Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011129.1 Corchorus capsularis cultivar CVL-1 contig11150, 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: 20044
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33


Found at i:283 original size:19 final size:19

Alignment explanation


    Indices: 261--298  Score: 58
    Period size: 19  Copynumber: 2.0  Consensus size: 19

        251 CCGACGTGGC

                     *         
        261 ATGCCACATGTACTAAAAA
          1 ATGCCACATATACTAAAAA

                   *           
        280 ATGCCACGTATACTAAAAA
          1 ATGCCACATATACTAAAAA

        299 GTTGGGTGCA


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  19   17  1.00

ACGTcount: A:0.47, C:0.21, G:0.11, T:0.21


Consensus pattern (19 bp):   
ATGCCACATATACTAAAAA

Found at i:14469 original size:2 final size:2

Alignment explanation


    Indices: 14451--14533  Score: 60
    Period size: 2  Copynumber: 39.5  Consensus size: 2

      14441 ATCATAACTG

                          *                                  *            
      14451 TA TA CTA TA TT TA TA TA TA TA TA TA TA TA TA TA GA TCA TA TCA
          1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T-A

                   **           *                        *              
      14494 TA -A CCG TA TA CTA CA TA TA TA TA TA TA TA TG TA TA TA TA T
          1 TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

      14534 TACAAATACC


Statistics
Matches: 64,  Mismatches: 11, Indels: 12
        0.74            0.13        0.14

Matches are distributed among these distances:
   1    1  0.02
   2   55  0.86
   3    8  0.12

ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45


Consensus pattern (2 bp):   
TA

Found at i:14486 original size:49 final size:49

Alignment explanation


    Indices: 14430--14532  Score: 170
    Period size: 49  Copynumber: 2.1  Consensus size: 49

      14420 TACGTACTAA

                               *        *  *                 
      14430 ATATAGATCATATCATAACTGTATACTATATTTATATATATATATATAT
          1 ATATAGATCATATCATAACCGTATACTACATATATATATATATATATAT

                                                         *   
      14479 ATATAGATCATATCATAACCGTATACTACATATATATATATATATGTAT
          1 ATATAGATCATATCATAACCGTATACTACATATATATATATATATATAT

                 
      14528 ATATA
          1 ATATA

      14533 TTACAAATAC


Statistics
Matches: 50,  Mismatches: 4, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  49   50  1.00

ACGTcount: A:0.44, C:0.10, G:0.05, T:0.42


Consensus pattern (49 bp):   
ATATAGATCATATCATAACCGTATACTACATATATATATATATATATAT
Done.