Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006930.1 Corchorus capsularis cultivar CVL-1 contig06951, 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: 12730
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Found at i:2065 original size:15 final size:15
Alignment explanation
Indices: 2047--2075 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2037 TCCAATTTGT
2047 AAATCAAATGCCTTA
1 AAATCAAATGCCTTA
2062 AAATCAAATGCCTT
1 AAATCAAATGCCTT
2076 GTATTTATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.45, C:0.21, G:0.07, T:0.28
Consensus pattern (15 bp):
AAATCAAATGCCTTA
Found at i:2641 original size:27 final size:27
Alignment explanation
Indices: 2568--2642 Score: 96
Period size: 27 Copynumber: 2.8 Consensus size: 27
2558 AAGTGACCTT
* * **
2568 AAAATGACCAAAATGCCCCTAAATGTG
1 AAAATGACCAAAATGCCCTTGAATGCA
*
2595 AAAATGATCAAAATGCCCTTGAATGCA
1 AAAATGACCAAAATGCCCTTGAATGCA
*
2622 AAAATGACCAAAATGGCCTTG
1 AAAATGACCAAAATGCCCTTG
2643 GATGACCCTA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.44, C:0.20, G:0.16, T:0.20
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCTTGAATGCA
Found at i:3034 original size:47 final size:47
Alignment explanation
Indices: 2977--3262 Score: 446
Period size: 47 Copynumber: 6.1 Consensus size: 47
2967 AAAACCCGTT
* *
2977 GACCAACTTTGGTCACTAAATTGAAAACTCGCGTGGAAGCGAGAGAA
1 GACCATCTTTGGTCACTAAATTGAAAACTCGCGTGGAAGCGAGAAAA
*
3024 GACCATCTTTGGTCACTAAATTGAAAACCCGCGTGGAAGCGAGAAAA
1 GACCATCTTTGGTCACTAAATTGAAAACTCGCGTGGAAGCGAGAAAA
* *
3071 GACCATCTTTGGTCACTAGATTGAAAACTCGCATGGAAGCGAGAAAA
1 GACCATCTTTGGTCACTAAATTGAAAACTCGCGTGGAAGCGAGAAAA
* *
3118 TACCATCTTTGGTCACTAAATTGAAAACTCGCGTGGAAGCGAGAAGA
1 GACCATCTTTGGTCACTAAATTGAAAACTCGCGTGGAAGCGAGAAAA
* *
3165 GACCATCTTTGGTCACTAAATTGAAAATTCGCGTGGAAGCGAGAGAA
1 GACCATCTTTGGTCACTAAATTGAAAACTCGCGTGGAAGCGAGAAAA
* * * * *
3212 GACTATCTTTGATCACTAGATTGAAAACTCGCATGGAAGCGAGAAAG
1 GACCATCTTTGGTCACTAAATTGAAAACTCGCGTGGAAGCGAGAAAA
3259 GACC
1 GACC
3263 GCCTGGATGG
Statistics
Matches: 217, Mismatches: 22, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 217 1.00
ACGTcount: A:0.35, C:0.19, G:0.24, T:0.21
Consensus pattern (47 bp):
GACCATCTTTGGTCACTAAATTGAAAACTCGCGTGGAAGCGAGAAAA
Found at i:3511 original size:69 final size:70
Alignment explanation
Indices: 3371--3666 Score: 330
Period size: 69 Copynumber: 4.3 Consensus size: 70
3361 CTCAATGAAC
* * *
3371 TTGGCTTATGGAAAAGCCCCTGAATG-CTCGGATGGAACCAAATCTTAAACTATCTCGCGTGGAA
1 TTGGCTTATGGAAAAGCCCCTGAATGCCT-GGATGGAACCAAAGCTGAAACTAACTCGCGTGGAA
*
3435 GCGAGT
65 ACGAGT
* ** * * * *
3441 TTGGCTTATGGAAAAGCCTCT-CTTGCCTGGATGGAACCGAAGCTGGATCTAACTCGTGTGGAAA
1 TTGGCTTATGGAAAAGCCCCTGAATGCCTGGATGGAACCAAAGCTGAAACTAACTCGCGTGGAAA
*
3505 CAAGT
66 CGAGT
* * * * * *
3510 TTGGCTTGTGGAAAAGCCCCTGAATGCTTTGATGGAACCAAATCTGAAACTATCTCGCGTGGAAG
1 TTGGCTTATGGAAAAGCCCCTGAATGCCTGGATGGAACCAAAGCTGAAACTAACTCGCGTGGAAA
3575 CGAGT
66 CGAGT
* * * * *
3580 TTGGCTTATGGAAAAGCCTCT--CTCGCCTGGATGGAACCAAAGCTGGAACTGACTCGTGTGGAA
1 TTGGCTTATGGAAAAGCCCCTGAAT-GCCTGGATGGAACCAAAGCTGAAACTAACTCGCGTGGAA
3643 ACGAGT
65 ACGAGT
*
3649 TTGGCTTGTGGAAAAGCC
1 TTGGCTTATGGAAAAGCC
3667 AGAGCATTCG
Statistics
Matches: 185, Mismatches: 38, Indels: 7
0.80 0.17 0.03
Matches are distributed among these distances:
68 1 0.01
69 107 0.58
70 77 0.42
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.25
Consensus pattern (70 bp):
TTGGCTTATGGAAAAGCCCCTGAATGCCTGGATGGAACCAAAGCTGAAACTAACTCGCGTGGAAA
CGAGT
Found at i:3623 original size:139 final size:139
Alignment explanation
Indices: 3371--3666 Score: 511
Period size: 139 Copynumber: 2.1 Consensus size: 139
3361 CTCAATGAAC
* *
3371 TTGGCTTATGGAAAAGCCCCTGAATGCTCGGATGGAACCAAATCTTAAACTATCTCGCGTGGAAG
1 TTGGCTTGTGGAAAAGCCCCTGAATGCTCGGATGGAACCAAATCTGAAACTATCTCGCGTGGAAG
* * *
3436 CGAGTTTGGCTTATGGAAAAGCCTCTCTTGCCTGGATGGAACCGAAGCTGGATCTAACTCGTGTG
66 CGAGTTTGGCTTATGGAAAAGCCTCTCTCGCCTGGATGGAACCAAAGCTGGAACTAACTCGTGTG
3501 GAAACAAGT
131 GAAACAAGT
**
3510 TTGGCTTGTGGAAAAGCCCCTGAATGCTTTGATGGAACCAAATCTGAAACTATCTCGCGTGGAAG
1 TTGGCTTGTGGAAAAGCCCCTGAATGCTCGGATGGAACCAAATCTGAAACTATCTCGCGTGGAAG
*
3575 CGAGTTTGGCTTATGGAAAAGCCTCTCTCGCCTGGATGGAACCAAAGCTGGAACTGACTCGTGTG
66 CGAGTTTGGCTTATGGAAAAGCCTCTCTCGCCTGGATGGAACCAAAGCTGGAACTAACTCGTGTG
*
3640 GAAACGAGT
131 GAAACAAGT
3649 TTGGCTTGTGGAAAAGCC
1 TTGGCTTGTGGAAAAGCC
3667 AGAGCATTCG
Statistics
Matches: 148, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
139 148 1.00
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.25
Consensus pattern (139 bp):
TTGGCTTGTGGAAAAGCCCCTGAATGCTCGGATGGAACCAAATCTGAAACTATCTCGCGTGGAAG
CGAGTTTGGCTTATGGAAAAGCCTCTCTCGCCTGGATGGAACCAAAGCTGGAACTAACTCGTGTG
GAAACAAGT
Found at i:3836 original size:30 final size:30
Alignment explanation
Indices: 3808--3866 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
3798 GTTCTGAATC
3808 TTTGCT-TTCTTGAATTTGCTTCCTTGAATCCT
1 TTTGCTCTTCTTG-ATTTG--TCCTTGAATCCT
*
3840 TTTGTTCTTCTTGATTTGTCCTTGAAT
1 TTTGCTCTTCTTGATTTGTCCTTGAAT
3867 TTGTTTTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 9 0.36
32 10 0.40
33 6 0.24
ACGTcount: A:0.12, C:0.19, G:0.14, T:0.56
Consensus pattern (30 bp):
TTTGCTCTTCTTGATTTGTCCTTGAATCCT
Found at i:3942 original size:29 final size:29
Alignment explanation
Indices: 3909--3969 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
3899 TTGCCCCAGA
3909 TCTGACTTGAATAGTATGCTTTGAAAGAT
1 TCTGACTTGAATAGTATGCTTTGAAAGAT
3938 TCTGACTTGAATAGTATGCTTTGAAAGAT
1 TCTGACTTGAATAGTATGCTTTGAAAGAT
3967 TCT
1 TCT
3970 TTTACTGATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.39
Consensus pattern (29 bp):
TCTGACTTGAATAGTATGCTTTGAAAGAT
Found at i:4281 original size:50 final size:50
Alignment explanation
Indices: 4217--4323 Score: 153
Period size: 50 Copynumber: 2.1 Consensus size: 50
4207 TAAAATGCCC
** *
4217 TTTGAAAAGTGAATTTTGATCTTGGACTCACAAATGGAATGCAATCTTAT
1 TTTGAAAAGTGAATTTTGATAATGGACTCACAAATGGAATGCAATCTCAT
* *
4267 TTTGAAAA-TCGAATTTTGATAATGGACTCACAAATGGAATGCCATGTCAT
1 TTTGAAAAGT-GAATTTTGATAATGGACTCACAAATGGAATGCAATCTCAT
4317 TTTGAAA
1 TTTGAAA
4324 CTTCTTGTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
49 1 0.02
50 50 0.98
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.35
Consensus pattern (50 bp):
TTTGAAAAGTGAATTTTGATAATGGACTCACAAATGGAATGCAATCTCAT
Found at i:5843 original size:46 final size:45
Alignment explanation
Indices: 5771--5918 Score: 226
Period size: 45 Copynumber: 3.3 Consensus size: 45
5761 AAAATGCAAC
* * * *
5771 TTTGGAAAACCCTTTTATTAAAACCTTTTGAAAACCATGACTTTTT
1 TTTGAAAAACCATTTTATTAACACCTTTTGAAAACCATGAC-TCTT
5817 TTTGAAAAACCATTTTATTAACACCTTTTGAAAACCATGACTCTT
1 TTTGAAAAACCATTTTATTAACACCTTTTGAAAACCATGACTCTT
* *
5862 TTTCAAAAACCATTTTATTAACACCTTTTGAAATCCATGACTCTT
1 TTTGAAAAACCATTTTATTAACACCTTTTGAAAACCATGACTCTT
5907 TTTG-AAAACCAT
1 TTTGAAAAACCAT
5919 CATTGCTTTT
Statistics
Matches: 95, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
44 8 0.08
45 49 0.52
46 38 0.40
ACGTcount: A:0.34, C:0.20, G:0.07, T:0.39
Consensus pattern (45 bp):
TTTGAAAAACCATTTTATTAACACCTTTTGAAAACCATGACTCTT
Found at i:5952 original size:10 final size:10
Alignment explanation
Indices: 5933--5997 Score: 62
Period size: 10 Copynumber: 6.4 Consensus size: 10
5923 GCTTTTGCTC
5933 TTTT-TCTTT
1 TTTTCTCTTT
5942 TTTTCTCTTT
1 TTTTCTCTTT
*
5952 TATTCT-TCTT
1 TTTTCTCT-TT
*
5962 TATTCTCTTT
1 TTTTCTCTTT
*
5972 TTCTCTTCTTT
1 TTTTC-TCTTT
5983 TTCTTCTCTTT
1 TT-TTCTCTTT
5994 TTTT
1 TTTT
5998 TTACTGGAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
9 5 0.11
10 25 0.53
11 15 0.32
12 2 0.04
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (10 bp):
TTTTCTCTTT
Found at i:5969 original size:20 final size:18
Alignment explanation
Indices: 5924--5986 Score: 76
Period size: 20 Copynumber: 3.4 Consensus size: 18
5914 ACCATCATTG
*
5924 CTTTTGCTC-TTTTTCTT
1 CTTTTTCTCTTTTTTCTT
5941 -TTTTTCTCTTTTATTCTT
1 CTTTTTCTCTTTT-TTCTT
5959 CTTTATTCTCTTTTTCTCTT
1 CTTT-TTCTCTTTTT-TCTT
5979 CTTTTTCT
1 CTTTTTCT
5987 TCTCTTTTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
16 7 0.17
17 3 0.08
18 5 0.12
19 8 0.20
20 17 0.43
ACGTcount: A:0.03, C:0.22, G:0.02, T:0.73
Consensus pattern (18 bp):
CTTTTTCTCTTTTTTCTT
Found at i:5981 original size:11 final size:10
Alignment explanation
Indices: 5940--5995 Score: 55
Period size: 9 Copynumber: 5.6 Consensus size: 10
5930 CTCTTTTTCT
5940 TTTTTTC-TC
1 TTTTTTCTTC
5949 TTTTATTCTTC
1 TTTT-TTCTTC
*
5960 TTTATTC-TC
1 TTTTTTCTTC
5969 TTTTTCTCTTC
1 TTTTT-TCTTC
5980 -TTTTTCTTC
1 TTTTTTCTTC
5989 TCTTTTT
1 T-TTTTT
5996 TTTTACTGGA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
9 15 0.38
10 12 0.31
11 12 0.31
ACGTcount: A:0.04, C:0.21, G:0.00, T:0.75
Consensus pattern (10 bp):
TTTTTTCTTC
Found at i:11661 original size:21 final size:21
Alignment explanation
Indices: 11635--11683 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
11625 TCTCACTAAA
*
11635 TCTGATTTGAAT-TTGAAAATC
1 TCTGATTTAAATCTTGAAAA-C
11656 TCTGA-TTAAATCTTGAAAAC
1 TCTGATTTAAATCTTGAAAAC
11676 TCTTGATT
1 TC-TGATT
11684 ACCAATTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 8 0.33
21 15 0.62
22 1 0.04
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (21 bp):
TCTGATTTAAATCTTGAAAAC
Done.