Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010100.1 Corchorus olitorius cultivar O-4 contig10132, 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: 6327
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34


Found at i:3578 original size:33 final size:31

Alignment explanation


    Indices: 3506--3595  Score: 100
    Period size: 30  Copynumber: 3.0  Consensus size: 31

       3496 TTTTGCTCGT

                                           *
       3506 CATACTTCGGAATATCATGAT-TTTTTTTTTT
          1 CATACTTCGG-ATATCATGATGTTTTTTTTTG

                 *                           
       3537 CA-A-ATCGGATATCATGCATGTTTTTTTTTGG
          1 CATACTTCGGATATCATG-ATGTTTTTTTTT-G

                                          
       3568 CATACTTCGGATATCAT-A-GTTTTTTTTT
          1 CATACTTCGGATATCATGATGTTTTTTTTT

       3596 TAAATCGAAA


Statistics
Matches: 51,  Mismatches: 3, Indels: 11
        0.78            0.05        0.17

Matches are distributed among these distances:
  28    8  0.16
  29    6  0.12
  30   20  0.39
  31    5  0.10
  32    1  0.02
  33   11  0.22

ACGTcount: A:0.22, C:0.13, G:0.13, T:0.51


Consensus pattern (31 bp):   
CATACTTCGGATATCATGATGTTTTTTTTTG

Found at i:3590 original size:29 final size:30

Alignment explanation


    Indices: 3506--3594  Score: 85
    Period size: 29  Copynumber: 2.9  Consensus size: 30

       3496 TTTTGCTCGT

                                *        **
       3506 CATACTTCGGAATATCATGATTTTTTTTTTT
          1 CATACTTCGG-ATATCATGAGTTTTTTTTGG

                 *                           
       3537 CA-A-ATCGGATATCATGCATGTTTTTTTTTGG
          1 CATACTTCGGATATCATG-A-G-TTTTTTTTGG

                                        
       3568 CATACTTCGGATATCAT-AGTTTTTTTT
          1 CATACTTCGGATATCATGAGTTTTTTTT

       3595 TTAAATCGAA


Statistics
Matches: 48,  Mismatches: 5, Indels: 12
        0.74            0.08        0.18

Matches are distributed among these distances:
  28    8  0.17
  29   13  0.27
  30    2  0.04
  31   13  0.27
  32    1  0.02
  33   11  0.23

ACGTcount: A:0.22, C:0.13, G:0.13, T:0.51


Consensus pattern (30 bp):   
CATACTTCGGATATCATGAGTTTTTTTTGG

Found at i:4906 original size:5 final size:5

Alignment explanation


    Indices: 4896--4931  Score: 58
    Period size: 5  Copynumber: 7.6  Consensus size: 5

       4886 TAATTACTAG

                                                         
       4896 TTATC TTATC TTA-C -TATC TTATC TTATC TTATC TTA
          1 TTATC TTATC TTATC TTATC TTATC TTATC TTATC TTA

       4932 CTAATTTACT


Statistics
Matches: 29,  Mismatches: 0, Indels: 4
        0.88            0.00        0.12

Matches are distributed among these distances:
   3    2  0.07
   4    2  0.07
   5   25  0.86

ACGTcount: A:0.22, C:0.19, G:0.00, T:0.58


Consensus pattern (5 bp):   
TTATC

Found at i:5207 original size:15 final size:15

Alignment explanation


    Indices: 5152--5211  Score: 52
    Period size: 15  Copynumber: 3.9  Consensus size: 15

       5142 AATAATGCAC

                             
       5152 TTAATTAATAATATACT
          1 TTAATT-ATAATATA-T

                      *   * 
       5169 TCTAA-TA-ATTATTT
          1 T-TAATTATAATATAT

                            
       5183 TTAGATTATAATATAT
          1 TTA-ATTATAATATAT

                         
       5199 TTAATTATAATAT
          1 TTAATTATAATAT

       5212 TAATTTATAG


Statistics
Matches: 35,  Mismatches: 4, Indels: 10
        0.71            0.08        0.20

Matches are distributed among these distances:
  13    2  0.06
  14    3  0.09
  15   16  0.46
  16    9  0.26
  17    2  0.06
  18    3  0.09

ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52


Consensus pattern (15 bp):   
TTAATTATAATATAT
Done.