Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005818.1 Corchorus capsularis cultivar CVL-1 contig05836, 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, 667

Length: 1113
ACGTcount: A:0.34, C:0.21, G:0.09, T:0.35


Found at i:134 original size:32 final size:32

Alignment explanation


    Indices: 66--138  Score: 85
    Period size: 32  Copynumber: 2.3  Consensus size: 32

         56 CTAATTAATC

                   *     *        *        *
         66 CTTTTACCTTGACTCTTAATTATTGACTTACC
          1 CTTTTACTTTGACCCTTAATTACTGACTTACA

                                         *   
         98 CTTTTACTTTGACCCTTAATTACTGA-TTGCTA
          1 CTTTTACTTTGACCCTTAATTACTGACTTAC-A

                     
        130 CTTTTACTT
          1 CTTTTACTT

        139 CCTCTCTTAG


Statistics
Matches: 35,  Mismatches: 5, Indels: 2
        0.83            0.12        0.05

Matches are distributed among these distances:
  31    3  0.09
  32   32  0.91

ACGTcount: A:0.21, C:0.23, G:0.07, T:0.49


Consensus pattern (32 bp):   
CTTTTACTTTGACCCTTAATTACTGACTTACA

Found at i:212 original size:38 final size:39

Alignment explanation


    Indices: 115--212  Score: 92
    Period size: 38  Copynumber: 2.5  Consensus size: 39

        105 TTTGACCCTT

                       *                     * * * 
        115 AATTACTGATTGCTACTTTTACTTCCTCTCTTAGTTATC
          1 AATTACTGATTACTACTTTTACTTCCTCTCTTAATCACC

                    *  * * *                        
        154 AATTTACTAATCAATCCTTTTACTT-C-CTCTTAATCACC
          1 AA-TTACTGATTACTACTTTTACTTCCTCTCTTAATCACC

                                 
        192 AATTGACTGATTACTACTTTT
          1 AATT-ACTGATTACTACTTTT

        213 TATCTTTTCA


Statistics
Matches: 45,  Mismatches: 12, Indels: 5
        0.73            0.19        0.08

Matches are distributed among these distances:
  37    2  0.04
  38   23  0.51
  39    3  0.07
  40   17  0.38

ACGTcount: A:0.26, C:0.23, G:0.05, T:0.46


Consensus pattern (39 bp):   
AATTACTGATTACTACTTTTACTTCCTCTCTTAATCACC

Found at i:1007 original size:2 final size:2

Alignment explanation


    Indices: 1000--1024  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

        990 AATCTATCCA

                                                 
       1000 AC AC AC AC AC AC AC AC AC AC AC AC A
          1 AC AC AC AC AC AC AC AC AC AC AC AC A

       1025 TATATATATA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00


Consensus pattern (2 bp):   
AC

Done.