Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014274.1 Corchorus capsularis cultivar CVL-1 contig14295, 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: 13854
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:667 original size:67 final size:68

Alignment explanation


    Indices: 459--732  Score: 308
    Period size: 67  Copynumber: 4.0  Consensus size: 68

        449 CTAAAGATGA

                                  *       *                  *              *
        459 TAATCAATCCATGCATGTTATTGCTAT-TTTATTAATCAATCAATCAATCAACGTATCATCAACC
          1 TAATCAATCCATGCATGTTATTTCTATCTTAATTAATCAATCAATCAATAAACGTATCATCAACT

               
        523 ATC
         66 ATC

                                      *                                *   * 
        526 TAATCAATCCATGCATGTTAATATTATTATCTTATTAATTAATCAATCAATCAATAAACATATAA
          1 TAATCAATCCATGCATGTT-AT-TT-CTATC---TTAATTAATCAATCAATCAATAAACGTATCA

                     
        591 TCAACTATC
         60 TCAACTATC

                 *                                           *             * 
        600 TAATCTATCCATGCATGTTATTTCTATCTT-ATTAATCAATCAATCAATTAACGTATCATCAATT
          1 TAATCAATCCATGCATGTTATTTCTATCTTAATTAATCAATCAATCAATAAACGTATCATCAACT

               
        664 ATC
         66 ATC

                                           *           *         ** *        
        667 TAATCAATCCATGCATGTTATTAT-TAT-TTCATTAATCAATCGAT--ATAAATATCTCATCAAC
          1 TAATCAATCCATGCATGTTATT-TCTATCTTAATTAATCAATCAATCAATAAACGTATCATCAAC

                
        728 TATC
         65 TATC

             
        732 T
          1 T

        733 TATAAATCAA


Statistics
Matches: 178,  Mismatches: 20, Indels: 20
        0.82            0.09        0.09

Matches are distributed among these distances:
  65   17  0.10
  66    2  0.01
  67   89  0.50
  68    5  0.03
  69    1  0.01
  70    3  0.02
  71    4  0.02
  72    2  0.01
  73    2  0.01
  74   53  0.30

ACGTcount: A:0.38, C:0.19, G:0.04, T:0.39


Consensus pattern (68 bp):   
TAATCAATCCATGCATGTTATTTCTATCTTAATTAATCAATCAATCAATAAACGTATCATCAACT
ATC

Found at i:742 original size:104 final size:104

Alignment explanation


    Indices: 623--844  Score: 356
    Period size: 104  Copynumber: 2.1  Consensus size: 104

        613 CATGTTATTT

                                     *   *  *      *                    *    
        623 CTATCTTATTAATCAATCAATCAATTAACGTATCATCAATTATCTAATCAATCCATGCATGTTAT
          1 CTATCTTATTAATCAATCAATCAATAAACATACCATCAACTATCTAATCAATCCATGCATATTAT

                                                    
        688 TATTAT-TTCATTAATCAATCGATATAAATATCTCATCAA
         66 TATTATCTT-ATTAATCAATCGATATAAATATCTCATCAA

                     *       *                                               
        727 CTATCTTATAAATCAATTAATCAATAAACATACCATCAACTATCTAATCAATCCATGCATATTAT
          1 CTATCTTATTAATCAATCAATCAATAAACATACCATCAACTATCTAATCAATCCATGCATATTAT

                                             *     
        792 TATTATCTTATTAATCAATCGATATAAATATCTTATCAA
         66 TATTATCTTATTAATCAATCGATATAAATATCTCATCAA

                          
        831 CTATCTTATTAATC
          1 CTATCTTATTAATC

        845 TATGCATGTT


Statistics
Matches: 108,  Mismatches: 9, Indels: 2
        0.91            0.08        0.02

Matches are distributed among these distances:
 104  106  0.98
 105    2  0.02

ACGTcount: A:0.40, C:0.18, G:0.03, T:0.39


Consensus pattern (104 bp):   
CTATCTTATTAATCAATCAATCAATAAACATACCATCAACTATCTAATCAATCCATGCATATTAT
TATTATCTTATTAATCAATCGATATAAATATCTCATCAA

Found at i:2317 original size:31 final size:31

Alignment explanation


    Indices: 2279--2344  Score: 123
    Period size: 31  Copynumber: 2.1  Consensus size: 31

       2269 TGTCAATTTA

                      *                    
       2279 GAAATATATATGAAAATAAAGGGTACAATCG
          1 GAAATATATACGAAAATAAAGGGTACAATCG

                                           
       2310 GAAATATATACGAAAATAAAGGGTACAATCG
          1 GAAATATATACGAAAATAAAGGGTACAATCG

                
       2341 GAAA
          1 GAAA

       2345 ACATAAAGTT


Statistics
Matches: 34,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  31   34  1.00

ACGTcount: A:0.53, C:0.08, G:0.20, T:0.20


Consensus pattern (31 bp):   
GAAATATATACGAAAATAAAGGGTACAATCG

Found at i:11472 original size:2 final size:2

Alignment explanation


    Indices: 11465--11492  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

      11455 AGAATAGAAT

                                                     
      11465 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

      11493 CTAGAATTTG


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

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


Consensus pattern (2 bp):   
TA

Done.