Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014241.1 Corchorus capsularis cultivar CVL-1 contig14262, 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: 10152
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33


Found at i:3913 original size:158 final size:162

Alignment explanation


    Indices: 3528--3959  Score: 500
    Period size: 167  Copynumber: 2.7  Consensus size: 162

       3518 ATGAGAAGCG

                                       *     *                 *             
       3528 AGAGAACTAATTTTTTTCATCTTTTCCCACTTGACAGATTACTTAAATGTCCTAACTTTTGATTC
          1 AGAGAACTAATTTTTTTCATCTTTTCCTACTTGGCAGATTACTTAAATGTCATAACTTTTGATTC

                                                        *     *         *    
       3593 TTGAGGGGATTAAATAACTAGA-CTTTTT-AGTCATTTCTCAATTGACTTTAATAGAGTAGTGGA
         66 TTGAGGGGATTAAATAACTA-ATCTTTTTGA-TCATTTCTCAATGGACTTGAATAGAGTACTGG-

                            *       *   * **       
       3656 ATCACTAAAAGATCCCTACCAAAGCTTGCTTTTAGAGTT
        128 A--ACT--AAGATCCCCACCAAAGATTGATGATAGAGTT

                    *         *                                *             
       3695 AGAGAACTTATTTTTTTCTTCTTTTCCTACTTGGCAGATTACTTAAATGTCTTAACTTTTGATTC
          1 AGAGAACTAATTTTTTTCATCTTTTCCTACTTGGCAGATTACTTAAATGTCATAACTTTTGATTC

                *            *                    *                          
       3760 TTGACGGGATTAAATAAGTAATCTTTTTGATCATTTCTTAATGGACTTGAATAGAGTACTGG-A-
         66 TTGAGGGGATTAAATAACTAATCTTTTTGATCATTTCTCAATGGACTTGAATAGAGTACTGGAAC

                       *   *                
       3823 T-AGATCCCCATCAAGGATTGATGAT-GAGTT
        131 TAAGATCCCCACCAAAGATTGATGATAGAGTT

                *      *      *     *           *           *      *         
       3853 AGAGCACTAATCTTTTTCGTCTTTACCTACTTGGCATATTACTTAAATATCATAATTTTTGATTC
          1 AGAGAACTAATTTTTTTCATCTTTTCCTACTTGGCAGATTACTTAAATGTCATAACTTTTGATTC

                                          *            
       3918 TTGAGGGGATTAAATAACTAAAT-TTTTTGGTCATTTCTCAAT
         66 TTGAGGGGATTAAATAACT-AATCTTTTTGATCATTTCTCAAT

       3960 TGACAAATGA


Statistics
Matches: 231,  Mismatches: 31, Indels: 15
        0.83            0.11        0.05

Matches are distributed among these distances:
 158   95  0.41
 159   20  0.09
 162    1  0.00
 163    1  0.00
 166    1  0.00
 167  112  0.48
 168    1  0.00

ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41


Consensus pattern (162 bp):   
AGAGAACTAATTTTTTTCATCTTTTCCTACTTGGCAGATTACTTAAATGTCATAACTTTTGATTC
TTGAGGGGATTAAATAACTAATCTTTTTGATCATTTCTCAATGGACTTGAATAGAGTACTGGAAC
TAAGATCCCCACCAAAGATTGATGATAGAGTT

Found at i:5512 original size:23 final size:23

Alignment explanation


    Indices: 5471--5528  Score: 66
    Period size: 23  Copynumber: 2.5  Consensus size: 23

       5461 GTTTGAAATT

                                     
       5471 GAGGGTTTGAGATCTAGGGATT-TA
          1 GAGGGTTTGA-ATCTAGGG-TTATA

                        *           
       5495 G-GGGTTTGAATTTGAGGGTTATA
          1 GAGGGTTTGAATCT-AGGGTTATA

                       
       5518 GAGGGTTTGAA
          1 GAGGGTTTGAA

       5529 ATCAAGAGTT


Statistics
Matches: 30,  Mismatches: 1, Indels: 6
        0.81            0.03        0.16

Matches are distributed among these distances:
  22    5  0.17
  23   15  0.50
  24   10  0.33

ACGTcount: A:0.24, C:0.02, G:0.40, T:0.34


Consensus pattern (23 bp):   
GAGGGTTTGAATCTAGGGTTATA
Done.