Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01016264.1 Corchorus capsularis cultivar CVL-1 contig16285, 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: 3085
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29


Found at i:1304 original size:26 final size:26

Alignment explanation


    Indices: 1229--1357  Score: 154
    Period size: 28  Copynumber: 4.8  Consensus size: 26

       1219 CCTAGGAAGA

                       *        *     
       1229 CCTCCCCTGGCTCGCTGCT-AGGGAG
          1 CCTCCCCTGGCGCGCTGCTGGGGGAG

                  *                      
       1254 CCTCCCTTGGCGCGC-GCTGTCGGGGGAG
          1 CCTCCCCTGGCGCGCTGC--T-GGGGGAG

            *                         
       1282 TCTCCCCTGGCGCGCTGCTGGGGGAG
          1 CCTCCCCTGGCGCGCTGCTGGGGGAG

                                        
       1308 CCTCCCCTGGCGCGCGCTGCTGGGGGAG
          1 CCTCCCCT-G-GCGCGCTGCTGGGGGAG

            *                     
       1336 TCTCCCCTGGCGCGCTGCTGGG
          1 CCTCCCCTGGCGCGCTGCTGGG

       1358 CCTCCTCTAG


Statistics
Matches: 90,  Mismatches: 7, Indels: 13
        0.82            0.06        0.12

Matches are distributed among these distances:
  24    2  0.02
  25   13  0.14
  26   28  0.31
  27    3  0.03
  28   42  0.47
  29    2  0.02

ACGTcount: A:0.04, C:0.38, G:0.40, T:0.19


Consensus pattern (26 bp):   
CCTCCCCTGGCGCGCTGCTGGGGGAG

Found at i:1320 original size:54 final size:54

Alignment explanation


    Indices: 1230--1357  Score: 206
    Period size: 54  Copynumber: 2.4  Consensus size: 54

       1220 CTAGGAAGAC

                      *        *           *                       
       1230 CTCCCCTGGCTCGCTGCT-AGGGAGCCTCCCTTGGCGCGCGCTG-TCGGGGGAGT
          1 CTCCCCTGGCGCGCTGCTGGGGGAGCCTCCCCTGGCGCGCGCTGCT-GGGGGAGT

                                                                  
       1283 CTCCCCTGGCGCGCTGCTGGGGGAGCCTCCCCTGGCGCGCGCTGCTGGGGGAGT
          1 CTCCCCTGGCGCGCTGCTGGGGGAGCCTCCCCTGGCGCGCGCTGCTGGGGGAGT

                                 
       1337 CTCCCCTGGCGCGCTGCTGGG
          1 CTCCCCTGGCGCGCTGCTGGG

       1358 CCTCCTCTAG


Statistics
Matches: 70,  Mismatches: 3, Indels: 3
        0.92            0.04        0.04

Matches are distributed among these distances:
  53   17  0.24
  54   52  0.74
  55    1  0.01

ACGTcount: A:0.04, C:0.38, G:0.40, T:0.19


Consensus pattern (54 bp):   
CTCCCCTGGCGCGCTGCTGGGGGAGCCTCCCCTGGCGCGCGCTGCTGGGGGAGT

Found at i:1587 original size:2 final size:2

Alignment explanation


    Indices: 1580--1609  Score: 60
    Period size: 2  Copynumber: 15.0  Consensus size: 2

       1570 AACATAAGTA

                                                        
       1580 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

       1610 GATCATGCTT


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):   
AT

Done.