Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007286.1 Corchorus capsularis cultivar CVL-1 contig07307, 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: 32588
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32


Found at i:6445 original size:34 final size:34

Alignment explanation


    Indices: 6397--6467  Score: 115
    Period size: 34  Copynumber: 2.1  Consensus size: 34

       6387 TTCAAAGCTT

                                      *       
       6397 TATTCCTATCTTCTTACTGCATACTAGTATTATA
          1 TATTCCTATCTTCTTACTGCATACTACTATTATA

                 *   *                        
       6431 TATTCGTATTTTCTTACTGCATACTACTATTATA
          1 TATTCCTATCTTCTTACTGCATACTACTATTATA

               
       6465 TAT
          1 TAT

       6468 ATATATATGA


Statistics
Matches: 34,  Mismatches: 3, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  34   34  1.00

ACGTcount: A:0.27, C:0.18, G:0.06, T:0.49


Consensus pattern (34 bp):   
TATTCCTATCTTCTTACTGCATACTACTATTATA

Found at i:6508 original size:29 final size:31

Alignment explanation


    Indices: 6448--6508  Score: 72
    Period size: 31  Copynumber: 2.0  Consensus size: 31

       6438 ATTTTCTTAC

                  *  *             *   *   
       6448 TGCATACTACTATTATATATATATATATGAT
          1 TGCATAATAATATTATATATATAGATACGAT

                                           
       6479 TGCATAATAATATTATATATAT-GA-ACGAT
          1 TGCATAATAATATTATATATATAGATACGAT

             
       6508 T
          1 T

       6509 TTTATTACTT


Statistics
Matches: 26,  Mismatches: 4, Indels: 2
        0.81            0.12        0.06

Matches are distributed among these distances:
  29    5  0.19
  30    1  0.04
  31   20  0.77

ACGTcount: A:0.41, C:0.08, G:0.08, T:0.43


Consensus pattern (31 bp):   
TGCATAATAATATTATATATATAGATACGAT

Found at i:22738 original size:23 final size:23

Alignment explanation


    Indices: 22695--22738  Score: 54
    Period size: 23  Copynumber: 1.9  Consensus size: 23

      22685 AAAATTTAAG

                      *  *         
      22695 TTTAAAATTTCAATAGCTTATTT
          1 TTTAAAATTTAAAAAGCTTATTT

                                  
      22718 TTTAAAAGTTTAAAAAG-TTAT
          1 TTTAAAA-TTTAAAAAGCTTAT

      22739 AGTTTTATAA


Statistics
Matches: 18,  Mismatches: 2, Indels: 2
        0.82            0.09        0.09

Matches are distributed among these distances:
  23   11  0.61
  24    7  0.39

ACGTcount: A:0.41, C:0.05, G:0.07, T:0.48


Consensus pattern (23 bp):   
TTTAAAATTTAAAAAGCTTATTT

Found at i:26420 original size:17 final size:17

Alignment explanation


    Indices: 26398--26432  Score: 70
    Period size: 17  Copynumber: 2.1  Consensus size: 17

      26388 GCATGACAAG

                             
      26398 AAGGTTCATCATAATTA
          1 AAGGTTCATCATAATTA

                             
      26415 AAGGTTCATCATAATTA
          1 AAGGTTCATCATAATTA

             
      26432 A
          1 A

      26433 GTTGCATAGG


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   18  1.00

ACGTcount: A:0.43, C:0.11, G:0.11, T:0.34


Consensus pattern (17 bp):   
AAGGTTCATCATAATTA

Found at i:31530 original size:31 final size:31

Alignment explanation


    Indices: 31494--31634  Score: 174
    Period size: 31  Copynumber: 4.5  Consensus size: 31

      31484 TCCTTTTGTG

                    *         *  *      ** 
      31494 CATGTGGCATGCCACGTGCCATTTTTTGAAA
          1 CATGTGGCGTGCCACGTGTCACTTTTTGGTA

                    *   *                  
      31525 CATGTGGCATGCTACGTGTCACTTTTTGGTA
          1 CATGTGGCGTGCCACGTGTCACTTTTTGGTA

              *        *  *                
      31556 CACGTGGCGTGACATGTGTCACTTTTTGGTA
          1 CATGTGGCGTGCCACGTGTCACTTTTTGGTA

                           *               
      31587 CATGTGGCGTGCCACATGTCACTTTTTGGTA
          1 CATGTGGCGTGCCACGTGTCACTTTTTGGTA

              *              
      31618 CACGTGGCGTGCCACGT
          1 CATGTGGCGTGCCACGT

      31635 CGGACACCAT


Statistics
Matches: 94,  Mismatches: 16, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  31   94  1.00

ACGTcount: A:0.17, C:0.23, G:0.27, T:0.33


Consensus pattern (31 bp):   
CATGTGGCGTGCCACGTGTCACTTTTTGGTA

Found at i:31962 original size:20 final size:21

Alignment explanation


    Indices: 31920--31962  Score: 54
    Period size: 20  Copynumber: 2.1  Consensus size: 21

      31910 TGGGTAAATA

                            *    
      31920 TTGACTAATAAAAATGTAATC
          1 TTGACTAATAAAAATGCAATC

                                  
      31941 TTGAC-AATAAAAAT-CAAGTC
          1 TTGACTAATAAAAATGCAA-TC

              
      31961 TT
          1 TT

      31963 TAGTCTAAAA


Statistics
Matches: 20,  Mismatches: 1, Indels: 3
        0.83            0.04        0.12

Matches are distributed among these distances:
  19    2  0.10
  20   13  0.65
  21    5  0.25

ACGTcount: A:0.47, C:0.12, G:0.09, T:0.33


Consensus pattern (21 bp):   
TTGACTAATAAAAATGCAATC
Done.