Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018518.1 Corchorus olitorius cultivar O-4 contig18551, 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: 7615
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.32


Found at i:249 original size:15 final size:16

Alignment explanation


    Indices: 231--263  Score: 50
    Period size: 15  Copynumber: 2.1  Consensus size: 16

        221 TAAAAAGTGA

                  *         
        231 TTTAAATAAAA-TATT
          1 TTTAAAAAAAATTATT

                            
        246 TTTAAAAAAAATTATT
          1 TTTAAAAAAAATTATT

              
        262 TT
          1 TT

        264 CTTCTGAATA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  15   10  0.62
  16    6  0.38

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


Consensus pattern (16 bp):   
TTTAAAAAAAATTATT

Found at i:393 original size:31 final size:31

Alignment explanation


    Indices: 294--433  Score: 133
    Period size: 31  Copynumber: 4.6  Consensus size: 31

        284 AGATGATAAG

                     *         *         ***
        294 CAAGCAATTTAGGATATAATGTTTTCTG-CCG
          1 CAAGCAATTAAGGATATAACGTTTTC-GATTT

                                    *   ***
        325 CAAGCAATTAAGGATATAACG-TTAC-AAAA
          1 CAAGCAATTAAGGATATAACGTTTTCGATTT

                                     *     
        354 CAAGCAATTAAGGATATAACGTTTTTGATTT
          1 CAAGCAATTAAGGATATAACGTTTTCGATTT

            *                * *           
        385 TAAGCAATTAAGGATATGATGTTTTCGATTT
          1 CAAGCAATTAAGGATATAACGTTTTCGATTT

                              
        416 CAAGCAATTAAGGATATA
          1 CAAGCAATTAAGGATATA

        434 GACATATAGT


Statistics
Matches: 89,  Mismatches: 17, Indels: 6
        0.79            0.15        0.05

Matches are distributed among these distances:
  29   21  0.24
  30    5  0.06
  31   63  0.71

ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33


Consensus pattern (31 bp):   
CAAGCAATTAAGGATATAACGTTTTCGATTT

Found at i:638 original size:29 final size:31

Alignment explanation


    Indices: 572--638  Score: 102
    Period size: 31  Copynumber: 2.2  Consensus size: 31

        562 CCTGACGGAC

                                           
        572 TATATCCTTAATTGCTCGTTTTTCGTAACGT
          1 TATATCCTTAATTGCTCGTTTTTCGTAACGT

                          * *              
        603 TATATCCTTAATTGTTTG-TTTT-GTAACGT
          1 TATATCCTTAATTGCTCGTTTTTCGTAACGT

                   
        632 TATATCC
          1 TATATCC

        639 CAAATTGCAT


Statistics
Matches: 34,  Mismatches: 2, Indels: 2
        0.89            0.05        0.05

Matches are distributed among these distances:
  29   14  0.41
  30    4  0.12
  31   16  0.47

ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51


Consensus pattern (31 bp):   
TATATCCTTAATTGCTCGTTTTTCGTAACGT

Found at i:6017 original size:6 final size:6

Alignment explanation


    Indices: 6006--6044  Score: 60
    Period size: 6  Copynumber: 6.5  Consensus size: 6

       5996 ATCGAACAAT

                                        *        *       
       6006 AAAAAG AAAAAG AAAAAG AAAAAG GAAAAG AAGAAG AAA
          1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAA

       6045 CGAATTCAAG


Statistics
Matches: 29,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
   6   29  1.00

ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00


Consensus pattern (6 bp):   
AAAAAG

Done.