Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016840.1 Corchorus olitorius cultivar O-4 contig16873, 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: 10701
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.32
Found at i:168 original size:27 final size:27
Alignment explanation
Indices: 105--179 Score: 80
Period size: 28 Copynumber: 2.7 Consensus size: 27
95 TTCGATGTTT
* *
105 AAGGGCAAATTGTAA-TTTAGTCAACC
1 AAGGGCAAATCGTAATTTTAGCCAACC
* * *
131 AAGGGTAAAATGGTAATTTTAGCCGACC
1 AAGGG-CAAATCGTAATTTTAGCCAACC
159 AAGGGCAAATACGTAATTTTA
1 AAGGGCAAAT-CGTAATTTTA
180 ACATCCTAAG
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
26 5 0.12
27 12 0.30
28 23 0.57
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.27
Consensus pattern (27 bp):
AAGGGCAAATCGTAATTTTAGCCAACC
Found at i:954 original size:23 final size:21
Alignment explanation
Indices: 928--1001 Score: 58
Period size: 23 Copynumber: 3.1 Consensus size: 21
918 TTCTCTTTAT
928 TTTCCTTATTTATTTATTTTCTC
1 TTTCCTT-TTT-TTTATTTTCTC
* *
951 TTTCCTTTTTTTTCTTTTTTTCTT
1 TTTCC--TTTTTT-TTATTTTCTC
975 TCTTCCTTTTCTTTTATTTTCTTC
1 T-TTCCTTTT-TTTTATTTTC-TC
999 TTT
1 TTT
1002 TAAAAAAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
23 19 0.46
24 16 0.39
25 6 0.15
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTCCTTTTTTTTATTTTCTC
Found at i:974 original size:22 final size:21
Alignment explanation
Indices: 944--989 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
934 TATTTATTTA
**
944 TTTTCTCTTTCCTTTTTTTTCT
1 TTTTCTCTTT-CTTCCTTTTCT
*
966 TTTTTTCTTTCTTCCTTTTCT
1 TTTTCTCTTTCTTCCTTTTCT
987 TTT
1 TTT
990 ATTTTCTTCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTTCTCTTTCTTCCTTTTCT
Found at i:989 original size:26 final size:24
Alignment explanation
Indices: 936--1002 Score: 80
Period size: 25 Copynumber: 2.7 Consensus size: 24
926 ATTTTCCTTA
*
936 TTTATTTATTTTCTCTTTCCTTTTT
1 TTTATTT-TTTTCTTTTTCCTTTTT
*
961 TTTCTTTTTTTCTTTCTTCCTTTTCT
1 TTTATTTTTTTCTTT-TTCCTTTT-T
*
987 TTTATTTTCTTCTTTT
1 TTTATTTTTTTCTTTT
1003 AAAAAAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
24 7 0.19
25 15 0.42
26 14 0.39
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (24 bp):
TTTATTTTTTTCTTTTTCCTTTTT
Found at i:999 original size:22 final size:23
Alignment explanation
Indices: 940--1000 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 23
930 TCCTTATTTA
*
940 TTTATTTTC-TCTTTCCTTTTTTT
1 TTTATTTTCTTC-TTCCTTTTTCT
*
963 TCTTTTTTTCTTTCTTCC-TTTTCT
1 T-TTATTTTC-TTCTTCCTTTTTCT
987 TTTATTTTCTTCTT
1 TTTATTTTCTTCTT
1001 TTAAAAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
22 5 0.16
23 8 0.25
24 13 0.41
25 4 0.12
26 2 0.06
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (23 bp):
TTTATTTTCTTCTTCCTTTTTCT
Found at i:6027 original size:13 final size:13
Alignment explanation
Indices: 5994--6046 Score: 60
Period size: 12 Copynumber: 4.4 Consensus size: 13
5984 GCACCCAAAA
*
5994 CATTTAT-TAAAA
1 CATTTATATAAAG
6006 CATTT-TATAAAG
1 CATTTATATAAAG
6018 CATTTATATAAAG
1 CATTTATATAAAG
*
6031 CAGTTATA-AAA-
1 CATTTATATAAAG
6042 CATTT
1 CATTT
6047 CCTCAACGGG
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
11 5 0.14
12 17 0.47
13 14 0.39
ACGTcount: A:0.45, C:0.09, G:0.06, T:0.40
Consensus pattern (13 bp):
CATTTATATAAAG
Found at i:7300 original size:22 final size:22
Alignment explanation
Indices: 7271--7343 Score: 78
Period size: 22 Copynumber: 3.2 Consensus size: 22
7261 TCCTTATTTA
7271 TTTATTTTCTCTTTCTTTTTTT
1 TTTATTTTCTCTTTCTTTTTTT
*
7293 TTCT-TTTTTTCTTTCTTCCTTTTCT
1 TT-TATTTTCTCTTTCTT--TTTT-T
7318 TTTATTTTCT-TCTTCTTTTTTT
1 TTTATTTTCTCT-TTCTTTTTTT
7340 TTTA
1 TTTA
7344 AATATTGGGC
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
22 19 0.44
23 5 0.12
24 6 0.14
25 13 0.30
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.79
Consensus pattern (22 bp):
TTTATTTTCTCTTTCTTTTTTT
Found at i:7339 original size:19 final size:19
Alignment explanation
Indices: 7293--7339 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
7283 TTCTTTTTTT
7293 TTCTTTTTTTCTTTCTTCC
1 TTCTTTTTTTCTTTCTTCC
7312 TT-TTCTTTTAT-TTTCTT-C
1 TTCTT-TTTT-TCTTTCTTCC
7330 TTCTTTTTTT
1 TTCTTTTTTT
7340 TTTAAATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
17 1 0.04
18 9 0.36
19 14 0.56
20 1 0.04
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (19 bp):
TTCTTTTTTTCTTTCTTCC
Found at i:10406 original size:2 final size:2
Alignment explanation
Indices: 10399--10517 Score: 184
Period size: 2 Copynumber: 59.5 Consensus size: 2
10389 GAAGATCTAT
10399 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
* * *
10441 TG TG TG TG TG TG TG TG TG CG TG TG TG TG TG TG CG CG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
** *
10483 CA TG TG TG TG TG TG TG TG TG TG TG CG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
10518 TTCTGAAGAC
Statistics
Matches: 107, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 107 1.00
ACGTcount: A:0.01, C:0.04, G:0.49, T:0.46
Consensus pattern (2 bp):
TG
Found at i:10600 original size:2 final size:2
Alignment explanation
Indices: 10593--10628 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
10583 CAGAGACATA
* *
10593 GT GT GT GT GT GT GT GC GT GT GT GT GC GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
10629 TTCTGAAGAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.06, G:0.50, T:0.44
Consensus pattern (2 bp):
GT
Found at i:10612 original size:10 final size:10
Alignment explanation
Indices: 10593--10627 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
10583 CAGAGACATA
*
10593 GTGTGTGTGT
1 GTGTGCGTGT
10603 GTGTGCGTGT
1 GTGTGCGTGT
10613 GTGTGCGTGT
1 GTGTGCGTGT
10623 GTGTG
1 GTGTG
10628 TTTCTGAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.00, C:0.06, G:0.51, T:0.43
Consensus pattern (10 bp):
GTGTGCGTGT
Found at i:10617 original size:111 final size:111
Alignment explanation
Indices: 10485--10688 Score: 399
Period size: 111 Copynumber: 1.8 Consensus size: 111
10475 CGTGTGTGCA
*
10485 TGTGTGTGTGTGTGTGTGTGTGCGTGTGTGTGTTTCTGAAGACATTGTTACTCTTATTGGTGTTC
1 TGTGTGTGTGTGCGTGTGTGTGCGTGTGTGTGTTTCTGAAGACATTGTTACTCTTATTGGTGTTC
10550 TTTAATGCAAAGTGAAAAGTTAGCATGGTTTAGCAGAGACATAGTG
66 TTTAATGCAAAGTGAAAAGTTAGCATGGTTTAGCAGAGACATAGTG
10596 TGTGTGTGTGTGCGTGTGTGTGCGTGTGTGTGTTTCTGAAGACATTGTTACTCTTATTGGTGTTC
1 TGTGTGTGTGTGCGTGTGTGTGCGTGTGTGTGTTTCTGAAGACATTGTTACTCTTATTGGTGTTC
10661 TTTAATGCAAAGTGAAAAGTTAGCATGG
66 TTTAATGCAAAGTGAAAAGTTAGCATGG
10689 GGGTGTGTGT
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
111 92 1.00
ACGTcount: A:0.20, C:0.09, G:0.31, T:0.40
Consensus pattern (111 bp):
TGTGTGTGTGTGCGTGTGTGTGCGTGTGTGTGTTTCTGAAGACATTGTTACTCTTATTGGTGTTC
TTTAATGCAAAGTGAAAAGTTAGCATGGTTTAGCAGAGACATAGTG
Done.