Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1922

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: 10316
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32


Found at i:1458 original size:40 final size:40

Alignment explanation


    Indices: 1402--1602  Score: 293
    Period size: 40  Copynumber: 5.1  Consensus size: 40

       1392 CAGATGATAA

                    *           *       *   *        
       1402 CCGGGCTAGGT-CCGAAGGCCTTTGTGCTAGTGACTA-ATT
          1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T

             *                                      
       1441 CTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-TATAT
          1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT

                                                    
       1480 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
          1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT

                    *                               
       1520 CCGGGCTAGGTCCCGAAGGCATTTGTGCGAGTTACTATAT
          1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT

                                     *               
       1560 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATAT
          1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT

               
       1600 CCG
          1 CCG

       1603 ACAAAATCCG


Statistics
Matches: 149,  Mismatches: 9, Indels: 7
        0.90            0.05        0.04

Matches are distributed among these distances:
  39   47  0.32
  40  102  0.68

ACGTcount: A:0.21, C:0.22, G:0.29, T:0.27


Consensus pattern (40 bp):   
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT

Found at i:1544 original size:79 final size:80

Alignment explanation


    Indices: 1402--1602  Score: 293
    Period size: 79  Copynumber: 2.5  Consensus size: 80

       1392 CAGATGATAA

                    *           *       *   *         *                      
       1402 CCGGGCTAGGT-CCGAAGGCCTTTGTGCTAGTGACTA-ATTCTGGGCTAAGTCCCGAAGGCATTT
          1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TCCGGGCTAAGTCCCGAAGGCATTT

                            
       1465 GTGCGAGTTA-TATAT
         65 GTGCGAGTTACTATAT

                                                            *                
       1480 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAGGTCCCGAAGGCATTTG
          1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG

                           
       1545 TGCGAGTTACTATAT
         66 TGCGAGTTACTATAT

                                     *                  
       1560 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATATCCG
          1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCCG

       1603 ACAAAATCCG


Statistics
Matches: 112,  Mismatches: 7, Indels: 6
        0.90            0.06        0.05

Matches are distributed among these distances:
  78   10  0.09
  79   57  0.51
  80   45  0.40

ACGTcount: A:0.21, C:0.22, G:0.29, T:0.27


Consensus pattern (80 bp):   
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
TGCGAGTTACTATAT

Found at i:9338 original size:40 final size:40

Alignment explanation


    Indices: 9237--9437  Score: 302
    Period size: 40  Copynumber: 5.1  Consensus size: 40

       9227 CGGATGATAA

                    *           *       *   *       
       9237 CCGGGCTAGGTCCCGAAGGCCTTTGTGCTAGTGACTA-AT
          1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT

            *                                       
       9276 TCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTATAT
          1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT

                                                    
       9315 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
          1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT

                    *                               
       9355 CC-GGCTAGGTCCCGAAGGCATTTGTGCGAGTTACTATAT
          1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT

                                     *               
       9394 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATAT
          1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT

                
       9434 CCGG
          1 CCGG

       9438 AAAATCCCGA


Statistics
Matches: 149,  Mismatches: 9, Indels: 7
        0.90            0.05        0.04

Matches are distributed among these distances:
  38   22  0.15
  39   61  0.41
  40   66  0.44

ACGTcount: A:0.21, C:0.23, G:0.29, T:0.26


Consensus pattern (40 bp):   
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT

Found at i:9396 original size:79 final size:78

Alignment explanation


    Indices: 9237--9437  Score: 298
    Period size: 79  Copynumber: 2.6  Consensus size: 78

       9227 CGGATGATAA

                    *           *       *   *         *                      
       9237 CCGGGCTAGGTCCCGAAGGCCTTTGTGCTAGTGACTA-ATTCGGGCTAAGTCCGAAGGCATTTGT
          1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TCCGGCTAAGTCCGAAGGCATTTGT

                          
       9301 GCGAGTTACTATAT
         65 GCGAGTTACTATAT

                                                           *                 
       9315 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGCTAGGTCCCGAAGGCATTTGT
          1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGCTAAGT-CCGAAGGCATTTGT

                          
       9380 GCGAGTTACTATAT
         65 GCGAGTTACTATAT

                                     *                   
       9394 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATATCCGG
          1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCCGG

       9438 AAAATCCCGA


Statistics
Matches: 113,  Mismatches: 7, Indels: 5
        0.90            0.06        0.04

Matches are distributed among these distances:
  78   44  0.39
  79   69  0.61

ACGTcount: A:0.21, C:0.23, G:0.29, T:0.26


Consensus pattern (78 bp):   
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGCTAAGTCCGAAGGCATTTGTG
CGAGTTACTATAT
Done.