Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019755.1 Corchorus olitorius cultivar O-4 contig19788, 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: 4336
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29


Found at i:984 original size:18 final size:18

Alignment explanation


    Indices: 961--995  Score: 54
    Period size: 18  Copynumber: 1.9  Consensus size: 18

        951 TATCAATTCG

                               
        961 CGTCAAT-TAGGGGCAGAC
          1 CGTCAATGT-GGGGCAGAC

                             
        979 CGTCAATGTGGGGCAGA
          1 CGTCAATGTGGGGCAGA

        996 ATCTTTTGGA


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

Matches are distributed among these distances:
  18   15  0.94
  19    1  0.06

ACGTcount: A:0.26, C:0.20, G:0.37, T:0.17


Consensus pattern (18 bp):   
CGTCAATGTGGGGCAGAC

Found at i:1141 original size:21 final size:21

Alignment explanation


    Indices: 1098--1138  Score: 66
    Period size: 20  Copynumber: 2.0  Consensus size: 21

       1088 CGAGAATTAC

                           *     
       1098 TTAAAAATTAAAAAACGAAAA
          1 TTAAAAATTAAAAAAAGAAAA

                                 
       1119 TTAAAAA-TAAAAAAAGAAAA
          1 TTAAAAATTAAAAAAAGAAAA

       1139 ATTGGCTTTA


Statistics
Matches: 19,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  20   12  0.63
  21    7  0.37

ACGTcount: A:0.76, C:0.02, G:0.05, T:0.17


Consensus pattern (21 bp):   
TTAAAAATTAAAAAAAGAAAA

Found at i:2355 original size:16 final size:16

Alignment explanation


    Indices: 2334--2368  Score: 61
    Period size: 16  Copynumber: 2.2  Consensus size: 16

       2324 TATGGTTAAA

                  *         
       2334 TTAAATGAATTTAATT
          1 TTAAATAAATTTAATT

                            
       2350 TTAAATAAATTTAATT
          1 TTAAATAAATTTAATT

               
       2366 TTA
          1 TTA

       2369 TTTCAAAATT


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  16   18  1.00

ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51


Consensus pattern (16 bp):   
TTAAATAAATTTAATT
Done.