Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015530.1 Corchorus olitorius cultivar O-4 contig15563, 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: 5578
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35


Found at i:1166 original size:27 final size:27

Alignment explanation


    Indices: 1118--1178  Score: 68
    Period size: 27  Copynumber: 2.3  Consensus size: 27

       1108 ATTACCAAAA

                 *           *    *    
       1118 TACCCGTGATGGACAAATTTACTATAT
          1 TACCCCTGATGGACAAAATTACGATAT

                      *  *           * 
       1145 TACCCCTGATTGATAAAATTACGATTT
          1 TACCCCTGATGGACAAAATTACGATAT

                   
       1172 TACCCCT
          1 TACCCCT

       1179 ATAATGAGGA


Statistics
Matches: 28,  Mismatches: 6, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  27   28  1.00

ACGTcount: A:0.31, C:0.23, G:0.11, T:0.34


Consensus pattern (27 bp):   
TACCCCTGATGGACAAAATTACGATAT

Found at i:4609 original size:29 final size:30

Alignment explanation


    Indices: 4543--4618  Score: 136
    Period size: 30  Copynumber: 2.6  Consensus size: 30

       4533 CTTTCTTCAT

                                          
       4543 AAAGGTTGTGCTGAATTTCTCATAAAAAAA
          1 AAAGGTTGTGCTGAATTTCTCATAAAAAAA

                                          
       4573 AAAGGTTGTGCTGAATTTCTCAT-AAAAAA
          1 AAAGGTTGTGCTGAATTTCTCATAAAAAAA

                       *     
       4602 AAAGGTTGTGCCGAATT
          1 AAAGGTTGTGCTGAATT

       4619 ACCTAAGAAC


Statistics
Matches: 45,  Mismatches: 1, Indels: 1
        0.96            0.02        0.02

Matches are distributed among these distances:
  29   22  0.49
  30   23  0.51

ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30


Consensus pattern (30 bp):   
AAAGGTTGTGCTGAATTTCTCATAAAAAAA
Done.