Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019516.1 Corchorus olitorius cultivar O-4 contig19549, 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: 12142
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:4242 original size:41 final size:41
Alignment explanation
Indices: 4173--4619 Score: 599
Period size: 41 Copynumber: 10.9 Consensus size: 41
4163 GTTTGATTTG
* * * * * * *
4173 ATTTGATTCAAGGGT-TGGGTGACTTGGTCTTGAATTAACA
1 ATTTAATTCAAGGGTCTCGATGACTCGTTCTTGAATTGATA
* * * *
4213 ATCTAATTCAAGGGTCTTGATGACTTGGTCTTGAATTGATA
1 ATTTAATTCAAGGGTCTCGATGACTCGTTCTTGAATTGATA
* * * *
4254 ATAATTCGATCCAAGAGTCTCGATGACTTGTTCTTGAATTGATA
1 AT--TT-AATTCAAGGGTCTCGATGACTCGTTCTTGAATTGATA
* *
4298 ATCTAATTCAAGGGTCTCGATGACTTGTTCTTGAATTGATA
1 ATTTAATTCAAGGGTCTCGATGACTCGTTCTTGAATTGATA
* **
4339 ATTTAATTTAAGGGTCTCGATGACTCAATCTTGAATTGATA
1 ATTTAATTCAAGGGTCTCGATGACTCGTTCTTGAATTGATA
*
4380 ATTTAATTCGAGGGTCTCGATGACTCGTTCTTGAATTGATA
1 ATTTAATTCAAGGGTCTCGATGACTCGTTCTTGAATTGATA
*
4421 ATTTAATTCAAGGGTCTTGATGACTCGTTCTTGAATTGATA
1 ATTTAATTCAAGGGTCTCGATGACTCGTTCTTGAATTGATA
*
4462 ATTTAATTCAAGGGTCTCGATGACTCGTTCTTCAATTGATA
1 ATTTAATTCAAGGGTCTCGATGACTCGTTCTTGAATTGATA
**
4503 ATTTAATTCAAGGGTCTCGATGACTCAATCTTGAATTGATA
1 ATTTAATTCAAGGGTCTCGATGACTCGTTCTTGAATTGATA
**
4544 ATTTAATTCAAGGGTCTCGATGACTCAATCTTGAATTGATA
1 ATTTAATTCAAGGGTCTCGATGACTCGTTCTTGAATTGATA
* *
4585 ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAA
1 ATTTAATTCAAGGGTCTCGATGACTCGTTCTTGAA
4620 CAAACGAAAA
Statistics
Matches: 369, Mismatches: 34, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
40 13 0.04
41 320 0.87
42 1 0.00
43 1 0.00
44 34 0.09
ACGTcount: A:0.28, C:0.14, G:0.20, T:0.38
Consensus pattern (41 bp):
ATTTAATTCAAGGGTCTCGATGACTCGTTCTTGAATTGATA
Found at i:5499 original size:63 final size:62
Alignment explanation
Indices: 5417--5545 Score: 177
Period size: 63 Copynumber: 2.1 Consensus size: 62
5407 AGTTCATTTA
* * ** * *
5417 TTTTTGTGCTTTAAGTTTTGCCAAAGTCGTCCTTTGTAGGATTTTCAACTTAGCGAGCTTTT
1 TTTTTGTGCTCTAACTTTTGCCAAAGTCGTCCTTTACAGGATTTTCAACTTAGCAAGCTCTT
* *
5479 TTTTTGGTGCTCTAACTTTTGCCTAAGTTGTCCTTTACAGGATTTTCAACTTAGCAAGCTCTT
1 TTTTT-GTGCTCTAACTTTTGCCAAAGTCGTCCTTTACAGGATTTTCAACTTAGCAAGCTCTT
5542 TTTT
1 TTTT
5546 CCCCCATTTT
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
62 5 0.09
63 53 0.91
ACGTcount: A:0.18, C:0.18, G:0.17, T:0.47
Consensus pattern (62 bp):
TTTTTGTGCTCTAACTTTTGCCAAAGTCGTCCTTTACAGGATTTTCAACTTAGCAAGCTCTT
Found at i:7343 original size:41 final size:41
Alignment explanation
Indices: 7273--7719 Score: 601
Period size: 41 Copynumber: 10.9 Consensus size: 41
7263 GTTTGATTTG
* * * *
7273 ATTTGATTCAAGGGT-T-GAATGACTTGGTCTTGAATTAACA
1 ATTTAATTCAAGGGTCTCG-ATGACTTGATCTTGAATTGATA
* * * *
7313 ATCTAATTCAAGGGTCTTGACGACTTGGTCTTGAATTGATA
1 ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAATTGATA
* * * *
7354 ATAATTCGATTCAAGAGTTTCGATGACTTGTTCTTGAATTGATA
1 AT--TT-AATTCAAGGGTCTCGATGACTTGATCTTGAATTGATA
** *
7398 ATCCAATTCAAGGGTCTCGATGACTTGTTCTTGAATTGATA
1 ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAATTGATA
**
7439 ATTTAATTCAAGGGTCTCGATGACTCAATCTTGAATTGATA
1 ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAATTGATA
*
7480 ATTTAATTCAAGGGTCTCGATGACTTGTTCTTGAATTGATA
1 ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAATTGATA
* *
7521 ATTTAATTCAAGGGTCTCGATGACTCGTTCTTGAATTGATA
1 ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAATTGATA
** *
7562 ATTTAATTCAAGGGTCTCGATGACTCAATCTTGAATTAATA
1 ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAATTGATA
**
7603 ATTTAATTCAAGGGTCTCGATGACTCAATCTTGAATTGATA
1 ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAATTGATA
* *
7644 ATTTAATTCAAGGGCCTCGATGACTTAATCTTGAATTGATA
1 ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAATTGATA
7685 ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAA
1 ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAA
7720 CAAACGAAAA
Statistics
Matches: 368, Mismatches: 34, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
40 13 0.04
41 320 0.87
42 1 0.00
43 1 0.00
44 33 0.09
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.38
Consensus pattern (41 bp):
ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAATTGATA
Found at i:10022 original size:2 final size:2
Alignment explanation
Indices: 10017--10052 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
10007 ACACACACAC
10017 AT 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
10053 TATTTTTCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11715 original size:29 final size:30
Alignment explanation
Indices: 11679--11744 Score: 100
Period size: 29 Copynumber: 2.2 Consensus size: 30
11669 ATTTGTACGG
11679 TTTGGACGCTTTGCCCCA-TAAACT-TCAAT
1 TTTGGACGCTTTG-CCCAGTAAACTCTCAAT
*
11708 TTTGGACGTTTTGCCCAGTAAACTCTCAAT
1 TTTGGACGCTTTGCCCAGTAAACTCTCAAT
11738 TTTGGAC
1 TTTGGAC
11745 ATTTTTGTCC
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
28 4 0.12
29 18 0.53
30 12 0.35
ACGTcount: A:0.23, C:0.24, G:0.17, T:0.36
Consensus pattern (30 bp):
TTTGGACGCTTTGCCCAGTAAACTCTCAAT
Done.