Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013570.1 Kokia drynarioides strain JFW-HI SEQ_128596, 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: 6737
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31


Found at i:228 original size:48 final size:48

Alignment explanation


    Indices: 172--273  Score: 141
    Period size: 48  Copynumber: 2.1  Consensus size: 48

        162 GGCATTTAAC

                                     *                      
        172 AAAGATGCATTTAACAAACAAAACATTTAATAATGAAAATTACTAAAA
          1 AAAGATGCATTTAACAAACAAAACACTTAATAATGAAAATTACTAAAA

                                 *         *   * *    *    *
        220 AAAGATGCATTTAACAAACAACACACTTAATGATGTAGATTATTAAAC
          1 AAAGATGCATTTAACAAACAAAACACTTAATAATGAAAATTACTAAAA

                  
        268 AAAGAT
          1 AAAGAT

        274 TCATGATACG


Statistics
Matches: 47,  Mismatches: 7, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  48   47  1.00

ACGTcount: A:0.54, C:0.12, G:0.09, T:0.25


Consensus pattern (48 bp):   
AAAGATGCATTTAACAAACAAAACACTTAATAATGAAAATTACTAAAA

Found at i:1285 original size:32 final size:32

Alignment explanation


    Indices: 1249--1311  Score: 90
    Period size: 32  Copynumber: 2.0  Consensus size: 32

       1239 GCCATCCATA

                         * *                
       1249 CATGTACCTAAAATATATTAATCAGCTAATTG
          1 CATGTACCTAAAACACATTAATCAGCTAATTG

                   * *                     
       1281 CATGTACTTGAAACACATTAATCAGCTAATT
          1 CATGTACCTAAAACACATTAATCAGCTAATT

       1312 AATTTCGGCT


Statistics
Matches: 27,  Mismatches: 4, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  32   27  1.00

ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33


Consensus pattern (32 bp):   
CATGTACCTAAAACACATTAATCAGCTAATTG

Found at i:1400 original size:39 final size:39

Alignment explanation


    Indices: 1357--1455  Score: 171
    Period size: 39  Copynumber: 2.5  Consensus size: 39

       1347 TTAATTTGTC

                   *      *                        
       1357 TCAAACTTAGACACCTTAAAAACAACTATTAAATATGTA
          1 TCAAACTAAGACACATTAAAAACAACTATTAAATATGTA

                 *                                 
       1396 TCAAAATAAGACACATTAAAAACAACTATTAAATATGTA
          1 TCAAACTAAGACACATTAAAAACAACTATTAAATATGTA

                                 
       1435 TCAAACTAAGACACATTAAAA
          1 TCAAACTAAGACACATTAAAA

       1456 CCCTATTTCA


Statistics
Matches: 56,  Mismatches: 4, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  39   56  1.00

ACGTcount: A:0.54, C:0.16, G:0.05, T:0.25


Consensus pattern (39 bp):   
TCAAACTAAGACACATTAAAAACAACTATTAAATATGTA

Found at i:4617 original size:13 final size:14

Alignment explanation


    Indices: 4583--4621  Score: 53
    Period size: 13  Copynumber: 2.9  Consensus size: 14

       4573 TATCTCTTTT

                *         
       4583 TCTTCCTTTTCATC
          1 TCTTTCTTTTCATC

             *            
       4597 TTTTTCTTTTC-TC
          1 TCTTTCTTTTCATC

                        
       4610 TCTTTCTTTTCA
          1 TCTTTCTTTTCA

       4622 CTTTCTTTGC


Statistics
Matches: 21,  Mismatches: 3, Indels: 2
        0.81            0.12        0.08

Matches are distributed among these distances:
  13   12  0.57
  14    9  0.43

ACGTcount: A:0.05, C:0.28, G:0.00, T:0.67


Consensus pattern (14 bp):   
TCTTTCTTTTCATC

Found at i:4678 original size:19 final size:20

Alignment explanation


    Indices: 4641--4679  Score: 69
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       4631 CTCTTTTCTC

                                
       4641 TCAATTTTCCTTTCTTTTTT
          1 TCAATTTTCCTTTCTTTTTT

                     *         
       4661 TCAATTTTCTTTTCTTTTT
          1 TCAATTTTCCTTTCTTTTT

       4680 CATTCTCACT


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  20   18  1.00

ACGTcount: A:0.10, C:0.18, G:0.00, T:0.72


Consensus pattern (20 bp):   
TCAATTTTCCTTTCTTTTTT
Done.