Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01003982.1 Corchorus capsularis cultivar CVL-1 contig03990, 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: 2654
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Found at i:1217 original size:15 final size:15
Alignment explanation
Indices: 1197--1227 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1187 CTACTTTTGC
*
1197 TACTTTTATCATTTT
1 TACTTTTACCATTTT
1212 TACTTTTACCATTTT
1 TACTTTTACCATTTT
1227 T
1 T
1228 CTTACTCTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.16, G:0.00, T:0.65
Consensus pattern (15 bp):
TACTTTTACCATTTT
Found at i:1227 original size:24 final size:24
Alignment explanation
Indices: 1182--1254 Score: 56
Period size: 24 Copynumber: 2.9 Consensus size: 24
1172 TACTGATTTC
* * * *
1182 CATTTCTACTTTTGCTACTTTTAT
1 CATTTTTACTTTTACCATTTTTAT
*
1206 CATTTTTACTTTTACCATTTTTCT
1 CATTTTTACTTTTACCATTTTTAT
* *
1230 TACTCTTTTACTTAATACCATTTTT
1 CA-T-TTTTACTT-TTACCATTTTT
1255 GTTTAATACC
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
24 20 0.51
25 1 0.03
26 8 0.21
27 10 0.26
ACGTcount: A:0.19, C:0.21, G:0.01, T:0.59
Consensus pattern (24 bp):
CATTTTTACTTTTACCATTTTTAT
Found at i:1341 original size:25 final size:25
Alignment explanation
Indices: 1313--1363 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
1303 CACCATTTTT
1313 TTTTAATTAATACCATTCTTTACTC
1 TTTTAATTAATACCATTCTTTACTC
* *
1338 TTTTACTTAATACCATTTTTTACTC
1 TTTTAATTAATACCATTCTTTACTC
1363 T
1 T
1364 ACACCATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.25, C:0.20, G:0.00, T:0.55
Consensus pattern (25 bp):
TTTTAATTAATACCATTCTTTACTC
Found at i:1412 original size:42 final size:42
Alignment explanation
Indices: 1322--1428 Score: 121
Period size: 42 Copynumber: 2.5 Consensus size: 42
1312 TTTTTAATTA
* * *
1322 ATACCATTCTTT-ACTCTT-TTACTTAATACCATTTTTTACTCT
1 ATACCATT-TTTGAC-CTTCTTACTCAATACCATATTTCACTCT
*
1364 ACACCATTTTTGACCTTCTTACTCAATACCATATTTCACT-T
1 ATACCATTTTTGACCTTCTTACTCAATACCATATTTCACTCT
*
1405 GATACCATCTTTGACCTTCTTACT
1 -ATACCATTTTTGACCTTCTTACT
1429 GATTACTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
41 7 0.12
42 49 0.88
ACGTcount: A:0.24, C:0.27, G:0.03, T:0.46
Consensus pattern (42 bp):
ATACCATTTTTGACCTTCTTACTCAATACCATATTTCACTCT
Found at i:1444 original size:15 final size:14
Alignment explanation
Indices: 1420--1455 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
1410 CATCTTTGAC
1420 CTTCTTACTGATTA
1 CTTCTTACTGATTA
1434 CTTCTTTACTGATTA
1 CTTC-TTACTGATTA
1449 CTT-TTAC
1 CTTCTTAC
1456 CTTTTTTTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 4 0.19
14 4 0.19
15 13 0.62
ACGTcount: A:0.19, C:0.22, G:0.06, T:0.53
Consensus pattern (14 bp):
CTTCTTACTGATTA
Found at i:1509 original size:20 final size:20
Alignment explanation
Indices: 1480--1518 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1470 CTTTGCCATT
* *
1480 TTTACTTTTTACTGATTACC
1 TTTACCTTTTACCGATTACC
1500 TTTACCTTTTACCGATTAC
1 TTTACCTTTTACCGATTAC
1519 TCTTAGCTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.23, G:0.05, T:0.51
Consensus pattern (20 bp):
TTTACCTTTTACCGATTACC
Found at i:1934 original size:39 final size:38
Alignment explanation
Indices: 1876--2182 Score: 427
Period size: 39 Copynumber: 8.0 Consensus size: 38
1866 TGTTTTTTTT
* * *
1876 TTACCTTGACTCTTGATTATCAATTCTACTGATTACTA
1 TTACTTTGACTCTTAATTATCAATTTTACTGATTACTA
* * *
1914 GTACCTTGACTCCTTAATTATCAATTTTAATGATTACTA
1 TTACTTTGACT-CTTAATTATCAATTTTACTGATTACTA
* *
1953 TTATTTTGACTCTTAATTTATTAATTTTACTGATTACTA
1 TTACTTTGACTCTTAA-TTATCAATTTTACTGATTACTA
*
1992 TTACTTTGACTCTTAATTATCAATTTTAATGATTACTA
1 TTACTTTGACTCTTAATTATCAATTTTACTGATTACTA
* *
2030 TTATTTTGACTCTTAATTTATTAATTTTACTGATTACTA
1 TTACTTTGACTCTTAA-TTATCAATTTTACTGATTACTA
*
2069 TTACTTTGACTCTTAATTATCAATTTTAATGATTACTA
1 TTACTTTGACTCTTAATTATCAATTTTACTGATTACTA
* *
2107 TTATTTTGACTCTTAATTTATTAATTTTACTGATTACTA
1 TTACTTTGACTCTTAA-TTATCAATTTTACTGATTACTA
**
2146 TTACTTTGACTCTTAATTATTGA-TTTACTGATTACTA
1 TTACTTTGACTCTTAATTATCAATTTTACTGATTACTA
2183 CTGCCTTAAT
Statistics
Matches: 242, Mismatches: 23, Indels: 9
0.88 0.08 0.03
Matches are distributed among these distances:
37 14 0.06
38 91 0.38
39 137 0.57
ACGTcount: A:0.29, C:0.14, G:0.06, T:0.51
Consensus pattern (38 bp):
TTACTTTGACTCTTAATTATCAATTTTACTGATTACTA
Found at i:2012 original size:77 final size:77
Alignment explanation
Indices: 1881--2182 Score: 509
Period size: 77 Copynumber: 3.9 Consensus size: 77
1871 TTTTTTTACC
* * * * *
1881 TTGACTCTTGA-TTATCAATTCTACTGATTACTAGTACCTTGACTCCTTAATTATCAATTTTAAT
1 TTGACTCTTAATTTATTAATTTTACTGATTACTATTACTTTGACT-CTTAATTATCAATTTTAAT
1945 GATTACTATTATT
65 GATTACTATTATT
1958 TTGACTCTTAATTTATTAATTTTACTGATTACTATTACTTTGACTCTTAATTATCAATTTTAATG
1 TTGACTCTTAATTTATTAATTTTACTGATTACTATTACTTTGACTCTTAATTATCAATTTTAATG
2023 ATTACTATTATT
66 ATTACTATTATT
2035 TTGACTCTTAATTTATTAATTTTACTGATTACTATTACTTTGACTCTTAATTATCAATTTTAATG
1 TTGACTCTTAATTTATTAATTTTACTGATTACTATTACTTTGACTCTTAATTATCAATTTTAATG
2100 ATTACTATTATT
66 ATTACTATTATT
** *
2112 TTGACTCTTAATTTATTAATTTTACTGATTACTATTACTTTGACTCTTAATTATTGA-TTTACTG
1 TTGACTCTTAATTTATTAATTTTACTGATTACTATTACTTTGACTCTTAATTATCAATTTTAATG
2176 ATTACTA
66 ATTACTA
2183 CTGCCTTAAT
Statistics
Matches: 216, Mismatches: 8, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
76 13 0.06
77 174 0.81
78 29 0.13
ACGTcount: A:0.29, C:0.13, G:0.06, T:0.51
Consensus pattern (77 bp):
TTGACTCTTAATTTATTAATTTTACTGATTACTATTACTTTGACTCTTAATTATCAATTTTAATG
ATTACTATTATT
Found at i:2333 original size:55 final size:53
Alignment explanation
Indices: 2205--2339 Score: 137
Period size: 55 Copynumber: 2.5 Consensus size: 53
2195 TCAATTTGCT
* * * *
2205 TGATTAATCCTTTTACTTTATTACTGATTTACTGAATATTATTACTTTAACTC
1 TGATTAATCCTTTTACTTAATTACTGATTTACTGAATACTATTACCTCAACTC
* * * * *
2258 TTATGT-ATCCTTTTTTACTTAATTTCTGATTTACTGATTACTATTGCCTCGACTC
1 TGAT-TAATCC--TTTTACTTAATTACTGATTTACTGAATACTATTACCTCAACTC
2313 TGATTAATCTCTTTTCACTTAATTACT
1 TGATTAATC-CTTTT-ACTTAATTACT
2340 ACTACTTTGA
Statistics
Matches: 65, Mismatches: 11, Indels: 10
0.76 0.13 0.12
Matches are distributed among these distances:
53 7 0.11
54 6 0.09
55 51 0.78
56 1 0.02
ACGTcount: A:0.24, C:0.18, G:0.07, T:0.51
Consensus pattern (53 bp):
TGATTAATCCTTTTACTTAATTACTGATTTACTGAATACTATTACCTCAACTC
Done.