Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009245.1 Corchorus capsularis cultivar CVL-1 contig09266, 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: 45580
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:6506 original size:3 final size:3
Alignment explanation
Indices: 6493--6527 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
6483 CAGTTCGCAG
6493 CTT CTTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT C-TT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
6528 GGTCTGAGGC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:7128 original size:32 final size:32
Alignment explanation
Indices: 7085--7149 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
7075 AATGCCTAAC
** *
7085 TTTTTTATTTTTTTCATAAATGAAATCCATGG
1 TTTTTTATTTTTGACAGAAATGAAATCCATGG
* *
7117 TTTTTTTTTTTTGAGAGAAATGAAATCCATGG
1 TTTTTTATTTTTGACAGAAATGAAATCCATGG
7149 T
1 T
7150 ATTTAATGTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.28, C:0.08, G:0.14, T:0.51
Consensus pattern (32 bp):
TTTTTTATTTTTGACAGAAATGAAATCCATGG
Found at i:8687 original size:63 final size:63
Alignment explanation
Indices: 8611--8733 Score: 237
Period size: 63 Copynumber: 2.0 Consensus size: 63
8601 AGAACAGTAT
*
8611 TTTTTATTCTAAAGTTAGCTGATTTTTATTTTAATTTTACATACTCTCATAATGTACTTAATA
1 TTTTTATTATAAAGTTAGCTGATTTTTATTTTAATTTTACATACTCTCATAATGTACTTAATA
8674 TTTTTATTATAAAGTTAGCTGATTTTTATTTTAATTTTACATACTCTCATAATGTACTTA
1 TTTTTATTATAAAGTTAGCTGATTTTTATTTTAATTTTACATACTCTCATAATGTACTTA
8734 TAATATCTTC
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 59 1.00
ACGTcount: A:0.30, C:0.11, G:0.07, T:0.53
Consensus pattern (63 bp):
TTTTTATTATAAAGTTAGCTGATTTTTATTTTAATTTTACATACTCTCATAATGTACTTAATA
Found at i:8885 original size:18 final size:20
Alignment explanation
Indices: 8849--8885 Score: 51
Period size: 18 Copynumber: 1.9 Consensus size: 20
8839 AATCGATTGA
8849 TTGATCAATGTATACAAGTT
1 TTGATCAATGTATACAAGTT
*
8869 TTGA-CAAT-TATATAAGT
1 TTGATCAATGTATACAAGT
8886 AATGTATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 8 0.50
19 4 0.25
20 4 0.25
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.41
Consensus pattern (20 bp):
TTGATCAATGTATACAAGTT
Found at i:13595 original size:2 final size:2
Alignment explanation
Indices: 13588--13622 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
13578 TCCTGATCCA
13588 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13623 TAATTTGTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:14775 original size:15 final size:15
Alignment explanation
Indices: 14743--14771 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
14733 TAAATTTAAT
14743 TTGTAACTTTGTAAC
1 TTGTAACTTTGTAAC
14758 TTGTAAC-TTGTAAC
1 TTGTAACTTTGTAAC
14772 CTTGGATGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.45
Consensus pattern (15 bp):
TTGTAACTTTGTAAC
Found at i:15421 original size:15 final size:15
Alignment explanation
Indices: 15385--15459 Score: 55
Period size: 15 Copynumber: 4.8 Consensus size: 15
15375 GCCAAAGGCA
* *
15385 GCAGAGAAGAAACCA
1 GCAGAGAAGAAGCCG
*
15400 GCGGAGAAGAAGCCG
1 GCAGAGAAGAAGCCG
15415 GCAGAG-A-AAGCTCCG
1 GCAGAGAAGAAG--CCG
*
15430 GCCGAGAAGAAGCCAAGG
1 GCAGAGAAGAAGCC---G
15448 GCAGAGAAGAAG
1 GCAGAGAAGAAG
15460 ATCCCGAAAG
Statistics
Matches: 47, Mismatches: 6, Indels: 11
0.73 0.09 0.17
Matches are distributed among these distances:
13 3 0.06
14 1 0.02
15 27 0.57
16 1 0.02
17 3 0.06
18 12 0.26
ACGTcount: A:0.41, C:0.20, G:0.37, T:0.01
Consensus pattern (15 bp):
GCAGAGAAGAAGCCG
Found at i:32239 original size:14 final size:13
Alignment explanation
Indices: 32213--32246 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
32203 TCACTTTCTA
*
32213 TTATTATTGTTTC
1 TTATTATTATTTC
32226 TTACTTATTATTTC
1 TTA-TTATTATTTC
32240 TTATTAT
1 TTATTAT
32247 AAATACACCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.21, C:0.09, G:0.03, T:0.68
Consensus pattern (13 bp):
TTATTATTATTTC
Found at i:33934 original size:32 final size:32
Alignment explanation
Indices: 33888--33959 Score: 126
Period size: 32 Copynumber: 2.2 Consensus size: 32
33878 CACCCAATTG
33888 TTTTTTTTTCTTCCAGAAATACCACACATAGT
1 TTTTTTTTTCTTCCAGAAATACCACACATAGT
* *
33920 TTTTTTTTTTTTCCAGAAATACCATACATAGT
1 TTTTTTTTTCTTCCAGAAATACCACACATAGT
33952 TTTTTTTT
1 TTTTTTTT
33960 AGCATAGCCG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.25, C:0.17, G:0.06, T:0.53
Consensus pattern (32 bp):
TTTTTTTTTCTTCCAGAAATACCACACATAGT
Found at i:35151 original size:72 final size:72
Alignment explanation
Indices: 35052--35202 Score: 221
Period size: 72 Copynumber: 2.1 Consensus size: 72
35042 TGAAGATCTT
* * * *
35052 GGTTTGTGGGATTCTAATTTTGATGCAAAGTTTTCTGCTGAAATCTTTAGATTGTCAAAAATTGA
1 GGTTTGTGGGATTCTAAGTTGGATGCAAAATTTTCTGCTGAAATCTTTAGATTATCAAAAATTGA
*
35117 TTTTGAA
66 TCTTGAA
** *
35124 GGTTTGTGGGATTCTTGGTTGGATGCAAAATTTTCTGCTGAAATTTTTAGATTATCAAAAATTGA
1 GGTTTGTGGGATTCTAAGTTGGATGCAAAATTTTCTGCTGAAATCTTTAGATTATCAAAAATTGA
*
35189 TCTTGAT
66 TCTTGAA
35196 GGTTTGT
1 GGTTTGT
35203 TTGCAAAAAC
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
72 70 1.00
ACGTcount: A:0.26, C:0.08, G:0.23, T:0.44
Consensus pattern (72 bp):
GGTTTGTGGGATTCTAAGTTGGATGCAAAATTTTCTGCTGAAATCTTTAGATTATCAAAAATTGA
TCTTGAA
Found at i:39054 original size:21 final size:21
Alignment explanation
Indices: 39030--39081 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
39020 AAATGACTAG
* *
39030 GAGACGACTTCCTCAGGCAGA
1 GAGACGACTTCCTCAAGCAAA
* *
39051 GAGACGGCTTCTTCAAGCAAA
1 GAGACGACTTCCTCAAGCAAA
39072 GAGACGACTT
1 GAGACGACTT
39082 TCATCCTCTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.31, C:0.25, G:0.27, T:0.17
Consensus pattern (21 bp):
GAGACGACTTCCTCAAGCAAA
Found at i:43996 original size:2 final size:2
Alignment explanation
Indices: 43951--43980 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
43941 ACGAAAAATA
43951 AT 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 AT
43981 TAGGTTTGGC
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):
AT
Done.