Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010686.1 Corchorus capsularis cultivar CVL-1 contig10707, 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: 29918
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32


Found at i:3369 original size:37 final size:38

Alignment explanation


    Indices: 3291--3368  Score: 106
    Period size: 39  Copynumber: 2.1  Consensus size: 38

       3281 CCTCTCTAAT

                                 *         *    *  
       3291 AAACTCCTTTGCTTATGTTTTTTGGCCACAAGAAAGGAA
          1 AAACTCCTTTGCTTA-GTTTTGTGGCCACAAAAAAGAAA

                                                  
       3330 AAACTCCTTTGCTTA-TTTTGTGGCCA-AAAAAAGAAA
          1 AAACTCCTTTGCTTAGTTTTGTGGCCACAAAAAAGAAA

               
       3366 AAA
          1 AAA

       3369 AAAAAAAAAA


Statistics
Matches: 36,  Mismatches: 3, Indels: 3
        0.86            0.07        0.07

Matches are distributed among these distances:
  36   11  0.31
  37   10  0.28
  39   15  0.42

ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31


Consensus pattern (38 bp):   
AAACTCCTTTGCTTAGTTTTGTGGCCACAAAAAAGAAA

Found at i:6166 original size:31 final size:31

Alignment explanation


    Indices: 6128--6195  Score: 91
    Period size: 31  Copynumber: 2.2  Consensus size: 31

       6118 TTAATTTGGC

                    *     * *            * 
       6128 CAAATAAGGGCCTACCGTTATCGAAAATGTT
          1 CAAATAAGAGCCTAACATTATCGAAAATGCT

                      *                    
       6159 CAAATAAGAGTCTAACATTATCGAAAATGCT
          1 CAAATAAGAGCCTAACATTATCGAAAATGCT

                  
       6190 CAAATA
          1 CAAATA

       6196 TGGGTCTGGT


Statistics
Matches: 32,  Mismatches: 5, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  31   32  1.00

ACGTcount: A:0.43, C:0.18, G:0.15, T:0.25


Consensus pattern (31 bp):   
CAAATAAGAGCCTAACATTATCGAAAATGCT

Found at i:6273 original size:31 final size:30

Alignment explanation


    Indices: 6235--6333  Score: 78
    Period size: 31  Copynumber: 3.3  Consensus size: 30

       6225 GAGACAGACT

                                           
       6235 CTTATTTGAGTATTTTGGCAAATGTTAGGCC
          1 CTTATTTGAGTATTTTGGCAAA-GTTAGGCC

                         **           **    
       6266 CTTATTTG-GCTAAATT--CAAAGATGGGGCC
          1 CTTATTTGAG-TATTTTGGCAAAG-TTAGGCC

                      *       *            
       6295 CTTATTTGAGCATTTTGGTAAACGTTAGGCC
          1 CTTATTTGAGTATTTTGGCAAA-GTTAGGCC

            *       
       6326 TTTATTTG
          1 CTTATTTG

       6334 GCCAAATTAA


Statistics
Matches: 51,  Mismatches: 11, Indels: 12
        0.69            0.15        0.16

Matches are distributed among these distances:
  28    1  0.02
  29   20  0.39
  30    2  0.04
  31   27  0.53
  32    1  0.02

ACGTcount: A:0.23, C:0.14, G:0.22, T:0.40


Consensus pattern (30 bp):   
CTTATTTGAGTATTTTGGCAAAGTTAGGCC

Found at i:6302 original size:60 final size:60

Alignment explanation


    Indices: 6235--6387  Score: 207
    Period size: 60  Copynumber: 2.5  Consensus size: 60

       6225 GAGACAGACT

                                  *                  *     *      *     
       6235 CTTATTTGAGTATTTTGGCAAATGTTAGGCCCTTATTTGGCTAAATTCAAAGATGGGGCC
          1 CTTATTTGAGTATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGGGCC

                      *       *            *                            
       6295 CTTATTTGAGCATTTTGGTAAACGTTAGGCCTTTATTTGGCCAAATTAAAAGATCGGGCC
          1 CTTATTTGAGTATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGGGCC

            *        *       *     *         
       6355 TTTATTTGAATATTTTGACAAACATTAGGCCCT
          1 CTTATTTGAGTATTTTGGCAAACGTTAGGCCCT

       6388 AACAATTAAC


Statistics
Matches: 79,  Mismatches: 14, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  60   79  1.00

ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37


Consensus pattern (60 bp):   
CTTATTTGAGTATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGGGCC

Found at i:8724 original size:34 final size:34

Alignment explanation


    Indices: 8686--8756  Score: 142
    Period size: 34  Copynumber: 2.1  Consensus size: 34

       8676 GTCAATCAAT

                                              
       8686 TTTTCCTCGTTGCCAAGTAAATATTATTGATAAG
          1 TTTTCCTCGTTGCCAAGTAAATATTATTGATAAG

                                              
       8720 TTTTCCTCGTTGCCAAGTAAATATTATTGATAAG
          1 TTTTCCTCGTTGCCAAGTAAATATTATTGATAAG

               
       8754 TTT
          1 TTT

       8757 GAAGACTAGA


Statistics
Matches: 37,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  34   37  1.00

ACGTcount: A:0.28, C:0.14, G:0.14, T:0.44


Consensus pattern (34 bp):   
TTTTCCTCGTTGCCAAGTAAATATTATTGATAAG

Found at i:13089 original size:17 final size:17

Alignment explanation


    Indices: 13044--13090  Score: 60
    Period size: 17  Copynumber: 2.7  Consensus size: 17

      13034 AAATCAGTTC

                             
      13044 TAATTAATATTTATTAT
          1 TAATTAATATTTATTAT

              *               
      13061 TATTTCAATATTTATT-T
          1 TAATT-AATATTTATTAT

                         
      13078 TAATTGAATATTT
          1 TAATT-AATATTT

      13091 GTGATCTCTT


Statistics
Matches: 26,  Mismatches: 3, Indels: 2
        0.84            0.10        0.06

Matches are distributed among these distances:
  17   16  0.62
  18   10  0.38

ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60


Consensus pattern (17 bp):   
TAATTAATATTTATTAT
Done.