Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006463.1 Corchorus capsularis cultivar CVL-1 contig06484, 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: 3591
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.27


Found at i:2595 original size:67 final size:68

Alignment explanation


    Indices: 2471--2751  Score: 317
    Period size: 65  Copynumber: 4.2  Consensus size: 68

       2461 AATGCTTCGA

                    *   *           * ** *       *                           
       2471 CTTTTCCATAAGTCAAACTCGTTTCCGTACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
          1 CTTTTCCACAAGCCAAACTCGTTTTCACATGAGTCA-ATCAAGCCTTGGTTCCATCCAAGCAGCA

            *   
       2536 GGGG
         65 AGGG

                                    *        *                 *             
       2540 CTTTTCCACAAGCCAAACTCG-TTCCACATGAGCCAATCAAGCCTTGGTTCTATCCAAGCAGCAA
          1 CTTTTCCACAAGCCAAACTCGTTTTCACATGAGTCAATCAAGCCTTGGTTCCATCCAAGCAGCAA

               
       2604 GGG
         66 GGG

                     *                            **                         
       2607 C--TTCCACCAGCCAAACTCGTTTTCACATGAGTC-ATTTAGCCTT-GTTCCATCCAAGCAGCAA
          1 CTTTTCCACAAGCCAAACTCGTTTTCACATGAGTCAATCAAGCCTTGGTTCCATCCAAGCAGCAA

               
       2668 GGG
         66 GGG

                                       *      * * **                         
       2671 CTTTTCCACAAGCCAAACTCGTTTTCATATGAGTTATTTTAGCCTTGGTTCCATCCAAGCAG---
          1 CTTTTCCACAAGCCAAACTCGTTTTCACATGAGTCAATCAAGCCTTGGTTCCATCCAAGCAGCAA

               
       2733 GGG
         66 GGG

                    *       
       2736 CTTTTCCATAAGCCAA
          1 CTTTTCCACAAGCCAA

       2752 GTTTCATTTC


Statistics
Matches: 187,  Mismatches: 20, Indels: 14
        0.85            0.09        0.06

Matches are distributed among these distances:
  64   21  0.11
  65   43  0.23
  66   40  0.21
  67   39  0.21
  68   25  0.13
  69   19  0.10

ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28


Consensus pattern (68 bp):   
CTTTTCCACAAGCCAAACTCGTTTTCACATGAGTCAATCAAGCCTTGGTTCCATCCAAGCAGCAA
GGG

Found at i:2750 original size:131 final size:134

Alignment explanation


    Indices: 2471--2751  Score: 340
    Period size: 131  Copynumber: 2.1  Consensus size: 134

       2461 AATGCTTCGA

                        *             **                                     
       2471 CTTTTCCATAAGTCAAACTCGTTTCCGTACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
          1 CTTTTCCATAAGCCAAACTCGTTTCCACACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA

            *                                                     *          
       2536 GGGGCTTTTCCACAAGCCAAACTCGTTCCACATGAGCCAATCAAGCCTTGGTTCTATCCAAGCAG
         66 AGGGCTTTTCCACAAGCCAAACTCGTTCCACATGAGCCAATCAAGCCTTGGTTCCATCCAAGCAG

                  
       2601 CAAGGG
        131 --AGGG

                    **              *    *          *                        
       2607 C--TTCCACCAGCCAAACTCGTTTTCACATGAGTCA-TT-TAGCCTT-GTTCCATCCAAGCAGCA
          1 CTTTTCCATAAGCCAAACTCGTTTCCACACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA

                                        *  *     ** * **                     
       2667 AGGGCTTTTCCACAAGCCAAACTCGTTTTCATATGAGTTATTTTAGCCTTGGTTCCATCCAAGCA
         66 AGGGCTTTTCCACAAGCCAAACTCG-TTCCACATGAGCCAATCAAGCCTTGGTTCCATCCAAGCA

                 
       2732 G-GGG
        130 GAGGG

                            
       2736 CTTTTCCATAAGCCAA
          1 CTTTTCCATAAGCCAA

       2752 GTTTCATTTC


Statistics
Matches: 123,  Mismatches: 19, Indels: 11
        0.80            0.12        0.07

Matches are distributed among these distances:
 129    4  0.03
 131   52  0.42
 132   38  0.31
 133    2  0.02
 134   26  0.21
 136    1  0.01

ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28


Consensus pattern (134 bp):   
CTTTTCCATAAGCCAAACTCGTTTCCACACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
AGGGCTTTTCCACAAGCCAAACTCGTTCCACATGAGCCAATCAAGCCTTGGTTCCATCCAAGCAG
AGGG
Done.