Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008866.1 Kokia drynarioides strain JFW-HI SEQ_123552, 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: 3275
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.34


Found at i:1990 original size:195 final size:194

Alignment explanation


    Indices: 1652--2098  Score: 553
    Period size: 195  Copynumber: 2.3  Consensus size: 194

       1642 ACTAGTACTT

                  *                                 *         *      *   *   
       1652 GATGCTGCTCACACGAGCTGTCGAGGACTCGCAACATATGTGGTACCCTAGCCATCGGTACGATA
          1 GATGCTACTCACACGAGCTGTCGAGGACTCGCAACATATGCGGTACCC-AACCATCGATACAATA

                                                                  *          
       1717 TCTATCTATAAACTATCCCCTAACAATGCTGCTCACACGAGCTATCGAGAATATGCATTCAAGCA
         65 TCTATCTATAAACTATCCCCTAACAATGCTGCTCACACGAGCTATCGAGAATATACATTCAAGCA

                                                                      *      
       1782 TAAATCCCAGCCATCGTAGGGCCTGTAATCC-TT-TTAAGGATTTCATATCTC-T-TTTTCGACT
        130 TAAATCCCAGCCATCGTAGGGCCTGTAATCCATTCTT--GGA-TTCATATCTCATCTTCTCGACT

               
       1843 CAC
        192 CAC

                                         *      *                   *        
       1846 GATGCTACTCACACGAGCTGTCGAGGACTTGCAACAAATGCGGTACCTCAACCATCTATACAATA
          1 GATGCTACTCACACGAGCTGTCGAGGACTCGCAACATATGCGGTACC-CAACCATCGATACAATA

               * *       * *         *                * *                  **
       1911 TCTGTGTATATAATTGTCCCCTAACGATGCTGCTCACACGAGTTGTCGAGAATATACACTT-ATT
         65 TCTATCTATA-AACTATCCCCTAACAATGCTGCTCACACGAGCTATCGAGAATATACA-TTCAAG

                    *              **                      *              *  
       1975 CATAAATCTCAGCCATCGTAGGGTTTGTAATCCATTCTTGGATTCATTTCTCATCTTCTCGATTC
        128 CATAAATCCCAGCCATCGTAGGGCCTGTAATCCATTCTTGGATTCATATCTCATCTTCTCGACTC

              
       2040 AC
        193 AC

                               *   *                                 
       2042 GATGCTACTCACACGAGCTATCGGGGACTCGCAACATATGCGGTACCCCAACCATCG
          1 GATGCTACTCACACGAGCTGTCGAGGACTCGCAACATATGCGGTA-CCCAACCATCG

       2099 CGTTGGTTTC


Statistics
Matches: 216,  Mismatches: 29, Indels: 14
        0.83            0.11        0.05

Matches are distributed among these distances:
 194   72  0.33
 195   77  0.36
 196   63  0.29
 197    4  0.02

ACGTcount: A:0.27, C:0.27, G:0.18, T:0.28


Consensus pattern (194 bp):   
GATGCTACTCACACGAGCTGTCGAGGACTCGCAACATATGCGGTACCCAACCATCGATACAATAT
CTATCTATAAACTATCCCCTAACAATGCTGCTCACACGAGCTATCGAGAATATACATTCAAGCAT
AAATCCCAGCCATCGTAGGGCCTGTAATCCATTCTTGGATTCATATCTCATCTTCTCGACTCAC

Found at i:2447 original size:28 final size:28

Alignment explanation


    Indices: 2424--2507  Score: 168
    Period size: 28  Copynumber: 3.0  Consensus size: 28

       2414 AAAATTGCAC

                                        
       2424 TTAACTTTTCACTTTTATTCAATTTAGT
          1 TTAACTTTTCACTTTTATTCAATTTAGT

                                        
       2452 TTAACTTTTCACTTTTATTCAATTTAGT
          1 TTAACTTTTCACTTTTATTCAATTTAGT

                                        
       2480 TTAACTTTTCACTTTTATTCAATTTAGT
          1 TTAACTTTTCACTTTTATTCAATTTAGT

       2508 CCCTTAGCTC


Statistics
Matches: 56,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  28   56  1.00

ACGTcount: A:0.25, C:0.14, G:0.04, T:0.57


Consensus pattern (28 bp):   
TTAACTTTTCACTTTTATTCAATTTAGT
Done.