Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013956.1 Kokia drynarioides strain JFW-HI SEQ_128986, 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: 2240
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33


Found at i:1503 original size:21 final size:22

Alignment explanation


    Indices: 1477--1564  Score: 97
    Period size: 23  Copynumber: 4.0  Consensus size: 22

       1467 TGGAACAAAT

                                  
       1477 AGAGAGTAC-CAAAGTACTAAC
          1 AGAGAGTACACAAAGTACTAAC

                  *     *   *      
       1498 AGAGAGCACACACAGTGCTAAAC
          1 AGAGAGTACACAAAGTACT-AAC

                                   
       1521 AGAGAGTACACAAAGTACTAATC
          1 AGAGAGTACACAAAGTACTAA-C

                  *     *   *    
       1544 AGAGAGCACACACAGTGCTAA
          1 AGAGAGTACACAAAGTACTAA

       1565 TAACATAAAG


Statistics
Matches: 55,  Mismatches: 9, Indels: 4
        0.81            0.13        0.06

Matches are distributed among these distances:
  21    8  0.15
  22    9  0.16
  23   38  0.69

ACGTcount: A:0.45, C:0.22, G:0.20, T:0.12


Consensus pattern (22 bp):   
AGAGAGTACACAAAGTACTAAC

Found at i:1521 original size:23 final size:23

Alignment explanation


    Indices: 1495--1598  Score: 111
    Period size: 23  Copynumber: 4.4  Consensus size: 23

       1485 CCAAAGTACT

                                   
       1495 AACAGAGAGCACACACAGTGCTA
          1 AACAGAGAGCACACACAGTGCTA

                     *     *   *   
       1518 AACAGAGAGTACACAAAGTACTA
          1 AACAGAGAGCACACACAGTGCTA

             *                      
       1541 ATCAGAGAGCACACACAGTGCTAA
          1 AACAGAGAGCACACACAGTGCT-A

                 * *       *         
       1565 TAACATAAAGCACGAGAC-GTGCTA
          1 -AACAGAGAGCAC-ACACAGTGCTA

                      
       1589 AACAGAGAGC
          1 AACAGAGAGC

       1599 GCGCTAGTGT


Statistics
Matches: 65,  Mismatches: 13, Indels: 6
        0.77            0.15        0.07

Matches are distributed among these distances:
  23   46  0.71
  24    2  0.03
  25   14  0.22
  26    3  0.05

ACGTcount: A:0.45, C:0.22, G:0.21, T:0.12


Consensus pattern (23 bp):   
AACAGAGAGCACACACAGTGCTA

Found at i:1553 original size:46 final size:44

Alignment explanation


    Indices: 1477--1564  Score: 158
    Period size: 46  Copynumber: 2.0  Consensus size: 44

       1467 TGGAACAAAT

                                                        
       1477 AGAGAGTACCAAAGTACTAACAGAGAGCACACACAGTGCTAAAC
          1 AGAGAGTACCAAAGTACTAACAGAGAGCACACACAGTGCTAAAC

                                                        
       1521 AGAGAGTACACAAAGTACTAATCAGAGAGCACACACAGTGCTAA
          1 AGAGAGTAC-CAAAGTACTAA-CAGAGAGCACACACAGTGCTAA

       1565 TAACATAAAG


Statistics
Matches: 42,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
  44    9  0.21
  45   11  0.26
  46   22  0.52

ACGTcount: A:0.45, C:0.22, G:0.20, T:0.12


Consensus pattern (44 bp):   
AGAGAGTACCAAAGTACTAACAGAGAGCACACACAGTGCTAAAC
Done.