Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023474.1 Corchorus olitorius cultivar O-4 contig23507, 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: 17840
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:146 original size:35 final size:35
Alignment explanation
Indices: 100--171 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
90 CTGTGAGACT
*
100 AAGTGAAAAAACTTTGTTCATAATGAGACTAAGCG
1 AAGTGAAAAAACTTTGTTCATAACGAGACTAAGCG
135 AAGTGAAAAAACTTTGTTCATAACGAGACTAAGCG
1 AAGTGAAAAAACTTTGTTCATAACGAGACTAAGCG
170 AA
1 AA
172 ATGTAAGCAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.24
Consensus pattern (35 bp):
AAGTGAAAAAACTTTGTTCATAACGAGACTAAGCG
Found at i:633 original size:30 final size:30
Alignment explanation
Indices: 598--687 Score: 135
Period size: 30 Copynumber: 3.0 Consensus size: 30
588 ATTTTATTAA
*
598 TTTCCAAAATCTTCTTTTGGATTTCTTTAT
1 TTTCCAAAATCTTCTTTTGGATTTCCTTAT
*
628 TTTCCAAAATCTTCTTTTGGAGTTACCTTAT
1 TTTCCAAAATCTTCTTTTGGA-TTTCCTTAT
* *
659 TTTCCAAAATCTTCTTCTGGATTTGCTTA
1 TTTCCAAAATCTTCTTTTGGATTTCCTTA
688 AGAAAAGTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
30 27 0.50
31 27 0.50
ACGTcount: A:0.21, C:0.19, G:0.09, T:0.51
Consensus pattern (30 bp):
TTTCCAAAATCTTCTTTTGGATTTCCTTAT
Found at i:662 original size:31 final size:30
Alignment explanation
Indices: 598--681 Score: 132
Period size: 31 Copynumber: 2.8 Consensus size: 30
588 ATTTTATTAA
* *
598 TTTCCAAAATCTTCTTTTGGATTTCTTTAT
1 TTTCCAAAATCTTCTTTTGGATTACCTTAT
628 TTTCCAAAATCTTCTTTTGGAGTTACCTTAT
1 TTTCCAAAATCTTCTTTTGGA-TTACCTTAT
*
659 TTTCCAAAATCTTCTTCTGGATT
1 TTTCCAAAATCTTCTTTTGGATT
682 TGCTTAAGAA
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
30 23 0.46
31 27 0.54
ACGTcount: A:0.21, C:0.19, G:0.08, T:0.51
Consensus pattern (30 bp):
TTTCCAAAATCTTCTTTTGGATTACCTTAT
Found at i:2901 original size:15 final size:15
Alignment explanation
Indices: 2881--2914 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2871 CAGTGAGCCT
* *
2881 AGAGAGTGTTTTTTG
1 AGAGAGGGTTTCTTG
2896 AGAGAGGGTTTCTTG
1 AGAGAGGGTTTCTTG
2911 AGAG
1 AGAG
2915 TATTTTCTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.03, G:0.38, T:0.35
Consensus pattern (15 bp):
AGAGAGGGTTTCTTG
Found at i:9934 original size:21 final size:21
Alignment explanation
Indices: 9910--9958 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
9900 ATAGTTTAGA
*
9910 TTTAATTTAGTTTGC-TTTATT
1 TTTAATTTAATTT-CTTTTATT
9931 TTTAATTTAATTTCTTTTATT
1 TTTAATTTAATTTCTTTTATT
*
9952 TATAATT
1 TTTAATT
9959 GTTATTCTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 1 0.04
21 24 0.96
ACGTcount: A:0.24, C:0.04, G:0.04, T:0.67
Consensus pattern (21 bp):
TTTAATTTAATTTCTTTTATT
Found at i:10733 original size:21 final size:21
Alignment explanation
Indices: 10709--10753 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
10699 GGCATCCACA
*
10709 TGGTTGCCTTGAGCACCCATG
1 TGGTTGCCTTGAGCACCCAGG
* *
10730 TGGTTTCCTTGAGGACCCAGG
1 TGGTTGCCTTGAGCACCCAGG
10751 TGG
1 TGG
10754 GCAGTGTCAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.13, C:0.24, G:0.33, T:0.29
Consensus pattern (21 bp):
TGGTTGCCTTGAGCACCCAGG
Done.