Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005261.1 Kokia drynarioides strain JFW-HI SEQ_119170, 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: 61735
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36


Found at i:5187 original size:12 final size:12

Alignment explanation


    Indices: 5170--5194  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

       5160 GAAACACCCA

                        
       5170 ACAATCTAAGAT
          1 ACAATCTAAGAT

                        
       5182 ACAATCTAAGAT
          1 ACAATCTAAGAT

             
       5194 A
          1 A

       5195 GTTGGGTGAC


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.52, C:0.16, G:0.08, T:0.24


Consensus pattern (12 bp):   
ACAATCTAAGAT

Found at i:16406 original size:18 final size:19

Alignment explanation


    Indices: 16383--16418  Score: 56
    Period size: 19  Copynumber: 1.9  Consensus size: 19

      16373 TATCTAATTC

                               
      16383 AAAAGA-AAAAAATTATAT
          1 AAAAGACAAAAAATTATAT

                   *          
      16401 AAAAGACGAAAAATTATA
          1 AAAAGACAAAAAATTATA

      16419 ATTATTTAAC


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    6  0.38
  19   10  0.62

ACGTcount: A:0.69, C:0.03, G:0.08, T:0.19


Consensus pattern (19 bp):   
AAAAGACAAAAAATTATAT

Found at i:25455 original size:2 final size:2

Alignment explanation


    Indices: 25450--25495  Score: 92
    Period size: 2  Copynumber: 23.0  Consensus size: 2

      25440 AAAGAACTAA

                                                                          
      25450 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                 
      25492 AT AT
          1 AT AT

      25496 TAATTTTTGA


Statistics
Matches: 44,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   44  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:28723 original size:48 final size:47

Alignment explanation


    Indices: 28658--28824  Score: 144
    Period size: 48  Copynumber: 3.6  Consensus size: 47

      28648 CCATCAGGAC

                     *  *          *                       *
      28658 ACAAAGTACGACTTAATGCTTCTGCTCTGTCCCGTTCTCCATCGAAAG
          1 ACAAAGTACAACCTAATGCTTCTACTCTGTCCC-TTCTCCATCGAAAA

                  *           *        *         *   *     
      28706 ACAAAGCACAACCTAATGTTTCTACTCCGTCCC--CTTCATTGAAAA
          1 ACAAAGTACAACCTAATGCTTCTACTCTGTCCCTTCTCCATCGAAAA

                     *   *          *               *       
      28751 ACAAAGTACGACCCAATGCTTCTATTCTGTCCCCTTCTCCCTC-AAAA
          1 ACAAAGTACAACCTAATGCTTCTACTCTGT-CCCTTCTCCATCGAAAA

                        *               
      28798 CACAAAGTACGATCC-AATGCTTCTACT
          1 -ACAAAGTAC-AACCTAATGCTTCTACT

      28825 GCTTCTACTT


Statistics
Matches: 93,  Mismatches: 21, Indels: 10
        0.75            0.17        0.08

Matches are distributed among these distances:
  45   33  0.35
  46    3  0.03
  47    4  0.04
  48   51  0.55
  49    2  0.02

ACGTcount: A:0.29, C:0.32, G:0.11, T:0.28


Consensus pattern (47 bp):   
ACAAAGTACAACCTAATGCTTCTACTCTGTCCCTTCTCCATCGAAAA

Found at i:31495 original size:52 final size:52

Alignment explanation


    Indices: 31437--31544  Score: 216
    Period size: 52  Copynumber: 2.1  Consensus size: 52

      31427 CGAAGATATA

                                                                
      31437 ACTTACAAGAATTTTTTAAATGTATTAAAAAGCTTTAAAAAAATCCTACCTT
          1 ACTTACAAGAATTTTTTAAATGTATTAAAAAGCTTTAAAAAAATCCTACCTT

                                                                
      31489 ACTTACAAGAATTTTTTAAATGTATTAAAAAGCTTTAAAAAAATCCTACCTT
          1 ACTTACAAGAATTTTTTAAATGTATTAAAAAGCTTTAAAAAAATCCTACCTT

                
      31541 ACTT
          1 ACTT

      31545 GTATCACGTA


Statistics
Matches: 56,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  52   56  1.00

ACGTcount: A:0.44, C:0.14, G:0.06, T:0.37


Consensus pattern (52 bp):   
ACTTACAAGAATTTTTTAAATGTATTAAAAAGCTTTAAAAAAATCCTACCTT

Found at i:60289 original size:19 final size:20

Alignment explanation


    Indices: 60267--60311  Score: 51
    Period size: 18  Copynumber: 2.4  Consensus size: 20

      60257 AAATCCCCAA

                                 
      60267 ATTTTATCCAAATT-T-ATTT
          1 ATTTTATCC-AATTCTAATTT

                   *            
      60286 A-TTTATTCAATTCTAATTT
          1 ATTTTATCCAATTCTAATTT

                   
      60305 ATTTTAT
          1 ATTTTAT

      60312 TTTAAGTTGA


Statistics
Matches: 22,  Mismatches: 1, Indels: 5
        0.79            0.04        0.18

Matches are distributed among these distances:
  17    4  0.18
  18    7  0.32
  19    6  0.27
  20    5  0.23

ACGTcount: A:0.31, C:0.09, G:0.00, T:0.60


Consensus pattern (20 bp):   
ATTTTATCCAATTCTAATTT

Found at i:61681 original size:2 final size:2

Alignment explanation


    Indices: 61644--61672  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

      61634 TATCAGTTTT

                                                       
      61644 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

      61673 CTGTATATAA


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Done.