Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024622.1 Corchorus olitorius cultivar O-4 contig24655, 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: 12941
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:431 original size:147 final size:147
Alignment explanation
Indices: 135--448 Score: 461
Period size: 147 Copynumber: 2.1 Consensus size: 147
125 GGAGAGCTAT
135 TGTTCATGACCTCTGCTGGGATGTCGAACACACTATCAAGCACTGTTGGGACCCACAGCAAGCTG
1 TGTTCATGACCTCTGCTGGGATGTCGAACACACTATCAAGCACTGTTGGGACCCACAGCAAGCTG
* *
200 ACTTGGGCAACACCCGAAACATGCTGATGGTGGGGCTCACTAATAGATGAGTTTATTGTTTTCAC
66 ACGTGGGCAACACCCGAAACATGCTGATAGTGGGGCTCACTAATAGATGAGTTTATTGTTTTCAC
*
265 CCTTGCTAGAAGGTCAC
131 CCTTGCTAGAAGATCAC
* * * *
282 TGTTCATGACCTCTGCTGGGATGTCGGACCCACTATCAGGCACTGTTGGGACCCACGGCAAGCTG
1 TGTTCATGACCTCTGCTGGGATGTCGAACACACTATCAAGCACTGTTGGGACCCACAGCAAGCTG
* * *
347 ACGT-GGCAACACCCGAGACATGCTGATAGTGGGGCTCACTAGTAGGA-GAGTTTATTGTTTTCG
66 ACGTGGGCAACACCCGAAACATGCTGATAGTGGGGCTCACTAATA-GATGAGTTTATTGTTTTCA
* * *
410 GCCTCTGCTGGAAGATTAC
130 CCCT-TGCTAGAAGATCAC
*
429 TGTTCATCAGCCTCTGCTGG
1 TGTTCATGA-CCTCTGCTGG
449 AGCATTGGGC
Statistics
Matches: 150, Mismatches: 14, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
146 55 0.37
147 85 0.57
148 10 0.07
ACGTcount: A:0.22, C:0.25, G:0.27, T:0.26
Consensus pattern (147 bp):
TGTTCATGACCTCTGCTGGGATGTCGAACACACTATCAAGCACTGTTGGGACCCACAGCAAGCTG
ACGTGGGCAACACCCGAAACATGCTGATAGTGGGGCTCACTAATAGATGAGTTTATTGTTTTCAC
CCTTGCTAGAAGATCAC
Found at i:902 original size:20 final size:21
Alignment explanation
Indices: 877--919 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
867 TGAAGGGAAT
877 CTTGT-CATAAGCATTAAATG
1 CTTGTCCATAAGCATTAAATG
* *
897 CTTGTCCTTGAGCATTAAATG
1 CTTGTCCATAAGCATTAAATG
918 CT
1 CT
920 GATGGGAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.37
Consensus pattern (21 bp):
CTTGTCCATAAGCATTAAATG
Found at i:1757 original size:46 final size:46
Alignment explanation
Indices: 1690--1798 Score: 200
Period size: 46 Copynumber: 2.4 Consensus size: 46
1680 TTAGATAAAA
*
1690 CTCTTGATCCAGTGTGAATTATCTCTTTTATTCTTTAAACAATTAC
1 CTCTTGATCCGGTGTGAATTATCTCTTTTATTCTTTAAACAATTAC
*
1736 CTCTTGATCCGGTGTGAATTATTTCTTTTATTCTTTAAACAATTAC
1 CTCTTGATCCGGTGTGAATTATCTCTTTTATTCTTTAAACAATTAC
1782 CTCTTGATCCGGTGTGA
1 CTCTTGATCCGGTGTGA
1799 TAATTGCTCA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 61 1.00
ACGTcount: A:0.23, C:0.19, G:0.13, T:0.45
Consensus pattern (46 bp):
CTCTTGATCCGGTGTGAATTATCTCTTTTATTCTTTAAACAATTAC
Found at i:3859 original size:13 final size:14
Alignment explanation
Indices: 3831--3864 Score: 52
Period size: 13 Copynumber: 2.4 Consensus size: 14
3821 TTGTTTCTAG
3831 TTTAATTGCTTTATT
1 TTTAATTGC-TTATT
3846 TTTAATTG-TTATT
1 TTTAATTGCTTATT
3859 TTTAAT
1 TTTAAT
3865 CCCCTGTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 11 0.58
15 8 0.42
ACGTcount: A:0.24, C:0.03, G:0.06, T:0.68
Consensus pattern (14 bp):
TTTAATTGCTTATT
Found at i:6791 original size:21 final size:22
Alignment explanation
Indices: 6767--6816 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
6757 GGAGCAGGCA
*
6767 TGGCCGGTCCTAGCTTGG-ATG
1 TGGCCGGTCCTAGCTCGGTATG
*
6788 TGGCCGGTCGTAGCTCGGTATG
1 TGGCCGGTCCTAGCTCGGTATG
6810 -GGCCGGT
1 TGGCCGGT
6817 GTTAGCCGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 23 0.88
22 3 0.12
ACGTcount: A:0.08, C:0.24, G:0.42, T:0.26
Consensus pattern (22 bp):
TGGCCGGTCCTAGCTCGGTATG
Found at i:10071 original size:11 final size:10
Alignment explanation
Indices: 10055--10101 Score: 53
Period size: 11 Copynumber: 4.7 Consensus size: 10
10045 AAGTTCGTGT
10055 TTGAAGACTTA
1 TTGAAGAC-TA
*
10066 TTGAAGACAA
1 TTGAAGACTA
10076 TTTGAAGA-T-
1 -TTGAAGACTA
10085 TTGAAGACTA
1 TTGAAGACTA
10095 TTGAAGA
1 TTGAAGA
10102 ATTATTTTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
8 7 0.23
9 1 0.03
10 8 0.26
11 15 0.48
ACGTcount: A:0.40, C:0.06, G:0.21, T:0.32
Consensus pattern (10 bp):
TTGAAGACTA
Found at i:10090 original size:19 final size:18
Alignment explanation
Indices: 10066--10101 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
10056 TGAAGACTTA
10066 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
10085 TTGAAGACTATTGAAGA
1 TTGAAGACAATTGAAGA
10102 ATTATTTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.06, G:0.22, T:0.31
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Done.