Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020244.1 Corchorus olitorius cultivar O-4 contig20277, 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: 58057
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:461 original size:49 final size:47
Alignment explanation
Indices: 392--532 Score: 162
Period size: 49 Copynumber: 3.0 Consensus size: 47
382 TCAAAGCAAT
* *
392 CTTTTACTTTTC--TGCACTTTTTCTCAATTTTTGCTACAAAATTGAA
1 CTTTTAATTTTCTTTGCACTTTTTCTCAATTTTTG-GACAAAATTGAA
* * * *
438 CTTTTATTTTTAC-TTGCGTCTTTTTCTCAATTTTTAAGACAAAATTGAT
1 CTTTTAATTTT-CTTTGC-ACTTTTTCTCAATTTTT-GGACAAAATTGAA
*
487 CTTTTAATTTTCTTTGCACTTTTTATCAATTTTTGGACAAAATTGA
1 CTTTTAATTTTCTTTGCACTTTTTCTCAATTTTTGGACAAAATTGA
533 TTGGCACGCT
Statistics
Matches: 81, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
46 10 0.12
47 12 0.15
48 19 0.23
49 40 0.49
ACGTcount: A:0.25, C:0.16, G:0.08, T:0.52
Consensus pattern (47 bp):
CTTTTAATTTTCTTTGCACTTTTTCTCAATTTTTGGACAAAATTGAA
Found at i:5468 original size:18 final size:18
Alignment explanation
Indices: 5441--5476 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
5431 AGTAGTTTTT
*
5441 GGTAGATTTTTTTAAATG
1 GGTAGATTTTTTAAAATG
*
5459 GGTAGTTTTTTTAAAATG
1 GGTAGATTTTTTAAAATG
5477 ATATAAATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.22, T:0.50
Consensus pattern (18 bp):
GGTAGATTTTTTAAAATG
Found at i:6013 original size:5 final size:5
Alignment explanation
Indices: 6005--6034 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
5995 TGAAGTAATT
*
6005 AAAGG AAAGG GAAGG AAAGG AAAGG AAAGG
1 AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG
6035 GGAGGGAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (5 bp):
AAAGG
Found at i:7013 original size:15 final size:15
Alignment explanation
Indices: 6993--7027 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
6983 TTTTTTATAA
6993 AAAAAT-TATTTTTTT
1 AAAAATATA-TTTTTT
7008 AAAAATATATTTTTT
1 AAAAATATATTTTTT
7023 AAAAA
1 AAAAA
7028 AAATTGGGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 17 0.89
16 2 0.11
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
AAAAATATATTTTTT
Found at i:8222 original size:19 final size:18
Alignment explanation
Indices: 8191--8245 Score: 92
Period size: 18 Copynumber: 3.0 Consensus size: 18
8181 GTCCCTGACT
*
8191 ATTTTTTTTAAAAAAATA
1 ATTTTTTATAAAAAAATA
8209 ATTTTTTATAAAAAAATA
1 ATTTTTTATAAAAAAATA
8227 ATTTTTTTATAAAAAAATA
1 A-TTTTTTATAAAAAAATA
8246 TGACGTGGCA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
18 18 0.51
19 17 0.49
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
ATTTTTTATAAAAAAATA
Found at i:19518 original size:42 final size:43
Alignment explanation
Indices: 19467--19560 Score: 138
Period size: 45 Copynumber: 2.2 Consensus size: 43
19457 AGTGCATTAC
*
19467 CTAA-ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAA
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAA
*
19508 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAA
19553 CTAATATT
1 CTAATATT
19561 AATTGTTGTT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
45 37 0.79
ACGTcount: A:0.39, C:0.22, G:0.04, T:0.34
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAA
Found at i:27931 original size:36 final size:36
Alignment explanation
Indices: 27891--27964 Score: 139
Period size: 36 Copynumber: 2.1 Consensus size: 36
27881 ATTTGTGTCG
*
27891 TTGCTTGATTTTCTCCATTTAACTCATTAGTGTTGA
1 TTGCTTGATTTTCTCCATTTAACTCATTAGTATTGA
27927 TTGCTTGATTTTCTCCATTTAACTCATTAGTATTGA
1 TTGCTTGATTTTCTCCATTTAACTCATTAGTATTGA
27963 TT
1 TT
27965 TTGTACCGTT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.20, C:0.16, G:0.12, T:0.51
Consensus pattern (36 bp):
TTGCTTGATTTTCTCCATTTAACTCATTAGTATTGA
Found at i:29811 original size:29 final size:29
Alignment explanation
Indices: 29755--29811 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
29745 AAAATATACC
* * ** *
29755 AAAAATAAAACATTAGGATGTAATATGAT
1 AAAAATAAAAAAGTAGGATACAAAATGAT
29784 AAAAATAAAAAAGTAGGATACAAAATGA
1 AAAAATAAAAAAGTAGGATACAAAATGA
29812 AAGCCCGTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.61, C:0.04, G:0.14, T:0.21
Consensus pattern (29 bp):
AAAAATAAAAAAGTAGGATACAAAATGAT
Found at i:31455 original size:27 final size:26
Alignment explanation
Indices: 31403--31457 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
31393 AAATTTTGAT
*
31403 ATTTAAATTTTATTTTTTATTCAAAA
1 ATTTAAATTTTATTTTTTATTAAAAA
*
31429 ATTTTAATTATTATTTTATT-TTAAAAA
1 ATTTAAATT-TTATTTT-TTATTAAAAA
31456 AT
1 AT
31458 AAATATGGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 8 0.32
27 15 0.60
28 2 0.08
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (26 bp):
ATTTAAATTTTATTTTTTATTAAAAA
Found at i:34695 original size:9 final size:11
Alignment explanation
Indices: 34670--34695 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
34660 TGCAGGTTTG
34670 CTCTCTTCCAC
1 CTCTCTTCCAC
34681 CTCTCTTCCAC
1 CTCTCTTCCAC
34692 CTCT
1 CTCT
34696 ATTTAACAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.54, G:0.00, T:0.38
Consensus pattern (11 bp):
CTCTCTTCCAC
Found at i:38311 original size:21 final size:21
Alignment explanation
Indices: 38285--38326 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
38275 AATAAGGAAA
*
38285 GTATAAAGATCATATCAGAAG
1 GTATAAAGATCAAATCAGAAG
**
38306 GTATAAATCTCAAATCAGAAG
1 GTATAAAGATCAAATCAGAAG
38327 TTGTGGAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.48, C:0.12, G:0.17, T:0.24
Consensus pattern (21 bp):
GTATAAAGATCAAATCAGAAG
Found at i:39663 original size:14 final size:14
Alignment explanation
Indices: 39646--39672 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
39636 GGTTTTTTTT
39646 AAAAGAGCCAAAAA
1 AAAAGAGCCAAAAA
39660 AAAAGAGCCAAAA
1 AAAAGAGCCAAAA
39673 TAATCATATA
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:0.70, C:0.15, G:0.15, T:0.00
Consensus pattern (14 bp):
AAAAGAGCCAAAAA
Found at i:39803 original size:20 final size:20
Alignment explanation
Indices: 39778--39816 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
39768 CATATAAAAT
*
39778 AATAATAACTAATTTTTAAA
1 AATAATAACTAATTATTAAA
39798 AATAATAACTAATTATTAA
1 AATAATAACTAATTATTAA
39817 TTTAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (20 bp):
AATAATAACTAATTATTAAA
Found at i:39927 original size:33 final size:33
Alignment explanation
Indices: 39890--39965 Score: 80
Period size: 33 Copynumber: 2.3 Consensus size: 33
39880 GCCATGGCTC
* * * *
39890 GGTCGCGAGCGGCTCGCGACTGTGCCGCAGCTT
1 GGTCGCGAGCGGCGCACGACCGAGCCGCAGCTT
* * *
39923 GGTCGTGAGCTGCGCACGACCGAGCCGCGGCTT
1 GGTCGCGAGCGGCGCACGACCGAGCCGCAGCTT
*
39956 GATCGCGAGC
1 GGTCGCGAGC
39966 CTTGGTCGCG
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.12, C:0.33, G:0.39, T:0.16
Consensus pattern (33 bp):
GGTCGCGAGCGGCGCACGACCGAGCCGCAGCTT
Found at i:40165 original size:17 final size:18
Alignment explanation
Indices: 40140--40186 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
40130 ATTGAGGTAT
*
40140 GAAAGTTTGAA-AATTGA
1 GAAAATTTGAAGAATTGA
40157 GAAAATTTGAGAGAATTGA
1 GAAAATTTGA-AGAATTGA
*
40176 -AAATTTTGAAG
1 GAAAATTTGAAG
40187 TTTGAAGGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 11 0.42
18 9 0.35
19 6 0.23
ACGTcount: A:0.47, C:0.00, G:0.23, T:0.30
Consensus pattern (18 bp):
GAAAATTTGAAGAATTGA
Found at i:41208 original size:74 final size:74
Alignment explanation
Indices: 41044--41195 Score: 243
Period size: 74 Copynumber: 2.1 Consensus size: 74
41034 GTATCTTTAA
* * * *
41044 AATAAAATTAAAAATTTCATTTGGGTTAAATTTAGTGACATTAGTTTTATATTTTATTTCTAAAA
1 AATAAAATTAAAATTTTAATTTGGGCTAAACTTAGTGACATTAGTTTTATATTTTATTTCTAAAA
41109 CCATATAAC
66 CCATATAAC
41118 AATAAAATTAAAATTTTAATTTGGGGCTAAACTTAGTGA-ATTAGTTTTATATTTTATTTCTAAA
1 AATAAAATTAAAATTTTAATTT-GGGCTAAACTTAGTGACATTAGTTTTATATTTTATTTCTAAA
*
41182 ACCCTATAAC
65 ACCATATAAC
41192 AATA
1 AATA
41196 TGTTATTAAT
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
74 58 0.81
75 14 0.19
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.42
Consensus pattern (74 bp):
AATAAAATTAAAATTTTAATTTGGGCTAAACTTAGTGACATTAGTTTTATATTTTATTTCTAAAA
CCATATAAC
Found at i:41280 original size:103 final size:102
Alignment explanation
Indices: 41126--41395 Score: 314
Period size: 103 Copynumber: 2.6 Consensus size: 102
41116 ACAATAAAAT
*
41126 TAAAA-TTTTAATTTGGGGCTAAACTTAGTG-AATTAGTTTTATATTTTATTTCTAAAACCCTAT
1 TAAAATTTTTAATTTGGGGCTAAACTTAATGAAATTAGTTTTATATTTTATTTCTAAAACCCTAT
**
41189 AACAATATGTTATTAATTTTGGAA-TTTACCCTT-AGAA
66 AACAATAAATTATTAATTTT-GAAGTTTACCCTTGA-AA
*
41226 TAAAATTTATTAATTTGGGGCTAAACTTATTGAAATTAGTTTTATATTTTATTTCTAAAACCCTA
1 TAAAATTT-TTAATTTGGGGCTAAACTTAATGAAATTAGTTTTATATTTTATTTCTAAAACCCTA
* * *
41291 TACCAATAAATTATTAATTTTTAAGTTTACTCTTGAAA
65 TAACAATAAATTATTAATTTTGAAGTTTACCCTTGAAA
* * * * *
41329 TAAAATTAAAAAATTTTAATTTGGGGCTAAACTTAAAGACATCAGTTTTATATCTAATTTCTAAA
1 TAAAA-T------TTTTAATTTGGGGCTAAACTTAATGAAATTAGTTTTATATTTTATTTCTAAA
41394 AC
59 AC
41396 TTTATAATAA
Statistics
Matches: 146, Mismatches: 12, Indels: 15
0.84 0.07 0.09
Matches are distributed among these distances:
100 5 0.03
101 2 0.01
102 24 0.16
103 65 0.45
104 2 0.01
109 46 0.32
110 2 0.01
ACGTcount: A:0.38, C:0.10, G:0.09, T:0.43
Consensus pattern (102 bp):
TAAAATTTTTAATTTGGGGCTAAACTTAATGAAATTAGTTTTATATTTTATTTCTAAAACCCTAT
AACAATAAATTATTAATTTTGAAGTTTACCCTTGAAA
Found at i:41429 original size:109 final size:109
Alignment explanation
Indices: 41235--41433 Score: 249
Period size: 109 Copynumber: 1.8 Consensus size: 109
41225 ATAAAATTTA
** * * * * *
41235 TTAATTTGGGGCTAAACTTATTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATACCAATAA
1 TTAATTTGGGGCTAAACTTAAAGAAATCAGTTTTATATCTAATTTCTAAAACCCTATAACAAAAA
*
41300 ATTATTAATTTTTAAGTTTACTCTTGAAATAAAATTAAAAAATT
66 ATTATTAATTTATAAGTTTACTCTTGAAATAAAATTAAAAAATT
* ** *
41344 TTAATTTGGGGCTAAACTTAAAGACATCAGTTTTATATCTAATTTCTAAAACTTTATAATAAAAA
1 TTAATTTGGGGCTAAACTTAAAGAAATCAGTTTTATATCTAATTTCTAAAACCCTATAACAAAAA
*
41409 ATTCTTTAATTTCAT-A-TTTACTCTT
66 ATT-ATTAATTT-ATAAGTTTACTCTT
41434 AACAATTTTG
Statistics
Matches: 75, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
109 66 0.88
110 8 0.11
111 1 0.01
ACGTcount: A:0.38, C:0.11, G:0.07, T:0.44
Consensus pattern (109 bp):
TTAATTTGGGGCTAAACTTAAAGAAATCAGTTTTATATCTAATTTCTAAAACCCTATAACAAAAA
ATTATTAATTTATAAGTTTACTCTTGAAATAAAATTAAAAAATT
Found at i:48178 original size:46 final size:46
Alignment explanation
Indices: 48122--48238 Score: 148
Period size: 45 Copynumber: 2.5 Consensus size: 46
48112 TCCATTTTAA
48122 TAAAGCCCATTTCCTCATTAGTTTCATTCAAAGTCCATTACCATTT
1 TAAAGCCCATTTCCTCATTAGTTTCATTCAAAGTCCATTACCATTT
* * * **
48168 TAGAGCCCATTTCCTCATTTAG--TAATTCAAAGTCCATTTCTTTTT
1 TAAAGCCCATTTCCTCA-TTAGTTTCATTCAAAGTCCATTACCATTT
*
48213 TAAAGACCCATTTCCTTATTAGTTTC
1 TAAAG-CCCATTTCCTCATTAGTTTC
48239 TCAAAATGTT
Statistics
Matches: 59, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
45 27 0.46
46 27 0.46
47 5 0.08
ACGTcount: A:0.26, C:0.24, G:0.08, T:0.42
Consensus pattern (46 bp):
TAAAGCCCATTTCCTCATTAGTTTCATTCAAAGTCCATTACCATTT
Found at i:48214 original size:45 final size:45
Alignment explanation
Indices: 48122--48236 Score: 142
Period size: 46 Copynumber: 2.5 Consensus size: 45
48112 TCCATTTTAA
*
48122 TAAAGCCCATTTCCTCATTAGTTTCATTCAAAGTCCATTACCATTT
1 TAAAGCCCATTTCCTCATTAG-TTAATTCAAAGTCCATTACCATTT
* * **
48168 TAGAGCCCATTTCCTCATTTAG-TAATTCAAAGTCCATTTCTTTTT
1 TAAAGCCCATTTCCTCA-TTAGTTAATTCAAAGTCCATTACCATTT
*
48213 TAAAGACCCATTTCCTTATTAGTT
1 TAAAG-CCCATTTCCTCATTAGTT
48237 TCTCAAAATG
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
45 27 0.46
46 28 0.47
47 4 0.07
ACGTcount: A:0.27, C:0.23, G:0.08, T:0.42
Consensus pattern (45 bp):
TAAAGCCCATTTCCTCATTAGTTAATTCAAAGTCCATTACCATTT
Found at i:56172 original size:21 final size:21
Alignment explanation
Indices: 56147--56202 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
56137 AAGAATTAGT
*
56147 GCGCCGAGATGAAGAGGCGAAA
1 GCGCCGAGAAGAAGAGGC-AAA
56169 -CGCCGAGAAGAAGAGGCAAA
1 GCGCCGAGAAGAAGAGGCAAA
56189 GCGCCGAGAAGAAG
1 GCGCCGAGAAGAAG
56203 CCACAAACGC
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
20 3 0.09
21 29 0.91
ACGTcount: A:0.39, C:0.20, G:0.39, T:0.02
Consensus pattern (21 bp):
GCGCCGAGAAGAAGAGGCAAA
Found at i:56209 original size:21 final size:21
Alignment explanation
Indices: 56147--56209 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
56137 AAGAATTAGT
* **
56147 GCGCCGAGATGAAGAGGCGAAA
1 GCGCCGAGAAGAAGACAC-AAA
**
56169 -CGCCGAGAAGAAGAGGCAAA
1 GCGCCGAGAAGAAGACACAAA
*
56189 GCGCCGAGAAGAAGCCACAAA
1 GCGCCGAGAAGAAGACACAAA
56210 CGCTCAGATG
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
20 3 0.08
21 33 0.92
ACGTcount: A:0.41, C:0.22, G:0.35, T:0.02
Consensus pattern (21 bp):
GCGCCGAGAAGAAGACACAAA
Done.