Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007597.1 Kokia drynarioides strain JFW-HI SEQ_122228, 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: 13042
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32


Found at i:7149 original size:19 final size:19

Alignment explanation


    Indices: 7113--7151  Score: 51
    Period size: 19  Copynumber: 2.1  Consensus size: 19

       7103 CACCTCATTT

                       * *     
       7113 ACATACTTCAATATACTTC
          1 ACATACTTCAAAACACTTC

                    *          
       7132 ACATACTTGAAAACACTTC
          1 ACATACTTCAAAACACTTC

             
       7151 A
          1 A

       7152 TTTTTTAGGA


Statistics
Matches: 17,  Mismatches: 3, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  19   17  1.00

ACGTcount: A:0.41, C:0.26, G:0.03, T:0.31


Consensus pattern (19 bp):   
ACATACTTCAAAACACTTC

Found at i:9746 original size:110 final size:111

Alignment explanation


    Indices: 9547--9758  Score: 315
    Period size: 110  Copynumber: 1.9  Consensus size: 111

       9537 TAGATATTCG

                      *              *  *                                    
       9547 ACAATTAACATTGAAATAAATAGTTGTAGTTATTGTCAACTGTTTCCGTAAATTCAATTCATTAG
          1 ACAATTAACAATGAAATAAATAGTTATAATTATTGTCAACTGTTTCCGTAAATTCAATTCATTAG

                       *              *                   
       9612 GAGAAAAACCATTAATACAATATTA-GTTATATTAAATGTTAAAGT
         66 GAGAAAAACCAATAATACAATATTATATTATATTAAATGTTAAAGT

                    *                                                        
       9657 ACAATTAATAATGAAATAAATAGTTATAATTATTGTCAACTGTTTCCGTAAATTCAATTCATTAG
          1 ACAATTAACAATGAAATAAATAGTTATAATTATTGTCAACTGTTTCCGTAAATTCAATTCATTAG

                                                    
       9722 GAG-AAAA-CAATAATA-AATTGTATTATATTATATTAAA
         66 GAGAAAAACCAATAATACAA---TATTATATTATATTAAA

       9759 ATAATAATTT


Statistics
Matches: 92,  Mismatches: 6, Indels: 7
        0.88            0.06        0.07

Matches are distributed among these distances:
 107    2  0.02
 108    7  0.08
 109    4  0.04
 110   69  0.75
 111   10  0.11

ACGTcount: A:0.44, C:0.09, G:0.10, T:0.37


Consensus pattern (111 bp):   
ACAATTAACAATGAAATAAATAGTTATAATTATTGTCAACTGTTTCCGTAAATTCAATTCATTAG
GAGAAAAACCAATAATACAATATTATATTATATTAAATGTTAAAGT

Found at i:10427 original size:17 final size:18

Alignment explanation


    Indices: 10407--10447  Score: 59
    Period size: 17  Copynumber: 2.4  Consensus size: 18

      10397 AATAAATAAA

                         *    
      10407 AAATATATAAAATCAT-T
          1 AAATATATAAAATAATAT

                              
      10424 AAATAT-TAAAATAATAT
          1 AAATATATAAAATAATAT

                   
      10441 AAATATA
          1 AAATATA

      10448 AATATTTTTT


Statistics
Matches: 21,  Mismatches: 1, Indels: 3
        0.84            0.04        0.12

Matches are distributed among these distances:
  16    8  0.38
  17   13  0.62

ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34


Consensus pattern (18 bp):   
AAATATATAAAATAATAT

Found at i:10449 original size:16 final size:15

Alignment explanation


    Indices: 10411--10449  Score: 51
    Period size: 16  Copynumber: 2.5  Consensus size: 15

      10401 AATAAAAAAT

                     *     
      10411 ATATAAAATCATTAA
          1 ATATAAAATAATTAA

                             
      10426 ATATTAAAATAATATAA
          1 ATA-TAAAATAAT-TAA

                   
      10443 ATATAAA
          1 ATATAAA

      10450 TATTTTTTAA


Statistics
Matches: 21,  Mismatches: 1, Indels: 3
        0.84            0.04        0.12

Matches are distributed among these distances:
  15    3  0.14
  16   12  0.57
  17    6  0.29

ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33


Consensus pattern (15 bp):   
ATATAAAATAATTAA

Found at i:10729 original size:19 final size:20

Alignment explanation


    Indices: 10693--10731  Score: 53
    Period size: 20  Copynumber: 2.0  Consensus size: 20

      10683 AATGAATTTC

                     * *        
      10693 TTAAAAAATCATTAATAATT
          1 TTAAAAAATAAATAATAATT

                                
      10713 TTAAAAAATAAAT-ATAATT
          1 TTAAAAAATAAATAATAATT

      10732 ACAAAATTTT


Statistics
Matches: 17,  Mismatches: 2, Indels: 1
        0.85            0.10        0.05

Matches are distributed among these distances:
  19    6  0.35
  20   11  0.65

ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38


Consensus pattern (20 bp):   
TTAAAAAATAAATAATAATT
Done.