Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005118.1 Corchorus capsularis cultivar CVL-1 contig05136, 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: 4086
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33


Found at i:116 original size:12 final size:13

Alignment explanation


    Indices: 99--127  Score: 51
    Period size: 13  Copynumber: 2.3  Consensus size: 13

         89 TTCAATTATA

                         
         99 AAAAT-AATAATT
          1 AAAATAAATAATT

                         
        111 AAAATAAATAATT
          1 AAAATAAATAATT

                
        124 AAAA
          1 AAAA

        128 GATAATTCTA


Statistics
Matches: 16,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  12    5  0.31
  13   11  0.69

ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28


Consensus pattern (13 bp):   
AAAATAAATAATT

Found at i:270 original size:26 final size:26

Alignment explanation


    Indices: 234--290  Score: 105
    Period size: 26  Copynumber: 2.2  Consensus size: 26

        224 GACTAAATAA

                *                     
        234 TAAAGATATGATTAAAATTCAAAAAC
          1 TAAAAATATGATTAAAATTCAAAAAC

                                      
        260 TAAAAATATGATTAAAATTCAAAAAC
          1 TAAAAATATGATTAAAATTCAAAAAC

                 
        286 TAAAA
          1 TAAAA

        291 GAAAGAATTG


Statistics
Matches: 30,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  26   30  1.00

ACGTcount: A:0.61, C:0.07, G:0.05, T:0.26


Consensus pattern (26 bp):   
TAAAAATATGATTAAAATTCAAAAAC

Found at i:1298 original size:16 final size:16

Alignment explanation


    Indices: 1277--1309  Score: 57
    Period size: 16  Copynumber: 2.1  Consensus size: 16

       1267 TTCAGAAAGC

                  *         
       1277 AGAAAAGCTCTGAAGT
          1 AGAAAAACTCTGAAGT

                            
       1293 AGAAAAACTCTGAAGT
          1 AGAAAAACTCTGAAGT

             
       1309 A
          1 A

       1310 TTTCAGATGT


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  16   16  1.00

ACGTcount: A:0.48, C:0.12, G:0.21, T:0.18


Consensus pattern (16 bp):   
AGAAAAACTCTGAAGT

Found at i:1423 original size:26 final size:26

Alignment explanation


    Indices: 1394--1448  Score: 67
    Period size: 26  Copynumber: 2.1  Consensus size: 26

       1384 TTCTTTCAAA

                  *                    
       1394 GAAGACTCAATTA-TTGGAGAATTATT
          1 GAAGACCCAATTATTTGG-GAATTATT

                     *          *     
       1420 GAAGACCCAGTTATTTGGGAGTTATT
          1 GAAGACCCAATTATTTGGGAATTATT

               
       1446 GAA
          1 GAA

       1449 AGAAGATCCA


Statistics
Matches: 25,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  26   21  0.84
  27    4  0.16

ACGTcount: A:0.35, C:0.09, G:0.24, T:0.33


Consensus pattern (26 bp):   
GAAGACCCAATTATTTGGGAATTATT

Found at i:1507 original size:91 final size:91

Alignment explanation


    Indices: 1352--1575  Score: 344
    Period size: 91  Copynumber: 2.5  Consensus size: 91

       1342 GCTTAAGAAA

                                      *                               *      
       1352 ATTGAAAGAAGATCCACGTATGTGGAAAATTCTTCTTTCAAAGAAGACTCAATTATTGGAGAATT
          1 ATTGAAAGAAGATCCACGTATGTGGAGAATTCTTCTTTCAAAGAAGACTCAATTATTGCAGAATT

             *                      *  
       1417 ATTGAAGACCCAGTTATTTGGG-AGTT
         66 ACTGAAGACCCAGTTA-TTGGGAAATT

                            *          *                                     
       1443 ATTGAAAGAAGATCCATGTATGTGGAGTATTCTTCTTTCAAAGAAGA-TCCAATTATTGCAGAAT
          1 ATTGAAAGAAGATCCACGTATGTGGAGAATTCTTCTTTCAAAGAAGACT-CAATTATTGCAGAAT

                                       
       1507 TACTGAAGACCCAGTTATTGGGAAATT
         65 TACTGAAGACCCAGTTATTGGGAAATT

                      *                *              
       1534 ATTGAAAGAAAATCCACGTATGTGGAGGATTCTTCTTTCAAA
          1 ATTGAAAGAAGATCCACGTATGTGGAGAATTCTTCTTTCAAA

       1576 TTATCAAAGA


Statistics
Matches: 122,  Mismatches: 9, Indels: 4
        0.90            0.07        0.03

Matches are distributed among these distances:
  90    6  0.05
  91  116  0.95

ACGTcount: A:0.35, C:0.13, G:0.20, T:0.32


Consensus pattern (91 bp):   
ATTGAAAGAAGATCCACGTATGTGGAGAATTCTTCTTTCAAAGAAGACTCAATTATTGCAGAATT
ACTGAAGACCCAGTTATTGGGAAATT

Found at i:3794 original size:13 final size:13

Alignment explanation


    Indices: 3776--3800  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       3766 AATATTCCTA

                         
       3776 TATATATATATAT
          1 TATATATATATAT

                        
       3789 TATATATATATA
          1 TATATATATATA

       3801 GCAGCGTCAA


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

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


Consensus pattern (13 bp):   
TATATATATATAT
Done.