Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012981.1 Corchorus capsularis cultivar CVL-1 contig13002, 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: 6399
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31


Found at i:900 original size:5 final size:5

Alignment explanation


    Indices: 890--923  Score: 52
    Period size: 5  Copynumber: 7.0  Consensus size: 5

        880 CTGGTCGGAA

                                             *       
        890 ATTTT ATTTT ATTTT ATTTT ATTTT -TTAT ATTTT
          1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT

        924 TCGATATAAC


Statistics
Matches: 26,  Mismatches: 2, Indels: 2
        0.87            0.07        0.07

Matches are distributed among these distances:
   4    3  0.12
   5   23  0.88

ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79


Consensus pattern (5 bp):   
ATTTT

Found at i:1168 original size:7 final size:7

Alignment explanation


    Indices: 1156--1183  Score: 56
    Period size: 7  Copynumber: 4.0  Consensus size: 7

       1146 TTGTATTAGA

                   
       1156 TTTAGGG
          1 TTTAGGG

                   
       1163 TTTAGGG
          1 TTTAGGG

                   
       1170 TTTAGGG
          1 TTTAGGG

                   
       1177 TTTAGGG
          1 TTTAGGG

       1184 ATACGAACCT


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   21  1.00

ACGTcount: A:0.14, C:0.00, G:0.43, T:0.43


Consensus pattern (7 bp):   
TTTAGGG

Found at i:2103 original size:12 final size:12

Alignment explanation


    Indices: 2072--2103  Score: 55
    Period size: 12  Copynumber: 2.7  Consensus size: 12

       2062 TCGCATGCGA

                   *    
       2072 TGGCCGGGCATG
          1 TGGCCGGTCATG

                        
       2084 TGGCCGGTCATG
          1 TGGCCGGTCATG

                    
       2096 TGGCCGGT
          1 TGGCCGGT

       2104 GTTGCGCGGC


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  12   19  1.00

ACGTcount: A:0.06, C:0.25, G:0.47, T:0.22


Consensus pattern (12 bp):   
TGGCCGGTCATG

Found at i:5311 original size:148 final size:148

Alignment explanation


    Indices: 5043--5330  Score: 515
    Period size: 148  Copynumber: 1.9  Consensus size: 148

       5033 GATCATTGGC

                             *                                               
       5043 GTCGAGTCCTTGTTGCCTTTGGCCTTGACGTCTTCTGGGACGAGAGACCAGAGCTTGTCAATGTT
          1 GTCGAGTCCTTGTTGCCATTGGCCTTGACGTCTTCTGGGACGAGAGACCAGAGCTTGTCAATGTT

            *                                                                
       5108 TACGATGGGGCAAGAGATGTCGAAGAGGATCCTGTGGTGCTGCATACCTCCGGCGTTACCACGAC
         66 GACGATGGGGCAAGAGATGTCGAAGAGGATCCTGTGGTGCTGCATACCTCCGGCGTTACCACGAC

                              
       5173 CTCCAGGTTGTTTGTGGT
        131 CTCCAGGTTGTTTGTGGT

                                                                       *     
       5191 GTCGAGTCCTTGTTGCCATTGGCCTTGACGTCTTCTGGGACGAGAGACCAGAGCTTGTCGATGTT
          1 GTCGAGTCCTTGTTGCCATTGGCCTTGACGTCTTCTGGGACGAGAGACCAGAGCTTGTCAATGTT

                                            *                            *   
       5256 GACGATGGGGC-AGTAGATGTCGAAGAGGATCTTGTGGTGCTGCATACCTCCGGCGTTACCGCGA
         66 GACGATGGGGCAAG-AGATGTCGAAGAGGATCCTGTGGTGCTGCATACCTCCGGCGTTACCACGA

                       
       5320 CCTCCAGGTTG
        130 CCTCCAGGTTG

       5331 CTTGCGTTGT


Statistics
Matches: 134,  Mismatches: 5, Indels: 2
        0.95            0.04        0.01

Matches are distributed among these distances:
 147    2  0.01
 148  132  0.99

ACGTcount: A:0.17, C:0.23, G:0.32, T:0.27


Consensus pattern (148 bp):   
GTCGAGTCCTTGTTGCCATTGGCCTTGACGTCTTCTGGGACGAGAGACCAGAGCTTGTCAATGTT
GACGATGGGGCAAGAGATGTCGAAGAGGATCCTGTGGTGCTGCATACCTCCGGCGTTACCACGAC
CTCCAGGTTGTTTGTGGT
Done.