Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009859.1 Corchorus olitorius cultivar O-4 contig09891, 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: 2418
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.38


Found at i:22 original size:15 final size:15

Alignment explanation


    Indices: 2--48  Score: 51
    Period size: 15  Copynumber: 3.1  Consensus size: 15

          1 T

                           
          2 AATATACAAAGTAAA
          1 AATATACAAAGTAAA

                   *  *    *
         17 AATATA-TAATTGAAT
          1 AATATACAAAGT-AAA

                           
         32 AATATACAAAGTAAA
          1 AATATACAAAGTAAA

              
         47 AA
          1 AA

         49 AAAACACAAT


Statistics
Matches: 24,  Mismatches: 6, Indels: 4
        0.71            0.18        0.12

Matches are distributed among these distances:
  14    3  0.12
  15   18  0.75
  16    3  0.12

ACGTcount: A:0.64, C:0.04, G:0.06, T:0.26


Consensus pattern (15 bp):   
AATATACAAAGTAAA

Found at i:310 original size:22 final size:23

Alignment explanation


    Indices: 267--311  Score: 67
    Period size: 22  Copynumber: 2.0  Consensus size: 23

        257 GAAAAGATTT

                                   
        267 TTTAAAAAATCAAACAAAATAAA
          1 TTTAAAAAATCAAACAAAATAAA

                                    
        290 TTTAGAAAAAT-AAA-AAAATAAA
          1 TTTA-AAAAATCAAACAAAATAAA

        312 GGAACTCATT


Statistics
Matches: 21,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  22    8  0.38
  23    7  0.33
  24    6  0.29

ACGTcount: A:0.71, C:0.04, G:0.02, T:0.22


Consensus pattern (23 bp):   
TTTAAAAAATCAAACAAAATAAA

Found at i:1568 original size:17 final size:16

Alignment explanation


    Indices: 1538--1594  Score: 64
    Period size: 17  Copynumber: 3.6  Consensus size: 16

       1528 CGTTAAAATG

                            
       1538 TCGGGTCA-TTTGGGT
          1 TCGGGTCATTTTGGGT

                             
       1553 TCGGGTCAATTTTGGGT
          1 TCGGGTC-ATTTTGGGT

                   *       * 
       1570 T-GGGTCGTTTTCGGTT
          1 TCGGGTCATTTT-GGGT

                     
       1586 TCGGGTCAT
          1 TCGGGTCAT

       1595 ACGGTTCAGA


Statistics
Matches: 35,  Mismatches: 3, Indels: 6
        0.80            0.07        0.14

Matches are distributed among these distances:
  15   11  0.31
  16   10  0.29
  17   14  0.40

ACGTcount: A:0.07, C:0.14, G:0.37, T:0.42


Consensus pattern (16 bp):   
TCGGGTCATTTTGGGT
Done.