Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012319.1 Corchorus capsularis cultivar CVL-1 contig12340, 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: 19908
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:2745 original size:13 final size:13

Alignment explanation


    Indices: 2729--2770  Score: 52
    Period size: 12  Copynumber: 3.4  Consensus size: 13

       2719 AATAGTTTTG

                         
       2729 AATTTATCCAATA
          1 AATTTATCCAATA

                  **     
       2742 AATTTAAGC-ATA
          1 AATTTATCCAATA

                         
       2754 AA-TTATCCAATA
          1 AATTTATCCAATA

                 
       2766 AATTT
          1 AATTT

       2771 CCGTCAGTGA


Statistics
Matches: 23,  Mismatches: 4, Indels: 4
        0.74            0.13        0.13

Matches are distributed among these distances:
  11    4  0.17
  12   10  0.43
  13    9  0.39

ACGTcount: A:0.48, C:0.12, G:0.02, T:0.38


Consensus pattern (13 bp):   
AATTTATCCAATA

Found at i:14106 original size:28 final size:29

Alignment explanation


    Indices: 14051--14109  Score: 93
    Period size: 28  Copynumber: 2.0  Consensus size: 29

      14041 TGAAGTTTGA

                                           
      14051 AGAATAAATAAGTAATAAAATAAATAAAGAG
          1 AGAATAAATAAG--ATAAAATAAATAAAGAG

                                         
      14082 AGAATAAATAAG-TAAAATAAATAAAGAG
          1 AGAATAAATAAGATAAAATAAATAAAGAG

      14110 TAACAAAATA


Statistics
Matches: 28,  Mismatches: 0, Indels: 3
        0.90            0.00        0.10

Matches are distributed among these distances:
  28   16  0.57
  31   12  0.43

ACGTcount: A:0.68, C:0.00, G:0.14, T:0.19


Consensus pattern (29 bp):   
AGAATAAATAAGATAAAATAAATAAAGAG

Found at i:14831 original size:81 final size:80

Alignment explanation


    Indices: 14685--14860  Score: 178
    Period size: 81  Copynumber: 2.2  Consensus size: 80

      14675 AACTGTCGAT

                          *       **           **                       *    
      14685 TTCAAAAATGGATTCGATGGACGGTGAGATTGTGCCCCTGTTACTTCCCCAACCTTGTTTGCTTC
          1 TTCAAAAATGGATTAGATGGACCCTGAGATTGT-CAACTGTTACTTCCCCAACCTTGTTTACTTC

               *             
      14750 CTCTTTG-TTTGAAGAC
         65 CTCATTGTTTTGAA-AC

                                                            *        *       
      14766 TTCAAAAATGGATTAGATGGACCCTGAGATTGT-AACTGATTCACTTCTCCAA-CTTTTTTCACT
          1 TTCAAAAATGGATTAGATGGACCCTGAGATTGTCAACTG-TT-ACTTCCCCAACCTTGTTT-ACT

                *         *   
      14829 TCCTGATTGTTTTGCAAC
         63 TCCTCATTGTTTTGAAAC

                  *       
      14847 TTCAAAGATGGATT
          1 TTCAAAAATGGATT

      14861 GGAACAACGT


Statistics
Matches: 79,  Mismatches: 12, Indels: 8
        0.80            0.12        0.08

Matches are distributed among these distances:
  79    3  0.04
  80    8  0.10
  81   63  0.80
  82    5  0.06

ACGTcount: A:0.24, C:0.21, G:0.18, T:0.37


Consensus pattern (80 bp):   
TTCAAAAATGGATTAGATGGACCCTGAGATTGTCAACTGTTACTTCCCCAACCTTGTTTACTTCC
TCATTGTTTTGAAAC
Done.