Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023427.1 Corchorus olitorius cultivar O-4 contig23460, 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: 7717
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.32


Found at i:549 original size:42 final size:43

Alignment explanation


    Indices: 475--559  Score: 154
    Period size: 42  Copynumber: 2.0  Consensus size: 43

        465 AATTGGGGAA

                                                       
        475 TGAATAATCAATCCAAAAAACAAACAATTTTCTATACTAAGTT
          1 TGAATAATCAATCCAAAAAACAAACAATTTTCTATACTAAGTT

                                               *       
        518 TGAATAATCAATCC-AAAAACAAACAATTTTCTATCCTAAGTT
          1 TGAATAATCAATCCAAAAAACAAACAATTTTCTATACTAAGTT

        560 CTCATACAAA


Statistics
Matches: 41,  Mismatches: 1, Indels: 1
        0.95            0.02        0.02

Matches are distributed among these distances:
  42   27  0.66
  43   14  0.34

ACGTcount: A:0.47, C:0.18, G:0.05, T:0.31


Consensus pattern (43 bp):   
TGAATAATCAATCCAAAAAACAAACAATTTTCTATACTAAGTT

Found at i:857 original size:30 final size:29

Alignment explanation


    Indices: 818--875  Score: 82
    Period size: 30  Copynumber: 2.0  Consensus size: 29

        808 GTTTATTAAT

                           *               
        818 GAAACTTGAAAATTAGAGACATAAAATAAAG
          1 GAAACTTGAAAATTAAAG-CAT-AAATAAAG

                                        
        849 GAAA-TTGAAAATTAAAGCATAAATAAA
          1 GAAACTTGAAAATTAAAGCATAAATAAA

        876 TAATCCTAAG


Statistics
Matches: 26,  Mismatches: 1, Indels: 3
        0.87            0.03        0.10

Matches are distributed among these distances:
  28    7  0.27
  29    3  0.12
  30   12  0.46
  31    4  0.15

ACGTcount: A:0.60, C:0.05, G:0.14, T:0.21


Consensus pattern (29 bp):   
GAAACTTGAAAATTAAAGCATAAATAAAG

Found at i:1865 original size:22 final size:22

Alignment explanation


    Indices: 1823--1870  Score: 53
    Period size: 22  Copynumber: 2.2  Consensus size: 22

       1813 CGATGGTTTG

                         *       *
       1823 CTTCCTCTTGAGTTGAAAATTT
          1 CTTCCTCTTGAGTCGAAAATTC

                             *     
       1845 CTTCCTCTT-AGTCGATTAATTC
          1 CTTCCTCTTGAGTCGA-AAATTC

                
       1867 CTTC
          1 CTTC

       1871 ACTTGAAATC


Statistics
Matches: 22,  Mismatches: 3, Indels: 2
        0.81            0.11        0.07

Matches are distributed among these distances:
  21    5  0.23
  22   17  0.77

ACGTcount: A:0.19, C:0.25, G:0.10, T:0.46


Consensus pattern (22 bp):   
CTTCCTCTTGAGTCGAAAATTC
Done.