Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009507.1 Corchorus olitorius cultivar O-4 contig09539, 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: 2166
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.32


Found at i:42 original size:13 final size:13

Alignment explanation


    Indices: 24--48  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

         14 AGGCGAAGGA

                         
         24 AAAAAGAAAAAAG
          1 AAAAAGAAAAAAG

                        
         37 AAAAAGAAAAAA
          1 AAAAAGAAAAAA

         49 AAATCAATTT


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00


Consensus pattern (13 bp):   
AAAAAGAAAAAAG

Found at i:158 original size:31 final size:30

Alignment explanation


    Indices: 93--186  Score: 129
    Period size: 31  Copynumber: 3.1  Consensus size: 30

         83 ACTAAATACT

                                           
         93 AAAAAAATCCCTAATG-TTTTCTTTTGGGAC
          1 AAAAAAATCCCT-ATGTTTTTCTTTTGGGAC

                                        *  
        123 -AAAAAATCCCATATGTTTTTCTTTTGGAAC
          1 AAAAAAATCCC-TATGTTTTTCTTTTGGGAC

                       *                   
        153 AAAAAAATCGCTTATGTTTTTCTTTTGGGAC
          1 AAAAAAATC-CCTATGTTTTTCTTTTGGGAC

               
        184 AAA
          1 AAA

        187 TCAGTCCCTT


Statistics
Matches: 57,  Mismatches: 3, Indels: 7
        0.85            0.04        0.10

Matches are distributed among these distances:
  29   13  0.23
  30   14  0.25
  31   29  0.51
  32    1  0.02

ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38


Consensus pattern (30 bp):   
AAAAAAATCCCTATGTTTTTCTTTTGGGAC

Found at i:376 original size:31 final size:29

Alignment explanation


    Indices: 310--389  Score: 97
    Period size: 29  Copynumber: 2.7  Consensus size: 29

        300 CTCATTTTTG

                *          *       **    
        310 AAACGTAAGGGATTAATTTGTCCTGAAAA
          1 AAACATAAGGGATTATTTTGTCCCAAAAA

                                           
        339 AAACATAAGGGATTATTTTGTCCCAAAAGCA
          1 AAACATAAGGGATTATTTTGTCCCAAAA--A

                          *     
        370 AAACATAAGGGATTTTTTTG
          1 AAACATAAGGGATTATTTTG

        390 GGTATTTAGC


Statistics
Matches: 44,  Mismatches: 5, Indels: 2
        0.86            0.10        0.04

Matches are distributed among these distances:
  29   24  0.55
  31   20  0.45

ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30


Consensus pattern (29 bp):   
AAACATAAGGGATTATTTTGTCCCAAAAA

Found at i:1436 original size:13 final size:13

Alignment explanation


    Indices: 1418--1443  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

       1408 ATAGTTGCAT

                         
       1418 CATCCTTCTTTTC
          1 CATCCTTCTTTTC

                         
       1431 CATCCTTCTTTTC
          1 CATCCTTCTTTTC

       1444 ATTTAAGCTT


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.08, C:0.38, G:0.00, T:0.54


Consensus pattern (13 bp):   
CATCCTTCTTTTC
Done.