Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01003749.1 Corchorus capsularis cultivar CVL-1 contig03757, 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, 704
Length: 1174
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.33
Found at i:712 original size:49 final size:49
Alignment explanation
Indices: 635--844 Score: 323
Period size: 49 Copynumber: 4.3 Consensus size: 49
625 TCTCTTAATT
* * * *
635 TTCAGTTTTTACCTACTTTTTCCTAAAGCGCCCTTCCCAGACGGAAGCCA
1 TTCA-TTTTTACTTGCTATTTCCCAAAGCGCCCTTCCCAGACGGAAGCCA
685 TTCATTTTTACTTGCTATTTCCCAAAGCGCCCTTCCCAGACGGAAGCCA
1 TTCATTTTTACTTGCTATTTCCCAAAGCGCCCTTCCCAGACGGAAGCCA
* *
734 TTTATTCTTACTTGCTATTTCCCAAAGCGCCCTTCCCAGACGGAAGCCAA
1 TTCATTTTTACTTGCTATTTCCCAAAGCGCCCTTCCCAGACGGAAGCC-A
**
784 TT-ATTTTCGCTTGCTATTTCCCAAAGCGCCCTTCCCAGACGGAAGCCA
1 TTCATTTTTACTTGCTATTTCCCAAAGCGCCCTTCCCAGACGGAAGCCA
832 TTCATTTTTACTT
1 TTCATTTTTACTT
845 ACGGAAGCCA
Statistics
Matches: 147, Mismatches: 11, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
48 3 0.02
49 137 0.93
50 7 0.05
ACGTcount: A:0.22, C:0.31, G:0.14, T:0.33
Consensus pattern (49 bp):
TTCATTTTTACTTGCTATTTCCCAAAGCGCCCTTCCCAGACGGAAGCCA
Found at i:822 original size:98 final size:98
Alignment explanation
Indices: 653--1160 Score: 572
Period size: 98 Copynumber: 4.9 Consensus size: 98
643 TTACCTACTT
*
653 TTTCCTAAAGCGCCCTTCCCAGACGGAAGCC-ATTCATTTTTACTTGCTATTTCCCAAAGCGCCC
1 TTTCCCAAAGCGCCCTTCCCAGACGGAAGCCAATT-ATTTTTACTTGCTATTTCCCAAAGCGCCC
*
717 TTCCCAGACGGAAGCCATTTATTCTTACTTGCTA
65 TTCCCAGACGGAAGCCATTTATTTTTACTTGCTA
**
751 TTTCCCAAAGCGCCCTTCCCAGACGGAAGCCAATTATTTTCGCTTGCTATTTCCCAAAGCGCCCT
1 TTTCCCAAAGCGCCCTTCCCAGACGGAAGCCAATTATTTTTACTTGCTATTTCCCAAAGCGCCCT
* *
816 TCCCAGACGGAAGCCATTCATTTTTACTTACGGAAGCCATT
66 TCCCAGACGGAAGCCATTTATTTTTACTT------G-C-TA
** ** * *
857 TATTCTTACTTGCTATTTCCCAAAGCGCCCTTCCCAGACGGAAGCC-ATTCATCTTTACTTGCTA
1 T-TTCCCA-AAGC----GCCC---------TTCCCAGACGGAAGCCAATT-ATTTTTACTTGCTA
* * *
921 TTTCACAAAACGCCCTTCCCAGACGGAAGCCATTCATTTTTACTTGCTA
50 TTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTTATTTTTACTTGCTA
* * *
970 TCTCCCAAAAGCGCCCTTCCCAGACGGAAGCCATTTATTTTTACTTGCTATTTCCCAAAG-GTTC
1 TTTCCC-AAAGCGCCCTTCCCAGACGGAAGCCAATTATTTTTACTTGCTATTTCCCAAAGCG-CC
1034 CTTCCCAGACGGAAGCCATTTATTTTTACTTGCTA
64 CTTCCCAGACGGAAGCCATTTATTTTTACTTGCTA
*
1069 TTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTTATTTTTACTTGCTATTTCCCAAAGCGCCCT
1 TTTCCCAAAGCGCCCTTCCCAGACGGAAGCCAATTATTTTTACTTGCTATTTCCCAAAGCGCCCT
*
1134 TCCCAGACGGAAGCCATTTATCTTTAC
66 TCCCAGACGGAAGCCATTTATTTTTAC
1161 CTACTTTCTC
Statistics
Matches: 349, Mismatches: 32, Indels: 58
0.79 0.07 0.13
Matches are distributed among these distances:
98 168 0.48
99 81 0.23
100 2 0.01
104 1 0.00
105 1 0.00
106 2 0.01
107 4 0.01
108 5 0.01
112 7 0.02
113 3 0.01
114 1 0.00
115 1 0.00
120 3 0.01
121 70 0.20
ACGTcount: A:0.23, C:0.31, G:0.14, T:0.31
Consensus pattern (98 bp):
TTTCCCAAAGCGCCCTTCCCAGACGGAAGCCAATTATTTTTACTTGCTATTTCCCAAAGCGCCCT
TCCCAGACGGAAGCCATTTATTTTTACTTGCTA
Found at i:852 original size:23 final size:23
Alignment explanation
Indices: 822--867 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
812 CCCTTCCCAG
*
822 ACGGAAGCCATTCATTTTTACTT
1 ACGGAAGCCATTCATTCTTACTT
*
845 ACGGAAGCCATTTATTCTTACTT
1 ACGGAAGCCATTCATTCTTACTT
868 GCTATTTCCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.26, C:0.22, G:0.13, T:0.39
Consensus pattern (23 bp):
ACGGAAGCCATTCATTCTTACTT
Found at i:890 original size:72 final size:72
Alignment explanation
Indices: 773--916 Score: 245
Period size: 72 Copynumber: 2.0 Consensus size: 72
763 CCCTTCCCAG
* *
773 ACGGAAGCCAATTATTTTCGCTTGCTATTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTCATT
1 ACGGAAGCCAATTATTTTCACTTGCTATTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTCATC
838 TTTACTT
66 TTTACTT
*
845 ACGGAAGCCATTTATTCTT-ACTTGCTATTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTCAT
1 ACGGAAGCCAATTATT-TTCACTTGCTATTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTCAT
909 CTTTACTT
65 CTTTACTT
917 GCTATTTCAC
Statistics
Matches: 68, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
72 66 0.97
73 2 0.03
ACGTcount: A:0.24, C:0.30, G:0.15, T:0.32
Consensus pattern (72 bp):
ACGGAAGCCAATTATTTTCACTTGCTATTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTCATC
TTTACTT
Found at i:938 original size:121 final size:121
Alignment explanation
Indices: 724--965 Score: 425
Period size: 121 Copynumber: 2.0 Consensus size: 121
714 CCCTTCCCAG
724 ACGGAAGCCATTTATTCTTACTTGCTATTTCCCAAAGCGCCCTTCCCAGACGGAAGCCAATTATT
1 ACGGAAGCCATTTATTCTTACTTGCTATTTCCCAAAGCGCCCTTCCCAGACGGAAGCCAATTATT
* * *
789 TTCGCTTGCTATTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTCATTTTTACTT
66 TTCACTTGCTATTTCACAAAACGCCCTTCCCAGACGGAAGCCATTCATTTTTACTT
845 ACGGAAGCCATTTATTCTTACTTGCTATTTCCCAAAGCGCCCTTCCCAGACGGAAGCC-ATTCAT
1 ACGGAAGCCATTTATTCTTACTTGCTATTTCCCAAAGCGCCCTTCCCAGACGGAAGCCAATT-AT
909 CTTT-ACTTGCTATTTCACAAAACGCCCTTCCCAGACGGAAGCCATTCATTTTTACTT
65 -TTTCACTTGCTATTTCACAAAACGCCCTTCCCAGACGGAAGCCATTCATTTTTACTT
966 GCTATCTCCC
Statistics
Matches: 116, Mismatches: 3, Indels: 4
0.94 0.02 0.03
Matches are distributed among these distances:
120 3 0.03
121 110 0.95
122 3 0.03
ACGTcount: A:0.24, C:0.31, G:0.14, T:0.31
Consensus pattern (121 bp):
ACGGAAGCCATTTATTCTTACTTGCTATTTCCCAAAGCGCCCTTCCCAGACGGAAGCCAATTATT
TTCACTTGCTATTTCACAAAACGCCCTTCCCAGACGGAAGCCATTCATTTTTACTT
Found at i:969 original size:170 final size:171
Alignment explanation
Indices: 675--1015 Score: 562
Period size: 170 Copynumber: 2.0 Consensus size: 171
665 CCCTTCCCAG
* *
675 ACGGAAGCCATTCATTTTTACTTGCTATTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTTATT
1 ACGGAAGCCATTCATTCTTACTTGCTATTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTCATT
* * * *
740 CTTACTTGCTATTTCCCAAAGCGCCCTTCCCAGACGGAAGCCAATTATTTTCGCTTGCTATTTCC
66 CTTACTTGCTATTTCACAAAACGCCCTTCCCAGACGGAAGCCAATTATTTTCACTTGCTATCTCC
805 C-AAAGCGCCCTTCCCAGACGGAAGCCATTCATTTTTACTT
131 CAAAAGCGCCCTTCCCAGACGGAAGCCATTCATTTTTACTT
*
845 ACGGAAGCCATTTATTCTTACTTGCTATTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTCA-T
1 ACGGAAGCCATTCATTCTTACTTGCTATTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTCATT
*
909 CTTTACTTGCTATTTCACAAAACGCCCTTCCCAGACGGAAGCC-ATTCATTTTTACTTGCTATCT
66 C-TTACTTGCTATTTCACAAAACGCCCTTCCCAGACGGAAGCCAATT-ATTTTCACTTGCTATCT
*
973 CCCAAAAGCGCCCTTCCCAGACGGAAGCCATTTATTTTTACTT
129 CCCAAAAGCGCCCTTCCCAGACGGAAGCCATTCATTTTTACTT
1016 GCTATTTCCC
Statistics
Matches: 159, Mismatches: 9, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
169 5 0.03
170 116 0.73
171 38 0.24
ACGTcount: A:0.24, C:0.31, G:0.14, T:0.31
Consensus pattern (171 bp):
ACGGAAGCCATTCATTCTTACTTGCTATTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTCATT
CTTACTTGCTATTTCACAAAACGCCCTTCCCAGACGGAAGCCAATTATTTTCACTTGCTATCTCC
CAAAAGCGCCCTTCCCAGACGGAAGCCATTCATTTTTACTT
Found at i:1113 original size:148 final size:147
Alignment explanation
Indices: 845--1160 Score: 526
Period size: 148 Copynumber: 2.1 Consensus size: 147
835 ATTTTTACTT
*
845 ACGGAAGCCATTTATTCTTACTTGCTATTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTCATC
1 ACGGAAGCCATTTATTTTTACTTGCTATTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTCATC
910 TTTACTTGCTATTTCACAAAACGCCCTTCCCAGACGGAAGCCATTCATTTTTACTTGCTATCTCC
66 TTTACTTGCTATTTCACAAAACGCCCTTCCCAGACGGAAGCCATTCATTTTTACTTGCTATCTCC
975 CAAAAGCGCCCTTCCCAG
131 C-AAAGCGCCCTTCCCAG
* *
993 ACGGAAGCCATTTATTTTTACTTGCTATTTCCCAAAG-GTTCCTTCCCAGACGGAAGCCATTTAT
1 ACGGAAGCCATTTATTTTTACTTGCTATTTCCCAAAGCG-CCCTTCCCAGACGGAAGCCATTCAT
* * * * *
1057 TTTTACTTGCTATTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTTATTTTTACTTGCTATTTC
65 CTTTACTTGCTATTTCACAAAACGCCCTTCCCAGACGGAAGCCATTCATTTTTACTTGCTATCTC
1122 CCAAAGCGCCCTTCCCAG
130 CCAAAGCGCCCTTCCCAG
*
1140 ACGGAAGCCATTTATCTTTAC
1 ACGGAAGCCATTTATTTTTAC
1161 CTACTTTCTC
Statistics
Matches: 158, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
147 37 0.23
148 121 0.77
ACGTcount: A:0.24, C:0.31, G:0.14, T:0.32
Consensus pattern (147 bp):
ACGGAAGCCATTTATTTTTACTTGCTATTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTCATC
TTTACTTGCTATTTCACAAAACGCCCTTCCCAGACGGAAGCCATTCATTTTTACTTGCTATCTCC
CAAAGCGCCCTTCCCAG
Found at i:1174 original size:49 final size:49
Alignment explanation
Indices: 845--1160 Score: 526
Period size: 49 Copynumber: 6.4 Consensus size: 49
835 ATTTTTACTT
*
845 ACGGAAGCCATTTATTCTTACTTGCTATTTCCCAAAGCGCCCTTCCCAG
1 ACGGAAGCCATTTATTTTTACTTGCTATTTCCCAAAGCGCCCTTCCCAG
* * * *
894 ACGGAAGCCATTCATCTTTACTTGCTATTTCACAAAACGCCCTTCCCAG
1 ACGGAAGCCATTTATTTTTACTTGCTATTTCCCAAAGCGCCCTTCCCAG
* *
943 ACGGAAGCCATTCATTTTTACTTGCTATCTCCCAAAAGCGCCCTTCCCAG
1 ACGGAAGCCATTTATTTTTACTTGCTATTTCCC-AAAGCGCCCTTCCCAG
*
993 ACGGAAGCCATTTATTTTTACTTGCTATTTCCCAAAG-GTTCCTTCCCAG
1 ACGGAAGCCATTTATTTTTACTTGCTATTTCCCAAAGCG-CCCTTCCCAG
1042 ACGGAAGCCATTTATTTTTACTTGCTATTTCCCAAAGCGCCCTTCCCAG
1 ACGGAAGCCATTTATTTTTACTTGCTATTTCCCAAAGCGCCCTTCCCAG
1091 ACGGAAGCCATTTATTTTTACTTGCTATTTCCCAAAGCGCCCTTCCCAG
1 ACGGAAGCCATTTATTTTTACTTGCTATTTCCCAAAGCGCCCTTCCCAG
*
1140 ACGGAAGCCATTTATCTTTAC
1 ACGGAAGCCATTTATTTTTAC
1161 CTACTTTCTC
Statistics
Matches: 250, Mismatches: 14, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
48 1 0.00
49 202 0.81
50 47 0.19
ACGTcount: A:0.24, C:0.31, G:0.14, T:0.32
Consensus pattern (49 bp):
ACGGAAGCCATTTATTTTTACTTGCTATTTCCCAAAGCGCCCTTCCCAG
Done.