Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011843.1 Corchorus olitorius cultivar O-4 contig11876, 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: 19467
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33


Found at i:3407 original size:2 final size:2

Alignment explanation


    Indices: 3400--3428  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

       3390 AAATTTTGTT

                                                       
       3400 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       3429 CTCAATAATA


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:8094 original size:29 final size:31

Alignment explanation


    Indices: 8039--8111  Score: 80
    Period size: 29  Copynumber: 2.4  Consensus size: 31

       8029 ACCGTAACAG

                     *                 *    
       8039 AGGGTGCAATGTGGAACAAAAATAAAATA-TT
          1 AGGGTGCAAAGT-GAACAAAAATAAAAAAGTT

                          *                
       8070 AGGGTGCAAAGTGATC-AAAATAAAAAAGTT
          1 AGGGTGCAAAGTGAACAAAAATAAAAAAGTT

                   *     
       8100 -GGGTGCGAAGTG
          1 AGGGTGCAAAGTG

       8112 GCAGTCCGTA


Statistics
Matches: 37,  Mismatches: 4, Indels: 4
        0.82            0.09        0.09

Matches are distributed among these distances:
  29   21  0.57
  30    5  0.14
  31   11  0.30

ACGTcount: A:0.44, C:0.07, G:0.29, T:0.21


Consensus pattern (31 bp):   
AGGGTGCAAAGTGAACAAAAATAAAAAAGTT

Found at i:13316 original size:3 final size:3

Alignment explanation


    Indices: 13308--13352  Score: 90
    Period size: 3  Copynumber: 15.0  Consensus size: 3

      13298 CCTTAATCAT

                                                                       
      13308 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
          1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA

      13353 TTTTGTGTTA


Statistics
Matches: 42,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   42  1.00

ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33


Consensus pattern (3 bp):   
ATA

Found at i:17311 original size:18 final size:18

Alignment explanation


    Indices: 17288--17326  Score: 78
    Period size: 18  Copynumber: 2.2  Consensus size: 18

      17278 CAAAAATCCA

                              
      17288 TGTGTTCAAGGGTAATTT
          1 TGTGTTCAAGGGTAATTT

                              
      17306 TGTGTTCAAGGGTAATTT
          1 TGTGTTCAAGGGTAATTT

               
      17324 TGT
          1 TGT

      17327 TGTTTGTTGC


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   21  1.00

ACGTcount: A:0.21, C:0.05, G:0.28, T:0.46


Consensus pattern (18 bp):   
TGTGTTCAAGGGTAATTT

Found at i:19344 original size:22 final size:23

Alignment explanation


    Indices: 19317--19374  Score: 84
    Period size: 22  Copynumber: 2.6  Consensus size: 23

      19307 TAATCCCTAT

                                   
      19317 AATTTTGATAACCACTC-TATGA
          1 AATTTTGATAACCACTCATATGA

                          *        
      19339 AATTTTGATAACC-TTCATATGA
          1 AATTTTGATAACCACTCATATGA

                   *      
      19361 AATTTTGGTAACCA
          1 AATTTTGATAACCA

      19375 TAGTATAATT


Statistics
Matches: 32,  Mismatches: 2, Indels: 3
        0.86            0.05        0.08

Matches are distributed among these distances:
  21    2  0.06
  22   30  0.94

ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38


Consensus pattern (23 bp):   
AATTTTGATAACCACTCATATGA

Found at i:19427 original size:42 final size:44

Alignment explanation


    Indices: 19334--19434  Score: 120
    Period size: 42  Copynumber: 2.4  Consensus size: 44

      19324 ATAACCACTC

                               *         *           *  
      19334 TATGAAATTTTGATAACCTTCATATGAAATTTTGGTAACCATAG
          1 TATGAAATTTTGATAACCTCCATATGAAAATTTGGTAACCAAAG

                       *         *                     *
      19378 TAT--AATTTTTATAACCTCCCTAT-AAAATTTGGT-ACCAAAT
          1 TATGAAATTTTGATAACCTCCATATGAAAATTTGGTAACCAAAG

                             
      19418 TATGAAATTTTGATAAC
          1 TATGAAATTTTGATAAC

      19435 ATTTCATTGG


Statistics
Matches: 48,  Mismatches: 7, Indels: 6
        0.79            0.11        0.10

Matches are distributed among these distances:
  40    8  0.17
  41    9  0.19
  42   28  0.58
  44    3  0.06

ACGTcount: A:0.38, C:0.13, G:0.10, T:0.40


Consensus pattern (44 bp):   
TATGAAATTTTGATAACCTCCATATGAAAATTTGGTAACCAAAG
Done.