Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006086.1 Corchorus olitorius cultivar O-4 contig06111, 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, 688

Length: 1148
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.38


Found at i:55 original size:39 final size:39

Alignment explanation


    Indices: 1--288  Score: 450
    Period size: 39  Copynumber: 7.4  Consensus size: 39

                      *                          **
          1 TGGAAACAGGCCATCTTTTCAGCATTTATCAAAGTTGGT
          1 TGGAAACAGGTCATCTTTTCAGCATTTATCAAAGTTGAC

                  *   *                            
         40 TGGAAATAGGCCATCTTTTCAGCATTTATCAAAGTTGAC
          1 TGGAAACAGGTCATCTTTTCAGCATTTATCAAAGTTGAC

                                                   
         79 TGGAAACAGGTCATCTTTTCAGCATTTATCAAAGTTGAC
          1 TGGAAACAGGTCATCTTTTCAGCATTTATCAAAGTTGAC

                            *                    **
        118 TGGAAACAGGTCATCTCTTCAGCATTTATCAAAGTTGGT
          1 TGGAAACAGGTCATCTTTTCAGCATTTATCAAAGTTGAC

                      *                            
        157 TGGAAACAGGCCATCTTTTCAGCATTTATCAAAGTTGAC
          1 TGGAAACAGGTCATCTTTTCAGCATTTATCAAAGTTGAC

                            *    *                 
        196 TGGAAACAGGTCATCTCTTCAACATTTATCAAAGTTGAC
          1 TGGAAACAGGTCATCTTTTCAGCATTTATCAAAGTTGAC

                               * **                
        235 TGGAAACAGGTCATCTTTTTAATATTTATCAAAGTTGAC
          1 TGGAAACAGGTCATCTTTTCAGCATTTATCAAAGTTGAC

                           
        274 TGGAAACAGGTCATC
          1 TGGAAACAGGTCATC

        289 CCTTCTCATT


Statistics
Matches: 231,  Mismatches: 18, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  39  231  1.00

ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33


Consensus pattern (39 bp):   
TGGAAACAGGTCATCTTTTCAGCATTTATCAAAGTTGAC

Found at i:347 original size:33 final size:30

Alignment explanation


    Indices: 305--423  Score: 132
    Period size: 33  Copynumber: 3.7  Consensus size: 30

        295 CATTTTTTAT

                                           
        305 TTCGACCTCAGACAGGTCTTTATCTTTCAAG
          1 TTCGACCTCAGACAGGTCTTTATCTTT-AAG

                                               *
        336 TTCCAGACCTCAGACAGGTCTTCCTCAGT-TTTAAA
          1 TT-C-GACCTCAGACAGGTCTT--T-A-TCTTTAAG

                                       *  
        371 TTCGACCTCAGACAGGTCTTTATCTTTTAG
          1 TTCGACCTCAGACAGGTCTTTATCTTTAAG

                                   
        401 TTTCGGACCTCAGACAGGTCTTT
          1 -TTC-GACCTCAGACAGGTCTTT

        424 CTTAGTTTTT


Statistics
Matches: 76,  Mismatches: 3, Indels: 17
        0.79            0.03        0.18

Matches are distributed among these distances:
  29    1  0.01
  30    5  0.07
  31    6  0.08
  32   19  0.25
  33   34  0.45
  34    1  0.01
  35    5  0.07
  36    4  0.05
  37    1  0.01

ACGTcount: A:0.22, C:0.26, G:0.17, T:0.35


Consensus pattern (30 bp):   
TTCGACCTCAGACAGGTCTTTATCTTTAAG

Found at i:435 original size:66 final size:66

Alignment explanation


    Indices: 305--432  Score: 204
    Period size: 65  Copynumber: 2.0  Consensus size: 66

        295 CATTTTTTAT

                                                                             
        305 TTCGACCTCAGACAGGTCTTTATCTTTCAAGTTCCAGACCTCAGACAGGTCTTCCTCAGTTTTAA
          1 TTCGACCTCAGACAGGTCTTTATCTTTCAAGTTCCAGACCTCAGACAGGTCTTCCTCAGTTTTAA

             
        370 A
         66 A

                                        *    * *                 *  *      
        371 TTCGACCTCAGACAGGTCTTTATCTTT-TAGTTTCGGACCTCAGACAGGTCTTTCTTAGTTTT
          1 TTCGACCTCAGACAGGTCTTTATCTTTCAAGTTCCAGACCTCAGACAGGTCTTCCTCAGTTTT

        433 TAAGGTCGAC


Statistics
Matches: 57,  Mismatches: 5, Indels: 1
        0.90            0.08        0.02

Matches are distributed among these distances:
  65   30  0.53
  66   27  0.47

ACGTcount: A:0.21, C:0.25, G:0.16, T:0.38


Consensus pattern (66 bp):   
TTCGACCTCAGACAGGTCTTTATCTTTCAAGTTCCAGACCTCAGACAGGTCTTCCTCAGTTTTAA
A

Found at i:442 original size:66 final size:66

Alignment explanation


    Indices: 306--442  Score: 195
    Period size: 66  Copynumber: 2.1  Consensus size: 66

        296 ATTTTTTATT

                                                                             
        306 TCGACCTCAGACAGGTCTTTATCTTTCAAGTTCCAGACCTCAGACAGGTCTTCCTCAGTTTTAAA
          1 TCGACCTCAGACAGGTCTTTATCTTTCAAGTTCCAGACCTCAGACAGGTCTTCCTCAGTTTTAAA

            *
        371 T
         66 G

                                       *    * *                 *  *         
        372 TCGACCTCAGACAGGTCTTTATCTTT-TAGTTTCGGACCTCAGACAGGTCTTTCTTAGTTTTTAA
          1 TCGACCTCAGACAGGTCTTTATCTTTCAAGTTCCAGACCTCAGACAGGTCTTCCTCAG-TTTTAA

            * 
        436 GG
         65 AG

                 
        438 TCGAC
          1 TCGAC

        443 TTCTTCAGTT


Statistics
Matches: 63,  Mismatches: 7, Indels: 2
        0.88            0.10        0.03

Matches are distributed among these distances:
  65   26  0.41
  66   37  0.59

ACGTcount: A:0.22, C:0.25, G:0.18, T:0.36


Consensus pattern (66 bp):   
TCGACCTCAGACAGGTCTTTATCTTTCAAGTTCCAGACCTCAGACAGGTCTTCCTCAGTTTTAAA
G
Done.