Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011695.1 Corchorus capsularis cultivar CVL-1 contig11716, 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: 13810
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.31


Found at i:590 original size:2 final size:2

Alignment explanation


    Indices: 583--618  Score: 72
    Period size: 2  Copynumber: 18.0  Consensus size: 2

        573 TATAATTAGA

                                                                 
        583 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

        619 GATAGGATAA


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   34  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:1272 original size:23 final size:23

Alignment explanation


    Indices: 1193--1237  Score: 63
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       1183 AACCCTAAAC

                                   
       1193 ATAACGTTAAGAATTTAATATAT
          1 ATAACGTTAAGAATTTAATATAT

                 *  *      *      
       1216 ATAACCTTGAGAATTAAATATA
          1 ATAACGTTAAGAATTTAATATA

       1238 ACGTTATATA


Statistics
Matches: 19,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  23   19  1.00

ACGTcount: A:0.49, C:0.07, G:0.09, T:0.36


Consensus pattern (23 bp):   
ATAACGTTAAGAATTTAATATAT

Found at i:1282 original size:22 final size:22

Alignment explanation


    Indices: 1242--1298  Score: 78
    Period size: 22  Copynumber: 2.5  Consensus size: 22

       1232 AATATAACGT

                    *              
       1242 TATATAACATTAAGAATTTAATA
          1 TATATAACGTT-AGAATTTAATA

                                 *
       1265 TATATAACGTTAGAATTTAATT
          1 TATATAACGTTAGAATTTAATA

              *         
       1287 TACATAACGTTA
          1 TATATAACGTTA

       1299 AAAATAAATA


Statistics
Matches: 31,  Mismatches: 3, Indels: 1
        0.89            0.09        0.03

Matches are distributed among these distances:
  22   21  0.68
  23   10  0.32

ACGTcount: A:0.46, C:0.07, G:0.07, T:0.40


Consensus pattern (22 bp):   
TATATAACGTTAGAATTTAATA

Found at i:1754 original size:13 final size:13

Alignment explanation


    Indices: 1736--1760  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       1726 TTCAATGTTC

                         
       1736 TAAATATTATTTA
          1 TAAATATTATTTA

                        
       1749 TAAATATTATTT
          1 TAAATATTATTT

       1761 GGAATTCAAA


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56


Consensus pattern (13 bp):   
TAAATATTATTTA

Found at i:2009 original size:30 final size:30

Alignment explanation


    Indices: 1973--2029  Score: 87
    Period size: 30  Copynumber: 1.9  Consensus size: 30

       1963 AGATTTCAAT

                                          
       1973 TGTAATTATTGGAAAAAGGGTTCGTTGAGA
          1 TGTAATTATTGGAAAAAGGGTTCGTTGAGA

                   *     *        *    
       2003 TGTAATTGTTGGAGAAAGGGTTTGTTG
          1 TGTAATTATTGGAAAAAGGGTTCGTTG

       2030 GCTCATAGAT


Statistics
Matches: 24,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  30   24  1.00

ACGTcount: A:0.28, C:0.02, G:0.33, T:0.37


Consensus pattern (30 bp):   
TGTAATTATTGGAAAAAGGGTTCGTTGAGA

Found at i:2229 original size:16 final size:16

Alignment explanation


    Indices: 2204--2253  Score: 55
    Period size: 16  Copynumber: 3.1  Consensus size: 16

       2194 TATCTTTTCA

                            
       2204 TTTTTCTTTGTGTTAC
          1 TTTTTCTTTGTGTTAC

                 *       ** *
       2220 TTTTTTTTTGTTGAAAA
          1 TTTTTCTTTG-TGTTAC

                            
       2237 TTTTTCTTTGTGTTAC
          1 TTTTTCTTTGTGTTAC

             
       2253 T
          1 T

       2254 CAAAGCTTGG


Statistics
Matches: 25,  Mismatches: 8, Indels: 2
        0.71            0.23        0.06

Matches are distributed among these distances:
  16   13  0.52
  17   12  0.48

ACGTcount: A:0.12, C:0.08, G:0.12, T:0.68


Consensus pattern (16 bp):   
TTTTTCTTTGTGTTAC
Done.