Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01001969.1 Corchorus olitorius cultivar O-4 contig01969, 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, 821
Length: 1369
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:182 original size:20 final size:22
Alignment explanation
Indices: 157--203 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 22
147 GGAAAGCGAA
157 AATCAA-TTT-GGCCATACGGT
1 AATCAACTTTAGGCCATACGGT
177 AATCAAGCTTTGAGGCCATACGGT
1 AATCAA-CTTT-AGGCCATACGGT
201 AAT
1 AAT
204 AAAACTGCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.26
22 3 0.13
24 14 0.61
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (22 bp):
AATCAACTTTAGGCCATACGGT
Found at i:708 original size:24 final size:24
Alignment explanation
Indices: 586--696 Score: 132
Period size: 24 Copynumber: 4.6 Consensus size: 24
576 AATCACACGG
* *
586 CCACATAGTGGTCATGAGAAACGG
1 CCACATAGTGGTCGTGAGAAACGA
* * **
610 CCACATAATGGCCGTGAGATTCGA
1 CCACATAGTGGTCGTGAGAAACGA
* * *
634 CCACATGGTGATTGTGAGAAACGA
1 CCACATAGTGGTCGTGAGAAACGA
*
658 CCACATGGTGGTCGTGAGAAACGA
1 CCACATAGTGGTCGTGAGAAACGA
682 CCACATAGTGGTCGT
1 CCACATAGTGGTCGT
697 ATGAAAAGAC
Statistics
Matches: 71, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 71 1.00
ACGTcount: A:0.30, C:0.22, G:0.29, T:0.20
Consensus pattern (24 bp):
CCACATAGTGGTCGTGAGAAACGA
Done.