Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009009.1 Kokia drynarioides strain JFW-HI SEQ_123707, 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: 7334
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.38

Warning! 51 characters in sequence are not A, C, G, or T


Found at i:1209 original size:21 final size:20

Alignment explanation


    Indices: 1185--1223  Score: 51
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       1175 TGATTACATG

                 *               
       1185 TTGTGTTGAGGTATATTGTTA
          1 TTGTGATGA-GTATATTGTTA

                     *        
       1206 TTGTGATGATTATATTGT
          1 TTGTGATGAGTATATTGT

       1224 GATGTGAAGA


Statistics
Matches: 16,  Mismatches: 2, Indels: 1
        0.84            0.11        0.05

Matches are distributed among these distances:
  20    8  0.50
  21    8  0.50

ACGTcount: A:0.21, C:0.00, G:0.26, T:0.54


Consensus pattern (20 bp):   
TTGTGATGAGTATATTGTTA

Found at i:1239 original size:19 final size:20

Alignment explanation


    Indices: 1197--1239  Score: 52
    Period size: 19  Copynumber: 2.2  Consensus size: 20

       1187 GTGTTGAGGT

                   *       *   *
       1197 ATATTGTTATTGTGATGATT
          1 ATATTGTGATTGTGAAGATG

                                
       1217 ATATTGTGA-TGTGAAGATG
          1 ATATTGTGATTGTGAAGATG

                
       1236 ATAT
          1 ATAT

       1240 GATTGAGGTT


Statistics
Matches: 20,  Mismatches: 3, Indels: 1
        0.83            0.12        0.04

Matches are distributed among these distances:
  19   12  0.60
  20    8  0.40

ACGTcount: A:0.30, C:0.00, G:0.23, T:0.47


Consensus pattern (20 bp):   
ATATTGTGATTGTGAAGATG

Found at i:2421 original size:10 final size:11

Alignment explanation


    Indices: 2405--2449  Score: 51
    Period size: 10  Copynumber: 4.4  Consensus size: 11

       2395 TTAATATTTA

                       
       2405 ATATTTATAAT
          1 ATATTTATAAT

                       
       2416 -TATTTA-AAT
          1 ATATTTATAAT

                     * 
       2425 ATATTTATATT
          1 ATATTTATAAT

            *          
       2436 TTA-TTATAAT
          1 ATATTTATAAT

                
       2446 ATAT
          1 ATAT

       2450 AAATTGAAGA


Statistics
Matches: 27,  Mismatches: 4, Indels: 6
        0.73            0.11        0.16

Matches are distributed among these distances:
   9    3  0.11
  10   20  0.74
  11    4  0.15

ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58


Consensus pattern (11 bp):   
ATATTTATAAT

Found at i:3126 original size:11 final size:11

Alignment explanation


    Indices: 3112--3150  Score: 51
    Period size: 11  Copynumber: 3.5  Consensus size: 11

       3102 AAATAACAAC

                    *  
       3112 AAAACAGTGAG
          1 AAAACAGTAAG

                       
       3123 AAAACAGTAAG
          1 AAAACAGTAAG

                  **   
       3134 AAAACAACAAG
          1 AAAACAGTAAG

                  
       3145 AAAACA
          1 AAAACA

       3151 ACATATTTTT


Statistics
Matches: 25,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  11   25  1.00

ACGTcount: A:0.67, C:0.13, G:0.15, T:0.05


Consensus pattern (11 bp):   
AAAACAGTAAG

Found at i:3822 original size:2 final size:2

Alignment explanation


    Indices: 3817--3847  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

       3807 AAAAAAAATA

                                                          
       3817 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       3848 CGGTTAAATT


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   29  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:4384 original size:5 final size:6

Alignment explanation


    Indices: 4367--4400  Score: 50
    Period size: 6  Copynumber: 5.5  Consensus size: 6

       4357 ACTTTTAATA

                                         *         
       4367 TATTTT TATTTT TATTTT TATTTAT AATTTT TAT
          1 TATTTT TATTTT TATTTT TATTT-T TATTTT TAT

       4401 GATTTTTAAA


Statistics
Matches: 25,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
   6   20  0.80
   7    5  0.20

ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76


Consensus pattern (6 bp):   
TATTTT

Done.