Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold6107.1

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: 13934
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29


Found at i:4797 original size:58 final size:58

Alignment explanation


    Indices: 4725--4840  Score: 223
    Period size: 58  Copynumber: 2.0  Consensus size: 58

       4715 GTCAATTTAT

                                                             *        
       4725 AGTGAATTTCCAAAGGCGGAACAGGGAATCCAGAAACTGTTCTGGCCCTGTTCCACAA
          1 AGTGAATTTCCAAAGGCGGAACAGGGAATCCAGAAACTGTTCTGGCCCTATTCCACAA

                                                                      
       4783 AGTGAATTTCCAAAGGCGGAACAGGGAATCCAGAAACTGTTCTGGCCCTATTCCACAA
          1 AGTGAATTTCCAAAGGCGGAACAGGGAATCCAGAAACTGTTCTGGCCCTATTCCACAA

       4841 GAACCCGAAT


Statistics
Matches: 57,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  58   57  1.00

ACGTcount: A:0.32, C:0.24, G:0.23, T:0.21


Consensus pattern (58 bp):   
AGTGAATTTCCAAAGGCGGAACAGGGAATCCAGAAACTGTTCTGGCCCTATTCCACAA

Found at i:5862 original size:79 final size:80

Alignment explanation


    Indices: 5761--5907  Score: 233
    Period size: 79  Copynumber: 1.9  Consensus size: 80

       5751 TCCTCGTTCA

                             *     *    *                                    
       5761 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-AATGCCTTCGGGACATAACCCGGAT
          1 AATGCCTTCGGGACATAACCCGGATTTAATAACTCACACGAATGCCTTCGGGACATAACCCGGAT

                           
       5825 TTAACAACTCGCACG
         66 TTAACAACTCGCACG

                          *                    *                  *          
       5840 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGAT
          1 AATGCCTTCGGGACATAACCCGGATTTAATAACTCACACGAATGCCTTCGGGACATAACCCGGAT

               
       5905 TTA
         66 TTA

       5908 GTATCTCGCA


Statistics
Matches: 61,  Mismatches: 6, Indels: 1
        0.90            0.09        0.01

Matches are distributed among these distances:
  79   34  0.56
  80   27  0.44

ACGTcount: A:0.27, C:0.28, G:0.20, T:0.24


Consensus pattern (80 bp):   
AATGCCTTCGGGACATAACCCGGATTTAATAACTCACACGAATGCCTTCGGGACATAACCCGGAT
TTAACAACTCGCACG

Found at i:5937 original size:40 final size:40

Alignment explanation


    Indices: 5761--5984  Score: 238
    Period size: 40  Copynumber: 5.6  Consensus size: 40

       5751 TCCTCGTTCA

                          *  *     *    *      *    
       5761 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
          1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG

                          *              *          
       5800 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
          1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG

                                                    
       5840 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
          1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG

                                        *  *       *
       5880 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
          1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG

              *      *         *      *  * *    *     
       5920 AAGGCCTT-TGGATCTTAATCCGGATATATTCACTTAGCAC-
          1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG

              *              *       
       5960 AAAGCCTTCGGGACTTAGCCCGGAT
          1 AATGCCTTCGGGACTTAACCCGGAT

       5985 AGCATTCAAT


Statistics
Matches: 159,  Mismatches: 22, Indels: 7
        0.85            0.12        0.04

Matches are distributed among these distances:
  39   37  0.23
  40  114  0.72
  41    8  0.05

ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25


Consensus pattern (40 bp):   
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG

Found at i:10265 original size:13 final size:13

Alignment explanation


    Indices: 10247--10271  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

      10237 GTATTGATCA

                         
      10247 TGTGTTCACACCT
          1 TGTGTTCACACCT

                        
      10260 TGTGTTCACACC
          1 TGTGTTCACACC

      10272 ATGATGACCA


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.16, C:0.32, G:0.16, T:0.36


Consensus pattern (13 bp):   
TGTGTTCACACCT
Done.