Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold5566.1

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: 21127
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.35


Found at i:7745 original size:17 final size:17

Alignment explanation


    Indices: 7723--7761  Score: 69
    Period size: 17  Copynumber: 2.3  Consensus size: 17

       7713 CCGTGTGTAT

                             
       7723 CAATTAGTAATAATATG
          1 CAATTAGTAATAATATG

                             
       7740 CAATTAGTAATAATATG
          1 CAATTAGTAATAATATG

            *    
       7757 TAATT
          1 CAATT

       7762 TAAATAATTT


Statistics
Matches: 21,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  17   21  1.00

ACGTcount: A:0.46, C:0.05, G:0.10, T:0.38


Consensus pattern (17 bp):   
CAATTAGTAATAATATG

Found at i:8109 original size:14 final size:14

Alignment explanation


    Indices: 8082--8119  Score: 51
    Period size: 14  Copynumber: 2.8  Consensus size: 14

       8072 TAGTCGGAAC

                          
       8082 TATATAATAAAATA
          1 TATATAATAAAATA

                 *   *    
       8096 TATATGATATAATA
          1 TATATAATAAAATA

                       
       8110 TATA-AATAAA
          1 TATATAATAAA

       8120 TGAAAATTTT


Statistics
Matches: 20,  Mismatches: 4, Indels: 1
        0.80            0.16        0.04

Matches are distributed among these distances:
  13    4  0.20
  14   16  0.80

ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37


Consensus pattern (14 bp):   
TATATAATAAAATA

Found at i:9320 original size:21 final size:22

Alignment explanation


    Indices: 9262--9321  Score: 70
    Period size: 21  Copynumber: 2.8  Consensus size: 22

       9252 TTATTAATTT

                                 *
       9262 TTTAAAAAATAA-TAAAAGATG
          1 TTTAAAAAATAATTAAAAGATA

                        *    *     
       9283 TTTAAAAACATAGTTAATAGA-A
          1 TTTAAAAA-ATAATTAAAAGATA

                             
       9305 TTTAAAAAATAATTAAA
          1 TTTAAAAAATAATTAAA

       9322 TAACATTAAA


Statistics
Matches: 32,  Mismatches: 5, Indels: 4
        0.78            0.12        0.10

Matches are distributed among these distances:
  21   15  0.47
  22   11  0.34
  23    6  0.19

ACGTcount: A:0.60, C:0.02, G:0.07, T:0.32


Consensus pattern (22 bp):   
TTTAAAAAATAATTAAAAGATA

Found at i:9323 original size:22 final size:23

Alignment explanation


    Indices: 9262--9323  Score: 69
    Period size: 22  Copynumber: 2.8  Consensus size: 23

       9252 TTATTAATTT

                                  *
       9262 TTTAAAAAATAA-TAAA-AGATG
          1 TTTAAAAAATAATTAAATAGATA

                        *           
       9283 TTTAAAAACATAGTT-AATAGA-A
          1 TTTAAAAA-ATAATTAAATAGATA

                               
       9305 TTTAAAAAATAATTAAATA
          1 TTTAAAAAATAATTAAATA

       9324 ACATTAAAAC


Statistics
Matches: 34,  Mismatches: 3, Indels: 7
        0.77            0.07        0.16

Matches are distributed among these distances:
  21   13  0.38
  22   17  0.50
  23    4  0.12

ACGTcount: A:0.60, C:0.02, G:0.06, T:0.32


Consensus pattern (23 bp):   
TTTAAAAAATAATTAAATAGATA

Found at i:12259 original size:25 final size:26

Alignment explanation


    Indices: 12231--12282  Score: 79
    Period size: 26  Copynumber: 2.0  Consensus size: 26

      12221 GGTTAGGGTA

                                      
      12231 GGTTGGGCTTA-ATTGGTTTAATTGG
          1 GGTTGGGCTTAGATTGGTTTAATTGG

                   *    *             
      12256 GGTTGGGTTTAGTTTGGTTTAATTGG
          1 GGTTGGGCTTAGATTGGTTTAATTGG

             
      12282 G
          1 G

      12283 TTGATGATTT


Statistics
Matches: 24,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  25   10  0.42
  26   14  0.58

ACGTcount: A:0.13, C:0.02, G:0.38, T:0.46


Consensus pattern (26 bp):   
GGTTGGGCTTAGATTGGTTTAATTGG

Found at i:13129 original size:22 final size:22

Alignment explanation


    Indices: 13091--13134  Score: 63
    Period size: 22  Copynumber: 2.0  Consensus size: 22

      13081 GATTGGTTCA

                                  
      13091 AATTCCAATCTATAATATAATT
          1 AATTCCAATCTATAATATAATT

                     *             
      13113 AATT-CAATTTATCAATATAATT
          1 AATTCCAATCTAT-AATATAATT

      13135 TTTTTTAAAA


Statistics
Matches: 20,  Mismatches: 1, Indels: 2
        0.87            0.04        0.09

Matches are distributed among these distances:
  21    7  0.35
  22   13  0.65

ACGTcount: A:0.45, C:0.11, G:0.00, T:0.43


Consensus pattern (22 bp):   
AATTCCAATCTATAATATAATT

Found at i:13171 original size:22 final size:23

Alignment explanation


    Indices: 13128--13171  Score: 72
    Period size: 23  Copynumber: 2.0  Consensus size: 23

      13118 AATTTATCAA

                     *             
      13128 TATAATTTTTTTTAAAATAAATT
          1 TATAATTTTGTTTAAAATAAATT

                                  
      13151 TATAATTTTGTTTAAAA-AAAT
          1 TATAATTTTGTTTAAAATAAAT

      13172 AAATTTATTG


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  22    4  0.20
  23   16  0.80

ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52


Consensus pattern (23 bp):   
TATAATTTTGTTTAAAATAAATT

Found at i:13500 original size:1 final size:1

Alignment explanation


    Indices: 13496--13520  Score: 50
    Period size: 1  Copynumber: 25.0  Consensus size: 1

      13486 TTCTTTTCCC

                                     
      13496 AAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAA

      13521 CCTTTTTTTT


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   24  1.00

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


Consensus pattern (1 bp):   
A

Done.