Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_5764

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: 9868
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.32


Found at i:2944 original size:35 final size:33

Alignment explanation


    Indices: 2827--2956  Score: 106
    Period size: 33  Copynumber: 3.9  Consensus size: 33

       2817 GGCTTAAGAC

                           *                 
       2827 CCGCAGGCTATGCTGAATTATATCCGGTTAAAT
          1 CCGCAGGCTATGCTGGATTATATCCGGTTAAAT

              *        * * *   *               
       2860 CCCCAGGGCT-CGGTTGA-AATATCCGGGTTAAAT
          1 CCGCA-GGCTATGCTGGATTATATCC-GGTTAAAT

                       *                        
       2893 CCCGCAGGCTCGTGCTGGTATTATATCCGGTTAAAT
          1 -CCGCAGGCT-ATGCTGG-ATTATATCCGGTTAAAT

                                     *    
       2929 CCGCAGGCCTATGCT-G-TTATATCTGGTT
          1 CCGCAGG-CTATGCTGGATTATATCCGGTT

       2957 TAAAATCCCG


Statistics
Matches: 76,  Mismatches: 13, Indels: 17
        0.72            0.12        0.16

Matches are distributed among these distances:
  32   17  0.22
  33   19  0.25
  34    9  0.12
  35   14  0.18
  36   11  0.14
  37    6  0.08

ACGTcount: A:0.22, C:0.24, G:0.25, T:0.30


Consensus pattern (33 bp):   
CCGCAGGCTATGCTGGATTATATCCGGTTAAAT

Found at i:2951 original size:69 final size:69

Alignment explanation


    Indices: 2811--2980  Score: 175
    Period size: 69  Copynumber: 2.4  Consensus size: 69

       2801 ATTTGATGTG

                                       *                               *  *  
       2811 TATCCGGGCTTAAGA-CCCGCAGGCT-ATGCT-GAATTATATCCGGTTAAATCCCCAGGGCTCGG
          1 TATCCGGG-TTAA-ATCCCGCAGGCTCGTGCTGGAATTATATCCGGTTAAATCCCCAGGCCTAGG

            *     
       2873 TTGAAA
         64 CTGAAA

                                            *                   *        *   
       2879 TATCCGGGTTAAATCCCGCAGGCTCGTGCTGGTATTATATCCGGTTAAATCCGCAGGCCTATGCT
          1 TATCCGGGTTAAATCCCGCAGGCTCGTGCTGGAATTATATCCGGTTAAATCCCCAGGCCTAGGCT

             ** 
       2944 GTTA
         66 GAAA

                *  *           *             
       2948 TATCTGGTTTAAAATCCCGTAGGCTTCGTGCTG
          1 TATCCGGGTT-AAATCCCGCAGGC-TCGTGCTG

       2981 TGTTATGTTG


Statistics
Matches: 85,  Mismatches: 12, Indels: 7
        0.82            0.12        0.07

Matches are distributed among these distances:
  66    1  0.01
  67   14  0.16
  68   12  0.14
  69   38  0.45
  70   12  0.14
  71    8  0.09

ACGTcount: A:0.22, C:0.24, G:0.25, T:0.29


Consensus pattern (69 bp):   
TATCCGGGTTAAATCCCGCAGGCTCGTGCTGGAATTATATCCGGTTAAATCCCCAGGCCTAGGCT
GAAA

Found at i:4456 original size:87 final size:85

Alignment explanation


    Indices: 4284--4448  Score: 208
    Period size: 87  Copynumber: 1.9  Consensus size: 85

       4274 AAATTTAAGT

                                 *                      **                 * 
       4284 TCGATGAATTCATCAAGTTGTTTCAATAGGACCACCAAACTCTGGGATATGAACTCATTAAGAGT
          1 TCGATGAATTCATCAAGTTGTATCAATAGGACCACCAAACTCTGCAATATGAACTCATTAAGAAT

                       *        
       4349 AATAAACTCAATCTCACATG
         66 AATAAACTCAACCTCACATG

                      *                                             *        
       4369 TCGATGAATTTATCAAGTTCGTATCAATAGGACCACCCAAA-TCCTGCAATATGAATTCATTAAG
          1 TCGATGAATTCATCAAGTT-GTATCAATAGGACCA-CCAAACT-CTGCAATATGAACTCATTAAG

               *  *          
       4433 AATGA-CAACTCAACCT
         63 AATAATAAACTCAACCT

       4449 TAGCATGTAC


Statistics
Matches: 68,  Mismatches: 9, Indels: 5
        0.83            0.11        0.06

Matches are distributed among these distances:
  85   18  0.26
  86   24  0.35
  87   26  0.38

ACGTcount: A:0.37, C:0.21, G:0.14, T:0.28


Consensus pattern (85 bp):   
TCGATGAATTCATCAAGTTGTATCAATAGGACCACCAAACTCTGCAATATGAACTCATTAAGAAT
AATAAACTCAACCTCACATG

Found at i:7530 original size:28 final size:28

Alignment explanation


    Indices: 7488--7545  Score: 82
    Period size: 28  Copynumber: 2.0  Consensus size: 28

       7478 CACACAGGCT

                                         
       7488 AGGACACGGGCGTGT-CATGGCCGTGTGA
          1 AGGACACGGGCGTGTCCA-GGCCGTGTGA

                      *                  
       7516 AGGACACGGGTGTGTGCCAGGCCGTGTGA
          1 AGGACACGGGCGTGT-CCAGGCCGTGTGA

             
       7545 A
          1 A

       7546 AACCCTTGTA


Statistics
Matches: 27,  Mismatches: 1, Indels: 3
        0.87            0.03        0.10

Matches are distributed among these distances:
  28   14  0.52
  29   11  0.41
  30    2  0.07

ACGTcount: A:0.19, C:0.21, G:0.43, T:0.17


Consensus pattern (28 bp):   
AGGACACGGGCGTGTCCAGGCCGTGTGA
Done.