Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009452.1 Kokia drynarioides strain JFW-HI SEQ_124159, 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: 4639
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.35


Found at i:529 original size:26 final size:23

Alignment explanation


    Indices: 450--530  Score: 65
    Period size: 25  Copynumber: 3.3  Consensus size: 23

        440 TTTTAGTTTA

                   *         **      
        450 ATATTTTATATTTATTCAAACTTGT
          1 ATATTTTTTATTTATTCTTA-TT-T

                                   
        475 ATATTTTTTATTTATTCTTATTT
          1 ATATTTTTTATTTATTCTTATTT

                                        
        498 CATATTTGTTTACTTTCATGTC-TATTT
          1 -ATATTT-TTTA-TTT-AT-TCTTATTT

                  
        525 ATATTT
          1 ATATTT

        531 ATGTTTTTTT


Statistics
Matches: 48,  Mismatches: 3, Indels: 9
        0.80            0.05        0.15

Matches are distributed among these distances:
  23    1  0.02
  24    8  0.17
  25   21  0.44
  26    9  0.19
  27    7  0.15
  28    2  0.04

ACGTcount: A:0.25, C:0.09, G:0.04, T:0.63


Consensus pattern (23 bp):   
ATATTTTTTATTTATTCTTATTT

Found at i:3716 original size:579 final size:577

Alignment explanation


    Indices: 2606--3749  Score: 1476
    Period size: 579  Copynumber: 2.0  Consensus size: 577

       2596 GCCCCTAAAT

                        **                    *                  *    *      
       2606 GTACTCCCGTTCGGTGTAGATTTAAGCTTTCTGCTAGTATACGAGACAAGTTGTAAATGTAGTGT
          1 GTACTCCCGTTCAATGTAGATTTAAGCTTTCTGCAAGTATACGAGACAAGTTGAAAATATAGTGT

                     *      *                                                
       2671 GTTACAACGGAACATTTAGTAGTACTCCAAGGATCGTACCCAAAGGAGGCTTAAAGCGATAGTAA
         66 GTTACAACGAAACATTGAGTAGTACTCCAAGGATCGTACCCAAAGGAGGCTTAAAGCGATAGTAA

                                                                             
       2736 ATCAAATACCTGCAAAGAGTAAAATTAATTAGTAATTATTTTAGGGTTTATAGTACGAAAAATAA
        131 ATCAAATACCTGCAAAGAGTAAAATTAATTAGTAATTATTTTAGGGTTTATAGTACGAAAAATAA

                        *                        *               *           
       2801 AAGTGTTTTGAGTGCATAAAAATAAAAAGATAAAATAGAATAGAAAATAAAAGCAAAAGATTGAG
        196 AAGTGTTTTGAGAGCATAAAAATAAAAAGATAAAATAAAATAGAAAATAAAAGAAAAAGATTGAG

            **                **          **             *         * *    *  
       2866 TTGTAGAAATCTTATAAATGGCTTTGGGGATTTTAGGTCGTTTCCGTATGAGTTATTTAATTTTT
        261 AAGTAGAAATCTTATAAACAGCTTTGGGGAAATTAGGTCGTTTCCATATGAGTTACTGAATTGTT

            *                                                *               
       2931 TGATTTTGAGGATTTTACTCCAATCAACTAGTCACTACCCTAGTTGGATCTCTTGATCTTCTGCC
        326 GGATTTTGAGGATTTTACTCCAATCAACTAGTCACTACCCTAGTTGGATATCTTGATCTTCTGCC

                 *   *                   *                                  *
       2996 AGCATGGCATGCCGATAGAGATTACTTATTGCTAGATGTCACAATCTAAACTGGTTTGGGGAAAG
        391 AGCATAGCAAGCCGATAGAGATTACTTATCGCTAGATGTCACAATCTAAACTGGTTTGGGGAAAA

            *       *                              *    *               *  * 
       3061 GGTGTTCATGGATGGACAATACCAATTTTGGGTTCATTCTCACCTAGATGACTTTCTAAGTTTGT
        456 CGTGTTCAAGGATGGACAATACCAATTTTGGGTTCATTCCCACCGAGATGACTTTCTAAGGTTAT

                              * *           *                        
       3126 CAAACCTAGTGTTTGTTCGATGCTCTTCCTTTTCCAAATAGCTGACTGCCCCCGAAC
        521 CAAACCTAGTGTTTGTTCAACGCTCTTCCTTTCCCAAATAGCTGACTGCCCCCGAAC

                                   **                   * ** *               
       3183 GTACTCCCGTTCAATGTAGATTTTGGCTTT-TCGCAAGTATACGGGTTAGGTTGAAAATATAGTG
          1 GTACTCCCGTTCAATGTAGATTTAAGCTTTCT-GCAAGTATACGAGACAAGTTGAAAATATAGTG

                                      *   *                                  
       3247 TGTTACAACGAAACACTTGA-TAGTATTCCGAGGATCGTACCCAAAGGAGGCTT-AAGACGATAG
         65 TGTTACAACGAAACA-TTGAGTAGTACTCCAAGGATCGTACCCAAAGGAGGCTTAAAG-CGATAG

                 **   *                          *  *                 *  *   
       3310 TAAATTGAATCCCTGCAAAGAGTAAAATTAATTAGTACTTGTTTTAGGGTTTATAGTATGAGAAA
        128 TAAATCAAATACCTGCAAAGAGTAAAATTAATTAGTAATTATTTTAGGGTTTATAGTACGAAAAA

                                *     *                      *               
       3375 TAAAAGAGTTGTTTTGAGAGTATAAATAT-AAAAGAT-AAATAAAATAGGAAATAAAAGAAAAAG
        193 T-AAA-AG-TGTTTTGAGAGCATAAAAATAAAAAGATAAAATAAAATAGAAAATAAAAGAAAAAG

            *                                            *           **  *   
       3438 TTTGAGAAGTAGAAAATCTTATAAACAGCTTTGGGGAAATTAGGTTGTTTCCATATGCTTTCCTG
        255 ATTGAGAAGTAG-AAATCTTATAAACAGCTTTGGGGAAATTAGGTCGTTTCCATATGAGTTACTG

            *        *     *       *  *                                   *  
       3503 GATTGTTGGGTTTTGGGGATTTTCCTTCAATCAACTAGTCACTACCCTAGTTGGATATCTTGGTC
        319 AATTGTTGGATTTTGAGGATTTTACTCCAATCAACTAGTCACTACCCTAGTTGGATATCTTGATC

                  *             *                                            
       3568 TT-TCGTC-GACATAGCAAGTCGATAGAGATTACTTATCGCTAGATGTCACAATCTAAA-TCGGT
        384 TTCT-GCCAG-CATAGCAAGCCGATAGAGATTACTTATCGCTAGATGTCACAATCTAAACT-GGT

                                     **                 *                    
       3630 TTGGGGAAAACGTGTTCAAGGATGGGTAATACCAATTTTGGGTTGATTCCCACCGAGATGACTTT
        446 TTGGGGAAAACGTGTTCAAGGATGGACAATACCAATTTTGGGTTCATTCCCACCGAGATGACTTT

               *        ***                 *                      
       3695 CTAGGGTTATCAGGTCTAGTGTTTGTTCAACGTTCTTCCTTTCCCAAATAGCTGA
        511 CTAAGGTTATCAAACCTAGTGTTTGTTCAACGCTCTTCCTTTCCCAAATAGCTGA

       3750 TTCGAAACGT


Statistics
Matches: 483,  Mismatches: 74, Indels: 18
        0.84            0.13        0.03

Matches are distributed among these distances:
 576    4  0.01
 577  161  0.33
 578   42  0.09
 579  259  0.54
 580   17  0.04

ACGTcount: A:0.32, C:0.15, G:0.21, T:0.33


Consensus pattern (577 bp):   
GTACTCCCGTTCAATGTAGATTTAAGCTTTCTGCAAGTATACGAGACAAGTTGAAAATATAGTGT
GTTACAACGAAACATTGAGTAGTACTCCAAGGATCGTACCCAAAGGAGGCTTAAAGCGATAGTAA
ATCAAATACCTGCAAAGAGTAAAATTAATTAGTAATTATTTTAGGGTTTATAGTACGAAAAATAA
AAGTGTTTTGAGAGCATAAAAATAAAAAGATAAAATAAAATAGAAAATAAAAGAAAAAGATTGAG
AAGTAGAAATCTTATAAACAGCTTTGGGGAAATTAGGTCGTTTCCATATGAGTTACTGAATTGTT
GGATTTTGAGGATTTTACTCCAATCAACTAGTCACTACCCTAGTTGGATATCTTGATCTTCTGCC
AGCATAGCAAGCCGATAGAGATTACTTATCGCTAGATGTCACAATCTAAACTGGTTTGGGGAAAA
CGTGTTCAAGGATGGACAATACCAATTTTGGGTTCATTCCCACCGAGATGACTTTCTAAGGTTAT
CAAACCTAGTGTTTGTTCAACGCTCTTCCTTTCCCAAATAGCTGACTGCCCCCGAAC
Done.