Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold955

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: 3897
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34


Found at i:3091 original size:72 final size:72

Alignment explanation


    Indices: 2953--3143  Score: 221
    Period size: 72  Copynumber: 2.6  Consensus size: 72

       2943 ATTACCGGTG

                 *                                                     *     
       2953 TTTTAGGTACAGCGCCGCAAAAAACCT-AGCGCAACGACGCCGTTTCAAGAGCATTTGGTGATTT
          1 TTTTAAGTA-AGCGCCGCAAAAAACCTAAGCGCAACGACGCCGTTTCAAGAGCATTTGGGGATTT

                    
       3017 AGCGGCGT
         65 AGCGGCGT

                               *   *       *       *        *                
       3025 TTTTAAGTAAGCGCCGCTAGAAACCCTAAGCCCAACGACACCGTTTC-TGAG-ATTTTGGGGATT
          1 TTTTAAGTAAGCGCCGC-AAAAAACCTAAGCGCAACGACGCCGTTTCAAGAGCA-TTTGGGGATT

                     
       3088 TAGCGGCGT
         64 TAGCGGCGT

                                      *                      
       3097 TTGTATAA--AAGCGCCGCAAAAAAAACTAAGCGCAACGACGCCGTTTC
          1 TT-T-TAAGTAAGCGCCGC-AAAAAACCTAAGCGCAACGACGCCGTTTC

       3144 CCGAGCTATT


Statistics
Matches: 101,  Mismatches: 13, Indels: 10
        0.81            0.10        0.08

Matches are distributed among these distances:
  71    9  0.09
  72   71  0.70
  73   18  0.18
  74    3  0.03

ACGTcount: A:0.29, C:0.24, G:0.24, T:0.23


Consensus pattern (72 bp):   
TTTTAAGTAAGCGCCGCAAAAAACCTAAGCGCAACGACGCCGTTTCAAGAGCATTTGGGGATTTA
GCGGCGT

Found at i:3348 original size:113 final size:114

Alignment explanation


    Indices: 3086--3372  Score: 309
    Period size: 113  Copynumber: 2.5  Consensus size: 114

       3076 ATTTTGGGGA

                           *                                   *   *         
       3086 TTTAGCGGCGTTTGTATAAAAGCGCCGCAAAAAAAACTAAGCGCAACGACGCCGTTTCCCGAGCT
          1 TTTAGCGGCGTTTGTGTAAAAGCGCCGCAAAAAAAACTAAGCGCAACGACGTCGTCTCCCGAGCT

                                                      *       
       3151 ATTCACGGAATTAGCGGCGCTTCCTATAAAGCGCCGCTAATGCTCAGGTC
         66 ATTCACGGAATTAGCGGCGCTT-CTATAAAGCGCCGCTAATGATCAGGTC

                             **      *          *              *             
       3201 TTTAGCGGCGTTTCG-GGGAAAGCGTCGCAAAAAAATCT-AGCGCAACGACATCGTCTCGCC-AG
          1 TTTAGCGGCGTTT-GTGTAAAAGCGCCGCAAAAAAAACTAAGCGCAACGACGTCGTCTC-CCGAG

                 * *   *    *                           *        
       3263 CT-TTTAGGGATTTAGTGGCGCTT-TATAGGAAGCGCCGCTAATTATCAGG-C
         64 CTATTCACGGAATTAGCGGCGCTTCTATA--AAGCGCCGCTAATGATCAGGTC

                                           *     *      *                
       3313 TTTTAGCGGCGTTTGTTGTAAAAGCGCCGC-TAAAAACCTAAGCCCAACGACGTCGTCTCC
          1 -TTTAGCGGCGTTTG-TGTAAAAGCGCCGCAAAAAAAACTAAGCGCAACGACGTCGTCTCC

       3373 TTATCTTTTG


Statistics
Matches: 143,  Mismatches: 21, Indels: 18
        0.79            0.12        0.10

Matches are distributed among these distances:
 111    4  0.03
 112    2  0.01
 113   56  0.39
 114   47  0.33
 115   33  0.23
 116    1  0.01

ACGTcount: A:0.26, C:0.25, G:0.25, T:0.24


Consensus pattern (114 bp):   
TTTAGCGGCGTTTGTGTAAAAGCGCCGCAAAAAAAACTAAGCGCAACGACGTCGTCTCCCGAGCT
ATTCACGGAATTAGCGGCGCTTCTATAAAGCGCCGCTAATGATCAGGTC

Found at i:3424 original size:113 final size:113

Alignment explanation


    Indices: 3086--3424  Score: 278
    Period size: 113  Copynumber: 3.0  Consensus size: 113

       3076 ATTTTGGGGA

                            **                  *      *       **   *        
       3086 TTTAGCGGCGTTT-GTATAAAAGCGCCGCAAAAAAAACTAAGCGCAACGACGCCGTTTC-CCGAG
          1 TTTAGCGGCGTTTCG-GGAAAAGCGCCGCAAAAAAACCT-AGCCCAACGACATCGTCTCGCC-AG

                 * *   *            **  *                       
       3149 CTATTCACGGAATTAGCGGCGCTTCCTATAAAGCGCCGCTAATGCTCAGGTC
         63 CT-TTTAGGGATTTAGCGGCGCTTTATAAAAAGCGCCGCTAATGCTCAGGTC

                             *      *          *     *                       
       3201 TTTAGCGGCGTTTCGGGGAAAGCGTCGCAAAAAAATCTAGCGCAACGACATCGTCTCGCCAGCTT
          1 TTTAGCGGCGTTTCGGGAAAAGCGCCGCAAAAAAACCTAGCCCAACGACATCGTCTCGCCAGCTT

                        *           **             **       
       3266 TTAGGGATTTAGTGGCGCTTTATAGGAAGCGCCGCTAATTATCAGG-C
         66 TTAGGGATTTAGCGGCGCTTTATAAAAAGCGCCGCTAATGCTCAGGTC

                               *            *                    *          *
       3313 TTTTAGCGGCGTTT-GTTGTAAAAGCGCCGC-TAAAAACCTAAGCCCAACGACGTCGTCTC-CTT
          1 -TTTAGCGGCGTTTCG--GGAAAAGCGCCGCAAAAAAACCT-AGCCCAACGACATCGTCTCGC-C

             *     *   *          *                            
       3375 ATCTTTTGGGGTTTTAGCGGCGTTTTA-AAAAAGCGCCGCTAATGCTCAGG
         61 AGCTTTTAGGGATTTAGCGGCGCTTTATAAAAAGCGCCGCTAATGCTCAGG

       3425 GATTTAAAAT


Statistics
Matches: 182,  Mismatches: 35, Indels: 16
        0.78            0.15        0.07

Matches are distributed among these distances:
 112    2  0.01
 113   77  0.42
 114   69  0.38
 115   33  0.18
 116    1  0.01

ACGTcount: A:0.25, C:0.24, G:0.25, T:0.25


Consensus pattern (113 bp):   
TTTAGCGGCGTTTCGGGAAAAGCGCCGCAAAAAAACCTAGCCCAACGACATCGTCTCGCCAGCTT
TTAGGGATTTAGCGGCGCTTTATAAAAAGCGCCGCTAATGCTCAGGTC

Found at i:3731 original size:8 final size:8

Alignment explanation


    Indices: 3718--3766  Score: 55
    Period size: 8  Copynumber: 6.2  Consensus size: 8

       3708 AGAGCTAGGA

                    
       3718 TTTAGGGG
          1 TTTAGGGG

                  * 
       3726 TTTAGGAG
          1 TTTAGGGG

                *   
       3734 TTTACGGG
          1 TTTAGGGG

                    
       3742 -TTAGGGG
          1 TTTAGGGG

                   *
       3749 TTTAGGGA
          1 TTTAGGGG

               *    
       3757 TTTGGGGG
          1 TTTAGGGG

              
       3765 TT
          1 TT

       3767 AGAGTTTGAA


Statistics
Matches: 33,  Mismatches: 7, Indels: 2
        0.79            0.17        0.05

Matches are distributed among these distances:
   7    6  0.18
   8   27  0.82

ACGTcount: A:0.14, C:0.02, G:0.45, T:0.39


Consensus pattern (8 bp):   
TTTAGGGG
Done.