Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01014762.1 Kokia drynarioides strain JFW-HI SEQ_129801, 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: 4292
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35


Found at i:1710 original size:326 final size:326

Alignment explanation


    Indices: 1225--1876  Score: 1214
    Period size: 326  Copynumber: 2.0  Consensus size: 326

       1215 AAAAATAATT

                 *  *                                                        
       1225 CTTTTGTTTTCCATTATAGTAACTCGGCGAGATCATTTGATTACTTCTAACTTCGAAATTTGAAT
          1 CTTTTATTGTCCATTATAGTAACTCGGCGAGATCATTTGATTACTTCTAACTTCGAAATTTGAAT

                                                                             
       1290 ATTTTTGAAATAGTTGCGAAAGATTAAAAAATTAAGAATAGAAAATTCCAGTTAACTTTGTAATC
         66 ATTTTTGAAATAGTTGCGAAAGATTAAAAAATTAAGAATAGAAAATTCCAGTTAACTTTGTAATC

                                *                                            
       1355 TCTCGATTTTTTTATTACCCTTTTTCAATCAAAAGAGATAAGAGCTGATGAATCAGAAACCAATA
        131 TCTCGATTTTTTTATTACCCCTTTTCAATCAAAAGAGATAAGAGCTGATGAATCAGAAACCAATA

                                                                             
       1420 ATTAAGAAAGAATAACAAAAAAGTTTTTATGGAGCATGCATATCAATATTCATGGATCATACCTT
        196 ATTAAGAAAGAATAACAAAAAAGTTTTTATGGAGCATGCATATCAATATTCATGGATCATACCTT

                                                                             
       1485 TTGTTCCACTTCCCATTCCTATTTTAATAGGAGTGGAACTCCTACTTTTTCCGACGGCAACAAAA
        261 TTGTTCCACTTCCCATTCCTATTTTAATAGGAGTGGAACTCCTACTTTTTCCGACGGCAACAAAA

             
       1550 A
        326 A

                                                                             
       1551 CTTTTATTGTCCATTATAGTAACTCGGCGAGATCATTTGATTACTTCTAACTTCGAAATTTGAAT
          1 CTTTTATTGTCCATTATAGTAACTCGGCGAGATCATTTGATTACTTCTAACTTCGAAATTTGAAT

                            *                                                
       1616 ATTTTTGAAATAGTTGTGAAAGATTAAAAAATTAAGAATAGAAAATTCCAGTTAACTTTGTAATC
         66 ATTTTTGAAATAGTTGCGAAAGATTAAAAAATTAAGAATAGAAAATTCCAGTTAACTTTGTAATC

                                                        *  *              *  
       1681 TCTCGATTTTTTTATTACCCCTTTTCAATCAAAAGAGATAAGAGTTGGTGAATCAGAAACCATTA
        131 TCTCGATTTTTTTATTACCCCTTTTCAATCAAAAGAGATAAGAGCTGATGAATCAGAAACCAATA

                   *                                                         
       1746 ATTAAGACAGAATAACAAAAAAGTTTTTATGGAGCATGCATATCAATATTCATGGATCATACCTT
        196 ATTAAGAAAGAATAACAAAAAAGTTTTTATGGAGCATGCATATCAATATTCATGGATCATACCTT

                                                               *     *       
       1811 TTGTTCCACTTCCCATTCCTATTTTAATAGGAGTGGAACTCCTACTTTTTCTGACGGTAACAAAA
        261 TTGTTCCACTTCCCATTCCTATTTTAATAGGAGTGGAACTCCTACTTTTTCCGACGGCAACAAAA

             
       1876 A
        326 A

       1877 ATCTTCGTCA


Statistics
Matches: 316,  Mismatches: 10, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
 326  316  1.00

ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35


Consensus pattern (326 bp):   
CTTTTATTGTCCATTATAGTAACTCGGCGAGATCATTTGATTACTTCTAACTTCGAAATTTGAAT
ATTTTTGAAATAGTTGCGAAAGATTAAAAAATTAAGAATAGAAAATTCCAGTTAACTTTGTAATC
TCTCGATTTTTTTATTACCCCTTTTCAATCAAAAGAGATAAGAGCTGATGAATCAGAAACCAATA
ATTAAGAAAGAATAACAAAAAAGTTTTTATGGAGCATGCATATCAATATTCATGGATCATACCTT
TTGTTCCACTTCCCATTCCTATTTTAATAGGAGTGGAACTCCTACTTTTTCCGACGGCAACAAAA
A

Found at i:3097 original size:15 final size:15

Alignment explanation


    Indices: 3077--3107  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       3067 TTGTATCAAT

                     *     
       3077 AATGAATCAGAGCAC
          1 AATGAATCAAAGCAC

                           
       3092 AATGAATCAAAGCAC
          1 AATGAATCAAAGCAC

             
       3107 A
          1 A

       3108 CAGAACCGTC


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.52, C:0.19, G:0.16, T:0.13


Consensus pattern (15 bp):   
AATGAATCAAAGCAC
Done.