Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007486.1 Corchorus capsularis cultivar CVL-1 contig07507, 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: 54880
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:3336 original size:18 final size:16
Alignment explanation
Indices: 3305--3338 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
3295 ACTGCTTAAC
3305 TCATAATAATATTACT
1 TCATAATAATATTACT
3321 TCATATATATATATTACT
1 TCATA-ATA-ATATTACT
3339 AATAAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 3 0.19
18 8 0.50
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.47
Consensus pattern (16 bp):
TCATAATAATATTACT
Found at i:27436 original size:2 final size:2
Alignment explanation
Indices: 27431--27462 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
27421 CTATATATGC
27431 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
27463 CTTTAAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:30730 original size:2 final size:2
Alignment explanation
Indices: 30723--30748 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
30713 TTTGTCATCC
30723 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
30749 GCTATGTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:33445 original size:2 final size:2
Alignment explanation
Indices: 33402--33434 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
33392 ATAGATATTG
*
33402 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
33435 GGTTATATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:33940 original size:20 final size:21
Alignment explanation
Indices: 33917--33960 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
33907 TACCATTCTC
33917 AGAT-CACCAGTAGTAATCTG
1 AGATACACCAGTAGTAATCTG
*
33937 AGATCACACCAGTAGTAATTTG
1 AGAT-ACACCAGTAGTAATCTG
33959 AG
1 AG
33961 GGATCCTAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.19
22 17 0.81
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.25
Consensus pattern (21 bp):
AGATACACCAGTAGTAATCTG
Found at i:36518 original size:6 final size:6
Alignment explanation
Indices: 36502--36549 Score: 71
Period size: 6 Copynumber: 7.8 Consensus size: 6
36492 TCCACTTCTT
36502 TTTTTC TTTTTTC TTTTTTC TTTTTC TTTTTC TTTTT- TTTTTC TTTTT
1 TTTTTC -TTTTTC -TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
36550 TGTCAAATCT
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.12
6 22 0.55
7 13 0.32
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (6 bp):
TTTTTC
Found at i:36550 original size:7 final size:7
Alignment explanation
Indices: 36501--36543 Score: 65
Period size: 7 Copynumber: 6.6 Consensus size: 7
36491 ATCCACTTCT
36501 TTTTTTC
1 TTTTTTC
36508 TTTTTTC
1 TTTTTTC
36515 TTTTTTC
1 TTTTTTC
36522 -TTTTTC
1 TTTTTTC
36528 -TTTTTC
1 TTTTTTC
36534 TTTTTT-
1 TTTTTTC
36540 TTTT
1 TTTT
36544 CTTTTTTGTC
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
6 16 0.46
7 19 0.54
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTC
Found at i:38458 original size:6 final size:6
Alignment explanation
Indices: 38449--38478 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
38439 AATAATAAAT
38449 ATATTA ATATTA ATATTA ATATTA ATATTA
1 ATATTA ATATTA ATATTA ATATTA ATATTA
38479 GTACTAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
ATATTA
Found at i:52939 original size:8 final size:8
Alignment explanation
Indices: 52926--52951 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
52916 ATATCAAACA
52926 CTCCTTCC
1 CTCCTTCC
52934 CTCCTTCC
1 CTCCTTCC
52942 CTCCTTCC
1 CTCCTTCC
52950 CT
1 CT
52952 TTAGAGCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (8 bp):
CTCCTTCC
Found at i:54232 original size:2 final size:2
Alignment explanation
Indices: 54225--54253 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
54215 CACCCAACTC
54225 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
54254 TTTCCCCGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.