Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010809.1 Corchorus capsularis cultivar CVL-1 contig10830, 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: 17756
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1494 original size:20 final size:21
Alignment explanation
Indices: 1466--1520 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
1456 CTTGATCTTG
*
1466 AGTCATTTG-CTCTTTAAGTA
1 AGTCATTTGACTCCTTAAGTA
* *
1486 AGTCGTTTGACTCCTTAAGCTG
1 AGTCATTTGACTCCTTAAG-TA
1508 AG-CATTTGACTCC
1 AGTCATTTGACTCC
1521 ATTATTCGAG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 8 0.28
21 18 0.62
22 3 0.10
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (21 bp):
AGTCATTTGACTCCTTAAGTA
Found at i:4664 original size:135 final size:131
Alignment explanation
Indices: 4385--4681 Score: 371
Period size: 135 Copynumber: 2.2 Consensus size: 131
4375 CAGAGGCGCA
* * * *
4385 GCACCAAGCGGCTGTTGGTGTTGCCCCCCAAGTCCTTGCCCCCCAAATCTTTCATCGATGAGACT
1 GCACCAAGCAGTTGTTGGTTTTGCCCCCCAAGTCCTTGCCCCCCAAATCTTTCATCGATGAGACC
* * * ** ** *
4450 AACCTGAGCACCTGTTGATTGTTCACCTGATGGTTAACTTGTTGAAGGGGAAGAGGATCGGGCTG
66 AACCTAACCACCTGTGGATTGTTCACCTGATGGTTAACTTGTTGAAAAGGAAGAACACCGGGCTG
4515 G
131 G
* *
4516 GCACCAAGCAGTTGTTGGTTTTGCCCCCCGAGTCCTTGCCCCCCAAGTCTTTCATCGATGAGACC
1 GCACCAAGCAGTTGTTGGTTTTGCCCCCCAAGTCCTTGCCCCCCAAATCTTTCATCGATGAGACC
* * * * *
4581 AATCTCAACCATGACTTGTGGGTTGTTCACCTGATGGTTGACTTGTTGAAAAGGCAGAACACCGG
66 AACCT-AACC---ACCTGTGGATTGTTCACCTGATGGTTAACTTGTTGAAAAGGAAGAACACCGG
4646 GCTGG
127 GCTGG
4651 GCACCAAGCAGTTGTTGGTTTT-CCCCTCCAA
1 GCACCAAGCAGTTGTTGGTTTTGCCCC-CCAA
4682 TTCTTTCTTC
Statistics
Matches: 141, Mismatches: 20, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
131 63 0.45
132 2 0.01
134 4 0.03
135 72 0.51
ACGTcount: A:0.21, C:0.27, G:0.26, T:0.27
Consensus pattern (131 bp):
GCACCAAGCAGTTGTTGGTTTTGCCCCCCAAGTCCTTGCCCCCCAAATCTTTCATCGATGAGACC
AACCTAACCACCTGTGGATTGTTCACCTGATGGTTAACTTGTTGAAAAGGAAGAACACCGGGCTG
G
Found at i:5026 original size:6 final size:6
Alignment explanation
Indices: 5017--5066 Score: 100
Period size: 6 Copynumber: 8.3 Consensus size: 6
5007 AAAAAATAAT
5017 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
5065 AA
1 AA
5067 CTCTCAGAGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:6618 original size:156 final size:156
Alignment explanation
Indices: 6387--6673 Score: 346
Period size: 156 Copynumber: 1.8 Consensus size: 156
6377 TTTGCCAAGG
* * * * *
6387 GACTTAGAATATCCACTTGAGACTATGGAAAAAATTCTAAGTAAAACCGAGCTCCCCTTGATGGT
1 GACTTAGAATATCCACTTAAGACTATGGAAAAAATTCTAAGTAAAACCGAACTCCCCTAGATAGA
* * ** * *
6452 GAACTAGGTTTCTCTCC-CTGAGTTGTCCTTAAATGAAAAACTAACATAAGTTTTTCATTCTAAG
66 GAACTAGGTTTCACTCCTC-AAACTATCCTTAAATGAAAAACTAACATAAGTTTTTCATACTAAG
6516 TCCAGCGAAGCTTATTCTCCACCAATA
130 TCCAGCGAAGCTTATTCTCCACCAATA
* * * *
6543 GACTTAGATTATCCCCATTAAGA-TATGGGAAAAATTCTAAGTAAAACCGAACT-CTCTAGCATA
1 GACTTAGAATATCCAC-TTAAGACTATGGAAAAAATTCTAAGTAAAACCGAACTCCCCTAG-ATA
* * * * *
6606 GAGAAGTTGGTTTGACTCCTCAAACTATCCTTAATTGAAAAACTAGCATAAGTTTTTCATACTAA
64 GAGAACTAGGTTTCACTCCTCAAACTATCCTTAAATGAAAAACTAACATAAGTTTTTCATACTAA
6671 GTC
129 GTC
6674 TGTTTGAGAT
Statistics
Matches: 108, Mismatches: 20, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
155 4 0.04
156 98 0.91
157 6 0.06
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.30
Consensus pattern (156 bp):
GACTTAGAATATCCACTTAAGACTATGGAAAAAATTCTAAGTAAAACCGAACTCCCCTAGATAGA
GAACTAGGTTTCACTCCTCAAACTATCCTTAAATGAAAAACTAACATAAGTTTTTCATACTAAGT
CCAGCGAAGCTTATTCTCCACCAATA
Found at i:9326 original size:28 final size:28
Alignment explanation
Indices: 9263--9318 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
9253 AAAAATAACC
9263 AAATTCATATAAAGTTATAGAGTTATAT
1 AAATTCATATAAAGTTATAGAGTTATAT
9291 AAATTCATATAAAGTTATAGAGTTATAT
1 AAATTCATATAAAGTTATAGAGTTATAT
9319 CCCTTCATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.46, C:0.04, G:0.11, T:0.39
Consensus pattern (28 bp):
AAATTCATATAAAGTTATAGAGTTATAT
Found at i:12532 original size:25 final size:24
Alignment explanation
Indices: 12499--12560 Score: 81
Period size: 25 Copynumber: 2.5 Consensus size: 24
12489 TTTGAGGTAC
* *
12499 AAAAATTAATTTTAATTATA-AGTG
1 AAAATTTAATTTTAACTATATA-TG
12523 AAAATTTTAATTTTAACTATATATG
1 AAAA-TTTAATTTTAACTATATATG
12548 AAAATTTAATTTT
1 AAAATTTAATTTT
12561 GTGGCATAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 13 0.38
25 20 0.59
26 1 0.03
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (24 bp):
AAAATTTAATTTTAACTATATATG
Found at i:17331 original size:16 final size:16
Alignment explanation
Indices: 17312--17347 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
17302 ACGGGTCTCG
17312 GGTCGTTTGGGTTTCA
1 GGTCGTTTGGGTTTCA
17328 GGTCGTTTGGGTTTCA
1 GGTCGTTTGGGTTTCA
17344 GGTC
1 GGTC
17348 ATCTAGGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.06, C:0.14, G:0.39, T:0.42
Consensus pattern (16 bp):
GGTCGTTTGGGTTTCA
Done.