Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006369.1 Corchorus capsularis cultivar CVL-1 contig06390, 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: 96884
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:2039 original size:51 final size:52
Alignment explanation
Indices: 1963--2062 Score: 159
Period size: 51 Copynumber: 1.9 Consensus size: 52
1953 CTGAGGACTC
*
1963 TGCTGGATGCGTGCTCTTCCTGGAGACCCAGGACGT-GAGGCTGCTATTCCT
1 TGCTGGATGCGTGCTCTGCCTGGAGACCCAGGACGTGGAGGCTGCTATTCCT
*
2014 TGCTGGATG-GATGCTCTGCCTGGAGACCTAGGACGTGGAGGCTGCTATT
1 TGCTGGATGCG-TGCTCTGCCTGGAGACCCAGGACGTGGAGGCTGCTATT
2063 GGCAAGGCGG
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
50 1 0.02
51 32 0.71
52 12 0.27
ACGTcount: A:0.15, C:0.24, G:0.34, T:0.27
Consensus pattern (52 bp):
TGCTGGATGCGTGCTCTGCCTGGAGACCCAGGACGTGGAGGCTGCTATTCCT
Found at i:13455 original size:19 final size:19
Alignment explanation
Indices: 13431--13468 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
13421 AATGCCCTTA
13431 TTTAAACTATTGTAGTTTT
1 TTTAAACTATTGTAGTTTT
13450 TTTAAACTATTGTAGTTTT
1 TTTAAACTATTGTAGTTTT
13469 ATTCTACTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.05, G:0.11, T:0.58
Consensus pattern (19 bp):
TTTAAACTATTGTAGTTTT
Found at i:13615 original size:22 final size:21
Alignment explanation
Indices: 13590--13640 Score: 50
Period size: 22 Copynumber: 2.3 Consensus size: 21
13580 TAATATACAG
13590 TTTTATTCTAATAAAAATTC-TA
1 TTTTATT-TAAT-AAAATTCATA
*
13612 TTTTCATTTAATTAAATTCAATA
1 TTTT-ATTTAATAAAATTC-ATA
13635 TTTTAT
1 TTTTAT
13641 AATTATTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
21 6 0.24
22 10 0.40
23 9 0.36
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTTATTTAATAAAATTCATA
Found at i:15248 original size:22 final size:21
Alignment explanation
Indices: 14906--15504 Score: 157
Period size: 22 Copynumber: 26.8 Consensus size: 21
14896 ATCTCTATGT
*
14906 GGTTATCAAAATTTTCATAAGAT
1 GGTTATCAAAA-TTTCAT-AGAA
* ** *
14929 GGTTATTATGATTTCATGAGGA
1 GGTTATCAAAATTTCAT-AGAA
**
14951 GGTTATCAAAA-TTCAATAGTGT
1 GGTTATCAAAATTTC-ATAG-AA
*
14973 GGTTA-CCAAATTCTCATATGGAA
1 GGTTATCAAAATT-TCATA--GAA
*
14996 -GTTATCAAAATTTCATACTG-T
1 GGTTATCAAAATTTCATA--GAA
* *
15017 GGTTACCAAAATTTCTTAGGATCA
1 GGTTATCAAAATTTCATA-GA--A
* * **
15041 GGTTATTAAAATTTCTTAGGTT
1 GGTTATCAAAATTTCATA-GAA
** **
15063 GGTTATTGAAATTTCATAGGGT
1 GGTTATCAAAATTTCATA-GAA
* * *
15085 GGTTAATTATCACAATTTTATATAAA
1 GG----TTATCAAAATTTCATA-GAA
* *
15111 GGTTATCAAAATGTCATAGCTA
1 GGTTATCAAAATTTCATAG-AA
* *
15133 GG-TACTAAAAATTTCATAGTAT
1 GGTTA-TCAAAATTTCATAG-AA
* *
15155 GGTAAACAAAATTTCATCACG-A
1 GGTTATCAAAATTTCAT-A-GAA
* *
15177 GGTTA-CAAATATTTCATGGGGA
1 GGTTATCAAA-ATTTCAT-AGAA
* *
15199 GGTTATCAAAATTTTATAG-T
1 GGTTATCAAAATTTCATAGAA
15219 GTGATTATCAAAATTTCATATGAA
1 G-G-TTATCAAAATTTCATA-GAA
* *
15243 GGTTAT-AAAAGTCTCATTTTCATAA
1 GGTTATCAAAA-TTTCA---T-AGAA
* * *
15268 GGAGTACCAAAATTTGATAGAA
1 GG-TTATCAAAATTTCATAGAA
*
15290 GGTTATC-AAATCTCATAG-A
1 GGTTATCAAAATTTCATAGAA
*
15309 GTGATTATCGAAATTTCATAGAGA
1 G-G-TTATCAAAATTTCATAGA-A
15333 TCGGATTATCAAAATTT-ATAGAAA
1 --GG-TTATCAAAATTTCATAG-AA
* *
15357 GATTATCAAAATTTCATAG-T
1 GGTTATCAAAATTTCATAGAA
* *
15377 GTTGTTATCAAAATTTCAAAGCGA
1 G--GTTATCAAAATTTCATAG-AA
* *
15401 GGTTATCAAAATTACATA-AT
1 GGTTATCAAAATTTCATAGAA
*
15421 GTGATTATCAGAAA-TTCATAGAGG
1 G-G-TTATCA-AAATTTCATAGA-A
* * * *
15445 GGTCAACAAAATTTTATAAAAA
1 GGTTATCAAAATTTCAT-AGAA
*
15467 GGTTATCAAAATTTCATAAAGA
1 GGTTATCAAAATTTCATAGA-A
*
15489 GGTTATCAAATTTTCA
1 GGTTATCAAAATTTCA
15505 AAATGTGATT
Statistics
Matches: 430, Mismatches: 91, Indels: 111
0.68 0.14 0.18
Matches are distributed among these distances:
19 2 0.00
20 13 0.03
21 50 0.12
22 260 0.60
23 32 0.07
24 29 0.07
25 19 0.04
26 21 0.05
27 4 0.01
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (21 bp):
GGTTATCAAAATTTCATAGAA
Found at i:15429 original size:44 final size:44
Alignment explanation
Indices: 15336--15526 Score: 158
Period size: 44 Copynumber: 4.4 Consensus size: 44
15326 ATAGAGATCG
* * * *
15336 GATTATCAAAATTT-ATAGAAAGATTATCAAAATTTCATAGTGTT
1 GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATG-T
* *
15380 G-TTATCAAAATTTCAAAGCGAGGTTATCAAAATTACATAATGT
1 GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGT
* * * * * ***
15423 GATTATCAGAAA-TTCATAGAGGGGTCAACAAAATTTTATAAAAA
1 GATTATCA-AAATTTCAAAGAGAGGTTATCAAAATTTCATAATGT
* * *
15467 GGTTATCAAAATTTCATAA-AGAGGTTATCAAATTTTCAAAATGT
1 GATTATCAAAATTTCA-AAGAGAGGTTATCAAAATTTCATAATGT
15511 GATTA-CAAAAATTTCA
1 GATTATC-AAAATTTCA
15527 TAGTGGTATT
Statistics
Matches: 113, Mismatches: 28, Indels: 12
0.74 0.18 0.08
Matches are distributed among these distances:
43 18 0.16
44 91 0.81
45 4 0.04
ACGTcount: A:0.44, C:0.09, G:0.13, T:0.34
Consensus pattern (44 bp):
GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGT
Found at i:15571 original size:22 final size:22
Alignment explanation
Indices: 15545--15878 Score: 120
Period size: 22 Copynumber: 15.7 Consensus size: 22
15535 TTTCTGGGGA
15545 GGTTATCAAAATTTCATAGTAT
1 GGTTATCAAAATTTCATAGTAT
* * *
15567 GGTTA-CCAAA--T--TAGGAA
1 GGTTATCAAAATTTCATAGTAT
* * *
15584 GGTTATTAAACTTT--TATTAT
1 GGTTATCAAAATTTCATAGTAT
* * *
15604 GGAGTAATCAAAATTTCA-AGGAG
1 GG-TTA-TCAAAATTTCATAGTAT
* *
15627 GGATATCAAAATTTCATA-TGAA
1 GGTTATCAAAATTTCATAGT-AT
*
15649 GGTTATCAAAATTTCATAGTTT
1 GGTTATCAAAATTTCATAGTAT
* * * *
15671 AGTTTTCAAAATGTCATAAG-AG
1 GGTTATCAAAATTTCAT-AGTAT
15693 GGTTATCAAAATTTCATAGTAT
1 GGTTATCAAAATTTCATAGTAT
* *
15715 -GTAGATCAAAATTTCATAGGGA-
1 GGT-TATCAAAATTTCATA-GTAT
* *
15737 GATTAACAAAATTTCATA--AT
1 GGTTATCAAAATTTCATAGTAT
* *
15757 GAGATTATCAAAA-ATCATAGGGA-
1 G-G-TTATCAAAATTTCATA-GTAT
15780 GGTTATCAAAA-TT--T-GTA-
1 GGTTATCAAAATTTCATAGTAT
* *
15797 -GTTATCAAGATTTCATAAG-AA
1 GGTTATCAAAATTTCAT-AGTAT
* * * *
15818 AGTTATCAAAATTTTATAGGAA
1 GGTTATCAAAATTTCATAGTAT
* *
15840 GATTTATCAAAATTTCATAGTGT
1 G-GTTATCAAAATTTCATAGTAT
* *
15863 GATAATCAAAATTTCA
1 GGTTATCAAAATTTCA
15879 GAGTGTGTGA
Statistics
Matches: 231, Mismatches: 51, Indels: 60
0.68 0.15 0.18
Matches are distributed among these distances:
16 9 0.04
17 13 0.06
18 2 0.01
19 4 0.02
20 8 0.03
21 39 0.17
22 127 0.55
23 28 0.12
24 1 0.00
ACGTcount: A:0.41, C:0.09, G:0.16, T:0.35
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAGTAT
Found at i:15706 original size:66 final size:64
Alignment explanation
Indices: 15578--15878 Score: 224
Period size: 66 Copynumber: 4.7 Consensus size: 64
15568 GTTACCAAAT
* * * * * * *
15578 TAGGAAGGTTATTAAACTTTTATTATGGAGTAATCAAAATTTCA-AGGAGGGATATCAAAATTTC
1 TAGGAAGGTTATCAAAATTTCA-TA-GTAGTTATCAAAATTTCATAAGAGGGTTATCAAAATTTC
15642 A
64 A
* * *
15643 TATGAAGGTTATCAAAATTTCATAGTTTAGTTTTCAAAATGTCATAAGAGGGTTATCAAAATTTC
1 TAGGAAGGTTATCAAAATTTCATAG--TAGTTATCAAAATTTCATAAGAGGGTTATCAAAATTTC
15708 A
64 A
* * * * * * *
15709 TA-GTATGTAGATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATGA-GATTATCAAAA-A
1 TAGGAAGGT-TATCAAAATTTCATA-GTAG-TTATCAAAATTTCATAA-GAGGGTTATCAAAATT
15771 TCA
62 TCA
* * ** *
15774 TAGGGAGGTTATCAAAA-TT--T-GTAGTTATCAAGATTTCATAAGAAAGTTATCAAAATTTTA
1 TAGGAAGGTTATCAAAATTTCATAGTAGTTATCAAAATTTCATAAGAGGGTTATCAAAATTTCA
*
15834 TAGGAAGATTTATCAAAATTTCATAGT-GTGATAATCAAAATTTCA
1 TAGGAAG-GTTATCAAAATTTCATAGTAGT--T-ATCAAAATTTCA
15879 GAGTGTGTGA
Statistics
Matches: 186, Mismatches: 32, Indels: 34
0.74 0.13 0.13
Matches are distributed among these distances:
58 2 0.01
59 24 0.13
60 11 0.06
61 9 0.05
62 3 0.02
63 1 0.01
64 7 0.04
65 51 0.27
66 64 0.34
67 14 0.08
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.35
Consensus pattern (64 bp):
TAGGAAGGTTATCAAAATTTCATAGTAGTTATCAAAATTTCATAAGAGGGTTATCAAAATTTCA
Found at i:15846 original size:23 final size:22
Alignment explanation
Indices: 15610--15859 Score: 135
Period size: 22 Copynumber: 11.7 Consensus size: 22
15600 TTATGGAGTA
** *
15610 ATCAAAATTTCA-AGGAGGGAT
1 ATCAAAATTTCATAGGAAAGTT
* *
15631 ATCAAAATTTCATATGAAGGTT
1 ATCAAAATTTCATAGGAAAGTT
***
15653 ATCAAAATTTCATAGTTTAGTT
1 ATCAAAATTTCATAGGAAAGTT
* * * **
15675 TTCAAAATGTCATAAGAGGGTT
1 ATCAAAATTTCATAGGAAAGTT
* * *
15697 ATCAAAATTTCATA-GTATGTAG
1 ATCAAAATTTCATAGGAAAGT-T
*
15719 ATCAAAATTTCATAGG-GAGATT
1 ATCAAAATTTCATAGGAAAG-TT
* * *
15741 AACAAAATTTCATAATGAGA-TT
1 ATCAAAATTTCAT-AGGAAAGTT
* * *
15763 ATCAAAA-ATCATAGGGAGGTT
1 ATCAAAATTTCATAGGAAAGTT
*
15784 ATCAAAA-TT--T--G-TAGTT
1 ATCAAAATTTCATAGGAAAGTT
* *
15800 ATCAAGATTTCATAAGAAAGTT
1 ATCAAAATTTCATAGGAAAGTT
* *
15822 ATCAAAATTTTATAGGAAGATTT
1 ATCAAAATTTCATAGGAA-AGTT
15845 ATCAAAATTTCATAG
1 ATCAAAATTTCATAG
15860 TGTGATAATC
Statistics
Matches: 173, Mismatches: 42, Indels: 26
0.72 0.17 0.11
Matches are distributed among these distances:
16 9 0.05
17 3 0.02
19 2 0.01
20 2 0.01
21 30 0.17
22 104 0.60
23 21 0.12
24 2 0.01
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.34
Consensus pattern (22 bp):
ATCAAAATTTCATAGGAAAGTT
Found at i:16178 original size:22 final size:22
Alignment explanation
Indices: 16150--16193 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
16140 GATCATAAAA
16150 AATAGTGTA-ATTATCATAATTT
1 AATAGTG-AGATTATCATAATTT
*
16172 AATAGTGAGGTTATCATAATTT
1 AATAGTGAGATTATCATAATTT
16194 CATATGAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.39, C:0.05, G:0.14, T:0.43
Consensus pattern (22 bp):
AATAGTGAGATTATCATAATTT
Found at i:17384 original size:3 final size:3
Alignment explanation
Indices: 17376--17434 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
17366 AATTAATTAT
17376 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
17424 ATA ATA ATA AT
1 ATA ATA ATA AT
17435 TCTCTTTGAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:18293 original size:15 final size:16
Alignment explanation
Indices: 18275--18308 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
18265 AACAATTGAC
18275 TTTATTATTTA-TATT
1 TTTATTATTTAGTATT
*
18290 TTTATTGTTTAGTATT
1 TTTATTATTTAGTATT
18306 TTT
1 TTT
18309 TTCTTACAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.74
Consensus pattern (16 bp):
TTTATTATTTAGTATT
Found at i:21824 original size:38 final size:39
Alignment explanation
Indices: 21766--21846 Score: 121
Period size: 38 Copynumber: 2.1 Consensus size: 39
21756 TTTAGCCATT
*
21766 ATTATACTATAATATTAAGGGTATTTTA-GTAATTGACTA
1 ATTATACAATAATATTAAGGGTA-TTTACGTAATTGACTA
*
21805 ATTATACAAT-ATTTTAAGGGTATTTACGTAATTGACTA
1 ATTATACAATAATATTAAGGGTATTTACGTAATTGACTA
21843 ATTA
1 ATTA
21847 AGATTTTTGA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
37 4 0.10
38 26 0.67
39 9 0.23
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.43
Consensus pattern (39 bp):
ATTATACAATAATATTAAGGGTATTTACGTAATTGACTA
Found at i:21878 original size:5 final size:5
Alignment explanation
Indices: 21868--21912 Score: 76
Period size: 5 Copynumber: 9.4 Consensus size: 5
21858 TTCGTAGTAC
21868 TAAGA TAAGA TAAGA T-AG- TAAGA TAAGA TAAGA TAAGA TAAGA TA
1 TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TA
21913 TAATGAAGTG
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
3 1 0.03
4 4 0.11
5 33 0.87
ACGTcount: A:0.58, C:0.00, G:0.20, T:0.22
Consensus pattern (5 bp):
TAAGA
Found at i:34278 original size:31 final size:31
Alignment explanation
Indices: 34237--34302 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
34227 AACATTATAT
* *
34237 TTTCCGATTGTACCCTTATT-TTTAAAACATA
1 TTTCCAATTGTACCCTT-TTCCTTAAAACATA
34268 TTTCCAATTGTACCCTTTTCCTTAAAACATA
1 TTTCCAATTGTACCCTTTTCCTTAAAACATA
34299 TTTC
1 TTTC
34303 TAAATTCCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 2 0.06
31 30 0.94
ACGTcount: A:0.27, C:0.23, G:0.05, T:0.45
Consensus pattern (31 bp):
TTTCCAATTGTACCCTTTTCCTTAAAACATA
Found at i:34863 original size:22 final size:21
Alignment explanation
Indices: 34809--34893 Score: 80
Period size: 22 Copynumber: 3.9 Consensus size: 21
34799 CTCTATGTGA
**
34809 TTATCAAAATTTCATAAAATGG
1 TTATCAAAATTTCATAGGA-GG
* *
34831 TTATTATAATTTCATGAGGAGG
1 TTATCAAAATTTCAT-AGGAGG
* *
34853 TTATCAAAATTCCATAGTGTGG
1 TTATCAAAATTTCATAG-GAGG
*
34875 TTACCAAAATTTCATAGGA
1 TTATCAAAATTTCATAGGA
34894 TCGGGTTAGT
Statistics
Matches: 50, Mismatches: 11, Indels: 5
0.76 0.17 0.08
Matches are distributed among these distances:
21 3 0.06
22 45 0.90
23 2 0.04
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (21 bp):
TTATCAAAATTTCATAGGAGG
Found at i:34907 original size:24 final size:22
Alignment explanation
Indices: 34858--34938 Score: 56
Period size: 22 Copynumber: 3.6 Consensus size: 22
34848 GGAGGTTATC
* **
34858 AAAATTCCATA-GTGTGGTTACC
1 AAAATTTCATAGGTG-GGTTAGT
34880 AAAATTTCATAGGATCGGGTTAGT
1 AAAATTTCATAGG-T-GGGTTAGT
* * * *
34904 AAAATCTCTTAGGTTGGTTATT
1 AAAATTTCATAGGTGGGTTAGT
*
34926 GAAATTTCATAGG
1 AAAATTTCATAGG
34939 GTGGTTAATT
Statistics
Matches: 46, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
22 26 0.57
23 2 0.04
24 17 0.37
25 1 0.02
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.36
Consensus pattern (22 bp):
AAAATTTCATAGGTGGGTTAGT
Found at i:35026 original size:22 final size:22
Alignment explanation
Indices: 34985--35039 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
34975 AAGAGATTAT
*
34985 CAAAATGTCATAGCGAGGTT-A
1 CAAAATTTCATAGCGAGGTTGA
* * *
35006 TAAGAATTTCATAGTGTGGTTGA
1 CAA-AATTTCATAGCGAGGTTGA
35029 CAAAATTTCAT
1 CAAAATTTCAT
35040 TAAATATTTC
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
21 2 0.07
22 22 0.81
23 3 0.11
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.33
Consensus pattern (22 bp):
CAAAATTTCATAGCGAGGTTGA
Found at i:35104 original size:22 final size:23
Alignment explanation
Indices: 35041--35110 Score: 69
Period size: 22 Copynumber: 3.1 Consensus size: 23
35031 AAATTTCATT
35041 AAATATTTCAT-TGAGAGGTTATCA
1 AAAT-TTTCATATGA-AGGTTATCA
*
35065 AAATTTT-ATAGTG-TGGTTATC-
1 AAATTTTCATA-TGAAGGTTATCA
35086 AAATTTTCATATGAAGGTTAT-A
1 AAATTTTCATATGAAGGTTATCA
35108 AAA
1 AAA
35111 GTCTCAATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
21 9 0.23
22 21 0.54
23 3 0.08
24 6 0.15
ACGTcount: A:0.39, C:0.06, G:0.16, T:0.40
Consensus pattern (23 bp):
AAATTTTCATATGAAGGTTATCA
Found at i:35163 original size:20 final size:23
Alignment explanation
Indices: 35140--35233 Score: 76
Period size: 21 Copynumber: 4.3 Consensus size: 23
35130 TACCAAACTT
35140 TCATAGAAG-G-TTATC-AAATC
1 TCATAGAAGTGATTATCAAAATC
*
35160 TCATAG-AGTGATTATCAAAATT
1 TCATAGAAGTGATTATCAAAATC
35182 TCATAG-AGTTCGGATTATCAAAAT-
1 TCATAGAAG-T--GATTATCAAAATC
* * *
35206 TTATAGAA-AGATTATCAAAATT
1 TCATAGAAGTGATTATCAAAATC
35228 TCATAG
1 TCATAG
35234 TGTTGTTATC
Statistics
Matches: 62, Mismatches: 4, Indels: 14
0.77 0.05 0.17
Matches are distributed among these distances:
19 2 0.03
20 7 0.11
21 17 0.27
22 17 0.27
23 1 0.02
24 5 0.08
25 13 0.21
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.34
Consensus pattern (23 bp):
TCATAGAAGTGATTATCAAAATC
Found at i:35185 original size:22 final size:22
Alignment explanation
Indices: 35133--35387 Score: 152
Period size: 22 Copynumber: 11.6 Consensus size: 22
35123 TAAGGGGTAC
*
35133 CAAACTTTCATAGAAG-G-TTAT
1 CAAAATTTCATAG-AGTGATTAT
*
35154 C-AAATCTCATAGAGTGATTAT
1 CAAAATTTCATAGAGTGATTAT
35175 CAAAATTTCATAGAGTTCGGATTAT
1 CAAAATTTCATAGAG-T--GATTAT
**
35200 CAAAATTT-ATAGAAAGATTAT
1 CAAAATTTCATAGAGTGATTAT
*
35221 CAAAATTTCATAGTGTTG-TTAT
1 CAAAATTTCATAGAG-TGATTAT
*
35243 CAAAATTTCAAAACGAG-G-TTAT
1 CAAAATTTC-ATA-GAGTGATTAT
* *
35265 CAAAATTACATA-ATGTGATTCT
1 CAAAATTTCATAGA-GTGATTAT
* * * * *
35287 CAGAATTTCATAGAGGGGTCAA
1 CAAAATTTCATAGAGTGATTAT
* * *
35309 CAAAATTTTATAAAGAGATTAT
1 CAAAATTTCATAGAGTGATTAT
* * * *
35331 AAAAATTTCATAAAGAGGTTAT
1 CAAAATTTCATAGAGTGATTAT
* *
35353 CAAATTTTCA-AAATGTGATTA-
1 CAAAATTTCATAGA-GTGATTAT
35374 CAAAAATTTCATAG
1 C-AAAATTTCATAG
35388 TGAATTTCTG
Statistics
Matches: 181, Mismatches: 36, Indels: 32
0.73 0.14 0.13
Matches are distributed among these distances:
19 3 0.02
20 11 0.06
21 27 0.15
22 113 0.62
23 6 0.03
24 7 0.04
25 14 0.08
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.34
Consensus pattern (22 bp):
CAAAATTTCATAGAGTGATTAT
Found at i:35524 original size:22 final size:20
Alignment explanation
Indices: 35470--35539 Score: 88
Period size: 19 Copynumber: 3.5 Consensus size: 20
35460 TGGAGTAATA
*
35470 AAAATTTCAAGGAGGATATC
1 AAAATTTCAAGAAGGATATC
*
35490 AAAA-TTCAAGAAGGATAAC
1 AAAATTTCAAGAAGGATATC
*
35509 AAAATTTCATATGAAGGTTATC
1 AAAATTTCA-A-GAAGGATATC
35531 AAAATTTCA
1 AAAATTTCA
35540 TAGTTTAGTT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
19 17 0.40
20 8 0.19
21 1 0.02
22 17 0.40
ACGTcount: A:0.49, C:0.10, G:0.14, T:0.27
Consensus pattern (20 bp):
AAAATTTCAAGAAGGATATC
Found at i:35540 original size:22 final size:22
Alignment explanation
Indices: 35470--35734 Score: 119
Period size: 22 Copynumber: 12.5 Consensus size: 22
35460 TGGAGTAATA
* *
35470 AAAATTTCA-A-GGAGGATATC
1 AAAATTTCATATGAAGGTTATC
* *
35490 AAAA-TTCA-A-GAAGGATAAC
1 AAAATTTCATATGAAGGTTATC
35509 AAAATTTCATATGAAGGTTATC
1 AAAATTTCATATGAAGGTTATC
** *
35531 AAAATTTCATAGTTTA-GTTTTC
1 AAAATTTCATA-TGAAGGTTATC
* * *
35553 AAAATTTCACAAGAGGGTTATC
1 AAAATTTCATATGAAGGTTATC
* * *
35575 AAAATTTCATA-GTATGTAGATC
1 AAAATTTCATATGAAGGT-TATC
* * * * *
35597 AAATTTTCATAGGTAGATTAAC
1 AAAATTTCATATGAAGGTTATC
35619 AAAATTTCATAATG-AGGTTATC
1 AAAATTTCAT-ATGAAGGTTATC
** * *
35641 AAAAAATCATAAGGAGGTTATC
1 AAAATTTCATATGAAGGTTATC
*
35663 -AAA-TT--T-TGTA-GTTATC
1 AAAATTTCATATGAAGGTTATC
* *
35679 AAGATTTCATAAG-AGGTTTATC
1 AAAATTTCATATGAAGG-TTATC
* * *
35701 AAAATTTTATAGGAAGATTTATC
1 AAAATTTCATATGAAG-GTTATC
*
35724 AAAACTTCATA
1 AAAATTTCATA
35735 GGTTATCACA
Statistics
Matches: 186, Mismatches: 41, Indels: 33
0.72 0.16 0.13
Matches are distributed among these distances:
16 6 0.03
17 4 0.02
18 3 0.02
19 17 0.09
20 11 0.06
21 11 0.06
22 110 0.59
23 24 0.13
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.34
Consensus pattern (22 bp):
AAAATTTCATATGAAGGTTATC
Found at i:35578 original size:66 final size:63
Alignment explanation
Indices: 35508--35742 Score: 196
Period size: 66 Copynumber: 3.7 Consensus size: 63
35498 AGAAGGATAA
* *
35508 CAAAATTTCATATGAAGGTTATCAAAATTTCATAGTTTAGTTTTCAAAATTTCACAAGAGGGTTA
1 CAAAATTTCATA-GAAGGTTATCAAAATTTCATAG--TAGTTATCAAAATTTCATAAGAGGGTTA
35573 T
63 T
* * * * *
35574 CAAAATTTCATAGTATGTAGATCAAATTTTCATAGGTAGATTAACAAAATTTCATAATGA-GGTT
1 CAAAATTTCATAGAAGGT-TATCAAAATTTCATA-GTAG-TTATCAAAATTTCATAA-GAGGGTT
35638 AT
62 AT
** * * *
35640 CAAAAAATCATAAGGAGGTTATC-AAATTT--T-GTAGTTATCAAGATTTCATAAGAGGTTTAT
1 CAAAATTTCAT-AGAAGGTTATCAAAATTTCATAGTAGTTATCAAAATTTCATAAGAGGGTTAT
* * *
35700 CAAAATTTTATAGGAAGATTTATCAAAACTTCATAG--GTTATCA
1 CAAAATTTCATA-GAAG-GTTATCAAAATTTCATAGTAGTTATCA
35743 CAATCATAGT
Statistics
Matches: 135, Mismatches: 22, Indels: 27
0.73 0.12 0.15
Matches are distributed among these distances:
59 3 0.02
60 31 0.23
61 9 0.07
62 5 0.04
63 8 0.06
64 1 0.01
65 13 0.10
66 57 0.42
67 8 0.06
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (63 bp):
CAAAATTTCATAGAAGGTTATCAAAATTTCATAGTAGTTATCAAAATTTCATAAGAGGGTTAT
Found at i:35821 original size:22 final size:22
Alignment explanation
Indices: 35796--35872 Score: 66
Period size: 22 Copynumber: 3.5 Consensus size: 22
35786 ATTTATATAA
*
35796 TTATCAATATATCATATGGAGG
1 TTATCAAAATATCATATGGAGG
* * **
35818 TTATCAACATCTCATAGTGTTGG
1 TTATCAAAATATCATA-TGGAGG
* *
35841 TTATCAAAATTTCATATTGAGG
1 TTATCAAAATATCATATGGAGG
35863 TCT-TCAAAAT
1 T-TATCAAAAT
35873 TCTTTAGGGA
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
22 25 0.57
23 19 0.43
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.39
Consensus pattern (22 bp):
TTATCAAAATATCATATGGAGG
Found at i:36117 original size:2 final size:2
Alignment explanation
Indices: 36110--36151 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
36100 TAAAACTAGA
*
36110 AT AT AT AT AT AT AT AT AT AT AT -T AT -T TT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36150 AT
1 AT
36152 TCTTATTCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
AT
Found at i:37547 original size:28 final size:29
Alignment explanation
Indices: 37513--37581 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
37503 ACTTGTTGCG
37513 TTTGGACGTTTACCCCATGAACTTC-ATT
1 TTTGGACGTTTACCCCATGAACTTCAATT
* * *
37541 TTTGGACATTTTGCCCCATGTACTTCAATT
1 TTTGGAC-GTTTACCCCATGAACTTCAATT
*
37571 TTGGGACGTTT
1 TTTGGACGTTT
37582 TAACCCCTCA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
28 7 0.21
29 18 0.53
30 9 0.26
ACGTcount: A:0.19, C:0.22, G:0.17, T:0.42
Consensus pattern (29 bp):
TTTGGACGTTTACCCCATGAACTTCAATT
Found at i:38193 original size:18 final size:18
Alignment explanation
Indices: 38166--38200 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
38156 GAGATGGTAT
*
38166 AAGTGTTCAAATTTACAA
1 AAGTGATCAAATTTACAA
*
38184 AAGTGATCAATTTTACA
1 AAGTGATCAAATTTACA
38201 TAAATCCATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.34
Consensus pattern (18 bp):
AAGTGATCAAATTTACAA
Found at i:40097 original size:40 final size:40
Alignment explanation
Indices: 40022--40102 Score: 110
Period size: 40 Copynumber: 2.0 Consensus size: 40
40012 GAAATTGGGG
* *
40022 AAACACAACCATGAAATGATGAATTATTATGATAAAGATA
1 AAACACAAACATGAAATAATGAATTATTATGATAAAGATA
* *
40062 AAACACAAACATG-AATAATGACTTATTAATTATAAAGATA
1 AAACACAAACATGAAATAATGAATTATT-ATGATAAAGATA
40102 A
1 A
40103 TAGCGCTAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
39 12 0.33
40 24 0.67
ACGTcount: A:0.54, C:0.10, G:0.10, T:0.26
Consensus pattern (40 bp):
AAACACAAACATGAAATAATGAATTATTATGATAAAGATA
Found at i:40523 original size:19 final size:19
Alignment explanation
Indices: 40499--40555 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
40489 TATTTTGTAT
40499 TCTTATTATGAAATTAATC
1 TCTTATTATGAAATTAATC
*
40518 TCTTATTTTG----T-AT-
1 TCTTATTATGAAATTAATC
40531 TCTTATTATGAAATTAATC
1 TCTTATTATGAAATTAATC
40550 TCTTAT
1 TCTTAT
40556 AGTGTATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 12
0.68 0.05 0.27
Matches are distributed among these distances:
13 9 0.30
14 2 0.07
15 1 0.03
17 1 0.03
18 2 0.07
19 15 0.50
ACGTcount: A:0.30, C:0.11, G:0.05, T:0.54
Consensus pattern (19 bp):
TCTTATTATGAAATTAATC
Found at i:40524 original size:32 final size:32
Alignment explanation
Indices: 40488--40555 Score: 136
Period size: 32 Copynumber: 2.1 Consensus size: 32
40478 TGCTTCTCAA
40488 TTATTTTGTATTCTTATTATGAAATTAATCTC
1 TTATTTTGTATTCTTATTATGAAATTAATCTC
40520 TTATTTTGTATTCTTATTATGAAATTAATCTC
1 TTATTTTGTATTCTTATTATGAAATTAATCTC
40552 TTAT
1 TTAT
40556 AGTGTATAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.28, C:0.09, G:0.06, T:0.57
Consensus pattern (32 bp):
TTATTTTGTATTCTTATTATGAAATTAATCTC
Found at i:40562 original size:32 final size:32
Alignment explanation
Indices: 40494--40562 Score: 120
Period size: 32 Copynumber: 2.2 Consensus size: 32
40484 TCAATTATTT
**
40494 TGTATTCTTATTATGAAATTAATCTCTTATTT
1 TGTATTCTTATTATGAAATTAATCTCTTATAG
40526 TGTATTCTTATTATGAAATTAATCTCTTATAG
1 TGTATTCTTATTATGAAATTAATCTCTTATAG
40558 TGTAT
1 TGTAT
40563 AAATATAAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.29, C:0.09, G:0.09, T:0.54
Consensus pattern (32 bp):
TGTATTCTTATTATGAAATTAATCTCTTATAG
Found at i:40690 original size:31 final size:31
Alignment explanation
Indices: 40652--40718 Score: 125
Period size: 31 Copynumber: 2.2 Consensus size: 31
40642 AAAATTGGTT
40652 GCTCACAAGTTGGGAAAAACAAAGACTAAAC
1 GCTCACAAGTTGGGAAAAACAAAGACTAAAC
40683 GCTCACAAGTTGGGAAAAACAAAGACTAAAC
1 GCTCACAAGTTGGGAAAAACAAAGACTAAAC
*
40714 ACTCA
1 GCTCA
40719 TTTTGTCCCC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.48, C:0.21, G:0.18, T:0.13
Consensus pattern (31 bp):
GCTCACAAGTTGGGAAAAACAAAGACTAAAC
Found at i:40803 original size:29 final size:28
Alignment explanation
Indices: 40741--40803 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 28
40731 AACTTGTAGC
** *
40741 ATTTGGATGTTTTGCCCCATGAACTTCA
1 ATTTGGACATTTTGCCCCATAAACTTCA
*
40769 ATTTTGGACATTTTGCCCCCTAAACTATCA
1 A-TTTGGACATTTTGCCCCATAAACT-TCA
40799 ATTTG
1 ATTTG
40804 TGCCTCCATT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
28 1 0.03
29 24 0.83
30 4 0.14
ACGTcount: A:0.24, C:0.22, G:0.14, T:0.40
Consensus pattern (28 bp):
ATTTGGACATTTTGCCCCATAAACTTCA
Found at i:44959 original size:33 final size:33
Alignment explanation
Indices: 44904--44971 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
44894 GAAGATTGTA
* *
44904 CAAAGACAATACAGAAGTTCTCACAAGGAGTCC
1 CAAAGACAATACAAAAGCTCTCACAAGGAGTCC
*
44937 CAAATACAATACAAAAGCTCTCACAAGGAGTCC
1 CAAAGACAATACAAAAGCTCTCACAAGGAGTCC
44970 CA
1 CA
44972 TATGCACATT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.44, C:0.26, G:0.15, T:0.15
Consensus pattern (33 bp):
CAAAGACAATACAAAAGCTCTCACAAGGAGTCC
Found at i:50267 original size:31 final size:30
Alignment explanation
Indices: 50169--50267 Score: 90
Period size: 31 Copynumber: 3.2 Consensus size: 30
50159 TTTTTTGGTA
* *
50169 CACGTGTCACTTTTTGTACATGTGACGTGACC
1 CACGTGTCACTTTTTGTACACGTGGCGTG--C
** * * *
50201 CATATGTCACTTTTTTTTACACGTTGCGTGA
1 CACGTGTCAC-TTTTTGTACACGTGGCGTGC
*
50232 CACGTGTCACTTTTTGGTACACGTGGCATGC
1 CACGTGTCACTTTTT-GTACACGTGGCGTGC
50263 CACGT
1 CACGT
50268 CGAACACCGT
Statistics
Matches: 52, Mismatches: 13, Indels: 5
0.74 0.19 0.07
Matches are distributed among these distances:
30 5 0.10
31 24 0.46
32 8 0.15
33 15 0.29
ACGTcount: A:0.18, C:0.24, G:0.21, T:0.36
Consensus pattern (30 bp):
CACGTGTCACTTTTTGTACACGTGGCGTGC
Found at i:50511 original size:31 final size:31
Alignment explanation
Indices: 50476--50537 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
50466 AAAGTCATTA
* *
50476 ATGAATATTGTGATTATTCATGAATCAAGAG
1 ATGAATATCGTAATTATTCATGAATCAAGAG
50507 ATGAATATCGTAATTATTCATGAATCAAGAG
1 ATGAATATCGTAATTATTCATGAATCAAGAG
50538 TTCTCTCGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.40, C:0.08, G:0.18, T:0.34
Consensus pattern (31 bp):
ATGAATATCGTAATTATTCATGAATCAAGAG
Found at i:51028 original size:19 final size:19
Alignment explanation
Indices: 51004--51061 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 19
50994 TGGATGAATA
51004 TTTTTGATTGACAAGGTTT
1 TTTTTGATTGACAAGGTTT
* * **
51023 TTTTTGCTATGAGACTGTTT
1 TTTTTGAT-TGACAAGGTTT
*
51043 TTTTTTATTGACAAGGTTT
1 TTTTTGATTGACAAGGTTT
51062 GATGCTGGAG
Statistics
Matches: 29, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.19, C:0.07, G:0.19, T:0.55
Consensus pattern (19 bp):
TTTTTGATTGACAAGGTTT
Found at i:52977 original size:30 final size:31
Alignment explanation
Indices: 52923--52987 Score: 96
Period size: 30 Copynumber: 2.1 Consensus size: 31
52913 AACTTTATGT
*
52923 TTTCCGATTGTACCATTATTTTTAAAACATA
1 TTTCCAATTGTACCATTATTTTTAAAACATA
* *
52954 TTTCCAATTGTACCCTT-TTTTTAAATCATA
1 TTTCCAATTGTACCATTATTTTTAAAACATA
52984 TTTC
1 TTTC
52988 TAAATTGCCA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
30 16 0.52
31 15 0.48
ACGTcount: A:0.28, C:0.18, G:0.05, T:0.49
Consensus pattern (31 bp):
TTTCCAATTGTACCATTATTTTTAAAACATA
Found at i:52994 original size:31 final size:31
Alignment explanation
Indices: 52929--52994 Score: 89
Period size: 30 Copynumber: 2.1 Consensus size: 31
52919 ATGTTTTCCG
*
52929 ATTGTACCATTATTTTTAAAACATATTTCCA
1 ATTGTACCATTATTTTTAAAACATATTTCAA
* *
52960 ATTGTACCCTT-TTTTTAAATCATATTTCTAA
1 ATTGTACCATTATTTTTAAAACATATTTC-AA
52991 ATTG
1 ATTG
52995 CCATTACTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 16 0.52
31 15 0.48
ACGTcount: A:0.32, C:0.15, G:0.05, T:0.48
Consensus pattern (31 bp):
ATTGTACCATTATTTTTAAAACATATTTCAA
Found at i:53125 original size:22 final size:22
Alignment explanation
Indices: 53100--53206 Score: 178
Period size: 22 Copynumber: 4.9 Consensus size: 22
53090 TCCATGAGGA
* *
53100 GGTTATCAAAATTCCATAGTGT
1 GGTTACCAAAATTTCATAGTGT
53122 GGTTACCAAAATTTCATAGTGT
1 GGTTACCAAAATTTCATAGTGT
53144 GGTTACCAAAATTTCATAGTGT
1 GGTTACCAAAATTTCATAGTGT
* *
53166 AGTTACCAAAATTTCATAGAGT
1 GGTTACCAAAATTTCATAGTGT
53188 GGTTACCAAAATTTCATAG
1 GGTTACCAAAATTTCATAG
53207 GATTAGGCTA
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 80 1.00
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.35
Consensus pattern (22 bp):
GGTTACCAAAATTTCATAGTGT
Found at i:53243 original size:22 final size:22
Alignment explanation
Indices: 53076--53260 Score: 119
Period size: 22 Copynumber: 8.3 Consensus size: 22
53066 ATATTTTACT
* *
53076 TTGGTTATTATAATTCCATGAGG
1 TTGGTTATTAAAATTTCAT-AGG
* * *
53099 -AGGTTATCAAAATTCCATA-G
1 TTGGTTATTAAAATTTCATAGG
**
53119 TGTGGTTACCAAAATTTCATA-G
1 T-TGGTTATTAAAATTTCATAGG
**
53141 TGTGGTTACCAAAATTTCATA-G
1 T-TGGTTATTAAAATTTCATAGG
* **
53163 TGTAGTTACCAAAATTTCATAGAG
1 T-TGGTTATTAAAATTTCATAG-G
**
53187 -TGGTTACCAAAATTTCATAGG
1 TTGGTTATTAAAATTTCATAGG
* *
53208 ATTAGGCTATTAAAATTTCTTAGG
1 -TT-GGTTATTAAAATTTCATAGG
53232 TTGGTTATTAAAATTTCATAGG
1 TTGGTTATTAAAATTTCATAGG
*
53254 GTGGTTA
1 TTGGTTA
53261 ATTATCACAA
Statistics
Matches: 140, Mismatches: 15, Indels: 15
0.82 0.09 0.09
Matches are distributed among these distances:
20 1 0.01
21 2 0.01
22 117 0.84
23 3 0.02
24 17 0.12
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.38
Consensus pattern (22 bp):
TTGGTTATTAAAATTTCATAGG
Found at i:53258 original size:68 final size:66
Alignment explanation
Indices: 53100--53260 Score: 182
Period size: 68 Copynumber: 2.4 Consensus size: 66
53090 TCCATGAGGA
* * *
53100 GGTTATCAAAATTCCATAGTGTGGTTACCAAAATTTCATAGTGTGGTTACCAAAATTTCATAGTG
1 GGTTATCAAAATTTCATAGAGTGGTTACCAAAATTTCATAGTGTGGCTACCAAAATTTCATAGTG
53165 T
66 T
* * ** *
53166 AGTTACCAAAATTTCATAGAGTGGTTACCAAAATTTCATAG-GATTAGGCTATTAAAATTTCTTA
1 GGTTATCAAAATTTCATAGAGTGGTTACCAAAATTTCATAGTG--T-GGCTACCAAAATTTCATA
53230 G-GTT
63 GTG-T
* *
53234 GGTTATTAAAATTTCATAGGGTGGTTA
1 GGTTATCAAAATTTCATAGAGTGGTTA
53261 ATTATCACAA
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
65 1 0.01
66 37 0.47
67 2 0.03
68 39 0.49
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (66 bp):
GGTTATCAAAATTTCATAGAGTGGTTACCAAAATTTCATAGTGTGGCTACCAAAATTTCATAGTG
T
Found at i:53537 original size:18 final size:19
Alignment explanation
Indices: 53514--53552 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
53504 TTTCATAAAG
53514 ATAT-GATTATCAAAATTT
1 ATATAGATTATCAAAATTT
53532 ATATGAAGATTATCAAAATTT
1 ATAT--AGATTATCAAAATTT
53553 CATAATGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.22
21 14 0.78
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (19 bp):
ATATAGATTATCAAAATTT
Found at i:53637 original size:87 final size:87
Alignment explanation
Indices: 53517--53679 Score: 222
Period size: 87 Copynumber: 1.9 Consensus size: 87
53507 CATAAAGATA
* * * * *
53517 TGATTATCAAAATTTATATGAAGATTATCAAAATTTCATAATGTTGTTATCAAAATTTCA-AAGC
1 TGATTATCAAAATTTATATGAAGATCAACAAAATTTCATAAAGATGTTATCAAAATTTCATAA-A
53581 GAGGTTATCAAAATTACATAATG
65 GAGGTTATCAAAATTACATAATG
* * *
53604 TGATTATCAAAATTTCATA-GAGGGTCAACAAAATTTTATAAAGATGTTATCAAAATTTCATAAA
1 TGATTATCAAAATTT-ATATGAAGATCAACAAAATTTCATAAAGATGTTATCAAAATTTCATAAA
53668 GAGGTTATCAAA
65 GAGGTTATCAAA
53680 TTTTCTGATT
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
87 61 0.92
88 5 0.08
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.35
Consensus pattern (87 bp):
TGATTATCAAAATTTATATGAAGATCAACAAAATTTCATAAAGATGTTATCAAAATTTCATAAAG
AGGTTATCAAAATTACATAATG
Found at i:53681 original size:43 final size:44
Alignment explanation
Indices: 53440--53684 Score: 179
Period size: 43 Copynumber: 5.6 Consensus size: 44
53430 TAAAAGTCTC
* * *
53440 AATTTCATAAGGA-G-TACCAAAATTTGATAGAAG--GTTATC-A
1 AATTTCATAAAGAGGTTATCAAAATTTCATA-AAGATGTTATCAA
* * * * *
53480 GATTTCATAGAGTGATTATCGAAATTTCATAAAGATATGATTATCAA
1 AATTTCATAAAGAGGTTATCAAAATTTCATAAAG--ATG-TTATCAA
* *
53527 AATTT-ATATGAAGA--TTATCAAAATTTCATAATGTTGTTATCAA
1 AATTTCATA--AAGAGGTTATCAAAATTTCATAAAGATGTTATCAA
* * *
53570 AATTTCA-AAGCGAGGTTATCAAAATTACATAATG-TGATTATCAA
1 AATTTCATAA-AGAGGTTATCAAAATTTCATAAAGATG-TTATCAA
* * * *
53614 AATTTCATAGAG-GGTCAACAAAATTTTATAAAGATGTTATCAA
1 AATTTCATAAAGAGGTTATCAAAATTTCATAAAGATGTTATCAA
*
53657 AATTTCATAAAGAGGTTATCAAATTTTC
1 AATTTCATAAAGAGGTTATCAAAATTTC
53685 TGATTACAAA
Statistics
Matches: 159, Mismatches: 28, Indels: 32
0.73 0.13 0.15
Matches are distributed among these distances:
40 9 0.06
41 4 0.03
42 14 0.09
43 49 0.31
44 49 0.31
45 2 0.01
46 25 0.16
47 5 0.03
48 2 0.01
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.35
Consensus pattern (44 bp):
AATTTCATAAAGAGGTTATCAAAATTTCATAAAGATGTTATCAA
Found at i:53815 original size:19 final size:19
Alignment explanation
Indices: 53785--53851 Score: 98
Period size: 19 Copynumber: 3.5 Consensus size: 19
53775 TGATGGAGTA
53785 ATCAAAATTTCAGGGAGGAT
1 ATCAAAA-TTCAGGGAGGAT
* *
53805 ACCAAAATTCAGGGAGGGT
1 ATCAAAATTCAGGGAGGAT
*
53824 ATCAAAATTCAGTGAGGAT
1 ATCAAAATTCAGGGAGGAT
53843 ATCAAAATT
1 ATCAAAATT
53852 TCATAAGGTT
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
19 36 0.86
20 6 0.14
ACGTcount: A:0.42, C:0.12, G:0.22, T:0.24
Consensus pattern (19 bp):
ATCAAAATTCAGGGAGGAT
Found at i:53865 original size:38 final size:39
Alignment explanation
Indices: 53785--53873 Score: 101
Period size: 38 Copynumber: 2.3 Consensus size: 39
53775 TGATGGAGTA
*
53785 ATCAAAATTTCAGGGAGGATACCAAAATTCAGGGAGGGT
1 ATCAAAATTTCAGGGAGGATACCAAAATTCAGGAAGGGT
* * * *
53824 ATCAAAA-TTCAGTGAGGATATCAAAATTTCA-TAAGGTT
1 ATCAAAATTTCAGGGAGGATACCAAAA-TTCAGGAAGGGT
*
53862 ATCAAATTTTCA
1 ATCAAAATTTCA
53874 TAGTTTAGTT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
38 27 0.64
39 15 0.36
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.28
Consensus pattern (39 bp):
ATCAAAATTTCAGGGAGGATACCAAAATTCAGGAAGGGT
Found at i:53910 original size:22 final size:20
Alignment explanation
Indices: 53379--53920 Score: 164
Period size: 22 Copynumber: 26.1 Consensus size: 20
53369 ACTTCATCGG
*
53379 GAGGTTATCAAAATTTTATA
1 GAGGTTATCAAAATTTCATA
*
53399 GTGTGGTTATCAAAATTTCATA
1 --GAGGTTATCAAAATTTCATA
*
53421 TGAAGGTTATAAAAGTCTCAATTTCATA
1 -G-AGGTTAT-CAA-----AATTTCATA
* * *
53449 -AGGAGTACCAAAATTTGATA
1 GAGG-TTATCAAAATTTCATA
*
53469 GAAGGTTATC-AGATTTCATA
1 G-AGGTTATCAAAATTTCATA
*
53489 GAGTGATTATCGAAATTTCATAAA
1 GAG-G-TTATCAAAATTTCAT--A
*
53513 GATATGATTATCAAAATTT-ATA
1 G--A-GGTTATCAAAATTTCATA
*
53535 TGAAGATTATCAAAATTTCATA
1 -G-AGGTTATCAAAATTTCATA
*
53557 -ATGTTGTTATCAAAATTTCAAA
1 GA-G--GTTATCAAAATTTCATA
*
53579 GCGAGGTTATCAAAATTACATA
1 --GAGGTTATCAAAATTTCATA
53601 -ATGTGATTATCAAAATTTCATA
1 GA-G-G-TTATCAAAATTTCATA
* * *
53623 GAGGGTCAACAAAATTTTATAAA
1 GA-GGTTATCAAAATTTCAT--A
*
53646 GATGTTATCAAAATTTCATAAA
1 GAGGTTATCAAAATTTCAT--A
*
53668 GAGGTTATCAAATTTTC-T-
1 GAGGTTATCAAAATTTCATA
53686 GA--TTA-CAAAAATTTCATA
1 GAGGTTATC-AAAATTTCATA
* * **
53704 GTGG-TAT-----TTTTAGG
1 GAGGTTATCAAAATTTCATA
53718 GAGGTTATCAAAATTTCATA
1 GAGGTTATCAAAATTTCATA
53738 GTATGGTTATC-AAA-TT-AT-
1 G-A-GGTTATCAAAATTTCATA
* * *
53756 GAAGGTTATTAAACTTTTAT-
1 G-AGGTTATCAAAATTTCATA
* **
53776 GATGGAGTAATCAAAATTTCAGG
1 GA--G-GTTATCAAAATTTCATA
* * **
53799 GAGGATACCAAAA-TTCAGG
1 GAGGTTATCAAAATTTCATA
*
53818 GAGGGTATCAAAA-TTCAGT-
1 GAGGTTATCAAAATTTCA-TA
*
53837 GAGGATATCAAAATTTCATA
1 GAGGTTATCAAAATTTCATA
*
53857 -AGGTTATCAAATTTTCATA
1 GAGGTTATCAAAATTTCATA
*
53876 GTTTA-GTTTTCAAAATTTCATAA
1 G---AGGTTATCAAAATTTCAT-A
53899 GAGGGTTATCAAAATTTCATA
1 GA-GGTTATCAAAATTTCATA
53920 G
1 G
53921 TATGTAGATC
Statistics
Matches: 397, Mismatches: 60, Indels: 127
0.68 0.10 0.22
Matches are distributed among these distances:
14 7 0.02
15 4 0.01
16 10 0.03
17 7 0.02
18 7 0.02
19 62 0.16
20 42 0.11
21 46 0.12
22 164 0.41
23 13 0.03
24 5 0.01
25 17 0.04
26 3 0.01
27 1 0.00
28 9 0.02
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.36
Consensus pattern (20 bp):
GAGGTTATCAAAATTTCATA
Found at i:53933 original size:44 final size:41
Alignment explanation
Indices: 53842--53941 Score: 114
Period size: 44 Copynumber: 2.4 Consensus size: 41
53832 TCAGTGAGGA
*
53842 TATCAAAATTTCAT-AAGGTTATCAAATTTTCATAGTTTAG
1 TATCAAAATTTCATAAAGGTTATCAAAATTTCATAGTTTAG
*
53882 TTTTCAAAATTTCATAAGAGGGTTATCAAAATTTCATAGTATGTAG
1 -TATCAAAATTTCATAA-A-GGTTATCAAAATTTCATAGT-T-TAG
*
53928 -ATCAAAATTGCATA
1 TATCAAAATTTCATA
53942 TAAATATTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
41 13 0.26
42 1 0.02
43 1 0.02
44 31 0.62
45 1 0.02
46 3 0.06
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (41 bp):
TATCAAAATTTCATAAAGGTTATCAAAATTTCATAGTTTAG
Found at i:54008 original size:2 final size:2
Alignment explanation
Indices: 54001--54032 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
53991 TAAAACTAGT
54001 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
54033 ATCGGATTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:54093 original size:2 final size:2
Alignment explanation
Indices: 54086--54119 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
54076 TTTCTTTTTA
54086 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
54120 TATGATCCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54233 original size:71 final size:65
Alignment explanation
Indices: 54100--54233 Score: 169
Period size: 65 Copynumber: 2.0 Consensus size: 65
54090 ATATATATAT
* ** *
54100 ATATATATATATATATATATTATGATCCTTGTTCCACTAGGACTCTAAAGTCGGTTTTTTTTTAA
1 ATATATATATATATATATATTATGATCCTTGTCCCACTAGGACTCTAAAGTCGGGGTGTTTTTAA
*
54165 ATATATATATATATTTATATTATGATCCTTGTCCCACTAGGAGTAGGACTCTAAAGTCGGGGTGT
1 ATATATATATATATATATATTATGATCCTTGTCCCAC------TAGGACTCTAAAGTCGGGGTGT
54230 TTTT
60 TTTT
54234 TTTTTTTTGA
Statistics
Matches: 58, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
65 35 0.60
71 23 0.40
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.43
Consensus pattern (65 bp):
ATATATATATATATATATATTATGATCCTTGTCCCACTAGGACTCTAAAGTCGGGGTGTTTTTAA
Found at i:57544 original size:78 final size:78
Alignment explanation
Indices: 57451--57615 Score: 285
Period size: 78 Copynumber: 2.1 Consensus size: 78
57441 GTTTTTTAAT
*
57451 TAAAATAGTAAAATGGTAAAATATAATAATTATAAGGTTAATAGATTTAATTATATAAAAATAGA
1 TAAAATAGTAAAATGGTAAAATATAATAATTATAAGGATAATAGATTTAATTATATAAAAATAGA
*
57516 TTTTTTAGTTGAG
66 GTTTTTAGTTGAG
* * *
57529 TAAAATAGTAAAATGGTATAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
1 TAAAATAGTAAAATGGTAAAATATAATAATTATAAGGATAATAGATTTAATTATATAAAAATAGA
57594 GTTTTTAGTTGAG
66 GTTTTTAGTTGAG
57607 TAAAATAGT
1 TAAAATAGT
57616 TATAAAGATA
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
78 82 1.00
ACGTcount: A:0.48, C:0.00, G:0.14, T:0.38
Consensus pattern (78 bp):
TAAAATAGTAAAATGGTAAAATATAATAATTATAAGGATAATAGATTTAATTATATAAAAATAGA
GTTTTTAGTTGAG
Found at i:57614 original size:57 final size:54
Alignment explanation
Indices: 57548--57665 Score: 146
Period size: 57 Copynumber: 2.1 Consensus size: 54
57538 AAAATGGTAT
* * * *
57548 AATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTTAGTTG
1 AATAAAATAGTTATAAAGATATTAGAGTTAA-TA-A-AAAAATAGAGTTTTTAGTCG
* * *
57605 AGTAAAATAGTTATAAAGATATTATAGTTAATAAAAAAATATAGTTTTTAGTCG
1 AATAAAATAGTTATAAAGATATTAGAGTTAATAAAAAAATAGAGTTTTTAGTCG
57659 AATAAAA
1 AATAAAA
57666 CTATAAAAAC
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
54 24 0.45
55 1 0.02
56 2 0.04
57 26 0.49
ACGTcount: A:0.48, C:0.01, G:0.13, T:0.38
Consensus pattern (54 bp):
AATAAAATAGTTATAAAGATATTAGAGTTAATAAAAAAATAGAGTTTTTAGTCG
Found at i:58889 original size:15 final size:16
Alignment explanation
Indices: 58850--58891 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
58840 ATTCCAAATT
*
58850 AAATTATTAAAAAAAC
1 AAATTAATAAAAAAAC
*
58866 AAATAAATAAAAAAAC
1 AAATTAATAAAAAAAC
*
58882 -CATTAATAAA
1 AAATTAATAAA
58892 TTTAATTTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.71, C:0.07, G:0.00, T:0.21
Consensus pattern (16 bp):
AAATTAATAAAAAAAC
Found at i:68288 original size:22 final size:22
Alignment explanation
Indices: 68263--68305 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
68253 TGAGATCGAT
*
68263 TTTCTCGGTTAGGATCAAACCC
1 TTTCTCAGTTAGGATCAAACCC
68285 TTTCTCAGTTAGGATCAAACC
1 TTTCTCAGTTAGGATCAAACC
68306 AATACTACTA
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:0.26, C:0.26, G:0.16, T:0.33
Consensus pattern (22 bp):
TTTCTCAGTTAGGATCAAACCC
Found at i:69371 original size:2 final size:2
Alignment explanation
Indices: 69364--69403 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
69354 GACTCGAAGC
* *
69364 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
69404 GGCTACGGGC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
AT
Found at i:70633 original size:30 final size:29
Alignment explanation
Indices: 70566--70637 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
70556 ACACTGAACC
****
70566 GTCAAATAAGCCCCTGAACTATTATTTCA
1 GTCAAATAAGCCCCTGAACTATTAAAAAA
* *
70595 GCCAAATAAGCCCCTGAACTCTTAAAAAAA
1 GTCAAATAAGCCCCTGAACTATT-AAAAAA
70625 GTCAAATAAGCCC
1 GTCAAATAAGCCC
70638 TGTTGCCAAG
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
29 21 0.60
30 14 0.40
ACGTcount: A:0.40, C:0.26, G:0.11, T:0.22
Consensus pattern (29 bp):
GTCAAATAAGCCCCTGAACTATTAAAAAA
Found at i:73419 original size:2 final size:2
Alignment explanation
Indices: 73374--73406 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
73364 TCCTATTTCA
*
73374 AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
73407 CTTACCTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:73559 original size:25 final size:24
Alignment explanation
Indices: 73500--73564 Score: 78
Period size: 23 Copynumber: 2.6 Consensus size: 24
73490 GTCATTGCTT
*
73500 AACTATTATAATTTTATTCTATTAAA
1 AACTATTAT--TTTTATTCAATTAAA
73526 AACTA-TATTTTTATTCAATTATAA
1 AACTATTATTTTTATTCAATTA-AA
*
73550 ATCTATTATTTTTAT
1 AACTATTATTTTTAT
73565 AATTACTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
23 12 0.34
24 6 0.17
25 12 0.34
26 5 0.14
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (24 bp):
AACTATTATTTTTATTCAATTAAA
Found at i:75279 original size:16 final size:16
Alignment explanation
Indices: 75252--75285 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
75242 TTAAATCTAA
75252 TATTTTTATACCTATTT
1 TATTTTTATACC-ATTT
75269 TATTTTT-TACCATTT
1 TATTTTTATACCATTT
75284 TA
1 TA
75286 CTAATTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 4 0.24
17 7 0.41
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.65
Consensus pattern (16 bp):
TATTTTTATACCATTT
Found at i:77134 original size:31 final size:31
Alignment explanation
Indices: 77090--77148 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
77080 GTTAGATAAG
* * *
77090 TAAGGATATAATAGGTATTTTAAAAGTTAAA
1 TAAGGATACAATAGGCATTTCAAAAGTTAAA
*
77121 TAAGGGTACAATAGGCATTTCAAAAGTT
1 TAAGGATACAATAGGCATTTCAAAAGTT
77149 TCTCAAAACT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.44, C:0.05, G:0.19, T:0.32
Consensus pattern (31 bp):
TAAGGATACAATAGGCATTTCAAAAGTTAAA
Found at i:77361 original size:30 final size:31
Alignment explanation
Indices: 77302--77392 Score: 157
Period size: 30 Copynumber: 3.0 Consensus size: 31
77292 ATTACACAAA
77302 CCGTCAAGACCCAACAATTGGTCCTGATATT
1 CCGTCAAGACCCAACAATTGGTCCTGATATT
*
77333 CCGTCAAGACCCAATAATTGGT-CTGATATT
1 CCGTCAAGACCCAACAATTGGTCCTGATATT
*
77363 CCGTCAGGACCCAACAATTGGTCCTGATAT
1 CCGTCAAGACCCAACAATTGGTCCTGATAT
77393 CAGCTCGACT
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
30 28 0.50
31 28 0.50
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (31 bp):
CCGTCAAGACCCAACAATTGGTCCTGATATT
Found at i:82645 original size:26 final size:26
Alignment explanation
Indices: 82616--82666 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
82606 ATTATTAAAA
82616 TATTTTATTTAGAAAAATTCAATTTT
1 TATTTTATTTAGAAAAATTCAATTTT
82642 TATTTTATTTAGAAAAATTCAATTT
1 TATTTTATTTAGAAAAATTCAATTT
82667 CTACAATATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.53
Consensus pattern (26 bp):
TATTTTATTTAGAAAAATTCAATTTT
Found at i:84239 original size:64 final size:63
Alignment explanation
Indices: 84121--84249 Score: 195
Period size: 64 Copynumber: 2.0 Consensus size: 63
84111 TAAATTATAA
* *
84121 TTAATTTCAATTATTTTAAAACTTTTTATTTTAAACGTGTTCCGCCACATGCCTGAAACTAGT
1 TTAATTTCAATTATTTTAAAACTTTTTACTTTAAACGTGTTCCACCACATGCCTGAAACTAGT
* * * *
84184 TTAATTTCAATTATTTTAATAATTTTTTACTTTAAACGTGTTTCACCACGTGCCTGGAACTAGT
1 TTAATTTCAATTATTTTAA-AACTTTTTACTTTAAACGTGTTCCACCACATGCCTGAAACTAGT
84248 TT
1 TT
84250 TTTTTTTTAA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
63 19 0.32
64 40 0.68
ACGTcount: A:0.29, C:0.16, G:0.10, T:0.45
Consensus pattern (63 bp):
TTAATTTCAATTATTTTAAAACTTTTTACTTTAAACGTGTTCCACCACATGCCTGAAACTAGT
Found at i:87261 original size:20 final size:20
Alignment explanation
Indices: 87236--87275 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
87226 ATCCCCCTGA
87236 AGTATCACAAAAAGAACACT
1 AGTATCACAAAAAGAACACT
* *
87256 AGTATCATAAAAAGGACACT
1 AGTATCACAAAAAGAACACT
87276 TTGGTCTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.53, C:0.17, G:0.12, T:0.17
Consensus pattern (20 bp):
AGTATCACAAAAAGAACACT
Found at i:91270 original size:7 final size:7
Alignment explanation
Indices: 91252--91285 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
91242 ACTCCCCTAT
91252 ATTATT-
1 ATTATTA
91258 ATTATTA
1 ATTATTA
91265 ATTATTA
1 ATTATTA
91272 ATTATTA
1 ATTATTA
91279 ATTATTA
1 ATTATTA
91286 TAAATAATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.22
7 21 0.78
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
ATTATTA
Found at i:91648 original size:18 final size:18
Alignment explanation
Indices: 91625--91668 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
91615 TATTTGATGT
91625 TGAGGATGTTTGTGAAGA
1 TGAGGATGTTTGTGAAGA
91643 TGAGGATGTTTGTGAAGA
1 TGAGGATGTTTGTGAAGA
*
91661 TGTGGATG
1 TGAGGATG
91669 AATTATTTCG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.25, C:0.00, G:0.41, T:0.34
Consensus pattern (18 bp):
TGAGGATGTTTGTGAAGA
Found at i:93519 original size:13 final size:13
Alignment explanation
Indices: 93503--93555 Score: 63
Period size: 13 Copynumber: 4.1 Consensus size: 13
93493 TATTCTTTAT
*
93503 TTTTTTAGATTAA
1 TTTTTTATATTAA
*
93516 TTTTTCATATTAA
1 TTTTTTATATTAA
93529 TTTTTT-TATTAA
1 TTTTTTATATTAA
*
93541 TATTTTATATATAA
1 TTTTTTATAT-TAA
93555 T
1 T
93556 GAATGATCTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
12 11 0.32
13 19 0.56
14 4 0.12
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (13 bp):
TTTTTTATATTAA
Found at i:93552 original size:27 final size:26
Alignment explanation
Indices: 93501--93555 Score: 69
Period size: 25 Copynumber: 2.1 Consensus size: 26
93491 TTTATTCTTT
93501 ATTTTTTTAGATTAATTTTTCATATTA
1 ATTTTTTTA-ATTAATTTTTCATATTA
93528 ATTTTTTT-ATTAATATTTT-ATATATA
1 ATTTTTTTAATTAAT-TTTTCATAT-TA
93554 AT
1 AT
93556 GAATGATCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
25 10 0.38
26 8 0.31
27 8 0.31
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (26 bp):
ATTTTTTTAATTAATTTTTCATATTA
Found at i:94093 original size:22 final size:22
Alignment explanation
Indices: 94051--94094 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
94041 TATTCATATG
*
94051 AAATTATGATAATCTCTCTATT
1 AAATTATGATAATCTCACTATT
94073 AAATTATGATAAT-TACACTATT
1 AAATTATGATAATCT-CACTATT
94095 TTTTATGATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.43
Consensus pattern (22 bp):
AAATTATGATAATCTCACTATT
Found at i:94172 original size:22 final size:23
Alignment explanation
Indices: 94147--94195 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
94137 GAATTTCGAG
*
94147 AACCTTTC-TATAAAATTTTTTT
1 AACCTTTCTTATAAAATTTTGTT
*
94169 AACC-TTCTTATGAAATTTTGTT
1 AACCTTTCTTATAAAATTTTGTT
94191 AACCT
1 AACCT
94196 CCCTAAGGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 3 0.13
22 20 0.87
ACGTcount: A:0.31, C:0.16, G:0.04, T:0.49
Consensus pattern (23 bp):
AACCTTTCTTATAAAATTTTGTT
Found at i:94428 original size:23 final size:23
Alignment explanation
Indices: 94380--94459 Score: 108
Period size: 23 Copynumber: 3.5 Consensus size: 23
94370 TCACACTCTG
* * *
94380 AAATTGTGAT-AACCTCGCTATG
1 AAATTTTGATAAACCTCCCTATA
* *
94402 AAATTTTGATAAATCTTCCTATA
1 AAATTTTGATAAACCTCCCTATA
94425 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAACCTCCCTATA
94448 AAATTTTGATAA
1 AAATTTTGATAA
94460 CTTTCTTATG
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
22 9 0.18
23 41 0.82
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.38
Consensus pattern (23 bp):
AAATTTTGATAAACCTCCCTATA
Found at i:94480 original size:45 final size:45
Alignment explanation
Indices: 94386--94490 Score: 131
Period size: 46 Copynumber: 2.3 Consensus size: 45
94376 TCTGAAATTG
* * *
94386 TGATAACCTCGCTATGAAATTTTGATAAATCTTCCTATAAAATTT
1 TGATAACCTCCCTATAAAATTTTGATAAATCTTCCTATAAAATCT
* * * *
94431 TGATAAACCTCCCTATAAAATTTTGATAACT-TTCTTATGAGATCT
1 TGAT-AACCTCCCTATAAAATTTTGATAAATCTTCCTATAAAATCT
94476 TGATAACCTCCCTAT
1 TGATAACCTCCCTAT
94491 GATTTTTTAA
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
44 11 0.21
45 18 0.35
46 23 0.44
ACGTcount: A:0.33, C:0.19, G:0.09, T:0.39
Consensus pattern (45 bp):
TGATAACCTCCCTATAAAATTTTGATAAATCTTCCTATAAAATCT
Found at i:94491 original size:22 final size:22
Alignment explanation
Indices: 94154--94608 Score: 165
Period size: 22 Copynumber: 20.7 Consensus size: 22
94144 GAGAACCTTT
* ** *
94154 CTATAAAATTTTTTTAACCTTC
1 CTATGAAATTTTGATAACCTCC
* *
94176 TTATGAAATTTTGTTAACCTCC
1 CTATGAAATTTTGATAACCTCC
* * ** *
94198 CTAAGGAATTTTGA-AGATTTCA
1 CTATGAAATTTTGATA-ACCTCC
* * *
94220 ATATGAAATTTTGATAACTTCG
1 CTATGAAATTTTGATAACCTCC
* * * *
94242 CAATGAAACTTTGATAACCAACA
1 CTATGAAATTTTGATAACC-TCC
* *
94265 ATAT-AAGATGTTGATAACCTCC
1 CTATGAA-ATTTTGATAACCTCC
* * ** * *
94287 ATATGATACATTGATAACCACG
1 CTATGAAATTTTGATAACCTCC
* * * *
94309 TTATGAAAATTTAAAAACCTCC
1 CTATGAAATTTTGATAACCTCC
* * * *
94331 ATATG-AATTGTT-AGTAATCACA
1 CTATGAAATT-TTGA-TAACCTCC
* * * *
94353 CTCTGAAATTTT-AGTAATCACA
1 CTATGAAATTTTGA-TAACCTCC
* * *
94375 CTCTGAAATTGTGATAACCTCG
1 CTATGAAATTTTGATAACCTCC
* *
94397 CTATGAAATTTTGATAAATCTTC
1 CTATGAAATTTTGAT-AACCTCC
*
94420 CTATAAAATTTTGATAAACCTCC
1 CTATGAAATTTTGAT-AACCTCC
* * *
94443 CTATAAAATTTTGATAACTTTC
1 CTATGAAATTTTGATAACCTCC
* * *
94465 TTATGAGATCTTGATAACCTCC
1 CTATGAAATTTTGATAACCTCC
** * *
94487 CTATGATTTTTTAATAACCTCA
1 CTATGAAATTTTGATAACCTCC
* * *
94509 TTATGAAATTTTGTTATCC-CC
1 CTATGAAATTTTGATAACCTCC
* * * *
94530 ATATGAAATTTTGATCTACAT-A
1 CTATGAAATTTTGAT-AACCTCC
*
94552 TTATGAAATTTTGATAACC-CTC
1 CTATGAAATTTTGATAACCTC-C
* **
94574 TTATGAAATTTTGATTTCCTCC
1 CTATGAAATTTTGATAACCTCC
94596 CTA--AAATTTTGAT
1 CTATGAAATTTTGAT
94609 TACTCCATAG
Statistics
Matches: 323, Mismatches: 95, Indels: 32
0.72 0.21 0.07
Matches are distributed among these distances:
20 10 0.03
21 21 0.07
22 232 0.72
23 60 0.19
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCTCC
Found at i:94740 original size:22 final size:22
Alignment explanation
Indices: 94721--94860 Score: 93
Period size: 22 Copynumber: 6.4 Consensus size: 22
94711 ATTTTGAACA
94721 TTTGATAACCTCTTTATGAAAT
1 TTTGATAACCTCTTTATGAAAT
* * *
94743 TTTGATTATCTCTTTATAAAAT
1 TTTGATAACCTCTTTATGAAAT
* * *
94765 TTTGTTGACCT-TTCTATTAAAT
1 TTTGATAACCTCTT-TATGAAAT
* * * * **
94787 TCTGATAATCACATTATGTGAT
1 TTTGATAACCTCTTTATGAAAT
** *
94809 TTTGATAACCTCGCTCTGAAAT
1 TTTGATAACCTCTTTATGAAAT
** **
94831 TTTGATAACAACACTATGAAAT
1 TTTGATAACCTCTTTATGAAAT
94853 TTTGATAA
1 TTTGATAA
94861 TCTGATCTCT
Statistics
Matches: 88, Mismatches: 28, Indels: 4
0.73 0.23 0.03
Matches are distributed among these distances:
21 2 0.02
22 85 0.97
23 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.10, T:0.44
Consensus pattern (22 bp):
TTTGATAACCTCTTTATGAAAT
Found at i:94744 original size:21 final size:21
Alignment explanation
Indices: 94715--94766 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
94705 AATCACATTT
94715 TGAACATTTGATAACCTCTTTA
1 TGAA-ATTTGATAACCTCTTTA
* *
94737 TGAAATTTTGATTATCTCTTTA
1 TGAAA-TTTGATAACCTCTTTA
*
94759 TAAAATTT
1 TGAAATTT
94767 TGTTGACCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 4 0.15
22 22 0.85
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.48
Consensus pattern (21 bp):
TGAAATTTGATAACCTCTTTA
Found at i:95051 original size:22 final size:21
Alignment explanation
Indices: 94945--95044 Score: 85
Period size: 22 Copynumber: 4.6 Consensus size: 21
94935 AAATTGAGAC
* *
94945 TTTTATAACCTTCATATGAAA
1 TTTTATAACCTCCCTATGAAA
*
94966 TTTTGATAACCTCCCCATGAAA
1 TTTT-ATAACCTCCCTATGAAA
*
94988 TATTAGTAACCT-CCTAATGAAA
1 TTTTA-TAACCTCCCT-ATGAAA
* * *
95010 TTTTTTTAACCACACTATGAAA
1 -TTTTATAACCTCCCTATGAAA
95032 TTCTTATAACCTC
1 TT-TTATAACCTC
95045 GTTATGACAT
Statistics
Matches: 62, Mismatches: 11, Indels: 11
0.74 0.13 0.13
Matches are distributed among these distances:
21 9 0.15
22 48 0.77
23 5 0.08
ACGTcount: A:0.35, C:0.21, G:0.06, T:0.38
Consensus pattern (21 bp):
TTTTATAACCTCCCTATGAAA
Found at i:95159 original size:24 final size:22
Alignment explanation
Indices: 95098--95213 Score: 83
Period size: 22 Copynumber: 5.2 Consensus size: 22
95088 TTGTGATAAT
* *
95098 TAACCACCCTATGAAATTTCAA
1 TAACCAACCTATGAAATTTTAA
*
95120 TAACCAACCTAAGAAATTTTAA
1 TAACCAACCTATGAAATTTTAA
** **
95142 TAACCTGGTCCTATGAAATTTTGG
1 TAACC--AACCTATGAAATTTTAA
* **
95166 TAACC-ACGCTATGAAGTTTTGG
1 TAACCAAC-CTATGAAATTTTAA
*
95188 TAACCATA-CTATGAAATTTTCA
1 TAACCA-ACCTATGAAATTTTAA
95210 TAAC
1 TAAC
95214 TTTCATATGA
Statistics
Matches: 76, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
21 1 0.01
22 57 0.75
24 18 0.24
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.32
Consensus pattern (22 bp):
TAACCAACCTATGAAATTTTAA
Found at i:95180 original size:22 final size:22
Alignment explanation
Indices: 95152--95258 Score: 108
Period size: 22 Copynumber: 4.9 Consensus size: 22
95142 TAACCTGGTC
*
95152 CTATGAAATTTTGGTAACCACG
1 CTATGAAATTTTGGTAACCACA
* *
95174 CTATGAAGTTTTGGTAACCATA
1 CTATGAAATTTTGGTAACCACA
** **
95196 CTATGAAATTTTCATAACTTTCA
1 CTATGAAATTTTGGTAAC-CACA
95219 -TATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGGTAACCACA
* * *
95240 CTATGGAATTCTGATAACC
1 CTATGAAATTTTGGTAACC
95259 TCCTCATGAA
Statistics
Matches: 67, Mismatches: 16, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
21 2 0.03
22 64 0.96
23 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.36
Consensus pattern (22 bp):
CTATGAAATTTTGGTAACCACA
Found at i:95279 original size:66 final size:66
Alignment explanation
Indices: 95153--95305 Score: 161
Period size: 66 Copynumber: 2.3 Consensus size: 66
95143 AACCTGGTCC
* * * * *
95153 TATGAAATTTTGGTAACCACGCTATGAAGTTTTGGTAACCATACTATGAAATTTTCATAA-C-TT
1 TATGAAATTTTGGTAACCACACTATGAAGTTCTGATAACCATACTATGAAATTATAATAACCATT
95216 T
66 T
* *
95217 CATATGAAATTTTGGTAACCACACTATGGAA-TTCTGATAACC-TCCTCATGAAGTTATAATAAC
1 --TATGAAATTTTGGTAACCACACTAT-GAAGTTCTGATAACCATACT-ATGAAATTATAATAAC
95280 CATTT
62 CATTT
* *
95285 TATGAGATTTTGATAACCACA
1 TATGAAATTTTGGTAACCACA
95306 TAGAGACAAG
Statistics
Matches: 74, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
65 3 0.04
66 64 0.86
67 4 0.05
68 3 0.04
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Consensus pattern (66 bp):
TATGAAATTTTGGTAACCACACTATGAAGTTCTGATAACCATACTATGAAATTATAATAACCATT
T
Found at i:95500 original size:19 final size:20
Alignment explanation
Indices: 95469--95506 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
95459 TATTGACATT
95469 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
95488 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
95507 AATAATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Found at i:95810 original size:168 final size:170
Alignment explanation
Indices: 95520--95862 Score: 439
Period size: 168 Copynumber: 2.0 Consensus size: 170
95510 AATAGTAAAG
* *
95520 GAAATTTACATGTTCATCAACTAAAATTAATTTGACAATCTTATAATTCGGTCTAAATTGAAATT
1 GAAATTTACATGTTCATCAACTAAAATCAATTTGACAAACTTATAATTCGGTCTAAATTGAAATT
95585 TTTAATTAATTTTTAAATAATAAAATAAAATAAATTTTAATAATGGAAATTTAGAAATATATTTG
66 TTTAATTAA-TTTT--AT-ATAAAAT-AAATAAATTTTAATAATGGAAATTTAGAAATATATTT-
* *
95650 GAAAAAAGGGTGCAATCACAAAACATAAAG-TTTCCTATTATTCGTA
125 GAAAAAAGAGTACAATCACAAAACATAAAGTTTTCC-ATTATTCGTA
* *
95696 GAAATTTGCATGTTCATCAA-TGAAAATCAATTTTACAAAACTTATAATTCGGTCTAAATTGAAA
1 GAAATTTACATGTTCATCAACT-AAAATCAATTTGAC-AAACTTATAATTCGGTCTAAATTGAAA
**
95760 TTTTATAATTAA-TTT-T-T-AAAT-AATAAATTTTAATAATGTCAATTTAGAAATATATTTGAA
64 TTTT-TAATTAATTTTATATAAAATAAATAAATTTTAATAATGGAAATTTAGAAATATATTTGAA
** **
95820 AAAAGAGTACAATCGGAGGACATAAAGTTTTCCATTATTCGTA
128 AAAAGAGTACAATCACAAAACATAAAGTTTTCCATTATTCGTA
95863 CTTTTATATA
Statistics
Matches: 151, Mismatches: 12, Indels: 17
0.84 0.07 0.09
Matches are distributed among these distances:
167 34 0.23
168 39 0.26
170 4 0.03
171 1 0.01
173 1 0.01
175 1 0.01
176 34 0.23
177 30 0.20
178 7 0.05
ACGTcount: A:0.44, C:0.09, G:0.10, T:0.37
Consensus pattern (170 bp):
GAAATTTACATGTTCATCAACTAAAATCAATTTGACAAACTTATAATTCGGTCTAAATTGAAATT
TTTAATTAATTTTATATAAAATAAATAAATTTTAATAATGGAAATTTAGAAATATATTTGAAAAA
AGAGTACAATCACAAAACATAAAGTTTTCCATTATTCGTA
Done.