Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000156.1 Kokia drynarioides strain JFW-HI SEQ_110818, 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: 16709
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36


Found at i:587 original size:44 final size:44

Alignment explanation


    Indices: 528--626  Score: 103
    Period size: 44  Copynumber: 2.2  Consensus size: 44

        518 AATTACTAAT

                *            *                    *        
        528 TAATCCTTGAATTTTT-TTAACCTTTCTTA-TTTAGACTACACATTC
          1 TAATTCTT-AATTTTTCCTAACC-TTCTTATTTTA-ACCACACATTC

                                *                  *    
        573 TAATTCTTAATTTTTCCTAATCTTCTTATTTTAACCACATATTC
          1 TAATTCTTAATTTTTCCTAACCTTCTTATTTTAACCACACATTC

               *      
        617 TAACTCTTAA
          1 TAATTCTTAA

        627 CTCGACACTA


Statistics
Matches: 46,  Mismatches: 6, Indels: 5
        0.81            0.11        0.09

Matches are distributed among these distances:
  44   31  0.67
  45   15  0.33

ACGTcount: A:0.28, C:0.20, G:0.02, T:0.49


Consensus pattern (44 bp):   
TAATTCTTAATTTTTCCTAACCTTCTTATTTTAACCACACATTC

Found at i:2049 original size:17 final size:18

Alignment explanation


    Indices: 2022--2055  Score: 61
    Period size: 17  Copynumber: 1.9  Consensus size: 18

       2012 GTTGCATATG

                              
       2022 TAAATTTTTAATATTAAT
          1 TAAATTTTTAATATTAAT

                             
       2040 TAAA-TTTTAATATTAA
          1 TAAATTTTTAATATTAA

       2056 AAATTTATAG


Statistics
Matches: 16,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  17   12  0.75
  18    4  0.25

ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53


Consensus pattern (18 bp):   
TAAATTTTTAATATTAAT

Found at i:2260 original size:3 final size:3

Alignment explanation


    Indices: 2252--2288  Score: 74
    Period size: 3  Copynumber: 12.3  Consensus size: 3

       2242 TCTTAATTCA

                                                             
       2252 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
          1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A

       2289 GAACAACAAT


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   34  1.00

ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65


Consensus pattern (3 bp):   
ATT

Found at i:13550 original size:5 final size:5

Alignment explanation


    Indices: 13540--13568  Score: 58
    Period size: 5  Copynumber: 5.8  Consensus size: 5

      13530 AGTGGATACA

                                              
      13540 CATCC CATCC CATCC CATCC CATCC CATC
          1 CATCC CATCC CATCC CATCC CATCC CATC

      13569 ACCTCACCTC


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   5   24  1.00

ACGTcount: A:0.21, C:0.59, G:0.00, T:0.21


Consensus pattern (5 bp):   
CATCC

Found at i:14011 original size:126 final size:126

Alignment explanation


    Indices: 13814--14065  Score: 504
    Period size: 126  Copynumber: 2.0  Consensus size: 126

      13804 TTATCTCTAA

                                                                             
      13814 TCAAGCGTTGATGTTGTTAGCAATATGAAAGCTTGGGTTCTTGAGTATTCATATTCAAGTCTTAC
          1 TCAAGCGTTGATGTTGTTAGCAATATGAAAGCTTGGGTTCTTGAGTATTCATATTCAAGTCTTAC

                                                                         
      13879 TCTACGTAGTTGCTATAGATAAATTTTATTCACTTATATCTTGGTATTTAGATATGTATTT
         66 TCTACGTAGTTGCTATAGATAAATTTTATTCACTTATATCTTGGTATTTAGATATGTATTT

                                                                             
      13940 TCAAGCGTTGATGTTGTTAGCAATATGAAAGCTTGGGTTCTTGAGTATTCATATTCAAGTCTTAC
          1 TCAAGCGTTGATGTTGTTAGCAATATGAAAGCTTGGGTTCTTGAGTATTCATATTCAAGTCTTAC

                                                                         
      14005 TCTACGTAGTTGCTATAGATAAATTTTATTCACTTATATCTTGGTATTTAGATATGTATTT
         66 TCTACGTAGTTGCTATAGATAAATTTTATTCACTTATATCTTGGTATTTAGATATGTATTT

      14066 ATACTTATAA


Statistics
Matches: 126,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
 126  126  1.00

ACGTcount: A:0.27, C:0.12, G:0.17, T:0.44


Consensus pattern (126 bp):   
TCAAGCGTTGATGTTGTTAGCAATATGAAAGCTTGGGTTCTTGAGTATTCATATTCAAGTCTTAC
TCTACGTAGTTGCTATAGATAAATTTTATTCACTTATATCTTGGTATTTAGATATGTATTT
Done.