Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014494.1 Corchorus olitorius cultivar O-4 contig14527, 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: 14834
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.34


Found at i:162 original size:51 final size:50

Alignment explanation


    Indices: 61--162  Score: 127
    Period size: 51  Copynumber: 2.0  Consensus size: 50

         51 GTTCTTCATA

                                                     * **     
         61 TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCTTTTAGTGT
          1 TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGT

                                            *                    
        111 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGACATACAAACACT-GTACACGTGT
          1 TTTTC-CTTGTTT-AGATCTTGTCTCCGGACAAACAAACACTCGTACA-GTGT

             
        162 T
          1 T

        163 CTTCATTCAG


Statistics
Matches: 45,  Mismatches: 4, Indels: 5
        0.83            0.07        0.09

Matches are distributed among these distances:
  50    7  0.16
  51   37  0.82
  52    1  0.02

ACGTcount: A:0.22, C:0.24, G:0.14, T:0.41


Consensus pattern (50 bp):   
TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGT

Found at i:10492 original size:11 final size:11

Alignment explanation


    Indices: 10476--10500  Score: 50
    Period size: 11  Copynumber: 2.3  Consensus size: 11

      10466 TTTATTATTA

                       
      10476 TATCTATATAC
          1 TATCTATATAC

                       
      10487 TATCTATATAC
          1 TATCTATATAC

               
      10498 TAT
          1 TAT

      10501 ATAAGTCTAA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   14  1.00

ACGTcount: A:0.36, C:0.16, G:0.00, T:0.48


Consensus pattern (11 bp):   
TATCTATATAC

Found at i:10775 original size:39 final size:40

Alignment explanation


    Indices: 10719--10799  Score: 137
    Period size: 39  Copynumber: 2.0  Consensus size: 40

      10709 TTTAATTCCT

                                                    
      10719 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
          1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA

                     *          *                   
      10759 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
          1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA

              
      10798 AT
          1 AT

      10800 TCTTAGGTAT


Statistics
Matches: 39,  Mismatches: 2, Indels: 1
        0.93            0.05        0.02

Matches are distributed among these distances:
  39   31  0.79
  40    8  0.21

ACGTcount: A:0.51, C:0.09, G:0.04, T:0.37


Consensus pattern (40 bp):   
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA

Found at i:11151 original size:204 final size:202

Alignment explanation


    Indices: 10909--11320  Score: 691
    Period size: 204  Copynumber: 2.0  Consensus size: 202

      10899 TTCCTTAATA

                        *                                                    
      10909 ATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTA
          1 ATAAATAAATCGAATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTA

                        *                                                   *
      10974 ATTTAATAAATCTACCACTAATGTTCAACTA-ATTTTTTTTGGTATAGTTATATATATATAATAG
         66 ATTTAATAAATCAACCACTAATGTTCAACTACATTTTTTTTGGTATAGTT-T-TATATATAATAA

                    *                                                        
      11038 TAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACAT
        129 TAATGTGTGGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACAT

                     
      11103 TCACCATTG
        194 TCACCATTG

                    *                                                        
      11112 ATAAATAAGTCGAATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
          1 ATAAATAAATCGAATC-TTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT

            *                         *       *                              
      11177 GATTTAATAAATCAACCACTAATGTTTAACTACTTTTTTTTTTGGTATAGTTTTATATATAATAA
         65 AATTTAATAAATCAACCACTAATGTTCAACTAC-ATTTTTTTTGGTATAGTTTTATATATAATAA

                                                       *          *          
      11242 TAATGTGTGGTATCTTATTCACTACAACTTTGTTAGTAATCTTTGACTTAAAAACTTAATAACAT
        129 TAATGTGTGGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACAT

                     
      11307 TCACCATTG
        194 TCACCATTG

                 
      11316 ATAAA
          1 ATAAA

      11321 GTTATTAAGC


Statistics
Matches: 196,  Mismatches: 10, Indels: 5
        0.93            0.05        0.02

Matches are distributed among these distances:
 203   14  0.07
 204  164  0.84
 205    1  0.01
 206   17  0.09

ACGTcount: A:0.35, C:0.11, G:0.09, T:0.45


Consensus pattern (202 bp):   
ATAAATAAATCGAATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTA
ATTTAATAAATCAACCACTAATGTTCAACTACATTTTTTTTGGTATAGTTTTATATATAATAATA
ATGTGTGGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTC
ACCATTG

Found at i:11879 original size:36 final size:36

Alignment explanation


    Indices: 11832--11901  Score: 113
    Period size: 36  Copynumber: 1.9  Consensus size: 36

      11822 GAGATTTTGG

                         *      *               
      11832 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
          1 AGAAATATGATAACCAAAATCACAAAAAATGTAATA

                                       *      
      11868 AGAAATATGATAACCAAAATCACAAAAGATGTAA
          1 AGAAATATGATAACCAAAATCACAAAAAATGTAA

      11902 GGTTATTGAA


Statistics
Matches: 31,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  36   31  1.00

ACGTcount: A:0.60, C:0.09, G:0.10, T:0.21


Consensus pattern (36 bp):   
AGAAATATGATAACCAAAATCACAAAAAATGTAATA
Done.