Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013644.1 Kokia drynarioides strain JFW-HI SEQ_128672, 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: 8498
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.33


Found at i:676 original size:19 final size:20

Alignment explanation


    Indices: 638--677  Score: 55
    Period size: 19  Copynumber: 2.0  Consensus size: 20

        628 TTGTATTTGT

                        *  *    
        638 AAAATAAATAAATAATAATA
          1 AAAATAAATAAAGAAAAATA

                                
        658 AAAATAAA-AAAGAAAAATA
          1 AAAATAAATAAAGAAAAATA

             
        677 A
          1 A

        678 TGTACTAGGC


Statistics
Matches: 18,  Mismatches: 2, Indels: 1
        0.86            0.10        0.05

Matches are distributed among these distances:
  19   10  0.56
  20    8  0.44

ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17


Consensus pattern (20 bp):   
AAAATAAATAAAGAAAAATA

Found at i:1352 original size:40 final size:40

Alignment explanation


    Indices: 1307--1453  Score: 113
    Period size: 40  Copynumber: 3.7  Consensus size: 40

       1297 GTTCGATTGT

                            *   *      *             
       1307 TTCAATTTTCCGC-ATGGTCGGGGTAAGAGATCTGATGGTC
          1 TTCAATTTTCC-CTATCGTCAGGGTAAAAGATCTGATGGTC

                  * *    *    *              *      
       1347 TTCAATCTGCCCTTTCGTTAGGGTAAAAGATCTTATGGTC
          1 TTCAATTTTCCCTATCGTCAGGGTAAAAGATCTGATGGTC

                         * *  *                  *   
       1387 TTCAATTTTCCCTCTGGTTAGGGTAAAAGAT-TGGATTG-C
          1 TTCAATTTTCCCTATCGTCAGGGTAAAAGATCT-GATGGTC

              *             *            
       1426 TTTAATTTGTCCC-ATGGTCAGGGTAAAA
          1 TTCAATTT-TCCCTATCGTCAGGGTAAAA

       1454 TACTCGGGGT


Statistics
Matches: 87,  Mismatches: 17, Indels: 7
        0.78            0.15        0.06

Matches are distributed among these distances:
  39   23  0.26
  40   64  0.74

ACGTcount: A:0.23, C:0.17, G:0.24, T:0.36


Consensus pattern (40 bp):   
TTCAATTTTCCCTATCGTCAGGGTAAAAGATCTGATGGTC

Found at i:1537 original size:50 final size:50

Alignment explanation


    Indices: 1482--1620  Score: 163
    Period size: 50  Copynumber: 2.8  Consensus size: 50

       1472 TGCTCTATTT

                  *   *    *                                   
       1482 CAGCTTCAGGAGTATAAGATTCGTCC-TTGCAACTTCAATTTGCCCCTCTA
          1 CAGCTTTAGGTGTATGAGATTCG-CCATTGCAACTTCAATTTGCCCCTCTA

                        *                  *   *         *    
       1532 CAGCTTTAGGTGAATGAGATTCGCCATTGCAGCTTTAATTTGCCCTTCTA
          1 CAGCTTTAGGTGTATGAGATTCGCCATTGCAACTTCAATTTGCCCCTCTA

                                 *  *     **       
       1582 CAGCTTTAGGTGTATGAGATTTGCAATTGCGGCTTCAAT
          1 CAGCTTTAGGTGTATGAGATTCGCCATTGCAACTTCAAT

       1621 CCGTTCCTCT


Statistics
Matches: 76,  Mismatches: 12, Indels: 2
        0.84            0.13        0.02

Matches are distributed among these distances:
  49    2  0.03
  50   74  0.97

ACGTcount: A:0.23, C:0.22, G:0.20, T:0.35


Consensus pattern (50 bp):   
CAGCTTTAGGTGTATGAGATTCGCCATTGCAACTTCAATTTGCCCCTCTA

Found at i:1637 original size:50 final size:49

Alignment explanation


    Indices: 1525--1654  Score: 136
    Period size: 50  Copynumber: 2.6  Consensus size: 49

       1515 TTCAATTTGC

                               *        *  *          *   ** 
       1525 CCCTCTACAGCTTTAGGTGAATGAGATTCGCCATTGCAGCTTTAATTTG
          1 CCCTCTACAGCTTTAGGTGTATGAGATTTGCAATTGCAGCTTCAATCCG

                                                  *           
       1574 CCCTTCTACAGCTTTAGGTGTATGAGATTTGCAATTGCGGCTTCAATCCG
          1 CCC-TCTACAGCTTTAGGTGTATGAGATTTGCAATTGCAGCTTCAATCCG

             *      *         *             
       1624 TTCCTCTATAGCTTTAGGGGTAT-AGCATTTG
          1 -CCCTCTACAGCTTTAGGTGTATGAG-ATTTG

       1655 TCGTTTTATC


Statistics
Matches: 68,  Mismatches: 10, Indels: 5
        0.82            0.12        0.06

Matches are distributed among these distances:
  49    5  0.07
  50   61  0.90
  51    2  0.03

ACGTcount: A:0.21, C:0.22, G:0.22, T:0.36


Consensus pattern (49 bp):   
CCCTCTACAGCTTTAGGTGTATGAGATTTGCAATTGCAGCTTCAATCCG
Done.