Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1735

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: 17937
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.30


Found at i:2202 original size:28 final size:27

Alignment explanation


    Indices: 2161--2266  Score: 106
    Period size: 27  Copynumber: 3.9  Consensus size: 27

       2151 TGGATAAGTT

                  *                    
       2161 GTAGAATTACCGAAATACCCCTATCGG
          1 GTAGAAATACCGAAATACCCCTATCGG

                   *               *     
       2188 GTAGAATTTACCGAAATACCCCTGTAC-G
          1 GTAGAA-ATACCGAAATACCCCTAT-CGG

            *         *         * * *  
       2216 ATAGAAATACTGAAATACCCTTGTAGG
          1 GTAGAAATACCGAAATACCCCTATCGG

                       *            
       2243 GTAGAAATACCAAAATACCCCTAT
          1 GTAGAAATACCGAAATACCCCTAT

       2267 AGACATAATT


Statistics
Matches: 65,  Mismatches: 11, Indels: 6
        0.79            0.13        0.07

Matches are distributed among these distances:
  27   41  0.63
  28   23  0.35
  29    1  0.02

ACGTcount: A:0.38, C:0.23, G:0.16, T:0.24


Consensus pattern (27 bp):   
GTAGAAATACCGAAATACCCCTATCGG

Found at i:2290 original size:53 final size:54

Alignment explanation


    Indices: 2163--2307  Score: 141
    Period size: 53  Copynumber: 2.7  Consensus size: 54

       2153 GATAAGTTGT

                *   *         * * *         *    *          *     *
       2163 AGAATTACCGAAATACCCCTATCGGGTAGAATTTACCGAAATACCCCTGTACGAT
          1 AGAAATACTGAAATACCCTTGTAGGGTAGAA-ATACCAAAATACCCCTATACGAC

                                                                  
       2218 AGAAATACTGAAATACCCTTGTAGGGTAGAAATACCAAAATACCCCTATA-GAC
          1 AGAAATACTGAAATACCCTTGTAGGGTAGAAATACCAAAATACCCCTATACGAC

             *  *      *          *               
       2271 ATAATTACTGAGATACCCTTGTGGGGTA-AAATTACCA
          1 AGAAATACTGAAATACCCTTGTAGGGTAGAAA-TACCA

       2308 TTTTGCCTCT


Statistics
Matches: 76,  Mismatches: 13, Indels: 4
        0.82            0.14        0.04

Matches are distributed among these distances:
  52    3  0.04
  53   31  0.41
  54   16  0.21
  55   26  0.34

ACGTcount: A:0.38, C:0.21, G:0.17, T:0.24


Consensus pattern (54 bp):   
AGAAATACTGAAATACCCTTGTAGGGTAGAAATACCAAAATACCCCTATACGAC

Found at i:11310 original size:79 final size:81

Alignment explanation


    Indices: 11174--11356  Score: 232
    Period size: 79  Copynumber: 2.3  Consensus size: 81

      11164 TCGAATGATG

                                    *              *                         
      11174 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
          1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT

                            
      11238 TGTGCGAGTTACTA-A
         66 TGTGCGAGTTACTATA

                                           *   *  *        **                
      11253 TTCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
          1 -TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA

                              
      11315 TTTGTGCGAGTTACTATA
         64 TTTGTGCGAGTTACTATA

            *        *              
      11333 ACCGGGCTATGTCCCGAAGGCATT
          1 TCCGGGCTAAGTCCCGAAGGCATT

      11357 TGAACGAGTA


Statistics
Matches: 90,  Mismatches: 9, Indels: 8
        0.84            0.08        0.07

Matches are distributed among these distances:
  78    1  0.01
  79   59  0.66
  80   30  0.33

ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25


Consensus pattern (81 bp):   
TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGTTACTATA

Found at i:11372 original size:40 final size:40

Alignment explanation


    Indices: 11175--11358  Score: 216
    Period size: 40  Copynumber: 4.6  Consensus size: 40

      11165 CGAATGATGT

                                         *   *  *   *
      11175 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
          1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA

                *                                    *
      11215 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA-ATT
          1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A

                                   *                
      11255 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AA
          1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA

                  *                                  
      11293 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
          1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA

                    *                
      11334 CCGGGCTATGTCCCGAAGGCATTTG
          1 CCGGGCTAAGTCCCGAAGGCATTTG

      11359 AACGAGTAGC


Statistics
Matches: 126,  Mismatches: 11, Indels: 14
        0.83            0.07        0.09

Matches are distributed among these distances:
  39   35  0.28
  40   81  0.64
  41   10  0.08

ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25


Consensus pattern (40 bp):   
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA

Found at i:11380 original size:79 final size:79

Alignment explanation


    Indices: 11227--11381  Score: 208
    Period size: 79  Copynumber: 2.0  Consensus size: 79

      11217 GGACTAAGAT

                                       *                        **           
      11227 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
          1 CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA

                          
      11292 ATCCGGGTTAAGTC
         66 ATCCGGGTTAAGTC

                                                 *              *            
      11306 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
          1 CCGAAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-C

              *           
      11369 TATATCC-GGTTAA
         63 TAAATCCGGGTTAA

      11382 ATTCGAAGGT


Statistics
Matches: 67,  Mismatches: 6, Indels: 6
        0.85            0.08        0.08

Matches are distributed among these distances:
  78    2  0.03
  79   41  0.61
  80   24  0.36

ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26


Consensus pattern (79 bp):   
CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
ATCCGGGTTAAGTC
Done.