Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007738.1 Kokia drynarioides strain JFW-HI SEQ_122371, 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: 2719
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.33


Found at i:120 original size:29 final size:29

Alignment explanation


    Indices: 5--319  Score: 191
    Period size: 29  Copynumber: 10.9  Consensus size: 29

          1 GAAG

                       *              *   
          5 AGTTTG-GGGTTAAAATGTAA-TTTTGGAA
          1 AGTTTGAGGGTAAAAATGTAATTTTTAG-A

                 *     *       *      **  
         33 AGTTTTAGGG-GAAAATGTCATTTTGGGGA
          1 AGTTTGAGGGTAAAAATGTAATTTT-TAGA

                *       * *    *  *   *  
         62 AGTTCGA-GGTAGACATGTGATCTTTGGA
          1 AGTTTGAGGGTAAAAATGTAATTTTTAGA

                                         
         90 AGTTTGAGGGTAAAAATGTAATTTTTAGA
          1 AGTTTGAGGGTAAAAATGTAATTTTTAGA

                               *           
        119 AGTTTG-GGAG-AAAAATGCAATTTTTTAGA
          1 AGTTTGAGG-GTAAAAATGTAA-TTTTTAGA

                  *   *      *           
        148 AGTTTGGGGGCAAAAATCTAATTTTTAGA
          1 AGTTTGAGGGTAAAAATGTAATTTTTAGA

                 *     *       *          
        177 AGTTTAAGGGTCAAAATGTGA-TTTTAGGA
          1 AGTTTGAGGGTAAAAATGTAATTTTTA-GA

                **          *             
        206 AGTTCAAGGGTAAAAAAGTAATTTTTAAGA
          1 AGTTTGAGGGTAAAAATGTAATTTTT-AGA

                *                *         
        236 AGTTCG-GGAGTAAAAATGTACTTTTTAAGA
          1 AGTTTGAGG-GTAAAAATGTAATTTTT-AGA

                * *    *       *           
        266 AGTTCGGGGGTCAAAATGTGA-TTTTAGAAA
          1 AGTTTGAGGGTAAAAATGTAATTTTTAG--A

                 *     *             
        296 AG-TTAAGGGTTAAAATGTAATTTT
          1 AGTTTGAGGGTAAAAATGTAATTTT

        320 GGAAAGTTTG


Statistics
Matches: 228,  Mismatches: 42, Indels: 32
        0.75            0.14        0.11

Matches are distributed among these distances:
  28   42  0.18
  29  120  0.53
  30   63  0.28
  31    3  0.01

ACGTcount: A:0.35, C:0.04, G:0.26, T:0.35


Consensus pattern (29 bp):   
AGTTTGAGGGTAAAAATGTAATTTTTAGA

Found at i:291 original size:89 final size:88

Alignment explanation


    Indices: 137--319  Score: 233
    Period size: 89  Copynumber: 2.1  Consensus size: 88

        127 AGAAAAATGC

                   *       *   *                        *                    
        137 AATTTTTTAGAAGTTTGGGGGCAAAAATCTAATTTTTAGAAGTTTAAGGGTCAAAATGTGATTTT
          1 AATTTTTAAGAAGTTCGGGAGCAAAAATCTAATTTTTAGAAGTTCAAGGGTCAAAATGTGATTTT

               *                    
        202 AG-GAAGTTCAAGGGTAAAAAAGT
         66 AGAAAAGTT-AAGGGTAAAAAAGT

                                 *      *  *              **                 
        225 AATTTTTAAGAAGTTCGGGAGTAAAAATGTACTTTTTAAGAAGTTCGGGGGTCAAAATGTGATTT
          1 AATTTTTAAGAAGTTCGGGAGCAAAAATCTAATTTTT-AGAAGTTCAAGGGTCAAAATGTGATTT

                            *    *  
        290 TAGAAAAGTTAAGGGTTAAAATGT
         65 TAGAAAAGTTAAGGGTAAAAAAGT

                  
        314 AATTTT
          1 AATTTT

        320 GGAAAGTTTG


Statistics
Matches: 81,  Mismatches: 12, Indels: 3
        0.84            0.12        0.03

Matches are distributed among these distances:
  88   31  0.38
  89   45  0.56
  90    5  0.06

ACGTcount: A:0.37, C:0.04, G:0.23, T:0.35


Consensus pattern (88 bp):   
AATTTTTAAGAAGTTCGGGAGCAAAAATCTAATTTTTAGAAGTTCAAGGGTCAAAATGTGATTTT
AGAAAAGTTAAGGGTAAAAAAGT

Found at i:1412 original size:13 final size:13

Alignment explanation


    Indices: 1394--1439  Score: 56
    Period size: 13  Copynumber: 3.4  Consensus size: 13

       1384 ATCTATTTAA

                         
       1394 TATTATACTTATT
          1 TATTATACTTATT

                    *      
       1407 TATTATTAGTATATT
          1 TATTA-TACT-TATT

                   *     
       1422 TATTATATTTATT
          1 TATTATACTTATT

                 
       1435 TATTA
          1 TATTA

       1440 AAACGTTTAG


Statistics
Matches: 29,  Mismatches: 2, Indels: 4
        0.83            0.06        0.11

Matches are distributed among these distances:
  13   14  0.48
  14    6  0.21
  15    9  0.31

ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63


Consensus pattern (13 bp):   
TATTATACTTATT

Found at i:1423 original size:15 final size:13

Alignment explanation


    Indices: 1376--1439  Score: 51
    Period size: 13  Copynumber: 4.7  Consensus size: 13

       1366 TTTTTATTAT

                      *  
       1376 TATTTATTATCTA
          1 TATTTATTATATA

                            
       1389 T-TTAATATTATACT-
          1 TATT--TATTATA-TA

                           
       1403 TATTTATTATTAGTA
          1 TATTTATTA-TA-TA

                        *
       1418 TATTTATTATATT
          1 TATTTATTATATA

                     
       1431 TATTTATTA
          1 TATTTATTA

       1440 AAACGTTTAG


Statistics
Matches: 42,  Mismatches: 3, Indels: 12
        0.74            0.05        0.21

Matches are distributed among these distances:
  12    2  0.05
  13   16  0.38
  14   12  0.29
  15   12  0.29

ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62


Consensus pattern (13 bp):   
TATTTATTATATA

Found at i:1994 original size:23 final size:23

Alignment explanation


    Indices: 1962--2009  Score: 78
    Period size: 23  Copynumber: 2.1  Consensus size: 23

       1952 AAAATTTGGA

                               *   
       1962 TTTTGGATTTGGACTTTTAGAAT
          1 TTTTGGATTTGGACTTTTAAAAT

                 *                 
       1985 TTTTGTATTTGGACTTTTAAAAT
          1 TTTTGGATTTGGACTTTTAAAAT

              
       2008 TT
          1 TT

       2010 AAATTTAAAA


Statistics
Matches: 23,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  23   23  1.00

ACGTcount: A:0.23, C:0.04, G:0.17, T:0.56


Consensus pattern (23 bp):   
TTTTGGATTTGGACTTTTAAAAT
Done.