Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014140.1 Corchorus capsularis cultivar CVL-1 contig14161, 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: 9209
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.29


Found at i:1105 original size:50 final size:49

Alignment explanation


    Indices: 1023--1166  Score: 207
    Period size: 50  Copynumber: 2.9  Consensus size: 49

       1013 ATCTCTTTGA

                                  *               *           
       1023 TTGTAATCAGTGAGGGGAGCACGTGTTTTAAGCTTGGGAAAAGCTTAGGT
          1 TTGTAATCAGTGAGGGGAGCACTTG-TTTAAGCTTGGGGAAAGCTTAGGT

                        *                                     
       1073 TTGTAATCAGTGCGGGGAGCACTTGTTCTAAGCTTGGGGAAAGCTTAGGT
          1 TTGTAATCAGTGAGGGGAGCACTTGTT-TAAGCTTGGGGAAAGCTTAGGT

                *  *    *               *               
       1123 TTGTGATTAGTGTGGGGAGCACTTGTTTGAGCTTGGGGAAAGCT
          1 TTGTAATCAGTGAGGGGAGCACTTGTTTAAGCTTGGGGAAAGCT

       1167 CGGTGTTGTC


Statistics
Matches: 86,  Mismatches: 7, Indels: 3
        0.90            0.07        0.03

Matches are distributed among these distances:
  49   18  0.21
  50   68  0.79

ACGTcount: A:0.22, C:0.11, G:0.35, T:0.31


Consensus pattern (49 bp):   
TTGTAATCAGTGAGGGGAGCACTTGTTTAAGCTTGGGGAAAGCTTAGGT

Found at i:1181 original size:26 final size:27

Alignment explanation


    Indices: 1152--1202  Score: 86
    Period size: 26  Copynumber: 1.9  Consensus size: 27

       1142 CACTTGTTTG

                                       
       1152 AGCTTGGGGAAAGCTCGG-TGTTGTCA
          1 AGCTTGGGGAAAGCTCGGTTGTTGTCA

                           *         
       1178 AGCTTGGGGAAAGCTTGGTTGTTGT
          1 AGCTTGGGGAAAGCTCGGTTGTTGT

       1203 AACGACTTGG


Statistics
Matches: 23,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  26   17  0.74
  27    6  0.26

ACGTcount: A:0.18, C:0.12, G:0.39, T:0.31


Consensus pattern (27 bp):   
AGCTTGGGGAAAGCTCGGTTGTTGTCA

Found at i:2581 original size:21 final size:21

Alignment explanation


    Indices: 2557--2596  Score: 71
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       2547 ACCATGAACG

                                 
       2557 AGACAGATACAGAAATGAAAA
          1 AGACAGATACAGAAATGAAAA

                    *          
       2578 AGACAGATTCAGAAATGAA
          1 AGACAGATACAGAAATGAA

       2597 GAAGTTCAAC


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.57, C:0.10, G:0.20, T:0.12


Consensus pattern (21 bp):   
AGACAGATACAGAAATGAAAA
Done.