Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001654.1 Corchorus capsularis cultivar CVL-1 contig01654, 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, 771

Length: 1286
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:96 original size:21 final size:21

Alignment explanation


    Indices: 70--115  Score: 67
    Period size: 21  Copynumber: 2.2  Consensus size: 21

         60 AAATGTTTAG

                                  
         70 AAAAGAATATAAAAAATATA-A
          1 AAAAGAATATAAAAAA-ATACA

                  *              
         91 AAAAGACTATAAAAAAATACA
          1 AAAAGAATATAAAAAAATACA

                
        112 AAAA
          1 AAAA

        116 TGAAAAAAGA


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

Matches are distributed among these distances:
  20    3  0.13
  21   20  0.87

ACGTcount: A:0.76, C:0.04, G:0.04, T:0.15


Consensus pattern (21 bp):   
AAAAGAATATAAAAAAATACA

Found at i:108 original size:22 final size:21

Alignment explanation


    Indices: 70--115  Score: 65
    Period size: 22  Copynumber: 2.1  Consensus size: 21

         60 AAATGTTTAG

                              *  
         70 AAAAGAATATAAAAAATATAA
          1 AAAAGAATATAAAAAATACAA

                  *               
         91 AAAAGACTATAAAAAAATACAA
          1 AAAAGAATAT-AAAAAATACAA

               
        113 AAA
          1 AAA

        116 TGAAAAAAGA


Statistics
Matches: 22,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  21    9  0.41
  22   13  0.59

ACGTcount: A:0.76, C:0.04, G:0.04, T:0.15


Consensus pattern (21 bp):   
AAAAGAATATAAAAAATACAA

Found at i:179 original size:20 final size:19

Alignment explanation


    Indices: 154--197  Score: 72
    Period size: 18  Copynumber: 2.3  Consensus size: 19

        144 TTATTATTAC

                                
        154 TATTTTCTATTTTTATATGT
          1 TATTTT-TATTTTTATATGT

                               
        174 TA-TTTTATTTTTATATGT
          1 TATTTTTATTTTTATATGT

                  
        192 TATTTT
          1 TATTTT

        198 ATCATATGTT


Statistics
Matches: 23,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  18   15  0.65
  19    6  0.26
  20    2  0.09

ACGTcount: A:0.20, C:0.02, G:0.05, T:0.73


Consensus pattern (19 bp):   
TATTTTTATTTTTATATGT

Found at i:184 original size:18 final size:18

Alignment explanation


    Indices: 161--199  Score: 78
    Period size: 18  Copynumber: 2.2  Consensus size: 18

        151 TACTATTTTC

                              
        161 TATTTTTATATGTTATTT
          1 TATTTTTATATGTTATTT

                              
        179 TATTTTTATATGTTATTT
          1 TATTTTTATATGTTATTT

               
        197 TAT
          1 TAT

        200 CATATGTTAT


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   21  1.00

ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72


Consensus pattern (18 bp):   
TATTTTTATATGTTATTT

Found at i:206 original size:15 final size:15

Alignment explanation


    Indices: 178--215  Score: 62
    Period size: 15  Copynumber: 2.7  Consensus size: 15

        168 ATATGTTATT

                           
        178 TTATTTT-T-ATATG
          1 TTATTTTATCATATG

                           
        191 TTATTTTATCATATG
          1 TTATTTTATCATATG

                      
        206 TTATTTTATC
          1 TTATTTTATC

        216 TTATCTGTTC


Statistics
Matches: 23,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
  13    7  0.30
  14    1  0.04
  15   15  0.65

ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66


Consensus pattern (15 bp):   
TTATTTTATCATATG

Found at i:401 original size:13 final size:13

Alignment explanation


    Indices: 383--407  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

        373 CTATAGCAGC

                         
        383 AATAATAAATAAG
          1 AATAATAAATAAG

                        
        396 AATAATAAATAA
          1 AATAATAAATAA

        408 AATTAAGAAT


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24


Consensus pattern (13 bp):   
AATAATAAATAAG
Done.