Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004300.1 Corchorus capsularis cultivar CVL-1 contig04308, 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, 646

Length: 1078
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36


Found at i:144 original size:29 final size:29

Alignment explanation


    Indices: 81--168  Score: 105
    Period size: 27  Copynumber: 3.1  Consensus size: 29

         71 CTTTTTGGTT

                                         *
         81 TAATTTTTTTATTATTATA-TATATAT-TT
          1 TAATTTTTTT-TTATTATATTATATATATA

                                     *    
        109 TAATTTTTTTATT-TTAT-TTAT-TTTATA
          1 TAATTTTTTT-TTATTATATTATATATATA

                                         
        136 TAATTTTTTTTTATTATATTATATATATA
          1 TAATTTTTTTTTATTATATTATATATATA

                
        165 TAAT
          1 TAAT

        169 ATTATAATAT


Statistics
Matches: 52,  Mismatches: 3, Indels: 9
        0.81            0.05        0.14

Matches are distributed among these distances:
  26    4  0.08
  27   22  0.42
  28   17  0.33
  29    9  0.17

ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68


Consensus pattern (29 bp):   
TAATTTTTTTTTATTATATTATATATATA

Found at i:146 original size:23 final size:26

Alignment explanation


    Indices: 81--252  Score: 96
    Period size: 24  Copynumber: 6.6  Consensus size: 26

         71 CTTTTTGGTT

                                        *
         81 TAATTTTT-TTATTATTATATATATATTT
          1 TAATTTTTATT-TTATTATAT-TATA-TA

                                   *    
        109 TAATTTTTTTATTTTATT-TATTTTATA
          1 TAA--TTTTTATTTTATTATATTATATA

                                      
        136 TAATTTTT-TTTTATTATATTATATA
          1 TAATTTTTATTTTATTATATTATATA

                 * *  *    *    *     
        161 T-A-TATAATATTATAATATAATAT-
          1 TAATTTTTATTTTATTATATTATATA

                                          
        184 TATATTTTTAATATATTATTATATT-TATA
          1 TA-ATTTTT-AT-T-TTATTATATTATATA

                 *                     
        213 TATATATTTA-TTTA-TATA-TATATA
          1 TA-ATTTTTATTTTATTATATTATATA

                             
        237 TATATTTTT-TTTTATT
          1 TA-ATTTTTATTTTATT

        253 TTTTTGTATA


Statistics
Matches: 114,  Mismatches: 15, Indels: 33
        0.70            0.09        0.20

Matches are distributed among these distances:
  23    4  0.04
  24   41  0.36
  25   19  0.17
  26    3  0.03
  27    6  0.05
  28   10  0.09
  29   19  0.17
  30   10  0.09
  31    2  0.02

ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65


Consensus pattern (26 bp):   
TAATTTTTATTTTATTATATTATATA

Found at i:160 original size:2 final size:2

Alignment explanation


    Indices: 150--241  Score: 76
    Period size: 2  Copynumber: 50.5  Consensus size: 2

        140 TTTTTTTTAT

                                                                          
        150 TA TA T- TA TA TA TA TA TA -A TA T- TA TA -A TA TA -A TA T- TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

                *  *                             *                 *     *
        186 TA TT TT TA -A TA TA T- TA T- TA TA TT TA TA TA TA TA TT TA TT
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

                                     
        225 TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA T

        242 TTTTTTTTAT


Statistics
Matches: 73,  Mismatches: 8, Indels: 18
        0.74            0.08        0.18

Matches are distributed among these distances:
   1    9  0.12
   2   64  0.88

ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57


Consensus pattern (2 bp):   
TA

Done.