Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017728.1 Corchorus olitorius cultivar O-4 contig17761, 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: 8707
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.36
Found at i:3894 original size:18 final size:18
Alignment explanation
Indices: 3871--3908 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
3861 TAGAGTACTA
3871 ATCTTATCTTATCTCACT
1 ATCTTATCTTATCTCACT
*
3889 ATCTTATCTTATCTTACT
1 ATCTTATCTTATCTCACT
3907 AT
1 AT
3909 ATATACTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCTTATCTCACT
Found at i:3918 original size:5 final size:5
Alignment explanation
Indices: 3903--3936 Score: 61
Period size: 5 Copynumber: 7.0 Consensus size: 5
3893 TATCTTATCT
3903 TACTA TA-TA TACTA TACTA TACTA TACTA TACTA
1 TACTA TACTA TACTA TACTA TACTA TACTA TACTA
3937 CTATATAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.14
5 24 0.86
ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41
Consensus pattern (5 bp):
TACTA
Found at i:3930 original size:15 final size:14
Alignment explanation
Indices: 3903--3943 Score: 64
Period size: 15 Copynumber: 2.8 Consensus size: 14
3893 TATCTTATCT
3903 TACTATATATACTA
1 TACTATATATACTA
3917 TACTATACTATACTA
1 TACTATA-TATACTA
3932 TACTACTATATA
1 TACTA-TATATA
3944 AAATCACGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.28
15 16 0.64
16 2 0.08
ACGTcount: A:0.41, C:0.17, G:0.00, T:0.41
Consensus pattern (14 bp):
TACTATATATACTA
Found at i:4746 original size:5 final size:5
Alignment explanation
Indices: 4736--4787 Score: 52
Period size: 5 Copynumber: 9.8 Consensus size: 5
4726 GTCCTTAATG
*
4736 AATAA AATAA AATAA AATAA TAA-AA TAATAA AATAA ATATAA TAATAT
1 AATAA AATAA AATAA AATAA -AATAA -AATAA AATAA A-ATAA -AATAA
4784 AATA
1 AATA
4788 TAATTTTTAT
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
5 30 0.71
6 11 0.26
7 1 0.02
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (5 bp):
AATAA
Found at i:4759 original size:8 final size:8
Alignment explanation
Indices: 4736--4787 Score: 59
Period size: 8 Copynumber: 6.1 Consensus size: 8
4726 GTCCTTAATG
4736 AATAAAAT
1 AATAAAAT
4744 AAAATAAAAT
1 --AATAAAAT
4754 AATAAAAT
1 AATAAAAT
4762 AATAAAAT
1 AATAAAAT
*
4770 AAATATAAT
1 -AATAAAAT
*
4779 AATATAAT
1 AATAAAAT
4787 A
1 A
4788 TAATTTTTAT
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
8 25 0.62
9 7 0.17
10 8 0.20
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (8 bp):
AATAAAAT
Found at i:4759 original size:13 final size:13
Alignment explanation
Indices: 4736--4791 Score: 69
Period size: 13 Copynumber: 4.2 Consensus size: 13
4726 GTCCTTAATG
4736 AATAAAATAAAAT
1 AATAAAATAAAAT
4749 AA-AATAATAAAAT
1 AATAA-AATAAAAT
4762 AATAAAATAAATAT
1 AATAAAATAAA-AT
* *
4776 AATAATATAATAT
1 AATAAAATAAAAT
4789 AAT
1 AAT
4792 TTTTATATGA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
12 2 0.05
13 23 0.61
14 13 0.34
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
AATAAAATAAAAT
Found at i:7663 original size:21 final size:22
Alignment explanation
Indices: 7639--7684 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
7629 TTACAATTGG
7639 ATATTTGAGAATGAT-ATATAT
1 ATATTTGAGAATGATGATATAT
7660 ATA-TTGAGAATGATGATATAT
1 ATATTTGAGAATGATGATATAT
7681 ATAT
1 ATAT
7685 GCTATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.43, C:0.00, G:0.15, T:0.41
Consensus pattern (22 bp):
ATATTTGAGAATGATGATATAT
Found at i:7692 original size:11 final size:11
Alignment explanation
Indices: 7676--7700 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
7666 AGAATGATGA
7676 TATATATATGC
1 TATATATATGC
7687 TATATATATGC
1 TATATATATGC
7698 TAT
1 TAT
7701 TGAGACATGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.48
Consensus pattern (11 bp):
TATATATATGC
Found at i:8509 original size:5 final size:5
Alignment explanation
Indices: 8499--8523 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
8489 GTTTCTTGTG
8499 ATTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT
8524 TCTCATTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Done.