Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005871.1 Corchorus capsularis cultivar CVL-1 contig05889, 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: 1688
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28


Found at i:134 original size:76 final size:82

Alignment explanation


    Indices: 25--236  Score: 276
    Period size: 76  Copynumber: 2.6  Consensus size: 82

         15 AGAATTAAAA

                        *                                                    
         25 ATGAGAATATTTCCTAAATCTTGCCAAATTGTGGGAGATTTAAGAGATATTTTAAG-AAATAAA-
          1 ATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAAGAGATATTTTAAGAAAATAAAT

                 *           
         88 AATAATGA-T-AAAG-T
         66 AATAAAGATTGAAAGAT

                                              *       *                      
        102 -TGAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTAGGAGATATTTTAAGAAACAAATA
          1 ATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAAGAGATATTTTAAG--A-AAATA

                *           *   
        166 AATATTAAAGATTGAATGAT
         63 AATAATAAAGATTGAAAGAT

                                                                
        186 AATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTT-AGAAGATAT
          1 -ATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAAG-AGATAT

        237 AAAAGGAAAT


Statistics
Matches: 116,  Mismatches: 8, Indels: 13
        0.85            0.06        0.09

Matches are distributed among these distances:
  76   52  0.45
  80    7  0.06
  81    6  0.05
  82    1  0.01
  83    3  0.03
  84    1  0.01
  85    1  0.01
  86   45  0.39

ACGTcount: A:0.42, C:0.07, G:0.17, T:0.34


Consensus pattern (82 bp):   
ATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAAGAGATATTTTAAGAAAATAAAT
AATAAAGATTGAAAGAT

Found at i:274 original size:86 final size:86

Alignment explanation


    Indices: 102--274  Score: 210
    Period size: 86  Copynumber: 2.0  Consensus size: 86

         92 ATGATAAAGT

                                                      *       **             
        102 TGAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTAGGAGATATTTTAAGAAACAAATAA
          1 TGAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTAGAAGATATTAAAAGAAACAAATAA

                       **   *    
        167 ATATTAAAGATTGAATGATAA
         66 ATATTAAAGATAAAATAATAA

                                             *                         *     
        188 TGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGAAGATA-TAAAAGGAAATATAAT
          1 TGAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTAGAAGATATTAAAA-GAAACA-AAT

                                     
        252 CAAA-ATT-AA-ATAAAAGTAATAA
         64 -AAATATTAAAGATAAAA-TAATAA

             
        274 T
          1 T

        275 AAAAAATAAT


Statistics
Matches: 75,  Mismatches: 8, Indels: 8
        0.82            0.09        0.09

Matches are distributed among these distances:
  85    7  0.09
  86   59  0.79
  87    6  0.08
  88    3  0.04

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


Consensus pattern (86 bp):   
TGAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTAGAAGATATTAAAAGAAACAAATAA
ATATTAAAGATAAAATAATAA

Found at i:279 original size:23 final size:24

Alignment explanation


    Indices: 247--295  Score: 64
    Period size: 23  Copynumber: 2.1  Consensus size: 24

        237 AAAAGGAAAT

                 *    *             
        247 ATAATCAAAATTAAATAAAAG-TA
          1 ATAATAAAAAATAAATAAAAGATA

                          *         
        270 ATAATAAAAAATAATTAAAAGATA
          1 ATAATAAAAAATAAATAAAAGATA

              
        294 AT
          1 AT

        296 TTTAGACTTT


Statistics
Matches: 22,  Mismatches: 3, Indels: 1
        0.85            0.12        0.04

Matches are distributed among these distances:
  23   18  0.82
  24    4  0.18

ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27


Consensus pattern (24 bp):   
ATAATAAAAAATAAATAAAAGATA
Done.