Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007857.1 Corchorus capsularis cultivar CVL-1 contig07878, 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: 8518
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34


Found at i:6171 original size:120 final size:120

Alignment explanation


    Indices: 6022--6237  Score: 360
    Period size: 120  Copynumber: 1.8  Consensus size: 120

       6012 TCCAGCGTTA

                        *   *                                *               
       6022 CTAGTCATCTAATCTTTCAAATATAAATTTTGACTCCGATTCTCAAAACTAGACAAACATTATCA
          1 CTAGTCATCTAAGCTTCCAAATATAAATTTTGACTCCGATTCTCAAAACCAGACAAACATTATCA

                     *                                             
       6087 CATGACATTTATACGTTACAGAATCCAAACATTATCATGTTACGTTTGAGTGTTG
         66 CATGACATTCATACGTTACAGAATCCAAACATTATCATGTTACGTTTGAGTGTTG

                 *              *               *                            
       6142 CTAGTTATCTAAGCTTCCAAGTATAAATTTTGACTCGGATTCTCAAAACCAGACAAACATTATCA
          1 CTAGTCATCTAAGCTTCCAAATATAAATTTTGACTCCGATTCTCAAAACCAGACAAACATTATCA

             *                             
       6207 CGTGACATTCATACGTTACAGAATCCAAACA
         66 CATGACATTCATACGTTACAGAATCCAAACA

       6238 ATTAATATCA


Statistics
Matches: 88,  Mismatches: 8, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
 120   88  1.00

ACGTcount: A:0.36, C:0.21, G:0.11, T:0.32


Consensus pattern (120 bp):   
CTAGTCATCTAAGCTTCCAAATATAAATTTTGACTCCGATTCTCAAAACCAGACAAACATTATCA
CATGACATTCATACGTTACAGAATCCAAACATTATCATGTTACGTTTGAGTGTTG

Found at i:6649 original size:26 final size:26

Alignment explanation


    Indices: 6613--6663  Score: 102
    Period size: 26  Copynumber: 2.0  Consensus size: 26

       6603 TTTATAAGTT

                                      
       6613 AAGGCATGCAATTGGATGAAAAAAAA
          1 AAGGCATGCAATTGGATGAAAAAAAA

                                     
       6639 AAGGCATGCAATTGGATGAAAAAAA
          1 AAGGCATGCAATTGGATGAAAAAAA

       6664 GGCATGCAAT


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  26   25  1.00

ACGTcount: A:0.53, C:0.08, G:0.24, T:0.16


Consensus pattern (26 bp):   
AAGGCATGCAATTGGATGAAAAAAAA

Found at i:6664 original size:23 final size:24

Alignment explanation


    Indices: 6613--6673  Score: 97
    Period size: 26  Copynumber: 2.5  Consensus size: 24

       6603 TTTATAAGTT

                                      
       6613 AAGGCATGCAATTGGATGAAAAAAAA
          1 AAGGCATGCAATTGGATG--AAAAAA

                                    
       6639 AAGGCATGCAATTGGATG-AAAAA
          1 AAGGCATGCAATTGGATGAAAAAA

                        
       6662 AAGGCATGCAAT
          1 AAGGCATGCAAT

       6674 CGACACTAAT


Statistics
Matches: 35,  Mismatches: 0, Indels: 3
        0.92            0.00        0.08

Matches are distributed among these distances:
  23   17  0.49
  26   18  0.51

ACGTcount: A:0.49, C:0.10, G:0.25, T:0.16


Consensus pattern (24 bp):   
AAGGCATGCAATTGGATGAAAAAA

Found at i:6939 original size:16 final size:16

Alignment explanation


    Indices: 6918--6950  Score: 50
    Period size: 15  Copynumber: 2.1  Consensus size: 16

       6908 TTATTAAACA

                             
       6918 TAATAAAATAATA-ATG
          1 TAAT-AAATAATATATG

                            
       6934 TAATAAATAATATATG
          1 TAATAAATAATATATG

             
       6950 T
          1 T

       6951 TTAATAGTCT


Statistics
Matches: 16,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  15    8  0.50
  16    8  0.50

ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36


Consensus pattern (16 bp):   
TAATAAATAATATATG

Found at i:7210 original size:42 final size:41

Alignment explanation


    Indices: 7130--7215  Score: 111
    Period size: 42  Copynumber: 2.1  Consensus size: 41

       7120 TCATGGGTTA

                           *        *                
       7130 ATATCCTTAATAAATTTAAAAAAAGTTACATAAATTAGTAT
          1 ATATCCTTAATAAATATAAAAAAACTTACATAAATTAGTAT

                                         *     *       
       7171 ATATCC-TAATAAATAATAAACAAAACTTGCATAATTTAGTAT
          1 ATATCCTTAATAAAT-ATAAA-AAAACTTACATAAATTAGTAT

               
       7213 ATA
          1 ATA

       7216 AATGAGATGG


Statistics
Matches: 39,  Mismatches: 4, Indels: 3
        0.85            0.09        0.07

Matches are distributed among these distances:
  40    8  0.21
  41   10  0.26
  42   21  0.54

ACGTcount: A:0.51, C:0.09, G:0.05, T:0.35


Consensus pattern (41 bp):   
ATATCCTTAATAAATATAAAAAAACTTACATAAATTAGTAT
Done.