Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010042.1 Corchorus capsularis cultivar CVL-1 contig10063, 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: 8749
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26


Found at i:2293 original size:66 final size:66

Alignment explanation


    Indices: 2190--2403  Score: 297
    Period size: 66  Copynumber: 3.2  Consensus size: 66

       2180 CCAAACAAAT

                        *            *     *  *                              
       2190 GATCCTTGAATCAT-AAACTTAAG-TACGACAAATGTCTCCCTTGAGACCGTTTTGCTAAAATGA
          1 GATCCTTGAATCGTAAAACTTAAGCGA-GACGAACGTCTCCCTTGAGACCGTTTTGCTAAAATGA

              
       2253 AC
         65 AC

                                            *              *      *     *    
       2255 GATCCTTGAATCGTAAAACTTAAGCGAGACGAGCGTCTCCCTTGAGATCGTTTTACTAAAGTGAA
          1 GATCCTTGAATCGTAAAACTTAAGCGAGACGAACGTCTCCCTTGAGACCGTTTTGCTAAAATGAA

             
       2320 C
         66 C

             *                                                         *   * 
       2321 GGTCCTTGAATCGTAAAACTTAAGCGAGACGAACGTCTCCCTTGAGACCGTTTTGCTAAGATAAA
          1 GATCCTTGAATCGTAAAACTTAAGCGAGACGAACGTCTCCCTTGAGACCGTTTTGCTAAAAT-GA

              
       2386 AC
         65 AC

                            
       2388 GATCCTTGAATCGTAA
          1 GATCCTTGAATCGTAA

       2404 GTTCGAGATT


Statistics
Matches: 130,  Mismatches: 16, Indels: 4
        0.87            0.11        0.03

Matches are distributed among these distances:
  65   13  0.10
  66   98  0.75
  67   19  0.15

ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28


Consensus pattern (66 bp):   
GATCCTTGAATCGTAAAACTTAAGCGAGACGAACGTCTCCCTTGAGACCGTTTTGCTAAAATGAA
C

Found at i:2364 original size:36 final size:36

Alignment explanation


    Indices: 2258--2365  Score: 104
    Period size: 36  Copynumber: 3.2  Consensus size: 36

       2248 AATGAACGAT

                                         *      
       2258 CCTTGAATCGTAAAACTTAAGCGAGACGAGCGTCTC
          1 CCTTGAATCGTAAAACTTAAGCGAGACGAACGTCTC

                        ***            *      *  
       2294 CCTTGAGATCGTTTTAC-TAA---AG-TGAACG-GT-
          1 CCTTGA-ATCGTAAAACTTAAGCGAGACGAACGTCTC

                                                
       2324 CCTTGAATCGTAAAACTTAAGCGAGACGAACGTCTC
          1 CCTTGAATCGTAAAACTTAAGCGAGACGAACGTCTC

                  
       2360 CCTTGA
          1 CCTTGA

       2366 GACCGTTTTG


Statistics
Matches: 53,  Mismatches: 11, Indels: 16
        0.66            0.14        0.20

Matches are distributed among these distances:
  29    7  0.13
  30    9  0.17
  31    1  0.02
  32    4  0.08
  33    4  0.08
  34    5  0.09
  35    1  0.02
  36   15  0.28
  37    7  0.13

ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26


Consensus pattern (36 bp):   
CCTTGAATCGTAAAACTTAAGCGAGACGAACGTCTC

Found at i:7452 original size:36 final size:36

Alignment explanation


    Indices: 7412--7486  Score: 89
    Period size: 36  Copynumber: 2.1  Consensus size: 36

       7402 ATGTGTTTTA

                          *                   *  
       7412 ACTTTGAACCAAAATAATAG-CTGCACAAAAATATAG
          1 ACTTTGAACCAAAAGAAT-GCCTGCACAAAAATAAAG

                  **                      *     
       7448 ACTTTGTGCCAAAAGAATGCCTGCACAAAAGTAAAG
          1 ACTTTGAACCAAAAGAATGCCTGCACAAAAATAAAG

               
       7484 ACT
          1 ACT

       7487 CCAAAGTTTG


Statistics
Matches: 33,  Mismatches: 5, Indels: 2
        0.82            0.12        0.05

Matches are distributed among these distances:
  35    1  0.03
  36   32  0.97

ACGTcount: A:0.45, C:0.19, G:0.15, T:0.21


Consensus pattern (36 bp):   
ACTTTGAACCAAAAGAATGCCTGCACAAAAATAAAG

Found at i:7597 original size:17 final size:17

Alignment explanation


    Indices: 7575--7613  Score: 53
    Period size: 17  Copynumber: 2.3  Consensus size: 17

       7565 ACCATAATCA

                              
       7575 TAAACTAAATACTAC-CC
          1 TAAACTAAAT-CTACTCC

                  *          
       7592 TAAACTTAATCTACTCC
          1 TAAACTAAATCTACTCC

                 
       7609 TAAAC
          1 TAAAC

       7614 CCTGCAGGTT


Statistics
Matches: 20,  Mismatches: 1, Indels: 2
        0.87            0.04        0.09

Matches are distributed among these distances:
  16    4  0.20
  17   16  0.80

ACGTcount: A:0.44, C:0.28, G:0.00, T:0.28


Consensus pattern (17 bp):   
TAAACTAAATCTACTCC
Done.