Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016259.1 Corchorus olitorius cultivar O-4 contig16292, 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: 10998
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Found at i:459 original size:33 final size:32
Alignment explanation
Indices: 417--1164 Score: 901
Period size: 32 Copynumber: 23.6 Consensus size: 32
407 CGAAGTTCCA
417 GACCTCAGACAGGTCTTTCTCAGTTTTTATTTC
1 GACCTCAGACAGGTCTTTCTCAG-TTTTATTTC
**
450 GACCTCAGACAGGTCTTTCTCAACTTTATTTC
1 GACCTCAGACAGGTCTTTCTCAGTTTTATTTC
*
482 GACCTCAGACAGGTCTTTTTCAGCTTTTATTTC
1 GACCTCAGACAGGTCTTTCTCAG-TTTTATTTC
* *
515 GACCTCAGAAAGGTCTTTCTCAGTTTAATTTC
1 GACCTCAGACAGGTCTTTCTCAGTTTTATTTC
*
547 GACCTCAGACAGGTCTTTTTCAGCTTTTATTTC
1 GACCTCAGACAGGTCTTTCTCAG-TTTTATTTC
* * *
580 GACCTCAGAAAGGTCTTTGTCAG-TTAATTTC
1 GACCTCAGACAGGTCTTTCTCAGTTTTATTTC
* *
611 GACCTCAGACAGGTCTTCCTCAGTTTAATTTC
1 GACCTCAGACAGGTCTTTCTCAGTTTTATTTC
*
643 GACCTCAGACAGGTCTTTCTCAGCTTTAATTTC
1 GACCTCAGACAGGTCTTTCTCAG-TTTTATTTC
676 GACCTCAGTACAGGTCTTTCTCAG-----TTTC
1 GACCTCAG-ACAGGTCTTTCTCAGTTTTATTTC
*
704 GACCTCAGAC-GGTCTCTACTCAGCTTTTATTTC
1 GACCTCAGACAGGTCT-TTCTCAG-TTTTATTTC
**
737 GACCTCAGACAGGTCTTTCTCAACTTTATTTC
1 GACCTCAGACAGGTCTTTCTCAGTTTTATTTC
*
769 GACCTCAGACAGGTCTTTTTCAGCTTTTATTTC
1 GACCTCAGACAGGTCTTTCTCAG-TTTTATTTC
* *
802 GACCTCAGAAAGGTCTTTCTCAGTTTAATTTC
1 GACCTCAGACAGGTCTTTCTCAGTTTTATTTC
* *
834 GACCTCAGACAGGTCTTCCTCAGTTTTAATTCC
1 GACCTCAGACAGGTCTTTCTCAGTTTT-ATTTC
867 GACCTCAGACAGGTC-TT-TC----TTATTTC
1 GACCTCAGACAGGTCTTTCTCAGTTTTATTTC
* ** *
893 GACCTCAGACAGGTCTTTAT-A-TTCCAATTCC
1 GACCTCAGACAGGTCTTTCTCAGTT-TTATTTC
*
924 GACCTCAGACAGGTCTTCCTCAGTTTTATTTC
1 GACCTCAGACAGGTCTTTCTCAGTTTTATTTC
956 GACCTCAGACAGGTCTTTCTCAGCTTTTAATTTC
1 GACCTCAGACAGGTCTTTCTCAG-TTTT-ATTTC
* *
990 GACCTCAGACAGGTCTTTCT-A-TTTCAATTCC
1 GACCTCAGACAGGTCTTTCTCAGTTT-TATTTC
* *
1021 AACCTCAGACAGGTCTTTCTCAGTTTTATTCC
1 GACCTCAGACAGGTCTTTCTCAGTTTTATTTC
1053 GACCTCAGACAGGTCTTTCTCAGTTTTTATTTTC
1 GACCTCAGACAGGTCTTTCTCAG-TTTTA-TTTC
1087 GACCTCAGACAGGTCTTTCTCA-----ATTTC
1 GACCTCAGACAGGTCTTTCTCAGTTTTATTTC
* * *
1114 GACCTCGGACAGGTCTTTCTAAGTTTCAGTTTC
1 GACCTCAGACAGGTCTTTCTCAGTTTTA-TTTC
*
1147 GACCTCAGACGGGTCTTT
1 GACCTCAGACAGGTCTTT
1165 ATCTTTCGAC
Statistics
Matches: 626, Mismatches: 53, Indels: 72
0.83 0.07 0.10
Matches are distributed among these distances:
26 24 0.04
27 36 0.06
28 14 0.02
31 77 0.12
32 206 0.33
33 199 0.32
34 70 0.11
ACGTcount: A:0.21, C:0.26, G:0.16, T:0.37
Consensus pattern (32 bp):
GACCTCAGACAGGTCTTTCTCAGTTTTATTTC
Found at i:483 original size:32 final size:32
Alignment explanation
Indices: 417--1164 Score: 715
Period size: 33 Copynumber: 23.6 Consensus size: 32
407 CGAAGTTCCA
**
417 GACCTCAGACAGGTCTTTCTCAGTTTTTATTTC
1 GACCTCAGACAGGTCTTTCTCA-ACTTTATTTC
450 GACCTCAGACAGGTCTTTCTCAACTTTATTTC
1 GACCTCAGACAGGTCTTTCTCAACTTTATTTC
* *
482 GACCTCAGACAGGTCTTTTTCAGCTTTTATTTC
1 GACCTCAGACAGGTCTTTCTCAAC-TTTATTTC
* *
515 GACCTCAGAAAGGTCTTTCTC-AGTTTAATTTC
1 GACCTCAGACAGGTCTTTCTCAACTTT-ATTTC
* *
547 GACCTCAGACAGGTCTTTTTCAGCTTTTATTTC
1 GACCTCAGACAGGTCTTTCTCAAC-TTTATTTC
* * * *
580 GACCTCAGAAAGGTCTTTGTC-AGTTAATTTC
1 GACCTCAGACAGGTCTTTCTCAACTTTATTTC
* *
611 GACCTCAGACAGGTCTTCCTC-AGTTTAATTTC
1 GACCTCAGACAGGTCTTTCTCAACTTT-ATTTC
*
643 GACCTCAGACAGGTCTTTCTCAGCTTTAATTTC
1 GACCTCAGACAGGTCTTTCTCAACTTT-ATTTC
*
676 GACCTCAGTACAGGTCTTTCTC-A----GTTTC
1 GACCTCAG-ACAGGTCTTTCTCAACTTTATTTC
* *
704 GACCTCAGAC-GGTCTCTACTCAGCTTTTATTTC
1 GACCTCAGACAGGTCT-TTCTCAAC-TTTATTTC
737 GACCTCAGACAGGTCTTTCTCAACTTTATTTC
1 GACCTCAGACAGGTCTTTCTCAACTTTATTTC
* *
769 GACCTCAGACAGGTCTTTTTCAGCTTTTATTTC
1 GACCTCAGACAGGTCTTTCTCAAC-TTTATTTC
* *
802 GACCTCAGAAAGGTCTTTCTC-AGTTTAATTTC
1 GACCTCAGACAGGTCTTTCTCAACTTT-ATTTC
* ** *
834 GACCTCAGACAGGTCTTCCTCAGTTTTAATTCC
1 GACCTCAGACAGGTCTTTCTCAACTTT-ATTTC
867 GACCTCAGACAGGTC-TT-T---C-TTATTTC
1 GACCTCAGACAGGTCTTTCTCAACTTTATTTC
* * *
893 GACCTCAGACAGGTCTTTAT--A-TTCCAATTCC
1 GACCTCAGACAGGTCTTTCTCAACTT--TATTTC
* **
924 GACCTCAGACAGGTCTTCCTCAGTTTTATTTC
1 GACCTCAGACAGGTCTTTCTCAACTTTATTTC
*
956 GACCTCAGACAGGTCTTTCTCAGCTTTTAATTTC
1 GACCTCAGACAGGTCTTTCTCAAC-TTT-ATTTC
*
990 GACCTCAGACAGGTCTTTCT--A-TTTCAATTCC
1 GACCTCAGACAGGTCTTTCTCAACTTT--ATTTC
* ** *
1021 AACCTCAGACAGGTCTTTCTCAGTTTTATTCC
1 GACCTCAGACAGGTCTTTCTCAACTTTATTTC
**
1053 GACCTCAGACAGGTCTTTCTCAGTTTTTATTTTC
1 GACCTCAGACAGGTCTTTCTCA-ACTTTA-TTTC
1087 GACCTCAGACAGGTCTTTCTC-A----ATTTC
1 GACCTCAGACAGGTCTTTCTCAACTTTATTTC
* *
1114 GACCTCGGACAGGTCTTTCT-AAGTTTCAGTTTC
1 GACCTCAGACAGGTCTTTCTCAACTTT-A-TTTC
*
1147 GACCTCAGACGGGTCTTT
1 GACCTCAGACAGGTCTTT
1165 ATCTTTCGAC
Statistics
Matches: 608, Mismatches: 65, Indels: 84
0.80 0.09 0.11
Matches are distributed among these distances:
26 24 0.04
27 34 0.06
28 14 0.02
29 1 0.00
30 3 0.00
31 82 0.13
32 187 0.31
33 188 0.31
34 75 0.12
ACGTcount: A:0.21, C:0.26, G:0.16, T:0.37
Consensus pattern (32 bp):
GACCTCAGACAGGTCTTTCTCAACTTTATTTC
Found at i:521 original size:65 final size:64
Alignment explanation
Indices: 417--1164 Score: 887
Period size: 65 Copynumber: 11.8 Consensus size: 64
407 CGAAGTTCCA
*
417 GACCTCAGACAGGTCTTTCTCAGTTTTTATTTCGACCTCAGACAGGTCTTTCTCAACTTTATTTC
1 GACCTCAGACAGGTCTTTCTCAG-TTTTATTTCGACCTCAGACAGGTCTTTCTCAGCTTTATTTC
* *
482 GACCTCAGACAGGTCTTTTTCAGCTTTTATTTCGACCTCAGAAAGGTCTTTCTCAG-TTTAATTT
1 GACCTCAGACAGGTCTTTCTCAG-TTTTATTTCGACCTCAGACAGGTCTTTCTCAGCTTT-ATTT
546 C
64 C
* * * *
547 GACCTCAGACAGGTCTTTTTCAGCTTTTATTTCGACCTCAGAAAGGTCTTTGTCAG-TTAATTTC
1 GACCTCAGACAGGTCTTTCTCAG-TTTTATTTCGACCTCAGACAGGTCTTTCTCAGCTTTATTTC
* *
611 GACCTCAGACAGGTCTTCCTCAGTTTAATTTCGACCTCAGACAGGTCTTTCTCAGCTTTAATTTC
1 GACCTCAGACAGGTCTTTCTCAGTTTTATTTCGACCTCAGACAGGTCTTTCTCAGCTTT-ATTTC
*
676 GACCTCAGTACAGGTCTTTCTCAG-----TTTCGACCTCAGAC-GGTCTCTACTCAGCTTTTATT
1 GACCTCAG-ACAGGTCTTTCTCAGTTTTATTTCGACCTCAGACAGGTCT-TTCTCAGC-TTTATT
735 TC
63 TC
** *
737 GACCTCAGACAGGTCTTTCTCAACTTTATTTCGACCTCAGACAGGTCTTTTTCAGCTTTTATTTC
1 GACCTCAGACAGGTCTTTCTCAGTTTTATTTCGACCTCAGACAGGTCTTTCTCAGC-TTTATTTC
* * * * *
802 GACCTCAGAAAGGTCTTTCTCAGTTTAATTTCGACCTCAGACAGGTCTTCCTCAGTTTTAATTCC
1 GACCTCAGACAGGTCTTTCTCAGTTTTATTTCGACCTCAGACAGGTCTTTCTCAGCTTT-ATTTC
* * *
867 GACCTCAGACAGGTC-TT-TC----TTATTTCGACCTCAGACAGGTCTTTAT-A--TTCCAATTC
1 GACCTCAGACAGGTCTTTCTCAGTTTTATTTCGACCTCAGACAGGTCTTTCTCAGCTT--TATTT
923 C
64 C
*
924 GACCTCAGACAGGTCTTCCTCAGTTTTATTTCGACCTCAGACAGGTCTTTCTCAGCTTTTAATTT
1 GACCTCAGACAGGTCTTTCTCAGTTTTATTTCGACCTCAGACAGGTCTTTCTCAGC-TTT-ATTT
989 C
64 C
* * * * *
990 GACCTCAGACAGGTCTTTCT-A-TTTCAATTCCAACCTCAGACAGGTCTTTCTCAGTTTTATTCC
1 GACCTCAGACAGGTCTTTCTCAGTTT-TATTTCGACCTCAGACAGGTCTTTCTCAGCTTTATTTC
1053 GACCTCAGACAGGTCTTTCTCAGTTTTTATTTTCGACCTCAGACAGGTCTTTCTCA-----ATTT
1 GACCTCAGACAGGTCTTTCTCAG-TTTTA-TTTCGACCTCAGACAGGTCTTTCTCAGCTTTATTT
1113 C
64 C
* * * *
1114 GACCTCGGACAGGTCTTTCTAAGTTTCAGTTTCGACCTCAGACGGGTCTTT
1 GACCTCAGACAGGTCTTTCTCAGTTTTA-TTTCGACCTCAGACAGGTCTTT
1165 ATCTTTCGAC
Statistics
Matches: 603, Mismatches: 49, Indels: 67
0.84 0.07 0.09
Matches are distributed among these distances:
56 2 0.00
57 20 0.03
58 2 0.00
59 26 0.04
60 44 0.07
61 59 0.10
62 3 0.00
63 81 0.13
64 44 0.07
65 251 0.42
66 69 0.11
67 2 0.00
ACGTcount: A:0.21, C:0.26, G:0.16, T:0.37
Consensus pattern (64 bp):
GACCTCAGACAGGTCTTTCTCAGTTTTATTTCGACCTCAGACAGGTCTTTCTCAGCTTTATTTC
Found at i:1181 original size:25 final size:25
Alignment explanation
Indices: 1143--1195 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
1133 TAAGTTTCAG
1143 TTTCGACCTCAGACGGGTCTTTATC
1 TTTCGACCTCAGACGGGTCTTTATC
*
1168 TTTCGACCTTAGACGGGTCTTTATC
1 TTTCGACCTCAGACGGGTCTTTATC
1193 TTT
1 TTT
1196 TAATAGTGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.15, C:0.25, G:0.19, T:0.42
Consensus pattern (25 bp):
TTTCGACCTCAGACGGGTCTTTATC
Found at i:3188 original size:23 final size:23
Alignment explanation
Indices: 3160--3204 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
3150 TCCAACTTCC
3160 AAAATTCAAATTTTGAAATTTCA
1 AAAATTCAAATTTTGAAATTTCA
*
3183 AAAATTCGAATTTTGAAATTTC
1 AAAATTCAAATTTTGAAATTTC
3205 GCGCCAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.44, C:0.09, G:0.07, T:0.40
Consensus pattern (23 bp):
AAAATTCAAATTTTGAAATTTCA
Found at i:9720 original size:21 final size:20
Alignment explanation
Indices: 9681--9720 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
9671 ATTTGATGGT
**
9681 GAAAATCCAAGCTTGATGAA
1 GAAAATCCAAGCTCCATGAA
9701 GAAAATCCCAAGCTCCATGA
1 GAAAAT-CCAAGCTCCATGA
9721 GAGGTCTCCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.42, C:0.23, G:0.17, T:0.17
Consensus pattern (20 bp):
GAAAATCCAAGCTCCATGAA
Found at i:10136 original size:36 final size:36
Alignment explanation
Indices: 10064--10139 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
10054 TGAGAAAAGG
* ** *
10064 CCAAGTACATAATTAAGTTGGCTTAATTCTATTGGC
1 CCAAATACATAATTAAGTTGGCCCAATTCTACTGGC
10100 CCAAATACATAATTAAGTTGGCCCAACTT-TACTGGC
1 CCAAATACATAATTAAGTTGGCCCAA-TTCTACTGGC
10136 CCAA
1 CCAA
10140 TACTACCAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 33 0.94
37 2 0.06
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.30
Consensus pattern (36 bp):
CCAAATACATAATTAAGTTGGCCCAATTCTACTGGC
Found at i:10299 original size:37 final size:37
Alignment explanation
Indices: 10258--10384 Score: 202
Period size: 37 Copynumber: 3.4 Consensus size: 37
10248 CCAAGAGTGA
* *
10258 AACAAGTCTTCATCAAAATTATTCATCAAAGTTCTTC
1 AACAAGTCTCCATCAAAGTTATTCATCAAAGTTCTTC
10295 AACAAGTCTCCA-CGAAAGTTATTCATCAAAGTTCTTC
1 AACAAGTCTCCATC-AAAGTTATTCATCAAAGTTCTTC
*
10332 AACAAGTCTCCACCAAAGTTATTCATCAAAGTTCTTC
1 AACAAGTCTCCATCAAAGTTATTCATCAAAGTTCTTC
*
10369 AACAAGTCTTCATCAA
1 AACAAGTCTCCATCAA
10385 GTTGTTCTTC
Statistics
Matches: 84, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
36 1 0.01
37 82 0.98
38 1 0.01
ACGTcount: A:0.37, C:0.24, G:0.08, T:0.31
Consensus pattern (37 bp):
AACAAGTCTCCATCAAAGTTATTCATCAAAGTTCTTC
Found at i:10384 original size:24 final size:24
Alignment explanation
Indices: 10279--10418 Score: 92
Period size: 24 Copynumber: 5.7 Consensus size: 24
10269 ATCAAAATTA
10279 TTCATCAAAGTTCTTCAACAAGTC
1 TTCATCAAAGTTCTTCAACAAGTC
* * *
10303 TCCA-CGAAAGTTATTCATCAAAGTTC
1 TTCATC-AAAGTTCTTCAAC-AAG-TC
* * * *
10329 TTCAAC-AAG-TCTCCACCAAAGTTA
1 TTCATCAAAGTTCTTCAAC-AAG-TC
10353 TTCATCAAAGTTCTTCAACAAGTC
1 TTCATCAAAGTTCTTCAACAAGTC
* *
10377 TTCATCAAGTTGTTCTTCAACAAGTT
1 TTCATCAA--AGTTCTTCAACAAGTC
10403 TTCACTC--AGTTCTTCA
1 TTCA-TCAAAGTTCTTCA
10419 TCAAATTTTC
Statistics
Matches: 92, Mismatches: 15, Indels: 19
0.73 0.12 0.15
Matches are distributed among these distances:
23 9 0.10
24 39 0.42
25 12 0.13
26 29 0.32
27 3 0.03
ACGTcount: A:0.31, C:0.25, G:0.09, T:0.34
Consensus pattern (24 bp):
TTCATCAAAGTTCTTCAACAAGTC
Found at i:10422 original size:26 final size:26
Alignment explanation
Indices: 10367--10422 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
10357 TCAAAGTTCT
* *
10367 TCAACAAGTCTTCATCAAGTTGTTCT
1 TCAACAAGTCTTCATCAAGTTCTTCA
*
10393 TCAACAAGTTTTCACTC-AGTTCTTCA
1 TCAACAAGTCTTCA-TCAAGTTCTTCA
10419 TCAA
1 TCAA
10423 ATTTTCCACC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 24 0.92
27 2 0.08
ACGTcount: A:0.29, C:0.25, G:0.09, T:0.38
Consensus pattern (26 bp):
TCAACAAGTCTTCATCAAGTTCTTCA
Done.