Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001701.1 Corchorus olitorius cultivar O-4 contig01701, 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, 637

Length: 1062
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35


Found at i:944 original size:50 final size:50

Alignment explanation


    Indices: 883--1059  Score: 248
    Period size: 50  Copynumber: 3.5  Consensus size: 50

        873 CGATCAACTT

                  *                     * *    *             * 
        883 CTTTGAGCTGTCTTCCAATTCAATCTT-CAGGGTATCGTCTTCCGCTTACC
          1 CTTTGAACTGTCTTCCAATTCAATCTTAAAAGG-ACCGTCTTCCGCTTATC

                                   *                          
        933 CTTTGAACTGTCTTCCAATTCAACCTTAAAAGGACCGTCTTCCGCTTATC
          1 CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC

            *                                        *        
        983 TTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTTCGCTTATC
          1 CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC

                 *        *            
       1033 CTTTGGACTGTCTTACAATTCAATCTT
          1 CTTTGAACTGTCTTCCAATTCAATCTT

       1060 TGG


Statistics
Matches: 114,  Mismatches: 12, Indels: 2
        0.89            0.09        0.02

Matches are distributed among these distances:
  50  111  0.97
  51    3  0.03

ACGTcount: A:0.21, C:0.27, G:0.13, T:0.38


Consensus pattern (50 bp):   
CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC

Found at i:1023 original size:27 final size:27

Alignment explanation


    Indices: 942--1023  Score: 73
    Period size: 27  Copynumber: 3.2  Consensus size: 27

        932 CCTTTGAACT

                          *            
        942 GTCTTCCAATTCAACCTTAAAAGGACC
          1 GTCTTCCAATTCAATCTTAAAAGGACC

                   **           ** *  *
        969 GTCTTCCGCTT--ATCTT--TTGAACT
          1 GTCTTCCAATTCAATCTTAAAAGGACC

                                       
        992 GTCTTCCAATTCAATCTTAAAAGGACC
          1 GTCTTCCAATTCAATCTTAAAAGGACC

                 
       1019 GTCTT
          1 GTCTT

       1024 TCGCTTATCC


Statistics
Matches: 38,  Mismatches: 13, Indels: 8
        0.64            0.22        0.14

Matches are distributed among these distances:
  23   12  0.32
  25    9  0.24
  27   17  0.45

ACGTcount: A:0.26, C:0.27, G:0.12, T:0.35


Consensus pattern (27 bp):   
GTCTTCCAATTCAATCTTAAAAGGACC
Done.