Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001386.1 Kokia drynarioides strain JFW-HI SEQ_112862, 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: 2020
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.39


Found at i:37 original size:16 final size:16

Alignment explanation


    Indices: 16--65  Score: 52
    Period size: 16  Copynumber: 3.2  Consensus size: 16

          6 TGATGGGGAT

                            
         16 ATTATTTTGATAATTA
          1 ATTATTTTGATAATTA

                     *       
         32 ATTATTTT-TTATATT-
          1 ATTATTTTGATA-ATTA

                     *      
         47 A-TATTTTGGTAATTA
          1 ATTATTTTGATAATTA

                
         62 ATTA
          1 ATTA

         66 GTTAGGTTTA


Statistics
Matches: 28,  Mismatches: 2, Indels: 8
        0.74            0.05        0.21

Matches are distributed among these distances:
  14    9  0.32
  15    6  0.21
  16   13  0.46

ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60


Consensus pattern (16 bp):   
ATTATTTTGATAATTA

Found at i:350 original size:20 final size:21

Alignment explanation


    Indices: 325--367  Score: 61
    Period size: 21  Copynumber: 2.1  Consensus size: 21

        315 TACTTACTAC

                                 
        325 TACTAAC-AACAAAATAAAAT
          1 TACTAACTAACAAAATAAAAT

                     *      *    
        345 TACTAACTAGCAAAATTAAAT
          1 TACTAACTAACAAAATAAAAT

              
        366 TA
          1 TA

        368 AAGTAAATTA


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  20    7  0.35
  21   13  0.65

ACGTcount: A:0.58, C:0.14, G:0.02, T:0.26


Consensus pattern (21 bp):   
TACTAACTAACAAAATAAAAT

Found at i:710 original size:4 final size:4

Alignment explanation


    Indices: 703--774  Score: 56
    Period size: 4  Copynumber: 17.0  Consensus size: 4

        693 TACTTTTTTT

                                   *      *      *                    
        703 TTTC TTTC TCCTTC TTCTC CTTC TTCC TTCTT TTTC TTTC TTTC TTTC
          1 TTTC TTTC T--TTC TT-TC TTTC TTTC TT-TC TTTC TTTC TTTC TTTC

                     *                    
        751 TTTC TCTTT TTTC TTTC TTT- TTTC
          1 TTTC T-TTC TTTC TTTC TTTC TTTC

        775 CTTCAATTTT


Statistics
Matches: 54,  Mismatches: 8, Indels: 12
        0.73            0.11        0.16

Matches are distributed among these distances:
   3    3  0.06
   4   39  0.72
   5    8  0.15
   6    4  0.07

ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71


Consensus pattern (4 bp):   
TTTC

Found at i:763 original size:17 final size:18

Alignment explanation


    Indices: 703--770  Score: 70
    Period size: 17  Copynumber: 3.8  Consensus size: 18

        693 TACTTTTTTT

                                
        703 TTTCTTTCTCCTTC-TTCTC
          1 TTTCTTTCT--TTCTTTCTC

            *       *      *  
        722 CTTC-TTCCTTCTTTTTC
          1 TTTCTTTCTTTCTTTCTC

                              
        739 TTTCTTTCTTTCTTTCTC
          1 TTTCTTTCTTTCTTTCTC

                           
        757 TTT-TTTCTTTCTTT
          1 TTTCTTTCTTTCTTT

        771 TTTCCTTCAA


Statistics
Matches: 41,  Mismatches: 6, Indels: 6
        0.77            0.11        0.11

Matches are distributed among these distances:
  16    3  0.07
  17   18  0.44
  18   17  0.41
  19    3  0.07

ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71


Consensus pattern (18 bp):   
TTTCTTTCTTTCTTTCTC
Done.