Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01008980.1 Corchorus olitorius cultivar O-4 contig09008, 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, 654

Length: 1091
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41


Found at i:62 original size:2 final size:2

Alignment explanation


    Indices: 55--118  Score: 51
    Period size: 2  Copynumber: 30.5  Consensus size: 2

         45 AATAATAATC

                            *                                           * 
         55 AT AT AT AT CAT GT CAT AT CAT AT A- AT AT AT AT AT AT AT AT GT
          1 AT AT AT AT -AT AT -AT AT -AT AT AT AT AT AT AT AT AT AT AT AT

                                             
         97 AT CAT AT AT CAT AT AT -T AT AT A
          1 AT -AT AT AT -AT AT AT AT AT AT A

        119 ATGATAACAA


Statistics
Matches: 51,  Mismatches: 4, Indels: 14
        0.74            0.06        0.20

Matches are distributed among these distances:
   1    2  0.04
   2   40  0.78
   3    9  0.18

ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45


Consensus pattern (2 bp):   
AT

Found at i:82 original size:10 final size:9

Alignment explanation


    Indices: 52--105  Score: 58
    Period size: 9  Copynumber: 6.0  Consensus size: 9

         42 AAAAATAATA

                     
         52 ATCATATAT
          1 ATCATATAT

                 *    
         61 ATCATGTCAT
          1 ATCATAT-AT

                      
         71 ATCATATAAT
          1 ATCATAT-AT

                     
         81 AT-ATATAT
          1 ATCATATAT

                   * 
         89 AT-ATATGT
          1 ATCATATAT

                     
         97 ATCATATAT
          1 ATCATATAT

        106 CATATATTAT


Statistics
Matches: 38,  Mismatches: 5, Indels: 4
        0.81            0.11        0.09

Matches are distributed among these distances:
   8   11  0.29
   9   15  0.39
  10   12  0.32

ACGTcount: A:0.43, C:0.09, G:0.04, T:0.44


Consensus pattern (9 bp):   
ATCATATAT

Found at i:108 original size:7 final size:6

Alignment explanation


    Indices: 55--118  Score: 51
    Period size: 7  Copynumber: 10.2  Consensus size: 6

         45 AATAATAATC

                        *                                  *           
         55 ATATAT ATCATGT CATATCAT ATA-AT ATATAT ATATAT ATGTAT CATATAT
          1 ATATAT AT-ATAT -ATAT-AT ATATAT ATATAT ATATAT ATATAT -ATATAT

                            
        106 CATATAT -TATAT A
          1 -ATATAT ATATAT A

        119 ATGATAACAA


Statistics
Matches: 48,  Mismatches: 4, Indels: 12
        0.75            0.06        0.19

Matches are distributed among these distances:
   5   10  0.21
   6   15  0.31
   7   20  0.42
   8    3  0.06

ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45


Consensus pattern (6 bp):   
ATATAT

Found at i:528 original size:82 final size:82

Alignment explanation


    Indices: 430--586  Score: 287
    Period size: 82  Copynumber: 1.9  Consensus size: 82

        420 CTCAAATATT

                                                                           * 
        430 CCGATTTAATTTGATTTGAATATTGTAAATCAAAATCAATTAGCATAAATGATATAATCACAATA
          1 CCGATTTAATTTGATTTGAATATTGTAAATCAAAATCAATTAGCATAAATGATATAATCACAACA

                             
        495 ATTTCCTTTTTTATCTA
         66 ATTTCCTTTTTTATCTA

                   *         *                                               
        512 CCGATTTGATTTGATTTTAATATTGTAAATCAAAATCAATTAGCATAAATGATATAATCACAACA
          1 CCGATTTAATTTGATTTGAATATTGTAAATCAAAATCAATTAGCATAAATGATATAATCACAACA

                      
        577 ATTTCCTTTT
         66 ATTTCCTTTT

        587 ATGATACCTA


Statistics
Matches: 72,  Mismatches: 3, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  82   72  1.00

ACGTcount: A:0.39, C:0.13, G:0.08, T:0.41


Consensus pattern (82 bp):   
CCGATTTAATTTGATTTGAATATTGTAAATCAAAATCAATTAGCATAAATGATATAATCACAACA
ATTTCCTTTTTTATCTA
Done.