Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_194 ID=scaffold_194-JGI_221_v2.0

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: 9526
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33


Found at i:2492 original size:44 final size:41

Alignment explanation


    Indices: 2439--2562  Score: 106
    Period size: 44  Copynumber: 2.9  Consensus size: 41

       2429 GATTATCGAA

                *                                       
       2439 TTCAATCTGCTCCACTGCAACCTTAGGGAGATAAGATTTGCTTC
          1 TTCAGTCTGCTCCACTGC-A-CTTAGGGAGATAAGATTTG-TTC

                      *       *                  *     *
       2483 TTCAGTCTGCCCCACTGTGACTTCAAGGG-GATAAGACTTGTTT
          1 TTCAGTCTGCTCCACTG-CACTT--AGGGAGATAAGATTTGTTC

                           *    *                
       2526 TCTCAGTCTGCTCCATTGCTGCTTAGGGAGATAAGAT
          1 T-TCAGTCTGCTCCACTGC-ACTTAGGGAGATAAGAT

       2563 CTATTGTTTT


Statistics
Matches: 64,  Mismatches: 10, Indels: 13
        0.74            0.11        0.15

Matches are distributed among these distances:
  42    4  0.06
  43   13  0.20
  44   43  0.67
  45    4  0.06

ACGTcount: A:0.23, C:0.23, G:0.22, T:0.32


Consensus pattern (41 bp):   
TTCAGTCTGCTCCACTGCACTTAGGGAGATAAGATTTGTTC

Found at i:2809 original size:87 final size:87

Alignment explanation


    Indices: 2689--3012  Score: 524
    Period size: 87  Copynumber: 3.7  Consensus size: 87

       2679 TTAGGGAGAT

                         *     *                                  *          
       2689 AAGATCTG-TAATTTTTAATCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGCTTTCGATCTG
          1 AAGATCTGCT-ATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTG

                                   
       2753 CTTCGCTGTCAATGTAGGAAGGC
         65 CTTCGCTGTCAATGTAGGAAGGC

                             *  *                                            
       2776 AAGATCTGCTATCTTTATCCTGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGC
          1 AAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGC

                  *              *
       2841 TTCGCTATCAATGTAGGAAGGT
         66 TTCGCTGTCAATGTAGGAAGGC

                                          *  *                               
       2863 AAGATCTGCTATCTTTAACCAGCTCCACTGTAATCGATGGAGGCAAGGCTTTGTTTTCGATCTGC
          1 AAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGC

                      *  *        
       2928 TTCGCTGTCAGTGCAGGAAGGC
         66 TTCGCTGTCAATGTAGGAAGGC

                    *                                                      
       2950 AAGATCTGTTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCT
          1 AAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCT

       3013 TCACTGATCT


Statistics
Matches: 218,  Mismatches: 18, Indels: 2
        0.92            0.08        0.01

Matches are distributed among these distances:
  87  217  1.00
  88    1  0.00

ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31


Consensus pattern (87 bp):   
AAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGC
TTCGCTGTCAATGTAGGAAGGC

Found at i:4277 original size:13 final size:12

Alignment explanation


    Indices: 4259--4288  Score: 51
    Period size: 13  Copynumber: 2.4  Consensus size: 12

       4249 TACTTTTTCG

                         
       4259 TCATTTTTCATTT
          1 TCATTTTTCA-TT

                        
       4272 TCATTTTTCATT
          1 TCATTTTTCATT

                 
       4284 TCATT
          1 TCATT

       4289 CATTTTTTTT


Statistics
Matches: 17,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  12    7  0.41
  13   10  0.59

ACGTcount: A:0.17, C:0.17, G:0.00, T:0.67


Consensus pattern (12 bp):   
TCATTTTTCATT
Done.