Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018366.1 Corchorus olitorius cultivar O-4 contig18399, 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, 646
Length: 1078
ACGTcount: A:0.33, C:0.20, G:0.28, T:0.20
Found at i:131 original size:38 final size:38
Alignment explanation
Indices: 88--636 Score: 214
Period size: 38 Copynumber: 13.2 Consensus size: 38
78 GCCAAAAATG
* *
88 GCCAAAATGCTAAAGGTGTTACATTATGAGCGTCGGGT
1 GCCAAAATGCCAAAGGTGTTACATCATGAGCGTCGGGT
* *
126 GCCAAAATGCCATAGGTGTTACATCATTAGCGTCGGGGGCAAAGATT
1 GCCAAAATGCCAAAGGTGTTACATCATGAGCGTC---GG----G--T
* *
173 GCTAAAATGCCAAAGGT-TAACCAGT-ATGAGCGTCGGGGGCCAAAAACT
1 GCCAAAATGCCAAAGGTGTTA-CA-TCATGAGCGTC--GGG--------T
*
221 GGCCAAAAATGCTAAAGGTGTTACATCATGAGCGTC-GGT
1 -GCC-AAAATGCCAAAGGTGTTACATCATGAGCGTCGGGT
* * *
260 GCCAAAATGCCATAGGTGTTACACCATTAGCGTCAGGGTAAAAGAT
1 GCCAAAATGCCAAAGGTGTTACATCATGAGCGTC--GG-----G-T
* * * *
306 GGCTAAAATGCCAAAGGT-TAACCACCATGAGCGTCGGGG
1 -GCCAAAATGCCAAAGGTGTTA-CATCATGAGCGTCGGGT
* * *
345 GCCAAAAAATGACCAAAACGCCAAAGGAGTTACACCATGAGCGTCGGGA
1 GCC--AAAAT---------GCCAAAGGTGTTACATCATGAGCGTCGGGT
* * * *
394 GACGAAATGCCATAGGTGTTACATCATGAGCGTCGGGG
1 GCCAAAATGCCAAAGGTGTTACATCATGAGCGTCGGGT
* * *
432 GCCAAAATGCCATAGCTGTTACATAATGAGCGTCGGG-
1 GCCAAAATGCCAAAGGTGTTACATCATGAGCGTCGGGT
**
469 GGAAAAATGGCCCAATGCCAAGTGTGTTACATCATGAGCGTCGGG-
1 GCCAAAAT-G-CC-A----AAG-GTGTTACATCATGAGCGTCGGGT
* * *
514 GCCAAAATGCCATAA-TTGTTACATTATGAGCGTCGGGG
1 GCCAAAATGCCA-AAGGTGTTACATCATGAGCGTCGGGT
* * * *
552 GCAAAAAATTCCATAGGTGTTACACCATGAGCGTCGGGT
1 GC-CAAAATGCCAAAGGTGTTACATCATGAGCGTCGGGT
* * *
591 GCCAAAAGGCCATAA-GTGTTACATCATTAGCGTCGGGG
1 GCCAAAATGCCA-AAGGTGTTACATCATGAGCGTCGGGT
*
629 GCAAAAAT
1 GCCAAAAT
637 TGGCTAAAAT
Statistics
Matches: 394, Mismatches: 61, Indels: 112
0.69 0.11 0.20
Matches are distributed among these distances:
37 53 0.13
38 131 0.33
39 35 0.09
40 8 0.02
41 2 0.01
42 2 0.01
43 2 0.01
44 3 0.01
45 30 0.08
46 9 0.02
47 59 0.15
48 3 0.01
49 29 0.07
50 26 0.07
51 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.28, T:0.20
Consensus pattern (38 bp):
GCCAAAATGCCAAAGGTGTTACATCATGAGCGTCGGGT
Found at i:252 original size:50 final size:48
Alignment explanation
Indices: 129--1077 Score: 339
Period size: 48 Copynumber: 21.7 Consensus size: 48
119 GTCGGGTGCC
* * * * *
129 AAAATGCCATAGGTGTTACATCATTAGCGTCGGGGG-CAAAGATTGCT
1 AAAATGCCAAAGGTGTTACATCATGAGCGTCGGGGGCCAAAAATGGCA
*
176 AAAATGCCAAAGGT-TAACCAGT-ATGAGCGTCGGGGGCCAAAAACTGGCCA
1 AAAATGCCAAAGGTGTTA-CA-TCATGAGCGTCGGGGGCCAAAAA-TGG-CA
* *
226 AAAATGCTAAAGGTGTTACATCATGAGCGTC---GG-------T-GCC
1 AAAATGCCAAAGGTGTTACATCATGAGCGTCGGGGGCCAAAAATGGCA
* * * * * *
263 AAAATGCCATAGGTGTTACACCATTAGCGTC-AGGG-TAAAAGATGGCT
1 AAAATGCCAAAGGTGTTACATCATGAGCGTCGGGGGCCAAAA-ATGGCA
* * * *
310 AAAATGCCAAAGGT-TAACCACCATGAGCGTCGGGGGCCAAAAAATGACC
1 AAAATGCCAAAGGTGTTA-CATCATGAGCGTCGGGGGCC-AAAAATGGCA
* * * *
359 AAAACGCCAAAGGAGTTACACCATGAGCGTC--GGG------A-GAC-
1 AAAATGCCAAAGGTGTTACATCATGAGCGTCGGGGGCCAAAAATGGCA
* *
397 GAAATGCCATAGGTGTTACATCATGAGCGTCGGGGG-C--------C-
1 AAAATGCCAAAGGTGTTACATCATGAGCGTCGGGGGCCAAAAATGGCA
* * *
435 AAAATGCCATAGCTGTTACATAATGAGCGTCGGGGG--AAAAATGGC-
1 AAAATGCCAAAGGTGTTACATCATGAGCGTCGGGGGCCAAAAATGGCA
**
480 CCAATGCC-AAGTGTGTTACATCATGAGCGTC-GGGGCC-AAAAT-GC-
1 AAAATGCCAAAG-GTGTTACATCATGAGCGTCGGGGGCCAAAAATGGCA
* * *
524 --CAT----AA-TTGTTACATTATGAGCGTCGGGGG-C----A----A
1 AAAATGCCAAAGGTGTTACATCATGAGCGTCGGGGGCCAAAAATGGCA
* * * *
556 AAAATTCCATAGGTGTTACACCATGAGCGTCGGGTGCC-AAAA-GGC-
1 AAAATGCCAAAGGTGTTACATCATGAGCGTCGGGGGCCAAAAATGGCA
* * *
601 --CAT----AA-GTGTTACATCATTAGCGTCGGGGG-CAAAAATTGGCT
1 AAAATGCCAAAGGTGTTACATCATGAGCGTCGGGGGCCAAAAA-TGGCA
* * * *
642 AAAATGCCAAAGCT-TAAGCAGCATGAGCGTCGGGGGCCAAAAATGGCC
1 AAAATGCCAAAGGTGTTA-CATCATGAGCGTCGGGGGCCAAAAATGGCA
* * *
690 AAAATGCTAAAGGTGTTACATTATGAGCGTCGGGTGCC-AAAAT-GC-
1 AAAATGCCAAAGGTGTTACATCATGAGCGTCGGGGGCCAAAAATGGCA
* * * * *
735 ----T---ATAGGTGTTACATCATTAGCGTCGGTGG-CAAAGAATTGCT
1 AAAATGCCAAAGGTGTTACATCATGAGCGTCGGGGGCCAAA-AATGGCA
* * * *
776 AAAATGCCAAAGGT-TAACCAGCATGAGCGTCGGGGGCCAAAACTGGCC
1 AAAATGCCAAAGGTGTTA-CATCATGAGCGTCGGGGGCCAAAAATGGCA
* * * *
824 AAAATGCTAAAGGTGTTACACCATGAGTGTC---GG----AAA---CT
1 AAAATGCCAAAGGTGTTACATCATGAGCGTCGGGGGCCAAAAATGGCA
** * *
862 AAAATGCCGTAGGTGTTACATCATGAGCGTCGGGGGCAAAAAATGGCT
1 AAAATGCCAAAGGTGTTACATCATGAGCGTCGGGGGCCAAAAATGGCA
* *
910 AAAATGCCAAAGGTGTTACACCATAAGCGTC-GGGG------A---CA
1 AAAATGCCAAAGGTGTTACATCATGAGCGTCGGGGGCCAAAAATGGCA
* *
948 AAAATGACAAAGGTGTTACATCATGAGCGTCGGGGG-CAAAATATGGCT
1 AAAATGCCAAAGGTGTTACATCATGAGCGTCGGGGGCCAAAA-ATGGCA
* * * * *
996 AAAATGCCAAAGGT-TAACCACCATGAGCGTCGCGGGCCAAAAATGACC
1 AAAATGCCAAAGGTGTTA-CATCATGAGCGTCGGGGGCCAAAAATGGCA
* ** *
1044 AAAACGCCAAAGGAATTACACCATGAGCGTCGGG
1 AAAATGCCAAAGGTGTTACATCATGAGCGTCGGG
1078 A
Statistics
Matches: 693, Mismatches: 106, Indels: 205
0.69 0.11 0.20
Matches are distributed among these distances:
34 3 0.00
37 48 0.07
38 172 0.25
39 36 0.05
40 10 0.01
41 6 0.01
42 2 0.00
43 5 0.01
44 8 0.01
45 36 0.05
46 7 0.01
47 77 0.11
48 197 0.28
49 53 0.08
50 31 0.04
51 2 0.00
ACGTcount: A:0.33, C:0.20, G:0.28, T:0.19
Consensus pattern (48 bp):
AAAATGCCAAAGGTGTTACATCATGAGCGTCGGGGGCCAAAAATGGCA
Found at i:261 original size:134 final size:133
Alignment explanation
Indices: 1--556 Score: 669
Period size: 134 Copynumber: 4.3 Consensus size: 133
* *
1 CCATAGGTGTTACATCATTAGCGTCGGGGGCAAAAATTGGCTAAAATGCCAAAGGTTAAGCAGCA
1 CCATAGGTGTTACATCATTAGCGTCGGGGGCAAAGATT-GCTAAAATGCCAAAGGTTAACCAGCA
* *
66 TGAGCGTCGAGGGCCAAAAATGGCCAAAATGCTAAAGGTGTTACATTATGAGCGTCGGGTGCCAA
65 TGAGCGTCGGGGGCCAAAAATGGCCAAAATGCTAAAGGTGTTACATCATGAGCGTCGGGTGCCAA
131 AATG
130 AATG
*
135 CCATAGGTGTTACATCATTAGCGTCGGGGGCAAAGATTGCTAAAATGCCAAAGGTTAACCAGTAT
1 CCATAGGTGTTACATCATTAGCGTCGGGGGCAAAGATTGCTAAAATGCCAAAGGTTAACCAGCAT
200 GAGCGTCGGGGGCCAAAAACTGGCCAAAAATGCTAAAGGTGTTACATCATGAGCGTC-GGTGCCA
66 GAGCGTCGGGGGCCAAAAA-TGGCC-AAAATGCTAAAGGTGTTACATCATGAGCGTCGGGTGCCA
264 AAATG
129 AAATG
* * ** * *
269 CCATAGGTGTTACACCATTAGCGTCAGGGTAAAAGATGGCTAAAATGCCAAAGGTTAACCACCAT
1 CCATAGGTGTTACATCATTAGCGTCGGGGGCAAAGATTGCTAAAATGCCAAAGGTTAACCAGCAT
* * * * * * * *
334 GAGCGTCGGGGGCCAAAAAATGACCAAAACGCCAAAGGAGTTACACCATGAGCGTCGGGAGACGA
66 GAGCGTCGGGGGCC-AAAAATGGCCAAAATGCTAAAGGTGTTACATCATGAGCGTCGGGTGCCAA
399 AATG
130 AATG
* * **
403 CCATAGGTGTTACATCATGAGCGTCGGGGGC--------C-AAAATGCCATAGCTGTT-A-CATA
1 CCATAGGTGTTACATCATTAGCGTCGGGGGCAAAGATTGCTAAAATGCCAAAG--GTTAACCAGC
* *
457 ATGAGCGTCGGGGG--AAAAATGGCC-CAATGC-CAAGTGTGTTACATCATGAGCGTCGGG-GCC
64 ATGAGCGTCGGGGGCCAAAAATGGCCAAAATGCTAAAG-GTGTTACATCATGAGCGTCGGGTGCC
517 AAAATG
128 AAAATG
** * *
523 CCATAATTGTTACATTATGAGCGTCGGGGGCAAA
1 CCATAGGTGTTACATCATTAGCGTCGGGGGCAAA
557 AAATTCCATA
Statistics
Matches: 373, Mismatches: 39, Indels: 31
0.84 0.09 0.07
Matches are distributed among these distances:
120 38 0.10
121 24 0.06
122 9 0.02
125 27 0.07
126 2 0.01
127 3 0.01
133 70 0.19
134 165 0.44
135 35 0.09
ACGTcount: A:0.32, C:0.20, G:0.28, T:0.20
Consensus pattern (133 bp):
CCATAGGTGTTACATCATTAGCGTCGGGGGCAAAGATTGCTAAAATGCCAAAGGTTAACCAGCAT
GAGCGTCGGGGGCCAAAAATGGCCAAAATGCTAAAGGTGTTACATCATGAGCGTCGGGTGCCAAA
ATG
Found at i:730 original size:38 final size:38
Alignment explanation
Indices: 687--760 Score: 121
Period size: 38 Copynumber: 1.9 Consensus size: 38
677 GCCAAAAATG
*
687 GCCAAAATGCTAAAGGTGTTACATTATGAGCGTCGGGT
1 GCCAAAATGCTAAAGGTGTTACATCATGAGCGTCGGGT
* *
725 GCCAAAATGCTATAGGTGTTACATCATTAGCGTCGG
1 GCCAAAATGCTAAAGGTGTTACATCATGAGCGTCGG
761 TGGCAAAGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.27
Consensus pattern (38 bp):
GCCAAAATGCTAAAGGTGTTACATCATGAGCGTCGGGT
Found at i:798 original size:134 final size:132
Alignment explanation
Indices: 566--953 Score: 535
Period size: 134 Copynumber: 2.9 Consensus size: 132
556 AAAATTCCAT
* *
566 AGGTGTTACACCATGAGCGTCGGGTGCCAAAAGGCCATAAGTGTTACATCATTAGCGTCGGGGGC
1 AGGTGTTACACCATGAGCGTCGGGTGCCAAAATGCCATAGGTGTTACATCATTAGCGTCGGGGGC
*
631 AAAAATTGGCTAAAATGCCAAAGCTTAAGCAGCATGAGCGTCGGGGGCCAAAAATGGCCAAAATG
66 AAAAATT-GCTAAAATGCCAAAGGTTAA-CAGCATGAGCGTCGGGGGCCAAAAATGGCCAAAATG
696 CTAA
129 CTAA
** * *
700 AGGTGTTACATTATGAGCGTCGGGTGCCAAAATGCTATAGGTGTTACATCATTAGCGTCGGTGGC
1 AGGTGTTACACCATGAGCGTCGGGTGCCAAAATGCCATAGGTGTTACATCATTAGCGTCGGGGGC
*
765 AAAGAATTGCTAAAATGCCAAAGGTTAACCAGCATGAGCGTCGGGGGCCAAAACTGGCCAAAATG
66 AAA-AATTGCTAAAATGCCAAAGGTTAA-CAGCATGAGCGTCGGGGGCCAAAAATGGCCAAAATG
830 CTAA
129 CTAA
* *** * * *
834 AGGTGTTACACCATGAGTGTCGGAAACTAAAATGCCGTAGGTGTTACATCATGAGCGTCGGGGGC
1 AGGTGTTACACCATGAGCGTCGGGTGCCAAAATGCCATAGGTGTTACATCATTAGCGTCGGGGGC
* * * * *
899 AAAAAATGGCTAAAATGCCAAAGGTGTTACACCATAAGCGTC-GGGGACAAAAATG
66 -AAAAATTGCTAAAATGCCAAAGGT-TAACAGCATGAGCGTCGGGGGCCAAAAATG
954 ACAAAGGTGT
Statistics
Matches: 225, Mismatches: 26, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
133 11 0.05
134 205 0.91
135 9 0.04
ACGTcount: A:0.33, C:0.19, G:0.28, T:0.20
Consensus pattern (132 bp):
AGGTGTTACACCATGAGCGTCGGGTGCCAAAATGCCATAGGTGTTACATCATTAGCGTCGGGGGC
AAAAATTGCTAAAATGCCAAAGGTTAACAGCATGAGCGTCGGGGGCCAAAAATGGCCAAAATGCT
AA
Found at i:864 original size:86 final size:86
Alignment explanation
Indices: 774--1027 Score: 325
Period size: 86 Copynumber: 3.0 Consensus size: 86
764 CAAAGAATTG
* * * * *
774 CTAAAATGCCAAAGGT-TAACCAGCATGAGCGTCGGGGGCCAAAACTGGCCAAAATGCTAAAGGT
1 CTAAAATGCCAAAGGTGTTA-CATCATGAGCGTCGGGGGCCAAAAATGGCTAAAATGCCAAAGGT
*
838 GTTACACCATGAGTGTCGGAAA
65 GTTACACCATGAGCGTCGGAAA
** *
860 CTAAAATGCCGTAGGTGTTACATCATGAGCGTCGGGGGCAAAAAATGGCTAAAATGCCAAAGGTG
1 CTAAAATGCCAAAGGTGTTACATCATGAGCGTCGGGGGCCAAAAATGGCTAAAATGCCAAAGGTG
* **
925 TTACACCATAAGCGTCGGGGA
66 TTACACCATGAGCGTCGGAAA
* *
946 CAAAAATGACAAAGGTGTTACATCATGAGCGTCGGGGG-CAAAATATGGCTAAAATGCCAAAGGT
1 CTAAAATGCCAAAGGTGTTACATCATGAGCGTCGGGGGCCAAAA-ATGGCTAAAATGCCAAAGGT
*
1010 -TAACCACCATGAGCGTCG
65 GTTA-CACCATGAGCGTCG
1028 CGGGCCAAAA
Statistics
Matches: 146, Mismatches: 19, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
85 6 0.04
86 138 0.95
87 2 0.01
ACGTcount: A:0.35, C:0.20, G:0.27, T:0.19
Consensus pattern (86 bp):
CTAAAATGCCAAAGGTGTTACATCATGAGCGTCGGGGGCCAAAAATGGCTAAAATGCCAAAGGTG
TTACACCATGAGCGTCGGAAA
Found at i:866 original size:220 final size:220
Alignment explanation
Indices: 640--1076 Score: 585
Period size: 220 Copynumber: 2.0 Consensus size: 220
630 CAAAAATTGG
* *
640 CTAAAATGCCAAAGCT-TAAGCAGCATGAGCGTCGGGGGCCAAAAATGGCCAAAATGCTAAAGGT
1 CTAAAATGCCAAAGCTGTAA-CAGCATGAGCGTCGGGGGCAAAAAATGGCCAAAATGCCAAAGGT
** * * * * *
704 GTTACATTATGAGCGTCGGGTG-CCAAAATG-CTATAGGTGTTACATCATTAGCGTCGGTGGCAA
65 GTTACACCATAAGCGTCGGG-GACAAAAATGAC-AAAGGTGTTACATCATGAGCGTCGGGGGCAA
* * * * * *
767 AGA-ATTGCTAAAATGCCAAAGGTTAACCAGCATGAGCGTCGGGGGCCAAAACTGGCCAAAATGC
128 A-ATATGGCTAAAATGCCAAAGGTTAACCACCATGAGCGTCGCGGGCCAAAAATGACCAAAACGC
* ** *
831 TAAAGGTGTTACACCATGAGTGTCGGAAA
192 CAAAGGAATTACACCATGAGCGTCGGAAA
** * * * *
860 CTAAAATGCCGTAGGTGTTACATCATGAGCGTCGGGGGCAAAAAATGGCTAAAATGCCAAAGGTG
1 CTAAAATGCCAAAGCTGTAACAGCATGAGCGTCGGGGGCAAAAAATGGCCAAAATGCCAAAGGTG
925 TTACACCATAAGCGTCGGGGACAAAAATGACAAAGGTGTTACATCATGAGCGTCGGGGGCAAAAT
66 TTACACCATAAGCGTCGGGGACAAAAATGACAAAGGTGTTACATCATGAGCGTCGGGGGCAAAAT
990 ATGGCTAAAATGCCAAAGGTTAACCACCATGAGCGTCGCGGGCCAAAAATGACCAAAACGCCAAA
131 ATGGCTAAAATGCCAAAGGTTAACCACCATGAGCGTCGCGGGCCAAAAATGACCAAAACGCCAAA
1055 GGAATTACACCATGAGCGTCGG
196 GGAATTACACCATGAGCGTCGG
1077 GA
Statistics
Matches: 188, Mismatches: 25, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
219 2 0.01
220 183 0.97
221 3 0.02
ACGTcount: A:0.34, C:0.20, G:0.27, T:0.19
Consensus pattern (220 bp):
CTAAAATGCCAAAGCTGTAACAGCATGAGCGTCGGGGGCAAAAAATGGCCAAAATGCCAAAGGTG
TTACACCATAAGCGTCGGGGACAAAAATGACAAAGGTGTTACATCATGAGCGTCGGGGGCAAAAT
ATGGCTAAAATGCCAAAGGTTAACCACCATGAGCGTCGCGGGCCAAAAATGACCAAAACGCCAAA
GGAATTACACCATGAGCGTCGGAAA
Found at i:961 original size:38 final size:38
Alignment explanation
Indices: 910--988 Score: 122
Period size: 38 Copynumber: 2.1 Consensus size: 38
900 AAAAATGGCT
*
910 AAAATGCCAAAGGTGTTACACCATAAGCGTCGGGGACA
1 AAAATGACAAAGGTGTTACACCATAAGCGTCGGGGACA
* * *
948 AAAATGACAAAGGTGTTACATCATGAGCGTCGGGGGCA
1 AAAATGACAAAGGTGTTACACCATAAGCGTCGGGGACA
986 AAA
1 AAA
989 TATGGCTAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.38, C:0.18, G:0.28, T:0.16
Consensus pattern (38 bp):
AAAATGACAAAGGTGTTACACCATAAGCGTCGGGGACA
Done.