Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01002016.1 Corchorus olitorius cultivar O-4 contig02016, 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, 699

Length: 1165
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35


Found at i:14 original size:3 final size:3

Alignment explanation


    Indices: 8--81  Score: 139
    Period size: 3  Copynumber: 24.7  Consensus size: 3

          1 ATAATAA

                                                                           
          8 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
          1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT

            *                                 
         56 GTT ATT ATT ATT ATT ATT ATT ATT AT
          1 ATT ATT ATT ATT ATT ATT ATT ATT AT

         82 AATACTCCTA


Statistics
Matches: 69,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
   3   69  1.00

ACGTcount: A:0.32, C:0.00, G:0.01, T:0.66


Consensus pattern (3 bp):   
ATT

Found at i:199 original size:2 final size:2

Alignment explanation


    Indices: 192--216  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

        182 ATGATAAACT

                                                 
        192 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 T

        217 GATAATAGGC


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:329 original size:31 final size:29

Alignment explanation


    Indices: 267--331  Score: 76
    Period size: 29  Copynumber: 2.2  Consensus size: 29

        257 CATAAATCTT

                     * *              *  
        267 AAATAAGGATCGAAACTTTAGAAAAGGTC
          1 AAATAAGGACCCAAACTTTAGAAAAGCTC

                                *          
        296 AAATAAGGACCCAAACTTTTTGAAAAAGCTC
          1 AAATAAGGACCCAAAC-TTTAG-AAAAGCTC

                 
        327 AAATA
          1 AAATA

        332 GGTCCAATCC


Statistics
Matches: 30,  Mismatches: 4, Indels: 2
        0.83            0.11        0.06

Matches are distributed among these distances:
  29   14  0.47
  30    4  0.13
  31   12  0.40

ACGTcount: A:0.49, C:0.14, G:0.15, T:0.22


Consensus pattern (29 bp):   
AAATAAGGACCCAAACTTTAGAAAAGCTC

Found at i:438 original size:25 final size:24

Alignment explanation


    Indices: 410--486  Score: 68
    Period size: 25  Copynumber: 3.2  Consensus size: 24

        400 GGCAGTTAAG

                                     
        410 TCCTTATTTTCCATTTTATTTAATT
          1 TCCTTATTTT-CATTTTATTTAATT

                  *            *    
        435 TCCTTAATTTC-TTTT-TTGAATT
          1 TCCTTATTTTCATTTTATTTAATT

             **   *                * 
        457 TGTTTCTTTTTCATTTTATTTAAAT
          1 TCCTT-ATTTTCATTTTATTTAATT

                 
        482 TCCTT
          1 TCCTT

        487 TTAATTTATT


Statistics
Matches: 39,  Mismatches: 10, Indels: 6
        0.71            0.18        0.11

Matches are distributed among these distances:
  22    9  0.23
  23    8  0.21
  24    5  0.13
  25   17  0.44

ACGTcount: A:0.18, C:0.14, G:0.03, T:0.65


Consensus pattern (24 bp):   
TCCTTATTTTCATTTTATTTAATT
Done.