Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012564.1 Corchorus capsularis cultivar CVL-1 contig12585, 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: 12405
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.32


Found at i:2993 original size:17 final size:17

Alignment explanation


    Indices: 2955--2987  Score: 66
    Period size: 17  Copynumber: 1.9  Consensus size: 17

       2945 CTCATGATAC

                             
       2955 CTAGGTAGTATGAGGTA
          1 CTAGGTAGTATGAGGTA

                            
       2972 CTAGGTAGTATGAGGT
          1 CTAGGTAGTATGAGGT

       2988 GATAGGCTGC


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   16  1.00

ACGTcount: A:0.27, C:0.06, G:0.36, T:0.30


Consensus pattern (17 bp):   
CTAGGTAGTATGAGGTA

Found at i:3535 original size:156 final size:156

Alignment explanation


    Indices: 3334--3723  Score: 432
    Period size: 156  Copynumber: 2.5  Consensus size: 156

       3324 AAACCGAGAG

                   *      *                                 *                
       3334 TCTCACCTCAAACTATCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGAATGAGC
          1 TCTCACCCCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATACTAAGTCTGAATGAGC

                    **      *                *                               
       3399 TGAAATTTTTCCAAG-GGACTTAGAATATC-CATATAAGACTAT-GGAAAAAATTCTAAGTAAAA
         66 TGAAATTTCACC-AGTAGACTTAGAATATCAC-CATAAGACTATGGGAAAAAA-TCTAAGTAAAA

                *       *    * *          
       3461 CCGAGCTCCCCTTG-ATGGTGAACTAGGTT
        128 CCGAACT-CCCTAGTATAGAGAACTAGGTT

                *  *   **                                            *  *    
       3490 TCTCTCCTCAAGTTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATACTAAGTC-CAACGAAG
          1 TCTCACCCCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATACTAAGTCTGAATG-AG

                *   *        *       *            *                          
       3554 CTGATATTCCACCAGTATACTTAGATTATCACCATAAGGCTATGGGAAAAAATCTAAGTAAAACC
         65 CTGAAATTTCACCAGTAGACTTAGAATATCACCATAAGACTATGGGAAAAAATCTAAGTAAAACC

                                * *    
       3619 GAACTCCCTAGTATAGAGAAGTTGGTT
        130 GAACTCCCTAGTATAGAGAACTAGGTT

             *                                                         **    
       3646 TGTCACCCCAAACTGTCCTTAACA-GAAAAACTAGCATAAGTTTTTCATACTAAGTCTGTTTGAG
          1 TCTCACCCCAAACTGTCCTTAA-ATGAAAAACTAGCATAAGTTTTTCATACTAAGTCTGAATGAG

            *             
       3710 ATGAAATTTCACCA
         65 CTGAAATTTCACCA

       3724 AGATGACCTA


Statistics
Matches: 193,  Mismatches: 34, Indels: 14
        0.80            0.14        0.06

Matches are distributed among these distances:
 155   10  0.05
 156  172  0.89
 157   11  0.06

ACGTcount: A:0.36, C:0.20, G:0.15, T:0.30


Consensus pattern (156 bp):   
TCTCACCCCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATACTAAGTCTGAATGAGC
TGAAATTTCACCAGTAGACTTAGAATATCACCATAAGACTATGGGAAAAAATCTAAGTAAAACCG
AACTCCCTAGTATAGAGAACTAGGTT

Found at i:4982 original size:14 final size:13

Alignment explanation


    Indices: 4944--4982  Score: 51
    Period size: 13  Copynumber: 2.9  Consensus size: 13

       4934 TTCACCGCAA

                *        
       4944 TTTTGAAAATCAC
          1 TTTTCAAAATCAC

                         
       4957 TTTTCAAAATCAC
          1 TTTTCAAAATCAC

                  *      
       4970 TTATTCCAAATCA
          1 TT-TTCAAAATCA

       4983 AACTTTTTCA


Statistics
Matches: 23,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  13   14  0.61
  14    9  0.39

ACGTcount: A:0.38, C:0.21, G:0.03, T:0.38


Consensus pattern (13 bp):   
TTTTCAAAATCAC

Found at i:11687 original size:17 final size:18

Alignment explanation


    Indices: 11653--11687  Score: 54
    Period size: 17  Copynumber: 2.0  Consensus size: 18

      11643 TAACCCAAAG

                         *    
      11653 TTTTCCTTCAATAGATTA
          1 TTTTCCTTCAATAAATTA

                              
      11671 TTTTCCTT-AATAAATTA
          1 TTTTCCTTCAATAAATTA

      11688 GTATGAAATA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  17    8  0.50
  18    8  0.50

ACGTcount: A:0.31, C:0.14, G:0.03, T:0.51


Consensus pattern (18 bp):   
TTTTCCTTCAATAAATTA
Done.