Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011242.1 Corchorus capsularis cultivar CVL-1 contig11263, 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: 4692
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34


Found at i:639 original size:43 final size:43

Alignment explanation


    Indices: 578--660  Score: 166
    Period size: 43  Copynumber: 1.9  Consensus size: 43

        568 ATCTATGAAC

                                                       
        578 TGAGTTATAAGTTGGCTTGAGTTATAATTTTTCATATTTGTGG
          1 TGAGTTATAAGTTGGCTTGAGTTATAATTTTTCATATTTGTGG

                                                    
        621 TGAGTTATAAGTTGGCTTGAGTTATAATTTTTCATATTTG
          1 TGAGTTATAAGTTGGCTTGAGTTATAATTTTTCATATTTG

        661 AATAGACTAT


Statistics
Matches: 40,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  43   40  1.00

ACGTcount: A:0.24, C:0.05, G:0.22, T:0.49


Consensus pattern (43 bp):   
TGAGTTATAAGTTGGCTTGAGTTATAATTTTTCATATTTGTGG

Found at i:790 original size:2 final size:2

Alignment explanation


    Indices: 783--815  Score: 66
    Period size: 2  Copynumber: 16.5  Consensus size: 2

        773 TAAAAAGGAG

                                                             
        783 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

        816 GTCAATAATG


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   31  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:3150 original size:179 final size:179

Alignment explanation


    Indices: 2838--3196  Score: 670
    Period size: 179  Copynumber: 2.0  Consensus size: 179

       2828 AAAGGACTAC

                                                                             
       2838 CATCCATAAGAGCTTTGTATAAATACAAAGAGCATCGATCCATGGTTTGGAGAGAGAAGAAAAAG
          1 CATCCATAAGAGCTTTGTATAAATACAAAGAGCATCGATCCATGGTTTGGAGAGAGAAGAAAAAG

                                                                             
       2903 AACTTGGAAAAAAAAAGAGAGAGAGAGAGAAGAAAACGAAACCATCTTTCCCATTAAACAATAAA
         66 AACTTGGAAAAAAAAAGAGAGAGAGAGAGAAGAAAACGAAACCATCTTTCCCATTAAACAATAAA

                                                             
       2968 GCAAAACTAATAAAGGGTATGGATCAGTTCAGCAGGGTTGTTTTTCTAG
        131 GCAAAACTAATAAAGGGTATGGATCAGTTCAGCAGGGTTGTTTTTCTAG

                                                                             
       3017 CATCCATAAGAGCTTTGTATAAATACAAAGAGCATCGATCCATGGTTTGGAGAGAGAAGAAAAAG
          1 CATCCATAAGAGCTTTGTATAAATACAAAGAGCATCGATCCATGGTTTGGAGAGAGAAGAAAAAG

                                                                             
       3082 AACTTGGAAAAAAAGAAGAGAGAGAGAGAGAAGAAAA-GAAACCCATCTTTCCCATT-AAC-ATA
         66 AACTTGGAAAAAAA-AAGAGAGAGAGAGAGAAGAAAACGAAA-CCATCTTTCCCATTAAACAAT-

                                                                
       3144 AAAGCAAAACTAATAAAGGGTATGGATCAGTTCAGCAGGGTTGTTTTTCTAG
        128 AAAGCAAAACTAATAAAGGGTATGGATCAGTTCAGCAGGGTTGTTTTTCTAG

             
       3196 C
          1 C

       3197 CCACTCCAAA


Statistics
Matches: 177,  Mismatches: 0, Indels: 6
        0.97            0.00        0.03

Matches are distributed among these distances:
 178    2  0.01
 179  139  0.79
 180   36  0.20

ACGTcount: A:0.43, C:0.14, G:0.22, T:0.21


Consensus pattern (179 bp):   
CATCCATAAGAGCTTTGTATAAATACAAAGAGCATCGATCCATGGTTTGGAGAGAGAAGAAAAAG
AACTTGGAAAAAAAAAGAGAGAGAGAGAGAAGAAAACGAAACCATCTTTCCCATTAAACAATAAA
GCAAAACTAATAAAGGGTATGGATCAGTTCAGCAGGGTTGTTTTTCTAG

Found at i:4512 original size:80 final size:80

Alignment explanation


    Indices: 4400--4556  Score: 224
    Period size: 80  Copynumber: 2.0  Consensus size: 80

       4390 CCAGATCTCG

                *                     *         * *        *        *        
       4400 AGCCGTGTAGGACTCCAATTGGGAGAGCCTCTTTTAGCCTCTATTTTTTCCATTTATAAGACTCG
          1 AGCCATGTAGGACTCCAATTGGGAGAACCTCTTTTAACATCTATTTTCTCCATTTACAAGACTCG

                           
       4465 AATTCCGAAACCTCC
         66 AATTCCGAAACCTCC

                    *              *                *                        
       4480 AGCCATGTCGGACTCCAATTGGGGGAACCTCTTTTAACATTTATTTTCTCCATTTACAAGACTCG
          1 AGCCATGTAGGACTCCAATTGGGAGAACCTCTTTTAACATCTATTTTCTCCATTTACAAGACTCG

                 *      
       4545 AATTCTGAAACC
         66 AATTCCGAAACC

       4557 ATTCTTAAGT


Statistics
Matches: 67,  Mismatches: 10, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  80   67  1.00

ACGTcount: A:0.25, C:0.25, G:0.17, T:0.32


Consensus pattern (80 bp):   
AGCCATGTAGGACTCCAATTGGGAGAACCTCTTTTAACATCTATTTTCTCCATTTACAAGACTCG
AATTCCGAAACCTCC

Found at i:4636 original size:2 final size:2

Alignment explanation


    Indices: 4629--4692  Score: 128
    Period size: 2  Copynumber: 32.0  Consensus size: 2

       4619 CCTTTGTTAT

                                                                          
       4629 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
          1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA

                                            
       4671 GA GA GA GA GA GA GA GA GA GA GA
          1 GA GA GA GA GA GA GA GA GA GA GA


Statistics
Matches: 62,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   62  1.00

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


Consensus pattern (2 bp):   
GA

Done.