Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014113.1 Corchorus olitorius cultivar O-4 contig14146, 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: 34790
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:8287 original size:14 final size:15

Alignment explanation


    Indices: 8249--8290  Score: 50
    Period size: 16  Copynumber: 2.7  Consensus size: 15

       8239 TTGATTAGCA

                            
       8249 AGAAAAGAAAATTAGT
          1 AGAAAA-AAAATTAGT

                *           
       8265 AGTAGAAAAAATTAG-
          1 AG-AAAAAAAATTAGT

                       
       8280 AGAAAAAAAAT
          1 AGAAAAAAAAT

       8291 GAAAAAGAGG


Statistics
Matches: 23,  Mismatches: 2, Indels: 4
        0.79            0.07        0.14

Matches are distributed among these distances:
  14    8  0.35
  15    2  0.09
  16   10  0.43
  17    3  0.13

ACGTcount: A:0.67, C:0.00, G:0.17, T:0.17


Consensus pattern (15 bp):   
AGAAAAAAAATTAGT

Found at i:14205 original size:3 final size:3

Alignment explanation


    Indices: 14197--14236  Score: 80
    Period size: 3  Copynumber: 13.3  Consensus size: 3

      14187 TCTTCTGTTT

                                                                 
      14197 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T

      14237 AACAATGTGT


Statistics
Matches: 37,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   37  1.00

ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68


Consensus pattern (3 bp):   
TTA

Found at i:26136 original size:68 final size:68

Alignment explanation


    Indices: 26056--26186  Score: 217
    Period size: 68  Copynumber: 1.9  Consensus size: 68

      26046 CAACTACCCT

                                                  *                          
      26056 CATTGGTAAACTCACCAACCAAACCTAGGTGCACGACCTGAGTCGAATCCGAATTAATCAACCGC
          1 CATTGGTAAACTCACCAACCAAACCTAGGTGCACGACCGGAGTCGAATCCGAATTAATCAACCGC

               
      26121 CCG
         66 CCG

                           *               *                   *    *      
      26124 CATTGGTAAACTCACTAACCAAACCTAGGTGTACGACCGGAGTCGAATCCGGATTAGTCAACC
          1 CATTGGTAAACTCACCAACCAAACCTAGGTGCACGACCGGAGTCGAATCCGAATTAATCAACC

      26187 AAACCTAGGT


Statistics
Matches: 58,  Mismatches: 5, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  68   58  1.00

ACGTcount: A:0.32, C:0.30, G:0.19, T:0.19


Consensus pattern (68 bp):   
CATTGGTAAACTCACCAACCAAACCTAGGTGCACGACCGGAGTCGAATCCGAATTAATCAACCGC
CCG

Found at i:26203 original size:43 final size:43

Alignment explanation


    Indices: 26140--26226  Score: 129
    Period size: 43  Copynumber: 2.0  Consensus size: 43

      26130 TAAACTCACT

                          **           *       *       
      26140 AACCAAACCTAGGTGTACGACCGGAGTCGAATCCGGATTAGTC
          1 AACCAAACCTAGGTACACGACCGGAGTAGAATCCGAATTAGTC

                                  *                    
      26183 AACCAAACCTAGGTACACGACCTGAGTAGAATCCGAATTAGTC
          1 AACCAAACCTAGGTACACGACCGGAGTAGAATCCGAATTAGTC

             
      26226 A
          1 A

      26227 GCCGCCCATT


Statistics
Matches: 39,  Mismatches: 5, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  43   39  1.00

ACGTcount: A:0.34, C:0.25, G:0.22, T:0.18


Consensus pattern (43 bp):   
AACCAAACCTAGGTACACGACCGGAGTAGAATCCGAATTAGTC

Found at i:26284 original size:109 final size:111

Alignment explanation


    Indices: 26071--26293  Score: 342
    Period size: 109  Copynumber: 2.0  Consensus size: 111

      26061 GTAAACTCAC

                           *            *                              *     
      26071 CAACCAAACCTAGGTGCACGACCTGAGTCGAATCCGAATTAATCAACCGCCCGCATTGGTAAACT
          1 CAACCAAACCTAGGTACACGACCTGAGTAGAATCCGAATTAATCAACCGCCCGCATTGGAAAACT

               *            *  *      *                 * 
      26136 CACTAACCAAACCTAGGTGTACGACCGGAGTCGAATCCGGATTAGT
         66 CACCAACCAAACCTAGATGCACGACCCGAGTCGAATCCGGATTAAT

                                                     *   *                   
      26182 CAACCAAACCTAGGTACACGACCTGAGTAGAATCCGAATTAGTCAGCCG-CC-CATTGGAAAACT
          1 CAACCAAACCTAGGTACACGACCTGAGTAGAATCCGAATTAATCAACCGCCCGCATTGGAAAACT

                                                          
      26245 CACCAACCAAACCTAGATGCACGACCCGAGTCGAATCCGGATTAAT
         66 CACCAACCAAACCTAGATGCACGACCCGAGTCGAATCCGGATTAAT

               
      26291 CAA
          1 CAA

      26294 AGCAACGAAG


Statistics
Matches: 102,  Mismatches: 10, Indels: 2
        0.89            0.09        0.02

Matches are distributed among these distances:
 109   55  0.54
 110    2  0.02
 111   45  0.44

ACGTcount: A:0.34, C:0.30, G:0.19, T:0.17


Consensus pattern (111 bp):   
CAACCAAACCTAGGTACACGACCTGAGTAGAATCCGAATTAATCAACCGCCCGCATTGGAAAACT
CACCAACCAAACCTAGATGCACGACCCGAGTCGAATCCGGATTAAT
Done.