Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016163.1 Corchorus olitorius cultivar O-4 contig16196, 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: 23684
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Found at i:360 original size:20 final size:20
Alignment explanation
Indices: 335--384 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
325 ATAGTCCAAG
*
335 AGGGGGTGGTGGCTAGTAAA
1 AGGGGGCGGTGGCTAGTAAA
355 AGGGGGCGGTGGCTAGTAAA
1 AGGGGGCGGTGGCTAGTAAA
375 AGGGGGCGGT
1 AGGGGGCGGT
385 ATTTAGTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.22, C:0.08, G:0.54, T:0.16
Consensus pattern (20 bp):
AGGGGGCGGTGGCTAGTAAA
Found at i:410 original size:18 final size:18
Alignment explanation
Indices: 387--429 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 18
377 GGGGCGGTAT
387 TTAGTAATACCTAAATAA
1 TTAGTAATACCTAAATAA
*
405 TTAGT-ATCCCTAAATAA
1 TTAGTAATACCTAAATAA
422 TTAG-AATA
1 TTAGTAATA
430 ATTAGTTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 17 0.77
18 5 0.23
ACGTcount: A:0.47, C:0.12, G:0.07, T:0.35
Consensus pattern (18 bp):
TTAGTAATACCTAAATAA
Found at i:469 original size:2 final size:2
Alignment explanation
Indices: 462--493 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
452 TTCATAGTAC
*
462 TA TA TA TA TC TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
494 CTAGTTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1526 original size:150 final size:149
Alignment explanation
Indices: 1291--1577 Score: 409
Period size: 150 Copynumber: 1.9 Consensus size: 149
1281 TCACAATCAC
* *
1291 CTTTTAAATTCAAATAGTAAAAATAAAATGATTATAAAAATATTGAATTTAATTAAATGAAAATA
1 CTTTTAAATTAAAATAGTAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATGAAAATA
** * *
1356 ATTTTTTTTGTAAAATAAAACTGTATATTAAAAAATCTTAATATATCCAAGTTTTTAATGAAAAA
66 ATACTTTTAGTAAAATAAAACTGTATATTAAAAAAT-TTAACATATCCAAG-TTTTAATGAAAAA
1421 TAGTAAAATGGTAGAAATAAA
129 TAGTAAAATGGTAGAAATAAA
1442 CTTTTAAATTAAAAT-GATAAAAATAAAATAATTAT-AAAATATTGAATTTAATTAAATGAAAAT
1 CTTTTAAATTAAAATAG-TAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATGAAAAT
* * ** *
1505 -ATAACTTTTAGTAGAATAAAACTGTATATTAAAATATTTTGCATATCCTAGTTTTAATGAAAAA
65 AAT-ACTTTTAGTAAAATAAAACTGTATATTAAAAAATTTAACATATCCAAGTTTTAATGAAAAA
*
1569 TATTAAAAT
129 TAGTAAAAT
1578 TAAAAAGAAA
Statistics
Matches: 122, Mismatches: 12, Indels: 7
0.87 0.09 0.05
Matches are distributed among these distances:
148 21 0.17
149 12 0.10
150 58 0.48
151 31 0.25
ACGTcount: A:0.51, C:0.04, G:0.07, T:0.37
Consensus pattern (149 bp):
CTTTTAAATTAAAATAGTAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATGAAAATA
ATACTTTTAGTAAAATAAAACTGTATATTAAAAAATTTAACATATCCAAGTTTTAATGAAAAATA
GTAAAATGGTAGAAATAAA
Found at i:2547 original size:17 final size:17
Alignment explanation
Indices: 2525--2574 Score: 82
Period size: 17 Copynumber: 2.9 Consensus size: 17
2515 CGAAAAACCC
*
2525 AAAACCCGAATGACCTA
1 AAAACCCGAGTGACCTA
2542 AAAACCCGAGTGACCTA
1 AAAACCCGAGTGACCTA
*
2559 AAAATCCGAGTGACCT
1 AAAACCCGAGTGACCT
2575 GAGGCCAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.42, C:0.28, G:0.16, T:0.14
Consensus pattern (17 bp):
AAAACCCGAGTGACCTA
Found at i:3303 original size:22 final size:22
Alignment explanation
Indices: 3278--3324 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
3268 TTTTTAGTTG
* *
3278 AGTAAAATTATAAAAGTAAAAT
1 AGTAAAATGATAAAAATAAAAT
*
3300 AGTAAAATGGTAAAAATAAAAT
1 AGTAAAATGATAAAAATAAAAT
3322 AGT
1 AGT
3325 TATAAGGATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.62, C:0.00, G:0.13, T:0.26
Consensus pattern (22 bp):
AGTAAAATGATAAAAATAAAAT
Found at i:3303 original size:93 final size:93
Alignment explanation
Indices: 3201--3385 Score: 307
Period size: 93 Copynumber: 2.0 Consensus size: 93
3191 ACTTTTTAAT
* *
3201 TAAATTAGTAATATCGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAG
1 TAAAATAGTAAAATCGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAG
* * *
3266 AGTTTTTAGTTGAGTAAAATTATAAAAG
66 AGTTTTTAGCTGACTAAAACTATAAAAG
* *
3294 TAAAATAGTAAAATGGTAAAAATAAAATAGTTATAAGGATATTAGATTTAATTAAATAAAAATAG
1 TAAAATAGTAAAATCGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAG
3359 AGTTTTTAGCTGACTAAAACTATAAAA
66 AGTTTTTAGCTGACTAAAACTATAAAA
3386 ATTTAAACAA
Statistics
Matches: 85, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 85 1.00
ACGTcount: A:0.52, C:0.02, G:0.13, T:0.33
Consensus pattern (93 bp):
TAAAATAGTAAAATCGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAG
AGTTTTTAGCTGACTAAAACTATAAAAG
Found at i:4422 original size:100 final size:102
Alignment explanation
Indices: 4257--4455 Score: 294
Period size: 100 Copynumber: 2.0 Consensus size: 102
4247 ATCTAAATTT
* * *
4257 TTTTAATTAAATTAGTAAAATGGTGAAAATAAAAAAGATATAAGGATATTAAAATTAATTAAATA
1 TTTTAATTAAAATACTAAAATGGTGAAAATAAAAAAGATATAAGGACATTAAAATTAATTAAATA
*
4322 AAAATAGAGTTTCTAGTTAAGTAAAGCTATAAAAGTA
66 AAAATAGAGTTTCTAGTTAAGTAAAACTATAAAAGTA
* * * *
4359 TTTTAATTAAAATACTAAAATGGT-AAAA-AAAATAGTTATAAGGACATTAGATTTAATTAAATA
1 TTTTAATTAAAATACTAAAATGGTGAAAATAAAAAAGATATAAGGACATTAAAATTAATTAAATA
* *
4422 AAAATAGAGTTTTTAGTTGAGTAAAACTATAAAA
66 AAAATAGAGTTTCTAGTTAAGTAAAACTATAAAA
4456 ATTTAAACAA
Statistics
Matches: 87, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
100 61 0.70
101 4 0.05
102 22 0.25
ACGTcount: A:0.52, C:0.03, G:0.12, T:0.33
Consensus pattern (102 bp):
TTTTAATTAAAATACTAAAATGGTGAAAATAAAAAAGATATAAGGACATTAAAATTAATTAAATA
AAAATAGAGTTTCTAGTTAAGTAAAACTATAAAAGTA
Found at i:9573 original size:37 final size:37
Alignment explanation
Indices: 9499--9573 Score: 84
Period size: 37 Copynumber: 2.0 Consensus size: 37
9489 CATTAATCAC
* *
9499 TATTATATTATTATATTATTATTATTATTGTACAATA
1 TATTATATTATTATATTACTATTATGATTGTACAATA
9536 TATTATATTA-TATGATATACTA-TATGATT-TACTAATA
1 TATTATATTATTAT-AT-TACTATTATGATTGTAC-AATA
9573 T
1 T
9574 GTTAGGTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
36 6 0.18
37 23 0.70
38 4 0.12
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.53
Consensus pattern (37 bp):
TATTATATTATTATATTACTATTATGATTGTACAATA
Found at i:11240 original size:14 final size:14
Alignment explanation
Indices: 11221--11247 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
11211 AACACTTGCA
11221 TTATATAAATTTAT
1 TTATATAAATTTAT
11235 TTATATAAATTTA
1 TTATATAAATTTA
11248 ATTACTTGCA
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:0.00, T:0.56
Consensus pattern (14 bp):
TTATATAAATTTAT
Found at i:12080 original size:2 final size:2
Alignment explanation
Indices: 12073--12106 Score: 52
Period size: 2 Copynumber: 17.0 Consensus size: 2
12063 TTAGTATAAA
12073 AT AT AT AT AT AT AT AT AT A- AT AT ACT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
12107 GTATCCTCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 27 0.90
3 2 0.07
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:13598 original size:7 final size:7
Alignment explanation
Indices: 13581--13621 Score: 66
Period size: 7 Copynumber: 5.9 Consensus size: 7
13571 CCCTCTCCAA
13581 AAAAAAT
1 AAAAAAT
13588 -AAAAAT
1 AAAAAAT
13594 AAAAAAT
1 AAAAAAT
13601 AAATAAAT
1 AAA-AAAT
13609 AAAAAAT
1 AAAAAAT
13616 AAAAAA
1 AAAAAA
13622 GATGGTTTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 6 0.19
7 19 0.59
8 7 0.22
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
AAAAAAT
Found at i:13599 original size:15 final size:15
Alignment explanation
Indices: 13579--13621 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
13569 CTCCCTCTCC
13579 AAAAAA-AATAAAAAT
1 AAAAAATAA-AAAAAT
*
13594 AAAAAATAAATAAAT
1 AAAAAATAAAAAAAT
13609 AAAAAATAAAAAA
1 AAAAAATAAAAAA
13622 GATGGTTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 23 0.92
16 2 0.08
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (15 bp):
AAAAAATAAAAAAAT
Found at i:13604 original size:11 final size:11
Alignment explanation
Indices: 13579--13618 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
13569 CTCCCTCTCC
13579 AAAAA-AAAT-
1 AAAAATAAATA
13588 AAAAATAAA-A
1 AAAAATAAATA
13598 AATAAATAAATA
1 AA-AAATAAATA
13610 AAAAATAAA
1 AAAAATAAA
13619 AAAGATGGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
9 5 0.19
10 5 0.19
11 14 0.52
12 3 0.11
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAAATAAATA
Found at i:20100 original size:2 final size:2
Alignment explanation
Indices: 20093--20125 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
20083 TGAATTAAAC
20093 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20126 TTGGTTATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:23591 original size:2 final size:2
Alignment explanation
Indices: 23584--23671 Score: 176
Period size: 2 Copynumber: 44.0 Consensus size: 2
23574 TTTCAAGGGG
23584 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
23626 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
23668 AC AC
1 AC AC
23672 TACTTGTTAC
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 86 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Done.