Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001955.1 Kokia drynarioides strain JFW-HI SEQ_113779, 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: 8707
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31


Found at i:3097 original size:21 final size:21

Alignment explanation


    Indices: 3041--3100  Score: 66
    Period size: 21  Copynumber: 2.9  Consensus size: 21

       3031 AACAGTACAG

                     *     *    *
       3041 ATTTCTACTAGTACATGTATT
          1 ATTTCTACTGGTACAAGTATA

             *      * *          
       3062 AGTTCTACCGATACAAGTATA
          1 ATTTCTACTGGTACAAGTATA

                              
       3083 ATTTCTACTGGTACAAGT
          1 ATTTCTACTGGTACAAGT

       3101 CATGCATCTA


Statistics
Matches: 30,  Mismatches: 9, Indels: 0
        0.77            0.23        0.00

Matches are distributed among these distances:
  21   30  1.00

ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38


Consensus pattern (21 bp):   
ATTTCTACTGGTACAAGTATA

Found at i:3229 original size:21 final size:24

Alignment explanation


    Indices: 3175--3231  Score: 66
    Period size: 21  Copynumber: 2.5  Consensus size: 24

       3165 CAAGCATGCA

                                    
       3175 AACTACCGATACTTCTATACATAC
          1 AACTACCGATACTTCTATACATAC

                 *                **
       3199 AACTATCGATAC-TC-ATA-ATTT
          1 AACTACCGATACTTCTATACATAC

                        
       3220 AACTACCGATAC
          1 AACTACCGATAC

       3232 AAATCAAGTC


Statistics
Matches: 29,  Mismatches: 4, Indels: 3
        0.81            0.11        0.08

Matches are distributed among these distances:
  21   13  0.45
  22    3  0.10
  23    2  0.07
  24   11  0.38

ACGTcount: A:0.39, C:0.26, G:0.05, T:0.30


Consensus pattern (24 bp):   
AACTACCGATACTTCTATACATAC

Found at i:3997 original size:51 final size:51

Alignment explanation


    Indices: 3873--4154  Score: 338
    Period size: 51  Copynumber: 5.5  Consensus size: 51

       3863 TCATATACAT

                       *                                  *       
       3873 ACGATGACACTAAGTCATCGGACCTTTAATTCGTCAT-GA--ATTCATTTACTC
          1 ACGATGACACTTAGTCATCGGACCTTTAA-TC--CATAGAGGATTCGTTTACTC

              *    *                 *   *                     
       3924 ACAATGATAC-TAGTCATCGGACCTGTAAACCATAGAGGATTCGTTTACTC
          1 ACGATGACACTTAGTCATCGGACCTTTAATCCATAGAGGATTCGTTTACTC

                                           **    *             
       3974 ACGATGACACTTAGTCATCGGACCTTTAATCTGTAGATGATTCGTTTACTC
          1 ACGATGACACTTAGTCATCGGACCTTTAATCCATAGAGGATTCGTTTACTC

             *   *                        * *         *        
       4025 ATGATTACACTTAGTCATCGGACCTTTAATTCGTAGAGGATTTGTTTACTC
          1 ACGATGACACTTAGTCATCGGACCTTTAATCCATAGAGGATTCGTTTACTC

                         *                     *       *       
       4076 ACGATGACACTTAATCATCGGACCTTTAATCCATAAAGGATTCATTTACTC
          1 ACGATGACACTTAGTCATCGGACCTTTAATCCATAGAGGATTCGTTTACTC

                     *                  
       4127 ACGATGACATTTAGTCATCGGACTCTTT
          1 ACGATGACACTTAGTCATCGGAC-CTTT

       4155 CATTTATAGC


Statistics
Matches: 197,  Mismatches: 29, Indels: 9
        0.84            0.12        0.04

Matches are distributed among these distances:
  47    3  0.02
  48    2  0.01
  49    1  0.01
  50   35  0.18
  51  152  0.77
  52    4  0.02

ACGTcount: A:0.29, C:0.22, G:0.16, T:0.34


Consensus pattern (51 bp):   
ACGATGACACTTAGTCATCGGACCTTTAATCCATAGAGGATTCGTTTACTC

Found at i:4132 original size:153 final size:153

Alignment explanation


    Indices: 3879--4154  Score: 405
    Period size: 153  Copynumber: 1.8  Consensus size: 153

       3869 ACATACGATG

                                                                *    *       
       3879 ACACTAAGTCATCGGACCTTTAATTCGTCATGAATTCATTTACTCACAATGATACTAGTCATCGG
          1 ACACTAAGTCATCGGACCTTTAATTCGTCATGAATTCATTTACTCACAATGACACTAATCATCGG

                          *       *                                          
       3944 ACCTGTAAACCATAGAGGATTCGTTTACTCACGATGACACTTAGTCATCGGAC-CTTTAATCTGT
         66 ACCTGTAAACCATAAAGGATTCATTTACTCACGATGACACTTAGTCATCGGACTCTTTAATCTGT

                                   
       4008 AGATGATTCGTTTACTCATGATT
        131 AGATGATTCGTTTACTCATGATT

                 *                                **         *               
       4031 ACACTTAGTCATCGGACCTTTAATTCGT-A-GAGGATTTGTTTACTCACGATGACACTTAATCAT
          1 ACACTAAGTCATCGGACCTTTAATTCGTCATGA--ATTCATTTACTCACAATGACAC-TAATCAT

                   *   *                              *                  
       4094 CGGACCTTTAATCCATAAAGGATTCATTTACTCACGATGACATTTAGTCATCGGACTCTTT
         63 CGGACCTGTAAACCATAAAGGATTCATTTACTCACGATGACACTTAGTCATCGGACTCTTT

       4155 CATTTATAGC


Statistics
Matches: 109,  Mismatches: 11, Indels: 6
        0.87            0.09        0.05

Matches are distributed among these distances:
 150    2  0.02
 151    1  0.01
 152   45  0.41
 153   57  0.52
 154    4  0.04

ACGTcount: A:0.29, C:0.22, G:0.16, T:0.34


Consensus pattern (153 bp):   
ACACTAAGTCATCGGACCTTTAATTCGTCATGAATTCATTTACTCACAATGACACTAATCATCGG
ACCTGTAAACCATAAAGGATTCATTTACTCACGATGACACTTAGTCATCGGACTCTTTAATCTGT
AGATGATTCGTTTACTCATGATT
Done.