Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015172.1 Corchorus olitorius cultivar O-4 contig15205, 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: 44167
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:1924 original size:166 final size:165
Alignment explanation
Indices: 1544--1930 Score: 501
Period size: 166 Copynumber: 2.3 Consensus size: 165
1534 TCAAGAATCG
* ** *
1544 GACGCCGCTATATATAATCAACATTGAGACAACTTCCT-GGACTTGCCCACGCCTGGGCAAGTCT
1 GACGCCGCTATATATAATCAAAATTGAGACAACTT-CTAGGACTTGCCCACGCCTGGGCAACCCC
* * * * *
1608 TACCCACGTCTGGGCAACCCCGGGATGTTGTCTCAATTTCTATTATATATAGCGGCGTCTTGCTT
65 TACCCACGCCTGGGCAACCCCAGGATGTTGTCTCAATTTCGATTATATATAGCGGCGTCGTGCTA
* * * * *
1673 TACAAGCGCCGCCATTATAGTGGCGTTTCTTCCCTAA
130 AACAAACGCCGCCAATATAGTGGCGTTTATTCAC-AA
* * *
1710 GACGCCGCTAAATATAATCAAAATTCAGACAACTTCGAGGACTTGCCCACGCCTGGGCAACCCCT
1 GACGCCGCTATATATAATCAAAATTGAGACAACTTCTAGGACTTGCCCACGCCTGGGCAACCCCT
*
1775 ATCCACGCCTGGGCAACCCCAGGATGTTGTCTCAATTTCGATTATATATAGCGGCGTCGTGCTAA
66 ACCCACGCCTGGGCAACCCCAGGATGTTGTCTCAATTTCGATTATATATAGCGGCGTCGTGCTAA
*
1840 ACAAACGCCGTCAATATAGTGGCGTTTATGGTCAC-A
131 ACAAACGCCGCCAATATAGTGGCGTTTAT--TCACAA
* * * *
1876 GACGCCGCCATATATAATCAAAATTGAGAAAACATCTTAGG-TTTGCCCACGCCTG
1 GACGCCGCTATATATAATCAAAATTGAGACAACTTC-TAGGACTTGCCCACGCCTG
1931 TGAAGCCGCA
Statistics
Matches: 191, Mismatches: 26, Indels: 8
0.85 0.12 0.04
Matches are distributed among these distances:
165 1 0.01
166 184 0.96
167 3 0.02
168 3 0.02
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (165 bp):
GACGCCGCTATATATAATCAAAATTGAGACAACTTCTAGGACTTGCCCACGCCTGGGCAACCCCT
ACCCACGCCTGGGCAACCCCAGGATGTTGTCTCAATTTCGATTATATATAGCGGCGTCGTGCTAA
ACAAACGCCGCCAATATAGTGGCGTTTATTCACAA
Found at i:2226 original size:131 final size:131
Alignment explanation
Indices: 1987--2229 Score: 398
Period size: 131 Copynumber: 1.9 Consensus size: 131
1977 TTTGATTAGT
1987 AAAACGCCGCTATATATTATAGGCGTAGAGTTGGAAAATTTCTTTGTTTTAGGAGGAGGGAATTT
1 AAAACGCCGCTATATATTATAGGCGTAGAGTTGGAAAATTTCTTTGTTTTAGGAGGAGGGAATTT
* *
2052 TTCCCTCCAAAAAAAGGGAAAAAAAAATCTCTCTCTCCATATATTAAAATAGCAGCGTCTGGTTT
66 TTCCCTCCAAAAAAAGGGAAAAAAAAATCTATCCCTCCATATATTAAAATAGCAGCGTCTGGTTT
2117 C
131 C
* * ** *
2118 AAAATGCCGCTATATATTATAGGTGTAGAGTTGGAAGCTTTCTTTGTTTTAGTAGGGAGGGAATT
1 AAAACGCCGCTATATATTATAGGCGTAGAGTTGGAAAATTTCTTTGTTTTAGGA-GGAGGGAATT
*
2183 TTTCCCTCCAAAAAAAGGG-GAAAAAAATCTATCCCTCCATATATTAA
65 TTTCCCTCCAAAAAAAGGGAAAAAAAAATCTATCCCTCCATATATTAA
2230 TATGGCGGCG
Statistics
Matches: 103, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
131 74 0.72
132 29 0.28
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.31
Consensus pattern (131 bp):
AAAACGCCGCTATATATTATAGGCGTAGAGTTGGAAAATTTCTTTGTTTTAGGAGGAGGGAATTT
TTCCCTCCAAAAAAAGGGAAAAAAAAATCTATCCCTCCATATATTAAAATAGCAGCGTCTGGTTT
C
Found at i:4921 original size:17 final size:18
Alignment explanation
Indices: 4883--4923 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
4873 TTTTTATTAT
*
4883 TTAAAAAATAGATTTCAA
1 TTAAAAAATAGATTTAAA
*
4901 -TAAAAAATATA-TTAAA
1 TTAAAAAATAGATTTAAA
4917 TTAAAAA
1 TTAAAAA
4924 TATTTAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.32
Consensus pattern (18 bp):
TTAAAAAATAGATTTAAA
Found at i:11601 original size:18 final size:18
Alignment explanation
Indices: 11578--11616 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
11568 CTTTTGTGGG
11578 TTTTTAGTT-TTGATCGTC
1 TTTTTA-TTCTTGATCGTC
*
11596 TTTTTATTCTTGTTCGTC
1 TTTTTATTCTTGATCGTC
11614 TTT
1 TTT
11617 ACATTCATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 2 0.11
18 17 0.89
ACGTcount: A:0.08, C:0.13, G:0.13, T:0.67
Consensus pattern (18 bp):
TTTTTATTCTTGATCGTC
Found at i:11795 original size:2 final size:2
Alignment explanation
Indices: 11788--11812 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11778 TCCACTGGTA
11788 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
11813 CTATTCCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:13904 original size:2 final size:2
Alignment explanation
Indices: 13894--13932 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
13884 ATGTTCACAC
13894 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13933 GTTATAACTT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:17444 original size:14 final size:14
Alignment explanation
Indices: 17425--17455 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
17415 ATGTGTAAGG
17425 CATAAAGTAAAAAC
1 CATAAAGTAAAAAC
17439 CATAAAGTAAAAAC
1 CATAAAGTAAAAAC
17453 CAT
1 CAT
17456 TGTTACAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.61, C:0.16, G:0.06, T:0.16
Consensus pattern (14 bp):
CATAAAGTAAAAAC
Found at i:22981 original size:14 final size:14
Alignment explanation
Indices: 22962--22988 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
22952 AAACACTGTG
22962 ACTCTGATGGTAAT
1 ACTCTGATGGTAAT
22976 ACTCTGATGGTAA
1 ACTCTGATGGTAA
22989 AATAGAATAC
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:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (14 bp):
ACTCTGATGGTAAT
Found at i:29590 original size:7 final size:7
Alignment explanation
Indices: 29580--29619 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
29570 TGACAGACAG
29580 ATTGGCA
1 ATTGGCA
29587 ATTGGCA
1 ATTGGCA
29594 ATTGGCA
1 ATTGGCA
29601 A-TGGC-
1 ATTGGCA
29606 A-TGGCAA
1 ATTGGC-A
29613 ATTGGCA
1 ATTGGCA
29620 GCTACCAGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
5 5 0.17
6 4 0.13
7 17 0.57
8 4 0.13
ACGTcount: A:0.30, C:0.15, G:0.30, T:0.25
Consensus pattern (7 bp):
ATTGGCA
Found at i:35448 original size:9 final size:10
Alignment explanation
Indices: 35436--35541 Score: 50
Period size: 9 Copynumber: 11.2 Consensus size: 10
35426 TTTTATTTAA
35436 ATTATATA-T
1 ATTATATATT
35445 ATTATATATT
1 ATTATATATT
35455 ATTA-AGTATT
1 ATTATA-TATT
*
35465 -TT-TATTTT
1 ATTATATATT
*
35473 ATT-TAAATT
1 ATTATATATT
35482 A-TATATTATAT
1 ATTATA-TAT-T
* *
35493 ATTATAAAGT
1 ATTATATATT
*
35503 ATT-TTTATT
1 ATTATATATT
* * *
35512 TTTATTTA-A
1 ATTATATATT
35521 ATTATATA-T
1 ATTATATATT
35530 ATTATATATT
1 ATTATATATT
35540 AT
1 AT
35542 AAAGTAGTAT
Statistics
Matches: 73, Mismatches: 14, Indels: 19
0.69 0.13 0.18
Matches are distributed among these distances:
8 4 0.05
9 40 0.55
10 22 0.30
11 3 0.04
12 4 0.05
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (10 bp):
ATTATATATT
Found at i:35544 original size:44 final size:44
Alignment explanation
Indices: 35418--35547 Score: 230
Period size: 44 Copynumber: 3.0 Consensus size: 44
35408 CGTCGTTTTG
*
35418 ATTTTTATTTTTATTTAAATTATATATATTATATATTATTAAGT
1 ATTTTTATTTTTATTTAAATTATATATATTATATATTATAAAGT
35462 ATTTTTA-TTTTATTTAAA-T-TATATATTATATATTATAAAGT
1 ATTTTTATTTTTATTTAAATTATATATATTATATATTATAAAGT
35503 ATTTTTATTTTTATTTAAATTATATATATTATATATTATAAAGT
1 ATTTTTATTTTTATTTAAATTATATATATTATATATTATAAAGT
35547 A
1 A
35548 GTATATGATA
Statistics
Matches: 82, Mismatches: 1, Indels: 6
0.92 0.01 0.07
Matches are distributed among these distances:
41 28 0.34
42 12 0.15
43 12 0.15
44 30 0.37
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.59
Consensus pattern (44 bp):
ATTTTTATTTTTATTTAAATTATATATATTATATATTATAAAGT
Found at i:35567 original size:85 final size:86
Alignment explanation
Indices: 35418--35584 Score: 230
Period size: 85 Copynumber: 2.0 Consensus size: 86
35408 CGTCGTTTTG
* * * ** *
35418 ATTTTTATTTTTATTTAAATTATATATATTATATATTATTAAGTATTTTTATTTTATTTAAATTA
1 ATTTTTATTTTTATTTAAATTATATATATTATATATTATAAAGTATGTATATGATATCTAAATTA
*
35483 -TATATTATATATTATAAAGT
66 TTATATAATATATTATAAAGT
*
35503 ATTTTTATTTTTATTTAAATTATATATATTATATATTATAAAGTA-GTATATGATATACTGAATT
1 ATTTTTATTTTTATTTAAATTATATATATTATATATTATAAAGTATGTATATGATAT-CTAAATT
*
35567 ATTATATAATTTATTATA
65 ATTATATAATATATTATA
35585 TATATTATAA
Statistics
Matches: 71, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
84 7 0.10
85 50 0.70
86 14 0.20
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.57
Consensus pattern (86 bp):
ATTTTTATTTTTATTTAAATTATATATATTATATATTATAAAGTATGTATATGATATCTAAATTA
TTATATAATATATTATAAAGT
Found at i:35573 original size:44 final size:45
Alignment explanation
Indices: 35433--35574 Score: 120
Period size: 44 Copynumber: 3.3 Consensus size: 45
35423 TATTTTTATT
* * * *
35433 TAAATTA-TATATATTATATATTATTAAGTATTTTTAT-TTTAT-
1 TAAATTATTATATATTATATATTATAAAGTATGTATATATATATC
* * * * * *
35475 TTAA--ATTATATATTATATATTATAAAGTATTTTTATTTTTATT
1 TAAATTATTATATATTATATATTATAAAGTATGTATATATATATC
35518 TAAATTA-TATATATTATATATTATAAAGTA-GTATATGATATA-C
1 TAAATTATTATATATTATATATTATAAAGTATGTATAT-ATATATC
*
35561 TGAATTATTATATA
1 TAAATTATTATATA
35575 ATTTATTATA
Statistics
Matches: 84, Mismatches: 9, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
40 1 0.01
41 29 0.35
42 8 0.10
43 13 0.15
44 32 0.38
45 1 0.01
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (45 bp):
TAAATTATTATATATTATATATTATAAAGTATGTATATATATATC
Found at i:42302 original size:25 final size:26
Alignment explanation
Indices: 42254--42302 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
42244 ACCCATATTT
*
42254 ATTTTTTAAAATAAAATAATAATTAA
1 ATTTTTTAAAATAAAATAACAATTAA
42280 ATTTTTTAATAA-AAAAT-ACAATT
1 ATTTTTTAA-AATAAAATAACAATT
42303 TAAACATGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 5 0.24
26 14 0.67
27 2 0.10
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (26 bp):
ATTTTTTAAAATAAAATAACAATTAA
Found at i:43525 original size:28 final size:28
Alignment explanation
Indices: 43485--43543 Score: 109
Period size: 28 Copynumber: 2.1 Consensus size: 28
43475 TTTCTGGAGG
*
43485 CATTTAAGCTTTCAAATCCAATGCCAAT
1 CATTTAAGCTTTCAAATCCAATGACAAT
43513 CATTTAAGCTTTCAAATCCAATGACAAT
1 CATTTAAGCTTTCAAATCCAATGACAAT
43541 CAT
1 CAT
43544 CCGGTGGAGG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.37, C:0.24, G:0.07, T:0.32
Consensus pattern (28 bp):
CATTTAAGCTTTCAAATCCAATGACAAT
Done.