Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000781.1 Corchorus olitorius cultivar O-4 contig00781, 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, 645

Length: 1075
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.33


Found at i:249 original size:29 final size:30

Alignment explanation


    Indices: 180--253  Score: 89
    Period size: 29  Copynumber: 2.4  Consensus size: 30

        170 AAATAGCCTT

                                           *
        180 TTTGCCCCCTGAACTTTGCAAATTTAGGCCAG
          1 TTTGCCCCCTGAACTTT-CAAATTTA-GCCAC

            *                              
        212 ATTGCCCCCTGAACTTT-AAATTGT-GCCAC
          1 TTTGCCCCCTGAACTTTCAAATT-TAGCCAC

                         
        241 TTTGCCCCCTGAA
          1 TTTGCCCCCTGAA

        254 TTTGTAAAAT


Statistics
Matches: 38,  Mismatches: 3, Indels: 5
        0.83            0.07        0.11

Matches are distributed among these distances:
  29   16  0.42
  30    5  0.13
  31    1  0.03
  32   16  0.42

ACGTcount: A:0.22, C:0.31, G:0.16, T:0.31


Consensus pattern (30 bp):   
TTTGCCCCCTGAACTTTCAAATTTAGCCAC

Found at i:497 original size:29 final size:30

Alignment explanation


    Indices: 447--524  Score: 72
    Period size: 32  Copynumber: 2.6  Consensus size: 30

        437 CCTGATTTCA

                     *        *            
        447 CAAA-TTCAAGGGGCAAAGTGG-CACAATAT
          1 CAAAGTTCAGGGGGCAAACTGGCCA-AATAT

                             *           * 
        476 -AAAGTTCAGGGGGCAATCTGGCCTAAATTT
          1 CAAAGTTCAGGGGGCAAACTGGCC-AAATAT

                               
        506 GCAAAGTTCAGGGGGCAAA
          1 -CAAAGTTCAGGGGGCAAA

        525 TGGGCTATTT


Statistics
Matches: 39,  Mismatches: 5, Indels: 7
        0.76            0.10        0.14

Matches are distributed among these distances:
  28    3  0.08
  29   14  0.36
  30    5  0.13
  31    1  0.03
  32   16  0.41

ACGTcount: A:0.36, C:0.17, G:0.28, T:0.19


Consensus pattern (30 bp):   
CAAAGTTCAGGGGGCAAACTGGCCAAATAT
Done.