Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01016124.1 Corchorus capsularis cultivar CVL-1 contig16145, 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: 20125
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35


Found at i:63 original size:24 final size:24

Alignment explanation


    Indices: 28--91  Score: 119
    Period size: 24  Copynumber: 2.7  Consensus size: 24

         18 TTAAGTTAGC

                   *                
         28 GGCGTCTAGACGCCGCCAAATAGT
          1 GGCGTCTTGACGCCGCCAAATAGT

                                    
         52 GGCGTCTTGACGCCGCCAAATAGT
          1 GGCGTCTTGACGCCGCCAAATAGT

                            
         76 GGCGTCTTGACGCCGC
          1 GGCGTCTTGACGCCGC

         92 TATGTTTTAT


Statistics
Matches: 39,  Mismatches: 1, Indels: 0
        0.98            0.03        0.00

Matches are distributed among these distances:
  24   39  1.00

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


Consensus pattern (24 bp):   
GGCGTCTTGACGCCGCCAAATAGT

Found at i:3649 original size:18 final size:17

Alignment explanation


    Indices: 3622--3655  Score: 50
    Period size: 18  Copynumber: 1.9  Consensus size: 17

       3612 ACATCTATGA

                              
       3622 TATCTCCATTTTGCAAAT
          1 TATCTCCATTTT-CAAAT

                 *          
       3640 TATCTGCATTTTCAAA
          1 TATCTCCATTTTCAAA

       3656 GCCATTCGGA


Statistics
Matches: 15,  Mismatches: 1, Indels: 1
        0.88            0.06        0.06

Matches are distributed among these distances:
  17    4  0.27
  18   11  0.73

ACGTcount: A:0.29, C:0.21, G:0.06, T:0.44


Consensus pattern (17 bp):   
TATCTCCATTTTCAAAT

Found at i:11835 original size:19 final size:19

Alignment explanation


    Indices: 11811--11849  Score: 69
    Period size: 19  Copynumber: 2.1  Consensus size: 19

      11801 TCCATTTTAT

                               
      11811 TCCCGAACCCAAACACGCC
          1 TCCCGAACCCAAACACGCC

                         *     
      11830 TCCCGAACCCAAATACGCC
          1 TCCCGAACCCAAACACGCC

             
      11849 T
          1 T

      11850 TATAGATGTA


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  19   19  1.00

ACGTcount: A:0.31, C:0.49, G:0.10, T:0.10


Consensus pattern (19 bp):   
TCCCGAACCCAAACACGCC

Found at i:19939 original size:20 final size:20

Alignment explanation


    Indices: 19914--19954  Score: 64
    Period size: 20  Copynumber: 2.0  Consensus size: 20

      19904 GATTTGAGAA

                                
      19914 TTACTAAATACCGCCCCCTT
          1 TTACTAAATACCGCCCCCTT

                  **            
      19934 TTACTAGGTACCGCCCCCTT
          1 TTACTAAATACCGCCCCCTT

             
      19954 T
          1 T

      19955 AGACTATTTT


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  20   19  1.00

ACGTcount: A:0.20, C:0.39, G:0.10, T:0.32


Consensus pattern (20 bp):   
TTACTAAATACCGCCCCCTT

Found at i:19960 original size:21 final size:20

Alignment explanation


    Indices: 19922--19960  Score: 60
    Period size: 20  Copynumber: 1.9  Consensus size: 20

      19912 AATTACTAAA

                         *      
      19922 TACCGCCCCCTTTTACTAGG
          1 TACCGCCCCCTTTGACTAGG

                               
      19942 TACCGCCCCCTTTAGACTA
          1 TACCGCCCCCTTT-GACTA

      19961 TTTTACCCTT


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  20   13  0.76
  21    4  0.24

ACGTcount: A:0.18, C:0.41, G:0.13, T:0.28


Consensus pattern (20 bp):   
TACCGCCCCCTTTGACTAGG
Done.