Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013361.1 Corchorus olitorius cultivar O-4 contig13394, 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: 54440
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:4100 original size:33 final size:31
Alignment explanation
Indices: 4027--4131 Score: 120
Period size: 33 Copynumber: 3.2 Consensus size: 31
4017 GCTATGATCA
** *
4027 ACCAAAACAGATTTGTTTTCATCACAATTAGC
1 ACCAAAACAGATTTG-TTTCATCACAAACAAC
4059 ATCCAAAACAGAATTTGTTTCATCACAAACAAC
1 A-CCAAAACAG-ATTTGTTTCATCACAAACAAC
*
4092 ACCTAAAACAGATTTAGTGTCATCACAAACAAC
1 ACC-AAAACAGATTT-GTTTCATCACAAACAAC
4125 ACTCAAA
1 AC-CAAA
4132 TTAGGTTTAA
Statistics
Matches: 64, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
32 7 0.11
33 51 0.80
34 6 0.09
ACGTcount: A:0.44, C:0.24, G:0.08, T:0.25
Consensus pattern (31 bp):
ACCAAAACAGATTTGTTTCATCACAAACAAC
Found at i:7570 original size:15 final size:15
Alignment explanation
Indices: 7550--7579 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
7540 ATCAGGCTGC
*
7550 CACGATACACGATAT
1 CACGATACACAATAT
7565 CACGATACACAATAT
1 CACGATACACAATAT
7580 TTCAACCGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.27, G:0.10, T:0.20
Consensus pattern (15 bp):
CACGATACACAATAT
Found at i:10727 original size:15 final size:15
Alignment explanation
Indices: 10707--10738 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
10697 GGGGATAAGG
10707 GATCTCCCTGTCTAA
1 GATCTCCCTGTCTAA
10722 GATCTCCCTGTCTAA
1 GATCTCCCTGTCTAA
10737 GA
1 GA
10739 CCTCTAGAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.22, C:0.31, G:0.16, T:0.31
Consensus pattern (15 bp):
GATCTCCCTGTCTAA
Found at i:14703 original size:26 final size:26
Alignment explanation
Indices: 14667--14716 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
14657 AAAGGTTTGT
14667 GGTTTTGGAGTCTATTTGGGGATTAG
1 GGTTTTGGAGTCTATTTGGGGATTAG
*
14693 GGTTTTGGAGTTTATTTGGGGATT
1 GGTTTTGGAGTCTATTTGGGGATT
14717 TCCTGATTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.14, C:0.02, G:0.38, T:0.46
Consensus pattern (26 bp):
GGTTTTGGAGTCTATTTGGGGATTAG
Found at i:25614 original size:31 final size:30
Alignment explanation
Indices: 25579--25648 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 30
25569 CAAATAATTT
**
25579 ATCAATCAACTAACAA-ATAATTGCAATTCAA
1 ATCAATCAA-TAACAAGAT-ATAACAATTCAA
*
25610 ATCAATCAATAGCAAGATATAACAATTCAA
1 ATCAATCAATAACAAGATATAACAATTCAA
25640 ATCAA-CAAT
1 ATCAATCAAT
25649 TGAAAGATAG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 4 0.11
30 20 0.57
31 11 0.31
ACGTcount: A:0.53, C:0.19, G:0.04, T:0.24
Consensus pattern (30 bp):
ATCAATCAATAACAAGATATAACAATTCAA
Found at i:27897 original size:25 final size:24
Alignment explanation
Indices: 27838--27898 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 24
27828 ATAAAAACAT
***
27838 GCAAGCAAAAATCAATTTAATTAA
1 GCAAGCAAAAATCAAGGGAATTAA
* *
27862 ACTAGCTAAAAATCAAGGGAATTAA
1 GCAAGC-AAAAATCAAGGGAATTAA
27887 GCAAGCAAAAAT
1 GCAAGCAAAAAT
27899 TCCAATCAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
24 10 0.34
25 19 0.66
ACGTcount: A:0.54, C:0.13, G:0.13, T:0.20
Consensus pattern (24 bp):
GCAAGCAAAAATCAAGGGAATTAA
Found at i:29438 original size:22 final size:21
Alignment explanation
Indices: 29413--29466 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
29403 GAAGTTCGTG
29413 TTTGAAGAGTTATTGAAGATAA
1 TTTGAAGA-TTATTGAAGATAA
*
29435 TTTGAAGA-T-TTGAAGATCA
1 TTTGAAGATTATTGAAGATAA
29454 -TTGAAGAATTATT
1 TTTGAAG-ATTATT
29467 TCGAGAAGCA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 6 0.21
19 10 0.36
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.02, G:0.20, T:0.39
Consensus pattern (21 bp):
TTTGAAGATTATTGAAGATAA
Found at i:33669 original size:11 final size:11
Alignment explanation
Indices: 33653--33682 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
33643 AATAGCACCT
33653 GAAGACCAAGA
1 GAAGACCAAGA
33664 GAAGACCAAGA
1 GAAGACCAAGA
33675 GAAGACCA
1 GAAGACCA
33683 CCTTTACCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.53, C:0.20, G:0.27, T:0.00
Consensus pattern (11 bp):
GAAGACCAAGA
Found at i:35392 original size:122 final size:122
Alignment explanation
Indices: 35254--35497 Score: 470
Period size: 122 Copynumber: 2.0 Consensus size: 122
35244 TGTTCTCTTC
35254 AATTACATCAATCATATGCATGTTTTTATTAGTTACTTTGGTCATATTCATGTTCATTTATTATT
1 AATTACATCAATCATATGCATGTTTTTATTAGTTACTTTGGTCATATTCATGTTCATTTATTATT
35319 AGGCATACTCATTTTTAATGTCATTTTTGTCTACCAATCATGTGTGCATTCAAACAA
66 AGGCATACTCATTTTTAATGTCATTTTTGTCTACCAATCATGTGTGCATTCAAACAA
35376 AATTACATCAATCATATGCATGTTTTTATTAGTTACTTTGGTCATATTCATGTTCATTTATTATT
1 AATTACATCAATCATATGCATGTTTTTATTAGTTACTTTGGTCATATTCATGTTCATTTATTATT
* *
35441 AGGCATACTCATTTTTTATGTCATTTTTGTCTACTAATCATGTGTGCATTCAAACAA
66 AGGCATACTCATTTTTAATGTCATTTTTGTCTACCAATCATGTGTGCATTCAAACAA
35498 GTCTTGCATT
Statistics
Matches: 120, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
122 120 1.00
ACGTcount: A:0.28, C:0.15, G:0.11, T:0.46
Consensus pattern (122 bp):
AATTACATCAATCATATGCATGTTTTTATTAGTTACTTTGGTCATATTCATGTTCATTTATTATT
AGGCATACTCATTTTTAATGTCATTTTTGTCTACCAATCATGTGTGCATTCAAACAA
Found at i:41532 original size:18 final size:18
Alignment explanation
Indices: 41509--41547 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
41499 AAAGGGTAAT
*
41509 TAAAAAAAATTGTTTTCA
1 TAAAAAAAAGTGTTTTCA
*
41527 TAAAAAGAAGTGTTTTCA
1 TAAAAAAAAGTGTTTTCA
41545 TAA
1 TAA
41548 TAGAGGAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.49, C:0.05, G:0.10, T:0.36
Consensus pattern (18 bp):
TAAAAAAAAGTGTTTTCA
Found at i:46231 original size:18 final size:19
Alignment explanation
Indices: 46208--46245 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
46198 GTGCATGGGC
*
46208 TGCATGGAG-GCATGGAGA
1 TGCATGGAGACCATGGAGA
46226 TGCATGGAGACCATGGAGA
1 TGCATGGAGACCATGGAGA
46245 T
1 T
46246 AAGGATGGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.29, C:0.13, G:0.39, T:0.18
Consensus pattern (19 bp):
TGCATGGAGACCATGGAGA
Found at i:48665 original size:20 final size:21
Alignment explanation
Indices: 48640--48681 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
48630 GGCTTTTGAT
48640 GAAAA-TGGGGTCTTGGCTGA
1 GAAAATTGGGGTCTTGGCTGA
**
48660 GAAAATTGTTGTCTTGGCTGA
1 GAAAATTGGGGTCTTGGCTGA
48681 G
1 G
48682 CATTAGATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.24, C:0.10, G:0.36, T:0.31
Consensus pattern (21 bp):
GAAAATTGGGGTCTTGGCTGA
Found at i:49861 original size:21 final size:21
Alignment explanation
Indices: 49838--49885 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
49828 ATTGAAACTG
*
49838 AAATTAAAAGCAAAGAAATCGA
1 AAATT-AAAGAAAAGAAATCGA
**
49860 AAATTAAAGAAAAGAAAAAGA
1 AAATTAAAGAAAAGAAATCGA
49881 AAATT
1 AAATT
49886 GCGATTAGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.69, C:0.04, G:0.12, T:0.15
Consensus pattern (21 bp):
AAATTAAAGAAAAGAAATCGA
Done.