Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024150.1 Corchorus olitorius cultivar O-4 contig24183, 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: 2346
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.31
Found at i:679 original size:68 final size:68
Alignment explanation
Indices: 560--1095 Score: 880
Period size: 68 Copynumber: 7.9 Consensus size: 68
550 TGCTTTGGCT
* * *
560 TTTC-CACAAGCCAAACTCGTTTCCATACGAGTCACTTTGAGCCTTGGTTCCATCCAAGCAGCAG
1 TTTCTCACAAGCCAAACTCGTTTCCATACGAGCCA-GTTAAGCCTTGGTTCCATCCAAGCAGCAG
624 AGGC
65 AGGC
*
628 TTTCTCACAAGCCAAACTCGTTTCCATACGAGCCAGTTAAGCCTTGGTTCCATCCAAGCAGCAGG
1 TTTCTCACAAGCCAAACTCGTTTCCATACGAGCCAGTTAAGCCTTGGTTCCATCCAAGCAGCAGA
693 GGC
66 GGC
*
696 TTTCTCGCAAGCCAAACTCGTTTCCATACGAGCCAGTTAAGCCTTGGTTCCATCCAAGCAGCAGA
1 TTTCTCACAAGCCAAACTCGTTTCCATACGAGCCAGTTAAGCCTTGGTTCCATCCAAGCAGCAGA
761 GGC
66 GGC
* *
764 TTTCTCACAAGCCAAACTCGTTTCCATACGAGCCAGTTAAGCCTTGGTTCCATCCAAACAGCAGG
1 TTTCTCACAAGCCAAACTCGTTTCCATACGAGCCAGTTAAGCCTTGGTTCCATCCAAGCAGCAGA
829 GGC
66 GGC
*
832 TTTCTCGCAAGCCAAACTCGTTTCCATACGAGCCAGTTAAGCCTTGGTTCCATCCAAGCAGCAGA
1 TTTCTCACAAGCCAAACTCGTTTCCATACGAGCCAGTTAAGCCTTGGTTCCATCCAAGCAGCAGA
897 GGC
66 GGC
*
900 TTTCTCACAAACCAAACTCGTTTCCATACGA-CCTAGTTAAGCCTTGGTTCCATCCAAGCAGCAG
1 TTTCTCACAAGCCAAACTCGTTTCCATACGAGCC-AGTTAAGCCTTGGTTCCATCCAAGCAGCAG
*
964 GGGC
65 AGGC
* * *
968 TTT-TCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAGACTTGGTTCCATCCAAGCAGCAG
1 TTTCT-CACAAGCCAAACTCGTTTCCATACGAGCCAGTTAAGCCTTGGTTCCATCCAAGCAGCAG
1032 AGGC
65 AGGC
* * *
1036 TTTCTCACAAGCCAAACCCGTTTCCATACGAGTCAGTTTAGCCTTGGTTCCATCCAAGCA
1 TTTCTCACAAGCCAAACTCGTTTCCATACGAGCCAGTTAAGCCTTGGTTCCATCCAAGCA
1096 TCCAGGGGCT
Statistics
Matches: 441, Mismatches: 22, Indels: 10
0.93 0.05 0.02
Matches are distributed among these distances:
67 3 0.01
68 407 0.92
69 31 0.07
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.25
Consensus pattern (68 bp):
TTTCTCACAAGCCAAACTCGTTTCCATACGAGCCAGTTAAGCCTTGGTTCCATCCAAGCAGCAGA
GGC
Found at i:1299 original size:38 final size:38
Alignment explanation
Indices: 1254--1437 Score: 278
Period size: 38 Copynumber: 4.8 Consensus size: 38
1244 TACCTTTCGT
* *
1254 TTATCAAAGTTGACTGGAAACAGGTCATCTTTCAATAG
1 TTATCAAAGTTGACTGGAAACAGGTCATCTTTCAACAA
* *
1292 TTATCAAAGTTGACTGGAAACATGTCATCTTTCAGCAA
1 TTATCAAAGTTGACTGGAAACAGGTCATCTTTCAACAA
*
1330 TTATCAAAGTTGACTGGAAACAGGTCATCTTTCAGCAA
1 TTATCAAAGTTGACTGGAAACAGGTCATCTTTCAACAA
** * *
1368 TTATCAAAGTTGACTGGAAACAAATCATCTTTCAATAG
1 TTATCAAAGTTGACTGGAAACAGGTCATCTTTCAACAA
*
1406 TTATCAAAGTTGACTGGAAACATGTCATCTTT
1 TTATCAAAGTTGACTGGAAACAGGTCATCTTT
1438 TCTTAGTCTT
Statistics
Matches: 134, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 134 1.00
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (38 bp):
TTATCAAAGTTGACTGGAAACAGGTCATCTTTCAACAA
Done.