Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013204.1 Corchorus capsularis cultivar CVL-1 contig13225, 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: 9667
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33


Found at i:311 original size:2 final size:2

Alignment explanation


    Indices: 304--372  Score: 54
    Period size: 2  Copynumber: 35.5  Consensus size: 2

        294 ATTCAAAGGA

                                                *     *      *         *   
        304 AT AT AT AT AT AT AT AT AT AT AT AT TT AT GT AT AC ACT AT AC AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT

             *        *                                
        347 AA AT -T AC AT -T AT AT AT AT -T AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

        373 ACGTAAATTA


Statistics
Matches: 51,  Mismatches: 12, Indels: 8
        0.72            0.17        0.11

Matches are distributed among these distances:
   1    3  0.06
   2   47  0.92
   3    1  0.02

ACGTcount: A:0.46, C:0.06, G:0.01, T:0.46


Consensus pattern (2 bp):   
AT

Found at i:325 original size:16 final size:15

Alignment explanation


    Indices: 304--412  Score: 53
    Period size: 14  Copynumber: 6.9  Consensus size: 15

        294 ATTCAAAGGA

                           
        304 ATATATATATATA-T
          1 ATATATATATATATT

                      *     
        318 ATATATATATTTATGT
          1 ATATATATATATAT-T

                      *   *   
        334 ATACACTATACATAAATT
          1 AT--A-TATATATATATT

             *             
        352 ACAT-TATATATATT
          1 ATATATATATATATT

                         *   
        366 ATATATA-ACGTAAATT
          1 ATATATATA--TATATT

             *               
        382 ACATTATATTATATATT
          1 ATA-TATA-TATATATT

               *  *       
        399 ATACATTTATATAT
          1 ATATATATATATAT

        413 ACATACATTA


Statistics
Matches: 70,  Mismatches: 14, Indels: 21
        0.67            0.13        0.20

Matches are distributed among these distances:
  14   24  0.34
  15   10  0.14
  16   13  0.19
  17   11  0.16
  18    3  0.04
  19    9  0.13

ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47


Consensus pattern (15 bp):   
ATATATATATATATT
Done.