Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013574.1 Corchorus capsularis cultivar CVL-1 contig13595, 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: 19819
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33


Found at i:18177 original size:23 final size:24

Alignment explanation


    Indices: 18151--18207  Score: 75
    Period size: 23  Copynumber: 2.5  Consensus size: 24

      18141 AAAAATACCC

                                    
      18151 TTCATCAATTATTAATTCTAAT-A
          1 TTCATCAATTATTAATTCTAATAA

                      *              
      18174 TTCATTC-ATGATTAATTCTAATAA
          1 TTCA-TCAATTATTAATTCTAATAA

                       
      18198 TTCAT-AATTA
          1 TTCATCAATTA

      18208 GAATACATGA


Statistics
Matches: 29,  Mismatches: 2, Indels: 6
        0.78            0.05        0.16

Matches are distributed among these distances:
  23   22  0.76
  24    7  0.24

ACGTcount: A:0.39, C:0.12, G:0.02, T:0.47


Consensus pattern (24 bp):   
TTCATCAATTATTAATTCTAATAA

Found at i:19313 original size:53 final size:53

Alignment explanation


    Indices: 19242--19345  Score: 163
    Period size: 53  Copynumber: 2.0  Consensus size: 53

      19232 TTTTTAATCA

                        *                  *                     
      19242 ATATATACATATCTATGAAATTCACGGGAAATATTTCAGTTCAGTTAATATAT
          1 ATATATACATATATATGAAATTCACGGGAAAGATTTCAGTTCAGTTAATATAT

                   *           *                      *        
      19295 ATATATATATATATATGAAGTTCACGGGAAAGATTTCAGTTCGGTTAATAT
          1 ATATATACATATATATGAAATTCACGGGAAAGATTTCAGTTCAGTTAATAT

      19346 TTGAAATATG


Statistics
Matches: 46,  Mismatches: 5, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  53   46  1.00

ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38


Consensus pattern (53 bp):   
ATATATACATATATATGAAATTCACGGGAAAGATTTCAGTTCAGTTAATATAT

Found at i:19807 original size:15 final size:14

Alignment explanation


    Indices: 19789--19819  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 14

      19779 AAATAAAATT

                           
      19789 TAAAATATATTTATA
          1 TAAAATATA-TTATA

                          
      19804 TAAAATATATTATA
          1 TAAAATATATTATA

              
      19818 TA
          1 TA


Statistics
Matches: 16,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14    7  0.44
  15    9  0.56

ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45


Consensus pattern (14 bp):   
TAAAATATATTATA
Done.