Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009805.1 Corchorus capsularis cultivar CVL-1 contig09826, 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: 5637
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Found at i:946 original size:44 final size:44
Alignment explanation
Indices: 878--972 Score: 181
Period size: 44 Copynumber: 2.2 Consensus size: 44
868 ATGGTCTTTG
878 AAGGGTCACCATCTTGGACCATGATCAAATGGTATTGCTCGAAA
1 AAGGGTCACCATCTTGGACCATGATCAAATGGTATTGCTCGAAA
*
922 AAGGGTCACCATCTTGGACGATGATCAAATGGTATTGCTCGAAA
1 AAGGGTCACCATCTTGGACCATGATCAAATGGTATTGCTCGAAA
966 AAGGGTC
1 AAGGGTC
973 TCCACATCTC
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 50 1.00
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.24
Consensus pattern (44 bp):
AAGGGTCACCATCTTGGACCATGATCAAATGGTATTGCTCGAAA
Found at i:993 original size:44 final size:44
Alignment explanation
Indices: 878--993 Score: 110
Period size: 44 Copynumber: 2.6 Consensus size: 44
868 ATGGTCTTTG
** ** *
878 AAGGGTCACCATCTTGGACCATGATCAAATGGTATTGCTCGAAA
1 AAGGGTCACCATCTTCCAAGATAATCAAATGGTATTGCTCGAAA
** * *
922 AAGGGTCACCATCTTGGACGATGATCAAATGGTATTGCTCGAAA
1 AAGGGTCACCATCTTCCAAGATAATCAAATGGTATTGCTCGAAA
*
966 AAGGGTCTCCA-CATCTCCAAGA-AATCAA
1 AAGGGTCACCATC-T-TCCAAGATAATCAA
994 GGTTTCTAAT
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
43 1 0.02
44 59 0.92
45 4 0.06
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.23
Consensus pattern (44 bp):
AAGGGTCACCATCTTCCAAGATAATCAAATGGTATTGCTCGAAA
Done.