Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012641.1 Corchorus capsularis cultivar CVL-1 contig12662, 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: 13461
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Found at i:571 original size:2 final size:2
Alignment explanation
Indices: 564--592 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
554 TAATGGAATA
564 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
593 ATGAACAATT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1182 original size:6 final size:6
Alignment explanation
Indices: 1165--1226 Score: 56
Period size: 6 Copynumber: 10.5 Consensus size: 6
1155 GATGATCATC
* * *
1165 ATTATG AATATG ATTATG ATTTTTG A-T-TG ATTATG GTTATG ATTATG
1 ATTATG ATTATG ATTATG A-TTATG ATTATG ATTATG ATTATG ATTATG
* *
1212 ATTAAG ATTACG ATT
1 ATTATG ATTATG ATT
1227 TTTATTGATT
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
4 3 0.07
5 2 0.04
6 36 0.78
7 5 0.11
ACGTcount: A:0.32, C:0.02, G:0.18, T:0.48
Consensus pattern (6 bp):
ATTATG
Found at i:9231 original size:53 final size:55
Alignment explanation
Indices: 9147--9253 Score: 155
Period size: 53 Copynumber: 2.0 Consensus size: 55
9137 TTCATTGATG
* **
9147 AGAGCTATTTTACAATGCTTCATGCCTTTTAAAGCATGCATTGCAAGCAAGATAA
1 AGAGCTATTTTACAAGGCTTCATGCCTTTTAAAGCATGCATCACAAGCAAGATAA
* *
9202 AGAGCTATTTT-CAAGGCTT-ATGCCTTTTAAATCTTGCATCACAAGCAAGATA
1 AGAGCTATTTTACAAGGCTTCATGCCTTTTAAAGCATGCATCACAAGCAAGATA
9254 CGTATGACTG
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
53 29 0.62
54 7 0.15
55 11 0.23
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.32
Consensus pattern (55 bp):
AGAGCTATTTTACAAGGCTTCATGCCTTTTAAAGCATGCATCACAAGCAAGATAA
Found at i:10635 original size:3 final size:3
Alignment explanation
Indices: 10627--10654 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
10617 CTTCATGCAG
10627 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
10655 TATTATTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:10659 original size:3 final size:3
Alignment explanation
Indices: 10653--10742 Score: 117
Period size: 3 Copynumber: 30.0 Consensus size: 3
10643 AATAATAATA
** * * *
10653 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AAA ATA ATA ATA
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
10701 ATA ATT ATT ATT ATC ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
10743 TCCTTATACT
Statistics
Matches: 81, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 81 1.00
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:11523 original size:110 final size:111
Alignment explanation
Indices: 11381--11603 Score: 403
Period size: 111 Copynumber: 2.0 Consensus size: 111
11371 TCTGTTTTAG
*
11381 AGAGGATTAGGATTTCAATGGCAGCAATTTCGCAAAATTGCAAATT-GGTATTTGGGTTTATGCA
1 AGAGGATTAGGATTTCAATGGCAGCAATTTCGCAAAATTGCAAATTGGGTATCTGGGTTTATGCA
*
11445 ATAATCGAATTTAATTCTTTTTAACCTTAAATAAAAATTACCAACA
66 ATAATCGAATTAAATTCTTTTTAACCTTAAATAAAAATTACCAACA
*
11491 AGAGGATTAGGATTTCAATGGTAGCAATTTCGCAAAATTGCAAATTGGGTATCTGGGTTTATGCA
1 AGAGGATTAGGATTTCAATGGCAGCAATTTCGCAAAATTGCAAATTGGGTATCTGGGTTTATGCA
*
11556 ATAATCGAATTAAATTCTTTTTAACCTTAAATTAAAATTACCAACA
66 ATAATCGAATTAAATTCTTTTTAACCTTAAATAAAAATTACCAACA
11602 AG
1 AG
11604 TAATTGAATA
Statistics
Matches: 108, Mismatches: 4, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
110 45 0.42
111 63 0.58
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (111 bp):
AGAGGATTAGGATTTCAATGGCAGCAATTTCGCAAAATTGCAAATTGGGTATCTGGGTTTATGCA
ATAATCGAATTAAATTCTTTTTAACCTTAAATAAAAATTACCAACA
Found at i:12888 original size:21 final size:21
Alignment explanation
Indices: 12862--12906 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
12852 TTTTACTGGA
12862 TTGCTAAACACCGCCCCATTT
1 TTGCTAAACACCGCCCCATTT
**
12883 TTGCTATTCACCGCCCCATTT
1 TTGCTAAACACCGCCCCATTT
12904 TTG
1 TTG
12907 ACGCATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.18, C:0.36, G:0.11, T:0.36
Consensus pattern (21 bp):
TTGCTAAACACCGCCCCATTT
Found at i:13156 original size:32 final size:32
Alignment explanation
Indices: 13122--13258 Score: 159
Period size: 32 Copynumber: 4.2 Consensus size: 32
13112 CCGTGGCGAA
* * *
13122 GCCGCCCCACTTGGGAGGCTTCGCCACGGCAA
1 GCCGCCCCACTGGGGCGGCTTCGCCACGGCAG
* *
13154 GCCGCCCTCA-TGGGGCGGCTTCACCATGGGCAG
1 GCCGCCC-CACTGGGGCGGCTTCGCCA-CGGCAG
* *
13187 GCCGCCCCACTGGGGCGGCTTAGCCAGGGCAG
1 GCCGCCCCACTGGGGCGGCTTCGCCACGGCAG
* **
13219 GCCGTCCCGGTGGGGCGGCTTCGCCACGGCAG
1 GCCGCCCCACTGGGGCGGCTTCGCCACGGCAG
13251 GCCGCCCC
1 GCCGCCCC
13259 GGTAGGGCGG
Statistics
Matches: 89, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
32 62 0.70
33 27 0.30
ACGTcount: A:0.11, C:0.40, G:0.37, T:0.12
Consensus pattern (32 bp):
GCCGCCCCACTGGGGCGGCTTCGCCACGGCAG
Found at i:13207 original size:65 final size:64
Alignment explanation
Indices: 13122--13258 Score: 168
Period size: 65 Copynumber: 2.1 Consensus size: 64
13112 CCGTGGCGAA
* * *
13122 GCCGCCCCACTTGGGAGGCTTCGCCACGGCAAGCCG-CCCTCATGGGGCGGCTTCACCATGGGCA
1 GCCGCCCCACTGGGGAGGCTTAGCCACGGCAAGCCGTCCC-CATGGGGCGGCTTCACCA-CGGCA
13186 G
64 G
* * * ** *
13187 GCCGCCCCACTGGGGCGGCTTAGCCAGGGCAGGCCGTCCCGGTGGGGCGGCTTCGCCACGGCAG
1 GCCGCCCCACTGGGGAGGCTTAGCCACGGCAAGCCGTCCCCATGGGGCGGCTTCACCACGGCAG
13251 GCCGCCCC
1 GCCGCCCC
13259 GGTAGGGCGG
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
64 13 0.21
65 46 0.74
66 3 0.05
ACGTcount: A:0.11, C:0.40, G:0.37, T:0.12
Consensus pattern (64 bp):
GCCGCCCCACTGGGGAGGCTTAGCCACGGCAAGCCGTCCCCATGGGGCGGCTTCACCACGGCAG
Found at i:13425 original size:33 final size:33
Alignment explanation
Indices: 13348--13429 Score: 101
Period size: 33 Copynumber: 2.5 Consensus size: 33
13338 CCGGTGCCGT
* * *
13348 CCCCCTGGGGCGGCACTACCATGGCCAGGCCGC
1 CCCCCTGGGGCGGCACTACCATGGACAGACCAC
* * * *
13381 CTCCCTAGGGCGGCCCTACCATGGATAGACCAC
1 CCCCCTGGGGCGGCACTACCATGGACAGACCAC
13414 CCCCCTGGGGCGGCAC
1 CCCCCTGGGGCGGCAC
13430 CGGTACTAAA
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.15, C:0.44, G:0.30, T:0.11
Consensus pattern (33 bp):
CCCCCTGGGGCGGCACTACCATGGACAGACCAC
Done.