Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013628.1 Corchorus olitorius cultivar O-4 contig13661, 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: 6110
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
Found at i:2597 original size:29 final size:27
Alignment explanation
Indices: 2565--2643 Score: 99
Period size: 29 Copynumber: 2.9 Consensus size: 27
2555 AAAGAAAAAT
*
2565 ATTTTTTTTCTAAAAACGCAGGAACAAGA
1 ATTTTTTTTCTAAAAACGCA-AAACAA-A
2594 ATTTTTTTT-TAGAAAACGCAAAACAAA
1 ATTTTTTTTCTA-AAAACGCAAAACAAA
*
2621 TTTTTTTTTC-AAAAACGCAAAAC
1 ATTTTTTTTCTAAAAACGCAAAAC
2644 TAATAAATTA
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
26 12 0.26
27 10 0.22
28 7 0.15
29 17 0.37
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (27 bp):
ATTTTTTTTCTAAAAACGCAAAACAAA
Found at i:2622 original size:26 final size:27
Alignment explanation
Indices: 2565--2643 Score: 99
Period size: 26 Copynumber: 2.9 Consensus size: 27
2555 AAAGAAAAAT
*
2565 ATTTTTTTTCTAAAAACGCAGGAACAAGA
1 ATTTTTTTT-TAAAAACGCA-AAACAAGA
2594 ATTTTTTTTTAGAAAACGCAAAAC-A-A
1 ATTTTTTTTTA-AAAACGCAAAACAAGA
2620 ATTTTTTTTTCAAAAACGCAAAAC
1 ATTTTTTTTT-AAAAACGCAAAAC
2644 TAATAAATTA
Statistics
Matches: 47, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
26 23 0.49
27 2 0.04
28 5 0.11
29 17 0.36
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (27 bp):
ATTTTTTTTTAAAAACGCAAAACAAGA
Found at i:2686 original size:28 final size:25
Alignment explanation
Indices: 2653--2706 Score: 81
Period size: 25 Copynumber: 2.0 Consensus size: 25
2643 CTAATAAATT
2653 AAAAACGCAAGAAAACTTTTTTTTTATG
1 AAAAACGC-A-AAAAC-TTTTTTTTATG
2681 AAAAACGCAAAAACTTTTTTTTATG
1 AAAAACGCAAAAACTTTTTTTTATG
2706 A
1 A
2707 CGCAGAAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
25 12 0.46
26 5 0.19
27 1 0.04
28 8 0.31
ACGTcount: A:0.44, C:0.11, G:0.09, T:0.35
Consensus pattern (25 bp):
AAAAACGCAAAAACTTTTTTTTATG
Found at i:2745 original size:22 final size:21
Alignment explanation
Indices: 2685--2758 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 21
2675 TTTATGAAAA
*
2685 ACGCAAAAACTTTTTTTTATG
1 ACGCAAAAAATTTTTTTTATG
**
2706 ACGCAGAAACAAAATTTTTTATG
1 ACGCA-AAA-AATTTTTTTTATG
2729 ACGCAAAAATATTTTTTTT-TCG
1 ACGCAAAAA-ATTTTTTTTAT-G
2751 ACGCAAAA
1 ACGCAAAA
2759 CACAAAACAA
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
21 7 0.16
22 22 0.50
23 15 0.34
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.35
Consensus pattern (21 bp):
ACGCAAAAAATTTTTTTTATG
Found at i:2746 original size:23 final size:23
Alignment explanation
Indices: 2685--2763 Score: 76
Period size: 23 Copynumber: 3.5 Consensus size: 23
2675 TTTATGAAAA
2685 ACGCAAAAAC--TTTTTTTTATG
1 ACGCAAAAACAATTTTTTTTATG
* **
2706 ACGCAGAAACAAAATTTTTTATG
1 ACGCAAAAACAATTTTTTTTATG
*
2729 ACGCAAAAA-TATTTTTTTT-TCG
1 ACGCAAAAACAATTTTTTTTAT-G
2751 ACGCAAAACACAA
1 ACGCAAAA-ACAA
2764 AACAAGTTTT
Statistics
Matches: 45, Mismatches: 8, Indels: 7
0.75 0.13 0.12
Matches are distributed among these distances:
21 10 0.22
22 16 0.36
23 18 0.40
24 1 0.02
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.33
Consensus pattern (23 bp):
ACGCAAAAACAATTTTTTTTATG
Found at i:3148 original size:16 final size:15
Alignment explanation
Indices: 3111--3151 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
3101 CAGAGATTGG
*
3111 CAGAAAGCAATTAAA
1 CAGAAAACAATTAAA
3126 CAGAAAACAATTAAA
1 CAGAAAACAATTAAA
3141 CTAGAAAACAA
1 C-AGAAAACAA
3152 AGCAAAGTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 15 0.62
16 9 0.38
ACGTcount: A:0.63, C:0.15, G:0.10, T:0.12
Consensus pattern (15 bp):
CAGAAAACAATTAAA
Found at i:3928 original size:11 final size:11
Alignment explanation
Indices: 3912--3937 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3902 CCTTTGCCTA
3912 AAAACTAGAAG
1 AAAACTAGAAG
3923 AAAACTAGAAG
1 AAAACTAGAAG
3934 AAAA
1 AAAA
3938 GAAATTATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08
Consensus pattern (11 bp):
AAAACTAGAAG
Found at i:5702 original size:19 final size:18
Alignment explanation
Indices: 5669--5704 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
5659 TTGAAATTAT
5669 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
5687 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
5705 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Done.