Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014962.1 Corchorus olitorius cultivar O-4 contig14995, 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: 3693
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31


Found at i:340 original size:33 final size:33

Alignment explanation


    Indices: 295--367  Score: 92
    Period size: 33  Copynumber: 2.2  Consensus size: 33

        285 GATGTTATTA

                   *                *        
        295 GTGATGATACTAAACCTAATTTAATTGTTGTTT
          1 GTGATGACACTAAACCTAATTTAAGTGTTGTTT

                          *  **    *         
        328 GTGATGACACTAAATCTGTTTTAGGTGTTGTTT
          1 GTGATGACACTAAACCTAATTTAAGTGTTGTTT

                   
        361 GTGATGA
          1 GTGATGA

        368 AACAAATTTT


Statistics
Matches: 34,  Mismatches: 6, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  33   34  1.00

ACGTcount: A:0.26, C:0.08, G:0.22, T:0.44


Consensus pattern (33 bp):   
GTGATGACACTAAACCTAATTTAAGTGTTGTTT

Found at i:381 original size:33 final size:33

Alignment explanation


    Indices: 320--417  Score: 94
    Period size: 33  Copynumber: 3.0  Consensus size: 33

        310 CTAATTTAAT

                           *                   
        320 TGTTGTTTGTGATGACACTAAA-TCTGTTTTAGG-
          1 TGTTGTTTGTGATGAAAC-AAATTCTGTTTT-GGA

                                   *         
        353 TGTTGTTTGTGATGAAACAAATTTTGTTTTGGA
          1 TGTTGTTTGTGATGAAACAAATTCTGTTTTGGA

              * **                  *        
        386 TGCTAATTGTGATGAAAACAAA-TATGTTTTGG
          1 TGTTGTTTGTGATG-AAACAAATTCTGTTTTGG

        418 TTGATCATAG


Statistics
Matches: 56,  Mismatches: 6, Indels: 6
        0.82            0.09        0.09

Matches are distributed among these distances:
  32    5  0.09
  33   44  0.79
  34    7  0.12

ACGTcount: A:0.27, C:0.06, G:0.23, T:0.44


Consensus pattern (33 bp):   
TGTTGTTTGTGATGAAACAAATTCTGTTTTGGA

Found at i:773 original size:30 final size:30

Alignment explanation


    Indices: 737--795  Score: 102
    Period size: 30  Copynumber: 2.0  Consensus size: 30

        727 TCTTCAAGGG

                                           
        737 GGAGGGAATGATGCGCCCAA-GGCTTATCAT
          1 GGAGGGAATGATGCG-CCAAGGGCTTATCAT

                                         
        767 GGAGGGAATGATGCGCCAAGGGCTTATCA
          1 GGAGGGAATGATGCGCCAAGGGCTTATCA

        796 AGGACATCAA


Statistics
Matches: 28,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
  29    4  0.14
  30   24  0.86

ACGTcount: A:0.27, C:0.19, G:0.36, T:0.19


Consensus pattern (30 bp):   
GGAGGGAATGATGCGCCAAGGGCTTATCAT
Done.