Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015232.1 Corchorus capsularis cultivar CVL-1 contig15253, 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: 28498
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.30


Found at i:6331 original size:2 final size:2

Alignment explanation


    Indices: 6324--6350  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

       6314 ATATTATAAC

                                                    
       6324 TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA T

       6351 CCATTTAGTA


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


Consensus pattern (2 bp):   
TA

Found at i:22302 original size:21 final size:20

Alignment explanation


    Indices: 22261--22304  Score: 52
    Period size: 21  Copynumber: 2.1  Consensus size: 20

      22251 TATAACACGC

                    *     * *   
      22261 GACTGACACATGCTGATATG
          1 GACTGACAAATGCTAACATG

                                 
      22281 GACTGAGCAAATGCTAACATG
          1 GACTGA-CAAATGCTAACATG

               
      22302 GAC
          1 GAC

      22305 AATAAGTATA


Statistics
Matches: 20,  Mismatches: 3, Indels: 1
        0.83            0.12        0.04

Matches are distributed among these distances:
  20    6  0.30
  21   14  0.70

ACGTcount: A:0.34, C:0.20, G:0.25, T:0.20


Consensus pattern (20 bp):   
GACTGACAAATGCTAACATG

Found at i:23701 original size:30 final size:31

Alignment explanation


    Indices: 23645--23710  Score: 89
    Period size: 30  Copynumber: 2.2  Consensus size: 31

      23635 TTTTTGCCTG

                    *            *         
      23645 AATTGACATAAAACGATAACGTTATATCCTA
          1 AATTGACACAAAACGATAACGGTATATCCTA

                        *                 *
      23676 AATTGACACAAATC-ATAACGGTATATCCTG
          1 AATTGACACAAAACGATAACGGTATATCCTA

                 
      23706 AATTG
          1 AATTG

      23711 CATTTTCGGC


Statistics
Matches: 31,  Mismatches: 4, Indels: 1
        0.86            0.11        0.03

Matches are distributed among these distances:
  30   19  0.61
  31   12  0.39

ACGTcount: A:0.42, C:0.17, G:0.12, T:0.29


Consensus pattern (31 bp):   
AATTGACACAAAACGATAACGGTATATCCTA

Found at i:27238 original size:3 final size:3

Alignment explanation


    Indices: 27230--27279  Score: 91
    Period size: 3  Copynumber: 16.7  Consensus size: 3

      27220 CGATTTACTT

                                              *                            
      27230 TTA TTA TTA TTA TTA TTA TTA TTA TTG TTA TTA TTA TTA TTA TTA TTA
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA

              
      27278 TT
          1 TT

      27280 TTCTTTTTTA


Statistics
Matches: 45,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
   3   45  1.00

ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68


Consensus pattern (3 bp):   
TTA

Found at i:28354 original size:2 final size:2

Alignment explanation


    Indices: 28347--28402  Score: 71
    Period size: 2  Copynumber: 28.5  Consensus size: 2

      28337 AAATTAGAGA

                                                     *  *                  
      28347 AT AT AT AT AT AT AT AT AT AT AT AT CA- AA AG A- 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 AT AT

                                  
      28388 AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT A

      28403 CTACATATTA


Statistics
Matches: 50,  Mismatches: 1, Indels: 6
        0.88            0.02        0.11

Matches are distributed among these distances:
   1    2  0.04
   2   47  0.94
   3    1  0.02

ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43


Consensus pattern (2 bp):   
AT

Done.