Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004842.1 Corchorus capsularis cultivar CVL-1 contig04860, 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: 8791
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33


Found at i:714 original size:186 final size:186

Alignment explanation


    Indices: 400--763  Score: 728
    Period size: 186  Copynumber: 2.0  Consensus size: 186

        390 AGCTGGAGAC

                                                                             
        400 ATGTCTCCATGCCACTAAGGAGTGTGTTTTTGCAGCTGATGTATGGTCCTATATATGGAATTTCT
          1 ATGTCTCCATGCCACTAAGGAGTGTGTTTTTGCAGCTGATGTATGGTCCTATATATGGAATTTCT

                                                                             
        465 TTATTCATGATGAATCCTTAAATCATGATAAGGATGAGGAATGGATAAAGGAAAACCTTGTCTCT
         66 TTATTCATGATGAATCCTTAAATCATGATAAGGATGAGGAATGGATAAAGGAAAACCTTGTCTCT

                                                                    
        530 AATTCTGACTGGTACCAGATTGTTTTGGTGACGGCATGGGCGGTTTGGTCCTATAT
        131 AATTCTGACTGGTACCAGATTGTTTTGGTGACGGCATGGGCGGTTTGGTCCTATAT

                                                                             
        586 ATGTCTCCATGCCACTAAGGAGTGTGTTTTTGCAGCTGATGTATGGTCCTATATATGGAATTTCT
          1 ATGTCTCCATGCCACTAAGGAGTGTGTTTTTGCAGCTGATGTATGGTCCTATATATGGAATTTCT

                                                                             
        651 TTATTCATGATGAATCCTTAAATCATGATAAGGATGAGGAATGGATAAAGGAAAACCTTGTCTCT
         66 TTATTCATGATGAATCCTTAAATCATGATAAGGATGAGGAATGGATAAAGGAAAACCTTGTCTCT

                                                            
        716 AATTCTGACTGGTACCAGATTGTTTTGGTGACGGCATGGGCGGTTTGG
        131 AATTCTGACTGGTACCAGATTGTTTTGGTGACGGCATGGGCGGTTTGG

        764 GGTGCTCGAA


Statistics
Matches: 178,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
 186  178  1.00

ACGTcount: A:0.26, C:0.15, G:0.25, T:0.35


Consensus pattern (186 bp):   
ATGTCTCCATGCCACTAAGGAGTGTGTTTTTGCAGCTGATGTATGGTCCTATATATGGAATTTCT
TTATTCATGATGAATCCTTAAATCATGATAAGGATGAGGAATGGATAAAGGAAAACCTTGTCTCT
AATTCTGACTGGTACCAGATTGTTTTGGTGACGGCATGGGCGGTTTGGTCCTATAT

Found at i:1529 original size:3 final size:3

Alignment explanation


    Indices: 1521--1577  Score: 50
    Period size: 3  Copynumber: 20.0  Consensus size: 3

       1511 TAATTTTCAA

                                        *   *   *                          
       1521 ATT ATT ATT ATT ATT -TT -TT GTT GTT GTT ATT ATT ATT ATT ATT -TT
          1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT

                            
       1566 ATT -TT ATAT ATT
          1 ATT ATT AT-T ATT

       1578 TATATTTATA


Statistics
Matches: 49,  Mismatches: 1, Indels: 8
        0.84            0.02        0.14

Matches are distributed among these distances:
   2    8  0.16
   3   38  0.78
   4    3  0.06

ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70


Consensus pattern (3 bp):   
ATT

Found at i:1577 original size:14 final size:14

Alignment explanation


    Indices: 1550--1590  Score: 50
    Period size: 14  Copynumber: 2.9  Consensus size: 14

       1540 GTTGTTGTTA

                           
       1550 TTATTATTAT-TATT
          1 TTATT-TTATATATT

                          
       1564 TTATTTTATATA-T
          1 TTATTTTATATATT

                          
       1577 TTATATTTATATAT
          1 TTAT-TTTATATAT

       1591 AGATGTATAA


Statistics
Matches: 24,  Mismatches: 0, Indels: 5
        0.83            0.00        0.17

Matches are distributed among these distances:
  13    9  0.38
  14   15  0.62

ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68


Consensus pattern (14 bp):   
TTATTTTATATATT

Found at i:8531 original size:2 final size:2

Alignment explanation


    Indices: 8522--8572  Score: 86
    Period size: 2  Copynumber: 26.0  Consensus size: 2

       8512 TATTGTTTTT

                                 *                                        
       8522 TA TA -A TA TA TA TA CA 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 TA TA TA TA TA

                          
       8563 TA TA TA TA TA
          1 TA TA TA TA TA

       8573 CCTTCTATAC


Statistics
Matches: 46,  Mismatches: 2, Indels: 2
        0.92            0.04        0.04

Matches are distributed among these distances:
   1    1  0.02
   2   45  0.98

ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47


Consensus pattern (2 bp):   
TA

Found at i:8726 original size:13 final size:13

Alignment explanation


    Indices: 8708--8732  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       8698 TTGAAATTCC

                         
       8708 AAATAATATTTAT
          1 AAATAATATTTAT

                        
       8721 AAATAATATTTA
          1 AAATAATATTTA

       8733 GAATATTGAA


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44


Consensus pattern (13 bp):   
AAATAATATTTAT
Done.