Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1469

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: 38581
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29


Found at i:20973 original size:21 final size:19

Alignment explanation


    Indices: 20933--20970  Score: 58
    Period size: 20  Copynumber: 1.9  Consensus size: 19

      20923 GTGACGAAAT

                      *        
      20933 CCATTTTTCATGTTTTTTA
          1 CCATTTTTCAAGTTTTTTA

                               
      20952 CCATATTTTCAAGTTTTTT
          1 CCAT-TTTTCAAGTTTTTT

      20971 TACACCAGTC


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  19    4  0.24
  20   13  0.76

ACGTcount: A:0.18, C:0.16, G:0.05, T:0.61


Consensus pattern (19 bp):   
CCATTTTTCAAGTTTTTTA

Found at i:22322 original size:50 final size:48

Alignment explanation


    Indices: 22147--22385  Score: 191
    Period size: 50  Copynumber: 4.8  Consensus size: 48

      22137 ATTTTGGTAA

                                           *         *         
      22147 AGGT-CCATGTAAGACCATGTCTGGGACCATAGCATTGGCATCAAATGAGG
          1 AGGTCCCATGTAAGACCATGTCTGGGA-CATGGC-TTGGCACCAAATGA-G

                          *                            *     
      22197 AGGTCCCATGT-AGGCCATGTCT-GGACATGGCTTGGCACCGAGATGAG
          1 AGGTCCCATGTAAGACCATGTCTGGGACATGGCTTGGCACC-AAATGAG

                            *     *                     *      
      22244 -GGTCCCATGTAAGATTCA-GTTTGGGACATGGCGTTTGGCACCCAATGAG
          1 AGGTCCCATGTAAGA-CCATGTCTGGGACATGGC--TTGGCACCAAATGAG

                   **               *           *     * *      
      22293 AGGTCCCCCGTAAGACCATGTCTGTGACATGGCATGAGGCACGATATGGAG
          1 AGGTCCCATGTAAGACCATGTCTGGGACATGGC-T-TGGCACCAAAT-GAG

              **                                      
      22344 AACATCCCATGTAAGACCATGTCATGGGACATGGCTTTGGCA
          1 -AGGTCCCATGTAAGACCATGTC-TGGGACATGGC-TTGGCA

      22386 TGTTATTCTC


Statistics
Matches: 150,  Mismatches: 26, Indels: 24
        0.75            0.13        0.12

Matches are distributed among these distances:
  46   10  0.07
  47   13  0.09
  48   21  0.14
  49   11  0.07
  50   53  0.35
  51    9  0.06
  52   22  0.15
  53   11  0.07

ACGTcount: A:0.26, C:0.22, G:0.30, T:0.23


Consensus pattern (48 bp):   
AGGTCCCATGTAAGACCATGTCTGGGACATGGCTTGGCACCAAATGAG

Found at i:30144 original size:21 final size:20

Alignment explanation


    Indices: 30120--30176  Score: 69
    Period size: 21  Copynumber: 2.7  Consensus size: 20

      30110 ATACAATCGT

                     *           
      30120 AGATTTGATATGTAACTTAGG
          1 AGATTTGATTTGTAACTTA-G

                *                 
      30141 AGATATGATTTTGTAAACTTAG
          1 AGATTTGA-TTTGT-AACTTAG

                          
      30163 AGATTTGATTTGTA
          1 AGATTTGATTTGTA

      30177 GATACCATTC


Statistics
Matches: 31,  Mismatches: 3, Indels: 5
        0.79            0.08        0.13

Matches are distributed among these distances:
  20    1  0.03
  21   12  0.39
  22   12  0.39
  23    6  0.19

ACGTcount: A:0.33, C:0.04, G:0.21, T:0.42


Consensus pattern (20 bp):   
AGATTTGATTTGTAACTTAG
Done.