Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007886.1 Corchorus capsularis cultivar CVL-1 contig07907, 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: 15619
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34


Found at i:2067 original size:40 final size:40

Alignment explanation


    Indices: 2021--2100  Score: 151
    Period size: 40  Copynumber: 2.0  Consensus size: 40

       2011 ATCTAATGAT

                                                    
       2021 CCTCATACTTTTATACTTTATGCTATTTAGTCATTTACAA
          1 CCTCATACTTTTATACTTTATGCTATTTAGTCATTTACAA

                                            *       
       2061 CCTCATACTTTTATACTTTATGCTATTTAGTCCTTTACAA
          1 CCTCATACTTTTATACTTTATGCTATTTAGTCATTTACAA

       2101 TTATAAGTTG


Statistics
Matches: 39,  Mismatches: 1, Indels: 0
        0.98            0.03        0.00

Matches are distributed among these distances:
  40   39  1.00

ACGTcount: A:0.26, C:0.21, G:0.05, T:0.47


Consensus pattern (40 bp):   
CCTCATACTTTTATACTTTATGCTATTTAGTCATTTACAA

Found at i:3240 original size:20 final size:20

Alignment explanation


    Indices: 3204--3241  Score: 51
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       3194 AAAAAACTAG

                        *       
       3204 TATTACTATAATCTAGACCA
          1 TATTACTATAATATAGACCA

                               
       3224 TATT-CTATATATATAGAC
          1 TATTACTATA-ATATAGAC

       3242 TTTTAATAAT


Statistics
Matches: 16,  Mismatches: 1, Indels: 2
        0.84            0.05        0.11

Matches are distributed among these distances:
  19    5  0.31
  20   11  0.69

ACGTcount: A:0.39, C:0.16, G:0.05, T:0.39


Consensus pattern (20 bp):   
TATTACTATAATATAGACCA

Found at i:11229 original size:75 final size:75

Alignment explanation


    Indices: 11100--11244  Score: 218
    Period size: 75  Copynumber: 1.9  Consensus size: 75

      11090 CTAAATTAAG

                                                **           *      **       
      11100 AAAAGACCAAAACGGGGGGAAAAGGTTCTCCCACGTTTAAAGTTGATGGGAGCTATTGGTAATTT
          1 AAAAGACCAAAACGGGGGGAAAAGGTTCTCCCACGTCGAAAGTTGATGGAAGCTATCAGTAATTT

                      
      11165 CCAGAGTAAT
         66 CCAGAGTAAT

                             *                             *                 
      11175 AAAAGACCAAAACGGGGTGAAAAGGTTCTCCCACGTCGAAAGTTGATTGAAGCTATCAGTAATTT
          1 AAAAGACCAAAACGGGGGGAAAAGGTTCTCCCACGTCGAAAGTTGATGGAAGCTATCAGTAATTT

            *    
      11240 TCAGA
         66 CCAGA

      11245 AGGTATTCAA


Statistics
Matches: 62,  Mismatches: 8, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  75   62  1.00

ACGTcount: A:0.36, C:0.16, G:0.25, T:0.23


Consensus pattern (75 bp):   
AAAAGACCAAAACGGGGGGAAAAGGTTCTCCCACGTCGAAAGTTGATGGAAGCTATCAGTAATTT
CCAGAGTAAT

Found at i:11520 original size:21 final size:21

Alignment explanation


    Indices: 11496--11538  Score: 68
    Period size: 21  Copynumber: 2.0  Consensus size: 21

      11486 TTGTAGCTCA

                                 
      11496 GGAGGCGCCTCCCTGCTTTCT
          1 GGAGGCGCCTCCCTGCTTTCT

                *  *             
      11517 GGAGTCGTCTCCCTGCTTTCT
          1 GGAGGCGCCTCCCTGCTTTCT

             
      11538 G
          1 G

      11539 TATTAAATGA


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  21   20  1.00

ACGTcount: A:0.05, C:0.35, G:0.28, T:0.33


Consensus pattern (21 bp):   
GGAGGCGCCTCCCTGCTTTCT

Found at i:14746 original size:37 final size:37

Alignment explanation


    Indices: 14696--14766  Score: 115
    Period size: 37  Copynumber: 1.9  Consensus size: 37

      14686 ATATGATTAT

                          *   *  *               
      14696 TCATAAAGTTATGTTTATTTGGAAAGACATGTATTGA
          1 TCATAAAGTTATGTCTATATGAAAAGACATGTATTGA

                                              
      14733 TCATAAAGTTATGTCTATATGAAAAGACATGTAT
          1 TCATAAAGTTATGTCTATATGAAAAGACATGTAT

      14767 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
Done.