Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01002416.1 Corchorus olitorius cultivar O-4 contig02416, 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, 942
Length: 1571
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.32
Found at i:1164 original size:27 final size:27
Alignment explanation
Indices: 1128--1327 Score: 328
Period size: 27 Copynumber: 7.2 Consensus size: 27
1118 AGAACTCCGA
1128 ATCATTCTCTTGAAGCTCATCCTTTTC
1 ATCATTCTCTTGAAGCTCATCCTTTTC
1155 ATCATTCTCTTGAAGCTCATCCTTTTC
1 ATCATTCTCTTGAAGCTCATCCTTTTC
1182 ATCATTCTCTTGAAGCTCATCCTTTTC
1 ATCATTCTCTTGAAGCTCATCCTTTTC
* *
1209 ATCATAAATGATCCGCTGAAGCTCATCCTTTTC
1 ATCAT---T-CT-C-TTGAAGCTCATCCTTTTC
1242 ATCATTCTCTTGAAGCTCATCCTTTTC
1 ATCATTCTCTTGAAGCTCATCCTTTTC
1269 ATCATTCTCTTGAAGCTCATCCTTTTC
1 ATCATTCTCTTGAAGCTCATCCTTTTC
1296 ATCATTCTCTTGAAGCTCATCCTTTTC
1 ATCATTCTCTTGAAGCTCATCCTTTTC
1323 ATCAT
1 ATCAT
1328 AAATGATCCG
Statistics
Matches: 163, Mismatches: 4, Indels: 12
0.91 0.02 0.07
Matches are distributed among these distances:
27 135 0.83
28 1 0.01
29 1 0.01
30 2 0.01
31 1 0.01
32 1 0.01
33 22 0.13
ACGTcount: A:0.20, C:0.29, G:0.08, T:0.42
Consensus pattern (27 bp):
ATCATTCTCTTGAAGCTCATCCTTTTC
Found at i:1284 original size:87 final size:87
Alignment explanation
Indices: 1138--1300 Score: 326
Period size: 87 Copynumber: 1.9 Consensus size: 87
1128 ATCATTCTCT
1138 TGAAGCTCATCCTTTTCATCATTCTCTTGAAGCTCATCCTTTTCATCATTCTCTTGAAGCTCATC
1 TGAAGCTCATCCTTTTCATCATTCTCTTGAAGCTCATCCTTTTCATCATTCTCTTGAAGCTCATC
1203 CTTTTCATCATAAATGATCCGC
66 CTTTTCATCATAAATGATCCGC
1225 TGAAGCTCATCCTTTTCATCATTCTCTTGAAGCTCATCCTTTTCATCATTCTCTTGAAGCTCATC
1 TGAAGCTCATCCTTTTCATCATTCTCTTGAAGCTCATCCTTTTCATCATTCTCTTGAAGCTCATC
1290 CTTTTCATCAT
66 CTTTTCATCAT
1301 TCTCTTGAAG
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
87 76 1.00
ACGTcount: A:0.21, C:0.29, G:0.09, T:0.42
Consensus pattern (87 bp):
TGAAGCTCATCCTTTTCATCATTCTCTTGAAGCTCATCCTTTTCATCATTCTCTTGAAGCTCATC
CTTTTCATCATAAATGATCCGC
Found at i:1328 original size:114 final size:114
Alignment explanation
Indices: 1128--1339 Score: 424
Period size: 114 Copynumber: 1.9 Consensus size: 114
1118 AGAACTCCGA
1128 ATCATTCTCTTGAAGCTCATCCTTTTCATCATTCTCTTGAAGCTCATCCTTTTCATCATTCTCTT
1 ATCATTCTCTTGAAGCTCATCCTTTTCATCATTCTCTTGAAGCTCATCCTTTTCATCATTCTCTT
1193 GAAGCTCATCCTTTTCATCATAAATGATCCGCTGAAGCTCATCCTTTTC
66 GAAGCTCATCCTTTTCATCATAAATGATCCGCTGAAGCTCATCCTTTTC
1242 ATCATTCTCTTGAAGCTCATCCTTTTCATCATTCTCTTGAAGCTCATCCTTTTCATCATTCTCTT
1 ATCATTCTCTTGAAGCTCATCCTTTTCATCATTCTCTTGAAGCTCATCCTTTTCATCATTCTCTT
1307 GAAGCTCATCCTTTTCATCATAAATGATCCGCT
66 GAAGCTCATCCTTTTCATCATAAATGATCCGCT
1340 TGCCCCGAAA
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
114 98 1.00
ACGTcount: A:0.21, C:0.29, G:0.08, T:0.42
Consensus pattern (114 bp):
ATCATTCTCTTGAAGCTCATCCTTTTCATCATTCTCTTGAAGCTCATCCTTTTCATCATTCTCTT
GAAGCTCATCCTTTTCATCATAAATGATCCGCTGAAGCTCATCCTTTTC
Done.