Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167915.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_18, whole genome shotgun sequence
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: 20765110
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 90000 characters in sequence are not A, C, G, or T
File 11 of 117
Found at i:3149911 original size:2 final size:2
Alignment explanation
Indices: 3149900--3149932 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3149890 AAAGGGGATT
3149900 GA GA -A GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3149933 TGGTGATGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3150374 original size:2 final size:2
Alignment explanation
Indices: 3150367--3150394 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3150357 TCTTCTTTCC
3150367 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3150395 TGAGCAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3160047 original size:14 final size:15
Alignment explanation
Indices: 3160023--3160051 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3160013 GATTATAATC
3160023 TTATCATTTGTATAT
1 TTATCATTTGTATAT
3160038 TTAT-ATTTGTATAT
1 TTATCATTTGTATAT
3160052 CTAAAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.03, G:0.07, T:0.62
Consensus pattern (15 bp):
TTATCATTTGTATAT
Found at i:3160065 original size:22 final size:22
Alignment explanation
Indices: 3160040--3160084 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
3160030 TTGTATATTT
3160040 ATATTTGTATATC-TAAAATTAA
1 ATATTTGTAT-TCTTAAAATTAA
3160062 ATATTTGTATTCTTAAAATTAA
1 ATATTTGTATTCTTAAAATTAA
3160084 A
1 A
3160085 GATAAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 2 0.09
22 20 0.91
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.47
Consensus pattern (22 bp):
ATATTTGTATTCTTAAAATTAA
Found at i:3163893 original size:180 final size:181
Alignment explanation
Indices: 3163532--3163900 Score: 492
Period size: 180 Copynumber: 2.0 Consensus size: 181
3163522 AACAACAAAT
* * * *
3163532 AACCTGATCATTGTCTTCTTTAATCATCACATTATCATCAGCTTCAATGTATGTGTTTTTAGCTG
1 AACCTGATCATTGTCTTCTTTAATCATCACATTATCATCAACTTCAATGTATGAGTATTTAGATG
* * * * *
3163597 ACCTAACATCAATATCAGGGGCAGTTCCACTACTTCTTCTGAAGTTTTTCTCTCTGAACAACTAG
66 ACCAAACATCAATATCAGAGACAGTTCCACTA-TTCTTCTGAAGCTTTTCTCTCTGAACAACAAG
* *
3163662 TAACCTGATCAACACTTTCAGAAAGCTTGCTTCCCATGTCATCTGCAATATC
130 TAACCTGATCAACACTTTCAGAAAGCTTGCTTCCCATATCACCTGCAATATC
* * * ** *
3163714 AATCTGATCATTGTCTTCTTTAATCATCATATTGTTGTCAATTTCAATGTATGAGTATTTAGATG
1 AACCTGATCATTGTCTTCTTTAATCATCACATTATCATCAACTTCAATGTATGAGTATTTAGATG
*
3163779 ACCAAACATCAATATTCA-AGACAGTTTCCACT-TT-TTCTGAGGCTTTTCTCTCTGAACAACAA
66 ACCAAACATCAATA-TCAGAGACAG-TTCCACTATTCTTCTGAAGCTTTTCTCTCTGAACAACAA
* * * *
3163841 GTAACCTGATCAACACTTTCAGAAGGCTTTCTTCTCATATCACCTTCAATATC
129 GTAACCTGATCAACACTTTCAGAAAGCTTGCTTCCCATATCACCTGCAATATC
3163894 AACCTGA
1 AACCTGA
3163901 AGGTGATTAC
Statistics
Matches: 162, Mismatches: 23, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
180 78 0.48
181 2 0.01
182 72 0.44
183 10 0.06
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.36
Consensus pattern (181 bp):
AACCTGATCATTGTCTTCTTTAATCATCACATTATCATCAACTTCAATGTATGAGTATTTAGATG
ACCAAACATCAATATCAGAGACAGTTCCACTATTCTTCTGAAGCTTTTCTCTCTGAACAACAAGT
AACCTGATCAACACTTTCAGAAAGCTTGCTTCCCATATCACCTGCAATATC
Found at i:3183181 original size:13 final size:13
Alignment explanation
Indices: 3183163--3183188 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3183153 AGCTTTCGAT
3183163 CAGGATTGTTGCA
1 CAGGATTGTTGCA
3183176 CAGGATTGTTGCA
1 CAGGATTGTTGCA
3183189 TGGCAATGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.15, G:0.31, T:0.31
Consensus pattern (13 bp):
CAGGATTGTTGCA
Found at i:3187691 original size:20 final size:21
Alignment explanation
Indices: 3187636--3187696 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
3187626 ATTAATACAT
* *
3187636 TTTTG-TAATATTTATATTAA
1 TTTTGATAATTTTTATATAAA
*
3187656 TATTGATAATTTTT-TATAAAA
1 TTTTGATAATTTTTATAT-AAA
3187677 TTTTGATAATTTTTAATATA
1 TTTTGATAATTTTT-ATATA
3187697 TATGAATATT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
20 7 0.21
21 22 0.67
22 1 0.03
23 3 0.09
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (21 bp):
TTTTGATAATTTTTATATAAA
Found at i:3187764 original size:21 final size:21
Alignment explanation
Indices: 3187740--3187817 Score: 54
Period size: 21 Copynumber: 3.8 Consensus size: 21
3187730 TTTGATATTA
*
3187740 TTTTGATAATTTTTTATATAG
1 TTTTGATAATCTTTTATATAG
* *
3187761 TTTT-AGTAATCTTCTAT-TAA
1 TTTTGA-TAATCTTTTATATAG
* * *
3187781 TTTTGAT-CTTTTTTGCTATAG
1 TTTTGATAATCTTTT-ATATAG
*
3187802 TTTTGGTAATCTTTTA
1 TTTTGATAATCTTTTA
3187818 AAATTTATGT
Statistics
Matches: 40, Mismatches: 12, Indels: 10
0.65 0.19 0.16
Matches are distributed among these distances:
19 4 0.10
20 9 0.22
21 22 0.55
22 5 0.12
ACGTcount: A:0.23, C:0.06, G:0.10, T:0.60
Consensus pattern (21 bp):
TTTTGATAATCTTTTATATAG
Found at i:3187794 original size:41 final size:40
Alignment explanation
Indices: 3187735--3187814 Score: 106
Period size: 41 Copynumber: 2.0 Consensus size: 40
3187725 AAACTTTTGA
*
3187735 TATTATTTTGATAATTTTTTATATAGTTTTAGTAATCTTC
1 TATTATTTTGATAATTTTTGATATAGTTTTAGTAATCTTC
** * *
3187775 TATTAATTTTGATCTTTTTTGCTATAGTTTTGGTAATCTT
1 TATT-ATTTTGATAATTTTTGATATAGTTTTAGTAATCTT
3187815 TTAAAATTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
40 4 0.12
41 30 0.88
ACGTcount: A:0.24, C:0.06, G:0.10, T:0.60
Consensus pattern (40 bp):
TATTATTTTGATAATTTTTGATATAGTTTTAGTAATCTTC
Found at i:3194892 original size:2 final size:2
Alignment explanation
Indices: 3194887--3194922 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3194877 AGAGAGTTTC
3194887 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3194923 TTGAGGATGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3205756 original size:17 final size:18
Alignment explanation
Indices: 3205724--3205761 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
3205714 GGGTTGCTTA
*
3205724 TTTTTTCTTTTATTTT-T
1 TTTTTTCTTGTATTTTGT
*
3205741 TTTTTTCTTGTGTTTTGT
1 TTTTTTCTTGTATTTTGT
3205759 TTT
1 TTT
3205762 GATTATTGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.03, C:0.05, G:0.08, T:0.84
Consensus pattern (18 bp):
TTTTTTCTTGTATTTTGT
Found at i:3213596 original size:3 final size:3
Alignment explanation
Indices: 3213588--3213634 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
3213578 CAAAATTAAC
*
3213588 ATT ATT ATT -TT ATT TTT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3213635 CTCCAACACT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
ATT
Found at i:3214240 original size:39 final size:38
Alignment explanation
Indices: 3214185--3214504 Score: 275
Period size: 39 Copynumber: 8.3 Consensus size: 38
3214175 GAGGGCAATG
**
3214185 AACTTTAAATTC-AAAAGCCCATTTAACCAAAGGCAATG
1 AACTTTAAATTCAAAAAGCCC-TTTAACCAAAGGCAACA
* * * * * * **
3214223 AATTTTAGATTCAAAAAGCTCATCTCACCAGAGATAACA
1 AACTTTAAATTCAAAAAGC-CCTTTAACCAAAGGCAACA
* * * *
3214262 AATTTTAAATCCAAAAAGCTCCTTCAGCCAAAGGCAACA
1 AACTTTAAATTCAAAAAGC-CCTTTAACCAAAGGCAACA
* * *
3214301 AATTTTAAATTCAAAAGGCCCCTCTT-ACTAAAGGCAACA
1 AACTTTAAATTCAAAAAG-CCCT-TTAACCAAAGGCAACA
* * * *
3214340 AACTTTAAATTCAAAAGGCTCCTCTCACCATAGGCAACA
1 AACTTTAAATTCAAAAAGC-CCTTTAACCAAAGGCAACA
* * *
3214379 AACTTTAAATCCAAAAAGCTTCTTTAAACAAAGGCAACA
1 AACTTTAAATTCAAAAAGC-CCTTTAACCAAAGGCAACA
* *
3214418 AACTTTAAATCCAAAAAGTCCTTTAACCAAAGGCAACA
1 AACTTTAAATTCAAAAAGCCCTTTAACCAAAGGCAACA
* * * * *
3214456 TACTTTAAATTCTAAAGGCTCCTCTAACCAAAGGCAACG
1 AACTTTAAATTCAAAAAGC-CCTTTAACCAAAGGCAACA
3214495 AACTTTAAAT
1 AACTTTAAAT
3214505 GGCTCATTTA
Statistics
Matches: 228, Mismatches: 47, Indels: 13
0.79 0.16 0.05
Matches are distributed among these distances:
38 43 0.19
39 182 0.80
40 3 0.01
ACGTcount: A:0.43, C:0.23, G:0.10, T:0.24
Consensus pattern (38 bp):
AACTTTAAATTCAAAAAGCCCTTTAACCAAAGGCAACA
Found at i:3214279 original size:78 final size:78
Alignment explanation
Indices: 3214144--3214577 Score: 293
Period size: 78 Copynumber: 5.7 Consensus size: 78
3214134 GAAGCTATAA
* * * ** *
3214144 AAATTTTAAATTTAAAAAGCTTATCTCACCAGAGGGCAATGAACTTTAAATTCAAAAGC-CCATT
1 AAATTTTAAATTCAAAAAGCTCATCTCACCAGAGGACAACAAACTTTAAATCCAAAAGCTCC-TT
* *
3214208 TAACCAAAGGCAAT
65 CAACCAAAGGCAAC
* * * *
3214222 GAATTTTAGATTCAAAAAGCTCATCTCACCAGA-GATAACAAATTTTAAATCCAAAAAGCTCCTT
1 AAATTTTAAATTCAAAAAGCTCATCTCACCAGAGGACAACAAACTTTAAATCC-AAAAGCTCCTT
*
3214286 CAGCCAAAGGCAAC
65 CAACCAAAGGCAAC
* * * * * * *
3214300 AAATTTTAAATTCAAAAGGCCCCTCTTACTAAAGG-CAACAAACTTTAAATTCAAAAGGCTCCTC
1 AAATTTTAAATTCAAAAAGCTCATCTCACCAGAGGACAACAAACTTTAAATCCAAAA-GCTCCT-
*
3214364 TC-ACCATAGGCAAC
64 TCAACCAAAGGCAAC
* * * * * *
3214378 AAACTTTAAATCCAAAAAGCTTC-TTTAAACAAAGG-CAACAAACTTTAAATCCAAAAAG-TCCT
1 AAATTTTAAATTCAAAAAGC-TCATCTCACCAGAGGACAACAAACTTTAAATCC-AAAAGCTCCT
*
3214440 TTAACCAAAGGCAAC
64 TCAACCAAAGGCAAC
* * * * * * * * * * *
3214455 ATACTTTAAATTCTAAAGGCTCCTCTAACCAAAGG-CAACGAACTTTAAAT-----GGCTCATTT
1 AAATTTTAAATTCAAAAAGCTCATCTCACCAGAGGACAACAAACTTTAAATCCAAAAGCTCCTTC
3214514 AACCAAAGGCAAC
66 AACCAAAGGCAAC
* * * * * * *
3214527 AAACTTTAAATGTTAAAAGGTTCTTCTGACCAGAGG-CAACGAACTTTAAAT
1 AAATTTTAAAT-TCAAAAAGCTCATCTCACCAGAGGACAACAAACTTTAAAT
3214578 GGCTCTTTTA
Statistics
Matches: 292, Mismatches: 53, Indels: 27
0.78 0.14 0.07
Matches are distributed among these distances:
71 1 0.00
72 28 0.10
73 33 0.11
76 3 0.01
77 72 0.25
78 145 0.50
79 10 0.03
ACGTcount: A:0.42, C:0.22, G:0.11, T:0.25
Consensus pattern (78 bp):
AAATTTTAAATTCAAAAAGCTCATCTCACCAGAGGACAACAAACTTTAAATCCAAAAGCTCCTTC
AACCAAAGGCAAC
Found at i:3214352 original size:117 final size:116
Alignment explanation
Indices: 3214185--3214504 Score: 374
Period size: 117 Copynumber: 2.8 Consensus size: 116
3214175 GAGGGCAATG
* ** * * * *
3214185 AACTTTAAATTCAAAAGCCCATTTAACCAAAGGCAATGAATTTTAGATTCAAAAAGCTCATCTCA
1 AACTTTAAATTCAAAAGCCCCTTTAACCAAAGGCAACAAACTTTAAATTCAAAAGGCTCCTCTCA
* * **
3214250 CCAGAGATAACAAATTTTAAATCCAAAAAGCTCCTTCAGCCAAAGGCAACA
66 CCAGAGACAACAAACTTTAAATCCAAAAAGCTCCTTCAAACAAAGGCAACA
* *
3214301 AATTTTAAATTCAAAAGGCCCCTCTT-ACTAAAGGCAACAAACTTTAAATTCAAAAGGCTCCTCT
1 AACTTTAAATTCAAAA-GCCCCT-TTAACCAAAGGCAACAAACTTTAAATTCAAAAGGCTCCTCT
* * * *
3214365 CACCATAGGCAACAAACTTTAAATCCAAAAAGCTTCTTTAAACAAAGGCAACA
64 CACCAGAGACAACAAACTTTAAATCCAAAAAGCTCCTTCAAACAAAGGCAACA
* * * * *
3214418 AACTTTAAATCCAAAAAG-TCCTTTAACCAAAGGCAACATACTTTAAATTCTAAAGGCTCCTCTA
1 AACTTTAAATTC-AAAAGCCCCTTTAACCAAAGGCAACAAACTTTAAATTCAAAAGGCTCCTCTC
* * *
3214482 ACCAAAGGCAACGAACTTTAAAT
65 ACCAGAGACAACAAACTTTAAAT
3214505 GGCTCATTTA
Statistics
Matches: 174, Mismatches: 26, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
115 2 0.01
116 74 0.43
117 92 0.53
118 6 0.03
ACGTcount: A:0.43, C:0.23, G:0.10, T:0.24
Consensus pattern (116 bp):
AACTTTAAATTCAAAAGCCCCTTTAACCAAAGGCAACAAACTTTAAATTCAAAAGGCTCCTCTCA
CCAGAGACAACAAACTTTAAATCCAAAAAGCTCCTTCAAACAAAGGCAACA
Found at i:3214517 original size:33 final size:32
Alignment explanation
Indices: 3214480--3214610 Score: 118
Period size: 33 Copynumber: 3.8 Consensus size: 32
3214470 AAGGCTCCTC
*
3214480 TAACCAAAGGCAACGAACTTTAAATGGCTCATT
1 TAACCAAAGGCAACAAACTTTAAATGGCTC-TT
*
3214513 TAACCAAAGGCAACAAACTTTAAATGTTAAAAGGTTCTT
1 TAACCAAAGGCAACAAACTTTAAA---T----GGCTCTT
* * *
3214552 CTGACCAGAGGCAACGAACTTTAAATGGCTCTTT
1 -TAACCAAAGGCAACAAACTTTAAATGGCTC-TT
*
3214586 TAACTAAAGGCAACAAACTTTAAAT
1 TAACCAAAGGCAACAAACTTTAAAT
3214611 TAAAGATCTA
Statistics
Matches: 79, Mismatches: 10, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
33 48 0.61
34 2 0.03
36 1 0.01
37 1 0.01
39 2 0.03
40 25 0.32
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.26
Consensus pattern (32 bp):
TAACCAAAGGCAACAAACTTTAAATGGCTCTT
Found at i:3214580 original size:73 final size:72
Alignment explanation
Indices: 3214289--3214611 Score: 272
Period size: 73 Copynumber: 4.3 Consensus size: 72
3214279 GCTCCTTCAG
* * * * * *
3214289 CCAAAGGCAACAAATTTTAAATTCAAAAGGCCCCTCTTACTAAAGGCAACAAACTTTAAATTCAA
1 CCAAAGGCAACAAACTTTAAATTCTAAAGGCTCCTCTAACCAAAGGCAACGAACTTTAAA-T---
* * *
3214354 AAGGCTCCTCTCA
62 --GGCTCATTTAA
* * * * * * * * *
3214367 CCATAGGCAACAAACTTTAAATCCAAAAAGCTTCTTTAAACAAAGGCAACAAACTTTAAAT-CCA
1 CCAAAGGCAACAAACTTTAAATTCTAAAGGCTCCTCTAACCAAAGGCAACGAACTTTAAATGGC-
*
3214431 AAAAGTCCTTTAA
65 -----TCATTTAA
*
3214444 CCAAAGGCAACATACTTTAAATTCTAAAGGCTCCTCTAACCAAAGGCAACGAACTTTAAATGGCT
1 CCAAAGGCAACAAACTTTAAATTCTAAAGGCTCCTCTAACCAAAGGCAACGAACTTTAAATGGCT
3214509 CATTTAA
66 CATTTAA
* * * *
3214516 CCAAAGGCAACAAACTTTAAATGT-TAAAAGGTTCTTCTGACCAGAGGCAACGAACTTTAAATGG
1 CCAAAGGCAACAAACTTTAAAT-TCT-AAAGGCTCCTCTAACCAAAGGCAACGAACTTTAAATGG
*
3214580 CTCTTTTAA
64 CTCATTTAA
*
3214589 CTAAAGGCAACAAACTTTAAATT
1 CCAAAGGCAACAAACTTTAAATT
3214612 AAAGATCTAA
Statistics
Matches: 205, Mismatches: 31, Indels: 24
0.79 0.12 0.09
Matches are distributed among these distances:
71 1 0.00
72 30 0.15
73 64 0.31
77 59 0.29
78 51 0.25
ACGTcount: A:0.41, C:0.22, G:0.11, T:0.25
Consensus pattern (72 bp):
CCAAAGGCAACAAACTTTAAATTCTAAAGGCTCCTCTAACCAAAGGCAACGAACTTTAAATGGCT
CATTTAA
Found at i:3214763 original size:40 final size:40
Alignment explanation
Indices: 3214698--3214866 Score: 193
Period size: 40 Copynumber: 4.3 Consensus size: 40
3214688 GAGGCTCTTA
* *
3214698 AAAT-TAAAAA-GCTTTTCTGATCAGAGGCAACAAACTTT
1 AAATGTAAAAAGGCTCTTCTGACCAGAGGCAACAAACTTT
3214736 AAAT-TCAAAAAGGCTCTTCTGACCAGAGGCAACAAACTTT
1 AAATGT-AAAAAGGCTCTTCTGACCAGAGGCAACAAACTTT
* * * *
3214776 AAATGTTAAAAGGCTCCTCTGACCATAAGCAACAAACTTT
1 AAATGTAAAAAGGCTCTTCTGACCAGAGGCAACAAACTTT
* * * *
3214816 AAATGTTAAAAGGCTCCTT-TAACCAAAGGCAATAAACTTT
1 AAATGTAAAAAGGCT-CTTCTGACCAGAGGCAACAAACTTT
*
3214856 AAATGTTAAAA
1 AAATGTAAAAA
3214867 TCTGAAAGGC
Statistics
Matches: 116, Mismatches: 11, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
38 5 0.04
39 5 0.04
40 103 0.89
41 3 0.03
ACGTcount: A:0.43, C:0.18, G:0.13, T:0.26
Consensus pattern (40 bp):
AAATGTAAAAAGGCTCTTCTGACCAGAGGCAACAAACTTT
Found at i:3226390 original size:3 final size:3
Alignment explanation
Indices: 3226382--3226430 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
3226372 CAAAATTACC
3226382 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3226430 A
1 A
3226431 ATCTTTAAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:3227267 original size:12 final size:12
Alignment explanation
Indices: 3227225--3227273 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
3227215 TTTTCTTTTT
*
3227225 ATTTTTCATTTTG
1 ATTTTT-ATGTTG
* *
3227238 ATTTTGATTTTG
1 ATTTTTATGTTG
3227250 ATTTTTTATGTTG
1 A-TTTTTATGTTG
3227263 ATTTTTATGTT
1 ATTTTTATGTT
3227274 ATTATTATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
12 17 0.53
13 15 0.47
ACGTcount: A:0.16, C:0.02, G:0.12, T:0.69
Consensus pattern (12 bp):
ATTTTTATGTTG
Found at i:3227280 original size:3 final size:3
Alignment explanation
Indices: 3227272--3227314 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
3227262 GATTTTTATG
*
3227272 TTA TTA TTA TTA TTA TTA TTA TTA TTG TTA TT- TTA -TA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3227315 CTGATAATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
2 4 0.11
3 32 0.89
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3228700 original size:38 final size:39
Alignment explanation
Indices: 3228591--3228743 Score: 168
Period size: 39 Copynumber: 4.0 Consensus size: 39
3228581 GGATAATAAG
* * *
3228591 AGGAGCCTTTTGAATTTAAAATTTGTTGCCTTTGGTTAA
1 AGGAGCCTTTTGAATTTAAAGTTCGTTGCCTTTGGTGAA
* ** * ** *
3228630 AAGAGTTTTTTGAATTTAAAGTTTGTTTTCTTTGGTGAT
1 AGGAGCCTTTTGAATTTAAAGTTCGTTGCCTTTGGTGAA
* *
3228669 AGGAGCCTTTTGAATTT-AAGTTCGTTGTCTTTGGTTAA
1 AGGAGCCTTTTGAATTTAAAGTTCGTTGCCTTTGGTGAA
3228707 ATGG-G-CTTTTGAATTTAAAGTTCGTTGCCTTTGGTGA
1 A-GGAGCCTTTTGAATTTAAAGTTCGTTGCCTTTGGTGA
3228744 GATAATTTTT
Statistics
Matches: 95, Mismatches: 17, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
37 11 0.12
38 37 0.39
39 47 0.49
ACGTcount: A:0.22, C:0.08, G:0.23, T:0.46
Consensus pattern (39 bp):
AGGAGCCTTTTGAATTTAAAGTTCGTTGCCTTTGGTGAA
Found at i:3228739 original size:76 final size:78
Alignment explanation
Indices: 3228591--3228743 Score: 211
Period size: 76 Copynumber: 2.0 Consensus size: 78
3228581 GGATAATAAG
* ** *
3228591 AGGAGCCTTTTGAATTTAAAATTTGTTGCCTTTGGTTAAAAGAGTTTTTTGAATTTAAAGTTTGT
1 AGGAGCCTTTTGAATTTAAAATTCGTTGCCTTTGGTTAAAAGAGGCTTTTGAATTTAAAGTTCGT
**
3228656 TTTCTTTGGTGAT
66 TGCCTTTGGTGAT
* * *
3228669 AGGAGCCTTTTGAATTT-AAGTTCGTTGTCTTTGGTTAAATG-GGCTTTTGAATTTAAAGTTCGT
1 AGGAGCCTTTTGAATTTAAAATTCGTTGCCTTTGGTTAAAAGAGGCTTTTGAATTTAAAGTTCGT
3228732 TGCCTTTGGTGA
66 TGCCTTTGGTGA
3228744 GATAATTTTT
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
76 29 0.44
77 20 0.30
78 17 0.26
ACGTcount: A:0.22, C:0.08, G:0.23, T:0.46
Consensus pattern (78 bp):
AGGAGCCTTTTGAATTTAAAATTCGTTGCCTTTGGTTAAAAGAGGCTTTTGAATTTAAAGTTCGT
TGCCTTTGGTGAT
Found at i:3229821 original size:12 final size:12
Alignment explanation
Indices: 3229804--3229881 Score: 52
Period size: 12 Copynumber: 6.4 Consensus size: 12
3229794 ATTTCGCAGG
* *
3229804 TTTTTCCTTTTC
1 TTTTTCATTTTA
*
3229816 TTTTTCTTTTTA
1 TTTTTCATTTTA
3229828 TTTTTCATTTTGA
1 TTTTTCATTTT-A
*
3229841 -TTTTGATTTTGA
1 TTTTTCATTTT-A
* *
3229853 TTTTTTATGTTGA
1 TTTTTCAT-TTTA
*
3229866 TTTTT-ATGTTA
1 TTTTTCATTTTA
3229877 TTTTT
1 TTTTT
3229882 TTATGATGCT
Statistics
Matches: 55, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
11 7 0.13
12 33 0.60
13 13 0.24
14 2 0.04
ACGTcount: A:0.12, C:0.06, G:0.08, T:0.74
Consensus pattern (12 bp):
TTTTTCATTTTA
Found at i:3229879 original size:11 final size:12
Alignment explanation
Indices: 3229827--3229881 Score: 58
Period size: 12 Copynumber: 4.5 Consensus size: 12
3229817 TTTTCTTTTT
*
3229827 ATTTTTCATTTTG
1 ATTTTT-ATGTTG
* *
3229840 ATTTTGATTTTG
1 ATTTTTATGTTG
3229852 ATTTTTTATGTTG
1 A-TTTTTATGTTG
3229865 ATTTTTATGTT-
1 ATTTTTATGTTG
3229876 ATTTTT
1 ATTTTT
3229882 TTATGATGCT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
11 6 0.16
12 17 0.45
13 15 0.39
ACGTcount: A:0.16, C:0.02, G:0.11, T:0.71
Consensus pattern (12 bp):
ATTTTTATGTTG
Found at i:3229897 original size:3 final size:3
Alignment explanation
Indices: 3229891--3229959 Score: 115
Period size: 3 Copynumber: 23.7 Consensus size: 3
3229881 TTTATGATGC
3229891 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
3229939 TAT TGT TAT T-T TA- TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TA
3229960 CTGGTAATAA
Statistics
Matches: 62, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
2 4 0.06
3 58 0.94
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3235111 original size:2 final size:2
Alignment explanation
Indices: 3235104--3235131 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3235094 CATTCAATTC
3235104 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3235132 AAATTCGCCG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3246373 original size:2 final size:2
Alignment explanation
Indices: 3246366--3246404 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
3246356 ACATCATGCT
*
3246366 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3246405 TAATCCCTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3249924 original size:19 final size:22
Alignment explanation
Indices: 3249884--3249928 Score: 69
Period size: 19 Copynumber: 2.2 Consensus size: 22
3249874 AAATCAAATT
3249884 ATATTAATTTATTAATAAATAA
1 ATATTAATTTATTAATAAATAA
3249906 ATATTAATTT-TT-A-AAATAA
1 ATATTAATTTATTAATAAATAA
3249925 ATAT
1 ATAT
3249929 ATAAAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 10 0.43
20 1 0.04
21 2 0.09
22 10 0.43
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATATTAATTTATTAATAAATAA
Found at i:3250438 original size:34 final size:34
Alignment explanation
Indices: 3250400--3250472 Score: 78
Period size: 34 Copynumber: 2.1 Consensus size: 34
3250390 TCGAATTTAA
*
3250400 TAAAT-TTAAAATTTTTTAAAAATA-TATTAAATGT
1 TAAATGTT-AAATATTTTAAAAATATTATTAAAT-T
* * *
3250434 TAAATGTTTAATATTTTAAATATATTTTTAAATT
1 TAAATGTTAAATATTTTAAAAATATTATTAAATT
3250468 TAAAT
1 TAAAT
3250473 AAGATTAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
34 24 0.73
35 9 0.27
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.51
Consensus pattern (34 bp):
TAAATGTTAAATATTTTAAAAATATTATTAAATT
Found at i:3251868 original size:26 final size:27
Alignment explanation
Indices: 3251816--3251869 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 27
3251806 TTATTAATTT
*
3251816 TTAAATTTTAATTATTTAAATACTAAA
1 TTAAATTTCAATTATTTAAATACTAAA
*
3251843 TTAAA-TTCAATTATCTTATATA-TAAA
1 TTAAATTTCAATTAT-TTAAATACTAAA
3251869 T
1 T
3251870 GAAAATAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 13 0.54
27 11 0.46
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (27 bp):
TTAAATTTCAATTATTTAAATACTAAA
Found at i:3259259 original size:15 final size:16
Alignment explanation
Indices: 3259223--3259265 Score: 56
Period size: 14 Copynumber: 2.9 Consensus size: 16
3259213 CGGGATCAAG
*
3259223 AATCACCCTAAAATTA
1 AATCACCCTAAAATAA
3259239 AA--ACCCTAAAA-AA
1 AATCACCCTAAAATAA
3259252 AATCACCCTAAAAT
1 AATCACCCTAAAAT
3259266 TCTTTTAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
13 3 0.13
14 9 0.39
15 9 0.39
16 2 0.09
ACGTcount: A:0.56, C:0.26, G:0.00, T:0.19
Consensus pattern (16 bp):
AATCACCCTAAAATAA
Found at i:3260710 original size:24 final size:23
Alignment explanation
Indices: 3260682--3260735 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
3260672 TTTAAAAGCA
* *
3260682 ATCAATTAGTTAATTTAATATGAT
1 ATCAATTACTCAATTTAATAT-AT
*
3260706 ATCAATAACTCAATTTAATATAT
1 ATCAATTACTCAATTTAATATAT
3260729 AT-AATTA
1 ATCAATTA
3260736 AGCTTTCTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
22 4 0.15
23 4 0.15
24 18 0.69
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (23 bp):
ATCAATTACTCAATTTAATATAT
Found at i:3277425 original size:2 final size:2
Alignment explanation
Indices: 3277418--3277451 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
3277408 CATCATTCAT
* *
3277418 TC TC TC TC TC TT TC TT TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3277452 CAAATGCGTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (2 bp):
TC
Found at i:3284379 original size:22 final size:24
Alignment explanation
Indices: 3284343--3284392 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 24
3284333 TCGATCCAAC
*
3284343 TTAAAATTAATAAAATA-TTATTT
1 TTAAAAATAATAAAATATTTATTT
3284366 TTAAAAAT-ATAAAATATTTATTT
1 TTAAAAATAATAAAATATTTATTT
3284389 TTAA
1 TTAA
3284393 TATAAATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 8 0.32
23 17 0.68
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
TTAAAAATAATAAAATATTTATTT
Found at i:3284396 original size:20 final size:20
Alignment explanation
Indices: 3284352--3284398 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 20
3284342 CTTAAAATTA
3284352 ATAAAATATTATTTTTAAAAAT
1 ATAAAATATTATTTTT--AAAT
3284374 ATAAAATATTTATTTTT-AAT
1 ATAAAATA-TTATTTTTAAAT
3284394 ATAAA
1 ATAAA
3284399 TATACAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.33
22 8 0.33
23 8 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATAAAATATTATTTTTAAAT
Found at i:3289960 original size:20 final size:22
Alignment explanation
Indices: 3289925--3290000 Score: 77
Period size: 23 Copynumber: 3.5 Consensus size: 22
3289915 TTATATATAT
*
3289925 TTATATATATTTAATAAATAAAA
1 TTAT-TATATTAAATAAATAAAA
3289948 TT-TT-TATTAAAT-AATATAAA
1 TTATTATATTAAATAAATA-AAA
*
3289968 TTATTATATTAAATTAATTAAAA
1 TTATTATATTAAA-TAAATAAAA
*
3289991 TTAATATATT
1 TTATTATATT
3290001 TTTATCAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
19 4 0.09
20 12 0.27
21 3 0.07
22 8 0.18
23 15 0.33
24 3 0.07
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TTATTATATTAAATAAATAAAA
Found at i:3290015 original size:22 final size:21
Alignment explanation
Indices: 3289987--3290034 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 21
3289977 TAAATTAATT
*
3289987 AAAATTAATATATTTTTATCAA
1 AAAATTAATATATATTTAT-AA
3290009 AAAATTAATATATATTTATAA
1 AAAATTAATATATATTTATAA
3290030 AAAAT
1 AAAAT
3290035 GATCTAACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 7 0.28
22 18 0.72
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
AAAATTAATATATATTTATAA
Found at i:3295157 original size:69 final size:69
Alignment explanation
Indices: 3295074--3295209 Score: 236
Period size: 69 Copynumber: 2.0 Consensus size: 69
3295064 TTTTGAGTCT
* *
3295074 GTCAGAAAATTTTCACATTGTTATTGTGGATATCATTGCGGGGCGATATATATTGTGCTTTGTTG
1 GTCAGAAAATTTTCACATTGTTATTGCGGATATCATTGCGGGGCAATATATATTGTGCTTTGTTG
3295139 CTAA
66 CTAA
* *
3295143 GTCAGACAATTTTCACATTGTTATTGCGGATATCATTGCGGGGCAATATATGTTGTGCTTTGTTG
1 GTCAGAAAATTTTCACATTGTTATTGCGGATATCATTGCGGGGCAATATATATTGTGCTTTGTTG
3295208 CT
66 CT
3295210 GACTACATTC
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
69 63 1.00
ACGTcount: A:0.23, C:0.13, G:0.24, T:0.40
Consensus pattern (69 bp):
GTCAGAAAATTTTCACATTGTTATTGCGGATATCATTGCGGGGCAATATATATTGTGCTTTGTTG
CTAA
Found at i:3302022 original size:15 final size:16
Alignment explanation
Indices: 3301992--3302025 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
3301982 GCATCTAAAA
*
3301992 ATTATAATTATTTTAT
1 ATTATAAATATTTTAT
3302008 ATTATAAAT-TTTTAT
1 ATTATAAATATTTTAT
3302023 ATT
1 ATT
3302026 TTCAAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
ATTATAAATATTTTAT
Found at i:3302913 original size:6 final size:6
Alignment explanation
Indices: 3302902--3302926 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3302892 GTGCCTGTAT
3302902 GCGGCA GCGGCA GCGGCA GCGGCA G
1 GCGGCA GCGGCA GCGGCA GCGGCA G
3302927 AGGATTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.32, G:0.52, T:0.00
Consensus pattern (6 bp):
GCGGCA
Found at i:3305203 original size:22 final size:21
Alignment explanation
Indices: 3305178--3305232 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 21
3305168 AACAGAACTC
3305178 ACACCAACCACAAAAAAA-AAAA
1 ACACCAA--ACAAAAAAATAAAA
*
3305200 ACA-CAAACAAAAAAATAGAA
1 ACACCAAACAAAAAAATAAAA
*
3305220 ACACAAAGACAAA
1 ACACCAA-ACAAA
3305233 CAGTCTTCCC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
19 9 0.32
20 6 0.21
21 5 0.18
22 8 0.29
ACGTcount: A:0.73, C:0.22, G:0.04, T:0.02
Consensus pattern (21 bp):
ACACCAAACAAAAAAATAAAA
Found at i:3305214 original size:20 final size:20
Alignment explanation
Indices: 3305189--3305226 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3305179 CACCAACCAC
3305189 AAAAAAAAAAAACACAAACA
1 AAAAAAAAAAAACACAAACA
* *
3305209 AAAAAATAGAAACACAAA
1 AAAAAAAAAAAACACAAA
3305227 GACAAACAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.82, C:0.13, G:0.03, T:0.03
Consensus pattern (20 bp):
AAAAAAAAAAAACACAAACA
Found at i:3306052 original size:23 final size:24
Alignment explanation
Indices: 3306026--3306070 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
3306016 GAAAACAAGT
3306026 AATA-ATT-AAAAATATATATTAAA
1 AATACATTAAAAAATA-ATATTAAA
*
3306049 AATACTTTAAAAAATAATATTA
1 AATACATTAAAAAATAATATTA
3306071 TTATTATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 4 0.21
24 8 0.42
25 7 0.37
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
AATACATTAAAAAATAATATTAAA
Found at i:3306376 original size:8 final size:8
Alignment explanation
Indices: 3306351--3306533 Score: 80
Period size: 8 Copynumber: 23.4 Consensus size: 8
3306341 ATTCATAATC
3306351 TCCTAAAA
1 TCCTAAAA
3306359 TCC-AAAA
1 TCCTAAAA
*
3306366 TCCTTAAA
1 TCCTAAAA
3306374 TCC-AAAA
1 TCCTAAAA
3306381 TCCTAAAA
1 TCCTAAAA
* * *
3306389 TTCGAAAC
1 TCCTAAAA
*
3306397 CCCTAAAAA
1 TCCT-AAAA
3306406 T-CTAAAA
1 TCCTAAAA
*
3306413 TCCCTTAAA
1 T-CCTAAAA
*
3306422 TCC-AAAC
1 TCCTAAAA
3306429 TCCTAAAA
1 TCCTAAAA
* *
3306437 TCCGAAAC
1 TCCTAAAA
*
3306445 CCCTAAAAA
1 TCCT-AAAA
3306454 T-CTAAAA
1 TCCTAAAA
*
3306461 TTCCTTAAA
1 -TCCTAAAA
3306470 TCC--AAA
1 TCCTAAAA
*
3306476 CCCTTAAAA
1 TCC-TAAAA
* *
3306485 TCCGAAAC
1 TCCTAAAA
*
3306493 TTCTAAAA
1 TCCTAAAA
3306501 TCC--AAA
1 TCCTAAAA
* *
3306507 CCCCAAAA
1 TCCTAAAA
*
3306515 ACC-AAAA
1 TCCTAAAA
3306522 TCCCTAAAA
1 T-CCTAAAA
3306531 TCC
1 TCC
3306534 AAACCCTTAA
Statistics
Matches: 127, Mismatches: 32, Indels: 32
0.66 0.17 0.17
Matches are distributed among these distances:
6 10 0.08
7 31 0.24
8 59 0.46
9 27 0.21
ACGTcount: A:0.47, C:0.30, G:0.02, T:0.21
Consensus pattern (8 bp):
TCCTAAAA
Found at i:3306443 original size:48 final size:47
Alignment explanation
Indices: 3306355--3306492 Score: 215
Period size: 48 Copynumber: 2.9 Consensus size: 47
3306345 ATAATCTCCT
* * *
3306355 AAAATCCAAAATCCTTAAATCCAAAATCCTAAAATTCGAAACCCCTA
1 AAAATCTAAAATCCTTAAATCCAAACTCCTAAAATCCGAAACCCCTA
3306402 AAAATCTAAAATCCCTTAAATCCAAACTCCTAAAATCCGAAACCCCTA
1 AAAATCTAAAAT-CCTTAAATCCAAACTCCTAAAATCCGAAACCCCTA
3306450 AAAATCTAAAATTCCTTAAATCCAAAC-CCTTAAAATCCGAAAC
1 AAAATCTAAAA-TCCTTAAATCCAAACTCC-TAAAATCCGAAAC
3306493 TTCTAAAATC
Statistics
Matches: 85, Mismatches: 3, Indels: 5
0.91 0.03 0.05
Matches are distributed among these distances:
47 13 0.15
48 71 0.84
49 1 0.01
ACGTcount: A:0.48, C:0.28, G:0.02, T:0.22
Consensus pattern (47 bp):
AAAATCTAAAATCCTTAAATCCAAACTCCTAAAATCCGAAACCCCTA
Found at i:3306499 original size:16 final size:15
Alignment explanation
Indices: 3306330--3306608 Score: 147
Period size: 16 Copynumber: 17.7 Consensus size: 15
3306320 TAGGTTTCTA
* *
3306330 AAACCCCTAAAATTC
1 AAACTCCTAAAATCC
3306345 ATAATCTCCTAAAATCC
1 A-AA-CTCCTAAAATCC
* *
3306362 AAAATCCTTAAATCC
1 AAACTCCTAAAATCC
* *
3306377 AAAATCCTAAAATTCG
1 AAACTCCTAAAA-TCC
* *
3306393 AAACCCCTAAAAATCT
1 AAACTCCT-AAAATCC
* *
3306409 AAAATCCCTTAAATCC
1 AAACT-CCTAAAATCC
3306425 AAACTCCTAAAATCC
1 AAACTCCTAAAATCC
* *
3306440 GAAACCCCTAAAAATCTA
1 -AAACTCCT-AAAATC-C
* *
3306458 AAATTCCTTAAATCC
1 AAACTCCTAAAATCC
3306473 AAAC-CCTTAAAATCC
1 AAACTCC-TAAAATCC
*
3306488 GAAACTTCTAAAATCC
1 -AAACTCCTAAAATCC
* *
3306504 AAAC-CCCAAAAACC
1 AAACTCCTAAAATCC
*
3306518 AAAATCCCTAAAATCC
1 AAACT-CCTAAAATCC
* *
3306534 AAAC-CCTTAAATCA
1 AAACTCCTAAAATCC
*
3306548 AAACCTCAAACCATAAAACCC
1 AAA-CT----CC-TAAAATCC
3306569 AAAC-CCTAAAATCTTC
1 AAACTCCTAAAATC--C
*
3306585 AAACT-CTAAAATCA
1 AAACTCCTAAAATCC
3306599 AAAC-CCTAAA
1 AAACTCCTAAA
3306609 CCTTTCATAT
Statistics
Matches: 202, Mismatches: 38, Indels: 49
0.70 0.13 0.17
Matches are distributed among these distances:
14 38 0.19
15 48 0.24
16 74 0.37
17 31 0.15
20 3 0.01
21 8 0.04
ACGTcount: A:0.48, C:0.30, G:0.01, T:0.20
Consensus pattern (15 bp):
AAACTCCTAAAATCC
Found at i:3306502 original size:31 final size:30
Alignment explanation
Indices: 3306354--3306544 Score: 145
Period size: 31 Copynumber: 6.1 Consensus size: 30
3306344 CATAATCTCC
* *
3306354 TAAAATCCAAAATCCTTAAATCCAAAATCC-
1 TAAAATCCAAAATCCTAAAATCC-AAACCCT
* ** *
3306384 TAAAATTCGAAACCCCTAAAAATCTAAAATCCCT
1 TAAAA-TCCAAAATCCT-AAAATC-CAAA-CCCT
*
3306418 T-AAATCCAAACTCCTAAAATCCGAAACCCCT
1 TAAAATCCAAAATCCTAAAATCC-AAA-CCCT
* * *
3306449 AAAAATCTAAAATTCCTTAAATCCAAACCCT
1 TAAAATCCAAAA-TCCTAAAATCCAAACCCT
* *
3306480 TAAAATCCGAAACTTCTAAAATCCAAACCC-
1 TAAAATCC-AAAATCCTAAAATCCAAACCCT
* *
3306510 CAAAAACCAAAATCCCTAAAATCCAAACCCT
1 TAAAATCCAAAAT-CCTAAAATCCAAACCCT
3306541 TAAA
1 TAAA
3306545 TCAAAACCTC
Statistics
Matches: 126, Mismatches: 24, Indels: 21
0.74 0.14 0.12
Matches are distributed among these distances:
29 4 0.03
30 26 0.21
31 49 0.39
32 31 0.25
33 15 0.12
34 1 0.01
ACGTcount: A:0.48, C:0.29, G:0.02, T:0.21
Consensus pattern (30 bp):
TAAAATCCAAAATCCTAAAATCCAAACCCT
Found at i:3306537 original size:30 final size:30
Alignment explanation
Indices: 3306430--3306539 Score: 105
Period size: 30 Copynumber: 3.5 Consensus size: 30
3306420 AATCCAAACT
* *
3306430 CCTAAAATCCGAAACCCCTAAAAATCTAAAATT
1 CCTAAAATCC-AAACCCC-AAAAA-CCAAAATC
* * * *
3306463 CCTTAAATCCAAACCCTTAAAATCCGAAA-C
1 CCTAAAATCCAAACCC-CAAAAACCAAAATC
*
3306493 TTCTAAAATCCAAACCCCAAAAACCAAAATC
1 -CCTAAAATCCAAACCCCAAAAACCAAAATC
3306524 CCTAAAATCCAAACCC
1 CCTAAAATCCAAACCC
3306540 TTAAATCAAA
Statistics
Matches: 62, Mismatches: 12, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
30 24 0.39
31 19 0.31
32 10 0.16
33 9 0.15
ACGTcount: A:0.47, C:0.33, G:0.02, T:0.18
Consensus pattern (30 bp):
CCTAAAATCCAAACCCCAAAAACCAAAATC
Found at i:3306544 original size:15 final size:15
Alignment explanation
Indices: 3306354--3306544 Score: 92
Period size: 15 Copynumber: 12.3 Consensus size: 15
3306344 CATAATCTCC
*
3306354 TAAAATCCAAAATCCT
1 TAAAATCC-AAACCCT
*
3306370 T-AAATCCAAAATCC-
1 TAAAATCC-AAACCCT
*
3306384 TAAAATTCGAAACCCCT
1 TAAAA-TCCAAA-CCCT
* *
3306401 AAAAATCTAAAATCCCT
1 TAAAATC-CAAA-CCCT
3306418 T-AAATCCAAACTCC-
1 TAAAATCCAAAC-CCT
3306432 TAAAATCCGAAACCCCT
1 TAAAATCC-AAA-CCCT
* * *
3306449 AAAAATCTAAAATTCCT
1 TAAAATC-CAAA-CCCT
3306466 T-AAATCCAAACCCT
1 TAAAATCCAAACCCT
*
3306480 TAAAATCCGAAA-CTT
1 TAAAATCC-AAACCCT
3306495 CTAAAATCCAAACCC-
1 -TAAAATCCAAACCCT
* *
3306510 CAAAAACCAAAATCCC-
1 TAAAATCC-AAA-CCCT
3306526 TAAAATCCAAACCCT
1 TAAAATCCAAACCCT
3306541 TAAA
1 TAAA
3306545 TCAAAACCTC
Statistics
Matches: 137, Mismatches: 20, Indels: 37
0.71 0.10 0.19
Matches are distributed among these distances:
14 16 0.12
15 54 0.39
16 43 0.31
17 24 0.18
ACGTcount: A:0.48, C:0.29, G:0.02, T:0.21
Consensus pattern (15 bp):
TAAAATCCAAACCCT
Found at i:3306571 original size:14 final size:15
Alignment explanation
Indices: 3306547--3306579 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
3306537 CCCTTAAATC
3306547 AAAACCTCAAACCAT
1 AAAACCTCAAACCAT
*
3306562 AAAACC-CAAACCCT
1 AAAACCTCAAACCAT
3306576 AAAA
1 AAAA
3306580 TCTTCAAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.58, C:0.33, G:0.00, T:0.09
Consensus pattern (15 bp):
AAAACCTCAAACCAT
Found at i:3306671 original size:31 final size:30
Alignment explanation
Indices: 3306591--3306676 Score: 77
Period size: 30 Copynumber: 2.8 Consensus size: 30
3306581 CTTCAAACTC
* * * *
3306591 TAAAATCAAAACCCT-AAACCTTTCATATCT
1 TAAAATCCAAACCTTAAAACCTCTAAT-TCT
* *
3306621 TAAAATTCAAGCCTTAAAACACTCTAATTCT
1 TAAAATCCAAACCTTAAAAC-CTCTAATTCT
3306652 TAAAA-CCAAACCTTCAAAACCTCTA
1 TAAAATCCAAACCTT-AAAACCTCTA
3306677 CTCAAGCTCT
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
30 23 0.51
31 17 0.38
32 5 0.11
ACGTcount: A:0.44, C:0.27, G:0.01, T:0.28
Consensus pattern (30 bp):
TAAAATCCAAACCTTAAAACCTCTAATTCT
Found at i:3315182 original size:58 final size:58
Alignment explanation
Indices: 3315118--3315243 Score: 252
Period size: 58 Copynumber: 2.2 Consensus size: 58
3315108 AGACATTCGT
3315118 ATTTGCATCACTTGCATTGACATTTGTATAAGACATTTGCATTCACACCATAAGAAGA
1 ATTTGCATCACTTGCATTGACATTTGTATAAGACATTTGCATTCACACCATAAGAAGA
3315176 ATTTGCATCACTTGCATTGACATTTGTATAAGACATTTGCATTCACACCATAAGAAGA
1 ATTTGCATCACTTGCATTGACATTTGTATAAGACATTTGCATTCACACCATAAGAAGA
3315234 ATTTGCATCA
1 ATTTGCATCA
3315244 TGGCATCTAT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 68 1.00
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.33
Consensus pattern (58 bp):
ATTTGCATCACTTGCATTGACATTTGTATAAGACATTTGCATTCACACCATAAGAAGA
Found at i:3315905 original size:22 final size:22
Alignment explanation
Indices: 3315880--3315922 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
3315870 GTCAATTCTG
* *
3315880 TAAGACCTCCGGGCATAATTTC
1 TAAGACCTACGGACATAATTTC
*
3315902 TAAGACTTACGGACATAATTT
1 TAAGACCTACGGACATAATTT
3315923 TGATTCGCAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (22 bp):
TAAGACCTACGGACATAATTTC
Found at i:3315979 original size:109 final size:109
Alignment explanation
Indices: 3315788--3316119 Score: 366
Period size: 109 Copynumber: 3.0 Consensus size: 109
3315778 GATTTTCATG
** * * *
3315788 ATTTCTAAGACCTTA-GGGTATAATTTTGATTCGTGGTGTTATCCCGATCGATTCGTTATTTTTC
1 ATTTCTAAGA-CTTACGGGTATAATTTTGATTCGCAGTGTTATTCCGATCGATTCTTTATTTTTT
* *
3315852 GACTACGATGTTATCCTAGTCAATTCTGTAAGACCTCCGGGCATA
65 GACTACGGTGTTATCCTAGTCGATTCTGTAAGACCTCCGGGCATA
**
3315897 ATTTCTAAGACTTACGGACATAATTTTGATTCGCAGTGTTATTCCGATCGATTCTTTATTTTTTG
1 ATTTCTAAGACTTACGGGTATAATTTTGATTCGCAGTGTTATTCCGATCGATTCTTTATTTTTTG
* * * * * *
3315962 ACTGCGGTGTTATCCTAGTCGATTTTGTAAGATCTCCAGACATT
66 ACTACGGTGTTATCCTAGTCGATTCTGTAAGACCTCCGGGCATA
* * *
3316006 ATTTCTAAGACCT-CTGGGTATAATTTCGATTCGCTA-TGTTA-TCCTGATCGATTTTTTATTTT
1 ATTTCTAAGACTTAC-GGGTATAATTTTGATTCGC-AGTGTTATTCC-GATCGATTCTTTATTTT
* * * * ** *
3316068 TTTAGTTACAGTGTTATCCCAGTCGATTCCATAAGACCTTCGGGCATA
63 TTGA-CTACGGTGTTATCCTAGTCGATTCTGTAAGACCTCCGGGCATA
3316116 ATTT
1 ATTT
3316120 TAATTCGTGG
Statistics
Matches: 185, Mismatches: 33, Indels: 9
0.81 0.15 0.04
Matches are distributed among these distances:
108 8 0.04
109 141 0.76
110 36 0.19
ACGTcount: A:0.23, C:0.18, G:0.17, T:0.41
Consensus pattern (109 bp):
ATTTCTAAGACTTACGGGTATAATTTTGATTCGCAGTGTTATTCCGATCGATTCTTTATTTTTTG
ACTACGGTGTTATCCTAGTCGATTCTGTAAGACCTCCGGGCATA
Found at i:3316254 original size:197 final size:198
Alignment explanation
Indices: 3315902--3316316 Score: 484
Period size: 197 Copynumber: 2.1 Consensus size: 198
3315892 GCATAATTTC
* * * * *
3315902 TAAGA-CTTACGGACATAATTTTGATTCGCAGTGTTATTCCGATCGATTCTTTATTTTTTGACTG
1 TAAGACCTTACGGACATAATTTTAATTCGCAGGGTTATCCCGATCGATTCTTTATCTTTCGACTG
* * * * * * *
3315966 CGGTGTTATCCTAGTCGATTTTGTAAGATCTCCAGACATTATTTCTAAGACCTCTGGGTATAATT
66 CGATGTTATCCTAGTCGATTCTGTAAGACCTCCAGACATGACTTCTAAGACCTCTGAGCATAATT
* ** * ** *
3316031 TCGATTCGCTATGTTATCCTGATCGATTTTTTATTTTTTTAGTTACAGTGTTATCCCAGTCGATT
131 TCGATTCGCTATGTTATCCCGATCGATTCCTTATATTTCGACTTACAGTGTTATCCCAGTCGATT
3316096 CCA
196 CCA
* **
3316099 TAAGACCTT-CGGGCATAATTTTAATTCGTGGGGTTATCCCGATCGATT-TCTTATCTTTCGACT
1 TAAGACCTTACGGACATAATTTTAATTCGCAGGGTTATCCCGATCGATTCT-TTATCTTTCGACT
*
3316162 GTGATGTTAT-CTCAGTCGATTCTGTAAGACCTCC-GAACATGACTTCTAAGACCTCTGAGCATA
65 GCGATGTTATCCT-AGTCGATTCTGTAAGACCTCCAG-ACATGACTTCTAAGACCTCTGAGCATA
* *
3316225 ATTTTGATTCG-TGATGTTATCCCGATCGATTCCTTATATTTCGACTTACGGTGTTATCCCAGTC
128 ATTTCGATTCGCT-ATGTTATCCCGATCGATTCCTTATATTTCGACTTACAGTGTTATCCCAGTC
**
3316289 GATTCTG
192 GATTCCA
* *
3316296 TAAGACC-TCCGGACATGATTT
1 TAAGACCTTACGGACATAATTT
3316317 CTAAGATCTC
Statistics
Matches: 183, Mismatches: 29, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
196 6 0.03
197 174 0.95
198 3 0.02
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.40
Consensus pattern (198 bp):
TAAGACCTTACGGACATAATTTTAATTCGCAGGGTTATCCCGATCGATTCTTTATCTTTCGACTG
CGATGTTATCCTAGTCGATTCTGTAAGACCTCCAGACATGACTTCTAAGACCTCTGAGCATAATT
TCGATTCGCTATGTTATCCCGATCGATTCCTTATATTTCGACTTACAGTGTTATCCCAGTCGATT
CCA
Found at i:3316328 original size:110 final size:108
Alignment explanation
Indices: 3316099--3316767 Score: 739
Period size: 110 Copynumber: 6.1 Consensus size: 108
3316089 GTCGATTCCA
* ** *
3316099 TAAGACCT-TCGGGCATAATTTTAATTCGTGGGGTTATCCCGATCGATTTCTTATCTTTCGACTG
1 TAAGACCTCT-GGGCATAATTTTGATTCGTGATGTTATCCCGATCGATTCCTTATCTTTCGACT-
* * *
3316163 T-GATGTTATCTCAGTCGATTCTGTAAGACCTCCGAACATGACTTC
64 TAGGTGTTATCCCAGTCGATTCTGTAAGACCTCCG-ACATGATTTC
* *
3316208 TAAGACCTCTGAGCATAATTTTGATTCGTGATGTTATCCCGATCGATTCCTTATATTTCGACTTA
1 TAAGACCTCTGGGCATAATTTTGATTCGTGATGTTATCCCGATCGATTCCTTATCTTTCGACTTA
3316273 CGGTGTTATCCCAGTCGATTCTGTAAGACCTCCGGACATGATTTC
66 -GGTGTTATCCCAGTCGATTCTGTAAGACCTCC-GACATGATTTC
* *** * * ** *
3316318 TAAGATCTCTGGGCATAATTTTGATTTACGATGTTATCTCAATCGATTTTTTATCTTTCAACTTG
1 TAAGACCTCTGGGCATAATTTTGATTCGTGATGTTATCCCGATCGATTCCTTATCTTTCGACTT-
* * *
3316383 TGGTGTTATCTCAGTCGATTCTGTAAGACCTCCGAGCATGATTTT
65 AGGTGTTATCCCAGTCGATTCTGTAAGACCTCCGA-CATGATTTC
* * * * * *
3316428 TAAGACTTTTGGGCATAATTTTGATTTGTGATTTTATCCAGATCGATTCCTTATCTTTTGACTTA
1 TAAGACCTCTGGGCATAATTTTGATTCGTGATGTTATCCCGATCGATTCCTTATCTTTCGACTTA
* * ** * **
3316493 TAGTATTATTTCAATCGATTCTGTAAGACCTTTAGACATGATTTC
66 -GGTGTTATCCCAGTCGATTCTGTAAGACC-TCCGACATGATTTC
* * * * *
3316538 TAAGACCTCTGGGCATAATTTCGATTCGCGGTATTATCCCGATCGATTTCTTATCTTTCGACTTG
1 TAAGACCTCTGGGCATAATTTTGATTCGTGATGTTATCCCGATCGATTCCTTATCTTTCGACTT-
* *
3316603 AGGTGTTATCCCAGTCGATTATGTAAGACCTCCGAGCATGATTTT
65 AGGTGTTATCCCAGTCGATTCTGTAAGACCTCCGA-CATGATTTC
* * * ** *
3316648 TAAGACCTCCGAGCATAATTTTGATTCGTGATTTTATCTTGATTGATTCCTTATCTTTCGACTTA
1 TAAGACCTCTGGGCATAATTTTGATTCGTGATGTTATCCCGATCGATTCCTTATCTTTCGACTTA
* * * *
3316713 CGATGTTATCCCAGTCGATTCTGTAAGACCTCTAGGCATGATTGTG
66 -GGTGTTATCCCAGTCGATTCTGTAAGACCTC-CGACATGATT-TC
3316759 TAAGACCTC
1 TAAGACCTC
3316768 CAGGCATTAT
Statistics
Matches: 469, Mismatches: 78, Indels: 24
0.82 0.14 0.04
Matches are distributed among these distances:
108 1 0.00
109 61 0.13
110 391 0.83
111 16 0.03
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.39
Consensus pattern (108 bp):
TAAGACCTCTGGGCATAATTTTGATTCGTGATGTTATCCCGATCGATTCCTTATCTTTCGACTTA
GGTGTTATCCCAGTCGATTCTGTAAGACCTCCGACATGATTTC
Found at i:3316446 original size:220 final size:220
Alignment explanation
Indices: 3316131--3316767 Score: 880
Period size: 220 Copynumber: 2.9 Consensus size: 220
3316121 AATTCGTGGG
*
3316131 GTTATCCCGATCGATTTCTTATCTTTCGAC-TGTGATGTTATCTCAGTCGATTCTGTAAGACCTC
1 GTTATCCCGATCGATTTCTTATCTTTCGACTTGTGGTGTTATCTCAGTCGATTCTGTAAGACCTC
* * * * *
3316195 CGAACATGACTTCTAAGACCTCTGAGCATAATTTTGATTCGTGATGTTATCCCGATCGATTCCTT
66 CGAGCATGATTTTTAAGACCTCTGAGCATAATTTTGATTCGTGATTTTATCCAGATCGATTCCTT
* * *
3316260 ATATTTCGACTTACGGTGTTATCCCAGTCGATTCTGTAAGACCTCCGGACATGATTTCTAAGATC
131 ATCTTTCGACTTACGGTGTTATCCCAGTCGATTCTGTAAGACCTCCAGACATGATTTCTAAGACC
* *
3316325 TCTGGGCATAATTTTGATTTACGAT
196 TCTGGGCATAATTTCGATTCACGAT
* * * *
3316350 GTTATCTCAATCGATTTTTTATCTTTCAACTTGTGGTGTTATCTCAGTCGATTCTGTAAGACCTC
1 GTTATCCCGATCGATTTCTTATCTTTCGACTTGTGGTGTTATCTCAGTCGATTCTGTAAGACCTC
* * * *
3316415 CGAGCATGATTTTTAAGACTTTTGGGCATAATTTTGATTTGTGATTTTATCCAGATCGATTCCTT
66 CGAGCATGATTTTTAAGACCTCTGAGCATAATTTTGATTCGTGATTTTATCCAGATCGATTCCTT
* ** * ** * **
3316480 ATCTTTTGACTTATAGTATTATTTCAATCGATTCTGTAAGACCTTTAGACATGATTTCTAAGACC
131 ATCTTTCGACTTACGGTGTTATCCCAGTCGATTCTGTAAGACCTCCAGACATGATTTCTAAGACC
* *
3316545 TCTGGGCATAATTTCGATTCGCGGT
196 TCTGGGCATAATTTCGATTCACGAT
* * * *
3316570 ATTATCCCGATCGATTTCTTATCTTTCGACTTGAGGTGTTATCCCAGTCGATTATGTAAGACCTC
1 GTTATCCCGATCGATTTCTTATCTTTCGACTTGTGGTGTTATCTCAGTCGATTCTGTAAGACCTC
* ** *
3316635 CGAGCATGATTTTTAAGACCTCCGAGCATAATTTTGATTCGTGATTTTATCTTGATTGATTCCTT
66 CGAGCATGATTTTTAAGACCTCTGAGCATAATTTTGATTCGTGATTTTATCCAGATCGATTCCTT
* * * *
3316700 ATCTTTCGACTTACGATGTTATCCCAGTCGATTCTGTAAGACCTCTAGGCATGATTGTGTAAGAC
131 ATCTTTCGACTTACGGTGTTATCCCAGTCGATTCTGTAAGACCTCCAGACATGATT-TCTAAGAC
3316765 CTC
195 CTC
3316768 CAGGCATTAT
Statistics
Matches: 359, Mismatches: 57, Indels: 2
0.86 0.14 0.00
Matches are distributed among these distances:
219 26 0.07
220 323 0.90
221 10 0.03
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.40
Consensus pattern (220 bp):
GTTATCCCGATCGATTTCTTATCTTTCGACTTGTGGTGTTATCTCAGTCGATTCTGTAAGACCTC
CGAGCATGATTTTTAAGACCTCTGAGCATAATTTTGATTCGTGATTTTATCCAGATCGATTCCTT
ATCTTTCGACTTACGGTGTTATCCCAGTCGATTCTGTAAGACCTCCAGACATGATTTCTAAGACC
TCTGGGCATAATTTCGATTCACGAT
Found at i:3316610 original size:330 final size:329
Alignment explanation
Indices: 3316099--3316780 Score: 836
Period size: 330 Copynumber: 2.1 Consensus size: 329
3316089 GTCGATTCCA
* * *
3316099 TAAGACCTTCGGGCATAATTTTAATTCGTGGGGTTATCCCGATCGATTTCTTATCTTTCGACTGT
1 TAAGACCTTCGGGCATAATTTTAATTCGTGAGGTTATCCAGATCGATTCCTTATCTTTCGACTGT
* *
3316164 GATGTTATCTCAGTCGATTCTGTAAGACCTCCGAACATGACTTCTAAGACCTCTGAGCATAATTT
66 GATGTTATCTCAATCGATTCTGTAAGACCTCAGAACATGACTTCTAAGACCTCTGAGCATAATTT
* * * *
3316229 TGATTCGTGATGTTATCCCGATCGATTCCTTATATTTCGACTTACGGTGTTATCCCAGTCGATTC
131 CGATTCGCGATATTATCCCGATCGATTCCTTATATTTCGACTTACGGTGTTATCCCAGTCGATTA
* * * *
3316294 TGTAAGACCTCCG-GACATGATTTCTAAGATCTCTGGGCATAATTTTGATTTACGATGTTATCTC
196 TGTAAGACCTCCGAG-CATGATTTCTAAGACCTCCGAGCATAATTTTGATTCACGATGTTATCTC
** ** * *
3316358 AATCGATTTTTTATCTTTCAACTTGTGGTGTTATCTCAGTCGATTCTGTAAGACCTCCGAGCATG
260 AATCGATTCCTTATCTTTCAACTTACGATGTTATCCCAGTCGATTCTGTAAGACCTCCGAGCATG
3316423 ATTTT
325 ATTTT
* * * * ** *
3316428 TAAGACTTTTGGGCATAATTTTGATTTGTGATTTTATCCAGATCGATTCCTTATCTTTTGACT-T
1 TAAGACCTTCGGGCATAATTTTAATTCGTGAGGTTATCCAGATCGATTCCTTATCTTTCGACTGT
* * * *
3316492 -ATAGTATTATTTCAATCGATTCTGTAAGACCTTTAG-ACATGATTTCTAAGACCTCTGGGCATA
66 GAT-G--TTATCTCAATCGATTCTGTAAGACC-TCAGAACATGACTTCTAAGACCTCTGAGCATA
* * *
3316555 ATTTCGATTCGCGGTATTATCCCGATCGATTTCTTATCTTTCGACTTGA-GGTGTTATCCCAGTC
127 ATTTCGATTCGCGATATTATCCCGATCGATTCCTTATATTTCGACTT-ACGGTGTTATCCCAGTC
* ** *
3316619 GATTATGTAAGACCTCCGAGCATGATTTTTAAGACCTCCGAGCATAATTTTGATTCGTGATTTTA
191 GATTATGTAAGACCTCCGAGCATGATTTCTAAGACCTCCGAGCATAATTTTGATTCACGATGTTA
** * * *
3316684 TCTTGATTGATTCCTTATCTTTCGACTTACGATGTTATCCCAGTCGATTCTGTAAGACCT-CTAG
256 TCTCAATCGATTCCTTATCTTTCAACTTACGATGTTATCCCAGTCGATTCTGTAAGACCTCCGA-
*
3316748 GCATGATTGTG
320 GCATGATT-TT
* * *
3316759 TAAGACCTCCAGGCATTATTTT
1 TAAGACCTTCGGGCATAATTTT
3316781 TAAGATCTCC
Statistics
Matches: 297, Mismatches: 48, Indels: 14
0.83 0.13 0.04
Matches are distributed among these distances:
327 2 0.01
328 2 0.01
329 55 0.19
330 216 0.73
331 22 0.07
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.39
Consensus pattern (329 bp):
TAAGACCTTCGGGCATAATTTTAATTCGTGAGGTTATCCAGATCGATTCCTTATCTTTCGACTGT
GATGTTATCTCAATCGATTCTGTAAGACCTCAGAACATGACTTCTAAGACCTCTGAGCATAATTT
CGATTCGCGATATTATCCCGATCGATTCCTTATATTTCGACTTACGGTGTTATCCCAGTCGATTA
TGTAAGACCTCCGAGCATGATTTCTAAGACCTCCGAGCATAATTTTGATTCACGATGTTATCTCA
ATCGATTCCTTATCTTTCAACTTACGATGTTATCCCAGTCGATTCTGTAAGACCTCCGAGCATGA
TTTT
Found at i:3316651 original size:22 final size:22
Alignment explanation
Indices: 3316626--3316669 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
3316616 GTCGATTATG
*
3316626 TAAGACCTCCGAGCATGATTTT
1 TAAGACCTCCGAGCATAATTTT
3316648 TAAGACCTCCGAGCATAATTTT
1 TAAGACCTCCGAGCATAATTTT
3316670 GATTCGTGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.32
Consensus pattern (22 bp):
TAAGACCTCCGAGCATAATTTT
Found at i:3316790 original size:22 final size:23
Alignment explanation
Indices: 3316729--3316774 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
3316719 TATCCCAGTC
* *
3316729 GATTCTGTAAGACCTCTAGGCAT
1 GATTGTGTAAGACCTCCAGGCAT
3316752 GATTGTGTAAGACCTCCAGGCAT
1 GATTGTGTAAGACCTCCAGGCAT
3316775 TATTTTTAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (23 bp):
GATTGTGTAAGACCTCCAGGCAT
Found at i:3316933 original size:40 final size:40
Alignment explanation
Indices: 3316878--3316957 Score: 124
Period size: 40 Copynumber: 2.0 Consensus size: 40
3316868 TGCTTTAAAA
* * *
3316878 AAAAATTCACAATTTGTTTTCAGACAAAATCGTTGTCTTT
1 AAAAATCCACAATTTGCTTTCAGACAAAATCATTGTCTTT
*
3316918 AAAAATCCACGATTTGCTTTCAGACAAAATCATTGTCTTT
1 AAAAATCCACAATTTGCTTTCAGACAAAATCATTGTCTTT
3316958 GTCTTTGCCC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (40 bp):
AAAAATCCACAATTTGCTTTCAGACAAAATCATTGTCTTT
Found at i:3317048 original size:3 final size:3
Alignment explanation
Indices: 3317042--3317080 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
3317032 TTATTAAAAT
* *
3317042 TAA TAA TAT TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3317081 ATATATATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:3317525 original size:26 final size:24
Alignment explanation
Indices: 3317480--3317529 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 24
3317470 CACCAACCAC
3317480 AAAAAAAAAAAAAAACACAAACAG
1 AAAAAAAAAAAAAAACACAAACAG
* *
3317504 AAAAACAAAAACACAAAGACAAACAG
1 AAAAA-AAAAA-AAAAACACAAACAG
3317530 TCCTCCCCGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 5 0.23
25 5 0.23
26 12 0.55
ACGTcount: A:0.78, C:0.16, G:0.06, T:0.00
Consensus pattern (24 bp):
AAAAAAAAAAAAAAACACAAACAG
Found at i:3318098 original size:56 final size:56
Alignment explanation
Indices: 3318007--3318119 Score: 217
Period size: 56 Copynumber: 2.0 Consensus size: 56
3317997 TAAAAATCAA
*
3318007 ATAATTTATTATTGCAAAACATTTCTTAAAATCTTTTCAAGAGTTAGAATAATTTC
1 ATAACTTATTATTGCAAAACATTTCTTAAAATCTTTTCAAGAGTTAGAATAATTTC
3318063 ATAACTTATTATTGCAAAACATTTCTTAAAATCTTTTCAAGAGTTAGAATAATTTC
1 ATAACTTATTATTGCAAAACATTTCTTAAAATCTTTTCAAGAGTTAGAATAATTTC
3318119 A
1 A
3318120 GTTATGATGA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.42
Consensus pattern (56 bp):
ATAACTTATTATTGCAAAACATTTCTTAAAATCTTTTCAAGAGTTAGAATAATTTC
Found at i:3318754 original size:2 final size:2
Alignment explanation
Indices: 3318747--3318782 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
3318737 TTTAAGTCAT
3318747 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3318783 TCGTTTCGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3319180 original size:19 final size:19
Alignment explanation
Indices: 3319154--3319194 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
3319144 ATTATTATAT
3319154 TATTTTA-TATTTT-T-AA
1 TATTTTATTATTTTATGAA
3319170 TATTTTATTATTTTATGAA
1 TATTTTATTATTTTATGAA
3319189 TATTTT
1 TATTTT
3319195 TTTTATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.32
17 6 0.27
18 1 0.05
19 8 0.36
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (19 bp):
TATTTTATTATTTTATGAA
Found at i:3320179 original size:31 final size:30
Alignment explanation
Indices: 3320143--3320210 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 30
3320133 TATATTTTAT
* *
3320143 ATTTTTATATGAACATAAATTATAAA-ATATA
1 ATTTTTATATAAAAAT-AA-TATAAATATATA
3320174 ATTTTTATATAAAAATAATATAAATATATA
1 ATTTTTATATAAAAATAATATAAATATATA
*
3320204 AATTTTA
1 ATTTTTA
3320211 ATATTTTATA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 6 0.18
30 13 0.39
31 14 0.42
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (30 bp):
ATTTTTATATAAAAATAATATAAATATATA
Found at i:3320210 original size:30 final size:31
Alignment explanation
Indices: 3320145--3320210 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 31
3320135 TATTTTATAT
* * *
3320145 TTTTATATGAACATAAATTATAAAATATAAT
1 TTTTATATAAAAATAAATTATAAAATATAAA
3320176 TTTTATATAAAAAT-AA-TATAAATATATAAA
1 TTTTATATAAAAATAAATTATAAA-ATATAAA
3320206 TTTTA
1 TTTTA
3320211 ATATTTTATA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 6 0.19
30 13 0.42
31 12 0.39
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (31 bp):
TTTTATATAAAAATAAATTATAAAATATAAA
Found at i:3322903 original size:2 final size:2
Alignment explanation
Indices: 3322896--3322940 Score: 65
Period size: 2 Copynumber: 22.5 Consensus size: 2
3322886 AACTAAAGTT
*
3322896 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG T- TA TA TA CTA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
3322938 TA T
1 TA T
3322941 TTTAGGTTGC
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
1 1 0.03
2 37 0.93
3 2 0.05
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3330897 original size:16 final size:17
Alignment explanation
Indices: 3330876--3330909 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
3330866 TTATCTTTTT
3330876 ATTTTTATCT-AAATAA
1 ATTTTTATCTCAAATAA
*
3330892 ATTTTTATTTCAAATAA
1 ATTTTTATCTCAAATAA
3330909 A
1 A
3330910 AAATTAGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTTTATCTCAAATAA
Found at i:3333542 original size:267 final size:267
Alignment explanation
Indices: 3333067--3333567 Score: 912
Period size: 267 Copynumber: 1.9 Consensus size: 267
3333057 CCGCGCGGGT
*
3333067 TCAGAGCTAGCCCTATACCGTTCGATCAACGCCAAGCGCAGGACGTCATGAGGTTGGGTGCGGGA
1 TCAGAGCTAGCCCTATACCGTTCGATCAACGCCAAGCGCAGGACGTCACGAGGTTGGGTGCGGGA
* *
3333132 GAATGCCACGGACCTAAGGAGGAGTCTTGAATCCTACATTGAACATAATAAGAGGGTCACTGAAG
66 GAATGCCACGGACCTAAGGAGGAGTCTTGAATCCCACATTGAACATAATAAGAGGCTCACTGAAG
* *
3333197 TATAAAAGGGTTCACACCATTTCTTACTTACGAAACATTTTTTGTAGGACAAAATCGTGAGGTAA
131 TATAAAAGGGTTCACACCATTTCTTACTTAAGAAACATTTTTTGTAGGACAAAATCGTGAGGCAA
3333262 AAAGATAAGAGCGGACAATACCTCACAAGAGTGTGAACCGAGTTCAGAGCTTAAGTCTCGTGACA
196 AAAGATAAGAGCGGACAATACCTCACAAGAGTGTGAACCGAGTTCAGAGCTTAAGTCTCGTGACA
3333327 AGTGGTA
261 AGTGGTA
3333334 TCAGAGCTAGCCCTATACCGTTCGATCAACGCCAAGCGCAGGACGTCACGAGGTTGGGTGCGGGA
1 TCAGAGCTAGCCCTATACCGTTCGATCAACGCCAAGCGCAGGACGTCACGAGGTTGGGTGCGGGA
**
3333399 GAATGCCACGGACCTAAGGAGGAGTCTTGAATCCCACATTGAACATAATAAGAGGCTCACTGGGG
66 GAATGCCACGGACCTAAGGAGGAGTCTTGAATCCCACATTGAACATAATAAGAGGCTCACTGAAG
3333464 TATAAAAGGGTTCACACCATTTCTTACTTAAGAAACATTTTTTGTAGGACAAAATCGTGAGGCAA
131 TATAAAAGGGTTCACACCATTTCTTACTTAAGAAACATTTTTTGTAGGACAAAATCGTGAGGCAA
* * *
3333529 AAAGATCAGAGCGGATAATACCTCACAAGGGTGTGAACC
196 AAAGATAAGAGCGGACAATACCTCACAAGAGTGTGAACC
3333568 CTGACAGTCA
Statistics
Matches: 224, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
267 224 1.00
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.22
Consensus pattern (267 bp):
TCAGAGCTAGCCCTATACCGTTCGATCAACGCCAAGCGCAGGACGTCACGAGGTTGGGTGCGGGA
GAATGCCACGGACCTAAGGAGGAGTCTTGAATCCCACATTGAACATAATAAGAGGCTCACTGAAG
TATAAAAGGGTTCACACCATTTCTTACTTAAGAAACATTTTTTGTAGGACAAAATCGTGAGGCAA
AAAGATAAGAGCGGACAATACCTCACAAGAGTGTGAACCGAGTTCAGAGCTTAAGTCTCGTGACA
AGTGGTA
Found at i:3333719 original size:121 final size:121
Alignment explanation
Indices: 3333501--3333740 Score: 426
Period size: 121 Copynumber: 2.0 Consensus size: 121
3333491 TTAAGAAACA
*
3333501 TTTTTTGTAGGACAAAATCGTGAGGCAAAAAGATCAGAGCGGATAATACCTCACAAGGGTGTGAA
1 TTTTTTGTAGGACAAAATCGTGAGGCAAAAAGATCAGAGCGGACAATACCTCACAAGGGTGTGAA
* * *
3333566 CCCTGACAGTCAGGCTGATCTGAGACGTCGGATGAGTGGATGCTCGGAACCTGGCG
66 CCCTGACAATCAGGCTGATCTGAGACGCCGGATGAGTGGATGCTCAGAACCTGGCG
3333622 TTTTTTGTAGGACAAAATCGTGAGGCAAAAAGATCAGAGCGGACAATACCTCACAAGGGTGTGAA
1 TTTTTTGTAGGACAAAATCGTGAGGCAAAAAGATCAGAGCGGACAATACCTCACAAGGGTGTGAA
* *
3333687 CCTTGACAATCAGGCTGATCTGAGACGCCGGATGAGTGGATGCTCAGATCCTGG
66 CCCTGACAATCAGGCTGATCTGAGACGCCGGATGAGTGGATGCTCAGAACCTGG
3333741 AGCCGCACAA
Statistics
Matches: 113, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
121 113 1.00
ACGTcount: A:0.30, C:0.19, G:0.30, T:0.22
Consensus pattern (121 bp):
TTTTTTGTAGGACAAAATCGTGAGGCAAAAAGATCAGAGCGGACAATACCTCACAAGGGTGTGAA
CCCTGACAATCAGGCTGATCTGAGACGCCGGATGAGTGGATGCTCAGAACCTGGCG
Found at i:3339814 original size:26 final size:26
Alignment explanation
Indices: 3339765--3339814 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
3339755 AATTTGAATC
* *
3339765 TAAAATAATTTAAATATGATATTTCA
1 TAAAAAAATTTAAATATGAAATTTCA
* *
3339791 TAAAAAAATTTAAATGTTAAATTT
1 TAAAAAAATTTAAATATGAAATTT
3339815 GAAATGATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (26 bp):
TAAAAAAATTTAAATATGAAATTTCA
Found at i:3348167 original size:3 final size:3
Alignment explanation
Indices: 3348159--3348274 Score: 83
Period size: 3 Copynumber: 38.7 Consensus size: 3
3348149 GATTAATGTG
* * * * **
3348159 GAA GAA GAA GAA GAA GAA GAA GAA GAA GCA GAA GAA CAG GAT GGC GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
** * * * * *
3348207 GAA GAA GAA TTA GAA GAT GAT GAA GTA GAA GAA GATA G-C GATG GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA-A GAA GA-A GAA
3348253 -AA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GA
3348275 CAACGATGGG
Statistics
Matches: 88, Mismatches: 21, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
2 3 0.03
3 81 0.92
4 4 0.05
ACGTcount: A:0.56, C:0.03, G:0.34, T:0.07
Consensus pattern (3 bp):
GAA
Found at i:3353019 original size:30 final size:31
Alignment explanation
Indices: 3352985--3353043 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
3352975 ATTATATTAA
* * *
3352985 ATTTATTTTTAATTAATTATTTA-ATTTTTT
1 ATTTATATATAATTAAATATTTATATTTTTT
*
3353015 ATTTATATATACTTAAATATTTATATTTT
1 ATTTATATATAATTAAATATTTATATTTT
3353044 AAAAAATAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 19 0.79
31 5 0.21
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (31 bp):
ATTTATATATAATTAAATATTTATATTTTTT
Found at i:3364572 original size:31 final size:30
Alignment explanation
Indices: 3364524--3364597 Score: 112
Period size: 31 Copynumber: 2.4 Consensus size: 30
3364514 TTATATAATG
3364524 TTAATAAATAAATCAAATGATGATAATTCA
1 TTAATAAATAAATCAAATGATGATAATTCA
* *
3364554 TTAATAAAATGAATCAAATGATGATATTTCA
1 TTAAT-AAATAAATCAAATGATGATAATTCA
*
3364585 TTAATGAATAAAT
1 TTAATAAATAAAT
3364598 TATTTTAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 11 0.28
31 28 0.72
ACGTcount: A:0.51, C:0.05, G:0.08, T:0.35
Consensus pattern (30 bp):
TTAATAAATAAATCAAATGATGATAATTCA
Found at i:3365831 original size:21 final size:22
Alignment explanation
Indices: 3365811--3365851 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
3365801 TTTTTTATTA
*
3365811 AAAAT-AATT-AAATAAAAATT
1 AAAATCAATTGAAAAAAAAATT
3365831 AAAATCAATTGAAAAAAAAAT
1 AAAATCAATTGAAAAAAAAAT
3365852 ATATAAGAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 4 0.22
22 9 0.50
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (22 bp):
AAAATCAATTGAAAAAAAAATT
Found at i:3368110 original size:39 final size:38
Alignment explanation
Indices: 3368067--3368164 Score: 90
Period size: 39 Copynumber: 2.5 Consensus size: 38
3368057 AAAAATATTA
* * *
3368067 TTTATCAAATGT-GAATTTCTCCGTTAATTGTATGAACAT
1 TTTATCAAAT-TAAAATTT-TCCGCTAATTATATGAACAT
* *
3368106 TTTATGCTAATTAAAATTTTTCGCTAATTATATGAACAT
1 TTTAT-CAAATTAAAATTTTCCGCTAATTATATGAACAT
*
3368145 TTTATCCTAATTAAACATTT
1 TTTAT-CAAATTAAA-ATTT
3368165 GATCACATTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
39 37 0.74
40 13 0.26
ACGTcount: A:0.34, C:0.12, G:0.08, T:0.46
Consensus pattern (38 bp):
TTTATCAAATTAAAATTTTCCGCTAATTATATGAACAT
Found at i:3368157 original size:22 final size:22
Alignment explanation
Indices: 3368091--3368157 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 22
3368081 ATTTCTCCGT
* *
3368091 TAATTGTATGAACATTTTATGC
1 TAATTATATGAACATTTTATCC
3368113 TAA-T-TA--AA-ATTTT-TCGC
1 TAATTATATGAACATTTTATC-C
3368130 TAATTATATGAACATTTTATCC
1 TAATTATATGAACATTTTATCC
3368152 TAATTA
1 TAATTA
3368158 AACATTTGAT
Statistics
Matches: 37, Mismatches: 1, Indels: 14
0.71 0.02 0.27
Matches are distributed among these distances:
16 1 0.03
17 9 0.24
18 3 0.08
19 2 0.05
20 2 0.05
21 3 0.08
22 15 0.41
23 2 0.05
ACGTcount: A:0.36, C:0.10, G:0.07, T:0.46
Consensus pattern (22 bp):
TAATTATATGAACATTTTATCC
Found at i:3368593 original size:21 final size:22
Alignment explanation
Indices: 3368551--3368598 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
3368541 TCTAAAATTA
3368551 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTATTTTTTAAAAT
3368573 ATAAAATATT-TATTTTT-AAAT
1 ATAAAATATTAT-TTTTTAAAAT
3368594 ATAAA
1 ATAAA
3368599 TTTATAAGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 10 0.40
22 15 0.60
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATAAAATATTATTTTTTAAAAT
Found at i:3375829 original size:8 final size:8
Alignment explanation
Indices: 3375796--3375855 Score: 56
Period size: 8 Copynumber: 7.8 Consensus size: 8
3375786 TTATTTTTTA
*
3375796 TTATGTAT
1 TTATATAT
3375804 TTA-AT-T
1 TTATATAT
3375810 TTATA-AT
1 TTATATAT
3375817 GTTATATAT
1 -TTATATAT
3375826 TTATATAT
1 TTATATAT
*
3375834 TTATTTAAT
1 TTATAT-AT
3375843 TT-TATAT
1 TTATATAT
3375850 TTATAT
1 TTATAT
3375856 TTATATAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
6 4 0.09
7 7 0.16
8 26 0.60
9 6 0.14
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (8 bp):
TTATATAT
Found at i:3375830 original size:6 final size:6
Alignment explanation
Indices: 3375821--3375861 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
3375811 TATAATGTTA
3375821 TATATT TATATAT T-TATT TA-ATTT TATATT TATATT TATAT
1 TATATT TATAT-T TATATT TATA-TT TATATT TATATT TATAT
3375862 AAAAATAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
5 3 0.10
6 25 0.81
7 3 0.10
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
TATATT
Found at i:3375844 original size:34 final size:30
Alignment explanation
Indices: 3375792--3375862 Score: 90
Period size: 34 Copynumber: 2.3 Consensus size: 30
3375782 ATAATTATTT
3375792 TTTAT-TATGTATTTAATTTTATAATGTTATATA
1 TTTATATATGTATTTAATTTTAT-A--TT-TATA
*
3375825 TTTATATATTTATTTAATTTTATATTTATA
1 TTTATATATGTATTTAATTTTATATTTATA
3375855 TTTATATA
1 TTTATATA
3375863 AAAATAATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
30 12 0.33
31 2 0.06
33 6 0.17
34 16 0.44
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (30 bp):
TTTATATATGTATTTAATTTTATATTTATA
Found at i:3375851 original size:46 final size:47
Alignment explanation
Indices: 3375761--3375863 Score: 113
Period size: 46 Copynumber: 2.2 Consensus size: 47
3375751 TCGAGGTTAG
*
3375761 ATTTTATAATCTAATATATATATAATTATTTTTTATTATGTATTTA-
1 ATTTTATAATCTAATATATATATAATTATTTTTTATTATATATTTAT
* * * *
3375807 ATTTTATAATGTTATATATTTAT-A-TATTTATTTAATTTTATATTTAT
1 ATTTTATAATCTAATATATATATAATTATTT-TTT-ATTATATATTTAT
3375854 ATTTATATAA
1 ATTT-TATAA
3375864 AAATAATATT
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
44 5 0.10
45 4 0.08
46 30 0.62
47 4 0.08
48 5 0.10
ACGTcount: A:0.37, C:0.01, G:0.02, T:0.60
Consensus pattern (47 bp):
ATTTTATAATCTAATATATATATAATTATTTTTTATTATATATTTAT
Found at i:3382642 original size:19 final size:19
Alignment explanation
Indices: 3382618--3382655 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
3382608 CCTCTAACTC
* *
3382618 AAGTTAATTTCAGCTAATT
1 AAGTTAATTCCAGCAAATT
3382637 AAGTTAATTCCAGCAAATT
1 AAGTTAATTCCAGCAAATT
3382656 CATTTCAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (19 bp):
AAGTTAATTCCAGCAAATT
Found at i:3387040 original size:22 final size:24
Alignment explanation
Indices: 3387013--3387061 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
3387003 ATTCAATTAC
3387013 TTAAA-TA-ATATAAATAATTTTT
1 TTAAATTATATATAAATAATTTTT
*
3387035 TTAAATTATTTATAAATAATTTTT
1 TTAAATTATATATAAATAATTTTT
3387059 TTA
1 TTA
3387062 CTCGATATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 5 0.21
23 2 0.08
24 17 0.71
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
TTAAATTATATATAAATAATTTTT
Found at i:3389366 original size:3 final size:3
Alignment explanation
Indices: 3389358--3389404 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
3389348 ATTCCCCCAT
3389358 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3389405 TCTTTTGAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3390301 original size:23 final size:23
Alignment explanation
Indices: 3390275--3390327 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
3390265 CACAGATAAC
* * * *
3390275 AAAAAAAGGGGAAACACATAATA
1 AAAAAAAGAGCAAACACAAAAAA
*
3390298 AAAAAAATAGCAAACACAAAAAA
1 AAAAAAAGAGCAAACACAAAAAA
3390321 AAAAAAA
1 AAAAAAA
3390328 TTTTGATAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.75, C:0.09, G:0.09, T:0.06
Consensus pattern (23 bp):
AAAAAAAGAGCAAACACAAAAAA
Found at i:3390791 original size:12 final size:13
Alignment explanation
Indices: 3390773--3390827 Score: 60
Period size: 13 Copynumber: 4.4 Consensus size: 13
3390763 TTTCGTAGGT
* *
3390773 TTTTTTTTTTTAA
1 TTTTTTATTTTGA
*
3390786 TTTTTTGTTTTGA
1 TTTTTTATTTTGA
*
3390799 -TTTTGATTTTGA
1 TTTTTTATTTTGA
3390811 TTTTTTATTTT-A
1 TTTTTTATTTTGA
3390823 TTTTT
1 TTTTT
3390828 ATGATGTTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
12 16 0.44
13 20 0.56
ACGTcount: A:0.13, C:0.00, G:0.07, T:0.80
Consensus pattern (13 bp):
TTTTTTATTTTGA
Found at i:3390827 original size:25 final size:25
Alignment explanation
Indices: 3390780--3390826 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
3390770 GGTTTTTTTT
*
3390780 TTTTAATTTTTTGTTTTGATTTTGA
1 TTTTAATTTTTTATTTTGATTTTGA
*
3390805 TTTTGATTTTTTATTTT-ATTTT
1 TTTTAATTTTTTATTTTGATTTT
3390827 TATGATGTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 5 0.25
25 15 0.75
ACGTcount: A:0.15, C:0.00, G:0.09, T:0.77
Consensus pattern (25 bp):
TTTTAATTTTTTATTTTGATTTTGA
Found at i:3390842 original size:3 final size:3
Alignment explanation
Indices: 3390834--3390862 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3390824 TTTTATGATG
3390834 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3390863 GGTAATAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3392281 original size:14 final size:15
Alignment explanation
Indices: 3392257--3392285 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3392247 GGATCTGTTT
3392257 ATTTCTTAAAAAATA
1 ATTTCTTAAAAAATA
3392272 ATTT-TTAAAAAATA
1 ATTTCTTAAAAAATA
3392286 CTTATATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (15 bp):
ATTTCTTAAAAAATA
Found at i:3392437 original size:34 final size:34
Alignment explanation
Indices: 3392385--3392465 Score: 96
Period size: 34 Copynumber: 2.4 Consensus size: 34
3392375 TATTTTTTTA
* *
3392385 AATTATATTAATATAATTATTAAAGTATTAA-AAAT
1 AATTATATTATTAAAATTATT-AA-TATTAAGAAAT
*
3392420 TATT-TATTATTAAAATTATTAATATTAAGAAAT
1 AATTATATTATTAAAATTATTAATATTAAGAAAT
3392453 AATTATATT-TTAA
1 AATTATATTATTAA
3392466 TAATAATATT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
32 6 0.15
33 13 0.32
34 18 0.45
35 3 0.08
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (34 bp):
AATTATATTATTAAAATTATTAATATTAAGAAAT
Found at i:3392447 original size:15 final size:15
Alignment explanation
Indices: 3392399--3392447 Score: 53
Period size: 15 Copynumber: 3.0 Consensus size: 15
3392389 ATATTAATAT
3392399 AATTATTAAAGTATTAAA
1 AATTATT-AA-TATT-AA
*
3392417 AATTATTTATTATTAA
1 AATTA-TTAATATTAA
3392433 AATTATTAATATTAA
1 AATTATTAATATTAA
3392448 GAAATAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
15 9 0.32
16 7 0.25
17 4 0.14
18 6 0.21
19 2 0.07
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (15 bp):
AATTATTAATATTAA
Found at i:3392557 original size:23 final size:23
Alignment explanation
Indices: 3392527--3392599 Score: 92
Period size: 28 Copynumber: 3.0 Consensus size: 23
3392517 ATTATTCTTT
3392527 ATATTATTTATTAATATATTATA
1 ATATTATTTATTAATATATTATA
*
3392550 ATATTATTTATTAAAATATTAAAATATA
1 ATATTATTTATT--AATA-T--ATTATA
3392578 ATATTATTTATTAATATATTAT
1 ATATTATTTATTAATATATTAT
3392600 TATTTATAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
23 16 0.37
25 5 0.12
26 5 0.12
28 17 0.40
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
ATATTATTTATTAATATATTATA
Found at i:3392561 original size:15 final size:15
Alignment explanation
Indices: 3392543--3392606 Score: 60
Period size: 15 Copynumber: 4.2 Consensus size: 15
3392533 TTTATTAATA
3392543 TATTATAATATTATT
1 TATTATAATATTATT
*
3392558 TATTAAAATATTA--
1 TATTATAATATTATT
* *
3392571 AAATATAATATTATT
1 TATTATAATATTATT
3392586 TATTAATATATTATTATT
1 TATT-ATA-A-TATTATT
3392604 TAT
1 TAT
3392607 AAGTAAAATT
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
13 10 0.26
15 14 0.37
16 3 0.08
17 1 0.03
18 10 0.26
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TATTATAATATTATT
Found at i:3392591 original size:20 final size:18
Alignment explanation
Indices: 3392527--3392606 Score: 69
Period size: 18 Copynumber: 4.6 Consensus size: 18
3392517 ATTATTCTTT
3392527 ATATTATTTATTAATATA
1 ATATTATTTATTAATATA
* * *
3392545 TTATAATATTATTTAT-TA
1 ATATTAT-TTATTAATATA
* *
3392563 A-AATA-TTA-AAATATA
1 ATATTATTTATTAATATA
3392578 ATATTATTTATTAATATA
1 ATATTATTTATTAATATA
*
3392596 TTATTATTTAT
1 ATATTATTTAT
3392607 AAGTAAAATT
Statistics
Matches: 46, Mismatches: 11, Indels: 10
0.69 0.16 0.15
Matches are distributed among these distances:
14 2 0.04
15 6 0.13
16 3 0.07
17 5 0.11
18 23 0.50
19 7 0.15
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
ATATTATTTATTAATATA
Found at i:3393843 original size:15 final size:15
Alignment explanation
Indices: 3393810--3393844 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
3393800 CTCGCGTCGT
*
3393810 CCACCTCCATATCCA
1 CCACCCCCATATCCA
3393825 CCACCCCCATATCCA
1 CCACCCCCATATCCA
3393840 CCACC
1 CCACC
3393845 GTTGCCGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.26, C:0.60, G:0.00, T:0.14
Consensus pattern (15 bp):
CCACCCCCATATCCA
Found at i:3396817 original size:28 final size:28
Alignment explanation
Indices: 3396785--3396885 Score: 96
Period size: 29 Copynumber: 3.5 Consensus size: 28
3396775 AAATTCTTAA
*
3396785 ATATTATTATTTTATTTAATAAATTTTT
1 ATATTTTTATTTTATTTAATAAATTTTT
*** *
3396813 ATATTTTTATTACGTTTAAATAACTTTTT
1 ATATTTTTATTTTATTT-AATAAATTTTT
* *
3396842 AAATTTTAATTTATATTTACATAAATTTTT
1 ATATTTTTATTT-TATTTA-ATAAATTTTT
*
3396872 A-ATTTTTAATTTAT
1 ATATTTTTATTTTAT
3396886 ACTAAAATAA
Statistics
Matches: 57, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
28 16 0.28
29 28 0.49
30 13 0.23
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (28 bp):
ATATTTTTATTTTATTTAATAAATTTTT
Found at i:3396873 original size:30 final size:29
Alignment explanation
Indices: 3396775--3396886 Score: 102
Period size: 30 Copynumber: 3.8 Consensus size: 29
3396765 AGGTTTAAAA
* *
3396775 AAATTCTTAAATATTATTATTT-TATTTAAT
1 AAATTTTTAAAT-TT-TAATTTATATTTAAT
* * **
3396805 AAATTTTTATATTTTTA-TTACGTTTAAAT
1 AAATTTTTAAATTTTAATTTATATTT-AAT
*
3396834 AACTTTTTAAATTTTAATTTATATTTACAT
1 AAATTTTTAAATTTTAATTTATATTTA-AT
*
3396864 AAATTTTTAATTTTTAATTTATA
1 AAATTTTTAAATTTTAATTTATA
3396887 CTAAAATAAA
Statistics
Matches: 67, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
27 2 0.03
28 6 0.09
29 20 0.30
30 39 0.58
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.58
Consensus pattern (29 bp):
AAATTTTTAAATTTTAATTTATATTTAAT
Found at i:3396896 original size:30 final size:30
Alignment explanation
Indices: 3396830--3396897 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 30
3396820 TATTACGTTT
* * *
3396830 AAATAACTTTTTAAATTTTAATTTATATTT
1 AAATAAATTTTTAAATTTTAATTTATACTA
* *
3396860 ACATAAATTTTTAATTTTTAATTTATACTA
1 AAATAAATTTTTAAATTTTAATTTATACTA
3396890 AAATAAAT
1 AAATAAAT
3396898 CATTAACAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.51
Consensus pattern (30 bp):
AAATAAATTTTTAAATTTTAATTTATACTA
Found at i:3398397 original size:2 final size:2
Alignment explanation
Indices: 3398390--3398420 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3398380 ACTTCCATAA
3398390 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3398421 AGATTGTACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3401282 original size:18 final size:18
Alignment explanation
Indices: 3401259--3401323 Score: 71
Period size: 18 Copynumber: 3.7 Consensus size: 18
3401249 TTTAATCAAA
**
3401259 TTAATTGATCGAATTAAT
1 TTAATTGATTAAATTAAT
* *
3401277 TTAATTTATTTAATTAA-
1 TTAATTGATTAAATTAAT
3401294 TTAATT-ATTAAATTAAT
1 TTAATTGATTAAATTAAT
3401311 TTCAATTGATTAA
1 TT-AATTGATTAA
3401324 CGAAAATGAT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
16 9 0.22
17 8 0.20
18 18 0.45
19 5 0.12
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.51
Consensus pattern (18 bp):
TTAATTGATTAAATTAAT
Found at i:3401686 original size:14 final size:14
Alignment explanation
Indices: 3401661--3401713 Score: 52
Period size: 15 Copynumber: 3.6 Consensus size: 14
3401651 TAAAAAAATA
*
3401661 AAATAATATAATTT
1 AAATAATTTAATTT
* *
3401675 GATTAATTTAATTTT
1 AAATAATTTAA-TTT
3401690 AAATAATTTAATTTT
1 AAATAATTTAA-TTT
3401705 AAATTAATT
1 AAA-TAATT
3401714 AAATCGATCG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
14 8 0.25
15 19 0.59
16 5 0.16
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (14 bp):
AAATAATTTAATTT
Found at i:3401715 original size:15 final size:16
Alignment explanation
Indices: 3401676--3401713 Score: 69
Period size: 15 Copynumber: 2.4 Consensus size: 16
3401666 ATATAATTTG
3401676 ATTAATTTAATTTTAA
1 ATTAATTTAATTTTAA
3401692 A-TAATTTAATTTTAA
1 ATTAATTTAATTTTAA
3401707 ATTAATT
1 ATTAATT
3401714 AAATCGATCG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 15 0.71
16 6 0.29
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
ATTAATTTAATTTTAA
Found at i:3409457 original size:15 final size:15
Alignment explanation
Indices: 3409437--3409471 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
3409427 CCATGGAACC
3409437 TTTCATGATAAATGA
1 TTTCATGATAAATGA
3409452 TTTCATGATAAATGA
1 TTTCATGATAAATGA
3409467 TTTCA
1 TTTCA
3409472 AATTAAACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.37, C:0.09, G:0.11, T:0.43
Consensus pattern (15 bp):
TTTCATGATAAATGA
Found at i:3410141 original size:9 final size:9
Alignment explanation
Indices: 3410127--3410163 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
3410117 AACTGTATCG
3410127 GTGGTTGAA
1 GTGGTTGAA
3410136 GTGGTTGAA
1 GTGGTTGAA
*
3410145 GTGGTCGAA
1 GTGGTTGAA
*
3410154 GTAGTTGAA
1 GTGGTTGAA
3410163 G
1 G
3410164 CACAATAACC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.24, C:0.03, G:0.43, T:0.30
Consensus pattern (9 bp):
GTGGTTGAA
Found at i:3426086 original size:14 final size:14
Alignment explanation
Indices: 3426067--3426100 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
3426057 AAAATATCAC
3426067 TTATAATT-ATTATA
1 TTATAATTAATTA-A
3426081 TTATAATTAATTAA
1 TTATAATTAATTAA
3426095 TTATAA
1 TTATAA
3426101 ATTCACATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 15 0.79
15 4 0.21
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TTATAATTAATTAA
Found at i:3427007 original size:18 final size:17
Alignment explanation
Indices: 3426965--3426999 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
3426955 TTGATATAAT
3426965 ATTAAATTTAAATTTGA
1 ATTAAATTTAAATTTGA
*
3426982 ATTGAATTTAAAATTTGA
1 ATTAAATTT-AAATTTGA
3427000 TTCAAATTCG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.46, C:0.00, G:0.09, T:0.46
Consensus pattern (17 bp):
ATTAAATTTAAATTTGA
Found at i:3427106 original size:22 final size:24
Alignment explanation
Indices: 3427081--3427135 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
3427071 ATTTTATTAT
3427081 ATTTAATTAATATA-T-AAAAAAA
1 ATTTAATTAATATATTCAAAAAAA
** *
3427103 ATTTAATTTTTATATTCAATAAAA
1 ATTTAATTAATATATTCAAAAAAA
3427127 ATTTAATTA
1 ATTTAATTA
3427136 TTTGTATTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 12 0.44
23 1 0.04
24 14 0.52
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (24 bp):
ATTTAATTAATATATTCAAAAAAA
Found at i:3427200 original size:22 final size:21
Alignment explanation
Indices: 3427175--3427226 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
3427165 AATTTTTATT
*
3427175 AATTAAATTTATAAATTATCTA
1 AATTAAATTTA-AAAATATCTA
* *
3427197 AATTAAATATAAAAATATTTA
1 AATTAAATTTAAAAATATCTA
*
3427218 AATTTAATT
1 AATTAAATT
3427227 AAATCGATAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 15 0.60
22 10 0.40
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
AATTAAATTTAAAAATATCTA
Found at i:3440800 original size:11 final size:12
Alignment explanation
Indices: 3440772--3440804 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
3440762 CATGAACAGC
*
3440772 AAATTTTCATGA
1 AAATTTACATGA
3440784 AAATTTACATG-
1 AAATTTACATGA
3440795 AAATTTACAT
1 AAATTTACAT
3440805 ATAAGATTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.45, C:0.09, G:0.06, T:0.39
Consensus pattern (12 bp):
AAATTTACATGA
Found at i:3446424 original size:6 final size:6
Alignment explanation
Indices: 3446413--3446450 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
3446403 TTTATAAATT
*
3446413 ATTTAA ATTT-A ATTTAA A-TAAA ATTTAA ATTTAA ATTT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTT
3446451 GATTATTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
5 9 0.32
6 19 0.68
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
ATTTAA
Found at i:3446427 original size:11 final size:11
Alignment explanation
Indices: 3446413--3446446 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
3446403 TTTATAAATT
3446413 ATTTAAATTTA
1 ATTTAAATTTA
**
3446424 ATTTAAATAAA
1 ATTTAAATTTA
3446435 ATTTAAATTTA
1 ATTTAAATTTA
3446446 A
1 A
3446447 ATTTGATTAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
ATTTAAATTTA
Found at i:3446445 original size:17 final size:16
Alignment explanation
Indices: 3446417--3446448 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
3446407 TAAATTATTT
3446417 AAATTTAATTTAAATA
1 AAATTTAATTTAAATA
3446433 AAATTTAAATTTAAAT
1 AAATTT-AATTTAAAT
3446449 TTGATTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AAATTTAATTTAAATA
Found at i:3446530 original size:21 final size:21
Alignment explanation
Indices: 3446505--3446565 Score: 67
Period size: 20 Copynumber: 3.0 Consensus size: 21
3446495 GATTGAATCA
3446505 AATTTAAATATTTTTATATTT
1 AATTTAAATATTTTTATATTT
*
3446526 AATTTAAATA-ATTTATGAATTT
1 AATTTAAATATTTTTAT--ATTT
3446548 AATTT--A-ATTTTTATATTT
1 AATTTAAATATTTTTATATTT
3446566 TGATAATTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
18 4 0.11
19 1 0.03
20 11 0.31
21 10 0.29
22 9 0.26
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (21 bp):
AATTTAAATATTTTTATATTT
Found at i:3446547 original size:22 final size:21
Alignment explanation
Indices: 3446505--3446565 Score: 67
Period size: 22 Copynumber: 3.0 Consensus size: 21
3446495 GATTGAATCA
*
3446505 AATTTAAATATTTTTATATTT
1 AATTTAAATATTTTGATATTT
3446526 AATTTAAATAATTTATGA-ATTT
1 AATTTAAAT-ATTT-TGATATTT
3446548 AATTT-AAT-TTTT-ATATTT
1 AATTTAAATATTTTGATATTT
3446566 TGATAATTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
17 1 0.03
18 5 0.14
19 3 0.08
21 12 0.33
22 13 0.36
23 2 0.06
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (21 bp):
AATTTAAATATTTTGATATTT
Found at i:3459801 original size:2 final size:2
Alignment explanation
Indices: 3459788--3459823 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
3459778 TCACAATTCA
*
3459788 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3459824 TTCGAATATG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3461384 original size:21 final size:21
Alignment explanation
Indices: 3461360--3461399 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3461350 TGGAGATGAG
* *
3461360 GAGGATGGTGTTGGTGGTGCT
1 GAGGAGGGTGGTGGTGGTGCT
3461381 GAGGAGGGTGGTGGTGGTG
1 GAGGAGGGTGGTGGTGGTG
3461400 GTGGAGATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.03, G:0.60, T:0.28
Consensus pattern (21 bp):
GAGGAGGGTGGTGGTGGTGCT
Done.