Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013089.1 Corchorus olitorius cultivar O-4 contig13122, 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: 8016
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Found at i:562 original size:25 final size:25
Alignment explanation
Indices: 532--579 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
522 ATGCAATGTC
*
532 AAATTAGATTTGAGTTACATGAATG
1 AAATTAGATTTGAGCTACATGAATG
*
557 AAATTAGCTTTGAGCTACATGAA
1 AAATTAGATTTGAGCTACATGAA
580 CGCAAAATAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.40, C:0.08, G:0.19, T:0.33
Consensus pattern (25 bp):
AAATTAGATTTGAGCTACATGAATG
Found at i:1191 original size:50 final size:50
Alignment explanation
Indices: 1127--1551 Score: 724
Period size: 50 Copynumber: 8.5 Consensus size: 50
1117 GAGAGATCCT
1127 CGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAA
1 CGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAA
* *
1177 CGAGCTTGGCTTGTGGAAAAGCCCATGTTGATAATTGACTCGTATGGAAA
1 CGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAA
* * *
1227 TGAGTTTGGCTTGTGGAAAACCCTATGTTGATAATTGACTCGAATGGAAA
1 CGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAA
* *
1277 CGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCATATGGAGA
1 CGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAA
* * *
1327 CGAGTTTGGCTTATGGAAAAGCCTGTGTTGATAATTTACTCGTATGGAAA
1 CGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAA
1377 CGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAA
1 CGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAA
*
1427 CGAGTTTGGCTTATGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAA
1 CGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAA
*
1477 CGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTAGGGAAA
1 CGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAA
*
1527 CGAGTTTGGGCTTATGGAAAAGCCT
1 CGAGTTT-GGCTTGTGGAAAAGCCT
1552 GTTGCTTCGA
Statistics
Matches: 350, Mismatches: 24, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
50 334 0.95
51 16 0.05
ACGTcount: A:0.28, C:0.13, G:0.28, T:0.31
Consensus pattern (50 bp):
CGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAA
Found at i:2026 original size:50 final size:50
Alignment explanation
Indices: 1946--2132 Score: 266
Period size: 50 Copynumber: 3.7 Consensus size: 50
1936 AAAATCGACC
* * * *
1946 TTTGGTCTTGGTCTCACAAATGGAGTGCAATCTTATTTTGAAAGGCGAAT
1 TTTGATCTTGGGCTCACAAATGGAATGCAATCTTATTTTGAAAAGCGAAT
**
1996 TTTGATCTTGGGCTCACAAATGGAATGCAATCTCGTTTTGAAAAGCGAAT
1 TTTGATCTTGGGCTCACAAATGGAATGCAATCTTATTTTGAAAAGCGAAT
** * * * *
2046 TTTGATCTTGAACTCACAAATGGAAAGCAATTTTACTTTGAAAAGCAAAT
1 TTTGATCTTGGGCTCACAAATGGAATGCAATCTTATTTTGAAAAGCGAAT
2096 TTTGATCTTGGGCTCACAAATGGAATGCAATCTTATT
1 TTTGATCTTGGGCTCACAAATGGAATGCAATCTTATT
2133 GTAAATATTC
Statistics
Matches: 118, Mismatches: 19, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 118 1.00
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (50 bp):
TTTGATCTTGGGCTCACAAATGGAATGCAATCTTATTTTGAAAAGCGAAT
Found at i:2720 original size:6 final size:6
Alignment explanation
Indices: 2709--2747 Score: 53
Period size: 6 Copynumber: 6.3 Consensus size: 6
2699 ATCCATTCTC
2709 TTTTGA TTTTGA TTTTTGA TTTTTGA TTTTGA -TTTGA TT
1 TTTTGA TTTTGA -TTTTGA -TTTTGA TTTTGA TTTTGA TT
2748 GATTTTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
5 5 0.16
6 13 0.42
7 13 0.42
ACGTcount: A:0.15, C:0.00, G:0.15, T:0.69
Consensus pattern (6 bp):
TTTTGA
Found at i:2734 original size:20 final size:21
Alignment explanation
Indices: 2709--2786 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 21
2699 ATCCATTCTC
2709 TTTTGATTTTGATTT-TTGAT
1 TTTTGATTTTGATTTATTGAT
2729 TTTTGATTTTGATTTGATTGAT
1 TTTTGATTTTGATTT-ATTGAT
**
2751 TTTTTTTTATTGACTTTGATTTGATT
1 TTTTGATT-TTGA-TTT-A-TTGA-T
2777 TTTTGATTTT
1 TTTTGATTTT
2787 TTTTTGAATT
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
20 15 0.31
22 11 0.23
23 4 0.08
24 5 0.10
25 6 0.12
26 7 0.15
ACGTcount: A:0.15, C:0.01, G:0.14, T:0.69
Consensus pattern (21 bp):
TTTTGATTTTGATTTATTGAT
Found at i:2754 original size:29 final size:29
Alignment explanation
Indices: 2717--2787 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 29
2707 TCTTTTGATT
*
2717 TTGATTTTTGATTTTTGATTTTGATTTGA
1 TTGATTTTTGATTTTTGACTTTGATTTGA
*
2746 TTGATTTTT-TTTTATTGACTTTGATTTGA
1 TTGATTTTTGATTT-TTGACTTTGATTTGA
2775 -T--TTTTTGATTTTT
1 TTGATTTTTGATTTTT
2788 TTTTGAATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
26 7 0.19
27 3 0.08
28 4 0.11
29 23 0.62
ACGTcount: A:0.15, C:0.01, G:0.14, T:0.69
Consensus pattern (29 bp):
TTGATTTTTGATTTTTGACTTTGATTTGA
Found at i:2783 original size:13 final size:11
Alignment explanation
Indices: 2765--2805 Score: 55
Period size: 12 Copynumber: 3.5 Consensus size: 11
2755 TTTTATTGAC
2765 TTTGATTTGATTT
1 TTTGATTT--TTT
2778 TTTGATTTTTT
1 TTTGATTTTTT
2789 TTTGAATTTTTT
1 TTTG-ATTTTTT
2801 TTTGA
1 TTTGA
2806 ATATCTTGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 8 0.30
12 11 0.41
13 8 0.30
ACGTcount: A:0.15, C:0.00, G:0.12, T:0.73
Consensus pattern (11 bp):
TTTGATTTTTT
Found at i:2789 original size:9 final size:8
Alignment explanation
Indices: 2715--2788 Score: 52
Period size: 8 Copynumber: 9.5 Consensus size: 8
2705 TCTCTTTTGA
2715 TTTTGA-T
1 TTTTGATT
2722 TTTTGA-T
1 TTTTGATT
2729 TTTTGA--
1 TTTTGATT
2735 TTTTGATT
1 TTTTGATT
*
2743 TGATTGATT
1 T-TTTGATT
2752 TTTT--TT
1 TTTTGATT
*
2758 TATTGACTT
1 TTTTGA-TT
2767 TGATTTGATT
1 T--TTTGATT
2777 TTTTGATT
1 TTTTGATT
2785 TTTT
1 TTTT
2789 TTTGAATTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 15
0.74 0.05 0.20
Matches are distributed among these distances:
6 11 0.20
7 13 0.24
8 14 0.25
9 10 0.18
10 3 0.05
11 4 0.07
ACGTcount: A:0.15, C:0.01, G:0.14, T:0.70
Consensus pattern (8 bp):
TTTTGATT
Found at i:2797 original size:12 final size:12
Alignment explanation
Indices: 2775--2807 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
2765 TTTGATTTGA
2775 TTTTTTG-ATTT
1 TTTTTTGAATTT
2786 TTTTTTGAATTT
1 TTTTTTGAATTT
2798 TTTTTTGAAT
1 TTTTTTGAAT
2808 ATCTTGATGG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 7 0.33
12 14 0.67
ACGTcount: A:0.15, C:0.00, G:0.09, T:0.76
Consensus pattern (12 bp):
TTTTTTGAATTT
Done.