Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015013.1 Corchorus olitorius cultivar O-4 contig15046, 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: 12788
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32


Found at i:1406 original size:30 final size:30

Alignment explanation


    Indices: 1331--1409  Score: 131
    Period size: 30  Copynumber: 2.6  Consensus size: 30

       1321 CATGAACTTC

                          *               
       1331 AATTTTGGACATTTGACCCCCTAAACTCTA
          1 AATTTTGGACATTTTACCCCCTAAACTCTA

                                          
       1361 AATTTTGGACATTTTACCCCCTAAACTCTA
          1 AATTTTGGACATTTTACCCCCTAAACTCTA

                     **        
       1391 AATTTTGGATGTTTTACCC
          1 AATTTTGGACATTTTACCC

       1410 TCTCAAATGA


Statistics
Matches: 46,  Mismatches: 3, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  30   46  1.00

ACGTcount: A:0.28, C:0.24, G:0.10, T:0.38


Consensus pattern (30 bp):   
AATTTTGGACATTTTACCCCCTAAACTCTA

Found at i:1602 original size:29 final size:30

Alignment explanation


    Indices: 1535--1610  Score: 111
    Period size: 30  Copynumber: 2.6  Consensus size: 30

       1525 CATTTGAGAG

                        *                 
       1535 GGGGCAAAATGTTCAAAATTGATAGTTCAA
          1 GGGGCAAAATGTCCAAAATTGATAGTTCAA

                                           
       1565 GGGGCAAAATGTCCAAAATTGA-AGTTCAAA
          1 GGGGCAAAATGTCCAAAATTGATAGTTC-AA

                     *       
       1595 GGGG-AAAACGTCCAAA
          1 GGGGCAAAATGTCCAAA

       1611 CGCTACATGT


Statistics
Matches: 43,  Mismatches: 2, Indels: 3
        0.90            0.04        0.06

Matches are distributed among these distances:
  29   16  0.37
  30   27  0.63

ACGTcount: A:0.42, C:0.13, G:0.25, T:0.20


Consensus pattern (30 bp):   
GGGGCAAAATGTCCAAAATTGATAGTTCAA

Found at i:2642 original size:4 final size:4

Alignment explanation


    Indices: 2633--2659  Score: 54
    Period size: 4  Copynumber: 6.8  Consensus size: 4

       2623 ATTGGGTAGC

                                             
       2633 TTAT TTAT TTAT TTAT TTAT TTAT TTA
          1 TTAT TTAT TTAT TTAT TTAT TTAT TTA

       2660 AAAATTCCTA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   4   23  1.00

ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74


Consensus pattern (4 bp):   
TTAT

Found at i:3329 original size:43 final size:43

Alignment explanation


    Indices: 3281--3363  Score: 148
    Period size: 43  Copynumber: 1.9  Consensus size: 43

       3271 TTAGGGCATT

                      *                                
       3281 GTTTTGTGAAGTGAACTGTTAAATATTAGGATTAGAATTCTTA
          1 GTTTTGTGAACTGAACTGTTAAATATTAGGATTAGAATTCTTA

                                 *                  
       3324 GTTTTGTGAACTGAACTGTTACATATTAGGATTAGAATTC
          1 GTTTTGTGAACTGAACTGTTAAATATTAGGATTAGAATTC

       3364 AATTCGTTGG


Statistics
Matches: 38,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  43   38  1.00

ACGTcount: A:0.31, C:0.07, G:0.20, T:0.41


Consensus pattern (43 bp):   
GTTTTGTGAACTGAACTGTTAAATATTAGGATTAGAATTCTTA

Found at i:6832 original size:18 final size:17

Alignment explanation


    Indices: 6794--6833  Score: 57
    Period size: 16  Copynumber: 2.4  Consensus size: 17

       6784 TCTCTCACTC

                             
       6794 TTTTTTTTTTCTCTGTT
          1 TTTTTTTTTTCTCTGTT

                              
       6811 TTTTTCTTTTTCT-T-TT
          1 TTTTT-TTTTTCTCTGTT

                   
       6827 TTTTTTT
          1 TTTTTTT

       6834 AAAAACTTTT


Statistics
Matches: 22,  Mismatches: 0, Indels: 4
        0.85            0.00        0.15

Matches are distributed among these distances:
  15    2  0.09
  16    7  0.32
  17    6  0.27
  18    7  0.32

ACGTcount: A:0.00, C:0.10, G:0.03, T:0.88


Consensus pattern (17 bp):   
TTTTTTTTTTCTCTGTT
Done.