Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005349.1 Kokia drynarioides strain JFW-HI SEQ_119314, 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: 3255
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37


Found at i:469 original size:26 final size:26

Alignment explanation


    Indices: 440--525  Score: 77
    Period size: 26  Copynumber: 3.2  Consensus size: 26

        430 CTCCTCTGAA

                                      
        440 TCAAATAAACTTAATTCTTCTCTCAT
          1 TCAAATAAACTTAATTCTTCTCTCAT

                    *    **               *
        466 TCAAACT-TA-TTTTTCTCTTCTCTCGTCAA
          1 TCAAA-TAAACTTAAT-TC-T-TCTC-TCAT

                                      
        495 TCAAATAAACTTAATTCTTCTCTCAT
          1 TCAAATAAACTTAATTCTTCTCTCAT

                 
        521 TCAAA
          1 TCAAA

        526 CTTATTTTTC


Statistics
Matches: 45,  Mismatches: 8, Indels: 14
        0.67            0.12        0.21

Matches are distributed among these distances:
  25    3  0.07
  26   16  0.36
  27    6  0.13
  28    6  0.13
  29   11  0.24
  30    3  0.07

ACGTcount: A:0.31, C:0.24, G:0.01, T:0.43


Consensus pattern (26 bp):   
TCAAATAAACTTAATTCTTCTCTCAT

Found at i:499 original size:55 final size:55

Alignment explanation


    Indices: 438--544  Score: 214
    Period size: 55  Copynumber: 1.9  Consensus size: 55

        428 CTCTCCTCTG

                                                                   
        438 AATCAAATAAACTTAATTCTTCTCTCATTCAAACTTATTTTTCTCTTCTCTCGTC
          1 AATCAAATAAACTTAATTCTTCTCTCATTCAAACTTATTTTTCTCTTCTCTCGTC

                                                                
        493 AATCAAATAAACTTAATTCTTCTCTCATTCAAACTTATTTTTCTCTTCTCTC
          1 AATCAAATAAACTTAATTCTTCTCTCATTCAAACTTATTTTTCTCTTCTCTC

        545 ATTTCTTCAT


Statistics
Matches: 52,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  55   52  1.00

ACGTcount: A:0.28, C:0.25, G:0.01, T:0.46


Consensus pattern (55 bp):   
AATCAAATAAACTTAATTCTTCTCTCATTCAAACTTATTTTTCTCTTCTCTCGTC

Found at i:539 original size:26 final size:26

Alignment explanation


    Indices: 455--547  Score: 91
    Period size: 26  Copynumber: 3.5  Consensus size: 26

        445 TAAACTTAAT

                                      
        455 TCTTCTCTCATTCAAACTTATTTTTC
          1 TCTTCTCTCATTCAAACTTATTTTTC

                         *        *    **  
        481 TCTTCTCTCGTCAATCAAA-TAAACTTAAT-
          1 TC-T-TCTC-TCATTCAAACT-TA-TTTTTC

                                      
        510 TCTTCTCTCATTCAAACTTATTTTTC
          1 TCTTCTCTCATTCAAACTTATTTTTC

                        
        536 TCTTCTCTCATT
          1 TCTTCTCTCATT

        548 TCTTCATCTT


Statistics
Matches: 52,  Mismatches: 8, Indels: 14
        0.70            0.11        0.19

Matches are distributed among these distances:
  25    3  0.06
  26   23  0.44
  27    6  0.12
  28    6  0.12
  29   11  0.21
  30    3  0.06

ACGTcount: A:0.23, C:0.27, G:0.01, T:0.49


Consensus pattern (26 bp):   
TCTTCTCTCATTCAAACTTATTTTTC
Done.