Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009679.1 Corchorus olitorius cultivar O-4 contig09711, 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: 2994
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33


Found at i:106 original size:18 final size:20

Alignment explanation


    Indices: 85--133  Score: 66
    Period size: 21  Copynumber: 2.5  Consensus size: 20

         75 ATTTTACCGC

                                
         85 TAATAATAA-TTAAT-ATAA
          1 TAATAATAAGTTAATAATAA

                               * 
        103 TAATAATAAGTTTAATAATTA
          1 TAATAATAAG-TTAATAATAA

                      
        124 TAATAATAAG
          1 TAATAATAAG

        134 AGGTTTAATG


Statistics
Matches: 27,  Mismatches: 1, Indels: 3
        0.87            0.03        0.10

Matches are distributed among these distances:
  18    9  0.33
  20    5  0.19
  21   13  0.48

ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39


Consensus pattern (20 bp):   
TAATAATAAGTTAATAATAA

Found at i:118 original size:15 final size:14

Alignment explanation


    Indices: 85--128  Score: 52
    Period size: 15  Copynumber: 3.0  Consensus size: 14

         75 ATTTTACCGC

                           
         85 TAATAATAATTAATA
          1 TAATAATAA-TAATA

                          *
        100 TAATAATAATAAGTT
          1 TAATAATAATAA-TA

                   *      
        115 TAATAATTATAATA
          1 TAATAATAATAATA

        129 ATAAGAGGTT


Statistics
Matches: 25,  Mismatches: 3, Indels: 3
        0.81            0.10        0.10

Matches are distributed among these distances:
  14    4  0.16
  15   21  0.84

ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41


Consensus pattern (14 bp):   
TAATAATAATAATA

Found at i:233 original size:110 final size:110

Alignment explanation


    Indices: 103--303  Score: 266
    Period size: 113  Copynumber: 1.8  Consensus size: 110

         93 ATTAATATAA

                            *                        *                       
        103 TAATAATAAGTTTAA-TA-ATTATAATAATAAGAGGTTTAATGTAAAAAAAATTGCTACTAATAT
          1 TAATAATAAGTTTAACAATATTATAATAATAAGAGGTTTAACGTAAAAAAAATTG-T--TAATAT

                                                             
        166 TTTAGA-TTTTGT-AATATGGAAAGAAAAACGTAATGATATGGAGTAAC
         63 TTTAGACTTTT-TAAATATGGAAAGAAAAACGTAATGATATGGAGTAAC

                     *                        **                       *     
        213 TAATAATAATTTTAACAATTATTATAATAATAAGTTGTTTAACGTAAAAAAAATTGTTATTATTT
          1 TAATAATAAGTTTAACAA-TATTATAATAATAAGAGGTTTAACGTAAAAAAAATTGTTAATATTT

                                 *    
        278 TAGACTTTTTAAATATGGAAATAAAA
         65 TAGACTTTTTAAATATGGAAAGAAAA

        304 TCTGGTTGAA


Statistics
Matches: 79,  Mismatches: 7, Indels: 9
        0.83            0.07        0.09

Matches are distributed among these distances:
 110   26  0.33
 111   19  0.24
 112    1  0.01
 113   33  0.42

ACGTcount: A:0.47, C:0.03, G:0.11, T:0.38


Consensus pattern (110 bp):   
TAATAATAAGTTTAACAATATTATAATAATAAGAGGTTTAACGTAAAAAAAATTGTTAATATTTT
AGACTTTTTAAATATGGAAAGAAAAACGTAATGATATGGAGTAAC
Done.