Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: 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: 93829987
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4250000 characters in sequence are not A, C, G, or T
File 148 of 295
Found at i:46210043 original size:27 final size:27
Alignment explanation
Indices: 46210013--46210189 Score: 156
Period size: 27 Copynumber: 6.5 Consensus size: 27
46210003 AAATTGTACA
*
46210013 GCACTAAGGGTGCGATTTGACTATGTT
1 GCACTAAGTGTGCGATTTGACTATGTT
** * *
46210040 GCACTAAGTGTGCGAAATGAATATGAT
1 GCACTAAGTGTGCGATTTGACTATGTT
* * * **
46210067 GCACTAGGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGATTTGACTATGTT
*
46210094 GCACTAAGTGTGCGAGTTTGACTATGTA
1 GCACTAAGTGTGCGA-TTTGACTATGTT
* * * *
46210122 GCACTAAGTGTGCGATTTTATTACGTA
1 GCACTAAGTGTGCGATTTGACTATGTT
* * * * *
46210149 GCACTAAGTGTGTGAGTTGATTATATA
1 GCACTAAGTGTGCGATTTGACTATGTT
*
46210176 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
46210190 GGCTCAACAT
Statistics
Matches: 123, Mismatches: 26, Indels: 2
0.81 0.17 0.01
Matches are distributed among these distances:
27 100 0.81
28 23 0.19
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.31
Consensus pattern (27 bp):
GCACTAAGTGTGCGATTTGACTATGTT
Found at i:46210080 original size:54 final size:55
Alignment explanation
Indices: 46210012--46210160 Score: 151
Period size: 55 Copynumber: 2.7 Consensus size: 55
46210002 TAAATTGTAC
*
46210012 AGCACTAAGG-GTGCGATTTGACTATGTTGCACTAAGTGTGCGA-AATGAATATG-
1 AGCACT-AGGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGAATGAATATGT
* * ** ** *
46210065 ATGCACTAGGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTTTGACTATGT
1 A-GCACTAGGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGAATGAATATGT
* * * *
46210121 AGCACTAAGTGTGCGATTTTATTACGTAGCACTAAGTGTG
1 AGCACTAGGTGTGCGATTTGACTATGTAGCACTAAGTGTG
46210161 TGAGTTGATT
Statistics
Matches: 77, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
53 4 0.05
54 34 0.44
55 38 0.49
56 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (55 bp):
AGCACTAGGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGAATGAATATGT
Found at i:46210180 original size:82 final size:81
Alignment explanation
Indices: 46210009--46210189 Score: 193
Period size: 82 Copynumber: 2.2 Consensus size: 81
46209999 GATTAAATTG
* * * *
46210009 TACAGCACTAAGGGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAG
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
46210074 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** * *
46210090 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTTATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* * **
46210154 AAGTGTGTGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
46210172 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
46210190 GGCTCAACAT
Statistics
Matches: 80, Mismatches: 18, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
81 17 0.21
82 63 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:46213569 original size:39 final size:40
Alignment explanation
Indices: 46213524--46213695 Score: 204
Period size: 40 Copynumber: 4.3 Consensus size: 40
46213514 GCTCCTCATT
* * *
46213524 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
**
46213564 C-AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * *
46213603 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * *
46213643 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGG-ATTTAGTAACTCGCA
*
46213683 CAAAAGCCTTCGG
1 CAAATGCCTTCGG
46213696 ATCTTAGTCC
Statistics
Matches: 117, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
39 34 0.29
40 79 0.68
41 4 0.03
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:46213708 original size:80 final size:79
Alignment explanation
Indices: 46213524--46213748 Score: 204
Period size: 80 Copynumber: 2.8 Consensus size: 79
46213514 GCTCCTCATT
* * * * * * *
46213524 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGG-
1 CAAAAGCCTTCGGGACTTAACCCGGATTTAGT-ACTCGCACAAAGCCTTCGGGACTTAACCCGGA
46213588 ATTTAACAACTCGCA
65 ATTTAACAACTCGCA
* * *
46213603 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGG
1 CAAAAGCCTTCGGGACTTAACCCGGATTTAGTA-CTCGCACAAA-GCCTTCGGGACTTAACCCGG
** *
46213668 AATTT-GTATCTCGCA
64 AATTTAACAACTCGCA
** * * * *
46213683 CAAAAGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAAAGCCTTCGGGA-CTTAACCCGGATTTAGT-AC-TCGCACAAAGCCTTCGGGACTTAACCCG
46213747 GA
63 GA
46213749 CAGCATTCAA
Statistics
Matches: 120, Mismatches: 20, Indels: 11
0.79 0.13 0.07
Matches are distributed among these distances:
78 1 0.01
79 39 0.32
80 67 0.56
81 13 0.11
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.24
Consensus pattern (79 bp):
CAAAAGCCTTCGGGACTTAACCCGGATTTAGTACTCGCACAAAGCCTTCGGGACTTAACCCGGAA
TTTAACAACTCGCA
Found at i:46213757 original size:41 final size:41
Alignment explanation
Indices: 46213680--46213757 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
46213670 TTTGTATCTC
* * *
46213680 GCACAAAAGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAAGCCTTCGGATCTTAGCCCGGACACATTCACTTA
46213721 GCAC-AAAGCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAAGCCTTC-GGATCTTAGCCCGGACA-CATTCA
46213758 ATTAAACATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 20 0.62
41 12 0.38
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (41 bp):
GCACAAAAGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:46220446 original size:39 final size:40
Alignment explanation
Indices: 46220403--46220512 Score: 159
Period size: 39 Copynumber: 2.8 Consensus size: 40
46220393 TCCTCGTTCA
* *
46220403 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACATAACCCGGATTTAGTAACTCACACG
** *
46220442 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACATAACCCGGATTTAGTAACTCACACG
*
46220482 AATGCCTTCGGGACTTAACCCGGATTTAGTA
1 AATGCCTTCGGGACATAACCCGGATTTAGTA
46220513 TCTTGCTCAA
Statistics
Matches: 62, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
39 34 0.55
40 28 0.45
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACATAACCCGGATTTAGTAACTCACACG
Found at i:46220501 original size:40 final size:39
Alignment explanation
Indices: 46220403--46220572 Score: 171
Period size: 40 Copynumber: 4.3 Consensus size: 39
46220393 TCCTCGTTCA
* * *
46220403 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCAC
**
46220442 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCAC
1 AATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCAC
* * * *
46220481 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTTGCTC
1 -AATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCAC
* * * *
46220521 AAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCAC
1 -AATGCCTTCGGGACATAACCCGG-ATTTAGTAACTCGCAC
*
46220561 AAAAGCCTTCGG
1 -AATGCCTTCGG
46220573 ATCTTAGTCC
Statistics
Matches: 112, Mismatches: 17, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
39 34 0.30
40 74 0.66
41 4 0.04
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (39 bp):
AATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCAC
Found at i:46220585 original size:80 final size:80
Alignment explanation
Indices: 46220401--46220625 Score: 190
Period size: 80 Copynumber: 2.8 Consensus size: 80
46220391 GCTCCTCGTT
* * * * * * * * *
46220401 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCA-CACAATGCCTTCGGGACATAACCCGG
1 CAAAAGCCTTCGGGACTTAACCCGGATATAGTCACTTAGCACAAAGCCTTCGGGACTTAACCCGG
** *
46220465 -ATTTAACAACTCGCA
66 AATTT-GTATCTCGCA
* * * * *
46220480 CGAATGCCTTCGGGACTTAACCCGGATTTAGT-ATCTT-GCTCAAAGGCCTTCGGGGCTTAACCC
1 CAAAAGCCTTCGGGACTTAACCCGGATATAGTCA-CTTAGCACAAA-GCCTTCGGGACTTAACCC
46220543 GGAATTTGTATCTCGCA
64 GGAATTTGTATCTCGCA
** * *
46220560 CAAAAGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAAAGCCTTCGGGA-CTTAACCCGGATATAGTCACTTAGCACAAAGCCTTCGGGACTTAACCCG
46220624 GA
65 GA
46220626 CAGCATTCAA
Statistics
Matches: 118, Mismatches: 21, Indels: 13
0.78 0.14 0.09
Matches are distributed among these distances:
78 1 0.01
79 37 0.31
80 69 0.58
81 11 0.09
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (80 bp):
CAAAAGCCTTCGGGACTTAACCCGGATATAGTCACTTAGCACAAAGCCTTCGGGACTTAACCCGG
AATTTGTATCTCGCA
Found at i:46220634 original size:41 final size:41
Alignment explanation
Indices: 46220557--46220634 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
46220547 TTTGTATCTC
* * *
46220557 GCACAAAAGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAAGCCTTCGGATCTTAGCCCGGACACATTCACTTA
46220598 GCAC-AAAGCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAAGCCTTC-GGATCTTAGCCCGGACA-CATTCA
46220635 ATTAAACATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 20 0.62
41 12 0.38
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (41 bp):
GCACAAAAGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:46224831 original size:30 final size:30
Alignment explanation
Indices: 46224797--46224854 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
46224787 TTTTCAAATA
* * *
46224797 TAGGGGTAAAATGGTCATTTTGCCAAAGTC
1 TAGGGGCAAAATGATCATTTTACCAAAGTC
46224827 TAGGGGCAAAATGATCATTTTACCAAAG
1 TAGGGGCAAAATGATCATTTTACCAAAG
46224855 ATGTGAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (30 bp):
TAGGGGCAAAATGATCATTTTACCAAAGTC
Found at i:46225354 original size:46 final size:46
Alignment explanation
Indices: 46225198--46225414 Score: 183
Period size: 46 Copynumber: 4.7 Consensus size: 46
46225188 TATGCGAGCT
* * **
46225198 AGTGTAAGACATGTCTGGGACATGCATCGGCCAC-A-TTGTGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGACGT-A-AGCC
** * * * *
46225244 AGTGTAAGACCATGTCTGGGACATAGCATTGGCATTGAGACGAAAGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCAGCCTCGAGACGTAAGCC
* *
46225292 AGAGTAAGACATGTCTGGGACATGCATCAGCCTCGGGACGTAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGACGTAAGCC
* * * *
46225338 AGTGTAAGACATGTCTGGGACATACATC-GACTACGAGATGT--GTC
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCT-CGAGACGTAAGCC
*
46225382 AGTGTAAAACCATGTCTGGGACATGGCATCAGC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCAGC
46225415 ACCTTACCCA
Statistics
Matches: 138, Mismatches: 25, Indels: 15
0.78 0.14 0.08
Matches are distributed among these distances:
44 10 0.07
45 17 0.12
46 61 0.44
47 29 0.21
48 18 0.13
49 2 0.01
50 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.22
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGACGTAAGCC
Found at i:46232364 original size:43 final size:42
Alignment explanation
Indices: 46232290--46232391 Score: 134
Period size: 43 Copynumber: 2.4 Consensus size: 42
46232280 AATGTCGTAT
* *
46232290 CCCAGATATGGTCTTACATGGAATCTCATATCGATGCCAATAG
1 CCCAGATATGGTCTTACATCGAATCTAATATCGATGCC-ATAG
* * *
46232333 CCCAGCTATAGTCTTACA-CGAAGTCTAATATCGATGCCATAT
1 CCCAGATATGGTCTTACATCGAA-TCTAATATCGATGCCATAG
46232375 CCCAGATATGGTCTTAC
1 CCCAGATATGGTCTTAC
46232392 GCGTAATCTC
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
42 21 0.41
43 30 0.59
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.28
Consensus pattern (42 bp):
CCCAGATATGGTCTTACATCGAATCTAATATCGATGCCATAG
Found at i:46235022 original size:15 final size:15
Alignment explanation
Indices: 46235002--46235041 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 15
46234992 TTATATATTA
46235002 TTTTATTCTTTTTAT
1 TTTTATTCTTTTTAT
46235017 TTTTA-T-TTTTTAT
1 TTTTATTCTTTTTAT
*
46235030 TCTT-TTCTTTTT
1 TTTTATTCTTTTT
46235042 CCTTTTCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
13 11 0.50
14 6 0.27
15 5 0.23
ACGTcount: A:0.10, C:0.07, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTATTCTTTTTAT
Found at i:46235732 original size:18 final size:18
Alignment explanation
Indices: 46235717--46235751 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
46235707 AATATGAACT
46235717 TGAATCAGAATGTGAATG
1 TGAATCAGAATGTGAATG
**
46235735 TGAATGTGAATGTGAAT
1 TGAATCAGAATGTGAAT
46235752 CTAAATCTAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.03, G:0.29, T:0.31
Consensus pattern (18 bp):
TGAATCAGAATGTGAATG
Found at i:46235733 original size:6 final size:6
Alignment explanation
Indices: 46235724--46235751 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
46235714 ACTTGAATCA
46235724 GAATGT GAATGT GAATGT GAATGT GAAT
1 GAATGT GAATGT GAATGT GAATGT GAAT
46235752 CTAAATCTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (6 bp):
GAATGT
Found at i:46239601 original size:23 final size:23
Alignment explanation
Indices: 46239575--46239643 Score: 120
Period size: 23 Copynumber: 3.0 Consensus size: 23
46239565 ATGAATATAT
46239575 AGTTGCTAATGTTGATGGTATTA
1 AGTTGCTAATGTTGATGGTATTA
46239598 AGTTGCTAATGTTGATGGTATTA
1 AGTTGCTAATGTTGATGGTATTA
* *
46239621 AGTTGCTAATTTTGATGGAATTA
1 AGTTGCTAATGTTGATGGTATTA
46239644 TTATAATTTC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.28, C:0.04, G:0.25, T:0.43
Consensus pattern (23 bp):
AGTTGCTAATGTTGATGGTATTA
Found at i:46240335 original size:24 final size:26
Alignment explanation
Indices: 46240299--46240346 Score: 64
Period size: 24 Copynumber: 1.9 Consensus size: 26
46240289 TTTAATAAGA
*
46240299 TTTTATTAAGATT-T-AATAAATTAT
1 TTTTAATAAGATTGTAAATAAATTAT
*
46240323 TTTTAATAGGATTGTAAATAAATT
1 TTTTAATAAGATTGTAAATAAATT
46240347 TATATGAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 11 0.55
25 1 0.05
26 8 0.40
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (26 bp):
TTTTAATAAGATTGTAAATAAATTAT
Found at i:46243920 original size:43 final size:44
Alignment explanation
Indices: 46243784--46243941 Score: 141
Period size: 43 Copynumber: 3.7 Consensus size: 44
46243774 TATGTGTTTT
*
46243784 CATGTAAGACCATGTTTGGGACATTGGCATC-A-ACTTATGATTTA
1 CATGTAAGACCATGTCTGGGACATTGGCATCGATA-TT-TGATTTA
* **
46243828 CGTGTAAGACCACATCTGGGAC-TTGGCATCG-TATTTGATTTCA
1 CATGTAAGACCATGTCTGGGACATTGGCATCGATATTTGATTT-A
* * *
46243871 CA--TAAGACCGTGTCTAGGACAGTGGCATCGATATTTG-TTTA
1 CATGTAAGACCATGTCTGGGACATTGGCATCGATATTTGATTTA
** * *
46243912 CATGTAAGACCACATCTGAGACGTTGGCAT
1 CATGTAAGACCATGTCTGGGACATTGGCAT
46243942 TGTACGAGCT
Statistics
Matches: 90, Mismatches: 17, Indels: 15
0.74 0.14 0.12
Matches are distributed among these distances:
41 17 0.19
42 17 0.19
43 37 0.41
44 19 0.21
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (44 bp):
CATGTAAGACCATGTCTGGGACATTGGCATCGATATTTGATTTA
Found at i:46246300 original size:16 final size:15
Alignment explanation
Indices: 46246274--46246303 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
46246264 AACTATTTTA
46246274 TTACAAATTTCACTC
1 TTACAAATTTCACTC
46246289 TTACATAATTTCACT
1 TTACA-AATTTCACT
46246304 TACTTCATTC
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:0.33, C:0.23, G:0.00, T:0.43
Consensus pattern (15 bp):
TTACAAATTTCACTC
Found at i:46246643 original size:100 final size:101
Alignment explanation
Indices: 46246507--46246690 Score: 280
Period size: 100 Copynumber: 1.8 Consensus size: 101
46246497 AGAGCTATCT
* * * *
46246507 GGTATGCATAGTAGCCAGCACTTAGTACTACACATGCGGCC-AACAATCCGGTACACATTGTACC
1 GGTACGCATAGTAGCCAGCACTTAGTACTACACATGCGACCTAACAATCCGGTACACATAGTAAC
* *
46246571 CTGCACTTAGTACTACACACGTGATTAAAGTTGTCG
66 CTACACATAGTACTACACACGTGATTAAAGTTGTCG
* * *
46246607 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTAACTATCTGGTACACATAGTAAC
1 GGTACGCATAGTAGCCAGCACTTAGTACTACACATGCGACCTAACAATCCGGTACACATAGTAAC
46246672 CTACACATAGTACTACACA
66 CTACACATAGTACTACACA
46246691 TGTGTTCTCA
Statistics
Matches: 74, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
100 38 0.51
101 36 0.49
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (101 bp):
GGTACGCATAGTAGCCAGCACTTAGTACTACACATGCGACCTAACAATCCGGTACACATAGTAAC
CTACACATAGTACTACACACGTGATTAAAGTTGTCG
Found at i:46246689 original size:12 final size:14
Alignment explanation
Indices: 46246659--46246691 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
46246649 AACTATCTGG
46246659 TACACATAGTAACC
1 TACACATAGTAACC
46246673 TACACATAGT-A-C
1 TACACATAGTAACC
46246685 TACACAT
1 TACACAT
46246692 GTGTTCTCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 8 0.42
13 1 0.05
14 10 0.53
ACGTcount: A:0.42, C:0.27, G:0.06, T:0.24
Consensus pattern (14 bp):
TACACATAGTAACC
Found at i:46253098 original size:6 final size:6
Alignment explanation
Indices: 46253080--46253173 Score: 68
Period size: 6 Copynumber: 15.3 Consensus size: 6
46253070 AAGAAACATT
* * *
46253080 ATCAGA A-CTAGA ATCAGA ATCAGA ATCAGA ATTAGT ATTAGGTA A-CAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA ATCA-G-A ATCAGA
* * *
46253129 ATCAAA ATCAGA ATCAGT ATCAGGTA A-CAGA ATCAAA ATCAGA AT
1 ATCAGA ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA AT
46253174 GTGAATGCAA
Statistics
Matches: 70, Mismatches: 10, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
5 5 0.07
6 57 0.81
7 6 0.09
8 2 0.03
ACGTcount: A:0.49, C:0.14, G:0.16, T:0.21
Consensus pattern (6 bp):
ATCAGA
Found at i:46253132 original size:31 final size:31
Alignment explanation
Indices: 46253094--46253173 Score: 133
Period size: 31 Copynumber: 2.6 Consensus size: 31
46253084 GAACTAGAAT
* * *
46253094 CAGAATCAGAATCAGAATTAGTATTAGGTAA
1 CAGAATCAAAATCAGAATCAGTATCAGGTAA
46253125 CAGAATCAAAATCAGAATCAGTATCAGGTAA
1 CAGAATCAAAATCAGAATCAGTATCAGGTAA
46253156 CAGAATCAAAATCAGAAT
1 CAGAATCAAAATCAGAAT
46253174 GTGAATGCAA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.49, C:0.14, G:0.16, T:0.21
Consensus pattern (31 bp):
CAGAATCAAAATCAGAATCAGTATCAGGTAA
Found at i:46253348 original size:27 final size:26
Alignment explanation
Indices: 46253305--46253406 Score: 123
Period size: 27 Copynumber: 3.8 Consensus size: 26
46253295 ACTCAGTTAT
** *
46253305 CAGATATTGTGATAGAGTCACCAGATA
1 CAGATATTGTGGCAGAGCCACCAGA-A
46253332 CAGATATTGTGGCAGAGCCACCAGAA
1 CAGATATTGTGGCAGAGCCACCAGAA
*
46253358 CAGATATTTGTGGCATAGCCACCAGAAA
1 CAGATA-TTGTGGCAGAGCCACCAG-AA
* *
46253386 CAGATAATGTGGCAAAGCCAC
1 CAGATATTGTGGCAGAGCCAC
46253407 TTAACAGAAT
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
26 7 0.10
27 52 0.78
28 8 0.12
ACGTcount: A:0.36, C:0.21, G:0.24, T:0.20
Consensus pattern (26 bp):
CAGATATTGTGGCAGAGCCACCAGAA
Found at i:46253593 original size:22 final size:21
Alignment explanation
Indices: 46253565--46253629 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 21
46253555 GCAAATACAT
46253565 TTGGCACACAACCATAATCAGG
1 TTGGCACA-AACCATAATCAGG
* *
46253587 TTGGCACAGAGCCAT-ATGTAGG
1 TTGGCACA-AACCATAAT-CAGG
*
46253609 TTGACACAAAGCCATAATCAG
1 TTGGCACAAA-CCATAATCAG
46253630 AAGGCTTTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
21 3 0.09
22 29 0.85
23 2 0.06
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.20
Consensus pattern (21 bp):
TTGGCACAAACCATAATCAGG
Found at i:46254094 original size:26 final size:27
Alignment explanation
Indices: 46254056--46254277 Score: 266
Period size: 27 Copynumber: 8.3 Consensus size: 27
46254046 GGGGCAAAAT
* * * *
46254056 GGTAATTTTACCCCACA-AGGTATCTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
46254082 GGTAATTCCACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
*
46254109 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
46254136 GGTAATTCTACCCTACATGGGTATTGC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
46254163 GATAATTCTACCTTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
46254190 GGTAATTTTACCCTATAGAGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
46254217 GATAATTCTACCCTATAGGGGTATTCC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
46254244 GATAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
46254271 GGTAATT
1 GGTAATT
46254278 TTGTAAACCA
Statistics
Matches: 166, Mismatches: 29, Indels: 1
0.85 0.15 0.01
Matches are distributed among these distances:
26 14 0.08
27 152 0.92
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.35
Consensus pattern (27 bp):
GGTAATTCTACCCTACAGGGGTATTTC
Found at i:46254289 original size:27 final size:27
Alignment explanation
Indices: 46254261--46254442 Score: 161
Period size: 27 Copynumber: 6.7 Consensus size: 27
46254251 CTACCCTACA
* *
46254261 AGGGTATTTCGGTAATTTTGTAAACCA
1 AGGGTATTTCGGTAATTTTATAAACCG
* * * *
46254288 AGTGTATTTTGGTAATGTTACAAACC-
1 AGGGTATTTCGGTAATTTTATAAACCG
* ** *
46254314 AGGGGTATTTTGGTAATTTTATTGATCG
1 A-GGGTATTTCGGTAATTTTATAAACCG
* * **
46254342 AGGGTATTTCAGTAATTTTGTAAATTG
1 AGGGTATTTCGGTAATTTTATAAACCG
* *
46254369 AGGGTATTTCGGTAATTTTACAAATCG
1 AGGGTATTTCGGTAATTTTATAAACCG
* *
46254396 AGGATATTTGGGTAATTTTATAAACCG
1 AGGGTATTTCGGTAATTTTATAAACCG
*
46254423 GGGGTACTTT-GGTAATTTTA
1 AGGGTA-TTTCGGTAATTTTA
46254443 CAACTGGGGG
Statistics
Matches: 125, Mismatches: 27, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
26 1 0.01
27 120 0.96
28 4 0.03
ACGTcount: A:0.28, C:0.08, G:0.24, T:0.41
Consensus pattern (27 bp):
AGGGTATTTCGGTAATTTTATAAACCG
Found at i:46254404 original size:81 final size:81
Alignment explanation
Indices: 46254261--46254416 Score: 206
Period size: 81 Copynumber: 1.9 Consensus size: 81
46254251 CTACCCTACA
* * * * *
46254261 AGGGTATTTCGGTAATTTTGTAAACCAAGTGTATTTTGGTAATGTTACAAACCAGGGGTATTTTG
1 AGGGTATTTCAGTAATTTTGTAAACCAAGGGTATTTCGGTAATGTTACAAACCAGGGATATTTGG
46254326 GTAATTTTATTGATCG
66 GTAATTTTATTGATCG
*** * *
46254342 AGGGTATTTCAGTAATTTTGTAAATTGAGGGTATTTCGGTAATTTTACAAATC-GAGGATATTTG
1 AGGGTATTTCAGTAATTTTGTAAACCAAGGGTATTTCGGTAATGTTACAAACCAG-GGATATTTG
46254406 GGTAATTTTAT
65 GGTAATTTTAT
46254417 AAACCGGGGG
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
80 1 0.02
81 63 0.98
ACGTcount: A:0.28, C:0.07, G:0.23, T:0.42
Consensus pattern (81 bp):
AGGGTATTTCAGTAATTTTGTAAACCAAGGGTATTTCGGTAATGTTACAAACCAGGGATATTTGG
GTAATTTTATTGATCG
Found at i:46254428 original size:81 final size:81
Alignment explanation
Indices: 46254261--46254441 Score: 204
Period size: 81 Copynumber: 2.2 Consensus size: 81
46254251 CTACCCTACA
* * * *
46254261 AGGGTATTTCGGTAATTTTGTAAACCAAGTGTATTTTGGTAATGTTACAAACCAGGGGTATTTTG
1 AGGGTATTTCGGTAATTTTGTAAACCAAGGGTATTTCGGTAATGTTACAAACCAGGGATATTTGG
** *
46254326 GTAATTTTATTGATCG
66 GTAATTTTATAAACCG
* *** * *
46254342 AGGGTATTTCAGTAATTTTGTAAATTGAGGGTATTTCGGTAATTTTACAAATC-GAGGATATTTG
1 AGGGTATTTCGGTAATTTTGTAAACCAAGGGTATTTCGGTAATGTTACAAACCAG-GGATATTTG
46254406 GGTAATTTTATAAACCG
65 GGTAATTTTATAAACCG
*
46254423 GGGGTACTTT-GGTAATTTT
1 AGGGTA-TTTCGGTAATTTT
46254442 ACAACTGGGG
Statistics
Matches: 83, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
80 1 0.01
81 79 0.95
82 3 0.04
ACGTcount: A:0.28, C:0.08, G:0.24, T:0.41
Consensus pattern (81 bp):
AGGGTATTTCGGTAATTTTGTAAACCAAGGGTATTTCGGTAATGTTACAAACCAGGGATATTTGG
GTAATTTTATAAACCG
Found at i:46254452 original size:27 final size:27
Alignment explanation
Indices: 46254291--46254466 Score: 101
Period size: 27 Copynumber: 6.6 Consensus size: 27
46254281 TAAACCAAGT
* * *
46254291 GTATTTTGGTAATGTTACAAAC-CAGGG
1 GTATTTCGGTAATTTTAC-AACTCGGGG
* ** *
46254318 GTATTTTGGTAATTTTATTGA-TCGAGG
1 GTATTTCGGTAATTTTA-CAACTCGGGG
* ** * * *
46254345 GTATTTCAGTAATTTTGTAAATTGAGG
1 GTATTTCGGTAATTTTACAACTCGGGG
* *
46254372 GTATTTCGGTAATTTTACAAATCGAGG
1 GTATTTCGGTAATTTTACAACTCGGGG
* * *
46254399 ATATTTGGGTAATTTTATAAAC-CGGGG
1 GTATTTCGGTAATTTTA-CAACTCGGGG
46254426 GTACTTT-GGTAATTTTACAACT-GGGG
1 GTA-TTTCGGTAATTTTACAACTCGGGG
**
46254452 GTATTTTAGTAATTT
1 GTATTTCGGTAATTT
46254467 GGTAAACTAA
Statistics
Matches: 120, Mismatches: 22, Indels: 15
0.76 0.14 0.10
Matches are distributed among these distances:
25 3 0.03
26 19 0.16
27 93 0.77
28 5 0.04
ACGTcount: A:0.27, C:0.07, G:0.24, T:0.41
Consensus pattern (27 bp):
GTATTTCGGTAATTTTACAACTCGGGG
Found at i:46254463 original size:26 final size:26
Alignment explanation
Indices: 46254261--46254466 Score: 98
Period size: 27 Copynumber: 7.7 Consensus size: 26
46254251 CTACCCTACA
**
46254261 AGGGTATTTCGGTAATTTTGTA-AACCA
1 AGGGTATTTCGGTAA-TTT-TACAACTG
* * * *
46254288 AGTGTATTTTGGTAATGTTACAAAC-C
1 AGGGTATTTCGGTAATTTTAC-AACTG
* **
46254314 AGGGGTATTTTGGTAATTTTATTGA-TCG
1 A-GGGTATTTCGGTAATTTTA-CAACT-G
* *
46254342 AGGGTATTTCAGTAATTTTGTA-AATTG
1 AGGGTATTTCGGTAA-TTT-TACAACTG
*
46254369 AGGGTATTTCGGTAATTTTACAAATCG
1 AGGGTATTTCGGTAATTTTACAACT-G
* * * *
46254396 AGGATATTTGGGTAATTTTATAAACCG
1 AGGGTATTTCGGTAATTTTA-CAACTG
*
46254423 GGGGTACTTT-GGTAATTTTACAACTG
1 AGGGTA-TTTCGGTAATTTTACAACTG
* **
46254449 GGGGTATTTTAGTAATTT
1 AGGGTATTTCGGTAATTT
46254467 GGTAAACTAA
Statistics
Matches: 141, Mismatches: 24, Indels: 29
0.73 0.12 0.15
Matches are distributed among these distances:
25 7 0.05
26 26 0.18
27 96 0.68
28 10 0.07
29 2 0.01
ACGTcount: A:0.28, C:0.08, G:0.24, T:0.41
Consensus pattern (26 bp):
AGGGTATTTCGGTAATTTTACAACTG
Found at i:46254474 original size:27 final size:25
Alignment explanation
Indices: 46254407--46254466 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
46254397 GGATATTTGG
* *
46254407 GTAATTTTATAAACCGGGGGTACTTTG
1 GTAA-TTT-TAAACTGGGGGTACTTTA
*
46254434 GTAATTTTACAACTGGGGGTATTTTA
1 GTAATTTTA-AACTGGGGGTACTTTA
46254460 GTAATTT
1 GTAATTT
46254467 GGTAAACTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
25 2 0.07
26 23 0.79
27 4 0.14
ACGTcount: A:0.27, C:0.08, G:0.23, T:0.42
Consensus pattern (25 bp):
GTAATTTTAAACTGGGGGTACTTTA
Found at i:46256793 original size:27 final size:27
Alignment explanation
Indices: 46256755--46256831 Score: 127
Period size: 27 Copynumber: 2.9 Consensus size: 27
46256745 TAAGACTCCG
**
46256755 ATTTGTAAAATTATCGAAATACCCTTA
1 ATTTGTAAAATTATCGAAATACCCCCA
46256782 ATTTGTAAAATTATCGAAATACCCCCA
1 ATTTGTAAAATTATCGAAATACCCCCA
*
46256809 GTTTGTAAAATTATCGAAATACC
1 ATTTGTAAAATTATCGAAATACC
46256832 TTTGTAGTGT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.40, C:0.17, G:0.09, T:0.34
Consensus pattern (27 bp):
ATTTGTAAAATTATCGAAATACCCCCA
Found at i:46256842 original size:27 final size:27
Alignment explanation
Indices: 46256757--46256846 Score: 103
Period size: 27 Copynumber: 3.3 Consensus size: 27
46256747 AGACTCCGAT
*
46256757 TTGTAAAATTATCGAAATACCCTT-AA
1 TTGTAAAATTATCGAAATACCCTTGTA
**
46256783 TTTGTAAAATTATCGAAATACCCCCAGT-
1 -TTGTAAAATTATCGAAATA-CCCTTGTA
*
46256811 TTGTAAAATTATCGAAATACCTTTGTA
1 TTGTAAAATTATCGAAATACCCTTGTA
*
46256838 GTGTAAAAT
1 TTGTAAAAT
46256847 GACTGTTTTG
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
26 4 0.08
27 46 0.87
28 3 0.06
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (27 bp):
TTGTAAAATTATCGAAATACCCTTGTA
Found at i:46257327 original size:27 final size:26
Alignment explanation
Indices: 46257238--46257333 Score: 66
Period size: 27 Copynumber: 3.6 Consensus size: 26
46257228 ATTATGGTTT
* **
46257238 TGTGCCAATCGTATTTACCTGTGGCTA
1 TGTGCCAATCATATTTACCCAT-GCTA
* *** *
46257265 TGTGCCTATCATATTTATTGATGACTC
1 TGTGCCAATCATATTTACCCATG-CTA
* *
46257292 TTTGTCAATCATATTTACCCATAGCTA
1 TGTGCCAATCATATTTACCCAT-GCTA
*
46257319 TGTGCCAATTATATT
1 TGTGCCAATCATATT
46257334 ACTGTCGCTG
Statistics
Matches: 50, Mismatches: 17, Indels: 4
0.70 0.24 0.06
Matches are distributed among these distances:
26 1 0.02
27 48 0.96
28 1 0.02
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.42
Consensus pattern (26 bp):
TGTGCCAATCATATTTACCCATGCTA
Found at i:46259473 original size:15 final size:16
Alignment explanation
Indices: 46259453--46259484 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
46259443 AAAACTGTAT
46259453 TATTACA-AATTTCAC
1 TATTACATAATTTCAC
46259468 TATTACATAATTTCAC
1 TATTACATAATTTCAC
46259484 T
1 T
46259485 TACTCCATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.38, C:0.19, G:0.00, T:0.44
Consensus pattern (16 bp):
TATTACATAATTTCAC
Found at i:46259736 original size:49 final size:50
Alignment explanation
Indices: 46259680--46259810 Score: 165
Period size: 49 Copynumber: 2.6 Consensus size: 50
46259670 AACCGAAGCT
* * * *
46259680 ATCTGGTACGCATAGTAGCCAGCACTTAGTACAACACATGCG-ACCAAGA
1 ATCTGGTACACGTAGTAGCCTGCACTTAGTACAACACATGCGAACCAACA
* * * * *
46259729 ATCTGGTACACGTAGTAGCCTGCACCTAGTACTACACATGTGAACTAACC
1 ATCTGGTACACGTAGTAGCCTGCACTTAGTACAACACATGCGAACCAACA
*
46259779 ATCTGATACACGTAGTAGCCTGCACTTAGTAC
1 ATCTGGTACACGTAGTAGCCTGCACTTAGTAC
46259811 TGCACACGTG
Statistics
Matches: 70, Mismatches: 11, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
49 36 0.51
50 34 0.49
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.23
Consensus pattern (50 bp):
ATCTGGTACACGTAGTAGCCTGCACTTAGTACAACACATGCGAACCAACA
Found at i:46259797 original size:50 final size:50
Alignment explanation
Indices: 46259692--46259971 Score: 208
Period size: 50 Copynumber: 5.6 Consensus size: 50
46259682 CTGGTACGCA
* * * * ** *
46259692 TAGTAGCCAGCACTTAGTACAACACATGCG-ACCAAGAATCTGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGTGAACTAACCATCTGATACACG
*
46259741 TAGTAGCCTGCACCTAGTACTACACATGTGAACTAACCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACATGTGAACTAACCATCTGATACACG
* * * *** * * *
46259791 TAGTAGCCTGCACTTAGTACTGCACACGTG-ATTGAAGTTGTCGGGTATGCATG
1 TAGTAGCCTGCACTTAGTACTACACATGTGAACT-AA-CCATC-TG-ATACACG
* * * * * *
46259844 -A-TAGCCTGCACTTAGTACTACACCTGCGACCTAACTATCTGGTACACT
1 TAGTAGCCTGCACTTAGTACTACACATGTGAACTAACCATCTGATACACG
* * * * * *
46259892 TAGTAGCCTACACTTAGTACTACACACGTGACCTAAAACCATCTTAAACACA
1 TAGTAGCCTGCACTTAGTACTACACATGTGAACT--AACCATCTGATACACG
*
46259944 TAGTAGCCTGCACATAGTACTACACATG
1 TAGTAGCCTGCACTTAGTACTACACATG
46259972 CGTTCTCCCA
Statistics
Matches: 178, Mismatches: 43, Indels: 17
0.75 0.18 0.07
Matches are distributed among these distances:
48 3 0.02
49 30 0.17
50 74 0.42
51 27 0.15
52 39 0.22
53 5 0.03
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (50 bp):
TAGTAGCCTGCACTTAGTACTACACATGTGAACTAACCATCTGATACACG
Found at i:46273791 original size:33 final size:33
Alignment explanation
Indices: 46273747--46273836 Score: 144
Period size: 33 Copynumber: 2.7 Consensus size: 33
46273737 AGTTTATTCT
*
46273747 GGATTAACAGTCCAGGATAAATCCAGTCAGTTA
1 GGATTAACAGTCCAGGCTAAATCCAGTCAGTTA
* * *
46273780 GGATTACCAGTCTAGGCTAAATCTAGTCAGTTA
1 GGATTAACAGTCCAGGCTAAATCCAGTCAGTTA
46273813 GGATTAACAGTCCAGGCTAAATCC
1 GGATTAACAGTCCAGGCTAAATCC
46273837 TAATTGAAAC
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (33 bp):
GGATTAACAGTCCAGGCTAAATCCAGTCAGTTA
Found at i:46313512 original size:47 final size:46
Alignment explanation
Indices: 46313394--46313526 Score: 169
Period size: 46 Copynumber: 2.9 Consensus size: 46
46313384 ATAATCTCAC
* * *
46313394 CCATAATGAACTCAGAACGCAACTCAACGAGCTCAGG-TGTTTGCAT
1 CCATAATGAACTCGGAACGCAACTCAACGAG-TTAGGATGCTTGCAT
* * *
46313440 CCATAATGAACTCGGAACACAACTCAATGAGTTTGGATGCTTGCAT
1 CCATAATGAACTCGGAACGCAACTCAACGAGTTAGGATGCTTGCAT
* *
46313486 CCATAAGTGAACTCGGAATGCAACTCAACGAGTTCGGATGC
1 CCATAA-TGAACTCGGAACGCAACTCAACGAGTTAGGATGC
46313527 CTCATAATTC
Statistics
Matches: 75, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
45 3 0.04
46 42 0.56
47 30 0.40
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.23
Consensus pattern (46 bp):
CCATAATGAACTCGGAACGCAACTCAACGAGTTAGGATGCTTGCAT
Found at i:46321868 original size:27 final size:26
Alignment explanation
Indices: 46321820--46321870 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
46321810 ATGTTTAAAA
*
46321820 ACTTTTTATTTATTATTTTTATTTTC
1 ACTTTTTATTTATTATTCTTATTTTC
46321846 ACTTTTATATTTATT-TATCTTATTT
1 ACTTTT-TATTTATTAT-TCTTATTT
46321871 AAGTACTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.22, C:0.08, G:0.00, T:0.71
Consensus pattern (26 bp):
ACTTTTTATTTATTATTCTTATTTTC
Found at i:46327784 original size:27 final size:27
Alignment explanation
Indices: 46327732--46327785 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
46327722 TTGAAATTAA
* **
46327732 AAGGTTAATTAAGTAAATTAACAAATT
1 AAGGTTAATTAAATAAAACAACAAATT
46327759 AAGGTTAATTATAATAAAACAA-AAATT
1 AAGGTTAATTA-AATAAAACAACAAATT
46327786 TCTATCTTCC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 16 0.70
28 7 0.30
ACGTcount: A:0.56, C:0.04, G:0.09, T:0.31
Consensus pattern (27 bp):
AAGGTTAATTAAATAAAACAACAAATT
Found at i:46329797 original size:42 final size:42
Alignment explanation
Indices: 46329738--46329818 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
46329728 TCCACATGGG
46329738 CAGAGACACAGGCATGTGTCTCAGTCGAGTGTGACACACTGT
1 CAGAGACACAGGCATGTGTCTCAGTCGAGTGTGACACACTGT
* * *
46329780 CAGAGACATAGGCATGTGTCTCAGTTGTGTGTGACACAC
1 CAGAGACACAGGCATGTGTCTCAGTCGAGTGTGACACAC
46329819 ATTCAGGTCA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.23
Consensus pattern (42 bp):
CAGAGACACAGGCATGTGTCTCAGTCGAGTGTGACACACTGT
Found at i:46336725 original size:43 final size:42
Alignment explanation
Indices: 46336676--46336845 Score: 173
Period size: 43 Copynumber: 4.0 Consensus size: 42
46336666 GGTTACCGAG
*
46336676 ATGTGATTACATGTAAGACCATGTATGGGACATTGGCATTGT
1 ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGT
* **
46336718 ACTGTGATTACATGTATGACCATGTCTGGGACATTGGCACCGTT
1 A-TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTG-T
** * **
46336762 AAT-CAATTTCATGTAAGACCATGTCTGGGACATTGGCATCAAT
1 -ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCAT-TGT
* * * *
46336805 ATGAGATAACATGTAAGACCATATCTGGGATA-TGGCATTGT
1 ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGT
46336846 GCGAGCTTAA
Statistics
Matches: 104, Mismatches: 19, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
41 1 0.01
42 9 0.09
43 91 0.88
44 2 0.02
45 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (42 bp):
ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGT
Found at i:46339712 original size:20 final size:20
Alignment explanation
Indices: 46339654--46339712 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
46339644 AAACATGGTC
*
46339654 TGTATGATATGCACATGAAA
1 TGTATGATATGCACATGATA
*
46339674 TGTATGCTATGCACATGATA
1 TGTATGATATGCACATGATA
46339694 TGTATGATATGCACATGAT
1 TGTATGATATGCACATGAT
46339713 GTATTCATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.34
Consensus pattern (20 bp):
TGTATGATATGCACATGATA
Found at i:46339855 original size:47 final size:48
Alignment explanation
Indices: 46339762--46339888 Score: 197
Period size: 47 Copynumber: 2.7 Consensus size: 48
46339752 GAGGAAGTGC
* *
46339762 AAAAGGGCTTATGCCCCAGTTATT-AAAGGGCTTATGCGCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCCCAATTATT
*
46339809 -CAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCCCAATTATT
1 AAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCCCAATTATT
46339856 AAAAGGGCTT-TGCCCCAGTTATTAAAAGAGGCT
1 AAAAGGGCTTATGCCCCAGTTATTAAAAG-GGCT
46339889 AGGCCTCCAG
Statistics
Matches: 73, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
46 22 0.30
47 39 0.53
48 12 0.16
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.28
Consensus pattern (48 bp):
AAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCCCAATTATT
Found at i:46339882 original size:23 final size:24
Alignment explanation
Indices: 46339762--46339902 Score: 200
Period size: 23 Copynumber: 6.0 Consensus size: 24
46339752 GAGGAAGTGC
46339762 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
46339786 -AAAGGGCTTATGCGCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
46339809 -CAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
46339832 AAAAGGGCTTATGCCCCAATTATT
1 AAAAGGGCTTATGCCCCAGTTATT
46339856 AAAAGGGCTT-TGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
46339879 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
46339903 ATGATAAAGC
Statistics
Matches: 106, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
23 61 0.58
24 37 0.35
25 8 0.08
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.28
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:46340130 original size:31 final size:31
Alignment explanation
Indices: 46340094--46340159 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
46340084 ACCGTGTACA
*
46340094 GAAAAGGCTTCGGCCTAGTAATATGAAATAT
1 GAAAAGGCTTCGGCCGAGTAATATGAAATAT
**
46340125 GAAAAGGCTTCGGCCGAGTGTTATGAAATAT
1 GAAAAGGCTTCGGCCGAGTAATATGAAATAT
46340156 GAAA
1 GAAA
46340160 TATGCAAAGG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.38, C:0.12, G:0.26, T:0.24
Consensus pattern (31 bp):
GAAAAGGCTTCGGCCGAGTAATATGAAATAT
Found at i:46350004 original size:40 final size:40
Alignment explanation
Indices: 46349949--46350225 Score: 448
Period size: 40 Copynumber: 6.9 Consensus size: 40
46349939 GCATGAGCAT
46349949 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
1 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
46349989 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
1 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
*
46350029 TTGATAAATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
1 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
* *
46350069 TTGATATATCTGGGCTAAAACCCGAAGGCATTTGTGCGAG
1 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
* *
46350109 TTGATATATCCGGGCTAAGACCCGAAGGCAATTATGC-AGG
1 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-G
*
46350149 TTGATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAG
1 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
* * * *
46350189 TTGCTATACCCGGGTTAAGACCCGAAGGCAATTGTGC
1 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGC
46350226 TTGCGGTTAT
Statistics
Matches: 219, Mismatches: 16, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
39 1 0.00
40 217 0.99
41 1 0.00
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (40 bp):
TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
Found at i:46356343 original size:31 final size:31
Alignment explanation
Indices: 46356306--46356375 Score: 113
Period size: 31 Copynumber: 2.3 Consensus size: 31
46356296 TTTGGACAGT
* *
46356306 CACACGCCCATGTGGGTAGGCTGTGTGGTCA
1 CACACGCCCATATGGGTAGGCCGTGTGGTCA
*
46356337 CACACGCCCGTATGGGTAGGCCGTGTGGTCA
1 CACACGCCCATATGGGTAGGCCGTGTGGTCA
46356368 CACACGCC
1 CACACGCC
46356376 TGTGTGACTT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.17, C:0.31, G:0.33, T:0.19
Consensus pattern (31 bp):
CACACGCCCATATGGGTAGGCCGTGTGGTCA
Found at i:46357877 original size:21 final size:21
Alignment explanation
Indices: 46357853--46357921 Score: 59
Period size: 21 Copynumber: 3.1 Consensus size: 21
46357843 CATCGTGAAC
46357853 TCAGACCATAACTTAATGAGT
1 TCAGACCATAACTTAATGAGT
* * **
46357874 TCAGATGCCACATA-TATCATGAAC
1 TCAGA--CCATA-ACT-TAATGAGT
46357898 TCAGACCATAACTTAATGAGT
1 TCAGACCATAACTTAATGAGT
46357919 TCA
1 TCA
46357922 ATCACATAGT
Statistics
Matches: 35, Mismatches: 8, Indels: 10
0.66 0.15 0.19
Matches are distributed among these distances:
21 14 0.40
22 5 0.14
23 5 0.14
24 11 0.31
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.28
Consensus pattern (21 bp):
TCAGACCATAACTTAATGAGT
Found at i:46361769 original size:43 final size:43
Alignment explanation
Indices: 46361681--46361775 Score: 120
Period size: 43 Copynumber: 2.2 Consensus size: 43
46361671 TATGAATACA
* * * *
46361681 TGTAAGACCGTGTATGGGACATTGGCATTGTATTGTGATTACG
1 TGTAAGACCATGTATGGGACATTGGCATCGTAATGCGATTACG
* *
46361724 TGTAAGACCATGTCTGGGACATTGGCATCGTTAAT-CGATTTCG
1 TGTAAGACCATGTATGGGACATTGGCATCG-TAATGCGATTACG
46361767 TGTAAGACC
1 TGTAAGACC
46361776 CTATCTAAGA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
43 42 0.93
44 3 0.07
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (43 bp):
TGTAAGACCATGTATGGGACATTGGCATCGTAATGCGATTACG
Found at i:46364396 original size:33 final size:33
Alignment explanation
Indices: 46364343--46364417 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 33
46364333 GGCCTTGTCG
*
46364343 TGGTCTT-TCATTCGTATGCCATAACCC-AGCTA
1 TGGTCTTATTATTCGTATGCCATAACCCGA-CTA
*
46364375 TGGTCTTATTATTCG-ATTGCCATAGCCCGACTA
1 TGGTCTTATTATTCGTA-TGCCATAACCCGACTA
46364408 TGGTCTTATT
1 TGGTCTTATT
46364418 TGGCAACTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
32 8 0.21
33 29 0.76
34 1 0.03
ACGTcount: A:0.20, C:0.24, G:0.17, T:0.39
Consensus pattern (33 bp):
TGGTCTTATTATTCGTATGCCATAACCCGACTA
Found at i:46364511 original size:30 final size:31
Alignment explanation
Indices: 46364452--46364511 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
46364442 TACTTTTCAT
*
46364452 TTAATATCTCAACATTTATTCAACAAAATAA
1 TTAATATCTCAACATTTATCCAACAAAATAA
*
46364483 TTAATATCTC-A-ATTTCATCCATCAAAATA
1 TTAATATCTCAACATTT-ATCCAACAAAATA
46364512 GATAGGTACA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 4 0.15
30 12 0.46
31 10 0.38
ACGTcount: A:0.45, C:0.18, G:0.00, T:0.37
Consensus pattern (31 bp):
TTAATATCTCAACATTTATCCAACAAAATAA
Found at i:46368561 original size:32 final size:33
Alignment explanation
Indices: 46368524--46368593 Score: 115
Period size: 35 Copynumber: 2.1 Consensus size: 33
46368514 ATATGTATTG
46368524 AATACCGG-GATGTCTGAGTCGAGGCTTGAATC
1 AATACCGGAGATGTCTGAGTCGAGGCTTGAATC
46368556 AATACCGGTAAGATGTCTGAGTCGAGGCTTGAATC
1 AATACCGG--AGATGTCTGAGTCGAGGCTTGAATC
46368591 AAT
1 AAT
46368594 GCCGATAATC
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
32 8 0.23
35 27 0.77
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.26
Consensus pattern (33 bp):
AATACCGGAGATGTCTGAGTCGAGGCTTGAATC
Found at i:46370160 original size:40 final size:40
Alignment explanation
Indices: 46370112--46370259 Score: 219
Period size: 40 Copynumber: 3.7 Consensus size: 40
46370102 AGCTACTGCT
46370112 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
46370152 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* * * * *
46370192 CAAATGCCTTCAGGACTT-GCCCGG-AACTAGTCACTAGCG
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCA
46370231 CAAATGCCTTCGGGACTTAGCCCGGTTAT
1 CAAATGCCTTCGGGACTTAGCCCGGTTAT
46370260 CATCCAAATA
Statistics
Matches: 97, Mismatches: 8, Indels: 6
0.87 0.07 0.05
Matches are distributed among these distances:
38 1 0.01
39 32 0.33
40 63 0.65
41 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:46370235 original size:79 final size:79
Alignment explanation
Indices: 46370090--46370255 Score: 223
Period size: 79 Copynumber: 2.1 Consensus size: 79
46370080 CCTTCAGGGT
* * * *
46370090 TTAG-CCGGATATAGCTACTGCTCAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACA
1 TTAGCCCGGATATAGCTACTGCACAAATGCCTTCAGGACTTAGCCCGGTAATAGTAACTAGCACA
46370154 AATGCCTTCGGGAC
66 AATGCCTTCGGGAC
*
46370168 TTAGCCCGGATATAG-TAACTCGCACAAATGCCTTCAGGACTT-GCCCGG-AACTAGTCACTAGC
1 TTAGCCCGGATATAGCT-ACT-GCACAAATGCCTTCAGGACTTAGCCCGGTAA-TAGTAACTAGC
*
46370230 GCAAATGCCTTCGGGAC
63 ACAAATGCCTTCGGGAC
46370247 TTAGCCCGG
1 TTAGCCCGG
46370256 TTATCATCCA
Statistics
Matches: 78, Mismatches: 6, Indels: 7
0.86 0.07 0.08
Matches are distributed among these distances:
78 6 0.08
79 53 0.68
80 19 0.24
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.23
Consensus pattern (79 bp):
TTAGCCCGGATATAGCTACTGCACAAATGCCTTCAGGACTTAGCCCGGTAATAGTAACTAGCACA
AATGCCTTCGGGAC
Found at i:46378253 original size:40 final size:40
Alignment explanation
Indices: 46378174--46378389 Score: 273
Period size: 40 Copynumber: 5.5 Consensus size: 40
46378164 CAGCCAAGTA
** *
46378174 CCTTCGGGGTTTAG-CCGGATATAGCT-ACT-GCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
46378212 CCTTCGGGACTTAGTCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
46378252 CCTTCGGGACTTAGCCCGGATATAGT-ACTTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAAC-TCGCACAAATG
46378292 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * * **
46378332 CCTTCGGGACTT-GCTCGGA-ACTAGTCACTAGCGTAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
46378371 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
46378390 TTATCATCCA
Statistics
Matches: 159, Mismatches: 12, Indels: 12
0.87 0.07 0.07
Matches are distributed among these distances:
38 14 0.09
39 46 0.29
40 97 0.61
41 2 0.01
ACGTcount: A:0.23, C:0.27, G:0.25, T:0.25
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:46378384 original size:119 final size:118
Alignment explanation
Indices: 46378174--46378389 Score: 287
Period size: 119 Copynumber: 1.8 Consensus size: 118
46378164 CAGCCAAGTA
** * *
46378174 CCTTCGGGGTTTAGCCGGATATAGCTACTGCTCAAATGCCTTCGGGACTTAGTCCGGTTATAGTA
1 CCTTCGGGACTTAGCCGGATATAGCTACTGCACAAATGCCTTCGGGACTTAGTCCGGTAATAGTA
*
46378239 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTACTTCGCACAAATG
66 ACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTACTTCGCACAAATG
46378292 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTT-G-CTCGG-AAC
1 CCTTCGGGACTTAG-CCGGATATAGCT-ACT-GCACAAATGCCTTCGGGACTTAGTC-CGGTAA-
* **
46378353 TAGTCACTAGCGTAAATGCCTTCGGGACTTAGCCCGG
61 TAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGG
46378390 TTATCATCCA
Statistics
Matches: 85, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
118 15 0.18
119 50 0.59
120 20 0.24
ACGTcount: A:0.23, C:0.27, G:0.25, T:0.25
Consensus pattern (118 bp):
CCTTCGGGACTTAGCCGGATATAGCTACTGCACAAATGCCTTCGGGACTTAGTCCGGTAATAGTA
ACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTACTTCGCACAAATG
Found at i:46381490 original size:29 final size:28
Alignment explanation
Indices: 46381444--46381528 Score: 116
Period size: 29 Copynumber: 3.0 Consensus size: 28
46381434 AGCATGACTG
*
46381444 TAAAAGTGATTGGGCCTAGTGGGCCATA
1 TAAATGTGATTGGGCCTAGTGGGCCATA
* *
46381472 TAGATGTGATTTGGGCCTAATGGGCCATA
1 TAAATGTGA-TTGGGCCTAGTGGGCCATA
* *
46381501 TAAATGAGATTGGGCCTAGTAGGCCATA
1 TAAATGTGATTGGGCCTAGTGGGCCATA
46381529 AGCATGTATG
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
28 24 0.49
29 25 0.51
ACGTcount: A:0.28, C:0.14, G:0.31, T:0.27
Consensus pattern (28 bp):
TAAATGTGATTGGGCCTAGTGGGCCATA
Found at i:46385168 original size:16 final size:15
Alignment explanation
Indices: 46385133--46385162 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
46385123 AGTAGATCGG
46385133 CAAAAGCCGAAATGC
1 CAAAAGCCGAAATGC
46385148 CAAAATGCCGAAATG
1 CAAAA-GCCGAAATG
46385163 TTAAAAAGCT
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:0.47, C:0.23, G:0.20, T:0.10
Consensus pattern (15 bp):
CAAAAGCCGAAATGC
Found at i:46385176 original size:16 final size:16
Alignment explanation
Indices: 46385134--46385176 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
46385124 GTAGATCGGC
46385134 AAAAGCCGAAATGCCA
1 AAAAGCCGAAATGCCA
* **
46385150 AAATGCCGAAATGTTA
1 AAAAGCCGAAATGCCA
*
46385166 AAAAGCTGAAA
1 AAAAGCCGAAA
46385177 GTTTGGCTAC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.51, C:0.16, G:0.19, T:0.14
Consensus pattern (16 bp):
AAAAGCCGAAATGCCA
Found at i:46385468 original size:28 final size:28
Alignment explanation
Indices: 46385394--46385473 Score: 101
Period size: 28 Copynumber: 2.8 Consensus size: 28
46385384 GACTGTAAAA
*
46385394 GTGATTGGGCCTAGTGGGCCTTATAGAT
1 GTGATTGGGCCTAGTGGGCCATATAGAT
*
46385422 GTGATTTGGGCCTAATGGGCCATAT-GAAT
1 GTGA-TTGGGCCTAGTGGGCCATATAG-AT
46385451 -TAGATTGGGCCTAGTGGGCCATA
1 GT-GATTGGGCCTAGTGGGCCATA
46385474 AGCATATATG
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
28 24 0.52
29 22 0.48
ACGTcount: A:0.21, C:0.15, G:0.34, T:0.30
Consensus pattern (28 bp):
GTGATTGGGCCTAGTGGGCCATATAGAT
Found at i:46385783 original size:43 final size:43
Alignment explanation
Indices: 46385717--46385803 Score: 129
Period size: 43 Copynumber: 2.0 Consensus size: 43
46385707 GCTAACGGGG
*
46385717 ATTTGCTAACGGGCAAAGGTAAGTAAAAACTCATAATAAAGGA
1 ATTTGCTAACGGGCAAAGGTAAGTAAAAACCCATAATAAAGGA
* * * *
46385760 ATTTTCTAACGGGCCAAGGTAAGTAAAAACCCGTACTAAAGGA
1 ATTTGCTAACGGGCAAAGGTAAGTAAAAACCCATAATAAAGGA
46385803 A
1 A
46385804 AATTATCGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.44, C:0.15, G:0.21, T:0.21
Consensus pattern (43 bp):
ATTTGCTAACGGGCAAAGGTAAGTAAAAACCCATAATAAAGGA
Found at i:46387497 original size:28 final size:29
Alignment explanation
Indices: 46387449--46387515 Score: 91
Period size: 28 Copynumber: 2.3 Consensus size: 29
46387439 AAGTCTACAT
* *
46387449 ACATGCATATGGTCCACTAGGCCC-AATC
1 ACATTCATATGGCCCACTAGGCCCAAATC
* *
46387477 TCATTCATATGGCCCATTAGGCCCAAATC
1 ACATTCATATGGCCCACTAGGCCCAAATC
46387506 ACATTCATAT
1 ACATTCATAT
46387516 TCATGCTTTC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
28 20 0.61
29 13 0.39
ACGTcount: A:0.30, C:0.30, G:0.13, T:0.27
Consensus pattern (29 bp):
ACATTCATATGGCCCACTAGGCCCAAATC
Found at i:46395105 original size:61 final size:61
Alignment explanation
Indices: 46394990--46395106 Score: 144
Period size: 61 Copynumber: 1.9 Consensus size: 61
46394980 ATGTGAAATC
* * *
46394990 AACATGGCCTGGACTTCCGTACACGGGCAAACCACACGCCCGTGTAGTTCTAGCAGGCTCT
1 AACACGGCCTGGACTTCCGTACACAGGCAAACCACACGCCCGTGTACTTCTAGCAGGCTCT
* * * * * * *
46395051 AACACGGCTTGGACTTCCTTACACAGGTAGACCACATGCCCGTGTCCTTTTAGCAG
1 AACACGGCCTGGACTTCCGTACACAGGCAAACCACACGCCCGTGTACTTCTAGCAG
46395107 AATCGAACAT
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
61 46 1.00
ACGTcount: A:0.23, C:0.32, G:0.23, T:0.22
Consensus pattern (61 bp):
AACACGGCCTGGACTTCCGTACACAGGCAAACCACACGCCCGTGTACTTCTAGCAGGCTCT
Found at i:46395377 original size:5 final size:5
Alignment explanation
Indices: 46395361--46395399 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
46395351 AGATAGATGG
* * *
46395361 AGAAA AAAAA AGGAA AGAAA AGAAA AGAAA GGAAA AGAA
1 AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAA
46395400 GGAAGAATGG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:46401945 original size:55 final size:56
Alignment explanation
Indices: 46401880--46401994 Score: 146
Period size: 55 Copynumber: 2.1 Consensus size: 56
46401870 AGCATGGCTG
* *
46401880 CCAGATACAGA-AAATGTGACAGAGTCACCAGATACAGATATTTTGTGGCAGT-GCCA
1 CCAGATACAGATAAATGTGACAGAGCCACCAGA-ACAGATAATTTGTGGCA-TAGCCA
* * *
46401936 CCAGA-ACAGATATATGTGGCAGGGCCACCAGAACAGATAATTTGTGGCATAGCCA
1 CCAGATACAGATAAATGTGACAGAGCCACCAGAACAGATAATTTGTGGCATAGCCA
46401991 CCAG
1 CCAG
46401995 GACGCTTCCT
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
54 1 0.02
55 29 0.56
56 22 0.42
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.19
Consensus pattern (56 bp):
CCAGATACAGATAAATGTGACAGAGCCACCAGAACAGATAATTTGTGGCATAGCCA
Found at i:46401957 original size:27 final size:27
Alignment explanation
Indices: 46401905--46401994 Score: 119
Period size: 27 Copynumber: 3.2 Consensus size: 27
46401895 GTGACAGAGT
46401905 CACCAGATACAGATATTTTGTGGCAGTGC
1 CACCAGA-ACAGATA-TTTGTGGCAGTGC
* *
46401934 CACCAGAACAGATATATGTGGCAGGGC
1 CACCAGAACAGATATTTGTGGCAGTGC
46401961 CACCAGAACAGATAATTTGTGGCA-TAGC
1 CACCAGAACAGAT-ATTTGTGGCAGT-GC
46401989 CACCAG
1 CACCAG
46401995 GACGCTTCCT
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
27 24 0.44
28 24 0.44
29 7 0.13
ACGTcount: A:0.32, C:0.23, G:0.24, T:0.20
Consensus pattern (27 bp):
CACCAGAACAGATATTTGTGGCAGTGC
Found at i:46402147 original size:28 final size:28
Alignment explanation
Indices: 46402100--46402166 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 28
46402090 AAATTAACCC
*
46402100 TAGGGGTATAAAGGTCATTTTGCATACA
1 TAGGGGTATAAAGGTAATTTTGCATACA
* *
46402128 TAGGGGTATTATGGTAATTTTGCATACA
1 TAGGGGTATAAAGGTAATTTTGCATACA
46402156 TAGGGGTATAA
1 TAGGGGTATAA
46402167 TAGTACATCT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.31, C:0.07, G:0.27, T:0.34
Consensus pattern (28 bp):
TAGGGGTATAAAGGTAATTTTGCATACA
Found at i:46403262 original size:5 final size:5
Alignment explanation
Indices: 46403243--46403281 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
46403233 ATATAGATGG
*
46403243 AGAAA A-AACA AGAAA AGAAA AGAAA AGAAA GGAAA AGAA
1 AGAAA AGAA-A AGAAA AGAAA AGAAA AGAAA AGAAA AGAA
46403282 GGAAGAATGG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
4 2 0.07
5 26 0.87
6 2 0.07
ACGTcount: A:0.77, C:0.03, G:0.21, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:46407142 original size:27 final size:27
Alignment explanation
Indices: 46407096--46407227 Score: 142
Period size: 27 Copynumber: 4.9 Consensus size: 27
46407086 TATGACCCTG
*
46407096 GATTGTAAAATTACCGAAATACTCCCA
1 GATTGTAAAATTACCGAAATACCCCCA
* * * *
46407123 GTTTGTAAATTTATCAAAATACCCCC-
1 GATTGTAAAATTACCGAAATACCCCCA
46407149 GAATTGTAAAATTACCGAAATACCCCCA
1 G-ATTGTAAAATTACCGAAATACCCCCA
*
46407177 -ATTGATAAAATTATCGAAATACCCCCA
1 GATTG-TAAAATTACCGAAATACCCCCA
* * * *
46407204 GTTTTTGAAATTACTGAAATACCC
1 GATTGTAAAATTACCGAAATACCC
46407228 TTGTAGCATA
Statistics
Matches: 86, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
26 5 0.06
27 79 0.92
28 2 0.02
ACGTcount: A:0.39, C:0.22, G:0.10, T:0.29
Consensus pattern (27 bp):
GATTGTAAAATTACCGAAATACCCCCA
Found at i:46407227 original size:54 final size:54
Alignment explanation
Indices: 46407097--46407202 Score: 160
Period size: 54 Copynumber: 2.0 Consensus size: 54
46407087 ATGACCCTGG
* * *
46407097 ATTGTAAAATTACCGAAATACTCCCAGTTTGTAAATTTATCAAAATACCCCCGA
1 ATTGTAAAATTACCGAAATACCCCCAGATTGTAAAATTATCAAAATACCCCCGA
*
46407151 ATTGTAAAATTACCGAAATACCCCCA-ATTGATAAAATTATCGAAATACCCCC
1 ATTGTAAAATTACCGAAATACCCCCAGATTG-TAAAATTATCAAAATACCCCC
46407203 AGTTTTTGAA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
53 3 0.06
54 44 0.94
ACGTcount: A:0.41, C:0.24, G:0.08, T:0.27
Consensus pattern (54 bp):
ATTGTAAAATTACCGAAATACCCCCAGATTGTAAAATTATCAAAATACCCCCGA
Found at i:46407254 original size:26 final size:27
Alignment explanation
Indices: 46407211--46407286 Score: 100
Period size: 26 Copynumber: 2.9 Consensus size: 27
46407201 CCAGTTTTTG
46407211 AAATTACTGAAATACCCTTGTAGCATA
1 AAATTACTGAAATACCCTTGTAGCATA
* * **
46407238 CAATTACCG-AATACCCTTGTAGTGTA
1 AAATTACTGAAATACCCTTGTAGCATA
*
46407264 AAATTACTGAAATACCCCTGTAG
1 AAATTACTGAAATACCCTTGTAG
46407287 GCCAAAATGA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
26 22 0.54
27 19 0.46
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.29
Consensus pattern (27 bp):
AAATTACTGAAATACCCTTGTAGCATA
Found at i:46407293 original size:27 final size:26
Alignment explanation
Indices: 46407211--46407294 Score: 91
Period size: 27 Copynumber: 3.2 Consensus size: 26
46407201 CCAGTTTTTG
46407211 AAATTACTGAAATACCCTTGTA-GCA
1 AAATTACTGAAATACCCTTGTAGGCA
* *
46407236 TACAATTACCG-AATACCCTTGTAGTGTA
1 -A-AATTACTGAAATACCCTTGTAG-GCA
*
46407264 AAATTACTGAAATACCCCTGTAGGCCA
1 AAATTACTGAAATACCCTTGTAGG-CA
46407291 AAAT
1 AAAT
46407295 GACTATTTTG
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
26 21 0.44
27 25 0.52
28 2 0.04
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.27
Consensus pattern (26 bp):
AAATTACTGAAATACCCTTGTAGGCA
Found at i:46407666 original size:22 final size:22
Alignment explanation
Indices: 46407638--46407697 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
46407628 GTAATCTGAT
46407638 TATGGCTCTGTGCCAACCTAAA
1 TATGGCTCTGTGCCAACCTAAA
* * * *
46407660 TATGGCTCTGTGCCATCTTGAG
1 TATGGCTCTGTGCCAACCTAAA
*
46407682 TATGGCTTTGTGCCAA
1 TATGGCTCTGTGCCAA
46407698 TCGTATTTAC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.33
Consensus pattern (22 bp):
TATGGCTCTGTGCCAACCTAAA
Found at i:46407774 original size:27 final size:27
Alignment explanation
Indices: 46407682--46407785 Score: 84
Period size: 27 Copynumber: 3.9 Consensus size: 27
46407672 CCATCTTGAG
* * *
46407682 TATGGCTTTGTGCCAATCGTATTTACC
1 TATGGCTATGTGCCGATCATATTTACC
* * * * *
46407709 TGTGGCTAAGTTCCTATCATATTTA-T
1 TATGGCTATGTGCCGATCATATTTACC
* * *
46407735 TGATGACTCTGTGTCGATCATATTTACC
1 T-ATGGCTATGTGCCGATCATATTTACC
*
46407763 TATGGCTATGTGCCGATTATATT
1 TATGGCTATGTGCCGATCATATT
46407786 ACTGTCGCTG
Statistics
Matches: 56, Mismatches: 19, Indels: 4
0.71 0.24 0.05
Matches are distributed among these distances:
26 1 0.02
27 54 0.96
28 1 0.02
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.42
Consensus pattern (27 bp):
TATGGCTATGTGCCGATCATATTTACC
Found at i:46407886 original size:22 final size:22
Alignment explanation
Indices: 46407839--46407901 Score: 56
Period size: 22 Copynumber: 2.9 Consensus size: 22
46407829 TAGCCTTGTG
* *
46407839 CCATCCTGATTATGGCTCTGTG
1 CCATCCTGATTATGGCTCTATA
*
46407861 CCATCCTGATTATGG-TTTATAA
1 CCATCCTGATTATGGCTCTAT-A
** *
46407883 CCATTTTGTTTATGGCTCT
1 CCATCCTGATTATGGCTCT
46407902 TATCCATTCT
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
21 3 0.09
22 27 0.84
23 2 0.06
ACGTcount: A:0.17, C:0.22, G:0.17, T:0.43
Consensus pattern (22 bp):
CCATCCTGATTATGGCTCTATA
Found at i:46414809 original size:20 final size:21
Alignment explanation
Indices: 46414777--46414834 Score: 66
Period size: 24 Copynumber: 2.7 Consensus size: 21
46414767 AGAGAAAAGA
46414777 AAGTAAGCT-TATAA-CTTAGT
1 AAGTAAG-TATATAAGCTTAGT
46414797 AAGTAAGTATATAAATAGCTTAGT
1 AAGTAAGTATAT--A-AGCTTAGT
46414821 AAGTAAGTATATAA
1 AAGTAAGTATATAA
46414835 ATAAAAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
19 1 0.03
20 10 0.30
21 1 0.03
22 2 0.06
23 1 0.03
24 18 0.55
ACGTcount: A:0.47, C:0.05, G:0.16, T:0.33
Consensus pattern (21 bp):
AAGTAAGTATATAAGCTTAGT
Found at i:46414818 original size:24 final size:24
Alignment explanation
Indices: 46414791--46414837 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
46414781 AAGCTTATAA
46414791 CTTAGTAAGTAAGTATATAAATAG
1 CTTAGTAAGTAAGTATATAAATAG
46414815 CTTAGTAAGTAAGTATATAAATA
1 CTTAGTAAGTAAGTATATAAATA
46414838 AAAAATAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.47, C:0.04, G:0.15, T:0.34
Consensus pattern (24 bp):
CTTAGTAAGTAAGTATATAAATAG
Found at i:46419236 original size:18 final size:18
Alignment explanation
Indices: 46419213--46419248 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
46419203 TTATTGCACA
46419213 TACATACTAATTAAATTG
1 TACATACTAATTAAATTG
46419231 TACATACTAATTAAATTG
1 TACATACTAATTAAATTG
46419249 AACTAATCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.11, G:0.06, T:0.39
Consensus pattern (18 bp):
TACATACTAATTAAATTG
Found at i:46443617 original size:46 final size:45
Alignment explanation
Indices: 46443562--46443736 Score: 203
Period size: 46 Copynumber: 3.8 Consensus size: 45
46443552 GGTTGAGCAT
46443562 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GAACGC
* * * *
46443608 CCGAGCTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAAC---GC
*
46443653 ATCCGAACTCGTCGAGTTGAGTCCGAGTTCACTTATGGATGTGAACGC
1 --CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GAACGC
* *
46443701 CCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
46443737 GCGGGTTACA
Statistics
Matches: 108, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 3 0.03
43 4 0.04
45 4 0.04
46 60 0.56
47 26 0.24
48 4 0.04
50 4 0.04
51 3 0.03
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.27
Consensus pattern (45 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAACGC
Found at i:46443717 original size:93 final size:93
Alignment explanation
Indices: 46443558--46443729 Score: 326
Period size: 93 Copynumber: 1.8 Consensus size: 93
46443548 GGATGGTTGA
*
46443558 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTCGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
46443623 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
46443651 GCATCCGAACTCGTCGAGTTGAGTCCGAGTTCACTTATGGATGTGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTCGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
46443716 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
46443730 CTTATGGGCG
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
93 77 1.00
ACGTcount: A:0.20, C:0.23, G:0.30, T:0.27
Consensus pattern (93 bp):
GCATCCGAACTCGTCGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:46446290 original size:16 final size:15
Alignment explanation
Indices: 46446269--46446307 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
46446259 CAAAAATAAG
46446269 AAATCCAAGACAAAAA
1 AAATCCAAGAC-AAAA
* *
46446285 AAATCCATGACAAAG
1 AAATCCAAGACAAAA
46446300 AAATCCAA
1 AAATCCAA
46446308 AATATATAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.62, C:0.21, G:0.08, T:0.10
Consensus pattern (15 bp):
AAATCCAAGACAAAA
Found at i:46446305 original size:15 final size:16
Alignment explanation
Indices: 46446266--46446307 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
46446256 AAACAAAAAT
46446266 AAGAAATCCAAGACAA
1 AAGAAATCCAAGACAA
* *
46446282 AAAAAATCCATGAC-A
1 AAGAAATCCAAGACAA
46446297 AAGAAATCCAA
1 AAGAAATCCAA
46446308 AATATATAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.62, C:0.19, G:0.10, T:0.10
Consensus pattern (16 bp):
AAGAAATCCAAGACAA
Found at i:46450386 original size:42 final size:43
Alignment explanation
Indices: 46450339--46450423 Score: 109
Period size: 42 Copynumber: 2.0 Consensus size: 43
46450329 GTCACAGGCA
*
46450339 TCACATCTACAATGAACTCAAACCACTCAAC-AGCCCGGATGC
1 TCACATCCACAATGAACTCAAACCACTCAACAAGCCCGGATGC
* * ** *
46450381 TCACATCCATAATGATCTCGGACCACTCAACAAGCTCGGATGC
1 TCACATCCACAATGAACTCAAACCACTCAACAAGCCCGGATGC
46450424 CGCATATCTC
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
42 26 0.72
43 10 0.28
ACGTcount: A:0.33, C:0.34, G:0.14, T:0.19
Consensus pattern (43 bp):
TCACATCCACAATGAACTCAAACCACTCAACAAGCCCGGATGC
Found at i:46463055 original size:27 final size:27
Alignment explanation
Indices: 46463025--46463116 Score: 96
Period size: 27 Copynumber: 3.4 Consensus size: 27
46463015 ATTACCAAAG
* * *
46463025 TACCTTCGATTTATAGAATTATTGTTT
1 TACCCTCGATTTACAAAATTATTGTTT
***
46463052 TACCCTCGATTTACAAAATTACCATTT
1 TACCCTCGATTTACAAAATTATTGTTT
**
46463079 TACTTTC-AGTTTACAAAATTATTGTTT
1 TACCCTCGA-TTTACAAAATTATTGTTT
46463106 TACCCTCGATT
1 TACCCTCGATT
46463117 GTAAAATTAC
Statistics
Matches: 50, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
26 1 0.02
27 48 0.96
28 1 0.02
ACGTcount: A:0.28, C:0.18, G:0.08, T:0.46
Consensus pattern (27 bp):
TACCCTCGATTTACAAAATTATTGTTT
Found at i:46463178 original size:27 final size:27
Alignment explanation
Indices: 46463115--46463298 Score: 176
Period size: 27 Copynumber: 6.8 Consensus size: 27
46463105 TTACCCTCGA
**
46463115 TTGTAAAATTACTGAAATACCCCT-GT
1 TTGTAAAATTACCAAAATACCCCTAGT
** *
46463141 AGGATAGAATTACCAAAATACCCCTAGT
1 TTG-TAAAATTACCAAAATACCCCTAGT
*
46463169 TTGTAAAATTACCAAAATACTCCTAGT
1 TTGTAAAATTACCAAAATACCCCTAGT
* *
46463196 TTGTAAAATTACCAAAATACCACTGGT
1 TTGTAAAATTACCAAAATACCCCTAGT
* *** *
46463223 TTGTGAAATTAATGAAATACCCTCAAG-
1 TTGTAAAATTACCAAAATACCC-CTAGT
*
46463250 TTGTAAAATTACCAAAATACCCCTAAT
1 TTGTAAAATTACCAAAATACCCCTAGT
**
46463277 TTACAAAATTA-CAGAAATACCC
1 TTGTAAAATTACCA-AAATACCC
46463299 TTGACTTTCT
Statistics
Matches: 126, Mismatches: 27, Indels: 9
0.78 0.17 0.06
Matches are distributed among these distances:
26 5 0.04
27 116 0.92
28 5 0.04
ACGTcount: A:0.42, C:0.20, G:0.10, T:0.29
Consensus pattern (27 bp):
TTGTAAAATTACCAAAATACCCCTAGT
Found at i:46463233 original size:81 final size:81
Alignment explanation
Indices: 46463148--46463297 Score: 196
Period size: 81 Copynumber: 1.9 Consensus size: 81
46463138 TGTAGGATAG
* * * * **
46463148 AATTACCAAAATACCC-CTAGTTTGTAAAATTACCAAAATACTCCTAGTTTGTAAAATTACCA-A
1 AATTAACAAAATACCCTCAAG-TTGTAAAATTACCAAAATACCCCTAATTTACAAAATTA-CAGA
46463211 AATACCACTGGTTTGTGA
64 AATACCACTGGTTTGTGA
**
46463229 AATTAATGAAATACCCTCAAGTTGTAAAATTACCAAAATACCCCTAATTTACAAAATTACAGAAA
1 AATTAACAAAATACCCTCAAGTTGTAAAATTACCAAAATACCCCTAATTTACAAAATTACAGAAA
46463294 TACC
66 TACC
46463298 CTTGACTTTC
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
80 2 0.03
81 54 0.92
82 3 0.05
ACGTcount: A:0.43, C:0.20, G:0.08, T:0.29
Consensus pattern (81 bp):
AATTAACAAAATACCCTCAAGTTGTAAAATTACCAAAATACCCCTAATTTACAAAATTACAGAAA
TACCACTGGTTTGTGA
Found at i:46463349 original size:27 final size:27
Alignment explanation
Indices: 46463276--46463361 Score: 95
Period size: 27 Copynumber: 3.1 Consensus size: 27
46463266 ATACCCCTAA
* *
46463276 TTTACAAAATTACAGAAATACCCTTGAC
1 TTTACAAAATTACTGAAATACCCTTG-G
*
46463304 TTT-CTAAAAATTA-TAGAAATACCATTGG
1 TTTAC--AAAATTACT-GAAATACCCTTGG
46463332 TTTACAAAATTACTGAAATACCCTTGG
1 TTTACAAAATTACTGAAATACCCTTGG
46463359 TTT
1 TTT
46463362 GTAGATTTAC
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
27 23 0.47
28 7 0.14
29 19 0.39
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.35
Consensus pattern (27 bp):
TTTACAAAATTACTGAAATACCCTTGG
Found at i:46463479 original size:27 final size:27
Alignment explanation
Indices: 46463415--46463479 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
46463405 ACCCTTAATA
*
46463415 GGTAAAAAGACCGTAAAGCCCCTATAG
1 GGTAAAATGACCGTAAAGCCCCTATAG
* * * *
46463442 GGTGAAGTGACCGTAATA-CCCCTGTAT
1 GGTAAAATGACCGTAA-AGCCCCTATAG
46463469 GGTAAAATGAC
1 GGTAAAATGAC
46463480 GAATATGCCC
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
27 29 0.97
28 1 0.03
ACGTcount: A:0.35, C:0.20, G:0.25, T:0.20
Consensus pattern (27 bp):
GGTAAAATGACCGTAAAGCCCCTATAG
Found at i:46464249 original size:16 final size:16
Alignment explanation
Indices: 46464228--46464258 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
46464218 CAACTATGGG
*
46464228 CATGACATTTTGCATA
1 CATGACATGTTGCATA
46464244 CATGACATGTTGCAT
1 CATGACATGTTGCAT
46464259 GGGTTGGGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.35
Consensus pattern (16 bp):
CATGACATGTTGCATA
Found at i:46464365 original size:24 final size:25
Alignment explanation
Indices: 46464289--46464358 Score: 104
Period size: 25 Copynumber: 2.8 Consensus size: 25
46464279 AGGAAGTGCT
* * * *
46464289 AAAACGGCTATGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTATCA
46464314 AAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTATCA
46464339 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
46464359 ATTAAAAGAG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.24
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTATCA
Found at i:46464371 original size:24 final size:24
Alignment explanation
Indices: 46464294--46464385 Score: 80
Period size: 25 Copynumber: 3.7 Consensus size: 24
46464284 GTGCTAAAAC
* *
46464294 GGCTATGCCCCAGTTTACCGAAAAG-
1 GGCTTTGCCCCAG-TTATC-AAAAGA
46464319 GGCTTTGCCCCAGTTTATCAAAA-A
1 GGCTTTGCCCCAG-TTATCAAAAGA
*
46464343 GGGCTTTGCCCCAGTTATTAAAAGA
1 -GGCTTTGCCCCAGTTATCAAAAGA
**
46464368 GGCTAGGCCTCCAGTTAT
1 GGCTTTGCC-CCAGTTAT
46464386 ATGATAAAGA
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
24 19 0.33
25 39 0.67
ACGTcount: A:0.26, C:0.25, G:0.23, T:0.26
Consensus pattern (24 bp):
GGCTTTGCCCCAGTTATCAAAAGA
Found at i:46484203 original size:24 final size:24
Alignment explanation
Indices: 46484176--46484221 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
46484166 TCCTAAATCC
*
46484176 CTCCATGATTTCCTCCCTAATCTT
1 CTCCATGATTTCCTCCATAATCTT
* *
46484200 CTCCTTGATTTTCTCCATAATC
1 CTCCATGATTTCCTCCATAATC
46484222 CATTCCTTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.17, C:0.35, G:0.04, T:0.43
Consensus pattern (24 bp):
CTCCATGATTTCCTCCATAATCTT
Found at i:46514907 original size:27 final size:27
Alignment explanation
Indices: 46514877--46515054 Score: 137
Period size: 27 Copynumber: 6.6 Consensus size: 27
46514867 ATATTGAGCC
* *
46514877 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * * *
46514904 CGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
* *
46514931 CGCACACTTAGTGCTACATAGTCAAACC
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
46514959 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
46514986 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
46515013 CGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCTACATAA-TCA-ACT
46515040 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
46515055 GTACAATTTA
Statistics
Matches: 121, Mismatches: 25, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
26 2 0.02
27 96 0.79
28 23 0.19
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:46514989 original size:55 final size:54
Alignment explanation
Indices: 46514877--46515054 Score: 164
Period size: 54 Copynumber: 3.3 Consensus size: 54
46514867 ATATTGAGCC
* * * * *
46514877 CGCACACTCAGTGCTATATAATCAACTCGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACCCGCACACTTAGTGCCACATAATCAAAT
* * ** *
46514931 CGCACACTTAGTGCTACATAGTCAAACCCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATC-AACCCGCACACTTAGTGCCACATAATCAAAT
* *** *
46514986 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCTA-CATAATCAACCCGCACACTTAGTGCCACATAA-TCA-AAT
46515040 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
46515055 GTACAATTTA
Statistics
Matches: 100, Mismatches: 19, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
53 1 0.01
54 55 0.55
55 44 0.44
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACCCGCACACTTAGTGCCACATAATCAAAT
Found at i:46520438 original size:93 final size:93
Alignment explanation
Indices: 46520324--46520494 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
46520314 GCCCCTAAGT
*
46520324 GAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGCTC-GGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
46520388 ACGAGTTCGGATGCCTAGTTACATCTCAC
65 ACGAGTTCGGATGCCTAGTTACATCTCAC
* * *
46520417 GAACTCGGACTCAAGTCAACGAGTTCGGACATTCGCATCCATAGGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
46520482 CGAGTTCGGATGC
66 CGAGTTCGGATGC
46520495 TCAACCATCC
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
92 2 0.03
93 71 0.97
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:46520489 original size:46 final size:45
Alignment explanation
Indices: 46520321--46520491 Score: 181
Period size: 46 Copynumber: 3.7 Consensus size: 45
46520311 CCCGCCCCTA
* *
46520321 AGTGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTC-GGACATTCGCATCCAT
*
46520366 AAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-C-T
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCAT
* *
46520414 CA-CGAACTCGGACTCAAGTCAACGAGTTCGGACATTCGCATCCAT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT
46520459 AGGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 A-GTGAACTCGGACTCAACTCAACGAGTTCGGA
46520492 TGCTCAACCA
Statistics
Matches: 105, Mismatches: 9, Indels: 22
0.77 0.07 0.16
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 3 0.03
45 3 0.03
46 56 0.53
47 28 0.27
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.22, T:0.21
Consensus pattern (45 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT
Found at i:46528000 original size:29 final size:30
Alignment explanation
Indices: 46527968--46528026 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
46527958 ATTTAATACG
46527968 AACTTTGGAAAAATTACACTTTT-CCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * * *
46527997 AACTTTTGCATAATTACGCTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
46528027 GGCTCAGAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 19 0.76
30 6 0.24
ACGTcount: A:0.29, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:46534535 original size:46 final size:45
Alignment explanation
Indices: 46534468--46534637 Score: 195
Period size: 46 Copynumber: 3.7 Consensus size: 45
46534458 AACCCGCCCC
*
46534468 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT-CA
*
46534514 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACATC-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTCGCATCA
* * * *
46534562 TCA-CGAACTC-GACTCAACTCAACGAGTTCGGACATTCGCATCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATCA
*
46534605 TAGGTGAACTCGGACTCAACTCAACGAGTTCGG
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG
46534638 ATGCTCAACC
Statistics
Matches: 105, Mismatches: 10, Indels: 19
0.78 0.07 0.14
Matches are distributed among these distances:
41 2 0.02
42 4 0.04
43 2 0.02
44 6 0.06
45 21 0.20
46 53 0.50
47 6 0.06
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (45 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATCA
Found at i:46534636 original size:91 final size:93
Alignment explanation
Indices: 46534473--46534641 Score: 288
Period size: 91 Copynumber: 1.8 Consensus size: 93
46534463 GCCCCTAAGT
* *
46534473 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
46534538 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* *
46534566 GAACTC-GACTCAACTCAACGAGTTCGGACATTCGCAT-CATAGGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
46534629 CGAGTTCGGATGC
66 CGAGTTCGGATGC
46534642 TCAACCATCC
Statistics
Matches: 72, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
91 38 0.53
92 28 0.39
93 6 0.08
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:46535091 original size:30 final size:30
Alignment explanation
Indices: 46535057--46535116 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
46535047 ATTTAATACG
46535057 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
46535087 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
46535117 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:46541658 original size:46 final size:46
Alignment explanation
Indices: 46541591--46541716 Score: 216
Period size: 46 Copynumber: 2.7 Consensus size: 46
46541581 AATCCGCCCC
* * *
46541591 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
46541637 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
*
46541683 TAGGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
46541717 TGCTCAACCA
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 76 1.00
ACGTcount: A:0.29, C:0.28, G:0.23, T:0.21
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:46542169 original size:30 final size:31
Alignment explanation
Indices: 46542135--46542192 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
46542125 ATTTAATATG
46542135 AACTTTGGAAAAATTACACTTTT-TCCCCTA
1 AACTTTGGAAAAATTACACTTTTGTCCCCTA
* * *
46542165 AACTTTTGCATAATTACACTTTTGTCCC
1 AACTTTGGAAAAATTACACTTTTGTCCC
46542193 TAGGCTCGGG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 20 0.83
31 4 0.17
ACGTcount: A:0.29, C:0.24, G:0.07, T:0.40
Consensus pattern (31 bp):
AACTTTGGAAAAATTACACTTTTGTCCCCTA
Found at i:46548790 original size:93 final size:93
Alignment explanation
Indices: 46548683--46548853 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
46548673 GCCCCTAAGT
*
46548683 GAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGCTC-GGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
46548747 ACGAGTTCGGATGCCTAGTTACATCTCAC
65 ACGAGTTCGGATGCCTAGTTACATCTCAC
* * *
46548776 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCTATAGGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
46548841 CGAGTTCGGATGC
66 CGAGTTCGGATGC
46548854 TCAACCATCC
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
92 2 0.03
93 71 0.97
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:46548848 original size:46 final size:45
Alignment explanation
Indices: 46548680--46548850 Score: 188
Period size: 46 Copynumber: 3.7 Consensus size: 45
46548670 CCCGCCCCTA
* * *
46548680 AGTGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTC-GGACATTCGCATCTAT
* *
46548725 AAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACATCT-C
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCTAT
*
46548774 A-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCTAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCTAT
46548818 AGGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 A-GTGAACTCGGACTCAACTCAACGAGTTCGGA
46548851 TGCTCAACCA
Statistics
Matches: 106, Mismatches: 9, Indels: 20
0.79 0.07 0.15
Matches are distributed among these distances:
42 2 0.02
43 6 0.06
44 2 0.02
45 2 0.02
46 57 0.54
47 29 0.27
48 1 0.01
49 1 0.01
50 4 0.04
51 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.22, T:0.22
Consensus pattern (45 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCTAT
Found at i:46549308 original size:30 final size:30
Alignment explanation
Indices: 46549274--46549333 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
46549264 ATTTAATACG
*
46549274 AACTTTGGAAAAATTACACTTTTTCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * * *
46549304 AACTTTTGCATAATTACGCTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
46549334 GGCTCGGGAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.28, C:0.25, G:0.08, T:0.38
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:46551724 original size:29 final size:29
Alignment explanation
Indices: 46551688--46551749 Score: 106
Period size: 29 Copynumber: 2.1 Consensus size: 29
46551678 AAAATTCAAA
* *
46551688 AAATAGCAAACGATGCCAAGCTGAAAACT
1 AAATAGCAAACAATGCCAAGCCGAAAACT
46551717 AAATAGCAAACAATGCCAAGCCGAAAACT
1 AAATAGCAAACAATGCCAAGCCGAAAACT
46551746 AAAT
1 AAAT
46551750 TCCTTTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.52, C:0.21, G:0.15, T:0.13
Consensus pattern (29 bp):
AAATAGCAAACAATGCCAAGCCGAAAACT
Found at i:46556244 original size:21 final size:21
Alignment explanation
Indices: 46556196--46556244 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
46556186 GTGTTATTAC
46556196 AGTT-ATTTTAAAGTTTCGAT
1 AGTTAATTTTAAAGTTTCGAT
***
46556216 AAAAAATTTTAAAGTTTCGAT
1 AGTTAATTTTAAAGTTTCGAT
46556237 AGTTAATT
1 AGTTAATT
46556245 AATTGAAAAG
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.39, C:0.04, G:0.12, T:0.45
Consensus pattern (21 bp):
AGTTAATTTTAAAGTTTCGAT
Found at i:46557557 original size:18 final size:17
Alignment explanation
Indices: 46557531--46557564 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
46557521 AAATATAATT
46557531 ATTAGTTTTATTATTATG
1 ATTAGTTTTATT-TTATG
*
46557549 ATTATTTTTATTTTAT
1 ATTAGTTTTATTTTAT
46557565 TATTCTCTCC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (17 bp):
ATTAGTTTTATTTTATG
Found at i:46562688 original size:64 final size:64
Alignment explanation
Indices: 46562608--46562791 Score: 189
Period size: 67 Copynumber: 2.8 Consensus size: 64
46562598 AGACATTATG
* * *
46562608 ATGTAGCTAGGTCGCATGGGTGATACTATATGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTATATGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * *
46562672 ATGTAGCTAGGTCGCATGCGTGGTTCTAGGTGAAAG-ACACCATGTAGACAAGAGAGCTACGAGT
1 ATGTAGCTAGGTCGCATGGGTGGTACTA--T--ATGTACACCATGTAGACAAGAGAGCTACGAGA
46562736 TAA
62 TAA
* *
46562739 ACTG--GCTAGGTCACATGGGTGGTACTA-AGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGGTACTATA-TGTACACCATGTAG-ACAAGAGAGC
46562792 CGAACTATAT
Statistics
Matches: 100, Mismatches: 12, Indels: 17
0.78 0.09 0.13
Matches are distributed among these distances:
61 1 0.01
62 2 0.02
63 18 0.18
64 25 0.25
66 21 0.21
67 29 0.29
68 4 0.04
ACGTcount: A:0.30, C:0.17, G:0.29, T:0.24
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGGTACTATATGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:46566612 original size:40 final size:40
Alignment explanation
Indices: 46566568--46566835 Score: 473
Period size: 40 Copynumber: 6.7 Consensus size: 40
46566558 GCAAACACAT
* *
46566568 TTGCCTTCGGGTCTTAGCCCGAACATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
46566608 TTGCCTTCGGGTCTTAGCCCGGATATATCATCTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
* *
46566648 TTGCCTTCGGGTTTTAGCCCGGATATATCATCTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
46566688 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
46566728 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
46566768 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
46566808 TTGCCTTCGGGTCATAGCCCGGATATAT
1 TTGCCTTCGGGTCTTAGCCCGGATATAT
46566836 TCCAATGCTC
Statistics
Matches: 219, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 219 1.00
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.31
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
Found at i:46575191 original size:40 final size:40
Alignment explanation
Indices: 46575147--46575414 Score: 473
Period size: 40 Copynumber: 6.7 Consensus size: 40
46575137 GCAAACACAT
* *
46575147 TTGCCTTCGGGTCTTAGCCCGAACATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
46575187 TTGCCTTCGGGTCTTAGCCCGGATATATCATCTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
* *
46575227 TTGCCTTCGGGTTTTAGCCCGGATATATCATCTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
46575267 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
46575307 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
46575347 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
46575387 TTGCCTTCGGGTCATAGCCCGGATATAT
1 TTGCCTTCGGGTCTTAGCCCGGATATAT
46575415 TCCAATGCTC
Statistics
Matches: 219, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 219 1.00
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.31
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
Found at i:46579320 original size:64 final size:63
Alignment explanation
Indices: 46579215--46579422 Score: 179
Period size: 67 Copynumber: 3.2 Consensus size: 63
46579205 GGTGCTGTGT
*
46579215 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATG
1 ACAAGAGAGCTACAAG--A-TA-AATGTAGCTAGGTCGCATGGGTGATACTA-GTGTACACCATG
46579280 TAG
61 TAG
** * * * * * * *
46579283 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAAGACACCAAGT
1 ACAAGAGAGCTACAAGATAAATGTAGCTAGGTCGCATGGGTGATACTA-GTG---TACACCATGT
46579348 AG
62 AG
* *
46579350 ACAAGAGAGCTACAAGATAAACTG--GCTAGGTCACATGGGTGATACTGAGTGTTCACCATGT-G
1 ACAAGAGAGCTACAAGATAAA-TGTAGCTAGGTCGCATGGGTGATACT-AGTGTACACCATGTAG
46579412 TACAAGAGAGC
1 -ACAAGAGAGC
46579423 CGAACTATAT
Statistics
Matches: 113, Mismatches: 21, Indels: 17
0.75 0.14 0.11
Matches are distributed among these distances:
62 1 0.01
63 17 0.15
64 27 0.24
65 2 0.02
66 21 0.19
67 29 0.26
68 16 0.14
ACGTcount: A:0.33, C:0.17, G:0.28, T:0.22
Consensus pattern (63 bp):
ACAAGAGAGCTACAAGATAAATGTAGCTAGGTCGCATGGGTGATACTAGTGTACACCATGTAG
Found at i:46600646 original size:9 final size:9
Alignment explanation
Indices: 46600632--46600663 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
46600622 TCTTTTATTT
46600632 TTATTTTTA
1 TTATTTTTA
46600641 TTA--TTTA
1 TTATTTTTA
46600648 TTATTTTTA
1 TTATTTTTA
46600657 TTATTTT
1 TTATTTT
46600664 ATCTATTTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
7 7 0.33
9 14 0.67
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (9 bp):
TTATTTTTA
Found at i:46600653 original size:16 final size:15
Alignment explanation
Indices: 46600626--46600663 Score: 67
Period size: 16 Copynumber: 2.5 Consensus size: 15
46600616 ACTCAATCTT
46600626 TTATTTTTATTTTTA
1 TTATTTTTATTTTTA
46600641 TTATTTATTATTTTTA
1 TTATTT-TTATTTTTA
46600657 TTATTTT
1 TTATTTT
46600664 ATCTATTTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (15 bp):
TTATTTTTATTTTTA
Found at i:46600672 original size:25 final size:22
Alignment explanation
Indices: 46600621--46600670 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
46600611 AGGCAACTCA
* *
46600621 ATCTTTTATTTTTATTTTTATT
1 ATCTATTATTTTTATTATTATT
*
46600643 ATTTATTATTTTTATTATT-TT
1 ATCTATTATTTTTATTATTATT
46600664 ATCTATT
1 ATCTATT
46600671 TAGATAAATG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 8 0.33
22 16 0.67
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (22 bp):
ATCTATTATTTTTATTATTATT
Found at i:46602120 original size:40 final size:40
Alignment explanation
Indices: 46602072--46602300 Score: 368
Period size: 40 Copynumber: 5.7 Consensus size: 40
46602062 GCTACTTGCT
46602072 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* *
46602112 CAATTGCCTTCGGGACTTAGCCCGGTTCTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* * *
46602152 CAATTGCCTTCGGGACTTGGCCCGGTTATAGTAACTCGTA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* **
46602192 CAAATGCCTTCGGGGCTTAGCCCGAATATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* *
46602232 CAAATGCCTTTGGGACTTAGCCCGGATATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
46602272 CAAATGCCTTCGGGACTTAGCCCGGTTAT
1 CAAATGCCTTCGGGACTTAGCCCGGTTAT
46602301 CAATCCGAAT
Statistics
Matches: 173, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 173 1.00
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Done.