Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004059.1 Kokia drynarioides strain JFW-HI SEQ_117212, 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: 7317
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35


Found at i:286 original size:10 final size:10

Alignment explanation


    Indices: 273--297  Score: 50
    Period size: 10  Copynumber: 2.5  Consensus size: 10

        263 TTTTTTGAGA

                      
        273 TTTTTCCATT
          1 TTTTTCCATT

                      
        283 TTTTTCCATT
          1 TTTTTCCATT

                 
        293 TTTTT
          1 TTTTT

        298 GTTTGTTTAC


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   15  1.00

ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76


Consensus pattern (10 bp):   
TTTTTCCATT

Found at i:2538 original size:35 final size:36

Alignment explanation


    Indices: 2453--2528  Score: 111
    Period size: 36  Copynumber: 2.1  Consensus size: 36

       2443 TGATGACTAT

                 *   *                          
       2453 TGTGAAAGTGAATATGTGGGTATGTTATTCAAGCCA
          1 TGTGACAGTAAATATGTGGGTATGTTATTCAAGCCA

                                                 
       2489 TGTGACAGTAAATATGTGGGTATGTT-TTCATA-CCA
          1 TGTGACAGTAAATATGTGGGTATGTTATTCA-AGCCA

                 
       2524 TGTGA
          1 TGTGA

       2529 TTGATAATAT


Statistics
Matches: 37,  Mismatches: 2, Indels: 3
        0.88            0.05        0.07

Matches are distributed among these distances:
  35   12  0.32
  36   25  0.68

ACGTcount: A:0.29, C:0.09, G:0.26, T:0.36


Consensus pattern (36 bp):   
TGTGACAGTAAATATGTGGGTATGTTATTCAAGCCA

Found at i:4466 original size:24 final size:21

Alignment explanation


    Indices: 4418--4491  Score: 60
    Period size: 21  Copynumber: 3.4  Consensus size: 21

       4408 CAACTTCTAA

                     *           
       4418 CGATACAAGTATCCTAACTAC
          1 CGATACAAGCATCCTAACTAC

                                   *
       4439 CGATACAAGCATACACTGAACTAT
          1 CGATACAAGCAT-C-CT-AACTAC

                   * *   *        
       4463 CGATACCTATCATGC-AACTAC
          1 CGATA-CAAGCATCCTAACTAC

                    
       4484 CGATACAA
          1 CGATACAA

       4492 CCCAAGTCAG


Statistics
Matches: 42,  Mismatches: 7, Indels: 9
        0.72            0.12        0.16

Matches are distributed among these distances:
  20    2  0.05
  21   21  0.50
  22    1  0.02
  23    3  0.07
  24   10  0.24
  25    5  0.12

ACGTcount: A:0.39, C:0.28, G:0.11, T:0.22


Consensus pattern (21 bp):   
CGATACAAGCATCCTAACTAC

Found at i:5150 original size:52 final size:52

Alignment explanation


    Indices: 5072--5263  Score: 278
    Period size: 52  Copynumber: 3.7  Consensus size: 52

       5062 GATTCATTTC

                                                   *            
       5072 ATTTA-ATACTCACGATGACACATAGTCATCGAACCTCACAATCCGTAAAGG
          1 ATTTATATACTCACGATGACACATAGTCATCGAACCTCATAATCCGTAAAGG

               *             *    *                 *           
       5123 ATTCATATACTCACGATAACACGTAGTCATCGAACCTCATTATCCGTAAAGG
          1 ATTTATATACTCACGATGACACATAGTCATCGAACCTCATAATCCGTAAAGG

            *       *    *     *  *                           * 
       5175 GTTTATATGCTCATGATGATACGTAGTCATCGAACCTCATAATCCGTAAAAG
          1 ATTTATATACTCACGATGACACATAGTCATCGAACCTCATAATCCGTAAAGG

                                                 
       5227 ATTTATATACTCACGATGACACATAGTCATCGAACCT
          1 ATTTATATACTCACGATGACACATAGTCATCGAACCT

       5264 TTTTCATTTA


Statistics
Matches: 122,  Mismatches: 18, Indels: 1
        0.87            0.13        0.01

Matches are distributed among these distances:
  51    4  0.03
  52  118  0.97

ACGTcount: A:0.35, C:0.23, G:0.14, T:0.28


Consensus pattern (52 bp):   
ATTTATATACTCACGATGACACATAGTCATCGAACCTCATAATCCGTAAAGG

Found at i:5727 original size:26 final size:27

Alignment explanation


    Indices: 5684--5745  Score: 92
    Period size: 26  Copynumber: 2.3  Consensus size: 27

       5674 TTCAACATTT

                                       
       5684 AAAT-CTTTTAATCCTAATTTCATCAA
          1 AAATCCTTTTAATCCTAATTTCATCAA

                          *            
       5710 AAATCCTTTT-ATCGTAATTTCATCAA
          1 AAATCCTTTTAATCCTAATTTCATCAA

                      
       5736 AAATCACTTT
          1 AAATC-CTTT

       5746 ACGAAAACAT


Statistics
Matches: 33,  Mismatches: 1, Indels: 3
        0.89            0.03        0.08

Matches are distributed among these distances:
  26   24  0.73
  27    9  0.27

ACGTcount: A:0.37, C:0.19, G:0.02, T:0.42


Consensus pattern (27 bp):   
AAATCCTTTTAATCCTAATTTCATCAA

Found at i:7113 original size:33 final size:32

Alignment explanation


    Indices: 7076--7150  Score: 80
    Period size: 33  Copynumber: 2.2  Consensus size: 32

       7066 AAAATAAATG

                                     *        
       7076 AAATAAAAACAAGAAGAAAAGATTCGAAAATCA-
          1 AAATAAAAACAAG--GAAAAGATTCAAAAATCAC

                    *                          
       7109 AAATAATCTAACAAGGAAAAGATTCAAAAATCATC
          1 AAATAA--AAACAAGGAAAAGATTCAAAAATCA-C

                   
       7144 AAATAAA
          1 AAATAAA

       7151 CAAACTTCTT


Statistics
Matches: 35,  Mismatches: 3, Indels: 8
        0.76            0.07        0.17

Matches are distributed among these distances:
  33   23  0.66
  35   12  0.34

ACGTcount: A:0.64, C:0.11, G:0.09, T:0.16


Consensus pattern (32 bp):   
AAATAAAAACAAGGAAAAGATTCAAAAATCAC
Done.