Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023035.1 Corchorus olitorius cultivar O-4 contig23068, 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: 8939
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.31
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:495 original size:27 final size:28
Alignment explanation
Indices: 464--536 Score: 103
Period size: 27 Copynumber: 2.6 Consensus size: 28
454 GGCGTATTTG
* *
464 AAATGACCAAAATGTCCCTGGACATGC-
1 AAATGACCAAAATGCCCCTAGACATGCA
* *
491 GAATGACAAAAATGCCCCTAGACATGCA
1 AAATGACCAAAATGCCCCTAGACATGCA
519 AAATGACCAAAATGCCCC
1 AAATGACCAAAATGCCCC
537 AAGAGAACCC
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
27 23 0.59
28 16 0.41
ACGTcount: A:0.41, C:0.27, G:0.16, T:0.15
Consensus pattern (28 bp):
AAATGACCAAAATGCCCCTAGACATGCA
Found at i:1382 original size:35 final size:35
Alignment explanation
Indices: 935--1380 Score: 766
Period size: 35 Copynumber: 12.7 Consensus size: 35
925 GAGCCCATAC
*
935 TGAAGATGCTACACCGAGTCATCTGAATTCATCTT
1 TGAAGATGCTACACCGAGTCATCTGAGTTCATCTT
970 TGAAGATGCTACACCGAGTCATCTGAGTTCATCTT
1 TGAAGATGCTACACCGAGTCATCTGAGTTCATCTT
1005 TGAAGATGCTACACCGAGTCATCTGAGTTCATCTT
1 TGAAGATGCTACACCGAGTCATCTGAGTTCATCTT
*
1040 TGAAGATGCTACACCGAGTCGTCTGAGTTCATCTT
1 TGAAGATGCTACACCGAGTCATCTGAGTTCATCTT
* *
1075 TGAGGATGCTACACCGAGTCATCTGAGTTCAACTT
1 TGAAGATGCTACACCGAGTCATCTGAGTTCATCTT
*
1110 TGAAGATGCTACACCGAGTCATCTGAGTTCAACTT
1 TGAAGATGCTACACCGAGTCATCTGAGTTCATCTT
1145 TGAAGATGCTACACCGAGTCATCTGAGTTCATCTT
1 TGAAGATGCTACACCGAGTCATCTGAGTTCATCTT
* * *
1180 TGAAGATGCTACACCCAGTCATCTGAATTCAACTT
1 TGAAGATGCTACACCGAGTCATCTGAGTTCATCTT
1215 TGAAGATGCTACACCGAGTCATCTGAGTTCATCTT
1 TGAAGATGCTACACCGAGTCATCTGAGTTCATCTT
* *
1250 TGAAGATGCTACACCGAGTCATCTGAATTCAACTT
1 TGAAGATGCTACACCGAGTCATCTGAGTTCATCTT
* *
1285 TGAAAATGCTACACCGAGTCATCTGAGTTCATTTT
1 TGAAGATGCTACACCGAGTCATCTGAGTTCATCTT
* *
1320 TGAAGATGCTACACCGAGTCATCTGAATTCAACTT
1 TGAAGATGCTACACCGAGTCATCTGAGTTCATCTT
1355 TGAAGATGCTACACCGAGTCATCTGA
1 TGAAGATGCTACACCGAGTCATCTGA
1381 ATCCCTGAAA
Statistics
Matches: 388, Mismatches: 23, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 388 1.00
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (35 bp):
TGAAGATGCTACACCGAGTCATCTGAGTTCATCTT
Done.