Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013185.1 Kokia drynarioides strain JFW-HI SEQ_128204, 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: 11946
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.33

Warning! 10 characters in sequence are not A, C, G, or T


Found at i:1071 original size:30 final size:31

Alignment explanation


    Indices: 1018--1292  Score: 197
    Period size: 30  Copynumber: 9.2  Consensus size: 31

       1008 TCCAGAAATC

                                          *
       1018 CCATTTTTGACCCCGAA-CTTCCAAAAA-TC
          1 CCATTTTTGACCCCGAACCTTCCAAAAATTA

                        *                  
       1047 CCATTTTTGACCTCGAACCTTCCAAAAATTA
          1 CCATTTTTGACCCCGAACCTTCCAAAAATTA

                     ********               *
       1078 CCATTTTNNNNNNNNNNAA-CTTCCAAAAA-TC
          1 CCATTTT--TGACCCCGAACCTTCCAAAAATTA

                        *                  
       1109 CCATTTTTGACCTCGAACCTTCCAAAAATTA
          1 CCATTTTTGACCCCGAACCTTCCAAAAATTA

                        *                     
       1140 CCATTTTTTGTTTCCCCGAACCTTCCAAAAATTA
          1 CCA-TTTTTG--ACCCCGAACCTTCCAAAAATTA

                    *                      *
       1174 CCA--TTTCACCCCCGAA-CTTCCAAAAA-TC
          1 CCATTTTTGA-CCCCGAACCTTCCAAAAATTA

                                           
       1202 CCATTTTTGA---C---CCTTCCAAAAATTA
          1 CCATTTTTGACCCCGAACCTTCCAAAAATTA

                    *     *  *            *
       1227 CCA--TTTCACCCCCAAACTTCCAAAAA-TC
          1 CCATTTTTGACCCCGAACCTTCCAAAAATTA

                        *                  
       1255 CCATTTTTGACCTCGAACCTTCCAAAAATTA
          1 CCATTTTTGACCCCGAACCTTCCAAAAATTA

                   
       1286 CCATTTT
          1 CCATTTT

       1293 ACCCTCGAAT


Statistics
Matches: 188,  Mismatches: 35, Indels: 44
        0.70            0.13        0.16

Matches are distributed among these distances:
  23    4  0.02
  24   10  0.05
  25    4  0.02
  26    2  0.01
  28    8  0.04
  29   38  0.20
  30   50  0.27
  31   31  0.16
  32   16  0.09
  33    2  0.01
  34   23  0.12

ACGTcount: A:0.31, C:0.31, G:0.04, T:0.30


Consensus pattern (31 bp):   
CCATTTTTGACCCCGAACCTTCCAAAAATTA

Found at i:1245 original size:53 final size:53

Alignment explanation


    Indices: 1160--1266  Score: 205
    Period size: 53  Copynumber: 2.0  Consensus size: 53

       1150 TTTCCCCGAA

                                       *                         
       1160 CCTTCCAAAAATTACCATTTCACCCCCGAACTTCCAAAAATCCCATTTTTGAC
          1 CCTTCCAAAAATTACCATTTCACCCCCAAACTTCCAAAAATCCCATTTTTGAC

                                                                 
       1213 CCTTCCAAAAATTACCATTTCACCCCCAAACTTCCAAAAATCCCATTTTTGAC
          1 CCTTCCAAAAATTACCATTTCACCCCCAAACTTCCAAAAATCCCATTTTTGAC

             
       1266 C
          1 C

       1267 TCGAACCTTC


Statistics
Matches: 53,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  53   53  1.00

ACGTcount: A:0.33, C:0.36, G:0.03, T:0.28


Consensus pattern (53 bp):   
CCTTCCAAAAATTACCATTTCACCCCCAAACTTCCAAAAATCCCATTTTTGAC

Found at i:7388 original size:26 final size:25

Alignment explanation


    Indices: 7344--7392  Score: 71
    Period size: 25  Copynumber: 1.9  Consensus size: 25

       7334 TATAGTGCTA

                        *            
       7344 ATAAAAAAATTCCTAATAATAAACT
          1 ATAAAAAAATTCATAATAATAAACT

                       *            
       7369 ATAAAAAAATTGATATATAATAAA
          1 ATAAAAAAATTCATA-ATAATAAA

       7393 TTAAACTCTT


Statistics
Matches: 21,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  25   13  0.62
  26    8  0.38

ACGTcount: A:0.63, C:0.06, G:0.02, T:0.29


Consensus pattern (25 bp):   
ATAAAAAAATTCATAATAATAAACT

Found at i:8405 original size:24 final size:24

Alignment explanation


    Indices: 8377--8425  Score: 98
    Period size: 24  Copynumber: 2.0  Consensus size: 24

       8367 CAAGTTAGCA

                                    
       8377 TTTTTCAATGTTGAAGGGTATCGT
          1 TTTTTCAATGTTGAAGGGTATCGT

                                    
       8401 TTTTTCAATGTTGAAGGGTATCGT
          1 TTTTTCAATGTTGAAGGGTATCGT

             
       8425 T
          1 T

       8426 GTAACTTCCC


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  24   25  1.00

ACGTcount: A:0.20, C:0.08, G:0.24, T:0.47


Consensus pattern (24 bp):   
TTTTTCAATGTTGAAGGGTATCGT
Done.