Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020225.1 Corchorus olitorius cultivar O-4 contig20258, 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: 15856
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36


Found at i:12795 original size:164 final size:164

Alignment explanation


    Indices: 12279--12777  Score: 838
    Period size: 164  Copynumber: 3.0  Consensus size: 164

      12269 ACAGACCAAG

                                                                          * *
      12279 GCAATGATTAGTTGG-TTTAAATTTAGTAAAAACTCACTTAAAAATTAAAATGACATAATTATCT
          1 GCAATGATTAGTTGGTTTTAAATTTAGTAAAAACTCAC-------TTAAAATGACATAATTACCC

                                                                             
      12343 TTTGTAAACAATTAATTAATAAATTTTCTCTCCCTTCCAGCTTTCCAAGACCATTTAAAAGTTCA
         59 TTTGTAAACAATTAATTAATAAATTTTCTCTCCCTTCCAGCTTTCCAAGACCATTTAAAAGTTCA

                *                                    
      12408 AGCATCTTAATTAACACTTAAGGGTATATATGGAAAAAAGA
        124 AGCACCTTAATTAACACTTAAGGGTATATATGGAAAAAAGA

                                                                         *   
      12449 GCAATGATTAGTTGGTTTTAAATTTAGTAAAAACTCACTTAAAATGACATAATTACCCTTTATAA
          1 GCAATGATTAGTTGGTTTTAAATTTAGTAAAAACTCACTTAAAATGACATAATTACCCTTTGTAA

                                                                             
      12514 ACAATTAATTAATAAATTTTCTCTCCCTTCCAGCTTTCCAAGACCATTTAAAAGTTCAAGCACCT
         66 ACAATTAATTAATAAATTTTCTCTCCCTTCCAGCTTTCCAAGACCATTTAAAAGTTCAAGCACCT

                                              
      12579 TAATTAACACTTAAGGGTATATATGGAAAAAAGA
        131 TAATTAACACTTAAGGGTATATATGGAAAAAAGA

                                                                             
      12613 GCAATGATTAGTTGGTTTTAAATTTAGTAAAAACTCACTTAAAATGACATAATTACCCTTTGTAA
          1 GCAATGATTAGTTGGTTTTAAATTTAGTAAAAACTCACTTAAAATGACATAATTACCCTTTGTAA

                           *    *    **                                *     
      12678 ACAATTAATTAATAATTTTTTTCTCATTTCCAGCTTTCCAAGACCATTTAAAAGTTCAAACACCT
         66 ACAATTAATTAATAAATTTTCTCTCCCTTCCAGCTTTCCAAGACCATTTAAAAGTTCAAGCACCT

                                       *      
      12743 TAATTAACACTTAAGGGTATATATGGATAAAAGA
        131 TAATTAACACTTAAGGGTATATATGGAAAAAAGA

             
      12777 G
          1 G

      12778 TAAAATTGCA


Statistics
Matches: 317,  Mismatches: 11, Indels: 8
        0.94            0.03        0.02

Matches are distributed among these distances:
 164  280  0.88
 170   15  0.05
 171   22  0.07

ACGTcount: A:0.40, C:0.15, G:0.11, T:0.35


Consensus pattern (164 bp):   
GCAATGATTAGTTGGTTTTAAATTTAGTAAAAACTCACTTAAAATGACATAATTACCCTTTGTAA
ACAATTAATTAATAAATTTTCTCTCCCTTCCAGCTTTCCAAGACCATTTAAAAGTTCAAGCACCT
TAATTAACACTTAAGGGTATATATGGAAAAAAGA

Found at i:12811 original size:25 final size:25

Alignment explanation


    Indices: 12777--12826  Score: 100
    Period size: 25  Copynumber: 2.0  Consensus size: 25

      12767 GGATAAAAGA

                                     
      12777 GTAAAATTGCATTGGTTTTGTGATT
          1 GTAAAATTGCATTGGTTTTGTGATT

                                     
      12802 GTAAAATTGCATTGGTTTTGTGATT
          1 GTAAAATTGCATTGGTTTTGTGATT

      12827 ATTTCACTTA


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

Matches are distributed among these distances:
  25   25  1.00

ACGTcount: A:0.24, C:0.04, G:0.24, T:0.48


Consensus pattern (25 bp):   
GTAAAATTGCATTGGTTTTGTGATT

Found at i:13961 original size:2 final size:2

Alignment explanation


    Indices: 13954--13982  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

      13944 ATCATAGATG

                                                       
      13954 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

      13983 AAAGTATGAA


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

Matches are distributed among these distances:
   2   27  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:14087 original size:24 final size:28

Alignment explanation


    Indices: 14035--14087  Score: 69
    Period size: 24  Copynumber: 2.0  Consensus size: 28

      14025 TTTTTTAAAA

                                    *   
      14035 AAATATATATTTCTAAATTGCCATTATT
          1 AAATATATATTTCTAAATTGCCATCATT

                                        
      14063 AAATA-ATATTT-T-AATT-CCATCATT
          1 AAATATATATTTCTAAATTGCCATCATT

             
      14087 A
          1 A

      14088 TTAAAATCAT


Statistics
Matches: 24,  Mismatches: 1, Indels: 4
        0.83            0.03        0.14

Matches are distributed among these distances:
  24    8  0.33
  25    4  0.17
  26    1  0.04
  27    6  0.25
  28    5  0.21

ACGTcount: A:0.42, C:0.11, G:0.02, T:0.45


Consensus pattern (28 bp):   
AAATATATATTTCTAAATTGCCATCATT
Done.