Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006542.1 Corchorus capsularis cultivar CVL-1 contig06563, 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: 24728
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34


Found at i:909 original size:5 final size:5

Alignment explanation


    Indices: 896--928  Score: 50
    Period size: 5  Copynumber: 6.8  Consensus size: 5

        886 TTTTTGCTAT

                *                                   
        896 AAAAA AAAAC AAAAC AAAAC AAAA- AAAAC AAAA
          1 AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAA

        929 ATAAAGTTTT


Statistics
Matches: 26,  Mismatches: 1, Indels: 2
        0.90            0.03        0.07

Matches are distributed among these distances:
   4    4  0.15
   5   22  0.85

ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00


Consensus pattern (5 bp):   
AAAAC

Found at i:923 original size:9 final size:9

Alignment explanation


    Indices: 897--929  Score: 57
    Period size: 9  Copynumber: 3.6  Consensus size: 9

        887 TTTTGCTATA

                     
        897 AAAAAAAAC
          1 AAAAAAAAC

                      
        906 AAAACAAAAC
          1 AAAA-AAAAC

                     
        916 AAAAAAAAC
          1 AAAAAAAAC

                 
        925 AAAAA
          1 AAAAA

        930 TAAAGTTTTG


Statistics
Matches: 23,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
   9   14  0.61
  10    9  0.39

ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00


Consensus pattern (9 bp):   
AAAAAAAAC

Found at i:8934 original size:7 final size:7

Alignment explanation


    Indices: 8923--8957  Score: 61
    Period size: 7  Copynumber: 5.0  Consensus size: 7

       8913 CATGAGAAGC

                   
       8923 CAAAAAA
          1 CAAAAAA

            *      
       8930 AAAAAAA
          1 CAAAAAA

                   
       8937 CAAAAAA
          1 CAAAAAA

                   
       8944 CAAAAAA
          1 CAAAAAA

                   
       8951 CAAAAAA
          1 CAAAAAA

       8958 AAACATATTG


Statistics
Matches: 26,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   7   26  1.00

ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00


Consensus pattern (7 bp):   
CAAAAAA

Found at i:20917 original size:139 final size:139

Alignment explanation


    Indices: 20667--20949  Score: 539
    Period size: 139  Copynumber: 2.0  Consensus size: 139

      20657 ATAATTAAAA

                                                               *             
      20667 TTGGATTATTTTCCAAGGAAAATGCTGATAAACCAAACCATTGAAACTACTTTCCATGGAATTTA
          1 TTGGATTATTTTCCAAGGAAAATGCTGATAAACCAAACCATTGAAACTACTCTCCATGGAATTTA

                                      *                                      
      20732 ATTGTTACTTTCCCTAGAGTTACTTTTCGTGGAATCACTCTCCCAAGAATCACTCTCCTATGGAG
         66 ATTGTTACTTTCCCTAGAGTTACTTTCCGTGGAATCACTCTCCCAAGAATCACTCTCCTATGGAG

                     
      20797 AGTTATTCC
        131 AGTTATTCC

                                                                             
      20806 TTGGATTATTTTCCAAGGAAAATGCTGATAAACCAAACCATTGAAACTACTCTCCATGGAATTTA
          1 TTGGATTATTTTCCAAGGAAAATGCTGATAAACCAAACCATTGAAACTACTCTCCATGGAATTTA

                                                                             
      20871 ATTGTTACTTTCCCTAGAGTTACTTTCCGTGGAATCACTCTCCCAAGAATCACTCTCCTATGGAG
         66 ATTGTTACTTTCCCTAGAGTTACTTTCCGTGGAATCACTCTCCCAAGAATCACTCTCCTATGGAG

                     
      20936 AGTTATTCC
        131 AGTTATTCC

            *    
      20945 ATGGA
          1 TTGGA

      20950 AAGCAACAAA


Statistics
Matches: 141,  Mismatches: 3, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
 139  141  1.00

ACGTcount: A:0.30, C:0.22, G:0.15, T:0.34


Consensus pattern (139 bp):   
TTGGATTATTTTCCAAGGAAAATGCTGATAAACCAAACCATTGAAACTACTCTCCATGGAATTTA
ATTGTTACTTTCCCTAGAGTTACTTTCCGTGGAATCACTCTCCCAAGAATCACTCTCCTATGGAG
AGTTATTCC

Found at i:22628 original size:37 final size:37

Alignment explanation


    Indices: 22578--22648  Score: 117
    Period size: 37  Copynumber: 1.9  Consensus size: 37

      22568 ATATAATTAT

                                  *               
      22578 TCATAAAGTTATGTCTAT-TTGGAAAGACATGTATTGA
          1 TCATAAAGTTATGTCTATATT-AAAAGACATGTATTGA

                                              
      22615 TCATAAAGTTATGTCTATATTAAAAGACATGTAT
          1 TCATAAAGTTATGTCTATATTAAAAGACATGTAT

      22649 GTTGATCAAG


Statistics
Matches: 32,  Mismatches: 1, Indels: 2
        0.91            0.03        0.06

Matches are distributed among these distances:
  37   30  0.94
  38    2  0.06

ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38


Consensus pattern (37 bp):   
TCATAAAGTTATGTCTATATTAAAAGACATGTATTGA
Done.