Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016019.1 Corchorus olitorius cultivar O-4 contig16052, 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: 8960
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32


Found at i:3818 original size:219 final size:216

Alignment explanation


    Indices: 3479--3879  Score: 599
    Period size: 219  Copynumber: 1.8  Consensus size: 216

       3469 TATGTTATAT

                             *         *          *            *             
       3479 TATGTTATATTATAATTTAAAATGCTATAAAGTCAAAAGTACCCTTGAAAGTTTGTGAGAATAAC
          1 TATGTTATATTATAATTAAAAATGCTAGAAAGTCAAAAATACCCTTGAAAGATTGTGAGAATAAC

                       *                 *                                   
       3544 AAAACAACCAATATTGAAATGACCAAAAAGCCATACTCAATATTAACCAAATTAATAAGGCAACA
         66 AAAACAACCAAGATTGAAATGACCAAAAAACCATACTCAATATTAACCAAATTAATAAGGCAACA

                                    * *                                      
       3609 T-TTTAGACATTTTTTTTTGTAATTTCACTTCTACATCTTATTGTTTCTTTATAATGTTAAATAG
        131 TCTTTAGACATTTTTTTTT-T--TATAACTTC-ACATCTTATTGTTTCTTTATAATGTTAAATAG

                                     
       3673 ACCACTCAACCAAACCATTTATAAA
        192 ACCACTCAACCAAACCATTTATAAA

                    *                    *            *   *                  
       3698 TATGTTATGTTATAATTAAAAATGCTAGAGAGTCAAAAATA-TCTTTAGAAGATTGTGAGAATAA
          1 TATGTTATATTATAATTAAAAATGCTAGAAAGTCAAAAATACCCTTGA-AAGATTGTGAGAATAA

                      *                                                   *  
       3762 CAAAACAACCGAGATTGAAATGACCAAAAAACCATACTCAATATTAACCAAATTAATAAGGCGAC
         65 CAAAACAACCAAGATTGAAATGACCAAAAAACCATACTCAATATTAACCAAATTAATAAGGCAAC

                      *               *                          
       3827 ATCTTTAGACCTTTTTTTTTTTATAATTTCACATCTTATTGTTTCTTTATAAT
        130 ATCTTTAGACATTTTTTTTTTTATAACTTCACATCTTATTGTTTCTTTATAAT

       3880 TAATAAGGCA


Statistics
Matches: 164,  Mismatches: 16, Indels: 7
        0.88            0.09        0.04

Matches are distributed among these distances:
 216   23  0.14
 217    6  0.04
 218    4  0.02
 219  115  0.70
 220   16  0.10

ACGTcount: A:0.41, C:0.14, G:0.10, T:0.35


Consensus pattern (216 bp):   
TATGTTATATTATAATTAAAAATGCTAGAAAGTCAAAAATACCCTTGAAAGATTGTGAGAATAAC
AAAACAACCAAGATTGAAATGACCAAAAAACCATACTCAATATTAACCAAATTAATAAGGCAACA
TCTTTAGACATTTTTTTTTTTATAACTTCACATCTTATTGTTTCTTTATAATGTTAAATAGACCA
CTCAACCAAACCATTTATAAA

Found at i:3946 original size:67 final size:64

Alignment explanation


    Indices: 3812--3946  Score: 182
    Period size: 65  Copynumber: 2.0  Consensus size: 64

       3802 ATATTAACCA

                        *                            *            *          
       3812 AATTAATAAGGCGACATCTTTAGACCTTTTTTTTTTTATAATTTCACATCTTATTGTTTCTTTAT
          1 AATTAATAAGGCAACATCTTTAGA-CTTTTTTTTTTTATAACTTCACATCTTATGGTTTCTTTAT

                                                     *                       
       3877 AATTAATAAGGCAACATCTTTAGA-TTTTTTTTTTTAATTTCACTTCTACATCTTATGGTTTCTT
          1 AATTAATAAGGCAACATCTTTAGACTTTTTTTTTTT-A--TAACTTC-ACATCTTATGGTTTCTT

               
       3941 TAT
         62 TAT

               
       3944 AAT
          1 AAT

       3947 ATATATATAT


Statistics
Matches: 62,  Mismatches: 4, Indels: 6
        0.86            0.06        0.08

Matches are distributed among these distances:
  63   11  0.18
  64    1  0.02
  65   23  0.37
  66    5  0.08
  67   22  0.35

ACGTcount: A:0.27, C:0.13, G:0.07, T:0.52


Consensus pattern (64 bp):   
AATTAATAAGGCAACATCTTTAGACTTTTTTTTTTTATAACTTCACATCTTATGGTTTCTTTAT
Done.