Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008494.1 Corchorus capsularis cultivar CVL-1 contig08515, 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: 43424
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.31


Found at i:112 original size:25 final size:25

Alignment explanation


    Indices: 63--113  Score: 61
    Period size: 25  Copynumber: 2.0  Consensus size: 25

         53 ATTTTTTCTT

                                *    
         63 TTATGTATGTATATACTTATTTATA
          1 TTATGTATGTATATACTTATATATA

                                       
         88 TTATGTAT-TATAATA-TATATATATA
          1 TTATGTATGTAT-ATACT-TATATATA

             
        113 T
          1 T

        114 ATTTATATAT


Statistics
Matches: 23,  Mismatches: 1, Indels: 4
        0.82            0.04        0.14

Matches are distributed among these distances:
  24    4  0.17
  25   19  0.83

ACGTcount: A:0.37, C:0.02, G:0.06, T:0.55


Consensus pattern (25 bp):   
TTATGTATGTATATACTTATATATA

Found at i:4214 original size:3 final size:3

Alignment explanation


    Indices: 4208--4242  Score: 70
    Period size: 3  Copynumber: 11.7  Consensus size: 3

       4198 TTCTTCTTTT

                                                          
       4208 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT

       4243 TATTCTTTTC


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   32  1.00

ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69


Consensus pattern (3 bp):   
TTA

Found at i:12512 original size:19 final size:18

Alignment explanation


    Indices: 12479--12514  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

      12469 TTGAAATAAT

                              
      12479 TCTTCAATGATCTTCAAA
          1 TCTTCAATGATCTTCAAA

                     *        
      12497 TCTTCAAATTATCTTCAA
          1 TCTTC-AATGATCTTCAA

      12515 TAAATCTTCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    5  0.31
  19   11  0.69

ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42


Consensus pattern (18 bp):   
TCTTCAATGATCTTCAAA

Found at i:13484 original size:20 final size:18

Alignment explanation


    Indices: 13459--13500  Score: 57
    Period size: 18  Copynumber: 2.2  Consensus size: 18

      13449 GAATGAATTT

                                
      13459 TTTTGATTTTGGTTTTTGAA
          1 TTTTGATTTT--TTTTTGAA

                            * 
      13479 TTTTGATTTTTTTTTGGA
          1 TTTTGATTTTTTTTTGAA

                
      13497 TTTT
          1 TTTT

      13501 TGAAAACCTT


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  18   11  0.52
  20   10  0.48

ACGTcount: A:0.12, C:0.00, G:0.17, T:0.71


Consensus pattern (18 bp):   
TTTTGATTTTTTTTTGAA

Found at i:25092 original size:21 final size:21

Alignment explanation


    Indices: 25063--25122  Score: 66
    Period size: 21  Copynumber: 2.9  Consensus size: 21

      25053 GCATAACTTT

                              *  
      25063 GAATCGATTGGAATATTCCTA
          1 GAATCGATTGGAATATTCATA

                *     * *  **    
      25084 GAATTGATTGTAGTAGACATA
          1 GAATCGATTGGAATATTCATA

                              
      25105 GAATCGATTGGAATATTC
          1 GAATCGATTGGAATATTC

      25123 TTGCTCCAAA


Statistics
Matches: 28,  Mismatches: 11, Indels: 0
        0.72            0.28        0.00

Matches are distributed among these distances:
  21   28  1.00

ACGTcount: A:0.35, C:0.10, G:0.22, T:0.33


Consensus pattern (21 bp):   
GAATCGATTGGAATATTCATA

Found at i:26601 original size:13 final size:12

Alignment explanation


    Indices: 26565--26611  Score: 51
    Period size: 13  Copynumber: 3.8  Consensus size: 12

      26555 TCAATCTTTA

                        *
      26565 TATATATTGATAA
          1 TATATATT-ATAT

                 *      
      26578 TA-ATGTTATAT
          1 TATATATTATAT

                         
      26589 TATATTATTATAT
          1 TATA-TATTATAT

                      
      26602 TATATATTAT
          1 TATATATTAT

      26612 CAATAAACTT


Statistics
Matches: 29,  Mismatches: 3, Indels: 5
        0.78            0.08        0.14

Matches are distributed among these distances:
  11    5  0.17
  12   11  0.38
  13   13  0.45

ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55


Consensus pattern (12 bp):   
TATATATTATAT
Done.