Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_131 ID=scaffold_131-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: 13424
ACGTcount: A:0.31, C:0.18, G:0.11, T:0.28

Warning! 1734 characters in sequence are not A, C, G, or T


Found at i:85 original size:20 final size:20

Alignment explanation


    Indices: 57--94  Score: 51
    Period size: 20  Copynumber: 1.9  Consensus size: 20

         47 TATAGACTAA

                                 
         57 AACAAAC-AACACATTTCATC
          1 AACAAACAAACA-ATTTCATC

                *             
         77 AACACACAAACAATTTCA
          1 AACAAACAAACAATTTCA

         95 CATTCAATTG


Statistics
Matches: 16,  Mismatches: 1, Indels: 2
        0.84            0.05        0.11

Matches are distributed among these distances:
  20   12  0.75
  21    4  0.25

ACGTcount: A:0.53, C:0.29, G:0.00, T:0.18


Consensus pattern (20 bp):   
AACAAACAAACAATTTCATC

Found at i:5453 original size:44 final size:44

Alignment explanation


    Indices: 5405--5526  Score: 124
    Period size: 44  Copynumber: 2.8  Consensus size: 44

       5395 ATGATGCTTC

                                                        
       5405 TGTCCCAGACAGGGTCTTACACGAAATCATATATTCGATGCCAA
          1 TGTCCCAGACAGGGTCTTACACGAAATCATATATTCGATGCCAA

                     * *           *           *          
       5449 TGTCCCAGATATGGTCTTACACATAAATC-TCA-AATCGATGCCAA
          1 TGTCCCAGACAGGGTCTTACAC-GAAATCAT-ATATTCGATGCCAA

            *    *                   *    *    
       5493 CGTCCTAGAC-GTGGTCTTACACGATATCACATAT
          1 TGTCCCAGACAG-GGTCTTACACGAAATCATATAT

       5527 CAGAATTCCA


Statistics
Matches: 61,  Mismatches: 12, Indels: 10
        0.73            0.14        0.12

Matches are distributed among these distances:
  43    5  0.08
  44   50  0.82
  45    6  0.10

ACGTcount: A:0.31, C:0.25, G:0.16, T:0.27


Consensus pattern (44 bp):   
TGTCCCAGACAGGGTCTTACACGAAATCATATATTCGATGCCAA

Found at i:9084 original size:138 final size:139

Alignment explanation


    Indices: 8835--9111  Score: 448
    Period size: 138  Copynumber: 2.0  Consensus size: 139

       8825 CTTCAAACTT

                                                  *    *                     
       8835 CGGATACATTTCTCGGAGGCTTCCAATCCAGTATAGCTGAAATCTTGATCGGATCAACCCGAATA
          1 CGGATACATTTCTCGGAGGCTTCCAATCCAGTATAGCTAAAATATTGATCGGATCAACCCGAATA

                                   *                                         
       8900 CCCGATGCTGATACAACATGTCCTAGAAAACTGACTTCTCGTAACCAAAACTCACATTTACTAAA
         66 CCCGATGCTGATACAACATGTCCCAGAAAACTGACTTCTCGTAACCAAAACTCACATTTACTAAA

                     
       8965 CTTCGCATA
        131 CTTCGCATA

                         *        *     *                  *        *        
       8974 CGGATACATTTCTTGGAGGCTTTCAATCTAGTATA-CTAAAATATTGCTCGGATCAGCCCGAATA
          1 CGGATACATTTCTCGGAGGCTTCCAATCCAGTATAGCTAAAATATTGATCGGATCAACCCGAATA

              *                                                 *         *  
       9038 CCTGATGCTGATACAACATGTCCCAGAAAACTGACTTCTCGTAACCAAAACTTACATTTACTGAA
         66 CCCGATGCTGATACAACATGTCCCAGAAAACTGACTTCTCGTAACCAAAACTCACATTTACTAAA

                     
       9103 CTTCGCATA
        131 CTTCGCATA

       9112 TAAATGCTTA


Statistics
Matches: 127,  Mismatches: 11, Indels: 1
        0.91            0.08        0.01

Matches are distributed among these distances:
 138   95  0.75
 139   32  0.25

ACGTcount: A:0.32, C:0.25, G:0.15, T:0.27


Consensus pattern (139 bp):   
CGGATACATTTCTCGGAGGCTTCCAATCCAGTATAGCTAAAATATTGATCGGATCAACCCGAATA
CCCGATGCTGATACAACATGTCCCAGAAAACTGACTTCTCGTAACCAAAACTCACATTTACTAAA
CTTCGCATA

Found at i:12518 original size:3 final size:3

Alignment explanation


    Indices: 12503--12556  Score: 99
    Period size: 3  Copynumber: 18.0  Consensus size: 3

      12493 TCTAGATGAT

                      *                                                    
      12503 AAC AAC AAT AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
          1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC

                   
      12551 AAC AAC
          1 AAC AAC

      12557 TATATACATG


Statistics
Matches: 49,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
   3   49  1.00

ACGTcount: A:0.67, C:0.31, G:0.00, T:0.02


Consensus pattern (3 bp):   
AAC

Done.