Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010610.1 Corchorus olitorius cultivar O-4 contig10642, 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: 2666
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.37


Found at i:506 original size:43 final size:43

Alignment explanation


    Indices: 425--509  Score: 131
    Period size: 42  Copynumber: 2.0  Consensus size: 43

        415 ATACCTAAGA

                                             *         
        425 ATTTAATTAATGTATAGTATTTCAGTTATTATAGTATTATTAC
          1 ATTTAATTAATGTATAGTATTTCAGTTATTATAATATTATTAC

                                  *                    
        468 ATTTAATTAATGTA-AGTATTTTAGTTATTAT-ATA-TATTAC
          1 ATTTAATTAATGTATAGTATTTCAGTTATTATAATATTATTAC

              
        508 AT
          1 AT

        510 AGGAATTAAT


Statistics
Matches: 40,  Mismatches: 2, Indels: 3
        0.89            0.04        0.07

Matches are distributed among these distances:
  40    8  0.20
  41    2  0.05
  42   16  0.40
  43   14  0.35

ACGTcount: A:0.36, C:0.04, G:0.08, T:0.52


Consensus pattern (43 bp):   
ATTTAATTAATGTATAGTATTTCAGTTATTATAATATTATTAC

Found at i:1227 original size:25 final size:24

Alignment explanation


    Indices: 1199--1245  Score: 85
    Period size: 25  Copynumber: 1.9  Consensus size: 24

       1189 ATTTTTACAC

                                     
       1199 AAATACCTAAGAATTTGAATTAAAA
          1 AAATACCTAAGAATTT-AATTAAAA

                                  
       1224 AAATACCTAAGAATTTAATTAA
          1 AAATACCTAAGAATTTAATTAA

       1246 TGTATAGTAT


Statistics
Matches: 22,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  24    6  0.27
  25   16  0.73

ACGTcount: A:0.55, C:0.09, G:0.06, T:0.30


Consensus pattern (24 bp):   
AAATACCTAAGAATTTAATTAAAA

Found at i:1310 original size:45 final size:44

Alignment explanation


    Indices: 1236--1320  Score: 136
    Period size: 45  Copynumber: 1.9  Consensus size: 44

       1226 ATACCTAAGA

                                                          
       1236 ATTTAATTAATGTATAGTATTTCAGTTATTATAGTATTATTATTAC
          1 ATTTAATTAATGTATAGTATTTCAGTTATTATA-TA-TATTATTAC

                                  *                 
       1282 ATTTAATTAATGTA-AGTATTTTAGTTATTATATATATTA
          1 ATTTAATTAATGTATAGTATTTCAGTTATTATATATATTA

       1321 CATAGGAATT


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

Matches are distributed among these distances:
  43    5  0.13
  44    2  0.05
  45   17  0.45
  46   14  0.37

ACGTcount: A:0.36, C:0.02, G:0.08, T:0.53


Consensus pattern (44 bp):   
ATTTAATTAATGTATAGTATTTCAGTTATTATATATATTATTAC

Found at i:1333 original size:45 final size:46

Alignment explanation


    Indices: 1238--1334  Score: 119
    Period size: 45  Copynumber: 2.1  Consensus size: 46

       1228 ACCTAAGAAT

                                                    *    *
       1238 TTAATTAATGTATAGTATTTCAGTTATTATAGTATTATTATTACAT
          1 TTAATTAATGTATAGTATTTCAGTTATTATAGTATTATTAATACAA

                                *                        *  
       1284 TTAATTAATGTA-AGTATTTTAGTTATTATA-TA-TATTACATAGGAA
          1 TTAATTAATGTATAGTATTTCAGTTATTATAGTATTATTA-ATA-CAA

                  
       1329 TTAATT
          1 TTAATT

       1335 GAAATTAGGG


Statistics
Matches: 45,  Mismatches: 4, Indels: 5
        0.83            0.07        0.09

Matches are distributed among these distances:
  43    5  0.11
  44    4  0.09
  45   24  0.53
  46   12  0.27

ACGTcount: A:0.37, C:0.03, G:0.09, T:0.51


Consensus pattern (46 bp):   
TTAATTAATGTATAGTATTTCAGTTATTATAGTATTATTAATACAA
Done.