Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005504.1 Corchorus capsularis cultivar CVL-1 contig05522, 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: 3723
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36


Found at i:1259 original size:24 final size:24

Alignment explanation


    Indices: 1232--1278  Score: 58
    Period size: 24  Copynumber: 2.0  Consensus size: 24

       1222 CTTTTAATTT

                         *          
       1232 ATTTATAATTTGATAAATTAAGTA
          1 ATTTATAATTTGAAAAATTAAGTA

                * **               
       1256 ATTTTTCTTTTGAAAAATTAAGT
          1 ATTTATAATTTGAAAAATTAAGT

       1279 GATTAACTCT


Statistics
Matches: 19,  Mismatches: 4, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  24   19  1.00

ACGTcount: A:0.40, C:0.02, G:0.09, T:0.49


Consensus pattern (24 bp):   
ATTTATAATTTGAAAAATTAAGTA

Found at i:2153 original size:197 final size:199

Alignment explanation


    Indices: 1779--2156  Score: 555
    Period size: 197  Copynumber: 1.9  Consensus size: 199

       1769 AATCACTTTA

                            *                    *                     *     
       1779 TATAATTTTTCTTATAGGATTATTATACAATACACTTTTCAGTGTAAATTTTACACTCCCTAAAC
          1 TATAATTTTTCTTATAAGATTATTATACAATACACTTGTCAGTGTAAATTTTACACTCCATAAAC

                                              *                              
       1844 GGGTTAAGAAATTGACACAATACCCCATTTCATAGTCAATTAAATATTTAATATTAATACATATT
         66 GGGTTAAGAAATTGACACAATACCCCATTTCATAATCAATTAAATATTTAATATTAATACATATT

                                         * **       *                        
       1909 CCTTAAGGGGACACATGTCAACCCTTAAATCTTGCACATGTAGTCTGCTAAATTCGACTGACGGT
        131 CCTTAAGGGGACACATGTCAACCCTTAAACCCCGCACATGCAGTCTGCTAAATTCGACTGACGGT

                
       1974 ATAG
        196 ATAG

                                           *                    **    *    * 
       1978 TATAATTTTTCTTATAAGATTATTATACAATCCA-TTGTCAGTGTAAATTTTGGACTCTATAAGC
          1 TATAATTTTTCTTATAAGATTATTATACAATACACTTGTCAGTGTAAATTTTACACTCCATAAAC

                      *       *     *           *                            
       2042 GGGTTAAGAAGTTGACA-TATACCTCATTTCATAATTAATTAAATATTTAATATTAATACATA-T
         66 GGGTTAAGAAATTGACACAATACCCCATTTCATAATCAATTAAATATTTAATATTAATACATATT

             *                                    *             
       2105 CTTCTAAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAA
        131 CCT-TAAGGGGACACATGTCAACCCTTAAACCCCGCACATGCAGTCTGCTAA

       2157 TGTGATATCA


Statistics
Matches: 159,  Mismatches: 19, Indels: 4
        0.87            0.10        0.02

Matches are distributed among these distances:
 196    3  0.02
 197   84  0.53
 198   40  0.25
 199   32  0.20

ACGTcount: A:0.34, C:0.18, G:0.12, T:0.35


Consensus pattern (199 bp):   
TATAATTTTTCTTATAAGATTATTATACAATACACTTGTCAGTGTAAATTTTACACTCCATAAAC
GGGTTAAGAAATTGACACAATACCCCATTTCATAATCAATTAAATATTTAATATTAATACATATT
CCTTAAGGGGACACATGTCAACCCTTAAACCCCGCACATGCAGTCTGCTAAATTCGACTGACGGT
ATAG
Done.