Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011822.1 Corchorus capsularis cultivar CVL-1 contig11843, 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: 9639
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Found at i:497 original size:86 final size:84
Alignment explanation
Indices: 351--602 Score: 395
Period size: 86 Copynumber: 3.0 Consensus size: 84
341 GACATGGAGG
351 TACACGAGAAGGACAGCGGCTCTCAGCAGTGAGGCTCTCAAAACGGCCGCCGACTACGAGGCTCG
1 TACACGAGAAGGACAGCGGCTCTCAGCAGTGAGGC-CTCAAAACGGCCGCCGACT-CGAGGCTCG
416 CGAACACGACACACACGAAGA
64 CGAACACGACACACACGAAGA
*
437 TACACGAGAAGGATAGCGGCTCTCAGCAGTGAGGCACTCAAAACGGCCGCCGACTGCGAGGCTCG
1 TACACGAGAAGGACAGCGGCTCTCAGCAGTGAGGC-CTCAAAACGGCCGCCGACT-CGAGGCTCG
* *
502 CGAACACGACACAAACGAAGG
64 CGAACACGACACACACGAAGA
523 TACACGAGAAGGACAGCGGCTCTCAGCAGTGAGGTCCTCAAAACGGCCGCCGA--C--GGCTCGC
1 TACACGAGAAGGACAGCGGCTCTCAGCAGTGAGG-CCTCAAAACGGCCGCCGACTCGAGGCTCGC
*
584 GGACACGACACACACGAAG
65 GAACACGACACACACGAAG
603 GCTCGCGAAC
Statistics
Matches: 157, Mismatches: 8, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
81 24 0.15
83 1 0.01
86 131 0.83
87 1 0.01
ACGTcount: A:0.31, C:0.31, G:0.29, T:0.09
Consensus pattern (84 bp):
TACACGAGAAGGACAGCGGCTCTCAGCAGTGAGGCCTCAAAACGGCCGCCGACTCGAGGCTCGCG
AACACGACACACACGAAGA
Found at i:614 original size:25 final size:25
Alignment explanation
Indices: 577--627 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
567 GGCCGCCGAC
*
577 GGCTCGCGGACACGACACACACGAA
1 GGCTCGCGAACACGACACACACGAA
602 GGCTCGCGAACACGACACACACGAA
1 GGCTCGCGAACACGACACACACGAA
627 G
1 G
628 ATACACGAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.33, C:0.35, G:0.27, T:0.04
Consensus pattern (25 bp):
GGCTCGCGAACACGACACACACGAA
Found at i:680 original size:106 final size:108
Alignment explanation
Indices: 495--714 Score: 338
Period size: 106 Copynumber: 2.0 Consensus size: 108
485 GCCGACTGCG
*
495 AGGCTCGCGAACACGACACAAACGAAGGTACACGAGAAGGACAGCGGCTCTCAGCAGTGAGGTCC
1 AGGCTCGCGAACACGACACAAACGAAGATACACGAGAAGGACAGCGGCTCTCAGCAGTGAGGTCC
* *
560 TCAAAACGGCCGCCGA-C-GGCTCGCGGACACGACACACACGA
66 TCAAAACGGCCGCCGACCAGGCTCGCGAACACGACACAAACGA
* *
601 AGGCTCGCGAACACGACACACACGAAGATACACGAGAAGGACAGCGGCTTTCAGCAGTGAGG-CA
1 AGGCTCGCGAACACGACACAAACGAAGATACACGAGAAGGACAGCGGCTCTCAGCAGTGAGGTC-
665 CTCAAAACGGCCGCCGACTGCGAGGCTCGCGAACACGACACAAACGA
65 CTCAAAACGGCCGCCGAC--C-AGGCTCGCGAACACGACACAAACGA
712 AGG
1 AGG
715 TACACGAGAA
Statistics
Matches: 103, Mismatches: 5, Indels: 7
0.90 0.04 0.06
Matches are distributed among these distances:
105 1 0.01
106 76 0.74
109 1 0.01
111 25 0.24
ACGTcount: A:0.32, C:0.31, G:0.29, T:0.08
Consensus pattern (108 bp):
AGGCTCGCGAACACGACACAAACGAAGATACACGAGAAGGACAGCGGCTCTCAGCAGTGAGGTCC
TCAAAACGGCCGCCGACCAGGCTCGCGAACACGACACAAACGA
Found at i:736 original size:192 final size:192
Alignment explanation
Indices: 409--795 Score: 731
Period size: 192 Copynumber: 2.0 Consensus size: 192
399 GCCGACTACG
*
409 AGGCTCGCGAACACGACACACACGAAGATACACGAGAAGGATAGCGGCTCTCAGCAGTGAGGCAC
1 AGGCTCGCGAACACGACACACACGAAGATACACGAGAAGGACAGCGGCTCTCAGCAGTGAGGCAC
474 TCAAAACGGCCGCCGACTGCGAGGCTCGCGAACACGACACAAACGAAGGTACACGAGAAGGACAG
66 TCAAAACGGCCGCCGACTGCGAGGCTCGCGAACACGACACAAACGAAGGTACACGAGAAGGACAG
*
539 CGGCTCTCAGCAGTGAGGTCCTCAAAACGGCCGCCGACGGCTCGCGGACACGACACACACGA
131 CGGCTCTCAGCAGTGAGGCCCTCAAAACGGCCGCCGACGGCTCGCGGACACGACACACACGA
*
601 AGGCTCGCGAACACGACACACACGAAGATACACGAGAAGGACAGCGGCTTTCAGCAGTGAGGCAC
1 AGGCTCGCGAACACGACACACACGAAGATACACGAGAAGGACAGCGGCTCTCAGCAGTGAGGCAC
666 TCAAAACGGCCGCCGACTGCGAGGCTCGCGAACACGACACAAACGAAGGTACACGAGAA-GAGCA
66 TCAAAACGGCCGCCGACTGCGAGGCTCGCGAACACGACACAAACGAAGGTACACGAGAAGGA-CA
730 GCGGCTCTCAGCAGTGAGGCCCTCAAAACGGCCGCCGACGGCTCGCGGACACGACACACACGA
130 GCGGCTCTCAGCAGTGAGGCCCTCAAAACGGCCGCCGACGGCTCGCGGACACGACACACACGA
793 AGG
1 AGG
796 TACACGAGAA
Statistics
Matches: 191, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
191 2 0.01
192 189 0.99
ACGTcount: A:0.31, C:0.31, G:0.29, T:0.08
Consensus pattern (192 bp):
AGGCTCGCGAACACGACACACACGAAGATACACGAGAAGGACAGCGGCTCTCAGCAGTGAGGCAC
TCAAAACGGCCGCCGACTGCGAGGCTCGCGAACACGACACAAACGAAGGTACACGAGAAGGACAG
CGGCTCTCAGCAGTGAGGCCCTCAAAACGGCCGCCGACGGCTCGCGGACACGACACACACGA
Found at i:746 original size:86 final size:86
Alignment explanation
Indices: 601--1047 Score: 629
Period size: 86 Copynumber: 5.3 Consensus size: 86
591 ACACACACGA
* *
601 AGGCTCGCGAACACGACACACACGAAGATACACGAGAAGGACAGCGGCTTTCAGCAGTGAGGCAC
1 AGGCTCGCGAACACGACACACACGAAGGTACACGAGAAGGACAGCGGCTCTCAGCAGTGAGGCAC
*
666 TCAAAACGGCCGCCGACTGCG
66 TCAAAACGGCCGCCGACTACG
* *
687 AGGCTCGCGAACACGACACAAACGAAGGTACACGAGAA-GAGCAGCGGCTCTCAGCAGTGAGGCC
1 AGGCTCGCGAACACGACACACACGAAGGTACACGAGAAGGA-CAGCGGCTCTCAGCAGTGAGGCA
751 CTCAAAACGGCCGCCG---AC-
65 CTCAAAACGGCCGCCGACTACG
* ***
769 -GGCTCGCGGACACGACACACACGAAGGTACACGAGAAGGACAGCGGCTCTCAGCAAAAAGGCAC
1 AGGCTCGCGAACACGACACACACGAAGGTACACGAGAAGGACAGCGGCTCTCAGCAGTGAGGCAC
*
833 TCAAAACGGCCGCCGACAACG
66 TCAAAACGGCCGCCGACTACG
* * * * *
854 AGACTCGCGAACACGACACACACGAAGGTACGCGTGAAGTACAGCAGCTCTCAGCAGTGAGGCAC
1 AGGCTCGCGAACACGACACACACGAAGGTACACGAGAAGGACAGCGGCTCTCAGCAGTGAGGCAC
*
919 TCAAAACAGCCGCCGACTACG
66 TCAAAACGGCCGCCGACTACG
* * *
940 AGGCTCGCGGACACAACACACACGAAGGTACACGAAAAGGACAGCGGCTCTCCA-CAGTGAGGCA
1 AGGCTCGCGAACACGACACACACGAAGGTACACGAGAAGGACAGCGGCTCT-CAGCAGTGAGGCA
* *
1004 CTCAAAACAGCCGCCGACTGCG
65 CTCAAAACGGCCGCCGACTACG
*
1026 AGGCTCGCGGACACGACACACA
1 AGGCTCGCGAACACGACACACA
1048 GAGGTGCTCC
Statistics
Matches: 321, Mismatches: 32, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
81 70 0.22
82 2 0.01
83 1 0.00
84 2 0.01
85 2 0.01
86 242 0.75
87 2 0.01
ACGTcount: A:0.32, C:0.32, G:0.28, T:0.08
Consensus pattern (86 bp):
AGGCTCGCGAACACGACACACACGAAGGTACACGAGAAGGACAGCGGCTCTCAGCAGTGAGGCAC
TCAAAACGGCCGCCGACTACG
Found at i:870 original size:278 final size:275
Alignment explanation
Indices: 351--881 Score: 827
Period size: 278 Copynumber: 1.9 Consensus size: 275
341 GACATGGAGG
*
351 TACACGAGAAGGACAGCGGCTCTCAGCAGTGAGGCTCTCAAAACGGCCGCCGACTACGAGGCTCG
1 TACACGAGAAGGACAGCGGCTCTCAGCAGTGAGGCACTCAAAACGGCCGCCGACTACGAGGCTCG
* *
416 CGAACACGACACACACGAAGATACACGAGAAGGATAGCGGCTCTCAGCAGTGAGGCACTCAAAAC
66 CGAACACGACACAAACGAAGATACACGAGAAGGACAGCGGCTCTCAGCAGTGAGGCACTCAAAAC
481 GGCCGCCGACTGCGAGGCTCGCGAACACGACACAAACGAAGGTACACGAGAAGGACAGCGGCTCT
131 GGCCGCCGAC--C-AGGCTCGCGAACACGACACAAACGAAGGTACACGAGAAGGACAGCGGCTCT
*** *
546 CAGCAGTGAGGTCCTCAAAACGGCCGCCGACGGCTCGCGGACACGACACACACGAAGGCTCGCGA
193 CAGCAAAAAGGTCCTCAAAACGGCCGCCGACGGCTCGCGAACACGACACACACGAAGGCTCGCGA
611 ACACGACACACACGAAGA
258 ACACGACACACACGAAGA
* *
629 TACACGAGAAGGACAGCGGCTTTCAGCAGTGAGGCACTCAAAACGGCCGCCGACTGCGAGGCTCG
1 TACACGAGAAGGACAGCGGCTCTCAGCAGTGAGGCACTCAAAACGGCCGCCGACTACGAGGCTCG
* *
694 CGAACACGACACAAACGAAGGTACACGAGAA-GAGCAGCGGCTCTCAGCAGTGAGGCCCTCAAAA
66 CGAACACGACACAAACGAAGATACACGAGAAGGA-CAGCGGCTCTCAGCAGTGAGGCACTCAAAA
* *
758 CGGCCGCCGA-C-GGCTCGCGGACACGACACACACGAAGGTACACGAGAAGGACAGCGGCTCTCA
130 CGGCCGCCGACCAGGCTCGCGAACACGACACAAACGAAGGTACACGAGAAGGACAGCGGCTCTCA
821 GCAAAAAGG-CACTCAAAACGGCCGCCGACAACGAGACTCGCGAACACGACACACACGAAGG
195 GCAAAAAGGTC-CTCAAAACGGCCGCCG---ACG-G-CTCGCGAACACGACACACACGAAGG
882 TACGCGTGAA
Statistics
Matches: 233, Mismatches: 13, Indels: 14
0.90 0.05 0.05
Matches are distributed among these distances:
272 1 0.00
273 72 0.31
275 1 0.00
276 3 0.01
277 3 0.01
278 153 0.66
ACGTcount: A:0.32, C:0.31, G:0.29, T:0.08
Consensus pattern (275 bp):
TACACGAGAAGGACAGCGGCTCTCAGCAGTGAGGCACTCAAAACGGCCGCCGACTACGAGGCTCG
CGAACACGACACAAACGAAGATACACGAGAAGGACAGCGGCTCTCAGCAGTGAGGCACTCAAAAC
GGCCGCCGACCAGGCTCGCGAACACGACACAAACGAAGGTACACGAGAAGGACAGCGGCTCTCAG
CAAAAAGGTCCTCAAAACGGCCGCCGACGGCTCGCGAACACGACACACACGAAGGCTCGCGAACA
CGACACACACGAAGA
Found at i:881 original size:167 final size:169
Alignment explanation
Indices: 601--1047 Score: 650
Period size: 167 Copynumber: 2.6 Consensus size: 169
591 ACACACACGA
* * *
601 AGGCTCGCGAACACGACACACACGAAGATACACGAGAAGGACAGCGGCTTTCAGCAGTGAGGCAC
1 AGGCTCGCGGACACGACACACACGAAGGTACACGAGAAGGACAGCGGCTCTCAGCAGTGAGGCAC
*
666 TCAAAACGGCCGCCGACTGCGAGGCTCGCGAACACGACACAAACGAAGGTACACGAGAAG-AGCA
66 TCAAAACGGCCGCCGACTGCGAGGCTCGCGAACACGACACACACGAAGGTACACGAGAAGTA-CA
* * *
730 GCGGCTCTCAGCAGTGAGGCCCTCAAAACGGCCGCCG-AC
130 GCAGCTCTCAGCAGTGAGGCACTCAAAACAGCCGCCGAAC
***
769 -GGCTCGCGGACACGACACACACGAAGGTACACGAGAAGGACAGCGGCTCTCAGCAAAAAGGCAC
1 AGGCTCGCGGACACGACACACACGAAGGTACACGAGAAGGACAGCGGCTCTCAGCAGTGAGGCAC
** * * *
833 TCAAAACGGCCGCCGACAACGAGACTCGCGAACACGACACACACGAAGGTACGCGTGAAGTACAG
66 TCAAAACGGCCGCCGACTGCGAGGCTCGCGAACACGACACACACGAAGGTACACGAGAAGTACAG
898 CAGCTCTCAGCAGTGAGGCACTCAAAACAGCCGCCGACTAC
131 CAGCTCTCAGCAGTGAGGCACTCAAAACAGCCGCCGA--AC
* *
939 GAGGCTCGCGGACACAACACACACGAAGGTACACGAAAAGGACAGCGGCTCTCCA-CAGTGAGGC
1 -AGGCTCGCGGACACGACACACACGAAGGTACACGAGAAGGACAGCGGCTCT-CAGCAGTGAGGC
* *
1003 ACTCAAAACAGCCGCCGACTGCGAGGCTCGCGGACACGACACACA
64 ACTCAAAACGGCCGCCGACTGCGAGGCTCGCGAACACGACACACA
1048 GAGGTGCTCC
Statistics
Matches: 247, Mismatches: 25, Indels: 10
0.88 0.09 0.04
Matches are distributed among these distances:
167 148 0.60
168 1 0.00
170 2 0.01
172 94 0.38
173 2 0.01
ACGTcount: A:0.32, C:0.32, G:0.28, T:0.08
Consensus pattern (169 bp):
AGGCTCGCGGACACGACACACACGAAGGTACACGAGAAGGACAGCGGCTCTCAGCAGTGAGGCAC
TCAAAACGGCCGCCGACTGCGAGGCTCGCGAACACGACACACACGAAGGTACACGAGAAGTACAG
CAGCTCTCAGCAGTGAGGCACTCAAAACAGCCGCCGAAC
Found at i:1139 original size:2 final size:2
Alignment explanation
Indices: 1132--1158 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1122 TCCCGGGGAA
1132 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1159 ATTAGTTCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4982 original size:2 final size:2
Alignment explanation
Indices: 4975--4999 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4965 CTAATTTCAT
4975 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
5000 TCACAAGGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5792 original size:2 final size:2
Alignment explanation
Indices: 5787--5816 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5777 TATAAACGGC
5787 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5817 GATTTCCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6774 original size:29 final size:27
Alignment explanation
Indices: 6707--6783 Score: 91
Period size: 29 Copynumber: 2.7 Consensus size: 27
6697 GAACTTACAC
6707 AAAACGGCCAAATAAGCCCCTGAACTCT
1 AAAA-GGCCAAATAAGCCCCTGAACTCT
**
6735 AATTGCAGCCAAATAAGCCCCTGAACTCTTT
1 AAAAG--GCCAAATAAGCCCCTGAACTC--T
6766 AAAAGGCCAAATAAGCCC
1 AAAAGGCCAAATAAGCCC
6784 TTTTCTGATG
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
27 1 0.02
28 2 0.05
29 34 0.83
31 4 0.10
ACGTcount: A:0.39, C:0.30, G:0.14, T:0.17
Consensus pattern (27 bp):
AAAAGGCCAAATAAGCCCCTGAACTCT
Done.