Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019787.1 Corchorus olitorius cultivar O-4 contig19820, 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: 6519
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31


Found at i:238 original size:13 final size:12

Alignment explanation


    Indices: 195--249  Score: 51
    Period size: 13  Copynumber: 4.5  Consensus size: 12

        185 TCATGCACCC

                       * 
        195 AAAACATTTTATT
          1 AAAACA-TTTAAT

                         
        208 AAAACCATTT-AT
          1 AAAA-CATTTAAT

                         
        220 AAAACATATTAAT
          1 AAAACAT-TTAAT

                   *    
        233 AAAACA-GTAAT
          1 AAAACATTTAAT

                  
        244 AAAACA
          1 AAAACA

        250 GTTCCTCAAC


Statistics
Matches: 37,  Mismatches: 2, Indels: 8
        0.79            0.04        0.17

Matches are distributed among these distances:
  11   13  0.35
  12    7  0.19
  13   15  0.41
  14    2  0.05

ACGTcount: A:0.58, C:0.11, G:0.02, T:0.29


Consensus pattern (12 bp):   
AAAACATTTAAT

Found at i:1433 original size:18 final size:18

Alignment explanation


    Indices: 1410--1452  Score: 50
    Period size: 18  Copynumber: 2.4  Consensus size: 18

       1400 TTAAATTCCC

                              
       1410 TTATTTCCCTTTTCCCTT
          1 TTATTTCCCTTTTCCCTT

                  ***    *    
       1428 TTATTTATTTTTTTCCTT
          1 TTATTTCCCTTTTCCCTT

                   
       1446 TTATTTC
          1 TTATTTC

       1453 AATTTGGGTC


Statistics
Matches: 20,  Mismatches: 5, Indels: 0
        0.80            0.20        0.00

Matches are distributed among these distances:
  18   20  1.00

ACGTcount: A:0.09, C:0.21, G:0.00, T:0.70


Consensus pattern (18 bp):   
TTATTTCCCTTTTCCCTT

Found at i:1531 original size:18 final size:18

Alignment explanation


    Indices: 1508--1542  Score: 52
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       1498 TGGGCCCATT

                  *    *      
       1508 TTATTTCATTTCATTTCA
          1 TTATTTAATTTAATTTCA

                             
       1526 TTATTTAATTTAATTTC
          1 TTATTTAATTTAATTTC

       1543 TTTTTTCGCT


Statistics
Matches: 15,  Mismatches: 2, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  18   15  1.00

ACGTcount: A:0.26, C:0.11, G:0.00, T:0.63


Consensus pattern (18 bp):   
TTATTTAATTTAATTTCA

Found at i:1640 original size:37 final size:37

Alignment explanation


    Indices: 1562--1634  Score: 101
    Period size: 38  Copynumber: 1.9  Consensus size: 37

       1552 TTGGGCCAAG

                         *        *  *           
       1562 GCTGGGCCGCCGCTGGCCCGCGTGCTTGGCCTGGCGC
          1 GCTGGGCCGCCGCAGGCCCGCGCGCCTGGCCTGGCGC

                       *                        
       1599 GCTGGGCCGCTTGCAGGCCCGCGCGCCTGGCCTGGC
          1 GCTGGGCCGC-CGCAGGCCCGCGCGCCTGGCCTGGC

       1635 TGCTGGCCCA


Statistics
Matches: 31,  Mismatches: 4, Indels: 1
        0.86            0.11        0.03

Matches are distributed among these distances:
  37   10  0.32
  38   21  0.68

ACGTcount: A:0.01, C:0.41, G:0.42, T:0.15


Consensus pattern (37 bp):   
GCTGGGCCGCCGCAGGCCCGCGCGCCTGGCCTGGCGC

Found at i:1689 original size:26 final size:26

Alignment explanation


    Indices: 1652--1710  Score: 84
    Period size: 26  Copynumber: 2.3  Consensus size: 26

       1642 CCAAGTTGGG

                         *             
       1652 CTTCTTTCTTTTTTCTT-TTCTTCTTT
          1 CTTCTTTCTTTTTCCTTCTTCTTC-TT

                   *                  
       1678 CTTCTTTTTTTTTCCTTCTTCTTCTT
          1 CTTCTTTCTTTTTCCTTCTTCTTCTT

                   
       1704 CTTCTTT
          1 CTTCTTT

       1711 GTGGCTACCG


Statistics
Matches: 30,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  26   24  0.80
  27    6  0.20

ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75


Consensus pattern (26 bp):   
CTTCTTTCTTTTTCCTTCTTCTTCTT
Done.