Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000475.1 Corchorus capsularis cultivar CVL-1 contig00475, 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, 700

Length: 1167
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.37


Found at i:312 original size:102 final size:102

Alignment explanation


    Indices: 221--426  Score: 358
    Period size: 102  Copynumber: 2.0  Consensus size: 102

        211 AGAGTTTTTT

                                                                             
        221 TACAGAAAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTATACAAAAAAATTTCTA
          1 TACAGAAAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTATACAAAAAAATTTCTA

                                                 
        286 ATACATCTAAGTTTTTTTAATTAAAATAGTAAAATGG
         66 ATACATCTAAGTTTTTTTAATTAAAATAGTAAAATGG

              * * ***                                                 *      
        323 TATATATTTATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTATACAAAAAATTTTCTA
          1 TACAGAAAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTATACAAAAAAATTTCTA

                                                 
        388 ATACATCTAAGTTTTTTTAATTAAAATAGTAAAATGG
         66 ATACATCTAAGTTTTTTTAATTAAAATAGTAAAATGG

              
        425 TA
          1 TA

        427 AAAATGATAT


Statistics
Matches: 98,  Mismatches: 6, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
 102   98  1.00

ACGTcount: A:0.48, C:0.05, G:0.10, T:0.36


Consensus pattern (102 bp):   
TACAGAAAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTATACAAAAAAATTTCTA
ATACATCTAAGTTTTTTTAATTAAAATAGTAAAATGG

Found at i:681 original size:25 final size:25

Alignment explanation


    Indices: 634--681  Score: 71
    Period size: 25  Copynumber: 1.9  Consensus size: 25

        624 AAATAATTAT

                              *      
        634 AAATATTGAATTTTTTGAGATGATA
          1 AAATATTGAATTTTTTGAAATGATA

                                    
        659 AAATATTGAATTTATTT-AAATGA
          1 AAATATTGAATTT-TTTGAAATGA

        682 AAATAGTGTT


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  25   18  0.86
  26    3  0.14

ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44


Consensus pattern (25 bp):   
AAATATTGAATTTTTTGAAATGATA

Found at i:943 original size:2 final size:2

Alignment explanation


    Indices: 921--970  Score: 55
    Period size: 2  Copynumber: 24.0  Consensus size: 2

        911 TCGTACTTTA

                             *     *                  *                     
        921 AT AT AT AGT AT AG AT AG AT AT AT AGT AT AG AT AT AT AT AT AT AT
          1 AT AT AT A-T AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT

                    
        965 AT AT AT
          1 AT AT AT

        971 CTTTATACTC


Statistics
Matches: 40,  Mismatches: 6, Indels: 4
        0.80            0.12        0.08

Matches are distributed among these distances:
   2   36  0.90
   3    4  0.10

ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42


Consensus pattern (2 bp):   
AT

Found at i:943 original size:17 final size:17

Alignment explanation


    Indices: 921--965  Score: 74
    Period size: 17  Copynumber: 2.7  Consensus size: 17

        911 TCGTACTTTA

                             
        921 ATATATAGTATAGATAG
          1 ATATATAGTATAGATAG

                            *
        938 ATATATAGTATAGATAT
          1 ATATATAGTATAGATAG

                        
        955 ATATATA-TATA
          1 ATATATAGTATA

        966 TATATCTTTA


Statistics
Matches: 27,  Mismatches: 1, Indels: 1
        0.93            0.03        0.03

Matches are distributed among these distances:
  16    4  0.15
  17   23  0.85

ACGTcount: A:0.49, C:0.00, G:0.11, T:0.40


Consensus pattern (17 bp):   
ATATATAGTATAGATAG

Done.