Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01014152.1 Kokia drynarioides strain JFW-HI SEQ_129185, 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: 2684
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.35

Warning! 50 characters in sequence are not A, C, G, or T


Found at i:1381 original size:25 final size:25

Alignment explanation


    Indices: 1324--1382  Score: 63
    Period size: 24  Copynumber: 2.5  Consensus size: 25

       1314 AAAGAAGGTT

                                    *
       1324 ATATATTAT--TTTTT-TTAATATT
          1 ATATATTATAATTTTTATTAATATC

                                     
       1346 ATATATTATAATTTTTATTAAT-TC
          1 ATATATTATAATTTTTATTAATATC

                *        
       1370 ATATTTTAATAAT
          1 ATATATT-ATAAT

       1383 AATTATATTA


Statistics
Matches: 31,  Mismatches: 2, Indels: 5
        0.82            0.05        0.13

Matches are distributed among these distances:
  22    9  0.29
  24   12  0.39
  25   10  0.32

ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61


Consensus pattern (25 bp):   
ATATATTATAATTTTTATTAATATC

Found at i:1508 original size:56 final size:55

Alignment explanation


    Indices: 1348--1510  Score: 150
    Period size: 56  Copynumber: 2.8  Consensus size: 55

       1338 TTAATATTAT

                    *                                          * *      
       1348 ATATTATAATTTTTATTAATTCATATTTTAATAATAAT-TATATTAAGAATGTTATTAAA
          1 ATATT-TATTTTTTATTAATT-ATA-TTTAATAATAATCT-TATTAA-AATATGATTAAA

            *   *    *            *                *                  
       1407 TTATATACTATTTTATTAAATTGTATTTAATAATAATC-AAGTTAAAATATGATTAAA
          1 ATATTTA-TTTTTTATT-AATTATATTTAATAATAATCTTA-TTAAAATATGATTAAA

                              *                            
       1464 ATATTTATTTTTTATTACGTTATATTTAATAATAATCTTATTAAAAT
          1 ATATTTATTTTTTATTA-ATTATATTTAATAATAATCTTATTAAAAT

       1511 TTAACAACAA


Statistics
Matches: 84,  Mismatches: 14, Indels: 15
        0.74            0.12        0.13

Matches are distributed among these distances:
  55    1  0.01
  56   32  0.38
  57   17  0.20
  58   18  0.21
  59   12  0.14
  60    4  0.05

ACGTcount: A:0.43, C:0.03, G:0.04, T:0.50


Consensus pattern (55 bp):   
ATATTTATTTTTTATTAATTATATTTAATAATAATCTTATTAAAATATGATTAAA

Found at i:1664 original size:44 final size:46

Alignment explanation


    Indices: 1601--1690  Score: 123
    Period size: 44  Copynumber: 2.0  Consensus size: 46

       1591 TATTACAACA

                                                 *         
       1601 TCATTCCATTCAACCAAAC-ACA-AGAATACT-ATTATAGCTCTATT
          1 TCATTCCATTCAACCAAACAACAGA-AATACTAATTACAGCTCTATT

                 *                *                       
       1645 TCATTTCATTCAACCAAACAACTGAAATACTAATTACAGCTCTATT
          1 TCATTCCATTCAACCAAACAACAGAAATACTAATTACAGCTCTATT

       1691 CTATTACAGC


Statistics
Matches: 40,  Mismatches: 3, Indels: 4
        0.85            0.06        0.09

Matches are distributed among these distances:
  44   18  0.45
  45    8  0.20
  46   14  0.35

ACGTcount: A:0.39, C:0.24, G:0.04, T:0.32


Consensus pattern (46 bp):   
TCATTCCATTCAACCAAACAACAGAAATACTAATTACAGCTCTATT
Done.