Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004483.1 Corchorus capsularis cultivar CVL-1 contig04491, 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, 739

Length: 1232
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36


Found at i:123 original size:20 final size:19

Alignment explanation


    Indices: 100--143  Score: 72
    Period size: 18  Copynumber: 2.3  Consensus size: 19

         90 TTATTATTAC

                                
        100 TATTTTCTATTTTTATATGT
          1 TATTTT-TATTTTTATATGT

                               
        120 TA-TTTTATTTTTATATGT
          1 TATTTTTATTTTTATATGT

                  
        138 TATTTT
          1 TATTTT

        144 ATCATATGTT


Statistics
Matches: 23,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  18   15  0.65
  19    6  0.26
  20    2  0.09

ACGTcount: A:0.20, C:0.02, G:0.05, T:0.73


Consensus pattern (19 bp):   
TATTTTTATTTTTATATGT

Found at i:130 original size:18 final size:18

Alignment explanation


    Indices: 107--145  Score: 78
    Period size: 18  Copynumber: 2.2  Consensus size: 18

         97 TACTATTTTC

                              
        107 TATTTTTATATGTTATTT
          1 TATTTTTATATGTTATTT

                              
        125 TATTTTTATATGTTATTT
          1 TATTTTTATATGTTATTT

               
        143 TAT
          1 TAT

        146 CATATGTTAT


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   21  1.00

ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72


Consensus pattern (18 bp):   
TATTTTTATATGTTATTT

Found at i:152 original size:15 final size:15

Alignment explanation


    Indices: 124--161  Score: 62
    Period size: 15  Copynumber: 2.7  Consensus size: 15

        114 ATATGTTATT

                           
        124 TTATTTT-T-ATATG
          1 TTATTTTATCATATG

                           
        137 TTATTTTATCATATG
          1 TTATTTTATCATATG

                      
        152 TTATTTTATC
          1 TTATTTTATC

        162 TTATCTGTTC


Statistics
Matches: 23,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
  13    7  0.30
  14    1  0.04
  15   15  0.65

ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66


Consensus pattern (15 bp):   
TTATTTTATCATATG

Found at i:346 original size:13 final size:13

Alignment explanation


    Indices: 328--352  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

        318 CTATAGCAGC

                         
        328 AATAATAAATAAG
          1 AATAATAAATAAG

                        
        341 AATAATAAATAA
          1 AATAATAAATAA

        353 AATTAAGAAT


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24


Consensus pattern (13 bp):   
AATAATAAATAAG
Done.