Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024575.1 Corchorus olitorius cultivar O-4 contig24608, 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: 11941
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33


Found at i:8 original size:2 final size:2

Alignment explanation


    Indices: 2--38  Score: 74
    Period size: 2  Copynumber: 18.5  Consensus size: 2

          1 A

                                                                   
          2 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

         39 CACACTTATT


Statistics
Matches: 35,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   35  1.00

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Found at i:7107 original size:3 final size:3

Alignment explanation


    Indices: 7099--7128  Score: 60
    Period size: 3  Copynumber: 10.0  Consensus size: 3

       7089 ATTTCTTAAA

                                                   
       7099 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
          1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT

       7129 ATATATATAT


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   27  1.00

ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67


Consensus pattern (3 bp):   
TAT

Found at i:7731 original size:86 final size:84

Alignment explanation


    Indices: 7571--7749  Score: 215
    Period size: 86  Copynumber: 2.2  Consensus size: 84

       7561 GGTTCAAGTA

                                         *  *                            *   
       7571 AAATAATAATAAAGTTGAATAATAATGAGGATGTTCTCTAAATCCTGCCAAATTGTGGAAGGTTT
          1 AAATAATAATAAAGTTGAATAATAATGAGAATATTCTCTAAATCCTGCCAAATTGTGGAAGATTT

                *              
       7636 AGGAGATATTTTAAGAAAT
         66 AGGAAATATTTTAAGAAAT

                    *                                      *             *   
       7655 AAATAAATTATAAAGATTGAATAATAATGAGAATATTCTTCT-AATCTTGCCAAATTGTGGGAGA
          1 AAAT-AATAATAAAG-TTGAATAATAATGAGAATATTC-TCTAAATCCTGCCAAATTGTGGAAGA

                        *      *  
       7719 TTT-GGAAA-ATATTAA-ATA-
         63 TTTAGGAAATATTTTAAGAAAT

                         
       7737 AAATAATAATAAA
          1 AAATAATAATAAA

       7750 AGGAAGTTAA


Statistics
Matches: 82,  Mismatches: 10, Indels: 9
        0.81            0.10        0.09

Matches are distributed among these distances:
  81    8  0.10
  82    4  0.05
  83    2  0.02
  84   10  0.12
  85   13  0.16
  86   42  0.51
  87    3  0.04

ACGTcount: A:0.46, C:0.06, G:0.16, T:0.32


Consensus pattern (84 bp):   
AAATAATAATAAAGTTGAATAATAATGAGAATATTCTCTAAATCCTGCCAAATTGTGGAAGATTT
AGGAAATATTTTAAGAAAT

Found at i:10952 original size:14 final size:15

Alignment explanation


    Indices: 10915--10969  Score: 53
    Period size: 15  Copynumber: 3.8  Consensus size: 15

      10905 TCAAAAGTCA

                  *        
      10915 AAAATGTTTTTCAAG
          1 AAAATGGTTTTCAAG

               *           
      10930 AAAGT-GTTTTC-AG
          1 AAAATGGTTTTCAAG

                            
      10943 AAAATGGTTTTCTAA-
          1 AAAATGGTTTTC-AAG

               *        
      10958 AAATTGGTTTTC
          1 AAAATGGTTTTC

      10970 GCAAGGGTTT


Statistics
Matches: 33,  Mismatches: 4, Indels: 6
        0.77            0.09        0.14

Matches are distributed among these distances:
  13    6  0.18
  14   11  0.33
  15   15  0.45
  16    1  0.03

ACGTcount: A:0.35, C:0.07, G:0.16, T:0.42


Consensus pattern (15 bp):   
AAAATGGTTTTCAAG
Done.