Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007388.1 Corchorus capsularis cultivar CVL-1 contig07409, 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: 4420
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33


Found at i:1197 original size:33 final size:32

Alignment explanation


    Indices: 1087--1191  Score: 149
    Period size: 32  Copynumber: 3.2  Consensus size: 32

       1077 ATTGGTCTAA

                                  *        *
       1087 CCGCCCCATGAGGGCGGCCTGCAGTGGCGAAA
          1 CCGCCCCATGAGGGCGGCCTGCCGTGGCGAAG

                                            
       1119 CCGCCCCATGAGGGCGGCCTGCCGTGGCGAAG
          1 CCGCCCCATGAGGGCGGCCTGCCGTGGCGAAG

                              *          *    
       1151 CCGCCCCAGTG-GGGCGGTCTGCCCGTGGTGAAG
          1 CCGCCCCA-TGAGGGCGGCCTG-CCGTGGCGAAG

                    
       1184 CCGCCCCA
          1 CCGCCCCA

       1192 GTGGGGAGGC


Statistics
Matches: 67,  Mismatches: 4, Indels: 3
        0.91            0.05        0.04

Matches are distributed among these distances:
  32   47  0.70
  33   20  0.30

ACGTcount: A:0.13, C:0.38, G:0.38, T:0.10


Consensus pattern (32 bp):   
CCGCCCCATGAGGGCGGCCTGCCGTGGCGAAG

Found at i:1210 original size:33 final size:32

Alignment explanation


    Indices: 1139--1219  Score: 101
    Period size: 33  Copynumber: 2.5  Consensus size: 32

       1129 AGGGCGGCCT

                   *                  *    *
       1139 GCCGTGGCGAAGCCGCCCCAGTGGGGCGGTCT
          1 GCCGTGGTGAAGCCGCCCCAGTGGGGAGGTCC

                                              
       1171 GCCCGTGGTGAAGCCGCCCCAGTGGGGAGGCTCC
          1 G-CCGTGGTGAAGCCGCCCCAGTGGGGAGG-TCC

                            
       1205 GCCGTGGCTG-AGCCG
          1 GCCGTGG-TGAAGCCG

       1220 TCCTAGTGAG


Statistics
Matches: 43,  Mismatches: 3, Indels: 5
        0.84            0.06        0.10

Matches are distributed among these distances:
  32    1  0.02
  33   37  0.86
  34    5  0.12

ACGTcount: A:0.10, C:0.35, G:0.43, T:0.12


Consensus pattern (32 bp):   
GCCGTGGTGAAGCCGCCCCAGTGGGGAGGTCC

Found at i:4394 original size:2 final size:2

Alignment explanation


    Indices: 4387--4420  Score: 68
    Period size: 2  Copynumber: 17.0  Consensus size: 2

       4377 ATCCTTACAG

                                                              
       4387 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   32  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Done.