Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_590 ID=scaffold_590-JGI_221_v2.0

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: 5418
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.30


Found at i:1451 original size:33 final size:33

Alignment explanation


    Indices: 1400--1543  Score: 146
    Period size: 33  Copynumber: 4.1  Consensus size: 33

       1390 AAATTTAAAC

                                              
       1400 AAATTAATTACTAACACTTATTTAAGCTGAACTA
          1 AAATTAATT-CTAACACTTATTTAAGCTGAACTA

                                  *          
       1434 AAATTAATTCTAACACTTATTTGAGCTGAACT-
          1 AAATTAATTCTAACACTTATTTAAGCTGAACTA

                       *             *                 
       1466 AAATATAATAAACTAACTCATTTAATTTATTTAAGCTGAACTA
          1 AAAT-TAAT--TCTAA--C-----ACTTATTTAAGCTGAACTA

                                  *          
       1509 AAATTAATTCTAACACTTATTTGAGCTGAACTA
          1 AAATTAATTCTAACACTTATTTAAGCTGAACTA

              
       1542 AA
          1 AA

       1544 TATAATAAAC


Statistics
Matches: 92,  Mismatches: 7, Indels: 23
        0.75            0.06        0.19

Matches are distributed among these distances:
  32    4  0.04
  33   45  0.49
  34    9  0.10
  35    4  0.04
  37    1  0.01
  38    1  0.01
  40    4  0.04
  42   20  0.22
  43    4  0.04

ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36


Consensus pattern (33 bp):   
AAATTAATTCTAACACTTATTTAAGCTGAACTA

Found at i:1502 original size:75 final size:75

Alignment explanation


    Indices: 1417--1571  Score: 310
    Period size: 75  Copynumber: 2.1  Consensus size: 75

       1407 TTACTAACAC

                                                                             
       1417 TTATTTAAGCTGAACTAAAATTAATTCTAACACTTATTTGAGCTGAACTAAATATAATAAACTAA
          1 TTATTTAAGCTGAACTAAAATTAATTCTAACACTTATTTGAGCTGAACTAAATATAATAAACTAA

                      
       1482 CTCATTTAAT
         66 CTCATTTAAT

                                                                             
       1492 TTATTTAAGCTGAACTAAAATTAATTCTAACACTTATTTGAGCTGAACTAAATATAATAAACTAA
          1 TTATTTAAGCTGAACTAAAATTAATTCTAACACTTATTTGAGCTGAACTAAATATAATAAACTAA

                      
       1557 CTCATTTAAT
         66 CTCATTTAAT

                 
       1567 TTATT
          1 TTATT

       1572 CCAGCAAATT


Statistics
Matches: 80,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  75   80  1.00

ACGTcount: A:0.42, C:0.13, G:0.06, T:0.39


Consensus pattern (75 bp):   
TTATTTAAGCTGAACTAAAATTAATTCTAACACTTATTTGAGCTGAACTAAATATAATAAACTAA
CTCATTTAAT

Found at i:1509 original size:42 final size:42

Alignment explanation


    Indices: 1450--1571  Score: 138
    Period size: 42  Copynumber: 3.1  Consensus size: 42

       1440 ATTCTAACAC

                                                      
       1450 TTATTTGAGCTGAACTAAATATAATAAACTAACTCATTTAAT
          1 TTATTTGAGCTGAACTAAATATAATAAACTAACTCATTTAAT

                  *                               *   *
       1492 TTATTTAAGCTGAACTAAA-AT--T-AA-T---TC--TAACAC
          1 TTATTTGAGCTGAACTAAATATAATAAACTAACTCATTTA-AT

                                                      
       1525 TTATTTGAGCTGAACTAAATATAATAAACTAACTCATTTAAT
          1 TTATTTGAGCTGAACTAAATATAATAAACTAACTCATTTAAT

                 
       1567 TTATT
          1 TTATT

       1572 CCAGCAAATT


Statistics
Matches: 63,  Mismatches: 6, Indels: 22
        0.69            0.07        0.24

Matches are distributed among these distances:
  32    2  0.03
  33   19  0.30
  34    4  0.06
  36    1  0.02
  37    3  0.05
  38    3  0.05
  39    1  0.02
  41    4  0.06
  42   24  0.38
  43    2  0.03

ACGTcount: A:0.42, C:0.12, G:0.07, T:0.39


Consensus pattern (42 bp):   
TTATTTGAGCTGAACTAAATATAATAAACTAACTCATTTAAT

Done.