Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010359.1 Kokia drynarioides strain JFW-HI SEQ_125230, 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: 5551
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28


Found at i:2144 original size:115 final size:114

Alignment explanation


    Indices: 1977--2192  Score: 362
    Period size: 115  Copynumber: 1.9  Consensus size: 114

       1967 ATAAATTCAC

                                                                     **      
       1977 ACTCGATGTGAGCAAATCTTCGAACTCCAGCTTCCTGATGAGATACTCAGAAGCAGGTTGAAGAA
          1 ACTCGATGTGAGCAAATCTTCGAACTCCAGCTTCCTGATGAGATACTCAGAAGCAGGGCGAAGAA

                                                              
       2042 ATAAAATGGTTAGCTTCCTGATGAGATACAGAGAAGTATACCAACTCAGG
         66 ATAAAA-GGTTAGCTTCCTGATGAGATACAGAGAAGTATACCAACTCAGG

                                                            *               *
       2092 ACTCGATGTGAGCAAATCTTCGAA-TCCCAGCTTCCTGATGAGATACTGAGAAGCAGGGCGAAGC
          1 ACTCGATGTGAGCAAATCTTCGAACT-CCAGCTTCCTGATGAGATACTCAGAAGCAGGGCGAAGA

                                         *       
       2156 AATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGT
         65 AATAAAAGGTTAGCTTCCTGATGAGATACAGAGAAGT

       2193 GGACCAAATC


Statistics
Matches: 95,  Mismatches: 5, Indels: 3
        0.92            0.05        0.03

Matches are distributed among these distances:
 114   30  0.32
 115   65  0.68

ACGTcount: A:0.34, C:0.19, G:0.24, T:0.23


Consensus pattern (114 bp):   
ACTCGATGTGAGCAAATCTTCGAACTCCAGCTTCCTGATGAGATACTCAGAAGCAGGGCGAAGAA
ATAAAAGGTTAGCTTCCTGATGAGATACAGAGAAGTATACCAACTCAGG

Found at i:2903 original size:37 final size:37

Alignment explanation


    Indices: 2854--2925  Score: 101
    Period size: 37  Copynumber: 1.9  Consensus size: 37

       2844 TTTAAATTCT

                  *           *           *       
       2854 TTTTTACATTTAAATTT-ATCTTAAATTTATATTTATA
          1 TTTTTAAATTTAAATTTGCT-TTAAATTTAAATTTATA

                                               
       2891 TTTTTAAATTTAAATTTGCTTTAAATTTAAATTTA
          1 TTTTTAAATTTAAATTTGCTTTAAATTTAAATTTA

       2926 ATCAAATATG


Statistics
Matches: 31,  Mismatches: 3, Indels: 2
        0.86            0.08        0.06

Matches are distributed among these distances:
  37   30  0.97
  38    1  0.03

ACGTcount: A:0.36, C:0.04, G:0.01, T:0.58


Consensus pattern (37 bp):   
TTTTTAAATTTAAATTTGCTTTAAATTTAAATTTATA

Found at i:3685 original size:3 final size:3

Alignment explanation


    Indices: 3622--3669  Score: 78
    Period size: 3  Copynumber: 15.7  Consensus size: 3

       3612 GCTCATAAGT

                                                                  *     
       3622 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATAA ATA ACA ATA
          1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA

              
       3668 AT
          1 AT

       3670 TGTTTTAATA


Statistics
Matches: 42,  Mismatches: 2, Indels: 2
        0.91            0.04        0.04

Matches are distributed among these distances:
   3   39  0.93
   4    3  0.07

ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31


Consensus pattern (3 bp):   
ATA

Found at i:4962 original size:96 final size:96

Alignment explanation


    Indices: 4845--5036  Score: 237
    Period size: 96  Copynumber: 2.0  Consensus size: 96

       4835 AAGACTTTCA

                    *                                  *                     
       4845 AATCGAGGTAATATTCTTTTAT-TTCAAGTT-TCAAAAATTTGTGCCTTAACTTACTAGGTGCAA
          1 AATCGAGGCAATATTCTTTTATCTTCAA-TTATCAAAAA-TTGCGCCTTAACTTACTAGGTGCAA

            **                               
       4908 TTTTTCTTCAAATCGAAATAATCGAATACCCTT
         64 CCTTTCTTCAAATCGAAATAATCGAATACCCTT

                        *              *     *   *                           
       4941 AATCGAGGCAATGTT-TCTTTATCTTCGATTATGAAATATTGCGCCTTAACTTACTAGGTGCAAC
          1 AATCGAGGCAATATTCT-TTTATCTTCAATTATCAAAAATTGCGCCTTAACTTACTAGGTGCAAC

                           *     *     *    
       5005 CTTTCTTCAAATCGAGATAATTGAATATCCTT
         65 CTTTCTTCAAATCGAAATAATCGAATACCCTT

       5037 TTCCCAAAAT


Statistics
Matches: 82,  Mismatches: 11, Indels: 6
        0.83            0.11        0.06

Matches are distributed among these distances:
  95    1  0.01
  96   72  0.88
  97    9  0.11

ACGTcount: A:0.31, C:0.18, G:0.13, T:0.39


Consensus pattern (96 bp):   
AATCGAGGCAATATTCTTTTATCTTCAATTATCAAAAATTGCGCCTTAACTTACTAGGTGCAACC
TTTCTTCAAATCGAAATAATCGAATACCCTT
Done.