Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006668.1 Corchorus capsularis cultivar CVL-1 contig06689, 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: 8311
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Found at i:153 original size:16 final size:16
Alignment explanation
Indices: 132--163 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
122 AGGGCGGCCT
132 GCCGTGGCAAAGCCGC
1 GCCGTGGCAAAGCCGC
*
148 GCCGTGGCGAAGCCGC
1 GCCGTGGCAAAGCCGC
164 CCCAGTGGGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.16, C:0.38, G:0.41, T:0.06
Consensus pattern (16 bp):
GCCGTGGCAAAGCCGC
Found at i:195 original size:33 final size:33
Alignment explanation
Indices: 150--212 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
140 AAAGCCGCGC
150 CGTGGCGAAGCCGCCCCAGTGGGGAGGCTCCGT
1 CGTGGCGAAGCCGCCCCAGTGGGGAGGCTCCGT
* *
183 CGTGGCTG-AGCCGTCCTAGTGGGGAGGCTC
1 CGTGGC-GAAGCCGCCCCAGTGGGGAGGCTC
213 AGTGTAAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
33 26 0.96
34 1 0.04
ACGTcount: A:0.11, C:0.30, G:0.43, T:0.16
Consensus pattern (33 bp):
CGTGGCGAAGCCGCCCCAGTGGGGAGGCTCCGT
Found at i:1680 original size:22 final size:22
Alignment explanation
Indices: 1654--1701 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
1644 TTCATTAAAT
*
1654 ATTTTATGGGGAGGTTATCAAA
1 ATTTTATAGGGAGGTTATCAAA
* *
1676 ATTTTATAGTGTGGTTATCAAA
1 ATTTTATAGGGAGGTTATCAAA
1698 ATTT
1 ATTT
1702 CATATGAAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.31, C:0.04, G:0.21, T:0.44
Consensus pattern (22 bp):
ATTTTATAGGGAGGTTATCAAA
Found at i:1851 original size:22 final size:22
Alignment explanation
Indices: 1780--1998 Score: 81
Period size: 22 Copynumber: 9.9 Consensus size: 22
1770 CATAAAGTGA
* *
1780 TTATCGAAATTTCATAGAGATCGG
1 TTATCAAAATTTCATAGTGAT--G
* *
1804 ATTATCAAAATTT-ATAG-AAAG
1 -TTATCAAAATTTCATAGTGATG
* *
1825 ATTATCAGAATTTCATAGTGTTG
1 -TTATCAAAATTTCATAGTGATG
* * *
1848 TTATCAAAATTTCAAAGCGAGG
1 TTATCAAAATTTCATAGTGATG
* * *
1870 TTATCAAAATTACATAAT-CTG
1 TTATCAAAATTTCATAGTGATG
* * **
1891 ATTATCAGAATTTCATAGAGGGG
1 -TTATCAAAATTTCATAGTGATG
* * * **
1914 TCAACAAAATTTTATAAAGATG
1 TTATCAAAATTTCATAGTGATG
* **
1936 TTATCAAAATTTTATAAAGA-G
1 TTATCAAAATTTCATAGTGATG
* * *
1957 CTTATCAAATTTTCAAAATGA-G
1 -TTATCAAAATTTCATAGTGATG
1979 ATTA-CAAAATTTTCATAGTG
1 -TTATCAAAA-TTTCATAGTG
1999 GTATTTCTGG
Statistics
Matches: 147, Mismatches: 41, Indels: 15
0.72 0.20 0.07
Matches are distributed among these distances:
21 19 0.13
22 110 0.75
23 3 0.02
24 4 0.03
25 11 0.07
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGATG
Found at i:1962 original size:66 final size:65
Alignment explanation
Indices: 1786--1968 Score: 156
Period size: 66 Copynumber: 2.8 Consensus size: 65
1776 GTGATTATCG
* * ** *
1786 AAATTTCATAGAGATCGGATTATCAAAA-TTTATAGAAAGATTATCAGAATTTCATAGTGTTGTT
1 AAATTTCAAAGAGA--GG-TTATCAAAATTTTATA-AAAGATTATCAGAATTTCATAGAGGGGTC
*
1850 ATCA
62 AACA
* ** **
1854 AAATTTCAAAGCGAGGTTATCAAAATTACATAATCTGATTATCAGAATTTCATAGAGGGGTCAAC
1 AAATTTCAAAGAGAGGTTATCAAAATTTTATAA-AAGATTATCAGAATTTCATAGAGGGGTCAAC
1919 A
65 A
* * *
1920 AAATTTTATAA-AGATGTTATCAAAATTTTATAAAGAGCTTATCA-AATTT
1 AAATTTCA-AAGAGAGGTTATCAAAATTTTATAAA-AGATTATCAGAATTT
1969 TCAAAATGAG
Statistics
Matches: 92, Mismatches: 19, Indels: 11
0.75 0.16 0.09
Matches are distributed among these distances:
65 15 0.16
66 63 0.68
67 2 0.02
68 12 0.13
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.35
Consensus pattern (65 bp):
AAATTTCAAAGAGAGGTTATCAAAATTTTATAAAAGATTATCAGAATTTCATAGAGGGGTCAACA
Found at i:2102 original size:20 final size:20
Alignment explanation
Indices: 2077--2132 Score: 78
Period size: 19 Copynumber: 2.8 Consensus size: 20
2067 TTATGGAGTA
2077 ATCAAAATTTCAATGAGGAT
1 ATCAAAATTTCAATGAGGAT
**
2097 ATCAAAA-TTCAGGGAGGAT
1 ATCAAAATTTCAATGAGGAT
2116 ATCAAAATTTCATATGA
1 ATCAAAATTTCA-ATGA
2133 AGGTTATGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 17 0.57
20 11 0.37
21 2 0.07
ACGTcount: A:0.45, C:0.11, G:0.16, T:0.29
Consensus pattern (20 bp):
ATCAAAATTTCAATGAGGAT
Found at i:2253 original size:22 final size:22
Alignment explanation
Indices: 2115--2411 Score: 139
Period size: 22 Copynumber: 13.7 Consensus size: 22
2105 TCAGGGAGGA
* *
2115 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATAGGAAAGT
* * ***
2137 TATGAAAAATTCATAGTTTAGT
1 TATCAAAATTTCATAGGAAAGT
* * *
2159 TTTCAAAATTTCACAAGAGAA-T
1 TATCAAAATTTCATAGGA-AAGT
* *
2181 TATCAAAATTTCATA-GTATGT
1 TATCAAAATTTCATAGGAAAGT
* *
2202 AGATCAAAATTTCATAGG-GAGAT
1 -TATCAAAATTTCATAGGAAAG-T
* **
2225 TAACAAAATTTCATAATAAAGT
1 TATCAAAATTTCATAGGAAAGT
** * *
2247 TATCAAAAAATCATAGGGAGGT
1 TATCAAAATTTCATAGGAAAGT
*
2269 TATCAAAA-TT--T--GTAA-T
1 TATCAAAATTTCATAGGAAAGT
* *
2285 TATCAAGATTTCATAAGAAAGT
1 TATCAAAATTTCATAGGAAAGT
* * *
2307 TATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATAGGAAAG-T
* * *
2330 TATCAAAATTTTATAAGAAGATT
1 TATCAAAATTTCATAGGAA-AGT
* *
2353 TATCAAGATTTCATAGCG-ATGT
1 TATCAAAATTTCATAG-GAAAGT
* **
2375 TATCACAATTTCATAGTGTGA-T
1 TATCAAAATTTCATAG-GAAAGT
2397 TATCAAAATTTCATA
1 TATCAAAATTTCATA
2412 TTGTGATTAC
Statistics
Matches: 200, Mismatches: 59, Indels: 32
0.69 0.20 0.11
Matches are distributed among these distances:
16 8 0.04
17 4 0.02
19 2 0.01
20 1 0.00
21 6 0.03
22 140 0.70
23 38 0.19
24 1 0.00
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (22 bp):
TATCAAAATTTCATAGGAAAGT
Found at i:2325 original size:60 final size:61
Alignment explanation
Indices: 2223--2340 Score: 175
Period size: 60 Copynumber: 2.0 Consensus size: 61
2213 TCATAGGGAG
*
2223 ATTAACAAAATTTCATAATAAAGTTATCAAAAAATCATAGGGAGG-TTATCAAAATTTGTA
1 ATTAACAAAATTTCATAAGAAAGTTATCAAAAAATCATAGGGAGGTTTATCAAAATTTGTA
* * ** *
2283 ATTATCAAGATTTCATAAGAAAGTTATCAAAATTTTATAGGGAGGTTTATCAAAATTT
1 ATTAACAAAATTTCATAAGAAAGTTATCAAAAAATCATAGGGAGGTTTATCAAAATTT
2341 TATAAGAAGA
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
60 39 0.76
61 12 0.24
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.35
Consensus pattern (61 bp):
ATTAACAAAATTTCATAAGAAAGTTATCAAAAAATCATAGGGAGGTTTATCAAAATTTGTA
Found at i:2348 original size:45 final size:45
Alignment explanation
Indices: 2110--2411 Score: 157
Period size: 44 Copynumber: 7.0 Consensus size: 45
2100 AAAATTCAGG
* * * * *
2110 GAGGATATCAAAATTTCATATGAAG-GTTATGAAAAATTCATAGTT
1 GAGGTTATCAAAATTTCATAAGAAGAGTTATCAAAATTTCATAG-C
* * * *
2155 TA-GTTTTCAAAATTTCACAAG-AGAATTATCAAAATTTCATAG-
1 GAGGTTATCAAAATTTCATAAGAAGAGTTATCAAAATTTCATAGC
* * * * * * **
2197 TATGTAGATCAAAATTTCATAGGGAGA-TTAACAAAATTTCATAAT
1 GAGGT-TATCAAAATTTCATAAGAAGAGTTATCAAAATTTCATAGC
* * ** * * *
2242 AAAGTTATCAAAAAATCATAGGGAG-GTTATCAAAATTT-GTA--
1 GAGGTTATCAAAATTTCATAAGAAGAGTTATCAAAATTTCATAGC
* * *
2283 -A--TTATCAAGATTTCATAAGAA-AGTTATCAAAATTTTATAGG
1 GAGGTTATCAAAATTTCATAAGAAGAGTTATCAAAATTTCATAGC
* * *
2324 GAGGTTTATCAAAATTTTATAAGAAGATTTATCAAGATTTCATAGC
1 GAGG-TTATCAAAATTTCATAAGAAGAGTTATCAAAATTTCATAGC
* * * *
2370 GATGTTATCACAATTTCAT-AG-TGTGATTATCAAAATTTCATA
1 GAGGTTATCAAAATTTCATAAGAAGAG-TTATCAAAATTTCATA
2412 TTGTGATTAC
Statistics
Matches: 201, Mismatches: 40, Indels: 33
0.73 0.15 0.12
Matches are distributed among these distances:
38 28 0.14
39 2 0.01
40 1 0.00
42 3 0.01
43 7 0.03
44 103 0.51
45 38 0.19
46 19 0.09
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.35
Consensus pattern (45 bp):
GAGGTTATCAAAATTTCATAAGAAGAGTTATCAAAATTTCATAGC
Found at i:2416 original size:22 final size:22
Alignment explanation
Indices: 2352--2420 Score: 86
Period size: 22 Copynumber: 3.1 Consensus size: 22
2342 ATAAGAAGAT
* *
2352 TTATCAAGATTTCATAGCGATG-
1 TTATCAAAATTTCATAGTG-TGA
*
2374 TTATCACAATTTCATAGTGTGA
1 TTATCAAAATTTCATAGTGTGA
*
2396 TTATCAAAATTTCATATTGTGA
1 TTATCAAAATTTCATAGTGTGA
2418 TTA
1 TTA
2421 CTAACAATTC
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
21 2 0.05
22 39 0.95
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.42
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGTGA
Found at i:2431 original size:22 final size:23
Alignment explanation
Indices: 2374--2434 Score: 76
Period size: 22 Copynumber: 2.8 Consensus size: 23
2364 CATAGCGATG
*
2374 TTATC-ACAATTTCATAGTGTGA
1 TTATCAACAATTTCATATTGTGA
2396 TTATCAA-AATTTCATATTGTGA
1 TTATCAACAATTTCATATTGTGA
2418 TTA-CTAACAA-TTCATAT
1 TTATC-AACAATTTCATAT
2435 GGAGGTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
21 1 0.03
22 31 0.89
23 3 0.09
ACGTcount: A:0.36, C:0.13, G:0.08, T:0.43
Consensus pattern (23 bp):
TTATCAACAATTTCATATTGTGA
Found at i:2630 original size:22 final size:22
Alignment explanation
Indices: 2599--2652 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
2589 AAGGTTCTCG
* * *
2599 AAATTCCATAGTATCGTTATCA
1 AAATTTCATAGGAACGTTATCA
*
2621 AAATTTCATAGGAAGGTTATCA
1 AAATTTCATAGGAACGTTATCA
2643 AAATTTCATA
1 AAATTTCATA
2653 ATGGGATCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.41, C:0.13, G:0.11, T:0.35
Consensus pattern (22 bp):
AAATTTCATAGGAACGTTATCA
Found at i:3501 original size:8 final size:8
Alignment explanation
Indices: 3477--3506 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
3467 AAAAGGCGTC
3477 TTTTTATT
1 TTTTTATT
3485 TTATTTATT
1 TT-TTTATT
3494 TTTTTATT
1 TTTTTATT
3502 TTTTT
1 TTTTT
3507 TGCTCTCCGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (8 bp):
TTTTTATT
Found at i:4347 original size:22 final size:22
Alignment explanation
Indices: 4321--4367 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
4311 ATTTATTCTT
4321 TATTAATTAACTATTAATTAGA
1 TATTAATTAACTATTAATTAGA
**
4343 TATTAATTAGTTATTAATTAGA
1 TATTAATTAACTATTAATTAGA
4365 TAT
1 TAT
4368 AGTATAATGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (22 bp):
TATTAATTAACTATTAATTAGA
Found at i:6163 original size:23 final size:23
Alignment explanation
Indices: 6085--6174 Score: 100
Period size: 23 Copynumber: 4.1 Consensus size: 23
6075 CTGATTATTC
*
6085 TTTA-TCTTGTACTGATTACTAT
1 TTTACTCTTGTACTGATTACCAT
*
6107 TTTACTCTTGT--TGATTACC-C
1 TTTACTCTTGTACTGATTACCAT
*
6127 TTTACT-TTTTACTGATTACCAT
1 TTTACTCTTGTACTGATTACCAT
* *
6149 TTTACTCTTTTACTGATTACTAT
1 TTTACTCTTGTACTGATTACCAT
6172 TTT
1 TTT
6175 CTGCTCCTTT
Statistics
Matches: 58, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
19 3 0.05
20 6 0.10
21 15 0.26
22 10 0.17
23 24 0.41
ACGTcount: A:0.20, C:0.18, G:0.07, T:0.56
Consensus pattern (23 bp):
TTTACTCTTGTACTGATTACCAT
Found at i:6305 original size:35 final size:35
Alignment explanation
Indices: 6266--6345 Score: 106
Period size: 35 Copynumber: 2.3 Consensus size: 35
6256 CTGGTTACTG
6266 TTTTACTCTTAATGACTACCTTCTACTGATCACTA
1 TTTTACTCTTAATGACTACCTTCTACTGATCACTA
* ** * * *
6301 TTTTACTCTTAATGGCTGTCTTTTGCTGATTACTA
1 TTTTACTCTTAATGACTACCTTCTACTGATCACTA
6336 TTTTACTCTT
1 TTTTACTCTT
6346 TACTGATTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.20, C:0.21, G:0.09, T:0.50
Consensus pattern (35 bp):
TTTTACTCTTAATGACTACCTTCTACTGATCACTA
Found at i:6382 original size:21 final size:22
Alignment explanation
Indices: 6336--6384 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
6326 CTGATTACTA
*
6336 TTTTACTCTTTACTGATTATTC
1 TTTTACTCTTTACTCATTATTC
*
6358 -TTTACTCTTTAC-CATTTTTC
1 TTTTACTCTTTACTCATTATTC
6378 TTTTACT
1 TTTTACT
6385 AATTACTCTC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 6 0.25
21 18 0.75
ACGTcount: A:0.16, C:0.20, G:0.02, T:0.61
Consensus pattern (22 bp):
TTTTACTCTTTACTCATTATTC
Found at i:6556 original size:31 final size:31
Alignment explanation
Indices: 6502--6567 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
6492 AATTACTGAT
*
6502 TTACTGATTACTATTTTTACCTTGACTTTTAA
1 TTACTGATTAC-ATTTTTACCTTGACTCTTAA
6534 TTACTGATTA-ATTTCTTACCTTGACTCTTAA
1 TTACTGATTACATTT-TTACCTTGACTCTTAA
6565 TTA
1 TTA
6568 TCAATTTACT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
30 4 0.12
31 18 0.56
32 10 0.31
ACGTcount: A:0.26, C:0.17, G:0.06, T:0.52
Consensus pattern (31 bp):
TTACTGATTACATTTTTACCTTGACTCTTAA
Found at i:6676 original size:47 final size:47
Alignment explanation
Indices: 6599--6805 Score: 319
Period size: 47 Copynumber: 4.4 Consensus size: 47
6589 TTTTACTTGA
* *
6599 TTACTGATTTACTGATTACTATTACCTTGACTTTTGATTAATCT-TTT
1 TTACTGATTTACTGATTACCATCACCTTGAC-TTTGATTAATCTCTTT
*
6646 TTACTGATTTACTGATTACCATCACTTTGACTTTGATTAATCTCTTT
1 TTACTGATTTACTGATTACCATCACCTTGACTTTGATTAATCTCTTT
* *
6693 TTACTGATTTACAGATTACCATCACTTTGACTTTGATTAATCTCTTT
1 TTACTGATTTACTGATTACCATCACCTTGACTTTGATTAATCTCTTT
* * *
6740 TTACTGATTTACTGATTACCATCACCTTGACTCTGTTTAAGCTCTTT
1 TTACTGATTTACTGATTACCATCACCTTGACTTTGATTAATCTCTTT
6787 TTACTGA-TTACTGATTACC
1 TTACTGATTTACTGATTACC
6806 CCTTTTTACT
Statistics
Matches: 150, Mismatches: 9, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
46 24 0.16
47 126 0.84
ACGTcount: A:0.24, C:0.19, G:0.09, T:0.48
Consensus pattern (47 bp):
TTACTGATTTACTGATTACCATCACCTTGACTTTGATTAATCTCTTT
Found at i:6710 original size:26 final size:25
Alignment explanation
Indices: 6680--6757 Score: 60
Period size: 26 Copynumber: 3.2 Consensus size: 25
6670 CTTTGACTTT
6680 GATTAATCTCTTTTTACTGATTTAC
1 GATTAATCTCTTTTTACTGATTTAC
* *
6705 AGATTACCATCAC-TTTGAC---TTT--
1 -GATTA--ATCTCTTTTTACTGATTTAC
6727 GATTAATCTCTTTTTACTGATTTAC
1 GATTAATCTCTTTTTACTGATTTAC
6752 TGATTA
1 -GATTA
6758 CCATCACCTT
Statistics
Matches: 39, Mismatches: 4, Indels: 18
0.64 0.07 0.30
Matches are distributed among these distances:
19 4 0.10
20 5 0.13
21 5 0.13
23 3 0.08
24 3 0.08
26 10 0.26
27 5 0.13
28 4 0.10
ACGTcount: A:0.26, C:0.17, G:0.09, T:0.49
Consensus pattern (25 bp):
GATTAATCTCTTTTTACTGATTTAC
Found at i:7509 original size:50 final size:51
Alignment explanation
Indices: 7405--7709 Score: 216
Period size: 50 Copynumber: 6.1 Consensus size: 51
7395 AACTAATCAA
** * * * *
7405 TTTATTTACTAATGGCCTAAAAGTTTAAACTTCTAATTCAAAGG-TAACAT-
1 TTTATTTACTAATTACTTAAAAGTTCAATCTT-TTATTCAAAGGTTAACATC
* *
7455 TTTATTTACTAATTACTTAAAAGTTCAATCTTTCATTCAAAGGTTAA-AGC
1 TTTATTTACTAATTACTTAAAAGTTCAATCTTTTATTCAAAGGTTAACATC
* * ** * ** *
7505 TTTATTTACCAATCACTCT-AAAGATTCAATCTTTTACCCGAA-CATAACATT
1 TTTATTTACTAATTACT-TAAAAG-TTCAATCTTTTATTCAAAGGTTAACATC
* * * *
7556 TTTACTTACCAATTACTTAAAAATTCAATCTTTTATTCAAAAGTTAA-ATC
1 TTTATTTACTAATTACTTAAAAGTTCAATCTTTTATTCAAAGGTTAACATC
** ** **
7606 TTTATTTACTAATTACTCT-AAAGATTCAATCTTTTACCCAAA-CATGCCAT-
1 TTTATTTACTAATTACT-TAAAAG-TTCAATCTTTTATTCAAAGGTTAACATC
** * *
7656 TTCGTTTACCAATTTACTTAAAAATTCAATCTTTTATTCAAAGGTTAA-ATC
1 TTTATTTACTAA-TTACTTAAAAGTTCAATCTTTTATTCAAAGGTTAACATC
7707 TTT
1 TTT
7710 TAGCAAAAGG
Statistics
Matches: 195, Mismatches: 46, Indels: 27
0.73 0.17 0.10
Matches are distributed among these distances:
49 11 0.06
50 117 0.60
51 67 0.34
ACGTcount: A:0.36, C:0.17, G:0.06, T:0.41
Consensus pattern (51 bp):
TTTATTTACTAATTACTTAAAAGTTCAATCTTTTATTCAAAGGTTAACATC
Found at i:7538 original size:51 final size:49
Alignment explanation
Indices: 7440--7709 Score: 222
Period size: 50 Copynumber: 5.4 Consensus size: 49
7430 TAAACTTCTA
* * *
7440 ATTCAAAGGTAACAT-TTTATTTACTAATTACTTAAA-AGTTCAATCTTTC
1 ATTCAAAGTTAA-ATCTTTATTTACCAATTACTTAAAGA-TTCAATCTTTT
* *
7489 ATTCAAAGGTTAAAGCTTTATTTACCAATCACTCTAAAGATTCAATCTTTT
1 ATTCAAA-GTTAAATCTTTATTTACCAATTACT-TAAAGATTCAATCTTTT
** * ** * * *
7540 ACCCGAACATAACATTTTTACTTACCAATTACTTAAAAATTCAATCTTTT
1 ATTCAAAGTTAA-ATCTTTATTTACCAATTACTTAAAGATTCAATCTTTT
*
7590 ATTCAAAAGTTAAATCTTTATTTACTAATTACTCTAAAGATTCAATCTTTT
1 ATTC-AAAGTTAAATCTTTATTTACCAATTACT-TAAAGATTCAATCTTTT
** * *** ** *
7641 ACCCAAACATGCCAT-TTCGTTTACCAATTTACTTAAAAATTCAATCTTTT
1 ATTCAAA-GTTAAATCTTTATTTACCAA-TTACTTAAAGATTCAATCTTTT
7691 ATTCAAAGGTTAAATCTTT
1 ATTCAAA-GTTAAATCTTT
7710 TAGCAAAAGG
Statistics
Matches: 169, Mismatches: 42, Indels: 18
0.74 0.18 0.08
Matches are distributed among these distances:
49 8 0.05
50 93 0.55
51 67 0.40
52 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.05, T:0.41
Consensus pattern (49 bp):
ATTCAAAGTTAAATCTTTATTTACCAATTACTTAAAGATTCAATCTTTT
Found at i:7583 original size:101 final size:100
Alignment explanation
Indices: 7449--7709 Score: 373
Period size: 101 Copynumber: 2.6 Consensus size: 100
7439 AATTCAAAGG
* * * *
7449 TAACA-TTTTATTTACTAATTACTTAAAAGTTCAATCTTTCATTCAAAGGTTAAAGCTTTATTTA
1 TAACATTTTTA-TTACCAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATCTTTATTTA
*
7513 CCAATCACTCTAAAGATTCAATCTTTTACCCGAACA
65 CCAATCACTCTAAAGATTCAATCTTTTACCCAAACA
*
7549 TAACATTTTTACTTACCAATTACTTAAAAATTCAATCTTTTATTCAAAAGTTAAATCTTTATTTA
1 TAACATTTTTA-TTACCAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATCTTTATTTA
* *
7614 CTAATTACTCTAAAGATTCAATCTTTTACCCAAACA
65 CCAATCACTCTAAAGATTCAATCTTTTACCCAAACA
** *
7650 TGCCATTTCGT-TTACCAATTTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATCTTT
1 TAACATTT-TTATTACCAA-TTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATCTTT
7710 TAGCAAAAGG
Statistics
Matches: 145, Mismatches: 13, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
100 12 0.08
101 132 0.91
102 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.05, T:0.41
Consensus pattern (100 bp):
TAACATTTTTATTACCAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATCTTTATTTAC
CAATCACTCTAAAGATTCAATCTTTTACCCAAACA
Found at i:7718 original size:20 final size:20
Alignment explanation
Indices: 7695--7733 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
7685 TCTTTTATTC
*
7695 AAAGGTTAAATCTTTTAGCA
1 AAAGGTTAAACCTTTTAGCA
*
7715 AAAGGTTACACCTTTTAGC
1 AAAGGTTAAACCTTTTAGC
7734 CAAATATCCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.33
Consensus pattern (20 bp):
AAAGGTTAAACCTTTTAGCA
Done.