Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01007730.1 Corchorus olitorius cultivar O-4 contig07756, 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: 2236
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37


Found at i:1439 original size:30 final size:29

Alignment explanation


    Indices: 1369--1445  Score: 93
    Period size: 29  Copynumber: 2.6  Consensus size: 29

       1359 GGATGTGGCA

                *                         
       1369 AAAAATACAAT-GTTATGGGAATTAATTTT
          1 AAAAGTACAATGGTT-TGGGAATTAATTTT

                               *    *    
       1398 AAAAGTACAATGGTTTGGGGATTATTTTT
          1 AAAAGTACAATGGTTTGGGAATTAATTTT

                 *             
       1427 AAGAATTACAATGGTTTGG
          1 AA-AAGTACAATGGTTTGG

       1446 TCAAAAACTC


Statistics
Matches: 42,  Mismatches: 4, Indels: 3
        0.86            0.08        0.06

Matches are distributed among these distances:
  29   24  0.57
  30   18  0.43

ACGTcount: A:0.38, C:0.04, G:0.21, T:0.38


Consensus pattern (29 bp):   
AAAAGTACAATGGTTTGGGAATTAATTTT

Found at i:1617 original size:16 final size:17

Alignment explanation


    Indices: 1582--1625  Score: 54
    Period size: 16  Copynumber: 2.6  Consensus size: 17

       1572 GTTATATATT

                         *    
       1582 AAATCAATATATTTAAGC
          1 AAATCAAT-TATTCAAGC

                             
       1600 AAATCAATT-TTCAAGC
          1 AAATCAATTATTCAAGC

               *      
       1616 AAACCAATTA
          1 AAATCAATTA

       1626 AACAAATCAA


Statistics
Matches: 23,  Mismatches: 2, Indels: 3
        0.82            0.07        0.11

Matches are distributed among these distances:
  16   14  0.61
  17    1  0.04
  18    8  0.35

ACGTcount: A:0.50, C:0.16, G:0.05, T:0.30


Consensus pattern (17 bp):   
AAATCAATTATTCAAGC

Found at i:2063 original size:11 final size:12

Alignment explanation


    Indices: 2033--2062  Score: 51
    Period size: 12  Copynumber: 2.5  Consensus size: 12

       2023 TACTATATTG

                   *    
       2033 AAATTTTTCATT
          1 AAATTTTGCATT

                        
       2045 AAATTTTGCATT
          1 AAATTTTGCATT

                  
       2057 AAATTT
          1 AAATTT

       2063 GGTAATATTC


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  12   17  1.00

ACGTcount: A:0.37, C:0.07, G:0.03, T:0.53


Consensus pattern (12 bp):   
AAATTTTGCATT
Done.