Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017412.1 Corchorus olitorius cultivar O-4 contig17445, 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: 11637
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--35  Score: 70
    Period size: 2  Copynumber: 17.5  Consensus size: 2

                                                                
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

         36 GAAAACTGAA


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   33  1.00

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
TA

Found at i:796 original size:30 final size:30

Alignment explanation


    Indices: 762--822  Score: 104
    Period size: 30  Copynumber: 2.0  Consensus size: 30

        752 TATCAATTTG

                       *      *           
        762 TTTCAAAGAGGTTCATAAGCAAATTTCTTT
          1 TTTCAAAGAGGATCATAAACAAATTTCTTT

                                          
        792 TTTCAAAGAGGATCATAAACAAATTTCTTT
          1 TTTCAAAGAGGATCATAAACAAATTTCTTT

             
        822 T
          1 T

        823 GTCAGAATGA


Statistics
Matches: 29,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  30   29  1.00

ACGTcount: A:0.36, C:0.13, G:0.11, T:0.39


Consensus pattern (30 bp):   
TTTCAAAGAGGATCATAAACAAATTTCTTT

Found at i:1205 original size:14 final size:14

Alignment explanation


    Indices: 1188--1223  Score: 65
    Period size: 14  Copynumber: 2.6  Consensus size: 14

       1178 ATATTTTCAG

                          
       1188 AATTATATATATAT
          1 AATTATATATATAT

                          
       1202 AATTATATATATAT
          1 AATTATATATATAT

                     
       1216 -ATTATATA
          1 AATTATATA

       1224 ACTAAAAACT


Statistics
Matches: 22,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  13    8  0.36
  14   14  0.64

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (14 bp):   
AATTATATATATAT

Found at i:9491 original size:13 final size:12

Alignment explanation


    Indices: 9468--9493  Score: 52
    Period size: 12  Copynumber: 2.2  Consensus size: 12

       9458 GCTCTGTTTA

                        
       9468 CTGTCTTTTTTT
          1 CTGTCTTTTTTT

                        
       9480 CTGTCTTTTTTT
          1 CTGTCTTTTTTT

              
       9492 CT
          1 CT

       9494 TATAATTTTA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   14  1.00

ACGTcount: A:0.00, C:0.19, G:0.08, T:0.73


Consensus pattern (12 bp):   
CTGTCTTTTTTT

Found at i:10477 original size:104 final size:104

Alignment explanation


    Indices: 10296--10507  Score: 415
    Period size: 104  Copynumber: 2.0  Consensus size: 104

      10286 TGCGAACCGA

                                                                             
      10296 GGAATGATTCATTTCTCCAAGCTAAATCCAATTAATTGTTGGCATGAAAATTTTTATTGCTGCAT
          1 GGAATGATTCATTTCTCCAAGCTAAATCCAATTAATTGTTGGCATGAAAATTTTTATTGCTGCAT

                                                   
      10361 GAATTTTGTGCTTAGAAATTAGAATACATCAAGCAGTAT
         66 GAATTTTGTGCTTAGAAATTAGAATACATCAAGCAGTAT

                                                                             
      10400 GGAATGATTCATTTCTCCAAGCTAAATCCAATTAATTGTTGGCATGAAAATTTTTATTGCTGCAT
          1 GGAATGATTCATTTCTCCAAGCTAAATCCAATTAATTGTTGGCATGAAAATTTTTATTGCTGCAT

                   *                               
      10465 GAATTTTTTGCTTAGAAATTAGAATACATCAAGCAGTAT
         66 GAATTTTGTGCTTAGAAATTAGAATACATCAAGCAGTAT

                
      10504 GGAA
          1 GGAA

      10508 ACTTCCCAAG


Statistics
Matches: 107,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
 104  107  1.00

ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36


Consensus pattern (104 bp):   
GGAATGATTCATTTCTCCAAGCTAAATCCAATTAATTGTTGGCATGAAAATTTTTATTGCTGCAT
GAATTTTGTGCTTAGAAATTAGAATACATCAAGCAGTAT

Found at i:11499 original size:161 final size:161

Alignment explanation


    Indices: 11323--11637  Score: 444
    Period size: 161  Copynumber: 2.0  Consensus size: 161

      11313 ACTTTTATTG

                                                                           * 
      11323 TTTTACTCAACTAAAAACTCTA-TTTTT-CCCTAAAAAAAAACTAAAAACTCTATTTTTATTTTA
          1 TTTTACTCAACTAAAAACTCTATTTTTTGCCC--AAAAAAAACTAAAAACTCTATTTTTATTTAA

             *                                    *                          
      11386 TTAAATATAATATCCTTATAACTA-TTTAATTTTTA-CCATTGTACT-ATTTAATTAAAAAAAAT
         64 TGAAATATAATATCCTTATAACTACTTT-ATTTTTATCAATT-TACTAATTTAATT-AAAAAAAT

              *               * *                
      11448 TATATA-TATTAGAATTTTTTAAATATATTTTTATAA
        126 TAGATATTA-TAGAATTTCTAAAATATATTTTTATAA

                                         *                                   
      11484 TTTTACTCAACTAAAAACTCTATTTTTTGGCCAAAAAAAACTAAAAACTCTATTTTTATTTAATG
          1 TTTTACTCAACTAAAAACTCTATTTTTTGCCCAAAAAAAACTAAAAACTCTATTTTTATTTAATG

                *             *                                       *      
      11549 AAATCTAATATCCTTATACCTACTTTATTTTTATCAATTTACTAATTTAATTAAAAAACTTAGAT
         66 AAATATAATATCCTTATAACTACTTTATTTTTATCAATTTACTAATTTAATTAAAAAAATTAGAT

                                    
      11614 ATTATAGAATTTCTAAAATATATT
        131 ATTATAGAATTTCTAAAATATATT


Statistics
Matches: 138,  Mismatches: 10, Indels: 12
        0.86            0.06        0.08

Matches are distributed among these distances:
 161  114  0.83
 162   22  0.16
 163    2  0.01

ACGTcount: A:0.42, C:0.12, G:0.02, T:0.44


Consensus pattern (161 bp):   
TTTTACTCAACTAAAAACTCTATTTTTTGCCCAAAAAAAACTAAAAACTCTATTTTTATTTAATG
AAATATAATATCCTTATAACTACTTTATTTTTATCAATTTACTAATTTAATTAAAAAAATTAGAT
ATTATAGAATTTCTAAAATATATTTTTATAA
Done.