Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_2827

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: 21541
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30


Found at i:3761 original size:11 final size:10

Alignment explanation


    Indices: 3734--3760  Score: 54
    Period size: 10  Copynumber: 2.7  Consensus size: 10

       3724 CTTTGATTTC

                      
       3734 TTTTTTTCTT
          1 TTTTTTTCTT

                      
       3744 TTTTTTTCTT
          1 TTTTTTTCTT

                   
       3754 TTTTTTT
          1 TTTTTTT

       3761 TTGACATGGC


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   17  1.00

ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93


Consensus pattern (10 bp):   
TTTTTTTCTT

Found at i:6274 original size:79 final size:81

Alignment explanation


    Indices: 6138--6320  Score: 205
    Period size: 79  Copynumber: 2.3  Consensus size: 81

       6128 TCGAATGATG

                                    *    *         *                         
       6138 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAGGTGACCATATCCGGACTAAGATCCGAAGGCATT
          1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCGAGGTGACCAAATCCGGACTAAGATCCGAAGGCATT

                            
       6202 TGTGAGAGATACTA-A
         66 TGTGAGAGATACTATA

                                               *  *        **                
       6217 TTCCGGGCTAAG-CCCGAAGGCATTGGTGCGA-GTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
          1 -TCCGGGCTAAGTCCCGAAGGCATTGGTGCGAGGTGACCAAATCCGGACTAAGAT-CCGAAGGCA

                  *   *       
       6279 TTTGTGCGAGTTACTATA
         64 TTTGTGAGAGATACTATA

            *        *  *           
       6297 ACCGGGCTATGTTCCGAAGGCATT
          1 TCCGGGCTAAGTCCCGAAGGCATT

       6321 TGAACGAGTA


Statistics
Matches: 87,  Mismatches: 12, Indels: 8
        0.81            0.11        0.07

Matches are distributed among these distances:
  78    1  0.01
  79   56  0.64
  80   30  0.34

ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25


Consensus pattern (81 bp):   
TCCGGGCTAAGTCCCGAAGGCATTGGTGCGAGGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGAGAGATACTATA

Found at i:6329 original size:40 final size:40

Alignment explanation


    Indices: 6139--6341  Score: 193
    Period size: 40  Copynumber: 5.1  Consensus size: 40

       6129 CGAATGATGT

                                        *    *  *   *
       6139 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAGGTGACCATAT
          1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGA-GTTACTATAA

                *                       *   *        *
       6179 CCGGACTAAGAT-CCGAAGGCATTTGTGAGAGATACTA-ATT
          1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A

                                   *                
       6219 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AA
          1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA

                  *                                  
       6257 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
          1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA

                    *  *             **              
       6298 CCGGGCTATGTTCCGAAGGCATTTGAACGAG-TAGCTATAA
          1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAA

                
       6338 CCGG
          1 CCGG

       6342 TTAAATTCTG


Statistics
Matches: 137,  Mismatches: 18, Indels: 16
        0.80            0.11        0.09

Matches are distributed among these distances:
  39   35  0.26
  40   92  0.67
  41   10  0.07

ACGTcount: A:0.26, C:0.22, G:0.29, T:0.24


Consensus pattern (40 bp):   
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA

Found at i:14447 original size:40 final size:40

Alignment explanation


    Indices: 14312--14490  Score: 190
    Period size: 40  Copynumber: 4.5  Consensus size: 40

      14302 AATGATGTCC

                                      *   *  * *     
      14312 GGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCG
          1 GGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCG

             *                           *      * *  
      14352 GACTAAGAT-CCGAAGGCATTTGTG-GAGATACTAATTTCG
          1 GGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAATCCG

                                *                   
      14391 GGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAATCCG
          1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCG

              *                                      
      14430 GGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCG
          1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AATCCG

                 *                
      14470 GGCTATGT-CCGAAGGCATTTG
          1 GGCTAAGTCCCGAAGGCATTTG

      14491 AACGAGTAGC


Statistics
Matches: 116,  Mismatches: 17, Indels: 13
        0.79            0.12        0.09

Matches are distributed among these distances:
  38   14  0.12
  39   45  0.39
  40   48  0.41
  41    9  0.08

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


Consensus pattern (40 bp):   
GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCG

Found at i:14497 original size:79 final size:77

Alignment explanation


    Indices: 14361--14513  Score: 175
    Period size: 79  Copynumber: 2.0  Consensus size: 77

      14351 GGACTAAGAT

                                      **                       **            
      14361 CCGAAGGCATTTGTGGAGATACTAATTTCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTA-CTAA
          1 CCGAAGGCATTTGTGGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAG-TAGCTAA

                          
      14425 ATCCGGGTTAAGTC
         65 ATCC-GGTTAAGTC

                               *                 * *           *             
      14439 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCGAAGGCATTTGAACGAGTAGCTA
          1 CCGAAGGCATTTGTG-GAGATACTAAT-ACCGGGCTAAGCCCGAAGGCATTGGAACGAGTAGCTA

            *          
      14503 TATCCGGTTAA
         64 AATCCGGTTAA

      14514 ATTCTGAAGG


Statistics
Matches: 63,  Mismatches: 9, Indels: 6
        0.81            0.12        0.08

Matches are distributed among these distances:
  78   25  0.40
  79   38  0.60

ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26


Consensus pattern (77 bp):   
CCGAAGGCATTTGTGGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTAGCTAAA
TCCGGTTAAGTC
Done.