Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004083.1 Corchorus capsularis cultivar CVL-1 contig04091, 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: 1710
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39
Found at i:1298 original size:56 final size:55
Alignment explanation
Indices: 1232--1418 Score: 151
Period size: 56 Copynumber: 3.5 Consensus size: 55
1222 CCTAGTCATT
* * *
1232 ATTTTATTCTTTACTGATTGCCATTTCTTTTTACTGATTAATATTTTACTCTTTACC
1 ATTTTACTCTTTACTGATTGCCTTTTC-TTTTACTGATTACTA-TTTACTCTTTACC
* * * * *
1289 ATTTT-TTCTTTAC-CA-T---TTTTC-TTTACTGATTTCTCTATAACTCTTTACC
1 ATTTTACTCTTTACTGATTGCCTTTTCTTTTACTGATTACTAT-TTACTCTTTACC
* * * *
1338 A-TTT-CTCTTTACTGATTACTTTTTACTCTTTACTGATTACCA-TTACTTTTTACC
1 ATTTTACTCTTTACTGATTGCCTTTT-CT-TTTACTGATTACTATTTACTCTTTACC
1392 ATTTTACTCTTTACTGATTGCCTTTTC
1 ATTTTACTCTTTACTGATTGCCTTTTC
1419 AATTTTTTAC
Statistics
Matches: 104, Mismatches: 15, Indels: 24
0.73 0.10 0.17
Matches are distributed among these distances:
48 11 0.11
49 24 0.23
50 1 0.01
51 4 0.04
53 4 0.04
54 13 0.12
55 5 0.05
56 37 0.36
57 5 0.05
ACGTcount: A:0.19, C:0.21, G:0.04, T:0.56
Consensus pattern (55 bp):
ATTTTACTCTTTACTGATTGCCTTTTCTTTTACTGATTACTATTTACTCTTTACC
Found at i:1305 original size:49 final size:48
Alignment explanation
Indices: 1252--1364 Score: 120
Period size: 49 Copynumber: 2.3 Consensus size: 48
1242 TTACTGATTG
* * *
1252 CCATTTCTTTTTACTGATTAATATTTTACTCTTTACCATTTTTTCTTTA
1 CCATTTCTTTTTACTGATTAATATATAACTCTTTACCA-TTTCTCTTTA
** *
1301 CCATTT-TTCTTTACTGATTTCTCTATAACTCTTTACCATTTCTCTTTA
1 CCATTTCTT-TTTACTGATTAATATATAACTCTTTACCATTTCTCTTTA
* *
1349 CTGATTACTTTTTACT
1 C-CATTTCTTTTTACT
1365 CTTTACTGAT
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
48 12 0.23
49 39 0.74
50 2 0.04
ACGTcount: A:0.19, C:0.21, G:0.03, T:0.57
Consensus pattern (48 bp):
CCATTTCTTTTTACTGATTAATATATAACTCTTTACCATTTCTCTTTA
Found at i:1309 original size:13 final size:14
Alignment explanation
Indices: 1281--1314 Score: 61
Period size: 13 Copynumber: 2.5 Consensus size: 14
1271 AATATTTTAC
1281 TCTTTACCATTTTT
1 TCTTTACCATTTTT
1295 TCTTTACCA-TTTT
1 TCTTTACCATTTTT
1308 TCTTTAC
1 TCTTTAC
1315 TGATTTCTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.15, C:0.24, G:0.00, T:0.62
Consensus pattern (14 bp):
TCTTTACCATTTTT
Found at i:1347 original size:13 final size:13
Alignment explanation
Indices: 1280--1349 Score: 51
Period size: 13 Copynumber: 5.6 Consensus size: 13
1270 TAATATTTTA
1280 CTCTTTACCATTTT
1 CTCTTTACCA-TTT
*
1294 TTCTTTACCATTT
1 CTCTTTACCATTT
* *
1307 TTCTTTACTGATTT
1 CTCTTTAC-CATTT
*
1321 CTCTATA--A---
1 CTCTTTACCATTT
1329 CTCTTTACCATTT
1 CTCTTTACCATTT
1342 CTCTTTAC
1 CTCTTTAC
1350 TGATTACTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
8 6 0.13
10 1 0.02
11 1 0.02
13 19 0.42
14 18 0.40
ACGTcount: A:0.17, C:0.26, G:0.01, T:0.56
Consensus pattern (13 bp):
CTCTTTACCATTT
Found at i:1551 original size:54 final size:55
Alignment explanation
Indices: 1486--1700 Score: 328
Period size: 55 Copynumber: 3.9 Consensus size: 55
1476 ACTATTACGC
*
1486 TTTTCTTACTC-TTTTTACTGAATATTGTTTCTTACTCTTTTTACTAATGACTCT
1 TTTTCTTACTCTTTTTTACTGAATATTGTTTCTTACTCTTTTTACTGATGACTCT
* *
1540 TTTTCTTACTCTTTTTTACTGAATACTGTTTCTTACTCTTTTTACTGATGGCTC-
1 TTTTCTTACTCTTTTTTACTGAATATTGTTTCTTACTCTTTTTACTGATGACTCT
*
1594 TTTTCTTAACTC-TTTTTACTGAATATTGTTTCTTACTCTTATTTACTGATGACCCT
1 TTTTCTT-ACTCTTTTTTACTGAATATTGTTTCTTACTCTT-TTTACTGATGACTCT
*
1650 TTTTCTTACTCTTTTTTACTGAATATTGTTTTTTTACTCTTTTTTACTGAT
1 TTTTCTTACTCTTTTTTACTGAATATTG-TTTCTTACTC-TTTTTACTGAT
1701 TACTATTACC
Statistics
Matches: 147, Mismatches: 7, Indels: 11
0.89 0.04 0.07
Matches are distributed among these distances:
54 45 0.31
55 59 0.40
56 23 0.16
57 18 0.12
58 2 0.01
ACGTcount: A:0.17, C:0.18, G:0.07, T:0.58
Consensus pattern (55 bp):
TTTTCTTACTCTTTTTTACTGAATATTGTTTCTTACTCTTTTTACTGATGACTCT
Found at i:1577 original size:81 final size:80
Alignment explanation
Indices: 1487--1699 Score: 238
Period size: 81 Copynumber: 2.6 Consensus size: 80
1477 CTATTACGCT
*
1487 TTTCTTACTCTTTTTACTGAATATTGTTTCTTACTCTTTTTACT-AATGACTCTTTTTCTTACTC
1 TTTCTTACTCTTTTTACTGAATATTGTTTCTTACTCTTTTTACTGAAT-A-T-TGTTTCTTACTC
*
1551 TTTTTTACTGAAT-A-CTG
63 TTATTTACTG-ATGACCTG
*
1568 TTTCTTACTCTTTTTACTG-ATGGCTCT-TTTCTTAACTCTTTTTACTGAATATTGTTTCTTACT
1 TTTCTTACTCTTTTTACTGAAT--AT-TGTTTCTT-ACTCTTTTTACTGAATATTGTTTCTTACT
*
1631 CTTATTTACTGATGACCCTT
62 CTTATTTACTGATGA-CCTG
*
1651 TTTCTTACTCTTTTTTACTGAATATTGTTTTTTTACTCTTTTTTACTGA
1 TTTCTTACTC-TTTTTACTGAATATTG-TTTCTTACTC-TTTTTACTGA
1700 TTACTATTAC
Statistics
Matches: 113, Mismatches: 6, Indels: 23
0.80 0.04 0.16
Matches are distributed among these distances:
80 4 0.04
81 40 0.35
82 9 0.08
83 31 0.27
84 27 0.24
85 2 0.02
ACGTcount: A:0.17, C:0.18, G:0.07, T:0.57
Consensus pattern (80 bp):
TTTCTTACTCTTTTTACTGAATATTGTTTCTTACTCTTTTTACTGAATATTGTTTCTTACTCTTA
TTTACTGATGACCTG
Found at i:1694 original size:28 final size:27
Alignment explanation
Indices: 1486--1704 Score: 218
Period size: 28 Copynumber: 8.0 Consensus size: 27
1476 ACTATTACGC
*
1486 TTTTCTTACTCTTTTTACTGAATATTG
1 TTTTCTTACTCTTTTTACTGAATACTG
*
1513 -TTTCTTACTCTTTTTACT-AATGACTCT
1 TTTTCTTACTCTTTTTACTGAAT-ACT-G
1540 TTTTCTTACTCTTTTTTACTGAATACTG
1 TTTTCTTACTC-TTTTTACTGAATACTG
* *
1568 -TTTCTTACTCTTTTTACTG-ATGGCTC
1 TTTTCTTACTCTTTTTACTGAAT-ACTG
*
1594 TTTTCTTAACTCTTTTTACTGAATATTG
1 TTTTCTT-ACTCTTTTTACTGAATACTG
1622 -TTTCTTACTCTTATTTACTG-ATGACCCT-
1 TTTTCTTACTCTT-TTTACTGAAT-A--CTG
*
1650 TTTTCTTACTCTTTTTTACTGAATATTG
1 TTTTCTTACTC-TTTTTACTGAATACTG
* *
1678 TTTTTTTACTCTTTTTTACTGATTACT
1 TTTTCTTACTC-TTTTTACTGAATACT
1705 ATTACC
Statistics
Matches: 162, Mismatches: 13, Indels: 33
0.78 0.06 0.16
Matches are distributed among these distances:
25 5 0.03
26 39 0.24
27 31 0.19
28 48 0.30
29 32 0.20
30 7 0.04
ACGTcount: A:0.17, C:0.18, G:0.07, T:0.58
Consensus pattern (27 bp):
TTTTCTTACTCTTTTTACTGAATACTG
Done.