Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011815.1 Corchorus capsularis cultivar CVL-1 contig11836, 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: 46620
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Found at i:1018 original size:5 final size:5
Alignment explanation
Indices: 1008--1062 Score: 87
Period size: 5 Copynumber: 11.4 Consensus size: 5
998 TATATAGTAG
*
1008 TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA T-AG- TAAGA TAATA
1 TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA
1056 TAAGA TA
1 TAAGA TA
1063 TATATGCACG
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
3 1 0.02
4 4 0.09
5 41 0.89
ACGTcount: A:0.58, C:0.00, G:0.18, T:0.24
Consensus pattern (5 bp):
TAAGA
Found at i:1197 original size:8 final size:8
Alignment explanation
Indices: 1186--1223 Score: 58
Period size: 8 Copynumber: 4.5 Consensus size: 8
1176 ATAAACTTTT
1186 AAAAAAAC
1 AAAAAAAC
1194 AAAAAAAC
1 AAAAAAAC
1202 AAAAAAAC
1 AAAAAAAC
1210 AAAACAAAAC
1 -AAA-AAAAC
1220 AAAA
1 AAAA
1224 CATGAAGATG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
8 17 0.61
9 6 0.21
10 5 0.18
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Found at i:1207 original size:16 final size:18
Alignment explanation
Indices: 1186--1223 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1176 ATAAACTTTT
1186 AAAAAAAC-AAA-AAAAC
1 AAAAAAACAAAACAAAAC
1202 AAAAAAACAAAACAAAAC
1 AAAAAAACAAAACAAAAC
1220 AAAA
1 AAAA
1224 CATGAAGATG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 8 0.40
17 3 0.15
18 9 0.45
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (18 bp):
AAAAAAACAAAACAAAAC
Found at i:7451 original size:2 final size:2
Alignment explanation
Indices: 7444--7470 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
7434 ATTTCCTCTT
7444 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
7471 GAAATAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:13121 original size:3 final size:3
Alignment explanation
Indices: 13113--13137 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
13103 ATTGTTTAAC
13113 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
13138 TGGATGGGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:15530 original size:29 final size:28
Alignment explanation
Indices: 15464--15524 Score: 122
Period size: 28 Copynumber: 2.2 Consensus size: 28
15454 TAAAATTGTA
15464 ATTTTATTTTACCACAAAAAAAGTTTAC
1 ATTTTATTTTACCACAAAAAAAGTTTAC
15492 ATTTTATTTTACCACAAAAAAAGTTTAC
1 ATTTTATTTTACCACAAAAAAAGTTTAC
15520 ATTTT
1 ATTTT
15525 TCTTTTCATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.41, C:0.13, G:0.03, T:0.43
Consensus pattern (28 bp):
ATTTTATTTTACCACAAAAAAAGTTTAC
Found at i:19360 original size:18 final size:19
Alignment explanation
Indices: 19323--19360 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
19313 CGGTCAAGGG
*
19323 AAAGGTCGAGGTCAAACTC
1 AAAGGTCGAAGTCAAACTC
*
19342 AAAGG-CGAAGTCGAACTC
1 AAAGGTCGAAGTCAAACTC
19360 A
1 A
19361 TCGTCGGTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.39, C:0.21, G:0.26, T:0.13
Consensus pattern (19 bp):
AAAGGTCGAAGTCAAACTC
Found at i:20051 original size:15 final size:15
Alignment explanation
Indices: 20031--20069 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
20021 ATGCAAGAAC
*
20031 ATGAAGAAGATGATG
1 ATGAAGAAGATGAAG
20046 ATGAAGAAGATGAAG
1 ATGAAGAAGATGAAG
*
20061 ATGATGAAG
1 ATGAAGAAG
20070 TTATGAGTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.49, C:0.00, G:0.33, T:0.18
Consensus pattern (15 bp):
ATGAAGAAGATGAAG
Found at i:31535 original size:2 final size:2
Alignment explanation
Indices: 31528--31561 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
31518 AAATTACTTC
*
31528 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31562 CAGCTATTGC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40136 original size:33 final size:31
Alignment explanation
Indices: 40087--40149 Score: 108
Period size: 33 Copynumber: 2.0 Consensus size: 31
40077 ACAAATTAAA
40087 AGTAAAAAGCAAGATAGATGGGATAAATGTG
1 AGTAAAAAGCAAGATAGATGGGATAAATGTG
40118 AGTAAAAACGACAAGATAGATGGGATAAATGT
1 AGTAAAAA-G-CAAGATAGATGGGATAAATGT
40150 CTGCATGGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 8 0.27
32 1 0.03
33 21 0.70
ACGTcount: A:0.49, C:0.05, G:0.27, T:0.19
Consensus pattern (31 bp):
AGTAAAAAGCAAGATAGATGGGATAAATGTG
Done.