Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000458.1 Corchorus capsularis cultivar CVL-1 contig00458, 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: 9315
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.31


Found at i:1065 original size:20 final size:19

Alignment explanation


    Indices: 1014--1081  Score: 61
    Period size: 20  Copynumber: 3.6  Consensus size: 19

       1004 ATAATATATA

                   *            
       1014 TATATATATATTAATTAA-T
          1 TATATATTTA-TAATTAATT

                 *             
       1033 TAT-TCTTT-TAATTAATT
          1 TATATATTTATAATTAATT

                               *
       1050 TATATATTTATGAATTAATA
          1 TATATATTTAT-AATTAATT

                   *    
       1070 TATATATATATA
          1 TATATATTTATA

       1082 TATATTTGTA


Statistics
Matches: 40,  Mismatches: 5, Indels: 8
        0.75            0.09        0.15

Matches are distributed among these distances:
  16    7  0.17
  17    4  0.10
  18    7  0.17
  19    5  0.12
  20   17  0.43

ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54


Consensus pattern (19 bp):   
TATATATTTATAATTAATT

Found at i:5044 original size:45 final size:46

Alignment explanation


    Indices: 4960--5050  Score: 123
    Period size: 45  Copynumber: 2.0  Consensus size: 46

       4950 ACATCTACAT

                                             **              
       4960 GAGATATGACTAGCAGGCAGGCTACAAGTAATAGGTAAAAATAAATAGA
          1 GAGATATGACTAGCA-G-AGGCTACAAGTAATAAATAAAAA-AAATAGA

                                                        
       5009 GAGATATGACTAGCA-A-GCTACAAGTAATAAATAAAAAAAATA
          1 GAGATATGACTAGCAGAGGCTACAAGTAATAAATAAAAAAAATA

       5051 AAAAAAGGGA


Statistics
Matches: 40,  Mismatches: 2, Indels: 5
        0.85            0.04        0.11

Matches are distributed among these distances:
  44    5  0.12
  45   19  0.47
  46    1  0.03
  49   15  0.38

ACGTcount: A:0.52, C:0.10, G:0.20, T:0.19


Consensus pattern (46 bp):   
GAGATATGACTAGCAGAGGCTACAAGTAATAAATAAAAAAAATAGA

Found at i:6609 original size:174 final size:175

Alignment explanation


    Indices: 6300--6643  Score: 566
    Period size: 174  Copynumber: 2.0  Consensus size: 175

       6290 CTAACAGTAT

                              *                                  *       *  *
       6300 ATTTTTGTGCAATCAGGTTCCTAAACTTTTCAATTTTTCAATTCTATCCCCCTGATTTATAGATT
          1 ATTTTTGTGCAATCAGGTCCCTAAACTTTTCAATTTTTCAATTCTATCCCCCTAATTTATAAATC

                                              *             *                
       6365 TATGCATTCACATCCCTCATTCATATATTCAACATAAAATCAATTTTCGCATGACAATACAAACT
         66 TATGCATTCACATCCCTCATTCATATATTCAACACAAAATCAATTTTCACATGACAATACAAACT

                  *                *                     
       6430 CATATCGAGCAACAAACACCAATTTACATTCTATAAGACACCATC
        131 CATATCAAGCAACAAACACCAATCTACATTCTATAAGACACCATC

                         *                *                                  
       6475 ATTTTT-TGCAATTAGGTCCCTAAACTTTTTAATTTTTCAATTCTATCCCCCTAATTTATAAATC
          1 ATTTTTGTGCAATCAGGTCCCTAAACTTTTCAATTTTTCAATTCTATCCCCCTAATTTATAAATC

                                                    *                        
       6539 TATGCATTCACATCCCTCATTCATATATTCAACACAAAATTAATTTTCACAT-AGCAATACAAAC
         66 TATGCATTCACATCCCTCATTCATATATTCAACACAAAATCAATTTTCACATGA-CAATACAAAC

                                                     
       6603 TCATATCAAGCAACAAACACCAATCTACATTCTATAAGACA
        130 TCATATCAAGCAACAAACACCAATCTACATTCTATAAGACA

       6644 TTACCCATCA


Statistics
Matches: 157,  Mismatches: 11, Indels: 3
        0.92            0.06        0.02

Matches are distributed among these distances:
 173    1  0.01
 174  150  0.96
 175    6  0.04

ACGTcount: A:0.36, C:0.24, G:0.06, T:0.35


Consensus pattern (175 bp):   
ATTTTTGTGCAATCAGGTCCCTAAACTTTTCAATTTTTCAATTCTATCCCCCTAATTTATAAATC
TATGCATTCACATCCCTCATTCATATATTCAACACAAAATCAATTTTCACATGACAATACAAACT
CATATCAAGCAACAAACACCAATCTACATTCTATAAGACACCATC
Done.