Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008582.1 Kokia drynarioides strain JFW-HI SEQ_123260, 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: 9131
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36


Found at i:274 original size:61 final size:60

Alignment explanation


    Indices: 199--362  Score: 190
    Period size: 60  Copynumber: 2.7  Consensus size: 60

        189 TTGGTACCTA

                                                               *          
        199 AACTTGACATTTTTTTTTCTAATTTGGTATCTAAACTTTTTTTTA-CTCAATTTGATAATTG
          1 AACTTGACA-TTTTTTTTCTAATTTGGTATCTAAACTTTTTTTTATC-CAAATTGATAATTG

            *        *     *            *   *          *          *  *   
        260 GACTTGACACTTTTTCT-TAATTTGGTACCTATACTTTTTTTGGATCCAAATTGGTACTTG
          1 AACTTGACATTTTTTTTCTAATTTGGTATCTAAACTTTTTTT-TATCCAAATTGATAATTG

                            *                           
        320 AACTTGACATTTTTTTCCTAATTTGGTATCTAAA-TTTTTTTTA
          1 AACTTGACATTTTTTTTCTAATTTGGTATCTAAACTTTTTTTTA

        363 AGATTCAATT


Statistics
Matches: 84,  Mismatches: 16, Indels: 8
        0.78            0.15        0.07

Matches are distributed among these distances:
  59   23  0.27
  60   38  0.45
  61   23  0.27

ACGTcount: A:0.24, C:0.13, G:0.10, T:0.52


Consensus pattern (60 bp):   
AACTTGACATTTTTTTTCTAATTTGGTATCTAAACTTTTTTTTATCCAAATTGATAATTG

Found at i:328 original size:60 final size:59

Alignment explanation


    Indices: 212--361  Score: 169
    Period size: 61  Copynumber: 2.5  Consensus size: 59

        202 TTGACATTTT

                                          *      *          *          
        212 TTTTTCTAATTTGGTATCTAAACTTTTTTTTACTCAATTTGATAATTGGACTTGACA-C
          1 TTTTTCTAATTTGGTATCTAAACTTTTTTTGACTCAAATTGATAATTGAACTTGACATC

                             *   *                      *  *             *
        270 TTTTTCTTAATTTGGTACCTATACTTTTTTTGGA-TCCAAATTGGTACTTGAACTTGACATT
          1 TTTTTC-TAATTTGGTATCTAAACTTTTTTT-GACT-CAAATTGATAATTGAACTTGACATC

                                   *       
        331 TTTTTCCTAATTTGGTATCTAAATTTTTTTT
          1 TTTTT-CTAATTTGGTATCTAAACTTTTTTT

        362 AAGATTCAAT


Statistics
Matches: 76,  Mismatches: 11, Indels: 7
        0.81            0.12        0.07

Matches are distributed among these distances:
  58    6  0.08
  59   23  0.30
  60   20  0.26
  61   26  0.34
  62    1  0.01

ACGTcount: A:0.23, C:0.13, G:0.11, T:0.53


Consensus pattern (59 bp):   
TTTTTCTAATTTGGTATCTAAACTTTTTTTGACTCAAATTGATAATTGAACTTGACATC

Found at i:965 original size:21 final size:20

Alignment explanation


    Indices: 942--979  Score: 60
    Period size: 20  Copynumber: 1.9  Consensus size: 20

        932 TTCATTTGAA

                                 
        942 AAAAAATGTT-TTTGAAAAAC
          1 AAAAAAT-TTCTTTGAAAAAC

                              
        962 AAAAAATTTCTTTGAAAA
          1 AAAAAATTTCTTTGAAAA

        980 GTGATTTGTT


Statistics
Matches: 17,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  19    2  0.12
  20   15  0.88

ACGTcount: A:0.55, C:0.05, G:0.08, T:0.32


Consensus pattern (20 bp):   
AAAAAATTTCTTTGAAAAAC

Found at i:7081 original size:3 final size:3

Alignment explanation


    Indices: 7073--7098  Score: 52
    Period size: 3  Copynumber: 8.7  Consensus size: 3

       7063 AGAGTCAACT

                                              
       7073 ATC ATC ATC ATC ATC ATC ATC ATC AT
          1 ATC ATC ATC ATC ATC ATC ATC ATC AT

       7099 TATTATTATT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   23  1.00

ACGTcount: A:0.35, C:0.31, G:0.00, T:0.35


Consensus pattern (3 bp):   
ATC

Done.