Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006168.1 Corchorus capsularis cultivar CVL-1 contig06186, 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: 12757
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32


Found at i:2241 original size:21 final size:21

Alignment explanation


    Indices: 2216--2267  Score: 59
    Period size: 21  Copynumber: 2.5  Consensus size: 21

       2206 GCGCTGGTCG

                          * *   *
       2216 CCCATGTGCTATGCTTGGCGC
          1 CCCATGTGCTATGCCTCGCGA

                    * *          
       2237 CCCATGTGGTTTGCCTCGCGA
          1 CCCATGTGCTATGCCTCGCGA

                      
       2258 CCCATGTGCT
          1 CCCATGTGCT

       2268 CCAGTGCTAT


Statistics
Matches: 25,  Mismatches: 6, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  21   25  1.00

ACGTcount: A:0.10, C:0.35, G:0.27, T:0.29


Consensus pattern (21 bp):   
CCCATGTGCTATGCCTCGCGA

Found at i:2710 original size:11 final size:10

Alignment explanation


    Indices: 2658--2733  Score: 55
    Period size: 11  Copynumber: 7.3  Consensus size: 10

       2648 GCGCCACCAT

                      
       2658 CGGCCATCAC
          1 CGGCCATCAC

              *    *   
       2668 CATGCCACCAC
          1 C-GGCCATCAC

               *    * 
       2679 CGGTCATCTC
          1 CGGCCATCAC

            *   *     
       2689 AGGCTATCAC
          1 CGGCCATCAC

                       
       2699 CGTGCCATCAC
          1 CG-GCCATCAC

                       
       2710 CGGCCA-CATC
          1 CGGCCATCA-C

                       
       2720 CGAGCCATCAC
          1 CG-GCCATCAC

               
       2731 CGG
          1 CGG

       2734 TCATGCATGC


Statistics
Matches: 49,  Mismatches: 12, Indels: 10
        0.69            0.17        0.14

Matches are distributed among these distances:
   9    2  0.04
  10   21  0.43
  11   24  0.49
  12    2  0.04

ACGTcount: A:0.21, C:0.45, G:0.20, T:0.14


Consensus pattern (10 bp):   
CGGCCATCAC

Found at i:2966 original size:21 final size:23

Alignment explanation


    Indices: 2927--2977  Score: 63
    Period size: 21  Copynumber: 2.3  Consensus size: 23

       2917 AGATCTTTAT

                         *          
       2927 TATGACTTATATGTTTTGAA-TGC
          1 TATGA-TTATATGCTTTGAATTGC

                                   
       2950 TATGATTA-ATGCTTTGAATTGC
          1 TATGATTATATGCTTTGAATTGC

                   
       2972 T-TGATT
          1 TATGATT

       2978 GGATCGACAC


Statistics
Matches: 26,  Mismatches: 1, Indels: 4
        0.84            0.03        0.13

Matches are distributed among these distances:
  21   14  0.54
  22    7  0.27
  23    5  0.19

ACGTcount: A:0.25, C:0.08, G:0.18, T:0.49


Consensus pattern (23 bp):   
TATGATTATATGCTTTGAATTGC

Found at i:4429 original size:19 final size:18

Alignment explanation


    Indices: 4405--4444  Score: 53
    Period size: 18  Copynumber: 2.2  Consensus size: 18

       4395 TTGAAGATTT

                    *          
       4405 ATTGAAGATAATTTGAAGA
          1 ATTGAAGACAA-TTGAAGA

                     *        
       4424 ATTGAAGACCATTGAAGA
          1 ATTGAAGACAATTGAAGA

               
       4442 ATT
          1 ATT

       4445 ATTTCAAGAA


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  18   10  0.53
  19    9  0.47

ACGTcount: A:0.45, C:0.05, G:0.20, T:0.30


Consensus pattern (18 bp):   
ATTGAAGACAATTGAAGA

Found at i:9717 original size:34 final size:33

Alignment explanation


    Indices: 9674--9741  Score: 118
    Period size: 34  Copynumber: 2.0  Consensus size: 33

       9664 TACCCGAGTG

                                              
       9674 TCCCTTGCTCGACTTGTCCCAGTCTCCCCCAACT
          1 TCCCTTGCTCGACTTGTCCCAGTCT-CCCCAACT

                        *                    
       9708 TCCCTTGCTCGAGTTGTCCCAGTCTCCCCAACT
          1 TCCCTTGCTCGACTTGTCCCAGTCTCCCCAACT

             
       9741 T
          1 T

       9742 TACCCTTCGC


Statistics
Matches: 33,  Mismatches: 1, Indels: 1
        0.94            0.03        0.03

Matches are distributed among these distances:
  33    9  0.27
  34   24  0.73

ACGTcount: A:0.12, C:0.44, G:0.13, T:0.31


Consensus pattern (33 bp):   
TCCCTTGCTCGACTTGTCCCAGTCTCCCCAACT
Done.