Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006516.1 Corchorus capsularis cultivar CVL-1 contig06537, 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: 22476
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32


Found at i:3453 original size:31 final size:31

Alignment explanation


    Indices: 3418--3493  Score: 109
    Period size: 30  Copynumber: 2.5  Consensus size: 31

       3408 GTCAAATAAC

                     *      *        *     
       3418 CAATTTGAGTCTAAACCTTTCAAAAGTTGCT
          1 CAATTTGAGCCTAAACATTTCAAAAATTGCT

                                           
       3449 CAA-TTGAGCCTAAACATTTCAAAAATTGCT
          1 CAATTTGAGCCTAAACATTTCAAAAATTGCT

                      *    
       3479 CAATTTGAGCTTAAA
          1 CAATTTGAGCCTAAA

       3494 AACTAAAAAA


Statistics
Matches: 40,  Mismatches: 4, Indels: 2
        0.87            0.09        0.04

Matches are distributed among these distances:
  30   27  0.68
  31   13  0.32

ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33


Consensus pattern (31 bp):   
CAATTTGAGCCTAAACATTTCAAAAATTGCT

Found at i:14557 original size:21 final size:21

Alignment explanation


    Indices: 14531--14581  Score: 84
    Period size: 21  Copynumber: 2.4  Consensus size: 21

      14521 TTGAAGCCGA

                      *        * 
      14531 AAATCATGTTGCTGTGTCCTC
          1 AAATCATGTTACTGTGTCCGC

                                 
      14552 AAATCATGTTACTGTGTCCGC
          1 AAATCATGTTACTGTGTCCGC

                     
      14573 AAATCATGT
          1 AAATCATGT

      14582 AGATTGATTC


Statistics
Matches: 28,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  21   28  1.00

ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35


Consensus pattern (21 bp):   
AAATCATGTTACTGTGTCCGC

Found at i:15719 original size:72 final size:72

Alignment explanation


    Indices: 15596--15737  Score: 196
    Period size: 72  Copynumber: 2.0  Consensus size: 72

      15586 AAAGACAAGC

                         *         *    *                                    
      15596 CAAGGTGTGAACATTGTCAAAAGGCGGGGCACACGAAAGACCAATGCTATGAGATCATTGGATAT
          1 CAAGGTGTGAACACTGTCAAAAGCCGGGACACACGAAAGACCAATGCTATGAGATCATTGGATAT

                   
      15661 CCTGCTG
         66 CCTGCTG

                     *         *           *         *     *                 
      15668 CAAGGTGTGGACACTGTCAGAAGCCGGGACATAC-AAACGATCAATGTTATGAGATCATTGGATA
          1 CAAGGTGTGAACACTGTCAAAAGCCGGGACACACGAAA-GACCAATGCTATGAGATCATTGGATA

                  
      15732 TCCTGC
         65 TCCTGC

      15738 GGGGTGGCGG


Statistics
Matches: 61,  Mismatches: 8, Indels: 2
        0.86            0.11        0.03

Matches are distributed among these distances:
  71    3  0.05
  72   58  0.95

ACGTcount: A:0.32, C:0.20, G:0.27, T:0.22


Consensus pattern (72 bp):   
CAAGGTGTGAACACTGTCAAAAGCCGGGACACACGAAAGACCAATGCTATGAGATCATTGGATAT
CCTGCTG

Found at i:16644 original size:33 final size:33

Alignment explanation


    Indices: 16607--16713  Score: 135
    Period size: 33  Copynumber: 3.2  Consensus size: 33

      16597 AGCACTAGTG

                    *            *           
      16607 ACCGGCCATGCGACTTGGAGAAGTCCGGCCAAC
          1 ACCGGCCACGCGACTTGGAGATGTCCGGCCAAC

                      *    *       *         
      16640 ACCGGCCACGTGACTCGGAGATGCCCGGCCAAC
          1 ACCGGCCACGCGACTTGGAGATGTCCGGCCAAC

                          *    *             
      16673 ACCGGCCACGCGACATGGACATGTCCGGCC-AC
          1 ACCGGCCACGCGACTTGGAGATGTCCGGCCAAC

                     
      16705 AACCGGCCA
          1 -ACCGGCCA

      16714 TCGCTAGGCG


Statistics
Matches: 63,  Mismatches: 10, Indels: 2
        0.84            0.13        0.03

Matches are distributed among these distances:
  32    2  0.03
  33   61  0.97

ACGTcount: A:0.23, C:0.38, G:0.29, T:0.09


Consensus pattern (33 bp):   
ACCGGCCACGCGACTTGGAGATGTCCGGCCAAC
Done.