Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013879.1 Corchorus capsularis cultivar CVL-1 contig13900, 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: 23323
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Found at i:5591 original size:32 final size:31
Alignment explanation
Indices: 5550--5611 Score: 97
Period size: 32 Copynumber: 2.0 Consensus size: 31
5540 ATATATTAAT
*
5550 AATCAAAATGAGTTTTTACAACCATAGCATAC
1 AATCAAAATGAGTTTTTAC-ACCATACCATAC
*
5582 AATCAAAATGGGTTTTTACACCATACCATA
1 AATCAAAATGAGTTTTTACACCATACCATA
5612 TAACTAGTGC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
31 10 0.36
32 18 0.64
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.29
Consensus pattern (31 bp):
AATCAAAATGAGTTTTTACACCATACCATAC
Found at i:5795 original size:2 final size:2
Alignment explanation
Indices: 5788--5813 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5778 CATAAAGCAT
5788 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
5814 GTAATCTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6570 original size:2 final size:2
Alignment explanation
Indices: 6563--6596 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
6553 GTACCATTGC
6563 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
6597 AGGAAAAGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:7701 original size:24 final size:24
Alignment explanation
Indices: 7639--7692 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
7629 GATGTTCTTC
* *
7639 TGGCCTTGAGGGTGGGACTGCAGT
1 TGGCCTTGACGGTGGGACTGCAGG
7663 TGGCCTTGACGGTGGGACTGCAGG
1 TGGCCTTGACGGTGGGACTGCAGG
7687 TGGCCT
1 TGGCCT
7693 CCTAGGTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.11, C:0.20, G:0.44, T:0.24
Consensus pattern (24 bp):
TGGCCTTGACGGTGGGACTGCAGG
Found at i:8414 original size:15 final size:15
Alignment explanation
Indices: 8394--8424 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
8384 TACATGGACA
8394 AAACAAAGTTTATAC
1 AAACAAAGTTTATAC
8409 AAACAAAGTTTATAC
1 AAACAAAGTTTATAC
8424 A
1 A
8425 TGGACATATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.55, C:0.13, G:0.06, T:0.26
Consensus pattern (15 bp):
AAACAAAGTTTATAC
Found at i:8501 original size:19 final size:19
Alignment explanation
Indices: 8477--8513 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
8467 TATTAAGTAA
*
8477 AAATCTCCACTAGCATAAT
1 AAATCTCCAATAGCATAAT
8496 AAATCTCCAATAGCATAA
1 AAATCTCCAATAGCATAA
8514 ATTATTAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.46, C:0.24, G:0.05, T:0.24
Consensus pattern (19 bp):
AAATCTCCAATAGCATAAT
Found at i:10294 original size:105 final size:105
Alignment explanation
Indices: 10058--10294 Score: 318
Period size: 105 Copynumber: 2.3 Consensus size: 105
10048 TTGTCAGAAA
* * **
10058 AGTATTAGTCGATGAAAACTTC-AGTATTAGTTCCAGTATTAATCGACTAAAACTCCAAGTCTTC
1 AGTATTAATCGATGAAAAC-TCAAGTTTTAGTTTTAGTATTAATCGACTAAAACTCCAAGTCTTC
*
10122 TCTTTAAAAAATGTGGCAGTGTTGACAGCGAACCTGAAGCC
65 TCTTTAAAAAATGTGGCAGTGTTGACAGCGAACCCGAAGCC
*
10163 AGTATTAATCGATGAAAACTCCAGTTTTAGTTTTAGTATTAATCGACTAAAACTCCAAGTCTT-T
1 AGTATTAATCGATGAAAACTCAAGTTTTAGTTTTAGTATTAATCGACTAAAACTCCAAGTCTTCT
* * *
10227 ACTTTGAAAAA-GTGGCAGTGTTGACAGCGAACCCGGAGCT
66 -CTTTAAAAAATGTGGCAGTGTTGACAGCGAACCCGAAGCC
* * *
10267 AGTATTAATTGATGGAATACTTAAGTTT
1 AGTATTAATCGAT-GAAAACTCAAGTTT
10295 CATGTTTCAA
Statistics
Matches: 117, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
104 41 0.35
105 76 0.65
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (105 bp):
AGTATTAATCGATGAAAACTCAAGTTTTAGTTTTAGTATTAATCGACTAAAACTCCAAGTCTTCT
CTTTAAAAAATGTGGCAGTGTTGACAGCGAACCCGAAGCC
Found at i:15607 original size:105 final size:105
Alignment explanation
Indices: 15371--15607 Score: 318
Period size: 105 Copynumber: 2.3 Consensus size: 105
15361 TTGTCAGAAA
* * **
15371 AGTATTAGTCGATGAAAACTTC-AGTATTAGTTCCAGTATTAATCGACTAAAACTCCAAGTCTTC
1 AGTATTAATCGATGAAAAC-TCAAGTTTTAGTTTTAGTATTAATCGACTAAAACTCCAAGTCTTC
15435 TCTTTAAAAAATATGGCAGTGTTGACAGCGAACCCGAAGCC
65 TCTTTAAAAAATATGGCAGTGTTGACAGCGAACCCGAAGCC
*
15476 AGTATTAATCGATGAAAACTCCAGTTTTAGTTTTAGTATTAATCGACTAAAACTCCAAGTCTT-T
1 AGTATTAATCGATGAAAACTCAAGTTTTAGTTTTAGTATTAATCGACTAAAACTCCAAGTCTTCT
* * * *
15540 ACTTTGAAAAA-GTGGCAGTGTTGACAGCGAACCCGGAGCT
66 -CTTTAAAAAATATGGCAGTGTTGACAGCGAACCCGAAGCC
* * *
15580 AGTATTAATTGATGGAATACTTAAGTTT
1 AGTATTAATCGAT-GAAAACTCAAGTTT
15608 CATGTTTCAA
Statistics
Matches: 117, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
104 41 0.35
105 76 0.65
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (105 bp):
AGTATTAATCGATGAAAACTCAAGTTTTAGTTTTAGTATTAATCGACTAAAACTCCAAGTCTTCT
CTTTAAAAAATATGGCAGTGTTGACAGCGAACCCGAAGCC
Found at i:22747 original size:13 final size:13
Alignment explanation
Indices: 22729--22754 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
22719 ATTCATTTTA
22729 TTTTTAGGTTATT
1 TTTTTAGGTTATT
22742 TTTTTAGGTTATT
1 TTTTTAGGTTATT
22755 GTTAGTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.15, T:0.69
Consensus pattern (13 bp):
TTTTTAGGTTATT
Done.