Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009001.1 Corchorus capsularis cultivar CVL-1 contig09022, 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: 40596
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.31
Found at i:2187 original size:3 final size:3
Alignment explanation
Indices: 2181--2219 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
2171 TAATCTTCTA
*
2181 ATT ATT ATT ATT ATT TTT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2220 TTGGTATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
ATT
Found at i:2475 original size:27 final size:28
Alignment explanation
Indices: 2425--2497 Score: 96
Period size: 27 Copynumber: 2.6 Consensus size: 28
2415 AGATGGACTC
*
2425 AAAATGACCGAAAT-CTCCCTTGAATGCA
1 AAAATGACCAAAATGC-CCCTTGAATGCA
**
2453 AAAATGACCAAAATGCCCC-TGAATGTG
1 AAAATGACCAAAATGCCCCTTGAATGCA
2480 AAAATGACCAAAATGCCC
1 AAAATGACCAAAATGCCC
2498 TTAGGTGACC
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
27 24 0.59
28 16 0.39
29 1 0.02
ACGTcount: A:0.42, C:0.25, G:0.15, T:0.18
Consensus pattern (28 bp):
AAAATGACCAAAATGCCCCTTGAATGCA
Found at i:2991 original size:70 final size:69
Alignment explanation
Indices: 2895--3165 Score: 371
Period size: 71 Copynumber: 3.9 Consensus size: 69
2885 TGGATCAATC
* * *
2895 GGAAACAACTGATGAAAAACCGCCCTGGGTCGACTGAATCGATCATTTTGACATAAACTTGGATA
1 GGAAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTGGATA
2960 AACAT
66 AAC-T
* * * * *
2965 GGAAACTACTGAAGAAAGACCACCCTGGGTCGACCGAATCGATCATTCCGACACAAACTTTGGAT
1 GGAAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAAC-TTGGAT
3030 AAACT
65 AAACT
*
3035 CAGAAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTGGAA
1 -GGAAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTGG-A
3100 TAAACTT
64 TAAAC-T
* * * * *
3107 GAAAATAACTAAAGAAAGACCGCCCTAGGTCGATTGAATCGATCATTCTGACATAAACT
1 GGAAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACT
3166 GAAGAAAGAC
Statistics
Matches: 177, Mismatches: 20, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
70 55 0.31
71 121 0.68
72 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (69 bp):
GGAAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTGGATA
AACT
Found at i:3249 original size:36 final size:36
Alignment explanation
Indices: 3145--3252 Score: 110
Period size: 36 Copynumber: 3.0 Consensus size: 36
3135 GTCGATTGAA
* * *
3145 TCGATCATTCTGACATAAACTGAAGAAAGACCGCCC
1 TCGATCATTCCGACATAAACTGAAGAAAAACCACCC
* * * * * * *
3181 TGGGTCA-ACCAAGATAGACTAAAGAAAAACCACCC
1 TCGATCATTCCGACATAAACTGAAGAAAAACCACCC
*
3216 TCGATCATTCCGACATATACTGAAGAAAAACCACCC
1 TCGATCATTCCGACATAAACTGAAGAAAAACCACCC
3252 T
1 T
3253 GGGTCAACTG
Statistics
Matches: 54, Mismatches: 17, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
35 25 0.46
36 29 0.54
ACGTcount: A:0.40, C:0.28, G:0.15, T:0.18
Consensus pattern (36 bp):
TCGATCATTCCGACATAAACTGAAGAAAAACCACCC
Found at i:3437 original size:141 final size:141
Alignment explanation
Indices: 3233--3546 Score: 477
Period size: 141 Copynumber: 2.2 Consensus size: 141
3223 TTCCGACATA
* * * *
3233 TACTGAAGAAAAACCACCCTGGGTCAACTGAATCGATCATTCTGACATAAACTTGGATAAACTTG
1 TACTGAAGAAAGACCACCCTGGGTCAACCGAATCGATCATTCCGACACAAACTTGGATAAACTTG
*
3298 AAAACAATTGAAGAAAGACCGCCCTGAGTCAACTAAATCGATCATTCTTACATAAACTTGG-ATA
66 AAAACAATTGAAGAAAGACCGCCCTGAGTCAACTAAATCGATCATTCTGACATAAACTTGGAATA
*
3362 AACATGGAAAC
131 AACATGAAAAC
* * *
3373 TACTGAAGAAAGACCACCCTGGGTCGACCGAATCGTTCCTTCCGACACAAACTTTGGATAAACTT
1 TACTGAAGAAAGACCACCCTGGGTCAACCGAATCGATCATTCCGACACAAAC-TTGGATAAACTT
* * *
3438 GGAAACAATTGAAGAAAGACCGCCCTGGGTCAACTGAATCGATCATTCTGACATAAACTTGGAAT
65 GAAAACAATTGAAGAAAGACCGCCCTGAGTCAACTAAATCGATCATTCTGACATAAACTTGGAAT
*
3503 AAACTTGAAAAC
130 AAACATGAAAAC
* *
3515 AACTGAAGAAAGACCGCCCTGGGTCAACCGAA
1 TACTGAAGAAAGACCACCCTGGGTCAACCGAA
3547 ATGAATTGTA
Statistics
Matches: 156, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
140 45 0.29
141 70 0.45
142 41 0.26
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.21
Consensus pattern (141 bp):
TACTGAAGAAAGACCACCCTGGGTCAACCGAATCGATCATTCCGACACAAACTTGGATAAACTTG
AAAACAATTGAAGAAAGACCGCCCTGAGTCAACTAAATCGATCATTCTGACATAAACTTGGAATA
AACATGAAAAC
Found at i:3457 original size:71 final size:70
Alignment explanation
Indices: 3234--3542 Score: 438
Period size: 70 Copynumber: 4.4 Consensus size: 70
3224 TCCGACATAT
* *
3234 ACTGAAGAAAAACCACCCTGGGTCAACTGAATCGATCATTCTGACATAAACTTGGATAAACTTGA
1 ACTGAAGAAAGACCGCCCTGGGTCAACTGAATCGATCATTCTGACATAAACTTGGATAAACTTGA
3299 AAACA
66 AAACA
* * * * * *
3304 ATTGAAGAAAGACCGCCCTGAGTCAACTAAATCGATCATTCTTACATAAACTTGGATAAACATGG
1 ACTGAAGAAAGACCGCCCTGGGTCAACTGAATCGATCATTCTGACATAAACTTGGATAAACTTGA
*
3369 AAACT
66 AAACA
* * * * * * *
3374 ACTGAAGAAAGACCACCCTGGGTCGACCGAATCGTTCCTTCCGACACAAACTTTGGATAAACTTG
1 ACTGAAGAAAGACCGCCCTGGGTCAACTGAATCGATCATTCTGACATAAAC-TTGGATAAACTTG
*
3439 GAAACA
65 AAAACA
*
3445 ATTGAAGAAAGACCGCCCTGGGTCAACTGAATCGATCATTCTGACATAAACTTGGAATAAACTTG
1 ACTGAAGAAAGACCGCCCTGGGTCAACTGAATCGATCATTCTGACATAAACTTGG-ATAAACTTG
3510 AAAACA
65 AAAACA
3516 ACTGAAGAAAGACCGCCCTGGGTCAAC
1 ACTGAAGAAAGACCGCCCTGGGTCAAC
3543 CGAAATGAAT
Statistics
Matches: 205, Mismatches: 32, Indels: 3
0.85 0.13 0.01
Matches are distributed among these distances:
70 105 0.51
71 100 0.49
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.21
Consensus pattern (70 bp):
ACTGAAGAAAGACCGCCCTGGGTCAACTGAATCGATCATTCTGACATAAACTTGGATAAACTTGA
AAACA
Found at i:3650 original size:35 final size:35
Alignment explanation
Indices: 3593--3727 Score: 119
Period size: 35 Copynumber: 3.8 Consensus size: 35
3583 ATCGATCATT
*
3593 CTGAAATAAAACCT-AAGAAAGACCACCCTGGGTAAA
1 CTGAAAT-AAA-CTGAAGAAAGACCGCCCTGGGTAAA
* * **
3629 CTGAAATAAGCTGAAGAAAGACCGCCCTGAGTCGA
1 CTGAAATAAACTGAAGAAAGACCGCCCTGGGTAAA
* * * * *
3664 CTGAAATAAACTCAAGAAAAATCGCCCTGGATTAA
1 CTGAAATAAACTGAAGAAAGACCGCCCTGGGTAAA
* * * *
3699 TTGAAATTATCTGAAGAAAGATCGCCCTG
1 CTGAAATAAACTGAAGAAAGACCGCCCTG
3728 AATTAATTAA
Statistics
Matches: 80, Mismatches: 18, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
34 2 0.03
35 71 0.89
36 7 0.09
ACGTcount: A:0.41, C:0.21, G:0.19, T:0.19
Consensus pattern (35 bp):
CTGAAATAAACTGAAGAAAGACCGCCCTGGGTAAA
Found at i:4894 original size:16 final size:17
Alignment explanation
Indices: 4875--4915 Score: 66
Period size: 16 Copynumber: 2.5 Consensus size: 17
4865 CATCATTCAT
4875 TTTTCTTTTTTC-CTTC
1 TTTTCTTTTTTCTCTTC
*
4891 TTTTCTTTTTTCTTTTC
1 TTTTCTTTTTTCTCTTC
4908 TTTTCTTT
1 TTTTCTTT
4916 CATCATTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 12 0.52
17 11 0.48
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (17 bp):
TTTTCTTTTTTCTCTTC
Found at i:4905 original size:12 final size:12
Alignment explanation
Indices: 4874--4911 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
4864 TCATCATTCA
4874 TTTTTCTTTT-T
1 TTTTTCTTTTCT
**
4885 TCCTTCTTTTCT
1 TTTTTCTTTTCT
4897 TTTTTCTTTTCT
1 TTTTTCTTTTCT
4909 TTT
1 TTT
4912 CTTTCATCAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
11 8 0.36
12 14 0.64
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTTCTTTTCT
Found at i:5750 original size:45 final size:44
Alignment explanation
Indices: 5683--5800 Score: 173
Period size: 44 Copynumber: 2.6 Consensus size: 44
5673 TGGAAAACCC
*
5683 TTTTATCAAAACCCTCTTGAAAACCATGATTCTTCTTGAAAAAACA
1 TTTTATCAAAA-CCTTTTGAAAACCATGATTCTTCTTG-AAAAACA
* * *
5729 TTTTATCAAAACCTTTTGAAAACCACGATTCTTTTTGAAAACCA
1 TTTTATCAAAACCTTTTGAAAACCATGATTCTTCTTGAAAAACA
*
5773 TTTTATCAAAACCTTTTGAAAGCCATGA
1 TTTTATCAAAACCTTTTGAAAACCATGA
5801 CTATTTTTTG
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
44 32 0.48
45 23 0.35
46 11 0.17
ACGTcount: A:0.37, C:0.20, G:0.08, T:0.35
Consensus pattern (44 bp):
TTTTATCAAAACCTTTTGAAAACCATGATTCTTCTTGAAAAACA
Found at i:5809 original size:45 final size:44
Alignment explanation
Indices: 5675--5818 Score: 191
Period size: 45 Copynumber: 3.2 Consensus size: 44
5665 TGCAACTTTG
* * *
5675 GAAAACCCTTTTATCAAAACCCTCTTGAAAACCATGATTCTTCTT
1 GAAAACCATTTTATCAAAA-CCTTTTGAAAACCATGATTCTTTTT
* *
5720 GAAAAAACATTTTATCAAAACCTTTTGAAAACCACGATTCTTTTT
1 G-AAAACCATTTTATCAAAACCTTTTGAAAACCATGATTCTTTTT
*
5765 GAAAACCATTTTATCAAAACCTTTTGAAAGCCATGACTAT-TTTTT
1 GAAAACCATTTTATCAAAACCTTTTGAAAACCATGA-T-TCTTTTT
5810 GAAAACCAT
1 GAAAACCAT
5819 CGTTGCTCTT
Statistics
Matches: 88, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
44 32 0.36
45 39 0.44
46 17 0.19
ACGTcount: A:0.38, C:0.21, G:0.08, T:0.34
Consensus pattern (44 bp):
GAAAACCATTTTATCAAAACCTTTTGAAAACCATGATTCTTTTT
Found at i:5855 original size:19 final size:18
Alignment explanation
Indices: 5827--5875 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
5817 ATCGTTGCTC
*
5827 TTTCTCTTTTCCTTTCTTT
1 TTTCTTTTTTCCTTT-TTT
*
5846 TTTCTTTTTTCATTTTTT
1 TTTCTTTTTTCCTTTTTT
*
5864 TTTCATTTTTCC
1 TTTCTTTTTTCC
5876 ACTTATCCCC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
18 13 0.50
19 13 0.50
ACGTcount: A:0.04, C:0.20, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTCTTTTTTCCTTTTTT
Found at i:6230 original size:14 final size:14
Alignment explanation
Indices: 6211--6237 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
6201 ACAGTGGAAA
6211 ATATGTATATATAT
1 ATATGTATATATAT
6225 ATATGTATATATA
1 ATATGTATATATA
6238 AAAAAGCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (14 bp):
ATATGTATATATAT
Found at i:11089 original size:3 final size:3
Alignment explanation
Indices: 11083--11121 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
11073 AAATCTTCTA
11083 ATT 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 ATT
11122 TTGGTATTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:11377 original size:27 final size:27
Alignment explanation
Indices: 11355--11428 Score: 139
Period size: 27 Copynumber: 2.7 Consensus size: 27
11345 CTTGAATGCA
11355 AAAATGACCAAAATGCCCCTGAATGTG
1 AAAATGACCAAAATGCCCCTGAATGTG
*
11382 AAAATGACCAAAATACCCCTGAATGTG
1 AAAATGACCAAAATGCCCCTGAATGTG
11409 AAAATGACCAAAATGCCCCT
1 AAAATGACCAAAATGCCCCT
11429 AGGTGACCCT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.43, C:0.24, G:0.15, T:0.18
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCCTGAATGTG
Found at i:15860 original size:22 final size:24
Alignment explanation
Indices: 15835--15878 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
15825 AAGCAGCATA
15835 TGAT-AAAATAAT-ATGAATATAT
1 TGATGAAAATAATGATGAATATAT
* *
15857 TGATGAATATATTGATGAATAT
1 TGATGAAAATAATGATGAATAT
15879 TACCTTATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 4 0.22
23 6 0.33
24 8 0.44
ACGTcount: A:0.48, C:0.00, G:0.14, T:0.39
Consensus pattern (24 bp):
TGATGAAAATAATGATGAATATAT
Found at i:15879 original size:10 final size:12
Alignment explanation
Indices: 15847--15878 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
15837 ATAAAATAAT
15847 ATGAATATATTG
1 ATGAATATATTG
15859 ATGAATATATTG
1 ATGAATATATTG
15871 ATGAATAT
1 ATGAATAT
15879 TACCTTATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.16, T:0.41
Consensus pattern (12 bp):
ATGAATATATTG
Found at i:29271 original size:22 final size:22
Alignment explanation
Indices: 29241--29285 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
29231 TTAATACAAC
29241 AACACAATATTATACACTTGAA
1 AACACAATATTATACACTTGAA
*
29263 AACAGAATATTATACACTTGAA
1 AACACAATATTATACACTTGAA
29285 A
1 A
29286 CTGCATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.51, C:0.16, G:0.07, T:0.27
Consensus pattern (22 bp):
AACACAATATTATACACTTGAA
Found at i:38915 original size:75 final size:75
Alignment explanation
Indices: 38792--38943 Score: 250
Period size: 75 Copynumber: 2.0 Consensus size: 75
38782 TTATCTAGAC
* *
38792 TGTGAGCAAAGGAATGATGAGTTTTAATCAAAAGATGTTTCAAAATCAGTTTTAATCCAAGAAAT
1 TGTGAGCAAAAGAATGATGAGTTTTAATCAAAAGATGTTTCAAAATCAGTTTTAATCAAAGAAAT
* *
38857 GGTTTCGAGG
66 GATTTCAAGG
* *
38867 TGTGAGCAAAAGAATGATGAGTTTTAATCAAAAGATGTTTCAAAATCAGTTTTAGTCAAAGCAAT
1 TGTGAGCAAAAGAATGATGAGTTTTAATCAAAAGATGTTTCAAAATCAGTTTTAATCAAAGAAAT
38932 GATTTCAAGG
66 GATTTCAAGG
38942 TG
1 TG
38944 ATTGAATCCA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
75 71 1.00
ACGTcount: A:0.38, C:0.09, G:0.22, T:0.31
Consensus pattern (75 bp):
TGTGAGCAAAAGAATGATGAGTTTTAATCAAAAGATGTTTCAAAATCAGTTTTAATCAAAGAAAT
GATTTCAAGG
Found at i:39365 original size:22 final size:21
Alignment explanation
Indices: 39340--39382 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
39330 GAAAAGCGAA
39340 AAGAAA-AAAAAGAAAGAAAAAG
1 AAGAAAGAAAAAG--AGAAAAAG
39362 AAGAAAGAAAAAGAGAAAAAG
1 AAGAAAGAAAAAGAGAAAAAG
39383 CAACGATGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 8 0.40
22 6 0.30
23 6 0.30
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (21 bp):
AAGAAAGAAAAAGAGAAAAAG
Found at i:39374 original size:13 final size:13
Alignment explanation
Indices: 39339--39379 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
39329 TGAAAAGCGA
*
39339 AAAGAAAAAAAAG
1 AAAGAAAAAGAAG
39352 AAAGAAAAAGAAG
1 AAAGAAAAAGAAG
39365 AAAGAAAAAG-AG
1 AAAGAAAAAGAAG
39377 AAA
1 AAA
39380 AAGCAACGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
12 5 0.19
13 22 0.81
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAGAAG
Done.