Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_6175

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: 8131
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.31


Found at i:4208 original size:39 final size:39

Alignment explanation


    Indices: 4154--4393  Score: 335
    Period size: 39  Copynumber: 6.2  Consensus size: 39

       4144 AACCCAAGTA

                     *             **     *        
       4154 CCTTCGGGATTTAGCCGGATATAACAACTCACACAAATG
          1 CCTTCGGGACTTAGCCGGATATAGTAACTCGCACAAATG

                 *                                 
       4193 CCTTCAGGACTTAGCCGGATATAGTAACTC-CACAAATG
          1 CCTTCGGGACTTAGCCGGATATAGTAACTCGCACAAATG

                          *                         
       4231 CCTTC-GGACTTAACCCGGATAT-GTAACTCGCACAAATG
          1 CCTTCGGGACTT-AGCCGGATATAGTAACTCGCACAAATG

                                                    
       4269 CCTTCGGGACTTAGCCCGGATATAGTAACTCGC-CAAATG
          1 CCTTCGGGACTTAG-CCGGATATAGTAACTCGCACAAATG

                          *                         
       4308 CCTTCGGGACTTAACCCGGATATAGTAACTCGCACAAATG
          1 CCTTCGGGACTT-AGCCGGATATAGTAACTCGCACAAATG

                         *           *   *         
       4348 CCTTCGGGACTTAACCGGATATAGTCACTAGCACAAATG
          1 CCTTCGGGACTTAGCCGGATATAGTAACTCGCACAAATG

                   
       4387 CCTTCGG
          1 CCTTCGG

       4394 ATCTTAGTCC


Statistics
Matches: 184,  Mismatches: 10, Indels: 14
        0.88            0.05        0.07

Matches are distributed among these distances:
  37   13  0.07
  38   36  0.20
  39  107  0.58
  40   28  0.15

ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23


Consensus pattern (39 bp):   
CCTTCGGGACTTAGCCGGATATAGTAACTCGCACAAATG

Found at i:4360 original size:79 final size:79

Alignment explanation


    Indices: 4154--4393  Score: 355
    Period size: 77  Copynumber: 3.1  Consensus size: 79

       4144 AACCCAAGTA

                        * *         **     *             *                   
       4154 CCTTCGGGA-TTTAGCCGGATATAACAACTCACACAAATGCCTTCAGGACTTAGCCGGATATAGT
          1 CCTTCGGGACTTAACCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCGGATATAGT

                          
       4218 AACTC-CACAAATG
         66 AACTCGCACAAATG

                                                                             
       4231 CCTTC-GGACTTAACCCGGATAT-GTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
          1 CCTTCGGGACTTAACCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAG-CCGGATATAG

                           
       4294 TAACTCGC-CAAATG
         65 TAACTCGCACAAATG

                                                                 *           
       4308 CCTTCGGGACTTAACCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCGGATATAGT
          1 CCTTCGGGACTTAACCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCGGATATAGT

            *   *         
       4373 CACTAGCACAAATG
         66 AACTCGCACAAATG

                   
       4387 CCTTCGG
          1 CCTTCGG

       4394 ATCTTAGTCC


Statistics
Matches: 148,  Mismatches: 9, Indels: 10
        0.89            0.05        0.06

Matches are distributed among these distances:
  76   29  0.20
  77   43  0.29
  78   34  0.23
  79   42  0.28

ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23


Consensus pattern (79 bp):   
CCTTCGGGACTTAACCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCGGATATAGT
AACTCGCACAAATG

Found at i:6158 original size:56 final size:55

Alignment explanation


    Indices: 6098--6219  Score: 199
    Period size: 56  Copynumber: 2.2  Consensus size: 55

       6088 GCCTTGCTCA

                           *                  *             *       
       6098 CACACATATATCGAAGTCACATAGCGATGCCAACGTATTAAACGTAGTTTTACTCG
          1 CACACATATATCGAACTCACATAGCGATGCCAACATATT-AACGTAGTCTTACTCG

                                   *                               
       6154 CACACATATATCGAACTCACATATCGATGCCAACATATTAACGTAGTCTTACTCG
          1 CACACATATATCGAACTCACATAGCGATGCCAACATATTAACGTAGTCTTACTCG

                       
       6209 CACACATATAT
          1 CACACATATAT

       6220 TGATGCCATG


Statistics
Matches: 62,  Mismatches: 4, Indels: 1
        0.93            0.06        0.01

Matches are distributed among these distances:
  55   26  0.42
  56   36  0.58

ACGTcount: A:0.35, C:0.25, G:0.12, T:0.27


Consensus pattern (55 bp):   
CACACATATATCGAACTCACATAGCGATGCCAACATATTAACGTAGTCTTACTCG

Found at i:7853 original size:18 final size:18

Alignment explanation


    Indices: 7827--7861  Score: 52
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       7817 TCGTAACATT

                *             
       7827 GTGTTGTTTGGAAAACAA
          1 GTGTCGTTTGGAAAACAA

                     *       
       7845 GTGTCGTTTTGAAAACA
          1 GTGTCGTTTGGAAAACA

       7862 TGTCCTAAGT


Statistics
Matches: 15,  Mismatches: 2, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  18   15  1.00

ACGTcount: A:0.31, C:0.09, G:0.26, T:0.34


Consensus pattern (18 bp):   
GTGTCGTTTGGAAAACAA
Done.