Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001364.1 Kokia drynarioides strain JFW-HI SEQ_112823, 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: 2449
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.36


Found at i:554 original size:43 final size:43

Alignment explanation


    Indices: 465--581  Score: 130
    Period size: 43  Copynumber: 2.7  Consensus size: 43

        455 TGGAAGTGTG

                   *    *                               
        465 TCCAACTGAAAGTGTTCTT-AGTGCCAACTCAGTTGAAAGCTAA
          1 TCCAACTAAAAGAGTT-TTCAGTGCCAACTCAGTTGAAAGCTAA

                *       *                               
        508 TCCAGCTAAAAGCGTTTTCAGTGCCAACTCAGTTGAAAGC-ACA
          1 TCCAACTAAAAGAGTTTTCAGTGCCAACTCAGTTGAAAGCTA-A

                 * **           *          
        551 TCCAATTGGAAGAGTTTTCACTGCCAACTCA
          1 TCCAACTAAAAGAGTTTTCAGTGCCAACTCA

        582 ACTAAAAGAG


Statistics
Matches: 63,  Mismatches: 9, Indels: 4
        0.83            0.12        0.05

Matches are distributed among these distances:
  42    3  0.05
  43   60  0.95

ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26


Consensus pattern (43 bp):   
TCCAACTAAAAGAGTTTTCAGTGCCAACTCAGTTGAAAGCTAA

Found at i:1356 original size:8 final size:9

Alignment explanation


    Indices: 1343--1524  Score: 61
    Period size: 9  Copynumber: 19.6  Consensus size: 9

       1333 TTATTAGAAT

                     
       1343 TTTTTAT-A
          1 TTTTTATAA

                     
       1351 TTTTTATAA
          1 TTTTTATAA

                       
       1360 TTTTTTATGAA
          1 -TTTTTAT-AA

              *   *  
       1371 TTCTTACAA
          1 TTTTTATAA

                       
       1380 GTTTTTATAAA
          1 -TTTTTAT-AA

            *        
       1391 ATTTTA-AA
          1 TTTTTATAA

                      
       1399 TGTTTTATAA
          1 T-TTTTATAA

                       
       1409 TTTATTACT-A
          1 TTT-TTA-TAA

            * ***   *
       1419 GTAGAAT-T
          1 TTTTTATAA

                     
       1427 TTTTTATAA
          1 TTTTTATAA

                     * 
       1436 GTTTTTTATGA
          1 --TTTTTATAA

                      
       1447 TTTTATATAA
          1 TTTT-TATAA

            *        
       1457 GTTTTATAA
          1 TTTTTATAA

              **     
       1466 TTGGTATAA
          1 TTTTTATAA

                    * 
       1475 TTTTATATTA
          1 TTTT-TATAA

            *         
       1485 GTTTTA-ATA
          1 TTTTTATA-A

                    *
       1494 TTTTTAT-T
          1 TTTTTATAA

                     
       1502 TTTTTATAA
          1 TTTTTATAA

               *   * 
       1511 TTTATATGA
          1 TTTTTATAA

                 
       1520 TTTTT
          1 TTTTT

       1525 TATGAGAAAA


Statistics
Matches: 124,  Mismatches: 33, Indels: 33
        0.65            0.17        0.17

Matches are distributed among these distances:
   8   20  0.16
   9   47  0.38
  10   44  0.35
  11   13  0.10

ACGTcount: A:0.31, C:0.02, G:0.07, T:0.61


Consensus pattern (9 bp):   
TTTTTATAA

Found at i:1361 original size:18 final size:20

Alignment explanation


    Indices: 1324--1367  Score: 65
    Period size: 18  Copynumber: 2.3  Consensus size: 20

       1314 ATTTTCTAAC

                                
       1324 TTTTATATCTTATTAGAATT
          1 TTTTATATCTTATTAGAATT

                           *    
       1344 TTTTATAT-TT-TTATAATT
          1 TTTTATATCTTATTAGAATT

                  
       1362 TTTTAT
          1 TTTTAT

       1368 GAATTCTTAC


Statistics
Matches: 23,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  18   13  0.57
  19    2  0.09
  20    8  0.35

ACGTcount: A:0.27, C:0.02, G:0.02, T:0.68


Consensus pattern (20 bp):   
TTTTATATCTTATTAGAATT

Done.