Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015711.1 Corchorus olitorius cultivar O-4 contig15744, 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: 2812
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.39


Found at i:1039 original size:36 final size:36

Alignment explanation


    Indices: 992--1061  Score: 113
    Period size: 36  Copynumber: 1.9  Consensus size: 36

        982 TCCAATAACC

                         *      *               
        992 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
          1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA

                  *                           
       1028 TTACATTTTTTGTAATTTTGATTATCATATTTCT
          1 TTACATCTTTTGTAATTTTGATTATCATATTTCT

       1062 CCAAAATCTC


Statistics
Matches: 31,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  36   31  1.00

ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60


Consensus pattern (36 bp):   
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA

Found at i:1247 original size:2 final size:2

Alignment explanation


    Indices: 1240--1266  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

       1230 AGAAATAATT

                                                    
       1240 TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA T

       1267 GCGTATCTTT


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:2138 original size:39 final size:40

Alignment explanation


    Indices: 2083--2163  Score: 128
    Period size: 39  Copynumber: 2.0  Consensus size: 40

       2073 ATACCTAAGA

                                             *      
       2083 ATTTAATTAATATAAGTATTTCAGTTATTATA-GTATTAC
          1 ATTTAATTAATATAAGTATTTCAGTTATTATATATATTAC

                       *         *                  
       2122 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
          1 ATTTAATTAATATAAGTATTTCAGTTATTATATATATTAC

              
       2162 AT
          1 AT

       2164 AGGAATTAAA


Statistics
Matches: 38,  Mismatches: 3, Indels: 1
        0.90            0.07        0.02

Matches are distributed among these distances:
  39   30  0.79
  40    8  0.21

ACGTcount: A:0.38, C:0.04, G:0.07, T:0.51


Consensus pattern (40 bp):   
ATTTAATTAATATAAGTATTTCAGTTATTATATATATTAC

Found at i:2518 original size:39 final size:40

Alignment explanation


    Indices: 2463--2543  Score: 128
    Period size: 39  Copynumber: 2.0  Consensus size: 40

       2453 ATACCTAAGA

                                             *      
       2463 ATTTAATTAATATAAGTATTTCAGTTATTATA-GTATTAC
          1 ATTTAATTAATATAAGTATTTCAGTTATTATATATATTAC

                       *         *                  
       2502 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
          1 ATTTAATTAATATAAGTATTTCAGTTATTATATATATTAC

              
       2542 AT
          1 AT

       2544 CGGAATTAAA


Statistics
Matches: 38,  Mismatches: 3, Indels: 1
        0.90            0.07        0.02

Matches are distributed among these distances:
  39   30  0.79
  40    8  0.21

ACGTcount: A:0.38, C:0.04, G:0.07, T:0.51


Consensus pattern (40 bp):   
ATTTAATTAATATAAGTATTTCAGTTATTATATATATTAC
Done.