Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold12843.1

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: 2044
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29


Found at i:108 original size:63 final size:63

Alignment explanation


    Indices: 4--133  Score: 226
    Period size: 63  Copynumber: 2.1  Consensus size: 63

          1 ATA

                                                *                           
          4 TTCAATGTCCTTTCGTTTCAAATCCGCATACGATTTTTGACGATCTGTGGCTG-CTTTCAGACT
          1 TTCAATGTCCTTTCGTTTCAAATCCGCATACGATTTCTGACGATCTGTGGCTGCCTTT-AGACT

                     *                                                     
         67 TTCAATGTCTTTTCGTTTCAAATCCGCATACGATTTCTGACGATCTGTGGCTGCCTTTAGACT
          1 TTCAATGTCCTTTCGTTTCAAATCCGCATACGATTTCTGACGATCTGTGGCTGCCTTTAGACT

                
        130 TTCA
          1 TTCA

        134 CGGATTACCC


Statistics
Matches: 64,  Mismatches: 2, Indels: 2
        0.94            0.03        0.03

Matches are distributed among these distances:
  63   60  0.94
  64    4  0.06

ACGTcount: A:0.19, C:0.24, G:0.17, T:0.40


Consensus pattern (63 bp):   
TTCAATGTCCTTTCGTTTCAAATCCGCATACGATTTCTGACGATCTGTGGCTGCCTTTAGACT

Found at i:884 original size:160 final size:160

Alignment explanation


    Indices: 614--933  Score: 604
    Period size: 160  Copynumber: 2.0  Consensus size: 160

        604 CTTAGTCAGT

                                                                *   *        
        614 CTATCAACAACAACCCAAATCGCATCCTTCTTACTTGTTGACAATGGCAGTCTGGATACAAAGTC
          1 CTATCAACAACAACCCAAATCGCATCCTTCTTACTTGTTGACAATGGCAGTCCGGACACAAAGTC

                                                               *             
        679 CATTGTGACTCGATCCCATTTCCACTCGGGTATCATGATCGGCTGAAGTAATCCTGAAGGCACTT
         66 CATTGTGACTCGATCCCATTTCCACTCGGGTATCATGATCGGCTGAAGTAACCCTGAAGGCACTT

                                          
        744 GATGTTCCGCTTTCACTTGTTGACATATTA
        131 GATGTTCCGCTTTCACTTGTTGACATATTA

                 *                                                           
        774 CTATCGACAACAACCCAAATCGCATCCTTCTTACTTGTTGACAATGGCAGTCCGGACACAAAGTC
          1 CTATCAACAACAACCCAAATCGCATCCTTCTTACTTGTTGACAATGGCAGTCCGGACACAAAGTC

                                                                             
        839 CATTGTGACTCGATCCCATTTCCACTCGGGTATCATGATCGGCTGAAGTAACCCTGAAGGCACTT
         66 CATTGTGACTCGATCCCATTTCCACTCGGGTATCATGATCGGCTGAAGTAACCCTGAAGGCACTT

                                          
        904 GATGTTCCGCTTTCACTTGTTGACATATTA
        131 GATGTTCCGCTTTCACTTGTTGACATATTA

        934 AACATCTCGA


Statistics
Matches: 156,  Mismatches: 4, Indels: 0
        0.98            0.03        0.00

Matches are distributed among these distances:
 160  156  1.00

ACGTcount: A:0.26, C:0.27, G:0.18, T:0.30


Consensus pattern (160 bp):   
CTATCAACAACAACCCAAATCGCATCCTTCTTACTTGTTGACAATGGCAGTCCGGACACAAAGTC
CATTGTGACTCGATCCCATTTCCACTCGGGTATCATGATCGGCTGAAGTAACCCTGAAGGCACTT
GATGTTCCGCTTTCACTTGTTGACATATTA

Found at i:1151 original size:73 final size:73

Alignment explanation


    Indices: 1032--1171  Score: 271
    Period size: 73  Copynumber: 1.9  Consensus size: 73

       1022 CGGGTGACTT

                                                                             
       1032 GACATTCGGCTACAATGGGCTTCGTTCAGAATCATCGAAATGAGTTCCGAACTCCTTGGAACACA
          1 GACATTCGGCTACAATGGGCTTCGTTCAGAATCATCGAAATGAGTTCCGAACTCCTTGGAACACA

                    
       1097 CAAACGAC
         66 CAAACGAC

                                                               *             
       1105 GACATTCGGCTACAATGGGCTTCGTTCAGAATCATCGAAATGAGTTCCGAATTCCTTGGAACACA
          1 GACATTCGGCTACAATGGGCTTCGTTCAGAATCATCGAAATGAGTTCCGAACTCCTTGGAACACA

              
       1170 CA
         66 CA

       1172 CATGATTTCT


Statistics
Matches: 66,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
  73   66  1.00

ACGTcount: A:0.31, C:0.25, G:0.21, T:0.24


Consensus pattern (73 bp):   
GACATTCGGCTACAATGGGCTTCGTTCAGAATCATCGAAATGAGTTCCGAACTCCTTGGAACACA
CAAACGAC

Found at i:1409 original size:56 final size:56

Alignment explanation


    Indices: 1348--1458  Score: 159
    Period size: 56  Copynumber: 2.0  Consensus size: 56

       1338 GTCAGGTAGA

                                *     *       *                     
       1348 ACAGACAAATGCACATTCATTGCTCGTAAAGCAACCAATGACTTCCGGCTTAAGGT
          1 ACAGACAAATGCACATTCATCGCTCGCAAAGCAAACAATGACTTCCGGCTTAAGGT

                    *  *                         *   *             
       1404 ACAGACAAGTGTACATTCATCGCTCGCAAAGCAAACAGTGATTTCCGGCTTAAGG
          1 ACAGACAAATGCACATTCATCGCTCGCAAAGCAAACAATGACTTCCGGCTTAAGG

       1459 CGTCCGCAAC


Statistics
Matches: 48,  Mismatches: 7, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  56   48  1.00

ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23


Consensus pattern (56 bp):   
ACAGACAAATGCACATTCATCGCTCGCAAAGCAAACAATGACTTCCGGCTTAAGGT
Done.