Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024076.1 Corchorus olitorius cultivar O-4 contig24109, 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: 19126
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32


Found at i:366 original size:22 final size:22

Alignment explanation


    Indices: 338--383  Score: 92
    Period size: 22  Copynumber: 2.1  Consensus size: 22

        328 ACTCTAGAAG

                                  
        338 GACTCCTTCTTTATTTTTTTCA
          1 GACTCCTTCTTTATTTTTTTCA

                                  
        360 GACTCCTTCTTTATTTTTTTCA
          1 GACTCCTTCTTTATTTTTTTCA

              
        382 GA
          1 GA

        384 GGGACAATAT


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  22   24  1.00

ACGTcount: A:0.15, C:0.22, G:0.07, T:0.57


Consensus pattern (22 bp):   
GACTCCTTCTTTATTTTTTTCA

Found at i:547 original size:17 final size:18

Alignment explanation


    Indices: 512--547  Score: 56
    Period size: 18  Copynumber: 2.1  Consensus size: 18

        502 CTCCTCTATC

                     *        
        512 ATGAAAACACTTCTTTTT
          1 ATGAAAACAATTCTTTTT

                              
        530 ATGAAAACAATT-TTTTT
          1 ATGAAAACAATTCTTTTT

             
        547 A
          1 A

        548 ATTACCCTTT


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  17    6  0.35
  18   11  0.65

ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44


Consensus pattern (18 bp):   
ATGAAAACAATTCTTTTT

Found at i:1189 original size:20 final size:20

Alignment explanation


    Indices: 1164--1207  Score: 54
    Period size: 20  Copynumber: 2.2  Consensus size: 20

       1154 CTAAGATGCA

                        *        
       1164 TAAAAAAT-AAATCTTAAATC
          1 TAAAAAATGAAAAC-TAAATC

                  *             
       1184 TAAAAACTGAAAACTAAATC
          1 TAAAAAATGAAAACTAAATC

                
       1204 TAAA
          1 TAAA

       1208 TTGGTTTATG


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  20   17  0.81
  21    4  0.19

ACGTcount: A:0.61, C:0.11, G:0.02, T:0.25


Consensus pattern (20 bp):   
TAAAAAATGAAAACTAAATC

Found at i:2302 original size:32 final size:32

Alignment explanation


    Indices: 2243--2304  Score: 81
    Period size: 32  Copynumber: 1.9  Consensus size: 32

       2233 GATCCCTTAG

                             *              
       2243 TTAGTCGACAAACTTAATTCAAAACTTGCTCT
          1 TTAGTCGACAAACTTAAGTCAAAACTTGCTCT

                                 * *       
       2275 TTAGTCGAC-AACTTCAAGTCGACACTTGCT
          1 TTAGTCGACAAACTT-AAGTCAAAACTTGCT

       2305 TTGTCGATTT


Statistics
Matches: 26,  Mismatches: 3, Indels: 2
        0.84            0.10        0.06

Matches are distributed among these distances:
  31    5  0.19
  32   21  0.81

ACGTcount: A:0.31, C:0.24, G:0.13, T:0.32


Consensus pattern (32 bp):   
TTAGTCGACAAACTTAAGTCAAAACTTGCTCT

Found at i:7007 original size:20 final size:20

Alignment explanation


    Indices: 6982--7025  Score: 79
    Period size: 20  Copynumber: 2.2  Consensus size: 20

       6972 AGTGAAAGCA

                     *          
       6982 TGTTGGTGACGGTTTCTTGT
          1 TGTTGGTGAAGGTTTCTTGT

                                
       7002 TGTTGGTGAAGGTTTCTTGT
          1 TGTTGGTGAAGGTTTCTTGT

                
       7022 TGTT
          1 TGTT

       7026 TTGCCAAAGA


Statistics
Matches: 23,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  20   23  1.00

ACGTcount: A:0.07, C:0.07, G:0.34, T:0.52


Consensus pattern (20 bp):   
TGTTGGTGAAGGTTTCTTGT

Found at i:9388 original size:19 final size:18

Alignment explanation


    Indices: 9355--9390  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       9345 TTGAAAGTAT

                              
       9355 TCTTCAATGGTCTTCAAA
          1 TCTTCAATGGTCTTCAAA

                     *        
       9373 TCTTCAAATTGTCTTCAA
          1 TCTTC-AATGGTCTTCAA

       9391 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:0.28, C:0.22, G:0.08, T:0.42


Consensus pattern (18 bp):   
TCTTCAATGGTCTTCAAA

Found at i:14397 original size:20 final size:21

Alignment explanation


    Indices: 14372--14414  Score: 70
    Period size: 21  Copynumber: 2.1  Consensus size: 21

      14362 TCAAGGTGTA

                           *     
      14372 ATCAAGT-CATGTGGTGAACC
          1 ATCAAGTACATGTGGGGAACC

                                 
      14392 ATCAAGTACATGTGGGGAACC
          1 ATCAAGTACATGTGGGGAACC

              
      14413 AT
          1 AT

      14415 GTATGATCTT


Statistics
Matches: 21,  Mismatches: 1, Indels: 1
        0.91            0.04        0.04

Matches are distributed among these distances:
  20    7  0.33
  21   14  0.67

ACGTcount: A:0.33, C:0.19, G:0.26, T:0.23


Consensus pattern (21 bp):   
ATCAAGTACATGTGGGGAACC

Done.