Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014943.1 Corchorus capsularis cultivar CVL-1 contig14964, 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: 19882
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.36


Found at i:55 original size:2 final size:2

Alignment explanation


    Indices: 43--83  Score: 75
    Period size: 2  Copynumber: 21.0  Consensus size: 2

         33 TATACCTTAA

                                                                          
         43 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

         84 TAAATCTATA


Statistics
Matches: 38,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
   1    1  0.03
   2   37  0.97

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Found at i:1496 original size:16 final size:16

Alignment explanation


    Indices: 1473--1519  Score: 60
    Period size: 15  Copynumber: 3.0  Consensus size: 16

       1463 ATTATAACCC

                            
       1473 GATAACCCGAAACCGA
          1 GATAACCCGAAACCGA

            **          *   
       1489 TTTAACCCG-AATCGA
          1 GATAACCCGAAACCGA

                            
       1504 GATAACCCGAAACCGA
          1 GATAACCCGAAACCGA

       1520 CAAAATCCGA


Statistics
Matches: 24,  Mismatches: 6, Indels: 2
        0.75            0.19        0.06

Matches are distributed among these distances:
  15   12  0.50
  16   12  0.50

ACGTcount: A:0.40, C:0.30, G:0.17, T:0.13


Consensus pattern (16 bp):   
GATAACCCGAAACCGA

Found at i:17268 original size:33 final size:34

Alignment explanation


    Indices: 17192--17337  Score: 158
    Period size: 33  Copynumber: 4.4  Consensus size: 34

      17182 TAGACAAAGG

                                    *    *     
      17192 GTCGCGTGGCCGGTTG-TGGCCGGGCATGGCCGA-
          1 GTCGCGTGGCCGGTTGATGGCCGGACATGTCC-AT

                **            *               
      17225 GTCGTTTGGCCGGTTG-TAGCCGGACATGTCCAT
          1 GTCGCGTGGCCGGTTGATGGCCGGACATGTCCAT

                                *             
      17258 GTCGCGTGGCCGG-TGATGGTCGGACATGTCCAT
          1 GTCGCGTGGCCGGTTGATGGCCGGACATGTCCAT

                *               *             
      17291 GTCGTGTGGCCGG-TGATGGTCGGACATGTCCAT
          1 GTCGCGTGGCCGGTTGATGGCCGGACATGTCCAT

              *  *        
      17324 GTTGCATGGCCGGT
          1 GTCGCGTGGCCGGT

      17338 CTTGTGGCCG


Statistics
Matches: 97,  Mismatches: 13, Indels: 5
        0.84            0.11        0.04

Matches are distributed among these distances:
  32    3  0.03
  33   94  0.97

ACGTcount: A:0.10, C:0.24, G:0.40, T:0.25


Consensus pattern (34 bp):   
GTCGCGTGGCCGGTTGATGGCCGGACATGTCCAT

Done.