Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_585 ID=scaffold_585-JGI_221_v2.0

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: 5471
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.30


Found at i:64 original size:42 final size:42

Alignment explanation


    Indices: 3--126  Score: 203
    Period size: 42  Copynumber: 2.9  Consensus size: 42

          1 CT

                                                      
          3 TAAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTATA
          1 TAAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTATA

             *                                     * *
         45 TGAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTC
          1 TAAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTATA

                    *                               
         87 TAAGCGCCTCTAAAGAACATGTTCTTTAGCGGCGCTTTTT
          1 TAAGCGCCGCTAAAGAACATGTTCTTTAGCGGCG-TTTTT

        127 TTCTTTAGCG


Statistics
Matches: 76,  Mismatches: 5, Indels: 1
        0.93            0.06        0.01

Matches are distributed among these distances:
  42   71  0.93
  43    5  0.07

ACGTcount: A:0.23, C:0.21, G:0.22, T:0.35


Consensus pattern (42 bp):   
TAAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTATA

Found at i:132 original size:19 final size:19

Alignment explanation


    Indices: 108--146  Score: 78
    Period size: 19  Copynumber: 2.1  Consensus size: 19

         98 AAAGAACATG

                               
        108 TTCTTTAGCGGCGCTTTTT
          1 TTCTTTAGCGGCGCTTTTT

                               
        127 TTCTTTAGCGGCGCTTTTT
          1 TTCTTTAGCGGCGCTTTTT

             
        146 T
          1 T

        147 ACAAAAACGC


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  19   20  1.00

ACGTcount: A:0.05, C:0.21, G:0.21, T:0.54


Consensus pattern (19 bp):   
TTCTTTAGCGGCGCTTTTT

Found at i:491 original size:21 final size:21

Alignment explanation


    Indices: 467--506  Score: 62
    Period size: 21  Copynumber: 1.9  Consensus size: 21

        457 TTCTTTTGAA

                      *          
        467 CCTCTACTTCTCTCGCTGCAG
          1 CCTCTACTTCCCTCGCTGCAG

                 *             
        488 CCTCTGCTTCCCTCGCTGC
          1 CCTCTACTTCCCTCGCTGC

        507 CGCATCTGCT


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  21   17  1.00

ACGTcount: A:0.05, C:0.47, G:0.15, T:0.33


Consensus pattern (21 bp):   
CCTCTACTTCCCTCGCTGCAG

Found at i:514 original size:21 final size:21

Alignment explanation


    Indices: 473--517  Score: 63
    Period size: 21  Copynumber: 2.1  Consensus size: 21

        463 TGAACCTCTA

                *           *    
        473 CTTCTCTCGCTGCAGCCTCTG
          1 CTTCCCTCGCTGCAGCATCTG

                         *       
        494 CTTCCCTCGCTGCCGCATCTG
          1 CTTCCCTCGCTGCAGCATCTG

               
        515 CTT
          1 CTT

        518 TAAGTTGTAG


Statistics
Matches: 21,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  21   21  1.00

ACGTcount: A:0.04, C:0.44, G:0.18, T:0.33


Consensus pattern (21 bp):   
CTTCCCTCGCTGCAGCATCTG

Found at i:570 original size:87 final size:87

Alignment explanation


    Indices: 402--561  Score: 230
    Period size: 87  Copynumber: 1.8  Consensus size: 87

        392 TTCTGCTCTG

                     *           *             *   *                  *      
        402 CTCTGCTTCTCTCGCTGCAGCCTCTGCTTTAAGTTTTAGTTGCAGTTCTTCATATTTCTTTTGAA
          1 CTCTGCTTCCCTCGCTGCAGCATCTGCTTTAAGTTGTAGCTGCAGTTCTTCATATTTCCTTTGAA

                *     *           
        467 CCTCTACTTCTCTCGCTGCAGC
         66 CCTCAACTTCGCTCGCTGCAGC

                              *                       *                      
        489 CTCTGCTTCCCTCGCTGCCGCATCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATTTCCTTTGAA
          1 CTCTGCTTCCCTCGCTGCAGCATCTGCTTTAAGTTGTAGCTGCAGTTCTTCATATTTCCTTTGAA

             *      
        554 CTTCAACT
         66 CCTCAACT

        562 GTGGTCGCTT


Statistics
Matches: 64,  Mismatches: 9, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  87   64  1.00

ACGTcount: A:0.14, C:0.29, G:0.16, T:0.41


Consensus pattern (87 bp):   
CTCTGCTTCCCTCGCTGCAGCATCTGCTTTAAGTTGTAGCTGCAGTTCTTCATATTTCCTTTGAA
CCTCAACTTCGCTCGCTGCAGC

Found at i:3972 original size:21 final size:22

Alignment explanation


    Indices: 3936--3977  Score: 68
    Period size: 21  Copynumber: 2.0  Consensus size: 22

       3926 AACATAGTAA

                                  
       3936 TTAAACACTGAAACCCTAAACT
          1 TTAAACACTGAAACCCTAAACT

                  *              
       3958 TTAAACTCT-AAACCCTAAAC
          1 TTAAACACTGAAACCCTAAAC

       3978 GCTATAAACC


Statistics
Matches: 19,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  21   11  0.58
  22    8  0.42

ACGTcount: A:0.45, C:0.29, G:0.02, T:0.24


Consensus pattern (22 bp):   
TTAAACACTGAAACCCTAAACT
Done.