Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014419.1 Corchorus olitorius cultivar O-4 contig14452, 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: 12094
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32


Found at i:8 original size:1 final size:1

Alignment explanation


    Indices: 3--28  Score: 52
    Period size: 1  Copynumber: 26.0  Consensus size: 1

          1 TT

                                      
          3 AAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAA

         29 CGATGACGCT


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   25  1.00

ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00


Consensus pattern (1 bp):   
A

Found at i:10329 original size:132 final size:132

Alignment explanation


    Indices: 10177--10429  Score: 402
    Period size: 133  Copynumber: 1.9  Consensus size: 132

      10167 GAATTTTTTT

                           *                   *                             
      10177 AAAATTATAATATATCTAAGT-TTTTTTAATTAAATTAGTAAAATGGTAAAAATAAAATA-TGTA
          1 AAAATTATAATATATATAAGTATTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAGT-TA

                       *                                                     
      10240 TAAGGATATTAGATTTAATTAATAAAAAATAGAGTTTTTAATTGAGTAAAACTATAAATGTATAT
         65 TAAGGATATTACATTTAATTAA-AAAAAATAGAGTTTTTAATTGAGTAAAACTATAAATGTATAT

                
      10305 TTAA
        129 TTAA

                  *  *                                            *          
      10309 AAAATTCTAGTATATATAAGTATTTTTTAATTAAAATAGTAAAATGGTAAAAATTAAATAGTTAT
          1 AAAATTATAATATATATAAGTATTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAGTTAT

                                  *               *                 
      10374 AAGGATATTACATTTAATTAAATAAAATAGAGTTTTTAGTTGAGTAAAACTATAAA
         66 AAGGATATTACATTTAATTAAAAAAAATAGAGTTTTTAATTGAGTAAAACTATAAA

      10430 AAGTTTAAAC


Statistics
Matches: 111,  Mismatches: 8, Indels: 4
        0.90            0.07        0.03

Matches are distributed among these distances:
 132   51  0.46
 133   59  0.53
 134    1  0.01

ACGTcount: A:0.49, C:0.02, G:0.10, T:0.39


Consensus pattern (132 bp):   
AAAATTATAATATATATAAGTATTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAGTTAT
AAGGATATTACATTTAATTAAAAAAAATAGAGTTTTTAATTGAGTAAAACTATAAATGTATATTT
AA

Found at i:12057 original size:2 final size:2

Alignment explanation


    Indices: 12050--12083  Score: 68
    Period size: 2  Copynumber: 17.0  Consensus size: 2

      12040 TAATATTTAG

                                                              
      12050 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

      12084 CTTAGTTTAC


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   32  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Done.