Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1068

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: 2724
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.29


Found at i:2439 original size:52 final size:52

Alignment explanation


    Indices: 2354--2478  Score: 223
    Period size: 52  Copynumber: 2.4  Consensus size: 52

       2344 ATATGAAAAG

                *                       *                       
       2354 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
          1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT

                                    *                           
       2406 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
          1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT

                                 
       2458 TTGCCTGCATGTATCGATACA
          1 TTGCCTGCATGTATCGATACA

       2479 AAGATCAGTG


Statistics
Matches: 70,  Mismatches: 3, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  52   70  1.00

ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36


Consensus pattern (52 bp):   
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT

Found at i:2491 original size:52 final size:51

Alignment explanation


    Indices: 2354--2498  Score: 211
    Period size: 52  Copynumber: 2.8  Consensus size: 51

       2344 ATATGAAAAG

                *                                               
       2354 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
          1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT

                                    *   *                       
       2406 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
          1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT

                                  *                   
       2458 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
          1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA

       2499 ATGTATCGAT


Statistics
Matches: 85,  Mismatches: 6, Indels: 4
        0.89            0.06        0.04

Matches are distributed among these distances:
  51    2  0.02
  52   83  0.98

ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34


Consensus pattern (51 bp):   
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT

Found at i:2505 original size:13 final size:13

Alignment explanation


    Indices: 2487--2511  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       2477 CAAAGATCAG

                         
       2487 TGTATCGATACAA
          1 TGTATCGATACAA

                        
       2500 TGTATCGATACA
          1 TGTATCGATACA

       2512 TGTGAGTAAT


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


Consensus pattern (13 bp):   
TGTATCGATACAA

Found at i:2595 original size:13 final size:13

Alignment explanation


    Indices: 2577--2601  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       2567 CAAAAAAATA

                         
       2577 TGTATCGATACAT
          1 TGTATCGATACAT

                        
       2590 TGTATCGATACA
          1 TGTATCGATACA

       2602 ACATTTTATG


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:2597 original size:33 final size:33

Alignment explanation


    Indices: 2555--2621  Score: 98
    Period size: 33  Copynumber: 2.0  Consensus size: 33

       2545 AGTAGCTTAA

                                             
       2555 ATTGTATCGATACAAAAAAATATGTATCGATAC
          1 ATTGTATCGATACAAAAAAATATGTATCGATAC

                           * ***             
       2588 ATTGTATCGATACAACATTTTATGTATCGATAC
          1 ATTGTATCGATACAAAAAAATATGTATCGATAC

             
       2621 A
          1 A

       2622 AATCGTTGAA


Statistics
Matches: 30,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  33   30  1.00

ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34


Consensus pattern (33 bp):   
ATTGTATCGATACAAAAAAATATGTATCGATAC
Done.