Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009764.1 Corchorus olitorius cultivar O-4 contig09796, 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: 3895
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.35


Found at i:910 original size:29 final size:30

Alignment explanation


    Indices: 849--921  Score: 76
    Period size: 29  Copynumber: 2.5  Consensus size: 30

        839 GTACCCGGGA

                                       ** 
        849 GGTCCCTGTACTATAAGATTTGTGCAATTT
          1 GGTCCCTGTACTATAAGATTTGTGCAAAAT

                           ***            
        879 GGTCCCTGTACTAT-TTTTTTGTGCAAAAT
          1 GGTCCCTGTACTATAAGATTTGTGCAAAAT

                *  *      
        908 GGTCTCTTTACTAT
          1 GGTCCCTGTACTAT

        922 CAAAAGTGAT


Statistics
Matches: 36,  Mismatches: 7, Indels: 1
        0.82            0.16        0.02

Matches are distributed among these distances:
  29   22  0.61
  30   14  0.39

ACGTcount: A:0.21, C:0.18, G:0.18, T:0.44


Consensus pattern (30 bp):   
GGTCCCTGTACTATAAGATTTGTGCAAAAT

Found at i:1091 original size:21 final size:22

Alignment explanation


    Indices: 1055--1096  Score: 68
    Period size: 21  Copynumber: 2.0  Consensus size: 22

       1045 CAAAAAATCA

                       *          
       1055 AAAATGTATTTTTTTAAAATAT
          1 AAAATGTATTTATTTAAAATAT

                                 
       1077 AAAAT-TATTTATTTAAAATA
          1 AAAATGTATTTATTTAAAATA

       1097 AAGAATTTTT


Statistics
Matches: 19,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  21   14  0.74
  22    5  0.26

ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48


Consensus pattern (22 bp):   
AAAATGTATTTATTTAAAATAT

Found at i:1103 original size:21 final size:20

Alignment explanation


    Indices: 1048--1103  Score: 67
    Period size: 21  Copynumber: 2.6  Consensus size: 20

       1038 AAAAAATCAA

                              *   
       1048 AAAATCAAAAATGTATTTTTTT
          1 AAAAT-AAAAAT-TATTTATTT

                                 
       1070 AAAATATAAAATTATTTATTT
          1 AAAATA-AAAATTATTTATTT

                         
       1091 AAAATAAAGAATT
          1 AAAATAAA-AATT

       1104 TTTTTTCTTA


Statistics
Matches: 31,  Mismatches: 1, Indels: 5
        0.84            0.03        0.14

Matches are distributed among these distances:
  20    2  0.06
  21   19  0.61
  22   10  0.32

ACGTcount: A:0.54, C:0.02, G:0.04, T:0.41


Consensus pattern (20 bp):   
AAAATAAAAATTATTTATTT
Done.