Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012156.1 Corchorus capsularis cultivar CVL-1 contig12177, 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: 27705
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.29


Found at i:3852 original size:27 final size:27

Alignment explanation


    Indices: 3822--3886  Score: 112
    Period size: 27  Copynumber: 2.4  Consensus size: 27

       3812 ATTTACCCAG

                  *                    
       3822 ATGCCCTTGGGTGCAAAAATGACCAAA
          1 ATGCCCCTGGGTGCAAAAATGACCAAA

                      *                
       3849 ATGCCCCTGGATGCAAAAATGACCAAA
          1 ATGCCCCTGGGTGCAAAAATGACCAAA

                       
       3876 ATGCCCCTGGG
          1 ATGCCCCTGGG

       3887 CGACCCTAAT


Statistics
Matches: 35,  Mismatches: 3, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  27   35  1.00

ACGTcount: A:0.34, C:0.26, G:0.23, T:0.17


Consensus pattern (27 bp):   
ATGCCCCTGGGTGCAAAAATGACCAAA

Found at i:5316 original size:53 final size:53

Alignment explanation


    Indices: 5233--5339  Score: 196
    Period size: 53  Copynumber: 2.0  Consensus size: 53

       5223 AAATAGCATC

                                     *                           
       5233 ATTGAGCATGTCATGCATAAAGGCTCTATCAATCCCCATGAAAGAGAGATTTT
          1 ATTGAGCATGTCATGCATAAAGGCTATATCAATCCCCATGAAAGAGAGATTTT

                                                *                
       5286 ATTGAGCATGTCATGCATAAAGGCTATATCAATCCCGATGAAAGAGAGATTTT
          1 ATTGAGCATGTCATGCATAAAGGCTATATCAATCCCCATGAAAGAGAGATTTT

             
       5339 A
          1 A

       5340 ACTCTTTAGA


Statistics
Matches: 52,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  53   52  1.00

ACGTcount: A:0.36, C:0.17, G:0.20, T:0.28


Consensus pattern (53 bp):   
ATTGAGCATGTCATGCATAAAGGCTATATCAATCCCCATGAAAGAGAGATTTT

Found at i:11167 original size:2 final size:2

Alignment explanation


    Indices: 11160--11186  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

      11150 TTCAACTGCA

                                                    
      11160 AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT A

      11187 AGCAGAAGCA


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:13200 original size:16 final size:17

Alignment explanation


    Indices: 13172--13209  Score: 53
    Period size: 16  Copynumber: 2.4  Consensus size: 17

      13162 GGTTCGGATC

                             
      13172 ATTAA-GGATTTTTCGG
          1 ATTAATGGATTTTTCGG

                             
      13188 ATTAATGGA-TTTTCGG
          1 ATTAATGGATTTTTCGG

            *     
      13204 TTTAAT
          1 ATTAAT

      13210 TTCAGGCGGT


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

Matches are distributed among these distances:
  16   17  0.85
  17    3  0.15

ACGTcount: A:0.26, C:0.05, G:0.21, T:0.47


Consensus pattern (17 bp):   
ATTAATGGATTTTTCGG

Found at i:19566 original size:17 final size:17

Alignment explanation


    Indices: 19540--19573  Score: 50
    Period size: 17  Copynumber: 2.0  Consensus size: 17

      19530 TTTTAATTTT

                 *           
      19540 GAAAATGGAAAAAACAG
          1 GAAAAGGGAAAAAACAG

                       *     
      19557 GAAAAGGGAAATAACAG
          1 GAAAAGGGAAAAAACAG

      19574 TGGTTAAAAG


Statistics
Matches: 15,  Mismatches: 2, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  17   15  1.00

ACGTcount: A:0.62, C:0.06, G:0.26, T:0.06


Consensus pattern (17 bp):   
GAAAAGGGAAAAAACAG

Found at i:27621 original size:13 final size:13

Alignment explanation


    Indices: 27603--27629  Score: 54
    Period size: 13  Copynumber: 2.1  Consensus size: 13

      27593 AAACTAATGC

                         
      27603 AAACAAAAACAAA
          1 AAACAAAAACAAA

                         
      27616 AAACAAAAACAAA
          1 AAACAAAAACAAA

             
      27629 A
          1 A

      27630 GGATCAAGAT


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   14  1.00

ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00


Consensus pattern (13 bp):   
AAACAAAAACAAA
Done.