Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011380.1 Corchorus capsularis cultivar CVL-1 contig11401, 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: 3714
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32


Found at i:1755 original size:91 final size:89

Alignment explanation


    Indices: 1619--1784  Score: 287
    Period size: 91  Copynumber: 1.8  Consensus size: 89

       1609 TGGAGGAGTC

                                                                             
       1619 CAACAAAATGGTTTTCAAAAGTCATGATTTCCAAAAGATTTTGATAAAATGGTTTTACAAAAATG
          1 CAACAAAATGGTTTTCAAAAGTCATGATTTCCAAAAGATTTTGATAAAATGGTTTTACAAAAATG

                                    
       1684 ATTTCAAACTTGAAATATGGTTTT
         66 ATTTCAAACTTGAAATATGGTTTT

                                     *      *                         *      
       1708 CAACAAAATGGTTTTCAAAAGAGTCGTGATTTTCAAAAGATTTTGATAAAATGGTTTTTCAAAAA
          1 CAACAAAATGGTTTTC-AAA-AGTCATGATTTCCAAAAGATTTTGATAAAATGGTTTTACAAAAA

                        
       1773 TGATTTCAAACT
         64 TGATTTCAAACT

       1785 CGTTTTCCCG


Statistics
Matches: 72,  Mismatches: 3, Indels: 2
        0.94            0.04        0.03

Matches are distributed among these distances:
  89   16  0.22
  90    3  0.04
  91   53  0.74

ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36


Consensus pattern (89 bp):   
CAACAAAATGGTTTTCAAAAGTCATGATTTCCAAAAGATTTTGATAAAATGGTTTTACAAAAATG
ATTTCAAACTTGAAATATGGTTTT

Found at i:3478 original size:58 final size:57

Alignment explanation


    Indices: 3388--3532  Score: 220
    Period size: 58  Copynumber: 2.5  Consensus size: 57

       3378 GCTGCAATTG

                                                     **                
       3388 CAATTCTTCAATTATCCAATGCTTCAATTTACTTCAATGATTTAGGGT-AGTCTTTCTT
          1 CAATTCTTCAA-TATCCAATGCTTCAATTTACTTCAATGATCCAGGGTGA-TCTTTCTT

                                                                      
       3446 CAATTCTTCAATCATCCAATGCTTCAATTTACTTCAATGATCCAGGGTGATCTTTCTT
          1 CAATTCTTCAAT-ATCCAATGCTTCAATTTACTTCAATGATCCAGGGTGATCTTTCTT

                           *             
       3504 CAATTCTTCAAGTATTCAATGCTTCAATT
          1 CAATTCTTCAA-TATCCAATGCTTCAATT

       3533 CCTCAATTAT


Statistics
Matches: 81,  Mismatches: 3, Indels: 6
        0.90            0.03        0.07

Matches are distributed among these distances:
  57    1  0.01
  58   78  0.96
  59    2  0.02

ACGTcount: A:0.27, C:0.21, G:0.10, T:0.42


Consensus pattern (57 bp):   
CAATTCTTCAATATCCAATGCTTCAATTTACTTCAATGATCCAGGGTGATCTTTCTT

Found at i:3512 original size:8 final size:8

Alignment explanation


    Indices: 3499--3547  Score: 53
    Period size: 8  Copynumber: 6.1  Consensus size: 8

       3489 AGGGTGATCT

                    
       3499 TTCTTCAA
          1 TTCTTCAA

                    
       3507 TTCTTCAA
          1 TTCTTCAA

            * *     
       3515 GTATTCAA
          1 TTCTTCAA

             *      
       3523 TGCTTCAA
          1 TTCTTCAA

               *    
       3531 TTCCTCAA
          1 TTCTTCAA

              *     
       3539 TTATTCAA
          1 TTCTTCAA

             
       3547 T
          1 T

       3548 GCCTCAATTT


Statistics
Matches: 32,  Mismatches: 9, Indels: 0
        0.78            0.22        0.00

Matches are distributed among these distances:
   8   32  1.00

ACGTcount: A:0.29, C:0.22, G:0.04, T:0.45


Consensus pattern (8 bp):   
TTCTTCAA

Found at i:3528 original size:24 final size:24

Alignment explanation


    Indices: 3501--3556  Score: 85
    Period size: 24  Copynumber: 2.3  Consensus size: 24

       3491 GGTGATCTTT

                     *              
       3501 CTTCAATTCTTCAAGTATTCAATG
          1 CTTCAATTCCTCAAGTATTCAATG

                          *         
       3525 CTTCAATTCCTCAATTATTCAATG
          1 CTTCAATTCCTCAAGTATTCAATG

             *      
       3549 CCTCAATT
          1 CTTCAATT

       3557 TCAAATCTTT


Statistics
Matches: 29,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  24   29  1.00

ACGTcount: A:0.29, C:0.25, G:0.05, T:0.41


Consensus pattern (24 bp):   
CTTCAATTCCTCAAGTATTCAATG

Found at i:3590 original size:14 final size:14

Alignment explanation


    Indices: 3571--3604  Score: 50
    Period size: 14  Copynumber: 2.4  Consensus size: 14

       3561 ATCTTTAACG

                     *    
       3571 CTTCAATTTCAATA
          1 CTTCAATTTAAATA

                         *
       3585 CTTCAATTTAAATT
          1 CTTCAATTTAAATA

                  
       3599 CTTCAA
          1 CTTCAA

       3605 ATTCCAAATC


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  14   18  1.00

ACGTcount: A:0.35, C:0.21, G:0.00, T:0.44


Consensus pattern (14 bp):   
CTTCAATTTAAATA

Found at i:3700 original size:20 final size:19

Alignment explanation


    Indices: 3634--3703  Score: 61
    Period size: 20  Copynumber: 3.4  Consensus size: 19

       3624 TATTTCGATG

                           **   
       3634 TTTCAATTTCAATATGCCAA
          1 TTTCAATTTCAAT-TTTCAA

                                   
       3654 TGCTTCAATTTCAATTCTTCGAA
          1 T--TTCAATTTCAATT-TTC-AA

                                
       3677 -TTCAATTTCAATGTTTCAA
          1 TTTCAATTTCAAT-TTTCAA

                    
       3696 TTTCAATT
          1 TTTCAATT

       3704 CTTAATCCAA


Statistics
Matches: 42,  Mismatches: 2, Indels: 12
        0.75            0.04        0.21

Matches are distributed among these distances:
  19    2  0.05
  20   23  0.55
  21    2  0.05
  22   13  0.31
  23    2  0.05

ACGTcount: A:0.30, C:0.19, G:0.06, T:0.46


Consensus pattern (19 bp):   
TTTCAATTTCAATTTTCAA
Done.