Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01002546.1 Corchorus capsularis cultivar CVL-1 contig02554, 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, 654
Length: 1091
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Found at i:233 original size:18 final size:18
Alignment explanation
Indices: 210--244 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
200 ATCATTATTG
210 ATTATTATATGATAATTA
1 ATTATTATATGATAATTA
228 ATTATTATATGATAATT
1 ATTATTATATGATAATT
245 CATTTTTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (18 bp):
ATTATTATATGATAATTA
Found at i:267 original size:21 final size:21
Alignment explanation
Indices: 243--317 Score: 69
Period size: 21 Copynumber: 3.2 Consensus size: 21
233 TATATGATAA
243 TTCATTTTTGAAATTTAGAAT
1 TTCATTTTTGAAATTTAGAAT
* *
264 TTCATCATTATTGATTATTATATGATAA
1 TTCAT--TT-TTGA-AATT-TA-GA-AT
292 TTCATTTTTGAAATTTAGAAT
1 TTCATTTTTGAAATTTAGAAT
313 TTCAT
1 TTCAT
318 CATTATTGAT
Statistics
Matches: 43, Mismatches: 4, Indels: 14
0.70 0.07 0.23
Matches are distributed among these distances:
21 11 0.26
22 2 0.05
23 4 0.09
24 7 0.16
25 7 0.16
26 4 0.09
27 2 0.05
28 6 0.14
ACGTcount: A:0.33, C:0.07, G:0.08, T:0.52
Consensus pattern (21 bp):
TTCATTTTTGAAATTTAGAAT
Found at i:272 original size:24 final size:24
Alignment explanation
Indices: 244--326 Score: 82
Period size: 24 Copynumber: 3.4 Consensus size: 24
234 ATATGATAAT
*
244 TCATTTTTGAAATTTAGAATTTCA
1 TCATTATTGAAATTTAGAATTTCA
* *
268 TCATTATTGATTATTATATGATAATTCA
1 TCATTATTGA-AATT-TA-GA-ATTTCA
296 T--TT-TTGAAATTTAGAATTTCA
1 TCATTATTGAAATTTAGAATTTCA
317 TCATTATTGA
1 TCATTATTGA
327 TTATTATATG
Statistics
Matches: 47, Mismatches: 5, Indels: 14
0.71 0.08 0.21
Matches are distributed among these distances:
21 6 0.13
22 2 0.04
23 4 0.09
24 16 0.34
25 7 0.15
26 4 0.09
27 2 0.04
28 6 0.13
ACGTcount: A:0.34, C:0.07, G:0.08, T:0.51
Consensus pattern (24 bp):
TCATTATTGAAATTTAGAATTTCA
Found at i:286 original size:49 final size:49
Alignment explanation
Indices: 228--352 Score: 250
Period size: 49 Copynumber: 2.6 Consensus size: 49
218 ATGATAATTA
228 ATTATTATATGATAATTCATTTTTGAAATTTAGAATTTCATCATTATTG
1 ATTATTATATGATAATTCATTTTTGAAATTTAGAATTTCATCATTATTG
277 ATTATTATATGATAATTCATTTTTGAAATTTAGAATTTCATCATTATTG
1 ATTATTATATGATAATTCATTTTTGAAATTTAGAATTTCATCATTATTG
326 ATTATTATATGATAATTCATTTTTGAA
1 ATTATTATATGATAATTCATTTTTGAA
353 TGATGATTTT
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 76 1.00
ACGTcount: A:0.35, C:0.06, G:0.08, T:0.51
Consensus pattern (49 bp):
ATTATTATATGATAATTCATTTTTGAAATTTAGAATTTCATCATTATTG
Found at i:296 original size:25 final size:25
Alignment explanation
Indices: 268--351 Score: 77
Period size: 25 Copynumber: 3.4 Consensus size: 25
258 TAGAATTTCA
268 TCATTATTGATTATTATATGATAAT
1 TCATTATTGATTATTATATGATAAT
* * *
293 TCATTTTTGA-AATT-TA-GA-ATTT
1 TCATTATTGATTATTATATGATA-AT
315 CATCATTATTGATTATTATATGATAAT
1 --TCATTATTGATTATTATATGATAAT
*
342 TCATTTTTGA
1 TCATTATTGA
352 ATGATGATTT
Statistics
Matches: 45, Mismatches: 7, Indels: 14
0.68 0.11 0.21
Matches are distributed among these distances:
21 1 0.02
22 3 0.07
23 2 0.04
24 12 0.27
25 21 0.47
26 2 0.04
27 3 0.07
28 1 0.02
ACGTcount: A:0.33, C:0.06, G:0.08, T:0.52
Consensus pattern (25 bp):
TCATTATTGATTATTATATGATAAT
Done.