Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009532.1 Kokia drynarioides strain JFW-HI SEQ_124244, 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: 11600
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32


Found at i:1025 original size:23 final size:22

Alignment explanation


    Indices: 995--1096  Score: 91
    Period size: 23  Copynumber: 4.5  Consensus size: 22

        985 ACGCTAGCAC

                         *         
        995 GCTTACTGCTTTGTACTTCGTGT
          1 GCTTACTG-TTTGCACTTCGTGT

                              *    
       1018 GCTTACTGTTTCGCACTTTGTGT
          1 GCTTACTGTTT-GCACTTCGTGT

                          *        *
       1041 GCTTACTGATTTGCGCTAT-GTGC
          1 GCTTACTG-TTTGCACT-TCGTGT

              *     *              
       1064 GCCTACTGATTGCACTGT-GTGT
          1 GCTTACTGTTTGCACT-TCGTGT

                       
       1086 GCTTACTGTTT
          1 GCTTACTGTTT

       1097 CCCCAGCACT


Statistics
Matches: 65,  Mismatches: 11, Indels: 7
        0.78            0.13        0.08

Matches are distributed among these distances:
  22   22  0.34
  23   39  0.60
  24    4  0.06

ACGTcount: A:0.11, C:0.22, G:0.24, T:0.44


Consensus pattern (22 bp):   
GCTTACTGTTTGCACTTCGTGT

Found at i:2544 original size:83 final size:83

Alignment explanation


    Indices: 2400--2565  Score: 278
    Period size: 83  Copynumber: 2.0  Consensus size: 83

       2390 TAAGATAAAT

                                                      *           * *        
       2400 ACCTTGATTAGGAAGTAAACAGAGCACACACGGCTTGTGACATGGGCTATCACATGGCCGTGTAT
          1 ACCTTGATTAGGAAGTAAACAGAGCACACACGGCTTGTGACACGGGCTATCACACGACCGTGTAT

                         *    
       2465 CATATTTTAAGTGTAGAG
         66 CATATTTTAAGTGCAGAG

                               *                            *                
       2483 ACCTTGATTAGGAAGTAAATAGAGCACACACGGCTTGTGACACGGGCTGTCACACGACCGTGTAT
          1 ACCTTGATTAGGAAGTAAACAGAGCACACACGGCTTGTGACACGGGCTATCACACGACCGTGTAT

                              
       2548 CATATTTTAAGTGCAGAG
         66 CATATTTTAAGTGCAGAG

       2566 CAGTTTACAC


Statistics
Matches: 77,  Mismatches: 6, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  83   77  1.00

ACGTcount: A:0.30, C:0.19, G:0.25, T:0.25


Consensus pattern (83 bp):   
ACCTTGATTAGGAAGTAAACAGAGCACACACGGCTTGTGACACGGGCTATCACACGACCGTGTAT
CATATTTTAAGTGCAGAG

Found at i:3413 original size:14 final size:17

Alignment explanation


    Indices: 3378--3415  Score: 55
    Period size: 17  Copynumber: 2.4  Consensus size: 17

       3368 ACTCATAAAC

                             
       3378 ATTAAAACAAAACAAAT
          1 ATTAAAACAAAACAAAT

                             
       3395 ATTAAAA-AAAA-AAAT
          1 ATTAAAACAAAACAAAT

                   
       3410 -TTAAAA
          1 ATTAAAA

       3416 TACATTAAAA


Statistics
Matches: 21,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  14    6  0.29
  15    4  0.19
  16    4  0.19
  17    7  0.33

ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21


Consensus pattern (17 bp):   
ATTAAAACAAAACAAAT

Found at i:3611 original size:12 final size:12

Alignment explanation


    Indices: 3552--3611  Score: 54
    Period size: 12  Copynumber: 5.2  Consensus size: 12

       3542 AAATAATATC

                  *     
       3552 AAAACAACAAAA
          1 AAAACAGCAAAA

             *          
       3564 ATAACAG-AAAA
          1 AAAACAGCAAAA

                         
       3575 AATAACAGCAAAA
          1 AA-AACAGCAAAA

                *    *  
       3588 AAAATA--ATAA
          1 AAAACAGCAAAA

                        
       3598 AAAACAGCAAAA
          1 AAAACAGCAAAA

              
       3610 AA
          1 AA

       3612 CACCATAAAC


Statistics
Matches: 37,  Mismatches: 7, Indels: 8
        0.71            0.13        0.15

Matches are distributed among these distances:
  10    8  0.22
  11    5  0.14
  12   18  0.49
  13    6  0.16

ACGTcount: A:0.77, C:0.12, G:0.05, T:0.07


Consensus pattern (12 bp):   
AAAACAGCAAAA

Found at i:3619 original size:22 final size:22

Alignment explanation


    Indices: 3552--3632  Score: 67
    Period size: 22  Copynumber: 3.7  Consensus size: 22

       3542 AAATAATATC

                  *      *      *  
       3552 AAAACAACAAAAATAACAGAAAA
          1 AAAACAGCAAAAAAAACA-ATAA

                             *     
       3575 AATAACAGCAAAAAAAATAATAA
          1 AA-AACAGCAAAAAAAACAATAA

                          *  *    
       3598 AAAACAGCAAAAAACACCATAA
          1 AAAACAGCAAAAAAAACAATAA

             *             
       3620 ACAACA--AAAAAAA
          1 AAAACAGCAAAAAAA

       3633 TATAATTTTT


Statistics
Matches: 48,  Mismatches: 9, Indels: 5
        0.77            0.15        0.08

Matches are distributed among these distances:
  20    6  0.12
  22   22  0.46
  23    7  0.15
  24   13  0.27

ACGTcount: A:0.75, C:0.15, G:0.04, T:0.06


Consensus pattern (22 bp):   
AAAACAGCAAAAAAAACAATAA

Found at i:4653 original size:6 final size:6

Alignment explanation


    Indices: 4642--4686  Score: 90
    Period size: 6  Copynumber: 7.5  Consensus size: 6

       4632 ATTCCAAATT

                                                                
       4642 TCCCCA TCCCCA TCCCCA TCCCCA TCCCCA TCCCCA TCCCCA TCC
          1 TCCCCA TCCCCA TCCCCA TCCCCA TCCCCA TCCCCA TCCCCA TCC

       4687 TTTCCTTCCA


Statistics
Matches: 39,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   39  1.00

ACGTcount: A:0.16, C:0.67, G:0.00, T:0.18


Consensus pattern (6 bp):   
TCCCCA

Done.