Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007860.1 Corchorus capsularis cultivar CVL-1 contig07881, 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: 4438
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33


Found at i:822 original size:62 final size:63

Alignment explanation


    Indices: 723--845  Score: 187
    Period size: 62  Copynumber: 2.0  Consensus size: 63

        713 TAATGAAGAG

                        *                                                  
        723 AAACCTAATCTATACTAATTTTTCAATATATTCTTATGTCATTTTGGTATAGTTGTTTTCAGA
          1 AAACCTAATCTACACTAATTTTTCAATATATTCTTATGTCATTTTGGTATAGTTGTTTTCAGA

                       *  *                         *                     
        786 AAACCTAATCTGCATTAA-TTTTCAATATACTT-TTATGTGATTTTGGTATAGTTGTTTTCA
          1 AAACCTAATCTACACTAATTTTTCAATATA-TTCTTATGTCATTTTGGTATAGTTGTTTTCA

        846 ATTGGTGCTC


Statistics
Matches: 55,  Mismatches: 4, Indels: 3
        0.89            0.06        0.05

Matches are distributed among these distances:
  62   38  0.69
  63   17  0.31

ACGTcount: A:0.29, C:0.12, G:0.11, T:0.48


Consensus pattern (63 bp):   
AAACCTAATCTACACTAATTTTTCAATATATTCTTATGTCATTTTGGTATAGTTGTTTTCAGA

Found at i:3421 original size:162 final size:162

Alignment explanation


    Indices: 3153--3477  Score: 623
    Period size: 162  Copynumber: 2.0  Consensus size: 162

       3143 GTAGAGTTAT

                                                                             
       3153 GTTCAACTTTTTACAGAGAAGATAAGAGAAACCGCAGGATAGCTCAATCAATCAGCTTTCTAAGG
          1 GTTCAACTTTTTACAGAGAAGATAAGAGAAACCGCAGGATAGCTCAATCAATCAGCTTTCTAAGG

                                                                             
       3218 AAATAAAACAACAATGAATTCTTTGCTCTCCAAAAGAAAATGTAATTAGCTTCTCTGATGTTCTC
         66 AAATAAAACAACAATGAATTCTTTGCTCTCCAAAAGAAAATGTAATTAGCTTCTCTGATGTTCTC

                                            
       3283 TAACCCAAATTTCAACCTAATTCTTGGGAAGA
        131 TAACCCAAATTTCAACCTAATTCTTGGGAAGA

                                            *                                
       3315 GTTCAACTTTTTACAGAGAAGATAAGAGAAACTGCAGGATAGCTCAATCAATCAGCTTTCTAAGG
          1 GTTCAACTTTTTACAGAGAAGATAAGAGAAACCGCAGGATAGCTCAATCAATCAGCTTTCTAAGG

                                              *                              
       3380 AAATAAAACAACAATGAATTCTTTGCTCTCCAAATGAAAATGTAATTAGCTTCTCTGATGTTCTC
         66 AAATAAAACAACAATGAATTCTTTGCTCTCCAAAAGAAAATGTAATTAGCTTCTCTGATGTTCTC

                                  *         
       3445 TAACCCAAATTTCAACCTAATTTTTGGGAAGA
        131 TAACCCAAATTTCAACCTAATTCTTGGGAAGA

             
       3477 G
          1 G

       3478 CTCCAGAAAT


Statistics
Matches: 160,  Mismatches: 3, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
 162  160  1.00

ACGTcount: A:0.37, C:0.18, G:0.15, T:0.29


Consensus pattern (162 bp):   
GTTCAACTTTTTACAGAGAAGATAAGAGAAACCGCAGGATAGCTCAATCAATCAGCTTTCTAAGG
AAATAAAACAACAATGAATTCTTTGCTCTCCAAAAGAAAATGTAATTAGCTTCTCTGATGTTCTC
TAACCCAAATTTCAACCTAATTCTTGGGAAGA
Done.