Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017161.1 Corchorus olitorius cultivar O-4 contig17194, 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: 26764
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34


Found at i:13551 original size:18 final size:19

Alignment explanation


    Indices: 13528--13563  Score: 65
    Period size: 18  Copynumber: 1.9  Consensus size: 19

      13518 TCTTATTCTA

                               
      13528 ATTTTAACT-TATTTAGTT
          1 ATTTTAACTCTATTTAGTT

                              
      13546 ATTTTAACTCTATTTAGT
          1 ATTTTAACTCTATTTAGT

      13564 GGTCAAACAG


Statistics
Matches: 17,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  18    9  0.53
  19    8  0.47

ACGTcount: A:0.28, C:0.08, G:0.06, T:0.58


Consensus pattern (19 bp):   
ATTTTAACTCTATTTAGTT

Found at i:15385 original size:19 final size:20

Alignment explanation


    Indices: 15347--15396  Score: 66
    Period size: 19  Copynumber: 2.5  Consensus size: 20

      15337 TAATAGTCTC

                                 
      15347 ATCTGTACAGTACCTAATCTA
          1 ATCTGTACAGTA-CTAATCTA

                        *      *
      15368 ATCTGTACAGT-GTAATCTT
          1 ATCTGTACAGTACTAATCTA

                      
      15387 ATCTGTACAG
          1 ATCTGTACAG

      15397 GTGTTAAACA


Statistics
Matches: 27,  Mismatches: 2, Indels: 2
        0.87            0.06        0.06

Matches are distributed among these distances:
  19   16  0.59
  21   11  0.41

ACGTcount: A:0.30, C:0.20, G:0.14, T:0.36


Consensus pattern (20 bp):   
ATCTGTACAGTACTAATCTA

Found at i:20819 original size:21 final size:21

Alignment explanation


    Indices: 20781--20824  Score: 52
    Period size: 21  Copynumber: 2.1  Consensus size: 21

      20771 AAGAGAAGCA

                  *     **    *  
      20781 TTAGCTTTTTTTTTTTTTTTT
          1 TTAGCTCTTTTTCCTTTTCTT

                                 
      20802 TTAGCTCTTTTTCCTTTTCTT
          1 TTAGCTCTTTTTCCTTTTCTT

              
      20823 TT
          1 TT

      20825 GCCTAAATTC


Statistics
Matches: 19,  Mismatches: 4, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  21   19  1.00

ACGTcount: A:0.05, C:0.14, G:0.05, T:0.77


Consensus pattern (21 bp):   
TTAGCTCTTTTTCCTTTTCTT

Found at i:26233 original size:16 final size:16

Alignment explanation


    Indices: 26212--26243  Score: 55
    Period size: 16  Copynumber: 2.0  Consensus size: 16

      26202 TATAATTATT

                            
      26212 TATATATTAATAATAA
          1 TATATATTAATAATAA

                     *      
      26228 TATATATTATTAATAA
          1 TATATATTAATAATAA

      26244 AAATAATAAT


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  16   15  1.00

ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47


Consensus pattern (16 bp):   
TATATATTAATAATAA

Found at i:26250 original size:25 final size:27

Alignment explanation


    Indices: 26220--26269  Score: 77
    Period size: 25  Copynumber: 1.9  Consensus size: 27

      26210 TTTATATATT

                                       
      26220 AATAATAATA-TATATTAT-TAATAAA
          1 AATAATAATATTATATTATCTAATAAA

                        *            
      26245 AATAATAATATTCTATTATCTAATA
          1 AATAATAATATTATATTATCTAATA

      26270 TATTTAAATT


Statistics
Matches: 22,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  25   10  0.45
  26    7  0.32
  27    5  0.23

ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42


Consensus pattern (27 bp):   
AATAATAATATTATATTATCTAATAAA
Done.