Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01006813.1 Corchorus olitorius cultivar O-4 contig06838, 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, 775
Length: 1293
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.42
Found at i:122 original size:21 final size:21
Alignment explanation
Indices: 96--183 Score: 89
Period size: 21 Copynumber: 4.4 Consensus size: 21
86 TTTATCTATT
96 TATTTATTTTTAACTATTATC
1 TATTTATTTTTAACTATTATC
* *
117 TATTTATTTTTAATTATCATC
1 TATTTATTTTTAACTATTATC
138 TATTTA--TTT-ACTATTTAT-
1 TATTTATTTTTAACTA-TTATC
*
156 T-TTT-TTTTCAACTATTATC
1 TATTTATTTTTAACTATTATC
*
175 TACTTATTT
1 TATTTATTT
184 ACTATTTATC
Statistics
Matches: 54, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
17 3 0.06
18 10 0.19
19 11 0.20
20 2 0.04
21 28 0.52
ACGTcount: A:0.26, C:0.10, G:0.00, T:0.64
Consensus pattern (21 bp):
TATTTATTTTTAACTATTATC
Found at i:203 original size:19 final size:18
Alignment explanation
Indices: 144--203 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 18
134 CATCTATTTA
144 TTTACTATTTAT-TTTTT
1 TTTACTATTTATCTTTTT
* *
161 TTTCAACTA-TTATCTACTTA
1 TTT--ACTATTTATCT-TTTT
181 TTTACTATTTATCTTTTT
1 TTTACTATTTATCTTTTT
199 GTTTA
1 -TTTA
204 TTTTTAATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
17 3 0.09
18 10 0.30
19 15 0.45
20 5 0.15
ACGTcount: A:0.22, C:0.12, G:0.02, T:0.65
Consensus pattern (18 bp):
TTTACTATTTATCTTTTT
Found at i:215 original size:81 final size:83
Alignment explanation
Indices: 71--242 Score: 244
Period size: 81 Copynumber: 2.1 Consensus size: 83
61 AAAAGACTTT
* *
71 TTTTATTTTTCACTATTTATCTATTTATTTATTTTTAACTATTATCTATTTATTTTTAATTATCA
1 TTTT-TTTTTCACTATTTATCTACTTATTTATATTTAACTATTATCTATTTATTTTTAATTATCA
136 TCTATTTATTTACTATTTA
65 TCTATTTATTTACTATTTA
* *
155 TTTTTTTTTCAACTA-TTATCTACTTATTTACTATTTATCT-TT-T-TGTTTATTTTTAATTATC
1 TTTTTTTTTC-ACTATTTATCTACTTATTTA-TATTTAACTATTATCTATTTATTTTTAATTATC
216 ATCTATTTATTTACTATTTA
64 ATCTATTTATTTACTATTTA
*
236 TCTTTTT
1 TTTTTTT
243 ATTTATTAAT
Statistics
Matches: 81, Mismatches: 5, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
81 43 0.53
82 1 0.01
83 22 0.27
84 15 0.19
ACGTcount: A:0.24, C:0.10, G:0.01, T:0.65
Consensus pattern (83 bp):
TTTTTTTTTCACTATTTATCTACTTATTTATATTTAACTATTATCTATTTATTTTTAATTATCAT
CTATTTATTTACTATTTA
Found at i:226 original size:44 final size:45
Alignment explanation
Indices: 142--274 Score: 155
Period size: 44 Copynumber: 3.0 Consensus size: 45
132 ATCATCTATT
* * * * *
142 TATTTA-CTATTTATTT-TTTTTTCAACTATTATCTACTTATTTAC
1 TATTTATCTTTTTATTTATTATTT-AATTATCATCTATTTATTTAC
*
186 TATTTATCTTTTTGTTTATT-TTTAATTATCATCTATTTATTTAC
1 TATTTATCTTTTTATTTATTATTTAATTATCATCTATTTATTTAC
* *
230 TATTTATCTTTTTATTTATTAATTTAGTTATTATCTATTTATTTA
1 TATTTATCTTTTTATTTATT-ATTTAATTATCATCTATTTATTTA
275 TTTATTATTA
Statistics
Matches: 77, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
44 43 0.56
45 11 0.14
46 23 0.30
ACGTcount: A:0.25, C:0.09, G:0.02, T:0.65
Consensus pattern (45 bp):
TATTTATCTTTTTATTTATTATTTAATTATCATCTATTTATTTAC
Found at i:227 original size:37 final size:36
Alignment explanation
Indices: 117--285 Score: 123
Period size: 37 Copynumber: 4.5 Consensus size: 36
107 AACTATTATC
117 TATTTATTTTTAATTATCATCTATTTATTTACTATT
1 TATTTATTTTTAATTATCATCTATTTATTTACTATT
* * * *
153 TATTTTTTTTTCAACTATTATCTACTTATTTACTATT
1 TATTTATTTTT-AATTATCATCTATTTATTTACTATT
190 TATCTTTTTGTTTATTTTTAATTATCATCTATTTATTTACTATT
1 TA--------TTTATTTTTAATTATCATCTATTTATTTACTATT
* * *
234 TATCTT-TTTATTTATTA--ATTTAGTTA-TTATCTATT
1 TAT-TTATTT-TTAATTATCATCTATTTATTTA-CTATT
269 TATTTATTTATT-ATTAT
1 TATTTATTT-TTAATTAT
286 TTCTTAGCTA
Statistics
Matches: 108, Mismatches: 11, Indels: 29
0.73 0.07 0.20
Matches are distributed among these distances:
34 9 0.08
35 21 0.19
36 14 0.13
37 32 0.30
44 24 0.22
45 8 0.07
ACGTcount: A:0.25, C:0.08, G:0.01, T:0.65
Consensus pattern (36 bp):
TATTTATTTTTAATTATCATCTATTTATTTACTATT
Found at i:254 original size:27 final size:27
Alignment explanation
Indices: 219--276 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
209 AATTATCATC
* *
219 TATTTATTTAC-TATTTATCTTTTTATT
1 TATTAATTTACTTA-TTATCTATTTATT
*
246 TATTAATTTAGTTATTATCTATTTATT
1 TATTAATTTACTTATTATCTATTTATT
273 TATT
1 TATT
277 TATTATTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 25 0.93
28 2 0.07
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (27 bp):
TATTAATTTACTTATTATCTATTTATT
Found at i:263 original size:19 final size:19
Alignment explanation
Indices: 241--283 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
231 ATTTATCTTT
241 TTATTTATTAATTTAGTTA
1 TTATTTATTAATTTAGTTA
* * *
260 TTATCTATTTATTTATTTA
1 TTATTTATTAATTTAGTTA
279 TTATT
1 TTATT
284 ATTTCTTAGC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (19 bp):
TTATTTATTAATTTAGTTA
Found at i:307 original size:4 final size:4
Alignment explanation
Indices: 84--280 Score: 67
Period size: 4 Copynumber: 50.0 Consensus size: 4
74 TATTTTTCAC
* * * *
84 TATT TATC TATT TATT TATT T-TT AACTAT TATC TATT TATT T-TT AATT
1 TATT TATT TATT TATT TATT TATT TA-T-T TATT TATT TATT TATT TATT
* * ** * *
132 ATCATC TATT TATT TA-C TATT TATT T-TT T-TT TCAAC TA-T TATC TACT
1 -T-ATT TATT TATT TATT TATT TATT TATT TATT T-ATT TATT TATT TATT
* * * *
179 TATT TA-C TATT TATCT T-TT TGTT TATT T-TT AATT ATCATC TATT TATT
1 TATT TATT TATT TAT-T TATT TATT TATT TATT TATT -T-ATT TATT TATT
* * * *
227 TA-C TATT TATCT T-TT TATT TATT AATT TAGT TA-T TATC TATT TATT
1 TATT TATT TAT-T TATT TATT TATT TATT TATT TATT TATT TATT TATT
273 TATT TATT
1 TATT TATT
281 ATTATTTCTT
Statistics
Matches: 140, Mismatches: 33, Indels: 40
0.66 0.15 0.19
Matches are distributed among these distances:
3 27 0.19
4 98 0.70
5 9 0.06
6 6 0.04
ACGTcount: A:0.25, C:0.09, G:0.01, T:0.65
Consensus pattern (4 bp):
TATT
Found at i:366 original size:13 final size:14
Alignment explanation
Indices: 350--384 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
340 TTTATTATTT
350 TTATTTTTTTAAA-
1 TTATTTTTTTAAAC
363 TTATTCTTTTTAAAC
1 TTATT-TTTTTAAAC
378 TTATTTT
1 TTATTTT
385 CCTATTTATC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 5 0.25
14 10 0.50
15 5 0.25
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.69
Consensus pattern (14 bp):
TTATTTTTTTAAAC
Done.