Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold542

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: 10786
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.36


Found at i:2688 original size:2 final size:2

Alignment explanation


    Indices: 2681--2711  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

       2671 TATCTATAAG

                                                          
       2681 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       2712 TAAAAATCTC


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   29  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:8220 original size:92 final size:92

Alignment explanation


    Indices: 8106--8319  Score: 216
    Period size: 91  Copynumber: 2.3  Consensus size: 92

       8096 TTATGGTGAG

                           *                 *           *       *          *
       8106 ATATTTAAAATCAATTAACTTTTCTTCTTTCTTTCCAAAAAG-AATTAGATTCTCACAAAAAATT
          1 ATATTTAAAATCAATCAACTTTTCTTCTTTCTTACCAAAAAGAAACTA-ATTCCCACAAAAAATA

               *                        
       8170 CATGTATTAATCTCATCCTTGCAGTGTA
         65 CATATATTAATCTCATCCTTGCAGTGTA

                   *   *           *           * *  *              *   *     
       8198 ATATTTACAATTAATCAACTTTTTTTC-TTCTTACTAGAAGGAAACTAATTCCCATAAAGAATAC
          1 ATATTTAAAATCAATCAACTTTTCTTCTTTCTTACCAAAAAGAAACTAATTCCCACAAAAAATAC

                        *       *     *
       8262 ATATATTAATCTTATCCTTGTAGTGTG
         66 ATATATTAATCTCATCCTTGCAGTGTA

             *     *           *           
       8289 ACATTTATAATCAATCAAAGTTTTCTTCTTT
          1 ATATTTAAAATCAATC-AACTTTTCTTCTTT

       8320 TCTATCAAAA


Statistics
Matches: 97,  Mismatches: 22, Indels: 5
        0.78            0.18        0.04

Matches are distributed among these distances:
  91   59  0.61
  92   36  0.37
  93    2  0.02

ACGTcount: A:0.35, C:0.16, G:0.07, T:0.42


Consensus pattern (92 bp):   
ATATTTAAAATCAATCAACTTTTCTTCTTTCTTACCAAAAAGAAACTAATTCCCACAAAAAATAC
ATATATTAATCTCATCCTTGCAGTGTA

Found at i:9150 original size:16 final size:16

Alignment explanation


    Indices: 9129--9176  Score: 53
    Period size: 16  Copynumber: 3.1  Consensus size: 16

       9119 TCGATTCAGG

                            
       9129 TTATTTCAAGTTTAAA
          1 TTATTTCAAGTTTAAA

                   * *   * *
       9145 TTATTT-GATTTTGAG
          1 TTATTTCAAGTTTAAA

                            
       9160 TTATTTCAAGTTTAAA
          1 TTATTTCAAGTTTAAA

             
       9176 T
          1 T

       9177 CATTCTGAGT


Statistics
Matches: 23,  Mismatches: 8, Indels: 2
        0.70            0.24        0.06

Matches are distributed among these distances:
  15   11  0.48
  16   12  0.52

ACGTcount: A:0.31, C:0.04, G:0.10, T:0.54


Consensus pattern (16 bp):   
TTATTTCAAGTTTAAA
Done.