Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009748.1 Corchorus olitorius cultivar O-4 contig09780, 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: 3155
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.37


Found at i:629 original size:331 final size:331

Alignment explanation


    Indices: 4--698  Score: 863
    Period size: 331  Copynumber: 2.1  Consensus size: 331

          1 CTG

                                  *     *   *            *                   
          4 GTTTCGATTTAATTAGAAATTATTTCGAGAAAGTAAAAGAAAAACTATATTAGAAGCGTGAGAAG
          1 GTTTCGATTTAATTAGAAATTAATTCGAAAAAATAAAAGAAAAACAATATTAGAAGCGTGAGAAG

            *                *         *              * *                    
         69 TCCTTCAATCTTTTTGGTGTTGAAATATATATTTTTTACGAGTTTTGATGGCCAAAAATTGAGAA
         66 CCCTTCAATCTTTTTGGCGTTGAAATAAATATTTTTTACGAGATATGATGGCCAAAAATTGAGAA

                   *                                     *          *        
        134 ATGATTTGGGTAAATTTTTTGCAAAATTTTAGCCGAAATCATGTATTAACCATCACGGTTTTGAC
        131 ATGATTTAGGTAAATTTTTTGCAAAATTTTAGCCGAAATCATGTACTAACCATCACAGTTTTGAC

                                                                    *        
        199 TAAAAACGCATTTCGGGGTCCCGGCTCAGTTTTGCATGATTTTTCGCGTCAAGCTTGATTGAAAT
        196 TAAAAACGCATTTCGGGGTCCCGGCTCAGTTTTGCATGATTTTTCGCGTCAAGCTTCATTGAAAT

                           * *  *              **           *                
        264 ATCTATATTCATCTAGCGAACGCTCAGACACATTGTCTTTAAGGAT-TTTTTTTAAGAGCATCTC
        261 ATCTATATTCATCTAACCAAAGCTCAGACACATTGGATTTAAGGATCTGTTTTTAAGAGCATCTC

                  
        328 AATC-C
        326 AATCAC

                                                *                            
        333 GATTTCGATTTAATTAGAAATTAATTCGAAAAAATAGAA-AAAAACAATATTAGAAGCGTGAGAA
          1 G-TTTCGATTTAATTAGAAATTAATTCGAAAAAATAAAAGAAAAACAATATTAGAAGCGTGAGAA

                                    **             *        *     **         
        397 GCCCTTCAATCTTTTTGGCGTTGAGTTAAATATTTTTTATGA-ATATGGTGGCCGGAAATTGAGG
         65 GCCCTTCAATCTTTTTGGCGTTGAAATAAATATTTTTTACGAGATATGATGGCCAAAAATT---G

                         *  *                     *                 *       *
        461 AGAAATG-TTTCATGTCAA-TTTTTGCAAAATTTTAGCTGAAAT-AGTGTACTAACGATCACAAT
        127 AGAAATGATTT-AGGTAAATTTTTTGCAAAATTTTAGCCGAAATCA-TGTACTAACCATCAC-AG

                            *                 *                *             
        523 TTTTGACTAAAAACGCGTTTCGGGGTCCCGGCTCTGTTTTGCATGATTTTTGGCG-CAAAG-TCT
        189 TTTTGACTAAAAACGCATTTCGGGGTCCCGGCTCAGTTTTGCATGATTTTTCGCGTC-AAGCT-T

                                           *                                 
        586 CATTGAAATATCTATA-TCTATCTAACCAAATCTCA-ACCACATTGGATTTAAGGATCTGTTTTT
        252 CATTGAAATATCTATATTC-ATCTAACCAAAGCTCAGA-CACATTGGATTTAAGGATCTGTTTTT

             *   *    *     *
        649 ACGAGTATCTGAATCAT
        315 AAGAGCATCTCAATCAC

                                             
        666 GTTTCGATTTAATTAGAAATTAATTCGAAAAAA
          1 GTTTCGATTTAATTAGAAATTAATTCGAAAAAA

        699 AATAGGAAAG


Statistics
Matches: 314,  Mismatches: 39, Indels: 23
        0.84            0.10        0.06

Matches are distributed among these distances:
 328   13  0.04
 329   62  0.20
 330   77  0.25
 331  111  0.35
 332   50  0.16
 333    1  0.00

ACGTcount: A:0.33, C:0.14, G:0.18, T:0.36


Consensus pattern (331 bp):   
GTTTCGATTTAATTAGAAATTAATTCGAAAAAATAAAAGAAAAACAATATTAGAAGCGTGAGAAG
CCCTTCAATCTTTTTGGCGTTGAAATAAATATTTTTTACGAGATATGATGGCCAAAAATTGAGAA
ATGATTTAGGTAAATTTTTTGCAAAATTTTAGCCGAAATCATGTACTAACCATCACAGTTTTGAC
TAAAAACGCATTTCGGGGTCCCGGCTCAGTTTTGCATGATTTTTCGCGTCAAGCTTCATTGAAAT
ATCTATATTCATCTAACCAAAGCTCAGACACATTGGATTTAAGGATCTGTTTTTAAGAGCATCTC
AATCAC

Found at i:2775 original size:2 final size:2

Alignment explanation


    Indices: 2768--2795  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

       2758 GCAATAGAAC

                                                     
       2768 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

       2796 GAGAGAAGAT


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

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


Consensus pattern (2 bp):   
AT

Done.