Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018380.1 Corchorus olitorius cultivar O-4 contig18413, 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: 20797
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:5625 original size:31 final size:30
Alignment explanation
Indices: 5581--5650 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 30
5571 AAATAAAAGA
* *
5581 AAAATATTTTTTTTCTA-AAAACGCAGGAAC
1 AAAATTTTTTTTTTCTAGAAAACGCA-AAAC
*
5611 AAGAATTTTTTTTTTTTAGAAAACGCAAAAC
1 AA-AATTTTTTTTTTCTAGAAAACGCAAAAC
5642 AAAATTTTT
1 AAAATTTTT
5651 ATGACGCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 9 0.26
31 18 0.51
32 8 0.23
ACGTcount: A:0.43, C:0.10, G:0.09, T:0.39
Consensus pattern (30 bp):
AAAATTTTTTTTTTCTAGAAAACGCAAAAC
Found at i:6099 original size:15 final size:16
Alignment explanation
Indices: 6075--6114 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
6065 AGAGGTTGAA
*
6075 AGAAAGCAATTATAC-
1 AGAAAACAATTATACT
6090 AGAAAACAATTATACT
1 AGAAAACAATTATACT
6106 AGAAAACAA
1 AGAAAACAA
6115 AACAAAGCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.60, C:0.12, G:0.10, T:0.17
Consensus pattern (16 bp):
AGAAAACAATTATACT
Found at i:7792 original size:11 final size:11
Alignment explanation
Indices: 7777--7864 Score: 53
Period size: 11 Copynumber: 8.5 Consensus size: 11
7767 TTATATATAA
7777 AATATATTTAT
1 AATATATTTAT
* * *
7788 GATATATATAA
1 AATATATTTAT
7799 AATATA-TT-T
1 AATATATTTAT
7808 AA-ATATTTAT
1 AATATATTTAT
*
7818 GATATA--TAT
1 AATATATTTAT
* *
7827 AAAATATTTTT
1 AATATATTTAT
7838 AAT-TATTTAT
1 AATATATTTAT
* * *
7848 GATATATATAA
1 AATATATTTAT
7859 AATATA
1 AATATA
7865 AAATATAAAA
Statistics
Matches: 55, Mismatches: 16, Indels: 12
0.66 0.19 0.14
Matches are distributed among these distances:
8 3 0.05
9 11 0.20
10 11 0.20
11 30 0.55
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (11 bp):
AATATATTTAT
Found at i:7815 original size:30 final size:30
Alignment explanation
Indices: 7780--7864 Score: 152
Period size: 30 Copynumber: 2.8 Consensus size: 30
7770 TATATAAAAT
7780 ATATTTATGATATATATAAAATATATTTAA
1 ATATTTATGATATATATAAAATATATTTAA
*
7810 ATATTTATGATATATATAAAATATTTTTAA
1 ATATTTATGATATATATAAAATATATTTAA
*
7840 TTATTTATGATATATATAAAATATA
1 ATATTTATGATATATATAAAATATA
7865 AAATATAAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 52 1.00
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (30 bp):
ATATTTATGATATATATAAAATATATTTAA
Found at i:7865 original size:7 final size:7
Alignment explanation
Indices: 7853--7885 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
7843 TTTATGATAT
7853 ATATAAA
1 ATATAAA
7860 ATATAAA
1 ATATAAA
7867 ATATAAA
1 ATATAAA
7874 ATATAAA
1 ATATAAA
7881 ATATA
1 ATATA
7886 TGTAAAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (7 bp):
ATATAAA
Found at i:7905 original size:9 final size:8
Alignment explanation
Indices: 7851--7929 Score: 51
Period size: 7 Copynumber: 9.9 Consensus size: 8
7841 TATTTATGAT
7851 ATATATAA
1 ATATATAA
7859 A-ATATAA
1 ATATATAA
7866 A-ATATAA
1 ATATATAA
7873 A-ATATAAA
1 ATATAT-AA
7881 ATATATGTAAA
1 ATATA--T-AA
7892 ATATATAA
1 ATATATAA
*
7900 AT-TATAT
1 ATATATAA
* *
7907 TTATGATAT
1 ATAT-ATAA
7916 ATATA-AA
1 ATATATAA
7923 ATATATA
1 ATATATA
7930 TAACAAAATT
Statistics
Matches: 60, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
7 29 0.48
8 11 0.18
9 11 0.18
11 9 0.15
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (8 bp):
ATATATAA
Found at i:12620 original size:28 final size:29
Alignment explanation
Indices: 12580--12638 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
12570 AAGTATTGTC
* * *
12580 CCTCTAAAGAAAA-AATGAGTGTTAGTAA
1 CCTCAAAAGAAAATAAAGAGAGTTAGTAA
*
12608 CCTCAAAAGAAAATAAAGGGAGTTAGTAA
1 CCTCAAAAGAAAATAAAGAGAGTTAGTAA
12637 CC
1 CC
12639 CCTAAATCAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 12 0.46
29 14 0.54
ACGTcount: A:0.47, C:0.14, G:0.19, T:0.20
Consensus pattern (29 bp):
CCTCAAAAGAAAATAAAGAGAGTTAGTAA
Found at i:18838 original size:21 final size:25
Alignment explanation
Indices: 18778--18839 Score: 62
Period size: 27 Copynumber: 2.6 Consensus size: 25
18768 TGTATACCCG
18778 ATAA-TAAAACATAAAATTTATATTA
1 ATAATTAAAA-ATAAAATTTATATTA
18803 ATAATTATAACAATAAAA-TTA-A-TA
1 ATAATTA-AA-AATAAAATTTATATTA
18827 A-AATTAAAAATAA
1 ATAATTAAAAATAA
18840 TAATAACATT
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
21 5 0.15
22 2 0.06
23 5 0.15
24 3 0.09
25 5 0.15
26 5 0.15
27 8 0.24
28 1 0.03
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (25 bp):
ATAATTAAAAATAAAATTTATATTA
Found at i:18843 original size:3 final size:3
Alignment explanation
Indices: 18801--18954 Score: 52
Period size: 3 Copynumber: 51.7 Consensus size: 3
18791 AAATTTATAT
* * *
18801 TAA TAA TTA TAA CAA TAA -AA TTAA TAA -AA TTAA AAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA -TAA TAA TAA TAA TAA
* * ** * * *
18846 CAT TAA TAA TAAA TGC TAC TAC TAA TAA TACA TAA TAC TAA TAA TAA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA
* * * *
18893 CAA TAT TAA -AA TTA -AA TAA -ATC TAA TAA TAA -AA -AA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA
* * *
18934 CAG TAA TAA CAA TAAA TAA TA
1 TAA TAA TAA TAA T-AA TAA TA
18955 TTTTAAGTTT
Statistics
Matches: 109, Mismatches: 30, Indels: 24
0.67 0.18 0.15
Matches are distributed among these distances:
2 12 0.11
3 83 0.76
4 14 0.13
ACGTcount: A:0.62, C:0.07, G:0.01, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:20458 original size:18 final size:19
Alignment explanation
Indices: 20426--20461 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
20416 TAACTACTAA
*
20426 TAATAAATAATACTAATAT
1 TAATAAATAACACTAATAT
20445 TAAT-AATAACACTAATA
1 TAATAAATAACACTAATA
20462 ATTATATTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.33
Consensus pattern (19 bp):
TAATAAATAACACTAATAT
Found at i:20496 original size:14 final size:14
Alignment explanation
Indices: 20479--20516 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
20469 TTGTAATTTT
20479 AATTATATAATTAA
1 AATTATATAATTAA
*
20493 AATTATATAACTAA
1 AATTATATAATTAA
20507 AATTAT-TAAT
1 AATTATATAAT
20517 AATTATCATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 3 0.14
14 19 0.86
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (14 bp):
AATTATATAATTAA
Done.