Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009745.1 Corchorus capsularis cultivar CVL-1 contig09766, 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: 39844
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Found at i:4599 original size:26 final size:26
Alignment explanation
Indices: 4570--4637 Score: 118
Period size: 26 Copynumber: 2.6 Consensus size: 26
4560 TTCCTTCATT
4570 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
4596 TTAATCATAAACTAATTAAATATTAA
1 TTAATCATAAACTAATTAAATACTAA
*
4622 TTAAACATAAACTAAT
1 TTAATCATAAACTAAT
4638 AAACTAAGTA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.35
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Found at i:4600 original size:15 final size:15
Alignment explanation
Indices: 4570--4614 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
4560 TTCCTTCATT
4570 TTAATCATAAACTAA
1 TTAATCATAAACTAA
4585 TTAA--AT--ACTAA
1 TTAATCATAAACTAA
4596 TTAATCATAAACTAA
1 TTAATCATAAACTAA
4611 TTAA
1 TTAA
4615 ATATTAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
11 9 0.35
13 4 0.15
15 13 0.50
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (15 bp):
TTAATCATAAACTAA
Found at i:4790 original size:12 final size:11
Alignment explanation
Indices: 4768--4796 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
4758 GGCTAGGCCA
4768 TTTTTAATTTT
1 TTTTTAATTTT
4779 TTTTTAATTTT
1 TTTTTAATTTT
4790 TTTTTAA
1 TTTTTAA
4797 AAATTCCAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTTAATTTT
Found at i:8790 original size:46 final size:44
Alignment explanation
Indices: 8737--8826 Score: 126
Period size: 46 Copynumber: 2.0 Consensus size: 44
8727 GAAATTTATG
*
8737 ACCATCAAATTGATTGAATTACATAGAATGTTTAGTCCCACTCTTC
1 ACCATCAAATTGATTGAATGACATAGAA--TTTAGTCCCACTCTTC
* * *
8783 ACCATCAAGTTGATTGAATGACATGGAATTTAGTCCCAGTCTTC
1 ACCATCAAATTGATTGAATGACATAGAATTTAGTCCCACTCTTC
8827 CTTCATTATC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 15 0.38
46 25 0.62
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.33
Consensus pattern (44 bp):
ACCATCAAATTGATTGAATGACATAGAATTTAGTCCCACTCTTC
Found at i:14206 original size:42 final size:42
Alignment explanation
Indices: 14160--14345 Score: 174
Period size: 42 Copynumber: 4.4 Consensus size: 42
14150 GGACCTATCG
*
14160 CGCCTTCTATAGTATCGATCATCTGGTGAGTAGGAACGGTCC
1 CGCCTTCTATAGTATCGATCATCTGGTGAGTAGGAACGGTCA
* ** * * ** * **
14202 CGCCTACGGTAGTAGCGGTCATCTGGCAAGTAGGACCTTTCA
1 CGCCTTCTATAGTATCGATCATCTGGTGAGTAGGAACGGTCA
* ** * * * **
14244 CGCCTACGGTAGTAGCGGTCATCTGGTGAGTAGGACCTATCA
1 CGCCTTCTATAGTATCGATCATCTGGTGAGTAGGAACGGTCA
* *
14286 CGCCTTCTATAGTATCGATCATCAGGAGAGTAGGAACGGTCA
1 CGCCTTCTATAGTATCGATCATCTGGTGAGTAGGAACGGTCA
*
14328 CGTCTTCTATAGTATCGA
1 CGCCTTCTATAGTATCGA
14346 GAATCTGGGG
Statistics
Matches: 119, Mismatches: 25, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 119 1.00
ACGTcount: A:0.23, C:0.24, G:0.27, T:0.26
Consensus pattern (42 bp):
CGCCTTCTATAGTATCGATCATCTGGTGAGTAGGAACGGTCA
Found at i:14318 original size:84 final size:84
Alignment explanation
Indices: 14142--14320 Score: 189
Period size: 84 Copynumber: 2.1 Consensus size: 84
14132 AGAGCCATAT
* * * * * *
14142 GGAGAGTAGGACCTATCGCGCCTTCTATAGTATCGATCATCTGGTGAGTAGGAACGGTCCCGCCT
1 GGAGAGTAGGACCTATCACGCCTACGATAGTAGCGATCATCTGGTGAGTAGGAACGATCACGCCT
* * *
14207 ACGGTAGTAGCGGTCATCT
66 ACGATAGTAGCGATCATCA
* * * * *
14226 GGCA-AGTAGGACCTTTCACGCCTACGGTAGTAGCGGTCATCTGGTGAGTAGGACCTATCACGCC
1 GG-AGAGTAGGACCTATCACGCCTACGATAGTAGCGATCATCTGGTGAGTAGGAACGATCACGCC
* * *
14290 TTCTATAGTATCGATCATCA
65 TACGATAGTAGCGATCATCA
14310 GGAGAGTAGGA
1 GGAGAGTAGGA
14321 ACGGTCACGT
Statistics
Matches: 76, Mismatches: 17, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
83 1 0.01
84 74 0.97
85 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.25
Consensus pattern (84 bp):
GGAGAGTAGGACCTATCACGCCTACGATAGTAGCGATCATCTGGTGAGTAGGAACGATCACGCCT
ACGATAGTAGCGATCATCA
Found at i:19960 original size:30 final size:30
Alignment explanation
Indices: 19924--19997 Score: 139
Period size: 30 Copynumber: 2.5 Consensus size: 30
19914 TTTGTAGTTT
*
19924 GAATCGGAGTAGACAAGTAGTGAAGGAACA
1 GAATCGGAGTAGACAAGTAGTGAAAGAACA
19954 GAATCGGAGTAGACAAGTAGTGAAAGAACA
1 GAATCGGAGTAGACAAGTAGTGAAAGAACA
19984 GAATCGGAGTAGAC
1 GAATCGGAGTAGAC
19998 GTCCAAGTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.43, C:0.11, G:0.32, T:0.14
Consensus pattern (30 bp):
GAATCGGAGTAGACAAGTAGTGAAAGAACA
Found at i:20309 original size:24 final size:24
Alignment explanation
Indices: 20274--20331 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
20264 TAATAAGTAA
* *
20274 TATTTTTA-AAATATTTTTAT-TTT
1 TATTTTTATAAAT-TTTATATCTAT
20297 TATTTTTATAAATTTTATATCTAT
1 TATTTTTATAAATTTTATATCTAT
*
20321 TATTTCTATAA
1 TATTTTTATAA
20332 CTAAAATTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
23 14 0.47
24 16 0.53
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (24 bp):
TATTTTTATAAATTTTATATCTAT
Found at i:20794 original size:22 final size:21
Alignment explanation
Indices: 20769--21053 Score: 243
Period size: 22 Copynumber: 13.1 Consensus size: 21
20759 GAAATTAAAC
* *
20769 TAACCTCCATATGAAATTTCGA
1 TAACCTCC-TATGAAATTTTGG
* *
20791 TAACCTTCATAT-AAATTATGG
1 TAACC-TCCTATGAAATTTTGG
** * *
20812 TAAATTTCCTATGAAAATTTGA
1 T-AACCTCCTATGAAATTTTGG
* * * *
20834 TAACCACGTAATTAAATCTTGG
1 TAACCTCCT-ATGAAATTTTGG
20856 TAA-CTCCTTATG-AATTTTGG
1 TAACCTCC-TATGAAATTTTGG
20876 TAACCTTCCTATGAAATTTTGG
1 TAACC-TCCTATGAAATTTTGG
20898 TAACCTACCTATGAAATTTTGG
1 TAACCT-CCTATGAAATTTTGG
*
20920 TAACTTCCCTATGAAATTTTGG
1 TAACCT-CCTATGAAATTTTGG
* *
20942 TAACCTCCCTATAAAATTTTTG
1 TAACCT-CCTATGAAATTTTGG
* *
20964 TAATCTCCTATGTAATTTTGG
1 TAACCTCCTATGAAATTTTGG
** *
20985 TAATTTCTCTATGATATTTTGG
1 TAACCTC-CTATGAAATTTTGG
*
21007 TAACCTCCATATGAAATTTTAG
1 TAACCTCC-TATGAAATTTTGG
*
21029 TAACCTCTCTATGAAATTTTTG
1 TAACCTC-CTATGAAATTTTGG
21051 TAA
1 TAA
21054 TCACCTTATG
Statistics
Matches: 212, Mismatches: 39, Indels: 24
0.77 0.14 0.09
Matches are distributed among these distances:
20 10 0.05
21 45 0.21
22 154 0.73
23 3 0.01
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.41
Consensus pattern (21 bp):
TAACCTCCTATGAAATTTTGG
Found at i:20885 original size:64 final size:66
Alignment explanation
Indices: 20803--21045 Score: 216
Period size: 65 Copynumber: 3.7 Consensus size: 66
20793 ACCTTCATAT
* ** * * *
20803 AAATTATGGTAAATTTCCTATGAAAATTTGATAACC-ACGTAATTAAATCTTGGTAAC-TCCTTA
1 AAATTTTGGTAACCTTCCTATGAAAATTTGATAACCTACCT-ATGAAATCTTGGTAACTTCCCTA
20866 TG
65 TG
* * *
20868 -AATTTTGGTAACCTTCCTATGAAATTTTGGTAACCTACCTATGAAATTTTGGTAACTTCCCTAT
1 AAATTTTGGTAACCTTCCTATGAAAATTTGATAACCTACCTATGAAATCTTGGTAACTTCCCTAT
20932 G
66 G
* * * * * *
20933 AAATTTTGGTAACCTCCCTAT-AAAATTTTTG-TAATCT-CCTATGTAATTTTGGTAATTTCTCT
1 AAATTTTGGTAACCTTCCTATGAAAA--TTTGATAACCTACCTATGAAATCTTGGTAACTTCCCT
20995 ATG
64 ATG
* *
20998 ATATTTTGGTAACC-TCCATATG-AAATTTTAGTAACCT-CTCTATGAAAT
1 AAATTTTGGTAACCTTCC-TATGAAAATTTGA-TAACCTAC-CTATGAAAT
21046 TTTTGTAATC
Statistics
Matches: 148, Mismatches: 20, Indels: 19
0.79 0.11 0.10
Matches are distributed among these distances:
63 3 0.02
64 46 0.31
65 63 0.43
66 32 0.22
67 4 0.03
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (66 bp):
AAATTTTGGTAACCTTCCTATGAAAATTTGATAACCTACCTATGAAATCTTGGTAACTTCCCTAT
G
Found at i:21079 original size:44 final size:43
Alignment explanation
Indices: 20847--21085 Score: 234
Period size: 44 Copynumber: 5.5 Consensus size: 43
20837 CCACGTAATT
* * *
20847 AAATCTTGGTAA-CTCCTTATG-AATTTTGGTAACCTTCCTATG
1 AAATTTTGGTAACCTCCCTATGAAATTTTGGTAATC-TCCTATG
*
20889 AAATTTTGGTAACCTACCTATGAAATTTTGGTAA-CTTCCCTATG
1 AAATTTTGGTAACCTCCCTATGAAATTTTGGTAATC-T-CCTATG
* *
20933 AAATTTTGGTAACCTCCCTATAAAATTTTTGTAATCTCCTATG
1 AAATTTTGGTAACCTCCCTATGAAATTTTGGTAATCTCCTATG
* ** * * *
20976 TAATTTTGGTAATTTCTCTATGATATTTTGGTAACCTCCATATG
1 AAATTTTGGTAACCTCCCTATGAAATTTTGGTAATCTCC-TATG
* * * *
21020 AAATTTTAGTAACCTCTCTATGAAATTTTTGTAATCACCTTATG
1 AAATTTTGGTAACCTCCCTATGAAATTTTGGTAATCTCC-TATG
* *
21064 TAATATTT-GTTACCTCCCTATG
1 AAAT-TTTGGTAACCTCCCTATG
21086 GTCGTGAAAA
Statistics
Matches: 165, Mismatches: 26, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
42 11 0.07
43 47 0.28
44 103 0.62
45 4 0.02
ACGTcount: A:0.28, C:0.18, G:0.12, T:0.43
Consensus pattern (43 bp):
AAATTTTGGTAACCTCCCTATGAAATTTTGGTAATCTCCTATG
Found at i:21733 original size:22 final size:22
Alignment explanation
Indices: 21470--21728 Score: 218
Period size: 22 Copynumber: 11.8 Consensus size: 22
21460 TGGATAACTA
*** *
21470 CCCTATGAAATTTCCCTGACCT
1 CCCTATGAAATTTTGGTAACCT
21492 CCCTATGAAATTTTGGTAACCT
1 CCCTATGAAATTTTGGTAACCT
* * *
21514 TCGTATGAAATTTTGGTAACCA
1 CCCTATGAAATTTTGGTAACCT
*
21536 CCATATG-AATTTATGGTAACCT
1 CCCTATGAAATTT-TGGTAACCT
* * * *
21558 CCATATGAAATCTTGCTAATCT
1 CCCTATGAAATTTTGGTAACCT
* *
21580 CCCTATGAAATCTTGGTAACGT
1 CCCTATGAAATTTTGGTAACCT
*
21602 CCCTATGAAATCTTGGTAACCT
1 CCCTATGAAATTTTGGTAACCT
* * * *
21624 ACATATGAGATTTTGGTAA-TT
1 CCCTATGAAATTTTGGTAACCT
* *
21645 GACATATGAAATTTTGGTAACCT
1 -CCCTATGAAATTTTGGTAACCT
* *
21668 CCGTATTG-AATTTTTGTAACCT
1 CCCTA-TGAAATTTTGGTAACCT
* * * * *
21690 TCTTGTGAAATTTTTGTAAACT
1 CCCTATGAAATTTTGGTAACCT
21712 CCCTATGAAATTTTGGT
1 CCCTATGAAATTTTGGT
21729 TAACTACTGA
Statistics
Matches: 195, Mismatches: 36, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
21 8 0.04
22 180 0.92
23 7 0.04
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.38
Consensus pattern (22 bp):
CCCTATGAAATTTTGGTAACCT
Found at i:23338 original size:13 final size:13
Alignment explanation
Indices: 23320--23354 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
23310 TTAATTATTG
23320 TTTGCTTTATTAA
1 TTTGCTTTATTAA
23333 TTTGCTTTATTAA
1 TTTGCTTTATTAA
*
23346 TCTGCTTTA
1 TTTGCTTTA
23355 GATTTAGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.20, C:0.11, G:0.09, T:0.60
Consensus pattern (13 bp):
TTTGCTTTATTAA
Found at i:23666 original size:22 final size:22
Alignment explanation
Indices: 23641--23713 Score: 83
Period size: 22 Copynumber: 3.3 Consensus size: 22
23631 GTAACTTATC
*
23641 TATGAAATTTTGGTAACATCCA
1 TATGAAATTTTGATAACATCCA
* *
23663 TATGAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACATCCA
* * * *
23685 TACGAAATTTTGACAATATCCC
1 TATGAAATTTTGATAACATCCA
23707 TATGAAA
1 TATGAAA
23714 CCTACCTATG
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (22 bp):
TATGAAATTTTGATAACATCCA
Found at i:24587 original size:22 final size:22
Alignment explanation
Indices: 24561--24635 Score: 73
Period size: 22 Copynumber: 3.4 Consensus size: 22
24551 TAACTATCTC
* *
24561 ATGAAATTTCCGTAACCTTCGT
1 ATGAAATTTCCGTAACCATCAT
*
24583 TTGAAATTT-CGATAACCATCAT
1 ATGAAATTTCCG-TAACCATCAT
* *
24605 ATGAAATTTCAGTAA-CTTACAT
1 ATGAAATTTCCGTAACCAT-CAT
24627 ATGAAATTT
1 ATGAAATTT
24636 TGGTAATCTC
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
21 4 0.09
22 39 0.89
23 1 0.02
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.37
Consensus pattern (22 bp):
ATGAAATTTCCGTAACCATCAT
Found at i:32261 original size:2 final size:2
Alignment explanation
Indices: 32254--32289 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
32244 AATTATATTA
32254 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
32290 TTTCTTCCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Done.