Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014836.1 Corchorus olitorius cultivar O-4 contig14869, 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: 13946
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32


Found at i:2552 original size:51 final size:50

Alignment explanation


    Indices: 2451--2552  Score: 120
    Period size: 51  Copynumber: 2.0  Consensus size: 50

       2441 GTTCTCCATA

                                                     * **     
       2451 TTTTTCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCTTTTAGTGT
          1 TTTTTCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGT

                                                                  
       2501 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGACATAA-AAACACT-GTACACGTGT
          1 TTTT-TCTTGTTT-AGATCTTGTCTCCGGACA-AACAAACACTCGTACA-GTGT

             
       2552 T
          1 T

       2553 CTTCATTCAG


Statistics
Matches: 45,  Mismatches: 3, Indels: 7
        0.82            0.05        0.13

Matches are distributed among these distances:
  50    6  0.13
  51   36  0.80
  52    3  0.07

ACGTcount: A:0.23, C:0.22, G:0.14, T:0.42


Consensus pattern (50 bp):   
TTTTTCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGT

Found at i:3146 original size:21 final size:22

Alignment explanation


    Indices: 3098--3152  Score: 67
    Period size: 22  Copynumber: 2.5  Consensus size: 22

       3088 CTTCAACGTA

                 *              * 
       3098 GAAAAATTGATAACCATATTGT
          1 GAAAATTTGATAACCATATTAT

                                   
       3120 GAAAATTTGATAACC-TCATTAT
          1 GAAAATTTGATAACCAT-ATTAT

                *      
       3142 GAAATTTTGAT
          1 GAAAATTTGAT

       3153 TTGGCAAAAA


Statistics
Matches: 29,  Mismatches: 3, Indels: 2
        0.85            0.09        0.06

Matches are distributed among these distances:
  21    1  0.03
  22   28  0.97

ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36


Consensus pattern (22 bp):   
GAAAATTTGATAACCATATTAT

Found at i:3213 original size:34 final size:34

Alignment explanation


    Indices: 3170--3239  Score: 131
    Period size: 34  Copynumber: 2.1  Consensus size: 34

       3160 AAAAAAAAAT

                                              
       3170 TATGAAATTTAATAACCTCATTATGAAATTTCGA
          1 TATGAAATTTAATAACCTCATTATGAAATTTCGA

                      *                       
       3204 TATGAAATTTGATAACCTCATTATGAAATTTCGA
          1 TATGAAATTTAATAACCTCATTATGAAATTTCGA

              
       3238 TA
          1 TA

       3240 ACCTCTATAT


Statistics
Matches: 35,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  34   35  1.00

ACGTcount: A:0.40, C:0.11, G:0.10, T:0.39


Consensus pattern (34 bp):   
TATGAAATTTAATAACCTCATTATGAAATTTCGA

Found at i:3242 original size:22 final size:21

Alignment explanation


    Indices: 3204--3286  Score: 96
    Period size: 22  Copynumber: 3.8  Consensus size: 21

       3194 GAAATTTCGA

                                 
       3204 TATGAAATTTGATAACCTCAT
          1 TATGAAATTTGATAACCTCAT

                                  
       3225 TATGAAATTTCGATAACCTC-T
          1 TATGAAATTT-GATAACCTCAT

                               *  *
       3246 ATATGAAAATTTGATAACCACAC
          1 -TATG-AAATTTGATAACCTCAT

             *                
       3269 TGTGAAATTTTGATAACC
          1 TATGAAA-TTTGATAACC

       3287 ATAGCTTTAT


Statistics
Matches: 54,  Mismatches: 3, Indels: 9
        0.82            0.05        0.14

Matches are distributed among these distances:
  21   14  0.26
  22   34  0.63
  23    6  0.11

ACGTcount: A:0.39, C:0.16, G:0.11, T:0.35


Consensus pattern (21 bp):   
TATGAAATTTGATAACCTCAT

Found at i:3275 original size:44 final size:43

Alignment explanation


    Indices: 3203--3286  Score: 123
    Period size: 44  Copynumber: 1.9  Consensus size: 43

       3193 TGAAATTTCG

                              *  *                     
       3203 ATATGAAATTTGATAACCTCATTATGAAATTTCGATAACCTCT
          1 ATATGAAATTTGATAACCACACTATGAAATTTCGATAACCTCT

                                    *        *       
       3246 ATATGAAAATTTGATAACCACACTGTGAAATTTTGATAACC
          1 ATATG-AAATTTGATAACCACACTATGAAATTTCGATAACC

       3287 ATAGCTTTAT


Statistics
Matches: 36,  Mismatches: 4, Indels: 1
        0.88            0.10        0.02

Matches are distributed among these distances:
  43    5  0.14
  44   31  0.86

ACGTcount: A:0.39, C:0.15, G:0.11, T:0.35


Consensus pattern (43 bp):   
ATATGAAATTTGATAACCACACTATGAAATTTCGATAACCTCT

Found at i:4990 original size:19 final size:19

Alignment explanation


    Indices: 4966--5002  Score: 65
    Period size: 19  Copynumber: 1.9  Consensus size: 19

       4956 GAATGTCAAG

                        *      
       4966 GTAAAGATTAATTAGTTTC
          1 GTAAAGATTAATCAGTTTC

                              
       4985 GTAAAGATTAATCAGTTT
          1 GTAAAGATTAATCAGTTT

       5003 ATTAATAAAT


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  19   17  1.00

ACGTcount: A:0.38, C:0.05, G:0.16, T:0.41


Consensus pattern (19 bp):   
GTAAAGATTAATCAGTTTC
Done.