Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006148.1 Corchorus capsularis cultivar CVL-1 contig06166, 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: 6883
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34


Found at i:161 original size:33 final size:33

Alignment explanation


    Indices: 64--168  Score: 122
    Period size: 33  Copynumber: 3.2  Consensus size: 33

         54 TTGCAAAGAA

                                     *      * 
         64 TGTTTT-AGATGTTGTTTGCGATGATACTAAACC
          1 TGTTTTAAG-TGTTGTTTGCGATGAAACTAAATC

             **                *    *       *
         97 TAATTTAAGTGTTGTTTGCAATGACACTAAATT
          1 TGTTTTAAGTGTTGTTTGCGATGAAACTAAATC

                              *              
        130 TGTTTTAAGTGTTGTTTGTGATGAAACTAAATC
          1 TGTTTTAAGTGTTGTTTGCGATGAAACTAAATC

                  
        163 TGTTTT
          1 TGTTTT

        169 GGATGCTAAT


Statistics
Matches: 59,  Mismatches: 12, Indels: 2
        0.81            0.16        0.03

Matches are distributed among these distances:
  33   57  0.97
  34    2  0.03

ACGTcount: A:0.27, C:0.09, G:0.19, T:0.46


Consensus pattern (33 bp):   
TGTTTTAAGTGTTGTTTGCGATGAAACTAAATC

Found at i:224 original size:33 final size:33

Alignment explanation


    Indices: 184--269  Score: 145
    Period size: 33  Copynumber: 2.6  Consensus size: 33

        174 CTAATTGTGA

                                         *   
        184 TGAAAATAATTCTGTTTTGGTTGATCATAGCAT
          1 TGAAAATAATTCTGTTTTGGTTGATCATAACAT

              *          *                   
        217 TGCAAATAATTCTATTTTGGTTGATCATAACAT
          1 TGAAAATAATTCTGTTTTGGTTGATCATAACAT

                                
        250 TGAAAATAATTCTGTTTTGG
          1 TGAAAATAATTCTGTTTTGG

        270 GTGAAAAGAA


Statistics
Matches: 48,  Mismatches: 5, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  33   48  1.00

ACGTcount: A:0.31, C:0.09, G:0.16, T:0.43


Consensus pattern (33 bp):   
TGAAAATAATTCTGTTTTGGTTGATCATAACAT

Found at i:1977 original size:30 final size:30

Alignment explanation


    Indices: 1937--1997  Score: 86
    Period size: 30  Copynumber: 2.0  Consensus size: 30

       1927 ATCCATTGGT

                                  *       
       1937 CGGTTATGGCCAGTTGCCCCATGCGATGGC
          1 CGGTTATGGCCAGTTGCCCCATCCGATGGC

                 *     *     *            
       1967 CGGTTGTGGCCGGTTGCTCCATCCGATGGC
          1 CGGTTATGGCCAGTTGCCCCATCCGATGGC

             
       1997 C
          1 C

       1998 CATGCGATGG


Statistics
Matches: 27,  Mismatches: 4, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  30   27  1.00

ACGTcount: A:0.10, C:0.31, G:0.34, T:0.25


Consensus pattern (30 bp):   
CGGTTATGGCCAGTTGCCCCATCCGATGGC

Found at i:5128 original size:13 final size:13

Alignment explanation


    Indices: 5110--5134  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       5100 ATAGGCCTAA

                         
       5110 TAAGAGTAACTTG
          1 TAAGAGTAACTTG

                        
       5123 TAAGAGTAACTT
          1 TAAGAGTAACTT

       5135 CTTTCTTCTC


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.40, C:0.08, G:0.20, T:0.32


Consensus pattern (13 bp):   
TAAGAGTAACTTG

Found at i:6399 original size:31 final size:31

Alignment explanation


    Indices: 6361--6422  Score: 88
    Period size: 31  Copynumber: 2.0  Consensus size: 31

       6351 TATGTTAGAC

                       *       *           
       6361 AAATAAGGATATAATAAACGTTTCAAAAGTT
          1 AAATAAGGATACAATAAACATTTCAAAAGTT

                    *       *              
       6392 AAATAAGGGTACAATAGACATTTCAAAAGTT
          1 AAATAAGGATACAATAAACATTTCAAAAGTT

       6423 TTACAAAACT


Statistics
Matches: 27,  Mismatches: 4, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  31   27  1.00

ACGTcount: A:0.50, C:0.08, G:0.15, T:0.27


Consensus pattern (31 bp):   
AAATAAGGATACAATAAACATTTCAAAAGTT

Found at i:6567 original size:21 final size:21

Alignment explanation


    Indices: 6541--6582  Score: 84
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       6531 CTTATCGTCC

                                 
       6541 CGTTTTAGTCATTTCTCACAT
          1 CGTTTTAGTCATTTCTCACAT

                                 
       6562 CGTTTTAGTCATTTCTCACAT
          1 CGTTTTAGTCATTTCTCACAT

       6583 GCGGTTACAC


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

Matches are distributed among these distances:
  21   21  1.00

ACGTcount: A:0.19, C:0.24, G:0.10, T:0.48


Consensus pattern (21 bp):   
CGTTTTAGTCATTTCTCACAT
Done.