Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019336.1 Corchorus olitorius cultivar O-4 contig19369, 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: 12826
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.34
Found at i:219 original size:23 final size:23
Alignment explanation
Indices: 187--251 Score: 112
Period size: 23 Copynumber: 2.8 Consensus size: 23
177 CACAATTGCT
*
187 TGGCGCCCGACCACTTCCAAACC
1 TGGCGACCGACCACTTCCAAACC
210 TGGCGACCGACCACTTCCAAACC
1 TGGCGACCGACCACTTCCAAACC
*
233 TGGCGACCGACTACTTCCA
1 TGGCGACCGACCACTTCCA
252 TAACGCGGCG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.23, C:0.43, G:0.18, T:0.15
Consensus pattern (23 bp):
TGGCGACCGACCACTTCCAAACC
Found at i:415 original size:26 final size:27
Alignment explanation
Indices: 354--421 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
344 AACCAGCTGG
*
354 CACC-CCACACGTGACCTCCAAACGTA
1 CACCTCCACACGTGACCTCCAAACGGA
*
380 CGACCT-CACACGTGATCTCC-AACGGA
1 C-ACCTCCACACGTGACCTCCAAACGGA
*
406 CACCTCCACATGTGAC
1 CACCTCCACACGTGAC
422 ATCGCGCGTG
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
25 4 0.11
26 15 0.43
27 16 0.46
ACGTcount: A:0.28, C:0.43, G:0.15, T:0.15
Consensus pattern (27 bp):
CACCTCCACACGTGACCTCCAAACGGA
Found at i:1185 original size:23 final size:20
Alignment explanation
Indices: 1133--1171 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1123 TTAAAAAAAA
*
1133 TTAATAATTAGTTATTATTT
1 TTAAAAATTAGTTATTATTT
1153 TTAAAAATTAGTTATTATT
1 TTAAAAATTAGTTATTATT
1172 ATTTTATATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (20 bp):
TTAAAAATTAGTTATTATTT
Found at i:4820 original size:17 final size:17
Alignment explanation
Indices: 4798--4848 Score: 54
Period size: 17 Copynumber: 3.0 Consensus size: 17
4788 CAAAATATCT
4798 GTTTCAATTAAGTCTGG
1 GTTTCAATTAAGTCTGG
4815 GTTTCAACTTTATA-TCT--
1 GTTTCAA--TTA-AGTCTGG
4832 GTTTCAATTAAGTCTGG
1 GTTTCAATTAAGTCTGG
4849 ATTTTGGTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 12
0.70 0.00 0.30
Matches are distributed among these distances:
14 1 0.04
15 6 0.21
17 14 0.50
19 6 0.21
20 1 0.04
ACGTcount: A:0.24, C:0.14, G:0.18, T:0.45
Consensus pattern (17 bp):
GTTTCAATTAAGTCTGG
Found at i:5506 original size:13 final size:13
Alignment explanation
Indices: 5488--5513 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5478 CATCGATACC
5488 TCGATATATCCGT
1 TCGATATATCCGT
5501 TCGATATATCCGT
1 TCGATATATCCGT
5514 GGATATCTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.38
Consensus pattern (13 bp):
TCGATATATCCGT
Found at i:6094 original size:15 final size:16
Alignment explanation
Indices: 6069--6098 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
6059 TGCCAGAGAT
6069 TTAATTTATATTTTAA
1 TTAATTTATATTTTAA
6085 TTAA-TTATATTTTA
1 TTAATTTATATTTTA
6099 TTTATTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TTAATTTATATTTTAA
Found at i:7205 original size:14 final size:14
Alignment explanation
Indices: 7186--7212 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
7176 AGAGGGAGTA
7186 CTTCTCTCTTCTTT
1 CTTCTCTCTTCTTT
7200 CTTCTCTCTTCTT
1 CTTCTCTCTTCTT
7213 GTTTCGGTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (14 bp):
CTTCTCTCTTCTTT
Done.