Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023107.1 Corchorus olitorius cultivar O-4 contig23140, 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: 5092
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Found at i:391 original size:28 final size:28
Alignment explanation
Indices: 377--453 Score: 154
Period size: 28 Copynumber: 2.8 Consensus size: 28
367 CCTAGCCTAA
377 CAAAATGACCAAAATGCCCTTGCTCATG
1 CAAAATGACCAAAATGCCCTTGCTCATG
405 CAAAATGACCAAAATGCCCTTGCTCATG
1 CAAAATGACCAAAATGCCCTTGCTCATG
433 CAAAATGACCAAAATGCCCTT
1 CAAAATGACCAAAATGCCCTT
454 TTAAGTGACC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 49 1.00
ACGTcount: A:0.38, C:0.29, G:0.13, T:0.21
Consensus pattern (28 bp):
CAAAATGACCAAAATGCCCTTGCTCATG
Found at i:751 original size:35 final size:35
Alignment explanation
Indices: 710--988 Score: 441
Period size: 35 Copynumber: 7.9 Consensus size: 35
700 CGAGTTCATA
* *
710 TTGAAGATGCTACATCGAGTCTCCTGAATTCGTTT
1 TTGAAGATGCTACACCGAGTCACCTGAATTCGTTT
* * *
745 TTGAAGATGCTACACCGAGTCACCTAAATTCATCT
1 TTGAAGATGCTACACCGAGTCACCTGAATTCGTTT
780 TTGAAGATGCTACACCGAGTCACCTGAATTCGTTTT
1 TTGAAGATGCTACACCGAGTCACCTGAATTCG-TTT
*
816 TTGAAGATGCTACACCGAGTCACCTGAATTCATTT
1 TTGAAGATGCTACACCGAGTCACCTGAATTCGTTT
851 TTGAAGATGCTACACCGAGTCACCTGAATTCGTTTT
1 TTGAAGATGCTACACCGAGTCACCTGAATTCG-TTT
* *
887 TTGAAAATGCTACACCGAGTCACCTGAATTCATTT
1 TTGAAGATGCTACACCGAGTCACCTGAATTCGTTT
*
922 TTGAAGATGCTACACTGAGTCACCTGAATTCGTTTT
1 TTGAAGATGCTACACCGAGTCACCTGAATTCG-TTT
*
958 TTGAAGATGCTACACCGAGTCACCTGGATTC
1 TTGAAGATGCTACACCGAGTCACCTGAATTC
989 CTGAGAATTT
Statistics
Matches: 224, Mismatches: 17, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
35 126 0.56
36 98 0.44
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (35 bp):
TTGAAGATGCTACACCGAGTCACCTGAATTCGTTT
Found at i:848 original size:71 final size:71
Alignment explanation
Indices: 710--988 Score: 488
Period size: 71 Copynumber: 3.9 Consensus size: 71
700 CGAGTTCATA
* * *
710 TTGAAGATGCTACATCGAGTCTCCTGAATTCG-TTTTTGAAGATGCTACACCGAGTCACCTAAAT
1 TTGAAGATGCTACACCGAGTCACCTGAATTCGTTTTTTGAAGATGCTACACCGAGTCACCTGAAT
*
774 TCATCT
66 TCATTT
780 TTGAAGATGCTACACCGAGTCACCTGAATTCGTTTTTTGAAGATGCTACACCGAGTCACCTGAAT
1 TTGAAGATGCTACACCGAGTCACCTGAATTCGTTTTTTGAAGATGCTACACCGAGTCACCTGAAT
845 TCATTT
66 TCATTT
*
851 TTGAAGATGCTACACCGAGTCACCTGAATTCGTTTTTTGAAAATGCTACACCGAGTCACCTGAAT
1 TTGAAGATGCTACACCGAGTCACCTGAATTCGTTTTTTGAAGATGCTACACCGAGTCACCTGAAT
916 TCATTT
66 TCATTT
* *
922 TTGAAGATGCTACACTGAGTCACCTGAATTCGTTTTTTGAAGATGCTACACCGAGTCACCTGGAT
1 TTGAAGATGCTACACCGAGTCACCTGAATTCGTTTTTTGAAGATGCTACACCGAGTCACCTGAAT
987 TC
66 TC
989 CTGAGAATTT
Statistics
Matches: 200, Mismatches: 8, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
70 30 0.15
71 170 0.85
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (71 bp):
TTGAAGATGCTACACCGAGTCACCTGAATTCGTTTTTTGAAGATGCTACACCGAGTCACCTGAAT
TCATTT
Found at i:858 original size:106 final size:106
Alignment explanation
Indices: 710--982 Score: 431
Period size: 106 Copynumber: 2.6 Consensus size: 106
700 CGAGTTCATA
* * *
710 TTGAAGATGCTACATCGAGTCTCCTGAATTCGTTTTTGAAGATGCTACACCGAGTCACCTAAATT
1 TTGAAGATGCTACACCGAGTCACCTGAATTCATTTTTGAAGATGCTACACCGAGTCACCTAAATT
* *
775 C-ATCTTTGAAGATGCTACACCGAGTCACCTGAATTCGTTTT
66 CGATCTTTGAAAATGCTACACCGAGTCACCTGAATTC-ATTT
*
816 TTGAAGATGCTACACCGAGTCACCTGAATTCATTTTTGAAGATGCTACACCGAGTCACCTGAATT
1 TTGAAGATGCTACACCGAGTCACCTGAATTCATTTTTGAAGATGCTACACCGAGTCACCTAAATT
* *
881 CGTTTTTTGAAAATGCTACACCGAGTCACCTGAATTCATTT
66 CGATCTTTGAAAATGCTACACCGAGTCACCTGAATTCATTT
* *
922 TTGAAGATGCTACACTGAGTCACCTGAATTCGTTTTTTGAAGATGCTACACCGAGTCACCT
1 TTGAAGATGCTACACCGAGTCACCTGAATTC-ATTTTTGAAGATGCTACACCGAGTCACCT
983 GGATTCCTGA
Statistics
Matches: 155, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
106 95 0.61
107 60 0.39
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (106 bp):
TTGAAGATGCTACACCGAGTCACCTGAATTCATTTTTGAAGATGCTACACCGAGTCACCTAAATT
CGATCTTTGAAAATGCTACACCGAGTCACCTGAATTCATTT
Done.