Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013462.1 Corchorus olitorius cultivar O-4 contig13495, 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: 26151
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31


Found at i:4472 original size:12 final size:12

Alignment explanation


    Indices: 4455--4496  Score: 57
    Period size: 12  Copynumber: 3.5  Consensus size: 12

       4445 ACGAAAATGG

                        
       4455 CTCTCCAACAAC
          1 CTCTCCAACAAC

                        
       4467 CTCTCCAACAAC
          1 CTCTCCAACAAC

                **  *   
       4479 CTCTGAAAAAAC
          1 CTCTCCAACAAC

                  
       4491 CTCTCC
          1 CTCTCC

       4497 TCAGAGTAAA


Statistics
Matches: 25,  Mismatches: 5, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  12   25  1.00

ACGTcount: A:0.33, C:0.45, G:0.02, T:0.19


Consensus pattern (12 bp):   
CTCTCCAACAAC

Found at i:4902 original size:49 final size:48

Alignment explanation


    Indices: 4837--4958  Score: 158
    Period size: 49  Copynumber: 2.5  Consensus size: 48

       4827 AATCTTTTAC

                                       **                 * 
       4837 TTTAC-TGCACTTTTTCTCAATTTTTACTACAAAATTGAACTTTTATT
          1 TTTACTTGCACTTTTTCTCAATTTTTAAGACAAAATTGAACTTTTAAT

                                                    *        
       4884 TTTACTTGCATCTTTTTCTCAATTTTTAAGACAAAATTGATCTTTTAAT
          1 TTTACTTGCA-CTTTTTCTCAATTTTTAAGACAAAATTGAACTTTTAAT

                   *         *         
       4933 TTT-CATCGCACTTTTTATCAATTTTT
          1 TTTAC-TTGCACTTTTTCTCAATTTTT

       4959 GGATAAAATT


Statistics
Matches: 66,  Mismatches: 6, Indels: 5
        0.86            0.08        0.06

Matches are distributed among these distances:
  47    5  0.08
  48   20  0.30
  49   41  0.62

ACGTcount: A:0.26, C:0.16, G:0.05, T:0.52


Consensus pattern (48 bp):   
TTTACTTGCACTTTTTCTCAATTTTTAAGACAAAATTGAACTTTTAAT

Found at i:7002 original size:19 final size:19

Alignment explanation


    Indices: 6952--7002  Score: 61
    Period size: 19  Copynumber: 2.7  Consensus size: 19

       6942 TGTGGGATTT

                               
       6952 TTAATAA-TAATTATTCAA
          1 TTAATAATTAATTATTCAA

              *              *  
       6970 TAAAATAATT-ATTATTTAA
          1 T-TAATAATTAATTATTCAA

                          
       6989 TTAATAATTAATTA
          1 TTAATAATTAATTA

       7003 ATTTCAGCCC


Statistics
Matches: 27,  Mismatches: 3, Indels: 5
        0.77            0.09        0.14

Matches are distributed among these distances:
  18    8  0.30
  19   18  0.67
  20    1  0.04

ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47


Consensus pattern (19 bp):   
TTAATAATTAATTATTCAA

Found at i:7374 original size:13 final size:13

Alignment explanation


    Indices: 7356--7381  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

       7346 AAGGTACCAA

                         
       7356 CAAAAATCATCAC
          1 CAAAAATCATCAC

                         
       7369 CAAAAATCATCAC
          1 CAAAAATCATCAC

       7382 TCATGCCAAG


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.54, C:0.31, G:0.00, T:0.15


Consensus pattern (13 bp):   
CAAAAATCATCAC

Found at i:14845 original size:15 final size:16

Alignment explanation


    Indices: 14821--14860  Score: 55
    Period size: 15  Copynumber: 2.6  Consensus size: 16

      14811 AGAGGTTGAA

                 *          
      14821 AGAAAGCAATTAAAC-
          1 AGAAAACAATTAAACT

                        *   
      14836 AGAAAACAATTATACT
          1 AGAAAACAATTAAACT

                     
      14852 AGAAAACAA
          1 AGAAAACAA

      14861 AACAAAGTAA


Statistics
Matches: 22,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  15   13  0.59
  16    9  0.41

ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15


Consensus pattern (16 bp):   
AGAAAACAATTAAACT

Done.