Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010523.1 Corchorus olitorius cultivar O-4 contig10555, 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: 5689
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31


Found at i:1093 original size:23 final size:23

Alignment explanation


    Indices: 1019--1251  Score: 290
    Period size: 23  Copynumber: 10.2  Consensus size: 23

       1009 TGTTTTTTTT

                       *          *
       1019 TGTTGAAAATGTTGCTG-TTTGT
          1 TGTTGAAAATGCTGCTGTTTTGC

                            *      
       1041 TGTTGAAAATGCTGCTATTTTG-
          1 TGTTGAAAATGCTGCTGTTTTGC

                                   
       1063 TGTTGAAAATGCTGCTGTTTTGC
          1 TGTTGAAAATGCTGCTGTTTTGC

                    *            * 
       1086 TGTTGAAATTGCTGCTGTTTTTC
          1 TGTTGAAAATGCTGCTGTTTTGC

                       *           
       1109 TGTTGAAAATGTTGCTGTTTTGC
          1 TGTTGAAAATGCTGCTGTTTTGC

                *  *   *          *
       1132 TGTTCAAGATGTTGCTGTTTTGA
          1 TGTTGAAAATGCTGCTGTTTTGC

                       *           
       1155 TGTTGAAAATGTTGCTGTTTTGC
          1 TGTTGAAAATGCTGCTGTTTTGC

                          *        
       1178 TGTTGAAAATGCTGTTGTTTTGC
          1 TGTTGAAAATGCTGCTGTTTTGC

                    *             * 
       1201 TGTTGAAATTGCTGCTGTTTTTTC
          1 TGTTGAAAATGCTGCTG-TTTTGC

             *         *  *        
       1225 TATTGAAAATGTTGTTGTTTTGC
          1 TGTTGAAAATGCTGCTGTTTTGC

                
       1248 TGTT
          1 TGTT

       1252 TTGATGTTCA


Statistics
Matches: 183,  Mismatches: 25, Indels: 5
        0.86            0.12        0.02

Matches are distributed among these distances:
  22   36  0.20
  23  129  0.70
  24   18  0.10

ACGTcount: A:0.17, C:0.09, G:0.24, T:0.49


Consensus pattern (23 bp):   
TGTTGAAAATGCTGCTGTTTTGC

Found at i:2144 original size:40 final size:40

Alignment explanation


    Indices: 2100--2176  Score: 120
    Period size: 40  Copynumber: 1.9  Consensus size: 40

       2090 GTCATTCACA

                           *                         
       2100 TTAAAAAT-ATAATCCAAAACAATTTGTTCTAATCCACACG
          1 TTAAAAATGA-AATCAAAAACAATTTGTTCTAATCCACACG

                         *                       
       2140 TTAAAAATGAAATTAAAAACAATTTGTTCTAATCCAC
          1 TTAAAAATGAAATCAAAAACAATTTGTTCTAATCCAC

       2177 TCATGTAGCA


Statistics
Matches: 34,  Mismatches: 2, Indels: 2
        0.89            0.05        0.05

Matches are distributed among these distances:
  40   33  0.97
  41    1  0.03

ACGTcount: A:0.47, C:0.17, G:0.05, T:0.31


Consensus pattern (40 bp):   
TTAAAAATGAAATCAAAAACAATTTGTTCTAATCCACACG

Found at i:2380 original size:17 final size:17

Alignment explanation


    Indices: 2344--2381  Score: 51
    Period size: 17  Copynumber: 2.2  Consensus size: 17

       2334 AAAGCAGTGG

                           * 
       2344 GAATATTGAACTTAGGA
          1 GAATATTGAACTTAGAA

                              
       2361 GAATATTGAA-TTATGAA
          1 GAATATTGAACTTA-GAA

                
       2378 GAAT
          1 GAAT

       2382 GTTTGAAAGG


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  16    3  0.16
  17   16  0.84

ACGTcount: A:0.45, C:0.03, G:0.21, T:0.32


Consensus pattern (17 bp):   
GAATATTGAACTTAGAA
Done.