Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01003458.1 Corchorus capsularis cultivar CVL-1 contig03466, 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, 657

Length: 1096
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.42


Found at i:77 original size:15 final size:15

Alignment explanation


    Indices: 57--85  Score: 58
    Period size: 15  Copynumber: 1.9  Consensus size: 15

         47 TTTTAAAAAA

                           
         57 AATTAATTAATTTTT
          1 AATTAATTAATTTTT

                          
         72 AATTAATTAATTTT
          1 AATTAATTAATTTT

         86 AATGTTTATG


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

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59


Consensus pattern (15 bp):   
AATTAATTAATTTTT

Found at i:144 original size:14 final size:15

Alignment explanation


    Indices: 127--168  Score: 50
    Period size: 15  Copynumber: 2.9  Consensus size: 15

        117 AAATTTAGTT

                           
        127 TGTTT-ATTAGTTTA
          1 TGTTTAATTAGTTTA

                      *    
        141 TGTTTAATTATTTTA
          1 TGTTTAATTAGTTTA

             **          
        156 TAATTAATTAGTT
          1 TGTTTAATTAGTT

        169 CATTATTTTT


Statistics
Matches: 23,  Mismatches: 4, Indels: 1
        0.82            0.14        0.04

Matches are distributed among these distances:
  14    5  0.22
  15   18  0.78

ACGTcount: A:0.29, C:0.00, G:0.10, T:0.62


Consensus pattern (15 bp):   
TGTTTAATTAGTTTA

Found at i:383 original size:15 final size:14

Alignment explanation


    Indices: 350--386  Score: 51
    Period size: 15  Copynumber: 2.7  Consensus size: 14

        340 AGTTTATTAA

                          
        350 AATTAGT-TTGTTT
          1 AATTAGTATTGTTT

                           
        363 -ATTAGTATATGTTT
          1 AATTAGTAT-TGTTT

                      
        377 AATTAGTATT
          1 AATTAGTATT

        387 TAATTAGTTT


Statistics
Matches: 21,  Mismatches: 0, Indels: 5
        0.81            0.00        0.19

Matches are distributed among these distances:
  12    6  0.29
  13    1  0.05
  14    6  0.29
  15    8  0.38

ACGTcount: A:0.30, C:0.00, G:0.14, T:0.57


Consensus pattern (14 bp):   
AATTAGTATTGTTT

Found at i:707 original size:24 final size:27

Alignment explanation


    Indices: 674--769  Score: 99
    Period size: 30  Copynumber: 3.4  Consensus size: 27

        664 CTCCGCCCGT

                 *                     
        674 AGGGACAGAGAGG-AGCA-TTTG-CAG
          1 AGGGAGAGAGAGGCAGCACTTTGCCAG

                              *           
        698 AGGGAGAGAGAGGCAGCAGTTGCTGCTCAG
          1 AGGGAGAGAGAGGCAGCACTT--TGC-CAG

                                          
        728 AGGGAGAGAGAGGCAGCAACTATTGCTCAG
          1 AGGGAGAGAGAGGCAGC-ACT-TTGC-CAG

                        
        758 AGGGAGAGAGAG
          1 AGGGAGAGAGAG

        770 CTTGCTGCTG


Statistics
Matches: 62,  Mismatches: 2, Indels: 10
        0.84            0.03        0.14

Matches are distributed among these distances:
  24   12  0.19
  25    4  0.06
  26    2  0.03
  28    2  0.03
  30   39  0.63
  31    2  0.03
  32    1  0.02

ACGTcount: A:0.32, C:0.14, G:0.43, T:0.11


Consensus pattern (27 bp):   
AGGGAGAGAGAGGCAGCACTTTGCCAG

Found at i:764 original size:28 final size:30

Alignment explanation


    Indices: 695--769  Score: 114
    Period size: 30  Copynumber: 2.5  Consensus size: 30

        685 GGAGCATTTG

                                 ** *     
        695 CAGAGGGAGAGAGAGGCAGCAGTTGCTGCT
          1 CAGAGGGAGAGAGAGGCAGCAACTACTGCT

                                     *    
        725 CAGAGGGAGAGAGAGGCAGCAACTATTGCT
          1 CAGAGGGAGAGAGAGGCAGCAACTACTGCT

                           
        755 CAGAGGGAGAGAGAG
          1 CAGAGGGAGAGAGAG

        770 CTTGCTGCTG


Statistics
Matches: 41,  Mismatches: 4, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  30   41  1.00

ACGTcount: A:0.32, C:0.15, G:0.43, T:0.11


Consensus pattern (30 bp):   
CAGAGGGAGAGAGAGGCAGCAACTACTGCT
Done.