Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01016403.1 Corchorus capsularis cultivar CVL-1 contig16424, 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: 9566
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.34


Found at i:665 original size:146 final size:148

Alignment explanation


    Indices: 385--683  Score: 433
    Period size: 146  Copynumber: 2.0  Consensus size: 148

        375 TTTAAAAAAA

                     *                                                 *     
        385 TAATACCTATTTTCCAAAAAATAACAAACACTTTTACAAACTCATGGGACTCGCCACTTTATATC
          1 TAATACCTACTTTCCAAAAAATAACAAACACTTTTACAAACTCATGGGACTCGCCACTTCATATC

                              *                           * *         *      
        450 ACTAACTTTTTACAAACTTATAGCACTAACTTTTTATGGAACTCGCCATTTCATATCAGTTGATC
         66 ACTAACTTTTTACAAACTGATAGCACTAACTTTTTATGGAACTCGCAACTTCATATCACTTGATC

                              
        515 AG-TATAATTGTAATGGC
        131 AGATATAATTGTAATGGC

                 *                 *                  *                      
        532 TAATATCTACTTTCC-AAAAATAGCAAACACTTTTACAAACTTATGGGACTCGCCACTTCATATC
          1 TAATACCTACTTTCCAAAAAATAACAAACACTTTTACAAACTCATGGGACTCGCCACTTCATATC

                                                    * *              *    *  
        596 ACTAACTTTTTACGAAA-TGATAGCACTAACTTTTTATGGGATTCGCAACTTCATATTACTTTAT
         66 ACTAACTTTTTAC-AAACTGATAGCACTAACTTTTTATGGAACTCGCAACTTCATATCACTTGAT

            *                   
        660 GAGTATATAATTGTAATGGC
        130 CAG-ATATAATTGTAATGGC

                
        680 TAAT
          1 TAAT

        684 TAGCCTTTTT


Statistics
Matches: 135,  Mismatches: 14, Indels: 5
        0.88            0.09        0.03

Matches are distributed among these distances:
 146  100  0.74
 147   16  0.12
 148   19  0.14

ACGTcount: A:0.34, C:0.20, G:0.10, T:0.35


Consensus pattern (148 bp):   
TAATACCTACTTTCCAAAAAATAACAAACACTTTTACAAACTCATGGGACTCGCCACTTCATATC
ACTAACTTTTTACAAACTGATAGCACTAACTTTTTATGGAACTCGCAACTTCATATCACTTGATC
AGATATAATTGTAATGGC

Found at i:2504 original size:20 final size:20

Alignment explanation


    Indices: 2466--2504  Score: 60
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       2456 ACAGTTTATA

                         **     
       2466 TAGATTAACATTTTTTTGTT
          1 TAGATTAACATTTACTTGTT

                               
       2486 TAGATTAACATTTACTTGT
          1 TAGATTAACATTTACTTGT

       2505 ATGTAATCTG


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  20   17  1.00

ACGTcount: A:0.28, C:0.08, G:0.10, T:0.54


Consensus pattern (20 bp):   
TAGATTAACATTTACTTGTT

Found at i:5783 original size:16 final size:16

Alignment explanation


    Indices: 5762--5796  Score: 61
    Period size: 16  Copynumber: 2.2  Consensus size: 16

       5752 ACAATTCAGA

                            
       5762 AAGCAGAAAAGCTCTG
          1 AAGCAGAAAAGCTCTG

                    *       
       5778 AAGCAGAAGAGCTCTG
          1 AAGCAGAAAAGCTCTG

               
       5794 AAG
          1 AAG

       5797 TATTTCAGAT


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  16   18  1.00

ACGTcount: A:0.43, C:0.17, G:0.29, T:0.11


Consensus pattern (16 bp):   
AAGCAGAAAAGCTCTG

Found at i:6198 original size:58 final size:61

Alignment explanation


    Indices: 6131--6247  Score: 168
    Period size: 62  Copynumber: 2.0  Consensus size: 61

       6121 ACGATCCTCG

                             *                    *            *         
       6131 AATCAAATCAAATTC-CCAA-GTCATCAA-TTCAAGATTAAGTCATTCGACTCTTGAATAA
          1 AATCAAATCAAATTCTCAAATGTCATCAAGTTCAAGATCAAGTCATTCGACCCTTGAATAA

                       *                                               
       6189 AATCAAATCAAGTTCTCAAATTGTCATCAAGTTCAAGATCAAGTCATTCGACCCTTGAA
          1 AATCAAATCAAATTCTCAAA-TGTCATCAAGTTCAAGATCAAGTCATTCGACCCTTGAA

       6248 GCAAATCTTG


Statistics
Matches: 51,  Mismatches: 4, Indels: 4
        0.86            0.07        0.07

Matches are distributed among these distances:
  58   14  0.27
  59    3  0.06
  61    8  0.16
  62   26  0.51

ACGTcount: A:0.39, C:0.21, G:0.10, T:0.29


Consensus pattern (61 bp):   
AATCAAATCAAATTCTCAAATGTCATCAAGTTCAAGATCAAGTCATTCGACCCTTGAATAA

Found at i:7520 original size:2 final size:2

Alignment explanation


    Indices: 7513--7539  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

       7503 CCTTAAACGT

                                                    
       7513 TC TC TC TC TC TC TC TC TC TC TC TC TC T
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC T

       7540 TTGGCCATTT


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

Matches are distributed among these distances:
   2   25  1.00

ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52


Consensus pattern (2 bp):   
TC

Done.