Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024122.1 Corchorus olitorius cultivar O-4 contig24155, 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: 19479
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35


Found at i:472 original size:28 final size:29

Alignment explanation


    Indices: 408--484  Score: 88
    Period size: 28  Copynumber: 2.7  Consensus size: 29

        398 TGTAAAGACA

                                *        
        408 TAAAATTACCGTTTTACCCTAAGAATGAG
          1 TAAAATTACCGTTTTACCCTTAGAATGAG

                *                        
        437 T-AAGTTACCGTTTTACCCTTAGAA-G-G
          1 TAAAATTACCGTTTTACCCTTAGAATGAG

                 *    *           
        463 TTAAATTTACAGTTTTACCCTT
          1 -TAAAATTACCGTTTTACCCTT

        485 TTAACCTTGT


Statistics
Matches: 42,  Mismatches: 4, Indels: 5
        0.82            0.08        0.10

Matches are distributed among these distances:
  26    1  0.02
  27    2  0.05
  28   38  0.90
  29    1  0.02

ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38


Consensus pattern (29 bp):   
TAAAATTACCGTTTTACCCTTAGAATGAG

Found at i:1034 original size:37 final size:37

Alignment explanation


    Indices: 984--1068  Score: 134
    Period size: 37  Copynumber: 2.3  Consensus size: 37

        974 CCCGTTGAGG

                             *                *  
        984 AAAATGTTTTATTACTGTTTTTATTTAAATGATTTAT
          1 AAAATGTTTTATTACTGATTTTATTTAAATGATTAAT

                                           *     
       1021 AAAATGTTTTATTACTGATTTTATTTAAATGCTTAAT
          1 AAAATGTTTTATTACTGATTTTATTTAAATGATTAAT

                 *     
       1058 AAAATATTTTA
          1 AAAATGTTTTA

       1069 ATAAATTATT


Statistics
Matches: 44,  Mismatches: 4, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  37   44  1.00

ACGTcount: A:0.36, C:0.04, G:0.07, T:0.53


Consensus pattern (37 bp):   
AAAATGTTTTATTACTGATTTTATTTAAATGATTAAT

Found at i:6452 original size:13 final size:13

Alignment explanation


    Indices: 6430--6463  Score: 50
    Period size: 13  Copynumber: 2.6  Consensus size: 13

       6420 ATCAATCTAT

                 *       
       6430 TTTTAATTTTATC
          1 TTTTATTTTTATC

                         
       6443 TTTTATTTTTATC
          1 TTTTATTTTTATC

            *       
       6456 ATTTATTT
          1 TTTTATTT

       6464 CATTTATGCC


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  13   19  1.00

ACGTcount: A:0.21, C:0.06, G:0.00, T:0.74


Consensus pattern (13 bp):   
TTTTATTTTTATC

Found at i:7336 original size:18 final size:16

Alignment explanation


    Indices: 7313--7350  Score: 51
    Period size: 16  Copynumber: 2.3  Consensus size: 16

       7303 TTTGTTAGGC

                              
       7313 TAAAAAGAATAAAAGAAA
          1 TAAAAAG-A-AAAAGAAA

                            
       7331 TAAAAAGAAAAAGAAA
          1 TAAAAAGAAAAAGAAA

                 
       7347 -AAAA
          1 TAAAA

       7351 TTAATGGTAT


Statistics
Matches: 20,  Mismatches: 0, Indels: 3
        0.87            0.00        0.13

Matches are distributed among these distances:
  15    4  0.20
  16    8  0.40
  17    1  0.05
  18    7  0.35

ACGTcount: A:0.82, C:0.00, G:0.11, T:0.08


Consensus pattern (16 bp):   
TAAAAAGAAAAAGAAA

Found at i:11276 original size:20 final size:20

Alignment explanation


    Indices: 11251--11292  Score: 68
    Period size: 20  Copynumber: 2.1  Consensus size: 20

      11241 TTTTATATAG

                                 
      11251 TAGTAATAGTAATAG-ACTAA
          1 TAGTAATAGTAA-AGTACTAA

                                
      11271 TAGTAATAGTAAAGTACTAA
          1 TAGTAATAGTAAAGTACTAA

              
      11291 TA
          1 TA

      11293 AGATGTGTAT


Statistics
Matches: 21,  Mismatches: 0, Indels: 2
        0.91            0.00        0.09

Matches are distributed among these distances:
  19    2  0.10
  20   19  0.90

ACGTcount: A:0.50, C:0.05, G:0.14, T:0.31


Consensus pattern (20 bp):   
TAGTAATAGTAAAGTACTAA

Found at i:14834 original size:61 final size:62

Alignment explanation


    Indices: 14742--14862  Score: 145
    Period size: 61  Copynumber: 2.0  Consensus size: 62

      14732 AAAGTATTTC

                    *       *                      *          *  *        
      14742 TATTTTATTTGATTTAGTCCTCCATCCTTATTTAAATT-TTAGGCATGCCCTCTAACATTCA
          1 TATTTTATCTGATTTAATCCTCCATCCTTATTTAAATTCATAGGCATGCCATCAAACATTCA

                              *  *    *      **                         
      14803 TATTTTATCTGATTTAATTCTTCATCTTTATTTCTATTCATAGGCATGCCATCAAACATT
          1 TATTTTATCTGATTTAATCCTCCATCCTTATTTAAATTCATAGGCATGCCATCAAACATT

      14863 TTCTATTCTA


Statistics
Matches: 49,  Mismatches: 10, Indels: 1
        0.82            0.17        0.02

Matches are distributed among these distances:
  61   31  0.63
  62   18  0.37

ACGTcount: A:0.26, C:0.20, G:0.07, T:0.47


Consensus pattern (62 bp):   
TATTTTATCTGATTTAATCCTCCATCCTTATTTAAATTCATAGGCATGCCATCAAACATTCA
Done.