Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009605.1 Hibiscus syriacus cultivar Beakdansim tig00116989_pilon, 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: 9158330
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 20 of 35
Found at i:4633860 original size:6 final size:6
Alignment explanation
Indices: 4633849--4633883 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
4633839 GTCATTATAT
4633849 ATTTCC ATTTCC ATTTCC ATTTCC ATTTCC ATTTC
1 ATTTCC ATTTCC ATTTCC ATTTCC ATTTCC ATTTC
4633884 ACTTCATTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.17, C:0.31, G:0.00, T:0.51
Consensus pattern (6 bp):
ATTTCC
Found at i:4634290 original size:20 final size:21
Alignment explanation
Indices: 4634265--4634309 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
4634255 ATCTGTTAGC
4634265 TTTTTTCGTTTATTATTAT-A
1 TTTTTTCGTTTATTATTATAA
* *
4634285 TTTTTTTGTTTATTCTTATAA
1 TTTTTTCGTTTATTATTATAA
4634306 TTTT
1 TTTT
4634310 GAATTAAACC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.18, C:0.04, G:0.04, T:0.73
Consensus pattern (21 bp):
TTTTTTCGTTTATTATTATAA
Found at i:4634735 original size:59 final size:60
Alignment explanation
Indices: 4634653--4634778 Score: 150
Period size: 59 Copynumber: 2.1 Consensus size: 60
4634643 TTGGTCCCTT
* * * * *
4634653 AACTTTTAAACATTTCAATTTCATCTTTAAACTATGACTA-TCATTCTAGATTAGT-CCTCA
1 AACTTTTAAACATTCCAATTTCATC-CTAAACTATGA-TATTCATGCTAAATTAGTCCCCCA
* *
4634713 AACTTTT-GACATTCCAATTTCATCCTAAACTATGATATTCATGCTAAATTGGTCCCCCA
1 AACTTTTAAACATTCCAATTTCATCCTAAACTATGATATTCATGCTAAATTAGTCCCCCA
4634772 AACTTTT
1 AACTTTT
4634779 TTGAACATTT
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
57 2 0.04
58 22 0.39
59 26 0.46
60 7 0.12
ACGTcount: A:0.32, C:0.22, G:0.06, T:0.40
Consensus pattern (60 bp):
AACTTTTAAACATTCCAATTTCATCCTAAACTATGATATTCATGCTAAATTAGTCCCCCA
Found at i:4637055 original size:18 final size:18
Alignment explanation
Indices: 4637029--4637080 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
4637019 ATTTTATATT
* *
4637029 ACATCTTAACTTAAATTC
1 ACATATTAACTTAAATTA
*
4637047 ACATATTAATTTAAATTA
1 ACATATTAACTTAAATTA
4637065 ACATATTAACATTAAA
1 ACATATTAAC-TTAAA
4637081 GATATGTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
18 24 0.83
19 5 0.17
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.38
Consensus pattern (18 bp):
ACATATTAACTTAAATTA
Found at i:4637188 original size:30 final size:32
Alignment explanation
Indices: 4637154--4637213 Score: 97
Period size: 30 Copynumber: 1.9 Consensus size: 32
4637144 TTAATTTTAA
4637154 TTTAACTTAAAAATTTA-A-TTTATTCTTACT
1 TTTAACTTAAAAATTTATATTTTATTCTTACT
*
4637184 TTTAACTTAAATATTTATATTTTATTCTTA
1 TTTAACTTAAAAATTTATATTTTATTCTTA
4637214 TAATATTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 16 0.59
31 1 0.04
32 10 0.37
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.57
Consensus pattern (32 bp):
TTTAACTTAAAAATTTATATTTTATTCTTACT
Found at i:4637849 original size:2 final size:2
Alignment explanation
Indices: 4637842--4637872 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4637832 AATATGTATG
4637842 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4637873 TGTGTATTCC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4638304 original size:28 final size:28
Alignment explanation
Indices: 4638264--4638318 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
4638254 TCAATATTTT
4638264 CATCAACTGTTGATATTAGTGATTGATC
1 CATCAACTGTTGATATTAGTGATTGATC
4638292 CATCAACTGTTGATATTAGTGATTGAT
1 CATCAACTGTTGATATTAGTGATTGAT
4638319 TGGTAATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.40
Consensus pattern (28 bp):
CATCAACTGTTGATATTAGTGATTGATC
Found at i:4641601 original size:17 final size:17
Alignment explanation
Indices: 4641579--4641614 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
4641569 CCAAATTGAT
4641579 AGAATGTATAAGTTTTA
1 AGAATGTATAAGTTTTA
4641596 AGAATGTATAAGTTTTA
1 AGAATGTATAAGTTTTA
4641613 AG
1 AG
4641615 GATTAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.19, T:0.39
Consensus pattern (17 bp):
AGAATGTATAAGTTTTA
Found at i:4643492 original size:178 final size:178
Alignment explanation
Indices: 4643187--4643527 Score: 637
Period size: 178 Copynumber: 1.9 Consensus size: 178
4643177 TTAGGGGGGT
*
4643187 GGGGGAATTTAGACCCTAATAAGGGATTTAAATTATAATTTGCATTTGTATTTTCAACCACGCTG
1 GGGGGAATTTAGACCCTAATAAGGGATTTAAATTACAATTTGCATTTGTATTTTCAACCACGCTG
*
4643252 CATTTATTGCTATTGCAAACATAACGAATGATATTACTGTTATTACAAGTATCGTGATTGTGAAT
66 CATTTATTGCTATTGCAAACATAACGAATGATATTACAGTTATTACAAGTATCGTGATTGTGAAT
4643317 TTTTAATAATATGTTATTGTGGATATAGCAATTTTTTGGTGGTCTTTG
131 TTTTAATAATATGTTATTGTGGATATAGCAATTTTTTGGTGGTCTTTG
* *
4643365 GGGGGGATTTAGACCCTAATAAGGGATTTAAATTACAATTTGCATTTGTATTTTCAACCACGTTG
1 GGGGGAATTTAGACCCTAATAAGGGATTTAAATTACAATTTGCATTTGTATTTTCAACCACGCTG
4643430 CATTTATTGCTATTGCAAACATAACGAATGATATTACAGTTATTACAAGTATCGTGATTGTGAAT
66 CATTTATTGCTATTGCAAACATAACGAATGATATTACAGTTATTACAAGTATCGTGATTGTGAAT
*
4643495 TTTTAATAATGTGTTATTGTGGATATAGCAATT
131 TTTTAATAATATGTTATTGTGGATATAGCAATT
4643528 ATGGACGATG
Statistics
Matches: 158, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
178 158 1.00
ACGTcount: A:0.31, C:0.11, G:0.18, T:0.40
Consensus pattern (178 bp):
GGGGGAATTTAGACCCTAATAAGGGATTTAAATTACAATTTGCATTTGTATTTTCAACCACGCTG
CATTTATTGCTATTGCAAACATAACGAATGATATTACAGTTATTACAAGTATCGTGATTGTGAAT
TTTTAATAATATGTTATTGTGGATATAGCAATTTTTTGGTGGTCTTTG
Found at i:4643768 original size:31 final size:32
Alignment explanation
Indices: 4643726--4643785 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
4643716 CAAATTTTGA
*
4643726 AAAAAACATTGGTCCTC-TAATAAAAAATACTG
1 AAAAAACATTGG-ACTCATAATAAAAAATACTG
4643758 AAAAAA-ATTGGACTCATAATAAAAAATA
1 AAAAAACATTGGACTCATAATAAAAAATA
4643786 TGCCCTTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 3 0.12
31 17 0.65
32 6 0.23
ACGTcount: A:0.57, C:0.12, G:0.08, T:0.23
Consensus pattern (32 bp):
AAAAAACATTGGACTCATAATAAAAAATACTG
Found at i:4646832 original size:21 final size:21
Alignment explanation
Indices: 4646803--4646849 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
4646793 TTTAGGTTCT
*
4646803 CATGCGCTCACATTGTTGCTA
1 CATGTGCTCACATTGTTGCTA
4646824 CATGTGCTCACATTGTTGCTA
1 CATGTGCTCACATTGTTGCTA
4646845 CATGT
1 CATGT
4646850 ATGCACATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.19, C:0.26, G:0.19, T:0.36
Consensus pattern (21 bp):
CATGTGCTCACATTGTTGCTA
Found at i:4646856 original size:21 final size:21
Alignment explanation
Indices: 4646810--4646857 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
4646800 TCTCATGCGC
*
4646810 TCACATTGTTGCTACATGTGC
1 TCACATTGTTGCTACATGTGA
4646831 TCACATTGTTGCTACATGT-A
1 TCACATTGTTGCTACATGTGA
4646851 TGCACAT
1 T-CACAT
4646858 CAATAACCCA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 1 0.04
21 24 0.96
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCACATTGTTGCTACATGTGA
Found at i:4647214 original size:23 final size:22
Alignment explanation
Indices: 4647188--4647230 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
4647178 AAATATTATG
4647188 TACTGTAACTATGTATTTTTTTA
1 TACTGTAACTATGT-TTTTTTTA
*
4647211 TACTGTAACTGTGTTTTTTT
1 TACTGTAACTATGTTTTTTT
4647231 AACTATGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.21, C:0.09, G:0.12, T:0.58
Consensus pattern (22 bp):
TACTGTAACTATGTTTTTTTTA
Found at i:4647229 original size:21 final size:22
Alignment explanation
Indices: 4647188--4647231 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
4647178 AAATATTATG
4647188 TACTGTAACTATGTATTTTTTTA
1 TACTGTAAC-ATGTATTTTTTTA
*
4647211 TACTGTAAC-TGTGTTTTTTTA
1 TACTGTAACATGTATTTTTTTA
4647232 ACTATGTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 11 0.55
23 9 0.45
ACGTcount: A:0.23, C:0.09, G:0.11, T:0.57
Consensus pattern (22 bp):
TACTGTAACATGTATTTTTTTA
Found at i:4647356 original size:42 final size:42
Alignment explanation
Indices: 4647303--4647384 Score: 146
Period size: 42 Copynumber: 2.0 Consensus size: 42
4647293 TAAGGAAAAA
*
4647303 TATTTTTGGACTTAATTGAATTTGTTCAAAGTCTTCAAAATT
1 TATTTTTGGACTTAATTGAATTTGTTAAAAGTCTTCAAAATT
*
4647345 TATTTTTGGACTTAATTGAATTTGTTAAAAGTTTTCAAAA
1 TATTTTTGGACTTAATTGAATTTGTTAAAAGTCTTCAAAA
4647385 ATAATTCAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.33, C:0.07, G:0.12, T:0.48
Consensus pattern (42 bp):
TATTTTTGGACTTAATTGAATTTGTTAAAAGTCTTCAAAATT
Found at i:4647794 original size:18 final size:17
Alignment explanation
Indices: 4647750--4647796 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
4647740 TGAATGAAAT
**
4647750 TTTTTAATTAAATTTTA
1 TTTTTAATTAAAAGTTA
4647767 -TTTTAATTAAAAGTTA
1 TTTTTAATTAAAAGTTA
4647783 TTTTTAAATTAAAA
1 TTTTT-AATTAAAA
4647797 AATTTTCATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 14 0.54
17 4 0.15
18 8 0.31
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (17 bp):
TTTTTAATTAAAAGTTA
Found at i:4651300 original size:21 final size:21
Alignment explanation
Indices: 4651274--4651318 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
4651264 GATTTCTGGG
* *
4651274 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
4651295 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
4651316 CAA
1 CAA
4651319 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:4652217 original size:31 final size:31
Alignment explanation
Indices: 4652179--4652334 Score: 233
Period size: 31 Copynumber: 5.0 Consensus size: 31
4652169 AGGGTCGAGG
*
4652179 GTTTACCTATGTTCTTCGGGATATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
4652210 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
4652241 GTTTACCTATGTTCTTCGGAACATACGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
4652272 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
4652303 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
4652334 G
1 G
4652335 GTCCTTCGGG
Statistics
Matches: 114, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
31 113 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:4655316 original size:21 final size:21
Alignment explanation
Indices: 4655290--4655334 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
4655280 GATTTCTGGG
* *
4655290 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
4655311 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
4655332 CAA
1 CAA
4655335 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:4656241 original size:31 final size:31
Alignment explanation
Indices: 4656203--4656355 Score: 215
Period size: 31 Copynumber: 5.0 Consensus size: 31
4656193 AGGGTCGAGG
4656203 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
4656234 GTTTACCTATGTTCTTCGGGAC--ATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
4656263 GTTTACCTATGTTC-TCGGAACATACGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
4656293 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
4656324 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
4656355 G
1 G
4656356 GTCCTTCGGG
Statistics
Matches: 109, Mismatches: 9, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
28 6 0.06
29 21 0.19
30 19 0.17
31 62 0.57
32 1 0.01
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.36
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:4656297 original size:59 final size:61
Alignment explanation
Indices: 4656203--4656344 Score: 216
Period size: 59 Copynumber: 2.3 Consensus size: 61
4656193 AGGGTCGAGG
* * *
4656203 GTTTACCTATGTTCTTCGGGACATATGGACTGTTTACCTATGTTCTTCGGGAC-ATGGACT
1 GTTTACCTATGTTCTTCGGAACATACGGACTGTTTACCTATGTCCTTCGGGACAATGGACT
4656263 GTTTACCTATGTTC-TCGGAACATACGGACTGTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATACGGACTGTTTACCTATGTCCTTCGGGACA-ATGGACT
* *
4656324 GATTACCTAGGTTCTTCGGAA
1 GTTTACCTATGTTCTTCGGAA
4656345 TCTATGGACT
Statistics
Matches: 74, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
59 35 0.47
60 14 0.19
61 19 0.26
62 6 0.08
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.36
Consensus pattern (61 bp):
GTTTACCTATGTTCTTCGGAACATACGGACTGTTTACCTATGTCCTTCGGGACAATGGACT
Found at i:4657341 original size:22 final size:21
Alignment explanation
Indices: 4657316--4657364 Score: 53
Period size: 22 Copynumber: 2.3 Consensus size: 21
4657306 AAATTACACA
* **
4657316 AATTTAAGAATAAAGTTAATAT
1 AATTTAAAAATAAAAATAAT-T
*
4657338 AATTAAAAAATAAAAATAATT
1 AATTTAAAAATAAAAATAATT
4657359 AATTTA
1 AATTTA
4657365 GATATATTTT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (21 bp):
AATTTAAAAATAAAAATAATT
Found at i:4657404 original size:25 final size:25
Alignment explanation
Indices: 4657355--4657404 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
4657345 AAATAAAAAT
* *
4657355 AATTAATTTAGATATATTTTTTAAG
1 AATTAATTTAGATATATTATGTAAG
* *
4657380 AATTGATTTAGATTTATTATGTAAG
1 AATTAATTTAGATATATTATGTAAG
4657405 CAAAATCACC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (25 bp):
AATTAATTTAGATATATTATGTAAG
Found at i:4666987 original size:201 final size:201
Alignment explanation
Indices: 4666490--4667144 Score: 883
Period size: 201 Copynumber: 3.3 Consensus size: 201
4666480 ATTCCTTCTG
* * * *
4666490 GACA-AAAAGTACACAAGTGTCGATACATTTTCTAAACCTATTCTCTCATAAAACCGGTATATTT
1 GACACAAAAGTACAAAAGTGTCGATACATTATCTAGACCTATTCTCACATAAAACCGGTATATTT
* * * *
4666554 ATACCGGTTACGTTGAAAAATTACCTATTATATTATAATTATGGGTTTCGATGTTTCTGGGATTG
66 ATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGAGTTTCGATGTTTCTGGGATCG
4666619 ATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCATTTTTTGGGCATTCATTCTGGACAA
131 ATACTTTTTATAAATGTATCGACACTTTATGCGTGCACC--TTTTTGGGCATTCATTCTGGACAA
*
4666684 AATGTATC
194 AAAGTATC
* * *
4666692 GACACAAAATTA-AAAAGTGTCGATACATTATGTAGATCTATTCTCACATAAAACCGGTATATTT
1 GACACAAAAGTACAAAAGTGTCGATACATTATCTAGACCTATTCTCACATAAAACCGGTATATTT
* *
4666756 ATACCGGTTATATT-ACAAAATTACCTATTACATTATAATTATGAGTTTCGATGTCTCTGGGATC
66 ATACCGGTTACATTGA-AAAATTACCTATTACATTATAATTATGAGTTTCGATGTTTCTGGGATC
* * * * * *
4666820 GACACTTTTTAAAAATATATCGACACTTTATGGGTGCATCCTTTTTGGGTATTCCTTCTGGACAA
130 GATACTTTTTATAAATGTATCGACACTTTATGCGTGCA-CCTTTTTGGGCATTCATTCTGGACAA
4666885 AAAGTATC
194 AAAGTATC
* * * * *
4666893 GACACAAAA-TACACAAGTGTC-AGTACATTTTCTAGACCTATTCTCTCATAAAACTGGTATAGT
1 GACACAAAAGTACAAAAGTGTCGA-TACATTATCTAGACCTATTCTCACATAAAACCGGTATATT
* * * *
4666956 TATATCGGTTACATTGTAAATTTATCTATTACATTATAATTAT-AGATTTCGATGTTTCTGGGAT
65 TATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGAG-TTTCGATGTTTCTGGGAT
* * *
4667020 CGATACTTTTTATAAATGTATCGACACTTTATGCGTTCACCATTTTGGGCATTCATTTTGGACAA
129 CGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCTTTTTGGGCATTCATTCTGGACAA
4667085 AAAGTATC
194 AAAGTATC
* * * *
4667093 GACAC-CAATTTCAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAA
1 GACACAAAAGTACAAAAGTGTCGATACATTATCTAGACCTATTCTCACATAAA
4667145 TACAAAATTA
Statistics
Matches: 396, Mismatches: 48, Indels: 20
0.85 0.10 0.04
Matches are distributed among these distances:
199 2 0.01
200 76 0.19
201 170 0.43
202 140 0.35
203 8 0.02
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (201 bp):
GACACAAAAGTACAAAAGTGTCGATACATTATCTAGACCTATTCTCACATAAAACCGGTATATTT
ATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGAGTTTCGATGTTTCTGGGATCG
ATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCTTTTTGGGCATTCATTCTGGACAAAA
AGTATC
Found at i:4667036 original size:403 final size:387
Alignment explanation
Indices: 4666285--4667144 Score: 1197
Period size: 403 Copynumber: 2.2 Consensus size: 387
4666275 ACTTTATGGG
* * * *
4666285 TTCTGGACAAAAAGTATCGACACAAAA-TACACAAGTGTCGATACATTTTCTAGACCTATTCTCT
1 TTCTGGACAAAAAGTATCGACACAAAATTA-AAAAGTGTCGATACATTATGTAGACCTATTCTCA
* *
4666349 CATAAAATCGGTATATTTATACCAGTTACATTAAAATTTACCTACTACATTATAATTATATATTT
65 CATAAAACCGGTATATTTATACCAGTTACATTAAAAATTACCTACTACATTATAATTATATATTT
* * * *
4666414 CTATGTTTTTGGGATCGAATCTTTTTAAAAATGTATCGACACTTTATGGGTACATCCTTTTTGGG
130 CGATGTCTCTGGGATCGAATCTTTTTAAAAATATATCGACACTTTATGGGTACATCCTTTTTGGG
4666479 CATTCCTTCTGGACAAAAAGTACACAAGTGTCGATACATTTTCTAAACCTATTCTCTCATAAAAC
195 CATTCCTTCTGGACAAAAAGTACACAAGTGTCGATACATTTTCTAAACCTATTCTCTCATAAAAC
* * * * *
4666544 CGGTATATTTATACCGGTTACGTTGAAAAATTACCTATTATATTATAATTATGGGTTTCGATGTT
260 CGGTATAGTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATAGATTTCGATGTT
*
4666609 TCTGGGATTGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCATTTTTTGGGCATTCA
325 TCTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCA--TTTTGGGCATTCA
* *
4666674 TTCTGGACAAAATGTATCGACACAAAATTAAAAAGTGTCGATACATTATGTAGATCTATTCTCAC
1 TTCTGGACAAAAAGTATCGACACAAAATTAAAAAGTGTCGATACATTATGTAGACCTATTCTCAC
* * * *
4666739 ATAAAACCGGTATATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGA-GTT
66 ATAAAACCGGTATATTTATACCAGTTACATTA-AAAATTACCTACTACATTATAATTAT-ATATT
*
4666803 TCGATGTCTCTGGGATCGACA-CTTTTTAAAAATATATCGACACTTTATGGGTGCATCCTTTTTG
129 TCGATGTCTCTGGGATCGA-ATCTTTTTAAAAATATATCGACACTTTATGGGTACATCCTTTTTG
* *
4666867 GGTATTCCTTCTGGACAAAAAGTATCGACACAAAATACACAAGTGTC-AGTACATTTTCTAGACC
193 GGCATTCCTTCTGGAC-AAAA--A--G--------TACACAAGTGTCGA-TACATTTTCTAAACC
* * * * *
4666931 TATTCTCTCATAAAACTGGTATAGTTATATCGGTTACATTGTAAATTTATCTATTACATTATAAT
244 TATTCTCTCATAAAACCGGTATAGTTATACCGGTTACATTGAAAAATTACCTATTACATTATAAT
*
4666996 TATAGATTTCGATGTTTCTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTTCACC
309 TATAGATTTCGATGTTTCTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACC
4667061 ATTTTGGGCATTCA
374 ATTTTGGGCATTCA
* * * *
4667075 TTTTGGACAAAAAGTATCGACACCAATTTCAAAAGTGTCGATACATTATGTAGACCTATTCTCAC
1 TTCTGGACAAAAAGTATCGACACAAAATTAAAAAGTGTCGATACATTATGTAGACCTATTCTCAC
4667140 ATAAA
66 ATAAA
4667145 TACAAAATTA
Statistics
Matches: 416, Mismatches: 37, Indels: 24
0.87 0.08 0.05
Matches are distributed among these distances:
389 85 0.20
390 100 0.24
391 6 0.01
393 1 0.00
395 1 0.00
401 77 0.19
402 1 0.00
403 145 0.35
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (387 bp):
TTCTGGACAAAAAGTATCGACACAAAATTAAAAAGTGTCGATACATTATGTAGACCTATTCTCAC
ATAAAACCGGTATATTTATACCAGTTACATTAAAAATTACCTACTACATTATAATTATATATTTC
GATGTCTCTGGGATCGAATCTTTTTAAAAATATATCGACACTTTATGGGTACATCCTTTTTGGGC
ATTCCTTCTGGACAAAAAGTACACAAGTGTCGATACATTTTCTAAACCTATTCTCTCATAAAACC
GGTATAGTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATAGATTTCGATGTTT
CTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCATTTTGGGCATTCA
Found at i:4667256 original size:15 final size:15
Alignment explanation
Indices: 4667238--4667272 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
4667228 TTACTTATTT
4667238 TTTGGAAACTTTACG
1 TTTGGAAACTTTACG
*
4667253 TTTGAAAACTTTACG
1 TTTGGAAACTTTACG
4667268 TTTGG
1 TTTGG
4667273 GAACCATACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.26, C:0.11, G:0.20, T:0.43
Consensus pattern (15 bp):
TTTGGAAACTTTACG
Found at i:4669526 original size:15 final size:15
Alignment explanation
Indices: 4669506--4669538 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
4669496 ACTCTGTTTT
4669506 CCCTCATCGTCATCC
1 CCCTCATCGTCATCC
4669521 CCCTCATCGTCATCC
1 CCCTCATCGTCATCC
4669536 CCC
1 CCC
4669539 AATACAACCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.12, C:0.58, G:0.06, T:0.24
Consensus pattern (15 bp):
CCCTCATCGTCATCC
Found at i:4671639 original size:170 final size:174
Alignment explanation
Indices: 4671353--4671695 Score: 658
Period size: 170 Copynumber: 2.0 Consensus size: 174
4671343 TTTCTATCTA
4671353 TAATCGATCTCAAATACTTCTTTACTCCAAAACCCCAAACAACACATAAAAACCCTATTTTTTAT
1 TAATCGATCTCAAATACTTCTTTACTCCAAAACCCCAAACAACACATAAAAACCCTATTTTTTAT
4671418 TACTAAAATAATAAAAAAACTAGGATTTCAACAACGTACTTTTTAATTCGACTGTAGCAACAAAC
66 TACTAAAATAATAAAAAAACTAGGATTTCAACAACGTACTTTTTAATTCGACTGTAGCAACAAAC
4671483 AAACAAATTTCGCTTTAGAAACGCCTTCTGAAATGCAGCAACAT
131 AAACAAATTTCGCTTTAGAAACGCCTTCTGAAATGCAGCAACAT
4671527 TAATCGATCTCAAATACTTC-TTACTCCAAAACCCCAAAC-ACACATAAAAACCCTATTTTTTA-
1 TAATCGATCTCAAATACTTCTTTACTCCAAAACCCCAAACAACACATAAAAACCCTATTTTTTAT
4671589 TACT-AAATAATAAAAAAACTAGGATTTCAACAACGTACTTTTTAATTCGACTGTAGCAACAAAC
66 TACTAAAATAATAAAAAAACTAGGATTTCAACAACGTACTTTTTAATTCGACTGTAGCAACAAAC
4671653 AAACAAATTTCGCTTTAGAAACGCCTTCTGAAATGCAGCAACA
131 AAACAAATTTCGCTTTAGAAACGCCTTCTGAAATGCAGCAACA
4671696 ATTACGCTTC
Statistics
Matches: 169, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
170 103 0.61
171 4 0.02
172 23 0.14
173 19 0.11
174 20 0.12
ACGTcount: A:0.42, C:0.23, G:0.08, T:0.28
Consensus pattern (174 bp):
TAATCGATCTCAAATACTTCTTTACTCCAAAACCCCAAACAACACATAAAAACCCTATTTTTTAT
TACTAAAATAATAAAAAAACTAGGATTTCAACAACGTACTTTTTAATTCGACTGTAGCAACAAAC
AAACAAATTTCGCTTTAGAAACGCCTTCTGAAATGCAGCAACAT
Found at i:4672264 original size:182 final size:180
Alignment explanation
Indices: 4671925--4672372 Score: 492
Period size: 182 Copynumber: 2.6 Consensus size: 180
4671915 ATATCAATAT
* *
4671925 ATTTTTATAAAGTATCGACACTTTATAGGCGCT-AAA-T-TGCTCTCTTTTAAATTCAC-AAGTG
1 ATTTTTATAAAGTATCGACACTTTATAAGCGCTAAAACTAT-TTCTCTTTTAAATTCACAAAGTG
* * * * *
4671986 TCTATAC-T-TATT-AATATCGACACTTTC---ATATCCGGAAGCGCTTTATCAGTTTTGTCATT
65 TCGATACTTATATTAAATTTCGACACTTTCAATATATTCGG-AGCGCTCTATCAGATTTGTCATT
* * * *
4672045 TCGAGACCGATTTTGTCATATTTTTACCTGTTATATCATTATGGATCGATAC
129 TAGAGACCGATTTTATCATATTTTTACCTATTATATCATTATAGATCGATAC
*
4672097 ATTTTTATAAAGTATTGACACTTTATAAGCGCTAAAACTATTTCTCTTTTAAATTCACAAAGTGT
1 ATTTTTATAAAGTATCGACACTTTATAAGCGCTAAAACTATTTCTCTTTTAAATTCACAAAGTGT
* * * *
4672162 CGATACTTATATTAAAGTTTCGACACTTTCAATATATTTGG-TCGCTCTATACCGATTTGATCCT
66 CGATACTTATATTAAA-TTTCGACACTTTCAATATATTCGGAGCGCTCTAT-CAGATTTG-TCAT
*
4672226 TTAGAGACCGATTTTATCATATTTTTACCTATTATATCATTGTAGATCGATAC
128 TTAGAGACCGATTTTATCATATTTTTACCTATTATATCATTATAGATCGATAC
* *
4672279 ATTATTATAAAGTATCG--AC------A---CTAAAACTACTTCTCTTTTAAATTCACAAAGTGT
1 ATTTTTATAAAGTATCGACACTTTATAAGCGCTAAAACTATTTCTCTTTTAAATTCACAAAGTGT
*
4672333 CGATACTTATATTAAAATATT-GTCACTTTCAATATATTCG
66 CGATACTTATATT-AAAT-TTCGACACTTTCAATATATTCG
4672373 TAGAGCAAGT
Statistics
Matches: 239, Mismatches: 22, Indels: 31
0.82 0.08 0.11
Matches are distributed among these distances:
171 64 0.27
172 36 0.15
173 3 0.01
174 18 0.08
175 12 0.05
176 1 0.00
177 4 0.02
178 2 0.01
179 12 0.05
180 9 0.04
181 6 0.03
182 72 0.30
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.41
Consensus pattern (180 bp):
ATTTTTATAAAGTATCGACACTTTATAAGCGCTAAAACTATTTCTCTTTTAAATTCACAAAGTGT
CGATACTTATATTAAATTTCGACACTTTCAATATATTCGGAGCGCTCTATCAGATTTGTCATTTA
GAGACCGATTTTATCATATTTTTACCTATTATATCATTATAGATCGATAC
Found at i:4673848 original size:23 final size:22
Alignment explanation
Indices: 4673822--4673866 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
4673812 ATCAATTTAC
*
4673822 CAATTCAACAAGCATCATTGCAT
1 CAATTCAACAAACATCA-TGCAT
*
4673845 CAATTCAGCAAACATCATGCAT
1 CAATTCAACAAACATCATGCAT
4673867 TAAGAAAGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.40, C:0.27, G:0.09, T:0.24
Consensus pattern (22 bp):
CAATTCAACAAACATCATGCAT
Found at i:4673987 original size:19 final size:20
Alignment explanation
Indices: 4673946--4673989 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
4673936 AACCCTTACA
* * *
4673946 AATATCAAGTAGAATCAAGC
1 AATATCAAGCAGAAGCAAAC
4673966 AATATCAA-CAGAAGCAAAC
1 AATATCAAGCAGAAGCAAAC
4673985 AATAT
1 AATAT
4673990 AAAACAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.55, C:0.16, G:0.11, T:0.18
Consensus pattern (20 bp):
AATATCAAGCAGAAGCAAAC
Found at i:4676109 original size:15 final size:14
Alignment explanation
Indices: 4676085--4676119 Score: 61
Period size: 15 Copynumber: 2.4 Consensus size: 14
4676075 AACTTTGAAT
4676085 TTATATAGTATAAA
1 TTATATAGTATAAA
4676099 TTATATAAGTATAAA
1 TTATAT-AGTATAAA
4676114 TTATAT
1 TTATAT
4676120 TATATATAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.46
Consensus pattern (14 bp):
TTATATAGTATAAA
Found at i:4676118 original size:27 final size:28
Alignment explanation
Indices: 4676088--4676162 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 28
4676078 TTTGAATTTA
* *
4676088 TATAGTATA-AATTATATAAGTATAAAT
1 TATAGTATATAATTATATAAATATAAAC
* * *
4676115 TATATTATATATAGTATATAAATATCAAC
1 TATAGTATATA-ATTATATAAATATAAAC
4676144 TATAGTATATAATTTATAT
1 TATAGTATATAA-TTATAT
4676163 GGTTTTTATA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
27 8 0.21
28 2 0.05
29 28 0.74
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.44
Consensus pattern (28 bp):
TATAGTATATAATTATATAAATATAAAC
Found at i:4676139 original size:20 final size:20
Alignment explanation
Indices: 4676098--4676235 Score: 69
Period size: 20 Copynumber: 7.1 Consensus size: 20
4676088 TATAGTATAA
4676098 ATTATATA-AGTATA-AATTAT
1 ATTATATATAGTATATAA--AT
4676118 ATTATATATAGTATATAAAT
1 ATTATATATAGTATATAAAT
*
4676138 ATCA-ACTATAGTATAT-AAT
1 ATTATA-TATAGTATATAAAT
* * * *
4676157 -TTATATGGT-TTTTATATAT
1 ATTATAT-ATAGTATATAAAT
* * *
4676176 AGTT-CATAT-GTAAAT-TAT
1 A-TTATATATAGTATATAAAT
* *
4676194 ATTATATATAGTTTATATAT
1 ATTATATATAGTATATAAAT
*
4676214 ATAATATATAGTATATAAAT
1 ATTATATATAGTATATAAAT
4676234 AT
1 AT
4676236 AAACTATAAT
Statistics
Matches: 90, Mismatches: 17, Indels: 22
0.70 0.13 0.17
Matches are distributed among these distances:
17 2 0.02
18 15 0.17
19 16 0.18
20 47 0.52
21 8 0.09
22 2 0.02
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (20 bp):
ATTATATATAGTATATAAAT
Found at i:4676198 original size:27 final size:29
Alignment explanation
Indices: 4676168--4676230 Score: 85
Period size: 27 Copynumber: 2.2 Consensus size: 29
4676158 TATATGGTTT
*
4676168 TTATATATAGTTCATATGTA-AAT-TATA
1 TTATATATAGTTCATATATATAATATATA
*
4676195 TTATATATAGTTTATATATATAATATATA
1 TTATATATAGTTCATATATATAATATATA
*
4676224 GTATATA
1 TTATATA
4676231 AATATAAACT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
27 18 0.58
28 3 0.10
29 10 0.32
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (29 bp):
TTATATATAGTTCATATATATAATATATA
Found at i:4676220 original size:7 final size:7
Alignment explanation
Indices: 4676191--4676298 Score: 68
Period size: 7 Copynumber: 16.0 Consensus size: 7
4676181 ATATGTAAAT
*
4676191 TATATTA
1 TATATAA
*
4676198 TATATAG
1 TATATAA
*
4676205 TTTAT-A
1 TATATAA
4676211 TATATAA
1 TATATAA
*
4676218 TATATAG
1 TATATAA
4676225 TATATAA
1 TATATAA
4676232 -ATATAA
1 TATATAA
4676238 -ACTATAA
1 TA-TATAA
*
4676245 TA-AGTAG
1 TATA-TAA
4676252 TATATAA
1 TATATAA
4676259 -ATATAA
1 TATATAA
4676265 -ACTATAA
1 TA-TATAA
*
4676272 TTTAT-A
1 TATATAA
*
4676278 TATATAG
1 TATATAA
*
4676285 TATATAC
1 TATATAA
4676292 TATATAA
1 TATATAA
4676299 ATAGTTTATA
Statistics
Matches: 79, Mismatches: 14, Indels: 16
0.72 0.13 0.15
Matches are distributed among these distances:
6 24 0.30
7 53 0.67
8 2 0.03
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.43
Consensus pattern (7 bp):
TATATAA
Found at i:4676236 original size:20 final size:20
Alignment explanation
Indices: 4676192--4676301 Score: 69
Period size: 20 Copynumber: 5.2 Consensus size: 20
4676182 TATGTAAATT
* * *
4676192 ATATTATATATAGTTTATAT
1 ATATAATATATAGTATATAA
4676212 ATATAATATATAGTATATAA
1 ATATAATATATAGTATATAA
4676232 ATATAAACTATAATAAGTAGTATATAA
1 ATAT--A--AT-AT-A-TAGTATATAA
* * *
4676259 ATATAA-ACTATAATTTATAT
1 ATATAATA-TATAGTATATAA
* *
4676279 ATATAGTATATACTATATAA
1 ATATAATATATAGTATATAA
4676299 ATA
1 ATA
4676302 GTTTATATAG
Statistics
Matches: 71, Mismatches: 10, Indels: 18
0.72 0.10 0.18
Matches are distributed among these distances:
20 45 0.63
21 3 0.04
22 2 0.03
23 1 0.01
24 2 0.03
25 3 0.04
26 1 0.01
27 14 0.20
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.42
Consensus pattern (20 bp):
ATATAATATATAGTATATAA
Found at i:4676243 original size:27 final size:27
Alignment explanation
Indices: 4676213--4676308 Score: 110
Period size: 27 Copynumber: 3.7 Consensus size: 27
4676203 AGTTTATATA
4676213 TATAATATATAGTATATAAATATAAAC
1 TATAATATATAGTATATAAATATAAAC
4676240 TATAATA-AGTAGTATATAAATATAAAC
1 TATAATATA-TAGTATATAAATATAAAC
* * *
4676267 TATAATTTATA-TATAT-AGTATATAC
1 TATAATATATAGTATATAAATATAAAC
* *
4676292 TAT-ATAAATAGTTTATA
1 TATAATATATAGTATATA
4676309 TAGTTCACTA
Statistics
Matches: 59, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
24 5 0.08
25 14 0.24
26 6 0.10
27 33 0.56
28 1 0.02
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (27 bp):
TATAATATATAGTATATAAATATAAAC
Found at i:4676358 original size:18 final size:18
Alignment explanation
Indices: 4676331--4676423 Score: 77
Period size: 18 Copynumber: 5.2 Consensus size: 18
4676321 AAACTATATA
4676331 TATAGTTCATATGTAAAC
1 TATAGTTCATATGTAAAC
*
4676349 TATAGCTCATATGTAAA-
1 TATAGTTCATATGTAAAC
** *
4676366 TATCAACT-ATA-GCTTATA-
1 TAT-AGTTCATATG--TAAAC
4676384 TATAGTTCATATGTAAAC
1 TATAGTTCATATGTAAAC
* *
4676402 TATAGTTCATATATCAAC
1 TATAGTTCATATGTAAAC
4676420 TATA
1 TATA
4676424 TAATTTATAT
Statistics
Matches: 61, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
16 1 0.02
17 11 0.18
18 48 0.79
19 1 0.02
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.39
Consensus pattern (18 bp):
TATAGTTCATATGTAAAC
Found at i:4676445 original size:31 final size:29
Alignment explanation
Indices: 4676402--4676503 Score: 102
Period size: 31 Copynumber: 3.5 Consensus size: 29
4676392 ATATGTAAAC
* *
4676402 TATAGTTCATATATCAACTATATAATTTA
1 TATAGTTTATATATAAACTATATAATTTA
* *
4676431 TATAGTTTATATATAAA-TATCAATTATAGTA
1 TATAGTTTATATATAAACTAT--ATAAT-TTA
*
4676462 TATAGTTTATATATAAAC--TATAGTTTA
1 TATAGTTTATATATAAACTATATAATTTA
*
4676489 TATAGTTTTTATATA
1 TATAGTTTATATATA
4676504 TAGTTCATAT
Statistics
Matches: 61, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
27 16 0.26
28 6 0.10
29 15 0.25
30 5 0.08
31 19 0.31
ACGTcount: A:0.41, C:0.05, G:0.06, T:0.48
Consensus pattern (29 bp):
TATAGTTTATATATAAACTATATAATTTA
Found at i:4676531 original size:58 final size:56
Alignment explanation
Indices: 4676379--4676548 Score: 152
Period size: 58 Copynumber: 2.9 Consensus size: 56
4676369 CAACTATAGC
* *
4676379 TTATATATAGTTCATATGTAAACTATAGTTCATATATCAACTATATAATTTATATAGTTT
1 TTATATATAGTTCATATGTAAATTATAGTT-ATATAT-AAC--TATAGTTTATATAGTTT
* * *
4676439 ATATATA-AATATCA-AT-TATAGTATATAGTTTATATATAAACTATAGTTTATATAGTTT
1 TTATATATAGT-TCATATGTA-AAT-TATAG-TTATATAT-AACTATAGTTTATATAGTTT
*
4676497 TTATATATAGTTCATATGTAAATTATA-CTATATAT-ACTATATAGTTTATATA
1 TTATATATAGTTCATATGTAAATTATAGTTATATATAAC--TATAGTTTATATA
4676549 TATAATATAT
Statistics
Matches: 91, Mismatches: 10, Indels: 22
0.74 0.08 0.18
Matches are distributed among these distances:
54 2 0.02
56 20 0.22
58 31 0.34
59 11 0.12
60 25 0.27
61 2 0.02
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (56 bp):
TTATATATAGTTCATATGTAAATTATAGTTATATATAACTATAGTTTATATAGTTT
Found at i:4676537 original size:7 final size:6
Alignment explanation
Indices: 4676520--4676633 Score: 63
Period size: 7 Copynumber: 17.7 Consensus size: 6
4676510 ATATGTAAAT
* *
4676520 TATACTA TATATA CTATATA GTTTATA TATATA -ATATA TAGTATA TAAATA
1 TATA-TA TATATA -TATATA -TATATA TATATA TATATA TA-TATA TATATA
* * *
4676571 TCA-ACTA TA-ATA TATAGTA TATAAA TATAAA CTATAGTT TATATA TATAGTA
1 T-ATA-TA TATATA TATA-TA TATATA TATATA -TATA-TA TATATA TATA-TA
4676623 TATACTA TATA
1 TATA-TA TATA
4676634 AAATAGTTTA
Statistics
Matches: 88, Mismatches: 9, Indels: 20
0.75 0.08 0.17
Matches are distributed among these distances:
5 9 0.10
6 28 0.32
7 51 0.58
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.43
Consensus pattern (6 bp):
TATATA
Found at i:4676541 original size:34 final size:36
Alignment explanation
Indices: 4676500--4676633 Score: 97
Period size: 34 Copynumber: 3.9 Consensus size: 36
4676490 ATAGTTTTTA
*
4676500 TATATAGTTCATATGTA-AAT-TATACTATATATAC
1 TATATAGTTCATATATATAATATATACTATATATAC
* *
4676534 TATATAGTTTATATATATAATATATAGTATATA-A-
1 TATATAGTTCATATATATAATATATACTATATATAC
** * * *
4676568 -ATATCAACT-ATAATATATAGTATATA-AATATAAAC
1 TATAT-AGTTCAT-ATATATAATATATACTATATATAC
* *
4676603 --TATAGTTTATATATATAGTATATACTATATA
1 TATATAGTTCATATATATAATATATACTATATA
4676634 AAATAGTTTA
Statistics
Matches: 82, Mismatches: 10, Indels: 16
0.76 0.09 0.15
Matches are distributed among these distances:
33 27 0.33
34 41 0.50
35 4 0.05
36 10 0.12
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.43
Consensus pattern (36 bp):
TATATAGTTCATATATATAATATATACTATATATAC
Found at i:4676571 original size:20 final size:19
Alignment explanation
Indices: 4676520--4676635 Score: 72
Period size: 20 Copynumber: 5.7 Consensus size: 19
4676510 ATATGTAAAT
* *
4676520 TATACTATATATACTATATAG
1 TATA-TATATATA-AATATAA
* *
4676541 TTTATATATATAATATATAG
1 TATATATATATAA-ATATAA
* *
4676561 TATATAAATATCAACTATAA
1 TATATATATAT-AAATATAA
4676581 TATATAGTATATAAATATAA
1 TATATA-TATATAAATATAA
* * *
4676601 -ACTATAGTTTATATATATAG
1 TA-TATA-TATATAAATATAA
4676621 TATATACTATATAAA
1 TATATA-TATATAAA
4676636 ATAGTTTATA
Statistics
Matches: 76, Mismatches: 14, Indels: 11
0.75 0.14 0.11
Matches are distributed among these distances:
19 1 0.01
20 65 0.86
21 10 0.13
ACGTcount: A:0.48, C:0.05, G:0.04, T:0.42
Consensus pattern (19 bp):
TATATATATATAAATATAA
Found at i:4676579 original size:27 final size:27
Alignment explanation
Indices: 4676549--4676619 Score: 108
Period size: 27 Copynumber: 2.7 Consensus size: 27
4676539 AGTTTATATA
*
4676549 TATAATATATAGTATATAAATATCAAC
1 TATAATATATAGTATATAAATATAAAC
4676576 TATAATATATAGTATATAAATATAAAC
1 TATAATATATAGTATATAAATATAAAC
* *
4676603 TATAGTTTATA-TATATA
1 TATAATATATAGTATATA
4676620 GTATATACTA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
26 6 0.15
27 35 0.85
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.41
Consensus pattern (27 bp):
TATAATATATAGTATATAAATATAAAC
Found at i:4676585 original size:47 final size:47
Alignment explanation
Indices: 4676529--4676618 Score: 119
Period size: 47 Copynumber: 1.9 Consensus size: 47
4676519 TTATACTATA
* * *
4676529 TATACTATATAGTTTATATATATAATA-TATAGTATATAAATATCAAC
1 TATAATATATAGTATATAAATATAA-ACTATAGTATATAAATATCAAC
* *
4676576 TATAATATATAGTATATAAATATAAACTATAGTTTATATATAT
1 TATAATATATAGTATATAAATATAAACTATAGTATATAAATAT
4676619 AGTATATACT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
46 1 0.03
47 36 0.97
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.43
Consensus pattern (47 bp):
TATAATATATAGTATATAAATATAAACTATAGTATATAAATATCAAC
Found at i:4676671 original size:24 final size:25
Alignment explanation
Indices: 4676610--4676691 Score: 87
Period size: 24 Copynumber: 3.2 Consensus size: 25
4676600 AACTATAGTT
*
4676610 TATATATATAGTATATACTATATAAAA
1 TATATATATAGT-TA-ACTATATAAAC
*
4676637 TAGTTTATATAGTTAACTA-ATAAAC
1 TA-TATATATAGTTAACTATATAAAC
* *
4676662 TATATATATAGGTAA-TATGTAAAC
1 TATATATATAGTTAACTATATAAAC
4676686 TATATA
1 TATATA
4676692 GTTTACATAT
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
23 2 0.04
24 22 0.46
25 7 0.15
26 4 0.08
27 4 0.08
28 9 0.19
ACGTcount: A:0.48, C:0.05, G:0.07, T:0.40
Consensus pattern (25 bp):
TATATATATAGTTAACTATATAAAC
Found at i:4676721 original size:30 final size:30
Alignment explanation
Indices: 4676686--4676762 Score: 100
Period size: 30 Copynumber: 2.6 Consensus size: 30
4676676 ATATGTAAAC
* *
4676686 TATATAGTTTACATATAGTATAAGATAGTA
1 TATATAGTTTACATATAGTAGAAGATAATA
* *
4676716 TATATAGTTTACATATAGTAGAAGTTAATT
1 TATATAGTTTACATATAGTAGAAGATAATA
* *
4676746 TATATTGTTTATATATA
1 TATATAGTTTACATATA
4676763 TAGTTTAAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.40, C:0.03, G:0.12, T:0.45
Consensus pattern (30 bp):
TATATAGTTTACATATAGTAGAAGATAATA
Found at i:4676863 original size:2 final size:2
Alignment explanation
Indices: 4676850--4677210 Score: 149
Period size: 2 Copynumber: 184.5 Consensus size: 2
4676840 ACCTTAAACC
* *
4676850 AT AT AT ACT AT AT AT AT AT AT AA ACT AT AT AGT TT AT AT -T A-
1 AT AT AT A-T AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT
* * *
4676891 AT AA ACT AT AT A- AT TT AT AT A- AT AT AT AT -T AT TT AT A- AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
4676930 -T AT AA AT TT AT AC A- AT AT AT AT -T AT TT AT A- AT -T AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
4676967 AT A- AT AT AT AA AT AT AA AT -T GT AT AGT TT AT AT AT A- AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
* * *
4677006 CAT AT AT AA AT -T AT AT AT AA ACT AT AT AGT AT -T AT AGT TT AT
1 -AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT A-T AT AT
* * * *
4677048 AC AT GGT AT AT AT AGT TT AT AC AT A- AT AT AT AT A- AT AT AT AGT
1 AT AT -AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
* * *
4677091 TT AT AT AT AGT AT AT A- AT A- AT AT AA AT AT AA AT -T AT AT AGT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
* * * *
4677132 TT AT AT AT AT A- AT AT AT AT ACT TT AT AT AT AA ACT AT AT -T GT
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT AT
*
4677174 TT AT AT 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 AT AT AT A
4677211 GTTGTTTCAA
Statistics
Matches: 265, Mismatches: 54, Indels: 80
0.66 0.14 0.20
Matches are distributed among these distances:
1 24 0.09
2 222 0.84
3 19 0.07
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4677010 original size:11 final size:10
Alignment explanation
Indices: 4676944--4677206 Score: 73
Period size: 11 Copynumber: 24.7 Consensus size: 10
4676934 AATTTATACA
4676944 ATATAT-ATT
1 ATATATAATT
*
4676953 ATTTATAATT
1 ATATATAATT
*
4676963 ATACATAATAT
1 ATATATAAT-T
4676974 ATAAATATAAATT
1 AT--ATAT-AATT
*
4676987 GTATAGT--TT
1 ATATA-TAATT
4676996 ATATATAATT
1 ATATATAATT
4677006 CATATATAAATT
1 -ATATAT-AATT
*
4677018 ATATATAAACT
1 ATATAT-AATT
4677029 ATATAGT-ATT
1 ATATA-TAATT
4677039 ATAGTTTATACATGGT
1 ATA---TATA-AT--T
*
4677055 ATATATAGTTT
1 ATATATA-ATT
*
4677066 ATACATAA-T
1 ATATATAATT
4677075 ATATATAA-T
1 ATATATAATT
4677084 ATATAGT--TT
1 ATATA-TAATT
*
4677093 ATATAT-AGT
1 ATATATAATT
4677102 ATATAATAATAT
1 ATAT-ATAAT-T
*
4677114 AAATATAAATT
1 ATATAT-AATT
4677125 ATATAGT--TT
1 ATATA-TAATT
*
4677134 ATATATATAAT
1 ATATATA-ATT
*
4677145 ATATATACTTT
1 ATATATA-ATT
*
4677156 ATATATAAACT
1 ATATAT-AATT
**
4677167 ATAT-TGTTT
1 ATATATAATT
4677176 ATATATATATAT
1 ATATATA-AT-T
4677188 ATATATATATAT
1 ATATATA-AT-T
4677200 ATATATA
1 ATATATA
4677207 TATAGTTGTT
Statistics
Matches: 193, Mismatches: 28, Indels: 63
0.68 0.10 0.22
Matches are distributed among these distances:
8 3 0.02
9 48 0.25
10 22 0.11
11 63 0.33
12 36 0.19
13 12 0.06
14 5 0.03
16 4 0.02
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (10 bp):
ATATATAATT
Found at i:4677087 original size:9 final size:9
Alignment explanation
Indices: 4676850--4677210 Score: 104
Period size: 9 Copynumber: 39.8 Consensus size: 9
4676840 ACCTTAAACC
*
4676850 ATATATACT
1 ATATATAAT
4676859 ATATAT-AT
1 ATATATAAT
4676867 ATATA-AACT
1 ATATATAA-T
*
4676876 ATATAGT-TT
1 ATATA-TAAT
4676885 ATAT-TAAT
1 ATATATAAT
4676893 AAACTATATAAT
1 --A-TATATAAT
*
4676905 TTATATAAT
1 ATATATAAT
4676914 ATATAT--T
1 ATATATAAT
*
4676921 ATTTATAAT
1 ATATATAAT
4676930 -TATA-AAT
1 ATATATAAT
* *
4676937 TTATACAAT
1 ATATATAAT
4676946 ATATAT--T
1 ATATATAAT
*
4676953 ATTTATAATT
1 ATATATAA-T
*
4676963 ATACATAAT
1 ATATATAAT
4676972 ATATA-AAT
1 ATATATAAT
*
4676980 ATA-A-ATT
1 ATATATAAT
* *
4676987 GTATAGT-TT
1 ATATA-TAAT
4676996 ATATATAATT
1 ATATATAA-T
4677006 CATATATAAATT
1 -ATATAT-AA-T
4677018 ATATATAA-
1 ATATATAAT
*
4677026 ACTATATAGT
1 A-TATATAAT
*
4677036 AT-TATAGTTT
1 ATATATA--AT
* **
4677046 ATACATGGT
1 ATATATAAT
*
4677055 ATATATAGTTT
1 ATATATA--AT
*
4677066 ATACATAAT
1 ATATATAAT
4677075 ATATATAAT
1 ATATATAAT
4677084 ATATAGT--T
1 ATATA-TAAT
4677092 -TATAT-AT
1 ATATATAAT
4677099 AGTATATAAT
1 A-TATATAAT
4677109 A-ATATAA-
1 ATATATAAT
4677116 ATATA-AATT
1 ATATATAA-T
*
4677125 ATATAGTTTAT
1 ATATA--TAAT
4677136 ATATATAAT
1 ATATATAAT
*
4677145 ATATATACTTT
1 ATATATA--AT
4677156 ATATATAA-
1 ATATATAAT
**
4677164 ACTATATTGT
1 A-TATATAAT
*
4677174 TTATATATAT
1 ATATATA-AT
4677184 ATATATATAT
1 ATATATA-AT
4677194 ATATATATAT
1 ATATATA-AT
4677204 ATATATA
1 ATATATA
4677211 GTTGTTTCAA
Statistics
Matches: 268, Mismatches: 38, Indels: 91
0.68 0.10 0.23
Matches are distributed among these distances:
6 1 0.00
7 29 0.11
8 39 0.15
9 106 0.40
10 46 0.17
11 38 0.14
12 9 0.03
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (9 bp):
ATATATAAT
Found at i:4677690 original size:213 final size:212
Alignment explanation
Indices: 4677309--4677801 Score: 792
Period size: 213 Copynumber: 2.3 Consensus size: 212
4677299 TTGATCCCTT
* *
4677309 TGTGTTGTTTAATTTATTTAAATTTTTATCTATAATTTCATATTTGTTCAATTTAGTCCTTAAAA
1 TGTGTTGTTTAATTTATTTAAA-TTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTT-AAA
4677374 TTATATTTGCATATGAAATTGCCCATACTTATTACTTATTTATATTTTTTAATTGGCCCATAACT
64 TTATATTTGCATATGAAATTGCCCATACTTATTACTTATTTATATTTTTTAATTGGCCCATAACT
* *
4677439 TTTTAAATGGGTATAATTTAGTACTTTTTGTATTAATTTAAACCTCACAATTTAAAATTATTTTG
129 TTTTAAATGGGTATAATATAGTACTTTTTGTATTAATTTAAACCTCACAATTTAAAATTATTTCG
* * *
4677504 ATTTGATCCCTCGTCAATG
194 ATTTGACCCCTCATAAATG
*
4677523 TGTGTTG-TTAATTTATTTAAATTTGTATTTGTAATTTCATTTTTGTTCAATTTAGTCCTTAAAT
1 TGTGTTGTTTAATTTATTTAAATTT-TATTTGTAATTTCATATTTGTTCAATTTAGTCCTTAAAT
* *
4677587 TATATTTGCATATGAAATTGGTCCATATTTATTACTTATTTATATTTTTTAATTGGCCCATAAC-
65 TATATTTGCATATGAAATT-GCCCATACTTATTACTTATTTATATTTTTTAATTGGCCCATAACT
* *
4677651 TTTTAAATGGGTATAATATAGTACTTTTTTGTTTTAATTTTAACCTCACAATTTAAAATTATTTC
129 TTTTAAATGGGTATAATATAGTAC-TTTTTGTATTAATTTAAACCTCACAATTTAAAATTATTTC
4677716 GATTTGACCCCTCATAAATG
193 GATTTGACCCCTCATAAATG
* *
4677736 CGTGTTGTTTAATTTATTTAAATTTTAATTTGTAATTTCATATTTGTTCAATTTAGTTCTTAAAT
1 TGTGTTGTTTAATTTATTTAAATTTT-ATTTGTAATTTCATATTTGTTCAATTTAGTCCTTAAAT
4677801 T
65 T
4677802 TTTATTTTTC
Statistics
Matches: 259, Mismatches: 15, Indels: 10
0.91 0.05 0.04
Matches are distributed among these distances:
212 49 0.19
213 149 0.58
214 61 0.24
ACGTcount: A:0.29, C:0.11, G:0.09, T:0.51
Consensus pattern (212 bp):
TGTGTTGTTTAATTTATTTAAATTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTTAAATT
ATATTTGCATATGAAATTGCCCATACTTATTACTTATTTATATTTTTTAATTGGCCCATAACTTT
TTAAATGGGTATAATATAGTACTTTTTGTATTAATTTAAACCTCACAATTTAAAATTATTTCGAT
TTGACCCCTCATAAATG
Found at i:4682923 original size:3 final size:3
Alignment explanation
Indices: 4682910--4682955 Score: 51
Period size: 3 Copynumber: 16.0 Consensus size: 3
4682900 TGAAACTCCA
* * *
4682910 AAG AA- AAG AAG AAG AAG AAC AAG AAG -AG AAG AAC AAG AAA AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
4682956 GTGGTGGGAA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
2 4 0.11
3 31 0.89
ACGTcount: A:0.70, C:0.04, G:0.26, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:4682939 original size:14 final size:15
Alignment explanation
Indices: 4682910--4682955 Score: 69
Period size: 14 Copynumber: 3.2 Consensus size: 15
4682900 TGAAACTCCA
4682910 AAGAA-AAGAAGAAG
1 AAGAACAAGAAGAAG
4682924 AAGAACAAGAAG-AG
1 AAGAACAAGAAGAAG
*
4682938 AAGAACAAGAAAAAG
1 AAGAACAAGAAGAAG
4682953 AAG
1 AAG
4682956 GTGGTGGGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 18 0.62
15 11 0.38
ACGTcount: A:0.70, C:0.04, G:0.26, T:0.00
Consensus pattern (15 bp):
AAGAACAAGAAGAAG
Found at i:4682939 original size:20 final size:20
Alignment explanation
Indices: 4682909--4682955 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
4682899 GTGAAACTCC
* *
4682909 AAAGAAAAGAAGAAGAAGAA
1 AAAGAAGAGAAGAACAAGAA
*
4682929 CAAGAAGAGAAGAACAAGAA
1 AAAGAAGAGAAGAACAAGAA
4682949 AAAGAAG
1 AAAGAAG
4682956 GTGGTGGGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.70, C:0.04, G:0.26, T:0.00
Consensus pattern (20 bp):
AAAGAAGAGAAGAACAAGAA
Found at i:4683467 original size:20 final size:20
Alignment explanation
Indices: 4683429--4683481 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
4683419 TGAAAATGAC
*
4683429 TTGATTTTG-AAAGCAAAAT
1 TTGATTTTGAAAAACAAAAT
4683448 TTGATTTTGAAAAACAAAAT
1 TTGATTTTGAAAAACAAAAT
***
4683468 GAAATTTTGAAAAA
1 TTGATTTTGAAAAA
4683482 TGATTTTGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 9 0.31
20 20 0.69
ACGTcount: A:0.49, C:0.04, G:0.13, T:0.34
Consensus pattern (20 bp):
TTGATTTTGAAAAACAAAAT
Found at i:4688446 original size:73 final size:72
Alignment explanation
Indices: 4688321--4688460 Score: 167
Period size: 73 Copynumber: 1.9 Consensus size: 72
4688311 TAAGTTCATC
* * * * **
4688321 CATTCATGCATATTCATGCAAGAAGCCAAATAGTCATGTTCACACAAGGGGA-GAAGAATTTCAG
1 CATTCATGAACATTCATCCAAGAAGACAAATAAACATGTTCACACAAGGGGAGGAAGAA-TTCAG
4688385 CCAAGATA
65 CCAAGATA
* *
4688393 CATTCATGAACATTCATCCATAGAAGACAAATCAAACATGTTCACAC-ATGGGAGGAAGGATTCA
1 CATTCATGAACATTCATCCA-AGAAGACAAAT-AAACATGTTCACACAAGGGGAGGAAGAATTCA
4688457 GCCA
64 GCCA
4688461 TGAAGATTTA
Statistics
Matches: 57, Mismatches: 8, Indels: 5
0.81 0.11 0.07
Matches are distributed among these distances:
72 17 0.30
73 23 0.40
74 17 0.30
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.21
Consensus pattern (72 bp):
CATTCATGAACATTCATCCAAGAAGACAAATAAACATGTTCACACAAGGGGAGGAAGAATTCAGC
CAAGATA
Found at i:4703360 original size:20 final size:22
Alignment explanation
Indices: 4703321--4703361 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
4703311 TTATTTTGCA
*
4703321 TAAAATCAATCCCTAACGGCTC
1 TAAAATCAATCCCCAACGGCTC
4703343 TAAAA-CAA-CCCCAACGGCT
1 TAAAATCAATCCCCAACGGCT
4703362 AGAAAATCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
21 3 0.17
22 5 0.28
ACGTcount: A:0.39, C:0.34, G:0.10, T:0.17
Consensus pattern (22 bp):
TAAAATCAATCCCCAACGGCTC
Found at i:4706112 original size:26 final size:26
Alignment explanation
Indices: 4706083--4706136 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
4706073 ACAAGATAAA
*
4706083 TTATTTGAAATAATTT-TTTTTCTTAT
1 TTATCTGAAATAATTTCTTTTT-TTAT
* *
4706109 TTATCTGAATTGATTTCTTTTTTTAT
1 TTATCTGAAATAATTTCTTTTTTTAT
4706135 TT
1 TT
4706137 GATTAAGCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 19 0.79
27 5 0.21
ACGTcount: A:0.22, C:0.06, G:0.06, T:0.67
Consensus pattern (26 bp):
TTATCTGAAATAATTTCTTTTTTTAT
Found at i:4706265 original size:20 final size:20
Alignment explanation
Indices: 4706229--4706266 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
4706219 CTCTTTTCTT
*
4706229 AAAATTTCATTTTGTTTTTC
1 AAAATTTCATTTAGTTTTTC
4706249 AAAA-TTCACTTTAGTTTT
1 AAAATTTCA-TTTAGTTTT
4706267 CAATAGAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.29, C:0.11, G:0.05, T:0.55
Consensus pattern (20 bp):
AAAATTTCATTTAGTTTTTC
Found at i:4709159 original size:15 final size:15
Alignment explanation
Indices: 4709139--4709172 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
4709129 TTTATTTTTC
**
4709139 AAAAAAAAGGCAAAA
1 AAAAAAAAAACAAAA
4709154 AAAAAAAAAACAAAA
1 AAAAAAAAAACAAAA
4709169 AAAA
1 AAAA
4709173 GTTAAAAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.88, C:0.06, G:0.06, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAACAAAA
Found at i:4722185 original size:21 final size:20
Alignment explanation
Indices: 4722143--4722185 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
4722133 TTGCCAATTC
*
4722143 ATAAATGAAATGAAACCTAT
1 ATAAATGAAATGAAACCAAT
4722163 ATAAATG-AATGTAAAACCAAT
1 ATAAATGAAATG--AAACCAAT
4722184 AT
1 AT
4722186 GAATCAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 4 0.20
20 7 0.35
21 9 0.45
ACGTcount: A:0.56, C:0.09, G:0.09, T:0.26
Consensus pattern (20 bp):
ATAAATGAAATGAAACCAAT
Found at i:4722887 original size:23 final size:24
Alignment explanation
Indices: 4722861--4722914 Score: 101
Period size: 23 Copynumber: 2.3 Consensus size: 24
4722851 GTTAAGAGAC
4722861 TAAAAAAAGAGAGTACATATTTA-
1 TAAAAAAAGAGAGTACATATTTAG
4722884 TAAAAAAAGAGAGTACATATTTAG
1 TAAAAAAAGAGAGTACATATTTAG
4722908 TAAAAAA
1 TAAAAAA
4722915 TAACAATTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 23 0.77
24 7 0.23
ACGTcount: A:0.59, C:0.04, G:0.13, T:0.24
Consensus pattern (24 bp):
TAAAAAAAGAGAGTACATATTTAG
Found at i:4723267 original size:157 final size:152
Alignment explanation
Indices: 4722935--4723268 Score: 352
Period size: 152 Copynumber: 2.2 Consensus size: 152
4722925 AGTTACATAG
* * * * *
4722935 GTATTCTATTATGGTATATGAGCATGTAGTTTAAATTTGGTAAAAAACAAACTTAAAATAAATGA
1 GTATTCTACTATGGTTTACGAGCATGTAGCTCAAATTTGGTAAAAAACAAACTTAAAATAAATGA
* * * * *
4723000 CAATTGAAAGCATAAGAAGATTATGAAAAATTGAAGGATTAAATTGGAAAAAAAATATTATCAAA
66 CAATTGAAAGAATAAGAAGATTATGAAAAATTGAAGGACTAAAATGAAAAAAAAATATTATAAAA
*
4723065 AAGAGGAATTTAAAGTAAACAT
131 AAGAGGAATTGAAAGTAAACAT
* * * **
4723087 GTATTATACTAT-GTGTTAGGAGCATGTGGCTCAAATTTGGTAAAAAACGGACTTAAAATAAATG
1 GTATTCTACTATGGT-TTACGAGCATGTAGCTCAAATTTGGTAAAAAACAAACTTAAAATAAATG
* * *
4723151 ATGAATTG-AAGAAATAA-AGATATTATG-AAAATTGAATGACTAAAATGAAAAATAAAAAAATT
65 A-CAATTGAAAG-AATAAGA-AGATTATGAAAAATTGAAGGACTAAAATG---AA-AAAAAAA-T
* ** *
4723213 GTTATAAAAAAGAGGAATTGAAAGTTCACGT
122 ATTATAAAAAAGAGGAATTGAAAGTAAACAT
4723244 GTATTCTACTATGGTTTACGAGCAT
1 GTATTCTACTATGGTTTACGAGCAT
4723269 TTAGTTTGGT
Statistics
Matches: 148, Mismatches: 24, Indels: 15
0.79 0.13 0.08
Matches are distributed among these distances:
151 2 0.01
152 74 0.50
153 16 0.11
155 1 0.01
156 7 0.05
157 46 0.31
158 2 0.01
ACGTcount: A:0.47, C:0.06, G:0.17, T:0.29
Consensus pattern (152 bp):
GTATTCTACTATGGTTTACGAGCATGTAGCTCAAATTTGGTAAAAAACAAACTTAAAATAAATGA
CAATTGAAAGAATAAGAAGATTATGAAAAATTGAAGGACTAAAATGAAAAAAAAATATTATAAAA
AAGAGGAATTGAAAGTAAACAT
Found at i:4726223 original size:89 final size:89
Alignment explanation
Indices: 4726127--4726300 Score: 222
Period size: 89 Copynumber: 2.0 Consensus size: 89
4726117 GGGACATGGT
* * * * * *
4726127 AGTAAAAAAAACAGGGACTAAAATGAAAATAAACTAAAAGTTCAATGATTACATTGTAAGTTTCA
1 AGTAAAAAAAACAAGGACTAAAATAAAAACAAACTAAAAGTTCAATAATTACATCGCAAGTTTCA
*
4726192 AAAGTTGGGTGACCAAAATGTGGC
66 AAAGTTGGGTGAACAAAATGTGGC
** * ** **
4726216 AGTAAAAAAGGCAAGGATTAAAATAAAAACAAACTAAAAGTTTGATAATTGTATCGCAAGTTTCA
1 AGTAAAAAAAACAAGGACTAAAATAAAAACAAACTAAAAGTTCAATAATTACATCGCAAGTTTCA
4726281 AAAGTTGGGTGAACAAAATG
66 AAAGTTGGGTGAACAAAATG
4726301 CAAGTGTCCT
Statistics
Matches: 71, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
89 71 1.00
ACGTcount: A:0.48, C:0.09, G:0.19, T:0.24
Consensus pattern (89 bp):
AGTAAAAAAAACAAGGACTAAAATAAAAACAAACTAAAAGTTCAATAATTACATCGCAAGTTTCA
AAAGTTGGGTGAACAAAATGTGGC
Found at i:4728087 original size:24 final size:24
Alignment explanation
Indices: 4728055--4728100 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
4728045 GCATGATATG
4728055 GTACATAGATGTTTTATACATCGT
1 GTACATAGATGTTTTATACATCGT
4728079 GTACATAGATGTTTTATACATC
1 GTACATAGATGTTTTATACATC
4728101 ATCTGTAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.41
Consensus pattern (24 bp):
GTACATAGATGTTTTATACATCGT
Found at i:4730403 original size:21 final size:22
Alignment explanation
Indices: 4730357--4730404 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 22
4730347 TATTTTAAAT
* * *
4730357 TAAATTATTTTTTTCTTTTTCA
1 TAAATTATTTTTATATTATTCA
4730379 -AAATTATTTTTATATTATT-A
1 TAAATTATTTTTATATTATTCA
4730399 TAAATT
1 TAAATT
4730405 TAAAATAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (22 bp):
TAAATTATTTTTATATTATTCA
Found at i:4733823 original size:11 final size:10
Alignment explanation
Indices: 4733790--4733823 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
4733780 ATAGCCTAAG
*
4733790 TTTCATGAAA
1 TTTCATGTAA
4733800 TTTCATGTAA
1 TTTCATGTAA
4733810 TTTCATGTTAA
1 TTTCATG-TAA
4733821 TTT
1 TTT
4733824 AACATTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 16 0.73
11 6 0.27
ACGTcount: A:0.29, C:0.09, G:0.09, T:0.53
Consensus pattern (10 bp):
TTTCATGTAA
Found at i:4735254 original size:21 final size:21
Alignment explanation
Indices: 4735217--4735256 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
4735207 AATTATCACA
*
4735217 AATAATAATAAGATTAATAAT
1 AATAATAATAAAATTAATAAT
4735238 AATAATAATAAAATTAATA
1 AATAATAATAAAATTAATA
4735257 TTATTATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (21 bp):
AATAATAATAAAATTAATAAT
Found at i:4738330 original size:78 final size:78
Alignment explanation
Indices: 4738236--4738380 Score: 263
Period size: 78 Copynumber: 1.9 Consensus size: 78
4738226 AAGGACCTGC
* * *
4738236 GGTAAGGACTTACCCTGAGCACAAAGTTGGGGAGCCTGAGGTAAGGACTTACCCTGAGCATAAAG
1 GGTAAGGACTTACCCTGAGCACAAAGTCGAGGAGCCTGAGGTAAGGACTTACCCTGAGCACAAAG
4738301 CCAAGGATCCTAT
66 CCAAGGATCCTAT
4738314 GGTAAGGACTTACCCTGAGCACAAAGTCGAGGAGCCTGAGGTAAGGACTTACCCTGAGCACAAAG
1 GGTAAGGACTTACCCTGAGCACAAAGTCGAGGAGCCTGAGGTAAGGACTTACCCTGAGCACAAAG
4738379 CC
66 CC
4738381 GAGAAGCCAA
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 64 1.00
ACGTcount: A:0.31, C:0.23, G:0.28, T:0.17
Consensus pattern (78 bp):
GGTAAGGACTTACCCTGAGCACAAAGTCGAGGAGCCTGAGGTAAGGACTTACCCTGAGCACAAAG
CCAAGGATCCTAT
Found at i:4738398 original size:78 final size:78
Alignment explanation
Indices: 4738238--4738403 Score: 251
Period size: 78 Copynumber: 2.1 Consensus size: 78
4738228 GGACCTGCGG
* * *
4738238 TAAGGACTTACCCTGAGCACAAAGTTGGGGAGCCTGAGGTAAGGACTTACCCTGAGCATAAAGCC
1 TAAGGACTTACCCTGAGCACAAAGTCGAGGAGCCTGAGGTAAGGACTTACCCTGAGCACAAAGCC
* * * * *
4738303 AAGGATCCTATGG
66 AAGAAGCCAACGA
4738316 TAAGGACTTACCCTGAGCACAAAGTCGAGGAGCCTGAGGTAAGGACTTACCCTGAGCACAAAGCC
1 TAAGGACTTACCCTGAGCACAAAGTCGAGGAGCCTGAGGTAAGGACTTACCCTGAGCACAAAGCC
*
4738381 GAGAAGCCAACGA
66 AAGAAGCCAACGA
4738394 TAAGGACTTA
1 TAAGGACTTA
4738404 AAAGTCATAA
Statistics
Matches: 79, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
78 79 1.00
ACGTcount: A:0.33, C:0.23, G:0.27, T:0.17
Consensus pattern (78 bp):
TAAGGACTTACCCTGAGCACAAAGTCGAGGAGCCTGAGGTAAGGACTTACCCTGAGCACAAAGCC
AAGAAGCCAACGA
Found at i:4738403 original size:39 final size:39
Alignment explanation
Indices: 4738227--4738388 Score: 220
Period size: 39 Copynumber: 4.2 Consensus size: 39
4738217 ACATAGCATA
* **
4738227 AGGA-CCTGCGGTAAGGACTTACCCTGAGCACAAAGTTG
1 AGGAGCCTGAGGTAAGGACTTACCCTGAGCACAAAGCCG
* * *
4738265 GGGAGCCTGAGGTAAGGACTTACCCTGAGCATAAAGCCA
1 AGGAGCCTGAGGTAAGGACTTACCCTGAGCACAAAGCCG
* *
4738304 AGGATCCT-ATGGTAAGGACTTACCCTGAGCACAAAGTCG
1 AGGAGCCTGA-GGTAAGGACTTACCCTGAGCACAAAGCCG
4738343 AGGAGCCTGAGGTAAGGACTTACCCTGAGCACAAAGCCG
1 AGGAGCCTGAGGTAAGGACTTACCCTGAGCACAAAGCCG
*
4738382 AGAAGCC
1 AGGAGCC
4738389 AACGATAAGG
Statistics
Matches: 107, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
38 4 0.04
39 102 0.95
40 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.29, T:0.16
Consensus pattern (39 bp):
AGGAGCCTGAGGTAAGGACTTACCCTGAGCACAAAGCCG
Found at i:4739798 original size:30 final size:30
Alignment explanation
Indices: 4739762--4739826 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
4739752 AAATTTGGAT
* *
4739762 TCGAATTTAATCAAAATTTTACTTTAGTCC
1 TCGAATTTAATCAAAATTTTAATTTACTCC
*
4739792 TCGAATTTAATTAAAATTTTAATTTACTCC
1 TCGAATTTAATCAAAATTTTAATTTACTCC
4739822 TCGAA
1 TCGAA
4739827 AAAAATTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.35, C:0.15, G:0.06, T:0.43
Consensus pattern (30 bp):
TCGAATTTAATCAAAATTTTAATTTACTCC
Found at i:4742614 original size:28 final size:26
Alignment explanation
Indices: 4742572--4742642 Score: 81
Period size: 28 Copynumber: 2.7 Consensus size: 26
4742562 TAATTCTTTC
* *
4742572 TTTTCAAAATGTTTATATATACTTATTA
1 TTTTCATAATATTTATATATA--TATTA
*
4742600 TTTTCATAATATTTATATGTATATTA
1 TTTTCATAATATTTATATATATATTA
*
4742626 TTTT-TTAATATTTATAT
1 TTTTCATAATATTTATAT
4742643 TTTATTTTCA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
25 12 0.31
26 9 0.23
28 18 0.46
ACGTcount: A:0.34, C:0.04, G:0.03, T:0.59
Consensus pattern (26 bp):
TTTTCATAATATTTATATATATATTA
Found at i:4744255 original size:12 final size:12
Alignment explanation
Indices: 4744235--4744286 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
4744225 ACATTCACAT
4744235 ATTTACATTTGC
1 ATTTACATTTGC
*
4744247 ATTTGCATTTGC
1 ATTTACATTTGC
** *
4744259 ATTTTTATGTTTGT
1 A--TTTACATTTGC
4744273 ATTTACATTTGC
1 ATTTACATTTGC
4744285 AT
1 AT
4744287 ATTTCCATAA
Statistics
Matches: 30, Mismatches: 8, Indels: 4
0.71 0.19 0.10
Matches are distributed among these distances:
12 22 0.73
14 8 0.27
ACGTcount: A:0.21, C:0.12, G:0.12, T:0.56
Consensus pattern (12 bp):
ATTTACATTTGC
Found at i:4744265 original size:26 final size:26
Alignment explanation
Indices: 4744213--4744286 Score: 67
Period size: 26 Copynumber: 2.8 Consensus size: 26
4744203 GTATTATACA
** *
4744213 ATTTGCATTGTTACATTCACATATTTAC
1 ATTTGCA-T-TTACATTTGCATTTTTAC
* *
4744241 ATTTGCATTTGCATTTGCATTTTTAT
1 ATTTGCATTTACATTTGCATTTTTAC
* *
4744267 GTTTGTATTTACATTTGCAT
1 ATTTGCATTTACATTTGCAT
4744287 ATTTCCATAA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
26 30 0.79
27 1 0.03
28 7 0.18
ACGTcount: A:0.23, C:0.14, G:0.11, T:0.53
Consensus pattern (26 bp):
ATTTGCATTTACATTTGCATTTTTAC
Found at i:4744289 original size:14 final size:14
Alignment explanation
Indices: 4744213--4744290 Score: 58
Period size: 14 Copynumber: 5.9 Consensus size: 14
4744203 GTATTATACA
4744213 ATTTGCAT-TGTTAC
1 ATTTGCATAT-TTAC
**
4744227 ATTCACATATTTAC
1 ATTTGCATATTTAC
*
4744241 ATTTGC--ATTTGC
1 ATTTGCATATTTAC
* *
4744253 ATTTGCATTTTTAT
1 ATTTGCATATTTAC
*
4744267 GTTTG--TATTTAC
1 ATTTGCATATTTAC
4744279 ATTTGCATATTT
1 ATTTGCATATTT
4744291 CCATAATTAA
Statistics
Matches: 47, Mismatches: 12, Indels: 10
0.68 0.17 0.14
Matches are distributed among these distances:
12 20 0.43
14 26 0.55
15 1 0.02
ACGTcount: A:0.23, C:0.13, G:0.10, T:0.54
Consensus pattern (14 bp):
ATTTGCATATTTAC
Found at i:4746987 original size:16 final size:15
Alignment explanation
Indices: 4746954--4747005 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
4746944 CATCCAGCAA
*
4746954 AAAAAGAAGAA-GAAG
1 AAAAAGAAAAATG-AG
*
4746969 AAAAATAAAAATGATG
1 AAAAAGAAAAATGA-G
4746985 AAAAAAGAAAAATGAG
1 -AAAAAGAAAAATGAG
4747001 AAAAA
1 AAAAA
4747006 ATGAAAAAGG
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
15 15 0.48
16 3 0.10
17 13 0.42
ACGTcount: A:0.75, C:0.00, G:0.17, T:0.08
Consensus pattern (15 bp):
AAAAAGAAAAATGAG
Found at i:4747006 original size:16 final size:17
Alignment explanation
Indices: 4746969--4747013 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 17
4746959 GAAGAAGAAG
*
4746969 AAAAATAAAAATGATGA
1 AAAAAGAAAAATGATGA
4746986 AAAAAGAAAAATGA-GA
1 AAAAAGAAAAATGATGA
4747002 AAAAATGAAAAA
1 AAAAA-GAAAAA
4747014 GGGAAAATAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 7 0.27
17 19 0.73
ACGTcount: A:0.76, C:0.00, G:0.13, T:0.11
Consensus pattern (17 bp):
AAAAAGAAAAATGATGA
Found at i:4748590 original size:9 final size:9
Alignment explanation
Indices: 4748567--4748605 Score: 62
Period size: 9 Copynumber: 4.4 Consensus size: 9
4748557 CAGTTTGCTT
4748567 TTATTTTTA
1 TTATTTTTA
4748576 TT-TTTTTA
1 TTATTTTTA
4748584 TTATTTTTA
1 TTATTTTTA
*
4748593 TTATTATTA
1 TTATTTTTA
4748602 TTAT
1 TTAT
4748606 ACATTATTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
8 8 0.29
9 20 0.71
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (9 bp):
TTATTTTTA
Found at i:4750952 original size:28 final size:27
Alignment explanation
Indices: 4750921--4750979 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 27
4750911 TAATTCTTTC
*
4750921 TTTTCAAAATTTTTATATATACTTATTA
1 TTTTCAAAATATTTATATATA-TTATTA
**
4750949 TTTTCCTAATATTTATATATATTATTA
1 TTTTCAAAATATTTATATATATTATTA
4750976 TTTT
1 TTTT
4750980 TATTAATGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 10 0.36
28 18 0.64
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (27 bp):
TTTTCAAAATATTTATATATATTATTA
Found at i:4753226 original size:14 final size:13
Alignment explanation
Indices: 4753209--4753282 Score: 69
Period size: 14 Copynumber: 5.4 Consensus size: 13
4753199 GCACAATTTG
*
4753209 CATTTTTATTGTTA
1 CATTTGTATT-TTA
*
4753223 CATTTGCATATTTA
1 CATTTGTAT-TTTA
4753237 CATTTGTATTTTA
1 CATTTGTATTTTA
4753250 CATTTTTGTATTTTTA
1 CA--TTTGTA-TTTTA
*
4753266 CGTTTGTA-TTTA
1 CATTTGTATTTTA
4753278 CATTT
1 CATTT
4753283 TCATTTTTGC
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
12 8 0.16
13 6 0.12
14 24 0.47
15 7 0.14
16 6 0.12
ACGTcount: A:0.22, C:0.09, G:0.08, T:0.61
Consensus pattern (13 bp):
CATTTGTATTTTA
Found at i:4756023 original size:19 final size:18
Alignment explanation
Indices: 4755998--4756050 Score: 97
Period size: 18 Copynumber: 2.9 Consensus size: 18
4755988 TATTATACTT
4755998 GAAAAAAAAGGAAAAAAG
1 GAAAAAAAAGGAAAAAAG
4756016 GAAAAAAAAGGAAAAAAG
1 GAAAAAAAAGGAAAAAAG
4756034 GAAAAAAAAAGGAAAAA
1 G-AAAAAAAAGGAAAAA
4756051 TGAAAAAAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 19 0.56
19 15 0.44
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (18 bp):
GAAAAAAAAGGAAAAAAG
Found at i:4756049 original size:26 final size:25
Alignment explanation
Indices: 4756001--4756059 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 25
4755991 TATACTTGAA
4756001 AAAAAAGGAAAAAAGGAAAAAAAAGG
1 AAAAAAGGAAAAAA-GAAAAAAAAGG
*
4756027 AAAAAAGGAAAAAA-AAAGGAAAAATG
1 AAAAAAGGAAAAAAGAAA--AAAAAGG
4756053 AAAAAAG
1 AAAAAAG
4756060 TGAACCAAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 3 0.10
26 27 0.90
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (25 bp):
AAAAAAGGAAAAAAGAAAAAAAAGG
Found at i:4756050 original size:8 final size:8
Alignment explanation
Indices: 4756001--4756040 Score: 62
Period size: 8 Copynumber: 4.8 Consensus size: 8
4755991 TATACTTGAA
4756001 AAAAAAGG
1 AAAAAAGG
4756009 AAAAAAGG
1 AAAAAAGG
4756017 AAAAAAAAGG
1 --AAAAAAGG
4756027 AAAAAAGG
1 AAAAAAGG
4756035 AAAAAA
1 AAAAAA
4756041 AAAGGAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
8 22 0.73
10 8 0.27
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (8 bp):
AAAAAAGG
Found at i:4756057 original size:19 final size:18
Alignment explanation
Indices: 4755999--4756058 Score: 93
Period size: 18 Copynumber: 3.3 Consensus size: 18
4755989 ATTATACTTG
*
4755999 AAAAAAAAGGAAAAAAGG
1 AAAAAAAAGGAAAAAAGA
4756017 AAAAAAAAGGAAAAAAGGA
1 AAAAAAAAGGAAAAAA-GA
*
4756036 AAAAAAAAGGAAAAATGA
1 AAAAAAAAGGAAAAAAGA
4756054 AAAAA
1 AAAAA
4756059 GTGAACCAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
18 23 0.59
19 16 0.41
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (18 bp):
AAAAAAAAGGAAAAAAGA
Found at i:4756549 original size:32 final size:32
Alignment explanation
Indices: 4756509--4756570 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
4756499 TCTGGAAACA
* * *
4756509 AGAAGTATCTCTACGAGATGAGCATAACAACG
1 AGAAGTATCTCTACCAAATAAGCATAACAACG
4756541 AGAAGTATCTCTACCAAATAAGCATAACAA
1 AGAAGTATCTCTACCAAATAAGCATAACAA
4756571 TAATTTCTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.45, C:0.19, G:0.16, T:0.19
Consensus pattern (32 bp):
AGAAGTATCTCTACCAAATAAGCATAACAACG
Found at i:4759202 original size:78 final size:79
Alignment explanation
Indices: 4759108--4759259 Score: 254
Period size: 78 Copynumber: 1.9 Consensus size: 79
4759098 GAAGGTTGGG
4759108 GGCATTTTGAAGGCCCAATTCAGACAGATCCAT-ACGAAACATCTTGAAAGCCCATATCAACCAG
1 GGCATTTTGAAGGCCCAATTCAGACAGATCCATGA-GAAACATCTTGAAAGCCCATATCAACCAG
4759172 AAA-TAGAATGGTAA
65 AAATTAGAATGGTAA
* * *
4759186 GGCATTTTGAAGGCCCAATTCAGACAGATCCATGAGGAACATCTTGAAAGCCCATTTCAATCAGA
1 GGCATTTTGAAGGCCCAATTCAGACAGATCCATGAGAAACATCTTGAAAGCCCATATCAACCAGA
4759251 AATTAGAAT
66 AATTAGAAT
4759260 AAGCATTTTG
Statistics
Matches: 69, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
78 62 0.90
79 7 0.10
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.22
Consensus pattern (79 bp):
GGCATTTTGAAGGCCCAATTCAGACAGATCCATGAGAAACATCTTGAAAGCCCATATCAACCAGA
AATTAGAATGGTAA
Found at i:4759239 original size:37 final size:38
Alignment explanation
Indices: 4759114--4759244 Score: 94
Period size: 37 Copynumber: 3.4 Consensus size: 38
4759104 TGGGGGCATT
* *
4759114 TTGAAGGCCCAATTCAGACAGATCCAT-ACGAAACATC
1 TTGAAAGCCCAATTCAGACAGATCCATGACGGAACATC
* * *
4759151 TTGAAAGCCC-ATATCA-ACCAGA--AATAGAATGGTAAGGCATT
1 TTGAAAGCCCAAT-TCAGA-CAGATCCAT-G-ACGG-AA--CATC
*
4759192 TTGAAGGCCCAATTCAGACAGATCCATGA-GGAACATC
1 TTGAAAGCCCAATTCAGACAGATCCATGACGGAACATC
*
4759229 TTGAAAGCCCATTTCA
1 TTGAAAGCCCAATTCA
4759245 ATCAGAAATT
Statistics
Matches: 72, Mismatches: 10, Indels: 24
0.68 0.09 0.23
Matches are distributed among these distances:
35 2 0.03
36 3 0.04
37 33 0.46
38 2 0.03
39 4 0.06
40 2 0.03
41 20 0.28
42 4 0.06
43 2 0.03
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (38 bp):
TTGAAAGCCCAATTCAGACAGATCCATGACGGAACATC
Found at i:4761417 original size:73 final size:72
Alignment explanation
Indices: 4761294--4761481 Score: 303
Period size: 73 Copynumber: 2.6 Consensus size: 72
4761284 CTATTTCCCA
4761294 CATCTGTAAGACCT-AGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGCC
1 CATCTGTAAGACCTCAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGCC
4761358 TCAGGGT
66 TCAGGGT
*
4761365 CATCCT-TAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTTGGGAGCTTTTTGATTTTAAAG
1 CAT-CTGTAAGACCT-CAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAG
4761429 CCTCAGGGT
64 CCTCAGGGT
*
4761438 CATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAA-CCTTCGGG
1 CATCTGTAAGACC-TCAGTGCATGATGTTTTCAAAAAGCCTTCGGG
4761482 TTATCTTTAA
Statistics
Matches: 109, Mismatches: 3, Indels: 10
0.89 0.02 0.08
Matches are distributed among these distances:
71 18 0.17
72 8 0.07
73 82 0.75
74 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (72 bp):
CATCTGTAAGACCTCAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGCC
TCAGGGT
Found at i:4761535 original size:118 final size:119
Alignment explanation
Indices: 4761361--4761594 Score: 337
Period size: 118 Copynumber: 2.0 Consensus size: 119
4761351 TAAAGCCTCA
4761361 GGGTCATCCTTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTTGGGAGCTTTTTGA-TTTT
1 GGGTCATCCTTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTTGGGAGCTTTTTGACTTTT
* * ** *
4761425 AAAGCCTCAGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTC
66 AAAGCCTCAGGGTCACCCGTAAGCCCTAAAGTGCAGGATGTTTTCAAAACCTTC
* * * * *
4761479 GGGTTATCTTTAAGCCCTTCAGTGCATGATGTTTTTAAAAAG-CTTTCGGGAGCTTTTTGACGTT
1 GGGTCATCCTTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTT-GGGAGCTTTTTGAC--T
4761543 TTTAAAGCCTCAGGGTCACCCGTAAGCCCTAAAGTGCAGGATGTTTTCAAAA
63 TTTAAAGCCTCAGGGTCACCCGTAAGCCCTAAAGTGCAGGATGTTTTCAAAA
4761595 AAGCCTTCTG
Statistics
Matches: 102, Mismatches: 10, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
117 4 0.04
118 50 0.49
121 48 0.47
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (119 bp):
GGGTCATCCTTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTTGGGAGCTTTTTGACTTTT
AAAGCCTCAGGGTCACCCGTAAGCCCTAAAGTGCAGGATGTTTTCAAAACCTTC
Found at i:4761595 original size:76 final size:75
Alignment explanation
Indices: 4761479--4761736 Score: 320
Period size: 77 Copynumber: 3.4 Consensus size: 75
4761469 CAAAACCTTC
* * * * * *
4761479 GGGTTATCTTTAAGCCCTTCAGTGCATGATGTTTTTAAAAAGCTTTCGGGAGCTTTTTGACGTTT
1 GGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGACG-TT
4761544 TTAAAGCCTCA
65 TTAAAGCCTCA
* * * * * * *
4761555 GGGTCACCCGTAAGCCCTAAAGTGCAGGATGTTTTCAAAAAAGCCTTCTGGAGCTTTTTGATGAT
1 GGGTCATCTGTAAGACCTACAGTGCATGATGTTTTC-AAAAAGCCTTCGGGAGCTTTTTGACG-T
* *
4761620 CTTAAAGCCTCC
64 TTTAAAGCCTCA
*
4761632 GGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGAC-ATT
1 GGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGACGTTT
4761696 TAAAGCCTCA
66 TAAAGCCTCA
* *
4761706 AGGTCATCTGTAAGACCTACAGTGCAAGATG
1 GGGTCATCTGTAAGACCTACAGTGCATGATG
4761737 ATAAGACCTC
Statistics
Matches: 155, Mismatches: 26, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
74 39 0.25
76 51 0.33
77 65 0.42
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (75 bp):
GGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGACGTTT
TAAAGCCTCA
Found at i:4763447 original size:29 final size:30
Alignment explanation
Indices: 4763399--4763457 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
4763389 AGGGCTGTAA
4763399 ATTTTAATATTTTATATTTTAATC-CTATT
1 ATTTTAATATTTTATATTTTAATCACTATT
* *
4763428 ATTTTAAT-TTTATATGTTTTAGTCACTATT
1 ATTTTAATATTT-TATATTTTAATCACTATT
4763458 TAATTGCAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 3 0.12
29 18 0.69
30 5 0.19
ACGTcount: A:0.29, C:0.07, G:0.03, T:0.61
Consensus pattern (30 bp):
ATTTTAATATTTTATATTTTAATCACTATT
Found at i:4763563 original size:2 final size:2
Alignment explanation
Indices: 4763546--4763585 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
4763536 TATATTACTC
* *
4763546 AT AT AA 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 AT AT
4763586 TTGTTTAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:4772939 original size:16 final size:16
Alignment explanation
Indices: 4772914--4772948 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
4772904 TACTTTTATC
* *
4772914 TTTATTTTTTATTGAT
1 TTTATCTTTTATGGAT
4772930 TTTATCTTTTATGGAT
1 TTTATCTTTTATGGAT
4772946 TTT
1 TTT
4772949 CGGGTATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.09, T:0.71
Consensus pattern (16 bp):
TTTATCTTTTATGGAT
Found at i:4781915 original size:13 final size:13
Alignment explanation
Indices: 4781893--4782001 Score: 92
Period size: 13 Copynumber: 8.2 Consensus size: 13
4781883 CGGGTAGAGC
*
4781893 TGAGTCAACTCGT
1 TGAGTCAACTCAT
*
4781906 TGAGTTAACTCAT
1 TGAGTCAACTCAT
* * *
4781919 TAAGTTAACTCAC
1 TGAGTCAACTCAT
* *
4781932 TAAGTCAACTCGGT
1 TGAGTCAACTC-AT
*
4781946 TGAGTTAACTCAT
1 TGAGTCAACTCAT
* *
4781959 TGAGTTAACTCAC
1 TGAGTCAACTCAT
*
4781972 TAAGTCAACTCAGT
1 TGAGTCAACTCA-T
*
4781986 TGAGTCAACTCTT
1 TGAGTCAACTCAT
4781999 TGA
1 TGA
4782002 CCGTAGACTT
Statistics
Matches: 78, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
13 59 0.76
14 19 0.24
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (13 bp):
TGAGTCAACTCAT
Found at i:4781953 original size:40 final size:39
Alignment explanation
Indices: 4781895--4781996 Score: 168
Period size: 40 Copynumber: 2.6 Consensus size: 39
4781885 GGTAGAGCTG
4781895 AGTCAACTCGTTGAGTTAACTCATTAAGTTAACTCACTA
1 AGTCAACTCGTTGAGTTAACTCATTAAGTTAACTCACTA
*
4781934 AGTCAACTCGGTTGAGTTAACTCATTGAGTTAACTCACTA
1 AGTCAACTC-GTTGAGTTAACTCATTAAGTTAACTCACTA
*
4781974 AGTCAACTCAGTTGAGTCAACTC
1 AGTCAACTC-GTTGAGTTAACTC
4781997 TTTGACCGTA
Statistics
Matches: 59, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
39 9 0.15
40 50 0.85
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (39 bp):
AGTCAACTCGTTGAGTTAACTCATTAAGTTAACTCACTA
Found at i:4783038 original size:53 final size:53
Alignment explanation
Indices: 4782975--4783084 Score: 211
Period size: 53 Copynumber: 2.1 Consensus size: 53
4782965 ACTAGGATAA
*
4782975 ACTTGAATGCTAAATGACCTAAGTACCCTCTTTGACCTAGAATTAAGTGGATG
1 ACTTGAATGCTAAATGACCTAAGTACCCTCTATGACCTAGAATTAAGTGGATG
4783028 ACTTGAATGCTAAATGACCTAAGTACCCTCTATGACCTAGAATTAAGTGGATG
1 ACTTGAATGCTAAATGACCTAAGTACCCTCTATGACCTAGAATTAAGTGGATG
4783081 ACTT
1 ACTT
4783085 AGATAAGTCT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 56 1.00
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (53 bp):
ACTTGAATGCTAAATGACCTAAGTACCCTCTATGACCTAGAATTAAGTGGATG
Found at i:4783816 original size:21 final size:21
Alignment explanation
Indices: 4783786--4783833 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
4783776 ATATGATTGT
*
4783786 TTTATTTATTCTGAAATGTGA
1 TTTATCTATTCTGAAATGTGA
4783807 TTTATCTATTCTGAAATGTGA
1 TTTATCTATTCTGAAATGTGA
4783828 TTTATC
1 TTTATC
4783834 GAAGTTATTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.08, G:0.12, T:0.52
Consensus pattern (21 bp):
TTTATCTATTCTGAAATGTGA
Found at i:4790005 original size:20 final size:20
Alignment explanation
Indices: 4789980--4790019 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
4789970 AGTGCAGAGG
4789980 CGTCATAGTTGCAAAGGGGA
1 CGTCATAGTTGCAAAGGGGA
4790000 CGTCATAGTTGCAAAGGGGA
1 CGTCATAGTTGCAAAGGGGA
4790020 TTTTGATAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.15, G:0.35, T:0.20
Consensus pattern (20 bp):
CGTCATAGTTGCAAAGGGGA
Found at i:4794887 original size:13 final size:13
Alignment explanation
Indices: 4794869--4794901 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
4794859 ATTTTGATAT
4794869 TCGAATAATTATA
1 TCGAATAATTATA
4794882 TCGAATAATTATA
1 TCGAATAATTATA
4794895 TCGAATA
1 TCGAATA
4794902 TACTTAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.36
Consensus pattern (13 bp):
TCGAATAATTATA
Found at i:4797393 original size:22 final size:22
Alignment explanation
Indices: 4797323--4797423 Score: 116
Period size: 22 Copynumber: 4.6 Consensus size: 22
4797313 ACCAGAACCC
* *
4797323 TCAA-GGGGTATCGATTCCCCT
1 TCAAGGGGGAATCGGTTCCCCT
* *
4797344 AC-AGGGGGAATCAGTTCCCCT
1 TCAAGGGGGAATCGGTTCCCCT
4797365 TCAAAGGGGGAATCGGTTCCCCT
1 TC-AAGGGGGAATCGGTTCCCCT
*
4797388 TCAAGGAGGAATCGGTTCCCCT
1 TCAAGGGGGAATCGGTTCCCCT
* *
4797410 TCAAGAGGGTATCG
1 TCAAGGGGGAATCG
4797424 ATTCTCTTTG
Statistics
Matches: 67, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
20 1 0.01
21 16 0.24
22 30 0.45
23 20 0.30
ACGTcount: A:0.23, C:0.26, G:0.29, T:0.23
Consensus pattern (22 bp):
TCAAGGGGGAATCGGTTCCCCT
Found at i:4797406 original size:45 final size:45
Alignment explanation
Indices: 4797327--4797418 Score: 123
Period size: 45 Copynumber: 2.0 Consensus size: 45
4797317 GAACCCTCAA
* *
4797327 GGGGTATCGATTCCCCTACAGGGGGAATCAGTTCCCCTTCAA-AG
1 GGGGAATCGATTCCCCTACAGGAGGAATCAGTTCCCCTTCAAGAG
* * *
4797371 GGGGAATCGGTTCCCCTTCAAGGAGGAATCGGTTCCCCTTCAAGAG
1 GGGGAATCGATTCCCCTAC-AGGAGGAATCAGTTCCCCTTCAAGAG
4797417 GG
1 GG
4797419 TATCGATTCT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
44 16 0.39
45 21 0.51
46 4 0.10
ACGTcount: A:0.22, C:0.26, G:0.30, T:0.22
Consensus pattern (45 bp):
GGGGAATCGATTCCCCTACAGGAGGAATCAGTTCCCCTTCAAGAG
Found at i:4804602 original size:20 final size:19
Alignment explanation
Indices: 4804577--4804620 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
4804567 TTTGCCATAT
4804577 GAAAATCTTAACACTCAAAA
1 GAAAATCTTAA-ACTCAAAA
* * *
4804597 GAAAATTTTAAAGTGAAAA
1 GAAAATCTTAAACTCAAAA
4804616 GAAAA
1 GAAAA
4804621 AAGAAAACAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.59, C:0.09, G:0.11, T:0.20
Consensus pattern (19 bp):
GAAAATCTTAAACTCAAAA
Found at i:4816081 original size:9 final size:9
Alignment explanation
Indices: 4816067--4816108 Score: 57
Period size: 9 Copynumber: 4.7 Consensus size: 9
4816057 TATTATTCTT
4816067 GAAGAATAA
1 GAAGAATAA
4816076 GAAGAATAA
1 GAAGAATAA
*
4816085 AAAGAATAA
1 GAAGAATAA
* *
4816094 AAAGAAAAA
1 GAAGAATAA
4816103 GAAGAA
1 GAAGAA
4816109 AAATAATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.74, C:0.00, G:0.19, T:0.07
Consensus pattern (9 bp):
GAAGAATAA
Found at i:4816178 original size:46 final size:44
Alignment explanation
Indices: 4816071--4816179 Score: 116
Period size: 46 Copynumber: 2.4 Consensus size: 44
4816061 ATTCTTGAAG
* *
4816071 AATAAGAAGAATAAAAAGAATAAAAAGAAAAAGAAGAAAAATAATA
1 AATAATAA-AATAAAAA-AATAAAAAGAAAAAGAAGAAAAATAAGA
4816117 AATAATAAAATAAAAAAATAAAAA-AAGGAAAGAAAGAAGAAA-AAGA
1 AATAATAAAATAAAAAAATAAAAAGAA--AAAG-AAGAA-AAATAAGA
4816163 AATAA-ATAAATAAAAAA
1 AATAATA-AAATAAAAAA
4816180 GGGTTCAAGA
Statistics
Matches: 56, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
43 2 0.04
44 8 0.14
45 13 0.23
46 30 0.54
47 3 0.05
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (44 bp):
AATAATAAAATAAAAAAATAAAAAGAAAAAGAAGAAAAATAAGA
Found at i:4816881 original size:6 final size:6
Alignment explanation
Indices: 4816869--4816967 Score: 84
Period size: 6 Copynumber: 17.2 Consensus size: 6
4816859 GAAAGAAAAG
* * * *
4816869 AAAGAA TAAGAA TAAGAA TAAGAA AAA-AA ATA-AA AAAGAA AAAG-A
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
*
4816914 AAAGAA AAA-AGA AAAGAA AAAG-A AAAGAA AAAGAGA AAA-AA ATAGAA
1 AAAGAA AAAGA-A AAAGAA AAAGAA AAAGAA AAAGA-A AAAGAA AAAGAA
*
4816961 GAAGAA A
1 AAAGAA A
4816968 CCAAAGTGAA
Statistics
Matches: 78, Mismatches: 8, Indels: 14
0.78 0.08 0.14
Matches are distributed among these distances:
5 22 0.28
6 51 0.65
7 5 0.06
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (6 bp):
AAAGAA
Found at i:4816887 original size:12 final size:11
Alignment explanation
Indices: 4816860--4816967 Score: 107
Period size: 11 Copynumber: 9.6 Consensus size: 11
4816850 AGACAAATTG
4816860 AAAG-AAAAG-
1 AAAGAAAAAGA
*
4816869 AAAGAATAAGA
1 AAAGAAAAAGA
*
4816880 ATAAGAATAAGA
1 A-AAGAAAAAGA
*
4816892 AAA-AAAATAAA
1 AAAGAAAA-AGA
4816903 AAAGAAAAAGA
1 AAAGAAAAAGA
4816914 AAAGAAAAAAGA
1 AAAG-AAAAAGA
4816926 AAAGAAAAAGA
1 AAAGAAAAAGA
4816937 AAAGAAAAAGA
1 AAAGAAAAAGA
4816948 GAAA-AAAATAGA
1 -AAAGAAAA-AGA
4816960 AGAAGAAA
1 A-AAGAAA
4816968 CCAAAGTGAA
Statistics
Matches: 85, Mismatches: 4, Indels: 16
0.81 0.04 0.15
Matches are distributed among these distances:
9 4 0.05
10 7 0.08
11 37 0.44
12 34 0.40
13 3 0.04
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.05
Consensus pattern (11 bp):
AAAGAAAAAGA
Found at i:4816905 original size:7 final size:7
Alignment explanation
Indices: 4816893--4816954 Score: 58
Period size: 7 Copynumber: 8.9 Consensus size: 7
4816883 AGAATAAGAA
*
4816893 AAAAAAT
1 AAAAAAG
4816900 AAAAAAG
1 AAAAAAG
4816907 -AAAAAG
1 AAAAAAG
4816913 --AAAAG
1 AAAAAAG
4816918 AAAAAAG
1 AAAAAAG
*
4816925 AAAAGAAA
1 AAAA-AAG
4816933 AAGAAAAG
1 AA-AAAAG
4816941 AAAAAGAG
1 AAAAA-AG
4816949 AAAAAA
1 AAAAAA
4816955 ATAGAAGAAG
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
5 5 0.11
6 6 0.13
7 19 0.40
8 15 0.32
9 2 0.04
ACGTcount: A:0.84, C:0.00, G:0.15, T:0.02
Consensus pattern (7 bp):
AAAAAAG
Found at i:4816907 original size:34 final size:34
Alignment explanation
Indices: 4816859--4816967 Score: 107
Period size: 34 Copynumber: 3.1 Consensus size: 34
4816849 AAGACAAATT
* *
4816859 GAAAGAAAAGAAAGAATAAGAATAAG-AATAAGAAAA
1 GAAA-AAAA-AAAGAAAAAGAA-AAGAAAAAAGAAAA
4816895 -AAAATAAAAAAGAAAAAGAAAAGAAAAAAGAAAA
1 GAAAA-AAAAAAGAAAAAGAAAAGAAAAAAGAAAA
* *
4816929 GAAAAAGAAAAGAAAAAGAGAAA-AAAATAGAAGAA
1 GAAAAAAAAAAGAAAAAGA-AAAGAAAAAAGAA-AA
4816964 GAAA
1 GAAA
4816968 CCAAAGTGAA
Statistics
Matches: 64, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
33 3 0.05
34 42 0.66
35 19 0.30
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (34 bp):
GAAAAAAAAAAGAAAAAGAAAAGAAAAAAGAAAA
Found at i:4817700 original size:131 final size:132
Alignment explanation
Indices: 4817480--4817772 Score: 324
Period size: 131 Copynumber: 2.2 Consensus size: 132
4817470 CAATCTTTTT
*
4817480 CTCGATTCTTCACAGAAGGAGTTGAATCAGCGTAACCTTATTTGGCTCGATTCTATCACAAAAGG
1 CTCGATTCTTCACAGAAGGAGTTGAATCAGCGTAACCTTATTTGGCTCGATTCAATCACAAAAGG
** * *
4817545 AAGTAGATCATCATCGCATTTTGTTTGATCCTTCA-AAGAAGGAGTTGGATCGACAATT-TCATT
66 AAGTAGATCATCATCGCAAATTGTTTGATCCTTCACAA-AAGGAGTTGGATCAACAATTGTCATG
4817608 TTA
130 TTA
* ** * * *
4817611 TTCGATTCTTCACAGAAGGAGTTGAATCATTGTAATCTTATTTTGCAT-GATTCAATCACAAAAT
1 CTCGATTCTTCACAGAAGGAGTTGAATCAGCGTAACCTTATTTGGC-TCGATTCAATCACAAAAG
* * * * * * * * *
4817675 GAGGTAGATCGGT-GTTGGAAATTGTTTGTTTCTTCACAAAATGAGTTGGATCAACATTTGTCAT
65 GAAGTAGATC-ATCATCGCAAATTGTTTGATCCTTCACAAAAGGAGTTGGATCAACAATTGTCAT
4817739 GTTA
129 GTTA
** *
4817743 CTCGACCCTTCACAGAAGGAGTTGGATCAG
1 CTCGATTCTTCACAGAAGGAGTTGAATCAG
4817773 TGACAACCTT
Statistics
Matches: 133, Mismatches: 25, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
131 97 0.73
132 36 0.27
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (132 bp):
CTCGATTCTTCACAGAAGGAGTTGAATCAGCGTAACCTTATTTGGCTCGATTCAATCACAAAAGG
AAGTAGATCATCATCGCAAATTGTTTGATCCTTCACAAAAGGAGTTGGATCAACAATTGTCATGT
TA
Found at i:4817838 original size:43 final size:43
Alignment explanation
Indices: 4817750--4817852 Score: 116
Period size: 43 Copynumber: 2.4 Consensus size: 43
4817740 TTACTCGACC
* **
4817750 CTTCACAGAAGGAGTTGGATCAGTGACAACCTTTCACTTTATT
1 CTTCACAGAAGGAGTTGGATCAGTGACAACCTTACACTCGATT
** * * * *
4817793 CTTCACAGAATTAGTTGGATCAGTGAGAATCTTACGCTCGGTT
1 CTTCACAGAAGGAGTTGGATCAGTGACAACCTTACACTCGATT
*
4817836 CTTCACAAAAGGAGTTG
1 CTTCACAGAAGGAGTTG
4817853 AATTCGCATC
Statistics
Matches: 48, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
43 48 1.00
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.31
Consensus pattern (43 bp):
CTTCACAGAAGGAGTTGGATCAGTGACAACCTTACACTCGATT
Found at i:4829410 original size:68 final size:69
Alignment explanation
Indices: 4829310--4829446 Score: 240
Period size: 68 Copynumber: 2.0 Consensus size: 69
4829300 CATTTCAAAA
4829310 TCGAAATATCAAATTAATTTTATTTTCAAAAATATTTTAATTATATATATTTTAAAGATTTAAAA
1 TCGAAATATCAAATTAATTTTATTTTCAAAAATATTTTAATTATATATATTTTAAAGATTTAAAA
4829375 CATC
66 CATC
* * *
4829379 TCGAAATATCAAATTAA-TTTATTTTCAAAAATATTTTAATTTTATGTATTTTAAAGATTTAATA
1 TCGAAATATCAAATTAATTTTATTTTCAAAAATATTTTAATTATATATATTTTAAAGATTTAAAA
4829443 CATC
66 CATC
4829447 ACATGTCTTC
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
68 48 0.74
69 17 0.26
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (69 bp):
TCGAAATATCAAATTAATTTTATTTTCAAAAATATTTTAATTATATATATTTTAAAGATTTAAAA
CATC
Found at i:4829637 original size:30 final size:30
Alignment explanation
Indices: 4829548--4829637 Score: 76
Period size: 30 Copynumber: 3.0 Consensus size: 30
4829538 ATTAGTCCTA
* * *
4829548 AAACTTTTGAACATTTCAACTTCAT-CCCT
1 AAACTTTTGAATATTTCAAATTTATCCCCT
** *
4829577 AAACTATTACAATTATTT-AAAATTAGTCCCCT
1 AAACT-TTTGAA-TATTTCAAATTTA-TCCCCT
*
4829609 AAACTTTTGAATATTTCAATTTTATCCCC
1 AAACTTTTGAATATTTCAAATTTATCCCC
4829638 CAATTCATTC
Statistics
Matches: 46, Mismatches: 10, Indels: 9
0.71 0.15 0.14
Matches are distributed among these distances:
29 5 0.11
30 18 0.39
31 14 0.30
32 9 0.20
ACGTcount: A:0.34, C:0.22, G:0.03, T:0.40
Consensus pattern (30 bp):
AAACTTTTGAATATTTCAAATTTATCCCCT
Found at i:4830486 original size:24 final size:26
Alignment explanation
Indices: 4830429--4830487 Score: 68
Period size: 24 Copynumber: 2.3 Consensus size: 26
4830419 ATATGTCATC
*
4830429 TTTTATAGAATTTTGAAAAATTTATA
1 TTTTATAAAATTTTGAAAAATTTATA
***
4830455 TAAAATAAAATTTTG-AAAA-TTATA
1 TTTTATAAAATTTTGAAAAATTTATA
4830479 TTTTATAAA
1 TTTTATAAA
4830488 TAAAAACCCT
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
24 11 0.42
25 4 0.15
26 11 0.42
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (26 bp):
TTTTATAAAATTTTGAAAAATTTATA
Found at i:4831369 original size:27 final size:29
Alignment explanation
Indices: 4831322--4831375 Score: 69
Period size: 27 Copynumber: 1.9 Consensus size: 29
4831312 CTTTTAATAT
*
4831322 TTATATTATATATGGTGTATA-ATTAAAA
1 TTATATTATATATGCTGTATATATTAAAA
4831350 TTATA-TATATAT-CTGATATATATTAA
1 TTATATTATATATGCTG-TATATATTAA
4831376 TCATAATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 2 0.09
27 11 0.48
28 10 0.43
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (29 bp):
TTATATTATATATGCTGTATATATTAAAA
Found at i:4831458 original size:27 final size:27
Alignment explanation
Indices: 4831420--4831473 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
4831410 TCATTCAATA
4831420 ACCTTGGGTGTAACCTTGTAGGTTCCT
1 ACCTTGGGTGTAACCTTGTAGGTTCCT
*
4831447 ACCTTGGGTGTAATCTTGTAGGTTCCT
1 ACCTTGGGTGTAACCTTGTAGGTTCCT
4831474 GTAACGTTAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.15, C:0.20, G:0.26, T:0.39
Consensus pattern (27 bp):
ACCTTGGGTGTAACCTTGTAGGTTCCT
Found at i:4839497 original size:20 final size:20
Alignment explanation
Indices: 4839472--4839517 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
4839462 TGAACAATAA
4839472 TGAACAATA-TCAATACTGTG
1 TGAACAATACT-AATACTGTG
* *
4839492 TGAACAGTACTGATACTGTG
1 TGAACAATACTAATACTGTG
4839512 TGAACA
1 TGAACA
4839518 GTAATGAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 22 0.96
21 1 0.04
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (20 bp):
TGAACAATACTAATACTGTG
Found at i:4848629 original size:2 final size:2
Alignment explanation
Indices: 4848622--4848673 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
4848612 AGCTAAAGTC
4848622 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4848664 AT AT AT AT AT
1 AT AT AT AT AT
4848674 TAAATCCAGT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4859014 original size:2 final size:2
Alignment explanation
Indices: 4859007--4859064 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
4858997 GCTAAAGTCT
4859007 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4859049 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
4859065 AATCCATTAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.