Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009510.1 Corchorus olitorius cultivar O-4 contig09542, 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, 787

Length: 1312
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.33


Found at i:283 original size:18 final size:18

Alignment explanation


    Indices: 260--308  Score: 50
    Period size: 15  Copynumber: 2.9  Consensus size: 18

        250 GAGCGACCAA

                              
        260 GGCTCGCGATCAAGCCAC
          1 GGCTCGCGATCAAGCCAC

                        *   * 
        278 GGCTCG-G-TCACG-CGC
          1 GGCTCGCGATCAAGCCAC

                     *      
        293 GGCTCGCGACCAAGCC
          1 GGCTCGCGATCAAGCC

        309 GCGACATAGT


Statistics
Matches: 24,  Mismatches: 4, Indels: 6
        0.71            0.12        0.18

Matches are distributed among these distances:
  15    8  0.33
  16    5  0.21
  17    4  0.17
  18    7  0.29

ACGTcount: A:0.16, C:0.41, G:0.33, T:0.10


Consensus pattern (18 bp):   
GGCTCGCGATCAAGCCAC

Found at i:454 original size:21 final size:22

Alignment explanation


    Indices: 430--475  Score: 76
    Period size: 21  Copynumber: 2.1  Consensus size: 22

        420 TTTTTTTAAA

                *                 
        430 TTAATAATTAGTTATTATT-TT
          1 TTAAAAATTAGTTATTATTATT

                                  
        451 TTAAAAATTAGTTATTATTATT
          1 TTAAAAATTAGTTATTATTATT

               
        473 TTA
          1 TTA

        476 TATGATTATT


Statistics
Matches: 23,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  21   18  0.78
  22    5  0.22

ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59


Consensus pattern (22 bp):   
TTAAAAATTAGTTATTATTATT

Found at i:827 original size:22 final size:22

Alignment explanation


    Indices: 802--844  Score: 86
    Period size: 22  Copynumber: 2.0  Consensus size: 22

        792 ATAGAACCAT

                                  
        802 AGAAAGGGATGAGAAATTAGAG
          1 AGAAAGGGATGAGAAATTAGAG

                                 
        824 AGAAAGGGATGAGAAATTAGA
          1 AGAAAGGGATGAGAAATTAGA

        845 AAATCTTGGC


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  22   21  1.00

ACGTcount: A:0.51, C:0.00, G:0.35, T:0.14


Consensus pattern (22 bp):   
AGAAAGGGATGAGAAATTAGAG

Found at i:1001 original size:21 final size:21

Alignment explanation


    Indices: 976--1018  Score: 68
    Period size: 21  Copynumber: 2.0  Consensus size: 21

        966 TAAACAAATA

                 *    *          
        976 TTATACTAGTTGATACATATT
          1 TTATAATAGTGGATACATATT

                                 
        997 TTATAATAGTGGATACATATT
          1 TTATAATAGTGGATACATATT

             
       1018 T
          1 T

       1019 CCAAAACTTG


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  21   20  1.00

ACGTcount: A:0.35, C:0.07, G:0.12, T:0.47


Consensus pattern (21 bp):   
TTATAATAGTGGATACATATT
Done.