Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009177.1 Corchorus olitorius cultivar O-4 contig09205, 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, 974

Length: 1624
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.35


Found at i:321 original size:21 final size:21

Alignment explanation


    Indices: 295--470  Score: 259
    Period size: 21  Copynumber: 8.4  Consensus size: 21

        285 TGCTAGAAGT

                                  
        295 TCATTGGAGCAA-GTTCCAAGC
          1 TCATTGGAG-AAGGTTCCAAGC

                                  
        316 TCATTGGAGCAA-GTTCCAAGC
          1 TCATTGGAG-AAGGTTCCAAGC

                                *
        337 TCATTGGAGAAGGTTCCAAGT
          1 TCATTGGAGAAGGTTCCAAGC

                                  
        358 TCATTGGAGCAA-GTTCCAAGC
          1 TCATTGGAG-AAGGTTCCAAGC

                                *
        379 TCATTGGAGAAGGTTCCAAGT
          1 TCATTGGAGAAGGTTCCAAGC

                                *
        400 TCATTGGAGAAGGTTCCAAGT
          1 TCATTGGAGAAGGTTCCAAGC

                                *
        421 TCATTGGAGAAGGTTCCAAGA
          1 TCATTGGAGAAGGTTCCAAGC

                           *     
        442 TCATTGGAGAAGGTTTCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                    
        463 TCATTGGA
          1 TCATTGGA

        471 AATGCCTAAG


Statistics
Matches: 146,  Mismatches: 6, Indels: 6
        0.92            0.04        0.04

Matches are distributed among these distances:
  20    4  0.03
  21  140  0.96
  22    2  0.01

ACGTcount: A:0.29, C:0.18, G:0.27, T:0.27


Consensus pattern (21 bp):   
TCATTGGAGAAGGTTCCAAGC

Found at i:364 original size:63 final size:63

Alignment explanation


    Indices: 291--470  Score: 301
    Period size: 63  Copynumber: 2.9  Consensus size: 63

        281 AAGATGCTAG

                                                                            
        291 AAGTTCATTGGAGCAAGTTCCAAGCTCATTGGAGCAA-GTTCCAAGCTCATTGGAGAAGGTTCC
          1 AAGTTCATTGGAGCAAGTTCCAAGCTCATTGGAG-AAGGTTCCAAGCTCATTGGAGAAGGTTCC

                                                         *                 
        354 AAGTTCATTGGAGCAAGTTCCAAGCTCATTGGAGAAGGTTCCAAGTTCATTGGAGAAGGTTCC
          1 AAGTTCATTGGAGCAAGTTCCAAGCTCATTGGAGAAGGTTCCAAGCTCATTGGAGAAGGTTCC

                                     *               *             
        417 AAGTTCATTGGAG-AAGGTTCCAAGATCATTGGAGAAGGTTTCAAGCTCATTGGA
          1 AAGTTCATTGGAGCAA-GTTCCAAGCTCATTGGAGAAGGTTCCAAGCTCATTGGA

        471 AATGCCTAAG


Statistics
Matches: 111,  Mismatches: 4, Indels: 4
        0.93            0.03        0.03

Matches are distributed among these distances:
  62    4  0.04
  63  107  0.96

ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27


Consensus pattern (63 bp):   
AAGTTCATTGGAGCAAGTTCCAAGCTCATTGGAGAAGGTTCCAAGCTCATTGGAGAAGGTTCC

Found at i:1541 original size:151 final size:152

Alignment explanation


    Indices: 1262--1624  Score: 622
    Period size: 151  Copynumber: 2.4  Consensus size: 152

       1252 TCGTATCATG

                                                                             
       1262 CACTGTGAAGTTTTTAGCTCATTTGGAACACTTTTTATTTTGAGCCTATCGGGGCCCATTAGTGA
          1 CACTGTGAAGTTTTTAGCTCATTTGGAACACTTTTTATTTTGAGCCTATCGGGGCCCATTA--GA

                             *                                               
       1327 CGTTTTGAATCGTCTTCGATTTGACAACCCTCAATGCTTTTTTTTCCATTGTTTATGGCCTAACT
         64 CGTTTTGAATCGTCTTCAATTTGACAACCCTCAATGCTTTTTTTTCCATTGTTTATGGCCTAACT

                                    
       1392 ATAATCATTTTGGTGAGATTAGTC
        129 ATAATCATTTTGGTGAGATTAGTC

                       *        *                                            
       1416 CACTGTGAAGTGTTTAGCTCTTTTGGAACACTTTTTATTTTGAGCCTATCGGGGCCCATTA-ACG
          1 CACTGTGAAGTTTTTAGCTCATTTGGAACACTTTTTATTTTGAGCCTATCGGGGCCCATTAGACG

                                                                             
       1480 TTTTGAATCGTCTTCAATTTGACAACCCTCAATGCTTTTTTTTCCATTGTTTATGGCCTAACTAT
         66 TTTTGAATCGTCTTCAATTTGACAACCCTCAATGCTTTTTTTTCCATTGTTTATGGCCTAACTAT

                                  
       1545 AATCATTTTGGTGAGATTAGTC
        131 AATCATTTTGGTGAGATTAGTC

                *          *                 *        *  *             
       1567 CACTTTGAAGTTTTTGGCTCATTTGGAACACTTGTTATTTTGGGCGTATC-GGGCCCAT
          1 CACTGTGAAGTTTTTAGCTCATTTGGAACACTTTTTATTTTGAGCCTATCGGGGCCCAT


Statistics
Matches: 199,  Mismatches: 10, Indels: 4
        0.93            0.05        0.02

Matches are distributed among these distances:
 150    8  0.04
 151  132  0.66
 154   59  0.30

ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41


Consensus pattern (152 bp):   
CACTGTGAAGTTTTTAGCTCATTTGGAACACTTTTTATTTTGAGCCTATCGGGGCCCATTAGACG
TTTTGAATCGTCTTCAATTTGACAACCCTCAATGCTTTTTTTTCCATTGTTTATGGCCTAACTAT
AATCATTTTGGTGAGATTAGTC
Done.