Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016574.1 Corchorus olitorius cultivar O-4 contig16607, 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: 4126
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.41


Found at i:226 original size:14 final size:13

Alignment explanation


    Indices: 207--245  Score: 51
    Period size: 14  Copynumber: 2.9  Consensus size: 13

        197 AAATTGTAAA

                         
        207 ATTTAAAAAATTT
          1 ATTTAAAAAATTT

                   *    * 
        220 CATTTAAGAAATAT
          1 -ATTTAAAAAATTT

                        
        234 ATTTAAAAAATT
          1 ATTTAAAAAATT

        246 CTAATATATA


Statistics
Matches: 21,  Mismatches: 4, Indels: 1
        0.81            0.15        0.04

Matches are distributed among these distances:
  13   10  0.48
  14   11  0.52

ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41


Consensus pattern (13 bp):   
ATTTAAAAAATTT

Found at i:476 original size:123 final size:127

Alignment explanation


    Indices: 231--483  Score: 381
    Period size: 131  Copynumber: 2.0  Consensus size: 127

        221 ATTTAAGAAA

                                                                             
        231 TATATTTAAAAAATTCTAATATATATAAGTTTTTAAAATAAAATAGTAAAACGGTAAAAATAAAA
          1 TATATTTAAAAAATTCTAATATATATAAGTTTTTAAAATAAAATAGTAAAACGGTAAAAAT---A

            *                                                          *     
        296 TAGGTATAAGGATATTAGATTTAATTAAATAAAAATTGAGTTTTTAGTTGAGTAAAACTGTAAAA
         63 CA-GTATAAGGATATTAGATTTAATTAAATAAAAATTGAGTTTTTAGTTGAGTAAAACTATAAAA

             
        361 G
        127 G

                                              *  *             *             
        362 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT-CA-
          1 TATATTTAAAAAATTCTAATATATATAAGTTTTTAAAATAAAATAGTAAAACGGTAAAAATACAG

                                                                          
        425 TA-AA-GATATTAGATTTAATTAAAT-AAAATTAGAGTTTTTAGTTGAGTAAAACTATAAAA
         66 TATAAGGATATTAGATTTAATTAAATAAAAATT-GAGTTTTTAGTTGAGTAAAACTATAAAA

        484 ATTTAAACAA


Statistics
Matches: 116,  Mismatches: 5, Indels: 10
        0.89            0.04        0.08

Matches are distributed among these distances:
 122    6  0.05
 123   47  0.41
 124    2  0.02
 125    2  0.02
 127    1  0.01
 131   58  0.50

ACGTcount: A:0.50, C:0.02, G:0.11, T:0.37


Consensus pattern (127 bp):   
TATATTTAAAAAATTCTAATATATATAAGTTTTTAAAATAAAATAGTAAAACGGTAAAAATACAG
TATAAGGATATTAGATTTAATTAAATAAAAATTGAGTTTTTAGTTGAGTAAAACTATAAAAG

Found at i:3595 original size:25 final size:24

Alignment explanation


    Indices: 3544--3600  Score: 80
    Period size: 25  Copynumber: 2.4  Consensus size: 24

       3534 GTAAGTCTTG

                                *   
       3544 AATTT-TTTAATGTTTAATTCTTA
          1 AATTTATTTAATGTTTAATTATTA

                                    *
       3567 AATTTATTTAATGTCTTAATTATTC
          1 AATTTATTTAATGT-TTAATTATTA

                     
       3592 AATTTATTT
          1 AATTTATTT

       3601 TACAATCCAC


Statistics
Matches: 30,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  23    5  0.17
  24    8  0.27
  25   17  0.57

ACGTcount: A:0.32, C:0.05, G:0.04, T:0.60


Consensus pattern (24 bp):   
AATTTATTTAATGTTTAATTATTA
Done.