Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011856.1 Corchorus capsularis cultivar CVL-1 contig11877, 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: 42249
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31


Found at i:13870 original size:16 final size:15

Alignment explanation


    Indices: 13845--13878  Score: 50
    Period size: 16  Copynumber: 2.2  Consensus size: 15

      13835 GGAATAAAAA

                           
      13845 TTAAATATTTTTACT
          1 TTAAATATTTTTACT

                          * 
      13860 TTAATATATTTTTATT
          1 TTAA-ATATTTTTACT

               
      13876 TTA
          1 TTA

      13879 TTGAAACGTA


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

Matches are distributed among these distances:
  15    4  0.24
  16   13  0.76

ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65


Consensus pattern (15 bp):   
TTAAATATTTTTACT

Found at i:30034 original size:13 final size:13

Alignment explanation


    Indices: 30016--30042  Score: 54
    Period size: 13  Copynumber: 2.1  Consensus size: 13

      30006 ATAATTATTG

                         
      30016 TTTGCTTTATTAA
          1 TTTGCTTTATTAA

                         
      30029 TTTGCTTTATTAA
          1 TTTGCTTTATTAA

             
      30042 T
          1 T

      30043 CTGTTTTAGA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   14  1.00

ACGTcount: A:0.22, C:0.07, G:0.07, T:0.63


Consensus pattern (13 bp):   
TTTGCTTTATTAA

Found at i:30849 original size:19 final size:18

Alignment explanation


    Indices: 30817--30852  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

      30807 TTGAAATAAT

                     *        
      30817 TCTTCAATTGTCTTCAAA
          1 TCTTCAATTATCTTCAAA

                              
      30835 TCTTCAAATTATCTTCAA
          1 TCTTC-AATTATCTTCAA

      30853 GAAATCTTCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    5  0.31
  19   11  0.69

ACGTcount: A:0.31, C:0.22, G:0.03, T:0.44


Consensus pattern (18 bp):   
TCTTCAATTATCTTCAAA

Found at i:31971 original size:69 final size:70

Alignment explanation


    Indices: 31856--31995  Score: 214
    Period size: 69  Copynumber: 2.0  Consensus size: 70

      31846 AAAACTAACA

                                             *     *                         
      31856 ACTAAGGAAAAAAATGGTGGAAGCACCATTAATTACATTTCAATGCTAAAATTACATATAAAGAC
          1 ACTAAGGAAAAAAATGGTGGAAGCACCATTAATAACATTCCAATGCTAAAATTACATATAAAGAC

                 
      31921 AATGC
         66 AATGC

                                    *                                        
      31926 ACTAAGG-AAAAAATGGTAGG-AGTACCATTAATAACA-TCCAGATGCTAAAATTACATATAAAG
          1 ACTAAGGAAAAAAATGGT-GGAAGCACCATTAATAACATTCCA-ATGCTAAAATTACATATAAAG

                   
      31988 ACAATGC
         64 ACAATGC

             
      31995 A
          1 A

      31996 TTTCAAGCAA


Statistics
Matches: 65,  Mismatches: 3, Indels: 5
        0.89            0.04        0.07

Matches are distributed among these distances:
  68    3  0.05
  69   53  0.82
  70    9  0.14

ACGTcount: A:0.48, C:0.14, G:0.15, T:0.23


Consensus pattern (70 bp):   
ACTAAGGAAAAAAATGGTGGAAGCACCATTAATAACATTCCAATGCTAAAATTACATATAAAGAC
AATGC

Found at i:40006 original size:19 final size:18

Alignment explanation


    Indices: 39973--40008  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

      39963 TTGAAATAAT

                              
      39973 TCTTCAATGATCTTCAAA
          1 TCTTCAATGATCTTCAAA

                     *        
      39991 TCTTCAAATTATCTTCAA
          1 TCTTC-AATGATCTTCAA

      40009 GAAATCTTCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    5  0.31
  19   11  0.69

ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42


Consensus pattern (18 bp):   
TCTTCAATGATCTTCAAA
Done.