Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012656.1 Corchorus capsularis cultivar CVL-1 contig12677, 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: 16602
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--36 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
37 CAGGGCTTCA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2202 original size:32 final size:32
Alignment explanation
Indices: 2161--2252 Score: 148
Period size: 32 Copynumber: 2.9 Consensus size: 32
2151 GGACTATTCA
* *
2161 AAATCTCCATTAACACTAGAAATTGTCATGAT
1 AAATCTCCATTGACACCAGAAATTGTCATGAT
2193 AAATCTCCATTGACACCAGAAATTGTCATGAT
1 AAATCTCCATTGACACCAGAAATTGTCATGAT
* *
2225 AAATCTCCACTGACACCAGAAGTTGTCA
1 AAATCTCCATTGACACCAGAAATTGTCA
2253 GTGGTCTTAC
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 56 1.00
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.27
Consensus pattern (32 bp):
AAATCTCCATTGACACCAGAAATTGTCATGAT
Found at i:2273 original size:31 final size:30
Alignment explanation
Indices: 2235--2743 Score: 599
Period size: 31 Copynumber: 16.6 Consensus size: 30
2225 AAATCTCCAC
*
2235 TGACACCAGAAGTTGTCAGTGGTCTTACAAT
1 TGACACCAGAAGTTGTCA-TGATCTTACAAT
2266 TGACACCAGAAGTTGTCTATGATCTTACAAT
1 TGACACCAGAAGTTGTC-ATGATCTTACAAT
*
2297 TGACACCAGAAGTTGTCAATGATCTTACAAA
1 TGACACCAGAAGTTGTC-ATGATCTTACAAT
* *
2328 TGACACCAGAAGTTGTCATGGTCTTACAAA
1 TGACACCAGAAGTTGTCATGATCTTACAAT
*
2358 TGACACCAGAAGTTGTCAATGATCTTACAAA
1 TGACACCAGAAGTTGTC-ATGATCTTACAAT
*
2389 TGACACCAGAAGTTGTCAATGATCTTACAAA
1 TGACACCAGAAGTTGTC-ATGATCTTACAAT
* * *
2420 TGACACCAAAAGTTGTCAATGGTCTTACAAA
1 TGACACCAGAAGTTGTC-ATGATCTTACAAT
*
2451 TGACACCAGAAGTTGTCATGATCTTACAAA
1 TGACACCAGAAGTTGTCATGATCTTACAAT
* *
2481 TGACACCAGAAGTTGTCATGGTCTTACAAA
1 TGACACCAGAAGTTGTCATGATCTTACAAT
*
2511 TAACACC-GAAAGTTGTCATGATCTTACAAT
1 TGACACCAG-AAGTTGTCATGATCTTACAAT
* * * *
2541 TGACACAAGAAGTTGTCATTGGTTTTAAAAT
1 TGACACCAGAAGTTGTCA-TGATCTTACAAT
* * * *
2572 TGATACCAGAAATTGTCATGATTTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTACAAT
*
2602 TGACACCAGAAGTTGTCATGA-CTTTGCAAT
1 TGACACCAGAAGTTGTCATGATC-TTACAAT
* * *
2632 TGACACTAGAAGTTGTCATGATTTTTGCAAT
1 TGACACCAGAAGTTGTCATGA-TCTTACAAT
* *
2663 TGACACCAGAAGTTGTCATGATTTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTACAAT
** * *
2693 TGACACTTGAAGATGTCATGATTTTATTCAAT
1 TGACACCAGAAGTTGTCATGATCTTA--CAAT
* *
2725 TGACCCCATAAGTTGTCAT
1 TGACACCAGAAGTTGTCAT
2744 ATACACCATG
Statistics
Matches: 429, Mismatches: 39, Indels: 19
0.88 0.08 0.04
Matches are distributed among these distances:
29 1 0.00
30 195 0.45
31 214 0.50
32 19 0.04
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Consensus pattern (30 bp):
TGACACCAGAAGTTGTCATGATCTTACAAT
Found at i:2376 original size:61 final size:61
Alignment explanation
Indices: 2235--2742 Score: 605
Period size: 61 Copynumber: 8.3 Consensus size: 61
2225 AAATCTCCAC
* * *
2235 TGACACCAGAAGTTGTCAGTGGTCTTACAATTGACACCAGAAGTTGTCTATGATCTTACAAT
1 TGACACCAGAAGTTGTCAATGATCTTACAAATGACACCAGAAGTTGTC-ATGATCTTACAAT
* *
2297 TGACACCAGAAGTTGTCAATGATCTTACAAATGACACCAGAAGTTGTCATGGTCTTACAAA
1 TGACACCAGAAGTTGTCAATGATCTTACAAATGACACCAGAAGTTGTCATGATCTTACAAT
*
2358 TGACACCAGAAGTTGTCAATGATCTTACAAATGACACCAGAAGTTGTCAATGATCTTACAAA
1 TGACACCAGAAGTTGTCAATGATCTTACAAATGACACCAGAAGTTGTC-ATGATCTTACAAT
* * *
2420 TGACACCAAAAGTTGTCAATGGTCTTACAAATGACACCAGAAGTTGTCATGATCTTACAAA
1 TGACACCAGAAGTTGTCAATGATCTTACAAATGACACCAGAAGTTGTCATGATCTTACAAT
* *
2481 TGACACCAGAAGTTGTC-ATGGTCTTACAAATAACACC-GAAAGTTGTCATGATCTTACAAT
1 TGACACCAGAAGTTGTCAATGATCTTACAAATGACACCAG-AAGTTGTCATGATCTTACAAT
* * * * * * * *
2541 TGACACAAGAAGTTGTCATTGGTTTTA-AAATTGATACCAGAAATTGTCATGATTTTGCAAT
1 TGACACCAGAAGTTGTCAATGATCTTACAAA-TGACACCAGAAGTTGTCATGATCTTACAAT
* * * * *
2602 TGACACCAGAAGTTGTC-ATGA-CTTTGCAATTGACACTAGAAGTTGTCATGATTTTTGCAAT
1 TGACACCAGAAGTTGTCAATGATC-TTACAAATGACACCAGAAGTTGTCATGA-TCTTACAAT
* * * ** * *
2663 TGACACCAGAAGTTGTC-ATGATTTTGCAATTGACACTTGAAGATGTCATGATTTTATTCAAT
1 TGACACCAGAAGTTGTCAATGATCTTACAAATGACACCAGAAGTTGTCATGATCTTA--CAAT
* *
2725 TGACCCCATAAGTTGTCA
1 TGACACCAGAAGTTGTCA
2743 TATACACCAT
Statistics
Matches: 400, Mismatches: 34, Indels: 23
0.88 0.07 0.05
Matches are distributed among these distances:
59 1 0.00
60 84 0.21
61 192 0.48
62 123 0.31
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Consensus pattern (61 bp):
TGACACCAGAAGTTGTCAATGATCTTACAAATGACACCAGAAGTTGTCATGATCTTACAAT
Found at i:13500 original size:13 final size:13
Alignment explanation
Indices: 13482--13508 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
13472 AAAAGGAGAG
13482 AAAGAAGAAAGAA
1 AAAGAAGAAAGAA
13495 AAAGAAGAAAGAA
1 AAAGAAGAAAGAA
13508 A
1 A
13509 TGTCGAGGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (13 bp):
AAAGAAGAAAGAA
Found at i:13595 original size:2 final size:2
Alignment explanation
Indices: 13588--13634 Score: 55
Period size: 2 Copynumber: 25.0 Consensus size: 2
13578 TTATTAATAG
* *
13588 TA TA TA TA TA TA TA -A AA TA TT TA T- TA -A TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13627 TA TA TA TA
1 TA TA TA TA
13635 GTCGGTCGGT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
1 3 0.08
2 36 0.92
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:14811 original size:37 final size:38
Alignment explanation
Indices: 14741--14837 Score: 117
Period size: 38 Copynumber: 2.6 Consensus size: 38
14731 AATTTGATTT
* *
14741 TTTGTTTCCAACGTCCTATTTAATTTTGTC-TTTTGTC
1 TTTGTTTCCAACGTCCGATTTAATTTTGACTTTTTGTC
**
14778 TTTGTTTCCAATCGTTGGATTTAATTTT-ACTTTTTGTC
1 TTTGTTTCCAA-CGTCCGATTTAATTTTGACTTTTTGTC
* *
14816 TTTGTCTCCAACGTCCTATTTA
1 TTTGTTTCCAACGTCCGATTTA
14838 GAATTAGATA
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
37 20 0.40
38 30 0.60
ACGTcount: A:0.15, C:0.19, G:0.11, T:0.55
Consensus pattern (38 bp):
TTTGTTTCCAACGTCCGATTTAATTTTGACTTTTTGTC
Found at i:15779 original size:27 final size:27
Alignment explanation
Indices: 15749--15802 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
15739 ACGGGATTGT
15749 CTGGTATCAGAGCCAGGGAGGAGCAGG
1 CTGGTATCAGAGCCAGGGAGGAGCAGG
15776 CTGGTATCAGAGCCAGGGAGGAGCAGG
1 CTGGTATCAGAGCCAGGGAGGAGCAGG
15803 TAATTCTAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.26, C:0.19, G:0.44, T:0.11
Consensus pattern (27 bp):
CTGGTATCAGAGCCAGGGAGGAGCAGG
Done.