Multiple sequence alignment - TraesCS2B01G433300

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2B01G433300 chr2B 100.000 2987 0 0 1 2987 622672493 622675479 0.000000e+00 5517
1 TraesCS2B01G433300 chr2B 96.332 627 22 1 2361 2987 622681838 622682463 0.000000e+00 1029
2 TraesCS2B01G433300 chr2B 95.056 627 30 1 2361 2987 114316862 114316237 0.000000e+00 985
3 TraesCS2B01G433300 chr2D 95.135 1521 53 9 833 2334 526346383 526347901 0.000000e+00 2379
4 TraesCS2B01G433300 chr2D 95.064 628 28 3 2361 2987 50320149 50319524 0.000000e+00 985
5 TraesCS2B01G433300 chr2D 83.019 212 36 0 1698 1909 542064118 542063907 3.040000e-45 193
6 TraesCS2B01G433300 chr2D 87.234 94 10 1 1905 1998 541549812 541549721 4.070000e-19 106
7 TraesCS2B01G433300 chr2A 93.399 1530 70 14 833 2334 671283379 671284905 0.000000e+00 2237
8 TraesCS2B01G433300 chr7A 97.839 833 18 0 1 833 279956126 279956958 0.000000e+00 1439
9 TraesCS2B01G433300 chr5A 97.842 834 17 1 1 834 494547099 494547931 0.000000e+00 1439
10 TraesCS2B01G433300 chr6B 97.716 832 19 0 1 832 500484828 500483997 0.000000e+00 1432
11 TraesCS2B01G433300 chr6B 96.717 853 27 1 1 853 559605639 559606490 0.000000e+00 1419
12 TraesCS2B01G433300 chr3B 97.716 832 19 0 1 832 338163317 338164148 0.000000e+00 1432
13 TraesCS2B01G433300 chr3B 97.596 832 20 0 1 832 144221327 144220496 0.000000e+00 1426
14 TraesCS2B01G433300 chr3B 97.476 832 21 0 1 832 454468452 454469283 0.000000e+00 1421
15 TraesCS2B01G433300 chr4B 97.488 836 20 1 1 836 65196280 65197114 0.000000e+00 1426
16 TraesCS2B01G433300 chr5B 97.479 833 21 0 1 833 602158356 602159188 0.000000e+00 1423
17 TraesCS2B01G433300 chr5B 94.904 628 30 2 2361 2987 518980292 518980918 0.000000e+00 981
18 TraesCS2B01G433300 chr5B 94.904 628 30 2 2361 2987 689957550 689958176 0.000000e+00 981
19 TraesCS2B01G433300 chr1D 95.382 628 26 3 2361 2987 122846133 122846758 0.000000e+00 996
20 TraesCS2B01G433300 chr1D 94.737 627 31 2 2361 2987 76083112 76082488 0.000000e+00 974
21 TraesCS2B01G433300 chr7B 94.745 628 31 2 2361 2987 15573916 15574542 0.000000e+00 976
22 TraesCS2B01G433300 chr1B 94.762 630 28 4 2360 2987 616739162 616739788 0.000000e+00 976


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G433300 chr2B 622672493 622675479 2986 False 5517 5517 100.000 1 2987 1 chr2B.!!$F1 2986
1 TraesCS2B01G433300 chr2B 622681838 622682463 625 False 1029 1029 96.332 2361 2987 1 chr2B.!!$F2 626
2 TraesCS2B01G433300 chr2B 114316237 114316862 625 True 985 985 95.056 2361 2987 1 chr2B.!!$R1 626
3 TraesCS2B01G433300 chr2D 526346383 526347901 1518 False 2379 2379 95.135 833 2334 1 chr2D.!!$F1 1501
4 TraesCS2B01G433300 chr2D 50319524 50320149 625 True 985 985 95.064 2361 2987 1 chr2D.!!$R1 626
5 TraesCS2B01G433300 chr2A 671283379 671284905 1526 False 2237 2237 93.399 833 2334 1 chr2A.!!$F1 1501
6 TraesCS2B01G433300 chr7A 279956126 279956958 832 False 1439 1439 97.839 1 833 1 chr7A.!!$F1 832
7 TraesCS2B01G433300 chr5A 494547099 494547931 832 False 1439 1439 97.842 1 834 1 chr5A.!!$F1 833
8 TraesCS2B01G433300 chr6B 500483997 500484828 831 True 1432 1432 97.716 1 832 1 chr6B.!!$R1 831
9 TraesCS2B01G433300 chr6B 559605639 559606490 851 False 1419 1419 96.717 1 853 1 chr6B.!!$F1 852
10 TraesCS2B01G433300 chr3B 338163317 338164148 831 False 1432 1432 97.716 1 832 1 chr3B.!!$F1 831
11 TraesCS2B01G433300 chr3B 144220496 144221327 831 True 1426 1426 97.596 1 832 1 chr3B.!!$R1 831
12 TraesCS2B01G433300 chr3B 454468452 454469283 831 False 1421 1421 97.476 1 832 1 chr3B.!!$F2 831
13 TraesCS2B01G433300 chr4B 65196280 65197114 834 False 1426 1426 97.488 1 836 1 chr4B.!!$F1 835
14 TraesCS2B01G433300 chr5B 602158356 602159188 832 False 1423 1423 97.479 1 833 1 chr5B.!!$F2 832
15 TraesCS2B01G433300 chr5B 518980292 518980918 626 False 981 981 94.904 2361 2987 1 chr5B.!!$F1 626
16 TraesCS2B01G433300 chr5B 689957550 689958176 626 False 981 981 94.904 2361 2987 1 chr5B.!!$F3 626
17 TraesCS2B01G433300 chr1D 122846133 122846758 625 False 996 996 95.382 2361 2987 1 chr1D.!!$F1 626
18 TraesCS2B01G433300 chr1D 76082488 76083112 624 True 974 974 94.737 2361 2987 1 chr1D.!!$R1 626
19 TraesCS2B01G433300 chr7B 15573916 15574542 626 False 976 976 94.745 2361 2987 1 chr7B.!!$F1 626
20 TraesCS2B01G433300 chr1B 616739162 616739788 626 False 976 976 94.762 2360 2987 1 chr1B.!!$F1 627

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
712 714 0.314302 AGTCTTTGTGGTCGAGTCCG 59.686 55.000 0.0 0.0 37.07 4.79 F
1234 1237 1.068333 CGCTTCTTTGGGGAATGTGTG 60.068 52.381 0.0 0.0 0.00 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1630 1653 0.914417 AACGTCATCACCCCCTCCAT 60.914 55.0 0.0 0.0 0.0 3.41 R
2347 2380 0.983467 TGCTAGGTGGAATGTGCTCA 59.017 50.0 0.0 0.0 0.0 4.26 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 3.147595 CGATGGAGGAGCCGACCA 61.148 66.667 9.95 9.95 40.66 4.02
132 133 2.746277 GGGGAGCGCATCAACGTT 60.746 61.111 11.47 0.00 34.88 3.99
323 324 2.522185 ACTGTCGTGGTTCTAAGCCTA 58.478 47.619 0.00 0.00 0.00 3.93
473 475 4.724303 CGGTCGAGTGGATTATGAGTATC 58.276 47.826 0.00 0.00 0.00 2.24
531 533 2.572104 GGGGGTGGCTTATATAGAGTGG 59.428 54.545 0.00 0.00 0.00 4.00
699 701 1.341531 CTGGTGGTCGAGTGAGTCTTT 59.658 52.381 0.00 0.00 0.00 2.52
712 714 0.314302 AGTCTTTGTGGTCGAGTCCG 59.686 55.000 0.00 0.00 37.07 4.79
913 915 4.291783 CCTCTCGCTCTTTTATAACCTCG 58.708 47.826 0.00 0.00 0.00 4.63
923 925 8.193438 GCTCTTTTATAACCTCGGAAACTACTA 58.807 37.037 0.00 0.00 0.00 1.82
927 929 8.814038 TTTATAACCTCGGAAACTACTACTCT 57.186 34.615 0.00 0.00 0.00 3.24
1234 1237 1.068333 CGCTTCTTTGGGGAATGTGTG 60.068 52.381 0.00 0.00 0.00 3.82
1371 1374 3.033764 CACGTCAACCCGGTCGTG 61.034 66.667 13.90 13.90 45.10 4.35
1548 1559 9.072375 CACTATTCCTAGTCATACATCTCAGAA 57.928 37.037 0.00 0.00 35.99 3.02
1662 1685 2.495409 TGACGTTCTTGCTCGTGTAA 57.505 45.000 0.00 0.00 40.39 2.41
1666 1689 1.862201 CGTTCTTGCTCGTGTAAACCA 59.138 47.619 0.00 0.00 0.00 3.67
2193 2220 7.652909 GCAATAATGGAAGCATGCTTGTAAATA 59.347 33.333 36.48 21.06 36.26 1.40
2200 2227 7.877097 TGGAAGCATGCTTGTAAATAATGTTTT 59.123 29.630 36.48 7.44 36.26 2.43
2201 2228 9.364989 GGAAGCATGCTTGTAAATAATGTTTTA 57.635 29.630 36.48 0.00 36.26 1.52
2273 2301 2.664402 ACTTTGAGCACATTCCACCT 57.336 45.000 0.00 0.00 0.00 4.00
2352 2385 5.726980 AAATGGAAGCAATACTTTGAGCA 57.273 34.783 0.00 0.00 39.29 4.26
2353 2386 4.708726 ATGGAAGCAATACTTTGAGCAC 57.291 40.909 0.00 0.00 39.29 4.40
2354 2387 3.485394 TGGAAGCAATACTTTGAGCACA 58.515 40.909 0.00 0.00 39.29 4.57
2355 2388 4.081406 TGGAAGCAATACTTTGAGCACAT 58.919 39.130 0.00 0.00 39.29 3.21
2356 2389 4.523943 TGGAAGCAATACTTTGAGCACATT 59.476 37.500 0.00 0.00 39.29 2.71
2357 2390 5.098211 GGAAGCAATACTTTGAGCACATTC 58.902 41.667 0.00 0.00 39.29 2.67
2358 2391 4.708726 AGCAATACTTTGAGCACATTCC 57.291 40.909 0.00 0.00 34.60 3.01
2399 2432 0.388649 CCTCGAAACACTGAGACCGG 60.389 60.000 0.00 0.00 34.04 5.28
2469 2502 6.549364 TGTTCACCATTGAAAACTACTCCATT 59.451 34.615 0.00 0.00 43.52 3.16
2504 2537 3.440173 CGGACATGGCTTAGTTGATTTGT 59.560 43.478 0.00 0.00 0.00 2.83
2506 2539 5.123186 CGGACATGGCTTAGTTGATTTGTAA 59.877 40.000 0.00 0.00 0.00 2.41
2509 2542 7.362920 GGACATGGCTTAGTTGATTTGTAACAT 60.363 37.037 0.00 0.00 0.00 2.71
2712 2747 7.928307 AAGCTAAGTTGAAAGATGATGCTAA 57.072 32.000 0.00 0.00 0.00 3.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 1.216178 CAACCGTCGACCCCGTATT 59.784 57.895 10.58 0.00 37.05 1.89
132 133 1.305633 CTCCAGGAGGCTCCACTCA 60.306 63.158 33.86 14.36 39.61 3.41
350 352 2.179204 TCCATAGCTAGGACCTTGCCTA 59.821 50.000 22.23 14.54 39.50 3.93
473 475 1.798813 GTTCGGCACCTTGTAACTCAG 59.201 52.381 0.00 0.00 0.00 3.35
699 701 1.105167 ACTTGACGGACTCGACCACA 61.105 55.000 0.00 0.00 40.11 4.17
712 714 2.350964 GGACTCACTCGACTGACTTGAC 60.351 54.545 0.00 0.00 0.00 3.18
913 915 5.135508 TGAACTGCAGAGTAGTAGTTTCC 57.864 43.478 23.35 0.00 43.10 3.13
923 925 0.671781 GCACGGATGAACTGCAGAGT 60.672 55.000 23.35 7.66 0.00 3.24
927 929 1.246649 ATTTGCACGGATGAACTGCA 58.753 45.000 0.00 0.00 39.15 4.41
989 991 1.210155 GACGCCATTGCCACAAGTC 59.790 57.895 0.00 0.00 0.00 3.01
1122 1124 2.669229 TCGGTCGACGTACTGGCA 60.669 61.111 9.92 0.00 44.69 4.92
1234 1237 2.821366 CGTGAGCATCCCTGGCAC 60.821 66.667 0.00 0.00 0.00 5.01
1367 1370 2.427905 CGAAGGCGAACGTCACGA 60.428 61.111 2.91 0.00 40.82 4.35
1630 1653 0.914417 AACGTCATCACCCCCTCCAT 60.914 55.000 0.00 0.00 0.00 3.41
1824 1847 1.664965 GAAGTCGCCGCTGACAACT 60.665 57.895 14.76 2.77 41.41 3.16
1956 1979 1.926511 CTGTTTCCACGCTCCCATGC 61.927 60.000 0.00 0.00 0.00 4.06
2033 2057 9.739276 ACATTAGTCCTGATCTTGAAACAATTA 57.261 29.630 0.00 0.00 0.00 1.40
2034 2058 8.517878 CACATTAGTCCTGATCTTGAAACAATT 58.482 33.333 0.00 0.00 0.00 2.32
2044 2068 5.869579 ACAAACACACATTAGTCCTGATCT 58.130 37.500 0.00 0.00 0.00 2.75
2201 2228 9.829507 CTCTAAGAGTTTATGATGATTGGACTT 57.170 33.333 0.00 0.00 0.00 3.01
2224 2252 6.252599 TCCATGGAATATGCTACAAACTCT 57.747 37.500 13.46 0.00 0.00 3.24
2238 2266 4.922206 TCAAAGTAGTGCTTCCATGGAAT 58.078 39.130 27.20 15.03 36.17 3.01
2334 2367 4.708726 ATGTGCTCAAAGTATTGCTTCC 57.291 40.909 0.00 0.00 36.17 3.46
2335 2368 5.098211 GGAATGTGCTCAAAGTATTGCTTC 58.902 41.667 0.00 0.00 36.17 3.86
2336 2369 4.523943 TGGAATGTGCTCAAAGTATTGCTT 59.476 37.500 0.00 0.00 39.52 3.91
2337 2370 4.081406 TGGAATGTGCTCAAAGTATTGCT 58.919 39.130 0.00 0.00 36.45 3.91
2338 2371 4.168760 GTGGAATGTGCTCAAAGTATTGC 58.831 43.478 0.00 0.00 36.45 3.56
2339 2372 4.460382 AGGTGGAATGTGCTCAAAGTATTG 59.540 41.667 0.00 0.00 37.92 1.90
2340 2373 4.666512 AGGTGGAATGTGCTCAAAGTATT 58.333 39.130 0.00 0.00 0.00 1.89
2341 2374 4.307032 AGGTGGAATGTGCTCAAAGTAT 57.693 40.909 0.00 0.00 0.00 2.12
2342 2375 3.788227 AGGTGGAATGTGCTCAAAGTA 57.212 42.857 0.00 0.00 0.00 2.24
2343 2376 2.664402 AGGTGGAATGTGCTCAAAGT 57.336 45.000 0.00 0.00 0.00 2.66
2344 2377 2.421424 GCTAGGTGGAATGTGCTCAAAG 59.579 50.000 0.00 0.00 0.00 2.77
2345 2378 2.224744 TGCTAGGTGGAATGTGCTCAAA 60.225 45.455 0.00 0.00 0.00 2.69
2346 2379 1.350684 TGCTAGGTGGAATGTGCTCAA 59.649 47.619 0.00 0.00 0.00 3.02
2347 2380 0.983467 TGCTAGGTGGAATGTGCTCA 59.017 50.000 0.00 0.00 0.00 4.26
2348 2381 2.338577 ATGCTAGGTGGAATGTGCTC 57.661 50.000 0.00 0.00 0.00 4.26
2349 2382 4.347876 TGTATATGCTAGGTGGAATGTGCT 59.652 41.667 0.00 0.00 0.00 4.40
2350 2383 4.641396 TGTATATGCTAGGTGGAATGTGC 58.359 43.478 0.00 0.00 0.00 4.57
2351 2384 6.101650 TCTGTATATGCTAGGTGGAATGTG 57.898 41.667 0.00 0.00 0.00 3.21
2352 2385 6.942163 ATCTGTATATGCTAGGTGGAATGT 57.058 37.500 0.00 0.00 0.00 2.71
2353 2386 7.930325 CCATATCTGTATATGCTAGGTGGAATG 59.070 40.741 0.00 0.00 42.48 2.67
2354 2387 7.419518 GCCATATCTGTATATGCTAGGTGGAAT 60.420 40.741 0.00 0.00 42.48 3.01
2355 2388 6.127054 GCCATATCTGTATATGCTAGGTGGAA 60.127 42.308 0.00 0.00 42.48 3.53
2356 2389 5.363868 GCCATATCTGTATATGCTAGGTGGA 59.636 44.000 0.00 0.00 42.48 4.02
2357 2390 5.453903 GGCCATATCTGTATATGCTAGGTGG 60.454 48.000 0.00 0.00 42.48 4.61
2358 2391 5.365025 AGGCCATATCTGTATATGCTAGGTG 59.635 44.000 5.01 0.00 42.48 4.00
2399 2432 6.740110 ACTATATGATTCACACTCGACCTTC 58.260 40.000 0.00 0.00 0.00 3.46
2469 2502 2.539476 CATGTCCGATCATCACGTGAA 58.461 47.619 24.13 7.48 40.97 3.18
2509 2542 8.548025 TCCCTCTAATCATTTAAGTGATCACAA 58.452 33.333 27.02 13.52 37.85 3.33
2796 2831 2.271173 CATCTGCAGCAGGCCTGA 59.729 61.111 37.21 14.99 44.64 3.86


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.