Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012013.1 Corchorus capsularis cultivar CVL-1 contig12034, 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: 36914
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4570 original size:6 final size:6
Alignment explanation
Indices: 4559--4584 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
4549 GTCCTCTCAA
4559 CAATTC CAATTC CAATTC CAATTC CA
1 CAATTC CAATTC CAATTC CAATTC CA
4585 TCAAAATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.31
Consensus pattern (6 bp):
CAATTC
Found at i:9567 original size:102 final size:104
Alignment explanation
Indices: 9431--9637 Score: 328
Period size: 102 Copynumber: 2.0 Consensus size: 104
9421 GTAGAATAAA
* *
9431 ACTGTAAAAATTTATACAATGTTATTTAAGAAATATATTTAAAAA-TTATAATATATCTAAGTTT
1 ACTGCAAAAATTTATACAATGTCATTTAAGAAATATATTTAAAAATTTATAATATATCTAAGTTT
*
9495 -TTTAATTAAAATAGTAAAATGGGAAAAATAAAATAGTT
66 CTTTAATTAAAATAGTAAAACGGGAAAAATAAAATAGTT
* * *
9533 ACTGCAAAAGTTTATACAATGTCATTTAAGAAATATATTTAAAAATTTCTAATATATTTAAGTTT
1 ACTGCAAAAATTTATACAATGTCATTTAAGAAATATATTTAAAAATTTATAATATATCTAAGTTT
* *
9598 CTTTTATTAAAATAGTAAAACGGTAAAAATAAAATAGTT
66 CTTTAATTAAAATAGTAAAACGGGAAAAATAAAATAGTT
9637 A
1 A
9638 TAAAGATATT
Statistics
Matches: 95, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
102 42 0.44
103 17 0.18
104 36 0.38
ACGTcount: A:0.48, C:0.05, G:0.09, T:0.38
Consensus pattern (104 bp):
ACTGCAAAAATTTATACAATGTCATTTAAGAAATATATTTAAAAATTTATAATATATCTAAGTTT
CTTTAATTAAAATAGTAAAACGGGAAAAATAAAATAGTT
Found at i:10121 original size:50 final size:50
Alignment explanation
Indices: 10015--10110 Score: 138
Period size: 50 Copynumber: 1.9 Consensus size: 50
10005 AAATTTCCTG
** * * *
10015 AAAAGTAGGACTGGAGAAGCTTTTTTCAACACGAAGCTATGTGGTTCAAT
1 AAAAGTAGGACTAAAGAAGATTTTTTCAACACCAAGCTATGCGGTTCAAT
*
10065 AAAAGTAGGACTAAAGAAGATTTTTTCAATACCAAGCTATGCGGTT
1 AAAAGTAGGACTAAAGAAGATTTTTTCAACACCAAGCTATGCGGTT
10111 TGGTAAAAGT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 40 1.00
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (50 bp):
AAAAGTAGGACTAAAGAAGATTTTTTCAACACCAAGCTATGCGGTTCAAT
Found at i:13883 original size:26 final size:26
Alignment explanation
Indices: 13830--13885 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
13820 GATGACATTA
* ** **
13830 TTTCTTTTATTCTTAGTATTTTTCCC
1 TTTCTTTTATTCTTAGGATGCTAACC
13856 TTTCTTTTATTCTTAGGATGCTAACC
1 TTTCTTTTATTCTTAGGATGCTAACC
13882 TTTC
1 TTTC
13886 CATTAATTAC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.14, C:0.20, G:0.07, T:0.59
Consensus pattern (26 bp):
TTTCTTTTATTCTTAGGATGCTAACC
Found at i:14900 original size:31 final size:31
Alignment explanation
Indices: 14843--14901 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
14833 ATGTTTTCCG
* *
14843 ATTGTACCCTTATTTTTAAAATATATTTACA
1 ATTGTACCCTTATTTTAAAAACATATTTACA
14874 ATTGTACCCTT-TTTTAAAAAACATATTT
1 ATTGTACCCTTATTTT-AAAAACATATTT
14902 CTAAATTGCC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 4 0.16
31 21 0.84
ACGTcount: A:0.36, C:0.14, G:0.03, T:0.47
Consensus pattern (31 bp):
ATTGTACCCTTATTTTAAAAACATATTTACA
Found at i:15112 original size:38 final size:38
Alignment explanation
Indices: 15038--15122 Score: 100
Period size: 38 Copynumber: 2.3 Consensus size: 38
15028 TTGTTTTCAA
* * *
15038 CGTTCTATTTAATTTTGCCTTTTGTCTTTGTTTCCAAT
1 CGTTCTATTTAATTTTGCCTTTTATCTTCGTCTCCAAT
* **
15076 CGTTGTATTTAATTTTGTTTTTTATCTTCGTCTCCAA-
1 CGTTCTATTTAATTTTGCCTTTTATCTTCGTCTCCAAT
*
15113 CGTCCTATTT
1 CGTTCTATTT
15123 GGGCTTATAA
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
37 8 0.21
38 31 0.79
ACGTcount: A:0.14, C:0.19, G:0.11, T:0.56
Consensus pattern (38 bp):
CGTTCTATTTAATTTTGCCTTTTATCTTCGTCTCCAAT
Found at i:15200 original size:22 final size:21
Alignment explanation
Indices: 15172--15555 Score: 183
Period size: 22 Copynumber: 17.6 Consensus size: 21
15162 TGGTCCAATT
*
15172 TCAAAATTTCAAAGCGAGGTTA
1 TCAAAATTTCATAG-GAGGTTA
* * * *
15194 TCAAAATTACATAATGCGATTA
1 TCAAAATTTCAT-AGGAGGTTA
*
15216 TCAAAAAATT-ATAGAGAGGTTA
1 TC-AAAATTTCATAG-GAGGTTA
*
15238 TCAAAATTT-GTA--A--TTA
1 TCAAAATTTCATAGGAGGTTA
*
15254 TCAAGATTTCATAAGGAGGTTA
1 TCAAAATTTCAT-AGGAGGTTA
* *
15276 TCAAAATTTTATAGGGAGATTTA
1 TCAAAATTTCATA-GGAG-GTTA
*
15299 TCAAAATTTTATAGGAAGGTTTA
1 TCAAAATTTCATAGG-AGG-TTA
*
15322 TCAAAATTTCATAGCGATGTTA
1 TCAAAATTTCATAG-GAGGTTA
* * *
15344 TCACAATTTCATAGTGTGATTA
1 TCAAAATTTCATAG-GAGGTTA
* * *
15366 TCAAAATTTCAGAGTGTGATTA
1 TCAAAATTTCATAG-GAGGTTA
* * *
15388 CTGACAA-TTCATATGGAGGTTT
1 -TCAAAATTTCATA-GGAGGTTA
* * * *
15410 TTAAATTTTCATAACGTGGTTA
1 TCAAAATTTCAT-AGGAGGTTA
* *
15432 TCAATATATCATATGGAGGTTA
1 TCAAAATTTCATA-GGAGGTTA
* * *
15454 TCAATATCTT-ATAGTGTTGATTA
1 TCAAAAT-TTCATAG-G-AGGTTA
*
15477 TCAAAATTTCATAGTGAGATCT-
1 TCAAAATTTCATAG-GAGGT-TA
* * *
15499 TTAAAATTCCTTAGGGAGGTTA
1 TCAAAATTTCATA-GGAGGTTA
*
15521 ACAAAATTTCATAGGAAGGTTA
1 TCAAAATTTCATAGG-AGGTTA
15543 TCAAAATTTCATA
1 TCAAAATTTCATA
15556 AGGATGTCAT
Statistics
Matches: 276, Mismatches: 59, Indels: 54
0.71 0.15 0.14
Matches are distributed among these distances:
16 11 0.04
17 1 0.00
18 2 0.01
20 1 0.00
21 18 0.07
22 175 0.63
23 67 0.24
24 1 0.00
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (21 bp):
TCAAAATTTCATAGGAGGTTA
Found at i:15254 original size:38 final size:38
Alignment explanation
Indices: 15212--15284 Score: 96
Period size: 38 Copynumber: 1.9 Consensus size: 38
15202 ACATAATGCG
15212 ATTATCAAAAAATT-AT-AGAGAGGTTATCAAAATTTGTA
1 ATTATC-AAAAATTCATAAG-GAGGTTATCAAAATTTGTA
* *
15250 ATTATCAAGATTTCATAAGGAGGTTATCAAAATTT
1 ATTATCAAAAATTCATAAGGAGGTTATCAAAATTT
15285 TATAGGGAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
37 5 0.16
38 24 0.77
39 2 0.06
ACGTcount: A:0.44, C:0.07, G:0.14, T:0.36
Consensus pattern (38 bp):
ATTATCAAAAATTCATAAGGAGGTTATCAAAATTTGTA
Found at i:15267 original size:60 final size:61
Alignment explanation
Indices: 15191--15307 Score: 146
Period size: 60 Copynumber: 1.9 Consensus size: 61
15181 CAAAGCGAGG
* *
15191 TTATCAAAATTACATAATGCGATTATCAAAAAATTATAGAGAG-GTTATCAAAATTTGTAA
1 TTATCAAAATTACATAAGGAGATTATCAAAAAATTATAGAGAGAGTTATCAAAATTTGTAA
* * * ** * *
15251 TTATCAAGATTTCATAAGGAGGTTATCAAAATTTTATAGGGAGATTTATCAAAATTT
1 TTATCAAAATTACATAAGGAGATTATCAAAAAATTATAGAGAGAGTTATCAAAATTT
15308 TATAGGAAGG
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
60 35 0.74
61 12 0.26
ACGTcount: A:0.43, C:0.08, G:0.14, T:0.36
Consensus pattern (61 bp):
TTATCAAAATTACATAAGGAGATTATCAAAAAATTATAGAGAGAGTTATCAAAATTTGTAA
Found at i:15345 original size:45 final size:43
Alignment explanation
Indices: 15172--15555 Score: 205
Period size: 44 Copynumber: 8.8 Consensus size: 43
15162 TGGTCCAATT
* * ** *
15172 TCAAAATTTCAAAGCGAGGTTATCAAAATTACATAATGCGATTA
1 TCAAAATTTCATAG-GAGGTTATCAAAATTTCATAGCGAGATTA
* *
15216 TCAAAAAATT-ATAGAGAGGTTATCAAAA-TT--T-G-TA-ATTA
1 TC-AAAATTTCATAG-GAGGTTATCAAAATTTCATAGCGAGATTA
* * *
15254 TCAAGATTTCATAAGGAGGTTATCAAAATTTTATAGGGAGATTTA
1 TCAAAATTTCAT-AGGAGGTTATCAAAATTTCATAGCGAGA-TTA
*
15299 TCAAAATTTTATAGGAAGGTTTATCAAAATTTCATAGCGATG-TTA
1 TCAAAATTTCATAGG-AGG-TTATCAAAATTTCATAGCGA-GATTA
* * * * * *
15344 TCACAATTTCATAGTGTGATTATCAAAATTTCAGAGTGTGATTA
1 TCAAAATTTCATAG-GAGGTTATCAAAATTTCATAGCGAGATTA
* * * * * * * *
15388 CTGACAA-TTCATATGGAGGTTTTTAAATTTTCATAACGTGGTTA
1 -TCAAAATTTCATA-GGAGGTTATCAAAATTTCATAGCGAGATTA
* * * * *
15432 TCAATATATCATATGGAGGTTATCAATATCTT-ATAGTGTTGATTA
1 TCAAAATTTCATA-GGAGGTTATCAAAAT-TTCATAGCG-AGATTA
* * * * * *
15477 TCAAAATTTCATAGTGAGATCT-TTAAAATTCCTTAGGGAGGTTA
1 TCAAAATTTCATAG-GAGGT-TATCAAAATTTCATAGCGAGATTA
*
15521 ACAAAATTTCATAGGAAGGTTATCAAAATTTCATA
1 TCAAAATTTCATAGG-AGGTTATCAAAATTTCATA
15556 AGGATGTCAT
Statistics
Matches: 258, Mismatches: 57, Indels: 50
0.71 0.16 0.14
Matches are distributed among these distances:
37 5 0.02
38 21 0.08
39 4 0.02
41 2 0.01
42 1 0.00
43 8 0.03
44 121 0.47
45 75 0.29
46 20 0.08
47 1 0.00
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (43 bp):
TCAAAATTTCATAGGAGGTTATCAAAATTTCATAGCGAGATTA
Found at i:15605 original size:62 final size:62
Alignment explanation
Indices: 15525--15676 Score: 241
Period size: 62 Copynumber: 2.5 Consensus size: 62
15515 AGGTTAACAA
** *
15525 AATTTCATAGGAAGGTTATCAAAATTTCATAAGGATGTCATGAAAAATAGTGTAATTATCAT
1 AATTTCATAGGAAGGTTATCAAAATTTCATAAGGACATCATAAAAAATAGTGTAATTATCAT
* *
15587 AATTTCATAGGAATGTTATCAAAATTTCATAAGGACATTATAAAAAATAGTGTAATTATCAT
1 AATTTCATAGGAAGGTTATCAAAATTTCATAAGGACATCATAAAAAATAGTGTAATTATCAT
* *
15649 AATTTAATAGGAAGGTTATCATAATTTC
1 AATTTCATAGGAAGGTTATCAAAATTTC
15677 GTATGAATAT
Statistics
Matches: 82, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
62 82 1.00
ACGTcount: A:0.43, C:0.08, G:0.14, T:0.36
Consensus pattern (62 bp):
AATTTCATAGGAAGGTTATCAAAATTTCATAAGGACATCATAAAAAATAGTGTAATTATCAT
Found at i:15627 original size:22 final size:20
Alignment explanation
Indices: 15473--15631 Score: 62
Period size: 22 Copynumber: 7.5 Consensus size: 20
15463 TATAGTGTTG
15473 ATTATCAAAATTTCATAGTGA
1 ATTATCAAAATTTCATAG-GA
* * *
15494 GATCT-TTAAAATTCCTTAGGGA
1 -AT-TATCAAAATTTCATA-GGA
* *
15516 GGTTAACAAAATTTCATAGGA
1 -ATTATCAAAATTTCATAGGA
15537 AGGTTATCAAAATTTCATAAGG-
1 A--TTATCAAAATTTCAT-AGGA
*
15559 ATGTCATGAAAA----ATAGTGTA
1 AT-T-ATCAAAATTTCATAG-G-A
*
15579 ATTATCATAATTTCATAGGA
1 ATTATCAAAATTTCATAGGA
15599 ATGTTATCAAAATTTCATAAGGA
1 A--TTATCAAAATTTCAT-AGGA
15622 CATTAT-AAAA
1 -ATTATCAAAA
15632 AATAGTGTAA
Statistics
Matches: 104, Mismatches: 14, Indels: 39
0.66 0.09 0.25
Matches are distributed among these distances:
17 2 0.02
18 8 0.08
19 1 0.01
20 5 0.05
21 10 0.10
22 68 0.65
23 9 0.09
24 1 0.01
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.34
Consensus pattern (20 bp):
ATTATCAAAATTTCATAGGA
Found at i:18538 original size:50 final size:50
Alignment explanation
Indices: 18476--18573 Score: 142
Period size: 50 Copynumber: 2.0 Consensus size: 50
18466 TGGGAATGTG
* * * *
18476 ATTCCCACAAAAAAATAAAGTGCAACCAAATCATGTCATATAAGATGTCC
1 ATTCCCAAAAAAAAAAAAAATGCAACCAAACCATGTCATATAAGATGTCC
* *
18526 ATTCCCAAAAAAAAAAAAAATGCAACCAAACCATGTCATGTGAGATGT
1 ATTCCCAAAAAAAAAAAAAATGCAACCAAACCATGTCATATAAGATGT
18574 GCCCACAGTA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 42 1.00
ACGTcount: A:0.48, C:0.20, G:0.11, T:0.20
Consensus pattern (50 bp):
ATTCCCAAAAAAAAAAAAAATGCAACCAAACCATGTCATATAAGATGTCC
Found at i:22237 original size:6 final size:6
Alignment explanation
Indices: 22217--22262 Score: 76
Period size: 6 Copynumber: 7.7 Consensus size: 6
22207 AGTTTTACTT
22217 AAAAA- AAATAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAA
1 AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAA
22263 TCTCTTGGTC
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
5 3 0.08
6 33 0.85
7 3 0.08
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:22472 original size:31 final size:31
Alignment explanation
Indices: 22437--22496 Score: 104
Period size: 31 Copynumber: 1.9 Consensus size: 31
22427 ATGTTTTTCG
22437 ATTGTACCCTTATT-TTTAAAACATATTTCCA
1 ATTGTACCCTT-TTCTTTAAAACATATTTCCA
22468 ATTGTACCCTTTTCTTTAAAACATATTTC
1 ATTGTACCCTTTTCTTTAAAACATATTTC
22497 TAAATTGCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 2 0.07
31 26 0.93
ACGTcount: A:0.30, C:0.20, G:0.03, T:0.47
Consensus pattern (31 bp):
ATTGTACCCTTTTCTTTAAAACATATTTCCA
Found at i:22836 original size:19 final size:21
Alignment explanation
Indices: 22804--22846 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 21
22794 TTCTTTACTA
22804 TTACTTTTTGAATTT-AATATT
1 TTACTTTTTGAATTTCAAT-TT
22825 TTAC-TTTT-AATTTCAATTT
1 TTACTTTTTGAATTTCAATTT
22844 TTA
1 TTA
22847 AATGTCAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 10 0.48
20 7 0.33
21 4 0.19
ACGTcount: A:0.28, C:0.07, G:0.02, T:0.63
Consensus pattern (21 bp):
TTACTTTTTGAATTTCAATTT
Found at i:23268 original size:22 final size:22
Alignment explanation
Indices: 23239--23403 Score: 88
Period size: 22 Copynumber: 7.5 Consensus size: 22
23229 TTCTTGTCTC
23239 TAAG-TGGTTATCAAAATTTCA
1 TAAGATGGTTATCAAAATTTCA
* *
23260 TAAGATGGTTATTATAATTTCA
1 TAAGATGGTTATCAAAATTTCA
* *
23282 TGAGGA-GGTTATCAAAATTCCA
1 T-AAGATGGTTATCAAAATTTCA
* *
23304 T-AGTGTGGTTACCAAAATTTCA
1 TAAG-ATGGTTATCAAAATTTCA
* *
23326 T-AGTGTGGTTA-CCAAATTTCA
1 TAAG-ATGGTTATCAAAATTTCA
* * * *
23347 TAGGATCAGGTTATTAAAATCTCT
1 TAAGAT--GGTTATCAAAATTTCA
* * **
23371 TAGGTTGGTTATTGAAATTTCA
1 TAAGATGGTTATCAAAATTTCA
* *
23393 TAGGGTGGTTA
1 TAAGATGGTTA
23404 ATTATCACAA
Statistics
Matches: 114, Mismatches: 22, Indels: 15
0.75 0.15 0.10
Matches are distributed among these distances:
20 1 0.01
21 15 0.13
22 79 0.69
23 8 0.07
24 11 0.10
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.38
Consensus pattern (22 bp):
TAAGATGGTTATCAAAATTTCA
Found at i:23344 original size:21 final size:22
Alignment explanation
Indices: 23242--23349 Score: 105
Period size: 22 Copynumber: 5.0 Consensus size: 22
23232 TTGTCTCTAA
*
23242 GTGGTTATCAAAATTTCATAAG-
1 GTGGTTACCAAAATTTCAT-AGT
* ** *
23264 ATGGTTATTATAATTTCATGAG-
1 GTGGTTACCAAAATTTCAT-AGT
* * *
23286 GAGGTTATCAAAATTCCATAGT
1 GTGGTTACCAAAATTTCATAGT
23308 GTGGTTACCAAAATTTCATAGT
1 GTGGTTACCAAAATTTCATAGT
23330 GTGGTTACC-AAATTTCATAG
1 GTGGTTACCAAAATTTCATAG
23350 GATCAGGTTA
Statistics
Matches: 73, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
21 13 0.18
22 60 0.82
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (22 bp):
GTGGTTACCAAAATTTCATAGT
Found at i:23498 original size:22 final size:23
Alignment explanation
Indices: 23439--23499 Score: 63
Period size: 24 Copynumber: 2.7 Consensus size: 23
23429 ATCAAAGAGA
*
23439 TTAT-CAAAATGTCATAGCGAGG
1 TTATACAAAATTTCATAGCGAGG
* * *
23461 TTATATAAGAATTTCATAGTGTGG
1 TTATACAA-AATTTCATAGCGAGG
23485 TTA-ACAAAATTTCAT
1 TTATACAAAATTTCAT
23500 TAAATATTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
22 12 0.38
23 5 0.16
24 15 0.47
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (23 bp):
TTATACAAAATTTCATAGCGAGG
Found at i:23531 original size:22 final size:22
Alignment explanation
Indices: 23512--23819 Score: 83
Period size: 22 Copynumber: 13.9 Consensus size: 22
23502 AATATTTAAT
23512 GGGAGGTTATCAAAATTTTATA
1 GGGAGGTTATCAAAATTTTATA
* * *
23534 GTGTGGTTATCAAAATTTCATA
1 GGGAGGTTATCAAAATTTTATA
* *
23556 TGAAGGTTAT-AAAAGTCTCAATTTCATA
1 GGGAGGTTATCAAAA---T---TTT-ATA
* *
23584 GGGA-G-TACCAAAATTTGATA
1 GGGAGGTTATCAAAATTTTATA
* * *
23604 -GAAGGTTATC-AAATCTCATA
1 GGGAGGTTATCAAAATTTTATA
* * * * *
23624 GAGTGATTATCGAAATTTCATA
1 GGGAGGTTATCAAAATTTTATA
* *
23646 GAGATCGTATTATCAAAA-TTTATA
1 GGGA--G-GTTATCAAAATTTTATA
** * *
23670 GAAAGATTATCAAAATTTCATA
1 GGGAGGTTATCAAAATTTTATA
* ** * *
23692 GTGTTGTTATCAAAATTTCAAA
1 GGGAGGTTATCAAAATTTTATA
* **
23714 GCGAGGTTATCAAAATTACATA
1 GGGAGGTTATCAAAATTTTATA
** * * * *
23736 ATGTGATTATCAGAATTTCATA
1 GGGAGGTTATCAAAATTTTATA
* *
23758 GAGG-GGTCAACAAAATTTTATA
1 G-GGAGGTTATCAAAATTTTATA
** *
23780 AAGAGGTTATCAAAATTTCATA
1 GGGAGGTTATCAAAATTTTATA
**
23802 AAGAGGTTATC-AAATTTT
1 GGGAGGTTATCAAAATTTT
23820 CAAAATGTGA
Statistics
Matches: 212, Mismatches: 56, Indels: 37
0.70 0.18 0.12
Matches are distributed among these distances:
19 2 0.01
20 12 0.06
21 32 0.15
22 131 0.62
23 1 0.00
24 11 0.05
25 9 0.04
26 2 0.01
27 7 0.03
28 5 0.02
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.34
Consensus pattern (22 bp):
GGGAGGTTATCAAAATTTTATA
Found at i:23746 original size:44 final size:44
Alignment explanation
Indices: 23654--24236 Score: 218
Period size: 44 Copynumber: 13.3 Consensus size: 44
23644 TAGAGATCGT
* * * *
23654 ATTATCAAAATTT-ATAGAAAGATTATCAAAATTTCATAGTGTTG
1 ATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATG-TG
* *
23698 -TTATCAAAATTTCAAAGCGAGGTTATCAAAATTACATAATGTG
1 ATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGTG
* * * * * * * *
23741 ATTATCAGAATTTCATAGAGGGGTCAACAAAATTTTATAAAGAG
1 ATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGTG
* * *
23785 GTTATCAAAATTTCATAA-AGAGGTTATCAAATTTTCAAAATGTG
1 ATTATCAAAATTTCA-AAGAGAGGTTATCAAAATTTCATAATGTG
* * *
23829 ATTA-CAAAAATTTCATAGTGGTATTTCTGGGGAGGTTATCAAAATTTCATAGTATG
1 ATTATC-AAAATTTCA-A-----A------GAGAGGTTATCAAAATTTCATAATGTG
* * * * * * *
23885 GTTA-CTAAA-TT--AGGA-AGGTTATTAAACTTTTATTATG-G
1 ATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGTG
* * **
23923 AGTAATCAAAATTTC-AAG-GAGGATATCAAAA-TTCAGGGA-G-G
1 A-TTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCA-TAATGTG
* * *
23964 A-TATCAAAATTTCATATGA-AGGTTATCAAAATTTCATAGT-TT
1 ATTATCAAAATTTCA-AAGAGAGGTTATCAAAATTTCATAATGTG
*
24006 AGTTTTCAAAATTTCACAAGAG-GGTTATCAAAATTTCATAGTATGT-
1 A-TTATCAAAATTTCA-AAGAGAGGTTATCAAAATTTCATA--ATGTG
* * * * * *
24052 A-GATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATGAG
1 ATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGTG
** * * *
24095 ATTATCAAAAAATCATATG-GATGTTATCAAAATTT-GT-A---G
1 ATTATCAAAATTTCA-AAGAGAGGTTATCAAAATTTCATAATGTG
* * * * *
24134 -TTATCAAGATTTCATAAGA-AAGTTATCAAAATTTTAT-AGGAAG
1 ATTATCAAAATTTCA-AAGAGAGGTTATCAAAATTTCATAATG-TG
* * * * *
24177 ATTTATCAAAATTTCATAGGGAGATTATCACAATTTCATAGTGTG
1 A-TTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGTG
24222 ATTATCAAAATTTCA
1 ATTATCAAAATTTCA
24237 GAGTGTGATT
Statistics
Matches: 395, Mismatches: 96, Indels: 96
0.67 0.16 0.16
Matches are distributed among these distances:
38 29 0.07
39 32 0.08
40 5 0.01
41 21 0.05
42 21 0.05
43 21 0.05
44 199 0.50
45 31 0.08
46 3 0.01
47 1 0.00
49 1 0.00
51 1 0.00
54 2 0.01
55 3 0.01
56 25 0.06
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (44 bp):
ATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGTG
Found at i:23772 original size:66 final size:66
Alignment explanation
Indices: 23674--23821 Score: 163
Period size: 66 Copynumber: 2.2 Consensus size: 66
23664 TTTATAGAAA
* ** * * *
23674 GATTATCAAAATTTCATAGTGTTGTTATCAAAATTTCA-AAGCGAGGTTATCAAAATTACATAAT
1 GATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAA-AGAGGTTATCAAAATTACATAAT
23738 GT
65 GT
* * * *
23740 GATTATCAGAATTTCATAGAGGGGTCAACAAAATTTTATAAAGAGGTTATCAAAATTTCATAAAG
1 GATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAAAGAGGTTATCAAAATTACATAATG
*
23805 A
66 T
* *
23806 GGTTATCAAATTTTCA
1 GATTATCAAAATTTCA
23822 AAATGTGATT
Statistics
Matches: 67, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
66 65 0.97
67 2 0.03
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (66 bp):
GATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAAAGAGGTTATCAAAATTACATAATG
T
Found at i:23820 original size:22 final size:22
Alignment explanation
Indices: 23592--23821 Score: 146
Period size: 22 Copynumber: 10.5 Consensus size: 22
23582 TAGGGAGTAC
* *
23592 CAAAATTTGATAGA-AGGTTAT
1 CAAAATTTCATAAAGAGGTTAT
* * * *
23613 C-AAATCTCATAGAGTGATTAT
1 CAAAATTTCATAAAGAGGTTAT
* * *
23634 CGAAATTTCATAGAGATCGTATTAT
1 CAAAATTTCATAAAGA--G-GTTAT
*
23659 CAAAATTT-ATAGAA-AGATTAT
1 CAAAATTTCATA-AAGAGGTTAT
** **
23680 CAAAATTTCATAGTGTTGTTAT
1 CAAAATTTCATAAAGAGGTTAT
*
23702 CAAAATTTCA-AAGCGAGGTTAT
1 CAAAATTTCATAA-AGAGGTTAT
* * * *
23724 CAAAATTACATAATGTGATTAT
1 CAAAATTTCATAAAGAGGTTAT
* * * * *
23746 CAGAATTTCATAGAGGGGTCAA
1 CAAAATTTCATAAAGAGGTTAT
*
23768 CAAAATTTTATAAAGAGGTTAT
1 CAAAATTTCATAAAGAGGTTAT
23790 CAAAATTTCATAAAGAGGTTAT
1 CAAAATTTCATAAAGAGGTTAT
*
23812 CAAATTTTCA
1 CAAAATTTCA
23822 AAATGTGATT
Statistics
Matches: 162, Mismatches: 37, Indels: 19
0.74 0.17 0.09
Matches are distributed among these distances:
20 10 0.06
21 21 0.13
22 111 0.69
23 2 0.01
24 5 0.03
25 13 0.08
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (22 bp):
CAAAATTTCATAAAGAGGTTAT
Found at i:23957 original size:19 final size:19
Alignment explanation
Indices: 23927--23974 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
23917 TTATGGAGTA
23927 ATCAAAATTTCAAGGAGGAT
1 ATCAAAA-TTCAAGGAGGAT
*
23947 ATCAAAATTCAGGGAGGAT
1 ATCAAAATTCAAGGAGGAT
23966 ATCAAAATT
1 ATCAAAATT
23975 TCATATGAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 20 0.74
20 7 0.26
ACGTcount: A:0.46, C:0.10, G:0.19, T:0.25
Consensus pattern (19 bp):
ATCAAAATTCAAGGAGGAT
Found at i:23993 original size:22 final size:22
Alignment explanation
Indices: 23965--24506 Score: 179
Period size: 22 Copynumber: 24.7 Consensus size: 22
23955 TCAGGGAGGA
23965 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
**
23987 TATCAAAATTTCATAGTTTA-GT
1 TATCAAAATTTCATA-TGAAGGT
* * * *
24009 TTTCAAAATTTCACAAGAGGGT
1 TATCAAAATTTCATATGAAGGT
* *
24031 TATCAAAATTTCATA-GTATGT
1 TATCAAAATTTCATATGAAGGT
* * * *
24052 AGATCAAAATTTCATAGGGAGAT
1 -TATCAAAATTTCATATGAAGGT
* *
24075 TAACAAAATTTCATAATG-AGAT
1 TATCAAAATTTCAT-ATGAAGGT
** * *
24097 TATCAAAAAATCATATGGATGT
1 TATCAAAATTTCATATGAAGGT
*
24119 TATCAAAA--T--T-TGTA-GT
1 TATCAAAATTTCATATGAAGGT
* * *
24135 TATCAAGATTTCATAAGAAAGT
1 TATCAAAATTTCATATGAAGGT
* * *
24157 TATCAAAATTTTATAGGAAGATT
1 TATCAAAATTTCATATGAAG-GT
* * *
24180 TATCAAAATTTCATAGGGAGAT
1 TATCAAAATTTCATATGAAGGT
* * *
24202 TATCACAATTTCATAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
* * *
24224 TATCAAAATTTCAGAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
24246 TA-CTAACAA-TTCATATTG-AGGT
1 TATC-AA-AATTTCATA-TGAAGGT
* * * * *
24268 TTTTAAATTTTCATAACG-TGGT
1 TATCAAAATTTCAT-ATGAAGGT
* * *
24290 TATCAATATATCATATGGAGGT
1 TATCAAAATTTCATATGAAGGT
* * **
24312 TATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATA-TGAAGGT
* *
24335 CATCAAAATTTCAT-TGGAAAGT
1 TATCAAAATTTCATAT-GAAGGT
24357 TATCAAAATTTCATATTG-AGGT
1 TATCAAAATTTCATA-TGAAGGT
* * * *
24379 CT-TCAAAATTCCTTAGGGAATTCCGT
1 -TATCAAAATTTCATA-TGAA---GGT
* * *
24405 TAACCAAATTTCATAAGAAGGT
1 TATCAAAATTTCATATGAAGGT
** **
24427 TAAAAAAATTT-ATAAAAAGGT
1 TATCAAAATTTCATATGAAGGT
* * * **
24448 TCTCGAAATTCCATA-GTATCGT
1 TATCAAAATTTCATATG-AAGGT
* *
24470 TATTAAAATTTCATAGGAAGGT
1 TATCAAAATTTCATATGAAGGT
24492 TATCAAAATTTCATA
1 TATCAAAATTTCATA
24507 ATGGGATCAT
Statistics
Matches: 388, Mismatches: 99, Indels: 66
0.70 0.18 0.12
Matches are distributed among these distances:
16 9 0.02
17 3 0.01
18 2 0.01
20 2 0.01
21 28 0.07
22 278 0.72
23 50 0.13
24 1 0.00
25 4 0.01
26 11 0.03
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:24042 original size:66 final size:63
Alignment explanation
Indices: 23927--24506 Score: 220
Period size: 66 Copynumber: 8.9 Consensus size: 63
23917 TTATGGAGTA
* * ** *
23927 ATCAAAATTTCA-AGGAGGATATCAAAA-TTCA-GGGAGGATATCAAAATTTCATATGAAGGTT
1 ATCAAAATTTCATAGTA-GTTATCAAAATTTCATAAGAGGTTATCAAAATTTCATATGAAGGTT
* * * *
23988 ATCAAAATTTCATAGTTTAGTTTTCAAAATTTCACAAGAGGGTTATCAAAATTTCATA-GTATGT
1 ATCAAAATTTCATAG--TAGTTATCAAAATTTCATAAGA-GGTTATCAAAATTTCATATGAAGGT
*
24052 AG
63 -T
* * * ** * *
24054 ATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATGAGATTATCAAAAAATCATATGGATGT
1 ATCAAAATTTCATA-GTAG-TTATCAAAATTTCATAA-GAGGTTATCAAAATTTCATATGAAGGT
24119 T
63 T
* * * * *
24120 ATCAAAA-TT--T-GTAGTTATCAAGATTTCATAAGAAAGTTATCAAAATTTTATAGGAAGATTT
1 ATCAAAATTTCATAGTAGTTATCAAAATTTCATAAG-AGGTTATCAAAATTTCATATGAAG-GTT
* * * * *
24181 ATCAAAATTTCATAGGGAGATTATCACAATTTCAT-AGTGTGATTATCAAAATTTCAGAGTG-TG
1 ATCAAAATTTCATA-GTAG-TTATCAAAATTTCATAAGAG-G-TTATCAAAATTTCATA-TGAAG
*
24244 ATT
61 GTT
* * * * * * * *
24247 A-CTAACAA-TTCATATTGAGGTTTTTAAATTTTCATAACGTGGTTATCAATATATCATATGGAG
1 ATC-AA-AATTTCATAGT-A-GTTATCAAAATTTCATAA-GAGGTTATCAAAATTTCATATGAAG
24310 GTT
61 GTT
* * ** *
24313 ATCAACATCTCATAGT-GTTGGTCATCAAAATTTCATTGGAAAGTTATCAAAATTTCATATTG-A
1 ATCAAAATTTCATAGTAG-T--T-ATCAAAATTTCATAAG-AGGTTATCAAAATTTCATA-TGAA
24376 GGTCT
60 GGT-T
* * * * * ** **
24381 -TCAAAATTCCTTAGGGAATTCCGTTAACCAAATTTCATAAGAAGGTTAAAAAAATTT-ATAAAA
1 ATCAAAATTTCATA--G---T-AGTTATCAAAATTTCATAAG-AGGTTATCAAAATTTCATATGA
24444 AGGTT
59 AGGTT
* * * * *
24449 CTCGAAATTCCATAGTATCGTTATTAAAATTTCATAGGAAGGTTATCAAAATTTCATA
1 ATCAAAATTTCATAGTA--GTTATCAAAATTTCATAAG-AGGTTATCAAAATTTCATA
24507 ATGGGATCAT
Statistics
Matches: 384, Mismatches: 85, Indels: 95
0.68 0.15 0.17
Matches are distributed among these distances:
59 1 0.00
60 31 0.08
61 24 0.06
62 4 0.01
63 10 0.03
64 8 0.02
65 43 0.11
66 126 0.33
67 81 0.21
68 8 0.02
69 19 0.05
70 25 0.07
71 1 0.00
72 1 0.00
73 1 0.00
74 1 0.00
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (63 bp):
ATCAAAATTTCATAGTAGTTATCAAAATTTCATAAGAGGTTATCAAAATTTCATATGAAGGTT
Found at i:26100 original size:3 final size:3
Alignment explanation
Indices: 26094--26118 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
26084 ACAGTTGTTG
26094 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
26119 GTAACATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:31329 original size:15 final size:15
Alignment explanation
Indices: 31309--31339 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
31299 AAAATCCATA
31309 TCTATAATGTAACAT
1 TCTATAATGTAACAT
31324 TCTATAATGTAACAT
1 TCTATAATGTAACAT
31339 T
1 T
31340 TTCAATCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.13, G:0.06, T:0.42
Consensus pattern (15 bp):
TCTATAATGTAACAT
Found at i:32268 original size:21 final size:20
Alignment explanation
Indices: 32239--32277 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
32229 AATTTATAAT
32239 AAAATATTT-AGAATAAAATC
1 AAAATATTTGA-AATAAAATC
32259 AAAATTATTTGAAATAAAA
1 AAAA-TATTTGAAATAAAA
32278 AATATAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 4 0.24
21 12 0.71
22 1 0.06
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.31
Consensus pattern (20 bp):
AAAATATTTGAAATAAAATC
Found at i:33089 original size:54 final size:54
Alignment explanation
Indices: 33007--33121 Score: 203
Period size: 54 Copynumber: 2.1 Consensus size: 54
32997 TAATTAAGTT
*
33007 CCCTTTATATGTAAAAAATTATTAGATAAGACTGTCCAAAATCTTGGGAACTTA
1 CCCTTTATATGTAAAAAATTATTAGATAAGACCGTCCAAAATCTTGGGAACTTA
* *
33061 CCCTTTATATGTAAGAAATTATTAGATAAGACCGTCCAAAATTTTGGGAACTTA
1 CCCTTTATATGTAAAAAATTATTAGATAAGACCGTCCAAAATCTTGGGAACTTA
33115 CCCTTTA
1 CCCTTTA
33122 CCTACCCACC
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 58 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.34
Consensus pattern (54 bp):
CCCTTTATATGTAAAAAATTATTAGATAAGACCGTCCAAAATCTTGGGAACTTA
Found at i:33949 original size:60 final size:60
Alignment explanation
Indices: 33880--34000 Score: 224
Period size: 60 Copynumber: 2.0 Consensus size: 60
33870 GGATAGACTT
* *
33880 TATTTTTTTGGTGAAATTAGGATAGACTTTTAGAAGATCAATAAGTTGTGACTATATAAG
1 TATTTTTTTGGTGAAATTAGGATAGACTTTTAAAAGATCAATAAGTTGTGAATATATAAG
33940 TATTTTTTTGGTGAAATTAGGATAGACTTTTAAAAGATCAATAAGTTGTGAATATATAAG
1 TATTTTTTTGGTGAAATTAGGATAGACTTTTAAAAGATCAATAAGTTGTGAATATATAAG
34000 T
1 T
34001 GGTTGCTCAT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.36, C:0.04, G:0.19, T:0.40
Consensus pattern (60 bp):
TATTTTTTTGGTGAAATTAGGATAGACTTTTAAAAGATCAATAAGTTGTGAATATATAAG
Found at i:35245 original size:19 final size:19
Alignment explanation
Indices: 35221--35262 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
35211 ACATCTCAGA
35221 GTAGGAAGCTAATCATTCT
1 GTAGGAAGCTAATCATTCT
35240 GTAGGAAGCTAATCATTCT
1 GTAGGAAGCTAATCATTCT
35259 GTAG
1 GTAG
35263 CTGAGTACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (19 bp):
GTAGGAAGCTAATCATTCT
Done.