Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004908.1 Corchorus capsularis cultivar CVL-1 contig04926, 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: 3703
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36


Found at i:1134 original size:31 final size:31

Alignment explanation


    Indices: 1098--1157  Score: 111
    Period size: 31  Copynumber: 1.9  Consensus size: 31

       1088 TGTTCATAAG

                                           
       1098 TGAACAATTATAAAGAGACTTATTTGTCTTA
          1 TGAACAATTATAAAGAGACTTATTTGTCTTA

                       *                 
       1129 TGAACAATTATGAAGAGACTTATTTGTCT
          1 TGAACAATTATAAAGAGACTTATTTGTCT

       1158 ATAATAGGTA


Statistics
Matches: 28,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  31   28  1.00

ACGTcount: A:0.37, C:0.10, G:0.15, T:0.38


Consensus pattern (31 bp):   
TGAACAATTATAAAGAGACTTATTTGTCTTA

Found at i:1228 original size:37 final size:37

Alignment explanation


    Indices: 1186--1256  Score: 115
    Period size: 37  Copynumber: 1.9  Consensus size: 37

       1176 ACATGATTAT

                          *   *  *               
       1186 TCATAAAGTTATGTTTATTTGGAAAGACATGTATTGA
          1 TCATAAAGTTATGTCTATATGAAAAGACATGTATTGA

                                              
       1223 TCATAAAGTTATGTCTATATGAAAAGACATGTAT
          1 TCATAAAGTTATGTCTATATGAAAAGACATGTAT

       1257 GTTGATCAAG


Statistics
Matches: 31,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  37   31  1.00

ACGTcount: A:0.38, C:0.07, G:0.17, T:0.38


Consensus pattern (37 bp):   
TCATAAAGTTATGTCTATATGAAAAGACATGTATTGA

Found at i:2870 original size:33 final size:33

Alignment explanation


    Indices: 2823--2899  Score: 138
    Period size: 33  Copynumber: 2.4  Consensus size: 33

       2813 ATTTATCAAA

                    *                        
       2823 TAATCC-TCACACTTTTTATGCTTTATGCTATT
          1 TAATCCTTTACACTTTTTATGCTTTATGCTATT

                                             
       2855 TAATCCTTTACACTTTTTATGCTTTATGCTATT
          1 TAATCCTTTACACTTTTTATGCTTTATGCTATT

                        
       2888 TAATCCTTTACA
          1 TAATCCTTTACA

       2900 ATTATGGGTT


Statistics
Matches: 43,  Mismatches: 1, Indels: 1
        0.96            0.02        0.02

Matches are distributed among these distances:
  32    6  0.14
  33   37  0.86

ACGTcount: A:0.23, C:0.21, G:0.05, T:0.51


Consensus pattern (33 bp):   
TAATCCTTTACACTTTTTATGCTTTATGCTATT

Found at i:2889 original size:16 final size:16

Alignment explanation


    Indices: 2837--2889  Score: 61
    Period size: 16  Copynumber: 3.2  Consensus size: 16

       2827 CCTCACACTT

                            
       2837 TTTATGCTTTATGCTA
          1 TTTATGCTTTATGCTA

                  *     **  *
       2853 TTTAATCCTTTACACTT
          1 TTT-ATGCTTTATGCTA

                            
       2870 TTTATGCTTTATGCTA
          1 TTTATGCTTTATGCTA

                
       2886 TTTA
          1 TTTA

       2890 ATCCTTTACA


Statistics
Matches: 28,  Mismatches: 8, Indels: 2
        0.74            0.21        0.05

Matches are distributed among these distances:
  16   16  0.57
  17   12  0.43

ACGTcount: A:0.21, C:0.15, G:0.08, T:0.57


Consensus pattern (16 bp):   
TTTATGCTTTATGCTA

Found at i:3462 original size:82 final size:83

Alignment explanation


    Indices: 3325--3476  Score: 225
    Period size: 82  Copynumber: 1.8  Consensus size: 83

       3315 GATTAGTTTA

                                         *                          *        
       3325 TATGATTTGGATATTGATTTTATTCTTTAGACAAGAAATTTAATTTGTACCAACAAGCA-TTTCT
          1 TATGATTTGGATATTGATTTTATTCTTTAAACAAGAAATTTAATTTGTACCAACAAACATTTTCT

                              
       3389 TATTTGGATTTTGTTTTT
         66 TATTTGGATTTTGTTTTT

                      * *        *           *  *     *                      
       3407 TATGATTTGGGTGTTGATTTTGTTCTTTAAACATGAGATTTAGTTTGTACCAACAAACATTTTCT
          1 TATGATTTGGATATTGATTTTATTCTTTAAACAAGAAATTTAATTTGTACCAACAAACATTTTCT

                 
       3472 TATTT
         66 TATTT

       3477 TGTTTTCATC


Statistics
Matches: 61,  Mismatches: 8, Indels: 1
        0.87            0.11        0.01

Matches are distributed among these distances:
  82   51  0.84
  83   10  0.16

ACGTcount: A:0.27, C:0.09, G:0.14, T:0.49


Consensus pattern (83 bp):   
TATGATTTGGATATTGATTTTATTCTTTAAACAAGAAATTTAATTTGTACCAACAAACATTTTCT
TATTTGGATTTTGTTTTT

Found at i:3530 original size:85 final size:85

Alignment explanation


    Indices: 3423--3590  Score: 318
    Period size: 85  Copynumber: 2.0  Consensus size: 85

       3413 TTGGGTGTTG

                     *                                     *                 
       3423 ATTTTGTTCTTTAAACATGAGATTTAGTTTGTACCAACAAACATTTTCTTATTTTGTTTTCATCA
          1 ATTTTGTTCATTAAACATGAGATTTAGTTTGTACCAACAAACATTTTATTATTTTGTTTTCATCA

                                
       3488 TCAATCATGTTTAATTTTTT
         66 TCAATCATGTTTAATTTTTT

                                                                             
       3508 ATTTTGTTCATTAAACATGAGATTTAGTTTGTACCAACAAACATTTTATTATTTTGTTTTCATCA
          1 ATTTTGTTCATTAAACATGAGATTTAGTTTGTACCAACAAACATTTTATTATTTTGTTTTCATCA

                              
       3573 TCAATCATGTTTAATTTT
         66 TCAATCATGTTTAATTTT

       3591 GTTCTGATTA


Statistics
Matches: 81,  Mismatches: 2, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  85   81  1.00

ACGTcount: A:0.29, C:0.12, G:0.08, T:0.51


Consensus pattern (85 bp):   
ATTTTGTTCATTAAACATGAGATTTAGTTTGTACCAACAAACATTTTATTATTTTGTTTTCATCA
TCAATCATGTTTAATTTTTT
Done.