Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006332.1 Kokia drynarioides strain JFW-HI SEQ_120907, 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: 1947
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.35


Found at i:1468 original size:58 final size:58

Alignment explanation


    Indices: 1351--1460  Score: 143
    Period size: 57  Copynumber: 1.9  Consensus size: 58

       1341 ATGACTATGG

                                *  *                         *        
       1351 TTTTCTCCAAAATGAAAATGTAATTAGAGAAATGAAATAATTTGAAAATGAATGTGAT
          1 TTTTCTCCAAAATGAAAATGAAAATAGAGAAATGAAATAATTTGAAAATAAATGTGAT

                          *                     * *               
       1409 TTTTCTCCAAAATGGAAATGAAAAT-GAGAAATGAATTCATTT-ACAAATAAAT
          1 TTTTCTCCAAAATGAAAATGAAAATAGAGAAATGAAATAATTTGA-AAATAAAT

       1461 AAGGATTTCT


Statistics
Matches: 45,  Mismatches: 6, Indels: 3
        0.83            0.11        0.06

Matches are distributed among these distances:
  56    1  0.02
  57   22  0.49
  58   22  0.49

ACGTcount: A:0.47, C:0.07, G:0.14, T:0.32


Consensus pattern (58 bp):   
TTTTCTCCAAAATGAAAATGAAAATAGAGAAATGAAATAATTTGAAAATAAATGTGAT

Found at i:1632 original size:26 final size:26

Alignment explanation


    Indices: 1592--1689  Score: 133
    Period size: 26  Copynumber: 3.8  Consensus size: 26

       1582 TTTTTTTAGA

                      *         **    
       1592 AATTTTATCAAGGGTAAAATTGTTAT
          1 AATTTTATCAGGGGTAAAATCATTAT

                    *                 
       1618 AATTTTATTAGGGGTAAAATCATTAT
          1 AATTTTATCAGGGGTAAAATCATTAT

                                   *  
       1644 AATTTTATCAGGGGTAAAATCATGAT
          1 AATTTTATCAGGGGTAAAATCATTAT

                    **          
       1670 AATTTTATTGGGGGTAAAAT
          1 AATTTTATCAGGGGTAAAAT

       1690 TATCATGCCT


Statistics
Matches: 64,  Mismatches: 8, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  26   64  1.00

ACGTcount: A:0.38, C:0.04, G:0.18, T:0.40


Consensus pattern (26 bp):   
AATTTTATCAGGGGTAAAATCATTAT

Found at i:1703 original size:52 final size:52

Alignment explanation


    Indices: 1595--1715  Score: 136
    Period size: 52  Copynumber: 2.3  Consensus size: 52

       1585 TTTTAGAAAT

                   *         ** *                         *    *
       1595 TTTATCAAGGGTAAAATTGTTATAATTTTATTAGGGGTAAAATCATTATAAT
          1 TTTATCAGGGGTAAAATCATGATAATTTTATTAGGGGTAAAATCATCATAAC

                                            *          *     ** 
       1647 TTTATCAGGGGTAAAATCATGATAATTTTATTGGGGGTAAAATTATCATGCC
          1 TTTATCAGGGGTAAAATCATGATAATTTTATTAGGGGTAAAATCATCATAAC

                              
       1699 TTTATC-GAGGGTAAAAT
          1 TTTATCAG-GGGTAAAAT

       1716 TGGGATGAGA


Statistics
Matches: 58,  Mismatches: 10, Indels: 2
        0.83            0.14        0.03

Matches are distributed among these distances:
  51    1  0.02
  52   57  0.98

ACGTcount: A:0.36, C:0.07, G:0.19, T:0.39


Consensus pattern (52 bp):   
TTTATCAGGGGTAAAATCATGATAATTTTATTAGGGGTAAAATCATCATAAC
Done.