Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01015069.1 Kokia drynarioides strain JFW-HI SEQ_130113, 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: 6074
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.31

Warning! 432 characters in sequence are not A, C, G, or T


Found at i:5375 original size:33 final size:32

Alignment explanation


    Indices: 5337--5430  Score: 76
    Period size: 26  Copynumber: 3.1  Consensus size: 32

       5327 AGCGTTCGAA

                                             
       5337 CAATTAAGTTCTTTGATAGTTAAAGTTAACAAT
          1 CAATTAAGTTCTTTGATAGTTAAAGTT-ACAAT

                            *  *    *  *    
       5370 CAATT-AG-----T-AAAGATAAAATTCCAAT
          1 CAATTAAGTTCTTTGATAGTTAAAGTTACAAT

            *                                
       5395 AAATTAAGTTCTTTGATAGTTAAAGTTCACAAT
          1 CAATTAAGTTCTTTGATAGTTAAAGTT-ACAAT

               
       5428 CAA
          1 CAA

       5431 CTATTAAAGA


Statistics
Matches: 43,  Mismatches: 10, Indels: 16
        0.62            0.14        0.23

Matches are distributed among these distances:
  25    8  0.19
  26   11  0.26
  27    1  0.02
  31    1  0.02
  32   11  0.26
  33   11  0.26

ACGTcount: A:0.44, C:0.11, G:0.11, T:0.35


Consensus pattern (32 bp):   
CAATTAAGTTCTTTGATAGTTAAAGTTACAAT

Found at i:5394 original size:25 final size:26

Alignment explanation


    Indices: 5366--5463  Score: 65
    Period size: 25  Copynumber: 3.6  Consensus size: 26

       5356 TTAAAGTTAA

                                      
       5366 CAATCAATT-AGTAAAGATAAAATTC
          1 CAATCAATTAAGTAAAGATAAAATTC

                *               *  *    *   
       5391 CAATAAATTAAGTTCTTTGATAGTTAAAGTTC
          1 CAATCAATTAAG-----T-AAAGATAAAATTC

                    *   *              
       5423 ACAATCAACT-ATTAAAGATAAAATTC
          1 -CAATCAATTAAGTAAAGATAAAATTC

                           
       5449 CAATCAATTAAGTAA
          1 CAATCAATTAAGTAA

       5464 TGGTGTAAGC


Statistics
Matches: 52,  Mismatches: 12, Indels: 17
        0.64            0.15        0.21

Matches are distributed among these distances:
  25   16  0.31
  26   16  0.31
  27    1  0.02
  31    1  0.02
  32   11  0.21
  33    7  0.13

ACGTcount: A:0.48, C:0.12, G:0.08, T:0.32


Consensus pattern (26 bp):   
CAATCAATTAAGTAAAGATAAAATTC

Found at i:5428 original size:58 final size:58

Alignment explanation


    Indices: 5338--5461  Score: 212
    Period size: 58  Copynumber: 2.1  Consensus size: 58

       5328 GCGTTCGAAC

                                               *                      
       5338 AATTAAGTTCTTTGATAGTTAAAGTTAACAATCAATTAGTAAAGATAAAATTCCAATA
          1 AATTAAGTTCTTTGATAGTTAAAGTTAACAATCAACTAGTAAAGATAAAATTCCAATA

                                      *           *                  *
       5396 AATTAAGTTCTTTGATAGTTAAAGTTCACAATCAACTATTAAAGATAAAATTCCAATC
          1 AATTAAGTTCTTTGATAGTTAAAGTTAACAATCAACTAGTAAAGATAAAATTCCAATA

                    
       5454 AATTAAGT
          1 AATTAAGT

       5462 AATGGTGTAA


Statistics
Matches: 62,  Mismatches: 4, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  58   62  1.00

ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35


Consensus pattern (58 bp):   
AATTAAGTTCTTTGATAGTTAAAGTTAACAATCAACTAGTAAAGATAAAATTCCAATA
Done.