Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: COLO4_23754

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: 4881
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26


Found at i:3841 original size:33 final size:33

Alignment explanation


    Indices: 3781--3901  Score: 138
    Period size: 33  Copynumber: 3.7  Consensus size: 33

       3771 AAGCATTACT

                               * * *          
       3781 ACCTTAGG-TGAAGAAACTTCAACCATTCCCACA
          1 ACCTT-GGCTGAAGAAACTCCTAGCATTCCCACA

            *          **                  *  
       3814 GCCTTGAG-TGCTGAAACTCCTAGCATTCCCGCA
          1 ACCTTG-GCTGAAGAAACTCCTAGCATTCCCACA

                                       *     
       3847 ACCTTGGCTGAAGAAACTCCTAGCATTTCCACA
          1 ACCTTGGCTGAAGAAACTCCTAGCATTCCCACA

                                  
       3880 ACCTTGGCTGAAGAAACTCCTA
          1 ACCTTGGCTGAAGAAACTCCTA

       3902 CCTATTCTGT


Statistics
Matches: 74,  Mismatches: 12, Indels: 4
        0.82            0.13        0.04

Matches are distributed among these distances:
  32    2  0.03
  33   72  0.97

ACGTcount: A:0.30, C:0.31, G:0.17, T:0.23


Consensus pattern (33 bp):   
ACCTTGGCTGAAGAAACTCCTAGCATTCCCACA

Found at i:4101 original size:33 final size:33

Alignment explanation


    Indices: 4024--4634  Score: 487
    Period size: 33  Copynumber: 18.5  Consensus size: 33

       4014 CACAGGTGTT

                   *  *             *  **  * 
       4024 GAAACTAAAATTGATCCTGCAACCCTGGGTGTG
          1 GAAACTACAACTGATCCTGCAACCTTGCATGAG

               * *           **              
       4057 GAAGCGACAACTGATCCCACAACCTTGCATGAG
          1 GAAACTACAACTGATCCTGCAACCTTGCATGAG

                  *       *  *           *   
       4090 GAAACTGCAACTGAACCGGCAACCTTGCACGAG
          1 GAAACTACAACTGATCCTGCAACCTTGCATGAG

                          *              *   
       4123 GAAACTACAACTGAACCTGCAACCTTGCACGAG
          1 GAAACTACAACTGATCCTGCAACCTTGCATGAG

                          *          **  *   
       4156 GAAACTACAACTGAACCTGCAACCTCACACGAG
          1 GAAACTACAACTGATCCTGCAACCTTGCATGAG

                          *              *   
       4189 GAAACTACAACTGAACCTGCAACCTTGCAAGAG
          1 GAAACTACAACTGATCCTGCAACCTTGCATGAG

                          *              *   
       4222 GAAACTACAACTGAACCTGCAACCTTGCACGAG
          1 GAAACTACAACTGATCCTGCAACCTTGCATGAG

                          *                  
       4255 GAAACTACAACTGAACCTGCAACCTTGCATGAG
          1 GAAACTACAACTGATCCTGCAACCTTGCATGAG

                       *  *       **         
       4288 GAAACTACAACCGAACCTGCAATTTTGCATGAG
          1 GAAACTACAACTGATCCTGCAACCTTGCATGAG

               *       * *                   
       4321 GAAGCTACAACAGTTCCTGCAACCTTGCATGAG
          1 GAAACTACAACTGATCCTGCAACCTTGCATGAG

                       *           **         
       4354 GAAACTACAACCGAAT-CTGCAATTTTGCATGAG
          1 GAAACTACAACTG-ATCCTGCAACCTTGCATGAG

               *  *    * *                   
       4387 GAAGCTGCAACAGTTCCTGCAACCTTGCATGAG
          1 GAAACTACAACTGATCCTGCAACCTTGCATGAG

               *             **    *           
       4420 GAAGCTACAACTGATCCCCCAACATTG-A-GCAAG
          1 GAAACTACAACTGATCCTGCAACCTTGCATG--AG

                  *          **    *   **    
       4453 GAAACTCCAACTGATCCCCCAACATTGGGTGAG
          1 GAAACTACAACTGATCCTGCAACCTTGCATGAG

                  *   *    *    *  *   ***   
       4486 GAAACTCCAAATGATTCTGCCACTTTGGGCGAG
          1 GAAACTACAACTGATCCTGCAACCTTGCATGAG

                  *                       **    
       4519 GAAACTCCAACTGATCC--C-ACTTCTCTGGGTGAG
          1 GAAACTACAACTGATCCTGCAAC--CT-TGCATGAG

                             ** *            
       4552 GAAACTACAACTGATCCCACCACCTTGCATGAG
          1 GAAACTACAACTGATCCTGCAACCTTGCATGAG

                  *  *    *  ** *            
       4585 GAAACTCCATCTGACCCCACCACCTTGCATGAG
          1 GAAACTACAACTGATCCTGCAACCTTGCATGAG

                  *     *    
       4618 GAAACTCCAACTAATCC
          1 GAAACTACAACTGATCC

       4635 AATGACCTTA


Statistics
Matches: 491,  Mismatches: 75, Indels: 24
        0.83            0.13        0.04

Matches are distributed among these distances:
  30    2  0.00
  31    2  0.00
  32    3  0.01
  33  477  0.97
  34    3  0.01
  35    2  0.00
  36    2  0.00

ACGTcount: A:0.33, C:0.29, G:0.19, T:0.18


Consensus pattern (33 bp):   
GAAACTACAACTGATCCTGCAACCTTGCATGAG

Found at i:4792 original size:33 final size:33

Alignment explanation


    Indices: 4755--4857  Score: 154
    Period size: 33  Copynumber: 3.1  Consensus size: 33

       4745 ACGAATCCAT

                                              
       4755 GGCTATGGAAGTGGAGACTGTACCCCCTGTCGA-
          1 GGCTATGGAAGTGGAGACTGTACCCCCTGTC-AC

                                  *          
       4788 GGCTATGGAAGTGGAGACTGTAACCCCTGTCAC
          1 GGCTATGGAAGTGGAGACTGTACCCCCTGTCAC

                           *    *    *       
       4821 GGCTATGGAAGTGGACACTGAACCCTCTGTCAC
          1 GGCTATGGAAGTGGAGACTGTACCCCCTGTCAC

                
       4854 GGCT
          1 GGCT

       4858 GAAAAAGAGG


Statistics
Matches: 64,  Mismatches: 5, Indels: 2
        0.90            0.07        0.03

Matches are distributed among these distances:
  32    1  0.02
  33   63  0.98

ACGTcount: A:0.22, C:0.25, G:0.31, T:0.21


Consensus pattern (33 bp):   
GGCTATGGAAGTGGAGACTGTACCCCCTGTCAC
Done.