Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018845.1 Corchorus olitorius cultivar O-4 contig18878, 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: 24291
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30


Found at i:2326 original size:17 final size:18

Alignment explanation


    Indices: 2300--2333  Score: 52
    Period size: 17  Copynumber: 1.9  Consensus size: 18

       2290 TTTTGAAAAA

                              
       2300 ATTTTCGAAA-AAAATTG
          1 ATTTTCGAAATAAAATTG

                 *           
       2317 ATTTTTGAAATAAAATT
          1 ATTTTCGAAATAAAATT

       2334 TAAAATTTTC


Statistics
Matches: 15,  Mismatches: 1, Indels: 1
        0.88            0.06        0.06

Matches are distributed among these distances:
  17    9  0.60
  18    6  0.40

ACGTcount: A:0.47, C:0.03, G:0.09, T:0.41


Consensus pattern (18 bp):   
ATTTTCGAAATAAAATTG

Found at i:20120 original size:6 final size:6

Alignment explanation


    Indices: 20100--20140  Score: 52
    Period size: 6  Copynumber: 7.3  Consensus size: 6

      20090 TATATTGCTG

                    *                                          
      20100 TTTGTT TGT-TT TTTGTT TTTGTT TTTGTT TTT-TT TTT-TT TT
          1 TTTGTT TTTGTT TTTGTT TTTGTT TTTGTT TTTGTT TTTGTT TT

      20141 GGAAAATCTT


Statistics
Matches: 32,  Mismatches: 2, Indels: 3
        0.86            0.05        0.08

Matches are distributed among these distances:
   5   13  0.41
   6   19  0.59

ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88


Consensus pattern (6 bp):   
TTTGTT

Found at i:20127 original size:23 final size:21

Alignment explanation


    Indices: 20100--20141  Score: 66
    Period size: 23  Copynumber: 1.9  Consensus size: 21

      20090 TATATTGCTG

                                   
      20100 TTTGTTTGTTTTTTGTTTTTGTT
          1 TTTGTTT-TTTTTT-TTTTTGTT

                               
      20123 TTTGTTTTTTTTTTTTTTG
          1 TTTGTTTTTTTTTTTTTTG

      20142 GAAAATCTTA


Statistics
Matches: 19,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  21    6  0.32
  22    6  0.32
  23    7  0.37

ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86


Consensus pattern (21 bp):   
TTTGTTTTTTTTTTTTTTGTT

Found at i:21425 original size:18 final size:18

Alignment explanation


    Indices: 21402--21447  Score: 56
    Period size: 18  Copynumber: 2.6  Consensus size: 18

      21392 TGAAATTAAT

                              
      21402 TAATTATTAATTAAATAA
          1 TAATTATTAATTAAATAA

                    **  *     
      21420 TAATTATTTTTTGAATAA
          1 TAATTATTAATTAAATAA

             *        
      21438 TTATTATTAA
          1 TAATTATTAA

      21448 GTTTCTAGTG


Statistics
Matches: 22,  Mismatches: 6, Indels: 0
        0.79            0.21        0.00

Matches are distributed among these distances:
  18   22  1.00

ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52


Consensus pattern (18 bp):   
TAATTATTAATTAAATAA

Found at i:22897 original size:51 final size:52

Alignment explanation


    Indices: 22796--22897  Score: 120
    Period size: 51  Copynumber: 2.0  Consensus size: 52

      22786 GTTCTTCATA

                                                     * **       
      22796 TTCTCCTTGTTTAGATCTTGTCTCCGAACAAACAAACACTCTTTTAGTGTTT
          1 TTCTCCTTGTTTAGATCTTGTCTCCGAACAAACAAACACTCGTACAGTGTTT

                                       *   *                     
      22848 TTCT-CTTGTTTCA-ATCTTGTCTCCGGACATACAAACACT-GTACACGTGTT
          1 TTCTCCTTGTTT-AGATCTTGTCTCCGAACAAACAAACACTCGTACA-GTGTT

      22898 CTTCATCCAA


Statistics
Matches: 43,  Mismatches: 5, Indels: 5
        0.81            0.09        0.09

Matches are distributed among these distances:
  50    2  0.05
  51   36  0.84
  52    5  0.12

ACGTcount: A:0.23, C:0.25, G:0.13, T:0.40


Consensus pattern (52 bp):   
TTCTCCTTGTTTAGATCTTGTCTCCGAACAAACAAACACTCGTACAGTGTTT
Done.