Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008337.1 Corchorus capsularis cultivar CVL-1 contig08358, 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: 41055
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:12 original size:2 final size:2
Alignment explanation
Indices: 6--71 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
1 AACTG
6 CT CT CT 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 CT CT CT
48 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
72 TAAAAGTTGA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2452 original size:2 final size:2
Alignment explanation
Indices: 2447--2473 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2437 TATAAAAAAC
2447 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
2474 ACCATGTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7481 original size:16 final size:16
Alignment explanation
Indices: 7462--7500 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
7452 TTTATATGTA
*
7462 TATATAAGAAATGATT
1 TATATAAGAAATAATT
* *
7478 TATATAATATATAATT
1 TATATAAGAAATAATT
7494 TATATAA
1 TATATAA
7501 TTCTATTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (16 bp):
TATATAAGAAATAATT
Found at i:8817 original size:17 final size:17
Alignment explanation
Indices: 8797--8830 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
8787 GAATAAAAAT
8797 AGAAAAAATGAATTTTA
1 AGAAAAAATGAATTTTA
* *
8814 AGAAAATATGATTTTTA
1 AGAAAAAATGAATTTTA
8831 TTAGTCACAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.12, T:0.35
Consensus pattern (17 bp):
AGAAAAAATGAATTTTA
Found at i:10857 original size:17 final size:17
Alignment explanation
Indices: 10806--10857 Score: 77
Period size: 17 Copynumber: 3.1 Consensus size: 17
10796 AAATTCTCCT
*
10806 TGTGGTACCAGGTAGCA
1 TGTGGTACTAGGTAGCA
**
10823 CATGGTACTAGGTAGCA
1 TGTGGTACTAGGTAGCA
10840 TGTGGTACTAGGTAGCA
1 TGTGGTACTAGGTAGCA
10857 T
1 T
10858 CTACTGTATC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.33, T:0.27
Consensus pattern (17 bp):
TGTGGTACTAGGTAGCA
Found at i:11548 original size:156 final size:155
Alignment explanation
Indices: 11191--11735 Score: 469
Period size: 156 Copynumber: 3.5 Consensus size: 155
11181 TGAACTAGGC
* * * **
11191 TTCACACCTCAAACTGTCCTTAAATGAAAAACTTGCATAAGTTTTTCA-CCTTAAGTCTGATTGA
1 TTCACACCCCAAACTGTCCTTAACTTAAAAACTTGCATAAGTTTTTCATCC-TAAGTCCAATTGA
* ** * * * * * * ** *
11255 GCTGAAACTTTTCCA-AGGGACTTAGATTCTCTCAACAAGACTATGGAAAAAA-TCCCAGTAAAA
65 GATG-AACTTGGCCACA-AGACTTAGACTATCTCCATAAAACTATGGAAAAAATTCTAACTAAAA
* * * ** *
11318 CCGAGCTCCCCT-TGATGGTGATCTTGGT
128 CCGAACT-CCCTATAATAGTGAAGTTAGT
** * ** * * * *
11346 TTTTCTCCCTGAACTGTCCTTAAATGAAAAACTTCCACAAGTTTTTCATCCTAAGTCCAA-TGAA
1 TTCACACCCCAAACTGTCCTTAACTTAAAAACTTGCATAAGTTTTTCATCCTAAGTCCAATTG-A
* ** * *
11410 GCTG-A-TTTTCCACCAGTAGGCTTAGATTAT-TCCCATAAAACTATGGAAAAAATTCTAACTAA
65 GATGAACTTGGCCA-CA--AGACTTAGACTATCT-CCATAAAACTATGGAAAAAATTCTAACTAA
* * *
11472 AACCTAACTTCCTATCATAGTGAAGTTAGT
126 AACCGAACTCCCTATAATAGTGAAGTTAGT
* *
11502 TTCACACCCCAAACTGTCCTTAACTTAAAAACTTGCATAAGTTTTTCATACTATGTCCAATTGAG
1 TTCACACCCCAAACTGTCCTTAACTTAAAAACTTGCATAAGTTTTTCATCCTAAGTCCAATTGAG
* * *
11567 ATGAAACTTGGCCACAAGACTTAGACTATCTCCATAAGACTATGGAAAAATTTCTAAGTAAAACC
66 ATG-AACTTGGCCACAAGACTTAGACTATCTCCATAAAACTATGGAAAAAATTCTAACTAAAACC
*
11632 GAACTCCCTATAATAGTGAAGTTGGT
130 GAACTCCCTATAATAGTGAAGTTAGT
* * * * *
11658 TTCACACCCCAAAATGTCCTTAAC-TAAAAGCTTGCATAAGTTTTTCATCTTAAGTCTATTTGAG
1 TTCACACCCCAAACTGTCCTTAACTTAAAAACTTGCATAAGTTTTTCATCCTAAGTCCAATTGAG
11722 ATGAAACTTGGCCA
66 ATG-AACTTGGCCA
11736 AGATGACCTA
Statistics
Matches: 319, Mismatches: 58, Indels: 26
0.79 0.14 0.06
Matches are distributed among these distances:
152 7 0.02
153 1 0.00
154 4 0.01
155 130 0.41
156 166 0.52
157 3 0.01
158 3 0.01
159 5 0.02
ACGTcount: A:0.34, C:0.22, G:0.14, T:0.31
Consensus pattern (155 bp):
TTCACACCCCAAACTGTCCTTAACTTAAAAACTTGCATAAGTTTTTCATCCTAAGTCCAATTGAG
ATGAACTTGGCCACAAGACTTAGACTATCTCCATAAAACTATGGAAAAAATTCTAACTAAAACCG
AACTCCCTATAATAGTGAAGTTAGT
Found at i:16988 original size:2 final size:2
Alignment explanation
Indices: 16981--17010 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
16971 TGCATGTCCC
16981 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17011 GATAAGAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17693 original size:21 final size:19
Alignment explanation
Indices: 17655--17694 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 19
17645 CTTTCACGTA
*
17655 TTTTCTTATTTGTATATAT
1 TTTTCTTATTTCTATATAT
17674 TTTTCTTATTCTACTATATAT
1 TTTTCTTATT-T-CTATATAT
17695 AGAATATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 1 0.06
21 7 0.39
ACGTcount: A:0.23, C:0.10, G:0.03, T:0.65
Consensus pattern (19 bp):
TTTTCTTATTTCTATATAT
Found at i:24255 original size:16 final size:17
Alignment explanation
Indices: 24234--24267 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
24224 ACCATTATTT
24234 ATAAAA-AATATTTAAA
1 ATAAAATAATATTTAAA
*
24250 ATAAAATAATTTTTAAA
1 ATAAAATAATATTTAAA
24267 A
1 A
24268 ATAACACTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
ATAAAATAATATTTAAA
Found at i:27641 original size:156 final size:155
Alignment explanation
Indices: 27113--27667 Score: 785
Period size: 154 Copynumber: 3.6 Consensus size: 155
27103 CTTCATAGCA
* * *
27113 AACTGGACTTCACACCTCAAACTATCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTC
1 AACT-GACTTCTCACCTCAAACTGTCCTTAAATGAAAAACTTGCATAAGTTTTTCATTCTAAGTC
** * * * * * *
27178 TGAATGAGCTGAAACTTT-TCCAAGGGACTTAGATTCTCTCCAAAAGAC-TATGGAAAAAATTCT
65 TGTTTGAGATGAAA-TTTGGCCAAGAGACTTATATTATCTCCACAA-ACTTATGGAAAAAATTCT
*
27241 AAGTAAAACCGAGCTCCCCTTGATAGTG
128 AAGTAAAACCGAACTCCCCTTGATAGTG
* * *
27269 AACTGACTTCTCACCTCAAAATGTCCTT-ATTGAAAAACTTGAATAAGTTTTTCATTCTAAGTCT
1 AACTGACTTCTCACCTCAAACTGTCCTTAAATGAAAAACTTGCATAAGTTTTTCATTCTAAGTCT
27333 GTTTGAGATGAAATTTGGCCAAGAGACTTATATTATCTCCACAAACTTATGGAAAAAATTCTAAG
66 GTTTGAGATGAAATTTGGCCAAGAGACTTATATTATCTCCACAAACTTATGGAAAAAATTCTAAG
27398 TAAAACCGAACTCCCCTTGATAGTG
131 TAAAACCGAACTCCCCTTGATAGTG
* *
27423 AACTGACTTCTCACCTCAAATTGTCCTTAACTGAAAAACTTGCATAAGTTTTTCATTCTAAGTCT
1 AACTGACTTCTCACCTCAAACTGTCCTTAAATGAAAAACTTGCATAAGTTTTTCATTCTAAGTCT
*
27488 GTTTGAGATGAAATTTGGCCAAGAGACTTATATTATCTCCACAAACTTATTGAAAAAAATTCTAA
66 GTTTGAGATGAAATTTGGCCAAGAGACTTATATTATCTCCACAAACTTA-TGGAAAAAATTCTAA
* *
27553 GTAAAACCGAACT-CCCTATCATGGTG
130 GTAAAACCGAACTCCCCT-TGATAGTG
* ** * * *
27579 AAGTGGTTTCTCACCCCAAACTGTCCTTAAATGAAAAACTTGCATAAGTTTTTCATTTTAAGTCC
1 AACTGACTTCTCACCTCAAACTGTCCTTAAATGAAAAACTTGCATAAGTTTTTCATTCTAAGTCT
* *
27644 GTTTGAGATGAAACTTAGCCAAGA
66 GTTTGAGATGAAATTTGGCCAAGA
27668 TGGTGCACGT
Statistics
Matches: 363, Mismatches: 31, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
153 5 0.01
154 134 0.37
155 108 0.30
156 116 0.32
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.31
Consensus pattern (155 bp):
AACTGACTTCTCACCTCAAACTGTCCTTAAATGAAAAACTTGCATAAGTTTTTCATTCTAAGTCT
GTTTGAGATGAAATTTGGCCAAGAGACTTATATTATCTCCACAAACTTATGGAAAAAATTCTAAG
TAAAACCGAACTCCCCTTGATAGTG
Found at i:33724 original size:32 final size:32
Alignment explanation
Indices: 33653--33724 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
33643 CGGATGCAAT
***
33653 AATAAACTAGTATATATACTCTGGTGCCATAA
1 AATAAACTAGTATATATACTCAAATGCCATAA
* **
33685 AAAAAACTAGTATATATACTCAAATTTCATAA
1 AATAAACTAGTATATATACTCAAATGCCATAA
*
33717 GATAAACT
1 AATAAACT
33725 TAATTAATGT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.47, C:0.14, G:0.08, T:0.31
Consensus pattern (32 bp):
AATAAACTAGTATATATACTCAAATGCCATAA
Done.