Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015422.1 Corchorus olitorius cultivar O-4 contig15455, 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: 25909
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:1556 original size:1 final size:1
Alignment explanation
Indices: 1550--1590 Score: 82
Period size: 1 Copynumber: 41.0 Consensus size: 1
1540 AGATAGAATG
1550 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1591 CTAGATTGTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:6772 original size:20 final size:20
Alignment explanation
Indices: 6744--6782 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
6734 AGGAAGCATA
*
6744 ATCATTCAAAATACATGGAG
1 ATCAATCAAAATACATGGAG
*
6764 ATCAATCAAGATACATGGA
1 ATCAATCAAAATACATGGA
6783 TAATTGGATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.23
Consensus pattern (20 bp):
ATCAATCAAAATACATGGAG
Found at i:7857 original size:3 final size:3
Alignment explanation
Indices: 7840--7932 Score: 170
Period size: 3 Copynumber: 31.3 Consensus size: 3
7830 TTTATCATTT
*
7840 TTA TTA GTA -TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
7887 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
7933 CTATACTAAT
Statistics
Matches: 88, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
2 2 0.02
3 86 0.98
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:8178 original size:19 final size:20
Alignment explanation
Indices: 8150--8187 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
8140 AATTCAAAAC
8150 AAAATAAAAACTACACATTT
1 AAAATAAAAACTACACATTT
*
8170 AAAAT-AAAACTACCCATT
1 AAAATAAAAACTACACATT
8188 ATTAGAGGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.58, C:0.18, G:0.00, T:0.24
Consensus pattern (20 bp):
AAAATAAAAACTACACATTT
Found at i:10144 original size:19 final size:18
Alignment explanation
Indices: 10102--10155 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 18
10092 TTAACCAAAA
*
10102 ATAATAATACTATAA-TAT
1 ATAATAATA-TATAATTAC
10120 ATAATAATATATAATCTAC
1 ATAATAATATATAAT-TAC
*
10139 ATAATATTATATAATTA
1 ATAATAATATATAATTA
10156 ATGAAAGAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 5 0.16
18 11 0.34
19 16 0.50
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.41
Consensus pattern (18 bp):
ATAATAATATATAATTAC
Found at i:10604 original size:12 final size:12
Alignment explanation
Indices: 10587--10619 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
10577 CTCTACTCCT
*
10587 CAGCAGCCACAG
1 CAGCAGCAACAG
10599 CAGCAGCAACAG
1 CAGCAGCAACAG
10611 CAGCAGCAA
1 CAGCAGCAA
10620 AGTCACAGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.39, C:0.36, G:0.24, T:0.00
Consensus pattern (12 bp):
CAGCAGCAACAG
Found at i:12000 original size:23 final size:23
Alignment explanation
Indices: 11970--12017 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
11960 TTATATTCAC
*
11970 TGAACAGGCATATTGTAGAATTT
1 TGAACAGGCATATCGTAGAATTT
11993 TGAACAGGCATATCGTAGAATTT
1 TGAACAGGCATATCGTAGAATTT
12016 TG
1 TG
12018 TAGGAGAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (23 bp):
TGAACAGGCATATCGTAGAATTT
Found at i:17528 original size:11 final size:11
Alignment explanation
Indices: 17514--17539 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
17504 ATATAGAGGC
17514 AATATATATAT
1 AATATATATAT
17525 AATATATATAT
1 AATATATATAT
17536 AATA
1 AATA
17540 CTAATAACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
AATATATATAT
Found at i:17561 original size:3 final size:3
Alignment explanation
Indices: 17523--17570 Score: 51
Period size: 3 Copynumber: 15.3 Consensus size: 3
17513 CAATATATAT
* * *
17523 ATA ATA TATA TATA ATA CTA ATA ACA ATA CTA ATA ATA ATA ATA ATA
1 ATA ATA -ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
17570 A
1 A
17571 ATACTACTAG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
3 31 0.82
4 7 0.18
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:17771 original size:6 final size:6
Alignment explanation
Indices: 17760--17789 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
17750 CAACGCATGC
17760 AGAAAA AGAAAA A-AAAA AGAAAA AGAAAA A
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA A
17790 AGAGAAACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:17778 original size:11 final size:12
Alignment explanation
Indices: 17760--17789 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
17750 CAACGCATGC
17760 AGAAAAAGAAAA
1 AGAAAAAGAAAA
17772 A-AAAAAGAAAA
1 AGAAAAAGAAAA
17783 AGAAAAA
1 AGAAAAA
17790 AGAGAAACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (12 bp):
AGAAAAAGAAAA
Found at i:18937 original size:4 final size:4
Alignment explanation
Indices: 18928--18961 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
18918 TTCATCACGT
18928 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT
18962 ATATATGGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Done.