Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013198.1 Corchorus capsularis cultivar CVL-1 contig13219, 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: 1812
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.33


Found at i:398 original size:35 final size:34

Alignment explanation


    Indices: 36--413  Score: 578
    Period size: 35  Copynumber: 10.8  Consensus size: 34

         26 CTGAAAATAT

                          *    *                
         36 GATCAACTCTGATCGT-TGGAAACTTCTTGAAATGA
          1 GATCAACTCTGA-CCTCTGAAAACTTCTTG-AATGA

                          *  *                 
         71 GATCAACTCTGACCCCTAAAAACTTCTTGATATGA
          1 GATCAACTCTGACCTCTGAAAACTTCTTGA-ATGA

                                               
        106 GATCAACTCTGACCTCTGAAAACTTCTTGGAATGA
          1 GATCAACTCTGACCTCTGAAAACTTCTT-GAATGA

                                               
        141 GATCAACTCTGACCTCTGAAAACTTCTTGGAATGA
          1 GATCAACTCTGACCTCTGAAAACTTCTT-GAATGA

                                               
        176 GATCAACTCTGACCTCTGAAAACTTCTTGAAGTGA
          1 GATCAACTCTGACCTCTGAAAACTTCTTGAA-TGA

                        *   *                  
        211 GATCAACTCTGATCTCAGAAAACTTCTTGGAATGA
          1 GATCAACTCTGACCTCTGAAAACTTCTT-GAATGA

                                               
        246 GATCAACTCTGACCTCTGAAAACTTCTTGCAATGA
          1 GATCAACTCTGACCTCTGAAAACTTCTTG-AATGA

                                            *  
        281 GATCAACTCTGACCTCTGAAAACTTCTTGATACGA
          1 GATCAACTCTGACCTCTGAAAACTTCTTGA-ATGA

                                               
        316 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
          1 GATCAACTCTGACCTCTGAAAACTTCTTG-AATGA

                                               
        351 GATCAACTCTGACCTCTGAAAACTTCTTGATATGA
          1 GATCAACTCTGACCTCTGAAAACTTCTTGA-ATGA

                                 *      
        386 GATCAACTCTGACCTCTGAAAGCTTCTT
          1 GATCAACTCTGACCTCTGAAAACTTCTT

        414 AAAATGACCG


Statistics
Matches: 321,  Mismatches: 13, Indels: 18
        0.91            0.04        0.05

Matches are distributed among these distances:
  34    8  0.02
  35  307  0.96
  36    6  0.02

ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29


Consensus pattern (34 bp):   
GATCAACTCTGACCTCTGAAAACTTCTTGAATGA

Found at i:1312 original size:20 final size:20

Alignment explanation


    Indices: 1284--1325  Score: 66
    Period size: 20  Copynumber: 2.1  Consensus size: 20

       1274 TCCCTTTTTC

                *               
       1284 TTCTTTTTTTTTTGAAACTT
          1 TTCTCTTTTTTTTGAAACTT

                         *      
       1304 TTCTCTTTTTTTTTAAACTT
          1 TTCTCTTTTTTTTGAAACTT

              
       1324 TT
          1 TT

       1326 TTTTTTGGAA


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  20   20  1.00

ACGTcount: A:0.14, C:0.12, G:0.02, T:0.71


Consensus pattern (20 bp):   
TTCTCTTTTTTTTGAAACTT

Found at i:1327 original size:22 final size:24

Alignment explanation


    Indices: 1277--1326  Score: 72
    Period size: 21  Copynumber: 2.2  Consensus size: 24

       1267 GAACCCCTCC

                                    
       1277 CTTTTTCTTCTTTTTTTTTTGAAA
          1 CTTTTTCTTCTTTTTTTTTTGAAA

                                    
       1301 C-TTTTC-TC-TTTTTTTTT-AAA
          1 CTTTTTCTTCTTTTTTTTTTGAAA

                  
       1321 CTTTTT
          1 CTTTTT

       1327 TTTTTGGAAA


Statistics
Matches: 25,  Mismatches: 0, Indels: 5
        0.83            0.00        0.17

Matches are distributed among these distances:
  20    4  0.16
  21   13  0.52
  22    2  0.08
  23    5  0.20
  24    1  0.04

ACGTcount: A:0.12, C:0.14, G:0.02, T:0.72


Consensus pattern (24 bp):   
CTTTTTCTTCTTTTTTTTTTGAAA
Done.