Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001859.1 Corchorus capsularis cultivar CVL-1 contig01860, 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: 2819
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.34


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--32  Score: 64
    Period size: 2  Copynumber: 16.0  Consensus size: 2

                                                           
          1 TA TA TA 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

         33 CTACATATAA


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   30  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:331 original size:166 final size:159

Alignment explanation


    Indices: 55--353  Score: 391
    Period size: 166  Copynumber: 1.8  Consensus size: 159

         45 AACATATGAA

                       *            *                               *    *   
         55 AATTACTAAAAGATCCCTACCCCGGATTAATGAGGAGCAAGATCATTTTCGTCTTTTCCCACTTG
          1 AATTACTAAAAAATCCCTACCCCGAATTAATGAGGAGCAAGATCATTTTCGTCTTTACCCAATTG

              *                                   *             *      *     
        120 ACCGATTACTTAAATGCCCTAACTTTTGATTCTAGAGGTGATTAAATAACTAGACTTTTTGGTCA
         66 ACAGATTACTTAAATGCCCTAACTTTTGATTCTAGAGGGGATTAAATAACTAAACTTTTAGGTCA

                                         
        185 TTTCTCAAATGACTTTAATAGAGTAGTGG
        131 TTTCTCAAATGACTTTAATAGAGTAGTGG

                                             *                 *             
        214 AATTACTAAAAAATCCCTACCCCGAATTAATGATGAGCTGGAGAAGTAATCTTTTTCGTCTTTAC
          1 AATTACTAAAAAATCCCTACCCCGAATTAATGAGGAGC-----AAG--ATCATTTTCGTCTTTAC

             *     *               *          *     *              *         
        279 CTAATTGGCAGATTACTTAAATGTCCTAACTTTTTATTCTTGAGGGGATTAAATATCTAAACTTT
         59 CCAATTGACAGATTACTTAAATGCCCTAACTTTTGATTCTAGAGGGGATTAAATAACTAAACTTT

                      
        344 TAGGTCATTT
        124 TAGGTCATTT

        354 TTACAAAAAA


Statistics
Matches: 117,  Mismatches: 16, Indels: 7
        0.84            0.11        0.05

Matches are distributed among these distances:
 159   35  0.30
 164    3  0.03
 166   79  0.68

ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36


Consensus pattern (159 bp):   
AATTACTAAAAAATCCCTACCCCGAATTAATGAGGAGCAAGATCATTTTCGTCTTTACCCAATTG
ACAGATTACTTAAATGCCCTAACTTTTGATTCTAGAGGGGATTAAATAACTAAACTTTTAGGTCA
TTTCTCAAATGACTTTAATAGAGTAGTGG

Found at i:960 original size:29 final size:30

Alignment explanation


    Indices: 935--1002  Score: 104
    Period size: 31  Copynumber: 2.3  Consensus size: 30

        925 ACGCAATTTG

                                          
        935 GGATATAACGTTAC-AAAACAAGCAATTAA
          1 GGATATAACGTTACGAAAACAAGCAATTAA

                                            
        964 GGATATAACGTTACGAAAACCGAA-CAATTAA
          1 GGATATAACGTTACGAAAA-C-AAGCAATTAA

                    
        995 GGATATAA
          1 GGATATAA

       1003 GGTTTGGCAT


Statistics
Matches: 36,  Mismatches: 0, Indels: 4
        0.90            0.00        0.10

Matches are distributed among these distances:
  29   14  0.39
  30    4  0.11
  31   16  0.44
  32    2  0.06

ACGTcount: A:0.50, C:0.13, G:0.16, T:0.21


Consensus pattern (30 bp):   
GGATATAACGTTACGAAAACAAGCAATTAA

Found at i:1164 original size:35 final size:31

Alignment explanation


    Indices: 1085--1165  Score: 90
    Period size: 31  Copynumber: 2.5  Consensus size: 31

       1075 CCCTAACTGA

                                   **    * 
       1085 TTATATCCTTAATTGCTTGAAATCGAAAATG
          1 TTATATCCTTAATTGCTTGAAATAAAAAACG

             *                                 
       1116 TGATATCCTTAATTGCTTGAAATAAAAAAAAAACG
          1 TTATATCCTTAATTGCTTGAAAT----AAAAAACG

                           
       1151 TTATATCCTTAATTG
          1 TTATATCCTTAATTG

       1166 TTCGTGGCAA


Statistics
Matches: 41,  Mismatches: 5, Indels: 4
        0.82            0.10        0.08

Matches are distributed among these distances:
  31   22  0.54
  35   19  0.46

ACGTcount: A:0.40, C:0.12, G:0.11, T:0.37


Consensus pattern (31 bp):   
TTATATCCTTAATTGCTTGAAATAAAAAACG
Done.