Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012464.1 Kokia drynarioides strain JFW-HI SEQ_127468, 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: 15139
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34


Found at i:561 original size:48 final size:48

Alignment explanation


    Indices: 509--629  Score: 127
    Period size: 49  Copynumber: 2.5  Consensus size: 48

        499 TTCGCCATTA

                                *   *    *  *          *     
        509 CGACTTAAACATTTCCCTT-GTGTCTTCGTGGTACTGGATCCGTCGTTG
          1 CGACTTAAAC-TTTCCCTTCATGTATTCGCGGCACTGGATCCGCCGTTG

                     *                               *       
        557 CGACTTAGATCTTTCCCTTCATGTATTCGCGGCACTGGATCTGCCGTTG
          1 CGACTTA-AACTTTCCCTTCATGTATTCGCGGCACTGGATCCGCCGTTG

              *              *      
        606 CGGCTTAAATCTTTCCCATCATGT
          1 CGACTTAAA-CTTTCCCTTCATGT

        630 CTCTGAGGTA


Statistics
Matches: 60,  Mismatches: 10, Indels: 5
        0.80            0.13        0.07

Matches are distributed among these distances:
  48   16  0.27
  49   44  0.73

ACGTcount: A:0.16, C:0.27, G:0.21, T:0.36


Consensus pattern (48 bp):   
CGACTTAAACTTTCCCTTCATGTATTCGCGGCACTGGATCCGCCGTTG

Found at i:651 original size:49 final size:49

Alignment explanation


    Indices: 598--739  Score: 151
    Period size: 50  Copynumber: 2.9  Consensus size: 49

        588 GCACTGGATC

                                                          *  
        598 TGCCGTTGCGGCTTAAATCTTTCCCATCATGTCTCTGAGGTACAAGGTT
          1 TGCCGTTGCGGCTTAAATCTTTCCCATCATGTCTCTGAGGTACAAGATT

                      *      * *      *  * *   *  *     *     
        647 TGCCGTTGCGACTTAAACCCTTCCCTTTCGTATCTTTGCGGTACTAGATT
          1 TGCCGTTGCGGCTTAAATCTTTCCC-ATCATGTCTCTGAGGTACAAGATT

                *                                       
        697 TGCCATTGCGGTCTTAAATCTTT-CCAGTCATGTCTCTGAGGTA
          1 TGCCGTTGCGG-CTTAAATCTTTCCCA-TCATGTCTCTGAGGTA

        740 TAGGGTTCGT


Statistics
Matches: 71,  Mismatches: 19, Indels: 5
        0.75            0.20        0.05

Matches are distributed among these distances:
  49   22  0.31
  50   40  0.56
  51    9  0.13

ACGTcount: A:0.18, C:0.25, G:0.20, T:0.37


Consensus pattern (49 bp):   
TGCCGTTGCGGCTTAAATCTTTCCCATCATGTCTCTGAGGTACAAGATT

Found at i:734 original size:100 final size:100

Alignment explanation


    Indices: 594--829  Score: 323
    Period size: 100  Copynumber: 2.4  Consensus size: 100

        584 CGCGGCACTG

                                                                   *        *
        594 GATCTGCCGTTGCGG-CTTAAATCTTTCCCA-TCATGTCTCTGAGGTACAAGGTTTGCCGTTGCG
          1 GATCTGCCGTTGCGGTCTTAAATCTTT-CCAGTCATGTCTCTGAGGTACAAGGTTCGCCGTTGCA

                                         *      
        657 ACTTAAACCCTTCCCTTTCGTATCTTTGCGGTACTA
         65 ACTTAAACCCTTCCCTTTCGTATCTTTGCAGTACTA

               *    *                                      * *      *        
        693 GATTTGCCATTGCGGTCTTAAATCTTTCCAGTCATGTCTCTGAGGTATAGGGTTCGTCGTTGCAA
          1 GATCTGCCGTTGCGGTCTTAAATCTTTCCAGTCATGTCTCTGAGGTACAAGGTTCGCCGTTGCAA

                             *                *
        758 CTTAAACCCTTCCCTTTTGTATCTTTGCAGTACTG
         66 CTTAAACCCTTCCCTTTCGTATCTTTGCAGTACTA

                **              *        *       
        793 GATCCACCGTTGCGGTCTTAGATCTTTCCCGTCATGT
          1 GATCTGCCGTTGCGGTCTTAAATCTTTCCAGTCATGT

        830 TTCATGGTGC


Statistics
Matches: 119,  Mismatches: 16, Indels: 3
        0.86            0.12        0.02

Matches are distributed among these distances:
  99   16  0.13
 100  103  0.87

ACGTcount: A:0.17, C:0.26, G:0.20, T:0.37


Consensus pattern (100 bp):   
GATCTGCCGTTGCGGTCTTAAATCTTTCCAGTCATGTCTCTGAGGTACAAGGTTCGCCGTTGCAA
CTTAAACCCTTCCCTTTCGTATCTTTGCAGTACTA

Found at i:5738 original size:16 final size:16

Alignment explanation


    Indices: 5705--5737  Score: 59
    Period size: 16  Copynumber: 2.1  Consensus size: 16

       5695 ATCCGTCATA

                            
       5705 TTAGACTTTTGATTTT
          1 TTAGACTTTTGATTTT

                            
       5721 TTAGACTTTT-ATTTT
          1 TTAGACTTTTGATTTT

              
       5736 TT
          1 TT

       5738 TCTTATTGTG


Statistics
Matches: 17,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  15    7  0.41
  16   10  0.59

ACGTcount: A:0.18, C:0.06, G:0.09, T:0.67


Consensus pattern (16 bp):   
TTAGACTTTTGATTTT
Done.