Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005396.1 Corchorus capsularis cultivar CVL-1 contig05414, 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: 12435
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33


Found at i:3912 original size:107 final size:105

Alignment explanation


    Indices: 3680--3942  Score: 386
    Period size: 107  Copynumber: 2.5  Consensus size: 105

       3670 AATTTTTCTA

                           *  *              *                               
       3680 ACCCTTAAAATAAAATTTTAATTTTAATTT-GGACTAAACTTAGTG-AATTAATTATATATTTTA
          1 ACCCTTAAAATAAAAATTAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAATTATATATTTTA

                                              *     
       3743 TTTCTAAAACCCTATAACAATATTATTAATTATGGAATTT
         66 TTTCTAAAACCCTATAACAATATTATTAATTATGAAATTT

                       *                      *                 *  * *       
       3783 ACCCTTAAAATGAAAATTAAATTTTAATTTGGGGTTAAACTTAGTGAAATTAGTTTTGTATTTTA
          1 ACCCTTAAAATAAAAATTAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAATTATATATTTTA

                                             *        
       3848 TTTCTAAAACCCTATAACAATAAATTATTAATTTTGAAATTT
         66 TTTCTAAAACCCTATAACAAT--ATTATTAATTATGAAATTT

                             *                         *         
       3890 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAATGAAATTAA
          1 ACCCTTAAAATAAAAATTAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAA

       3943 GACTAAACTT


Statistics
Matches: 141,  Mismatches: 15, Indels: 4
        0.88            0.09        0.03

Matches are distributed among these distances:
 103   27  0.19
 104   13  0.09
 105   36  0.26
 107   65  0.46

ACGTcount: A:0.42, C:0.09, G:0.08, T:0.41


Consensus pattern (105 bp):   
ACCCTTAAAATAAAAATTAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAATTATATATTTTA
TTTCTAAAACCCTATAACAATATTATTAATTATGAAATTT

Found at i:4262 original size:21 final size:21

Alignment explanation


    Indices: 4228--4282  Score: 67
    Period size: 21  Copynumber: 2.7  Consensus size: 21

       4218 AAAATAACAA

                           ***   
       4228 TAAACTT-TTAAAATTGGGGC
          1 TAAACTTATTAAAATCAAGGC

                    *            
       4248 TAAACTTAGTAAAATCAAGGC
          1 TAAACTTATTAAAATCAAGGC

                          
       4269 TAAACTTATTAAAA
          1 TAAACTTATTAAAA

       4283 AAGGAAAAAA


Statistics
Matches: 29,  Mismatches: 5, Indels: 1
        0.83            0.14        0.03

Matches are distributed among these distances:
  20    7  0.24
  21   22  0.76

ACGTcount: A:0.45, C:0.11, G:0.13, T:0.31


Consensus pattern (21 bp):   
TAAACTTATTAAAATCAAGGC

Found at i:4298 original size:14 final size:13

Alignment explanation


    Indices: 4279--4308  Score: 51
    Period size: 13  Copynumber: 2.3  Consensus size: 13

       4269 TAAACTTATT

                  *      
       4279 AAAAAAGGAAAAA
          1 AAAAAAAGAAAAA

                         
       4292 AAAAAAAGAAAAA
          1 AAAAAAAGAAAAA

                
       4305 AAAA
          1 AAAA

       4309 GGTGAAGACA


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  13   16  1.00

ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00


Consensus pattern (13 bp):   
AAAAAAAGAAAAA

Found at i:5508 original size:26 final size:26

Alignment explanation


    Indices: 5447--5542  Score: 97
    Period size: 26  Copynumber: 3.6  Consensus size: 26

       5437 TTAGTTTATG

                                   *     
       5447 ATTAGTTTTAATTAGTTAATTAAAAT-TA
          1 ATTAG-TTT-ATTA-TTAATTAATATCTA

            *                   *      
       5475 CTTAGTTTATGT-TTAATTAGTATCTA
          1 ATTAGTTTAT-TATTAATTAATATCTA

                                   *  
       5501 ATTAGTTTATTATTAATTAATATTTA
          1 ATTAGTTTATTATTAATTAATATCTA

                      *     
       5527 ATTAGTTTATAATTAA
          1 ATTAGTTTATTATTAA

       5543 AATGAAGGAA


Statistics
Matches: 58,  Mismatches: 7, Indels: 8
        0.79            0.10        0.11

Matches are distributed among these distances:
  25   10  0.17
  26   40  0.69
  27    4  0.07
  28    4  0.07

ACGTcount: A:0.38, C:0.02, G:0.07, T:0.53


Consensus pattern (26 bp):   
ATTAGTTTATTATTAATTAATATCTA

Found at i:5586 original size:24 final size:24

Alignment explanation


    Indices: 5552--5602  Score: 86
    Period size: 25  Copynumber: 2.1  Consensus size: 24

       5542 AAATGAAGGA

                                    
       5552 AAATGAATTTGAAGAT-TTGTTAG
          1 AAATGAATTTGAAGATGTTGTTAG

                                     
       5575 AAATGAAGTTTGAAGATGTTGTTAG
          1 AAATGAA-TTTGAAGATGTTGTTAG

               
       5600 AAA
          1 AAA

       5603 ATTCAAAATA


Statistics
Matches: 26,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
  23    7  0.27
  24    9  0.35
  25   10  0.38

ACGTcount: A:0.41, C:0.00, G:0.24, T:0.35


Consensus pattern (24 bp):   
AAATGAATTTGAAGATGTTGTTAG

Found at i:5659 original size:20 final size:20

Alignment explanation


    Indices: 5634--5675  Score: 57
    Period size: 20  Copynumber: 2.1  Consensus size: 20

       5624 CAAAAATGTA

                  *             
       5634 AAAAGAGGGCGGTATTTAGC
          1 AAAAGAAGGCGGTATTTAGC

                    *    *      
       5654 AAAAGAAGTCGGTGTTTAGC
          1 AAAAGAAGGCGGTATTTAGC

              
       5674 AA
          1 AA

       5676 TCCGGTTGGT


Statistics
Matches: 19,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  20   19  1.00

ACGTcount: A:0.38, C:0.10, G:0.31, T:0.21


Consensus pattern (20 bp):   
AAAAGAAGGCGGTATTTAGC
Done.