Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01014488.1 Kokia drynarioides strain JFW-HI SEQ_129527, 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: 16520
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34


Found at i:3747 original size:31 final size:31

Alignment explanation


    Indices: 3712--3786  Score: 105
    Period size: 31  Copynumber: 2.4  Consensus size: 31

       3702 AACTACTTAG

                                           
       3712 TTGGTCATTCAAATTTTAGGGCACTTTCATT
          1 TTGGTCATTCAAATTTTAGGGCACTTTCATT

                   *    *       **         
       3743 TTGGTCACTCAATTTTTAGGTTACTTTCATT
          1 TTGGTCATTCAAATTTTAGGGCACTTTCATT

                    *    
       3774 TTGGTCATCCAAA
          1 TTGGTCATTCAAA

       3787 AAATATATTT


Statistics
Matches: 37,  Mismatches: 7, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  31   37  1.00

ACGTcount: A:0.23, C:0.17, G:0.15, T:0.45


Consensus pattern (31 bp):   
TTGGTCATTCAAATTTTAGGGCACTTTCATT

Found at i:13513 original size:28 final size:28

Alignment explanation


    Indices: 13482--13548  Score: 80
    Period size: 28  Copynumber: 2.4  Consensus size: 28

      13472 AAGAACAGAT

                  *     **              
      13482 AGCACATAAAGCGTTAATCACAATAGAG
          1 AGCACACAAAGCACTAATCACAATAGAG

                       *        * *     
      13510 AGCACACAAAGTACTAATCAGACTAGAG
          1 AGCACACAAAGCACTAATCACAATAGAG

                       
      13538 AGCACACAAAG
          1 AGCACACAAAG

      13549 TGCTAAATAT


Statistics
Matches: 33,  Mismatches: 6, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  28   33  1.00

ACGTcount: A:0.48, C:0.21, G:0.18, T:0.13


Consensus pattern (28 bp):   
AGCACACAAAGCACTAATCACAATAGAG

Found at i:13549 original size:28 final size:28

Alignment explanation


    Indices: 13496--13554  Score: 91
    Period size: 28  Copynumber: 2.1  Consensus size: 28

      13486 CATAAAGCGT

                                        
      13496 TAATCACAATAGAGAGCACACAAAGTAC
          1 TAATCACAATAGAGAGCACACAAAGTAC

                  * *                 * 
      13524 TAATCAGACTAGAGAGCACACAAAGTGC
          1 TAATCACAATAGAGAGCACACAAAGTAC

               
      13552 TAA
          1 TAA

      13555 ATATACGTAG


Statistics
Matches: 28,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  28   28  1.00

ACGTcount: A:0.47, C:0.20, G:0.17, T:0.15


Consensus pattern (28 bp):   
TAATCACAATAGAGAGCACACAAAGTAC

Found at i:13669 original size:3 final size:3

Alignment explanation


    Indices: 13661--13695  Score: 70
    Period size: 3  Copynumber: 11.7  Consensus size: 3

      13651 AATAATTCTA

                                                          
      13661 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
          1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA

      13696 TAATAATAAT


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   32  1.00

ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00


Consensus pattern (3 bp):   
AAC

Found at i:13700 original size:3 final size:3

Alignment explanation


    Indices: 13694--13786  Score: 59
    Period size: 3  Copynumber: 31.7  Consensus size: 3

      13684 CAACAACAAC

                                                *    *      *    *    *  * 
      13694 AAT AAT AAT AAT AAT AAT AAT AAT AAT GAT AGT AAT TAT AGT AAC AGT
          1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT

            *            *            *                                  
      13742 TAT AAT AAT ACT AA- AA- AAA AAT AAT AA- AAT AACT AA- ATAT AAT
          1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT A-AT AAT

              
      13785 AA
          1 AA

      13787 ATATAACAAA


Statistics
Matches: 68,  Mismatches: 17, Indels: 10
        0.72            0.18        0.11

Matches are distributed among these distances:
   2    7  0.10
   3   57  0.84
   4    4  0.06

ACGTcount: A:0.62, C:0.03, G:0.04, T:0.30


Consensus pattern (3 bp):   
AAT

Done.