Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015552.1 Corchorus capsularis cultivar CVL-1 contig15573, 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: 7916
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.33


Found at i:4440 original size:31 final size:31

Alignment explanation


    Indices: 4405--4469  Score: 96
    Period size: 31  Copynumber: 2.1  Consensus size: 31

       4395 ACGGTGCCAC

                         *                  
       4405 CCTGCGAGGACGGTTTGCCATGGTGT-TGCCG
          1 CCTGCGAGGACGGCTTGCCATGGT-TATGCCG

                 *                         
       4436 CCTGCTAGGACGGCTTGCCATGGTTATGCCG
          1 CCTGCGAGGACGGCTTGCCATGGTTATGCCG

               
       4467 CCT
          1 CCT

       4470 TGACAGGGCG


Statistics
Matches: 31,  Mismatches: 2, Indels: 2
        0.89            0.06        0.06

Matches are distributed among these distances:
  30    1  0.03
  31   30  0.97

ACGTcount: A:0.11, C:0.29, G:0.34, T:0.26


Consensus pattern (31 bp):   
CCTGCGAGGACGGCTTGCCATGGTTATGCCG

Found at i:4562 original size:33 final size:32

Alignment explanation


    Indices: 4472--4567  Score: 133
    Period size: 32  Copynumber: 3.0  Consensus size: 32

       4462 TGCCGCCTTG

                                             
       4472 ACAGGGCGGCACGC-CCATGGGATGCCGTCCTC
          1 ACAGGGCGGCA-GCACCATGGGATGCCGTCCTC

                       *                    
       4504 ACAGGGCGGCAACACCATGGGATGCCGTCCT-
          1 ACAGGGCGGCAGCACCATGGGATGCCGTCCTC

                                  *          
       4535 AGCAGGGCGGCATGCACCATGGCATGCCGTCCT
          1 A-CAGGGCGGCA-GCACCATGGGATGCCGTCCT

       4568 GCTAGGCCGG


Statistics
Matches: 58,  Mismatches: 3, Indels: 5
        0.88            0.05        0.08

Matches are distributed among these distances:
  31    2  0.03
  32   38  0.66
  33   18  0.31

ACGTcount: A:0.19, C:0.34, G:0.33, T:0.14


Consensus pattern (32 bp):   
ACAGGGCGGCAGCACCATGGGATGCCGTCCTC

Found at i:6384 original size:27 final size:26

Alignment explanation


    Indices: 6352--6419  Score: 100
    Period size: 26  Copynumber: 2.6  Consensus size: 26

       6342 GTCCAAGGGT

                                       
       6352 ATTTTGGTCATTTTTGCACCCAGGGGC
          1 ATTTTGGTCATTTTT-CACCCAGGGGC

                           *  *       
       6379 ATTTTGGTCATTTTTTACTCAGGGGC
          1 ATTTTGGTCATTTTTCACCCAGGGGC

                 *         
       6405 ATTTTAGTCATTTTT
          1 ATTTTGGTCATTTTT

       6420 AGGTTCACCT


Statistics
Matches: 38,  Mismatches: 3, Indels: 1
        0.90            0.07        0.02

Matches are distributed among these distances:
  26   23  0.61
  27   15  0.39

ACGTcount: A:0.16, C:0.16, G:0.21, T:0.47


Consensus pattern (26 bp):   
ATTTTGGTCATTTTTCACCCAGGGGC
Done.