Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009676.1 Corchorus capsularis cultivar CVL-1 contig09697, 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: 28803
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34


Found at i:3510 original size:26 final size:25

Alignment explanation


    Indices: 3463--3514  Score: 59
    Period size: 26  Copynumber: 2.0  Consensus size: 25

       3453 TAATTAATTA

                             *        
       3463 TATAATGAATTATGTGTTTAATTGCT
          1 TATAATGAATTATGTGTCTAA-TGCT

                *      * *           
       3489 TATACTGAATTTTTTGTCTAATGCT
          1 TATAATGAATTATGTGTCTAATGCT

             
       3514 T
          1 T

       3515 GCTTAAAAAT


Statistics
Matches: 22,  Mismatches: 4, Indels: 1
        0.81            0.15        0.04

Matches are distributed among these distances:
  25    5  0.23
  26   17  0.77

ACGTcount: A:0.27, C:0.08, G:0.13, T:0.52


Consensus pattern (25 bp):   
TATAATGAATTATGTGTCTAATGCT

Found at i:5173 original size:70 final size:70

Alignment explanation


    Indices: 5099--5237  Score: 251
    Period size: 70  Copynumber: 2.0  Consensus size: 70

       5089 ATAGGGGCTT

                                                                             
       5099 TTTTTTTTATTTGAAAATCGGGTTCGGGGTGGATCAGATCGATTTTTTATTGTTTGAGAGTCAAG
          1 TTTTTTTTATTTGAAAATCGGGTTCGGGGTGGATCAGATCGATTTTTTATTGTTTGAGAGTCAAG

                 
       5164 GTCGA
         66 GTCGA

                    *               *                       *                
       5169 TTTTTTTTGTTTGAAAATCGGGTTTGGGGTGGATCAGATCGATTTTTTTTTGTTTGAGAGTCAAG
          1 TTTTTTTTATTTGAAAATCGGGTTCGGGGTGGATCAGATCGATTTTTTATTGTTTGAGAGTCAAG

                
       5234 GTCG
         66 GTCG

       5238 GTGTTAGATA


Statistics
Matches: 66,  Mismatches: 3, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  70   66  1.00

ACGTcount: A:0.19, C:0.08, G:0.28, T:0.45


Consensus pattern (70 bp):   
TTTTTTTTATTTGAAAATCGGGTTCGGGGTGGATCAGATCGATTTTTTATTGTTTGAGAGTCAAG
GTCGA

Found at i:14984 original size:15 final size:15

Alignment explanation


    Indices: 14960--15017  Score: 62
    Period size: 15  Copynumber: 3.9  Consensus size: 15

      14950 ACTTTCCATG

                           
      14960 GGAGAGTGATTCCCA
          1 GGAGAGTGATTCCCA

                 *    *    
      14975 GGAGAATGATACCCA
          1 GGAGAGTGATTCCCA

             *          ***
      14990 GAAGAGTGATTCTTG
          1 GGAGAGTGATTCCCA

                         
      15005 GGAGAGTGATTCC
          1 GGAGAGTGATTCC

      15018 TGGAAAAGTA


Statistics
Matches: 33,  Mismatches: 10, Indels: 0
        0.77            0.23        0.00

Matches are distributed among these distances:
  15   33  1.00

ACGTcount: A:0.29, C:0.16, G:0.33, T:0.22


Consensus pattern (15 bp):   
GGAGAGTGATTCCCA

Found at i:15419 original size:21 final size:21

Alignment explanation


    Indices: 15395--15450  Score: 78
    Period size: 21  Copynumber: 2.7  Consensus size: 21

      15385 AGGATACGGC

                                  
      15395 AAAGTGGAGGAATGGAG-GTCA
          1 AAAGTGGAGGAATGGAGAG-CA

                     *           
      15416 AAAGTGGAGCAATGGAGAGCA
          1 AAAGTGGAGGAATGGAGAGCA

               *          
      15437 AAAATGGAGGAATG
          1 AAAGTGGAGGAATG

      15451 AAGTGTTGGA


Statistics
Matches: 31,  Mismatches: 3, Indels: 2
        0.86            0.08        0.06

Matches are distributed among these distances:
  21   30  0.97
  22    1  0.03

ACGTcount: A:0.43, C:0.05, G:0.39, T:0.12


Consensus pattern (21 bp):   
AAAGTGGAGGAATGGAGAGCA

Found at i:16375 original size:15 final size:15

Alignment explanation


    Indices: 16355--16385  Score: 62
    Period size: 15  Copynumber: 2.1  Consensus size: 15

      16345 ATAGTGTTTA

                           
      16355 GTATAACTAATAAGT
          1 GTATAACTAATAAGT

                           
      16370 GTATAACTAATAAGT
          1 GTATAACTAATAAGT

             
      16385 G
          1 G

      16386 ACTTGTTATT


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.45, C:0.06, G:0.16, T:0.32


Consensus pattern (15 bp):   
GTATAACTAATAAGT
Done.