Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01003168.1 Corchorus capsularis cultivar CVL-1 contig03176, 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: 1809
ACGTcount: A:0.25, C:0.22, G:0.12, T:0.40
Found at i:1046 original size:25 final size:26
Alignment explanation
Indices: 1012--1073 Score: 81
Period size: 25 Copynumber: 2.3 Consensus size: 26
1002 TCTTACCGAT
*
1012 TACCATTTTTGCTTTTGCTAC-TGAA
1 TACCATTTTTACTTTTGCTACTTGAA
*
1037 TACCATTTTTACTTTTTCTACTATTGAA
1 TACCATTTTTACTTTTGCTAC--TTGAA
1065 TACCATTTT
1 TACCATTTT
1074 GATCCTTTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
25 19 0.59
28 13 0.41
ACGTcount: A:0.23, C:0.19, G:0.06, T:0.52
Consensus pattern (26 bp):
TACCATTTTTACTTTTGCTACTTGAA
Found at i:1088 original size:30 final size:28
Alignment explanation
Indices: 1012--1088 Score: 79
Period size: 25 Copynumber: 2.8 Consensus size: 28
1002 TCTTACCGAT
* *
1012 TACCATTTTTGCTTTTGCTAC---TGAA
1 TACCATTTTTACTTTTCCTACTATTGAA
*
1037 TACCATTTTTACTTTTTCTACTATTGAA
1 TACCATTTTTACTTTTCCTACTATTGAA
*
1065 TACCATTTTGATCCTTTTCCTACT
1 TACCATTTT--TACTTTTCCTACT
1089 TACCATTTAC
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
25 19 0.44
28 13 0.30
30 11 0.26
ACGTcount: A:0.21, C:0.22, G:0.06, T:0.51
Consensus pattern (28 bp):
TACCATTTTTACTTTTCCTACTATTGAA
Found at i:1192 original size:7 final size:7
Alignment explanation
Indices: 1171--1299 Score: 68
Period size: 7 Copynumber: 17.7 Consensus size: 7
1161 TGCCATTTTT
1171 CTCTTTA
1 CTCTTTA
**
1178 CTGATTA
1 CTCTTTA
1185 CTCTTTA
1 CTCTTTA
1192 C-CTTTTA
1 CTC-TTTA
1199 C-CATTTTA
1 CTC--TTTA
1207 CTCTTTTA
1 CTC-TTTA
**
1215 CTGATTA
1 CTCTTTA
1222 CTCTTTA
1 CTCTTTA
*
1229 CTTTTTA
1 CTCTTTA
1236 C-CATTTTA
1 CTC--TTTA
1244 CTCTTTA
1 CTCTTTA
**
1251 CTGATTA
1 CTCTTTA
1258 CTCTTTA
1 CTCTTTA
*
1265 CTTTTTA
1 CTCTTTA
1272 -TCATCTTA
1 CTC-T-TTA
1280 CTCTTTA
1 CTCTTTA
*
1287 CTATTTTA
1 CT-CTTTA
1295 CTCTT
1 CTCTT
1300 ACTAATTACC
Statistics
Matches: 94, Mismatches: 18, Indels: 20
0.71 0.14 0.15
Matches are distributed among these distances:
6 2 0.02
7 60 0.64
8 28 0.30
9 4 0.04
ACGTcount: A:0.19, C:0.23, G:0.02, T:0.56
Consensus pattern (7 bp):
CTCTTTA
Found at i:1234 original size:29 final size:29
Alignment explanation
Indices: 1202--1336 Score: 86
Period size: 29 Copynumber: 4.7 Consensus size: 29
1192 CCTTTTACCA
1202 TTTTACTCTTTTACTGATTACTCTTTACT
1 TTTTACTCTTTTACTGATTACTCTTTACT
** **
1231 TTTTAC-CATTTTACTCTTTACTGATTACT
1 TTTTACTC-TTTTACTGATTACTCTTTACT
* *
1260 CTTTACT-TTTTATCAT-CTTACTCTTTACT
1 TTTTACTCTTTTA-C-TGATTACTCTTTACT
*
1289 ATTTTACTC--TTACTAATTAC-CTTTTACT
1 -TTTTACTCTTTTACTGATTACTC-TTTACT
** *
1317 GATTACTATTTTACTG-TTAC
1 TTTTACTCTTTTACTGATTAC
1337 CACTTTGCTC
Statistics
Matches: 82, Mismatches: 14, Indels: 21
0.70 0.12 0.18
Matches are distributed among these distances:
27 7 0.09
28 21 0.26
29 47 0.57
30 7 0.09
ACGTcount: A:0.21, C:0.21, G:0.03, T:0.56
Consensus pattern (29 bp):
TTTTACTCTTTTACTGATTACTCTTTACT
Found at i:1283 original size:22 final size:21
Alignment explanation
Indices: 1255--1302 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 21
1245 TCTTTACTGA
1255 TTACTCTTTACT-TTTTATCATC
1 TTACTCTTTACTATTTTA-C-TC
1277 TTACTCTTTACTATTTTACTC
1 TTACTCTTTACTATTTTACTC
1298 TTACT
1 TTACT
1303 AATTACCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 7 0.28
22 13 0.52
23 5 0.20
ACGTcount: A:0.19, C:0.23, G:0.00, T:0.58
Consensus pattern (21 bp):
TTACTCTTTACTATTTTACTC
Found at i:1296 original size:73 final size:72
Alignment explanation
Indices: 1157--1316 Score: 209
Period size: 73 Copynumber: 2.2 Consensus size: 72
1147 TATATTTTTT
* * *
1157 TTTTTGCCATTTTTCTCTTTACTGATTACTCTTTACCTTTTACCATTTTACTCTTTTACTGATTA
1 TTTTTACCATTTTACTCTTTACTGATTACTCTTTACCTTTTACCATCTTACTCTTTTACTGATTA
1222 CTCTTTAC
66 CTC-TTAC
* *
1230 TTTTTACCATTTTACTCTTTACTGATTACTCTTTACTTTTTATCATCTTACTC-TTTACT-ATTT
1 TTTTTACCATTTTACTCTTTACTGATTACTCTTTACCTTTTACCATCTTACTCTTTTACTGA--T
1293 TACTCTTAC
64 TACTCTTAC
**
1302 TAATTACC-TTTTACT
1 TTTTTACCATTTTACT
1317 GATTACTATT
Statistics
Matches: 78, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
71 8 0.10
72 16 0.21
73 54 0.69
ACGTcount: A:0.19, C:0.23, G:0.03, T:0.56
Consensus pattern (72 bp):
TTTTTACCATTTTACTCTTTACTGATTACTCTTTACCTTTTACCATCTTACTCTTTTACTGATTA
CTCTTAC
Found at i:1302 original size:36 final size:36
Alignment explanation
Indices: 1157--1288 Score: 210
Period size: 36 Copynumber: 3.6 Consensus size: 36
1147 TATATTTTTT
* *
1157 TTTTTGCCATTTTTCTCTTTACTGATTACTCTTTAC
1 TTTTTACCATTTTACTCTTTACTGATTACTCTTTAC
*
1193 CTTTTACCATTTTACTCTTTTACTGATTACTCTTTAC
1 TTTTTACCATTTTACTC-TTTACTGATTACTCTTTAC
1230 TTTTTACCATTTTACTCTTTACTGATTACTCTTTAC
1 TTTTTACCATTTTACTCTTTACTGATTACTCTTTAC
* *
1266 TTTTTATCATCTTACTCTTTACT
1 TTTTTACCATTTTACTCTTTACT
1289 ATTTTACTCT
Statistics
Matches: 89, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
36 54 0.61
37 35 0.39
ACGTcount: A:0.17, C:0.23, G:0.03, T:0.57
Consensus pattern (36 bp):
TTTTTACCATTTTACTCTTTACTGATTACTCTTTAC
Found at i:1323 original size:35 final size:35
Alignment explanation
Indices: 1284--1396 Score: 145
Period size: 35 Copynumber: 3.2 Consensus size: 35
1274 ATCTTACTCT
*
1284 TTACTATTTTACTCTTACTAATTACCTTTTACTGA
1 TTACTATTTTACTCTTACCAATTACCTTTTACTGA
* * ** *
1319 TTACTATTTTACTGTTACCACTTTGCTCTTACTGA
1 TTACTATTTTACTCTTACCAATTACCTTTTACTGA
* * *
1354 TTATTATTTTACTCTTACCGATTACTTTTTACTGA
1 TTACTATTTTACTCTTACCAATTACCTTTTACTGA
1389 TTACTATT
1 TTACTATT
1397 ATCCAATTAC
Statistics
Matches: 63, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
35 63 1.00
ACGTcount: A:0.23, C:0.19, G:0.05, T:0.52
Consensus pattern (35 bp):
TTACTATTTTACTCTTACCAATTACCTTTTACTGA
Found at i:1370 original size:21 final size:20
Alignment explanation
Indices: 1344--1386 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
1334 TACCACTTTG
* *
1344 CTCTTACTGATTATTATTTTA
1 CTCTTACCGATTACT-TTTTA
1365 CTCTTACCGATTACTTTTTA
1 CTCTTACCGATTACTTTTTA
1385 CT
1 CT
1387 GATTACTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.21, C:0.21, G:0.05, T:0.53
Consensus pattern (20 bp):
CTCTTACCGATTACTTTTTA
Found at i:1684 original size:16 final size:16
Alignment explanation
Indices: 1663--1726 Score: 51
Period size: 16 Copynumber: 4.1 Consensus size: 16
1653 ATAATTACCA
1663 TTTTACTGATTACTTC
1 TTTTACTGATTACTTC
** *
1679 TTTTACT--TTTGTCCC
1 TTTTACTGATTACT-TC
*
1694 TTTTACCGATTACTTC
1 TTTTACTGATTACTTC
* *
1710 CTTTACTGATTATTTC
1 TTTTACTGATTACTTC
1726 T
1 T
1727 CTTGATTGCC
Statistics
Matches: 34, Mismatches: 11, Indels: 6
0.67 0.22 0.12
Matches are distributed among these distances:
14 3 0.09
15 7 0.21
16 21 0.62
17 3 0.09
ACGTcount: A:0.16, C:0.22, G:0.06, T:0.56
Consensus pattern (16 bp):
TTTTACTGATTACTTC
Done.