Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014474.1 Corchorus capsularis cultivar CVL-1 contig14495, 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: 33811
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33


Found at i:13098 original size:4 final size:4

Alignment explanation


    Indices: 13089--13135  Score: 94
    Period size: 4  Copynumber: 11.8  Consensus size: 4

      13079 ATTGAATATG

                                                                      
      13089 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
          1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA

      13136 GGATAATAAG


Statistics
Matches: 43,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   4   43  1.00

ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26


Consensus pattern (4 bp):   
ATAC

Found at i:14523 original size:30 final size:29

Alignment explanation


    Indices: 14461--14530  Score: 86
    Period size: 29  Copynumber: 2.4  Consensus size: 29

      14451 ATCGAACCGT

                                  ***    
      14461 CAAATAAGCCCCTGAACTATTATTTCGGC
          1 CAAATAAGCCCCTGAACTATTAAAACGGC

                              *       *   
      14490 CAAATAAGCCCCTGAACTCTTAAAAAGGGC
          1 CAAATAAGCCCCTGAACTATT-AAAACGGC

                       
      14520 CAAATAAGCCC
          1 CAAATAAGCCC

      14531 TGTTGCCAAG


Statistics
Matches: 35,  Mismatches: 5, Indels: 1
        0.85            0.12        0.02

Matches are distributed among these distances:
  29   20  0.57
  30   15  0.43

ACGTcount: A:0.37, C:0.29, G:0.14, T:0.20


Consensus pattern (29 bp):   
CAAATAAGCCCCTGAACTATTAAAACGGC

Found at i:17089 original size:6 final size:7

Alignment explanation


    Indices: 17072--17096  Score: 50
    Period size: 7  Copynumber: 3.6  Consensus size: 7

      17062 ATGGGTTTAT

                   
      17072 TTTTTTG
          1 TTTTTTG

                   
      17079 TTTTTTG
          1 TTTTTTG

                   
      17086 TTTTTTG
          1 TTTTTTG

                
      17093 TTTT
          1 TTTT

      17097 CATTTTATAT


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   18  1.00

ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88


Consensus pattern (7 bp):   
TTTTTTG

Found at i:18530 original size:15 final size:15

Alignment explanation


    Indices: 18510--18538  Score: 58
    Period size: 15  Copynumber: 1.9  Consensus size: 15

      18500 AAAGTCCCAC

                           
      18510 ATATATATAAAAAAT
          1 ATATATATAAAAAAT

                          
      18525 ATATATATAAAAAA
          1 ATATATATAAAAAA

      18539 GAAGGAAAAC


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:0.69, C:0.00, G:0.00, T:0.31


Consensus pattern (15 bp):   
ATATATATAAAAAAT

Found at i:32946 original size:1 final size:1

Alignment explanation


    Indices: 32940--32964  Score: 50
    Period size: 1  Copynumber: 25.0  Consensus size: 1

      32930 AATGAAAAGT

                                     
      32940 AAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAA

      32965 CAGCACAAAC


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   24  1.00

ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00


Consensus pattern (1 bp):   
A

Found at i:33636 original size:21 final size:21

Alignment explanation


    Indices: 33610--33651  Score: 57
    Period size: 21  Copynumber: 2.0  Consensus size: 21

      33600 ATAAAGGGGA

                    *            
      33610 TTACTAAATACCGCCCCCTTT
          1 TTACTAAACACCGCCCCCTTT

                  **             
      33631 TTACTAGGCACCGCCCCCTTT
          1 TTACTAAACACCGCCCCCTTT

      33652 GGACTATTTT


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.19, C:0.40, G:0.10, T:0.31


Consensus pattern (21 bp):   
TTACTAAACACCGCCCCCTTT
Done.