Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01002517.1 Corchorus olitorius cultivar O-4 contig02517, 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, 747

Length: 1246
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35


Found at i:469 original size:24 final size:24

Alignment explanation


    Indices: 431--723  Score: 344
    Period size: 24  Copynumber: 12.2  Consensus size: 24

        421 GACTCCTTGC

                                 *   
        431 ATCATTATCAGAACTTTC-TGATAA
          1 ATCATTATCAGAACTTTCAT-CTAA

                    * *          *   
        455 ATCATTATAATAACTTTC-TGATAA
          1 ATCATTATCAGAACTTTCAT-CTAA

                                    
        479 ATCATTATCAGAACTTTCATCTAA
          1 ATCATTATCAGAACTTTCATCTAA

                    * *             
        503 ATCATTATAATAACTTTCATCTAA
          1 ATCATTATCAGAACTTTCATCTAA

                              *  *   
        527 ATCATTATCAGAACTTT-TTGATAA
          1 ATCATTATCAGAACTTTCAT-CTAA

            *                       
        551 GTCATTATCAGAACTTTCATCTAA
          1 ATCATTATCAGAACTTTCATCTAA

                    * *             
        575 ATCATTATAATAACTTTCATCTAA
          1 ATCATTATCAGAACTTTCATCTAA

                              *  *   
        599 ATCATTATCAGAACTTT-TTGATAA
          1 ATCATTATCAGAACTTTCAT-CTAA

                                    
        623 ATCATTATCAGAACTTTCATCTAA
          1 ATCATTATCAGAACTTTCATCTAA

                    * *             
        647 ATCATTATAATAACTTTCATCTAA
          1 ATCATTATCAGAACTTTCATCTAA

                    * *          *   
        671 ATCATTATAATAACTTTC-TGATAA
          1 ATCATTATCAGAACTTTCAT-CTAA

                                    
        695 ATCATTATCAGAACTTTCATCTAA
          1 ATCATTATCAGAACTTTCATCTAA

                 
        719 ATCAT
          1 ATCAT

        724 AACCACTTGT


Statistics
Matches: 233,  Mismatches: 29, Indels: 14
        0.84            0.11        0.05

Matches are distributed among these distances:
  23    3  0.01
  24  226  0.97
  25    4  0.02

ACGTcount: A:0.39, C:0.17, G:0.04, T:0.40


Consensus pattern (24 bp):   
ATCATTATCAGAACTTTCATCTAA

Found at i:549 original size:72 final size:72

Alignment explanation


    Indices: 452--723  Score: 481
    Period size: 72  Copynumber: 3.8  Consensus size: 72

        442 AACTTTCTGA

                         *                                                   
        452 TAAATCATTATAATAACTTTCTGATAAATCATTATCAGAACTTTCATCTAAATCATTATAATAAC
          1 TAAATCATTATAAGAACTTTCTGATAAATCATTATCAGAACTTTCATCTAAATCATTATAATAAC

                   
        517 TTTCATC
         66 TTTCATC

                       *        *      *                                     
        524 TAAATCATTATCAGAACTTTTTGATAAGTCATTATCAGAACTTTCATCTAAATCATTATAATAAC
          1 TAAATCATTATAAGAACTTTCTGATAAATCATTATCAGAACTTTCATCTAAATCATTATAATAAC

                   
        589 TTTCATC
         66 TTTCATC

                       *        *                                            
        596 TAAATCATTATCAGAACTTTTTGATAAATCATTATCAGAACTTTCATCTAAATCATTATAATAAC
          1 TAAATCATTATAAGAACTTTCTGATAAATCATTATCAGAACTTTCATCTAAATCATTATAATAAC

                   
        661 TTTCATC
         66 TTTCATC

                         *                                          
        668 TAAATCATTATAATAACTTTCTGATAAATCATTATCAGAACTTTCATCTAAATCAT
          1 TAAATCATTATAAGAACTTTCTGATAAATCATTATCAGAACTTTCATCTAAATCAT

        724 AACCACTTGT


Statistics
Matches: 192,  Mismatches: 8, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  72  192  1.00

ACGTcount: A:0.39, C:0.17, G:0.04, T:0.40


Consensus pattern (72 bp):   
TAAATCATTATAAGAACTTTCTGATAAATCATTATCAGAACTTTCATCTAAATCATTATAATAAC
TTTCATC

Found at i:1060 original size:15 final size:15

Alignment explanation


    Indices: 1040--1070  Score: 62
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       1030 AATTACAATG

                           
       1040 ATCATAGTTAATGTT
          1 ATCATAGTTAATGTT

                           
       1055 ATCATAGTTAATGTT
          1 ATCATAGTTAATGTT

             
       1070 A
          1 A

       1071 ATGTTAACTA


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.35, C:0.06, G:0.13, T:0.45


Consensus pattern (15 bp):   
ATCATAGTTAATGTT
Done.