTTGAAAAAA
1 TTTAAATATTAATTTATCAATA-TT--AAAAA
* *
46672019 TTTAATTATTAATTTATGAATATTAAAAA
1 TTTAAATATTAATTTATCAATATTAAAAA
46672048 TTTAAA-ATTAAT
1 TTTAAATATTAAT
46672060 ATATTCTTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
28 6 0.17
29 10 0.28
31 2 0.06
32 18 0.50
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (29 bp):
TTTAAATATTAATTTATCAATATTAAAAA
Found at i:46674840 original size:11 final size:12
Alignment explanation
Indices: 46674813--46674839 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
46674803 TCCTTTCTTT
46674813 AAAACTAAAAAA
1 AAAACTAAAAAA
46674825 AAAACTAAAAAA
1 AAAACTAAAAAA
46674837 AAA
1 AAA
46674840 CCTCCCAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.85, C:0.07, G:0.00, T:0.07
Consensus pattern (12 bp):
AAAACTAAAAAA
Found at i:46677555 original size:13 final size:13
Alignment explanation
Indices: 46677539--46677568 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
46677529 AACTATTTTT
46677539 AAAAATTTGTTTC
1 AAAAATTTGTTTC
46677552 AAAAATTTGTTTC
1 AAAAATTTGTTTC
46677565 AAAA
1 AAAA
46677569 CTTTTTTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (13 bp):
AAAAATTTGTTTC
Found at i:46678267 original size:35 final size:36
Alignment explanation
Indices: 46678216--46678306 Score: 96
Period size: 36 Copynumber: 2.5 Consensus size: 36
46678206 TAATTTTTAA
* *
46678216 AATAATTATTATAATAATAAA-TTTC-ATGTAAAAGAT
1 AATAA-TATTTTAATAATAAAGTTCCTAT-TAAAAGAT
* *
46678252 AATAATATTTTAATAAAAAAGTTCCTATTAAAATAT
1 AATAATATTTTAATAATAAAGTTCCTATTAAAAGAT
*
46678288 ACTAATATTTTAAGTAATA
1 AATAATATTTTAA-TAATA
46678307 TTTGTCTAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
35 13 0.28
36 27 0.59
37 6 0.13
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.40
Consensus pattern (36 bp):
AATAATATTTTAATAATAAAGTTCCTATTAAAAGAT
Found at i:46691236 original size:29 final size:28
Alignment explanation
Indices: 46691197--46691284 Score: 79
Period size: 30 Copynumber: 3.0 Consensus size: 28
46691187 ATTAACAGTT
* *
46691197 AAAATTGAATTTAAAATCTAAAAAATAG
1 AAAATTAAATTTAAAATATAAAAAATAG
*
46691225 AGAAATTAAATTTTTAAAA-ATAAAAAATAT
1 A-AAATTAAA--TTTAAAATATAAAAAATAG
*
46691255 AATAATTAAATTTCAAAATTATGAAAAATA
1 AA-AATTAAATTT-AAAA-TATAAAAAATA
46691285 CACCTATTTC
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
28 4 0.08
29 12 0.24
30 17 0.35
31 16 0.33
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (28 bp):
AAAATTAAATTTAAAATATAAAAAATAG
Found at i:46691251 original size:30 final size:31
Alignment explanation
Indices: 46691206--46691284 Score: 83
Period size: 30 Copynumber: 2.6 Consensus size: 31
46691196 TAAAATTGAA
*
46691206 TTTAAAATCTAAAAAATAGAGA-AATTAAATT
1 TTTAAAATATAAAAAATAGA-ATAATTAAATT
*
46691237 TTTAAAA-ATAAAAAATATAATAATTAAA-T
1 TTTAAAATATAAAAAATAGAATAATTAAATT
* *
46691266 TTCAAAATTATGAAAAATA
1 TTTAAAA-TATAAAAAATA
46691285 CACCTATTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
29 8 0.20
30 17 0.41
31 16 0.39
ACGTcount: A:0.61, C:0.03, G:0.04, T:0.33
Consensus pattern (31 bp):
TTTAAAATATAAAAAATAGAATAATTAAATT
Found at i:46701262 original size:9 final size:9
Alignment explanation
Indices: 46701248--46701278 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
46701238 GTTAAACGAA
46701248 TCGAGTTAT
1 TCGAGTTAT
*
46701257 TCGAGTTAA
1 TCGAGTTAT
46701266 TCGAGTTAT
1 TCGAGTTAT
46701275 TCGA
1 TCGA
46701279 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:46701349 original size:9 final size:9
Alignment explanation
Indices: 46701332--46701368 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
46701322 TGAGTTTTCG
46701332 AATTCGAAT
1 AATTCGAAT
*
46701341 AACTCGAAT
1 AATTCGAAT
46701350 AATTCGAAT
1 AATTCGAAT
46701359 AATTCGAAT
1 AATTCGAAT
46701368 A
1 A
46701369 TCAAACTATA
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:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:46702406 original size:5 final size:5
Alignment explanation
Indices: 46702396--46702421 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
46702386 CTCGAAAATT
46702396 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
46702422 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:46710043 original size:16 final size:16
Alignment explanation
Indices: 46710022--46710078 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
46710012 AAGTTTCTAA
46710022 TTTGGATTTATGATTT
1 TTTGGATTTATGATTT
* **
46710038 TTTGGATTTAGAGAGAT
1 TTTGGATTTA-TGATTT
* *
46710055 TTAGG-TTTATTATTT
1 TTTGGATTTATGATTT
46710070 TTTGGATTT
1 TTTGGATTT
46710079 TTTTTGTTAA
Statistics
Matches: 30, Mismatches: 9, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
15 6 0.20
16 17 0.57
17 7 0.23
ACGTcount: A:0.21, C:0.00, G:0.21, T:0.58
Consensus pattern (16 bp):
TTTGGATTTATGATTT
Found at i:46710548 original size:15 final size:16
Alignment explanation
Indices: 46710528--46710557 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
46710518 TCAATAGGAG
46710528 TGTATTGTGT-ATGTT
1 TGTATTGTGTGATGTT
46710543 TGTATTGTGTGATGT
1 TGTATTGTGTGATGT
46710558 CCTTTGTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.13, C:0.00, G:0.30, T:0.57
Consensus pattern (16 bp):
TGTATTGTGTGATGTT
Found at i:46711758 original size:45 final size:45
Alignment explanation
Indices: 46711709--46711812 Score: 145
Period size: 45 Copynumber: 2.3 Consensus size: 45
46711699 CCAAATGATT
* * *
46711709 CCATTTCTCTTTTTCAGAGAAAACAATAATTATTTCTGAATGTTC
1 CCATTTCTCTTTTTCAAAGAAAACAATAATCATTCCTGAATGTTC
**
46711754 CCATTTCTCCATTTCAAAGAAAACAATAATCATTCCTGAATGTTC
1 CCATTTCTCTTTTTCAAAGAAAACAATAATCATTCCTGAATGTTC
46711799 CCTATTTCTTCTTT
1 CC-ATTTC-TCTTT
46711813 CCTATTCATT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
45 42 0.84
46 5 0.10
47 3 0.06
ACGTcount: A:0.30, C:0.22, G:0.07, T:0.41
Consensus pattern (45 bp):
CCATTTCTCTTTTTCAAAGAAAACAATAATCATTCCTGAATGTTC
Found at i:46721328 original size:272 final size:275
Alignment explanation
Indices: 46720821--46721370 Score: 788
Period size: 272 Copynumber: 2.0 Consensus size: 275
46720811 TGGTATAGCG
* * *
46720821 AGGAGCAAAGGAATAAAAAATAGCTTTAAAGAGGAAAAAAATAGTAGATGGCCATGTGAGCCACA
1 AGGAACAAAAGAATAAAAAATAGCTTTAAAGAGGAAAAAAATAGTACATGGCCATGTGAGCCACA
* *
46720886 CGACCATGTGGAATTAGTCAGGCCGTGTGTGATAAAAAATAGGTAAAAATAAGCCTAGTATCCAT
66 CGACCATGTGGAATCAGTCAGACCGTGTGTGATAAAAAATAGGTAAAAATAAGCCTAGTATCCAT
* ** * **
46720951 ACAGCCTAGGACATGCCCGTGTGTCAAACACGATCGTGTGAAATCATTGTTCGCTTCTCCCACGC
131 ACAGCCTAGGACACGCCAATGTGTCAAACACGACCGTGTGAAATCATCATTCGCTTCTCCCACGC
* * *
46721016 CCGTGTGTGAGGGCATGTGGGTCACACGGTCTATCACATGCCCGTGTTCTAGGCCGTGTGTCTCA
196 CCGTGTGTGAGGGCACGTGGGTCACACGGTCTACCACATGCCCGTGTTCTAGGCCGTATGTCTCA
46721081 CACGACCATGTCTCT
261 CACGACCATGTCTCT
46721096 AGGAACAAAAGAATAAAAAATAGCTTTAAAGAGGAAAAAAA-AGTACATGGCCATGTGAGCCACA
1 AGGAACAAAAGAATAAAAAATAGCTTTAAAGAGGAAAAAAATAGTACATGGCCATGTGAGCCACA
* *
46721160 CGACCCTGTGGAATCAGTCAGATCGTGTGTGAT-AAAAATAGGTAAAAATAAGCC-AGTATCCAT
66 CGACCATGTGGAATCAGTCAGACCGTGTGTGATAAAAAATAGGTAAAAATAAGCCTAGTATCCAT
* * * * ** *
46721223 ACTGCTTAGGGCACGCCAATGTGTTACATACA-G-CCGTGTGCGATGATCATTCGCTTCTCCCAC
131 ACAGCCTAGGACACGCCAATGTG-T-CAAACACGACCGTGTGAAATCATCATTCGCTTCTCCCAC
* * *
46721286 GCTCGTGTGTGAGGGCGCGTGGGTCACACGGTGC-ACCACATGCCCGTGTTCTAGGCTGTATGTC
194 GCCCGTGTGTGAGGGCACGTGGGTCACACGGT-CTACCACATGCCCGTGTTCTAGGCCGTATGTC
*
46721350 TCACACGGCCATGTCTCT
258 TCACACGACCATGTCTCT
46721368 AGG
1 AGG
46721371 GCGTGTAACT
Statistics
Matches: 245, Mismatches: 27, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
272 126 0.51
273 24 0.10
274 56 0.23
275 39 0.16
ACGTcount: A:0.30, C:0.22, G:0.25, T:0.23
Consensus pattern (275 bp):
AGGAACAAAAGAATAAAAAATAGCTTTAAAGAGGAAAAAAATAGTACATGGCCATGTGAGCCACA
CGACCATGTGGAATCAGTCAGACCGTGTGTGATAAAAAATAGGTAAAAATAAGCCTAGTATCCAT
ACAGCCTAGGACACGCCAATGTGTCAAACACGACCGTGTGAAATCATCATTCGCTTCTCCCACGC
CCGTGTGTGAGGGCACGTGGGTCACACGGTCTACCACATGCCCGTGTTCTAGGCCGTATGTCTCA
CACGACCATGTCTCT
Found at i:46726380 original size:25 final size:25
Alignment explanation
Indices: 46726345--46726431 Score: 113
Period size: 25 Copynumber: 3.5 Consensus size: 25
46726335 GACACACCAT
46726345 AGCTCGTATGAGCTTCCCGTTATAC
1 AGCTCGTATGAGCTTCCCGTTATAC
* *
46726370 AGCTCGCATGAGCTTCCCGTTATTC
1 AGCTCGTATGAGCTTCCCGTTATAC
* * * *
46726395 AGCTAGGAGGAGCTTCCTGTT-TAC
1 AGCTCGTATGAGCTTCCCGTTATAC
46726419 AGCTCGTATGAGC
1 AGCTCGTATGAGC
46726432 ATACATGAAT
Statistics
Matches: 52, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
24 12 0.23
25 40 0.77
ACGTcount: A:0.20, C:0.26, G:0.24, T:0.30
Consensus pattern (25 bp):
AGCTCGTATGAGCTTCCCGTTATAC
Found at i:46729689 original size:20 final size:20
Alignment explanation
Indices: 46729664--46729712 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
46729654 AATAGAAACC
*
46729664 AATATAAATTTTAT-TTTGGA
1 AATATAAATTTAATATTT-GA
*
46729684 AATATATATTTAATATTTGA
1 AATATAAATTTAATATTTGA
46729704 AA-ATAAATT
1 AATATAAATT
46729713 ATATCTATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 6 0.24
20 16 0.64
21 3 0.12
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (20 bp):
AATATAAATTTAATATTTGA
Found at i:46731843 original size:43 final size:43
Alignment explanation
Indices: 46731782--46731867 Score: 147
Period size: 43 Copynumber: 2.0 Consensus size: 43
46731772 ACCGAATTGG
*
46731782 GTCGGTGGATAGTGTGAGTGATC-TCTGCCAAATTTCCAACCCA
1 GTCGGTGGATAGTGTGAGTGATCTTC-ACCAAATTTCCAACCCA
46731825 GTCGGTGGATAGTGTGAGTGATCTTCACCAAATTTCCAACCCA
1 GTCGGTGGATAGTGTGAGTGATCTTCACCAAATTTCCAACCCA
46731868 ACGAGCCTCC
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
43 39 0.95
44 2 0.05
ACGTcount: A:0.24, C:0.23, G:0.24, T:0.28
Consensus pattern (43 bp):
GTCGGTGGATAGTGTGAGTGATCTTCACCAAATTTCCAACCCA
Found at i:46732407 original size:24 final size:24
Alignment explanation
Indices: 46732377--46732427 Score: 86
Period size: 24 Copynumber: 2.1 Consensus size: 24
46732367 AAAGAATCTA
46732377 TAACGGGTAGCTCC-AGAGAGCAAT
1 TAACGGGTAGCTCCGA-AGAGCAAT
46732401 TAACGGGTAGCTCCGAAGAGCAAT
1 TAACGGGTAGCTCCGAAGAGCAAT
46732425 TAA
1 TAA
46732428 TCAGAAGCAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 25 0.96
25 1 0.04
ACGTcount: A:0.35, C:0.20, G:0.27, T:0.18
Consensus pattern (24 bp):
TAACGGGTAGCTCCGAAGAGCAAT
Found at i:46732500 original size:25 final size:27
Alignment explanation
Indices: 46732472--46732526 Score: 87
Period size: 26 Copynumber: 2.1 Consensus size: 27
46732462 CAAGCGAGCA
*
46732472 ATAAT-GGGAAGCTCACAGAGAGCC-T
1 ATAATCGGGAAGCTCACAAAGAGCCAT
46732497 ATAATCGGGAAGCTCACAAAGAGCCAT
1 ATAATCGGGAAGCTCACAAAGAGCCAT
46732524 ATA
1 ATA
46732527 CGAGATACTC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 5 0.19
26 18 0.67
27 4 0.15
ACGTcount: A:0.40, C:0.20, G:0.24, T:0.16
Consensus pattern (27 bp):
ATAATCGGGAAGCTCACAAAGAGCCAT
Found at i:46735913 original size:36 final size:36
Alignment explanation
Indices: 46735872--46735945 Score: 103
Period size: 36 Copynumber: 2.1 Consensus size: 36
46735862 GACTTACTAG
* * * *
46735872 CTAGATGTAGTGTGTAGCGATATCATTAGGGCTTTT
1 CTAGATGTAGTGTGTAACAATACCATTAGGACTTTT
*
46735908 CTAGATGTTGTGTGTAACAATACCATTAGGACTTTT
1 CTAGATGTAGTGTGTAACAATACCATTAGGACTTTT
46735944 CT
1 CT
46735946 TGGTAGAGTG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.24, C:0.14, G:0.23, T:0.39
Consensus pattern (36 bp):
CTAGATGTAGTGTGTAACAATACCATTAGGACTTTT
Found at i:46735980 original size:16 final size:16
Alignment explanation
Indices: 46735961--46735995 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
46735951 GAGTGGAAAC
46735961 AAATTAGAAAAATGGA
1 AAATTAGAAAAATGGA
* *
46735977 AAATTATAAAGATGGA
1 AAATTAGAAAAATGGA
46735993 AAA
1 AAA
46735996 ATAAAAAGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.17, T:0.20
Consensus pattern (16 bp):
AAATTAGAAAAATGGA
Found at i:46736003 original size:16 final size:16
Alignment explanation
Indices: 46735968--46736005 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
46735958 AACAAATTAG
*
46735968 AAAA-ATGGAAAATTA
1 AAAAGATGGAAAAATA
*
46735983 TAAAGATGGAAAAATA
1 AAAAGATGGAAAAATA
46735999 AAAAGAT
1 AAAAGAT
46736006 AAAAAAAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 3 0.16
16 16 0.84
ACGTcount: A:0.66, C:0.00, G:0.16, T:0.18
Consensus pattern (16 bp):
AAAAGATGGAAAAATA
Found at i:46745005 original size:14 final size:14
Alignment explanation
Indices: 46744986--46745016 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
46744976 GTTGTCATAT
46744986 ATATATACACACGG
1 ATATATACACACGG
*
46745000 ATATATATACACGG
1 ATATATACACACGG
46745014 ATA
1 ATA
46745017 ATGTGAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.45, C:0.16, G:0.13, T:0.26
Consensus pattern (14 bp):
ATATATACACACGG
Found at i:46747051 original size:2 final size:2
Alignment explanation
Indices: 46747003--46747036 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
46746993 AAAAATGATG
*
46747003 AT AT TT AT A- 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 AT AT A
46747037 ATTTTTAGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46753261 original size:5 final size:5
Alignment explanation
Indices: 46753253--46753281 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
46753243 TTAGTTTTGA
46753253 TCTAC TCTAC TCTAC TCTAC TCTAC TCTA
1 TCTAC TCTAC TCTAC TCTAC TCTAC TCTA
46753282 ATATAATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.38, G:0.00, T:0.41
Consensus pattern (5 bp):
TCTAC
Found at i:46755571 original size:22 final size:23
Alignment explanation
Indices: 46755509--46755573 Score: 71
Period size: 22 Copynumber: 2.9 Consensus size: 23
46755499 TTCAATATAA
46755509 AACTAATAATTTAATAATCAAGT
1 AACTAATAATTTAATAATCAAGT
* * * * *
46755532 TA-TAACAAATAAAAAATCAA-T
1 AACTAATAATTTAATAATCAAGT
46755553 AACTAATAATTTAATAATCAA
1 AACTAATAATTTAATAATCAA
46755574 AGTTTTGTAA
Statistics
Matches: 31, Mismatches: 10, Indels: 3
0.70 0.23 0.07
Matches are distributed among these distances:
21 2 0.06
22 28 0.90
23 1 0.03
ACGTcount: A:0.58, C:0.09, G:0.02, T:0.31
Consensus pattern (23 bp):
AACTAATAATTTAATAATCAAGT
Found at i:46755897 original size:25 final size:28
Alignment explanation
Indices: 46755849--46755900 Score: 83
Period size: 25 Copynumber: 2.0 Consensus size: 28
46755839 ATAAAAATTA
46755849 ACCAAAATATTATAACTTTTTTTTATTT
1 ACCAAAATATTATAACTTTTTTTTATTT
46755877 ACCAAAATA-T-T-ACTTTTTTTTATT
1 ACCAAAATATTATAACTTTTTTTTATT
46755901 ATTTACGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 13 0.54
26 1 0.04
27 1 0.04
28 9 0.38
ACGTcount: A:0.35, C:0.12, G:0.00, T:0.54
Consensus pattern (28 bp):
ACCAAAATATTATAACTTTTTTTTATTT
Found at i:46756135 original size:19 final size:19
Alignment explanation
Indices: 46756108--46756177 Score: 97
Period size: 19 Copynumber: 3.7 Consensus size: 19
46756098 TCAACTCATT
*
46756108 TTTTTATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
*
46756127 TTTTAATTTAATAA-ACTA
1 TTTTAATTTAATAACTCTA
* *
46756145 TTCTCATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
46756164 TTTTAATTTAATAA
1 TTTTAATTTAATAA
46756178 ACTATTAAGT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
18 15 0.35
19 28 0.65
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTTAATTTAATAACTCTA
Found at i:46756156 original size:37 final size:37
Alignment explanation
Indices: 46756113--46756183 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
46756103 TCATTTTTTT
46756113 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
1 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
46756150 ATTTAATAACTCTATTTTAATTTAATAAACTATT
1 ATTTAATAACTCTATTTTAATTTAATAAACTATT
46756184 AAGTAATACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.49
Consensus pattern (37 bp):
ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
Found at i:46756402 original size:19 final size:19
Alignment explanation
Indices: 46756378--46756432 Score: 76
Period size: 18 Copynumber: 2.9 Consensus size: 19
46756368 TCTAATTAAG
46756378 TAATAACTCTATTTTAATT
1 TAATAACTCTATTTTAATT
* * *
46756397 TAATAA-ACTATTCTCATT
1 TAATAACTCTATTTTAATT
46756415 TAATAACTCTATTTTAAT
1 TAATAACTCTATTTTAAT
46756433 NNNNNNNNNN
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
18 15 0.52
19 14 0.48
ACGTcount: A:0.38, C:0.13, G:0.00, T:0.49
Consensus pattern (19 bp):
TAATAACTCTATTTTAATT
Done.