Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014239.1 Corchorus capsularis cultivar CVL-1 contig14260, 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: 10149
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37


Found at i:750 original size:22 final size:22

Alignment explanation


    Indices: 669--755  Score: 70
    Period size: 22  Copynumber: 3.8  Consensus size: 22

        659 ATTAAATTAT

                                *  
        669 TTTATTTATCTATCTATTTATTA
          1 TTTATTT-TCTATCTATTTACTA

                   *         *      
        692 -TTATCTATCTATCTATCTACTTA
          1 TTTAT-TTTCTATCTATTTAC-TA

                      *             
        715 GTTT-TTGTTTTATCTATTTACTA
          1 -TTTATT-TTCTATCTATTTACTA

                    *         
        738 TTTATTTTTTATCTATTT
          1 TTTATTTTCTATCTATTT

        756 GTAATCATTA


Statistics
Matches: 52,  Mismatches: 6, Indels: 13
        0.73            0.08        0.18

Matches are distributed among these distances:
  22   30  0.58
  23    8  0.15
  24   12  0.23
  25    2  0.04

ACGTcount: A:0.22, C:0.11, G:0.02, T:0.64


Consensus pattern (22 bp):   
TTTATTTTCTATCTATTTACTA

Found at i:793 original size:17 final size:17

Alignment explanation


    Indices: 771--810  Score: 71
    Period size: 17  Copynumber: 2.4  Consensus size: 17

        761 CATTATTTAT

                         *   
        771 TATTATCTATTTAGTAC
          1 TATTATCTATTTAATAC

                             
        788 TATTATCTATTTAATAC
          1 TATTATCTATTTAATAC

                  
        805 TATTAT
          1 TATTAT

        811 TTATCTATCT


Statistics
Matches: 22,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  17   22  1.00

ACGTcount: A:0.33, C:0.10, G:0.03, T:0.55


Consensus pattern (17 bp):   
TATTATCTATTTAATAC

Found at i:2874 original size:2 final size:2

Alignment explanation


    Indices: 2867--2895  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

       2857 ATATCCTTCA

                                                       
       2867 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       2896 AAGTTATAAA


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:6356 original size:11 final size:11

Alignment explanation


    Indices: 6340--6392  Score: 70
    Period size: 11  Copynumber: 4.5  Consensus size: 11

       6330 TAGATAGAGG

                       
       6340 TATAGATATGA
          1 TATAGATATGA

                       
       6351 TATAGATATGA
          1 TATAGATATGA

                        
       6362 TATATGATATGA
          1 TATA-GATATGA

                          
       6374 TATAGTCATATAGA
          1 TATAG--ATAT-GA

                 
       6388 TATAG
          1 TATAG

       6393 GTACAGATAG


Statistics
Matches: 38,  Mismatches: 0, Indels: 5
        0.88            0.00        0.12

Matches are distributed among these distances:
  11   16  0.42
  12   11  0.29
  13    4  0.11
  14    7  0.18

ACGTcount: A:0.43, C:0.02, G:0.17, T:0.38


Consensus pattern (11 bp):   
TATAGATATGA
Done.