Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024890.1 Corchorus olitorius cultivar O-4 contig24923, 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: 7914
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Found at i:1162 original size:16 final size:16
Alignment explanation
Indices: 1133--1207 Score: 52
Period size: 16 Copynumber: 5.0 Consensus size: 16
1123 TGGAAATATT
*
1133 CATGAACATGTATTTA
1 CATGAACATATATTTA
*
1149 CATGAACCTATA-TTA
1 CATGAACATATATTTA
* **
1164 -AT-TAGGTATA-TT-
1 CATGAACATATATTTA
*
1176 CATGAACATGTATTTA
1 CATGAACATATATTTA
*
1192 CATGAACCTATATTTA
1 CATGAACATATATTTA
1208 TTAGGTGCAT
Statistics
Matches: 44, Mismatches: 11, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
13 9 0.20
14 6 0.14
15 5 0.11
16 24 0.55
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (16 bp):
CATGAACATATATTTA
Found at i:1189 original size:43 final size:43
Alignment explanation
Indices: 1128--1213 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
1118 TGCATTGGAA
1128 ATATTCATGAACATGTATTTACATGAACCTATATTAATTAGGT
1 ATATTCATGAACATGTATTTACATGAACCTATATTAATTAGGT
*
1171 ATATTCATGAACATGTATTTACATGAACCTATATTTATTAGGT
1 ATATTCATGAACATGTATTTACATGAACCTATATTAATTAGGT
1214 GCATTAAGAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.41
Consensus pattern (43 bp):
ATATTCATGAACATGTATTTACATGAACCTATATTAATTAGGT
Found at i:3392 original size:12 final size:13
Alignment explanation
Indices: 3369--3397 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
3359 TCAAAAAAAA
3369 ATATATGATATAG
1 ATATATGATATAG
3382 ATATA-GATATAG
1 ATATATGATATAG
3394 ATAT
1 ATAT
3398 TTAGTATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.48, C:0.00, G:0.14, T:0.38
Consensus pattern (13 bp):
ATATATGATATAG
Found at i:4040 original size:9 final size:9
Alignment explanation
Indices: 4026--4051 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
4016 ATCAGCCACT
4026 AACACCTCC
1 AACACCTCC
4035 AACACCTCC
1 AACACCTCC
4044 AACACCTC
1 AACACCTC
4052 AATCAAGGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.54, G:0.00, T:0.12
Consensus pattern (9 bp):
AACACCTCC
Found at i:7282 original size:30 final size:31
Alignment explanation
Indices: 7248--7306 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
7238 AACTTGTTTT
*
7248 CTGAA-TTTCCAAATTTAGGACAATTTGCTC
1 CTGAACTTTCCAAATATAGGACAATTTGCTC
*
7278 CTGAACTTTCCAAATATAGGACCATTTGC
1 CTGAACTTTCCAAATATAGGACAATTTGC
7307 CCCCTACATA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 5 0.19
31 21 0.81
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.34
Consensus pattern (31 bp):
CTGAACTTTCCAAATATAGGACAATTTGCTC
Done.