Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021914.1 Corchorus olitorius cultivar O-4 contig21947, 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: 18592
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:1259 original size:22 final size:22

Alignment explanation


    Indices: 1240--1296  Score: 114
    Period size: 22  Copynumber: 2.6  Consensus size: 22

       1230 CCATGACCCG

                                  
       1240 GCCATGCCGCACACCAGACCAA
          1 GCCATGCCGCACACCAGACCAA

                                  
       1262 GCCATGCCGCACACCAGACCAA
          1 GCCATGCCGCACACCAGACCAA

                         
       1284 GCCATGCCGCACA
          1 GCCATGCCGCACA

       1297 TGACCGAGCC


Statistics
Matches: 35,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  22   35  1.00

ACGTcount: A:0.30, C:0.46, G:0.19, T:0.05


Consensus pattern (22 bp):   
GCCATGCCGCACACCAGACCAA

Found at i:8979 original size:14 final size:14

Alignment explanation


    Indices: 8960--8993  Score: 68
    Period size: 14  Copynumber: 2.4  Consensus size: 14

       8950 CTGTCGCGGA

                          
       8960 CGCGGTCACGGTGT
          1 CGCGGTCACGGTGT

                          
       8974 CGCGGTCACGGTGT
          1 CGCGGTCACGGTGT

                  
       8988 CGCGGT
          1 CGCGGT

       8994 TGCGGGTGTC


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   20  1.00

ACGTcount: A:0.06, C:0.29, G:0.44, T:0.21


Consensus pattern (14 bp):   
CGCGGTCACGGTGT

Found at i:10492 original size:35 final size:36

Alignment explanation


    Indices: 10438--10510  Score: 105
    Period size: 35  Copynumber: 2.1  Consensus size: 36

      10428 GTTATCGTAT

                                                
      10438 AATTATAAAGATTCCTACCAAAG-CAAAGTACGCTG
          1 AATTATAAAGATTCCTACCAAAGACAAAGTACGCTG

                           *            *        
      10473 AATTATTAAA-ATTCTTACCAAAGACAACGTACGCTG
          1 AATTA-TAAAGATTCCTACCAAAGACAAAGTACGCTG

              
      10509 AA
          1 AA

      10511 GTTTGGCAGT


Statistics
Matches: 34,  Mismatches: 2, Indels: 3
        0.87            0.05        0.08

Matches are distributed among these distances:
  35   17  0.50
  36   17  0.50

ACGTcount: A:0.44, C:0.19, G:0.12, T:0.25


Consensus pattern (36 bp):   
AATTATAAAGATTCCTACCAAAGACAAAGTACGCTG

Found at i:14221 original size:82 final size:81

Alignment explanation


    Indices: 14157--14324  Score: 246
    Period size: 82  Copynumber: 2.0  Consensus size: 81

      14147 TTTCTTATTT

                   *                *                                        
      14157 GAATTTATTAAAAAAAACTACAGGGCTATTAAGAACGAAGTTAAACATTAATCAATTAAAAAGGT
          1 GAATTTACT-AAAAAAACTACAGGACTATTAAGAACGAAGTTAAACATTAATCAATTAAAAAGGT

                *             
      14222 TATCGATCTCTGATGCAA
         65 TATCAATCTCTGAT-CAA

                                              *                       *      
      14240 GAATTTACTAAAAAAACTACAGGACTATTAAGAATGAAGTTAAACATTAATCAATTAAGAAGGTT
          1 GAATTTACTAAAAAAACTACAGGACTATTAAGAACGAAGTTAAACATTAATCAATTAAAAAGGTT

               *      *      
      14305 ATCGATCTCTAATGCAA
         66 ATCAATCTCTGAT-CAA

               
      14322 GAA
          1 GAA

      14325 GATTATAATT


Statistics
Matches: 80,  Mismatches: 5, Indels: 1
        0.93            0.06        0.01

Matches are distributed among these distances:
  82   72  0.90
  83    8  0.10

ACGTcount: A:0.46, C:0.12, G:0.14, T:0.27


Consensus pattern (81 bp):   
GAATTTACTAAAAAAACTACAGGACTATTAAGAACGAAGTTAAACATTAATCAATTAAAAAGGTT
ATCAATCTCTGATCAA

Found at i:14760 original size:21 final size:20

Alignment explanation


    Indices: 14718--14761  Score: 52
    Period size: 21  Copynumber: 2.1  Consensus size: 20

      14708 TCTTGTAATC

                             *  
      14718 TAAAATTACTAAAAAAGTTA
          1 TAAAATTACTAAAAAAGCTA

                     *     *     
      14738 TAAAATGTATTAAAATAGCTA
          1 TAAAAT-TACTAAAAAAGCTA

               
      14759 TAA
          1 TAA

      14762 CGCTTTCTCA


Statistics
Matches: 20,  Mismatches: 3, Indels: 1
        0.83            0.12        0.04

Matches are distributed among these distances:
  20    6  0.30
  21   14  0.70

ACGTcount: A:0.57, C:0.05, G:0.07, T:0.32


Consensus pattern (20 bp):   
TAAAATTACTAAAAAAGCTA

Found at i:16375 original size:36 final size:35

Alignment explanation


    Indices: 16315--16383  Score: 93
    Period size: 36  Copynumber: 1.9  Consensus size: 35

      16305 TTCAATAACG

                              **               
      16315 TTACATTTTTGTAATTATGGTTATCATAATTCTTA
          1 TTACATTTTTGTAATTATAATTATCATAATTCTTA

                             *           *    
      16350 TTACATTTTTTGTAATTTTAATTATCATATTTCT
          1 TTACA-TTTTTGTAATTATAATTATCATAATTCT

      16384 CCAAAATCTC


Statistics
Matches: 29,  Mismatches: 4, Indels: 1
        0.85            0.12        0.03

Matches are distributed among these distances:
  35    5  0.17
  36   24  0.83

ACGTcount: A:0.28, C:0.09, G:0.06, T:0.58


Consensus pattern (35 bp):   
TTACATTTTTGTAATTATAATTATCATAATTCTTA
Done.