Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015342.1 Corchorus olitorius cultivar O-4 contig15375, 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: 23600
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32


Found at i:1208 original size:17 final size:18

Alignment explanation


    Indices: 1179--1218  Score: 57
    Period size: 17  Copynumber: 2.3  Consensus size: 18

       1169 GGCGGTTGCT

                              
       1179 GTTTT-ATTGTTTTTTTG
          1 GTTTTGATTGTTTTTTTG

                              
       1196 GTTTTGATT-TTTTTTTG
          1 GTTTTGATTGTTTTTTTG

            *     
       1213 TTTTTG
          1 GTTTTG

       1219 TAATAAGTTT


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  17   18  0.86
  18    3  0.14

ACGTcount: A:0.05, C:0.00, G:0.17, T:0.78


Consensus pattern (18 bp):   
GTTTTGATTGTTTTTTTG

Found at i:1499 original size:27 final size:28

Alignment explanation


    Indices: 1461--1532  Score: 92
    Period size: 27  Copynumber: 2.6  Consensus size: 28

       1451 CGGCTCATTG

                                        
       1461 AGGTTGGTTGAGTTGATCAGATCAA-TC
          1 AGGTTGGTTGAGTTGATCAGATCAATTC

                              * *      *
       1488 AGGTTGGTTGAGTTGATCTGGTCAATTG
          1 AGGTTGGTTGAGTTGATCAGATCAATTC

             **              
       1516 AATTTGGTTGAGTTGAT
          1 AGGTTGGTTGAGTTGAT

       1533 AAAGCCTCAA


Statistics
Matches: 39,  Mismatches: 5, Indels: 1
        0.87            0.11        0.02

Matches are distributed among these distances:
  27   23  0.59
  28   16  0.41

ACGTcount: A:0.22, C:0.07, G:0.32, T:0.39


Consensus pattern (28 bp):   
AGGTTGGTTGAGTTGATCAGATCAATTC

Found at i:11555 original size:26 final size:26

Alignment explanation


    Indices: 11519--11574  Score: 94
    Period size: 26  Copynumber: 2.2  Consensus size: 26

      11509 AAGATTTCTA

                                      
      11519 GTAACTGGAACTTAGCTATCCCTGGT
          1 GTAACTGGAACTTAGCTATCCCTGGT

                           *    *     
      11545 GTAACTGGAACTTAGTTATCTCTGGT
          1 GTAACTGGAACTTAGCTATCCCTGGT

                
      11571 GTAA
          1 GTAA

      11575 TTAGCTAAGC


Statistics
Matches: 28,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  26   28  1.00

ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34


Consensus pattern (26 bp):   
GTAACTGGAACTTAGCTATCCCTGGT

Found at i:11892 original size:12 final size:12

Alignment explanation


    Indices: 11875--11899  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

      11865 GCAAAACTAA

                        
      11875 AACTAGACATAG
          1 AACTAGACATAG

                        
      11887 AACTAGACATAG
          1 AACTAGACATAG

             
      11899 A
          1 A

      11900 GATGCATCAA


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:0.52, C:0.16, G:0.16, T:0.16


Consensus pattern (12 bp):   
AACTAGACATAG

Found at i:14637 original size:23 final size:23

Alignment explanation


    Indices: 14611--14656  Score: 58
    Period size: 23  Copynumber: 2.0  Consensus size: 23

      14601 GCAATCAAAC

                                    
      14611 ATTA-ATTGCTACAGAAGAAAATG
          1 ATTATATTGCTA-AGAAGAAAATG

                 *       *         
      14634 ATTATGTTGCTAATAAGAAAATG
          1 ATTATATTGCTAAGAAGAAAATG

      14657 GAATGGGAGA


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  23   14  0.70
  24    6  0.30

ACGTcount: A:0.46, C:0.07, G:0.17, T:0.30


Consensus pattern (23 bp):   
ATTATATTGCTAAGAAGAAAATG

Found at i:15084 original size:30 final size:30

Alignment explanation


    Indices: 15050--15115  Score: 123
    Period size: 30  Copynumber: 2.2  Consensus size: 30

      15040 ATTTTTATCT

                                          
      15050 TGACTTTCCTCTTATACCCTCAAATTTTAA
          1 TGACTTTCCTCTTATACCCTCAAATTTTAA

                   *                      
      15080 TGACTTTTCTCTTATACCCTCAAATTTTAA
          1 TGACTTTCCTCTTATACCCTCAAATTTTAA

                  
      15110 TGACTT
          1 TGACTT

      15116 ATTAATTATT


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

Matches are distributed among these distances:
  30   35  1.00

ACGTcount: A:0.26, C:0.24, G:0.05, T:0.45


Consensus pattern (30 bp):   
TGACTTTCCTCTTATACCCTCAAATTTTAA

Found at i:17062 original size:27 final size:27

Alignment explanation


    Indices: 17008--17064  Score: 71
    Period size: 27  Copynumber: 2.1  Consensus size: 27

      16998 CAAAAATGAG

                                  **   
      17008 TCAAACCCCAAGAAGGATCTAATTTTA
          1 TCAAACCCCAAGAAGGATCTAACATTA

                          *             
      17035 TCAAACCCCAA-ACTGGATCTAACATTA
          1 TCAAACCCCAAGA-AGGATCTAACATTA

               
      17062 TCA
          1 TCA

      17065 GAAGATACAT


Statistics
Matches: 26,  Mismatches: 3, Indels: 2
        0.84            0.10        0.06

Matches are distributed among these distances:
  26    1  0.04
  27   25  0.96

ACGTcount: A:0.40, C:0.26, G:0.09, T:0.25


Consensus pattern (27 bp):   
TCAAACCCCAAGAAGGATCTAACATTA
Done.