Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2098

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: 16426
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.32


Found at i:152 original size:60 final size:59

Alignment explanation


    Indices: 49--181  Score: 148
    Period size: 60  Copynumber: 2.2  Consensus size: 59

         39 GTGTTAACTT

                                *                                         
         49 GGCCTAGCCCATATCAATATTAATCTAGGCCATAGCCATTTAC-AGTATC-AGAGTATATTG
          1 GGCCTAGCCCATATCAATATCAATCTAGGCCATAGCCATTTACAAG--TCGAGA-TATATTG

                            *             *       *                      
        109 GGCCTAGCCCATATCAGTATCAATCTA-G-TAGTAGCCCTATTACAAGTCGAGATATATTG
          1 GGCCTAGCCCATATCAATATCAATCTAGGCCA-TAGCCAT-TTACAAGTCGAGATATATTG

                 *        
        168 GGCCTTGCCCATAT
          1 GGCCTAGCCCATAT

        182 TAACATAGTT


Statistics
Matches: 64,  Mismatches: 5, Indels: 9
        0.82            0.06        0.12

Matches are distributed among these distances:
  58    1  0.02
  59   29  0.45
  60   32  0.50
  61    2  0.03

ACGTcount: A:0.29, C:0.23, G:0.18, T:0.29


Consensus pattern (59 bp):   
GGCCTAGCCCATATCAATATCAATCTAGGCCATAGCCATTTACAAGTCGAGATATATTG

Found at i:6703 original size:102 final size:102

Alignment explanation


    Indices: 6497--6720  Score: 341
    Period size: 104  Copynumber: 2.2  Consensus size: 102

       6487 TTGTATATAA

                      **                             *                       
       6497 AGGGGTTGCTGTGTGCTGATTCCCCGATTATGGTGGTGCTATGTGCGTGATCCACCATATCTTTG
          1 AGGGGTTGCTAAGTGCTGATTCCCCGATTATGGTGGTGCTAAGTGCGTGATCCACCATATCTTTG

                  *                              
       6562 AAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
         66 AAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCCG

                                      *                                      
       6599 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
          1 AGGGGTTGCTAAGTGCTGATTCCCCGATT-A-TGGTGGTGCTAAGTGCG-TGATCCACCATATCT

                                                    
       6663 TTGAAATG-AAAAGGGGGTTGCTATGTGCTGATT-CCCCG
         63 TTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCCG

                                  
       6701 A--GGTTGCTAAGTGCTGATTC
          1 AGGGGTTGCTAAGTGCTGATTC

       6721 AGTGGTGGTG


Statistics
Matches: 114,  Mismatches: 5, Indels: 8
        0.90            0.04        0.06

Matches are distributed among these distances:
 100   19  0.17
 102   32  0.28
 103   25  0.22
 104   37  0.32
 105    1  0.01

ACGTcount: A:0.19, C:0.19, G:0.30, T:0.32


Consensus pattern (102 bp):   
AGGGGTTGCTAAGTGCTGATTCCCCGATTATGGTGGTGCTAAGTGCGTGATCCACCATATCTTTG
AAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCCG

Found at i:12778 original size:32 final size:33

Alignment explanation


    Indices: 12722--12786  Score: 123
    Period size: 32  Copynumber: 2.0  Consensus size: 33

      12712 GGTAAGATTT

                                             
      12722 TCGGGGACGAAAATCCCTAAGGGGGGAGAGTTG
          1 TCGGGGACGAAAATCCCTAAGGGGGGAGAGTTG

                                             
      12755 TCGGGGACGAAAAT-CCTAAGGGGGGAGAGTTG
          1 TCGGGGACGAAAATCCCTAAGGGGGGAGAGTTG

      12787 AAGTTCTGGG


Statistics
Matches: 32,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
  32   18  0.56
  33   14  0.44

ACGTcount: A:0.28, C:0.14, G:0.43, T:0.15


Consensus pattern (33 bp):   
TCGGGGACGAAAATCCCTAAGGGGGGAGAGTTG

Found at i:14159 original size:102 final size:100

Alignment explanation


    Indices: 13959--14216  Score: 323
    Period size: 102  Copynumber: 2.6  Consensus size: 100

      13949 TGTATATAAA

                      **                    *          *                     
      13959 AGGGGTTGCTGTGTGCTGATTCCCGATTT--TGGGTGGTGCTATGTG-GTGAT-CA-CATATCTT
          1 AGGGGTTGCTAAGTGCTGATTCCCGATTTCATTGGTGGTGCTAAGTGCGT-ATCCACCATATCTT

                        *                    *   
      14019 GAAATGTGAAAGTGGGTTGCTATGTGCTGATTCCCCG
         65 GAAA-GTGAAAGGGGGTTGCTATGTGCTGATTCACCG

                                                                           * 
      14056 AGGGGTTGCTAAGTGCTGATTCCCGATTTCATTGGTGGTGCTAAGTGCGATATCCACCATATATT
          1 AGGGGTTGCTAAGTGCTGATTCCCGATTTCATTGGTGGTGCTAAGTGCG-TATCCACCATAT-CT

                                                  
      14121 TGAAA-TGAAAGGGGGGTTGCTATGTGCTGATTCACCG
         64 TGAAAGTGAAA-GGGGGTTGCTATGTGCTGATTCACCG

                                            *                  *        
      14158 AGGGGTTGCTAAGTGCTGATTCCCCGA-TTCAGTGGTGGTGCTAAGTGCGGGATCCACCA
          1 AGGGGTTGCTAAGTGCTGATT-CCCGATTTCATTGGTGGTGCTAAGTGC-GTATCCACCA

      14217 ATAACGGCTA


Statistics
Matches: 142,  Mismatches: 9, Indels: 15
        0.86            0.05        0.09

Matches are distributed among these distances:
  97   27  0.19
  99   14  0.10
 100    3  0.02
 101    8  0.06
 102   78  0.55
 103   12  0.08

ACGTcount: A:0.19, C:0.17, G:0.32, T:0.31


Consensus pattern (100 bp):   
AGGGGTTGCTAAGTGCTGATTCCCGATTTCATTGGTGGTGCTAAGTGCGTATCCACCATATCTTG
AAAGTGAAAGGGGGTTGCTATGTGCTGATTCACCG

Found at i:14168 original size:26 final size:26

Alignment explanation


    Indices: 14133--14184  Score: 86
    Period size: 26  Copynumber: 2.0  Consensus size: 26

      14123 AAATGAAAGG

                      *               
      14133 GGGGTTGCTATGTGCTGATTCACCGA
          1 GGGGTTGCTAAGTGCTGATTCACCGA

                                 *    
      14159 GGGGTTGCTAAGTGCTGATTCCCCGA
          1 GGGGTTGCTAAGTGCTGATTCACCGA

      14185 TTCAGTGGTG


Statistics
Matches: 24,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  26   24  1.00

ACGTcount: A:0.15, C:0.21, G:0.35, T:0.29


Consensus pattern (26 bp):   
GGGGTTGCTAAGTGCTGATTCACCGA
Done.