Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005123.1 Corchorus capsularis cultivar CVL-1 contig05141, 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: 4663
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32


Found at i:908 original size:36 final size:36

Alignment explanation


    Indices: 806--977  Score: 136
    Period size: 36  Copynumber: 4.8  Consensus size: 36

        796 TAAGATAAAT

                                *         **     
        806 AACTGAAGAAAGACCACCCTGGATCATTCTAAACTG-
          1 AACTGAAGAAAGACCACCCTCGATCATTC-CGACTGA

                *     *    *                     
        842 AACTAAAGAATGACCGCCCTCGATCATTCCGGAC-GA
          1 AACTGAAGAAAGACCACCCTCGATCATTCC-GACTGA

                                              * 
        878 AACTGAAGAAAGACCACCCTCGATCATTCCGACTCA
          1 AACTGAAGAAAGACCACCCTCGATCATTCCGACTGA

               *            *    * *    * *   *   
        914 AACCGAAGAAAAGACCGCCCTGGGTCA-ACTGAAAT-A
          1 AACTGAAG-AAAGACCACCCTCGATCATTCCG-ACTGA

                *     *                 
        950 AACTTAAGAACGACCACCCTCGATCATT
          1 AACTGAAGAAAGACCACCCTCGATCATT

        978 GAAAAATGGT


Statistics
Matches: 106,  Mismatches: 24, Indels: 12
        0.75            0.17        0.08

Matches are distributed among these distances:
  35   18  0.17
  36   71  0.67
  37   17  0.16

ACGTcount: A:0.37, C:0.29, G:0.17, T:0.17


Consensus pattern (36 bp):   
AACTGAAGAAAGACCACCCTCGATCATTCCGACTGA

Found at i:1189 original size:29 final size:29

Alignment explanation


    Indices: 1144--1199  Score: 78
    Period size: 29  Copynumber: 1.9  Consensus size: 29

       1134 AAACTATCTA

                                          
       1144 AAAGACCATCCTAGGTC-ATGTAACTGAGG
          1 AAAGACCATCCTAGGTCAAT-TAACTGAGG

                 *      *              
       1173 AAAGATCATCCTGGGTCAATTAACTGA
          1 AAAGACCATCCTAGGTCAATTAACTGA

       1200 AGATGGACCA


Statistics
Matches: 24,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  29   22  0.92
  30    2  0.08

ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23


Consensus pattern (29 bp):   
AAAGACCATCCTAGGTCAATTAACTGAGG

Found at i:1363 original size:35 final size:34

Alignment explanation


    Indices: 1281--1363  Score: 105
    Period size: 35  Copynumber: 2.4  Consensus size: 34

       1271 GAAGAAGGAT

                  *               *        *  
       1281 CGCCCTAGGTCAATTGAAATTATTGAAGAGAGAC
          1 CGCCCTGGGTCAATTGAAATTACTGAAGAGAAAC

                    *                           
       1315 CGCCCTGGATCAATTGAAATTTACTGAATG-GAAAC
          1 CGCCCTGGGTCAATTGAAA-TTACTGAA-GAGAAAC

                          
       1350 CGCCCTGGGTCAAT
          1 CGCCCTGGGTCAAT

       1364 CAACTGAATG


Statistics
Matches: 42,  Mismatches: 5, Indels: 3
        0.84            0.10        0.06

Matches are distributed among these distances:
  34   17  0.40
  35   24  0.57
  36    1  0.02

ACGTcount: A:0.31, C:0.22, G:0.23, T:0.24


Consensus pattern (34 bp):   
CGCCCTGGGTCAATTGAAATTACTGAAGAGAAAC

Found at i:3419 original size:2 final size:2

Alignment explanation


    Indices: 3412--3442  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

       3402 GAACAGCAGA

                                                          
       3412 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       3443 CAAAAAGCAG


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   29  1.00

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


Consensus pattern (2 bp):   
AT

Done.