Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007392.1 Corchorus capsularis cultivar CVL-1 contig07413, 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: 17802
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.35
Found at i:100 original size:33 final size:34
Alignment explanation
Indices: 1--88 Score: 155
Period size: 33 Copynumber: 2.7 Consensus size: 34
1 CTGCCCAATGGTGAAGCCGCCCTAGTGGGGCGGC
1 CTGCCCAATGGTGAAGCCGCCCTAGTGGGGCGGC
35 CTGCCCAATGGTGAAG-CGCCCTAGTGGGGCGGC
1 CTGCCCAATGGTGAAGCCGCCCTAGTGGGGCGGC
68 CTGCCC-ATGGT-AAGCCGCCCT
1 CTGCCCAATGGTGAAGCCGCCCT
89 CTTTGGGGCG
Statistics
Matches: 53, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
31 3 0.06
32 11 0.21
33 23 0.43
34 16 0.30
ACGTcount: A:0.15, C:0.34, G:0.35, T:0.16
Consensus pattern (34 bp):
CTGCCCAATGGTGAAGCCGCCCTAGTGGGGCGGC
Found at i:5558 original size:14 final size:14
Alignment explanation
Indices: 5539--5568 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5529 CCTGTGCATG
*
5539 GGTATGTTGTAAAT
1 GGTATGTGGTAAAT
5553 GGTATGTGGTAAAT
1 GGTATGTGGTAAAT
5567 GG
1 GG
5569 CCTTTTCGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.37, T:0.37
Consensus pattern (14 bp):
GGTATGTGGTAAAT
Found at i:7577 original size:14 final size:15
Alignment explanation
Indices: 7558--7587 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
7548 TTCCCCTCCC
7558 TTTCTTTT-TTTTTT
1 TTTCTTTTCTTTTTT
7572 TTTCTTTTCTTTTTT
1 TTTCTTTTCTTTTTT
7587 T
1 T
7588 CACCCTTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (15 bp):
TTTCTTTTCTTTTTT
Found at i:9308 original size:156 final size:156
Alignment explanation
Indices: 9002--9353 Score: 343
Period size: 156 Copynumber: 2.3 Consensus size: 156
8992 TCATCTCAAA
* * * ** *
9002 CAGACTTAGTATGAAAAACTTATGCTAGTTTTTCAGTTAAGGAC-AGTTTGAGGAGTCAAACCAA
1 CAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAACTCAGAGGAGACAAACCAA
* * * * *
9066 CTTCTCTATGCTAGAGAGTTCGGTTTTACTTAGAATTTTCCCCATAGCTTTATGGTGATAATCTA
66 CTTCACCATGCAAGAGAGCTCGGTTTTACTTAGAATTTTCCCCATAGCTTCATGGTGATAATCTA
* *
9131 AGTCTACTGGTGGAAAATCAGCTTCGTT
131 AGACTACT-GTGGAAAATCAGC-TCATT
* * *
9159 -GGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAACTCAG-GGAGAGAAACCTA
1 CAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAACTCAGAGGAGACAAACCAA
* ** *
9222 GTTCACCAT-CAAGAGGAGCTCGGTTTTACTTAGAATTTTTTCCATAG-TCTCAT-GTGGATATT
66 CTTCACCATGCAAGA-GAGCTCGGTTTTACTTAGAATTTTCCCCATAGCT-TCATGGT-GATAAT
*
9284 CTAAGAC-CCT-TGGCAAAATTTCAGCTCATT
128 CTAAGACTACTGTGG-AAAA--TCAGCTCATT
*
9314 CAAACTT--AATGAAAAA---ATGCTAGTTTTTCATTTAAGGACA
1 CAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACA
9354 GTTTGAGGTG
Statistics
Matches: 164, Mismatches: 23, Indels: 22
0.78 0.11 0.11
Matches are distributed among these distances:
151 24 0.15
153 3 0.02
154 13 0.08
155 13 0.08
156 108 0.66
157 3 0.02
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (156 bp):
CAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAACTCAGAGGAGACAAACCAA
CTTCACCATGCAAGAGAGCTCGGTTTTACTTAGAATTTTCCCCATAGCTTCATGGTGATAATCTA
AGACTACTGTGGAAAATCAGCTCATT
Found at i:9733 original size:17 final size:17
Alignment explanation
Indices: 9713--9745 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
9703 GCAGCCTATC
9713 ACCTCATACTACCTAGT
1 ACCTCATACTACCTAGT
9730 ACCTCATACTACCTAG
1 ACCTCATACTACCTAG
9746 GTACTATGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.36, G:0.06, T:0.27
Consensus pattern (17 bp):
ACCTCATACTACCTAGT
Found at i:9919 original size:21 final size:21
Alignment explanation
Indices: 9893--9932 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
9883 CAGAAGAGTT
*
9893 CGCCTTCCTGAGCAAGTAAAA
1 CGCCTTCCTCAGCAAGTAAAA
9914 CGCCTTCCTCAGCAAGTAA
1 CGCCTTCCTCAGCAAGTAA
9933 TGCCCACCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.33, G:0.17, T:0.20
Consensus pattern (21 bp):
CGCCTTCCTCAGCAAGTAAAA
Found at i:10428 original size:18 final size:18
Alignment explanation
Indices: 10405--10440 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
10395 TCTCTTTGTC
10405 AATTTCAGCAAATTGACT
1 AATTTCAGCAAATTGACT
10423 AATTTCAGCAAATTGACT
1 AATTTCAGCAAATTGACT
10441 GGCACGCCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (18 bp):
AATTTCAGCAAATTGACT
Done.