Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold740

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: 26482
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30


Found at i:10295 original size:26 final size:26

Alignment explanation


    Indices: 10263--10366  Score: 156
    Period size: 26  Copynumber: 4.0  Consensus size: 26

      10253 ATTCCCATCG

                                      
      10263 TGGAACATTTACCTAAACCATTATCA
          1 TGGAACATTTACCTAAACCATTATCA

              *                        
      10289 TGAAACATTTACCT-AACGCATTATCA
          1 TGGAACATTTACCTAAAC-CATTATCA

                 *          *         
      10315 TGGAATATTTACCTAATCCATTATCA
          1 TGGAACATTTACCTAAACCATTATCA

                            *         
      10341 TGGAACATTTACCTAACCCATTATCA
          1 TGGAACATTTACCTAAACCATTATCA

      10367 ATTTGTATCA


Statistics
Matches: 70,  Mismatches: 6, Indels: 4
        0.88            0.08        0.05

Matches are distributed among these distances:
  25    3  0.04
  26   65  0.93
  27    2  0.03

ACGTcount: A:0.37, C:0.23, G:0.08, T:0.33


Consensus pattern (26 bp):   
TGGAACATTTACCTAAACCATTATCA

Found at i:10341 original size:52 final size:52

Alignment explanation


    Indices: 10263--10366  Score: 172
    Period size: 52  Copynumber: 2.0  Consensus size: 52

      10253 ATTCCCATCG

                                                       *        
      10263 TGGAACATTTACCTAAACCATTATCATGAAACATTTACCTAACGCATTATCA
          1 TGGAACATTTACCTAAACCATTATCATGAAACATTTACCTAACCCATTATCA

                 *          *           *                       
      10315 TGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATTATCA
          1 TGGAACATTTACCTAAACCATTATCATGAAACATTTACCTAACCCATTATCA

      10367 ATTTGTATCA


Statistics
Matches: 48,  Mismatches: 4, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  52   48  1.00

ACGTcount: A:0.37, C:0.23, G:0.08, T:0.33


Consensus pattern (52 bp):   
TGGAACATTTACCTAAACCATTATCATGAAACATTTACCTAACCCATTATCA

Found at i:16399 original size:26 final size:25

Alignment explanation


    Indices: 16344--16422  Score: 142
    Period size: 26  Copynumber: 3.2  Consensus size: 25

      16334 CATGAAATTC

                                     
      16344 ATCAT-GAACATTTACCTAACCATT
          1 ATCATGGAACATTTACCTAACCATT

                                      
      16368 ATCATGGAACATTTACCTAACCCATT
          1 ATCATGGAACATTTACCTAA-CCATT

                                     
      16394 ATCATGGAACATTTACCTAACCATT
          1 ATCATGGAACATTTACCTAACCATT

                
      16419 ATCA
          1 ATCA

      16423 ATTTGTATCA


Statistics
Matches: 53,  Mismatches: 0, Indels: 3
        0.95            0.00        0.05

Matches are distributed among these distances:
  24    5  0.09
  25   23  0.43
  26   25  0.47

ACGTcount: A:0.37, C:0.25, G:0.06, T:0.32


Consensus pattern (25 bp):   
ATCATGGAACATTTACCTAACCATT

Found at i:23311 original size:26 final size:26

Alignment explanation


    Indices: 23273--23330  Score: 98
    Period size: 26  Copynumber: 2.2  Consensus size: 26

      23263 CATGAAATTC

                                      
      23273 TTATCATGAAACATTTACCTAACCCA
          1 TTATCATGAAACATTTACCTAACCCA

                    *               * 
      23299 TTATCATGGAACATTTACCTAACCTA
          1 TTATCATGAAACATTTACCTAACCCA

                  
      23325 TTATCA
          1 TTATCA

      23331 ATTTGTATCA


Statistics
Matches: 30,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  26   30  1.00

ACGTcount: A:0.36, C:0.24, G:0.05, T:0.34


Consensus pattern (26 bp):   
TTATCATGAAACATTTACCTAACCCA

Found at i:25059 original size:31 final size:31

Alignment explanation


    Indices: 25012--25077  Score: 96
    Period size: 31  Copynumber: 2.1  Consensus size: 31

      25002 TGGTATTTTT

                                 *        *
      25012 ATGCTACATTTGCTGTTTTTGGTTGGATTTC
          1 ATGCTACATTTGCTGTTTTTGCTTGGATTTA

                  *    *                   
      25043 ATGCTATATTTTCTGTTTTTGCTTGGATTTA
          1 ATGCTACATTTGCTGTTTTTGCTTGGATTTA

                
      25074 ATGC
          1 ATGC

      25078 AGGAAGGTTA


Statistics
Matches: 31,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  31   31  1.00

ACGTcount: A:0.15, C:0.12, G:0.20, T:0.53


Consensus pattern (31 bp):   
ATGCTACATTTGCTGTTTTTGCTTGGATTTA
Done.