Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014378.1 Corchorus olitorius cultivar O-4 contig14411, 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: 5229
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Found at i:1001 original size:13 final size:13
Alignment explanation
Indices: 983--1033 Score: 52
Period size: 13 Copynumber: 3.8 Consensus size: 13
973 TTTTGTGTGA
983 TTGATTTTTTTAT
1 TTGATTTTTTTAT
996 TTGATTTTTTT-T
1 TTGATTTTTTTAT
*
1008 GTT-TTTTTTTTATTT
1 -TTGATTTTTTTA--T
1023 TTGATTTTTTT
1 TTGATTTTTTT
1034 TTGTTCTTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
12 8 0.26
13 13 0.42
14 2 0.06
15 8 0.26
ACGTcount: A:0.10, C:0.00, G:0.08, T:0.82
Consensus pattern (13 bp):
TTGATTTTTTTAT
Found at i:1004 original size:1 final size:1
Alignment explanation
Indices: 1000--1056 Score: 51
Period size: 1 Copynumber: 57.0 Consensus size: 1
990 TTTTATTTGA
* * ** * * *
1000 TTTTTTTTGTTTTTTTTTTATTTTTGATTTTTTTTTGTTCTTTGTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1057 GGAATTTCTT
Statistics
Matches: 43, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.04, C:0.02, G:0.07, T:0.88
Consensus pattern (1 bp):
T
Found at i:1008 original size:10 final size:9
Alignment explanation
Indices: 989--1056 Score: 61
Period size: 8 Copynumber: 7.6 Consensus size: 9
979 GTGATTGATT
989 TTTTTATTTG
1 TTTTT-TTTG
999 ATTTTTTTTG
1 -TTTTTTTTG
1009 TTTTTTTT-
1 TTTTTTTTG
*
1017 TTATTTTTG
1 TTTTTTTTG
1026 ATTTTTTTT-
1 -TTTTTTTTG
* *
1035 TGTTCTTTG
1 TTTTTTTTG
1044 TTTTTTTT-
1 TTTTTTTTG
1052 TTTTT
1 TTTTT
1057 GGAATTTCTT
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
8 18 0.38
9 14 0.29
10 11 0.23
11 5 0.10
ACGTcount: A:0.06, C:0.01, G:0.07, T:0.85
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:1021 original size:25 final size:28
Alignment explanation
Indices: 987--1053 Score: 86
Period size: 28 Copynumber: 2.4 Consensus size: 28
977 GTGTGATTGA
987 TTTTTTTA-TTTGA-TTTTTTTTGTT-T
1 TTTTTTTATTTTGATTTTTTTTTGTTCT
1012 TTTTTTTATTTTTGATTTTTTTTTGTTCT
1 TTTTTTTA-TTTTGATTTTTTTTTGTTCT
*
1041 TTGTTTTTTTTTT
1 TT-TTTTTATTTT
1054 TTTGGAATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
25 8 0.22
27 5 0.14
28 11 0.31
29 7 0.19
30 5 0.14
ACGTcount: A:0.06, C:0.01, G:0.07, T:0.85
Consensus pattern (28 bp):
TTTTTTTATTTTGATTTTTTTTTGTTCT
Found at i:1030 original size:18 final size:16
Alignment explanation
Indices: 1000--1056 Score: 78
Period size: 17 Copynumber: 3.4 Consensus size: 16
990 TTTTATTTGA
1000 TTTTTTTTGTTTTTTT
1 TTTTTTTTGTTTTTTT
1016 TTTATTTTTGATTTTTTT
1 TTT-TTTTTG-TTTTTTT
*
1034 TTGTTCTTTGTTTTTTT
1 TT-TTTTTTGTTTTTTT
1051 TTTTTT
1 TTTTTT
1057 GGAATTTCTT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
16 6 0.17
17 15 0.42
18 14 0.39
19 1 0.03
ACGTcount: A:0.04, C:0.02, G:0.07, T:0.88
Consensus pattern (16 bp):
TTTTTTTTGTTTTTTT
Found at i:1450 original size:10 final size:10
Alignment explanation
Indices: 1435--1460 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1425 AGTGCCTTAA
1435 TTTTTTTCAT
1 TTTTTTTCAT
1445 TTTTTTTCAT
1 TTTTTTTCAT
1455 TTTTTT
1 TTTTTT
1461 CAGTTTTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTTTTCAT
Found at i:1467 original size:10 final size:9
Alignment explanation
Indices: 1434--1474 Score: 57
Period size: 9 Copynumber: 4.6 Consensus size: 9
1424 AAGTGCCTTA
1434 ATTTTTTTC
1 ATTTTTTTC
1443 ATTTTTTTTC
1 A-TTTTTTTC
1453 ATTTTTTTC
1 ATTTTTTTC
*
1462 A-GTTTTTC
1 ATTTTTTTC
1470 ATTTT
1 ATTTT
1475 CATCATCATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
8 7 0.25
9 12 0.43
10 9 0.32
ACGTcount: A:0.12, C:0.10, G:0.02, T:0.76
Consensus pattern (9 bp):
ATTTTTTTC
Found at i:3000 original size:15 final size:16
Alignment explanation
Indices: 2980--3013 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
2970 TGACATAAAG
2980 CAATTAAAC-AGAAAA
1 CAATTAAACTAGAAAA
2995 CAATTAAACTAGAAAA
1 CAATTAAACTAGAAAA
3011 CAA
1 CAA
3014 AGCAAAGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.65, C:0.15, G:0.06, T:0.15
Consensus pattern (16 bp):
CAATTAAACTAGAAAA
Found at i:4232 original size:16 final size:16
Alignment explanation
Indices: 4207--4237 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4197 CAGATACTTA
4207 TGATGATTTGCATGAC
1 TGATGATTTGCATGAC
*
4223 TGATGCTTTGCATGA
1 TGATGATTTGCATGA
4238 ATGCATTCGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.13, G:0.26, T:0.39
Consensus pattern (16 bp):
TGATGATTTGCATGAC
Done.