Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017789.1 Corchorus olitorius cultivar O-4 contig17822, 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: 5820
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30


Found at i:1171 original size:44 final size:45

Alignment explanation


    Indices: 1101--1191  Score: 166
    Period size: 44  Copynumber: 2.0  Consensus size: 45

       1091 AAATTACCCC

                                                         
       1101 TATTAACTCCCCAAAGGGAGCCAAGAATACATATATATATATATA
          1 TATTAACTCCCCAAAGGGAGCCAAGAATACATATATATATATATA

                                         *               
       1146 TATTAACTCCCC-AAGGGAGCCAAGAATATATATATATATATATA
          1 TATTAACTCCCCAAAGGGAGCCAAGAATACATATATATATATATA

              
       1190 TA
          1 TA

       1192 ATTTTGGGAA


Statistics
Matches: 45,  Mismatches: 1, Indels: 1
        0.96            0.02        0.02

Matches are distributed among these distances:
  44   33  0.73
  45   12  0.27

ACGTcount: A:0.44, C:0.16, G:0.11, T:0.29


Consensus pattern (45 bp):   
TATTAACTCCCCAAAGGGAGCCAAGAATACATATATATATATATA

Found at i:3141 original size:22 final size:25

Alignment explanation


    Indices: 3107--3164  Score: 61
    Period size: 22  Copynumber: 2.4  Consensus size: 25

       3097 TAAATGTAGC

                           *       * 
       3107 TGATAA-TCTTCT-CTTTTATC-TT
          1 TGATAATTCTTCTCCATTTATCACT

                                     
       3129 TGATAATTC-TCTCCATTTATCACT
          1 TGATAATTCTTCTCCATTTATCACT

                        
       3153 TGATAATATCTT
          1 TGATAAT-TCTT

       3165 GCCAGGTAAA


Statistics
Matches: 29,  Mismatches: 2, Indels: 6
        0.78            0.05        0.16

Matches are distributed among these distances:
  22    9  0.31
  23    9  0.31
  24    8  0.28
  25    2  0.07
  26    1  0.03

ACGTcount: A:0.24, C:0.19, G:0.05, T:0.52


Consensus pattern (25 bp):   
TGATAATTCTTCTCCATTTATCACT
Done.