Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009727.1 Corchorus olitorius cultivar O-4 contig09759, 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: 5779
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34


Found at i:94 original size:60 final size:60

Alignment explanation


    Indices: 1--143  Score: 182
    Period size: 60  Copynumber: 2.4  Consensus size: 60

                                                       **                
          1 CGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGG-TTCTTATTTGAGCATTTT
          1 CGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGAT-AGGAGCCTTATTTGAGCATTTT

                  *       *                       *                     
         61 CGATAATGTTAGGCTCTTATTTGGCCAAATTAAAAGATTGGAGCCTTATTTGAGCATTTT
          1 CGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATAGGAGCCTTATTTGAGCATTTT

                *   *     *         
        121 -GACAAACATTAGGTCCTTATTTG
          1 CGA-TAACGTTAGGCCCTTATTTG

        144 AGCAATTAAC


Statistics
Matches: 71,  Mismatches: 10, Indels: 4
        0.84            0.12        0.05

Matches are distributed among these distances:
  59    4  0.06
  60   67  0.94

ACGTcount: A:0.29, C:0.15, G:0.19, T:0.37


Consensus pattern (60 bp):   
CGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATAGGAGCCTTATTTGAGCATTTT

Found at i:298 original size:15 final size:16

Alignment explanation


    Indices: 279--315  Score: 58
    Period size: 15  Copynumber: 2.4  Consensus size: 16

        269 TATAAATAAT

                            
        279 AATATTATAAT-TAAA
          1 AATATTATAATCTAAA

            *               
        294 TATATTATAATCTAAA
          1 AATATTATAATCTAAA

                  
        310 AATATT
          1 AATATT

        316 TATTAGAAGT


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

Matches are distributed among these distances:
  15   10  0.53
  16    9  0.47

ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43


Consensus pattern (16 bp):   
AATATTATAATCTAAA

Found at i:578 original size:8 final size:8

Alignment explanation


    Indices: 565--626  Score: 56
    Period size: 8  Copynumber: 7.2  Consensus size: 8

        555 TTTTATATAG

                    
        565 TAGTAAGA
          1 TAGTAAGA

                    
        573 TAGTAAGA
          1 TAGTAAGA

                    
        581 TAGT-AG-
          1 TAGTAAGA

                      
        587 TAAGATAAGA
          1 T-AG-TAAGA

                      
        597 TAAGATAAGA
          1 T-AG-TAAGA

                      
        607 TAGTAAGATA
          1 TAGTAAG--A

                    
        617 TAGTAAGA
          1 TAGTAAGA

              
        625 TA
          1 TA

        627 TATGAACTTT


Statistics
Matches: 48,  Mismatches: 0, Indels: 12
        0.80            0.00        0.20

Matches are distributed among these distances:
   6    1  0.02
   7    4  0.08
   8   20  0.42
   9    4  0.08
  10   19  0.40

ACGTcount: A:0.52, C:0.00, G:0.23, T:0.26


Consensus pattern (8 bp):   
TAGTAAGA

Found at i:597 original size:5 final size:5

Alignment explanation


    Indices: 587--626  Score: 50
    Period size: 5  Copynumber: 8.4  Consensus size: 5

        577 AAGATAGTAG

                                                               
        587 TAAGA TAAGA TAAGA TAAGA T-AG- TAAGA TATAG- TAAGA TA
          1 TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TA-AGA TAAGA TA

        627 TATGAACTTT


Statistics
Matches: 31,  Mismatches: 0, Indels: 8
        0.79            0.00        0.21

Matches are distributed among these distances:
   3    1  0.03
   4    6  0.19
   5   22  0.71
   6    2  0.06

ACGTcount: A:0.55, C:0.00, G:0.20, T:0.25


Consensus pattern (5 bp):   
TAAGA

Found at i:627 original size:10 final size:10

Alignment explanation


    Indices: 572--628  Score: 62
    Period size: 10  Copynumber: 5.3  Consensus size: 10

        562 TAGTAGTAAG

                      
        572 ATAGTAAGAT
          1 ATAGTAAGAT

                       
        582 AGTAGTAAGAT
          1 A-TAGTAAGAT

                       
        593 A-AGATAAGAT
          1 ATAG-TAAGAT

                         
        603 AAGATAGTAAGAT
          1 ---ATAGTAAGAT

                      
        616 ATAGTAAGAT
          1 ATAGTAAGAT

               
        626 ATA
          1 ATA

        629 TGAACTTTCT


Statistics
Matches: 41,  Mismatches: 0, Indels: 12
        0.77            0.00        0.23

Matches are distributed among these distances:
   9    2  0.05
  10   20  0.49
  11   10  0.24
  13    7  0.17
  14    2  0.05

ACGTcount: A:0.53, C:0.00, G:0.21, T:0.26


Consensus pattern (10 bp):   
ATAGTAAGAT

Found at i:4015 original size:62 final size:62

Alignment explanation


    Indices: 3938--4061  Score: 230
    Period size: 62  Copynumber: 2.0  Consensus size: 62

       3928 CCACCCTGAA

                                  *                                       
       3938 AAATATTTATGGATCCGCCATCGCCTTTTCATCTCCTTTTAAATACTATAAACCTACAATAG
          1 AAATATTTATGGATCCGCCATCACCTTTTCATCTCCTTTTAAATACTATAAACCTACAATAG

                                 *                                        
       4000 AAATATTTATGGATCCGCCATTACCTTTTCATCTCCTTTTAAATACTATAAACCTACAATAG
          1 AAATATTTATGGATCCGCCATCACCTTTTCATCTCCTTTTAAATACTATAAACCTACAATAG

       4062 GATTAACAAT


Statistics
Matches: 60,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  62   60  1.00

ACGTcount: A:0.33, C:0.23, G:0.07, T:0.36


Consensus pattern (62 bp):   
AAATATTTATGGATCCGCCATCACCTTTTCATCTCCTTTTAAATACTATAAACCTACAATAG
Done.