Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004910.1 Corchorus capsularis cultivar CVL-1 contig04928, 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: 16638
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.35


Found at i:6138 original size:11 final size:10

Alignment explanation


    Indices: 6122--6169  Score: 62
    Period size: 11  Copynumber: 4.7  Consensus size: 10

       6112 AAGAATGTCA

                       
       6122 TTTTAAGTTAT
          1 TTTTAA-TTAT

                      
       6133 TTTTAATTAT
          1 TTTTAATTAT

                *     
       6143 TTTTTATT-T
          1 TTTTAATTAT

                       
       6152 TTTTAATTCAT
          1 TTTTAATT-AT

                   
       6163 TTTTAAT
          1 TTTTAAT

       6170 CCATTCTTAT


Statistics
Matches: 33,  Mismatches: 2, Indels: 4
        0.85            0.05        0.10

Matches are distributed among these distances:
   9    8  0.24
  10   11  0.33
  11   14  0.42

ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71


Consensus pattern (10 bp):   
TTTTAATTAT

Found at i:11144 original size:23 final size:23

Alignment explanation


    Indices: 11118--11163  Score: 65
    Period size: 23  Copynumber: 2.0  Consensus size: 23

      11108 TTTTAATTTC

                 *                 
      11118 AAATTGTAAATTTTTAATGAAAT
          1 AAATTATAAATTTTTAATGAAAT

                   *          *    
      11141 AAATTATTAATTTTTAATTAAAT
          1 AAATTATAAATTTTTAATGAAAT

      11164 TTTATGTTTC


Statistics
Matches: 20,  Mismatches: 3, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  23   20  1.00

ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48


Consensus pattern (23 bp):   
AAATTATAAATTTTTAATGAAAT

Found at i:11928 original size:2 final size:2

Alignment explanation


    Indices: 11921--11945  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

      11911 CTAGTATACA

                                                 
      11921 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 A

      11946 GGGTGATTAT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:12191 original size:23 final size:20

Alignment explanation


    Indices: 12139--12184  Score: 74
    Period size: 20  Copynumber: 2.2  Consensus size: 20

      12129 GCCATATATA

                                 
      12139 TATTATAATACATATCTTTAT
          1 TATT-TAATACATATCTTTAT

                               *
      12160 TATTTAATACATATCTTTAC
          1 TATTTAATACATATCTTTAT

                 
      12180 TATTT
          1 TATTT

      12185 TTAAATATAT


Statistics
Matches: 24,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  20   20  0.83
  21    4  0.17

ACGTcount: A:0.35, C:0.11, G:0.00, T:0.54


Consensus pattern (20 bp):   
TATTTAATACATATCTTTAT

Found at i:12680 original size:22 final size:22

Alignment explanation


    Indices: 12655--12698  Score: 70
    Period size: 22  Copynumber: 2.0  Consensus size: 22

      12645 ACTCTAAGAC

                     *            
      12655 TTTTAATTTTTTTTAATTAATA
          1 TTTTAATTTATTTTAATTAATA

                *                 
      12677 TTTTGATTTATTTTAATTAATA
          1 TTTTAATTTATTTTAATTAATA

      12699 CTAATTATTC


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  22   20  1.00

ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66


Consensus pattern (22 bp):   
TTTTAATTTATTTTAATTAATA

Found at i:14932 original size:158 final size:164

Alignment explanation


    Indices: 14703--15021  Score: 488
    Period size: 158  Copynumber: 2.0  Consensus size: 164

      14693 ATATAATAAA

                                 **                          *               
      14703 TACAATCTACAATTTGATAACCCAAAAATATCATTACGTCCATGATTATCATAAATCTCTTTTGT
          1 TACAATCTACAATTTGATAACAAAAAAATATCATTACGTCCATGATTATAATAAATCTCTTTTGT

                           *                                      *          
      14768 CAAAACCTCATCAATTATTGATTT-TTTTT-TTCAATTATTGTCTACTAATTGTGTTTAATAAT-
         66 CAAAACCTCATCAATGATTGATTTATTTTTGTTCAATTATTGTCTACTAATTGTATTTAATAATA

                      * *                     
      14830 AT-A-ATAAATATTAATAATAATATCTATATCCG
        131 ATAATATAAAAAATAATAATAATATCTATATCCG

                                                                             
      14862 TACAATCTACAATTTGATAACAAAAAAATAT-ATTACGTCCATGATTATAATAAATCTCTTTTGT
          1 TACAATCTACAATTTGATAACAAAAAAATATCATTACGTCCATGATTATAATAAATCTCTTTTGT

             *                  *                                        *   
      14926 CCAAACCTCATCAATGATTGGTTTATTTTTGGGTTCAATTATTGTCTACTAATTGTATTTATTAA
         66 CAAAACCTCATCAATGATTGATTTATTTTT--GTTCAATTATTGTCTACTAATTGTATTTAATAA

                                           
      14991 TAATAATATAAAAAATAATAATAATATCTAT
        129 TAATAATATAAAAAATAATAATAATATCTAT

      15022 TATCTATATC


Statistics
Matches: 143,  Mismatches: 10, Indels: 8
        0.89            0.06        0.05

Matches are distributed among these distances:
 158   53  0.37
 159   34  0.24
 162   31  0.22
 163    2  0.01
 164    1  0.01
 165   22  0.15

ACGTcount: A:0.39, C:0.13, G:0.07, T:0.41


Consensus pattern (164 bp):   
TACAATCTACAATTTGATAACAAAAAAATATCATTACGTCCATGATTATAATAAATCTCTTTTGT
CAAAACCTCATCAATGATTGATTTATTTTTGTTCAATTATTGTCTACTAATTGTATTTAATAATA
ATAATATAAAAAATAATAATAATATCTATATCCG
Done.