Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007558.1 Kokia drynarioides strain JFW-HI SEQ_122186, 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: 8751
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36


Found at i:2288 original size:14 final size:16

Alignment explanation


    Indices: 2269--2305  Score: 53
    Period size: 13  Copynumber: 2.5  Consensus size: 16

       2259 GAATTAGGGA

                            
       2269 TTTTTTTTT-TC-C-T
          1 TTTTTTTTTCTCTCAT

                            
       2282 TTTTTTTTTCTCTCAT
          1 TTTTTTTTTCTCTCAT

                    
       2298 TTTTTTTT
          1 TTTTTTTT

       2306 GTGTTTTGAA


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

Matches are distributed among these distances:
  13    9  0.43
  14    2  0.10
  15    1  0.05
  16    9  0.43

ACGTcount: A:0.03, C:0.14, G:0.00, T:0.84


Consensus pattern (16 bp):   
TTTTTTTTTCTCTCAT

Found at i:6560 original size:9 final size:9

Alignment explanation


    Indices: 6518--6635  Score: 53
    Period size: 9  Copynumber: 12.6  Consensus size: 9

       6508 ATTTAGAATA

                *    
       6518 TATATAAAT
          1 TATAAAAAT

              *      
       6527 TACAAAAA-
          1 TATAAAAAT

                      
       6535 TATAACAAAT
          1 TATAA-AAAT

             *       
       6545 TGT-AAAAT
          1 TATAAAAAT

                     
       6553 TATAAAAAT
          1 TATAAAAAT

              * *    *
       6562 ATTTGAAAAC
          1 -TATAAAAAT

                   *  
       6572 TATAGAAGAT
          1 TATA-AAAAT

                      
       6582 GTA-AAAAAT
          1 -TATAAAAAT

                        
       6591 TATTAAAAAGCT
          1 TA-TAAAAA--T

              *       
       6603 TACAAAATAT
          1 TATAAAA-AT

                    *
       6613 TATAAAAAG
          1 TATAAAAAT

                     
       6622 TATAAAAAT
          1 TATAAAAAT

            *    
       6631 CATAA
          1 TATAA

       6636 GACAAAATAA


Statistics
Matches: 80,  Mismatches: 18, Indels: 22
        0.67            0.15        0.18

Matches are distributed among these distances:
   8   12  0.15
   9   34  0.43
  10   24  0.30
  11    6  0.08
  12    4  0.05

ACGTcount: A:0.59, C:0.05, G:0.06, T:0.30


Consensus pattern (9 bp):   
TATAAAAAT

Found at i:6628 original size:19 final size:21

Alignment explanation


    Indices: 6583--6629  Score: 55
    Period size: 21  Copynumber: 2.3  Consensus size: 21

       6573 ATAGAAGATG

                                 
       6583 TAAAAAATTATTAAAAAGCT-
          1 TAAAAAATTATTAAAAAGCTA

                                   
       6603 TACAAAATATTA-TAAAAAG-TA
          1 TA-AAAA-ATTATTAAAAAGCTA

                  
       6624 TAAAAA
          1 TAAAAA

       6630 TCATAAGACA


Statistics
Matches: 24,  Mismatches: 0, Indels: 6
        0.80            0.00        0.20

Matches are distributed among these distances:
  20    7  0.29
  21   13  0.54
  22    4  0.17

ACGTcount: A:0.64, C:0.04, G:0.04, T:0.28


Consensus pattern (21 bp):   
TAAAAAATTATTAAAAAGCTA

Found at i:8626 original size:153 final size:153

Alignment explanation


    Indices: 8430--8751  Score: 504
    Period size: 153  Copynumber: 2.1  Consensus size: 153

       8420 CTCACTTGCA

                             *                *                              
       8430 CAAAAAAAATCAGACTTGACTTTGAGAATAATTGTCTAGTTTAAAGACTAATTT-GGAAAATAA-
          1 CAAAAAAAATCAGACTTCACTTTGAGAATAATTGCCTAGTTTAAAGACTAATTTGGGAAAA-AAG

                            *                             *                  
       8493 AGTTTACCAAATTAAAGGACTAATTTAGACAAAAAAAAGGATTTAATTCTCAATGTGAAAATAAT
         65 AGTTTACCAAATTAAAAGACTAATTTAGAC-AAAAAAAGGATTTAAGTCTCAATGTGAAAATAAT

               *          *          
       8558 TGTTAAGTTGAGACTCCAAAACTTG
        129 TGTCAAGTTGAGACCCCAAAACTTG

                          *                                                  
       8583 CAAAAAAAATCAGATTTCACTTTGAGAATAATTGCCTAGTTTAAAGACTAATTTGGGAAAAAAGA
          1 CAAAAAAAATCAGACTTCACTTTGAGAATAATTGCCTAGTTTAAAGACTAATTTGGGAAAAAAGA

                              *                              *               
       8648 GTTTACCAAATTAAAAGATTAATTTAGACAAAAAAAGGATTTAAGTCTCGATGTGAAAATAATTG
         66 GTTTACCAAATTAAAAGACTAATTTAGACAAAAAAAGGATTTAAGTCTCAATGTGAAAATAATTG

                                   
       8713 TCAAGTTGAGACCCCAAAACTTG
        131 TCAAGTTGAGACCCCAAAACTTG

                  *         
       8736 CACACACAAAATCAGA
          1 CA-A-AAAAAATCAGA


Statistics
Matches: 155,  Mismatches: 10, Indels: 6
        0.91            0.06        0.04

Matches are distributed among these distances:
 153  110  0.71
 154   35  0.23
 155   10  0.06

ACGTcount: A:0.45, C:0.12, G:0.15, T:0.28


Consensus pattern (153 bp):   
CAAAAAAAATCAGACTTCACTTTGAGAATAATTGCCTAGTTTAAAGACTAATTTGGGAAAAAAGA
GTTTACCAAATTAAAAGACTAATTTAGACAAAAAAAGGATTTAAGTCTCAATGTGAAAATAATTG
TCAAGTTGAGACCCCAAAACTTG
Done.