Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005876.1 Kokia drynarioides strain JFW-HI SEQ_120205, 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: 12104
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.27


Found at i:461 original size:30 final size:30

Alignment explanation


    Indices: 400--656  Score: 290
    Period size: 30  Copynumber: 8.6  Consensus size: 30

        390 CTAAACTATT

                   *        *     **      
        400 CAAAAATTCCA-TTTTCACCCCCGAACTTC
          1 CAAAAATCCCATTTTTAACCCCAAAACTTC

                            *          *  
        429 CAAAAATCCCATTTTTTACCCCAAAACCTC
          1 CAAAAATCCCATTTTTAACCCCAAAACTTC

                   *              *        
        459 CAAAAATTCCATTTTTTAACCCTAAAA-TTC
          1 CAAAAATCCCA-TTTTTAACCCCAAAACTTC

                                 *        
        489 CAAAAATCCCATTTTTAACCCTAAAACTTC
          1 CAAAAATCCCATTTTTAACCCCAAAACTTC

                                * *       
        519 CAAAAATCCCATTTTTAACCTCGAAACTTC
          1 CAAAAATCCCATTTTTAACCCCAAAACTTC

                                       *   
        549 CAAAAA-CTCCATTTTT-ACCCCAAAAATTC
          1 CAAAAATC-CCATTTTTAACCCCAAAACTTC

            *                     *       
        578 TAAAAATCCCATTTTTAACCCCGAAACTTC
          1 CAAAAATCCCATTTTTAACCCCAAAACTTC

                                * *        
        608 CAAAAATCCCATTTTTAACCTCGAAACTTGC
          1 CAAAAATCCCATTTTTAACCCCAAAACTT-C

            *                  
        639 AAAAAATTCCC-TTTTTAA
          1 CAAAAA-TCCCATTTTTAA

        657 ACCTGAATTT


Statistics
Matches: 198,  Mismatches: 22, Indels: 14
        0.85            0.09        0.06

Matches are distributed among these distances:
  29   49  0.25
  30  119  0.60
  31   26  0.13
  32    4  0.02

ACGTcount: A:0.38, C:0.30, G:0.02, T:0.30


Consensus pattern (30 bp):   
CAAAAATCCCATTTTTAACCCCAAAACTTC

Found at i:577 original size:89 final size:90

Alignment explanation


    Indices: 400--643  Score: 339
    Period size: 89  Copynumber: 2.7  Consensus size: 90

        390 CTAAACTATT

                   *        *     **                      *   * *    *       
        400 CAAAAATTCCA-TTTTCACCCCCGAACTTCCAAAAATCCCATTTTTTACCCCAAAACCTCCAAAA
          1 CAAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATCCCATTTTTAACCTCGAAACTTCCAAAA

             *               *       
        464 ATTCCATTTTTTAACCCTAAAATTC
         66 ACTCCATTTTTTAACCCAAAAATTC

                                 *                                           
        489 CAAAAATCCCATTTTTAACCCTAAAACTTCCAAAAATCCCATTTTTAACCTCGAAACTTCCAAAA
          1 CAAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATCCCATTTTTAACCTCGAAACTTCCAAAA

                         *           
        554 ACTCCA-TTTTTACCCCAAAAATTC
         66 ACTCCATTTTTTAACCCAAAAATTC

            *                     *                                    *     
        578 TAAAAATCCCATTTTTAACCCCGAAACTTCCAAAAATCCCATTTTTAACCTCGAAACTTGCAAAA
          1 CAAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATCCCATTTTTAACCTCGAAACTTCCAAAA

             
        643 A
         66 A

        644 ATTCCCTTTT


Statistics
Matches: 138,  Mismatches: 16, Indels: 2
        0.88            0.10        0.01

Matches are distributed among these distances:
  89   88  0.64
  90   50  0.36

ACGTcount: A:0.39, C:0.30, G:0.02, T:0.29


Consensus pattern (90 bp):   
CAAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATCCCATTTTTAACCTCGAAACTTCCAAAA
ACTCCATTTTTTAACCCAAAAATTC

Found at i:6045 original size:22 final size:21

Alignment explanation


    Indices: 6020--6062  Score: 52
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       6010 CCTTGCTAGA

                                   
       6020 AGAAGGAGCTTGAA-AAATTAAG
          1 AGAA-GAG-TTGAAGAAATTAAG

                 *               
       6042 AGAAGTGTTGAAGAAATTAAG
          1 AGAAGAGTTGAAGAAATTAAG

       6063 TCTCAACTTC


Statistics
Matches: 19,  Mismatches: 1, Indels: 3
        0.83            0.04        0.13

Matches are distributed among these distances:
  20    5  0.26
  21   10  0.53
  22    4  0.21

ACGTcount: A:0.49, C:0.02, G:0.28, T:0.21


Consensus pattern (21 bp):   
AGAAGAGTTGAAGAAATTAAG
Done.