Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020836.1 Corchorus olitorius cultivar O-4 contig20869, 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: 42544
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33


Found at i:22050 original size:14 final size:14

Alignment explanation


    Indices: 22031--22074  Score: 54
    Period size: 14  Copynumber: 3.1  Consensus size: 14

      22021 TGGAAAAATG

                          
      22031 CTTCTTCTCTTCTT
          1 CTTCTTCTCTTCTT

                           
      22045 CTTCTTCT-TTCTTT
          1 CTTCTTCTCTTC-TT

            *              
      22059 TTTCTTCTCTCTCTT
          1 CTTCTTCTCT-TCTT

             
      22074 C
          1 C

      22075 CCTCCCCTCT


Statistics
Matches: 25,  Mismatches: 2, Indels: 5
        0.78            0.06        0.16

Matches are distributed among these distances:
  13    3  0.12
  14   17  0.68
  15    3  0.12
  16    2  0.08

ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66


Consensus pattern (14 bp):   
CTTCTTCTCTTCTT

Found at i:22053 original size:17 final size:16

Alignment explanation


    Indices: 22031--22074  Score: 56
    Period size: 16  Copynumber: 2.8  Consensus size: 16

      22021 TGGAAAAATG

                             
      22031 CTTCTTCTCTTCTTCTT
          1 CTTCTTCTCTTCTT-TT

                            
      22048 CTTCTT-TCTT-TTTT
          1 CTTCTTCTCTTCTTTT

                         
      22062 CTTCTCTCTCTTC
          1 CTTCT-TCTCTTC

      22075 CCTCCCCTCT


Statistics
Matches: 24,  Mismatches: 0, Indels: 6
        0.80            0.00        0.20

Matches are distributed among these distances:
  14    7  0.29
  15    3  0.12
  16    8  0.33
  17    6  0.25

ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66


Consensus pattern (16 bp):   
CTTCTTCTCTTCTTTT

Found at i:32973 original size:2 final size:2

Alignment explanation


    Indices: 32966--32999  Score: 68
    Period size: 2  Copynumber: 17.0  Consensus size: 2

      32956 ACTCCGCCAC

                                                              
      32966 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

      33000 ATTACAATTA


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   32  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:33832 original size:22 final size:22

Alignment explanation


    Indices: 33807--33849  Score: 59
    Period size: 22  Copynumber: 2.0  Consensus size: 22

      33797 TGTTTAATTA

                  *  *            
      33807 ATTAATTTATTATATTATTATT
          1 ATTAATATAATATATTATTATT

                *                
      33829 ATTACTATAATATATTATTAT
          1 ATTAATATAATATATTATTAT

      33850 AGTACATTAT


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  22   18  1.00

ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58


Consensus pattern (22 bp):   
ATTAATATAATATATTATTATT

Found at i:33860 original size:16 final size:15

Alignment explanation


    Indices: 33813--33862  Score: 50
    Period size: 16  Copynumber: 3.3  Consensus size: 15

      33803 ATTAATTAAT

                      *    
      33813 TTATTA-TATTATTA
          1 TTATTACTATAATTA

                            
      33827 TTATTACTATAATATA
          1 TTATTACTATAAT-TA

                             
      33843 TTATTA-TAGTACATTA
          1 TTATTACTA-TA-ATTA

                
      33859 TTAT
          1 TTAT

      33863 GAAGTCTATA


Statistics
Matches: 31,  Mismatches: 1, Indels: 6
        0.82            0.03        0.16

Matches are distributed among these distances:
  14    6  0.19
  15    7  0.23
  16   16  0.52
  17    2  0.06

ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56


Consensus pattern (15 bp):   
TTATTACTATAATTA

Found at i:41095 original size:34 final size:34

Alignment explanation


    Indices: 41052--41121  Score: 140
    Period size: 34  Copynumber: 2.1  Consensus size: 34

      41042 GCCTGCAACA

                                              
      41052 TTCGGTTTGGATGTTGGCCCGATGCATCTAACGG
          1 TTCGGTTTGGATGTTGGCCCGATGCATCTAACGG

                                              
      41086 TTCGGTTTGGATGTTGGCCCGATGCATCTAACGG
          1 TTCGGTTTGGATGTTGGCCCGATGCATCTAACGG

              
      41120 TT
          1 TT

      41122 GCAAAATAGT


Statistics
Matches: 36,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  34   36  1.00

ACGTcount: A:0.14, C:0.20, G:0.31, T:0.34


Consensus pattern (34 bp):   
TTCGGTTTGGATGTTGGCCCGATGCATCTAACGG
Done.