Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022893.1 Corchorus olitorius cultivar O-4 contig22926, 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: 4269
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.37


Found at i:1560 original size:10 final size:10

Alignment explanation


    Indices: 1547--1576  Score: 51
    Period size: 10  Copynumber: 2.9  Consensus size: 10

       1537 ACATTAATAC

                      
       1547 TAATTGATTT
          1 TAATTGATTT

                      
       1557 TAATTGATTT
          1 TAATTGATTT

                      
       1567 TAATCTGATT
          1 TAAT-TGATT

       1577 AATATTCAAA


Statistics
Matches: 19,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  10   14  0.74
  11    5  0.26

ACGTcount: A:0.30, C:0.03, G:0.10, T:0.57


Consensus pattern (10 bp):   
TAATTGATTT

Found at i:1791 original size:73 final size:69

Alignment explanation


    Indices: 1585--1801  Score: 346
    Period size: 69  Copynumber: 3.1  Consensus size: 69

       1575 TTAATATTCA

                                                          *               *  
       1585 AATCAATCAATCAATTT-ATATCATTAGTACTAATTGATTCTAATTTGATCAAGATATTCAACTC
          1 AATCAATCAATCAATTTAATATCATTAGTACTAATTGATTCTAATTGGATCAAGATATTCAAATC

                
       1649 AATC
         66 AATC

                                          *                                  
       1653 AATCAATCAATCAATTTAATATCATTAGTAATAATTGATTCTAATTGGATCAAGATATTCAAATC
          1 AATCAATCAATCAATTTAATATCATTAGTACTAATTGATTCTAATTGGATCAAGATATTCAAATC

                
       1718 AATC
         66 AATC

                       *                                             *       
       1722 AATCAATCAATTAATTTAATATCATTTTAGTACTAATTGATTCTAATTGGATCAAAATATATTCA
          1 AATCAATCAATCAATTTAATATCA--TTAGTACTAATTGATTCTAATTGGATC--AAGATATTCA

                    
       1787 AATCAATC
         62 AATCAATC

                   
       1795 AATCAAT
          1 AATCAAT

       1802 TTAATAGATA


Statistics
Matches: 138,  Mismatches: 6, Indels: 5
        0.93            0.04        0.03

Matches are distributed among these distances:
  68   17  0.12
  69   71  0.51
  71   26  0.19
  73   24  0.17

ACGTcount: A:0.42, C:0.14, G:0.06, T:0.38


Consensus pattern (69 bp):   
AATCAATCAATCAATTTAATATCATTAGTACTAATTGATTCTAATTGGATCAAGATATTCAAATC
AATC

Found at i:3372 original size:16 final size:16

Alignment explanation


    Indices: 3343--3384  Score: 50
    Period size: 16  Copynumber: 2.6  Consensus size: 16

       3333 ATTATATTCC

                             
       3343 ATATCAA-TGTCTAAAT
          1 ATATCAATTG-CTAAAT

              *           * 
       3359 ATGTCAATTGCTAATT
          1 ATATCAATTGCTAAAT

                      
       3375 ATATCAATTG
          1 ATATCAATTG

       3385 ATTTATAATC


Statistics
Matches: 22,  Mismatches: 3, Indels: 2
        0.81            0.11        0.07

Matches are distributed among these distances:
  16   20  0.91
  17    2  0.09

ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40


Consensus pattern (16 bp):   
ATATCAATTGCTAAAT
Done.