Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013965.1 Corchorus olitorius cultivar O-4 contig13998, 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: 9853
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.35


Found at i:974 original size:49 final size:47

Alignment explanation


    Indices: 897--1037  Score: 160
    Period size: 49  Copynumber: 2.9  Consensus size: 47

        887 CAAGCAATCC

                *      *                                    
        897 TTTACTTTTCACTGCACTTTTTCTCAATTTTTACTACAAAATTGAACT
          1 TTTAATTTTCATTGCACTTTTTCTCAATTTTTA-TACAAAATTGAACT

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

                        *         *                      
        994 TTTAATTTTCATCGCACTTTTTATCAATTTTT-TGACAAAATTGA
          1 TTTAATTTTCATTGCACTTTTTCTCAATTTTTAT-ACAAAATTGA

       1038 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:1802 original size:78 final size:77

Alignment explanation


    Indices: 1673--1821  Score: 244
    Period size: 78  Copynumber: 1.9  Consensus size: 77

       1663 CACCATAACT

                                               * *                          *
       1673 AGGTGCGCGACGCGGGTCGGATCCGGATTAGTCAGGGTAAAGCCCTGGATACCGCATGGGATACC
          1 AGGTGCGCGACGCGGGTCGGATCCGGATTAGTCAGAGCAAAGCCCTGGATACCGCATGGGATA-A

                         
       1738 AAAAAAATAAATA
         65 AAAAAAATAAATA

                                            *                     *          
       1751 AGGTGCGCGACGCGGGTCGGATCCGGATTAGTTAGAGCAAAGCCCTGGATACCGGATGGGATAAA
          1 AGGTGCGCGACGCGGGTCGGATCCGGATTAGTCAGAGCAAAGCCCTGGATACCGCATGGGATAAA

                  
       1816 AAAAAA
         66 AAAAAA

       1822 CTTATTATAT


Statistics
Matches: 66,  Mismatches: 5, Indels: 1
        0.92            0.07        0.01

Matches are distributed among these distances:
  77    7  0.11
  78   59  0.89

ACGTcount: A:0.32, C:0.19, G:0.32, T:0.16


Consensus pattern (77 bp):   
AGGTGCGCGACGCGGGTCGGATCCGGATTAGTCAGAGCAAAGCCCTGGATACCGCATGGGATAAA
AAAAAATAAATA

Found at i:2127 original size:15 final size:15

Alignment explanation


    Indices: 2086--2129  Score: 52
    Period size: 15  Copynumber: 2.9  Consensus size: 15

       2076 CATATCAATT

                           
       2086 TTTTATTAAAAAAAA
          1 TTTTATTAAAAAAAA

            **  *  *       
       2101 AATTCTTCAAAAAAA
          1 TTTTATTAAAAAAAA

                          
       2116 TTTTATTAAAAAAA
          1 TTTTATTAAAAAAA

       2130 TATATAAAAA


Statistics
Matches: 21,  Mismatches: 8, Indels: 0
        0.72            0.28        0.00

Matches are distributed among these distances:
  15   21  1.00

ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36


Consensus pattern (15 bp):   
TTTTATTAAAAAAAA

Found at i:2231 original size:32 final size:30

Alignment explanation


    Indices: 2188--2248  Score: 77
    Period size: 30  Copynumber: 2.0  Consensus size: 30

       2178 CACCCTCTAA

                  *           *    *        
       2188 ATATAATAATAATCTAAATAAAATAAAAAAAT
          1 ATATAACAATAA--TAAAAAAAAGAAAAAAAT

                                         
       2220 ATATAACAATAATAAAAAAAAGAAAAAAA
          1 ATATAACAATAATAAAAAAAAGAAAAAAA

       2249 AAGACAGAAA


Statistics
Matches: 26,  Mismatches: 3, Indels: 2
        0.84            0.10        0.06

Matches are distributed among these distances:
  30   15  0.58
  32   11  0.42

ACGTcount: A:0.74, C:0.03, G:0.02, T:0.21


Consensus pattern (30 bp):   
ATATAACAATAATAAAAAAAAGAAAAAAAT

Found at i:9576 original size:82 final size:82

Alignment explanation


    Indices: 9439--9603  Score: 321
    Period size: 82  Copynumber: 2.0  Consensus size: 82

       9429 TGAAGCGTCA

                    *                                                        
       9439 AGAACACGGCCTTCACCTCTTGTCTAAGGTTTGCCTTTTCTCGTCGTAATGCAATTTTCTTTTTA
          1 AGAACACGCCCTTCACCTCTTGTCTAAGGTTTGCCTTTTCTCGTCGTAATGCAATTTTCTTTTTA

                             
       9504 CCAGATCGTCGTAATGC
         66 CCAGATCGTCGTAATGC

                                                                             
       9521 AGAACACGCCCTTCACCTCTTGTCTAAGGTTTGCCTTTTCTCGTCGTAATGCAATTTTCTTTTTA
          1 AGAACACGCCCTTCACCTCTTGTCTAAGGTTTGCCTTTTCTCGTCGTAATGCAATTTTCTTTTTA

                             
       9586 CCAGATCGTCGTAATGC
         66 CCAGATCGTCGTAATGC

             
       9603 A
          1 A

       9604 ATTTATTACT


Statistics
Matches: 82,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
  82   82  1.00

ACGTcount: A:0.20, C:0.26, G:0.16, T:0.38


Consensus pattern (82 bp):   
AGAACACGCCCTTCACCTCTTGTCTAAGGTTTGCCTTTTCTCGTCGTAATGCAATTTTCTTTTTA
CCAGATCGTCGTAATGC

Found at i:9812 original size:14 final size:14

Alignment explanation


    Indices: 9795--9823  Score: 58
    Period size: 14  Copynumber: 2.1  Consensus size: 14

       9785 AATGTGACAA

                          
       9795 ATAAAAAGGAATGG
          1 ATAAAAAGGAATGG

                          
       9809 ATAAAAAGGAATGG
          1 ATAAAAAGGAATGG

             
       9823 A
          1 A

       9824 GGGAGTATAA


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   15  1.00

ACGTcount: A:0.59, C:0.00, G:0.28, T:0.14


Consensus pattern (14 bp):   
ATAAAAAGGAATGG
Done.