Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016302.1 Corchorus olitorius cultivar O-4 contig16335, 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: 12711
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.31

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:1150 original size:16 final size:18

Alignment explanation


    Indices: 1106--1153  Score: 57
    Period size: 16  Copynumber: 2.8  Consensus size: 18

       1096 AACAAGCTAG

                              
       1106 AAAAC-AAAACAAAGACT
          1 AAAACTAAAACAAAGACT

                   *           
       1123 AAAAACTTAAACAAA-ACT
          1 -AAAACTAAAACAAAGACT

                          
       1141 -AAACTAAAACAAA
          1 AAAACTAAAACAAA

       1154 CAAATGCATA


Statistics
Matches: 27,  Mismatches: 2, Indels: 4
        0.82            0.06        0.12

Matches are distributed among these distances:
  16   12  0.44
  18    8  0.30
  19    7  0.26

ACGTcount: A:0.71, C:0.17, G:0.02, T:0.10


Consensus pattern (18 bp):   
AAAACTAAAACAAAGACT

Found at i:4288 original size:8 final size:8

Alignment explanation


    Indices: 4275--4315  Score: 82
    Period size: 8  Copynumber: 5.1  Consensus size: 8

       4265 TGCAAAATTA

                    
       4275 ACAAAAAC
          1 ACAAAAAC

                    
       4283 ACAAAAAC
          1 ACAAAAAC

                    
       4291 ACAAAAAC
          1 ACAAAAAC

                    
       4299 ACAAAAAC
          1 ACAAAAAC

                    
       4307 ACAAAAAC
          1 ACAAAAAC

             
       4315 A
          1 A

       4316 AAATACGAAA


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   8   33  1.00

ACGTcount: A:0.76, C:0.24, G:0.00, T:0.00


Consensus pattern (8 bp):   
ACAAAAAC

Found at i:9717 original size:27 final size:27

Alignment explanation


    Indices: 9673--9730  Score: 64
    Period size: 27  Copynumber: 2.1  Consensus size: 27

       9663 GCCCCACCTG

                *        *    *         
       9673 TTTATATATTATATATTATTTAATCTAT
          1 TTTAAATATTATACATTAGTT-ATCTAT

                                   *   
       9701 TTTAAATA-TATACATTAGTTATTTAT
          1 TTTAAATATTATACATTAGTTATCTAT

                
       9727 TTTA
          1 TTTA

       9731 GATTTATTTA


Statistics
Matches: 26,  Mismatches: 4, Indels: 2
        0.81            0.12        0.06

Matches are distributed among these distances:
  26    9  0.35
  27   10  0.38
  28    7  0.27

ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59


Consensus pattern (27 bp):   
TTTAAATATTATACATTAGTTATCTAT
Done.