Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1420

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: 27225
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32


Found at i:3577 original size:37 final size:37

Alignment explanation


    Indices: 3520--3593  Score: 132
    Period size: 37  Copynumber: 2.0  Consensus size: 37

       3510 GTTCATCTTT

                                                 
       3520 TTCATTTCTTTTGGCCAAAATTCTAAGGAAGGAGGAA
          1 TTCATTTCTTTTGGCCAAAATTCTAAGGAAGGAGGAA

                                                  
       3557 TTCATTTC-TTTGGCCGAAAATTCTAAGGAAGGAGGAA
          1 TTCATTTCTTTTGGCC-AAAATTCTAAGGAAGGAGGAA

       3594 GGAGTTCTTG


Statistics
Matches: 36,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
  36    7  0.19
  37   29  0.81

ACGTcount: A:0.32, C:0.14, G:0.23, T:0.31


Consensus pattern (37 bp):   
TTCATTTCTTTTGGCCAAAATTCTAAGGAAGGAGGAA

Found at i:3602 original size:36 final size:36

Alignment explanation


    Indices: 3529--3602  Score: 105
    Period size: 37  Copynumber: 2.1  Consensus size: 36

       3519 TTTCATTTCT

                                         *  *   
       3529 TTTGGCCAAAATTCTAAGGAAGGAGGAATTCATTTC
          1 TTTGGCCAAAATTCTAAGGAAGGAGGAATGCAGTTC

                                           *     
       3565 TTTGGCCGAAAATTCTAAGGAAGGAGGAA-GGAGTTC
          1 TTTGGCC-AAAATTCTAAGGAAGGAGGAATGCAGTTC

              
       3601 TT
          1 TT

       3603 GCTTCATGTT


Statistics
Matches: 34,  Mismatches: 3, Indels: 2
        0.87            0.08        0.05

Matches are distributed among these distances:
  36   13  0.38
  37   21  0.62

ACGTcount: A:0.32, C:0.12, G:0.27, T:0.28


Consensus pattern (36 bp):   
TTTGGCCAAAATTCTAAGGAAGGAGGAATGCAGTTC

Found at i:4876 original size:40 final size:40

Alignment explanation


    Indices: 4782--4926  Score: 193
    Period size: 40  Copynumber: 3.6  Consensus size: 40

       4772 TACTCGAATG

                                    *                
       4782 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
          1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT

             *      *                                
       4823 ACATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
          1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACT

                                        *      *   *
       4863 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
          1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT

                     *    *         
       4903 ATATCCGGGTTAAGACCCGAAGGC
          1 ATATCCGGGCTAAGTCCCGAAGGC

       4927 CTTGTGCGAG


Statistics
Matches: 92,  Mismatches: 10, Indels: 5
        0.86            0.09        0.05

Matches are distributed among these distances:
  39    1  0.01
  40   62  0.67
  41   28  0.30
  42    1  0.01

ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23


Consensus pattern (40 bp):   
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT

Found at i:17447 original size:28 final size:29

Alignment explanation


    Indices: 17415--17513  Score: 107
    Period size: 28  Copynumber: 3.5  Consensus size: 29

      17405 ATAATAAGCC

                                 *       
      17415 CGCACACTTAGTGCTTA-ATAGTCGAACT
          1 CGCACACTTAGTGCTTACATAATCGAACT

                             *            
      17443 CGCACACTTAGTGC-TATATAATC-AACCT
          1 CGCACACTTAGTGCTTACATAATCGAA-CT

                                  * *    *
      17471 CGCACACTTAGTGCTATACA-ATTTGAACC
          1 CGCACACTTAGTGCT-TACATAATCGAACT

                          
      17500 CGCACACTTAGTGC
          1 CGCACACTTAGTGC

      17514 CAATCTCATG


Statistics
Matches: 61,  Mismatches: 5, Indels: 9
        0.81            0.07        0.12

Matches are distributed among these distances:
  27    4  0.07
  28   35  0.57
  29   17  0.28
  30    5  0.08

ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27


Consensus pattern (29 bp):   
CGCACACTTAGTGCTTACATAATCGAACT

Found at i:25486 original size:26 final size:26

Alignment explanation


    Indices: 25421--25518  Score: 108
    Period size: 28  Copynumber: 3.6  Consensus size: 26

      25411 TATAATAAGC

                                  *     
      25421 CCGCACACTTAGTGCT-TAATAGTCGAA
          1 CCGCACACTTAGTGCTAT-ATAATC-AA

                                       
      25448 CTCGCACACTTAGTGCTATATAATCAA
          1 C-CGCACACTTAGTGCTATATAATCAA

                               *     *  
      25475 CCGCACACTTAGTGCTATACAATTTGAA
          1 CCGCACACTTAGTGCTATATAA--TCAA

                            
      25503 CCCGCACACTTAGTGC
          1 -CCGCACACTTAGTGC

      25519 CAATCTCATG


Statistics
Matches: 63,  Mismatches: 3, Indels: 8
        0.85            0.04        0.11

Matches are distributed among these distances:
  26   20  0.32
  27    4  0.06
  28   23  0.37
  29   16  0.25

ACGTcount: A:0.30, C:0.29, G:0.15, T:0.27


Consensus pattern (26 bp):   
CCGCACACTTAGTGCTATATAATCAA
Done.