Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005656.1 Corchorus capsularis cultivar CVL-1 contig05674, 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: 5226
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Found at i:2943 original size:9 final size:9
Alignment explanation
Indices: 2929--2985 Score: 78
Period size: 9 Copynumber: 6.1 Consensus size: 9
2919 GGTTTGCATG
2929 TTTTTCTTT
1 TTTTTCTTT
2938 TTTTTCTTT
1 TTTTTCTTT
*
2947 TTTCTCTTT
1 TTTTTCTTT
*
2956 TTTTTATTT
1 TTTTTCTTT
2965 CTTTTTCTTT
1 -TTTTTCTTT
2975 TCTTTTCTTT
1 T-TTTTCTTT
2985 T
1 T
2986 CTCTCTCTCT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
9 25 0.60
10 17 0.40
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:2947 original size:5 final size:5
Alignment explanation
Indices: 2930--2987 Score: 61
Period size: 5 Copynumber: 12.2 Consensus size: 5
2920 GTTTGCATGT
* *
2930 TTTTC TTTT- TTTTC TTTT- TTCTC TTTT- TTTT- ATTTC TTTTTC TTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC -TTTTC TTTTC
2977 TTTTC TTTTC T
1 TTTTC TTTTC T
2988 CTCTCTCTCT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
4 14 0.31
5 27 0.60
6 4 0.09
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTC
Found at i:2948 original size:10 final size:10
Alignment explanation
Indices: 2929--2987 Score: 59
Period size: 11 Copynumber: 5.7 Consensus size: 10
2919 GGTTTGCATG
2929 TTTTTC-TTT
1 TTTTTCTTTT
2938 TTTTTCTTTT
1 TTTTTCTTTT
2948 TTCTCTT-TTTT
1 TT-T-TTCTTTT
2959 TTATTTCTTTT
1 TT-TTTCTTTT
2970 TCTTTTCTTTT
1 T-TTTTCTTTT
*
2981 CTTTTCT
1 TTTTTCT
2988 CTCTCTCTCT
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
9 6 0.14
10 13 0.30
11 21 0.49
12 3 0.07
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:2948 original size:16 final size:15
Alignment explanation
Indices: 2929--2985 Score: 69
Period size: 16 Copynumber: 3.7 Consensus size: 15
2919 GGTTTGCATG
2929 TTTTTCTTTTTTTTCT
1 TTTTTCTTTTTTTT-T
*
2945 TTTTTCTCTTTTTTT
1 TTTTTCTTTTTTTTT
*
2960 TATTTCTTTTTCTTTT
1 TTTTTCTTTTT-TTTT
*
2976 CTTTTCTTTT
1 TTTTTCTTTT
2986 CTCTCTCTCT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
15 10 0.29
16 25 0.71
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTTTCTTTTTTTTT
Found at i:3016 original size:5 final size:6
Alignment explanation
Indices: 2929--3024 Score: 74
Period size: 6 Copynumber: 15.8 Consensus size: 6
2919 GGTTTGCATG
*
2929 TTTTTC TTTTT- TTTCTT- TTTTCTC TTTTTT TTATTTC TTTTTC -TTTTC
1 TTTTTC TTTTTC TTT-TTC TTTT-TC TTTTTC TT-TTTC TTTTTC TTTTTC
* * * *
2977 -TTTTC TTTTCTC TCTCTC TCTCTC TTTTTC TTTTTC TTTTTCC TTTTT
1 TTTTTC TTTT-TC TTTTTC TTTTTC TTTTTC TTTTTC TTTTT-C TTTTT
3025 TAAGACCTAC
Statistics
Matches: 77, Mismatches: 6, Indels: 13
0.80 0.06 0.14
Matches are distributed among these distances:
5 14 0.18
6 44 0.57
7 19 0.25
ACGTcount: A:0.01, C:0.21, G:0.00, T:0.78
Consensus pattern (6 bp):
TTTTTC
Found at i:3129 original size:47 final size:47
Alignment explanation
Indices: 3075--3313 Score: 216
Period size: 47 Copynumber: 5.1 Consensus size: 47
3065 GAAAACCCGC
* *
3075 TGACCAACTTTGCTCACTAAATTGAAAATTCGCATGGAAGCGAGATAA
1 TGACCAACTTTGC-CACTAAATTGAAAACTCGCATGGAAGCGAGAGAA
* ** *
3123 -GACCAACTTTGGCCACTAGATTGCTAACTCGCGTGGAAGCGAGAGAA
1 TGACCAACTTT-GCCACTAAATTGAAAACTCGCATGGAAGCGAGAGAA
* *** * * *
3170 TG-CCAACTTTGGCCACTGAATTGCTTACTCGCGTGAAAGCGAAAGAA
1 TGACCAACTTT-GCCACTAAATTGAAAACTCGCATGGAAGCGAGAGAA
** *
3217 TG-CCAACTTTGGCCACTAAATTGCTAACTCGCGTGGAAGCGAGAGAA
1 TGACCAACTTT-GCCACTAAATTGAAAACTCGCATGGAAGCGAGAGAA
* *** *
3264 TG-CCAACTTTGGCCACTGAATTGCTTACTCGCGTGGAAGCGAGAGAA
1 TGACCAACTTT-GCCACTAAATTGAAAACTCGCATGGAAGCGAGAGAA
3311 TGA
1 TGA
3314 TTGCCTGGAT
Statistics
Matches: 171, Mismatches: 17, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
47 168 0.98
48 3 0.02
ACGTcount: A:0.31, C:0.22, G:0.25, T:0.23
Consensus pattern (47 bp):
TGACCAACTTTGCCACTAAATTGAAAACTCGCATGGAAGCGAGAGAA
Found at i:3240 original size:94 final size:94
Alignment explanation
Indices: 3125--3312 Score: 349
Period size: 94 Copynumber: 2.0 Consensus size: 94
3115 CGAGATAAGA
*
3125 CCAACTTTGGCCACTAGATTGCTAACTCGCGTGGAAGCGAGAGAATGCCAACTTTGGCCACTGAA
1 CCAACTTTGGCCACTAAATTGCTAACTCGCGTGGAAGCGAGAGAATGCCAACTTTGGCCACTGAA
3190 TTGCTTACTCGCGTGAAAGCGAAAGAATG
66 TTGCTTACTCGCGTGAAAGCGAAAGAATG
3219 CCAACTTTGGCCACTAAATTGCTAACTCGCGTGGAAGCGAGAGAATGCCAACTTTGGCCACTGAA
1 CCAACTTTGGCCACTAAATTGCTAACTCGCGTGGAAGCGAGAGAATGCCAACTTTGGCCACTGAA
* *
3284 TTGCTTACTCGCGTGGAAGCGAGAGAATG
66 TTGCTTACTCGCGTGAAAGCGAAAGAATG
3313 ATTGCCTGGA
Statistics
Matches: 91, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
94 91 1.00
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.22
Consensus pattern (94 bp):
CCAACTTTGGCCACTAAATTGCTAACTCGCGTGGAAGCGAGAGAATGCCAACTTTGGCCACTGAA
TTGCTTACTCGCGTGAAAGCGAAAGAATG
Found at i:3555 original size:69 final size:69
Alignment explanation
Indices: 3422--3782 Score: 394
Period size: 69 Copynumber: 5.3 Consensus size: 69
3412 CCTCACTGTA
* ** * * *
3422 TTTGGCTTATGGAAAAGCCCCTGAATGCTTGGATGGAACCAAATCTTAAACT-ATCTCGCGTGGA
1 TTTGGCTTATGGAAAAGCCTCT-TTTGCTTGGATGGAACCAAAGCTGAAACTGA-CTCGTGTGGA
3486 AACGAG
64 AACGAG
* * * * *
3492 TTTGGCTTATGGAAAAGCCACTTTTGCCTGGATGAAACCAAAGCTGGATCTGACTCGTGTGGAAA
1 TTTGGCTTATGGAAAAGCCTCTTTTGCTTGGATGGAACCAAAGCTGAAACTGACTCGTGTGGAAA
3557 CGAG
66 CGAG
* * * *
3561 TTTGGCTTGTGGAAAAG-C-C-TTTGTTTGGATGGAACCAAAGCTTAAACT-ATCTCGTATGGAA
1 TTTGGCTTATGGAAAAGCCTCTTTTGCTTGGATGGAACCAAAGCTGAAACTGA-CTCGTGTGGAA
3622 ACGAG
65 ACGAG
* * * * *
3627 TTTGGCTTGTAGAAAAGCCTCTGTTGCTTGGATGGAACC-AAGACT-TAACTGACTCGTATGGAA
1 TTTGGCTTATGGAAAAGCCTCTTTTGCTTGGATGGAACCAAAG-CTGAAACTGACTCGTGTGGAA
3690 ACGAG
65 ACGAG
* * * * **
3695 TTTGGCTTATGGAAAAGCCTCTCTTGCCTGGATGGAATCAAAGCTGGATTTGACTCGTGTGGAAA
1 TTTGGCTTATGGAAAAGCCTCTTTTGCTTGGATGGAACCAAAGCTGAAACTGACTCGTGTGGAAA
3760 CGAG
66 CGAG
*
3764 TTTGGCTTGTGGAAAAGCC
1 TTTGGCTTATGGAAAAGCC
3783 GAAGCATTCG
Statistics
Matches: 250, Mismatches: 32, Indels: 19
0.83 0.11 0.06
Matches are distributed among these distances:
65 1 0.00
66 54 0.22
67 2 0.01
68 61 0.24
69 110 0.44
70 22 0.09
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.28
Consensus pattern (69 bp):
TTTGGCTTATGGAAAAGCCTCTTTTGCTTGGATGGAACCAAAGCTGAAACTGACTCGTGTGGAAA
CGAG
Found at i:3613 original size:135 final size:137
Alignment explanation
Indices: 3422--3782 Score: 444
Period size: 135 Copynumber: 2.6 Consensus size: 137
3412 CCTCACTGTA
* ** * *
3422 TTTGGCTTATGGAAAAGCCCCTGAATGCTTGGATGGAACCAAATCTTAAACTATCTCGCGTGGAA
1 TTTGGCTTATGGAAAAGCCTCT-CTTGCTTGGATGGAACCAAAGCTTAAACTATCTCGTGTGGAA
* * * *
3487 ACGAGTTTGGCTTATGGAAAAGCCACTTTTGCCTGGATGAAACCAA-AGCTGGATCTGACTCGTG
65 ACGAGTTTGGCTTGTGGAAAAGCCACTGTTGCCTGGATGAAACCAAGA-CT-GAACTGACTCGTA
3551 TGGAAACGAG
128 TGGAAACGAG
* * *
3561 TTTGGCTTGTGGAAAAG-C-CT-TTGTTTGGATGGAACCAAAGCTTAAACTATCTCGTATGGAAA
1 TTTGGCTTATGGAAAAGCCTCTCTTGCTTGGATGGAACCAAAGCTTAAACTATCTCGTGTGGAAA
* * * * *
3623 CGAGTTTGGCTTGTAGAAAAGCCTCTGTTGCTTGGATGGAACCAAGACTTAACTGACTCGTATGG
66 CGAGTTTGGCTTGTGGAAAAGCCACTGTTGCCTGGATGAAACCAAGACTGAACTGACTCGTATGG
3688 AAACGAG
131 AAACGAG
* * ** **
3695 TTTGGCTTATGGAAAAGCCTCTCTTGCCTGGATGGAATCAAAGCTGGATTTGA-CTCGTGTGGAA
1 TTTGGCTTATGGAAAAGCCTCTCTTGCTTGGATGGAACCAAAGCTTAAACT-ATCTCGTGTGGAA
3759 ACGAGTTTGGCTTGTGGAAAAGCC
65 ACGAGTTTGGCTTGTGGAAAAGCC
3783 GAAGCATTCG
Statistics
Matches: 192, Mismatches: 25, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
134 36 0.19
135 79 0.41
136 3 0.02
137 56 0.29
138 2 0.01
139 16 0.08
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.28
Consensus pattern (137 bp):
TTTGGCTTATGGAAAAGCCTCTCTTGCTTGGATGGAACCAAAGCTTAAACTATCTCGTGTGGAAA
CGAGTTTGGCTTGTGGAAAAGCCACTGTTGCCTGGATGAAACCAAGACTGAACTGACTCGTATGG
AAACGAG
Found at i:4340 original size:50 final size:50
Alignment explanation
Indices: 4284--4383 Score: 146
Period size: 50 Copynumber: 2.0 Consensus size: 50
4274 AAAATACCCC
* * *
4284 TTGAAAAGCAAATTTTGATCTTGAACTCACAAATGGAATGCAATCTTATT
1 TTGAAAAGCAAATCTTGATATTGAACTCACAAATGAAATGCAATCTTATT
* * *
4334 TTGAAAATCGAATCTTGATATTGGACTCACAAATGAAATGCAATCTTATT
1 TTGAAAAGCAAATCTTGATATTGAACTCACAAATGAAATGCAATCTTATT
4384 ATAAAACCTC
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 44 1.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (50 bp):
TTGAAAAGCAAATCTTGATATTGAACTCACAAATGAAATGCAATCTTATT
Found at i:4695 original size:14 final size:14
Alignment explanation
Indices: 4678--4719 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
4668 TTCATTCTCA
4678 TTCTCTTTTTCTTT
1 TTCTCTTTTTCTTT
*
4692 TTCTCTTTTTTTTCT
1 TTCTCTTTTTCTT-T
4707 TTC-CTTTTTCTTT
1 TTCTCTTTTTCTTT
4720 CATCACATAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 1 0.04
14 20 0.80
15 4 0.16
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (14 bp):
TTCTCTTTTTCTTT
Found at i:5051 original size:145 final size:145
Alignment explanation
Indices: 4788--5081 Score: 570
Period size: 145 Copynumber: 2.0 Consensus size: 145
4778 CCCAAAACAT
*
4788 TTTGCAAAAAAGGACTGTTATTTTTGTTGAGGAAAAATCTCCTCTCGAATGTCCTCACAAAATCA
1 TTTGCAAAAAAGGACTGTTATTTTTGTTGAGGAAAAATCTCCTCTCGAAGGTCCTCACAAAATCA
4853 AAGATGGACTTTTATTAGGCACGTAATGTAGGCTAGGGTTTTGGGTTGCCAAAGAAAGGATATAA
66 AAGATGGACTTTTATTAGGCACGTAATGTAGGCTAGGGTTTTGGGTTGCCAAAGAAAGGATATAA
*
4918 CGGCTCAACAATGTG
131 CGACTCAACAATGTG
4933 TTTGCAAAAAAGGACTGTTATTTTTGTTGAGGAAAAATCTCCTCTCGAAGGTCCTCACAAAATCA
1 TTTGCAAAAAAGGACTGTTATTTTTGTTGAGGAAAAATCTCCTCTCGAAGGTCCTCACAAAATCA
4998 AAGATGGACTTTTATTAGGCACGTAATGTAGGCTAGGGTTTTGGGTTGCCAAAGAAAGGATATAA
66 AAGATGGACTTTTATTAGGCACGTAATGTAGGCTAGGGTTTTGGGTTGCCAAAGAAAGGATATAA
5063 CGACTCAACAATGTG
131 CGACTCAACAATGTG
5078 TTTG
1 TTTG
5082 AGGATATTTC
Statistics
Matches: 147, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
145 147 1.00
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (145 bp):
TTTGCAAAAAAGGACTGTTATTTTTGTTGAGGAAAAATCTCCTCTCGAAGGTCCTCACAAAATCA
AAGATGGACTTTTATTAGGCACGTAATGTAGGCTAGGGTTTTGGGTTGCCAAAGAAAGGATATAA
CGACTCAACAATGTG
Found at i:5200 original size:20 final size:20
Alignment explanation
Indices: 5172--5219 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
5162 TCACTCTTCC
*
5172 TTTCACTTTTA-TCTTCAATT
1 TTTCACTTTCACT-TTCAATT
*
5192 TTTCCCTTTCACTTTCAA-T
1 TTTCACTTTCACTTTCAATT
5211 TTTCACTTT
1 TTTCACTTT
5220 TTCTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 9 0.38
20 14 0.58
21 1 0.04
ACGTcount: A:0.17, C:0.25, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTCACTTTCACTTTCAATT
Done.