Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007034.1 Kokia drynarioides strain JFW-HI SEQ_121642, 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: 18865
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30

Warning! 32 characters in sequence are not A, C, G, or T


Found at i:3812 original size:16 final size:17

Alignment explanation


    Indices: 3791--3825  Score: 63
    Period size: 16  Copynumber: 2.1  Consensus size: 17

       3781 TTTAATAATT

                             
       3791 ATATTTATTTTTA-TAA
          1 ATATTTATTTTTACTAA

                             
       3807 ATATTTATTTTTACTAA
          1 ATATTTATTTTTACTAA

              
       3824 AT
          1 AT

       3826 GGTACAGATT


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  16   13  0.72
  17    5  0.28

ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60


Consensus pattern (17 bp):   
ATATTTATTTTTACTAA

Found at i:17019 original size:20 final size:21

Alignment explanation


    Indices: 16996--17035  Score: 64
    Period size: 20  Copynumber: 2.0  Consensus size: 21

      16986 TAAATTTAGT

                    *            
      16996 TAATTAAAGGTT-AACTAAAC
          1 TAATTAAAAGTTAAACTAAAC

                                
      17016 TAATTAAAAGTTAAACTAAA
          1 TAATTAAAAGTTAAACTAAA

      17036 TACATAAGTA


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  20   11  0.61
  21    7  0.39

ACGTcount: A:0.55, C:0.07, G:0.07, T:0.30


Consensus pattern (21 bp):   
TAATTAAAAGTTAAACTAAAC

Found at i:17025 original size:21 final size:20

Alignment explanation


    Indices: 16996--17035  Score: 55
    Period size: 21  Copynumber: 1.9  Consensus size: 20

      16986 TAAATTTAGT

                                 
      16996 TAATTAAAGGTT-AACTAAAC
          1 TAATTAAA-GTTAAACTAAAC

                                
      17016 TAATTAAAAGTTAAACTAAA
          1 TAATT-AAAGTTAAACTAAA

      17036 TACATAAGTA


Statistics
Matches: 18,  Mismatches: 0, Indels: 3
        0.86            0.00        0.14

Matches are distributed among these distances:
  20    8  0.44
  21   10  0.56

ACGTcount: A:0.55, C:0.07, G:0.07, T:0.30


Consensus pattern (20 bp):   
TAATTAAAGTTAAACTAAAC

Found at i:18198 original size:22 final size:22

Alignment explanation


    Indices: 18142--18251  Score: 98
    Period size: 22  Copynumber: 5.0  Consensus size: 22

      18132 GTCCTATTAA

                         * *      
      18142 TTGATTAGCACTTTTGTGCTCT
          1 TTGATTAGCACTTCTATGCTCT

                    *      *       
      18164 TTG-TTCAACACTTCAATGCTCT
          1 TTGATT-AGCACTTCTATGCTCT

                    *      *      
      18186 TTGATTAGGACTTCTGTGCTCT
          1 TTGATTAGCACTTCTATGCTCT

                            * *    
      18208 GTT-ATTAGCACTTCTTTTCTCT
          1 -TTGATTAGCACTTCTATGCTCT

               *          *       
      18230 TTGTTTAGCACTTCGATGCTCT
          1 TTGATTAGCACTTCTATGCTCT

      18252 CTAATGGATT


Statistics
Matches: 69,  Mismatches: 15, Indels: 8
        0.75            0.16        0.09

Matches are distributed among these distances:
  21    4  0.06
  22   61  0.88
  23    4  0.06

ACGTcount: A:0.15, C:0.22, G:0.15, T:0.47


Consensus pattern (22 bp):   
TTGATTAGCACTTCTATGCTCT

Found at i:18230 original size:44 final size:44

Alignment explanation


    Indices: 18142--18251  Score: 116
    Period size: 44  Copynumber: 2.5  Consensus size: 44

      18132 GTCCTATTAA

                         *          *                   
      18142 TTGATTAGCACTTTTGTGCTCTTTGTTCAACACTTCAATGCTCT
          1 TTGATTAGCACTTCTGTGCTCTTTATTCAACACTTCAATGCTCT

                    *                     *      ** *    
      18186 TTGATTAGGACTTCTGTGCTCTGTTATT-AGCACTTCTTTTCTCT
          1 TTGATTAGCACTTCTGTGCTCT-TTATTCAACACTTCAATGCTCT

               *                   
      18230 TTGTTTAGCACTTC-GATGCTCT
          1 TTGATTAGCACTTCTG-TGCTCT

      18252 CTAATGGATT


Statistics
Matches: 55,  Mismatches: 9, Indels: 4
        0.81            0.13        0.06

Matches are distributed among these distances:
  43    1  0.02
  44   50  0.91
  45    4  0.07

ACGTcount: A:0.15, C:0.22, G:0.15, T:0.47


Consensus pattern (44 bp):   
TTGATTAGCACTTCTGTGCTCTTTATTCAACACTTCAATGCTCT
Done.