Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011573.1 Corchorus capsularis cultivar CVL-1 contig11594, 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: 19331
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32


Found at i:136 original size:25 final size:23

Alignment explanation


    Indices: 100--145  Score: 65
    Period size: 25  Copynumber: 1.9  Consensus size: 23

         90 ATTAAATTTA

                            *      
        100 ATTTATTAATTTAATTTTAATTG
          1 ATTTATTAATTTAATTATAATTG

                                   
        123 ATTTATTATCATTTAATTATAAT
          1 ATTTATTA--ATTTAATTATAAT

        146 GCAAAAGAAT


Statistics
Matches: 20,  Mismatches: 1, Indels: 2
        0.87            0.04        0.09

Matches are distributed among these distances:
  23    8  0.40
  25   12  0.60

ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59


Consensus pattern (23 bp):   
ATTTATTAATTTAATTATAATTG

Found at i:578 original size:92 final size:92

Alignment explanation


    Indices: 421--595  Score: 341
    Period size: 92  Copynumber: 1.9  Consensus size: 92

        411 AGACACTAAG

                                                                             
        421 TGATTATTTTTTTTTGAGTAAATAATCAAAATTTCATTAATCAATAATTAGAGATTACAAACACC
          1 TGATTATTTTTTTTTGAGTAAATAATCAAAATTTCATTAATCAATAATTAGAGATTACAAACACC

                                       
        486 GGGAGAAATAGTCCCACATCCACACAA
         66 GGGAGAAATAGTCCCACATCCACACAA

                                                                             
        513 TGATTATTTTTTTTTGAGTAAATAATCAAAATTTCATTAATCAATAATTAGAGATTACAAACACC
          1 TGATTATTTTTTTTTGAGTAAATAATCAAAATTTCATTAATCAATAATTAGAGATTACAAACACC

                         *    
        578 GGGAGAAATAGTCTCACA
         66 GGGAGAAATAGTCCCACA

        596 CCCAAACTTA


Statistics
Matches: 82,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
  92   82  1.00

ACGTcount: A:0.41, C:0.14, G:0.11, T:0.33


Consensus pattern (92 bp):   
TGATTATTTTTTTTTGAGTAAATAATCAAAATTTCATTAATCAATAATTAGAGATTACAAACACC
GGGAGAAATAGTCCCACATCCACACAA

Found at i:1043 original size:5 final size:5

Alignment explanation


    Indices: 1035--1060  Score: 52
    Period size: 5  Copynumber: 5.2  Consensus size: 5

       1025 TGAATTCTTC

                                           
       1035 AGAAA AGAAA AGAAA AGAAA AGAAA A
          1 AGAAA AGAAA AGAAA AGAAA AGAAA A

       1061 AAAGGAGATA


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   5   21  1.00

ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00


Consensus pattern (5 bp):   
AGAAA

Found at i:10378 original size:125 final size:122

Alignment explanation


    Indices: 10124--10370  Score: 350
    Period size: 131  Copynumber: 2.0  Consensus size: 122

      10114 ACCATGTTAC

                                                     *                       
      10124 CATTTTCCTTTTTCGGATAAATATCATGTTACCATTTTCAGTCAAAGAGAATATAAGAAAGATTT
          1 CATTTTCCTTTTTCGGATAAATATCATGTTACCATTTTCAGCCAAAGAGAATATAAGAAAGATTT

               *                                                       *
      10189 CAACTTTTGATCAAACATACAAGTACTAACTTTGCATTTATAAATAGGAAACCATGTTAC
         66 CAAATTTTGATCAAACATACAAGTACTAACTTTGCATTTATAAATAGGAAA-CA--TTAA

                         *             *               *                     
      10249 CATTTTCCTTTTTTGGATAAATATCATTTTACCATTTTCAGCCGAAGAGAATATAAGAAAACTTC
          1 CATTTTCCTTTTTCGGATAAATATCATGTTACCATTTTCAGCCAAAGAGAATATAAG--AA----

                                                         *           
      10314 AGATTTCAAATTTTGATCAAACATACAAGTACTAACTTTGCATTTCTAAATAGGAAA
         60 AGATTTCAAATTTTGATCAAACATACAAGTACTAACTTTGCATTTATAAATAGGAAA

      10371 TAACATTTGA


Statistics
Matches: 110,  Mismatches: 6, Indels: 6
        0.90            0.05        0.05

Matches are distributed among these distances:
 125   53  0.48
 127    2  0.02
 131   55  0.50

ACGTcount: A:0.38, C:0.16, G:0.11, T:0.36


Consensus pattern (122 bp):   
CATTTTCCTTTTTCGGATAAATATCATGTTACCATTTTCAGCCAAAGAGAATATAAGAAAGATTT
CAAATTTTGATCAAACATACAAGTACTAACTTTGCATTTATAAATAGGAAACATTAA

Found at i:11960 original size:38 final size:38

Alignment explanation


    Indices: 11888--11960  Score: 110
    Period size: 38  Copynumber: 1.9  Consensus size: 38

      11878 CACCACCCCA

                                   * *   *        
      11888 TATAATAAGTTTTCAAAGCCACTTAGAGGTGCCTTCCG
          1 TATAATAAGTTTTCAAAGCCACTAAAAGGAGCCTTCCG

                                       *       
      11926 TATAATAAGTTTTCAAAGCCACTAAAATGAGCCTT
          1 TATAATAAGTTTTCAAAGCCACTAAAAGGAGCCTT

      11961 AACTCAGCAC


Statistics
Matches: 31,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  38   31  1.00

ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32


Consensus pattern (38 bp):   
TATAATAAGTTTTCAAAGCCACTAAAAGGAGCCTTCCG

Found at i:13850 original size:28 final size:28

Alignment explanation


    Indices: 13810--13867  Score: 116
    Period size: 28  Copynumber: 2.1  Consensus size: 28

      13800 GTGATGAAGG

                                        
      13810 ACTAATTAGCTTTTTCAAATTAAATAAA
          1 ACTAATTAGCTTTTTCAAATTAAATAAA

                                        
      13838 ACTAATTAGCTTTTTCAAATTAAATAAA
          1 ACTAATTAGCTTTTTCAAATTAAATAAA

              
      13866 AC
          1 AC

      13868 GGCATTTTCT


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  28   30  1.00

ACGTcount: A:0.47, C:0.12, G:0.03, T:0.38


Consensus pattern (28 bp):   
ACTAATTAGCTTTTTCAAATTAAATAAA
Done.