Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023019.1 Corchorus olitorius cultivar O-4 contig23052, 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: 32902
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:270 original size:4 final size:4
Alignment explanation
Indices: 248--371 Score: 117
Period size: 4 Copynumber: 31.5 Consensus size: 4
238 TGTGTCTATG
* * * * * * *
248 TATA TACA TACA TACA TATA TATC TATA TATG TATA TGTA TATG TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* *
296 TATA TATA TAAA TAT- TATA TATA TATA T-TA TTTA TATA TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* * * *
342 CATA TACA TATA TAGA TATA TATG TATA TA
1 TATA TATA TATA TATA TATA TATA TATA TA
372 CTCCCTCAGT
Statistics
Matches: 97, Mismatches: 21, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
3 6 0.06
4 91 0.94
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (4 bp):
TATA
Found at i:303 original size:6 final size:6
Alignment explanation
Indices: 248--371 Score: 117
Period size: 6 Copynumber: 21.0 Consensus size: 6
238 TGTGTCTATG
* * * * * * *
248 TATATA CATACA TACATA TATATC TATATA TGTATA TGTATA TGTATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* *
296 TATATA TATAAA TAT-TA TATATA TATAT- TATTTA TATATA TATATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * *
342 CATATA CATATA TAGATA TATATG TATATA
1 TATATA TATATA TATATA TATATA TATATA
372 CTCCCTCAGT
Statistics
Matches: 96, Mismatches: 20, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
5 8 0.08
6 88 0.92
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (6 bp):
TATATA
Found at i:1610 original size:17 final size:17
Alignment explanation
Indices: 1588--1621 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1578 CACATGTGTA
*
1588 ATTTATGATTCTTACTG
1 ATTTATGAGTCTTACTG
*
1605 ATTTATGGGTCTTACTG
1 ATTTATGAGTCTTACTG
1622 TTCAAGTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.12, G:0.18, T:0.50
Consensus pattern (17 bp):
ATTTATGAGTCTTACTG
Found at i:9112 original size:27 final size:28
Alignment explanation
Indices: 9080--9132 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
9070 TAACCTGATT
9080 ATTTATC-TT-GGTATTTTATGATTTCAG
1 ATTTATCTTTAGGT-TTTTATGATTTCAG
*
9107 ATTTATCTTTATGTTTTTATGATTTC
1 ATTTATCTTTAGGTTTTTATGATTTC
9133 TAATTGATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 7 0.30
28 14 0.61
29 2 0.09
ACGTcount: A:0.21, C:0.08, G:0.11, T:0.60
Consensus pattern (28 bp):
ATTTATCTTTAGGTTTTTATGATTTCAG
Found at i:9594 original size:24 final size:25
Alignment explanation
Indices: 9560--9610 Score: 79
Period size: 24 Copynumber: 2.1 Consensus size: 25
9550 ATTGGAGTAT
9560 TTATTTATCTTG-TTATTTAATTTTA
1 TTATTTATCTTGTTTATTT-ATTTTA
9585 TTATTT-TCTTGTTTATTTATTTTA
1 TTATTTATCTTGTTTATTTATTTTA
9609 TT
1 TT
9611 GTTCACATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 13 0.52
25 12 0.48
ACGTcount: A:0.20, C:0.04, G:0.04, T:0.73
Consensus pattern (25 bp):
TTATTTATCTTGTTTATTTATTTTA
Found at i:19128 original size:18 final size:18
Alignment explanation
Indices: 19083--19147 Score: 64
Period size: 18 Copynumber: 3.8 Consensus size: 18
19073 ATAAGGAATC
*
19083 TGATTTTGATGATGCTCT
1 TGATTTTGATGATGCTGT
*
19101 TG-TATT--TGATGCTGT
1 TGATTTTGATGATGCTGT
* *
19116 TGATTTTGATGATGTTGA
1 TGATTTTGATGATGCTGT
*
19134 TGATTCTGATGATG
1 TGATTTTGATGATG
19148 ATGATTATGT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
15 10 0.26
16 3 0.08
17 3 0.08
18 22 0.58
ACGTcount: A:0.18, C:0.06, G:0.26, T:0.49
Consensus pattern (18 bp):
TGATTTTGATGATGCTGT
Found at i:20641 original size:18 final size:18
Alignment explanation
Indices: 20618--20653 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
20608 AGTCTCAGAC
20618 TCAAAGGACTTGATAATA
1 TCAAAGGACTTGATAATA
20636 TCAAAGGACTTGATAATA
1 TCAAAGGACTTGATAATA
20654 CCGTTGATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.11, G:0.17, T:0.28
Consensus pattern (18 bp):
TCAAAGGACTTGATAATA
Found at i:21732 original size:2 final size:2
Alignment explanation
Indices: 21725--21759 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
21715 TCAAAACTTT
21725 TA TA TA 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 TA TA TA T
21760 CTAGGCAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:29657 original size:8 final size:8
Alignment explanation
Indices: 29644--29676 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
29634 ACAGCAGGAG
29644 GAGGAAGA
1 GAGGAAGA
*
29652 GAGGAAAA
1 GAGGAAGA
29660 GAGGAAGA
1 GAGGAAGA
29668 GAGG-AGA
1 GAGGAAGA
29675 GA
1 GA
29677 AAGAAGATTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
7 5 0.22
8 18 0.78
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (8 bp):
GAGGAAGA
Found at i:32368 original size:68 final size:68
Alignment explanation
Indices: 32259--32392 Score: 250
Period size: 68 Copynumber: 2.0 Consensus size: 68
32249 ACAAGGTATA
* *
32259 TCACAAGGGACATGTGGCATGATTTGGTGAATGGGGCATGAAGTGGGGCACAGAACTTGGGGCAG
1 TCACAAGGGACATGTGGCATGATTTGGTGAATGAGGCATGAAGTGGGGCACAGAACTTGGGACAG
32324 GAG
66 GAG
32327 TCACAAGGGACATGTGGCATGATTTGGTGAATGAGGCATGAAGTGGGGCACAGAACTTGGGACAG
1 TCACAAGGGACATGTGGCATGATTTGGTGAATGAGGCATGAAGTGGGGCACAGAACTTGGGACAG
32392 G
66 G
32393 GGATTTCCAT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 64 1.00
ACGTcount: A:0.28, C:0.13, G:0.40, T:0.19
Consensus pattern (68 bp):
TCACAAGGGACATGTGGCATGATTTGGTGAATGAGGCATGAAGTGGGGCACAGAACTTGGGACAG
GAG
Found at i:32882 original size:2 final size:2
Alignment explanation
Indices: 32875--32902 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
32865 ATTATAAAAC
32875 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.