Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold5459.1

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: 23453
ACGTcount: A:0.29, C:0.11, G:0.14, T:0.30

Warning! 3712 characters in sequence are not A, C, G, or T


Found at i:5106 original size:19 final size:19

Alignment explanation


    Indices: 5061--5128  Score: 100
    Period size: 19  Copynumber: 3.5  Consensus size: 19

       5051 TTAGCTCTTA

                                *
       5061 CGAGCTTCTGTTCAGCTCTCA
          1 CGAGCTTCTGTTCAGCT-T-T

                          *    
       5082 CGAGCTTCTGTTCAACTTT
          1 CGAGCTTCTGTTCAGCTTT

                               
       5101 CGAGCTTCTGTTCAGCTTT
          1 CGAGCTTCTGTTCAGCTTT

                     
       5120 CGAGCTTCT
          1 CGAGCTTCT

       5129 ATTGACGATG


Statistics
Matches: 44,  Mismatches: 3, Indels: 2
        0.90            0.06        0.04

Matches are distributed among these distances:
  19   27  0.61
  20    1  0.02
  21   16  0.36

ACGTcount: A:0.13, C:0.29, G:0.19, T:0.38


Consensus pattern (19 bp):   
CGAGCTTCTGTTCAGCTTT

Found at i:9091 original size:20 final size:20

Alignment explanation


    Indices: 9059--9096  Score: 51
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       9049 TGTTTCACAT

                                
       9059 TCATATAACTAATATTTATA
          1 TCATATAACTAATATTTATA

                          *    
       9079 TCAT-TAACATAATTTTTA
          1 TCATATAAC-TAATATTTA

       9097 ACTTAATAAC


Statistics
Matches: 16,  Mismatches: 1, Indels: 2
        0.84            0.05        0.11

Matches are distributed among these distances:
  19    4  0.25
  20   12  0.75

ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47


Consensus pattern (20 bp):   
TCATATAACTAATATTTATA

Found at i:15279 original size:21 final size:21

Alignment explanation


    Indices: 15253--15296  Score: 54
    Period size: 21  Copynumber: 2.1  Consensus size: 21

      15243 TTAGTTAAAT

                  *               
      15253 GGGCGTGTGGAGT-AGCCACAC
          1 GGGCGTATGGAGTAAG-CACAC

                      *          
      15274 GGGCGTATGGGGTAAGCACAC
          1 GGGCGTATGGAGTAAGCACAC

              
      15295 GG
          1 GG

      15297 CTATGTTCTA


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  21   18  0.90
  22    2  0.10

ACGTcount: A:0.20, C:0.20, G:0.45, T:0.14


Consensus pattern (21 bp):   
GGGCGTATGGAGTAAGCACAC

Found at i:16021 original size:15 final size:15

Alignment explanation


    Indices: 16001--16031  Score: 62
    Period size: 15  Copynumber: 2.1  Consensus size: 15

      15991 ATAGCCTCTT

                           
      16001 GCTATCCTATAAATA
          1 GCTATCCTATAAATA

                           
      16016 GCTATCCTATAAATA
          1 GCTATCCTATAAATA

             
      16031 G
          1 G

      16032 GAGAATAATA


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32


Consensus pattern (15 bp):   
GCTATCCTATAAATA

Found at i:16312 original size:27 final size:27

Alignment explanation


    Indices: 16281--16340  Score: 77
    Period size: 27  Copynumber: 2.2  Consensus size: 27

      16271 AGTGATATAT

                                *       
      16281 AATAAATAATAAAATGTATAGT-TTGAA
          1 AATAAATAATAAAATGTATAATATT-AA

                 *      *              
      16308 AATAATTAATAATATGTATAATATTAA
          1 AATAAATAATAAAATGTATAATATTAA

                  
      16335 AATAAA
          1 AATAAA

      16341 AAATTAGATT


Statistics
Matches: 28,  Mismatches: 4, Indels: 2
        0.82            0.12        0.06

Matches are distributed among these distances:
  27   26  0.93
  28    2  0.07

ACGTcount: A:0.58, C:0.00, G:0.07, T:0.35


Consensus pattern (27 bp):   
AATAAATAATAAAATGTATAATATTAA

Found at i:17410 original size:15 final size:15

Alignment explanation


    Indices: 17383--17430  Score: 53
    Period size: 15  Copynumber: 3.1  Consensus size: 15

      17373 ATCGAAATTA

                            
      17383 AATTGTATATTTTTAT
          1 AATT-TATATTTTTAT

            *            *  
      17399 TA-TTATTATTTTAAT
          1 AATTTA-TATTTTTAT

                           
      17414 AATTTATATTTTTAT
          1 AATTTATATTTTTAT

              
      17429 AA
          1 AA

      17431 CTTTTAAAAG


Statistics
Matches: 26,  Mismatches: 4, Indels: 5
        0.74            0.11        0.14

Matches are distributed among these distances:
  14    2  0.08
  15   20  0.77
  16    4  0.15

ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62


Consensus pattern (15 bp):   
AATTTATATTTTTAT

Found at i:17418 original size:24 final size:25

Alignment explanation


    Indices: 17391--17437  Score: 60
    Period size: 24  Copynumber: 1.9  Consensus size: 25

      17381 TAAATTGTAT

                *         *          
      17391 ATTTTTATTATTATTA-TTTTAATA
          1 ATTTATATTATTATAACTTTTAATA

                     *             
      17415 ATTTATATTTTTATAACTTTTAA
          1 ATTTATATTATTATAACTTTTAA

      17438 AAGATTAAAT


Statistics
Matches: 19,  Mismatches: 3, Indels: 1
        0.83            0.13        0.04

Matches are distributed among these distances:
  24   13  0.68
  25    6  0.32

ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64


Consensus pattern (25 bp):   
ATTTATATTATTATAACTTTTAATA
Done.