Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012927.1 Corchorus capsularis cultivar CVL-1 contig12948, 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: 11927
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31


Found at i:561 original size:19 final size:18

Alignment explanation


    Indices: 528--563  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

        518 TTGAAATAAT

                              
        528 TCTTCAATGATCTTCAAA
          1 TCTTCAATGATCTTCAAA

                     *        
        546 TCTTCAAATTATCTTCAA
          1 TCTTC-AATGATCTTCAA

        564 GAAATCTTGA


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

Found at i:8341 original size:33 final size:33

Alignment explanation


    Indices: 8303--8407  Score: 122
    Period size: 33  Copynumber: 3.2  Consensus size: 33

       8293 CGCGAGTGAT

                  *            *             
       8303 CGGCCATGCGACTTGGAGAAGCCCGGCCAACAC
          1 CGGCCACGCGACTTGGAGATGCCCGGCCAACAC

                   *     *               *   
       8336 CGGCCACACGACTCGGAGATGCCCGGCCATCAC
          1 CGGCCACGCGACTTGGAGATGCCCGGCCAACAC

            *           *    *                
       8369 TGGCCACGCGACATGGACATGCCCGGCC-ACAAC
          1 CGGCCACGCGACTTGGAGATGCCCGGCCAAC-AC

                  
       8402 CGGCCA
          1 CGGCCA

       8408 TCGCTTGGCG


Statistics
Matches: 59,  Mismatches: 12, Indels: 2
        0.81            0.16        0.03

Matches are distributed among these distances:
  32    1  0.02
  33   58  0.98

ACGTcount: A:0.23, C:0.40, G:0.29, T:0.09


Consensus pattern (33 bp):   
CGGCCACGCGACTTGGAGATGCCCGGCCAACAC

Found at i:9496 original size:5 final size:5

Alignment explanation


    Indices: 9481--9515  Score: 61
    Period size: 5  Copynumber: 7.0  Consensus size: 5

       9471 GTTATATCGA

                   *                                 
       9481 AAAAT ATAAT AAAAT AAAAT AAAAT AAAAT AAAAT
          1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT

       9516 TTCGACCAGA


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

Matches are distributed among these distances:
   5   28  1.00

ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23


Consensus pattern (5 bp):   
AAAAT

Found at i:10988 original size:33 final size:33

Alignment explanation


    Indices: 10905--10997  Score: 123
    Period size: 33  Copynumber: 2.8  Consensus size: 33

      10895 TTTTAGATGA

                               *  **   *     
      10905 TGTTTGCGATGATACTAAACCTAATTTGAGTGT
          1 TGTTTGCGATGATACTAAATCTGTTTTAAGTGT

                   *    *                    
      10938 TGTTTGCAATGACACTAAATCTGTTTTAAGTGT
          1 TGTTTGCGATGATACTAAATCTGTTTTAAGTGT

                  *                    
      10971 TGTTTGTGATGATACTAAATCTGTTTT
          1 TGTTTGCGATGATACTAAATCTGTTTT

      10998 GGATGCTAAT


Statistics
Matches: 51,  Mismatches: 9, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  33   51  1.00

ACGTcount: A:0.26, C:0.11, G:0.19, T:0.44


Consensus pattern (33 bp):   
TGTTTGCGATGATACTAAATCTGTTTTAAGTGT

Found at i:11053 original size:33 final size:32

Alignment explanation


    Indices: 11016--11097  Score: 84
    Period size: 27  Copynumber: 2.7  Consensus size: 32

      11006 ATTGTGATGA

                                             
      11016 AAATAATTATGTTTTGGTTGATCATAGCATTAC
          1 AAATAA-TATGTTTTGGTTGATCATAGCATTAC

                      *                   * 
      11049 AAAT-A-A--CTTT-GTTGATCATAGCATTGC
          1 AAATAATATGTTTTGGTTGATCATAGCATTAC

                    *             
      11076 AAATAATCCTGTTTTGGTTGAT
          1 AAATAAT-ATGTTTTGGTTGAT

      11098 GGCATTGAAA


Statistics
Matches: 39,  Mismatches: 4, Indels: 12
        0.71            0.07        0.22

Matches are distributed among these distances:
  27   20  0.51
  28    4  0.10
  30    1  0.03
  32    4  0.10
  33   10  0.26

ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41


Consensus pattern (32 bp):   
AAATAATATGTTTTGGTTGATCATAGCATTAC
Done.