Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016653.1 Corchorus olitorius cultivar O-4 contig16686, 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: 9288
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Found at i:449 original size:51 final size:51
Alignment explanation
Indices: 365--467 Score: 127
Period size: 51 Copynumber: 2.0 Consensus size: 51
355 TTCATATTTT
** *
365 TCTTGTTTAGATCTTGTCTCAGGACACCCAAACACTCTTTTAGTGTTTCTC
1 TCTTGTTTAGATCTTGTCTCAGGACACAAAAACACTCTATTAGTGTTTCTC
* * * *
416 TCTTGTTTCA-ATCTTGTCTCCGGACATAAAAACACTGTATTCGTGTTTCTC
1 TCTTGTTT-AGATCTTGTCTCAGGACACAAAAACACTCTATTAGTGTTTCTC
467 T
1 T
468 TTCAGAAATA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
51 43 0.98
52 1 0.02
ACGTcount: A:0.20, C:0.24, G:0.14, T:0.42
Consensus pattern (51 bp):
TCTTGTTTAGATCTTGTCTCAGGACACAAAAACACTCTATTAGTGTTTCTC
Found at i:2052 original size:42 final size:42
Alignment explanation
Indices: 2001--2084 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
1991 CTCATCAAAC
* * * *
2001 CAACTTTTAAATCCGTATATATTTTCTTTTACCTTAATTAAA
1 CAACATTTAAATCAGTATATATTTACTTTCACCTTAATTAAA
* * *
2043 CAACATTTAATTCATTATATGTTTACTTTCACCTTAATTAAA
1 CAACATTTAAATCAGTATATATTTACTTTCACCTTAATTAAA
2085 TAAAAAAAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.35, C:0.17, G:0.02, T:0.46
Consensus pattern (42 bp):
CAACATTTAAATCAGTATATATTTACTTTCACCTTAATTAAA
Found at i:3759 original size:22 final size:22
Alignment explanation
Indices: 3687--3793 Score: 76
Period size: 22 Copynumber: 4.9 Consensus size: 22
3677 TTGAACTTTA
* * * *
3687 ATAACTACAATATGAAATTCTA
1 ATAACCACACTATGAAATTTTG
3709 ATAACCATC-CTATGAAATTTTG
1 ATAACCA-CACTATGAAATTTTG
* * *
3731 GTCACCACACTCTGAAATTTTG
1 ATAACCACACTATGAAATTTTG
* *
3753 ATAACCACAGTAT-AAACTTGTG
1 ATAACCACACTATGAAA-TTTTG
*
3775 ATAACCTCTA-TATGAAATT
1 ATAACCAC-ACTATGAAATT
3794 AATTTTGATG
Statistics
Matches: 67, Mismatches: 13, Indels: 10
0.74 0.14 0.11
Matches are distributed among these distances:
21 4 0.06
22 58 0.87
23 5 0.07
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.33
Consensus pattern (22 bp):
ATAACCACACTATGAAATTTTG
Found at i:3910 original size:22 final size:22
Alignment explanation
Indices: 3862--4050 Score: 123
Period size: 22 Copynumber: 8.5 Consensus size: 22
3852 GATTTGGTAG
* * **
3862 ACTATGAAATTTGGATAATCAA
1 ACTATGAAATTTTGATAACCTC
3884 ACTATGAAATTTTGATAACCTC
1 ACTATGAAATTTTGATAACCTC
* * * *
3906 CCTATGGAATGTTGATAACTTC
1 ACTATGAAATTTTGATAACCTC
* * *
3928 CCTAT-AGAATTTAGTGTTAATCTC
1 ACTATGA-AATTT--TGATAACCTC
* *
3952 ACTATGAAATTTTGATAAACAC
1 ACTATGAAATTTTGATAACCTC
* * *
3974 AATATGAAACTTTGATTACCT-
1 ACTATGAAATTTTGATAACCTC
* * *
3995 TCTATGAAATTTTTG-TAATCAC
1 ACTATGAAA-TTTTGATAACCTC
* * *
4017 ATTATGAAATTTTGATAGCCAC
1 ACTATGAAATTTTGATAACCTC
4039 ACTATGAAATTT
1 ACTATGAAATTT
4051 CAATAATCTA
Statistics
Matches: 127, Mismatches: 33, Indels: 14
0.73 0.19 0.08
Matches are distributed among these distances:
21 15 0.12
22 95 0.75
24 16 0.13
25 1 0.01
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.38
Consensus pattern (22 bp):
ACTATGAAATTTTGATAACCTC
Found at i:4333 original size:12 final size:12
Alignment explanation
Indices: 4316--4342 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
4306 GGTCAAGACT
4316 TTAAATTTATAA
1 TTAAATTTATAA
4328 TTAAATTTATAA
1 TTAAATTTATAA
4340 TTA
1 TTA
4343 TTTTCTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTAAATTTATAA
Found at i:7259 original size:18 final size:17
Alignment explanation
Indices: 7229--7264 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
7219 GCTCTAATTT
7229 ATTTTTTGAGTAAAAAA
1 ATTTTTTGAGTAAAAAA
*
7246 ATTTCTTTGTGTAAAAAA
1 ATTT-TTTGAGTAAAAAA
7264 A
1 A
7265 ATTATTAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.44, C:0.03, G:0.11, T:0.42
Consensus pattern (17 bp):
ATTTTTTGAGTAAAAAA
Found at i:8659 original size:14 final size:13
Alignment explanation
Indices: 8640--8670 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
8630 GTTTCCTTAG
8640 TTTTTTGTTTTTGT
1 TTTTTTGTTTTT-T
8654 TTTTTTGTTTTTT
1 TTTTTTGTTTTTT
8667 TTTT
1 TTTT
8671 AATCAAACCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (13 bp):
TTTTTTGTTTTTT
Found at i:9255 original size:3 final size:3
Alignment explanation
Indices: 9247--9286 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
9237 TCTTAAAACA
9247 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
9287 TA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Done.