Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013261.1 Corchorus capsularis cultivar CVL-1 contig13282, 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: 46869
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34


Found at i:439 original size:15 final size:15

Alignment explanation


    Indices: 415--444  Score: 51
    Period size: 15  Copynumber: 2.0  Consensus size: 15

        405 ATTCGTCTCC

                 *         
        415 GAATATGTGTTTGAA
          1 GAATACGTGTTTGAA

                           
        430 GAATACGTGTTTGAA
          1 GAATACGTGTTTGAA

        445 TGATTGAACT


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

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.33, C:0.03, G:0.27, T:0.37


Consensus pattern (15 bp):   
GAATACGTGTTTGAA

Found at i:5114 original size:30 final size:32

Alignment explanation


    Indices: 5078--5143  Score: 91
    Period size: 34  Copynumber: 2.1  Consensus size: 32

       5068 CACGATTAAT

                                *           
       5078 TTGGAGTTGC-G-TCGAACCTTTACTCTTCAA
          1 TTGGAGTTGCTGATCGAACCCTTACTCTTCAA

                                              
       5108 TTGGAGTTGCATTGATCGAACCCTTACTCTTCAA
          1 TTGGAGTTGC--TGATCGAACCCTTACTCTTCAA

              
       5142 TT
          1 TT

       5144 ATGAAGTATT


Statistics
Matches: 31,  Mismatches: 1, Indels: 4
        0.86            0.03        0.11

Matches are distributed among these distances:
  30   10  0.32
  33    1  0.03
  34   20  0.65

ACGTcount: A:0.21, C:0.23, G:0.18, T:0.38


Consensus pattern (32 bp):   
TTGGAGTTGCTGATCGAACCCTTACTCTTCAA

Found at i:27953 original size:3 final size:3

Alignment explanation


    Indices: 27945--27982  Score: 76
    Period size: 3  Copynumber: 12.7  Consensus size: 3

      27935 TTTTAAATTA

                                                              
      27945 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
          1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA

      27983 ACAAACACTT


Statistics
Matches: 35,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   35  1.00

ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32


Consensus pattern (3 bp):   
AAT

Found at i:42494 original size:29 final size:29

Alignment explanation


    Indices: 42429--42509  Score: 99
    Period size: 29  Copynumber: 2.7  Consensus size: 29

      42419 ACTTAATACC

                  *              **        
      42429 CAAATTAACCCCTTAACTATCCATTTTGGGA
          1 CAAATTGACCCCTTAACT-T-TTTTTTGGGA

                   **                    
      42460 CAAATTGGTCCCTTAACTTTTTTTTGGGA
          1 CAAATTGACCCCTTAACTTTTTTTTGGGA

                                 
      42489 CAAATTGACCCCTTAACTTTT
          1 CAAATTGACCCCTTAACTTTT

      42510 AAAAACGAGA


Statistics
Matches: 43,  Mismatches: 7, Indels: 2
        0.83            0.13        0.04

Matches are distributed among these distances:
  29   27  0.63
  30    1  0.02
  31   15  0.35

ACGTcount: A:0.27, C:0.23, G:0.11, T:0.38


Consensus pattern (29 bp):   
CAAATTGACCCCTTAACTTTTTTTTGGGA

Found at i:43245 original size:29 final size:29

Alignment explanation


    Indices: 43198--43255  Score: 73
    Period size: 29  Copynumber: 2.0  Consensus size: 29

      43188 TTTCGTTTTT

                                *        
      43198 AAAAGTTAAGGGGCTAATTTGTCCAAAAA
          1 AAAAGTTAAGGGGCTAATTTATCCAAAAA

                         *           *    
      43227 AAAAGTTAA-GGGATCAATTTATCCCAAAA
          1 AAAAGTTAAGGGGCT-AATTTATCCAAAAA

      43256 TGGATAGTTA


Statistics
Matches: 25,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  28    4  0.16
  29   21  0.84

ACGTcount: A:0.47, C:0.12, G:0.17, T:0.24


Consensus pattern (29 bp):   
AAAAGTTAAGGGGCTAATTTATCCAAAAA

Found at i:43444 original size:54 final size:54

Alignment explanation


    Indices: 43362--43480  Score: 238
    Period size: 54  Copynumber: 2.2  Consensus size: 54

      43352 TTTTTCTCAA

                                                                  
      43362 GAACTATTTCCGGGAATTTTTCTCAACACTTATTTTCTTTACTTGATAGACATC
          1 GAACTATTTCCGGGAATTTTTCTCAACACTTATTTTCTTTACTTGATAGACATC

                                                                  
      43416 GAACTATTTCCGGGAATTTTTCTCAACACTTATTTTCTTTACTTGATAGACATC
          1 GAACTATTTCCGGGAATTTTTCTCAACACTTATTTTCTTTACTTGATAGACATC

                       
      43470 GAACTATTTCC
          1 GAACTATTTCC

      43481 ACTAAACCGA


Statistics
Matches: 65,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  54   65  1.00

ACGTcount: A:0.26, C:0.21, G:0.11, T:0.42


Consensus pattern (54 bp):   
GAACTATTTCCGGGAATTTTTCTCAACACTTATTTTCTTTACTTGATAGACATC

Found at i:43841 original size:11 final size:11

Alignment explanation


    Indices: 43825--43869  Score: 54
    Period size: 11  Copynumber: 4.0  Consensus size: 11

      43815 TCTCTCTTTC

                       
      43825 TTTTCTTTTTT
          1 TTTTCTTTTTT

                       
      43836 TTTTCTTTTTT
          1 TTTTCTTTTTT

                *     **
      43847 TTTCCCTTTTCC
          1 TTT-TCTTTTTT

                       
      43859 TTTTCTTTTTT
          1 TTTTCTTTTTT

      43870 GTATAGTTTT


Statistics
Matches: 27,  Mismatches: 6, Indels: 2
        0.77            0.17        0.06

Matches are distributed among these distances:
  11   19  0.70
  12    8  0.30

ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82


Consensus pattern (11 bp):   
TTTTCTTTTTT
Done.