Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020261.1 Corchorus olitorius cultivar O-4 contig20294, 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: 6331
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37


Found at i:235 original size:22 final size:21

Alignment explanation


    Indices: 188--228  Score: 57
    Period size: 22  Copynumber: 2.0  Consensus size: 21

        178 TGTATTGAAT

                            *     
        188 AAATGATAATTTAGCTTATAAA
          1 AAATGATAATTTAGC-AATAAA

                                
        210 AAATGATAATTTAG-AATAA
          1 AAATGATAATTTAGCAATAA

        229 GTAAAATTAT


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  20    4  0.22
  22   14  0.78

ACGTcount: A:0.54, C:0.02, G:0.10, T:0.34


Consensus pattern (21 bp):   
AAATGATAATTTAGCAATAAA

Found at i:302 original size:22 final size:23

Alignment explanation


    Indices: 272--317  Score: 76
    Period size: 22  Copynumber: 2.0  Consensus size: 23

        262 TTTTAGTTTA

                                   
        272 TAACATTCTCGAGTTATTCGGGT
          1 TAACATTCTCGAGTTATTCGGGT

                              *    
        295 TAAC-TTCTCGAGTTATTTGGGT
          1 TAACATTCTCGAGTTATTCGGGT

             
        317 T
          1 T

        318 TCGGGTCATC


Statistics
Matches: 22,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  22   18  0.82
  23    4  0.18

ACGTcount: A:0.20, C:0.15, G:0.22, T:0.43


Consensus pattern (23 bp):   
TAACATTCTCGAGTTATTCGGGT

Found at i:1084 original size:28 final size:28

Alignment explanation


    Indices: 1045--1117  Score: 69
    Period size: 31  Copynumber: 2.5  Consensus size: 28

       1035 CCAAATTGCG

                *                        
       1045 AGTTCAGGGGCAAACATCCAAAAT-TA-A
          1 AGTTTAGGGGCAAACAT-CAAAATCTAGA

                             *             
       1072 AGTTTAGGAGGCAAAACGTCAAAATCGTAGA
          1 AGTTTAGG-GGC-AAACATCAAAATC-TAGA

                           
       1103 AGTTTAGGGGGCAAA
          1 AGTTTA-GGGGCAAA

       1118 AGGGCATTGA


Statistics
Matches: 38,  Mismatches: 2, Indels: 9
        0.78            0.04        0.18

Matches are distributed among these distances:
  27    7  0.18
  28    9  0.24
  29    5  0.13
  30    5  0.13
  31   10  0.26
  32    2  0.05

ACGTcount: A:0.41, C:0.14, G:0.26, T:0.19


Consensus pattern (28 bp):   
AGTTTAGGGGCAAACATCAAAATCTAGA

Found at i:2813 original size:4 final size:4

Alignment explanation


    Indices: 2804--2831  Score: 56
    Period size: 4  Copynumber: 7.0  Consensus size: 4

       2794 GTATTGTTCA

                                              
       2804 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
          1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT

       2832 TGTCAGTTAG


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   4   24  1.00

ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75


Consensus pattern (4 bp):   
ATTT

Found at i:4617 original size:12 final size:12

Alignment explanation


    Indices: 4600--4624  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

       4590 ATTAATCGGG

                        
       4600 TGAAAAATTAAT
          1 TGAAAAATTAAT

                        
       4612 TGAAAAATTAAT
          1 TGAAAAATTAAT

             
       4624 T
          1 T

       4625 ATCATACTGA


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36


Consensus pattern (12 bp):   
TGAAAAATTAAT
Done.