Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020912.1 Corchorus olitorius cultivar O-4 contig20945, 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: 8239
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32


Found at i:2765 original size:33 final size:34

Alignment explanation


    Indices: 2728--2813  Score: 138
    Period size: 35  Copynumber: 2.5  Consensus size: 34

       2718 AATCTATTCC

                                              
       2728 AAGTAAACTAACCAATTTTGTTGT-AAAAAAAAA
          1 AAGTAAACTAACCAATTTTGTTGTAAAAAAAAAA

                                               
       2761 AAGTAAACTAACCAATTTTTGTTGTAAAAAAAAAA
          1 AAGTAAACTAACCAA-TTTTGTTGTAAAAAAAAAA

              **              
       2796 AAAAAAACTAACCAATTT
          1 AAGTAAACTAACCAATTT

       2814 CTAGTCAGGG


Statistics
Matches: 49,  Mismatches: 2, Indels: 3
        0.91            0.04        0.06

Matches are distributed among these distances:
  33   15  0.31
  34   12  0.24
  35   22  0.45

ACGTcount: A:0.56, C:0.10, G:0.07, T:0.27


Consensus pattern (34 bp):   
AAGTAAACTAACCAATTTTGTTGTAAAAAAAAAA

Found at i:5084 original size:65 final size:64

Alignment explanation


    Indices: 4865--5245  Score: 317
    Period size: 65  Copynumber: 5.8  Consensus size: 64

       4855 ACAAAGTTCG

                 *           *               * *      *      *               
       4865 CCCTTTGACCGAAAGGGCATTTTTGGAAAGT-AGAGTAAACTGAAATGTGAAAATGATGAAACTG
          1 CCCTTCGACCGAAAGGGTATTTTTGGAAAGTAAAACTAAACTTAAATG-CAAAA-GATGAAACTG

             
       4929 A
         64 A

                                     *               *                 *     
       4930 CCCTTTC-ACCGAAAGGGTATTTTTTGAAA-TCAAAAGCTAGACTTAAATGCATTAACCTGATGA
          1 CCC-TTCGACCGAAAGGGTATTTTTGGAAAGT-AAAA-CTAAACTTAAATGCA--AA--AGATGA

                  
       4993 AACTGA
         59 AACTGA

                       *                                             *       
       4999 CCCTTCGACCGGAAGGGTATTTTTGGAAAGTAAAACTAAAACTTAAATGCAAAAGACGGAAA-TG
          1 CCCTTCGACCGAAAGGGTATTTTTGGAAAGTAAAACT-AAACTTAAATGCAAAAGA-TGAAACTG

             
       5063 A
         64 A

                                             *                         *    *
       5064 CCCTTCGACCGAAAGGGTA-TTTTGGAAATTTGAAAATACTAAACTTAAATGCAAAAGACGAAAA
          1 CCCTTCGACCGAAAGGGTATTTTTGGAAA---GTAAA-ACTAAACTTAAATGCAAAAGATGAAAC

               
       5128 TGA
         62 TGA

                          *    *   *                         * *     *     * 
       5131 CCCTTCGACCGAAATGGTACTTTGGGAAAAG-AAAACT-AACTTAGATACGGAAAAGTTGAAATT
          1 CCCTTCGACCGAAAGGGTATTTTTGG-AAAGTAAAACTAAACTTA-A-ATGCAAAAGATGAAACT

              
       5194 GA
         63 GA

                                   *       *       *          
       5196 CCCTTCGACCGAAAGGGTATTTTCGGAAATGAAAATACTGAACTTAAATG
          1 CCCTTCGACCGAAAGGGTATTTTTGGAAA-GTAAA-ACTAAACTTAAATG

       5246 GGAACCTTCC


Statistics
Matches: 263,  Mismatches: 28, Indels: 49
        0.77            0.08        0.14

Matches are distributed among these distances:
  63    6  0.02
  64   17  0.06
  65   87  0.33
  66   19  0.07
  67   59  0.22
  68   21  0.08
  69   53  0.20
  70    1  0.00

ACGTcount: A:0.39, C:0.16, G:0.20, T:0.25


Consensus pattern (64 bp):   
CCCTTCGACCGAAAGGGTATTTTTGGAAAGTAAAACTAAACTTAAATGCAAAAGATGAAACTGA

Found at i:5166 original size:132 final size:131

Alignment explanation


    Indices: 4922--5245  Score: 338
    Period size: 132  Copynumber: 2.4  Consensus size: 131

       4912 TGAAAATGAT

                *                           **     *     *   *               
       4922 GAAACTGACCCTTTC-ACCGAAAGGGTATTTTTTGAAATCAAAA-GCTAGACTTAAATGCATTAA
          1 GAAATTGACCC-TTCGACCGAAAGGGTATTTTCGGAAATGAAAATACTAAACTTAAATGCA--AA

              *  *    *              *       *   *                         * 
       4985 CCTGATGAAACTGACCCTTCGACCGGAAGGGTATTTTTGGAAAGTAAAACTAAAACTTA-A-ATG
         63 --AGACGAAAATGACCCTTCGACCGAAAGGGTACTTTGGGAAAGTAAAACT--AACTTAGATACG

                     
       5048 CAAAAGACG
        124 CAAAAG-CG

                                                                             
       5057 GAAA-TGACCCTTCGACCGAAAGGGTATTTT-GGAAATTTGAAAATACTAAACTTAAATGCAAAA
          1 GAAATTGACCCTTCGACCGAAAGGGTATTTTCGGAAA--TGAAAATACTAAACTTAAATGCAAAA

                                     *                                   *   
       5120 GACGAAAATGACCCTTCGACCGAAATGGTACTTTGGGAAAAG-AAAACTAACTTAGATACGGAAA
         64 GACGAAAATGACCCTTCGACCGAAAGGGTACTTTGGG-AAAGTAAAACTAACTTAGATACGCAAA

              **
       5184 AGTT
        128 AGCG

                                                           *          
       5188 GAAATTGACCCTTCGACCGAAAGGGTATTTTCGGAAATGAAAATACTGAACTTAAATG
          1 GAAATTGACCCTTCGACCGAAAGGGTATTTTCGGAAATGAAAATACTAAACTTAAATG

       5246 GGAACCTTCC


Statistics
Matches: 164,  Mismatches: 16, Indels: 22
        0.81            0.08        0.11

Matches are distributed among these distances:
 130    6  0.04
 131   25  0.15
 132   70  0.43
 133   16  0.10
 134   24  0.15
 135    9  0.05
 136   14  0.09

ACGTcount: A:0.40, C:0.16, G:0.19, T:0.24


Consensus pattern (131 bp):   
GAAATTGACCCTTCGACCGAAAGGGTATTTTCGGAAATGAAAATACTAAACTTAAATGCAAAAGA
CGAAAATGACCCTTCGACCGAAAGGGTACTTTGGGAAAGTAAAACTAACTTAGATACGCAAAAGC
G

Found at i:7977 original size:8 final size:9

Alignment explanation


    Indices: 7953--7978  Score: 52
    Period size: 9  Copynumber: 2.9  Consensus size: 9

       7943 CCTGCATTAG

                     
       7953 CTGTTTTTT
          1 CTGTTTTTT

                     
       7962 CTGTTTTTT
          1 CTGTTTTTT

                    
       7971 CTGTTTTT
          1 CTGTTTTT

       7979 GCCTTCCATG


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   9   17  1.00

ACGTcount: A:0.00, C:0.12, G:0.12, T:0.77


Consensus pattern (9 bp):   
CTGTTTTTT
Done.