Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018342.1 Corchorus olitorius cultivar O-4 contig18375, 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: 3290
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34


Found at i:791 original size:11 final size:10

Alignment explanation


    Indices: 775--828  Score: 54
    Period size: 11  Copynumber: 4.9  Consensus size: 10

        765 AACCTTTTGA

                       
        775 TTTTTCTTTCT
          1 TTTTTCTTT-T

                       
        786 TTTTTCTCTTT
          1 TTTTTCT-TTT

                      
        797 TTTTTCTTTT
          1 TTTTTCTTTT

                 *       
        807 GCTTTCTCTTTTT
          1 --TTTTTC-TTTT

                     
        820 TTTTTCTTT
          1 TTTTTCTTT

        829 AGATTGCTGC


Statistics
Matches: 37,  Mismatches: 2, Indels: 9
        0.77            0.04        0.19

Matches are distributed among these distances:
  10    6  0.16
  11   20  0.54
  12    7  0.19
  13    4  0.11

ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81


Consensus pattern (10 bp):   
TTTTTCTTTT

Found at i:1544 original size:14 final size:13

Alignment explanation


    Indices: 1479--1543  Score: 87
    Period size: 14  Copynumber: 4.8  Consensus size: 13

       1469 ACTCAAAACC

                          
       1479 TTTTTGAAAACTCA
          1 TTTTTGAAAA-TCA

                         
       1493 TTTTTGAAAATCA
          1 TTTTTGAAAATCA

                           
       1506 TTTCTTGAAAA-CAA
          1 TTT-TTGAAAATC-A

                          
       1520 TTTCTTGAAAATCA
          1 TTT-TTGAAAATCA

                      
       1534 TTTTTGAAAA
          1 TTTTTGAAAA

       1544 ACGTCCTTTA


Statistics
Matches: 48,  Mismatches: 0, Indels: 7
        0.87            0.00        0.13

Matches are distributed among these distances:
  13   14  0.29
  14   33  0.69
  15    1  0.02

ACGTcount: A:0.38, C:0.11, G:0.08, T:0.43


Consensus pattern (13 bp):   
TTTTTGAAAATCA

Found at i:1545 original size:28 final size:27

Alignment explanation


    Indices: 1479--1543  Score: 96
    Period size: 28  Copynumber: 2.4  Consensus size: 27

       1469 ACTCAAAACC

                        *              
       1479 TTTTTGAAAACTCATTTTTGAAAATCA
          1 TTTTTGAAAACTAATTTTTGAAAATCA

                                         
       1506 TTTCTTGAAAAC-AATTTCTTGAAAATCA
          1 TTT-TTGAAAACTAATTT-TTGAAAATCA

                      
       1534 TTTTTGAAAA
          1 TTTTTGAAAA

       1544 ACGTCCTTTA


Statistics
Matches: 35,  Mismatches: 1, Indels: 4
        0.88            0.03        0.10

Matches are distributed among these distances:
  27   14  0.40
  28   21  0.60

ACGTcount: A:0.38, C:0.11, G:0.08, T:0.43


Consensus pattern (27 bp):   
TTTTTGAAAACTAATTTTTGAAAATCA
Done.