Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2598

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: 7725
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35


Found at i:3647 original size:17 final size:17

Alignment explanation


    Indices: 3625--3658  Score: 68
    Period size: 17  Copynumber: 2.0  Consensus size: 17

       3615 ATACTTCATC

                             
       3625 TGGAGCAGCTTTGTCAG
          1 TGGAGCAGCTTTGTCAG

                             
       3642 TGGAGCAGCTTTGTCAG
          1 TGGAGCAGCTTTGTCAG

       3659 AACAAATAGC


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   17  1.00

ACGTcount: A:0.18, C:0.18, G:0.35, T:0.29


Consensus pattern (17 bp):   
TGGAGCAGCTTTGTCAG

Found at i:4493 original size:37 final size:38

Alignment explanation


    Indices: 4452--4524  Score: 121
    Period size: 38  Copynumber: 1.9  Consensus size: 38

       4442 CCTTAGTCAC

                                                  
       4452 AGCCACTAGCCAATTCT-AATTGAATTCTCTAGTCGCT
          1 AGCCACTAGCCAATTCTAAATTGAATTCTCTAGTCGCT

                 * *                            
       4489 AGCCATTGGCCAATTCTAAATTGAATTCTCTAGTCG
          1 AGCCACTAGCCAATTCTAAATTGAATTCTCTAGTCG

       4525 TCAGTCGCCA


Statistics
Matches: 33,  Mismatches: 2, Indels: 1
        0.92            0.06        0.03

Matches are distributed among these distances:
  37   15  0.45
  38   18  0.55

ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33


Consensus pattern (38 bp):   
AGCCACTAGCCAATTCTAAATTGAATTCTCTAGTCGCT

Found at i:4548 original size:38 final size:38

Alignment explanation


    Indices: 4506--4606  Score: 157
    Period size: 38  Copynumber: 2.7  Consensus size: 38

       4496 GGCCAATTCT

                           *                      
       4506 AAATTGAATTCTCTAGTCGTCAGTCGCCAGCTAATTTC
          1 AAATTGAATTCTCTAATCGTCAGTCGCCAGCTAATTTC

                 *             *    *             
       4544 AAATTAAATTCTCTAATCGGCAGTTGCCAGCTAATTTC
          1 AAATTGAATTCTCTAATCGTCAGTCGCCAGCTAATTTC

                            *        
       4582 AAATTGAATTCTCTAACCGTCAGTC
          1 AAATTGAATTCTCTAATCGTCAGTC

       4607 AATTCAATTT


Statistics
Matches: 55,  Mismatches: 8, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  38   55  1.00

ACGTcount: A:0.30, C:0.23, G:0.14, T:0.34


Consensus pattern (38 bp):   
AAATTGAATTCTCTAATCGTCAGTCGCCAGCTAATTTC

Found at i:6190 original size:11 final size:13

Alignment explanation


    Indices: 6173--6238  Score: 50
    Period size: 13  Copynumber: 5.2  Consensus size: 13

       6163 TACAAACACA

                     *   
       6173 TTTTTT-TCCTTC
          1 TTTTTTCTCTTTC

                         
       6185 TTTTTTCTCTTTC
          1 TTTTTTCTCTTTC

                      *  
       6198 --TTTTCTCTATC
          1 TTTTTTCTCTTTC

                    *    *
       6209 TTTTCTTCCCTTTT
          1 TTTT-TTCTCTTTC

                          
       6223 TATTTTTCT-TTTC
          1 T-TTTTTCTCTTTC

               
       6236 TTT
          1 TTT

       6239 CTTCCCTTCT


Statistics
Matches: 42,  Mismatches: 7, Indels: 10
        0.71            0.12        0.17

Matches are distributed among these distances:
  11   10  0.24
  12    8  0.19
  13   11  0.26
  14   10  0.24
  15    3  0.07

ACGTcount: A:0.03, C:0.23, G:0.00, T:0.74


Consensus pattern (13 bp):   
TTTTTTCTCTTTC
Done.