Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013738.1 Corchorus capsularis cultivar CVL-1 contig13759, 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: 22828
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33


Found at i:4112 original size:2 final size:2

Alignment explanation


    Indices: 4105--4142  Score: 76
    Period size: 2  Copynumber: 19.0  Consensus size: 2

       4095 GCTCTGCTGA

                                                                    
       4105 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       4143 CTTCCCTCAA


Statistics
Matches: 36,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   36  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:6281 original size:13 final size:13

Alignment explanation


    Indices: 6263--6287  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       6253 TTTGCAAAAA

                         
       6263 GTGCTTTTGAAAT
          1 GTGCTTTTGAAAT

                        
       6276 GTGCTTTTGAAA
          1 GTGCTTTTGAAA

       6288 ATAGCTGTAG


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.24, C:0.08, G:0.24, T:0.44


Consensus pattern (13 bp):   
GTGCTTTTGAAAT

Found at i:9309 original size:6 final size:6

Alignment explanation


    Indices: 9298--9330  Score: 66
    Period size: 6  Copynumber: 5.5  Consensus size: 6

       9288 AAAGCAAAGC

                                                  
       9298 AAATCT AAATCT AAATCT AAATCT AAATCT AAA
          1 AAATCT AAATCT AAATCT AAATCT AAATCT AAA

       9331 GCAGATTAAT


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   27  1.00

ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30


Consensus pattern (6 bp):   
AAATCT

Found at i:10264 original size:10 final size:10

Alignment explanation


    Indices: 10249--10273  Score: 50
    Period size: 10  Copynumber: 2.5  Consensus size: 10

      10239 GAGGACTCTA

                      
      10249 GAATTTTCTG
          1 GAATTTTCTG

                      
      10259 GAATTTTCTG
          1 GAATTTTCTG

                 
      10269 GAATT
          1 GAATT

      10274 GAGCAGGGAC


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   15  1.00

ACGTcount: A:0.24, C:0.08, G:0.20, T:0.48


Consensus pattern (10 bp):   
GAATTTTCTG

Found at i:17856 original size:61 final size:61

Alignment explanation


    Indices: 17761--17890  Score: 253
    Period size: 61  Copynumber: 2.1  Consensus size: 61

      17751 ATATCTGTAT

                                                                         
      17761 ATATTAATTTGGATGAGTGCTTCCTAAACACACAATCATCGTCACATCCTTCTTTAATTAC
          1 ATATTAATTTGGATGAGTGCTTCCTAAACACACAATCATCGTCACATCCTTCTTTAATTAC

                                                                         
      17822 ATATTAATTTGGATGAGTGCTTCCTAAACACACAATCATCGTCACATCCTTCTTTAATTAC
          1 ATATTAATTTGGATGAGTGCTTCCTAAACACACAATCATCGTCACATCCTTCTTTAATTAC

                     
      17883 ATA-TAATT
          1 ATATTAATT

      17891 ATGTATAACA


Statistics
Matches: 69,  Mismatches: 0, Indels: 1
        0.99            0.00        0.01

Matches are distributed among these distances:
  60    5  0.07
  61   64  0.93

ACGTcount: A:0.32, C:0.22, G:0.09, T:0.37


Consensus pattern (61 bp):   
ATATTAATTTGGATGAGTGCTTCCTAAACACACAATCATCGTCACATCCTTCTTTAATTAC

Found at i:20205 original size:2 final size:2

Alignment explanation


    Indices: 20198--20249  Score: 79
    Period size: 2  Copynumber: 26.5  Consensus size: 2

      20188 GGGTGGGACA

                                                            *        *    
      20198 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT CT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                            
      20240 AT AT -T AT AT A
          1 AT AT AT AT AT A

      20250 AGTCTAAATT


Statistics
Matches: 45,  Mismatches: 4, Indels: 2
        0.88            0.08        0.04

Matches are distributed among these distances:
   1    1  0.02
   2   44  0.98

ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:22115 original size:20 final size:20

Alignment explanation


    Indices: 22077--22114  Score: 60
    Period size: 19  Copynumber: 1.9  Consensus size: 20

      22067 GAATTTATAA

                                
      22077 ATAACCTTATAACTGTTTTG
          1 ATAACCTTATAACTGTTTTG

                        *      
      22097 ATAACC-TATAATTGTTTT
          1 ATAACCTTATAACTGTTTT

      22115 TTAGTAATCA


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  19   11  0.65
  20    6  0.35

ACGTcount: A:0.32, C:0.13, G:0.08, T:0.47


Consensus pattern (20 bp):   
ATAACCTTATAACTGTTTTG
Done.