Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022736.1 Corchorus olitorius cultivar O-4 contig22769, 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: 7633
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:2464 original size:38 final size:38

Alignment explanation


    Indices: 2413--2491  Score: 131
    Period size: 38  Copynumber: 2.1  Consensus size: 38

       2403 TTAGAGTTGC

                    *              *              
       2413 CATTTAAGTAAACCTGCTTAGGTTTACGTTTAGAATCT
          1 CATTTAAGGAAACCTGCTTAGGTCTACGTTTAGAATCT

                                      *           
       2451 CATTTAAGGAAACCTGCTTAGGTCTATGTTTAGAATCT
          1 CATTTAAGGAAACCTGCTTAGGTCTACGTTTAGAATCT

               
       2489 CAT
          1 CAT

       2492 CAGAATTTCT


Statistics
Matches: 38,  Mismatches: 3, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  38   38  1.00

ACGTcount: A:0.29, C:0.16, G:0.16, T:0.38


Consensus pattern (38 bp):   
CATTTAAGGAAACCTGCTTAGGTCTACGTTTAGAATCT

Found at i:2593 original size:39 final size:39

Alignment explanation


    Indices: 2493--2640  Score: 190
    Period size: 39  Copynumber: 3.8  Consensus size: 39

       2483 GAATCTCATC

                    *       *                ** *  
       2493 AGAATTTCTGTTTAAGAAAACCTGCTTAGGTCCCCGCTT
          1 AGAATTTCCGTTTAAGCAAACCTGCTTAGGTCCTTGTTT

                 *       * **                      
       2532 AGAATCT-CGTTTGATTAAACCTGCTTAGGTCCTTGTTT
          1 AGAATTTCCGTTTAAGCAAACCTGCTTAGGTCCTTGTTT

                                        *          
       2570 AGAATTTCCGTTTAAGCAAACCTGCTTACGTCCTTGTTT
          1 AGAATTTCCGTTTAAGCAAACCTGCTTAGGTCCTTGTTT

                                 *          
       2609 AGAATTTCCGTTTAAGCAAACTTGCTTAGGTC
          1 AGAATTTCCGTTTAAGCAAACCTGCTTAGGTC

       2641 TCTGTTCCGT


Statistics
Matches: 93,  Mismatches: 15, Indels: 2
        0.85            0.14        0.02

Matches are distributed among these distances:
  38   30  0.32
  39   63  0.68

ACGTcount: A:0.24, C:0.21, G:0.18, T:0.37


Consensus pattern (39 bp):   
AGAATTTCCGTTTAAGCAAACCTGCTTAGGTCCTTGTTT

Found at i:2824 original size:38 final size:36

Alignment explanation


    Indices: 2695--2825  Score: 120
    Period size: 39  Copynumber: 3.4  Consensus size: 36

       2685 TCATTCGAGT

                                    *              
       2695 AAACCTGCTTAGGTCTTCGTTTAAAAGTTTCGTTTAATC
          1 AAACCTGCTTAGGTCTT-GTTT-AGAGTTTCG-TTAATC

                 *                *     *           
       2734 AAACCCGCTTAGGTTCTTGTTTGGAGTTCCTGCTTAAGT-
          1 AAACCTGCTTAGG-TCTTGTTTAGAGTTTC-G-TTAA-TC

            *                  *                  
       2773 GAACCTGCTTAGGTCTATGCTTAGAGTTTCGTTCAATC
          1 AAACCTGCTTAGGTCT-TGTTTAGAGTTTCGTT-AATC

                           
       2811 AAACCTGCTTAGGTC
          1 AAACCTGCTTAGGTC

       2826 CCTCTTTTTA


Statistics
Matches: 75,  Mismatches: 11, Indels: 13
        0.76            0.11        0.13

Matches are distributed among these distances:
  37    3  0.04
  38   25  0.33
  39   42  0.56
  40    5  0.07

ACGTcount: A:0.22, C:0.21, G:0.20, T:0.37


Consensus pattern (36 bp):   
AAACCTGCTTAGGTCTTGTTTAGAGTTTCGTTAATC

Found at i:3992 original size:43 final size:43

Alignment explanation


    Indices: 3945--4033  Score: 169
    Period size: 43  Copynumber: 2.1  Consensus size: 43

       3935 CATATCACCC

                             *                         
       3945 ATTTTGAACTTAGCCAGTATATAGCATTCTCAACACTGCATCG
          1 ATTTTGAACTTAGCCAGCATATAGCATTCTCAACACTGCATCG

                                                       
       3988 ATTTTGAACTTAGCCAGCATATAGCATTCTCAACACTGCATCG
          1 ATTTTGAACTTAGCCAGCATATAGCATTCTCAACACTGCATCG

               
       4031 ATT
          1 ATT

       4034 GAGTAACACA


Statistics
Matches: 45,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  43   45  1.00

ACGTcount: A:0.30, C:0.24, G:0.13, T:0.33


Consensus pattern (43 bp):   
ATTTTGAACTTAGCCAGCATATAGCATTCTCAACACTGCATCG
Done.