Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004920.1 Corchorus capsularis cultivar CVL-1 contig04938, 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: 10229
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.31


Found at i:1600 original size:66 final size:66

Alignment explanation


    Indices: 1510--1741  Score: 410
    Period size: 66  Copynumber: 3.5  Consensus size: 66

       1500 CTCAAAGAAT

                                      *                                      
       1510 GTTTTTATTTTGGTAAAACGGTCTCGTGGGAGACGTTCGTTTTACCTAAGTTACGATTCAAGGAT
          1 GTTTTTATTTTGGTAAAACGGTCTCGAGGGAGACGTTCGTTTTACCTAAGTTACGATTCAAGGAT

             
       1575 C
         66 C

                                                  * *                        
       1576 GTTTTTATTTTGGTAAAACGGTCTCGAGGGAGACGTTCATCTTACCTAAGTTACGATTCAAGGAT
          1 GTTTTTATTTTGGTAAAACGGTCTCGAGGGAGACGTTCGTTTTACCTAAGTTACGATTCAAGGAT

             
       1641 C
         66 C

                              *       *                                  *   
       1642 GTTTTTATTTTGGTAAAATGGTCTCGTGGGAGACGTTCGTTTTACCTAAGTTACGATTCAATGAT
          1 GTTTTTATTTTGGTAAAACGGTCTCGAGGGAGACGTTCGTTTTACCTAAGTTACGATTCAAGGAT

             
       1707 C
         66 C

                                              
       1708 GTTTTTATTTTGGTAAAACGGTCTCGAGGGAGAC
          1 GTTTTTATTTTGGTAAAACGGTCTCGAGGGAGAC

       1742 AAATGCATCA


Statistics
Matches: 156,  Mismatches: 10, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  66  156  1.00

ACGTcount: A:0.24, C:0.15, G:0.24, T:0.38


Consensus pattern (66 bp):   
GTTTTTATTTTGGTAAAACGGTCTCGAGGGAGACGTTCGTTTTACCTAAGTTACGATTCAAGGAT
C

Found at i:1680 original size:132 final size:125

Alignment explanation


    Indices: 1458--1741  Score: 435
    Period size: 132  Copynumber: 2.2  Consensus size: 125

       1448 ATCGTACAAT

                  *                        *                                 
       1458 TTTTGGCAAAACGGTCTCGAGGGAGACGTTCGTCTTTTACGACTCAAAGAATGTTTTTATTTTGG
          1 TTTTGGTAAAACGGTCTCGAGGGAGACGTTCATCTTTTACGACTCAAAGAATGTTTTTATTTTGG

                                                                        
       1523 TAAAACGGTCTCGTGGGAGACGTTCGTTTTACCTAAGTTACGATTCAAGGATCGTTTTTA
         66 TAAAACGGTCTCGTGGGAGACGTTCGTTTTACCTAAGTTACGATTCAAGGATCGTTTTTA

                                                             *      *        
       1583 TTTTGGTAAAACGGTCTCGAGGGAGACGTTCATCTTACCTAAGTTACGATTC-AAGGATCGTTTT
          1 TTTTGGTAAAACGGTCTCGAGGGAGACGTTCATC-T---T---TTACGACTCAAAGAAT-GTTTT

                         *                                          *        
       1647 TATTTTGGTAAAATGGTCTCGTGGGAGACGTTCGTTTTACCTAAGTTACGATTCAATGATCGTTT
         58 TATTTTGGTAAAACGGTCTCGTGGGAGACGTTCGTTTTACCTAAGTTACGATTCAAGGATCGTTT

               
       1712 TTA
        123 TTA

                                       
       1715 TTTTGGTAAAACGGTCTCGAGGGAGAC
          1 TTTTGGTAAAACGGTCTCGAGGGAGAC

       1742 AAATGCATCA


Statistics
Matches: 145,  Mismatches: 6, Indels: 9
        0.91            0.04        0.06

Matches are distributed among these distances:
 125   32  0.22
 126    1  0.01
 129    1  0.01
 131    5  0.03
 132  106  0.73

ACGTcount: A:0.24, C:0.15, G:0.24, T:0.36


Consensus pattern (125 bp):   
TTTTGGTAAAACGGTCTCGAGGGAGACGTTCATCTTTTACGACTCAAAGAATGTTTTTATTTTGG
TAAAACGGTCTCGTGGGAGACGTTCGTTTTACCTAAGTTACGATTCAAGGATCGTTTTTA

Found at i:3579 original size:29 final size:32

Alignment explanation


    Indices: 3522--3582  Score: 83
    Period size: 33  Copynumber: 2.0  Consensus size: 32

       3512 CATTGCTGTT

                                             
       3522 ACAAACTATTACTGACAATAATATATTCTTCAA
          1 ACAAACTATTACTGA-AATAATATATTCTTCAA

                   *                       
       3555 ACAAACTGTTACTG-AA-AATAT-TTCTTCA
          1 ACAAACTATTACTGAAATAATATATTCTTCA

       3583 GGTGAATAGC


Statistics
Matches: 27,  Mismatches: 1, Indels: 4
        0.84            0.03        0.12

Matches are distributed among these distances:
  29    7  0.26
  30    5  0.19
  31    2  0.07
  33   13  0.48

ACGTcount: A:0.43, C:0.18, G:0.05, T:0.34


Consensus pattern (32 bp):   
ACAAACTATTACTGAAATAATATATTCTTCAA
Done.