Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017699.1 Corchorus olitorius cultivar O-4 contig17732, 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: 22000
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.31


Found at i:7493 original size:30 final size:30

Alignment explanation


    Indices: 7436--7505  Score: 81
    Period size: 30  Copynumber: 2.4  Consensus size: 30

       7426 CAATTCTTGC

                      *          **       
       7436 TTCTTGAAATAATTCTTCAATGGTCTTCAA
          1 TTCTTGAAATTATTCTTCAATAATCTTCAA

                                           
       7466 TTCTTGAAATTA-TCTTCAATAAATCTTCAA
          1 TTCTTGAAATTATTCTTCAAT-AATCTTCAA

               *       
       7496 -TCATGAAATT
          1 TTCTTGAAATT

       7506 TGAATTTTCA


Statistics
Matches: 35,  Mismatches: 4, Indels: 3
        0.83            0.10        0.07

Matches are distributed among these distances:
  29   17  0.49
  30   18  0.51

ACGTcount: A:0.34, C:0.16, G:0.07, T:0.43


Consensus pattern (30 bp):   
TTCTTGAAATTATTCTTCAATAATCTTCAA

Found at i:12987 original size:66 final size:66

Alignment explanation


    Indices: 12905--13060  Score: 276
    Period size: 66  Copynumber: 2.4  Consensus size: 66

      12895 TTGGAAATAG

                                        *                                    
      12905 TGTTTTAGATGTTGTTTGCGATGATACTGAACCTAATTTGAGTGTTGTTTGTGATGACACTAAAT
          1 TGTTTTAGATGTTGTTTGCGATGATACTAAACCTAATTTGAGTGTTGTTTGTGATGACACTAAAT

             
      12970 C
         66 C

                                                                             
      12971 TGTTTTAGATGTTGTTTGCGATGATACTAAACCTAATTTGAGTGTTGTTTGTGATGACACTAAAT
          1 TGTTTTAGATGTTGTTTGCGATGATACTAAACCTAATTTGAGTGTTGTTTGTGATGACACTAAAT

             
      13036 C
         66 C

                    * *       *     
      13037 TGTTTTAGGTATTGTTTGTGATGA
          1 TGTTTTAGATGTTGTTTGCGATGA

      13061 AACGAATTCT


Statistics
Matches: 86,  Mismatches: 4, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  66   86  1.00

ACGTcount: A:0.24, C:0.09, G:0.23, T:0.44


Consensus pattern (66 bp):   
TGTTTTAGATGTTGTTTGCGATGATACTAAACCTAATTTGAGTGTTGTTTGTGATGACACTAAAT
C

Found at i:13052 original size:33 final size:33

Alignment explanation


    Indices: 12905--13075  Score: 157
    Period size: 33  Copynumber: 5.2  Consensus size: 33

      12895 TTGGAAATAG

                    *         *     *   *  * 
      12905 TGTTTTAGATGTTGTTTGCGATGATACTGAACC
          1 TGTTTTAGGTGTTGTTTGTGATGACACTAAATC

             **                               
      12938 TAATTT-GAGTGTTGTTTGTGATGACACTAAATC
          1 TGTTTTAG-GTGTTGTTTGTGATGACACTAAATC

                    *         *     *      * 
      12971 TGTTTTAGATGTTGTTTGCGATGATACTAAACC
          1 TGTTTTAGGTGTTGTTTGTGATGACACTAAATC

             **                               
      13004 TAATTT-GAGTGTTGTTTGTGATGACACTAAATC
          1 TGTTTTAG-GTGTTGTTTGTGATGACACTAAATC

                      *             *  *  *  
      13037 TGTTTTAGGTATTGTTTGTGATGAAACGAATTC
          1 TGTTTTAGGTGTTGTTTGTGATGACACTAAATC

                  
      13070 TGTTTT
          1 TGTTTT

      13076 GGATGCTAAT


Statistics
Matches: 109,  Mismatches: 25, Indels: 8
        0.77            0.18        0.06

Matches are distributed among these distances:
  32    2  0.02
  33  105  0.96
  34    2  0.02

ACGTcount: A:0.24, C:0.09, G:0.22, T:0.44


Consensus pattern (33 bp):   
TGTTTTAGGTGTTGTTTGTGATGACACTAAATC

Found at i:14880 original size:21 final size:21

Alignment explanation


    Indices: 14854--14903  Score: 84
    Period size: 21  Copynumber: 2.4  Consensus size: 21

      14844 TGCTAGGAGA

                                  
      14854 TCATTGGAGCAA-GTTCCAAGC
          1 TCATTGGAG-AAGGTTCCAAGC

                                 
      14875 TCATTGGAGAAGGTTCCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                    
      14896 TCATTGGA
          1 TCATTGGA

      14904 ATTGCCTAAG


Statistics
Matches: 28,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
  20    2  0.07
  21   26  0.93

ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26


Consensus pattern (21 bp):   
TCATTGGAGAAGGTTCCAAGC
Done.