Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2375

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: 4477
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26


Found at i:4028 original size:55 final size:55

Alignment explanation


    Indices: 3963--4066  Score: 131
    Period size: 54  Copynumber: 1.9  Consensus size: 55

       3953 AGCATGGCTG

                                     *               *               
       3963 CCAGATACAGAAAAT-GTGACAGAGTCACCAGATACAGATATTTTGTGGCAGTGCCA
          1 CCAGATACAG-AAATCGTGACAGAGCCACCAGA-ACAGATAATTTGTGGCAGTGCCA

                       *      *   *                          
       4019 CCAGA-ACAGATATCGTGGCAGGGCCACCAGAACAGATAATTTGTGGCA
          1 CCAGATACAGAAATCGTGACAGAGCCACCAGAACAGATAATTTGTGGCA

       4067 TAGCACCAGG


Statistics
Matches: 42,  Mismatches: 5, Indels: 4
        0.82            0.10        0.08

Matches are distributed among these distances:
  54   19  0.45
  55   18  0.43
  56    5  0.12

ACGTcount: A:0.35, C:0.21, G:0.25, T:0.19


Consensus pattern (55 bp):   
CCAGATACAGAAATCGTGACAGAGCCACCAGAACAGATAATTTGTGGCAGTGCCA

Found at i:4044 original size:26 final size:27

Alignment explanation


    Indices: 3988--4066  Score: 97
    Period size: 26  Copynumber: 2.9  Consensus size: 27

       3978 GTGACAGAGT

                              *       *  
       3988 CACCAGATACAGATATTTTGTGGCAGTGC
          1 CACCAGA-ACAGATA-TTCGTGGCAGGGC

                                       
       4017 CACCAGAACAGATA-TCGTGGCAGGGC
          1 CACCAGAACAGATATTCGTGGCAGGGC

                             *      
       4043 CACCAGAACAGATAATTTGTGGCA
          1 CACCAGAACAGAT-ATTCGTGGCA

       4067 TAGCACCAGG


Statistics
Matches: 45,  Mismatches: 3, Indels: 5
        0.85            0.06        0.09

Matches are distributed among these distances:
  26   23  0.51
  27    1  0.02
  28   14  0.31
  29    7  0.16

ACGTcount: A:0.32, C:0.23, G:0.25, T:0.20


Consensus pattern (27 bp):   
CACCAGAACAGATATTCGTGGCAGGGC

Found at i:4232 original size:27 final size:26

Alignment explanation


    Indices: 4181--4266  Score: 124
    Period size: 26  Copynumber: 3.3  Consensus size: 26

       4171 AAATTAACCC

                                       
       4181 TAGGGGTATAA-GTCATTTTGCATACA
          1 TAGGGGTATAATGT-ATTTTGCATACA

                                       
       4207 TAGGGGTATAATGGTATTTTGCATACA
          1 TAGGGGTATAAT-GTATTTTGCATACA

                           *          
       4234 TA-GGGTATAAT-TAATTTGCATACA
          1 TAGGGGTATAATGTATTTTGCATACA

                     
       4258 TAGGGGTAT
          1 TAGGGGTAT

       4267 TCTAGTACAT


Statistics
Matches: 56,  Mismatches: 1, Indels: 7
        0.88            0.02        0.11

Matches are distributed among these distances:
  24   14  0.25
  25    6  0.11
  26   20  0.36
  27   14  0.25
  28    2  0.04

ACGTcount: A:0.31, C:0.08, G:0.24, T:0.36


Consensus pattern (26 bp):   
TAGGGGTATAATGTATTTTGCATACA

Found at i:4256 original size:24 final size:25

Alignment explanation


    Indices: 4184--4262  Score: 99
    Period size: 24  Copynumber: 3.1  Consensus size: 25

       4174 TTAACCCTAG

                         *            
       4184 GGGTATAA-GTCATTTTGCATACATA
          1 GGGTATAATGT-AATTTGCATACATA

                          *            
       4209 GGGGTATAATGGTATTTTGCATACATA
          1 -GGGTATAAT-GTAATTTGCATACATA

                                     
       4236 GGGTATAAT-TAATTTGCATACATA
          1 GGGTATAATGTAATTTGCATACATA

               
       4260 GGG
          1 GGG

       4263 GTATTCTAGT


Statistics
Matches: 50,  Mismatches: 1, Indels: 6
        0.88            0.02        0.11

Matches are distributed among these distances:
  24   17  0.34
  26   17  0.34
  27   14  0.28
  28    2  0.04

ACGTcount: A:0.32, C:0.09, G:0.24, T:0.35


Consensus pattern (25 bp):   
GGGTATAATGTAATTTGCATACATA
Done.