Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010486.1 Corchorus capsularis cultivar CVL-1 contig10507, 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: 22127
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32


Found at i:168 original size:13 final size:13

Alignment explanation


    Indices: 148--179  Score: 55
    Period size: 13  Copynumber: 2.5  Consensus size: 13

        138 CTGCCAACAC

                         
        148 CCATGCACCCATG
          1 CCATGCACCCATG

             *           
        161 CTATGCACCCATG
          1 CCATGCACCCATG

                  
        174 CCATGC
          1 CCATGC

        180 CGTACTCACC


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  13   17  1.00

ACGTcount: A:0.22, C:0.44, G:0.16, T:0.19


Consensus pattern (13 bp):   
CCATGCACCCATG

Found at i:6409 original size:24 final size:24

Alignment explanation


    Indices: 6341--6408  Score: 84
    Period size: 24  Copynumber: 2.8  Consensus size: 24

       6331 GAAAGTCAAA

                 *               *  
       6341 GAGCAGCAGAAAAAGAAAAAGGGT
          1 GAGCAACAGAAAAAGAAAAAGAGT

               *                     
       6365 GAGAAACA-ACAAAAGAAAAAGAGT
          1 GAGCAACAGA-AAAAGAAAAAGAGT

                                
       6389 GAGCAACAGGAAAAAGAAAA
          1 GAGCAACA-GAAAAAGAAAA

       6409 GGATGCTAAA


Statistics
Matches: 37,  Mismatches: 4, Indels: 5
        0.80            0.09        0.11

Matches are distributed among these distances:
  23    1  0.03
  24   26  0.70
  25    9  0.24
  26    1  0.03

ACGTcount: A:0.62, C:0.09, G:0.26, T:0.03


Consensus pattern (24 bp):   
GAGCAACAGAAAAAGAAAAAGAGT

Found at i:9198 original size:40 final size:40

Alignment explanation


    Indices: 9143--9218  Score: 143
    Period size: 40  Copynumber: 1.9  Consensus size: 40

       9133 CAAAAGGGTC

                                                    
       9143 AAGTGGCCGGTTGTGCCCGGTTGGCGCATGCGTTGGGCCG
          1 AAGTGGCCGGTTGTGCCCGGTTGGCGCATGCGTTGGGCCG

                                          *     
       9183 AAGTGGCCGGTTGTGCCCGGTTGGCGCATGTGTTGG
          1 AAGTGGCCGGTTGTGCCCGGTTGGCGCATGCGTTGG

       9219 CCCGTGCGAT


Statistics
Matches: 35,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  40   35  1.00

ACGTcount: A:0.08, C:0.22, G:0.45, T:0.25


Consensus pattern (40 bp):   
AAGTGGCCGGTTGTGCCCGGTTGGCGCATGCGTTGGGCCG

Found at i:13681 original size:18 final size:18

Alignment explanation


    Indices: 13647--13686  Score: 55
    Period size: 18  Copynumber: 2.2  Consensus size: 18

      13637 TGGGCCGAAG

                             *
      13647 TGGCCGGTTGTGCCCGGT
          1 TGGCCGGTTGTGCCCGGA

                               
      13665 TGGCCGGTTGTTG-CCGGA
          1 TGGCCGGTTG-TGCCCGGA

                
      13683 TGGC
          1 TGGC

      13687 TTGTGCAATG


Statistics
Matches: 20,  Mismatches: 1, Indels: 2
        0.87            0.04        0.09

Matches are distributed among these distances:
  18   18  0.90
  19    2  0.10

ACGTcount: A:0.03, C:0.25, G:0.45, T:0.28


Consensus pattern (18 bp):   
TGGCCGGTTGTGCCCGGA

Found at i:16688 original size:17 final size:16

Alignment explanation


    Indices: 16666--16707  Score: 57
    Period size: 17  Copynumber: 2.5  Consensus size: 16

      16656 CGATAAACTG

                       *     
      16666 ATTTTTGCTTGCATGTT
          1 ATTTTTGCTTGAAT-TT

                            
      16683 ATTTTTGCTTGAATTT
          1 ATTTTTGCTTGAATTT

                     
      16699 AGTTTTTGC
          1 A-TTTTTGC

      16708 ATTTAGATTA


Statistics
Matches: 23,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  16    3  0.13
  17   20  0.87

ACGTcount: A:0.14, C:0.10, G:0.17, T:0.60


Consensus pattern (16 bp):   
ATTTTTGCTTGAATTT

Found at i:18648 original size:20 final size:21

Alignment explanation


    Indices: 18625--18667  Score: 54
    Period size: 20  Copynumber: 2.1  Consensus size: 21

      18615 GAATTGGCAT

                               * 
      18625 ATTTTGCTA-TTGATTGATTG
          1 ATTTTGCTAGTTGATTGATAG

                  *              
      18645 A-TTTGTTAGTTGATTGATAG
          1 ATTTTGCTAGTTGATTGATAG

               
      18665 ATT
          1 ATT

      18668 GTTTGTATGT


Statistics
Matches: 19,  Mismatches: 2, Indels: 3
        0.79            0.08        0.12

Matches are distributed among these distances:
  19    6  0.32
  20   12  0.63
  21    1  0.05

ACGTcount: A:0.23, C:0.02, G:0.21, T:0.53


Consensus pattern (21 bp):   
ATTTTGCTAGTTGATTGATAG

Found at i:21855 original size:26 final size:26

Alignment explanation


    Indices: 21819--21881  Score: 126
    Period size: 26  Copynumber: 2.4  Consensus size: 26

      21809 ACCACCCTTC

                                      
      21819 TTGAAAATTCAAAAAAATCAGCAACT
          1 TTGAAAATTCAAAAAAATCAGCAACT

                                      
      21845 TTGAAAATTCAAAAAAATCAGCAACT
          1 TTGAAAATTCAAAAAAATCAGCAACT

                       
      21871 TTGAAAATTCA
          1 TTGAAAATTCA

      21882 TAGCCGATTC


Statistics
Matches: 37,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  26   37  1.00

ACGTcount: A:0.52, C:0.14, G:0.08, T:0.25


Consensus pattern (26 bp):   
TTGAAAATTCAAAAAAATCAGCAACT
Done.