Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016012.1 Corchorus capsularis cultivar CVL-1 contig16033, 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: 99014
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:396 original size:2 final size:2
Alignment explanation
Indices: 389--418 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
379 ATTTTTGTTT
389 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
419 ATAATAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3745 original size:158 final size:156
Alignment explanation
Indices: 3557--3863 Score: 481
Period size: 158 Copynumber: 2.0 Consensus size: 156
3547 AGGTGAGTTC
* * *
3557 GTTTGGTATTATTTTTGTTTTCTGTTTTCTGTTGTCAATTTCCTGTTTTTTGAAACAAAACAGTG
1 GTTTGGCATTATTTTTGTTTTCTGTTTTCTGTTGCCAATTTCCTGTTTTTGGAAACAAAACAGTG
*
3622 AAAACACGTTTGGCAGGCTGTTTCCGTTTTAAAAAATTTTGGAAACAGAAGCAGTATTTTGGAAA
66 AAAACACGTTTGGCAGGCTGTTTCCGTTTT-AAAAATTTTGAAAACAGAAGCAGTATTTTGG-AA
3687 AAAAGTGGAAGCAAAAATTTTAGGGCTT
129 AAAAGTGGAAGCAAAAATTTTAGGGCTT
* *
3715 GTTTGGCATTGTTTTTG-TTTCTGTTTTTCTGTTGCCAATTTTCTGTTTTTGGAAACAAAACAGT
1 GTTTGGCATTATTTTTGTTTTCTG-TTTTCTGTTGCCAATTTCCTGTTTTTGGAAACAAAACAGT
* * * * *
3779 GAAAACATGTTTGGCAGGTTGTTTCTGTTTTCAAAATTTTGAAAACAGAATCAGTATTTTGGAAA
65 GAAAACACGTTTGGCAGGCTGTTTCCGTTTTAAAAATTTTGAAAACAGAAGCAGTATTTTGGAAA
3844 AAAGTGGAAGCAAAAATTTT
130 AAAGTGGAAGCAAAAATTTT
3864 GTGCTTTCAT
Statistics
Matches: 137, Mismatches: 11, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
156 23 0.17
157 34 0.25
158 80 0.58
ACGTcount: A:0.29, C:0.10, G:0.20, T:0.40
Consensus pattern (156 bp):
GTTTGGCATTATTTTTGTTTTCTGTTTTCTGTTGCCAATTTCCTGTTTTTGGAAACAAAACAGTG
AAAACACGTTTGGCAGGCTGTTTCCGTTTTAAAAATTTTGAAAACAGAAGCAGTATTTTGGAAAA
AAGTGGAAGCAAAAATTTTAGGGCTT
Found at i:4050 original size:11 final size:11
Alignment explanation
Indices: 4026--4077 Score: 54
Period size: 11 Copynumber: 4.8 Consensus size: 11
4016 TTGACAACGC
4026 AACAAAAACAA
1 AACAAAAACAA
* *
4037 AACGAAAACGA
1 AACAAAAACAA
4048 AACAAAAACAA
1 AACAAAAACAA
4059 AA-AACAAA-AA
1 AACAA-AAACAA
*
4069 AACGAAAAC
1 AACAAAAAC
4078 GATGCCAAAC
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
10 9 0.27
11 24 0.73
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:4050 original size:16 final size:16
Alignment explanation
Indices: 4031--4079 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 16
4021 AACGCAACAA
4031 AAACAAAACGAAAACG
1 AAACAAAACGAAAACG
*
4047 AAACAAAAACAAAAAAC-
1 AAAC-AAAAC-GAAAACG
4064 AAA-AAAACGAAAACG
1 AAACAAAACGAAAACG
4079 A
1 A
4080 TGCCAAACGG
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
14 5 0.18
15 6 0.21
16 4 0.14
17 8 0.29
18 5 0.18
ACGTcount: A:0.76, C:0.16, G:0.08, T:0.00
Consensus pattern (16 bp):
AAACAAAACGAAAACG
Found at i:4281 original size:11 final size:11
Alignment explanation
Indices: 4257--4291 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
4247 TTGACAGCAC
4257 AACAAAAACAA
1 AACAAAAACAA
* *
4268 AACGAAAACGA
1 AACAAAAACAA
4279 AACAAAAACAA
1 AACAAAAACAA
4290 AA
1 AA
4292 AAACAAATTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:4295 original size:232 final size:231
Alignment explanation
Indices: 3872--4326 Score: 682
Period size: 232 Copynumber: 2.0 Consensus size: 231
3862 TTGTGCTTTC
* *
3872 ATGTATTTCCAAAACACTTTCAAAACACAGAAGCACAGTCATGAACAGTAACTCACACACATTTT
1 ATGTATTTCCAAAACACTTCCAAAACACAGAAGCACAATCATGAACAGTAACTCACACACATTTT
*
3937 TACTTTTTTTTTTTAAACTTTGTTATTTAAAAACATACAACAAAATTGTATATCCAAACATGTTT
66 TACTTTTTTCTTTT-AACTTTGTTATTTAAAAACATACAACAAAATTGTATATCCAAACATGTTT
*
4002 TTGTTTTCAAAAAATTGACAACGCAACAAAAACAAAACGAAAACGAAACAAAAACAAAAAACAAA
130 TTGTTTTCAAAAAATTGACAACACAACAAAAACAAAACGAAAACGAAACAAAAACAAAAAACAAA
*
4067 AAAACGAAAACGATGCCAAACGGCCCCTTATGTTTTT
195 AAAACGAAAACGATGCCAAACGACCCCTTATGTTTTT
* * * * * **
4104 ATGTTTTTCCAAAACACTTCCAAAACACAGGAGTAGAATGATGAACAGTAACTCACATGC-TTTT
1 ATGTATTTCCAAAACACTTCCAAAACACAGAAGCACAATCATGAACAGTAACTCACACACATTTT
* *
4168 TAACCATTTTTTCTTTT-ACTTTTTTATTTAAAAACATACAACCAAATTGTATATCCAAACATGT
66 T-A-C-TTTTTTCTTTTAACTTTGTTATTTAAAAACATACAACAAAATTGTATATCCAAACATGT
*
4232 TTTTGTTTTC-AAAAATTGACAGCACAACAAAAACAAAACGAAAACGAAACAAAAACAAAAAAAC
128 TTTTGTTTTCAAAAAATTGACAACACAACAAAAACAAAACGAAAACGAAACAAAAAC-AAAAAAC
** *
4296 AAATTAACGAAAACGATGTCAAACGACCCCT
192 AAAAAAACGAAAACGATGCCAAACGACCCCT
4327 ACCAAATTCC
Statistics
Matches: 201, Mismatches: 18, Indels: 8
0.89 0.08 0.04
Matches are distributed among these distances:
231 49 0.24
232 141 0.70
233 1 0.00
234 10 0.05
ACGTcount: A:0.45, C:0.19, G:0.09, T:0.27
Consensus pattern (231 bp):
ATGTATTTCCAAAACACTTCCAAAACACAGAAGCACAATCATGAACAGTAACTCACACACATTTT
TACTTTTTTCTTTTAACTTTGTTATTTAAAAACATACAACAAAATTGTATATCCAAACATGTTTT
TGTTTTCAAAAAATTGACAACACAACAAAAACAAAACGAAAACGAAACAAAAACAAAAAACAAAA
AAACGAAAACGATGCCAAACGACCCCTTATGTTTTT
Found at i:4849 original size:30 final size:32
Alignment explanation
Indices: 4790--4851 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 32
4780 GGGGAAACTT
*
4790 TATATTTTCCGATTGTACCCTTATTTTTAAAA
1 TATATTTTCCAATTGTACCCTTATTTTTAAAA
*
4822 TATA-TTTCCAATTGTACTCTT-TTTTTAAAA
1 TATATTTTCCAATTGTACCCTTATTTTTAAAA
4852 AAAAAAACAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 9 0.32
31 15 0.54
32 4 0.14
ACGTcount: A:0.29, C:0.15, G:0.05, T:0.52
Consensus pattern (32 bp):
TATATTTTCCAATTGTACCCTTATTTTTAAAA
Found at i:5133 original size:22 final size:23
Alignment explanation
Indices: 5082--5304 Score: 141
Period size: 22 Copynumber: 10.1 Consensus size: 23
5072 AAGGAGTACA
* *
5082 AAAATTTAATAGA-A-GGTTATC
1 AAAATTTCATAGAGATGATTATC
*
5103 -AAATCTCATAGAG-TGATTATC
1 AAAATTTCATAGAGATGATTATC
*
5124 TAAATTTCATAGAGATCAGATTATC
1 AAAATTTCATAGAGAT--GATTATC
*
5149 AAAATTT-ATAG-GAAGATTATC
1 AAAATTTCATAGAGATGATTATC
* *
5170 AAAATTTCATAGTGTTG-TTATC
1 AAAATTTCATAGAGATGATTATC
*
5192 AAAATTTCA-ACGCGA-GATTATC
1 AAAATTTCATA-GAGATGATTATC
*
5214 AAAATTACATA-ATG-TGATTATC
1 AAAATTTCATAGA-GATGATTATC
* * * * *
5236 AGAATTTCATAGAG-GGGTCAAC
1 AAAATTTCATAGAGATGATTATC
* * *
5258 AAAATTTTATAAAGA-GGTTATC
1 AAAATTTCATAGAGATGATTATC
* *
5280 AAAATTTCATAAAGA-GGTTATC
1 AAAATTTCATAGAGATGATTATC
5302 AAA
1 AAA
5305 TTCTCAAAAA
Statistics
Matches: 163, Mismatches: 24, Indels: 29
0.75 0.11 0.13
Matches are distributed among these distances:
20 10 0.06
21 22 0.13
22 107 0.66
23 7 0.04
24 4 0.02
25 13 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (23 bp):
AAAATTTCATAGAGATGATTATC
Found at i:5319 original size:30 final size:30
Alignment explanation
Indices: 5278--5336 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
5268 AAAGAGGTTA
*
5278 TCAAAATTTCATAAAGAGGTTATCAAATTC
1 TCAAAAATTCATAAAGAGGTTATCAAATTC
5308 TCAAAAATTCATAAAGAGGTTATCAAATT
1 TCAAAAATTCATAAAGAGGTTATCAAATT
5337 TTTAAAATGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.32
Consensus pattern (30 bp):
TCAAAAATTCATAAAGAGGTTATCAAATTC
Found at i:5573 original size:22 final size:22
Alignment explanation
Indices: 5446--5960 Score: 155
Period size: 22 Copynumber: 23.6 Consensus size: 22
5436 TTATGGAGTA
*
5446 ATCAAAATTT--TAGGGAGGAT
1 ATCAAAATTTCATAGGGAGGTT
**
5466 ATCAAAATTTCATAGTTTA-GTT
1 ATCAAAATTTCATAG-GGAGGTT
* **
5488 TTCAAAATTTCATA-AAAGGGTT
1 ATCAAAATTTCATAGGGA-GGTT
*
5510 ATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATAGGGAGGTT
* **
5532 AACAAAATTTCATAATGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
** *
5554 ATCAAAAAATCATAGGGAGGTG
1 ATCAAAATTTCATAGGGAGGTT
* *
5576 ATTAAAA-TT--T--GTA-GTT
1 ATCAAAATTTCATAGGGAGGTT
* * * * *
5592 ATCAAGATTTCAGAAGAAAGTT
1 ATCAAAATTTCATAGGGAGGTT
*
5614 ATCAAAATTTTATAGGGAGGTTTAT
1 ATCAAAATTTCATAGGGAGG--T-T
* * *
5639 ATCAAAATTTTATAGGAAGATTT
1 ATCAAAATTTCATAGGGAG-GTT
* ***
5662 ATTAAAATTTCATAACAAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * * *
5684 ATCATAATTTCATAGTGTGATT
1 ATCAAAATTTCATAGGGAGGTT
* * *
5706 ATCAAAATTTCAGAGTGTGGTT
1 ATCAAAATTTCATAGGGAGGTT
5728 A-CTAACAA-TTCATAGGGAGGTT
1 ATC-AA-AATTTCATAGGGAGGTT
* * * * ** *
5750 TTTACATTTTCATAACGTGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * * ***
5772 ATCAATATATCATATGGAGAAG
1 ATCAAAATTTCATAGGGAGGTT
* * **
5794 AT-AACATCTCATAGTGTTGGTT
1 ATCAAAATTTCATAG-GGAGGTT
**
5816 ATCAAAATTTCATATTGAGGTGT
1 ATCAAAATTTCATAGGGAGGT-T
**
5839 -TCAAAATTTTTTAGGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * *
5860 AACAAAATTTCATAAGAAGGTT
1 ATCAAAATTTCATAGGGAGGTT
** ***
5882 AAAAAAAATTT-ATAAAAAGGTT
1 -ATCAAAATTTCATAGGGAGGTT
* * * * **
5904 CTCGAAA-TTCAGA-GTATCATT
1 ATCAAAATTTCATAGGGA-GGTT
* *
5925 ATTAAAATTTCATAGGAAGGTT
1 ATCAAAATTTCATAGGGAGGTT
5947 ATCAAAATTTCATA
1 ATCAAAATTTCATA
5961 ATGGGATCAT
Statistics
Matches: 351, Mismatches: 115, Indels: 56
0.67 0.22 0.11
Matches are distributed among these distances:
16 7 0.02
17 4 0.01
19 1 0.00
20 14 0.04
21 26 0.07
22 237 0.68
23 41 0.12
24 2 0.01
25 19 0.05
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.36
Consensus pattern (22 bp):
ATCAAAATTTCATAGGGAGGTT
Found at i:5641 original size:25 final size:25
Alignment explanation
Indices: 5613--5671 Score: 86
Period size: 25 Copynumber: 2.4 Consensus size: 25
5603 AGAAGAAAGT
* *
5613 TATCAAAATTTTATAGGGAGGTTTA
1 TATCAAAATTTTATAGGAAGATTTA
5638 TATCAAAATTTTATAGGAAGATTTA
1 TATCAAAATTTTATAGGAAGATTTA
5663 T-T-AAAATTT
1 TATCAAAATTT
5672 CATAACAAGG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
23 7 0.22
24 1 0.03
25 24 0.75
ACGTcount: A:0.41, C:0.03, G:0.14, T:0.42
Consensus pattern (25 bp):
TATCAAAATTTTATAGGAAGATTTA
Found at i:11709 original size:22 final size:22
Alignment explanation
Indices: 11667--11710 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
11657 TATTTATATG
*
11667 AAATTATGATAATATCCCTATT
1 AAATTATGATAATATCACTATT
11689 AAATTATGATAATTAT-ACTATT
1 AAATTATGATAA-TATCACTATT
11711 TTTTATAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 17 0.85
23 3 0.15
ACGTcount: A:0.43, C:0.09, G:0.05, T:0.43
Consensus pattern (22 bp):
AAATTATGATAATATCACTATT
Found at i:11740 original size:22 final size:21
Alignment explanation
Indices: 11710--11785 Score: 71
Period size: 22 Copynumber: 3.5 Consensus size: 21
11700 ATTATACTAT
* *
11710 TTTTTATAATCTCCTTATGAAA
1 TTTTGATAACCTCC-TATGAAA
* *
11732 TTTTGATAATCTTCCGATGAAA
1 TTTTGATAA-CCTCCTATGAAA
*
11754 TTTTGATAAACTTCCTATGAAA
1 TTTTGAT-AACCTCCTATGAAA
*
11776 TTTTAATAAC
1 TTTTGATAAC
11786 GATACTACGG
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
21 3 0.07
22 38 0.83
23 5 0.11
ACGTcount: A:0.34, C:0.13, G:0.08, T:0.45
Consensus pattern (21 bp):
TTTTGATAACCTCCTATGAAA
Found at i:12088 original size:23 final size:23
Alignment explanation
Indices: 12058--12124 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
12048 CCTCGTTATT
12058 AAATTTTGATAAATCTTCCTATA
1 AAATTTTGATAAATCTTCCTATA
12081 AAATTTTGATAAA-CTTCCCTATA
1 AAATTTTGATAAATCTT-CCTATA
*
12104 AAATTTTGAT-AATCTCCCTAT
1 AAATTTTGATAAATCTTCCTAT
12125 GATTTTTTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
22 10 0.24
23 31 0.76
ACGTcount: A:0.37, C:0.16, G:0.04, T:0.42
Consensus pattern (23 bp):
AAATTTTGATAAATCTTCCTATA
Found at i:12124 original size:45 final size:45
Alignment explanation
Indices: 11883--12265 Score: 172
Period size: 45 Copynumber: 8.7 Consensus size: 45
11873 CCTCATTTTG
* * * *
11883 AAATTTTGATAA-CTTCCCAATGAAATTTTGATAACCAACACTATG
1 AAATTTTGATAATC-TCCCTATGAAATTTTGATAAACTACACTATA
* * * * * * * **
11928 AGATGTTGATAACCTCCATATGATATATTGAT-AACCACGTTATGA
1 AAATTTTGATAATCTCCCTATGAAATTTTGATAAACTACACTAT-A
* * * * * *
11973 AAA-TTTAAAAACCTCCATATG-AATTGTT-AGTAATC-ACACTATG
1 AAATTTTGATAATCTCCCTATGAAATT-TTGA-TAAACTACACTATA
* * * * * ** *
12016 AAATTTTGAT-A-CGCACTATGAAATTGTAATAACCT-CGTTATT
1 AAATTTTGATAATCTCCCTATGAAATTTTGATAAACTACACTATA
* * * *
12058 AAATTTTGATAAATCTTCCTATAAAATTTTGATAAACTTCCCTATA
1 AAATTTTGAT-AATCTCCCTATGAAATTTTGATAAACTACACTATA
** * * * *
12104 AAATTTTGATAATCTCCCTATGATTTTTTTAATAACCT-CATTATG
1 AAATTTTGATAATCTCCCTATGA-AATTTTGATAAACTACACTATA
* *
12149 AAATTTTGTTAATCTCCCTATGAAATTTTGAT---CTACACTATG
1 AAATTTTGATAATCTCCCTATGAAATTTTGATAAACTACACTATA
* *
12191 AAATTTTAATAA-C-CCTCT-T-ATAATTTTGA-AAACTAAACTATA
1 AAATTTTGATAATCTCC-CTATGA-AATTTTGATAAACTACACTATA
* * *
12233 AAATTTTGATAACCTTCATATGAAATTTTGATA
1 AAATTTTGATAATCTCCCTATGAAATTTTGATA
12266 TCCTCCCTGA
Statistics
Matches: 251, Mismatches: 62, Indels: 50
0.69 0.17 0.14
Matches are distributed among these distances:
39 1 0.00
40 11 0.04
41 5 0.02
42 60 0.24
43 14 0.06
44 51 0.20
45 84 0.33
46 25 0.10
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.39
Consensus pattern (45 bp):
AAATTTTGATAATCTCCCTATGAAATTTTGATAAACTACACTATA
Found at i:12133 original size:23 final size:22
Alignment explanation
Indices: 11881--12284 Score: 147
Period size: 22 Copynumber: 18.5 Consensus size: 22
11871 GACCTCATTT
*
11881 TGAAATTTTGATAA-CTTCCCAA
1 TGAAATTTTGATAATC-TCCCTA
* * *
11903 TGAAATTTTGATAACCAACACTA
1 TGAAATTTTGATAATC-TCCCTA
* * * *
11926 TGAGATGTTGATAACCTCCATA
1 TGAAATTTTGATAATCTCCCTA
* * * * **
11948 TGATATATTGATAACCACGTTA
1 TGAAATTTTGATAATCTCCCTA
* * * * *
11970 TGAAAATTTAAAAACCTCCATA
1 TGAAATTTTGATAATCTCCCTA
* *
11992 TG-AATTGTT-AGTAATCACACTA
1 TGAAATT-TTGA-TAATCTCCCTA
* *
12014 TGAAATTTTGAT-A-CGCACTA
1 TGAAATTTTGATAATCTCCCTA
* * * **
12034 TGAAATTGTAATAACCTCGTTA
1 TGAAATTTTGATAATCTCCCTA
* *
12056 TTAAATTTTGATAAATCTTCCTA
1 TGAAATTTTGAT-AATCTCCCTA
* *
12079 TAAAATTTTGATAAACTTCCCTA
1 TGAAATTTTGATAATC-TCCCTA
*
12102 TAAAATTTTGATAATCTCCCTA
1 TGAAATTTTGATAATCTCCCTA
** * * **
12124 TGATTTTTTTAATAACCTCATTA
1 TGA-AATTTTGATAATCTCCCTA
*
12147 TGAAATTTTGTTAATCTCCCTA
1 TGAAATTTTGATAATCTCCCTA
*
12169 TGAAATTTTG---ATCTACACTA
1 TGAAATTTTGATAATCT-CCCTA
*
12189 TGAAATTTTAATAA-C-CCTCT-
1 TGAAATTTTGATAATCTCC-CTA
* **
12209 T-ATAATTTTGA-AAACTAAACTA
1 TGA-AATTTTGATAATCT-CCCTA
* * * *
12231 TAAAATTTTGATAACCTTCATA
1 TGAAATTTTGATAATCTCCCTA
12253 TGAAATTTTGAT-ATCCTCCC--
1 TGAAATTTTGATAAT-CTCCCTA
12273 TGAAATTTTGAT
1 TGAAATTTTGAT
12285 TACTCCATAA
Statistics
Matches: 286, Mismatches: 73, Indels: 48
0.70 0.18 0.12
Matches are distributed among these distances:
19 7 0.02
20 51 0.18
21 11 0.04
22 135 0.47
23 82 0.29
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.39
Consensus pattern (22 bp):
TGAAATTTTGATAATCTCCCTA
Found at i:12149 original size:155 final size:151
Alignment explanation
Indices: 11976--12273 Score: 358
Period size: 155 Copynumber: 1.9 Consensus size: 151
11966 GTTATGAAAA
*
11976 TTTAAAAACCTCCATATG-AATTGTTAG-TAATCACACTATGAAATTTTGATAC-GCACTATGAA
1 TTTAAAAACCTCCATATGAAATT-TT-GTTAATCACACTATGAAATTTTGAT-CTACACTATGAA
** *
12038 ATTGTAATAA-CCTCGTTATTAAATTTTGATAAATCT-TCCTATAAAATTTTGATAAACTTCCCT
63 ATTGTAATAACCCTC-TTA-T-AATTTTGA-AAA-CTAAACTATAAAATTTTGATAAACTT-CAT
12101 ATAAAATTTTGATAAT-CTCCCTATGATTTT
122 ATAAAATTTTGAT-ATCCTCCCTATGATTTT
* * *
12131 TTTAATAACCT-CATTATGAAATTTTGTTAATCTCCCTATGAAATTTTGATCTACACTATGAAAT
1 TTTAAAAACCTCCA-TATGAAATTTTGTTAATCACACTATGAAATTTTGATCTACACTATGAAAT
* * *
12195 TTTAATAACCCTCTTATAATTTTGAAAACTAAACTATAAAATTTTGATAACCTTCATATGAAATT
65 TGTAATAACCCTCTTATAATTTTGAAAACTAAACTATAAAATTTTGATAAACTTCATATAAAATT
12260 TTGATATCCTCCCT
130 TTGATATCCTCCCT
12274 GAAATTTTGA
Statistics
Matches: 126, Mismatches: 10, Indels: 18
0.82 0.06 0.12
Matches are distributed among these distances:
150 2 0.02
151 22 0.17
152 23 0.18
153 8 0.06
154 5 0.04
155 58 0.46
156 8 0.06
ACGTcount: A:0.36, C:0.16, G:0.07, T:0.41
Consensus pattern (151 bp):
TTTAAAAACCTCCATATGAAATTTTGTTAATCACACTATGAAATTTTGATCTACACTATGAAATT
GTAATAACCCTCTTATAATTTTGAAAACTAAACTATAAAATTTTGATAAACTTCATATAAAATTT
TGATATCCTCCCTATGATTTT
Found at i:12592 original size:22 final size:21
Alignment explanation
Indices: 12565--12688 Score: 87
Period size: 22 Copynumber: 5.8 Consensus size: 21
12555 AAAACCTCCA
12565 TATGAATTATT-AGTAATCATAC
1 TATGAATT-TTGA-TAATCATAC
*
12587 TCTGAAATTTTGATAATCATAC
1 TATG-AATTTTGATAATCATAC
* * *
12609 TATGAAATTGTGATAA-CCTCGC
1 TATG-AATTTTGATAATCAT-AC
12631 TATGAAATTTTGATAA-C--AC
1 TATG-AATTTTGATAATCATAC
* *
12650 TATGAAATTTTGATAATCTTCC
1 TATG-AATTTTGATAATCATAC
*
12672 TATAAATTTTGATAATC
1 TATGAATTTTGATAATC
12689 CGATCTCTAT
Statistics
Matches: 87, Mismatches: 9, Indels: 13
0.80 0.08 0.12
Matches are distributed among these distances:
19 17 0.20
20 1 0.01
21 15 0.17
22 49 0.56
23 5 0.06
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.40
Consensus pattern (21 bp):
TATGAATTTTGATAATCATAC
Found at i:12664 original size:41 final size:43
Alignment explanation
Indices: 12589--12688 Score: 136
Period size: 41 Copynumber: 2.4 Consensus size: 43
12579 AATCATACTC
12589 TGAAATTTTGATAATCATACTATGAAATTGTGATAA-CCTCGCTA
1 TGAAATTTTGATAATCA-ACTATGAAATTGTGATAATCCTC-CTA
* *
12633 TGAAATTTTGATAA-C-ACTATGAAATTTTGATAATCTTCCTA
1 TGAAATTTTGATAATCAACTATGAAATTGTGATAATCCTCCTA
12674 T-AAATTTTGATAATC
1 TGAAATTTTGATAATC
12689 CGATCTCTAT
Statistics
Matches: 52, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
40 12 0.23
41 22 0.42
42 3 0.06
43 1 0.02
44 14 0.27
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.40
Consensus pattern (43 bp):
TGAAATTTTGATAATCAACTATGAAATTGTGATAATCCTCCTA
Found at i:12801 original size:22 final size:22
Alignment explanation
Indices: 12786--12933 Score: 131
Period size: 22 Copynumber: 6.7 Consensus size: 22
12776 ATAACATTCA
12786 TATGAAATTTTGATAACCACAC
1 TATGAAATTTTGATAACCACAC
**
12808 TAAAAAATTTTGATAACCACAC
1 TATGAAATTTTGATAACCACAC
* *
12830 TATGAAATTTTGATAACCTCTC
1 TATGAAATTTTGATAACCACAC
* * * *
12852 CATGATATATT-AGTAACCTC-C
1 TATGAAATTTTGA-TAACCACAC
*
12873 TTATGAAATTTTGTTAACCACAC
1 -TATGAAATTTTGATAACCACAC
* **
12896 TATGAAATTCTT-ATAACCTCGT
1 TATGAAATT-TTGATAACCACAC
*
12918 TATGACATTTTGATAA
1 TATGAAATTTTGATAA
12934 TAATCTCTTT
Statistics
Matches: 101, Mismatches: 19, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
21 4 0.04
22 94 0.93
23 3 0.03
ACGTcount: A:0.37, C:0.18, G:0.09, T:0.36
Consensus pattern (22 bp):
TATGAAATTTTGATAACCACAC
Found at i:12913 original size:44 final size:43
Alignment explanation
Indices: 12772--13141 Score: 175
Period size: 44 Copynumber: 8.5 Consensus size: 43
12762 AAATTGAGAC
* * * **
12772 TTTTATAACATTCATATGAAATTTTGATAACCACACTAAAAAA
1 TTTTATAACCTCCTTATGAAATTTTGATAACCACACTATGAAA
* * * * *
12815 TTTTGATAACCACAC-TATGAAATTTTGATAACCTCTCCATGATA
1 TTTT-ATAACCTC-CTTATGAAATTTTGATAACCACACTATGAAA
* *
12859 TATTAGTAACCTCCTTATGAAATTTTGTTAACCACACTATGAAA
1 TTTTA-TAACCTCCTTATGAAATTTTGATAACCACACTATGAAA
* * * * *
12903 TTCTTATAACCTCGTTATGACATTTTGATAA-TA-A-TCT---C
1 TT-TTATAACCTCCTTATGAAATTTTGATAACCACACTATGAAA
* * ** * * *
12941 TTTGATAACTTTTTTATAAAATTGTGATAATCACACTATGAAA
1 TTTTATAACCTCCTTATGAAATTTTGATAACCACACTATGAAA
* * * **
12984 TTTCAATAACCTTCC-TAAGAAATTTTAATAACCTATTTCTATGAAA
1 TTT-TATAACC-TCCTTATGAAATTTTGATAACC-A-CACTATGAAA
* * ** **
13030 TTTTGGTAACCACAGTATGAAATTTTGATAACC-TTCTCATGAAA
1 TTTT-ATAACCTCCTTATGAAATTTTGATAACCACACT-ATGAAA
* * * * *
13074 TTTTGATAA-CTTCTATATAAAAGTTTGGTAACCACACTATGGAA
1 TTTT-ATAACCTCCT-TATGAAATTTTGATAACCACACTATGAAA
* *
13118 TTTTGATAACCTACTCATGAAATT
1 TTTT-ATAACCTCCTTATGAAATT
13142 ATAACGGTCA
Statistics
Matches: 241, Mismatches: 65, Indels: 41
0.69 0.19 0.12
Matches are distributed among these distances:
37 21 0.09
38 3 0.01
39 1 0.00
40 2 0.01
41 2 0.01
42 1 0.00
43 15 0.06
44 151 0.63
45 13 0.05
46 32 0.13
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.38
Consensus pattern (43 bp):
TTTTATAACCTCCTTATGAAATTTTGATAACCACACTATGAAA
Found at i:13040 original size:46 final size:45
Alignment explanation
Indices: 12976--13083 Score: 112
Period size: 46 Copynumber: 2.4 Consensus size: 45
12966 GATAATCACA
** * *
12976 CTATGAAATTTCAATAACCTTC-CTAAGAAATTTTAATAACCTATTT
1 CTATGAAATTTTGATAACC-ACACTAAGAAATTTTAATAACCT-TCT
* * * *
13022 CTATGAAATTTTGGTAACCACAGTATGAAATTTTGATAACCTTCT
1 CTATGAAATTTTGATAACCACACTAAGAAATTTTAATAACCTTCT
13067 C-ATGAAATTTTGATAAC
1 CTATGAAATTTTGATAAC
13084 TTCTATATAA
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
44 15 0.29
45 4 0.08
46 33 0.63
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.38
Consensus pattern (45 bp):
CTATGAAATTTTGATAACCACACTAAGAAATTTTAATAACCTTCT
Found at i:13051 original size:22 final size:21
Alignment explanation
Indices: 13023--13175 Score: 91
Period size: 22 Copynumber: 7.0 Consensus size: 21
13013 AACCTATTTC
*
13023 TATGAAATTTTGGTAACCACA
1 TATGAAATTTTGATAACCACA
*
13044 GTATGAAATTTTGATAACCTTC-
1 -TATGAAATTTTGATAACC-ACA
**
13066 TCATGAAATTTTGATAACTTCTA
1 T-ATGAAATTTTGATAACCAC-A
* * *
13089 TATAAAAGTTTGGTAACCACA
1 TATGAAATTTTGATAACCACA
*
13110 CTATGGAATTTTGATAACCTAC-
1 -TATGAAATTTTGATAACC-ACA
*
13132 TCATGAAA--TT-ATAACGGTCATCT
1 T-ATGAAATTTTGATAAC---CA-CA
13155 TATGAAATTTTGATAACCACA
1 TATGAAATTTTGATAACCACA
13176 CAGAGACAAG
Statistics
Matches: 102, Mismatches: 14, Indels: 31
0.69 0.10 0.21
Matches are distributed among these distances:
19 5 0.05
20 2 0.02
21 7 0.07
22 76 0.75
23 5 0.05
24 2 0.02
25 5 0.05
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.36
Consensus pattern (21 bp):
TATGAAATTTTGATAACCACA
Found at i:13124 original size:66 final size:65
Alignment explanation
Indices: 12941--13141 Score: 224
Period size: 66 Copynumber: 3.0 Consensus size: 65
12931 TAATAATCTC
* * * ** *
12941 TTTGATAACTTTTTTATAAAATTGTGATAATCACACTATGAAATTTCAATAACCTTC-CTAAGAA
1 TTTGATAACTTTTATATAAAATT-TGGTAACCACACTATGAAATTTTGATAACCTTCTC-ATGAA
13005 AT
64 AT
* * * *
13007 TTTAATAACCTATTTCTATGAAATTTTGGTAACCACAGTATGAAATTTTGATAACCTTCTCATGA
1 TTTGATAA-CT-TTTATAT-AAAATTTGGTAACCACACTATGAAATTTTGATAACCTTCTCATGA
13072 AAT
63 AAT
* * *
13075 TTTGATAACTTCTATATAAAAGTTTGGTAACCACACTATGGAATTTTGATAACCTACTCATGAAA
1 TTTGATAACTTTTATATAAAA-TTTGGTAACCACACTATGAAATTTTGATAACCTTCTCATGAAA
13140 T
65 T
13141 T
1 T
13142 ATAACGGTCA
Statistics
Matches: 114, Mismatches: 16, Indels: 10
0.81 0.11 0.07
Matches are distributed among these distances:
65 3 0.03
66 54 0.47
67 4 0.04
68 47 0.41
69 6 0.05
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.39
Consensus pattern (65 bp):
TTTGATAACTTTTATATAAAATTTGGTAACCACACTATGAAATTTTGATAACCTTCTCATGAAAT
Found at i:13172 original size:66 final size:65
Alignment explanation
Indices: 12941--13176 Score: 192
Period size: 66 Copynumber: 3.6 Consensus size: 65
12931 TAATAATCTC
* * * * * * ** * *
12941 TTTGATAACTTTTTTATAAAATTGTGATAATCACACTATGAAATTTCAATAACCTTC-CTAAGAA
1 TTTGATAACTTCTATATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTACTC-ATGAA
13005 A
65 A
* * * * *
13006 TTTTAATAACCTATTTCTATGAAATTTTGGTAACCACAGTATGAAATTTTGATAACCTTCTCATG
1 -TTTGATAA-CT-TCTATATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTACTCATG
13071 AAA
63 AAA
* * *
13074 TTTTGATAACTTCTATATAAAAGTTTGGTAACCACACTATGGAATTTTGATAACCTACTCATGAA
1 -TTTGATAACTTCTATATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTACTCATGAA
13139 A
65 A
*
13140 -TT-ATAACGGTCATCT-TATGAAATTTTGATAACCACAC
1 TTTGATAAC--T--TCTATATGAAATTTTGGTAACCACAC
13177 AGAGACAAGA
Statistics
Matches: 142, Mismatches: 21, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
63 5 0.04
64 2 0.01
65 1 0.01
66 74 0.52
67 7 0.05
68 52 0.37
69 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.38
Consensus pattern (65 bp):
TTTGATAACTTCTATATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTACTCATGAAA
Found at i:14408 original size:31 final size:28
Alignment explanation
Indices: 14353--14415 Score: 72
Period size: 31 Copynumber: 2.1 Consensus size: 28
14343 TGGCAATTTA
* *
14353 GAAATATATTTGAAAAAAGTTACAATCG
1 GAAATATATTTAAAAAAAGATACAATCG
*
14381 GAAACTATATTTTAAAAAAAGGATACAATTG
1 GAAA-TATA-TTTAAAAAAA-GATACAATCG
14412 GAAA
1 GAAA
14416 ACATAAAGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 4 0.14
29 4 0.14
30 9 0.31
31 12 0.41
ACGTcount: A:0.52, C:0.06, G:0.14, T:0.27
Consensus pattern (28 bp):
GAAATATATTTAAAAAAAGATACAATCG
Found at i:14602 original size:22 final size:22
Alignment explanation
Indices: 14577--14745 Score: 67
Period size: 22 Copynumber: 7.6 Consensus size: 22
14567 TCCCATTATA
14577 AAATTTTGATAACCTTCCTATG
1 AAATTTTGATAACCTTCCTATG
* *** *
14599 AAATTTTAATAATGATACTATG
1 AAATTTTGATAACCTTCCTATG
* ** * **
14621 GAATTTCAAGAACCTTTTTATG
1 AAATTTTGATAACCTTCCTATG
** * ** *
14643 ATTTTTTTA-AATTTTCTTATG
1 AAATTTTGATAACCTTCCTATG
* * * *
14664 ATATTTTGTTAACCTCCCTAAG
1 AAATTTTGATAACCTTCCTATG
*
14686 AAATTTTGA-AGACC-TCAATATG
1 AAATTTTGATA-ACCTTC-CTATG
14708 AAATTTTGATAA-CTTCCCAATATG
1 AAATTTTGATAACCTT-CC--TATG
14732 AAATTTTGATAACC
1 AAATTTTGATAACC
14746 AACACTATGA
Statistics
Matches: 103, Mismatches: 35, Indels: 15
0.67 0.23 0.10
Matches are distributed among these distances:
21 18 0.17
22 66 0.64
23 2 0.02
24 16 0.16
25 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (22 bp):
AAATTTTGATAACCTTCCTATG
Found at i:14839 original size:22 final size:21
Alignment explanation
Indices: 14812--14893 Score: 60
Period size: 22 Copynumber: 3.7 Consensus size: 21
14802 AAAACCTCCA
14812 TATGAATTATT-AGTAATCATAC
1 TATGAATT-TTGA-TAATCATAC
*
14834 TCTGAAATTTTGATAATCATAC
1 TATG-AATTTTGATAATCATAC
* * *
14856 TATGAAATTGTGATAA-CCTCGC
1 TATG-AATTTTGATAATCAT-AC
14878 TATGAAATTTTGATAA
1 TATG-AATTTTGATAA
14894 ATCTTCCTAT
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
21 2 0.04
22 44 0.86
23 5 0.10
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.39
Consensus pattern (21 bp):
TATGAATTTTGATAATCATAC
Found at i:14927 original size:25 final size:25
Alignment explanation
Indices: 14870--14940 Score: 92
Period size: 25 Copynumber: 2.9 Consensus size: 25
14860 AAATTGTGAT
* *
14870 AACCTCGCTATGAAATTTTG--ATA
1 AACCTCCCTATAAAATTTTGATATA
* *
14893 AATCTTCCTATAAAATTTTGATATA
1 AACCTCCCTATAAAATTTTGATATA
14918 AACCTCCCTATAAAATTTTGATA
1 AACCTCCCTATAAAATTTTGATA
14941 ACTTTCTTAT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
23 16 0.40
25 24 0.60
ACGTcount: A:0.38, C:0.17, G:0.07, T:0.38
Consensus pattern (25 bp):
AACCTCCCTATAAAATTTTGATATA
Found at i:14937 original size:48 final size:45
Alignment explanation
Indices: 14838--14941 Score: 120
Period size: 48 Copynumber: 2.3 Consensus size: 45
14828 TCATACTCTG
* * *
14838 AAATTTTGAT-AATCATACTATGAAATTGTGATAACCTCGCTATG
1 AAATTTTGATAAATCATACTATAAAATTGTGATAACCTCCCTATA
* * *
14882 AAATTTTGATAAATCTTCCTATAAAATTTTGATATAAACCTCCCTATA
1 AAATTTTGATAAATCATACTATAAAATTGTG--AT-AACCTCCCTATA
14930 AAATTTTGATAA
1 AAATTTTGATAA
14942 CTTTCTTATG
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
44 10 0.20
45 16 0.32
47 2 0.04
48 22 0.44
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.38
Consensus pattern (45 bp):
AAATTTTGATAAATCATACTATAAAATTGTGATAACCTCCCTATA
Found at i:15018 original size:22 final size:22
Alignment explanation
Indices: 14836--15086 Score: 103
Period size: 22 Copynumber: 11.5 Consensus size: 22
14826 AATCATACTC
14836 TGAAATTTTGATAA--TCATACTA
1 TGAAATTTTGATAACCTCAT--TA
* **
14858 TGAAATTGTGATAACCTCGCTA
1 TGAAATTTTGATAACCTCATTA
* *
14880 TGAAATTTTGATAAATCTTC-CTA
1 TGAAATTTTGAT-AA-CCTCATTA
* **
14903 TAAAATTTTGATATAAACCTCCCTA
1 TGAAATTTTG--AT-AACCTCATTA
* *
14928 TAAAATTTTGATAACTTTC-TTA
1 TGAAATTTTGATAAC-CTCATTA
*
14950 TGAAATCTTGATAA---C--TA
1 TGAAATTTTGATAACCTCATTA
* * *
14967 -CAAATTTTAATAACCTCCTTA
1 TGAAATTTTGATAACCTCATTA
**
14988 TGATTTTTTGATAACCTCATTA
1 TGAAATTTTGATAACCTCATTA
* * * * **
15010 AGAAATTTTGTTGATCTCCCTA
1 TGAAATTTTGATAACCTCATTA
* * *
15032 TGAAATTTTGATTTACAT-ACTA
1 TGAAATTTTGA-TAACCTCATTA
15054 TGAAATTTTGATAACCCTC-TTA
1 TGAAATTTTGATAA-CCTCATTA
15076 TGAAATTTTGA
1 TGAAATTTTGA
15087 AAAGTAAACT
Statistics
Matches: 176, Mismatches: 36, Indels: 34
0.72 0.15 0.14
Matches are distributed among these distances:
16 10 0.06
17 2 0.01
18 1 0.01
19 1 0.01
21 4 0.02
22 111 0.63
23 21 0.12
24 8 0.05
25 18 0.10
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.41
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCATTA
Found at i:15260 original size:22 final size:22
Alignment explanation
Indices: 15235--15314 Score: 83
Period size: 22 Copynumber: 3.6 Consensus size: 22
15225 AATCACATTC
*
15235 TGAAAATTTGATAACCTCTTTA
1 TGAAAATTTGATAACCTCTATA
*
15257 TGAAATTTTGATAACCTCTATA
1 TGAAAATTTGATAACCTCTATA
* * *
15279 T-AAAATTTTGTTGACCTCTCTA
1 TGAAAA-TTTGATAACCTCTATA
15301 TG-AAATTCTGATAA
1 TGAAAATT-TGATAA
15315 TTACATTATA
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
21 5 0.11
22 42 0.89
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (22 bp):
TGAAAATTTGATAACCTCTATA
Found at i:15396 original size:21 final size:24
Alignment explanation
Indices: 15364--15428 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 24
15354 GATAACAAAA
*
15364 CTATGGAATTTTGATAATCT-TC-
1 CTATGAAATTTTGATAATCTATCG
15386 CTAT-AAATTTTGATAATCTGATCG
1 CTATGAAATTTTGATAATCT-ATCG
15410 CTATGAAATTTTGATAATC
1 CTATGAAATTTTGATAATC
15429 ACTCTGAGAT
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
21 14 0.37
22 4 0.11
23 2 0.05
24 4 0.11
25 14 0.37
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.43
Consensus pattern (24 bp):
CTATGAAATTTTGATAATCTATCG
Found at i:15700 original size:30 final size:31
Alignment explanation
Indices: 15664--15725 Score: 99
Period size: 30 Copynumber: 2.0 Consensus size: 31
15654 TAATGAAAAT
*
15664 TTAGAAATATGTTTTAAAAA-AAAGGTACAA
1 TTAGAAATATATTTTAAAAATAAAGGTACAA
*
15694 TTAGAAATATATTTTAAAAATAAGGGTACAA
1 TTAGAAATATATTTTAAAAATAAAGGTACAA
15725 T
1 T
15726 CGGAAAACAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 19 0.66
31 10 0.34
ACGTcount: A:0.52, C:0.03, G:0.13, T:0.32
Consensus pattern (31 bp):
TTAGAAATATATTTTAAAAATAAAGGTACAA
Found at i:16387 original size:11 final size:11
Alignment explanation
Indices: 16344--16381 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
16334 TTCCTATATA
*
16344 AAATAAATTAT
1 AAATTAATTAT
16355 CAAA-TAATTAT
1 -AAATTAATTAT
16366 AAATTAATTAT
1 AAATTAATTAT
16377 AAATT
1 AAATT
16382 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:16629 original size:16 final size:16
Alignment explanation
Indices: 16584--16631 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
16574 CTCCCTTCTT
*
16584 CATATTCTCTTCTTCTC
1 CATATTCTCTT-GTCTC
* *
16601 CATATTTTATTGTCTC
1 CATATTCTCTTGTCTC
*
16617 TATATTCTCTTGTCT
1 CATATTCTCTTGTCT
16632 TTTCCATACT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
16 16 0.64
17 9 0.36
ACGTcount: A:0.15, C:0.25, G:0.04, T:0.56
Consensus pattern (16 bp):
CATATTCTCTTGTCTC
Found at i:17386 original size:2 final size:2
Alignment explanation
Indices: 17379--17404 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
17369 AATACAAGTC
17379 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
17405 CTACTTGATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:18945 original size:8 final size:8
Alignment explanation
Indices: 18932--18958 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
18922 TATTATATAC
18932 ATACATAT
1 ATACATAT
18940 ATACATAT
1 ATACATAT
18948 ATACATAT
1 ATACATAT
18956 ATA
1 ATA
18959 AAAGTTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (8 bp):
ATACATAT
Found at i:19526 original size:214 final size:214
Alignment explanation
Indices: 19157--19585 Score: 840
Period size: 214 Copynumber: 2.0 Consensus size: 214
19147 AGCCCGCTCG
*
19157 ATATTTGAGAGGGTTTAGGACAAAAATTTGAAATCTGTTAGATGAGTTTGGATATTAAGGTTCGT
1 ATATTTGAGAGGGTTTAGGACAAAAATTTGAAATCTGTTAGATGAGTTTGGATATTAAGGTCCGT
19222 TTAAAAAATAGGTCGAGTTTGGTCTTAGCCATAAAAGTCCGGTCCAAACCTGATCTGTATTGTGA
66 TTAAAAAATAGGTCGAGTTTGGTCTTAGCCATAAAAGTCCGGTCCAAACCTGATCTGTATTGTGA
*
19287 AATAATTAGATCATTTTATTTTATTTTAAATAGATTGGATAATTAAAATATTTATTAGATGTGTA
131 AATAATTAGATCATTTTATTTTATTTTAAACAGATTGGATAATTAAAATATTTATTAGATGTGTA
19352 AATTAATTATTTTGAAAAA
196 AATTAATTATTTTGAAAAA
19371 ATATTTGAGAGGGTTTAGGACAAAAATTTGAAATCTGTTAGATGAGTTTGGATATTAAGGTCCGT
1 ATATTTGAGAGGGTTTAGGACAAAAATTTGAAATCTGTTAGATGAGTTTGGATATTAAGGTCCGT
19436 TTAAAAAATAGGTCGAGTTTGGTCTTAGCCATAAAAGTCCGGTCCAAACCTGATCTGTATTGTGA
66 TTAAAAAATAGGTCGAGTTTGGTCTTAGCCATAAAAGTCCGGTCCAAACCTGATCTGTATTGTGA
19501 AATAATTAGATCATTTTATTTTATTTTAAACAGATTGGATAATTAAAATATTTATTAGATGTGTA
131 AATAATTAGATCATTTTATTTTATTTTAAACAGATTGGATAATTAAAATATTTATTAGATGTGTA
19566 AATTAATTATTTTGAAAAA
196 AATTAATTATTTTGAAAAA
19585 A
1 A
19586 ATATATTATT
Statistics
Matches: 213, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
214 213 1.00
ACGTcount: A:0.36, C:0.07, G:0.18, T:0.38
Consensus pattern (214 bp):
ATATTTGAGAGGGTTTAGGACAAAAATTTGAAATCTGTTAGATGAGTTTGGATATTAAGGTCCGT
TTAAAAAATAGGTCGAGTTTGGTCTTAGCCATAAAAGTCCGGTCCAAACCTGATCTGTATTGTGA
AATAATTAGATCATTTTATTTTATTTTAAACAGATTGGATAATTAAAATATTTATTAGATGTGTA
AATTAATTATTTTGAAAAA
Found at i:19798 original size:68 final size:70
Alignment explanation
Indices: 19724--19852 Score: 217
Period size: 70 Copynumber: 1.9 Consensus size: 70
19714 AAGAAACCCT
* *
19724 TCAATTACTTTCTTACATTTTC-TT-TCGCCTACCCTATTTTGGTAATAAATAGTGTCATTAATA
1 TCAATTAATTTCTTACATTTTCTTTCTCCCCTACCCTATTTTGGTAATAAATAGTGTCATTAATA
19787 GTACA
66 GTACA
*
19792 TCAATTAATTTCTTACATTTTCTTTCTCCCCTGCCCTATTTTGGTAATAAATAGTGTCATT
1 TCAATTAATTTCTTACATTTTCTTTCTCCCCTACCCTATTTTGGTAATAAATAGTGTCATT
19853 TAGATGTAAT
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
68 21 0.38
69 2 0.04
70 33 0.59
ACGTcount: A:0.26, C:0.20, G:0.09, T:0.46
Consensus pattern (70 bp):
TCAATTAATTTCTTACATTTTCTTTCTCCCCTACCCTATTTTGGTAATAAATAGTGTCATTAATA
GTACA
Found at i:26316 original size:65 final size:66
Alignment explanation
Indices: 26186--26317 Score: 194
Period size: 69 Copynumber: 2.0 Consensus size: 66
26176 CGGTGAGATT
*
26186 TGAGATTTGTATAGATGAAAATGATGGAAAAACTGAATCTTAGATAGGATAACACTTGAGACTCC
1 TGAGATTTGTATAAATGAAAATGATGGAAAAACTGAA---TAGATAGGATAACACTTGAGACTCC
26251 GATA
63 GATA
* * *
26255 TGAGATTTGTATAAATGAGAATGGTGGAACAACTGAA-AGATAGGATAACACTTGAGACTCCGA
1 TGAGATTTGTATAAATGAAAATGATGGAAAAACTGAATAGATAGGATAACACTTGAGACTCCGA
26318 ACAAGATTGT
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
65 26 0.44
69 33 0.56
ACGTcount: A:0.40, C:0.11, G:0.23, T:0.26
Consensus pattern (66 bp):
TGAGATTTGTATAAATGAAAATGATGGAAAAACTGAATAGATAGGATAACACTTGAGACTCCGAT
A
Found at i:35892 original size:4 final size:4
Alignment explanation
Indices: 35883--35924 Score: 84
Period size: 4 Copynumber: 10.5 Consensus size: 4
35873 ATGTTCAACA
35883 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GT
35925 TGTGGTGGCC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (4 bp):
GTAT
Found at i:45553 original size:2 final size:2
Alignment explanation
Indices: 45546--45572 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
45536 AAAGCATTTC
45546 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 T
45573 TCCAACCTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:50440 original size:45 final size:45
Alignment explanation
Indices: 50390--50479 Score: 153
Period size: 45 Copynumber: 2.0 Consensus size: 45
50380 GATTACTTCT
50390 CCAGCTCATCATTAATCCGGGGTAGGGATCTTTCAGTAATTCCAC
1 CCAGCTCATCATTAATCCGGGGTAGGGATCTTTCAGTAATTCCAC
* * *
50435 CCAGCTTATCATTAATTCGGGGTAGGGATCTTTTAGTAATTCCAC
1 CCAGCTCATCATTAATCCGGGGTAGGGATCTTTCAGTAATTCCAC
50480 TACTCTATTA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.32
Consensus pattern (45 bp):
CCAGCTCATCATTAATCCGGGGTAGGGATCTTTCAGTAATTCCAC
Found at i:50681 original size:2 final size:2
Alignment explanation
Indices: 50674--50708 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
50664 TAATATGTAG
50674 TA TA 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 TA TA T
50709 GACATGACAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:59927 original size:1 final size:1
Alignment explanation
Indices: 59921--59950 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
59911 CCAGGTATGC
59921 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
59951 CTGATTTATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:66361 original size:2 final size:2
Alignment explanation
Indices: 66354--66386 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
66344 AACCCATTAA
66354 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 A
66387 AGTAATAAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:66553 original size:32 final size:32
Alignment explanation
Indices: 66508--66571 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
66498 AGCTTCAAAA
*
66508 TAGTTCTTGTAAGAGCTACATATTTAATCAAG
1 TAGTTCTTATAAGAGCTACATATTTAATCAAG
66540 TAGTTCTTATAAGAGCTACATATTTAATCAAG
1 TAGTTCTTATAAGAGCTACATATTTAATCAAG
66572 AAGAGTGAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (32 bp):
TAGTTCTTATAAGAGCTACATATTTAATCAAG
Found at i:68702 original size:24 final size:24
Alignment explanation
Indices: 68598--68730 Score: 136
Period size: 22 Copynumber: 5.8 Consensus size: 24
68588 AATCATATGG
* *
68598 AGGTTATTAAAATTTCATAGG--G
1 AGGTTATCAAAATTTCATAGGATT
*
68620 AGGTTATCAAAATTCCATA-G-TGT
1 AGGTTATCAAAATTTCATAGGAT-T
*
68643 -GGTTATCAGAATTTCATAGGAATT
1 AGGTTATCAAAATTTCATAGG-ATT
*
68667 AGGTTACCAAAATTTCATAGGATT
1 AGGTTATCAAAATTTCATAGGATT
* *
68691 AGATTATTAAAATTTCATAGGA--
1 AGGTTATCAAAATTTCATAGGATT
68713 AGGTTATCAAAATTTCAT
1 AGGTTATCAAAATTTCAT
68731 GATGTTATCA
Statistics
Matches: 93, Mismatches: 12, Indels: 12
0.79 0.10 0.10
Matches are distributed among these distances:
21 1 0.01
22 49 0.53
23 1 0.01
24 23 0.25
25 19 0.20
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (24 bp):
AGGTTATCAAAATTTCATAGGATT
Found at i:75331 original size:22 final size:22
Alignment explanation
Indices: 75295--75551 Score: 175
Period size: 22 Copynumber: 11.6 Consensus size: 22
75285 CTATGTGGTC
* *
75295 ATCAAAATTTTATAAAGAGGTT
1 ATCAAAATTTCATAAGGAGGTT
* *
75317 ATTATAATTTCATAAGGAGGTT
1 ATCAAAATTTCATAAGGAGGTT
* * *
75339 ATCAAAATTTTATAATGTGGTT
1 ATCAAAATTTCATAAGGAGGTT
* * **
75361 ACCAAAATATCATATTGAGGTT
1 ATCAAAATTTCATAAGGAGGTT
* *
75383 ATAAAAATTTCATATGGAGGTT
1 ATCAAAATTTCATAAGGAGGTT
*
75405 ATCAAAATTTCAT-AGTATGGTT
1 ATCAAAATTTCATAAGGA-GGTT
* * * *
75427 ACCAAAATATCATATGGCGGTT
1 ATCAAAATTTCATAAGGAGGTT
*
75449 AT-AACAATTTCATAGGGAGGTT
1 ATCAA-AATTTCATAAGGAGGTT
*
75471 ATCAAAATTTTAT-AGTGTA-GTT
1 ATCAAAATTTCATAAG-G-AGGTT
* * *
75493 ACCAAAA-TTCAT-TGAGTGGTT
1 ATCAAAATTTCATAAG-GAGGTT
**
75514 ATCAAAATTTCATATGATCAGGTT
1 ATCAAAATTTCATA--AGGAGGTT
*
75538 ATTAAAATTTCATA
1 ATCAAAATTTCATA
75552 GGAAGGTCAT
Statistics
Matches: 181, Mismatches: 43, Indels: 20
0.74 0.18 0.08
Matches are distributed among these distances:
21 20 0.11
22 140 0.77
23 4 0.02
24 17 0.09
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.37
Consensus pattern (22 bp):
ATCAAAATTTCATAAGGAGGTT
Found at i:75361 original size:44 final size:44
Alignment explanation
Indices: 75295--75791 Score: 234
Period size: 44 Copynumber: 10.9 Consensus size: 44
75285 CTATGTGGTC
* * *
75295 ATCAAAATTTTATAAAGAGGTTATTATAATTTCATAAGGAGGTT
1 ATCAAAATTTTATAATGAGGTTATCAAAATTTCATAAGGAGGTT
* * * **
75339 ATCAAAATTTTATAATGTGGTTACCAAAATATCATATTGAGGTT
1 ATCAAAATTTTATAATGAGGTTATCAAAATTTCATAAGGAGGTT
* * *
75383 ATAAAAATTTCAT-ATGGAGGTTATCAAAATTTCAT-AGTATGGTT
1 ATCAAAATTTTATAAT-GAGGTTATCAAAATTTCATAAGGA-GGTT
* * * * *
75427 ACCAAAATATCAT-ATGGCGGTTAT-AACAATTTCATAGGGAGGTT
1 ATCAAAATTTTATAAT-GAGGTTATCAA-AATTTCATAAGGAGGTT
* * * *
75471 ATCAAAATTTTATAGTGTA-GTTACCAAAA-TTCAT-TGAGTGGTT
1 ATCAAAATTTTATAATG-AGGTTATCAAAATTTCATAAG-GAGGTT
* * *
75514 ATCAAAATTTCATATGATCAGGTTATTAAAATTTCATAGGAAGGTCATGATGTT
1 ATCAAAATTT--TATAATGAGGTTATCAAAATTTCAT---AAGG--A-G--GTT
* *
75568 ACCAAATTATAATTTCATAA-GAAGGTTATCAAAATTTCAT-AGTACTTTGGTT
1 ATCAAA--AT--TTT-ATAATG-AGGTTATCAAAATTTCATAAGGA----GGTT
* * * *
75620 ACCAAAATATCAT-ATGGAGGTTATAAAAATTTCATAAGGAGGTT
1 ATCAAAATTTTATAAT-GAGGTTATCAAAATTTCATAAGGAGGTT
* * *
75664 ATCAAAAATTTCATAATGTGGTTACCAAAATTTCAT-AGGAAGGTT
1 ATC-AAAATTTTATAATGAGGTTATCAAAATTTCATAAGG-AGGTT
* * * * *
75709 ACCAAAAATTTCATAGA-GTGGTTACCAAAATTTCAT-AGAGTGGTT
1 ATC-AAAATTTTATA-ATGAGGTTATCAAAATTTCATAAG-GAGGTT
*
75754 ATCAAAATTTCAT-A-GAGTAGTTATCAAAATTTCA-AAGG
1 ATCAAAATTTTATAATGAG--GTTATCAAAATTTCATAAGG
75792 GAGATTTCAT
Statistics
Matches: 356, Mismatches: 56, Indels: 83
0.72 0.11 0.17
Matches are distributed among these distances:
42 4 0.01
43 26 0.07
44 152 0.43
45 88 0.25
46 10 0.03
47 19 0.05
48 5 0.01
49 1 0.00
50 3 0.01
51 1 0.00
52 10 0.03
53 2 0.01
54 10 0.03
56 3 0.01
57 20 0.06
58 2 0.01
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (44 bp):
ATCAAAATTTTATAATGAGGTTATCAAAATTTCATAAGGAGGTT
Found at i:75367 original size:66 final size:66
Alignment explanation
Indices: 75287--75527 Score: 279
Period size: 66 Copynumber: 3.7 Consensus size: 66
75277 TGTCGTCTCT
* * * * * * *
75287 ATGTGGTCATCAAAATTTTATAAAGAGGTTATTATAATTTCATAAGGAGGTTATCAAAATTTTAT
1 ATGTGGTTACCAAAATATCATATAGAGGTTATAAAAATTTCATAAGGAGGTTATCAAAATTTTAT
75352 A
66 A
* * *
75353 ATGTGGTTACCAAAATATCATATTGAGGTTATAAAAATTTCATATGGAGGTTATCAAAATTTCAT
1 ATGTGGTTACCAAAATATCATATAGAGGTTATAAAAATTTCATAAGGAGGTTATCAAAATTTTAT
75418 A
66 A
* * * * * *
75419 GTATGGTTACCAAAATATCATATGGCGGTTATAACAATTTCATAGGGAGGTTATCAAAATTTTAT
1 ATGTGGTTACCAAAATATCATATAGAGGTTATAAAAATTTCATAAGGAGGTTATCAAAATTTTAT
75484 A
66 A
* * * *
75485 GTGTAGTTACCAAAAT-TCAT-TGAGTGGTTATCAAAATTTCATA
1 ATGTGGTTACCAAAATATCATAT-AGAGGTTATAAAAATTTCATA
75528 TGATCAGGTT
Statistics
Matches: 151, Mismatches: 23, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
64 1 0.01
65 21 0.14
66 129 0.85
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.37
Consensus pattern (66 bp):
ATGTGGTTACCAAAATATCATATAGAGGTTATAAAAATTTCATAAGGAGGTTATCAAAATTTTAT
A
Found at i:75603 original size:22 final size:22
Alignment explanation
Indices: 75578--75787 Score: 160
Period size: 22 Copynumber: 9.3 Consensus size: 22
75568 ACCAAATTAT
75578 AATTTCATAAGAAGGTTATCAA
1 AATTTCATAAGAAGGTTATCAA
* *
75600 AATTTCAT-AGTACTTTGGTTACCAA
1 AATTTCATAAG-A---AGGTTATCAA
* * * *
75625 AATATCATATGGAGGTTATAAA
1 AATTTCATAAGAAGGTTATCAA
*
75647 AATTTCATAAGGAGGTTATCAAA
1 AATTTCATAAGAAGGTTATC-AA
* *
75670 AATTTCATAATG-TGGTTACCAA
1 AATTTCATAA-GAAGGTTATCAA
* *
75692 AATTTCATAGGAAGGTTACCAAA
1 AATTTCATAAGAAGGTTATC-AA
* *
75715 AATTTCAT-AGAGTGGTTACCAA
1 AATTTCATAAGA-AGGTTATCAA
*
75737 AATTTCAT-AGAGTGGTTATCAA
1 AATTTCATAAGA-AGGTTATCAA
*
75759 AATTTCATAGAGTA-GTTATCAA
1 AATTTCATA-AGAAGGTTATCAA
75781 AATTTCA
1 AATTTCA
75788 AAGGGAGATT
Statistics
Matches: 156, Mismatches: 20, Indels: 24
0.78 0.10 0.12
Matches are distributed among these distances:
21 3 0.02
22 99 0.63
23 35 0.22
24 3 0.02
25 15 0.10
26 1 0.01
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.34
Consensus pattern (22 bp):
AATTTCATAAGAAGGTTATCAA
Found at i:75687 original size:45 final size:44
Alignment explanation
Indices: 75645--75787 Score: 200
Period size: 45 Copynumber: 3.2 Consensus size: 44
75635 GGAGGTTATA
75645 AAAATTTCATAAGGAGGTTATCAAAAATTTCATA-ATGTGGTTACC
1 AAAATTTCAT-AGGAGGTTATCAAAAATTTCATAGA-GTGGTTACC
*
75690 AAAATTTCATAGGAAGGTTACCAAAAATTTCATAGAGTGGTTACC
1 AAAATTTCATAGG-AGGTTATCAAAAATTTCATAGAGTGGTTACC
* * *
75735 AAAATTTCATAGAGTGGTTATC-AAAATTTCATAGAGTAGTTATC
1 AAAATTTCATAG-GAGGTTATCAAAAATTTCATAGAGTGGTTACC
75779 AAAATTTCA
1 AAAATTTCA
75788 AAGGGAGATT
Statistics
Matches: 90, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
44 32 0.36
45 56 0.62
46 2 0.02
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (44 bp):
AAAATTTCATAGGAGGTTATCAAAAATTTCATAGAGTGGTTACC
Found at i:75708 original size:67 final size:66
Alignment explanation
Indices: 75578--75791 Score: 240
Period size: 67 Copynumber: 3.2 Consensus size: 66
75568 ACCAAATTAT
* * *
75578 AATTTCATAAGAAGGTTATCAAAATTTCATAGTACTTTGGTTACCAAAATATCATATGGAGGTTA
1 AATTTCATAAGGAGGTTATCAAAATTTCATAG-A-TGTGGTTACCAAAATTTCATA-GGAGGTTA
75643 TAAA
63 TAAA
75647 AATTTCATAAGGAGGTTATCAAAAATTTCATA-ATGTGGTTACCAAAATTTCATAGGAAGGTTAC
1 AATTTCATAAGGAGGTTATC-AAAATTTCATAGATGTGGTTACCAAAATTTCATAGG-AGGTTA-
*
75711 CAAA
63 TAAA
* * *
75715 AATTTCAT-AGAGTGGTTACCAAAATTTCATAGA-GTGGTTATCAAAATTTCATA-GAGTAGTTA
1 AATTTCATAAG-GAGGTTATCAAAATTTCATAGATGTGGTTACCAAAATTTCATAGGAG--GTTA
*
75777 TCAA
63 TAAA
75781 AATTTCA-AAGG
1 AATTTCATAAGG
75792 GAGATTTCAT
Statistics
Matches: 128, Mismatches: 9, Indels: 20
0.82 0.06 0.13
Matches are distributed among these distances:
65 3 0.02
66 14 0.11
67 61 0.48
68 20 0.16
69 19 0.15
70 11 0.09
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.33
Consensus pattern (66 bp):
AATTTCATAAGGAGGTTATCAAAATTTCATAGATGTGGTTACCAAAATTTCATAGGAGGTTATAA
A
Found at i:75875 original size:21 final size:21
Alignment explanation
Indices: 75851--76021 Score: 80
Period size: 22 Copynumber: 8.0 Consensus size: 21
75841 AAATTTATTT
*
75851 TGGAATAATCAAAATTTCATA
1 TGGAATTATCAAAATTTCATA
* *
75872 TGGAGGTTATGAAAATTTCATA
1 TGGA-ATTATCAAAATTTCATA
*
75894 TGAGGATTATCAAAATTTCATA
1 TG-GAATTATCAAAATTTCATA
** **
75916 -AAAAGGTTATTGAAATTTCATA
1 TGGAA--TTATCAAAATTTCATA
** * * *
75938 GTTTATTTTTCCAAATTTC--A
1 -TGGAATTATCAAAATTTCATA
75958 TGGAAGTTATCAAAATTTCATA
1 TGGAA-TTATCAAAATTTCATA
** * *
75980 GTTTATTTTTCAAAATTTCAT-
1 -TGGAATTATCAAAATTTCATA
* *
76001 GGGAGTTATCAAAATTTCATA
1 TGGAATTATCAAAATTTCATA
76022 GTATGTAGAT
Statistics
Matches: 108, Mismatches: 31, Indels: 22
0.67 0.19 0.14
Matches are distributed among these distances:
19 2 0.02
20 28 0.26
21 4 0.04
22 70 0.65
23 3 0.03
24 1 0.01
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.40
Consensus pattern (21 bp):
TGGAATTATCAAAATTTCATA
Found at i:75888 original size:22 final size:21
Alignment explanation
Indices: 75861--75937 Score: 84
Period size: 22 Copynumber: 3.5 Consensus size: 21
75851 TGGAATAATC
75861 AAAATTTCATATGGAGGTTATG
1 AAAATTTCATAT-GAGGTTATG
*
75883 AAAATTTCATATGAGGATTATC
1 AAAATTTCATATGAGG-TTATG
**
75905 AAAATTTCATAAAAAGGTTATTG
1 AAAATTTCAT-ATGAGGTTA-TG
75928 -AAATTTCATA
1 AAAATTTCATA
75938 GTTTATTTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
21 5 0.10
22 38 0.79
23 5 0.10
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.36
Consensus pattern (21 bp):
AAAATTTCATATGAGGTTATG
Found at i:75953 original size:22 final size:22
Alignment explanation
Indices: 75928--76000 Score: 87
Period size: 22 Copynumber: 3.4 Consensus size: 22
75918 AAGGTTATTG
*
75928 AAATTTCATAGTTTATTTTTCC
1 AAATTTCATAGTTTATTTTTCA
** * *
75950 AAATTTCAT-G-GAAGTTATCA
1 AAATTTCATAGTTTATTTTTCA
75970 AAATTTCATAGTTTATTTTTCA
1 AAATTTCATAGTTTATTTTTCA
75992 AAATTTCAT
1 AAATTTCAT
76001 GGGAGTTATC
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
20 14 0.35
21 2 0.05
22 24 0.60
ACGTcount: A:0.34, C:0.11, G:0.07, T:0.48
Consensus pattern (22 bp):
AAATTTCATAGTTTATTTTTCA
Found at i:75975 original size:20 final size:20
Alignment explanation
Indices: 75950--76020 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
75940 TTATTTTTCC
75950 AAATTTCATGGAAGTTATCA
1 AAATTTCATGGAAGTTATCA
** * *
75970 AAATTTCATAGTTTATTTTTCA
1 AAATTTCAT-G-GAAGTTATCA
*
75992 AAATTTCATGGGAGTTATCA
1 AAATTTCATGGAAGTTATCA
76012 AAATTTCAT
1 AAATTTCAT
76021 AGTATGTAGA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
20 24 0.59
21 2 0.05
22 15 0.37
ACGTcount: A:0.37, C:0.10, G:0.11, T:0.42
Consensus pattern (20 bp):
AAATTTCATGGAAGTTATCA
Found at i:75980 original size:42 final size:42
Alignment explanation
Indices: 75928--76023 Score: 174
Period size: 42 Copynumber: 2.3 Consensus size: 42
75918 AAGGTTATTG
*
75928 AAATTTCATAGTTTATTTTTCCAAATTTCATGGAAGTTATCA
1 AAATTTCATAGTTTATTTTTCAAAATTTCATGGAAGTTATCA
*
75970 AAATTTCATAGTTTATTTTTCAAAATTTCATGGGAGTTATCA
1 AAATTTCATAGTTTATTTTTCAAAATTTCATGGAAGTTATCA
76012 AAATTTCATAGT
1 AAATTTCATAGT
76024 ATGTAGATCA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.45
Consensus pattern (42 bp):
AAATTTCATAGTTTATTTTTCAAAATTTCATGGAAGTTATCA
Found at i:76035 original size:42 final size:42
Alignment explanation
Indices: 75950--76041 Score: 130
Period size: 42 Copynumber: 2.2 Consensus size: 42
75940 TTATTTTTCC
* ***
75950 AAATTTCATGGAAGTTATCAAAATTTCATAGTTTATTTTTCA
1 AAATTTCATGGAAGTTATCAAAATTTCATAGTATATAGATCA
* *
75992 AAATTTCATGGGAGTTATCAAAATTTCATAGTATGTAGATCA
1 AAATTTCATGGAAGTTATCAAAATTTCATAGTATATAGATCA
76034 AAATTTCA
1 AAATTTCA
76042 CATATAGGGA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (42 bp):
AAATTTCATGGAAGTTATCAAAATTTCATAGTATATAGATCA
Found at i:76116 original size:16 final size:18
Alignment explanation
Indices: 76095--76139 Score: 67
Period size: 16 Copynumber: 2.6 Consensus size: 18
76085 TATAAAGGAA
76095 GTTATCAAAATTT-TT-G
1 GTTATCAAAATTTATTAG
76111 GTTATCAAAATTTATTAAG
1 GTTATCAAAATTTATT-AG
76130 GTTATCAAAA
1 GTTATCAAAA
76140 AATTTTAGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
16 13 0.50
17 2 0.08
19 11 0.42
ACGTcount: A:0.40, C:0.07, G:0.11, T:0.42
Consensus pattern (18 bp):
GTTATCAAAATTTATTAG
Found at i:76256 original size:22 final size:22
Alignment explanation
Indices: 76178--76246 Score: 75
Period size: 22 Copynumber: 3.1 Consensus size: 22
76168 TAGGAAGGTT
** * *
76178 TTATCAAAATTTTACGATGAGA
1 TTATCAAAATTTCGCAATGTGA
* * *
76200 TTATCACAATTTCGTAGTGTGA
1 TTATCAAAATTTCGCAATGTGA
76222 TTATCAAAATTTCGCAATGTGA
1 TTATCAAAATTTCGCAATGTGA
76244 TTA
1 TTA
76247 CTAACATTTC
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Consensus pattern (22 bp):
TTATCAAAATTTCGCAATGTGA
Found at i:76323 original size:22 final size:22
Alignment explanation
Indices: 76293--76531 Score: 215
Period size: 22 Copynumber: 10.9 Consensus size: 22
76283 TATAACAGGG
*
76293 AGGTTATCAAAATTTCATAGTGT
1 AGGTTATCAAAATTTCATAG-GA
76316 A-GTTATCAAAATTTCATTAGG-
1 AGGTTATCAAAATTTCA-TAGGA
*
76337 AGGTTATCAAAATTCCATAGTG-
1 AGGTTATCAAAATTTCATAG-GA
* * *
76359 AGGTTTTCAAAATTCCATAGGG
1 AGGTTATCAAAATTTCATAGGA
* *
76381 ATGTTAACAAAAATTTCATAGGA
1 AGGTTATC-AAAATTTCATAGGA
* *
76404 ATGTTAACAAAATTTCATAGGA
1 AGGTTATCAAAATTTCATAGGA
* *
76426 AGGTTCTCAAAATTTTATAGGA
1 AGGTTATCAAAATTTCATAGGA
* *
76448 AGGCTATCAAAATTTTATAAGG-
1 AGGTTATCAAAATTTCAT-AGGA
76470 AGGTTATCAAAATTTCAGT-GTG-
1 AGGTTATCAAAATTTCA-TAG-GA
*
76492 A--TTATCATAATTTCATAGGAA
1 AGGTTATCAAAATTTCATAGG-A
*
76513 AGGTTATCATAATTTCATA
1 AGGTTATCAAAATTTCATA
76532 ATATAGTTAT
Statistics
Matches: 187, Mismatches: 16, Indels: 26
0.82 0.07 0.11
Matches are distributed among these distances:
19 2 0.01
20 14 0.07
21 7 0.04
22 120 0.64
23 44 0.24
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.35
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATAGGA
Found at i:76481 original size:89 final size:88
Alignment explanation
Indices: 76291--76486 Score: 227
Period size: 89 Copynumber: 2.2 Consensus size: 88
76281 AGTATAACAG
* *
76291 GGAGGTTATCAAAATTTCATAGTGTAGTTATCAAAATTTCATTAGGAGGTTATCAAAATTCCATA
1 GGAGGTTATCAAAATTTCATAGTGAAGTTAACAAAATTTCATTAGGAGGTTATCAAAATTCCATA
* * *
76356 GTGAGGTTTTCAAAATTCCATAG
66 GTGAGGCTATCAAAATTCCATAA
* * * **
76379 GGATGTTAACAAAAATTTCATAG-GAATGTTAACAAAATTTCA-TAGGAAGGTTCTCAAAATTTT
1 GGAGGTTATC-AAAATTTCATAGTGAA-GTTAACAAAATTTCATTAGG-AGGTTATCAAAATTCC
**
76442 ATAG-GAAGGCTATCAAAATTTTATAA
63 ATAGTG-AGGCTATCAAAATTCCATAA
76468 GGAGGTTATCAAAATTTCA
1 GGAGGTTATCAAAATTTCA
76487 GTGTGATTAT
Statistics
Matches: 90, Mismatches: 14, Indels: 8
0.80 0.12 0.07
Matches are distributed among these distances:
88 24 0.27
89 66 0.73
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.34
Consensus pattern (88 bp):
GGAGGTTATCAAAATTTCATAGTGAAGTTAACAAAATTTCATTAGGAGGTTATCAAAATTCCATA
GTGAGGCTATCAAAATTCCATAA
Found at i:98605 original size:210 final size:212
Alignment explanation
Indices: 98188--98605 Score: 768
Period size: 212 Copynumber: 2.0 Consensus size: 212
98178 ACCCTTTTTT
**
98188 AATTTTAAAATTTTAGTTATATTTTTAAGGGTTAATATGTAATCTAATACTATCTCTTTTAATTT
1 AATTTTAAAATTTTAACTATATTTTTAAGGGTTAATATGTAATCTAATACTATCTCTTTTAATTT
*
98253 TAAAATTAATGCAATCAAAACCACGTTAAGCATCTTATTATTATAATAATATATATTAAGCTTCT
66 TAAAATTAATGCAATCAAAACCACGTTAAGCATCTTATTATTATAAT-ATATATATTAAACTTCT
98318 TATTATTATAAAATAATTAGTAGTAGTAAAATTGTTATTAGTTATAAACTTCTTTTTGTCGAGAA
130 TATTATTATAAAATAATTAGTAGTAGTAAAATTGTTATTAGTTATAAACTTCTTTTTGTCGAGAA
98383 AATATTTTGAAATTCATA
195 AATATTTTGAAATTCATA
98401 AATTTTAAAA-TTTAACTATATTTTTAAGGGTTAATATGTAATCTAATACTATCTCTTTTAATTT
1 AATTTTAAAATTTTAACTATATTTTTAAGGGTTAATATGTAATCTAATACTATCTCTTTTAATTT
* *
98465 TAAAATTAATGCAATCAAAACCACGTTAAGCGTCTTATTGTTATAAT-TATATATTAAACTTCTT
66 TAAAATTAATGCAATCAAAACCACGTTAAGCATCTTATTATTATAATATATATATTAAACTTCTT
98529 ATTATTATAAAATAATTAGTAGTAGTAAAATTGTTATTAGTTATAAACTTCTTTTTGTCGAGAAA
131 ATTATTATAAAATAATTAGTAGTAGTAAAATTGTTATTAGTTATAAACTTCTTTTTGTCGAGAAA
98594 ATATTTTGAAAT
196 ATATTTTGAAAT
98606 ATTTTGAAAT
Statistics
Matches: 200, Mismatches: 5, Indels: 3
0.96 0.02 0.01
Matches are distributed among these distances:
210 93 0.47
212 97 0.49
213 10 0.05
ACGTcount: A:0.39, C:0.08, G:0.09, T:0.44
Consensus pattern (212 bp):
AATTTTAAAATTTTAACTATATTTTTAAGGGTTAATATGTAATCTAATACTATCTCTTTTAATTT
TAAAATTAATGCAATCAAAACCACGTTAAGCATCTTATTATTATAATATATATATTAAACTTCTT
ATTATTATAAAATAATTAGTAGTAGTAAAATTGTTATTAGTTATAAACTTCTTTTTGTCGAGAAA
ATATTTTGAAATTCATA
Done.