Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017141.1 Corchorus olitorius cultivar O-4 contig17174, 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: 17670
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31


Found at i:304 original size:16 final size:15

Alignment explanation


    Indices: 283--324  Score: 57
    Period size: 15  Copynumber: 2.7  Consensus size: 15

        273 TTACTTTGTT

                            
        283 TTGTTTTCTAGTTTAA
          1 TTGTTTTCT-GTTTAA

                   *       
        299 TTGTTTTATGTTTAA
          1 TTGTTTTCTGTTTAA

            *          
        314 ATGTTTTCTGT
          1 TTGTTTTCTGT

        325 CAATCTCTGT


Statistics
Matches: 23,  Mismatches: 3, Indels: 1
        0.85            0.11        0.04

Matches are distributed among these distances:
  15   15  0.65
  16    8  0.35

ACGTcount: A:0.17, C:0.05, G:0.14, T:0.64


Consensus pattern (15 bp):   
TTGTTTTCTGTTTAA

Found at i:2219 original size:15 final size:15

Alignment explanation


    Indices: 2189--2230  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       2179 TTACTTTGCT

                            
       2189 TTGTTTTCTAGTTTAA
          1 TTGTTTTCT-GTTTAA

                           
       2205 TTGTTTTCTGTTTAA
          1 TTGTTTTCTGTTTAA

               *       
       2220 TTGCTTTCTGT
          1 TTGTTTTCTGT

       2231 CAATCTCTGT


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  15   16  0.64
  16    9  0.36

ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64


Consensus pattern (15 bp):   
TTGTTTTCTGTTTAA

Found at i:9419 original size:117 final size:117

Alignment explanation


    Indices: 9213--9443  Score: 383
    Period size: 117  Copynumber: 2.0  Consensus size: 117

       9203 ATGATCGACA

                        *                                      *   *         
       9213 GAGAACATGTTCTATCAGCCCTGGCCAGTGGGTTATAATAACTGGAAAACGGCCCTGCTAACGGG
          1 GAGAACATGTTCAATCAGCCCTGGCCAGTGGGTTATAATAACTGGAAAACGACCCCGCTAACGGG

                                                                 
       9278 TTATAGTAGTTAGCTTAAGGCCCTGCTAAC-GGATTATAGTAGTTAGCAAATG
         66 TTATAGTAGTTAGCTTAAGGCCCTGCTAACAGG-TTATAGTAGTTAGCAAATG

                            *   *                *                           
       9330 GAGAACATGTTCAATCGGCCTTGGCCAGTGGGTTATAGTAACTGGAAAACGACCCCGCTAACGGG
          1 GAGAACATGTTCAATCAGCCCTGGCCAGTGGGTTATAATAACTGGAAAACGACCCCGCTAACGGG

                        *                                    
       9395 TTATAGTAGTTATCTTAAGGCCCTGCTAACAGGTTATAGTAGTTAGCAA
         66 TTATAGTAGTTAGCTTAAGGCCCTGCTAACAGGTTATAGTAGTTAGCAA

       9444 TTGTCGATAT


Statistics
Matches: 106,  Mismatches: 7, Indels: 2
        0.92            0.06        0.02

Matches are distributed among these distances:
 117  104  0.98
 118    2  0.02

ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26


Consensus pattern (117 bp):   
GAGAACATGTTCAATCAGCCCTGGCCAGTGGGTTATAATAACTGGAAAACGACCCCGCTAACGGG
TTATAGTAGTTAGCTTAAGGCCCTGCTAACAGGTTATAGTAGTTAGCAAATG

Found at i:16783 original size:21 final size:23

Alignment explanation


    Indices: 16758--16800  Score: 63
    Period size: 22  Copynumber: 2.0  Consensus size: 23

      16748 TTGAATCAAA

                                   
      16758 TTTTCTA-TCTGTTCTT-TTCAT
          1 TTTTCTATTCTGTTCTTGTTCAT

                     *            
      16779 TTTTCTATTGTGTTCTTGTTCA
          1 TTTTCTATTCTGTTCTTGTTCA

      16801 ATTTCATACT


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

Matches are distributed among these distances:
  21    7  0.37
  22    8  0.42
  23    4  0.21

ACGTcount: A:0.09, C:0.16, G:0.09, T:0.65


Consensus pattern (23 bp):   
TTTTCTATTCTGTTCTTGTTCAT

Found at i:16805 original size:22 final size:21

Alignment explanation


    Indices: 16759--16805  Score: 51
    Period size: 22  Copynumber: 2.2  Consensus size: 21

      16749 TGAATCAAAT

                                *
      16759 TTTCTATCTGTTCTTTTCATT
          1 TTTCTATCTGTTCTTTTCATA

                    *              
      16780 TTTCTATTGTGTTCTTGTTCA-A
          1 TTTCTA-TCTGTTCTT-TTCATA

                
      16802 TTTC
          1 TTTC

      16806 ATACTTTGAA


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

Matches are distributed among these distances:
  21    6  0.27
  22   12  0.55
  23    4  0.18

ACGTcount: A:0.11, C:0.17, G:0.09, T:0.64


Consensus pattern (21 bp):   
TTTCTATCTGTTCTTTTCATA
Done.