Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01014791.1 Kokia drynarioides strain JFW-HI SEQ_129833, 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: 13471
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35


Found at i:1719 original size:153 final size:153

Alignment explanation


    Indices: 1427--1728  Score: 360
    Period size: 153  Copynumber: 2.0  Consensus size: 153

       1417 ACTAAGCGAC

                  *                        *                              * *
       1427 TGCAATCTTGGTGAAGAAGATATTCCTAGTGCTATTTCTCGTCTATCCTCATTGCGATGTCTTGC
          1 TGCAATATTGGTGAAGAAGATATTCCTAGTGATATTTCTCGTCTATCCTCATTGCGATGTCTAGA

                                                               * *      ***  
       1492 TCTTAGGGGAAACAATTTCAACAGCATACCGGCGTCTCTTACTCGACTCTCGAGGCTTCACTTTC
         66 TCTTAGGGGAAACAATTTCAACAGCATACCGGCGTCTCTTACTCGACTCTCCAAGCTTCAAAATC

                                   
       1557 TTGATTTGTCAAATTGCAGCCTG
        131 TTGATTTGTCAAATTGCAGCCTG

                            *          *           *                   *     
       1580 TGCAATATTGGTGAAGGAGATATTCCTGGTGATATTTCTGGTCTATCCTCATTG-GATATTCTAG
          1 TGCAATATTGGTGAAGAAGATATTCCTAGTGATATTTCTCGTCTATCCTCATTGCGAT-GTCTAG

                    *             *    *  * *    *             *             
       1644 ATCTTA-GTGATAACAATTTCACCAGCGTAGCTGCGTTTCTTACTC-ATCTTTCCAAGCTTCAAA
         65 ATCTTAGGGGA-AACAATTTCAACAGCATACCGGCGTCTCTTACTCGA-CTCTCCAAGCTTCAAA

                                   
       1707 ATCTTAGA-TTGTCAAATTGCAG
        128 ATCTT-GATTTGTCAAATTGCAG

       1729 TGAGCTTGAA


Statistics
Matches: 125,  Mismatches: 20, Indels: 8
        0.82            0.13        0.05

Matches are distributed among these distances:
 152    7  0.06
 153  116  0.93
 154    2  0.02

ACGTcount: A:0.24, C:0.22, G:0.19, T:0.36


Consensus pattern (153 bp):   
TGCAATATTGGTGAAGAAGATATTCCTAGTGATATTTCTCGTCTATCCTCATTGCGATGTCTAGA
TCTTAGGGGAAACAATTTCAACAGCATACCGGCGTCTCTTACTCGACTCTCCAAGCTTCAAAATC
TTGATTTGTCAAATTGCAGCCTG

Found at i:6560 original size:22 final size:20

Alignment explanation


    Indices: 6528--6580  Score: 72
    Period size: 22  Copynumber: 2.6  Consensus size: 20

       6518 CATTACATAA

                        *       
       6528 AATAATATAAATTTTTAAAT
          1 AATAATATAAATCTTTAAAT

                                  
       6548 AGATAATCATAAATCTTTAAAT
          1 A-ATAAT-ATAAATCTTTAAAT

                        
       6570 AATAAT-TAAAT
          1 AATAATATAAAT

       6581 AAACTAATTA


Statistics
Matches: 30,  Mismatches: 1, Indels: 5
        0.83            0.03        0.14

Matches are distributed among these distances:
  19    5  0.17
  20    1  0.03
  21   10  0.33
  22   14  0.47

ACGTcount: A:0.55, C:0.04, G:0.02, T:0.40


Consensus pattern (20 bp):   
AATAATATAAATCTTTAAAT

Found at i:11937 original size:153 final size:153

Alignment explanation


    Indices: 11636--11914  Score: 339
    Period size: 153  Copynumber: 1.8  Consensus size: 153

      11626 TCTAAGGGAC

                  * *                      *                  *              
      11636 TGCAATCTTGGTGAAGGAGATATTCCTAGTGCTATTTCTCGTCTATCATCTTTGAAACATCTTGA
          1 TGCAATATGGGTGAAGGAGATATTCCTAGTGATATTTCTCGTCTATCATCATTGAAACATCTTGA

                     *     *                                          *      
      11701 TCTTAAGGGTAACAATTTCAACAGCATACCGACATCTCTTACTCGACTCTCCAAGCTTGAATATC
         66 TCTTAAGGGAAACAAATTCAACAGCATACCGACATCTCTTACTCGACTCTCCAAGCTTCAATATC

                 *       *         
      11766 TTAAATTGTCAAATTGCAGCCTG
        131 TTAAAGTGTCAAACTGCAGCCTG

                                                   *       *       * **      
      11789 TGCAATATGGGTGAAGGAGATATTCCTAGTGATATTTCTGGTCTATCCTCATTGAGATTTCTT-A
          1 TGCAATATGGGTGAAGGAGATATTCCTAGTGATATTTCTCGTCTATCATCATTGAAACATCTTGA

                                  *             *           *  *     *      
      11853 GTCTT-AGTGGAAACAAATTCACCAGCATAGCCG-CGTCTCTTACTCGTCTTTCCAATCTTCAA
         66 -TCTTAAG-GGAAACAAATTCAACAGCATA-CCGACATCTCTTACTCGACTCTCCAAGCTTCAA

      11915 AGTCTTGGAG


Statistics
Matches: 106,  Mismatches: 17, Indels: 6
        0.82            0.13        0.05

Matches are distributed among these distances:
 152    3  0.03
 153  100  0.94
 154    3  0.03

ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34


Consensus pattern (153 bp):   
TGCAATATGGGTGAAGGAGATATTCCTAGTGATATTTCTCGTCTATCATCATTGAAACATCTTGA
TCTTAAGGGAAACAAATTCAACAGCATACCGACATCTCTTACTCGACTCTCCAAGCTTCAATATC
TTAAAGTGTCAAACTGCAGCCTG
Done.