Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01014949.1 Kokia drynarioides strain JFW-HI SEQ_129992, 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: 8351
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34


Found at i:377 original size:17 final size:16

Alignment explanation


    Indices: 346--379  Score: 50
    Period size: 17  Copynumber: 2.1  Consensus size: 16

        336 TTATATTTTA

                    *       
        346 TAATTAAAGTTATATT
          1 TAATTAAAATTATATT

                             
        362 TAATTAATAATTATATT
          1 TAATTAA-AATTATATT

             
        379 T
          1 T

        380 TAAAATAAAT


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  16    7  0.44
  17    9  0.56

ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53


Consensus pattern (16 bp):   
TAATTAAAATTATATT

Found at i:1039 original size:91 final size:91

Alignment explanation


    Indices: 928--1105  Score: 311
    Period size: 91  Copynumber: 2.0  Consensus size: 91

        918 TACATGATTA

                                             *                               
        928 TCGAGAAAGGATTGGATGAAACAGTTACGCCACGTCATCCATATCCCTTTCCAATCATTTAATGA
          1 TCGAGAAAGGATTGGATGAAACAGTTACGCCACATCATCCATATCCCTTTCCAATCATTTAATGA

            *                         
        993 TATGTGGATTAATTTTGACATCCCAT
         66 CATGTGGATTAATTTTGACATCCCAT

                    *      *                      *                          
       1019 TCGAGAAATGATTGGTTGAAACAGTTACGCCACATCATTCATATCCCTTTCCAATCATTTAATGA
          1 TCGAGAAAGGATTGGATGAAACAGTTACGCCACATCATCCATATCCCTTTCCAATCATTTAATGA

                                  
       1084 CATGTGGATTAATTTTGACATC
         66 CATGTGGATTAATTTTGACATC

       1106 TTATTCACAC


Statistics
Matches: 82,  Mismatches: 5, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  91   82  1.00

ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33


Consensus pattern (91 bp):   
TCGAGAAAGGATTGGATGAAACAGTTACGCCACATCATCCATATCCCTTTCCAATCATTTAATGA
CATGTGGATTAATTTTGACATCCCAT

Found at i:4717 original size:30 final size:30

Alignment explanation


    Indices: 4683--4747  Score: 78
    Period size: 31  Copynumber: 2.1  Consensus size: 30

       4673 TCAAATTATG

                                           
       4683 TAATTTATATTCGAGTTAAAT-CAAATAACT
          1 TAATTTATATTCGAGTT-AATCCAAATAACT

                   *    *     *            
       4713 TAATTTTTTATTGGAGTTTATCCAAATAACT
          1 TAA-TTTATATTCGAGTTAATCCAAATAACT

                
       4744 TAAT
          1 TAAT

       4748 AATTCAAATA


Statistics
Matches: 30,  Mismatches: 3, Indels: 4
        0.81            0.08        0.11

Matches are distributed among these distances:
  30    6  0.20
  31   24  0.80

ACGTcount: A:0.38, C:0.09, G:0.08, T:0.45


Consensus pattern (30 bp):   
TAATTTATATTCGAGTTAATCCAAATAACT

Found at i:7967 original size:105 final size:105

Alignment explanation


    Indices: 7781--7972  Score: 339
    Period size: 105  Copynumber: 1.8  Consensus size: 105

       7771 AAACACTTAC

                    *                                                        
       7781 ACAAACCATATACAACATTAATTTACTAAATTTCATTTAAATCCTTCAAGAATTATAATGTTTGT
          1 ACAAACCAAATACAACATTAATTTACTAAATTTCATTTAAATCCTTCAAGAATTATAATGTTTGT

                   *   *     *                      
       7846 AGCATGATCCACAATATTCAAAATCCTTAACTTAAAATAT
         66 AGCATGACCCAAAATATACAAAATCCTTAACTTAAAATAT

                          *                                                  
       7886 ACAAACCAAATACAGCATTAATTTACTAAATTTCATTTAAATCCTTCAAGAATTATAATGTTTGT
          1 ACAAACCAAATACAACATTAATTTACTAAATTTCATTTAAATCCTTCAAGAATTATAATGTTTGT

                                  
       7951 AGCATGACCCAAAATATACAAA
         66 AGCATGACCCAAAATATACAAA

       7973 CCATATTGAC


Statistics
Matches: 82,  Mismatches: 5, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
 105   82  1.00

ACGTcount: A:0.44, C:0.17, G:0.06, T:0.33


Consensus pattern (105 bp):   
ACAAACCAAATACAACATTAATTTACTAAATTTCATTTAAATCCTTCAAGAATTATAATGTTTGT
AGCATGACCCAAAATATACAAAATCCTTAACTTAAAATAT
Done.