Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01011336.1 Kokia drynarioides strain JFW-HI SEQ_126316, 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: 2545
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.33

Warning! 50 characters in sequence are not A, C, G, or T


Found at i:2429 original size:4 final size:4

Alignment explanation


    Indices: 2420--2507  Score: 56
    Period size: 4  Copynumber: 21.5  Consensus size: 4

       2410 AAACACATTA

                        *                     *                          *
       2420 TCTT TCTT TCAT TC-T TCTT TCTT TCCTC TCTT TC-T TCATT TCTT TCCTC
          1 TCTT TCTT TCTT TCTT TCTT TCTT T-CTT TCTT TCTT TC-TT TCTT T-CTT

              *     *                                  *     
       2469 TCCT TC-A TCTTT TCTT TCTT TCTTT TCTT TCTT TTTT TC
          1 TCTT TCTT TC-TT TCTT TCTT TC-TT TCTT TCTT TCTT TC

       2508 CCGTTTATTT


Statistics
Matches: 66,  Mismatches: 10, Indels: 16
        0.72            0.11        0.17

Matches are distributed among these distances:
   3    8  0.12
   4   43  0.65
   5   15  0.23

ACGTcount: A:0.03, C:0.30, G:0.00, T:0.67


Consensus pattern (4 bp):   
TCTT

Found at i:2463 original size:21 final size:20

Alignment explanation


    Indices: 2431--2502  Score: 78
    Period size: 21  Copynumber: 3.6  Consensus size: 20

       2421 CTTTCTTTCA

                               *
       2431 TTCTTCTTTCTTTCCTCTCT
          1 TTCTTCTTTCTTTCCTCTCC

                                 
       2451 TTCTTCATTTCTTTCCTCTCC
          1 TTCTTC-TTTCTTTCCTCTCC

               *               * 
       2472 TTCATCTTTTCTTT-CT-TTC
          1 TTCTTC-TTTCTTTCCTCTCC

                         
       2491 TT-TTCTTTCTTT
          1 TTCTTCTTTCTTT

       2503 TTTTCCCGTT


Statistics
Matches: 46,  Mismatches: 5, Indels: 5
        0.82            0.09        0.09

Matches are distributed among these distances:
  17    7  0.15
  18    2  0.04
  19    4  0.09
  20    8  0.17
  21   25  0.54

ACGTcount: A:0.03, C:0.31, G:0.00, T:0.67


Consensus pattern (20 bp):   
TTCTTCTTTCTTTCCTCTCC

Found at i:2479 original size:28 final size:27

Alignment explanation


    Indices: 2419--2493  Score: 75
    Period size: 29  Copynumber: 2.7  Consensus size: 27

       2409 TAAACACATT

                                   *     
       2419 ATCTTTCTTTCATTCTTCTTTCTTTCCTC
          1 ATCTTTCTTTCA-T-TTCTTTCTCTCCTC

                                         
       2448 -TCTTTC-TTCATTTCTTTCCTCTCCTTC
          1 ATCTTTCTTTCATTTCTTT-CTCTCC-TC

                                
       2475 ATCTTTTCTTTC-TTTCTTT
          1 ATC-TTTCTTTCATTTCTTT

       2494 TCTTTCTTTT


Statistics
Matches: 40,  Mismatches: 1, Indels: 10
        0.78            0.02        0.20

Matches are distributed among these distances:
  25    6  0.15
  26    6  0.15
  27    6  0.15
  28    8  0.20
  29   11  0.28
  30    3  0.08

ACGTcount: A:0.05, C:0.31, G:0.00, T:0.64


Consensus pattern (27 bp):   
ATCTTTCTTTCATTTCTTTCTCTCCTC
Done.