Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003585.1 Kokia drynarioides strain JFW-HI SEQ_116459, 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: 18623
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36


Found at i:2014 original size:18 final size:18

Alignment explanation


    Indices: 1991--2026  Score: 54
    Period size: 18  Copynumber: 2.0  Consensus size: 18

       1981 TCAATAACCC

                              
       1991 AAAATAAATTTAAAATTT
          1 AAAATAAATTTAAAATTT

                  *    *      
       2009 AAAATATATTTTAAATTT
          1 AAAATAAATTTAAAATTT

       2027 TTTTGTTCTA


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  18   16  1.00

ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44


Consensus pattern (18 bp):   
AAAATAAATTTAAAATTT

Found at i:4982 original size:21 final size:20

Alignment explanation


    Indices: 4956--4998  Score: 68
    Period size: 21  Copynumber: 2.1  Consensus size: 20

       4946 AAACCATTCC

                                 
       4956 AAACAACAAAACAAAAAATAA
          1 AAACAACAAAAC-AAAAATAA

                    *           
       4977 AAACAACACAACAAAAATAA
          1 AAACAACAAAACAAAAATAA

              
       4997 AA
          1 AA

       4999 TAAACGAACA


Statistics
Matches: 21,  Mismatches: 1, Indels: 1
        0.91            0.04        0.04

Matches are distributed among these distances:
  20   10  0.48
  21   11  0.52

ACGTcount: A:0.79, C:0.16, G:0.00, T:0.05


Consensus pattern (20 bp):   
AAACAACAAAACAAAAATAA

Found at i:5273 original size:58 final size:58

Alignment explanation


    Indices: 5209--5319  Score: 172
    Period size: 58  Copynumber: 1.9  Consensus size: 58

       5199 GAATTGTTTC

                                                                        
       5209 TGAGTGTTATTT--AAGAATAAAATTATATTTGGGTTTAAAAATATTTGGATTTAATTTA
          1 TGAGTGTT-TTTGAAAG-ATAAAATTATATTTGGGTTTAAAAATATTTGGATTTAATTTA

                              *                             *    
       5267 TGAGTGTTTTTGAAAGATGAAATTATATTTGGGTTTAAAAATATTTGGGTTTA
          1 TGAGTGTTTTTGAAAGATAAAATTATATTTGGGTTTAAAAATATTTGGATTTA

       5320 GTTTGTTGAT


Statistics
Matches: 49,  Mismatches: 2, Indels: 4
        0.89            0.04        0.07

Matches are distributed among these distances:
  57    3  0.06
  58   43  0.88
  59    3  0.06

ACGTcount: A:0.35, C:0.00, G:0.19, T:0.46


Consensus pattern (58 bp):   
TGAGTGTTTTTGAAAGATAAAATTATATTTGGGTTTAAAAATATTTGGATTTAATTTA

Found at i:7663 original size:21 final size:22

Alignment explanation


    Indices: 7637--7682  Score: 67
    Period size: 22  Copynumber: 2.1  Consensus size: 22

       7627 ATCCTTGAAA

                              *   
       7637 TTTAAATA-TCTTTAATATTTT
          1 TTTAAATATTCTTTAATAATTT

                          *       
       7658 TTTAAATATTCTTTTATAATTT
          1 TTTAAATATTCTTTAATAATTT

               
       7680 TTT
          1 TTT

       7683 GTAATATTTA


Statistics
Matches: 22,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  21    8  0.36
  22   14  0.64

ACGTcount: A:0.30, C:0.04, G:0.00, T:0.65


Consensus pattern (22 bp):   
TTTAAATATTCTTTAATAATTT

Found at i:7679 original size:23 final size:22

Alignment explanation


    Indices: 7637--7690  Score: 67
    Period size: 23  Copynumber: 2.5  Consensus size: 22

       7627 ATCCTTGAAA

                                  
       7637 TTTAAATA-TCTTTAATATTTT
          1 TTTAAATATTCTTTAATATTTT

                          *        
       7658 TTTAAATATTCTTTTATAATTTT
          1 TTTAAATATTCTTTAAT-ATTTT

                       
       7681 TTGT-AATATT
          1 TT-TAAATATT

       7691 TACAATTTTT


Statistics
Matches: 29,  Mismatches: 1, Indels: 4
        0.85            0.03        0.12

Matches are distributed among these distances:
  21    8  0.28
  22    7  0.24
  23   13  0.45
  24    1  0.03

ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63


Consensus pattern (22 bp):   
TTTAAATATTCTTTAATATTTT

Found at i:11420 original size:2 final size:2

Alignment explanation


    Indices: 11413--11448  Score: 72
    Period size: 2  Copynumber: 18.0  Consensus size: 2

      11403 TACCTTCTGT

                                                                 
      11413 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
          1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA

      11449 TATATATATA


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   34  1.00

ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00


Consensus pattern (2 bp):   
CA

Found at i:12698 original size:61 final size:61

Alignment explanation


    Indices: 12631--12746  Score: 169
    Period size: 61  Copynumber: 1.9  Consensus size: 61

      12621 AAATAAACTT

                    *          *    *   *    *            *              
      12631 CAAATCTTGAACCCAAATCGAAAATTCCTAAATTAAGAACTCTCAATTTGGAAACTTCTTC
          1 CAAATCTTAAACCCAAATCAAAAAATCCAAAATAAAGAACTCTCAAATTGGAAACTTCTTC

                                                       *           
      12692 CAAATCTTAAACCCAAATCAAAAAATCCAAAATAAAGAACTCTTAAATTGGAAAC
          1 CAAATCTTAAACCCAAATCAAAAAATCCAAAATAAAGAACTCTCAAATTGGAAAC

      12747 CCATAAATCA


Statistics
Matches: 48,  Mismatches: 7, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  61   48  1.00

ACGTcount: A:0.47, C:0.22, G:0.07, T:0.25


Consensus pattern (61 bp):   
CAAATCTTAAACCCAAATCAAAAAATCCAAAATAAAGAACTCTCAAATTGGAAACTTCTTC
Done.