Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008839.1 Kokia drynarioides strain JFW-HI SEQ_123523, 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: 5988
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34


Found at i:3564 original size:22 final size:21

Alignment explanation


    Indices: 3521--3564  Score: 52
    Period size: 22  Copynumber: 2.0  Consensus size: 21

       3511 TATTTATTTA

                             *   
       3521 TTTAATTTTTTTCATAATTAT
          1 TTTAATTTTTTTCATAAATAT

                *            *    
       3542 TTTATTTTATTTTCATACATAT
          1 TTTAATTT-TTTTCATAAATAT

             
       3564 T
          1 T

       3565 ATATATGTGT


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

Matches are distributed among these distances:
  21    7  0.37
  22   12  0.63

ACGTcount: A:0.27, C:0.07, G:0.00, T:0.66


Consensus pattern (21 bp):   
TTTAATTTTTTTCATAAATAT

Found at i:3959 original size:21 final size:21

Alignment explanation


    Indices: 3919--3959  Score: 55
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       3909 CTTATTTATA

                          **     
       3919 TTTTAATTAATCATGTTTTAG
          1 TTTTAATTAATCATAATTTAG

                        *       
       3940 TTTTAATTAATCTTAATTTA
          1 TTTTAATTAATCATAATTTA

       3960 CATAATTAAG


Statistics
Matches: 17,  Mismatches: 3, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  21   17  1.00

ACGTcount: A:0.32, C:0.05, G:0.05, T:0.59


Consensus pattern (21 bp):   
TTTTAATTAATCATAATTTAG

Found at i:4788 original size:145 final size:145

Alignment explanation


    Indices: 4639--4942  Score: 436
    Period size: 144  Copynumber: 2.1  Consensus size: 145

       4629 GTCGATGTGA

                                   *                                         
       4639 AATTGTTGGTCCAATTCCCTTCTTCTTTGGGCCAATTAACCAATCTCCAATCTCTGATCCTT-G-
          1 AATTGTTGGTCCAATTCCCTTCTGCTTTGGGCCAATTAACCAATCTCCAATCTCTGATCCTTCGA

                                                                *       *    
       4702 GGATAAACAAAATCAATGGATCTATCCCATTAGAAATTGGATATTTGAGAAATTTGACTTGTTTG
         66 GG--AAACAAAATCAATGGATCTATCCCATTAGAAATTGGATATTTGAGAAAATTGACTTATTTG

                      *       
       4767 -AGTCTCTCCGACAATAG
        129 TA-TCTCTCCAACAATAG

                                           * *        *                      
       4784 AATTGTTGGTCCAA-TCCCTTCTGCTTTGGGTCTATTAACCAGTCTCCAATCTCTGATCCTTCGA
          1 AATTGTTGGTCCAATTCCCTTCTGCTTTGGGCCAATTAACCAATCTCCAATCTCTGATCCTTCGA

              *   *      *                                         *         
       4848 GGGAACCAAATCAGTGGATCTATCCCATTAGAAATTGGATATTTGAGAAAATTGATTTATTTGTA
         66 GGAAACAAAATCAATGGATCTATCCCATTAGAAATTGGATATTTGAGAAAATTGACTTATTTGTA

                           
       4913 TCTCTCCAACAATAG
        131 TCTCTCCAACAATAG

             *        *    
       4928 ACTTGTTGGTTCAAT
          1 AATTGTTGGTCCAAT

       4943 ACCCATTACT


Statistics
Matches: 142,  Mismatches: 13, Indels: 8
        0.87            0.08        0.05

Matches are distributed among these distances:
 144  124  0.87
 145   16  0.11
 146    2  0.01

ACGTcount: A:0.28, C:0.20, G:0.16, T:0.35


Consensus pattern (145 bp):   
AATTGTTGGTCCAATTCCCTTCTGCTTTGGGCCAATTAACCAATCTCCAATCTCTGATCCTTCGA
GGAAACAAAATCAATGGATCTATCCCATTAGAAATTGGATATTTGAGAAAATTGACTTATTTGTA
TCTCTCCAACAATAG

Done.