Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015340.1 Corchorus capsularis cultivar CVL-1 contig15361, 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: 15198
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.34


Found at i:442 original size:22 final size:22

Alignment explanation


    Indices: 417--464  Score: 62
    Period size: 22  Copynumber: 2.2  Consensus size: 22

        407 GAAAAAAAAA

                *                  
        417 ATCAGATTTCT-TTTTTCAGTTG
          1 ATCACATTTCTCTTTTT-AGTTG

                 *                
        439 ATCACTTTTCTCTTTTTAGTTG
          1 ATCACATTTCTCTTTTTAGTTG

                
        461 ATCA
          1 ATCA

        465 TTATCCACCC


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
  22   18  0.78
  23    5  0.22

ACGTcount: A:0.19, C:0.17, G:0.10, T:0.54


Consensus pattern (22 bp):   
ATCACATTTCTCTTTTTAGTTG

Found at i:1584 original size:35 final size:35

Alignment explanation


    Indices: 1545--1613  Score: 95
    Period size: 35  Copynumber: 2.0  Consensus size: 35

       1535 ATCAAGTTAA

                    *                           
       1545 ATAAAATAGTAAAAAATATAATCAA-ATAACATAAC
          1 ATAAAATAATAAAAAATATAAT-AACATAACATAAC

                      *        *              
       1580 ATAAAATAATTAAAAATATGATAACATAACATAA
          1 ATAAAATAATAAAAAATATAATAACATAACATAA

       1614 AAAAAAAGCA


Statistics
Matches: 30,  Mismatches: 3, Indels: 2
        0.86            0.09        0.06

Matches are distributed among these distances:
  34    2  0.07
  35   28  0.93

ACGTcount: A:0.65, C:0.07, G:0.03, T:0.25


Consensus pattern (35 bp):   
ATAAAATAATAAAAAATATAATAACATAACATAAC

Found at i:1596 original size:25 final size:23

Alignment explanation


    Indices: 1568--1631  Score: 67
    Period size: 25  Copynumber: 2.7  Consensus size: 23

       1558 AAATATAATC

                                     
       1568 AAATAACATAACATAAAATAATTAA
          1 AAATAACATAACATAAAATAA--AA

                 **         *      
       1593 AAATATGATAACATAACATAAAA
          1 AAATAACATAACATAAAATAAAA

                             
       1616 AAA-AAGCATAACATAA
          1 AAATAA-CATAACATAA

       1632 TGTCTGAGGG


Statistics
Matches: 33,  Mismatches: 5, Indels: 4
        0.79            0.12        0.10

Matches are distributed among these distances:
  22    1  0.03
  23   14  0.42
  25   18  0.55

ACGTcount: A:0.67, C:0.09, G:0.03, T:0.20


Consensus pattern (23 bp):   
AAATAACATAACATAAAATAAAA

Found at i:1742 original size:2 final size:2

Alignment explanation


    Indices: 1735--1764  Score: 60
    Period size: 2  Copynumber: 15.0  Consensus size: 2

       1725 TATAATTATG

                                                        
       1735 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       1765 GTTAGTACTT


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   28  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:11918 original size:31 final size:32

Alignment explanation


    Indices: 11847--11918  Score: 94
    Period size: 31  Copynumber: 2.3  Consensus size: 32

      11837 TAAGAAAATG

                          *       *         
      11847 CCACTTTGCACCCTTATATTTTTTATTTTGAT
          1 CCACTTTGCACCCTAATATTTTATATTTTGAT

                                          * 
      11879 -CACTTTGCACCCTAATATTTTAT-TTTTGTT
          1 CCACTTTGCACCCTAATATTTTATATTTTGAT

                *     
      11909 CCACGTTGCA
          1 CCACTTTGCA

      11919 TCTCCGTTAT


Statistics
Matches: 35,  Mismatches: 4, Indels: 3
        0.83            0.10        0.07

Matches are distributed among these distances:
  30    6  0.17
  31   29  0.83

ACGTcount: A:0.19, C:0.24, G:0.08, T:0.49


Consensus pattern (32 bp):   
CCACTTTGCACCCTAATATTTTATATTTTGAT

Found at i:12163 original size:29 final size:29

Alignment explanation


    Indices: 12126--12185  Score: 86
    Period size: 29  Copynumber: 2.1  Consensus size: 29

      12116 AGCGTGAAAC

                                          
      12126 AAAAATAAAATATCAA-GGTGCAAAGTGAT
          1 AAAAATAAAA-ATCAAGGGTGCAAAGTGAT

                        *           *    
      12155 AAAAATAAAAATTAAGGGTGCAAATTGAT
          1 AAAAATAAAAATCAAGGGTGCAAAGTGAT

              
      12184 AA
          1 AA

      12186 TCCGTATAAA


Statistics
Matches: 28,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  28    4  0.14
  29   24  0.86

ACGTcount: A:0.57, C:0.05, G:0.17, T:0.22


Consensus pattern (29 bp):   
AAAAATAAAAATCAAGGGTGCAAAGTGAT
Done.