Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A07
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 92880876
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2857347 characters in sequence are not A, C, G, or T
File 93 of 290
Found at i:28565623 original size:26 final size:26
Alignment explanation
Indices: 28565587--28565693 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
28565577 TGAAATGCCC
*
28565587 ATCAT-GAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
28565612 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
28565638 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
28565664 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
28565690 ATCA
1 ATCA
28565694 ATTTGTATCA
Statistics
Matches: 76, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
25 5 0.07
26 71 0.93
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:28569248 original size:12 final size:12
Alignment explanation
Indices: 28569231--28569259 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
28569221 TGCTTCCGTA
28569231 TTTAATTTTATT
1 TTTAATTTTATT
28569243 TTTAA-TTTATT
1 TTTAATTTTATT
28569254 TTTAAT
1 TTTAAT
28569260 AATTTAACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (12 bp):
TTTAATTTTATT
Found at i:28572259 original size:25 final size:25
Alignment explanation
Indices: 28572212--28572259 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
28572202 TTTCATGTAC
* * * *
28572212 TTATACTTATTTCTTTTATCTATCG
1 TTATAATTATTTCATATAACTATCG
28572237 TTATAATTATTTCATATAACTAT
1 TTATAATTATTTCATATAACTAT
28572260 TTTGTACATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.29, C:0.12, G:0.02, T:0.56
Consensus pattern (25 bp):
TTATAATTATTTCATATAACTATCG
Found at i:28572720 original size:46 final size:46
Alignment explanation
Indices: 28572410--28572718 Score: 424
Period size: 46 Copynumber: 6.7 Consensus size: 46
28572400 TTATCTTTGA
* * * * *
28572410 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCA-TTTCATGT
*
28572456 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
28572502 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
* * **
28572548 CACGCTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCCCGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
* * * *
28572594 CATGTTGTCATGGTATCTTTCAACCATGG-CCTATTCTTTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
* * ** *
28572639 CAAGTTCCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
28572685 CATGTTGCCATGGTATCTTTCAACCATGGTCTTA
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTA
28572719 CATATTTCAT
Statistics
Matches: 233, Mismatches: 28, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
45 41 0.18
46 192 0.82
ACGTcount: A:0.20, C:0.24, G:0.15, T:0.41
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
Found at i:28572726 original size:137 final size:138
Alignment explanation
Indices: 28572410--28572719 Score: 460
Period size: 137 Copynumber: 2.3 Consensus size: 138
28572400 TTATCTTTGA
* * * * *
28572410 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTCTGTCATGTTGCCATGGTATCTT
1 CATGATGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCCCGTCATGTTGCCATGGTATCTT
* * * * **
28572475 TCAACCATGGTCTTATTCTTTTCATGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCA
66 TCAACCATGGTCCTATTCTTTTCATATCAAGTTCCCATGGTATCTTTCAACCATGGTCTTACACA
*
28572540 TTTCATGT
131 TTTCATAT
* * * *
28572548 CACGCTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCCCGTCATGTTGTCATGGTATCTT
1 CATGATGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCCCGTCATGTTGCCATGGTATCTT
28572613 TCAACCATGG-CCTATTCTTTTCATATCAAGTTCCCATGGTATCTTTCAACCATGGTCTTACACA
66 TCAACCATGGTCCTATTCTTTTCATATCAAGTTCCCATGGTATCTTTCAACCATGGTCTTACACA
28572677 TTTCATAT
131 TTTCATAT
*
28572685 CATGTTGCCATGGTATCTTTCAACCATGGTCTTAC
1 CATGATGCCATGGTATCTTTCAACCATGGTCTTAC
28572720 ATATTTCATT
Statistics
Matches: 153, Mismatches: 19, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
137 87 0.57
138 66 0.43
ACGTcount: A:0.20, C:0.24, G:0.15, T:0.41
Consensus pattern (138 bp):
CATGATGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCCCGTCATGTTGCCATGGTATCTT
TCAACCATGGTCCTATTCTTTTCATATCAAGTTCCCATGGTATCTTTCAACCATGGTCTTACACA
TTTCATAT
Found at i:28575095 original size:15 final size:15
Alignment explanation
Indices: 28575067--28575100 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
28575057 GGATTGAATG
28575067 TTGTAAATGTTATGA
1 TTGTAAATGTTATGA
28575082 TTGTGAAATG-TATGA
1 TTGT-AAATGTTATGA
28575097 TTGT
1 TTGT
28575101 CTGACAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.47
Consensus pattern (15 bp):
TTGTAAATGTTATGA
Found at i:28575409 original size:25 final size:24
Alignment explanation
Indices: 28575367--28575424 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
28575357 TACAAATGCA
*
28575367 GCTCTTTATGAGCGTCCTGATATAG
1 GCTCTTTGTGAGCGTCCTGATAT-G
* * *
28575392 GCTCTTTGTTAGCTTCCTGGTATG
1 GCTCTTTGTGAGCGTCCTGATATG
28575416 GCTCGTTTG
1 GCTC-TTTG
28575425 AACATCCTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 5 0.18
25 23 0.82
ACGTcount: A:0.12, C:0.21, G:0.26, T:0.41
Consensus pattern (24 bp):
GCTCTTTGTGAGCGTCCTGATATG
Found at i:28582586 original size:25 final size:25
Alignment explanation
Indices: 28582558--28582605 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
28582548 GACTACCACA
28582558 GCTCTTTGTGAGCATCCTGATATAG
1 GCTCTTTGTGAGCATCCTGATATAG
* *
28582583 GCTCTTTTTGAGCCTCCTGATAT
1 GCTCTTTGTGAGCATCCTGATAT
28582606 CGCTCGCTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.17, C:0.23, G:0.21, T:0.40
Consensus pattern (25 bp):
GCTCTTTGTGAGCATCCTGATATAG
Found at i:28591291 original size:6 final size:6
Alignment explanation
Indices: 28591274--28591307 Score: 59
Period size: 6 Copynumber: 5.5 Consensus size: 6
28591264 GAAAACAAAT
28591274 GGGAGAA GGGAGA GGGAGA GGGAGA GGGAGA GGG
1 GGGAG-A GGGAGA GGGAGA GGGAGA GGGAGA GGG
28591308 GAAGGAGGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 22 0.81
7 5 0.19
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (6 bp):
GGGAGA
Found at i:28597075 original size:34 final size:34
Alignment explanation
Indices: 28597032--28597104 Score: 130
Period size: 34 Copynumber: 2.1 Consensus size: 34
28597022 GTAATACTAA
28597032 CATTCTTTCTTC-AGAATATTATAAAGTTAAATAG
1 CATTCTTTCTTCGA-AATATTATAAAGTTAAATAG
28597066 CATTCTTTCTTCGAAATATTATAAAGTTAAATAG
1 CATTCTTTCTTCGAAATATTATAAAGTTAAATAG
28597100 CATTC
1 CATTC
28597105 AACAAATCAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
34 37 0.97
35 1 0.03
ACGTcount: A:0.37, C:0.14, G:0.08, T:0.41
Consensus pattern (34 bp):
CATTCTTTCTTCGAAATATTATAAAGTTAAATAG
Found at i:28599076 original size:21 final size:23
Alignment explanation
Indices: 28599029--28599082 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 23
28599019 CATTCAAGAT
**
28599029 AAAATAATATATAAAACTCTTTA
1 AAAATAATATATAAAACTAATTA
*
28599052 AAAATAATATAT-AAAC-AATTC
1 AAAATAATATATAAAACTAATTA
28599073 AAAAT-ATATA
1 AAAATAATATA
28599083 ATGTGTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 5 0.18
21 7 0.25
22 4 0.14
23 12 0.43
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.31
Consensus pattern (23 bp):
AAAATAATATATAAAACTAATTA
Found at i:28599315 original size:25 final size:23
Alignment explanation
Indices: 28599260--28599315 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
28599250 ATAATAATGA
*
28599260 AAATAATAATAGTATATAAATAG
1 AAATAATAATAGTATAGAAATAG
*
28599283 AAAT-ATAATAGTAGTAGAAATAT
1 AAATAATAATAGTA-TAGAAATAG
28599306 AAATAGATAA
1 AAATA-ATAA
28599316 ATAAAATTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 9 0.32
23 15 0.54
25 4 0.14
ACGTcount: A:0.61, C:0.00, G:0.11, T:0.29
Consensus pattern (23 bp):
AAATAATAATAGTATAGAAATAG
Found at i:28599326 original size:14 final size:13
Alignment explanation
Indices: 28599300--28599338 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
28599290 ATAGTAGTAG
28599300 AAATATAAATAGAT
1 AAATA-AAATAGAT
28599314 AAATAAAATTAGAT
1 AAATAAAA-TAGAT
28599328 AAATAATAATA
1 AAATAA-AATA
28599339 ATATTAGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 3 0.13
14 18 0.78
15 2 0.09
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (13 bp):
AAATAAAATAGAT
Found at i:28599345 original size:20 final size:22
Alignment explanation
Indices: 28599304--28599346 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
28599294 TAGTAGAAAT
28599304 ATAAATAGATAAATAAAATTAG
1 ATAAATAGATAAATAAAATTAG
*
28599326 ATAAATA-AT-AATAATATTAG
1 ATAAATAGATAAATAAAATTAG
28599346 A
1 A
28599347 ATAAGAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 11 0.55
21 2 0.10
22 7 0.35
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (22 bp):
ATAAATAGATAAATAAAATTAG
Found at i:28599633 original size:17 final size:17
Alignment explanation
Indices: 28599611--28599652 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
28599601 TTTTAGGGCC
*
28599611 AAAATTAAGAATAATGA
1 AAAATTAAGAATAACGA
28599628 AAAATTAAGAATAACGA
1 AAAATTAAGAATAACGA
*
28599645 AAACTTAA
1 AAAATTAA
28599653 TTGCAAAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.64, C:0.05, G:0.10, T:0.21
Consensus pattern (17 bp):
AAAATTAAGAATAACGA
Found at i:28600408 original size:44 final size:44
Alignment explanation
Indices: 28600340--28600886 Score: 233
Period size: 44 Copynumber: 12.5 Consensus size: 44
28600330 GGAACTTAAA
* *
28600340 GGAGATAAAATCTAGTAATCTTCAGTCTGCTCCACTACTGCTTAG
1 GGAGATAAGATCT-GTAATTTTCAGTCTGCTCCACTACTGCTTAG
* * * * *
28600385 TGAGATAAGATCTGTAATTTTCAGCCTACTCCAC-ACTACTCAG
1 GGAGATAAGATCTGTAATTTTCAGTCTGCTCCACTACTGCTTAG
* ** * *
28600428 GGAGATAAGGCTCACT-GTTTTC-GATCTGCTCCGCTACTGCTTAG
1 GGAGATAA-GATCTGTAATTTTCAG-TCTGCTCCACTACTGCTTAG
* *
28600472 GGAGATAAGATATGTAATTTTCAG-CTTGTTTCC-CTACTGCTTAG
1 GGAGATAAGATCTGTAATTTTCAGTC-TG-CTCCACTACTGCTTAG
* * * * * *
28600516 GGAGATAAGATTTCTAAATTT-AGCCTGTTTCC-CCACTGCTTAG
1 GGAGATAAGATCTGTAATTTTCAGTCTG-CTCCACTACTGCTTAG
* * * * * *
28600559 GGGGATAAGGT-T-CACCGTCTTC-GATCTGTTCCACTACTGCTTAG
1 GGAGATAAGATCTGTA--ATTTTCAG-TCTGCTCCACTACTGCTTAG
* * *
28600603 GGAGATAAGATCTGTAATTTTCAGCCTGTTACC-TTACTGCTTAG
1 GGAGATAAGATCTGTAATTTTCAGTCTGCT-CCACTACTGCTTAG
* * * * *
28600647 GGGGTTAAG-GCT-TACCCTCTTC-GATCTGCTCCACTACTGCTTAG
1 GGAGATAAGATCTGTA--ATTTTCAG-TCTGCTCCACTACTGCTTAG
* * * * *
28600691 AGAGATAATATCTGTAATTTTCAGCCTGTTACC-CTACTACTTAAG
1 GGAGATAAGATCTGTAATTTTCAGTCTGCT-CCACTACTGCTT-AG
** * * * * *
28600736 GG-CTTAAG-GCT-CACCCTCTTC-GATCTACTCCACTACTGCTTAG
1 GGAGATAAGATCTGTA--ATTTTCAG-TCTGCTCCACTACTGCTTAG
* * *
28600779 AGAGATAAGATCTGTAATTTTCAGCCTGTTACC-CTACTGCTTAG
1 GGAGATAAGATCTGTAATTTTCAGTCTGCT-CCACTACTGCTTAG
* * * * * * *
28600823 GGGGTTAAG-GCTTGCT-GTCTTCAATCTGCTCCACTACTGTTTA-
1 GGAGATAAGATC-TG-TAATTTTCAGTCTGCTCCACTACTGCTTAG
28600866 GG-GATAAGATCTGTAATTTTC
1 GGAGATAAGATCTGTAATTTTC
28600887 TAGCCTATTA
Statistics
Matches: 366, Mismatches: 96, Indels: 83
0.67 0.18 0.15
Matches are distributed among these distances:
41 2 0.01
42 16 0.04
43 84 0.23
44 227 0.62
45 33 0.09
46 4 0.01
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.34
Consensus pattern (44 bp):
GGAGATAAGATCTGTAATTTTCAGTCTGCTCCACTACTGCTTAG
Found at i:28600559 original size:43 final size:44
Alignment explanation
Indices: 28600463--28600567 Score: 149
Period size: 43 Copynumber: 2.4 Consensus size: 44
28600453 CTGCTCCGCT
* * * *
28600463 ACTGCTTAGGGAGATAAGATATGTAATTTTCAGCTTGTTTCCCT
1 ACTGCTTAGGGAGATAAGATATCTAAATTTCAGCCTGTTTCCCC
*
28600507 ACTGCTTAGGGAGATAAGATTTCTAAATTT-AGCCTGTTTCCCC
1 ACTGCTTAGGGAGATAAGATATCTAAATTTCAGCCTGTTTCCCC
*
28600550 ACTGCTTAGGGGGATAAG
1 ACTGCTTAGGGAGATAAG
28600568 GTTCACCGTC
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
43 28 0.51
44 27 0.49
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (44 bp):
ACTGCTTAGGGAGATAAGATATCTAAATTTCAGCCTGTTTCCCC
Found at i:28600596 original size:131 final size:131
Alignment explanation
Indices: 28600374--28600648 Score: 363
Period size: 131 Copynumber: 2.1 Consensus size: 131
28600364 GTCTGCTCCA
* * *
28600374 CTACTGCTTAGTGAGATAAGATCTGTAATTTTCAGCCTACTCCACACTACTCAGGGAGATAAGGC
1 CTACTGCTTAGGGAGATAAGATCTCTAAATTTCAGCCTACTCCACACTACTCAGGGAGATAAGGC
* * * * *
28600439 TCACTGTTTTCGATCTGCTCCGCTACTGCTTAGGGAGATAAGATATGTAATTTTCAGCTTGTTTC
66 TCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATATGTAATTTTCAGCCTGTTAC
28600504 C
131 C
* ** * * * *
28600505 CTACTGCTTAGGGAGATAAGATTTCTAAATTT-AGCCTGTTTCCCCACTGCTTAGGGGGATAAGG
1 CTACTGCTTAGGGAGATAAGATCTCTAAATTTCAGCCT-ACTCCACACTACTCAGGGAGATAAGG
* * *
28600569 TTCACCGTCTTCGATCTGTTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTA
65 CTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATATGTAATTTTCAGCCTGTTA
28600634 CC
130 CC
*
28600636 TTACTGCTTAGGG
1 CTACTGCTTAGGG
28600649 GGTTAAGGCT
Statistics
Matches: 124, Mismatches: 19, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
130 5 0.04
131 119 0.96
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.34
Consensus pattern (131 bp):
CTACTGCTTAGGGAGATAAGATCTCTAAATTTCAGCCTACTCCACACTACTCAGGGAGATAAGGC
TCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATATGTAATTTTCAGCCTGTTAC
C
Found at i:28600656 original size:88 final size:88
Alignment explanation
Indices: 28600505--28601108 Score: 768
Period size: 88 Copynumber: 7.0 Consensus size: 88
28600495 GCTTGTTTCC
* * * * * *
28600505 CTACTGCTTAGGGAGATAAGATTTCTAAATTT-AGCCTGTTTCCCCACTGCTTAGGGGGATAAGG
1 CTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGG
*
28600569 -TTCACCGTCTTCGATCTGTTCCA
66 CTT-ACCGTCTTCGATCTGCTCCA
*
28600592 CTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTACCTTACTGCTTAGGGGGTTAAGG
1 CTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGG
*
28600657 CTTACCCTCTTCGATCTGCTCCA
66 CTTACCGTCTTCGATCTGCTCCA
* * * * *
28600680 CTACTGCTTAGAGAGATAATATCTGTAATTTTCAGCCTGTTACCCTACTACTTAAGGGCTTAAGG
1 CTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGG
* * *
28600745 CTCACCCTCTTCGATCTACTCCA
66 CTTACCGTCTTCGATCTGCTCCA
*
28600768 CTACTGCTTAGAGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGG
1 CTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGG
* * *
28600833 CTTGCTGTCTTCAATCTGCTCCA
66 CTTACCGTCTTCGATCTGCTCCA
* * *
28600856 CTACTGTTTA-GG-GATAAGATCTGTAATTTTCTAGCCTATTACCCTACTGCTTAGAGGGTTAAG
1 CTACTGCTTAGGGAGATAAGATCTGTAATTTTC-AGCCTGTTACCCTACTGCTTAGGGGGTTAAG
* *
28600919 GCTTACTGTCTTCGATTTGCTCCA
65 GCTTACCGTCTTCGATCTGCTCCA
* *
28600943 CTACTGTTTAGGG-G---AGATCTGT-ATTTTCCAGCCTGTTACCTTACTGCTTAGGGGGTTAAG
1 CTACTGCTTAGGGAGATAAGATCTGTAATTTT-CAGCCTGTTACCCTACTGCTTAGGGGGTTAAG
* *
28601003 GCTTGCTGTCTTCGATCTGCTCCA
65 GCTTACCGTCTTCGATCTGCTCCA
*
28601027 CTACTGTTTAGGG-G---AGATCTGT-ATTTTCCAGCCTGTTACCCTACTGCTTAGGGGGTTAAG
1 CTACTGCTTAGGGAGATAAGATCTGTAATTTT-CAGCCTGTTACCCTACTGCTTAGGGGGTTAAG
* * *
28601087 GCTTGCTGTCTTTGATCTGCTC
65 GCTTACCGTCTTCGATCTGCTC
28601109 AATTATTGTT
Statistics
Matches: 471, Mismatches: 41, Indels: 13
0.90 0.08 0.02
Matches are distributed among these distances:
84 135 0.29
85 9 0.02
86 19 0.04
87 90 0.19
88 216 0.46
89 2 0.00
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.35
Consensus pattern (88 bp):
CTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGG
CTTACCGTCTTCGATCTGCTCCA
Found at i:28601078 original size:40 final size:40
Alignment explanation
Indices: 28600943--28601080 Score: 111
Period size: 40 Copynumber: 3.4 Consensus size: 40
28600933 ATTTGCTCCA
*
28600943 CTACTGTTTAGGGGAGATCTGTATTTTCCAGCCTGTTACC
1 CTACTGCTTAGGGGAGATCTGTATTTTCCAGCCTGTTACC
* * * * * * *
28600983 TTACTGCTTAGGGG-GTTAAGGCTTGCTGTCTTCGA-TCTGCT-CC
1 CTACTGCTTAGGGGAG---A-TC-TG-TATTTTCCAGCCTGTTACC
*
28601026 ACTACTGTTTAGGGGAGATCTGTATTTTCCAGCCTGTTACC
1 -CTACTGCTTAGGGGAGATCTGTATTTTCCAGCCTGTTACC
28601067 CTACTGCTTAGGGG
1 CTACTGCTTAGGGG
28601081 GTTAAGGCTT
Statistics
Matches: 71, Mismatches: 17, Indels: 20
0.66 0.16 0.19
Matches are distributed among these distances:
39 7 0.10
40 31 0.44
41 3 0.04
42 2 0.03
43 3 0.04
44 18 0.25
45 7 0.10
ACGTcount: A:0.16, C:0.22, G:0.25, T:0.36
Consensus pattern (40 bp):
CTACTGCTTAGGGGAGATCTGTATTTTCCAGCCTGTTACC
Found at i:28601496 original size:45 final size:45
Alignment explanation
Indices: 28601409--28601496 Score: 115
Period size: 45 Copynumber: 2.0 Consensus size: 45
28601399 GGTGGCTAAA
** * *
28601409 ATCTGCTCTGTAGCCAATACATGGAGATAAGACTTTCCATTTTTG
1 ATCTGCTCCATAGCCAATACATGGAGATAAGACTGTCAATTTTTG
*
28601454 ATCTGCTCCATAGCCGATACATGGAGATAAGATCTGT-AATTTT
1 ATCTGCTCCATAGCCAATACATGGAGATAAGA-CTGTCAATTTT
28601497 CAGTCTGCTT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
45 34 0.92
46 3 0.08
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.34
Consensus pattern (45 bp):
ATCTGCTCCATAGCCAATACATGGAGATAAGACTGTCAATTTTTG
Found at i:28601617 original size:178 final size:177
Alignment explanation
Indices: 28601125--28601796 Score: 868
Period size: 178 Copynumber: 3.8 Consensus size: 177
28601115 TGTTTAGGGG
* * *
28601125 AGATCTGTATTTTTCAGTCTGCTCCATAGCTGA-TACATGAAGATAAGACCTGTAATTTTCAACC
1 AGATCTGTAATTTTCAGTCTGCTCCATAGCT-ACT-CAGGAAGATAAGACTTGT-ATTTTCAACC
* * * * * * *
28601189 TGTTCTCCTGCTAGCTCAGAGAGATAAGGTTGGTAGCTAAAATCTGCTCCATAGCTGAGACATGG
63 TGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTAAAATCTGCTCCATAGCCGATACATGG
* * *
28601254 AGATAGGACTCGCCATTTTCGATCTGCTCCATAGCCGATACATAGAGATA
128 AGATAAGACTCGCCATTTTTGATCTGCTCCATAGCCGATACATGGAGATA
* * * * ***
28601304 AGATCTGTAATTCTCAGTCTGCTCCATAGCCGATTCATGG-AGTTAAGACCTACAATTTTCAACC
1 AGATCTGTAATTTTCAGTCTGCTCCATAG-CTACTCA-GGAAGATAAGA-CTTGTATTTTCAACC
* * * ** *
28601368 TACTCTCTTGCTACTTCGGAGAGATAAGGCTGGTGGCTAAAATCTGCTCTGTAGCCAATACATGG
63 TGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTAAAATCTGCTCCATAGCCGATACATGG
**
28601433 AGATAAGACTTTCCATTTTTGATCTGCTCCATAGCCGATACATGGAGATA
128 AGATAAGACTCGCCATTTTTGATCTGCTCCATAGCCGATACATGGAGATA
*
28601483 AGATCTGTAATTTTCAGTCTGCTTCC-TTGCTACCTCAGGAAGATAAGACTTGTATCTTT-AACC
1 AGATCTGTAATTTTCAGTCTGC-TCCATAGCTA-CTCAGGAAGATAAGACTTGTAT-TTTCAACC
28601546 TGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTAAAATCTGCTCCATAGCCGATACATGG
63 TGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTAAAATCTGCTCCATAGCCGATACATGG
* *
28601611 AGATAAGACTCGCCATTTTTTATCTGCTCCATAGTCGATACATGGAGATA
128 AGATAAGACTCGCCATTTTTGATCTGCTCCATAGCCGATACATGGAGATA
* * * * * *
28601661 AGATTTGTAATTTTTAGTCTGCTTCC-TTGCTACCTTAGGAAGATAAGACTTGTATCTTCAACTT
1 AGATCTGTAATTTTCAGTCTGC-TCCATAGCTA-CTCAGGAAGATAAGACTTGTATTTTCAACCT
*
28601725 GCTCTCTTGCTACCTCAGAAAGATAAGGCTGGTGGCTAAAATCTGCTCCATAGCCGATACATGGA
64 GCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTAAAATCTGCTCCATAGCCGATACATGGA
28601790 GATAAGA
129 GATAAGA
28601797 TCTGTAATTT
Statistics
Matches: 433, Mismatches: 51, Indels: 19
0.86 0.10 0.04
Matches are distributed among these distances:
177 2 0.00
178 244 0.56
179 180 0.42
180 7 0.02
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.31
Consensus pattern (177 bp):
AGATCTGTAATTTTCAGTCTGCTCCATAGCTACTCAGGAAGATAAGACTTGTATTTTCAACCTGC
TCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTAAAATCTGCTCCATAGCCGATACATGGAGA
TAAGACTCGCCATTTTTGATCTGCTCCATAGCCGATACATGGAGATA
Found at i:28601674 original size:45 final size:44
Alignment explanation
Indices: 28601587--28601683 Score: 131
Period size: 45 Copynumber: 2.2 Consensus size: 44
28601577 GGTGGCTAAA
*
28601587 ATCTGCTCCATAGCCGATACATGGAGATAAGACTCGCCATTTTTT
1 ATCTGCTCCATAGCCGATACATGGAGATAAGACTCG-CAATTTTT
* * * *
28601632 ATCTGCTCCATAGTCGATACATGGAGATAAGATTTGTAATTTTT
1 ATCTGCTCCATAGCCGATACATGGAGATAAGACTCGCAATTTTT
28601676 AGTCTGCT
1 A-TCTGCT
28601684 TCCTTGCTAC
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 7 0.15
45 39 0.85
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.35
Consensus pattern (44 bp):
ATCTGCTCCATAGCCGATACATGGAGATAAGACTCGCAATTTTT
Found at i:28607992 original size:126 final size:127
Alignment explanation
Indices: 28607849--28608092 Score: 301
Period size: 131 Copynumber: 1.9 Consensus size: 127
28607839 TATCTAATTT
* *
28607849 CCAAATACAAAACATTGCCTCATTTTAA-TTTGAGAAAACATGGATGAAATTTCAAAAGGATATT
1 CCAAACACAAAACATTGCCTCATTTTAATTTTGAAAAAACATGGATGAAATTTCAAAAGGATATT
* * * * * *
28607913 CTGTATTTTAGTAGAATGGAAAATCGAAGCCCAGCACGATTGGACACGACCTCCCAAACCCC
66 CCGCATTTTAGTAGAACGAAAAATCGAAACCCAGCACGATAGGACACGACCTCCCAAACCCC
* ** *
28607975 CCAAACACAAAATATTGCCTTGTTTTAATTTTTTTTTAAAAAACATGGATGAAATTTCAAAAGGA
1 CCAAACACAAAACATTGCCTCATTTTAA----TTTTGAAAAAACATGGATGAAATTTCAAAAGGA
* * * *
28608040 TATTCCGCATTTTAGTTGAACGAAAAATTGAAACCCAGTACGATAGGGCACGA
62 TATTCCGCATTTTAGTAGAACGAAAAATCGAAACCCAGCACGATAGGACACGA
28608093 TTCCTCGAAC
Statistics
Matches: 97, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
126 24 0.25
131 73 0.75
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (127 bp):
CCAAACACAAAACATTGCCTCATTTTAATTTTGAAAAAACATGGATGAAATTTCAAAAGGATATT
CCGCATTTTAGTAGAACGAAAAATCGAAACCCAGCACGATAGGACACGACCTCCCAAACCCC
Found at i:28608264 original size:21 final size:23
Alignment explanation
Indices: 28608217--28608270 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 23
28608207 CATTCAAGAT
**
28608217 AAAATAATATATAAAACTCTTTA
1 AAAATAATATATAAAACTAATTA
*
28608240 AAAATAATATAT-AAAC-AATTC
1 AAAATAATATATAAAACTAATTA
28608261 AAAAT-ATATA
1 AAAATAATATA
28608271 ATGTGTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 5 0.18
21 7 0.25
22 4 0.14
23 12 0.43
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.31
Consensus pattern (23 bp):
AAAATAATATATAAAACTAATTA
Found at i:28608323 original size:51 final size:49
Alignment explanation
Indices: 28608243--28608340 Score: 128
Period size: 51 Copynumber: 2.0 Consensus size: 49
28608233 CTCTTTAAAA
*
28608243 ATAATATATAAACAATTCAAAATATATAATGTGTAAAAATGTTTGAAATAC
1 ATAATATATAAACAATTCAAAATAAATAATGTGTAAAAA--TTTGAAATAC
*
28608294 ATAATATATGAAA-ATATT-AAAGTAAATAATGTGTAAAAATTTGAAAT
1 ATAATATAT-AAACA-ATTCAAAATAAATAATGTGTAAAAATTTGAAAT
28608341 GAGCGTTGTG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
49 8 0.19
51 29 0.67
52 6 0.14
ACGTcount: A:0.54, C:0.03, G:0.09, T:0.34
Consensus pattern (49 bp):
ATAATATATAAACAATTCAAAATAAATAATGTGTAAAAATTTGAAATAC
Found at i:28608332 original size:25 final size:26
Alignment explanation
Indices: 28608262--28608340 Score: 67
Period size: 25 Copynumber: 3.2 Consensus size: 26
28608252 AAACAATTCA
* *
28608262 AAATATATAATGTGTAAAAATGTTTG
1 AAATAAATAATGTGTAAAAATGATTG
* * * *
28608288 AAATACATAATATATGAAAAT-ATT-
1 AAATAAATAATGTGTAAAAATGATTG
28608312 AAAGTAAATAATGTGTAAAAAT--TTG
1 AAA-TAAATAATGTGTAAAAATGATTG
28608337 AAAT
1 AAAT
28608341 GAGCGTTGTG
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
24 6 0.14
25 19 0.45
26 17 0.40
ACGTcount: A:0.53, C:0.01, G:0.11, T:0.34
Consensus pattern (26 bp):
AAATAAATAATGTGTAAAAATGATTG
Found at i:28608512 original size:14 final size:13
Alignment explanation
Indices: 28608463--28608561 Score: 55
Period size: 14 Copynumber: 7.2 Consensus size: 13
28608453 ATTAGTATAT
28608463 AAATAGA-AATATA
1 AAATAGATAA-ATA
*
28608476 ATAATAGTAGAAATA
1 A-AATAG-ATAAATA
28608491 CAAATAGATAAATA
1 -AAATAGATAAATA
28608505 AAATTAGATAAATA
1 AAA-TAGATAAATA
*
28608519 ATAATA-TTAGAATA
1 A-AATAGATA-AATA
28608533 AGAA-A-ATAAATA
1 A-AATAGATAAATA
28608545 TAAATAGA-AACATA
1 -AAATAGATAA-ATA
28608559 AAA
1 AAA
28608562 ATAATAGCAA
Statistics
Matches: 71, Mismatches: 4, Indels: 22
0.73 0.04 0.23
Matches are distributed among these distances:
12 6 0.08
13 16 0.23
14 35 0.49
15 11 0.15
16 3 0.04
ACGTcount: A:0.66, C:0.02, G:0.08, T:0.24
Consensus pattern (13 bp):
AAATAGATAAATA
Found at i:28608568 original size:17 final size:17
Alignment explanation
Indices: 28608492--28608565 Score: 51
Period size: 18 Copynumber: 4.1 Consensus size: 17
28608482 GTAGAAATAC
*
28608492 AAATAGATAAATAAAATT
1 AAATAGA-AAATAAAAAT
* * *
28608510 AGATA-AATAATAATATT
1 AAATAGAA-AATAAAAAT
*
28608527 AGAATAAGAAAATAAATAT
1 A-AAT-AGAAAATAAAAAT
28608546 AAATAGAAACATAAAAAT
1 AAATAGAAA-ATAAAAAT
28608564 AA
1 AA
28608566 TAGCAATAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 10
0.72 0.11 0.16
Matches are distributed among these distances:
16 1 0.02
17 15 0.34
18 18 0.41
19 8 0.18
20 2 0.05
ACGTcount: A:0.68, C:0.01, G:0.07, T:0.24
Consensus pattern (17 bp):
AAATAGAAAATAAAAAT
Found at i:28608819 original size:17 final size:17
Alignment explanation
Indices: 28608797--28608838 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
28608787 TTTTAGAGCC
*
28608797 AAAATTAAGAATAATGA
1 AAAATTAAGAATAACGA
28608814 AAAATTAAGAATAACGA
1 AAAATTAAGAATAACGA
*
28608831 AAACTTAA
1 AAAATTAA
28608839 TTGCAAAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.64, C:0.05, G:0.10, T:0.21
Consensus pattern (17 bp):
AAAATTAAGAATAACGA
Found at i:28611642 original size:6 final size:6
Alignment explanation
Indices: 28611627--28611661 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
28611617 CTAAAAAATT
* *
28611627 CTACTA CTACTC CTACTC CTACTC TTACTC CTACT
1 CTACTC CTACTC CTACTC CTACTC CTACTC CTACT
28611662 TAAGATAAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.20, C:0.43, G:0.00, T:0.37
Consensus pattern (6 bp):
CTACTC
Found at i:28613106 original size:36 final size:36
Alignment explanation
Indices: 28613062--28613136 Score: 141
Period size: 36 Copynumber: 2.1 Consensus size: 36
28613052 TGCTATTTTC
*
28613062 TTTTATTATTATAAAAACCCTAAAACTTCCCTTTAT
1 TTTTATTATTATAAAAACCCTAAAAATTCCCTTTAT
28613098 TTTTATTATTATAAAAACCCTAAAAATTCCCTTTAT
1 TTTTATTATTATAAAAACCCTAAAAATTCCCTTTAT
28613134 TTT
1 TTT
28613137 AACTTTTTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.36, C:0.17, G:0.00, T:0.47
Consensus pattern (36 bp):
TTTTATTATTATAAAAACCCTAAAAATTCCCTTTAT
Found at i:28621007 original size:14 final size:15
Alignment explanation
Indices: 28620968--28621011 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 15
28620958 TTAACGTTTA
28620968 TTATTAAAATAAATT
1 TTATTAAAATAAATT
28620983 TATAATATAAAATAAA-T
1 T-T-AT-TAAAATAAATT
28621000 TTATTAAAATAA
1 TTATTAAAATAA
28621012 TCATTTTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
14 8 0.31
15 3 0.12
16 2 0.08
17 4 0.15
18 9 0.35
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TTATTAAAATAAATT
Found at i:28624025 original size:25 final size:25
Alignment explanation
Indices: 28623995--28624044 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
28623985 CTAGAAAGTA
*
28623995 TGACTTGAGAATGTATAGGTGATTT
1 TGACTTGAGAATGTATAAGTGATTT
28624020 TGACTTGAGAATGTATAAGTGATTT
1 TGACTTGAGAATGTATAAGTGATTT
28624045 AACATAAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.30, C:0.04, G:0.26, T:0.40
Consensus pattern (25 bp):
TGACTTGAGAATGTATAAGTGATTT
Found at i:28630595 original size:3 final size:3
Alignment explanation
Indices: 28630587--28630618 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
28630577 TACTTCATTG
28630587 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
28630619 TATTTGTTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:28632287 original size:16 final size:15
Alignment explanation
Indices: 28632266--28632313 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
28632256 ATTTTGAATA
28632266 TTATTTAATATTATTT
1 TTATTT-ATATTATTT
* *
28632282 TTATTTATGTAATTT
1 TTATTTATATTATTT
*
28632297 TTATTTTATAATATTT
1 TTA-TTTATATTATTT
28632313 T
1 T
28632314 ATAACAGCAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 10 0.38
16 16 0.62
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (15 bp):
TTATTTATATTATTT
Found at i:28640817 original size:125 final size:126
Alignment explanation
Indices: 28640655--28641174 Score: 525
Period size: 125 Copynumber: 4.2 Consensus size: 126
28640645 GCCAATCAAG
* ** * * *
28640655 AACTACTGTAGAAAAAGAGCATCCACATGGGAGCTTTTTTTAATAATTTTACTGACAGTGCATCC
1 AACTACTATAGAAAAA-AAAATCCACATGGGAGCTTTTTTCAGTAATTTTACTAACAGTGCATCC
* *
28640720 TGCTTGAAGCGTTTTTGACACT-TTTTTTCCAGAACCATCTTCTCAAAATTATTTTTCTAGG
65 TGCTTGAAGCGTTTTTGACACTATTTTTTCCAGAACTATCTTCTCAAAATTATTTTTCTAGA
* ** * * *
28640781 AACTAGTATAGAAAAAAAAATCCACATAAGAGCTTTTTTCAGTAATTTTGCTAACAATACATCCT
1 AACTACTATAGAAAAAAAAATCCACATGGGAGCTTTTTTCAGTAATTTTACTAACAGTGCATCCT
* * *
28640846 GCTTGAAGTGTTTTTGACACTATTTTTT--AGAACTGTCTTCTCAAAATTATATTTTCAAG-
66 GCTTGAAGCGTTTTTGACACTATTTTTTCCAGAACTATCTTCTCAAAATTAT-TTTTCTAGA
* *** * * * * * *
28640905 AACTACTATAGGAAAAAGCGTCCAC--GTGAGTTTTTTTTAGTAATTTTACTGACACTGCATCCC
1 AACTACTATAGAAAAAAAAATCCACATGGGAGCTTTTTTCAGTAATTTTACTAACAGTGCATCCT
* * * * * * * *
28640968 GCTTGAAGCATTTTTTACATTATTTTTTTCAAAATTTTCTTCTCAAAATTATTTTTTTAGA
66 GCTTGAAGCGTTTTTGACACTATTTTTTCCAGAACTATCTTCTCAAAATTATTTTTCTAGA
* *** * * * *
28641029 AACTACTGTAGAAAAAGAGTGTCCACGTGGGAGCTTCTTTCAGTAATTTTGCTAACAGTGTATCC
1 AACTACTATAGAAAAA-AAAATCCACATGGGAGCTTTTTTCAGTAATTTTACTAACAGTGCATCC
* * * *
28641094 TGCTTAAAGCGTTTTTGACATTATCTTCT-CAGAACTATCTTCTCAAAATTAATTTTTCTA-A
65 TGCTTGAAGCGTTTTTGACACTATTTTTTCCAGAACTATCTTCTCAAAATT-ATTTTTCTAGA
28641155 AACTACTATAGAAAAAAAAA
1 AACTACTATAGAAAAAAAAA
28641175 CAAAAGCCTT
Statistics
Matches: 321, Mismatches: 64, Indels: 19
0.79 0.16 0.05
Matches are distributed among these distances:
122 53 0.17
123 6 0.02
124 73 0.23
125 75 0.23
126 54 0.17
127 60 0.19
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (126 bp):
AACTACTATAGAAAAAAAAATCCACATGGGAGCTTTTTTCAGTAATTTTACTAACAGTGCATCCT
GCTTGAAGCGTTTTTGACACTATTTTTTCCAGAACTATCTTCTCAAAATTATTTTTCTAGA
Found at i:28640942 original size:124 final size:124
Alignment explanation
Indices: 28640652--28641171 Score: 523
Period size: 124 Copynumber: 4.2 Consensus size: 124
28640642 AAGGCCAATC
* * * * *
28640652 AAGAACTACTGTAG-AAAAAGAGCATCCACATGGGAGCTTTTTTTAATAATTTTACTGACAGTGC
1 AAGAACTACTATAGAAAAAAGAG--TCCACGTGAGAGC-TTTTTTAGTAATTTTACTAACAGTGC
*
28640716 ATCCTGCTTGAAGCGTTTTTGACACT-TTTTTTCCAGAACCATCTTCTCAAAATTATTTTTCT
63 ATCCTGCTTGAAGCGTTTTTGACACTATTTTTT-CAGAACTATCTTCTCAAAATTATTTTTCT
* * * * * * * * *
28640778 AGGAACTAGTATAGAAAAAAAAATCCACATAAGAGCTTTTTTCAGTAATTTTGCTAACAATACAT
1 AAGAACTACTATAGAAAAAAGAGTCCACGTGAGAGCTTTTTT-AGTAATTTTACTAACAGTGCAT
* *
28640843 CCTGCTTGAAGTGTTTTTGACACTATTTTTT-AGAACTGTCTTCTCAAAATTATATTTTC-
65 CCTGCTTGAAGCGTTTTTGACACTATTTTTTCAGAACTATCTTCTCAAAATTAT-TTTTCT
* * ** * *
28640902 AAGAACTACTATAGGAAAAAGCGTCCACGTGAG-TTTTTTTTAGTAATTTTACTGACACTGCATC
1 AAGAACTACTATAGAAAAAAGAGTCCACGTGAGAGCTTTTTTAGTAATTTTACTAACAGTGCATC
* * * * * * *
28640966 CCGCTTGAAGCATTTTTTACATTATTTTTTTCAAAATTTTCTTCTCAAAATTATTTTT-T
66 CTGCTTGAAGCGTTTTTGACACTA-TTTTTTCAGAACTATCTTCTCAAAATTATTTTTCT
* * * * * * *
28641025 TAGAAACTACTGTAGAAAAAGAGTGTCCACGTGGGAGCTTCTTTCAGTAATTTTGCTAACAGTGT
1 AAG-AACTACTATAGAAAAA-AGAGTCCACGTGAGAGCTT-TTTTAGTAATTTTACTAACAGTGC
* * * *
28641090 ATCCTGCTTAAAGCGTTTTTGACATTATCTTCTCAGAACTATCTTCTCAAAATTAATTTTTCT
63 ATCCTGCTTGAAGCGTTTTTGACACTATTTTTTCAGAACTATCTTCTCAAAATT-ATTTTTCT
28641153 AA-AACTACTATAGAAAAAA
1 AAGAACTACTATAGAAAAAA
28641172 AAACAAAAGC
Statistics
Matches: 321, Mismatches: 60, Indels: 27
0.79 0.15 0.07
Matches are distributed among these distances:
122 38 0.12
123 18 0.06
124 84 0.26
125 69 0.21
126 56 0.17
127 54 0.17
128 2 0.01
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (124 bp):
AAGAACTACTATAGAAAAAAGAGTCCACGTGAGAGCTTTTTTAGTAATTTTACTAACAGTGCATC
CTGCTTGAAGCGTTTTTGACACTATTTTTTCAGAACTATCTTCTCAAAATTATTTTTCT
Found at i:28641335 original size:34 final size:34
Alignment explanation
Indices: 28641262--28641385 Score: 141
Period size: 34 Copynumber: 3.7 Consensus size: 34
28641252 CAAAAATTAT
** *
28641262 TTTAAAAAAACTAAACCCTAATTTAATCAATTT-
1 TTTAAAAACTCTAAACCCTAATTTAATTAATTTA
*
28641295 TCTTAAAAACTCTAAACCCTAATTTAATTTATTTA
1 T-TTAAAAACTCTAAACCCTAATTTAATTAATTTA
* *
28641330 TTT-AAAACCCTTAAAACCTAATTTAATTAATTTA
1 TTTAAAAACTC-TAAACCCTAATTTAATTAATTTA
28641364 ---AAAAACTCTAAACCCTAATTTA
1 TTTAAAAACTCTAAACCCTAATTTA
28641386 TTTTTTAAAA
Statistics
Matches: 78, Mismatches: 9, Indels: 10
0.80 0.09 0.10
Matches are distributed among these distances:
31 13 0.17
32 6 0.08
33 7 0.09
34 51 0.65
35 1 0.01
ACGTcount: A:0.45, C:0.17, G:0.00, T:0.38
Consensus pattern (34 bp):
TTTAAAAACTCTAAACCCTAATTTAATTAATTTA
Found at i:28641458 original size:8 final size:8
Alignment explanation
Indices: 28641445--28641481 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
28641435 ACAGAACATT
28641445 AACCCTAC
1 AACCCTAC
*
28641453 AACCCTAA
1 AACCCTAC
28641461 AACCCT--
1 AACCCTAC
28641467 AACCCTAC
1 AACCCTAC
28641475 AACCCTA
1 AACCCTA
28641482 GGCACTAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
6 6 0.23
8 20 0.77
ACGTcount: A:0.41, C:0.46, G:0.00, T:0.14
Consensus pattern (8 bp):
AACCCTAC
Found at i:28645660 original size:15 final size:15
Alignment explanation
Indices: 28645639--28645682 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
28645629 CAATTTTAAT
* *
28645639 AAAATGTGATTTTTT
1 AAAATGTGATTGTTG
* *
28645654 TAAATGTAATTGTTG
1 AAAATGTGATTGTTG
28645669 AAAATGTGATTGTT
1 AAAATGTGATTGTT
28645683 ATATTGCTTA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.18, T:0.48
Consensus pattern (15 bp):
AAAATGTGATTGTTG
Found at i:28649358 original size:21 final size:22
Alignment explanation
Indices: 28649334--28649377 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
28649324 TTAAATCAGT
*
28649334 TTTAATTTAAGAGTTT-GTTTA
1 TTTAATTAAAGAGTTTAGTTTA
*
28649355 TTTAATTAAAGTGTTTAGTTTA
1 TTTAATTAAAGAGTTTAGTTTA
28649377 T
1 T
28649378 ACTTTTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.30, C:0.00, G:0.14, T:0.57
Consensus pattern (22 bp):
TTTAATTAAAGAGTTTAGTTTA
Found at i:28650565 original size:42 final size:42
Alignment explanation
Indices: 28650519--28650605 Score: 174
Period size: 42 Copynumber: 2.1 Consensus size: 42
28650509 CTCAAAAAAA
28650519 AAAATGAAATGTTCCAAAGAAATATTAATTTTATAATAAATT
1 AAAATGAAATGTTCCAAAGAAATATTAATTTTATAATAAATT
28650561 AAAATGAAATGTTCCAAAGAAATATTAATTTTATAATAAATT
1 AAAATGAAATGTTCCAAAGAAATATTAATTTTATAATAAATT
28650603 AAA
1 AAA
28650606 CCTATAACCT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.54, C:0.05, G:0.07, T:0.34
Consensus pattern (42 bp):
AAAATGAAATGTTCCAAAGAAATATTAATTTTATAATAAATT
Found at i:28650945 original size:16 final size:15
Alignment explanation
Indices: 28650906--28650947 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
28650896 TACATTTATT
28650906 AATAGATT-A-ATAA
1 AATAGATTAATATAA
*
28650919 TATAGATTAATATAA
1 AATAGATTAATATAA
28650934 AATAGAATTAATAT
1 AATAG-ATTAATAT
28650948 TGTTTGTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 7 0.29
14 1 0.04
15 8 0.33
16 8 0.33
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (15 bp):
AATAGATTAATATAA
Found at i:28653769 original size:10 final size:10
Alignment explanation
Indices: 28653737--28653773 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
28653727 GGAAAAATAT
28653737 AAAAAATTTAC
1 AAAAAATTT-C
28653748 AAAAAA-TT-
1 AAAAAATTTC
28653756 AAAAAATTTC
1 AAAAAATTTC
28653766 AAAAAATT
1 AAAAAATT
28653774 ATTTAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
8 6 0.25
9 2 0.08
10 10 0.42
11 6 0.25
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (10 bp):
AAAAAATTTC
Found at i:28653769 original size:29 final size:28
Alignment explanation
Indices: 28653720--28653798 Score: 63
Period size: 29 Copynumber: 2.8 Consensus size: 28
28653710 AAATAACCTT
**
28653720 AAAAAATGGAAAAATATAAAAAATT-TAC
1 AAAAAATTAAAAAAT-TAAAAAATTATAC
*
28653748 AAAAAATTAAAAAATTTCAAAAAATTAT-T
1 AAAAAATTAAAAAA-TT-AAAAAATTATAC
* *
28653777 TAAAAATTACAAACATTAAAAA
1 AAAAAATTA-AAAAATTAAAAA
28653799 CTGATCCAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
28 18 0.43
29 19 0.45
30 5 0.12
ACGTcount: A:0.67, C:0.05, G:0.03, T:0.25
Consensus pattern (28 bp):
AAAAAATTAAAAAATTAAAAAATTATAC
Found at i:28653770 original size:18 final size:19
Alignment explanation
Indices: 28653729--28653774 Score: 76
Period size: 18 Copynumber: 2.4 Consensus size: 19
28653719 TAAAAAATGG
28653729 AAAAATATAAAAAATTTACA
1 AAAAAT-TAAAAAATTTACA
28653749 AAAAATTAAAAAATTT-CA
1 AAAAATTAAAAAATTTACA
28653767 AAAAATTA
1 AAAAATTA
28653775 TTTAAAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 10 0.38
19 10 0.38
20 6 0.23
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (19 bp):
AAAAATTAAAAAATTTACA
Found at i:28653993 original size:20 final size:18
Alignment explanation
Indices: 28653970--28654029 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 18
28653960 TTTTTAATAT
28653970 TTTTTAATAATTTTAGTAAA
1 TTTTTAATAATTTTA-T-AA
*
28653990 TTTTTATATATTTTTATAA
1 TTTTTA-ATAATTTTATAA
* *
28654009 -TTTT-GTAATTTTATAC
1 TTTTTAATAATTTTATAA
28654025 TTTTT
1 TTTTT
28654030 TTTTCTATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
16 9 0.26
17 4 0.12
18 4 0.12
19 2 0.06
20 7 0.21
21 8 0.24
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.65
Consensus pattern (18 bp):
TTTTTAATAATTTTATAA
Found at i:28653994 original size:11 final size:10
Alignment explanation
Indices: 28653955--28654012 Score: 50
Period size: 10 Copynumber: 5.8 Consensus size: 10
28653945 GTAAAAATAT
28653955 TAAATTTTT-
1 TAAATTTTTA
28653964 TAATATTTTT-
1 TAA-ATTTTTA
*
28653974 TAATAATTTTA
1 TAA-ATTTTTA
28653985 GTAAATTTTTA
1 -TAAATTTTTA
*
28653996 TATATTTTTA
1 TAAATTTTTA
28654006 T-AATTTT
1 TAAATTTT
28654013 GTAATTTTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
9 8 0.19
10 25 0.60
11 6 0.14
12 3 0.07
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (10 bp):
TAAATTTTTA
Found at i:28654010 original size:19 final size:18
Alignment explanation
Indices: 28653960--28654062 Score: 57
Period size: 20 Copynumber: 5.4 Consensus size: 18
28653950 AATATTAAAT
28653960 TTTTTAATATTTTTTAATAA
1 TTTTTAATA-TTTTT-ATAA
28653980 TTTTAGTAA-ATTTTTATATA
1 TTTT--TAATATTTTTATA-A
* *
28654000 TTTTT-ATAATTTTGTAA
1 TTTTTAATATTTTTATAA
* * * *
28654017 TTTTATACTTTTTTTTTCTA
1 TTTT-TAATATTTTTAT-AA
*
28654037 TTTTTAATCATTTTTGTAA
1 TTTTTAAT-ATTTTTATAA
28654056 TTTTTAA
1 TTTTTAA
28654063 ATAACTCTTT
Statistics
Matches: 64, Mismatches: 11, Indels: 17
0.70 0.12 0.18
Matches are distributed among these distances:
17 6 0.09
18 9 0.14
19 20 0.31
20 25 0.39
21 1 0.02
22 3 0.05
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.66
Consensus pattern (18 bp):
TTTTTAATATTTTTATAA
Found at i:28656861 original size:14 final size:14
Alignment explanation
Indices: 28656842--28656868 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28656832 TTGTTTTTAT
28656842 ATATATGTATATAG
1 ATATATGTATATAG
28656856 ATATATGTATATA
1 ATATATGTATATA
28656869 TATAGTAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (14 bp):
ATATATGTATATAG
Found at i:28657056 original size:23 final size:23
Alignment explanation
Indices: 28657015--28657063 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
28657005 TTGTTACACC
*
28657015 TTTTACTATTATTACTATTGTAT
1 TTTTACTATTATTACTATTATAT
**
28657038 TTTTACTATTATTGTTATTATAT
1 TTTTACTATTATTACTATTATAT
28657061 TTT
1 TTT
28657064 CCTCTTTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.24, C:0.06, G:0.04, T:0.65
Consensus pattern (23 bp):
TTTTACTATTATTACTATTATAT
Found at i:28663419 original size:27 final size:27
Alignment explanation
Indices: 28663381--28663493 Score: 133
Period size: 27 Copynumber: 4.2 Consensus size: 27
28663371 AGCATAGCTG
* *
28663381 CCAGA-ACAGATAATGTGACAGAGTCA
1 CCAGATACAGATAATGTGGCAGAGCCA
*
28663407 CCAGATATAGATAATCGTGGCAGAGCCA
1 CCAGATACAGATAAT-GTGGCAGAGCCA
28663435 CCAGA-ACAGATATATGTGGCAGAGCCA
1 CCAGATACAGATA-ATGTGGCAGAGCCA
* *
28663462 CCAGAT-CAGATATTTGTGGCATAGCCA
1 CCAGATACAGATA-ATGTGGCAGAGCCA
28663489 CCAGA
1 CCAGA
28663494 ACGCTTCCTC
Statistics
Matches: 77, Mismatches: 6, Indels: 7
0.86 0.07 0.08
Matches are distributed among these distances:
26 5 0.06
27 55 0.71
28 17 0.22
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18
Consensus pattern (27 bp):
CCAGATACAGATAATGTGGCAGAGCCA
Found at i:28663445 original size:54 final size:54
Alignment explanation
Indices: 28663381--28663495 Score: 160
Period size: 54 Copynumber: 2.1 Consensus size: 54
28663371 AGCATAGCTG
* *
28663381 CCAGAACAGATA-ATGTGACAGAGTCACCAGATATAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA
* * * *
28663435 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
28663489 CCAGAAC
1 CCAGAAC
28663496 GCTTCCTCCA
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
54 36 0.67
55 18 0.33
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
Found at i:28665149 original size:26 final size:26
Alignment explanation
Indices: 28665113--28665222 Score: 177
Period size: 26 Copynumber: 4.2 Consensus size: 26
28665103 CATGAAATTC
28665113 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
28665139 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
28665165 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
*
28665191 TTATCATTG-AACATTTACCTAACCTA
1 TTATCA-TGAAACATTTACCTAACCCA
28665217 TTATCA
1 TTATCA
28665223 ATTTGTACCA
Statistics
Matches: 81, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
26 79 0.98
27 2 0.02
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.35
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:28672637 original size:44 final size:44
Alignment explanation
Indices: 28672549--28672638 Score: 110
Period size: 43 Copynumber: 2.0 Consensus size: 44
28672539 CAAAAATAAT
*
28672549 GACCTTTAACCCCCTAAGCAGTAGGGTAACAAGCCAAATTTACA
1 GACCTTTAACCCCCTAAGCAGTAGGGTAACAAGCCAAAATTACA
* * * * *
28672593 GACC-TTAACCCCTTAAGTAGTAGGGTAATAGGCTGAAAATTACA
1 GACCTTTAACCCCCTAAGCAGTAGGGTAACAAGC-CAAAATTACA
28672637 GA
1 GA
28672639 TTTTGTCTCC
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
43 25 0.64
44 14 0.36
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (44 bp):
GACCTTTAACCCCCTAAGCAGTAGGGTAACAAGCCAAAATTACA
Found at i:28674251 original size:14 final size:14
Alignment explanation
Indices: 28674232--28674258 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28674222 TTGTTTTTAT
28674232 ATATATGTATATAG
1 ATATATGTATATAG
28674246 ATATATGTATATA
1 ATATATGTATATA
28674259 TATAGTAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (14 bp):
ATATATGTATATAG
Found at i:28674446 original size:23 final size:23
Alignment explanation
Indices: 28674405--28674453 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
28674395 TTGTTACACC
*
28674405 TTTTACTATTATTACTATTGTAT
1 TTTTACTATTATTACTATTATAT
**
28674428 TTTTACTATTATTGTTATTATAT
1 TTTTACTATTATTACTATTATAT
28674451 TTT
1 TTT
28674454 CCTCTTTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.24, C:0.06, G:0.04, T:0.65
Consensus pattern (23 bp):
TTTTACTATTATTACTATTATAT
Found at i:28674667 original size:3 final size:3
Alignment explanation
Indices: 28674659--28674784 Score: 53
Period size: 3 Copynumber: 42.7 Consensus size: 3
28674649 TGTATTTACC
* * * *
28674659 ATT ATT ATT ACT ATT ATT -TT CATT -TT -TT ATT ACT ATT ACT AAT
1 ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT
* ** * * * *
28674702 ATC ATT CCT -TT ATT ATT TTCT ATT ATT ATT ATC ACT ATT ATT AAT
1 ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT
* * * * * *
28674747 ATA AAT ATT AAT ACT CTT ATT ATT ATT TTT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
28674785 CAATATTATA
Statistics
Matches: 87, Mismatches: 31, Indels: 10
0.68 0.24 0.08
Matches are distributed among these distances:
2 7 0.08
3 76 0.87
4 4 0.05
ACGTcount: A:0.32, C:0.10, G:0.00, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:28674845 original size:18 final size:18
Alignment explanation
Indices: 28674824--28674862 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
28674814 CATTATCGAC
* *
28674824 ATTATTATTTTTATTATT
1 ATTATTATTTTCATCATT
*
28674842 ATTATTGTTTTCATCATT
1 ATTATTATTTTCATCATT
28674860 ATT
1 ATT
28674863 GTCCTTTTTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.67
Consensus pattern (18 bp):
ATTATTATTTTCATCATT
Found at i:28678792 original size:56 final size:56
Alignment explanation
Indices: 28678706--28678817 Score: 197
Period size: 56 Copynumber: 2.0 Consensus size: 56
28678696 AAAATAAATG
*
28678706 TTGAAATAACTTAAATGATCGCTTAGAATCAAACTTCACAGGTGAAGTGGTGCCTA
1 TTGAAATAACTTAAATGATCGCTTAGAATCAAACTTCACAGATGAAGTGGTGCCTA
* *
28678762 TTGAAATTACTTAAATGATTGCTTAGAATCAAACTTCACAGATGAAGTGGTGCCTA
1 TTGAAATAACTTAAATGATCGCTTAGAATCAAACTTCACAGATGAAGTGGTGCCTA
28678818 AGGTGGTGGG
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (56 bp):
TTGAAATAACTTAAATGATCGCTTAGAATCAAACTTCACAGATGAAGTGGTGCCTA
Found at i:28684025 original size:20 final size:19
Alignment explanation
Indices: 28683993--28684043 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 19
28683983 ATATTTGCAT
*
28683993 AAAAATAAT-AAAATAGAAG
1 AAAAA-AATAAAAAGAGAAG
*
28684012 AAAAAAAGTAAAAAGAGAAT
1 AAAAAAA-TAAAAAGAGAAG
*
28684032 AGAAAAATAAAA
1 AAAAAAATAAAA
28684044 TGTAATTATC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 2 0.07
19 11 0.41
20 14 0.52
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (19 bp):
AAAAAAATAAAAAGAGAAG
Found at i:28689973 original size:25 final size:25
Alignment explanation
Indices: 28689945--28690005 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
28689935 TAAAATATGC
* *
28689945 TATGTTATGATTCGATATAACATGA
1 TATGTTAAGATTCAATATAACATGA
* * *
28689970 TATGCTAAGATTCAATATGATATGA
1 TATGTTAAGATTCAATATAACATGA
*
28689995 TACGTTAAGAT
1 TATGTTAAGAT
28690006 ATGATTTGTA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.38, C:0.08, G:0.16, T:0.38
Consensus pattern (25 bp):
TATGTTAAGATTCAATATAACATGA
Found at i:28690831 original size:12 final size:12
Alignment explanation
Indices: 28690814--28690843 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
28690804 AAATCACTCT
28690814 ATATTTTGATAA
1 ATATTTTGATAA
28690826 ATATTTTGATAA
1 ATATTTTGATAA
*
28690838 AAATTT
1 ATATTT
28690844 AAAACAGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (12 bp):
ATATTTTGATAA
Found at i:28692576 original size:51 final size:51
Alignment explanation
Indices: 28692499--28692697 Score: 285
Period size: 51 Copynumber: 3.9 Consensus size: 51
28692489 CGGATACACG
* * * *
28692499 GTGGCTTTCACATAGTACCACCCTTGTAG-CTAAAGCTATTTTATTCACAAA
1 GTGGCCTTCACATAGTACCACACTTGT-GTCCAAAGCTATTATATTCACAAA
28692550 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTATATTCACAAA
1 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTATATTCACAAA
*
28692601 GTGGCATTCACATAGTACCACA-TATGTGTCCAAAGCTATTATATTCACAAA
1 GTGGCCTTCACATAGTACCACACT-TGTGTCCAAAGCTATTATATTCACAAA
* * * *
28692652 GTGGCCTTCATATAGTACCACAATTGTGTCCAAGGCTATTTTATTC
1 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTATATTC
28692698 CTAAGGTTCA
Statistics
Matches: 136, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
50 2 0.01
51 133 0.98
52 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (51 bp):
GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTATATTCACAAA
Found at i:28692781 original size:24 final size:24
Alignment explanation
Indices: 28692733--28692833 Score: 130
Period size: 24 Copynumber: 4.0 Consensus size: 24
28692723 ACTTAGCATA
*
28692733 ATGCCATGAACTTTATTTCACTTAG
1 ATGCCATGGAC-TTATTTCACTTAG
*
28692758 ATGCCATGGACTTATTTCATTTAG
1 ATGCCATGGACTTATTTCACTTAG
28692782 CACATTGCCATGGACTTATTTCACTTAG
1 ---A-TGCCATGGACTTATTTCACTTAG
*
28692810 ATGCCATGGTCTTATTTCACTTAG
1 ATGCCATGGACTTATTTCACTTAG
28692834 CACAAGGTCA
Statistics
Matches: 68, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
24 34 0.50
25 11 0.16
27 1 0.01
28 22 0.32
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.40
Consensus pattern (24 bp):
ATGCCATGGACTTATTTCACTTAG
Found at i:28692791 original size:28 final size:27
Alignment explanation
Indices: 28692721--28692837 Score: 129
Period size: 24 Copynumber: 4.4 Consensus size: 27
28692711 GGGAAATTTC
* *
28692721 TCACTTAGCATAATGCCATGAACTTTATT
1 TCACTTAGCA-CATGCCATGGAC-TTATT
28692750 TCACTTAG---ATGCCATGGACTTATT
1 TCACTTAGCACATGCCATGGACTTATT
*
28692774 TCATTTAGCACATTGCCATGGACTTATT
1 TCACTTAGCACA-TGCCATGGACTTATT
*
28692802 TCACTTAG---ATGCCATGGTCTTATT
1 TCACTTAGCACATGCCATGGACTTATT
28692826 TCACTTAGCACA
1 TCACTTAGCACA
28692838 AGGTCATATC
Statistics
Matches: 77, Mismatches: 4, Indels: 16
0.79 0.04 0.16
Matches are distributed among these distances:
24 34 0.44
25 11 0.14
27 2 0.03
28 22 0.29
29 8 0.10
ACGTcount: A:0.26, C:0.22, G:0.14, T:0.38
Consensus pattern (27 bp):
TCACTTAGCACATGCCATGGACTTATT
Found at i:28692809 original size:52 final size:53
Alignment explanation
Indices: 28692721--28692838 Score: 184
Period size: 52 Copynumber: 2.2 Consensus size: 53
28692711 GGGAAATTTC
*
28692721 TCACTTAGCATAATGCCATGAACTTTATTTCACTTAGATGCCATGGACTTATT
1 TCACTTAGCACAATGCCATGAACTTTATTTCACTTAGATGCCATGGACTTATT
* * * *
28692774 TCATTTAGCACATTGCCATGGAC-TTATTTCACTTAGATGCCATGGTCTTATT
1 TCACTTAGCACAATGCCATGAACTTTATTTCACTTAGATGCCATGGACTTATT
28692826 TCACTTAGCACAA
1 TCACTTAGCACAA
28692839 GGTCATATCC
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
52 39 0.67
53 19 0.33
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.37
Consensus pattern (53 bp):
TCACTTAGCACAATGCCATGAACTTTATTTCACTTAGATGCCATGGACTTATT
Found at i:28699680 original size:25 final size:25
Alignment explanation
Indices: 28699652--28699712 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
28699642 TAAAATATGC
* *
28699652 TATGTTATGATTCGATATAACATGA
1 TATGTTAAGATTCAATATAACATGA
* * *
28699677 TATGCTAAGATTCAATATGATATGA
1 TATGTTAAGATTCAATATAACATGA
*
28699702 TACGTTAAGAT
1 TATGTTAAGAT
28699713 ATGATTTGTA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.38, C:0.08, G:0.16, T:0.38
Consensus pattern (25 bp):
TATGTTAAGATTCAATATAACATGA
Found at i:28707631 original size:15 final size:16
Alignment explanation
Indices: 28707608--28707644 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
28707598 GAATTTAATC
28707608 AAAAA-CAC-ATCAAT
1 AAAAATCACAATCAAT
28707622 AAAAATCACAAATCAAT
1 AAAAATCAC-AATCAAT
28707639 AAAAAT
1 AAAAAT
28707645 TCATTCTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 5 0.25
15 3 0.15
17 12 0.60
ACGTcount: A:0.68, C:0.16, G:0.00, T:0.16
Consensus pattern (16 bp):
AAAAATCACAATCAAT
Found at i:28709500 original size:20 final size:20
Alignment explanation
Indices: 28709475--28709541 Score: 57
Period size: 20 Copynumber: 3.4 Consensus size: 20
28709465 AATAATGATA
28709475 TAAAAATAATAGGAGGCCTG
1 TAAAAATAATAGGAGGCCTG
** * * *
28709495 TAAAAATCAA-ACAAATG-ATA
1 TAAAAAT-AATA-GGAGGCCTG
28709515 TAAAAATAATAGGAGGCCTG
1 TAAAAATAATAGGAGGCCTG
28709535 TAAAAAT
1 TAAAAAT
28709542 CAAACAAAAC
Statistics
Matches: 33, Mismatches: 10, Indels: 8
0.65 0.20 0.16
Matches are distributed among these distances:
19 4 0.12
20 25 0.76
21 4 0.12
ACGTcount: A:0.54, C:0.09, G:0.16, T:0.21
Consensus pattern (20 bp):
TAAAAATAATAGGAGGCCTG
Found at i:28709514 original size:40 final size:40
Alignment explanation
Indices: 28709468--28709549 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
28709458 AATCAAGAAT
28709468 AATGATATAAAAATAATAGGAGGCCTGTAAAAATCAAACA
1 AATGATATAAAAATAATAGGAGGCCTGTAAAAATCAAACA
28709508 AATGATATAAAAATAATAGGAGGCCTGTAAAAATCAAACA
1 AATGATATAAAAATAATAGGAGGCCTGTAAAAATCAAACA
28709548 AA
1 AA
28709550 ACTAAAAATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.20
Consensus pattern (40 bp):
AATGATATAAAAATAATAGGAGGCCTGTAAAAATCAAACA
Found at i:28709745 original size:18 final size:19
Alignment explanation
Indices: 28709707--28709760 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 19
28709697 AGAATAAAAC
28709707 AAATAAATGATAATAAG-A
1 AAATAAATGATAATAAGAA
*
28709725 AAATAAATGA-AATAAATAA
1 AAATAAATGATAAT-AAGAA
*
28709744 AAATAAAAGAATAATAA
1 AAATAAATG-ATAATAA
28709761 TTAAGAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
17 3 0.10
18 12 0.40
19 9 0.30
20 3 0.10
21 3 0.10
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.20
Consensus pattern (19 bp):
AAATAAATGATAATAAGAA
Found at i:28716773 original size:17 final size:17
Alignment explanation
Indices: 28716748--28716781 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
28716738 TTTAATTCAA
*
28716748 AATAGATTAATAAAAAT
1 AATAAATTAATAAAAAT
*
28716765 AATAAATTAATTAAAAT
1 AATAAATTAATAAAAAT
28716782 TTATTCTAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (17 bp):
AATAAATTAATAAAAAT
Found at i:28725325 original size:38 final size:38
Alignment explanation
Indices: 28725264--28725376 Score: 127
Period size: 38 Copynumber: 2.9 Consensus size: 38
28725254 ATTTGATGTG
*
28725264 TATCCGGGATTAAAGACCCGCAGGCTTCGTGCTGGTAAAA
1 TATCCGGG-TTAAA-TCCCGCAGGCTTCGTGCTGGTAAAA
* **
28725304 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTAGTATTA
1 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAAAA
* ** * *
28725342 TATCCGGGATAAATCCTACAGGCCTAGTGCTGGTA
1 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTA
28725377 TTATATTCGG
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
38 50 0.79
39 5 0.08
40 8 0.13
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.27
Consensus pattern (38 bp):
TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAAAA
Found at i:28725449 original size:43 final size:43
Alignment explanation
Indices: 28725380--28725620 Score: 428
Period size: 43 Copynumber: 5.6 Consensus size: 43
28725370 GCTGGTATTA
*
28725380 TATTCGGGCCTTCGTGCCTAGTAGGCTTCGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
**
28725423 TATTCGGGCCTTCGTAACTAGCAGGCTTCGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
28725466 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
* * *
28725509 TATTTGGGCCTTCGTGCCTAGCAAGCTTCGTGCCAGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
28725552 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
28725595 TATTCGGGCCTTCGTGCCTAGCAGGC
1 TATTCGGGCCTTCGTGCCTAGCAGGC
28725621 GTAATGCCAG
Statistics
Matches: 187, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 187 1.00
ACGTcount: A:0.11, C:0.25, G:0.33, T:0.31
Consensus pattern (43 bp):
TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
Found at i:28730073 original size:26 final size:26
Alignment explanation
Indices: 28730043--28730150 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
28730033 TGAAATTCCC
28730043 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
28730069 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
28730095 ATCATGAAACATTTACCTAACTCATT
1 ATCATGGAACATTTACCTAACCCATT
*
28730121 ATCATGGAACATTTACCTAACACATT
1 ATCATGGAACATTTACCTAACCCATT
28730147 ATCA
1 ATCA
28730151 ATTTGTATCA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 78 1.00
ACGTcount: A:0.37, C:0.25, G:0.06, T:0.31
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:28732967 original size:28 final size:28
Alignment explanation
Indices: 28732927--28733005 Score: 88
Period size: 28 Copynumber: 2.9 Consensus size: 28
28732917 TCCAGAAAAG
28732927 GGAA-GTCTGCCAAGGGCTATCTTAGGT
1 GGAATGTCTGCCAAGGGCTATCTTAGGT
* * *
28732954 GGAATGTCCGCCAAAGGCTATTTTAGGT
1 GGAATGTCTGCCAAGGGCTATCTTAGGT
** * *
28732982 CAAATGTTTGCCAAGGACTATCTT
1 GGAATGTCTGCCAAGGGCTATCTT
28733006 GAAGACATGA
Statistics
Matches: 41, Mismatches: 10, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
27 4 0.10
28 37 0.90
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (28 bp):
GGAATGTCTGCCAAGGGCTATCTTAGGT
Found at i:28744590 original size:25 final size:25
Alignment explanation
Indices: 28744562--28744613 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
28744552 CCGACACTAG
28744562 ATCAATACTAAATTCAACTTCTCTA
1 ATCAATACTAAATTCAACTTCTCTA
28744587 ATCAATACTAAATTCAACTTCTCTA
1 ATCAATACTAAATTCAACTTCTCTA
28744612 AT
1 AT
28744614 AGGAGGCAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.40, C:0.23, G:0.00, T:0.37
Consensus pattern (25 bp):
ATCAATACTAAATTCAACTTCTCTA
Found at i:28753272 original size:18 final size:19
Alignment explanation
Indices: 28753244--28753280 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
28753234 ATTAAATTAA
28753244 TTGATTGAATCGATCTAAT
1 TTGATTGAATCGATCTAAT
28753263 TTGATT-AATCGATCTAAT
1 TTGATTGAATCGATCTAAT
28753281 CAATCGGAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (19 bp):
TTGATTGAATCGATCTAAT
Found at i:28755359 original size:30 final size:30
Alignment explanation
Indices: 28755323--28755384 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
28755313 CTTAACAAGT
*
28755323 AAATGCCTCTAAGATAATAA-ACAAATTAAC
1 AAATGCCTCTAAAATAATAATA-AAATTAAC
*
28755353 AAATGCCTTTAAAATAATAATAAAATTAAC
1 AAATGCCTCTAAAATAATAATAAAATTAAC
28755383 AA
1 AA
28755385 GAAAATAAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 28 0.97
31 1 0.03
ACGTcount: A:0.56, C:0.13, G:0.05, T:0.26
Consensus pattern (30 bp):
AAATGCCTCTAAAATAATAATAAAATTAAC
Found at i:28762681 original size:19 final size:20
Alignment explanation
Indices: 28762659--28762715 Score: 66
Period size: 19 Copynumber: 3.0 Consensus size: 20
28762649 GAAAAGTTTA
28762659 TAAATAAATAATAATAATT-
1 TAAATAAATAATAATAATTG
*
28762678 TAAATATAATTA-AAT-ATTG
1 TAAATA-AATAATAATAATTG
*
28762697 TAAATAAATATTAATAATT
1 TAAATAAATAATAATAATT
28762716 ATCGAGGTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
18 6 0.19
19 18 0.58
20 7 0.23
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (20 bp):
TAAATAAATAATAATAATTG
Found at i:28769536 original size:106 final size:106
Alignment explanation
Indices: 28769346--28769558 Score: 390
Period size: 106 Copynumber: 2.0 Consensus size: 106
28769336 AGCTTTCAAC
*
28769346 AAAATGCTTTAAATTTTATAATTGTTCTATGAATAGTTTCTTCAGTTATCGACTGATAATTACAA
1 AAAATGCTTTAAATTTTATAATTGTTCCATGAATAGTTTCTTCAGTTATCGACTGATAATTACAA
* * *
28769411 GAGACCTTTATGCCGATCATGCATGTGTCTTGCATTAACCA
66 GACACCTTTATGCCAATCATGCATGTGCCTTGCATTAACCA
28769452 AAAATGCTTTAAATTTTATAATTGTTCCATGAATAGTTTCTTCAGTTATCGACTGATAATTACAA
1 AAAATGCTTTAAATTTTATAATTGTTCCATGAATAGTTTCTTCAGTTATCGACTGATAATTACAA
28769517 GACACCTTTATGCCAATCATGCATGTGCCTTGCATTAACCA
66 GACACCTTTATGCCAATCATGCATGTGCCTTGCATTAACCA
28769558 A
1 A
28769559 CTTGATCTAC
Statistics
Matches: 103, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
106 103 1.00
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (106 bp):
AAAATGCTTTAAATTTTATAATTGTTCCATGAATAGTTTCTTCAGTTATCGACTGATAATTACAA
GACACCTTTATGCCAATCATGCATGTGCCTTGCATTAACCA
Found at i:28787353 original size:20 final size:20
Alignment explanation
Indices: 28787328--28787366 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
28787318 TAAAGAACAC
28787328 GGGTGTGTCCCAATGCACAT
1 GGGTGTGTCCCAATGCACAT
28787348 GGGTGTGTCCCAATGCACA
1 GGGTGTGTCCCAATGCACA
28787367 CGGTCATGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.21, C:0.26, G:0.31, T:0.23
Consensus pattern (20 bp):
GGGTGTGTCCCAATGCACAT
Found at i:28787376 original size:22 final size:20
Alignment explanation
Indices: 28787324--28787369 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
28787314 AGGGTAAAGA
*
28787324 ACACGGGTGTGTCCCAATGC
1 ACACGGATGTGTCCCAATGC
* *
28787344 ACATGGGTGTGTCCCAATGC
1 ACACGGATGTGTCCCAATGC
28787364 ACACGG
1 ACACGG
28787370 TCATGTGCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.22, C:0.28, G:0.30, T:0.20
Consensus pattern (20 bp):
ACACGGATGTGTCCCAATGC
Found at i:28789978 original size:23 final size:21
Alignment explanation
Indices: 28789951--28789993 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
28789941 TATTAATAAC
*
28789951 AATATTTAATAAATTTGAAAATG
1 AATATTT-ATAAAATT-AAAATG
28789974 AATATTTATAAAATTAAAAT
1 AATATTTATAAAATTAAAAT
28789994 ATGCGAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 7 0.37
23 7 0.37
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.40
Consensus pattern (21 bp):
AATATTTATAAAATTAAAATG
Found at i:28791898 original size:28 final size:28
Alignment explanation
Indices: 28791858--28791911 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
28791848 ACACGGAGAG
28791858 TAGAACACAGAAAACACTCAAGTTCAAC
1 TAGAACACAGAAAACACTCAAGTTCAAC
*
28791886 TAGAACATAGAAAACACTCAAGTTCA
1 TAGAACACAGAAAACACTCAAGTTCA
28791912 GCCACAGAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.50, C:0.22, G:0.11, T:0.17
Consensus pattern (28 bp):
TAGAACACAGAAAACACTCAAGTTCAAC
Found at i:28793018 original size:161 final size:161
Alignment explanation
Indices: 28792753--28793345 Score: 999
Period size: 161 Copynumber: 3.7 Consensus size: 161
28792743 ACGACCATCA
* * * *
28792753 CAGTGTTGGTCAACTTAAAAAGCTCATCAAAGAAGCTATAAAAGACCAATTTTAAAGTGTTGATC
1 CAGTGTTGGTCAACTCAAAGAGCTCATCAAAGAAGCTATAAAAGACCAATTTGAAAGTATTGATC
* *
28792818 CACTTTCATATACATACTCAAATCCATACACACAAATGATTGATCGTCCAATATACAAGTTGCCA
66 CACTTTCATATACATACTCAAATCCATACACACAAAGGATTGATCGTCCAATGTACAAGTTGCCA
28792883 AAGATCTTTAACCAACAATCAATGAAGTTTT
131 AAGATCTTTAACCAACAATCAATGAAGTTTT
28792914 CAGTGTTGGTCAACTCAAAGAGCTCATCAAAGAAGCTATAAAAGACCAATTTGAAAGTATTGATC
1 CAGTGTTGGTCAACTCAAAGAGCTCATCAAAGAAGCTATAAAAGACCAATTTGAAAGTATTGATC
*
28792979 CACTTTCATATACATACTCAAATCCATACACACAAATGATTGATCGTCCAATGTACAAGTTGCCA
66 CACTTTCATATACATACTCAAATCCATACACACAAAGGATTGATCGTCCAATGTACAAGTTGCCA
28793044 AAGATCTTTAACCAACAATCAATGAAGTTTT
131 AAGATCTTTAACCAACAATCAATGAAGTTTT
* * * **
28793075 CAGTCTTGGTCAACTCAAAGAGCTTATCAAATAAGCTATAAAAGTTCAATTTGAAAGTATTGATC
1 CAGTGTTGGTCAACTCAAAGAGCTCATCAAAGAAGCTATAAAAGACCAATTTGAAAGTATTGATC
* *
28793140 CACCTTCATATACATACTCAAATCCATACACACGAAGGATTGATCGTCCAATGTACAAGTTGCCA
66 CACTTTCATATACATACTCAAATCCATACACACAAAGGATTGATCGTCCAATGTACAAGTTGCCA
28793205 AAGATCTTTAACCAACAATCAATGAAGTTTT
131 AAGATCTTTAACCAACAATCAATGAAGTTTT
* * * *
28793236 CAGTGTTGGTCAACTCAAAGGGATCATCAAAGAAGCTATAAAACACCAATTTGAAAGTGTTGATC
1 CAGTGTTGGTCAACTCAAAGAGCTCATCAAAGAAGCTATAAAAGACCAATTTGAAAGTATTGATC
*
28793301 CACCTTT-ATATACATACTCAAAGCCATACACACAAAGGATTGATC
66 CA-CTTTCATATACATACTCAAATCCATACACACAAAGGATTGATC
28793346 ATCTGATAAA
Statistics
Matches: 406, Mismatches: 25, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
161 403 0.99
162 3 0.01
ACGTcount: A:0.39, C:0.20, G:0.13, T:0.27
Consensus pattern (161 bp):
CAGTGTTGGTCAACTCAAAGAGCTCATCAAAGAAGCTATAAAAGACCAATTTGAAAGTATTGATC
CACTTTCATATACATACTCAAATCCATACACACAAAGGATTGATCGTCCAATGTACAAGTTGCCA
AAGATCTTTAACCAACAATCAATGAAGTTTT
Found at i:28797735 original size:33 final size:35
Alignment explanation
Indices: 28797640--28797736 Score: 89
Period size: 33 Copynumber: 2.8 Consensus size: 35
28797630 TTAATATTTT
*
28797640 AATATATGAAATATAAATTTTAAATATTT--TTAAGC
1 AATATAT-AAAT-TATATTTTAAATATTTAATTAAGC
* *
28797675 AATAAATATTAATTAT-TTATAAA-ATTTAATT-AG-
1 AAT--ATATAAATTATATTTTAAATATTTAATTAAGC
28797708 AATATATAAATTATATTTTAAATATTTAA
1 AATATATAAATTATATTTTAAATATTTAA
28797737 ATATAACCAT
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
31 10 0.20
32 6 0.12
33 13 0.25
34 8 0.16
35 7 0.14
36 3 0.06
37 4 0.08
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (35 bp):
AATATATAAATTATATTTTAAATATTTAATTAAGC
Found at i:28801746 original size:6 final size:6
Alignment explanation
Indices: 28801735--28801771 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
28801725 AAAATTTATA
* *
28801735 AATGTC AATGTC AAGGTC AATGTC AATATC AATGTC A
1 AATGTC AATGTC AATGTC AATGTC AATGTC AATGTC A
28801772 TAAATGATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (6 bp):
AATGTC
Found at i:28805351 original size:39 final size:39
Alignment explanation
Indices: 28805308--28805460 Score: 252
Period size: 39 Copynumber: 3.9 Consensus size: 39
28805298 CTGGACATAT
* * *
28805308 TTCCAGCACGTAGCCTGCGGACCTTAAGTCCGGTTATAA
1 TTCCAGCACGTAGCCTACGGACCCTAAGTCCGGATATAA
*
28805347 TTCCAGCACATAGCCTACGGACCCTAAGTCCGGATATAA
1 TTCCAGCACGTAGCCTACGGACCCTAAGTCCGGATATAA
28805386 TTCCAGCACGTAGCCTACGGACCCTAAGTCCGGATATAA
1 TTCCAGCACGTAGCCTACGGACCCTAAGTCCGGATATAA
* *
28805425 TTCCAGCACGTAGCCTGCGGACCCTAAGTTCGGATA
1 TTCCAGCACGTAGCCTACGGACCCTAAGTCCGGATA
28805461 AACATCGCTG
Statistics
Matches: 107, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 107 1.00
ACGTcount: A:0.26, C:0.30, G:0.22, T:0.22
Consensus pattern (39 bp):
TTCCAGCACGTAGCCTACGGACCCTAAGTCCGGATATAA
Found at i:28813080 original size:39 final size:39
Alignment explanation
Indices: 28812989--28813189 Score: 244
Period size: 39 Copynumber: 5.2 Consensus size: 39
28812979 AAATTTAAAC
* * * * *
28812989 CCGG-TATAATACCAGCTCGAAGCTTGCGGGA-CTTTAGC
1 CCGGATATAATTCCAGCACGTAGCTTGC-GGACCTTAAGT
* *
28813027 CCGGACATATTTCCAGCACGTAGCTTGCGGACCTTAAGT
1 CCGGATATAATTCCAGCACGTAGCTTGCGGACCTTAAGT
* * * **
28813066 CCGGTTATAATTCCAGCACATAGCCTGTTGACCTTAAGT
1 CCGGATATAATTCCAGCACGTAGCTTGCGGACCTTAAGT
28813105 CCGGATATAATTCCAGCACGTAGCTTGCGGACCTTAAGT
1 CCGGATATAATTCCAGCACGTAGCTTGCGGACCTTAAGT
* *
28813144 CCGGATATAATTCCAGCACGTAGCCTGCGGACCCTAAGT
1 CCGGATATAATTCCAGCACGTAGCTTGCGGACCTTAAGT
*
28813183 CCAGATA
1 CCGGATA
28813190 AACATCGCTG
Statistics
Matches: 139, Mismatches: 22, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
38 7 0.05
39 132 0.95
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (39 bp):
CCGGATATAATTCCAGCACGTAGCTTGCGGACCTTAAGT
Found at i:28816287 original size:43 final size:43
Alignment explanation
Indices: 28816206--28816291 Score: 113
Period size: 43 Copynumber: 2.0 Consensus size: 43
28816196 AAATAGTACA
* **
28816206 ATGCCAACGTCCCAGACATGGTCTTACATGTAGCCACATATCG
1 ATGCCAACGTCCCAGACAGGGTCTTACATGTAAACACATATCG
28816249 ATGCC-ACTGTCCCAGACAGGGTCTTAC-TCGTAAACACATATCG
1 ATGCCAAC-GTCCCAGACAGGGTCTTACAT-GTAAACACATATCG
28816292 GAATCACAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
42 3 0.08
43 35 0.92
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.23
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACAGGGTCTTACATGTAAACACATATCG
Found at i:28830942 original size:17 final size:18
Alignment explanation
Indices: 28830910--28830945 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
28830900 TTGGGCCAGG
*
28830910 ATGGGCCATGTGGGCCCA
1 ATGGGCCATATGGGCCCA
28830928 ATGGGCC-TATGGGCCCA
1 ATGGGCCATATGGGCCCA
28830945 A
1 A
28830946 GTGGATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.19, C:0.28, G:0.36, T:0.17
Consensus pattern (18 bp):
ATGGGCCATATGGGCCCA
Found at i:28831128 original size:27 final size:26
Alignment explanation
Indices: 28831079--28831177 Score: 87
Period size: 27 Copynumber: 3.7 Consensus size: 26
28831069 TTTGGTTTAC
28831079 AAAATTACTG-AATA-CCCTCAATTAGT
1 AAAATTACTGAAATACCCCT-AATT-GT
* *
28831105 AAAATTACCGAAATACCCCTAATTTTT
1 AAAATTACTGAAATACCCCTAA-TTGT
* * *
28831132 GAAATTACTGAAATACCCTCGACTTGT
1 AAAATTACTGAAATACCC-CTAATTGT
28831159 AAAATTA-TAGAAATACCCC
1 AAAATTACT-GAAATACCCC
28831178 AAATACCCCT
Statistics
Matches: 60, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
26 11 0.18
27 41 0.68
28 8 0.13
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.29
Consensus pattern (26 bp):
AAAATTACTGAAATACCCCTAATTGT
Found at i:28831182 original size:36 final size:36
Alignment explanation
Indices: 28831142--28831212 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 36
28831132 GAAATTACTG
*
28831142 AAATA-CCCTCGACTTGTAAAATTA-TAGAAATACCCC
1 AAATACCCCT-GACTTGAAAAATTACTA-AAATACCCC
*
28831178 AAATACCCCTGATTTGAAAAATTACTAAAATACCC
1 AAATACCCCTGACTTGAAAAATTACTAAAATACCC
28831213 TTGATTTGGA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 25 0.81
37 6 0.19
ACGTcount: A:0.44, C:0.24, G:0.07, T:0.25
Consensus pattern (36 bp):
AAATACCCCTGACTTGAAAAATTACTAAAATACCCC
Found at i:28831199 original size:27 final size:26
Alignment explanation
Indices: 28831169--28831246 Score: 68
Period size: 27 Copynumber: 2.9 Consensus size: 26
28831159 AAAATTATAG
*
28831169 AAATACCCCAAATACCCCTGATTTGAA
1 AAATA-CCAAAATACCCCTGATTTGAA
* *
28831196 AAATTACTAAAATACCCTTGATTTGGAA
1 AAA-TACCAAAATACCCCTGATTT-GAA
* *
28831224 AATTA-CAAAAGTACCCTTGATTT
1 AAATACCAAAA-TACCCCTGATTT
28831247 ATAAAATTAC
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
26 4 0.09
27 32 0.74
28 7 0.16
ACGTcount: A:0.41, C:0.21, G:0.09, T:0.29
Consensus pattern (26 bp):
AAATACCAAAATACCCCTGATTTGAA
Found at i:28831239 original size:63 final size:63
Alignment explanation
Indices: 28831115--28831239 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
28831105 AAAATTACCG
*** * * *
28831115 AAATACCCCTAATTTTTGAAATTACTGAAATACCCTCGACTTGTAAAATTATAGAAATACCCC
1 AAATACCCCTAATTTGAAAAATTACTAAAATACCCTCGACTTGGAAAATTACAGAAATACCCC
* * *
28831178 AAATACCCCTGATTTGAAAAATTACTAAAATACCCTTGATTTGGAAAATTACA-AAAGTACCC
1 AAATACCCCTAATTTGAAAAATTACTAAAATACCCTCGACTTGGAAAATTACAGAAA-TACCC
28831240 TTGATTTATA
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
62 3 0.06
63 49 0.94
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.29
Consensus pattern (63 bp):
AAATACCCCTAATTTGAAAAATTACTAAAATACCCTCGACTTGGAAAATTACAGAAATACCCC
Found at i:28831325 original size:27 final size:27
Alignment explanation
Indices: 28831178--28831329 Score: 139
Period size: 27 Copynumber: 5.6 Consensus size: 27
28831168 GAAATACCCC
* * *
28831178 AAATACCCCTGATTTGAAAAATTACTA
1 AAATACCCTTGATTTGCAAAATTACTG
* *
28831205 AAATACCCTTGATTTGGAAAATTAC-A
1 AAATACCCTTGATTTGCAAAATTACTG
** *
28831231 AAAGTACCCTTGATTTATAAAATTACAG
1 AAA-TACCCTTGATTTGCAAAATTACTG
*
28831259 AAATACCTTTGACTTT-CAAAAATTA-TAG
1 AAATACCCTTGA-TTTGC-AAAATTACT-G
* *
28831287 AAATACCATTGGTTTGCAAAATTACTG
1 AAATACCCTTGATTTGCAAAATTACTG
*
28831314 AAATACCCTTGGTTTG
1 AAATACCCTTGATTTG
28831330 TAGATTTACC
Statistics
Matches: 107, Mismatches: 11, Indels: 14
0.81 0.08 0.11
Matches are distributed among these distances:
26 4 0.04
27 77 0.72
28 26 0.24
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (27 bp):
AAATACCCTTGATTTGCAAAATTACTG
Found at i:28831638 original size:41 final size:41
Alignment explanation
Indices: 28831589--28831711 Score: 185
Period size: 41 Copynumber: 3.0 Consensus size: 41
28831579 GGAGGAAGAA
*
28831589 ATTAAGGATCGCATGGTTGCTTGACAACTGTGGATCCACCG
1 ATTAAGGATCGCATGGTTGCTTGACGACTGTGGATCCACCG
* * **
28831630 ATTGAGGATCGCATGGTTGCTTGATGA-TCGTGGATCCATAG
1 ATTAAGGATCGCATGGTTGCTTGACGACT-GTGGATCCACCG
28831671 ATTAAGGATCGCATGGTTGCTTGACGACTGTGGATCCACCG
1 ATTAAGGATCGCATGGTTGCTTGACGACTGTGGATCCACCG
28831712 GTGGCTTTTA
Statistics
Matches: 71, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
40 1 0.01
41 69 0.97
42 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.28
Consensus pattern (41 bp):
ATTAAGGATCGCATGGTTGCTTGACGACTGTGGATCCACCG
Found at i:28831886 original size:22 final size:22
Alignment explanation
Indices: 28831852--28831917 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
28831842 AGCCAATTAT
* *
28831852 CCTGATTATGGCTTTGTGCCAA
1 CCTGAATATGGCTATGTGCCAA
*
28831874 CCT-ACATATGGCTCTGTGCCAA
1 CCTGA-ATATGGCTATGTGCCAA
*
28831896 CCTGATTATGGCTATGTGCCAA
1 CCTGAATATGGCTATGTGCCAA
28831918 ACGTATTTGC
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
21 1 0.03
22 36 0.95
23 1 0.03
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.32
Consensus pattern (22 bp):
CCTGAATATGGCTATGTGCCAA
Found at i:28832144 original size:22 final size:22
Alignment explanation
Indices: 28832119--28832161 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
28832109 GTTGTTGCGA
*
28832119 TGTTTATGGCTATGTGCTGTCT
1 TGTTTACGGCTATGTGCTGTCT
28832141 TGTTTACGGCTATGTGCTGTC
1 TGTTTACGGCTATGTGCTGTC
28832162 CTGTCTACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.09, C:0.16, G:0.28, T:0.47
Consensus pattern (22 bp):
TGTTTACGGCTATGTGCTGTCT
Found at i:28833552 original size:7 final size:7
Alignment explanation
Indices: 28833540--28833566 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
28833530 GTGATATTAT
28833540 TGATATA
1 TGATATA
28833547 TGATATA
1 TGATATA
28833554 TGATATA
1 TGATATA
28833561 TGATAT
1 TGATAT
28833567 TAAAATGATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (7 bp):
TGATATA
Found at i:28841810 original size:16 final size:15
Alignment explanation
Indices: 28841780--28841815 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
28841770 GAGAGAAAAA
28841780 TAAAATAAAATAAAT
1 TAAAATAAAATAAAT
*
28841795 TAAAACTAAGATAAAT
1 TAAAA-TAAAATAAAT
28841811 TAAAA
1 TAAAA
28841816 GATTTCAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.25
Consensus pattern (15 bp):
TAAAATAAAATAAAT
Found at i:28843382 original size:21 final size:21
Alignment explanation
Indices: 28843358--28843418 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
28843348 TTTTGCTCTG
28843358 CTCTG-CTGCCATCGCTGCTAC
1 CTCTGCCT-CCATCGCTGCTAC
* *
28843379 CTCTGCCTCCCTCGCTGCTGC
1 CTCTGCCTCCATCGCTGCTAC
* *
28843400 CGCTGCCTCCCTCGCTGCT
1 CTCTGCCTCCATCGCTGCT
28843419 GCACAGTATC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 34 0.94
22 2 0.06
ACGTcount: A:0.03, C:0.49, G:0.20, T:0.28
Consensus pattern (21 bp):
CTCTGCCTCCATCGCTGCTAC
Found at i:28843419 original size:21 final size:21
Alignment explanation
Indices: 28843369--28843420 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
28843359 TCTGCTGCCA
* *
28843369 TCGCTGCTACCTCTGCCTCCC
1 TCGCTGCTGCCGCTGCCTCCC
28843390 TCGCTGCTGCCGCTGCCTCCC
1 TCGCTGCTGCCGCTGCCTCCC
28843411 TCGCTGCTGC
1 TCGCTGCTGC
28843421 ACAGTATCCC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.02, C:0.50, G:0.21, T:0.27
Consensus pattern (21 bp):
TCGCTGCTGCCGCTGCCTCCC
Found at i:28843882 original size:13 final size:14
Alignment explanation
Indices: 28843857--28843885 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
28843847 TGATGAATTG
28843857 AATTAAACAATTAT
1 AATTAAACAATTAT
28843871 AATTAAAC-ATTAT
1 AATTAAACAATTAT
28843884 AA
1 AA
28843886 ATATTTAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTAAACAATTAT
Found at i:28844089 original size:16 final size:17
Alignment explanation
Indices: 28844052--28844090 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
28844042 AAAATATTAT
*
28844052 TTAATATTAGAAAGTTA
1 TTAATATTAGAAAGTAA
*
28844069 TTAATATTTGAAAG-AA
1 TTAATATTAGAAAGTAA
28844085 TTAATA
1 TTAATA
28844091 AAATTATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (17 bp):
TTAATATTAGAAAGTAA
Found at i:28845168 original size:30 final size:30
Alignment explanation
Indices: 28845134--28845242 Score: 132
Period size: 30 Copynumber: 3.5 Consensus size: 30
28845124 TACATATAAG
28845134 ATTATGTAAGTTATGAAATTTGATCTTTAA
1 ATTATGTAAGTTATGAAATTTGATCTTTAA
*
28845164 ATTATGTAAGTTATG-TATTATGTAAGT-TATGTAA
1 ATTATGTAAGTTATGAAATT-TG--A-TCT-T-TAA
*
28845198 ATTATGTAAGTTATAAAATTTGATCTTTAA
1 ATTATGTAAGTTATGAAATTTGATCTTTAA
28845228 ATTATGTAAGTTATG
1 ATTATGTAAGTTATG
28845243 TATTATGTAA
Statistics
Matches: 67, Mismatches: 4, Indels: 16
0.77 0.05 0.18
Matches are distributed among these distances:
29 3 0.04
30 34 0.51
31 2 0.03
32 4 0.06
33 2 0.03
34 19 0.28
35 3 0.04
ACGTcount: A:0.37, C:0.02, G:0.15, T:0.47
Consensus pattern (30 bp):
ATTATGTAAGTTATGAAATTTGATCTTTAA
Found at i:28845179 original size:9 final size:9
Alignment explanation
Indices: 28845165--28845260 Score: 83
Period size: 9 Copynumber: 10.8 Consensus size: 9
28845155 GATCTTTAAA
28845165 TTATGTAAG
1 TTATGTAAG
28845174 TTATGT-A-
1 TTATGTAAG
28845181 TTATGTAAG
1 TTATGTAAG
*
28845190 TTATGTAAA
1 TTATGTAAG
28845199 TTATGTAAG
1 TTATGTAAG
** *
28845208 TTATAAAAT
1 TTATGTAAG
* *
28845217 TTGATCTTTAAA
1 TT-A--TGTAAG
28845229 TTATGTAAG
1 TTATGTAAG
28845238 TTATGT-A-
1 TTATGTAAG
28845245 TTATGTAAG
1 TTATGTAAG
28845254 TTATGTA
1 TTATGTA
28845261 TTAAATAATA
Statistics
Matches: 70, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
7 12 0.17
8 4 0.06
9 47 0.67
10 1 0.01
11 1 0.01
12 5 0.07
ACGTcount: A:0.35, C:0.01, G:0.16, T:0.48
Consensus pattern (9 bp):
TTATGTAAG
Found at i:28845185 original size:16 final size:16
Alignment explanation
Indices: 28845164--28845263 Score: 98
Period size: 16 Copynumber: 6.2 Consensus size: 16
28845154 TGATCTTTAA
28845164 ATTATGTAAGTTATGT
1 ATTATGTAAGTTATGT
28845180 ATTATGTAAGTTATGT
1 ATTATGTAAGTTATGT
**
28845196 AAATTATGTAAGTTATAAA
1 --ATTATGTAAGTTAT-GT
** **
28845215 ATT-TG-ATCTT-TAA
1 ATTATGTAAGTTATGT
28845228 ATTATGTAAGTTATGT
1 ATTATGTAAGTTATGT
28845244 ATTATGTAAGTTATGT
1 ATTATGTAAGTTATGT
28845260 ATTA
1 ATTA
28845264 AATAATATTT
Statistics
Matches: 70, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
13 5 0.07
14 3 0.04
15 6 0.09
16 39 0.56
17 3 0.04
18 14 0.20
ACGTcount: A:0.36, C:0.01, G:0.15, T:0.48
Consensus pattern (16 bp):
ATTATGTAAGTTATGT
Found at i:28845202 original size:25 final size:25
Alignment explanation
Indices: 28845134--28845205 Score: 82
Period size: 25 Copynumber: 3.0 Consensus size: 25
28845124 TACATATAAG
28845134 ATTATGTAAGTTATG-AAATT-TG-
1 ATTATGTAAGTTATGTAAATTATGT
* *
28845156 ATCT-T-TAAATTATGTAAGTTATGT
1 AT-TATGTAAGTTATGTAAATTATGT
28845180 ATTATGTAAGTTATGTAAATTATGT
1 ATTATGTAAGTTATGTAAATTATGT
28845205 A
1 A
28845206 AGTTATAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
21 8 0.20
22 7 0.17
23 4 0.10
24 3 0.08
25 18 0.45
ACGTcount: A:0.36, C:0.01, G:0.15, T:0.47
Consensus pattern (25 bp):
ATTATGTAAGTTATGTAAATTATGT
Found at i:28845208 original size:64 final size:64
Alignment explanation
Indices: 28845134--28845260 Score: 245
Period size: 64 Copynumber: 2.0 Consensus size: 64
28845124 TACATATAAG
*
28845134 ATTATGTAAGTTATGAAATTTGATCTTTAAATTATGTAAGTTATGTATTATGTAAGTTATGTAA
1 ATTATGTAAGTTATAAAATTTGATCTTTAAATTATGTAAGTTATGTATTATGTAAGTTATGTAA
28845198 ATTATGTAAGTTATAAAATTTGATCTTTAAATTATGTAAGTTATGTATTATGTAAGTTATGTA
1 ATTATGTAAGTTATAAAATTTGATCTTTAAATTATGTAAGTTATGTATTATGTAAGTTATGTA
28845261 TTAAATAATA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 62 1.00
ACGTcount: A:0.36, C:0.02, G:0.15, T:0.47
Consensus pattern (64 bp):
ATTATGTAAGTTATAAAATTTGATCTTTAAATTATGTAAGTTATGTATTATGTAAGTTATGTAA
Found at i:28845569 original size:16 final size:16
Alignment explanation
Indices: 28845550--28845583 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
28845540 AAATATTAAA
*
28845550 TATTAAAATCAAACAT
1 TATTAAAATCAAAAAT
*
28845566 TATTAATATCAAAAAT
1 TATTAAAATCAAAAAT
28845582 TA
1 TA
28845584 AGCAATATGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (16 bp):
TATTAAAATCAAAAAT
Found at i:28846571 original size:25 final size:25
Alignment explanation
Indices: 28846496--28846572 Score: 109
Period size: 25 Copynumber: 3.1 Consensus size: 25
28846486 GGCAGAAAAC
* *
28846496 TGGAGAAGCAGCAGAGGGATGCCGA
1 TGGAGATGTAGCAGAGGGATGCCGA
* *
28846521 CGGAGATGTAGAAGAGGGATGCCGA
1 TGGAGATGTAGCAGAGGGATGCCGA
*
28846546 TGGAGATGTAGCAGAGGGCTGCCGA
1 TGGAGATGTAGCAGAGGGATGCCGA
28846571 TG
1 TG
28846573 ACGATGCAGA
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 45 1.00
ACGTcount: A:0.29, C:0.14, G:0.44, T:0.13
Consensus pattern (25 bp):
TGGAGATGTAGCAGAGGGATGCCGA
Found at i:28846584 original size:22 final size:22
Alignment explanation
Indices: 28846556--28846603 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
28846546 TGGAGATGTA
* * *
28846556 GCAGAGGGCTGCCGATGACGAT
1 GCAGAGGACTACCGAAGACGAT
*
28846578 GCAGAGGACTACCGAAGGCGAT
1 GCAGAGGACTACCGAAGACGAT
28846600 GCAG
1 GCAG
28846604 CAGACGTAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.23, G:0.40, T:0.10
Consensus pattern (22 bp):
GCAGAGGACTACCGAAGACGAT
Found at i:28848594 original size:18 final size:18
Alignment explanation
Indices: 28848571--28848606 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
28848561 TGAGAAAGGC
28848571 TGAGAAAGAAAAGGGAAT
1 TGAGAAAGAAAAGGGAAT
28848589 TGAGAAAGAAAAGGGAAT
1 TGAGAAAGAAAAGGGAAT
28848607 CGGGGGAGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.33, T:0.11
Consensus pattern (18 bp):
TGAGAAAGAAAAGGGAAT
Found at i:28848644 original size:72 final size:71
Alignment explanation
Indices: 28848557--28848692 Score: 195
Period size: 72 Copynumber: 1.9 Consensus size: 71
28848547 GAAATGGCTT
*
28848557 AGGCTGAGAAAGGCTGAGAAAGAAAAG-GGAATTGAGAAAGAAAAGGGAA-TCGGGGGAGAGAAA
1 AGGCTGAGAAAGGCTGAGAAAG-AAAGTGGAATCGAGAAAG--AAGGGAATTCGGGGGAGAGAAA
28848620 TAGAAGTAC
63 TAGAAGTAC
* * *
28848629 AGGCTGAGAATGGCTGAGAAAGAAAGTGGAATCGGGAAAGAAGGGAATTGGGGGGAGAGAAATA
1 AGGCTGAGAAAGGCTGAGAAAGAAAGTGGAATCGAGAAAGAAGGGAATTCGGGGGAGAGAAATA
28848693 AAAACGCGTC
Statistics
Matches: 58, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
70 7 0.12
71 19 0.33
72 32 0.55
ACGTcount: A:0.44, C:0.05, G:0.40, T:0.11
Consensus pattern (71 bp):
AGGCTGAGAAAGGCTGAGAAAGAAAGTGGAATCGAGAAAGAAGGGAATTCGGGGGAGAGAAATAG
AAGTAC
Found at i:28848858 original size:40 final size:40
Alignment explanation
Indices: 28848782--28848858 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
28848772 CTTTTTTACA
* * * *
28848782 GCGTTTTTGTCATAAACGCCGCTATTGCTTGCCTTTTGTG
1 GCGTTCTTATCATAAACGCCGCTAATGCTTGACTTTTGTG
*
28848822 GCGTTCTTATCATAAACGCCGCTAATGTTTGACTTTT
1 GCGTTCTTATCATAAACGCCGCTAATGCTTGACTTTT
28848859 TTATAATTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.17, C:0.22, G:0.19, T:0.42
Consensus pattern (40 bp):
GCGTTCTTATCATAAACGCCGCTAATGCTTGACTTTTGTG
Found at i:28848884 original size:22 final size:20
Alignment explanation
Indices: 28848857--28848913 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 20
28848847 TGTTTGACTT
28848857 TTTTATAATTTTTATATTGAA
1 TTTTATAATTTTTATATT-AA
28848878 TTATTAT-ATCTTTTATATTAA
1 TT-TTATAAT-TTTTATATTAA
28848899 TTTTAAATAATTTTT
1 TTTT--ATAATTTTT
28848914 TAAAAAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
20 2 0.06
21 8 0.26
22 19 0.61
23 2 0.06
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (20 bp):
TTTTATAATTTTTATATTAA
Done.