Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022796.1 Corchorus olitorius cultivar O-4 contig22829, 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: 1815
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.27


Found at i:555 original size:47 final size:46

Alignment explanation


    Indices: 489--619  Score: 172
    Period size: 48  Copynumber: 2.8  Consensus size: 46

        479 CGGCAAAGCA

                                                          
        489 AAATTGATCTTGATGGTGTGAAGAAATTTATACCATCAGCACGGAG
          1 AAATTGATCTTGATGGTGTGAAGAAATTTATACCATCAGCACGGAG

                                    *              * * *    
        535 AAATTGATCTTTGATGGTGTGAAAAAAATTTATACCATCTGGATGGAG
          1 AAATTGATC-TTGATGGTGTG-AAGAAATTTATACCATCAGCACGGAG

                  *  *          *        *       
        583 AAATTGGTCCTGATGGTGTGGAGAAATTTGTACCATC
          1 AAATTGATCTTGATGGTGTGAAGAAATTTATACCATC

        620 TGGATGGAAA


Statistics
Matches: 74,  Mismatches: 9, Indels: 4
        0.85            0.10        0.05

Matches are distributed among these distances:
  46   23  0.31
  47   21  0.28
  48   30  0.41

ACGTcount: A:0.33, C:0.11, G:0.24, T:0.31


Consensus pattern (46 bp):   
AAATTGATCTTGATGGTGTGAAGAAATTTATACCATCAGCACGGAG

Found at i:587 original size:23 final size:23

Alignment explanation


    Indices: 560--633  Score: 71
    Period size: 23  Copynumber: 3.2  Consensus size: 23

        550 GGTGTGAAAA

                  *                
        560 AAATTTATACCATCTGGATGGAG
          1 AAATTTGTACCATCTGGATGGAG

                 *        *    *     
        583 AAATTGGT-CC-TGATGGTGTGGAG
          1 AAATTTGTACCAT-CTGG-ATGGAG

                                  *
        606 AAATTTGTACCATCTGGATGGAA
          1 AAATTTGTACCATCTGGATGGAG

                 
        629 AAATT
          1 AAATT

        634 GGAAGAAATT


Statistics
Matches: 39,  Mismatches: 8, Indels: 8
        0.71            0.15        0.15

Matches are distributed among these distances:
  21    1  0.03
  22    5  0.13
  23   27  0.69
  24    5  0.13
  25    1  0.03

ACGTcount: A:0.32, C:0.11, G:0.26, T:0.31


Consensus pattern (23 bp):   
AAATTTGTACCATCTGGATGGAG

Found at i:621 original size:46 final size:46

Alignment explanation


    Indices: 489--634  Score: 193
    Period size: 46  Copynumber: 3.1  Consensus size: 46

        479 CGGCAAAGCA

                                                 * * *    
        489 AAATTGATCTTGATGGTGTGAAGAAATTTATACCATCAGCACGGAG
          1 AAATTGATCTTGATGGTGTGAAGAAATTTATACCATCTGGATGGAG

                                    *                       
        535 AAATTGATCTTTGATGGTGTGAAAAAAATTTATACCATCTGGATGGAG
          1 AAATTGATC-TTGATGGTGTG-AAGAAATTTATACCATCTGGATGGAG

                  *  *          *        *               *
        583 AAATTGGTCCTGATGGTGTGGAGAAATTTGTACCATCTGGATGGAA
          1 AAATTGATCTTGATGGTGTGAAGAAATTTATACCATCTGGATGGAG

                  
        629 AAATTG
          1 AAATTG

        635 GAAGAAATTC


Statistics
Matches: 88,  Mismatches: 10, Indels: 4
        0.86            0.10        0.04

Matches are distributed among these distances:
  46   37  0.42
  47   21  0.24
  48   30  0.34

ACGTcount: A:0.34, C:0.10, G:0.25, T:0.31


Consensus pattern (46 bp):   
AAATTGATCTTGATGGTGTGAAGAAATTTATACCATCTGGATGGAG

Found at i:1118 original size:21 final size:21

Alignment explanation


    Indices: 1079--1119  Score: 55
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       1069 AGCTTGAAGA

                *         *      
       1079 TCAGTAATCTTGCGCTCAACC
          1 TCAGAAATCTTGCGATCAACC

                         *      
       1100 TCAGAAATCTTGCTATCAAC
          1 TCAGAAATCTTGCGATCAAC

       1120 TTTAAATTCC


Statistics
Matches: 17,  Mismatches: 3, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  21   17  1.00

ACGTcount: A:0.29, C:0.29, G:0.12, T:0.29


Consensus pattern (21 bp):   
TCAGAAATCTTGCGATCAACC
Done.