Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022348.1 Corchorus olitorius cultivar O-4 contig22381, 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: 3709
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.33


Found at i:272 original size:2 final size:2

Alignment explanation


    Indices: 267--294  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

        257 CATATATGTG

                                                     
        267 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA

        295 AACATGGGCC


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):   
TA

Found at i:554 original size:43 final size:42

Alignment explanation


    Indices: 415--576  Score: 220
    Period size: 43  Copynumber: 3.8  Consensus size: 42

        405 ATAAGGAGAA

                 *  *                                   
        415 ATGCCTCTTTGTTATATATGTGTTTGAGGACTTTTGTAATAGAG
          1 ATGCCCCTGTGTTATATATGTGTTTGAGGAC-TTTGT-ATAGAG

                                      *                
        459 ATGCCCCTGTGTTATATATGTGTTTGGGGACTTTGATATA-A-
          1 ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTG-TATAGAG

                 *                                     
        500 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAGTAGAG
          1 ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTA-TAGAG

            *                         *       
        543 TTGCCCCTGTGTTATATATGTGTTTGGGGACTTT
          1 ATGCCCCTGTGTTATATATGTGTTTGAGGACTTT

        577 TTGGCTATTG


Statistics
Matches: 106,  Mismatches: 8, Indels: 9
        0.86            0.07        0.07

Matches are distributed among these distances:
  40    2  0.02
  41   35  0.33
  42    2  0.02
  43   38  0.36
  44   29  0.27

ACGTcount: A:0.20, C:0.11, G:0.25, T:0.44


Consensus pattern (42 bp):   
ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTATAGAG

Found at i:567 original size:84 final size:85

Alignment explanation


    Indices: 413--576  Score: 294
    Period size: 84  Copynumber: 1.9  Consensus size: 85

        403 CCATAAGGAG

                      *                                                      
        413 AAATGCCTCTTTGTTATATATGTGTTTGAGGACTTTTGTAATAGAGATGCCCCTGTGTTATATAT
          1 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGTAATAGAGATGCCCCTGTGTTATATAT

                                
        478 GTGTTTGGGGACTTTGATAT
         66 GTGTTTGGGGACTTTGATAT

                                                    *     *                  
        498 AAATGCCTCTGTGTTATATATGTGTTTGAGGAC-TTTGTAGTAGAGTTGCCCCTGTGTTATATAT
          1 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGTAATAGAGATGCCCCTGTGTTATATAT

                           
        562 GTGTTTGGGGACTTT
         66 GTGTTTGGGGACTTT

        577 TTGGCTATTG


Statistics
Matches: 76,  Mismatches: 3, Indels: 1
        0.95            0.04        0.01

Matches are distributed among these distances:
  84   44  0.58
  85   32  0.42

ACGTcount: A:0.21, C:0.11, G:0.25, T:0.43


Consensus pattern (85 bp):   
AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGTAATAGAGATGCCCCTGTGTTATATAT
GTGTTTGGGGACTTTGATAT

Found at i:1151 original size:23 final size:23

Alignment explanation


    Indices: 1124--1174  Score: 75
    Period size: 23  Copynumber: 2.2  Consensus size: 23

       1114 CGAAATCAAA

                                   
       1124 ACCGAACCCGAACCCGACCCGAG
          1 ACCGAACCCGAACCCGACCCGAG

            *      *       *       
       1147 CCCGAACTCGAACCCTACCCGAG
          1 ACCGAACCCGAACCCGACCCGAG

                 
       1170 ACCGA
          1 ACCGA

       1175 CATAACCCGA


Statistics
Matches: 24,  Mismatches: 4, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  23   24  1.00

ACGTcount: A:0.29, C:0.47, G:0.20, T:0.04


Consensus pattern (23 bp):   
ACCGAACCCGAACCCGACCCGAG

Found at i:1206 original size:16 final size:16

Alignment explanation


    Indices: 1187--1220  Score: 50
    Period size: 16  Copynumber: 2.1  Consensus size: 16

       1177 TAACCCGAGT

                   * *      
       1187 CCGAAAATAGCCGAAC
          1 CCGAAAAAACCCGAAC

                            
       1203 CCGAAAAAACCCGAAC
          1 CCGAAAAAACCCGAAC

              
       1219 CC
          1 CC

       1221 AAAGTACCTG


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  16   16  1.00

ACGTcount: A:0.44, C:0.38, G:0.15, T:0.03


Consensus pattern (16 bp):   
CCGAAAAAACCCGAAC
Done.