Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010400.1 Corchorus olitorius cultivar O-4 contig10432, 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: 2849
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35


Found at i:51 original size:35 final size:35

Alignment explanation


    Indices: 5--284  Score: 352
    Period size: 35  Copynumber: 7.9  Consensus size: 35

          1 TCGT

                        *                      
          5 TTCAAGAAGTTTACGATGATCAGAGTTGATCTCGC
          1 TTCAAGAAGTTTTCGATGATCAGAGTTGATCTCGC

                           *                   
         40 TTCAAGAAGTTTTCGGTGATCAGAGTTGATCTC-C
          1 TTCAAGAAGTTTTCGATGATCAGAGTTGATCTCGC

                                            * **
         74 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCGCAT
          1 -TTCAAGAAGTTTTCGATGATCAGAGTTGATCTCGC

                                   *            
        110 TTCAAGAAGTTTTCGATGATCAGTGTTGATCATCGC
          1 TTCAAGAAGTTTTCGATGATCAGAGTTGATC-TCGC

                                                *
        146 ATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCGT
          1 --TTCAAGAAGTTTTCGATGATCAGAGTTGATCTCGC

                          *             *    **
        183 TTCAAGAAGTTTTCAATGATCAGAGTTGGTCTCAT
          1 TTCAAGAAGTTTTCGATGATCAGAGTTGATCTCGC

                          *                    
        218 TTCAAGAAGTTTT-TATGATCAGAGTTGATCTC-C
          1 TTCAAGAAGTTTTCGATGATCAGAGTTGATCTCGC

               *          *                    
        251 TTTTAAGAAGTTTTTG-TCGATCAGAGTTGATCTC
          1 -TTCAAGAAGTTTTCGAT-GATCAGAGTTGATCTC

        285 ATTTTGGTCA


Statistics
Matches: 218,  Mismatches: 19, Indels: 16
        0.86            0.08        0.06

Matches are distributed among these distances:
  34   31  0.14
  35  153  0.70
  36    1  0.00
  37    3  0.01
  38   30  0.14

ACGTcount: A:0.26, C:0.15, G:0.21, T:0.37


Consensus pattern (35 bp):   
TTCAAGAAGTTTTCGATGATCAGAGTTGATCTCGC

Found at i:117 original size:70 final size:70

Alignment explanation


    Indices: 4--284  Score: 395
    Period size: 70  Copynumber: 4.0  Consensus size: 70

          1 TCG

                         *                     *               *             
          4 TTTCAAGAAGTTTACGATGATCAGAGTTGATCTCGCTTCAAGAAGTTTTCGGTGATCAGAGTTGA
          1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTTCAAGAAGTTTTCGATGATCAGAGTTGA

                 
         69 TCTCC
         66 TCTCC

                                            * *                        *     
         74 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCGCATTTCAAGAAGTTTTCGATGATCAGTGTTGA
          1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTTCAAGAAGTTTTCGATGATCAGAGTTGA

                   
        139 TCATCGC
         66 TC-TC-C

                                                               *             
        146 ATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTTCAAGAAGTTTTCAATGATCAGAGTTG
          1 -TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTTCAAGAAGTTTTCGATGATCAGAGTTG

            *    *
        211 GTCTCA
         65 ATCTCC

                           *                  *   *          *               
        217 TTTCAAGAAGTTTT-TATGATCAGAGTTGATCTCCTTTTAAGAAGTTTTTG-TCGATCAGAGTTG
          1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTTCAAGAAGTTTTCGAT-GATCAGAGTTG

                 
        280 ATCTC
         65 ATCTC

        285 ATTTTGGTCA


Statistics
Matches: 189,  Mismatches: 18, Indels: 9
        0.88            0.08        0.04

Matches are distributed among these distances:
  68    1  0.01
  69   46  0.24
  70   75  0.40
  71    2  0.01
  72    3  0.02
  73   62  0.33

ACGTcount: A:0.26, C:0.15, G:0.21, T:0.37


Consensus pattern (70 bp):   
TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTTCAAGAAGTTTTCGATGATCAGAGTTGA
TCTCC

Found at i:367 original size:94 final size:90

Alignment explanation


    Indices: 202--377  Score: 246
    Period size: 94  Copynumber: 1.9  Consensus size: 90

        192 TTTTCAATGA

                     *                                      *   *          * 
        202 TCAGAGTTGGTCTCATTTCAAGAAGTTTTTATGATCAGAGTTGATCTCCTTTTAAGAAGTTTTTG
          1 TCAGAGTTGATCTCATTTCAAGAAGTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCG

                                     
        267 TCGATCAGAGTTGATCTCATTTTGG
         66 TCGATCAGAGTTGATCTCATTTTGG

                          *                                    *             
        292 TCAGAGTTGATCTCCTTTCAAGAAGTTTTTTTTTATGATCAGAGTTGATCTTATTTCAAGAAGTT
          1 TCAGAGTTGATCTCATTTCAAGAAG----TTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTT

                                  
        357 TTCGAT-GATCAGAGTTGATCT
         62 TTCG-TCGATCAGAGTTGATCT

        378 TCACATTGAT


Statistics
Matches: 75,  Mismatches: 6, Indels: 6
        0.86            0.07        0.07

Matches are distributed among these distances:
  90   23  0.31
  94   51  0.68
  95    1  0.01

ACGTcount: A:0.24, C:0.13, G:0.20, T:0.43


Consensus pattern (90 bp):   
TCAGAGTTGATCTCATTTCAAGAAGTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCG
TCGATCAGAGTTGATCTCATTTTGG

Found at i:372 original size:35 final size:36

Alignment explanation


    Indices: 292--378  Score: 113
    Period size: 38  Copynumber: 2.4  Consensus size: 36

        282 CTCATTTTGG

                         **                 **    
        292 TCAGAGTTGATCTCCTTTCAAGAAGTTTTTTTTTATGA
          1 TCAGAGTTGATCTTATTTCAAGAAG--TTTTTCGATGA

                                                
        330 TCAGAGTTGATCTTATTTCAAGAAG-TTTTCGATGA
          1 TCAGAGTTGATCTTATTTCAAGAAGTTTTTCGATGA

                          
        365 TCAGAGTTGATCTT
          1 TCAGAGTTGATCTT

        379 CACATTGATC


Statistics
Matches: 45,  Mismatches: 4, Indels: 3
        0.87            0.08        0.06

Matches are distributed among these distances:
  35   22  0.49
  38   23  0.51

ACGTcount: A:0.25, C:0.13, G:0.18, T:0.44


Consensus pattern (36 bp):   
TCAGAGTTGATCTTATTTCAAGAAGTTTTTCGATGA
Done.