Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015355.1 Corchorus olitorius cultivar O-4 contig15388, 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: 2676
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34


Found at i:278 original size:21 final size:21

Alignment explanation


    Indices: 252--364  Score: 147
    Period size: 21  Copynumber: 5.4  Consensus size: 21

        242 TGCTAGAAGT

                                 
        252 TCATTGGAGCAAGTTCCAAGC
          1 TCATTGGAGCAAGTTCCAAGC

                                 
        273 TCATTGGAGCAAGTTCCAAGC
          1 TCATTGGAGCAAGTTCCAAGC

                       *   *    *
        294 TCATTGGAGCAGGTTACAAGT
          1 TCATTGGAGCAAGTTCCAAGC

                     * *        *
        315 TCATTGGAGGAGGTTCCAAGA
          1 TCATTGGAGCAAGTTCCAAGC

                            *     
        336 TCATTGGAG-AAGGTTTCAAGC
          1 TCATTGGAGCAA-GTTCCAAGC

                    
        357 TCATTGGA
          1 TCATTGGA

        365 AATGCCTAAG


Statistics
Matches: 82,  Mismatches: 9, Indels: 2
        0.88            0.10        0.02

Matches are distributed among these distances:
  20    1  0.01
  21   81  0.99

ACGTcount: A:0.28, C:0.18, G:0.27, T:0.27


Consensus pattern (21 bp):   
TCATTGGAGCAAGTTCCAAGC

Found at i:502 original size:20 final size:21

Alignment explanation


    Indices: 479--521  Score: 61
    Period size: 21  Copynumber: 2.1  Consensus size: 21

        469 ATCTTGAAGA

                                 
        479 ATTTAAAG-CCATCGGAGATC
          1 ATTTAAAGCCCATCGGAGATC

                *        *       
        499 ATTTGAAGCCCATTGGAGATC
          1 ATTTAAAGCCCATCGGAGATC

              
        520 AT
          1 AT

        522 CAACAAAGGA


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

Matches are distributed among these distances:
  20    7  0.35
  21   13  0.65

ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28


Consensus pattern (21 bp):   
ATTTAAAGCCCATCGGAGATC

Found at i:1287 original size:21 final size:21

Alignment explanation


    Indices: 1261--1373  Score: 149
    Period size: 21  Copynumber: 5.4  Consensus size: 21

       1251 TGCTAGAAGT

                                 
       1261 TCATTGGAGCAAGTTCCAAGC
          1 TCATTGGAGCAAGTTCCAAGC

                                 
       1282 TCATTGGAGCAAGTTCCAAGC
          1 TCATTGGAGCAAGTTCCAAGC

                       *        *
       1303 TCATTGGAGCAGGTTCCAAGT
          1 TCATTGGAGCAAGTTCCAAGC

                                 *
       1324 TCATTGGAG-AAGGTTCCAAGA
          1 TCATTGGAGCAA-GTTCCAAGC

                *           *     
       1345 TCATAGGAG-AAGGTTTCAAGC
          1 TCATTGGAGCAA-GTTCCAAGC

                    
       1366 TCATTGGA
          1 TCATTGGA

       1374 AATGCCTAAG


Statistics
Matches: 83,  Mismatches: 8, Indels: 2
        0.89            0.09        0.02

Matches are distributed among these distances:
  20    1  0.01
  21   82  0.99

ACGTcount: A:0.29, C:0.19, G:0.27, T:0.26


Consensus pattern (21 bp):   
TCATTGGAGCAAGTTCCAAGC

Found at i:2536 original size:144 final size:144

Alignment explanation


    Indices: 2335--2609  Score: 460
    Period size: 144  Copynumber: 1.9  Consensus size: 144

       2325 TGTTTATGGC

                                      **                  *                  
       2335 CTAACTATAACCATTTTGGTGAGATTGGTCCACTGTGAAGTTCTTAGCTCATTTGGAACACTTGT
          1 CTAACTATAACCATTTTGGTGAGATTACTCCACTGTGAAGTTCTTAACTCATTTGGAACACTTGT

                          *           *                                      
       2400 TATGTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAACCCTCAAT
         66 TATGTTGGGCCTATAGGGGCCCATTAATGACGTTTTGAATCGTCTTCGATTTGGCAACCCTCAAT

                          
       2465 GTTCTTTTAATAGG
        131 GTTCTTTTAATAGG

                      *                               *                      
       2479 CTAACTATAATCATTTTGGTGAGATTACTCCACTGTGAAGTTTTTAACTCATTTGGAACACTTGT
          1 CTAACTATAACCATTTTGGTGAGATTACTCCACTGTGAAGTTCTTAACTCATTTGGAACACTTGT

               *                        **                                   
       2544 TATTTTGGGCCTATAGGGGCCCATTAATTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAAT
         66 TATGTTGGGCCTATAGGGGCCCATTAATGACGTTTTGAATCGTCTTCGATTTGGCAACCCTCAAT

             
       2609 G
        131 G

       2610 CTTTTTTTTT


Statistics
Matches: 121,  Mismatches: 10, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
 144  121  1.00

ACGTcount: A:0.23, C:0.20, G:0.20, T:0.37


Consensus pattern (144 bp):   
CTAACTATAACCATTTTGGTGAGATTACTCCACTGTGAAGTTCTTAACTCATTTGGAACACTTGT
TATGTTGGGCCTATAGGGGCCCATTAATGACGTTTTGAATCGTCTTCGATTTGGCAACCCTCAAT
GTTCTTTTAATAGG
Done.