Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023713.1 Corchorus olitorius cultivar O-4 contig23746, 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: 13570
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.30
Found at i:3113 original size:17 final size:17
Alignment explanation
Indices: 3093--3163 Score: 65
Period size: 17 Copynumber: 4.1 Consensus size: 17
3083 TAATTTTCTA
3093 TTTTCTCTTATTT-CTTT
1 TTTTCTCTT-TTTCCTTT
*
3110 TTTTTTCTTTTTCCTTT
1 TTTTCTCTTTTTCCTTT
* *
3127 TTCTTTTC-TTTTCTTTT
1 TT-TTCTCTTTTTCCTTT
*
3144 TCTTTCTCTTTTCCCTTT
1 T-TTTCTCTTTTTCCTTT
3162 TT
1 TT
3164 CCCCATTTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
16 3 0.07
17 28 0.62
18 14 0.31
ACGTcount: A:0.01, C:0.21, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTCTCTTTTTCCTTT
Found at i:3116 original size:10 final size:10
Alignment explanation
Indices: 3103--3155 Score: 52
Period size: 10 Copynumber: 4.8 Consensus size: 10
3093 TTTTCTCTTA
3103 TTTCTTTTTT
1 TTTCTTTTTT
3113 TTTCTTTTTCCTT
1 TTTC-TTTT--TT
*
3126 TTTCTTTTCT
1 TTTCTTTTTT
3136 TTTCTTTTTCT
1 TTTCTTTTT-T
3147 TTCTCTTTT
1 TT-TCTTTT
3156 CCCTTTTTCC
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
10 13 0.36
11 7 0.19
12 10 0.28
13 6 0.17
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTCTTTTTT
Found at i:3122 original size:6 final size:6
Alignment explanation
Indices: 3093--3155 Score: 62
Period size: 6 Copynumber: 10.7 Consensus size: 6
3083 TAATTTTCTA
3093 TTTTCTC TTATTTC -TTTT- TTTTTC TTTTTCC TTTTTC -TTTTC -TTTTC
1 TTTT-TC TT-TTTC TTTTTC TTTTTC TTTTT-C TTTTTC TTTTTC TTTTTC
*
3140 TTTTTC TTTCTC TTTT
1 TTTTTC TTTTTC TTTT
3156 CCCTTTTTCC
Statistics
Matches: 49, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
5 17 0.35
6 20 0.41
7 10 0.20
8 2 0.04
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTTTC
Found at i:3129 original size:23 final size:23
Alignment explanation
Indices: 3086--3156 Score: 90
Period size: 23 Copynumber: 3.0 Consensus size: 23
3076 TTATCCATAA
*
3086 TTTTCTATTTTCTCTTATTTCTTTTT
1 TTTTCT-TTTTC-CTT-TTTCTTTTC
3112 TTTTCTTTTTCCTTTTTCTTTTC
1 TTTTCTTTTTCCTTTTTCTTTTC
*
3135 TTTTCTTTTT-CTTTCTCTTTTC
1 TTTTCTTTTTCCTTTTTCTTTTC
3157 CCTTTTTCCC
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
22 11 0.26
23 18 0.42
24 3 0.07
25 5 0.12
26 6 0.14
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (23 bp):
TTTTCTTTTTCCTTTTTCTTTTC
Found at i:3310 original size:3 final size:3
Alignment explanation
Indices: 3299--3340 Score: 59
Period size: 3 Copynumber: 14.0 Consensus size: 3
3289 TTTATTTTTT
*
3299 TTC TT- TTC TTC TTC TTC TTTC TTC TTC TTC TTC TTC TCC TTC
1 TTC TTC TTC TTC TTC TTC -TTC TTC TTC TTC TTC TTC TTC TTC
3341 CGGTAACCGA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 30 0.86
4 3 0.09
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:3328 original size:19 final size:18
Alignment explanation
Indices: 3298--3335 Score: 67
Period size: 19 Copynumber: 2.1 Consensus size: 18
3288 TTTTATTTTT
3298 TTTCTTTTCTTCTTCTTC
1 TTTCTTTTCTTCTTCTTC
3316 TTTCTTCTTCTTCTTCTTC
1 TTTCTT-TTCTTCTTCTTC
3335 T
1 T
3336 CCTTCCGGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTCTTTTCTTCTTCTTC
Found at i:9322 original size:7 final size:6
Alignment explanation
Indices: 9303--9372 Score: 62
Period size: 5 Copynumber: 12.3 Consensus size: 6
9293 TTATTTCCTA
9303 TTTCTT TTT-TT TTTCCTT TTTC-T TTTC-T TTTCTT TTTC-T TTT-TT
1 TTTCTT TTTCTT TTT-CTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
* *
9347 TTTCTT TTCCCTC TTTC-T TTTCTT TT
1 TTTCTT TT-TCTT TTTCTT TTTCTT TT
9373 CCCTTTTTCC
Statistics
Matches: 53, Mismatches: 4, Indels: 14
0.75 0.06 0.20
Matches are distributed among these distances:
5 27 0.51
6 17 0.32
7 9 0.17
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTCTT
Found at i:9322 original size:11 final size:10
Alignment explanation
Indices: 9303--9354 Score: 68
Period size: 11 Copynumber: 4.8 Consensus size: 10
9293 TTATTTCCTA
9303 TTTCTTTTTTT
1 TTTC-TTTTTT
9314 TTTCCTTTTTCT
1 TTT-CTTTTT-T
9326 TTTCTTTTCTT
1 TTTCTTTT-TT
9337 TTTCTTTTTT
1 TTTCTTTTTT
9347 TTTCTTTT
1 TTTCTTTT
9355 CCCTCTTTCT
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
10 10 0.26
11 22 0.58
12 6 0.16
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTCTTTTTT
Found at i:9328 original size:5 final size:5
Alignment explanation
Indices: 9320--9373 Score: 63
Period size: 5 Copynumber: 10.0 Consensus size: 5
9310 TTTTTTTCCT
*
9320 TTTTC TTTTC TTTTC TTTTTC TTTTT TTTTC TTTTCCC TCTTTC TTTTC
1 TTTTC TTTTC TTTTC -TTTTC TTTTC TTTTC TTTT--C T-TTTC TTTTC
9369 TTTTC
1 TTTTC
9374 CCTTTTTCCC
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
5 31 0.72
6 7 0.16
7 2 0.05
8 3 0.07
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTTC
Found at i:9330 original size:39 final size:39
Alignment explanation
Indices: 9286--9369 Score: 91
Period size: 39 Copynumber: 2.2 Consensus size: 39
9276 TAATTTTCTA
* *
9286 TTTTCTCTT-ATTTCCTATTTCTTTTT-TTTTTCCTTTTTC
1 TTTTCTCTTCATTTCCT-TTT-TTTTTCTTTTCCCTCTTTC
* * *
9325 TTTTCTTTTCTTTTTCTTTTTTTTTCTTTTCCCTCTTTC
1 TTTTCTCTTCATTTCCTTTTTTTTTCTTTTCCCTCTTTC
9364 TTTTCT
1 TTTTCT
9370 TTTCCCTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
38 5 0.13
39 28 0.74
40 5 0.13
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.76
Consensus pattern (39 bp):
TTTTCTCTTCATTTCCTTTTTTTTTCTTTTCCCTCTTTC
Found at i:9364 original size:34 final size:34
Alignment explanation
Indices: 9303--9372 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 34
9293 TTATTTCCTA
*
9303 TTTCTTTTTTTTTTCCTTTTTCTTTTCTTTTCTT
1 TTTCTTTTTTTTTTCCTTTTCCTTTTCTTTTCTT
9337 TTTC-TTTTTTTTT-CTTTTCCCTCTTTCTTTTCTT
1 TTTCTTTTTTTTTTCCTTTT-CCT-TTTCTTTTCTT
9371 TT
1 TT
9373 CCCTTTTTCC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
32 5 0.15
33 11 0.33
34 17 0.52
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (34 bp):
TTTCTTTTTTTTTTCCTTTTCCTTTTCTTTTCTT
Found at i:9381 original size:18 final size:18
Alignment explanation
Indices: 9325--9381 Score: 82
Period size: 18 Copynumber: 3.3 Consensus size: 18
9315 TTCCTTTTTC
*
9325 TTTTCTTTTCTTTT-TCT
1 TTTTCTTTTCTTTTCCCT
9342 TTTT-TTTTCTTTTCCCT
1 TTTTCTTTTCTTTTCCCT
*
9359 CTTTCTTTTCTTTTCCCT
1 TTTTCTTTTCTTTTCCCT
9377 TTTTC
1 TTTTC
9382 CCCATTTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
16 9 0.26
17 9 0.26
18 17 0.49
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTTCTTTTCTTTTCCCT
Done.