Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013006.1 Corchorus olitorius cultivar O-4 contig13039, 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: 23759
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:6742 original size:35 final size:35
Alignment explanation
Indices: 6703--6773 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
6693 ACAAAAAGAC
*
6703 TTGAAGAATTAATATTGTATCATTAAAAATAAGTT
1 TTGAAGAATTAATATTGTATCAATAAAAATAAGTT
* *
6738 TTGAAGAGTTAATATTGTATGAATAAAAATAAGTT
1 TTGAAGAATTAATATTGTATCAATAAAAATAAGTT
6773 T
1 T
6774 CACTCCCCAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.45, C:0.01, G:0.14, T:0.39
Consensus pattern (35 bp):
TTGAAGAATTAATATTGTATCAATAAAAATAAGTT
Found at i:7653 original size:193 final size:193
Alignment explanation
Indices: 7320--7705 Score: 756
Period size: 193 Copynumber: 2.0 Consensus size: 193
7310 AATATATATA
7320 TATACTATATATACTAAATATTATTTGAAAGACCCAGGAAATTTACCAAAGGCCCCTTTGAGAAT
1 TATACTATATATACTAAATATTATTTGAAAGACCCAGGAAATTTACCAAAGGCCCCTTTGAGAAT
7385 CGATGAGGAGACTCCATTTGAACTTTTTTTGTCCTTTTCTGTCTTTTCTCACTTGCCAAATTACT
66 CGATGAGGAGACTCCATTTGAACTTTTTTTGTCCTTTTCTGTCTTTTCTCACTTGCCAAATTACT
7450 AAGAAGACCCTAGGTTAGTTTCTTACCCTTGAGCCCTTCTTTGTAATTATCCTTTACTTTCAC
131 AAGAAGACCCTAGGTTAGTTTCTTACCCTTGAGCCCTTCTTTGTAATTATCCTTTACTTTCAC
7513 TATA-TATATATACTAAATATTATTTGAAAGACCCAGGAAATTTACCAAAGGCCCCTTTTGAGAA
1 TATACTATATATACTAAATATTATTTGAAAGACCCAGGAAATTTACCAAAGGCCCC-TTTGAGAA
7577 TCGATGAGGAGACTCCATTTGAACTTTTTTTGTCCTTTTCTGTCTTTTCTCACTTGCCAAATTAC
65 TCGATGAGGAGACTCCATTTGAACTTTTTTTGTCCTTTTCTGTCTTTTCTCACTTGCCAAATTAC
7642 TAAGAAGACCCTAGGTTAGTTTCTTACCCTTGAGCCCTTCTTTGTAATTATCCTTTACTTTCAC
130 TAAGAAGACCCTAGGTTAGTTTCTTACCCTTGAGCCCTTCTTTGTAATTATCCTTTACTTTCAC
7706 ATAAATGTTA
Statistics
Matches: 192, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
192 51 0.27
193 141 0.73
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.39
Consensus pattern (193 bp):
TATACTATATATACTAAATATTATTTGAAAGACCCAGGAAATTTACCAAAGGCCCCTTTGAGAAT
CGATGAGGAGACTCCATTTGAACTTTTTTTGTCCTTTTCTGTCTTTTCTCACTTGCCAAATTACT
AAGAAGACCCTAGGTTAGTTTCTTACCCTTGAGCCCTTCTTTGTAATTATCCTTTACTTTCAC
Found at i:21052 original size:6 final size:6
Alignment explanation
Indices: 21038--21092 Score: 74
Period size: 6 Copynumber: 8.7 Consensus size: 6
21028 TTTCCTTTAG
*
21038 TTTTGT TTTTAT TTTTCGT ATTTTGT TTTTGT TTTTGT TTTTGT TTTTGT
1 TTTTGT TTTTGT TTTT-GT -TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT
21088 GTTTT
1 -TTTT
21093 TGTGCTTTTG
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
6 33 0.75
7 7 0.16
8 4 0.09
ACGTcount: A:0.04, C:0.02, G:0.15, T:0.80
Consensus pattern (6 bp):
TTTTGT
Found at i:21072 original size:26 final size:26
Alignment explanation
Indices: 21038--21095 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 26
21028 TTTCCTTTAG
21038 TTTTGTTTTTATTTTTCGTATTT-TGT
1 TTTTGTTTTTATTTTT-GTATTTGTGT
* *
21064 TTTTGTTTTTGTTTTTGTTTTTGTGT
1 TTTTGTTTTTATTTTTGTATTTGTGT
21090 TTTTGT
1 TTTTGT
21096 GCTTTTGTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 5 0.17
26 24 0.83
ACGTcount: A:0.03, C:0.02, G:0.16, T:0.79
Consensus pattern (26 bp):
TTTTGTTTTTATTTTTGTATTTGTGT
Found at i:21090 original size:20 final size:20
Alignment explanation
Indices: 21038--21095 Score: 68
Period size: 19 Copynumber: 3.0 Consensus size: 20
21028 TTTCCTTTAG
*
21038 TTTTGTTTTTAT-TTTTCGTA
1 TTTTGTTTTT-TGTTTTTGTA
21058 TTTTG-TTTTTGTTTTTGT-
1 TTTTGTTTTTTGTTTTTGTA
21076 TTTTGTTTTTGTGTTTTTGT
1 TTTTGTTTTT-TGTTTTTGT
21096 GCTTTTGTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
18 6 0.18
19 14 0.41
20 14 0.41
ACGTcount: A:0.03, C:0.02, G:0.16, T:0.79
Consensus pattern (20 bp):
TTTTGTTTTTTGTTTTTGTA
Found at i:23408 original size:10 final size:10
Alignment explanation
Indices: 23393--23424 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
23383 TTTTTTCAAA
23393 AAAAAAAATG
1 AAAAAAAATG
23403 AAAAAAAATG
1 AAAAAAAATG
23413 AAAAAAAA-G
1 AAAAAAAATG
23422 AAA
1 AAA
23425 CTTGTGCTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 4 0.18
10 18 0.82
ACGTcount: A:0.84, C:0.00, G:0.09, T:0.06
Consensus pattern (10 bp):
AAAAAAAATG
Done.