Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021265.1 Corchorus olitorius cultivar O-4 contig21298, 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: 10471
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27


Found at i:404 original size:49 final size:47

Alignment explanation


    Indices: 327--467  Score: 160
    Period size: 49  Copynumber: 2.9  Consensus size: 47

        317 CAAGCAATCC

                *      *                                    
        327 TTTACTTTTCACTGCACTTTTTCTCAATTTTTACTACAAAATTGAACT
          1 TTTAATTTTCATTGCACTTTTTCTCAATTTTTA-TACAAAATTGAACT

                     *                          *          *  
        375 TTT-ATTTTTACTTGCATCTTTTTCTCAATTTTTAAGACAAAATTGATCT
          1 TTTAATTTTCA-TTGCA-CTTTTTCTCAATTTTT-ATACAAAATTGAACT

                        *         *                      
        424 TTTAATTTTCATCGCACTTTTTATCAATTTTT-TGACAAAATTGA
          1 TTTAATTTTCATTGCACTTTTTCTCAATTTTTAT-ACAAAATTGA

        468 TTGGCACGCT


Statistics
Matches: 79,  Mismatches: 9, Indels: 11
        0.80            0.09        0.11

Matches are distributed among these distances:
  47   15  0.19
  48   22  0.28
  49   35  0.44
  50    7  0.09

ACGTcount: A:0.28, C:0.16, G:0.06, T:0.50


Consensus pattern (47 bp):   
TTTAATTTTCATTGCACTTTTTCTCAATTTTTATACAAAATTGAACT

Found at i:1312 original size:15 final size:16

Alignment explanation


    Indices: 1292--1329  Score: 51
    Period size: 15  Copynumber: 2.4  Consensus size: 16

       1282 TGCTAGGGTG

                            
       1292 AATGGTGCAAAC-AAC
          1 AATGGTGCAAACAAAC

                   **       
       1307 AATGGTGTGAACAAAC
          1 AATGGTGCAAACAAAC

                   
       1323 AATGGTG
          1 AATGGTG

       1330 TGAACAATAA


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  15   10  0.50
  16   10  0.50

ACGTcount: A:0.42, C:0.13, G:0.26, T:0.18


Consensus pattern (16 bp):   
AATGGTGCAAACAAAC

Found at i:1323 original size:19 final size:18

Alignment explanation


    Indices: 1299--1336  Score: 53
    Period size: 16  Copynumber: 2.2  Consensus size: 18

       1289 GTGAATGGTG

                               
       1299 CAAACAACAATGGTGTGAA
          1 CAAA-AACAATGGTGTGAA

                              
       1318 C--AAACAATGGTGTGAA
          1 CAAAAACAATGGTGTGAA

               
       1334 CAA
          1 CAA

       1337 TAATGGAAAC


Statistics
Matches: 17,  Mismatches: 0, Indels: 5
        0.77            0.00        0.23

Matches are distributed among these distances:
  16   15  0.88
  17    1  0.06
  19    1  0.06

ACGTcount: A:0.47, C:0.16, G:0.21, T:0.16


Consensus pattern (18 bp):   
CAAAAACAATGGTGTGAA

Found at i:1325 original size:16 final size:16

Alignment explanation


    Indices: 1304--1336  Score: 66
    Period size: 16  Copynumber: 2.1  Consensus size: 16

       1294 TGGTGCAAAC

                            
       1304 AACAATGGTGTGAACA
          1 AACAATGGTGTGAACA

                            
       1320 AACAATGGTGTGAACA
          1 AACAATGGTGTGAACA

             
       1336 A
          1 A

       1337 TAATGGAAAC


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   17  1.00

ACGTcount: A:0.45, C:0.12, G:0.24, T:0.18


Consensus pattern (16 bp):   
AACAATGGTGTGAACA
Done.