Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3308

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: 29795
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32


Found at i:7561 original size:22 final size:23

Alignment explanation


    Indices: 7535--7583  Score: 57
    Period size: 24  Copynumber: 2.1  Consensus size: 23

       7525 TACAAGCACT

                    *               
       7535 TATA-TGATAATA-ATAAGATATA
          1 TATACTGAAAATACATAAG-TATA

                                    
       7557 TATATCTGAAAATACATAAGTATA
          1 TATA-CTGAAAATACATAAGTATA

               
       7581 TAT
          1 TAT

       7584 GAATAGAGAT


Statistics
Matches: 23,  Mismatches: 1, Indels: 4
        0.82            0.04        0.14

Matches are distributed among these distances:
  22    4  0.17
  24   14  0.61
  25    5  0.22

ACGTcount: A:0.51, C:0.04, G:0.08, T:0.37


Consensus pattern (23 bp):   
TATACTGAAAATACATAAGTATA

Found at i:7628 original size:3 final size:3

Alignment explanation


    Indices: 7617--7670  Score: 56
    Period size: 3  Copynumber: 17.7  Consensus size: 3

       7607 CAATAATACC

                 *           *           *                               
       7617 AAT ACT AAT AAT AGT AA- AGAT GAT AAT AAT AAT AAT ATAT AAT AAT
          1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT A-AT AAT AAT

                      
       7663 AAT AAT AA
          1 AAT AAT AA

       7671 AGTTAACAAA


Statistics
Matches: 42,  Mismatches: 6, Indels: 6
        0.78            0.11        0.11

Matches are distributed among these distances:
   2    1  0.02
   3   38  0.90
   4    3  0.07

ACGTcount: A:0.61, C:0.02, G:0.06, T:0.31


Consensus pattern (3 bp):   
AAT

Found at i:7660 original size:16 final size:16

Alignment explanation


    Indices: 7639--7669  Score: 62
    Period size: 16  Copynumber: 1.9  Consensus size: 16

       7629 AGTAAAGATG

                            
       7639 ATAATAATAATAATAT
          1 ATAATAATAATAATAT

                           
       7655 ATAATAATAATAATA
          1 ATAATAATAATAATA

       7670 AAGTTAACAA


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   15  1.00

ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35


Consensus pattern (16 bp):   
ATAATAATAATAATAT

Found at i:12917 original size:3 final size:3

Alignment explanation


    Indices: 12897--12939  Score: 59
    Period size: 3  Copynumber: 14.3  Consensus size: 3

      12887 CAAGTGATTT

                     *    *  *                                       
      12897 ATC ATC AAC ATG ACC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
          1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A

      12940 CACCATTCTA


Statistics
Matches: 34,  Mismatches: 6, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
   3   34  1.00

ACGTcount: A:0.37, C:0.33, G:0.02, T:0.28


Consensus pattern (3 bp):   
ATC

Found at i:20416 original size:14 final size:15

Alignment explanation


    Indices: 20379--20417  Score: 62
    Period size: 14  Copynumber: 2.7  Consensus size: 15

      20369 CTTTGCAAAA

                           
      20379 GGCCTAAAAATTAAT
          1 GGCCTAAAAATTAAT

              *            
      20394 -GACTAAAAATTAAT
          1 GGCCTAAAAATTAAT

                      
      20408 GGCCTAAAAA
          1 GGCCTAAAAA

      20418 AAAAATAGAT


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  14   13  0.62
  15    8  0.38

ACGTcount: A:0.51, C:0.13, G:0.13, T:0.23


Consensus pattern (15 bp):   
GGCCTAAAAATTAAT

Found at i:26090 original size:20 final size:21

Alignment explanation


    Indices: 26052--26091  Score: 64
    Period size: 21  Copynumber: 2.0  Consensus size: 21

      26042 ATCTGCTCAA

                        *        
      26052 ACTCCACCTGTTTTGGAGTAC
          1 ACTCCACCTGTTGTGGAGTAC

                                
      26073 ACTCCACCTG-TGTGGAGTA
          1 ACTCCACCTGTTGTGGAGTA

      26092 TTGCTCGTCT


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  20    8  0.44
  21   10  0.56

ACGTcount: A:0.20, C:0.28, G:0.23, T:0.30


Consensus pattern (21 bp):   
ACTCCACCTGTTGTGGAGTAC
Done.