Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007025.1 Corchorus capsularis cultivar CVL-1 contig07046, 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: 10646
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:105 original size:50 final size:50

Alignment explanation


    Indices: 41--396  Score: 358
    Period size: 50  Copynumber: 7.1  Consensus size: 50

         31 GACGACATTT

                     *              *                  *       
         41 TTTATTTACCAATTACTT-AAAATCCAAATCTTTTATTCAAAGGTTAAATC
          1 TTTATTTACTAATTACTTAAAAATTC-AATCTTTTATTCAAAGATTAAATC

                                  *             **       * *  *
         91 TTTATTTACTAATTACTCTAAAGATTCAATCTTTTACCCAAAGATGACATT
          1 TTTATTTACTAATTACT-TAAAAATTCAATCTTTTATTCAAAGATTAAATC

                     *                   *            *       
        142 TTTATTTACCAATTACTTAAAAATTCAATGTTTTATTCAAAGGTTAAATC
          1 TTTATTTACTAATTACTTAAAAATTCAATCTTTTATTCAAAGATTAAATC

            *                          *        **    *  * *  *
        192 CTTATTTACTAATTACTCTAAAAATTCGATCTTTTACCCAAACATGACATT
          1 TTTATTTACTAATTACT-TAAAAATTCAATCTTTTATTCAAAGATTAAATC

                *    *                                *        
        243 TTTACTTACCAATTACTTAAAAATTCAATCTTTTATTCAAAGCTTAAAAT-
          1 TTTATTTACTAATTACTTAAAAATTCAATCTTTTATTCAAAGATT-AAATC

                         *                      **       * *  *
        293 TTTATTTACTAATCACTCTAAAAATTCAATCTTTTACCCAAAGATGACATT
          1 TTTATTTACTAATTACT-TAAAAATTCAATCTTTTATTCAAAGATTAAATC

                                                       *   *   
        344 TTTATTTA-TCAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTATATC
          1 TTTATTTACT-AATTACTTAAAAATTCAATCTTTTATTCAAAGATTAAATC

               
        394 TTT
          1 TTT

        397 TAGCCAAGTA


Statistics
Matches: 245,  Mismatches: 54, Indels: 14
        0.78            0.17        0.04

Matches are distributed among these distances:
  50  126  0.51
  51  114  0.47
  52    5  0.02

ACGTcount: A:0.37, C:0.16, G:0.04, T:0.43


Consensus pattern (50 bp):   
TTTATTTACTAATTACTTAAAAATTCAATCTTTTATTCAAAGATTAAATC

Found at i:179 original size:101 final size:101

Alignment explanation


    Indices: 1--396  Score: 616
    Period size: 101  Copynumber: 3.9  Consensus size: 101

                      *                     *                               *
          1 ACTCTAAAGATTTCAATCTTTTTACCCAAAGACGACATTTTTTATTTACCAATTACTT-AAAATC
          1 ACTCTAAA-AATTCAATC-TTTTACCCAAAGATGACA-TTTTTATTTACCAATTACTTAAAAATT

                                                    
         65 CAAATCTTTTATTCAAAGGTTAAATCTTTATTTACTAATT
         63 C-AATCTTTTATTCAAAGGTTAAATCTTTATTTACTAATT

                    *                                                        
        105 ACTCTAAAGATTCAATCTTTTACCCAAAGATGACATTTTTATTTACCAATTACTTAAAAATTCAA
          1 ACTCTAAAAATTCAATCTTTTACCCAAAGATGACATTTTTATTTACCAATTACTTAAAAATTCAA

             *                    *             
        170 TGTTTTATTCAAAGGTTAAATCCTTATTTACTAATT
         66 TCTTTTATTCAAAGGTTAAATCTTTATTTACTAATT

                         *              *            *                       
        206 ACTCTAAAAATTCGATCTTTTACCCAAACATGACATTTTTACTTACCAATTACTTAAAAATTCAA
          1 ACTCTAAAAATTCAATCTTTTACCCAAAGATGACATTTTTATTTACCAATTACTTAAAAATTCAA

                          *                     *
        271 TCTTTTATTCAAAGCTTAAAAT-TTTATTTACTAATC
         66 TCTTTTATTCAAAGGTT-AAATCTTTATTTACTAATT

                                                         *                   
        307 ACTCTAAAAATTCAATCTTTTACCCAAAGATGACATTTTTATTTATCAATTACTTAAAAATTCAA
          1 ACTCTAAAAATTCAATCTTTTACCCAAAGATGACATTTTTATTTACCAATTACTTAAAAATTCAA

                              *      
        372 TCTTTTATTCAAAGGTTATATCTTT
         66 TCTTTTATTCAAAGGTTAAATCTTT

        397 TAGCCAAGTA


Statistics
Matches: 269,  Mismatches: 20, Indels: 9
        0.90            0.07        0.03

Matches are distributed among these distances:
 100    3  0.01
 101  224  0.83
 102   27  0.10
 103    7  0.03
 104    8  0.03

ACGTcount: A:0.37, C:0.17, G:0.05, T:0.42


Consensus pattern (101 bp):   
ACTCTAAAAATTCAATCTTTTACCCAAAGATGACATTTTTATTTACCAATTACTTAAAAATTCAA
TCTTTTATTCAAAGGTTAAATCTTTATTTACTAATT

Found at i:3372 original size:27 final size:27

Alignment explanation


    Indices: 3342--3410  Score: 93
    Period size: 27  Copynumber: 2.6  Consensus size: 27

       3332 AGGTGAACTT

                     **     *          
       3342 AAAAATGACTGAAATGTCCCTGAGTGC
          1 AAAAATGACCAAAATGCCCCTGAGTGC

                 *                *    
       3369 AAAAAAGACCAAAATGCCCCTGGGTGC
          1 AAAAATGACCAAAATGCCCCTGAGTGC

                           
       3396 AAAAATGACCAAAAT
          1 AAAAATGACCAAAAT

       3411 ACCCTTGGGG


Statistics
Matches: 36,  Mismatches: 6, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  27   36  1.00

ACGTcount: A:0.45, C:0.20, G:0.19, T:0.16


Consensus pattern (27 bp):   
AAAAATGACCAAAATGCCCCTGAGTGC

Found at i:3419 original size:27 final size:27

Alignment explanation


    Indices: 3359--3419  Score: 86
    Period size: 27  Copynumber: 2.3  Consensus size: 27

       3349 ACTGAAATGT

                 *                   * 
       3359 CCCTGAGTGCAAAAAAGACCAAAATGC
          1 CCCTGGGTGCAAAAAAGACCAAAATAC

                           *           
       3386 CCCTGGGTGCAAAAATGACCAAAATAC
          1 CCCTGGGTGCAAAAAAGACCAAAATAC

              *    
       3413 CCTTGGG
          1 CCCTGGG

       3420 GGGCCTAATG


Statistics
Matches: 30,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  27   30  1.00

ACGTcount: A:0.38, C:0.26, G:0.21, T:0.15


Consensus pattern (27 bp):   
CCCTGGGTGCAAAAAAGACCAAAATAC
Done.