Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011529.1 Corchorus capsularis cultivar CVL-1 contig11550, 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: 18939
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Found at i:25 original size:2 final size:2
Alignment explanation
Indices: 20--54 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
10 TTTACTGTTG
20 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
55 GCTTGAGTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1895 original size:69 final size:69
Alignment explanation
Indices: 1764--2405 Score: 838
Period size: 70 Copynumber: 9.2 Consensus size: 69
1754 CTCATTGAAC
* * * * * * *
1764 TTGGCTTATGGAAAAACCCATGTTGCTTGGATGGAACCAAAGCTTGAATTGACTTGTGTGGAAAC
1 TTGGCTTGTGGAAAAGCCCCTGCTGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAAC
1829 GAGT
66 GAGT
* * * *
1833 TTGGTTTGTGGAAAAGCCCCTGCTGCTTGGATAGAACCAAGGCTTGAACTAACTCGTATGGAAAC
1 TTGGCTTGTGGAAAAGCCCCTGCTGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAAC
1898 GAGT
66 GAGT
* * * *
1902 TTGGCTTGTGGAAAAGGCCCTGCTGCTTGGATAGAACCAAGGCTTGAACTGGCTCGTATGGAAAC
1 TTGGCTTGTGGAAAAGCCCCTGCTGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAAC
*
1967 AAGT
66 GAGT
* * * *
1971 TTGCCTTGTGGAAAAGCCCCTGAATGCTTGGATGGAACCAAAGCTTGAACTGACTCGCATGTAAA
1 TTGGCTTGTGGAAAAGCCCCTG-CTGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAA
2036 CGAGT
65 CGAGT
* * * * *
2041 TTGGCTTGTGAAAAAGGCCCTGCTGCTTGGATAGAACCAAGGCTTGAACTGGCTCGTATGGAAAC
1 TTGGCTTGTGGAAAAGCCCCTGCTGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAAC
*
2106 AAGT
66 GAGT
* * *
2110 TTGCCTTGTGGAAAAGCCCCTGAATGCTTGGATGGAACCAAAGCTTGAACTGACTCGCATGGAAA
1 TTGGCTTGTGGAAAAGCCCCTG-CTGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAA
2175 CGAGT
65 CGAGT
* *
2180 TTGGCTTGTGGAAAAGCCCTTGCATTCTTGGATGGAACCAAAGCTTGAACT-ATCTCGTATGGAA
1 TTGGCTTGTGGAAAAGCCCCTGC-TGCTTGGATGGAACCAAAGCTTGAACTGA-CTCGTATGGAA
2244 ACGAGT
64 ACGAGT
* *
2250 TTGGCTTGTGGAAAAGCCCCTGCACGCTTGGATGGAAGCAAAGCTTGAACT-ATCTCGTATGGAA
1 TTGGCTTGTGGAAAAGCCCCTGC-TGCTTGGATGGAACCAAAGCTTGAACTGA-CTCGTATGGAA
2314 ACGAGT
64 ACGAGT
* * * * **
2320 CTGGCTTGTGGAAAAGCCGCTCCACGCTTGGATGGAACCAAAGCTTGAACTGACTCGTACAGAAA
1 TTGGCTTGTGGAAAAGCCCCTGC-TGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAA
2385 CGAGT
65 CGAGT
* *
2390 TTGACTTATGGAAAAG
1 TTGGCTTGTGGAAAAG
2406 TCAAAGCATT
Statistics
Matches: 506, Mismatches: 62, Indels: 9
0.88 0.11 0.02
Matches are distributed among these distances:
69 202 0.40
70 303 0.60
71 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (69 bp):
TTGGCTTGTGGAAAAGCCCCTGCTGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAAC
GAGT
Found at i:2061 original size:139 final size:139
Alignment explanation
Indices: 1764--2405 Score: 855
Period size: 139 Copynumber: 4.6 Consensus size: 139
1754 CTCATTGAAC
* * * * * *
1764 TTGGCTTATGGAAAAACCCATG-TTGCTTGGATGGAACCAAAGCTTGAATTGACTTGTGTGGAAA
1 TTGGCTTGTGGAAAAGCCC-TGCATGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAA
** * * * * *
1828 CGAGTTTGGTTTGTGGAAAAGCCCCTG-CTGCTTGGATAGAACCAAGGCTTGAACTAACTCGTAT
65 CGAGTTTGCCTTGTGGAAAAGCCCCTGAATGCTTGGATGGAACCAAAGCTTGAACTGACTCGCAT
1892 GGAAACGAGT
130 GGAAACGAGT
* * *
1902 TTGGCTTGTGGAAAAGGCCCTGC-TGCTTGGATAGAACCAAGGCTTGAACTGGCTCGTATGGAAA
1 TTGGCTTGTGGAAAA-GCCCTGCATGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAA
*
1966 CAAGTTTGCCTTGTGGAAAAGCCCCTGAATGCTTGGATGGAACCAAAGCTTGAACTGACTCGCAT
65 CGAGTTTGCCTTGTGGAAAAGCCCCTGAATGCTTGGATGGAACCAAAGCTTGAACTGACTCGCAT
*
2031 GTAAACGAGT
130 GGAAACGAGT
* * * *
2041 TTGGCTTGTGAAAAAGGCCCTGC-TGCTTGGATAGAACCAAGGCTTGAACTGGCTCGTATGGAAA
1 TTGGCTTGTGGAAAA-GCCCTGCATGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAA
*
2105 CAAGTTTGCCTTGTGGAAAAGCCCCTGAATGCTTGGATGGAACCAAAGCTTGAACTGACTCGCAT
65 CGAGTTTGCCTTGTGGAAAAGCCCCTGAATGCTTGGATGGAACCAAAGCTTGAACTGACTCGCAT
2170 GGAAACGAGT
130 GGAAACGAGT
*
2180 TTGGCTTGTGGAAAAGCCCTTGCATTCTTGGATGGAACCAAAGCTTGAACT-ATCTCGTATGGAA
1 TTGGCTTGTGGAAAAGCCC-TGCATGCTTGGATGGAACCAAAGCTTGAACTGA-CTCGTATGGAA
* * * * *
2244 ACGAGTTTGGCTTGTGGAAAAGCCCCTGCACGCTTGGATGGAAGCAAAGCTTGAACT-ATCTCGT
64 ACGAGTTTGCCTTGTGGAAAAGCCCCTGAATGCTTGGATGGAACCAAAGCTTGAACTGA-CTCGC
2308 ATGGAAACGAGT
128 ATGGAAACGAGT
* * * **
2320 CTGGCTTGTGGAAAAGCCGCTCCACGCTTGGATGGAACCAAAGCTTGAACTGACTCGTACAGAAA
1 TTGGCTTGTGGAAAAGCC-CTGCATGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAA
* *
2385 CGAGTTTGACTTATGGAAAAG
65 CGAGTTTGCCTTGTGGAAAAG
2406 TCAAAGCATT
Statistics
Matches: 457, Mismatches: 38, Indels: 16
0.89 0.07 0.03
Matches are distributed among these distances:
138 79 0.17
139 199 0.44
140 177 0.39
141 2 0.00
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (139 bp):
TTGGCTTGTGGAAAAGCCCTGCATGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAAC
GAGTTTGCCTTGTGGAAAAGCCCCTGAATGCTTGGATGGAACCAAAGCTTGAACTGACTCGCATG
GAAACGAGT
Found at i:2958 original size:41 final size:41
Alignment explanation
Indices: 2913--2994 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 41
2903 TTTTGAAAAG
* * *
2913 CGAATTTTAATCTTGGACTCACAAATGGAATGCAATCTTAT
1 CGAATTTTAATATTGGACCCACAAATGAAATGCAATCTTAT
* * *
2954 CGAATTTTGATATTGGACCCATAAATGAAATGCAGTCTTAT
1 CGAATTTTAATATTGGACCCACAAATGAAATGCAATCTTAT
2995 TATAAAACTT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (41 bp):
CGAATTTTAATATTGGACCCACAAATGAAATGCAATCTTAT
Found at i:3303 original size:10 final size:10
Alignment explanation
Indices: 3277--3351 Score: 75
Period size: 10 Copynumber: 7.4 Consensus size: 10
3267 TTTTCTTCAT
3277 TTTC-TTTT-
1 TTTCTTTTTC
3285 TTTCTTTTTC
1 TTTCTTTTTC
3295 TTTCATTTTTTC
1 TTTC--TTTTTC
*
3307 TCTCATTTTTTC
1 TTTC--TTTTTC
3319 TTTCTTTTTC
1 TTTCTTTTTC
*
3329 TTTTTTTTTC
1 TTTCTTTTTC
3339 TTT-TTTTTC
1 TTTCTTTTTC
3348 TTTC
1 TTTC
3352 AATTTTTTAC
Statistics
Matches: 59, Mismatches: 3, Indels: 8
0.84 0.04 0.11
Matches are distributed among these distances:
8 4 0.07
9 13 0.22
10 22 0.37
12 20 0.34
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTCTTTTTC
Found at i:3318 original size:30 final size:29
Alignment explanation
Indices: 3282--3351 Score: 88
Period size: 30 Copynumber: 2.4 Consensus size: 29
3272 TTCATTTTCT
3282 TTTTTTCTTT-TTCTTTCATTTTTTCTCTCA
1 TTTTTTCTTTCTT-TTTCATTTTTTCTCT-A
* * *
3312 TTTTTTCTTTCTTTTTCTTTTTTTTTCTT
1 TTTTTTCTTTCTTTTTCATTTTTTCTCTA
3341 TTTTTTCTTTC
1 TTTTTTCTTTC
3352 AATTTTTTAC
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 11 0.31
30 23 0.64
31 2 0.06
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (29 bp):
TTTTTTCTTTCTTTTTCATTTTTTCTCTA
Found at i:4006 original size:19 final size:19
Alignment explanation
Indices: 3962--4016 Score: 53
Period size: 19 Copynumber: 3.0 Consensus size: 19
3952 TAGGCCAAGC
3962 TTTTT-CTTTTCTTT-TTT-
1 TTTTTCCTTTT-TTTCTTTG
*
3979 TTTTCCCTTTTTTTCTTTG
1 TTTTTCCTTTTTTTCTTTG
* *
3998 TTTTTCCTTCTTTACTTTG
1 TTTTTCCTTTTTTTCTTTG
4017 AATGCGAAGG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
17 7 0.23
18 8 0.26
19 16 0.52
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.76
Consensus pattern (19 bp):
TTTTTCCTTTTTTTCTTTG
Found at i:4601 original size:45 final size:44
Alignment explanation
Indices: 4551--4651 Score: 175
Period size: 45 Copynumber: 2.3 Consensus size: 44
4541 CACAACTTTG
4551 GAAAACCATTTTATCAAAACCTTTTGAAAACCATGACTCTTTCT
1 GAAAACCATTTTATCAAAACCTTTTGAAAACCATGACTCTTTCT
* *
4595 GAAAAACCGTTTTATCAAAACCTTTTGAAAACCATGACTCTTTTT
1 G-AAAACCATTTTATCAAAACCTTTTGAAAACCATGACTCTTTCT
4640 GAAAACCATTTT
1 GAAAACCATTTT
4652 TGCTTTTTCT
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
44 11 0.21
45 42 0.79
ACGTcount: A:0.37, C:0.21, G:0.08, T:0.35
Consensus pattern (44 bp):
GAAAACCATTTTATCAAAACCTTTTGAAAACCATGACTCTTTCT
Found at i:5177 original size:75 final size:75
Alignment explanation
Indices: 5081--5225 Score: 236
Period size: 75 Copynumber: 1.9 Consensus size: 75
5071 ATTTTAGTCC
* * * * *
5081 CCTCGAAATCATTGCTTTGATTGAAACTGATTTTGAAATCTATTTTGATTAAAACTCATCATTCT
1 CCTCGAAACCATTGCTTTGATTGAAAATGATTTTGAAACCTATTTTGATTAAAACCCATCATTCC
5146 TTTGCCTACT
66 TTTGCCTACT
*
5156 CCTCGAAACCATTGCTTTGATTGAAAATGATTTTGAAACCTGTTTTGATTAAAACCCATCATTCC
1 CCTCGAAACCATTGCTTTGATTGAAAATGATTTTGAAACCTATTTTGATTAAAACCCATCATTCC
5221 TTTGC
66 TTTGC
5226 TCACAGTCTA
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
75 64 1.00
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.40
Consensus pattern (75 bp):
CCTCGAAACCATTGCTTTGATTGAAAATGATTTTGAAACCTATTTTGATTAAAACCCATCATTCC
TTTGCCTACT
Found at i:5372 original size:3 final size:3
Alignment explanation
Indices: 5366--5402 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
5356 TTTTATCCCT
5366 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
5403 CTAATGTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5522 original size:66 final size:66
Alignment explanation
Indices: 5416--5548 Score: 257
Period size: 66 Copynumber: 2.0 Consensus size: 66
5406 ATGTAAACTC
5416 ATGCAAATATTTACCAAAGAAGTCTTTTATCTACCAAATGCATATTTCAAAATAAATAAGAAAGT
1 ATGCAAATATTTACCAAAGAAGTCTTTTATCTACCAAATGCATATTTCAAAATAAATAAGAAAGT
5481 A
66 A
*
5482 ATGCAAATGTTTACCAAAGAAGTCTTTTATCTACCAAATGCATATTTCAAAATAAATAAGAAAGT
1 ATGCAAATATTTACCAAAGAAGTCTTTTATCTACCAAATGCATATTTCAAAATAAATAAGAAAGT
5547 A
66 A
5548 A
1 A
5549 GGAAAATGCC
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.47, C:0.14, G:0.10, T:0.30
Consensus pattern (66 bp):
ATGCAAATATTTACCAAAGAAGTCTTTTATCTACCAAATGCATATTTCAAAATAAATAAGAAAGT
A
Found at i:7472 original size:6 final size:6
Alignment explanation
Indices: 7457--7488 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
7447 AAAGCAAAAC
7457 AAAT-T AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAATCT AAA
7489 GCAGATTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (6 bp):
AAATCT
Found at i:7503 original size:13 final size:13
Alignment explanation
Indices: 7485--7519 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
7475 AATCTAAATC
*
7485 TAAAGCAGATTAA
1 TAAAGCAAATTAA
7498 TAAAGCAAATTAA
1 TAAAGCAAATTAA
7511 TAAAGCAAA
1 TAAAGCAAA
7520 CAATAATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.60, C:0.09, G:0.11, T:0.20
Consensus pattern (13 bp):
TAAAGCAAATTAA
Found at i:8407 original size:10 final size:10
Alignment explanation
Indices: 8392--8419 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
8382 AGATGAGGAC
8392 TCTGGAATTT
1 TCTGGAATTT
8402 TCTGGAATTT
1 TCTGGAATTT
8412 TCTGGAAT
1 TCTGGAAT
8420 CTGGCAGCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.21, C:0.11, G:0.21, T:0.46
Consensus pattern (10 bp):
TCTGGAATTT
Found at i:10638 original size:21 final size:21
Alignment explanation
Indices: 10614--10670 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
10604 GTGGTGGCGC
*
10614 GGCATGGTACGCGGATGGCTT
1 GGCATGGTACGCGGATGGCTG
* **
10635 GGCAAGGGCCG-GGCATGGCTG
1 GGCATGGTACGCGG-ATGGCTG
*
10656 GGCATGGTGCGCGGA
1 GGCATGGTACGCGGA
10671 CAAGGCCGGG
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
20 2 0.07
21 23 0.85
22 2 0.07
ACGTcount: A:0.14, C:0.21, G:0.49, T:0.16
Consensus pattern (21 bp):
GGCATGGTACGCGGATGGCTG
Found at i:14218 original size:50 final size:49
Alignment explanation
Indices: 14121--14218 Score: 108
Period size: 50 Copynumber: 2.0 Consensus size: 49
14111 GGAAAAACGG
* ** *
14121 AAAAGGAAAATTAATTTTTTTTAAAGAAAAATCGGAAACCCTAAAATTA
1 AAAAGGAAAAATAATTTTTTTTAAAGAAAAATCGGAAAAACGAAAATTA
* * *
14170 AAAACGGAAAAATAATTTTTTTTTTAGGAAAAA-CGGAAAAACGGAAATT
1 AAAA-GGAAAAATAA-TTTTTTTTAAAGAAAAATCGGAAAAACGAAAATT
14219 TTTTTTTTCG
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
49 4 0.10
50 21 0.52
51 15 0.38
ACGTcount: A:0.52, C:0.07, G:0.13, T:0.28
Consensus pattern (49 bp):
AAAAGGAAAAATAATTTTTTTTAAAGAAAAATCGGAAAAACGAAAATTA
Found at i:18674 original size:38 final size:38
Alignment explanation
Indices: 18632--18727 Score: 106
Period size: 39 Copynumber: 2.5 Consensus size: 38
18622 TTTTGACGAG
18632 ATCTTTCCCTAAATTGAAGACTTTGAAA-ACTGGATGGA
1 ATCTTTCCCTAAATTGAA-ACTTTGAAAGACTGGATGGA
* ** *
18670 ATCTTTCCCTAAATCT-AAAATTAAAAAAGACTGGATGGG
1 ATCTTTCCCTAAAT-TGAAACTT-TGAAAGACTGGATGGA
*
18709 ATTTTTCCCTAAATTGAAA
1 ATCTTTCCCTAAATTGAAA
18728 ACATTGAAGA
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
37 3 0.06
38 20 0.41
39 26 0.53
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.32
Consensus pattern (38 bp):
ATCTTTCCCTAAATTGAAACTTTGAAAGACTGGATGGA
Done.