Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020699.1 Corchorus olitorius cultivar O-4 contig20732, 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: 2925
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.34
Found at i:754 original size:35 final size:35
Alignment explanation
Indices: 698--1167 Score: 403
Period size: 35 Copynumber: 13.0 Consensus size: 35
688 ATGCAGTCTA
* **
698 ATTTTAAGAAGTTTTCGATGATCAGAGTTGATCTC
1 ATTTCAAGAAGTTTTTTATGATCAGAGTTGATCTC
*
733 CTTTCAAGAAGTTTTTTATGATCAGAGTTGATCTC
1 ATTTCAAGAAGTTTTTTATGATCAGAGTTGATCTC
** * * *
768 ATTTCAAGAAGTTTTTTTTATGATCAGAGAAGTTTTTT
1 ATTTCAAGAAG--TTTTTTATGATCAGAGTTG-ATCTC
* * ** * * * *
806 ATGATC-AG-AGTTGATCTCCT-TTCAAGAAGTT-TTTTT
1 AT-TTCAAGAAGTT--TTTTATGATC-AG-AGTTGATCTC
*
842 ATGATCAGAGAAGTTTTTTATGATCAGAGTTGATCTC
1 AT-TTCA-AGAAGTTTTTTATGATCAGAGTTGATCTC
* *
879 CTTTCAAGAAGCTTTTTTATGATCAAAGTTGATCTC
1 ATTTCAAGAAG-TTTTTTATGATCAGAGTTGATCTC
* *
915 GTTTCAAGAAGTTTTCGT-TGATCAGAGTTGATCTC
1 ATTTCAAGAAGTTTT-TTATGATCAGAGTTGATCTC
* *
950 GTTTCAAGAAGTTTCTTATGATCAGAGTTGATCTC
1 ATTTCAAGAAGTTTTTTATGATCAGAGTTGATCTC
* **
985 CTTTCAAGAAGATTTCGT-TGATCAGAGTTGATCTC
1 ATTTCAAGAAG-TTTTTTATGATCAGAGTTGATCTC
*
1020 ATTTCAAGATGTTCTTTTTTTTTCATGATCAGAGTTGATCTC
1 ATTTCAAGAAG------TTTTTT-ATGATCAGAGTTGATCTC
*
1062 ATTCCAAGAAGTTTTTTTTATGATCAGAGTTGATCTC
1 ATTTCAAGAAG--TTTTTTATGATCAGAGTTGATCTC
* **
1099 CTTTCAAGAAGTTTTCGATGATCAGAGTTGATCTC
1 ATTTCAAGAAGTTTTTTATGATCAGAGTTGATCTC
*
1134 GTTTCAAGAAGTTTTTTATGATCAGAGTTGATCT
1 ATTTCAAGAAGTTTTTTATGATCAGAGTTGATCT
1168 TCACATTGAT
Statistics
Matches: 363, Mismatches: 48, Indels: 48
0.79 0.10 0.10
Matches are distributed among these distances:
34 1 0.00
35 188 0.52
36 59 0.16
37 59 0.16
38 20 0.06
39 6 0.02
40 4 0.01
42 26 0.07
ACGTcount: A:0.26, C:0.13, G:0.18, T:0.42
Consensus pattern (35 bp):
ATTTCAAGAAGTTTTTTATGATCAGAGTTGATCTC
Found at i:805 original size:19 final size:20
Alignment explanation
Indices: 781--870 Score: 84
Period size: 19 Copynumber: 4.8 Consensus size: 20
771 TCAAGAAGTT
781 TTTTTTATGATCAGAGAAG-
1 TTTTTTATGATCAGAGAAGA
**
800 TTTTTTATGATCAGAGTTGA
1 TTTTTTATGATCAGAGAAGA
* ** *
820 TCTCCT-T--TCA-AGAAGT
1 TTTTTTATGATCAGAGAAGA
836 TTTTTTATGATCAGAGAAG-
1 TTTTTTATGATCAGAGAAGA
855 TTTTTTATGATCAGAG
1 TTTTTTATGATCAGAG
871 TTGATCTCCT
Statistics
Matches: 55, Mismatches: 11, Indels: 10
0.72 0.14 0.13
Matches are distributed among these distances:
16 6 0.11
17 4 0.07
19 37 0.67
20 8 0.15
ACGTcount: A:0.28, C:0.09, G:0.19, T:0.44
Consensus pattern (20 bp):
TTTTTTATGATCAGAGAAGA
Found at i:846 original size:55 final size:55
Alignment explanation
Indices: 739--903 Score: 303
Period size: 55 Copynumber: 3.0 Consensus size: 55
729 TCTCCTTTCA
*
739 AGAAGTTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTTTTTTATGATCAG
1 AGAAGTTTTTTATGATCAGAGTTGATCTCCTTTCAAGAAG-TTTTTTTATGATCAG
795 AGAAGTTTTTTATGATCAGAGTTGATCTCCTTTCAAGAAGTTTTTTTATGATCAG
1 AGAAGTTTTTTATGATCAGAGTTGATCTCCTTTCAAGAAGTTTTTTTATGATCAG
*
850 AGAAGTTTTTTATGATCAGAGTTGATCTCCTTTCAAGAAGCTTTTTTATGATCA
1 AGAAGTTTTTTATGATCAGAGTTGATCTCCTTTCAAGAAGTTTTTTTATGATCA
904 AAGTTGATCT
Statistics
Matches: 107, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
55 68 0.64
56 39 0.36
ACGTcount: A:0.28, C:0.11, G:0.18, T:0.44
Consensus pattern (55 bp):
AGAAGTTTTTTATGATCAGAGTTGATCTCCTTTCAAGAAGTTTTTTTATGATCAG
Found at i:962 original size:19 final size:19
Alignment explanation
Indices: 904--962 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 19
894 TTTATGATCA
904 AAGTTGATCTCGTTTCAAG
1 AAGTTGATCTCGTTTCAAG
923 AAGTT--T-TCGTTGATC-AG
1 AAGTTGATCTCGTT--TCAAG
940 -AGTTGATCTCGTTTCAAG
1 AAGTTGATCTCGTTTCAAG
958 AAGTT
1 AAGTT
963 TCTTATGATC
Statistics
Matches: 33, Mismatches: 0, Indels: 14
0.70 0.00 0.30
Matches are distributed among these distances:
16 9 0.27
17 5 0.15
18 5 0.15
19 14 0.42
ACGTcount: A:0.25, C:0.14, G:0.22, T:0.39
Consensus pattern (19 bp):
AAGTTGATCTCGTTTCAAG
Found at i:1131 original size:114 final size:111
Alignment explanation
Indices: 850--1150 Score: 389
Period size: 114 Copynumber: 2.7 Consensus size: 111
840 TTATGATCAG
* * ** *
850 AGAAGTTTTTTATGATCAGAGTTGATCTCCTTTCAAGAAGCTTTTTTATGATCAAAGTTGATCTC
1 AGAAGTTTCTTATGATCAGAGTTGATCTCCTTTCAAGAAG-ATTTCGATGATCAGAGTTGATCTC
* ** * *
915 GTTTCAAGAAG----TTTTCGT--TGATCAGAGTTGATCTCGTTTCA
65 ATTTCAAGAAGTTTTTTTTTTTCATGATCAGAGTTGATCTCATTCCA
*
956 AGAAGTTTCTTATGATCAGAGTTGATCTCCTTTCAAGAAGATTTCGTTGATCAGAGTTGATCTCA
1 AGAAGTTTCTTATGATCAGAGTTGATCTCCTTTCAAGAAGATTTCGATGATCAGAGTTGATCTCA
*
1021 TTTCAAGATGTTCTTTTTTTTTCATGATCAGAGTTGATCTCATTCCA
66 TTTCAAGAAGTT-TTTTTTTTTCATGATCAGAGTTGATCTCATTCCA
* *
1068 AGAAGTTTTTTTTATGATCAGAGTTGATCTCCTTTCAAGAAGTTTTCGATGATCAGAGTTGATCT
1 AGAAG--TTTCTTATGATCAGAGTTGATCTCCTTTCAAGAAGATTTCGATGATCAGAGTTGATCT
*
1133 CGTTTCAAGAAGTTTTTT
64 CATTTCAAGAAGTTTTTT
1151 ATGATCAGAG
Statistics
Matches: 169, Mismatches: 17, Indels: 11
0.86 0.09 0.06
Matches are distributed among these distances:
105 28 0.17
106 39 0.23
110 5 0.03
112 26 0.15
113 4 0.02
114 67 0.40
ACGTcount: A:0.25, C:0.14, G:0.18, T:0.42
Consensus pattern (111 bp):
AGAAGTTTCTTATGATCAGAGTTGATCTCCTTTCAAGAAGATTTCGATGATCAGAGTTGATCTCA
TTTCAAGAAGTTTTTTTTTTTCATGATCAGAGTTGATCTCATTCCA
Done.