Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013217.1 Corchorus olitorius cultivar O-4 contig13250, 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: 2455
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Found at i:1553 original size:112 final size:112
Alignment explanation
Indices: 1356--1559 Score: 309
Period size: 112 Copynumber: 1.8 Consensus size: 112
1346 AGAAATAAAT
* * * *
1356 AAATGATATTTTTGATACTTTTTTGGTGGGTTTTGATTCAGCTTTGGTGGTTTTGAAACCACTAG
1 AAATGATATCTTTGATACTTTTTTGGTGGATTTTGATTCAGCCTTGGTGGTTTTGAAACCACCAG
*
1421 TTAAAGAAGCTATCTTTGCTTCTTCAAAAAAATAAAAAATAAGAAAA
66 TTAAAAAAGCTATCTTTGCTTCTTCAAAAAAATAAAAAATAAGAAAA
* ** * * *
1468 AAATGATATCTTTGATACTTTTTTGGTGGATTTTGGTTTGGCCTTGTTGGTTTTGGAACCACCGG
1 AAATGATATCTTTGATACTTTTTTGGTGGATTTTGATTCAGCCTTGGTGGTTTTGAAACCACCAG
1533 TTAAAAAAGCTATCTTTGCTTCTTCAA
66 TTAAAAAAGCTATCTTTGCTTCTTCAA
1560 CCTTCCCACA
Statistics
Matches: 81, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
112 81 1.00
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.41
Consensus pattern (112 bp):
AAATGATATCTTTGATACTTTTTTGGTGGATTTTGATTCAGCCTTGGTGGTTTTGAAACCACCAG
TTAAAAAAGCTATCTTTGCTTCTTCAAAAAAATAAAAAATAAGAAAA
Found at i:2042 original size:15 final size:14
Alignment explanation
Indices: 2007--2090 Score: 57
Period size: 15 Copynumber: 5.9 Consensus size: 14
1997 TAATTTAGAC
2007 TTATTATTATTATAA
1 TTATTATTATTA-AA
2022 -TA--ATTATTAAA
1 TTATTATTATTAAA
***
2033 CTTATTATTAGTGGTA
1 -TTATTATTA-TTAAA
*
2049 TTATAATTATTAAA
1 TTATTATTATTAAA
2063 CTTATTATTATTATAA
1 -TTATTATTATTA-AA
*
2079 TAATTATTATTA
1 TTATTATTATTA
2091 GTGGTATGTA
Statistics
Matches: 53, Mismatches: 9, Indels: 14
0.70 0.12 0.18
Matches are distributed among these distances:
11 2 0.04
12 7 0.13
13 2 0.04
14 4 0.08
15 34 0.64
16 4 0.08
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (14 bp):
TTATTATTATTAAA
Found at i:2055 original size:30 final size:27
Alignment explanation
Indices: 2005--2087 Score: 130
Period size: 30 Copynumber: 3.0 Consensus size: 27
1995 GTTAATTTAG
2005 ACTTATTATTATTATAATAATTATTAA
1 ACTTATTATTATTATAATAATTATTAA
*
2032 ACTTATTATTAGTGGTATTATAATTATTAA
1 ACTTATTATTA-T--TATAATAATTATTAA
2062 ACTTATTATTATTATAATAATTATTA
1 ACTTATTATTATTATAATAATTATTA
2088 TTAGTGGTAT
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
27 24 0.47
28 1 0.02
29 1 0.02
30 25 0.49
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.52
Consensus pattern (27 bp):
ACTTATTATTATTATAATAATTATTAA
Found at i:2059 original size:9 final size:9
Alignment explanation
Indices: 2007--2088 Score: 60
Period size: 9 Copynumber: 8.8 Consensus size: 9
1997 TAATTTAGAC
*
2007 TTATTATTA
1 TTATTATAA
*
2016 TTATAATAA
1 TTATTATAA
2025 TTATTA-AA
1 TTATTATAA
*
2033 CTTATTATTAG
1 -TTATTA-TAA
2044 TGGTATTATAA
1 T--TATTATAA
2055 TTATTA-AA
1 TTATTATAA
*
2063 CTTATTATTA
1 -TTATTATAA
*
2073 TTATAATAA
1 TTATTATAA
2082 TTATTAT
1 TTATTAT
2089 TAGTGGTATG
Statistics
Matches: 57, Mismatches: 9, Indels: 14
0.71 0.11 0.17
Matches are distributed among these distances:
8 4 0.07
9 42 0.74
10 2 0.04
11 4 0.07
12 5 0.09
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (9 bp):
TTATTATAA
Done.