Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021008.1 Corchorus olitorius cultivar O-4 contig21041, 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: 5177
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30


Found at i:1174 original size:21 final size:21

Alignment explanation


    Indices: 1148--1302  Score: 258
    Period size: 21  Copynumber: 7.4  Consensus size: 21

       1138 TGCTAGGAGT

                                  
       1148 TCATTGGAGCAA-GTTCCAAGC
          1 TCATTGGAG-AAGGTTCCAAGC

                     *           
       1169 TCATTGGAGCAGGTTCCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                                 
       1190 TCATTGGAGAAGGTTCCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                                 
       1211 TCATTGGAGAAGGTTCCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                                 
       1232 TCATTGGAGAAGGTTCCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                    *          * 
       1253 TCATTGGATAAGGTTCCAATC
          1 TCATTGGAGAAGGTTCCAAGC

                           *     
       1274 TCATTGGAGAAGGTTTCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                    
       1295 TCATTGGA
          1 TCATTGGA

       1303 ATTGCCTAAG


Statistics
Matches: 126,  Mismatches: 7, Indels: 2
        0.93            0.05        0.01

Matches are distributed among these distances:
  20    1  0.01
  21  125  0.99

ACGTcount: A:0.28, C:0.19, G:0.26, T:0.26


Consensus pattern (21 bp):   
TCATTGGAGAAGGTTCCAAGC

Found at i:1320 original size:42 final size:41

Alignment explanation


    Indices: 1148--1320  Score: 164
    Period size: 42  Copynumber: 4.1  Consensus size: 41

       1138 TGCTAGGAGT

                                                         
       1148 TCATTGGAGCAA-GTTCCAAGCTCATTGGAGCAGGTTCCAAG--C
          1 TCATTGGAG-AAGGTTCCAAGCTCATTGGA--A-GTTCCAAGATC

                                                        
       1190 TCATTGGAGAAGGTTCCAAGCTCATTGGAGAAGGTTCCAAG--C
          1 TCATTGGAGAAGGTTCCAAGCTCATT-G-GAA-GTTCCAAGATC

                                                        
       1232 TCATTGGAGAAGGTTCCAAGCTCATTGGATAAGGTTCC-A-ATC
          1 TCATTGGAGAAGGTTCCAAGCTCATTGG--AA-GTTCCAAGATC

                           *                          *
       1274 TCATTGGAGAAGGTTTCAAGCTCATTGGAA-TTGCCTAAGATG
          1 TCATTGGAGAAGGTTCCAAGCTCATTGGAAGTT-CC-AAGATC

                 
       1316 TCATT
          1 TCATT

       1321 TGATCCATTG


Statistics
Matches: 118,  Mismatches: 2, Indels: 22
        0.83            0.01        0.15

Matches are distributed among these distances:
  38    2  0.02
  39    2  0.02
  40    3  0.03
  41    5  0.04
  42  103  0.87
  43    1  0.01
  44    2  0.02

ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28


Consensus pattern (41 bp):   
TCATTGGAGAAGGTTCCAAGCTCATTGGAAGTTCCAAGATC

Found at i:1606 original size:65 final size:65

Alignment explanation


    Indices: 1497--1625  Score: 231
    Period size: 65  Copynumber: 2.0  Consensus size: 65

       1487 CTTGCTATTG

                *                                                      *     
       1497 ATTCCAACTTTCTGCACTAGCCCAGGCGTGGGTAGGCCAAGGGTACCCCATGCATGGGTTGGACA
          1 ATTCAAACTTTCTGCACTAGCCCAGGCGTGGGTAGGCCAAGGGTACCCCATGCATGGGTAGGACA

                                 *                                          
       1562 ATTCAAACTTTCTGCACTAGCTCAGGCGTGGGTAGGCCAAGGGTACCCCATGCATGGGTAGGAC
          1 ATTCAAACTTTCTGCACTAGCCCAGGCGTGGGTAGGCCAAGGGTACCCCATGCATGGGTAGGAC

       1626 CAGTTTTTCC


Statistics
Matches: 61,  Mismatches: 3, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  65   61  1.00

ACGTcount: A:0.22, C:0.26, G:0.29, T:0.22


Consensus pattern (65 bp):   
ATTCAAACTTTCTGCACTAGCCCAGGCGTGGGTAGGCCAAGGGTACCCCATGCATGGGTAGGACA

Found at i:4395 original size:17 final size:17

Alignment explanation


    Indices: 4373--4405  Score: 57
    Period size: 17  Copynumber: 1.9  Consensus size: 17

       4363 TGAAAAAGAT

                             
       4373 AAGAGAATATAGAGAAC
          1 AAGAGAATATAGAGAAC

                      *     
       4390 AAGAGAATATGGAGAA
          1 AAGAGAATATAGAGAA

       4406 GGGGAGAAAT


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  17   15  1.00

ACGTcount: A:0.58, C:0.03, G:0.27, T:0.12


Consensus pattern (17 bp):   
AAGAGAATATAGAGAAC
Done.