Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01011644.1 Kokia drynarioides strain JFW-HI SEQ_126636, 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: 42861
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33


Found at i:5048 original size:44 final size:44

Alignment explanation


    Indices: 4975--5061  Score: 120
    Period size: 44  Copynumber: 2.0  Consensus size: 44

       4965 GTTTGAAATG

                    *              *      *    *        
       4975 ATACATTTTATTATTTATTGTATGCTATTTTTAAATGAATACTC
          1 ATACATTTCATTATTTATTGTATACTATTTATAAAAGAATACTC

                *                   *                  
       5019 ATACGTTTCATTATTTATTGTATATTATTTATAAAAGAATACT
          1 ATACATTTCATTATTTATTGTATACTATTTATAAAAGAATACT

       5062 TATATTCTAC


Statistics
Matches: 37,  Mismatches: 6, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  44   37  1.00

ACGTcount: A:0.34, C:0.08, G:0.07, T:0.51


Consensus pattern (44 bp):   
ATACATTTCATTATTTATTGTATACTATTTATAAAAGAATACTC

Found at i:17199 original size:114 final size:114

Alignment explanation


    Indices: 16996--17222  Score: 359
    Period size: 114  Copynumber: 2.0  Consensus size: 114

      16986 GATTAAGAGT

                                            *                         *      
      16996 ACTCCTTGTTGAGACCCAAAAAGAACATCAGGTTCGCATTCTCGATTCTGCTTTGCTTTGCCACA
          1 ACTCCTTGTTGAGACCCAAAAAGAACATCAGGCTCGCATTCTCGATTCTGCTTTGCTTCGCCACA

                    **               *             *         
      17061 GCAACATCTGTTTGCTTTGATGGTTTTTGCTACAGCATTGTCGAGCTCC
         66 GCAACATCACTTTGCTTTGATGGTTCTTGCTACAGCATTATCGAGCTCC

                                                              *              
      17110 ACTCCTTGTTGAGACCCAAAAAGAACATCAGGCTCGCATTC-CTGATTCTTCTTTGCTTCGCCAC
          1 ACTCCTTGTTGAGACCCAAAAAGAACATCAGGCTCGCATTCTC-GATTCTGCTTTGCTTCGCCAC

                                                              
      17174 AGCAACATCACTTTGCTTT-AGTGGTTCTTGCTACAGCATTATCGAGCTC
         65 AGCAACATCACTTTGCTTTGA-TGGTTCTTGCTACAGCATTATCGAGCTC

      17223 TGCTCCCAGC


Statistics
Matches: 104,  Mismatches: 7, Indels: 4
        0.90            0.06        0.03

Matches are distributed among these distances:
 113    2  0.02
 114  102  0.98

ACGTcount: A:0.22, C:0.27, G:0.18, T:0.33


Consensus pattern (114 bp):   
ACTCCTTGTTGAGACCCAAAAAGAACATCAGGCTCGCATTCTCGATTCTGCTTTGCTTCGCCACA
GCAACATCACTTTGCTTTGATGGTTCTTGCTACAGCATTATCGAGCTCC

Found at i:31712 original size:24 final size:24

Alignment explanation


    Indices: 31676--31753  Score: 104
    Period size: 24  Copynumber: 3.3  Consensus size: 24

      31666 AATCTTCTAG

                                  * 
      31676 TTAAAC-ATATTTATTTGTTTCGA
          1 TTAAACTATATTTATTTGTTTCAA

                   *                
      31699 TTAAACTCTATTTATTTGTTTCAA
          1 TTAAACTATATTTATTTGTTTCAA

                     *           *  
      31723 TTAAACTATGTTTATTTGTTTTAA
          1 TTAAACTATATTTATTTGTTTCAA

             *     
      31747 TCAAACT
          1 TTAAACT

      31754 CTTATTAGTT


Statistics
Matches: 48,  Mismatches: 6, Indels: 1
        0.87            0.11        0.02

Matches are distributed among these distances:
  23    6  0.12
  24   42  0.88

ACGTcount: A:0.31, C:0.10, G:0.06, T:0.53


Consensus pattern (24 bp):   
TTAAACTATATTTATTTGTTTCAA

Found at i:38924 original size:13 final size:13

Alignment explanation


    Indices: 38906--38937  Score: 57
    Period size: 13  Copynumber: 2.5  Consensus size: 13

      38896 GGGTTGCTAT

                         
      38906 ATATCTAACGTAA
          1 ATATCTAACGTAA

                         
      38919 ATATCTAACGTAA
          1 ATATCTAACGTAA

                   
      38932 AT-TCTA
          1 ATATCTA

      38938 TCACCACTTC


Statistics
Matches: 19,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  12    4  0.21
  13   15  0.79

ACGTcount: A:0.44, C:0.16, G:0.06, T:0.34


Consensus pattern (13 bp):   
ATATCTAACGTAA
Done.