Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021043.1 Corchorus olitorius cultivar O-4 contig21076, 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: 21479
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:1069 original size:19 final size:19
Alignment explanation
Indices: 1045--1081 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1035 TGTTTTATCA
* *
1045 ATTTCTGTCTTTGAATCTC
1 ATTTCTCTCTTTCAATCTC
1064 ATTTCTCTCTTTCAATCT
1 ATTTCTCTCTTTCAATCT
1082 TGCTTTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.16, C:0.24, G:0.05, T:0.54
Consensus pattern (19 bp):
ATTTCTCTCTTTCAATCTC
Found at i:3508 original size:20 final size:21
Alignment explanation
Indices: 3466--3508 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 21
3456 CCCAGTCTTC
3466 TTTTTGAAATTTCTTATGCTGTT
1 TTTTTGAAATTTCTTA--CTGTT
3489 TTTTTGAAATTTCTTA-TGTT
1 TTTTTGAAATTTCTTACTGTT
3509 GGTATTGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
23 16 0.80
ACGTcount: A:0.19, C:0.07, G:0.12, T:0.63
Consensus pattern (21 bp):
TTTTTGAAATTTCTTACTGTT
Found at i:5229 original size:4 final size:4
Alignment explanation
Indices: 5220--5263 Score: 88
Period size: 4 Copynumber: 11.0 Consensus size: 4
5210 CCTCTCTAGG
5220 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
5264 TATGATGTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 40 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:10688 original size:17 final size:14
Alignment explanation
Indices: 10651--10679 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
10641 TTATATATAA
10651 TGAAATATATGTAG
1 TGAAATATATGTAG
10665 TGAAATATATGTAG
1 TGAAATATATGTAG
10679 T
1 T
10680 TGTGAAATAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.21, T:0.38
Consensus pattern (14 bp):
TGAAATATATGTAG
Found at i:11836 original size:34 final size:34
Alignment explanation
Indices: 11793--11862 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
11783 ATGGACACAA
11793 TACTCCGTTCACTCCCTGATATAATCATTTCTCT
1 TACTCCGTTCACTCCCTGATATAATCATTTCTCT
*
11827 TACTCCGTTCACTCCCTGTTATAATCATTTCTCT
1 TACTCCGTTCACTCCCTGATATAATCATTTCTCT
11861 TA
1 TA
11863 ACCAGTAATC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.20, C:0.31, G:0.06, T:0.43
Consensus pattern (34 bp):
TACTCCGTTCACTCCCTGATATAATCATTTCTCT
Found at i:14000 original size:2 final size:2
Alignment explanation
Indices: 13993--14022 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
13983 ATTGGCTTGT
13993 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
14023 ACTACCAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:14165 original size:19 final size:20
Alignment explanation
Indices: 14138--14177 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
14128 AAACTAACAA
*
14138 ATTATTATCA-CAAAAAAAT
1 ATTAATATCACCAAAAAAAT
14157 ATTAATATCATCCAAAAAAAT
1 ATTAATATCA-CCAAAAAAAT
14178 CTAACAAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
21 9 0.50
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.30
Consensus pattern (20 bp):
ATTAATATCACCAAAAAAAT
Found at i:15324 original size:16 final size:16
Alignment explanation
Indices: 15303--15336 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
15293 AAATACAAAC
*
15303 TTTGTATTTTATTCAG
1 TTTGTATTTAATTCAG
15319 TTTGTATTTAATTCAG
1 TTTGTATTTAATTCAG
15335 TT
1 TT
15337 AAGGACAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.21, C:0.06, G:0.12, T:0.62
Consensus pattern (16 bp):
TTTGTATTTAATTCAG
Found at i:16228 original size:25 final size:25
Alignment explanation
Indices: 16192--16286 Score: 120
Period size: 25 Copynumber: 3.8 Consensus size: 25
16182 GTGCCTATTT
*
16192 TCTCTCAAGCCCTGCGCCACTTTCC
1 TCTCTCAGGCCCTGCGCCACTTTCC
*
16217 TCTCCCAGGCCCTGCGCCAC-TTCC
1 TCTCTCAGGCCCTGCGCCACTTTCC
* * *
16241 TTTTCTCAGGCCCTGCGCCATTTTCT
1 -TCTCTCAGGCCCTGCGCCACTTTCC
*
16267 TCTATCAGGCCCTGCGCCAC
1 TCTCTCAGGCCCTGCGCCAC
16287 CCTCTACAGC
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
24 4 0.07
25 52 0.88
26 3 0.05
ACGTcount: A:0.11, C:0.45, G:0.16, T:0.28
Consensus pattern (25 bp):
TCTCTCAGGCCCTGCGCCACTTTCC
Found at i:17160 original size:29 final size:31
Alignment explanation
Indices: 17121--17179 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 31
17111 GTGCATTTCG
* *
17121 GTCCCTGAAGTGAA-A-AAGTGAGCAATTGA
1 GTCCCTAAAGTGAAGATAAGGGAGCAATTGA
17150 GTCCCTAAAGTGAAGATAAGGGAGCAATTG
1 GTCCCTAAAGTGAAGATAAGGGAGCAATTG
17180 GATCCCTGTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 13 0.50
30 1 0.04
31 12 0.46
ACGTcount: A:0.37, C:0.14, G:0.29, T:0.20
Consensus pattern (31 bp):
GTCCCTAAAGTGAAGATAAGGGAGCAATTGA
Found at i:20957 original size:22 final size:20
Alignment explanation
Indices: 20918--20965 Score: 53
Period size: 22 Copynumber: 2.3 Consensus size: 20
20908 AAATACAACA
*
20918 ATATAAATAAACATAATAATAC
1 ATATTAATAAACATAAT-AT-C
20940 ATATTAAT-AACATAAATATC
1 ATATTAATAAACAT-AATATC
20960 ATATTA
1 ATATTA
20966 GTAATAAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 7 0.29
21 7 0.29
22 10 0.42
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.33
Consensus pattern (20 bp):
ATATTAATAAACATAATATC
Done.