Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010247.1 Corchorus capsularis cultivar CVL-1 contig10268, 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: 8156
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38


Found at i:186 original size:2 final size:2

Alignment explanation


    Indices: 179--210  Score: 64
    Period size: 2  Copynumber: 16.0  Consensus size: 2

        169 TGTTATAGTG

                                                           
        179 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

        211 ATTACATAAC


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   30  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:779 original size:97 final size:97

Alignment explanation


    Indices: 670--866  Score: 376
    Period size: 97  Copynumber: 2.0  Consensus size: 97

        660 AATTTATTTC

                                               *    *                        
        670 ATTGTTAATATTTATTTTAATGATCAAATCAACCTGAATAGTCGATGTTTGGGATTAGAGATTTT
          1 ATTGTTAATATTTATTTTAATGATCAAATCAACCTAAATAATCGATGTTTGGGATTAGAGATTTT

                                            
        735 ATTTGTCTTGTTTCTTAATTTTTTTTCTGCTT
         66 ATTTGTCTTGTTTCTTAATTTTTTTTCTGCTT

                                                                             
        767 ATTGTTAATATTTATTTTAATGATCAAATCAACCTAAATAATCGATGTTTGGGATTAGAGATTTT
          1 ATTGTTAATATTTATTTTAATGATCAAATCAACCTAAATAATCGATGTTTGGGATTAGAGATTTT

                                            
        832 ATTTGTCTTGTTTCTTAATTTTTTTTCTGCTT
         66 ATTTGTCTTGTTTCTTAATTTTTTTTCTGCTT

               
        864 ATT
          1 ATT

        867 TATTTTATAT


Statistics
Matches: 98,  Mismatches: 2, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  97   98  1.00

ACGTcount: A:0.26, C:0.09, G:0.13, T:0.52


Consensus pattern (97 bp):   
ATTGTTAATATTTATTTTAATGATCAAATCAACCTAAATAATCGATGTTTGGGATTAGAGATTTT
ATTTGTCTTGTTTCTTAATTTTTTTTCTGCTT

Found at i:3036 original size:31 final size:31

Alignment explanation


    Indices: 2998--3060  Score: 92
    Period size: 31  Copynumber: 2.0  Consensus size: 31

       2988 AGTTTTGTAA

                                  *         
       2998 AATTTTTGAAACGCCTA-TTATGTCCTTATTT
          1 AATTTTTGAAACGCC-ACTTATATCCTTATTT

                         *                 
       3029 AATTTTTGAAACGTCACTTATATCCTTATTT
          1 AATTTTTGAAACGCCACTTATATCCTTATTT

             
       3060 A
          1 A

       3061 TCTAACATAT


Statistics
Matches: 29,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  30    1  0.03
  31   28  0.97

ACGTcount: A:0.29, C:0.16, G:0.08, T:0.48


Consensus pattern (31 bp):   
AATTTTTGAAACGCCACTTATATCCTTATTT

Found at i:3429 original size:7 final size:7

Alignment explanation


    Indices: 3405--3444  Score: 53
    Period size: 7  Copynumber: 5.4  Consensus size: 7

       3395 GATCATTCGA

                *  
       3405 GTCTCGG
          1 GTCTGGG

                     
       3412 GTCTGCTGG
          1 GTCTG--GG

                   
       3421 GTCTGGG
          1 GTCTGGG

                   
       3428 GTCTGGG
          1 GTCTGGG

                   
       3435 GTCTGGG
          1 GTCTGGG

               
       3442 GTC
          1 GTC

       3445 AGGCGGGTTC


Statistics
Matches: 30,  Mismatches: 1, Indels: 4
        0.86            0.03        0.11

Matches are distributed among these distances:
   7   23  0.77
   9    7  0.23

ACGTcount: A:0.00, C:0.20, G:0.50, T:0.30


Consensus pattern (7 bp):   
GTCTGGG

Found at i:5624 original size:24 final size:24

Alignment explanation


    Indices: 5579--5628  Score: 64
    Period size: 24  Copynumber: 2.1  Consensus size: 24

       5569 CTCTCTGACG

                    *    *          
       5579 TCTCTCCCTTTCACATCAGTTTCT
          1 TCTCTCCCCTTCAAATCAGTTTCT

                            **      
       5603 TCTCTCCCCTTCAAATTTGTTTCT
          1 TCTCTCCCCTTCAAATCAGTTTCT

              
       5627 TC
          1 TC

       5629 AGTTTTCAAA


Statistics
Matches: 22,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  24   22  1.00

ACGTcount: A:0.12, C:0.36, G:0.04, T:0.48


Consensus pattern (24 bp):   
TCTCTCCCCTTCAAATCAGTTTCT
Done.