Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012077.1 Corchorus olitorius cultivar O-4 contig12110, 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: 29625
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:656 original size:72 final size:73
Alignment explanation
Indices: 554--709 Score: 260
Period size: 72 Copynumber: 2.2 Consensus size: 73
544 TCCGATTAGC
* *
554 TGTAGGTATATAGCCTACCTATATTAATGGATAGCAGTGGACAGGACTAGCTTATACCATCGGGT
1 TGTAGGTATATAGCCTACCTATATTAATGGATAGAAGTGGACAGGACTAGCTTATACCATCGGGC
619 ATAAATGG
66 ATAAATGG
* *
627 TGTAGGTATATAG-CTGCCTATATTAATGGATAGAAGTGGACATGACTAGCTTATACCATCGGGC
1 TGTAGGTATATAGCCTACCTATATTAATGGATAGAAGTGGACAGGACTAGCTTATACCATCGGGC
691 ATAAATGG
66 ATAAATGG
*
699 TGTAGTTATAT
1 TGTAGGTATAT
710 CTGATATATA
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
72 65 0.83
73 13 0.17
ACGTcount: A:0.31, C:0.13, G:0.24, T:0.31
Consensus pattern (73 bp):
TGTAGGTATATAGCCTACCTATATTAATGGATAGAAGTGGACAGGACTAGCTTATACCATCGGGC
ATAAATGG
Found at i:2344 original size:31 final size:31
Alignment explanation
Indices: 2308--2505 Score: 234
Period size: 31 Copynumber: 6.4 Consensus size: 31
2298 TTTTGTGCAT
* * **
2308 GTGGCATGCCACGTGTCACTTTTTGAAACAC
1 GTGGCGTGCCACATGTCACTTTTTGGTACAC
* * * *
2339 ATGGCATGCCACATATCACTTTTGGGTACAC
1 GTGGCGTGCCACATGTCACTTTTTGGTACAC
* ** * *
2370 ATGGCGTGATACGTGTCACTTTTTGGTGCAC
1 GTGGCGTGCCACATGTCACTTTTTGGTACAC
* *
2401 GTGGCGTGCCACATATCACTTTTTGGTGCAC
1 GTGGCGTGCCACATGTCACTTTTTGGTACAC
*
2432 GTGGCGTGCCACATGTCGCTTTTTGGTACAC
1 GTGGCGTGCCACATGTCACTTTTTGGTACAC
*
2463 GTGGTGTGCCACATGTCACTTTTTGGTACAC
1 GTGGCGTGCCACATGTCACTTTTTGGTACAC
*
2494 GTGGCTTGCCAC
1 GTGGCGTGCCAC
2506 GTCGGACACC
Statistics
Matches: 142, Mismatches: 25, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 142 1.00
ACGTcount: A:0.18, C:0.25, G:0.26, T:0.32
Consensus pattern (31 bp):
GTGGCGTGCCACATGTCACTTTTTGGTACAC
Found at i:7045 original size:16 final size:15
Alignment explanation
Indices: 7007--7048 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
6997 ACAGAGGTTG
7007 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
7022 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
7037 ACTAGAAAACAA
1 AC-AGAAAACAA
7049 AACAAAGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.67, C:0.14, G:0.07, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:9921 original size:14 final size:15
Alignment explanation
Indices: 9902--9931 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
9892 CAATCAAAGC
9902 AATAAT-CAAGGAAA
1 AATAATGCAAGGAAA
9916 AATAATGCAAGGAAA
1 AATAATGCAAGGAAA
9931 A
1 A
9932 TTAAAGAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.63, C:0.07, G:0.17, T:0.13
Consensus pattern (15 bp):
AATAATGCAAGGAAA
Found at i:10311 original size:21 final size:21
Alignment explanation
Indices: 10287--10338 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
10277 GGCAGTGAAT
* *
10287 GGTGATGGCACGGGCATAGCC
1 GGTGGTGGCACGGGCATAACC
*
10308 GGTGGTGGCACGGGCTTAACC
1 GGTGGTGGCACGGGCATAACC
10329 GGTGGTGGCA
1 GGTGGTGGCA
10339 TGGTAATGGG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.15, C:0.21, G:0.46, T:0.17
Consensus pattern (21 bp):
GGTGGTGGCACGGGCATAACC
Found at i:13853 original size:13 final size:13
Alignment explanation
Indices: 13835--13861 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
13825 AATTTAGCTA
13835 CTCATGGATTTTC
1 CTCATGGATTTTC
13848 CTCATGGATTTTC
1 CTCATGGATTTTC
13861 C
1 C
13862 ATGAGAGGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.26, G:0.15, T:0.44
Consensus pattern (13 bp):
CTCATGGATTTTC
Found at i:17907 original size:14 final size:14
Alignment explanation
Indices: 17888--17914 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
17878 CTATTATATG
17888 AAATAATAATTATA
1 AAATAATAATTATA
17902 AAATAATAATTAT
1 AAATAATAATTAT
17915 TATTCAATAA
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:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
AAATAATAATTATA
Found at i:20532 original size:25 final size:27
Alignment explanation
Indices: 20494--20546 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 27
20484 TTTGAATATC
20494 TCCAAACAATCAAAATATAT-ACTTGTA
1 TCCAAACAATCAAAA-ATATCACTTGTA
*
20521 TCCAAAC-A-CAAAAATATCTCTTGTA
1 TCCAAACAATCAAAAATATCACTTGTA
20546 T
1 T
20547 TGTAGAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 4 0.17
25 12 0.50
26 1 0.04
27 7 0.29
ACGTcount: A:0.45, C:0.21, G:0.04, T:0.30
Consensus pattern (27 bp):
TCCAAACAATCAAAAATATCACTTGTA
Found at i:23865 original size:3 final size:3
Alignment explanation
Indices: 23857--23916 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
23847 ACGCATAAAT
23857 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
23905 ATA ATA ATA ATA
1 ATA ATA ATA ATA
23917 TGTTATGGAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:25091 original size:30 final size:30
Alignment explanation
Indices: 25055--25367 Score: 356
Period size: 30 Copynumber: 10.0 Consensus size: 30
25045 TAATATACGT
25055 TGACACCAGAAGTTGTCATGGCCTTGCAAA
1 TGACACCAGAAGTTGTCATGGCCTTGCAAA
25085 TGACACCAGAAGTTGTCATGGCCTTGCAAA
1 TGACACCAGAAGTTGTCATGGCCTTGCAAA
25115 TGACACCAGAAGTTGTCATGGCCTTGCAAA
1 TGACACCAGAAGTTGTCATGGCCTTGCAAA
*
25145 TGACACCAGAAGTTGTCATGGCCTTGCAAT
1 TGACACCAGAAGTTGTCATGGCCTTGCAAA
25175 TGACACCAGAAGTTGTCATGGCCTTGCGATTTGCAA
1 TGACACCAGAAGTTGTCATGGCCTTGC-A-----AA
25211 TTGACACCAGAAGTTGTCATGGCCTTGCAATTTGCAA
1 -TGACACCAGAAGTTGTCATGGCCTTGC-A-----AA
* *
25248 TTGACACCAGAAGTTGTCATGGTCTTGCAAT
1 -TGACACCAGAAGTTGTCATGGCCTTGCAAA
* *** *
25279 TGACACCAGAAGCTGTCATGATGTTGCAAT
1 TGACACCAGAAGTTGTCATGGCCTTGCAAA
* *** *
25309 TGACACCAGAAGCTGTCATGATGTTGCAAT
1 TGACACCAGAAGTTGTCATGGCCTTGCAAA
* **
25339 TGACACCAGAAGCTGTCATGATCTTGCAA
1 TGACACCAGAAGTTGTCATGGCCTTGCAA
25368 TAGACACTTG
Statistics
Matches: 267, Mismatches: 9, Indels: 14
0.92 0.03 0.05
Matches are distributed among these distances:
30 201 0.75
31 2 0.01
36 2 0.01
37 62 0.23
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (30 bp):
TGACACCAGAAGTTGTCATGGCCTTGCAAA
Found at i:25218 original size:37 final size:37
Alignment explanation
Indices: 25168--25279 Score: 206
Period size: 37 Copynumber: 3.0 Consensus size: 37
25158 TGTCATGGCC
*
25168 TTGCAATTGACACCAGAAGTTGTCATGGCCTTGCGAT
1 TTGCAATTGACACCAGAAGTTGTCATGGCCTTGCAAT
25205 TTGCAATTGACACCAGAAGTTGTCATGGCCTTGCAAT
1 TTGCAATTGACACCAGAAGTTGTCATGGCCTTGCAAT
*
25242 TTGCAATTGACACCAGAAGTTGTCATGGTCTTGCAAT
1 TTGCAATTGACACCAGAAGTTGTCATGGCCTTGCAAT
25279 T
1 T
25280 GACACCAGAA
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 73 1.00
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (37 bp):
TTGCAATTGACACCAGAAGTTGTCATGGCCTTGCAAT
Found at i:25311 original size:134 final size:120
Alignment explanation
Indices: 25054--25367 Score: 376
Period size: 134 Copynumber: 2.5 Consensus size: 120
25044 CTAATATACG
25054 TTGACACCAGAAGTTGTCATGGCCTTGCAAATGACACCAGAAGTTGTCATGGCCTTGCAAATGAC
1 TTGACACCAGAAGTTGTCATGGCCTTGCAAATGACACCAGAAGTTGTCATGGCCTTGCAAATGAC
* *
25119 ACCAGAAGTTGTCATGGCCTTGCAAATGACACCAGAAGTTGTCATGGCCTTGCAA
66 ACCAGAAGTTGTCATGGCCTTGCAAATGACACCAGAAGCTGTCATGACCTTGCAA
25174 TTGACACCAGAAGTTGTCATGGCCTTGCGATTTGCAATTGACACCAGAAGTTGTCATGGCCTTGC
1 TTGACACCAGAAGTTGTCATGGCCTTGC-A-----AA-TGACACCAGAAGTTGTCATGGCCTTGC
* * **
25239 AATTTGCAATTGACACCAGAAGTTGTCATGGTCTTGCAATTGACACCAGAAGCTGTCATGATGTT
59 -A-----AA-TGACACCAGAAGTTGTCATGGCCTTGCAAATGACACCAGAAGCTGTCATGACCTT
25304 GCAA
117 GCAA
* *** * * **
25308 TTGACACCAGAAGCTGTCATGATGTTGCAATTGACACCAGAAGCTGTCATGATCTTGCAA
1 TTGACACCAGAAGTTGTCATGGCCTTGCAAATGACACCAGAAGTTGTCATGGCCTTGCAA
25368 TAGACACTTG
Statistics
Matches: 166, Mismatches: 14, Indels: 27
0.80 0.07 0.13
Matches are distributed among these distances:
120 28 0.17
121 2 0.01
126 3 0.02
127 51 0.31
128 2 0.01
133 3 0.02
134 77 0.46
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (120 bp):
TTGACACCAGAAGTTGTCATGGCCTTGCAAATGACACCAGAAGTTGTCATGGCCTTGCAAATGAC
ACCAGAAGTTGTCATGGCCTTGCAAATGACACCAGAAGCTGTCATGACCTTGCAA
Found at i:25318 original size:164 final size:157
Alignment explanation
Indices: 25054--25358 Score: 439
Period size: 164 Copynumber: 1.9 Consensus size: 157
25044 CTAATATACG
25054 TTGACACCAGAAGTTGTCATGGCCTTGCAAATGACACCAGAAGTTGTCATGGCCTTGCAAATGAC
1 TTGACACCAGAAGTTGTCATGGCCTTGCAAATGACACCAGAAGTTGTCATGGCCTTGCAAATGAC
* * * *
25119 ACCAGAAGTTGTCATGGCCTTGCAAATGACACCAGAAGTTGTCATGGCCTTGCAATTGACACCAG
66 ACCAGAAGCTGTCATGACCTTGCAAATGACACCAGAAGCTGTCATGACCTTGCAATTGACACCAG
*
25184 AAGTTGTCATGGCCTTGCGATTTGCAA
131 AAGCTGTCATGGCCTTGCGATTTGCAA
*
25211 TTGACACCAGAAGTTGTCATGGCCTTGCAATTTGCAATTGACACCAGAAGTTGTCATGGTCTTGC
1 TTGACACCAGAAGTTGTCATGGCCTTGC-A-----AA-TGACACCAGAAGTTGTCATGGCCTTGC
* ** * **
25276 AATTGACACCAGAAGCTGTCATGATGTTGCAATTGACACCAGAAGCTGTCATGATGTTGCAATTG
59 AAATGACACCAGAAGCTGTCATGACCTTGCAAATGACACCAGAAGCTGTCATGACCTTGCAATTG
25341 ACACCAGAAGCTGTCATG
124 ACACCAGAAGCTGTCATG
25359 ATCTTGCAAT
Statistics
Matches: 129, Mismatches: 12, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
157 28 0.22
158 1 0.01
163 2 0.02
164 98 0.76
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (157 bp):
TTGACACCAGAAGTTGTCATGGCCTTGCAAATGACACCAGAAGTTGTCATGGCCTTGCAAATGAC
ACCAGAAGCTGTCATGACCTTGCAAATGACACCAGAAGCTGTCATGACCTTGCAATTGACACCAG
AAGCTGTCATGGCCTTGCGATTTGCAA
Found at i:25368 original size:30 final size:30
Alignment explanation
Indices: 25242--25422 Score: 227
Period size: 30 Copynumber: 6.0 Consensus size: 30
25232 GCCTTGCAAT
* *
25242 TTGCAATTGACACCAGAAGTTGTCATGGTC
1 TTGCAATTGACACCAGAAGCTGTCATGATC
*
25272 TTGCAATTGACACCAGAAGCTGTCATGATG
1 TTGCAATTGACACCAGAAGCTGTCATGATC
*
25302 TTGCAATTGACACCAGAAGCTGTCATGATG
1 TTGCAATTGACACCAGAAGCTGTCATGATC
25332 TTGCAATTGACACCAGAAGCTGTCATGATC
1 TTGCAATTGACACCAGAAGCTGTCATGATC
* ** * * *
25362 TTGCAATAGACACTTGAAGATGTCATAATTT
1 TTGCAATTGACACCAGAAGCTGTCATGA-TC
* * *
25393 TATTCAATTGACACCAGAAGTTTTCATGAT
1 T-TGCAATTGACACCAGAAGCTGTCATGAT
25423 AAATTTCCAA
Statistics
Matches: 132, Mismatches: 17, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
30 109 0.83
31 3 0.02
32 20 0.15
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (30 bp):
TTGCAATTGACACCAGAAGCTGTCATGATC
Found at i:25452 original size:65 final size:62
Alignment explanation
Indices: 25275--25453 Score: 200
Period size: 60 Copynumber: 2.9 Consensus size: 62
25265 CATGGTCTTG
* * * ** * * * *
25275 CAATTGACACCAGAAGCTGTCATGATGTTGCAATTGACACCAGAAGCTGTCATGA-TGT-TG
1 CAATTGACACCAGAAGCTGTCATGATCTTCCAATAGACACTTGAAGATGTCATAATTTTATT
*
25335 CAATTGACACCAGAAGCTGTCATGATCTTGCAATAGACACTTGAAGATGTCATAATTTTATT
1 CAATTGACACCAGAAGCTGTCATGATCTTCCAATAGACACTTGAAGATGTCATAATTTTATT
* * *
25397 CAATTGACACCAGAAGTTTTCATGATAAATTTCCAATAGACACTTGAAGATGTCATA
1 CAATTGACACCAGAAGCTGTCATGAT---CTTCCAATAGACACTTGAAGATGTCATA
25454 TGCACTATTA
Statistics
Matches: 102, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
60 49 0.48
61 2 0.02
62 25 0.25
65 26 0.25
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (62 bp):
CAATTGACACCAGAAGCTGTCATGATCTTCCAATAGACACTTGAAGATGTCATAATTTTATT
Found at i:27516 original size:33 final size:33
Alignment explanation
Indices: 27453--27516 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
27443 ATACTGAATA
**
27453 ATATTGCCCCTGAAGAGGCATAAATTCATGAGC
1 ATATTGCCCCTGAAGAGGCATAAACCCATGAGC
* *
27486 ATATTGCCCCTGTAGTGGCATAAACCCATGA
1 ATATTGCCCCTGAAGAGGCATAAACCCATGA
27517 AAAGATCACT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.25
Consensus pattern (33 bp):
ATATTGCCCCTGAAGAGGCATAAACCCATGAGC
Done.