Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1218

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: 18970
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


Found at i:2443 original size:13 final size:13

Alignment explanation


    Indices: 2425--2449  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       2415 AGATTGCATA

                         
       2425 GTATCGATACATT
          1 GTATCGATACATT

                        
       2438 GTATCGATACAT
          1 GTATCGATACAT

       2450 GACCAAATGT


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36


Consensus pattern (13 bp):   
GTATCGATACATT

Found at i:2462 original size:20 final size:21

Alignment explanation


    Indices: 2437--2489  Score: 65
    Period size: 20  Copynumber: 2.6  Consensus size: 21

       2427 ATCGATACAT

                             *    
       2437 TGTATCGATACATG-ACCA-AA
          1 TGTATCGATACATGTA-AAGAA

                       *         
       2457 TGTATCGATACTTGTAAAGAA
          1 TGTATCGATACATGTAAAGAA

                        
       2478 TGTATCGATACA
          1 TGTATCGATACA

       2490 GGTCATTGGC


Statistics
Matches: 28,  Mismatches: 3, Indels: 3
        0.82            0.09        0.09

Matches are distributed among these distances:
  20   14  0.50
  21   14  0.50

ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30


Consensus pattern (21 bp):   
TGTATCGATACATGTAAAGAA

Found at i:8671 original size:13 final size:13

Alignment explanation


    Indices: 8653--8677  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       8643 TAGCATTCTC

                         
       8653 TGTATCGATACAT
          1 TGTATCGATACAT

                        
       8666 TGTATCGATACA
          1 TGTATCGATACA

       8678 AACGGTTTAT


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36


Consensus pattern (13 bp):   
TGTATCGATACAT

Found at i:10562 original size:21 final size:22

Alignment explanation


    Indices: 10522--10566  Score: 74
    Period size: 22  Copynumber: 2.0  Consensus size: 22

      10512 AGAAATTGTT

                                  
      10522 AAATTGTTTTATTAAGGGGGAG
          1 AAATTGTTTTATTAAGGGGGAG

                                   
      10544 AAATT-TTTTGATTAAGGGGGAG
          1 AAATTGTTTT-ATTAAGGGGGAG

             
      10566 A
          1 A

      10567 GATAAGAAAA


Statistics
Matches: 22,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
  21    4  0.18
  22   18  0.82

ACGTcount: A:0.33, C:0.00, G:0.31, T:0.36


Consensus pattern (22 bp):   
AAATTGTTTTATTAAGGGGGAG

Found at i:11139 original size:13 final size:13

Alignment explanation


    Indices: 11121--11145  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

      11111 AGATTGCACA

                         
      11121 GTATCGATACATT
          1 GTATCGATACATT

                        
      11134 GTATCGATACAT
          1 GTATCGATACAT

      11146 GACCAAATGT


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36


Consensus pattern (13 bp):   
GTATCGATACATT

Found at i:11253 original size:13 final size:13

Alignment explanation


    Indices: 11235--11260  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

      11225 ACACACAATA

                         
      11235 TGTATCGATACAT
          1 TGTATCGATACAT

                         
      11248 TGTATCGATACAT
          1 TGTATCGATACAT

      11261 CCCAAAATGT


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:0.31, C:0.15, G:0.15, T:0.38


Consensus pattern (13 bp):   
TGTATCGATACAT

Found at i:11276 original size:33 final size:32

Alignment explanation


    Indices: 11215--11282  Score: 109
    Period size: 33  Copynumber: 2.1  Consensus size: 32

      11205 CTTTAACTGT

                              *             
      11215 TTGTATCGATACACACAATATGTATCGATACA
          1 TTGTATCGATACACACAAAATGTATCGATACA

                           *                 
      11247 TTGTATCGATACATCCCAAAATGTATCGATACA
          1 TTGTATCGATACA-CACAAAATGTATCGATACA

               
      11280 TTG
          1 TTG

      11283 GCTTGTAACG


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

Matches are distributed among these distances:
  32   13  0.39
  33   20  0.61

ACGTcount: A:0.35, C:0.19, G:0.13, T:0.32


Consensus pattern (32 bp):   
TTGTATCGATACACACAAAATGTATCGATACA

Found at i:12546 original size:13 final size:13

Alignment explanation


    Indices: 12528--12553  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

      12518 CAATTTTTTG

                         
      12528 TGTATCGATACAT
          1 TGTATCGATACAT

                         
      12541 TGTATCGATACAT
          1 TGTATCGATACAT

      12554 ACTTGCTGTA


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:0.31, C:0.15, G:0.15, T:0.38


Consensus pattern (13 bp):   
TGTATCGATACAT
Done.