Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01015233.1 Kokia drynarioides strain JFW-HI SEQ_130278, 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: 371888
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34

Warning! 345 characters in sequence are not A, C, G, or T


File 2 of 2

Found at i:353731 original size:13 final size:14

Alignment explanation


    Indices: 353713--353741  Score: 51
    Period size: 14  Copynumber: 2.1  Consensus size: 14

     353703 CCCGTTTTGT

                          
     353713 AAACATC-ATTTTA
          1 AAACATCAATTTTA

                          
     353726 AAACATCAATTTTA
          1 AAACATCAATTTTA

              
     353740 AA
          1 AA

     353742 CAGCTTTTTA


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  13    7  0.47
  14    8  0.53

ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34


Consensus pattern (14 bp):   
AAACATCAATTTTA

Found at i:354061 original size:2 final size:2

Alignment explanation


    Indices: 354054--354078  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

     354044 TACATACATG

                                                 
     354054 AC AC AC AC AC AC AC AC AC AC AC AC A
          1 AC AC AC AC AC AC AC AC AC AC AC AC A

     354079 TATGTATATA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00


Consensus pattern (2 bp):   
AC

Found at i:361436 original size:33 final size:35

Alignment explanation


    Indices: 361367--361436  Score: 101
    Period size: 33  Copynumber: 2.1  Consensus size: 35

     361357 TATTTTTCTG

                                           *   
     361367 TTATGTTATGCTTGAAAGTTTTGTTAAGAGATTAC
          1 TTATGTTATGCTTGAAAGTTTTGTTAAGAGACTAC

                                                
     361402 TTATGTT-TGCTTGAAAG-TTTGTTAATGA-ACTAC
          1 TTATGTTATGCTTGAAAGTTTTGTTAA-GAGACTAC

              
     361435 TT
          1 TT

     361437 GTATTTATAT


Statistics
Matches: 33,  Mismatches: 1, Indels: 4
        0.87            0.03        0.11

Matches are distributed among these distances:
  33   14  0.42
  34   12  0.36
  35    7  0.21

ACGTcount: A:0.27, C:0.07, G:0.19, T:0.47


Consensus pattern (35 bp):   
TTATGTTATGCTTGAAAGTTTTGTTAAGAGACTAC

Found at i:371814 original size:26 final size:28

Alignment explanation


    Indices: 371785--371841  Score: 82
    Period size: 26  Copynumber: 2.1  Consensus size: 28

     371775 CATGCATTGA

                        *  *            
     371785 AATTTAGTTTAGTTTTA-AC-TTAGATT
          1 AATTTAGTTTAGATTAATACTTTAGATT

                                        
     371811 AATTTAGTTTAGATTAATACTTTAGATT
          1 AATTTAGTTTAGATTAATACTTTAGATT

               
     371839 AAT
          1 AAT

     371842 ATCCTCCACA


Statistics
Matches: 27,  Mismatches: 2, Indels: 2
        0.87            0.06        0.06

Matches are distributed among these distances:
  26   15  0.56
  27    2  0.07
  28   10  0.37

ACGTcount: A:0.35, C:0.04, G:0.11, T:0.51


Consensus pattern (28 bp):   
AATTTAGTTTAGATTAATACTTTAGATT

Found at i:371836 original size:13 final size:13

Alignment explanation


    Indices: 371804--371842  Score: 51
    Period size: 13  Copynumber: 2.8  Consensus size: 13

     371794 TAGTTTTAAC

                         * 
     371804 TTAGATTAATTTAGT
          1 TTAGATTAA--TACT

                         
     371819 TTAGATTAATACT
          1 TTAGATTAATACT

                       
     371832 TTAGATTAATA
          1 TTAGATTAATA

     371843 TCCTCCACAA


Statistics
Matches: 23,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  13   14  0.61
  15    9  0.39

ACGTcount: A:0.38, C:0.03, G:0.10, T:0.49


Consensus pattern (13 bp):   
TTAGATTAATACT

Done.