Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010214.1 Corchorus capsularis cultivar CVL-1 contig10235, 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: 34389
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:87 original size:15 final size:15
Alignment explanation
Indices: 69--117 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
59 AAATTAACTG
69 AAACTGACCTAACCC
1 AAACTGACCTAACCC
**
84 AAACTTTCCTTAACCC
1 AAACTGACC-TAACCC
* *
100 GAACTGACCTAACTC
1 AAACTGACCTAACCC
115 AAA
1 AAA
118 TCTAATCCGA
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
15 14 0.54
16 12 0.46
ACGTcount: A:0.39, C:0.35, G:0.06, T:0.20
Consensus pattern (15 bp):
AAACTGACCTAACCC
Found at i:3530 original size:123 final size:123
Alignment explanation
Indices: 3286--3530 Score: 282
Period size: 124 Copynumber: 2.0 Consensus size: 123
3276 CTTTTTAAAT
* *
3286 TAAAATGGTAAAAATAAAATAATTATAAAATATTGAATTTAATTAAATGAAAATATAGTTTTTAA
1 TAAAATGGTAAAAATAAAATAATTATAAAATATTGAATTTAATTAAATAAAAATAGAGTTTTTAA
* ** * * *
3351 TAGAATAAAAATGTATATTAAAAAATTTTTATGTATCCAAATTTTTATTGAAAAATAG
66 TAGAATAAAAATATATATTAAAAAATTGGTATGTATACAAATATGTATTGAAAAATAG
* * *
3409 TAAAATGGTAAACATAAAGTAATTATAAAGATATT-AGATTTAATTGAATAAAAATAGAGTTTTT
1 TAAAATGGTAAAAATAAAATAATTATAAA-ATATTGA-ATTTAATTAAATAAAAATAGAGTTTTT
* * * * *
3473 AGTAGAATAAAACTATAATAATTAAACAA-TGGTATTTA-AGAAATATGT-TTGAAAAATA
64 AATAGAATAAAAATAT-AT-ATTAAAAAATTGGTATGTATACAAATATGTATTGAAAAATA
3531 AAGGTATAAT
Statistics
Matches: 102, Mismatches: 16, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
123 38 0.37
124 48 0.47
125 8 0.08
126 8 0.08
ACGTcount: A:0.52, C:0.02, G:0.10, T:0.36
Consensus pattern (123 bp):
TAAAATGGTAAAAATAAAATAATTATAAAATATTGAATTTAATTAAATAAAAATAGAGTTTTTAA
TAGAATAAAAATATATATTAAAAAATTGGTATGTATACAAATATGTATTGAAAAATAG
Found at i:4733 original size:109 final size:109
Alignment explanation
Indices: 4604--4830 Score: 404
Period size: 109 Copynumber: 2.1 Consensus size: 109
4594 AAAAAATTTA
4604 TATAAA-ATATTGAATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGA
1 TATAAAGATATTGAATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGA
4668 AAAAATTGTAATATATCCAAATTTTTTGGTAAAAATAAAGTAAT
66 AAAAATTGTAATATATCCAAATTTTTTGGTAAAAATAAAGTAAT
*
4712 TATAAAGATATT-AGATTTAATTAAATGAAAATTGAGTTTTTAGTAGAATAAAATTGTATATTAG
1 TATAAAGATATTGA-ATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAG
* *
4776 AAAAAATTTTAGTATATCCAAATTTTTTGGTAAAAATAAAGTAAT
65 AAAAAATTGTAATATATCCAAATTTTTTGGTAAAAATAAAGTAAT
4821 TATAAAGATA
1 TATAAAGATA
4831 AAGATATTAG
Statistics
Matches: 114, Mismatches: 3, Indels: 3
0.95 0.03 0.03
Matches are distributed among these distances:
108 7 0.06
109 107 0.94
ACGTcount: A:0.48, C:0.02, G:0.11, T:0.38
Consensus pattern (109 bp):
TATAAAGATATTGAATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGA
AAAAATTGTAATATATCCAAATTTTTTGGTAAAAATAAAGTAAT
Found at i:4982 original size:2 final size:2
Alignment explanation
Indices: 4975--5021 Score: 60
Period size: 2 Copynumber: 23.5 Consensus size: 2
4965 CTCGTACTTT
*
4975 TA TA TA TA GTA TA GA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
5017 GA TA T
1 TA TA T
5022 GCATGTTATG
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
1 1 0.03
2 36 0.92
3 2 0.05
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (2 bp):
TA
Found at i:6848 original size:27 final size:27
Alignment explanation
Indices: 6815--6868 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
6805 AATGACCTAG
* *
6815 CAACATATTATTACATAATTTTGGATT
1 CAACATACTATTACATAAATTTGGATT
6842 CAACATACTATTACATAAATTTGGATT
1 CAACATACTATTACATAAATTTGGATT
6869 TGATTAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.39, C:0.13, G:0.07, T:0.41
Consensus pattern (27 bp):
CAACATACTATTACATAAATTTGGATT
Found at i:16980 original size:2 final size:2
Alignment explanation
Indices: 16973--16997 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16963 TATTTTAGAT
16973 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
16998 TTGTTTCCGA
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:17655 original size:14 final size:14
Alignment explanation
Indices: 17632--17674 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
17622 TTTTGATTTT
*
17632 ATAATGATAATAAA
1 ATAATAATAATAAA
*
17646 ATAATAATAATAAT
1 ATAATAATAATAAA
17660 AT-ATAAATAATAAA
1 ATAAT-AATAATAAA
17674 A
1 A
17675 AAAAACCAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 2 0.08
14 23 0.92
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (14 bp):
ATAATAATAATAAA
Found at i:19119 original size:166 final size:165
Alignment explanation
Indices: 18844--19159 Score: 510
Period size: 166 Copynumber: 1.9 Consensus size: 165
18834 TTGAGTCATT
* *
18844 TGTCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAATCCCCTCAAGATAAAAAGTTAGGATAT
1 TGTCAATTGAGAAATGACCAAAAAGTCTAGTTATTTAATCCCCTCAAGATAAAAAGTTAGGACAT
*
18909 TTAAGTAATCTGCCAAGTAGATAAAGACGAAAAAGATTAGTTCTC-CAGCTCATCATTAATCCGG
66 TTAAGTAATCTGCCAAGTAGATAAAGACGAAAAAAATTAGTTCTCTC-GCTCATCATTAATCCGG
*
18973 GGTAGGGATCTTTTAGTAATTCCACTACTCTATTAA
130 AGTAGGGATCTTTTAGTAATTCCACTACTCTATTAA
* *
19009 TGTCAATTGAGAACTGACCAAAAAGTCTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACA
1 TGTCAATTGAGAAATGACCAAAAAGTCTAGTTATTTAATCCCCTCAAG-ATAAAAAGTTAGGACA
* * *
19074 TTTAAGTAATCTGTCAAGTGGGA-AAAGACGAAAAAAATTAGTTCTCTCGCTCCTCATTAATCCG
65 TTTAAGTAATCTGCCAAGT-AGATAAAGACGAAAAAAATTAGTTCTCTCGCTCATCATTAATCCG
19138 GAGTAGGGATCTTTTAGTAATT
129 GAGTAGGGATCTTTTAGTAATT
19160 TCACATGTTT
Statistics
Matches: 139, Mismatches: 9, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
165 46 0.33
166 90 0.65
167 3 0.02
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.30
Consensus pattern (165 bp):
TGTCAATTGAGAAATGACCAAAAAGTCTAGTTATTTAATCCCCTCAAGATAAAAAGTTAGGACAT
TTAAGTAATCTGCCAAGTAGATAAAGACGAAAAAAATTAGTTCTCTCGCTCATCATTAATCCGGA
GTAGGGATCTTTTAGTAATTCCACTACTCTATTAA
Found at i:22529 original size:99 final size:99
Alignment explanation
Indices: 22310--22510 Score: 261
Period size: 99 Copynumber: 2.1 Consensus size: 99
22300 ATGAGTTACA
*
22310 ACTTACAATTGGAT-CTTTAATCCTTTTTATACTTTCAATAATACCTCACCGTGATATATACATT
1 ACTTA-AATTGGATACTTTAATTCTTTTTATACTTTCAATAATACCTCACCGTGATATATACATT
22374 ACATTCAAATTCAAATAATAATTCCAATTAAAGTG
65 ACATTCAAATTCAAATAATAATTCCAATTAAAGTG
* * * *
22409 AGTTACAATTGGGTA-TTTAATTCTTTTTAT-CATTTCAATAACT-CCTCACTGTTATATATACA
1 ACTTA-AATTGGATACTTTAATTCTTTTTATAC-TTTCAATAA-TACCTCACCGTGATATATACA
* *
22471 -TACATT-ACATTCAAATAATAATTCCAATTAAAGTT
63 TTACATTCAAATTCAAATAATAATTCCAATTAAAGTG
22506 ACTTA
1 ACTTA
22511 GTTGGCATAT
Statistics
Matches: 91, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
97 31 0.34
98 7 0.08
99 52 0.57
100 1 0.01
ACGTcount: A:0.37, C:0.17, G:0.06, T:0.40
Consensus pattern (99 bp):
ACTTAAATTGGATACTTTAATTCTTTTTATACTTTCAATAATACCTCACCGTGATATATACATTA
CATTCAAATTCAAATAATAATTCCAATTAAAGTG
Found at i:27317 original size:16 final size:14
Alignment explanation
Indices: 27296--27331 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 14
27286 AAAATTTAGG
27296 AAAAAAAGAAGGAAA
1 AAAAAAAGAA-GAAA
27311 AAGAAAAAGAAGAAA
1 AA-AAAAAGAAGAAA
27326 AAAAAA
1 AAAAAA
27332 CTGTAGCGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 4 0.20
15 8 0.40
16 8 0.40
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (14 bp):
AAAAAAAGAAGAAA
Found at i:34156 original size:3 final size:3
Alignment explanation
Indices: 34138--34173 Score: 54
Period size: 3 Copynumber: 11.3 Consensus size: 3
34128 AAAATTAGCT
34138 TAA TATA TATA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TA-A TA-A TAA TAA TAA TAA TAA TAA TAA TAA T
34174 TTGACCTGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 25 0.78
4 7 0.22
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Done.