Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold2348

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, 587

Length: 979
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32


Found at i:255 original size:24 final size:22

Alignment explanation


    Indices: 227--279  Score: 67
    Period size: 19  Copynumber: 2.5  Consensus size: 22

        217 AATTTAAAAA

                                    
        227 ATAAAACATAATATAATATTTATC
          1 ATAAAA-ATAATA-AATATTTATC

                                  
        251 AT--AAA-AATAAATATTTATC
          1 ATAAAAATAATAAATATTTATC

                      
        270 ATAAAAATAA
          1 ATAAAAATAA

        280 ATATTTCATT


Statistics
Matches: 26,  Mismatches: 0, Indels: 8
        0.76            0.00        0.24

Matches are distributed among these distances:
  19   12  0.46
  20    4  0.15
  21    4  0.15
  22    4  0.15
  24    2  0.08

ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34


Consensus pattern (22 bp):   
ATAAAAATAATAAATATTTATC

Found at i:265 original size:19 final size:19

Alignment explanation


    Indices: 236--285  Score: 91
    Period size: 19  Copynumber: 2.6  Consensus size: 19

        226 AATAAAACAT

                                
        236 AATATAATATTTATCATAAA
          1 AATA-AATATTTATCATAAA

                               
        256 AATAAATATTTATCATAAA
          1 AATAAATATTTATCATAAA

                       
        275 AATAAATATTT
          1 AATAAATATTT

        286 CATTTGATTA


Statistics
Matches: 30,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
  19   26  0.87
  20    4  0.13

ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40


Consensus pattern (19 bp):   
AATAAATATTTATCATAAA

Found at i:619 original size:127 final size:129

Alignment explanation


    Indices: 358--670  Score: 382
    Period size: 127  Copynumber: 2.4  Consensus size: 129

        348 AAAAGTTTGT

                                      *            **  *    * *       *     *
        358 TCTATAGCGGCGTTTGTGGGAAAAGCACCGCTAAAGGTCCCGAGCTATGGTGGCGTTTGTGGGAT
          1 TCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTATGGGAA

                                                              *             
        423 AAGCGCCGCTAAAGGCCTTGAGCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGA
         66 AAGCGCCGCTAAAGGCCTTGAGCTATAGCGGCGTTTGTGGGAAAAGCGCCACTAAAGGTCATGA

                  *   *                                    *   *          *  
        487 TCTATATCGGTGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGATCTACAGCAGCGTTTAT-GTAA
          1 TCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTATGGGAA

               *           *     *                                       * * 
        551 AAGTGCCGCTAAAGGTC-TGATCTATAGCGGCGTTTGT-GGAAAATGCGCCACTAAAGGTCCTTA
         66 AAGCGCCGCTAAAGGCCTTGAGCTATAGCGGCGTTTGTGGGAAAA-GCGCCACTAAAGGTCATGA

                       *   *           *                              
        614 TCTATAGCGGCATTTTTGGGAAAAGCGTCGCTAAAGGT-TATGATCTATAGCGGCGTT
          1 TCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCT-TGATCTATAGCGGCGTT

        671 GACAACAGCG


Statistics
Matches: 156,  Mismatches: 26, Indels: 6
        0.83            0.14        0.03

Matches are distributed among these distances:
 126    7  0.04
 127   83  0.53
 128   17  0.11
 129   49  0.31

ACGTcount: A:0.25, C:0.19, G:0.30, T:0.27


Consensus pattern (129 bp):   
TCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTATGGGAA
AAGCGCCGCTAAAGGCCTTGAGCTATAGCGGCGTTTGTGGGAAAAGCGCCACTAAAGGTCATGA

Found at i:660 original size:43 final size:43

Alignment explanation


    Indices: 358--670  Score: 341
    Period size: 43  Copynumber: 7.3  Consensus size: 43

        348 AAAAGTTTGT

                                      *           * *  
        358 TCTATAGCGGCGTTTGTGGGAAAAGCACCGCTAAAGGTCCCGA
          1 TCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTTCTGA

            *    * *             *                *     
        401 GCTATGGTGGCGTTTGTGGGATAAGCGCCGCTAAAGG-CCTTGA
          1 TCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTTC-TGA

            *                                           
        444 GCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGG-TCATGA
          1 TCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTTC-TGA

                  *   *                                 
        487 TCTATATCGGTGTTTGTGGGAAAAGCGCCGCTAAAGG-TCTTGA
          1 TCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTTC-TGA

                *   *      *   *     *                 
        530 TCTACAGCAGCGTTTAT-GTAAAAGTGCCGCTAAAGG-TCTGA
          1 TCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTTCTGA

                                          *        *  * 
        571 TCTATAGCGGCGTTTGT-GGAAAATGCGCCACTAAAGGTCCTTA
          1 TCTATAGCGGCGTTTGTGGGAAAA-GCGCCGCTAAAGGTTCTGA

                       *   *           *           *   
        614 TCTATAGCGGCATTTTTGGGAAAAGCGTCGCTAAAGGTTATGA
          1 TCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTTCTGA

                          
        657 TCTATAGCGGCGTT
          1 TCTATAGCGGCGTT

        671 GACAACAGCG


Statistics
Matches: 228,  Mismatches: 38, Indels: 8
        0.83            0.14        0.03

Matches are distributed among these distances:
  41   22  0.10
  42   32  0.14
  43  168  0.74
  44    6  0.03

ACGTcount: A:0.25, C:0.19, G:0.30, T:0.27


Consensus pattern (43 bp):   
TCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTTCTGA

Found at i:759 original size:22 final size:22

Alignment explanation


    Indices: 731--773  Score: 77
    Period size: 22  Copynumber: 2.0  Consensus size: 22

        721 TAGTGGCGCT

                            *     
        731 AAAAAGCGCCGCTAAAGGCCTA
          1 AAAAAGCGCCGCTAAAAGCCTA

                                 
        753 AAAAAGCGCCGCTAAAAGCCT
          1 AAAAAGCGCCGCTAAAAGCCT

        774 GTTTTGGTGT


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  22   20  1.00

ACGTcount: A:0.42, C:0.28, G:0.21, T:0.09


Consensus pattern (22 bp):   
AAAAAGCGCCGCTAAAAGCCTA
Done.