Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023233.1 Corchorus olitorius cultivar O-4 contig23266, 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: 29346
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.30
Found at i:2416 original size:21 final size:22
Alignment explanation
Indices: 2392--2432 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
2382 TAATTAAATG
*
2392 CAATTTGGCCCCTG-TTTTATT
1 CAATTTGACCCCTGATTTTATT
2413 CAATTTGACCCCTGATTTTA
1 CAATTTGACCCCTGATTTTA
2433 GAAATTATGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.20, C:0.24, G:0.12, T:0.44
Consensus pattern (22 bp):
CAATTTGACCCCTGATTTTATT
Found at i:3543 original size:14 final size:15
Alignment explanation
Indices: 3518--3547 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
3508 AAGAAGCAAT
3518 AAAAGGTGTTTTCAA
1 AAAAGGTGTTTTCAA
3533 AAAAGGT-TTTTCAA
1 AAAAGGTGTTTTCAA
3547 A
1 A
3548 TCATGTTCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.43, C:0.07, G:0.17, T:0.33
Consensus pattern (15 bp):
AAAAGGTGTTTTCAA
Found at i:5045 original size:15 final size:14
Alignment explanation
Indices: 5016--5053 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
5006 AATAAAACAT
*
5016 CAAAGCAAACGAAA
1 CAAAACAAACGAAA
5030 CAAAACAAACCGAAA
1 CAAAACAAA-CGAAA
5045 CAAAACAAA
1 CAAAACAAA
5054 GCAACCATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 8 0.36
15 14 0.64
ACGTcount: A:0.68, C:0.24, G:0.08, T:0.00
Consensus pattern (14 bp):
CAAAACAAACGAAA
Found at i:9599 original size:27 final size:27
Alignment explanation
Indices: 9559--9631 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
9549 AAAGTGAACT
* *
9559 AAAAATGACTAAAACGCCCTTGAATGT-
1 AAAAATGACCAAAATGCCCTT-AATGTA
**
9586 GCAAATGACCAAAATGCCCTTAATGTA
1 AAAAATGACCAAAATGCCCTTAATGTA
9613 AAAAATGACCAAAATGCCC
1 AAAAATGACCAAAATGCCC
9632 CTGGGTGACC
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
26 5 0.13
27 34 0.87
ACGTcount: A:0.45, C:0.22, G:0.14, T:0.19
Consensus pattern (27 bp):
AAAAATGACCAAAATGCCCTTAATGTA
Found at i:10426 original size:84 final size:84
Alignment explanation
Indices: 10285--10614 Score: 434
Period size: 84 Copynumber: 3.9 Consensus size: 84
10275 GTAAAGAGAA
* * *
10285 ATGCCTCTGTGTTATAAATGTATTTGAGGACTTTGAGATAGAGGTG-CCCTTGTGTTATAAATGT
1 ATGCCTCTGTGTTATAAATGTGTTTGAGGACTTTGAGAGAGAAGTGACCC-TGTGTTATAAATGT
* *
10349 GTTTGGGGATTTTAGTATGG
65 GTTTGGGGACTTTAGTATAG
* * *
10369 ATGCCTCTGTGTTATAAATGTGTTTGAGGACTTTTAGAGAGAATTG-CCTCTGTGTTATAATTGT
1 ATGCCTCTGTGTTATAAATGTGTTTGAGGACTTTGAGAGAGAAGTGACC-CTGTGTTATAAATGT
*
10433 GTTTGGGGACTTTGGTATAG
65 GTTTGGGGACTTTAGTATAG
* *
10453 ATGCCTCTGTGTTATAAATGTGTTTGAGGACTTTGAAATA-AAGGTGACCCTGTGTTATAAATGT
1 ATGCCTCTGTGTTATAAATGTGTTTGAGGACTTTGAGAGAGAA-GTGACCCTGTGTTATAAATGT
10517 GTTTGGGGACTTT-GATATAG
65 GTTTGGGGACTTTAG-TATAG
* * * * * *
10537 ATGCCTCTGTGTTATAATTGTGTTTGAGGACTTTAGAAAGAGAATTGTCCATGTGTTATAATTGT
1 ATGCCTCTGTGTTATAAATGTGTTTGAGGACTTT-GAGAGAGAAGTGACCCTGTGTTATAAATGT
10602 GTTTGGGGACTTT
65 GTTTGGGGACTTT
10615 TAGTTATTGG
Statistics
Matches: 220, Mismatches: 20, Indels: 11
0.88 0.08 0.04
Matches are distributed among these distances:
83 3 0.01
84 177 0.80
85 38 0.17
86 2 0.01
ACGTcount: A:0.23, C:0.09, G:0.27, T:0.41
Consensus pattern (84 bp):
ATGCCTCTGTGTTATAAATGTGTTTGAGGACTTTGAGAGAGAAGTGACCCTGTGTTATAAATGTG
TTTGGGGACTTTAGTATAG
Found at i:10434 original size:43 final size:42
Alignment explanation
Indices: 10279--10617 Score: 297
Period size: 43 Copynumber: 8.0 Consensus size: 42
10269 TTTTCCGTAA
* *
10279 AGAGA-AATGCCTCTGTGTTATAAATGTATTTGAGGACTTTG
1 AGAGAGAATGCCTCTGTGTTATAAATGTGTTTGAGGACTTTT
* * *
10320 AGATAGAGGTGCC-CTTGTGTTATAAATGTGTTTGGGGA-TTTT
1 AGAGAGA-ATGCCTC-TGTGTTATAAATGTGTTTGAGGACTTTT
10362 AGTATG-G-ATGCCTCTGTGTTATAAATGTGTTTGAGGACTTTT
1 AG-A-GAGAATGCCTCTGTGTTATAAATGTGTTTGAGGACTTTT
* *
10404 AGAGAGAATTGCCTCTGTGTTATAATTGTGTTTGGGGAC-TTT
1 AGAGAGAA-TGCCTCTGTGTTATAAATGTGTTTGAGGACTTTT
* * *
10446 GGTATAG-ATGCCTCTGTGTTATAAATGTGTTTGAGGACTTTG
1 AG-AGAGAATGCCTCTGTGTTATAAATGTGTTTGAGGACTTTT
* * * *
10488 AAATA-AAGGTGACC-CTGTGTTATAAATGTGTTTGGGGACTTTG
1 AGAGAGAA--TG-CCTCTGTGTTATAAATGTGTTTGAGGACTTTT
* * *
10531 ATATAG-ATGCCTCTGTGTTATAATTGTGTTTGAGGAC-TTT
1 AGAGAGAATGCCTCTGTGTTATAAATGTGTTTGAGGACTTTT
* * *
10571 AGAAAGAGAATTGTCC-ATGTGTTATAATTGTGTTTGGGGACTTTT
1 AG--AGAGAA-TG-CCTCTGTGTTATAAATGTGTTTGAGGACTTTT
10616 AG
1 AG
10618 TTATTGGGTA
Statistics
Matches: 248, Mismatches: 26, Indels: 44
0.78 0.08 0.14
Matches are distributed among these distances:
40 6 0.02
41 89 0.36
42 25 0.10
43 94 0.38
44 27 0.11
45 7 0.03
ACGTcount: A:0.24, C:0.09, G:0.27, T:0.40
Consensus pattern (42 bp):
AGAGAGAATGCCTCTGTGTTATAAATGTGTTTGAGGACTTTT
Found at i:10563 original size:168 final size:168
Alignment explanation
Indices: 10285--10614 Score: 524
Period size: 168 Copynumber: 2.0 Consensus size: 168
10275 GTAAAGAGAA
* *
10285 ATGCCTCTGTGTTATAAATGTATTTGAGGACTTTGAGATAGAGGTGCCCTTGTGTTATAAATGTG
1 ATGCCTCTGTGTTATAAATGTATTTGAGGACTTTGAAATAAAGGTGCCCTTGTGTTATAAATGTG
* *
10350 TTTGGGGATTTTAGTATGGATGCCTCTGTGTTATAAATGTGTTTGAGGACTTTTAG-AGAGAATT
66 TTTGGGGATTTGAGTATAGATGCCTCTGTGTTATAAATGTGTTTGAGGAC-TTTAGAAGAGAATT
*
10414 G-CCTCTGTGTTATAATTGTGTTTGGGGACTTTGGTATAG
130 GTCC-ATGTGTTATAATTGTGTTTGGGGACTTTGGTATAG
*
10453 ATGCCTCTGTGTTATAAATGTGTTTGAGGACTTTGAAATAAAGGTGACCC-TGTGTTATAAATGT
1 ATGCCTCTGTGTTATAAATGTATTTGAGGACTTTGAAATAAAGGTG-CCCTTGTGTTATAAATGT
*
10517 GTTTGGGGACTTTGA-TATAGATGCCTCTGTGTTATAATTGTGTTTGAGGACTTTAGAAAGAGAA
65 GTTTGGGGA-TTTGAGTATAGATGCCTCTGTGTTATAAATGTGTTTGAGGACTTTAG-AAGAGAA
10581 TTGTCCATGTGTTATAATTGTGTTTGGGGACTTT
128 TTGTCCATGTGTTATAATTGTGTTTGGGGACTTT
10615 TAGTTATTGG
Statistics
Matches: 150, Mismatches: 7, Indels: 9
0.90 0.04 0.05
Matches are distributed among these distances:
167 5 0.03
168 100 0.67
169 43 0.29
170 2 0.01
ACGTcount: A:0.23, C:0.09, G:0.27, T:0.41
Consensus pattern (168 bp):
ATGCCTCTGTGTTATAAATGTATTTGAGGACTTTGAAATAAAGGTGCCCTTGTGTTATAAATGTG
TTTGGGGATTTGAGTATAGATGCCTCTGTGTTATAAATGTGTTTGAGGACTTTAGAAGAGAATTG
TCCATGTGTTATAATTGTGTTTGGGGACTTTGGTATAG
Found at i:22308 original size:18 final size:18
Alignment explanation
Indices: 22285--22321 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
22275 TTGGACTATT
22285 ACATTCTGTACGAGGAAA
1 ACATTCTGTACGAGGAAA
22303 ACATTCTGTACGAGGAAA
1 ACATTCTGTACGAGGAAA
22321 A
1 A
22322 GAACCGGCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.16, G:0.22, T:0.22
Consensus pattern (18 bp):
ACATTCTGTACGAGGAAA
Found at i:24443 original size:118 final size:118
Alignment explanation
Indices: 24235--24472 Score: 449
Period size: 118 Copynumber: 2.0 Consensus size: 118
24225 ACAGAATTCT
* *
24235 CAATGGGTATAGGTATATAAGTACTTTTATGAGTTAATGACAAAAGCTAAAACTCATGTCAGCTT
1 CAATGGGTATAGGTATATAAGTACTTTTATGAATTAATGACAAAAGCTAAAACTCATGTAAGCTT
24300 ATCACAGTCACTGAGAACAAATGCATTCTTCACAACCAGTACTACTGAAGTCC
66 ATCACAGTCACTGAGAACAAATGCATTCTTCACAACCAGTACTACTGAAGTCC
24353 CAATGGGTATAGGTATATAAGTACTTTTATGAATTAATGACAAAAGCTAAAACTCATGTAAGCTT
1 CAATGGGTATAGGTATATAAGTACTTTTATGAATTAATGACAAAAGCTAAAACTCATGTAAGCTT
*
24418 ATCACAGTCACTGAGACCAAATGCATTCTTCACAACCAGTACTACTGAAGTCC
66 ATCACAGTCACTGAGAACAAATGCATTCTTCACAACCAGTACTACTGAAGTCC
24471 CA
1 CA
24473 TTGGAATACT
Statistics
Matches: 117, Mismatches: 3, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
118 117 1.00
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.28
Consensus pattern (118 bp):
CAATGGGTATAGGTATATAAGTACTTTTATGAATTAATGACAAAAGCTAAAACTCATGTAAGCTT
ATCACAGTCACTGAGAACAAATGCATTCTTCACAACCAGTACTACTGAAGTCC
Done.