Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013772.1 Corchorus olitorius cultivar O-4 contig13805, 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: 21599
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37


Found at i:162 original size:3 final size:3

Alignment explanation


    Indices: 24--153  Score: 251
    Period size: 3  Copynumber: 43.0  Consensus size: 3

         14 ACTTTAAGTA

                                                                        
         24 TAT TAAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
          1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT

                                                                           
         70 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
          1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT

                                                           
        118 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
          1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT

        154 ACATTATTAA


Statistics
Matches: 126,  Mismatches: 0, Indels: 2
        0.98            0.00        0.02

Matches are distributed among these distances:
   3  123  0.98
   4    3  0.02

ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66


Consensus pattern (3 bp):   
TAT

Found at i:1388 original size:5 final size:5

Alignment explanation


    Indices: 1380--1408  Score: 58
    Period size: 5  Copynumber: 5.8  Consensus size: 5

       1370 GCTTTTTTGT

                                              
       1380 TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
          1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTT

       1409 GAGGAATGCA


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   5   24  1.00

ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83


Consensus pattern (5 bp):   
TTTTC

Found at i:12981 original size:3 final size:3

Alignment explanation


    Indices: 12973--13005  Score: 66
    Period size: 3  Copynumber: 11.0  Consensus size: 3

      12963 TCTTTCCTTT

                                                       
      12973 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
          1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA

      13006 CGCTGGAGTC


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   30  1.00

ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33


Consensus pattern (3 bp):   
ATA

Found at i:16699 original size:26 final size:26

Alignment explanation


    Indices: 16663--16715  Score: 106
    Period size: 26  Copynumber: 2.0  Consensus size: 26

      16653 TGGAATGTGA

                                      
      16663 TTGTTTTTTTGCCTTTGCAATTTGCT
          1 TTGTTTTTTTGCCTTTGCAATTTGCT

                                      
      16689 TTGTTTTTTTGCCTTTGCAATTTGCT
          1 TTGTTTTTTTGCCTTTGCAATTTGCT

             
      16715 T
          1 T

      16716 CCGCAACTTT


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  26   27  1.00

ACGTcount: A:0.08, C:0.15, G:0.15, T:0.62


Consensus pattern (26 bp):   
TTGTTTTTTTGCCTTTGCAATTTGCT

Found at i:17401 original size:16 final size:15

Alignment explanation


    Indices: 17356--17406  Score: 50
    Period size: 16  Copynumber: 3.2  Consensus size: 15

      17346 CTCATCTTTC

                             
      17356 TTTCTTTCTTCCTTCTT
          1 TTTCTTTCTT--TTCTT

                    *       
      17373 TCTTCTTTGTTTTCTT
          1 T-TTCTTTCTTTTCTT

                            
      17389 TTTCTTTTCTTTT-TT
          1 TTTC-TTTCTTTTCTT

               
      17404 TTT
          1 TTT

      17407 TGTCCTGTTC


Statistics
Matches: 30,  Mismatches: 2, Indels: 6
        0.79            0.05        0.16

Matches are distributed among these distances:
  15    8  0.27
  16   13  0.43
  17    1  0.03
  18    8  0.27

ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78


Consensus pattern (15 bp):   
TTTCTTTCTTTTCTT

Found at i:21445 original size:59 final size:59

Alignment explanation


    Indices: 21348--21526  Score: 322
    Period size: 59  Copynumber: 3.0  Consensus size: 59

      21338 TGGTATTCAT

                               *       *   * *                         
      21348 TCTCTTCTATCCTTCATTAGTTGAAGCGTTTATCGCAACAAATGTTTATAAGAAAAATG
          1 TCTCTTCTATCCTTCATTAATTGAAGCATTTCTTGCAACAAATGTTTATAAGAAAAATG

                                                                       
      21407 TCTCTTCTATCCTTCATTAATTGAAGCATTTCTTGCAACAAATGTTTATAAGAAAAATG
          1 TCTCTTCTATCCTTCATTAATTGAAGCATTTCTTGCAACAAATGTTTATAAGAAAAATG

                                                                       
      21466 TCTCTTCTATCCTTCATTAATTGAAGCATTTCTTGCAACAAATGTTTATAAGAAAAATG
          1 TCTCTTCTATCCTTCATTAATTGAAGCATTTCTTGCAACAAATGTTTATAAGAAAAATG

              
      21525 TC
          1 TC

      21527 ATTTCTTCCT


Statistics
Matches: 116,  Mismatches: 4, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  59  116  1.00

ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39


Consensus pattern (59 bp):   
TCTCTTCTATCCTTCATTAATTGAAGCATTTCTTGCAACAAATGTTTATAAGAAAAATG
Done.