Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011330.1 Corchorus capsularis cultivar CVL-1 contig11351, 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: 19605
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:2752 original size:26 final size:25
Alignment explanation
Indices: 2723--2776 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 25
2713 TTTTAATATA
2723 TTTCTTAAATTTCATCATCTAAACGT
1 TTTCTTAAATTTCATCATCTAAAC-T
2749 TTTCTTAAATTTCATCATCTAAACT
1 TTTCTTAAATTTCATCATCTAAACT
2774 TTT
1 TTT
2777 ACAGTTTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 4 0.14
26 24 0.86
ACGTcount: A:0.30, C:0.19, G:0.02, T:0.50
Consensus pattern (25 bp):
TTTCTTAAATTTCATCATCTAAACT
Found at i:3623 original size:11 final size:11
Alignment explanation
Indices: 3609--3646 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
3599 ATCCATAACA
3609 AATTTATAATT
1 AATTTATAATT
3620 AATTTATAATT
1 AATTTATAATT
3631 -ATTTGATAATT
1 AATTT-ATAATT
*
3642 TATTT
1 AATTT
3647 TATATATAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:5774 original size:8 final size:8
Alignment explanation
Indices: 5750--5802 Score: 53
Period size: 8 Copynumber: 7.1 Consensus size: 8
5740 GTACTTTTTA
5750 ATAG-TAT
1 ATAGATAT
5757 ATA-A-AT
1 ATAGATAT
*
5763 ATAGATAG
1 ATAGATAT
5771 ATAG--AT
1 ATAGATAT
5777 ATAGATATT
1 ATAGATA-T
5786 ATAGATAT
1 ATAGATAT
5794 ATAGATAT
1 ATAGATAT
5802 A
1 A
5803 AAATTAAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
6 10 0.26
7 4 0.11
8 16 0.42
9 8 0.21
ACGTcount: A:0.51, C:0.00, G:0.13, T:0.36
Consensus pattern (8 bp):
ATAGATAT
Found at i:5802 original size:14 final size:14
Alignment explanation
Indices: 5750--5794 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
5740 GTACTTTTTA
*
5750 ATAG-TATATAAAT
1 ATAGATATATAGAT
*
5763 ATAGATAGATAGAT
1 ATAGATATATAGAT
5777 ATAGATATTATAGAT
1 ATAGATA-TATAGAT
5792 ATA
1 ATA
5795 TAGATATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 4 0.15
14 14 0.52
15 9 0.33
ACGTcount: A:0.51, C:0.00, G:0.13, T:0.36
Consensus pattern (14 bp):
ATAGATATATAGAT
Found at i:7268 original size:11 final size:9
Alignment explanation
Indices: 7243--7267 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
7233 GTTAAAAATA
7243 ATATATAGT
1 ATATATAGT
7252 ATATATAGT
1 ATATATAGT
7261 ATATATA
1 ATATATA
7268 TGGGTTAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (9 bp):
ATATATAGT
Found at i:7661 original size:9 final size:9
Alignment explanation
Indices: 7637--7674 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
7627 AAAAACCTTT
7637 AAAGAAGAA
1 AAAGAAGAA
7646 AAA-AAGAA
1 AAAGAAGAA
7654 AAAGAAGAA
1 AAAGAAGAA
*
7663 GAAGAAGAA
1 AAAGAAGAA
7672 AAA
1 AAA
7675 AAAGGAAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
8 8 0.31
9 18 0.69
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (9 bp):
AAAGAAGAA
Found at i:10430 original size:16 final size:16
Alignment explanation
Indices: 10404--10515 Score: 154
Period size: 16 Copynumber: 6.9 Consensus size: 16
10394 TTGGTGACCT
10404 CACCAGGTGAGTATTG
1 CACCAGGTGAGTATTG
* **
10420 TACTGGGTGAGTATCT-
1 CACCAGGTGAGTAT-TG
*
10436 CACCATGTGAGTATTG
1 CACCAGGTGAGTATTG
10452 CACCAGGTGAGTATTG
1 CACCAGGTGAGTATTG
10468 CACCAGGTGAGTATTG
1 CACCAGGTGAGTATTG
10484 CACCAGGTGAGTATTTG
1 CACCAGGTGAGTA-TTG
*
10501 TACCAGGTGAGTATT
1 CACCAGGTGAGTATT
10516 TGTATTGGGT
Statistics
Matches: 84, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
15 1 0.01
16 67 0.80
17 16 0.19
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.29
Consensus pattern (16 bp):
CACCAGGTGAGTATTG
Found at i:11600 original size:3 final size:3
Alignment explanation
Indices: 11594--11629 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
11584 TTTTTTAAAC
11594 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
11630 TGTGTTTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:11688 original size:27 final size:28
Alignment explanation
Indices: 11650--11835 Score: 159
Period size: 29 Copynumber: 6.5 Consensus size: 28
11640 TTTTTTAGTT
* * * *
11650 GGGATTCT-TCCCTTGGTACAGCACT-A
1 GGGAGTCTCTCCCTTGGTGCGGCACTGG
11676 GGGAGTCTCTCCCCCTTGGTGCGCGGCACTGG
1 GGGAGTCTCT--CCCTTGGT--GCGGCACTGG
11708 GGGAGTCTCTCCCTT-GTGCGGCACTGG
1 GGGAGTCTCTCCCTTGGTGCGGCACTGG
* * * *
11735 GGGAGTCTCTCCCCTGGTGTGACACTTG
1 GGGAGTCTCTCCCTTGGTGCGGCACTGG
*
11763 GGGAGTCTCTCCCCTGGTGCGCGGACACTGG
1 GGGAGTCTCTCCCTTGGT--GCGG-CACTGG
11794 GGGAGTCTC-CCC-TGGTGCGCGGACACTGG
1 GGGAGTCTCTCCCTTGGT--GCGG-CACTGG
11823 GGGAGTCTC-CCCT
1 GGGAGTCTCTCCCT
11836 AGTGCGCCCC
Statistics
Matches: 138, Mismatches: 11, Indels: 18
0.83 0.07 0.11
Matches are distributed among these distances:
26 7 0.05
27 25 0.18
28 27 0.20
29 39 0.28
30 10 0.07
31 20 0.14
32 10 0.07
ACGTcount: A:0.10, C:0.31, G:0.35, T:0.24
Consensus pattern (28 bp):
GGGAGTCTCTCCCTTGGTGCGGCACTGG
Found at i:11760 original size:28 final size:30
Alignment explanation
Indices: 11676--11831 Score: 184
Period size: 29 Copynumber: 5.3 Consensus size: 30
11666 TACAGCACTA
11676 GGGAGTCTCTCCCCCTTGGTGCGCGG-CACTGG
1 GGGAGTCTCT-CCCC-TGGT-CGCGGACACTGG
*
11708 GGGAGTCTCT-CCCTTGT-GCGG-CACTGG
1 GGGAGTCTCTCCCCTGGTCGCGGACACTGG
* *
11735 GGGAGTCTCTCCCCTGGT-G-TGACACTTG
1 GGGAGTCTCTCCCCTGGTCGCGGACACTGG
11763 GGGAGTCTCTCCCCTGGTGCGCGGACACTGG
1 GGGAGTCTCTCCCCTGGT-CGCGGACACTGG
11794 GGGAG--TCTCCCCTGGTGCGCGGACACTGG
1 GGGAGTCTCTCCCCTGGT-CGCGGACACTGG
11823 GGGAGTCTC
1 GGGAGTCTC
11832 CCCTAGTGCG
Statistics
Matches: 111, Mismatches: 6, Indels: 15
0.84 0.05 0.11
Matches are distributed among these distances:
27 21 0.19
28 30 0.27
29 32 0.29
30 4 0.04
31 14 0.13
32 10 0.09
ACGTcount: A:0.09, C:0.31, G:0.38, T:0.22
Consensus pattern (30 bp):
GGGAGTCTCTCCCCTGGTCGCGGACACTGG
Found at i:13599 original size:12 final size:12
Alignment explanation
Indices: 13582--13618 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
13572 AAAGGGACCA
13582 CTCAAGAGAAAT
1 CTCAAGAGAAAT
13594 CTCAAGAGAAAT
1 CTCAAGAGAAAT
* *
13606 CCCAGGAGAAAT
1 CTCAAGAGAAAT
13618 C
1 C
13619 CAAAGGGAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.46, C:0.22, G:0.19, T:0.14
Consensus pattern (12 bp):
CTCAAGAGAAAT
Found at i:13749 original size:2 final size:2
Alignment explanation
Indices: 13744--13771 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
13734 TTTTACAGGC
13744 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13772 GTATCTATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15190 original size:28 final size:28
Alignment explanation
Indices: 15152--15228 Score: 100
Period size: 28 Copynumber: 2.8 Consensus size: 28
15142 GCTCGCTACT
*
15152 GGGGAGCCTCCCTTGGCGCGCGCTGCCG
1 GGGGAGCCTCCCTTGGCGCGCGCTGCCA
* * * *
15180 GGGGAGTCTCCCTTGGCGCACGTTGCTA
1 GGGGAGCCTCCCTTGGCGCGCGCTGCCA
*
15208 GGGGAGCCTCCCCTGGCGCGC
1 GGGGAGCCTCCCTTGGCGCGC
15229 ATTGTTGGGC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.06, C:0.36, G:0.40, T:0.17
Consensus pattern (28 bp):
GGGGAGCCTCCCTTGGCGCGCGCTGCCA
Done.