Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013791.1 Kokia drynarioides strain JFW-HI SEQ_128819, 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: 15777
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35

Warning! 19 characters in sequence are not A, C, G, or T


Found at i:654 original size:205 final size:207

Alignment explanation


    Indices: 337--794  Score: 654
    Period size: 205  Copynumber: 2.2  Consensus size: 207

        327 CGTATTTCAC

                         **               *        *  *        *             
        337 CAGGAAGCTAATCGTTTTATTACTTCGAC-TTGCTTCTCAGTGTCTCATCAGGAAGCTAGGGTTC
          1 CAGGAAGCTAA-CCCTTTATTACTTC-ACACTGCTTCTCCGTATCTCATCAAGAAGCTAGGGTTC

                            *                                                
        401 GAAGATTTGCTCACATTAGGCGTGAGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGAT
         64 GAAGATTTGCTCACATCAGGCGTGAGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGAT

                                                                    *        
        466 GACTGCGTCGTTTGTTTCAATTCGCTTCTCTGTATCTCATCAGGAAGACGAATTT-TATCCACTT
        129 GACTGCGTCGTTTGTTTCAATTCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGATCCACTT

                          
        530 CTCAG-TATCTCAT
        194 CTCAGCTATCTCAT

                                    *  *                            *        
        543 CAGGAAGCTAACCCTTTATTACTTTACCCTGCTTCTCCGTATCTCATCAAGAAGCTGGGGTTC-A
          1 CAGGAAGCTAACCCTTTATTACTTCACACTGCTTCTCCGTATCTCATCAAGAAGCTAGGGTTCGA

                    *       *                                                
        607 AGGATTTGTTCACATCGGGCGTGAGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATG
         66 A-GATTTGCTCACATCAGGCGTGAGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATG

             *                          *                 * *       *        
        672 ATTGCGTCGTTTGTTTCAATTCGCTTCTGTGTATCTCATCAGGAAGGCTAATTTGGGTCCACTTC
        130 ACTGCGTCGTTTGTTTCAATTCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGATCCACTTC

                         
        737 TCAGCTATCTCAT
        195 TCAGCTATCTCAT

            *    *       *      *        *               
        750 TAGGAGGCTAACCTTTTATTGCTTCACACAGCTTCTCCGTATCTC
          1 CAGGAAGCTAACCCTTTATTACTTCACACTGCTTCTCCGTATCTC

        795 TAGGGTTCGA


Statistics
Matches: 224,  Mismatches: 24, Indels: 7
        0.88            0.09        0.03

Matches are distributed among these distances:
 204    4  0.02
 205  151  0.67
 206   23  0.10
 207   46  0.21

ACGTcount: A:0.21, C:0.23, G:0.20, T:0.36


Consensus pattern (207 bp):   
CAGGAAGCTAACCCTTTATTACTTCACACTGCTTCTCCGTATCTCATCAAGAAGCTAGGGTTCGA
AGATTTGCTCACATCAGGCGTGAGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGA
CTGCGTCGTTTGTTTCAATTCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGATCCACTTCT
CAGCTATCTCAT

Found at i:11768 original size:21 final size:22

Alignment explanation


    Indices: 11742--11804  Score: 78
    Period size: 21  Copynumber: 3.0  Consensus size: 22

      11732 TCTCCTTTTT

                                  
      11742 TATTATTATTATTAAT-AATAA
          1 TATTATTATTATTAATCAATAA

                                  
      11763 TATTATTATTATT-ATCAA-AA
          1 TATTATTATTATTAATCAATAA

            *                *    
      11783 CATTTATTATTATTAATGAATA
          1 TA-TTATTATTATTAATCAATA

      11805 TTAAGAAAAA


Statistics
Matches: 36,  Mismatches: 2, Indels: 6
        0.82            0.05        0.14

Matches are distributed among these distances:
  20    5  0.14
  21   26  0.72
  22    4  0.11
  23    1  0.03

ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51


Consensus pattern (22 bp):   
TATTATTATTATTAATCAATAA

Found at i:12568 original size:6 final size:6

Alignment explanation


    Indices: 12559--12605  Score: 51
    Period size: 6  Copynumber: 8.0  Consensus size: 6

      12549 GTTTTTAATT

                               *     *       *      *              
      12559 TTAAAA TTAAAA TTAAAT TTAAGA TT-AAT TTAAAT TTAAAA TTAAAA
          1 TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA

      12606 AGGGGTTCGA


Statistics
Matches: 34,  Mismatches: 6, Indels: 2
        0.81            0.14        0.05

Matches are distributed among these distances:
   5    3  0.09
   6   31  0.91

ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40


Consensus pattern (6 bp):   
TTAAAA

Done.