Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010090.1 Corchorus olitorius cultivar O-4 contig10122, 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: 4156
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Found at i:149 original size:30 final size:30
Alignment explanation
Indices: 113--188 Score: 134
Period size: 30 Copynumber: 2.5 Consensus size: 30
103 TCAACAGCTA
* *
113 CATCTATACCATCACCATTACCTACACCAC
1 CATCTATGCCTTCACCATTACCTACACCAC
143 CATCTATGCCTTCACCATTACCTACACCAC
1 CATCTATGCCTTCACCATTACCTACACCAC
173 CATCTATGCCTTCACC
1 CATCTATGCCTTCACC
189 TTCACCAGGA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.28, C:0.43, G:0.03, T:0.26
Consensus pattern (30 bp):
CATCTATGCCTTCACCATTACCTACACCAC
Found at i:158 original size:18 final size:18
Alignment explanation
Indices: 137--188 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 18
127 CCATTACCTA
137 CACCACCATCTATGCCTT
1 CACCACCATCTATGCCTT
*
155 ---CACCAT-TA--CCTA
1 CACCACCATCTATGCCTT
167 CACCACCATCTATGCCTT
1 CACCACCATCTATGCCTT
185 CACC
1 CACC
189 TTCACCAGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 12
0.65 0.05 0.30
Matches are distributed among these distances:
12 3 0.12
14 2 0.08
15 12 0.46
16 2 0.08
18 7 0.27
ACGTcount: A:0.25, C:0.46, G:0.04, T:0.25
Consensus pattern (18 bp):
CACCACCATCTATGCCTT
Found at i:206 original size:21 final size:21
Alignment explanation
Indices: 191--251 Score: 113
Period size: 21 Copynumber: 2.9 Consensus size: 21
181 CCTTCACCTT
191 CACCAGGATGAGCTTCTCCAC
1 CACCAGGATGAGCTTCTCCAC
*
212 CCCCAGGATGAGCTTCTCCAC
1 CACCAGGATGAGCTTCTCCAC
233 CACCAGGATGAGCTTCTCC
1 CACCAGGATGAGCTTCTCC
252 TTCCACATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.21, C:0.39, G:0.20, T:0.20
Consensus pattern (21 bp):
CACCAGGATGAGCTTCTCCAC
Found at i:349 original size:21 final size:21
Alignment explanation
Indices: 324--366 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
314 CTACATCATT
324 CCCACCACCATGAATAACATC
1 CCCACCACCATGAATAACATC
*
345 CCCACCACCATGAATATCATC
1 CCCACCACCATGAATAACATC
366 C
1 C
367 ACAGCTTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.35, C:0.44, G:0.05, T:0.16
Consensus pattern (21 bp):
CCCACCACCATGAATAACATC
Found at i:1492 original size:31 final size:29
Alignment explanation
Indices: 1457--1553 Score: 81
Period size: 31 Copynumber: 3.2 Consensus size: 29
1447 CGTCCAAAAT
*
1457 TATCC-TTATTTGACGCTTTTGGGTAACGTTA
1 TATCCTTTA-TTGACG-TTTT-GGAAACGTTA
*
1488 TATCCTTTATTGACGTTTTTGAAACGTTA
1 TATCCTTTATTGACGTTTTGGAAACGTTA
** *
1517 TATCCTGAATTGA-TTTTTCAGGCAAACGTTA
1 TATCCTTTATTGACGTTTT--GG-AAACGTTA
1548 TATCCT
1 TATCCT
1554 GAATTGATTA
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
28 4 0.07
29 19 0.34
30 5 0.09
31 25 0.45
32 3 0.05
ACGTcount: A:0.24, C:0.16, G:0.15, T:0.44
Consensus pattern (29 bp):
TATCCTTTATTGACGTTTTGGAAACGTTA
Found at i:1528 original size:29 final size:29
Alignment explanation
Indices: 1481--1569 Score: 101
Period size: 31 Copynumber: 3.0 Consensus size: 29
1471 GCTTTTGGGT
**
1481 AACGTTATATCCTTTATTGACGTTTTT-G-A
1 AACGTTATATCCTGAATTGA--TTTTTAGCA
1510 AACGTTATATCCTGAATTGATTTTTCAGGCA
1 AACGTTATATCCTGAATTGATTTTT-A-GCA
1541 AACGTTATATCCTGAATTGATTATTTAGC
1 AACGTTATATCCTGAATTGATT-TTTAGC
1570 CCCTTTACCG
Statistics
Matches: 53, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
27 5 0.09
29 18 0.34
30 3 0.06
31 24 0.45
32 3 0.06
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.43
Consensus pattern (29 bp):
AACGTTATATCCTGAATTGATTTTTAGCA
Found at i:3561 original size:2 final size:2
Alignment explanation
Indices: 3549--3581 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
3539 ACTAAAAATA
3549 AT AT AT A- AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3582 ATGGTAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.