Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003583.1 Kokia drynarioides strain JFW-HI SEQ_116456, 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: 2127
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36


Found at i:1302 original size:30 final size:30

Alignment explanation


    Indices: 1269--1618  Score: 316
    Period size: 30  Copynumber: 11.9  Consensus size: 30

       1259 TCTAAAAAAC

                   *                     *
       1269 ACATTTTGACCCCTAAACTTTTCCAAAATC
          1 ACATTTTAACCCCTAAACTTTTCCAAAATT

                        * * *            *
       1299 ACATTTTAACCCTTTAGCTTTTCCAAAATC
          1 ACATTTTAACCCCTAAACTTTTCCAAAATT

                   *    *                 
       1329 ACATTTTGACCCTTAAACTTTTCCAAAATT
          1 ACATTTTAACCCCTAAACTTTTCCAAAATT

                        *                *
       1359 ACATTTTAACCCATAAACTTTTCCAAAATC
          1 ACATTTTAACCCCTAAACTTTTCCAAAATT

                          *   *           
       1389 ACATTTTAACCCCTTAACCTTTCCAAAATT
          1 ACATTTTAACCCCTAAACTTTTCCAAAATT

                   *            *  *      
       1419 ACATTTTGA-CCCTAAACTTCTCTAAAATT
          1 ACATTTTAACCCCTAAACTTTTCCAAAATT

                        *          *      
       1448 ACATTTTAACCCTTAAACTTTTCAAAAATT
          1 ACATTTTAACCCCTAAACTTTTCCAAAATT

                                *         
       1478 ACA-TTTAA-CCCTAAACTTCTCCAAAATT
          1 ACATTTTAACCCCTAAACTTTTCCAAAATT

              *                  *          
       1506 ATGATTTT-ACCCCTAAAC--ATCCAAAAATT
          1 A-CATTTTAACCCCTAAACTTTTCC-AAAATT

                                     *     *
       1535 ACCA-TTT-ACCCCTAAA--TTTCTAAAAATC
          1 A-CATTTTAACCCCTAAACTTTTC-CAAAATT

                         *                  
       1563 ACATTTTCAA-CCTTAAA-TTTTCCAAAAGTT
          1 ACATTTT-AACCCCTAAACTTTTCCAAAA-TT

                      *                  
       1593 -CGATTTTAATCCC-AAA-TTTTCCAAAA
          1 AC-ATTTTAACCCCTAAACTTTTCCAAAA

       1619 ATTTCAATTT


Statistics
Matches: 268,  Mismatches: 38, Indels: 29
        0.80            0.11        0.09

Matches are distributed among these distances:
  27    2  0.01
  28   44  0.16
  29   65  0.24
  30  157  0.59

ACGTcount: A:0.37, C:0.25, G:0.02, T:0.36


Consensus pattern (30 bp):   
ACATTTTAACCCCTAAACTTTTCCAAAATT

Found at i:1790 original size:22 final size:21

Alignment explanation


    Indices: 1738--1791  Score: 56
    Period size: 22  Copynumber: 2.4  Consensus size: 21

       1728 CCTACACAAA

                                  
       1738 TTTAATTATTATTCTTTCTTAT
          1 TTTAATTA-TATTCTTTCTTAT

                *                  
       1760 TTTGTATTATATTACTTT-TTAT
          1 TTT-AATTATATT-CTTTCTTAT

                      
       1782 GTTTAATTAT
          1 -TTTAATTAT

       1792 TTTATGCATT


Statistics
Matches: 27,  Mismatches: 2, Indels: 6
        0.77            0.06        0.17

Matches are distributed among these distances:
  22   16  0.59
  23   11  0.41

ACGTcount: A:0.24, C:0.06, G:0.04, T:0.67


Consensus pattern (21 bp):   
TTTAATTATATTCTTTCTTAT
Done.