Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019641.1 Corchorus olitorius cultivar O-4 contig19674, 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: 3781
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31


Found at i:158 original size:21 final size:21

Alignment explanation


    Indices: 105--165  Score: 59
    Period size: 21  Copynumber: 2.9  Consensus size: 21

         95 TATAGCATAA

                  *    *   *     
        105 AAAAATTATAGCGAGATTAAC
          1 AAAAATCATAGGGAGGTTAAC

                 *              * 
        126 AAAATCTCATAGGGAGGTTATC
          1 AAAA-ATCATAGGGAGGTTAAC

                        *     
        148 AAAAATCATAGGAAGGTT
          1 AAAAATCATAGGGAGGTT

        166 TATTAAAATT


Statistics
Matches: 32,  Mismatches: 7, Indels: 2
        0.78            0.17        0.05

Matches are distributed among these distances:
  21   16  0.50
  22   16  0.50

ACGTcount: A:0.46, C:0.10, G:0.20, T:0.25


Consensus pattern (21 bp):   
AAAAATCATAGGGAGGTTAAC

Found at i:212 original size:22 final size:22

Alignment explanation


    Indices: 186--267  Score: 96
    Period size: 22  Copynumber: 3.8  Consensus size: 22

        176 TCATAGTTAG

                                   
        186 ATTATCAAAATTTCATATGGA-A
          1 ATTATCAAAATTTCATA-GGACA

            *      *            * 
        208 TTTATCACAATTTCATA-GATA
          1 ATTATCAAAATTTCATAGGACA

                         *        
        229 ATTATCAAAATTTAATAGGACA
          1 ATTATCAAAATTTCATAGGACA

            *                
        251 GTTATCAAAATTTCATA
          1 ATTATCAAAATTTCATA

        268 AAAATATTTA


Statistics
Matches: 50,  Mismatches: 8, Indels: 4
        0.81            0.13        0.06

Matches are distributed among these distances:
  20    2  0.04
  21   15  0.30
  22   33  0.66

ACGTcount: A:0.44, C:0.11, G:0.07, T:0.38


Consensus pattern (22 bp):   
ATTATCAAAATTTCATAGGACA

Found at i:234 original size:43 final size:44

Alignment explanation


    Indices: 165--267  Score: 138
    Period size: 43  Copynumber: 2.4  Consensus size: 44

        155 ATAGGAAGGT

                *            *                *         *
        165 TTATTAAAATTTCATAGTTAGATTATCAAAATTTCATATGGA-AT
          1 TTATCAAAATTTCATAGATAGATTATCAAAATTTAATA-GGACAG

                  *                                     
        209 TTATCACAATTTCATAGATA-ATTATCAAAATTTAATAGGACAG
          1 TTATCAAAATTTCATAGATAGATTATCAAAATTTAATAGGACAG

                            
        252 TTATCAAAATTTCATA
          1 TTATCAAAATTTCATA

        268 AAAATATTTA


Statistics
Matches: 52,  Mismatches: 6, Indels: 3
        0.85            0.10        0.05

Matches are distributed among these distances:
  42    3  0.06
  43   32  0.62
  44   17  0.33

ACGTcount: A:0.43, C:0.10, G:0.08, T:0.40


Consensus pattern (44 bp):   
TTATCAAAATTTCATAGATAGATTATCAAAATTTAATAGGACAG

Found at i:1378 original size:2 final size:2

Alignment explanation


    Indices: 1371--1397  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

       1361 AATTGATGAT

                                                    
       1371 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

       1398 GTTGTCATTA


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

Done.