Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013786.1 Corchorus capsularis cultivar CVL-1 contig13807, 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: 11158
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29


Found at i:1207 original size:13 final size:13

Alignment explanation


    Indices: 1189--1215  Score: 54
    Period size: 13  Copynumber: 2.1  Consensus size: 13

       1179 TTAATTATTG

                         
       1189 TTTGCTTTATTAA
          1 TTTGCTTTATTAA

                         
       1202 TTTGCTTTATTAA
          1 TTTGCTTTATTAA

             
       1215 T
          1 T

       1216 CTACTTTAGA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   14  1.00

ACGTcount: A:0.22, C:0.07, G:0.07, T:0.63


Consensus pattern (13 bp):   
TTTGCTTTATTAA

Found at i:1231 original size:6 final size:6

Alignment explanation


    Indices: 1220--1246  Score: 54
    Period size: 6  Copynumber: 4.5  Consensus size: 6

       1210 ATTAATCTAC

                                           
       1220 TTTAGA TTTAGA TTTAGA TTTAGA TTT
          1 TTTAGA TTTAGA TTTAGA TTTAGA TTT

       1247 GCTTTGCTTT


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   21  1.00

ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56


Consensus pattern (6 bp):   
TTTAGA

Found at i:1729 original size:40 final size:41

Alignment explanation


    Indices: 1653--1735  Score: 116
    Period size: 41  Copynumber: 2.0  Consensus size: 41

       1643 TAAATTAGGG

                                         *        *  
       1653 TTTCCGATTTTTCCTTTTAAAAAAAATAATTAATTTTTCTT
          1 TTTCCGATTTTTCCTTTTAAAAAAAATAAATAATTTTTATT

                  *                                   
       1694 TTTCCGTTTTTTCCTTTTAAAATAAAA-AAAT-ATTTTTATT
          1 TTTCCGATTTTTCCTTTTAAAA-AAAATAAATAATTTTTATT

              
       1734 TT
          1 TT

       1736 CTGTTTCTGC


Statistics
Matches: 38,  Mismatches: 3, Indels: 3
        0.86            0.07        0.07

Matches are distributed among these distances:
  40   10  0.26
  41   24  0.63
  42    4  0.11

ACGTcount: A:0.31, C:0.11, G:0.02, T:0.55


Consensus pattern (41 bp):   
TTTCCGATTTTTCCTTTTAAAAAAAATAAATAATTTTTATT

Found at i:6506 original size:33 final size:33

Alignment explanation


    Indices: 6467--6548  Score: 164
    Period size: 33  Copynumber: 2.5  Consensus size: 33

       6457 CGGCCACAAG

                                             
       6467 ACCGGCCACGCGACATGGACATGTCCGGCCATC
          1 ACCGGCCACGCGACATGGACATGTCCGGCCATC

                                             
       6500 ACCGGCCACGCGACATGGACATGTCCGGCCATC
          1 ACCGGCCACGCGACATGGACATGTCCGGCCATC

                            
       6533 ACCGGCCACGCGACAT
          1 ACCGGCCACGCGACAT

       6549 TGGGTTGGGC


Statistics
Matches: 49,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  33   49  1.00

ACGTcount: A:0.22, C:0.40, G:0.27, T:0.11


Consensus pattern (33 bp):   
ACCGGCCACGCGACATGGACATGTCCGGCCATC

Found at i:7296 original size:10 final size:9

Alignment explanation


    Indices: 7283--7317  Score: 52
    Period size: 10  Copynumber: 3.7  Consensus size: 9

       7273 AGTTATATCG

                      
       7283 AAAAATATAA
          1 AAAAATA-AA

                     
       7293 AAAAATAAA
          1 AAAAATAAA

                      
       7302 ATAAAATAAA
          1 A-AAAATAAA

                  
       7312 AAAAAT
          1 AAAAAT

       7318 TTCGACCAGA


Statistics
Matches: 24,  Mismatches: 0, Indels: 3
        0.89            0.00        0.11

Matches are distributed among these distances:
   9    8  0.33
  10   16  0.67

ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17


Consensus pattern (9 bp):   
AAAAATAAA

Found at i:9332 original size:33 final size:33

Alignment explanation


    Indices: 9295--9401  Score: 144
    Period size: 33  Copynumber: 3.2  Consensus size: 33

       9285 CGCCTAGCGA

                                  *    *      
       9295 TGGCCGGTTG-TGGCCGGACATGTCCATGTCGCG
          1 TGGCCGG-TGATGGCCGGACATCTCCAAGTCGCG

                             *               
       9328 TGGCCGGTGATGGCCGGGCATCTCCAAGTCGCG
          1 TGGCCGGTGATGGCCGGACATCTCCAAGTCGCG

                     *         *            *
       9361 TGGCCGGTGTTGGCCGGACTTCTCCAAGTCGCA
          1 TGGCCGGTGATGGCCGGACATCTCCAAGTCGCG

                    
       9394 TGGCCGGT
          1 TGGCCGGT

       9402 CACTAGTGCT


Statistics
Matches: 66,  Mismatches: 7, Indels: 2
        0.88            0.09        0.03

Matches are distributed among these distances:
  32    2  0.03
  33   64  0.97

ACGTcount: A:0.10, C:0.29, G:0.38, T:0.22


Consensus pattern (33 bp):   
TGGCCGGTGATGGCCGGACATCTCCAAGTCGCG
Done.