Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015803.1 Corchorus capsularis cultivar CVL-1 contig15824, 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: 3688
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34


Found at i:2965 original size:26 final size:25

Alignment explanation


    Indices: 2929--2993  Score: 112
    Period size: 25  Copynumber: 2.6  Consensus size: 25

       2919 TGCATATAGC

                                      
       2929 GGCGTCTAGACGCCACTATTTTTAGA
          1 GGCGTCTAGACGCCACTA-TTTTAGA

                                    *
       2955 GGCGTCTAGACGCCACTATTTTAGC
          1 GGCGTCTAGACGCCACTATTTTAGA

                          
       2980 GGCGTCTAGACGCC
          1 GGCGTCTAGACGCC

       2994 GCTACTTATA


Statistics
Matches: 38,  Mismatches: 1, Indels: 1
        0.95            0.03        0.03

Matches are distributed among these distances:
  25   20  0.53
  26   18  0.47

ACGTcount: A:0.20, C:0.28, G:0.26, T:0.26


Consensus pattern (25 bp):   
GGCGTCTAGACGCCACTATTTTAGA

Found at i:2983 original size:25 final size:26

Alignment explanation


    Indices: 2925--2993  Score: 122
    Period size: 26  Copynumber: 2.7  Consensus size: 26

       2915 AATTTGCATA

                                      
       2925 TAGCGGCGTCTAGACGCCACTATTTT
          1 TAGCGGCGTCTAGACGCCACTATTTT

               *                      
       2951 TAGAGGCGTCTAGACGCCACTA-TTT
          1 TAGCGGCGTCTAGACGCCACTATTTT

                              
       2976 TAGCGGCGTCTAGACGCC
          1 TAGCGGCGTCTAGACGCC

       2994 GCTACTTATA


Statistics
Matches: 41,  Mismatches: 2, Indels: 1
        0.93            0.05        0.02

Matches are distributed among these distances:
  25   20  0.49
  26   21  0.51

ACGTcount: A:0.20, C:0.28, G:0.26, T:0.26


Consensus pattern (26 bp):   
TAGCGGCGTCTAGACGCCACTATTTT

Found at i:3106 original size:32 final size:31

Alignment explanation


    Indices: 3070--3140  Score: 81
    Period size: 32  Copynumber: 2.2  Consensus size: 31

       3060 ACTATGGCGC

                                             
       3070 GGCGTTTGGATATTTAGACGCCACTAAATA-AG
          1 GGCGTTT-GATATTTAGACGCCACTAAA-AGAG

                     * *          *         
       3102 GGCGTCTTGTTCTTTAGACGCCGCTAAAAGAG
          1 GGCGT-TTGATATTTAGACGCCACTAAAAGAG

                   
       3134 GGCGTTT
          1 GGCGTTT

       3141 TCTTTTCATG


Statistics
Matches: 34,  Mismatches: 3, Indels: 5
        0.81            0.07        0.12

Matches are distributed among these distances:
  31    3  0.09
  32   29  0.85
  33    2  0.06

ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30


Consensus pattern (31 bp):   
GGCGTTTGATATTTAGACGCCACTAAAAGAG
Done.