Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007187.1 Kokia drynarioides strain JFW-HI SEQ_121800, 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: 12185
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30


Found at i:4422 original size:3 final size:3

Alignment explanation


    Indices: 4405--4462  Score: 66
    Period size: 3  Copynumber: 20.0  Consensus size: 3

       4395 GTATCTCCAT

                          *               *      *                   *     
       4405 TTC TTC -TC TTT TTC TTC TTC TTT TTC TCC TTC TTC -TC TTC TAC TTC
          1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC

                           
       4451 TTC TTC TTC TTC
          1 TTC TTC TTC TTC

       4463 CACAAGCCAG


Statistics
Matches: 45,  Mismatches: 8, Indels: 4
        0.79            0.14        0.07

Matches are distributed among these distances:
   2    4  0.09
   3   41  0.91

ACGTcount: A:0.02, C:0.33, G:0.00, T:0.66


Consensus pattern (3 bp):   
TTC

Found at i:4424 original size:14 final size:14

Alignment explanation


    Indices: 4405--4454  Score: 57
    Period size: 14  Copynumber: 3.5  Consensus size: 14

       4395 GTATCTCCAT

                          
       4405 TTCTTCTCTTTTTC
          1 TTCTTCTCTTTTTC

                            
       4419 TTCTTCT-TTTTCTCC
          1 TTCTTCTCTTTT-T-C

                      * * 
       4434 TTCTTCTCTTCTAC
          1 TTCTTCTCTTTTTC

                   
       4448 TTCTTCT
          1 TTCTTCT

       4455 TCTTCTTCCA


Statistics
Matches: 31,  Mismatches: 2, Indels: 6
        0.79            0.05        0.15

Matches are distributed among these distances:
  13    4  0.13
  14   16  0.52
  15    8  0.26
  16    3  0.10

ACGTcount: A:0.02, C:0.32, G:0.00, T:0.66


Consensus pattern (14 bp):   
TTCTTCTCTTTTTC

Found at i:4442 original size:29 final size:29

Alignment explanation


    Indices: 4405--4460  Score: 85
    Period size: 29  Copynumber: 1.9  Consensus size: 29

       4395 GTATCTCCAT

                      * *         *      
       4405 TTCTTCTCTTTTTCTTCTTCTTTTTCTCC
          1 TTCTTCTCTTCTACTTCTTCTTCTTCTCC

                                       
       4434 TTCTTCTCTTCTACTTCTTCTTCTTCT
          1 TTCTTCTCTTCTACTTCTTCTTCTTCT

       4461 TCCACAAGCC


Statistics
Matches: 24,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  29   24  1.00

ACGTcount: A:0.02, C:0.32, G:0.00, T:0.66


Consensus pattern (29 bp):   
TTCTTCTCTTCTACTTCTTCTTCTTCTCC

Found at i:5493 original size:87 final size:89

Alignment explanation


    Indices: 5341--5514  Score: 289
    Period size: 87  Copynumber: 2.0  Consensus size: 89

       5331 CCCTGCATCG

                                              *          *              *    
       5341 TCTCATTCTCTTTTGTCGATCGAATAACAGAAAATGATGCACTGCTGCAAATCTTTTTCTGCATT
          1 TCTCATTCTCTTTTGTCGATCGAATAACAGAAAAAGATGCACTGCCGCAAATCTTTTTCTACATT

              *                     
       5406 T-TAACCTCCCACTTAATAAGAGT
         66 TGAAACCTCCCACTTAATAAGAGT

                            *                                                
       5429 TCTCATTCTC-TTTGTTGATCGAATAACAGAAAAAGATGCACTGCCGCAAATCTTTTTCTACATT
          1 TCTCATTCTCTTTTGTCGATCGAATAACAGAAAAAGATGCACTGCCGCAAATCTTTTTCTACATT

                                  
       5493 TGAAACCTCCCACTTAATAAGA
         66 TGAAACCTCCCACTTAATAAGA

       5515 TAACTCATTA


Statistics
Matches: 80,  Mismatches: 5, Indels: 2
        0.92            0.06        0.02

Matches are distributed among these distances:
  87   51  0.64
  88   29  0.36

ACGTcount: A:0.30, C:0.23, G:0.12, T:0.34


Consensus pattern (89 bp):   
TCTCATTCTCTTTTGTCGATCGAATAACAGAAAAAGATGCACTGCCGCAAATCTTTTTCTACATT
TGAAACCTCCCACTTAATAAGAGT

Found at i:9471 original size:20 final size:19

Alignment explanation


    Indices: 9437--9476  Score: 55
    Period size: 20  Copynumber: 2.1  Consensus size: 19

       9427 GTTGACACGA

                                
       9437 TTTTTTCTTTGGTTTTCTTG
          1 TTTTTTCTTTGGTTTT-TTG

                                
       9457 TTTTTTC-TTGTGTTTTTTG
          1 TTTTTTCTTTG-GTTTTTTG

             
       9476 T
          1 T

       9477 GAACTCGTTG


Statistics
Matches: 19,  Mismatches: 0, Indels: 3
        0.86            0.00        0.14

Matches are distributed among these distances:
  19    7  0.37
  20   12  0.63

ACGTcount: A:0.00, C:0.07, G:0.15, T:0.78


Consensus pattern (19 bp):   
TTTTTTCTTTGGTTTTTTG
Done.