Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001335.1 Corchorus olitorius cultivar O-4 contig01335, 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: 1856
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32


Found at i:180 original size:17 final size:17

Alignment explanation


    Indices: 158--191  Score: 59
    Period size: 17  Copynumber: 2.0  Consensus size: 17

        148 CTGTTGGTTT

                             
        158 CTGCAAGATACGAAGGA
          1 CTGCAAGATACGAAGGA

                      *      
        175 CTGCAAGATATGAAGGA
          1 CTGCAAGATACGAAGGA

        192 AAGAACTAAT


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

Matches are distributed among these distances:
  17   16  1.00

ACGTcount: A:0.41, C:0.15, G:0.29, T:0.15


Consensus pattern (17 bp):   
CTGCAAGATACGAAGGA

Found at i:254 original size:33 final size:33

Alignment explanation


    Indices: 216--296  Score: 153
    Period size: 33  Copynumber: 2.5  Consensus size: 33

        206 CATGGTTTAC

                                        *    
        216 ATATAATACACTGTTCCTTCAAAAAAAATATAT
          1 ATATAATACACTGTTCCTTCAAAAAAAAAATAT

                                             
        249 ATATAATACACTGTTCCTTCAAAAAAAAAATAT
          1 ATATAATACACTGTTCCTTCAAAAAAAAAATAT

                           
        282 ATATAATACACTGTT
          1 ATATAATACACTGTT

        297 AGTGGATTTT


Statistics
Matches: 47,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  33   47  1.00

ACGTcount: A:0.48, C:0.15, G:0.04, T:0.33


Consensus pattern (33 bp):   
ATATAATACACTGTTCCTTCAAAAAAAAAATAT

Found at i:1526 original size:18 final size:18

Alignment explanation


    Indices: 1498--1532  Score: 54
    Period size: 17  Copynumber: 1.9  Consensus size: 18

       1488 TGTTTAAATA

                               
       1498 AATTGAAAATTAAATTAAT
          1 AATTGAAAATT-AATTAAT

                             
       1517 AATT-AAAATTAATTAA
          1 AATTGAAAATTAATTAA

       1533 CACCGTATAT


Statistics
Matches: 16,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  17    6  0.38
  18    6  0.38
  19    4  0.25

ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37


Consensus pattern (18 bp):   
AATTGAAAATTAATTAAT
Done.