Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011282.1 Corchorus capsularis cultivar CVL-1 contig11303, 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: 12334
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


Found at i:4479 original size:27 final size:27

Alignment explanation


    Indices: 4424--4475  Score: 70
    Period size: 26  Copynumber: 2.0  Consensus size: 27

       4414 ACCAACAAAG

                                *  *   
       4424 TTAGATGGTTGTTTTTTTGACATCAAT
          1 TTAGATGGTTGTTTTTTTGAAATAAAT

                      *               
       4451 TTAGAT-GTTTTTTTTTTGAAATAAA
          1 TTAGATGGTTGTTTTTTTGAAATAAA

       4476 ATTTCGAGTT


Statistics
Matches: 22,  Mismatches: 3, Indels: 1
        0.85            0.12        0.04

Matches are distributed among these distances:
  26   16  0.73
  27    6  0.27

ACGTcount: A:0.27, C:0.04, G:0.15, T:0.54


Consensus pattern (27 bp):   
TTAGATGGTTGTTTTTTTGAAATAAAT

Found at i:6199 original size:12 final size:12

Alignment explanation


    Indices: 6182--6208  Score: 54
    Period size: 12  Copynumber: 2.2  Consensus size: 12

       6172 ATAAGTATCC

                        
       6182 ATATCCATTTTA
          1 ATATCCATTTTA

                        
       6194 ATATCCATTTTA
          1 ATATCCATTTTA

               
       6206 ATA
          1 ATA

       6209 ACTGAATTGC


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   15  1.00

ACGTcount: A:0.37, C:0.15, G:0.00, T:0.48


Consensus pattern (12 bp):   
ATATCCATTTTA

Found at i:12115 original size:28 final size:29

Alignment explanation


    Indices: 12057--12135  Score: 106
    Period size: 28  Copynumber: 2.7  Consensus size: 29

      12047 CTAAATACCC

                                     *      
      12057 AAATAAATCCCTTATGTTTTGCTTTTGGGACA
          1 AAAT-AATCCCTTATG-TTT-CTTTCGGGACA

                                         
      12089 AAATAATCCCTTATGTTT-TTTCGGGACA
          1 AAATAATCCCTTATGTTTCTTTCGGGACA

              *                
      12117 AATTAATCCCTTATGTTTC
          1 AAATAATCCCTTATGTTTC

      12136 AAAAATGAGC


Statistics
Matches: 44,  Mismatches: 2, Indels: 5
        0.86            0.04        0.10

Matches are distributed among these distances:
  28   26  0.59
  30    3  0.07
  31   11  0.25
  32    4  0.09

ACGTcount: A:0.28, C:0.18, G:0.13, T:0.42


Consensus pattern (29 bp):   
AAATAATCCCTTATGTTTCTTTCGGGACA
Done.