Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010156.1 Kokia drynarioides strain JFW-HI SEQ_124959, 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: 10719
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.36

Warning! 67 characters in sequence are not A, C, G, or T


Found at i:39 original size:4 final size:4

Alignment explanation


    Indices: 32--74  Score: 61
    Period size: 4  Copynumber: 10.8  Consensus size: 4

         22 TTCTTCCTTC

                                             *                    
         32 TTCT TTCT TTCT TTCT TTCT TTCT ATTTT TTCT TTCT TT-T TTC
          1 TTCT TTCT TTCT TTCT TTCT TTCT -TTCT TTCT TTCT TTCT TTC

         75 CTTCATTTTT


Statistics
Matches: 35,  Mismatches: 2, Indels: 4
        0.85            0.05        0.10

Matches are distributed among these distances:
   3    3  0.09
   4   29  0.83
   5    3  0.09

ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77


Consensus pattern (4 bp):   
TTCT

Found at i:83 original size:12 final size:11

Alignment explanation


    Indices: 29--85  Score: 60
    Period size: 11  Copynumber: 4.8  Consensus size: 11

         19 TCCTTCTTCC

                 *     
         29 TTCTTCTTTCT
          1 TTCTTTTTTCT

                        
         40 TTCTTTCTTTCT
          1 TTCTTT-TTTCT

                         
         52 TTCTATTTTTTCT
          1 TTC--TTTTTTCT

                      *
         65 TTCTTTTTTCC
          1 TTCTTTTTTCT

                      
         76 TTCATTTTTT
          1 TTC-TTTTTT

         86 GTTGGTCCCC


Statistics
Matches: 40,  Mismatches: 2, Indels: 7
        0.82            0.04        0.14

Matches are distributed among these distances:
  11   15  0.38
  12   14  0.35
  13    8  0.20
  14    3  0.08

ACGTcount: A:0.04, C:0.21, G:0.00, T:0.75


Consensus pattern (11 bp):   
TTCTTTTTTCT

Found at i:4296 original size:13 final size:13

Alignment explanation


    Indices: 4248--4304  Score: 53
    Period size: 13  Copynumber: 4.2  Consensus size: 13

       4238 TCGAACCTCA

                          
       4248 AACCTTGAACCCTG
          1 AACCTTGAACCC-G

                          
       4262 AACCCTT-AACCCG
          1 AA-CCTTGAACCCG

              * *     *  
       4275 AATCGTGAACACG
          1 AACCTTGAACCCG

                          
       4288 AACCTTGAACCCCG
          1 AACCTTGAA-CCCG

               
       4302 AAC
          1 AAC

       4305 TCAAACCTTG


Statistics
Matches: 34,  Mismatches: 6, Indels: 6
        0.74            0.13        0.13

Matches are distributed among these distances:
  12    2  0.06
  13   15  0.44
  14   13  0.38
  15    4  0.12

ACGTcount: A:0.33, C:0.37, G:0.14, T:0.16


Consensus pattern (13 bp):   
AACCTTGAACCCG

Found at i:4826 original size:3 final size:3

Alignment explanation


    Indices: 4818--4849  Score: 64
    Period size: 3  Copynumber: 10.7  Consensus size: 3

       4808 TCGTGCATGT

                                                      
       4818 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
          1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT

       4850 CGAGAGATTA


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   29  1.00

ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34


Consensus pattern (3 bp):   
ATA

Found at i:5416 original size:29 final size:28

Alignment explanation


    Indices: 5348--5421  Score: 71
    Period size: 27  Copynumber: 2.6  Consensus size: 28

       5338 GTCATGTCAA

                *    *    *             
       5348 CAAATAATTTAAAATTTATAAAAATATT
          1 CAAAAAATTAAAAAATTATAAAAATATT

               *                         
       5376 CAAGAAA-TAAAAAATTATAAAAA-AGTT
          1 CAAAAAATTAAAAAATTATAAAAATA-TT

                          *    
       5403 CATAAAAATTAAAAGATTA
          1 CA-AAAAATTAAAAAATTA

       5422 GCATGAAGTA


Statistics
Matches: 37,  Mismatches: 6, Indels: 5
        0.77            0.12        0.10

Matches are distributed among these distances:
  26    1  0.03
  27   18  0.49
  28    9  0.24
  29    9  0.24

ACGTcount: A:0.62, C:0.04, G:0.04, T:0.30


Consensus pattern (28 bp):   
CAAAAAATTAAAAAATTATAAAAATATT
Done.