Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005974.1 Corchorus capsularis cultivar CVL-1 contig05992, 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: 4298
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29


Found at i:1493 original size:33 final size:33

Alignment explanation


    Indices: 1424--1529  Score: 99
    Period size: 33  Copynumber: 3.2  Consensus size: 33

       1414 AAGGATCATA

                   *      *                ** 
       1424 TGGCCGGTTGTGGCAGGGCATGGCCGA-GTCATG
          1 TGGCCGGGTGTGGCCGGGCATGGCC-ATGTCGCG

                               *             
       1457 TGGCCGGGTGTGGCCGGGCTTGGCCATGTCGCG
          1 TGGCCGGGTGTGGCCGGGCATGGCCATGTCGCG

                          *       **         *
       1490 TGGCC-GGTGATGGTCGGGCATCTCCATGTCGCA
          1 TGGCCGGGTG-TGGCCGGGCATGGCCATGTCGCG

                   
       1523 TGGCCGG
          1 TGGCCGG

       1530 TGTTGCGCGG


Statistics
Matches: 60,  Mismatches: 10, Indels: 5
        0.80            0.13        0.07

Matches are distributed among these distances:
  32    5  0.08
  33   54  0.90
  34    1  0.02

ACGTcount: A:0.08, C:0.25, G:0.44, T:0.22


Consensus pattern (33 bp):   
TGGCCGGGTGTGGCCGGGCATGGCCATGTCGCG

Found at i:1530 original size:33 final size:33

Alignment explanation


    Indices: 1480--1562  Score: 105
    Period size: 33  Copynumber: 2.5  Consensus size: 33

       1470 CCGGGCTTGG

                                         *    
       1480 CCATGTCGCGTGGCCGGTGATG-GTCGGGCATCT
          1 CCATGTCGCGTGGCCGGTGATGCG-CGGGAATCT

                     *         *             
       1513 CCATGTCGCATGGCCGGTGTTGCGCGGGAATCT
          1 CCATGTCGCGTGGCCGGTGATGCGCGGGAATCT

               **            
       1546 CCAAATCGCGTGGCCGG
          1 CCATGTCGCGTGGCCGG

       1563 ATCTCTAAGT


Statistics
Matches: 43,  Mismatches: 6, Indels: 2
        0.84            0.12        0.04

Matches are distributed among these distances:
  33   42  0.98
  34    1  0.02

ACGTcount: A:0.12, C:0.29, G:0.37, T:0.22


Consensus pattern (33 bp):   
CCATGTCGCGTGGCCGGTGATGCGCGGGAATCT

Found at i:1575 original size:21 final size:21

Alignment explanation


    Indices: 1542--1583  Score: 57
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       1532 TTGCGCGGGA

                         *       
       1542 ATCTCCAAATCGCGTGGCCGG
          1 ATCTCCAAATCGCATGGCCGG

                 *  *            
       1563 ATCTCTAAGTCGCATGGCCGG
          1 ATCTCCAAATCGCATGGCCGG

       1584 TCACTTGTGC


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.19, C:0.31, G:0.29, T:0.21


Consensus pattern (21 bp):   
ATCTCCAAATCGCATGGCCGG

Found at i:1856 original size:6 final size:6

Alignment explanation


    Indices: 1845--1874  Score: 60
    Period size: 6  Copynumber: 5.0  Consensus size: 6

       1835 GCAAAGCAAT

                                              
       1845 TCTAAA TCTAAA TCTAAA TCTAAA TCTAAA
          1 TCTAAA TCTAAA TCTAAA TCTAAA TCTAAA

       1875 GCAAATTAAT


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   24  1.00

ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33


Consensus pattern (6 bp):   
TCTAAA

Found at i:1889 original size:13 final size:13

Alignment explanation


    Indices: 1871--1901  Score: 62
    Period size: 13  Copynumber: 2.4  Consensus size: 13

       1861 AATCTAAATC

                         
       1871 TAAAGCAAATTAA
          1 TAAAGCAAATTAA

                         
       1884 TAAAGCAAATTAA
          1 TAAAGCAAATTAA

                 
       1897 TAAAG
          1 TAAAG

       1902 AAAACAATAA


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   18  1.00

ACGTcount: A:0.61, C:0.06, G:0.10, T:0.23


Consensus pattern (13 bp):   
TAAAGCAAATTAA

Found at i:2832 original size:10 final size:10

Alignment explanation


    Indices: 2817--2842  Score: 52
    Period size: 10  Copynumber: 2.6  Consensus size: 10

       2807 GAGGACTCTA

                      
       2817 GAATTTTCTG
          1 GAATTTTCTG

                      
       2827 GAATTTTCTG
          1 GAATTTTCTG

                  
       2837 GAATTT
          1 GAATTT

       2843 GGCAGCAACT


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

Matches are distributed among these distances:
  10   16  1.00

ACGTcount: A:0.23, C:0.08, G:0.19, T:0.50


Consensus pattern (10 bp):   
GAATTTTCTG
Done.