Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019525.1 Corchorus olitorius cultivar O-4 contig19558, 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: 25645
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31


Found at i:8806 original size:21 final size:20

Alignment explanation


    Indices: 8780--8839  Score: 68
    Period size: 19  Copynumber: 3.0  Consensus size: 20

       8770 CGCTGCTCTA

                                 
       8780 ATAATCTCATCTGTACAGTAT
          1 ATAATCTCATCTGTACAGT-T

                   *    *  *    
       8801 ATAATCTAATCTATATAG-T
          1 ATAATCTCATCTGTACAGTT

            *                   
       8820 GTAATCTCATCTGTACAGTT
          1 ATAATCTCATCTGTACAGTT

       8840 GCCAAACAAT


Statistics
Matches: 31,  Mismatches: 7, Indels: 3
        0.76            0.17        0.07

Matches are distributed among these distances:
  19   15  0.48
  20    1  0.03
  21   15  0.48

ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40


Consensus pattern (20 bp):   
ATAATCTCATCTGTACAGTT

Found at i:9703 original size:54 final size:54

Alignment explanation


    Indices: 9656--9768  Score: 190
    Period size: 54  Copynumber: 2.1  Consensus size: 54

       9646 ACATATTTTT

                                           *                      
       9656 TGAATTTATTGCTTATAATGATTGGGGATAATGATTACATAAAAACATAGGCAA
          1 TGAATTTATTGCTTATAATGATTGGGGATAACGATTACATAAAAACATAGGCAA

                                       *                 **       
       9710 TGAATTTATTGCTTATAATGATTGGGGGTAACGATTACATAAAAATGTAGGCAA
          1 TGAATTTATTGCTTATAATGATTGGGGATAACGATTACATAAAAACATAGGCAA

                 
       9764 TGAAT
          1 TGAAT

       9769 CTCTATATGC


Statistics
Matches: 55,  Mismatches: 4, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  54   55  1.00

ACGTcount: A:0.39, C:0.07, G:0.20, T:0.34


Consensus pattern (54 bp):   
TGAATTTATTGCTTATAATGATTGGGGATAACGATTACATAAAAACATAGGCAA

Found at i:12643 original size:108 final size:108

Alignment explanation


    Indices: 12428--12791  Score: 468
    Period size: 117  Copynumber: 3.3  Consensus size: 108

      12418 TTTTTTATGT

                    *                *         *                 *  *        
      12428 ATCCGGATTCGACCCGCGTCGCGCATCTGGTTATGAGGATCCGACCC-A-A-TATTATTTTTTTT
          1 ATCCGGATCCGACCCGCGTCGCGCACCTGGTTATGTGGATCCGACCCGATATTTTTTTTTTTTTT

                                   *                   
      12490 -TTATCCCATCCCCATCCGGTATCCAAGGCTTAGCCCTGACTA
         66 GTTATCCCATCCCCATCCGGTATTCAAGGCTTAGCCCTGACTA

                       *                                                     
      12532 ATCCGGATCCGCCCCGCGTCGCGCACCTGGTTATGTGGATCCGACCCGATATTTTTTTTTTTTTT
          1 ATCCGGATCCGACCCGCGTCGCGCACCTGGTTATGTGGATCCGACCCGATATTTTTTTTTTTTTT

                                             *         
      12597 GTTATCCCATCCCCATCCGGTATTCAAGGCTTATCCCTGACTA
         66 GTTATCCCATCCCCATCCGGTATTCAAGGCTTAGCCCTGACTA

                    *               *                                 * *    
      12640 ATCCGGATTCGACCCGCATCGCGCACGGGAACGCACCTGGTTATGTGGATCCGACCCGTTTTTTT
          1 ATCCGGATCCGA--C-C--CGCG-TC--G--CGCACCTGGTTATGTGGATCCGACCCGATATTTT

                                                                 
      12705 TTTTTTTTTTG-TATCCCATCCCCATCCGGTATTCAAGGCTTAGCCCTGACTA
         56 TTTTTTTTTTGTTATCCCATCCCCATCCGGTATTCAAGGCTTAGCCCTGACTA

                             *  *        *     
      12757 ATCCGGATCCGACCCGCATCACGCACCTGATTATG
          1 ATCCGGATCCGACCCGCGTCGCGCACCTGGTTATG

      12792 GTGGGTGAGT


Statistics
Matches: 227,  Mismatches: 19, Indels: 25
        0.84            0.07        0.09

Matches are distributed among these distances:
 104   43  0.19
 105    1  0.00
 106    1  0.00
 107   24  0.11
 108   50  0.22
 110    1  0.00
 111    2  0.01
 112    3  0.01
 113    4  0.02
 114    2  0.01
 115    1  0.00
 116    1  0.00
 117   51  0.22
 118   43  0.19

ACGTcount: A:0.18, C:0.31, G:0.19, T:0.31


Consensus pattern (108 bp):   
ATCCGGATCCGACCCGCGTCGCGCACCTGGTTATGTGGATCCGACCCGATATTTTTTTTTTTTTT
GTTATCCCATCCCCATCCGGTATTCAAGGCTTAGCCCTGACTA

Found at i:15367 original size:17 final size:17

Alignment explanation


    Indices: 15335--15368  Score: 50
    Period size: 17  Copynumber: 2.0  Consensus size: 17

      15325 TCACACTACC

                       *     
      15335 TTATATTTCTGTTATTA
          1 TTATATTTCTGGTATTA

                    *        
      15352 TTATATTTTTGGTATTA
          1 TTATATTTCTGGTATTA

      15369 GAGAAACAGA


Statistics
Matches: 15,  Mismatches: 2, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  17   15  1.00

ACGTcount: A:0.24, C:0.03, G:0.09, T:0.65


Consensus pattern (17 bp):   
TTATATTTCTGGTATTA
Done.