Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022878.1 Corchorus olitorius cultivar O-4 contig22911, 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: 6977
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.28


Found at i:5133 original size:3 final size:3

Alignment explanation


    Indices: 5125--5210  Score: 172
    Period size: 3  Copynumber: 28.7  Consensus size: 3

       5115 GGCAGCCTTT

                                                                           
       5125 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA

                                                              
       5173 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT

       5211 TCTTATATAT


Statistics
Matches: 83,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   83  1.00

ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67


Consensus pattern (3 bp):   
TTA

Found at i:5226 original size:16 final size:16

Alignment explanation


    Indices: 5125--5227  Score: 110
    Period size: 15  Copynumber: 6.8  Consensus size: 16

       5115 GGCAGCCTTT

                        *   
       5125 TTATTATTA-TTATTA
          1 TTATTATTATTTCTTA

                        *   
       5140 TTATTATTA-TTATTA
          1 TTATTATTATTTCTTA

                        *   
       5155 TTATTATTA-TTATTA
          1 TTATTATTATTTCTTA

                        *   
       5170 TTATTATTA-TTATTA
          1 TTATTATTATTTCTTA

                        *   
       5185 TTATTATTA-TTATTA
          1 TTATTATTATTTCTTA

                            
       5200 TTATTATTATTTCTTA
          1 TTATTATTATTTCTTA

                         
       5216 TATATTA-TATTT
          1 T-TATTATTATTT

       5228 TGTGAACCAC


Statistics
Matches: 85,  Mismatches: 1, Indels: 3
        0.96            0.01        0.03

Matches are distributed among these distances:
  15   69  0.81
  16   11  0.13
  17    5  0.06

ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67


Consensus pattern (16 bp):   
TTATTATTATTTCTTA

Found at i:5854 original size:38 final size:38

Alignment explanation


    Indices: 5812--6021  Score: 226
    Period size: 38  Copynumber: 5.5  Consensus size: 38

       5802 GTTTTATCAT

                                                  
       5812 AGCAAACCTGCTTAGGTCTATGTTTAGAATTTTATTTA
          1 AGCAAACCTGCTTAGGTCTATGTTTAGAATTTTATTTA

                                            *  *  
       5850 AGCAAACCTGCTTAGGTCTATGTTTAGAATTTCATCTA
          1 AGCAAACCTGCTTAGGTCTATGTTTAGAATTTTATTTA

              *                   * *          *  * 
       5888 AGTAAACCTGCTTAGGTCCT-TATCTAGAATTTTCGTTCA
          1 AGCAAACCTGCTTAGGT-CTATGTTTAGAATTTT-ATTTA

             *   *                          *  *  
       5927 ATCAAGCCTGCTTAGGTCTATGTTTAGAATTTCATCTA
          1 AGCAAACCTGCTTAGGTCTATGTTTAGAATTTTATTTA

              *                   *            *  * 
       5965 AGTAAACCTGCTTAGGTCCT-TATTTAGAATTTTCGTTCA
          1 AGCAAACCTGCTTAGGT-CTATGTTTAGAATTTT-ATTTA

             *                
       6004 ATCAAACCTGCTTAGGTC
          1 AGCAAACCTGCTTAGGTC

       6022 CCTGTGTAAA


Statistics
Matches: 139,  Mismatches: 28, Indels: 10
        0.79            0.16        0.06

Matches are distributed among these distances:
  38   92  0.66
  39   47  0.34

ACGTcount: A:0.27, C:0.19, G:0.16, T:0.39


Consensus pattern (38 bp):   
AGCAAACCTGCTTAGGTCTATGTTTAGAATTTTATTTA

Found at i:5956 original size:77 final size:77

Alignment explanation


    Indices: 5815--6021  Score: 337
    Period size: 77  Copynumber: 2.7  Consensus size: 77

       5805 TTATCATAGC

                               *            *  *  *                          
       5815 AAACCTGCTTAGGT-CTATGTTTAGAATTTT-ATTTAAGCAAACCTGCTTAGGTCTATGTTTAGA
          1 AAACCTGCTTAGGTCCT-TATTTAGAATTTTCGTTCAATCAAACCTGCTTAGGTCTATGTTTAGA

                         
       5878 ATTTCATCTAAGT
         65 ATTTCATCTAAGT

                                *                    *                       
       5891 AAACCTGCTTAGGTCCTTATCTAGAATTTTCGTTCAATCAAGCCTGCTTAGGTCTATGTTTAGAA
          1 AAACCTGCTTAGGTCCTTATTTAGAATTTTCGTTCAATCAAACCTGCTTAGGTCTATGTTTAGAA

                        
       5956 TTTCATCTAAGT
         66 TTTCATCTAAGT

                                                                  
       5968 AAACCTGCTTAGGTCCTTATTTAGAATTTTCGTTCAATCAAACCTGCTTAGGTC
          1 AAACCTGCTTAGGTCCTTATTTAGAATTTTCGTTCAATCAAACCTGCTTAGGTC

       6022 CCTGTGTAAA


Statistics
Matches: 121,  Mismatches: 8, Indels: 3
        0.92            0.06        0.02

Matches are distributed among these distances:
  76   25  0.21
  77   96  0.79

ACGTcount: A:0.27, C:0.18, G:0.15, T:0.39


Consensus pattern (77 bp):   
AAACCTGCTTAGGTCCTTATTTAGAATTTTCGTTCAATCAAACCTGCTTAGGTCTATGTTTAGAA
TTTCATCTAAGT

Found at i:6041 original size:39 final size:39

Alignment explanation


    Indices: 5887--6058  Score: 113
    Period size: 39  Copynumber: 4.4  Consensus size: 39

       5877 AATTTCATCT

                                *   *  *    **     
       5887 AAGTAAACCTGCTTAGGTCCTTATCTAGAATTTTCGTTC
          1 AAGTAAACCTGCTTAGGTCCCTATGTAAAATTACCGTTC

                   *                      *     *  *  
       5926 AA-TCAAGCCTGCTTAGGT--CTATGTTTAGAATT-TC-ATC
          1 AAGT-AAACCTGCTTAGGTCCCTATG--TAAAATTACCGTTC

                                 *   *  *    **     
       5963 TAAGTAAACCTGCTTAGGTCCTTATTTAGAATTTTCGTTC
          1 -AAGTAAACCTGCTTAGGTCCCTATGTAAAATTACCGTTC

                                   *                
       6003 AA-TCAAACCTGCTTAGGTCCCTGTGTAAAATTACCGTTC
          1 AAGT-AAACCTGCTTAGGTCCCTATGTAAAATTACCGTTC

                *            
       6042 AAGTGAACCTGCTTAGG
          1 AAGTAAACCTGCTTAGG

       6059 ATCTCTGCTT


Statistics
Matches: 107,  Mismatches: 15, Indels: 22
        0.74            0.10        0.15

Matches are distributed among these distances:
  37    5  0.05
  38   26  0.24
  39   70  0.65
  40    6  0.06

ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36


Consensus pattern (39 bp):   
AAGTAAACCTGCTTAGGTCCCTATGTAAAATTACCGTTC
Done.