Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024555.1 Corchorus olitorius cultivar O-4 contig24588, 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: 11360
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.36


Found at i:4882 original size:129 final size:129

Alignment explanation


    Indices: 4738--4996  Score: 421
    Period size: 129  Copynumber: 2.0  Consensus size: 129

       4728 TTGTTTAAAC

                   *                         *        *                      
       4738 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAAACTAATATCCTTATAACTA
          1 TTTTATAATTTTACTCAACTAAAAACTCTATTTCTATTTAATCAAAACTAATATCCTTATAACTA

                                  *                                     *    
       4803 TTTTATTTTTACCATTTTACTATTTTAATTAAAAAAACTT-ATATATTAGAATTTGTTAATATAT
         66 TTTTATTTTTACCATTTTACTAATTTAATTAAAAAAACTTAATATATTAGAATTT-TTAAAATAT

                                                          *        *     *   
       4867 TTTTATAATTTTACTCAACTAAAAACTCTATTTCTATTTAATCAAATCTAATATCTTTATACCTA
          1 TTTTATAATTTTACTCAACTAAAAACTCTATTTCTATTTAATCAAAACTAATATCCTTATAACTA

                                                                             
       4932 TTTTATTTTTACCATTTTACTAATTTAATTAAAAAAACTTAGATATATTAGAATTTTTAAAATAT
         66 TTTTATTTTTACCATTTTACTAATTTAATTAAAAAAACTTA-ATATATTAGAATTTTTAAAATAT

       4997 ATTTCTCAAA


Statistics
Matches: 120,  Mismatches: 8, Indels: 3
        0.92            0.06        0.02

Matches are distributed among these distances:
 129   98  0.82
 130    8  0.07
 131   14  0.12

ACGTcount: A:0.39, C:0.11, G:0.02, T:0.49


Consensus pattern (129 bp):   
TTTTATAATTTTACTCAACTAAAAACTCTATTTCTATTTAATCAAAACTAATATCCTTATAACTA
TTTTATTTTTACCATTTTACTAATTTAATTAAAAAAACTTAATATATTAGAATTTTTAAAATAT

Found at i:7512 original size:24 final size:25

Alignment explanation


    Indices: 7480--7536  Score: 82
    Period size: 25  Copynumber: 2.4  Consensus size: 25

       7470 GTCAGCCTTG

                                 *   
       7480 AATTT-TTTAATGT-TTAATTCTTA
          1 AATTTATTTAATGTCTTAATTATTA

                                    *
       7503 AATTTATTTAATGTCTTAATTATTC
          1 AATTTATTTAATGTCTTAATTATTA

                     
       7528 AATTTATTT
          1 AATTTATTT

       7537 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 (25 bp):   
AATTTATTTAATGTCTTAATTATTA

Found at i:10240 original size:57 final size:57

Alignment explanation


    Indices: 10132--10240  Score: 130
    Period size: 58  Copynumber: 1.9  Consensus size: 57

      10122 ATTAATCAAA

                                                      * * *           
      10132 TATCAAGTGACATGTTCTTTTTTAGATGCATAAAAAAAGACATTTTCGGACCAAGACT
          1 TATCAAGTGACATGTTCTTTTTTAGATGCAT-AAAAAAGACACTCTAGGACCAAGACT

                *           *             *          *          
      10190 TATCGAGTGACATGTTTTTTTATTAGATGCCT-AAAAAGACGCTCTAGGACC
          1 TATCAAGTGACATGTTCTTTT-TTAGATGCATAAAAAAGACACTCTAGGACC

      10241 GAGGTATGAT


Statistics
Matches: 43,  Mismatches: 7, Indels: 3
        0.81            0.13        0.06

Matches are distributed among these distances:
  57   15  0.35
  58   19  0.44
  59    9  0.21

ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


Consensus pattern (57 bp):   
TATCAAGTGACATGTTCTTTTTTAGATGCATAAAAAAGACACTCTAGGACCAAGACT
Done.