Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010310.1 Corchorus olitorius cultivar O-4 contig10342, 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, 947

Length: 1579
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37


Found at i:531 original size:16 final size:16

Alignment explanation


    Indices: 510--542  Score: 57
    Period size: 16  Copynumber: 2.1  Consensus size: 16

        500 TGCTGATTCT

                            
        510 GTCCATCTGTCCAGTC
          1 GTCCATCTGTCCAGTC

                        *   
        526 GTCCATCTGTCCCGTC
          1 GTCCATCTGTCCAGTC

             
        542 G
          1 G

        543 CCGACATATT


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  16   16  1.00

ACGTcount: A:0.09, C:0.39, G:0.21, T:0.30


Consensus pattern (16 bp):   
GTCCATCTGTCCAGTC

Found at i:1516 original size:22 final size:22

Alignment explanation


    Indices: 1424--1551  Score: 84
    Period size: 22  Copynumber: 5.8  Consensus size: 22

       1414 TGGATATTTT

                                  *
       1424 TATGAAATTTTGATAACC-ACAT
          1 TATGAAATTTTGATAACCTA-AC

                               *  * 
       1446 TATGAAATTTTTTGATAA-TTATC
          1 TATGAAA--TTTTGATAACCTAAC

                     *       * ** 
       1469 TATGAAATTGTGATAA-ATTCC
          1 TATGAAATTTTGATAACCTAAC

                    *              
       1490 ATATGAAACTTTGATAACCTAAC
          1 -TATGAAATTTTGATAACCTAAC

                       *        ** 
       1513 TATGAAATTTTAATAAACCTTCC
          1 TATGAAATTTTGAT-AACCTAAC

                             
       1536 TATGAAATTTTG-TAAC
          1 TATGAAATTTTGATAAC

       1552 TTTCCCTATG


Statistics
Matches: 83,  Mismatches: 17, Indels: 13
        0.73            0.15        0.12

Matches are distributed among these distances:
  21   13  0.16
  22   34  0.41
  23   26  0.31
  24   10  0.12

ACGTcount: A:0.39, C:0.12, G:0.09, T:0.40


Consensus pattern (22 bp):   
TATGAAATTTTGATAACCTAAC

Found at i:1529 original size:44 final size:43

Alignment explanation


    Indices: 1468--1551  Score: 107
    Period size: 44  Copynumber: 1.9  Consensus size: 43

       1458 TGATAATTAT

                        *                                
       1468 CTATGAAATTGTGATAAA-TTCCATATGAAACTTTGATAACCTAA
          1 CTATGAAATTGTAATAAACTTCC-TATGAAACTTTG-TAACCTAA

                      *                    *        
       1512 CTATGAAATTTTAATAAACCTTCCTATGAAATTTTGTAAC
          1 CTATGAAATTGTAATAAA-CTTCCTATGAAACTTTGTAAC

       1552 TTTCCCTATG


Statistics
Matches: 35,  Mismatches: 3, Indels: 4
        0.83            0.07        0.10

Matches are distributed among these distances:
  44   20  0.57
  45   11  0.31
  46    4  0.11

ACGTcount: A:0.39, C:0.14, G:0.10, T:0.37


Consensus pattern (43 bp):   
CTATGAAATTGTAATAAACTTCCTATGAAACTTTGTAACCTAA

Found at i:1538 original size:23 final size:23

Alignment explanation


    Indices: 1468--1569  Score: 88
    Period size: 22  Copynumber: 4.6  Consensus size: 23

       1458 TGATAATTAT

                      *            
       1468 CTATGAAATTGTGATAAA--TTC
          1 CTATGAAATTTTGATAAACCTTC

                     *            **
       1489 CATATGAAACTTTGAT-AACCTAA
          1 C-TATGAAATTTTGATAAACCTTC

                        *          
       1512 CTATGAAATTTTAATAAACCTTC
          1 CTATGAAATTTTGATAAACCTTC

                               *    
       1535 CTATGAAATTTTG-T-AACTTTCC
          1 CTATGAAATTTTGATAAACCTT-C

                  *      
       1557 CTATGAGATTTTG
          1 CTATGAAATTTTG

       1570 TTAATCTCCT


Statistics
Matches: 65,  Mismatches: 11, Indels: 9
        0.76            0.13        0.11

Matches are distributed among these distances:
  21    8  0.12
  22   38  0.58
  23   19  0.29

ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39


Consensus pattern (23 bp):   
CTATGAAATTTTGATAAACCTTC

Done.