Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019792.1 Corchorus olitorius cultivar O-4 contig19825, 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: 5758
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.30


Found at i:193 original size:12 final size:12

Alignment explanation


    Indices: 177--245  Score: 57
    Period size: 13  Copynumber: 5.5  Consensus size: 12

        167 CCGGTTTTCC

                  *      
        177 CTTTTTTTTTCTT
          1 CTTTTTCTTT-TT

            *           
        190 TTTTTTCTTTTT
          1 CTTTTTCTTTTT

                  *      
        202 CCTTTTCCTTTTT
          1 -CTTTTTCTTTTT

                        *
        215 CTTTTTCCTTTTC
          1 CTTTTT-CTTTTT

                 *     *
        228 CTTTTCCTTTTC
          1 CTTTTTCTTTTT

                  
        240 CTTTTT
          1 CTTTTT

        246 TTTCTTTCCT


Statistics
Matches: 46,  Mismatches: 8, Indels: 5
        0.78            0.14        0.08

Matches are distributed among these distances:
  12   18  0.39
  13   28  0.61

ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77


Consensus pattern (12 bp):   
CTTTTTCTTTTT

Found at i:199 original size:19 final size:20

Alignment explanation


    Indices: 177--252  Score: 61
    Period size: 19  Copynumber: 3.8  Consensus size: 20

        167 CCGGTTTTCC

                                
        177 CTTTTT-TTTTCTTTTTTTT
          1 CTTTTTCTTTTCTTTTTTTT

                           *     
        196 CTTTTTCCTTTTC--CTTTTT
          1 CTTTTT-CTTTTCTTTTTTTT

                                    
        215 CTTTTTCCTTTTCCTTTTCCTTTT
          1 CTTTTT-CTTTT-CTTTT--TTTT

             *             
        239 CCTTTT-TTTTCTTT
          1 CTTTTTCTTTTCTTT

        253 CCTCTCTTTT


Statistics
Matches: 47,  Mismatches: 3, Indels: 12
        0.76            0.05        0.19

Matches are distributed among these distances:
  19   23  0.49
  20    1  0.02
  21    9  0.19
  22    5  0.11
  24    9  0.19

ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78


Consensus pattern (20 bp):   
CTTTTTCTTTTCTTTTTTTT

Found at i:200 original size:6 final size:6

Alignment explanation


    Indices: 177--245  Score: 57
    Period size: 6  Copynumber: 11.0  Consensus size: 6

        167 CCGGTTTTCC

                   *       *                   *                     *
        177 CTTTTT TTTTCTT TTTTTT CTTTTT CCTTTTC CTTTTT CTTTTT CCTTTTC
          1 CTTTTT CTTT-TT CTTTTT CTTTTT -CTTTTT CTTTTT CTTTTT -CTTTTT

                 *      *       
        228 CTTTTC CTTTTC CTTTTT
          1 CTTTTT CTTTTT CTTTTT

        246 TTTCTTTCCT


Statistics
Matches: 54,  Mismatches: 6, Indels: 6
        0.82            0.09        0.09

Matches are distributed among these distances:
   6   38  0.70
   7   16  0.30

ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77


Consensus pattern (6 bp):   
CTTTTT

Found at i:4572 original size:11 final size:11

Alignment explanation


    Indices: 4537--4593  Score: 60
    Period size: 12  Copynumber: 4.8  Consensus size: 11

       4527 TTATGCACCA

                        
       4537 AAAACATTTATT
          1 AAAACATTTA-T

                        
       4549 AAAACATTTTAT
          1 AAAACA-TTTAT

               *       
       4561 AAAGCATTTAT
          1 AAAACATTTAT

                    *    
       4572 ATAAAGCAGTTAT
          1 A-AAA-CATTTAT

                     
       4585 AAAACATTT
          1 AAAACATTT

       4594 TCTCAACGGA


Statistics
Matches: 38,  Mismatches: 4, Indels: 7
        0.78            0.08        0.14

Matches are distributed among these distances:
  11   10  0.26
  12   17  0.45
  13   11  0.29

ACGTcount: A:0.49, C:0.09, G:0.05, T:0.37


Consensus pattern (11 bp):   
AAAACATTTAT
Done.