Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007091.1 Corchorus capsularis cultivar CVL-1 contig07112, 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: 18384
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29


Found at i:402 original size:32 final size:32

Alignment explanation


    Indices: 358--464  Score: 144
    Period size: 32  Copynumber: 3.3  Consensus size: 32

        348 TTCCATGTAG

                                            
        358 AACGCCCCTATTTAGAGGCGTTTCTCATATAA
          1 AACGCCCCTATTTAGAGGCGTTTCTCATATAA

              *    *     *       *        * 
        390 AAGGCCCTTATTTTGAGGCGTATCTCATATGA
          1 AACGCCCCTATTTAGAGGCGTTTCTCATATAA

                           *                 
        422 AACGCCCCTATTTAGCGGCGTGTT-TCATATAA
          1 AACGCCCCTATTTAGAGGCGT-TTCTCATATAA

                       
        454 AACGCCCCTAT
          1 AACGCCCCTAT

        465 CTAAGCGGAG


Statistics
Matches: 63,  Mismatches: 11, Indels: 2
        0.83            0.14        0.03

Matches are distributed among these distances:
  32   62  0.98
  33    1  0.02

ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31


Consensus pattern (32 bp):   
AACGCCCCTATTTAGAGGCGTTTCTCATATAA

Found at i:1534 original size:9 final size:9

Alignment explanation


    Indices: 1520--1544  Score: 50
    Period size: 9  Copynumber: 2.8  Consensus size: 9

       1510 TATGCATGAA

                     
       1520 TTCAAAATT
          1 TTCAAAATT

                     
       1529 TTCAAAATT
          1 TTCAAAATT

                   
       1538 TTCAAAA
          1 TTCAAAA

       1545 AAATTTCATG


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   9   16  1.00

ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40


Consensus pattern (9 bp):   
TTCAAAATT

Found at i:1922 original size:16 final size:15

Alignment explanation


    Indices: 1901--1948  Score: 62
    Period size: 16  Copynumber: 3.1  Consensus size: 15

       1891 AGAAATAGGC

                           
       1901 AATCAATCAAAGAAA
          1 AATCAATCAAAGAAA

                         *  
       1916 TAATCAATCAAAGCAA
          1 -AATCAATCAAAGAAA

                            
       1932 AA-CAATGCAAAGAAA
          1 AATCAAT-CAAAGAAA

              
       1947 AA
          1 AA

       1949 GTAAATGGAG


Statistics
Matches: 29,  Mismatches: 2, Indels: 3
        0.85            0.06        0.09

Matches are distributed among these distances:
  14    4  0.14
  15   11  0.38
  16   14  0.48

ACGTcount: A:0.65, C:0.15, G:0.08, T:0.12


Consensus pattern (15 bp):   
AATCAATCAAAGAAA

Found at i:1923 original size:20 final size:19

Alignment explanation


    Indices: 1886--1926  Score: 55
    Period size: 20  Copynumber: 2.1  Consensus size: 19

       1876 AACTAATTCA

                        *      
       1886 AATCAAGAAATAGGCAATC
          1 AATCAAGAAATAAGCAATC

                          *     
       1905 AATCAAAGAAATAATCAATC
          1 AATC-AAGAAATAAGCAATC

              
       1925 AA
          1 AA

       1927 AGCAAAACAA


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

Matches are distributed among these distances:
  19    4  0.21
  20   15  0.79

ACGTcount: A:0.59, C:0.15, G:0.10, T:0.17


Consensus pattern (19 bp):   
AATCAAGAAATAAGCAATC

Found at i:3501 original size:21 final size:21

Alignment explanation


    Indices: 3489--3528  Score: 71
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       3479 GAAACTTTGA

                                 
       3489 AATATAAATAAGAAACCTCTG
          1 AATATAAATAAGAAACCTCTG

                         *     
       3510 AATATAAATAAGAGACCTC
          1 AATATAAATAAGAAACCTC

       3529 CAACATAGGA


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.53, C:0.15, G:0.10, T:0.23


Consensus pattern (21 bp):   
AATATAAATAAGAAACCTCTG
Done.