Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1628

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: 9869
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33


Found at i:635 original size:31 final size:31

Alignment explanation


    Indices: 600--658  Score: 75
    Period size: 31  Copynumber: 1.9  Consensus size: 31

        590 AAGCCACCCA

                                            
        600 TTTGT-ATTGGTCAAAAAATGGTGTTTTTATT
          1 TTTGTGATTGGTC-AAAAATGGTGTTTTTATT

                  *  *   *              
        631 TTTGTGTTTTGTCCAAAATGGTGTTTTT
          1 TTTGTGATTGGTCAAAAATGGTGTTTTT

        659 CTTATATTTT


Statistics
Matches: 24,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  31   19  0.79
  32    5  0.21

ACGTcount: A:0.20, C:0.05, G:0.20, T:0.54


Consensus pattern (31 bp):   
TTTGTGATTGGTCAAAAATGGTGTTTTTATT

Found at i:5942 original size:28 final size:29

Alignment explanation


    Indices: 5883--5941  Score: 86
    Period size: 27  Copynumber: 2.1  Consensus size: 29

       5873 AAAGCACCCA

                       *                 
       5883 TTTGTTTTTGTTTCAAAAATGGTGGTTAT
          1 TTTGTTTTTGTGTCAAAAATGGTGGTTAT

                                       * 
       5912 TTTG-TTTTGTGTC-AAAATGGTGGTTTT
          1 TTTGTTTTTGTGTCAAAAATGGTGGTTAT

               
       5939 TTT
          1 TTT

       5942 TCACCCCTTT


Statistics
Matches: 28,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  27   16  0.57
  28    8  0.29
  29    4  0.14

ACGTcount: A:0.17, C:0.03, G:0.22, T:0.58


Consensus pattern (29 bp):   
TTTGTTTTTGTGTCAAAAATGGTGGTTAT

Found at i:7939 original size:12 final size:12

Alignment explanation


    Indices: 7914--7960  Score: 58
    Period size: 12  Copynumber: 3.8  Consensus size: 12

       7904 TCGATATTTT

                         
       7914 ATTATAATTAATA
          1 ATTATAA-TAATA

              *         
       7927 ATAATAATAATA
          1 ATTATAATAATA

                  * *   
       7939 ATTATATTTATA
          1 ATTATAATAATA

                      
       7951 ATTATAATAA
          1 ATTATAATAA

       7961 ATATAATATG


Statistics
Matches: 28,  Mismatches: 6, Indels: 1
        0.80            0.17        0.03

Matches are distributed among these distances:
  12   22  0.79
  13    6  0.21

ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45


Consensus pattern (12 bp):   
ATTATAATAATA

Found at i:9035 original size:26 final size:26

Alignment explanation


    Indices: 9006--9099  Score: 100
    Period size: 26  Copynumber: 3.6  Consensus size: 26

       8996 ATTTATTTAA

                              *  *    
       9006 TTTAAATAAATAAATATATATTTAAT
          1 TTTAAATAAATAAATATAAATATAAT

                            *    * *   
       9032 TTTAAATAAATTAAATCTAAACACAAT
          1 TTTAAATAAA-TAAATATAAATATAAT

                                   *   
       9059 TTTAAA-AAATCAAATATAAATAAAAT
          1 TTTAAATAAAT-AAATATAAATATAAT

              *            
       9085 TTAAAATAAATAAAT
          1 TTTAAATAAATAAAT

       9100 GAACATAAAT


Statistics
Matches: 56,  Mismatches: 9, Indels: 6
        0.79            0.13        0.08

Matches are distributed among these distances:
  25    1  0.02
  26   34  0.61
  27   21  0.38

ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36


Consensus pattern (26 bp):   
TTTAAATAAATAAATATAAATATAAT
Done.