Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009661.1 Corchorus capsularis cultivar CVL-1 contig09682, 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: 64277
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:5033 original size:7 final size:7
Alignment explanation
Indices: 5018--5055 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
5008 GGATATCTGG
*
5018 TTAATGA
1 TTAAAGA
5025 TTAAAGA
1 TTAAAGA
5032 TTAAAGA
1 TTAAAGA
5039 TTAAAGA
1 TTAAAGA
5046 TTAAAGA
1 TTAAAGA
5053 TTA
1 TTA
5056 TTGCTTTAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.13, T:0.34
Consensus pattern (7 bp):
TTAAAGA
Found at i:5646 original size:12 final size:12
Alignment explanation
Indices: 5629--5654 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5619 TAGCAAGGAC
5629 AGCAAATTCGAA
1 AGCAAATTCGAA
5641 AGCAAATTCGAA
1 AGCAAATTCGAA
5653 AG
1 AG
5655 TAACGGTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.15, G:0.19, T:0.15
Consensus pattern (12 bp):
AGCAAATTCGAA
Found at i:11624 original size:31 final size:31
Alignment explanation
Indices: 11589--11654 Score: 107
Period size: 31 Copynumber: 2.1 Consensus size: 31
11579 AACTTTATGT
*
11589 TTTCCGATTGTACCCTTATT-TTTAAAACATA
1 TTTCCAATTGTACCCTT-TTCTTTAAAACATA
11620 TTTCCAATTGTACCCTTTTCTTTAAAACATA
1 TTTCCAATTGTACCCTTTTCTTTAAAACATA
11651 TTTC
1 TTTC
11655 TAAATTGCCA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
30 2 0.06
31 31 0.94
ACGTcount: A:0.27, C:0.21, G:0.05, T:0.47
Consensus pattern (31 bp):
TTTCCAATTGTACCCTTTTCTTTAAAACATA
Found at i:11674 original size:123 final size:123
Alignment explanation
Indices: 11455--11694 Score: 444
Period size: 123 Copynumber: 2.0 Consensus size: 123
11445 GAATAAGGGA
* *
11455 AAACTTTATGTTTTCTGATTATACCCTTATTTTTAAAACATATTTCCAATTGTACCTTTTTCTTT
1 AAACTTTATGTTTTCCGATTATACCCTTATTTTTAAAACATATTTCCAATTGTACCCTTTTCTTT
*
11520 AACACATATTTCTAAATTGCCATTACTAAATAATATTTTAATTATTCCATTATTAGTT
66 AAAACATATTTCTAAATTGCCATTACTAAATAATATTTTAATTATTCCATTATTAGTT
*
11578 AAACTTTATGTTTTCCGATTGTACCCTTATTTTTAAAACATATTTCCAATTGTACCCTTTTCTTT
1 AAACTTTATGTTTTCCGATTATACCCTTATTTTTAAAACATATTTCCAATTGTACCCTTTTCTTT
11643 AAAACATATTTCTAAATTGCCATTACTAAATAATATTTTAATTATTCCATTA
66 AAAACATATTTCTAAATTGCCATTACTAAATAATATTTTAATTATTCCATTA
11695 CTTTTTTAAT
Statistics
Matches: 113, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
123 113 1.00
ACGTcount: A:0.32, C:0.16, G:0.04, T:0.47
Consensus pattern (123 bp):
AAACTTTATGTTTTCCGATTATACCCTTATTTTTAAAACATATTTCCAATTGTACCCTTTTCTTT
AAAACATATTTCTAAATTGCCATTACTAAATAATATTTTAATTATTCCATTATTAGTT
Found at i:12695 original size:22 final size:22
Alignment explanation
Indices: 12635--12695 Score: 81
Period size: 20 Copynumber: 2.9 Consensus size: 22
12625 TTCATGAGGA
* * *
12635 GGTTATCAAAATTCCATAGTGT
1 GGTTACCAAAATTTCATAGTCT
12657 GGTTACC-AAA-TTCATAGTCT
1 GGTTACCAAAATTTCATAGTCT
12677 GGTTACCAAAATTTCATAG
1 GGTTACCAAAATTTCATAG
12696 GATCATGTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 15 0.44
21 6 0.18
22 13 0.38
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Consensus pattern (22 bp):
GGTTACCAAAATTTCATAGTCT
Found at i:12711 original size:24 final size:22
Alignment explanation
Indices: 12590--12749 Score: 89
Period size: 22 Copynumber: 7.3 Consensus size: 22
12580 TGTCTCTATG
* * *
12590 TGGTTATCAAAATTTCATAAGA
1 TGGTTATTAAAATTTCATAGGT
*
12612 TGGTTATTATAATTTCATGAGG-
1 TGGTTATTAAAATTTCAT-AGGT
* * *
12634 AGGTTATCAAAATTCCATA-GT
1 TGGTTATTAAAATTTCATAGGT
**
12655 GTGGTTA-CCAAA-TTCATA-GT
1 -TGGTTATTAAAATTTCATAGGT
**
12675 CTGGTTACCAAAATTTCATAGGAT
1 -TGGTTATTAAAATTTCATAGG-T
* *
12699 CAT-GTTATTAAAATCTCTTAGGT
1 --TGGTTATTAAAATTTCATAGGT
* *
12722 TGGTTATTGAAATTTCATAGGG
1 TGGTTATTAAAATTTCATAGGT
12744 TGGTTA
1 TGGTTA
12750 ATTATCACAA
Statistics
Matches: 108, Mismatches: 21, Indels: 18
0.73 0.14 0.12
Matches are distributed among these distances:
20 14 0.13
21 10 0.09
22 63 0.58
23 4 0.04
24 16 0.15
25 1 0.01
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.39
Consensus pattern (22 bp):
TGGTTATTAAAATTTCATAGGT
Found at i:12810 original size:22 final size:22
Alignment explanation
Indices: 12785--12843 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
12775 ACCAAAGAGA
*
12785 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAGCGAGG
* *
12807 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAGCGAGG
*
12829 TTAACAAAATTTCAT
1 TTATCAAAATTTCAT
12844 TAAATATTCC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 2 0.06
22 27 0.87
23 2 0.06
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATAGCGAGG
Found at i:12882 original size:23 final size:23
Alignment explanation
Indices: 12856--12914 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 23
12846 AATATTCCAT
* *
12856 GTGTAGGTTATCAAATTTTTATA
1 GTGTAGGTTATCAAAATTTCATA
*
12879 GTGT-GGTTCTCAAAATTTCATA
1 GTGTAGGTTATCAAAATTTCATA
*
12901 -TGAAGGTTAT-AAAA
1 GTGTAGGTTATCAAAA
12915 GTCTCAATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
21 6 0.20
22 20 0.67
23 4 0.13
ACGTcount: A:0.34, C:0.07, G:0.19, T:0.41
Consensus pattern (23 bp):
GTGTAGGTTATCAAAATTTCATA
Found at i:13068 original size:22 final size:22
Alignment explanation
Indices: 12971--13075 Score: 72
Period size: 22 Copynumber: 4.7 Consensus size: 22
12961 ATCTCTTAGA
*
12971 GAGATTATCGAAATTTCATAGAGATC
1 GAGATTATCAAAATTTCA-A-AG--C
* *
12997 G-GATTATCAAAATTT-ATAGA
1 GAGATTATCAAAATTTCAAAGC
* * * *
13017 AAGATTACCAAAATTTCATAGT
1 GAGATTATCAAAATTTCAAAGC
*
13039 GTTG-TTATCAAAATTTCAAAGC
1 G-AGATTATCAAAATTTCAAAGC
13061 GAGATTATCAAAATT
1 GAGATTATCAAAATT
13076 ATATAATGTG
Statistics
Matches: 63, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
21 14 0.22
22 33 0.52
23 1 0.02
24 1 0.02
25 13 0.21
26 1 0.02
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.33
Consensus pattern (22 bp):
GAGATTATCAAAATTTCAAAGC
Found at i:13074 original size:44 final size:46
Alignment explanation
Indices: 12968--13075 Score: 123
Period size: 46 Copynumber: 2.4 Consensus size: 46
12958 TAAATCTCTT
* *
12968 AGAGAGATTATCGAAATTTCATAGAGATCGGATTATCAAAATTTAT
1 AGAGAGATTATCAAAATTTCATAGAGATCGGATTATCAAAATTTAA
* * * *
13014 AGAAAGATTACCAAAATTTCATAGTG-T-TG-TTATCAAAATTTCAA
1 AGAGAGATTATCAAAATTTCATAGAGATCGGATTATCAAAATTT-AA
*
13058 AGCGAGATTATCAAAATT
1 AGAGAGATTATCAAAATT
13076 ATATAATGTG
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
43 12 0.23
44 17 0.33
45 1 0.02
46 22 0.42
ACGTcount: A:0.43, C:0.10, G:0.15, T:0.32
Consensus pattern (46 bp):
AGAGAGATTATCAAAATTTCATAGAGATCGGATTATCAAAATTTAA
Found at i:13091 original size:44 final size:45
Alignment explanation
Indices: 12998--13100 Score: 106
Period size: 44 Copynumber: 2.4 Consensus size: 45
12988 ATAGAGATCG
* *
12998 GATTATCAAAATTT-ATAGAAAGATTACCAAAATTTCATAGTGTT
1 GATTATCAAAATTTCAAAGAAAGATTACCAAAATTTCATAATGTT
** *
13042 G-TTATCAAAATTTCAAAGCGAGATTATCAAAATTAT-ATAATG-T
1 GATTATCAAAATTTCAAAGAAAGATTACCAAAATT-TCATAATGTT
**
13085 GATTATCGGAATTTCA
1 GATTATCAAAATTTCA
13101 TGGAGGGGTC
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
43 14 0.29
44 34 0.69
45 1 0.02
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.36
Consensus pattern (45 bp):
GATTATCAAAATTTCAAAGAAAGATTACCAAAATTTCATAATGTT
Found at i:13453 original size:222 final size:222
Alignment explanation
Indices: 13186--13647 Score: 897
Period size: 222 Copynumber: 2.1 Consensus size: 222
13176 TTCTGGGGCG
13186 GTTATCAAAATTTCATAGTATGGTTACCAAATTAGGAAGGTTATCAAACTTTTATTATATCAAAA
1 GTTATCAAAATTTCATAGTATGGTTACCAAATTAGGAAGGTTATCAAACTTTTATTATATCAAAA
13251 TTTAGGGAGGATATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGTTTAGTTTTCAAAATT
66 TTTAGGGAGGATATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGTTTAGTTTTCAAAATT
*
13316 TCACAAGAGGGTTATCAAAATTTCATAGTATGTAGATCAAAATTTCATAAGGAGATTAACAAAAT
131 TCACAAGAGGGTTATCAAAATTTCATAGCATGTAGATCAAAATTTCATAAGGAGATTAACAAAAT
13381 TTGTAGTTATCAAGATTTCATAAGAAA
196 TTGTAGTTATCAAGATTTCATAAGAAA
13408 GTTATCAAAATTTCATAGTATGGTTACCAAATTAGGAAGGTTATCAAACTTTTATTATATCAAAA
1 GTTATCAAAATTTCATAGTATGGTTACCAAATTAGGAAGGTTATCAAACTTTTATTATATCAAAA
13473 TTTAGGGAGGATATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGTTTAGTTTTCAAAATT
66 TTTAGGGAGGATATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGTTTAGTTTTCAAAATT
*
13538 TCACAAGAGGGTTATCAAAATTTCATAGCATGTAGATCAAAATTTCATAGGGAGATTAACAAAAT
131 TCACAAGAGGGTTATCAAAATTTCATAGCATGTAGATCAAAATTTCATAAGGAGATTAACAAAAT
13603 TTGTAGTTATCAAGATTTCATAAGAAA
196 TTGTAGTTATCAAGATTTCATAAGAAA
*
13630 GTTATCAAAATTTTATAG
1 GTTATCAAAATTTCATAG
13648 GGAGGTTTAT
Statistics
Matches: 237, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
222 237 1.00
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.36
Consensus pattern (222 bp):
GTTATCAAAATTTCATAGTATGGTTACCAAATTAGGAAGGTTATCAAACTTTTATTATATCAAAA
TTTAGGGAGGATATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGTTTAGTTTTCAAAATT
TCACAAGAGGGTTATCAAAATTTCATAGCATGTAGATCAAAATTTCATAAGGAGATTAACAAAAT
TTGTAGTTATCAAGATTTCATAAGAAA
Found at i:13640 original size:82 final size:84
Alignment explanation
Indices: 13524--13688 Score: 199
Period size: 82 Copynumber: 2.0 Consensus size: 84
13514 TTTCATAGTT
* ** *
13524 TAGTTTTCAAAATTTCACAAGAGGGTTATCAAAATTTCATA-GCATGTAGATCAAAATTTCATAG
1 TAGTTATCAAAATTTCACAAGAAAGTTATCAAAATTTCATAGGCAGGTAGATCAAAATTTCATAG
*
13588 GGAGA-TTAACAAAATTTG
66 GAAGATTTAACAAAATTTG
* * * * ** *
13606 TAGTTATCAAGATTTCATAAGAAAGTTATCAAAATTTTATAGGGAGGTTTATCAAAATTTTATAG
1 TAGTTATCAAAATTTCACAAGAAAGTTATCAAAATTTCATAGGCAGGTAGATCAAAATTTCATAG
*
13671 GAAGATTTATCAAAATTT
66 GAAGATTTAACAAAATTT
13689 CATAGCGAGG
Statistics
Matches: 68, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
82 35 0.51
83 22 0.32
84 11 0.16
ACGTcount: A:0.41, C:0.08, G:0.15, T:0.36
Consensus pattern (84 bp):
TAGTTATCAAAATTTCACAAGAAAGTTATCAAAATTTCATAGGCAGGTAGATCAAAATTTCATAG
GAAGATTTAACAAAATTTG
Found at i:13661 original size:23 final size:23
Alignment explanation
Indices: 13631--13700 Score: 104
Period size: 23 Copynumber: 3.0 Consensus size: 23
13621 CATAAGAAAG
13631 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGGAGGT
* *
13654 TTATCAAAATTTTATAGGAAGAT
1 TTATCAAAATTTTATAGGGAGGT
* *
13677 TTATCAAAATTTCATAGCGAGGT
1 TTATCAAAATTTTATAGGGAGGT
13700 T
1 T
13701 ATTGCAATTT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.39
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGGAGGT
Found at i:13683 original size:46 final size:45
Alignment explanation
Indices: 13609--13734 Score: 121
Period size: 45 Copynumber: 2.8 Consensus size: 45
13599 AAATTTGTAG
* * *
13609 TTATCAAGATTTCATAAGAAAGTTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTCATAAGAAAGTTATCAAAATTTCATAGCGAGGT
* * *
13654 TTATCAAAATTTTATAGGAAGATTTATCAAAATTTCATAGCGAGG-
1 TTATCAAAATTTCATAAGAA-AGTTATCAAAATTTCATAGCGAGGT
*** **
13699 TTATTGCAATTTCATAATGTGA-TTATCAAAATTTCA
1 TTATCAAAATTTCATAA-GAAAGTTATCAAAATTTCA
13735 GAGTGTGATT
Statistics
Matches: 66, Mismatches: 13, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
44 14 0.21
45 30 0.45
46 22 0.33
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.38
Consensus pattern (45 bp):
TTATCAAAATTTCATAAGAAAGTTATCAAAATTTCATAGCGAGGT
Found at i:13843 original size:23 final size:22
Alignment explanation
Indices: 13253--13866 Score: 207
Period size: 22 Copynumber: 29.1 Consensus size: 22
13243 TATCAAAATT
* *
13253 TAGGGAGGATATCAAAATTTCA
1 TAGGTAGGTTATCAAAATTTCA
* *
13275 TATGAAGGTTATCAAAATTTCA
1 TAGGTAGGTTATCAAAATTTCA
* *
13297 TAGTTTA-GTTTTCAAAATTTCA
1 TAG-GTAGGTTATCAAAATTTCA
* *
13319 CAAG-AGGGTTATCAAAATTTCA
1 TAGGTA-GGTTATCAAAATTTCA
* *
13341 TA-GTATGTAGATCAAAATTTCA
1 TAGGTAGGT-TATCAAAATTTCA
* *
13363 TAAGG-AGATTAACAAAA-TT--
1 T-AGGTAGGTTATCAAAATTTCA
*
13382 T--GTA-GTTATCAAGATTTCA
1 TAGGTAGGTTATCAAAATTTCA
* * *
13401 TAAGAAAGTTATCAAAATTTCA
1 TAGGTAGGTTATCAAAATTTCA
*
13423 TA-GTATGGTTA-CCAAA--T--
1 TAGGTA-GGTTATCAAAATTTCA
* *
13440 TAGGAAGGTTATCAAACTTT--
1 TAGGTAGGTTATCAAAATTTCA
*
13460 TA-TTA---TATCAAAA-TT--
1 TAGGTAGGTTATCAAAATTTCA
* *
13475 TAGGGAGGATATCAAAATTTCA
1 TAGGTAGGTTATCAAAATTTCA
* *
13497 TATGAAGGTTATCAAAATTTCA
1 TAGGTAGGTTATCAAAATTTCA
* *
13519 TAGTTTA-GTTTTCAAAATTTCA
1 TAG-GTAGGTTATCAAAATTTCA
* *
13541 CAAG-AGGGTTATCAAAATTTCA
1 TAGGTA-GGTTATCAAAATTTCA
* * *
13563 TA-GCATGTAGATCAAAATTTCA
1 TAGGTAGGT-TATCAAAATTTCA
* * *
13585 TAGGGAGATTAACAAAA-TT--
1 TAGGTAGGTTATCAAAATTTCA
*
13604 T--GTA-GTTATCAAGATTTCA
1 TAGGTAGGTTATCAAAATTTCA
* * * *
13623 TAAGAAAGTTATCAAAATTTTA
1 TAGGTAGGTTATCAAAATTTCA
* *
13645 TAGGGAGGTTTATCAAAATTTTA
1 TAGGTAGG-TTATCAAAATTTCA
* *
13668 TAGGAAGATTTATCAAAATTTCA
1 TAGGTAG-GTTATCAAAATTTCA
***
13691 TAGCG-AGGTTATTGCAATTTCA
1 TAG-GTAGGTTATCAAAATTTCA
* *
13713 TAATGT-GATTATCAAAATTTCA
1 T-AGGTAGGTTATCAAAATTTCA
* * *
13735 GAGTGT-GATTA-C-TAA-TTCA
1 TAG-GTAGGTTATCAAAATTTCA
* * *
13754 TATGG-AGGTTTTTAAATTTTCA
1 TA-GGTAGGTTATCAAAATTTCA
* * * *
13776 TAACGT-GGTTATCAATATATGA
1 T-AGGTAGGTTATCAAAATTTCA
* *
13798 TATGG-AGGTTATCAACATCTCA
1 TA-GGTAGGTTATCAAAATTTCA
*
13820 TAGTGTTGGTTATCAAAATTTCA
1 TAG-GTAGGTTATCAAAATTTCA
* *
13843 TTGGTAAGTTATCAAAATTTCA
1 TAGGTAGGTTATCAAAATTTCA
13865 TA
1 TA
13867 TTGAGCTCTT
Statistics
Matches: 435, Mismatches: 102, Indels: 110
0.67 0.16 0.17
Matches are distributed among these distances:
15 4 0.01
16 23 0.05
17 14 0.03
18 5 0.01
19 23 0.05
20 10 0.02
21 25 0.06
22 265 0.61
23 64 0.15
24 2 0.00
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.37
Consensus pattern (22 bp):
TAGGTAGGTTATCAAAATTTCA
Found at i:14996 original size:32 final size:33
Alignment explanation
Indices: 14926--15034 Score: 100
Period size: 33 Copynumber: 3.3 Consensus size: 33
14916 GCCGCCCTAG
* *
14926 TGGGGCGACAC-AGCCGTGGCTAAGCCG-CCCCAC
1 TGGGGCGGCACTAGCCATGGC-AAGCCGTCCCC-C
* *
14959 CGGGGCGGC-CT-GCCCTGGCACAGCCGTCCCCC
1 TGGGGCGGCACTAGCCATGGCA-AGCCGTCCCCC
* *
14991 TGGGGCGGCACTAGCCATGGGAAGCCGTCCTCC
1 TGGGGCGGCACTAGCCATGGCAAGCCGTCCCCC
*
15024 TGAGGCGGCAC
1 TGGGGCGGCAC
15035 GCGCATCAGC
Statistics
Matches: 63, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
31 1 0.02
32 22 0.35
33 33 0.52
34 7 0.11
ACGTcount: A:0.14, C:0.39, G:0.36, T:0.11
Consensus pattern (33 bp):
TGGGGCGGCACTAGCCATGGCAAGCCGTCCCCC
Found at i:18579 original size:9 final size:9
Alignment explanation
Indices: 18565--18614 Score: 50
Period size: 9 Copynumber: 5.7 Consensus size: 9
18555 TAGATTTATG
18565 ATATATAAT
1 ATATATAAT
18574 ATATATAAT
1 ATATATAAT
18583 AT-T-TAATT
1 ATATATAA-T
* *
18591 ATTTATGAT
1 ATATATAAT
*
18600 ATATATAAA
1 ATATATAAT
18609 ATATAT
1 ATATAT
18615 GTAAAATATA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
7 3 0.09
8 4 0.12
9 25 0.74
10 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (9 bp):
ATATATAAT
Found at i:18646 original size:20 final size:20
Alignment explanation
Indices: 18590--18646 Score: 51
Period size: 20 Copynumber: 2.8 Consensus size: 20
18580 AATATTTAAT
18590 TATTTATGATATATATAAAATA
1 TATTTATGAT-T-TATAAAATA
* ** * *
18612 TATGTAAAATATATAAATTA
1 TATTTATGATTTATAAAATA
18632 TATTTATGATTTATA
1 TATTTATGATTTATA
18647 TAAAAGATAT
Statistics
Matches: 26, Mismatches: 9, Indels: 2
0.70 0.24 0.05
Matches are distributed among these distances:
20 19 0.73
22 7 0.27
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (20 bp):
TATTTATGATTTATAAAATA
Found at i:26801 original size:2 final size:2
Alignment explanation
Indices: 26796--26820 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
26786 ATTGTGTGTG
26796 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 T
26821 CTTAATATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:26904 original size:33 final size:33
Alignment explanation
Indices: 26862--26957 Score: 183
Period size: 33 Copynumber: 2.9 Consensus size: 33
26852 GTATATATAA
*
26862 TTCAAAAACAGGAGGCAAAAAAGGAAGAGATAG
1 TTCAAAAACATGAGGCAAAAAAGGAAGAGATAG
26895 TTCAAAAACATGAGGCAAAAAAGGAAGAGATAG
1 TTCAAAAACATGAGGCAAAAAAGGAAGAGATAG
26928 TTCAAAAACATGAGGCAAAAAAGGAAGAGA
1 TTCAAAAACATGAGGCAAAAAAGGAAGAGA
26958 AACAATATAT
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 62 1.00
ACGTcount: A:0.55, C:0.09, G:0.25, T:0.10
Consensus pattern (33 bp):
TTCAAAAACATGAGGCAAAAAAGGAAGAGATAG
Found at i:27977 original size:4 final size:4
Alignment explanation
Indices: 27970--27994 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
27960 AAGACTAACA
27970 TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT T
27995 ATGGAACTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:32569 original size:23 final size:23
Alignment explanation
Indices: 32539--32584 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
32529 GATTAGTTTG
*
32539 TAGAGACCGAGCGAGAGTGCTCA
1 TAGAGACCGAACGAGAGTGCTCA
32562 TAGAGACCGAACGAGAGTGCTCA
1 TAGAGACCGAACGAGAGTGCTCA
32585 AGATTGTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.33, C:0.22, G:0.33, T:0.13
Consensus pattern (23 bp):
TAGAGACCGAACGAGAGTGCTCA
Found at i:33975 original size:27 final size:28
Alignment explanation
Indices: 33937--33993 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 28
33927 ATCCTAAAAG
* *
33937 TACTGATCTTTCAATTATTATA-CCTCC
1 TACTGAACTTTCAATTATGATATCCTCC
33964 TACTGAACTTTCAATTATGATATCCTCC
1 TACTGAACTTTCAATTATGATATCCTCC
33992 TA
1 TA
33994 AAAGAATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 20 0.74
28 7 0.26
ACGTcount: A:0.28, C:0.25, G:0.05, T:0.42
Consensus pattern (28 bp):
TACTGAACTTTCAATTATGATATCCTCC
Found at i:36086 original size:41 final size:40
Alignment explanation
Indices: 36026--36103 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 40
36016 CGCATTAACC
36026 TTCAATCTACAAAGCTGACATTTTATGACATCTGTTCTGGT
1 TTCAATCTACAAAGCTGACATTTTATGACATCT-TTCTGGT
*
36067 TTCAATCTACAAAGGTGACATTTTATGACATCTTTCT
1 TTCAATCTACAAAGCTGACATTTTATGACATCTTTCT
36104 TAACCCTGTT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
40 4 0.11
41 32 0.89
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (40 bp):
TTCAATCTACAAAGCTGACATTTTATGACATCTTTCTGGT
Found at i:38324 original size:30 final size:28
Alignment explanation
Indices: 38260--38321 Score: 101
Period size: 26 Copynumber: 2.3 Consensus size: 28
38250 ATCAAACTAG
*
38260 AAACAAACTACCTGCCTAACAAATACAT
1 AAACAAACTACCTACCTAACAAATACAT
38288 AAACAAAC-A-CTACCTAACAAATACAT
1 AAACAAACTACCTACCTAACAAATACAT
38314 AAACAAAC
1 AAACAAAC
38322 AAATTACAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
26 24 0.73
27 1 0.03
28 8 0.24
ACGTcount: A:0.56, C:0.27, G:0.02, T:0.15
Consensus pattern (28 bp):
AAACAAACTACCTACCTAACAAATACAT
Found at i:38642 original size:22 final size:22
Alignment explanation
Indices: 38598--38643 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
38588 GCTGGTTTGC
* *
38598 TTGGACCACATAATAGCATATA
1 TTGGAACACATAATAACATATA
38620 TTGGAACACTATAATAACAATATA
1 TTGGAACAC-ATAATAAC-ATATA
38644 ATCAGGCTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 8 0.40
23 7 0.35
24 5 0.25
ACGTcount: A:0.46, C:0.15, G:0.11, T:0.28
Consensus pattern (22 bp):
TTGGAACACATAATAACATATA
Found at i:39941 original size:167 final size:165
Alignment explanation
Indices: 39570--40015 Score: 588
Period size: 167 Copynumber: 2.7 Consensus size: 165
39560 TGAGTCATTT
*
39570 GTCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGGCAT
1 GTCAATTGAGAAATGACCAAAAA-ATTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGGCAT
* * * ** * *
39635 TTAAGTAATCTGCCAAGTAGGTAAAGACGAAAAAAAAAAGAGTTCTCTAGCTCATCATCAATCAT
65 TTAAGTAATCTGCCAAGTAGGAAAAGACG-AAAAAAATA-AGTTCTCTAACTCAAAAGCAAGCAT
* * *
39700 TGATGGGGATCTTTTATTAATTCCACTACTCTATTCAA
128 TGATAGGGATCTTTTAGTAATTCCACTACTCTATTAAA
* * * *
39738 GTCCATTGAGAATTGACCAAAAAAATTACTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
1 GTCAATTGAGAAATGACC-AAAAAATTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGGCAT
* * * *
39803 TTAAGTAATTTACCAAGTAGGAAAAGACGAAAAAAATAAGTTCTGTAACTCTAAAAGCAAGCCTT
65 TTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAATAAGTTCTCTAACTC-AAAAGCAAGCATT
* * *
39868 GGTATGGATCTTTTAGTAATTCCACTACTTTATTAAA
129 GATAGGGATCTTTTAGTAATTCCACTACTCTATTAAA
*
39905 GTCAATTGAGAAATGACCAAAAAATCTAGTTATTTAATCACCTCAAGAATCAAAAGTTAGGGCAT
1 GTCAATTGAGAAATGACCAAAAAAT-TAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGGCAT
* * *
39970 TTAAGTAATCGGTCAAGT-GTGAAAAGACGAAAAAAATTAGTTCTCT
65 TTAAGTAATCTGCCAAGTAG-GAAAAGACGAAAAAAATAAGTTCTCT
40016 CGCTCCTCAT
Statistics
Matches: 241, Mismatches: 33, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
166 19 0.08
167 137 0.57
168 80 0.33
169 5 0.02
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.29
Consensus pattern (165 bp):
GTCAATTGAGAAATGACCAAAAAATTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGGCATT
TAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAATAAGTTCTCTAACTCAAAAGCAAGCATTGA
TAGGGATCTTTTAGTAATTCCACTACTCTATTAAA
Found at i:41051 original size:45 final size:45
Alignment explanation
Indices: 41001--41086 Score: 138
Period size: 45 Copynumber: 1.9 Consensus size: 45
40991 ACTTCTCCAG
* *
41001 CTCATCATTAA-TCTGGGGTAGGGATCTTTTAGTAATTCCACCCAC
1 CTCATCATTAATTC-GGGGAAGGGATCTTTTAGTAATACCACCCAC
41046 CTCATCATTAATTCGGGGAAGGGATCTTTTAGTAATACCAC
1 CTCATCATTAATTCGGGGAAGGGATCTTTTAGTAATACCAC
41087 GACTCTATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
45 36 0.95
46 2 0.05
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.33
Consensus pattern (45 bp):
CTCATCATTAATTCGGGGAAGGGATCTTTTAGTAATACCACCCAC
Found at i:41284 original size:2 final size:2
Alignment explanation
Indices: 41277--41317 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
41267 TAATATGTAG
41277 TA TA TA 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 TA TA TA T
41318 GTTTGGTGTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:41684 original size:29 final size:31
Alignment explanation
Indices: 41652--41718 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
41642 ATGCAATTTG
41652 GGATATAACGTTAC-AAAA-CAAACAATTAA
1 GGATATAACGTTACGAAAATCAAACAATTAA
* * *
41681 GGATATAATGTTACGAAAATCGAGCAATTAA
1 GGATATAACGTTACGAAAATCAAACAATTAA
41712 GGATATA
1 GGATATA
41719 GTCCGTTAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 13 0.39
30 4 0.12
31 16 0.48
ACGTcount: A:0.49, C:0.10, G:0.16, T:0.24
Consensus pattern (31 bp):
GGATATAACGTTACGAAAATCAAACAATTAA
Found at i:42863 original size:3 final size:3
Alignment explanation
Indices: 42855--42907 Score: 88
Period size: 3 Copynumber: 17.7 Consensus size: 3
42845 AAAATTTAGG
* *
42855 ATT ATT ATT GTT GTT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
42903 ATT AT
1 ATT AT
42908 AAAATACGGG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:42989 original size:31 final size:31
Alignment explanation
Indices: 42948--43055 Score: 105
Period size: 31 Copynumber: 3.5 Consensus size: 31
42938 GTCAAATACC
* *
42948 CAATTTAGGATATAACGTTTGCTGCCGCAAG
1 CAATTAAGGATATAACGTTTGCTGTCGCAAG
* *
42979 CAATTAAGGATATAACGTTTTTGATTTCG--AG
1 CAATTAAGGATATAACG--TTTGCTGTCGCAAG
* **
43010 CAATTAAGGATATAACGTTTTC-GATTTCAAG
1 CAATTAAGGATATAACGTTTGCTG-TCGCAAG
43041 CAATTAAGGATATAA
1 CAATTAAGGATATAA
43056 TCAGTTAGGG
Statistics
Matches: 63, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
29 4 0.06
31 52 0.83
33 7 0.11
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (31 bp):
CAATTAAGGATATAACGTTTGCTGTCGCAAG
Found at i:43208 original size:31 final size:29
Alignment explanation
Indices: 43173--43239 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 29
43163 CTCTAACGGA
43173 TTATATCCTTAATTGCTCGCTTTTGGTAACG
1 TTATATCCTTAATTGCTCG-TTTT-GTAACG
*
43204 TTATATCCTTAATTGCTTGTTTTGTAACG
1 TTATATCCTTAATTGCTCGTTTTGTAACG
43233 TTATATC
1 TTATATC
43240 TCAAATTGCA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
29 13 0.37
30 4 0.11
31 18 0.51
ACGTcount: A:0.21, C:0.16, G:0.13, T:0.49
Consensus pattern (29 bp):
TTATATCCTTAATTGCTCGTTTTGTAACG
Found at i:43246 original size:29 final size:31
Alignment explanation
Indices: 43173--43248 Score: 95
Period size: 29 Copynumber: 2.5 Consensus size: 31
43163 CTCTAACGGA
*
43173 TTATATCCTTAATTGCTCGCTTTTGGTAACG
1 TTATATCCTAAATTGCTCGCTTTTGGTAACG
* *
43204 TTATATCCTTAATTGCTTG-TTTT-GTAACG
1 TTATATCCTAAATTGCTCGCTTTTGGTAACG
43233 TTATAT-CTCAAATTGC
1 TTATATCCT-AAATTGC
43249 ATTTTGAAGC
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
28 2 0.05
29 18 0.43
30 4 0.10
31 18 0.43
ACGTcount: A:0.22, C:0.17, G:0.13, T:0.47
Consensus pattern (31 bp):
TTATATCCTAAATTGCTCGCTTTTGGTAACG
Found at i:44636 original size:30 final size:30
Alignment explanation
Indices: 44602--44660 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
44592 GCAGAAATGA
* * *
44602 TAGTGGAAGAGGTGGAAACTGTGGCGGAGG
1 TAGTGGAAAAGGTAGAAACCGTGGCGGAGG
*
44632 TAGTGGAAAAGGTAGCAACCGTGGCGGAG
1 TAGTGGAAAAGGTAGAAACCGTGGCGGAG
44661 AAGGTATCAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.29, C:0.10, G:0.46, T:0.15
Consensus pattern (30 bp):
TAGTGGAAAAGGTAGAAACCGTGGCGGAGG
Found at i:46652 original size:11 final size:11
Alignment explanation
Indices: 46636--46660 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
46626 AGAGTACTCA
46636 AAAACACAATT
1 AAAACACAATT
46647 AAAACACAATT
1 AAAACACAATT
46658 AAA
1 AAA
46661 GAGAAAAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.16, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAACACAATT
Found at i:47154 original size:54 final size:54
Alignment explanation
Indices: 47069--47186 Score: 200
Period size: 54 Copynumber: 2.2 Consensus size: 54
47059 AGAATGGCTT
* * *
47069 GGTGCAGGAGCCGCTACAGGGGACTTGGTGGGGCCAGAGTGTACGACGGGAGAC
1 GGTGCAGGAGCCGCTACAGGGGACATAGTGGGGCCAGAGTGGACGACGGGAGAC
*
47123 GGTGCAGGAGCCGCTACAGGTGACATAGTGGGGCCAGAGTGGACGACGGGAGAC
1 GGTGCAGGAGCCGCTACAGGGGACATAGTGGGGCCAGAGTGGACGACGGGAGAC
47177 GGTGCAGGAG
1 GGTGCAGGAG
47187 ACGGTGGGTT
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 60 1.00
ACGTcount: A:0.22, C:0.19, G:0.47, T:0.12
Consensus pattern (54 bp):
GGTGCAGGAGCCGCTACAGGGGACATAGTGGGGCCAGAGTGGACGACGGGAGAC
Found at i:47284 original size:87 final size:82
Alignment explanation
Indices: 47157--47441 Score: 366
Period size: 81 Copynumber: 3.5 Consensus size: 82
47147 ATAGTGGGGC
*
47157 CAGAGTGGACGACGGGAGACGGTGCAGGAGACGGTGGGTTAACGGGATGACTTGGCGCATGAGAA
1 CAGAGTGGACGACGGGAGACGGTGCAGGAGACGGTGGGTTAACGGGATGGCTTGGCGCATGAGAA
47222 GGAACAGGAGACTGGGTGGGTG
66 GGAACAGGAGA-----TGGGTG
* * * *
47244 CAGAGTGGACAACGGGGGACGGTGCAGGAGACGGTGGGTTAACGGAATGGCTTGGAGCATGAGAA
1 CAGAGTGGACGACGGGAGACGGTGCAGGAGACGGTGGGTTAACGGGATGGCTTGGCGCATGAGAA
47309 GGAACAGGA-ATGGGTG
66 GGAACAGGAGATGGGTG
* * *
47325 CAGAGTGGACGACGGGTGACGGTGCATGAG-CTGGTGGGTTGACGGGATGGCTTGGCGCATGAGA
1 CAGAGTGGACGACGGGAGACGGTGCAGGAGAC-GGTGGGTTAACGGGATGGCTTGGCGCATGAGA
47389 AGGAACAGGAGA----TG
65 AGGAACAGGAGATGGGTG
* * * *
47403 CAGAGTGGACGACGGGAGATGGCGCATGAGCCGGTGGGT
1 CAGAGTGGACGACGGGAGACGGTGCAGGAGACGGTGGGT
47442 GATTACGATG
Statistics
Matches: 181, Mismatches: 14, Indels: 15
0.86 0.07 0.07
Matches are distributed among these distances:
78 36 0.20
79 1 0.01
80 1 0.01
81 72 0.40
82 1 0.01
86 1 0.01
87 69 0.38
ACGTcount: A:0.25, C:0.14, G:0.47, T:0.14
Consensus pattern (82 bp):
CAGAGTGGACGACGGGAGACGGTGCAGGAGACGGTGGGTTAACGGGATGGCTTGGCGCATGAGAA
GGAACAGGAGATGGGTG
Found at i:50434 original size:32 final size:31
Alignment explanation
Indices: 50398--50467 Score: 104
Period size: 32 Copynumber: 2.2 Consensus size: 31
50388 AACAATAGTG
* *
50398 ATGATTTTTTTTTTTTGCTACTAAGAATAATA
1 ATGATTTTTTTTTTTTGCCA-GAAGAATAATA
50430 ATGATTTTTTTTTTTTTGCCAGAAGAATAATA
1 ATGA-TTTTTTTTTTTTGCCAGAAGAATAATA
50462 ATGATT
1 ATGATT
50468 AAAAAAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
31 2 0.06
32 18 0.51
33 15 0.43
ACGTcount: A:0.31, C:0.06, G:0.11, T:0.51
Consensus pattern (31 bp):
ATGATTTTTTTTTTTTGCCAGAAGAATAATA
Found at i:51375 original size:1 final size:1
Alignment explanation
Indices: 51364--51411 Score: 78
Period size: 1 Copynumber: 48.0 Consensus size: 1
51354 GAAGAAGAAG
* *
51364 AAAAGAAAAAAAAAAAAAAAAAAAAATAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
51412 CTCTTGAGGA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.96, C:0.00, G:0.02, T:0.02
Consensus pattern (1 bp):
A
Found at i:51389 original size:22 final size:22
Alignment explanation
Indices: 51364--51411 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
51354 GAAGAAGAAG
51364 AAAAGAAAAAAAAAAAAAAAAA
1 AAAAGAAAAAAAAAAAAAAAAA
*
51386 AAAATAAAAAAAAAAAAAAAAA
1 AAAAGAAAAAAAAAAAAAAAAA
51408 AAAA
1 AAAA
51412 CTCTTGAGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.96, C:0.00, G:0.02, T:0.02
Consensus pattern (22 bp):
AAAAGAAAAAAAAAAAAAAAAA
Found at i:62667 original size:15 final size:16
Alignment explanation
Indices: 62647--62688 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
62637 AATCAAAACA
62647 TAATTTT-TAAAATTT
1 TAATTTTATAAAATTT
*
62662 TAATTTTATATAATTT
1 TAATTTTATAAAATTT
**
62678 TTTTTTTATAA
1 TAATTTTATAA
62689 TTAAGGGTCA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TAATTTTATAAAATTT
Found at i:62678 original size:16 final size:15
Alignment explanation
Indices: 62647--62690 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
62637 AATCAAAACA
*
62647 TAATTTTTAAAATTT
1 TAATTTTTATAATTT
62662 TAATTTTATATAATTT
1 TAATTTT-TATAATTT
*
62678 T-TTTTTTATAATT
1 TAATTTTTATAATT
62691 AAGGGTCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
14 7 0.27
15 11 0.42
16 8 0.31
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTATAATTT
Done.