Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015000.1 Corchorus capsularis cultivar CVL-1 contig15021, 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: 24350
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33


Found at i:760 original size:19 final size:20

Alignment explanation


    Indices: 728--773  Score: 69
    Period size: 19  Copynumber: 2.4  Consensus size: 20

        718 TTTCCTAACA

                                
        728 AACT-AACTAACTGTTAATT
          1 AACTAAACTAACTGTTAATT

                      *         
        747 AAC-AAACTATCTGTTAATT
          1 AACTAAACTAACTGTTAATT

                    
        766 AACTAAAC
          1 AACTAAAC

        774 AATGGTTAAC


Statistics
Matches: 24,  Mismatches: 1, Indels: 3
        0.86            0.04        0.11

Matches are distributed among these distances:
  19   20  0.83
  20    4  0.17

ACGTcount: A:0.46, C:0.17, G:0.04, T:0.33


Consensus pattern (20 bp):   
AACTAAACTAACTGTTAATT

Found at i:781 original size:19 final size:19

Alignment explanation


    Indices: 740--782  Score: 52
    Period size: 19  Copynumber: 2.3  Consensus size: 19

        730 CTAACTAACT

                          *   *
        740 GTTAATTAACAAACTATCT
          1 GTTAATTAACAAACAATCG

                                
        759 GTTAATTAACTAAACAAT-G
          1 GTTAATTAAC-AAACAATCG

                 
        778 GTTAA
          1 GTTAA

        783 CTAAGTATAT


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  19   15  0.71
  20    6  0.29

ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35


Consensus pattern (19 bp):   
GTTAATTAACAAACAATCG

Found at i:2439 original size:20 final size:19

Alignment explanation


    Indices: 2414--2453  Score: 53
    Period size: 20  Copynumber: 2.1  Consensus size: 19

       2404 CCAGAAACAT

                      *         
       2414 ATTAAAAAAATAAAAGAAAA
          1 ATTAAAAAAAGAAAA-AAAA

                  *            
       2434 ATTAAAGAAAGAAAAAAAA
          1 ATTAAAAAAAGAAAAAAAA

             
       2453 A
          1 A

       2454 GCACCATAAA


Statistics
Matches: 18,  Mismatches: 2, Indels: 1
        0.86            0.10        0.05

Matches are distributed among these distances:
  19    5  0.28
  20   13  0.72

ACGTcount: A:0.80, C:0.00, G:0.07, T:0.12


Consensus pattern (19 bp):   
ATTAAAAAAAGAAAAAAAA

Found at i:3411 original size:4 final size:4

Alignment explanation


    Indices: 3402--3432  Score: 53
    Period size: 4  Copynumber: 7.8  Consensus size: 4

       3392 GAAAGGTAAT

                                           *      
       3402 TTTA TTTA TTTA TTTA TTTA TTTA TGTA TTT
          1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT

       3433 TTACAATAGT


Statistics
Matches: 25,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   4   25  1.00

ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74


Consensus pattern (4 bp):   
TTTA

Found at i:4205 original size:35 final size:35

Alignment explanation


    Indices: 4159--4231  Score: 137
    Period size: 35  Copynumber: 2.1  Consensus size: 35

       4149 CACGTTCTCT

                                      *        
       4159 CTGTATATGCAACAGTGTTATGCTTTCATCCATTG
          1 CTGTATATGCAACAGTGTTATGCTTTAATCCATTG

                                               
       4194 CTGTATATGCAACAGTGTTATGCTTTAATCCATTG
          1 CTGTATATGCAACAGTGTTATGCTTTAATCCATTG

               
       4229 CTG
          1 CTG

       4232 AAGATATGTA


Statistics
Matches: 37,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  35   37  1.00

ACGTcount: A:0.23, C:0.19, G:0.18, T:0.40


Consensus pattern (35 bp):   
CTGTATATGCAACAGTGTTATGCTTTAATCCATTG

Found at i:9315 original size:52 final size:52

Alignment explanation


    Indices: 9233--9338  Score: 185
    Period size: 52  Copynumber: 2.0  Consensus size: 52

       9223 TCGATTCTTC

                         *           *                          
       9233 TCCTAACATTGATGTATTTACTTGACAGTGCAAATAATCCCGTTGCTTGGCA
          1 TCCTAACATTGATATATTTACTTGAAAGTGCAAATAATCCCGTTGCTTGGCA

                                                    *           
       9285 TCCTAACATTGATATATTTACTTGAAAGTGCAAATAATCCTGTTGCTTGGCA
          1 TCCTAACATTGATATATTTACTTGAAAGTGCAAATAATCCCGTTGCTTGGCA

              
       9337 TC
          1 TC

       9339 ATATGATAAA


Statistics
Matches: 51,  Mismatches: 3, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  52   51  1.00

ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36


Consensus pattern (52 bp):   
TCCTAACATTGATATATTTACTTGAAAGTGCAAATAATCCCGTTGCTTGGCA
Done.