Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023711.1 Corchorus olitorius cultivar O-4 contig23744, 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: 3968
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Found at i:3171 original size:38 final size:35
Alignment explanation
Indices: 3129--3224 Score: 88
Period size: 35 Copynumber: 2.6 Consensus size: 35
3119 TTATTCATAA
* *
3129 TTTTCTATTTTCTCTTATTTCTTATTTCTTTCTCTTTT
1 TTTTCT-TTTTCTCTT-TTTCTTATTT-TTCCTCTTTC
3167 TTTTCCTTTTTCT-TTTCTT-TTATTTTTCCTCTTTC
1 TTTT-CTTTTTCTCTTT-TTCTTATTTTTCCTCTTTC
*
3202 TTTTCTTTTCTTTTCTTTTTCTT
1 TTTTC-TTT-TTCTCTTTTTCTT
3225 TTCCCTTTTC
Statistics
Matches: 49, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
34 1 0.02
35 15 0.31
36 12 0.24
37 9 0.18
38 10 0.20
39 2 0.04
ACGTcount: A:0.04, C:0.20, G:0.00, T:0.76
Consensus pattern (35 bp):
TTTTCTTTTTCTCTTTTTCTTATTTTTCCTCTTTC
Found at i:3176 original size:7 final size:6
Alignment explanation
Indices: 3136--3226 Score: 61
Period size: 6 Copynumber: 15.7 Consensus size: 6
3126 TAATTTTCTA
* *
3136 TTTTCTC TTATTTC TTATTTC TTTCTC -TTTT- TTTTCC TTTTTC -TTTTC
1 TTTT-TC TT-TTTC TT-TTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
* *
3184 TTTTAT- TTTTCC TCTTTC -TTTTC -TTTTC -TTTTC TTTTTC TTTT
1 TTTT-TC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTT
3227 CCCTTTTCCC
Statistics
Matches: 69, Mismatches: 8, Indels: 15
0.75 0.09 0.16
Matches are distributed among these distances:
5 25 0.36
6 28 0.41
7 14 0.20
8 2 0.03
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (6 bp):
TTTTTC
Found at i:3184 original size:5 final size:5
Alignment explanation
Indices: 3153--3227 Score: 71
Period size: 5 Copynumber: 13.8 Consensus size: 5
3143 TTATTTCTTA
*
3153 TTTCT TTCTCT TTT-T TTTCCTT TTTCT TTTCT TTTATT TTTCCT CTTTCT
1 TTTCT TT-TCT TTTCT TTT-C-T TTTCT TTTCT TTT-CT TTT-CT -TTTCT
3203 TTTCT TTTCT TTTCTT TTTCT TTTC
1 TTTCT TTTCT TTTC-T TTTCT TTTC
3228 CCTTTTCCCC
Statistics
Matches: 60, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
4 4 0.07
5 31 0.52
6 18 0.30
7 7 0.12
ACGTcount: A:0.01, C:0.21, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTCT
Found at i:3192 original size:23 final size:22
Alignment explanation
Indices: 3153--3227 Score: 100
Period size: 23 Copynumber: 3.4 Consensus size: 22
3143 TTATTTCTTA
3153 TTTC-TTTCTCTTTTTTTTCCTT
1 TTTCTTTTCT-TTTTTTTTCCTT
*
3175 TTTCTTTTCTTTTATTTTTCCTC
1 TTTCTTTTCTTTT-TTTTTCCTT
*
3198 TTTCTTTTCTTTTCTTTT-CTT
1 TTTCTTTTCTTTTTTTTTCCTT
3219 TTTCTTTTC
1 TTTCTTTTC
3228 CCTTTTCCCC
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.23
22 11 0.23
23 26 0.54
ACGTcount: A:0.01, C:0.21, G:0.00, T:0.77
Consensus pattern (22 bp):
TTTCTTTTCTTTTTTTTTCCTT
Found at i:3305 original size:23 final size:26
Alignment explanation
Indices: 3263--3319 Score: 66
Period size: 25 Copynumber: 2.2 Consensus size: 26
3253 TGGGCCTCAC
3263 CAGGCCCGCGCGCCTGGGCC-GCGCA
1 CAGGCCCGCGCGCCTGGGCCGGCGCA
*
3288 CAGGCCTGCGCG-CT-GGCCTGGCGCA
1 CAGGCCCGCGCGCCTGGGCC-GGCGCA
3313 CTAGGCC
1 C-AGGCC
3320 GGCTAGGCAC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 4 0.14
24 2 0.07
25 17 0.61
26 5 0.18
ACGTcount: A:0.09, C:0.44, G:0.39, T:0.09
Consensus pattern (26 bp):
CAGGCCCGCGCGCCTGGGCCGGCGCA
Found at i:3363 original size:3 final size:3
Alignment explanation
Indices: 3352--3394 Score: 52
Period size: 3 Copynumber: 14.0 Consensus size: 3
3342 CTTATTTTTT
*
3352 TTC TT- TTC TTC TTC TTTC TTTC TTC TTC TTC TTC TTC TCC TTC
1 TTC TTC TTC TTC TTC -TTC -TTC TTC TTC TTC TTC TTC TTC TTC
3395 CGGTAACCAG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 27 0.75
4 7 0.19
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Done.