Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012909.1 Corchorus olitorius cultivar O-4 contig12942, 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: 16393
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.32


Found at i:309 original size:14 final size:14

Alignment explanation


    Indices: 290--320  Score: 62
    Period size: 14  Copynumber: 2.2  Consensus size: 14

        280 GCATTAGATT

                          
        290 ATTAATATATAATA
          1 ATTAATATATAATA

                          
        304 ATTAATATATAATA
          1 ATTAATATATAATA

               
        318 ATT
          1 ATT

        321 GGCTTGTCAA


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   17  1.00

ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45


Consensus pattern (14 bp):   
ATTAATATATAATA

Found at i:3356 original size:1 final size:1

Alignment explanation


    Indices: 3350--3375  Score: 52
    Period size: 1  Copynumber: 26.0  Consensus size: 1

       3340 ATATAATTAT

                                      
       3350 AAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAA

       3376 CGATCATGAG


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   25  1.00

ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00


Consensus pattern (1 bp):   
A

Found at i:7414 original size:124 final size:124

Alignment explanation


    Indices: 7181--7428  Score: 286
    Period size: 124  Copynumber: 2.0  Consensus size: 124

       7171 GATGAGTCTC

                           *  *     *       *     *   *    *             *   
       7181 AGGTTCAAAGAGTTTGTGGATACCTTTGATCAGACCAGGAAATTTTATAGAAAACAATCATGATA
          1 AGGTTCAAAGAGTTTCTGAATACCATTGATCAAACCAGCAAACTTTAGAGAAAACAATCATAATA

            **     *      *      *   *                      *          
       7246 TGCCGATCCAATTATTTTAACTAACGTTATAAATTTAATCAATAATGTTACATTAACTA
         66 AACCGATACAATTACTTTAACCAACATTATAAATTTAATCAATAATGTAACATTAACTA

                                               *                             
       7305 AGGTTCAAAG-GATTTCTGAATACCATTGATCAAATCAGACAAACTTTAGAGAAAACAATCATAA
          1 AGGTTCAAAGAG-TTTCTGAATACCATTGATCAAACCAG-CAAACTTTAGAGAAAACAATCATAA

                                             *      *                     
       7369 TAAACCGATACAATGT-CTTTAACCAACATTATGAATTT-GTCAATAATGTAACATTAACTA
         64 TAAACCGATACAAT-TACTTTAACCAACATTATAAATTTAATCAATAATGTAACATTAACTA

       7429 TCACACTAGT


Statistics
Matches: 103,  Mismatches: 18, Indels: 6
        0.81            0.14        0.05

Matches are distributed among these distances:
 123    1  0.01
 124   51  0.50
 125   50  0.49
 126    1  0.01

ACGTcount: A:0.41, C:0.15, G:0.12, T:0.31


Consensus pattern (124 bp):   
AGGTTCAAAGAGTTTCTGAATACCATTGATCAAACCAGCAAACTTTAGAGAAAACAATCATAATA
AACCGATACAATTACTTTAACCAACATTATAAATTTAATCAATAATGTAACATTAACTA

Found at i:7590 original size:23 final size:24

Alignment explanation


    Indices: 7542--7603  Score: 67
    Period size: 23  Copynumber: 2.7  Consensus size: 24

       7532 ATGCTATTTG

                               **   
       7542 AATAATATATAAATA-AATTGTAT
          1 AATAATATATAAATATAATAATAT

                 *                  
       7565 AATAACATATAAATATAATAAT-T
          1 AATAATATATAAATATAATAATAT

               *             
       7588 AATTATA-ATAAATATA
          1 AATAATATATAAATATA

       7604 GTTGTTAGCT


Statistics
Matches: 33,  Mismatches: 5, Indels: 3
        0.80            0.12        0.07

Matches are distributed among these distances:
  22    9  0.27
  23   20  0.61
  24    4  0.12

ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37


Consensus pattern (24 bp):   
AATAATATATAAATATAATAATAT

Found at i:16362 original size:2 final size:2

Alignment explanation


    Indices: 16357--16388  Score: 64
    Period size: 2  Copynumber: 16.0  Consensus size: 2

      16347 TGTGTGTGTT

                                                           
      16357 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

      16389 GTAGT


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

Matches are distributed among these distances:
   2   30  1.00

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


Consensus pattern (2 bp):   
TA

Done.