Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_3657

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: 17682
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34


Found at i:5085 original size:3 final size:3

Alignment explanation


    Indices: 5070--5103  Score: 50
    Period size: 3  Copynumber: 11.3  Consensus size: 3

       5060 AGGAACTATT

                    *                *                   
       5070 CTG CTG TTG CTG CTG CTG CGG CTG CTG CTG CTG C
          1 CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG C

       5104 GGAAAGTGAT


Statistics
Matches: 27,  Mismatches: 4, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
   3   27  1.00

ACGTcount: A:0.00, C:0.32, G:0.35, T:0.32


Consensus pattern (3 bp):   
CTG

Found at i:5104 original size:15 final size:15

Alignment explanation


    Indices: 5077--5105  Score: 58
    Period size: 15  Copynumber: 1.9  Consensus size: 15

       5067 ATTCTGCTGT

                           
       5077 TGCTGCTGCTGCGGC
          1 TGCTGCTGCTGCGGC

                          
       5092 TGCTGCTGCTGCGG
          1 TGCTGCTGCTGCGG

       5106 AAAGTGATGA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.00, C:0.31, G:0.41, T:0.28


Consensus pattern (15 bp):   
TGCTGCTGCTGCGGC

Found at i:5138 original size:15 final size:15

Alignment explanation


    Indices: 5120--5159  Score: 53
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       5110 TGATGAGGAG

                 *         
       5120 GAGGGTGAGGAAAGC
          1 GAGGGAGAGGAAAGC

                          *
       5135 GAGGGAGAGGAAAGT
          1 GAGGGAGAGGAAAGC

              *       
       5150 GAAGGAGAGG
          1 GAGGGAGAGG

       5160 GAGAGGAGAG


Statistics
Matches: 22,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  15   22  1.00

ACGTcount: A:0.38, C:0.03, G:0.55, T:0.05


Consensus pattern (15 bp):   
GAGGGAGAGGAAAGC

Found at i:5159 original size:21 final size:21

Alignment explanation


    Indices: 5135--5175  Score: 64
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       5125 TGAGGAAAGC

                          *      
       5135 GAGGGAGAGGAAAGTGAAGGA
          1 GAGGGAGAGGAAAGGGAAGGA

                       *        
       5156 GAGGGAGAGGAGAGGGAAGG
          1 GAGGGAGAGGAAAGGGAAGG

       5176 GATGAAGAGA


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.39, C:0.00, G:0.59, T:0.02


Consensus pattern (21 bp):   
GAGGGAGAGGAAAGGGAAGGA

Found at i:11381 original size:3 final size:3

Alignment explanation


    Indices: 11375--11412  Score: 67
    Period size: 3  Copynumber: 12.7  Consensus size: 3

      11365 AAACAAATTT

                            *                                 
      11375 TTA TTA TTA TTA GTA TTA TTA TTA TTA TTA TTA TTA TT
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT

      11413 TTGCATGATA


Statistics
Matches: 33,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   3   33  1.00

ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66


Consensus pattern (3 bp):   
TTA

Found at i:15514 original size:13 final size:13

Alignment explanation


    Indices: 15496--15521  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

      15486 TTATCGAAAT

                         
      15496 AAAAAAAAAAGAA
          1 AAAAAAAAAAGAA

                         
      15509 AAAAAAAAAAGAA
          1 AAAAAAAAAAGAA

      15522 GATAATCAAC


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00


Consensus pattern (13 bp):   
AAAAAAAAAAGAA

Found at i:17103 original size:1 final size:1

Alignment explanation


    Indices: 17051--17088  Score: 76
    Period size: 1  Copynumber: 38.0  Consensus size: 1

      17041 CTAACCTTAC

                                                  
      17051 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
          1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

      17089 ATACTTGCGG


Statistics
Matches: 37,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   37  1.00

ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00


Consensus pattern (1 bp):   
T
Done.