Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024808.1 Corchorus olitorius cultivar O-4 contig24841, 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: 12582
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:1564 original size:19 final size:18

Alignment explanation


    Indices: 1531--1566  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       1521 TTGAGAATAT

                              
       1531 TCTTCAATGATCTTCAAA
          1 TCTTCAATGATCTTCAAA

                     *        
       1549 TCTTCAAATTATCTTCAA
          1 TCTTC-AATGATCTTCAA

       1567 TAAGTCTTCA


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

Matches are distributed among these distances:
  18    5  0.31
  19   11  0.69

ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42


Consensus pattern (18 bp):   
TCTTCAATGATCTTCAAA

Found at i:4314 original size:30 final size:29

Alignment explanation


    Indices: 4260--4319  Score: 75
    Period size: 29  Copynumber: 2.0  Consensus size: 29

       4250 AAACTAAAAT

                       *     *       *   
       4260 TAGTGGCGTTTCTTTTCTAAACGCCCCTA
          1 TAGTGGCGTTTATTTTCAAAACGCCACTA

                             *            
       4289 TAGTGGCGTTTATTTGTGAAAACGCCACTA
          1 TAGTGGCGTTTATTT-TCAAAACGCCACTA

             
       4319 T
          1 T

       4320 TTAGAATAAA


Statistics
Matches: 26,  Mismatches: 4, Indels: 1
        0.84            0.13        0.03

Matches are distributed among these distances:
  29   14  0.54
  30   12  0.46

ACGTcount: A:0.22, C:0.22, G:0.20, T:0.37


Consensus pattern (29 bp):   
TAGTGGCGTTTATTTTCAAAACGCCACTA

Found at i:4479 original size:17 final size:17

Alignment explanation


    Indices: 4457--4490  Score: 59
    Period size: 17  Copynumber: 2.0  Consensus size: 17

       4447 AGCTAAAACC

                       *     
       4457 AAGTTTTATATTTTAAA
          1 AAGTTTTATATGTTAAA

                             
       4474 AAGTTTTATATGTTAAA
          1 AAGTTTTATATGTTAAA

       4491 GATATAGTAT


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:0.41, C:0.00, G:0.09, T:0.50


Consensus pattern (17 bp):   
AAGTTTTATATGTTAAA

Found at i:8334 original size:32 final size:32

Alignment explanation


    Indices: 8276--8392  Score: 128
    Period size: 32  Copynumber: 3.7  Consensus size: 32

       8266 TAAAAGGCCA

                             **              
       8276 AAATAGCGGCGTTTAAAGAT-AGAAACGCCGCT
          1 AAATAGCGGCGTTTAAATTTCA-AAACGCCGCT

             **                          *  
       8308 ATTTAGCGGCGTTTAAATTTCAAAACGCCACT
          1 AAATAGCGGCGTTTAAATTTCAAAACGCCGCT

                 *          *    *        * 
       8340 AAATAACGGCGTTTAATTTTCCAAACGCCGTT
          1 AAATAGCGGCGTTTAAATTTCAAAACGCCGCT

                        *        
       8372 AAATAGCGGCGTCTAAATTTC
          1 AAATAGCGGCGTTTAAATTTC

       8393 GAGAAATATC


Statistics
Matches: 69,  Mismatches: 15, Indels: 2
        0.80            0.17        0.02

Matches are distributed among these distances:
  32   68  0.99
  33    1  0.01

ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27


Consensus pattern (32 bp):   
AAATAGCGGCGTTTAAATTTCAAAACGCCGCT

Found at i:12243 original size:2 final size:2

Alignment explanation


    Indices: 12236--12263  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

      12226 TGCTTTATTC

                                                     
      12236 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      12264 GCTTTATTTA


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:12539 original size:1 final size:1

Alignment explanation


    Indices: 12533--12578  Score: 74
    Period size: 1  Copynumber: 46.0  Consensus size: 1

      12523 CCTTGTAATT

                                       **                 
      12533 AAAAAAAAAAAAAAAAAAAAAAAAAAACCAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

      12579 CCCA


Statistics
Matches: 43,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
   1   43  1.00

ACGTcount: A:0.96, C:0.04, G:0.00, T:0.00


Consensus pattern (1 bp):   
A

Found at i:12579 original size:19 final size:19

Alignment explanation


    Indices: 12533--12580  Score: 82
    Period size: 19  Copynumber: 2.6  Consensus size: 19

      12523 CCTTGTAATT

                               
      12533 AAAAAAAAAA--AAAAAAA
          1 AAAAAAAAAACCAAAAAAA

                               
      12550 AAAAAAAAAACCAAAAAAA
          1 AAAAAAAAAACCAAAAAAA

                        
      12569 AAAAAAAAAACC
          1 AAAAAAAAAACC

      12581 CA


Statistics
Matches: 29,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
  17   10  0.34
  19   19  0.66

ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00


Consensus pattern (19 bp):   
AAAAAAAAAACCAAAAAAA
Done.