Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01006345.1 Corchorus olitorius cultivar O-4 contig06370, 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, 755
Length: 1259
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Found at i:53 original size:37 final size:37
Alignment explanation
Indices: 3--497 Score: 740
Period size: 37 Copynumber: 13.1 Consensus size: 37
1 CA
3 TTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAG
1 TTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAG
*
40 TTTATCAAAGTTGACTGGGAACAGGTCATCTTTTCA-
1 TTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAG
76 TTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAG
1 TTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAG
* * *
113 TTTATCAAAGTTGATTGGGAACAGGTCATCTTTTTAGCG
1 TTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCA--G
152 TTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAG
1 TTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAG
*
189 TTTATCAAAGTTGACTGAAAACAGGTCATCTTTTCAG
1 TTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAG
*
226 CACTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAG
1 --TTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAG
265 TTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAG
1 TTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAG
* *
302 CATTTATCAAAGTCGACTGGAAACAGGTCATCTTTTTAG
1 --TTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAG
* *
341 ATTATCAGAGTTGACTGGAAACAGGTCATCTTTTCAG
1 TTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAG
*
378 CATTTATCAAAGTCGACTGGAAACAGGTCATCTTTTCAG
1 --TTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAG
* *
417 ATTATCAAAGTTGACTGGAAACAAGTCATCTTTTCAG
1 TTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAG
* *
454 CATTTATCAAAGTTGATTGGAAACAAGTCATCTTTCCTCAG
1 --TTTATCAAAGTTGACTGGAAACAGGTCATCTTT--TCAG
495 TTT
1 TTT
498 TAACTTCGAC
Statistics
Matches: 419, Mismatches: 26, Indels: 24
0.89 0.06 0.05
Matches are distributed among these distances:
36 35 0.08
37 208 0.50
39 172 0.41
41 4 0.01
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (37 bp):
TTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAG
Found at i:199 original size:76 final size:76
Alignment explanation
Indices: 1--497 Score: 811
Period size: 76 Copynumber: 6.6 Consensus size: 76
*
1 CATTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGTTTATCAAAGTTGACTGGGAACAGGT
1 CATTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGTTTATCAAAGTTGACTGGAAACAGGT
66 CATCTTTT---
66 CATCTTTTCAG
* *
74 CATTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGTTTATCAAAGTTGATTGGGAACAGGT
1 CATTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGTTTATCAAAGTTGACTGGAAACAGGT
*
139 CATCTTTTTAG
66 CATCTTTTCAG
* *
150 CGTTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGTTTATCAAAGTTGACTGAAAACAGGT
1 CATTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGTTTATCAAAGTTGACTGGAAACAGGT
215 CATCTTTTCAG
66 CATCTTTTCAG
*
226 CACTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGTTTATCAAAGTTGACTGGAAACAGGT
1 CATTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGTTTATCAAAGTTGACTGGAAACAGGT
291 CATCTTTTCAG
66 CATCTTTTCAG
* * * *
302 CATTTATCAAAGTCGACTGGAAACAGGTCATCTTTTTAGATTATCAGAGTTGACTGGAAACAGGT
1 CATTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGTTTATCAAAGTTGACTGGAAACAGGT
367 CATCTTTTCAG
66 CATCTTTTCAG
* * *
378 CATTTATCAAAGTCGACTGGAAACAGGTCATCTTTTCAGATTATCAAAGTTGACTGGAAACAAGT
1 CATTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGTTTATCAAAGTTGACTGGAAACAGGT
443 CATCTTTTCAG
66 CATCTTTTCAG
* *
454 CATTTATCAAAGTTGATTGGAAACAAGTCATCTTTCCTCAGTTT
1 CATTTATCAAAGTTGACTGGAAACAGGTCATCTTT--TCAGTTT
498 TAACTTCGAC
Statistics
Matches: 398, Mismatches: 21, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
73 72 0.18
76 320 0.80
78 6 0.02
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.34
Consensus pattern (76 bp):
CATTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGTTTATCAAAGTTGACTGGAAACAGGT
CATCTTTTCAG
Found at i:522 original size:34 final size:33
Alignment explanation
Indices: 484--599 Score: 128
Period size: 34 Copynumber: 3.5 Consensus size: 33
474 AAACAAGTCA
* *
484 TCTTTCCTCAGTTTTAACTTCGACCTCAAACAGG
1 TCTTT-CTCAGTTTTAAATTCGACCTCAGACAGG
* *
518 TCTTTATC--TTTCAAATTCGACCTCAGACAGG
1 TCTTTCTCAGTTTTAAATTCGACCTCAGACAGG
* * *
549 TCTTTCTCAGTTTTTAATTTCAACCCCAGACAGG
1 TCTTTCTCAG-TTTTAAATTCGACCTCAGACAGG
*
583 TCTTTCTTAGTTTTAAA
1 TCTTTCTCAGTTTTAAA
600 AGGTTATCCA
Statistics
Matches: 68, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
31 27 0.40
33 8 0.12
34 33 0.49
ACGTcount: A:0.24, C:0.25, G:0.11, T:0.40
Consensus pattern (33 bp):
TCTTTCTCAGTTTTAAATTCGACCTCAGACAGG
Found at i:838 original size:46 final size:47
Alignment explanation
Indices: 750--868 Score: 129
Period size: 46 Copynumber: 2.6 Consensus size: 47
740 AGACACATTA
* *
750 TTTAAAGCCCATTTCCTCA-TTAGTTTCATTCAAAGTCCATTCC-CAT
1 TTTAAAGCCCATTTCCTTATTTAG-TTAATTCAAAGTCCATTCCTCAT
* **
796 TTTAAAGCCCATTTCCTTATTTAG-TAATTCAAGGTCCAATTCCTTTT
1 TTTAAAGCCCATTTCCTTATTTAGTTAATTCAAAGTCC-ATTCCTCAT
*
843 TTTTAAGACCCATTTCCTTA-TTAGTT
1 TTTAAAG-CCCATTTCCTTATTTAGTT
869 TCTCAAAATG
Statistics
Matches: 62, Mismatches: 6, Indels: 8
0.82 0.08 0.11
Matches are distributed among these distances:
45 11 0.18
46 23 0.37
47 15 0.24
48 13 0.21
ACGTcount: A:0.25, C:0.24, G:0.08, T:0.44
Consensus pattern (47 bp):
TTTAAAGCCCATTTCCTTATTTAGTTAATTCAAAGTCCATTCCTCAT
Done.