Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015374.1 Corchorus olitorius cultivar O-4 contig15407, 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: 27029
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:6491 original size:29 final size:29
Alignment explanation
Indices: 6457--6522 Score: 89
Period size: 28 Copynumber: 2.3 Consensus size: 29
6447 AGAAAATACT
** *
6457 TAAATAAGGGTTCGATTTTTTAATTTGGC
1 TAAATAAGGGCCCGATCTTTTAATTTGGC
6486 TAAAT-AGGGCCCGATCTTTTAATTTGGC
1 TAAATAAGGGCCCGATCTTTTAATTTGGC
*
6514 CAAATAAGG
1 TAAATAAGG
6523 ATCTAACGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 24 0.75
29 8 0.25
ACGTcount: A:0.30, C:0.12, G:0.21, T:0.36
Consensus pattern (29 bp):
TAAATAAGGGCCCGATCTTTTAATTTGGC
Found at i:7659 original size:18 final size:20
Alignment explanation
Indices: 7638--7678 Score: 68
Period size: 18 Copynumber: 2.1 Consensus size: 20
7628 TACTATTAAA
7638 TAAATAATAAAT-ATAT-TT
1 TAAATAATAAATAATATATT
7656 TAAATAATAAATAATATATT
1 TAAATAATAAATAATATATT
7676 TAA
1 TAA
7679 TTACTAAACG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 12 0.57
19 4 0.19
20 5 0.24
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TAAATAATAAATAATATATT
Found at i:7664 original size:21 final size:22
Alignment explanation
Indices: 7633--7676 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 22
7623 ATATATACTA
7633 TTAAATAAAT-AATAAATATATT
1 TTAAATAAATAAAT-AATATATT
7655 TTAAAT-AATAAATAATATATT
1 TTAAATAAATAAATAATATATT
7676 T
1 T
7677 AATTACTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TTAAATAAATAAATAATATATT
Found at i:7686 original size:20 final size:21
Alignment explanation
Indices: 7633--7676 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 21
7623 ATATATACTA
7633 TTAAATAA-ATAATAAATATATT
1 TTAAATAATA-AAT-AATATATT
7655 TTAAATAATAAATAATATATT
1 TTAAATAATAAATAATATATT
7676 T
1 T
7677 AATTACTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 9 0.43
22 11 0.52
23 1 0.05
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TTAAATAATAAATAATATATT
Found at i:10636 original size:14 final size:14
Alignment explanation
Indices: 10617--10644 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
10607 CTTCCCATGT
10617 CCAAAAAAAAAAAA
1 CCAAAAAAAAAAAA
10631 CCAAAAAAAAAAAA
1 CCAAAAAAAAAAAA
10645 AACTTTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (14 bp):
CCAAAAAAAAAAAA
Found at i:15525 original size:28 final size:30
Alignment explanation
Indices: 15463--15526 Score: 78
Period size: 28 Copynumber: 2.2 Consensus size: 30
15453 GGGTAAAATA
*
15463 TCCAAAATTGAAAGTTCAAAAGGCAAAATG
1 TCCAAAATTGAAAGTTCAAAAGGCAAAACG
* **
15493 GCCAAAATT-AAAGTTC-AGGGGCAAAACG
1 TCCAAAATTGAAAGTTCAAAAGGCAAAACG
15521 TCCAAA
1 TCCAAA
15527 CCCTACAAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
28 14 0.48
29 7 0.24
30 8 0.28
ACGTcount: A:0.47, C:0.17, G:0.19, T:0.17
Consensus pattern (30 bp):
TCCAAAATTGAAAGTTCAAAAGGCAAAACG
Found at i:16345 original size:40 final size:40
Alignment explanation
Indices: 16290--16367 Score: 147
Period size: 40 Copynumber: 1.9 Consensus size: 40
16280 TTTTCCCCCC
*
16290 TGAACTTTTAATTTGAAACTTTCAGCCCTTAAACTATCCT
1 TGAACTTTTAATTTGAAACTTTCACCCCTTAAACTATCCT
16330 TGAACTTTTAATTTGAAACTTTCACCCCTTAAACTATC
1 TGAACTTTTAATTTGAAACTTTCACCCCTTAAACTATC
16368 AAAATCGAGA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.31, C:0.23, G:0.06, T:0.40
Consensus pattern (40 bp):
TGAACTTTTAATTTGAAACTTTCACCCCTTAAACTATCCT
Found at i:16546 original size:49 final size:49
Alignment explanation
Indices: 16490--16585 Score: 183
Period size: 49 Copynumber: 2.0 Consensus size: 49
16480 TCAAATTAAA
*
16490 AATTCAAGAGGGAAAATGTTCATATTGTGAAAGTTTGGGGGGGGGGGGG
1 AATTCAAGAGGGAAAATGTTCATATTGTGAAAGTTTAGGGGGGGGGGGG
16539 AATTCAAGAGGGAAAATGTTCATATTGTGAAAGTTTAGGGGGGGGGG
1 AATTCAAGAGGGAAAATGTTCATATTGTGAAAGTTTAGGGGGGGGGG
16586 TAATGATCAT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.30, C:0.04, G:0.41, T:0.25
Consensus pattern (49 bp):
AATTCAAGAGGGAAAATGTTCATATTGTGAAAGTTTAGGGGGGGGGGGG
Done.