Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007905.1 Corchorus capsularis cultivar CVL-1 contig07926, 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: 18646
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37


Found at i:4396 original size:27 final size:27

Alignment explanation


    Indices: 4366--4439  Score: 121
    Period size: 27  Copynumber: 2.7  Consensus size: 27

       4356 AGGGTCATCT

                                       
       4366 AGGGGCATTTTGGTCATTTTTACATTC
          1 AGGGGCATTTTGGTCATTTTTACATTC

                      *          *     
       4393 AGGGGCATTTAGGTCATTTTTGCATTC
          1 AGGGGCATTTTGGTCATTTTTACATTC

                 *              
       4420 AGGGGAATTTTGGTCATTTT
          1 AGGGGCATTTTGGTCATTTT

       4440 AAGTCCACTT


Statistics
Matches: 43,  Mismatches: 4, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  27   43  1.00

ACGTcount: A:0.19, C:0.12, G:0.26, T:0.43


Consensus pattern (27 bp):   
AGGGGCATTTTGGTCATTTTTACATTC

Found at i:11497 original size:110 final size:110

Alignment explanation


    Indices: 11367--11684  Score: 512
    Period size: 110  Copynumber: 2.9  Consensus size: 110

      11357 TGTTGATTCA

                          *                  *                      *        
      11367 AAAATGGGTCATTTAATTTAGGAATGTTGGTGTCAGGGCCTTAAGTTTACTTATAACTTATGCTT
          1 AAAATGGGTCATTTGATTTAGGAATGTTGGTGTTAGGGCCTTAAGTTTACTTATAAATTATGCTT

                          *                        *     
      11432 ATTTATATTTAAGGATGAGTTTGGGTTATAAATTATTATGCTTAC
         66 ATTTATATTTAAGGGTGAGTTTGGGTTATAAATTATTATACTTAC

                                                                             
      11477 AAAATGGGTCATTTGATTTAGGAATGTTGGTGTTAGGGCCTTAAGTTTACTTATAAATTATGCTT
          1 AAAATGGGTCATTTGATTTAGGAATGTTGGTGTTAGGGCCTTAAGTTTACTTATAAATTATGCTT

                              *             *            
      11542 ATTTATATTTAAGGGTGAATTTGGGTTATAAACTATTATACTTAC
         66 ATTTATATTTAAGGGTGAGTTTGGGTTATAAATTATTATACTTAC

                 *                                *     *    *            *  
      11587 AAAATAGGTCATTTGA-TTAGGAATGTTGGTGTTAGGGTCTTAATTTTAATTATAAATTATGTTT
          1 AAAATGGGTCATTTGATTTAGGAATGTTGGTGTTAGGGCCTTAAGTTTACTTATAAATTATGCTT

             *                                
      11651 AGTTATATTTAAGGGTGAGTTTGGGTTATAAATT
         66 ATTTATATTTAAGGGTGAGTTTGGGTTATAAATT

      11685 TTGGTCCATT


Statistics
Matches: 193,  Mismatches: 15, Indels: 1
        0.92            0.07        0.00

Matches are distributed among these distances:
 109   75  0.39
 110  118  0.61

ACGTcount: A:0.30, C:0.06, G:0.21, T:0.43


Consensus pattern (110 bp):   
AAAATGGGTCATTTGATTTAGGAATGTTGGTGTTAGGGCCTTAAGTTTACTTATAAATTATGCTT
ATTTATATTTAAGGGTGAGTTTGGGTTATAAATTATTATACTTAC

Found at i:12015 original size:21 final size:20

Alignment explanation


    Indices: 11966--12015  Score: 57
    Period size: 21  Copynumber: 2.4  Consensus size: 20

      11956 TTTCATCTTT

                                 
      11966 TCTCTCTTTTTTCCCCGTTTC
          1 TCTCTCTTTTTTCCCCG-TTC

               *                 
      11987 TCTTTCTTTCTTTCCCC-TTC
          1 TCTCTCTTT-TTTCCCCGTTC

                     
      12007 ATCTCTCTT
          1 -TCTCTCTT

      12016 CTCCATATAA


Statistics
Matches: 25,  Mismatches: 2, Indels: 4
        0.81            0.06        0.13

Matches are distributed among these distances:
  20    3  0.12
  21   15  0.60
  22    7  0.28

ACGTcount: A:0.02, C:0.38, G:0.02, T:0.58


Consensus pattern (20 bp):   
TCTCTCTTTTTTCCCCGTTC

Found at i:15814 original size:8 final size:8

Alignment explanation


    Indices: 15801--15830  Score: 53
    Period size: 8  Copynumber: 3.9  Consensus size: 8

      15791 AAATATTGTG

                    
      15801 TATCGTGA
          1 TATCGTGA

                    
      15809 TATCGTGA
          1 TATCGTGA

                    
      15817 TATCGTG-
          1 TATCGTGA

                   
      15824 TATCGTG
          1 TATCGTG

      15831 GCAGCCTGAT


Statistics
Matches: 22,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
   7    7  0.32
   8   15  0.68

ACGTcount: A:0.20, C:0.13, G:0.27, T:0.40


Consensus pattern (8 bp):   
TATCGTGA

Found at i:15822 original size:16 final size:15

Alignment explanation


    Indices: 15801--15830  Score: 51
    Period size: 15  Copynumber: 1.9  Consensus size: 15

      15791 AAATATTGTG

                            
      15801 TATCGTGATATCGTGA
          1 TATCGTG-TATCGTGA

                          
      15817 TATCGTGTATCGTG
          1 TATCGTGTATCGTG

      15831 GCAGCCTGAT


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  15    7  0.50
  16    7  0.50

ACGTcount: A:0.20, C:0.13, G:0.27, T:0.40


Consensus pattern (15 bp):   
TATCGTGTATCGTGA

Found at i:18550 original size:30 final size:28

Alignment explanation


    Indices: 18479--18556  Score: 86
    Period size: 29  Copynumber: 2.7  Consensus size: 28

      18469 GAACTTACAC

                *               *       
      18479 AAAACGGCCAAATAAGCCCCTGAACTCT
          1 AAAAAGGCCAAATAAGCCCCCGAACTCT

                 *                          
      18507 AATTACA-GCCAAATAAGCCCCCGAACTCTTT
          1 AA--AAAGGCCAAATAAGCCCCCGAACTC--T

                               
      18538 AAAAAGGCCAAATAAGCCC
          1 AAAAAGGCCAAATAAGCCC

      18557 TTTTCTGATG


Statistics
Matches: 41,  Mismatches: 4, Indels: 8
        0.77            0.08        0.15

Matches are distributed among these distances:
  28    2  0.05
  29   22  0.54
  30   14  0.34
  31    3  0.07

ACGTcount: A:0.41, C:0.31, G:0.13, T:0.15


Consensus pattern (28 bp):   
AAAAAGGCCAAATAAGCCCCCGAACTCT
Done.