Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017961.1 Corchorus olitorius cultivar O-4 contig17994, 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: 30842
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34


Found at i:7285 original size:21 final size:21

Alignment explanation


    Indices: 7261--7305  Score: 90
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       7251 CTTAATCCGT

                                 
       7261 TTACGGAATCTATAATTTACA
          1 TTACGGAATCTATAATTTACA

                                 
       7282 TTACGGAATCTATAATTTACA
          1 TTACGGAATCTATAATTTACA

               
       7303 TTA
          1 TTA

       7306 ACAGTATATC


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  21   24  1.00

ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40


Consensus pattern (21 bp):   
TTACGGAATCTATAATTTACA

Found at i:18134 original size:30 final size:31

Alignment explanation


    Indices: 18100--18183  Score: 118
    Period size: 30  Copynumber: 2.7  Consensus size: 31

      18090 GGTTTTGCTG

                                  *        
      18100 TTATTTTCTGCACTGTTTAATTCGTTTCTA-
          1 TTATTTTCTGCACTGTTTAATTAGTTTCTAT

                                             
      18130 TTATTTTCTGCACT-TTATAATTAGTTTCTATT
          1 TTATTTTCTGCACTGTT-TAATTAGTTTCTA-T

                            *     
      18162 TTATTTTCTGCACTGTATAATT
          1 TTATTTTCTGCACTGTTTAATT

      18184 GTGATCATTA


Statistics
Matches: 48,  Mismatches: 2, Indels: 6
        0.86            0.04        0.11

Matches are distributed among these distances:
  29    2  0.04
  30   26  0.54
  32   19  0.40
  33    1  0.02

ACGTcount: A:0.20, C:0.14, G:0.08, T:0.57


Consensus pattern (31 bp):   
TTATTTTCTGCACTGTTTAATTAGTTTCTAT

Found at i:23808 original size:29 final size:31

Alignment explanation


    Indices: 23739--23811  Score: 132
    Period size: 31  Copynumber: 2.4  Consensus size: 31

      23729 TCAAGTCGTC

                                           
      23739 AACATATGACCAAAATATTTCACCAACAAAA
          1 AACATATGACCAAAATATTTCACCAACAAAA

                                           
      23770 AACATATGACCAAAATATTTCACC-A-AAAA
          1 AACATATGACCAAAATATTTCACCAACAAAA

                         
      23799 AACATATGACCAA
          1 AACATATGACCAA

      23812 TAGGCTCAAC


Statistics
Matches: 42,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
  29   17  0.40
  30    1  0.02
  31   24  0.57

ACGTcount: A:0.55, C:0.22, G:0.04, T:0.19


Consensus pattern (31 bp):   
AACATATGACCAAAATATTTCACCAACAAAA

Found at i:24891 original size:14 final size:15

Alignment explanation


    Indices: 24865--24893  Score: 51
    Period size: 14  Copynumber: 2.0  Consensus size: 15

      24855 TCCCACCGGC

                           
      24865 TTCTTTCCTTTTTTT
          1 TTCTTTCCTTTTTTT

                           
      24880 TTCTTT-CTTTTTTT
          1 TTCTTTCCTTTTTTT

      24894 GGCACAGAGA


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  14    8  0.57
  15    6  0.43

ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83


Consensus pattern (15 bp):   
TTCTTTCCTTTTTTT

Found at i:30200 original size:13 final size:14

Alignment explanation


    Indices: 30176--30207  Score: 57
    Period size: 13  Copynumber: 2.4  Consensus size: 14

      30166 AGCCATCAAC

                          
      30176 TATTTGAAATTATA
          1 TATTTGAAATTATA

                          
      30190 TATTT-AAATTATA
          1 TATTTGAAATTATA

                 
      30203 TATTT
          1 TATTT

      30208 TATGAGTATT


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

Matches are distributed among these distances:
  13   13  0.72
  14    5  0.28

ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56


Consensus pattern (14 bp):   
TATTTGAAATTATA

Done.