Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005678.1 Corchorus capsularis cultivar CVL-1 contig05696, 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: 7013
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33


Found at i:904 original size:26 final size:26

Alignment explanation


    Indices: 864--914  Score: 86
    Period size: 26  Copynumber: 2.0  Consensus size: 26

        854 CCTTGTAGGG

                                      
        864 GTCGTACGTGCGAGGTCACGTGTGGA
          1 GTCGTACGTGCGAGGTCACGTGTGGA

                                      
        890 GTCGTACGTTG-GAGGTCACGTGTGG
          1 GTCGTACG-TGCGAGGTCACGTGTGG

        915 GGTGCCAGCT


Statistics
Matches: 24,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
  26   22  0.92
  27    2  0.08

ACGTcount: A:0.14, C:0.18, G:0.43, T:0.25


Consensus pattern (26 bp):   
GTCGTACGTGCGAGGTCACGTGTGGA

Found at i:1121 original size:2 final size:2

Alignment explanation


    Indices: 1116--1145  Score: 60
    Period size: 2  Copynumber: 15.0  Consensus size: 2

       1106 TTGAAAAGTT

                                                        
       1116 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

       1146 AAAGAACTAC


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   28  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:4057 original size:29 final size:30

Alignment explanation


    Indices: 3993--4056  Score: 98
    Period size: 29  Copynumber: 2.2  Consensus size: 30

       3983 AGCAACTAAA

                              *           
       3993 GGAAAAATGTTTTTTTTTGTGCCAAAAAAC
          1 GGAAAAATGTTTTTTTTTCTGCCAAAAAAC

                                          
       4023 GGAAAAATG-TTTTTTTTCTGCC-AAAAA-
          1 GGAAAAATGTTTTTTTTTCTGCCAAAAAAC

                   
       4050 GGAAAAA
          1 GGAAAAA

       4057 ATGATTAGTA


Statistics
Matches: 33,  Mismatches: 1, Indels: 3
        0.89            0.03        0.08

Matches are distributed among these distances:
  27    7  0.21
  28    5  0.15
  29   12  0.36
  30    9  0.27

ACGTcount: A:0.41, C:0.09, G:0.17, T:0.33


Consensus pattern (30 bp):   
GGAAAAATGTTTTTTTTTCTGCCAAAAAAC
Done.