Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_3270

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: 19434
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34


Found at i:6153 original size:40 final size:40

Alignment explanation


    Indices: 5924--6146  Score: 258
    Period size: 40  Copynumber: 5.6  Consensus size: 40

       5914 GAATGATGTT

                                        *   *  * *   
       5924 CGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATC
          1 CGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATC

               *        *                         *  
       5964 CGGACTAAGAT-TCGAAGGCATTTGTGCGAGTTACTAATTC
          1 CGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAATC

                                  *                 
       6004 CGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAATC
          1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATC

                *                                    
       6043 CGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-C
          1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AATC

                *             *            *         
       6083 CGGGTTAAGTCCCGAAGGTATTTGTGCGAGTCACTATAAT-
          1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AATC

                   *                
       6123 CGGGCTATGTCCCGAAGGCATTTG
          1 CGGGCTAAGTCCCGAAGGCATTTG

       6147 AACGAGTAGC


Statistics
Matches: 159,  Mismatches: 18, Indels: 12
        0.84            0.10        0.06

Matches are distributed among these distances:
  39   34  0.21
  40  115  0.72
  41   10  0.06

ACGTcount: A:0.24, C:0.21, G:0.28, T:0.26


Consensus pattern (40 bp):   
CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATC

Found at i:10546 original size:45 final size:45

Alignment explanation


    Indices: 10477--10613  Score: 179
    Period size: 45  Copynumber: 3.0  Consensus size: 45

      10467 AGTCTTACTC

                              *                            
      10477 ATTCATTTTC-TGTCATGTTGCCATGATATCTTTCAACCATGGTCTT
          1 ATTC-TTTTCATGTCA-GGTGCCATGATATCTTTCAACCATGGTCTT

                                                         
      10523 ATTCTTTTCATGTCAGGTGCCATGATATCTTTCAA-CATGGTCTT
          1 ATTCTTTTCATGTCAGGTGCCATGATATCTTTCAACCATGGTCTT

             ** *      *             *                    
      10567 ACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTT
          1 ATTCTTTTCATGTCAGG-TGCCATGATATCTTTCAACCATGGTCTT

             
      10613 A
          1 A

      10614 CACATTTCAT


Statistics
Matches: 82,  Mismatches: 6, Indels: 6
        0.87            0.06        0.06

Matches are distributed among these distances:
  44   22  0.27
  45   41  0.50
  46   19  0.23

ACGTcount: A:0.22, C:0.22, G:0.15, T:0.42


Consensus pattern (45 bp):   
ATTCTTTTCATGTCAGGTGCCATGATATCTTTCAACCATGGTCTT

Found at i:10621 original size:46 final size:46

Alignment explanation


    Indices: 10493--10628  Score: 213
    Period size: 45  Copynumber: 3.0  Consensus size: 46

      10483 TTTCTGTCAT

                                           ** *      *    
      10493 GTTGCCATGATATCTTTCAACCATGGTCTTATTCTTTTCATGTCAG
          1 GTTGCCATGATATCTTTCAACCATGGTCTTACACATTTCATATCAG

                                                          
      10539 G-TGCCATGATATCTTTCAA-CATGGTCTTACACATTTCATATCAG
          1 GTTGCCATGATATCTTTCAACCATGGTCTTACACATTTCATATCAG

                     *                                    
      10583 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
          1 GTTGCCATGATATCTTTCAACCATGGTCTTACACATTTCATATCAG

      10629 AAAGTACACT


Statistics
Matches: 83,  Mismatches: 5, Indels: 4
        0.90            0.05        0.04

Matches are distributed among these distances:
  44   22  0.27
  45   35  0.42
  46   26  0.31

ACGTcount: A:0.24, C:0.23, G:0.15, T:0.39


Consensus pattern (46 bp):   
GTTGCCATGATATCTTTCAACCATGGTCTTACACATTTCATATCAG

Found at i:14026 original size:14 final size:13

Alignment explanation


    Indices: 13999--14034  Score: 56
    Period size: 14  Copynumber: 2.8  Consensus size: 13

      13989 AGGGTTTTAT

                         
      13999 AAGAAA-AAATAA
          1 AAGAAATAAATAA

                          
      14011 AAGAAATAACATAA
          1 AAGAAATAA-ATAA

                      
      14025 AAGAAATAAA
          1 AAGAAATAAA

      14035 AGTTCAAGAG


Statistics
Matches: 22,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  12    6  0.27
  13    3  0.14
  14   13  0.59

ACGTcount: A:0.78, C:0.03, G:0.08, T:0.11


Consensus pattern (13 bp):   
AAGAAATAAATAA
Done.