Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010133.1 Corchorus olitorius cultivar O-4 contig10165, 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: 5644
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32


Found at i:1190 original size:22 final size:23

Alignment explanation


    Indices: 1165--1208  Score: 63
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       1155 TCTTTCAAAA

                             *     
       1165 TTTTCTA-TCTGTTCTTTTTCAT
          1 TTTTCTATTCTGTTCTTGTTCAT

                     *            
       1187 TTTTCTATTGTGTTCTTGTTCA
          1 TTTTCTATTCTGTTCTTGTTCA

       1209 ATTTCATACT


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  22    7  0.37
  23   12  0.63

ACGTcount: A:0.09, C:0.16, G:0.09, T:0.66


Consensus pattern (23 bp):   
TTTTCTATTCTGTTCTTGTTCAT

Found at i:1213 original size:22 final size:22

Alignment explanation


    Indices: 1166--1213  Score: 53
    Period size: 23  Copynumber: 2.2  Consensus size: 22

       1156 CTTTCAAAAT

                           *     *
       1166 TTTCTATCTGTTCTTTTTCATT
          1 TTTCTATCTGTTCTTGTTCATA

                    *              
       1188 TTTCTATTGTGTTCTTGTTCA-A
          1 TTTCTA-TCTGTTCTTGTTCATA

                
       1210 TTTC
          1 TTTC

       1214 ATACTTTGAA


Statistics
Matches: 22,  Mismatches: 3, Indels: 2
        0.81            0.11        0.07

Matches are distributed among these distances:
  22   10  0.45
  23   12  0.55

ACGTcount: A:0.10, C:0.17, G:0.08, T:0.65


Consensus pattern (22 bp):   
TTTCTATCTGTTCTTGTTCATA

Found at i:5489 original size:10 final size:10

Alignment explanation


    Indices: 5474--5564  Score: 62
    Period size: 10  Copynumber: 10.1  Consensus size: 10

       5464 CAAAATTTTC

                      
       5474 AATTCTCTCA
          1 AATTCTCTCA

                      
       5484 AATTCTCTC-
          1 AATTCTCTCA

               *       
       5493 AA-CCT-TCAA
          1 AATTCTCTC-A

                      
       5502 AATT-T-TC-
          1 AATTCTCTCA

                      
       5509 AATTCTCTCA
          1 AATTCTCTCA

                      
       5519 AATTCTCTC-
          1 AATTCTCTCA

               *       
       5528 AA-CCT-TCAA
          1 AATTCTCTC-A

                      
       5537 AATT-T-TC-
          1 AATTCTCTCA

                      
       5544 AATTCTCTCA
          1 AATTCTCTCA

                      
       5554 AATTCTCTCA
          1 AATTCTCTCA

             
       5564 A
          1 A

       5565 CCTTCAAACT


Statistics
Matches: 65,  Mismatches: 4, Indels: 24
        0.70            0.04        0.26

Matches are distributed among these distances:
   7   12  0.18
   8    6  0.09
   9   18  0.28
  10   29  0.45

ACGTcount: A:0.32, C:0.29, G:0.00, T:0.40


Consensus pattern (10 bp):   
AATTCTCTCA

Found at i:5500 original size:35 final size:35

Alignment explanation


    Indices: 5452--5572  Score: 226
    Period size: 35  Copynumber: 3.5  Consensus size: 35

       5442 TTACTTTATT

                     *                         
       5452 TTCT-TCAATCTTCAAAATTTTCAATTCTCTCAAA
          1 TTCTCTCAACCTTCAAAATTTTCAATTCTCTCAAA

                                               
       5486 TTCTCTCAACCTTCAAAATTTTCAATTCTCTCAAA
          1 TTCTCTCAACCTTCAAAATTTTCAATTCTCTCAAA

                                               
       5521 TTCTCTCAACCTTCAAAATTTTCAATTCTCTCAAA
          1 TTCTCTCAACCTTCAAAATTTTCAATTCTCTCAAA

                             
       5556 TTCTCTCAACCTTCAAA
          1 TTCTCTCAACCTTCAAA

       5573 CTTTCAAAAC


Statistics
Matches: 85,  Mismatches: 1, Indels: 1
        0.98            0.01        0.01

Matches are distributed among these distances:
  34    4  0.05
  35   81  0.95

ACGTcount: A:0.31, C:0.28, G:0.00, T:0.40


Consensus pattern (35 bp):   
TTCTCTCAACCTTCAAAATTTTCAATTCTCTCAAA

Found at i:5501 original size:17 final size:17

Alignment explanation


    Indices: 5481--5572  Score: 84
    Period size: 17  Copynumber: 5.3  Consensus size: 17

       5471 TTCAATTCTC

                             
       5481 TCAAATTCTCTCAACCT
          1 TCAAATTCTCTCAACCT

                            *  
       5498 TCAAAATT-T-TCAATTCT
          1 TC-AAATTCTCTCAA-CCT

                              
       5515 CTCAAATTCTCTCAACCT
          1 -TCAAATTCTCTCAACCT

                            *  
       5533 TCAAAATT-T-TCAATTCT
          1 TC-AAATTCTCTCAA-CCT

                              
       5550 CTCAAATTCTCTCAACCT
          1 -TCAAATTCTCTCAACCT

                 
       5568 TCAAA
          1 TCAAA

       5573 CTTTCAAAAC


Statistics
Matches: 61,  Mismatches: 4, Indels: 20
        0.72            0.05        0.24

Matches are distributed among these distances:
  16    8  0.13
  17   25  0.41
  18   20  0.33
  19    8  0.13

ACGTcount: A:0.33, C:0.29, G:0.00, T:0.38


Consensus pattern (17 bp):   
TCAAATTCTCTCAACCT
Done.