Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005944.1 Corchorus capsularis cultivar CVL-1 contig05962, 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: 3033
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29


Found at i:82 original size:33 final size:33

Alignment explanation


    Indices: 6--118  Score: 140
    Period size: 33  Copynumber: 3.4  Consensus size: 33

          1 AAAGG

                                   *    *     
          6 GTCGCGTGGCCGGTTGTGGCCGGGCATGGCCGA-
          1 GTCGCGTGGCCGGTTGTGGCCGGACATGTCC-AT

                **           *               
         39 GTCGTTTGGCCGGTTGTAGCCGGACATGTCCAT
          1 GTCGCGTGGCCGGTTGTGGCCGGACATGTCCAT

                                  *           
         72 GTCGCGTGGCCGG-TGATGGCCAGACATGTCCAT
          1 GTCGCGTGGCCGGTTG-TGGCCGGACATGTCCAT

                          
        105 GTCGCGTGGCCGGT
          1 GTCGCGTGGCCGGT

        119 GTTGCGCGGC


Statistics
Matches: 68,  Mismatches: 9, Indels: 5
        0.83            0.11        0.06

Matches are distributed among these distances:
  32    3  0.04
  33   65  0.96

ACGTcount: A:0.10, C:0.27, G:0.41, T:0.23


Consensus pattern (33 bp):   
GTCGCGTGGCCGGTTGTGGCCGGACATGTCCAT

Found at i:958 original size:33 final size:33

Alignment explanation


    Indices: 882--1027  Score: 152
    Period size: 33  Copynumber: 4.4  Consensus size: 33

        872 TAGACAAAGG

                       *         * *    *     
        882 GTCGCGTGGCCAGTTGTGGCCGGGCATGGCCGA-
          1 GTCGCGTGGCCGGTTGTGGCCAGACATGTCC-AT

                **           *   *           
        915 GTCGTTTGGCCGGTTGTAGCCGGACATGTCCAT
          1 GTCGCGTGGCCGGTTGTGGCCAGACATGTCCAT

                       *   *                 
        948 GTCGCGTGGCCTGTTATGGCCAGACATGTCCAT
          1 GTCGCGTGGCCGGTTGTGGCCAGACATGTCCAT

                *      *                      
        981 GTCGAGTGGCCTG-TGATGGCCAGACATGTCCAT
          1 GTCGCGTGGCCGGTTG-TGGCCAGACATGTCCAT

                          
       1014 GTCGCGTGGCCGGT
          1 GTCGCGTGGCCGGT

       1028 CTTGAGGCCA


Statistics
Matches: 94,  Mismatches: 16, Indels: 5
        0.82            0.14        0.04

Matches are distributed among these distances:
  32    2  0.02
  33   92  0.98

ACGTcount: A:0.12, C:0.26, G:0.37, T:0.25


Consensus pattern (33 bp):   
GTCGCGTGGCCGGTTGTGGCCAGACATGTCCAT

Found at i:2964 original size:33 final size:33

Alignment explanation


    Indices: 2869--2970  Score: 129
    Period size: 33  Copynumber: 3.2  Consensus size: 33

       2859 ATCAGATTTA

                                        *   *
       2869 TTTTCAATGC--T-ATCAACCAAAACAGGATTA
          1 TTTTCAATGCTATAATCAACCAAAACAGAATTG

               *                             
       2899 TTTGCAATGCTATAATCAACCAAAACAGAATTG
          1 TTTTCAATGCTATAATCAACCAAAACAGAATTG

                *        **                  
       2932 TTTTTAATGCTATGTTCAACCAAAACAGAATTG
          1 TTTTCAATGCTATAATCAACCAAAACAGAATTG

                  
       2965 TTTTCA
          1 TTTTCA

       2971 TCACAATTAG


Statistics
Matches: 61,  Mismatches: 8, Indels: 3
        0.85            0.11        0.04

Matches are distributed among these distances:
  30    9  0.15
  32    1  0.02
  33   51  0.84

ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33


Consensus pattern (33 bp):   
TTTTCAATGCTATAATCAACCAAAACAGAATTG
Done.