Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011492.1 Corchorus olitorius cultivar O-4 contig11525, 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: 14471
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.30
Found at i:2828 original size:30 final size:30
Alignment explanation
Indices: 2793--3327 Score: 679
Period size: 30 Copynumber: 18.0 Consensus size: 30
2783 ACTGATGAAA
* *
2793 CAATGATCCTAAACCAGGGTTAAAATAAAG
1 CAATGATCCTCAACCAGGATTAAAATAAAG
*
2823 CAATGATCCTCAACCAGGATTAAAATGAAG
1 CAATGATCCTCAACCAGGATTAAAATAAAG
2853 CAATGATCCTCAACCAGGATTAAAATAAAG
1 CAATGATCCTCAACCAGGATTAAAATAAAG
* *
2883 CAACGATCCTCAACCAGGATTAAAGTAAAG
1 CAATGATCCTCAACCAGGATTAAAATAAAG
*
2913 CAATTATCCTCAACCAGGATTAAAATAAAG
1 CAATGATCCTCAACCAGGATTAAAATAAAG
*
2943 CAATGATCCTCAAACAGGATTAAAATAAAG
1 CAATGATCCTCAACCAGGATTAAAATAAAG
* * *
2973 CAATGATCCTCAACCAAGATTAAAATGACG
1 CAATGATCCTCAACCAGGATTAAAATAAAG
* * *
3003 CAATGATCCTCAAACATGATTAAAATGAAG
1 CAATGATCCTCAACCAGGATTAAAATAAAG
* * *
3033 CAGTGATCCTCAAACAGGATTAAAACAAAG
1 CAATGATCCTCAACCAGGATTAAAATAAAG
* *
3063 CAACGATCCTCAACCAGGATTAAAGTAAAG
1 CAATGATCCTCAACCAGGATTAAAATAAAG
*
3093 C-ATCTATCCTCAACCAGGATTAAAATAAAG
1 CAAT-GATCCTCAACCAGGATTAAAATAAAG
* * *
3123 CAACGATCCTCAAACAGGATTAAAACAAAG
1 CAATGATCCTCAACCAGGATTAAAATAAAG
* * *
3153 CAAAGATCCTCAAACAGGATTAAAACAAAG
1 CAATGATCCTCAACCAGGATTAAAATAAAG
* *
3183 CAAAGATCCTCAAACAGGATTAAAATAAAG
1 CAATGATCCTCAACCAGGATTAAAATAAAG
* **
3213 CACAT-ATCCTCAAACAGGATTAAAATGGAG
1 CA-ATGATCCTCAACCAGGATTAAAATAAAG
* ***
3243 TACCAATCCTCAACCAGGATTAAAAT-AA-
1 CAATGATCCTCAACCAGGATTAAAATAAAG
3271 C---GATCCTCAACCAGGATTAAAATAAAG
1 CAATGATCCTCAACCAGGATTAAAATAAAG
* *
3298 TAACGATCCTCAACCAGGATTAAAATAAAG
1 CAATGATCCTCAACCAGGATTAAAATAAAG
3328 TAACACAATG
Statistics
Matches: 449, Mismatches: 47, Indels: 18
0.87 0.09 0.04
Matches are distributed among these distances:
25 21 0.05
26 2 0.00
29 2 0.00
30 422 0.94
31 2 0.00
ACGTcount: A:0.47, C:0.21, G:0.14, T:0.19
Consensus pattern (30 bp):
CAATGATCCTCAACCAGGATTAAAATAAAG
Found at i:3673 original size:69 final size:69
Alignment explanation
Indices: 3543--3790 Score: 433
Period size: 69 Copynumber: 3.6 Consensus size: 69
3533 AAGTAAGGCT
* *
3543 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAAGCCCATGTGACTTGGATGGAACCAAGGCT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGG-AAAAGCCTATGTGGCTTGGATGGAACCAAGGCT
3608 TAAAC
65 TAAAC
* *
3613 TAACTCATATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTT
3678 AAAC
66 AAAC
*
3682 TGACTCGTATGGAAATGAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTT
3747 AAAC
66 AAAC
*
3751 TGACTCGTATCGAAACGAGTTTGGCTTGTGGAAAAGCCTA
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTA
3791 ATCATTCGGA
Statistics
Matches: 169, Mismatches: 9, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
69 140 0.83
70 29 0.17
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.26
Consensus pattern (69 bp):
TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTT
AAAC
Found at i:5103 original size:13 final size:12
Alignment explanation
Indices: 5085--5126 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
5075 TTCTCTTTTT
5085 TCTTTTTTCTTCA
1 TCTTTTTT-TTCA
5098 TC-TTTTTTTCA
1 TCTTTTTTTTCA
5109 TCTTTTTTTT-A
1 TCTTTTTTTTCA
5120 T-TTTTTT
1 TCTTTTTT
5127 GTGCACTTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
10 6 0.21
11 8 0.29
12 12 0.43
13 2 0.07
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.79
Consensus pattern (12 bp):
TCTTTTTTTTCA
Found at i:5117 original size:11 final size:11
Alignment explanation
Indices: 5071--5126 Score: 59
Period size: 11 Copynumber: 5.5 Consensus size: 11
5061 TATTCCTTCC
5071 TTTTTTC-TC-
1 TTTTTTCATCT
5080 TTTTTTC-T-T
1 TTTTTTCATCT
5089 TTTTCTTCATCT
1 TTTT-TTCATCT
5101 TTTTTTCATCT
1 TTTTTTCATCT
*
5112 TTTTTTTAT-T
1 TTTTTTCATCT
5122 TTTTT
1 TTTTT
5127 GTGCACTTGA
Statistics
Matches: 42, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
9 12 0.29
10 9 0.21
11 16 0.38
12 5 0.12
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTTTCATCT
Found at i:5436 original size:12 final size:13
Alignment explanation
Indices: 5408--5472 Score: 62
Period size: 14 Copynumber: 4.8 Consensus size: 13
5398 ATCAATTCCC
5408 TTTTTGATTTTGA
1 TTTTTGATTTTGA
5421 -TTTTGA-TTTGA
1 TTTTTGATTTTGA
* *
5432 TTTTTTTATTTTTTA
1 -TTTTTGA-TTTTGA
5447 TTTTTGATTTTTGA
1 TTTTTGA-TTTTGA
5461 TTTTTTGATTTT
1 -TTTTTGATTTT
5473 TTTGTTTTTG
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
11 5 0.12
12 6 0.14
13 5 0.12
14 16 0.37
15 11 0.26
ACGTcount: A:0.14, C:0.00, G:0.11, T:0.75
Consensus pattern (13 bp):
TTTTTGATTTTGA
Found at i:5444 original size:8 final size:8
Alignment explanation
Indices: 5427--5474 Score: 66
Period size: 8 Copynumber: 6.4 Consensus size: 8
5417 TTGATTTTGA
5427 TTTGATTT
1 TTTGATTT
*
5435 TTTTATTT
1 TTTGATTT
5443 TTT-A-TT
1 TTTGATTT
5449 TTTGA-TT
1 TTTGATTT
5456 TTTGATTT
1 TTTGATTT
5464 TTTGATTT
1 TTTGATTT
5472 TTT
1 TTT
5475 TGTTTTTGAT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
6 5 0.14
7 9 0.24
8 23 0.62
ACGTcount: A:0.12, C:0.00, G:0.08, T:0.79
Consensus pattern (8 bp):
TTTGATTT
Found at i:5445 original size:7 final size:7
Alignment explanation
Indices: 5433--5474 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
5423 TTGATTTGAT
5433 TTTTTTA
1 TTTTTTA
5440 TTTTTTA
1 TTTTTTA
*
5447 TTTTTGA
1 TTTTTTA
*
5454 TTTTTGA
1 TTTTTTA
5461 TTTTTTGA
1 TTTTTT-A
5469 TTTTTT
1 TTTTTT
5475 TGTTTTTGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
7 25 0.78
8 7 0.22
ACGTcount: A:0.12, C:0.00, G:0.07, T:0.81
Consensus pattern (7 bp):
TTTTTTA
Found at i:5451 original size:15 final size:15
Alignment explanation
Indices: 5431--5485 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
5421 TTTTGATTTG
*
5431 ATTTTTTTATTTTTT
1 ATTTTTTGATTTTTT
*
5446 A-TTTTTGATTTTTG
1 ATTTTTTGATTTTTT
5460 ATTTTTTGATTTTTT
1 ATTTTTTGATTTTTT
5475 -TGTTTTTGATT
1 AT-TTTTTGATT
5486 GAATTTCTTG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
14 13 0.37
15 22 0.63
ACGTcount: A:0.13, C:0.00, G:0.09, T:0.78
Consensus pattern (15 bp):
ATTTTTTGATTTTTT
Found at i:5883 original size:8 final size:8
Alignment explanation
Indices: 5870--5898 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
5860 TTTATTTCCA
5870 TTTTCATT
1 TTTTCATT
5878 TTTTCATT
1 TTTTCATT
5886 TTTTCATT
1 TTTTCATT
5894 TTTTC
1 TTTTC
5899 CCATTACTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.10, C:0.14, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTTCATT
Found at i:10694 original size:22 final size:21
Alignment explanation
Indices: 10647--10695 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
10637 AGAGCGTGGA
10647 GATGAGAGAGGGTGATGAGAT
1 GATGAGAGAGGGTGATGAGAT
*
10668 G-TGAGAGAGAAGTTGA-GAGAT
1 GATGAGAGAG--GGTGATGAGAT
10689 GATGAGA
1 GATGAGA
10696 TGAATATCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 8 0.33
21 7 0.29
22 9 0.38
ACGTcount: A:0.37, C:0.00, G:0.45, T:0.18
Consensus pattern (21 bp):
GATGAGAGAGGGTGATGAGAT
Found at i:12773 original size:30 final size:30
Alignment explanation
Indices: 12738--13356 Score: 705
Period size: 30 Copynumber: 21.0 Consensus size: 30
12728 ACTGATGAAA
* *
12738 CAATGATCCTAAACCAGGGTTAAAATAAAG
1 CAATGATCCTCAACCAGGATTAAAATAAAG
*
12768 CAATGATCCTCAACCGGGATTAAAATAAAG
1 CAATGATCCTCAACCAGGATTAAAATAAAG
*
12798 CAACGATCCTCAACCAGGATTAAAATAAAG
1 CAATGATCCTCAACCAGGATTAAAATAAAG
* *
12828 TAATGATCCTCAACCAGGATTAAAATGAAG
1 CAATGATCCTCAACCAGGATTAAAATAAAG
* *
12858 CAATGATCCTCGACCAGGATTAAAATAAGG
1 CAATGATCCTCAACCAGGATTAAAATAAAG
* *
12888 TAATGATCCTCAACCAGGATTAAAATAAGG
1 CAATGATCCTCAACCAGGATTAAAATAAAG
* *
12918 TAATGATCCTCAACCAGGATTAAAAATAAGG
1 CAATGATCCTCAACCAGGATT-AAAATAAAG
* *
12949 TAATGATCCTCAACCAGGATTAAAATGAAG
1 CAATGATCCTCAACCAGGATTAAAATAAAG
*
12979 CAATGATCCTCGACCAGGATTAAAATGAAA-
1 CAATGATCCTCAACCAGGATTAAAAT-AAAG
*
13009 CAATGATCCTCAACCAGGATTAAAATGAAG
1 CAATGATCCTCAACCAGGATTAAAATAAAG
* *
13039 GAATGATCCTCAACCAGGATTAAAATGAAGG
1 CAATGATCCTCAACCAGGATTAAAAT-AAAG
* *
13070 TAATGATCCTCAAACAGGATTAAAATAAAG
1 CAATGATCCTCAACCAGGATTAAAATAAAG
* * * *
13100 CAACGATCCTCAAACAGGAGATAAAACAAAG
1 CAATGATCCTCAACCAGGA-TTAAAATAAAG
** * *
13131 CAGCGATCCTCAAACAGGAATTAAAACAAAG
1 CAATGATCCTCAACCAGG-ATTAAAATAAAG
* **
13162 CAAAGATCCTCAAATAGGATTAAAATAAAG
1 CAATGATCCTCAACCAGGATTAAAATAAAG
** **
13192 CACA-GATCCTCAAATAGGATTAAAATGGAG
1 CA-ATGATCCTCAACCAGGATTAAAATAAAG
* **
13222 TAACAATCCTCAACCAGGATTAAAAT-AA-
1 CAATGATCCTCAACCAGGATTAAAATAAAG
13250 C---GATCCTCAACCAGGATTAAAAT-AA-
1 CAATGATCCTCAACCAGGATTAAAATAAAG
13275 C---GATCCTCAACCAGGATTAAAAT-AA-
1 CAATGATCCTCAACCAGGATTAAAATAAAG
13300 C---GATCCTCAACCAGGATTAAAATAAAG
1 CAATGATCCTCAACCAGGATTAAAATAAAG
* *
13327 TAACGATCCTCAACCAGGATTAAAATAAAG
1 CAATGATCCTCAACCAGGATTAAAATAAAG
13357 TAACACAATG
Statistics
Matches: 529, Mismatches: 47, Indels: 26
0.88 0.08 0.04
Matches are distributed among these distances:
25 71 0.13
26 2 0.00
29 4 0.01
30 341 0.64
31 110 0.21
32 1 0.00
ACGTcount: A:0.46, C:0.19, G:0.16, T:0.20
Consensus pattern (30 bp):
CAATGATCCTCAACCAGGATTAAAATAAAG
Found at i:12996 original size:121 final size:120
Alignment explanation
Indices: 12732--13356 Score: 717
Period size: 121 Copynumber: 5.3 Consensus size: 120
12722 GGATTAACTG
* * * * *
12732 ATGAAACAATGATCCTAAACCAGGGTTAAAATAAAGCAATGATCCTCAACCGGGATTAAAATAAA
1 ATGAAGCAACGATCCTCAACCAGGATTAAAATAAAGCAATGATCCTCAACCAGGATTAAAATAAA
12797 GCAACGATCCTCAACCAGGATTAAAATAAAGTAATGATCCTCAACCAGGATTAAA
66 GCAACGATCCTCAACCAGGATTAAAATAAAGTAATGATCCTCAACCAGGATTAAA
* * * * *
12852 ATGAAGCAATGATCCTCGACCAGGATTAAAATAAGGTAATGATCCTCAACCAGGATTAAAATAAG
1 ATGAAGCAACGATCCTCAACCAGGATTAAAATAAAGCAATGATCCTCAACCAGGATTAAAATAAA
* * *
12917 GTAATGATCCTCAACCAGGATTAAAAATAAGGTAATGATCCTCAACCAGGATTAAA
66 GCAACGATCCTCAACCAGGATT-AAAATAAAGTAATGATCCTCAACCAGGATTAAA
* * *
12973 ATGAAGCAATGATCCTCGACCAGGATTAAAATGAAA-CAATGATCCTCAACCAGGATTAAAATGA
1 ATGAAGCAACGATCCTCAACCAGGATTAAAAT-AAAGCAATGATCCTCAACCAGGATTAAAATAA
* * * *
13037 AGGAATGATCCTCAACCAGGATTAAAATGAAGGTAATGATCCTCAAACAGGATTAAA
65 AGCAACGATCCTCAACCAGGATTAAAAT-AAAGTAATGATCCTCAACCAGGATTAAA
* * * * ** * *
13094 ATAAAGCAACGATCCTCAAACAGGAGATAAAACAAAGCAGCGATCCTCAAACAGGAATTAAAACA
1 ATGAAGCAACGATCCTCAACCAGGA-TTAAAATAAAGCAATGATCCTCAACCAGG-ATTAAAATA
* ** * **
13159 AAGCAAAGATCCTCAAATAGGATTAAAATAAAGCACA-GATCCTCAAATAGGATTAAA
64 AAGCAACGATCCTCAACCAGGATTAAAATAAAGTA-ATGATCCTCAACCAGGATTAAA
* * *
13216 ATGGAGTAACAATCCTCAACCAGGATTAAAAT-AA-C---GATCCTCAACCAGGATTAAAAT---
1 ATGAAGCAACGATCCTCAACCAGGATTAAAATAAAGCAATGATCCTCAACCAGGATTAAAATAAA
*
13273 --AACGATCCTCAACCAGGATT---A-AAA-TAACGATCCTCAACCAGGATTAAA
66 GCAACGATCCTCAACCAGGATTAAAATAAAGTAATGATCCTCAACCAGGATTAAA
* *
13321 ATAAAGTAACGATCCTCAACCAGGATTAAAATAAAG
1 ATGAAGCAACGATCCTCAACCAGGATTAAAATAAAG
13357 TAACACAATG
Statistics
Matches: 442, Mismatches: 53, Indels: 33
0.84 0.10 0.06
Matches are distributed among these distances:
104 1 0.00
105 48 0.11
106 5 0.01
107 1 0.00
110 17 0.04
115 7 0.02
116 13 0.03
119 1 0.00
120 84 0.19
121 167 0.38
122 65 0.15
123 33 0.07
ACGTcount: A:0.46, C:0.19, G:0.16, T:0.20
Consensus pattern (120 bp):
ATGAAGCAACGATCCTCAACCAGGATTAAAATAAAGCAATGATCCTCAACCAGGATTAAAATAAA
GCAACGATCCTCAACCAGGATTAAAATAAAGTAATGATCCTCAACCAGGATTAAA
Found at i:13256 original size:25 final size:25
Alignment explanation
Indices: 13222--13354 Score: 212
Period size: 25 Copynumber: 5.1 Consensus size: 25
13212 TAAAATGGAG
*
13222 TAACAATCCTCAACCAGGATTAAAA
1 TAACGATCCTCAACCAGGATTAAAA
13247 TAACGATCCTCAACCAGGATTAAAA
1 TAACGATCCTCAACCAGGATTAAAA
13272 TAACGATCCTCAACCAGGATTAAAA
1 TAACGATCCTCAACCAGGATTAAAA
13297 TAACGATCCTCAACCAGGATTAAAATAAA
1 TAACGATCCTCAACCAGGATT---A-AAA
13326 GTAACGATCCTCAACCAGGATTAAAA
1 -TAACGATCCTCAACCAGGATTAAAA
13352 TAA
1 TAA
13355 AGTAACACAA
Statistics
Matches: 102, Mismatches: 1, Indels: 10
0.90 0.01 0.09
Matches are distributed among these distances:
25 73 0.72
26 3 0.03
27 1 0.01
28 1 0.01
29 3 0.03
30 21 0.21
ACGTcount: A:0.46, C:0.23, G:0.11, T:0.20
Consensus pattern (25 bp):
TAACGATCCTCAACCAGGATTAAAA
Found at i:13914 original size:35 final size:35
Alignment explanation
Indices: 13849--14302 Score: 447
Period size: 35 Copynumber: 13.1 Consensus size: 35
13839 ATTTGCGGTA
* * *
13849 AACTGAAGTAAACTGCAGAAAAGATCGCCCTGGATC
1 AACTGAAATAAATTGAAG-AAAGATCGCCCTGGATC
*
13885 AACTGAAATAAATTGAAGAAAGACCGCCCTGGATC
1 AACTGAAATAAATTGAAGAAAGATCGCCCTGGATC
* *
13920 AACTGAAATAAATTGAAGAAAGATCACACTGGATC
1 AACTGAAATAAATTGAAGAAAGATCGCCCTGGATC
*
13955 AACTGAAATAAACTGAAGAAAAGATCGCCCTGGATC
1 AACTGAAATAAATTGAAG-AAAGATCGCCCTGGATC
* *
13991 AACTGAAATAAATTGAAGAAAAATC-CCTTGGATC
1 AACTGAAATAAATTGAAGAAAGATCGCCCTGGATC
* * * * * * *
14025 AATTAAAATGAATTGAAGAAGGACCGCCTTGGGTC
1 AACTGAAATAAATTGAAGAAAGATCGCCCTGGATC
* * * * *
14060 AACTGAAATCAACTAAAGAAAGACCGCCCTGGGTC
1 AACTGAAATAAATTGAAGAAAGATCGCCCTGGATC
* *
14095 AACTGAAATAAACTGAAGAAAGACCGCCCTGGATC
1 AACTGAAATAAATTGAAGAAAGATCGCCCTGGATC
* * * *
14130 AACTGAAATAAACTGGAGAAAGACCGCCCTGGGTC
1 AACTGAAATAAATTGAAGAAAGATCGCCCTGGATC
* *
14165 AA--G---TAAGTTGAAGAAAAGATCGCCCTAGATC
1 AACTGAAATAAATTGAAG-AAAGATCGCCCTGGATC
* * * * * * *
14196 CATTAAAATGAATTGAAGAAGGACCGCCCTGGGTC
1 AACTGAAATAAATTGAAGAAAGATCGCCCTGGATC
* *
14231 AACTGAAATAAACTGAAATAAAGATCGCCCTGGATC
1 AACTGAAATAAATTG-AAGAAAGATCGCCCTGGATC
* *
14267 AACTGAAGT-AATTG-AGTAGAGATCGCCCTGGATC
1 AACTGAAATAAATTGAAG-AAAGATCGCCCTGGATC
14301 AA
1 AA
14303 TTAAAATGAA
Statistics
Matches: 349, Mismatches: 59, Indels: 22
0.81 0.14 0.05
Matches are distributed among these distances:
30 7 0.02
31 15 0.04
33 2 0.01
34 45 0.13
35 201 0.58
36 79 0.23
ACGTcount: A:0.41, C:0.19, G:0.21, T:0.19
Consensus pattern (35 bp):
AACTGAAATAAATTGAAGAAAGATCGCCCTGGATC
Done.