Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004270.1 Kokia drynarioides strain JFW-HI SEQ_117558, 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: 7262
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32


Found at i:534 original size:172 final size:172

Alignment explanation


    Indices: 238--550  Score: 378
    Period size: 172  Copynumber: 1.8  Consensus size: 172

        228 CTTTTAGCTG

                   *                                     *                   
        238 TGTCACAGTTTATGGATCATAGTGATGGTTATCAATATTGATGATGTGATATACTGCTTAGATAT
          1 TGTCACAATTTATGGATCATAGTGATGGTTATCAATATTGATGATCTGATATACTGCTTAGATAT

            *        * *               *                    *   *            
        303 TCCACGTTAGTTTATGTTACCCGGACTTGAGGATGACCGCATATCATTTTCCCGATATGTGTCT-
         66 GCCACGTTAATCTATGTTACCCGGACTCGAGGATGACCGCATATCATTATCCAGATATGTGT-TG

            *                                          
        367 TACATAGGTGTTGGACACAGGTTTAGGAAAAACAAAGAATCTA
        130 CACATAGGTGTTGGACACAGGTTTAGGAAAAACAAAGAATCTA

                                *            **                 **           
        410 TGTCACAATTTATGGATCATGGTGATGGTTATCGTTATTGATGATCTGATATGTTGCTTAGATAT
          1 TGTCACAATTTATGGATCATAGTGATGGTTATCAATATTGATGATCTGATATACTGCTTAGATAT

              ****       *      *               ***             *            
        475 GCTGTTTTAATCTCTGTTACTCGGACTCGAGGATGAGTTCATATCCA-TATCTAGATATGTGTTG
         66 GCCACGTTAATCTATGTTACCCGGACTCGAGGATGACCGCATAT-CATTATCCAGATATGTGTTG

                        
        539 CACATAGGTGTT
        130 CACATAGGTGTT

        551 AGCCATGGGT


Statistics
Matches: 115,  Mismatches: 24, Indels: 4
        0.80            0.17        0.03

Matches are distributed among these distances:
 171    1  0.01
 172  112  0.97
 173    2  0.02

ACGTcount: A:0.27, C:0.14, G:0.22, T:0.37


Consensus pattern (172 bp):   
TGTCACAATTTATGGATCATAGTGATGGTTATCAATATTGATGATCTGATATACTGCTTAGATAT
GCCACGTTAATCTATGTTACCCGGACTCGAGGATGACCGCATATCATTATCCAGATATGTGTTGC
ACATAGGTGTTGGACACAGGTTTAGGAAAAACAAAGAATCTA

Found at i:2575 original size:43 final size:43

Alignment explanation


    Indices: 2514--2602  Score: 169
    Period size: 43  Copynumber: 2.1  Consensus size: 43

       2504 TAGAAACATA

                                                       
       2514 CTTAATCAATCACCATCTTTCAGTTTCCATAATTCGTTGGACC
          1 CTTAATCAATCACCATCTTTCAGTTTCCATAATTCGTTGGACC

                                       *               
       2557 CTTAATCAATCACCATCTTTCAGTTTCTATAATTCGTTGGACC
          1 CTTAATCAATCACCATCTTTCAGTTTCCATAATTCGTTGGACC

               
       2600 CTT
          1 CTT

       2603 CTGAACATTG


Statistics
Matches: 45,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  43   45  1.00

ACGTcount: A:0.25, C:0.27, G:0.09, T:0.39


Consensus pattern (43 bp):   
CTTAATCAATCACCATCTTTCAGTTTCCATAATTCGTTGGACC
Done.