Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015545.1 Corchorus capsularis cultivar CVL-1 contig15566, 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: 20561
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:1893 original size:23 final size:23
Alignment explanation
Indices: 1863--1908 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
1853 ACTATTACCA
1863 AAATCCAATTATATTAATACTTT
1 AAATCCAATTATATTAATACTTT
1886 AAATCCAATTATATTAATACTTT
1 AAATCCAATTATATTAATACTTT
1909 TTATAAAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.13, G:0.00, T:0.43
Consensus pattern (23 bp):
AAATCCAATTATATTAATACTTT
Found at i:3974 original size:185 final size:185
Alignment explanation
Indices: 3657--4018 Score: 688
Period size: 185 Copynumber: 2.0 Consensus size: 185
3647 AATCCCCACT
3657 AGTGTCTCTAATCAAGCCACCAGCAGAGGAATGTCCATCATCATATCGTCGTGACCCATCCATGT
1 AGTGTCTCTAATCAAGCCACCAGCAGAGGAATGTCCATCATCATATCGTCGTGACCCATCCATGT
* *
3722 TCAGTATGAACACACCATCTAGTGGTCGTTTCCATATGATCATTCTACCCGAAGGCGTAGGCAGG
66 TCAGTATGAACACACCATCTAGTGGTAGTTTCCATATGATCATTCTACCCGAAGGCGTAGACAGG
3787 GTGTGGTGAGAATTATGTACCTGATAAGAATCTCTCGCTAAAGCAAGTCCCCTCC
131 GTGTGGTGAGAATTATGTACCTGATAAGAATCTCTCGCTAAAGCAAGTCCCCTCC
* *
3842 AGTGTCTCTAATCAAGCCACCAGCAGAGGCATGTCCATCATCATGTCGTCGTGACCCATCCATGT
1 AGTGTCTCTAATCAAGCCACCAGCAGAGGAATGTCCATCATCATATCGTCGTGACCCATCCATGT
3907 TCAGTATGAACACACCATCTAGTGGTAGTTTCCATATGATCATTCTACCCGAAGGCGTAGACAGG
66 TCAGTATGAACACACCATCTAGTGGTAGTTTCCATATGATCATTCTACCCGAAGGCGTAGACAGG
3972 GTGTGGTGAGAATTATGTACCTGATAAGAATCTCTCGCTAAAGCAAG
131 GTGTGGTGAGAATTATGTACCTGATAAGAATCTCTCGCTAAAGCAAG
4019 AGAATACTGT
Statistics
Matches: 173, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
185 173 1.00
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.26
Consensus pattern (185 bp):
AGTGTCTCTAATCAAGCCACCAGCAGAGGAATGTCCATCATCATATCGTCGTGACCCATCCATGT
TCAGTATGAACACACCATCTAGTGGTAGTTTCCATATGATCATTCTACCCGAAGGCGTAGACAGG
GTGTGGTGAGAATTATGTACCTGATAAGAATCTCTCGCTAAAGCAAGTCCCCTCC
Found at i:5516 original size:7 final size:6
Alignment explanation
Indices: 5487--5520 Score: 59
Period size: 6 Copynumber: 5.5 Consensus size: 6
5477 AAAGCAAAGC
5487 AAATCT AAATCT AAATCT AAATCTT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATC-T AAATCT AAA
5521 GCAGATTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 21 0.78
7 6 0.22
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.32
Consensus pattern (6 bp):
AAATCT
Found at i:5533 original size:13 final size:13
Alignment explanation
Indices: 5517--5551 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
5507 ATCTTAAATC
*
5517 TAAAGCAGATTAA
1 TAAAGCAAATTAA
*
5530 TAAAGTAAATTAA
1 TAAAGCAAATTAA
5543 TAAAGCAAA
1 TAAAGCAAA
5552 CAATAATTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.60, C:0.06, G:0.11, T:0.23
Consensus pattern (13 bp):
TAAAGCAAATTAA
Found at i:12760 original size:13 final size:13
Alignment explanation
Indices: 12744--12778 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
12734 ATCTTAAATC
*
12744 TAAAGCAGATTAA
1 TAAAGCAAATTAA
*
12757 TAAAGTAAATTAA
1 TAAAGCAAATTAA
12770 TAAAGCAAA
1 TAAAGCAAA
12779 CAATAATTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.60, C:0.06, G:0.11, T:0.23
Consensus pattern (13 bp):
TAAAGCAAATTAA
Found at i:14337 original size:2 final size:2
Alignment explanation
Indices: 14330--14358 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
14320 AATAGTAGCT
14330 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 T
14359 CCATAGAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16674 original size:31 final size:34
Alignment explanation
Indices: 16621--16715 Score: 99
Period size: 34 Copynumber: 2.8 Consensus size: 34
16611 TACTCACTAC
* *
16621 GTGAGTATATATACGAAGATAAAAGA-T-AAA-ATA
1 GTGAGTATATAT--GAAAATAAAAAATTAAAAGATA
16654 GTGAGTATATATGAAAATAAAAAATTAGAAAGATA
1 GTGAGTATATATGAAAATAAAAAATTA-AAAGATA
*
16689 GT-AATATATATGAAAATAAAATAATTA
1 GTGAGTATATATGAAAATAAAA-AATTA
16716 TAGAAAGATA
Statistics
Matches: 54, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
31 10 0.19
32 1 0.02
33 12 0.22
34 21 0.39
35 10 0.19
ACGTcount: A:0.57, C:0.01, G:0.15, T:0.27
Consensus pattern (34 bp):
GTGAGTATATATGAAAATAAAAAATTAAAAGATA
Found at i:16700 original size:34 final size:37
Alignment explanation
Indices: 16659--16727 Score: 117
Period size: 34 Copynumber: 1.9 Consensus size: 37
16649 AAATAGTGAG
16659 TATATATGAAAATAAAA-AA-T-TAGAAAGATAGTAA
1 TATATATGAAAATAAAATAATTATAGAAAGATAGTAA
16693 TATATATGAAAATAAAATAATTATAGAAAGATAGT
1 TATATATGAAAATAAAATAATTATAGAAAGATAGT
16728 TTATGTTACA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
34 17 0.53
35 2 0.06
36 1 0.03
37 12 0.38
ACGTcount: A:0.59, C:0.00, G:0.12, T:0.29
Consensus pattern (37 bp):
TATATATGAAAATAAAATAATTATAGAAAGATAGTAA
Done.