Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013000.1 Corchorus olitorius cultivar O-4 contig13033, 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: 7168
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Found at i:1092 original size:35 final size:35
Alignment explanation
Indices: 1046--1433 Score: 485
Period size: 35 Copynumber: 11.0 Consensus size: 35
1036 ATCAATGTGA
* *
1046 AGATCAACTCTGATCACCGAAAACTTCTTGAAATG
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
*
1081 AGATCAACTCTGATCAT--AAAACATCTTGAAAATG
1 AGATCAACTCTGATCATCAAAAACTTCTTG-AAATG
* * * *
1115 AGATCAACTTTGATCATAAAAAACTTCCTGAAAGG
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
*
1150 AGATCAACTCTGATCATCAAAAACTTCTTGAAACG
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
* * *
1185 AGATGAACTCTGATCATCGAAAACTTCTTGAAATA
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
* *
1220 AGATCAACTCTGATCATAAAAAAAACTTCTTGAAAGG
1 AGATCAACTCTGATCAT--CAAAAACTTCTTGAAATG
*
1257 AGATCAACTCTGATCAT-AAAAACATCTTGAAAATG
1 AGATCAACTCTGATCATCAAAAACTTCTTG-AAATG
* * *
1292 AGATCAACTCTGATCATAAAAAAACTTCCTGAAAGG
1 AGATCAACTCTGATCAT-CAAAAACTTCTTGAAATG
* * *
1328 AGATCAACTCTGATCACCGAAAACTTCTTGAAACG
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
* *
1363 AGATCAACTCTGATCATCGAAAACTTCTTGAAACG
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
* * *
1398 AGATCAACTCTAATCATCGAAAACTTCTTGGAATG
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
1433 A
1 A
1434 CCGCACTGGA
Statistics
Matches: 312, Mismatches: 33, Indels: 16
0.86 0.09 0.04
Matches are distributed among these distances:
33 10 0.03
34 32 0.10
35 200 0.64
36 29 0.09
37 41 0.13
ACGTcount: A:0.41, C:0.20, G:0.13, T:0.26
Consensus pattern (35 bp):
AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
Found at i:1353 original size:178 final size:176
Alignment explanation
Indices: 1065--1414 Score: 610
Period size: 178 Copynumber: 2.0 Consensus size: 176
1055 CTGATCACCG
* *
1065 AAAACTTCTTGAAATGAGATCAACTCTGATCATAAAACATCTTGAAAATGAGATCAACTTTGATC
1 AAAACTTCTTGAAAGGAGATCAACTCTGATCATAAAACATCTTGAAAATGAGATCAACTCTGATC
* *
1130 ATAAAAAACTTCCTGAAAGGAGATCAACTCTGATCATCAAAAACTTCTTGAAACGAGATGAACTC
66 ATAAAAAACTTCCTGAAAGGAGATCAACTCTGATCACCAAAAACTTCTTGAAACGAGATCAACTC
* *
1195 TGATCATCGAAAACTTCTTGAAATAAGATCAACTCTGATCATAAAA
131 TGATCATCGAAAACTTCTTGAAACAAGATCAACTCTAATCATAAAA
1241 AAAACTTCTTGAAAGGAGATCAACTCTGATCATAAAAACATCTTGAAAATGAGATCAACTCTGAT
1 AAAACTTCTTGAAAGGAGATCAACTCTGATCAT-AAAACATCTTGAAAATGAGATCAACTCTGAT
*
1306 CATAAAAAAACTTCCTGAAAGGAGATCAACTCTGATCACCGAAAACTTCTTGAAACGAGATCAAC
65 CAT-AAAAAACTTCCTGAAAGGAGATCAACTCTGATCACCAAAAACTTCTTGAAACGAGATCAAC
*
1371 TCTGATCATCGAAAACTTCTTGAAACGAGATCAACTCTAATCAT
129 TCTGATCATCGAAAACTTCTTGAAACAAGATCAACTCTAATCAT
1415 CGAAAACTTC
Statistics
Matches: 164, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
176 32 0.20
177 33 0.20
178 99 0.60
ACGTcount: A:0.42, C:0.19, G:0.13, T:0.26
Consensus pattern (176 bp):
AAAACTTCTTGAAAGGAGATCAACTCTGATCATAAAACATCTTGAAAATGAGATCAACTCTGATC
ATAAAAAACTTCCTGAAAGGAGATCAACTCTGATCACCAAAAACTTCTTGAAACGAGATCAACTC
TGATCATCGAAAACTTCTTGAAACAAGATCAACTCTAATCATAAAA
Found at i:1377 original size:213 final size:211
Alignment explanation
Indices: 1046--1427 Score: 579
Period size: 213 Copynumber: 1.8 Consensus size: 211
1036 ATCAATGTGA
* * *
1046 AGATCAACTCTGATCACCGAAAACTTCTTGAAATGAGATCAACTCTGATCATAAAACATCTTGAA
1 AGATCAACTCTGATCACCAAAAACATCTTGAAATGAGATCAACTCTGATCATAAAACATCCTGAA
* * * *
1111 AATGAGATCAACTTTGATCATAAAAAACTTCCTGAAAGGAGATCAACTCTGATCATCAAAAACTT
66 AAGGAGATCAACTCTGATCACAAAAAACTTCCTGAAACGAGATCAACTCTGATCATCAAAAACTT
* *
1176 CTTGAAACGAGATGAACTCTGATCATCGAAAACTTCTTGAAATAAGATCAACTCTGATCATAAAA
131 CTTGAAACGAGATCAACTCTAATCATCGAAAACTTCTTGAAATAAGATCAACTCTGATCATAAAA
1241 AAAACTTCTTGAAAGG
196 AAAACTTCTTGAAAGG
* *
1257 AGATCAACTCTGATCA-TAAAAACATCTTGAAAATGAGATCAACTCTGATCATAAAAAAACTTCC
1 AGATCAACTCTGATCACCAAAAACATCTTG-AAATGAGATCAACTCTGATCAT---AAAACATCC
** * *
1321 TG-AAAGGAGATCAACTCTGATCACCGAAAACTTCTTGAAACGAGATCAACTCTGATCATCGAAA
62 TGAAAAGGAGATCAACTCTGATCACAAAAAACTTCCTGAAACGAGATCAACTCTGATCATCAAAA
1385 ACTTCTTGAAACGAGATCAACTCTAATCATCGAAAACTTCTTG
127 ACTTCTTGAAACGAGATCAACTCTAATCATCGAAAACTTCTTG
1428 GAATGACCGC
Statistics
Matches: 152, Mismatches: 15, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
210 10 0.07
211 38 0.25
213 95 0.62
214 9 0.06
ACGTcount: A:0.41, C:0.20, G:0.13, T:0.26
Consensus pattern (211 bp):
AGATCAACTCTGATCACCAAAAACATCTTGAAATGAGATCAACTCTGATCATAAAACATCCTGAA
AAGGAGATCAACTCTGATCACAAAAAACTTCCTGAAACGAGATCAACTCTGATCATCAAAAACTT
CTTGAAACGAGATCAACTCTAATCATCGAAAACTTCTTGAAATAAGATCAACTCTGATCATAAAA
AAAACTTCTTGAAAGG
Found at i:1485 original size:54 final size:54
Alignment explanation
Indices: 1398--1506 Score: 164
Period size: 54 Copynumber: 2.0 Consensus size: 54
1388 TCTTGAAACG
* * *
1398 AGATCAACTCTAATCATCGAAAACTTCTTGGAATGACCGCACTGGATCATCTGA
1 AGATCAACTCTAACCATCGAAAACTTCTTGGAATGAACGCACTAGATCATCTGA
* * *
1452 AGATTAACTCTGACCATTGAAAACTTCTTGGAATGAACGCACTAGATCATCTGA
1 AGATCAACTCTAACCATCGAAAACTTCTTGGAATGAACGCACTAGATCATCTGA
1506 A
1 A
1507 CACCTGTTTC
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.27
Consensus pattern (54 bp):
AGATCAACTCTAACCATCGAAAACTTCTTGGAATGAACGCACTAGATCATCTGA
Done.