Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014748.1 Corchorus olitorius cultivar O-4 contig14781, 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: 4784
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.34


Found at i:2458 original size:33 final size:33

Alignment explanation


    Indices: 2421--2580  Score: 105
    Period size: 33  Copynumber: 4.9  Consensus size: 33

       2411 CTAATTTGAG

                      *       *              
       2421 TGTTGTTTGTAATGACACGAAATCTGTTTTAGA
          1 TGTTGTTTGTGATGACACTAAATCTGTTTTAGA

                   *       *      *  **      
       2454 TGTTGTTAGTGATGATACTAAACCTAATTT-GA
          1 TGTTGTTTGTGATGACACTAAATCTGTTTTAGA

              *         *                    *
       2486 GTATTG-TT-TGCTGACACTAAATCTGTTTTAGG
          1 -TGTTGTTTGTGATGACACTAAATCTGTTTTAGA

             *             *               *  
       2518 TATTGTTTGTGATGAAAC-AAATTCTGTTTTGGA
          1 TGTTGTTTGTGATGACACTAAA-TCTGTTTTAGA

              * **          *              
       2551 TGCTAATTGTGATGAAAAC-AAATCTGTTTT
          1 TGTTGTTTGTGATG-ACACTAAATCTGTTTT

       2581 GGTTGATCAT


Statistics
Matches: 98,  Mismatches: 23, Indels: 12
        0.74            0.17        0.09

Matches are distributed among these distances:
  31   21  0.21
  32    9  0.09
  33   61  0.62
  34    7  0.07

ACGTcount: A:0.28, C:0.09, G:0.20, T:0.42


Consensus pattern (33 bp):   
TGTTGTTTGTGATGACACTAAATCTGTTTTAGA

Found at i:2521 original size:31 final size:31

Alignment explanation


    Indices: 2423--2526  Score: 84
    Period size: 31  Copynumber: 3.2  Consensus size: 31

       2413 AATTTGAGTG

                            *             * *
       2423 TTGTTTGTAATGACACGAAATCTGTTTTAGATG
          1 TTGTTTG--ATGACACTAAATCTGTTTTAGGTA

                         *      *  **         
       2456 TTGTTAGTGATGATACTAAACCTAATTT-GAGTA
          1 TTGTT--TGATGACACTAAATCTGTTTTAG-GTA

                   *                       
       2489 TTGTTTGCTGACACTAAATCTGTTTTAGGTA
          1 TTGTTTGATGACACTAAATCTGTTTTAGGTA

                   
       2520 TTGTTTG
          1 TTGTTTG

       2527 TGATGAAACA


Statistics
Matches: 55,  Mismatches: 12, Indels: 10
        0.71            0.16        0.13

Matches are distributed among these distances:
  31   26  0.47
  32    2  0.04
  33   25  0.45
  35    2  0.04

ACGTcount: A:0.26, C:0.10, G:0.20, T:0.44


Consensus pattern (31 bp):   
TTGTTTGATGACACTAAATCTGTTTTAGGTA

Found at i:2524 original size:64 final size:65

Alignment explanation


    Indices: 2408--2532  Score: 180
    Period size: 64  Copynumber: 1.9  Consensus size: 65

       2398 AGTAATTCTG

                          *                                *                 
       2408 AACCTAATTTGAGTGTTGTTTGTAATGACACGAAATCTGTTTTAGATGTTGTTAGTGATGATACT
          1 AACCTAATTTGAGTATTGTTTG-AATGACACGAAATCTGTTTTAGATATTGTTAGTGATGATACT

             
       2473 A
         65 A

                                   *      *             *       *       
       2474 AACCTAATTTGAGTATTGTTTG-CTGACACTAAATCTGTTTTAGGTATTGTTTGTGATGA
          1 AACCTAATTTGAGTATTGTTTGAATGACACGAAATCTGTTTTAGATATTGTTAGTGATGA

       2533 AACAAATTCT


Statistics
Matches: 53,  Mismatches: 6, Indels: 2
        0.87            0.10        0.03

Matches are distributed among these distances:
  64   32  0.60
  66   21  0.40

ACGTcount: A:0.27, C:0.10, G:0.21, T:0.42


Consensus pattern (65 bp):   
AACCTAATTTGAGTATTGTTTGAATGACACGAAATCTGTTTTAGATATTGTTAGTGATGATACTA
Done.