Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008050.1 Kokia drynarioides strain JFW-HI SEQ_122706, 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: 12593
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35


Found at i:2315 original size:17 final size:18

Alignment explanation


    Indices: 2293--2326  Score: 52
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       2283 TTGTTAAGTT

                              
       2293 TTGTATT-TGTTTATTTA
          1 TTGTATTATGTTTATTTA

                     *       
       2310 TTGTATTATTTTTATTT
          1 TTGTATTATGTTTATTT

       2327 GATTTAGACT


Statistics
Matches: 15,  Mismatches: 1, Indels: 1
        0.88            0.06        0.06

Matches are distributed among these distances:
  17    7  0.47
  18    8  0.53

ACGTcount: A:0.18, C:0.00, G:0.09, T:0.74


Consensus pattern (18 bp):   
TTGTATTATGTTTATTTA

Found at i:3276 original size:41 final size:41

Alignment explanation


    Indices: 3228--3311  Score: 150
    Period size: 41  Copynumber: 2.0  Consensus size: 41

       3218 TAAAATGTTA

                               *             *       
       3228 ATAAATAAATTATGAGTTGGTGAAAGTTAATAATAAATTTG
          1 ATAAATAAATTATGAGTTGATGAAAGTTAATAACAAATTTG

                                                     
       3269 ATAAATAAATTATGAGTTGATGAAAGTTAATAACAAATTTG
          1 ATAAATAAATTATGAGTTGATGAAAGTTAATAACAAATTTG

              
       3310 AT
          1 AT

       3312 TACGATGCGT


Statistics
Matches: 41,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  41   41  1.00

ACGTcount: A:0.48, C:0.01, G:0.15, T:0.36


Consensus pattern (41 bp):   
ATAAATAAATTATGAGTTGATGAAAGTTAATAACAAATTTG

Found at i:6113 original size:24 final size:24

Alignment explanation


    Indices: 6068--6113  Score: 56
    Period size: 24  Copynumber: 1.9  Consensus size: 24

       6058 GTGAAATGAA

                          *  *      
       6068 ATTTAAGTCAAATTGAATAAATTT
          1 ATTTAAGTCAAATTAAAAAAATTT

                *   *             
       6092 ATTTGAGTTAAATTAAAAAAAT
          1 ATTTAAGTCAAATTAAAAAAAT

       6114 AAATCAATCA


Statistics
Matches: 18,  Mismatches: 4, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  24   18  1.00

ACGTcount: A:0.50, C:0.02, G:0.09, T:0.39


Consensus pattern (24 bp):   
ATTTAAGTCAAATTAAAAAAATTT

Found at i:6340 original size:20 final size:20

Alignment explanation


    Indices: 6318--6361  Score: 70
    Period size: 20  Copynumber: 2.1  Consensus size: 20

       6308 TAATTAAACA

                              *  
       6318 TTTTTTTATATATTTTAAGAT
          1 TTTTTTTATA-ATTTTAAAAT

                                
       6339 TTTTTTTATAATTTTAAAAT
          1 TTTTTTTATAATTTTAAAAT

               
       6359 TTT
          1 TTT

       6362 AAAATTATAT


Statistics
Matches: 22,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  20   12  0.55
  21   10  0.45

ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68


Consensus pattern (20 bp):   
TTTTTTTATAATTTTAAAAT

Found at i:9504 original size:6 final size:7

Alignment explanation


    Indices: 9489--9514  Score: 52
    Period size: 7  Copynumber: 3.7  Consensus size: 7

       9479 TATGATTCAA

                   
       9489 TTTTATT
          1 TTTTATT

                   
       9496 TTTTATT
          1 TTTTATT

                   
       9503 TTTTATT
          1 TTTTATT

                 
       9510 TTTTA
          1 TTTTA

       9515 ATTATATAAT


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   19  1.00

ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85


Consensus pattern (7 bp):   
TTTTATT

Found at i:10290 original size:54 final size:52

Alignment explanation


    Indices: 10150--10315  Score: 167
    Period size: 54  Copynumber: 3.1  Consensus size: 52

      10140 CCAAAAATAC

                               *    *   *     *    *       *    
      10150 TTTTTTTTTATCTGAAAAATGAGTGATGACCATGGCTTGACAAACACTAAAA
          1 TTTTTTTTTATCTGAAAAAAGAGTAATGGCCATGACTTGGCAAACACCAAAA

                          *             *                   *      
      10202 TTTTTTTTTATTATTTGAAAAAAGA--AGT-GCCATGACTTGGCAAACCCCAAAA
          1 --TTTTTTT-TTATCTGAAAAAAGAGTAATGGCCATGACTTGGCAAACACCAAAA

                                                         *         
      10254 TATTTTTTTTATCTGAAAAAAAGAGTAATGGCCATGACTTGGCAAGCATCCAAAA
          1 T-TTTTTTTTATCTG-AAAAAAGAGTAATGGCCATGACTTGGCAAACA-CCAAAA

                   
      10309 TTTTTTT
          1 TTTTTTT

      10316 ATCTAATAAA


Statistics
Matches: 92,  Mismatches: 13, Indels: 14
        0.77            0.11        0.12

Matches are distributed among these distances:
  50    7  0.08
  51   14  0.15
  52   19  0.21
  53    3  0.03
  54   29  0.32
  55   20  0.22

ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36


Consensus pattern (52 bp):   
TTTTTTTTTATCTGAAAAAAGAGTAATGGCCATGACTTGGCAAACACCAAAA

Found at i:12585 original size:20 final size:21

Alignment explanation


    Indices: 12544--12586  Score: 61
    Period size: 21  Copynumber: 2.1  Consensus size: 21

      12534 TAATTTACTT

                                 
      12544 TAATTTAATTTTGCTAGTTAG
          1 TAATTTAATTTTGCTAGTTAG

                  *        *     
      12565 TAATTTTATTTTG-TTGTTAG
          1 TAATTTAATTTTGCTAGTTAG

              
      12585 TA
          1 TA

      12587 GTAGTAA


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  20    8  0.40
  21   12  0.60

ACGTcount: A:0.26, C:0.02, G:0.14, T:0.58


Consensus pattern (21 bp):   
TAATTTAATTTTGCTAGTTAG
Done.