Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014208.1 Corchorus capsularis cultivar CVL-1 contig14229, 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: 16675
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:197 original size:30 final size:30
Alignment explanation
Indices: 161--221 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
151 TTCAAGGGGG
161 AGGGAATGATGCGCCCAA-GACTTATCATGA
1 AGGGAATGATGCG-CCAAGGACTTATCATGA
*
191 AGGGAATGATGCGCCAAGGACTTATTATGA
1 AGGGAATGATGCGCCAAGGACTTATCATGA
221 A
1 A
222 CTTGAAGACA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 4 0.14
30 25 0.86
ACGTcount: A:0.34, C:0.16, G:0.28, T:0.21
Consensus pattern (30 bp):
AGGGAATGATGCGCCAAGGACTTATCATGA
Found at i:2852 original size:33 final size:33
Alignment explanation
Indices: 2774--2852 Score: 113
Period size: 33 Copynumber: 2.4 Consensus size: 33
2764 TTGCAAAGTG
*
2774 TGTTTTAGATGTTGTTTGCAATGATACTAAACC
1 TGTTTTAGGTGTTGTTTGCAATGATACTAAACC
** * *
2807 TAATTTAAGTGTTGTTTGCAATGATACTAAATC
1 TGTTTTAGGTGTTGTTTGCAATGATACTAAACC
2840 TGTTTTAGGTGTT
1 TGTTTTAGGTGTT
2853 ATTGGTGATG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.27, C:0.09, G:0.19, T:0.46
Consensus pattern (33 bp):
TGTTTTAGGTGTTGTTTGCAATGATACTAAACC
Found at i:2941 original size:33 final size:33
Alignment explanation
Indices: 2904--3010 Score: 205
Period size: 33 Copynumber: 3.2 Consensus size: 33
2894 TGAAAACAAA
2904 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
1 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
*
2937 TCTGTTTTAGTTGATCATAGCATTGCAAATAAT
1 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
2970 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
1 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
3003 TCTGTTTT
1 TCTGTTTT
3011 AGGTGAAAAG
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 72 1.00
ACGTcount: A:0.26, C:0.12, G:0.17, T:0.45
Consensus pattern (33 bp):
TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
Found at i:3356 original size:30 final size:30
Alignment explanation
Indices: 3320--3380 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
3310 TTCAAGGGGG
*
3320 AGGGAATGATGTGCCCAA-GACTTATCATGA
1 AGGGAATGATGCG-CCAAGGACTTATCATGA
*
3350 AGGGAATGATGCGCCAAGGACTTATTATGA
1 AGGGAATGATGCGCCAAGGACTTATCATGA
3380 A
1 A
3381 CTTGAAGACA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 4 0.14
30 24 0.86
ACGTcount: A:0.34, C:0.15, G:0.28, T:0.23
Consensus pattern (30 bp):
AGGGAATGATGCGCCAAGGACTTATCATGA
Found at i:3447 original size:18 final size:18
Alignment explanation
Indices: 3424--3461 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
3414 GTGCAAGGGC
3424 TGCAAGGAAG-CATGGAGA
1 TGCAA-GAAGACATGGAGA
3442 TGCAAGAAGATCATGGAGA
1 TGCAAGAAGA-CATGGAGA
3461 T
1 T
3462 ATTGATGATC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.22
18 5 0.28
19 9 0.50
ACGTcount: A:0.39, C:0.11, G:0.34, T:0.16
Consensus pattern (18 bp):
TGCAAGAAGACATGGAGA
Found at i:4751 original size:20 final size:22
Alignment explanation
Indices: 4717--4760 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 22
4707 AAAATTATGC
*
4717 ATATTTTTATAGCTATTTTTAT
1 ATATTTTTATAGCTACTTTTAT
4739 ATATTTTT-T-GCTACTTTTAT
1 ATATTTTTATAGCTACTTTTAT
4759 AT
1 AT
4761 GTGTTTTTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 12 0.57
21 1 0.05
22 8 0.38
ACGTcount: A:0.25, C:0.07, G:0.05, T:0.64
Consensus pattern (22 bp):
ATATTTTTATAGCTACTTTTAT
Found at i:4767 original size:20 final size:20
Alignment explanation
Indices: 4728--4767 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
4718 TATTTTTATA
* *
4728 GCTATTTTTATATATTTTTT
1 GCTACTTTTATATATGTTTT
*
4748 GCTACTTTTATATGTGTTTT
1 GCTACTTTTATATATGTTTT
4768 TACCCTATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.17, C:0.07, G:0.10, T:0.65
Consensus pattern (20 bp):
GCTACTTTTATATATGTTTT
Found at i:15953 original size:35 final size:35
Alignment explanation
Indices: 15913--15995 Score: 139
Period size: 35 Copynumber: 2.4 Consensus size: 35
15903 TTTAGTTTCA
15913 GAACAATGGTTTGTAATCCTTAATTCCTAGTATCG
1 GAACAATGGTTTGTAATCCTTAATTCCTAGTATCG
* * *
15948 GAACAATGGTTTGTAATCCTTGATTTCTAGTCTCG
1 GAACAATGGTTTGTAATCCTTAATTCCTAGTATCG
15983 GAACAATGGTTTG
1 GAACAATGGTTTG
15996 ATGTTGGCAG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 45 1.00
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (35 bp):
GAACAATGGTTTGTAATCCTTAATTCCTAGTATCG
Found at i:16533 original size:6 final size:6
Alignment explanation
Indices: 16524--16562 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
16514 AAAGCAAAGC
16524 AAATCT AAATCT AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAATCT AAATCT AAA
16563 GCAGATTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (6 bp):
AAATCT
Found at i:16574 original size:12 final size:12
Alignment explanation
Indices: 16559--16595 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
16549 AATCTAAATC
16559 TAAAGCAGATTA
1 TAAAGCAGATTA
*
16571 TAAAGCAAATTAA
1 TAAAGCAGATT-A
16584 TAAAGCAGATTA
1 TAAAGCAGATTA
16596 ACAAAGCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.54, C:0.08, G:0.14, T:0.24
Consensus pattern (12 bp):
TAAAGCAGATTA
Found at i:16588 original size:13 final size:13
Alignment explanation
Indices: 16559--16605 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 13
16549 AATCTAAATC
*
16559 TAAAGCAGATT-A
1 TAAAGCAAATTAA
16571 TAAAGCAAATTAA
1 TAAAGCAAATTAA
*
16584 TAAAGCAGATTAA
1 TAAAGCAAATTAA
*
16597 CAAAGCAAA
1 TAAAGCAAA
16606 CAATAATTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
12 10 0.33
13 20 0.67
ACGTcount: A:0.57, C:0.11, G:0.13, T:0.19
Consensus pattern (13 bp):
TAAAGCAAATTAA
Found at i:16610 original size:25 final size:25
Alignment explanation
Indices: 16559--16611 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
16549 AATCTAAATC
* *
16559 TAAAGCAGATTATAAAGCAAATTAA
1 TAAAGCAGATTACAAAGCAAATCAA
16584 TAAAGCAGATTAACAAAGCAAA-CAA
1 TAAAGCAGATT-ACAAAGCAAATCAA
16609 TAA
1 TAA
16612 TTAAAAAGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 16 0.64
26 9 0.36
ACGTcount: A:0.58, C:0.11, G:0.11, T:0.19
Consensus pattern (25 bp):
TAAAGCAGATTACAAAGCAAATCAA
Done.