Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_4701

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: 13805
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33


Found at i:4567 original size:27 final size:28

Alignment explanation


    Indices: 4537--4598  Score: 67
    Period size: 27  Copynumber: 2.3  Consensus size: 28

       4527 ATATTTGGTA

                                      *  
       4537 ATAATAATATA-AAATA-ATAATATGTAC
          1 ATAATAA-ATACAAATATATAATATGCAC

                        *              *
       4564 ATAA-AAATACATATATATAATATGCAT
          1 ATAATAAATACAAATATATAATATGCAC

                    
       4591 ATAATAAA
          1 ATAATAAA

       4599 AGTATGTAAT


Statistics
Matches: 29,  Mismatches: 3, Indels: 5
        0.78            0.08        0.14

Matches are distributed among these distances:
  25    3  0.10
  26    6  0.21
  27   17  0.59
  28    3  0.10

ACGTcount: A:0.60, C:0.05, G:0.03, T:0.32


Consensus pattern (28 bp):   
ATAATAAATACAAATATATAATATGCAC

Found at i:10093 original size:22 final size:22

Alignment explanation


    Indices: 10068--10110  Score: 59
    Period size: 22  Copynumber: 2.0  Consensus size: 22

      10058 TATCTAAACA

                                  
      10068 ATAATAACAAAATAGTAGCAAC
          1 ATAATAACAAAATAGTAGCAAC

                   **    *       
      10090 ATAATAATTAAATGGTAGCAA
          1 ATAATAACAAAATAGTAGCAA

      10111 AATAGTGAGA


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  22   18  1.00

ACGTcount: A:0.56, C:0.09, G:0.12, T:0.23


Consensus pattern (22 bp):   
ATAATAACAAAATAGTAGCAAC

Found at i:11554 original size:26 final size:26

Alignment explanation


    Indices: 11525--11580  Score: 112
    Period size: 26  Copynumber: 2.2  Consensus size: 26

      11515 TGATACAAAT

                                      
      11525 TGATAATGGGTTAGGTAAATGTTCCA
          1 TGATAATGGGTTAGGTAAATGTTCCA

                                      
      11551 TGATAATGGGTTAGGTAAATGTTCCA
          1 TGATAATGGGTTAGGTAAATGTTCCA

                
      11577 TGAT
          1 TGAT

      11581 GGGAATTCAT


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  26   30  1.00

ACGTcount: A:0.30, C:0.07, G:0.27, T:0.36


Consensus pattern (26 bp):   
TGATAATGGGTTAGGTAAATGTTCCA

Found at i:13195 original size:26 final size:28

Alignment explanation


    Indices: 13149--13208  Score: 88
    Period size: 27  Copynumber: 2.2  Consensus size: 28

      13139 AGGAAGCGTC

                      *                 
      13149 CTGGTGGCTATGCCACAATTATCTG-AT
          1 CTGGTGGCTACGCCACAATTATCTGTAT

                           *            
      13176 CTGGTGGCT-CGCCATAATTATCTGTAT
          1 CTGGTGGCTACGCCACAATTATCTGTAT

                  
      13203 CTGGTG
          1 CTGGTG

      13209 ACTCTGTCAC


Statistics
Matches: 30,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  26   13  0.43
  27   17  0.57

ACGTcount: A:0.18, C:0.22, G:0.25, T:0.35


Consensus pattern (28 bp):   
CTGGTGGCTACGCCACAATTATCTGTAT

Done.