Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold775

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: 25209
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31


Found at i:1170 original size:32 final size:32

Alignment explanation


    Indices: 1127--1188  Score: 115
    Period size: 32  Copynumber: 1.9  Consensus size: 32

       1117 GAGCTTTTGG

                                            
       1127 TTTTTCATGTTGTCAAAGAGTTGAACAATGGA
          1 TTTTTCATGTTGTCAAAGAGTTGAACAATGGA

                  *                       
       1159 TTTTTCGTGTTGTCAAAGAGTTGAACAATG
          1 TTTTTCATGTTGTCAAAGAGTTGAACAATG

       1189 AAAATAGATG


Statistics
Matches: 29,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  32   29  1.00

ACGTcount: A:0.29, C:0.10, G:0.23, T:0.39


Consensus pattern (32 bp):   
TTTTTCATGTTGTCAAAGAGTTGAACAATGGA

Found at i:13102 original size:14 final size:14

Alignment explanation


    Indices: 13083--13111  Score: 58
    Period size: 14  Copynumber: 2.1  Consensus size: 14

      13073 ACAGATGGAT

                          
      13083 TCGTATAATTCTTA
          1 TCGTATAATTCTTA

                          
      13097 TCGTATAATTCTTA
          1 TCGTATAATTCTTA

             
      13111 T
          1 T

      13112 ATATATTGTA


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   15  1.00

ACGTcount: A:0.28, C:0.14, G:0.07, T:0.52


Consensus pattern (14 bp):   
TCGTATAATTCTTA

Found at i:17335 original size:20 final size:21

Alignment explanation


    Indices: 17269--17337  Score: 95
    Period size: 21  Copynumber: 3.3  Consensus size: 21

      17259 TCACTTCGTT

                                 
      17269 TCTTTTTGTCCAAGTTACTTC
          1 TCTTTTTGTCCAAGTTACTTC

                            *    
      17290 TCTTTTTGTCCAAGTTGCTTC
          1 TCTTTTTGTCCAAGTTACTTC

                      *  * *     
      17311 TCTTTTTGTCTAACTCACTTC
          1 TCTTTTTGTCCAAGTTACTTC

                   
      17332 -CTTTTT
          1 TCTTTTT

      17338 TCTTTGTGAG


Statistics
Matches: 43,  Mismatches: 5, Indels: 1
        0.88            0.10        0.02

Matches are distributed among these distances:
  20    6  0.14
  21   37  0.86

ACGTcount: A:0.12, C:0.25, G:0.09, T:0.55


Consensus pattern (21 bp):   
TCTTTTTGTCCAAGTTACTTC

Found at i:19730 original size:18 final size:18

Alignment explanation


    Indices: 19697--19790  Score: 131
    Period size: 18  Copynumber: 5.4  Consensus size: 18

      19687 AAGGTTTTCT

                              
      19697 TATTGATGATA-T--CGA
          1 TATTGATGATAGTGACGA

                              
      19712 TATTGATGATAGTGACGA
          1 TATTGATGATAGTGACGA

                    *         
      19730 TATTGATGCTAGTGACGA
          1 TATTGATGATAGTGACGA

                    *        *
      19748 TATTGATGCTAGTGACGC
          1 TATTGATGATAGTGACGA

                             *
      19766 TATTGATGATAGTGACGC
          1 TATTGATGATAGTGACGA

                   
      19784 TATTGAT
          1 TATTGAT

      19791 CGTGACCTTG


Statistics
Matches: 73,  Mismatches: 3, Indels: 3
        0.92            0.04        0.04

Matches are distributed among these distances:
  15   11  0.15
  16    1  0.01
  18   61  0.84

ACGTcount: A:0.29, C:0.10, G:0.26, T:0.36


Consensus pattern (18 bp):   
TATTGATGATAGTGACGA

Done.