Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013862.1 Corchorus olitorius cultivar O-4 contig13895, 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: 19745
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35


Found at i:9732 original size:36 final size:35

Alignment explanation


    Indices: 9692--9796  Score: 85
    Period size: 32  Copynumber: 3.1  Consensus size: 35

       9682 ATCTCTACTT

                                                
       9692 ATTGTTGATTTAAATTATAGTCTATTTGATTTAGGA
          1 ATTGTTGATTTAAATTATAGTC-ATTTGATTTAGGA

                 * **         * *           *   
       9728 ATTGTGGCCTT-AATT-TTGAC-TTT-ATTTTTGG-
          1 ATTGTTGATTTAAATTATAGTCATTTGA-TTTAGGA

            *                                   
       9759 GTTGTTGATTTAAATTATAGTCCATTTGATTTAGGA
          1 ATTGTTGATTTAAATTATAGT-CATTTGATTTAGGA

              
       9795 AT
          1 AT

       9797 AATCACACTA


Statistics
Matches: 48,  Mismatches: 14, Indels: 14
        0.63            0.18        0.18

Matches are distributed among these distances:
  31    8  0.17
  32   12  0.25
  33    2  0.04
  34    4  0.08
  35   12  0.25
  36   10  0.21

ACGTcount: A:0.26, C:0.06, G:0.18, T:0.50


Consensus pattern (35 bp):   
ATTGTTGATTTAAATTATAGTCATTTGATTTAGGA

Found at i:10704 original size:22 final size:22

Alignment explanation


    Indices: 10659--10707  Score: 62
    Period size: 22  Copynumber: 2.2  Consensus size: 22

      10649 AAAATTAATG

                           * * *  
      10659 AATTACTTAATTTATTAGTTTT
          1 AATTACTTAATTTATGACTGTT

                 *                
      10681 AATTAGTTAATTTATGACTGTT
          1 AATTACTTAATTTATGACTGTT

                 
      10703 AATTA
          1 AATTA

      10708 ATAAAAATTT


Statistics
Matches: 23,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  22   23  1.00

ACGTcount: A:0.35, C:0.04, G:0.08, T:0.53


Consensus pattern (22 bp):   
AATTACTTAATTTATGACTGTT

Found at i:11217 original size:12 final size:13

Alignment explanation


    Indices: 11200--11233  Score: 52
    Period size: 13  Copynumber: 2.7  Consensus size: 13

      11190 TTTAGGGTTT

                        *
      11200 AATTAATTT-ATG
          1 AATTAATTTAATA

                         
      11212 AATTAATTTAATA
          1 AATTAATTTAATA

                     
      11225 AATTAATTT
          1 AATTAATTT

      11234 GAGTTATTAT


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  12    9  0.45
  13   11  0.55

ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50


Consensus pattern (13 bp):   
AATTAATTTAATA

Found at i:15575 original size:21 final size:21

Alignment explanation


    Indices: 15545--15584  Score: 62
    Period size: 21  Copynumber: 1.9  Consensus size: 21

      15535 CTAAAAACAG

                 *               
      15545 GACAAGTCCTGCCCAGGACTT
          1 GACAACTCCTGCCCAGGACTT

                        *      
      15566 GACAACTCCTGCTCAGGAC
          1 GACAACTCCTGCCCAGGAC

      15585 CTGGTCTGTT


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  21   17  1.00

ACGTcount: A:0.25, C:0.35, G:0.23, T:0.17


Consensus pattern (21 bp):   
GACAACTCCTGCCCAGGACTT

Found at i:15642 original size:50 final size:50

Alignment explanation


    Indices: 15567--15688  Score: 199
    Period size: 50  Copynumber: 2.4  Consensus size: 50

      15557 CCAGGACTTG

                       *      *                               
      15567 ACAACTCCTGCTCAGGACCTGGTCTGTTGAAAGACGGAAGAAAAATCAGA
          1 ACAACTCCTGCCCAGGACTTGGTCTGTTGAAAGACGGAAGAAAAATCAGA

                                                        *     
      15617 ACAACTCCTGCCCAGGACTTGGTCTGTTGAAAGACGGAAGAAAATTCAGA
          1 ACAACTCCTGCCCAGGACTTGGTCTGTTGAAAGACGGAAGAAAAATCAGA

                *     *           
      15667 ACAAATCCTGTCCAGGACTTGG
          1 ACAACTCCTGCCCAGGACTTGG

      15689 ACAACTCTTG


Statistics
Matches: 67,  Mismatches: 5, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  50   67  1.00

ACGTcount: A:0.34, C:0.23, G:0.24, T:0.20


Consensus pattern (50 bp):   
ACAACTCCTGCCCAGGACTTGGTCTGTTGAAAGACGGAAGAAAAATCAGA

Found at i:17931 original size:33 final size:33

Alignment explanation


    Indices: 17830--17967  Score: 129
    Period size: 33  Copynumber: 4.2  Consensus size: 33

      17820 TTGCAAAGAG

                    *       *       *      * 
      17830 TGTTTTAGATGTTGTTAGTGATGATACTAAACC
          1 TGTTTTAGGTGTTGTTTGTGATGAAACTAAATC

             **    *                *        
      17863 TAATTTAAGTGTTGTTTGTGATGACACTAAATC
          1 TGTTTTAGGTGTTGTTTGTGATGAAACTAAATC

                                              
      17896 TGTTTTAGGTGTTGTTTGTGATGAAAC-AAATTC
          1 TGTTTTAGGTGTTGTTTGTGATGAAACTAAA-TC

                        * **                   
      17929 TGTTTT-GGATGCTAATTGTGATGAAAAC-AAATC
          1 TGTTTTAGG-TGTTGTTTGTGATG-AAACTAAATC

                  
      17962 TGTTTT
          1 TGTTTT

      17968 GGTTGATCAT


Statistics
Matches: 88,  Mismatches: 14, Indels: 6
        0.81            0.13        0.06

Matches are distributed among these distances:
  32    5  0.06
  33   76  0.86
  34    7  0.08

ACGTcount: A:0.28, C:0.08, G:0.21, T:0.43


Consensus pattern (33 bp):   
TGTTTTAGGTGTTGTTTGTGATGAAACTAAATC
Done.