Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006870.1 Kokia drynarioides strain JFW-HI SEQ_121470, whole genome shotgun sequence

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: 13789
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35


Found at i:1433 original size:31 final size:32

Alignment explanation


    Indices: 1395--1463  Score: 81
    Period size: 31  Copynumber: 2.2  Consensus size: 32

       1385 TAGGTCAAAT

                             * *             
       1395 TTAAAATTTG-AGAATTTAGAAAATA-AAAAGA
          1 TTAAAATTTGAAGAATTCAAAAAATACAAAA-A

                        *                   
       1426 TTAAAA-TTGAATAATTCAAAAAATACAAAAA
          1 TTAAAATTTGAAGAATTCAAAAAATACAAAAA

                   
       1457 TTAAAAT
          1 TTAAAAT

       1464 AAATCAAATT


Statistics
Matches: 32,  Mismatches: 3, Indels: 5
        0.80            0.08        0.12

Matches are distributed among these distances:
  30    3  0.09
  31   25  0.78
  32    4  0.12

ACGTcount: A:0.61, C:0.03, G:0.07, T:0.29


Consensus pattern (32 bp):   
TTAAAATTTGAAGAATTCAAAAAATACAAAAA

Found at i:13578 original size:19 final size:19

Alignment explanation


    Indices: 13554--13590  Score: 56
    Period size: 19  Copynumber: 1.9  Consensus size: 19

      13544 TATTATTAAG

                         *     
      13554 ATATTTATAATTATAATAA
          1 ATATTTATAATTAAAATAA

                    *         
      13573 ATATTTATTATTAAAATA
          1 ATATTTATAATTAAAATA

      13591 TTAATAATTA


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  19   16  1.00

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (19 bp):   
ATATTTATAATTAAAATAA

Found at i:13591 original size:15 final size:15

Alignment explanation


    Indices: 13536--13592  Score: 60
    Period size: 15  Copynumber: 3.5  Consensus size: 15

      13526 TTTATATTAC

                           
      13536 AAAATATTTATTATT
          1 AAAATATTTATTATT

              *              *
      13551 AAGATATTTATAATTATA
          1 AAAATA-TT-T-ATTATT

                            
      13569 ATAAATATTTATTATT
          1 A-AAATATTTATTATT

                    
      13585 AAAATATT
          1 AAAATATT

      13593 AATAATTAAC


Statistics
Matches: 34,  Mismatches: 4, Indels: 8
        0.74            0.09        0.17

Matches are distributed among these distances:
  15   12  0.35
  16    8  0.24
  17    2  0.06
  18    8  0.24
  19    4  0.12

ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49


Consensus pattern (15 bp):   
AAAATATTTATTATT
Done.