Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01011220.1 Kokia drynarioides strain JFW-HI SEQ_126198, 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: 9525
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.33


Found at i:3031 original size:36 final size:36

Alignment explanation


    Indices: 2984--3062  Score: 158
    Period size: 36  Copynumber: 2.2  Consensus size: 36

       2974 TGTGTAACAA

                                                
       2984 TAATGTTTTGGGTGATTGATATTAATATGGATATTT
          1 TAATGTTTTGGGTGATTGATATTAATATGGATATTT

                                                
       3020 TAATGTTTTGGGTGATTGATATTAATATGGATATTT
          1 TAATGTTTTGGGTGATTGATATTAATATGGATATTT

                   
       3056 TAATGTT
          1 TAATGTT

       3063 CTTATTGACT


Statistics
Matches: 43,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  36   43  1.00

ACGTcount: A:0.28, C:0.00, G:0.22, T:0.51


Consensus pattern (36 bp):   
TAATGTTTTGGGTGATTGATATTAATATGGATATTT

Found at i:3609 original size:19 final size:18

Alignment explanation


    Indices: 3581--3621  Score: 73
    Period size: 19  Copynumber: 2.2  Consensus size: 18

       3571 CCTTGATCGC

                              
       3581 TTTTAGTAATTTTTATGT
          1 TTTTAGTAATTTTTATGT

                               
       3599 TTTTAAGTAATTTTTATGT
          1 TTTT-AGTAATTTTTATGT

                
       3618 TTTT
          1 TTTT

       3622 GAGTCCGTGT


Statistics
Matches: 22,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  18    4  0.18
  19   18  0.82

ACGTcount: A:0.22, C:0.00, G:0.10, T:0.68


Consensus pattern (18 bp):   
TTTTAGTAATTTTTATGT

Found at i:5208 original size:116 final size:116

Alignment explanation


    Indices: 4995--5247  Score: 364
    Period size: 116  Copynumber: 2.2  Consensus size: 116

       4985 CGGTAAAACT

                      * *                                                    
       4995 AATGCTTGTAACAGTAGAAGTACAGGGTAGGAGAGAGGTTGTTCTCTGACTTGAGTTGTTTCAGT
          1 AATGCTTGTATCGGTAGAAGTACAGGGTAGGAGAGAGGTTGTTCTCTGACTTGAGTTGTTTCAGT

                                       *       *           *   
       5060 AGTTGTATAACAGGTATCGATAATTCTTTACATTGTGGTATTGGTAGTTTA
         66 AGTTGTATAACAGGTATCGATAATTCTGTACATTGAGGTATTGGTAGCTTA

                             *                   *           *           **  
       5111 AATGCTTGTATCGGTAGTAGTACAGGGTAGGAGAGAGTTTGTTCTCTGATTTGAGTTGTTTTGGT
          1 AATGCTTGTATCGGTAGAAGTACAGGGTAGGAGAGAGGTTGTTCTCTGACTTGAGTTGTTTCAGT

                      *            *                            
       5176 AGTTGTATAATAGGTATC-AGTAGTTCTGTACATTGAGGTATTGGTAGCTTA
         66 AGTTGTATAACAGGTATCGA-TAATTCTGTACATTGAGGTATTGGTAGCTTA

               *         *       
       5227 AATACTTGTATCGATAGAAGT
          1 AATGCTTGTATCGGTAGAAGT

       5248 TGTAGGCTAG


Statistics
Matches: 121,  Mismatches: 15, Indels: 2
        0.88            0.11        0.01

Matches are distributed among these distances:
 115    1  0.01
 116  120  0.99

ACGTcount: A:0.26, C:0.09, G:0.27, T:0.38


Consensus pattern (116 bp):   
AATGCTTGTATCGGTAGAAGTACAGGGTAGGAGAGAGGTTGTTCTCTGACTTGAGTTGTTTCAGT
AGTTGTATAACAGGTATCGATAATTCTGTACATTGAGGTATTGGTAGCTTA

Found at i:8480 original size:147 final size:147

Alignment explanation


    Indices: 8213--8504  Score: 476
    Period size: 147  Copynumber: 2.0  Consensus size: 147

       8203 GACTAAGGCC

                                 *                    * *                    
       8213 ATGTGAAAATCGAAAAACCTTGGGTTTTTGGGGAACATAATCGTGTGATGGTCTGTGTGGTCCAC
          1 ATGTGAAAATCGAAAAACCTTAGGTTTTTGGGGAACATAATCATATGATGGTCTGTGTGGTCCAC

                **       *         **     *                                  
       8278 GAGTGGCCCTAGGCACAATTTTCGTTGATTTGATTGTAAAAGAACACATGCATGTTACCAGAATC
         66 GAGTCACCCTAGGAACAATTTTCCCTGATTCGATTGTAAAAGAACACATGCATGTTACCAGAATC

              *              
       8343 TCGAGCGATGTCCCTTA
        131 TCAAGCGATGTCCCTTA

                                                                *            
       8360 ATGTGAAAATCGAAAAACCTTAGGTTTTTGGGGAACATAATCATATGATGGTTTGTGTGGTCCAC
          1 ATGTGAAAATCGAAAAACCTTAGGTTTTTGGGGAACATAATCATATGATGGTCTGTGTGGTCCAC

                             *                                               
       8425 GAGTCACCCTAGGAACATTTTTCCCTGATTCGATTGTAAAAGAACACATGCATGTTACCAGAATC
         66 GAGTCACCCTAGGAACAATTTTCCCTGATTCGATTGTAAAAGAACACATGCATGTTACCAGAATC

                           
       8490 TCAAGCGATGTCCCT
        131 TCAAGCGATGTCCCT

       8505 CATGTTCAAA


Statistics
Matches: 133,  Mismatches: 12, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
 147  133  1.00

ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30


Consensus pattern (147 bp):   
ATGTGAAAATCGAAAAACCTTAGGTTTTTGGGGAACATAATCATATGATGGTCTGTGTGGTCCAC
GAGTCACCCTAGGAACAATTTTCCCTGATTCGATTGTAAAAGAACACATGCATGTTACCAGAATC
TCAAGCGATGTCCCTTA
Done.