Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019247.1 Corchorus olitorius cultivar O-4 contig19280, 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: 3589
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.39


Found at i:1374 original size:260 final size:257

Alignment explanation


    Indices: 889--1407  Score: 860
    Period size: 260  Copynumber: 2.0  Consensus size: 257

        879 TATTATCAAA

                                  *               *     *                    
        889 TATAACATATATTAAAGTTGAATATGAATTACCCTTCTGTCCAATTATAAGATGCACCACATTCA
          1 TATAACATATATTAAAGTTGAAAATGAATTACCCTTCTATCCAACTATAAGATGCACCACATTCA

                                                                             
        954 CCCAAGAACAAATTGTCAGGGGTATTTTGGTACTTTCATACTCGGTTTCTCGCTATTTAGGTTGA
         66 CCCAAGAACAAATTGTCAGGGGTATTTTGGTACTTTCATACTCGGTTTCTCGCTATTTAGGTTGA

                            *           *          *                    *    
       1019 TAGCCAAGGGCATTTTTGGAACTTTGATTAAAAGTTACTTTTAGTGGGTCCCACTCTCAATAAAC
        131 TAGCCAAGGGCATTTTGGGAACTTTGATCAAAAGTTACTATTAGTGGGTCCCACTCTCAACAAAC

                          *                                   *           
       1084 TAATCTTTTTTTTGGTGGAATATTTAGCAAATGATCCCTATACTTTTATGTTTTATGCTATT
        196 TAATCTTTTTTTTGCTGGAATATTTAGCAAATGATCCCTATACTTTTATGCTTTATGCTATT

                                                 *      *                    
       1146 TATAACATATATTAAAGTTGAAAATGAAATTACCCTTTTATCCAGCTATAAGATGCA-CACCATT
          1 TATAACATATATTAAAGTTGAAAATG-AATTACCCTTCTATCCAACTATAAGATGCACCA-CATT

                                                                *            
       1210 CACCCAAGAACAAATTGTCAGGGGTATTTTGGTACTTTCATACTCGGTTTTTTTCGCTATTTAGG
         64 CACCCAAGAACAAATTGTCAGGGGTATTTTGGTACTTTCATACTCGG--TTTCTCGCTATTTAGG

                           *                                             *   
       1275 TTGATAGCCAAGGGCGTTTTGGGAACTTTGATCAAAAGTTACTATTAGTGGGTCCCACTCTGAAC
        127 TTGATAGCCAAGGGCATTTTGGGAACTTTGATCAAAAGTTACTATTAGTGGGTCCCACTCTCAAC

                                  *                                          
       1340 AAACTAATCTTTTTTTTGCTGGGATATTTAGCAAATGATCCCTATACTTTTATGCTTTATGCTAT
        192 AAACTAATCTTTTTTTTGCTGGAATATTTAGCAAATGATCCCTATACTTTTATGCTTTATGCTAT

             
       1405 T
        257 T

              
       1406 TA
          1 TA

       1408 ATCTCTCACA


Statistics
Matches: 243,  Mismatches: 15, Indels: 5
        0.92            0.06        0.02

Matches are distributed among these distances:
 257   27  0.11
 258   77  0.32
 260  139  0.57

ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38


Consensus pattern (257 bp):   
TATAACATATATTAAAGTTGAAAATGAATTACCCTTCTATCCAACTATAAGATGCACCACATTCA
CCCAAGAACAAATTGTCAGGGGTATTTTGGTACTTTCATACTCGGTTTCTCGCTATTTAGGTTGA
TAGCCAAGGGCATTTTGGGAACTTTGATCAAAAGTTACTATTAGTGGGTCCCACTCTCAACAAAC
TAATCTTTTTTTTGCTGGAATATTTAGCAAATGATCCCTATACTTTTATGCTTTATGCTATT

Found at i:3549 original size:11 final size:11

Alignment explanation


    Indices: 3533--3567  Score: 61
    Period size: 11  Copynumber: 3.2  Consensus size: 11

       3523 TTGACAGCTT

                       
       3533 AACAAAAACAA
          1 AACAAAAACAA

                     * 
       3544 AACAAAAACGA
          1 AACAAAAACAA

                       
       3555 AACAAAAACAA
          1 AACAAAAACAA

              
       3566 AA
          1 AA

       3568 AATAAAAAAC


Statistics
Matches: 22,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  11   22  1.00

ACGTcount: A:0.80, C:0.17, G:0.03, T:0.00


Consensus pattern (11 bp):   
AACAAAAACAA
Done.