Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023246.1 Corchorus olitorius cultivar O-4 contig23279, 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: 5155
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34


Found at i:1569 original size:17 final size:17

Alignment explanation


    Indices: 1547--1580  Score: 59
    Period size: 17  Copynumber: 2.0  Consensus size: 17

       1537 CTCAAAAGTC

                             
       1547 CTCTCCGTCTTCCCTCT
          1 CTCTCCGTCTTCCCTCT

                  *          
       1564 CTCTCCTTCTTCCCTCT
          1 CTCTCCGTCTTCCCTCT

       1581 TTCTTTTATG


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

Matches are distributed among these distances:
  17   16  1.00

ACGTcount: A:0.00, C:0.53, G:0.03, T:0.44


Consensus pattern (17 bp):   
CTCTCCGTCTTCCCTCT

Found at i:3400 original size:27 final size:27

Alignment explanation


    Indices: 3364--3427  Score: 80
    Period size: 27  Copynumber: 2.4  Consensus size: 27

       3354 TCTAATTTTC

                                          
       3364 TATTATTTTAATAATGG-AATAATTA-AAA
          1 TATTA-TTTAATAATGGCAAT--TTAGAAA

                                       
       3392 TATTATTTAATAATGGCAATTTAGAAA
          1 TATTATTTAATAATGGCAATTTAGAAA

                      
       3419 TA-TATTTAA
          1 TATTATTTAA

       3428 AAAGAAAGGG


Statistics
Matches: 34,  Mismatches: 0, Indels: 6
        0.85            0.00        0.15

Matches are distributed among these distances:
  26   10  0.29
  27   16  0.47
  28    8  0.24

ACGTcount: A:0.47, C:0.02, G:0.08, T:0.44


Consensus pattern (27 bp):   
TATTATTTAATAATGGCAATTTAGAAA

Found at i:4316 original size:19 final size:19

Alignment explanation


    Indices: 4277--4328  Score: 74
    Period size: 18  Copynumber: 2.9  Consensus size: 19

       4267 TTATTTTTAA

                    *          
       4277 AAAAAATTGTAA-A-ATTT
          1 AAAAAATTATAATATATTT

                               
       4294 AAAAAATTA-AATATATTT
          1 AAAAAATTATAATATATTT

                             
       4312 AAAAAATTATAATATAT
          1 AAAAAATTATAATATAT

       4329 ATAAGTTTTT


Statistics
Matches: 31,  Mismatches: 1, Indels: 4
        0.86            0.03        0.11

Matches are distributed among these distances:
  16    2  0.06
  17    9  0.29
  18   13  0.42
  19    7  0.23

ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37


Consensus pattern (19 bp):   
AAAAAATTATAATATATTT

Found at i:4448 original size:129 final size:123

Alignment explanation


    Indices: 4305--4541  Score: 348
    Period size: 129  Copynumber: 1.9  Consensus size: 123

       4295 AAAAATTAAA

                                                            *                
       4305 TATATTTAAAAAATTATAATATATATAAGTTTTTTAAATAAAATAGTACAATGGTAAATAAAATA
          1 TATATTTAAAAAATTATAATATATATAAGTTTTTTAAATAAAATAGTAAAATGGT--A-AAAAT-

                   *    *                     *                             
       4370 GGTATAAGGATATTAGATTTAATTAAATAAAAATGGAGTTTTTAGTTGAGTAAAGCTGTAAAAG
         62 --TATAAAGATAATAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAGCTGTAAAAG

                           *                     *                           
       4434 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATTATA
          1 TATATTTAAAAAATTATAATATATATAAGTTTTTTAAATAAAATAGTAAAATGGTAAAAATTATA

                                    * *                
       4499 AAGATAATAGATTTAATTAAATAACATTAGAGTTTTTAGTTGA
         66 AAGATAATAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGA

       4542 ATAATACTAA


Statistics
Matches: 100,  Mismatches: 8, Indels: 6
        0.88            0.07        0.05

Matches are distributed among these distances:
 123   42  0.42
 126    5  0.05
 127    1  0.01
 129   52  0.52

ACGTcount: A:0.48, C:0.02, G:0.12, T:0.38


Consensus pattern (123 bp):   
TATATTTAAAAAATTATAATATATATAAGTTTTTTAAATAAAATAGTAAAATGGTAAAAATTATA
AAGATAATAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAGCTGTAAAAG

Found at i:4583 original size:123 final size:126

Alignment explanation


    Indices: 4312--4583  Score: 275
    Period size: 123  Copynumber: 2.2  Consensus size: 126

       4302 AAATATATTT

                    *   * *                          *                       
       4312 AAAAAATTATAATATATATAAGTTTTTTAAATAAAATAGTACAATGGTAAATAAAATAGGTATAA
          1 AAAAAATTCTAAAAAATATAAGTTTTTTAAATAAAATAGTAAAATGGT-AATAAAAT--GTATAA

            *    *                     *              *       **         ***
       4377 GGATATTAGATTTAATTAAATAAAAATGGAGTTTTTAGTTGAGTAAAGCTGTAAAAGTATATTT
         63 AGATAATAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAATAAAGCTAAAAAAGTATAAAC

                        * *               *                                  
       4441 AAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGT-A-AAAAT-TATAAAGA
          1 AAAAAATTCTAAAAAATATAAGTTTTTTAAATAAAATAGTAAAATGGTAATAAAATGTATAAAGA

                                * *                                 *     
       4503 TAATAGATTTAATTAAATAACATTAGAGTTTTTAGTTGAATAATA-CTAAAAAAGTTTAAAC
         66 TAATAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAATAA-AGCTAAAAAAGTATAAAC

               * *               
       4564 AATGACATT-TAAAAAATATA
          1 AA-AAAATTCTAAAAAATATA

       4584 TTCGAAAAAT


Statistics
Matches: 122,  Mismatches: 19, Indels: 10
        0.81            0.13        0.07

Matches are distributed among these distances:
 123   66  0.54
 124    5  0.04
 126    5  0.04
 127    1  0.01
 129   45  0.37

ACGTcount: A:0.50, C:0.03, G:0.11, T:0.36


Consensus pattern (126 bp):   
AAAAAATTCTAAAAAATATAAGTTTTTTAAATAAAATAGTAAAATGGTAATAAAATGTATAAAGA
TAATAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAATAAAGCTAAAAAAGTATAAAC
Done.