Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021033.1 Corchorus olitorius cultivar O-4 contig21066, 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: 6895
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35


Found at i:5041 original size:29 final size:30

Alignment explanation


    Indices: 4987--5060  Score: 105
    Period size: 29  Copynumber: 2.5  Consensus size: 30

       4977 TACCCAGAAA

                                *          
       4987 AATCCCTTATGTTTTGCTTTTGGGACAAAAT
          1 AATCCCTTATGTTTT-CTTTCGGGACAAAAT

                                        * 
       5018 AATCCCTTATGTTTT-TTTCGGGACAAATT
          1 AATCCCTTATGTTTTCTTTCGGGACAAAAT

                     *    
       5047 AATCCCTTACGTTT
          1 AATCCCTTATGTTT

       5061 CAAAAATGAG


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

Matches are distributed among these distances:
  29   25  0.62
  31   15  0.38

ACGTcount: A:0.24, C:0.19, G:0.14, T:0.43


Consensus pattern (30 bp):   
AATCCCTTATGTTTTCTTTCGGGACAAAAT

Found at i:5244 original size:31 final size:32

Alignment explanation


    Indices: 5204--5298  Score: 137
    Period size: 31  Copynumber: 3.1  Consensus size: 32

       5194 AAGGGACTAA

                                            
       5204 TTTGT-CCAAAA-AAAAA-ATAAGGGTATTTT
          1 TTTGTCCCAAAAGAAAAACATAAGGGTATTTT

                                             
       5233 TTTGTACCCAAAAGAAAAACATAAGGGT-TTTT
          1 TTTGT-CCCAAAAGAAAAACATAAGGGTATTTT

                                 *          
       5265 TTTGTCCCAAAAGAAAAACATTAGGG-ATTTT
          1 TTTGTCCCAAAAGAAAAACATAAGGGTATTTT

               
       5296 TTT
          1 TTT

       5299 AGTATTTAGT


Statistics
Matches: 60,  Mismatches: 1, Indels: 8
        0.87            0.01        0.12

Matches are distributed among these distances:
  29    5  0.08
  31   33  0.55
  32   14  0.23
  33    8  0.13

ACGTcount: A:0.40, C:0.11, G:0.15, T:0.35


Consensus pattern (32 bp):   
TTTGTCCCAAAAGAAAAACATAAGGGTATTTT

Found at i:5665 original size:127 final size:124

Alignment explanation


    Indices: 5451--5690  Score: 326
    Period size: 126  Copynumber: 1.9  Consensus size: 124

       5441 ATTCCCTAAA

                       *                                *                    
       5451 AAAATGGTAAAGATAAAATAGTTATAAAAATATTGAATTTAATTGAATAAAAATAGAAGTTTTGG
          1 AAAATGGTAAAAATAAAATAGTTATAAAAATATTGAATTTAATTAAATAAAAATAGAAGTTTT-G

                                                   *                      
       5516 TAAAATAAAACTGTAAAAGTTTAAATAAT-GTCATTTAAGAAATATATTTAATTAAAATAGT
         65 TAAAATAAAACTGTAAAAGTTTAAA-AATGGT-ATTTAAAAAATATATTTAATTAAAATAGT

                                                      *                      
       5577 AAAATGGTAAAAATAAAATAGTTATAAAATATATT-AGATTTGATTAAATAAAAATAG-AGTTTT
          1 AAAATGGTAAAAATAAAATAGTTATAAAA-ATATTGA-ATTTAATTAAATAAAAATAGAAGTTTT

                    *     *                                     
       5640 -TAATTGAGTAAAATTGTAAAAGTTTAAAAATGGTATTTAAAAAATATATTT
         64 GTAA---AATAAAACTGTAAAAGTTTAAAAATGGTATTTAAAAAATATATTT

       5691 GAAAAATAAG


Statistics
Matches: 102,  Mismatches: 6, Indels: 12
        0.85            0.05        0.10

Matches are distributed among these distances:
 124    3  0.03
 126   54  0.53
 127   45  0.44

ACGTcount: A:0.52, C:0.01, G:0.12, T:0.35


Consensus pattern (124 bp):   
AAAATGGTAAAAATAAAATAGTTATAAAAATATTGAATTTAATTAAATAAAAATAGAAGTTTTGT
AAAATAAAACTGTAAAAGTTTAAAAATGGTATTTAAAAAATATATTTAATTAAAATAGT

Found at i:6336 original size:32 final size:32

Alignment explanation


    Indices: 6300--6366  Score: 107
    Period size: 32  Copynumber: 2.1  Consensus size: 32

       6290 ATTGAATACT

                   *  *                     
       6300 AAAAAAATTCTCTTATATTTTTCTTTTGGGAC
          1 AAAAAAAATCCCTTATATTTTTCTTTTGGGAC

                            *               
       6332 AAAAAAAATCCCTTATGTTTTTCTTTTGGGAC
          1 AAAAAAAATCCCTTATATTTTTCTTTTGGGAC

               
       6364 AAA
          1 AAA

       6367 TCAGTCCCTT


Statistics
Matches: 32,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  32   32  1.00

ACGTcount: A:0.34, C:0.13, G:0.10, T:0.42


Consensus pattern (32 bp):   
AAAAAAAATCCCTTATATTTTTCTTTTGGGAC

Found at i:6570 original size:31 final size:30

Alignment explanation


    Indices: 6490--6570  Score: 92
    Period size: 30  Copynumber: 2.7  Consensus size: 30

       6480 CTCATTTTTG

                *          *              
       6490 AAACGTAAGGGATTAATTTGTCCCGAAAAA
          1 AAACATAAGGGATTATTTTGTCCCGAAAAA

                                            
       6520 AAACATAAGGGATTATTTTGTCCC-AAAAGCA
          1 AAACATAAGGGATTATTTTGTCCCGAAAA--A

               *    *     *     
       6551 AAATATAATGGATTTTTTTG
          1 AAACATAAGGGATTATTTTG

       6571 GGTATTTAAC


Statistics
Matches: 44,  Mismatches: 5, Indels: 3
        0.85            0.10        0.06

Matches are distributed among these distances:
  29    4  0.09
  30   22  0.50
  31   18  0.41

ACGTcount: A:0.41, C:0.11, G:0.17, T:0.31


Consensus pattern (30 bp):   
AAACATAAGGGATTATTTTGTCCCGAAAAA
Done.