Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013189.1 Corchorus capsularis cultivar CVL-1 contig13210, 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: 23848
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Found at i:2581 original size:30 final size:31
Alignment explanation
Indices: 2547--2608 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
2537 TAATTGATCA
2547 ACCCC-GAAAACGTTTGGCCCCAAATCGAGC
1 ACCCCGGAAAACGTTTGGCCCCAAATCGAGC
* *
2577 ACCCCGGCAAACGTTTGGCCCCAAATTGAGC
1 ACCCCGGAAAACGTTTGGCCCCAAATCGAGC
2608 A
1 A
2609 TTTAGCCGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 5 0.17
31 24 0.83
ACGTcount: A:0.29, C:0.35, G:0.21, T:0.15
Consensus pattern (31 bp):
ACCCCGGAAAACGTTTGGCCCCAAATCGAGC
Found at i:4755 original size:33 final size:33
Alignment explanation
Indices: 4713--4800 Score: 142
Period size: 33 Copynumber: 2.7 Consensus size: 33
4703 GCCGAGTCAT
4713 GTGGCCGGTTGTGGCCGGGCATGGTCATGTCGC
1 GTGGCCGGTTGTGGCCGGGCATGGTCATGTCGC
*
4746 GTGGTCGGTTGTGGCCGGGCATGGTCATGTCGC
1 GTGGCCGGTTGTGGCCGGGCATGGTCATGTCGC
*
4779 GTGACCGG-TGTTGGCCGGGCAT
1 GTGGCCGGTTG-TGGCCGGGCAT
4801 CTCCAAATCG
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
32 2 0.04
33 49 0.96
ACGTcount: A:0.07, C:0.23, G:0.45, T:0.25
Consensus pattern (33 bp):
GTGGCCGGTTGTGGCCGGGCATGGTCATGTCGC
Found at i:5363 original size:11 final size:10
Alignment explanation
Indices: 5345--5378 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
5335 GAAGTTCGTG
5345 TTTTGAAGAT
1 TTTTGAAGAT
5355 TTCTTGAAGAT
1 TT-TTGAAGAT
5366 ATTTTGAAGAT
1 -TTTTGAAGAT
5377 TT
1 TT
5379 GAAGACAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.29, C:0.03, G:0.18, T:0.50
Consensus pattern (10 bp):
TTTTGAAGAT
Found at i:7611 original size:21 final size:21
Alignment explanation
Indices: 7585--7635 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
7575 CCTTTGCTTA
*
7585 TGATCTTCAATGCTCTCCAAT
1 TGATCTTCAATGATCTCCAAT
*
7606 TGATCTTCAATGATCTTCAAT
1 TGATCTTCAATGATCTCCAAT
*
7627 GGA-CTTCAA
1 TGATCTTCAA
7636 GCCTTTAAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 6 0.22
21 21 0.78
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.37
Consensus pattern (21 bp):
TGATCTTCAATGATCTCCAAT
Found at i:7635 original size:10 final size:10
Alignment explanation
Indices: 7584--7627 Score: 61
Period size: 10 Copynumber: 4.3 Consensus size: 10
7574 TCCTTTGCTT
7584 ATGATCTTCA
1 ATGATCTTCA
* *
7594 ATGCTCTCCA
1 ATGATCTTCA
7604 ATTGATCTTCA
1 A-TGATCTTCA
7615 ATGATCTTCA
1 ATGATCTTCA
7625 ATG
1 ATG
7628 GACTTCAAGC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
10 21 0.72
11 8 0.28
ACGTcount: A:0.27, C:0.23, G:0.11, T:0.39
Consensus pattern (10 bp):
ATGATCTTCA
Found at i:9518 original size:17 final size:17
Alignment explanation
Indices: 9493--9527 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
9483 TGCATAATGT
9493 TAATATGCCAACAAGAA
1 TAATATGCCAACAAGAA
* *
9510 TAATGTGCCACCAAGAA
1 TAATATGCCAACAAGAA
9527 T
1 T
9528 GCACTTTTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.46, C:0.20, G:0.14, T:0.20
Consensus pattern (17 bp):
TAATATGCCAACAAGAA
Found at i:10370 original size:27 final size:27
Alignment explanation
Indices: 10332--10452 Score: 152
Period size: 27 Copynumber: 4.4 Consensus size: 27
10322 CGACCCGAGG
10332 CGAAGTGGGAGGATCCACTGCTGGGGT
1 CGAAGTGGGAGGATCCACTGCTGGGGT
* *
10359 CGAAGTGGGAGGAACCACTGCTTGGGT
1 CGAAGTGGGAGGATCCACTGCTGGGGT
* * * *
10386 TGCAGTGGGAGGATCCACTTCTAGGGT
1 CGAAGTGGGAGGATCCACTGCTGGGGT
* * *
10413 CGCAGTGGGAGGATCCACTTCTGAGGT
1 CGAAGTGGGAGGATCCACTGCTGGGGT
10440 CGAAGTGTGGAGG
1 CGAAGTG-GGAGG
10453 GCCGAAACAG
Statistics
Matches: 82, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
27 77 0.94
28 5 0.06
ACGTcount: A:0.20, C:0.18, G:0.41, T:0.21
Consensus pattern (27 bp):
CGAAGTGGGAGGATCCACTGCTGGGGT
Found at i:10507 original size:24 final size:24
Alignment explanation
Indices: 10475--10529 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
10465 ACATCCTCTC
10475 CATTTGCAGCCTCAATGGGGTCGT
1 CATTTGCAGCCTCAATGGGGTCGT
*
10499 CATTTGCAGCCTCAATTGGGTCGT
1 CATTTGCAGCCTCAATGGGGTCGT
10523 CATTTGC
1 CATTTGC
10530 TGCTAAATCC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.16, C:0.25, G:0.25, T:0.33
Consensus pattern (24 bp):
CATTTGCAGCCTCAATGGGGTCGT
Found at i:15107 original size:33 final size:33
Alignment explanation
Indices: 15060--15184 Score: 148
Period size: 33 Copynumber: 3.8 Consensus size: 33
15050 AGCTAAAGGA
* *
15060 TCATGTGGCCGGTTGTGGCTGGGCATGGCCGA-G
1 TCATGTGGCCGGTTGTGGCCGGGCATGG-CAATG
*
15093 TCATATGGCCGGTTGTGGCCGGGCATGGCAATG
1 TCATGTGGCCGGTTGTGGCCGGGCATGGCAATG
**
15126 TCGCGTGGCCGGTTGTGGCCGGGCATGGTC-ATG
1 TCATGTGGCCGGTTGTGGCCGGGCATGG-CAATG
*
15159 TCACGTGGCCGG-TGTTGGCCGGGCAT
1 TCATGTGGCCGGTTG-TGGCCGGGCAT
15185 CTCCAAGTCG
Statistics
Matches: 82, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
32 4 0.05
33 77 0.94
34 1 0.01
ACGTcount: A:0.10, C:0.23, G:0.43, T:0.24
Consensus pattern (33 bp):
TCATGTGGCCGGTTGTGGCCGGGCATGGCAATG
Found at i:19152 original size:9 final size:9
Alignment explanation
Indices: 19138--19172 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
19128 TTCTAGTCGA
19138 ATTTTTTTT
1 ATTTTTTTT
*
19147 ATTTTTTTG
1 ATTTTTTTT
19156 ATTTTTTTT
1 ATTTTTTTT
19165 ATATTTTT
1 AT-TTTTT
19173 CAATATAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 18 0.78
10 5 0.22
ACGTcount: A:0.14, C:0.00, G:0.03, T:0.83
Consensus pattern (9 bp):
ATTTTTTTT
Found at i:20175 original size:33 final size:33
Alignment explanation
Indices: 20148--20257 Score: 125
Period size: 33 Copynumber: 3.3 Consensus size: 33
20138 TGGCCGGTTG
* *
20148 TGGCCGGGCATGGCCGA-GTCATGTGGCCGGTTG
1 TGGCCGGGCATGGTC-ATGTCACGTGGCCGGTTG
* * * *
20181 TGGCCGAGCGTGGTCATGTCGCGTGGCTGGTTG
1 TGGCCGGGCATGGTCATGTCACGTGGCCGGTTG
*
20214 TGGCCGGGCATGGTCATGTCGCGTGGCCGG-TG
1 TGGCCGGGCATGGTCATGTCACGTGGCCGGTTG
20246 TTGGCCGGGCAT
1 -TGGCCGGGCAT
20258 CTCCAAGTTG
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
32 3 0.05
33 63 0.95
ACGTcount: A:0.07, C:0.24, G:0.45, T:0.24
Consensus pattern (33 bp):
TGGCCGGGCATGGTCATGTCACGTGGCCGGTTG
Done.