Multiple sequence alignment - TraesCS2A01G366300

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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 TraesCS2A01G366300 chr2A 100.000 2375 0 0 1 2375 610789242 610791616 0.000000e+00 4386
1 TraesCS2A01G366300 chr7A 96.089 2327 70 8 1 2309 56073899 56076222 0.000000e+00 3773
2 TraesCS2A01G366300 chr1D 94.694 2337 96 13 1 2314 463793643 463791312 0.000000e+00 3603
3 TraesCS2A01G366300 chr1D 93.103 1450 53 13 904 2310 336729287 336727842 0.000000e+00 2080
4 TraesCS2A01G366300 chr4D 93.915 2350 93 12 1 2309 236672657 236670317 0.000000e+00 3502
5 TraesCS2A01G366300 chr4D 86.840 1421 123 38 905 2309 239784686 239783314 0.000000e+00 1530
6 TraesCS2A01G366300 chr4D 85.281 231 11 2 1390 1597 125903980 125903750 1.430000e-52 217
7 TraesCS2A01G366300 chr4D 97.333 75 2 0 2298 2372 89064235 89064309 6.890000e-26 128
8 TraesCS2A01G366300 chr2D 92.748 2358 101 22 1 2310 645236663 645234328 0.000000e+00 3343
9 TraesCS2A01G366300 chr2D 92.683 82 5 1 2294 2375 55530369 55530289 1.490000e-22 117
10 TraesCS2A01G366300 chr5B 95.526 2101 60 13 1 2098 56336221 56338290 0.000000e+00 3328
11 TraesCS2A01G366300 chr4A 92.912 2328 104 18 1 2309 129030524 129032809 0.000000e+00 3328
12 TraesCS2A01G366300 chr4A 95.978 920 33 4 1 918 433607523 433606606 0.000000e+00 1491
13 TraesCS2A01G366300 chr4A 97.222 72 2 0 2304 2375 576483849 576483778 3.210000e-24 122
14 TraesCS2A01G366300 chr5A 91.585 2353 126 14 1 2310 235675095 235677418 0.000000e+00 3182
15 TraesCS2A01G366300 chr2B 88.663 2364 186 51 1 2309 149803143 149805479 0.000000e+00 2806
16 TraesCS2A01G366300 chr7D 93.719 1417 66 14 901 2309 79227533 79228934 0.000000e+00 2102
17 TraesCS2A01G366300 chr7D 93.123 1425 70 14 1 1399 501764135 501765557 0.000000e+00 2063
18 TraesCS2A01G366300 chr5D 93.137 1457 48 16 904 2315 384511181 384509732 0.000000e+00 2089
19 TraesCS2A01G366300 chr5D 96.855 922 29 0 1 922 384512118 384511197 0.000000e+00 1543
20 TraesCS2A01G366300 chr5D 92.958 852 32 13 904 1728 363991505 363990655 0.000000e+00 1216
21 TraesCS2A01G366300 chr5D 91.162 826 53 13 1492 2309 140951674 140950861 0.000000e+00 1103
22 TraesCS2A01G366300 chr6D 92.355 1452 59 25 901 2310 297170564 297169123 0.000000e+00 2019
23 TraesCS2A01G366300 chr6D 96.095 922 36 0 1 922 297171498 297170577 0.000000e+00 1504
24 TraesCS2A01G366300 chr6D 95.536 112 4 1 1435 1545 46519263 46519152 6.750000e-41 178
25 TraesCS2A01G366300 chr3A 93.878 833 46 3 546 1375 706571677 706570847 0.000000e+00 1251
26 TraesCS2A01G366300 chr3A 91.453 702 36 7 901 1597 702241614 702242296 0.000000e+00 942
27 TraesCS2A01G366300 chrUn 100.000 67 0 0 2309 2375 21074330 21074396 8.910000e-25 124
28 TraesCS2A01G366300 chrUn 100.000 67 0 0 2309 2375 48315985 48315919 8.910000e-25 124
29 TraesCS2A01G366300 chrUn 100.000 67 0 0 2309 2375 69432187 69432253 8.910000e-25 124
30 TraesCS2A01G366300 chrUn 100.000 67 0 0 2309 2375 69438190 69438256 8.910000e-25 124
31 TraesCS2A01G366300 chr3B 94.872 78 3 1 2298 2375 76286279 76286355 1.150000e-23 121
32 TraesCS2A01G366300 chr3D 92.683 82 4 1 2296 2375 498578470 498578389 1.490000e-22 117


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 TraesCS2A01G366300 chr2A 610789242 610791616 2374 False 4386.0 4386 100.000 1 2375 1 chr2A.!!$F1 2374
1 TraesCS2A01G366300 chr7A 56073899 56076222 2323 False 3773.0 3773 96.089 1 2309 1 chr7A.!!$F1 2308
2 TraesCS2A01G366300 chr1D 463791312 463793643 2331 True 3603.0 3603 94.694 1 2314 1 chr1D.!!$R2 2313
3 TraesCS2A01G366300 chr1D 336727842 336729287 1445 True 2080.0 2080 93.103 904 2310 1 chr1D.!!$R1 1406
4 TraesCS2A01G366300 chr4D 236670317 236672657 2340 True 3502.0 3502 93.915 1 2309 1 chr4D.!!$R2 2308
5 TraesCS2A01G366300 chr4D 239783314 239784686 1372 True 1530.0 1530 86.840 905 2309 1 chr4D.!!$R3 1404
6 TraesCS2A01G366300 chr2D 645234328 645236663 2335 True 3343.0 3343 92.748 1 2310 1 chr2D.!!$R2 2309
7 TraesCS2A01G366300 chr5B 56336221 56338290 2069 False 3328.0 3328 95.526 1 2098 1 chr5B.!!$F1 2097
8 TraesCS2A01G366300 chr4A 129030524 129032809 2285 False 3328.0 3328 92.912 1 2309 1 chr4A.!!$F1 2308
9 TraesCS2A01G366300 chr4A 433606606 433607523 917 True 1491.0 1491 95.978 1 918 1 chr4A.!!$R1 917
10 TraesCS2A01G366300 chr5A 235675095 235677418 2323 False 3182.0 3182 91.585 1 2310 1 chr5A.!!$F1 2309
11 TraesCS2A01G366300 chr2B 149803143 149805479 2336 False 2806.0 2806 88.663 1 2309 1 chr2B.!!$F1 2308
12 TraesCS2A01G366300 chr7D 79227533 79228934 1401 False 2102.0 2102 93.719 901 2309 1 chr7D.!!$F1 1408
13 TraesCS2A01G366300 chr7D 501764135 501765557 1422 False 2063.0 2063 93.123 1 1399 1 chr7D.!!$F2 1398
14 TraesCS2A01G366300 chr5D 384509732 384512118 2386 True 1816.0 2089 94.996 1 2315 2 chr5D.!!$R3 2314
15 TraesCS2A01G366300 chr5D 363990655 363991505 850 True 1216.0 1216 92.958 904 1728 1 chr5D.!!$R2 824
16 TraesCS2A01G366300 chr5D 140950861 140951674 813 True 1103.0 1103 91.162 1492 2309 1 chr5D.!!$R1 817
17 TraesCS2A01G366300 chr6D 297169123 297171498 2375 True 1761.5 2019 94.225 1 2310 2 chr6D.!!$R2 2309
18 TraesCS2A01G366300 chr3A 706570847 706571677 830 True 1251.0 1251 93.878 546 1375 1 chr3A.!!$R1 829
19 TraesCS2A01G366300 chr3A 702241614 702242296 682 False 942.0 942 91.453 901 1597 1 chr3A.!!$F1 696

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
104 105 1.135139 CTGGTGGAGATGTGGTCTACG 59.865 57.143 0.0 0.0 41.05 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1487 1652 0.179018 GTGCTCCCAGGTTCACTTGT 60.179 55.0 0.0 0.0 0.0 3.16 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
104 105 1.135139 CTGGTGGAGATGTGGTCTACG 59.865 57.143 0.00 0.0 41.05 3.51
179 180 6.847421 TGATATGCTAGTGCTAGATCATGT 57.153 37.500 10.17 3.8 40.48 3.21
186 187 3.529533 AGTGCTAGATCATGTTGACAGC 58.470 45.455 0.00 0.0 0.00 4.40
347 349 9.357652 CGTTTGATCCTCATTGAATAACATTTT 57.642 29.630 0.00 0.0 0.00 1.82
610 659 2.167693 AGAACCAGTCAAGAACACACGA 59.832 45.455 0.00 0.0 0.00 4.35
1024 1148 1.231958 AAAAATGAAGGACGCGCCGA 61.232 50.000 5.73 0.0 43.43 5.54
1404 1538 4.229876 GCAGTTTGTCTTTGAACCTATGC 58.770 43.478 0.00 0.0 0.00 3.14
1518 1768 0.108585 GGGAGCACTTGTGAACCTGA 59.891 55.000 4.79 0.0 0.00 3.86
1952 2320 6.256321 GCAGATGAGCAAAACAAAGAGAAAAA 59.744 34.615 0.00 0.0 0.00 1.94
2072 2445 2.661537 CACGTCAGCTTGCCACGA 60.662 61.111 17.73 0.0 37.00 4.35
2170 2545 3.389925 AAACGTCTACGACCATTCCAA 57.610 42.857 9.86 0.0 43.02 3.53
2293 2679 6.122277 CCAATAGTGGTGGTCATAAGTTGAT 58.878 40.000 0.00 0.0 40.42 2.57
2324 2710 9.444600 TTCTTGTAGTGGTAGAACAAATATTCC 57.555 33.333 0.00 0.0 33.05 3.01
2325 2711 8.044908 TCTTGTAGTGGTAGAACAAATATTCCC 58.955 37.037 0.00 0.0 33.05 3.97
2326 2712 7.504926 TGTAGTGGTAGAACAAATATTCCCT 57.495 36.000 0.00 0.0 0.00 4.20
2327 2713 7.562135 TGTAGTGGTAGAACAAATATTCCCTC 58.438 38.462 0.00 0.0 0.00 4.30
2328 2714 6.636454 AGTGGTAGAACAAATATTCCCTCA 57.364 37.500 0.00 0.0 0.00 3.86
2329 2715 7.027874 AGTGGTAGAACAAATATTCCCTCAA 57.972 36.000 0.00 0.0 0.00 3.02
2330 2716 7.112779 AGTGGTAGAACAAATATTCCCTCAAG 58.887 38.462 0.00 0.0 0.00 3.02
2331 2717 6.884836 GTGGTAGAACAAATATTCCCTCAAGT 59.115 38.462 0.00 0.0 0.00 3.16
2332 2718 7.393515 GTGGTAGAACAAATATTCCCTCAAGTT 59.606 37.037 0.00 0.0 0.00 2.66
2333 2719 7.610305 TGGTAGAACAAATATTCCCTCAAGTTC 59.390 37.037 0.00 0.0 35.58 3.01
2334 2720 7.829706 GGTAGAACAAATATTCCCTCAAGTTCT 59.170 37.037 0.00 0.0 44.45 3.01
2335 2721 9.886132 GTAGAACAAATATTCCCTCAAGTTCTA 57.114 33.333 0.00 0.0 42.83 2.10
2337 2723 9.620259 AGAACAAATATTCCCTCAAGTTCTATC 57.380 33.333 0.00 0.0 41.64 2.08
2338 2724 8.438676 AACAAATATTCCCTCAAGTTCTATCG 57.561 34.615 0.00 0.0 0.00 2.92
2339 2725 7.792032 ACAAATATTCCCTCAAGTTCTATCGA 58.208 34.615 0.00 0.0 0.00 3.59
2340 2726 7.711339 ACAAATATTCCCTCAAGTTCTATCGAC 59.289 37.037 0.00 0.0 0.00 4.20
2341 2727 4.674281 ATTCCCTCAAGTTCTATCGACC 57.326 45.455 0.00 0.0 0.00 4.79
2342 2728 3.095912 TCCCTCAAGTTCTATCGACCA 57.904 47.619 0.00 0.0 0.00 4.02
2343 2729 2.758979 TCCCTCAAGTTCTATCGACCAC 59.241 50.000 0.00 0.0 0.00 4.16
2344 2730 2.159085 CCCTCAAGTTCTATCGACCACC 60.159 54.545 0.00 0.0 0.00 4.61
2345 2731 2.479730 CCTCAAGTTCTATCGACCACCG 60.480 54.545 0.00 0.0 40.25 4.94
2355 2741 1.830279 TCGACCACCGATACAACTCT 58.170 50.000 0.00 0.0 43.23 3.24
2356 2742 2.989909 TCGACCACCGATACAACTCTA 58.010 47.619 0.00 0.0 43.23 2.43
2357 2743 2.679837 TCGACCACCGATACAACTCTAC 59.320 50.000 0.00 0.0 43.23 2.59
2358 2744 2.538333 CGACCACCGATACAACTCTACG 60.538 54.545 0.00 0.0 41.76 3.51
2359 2745 1.133790 ACCACCGATACAACTCTACGC 59.866 52.381 0.00 0.0 0.00 4.42
2360 2746 1.133598 CCACCGATACAACTCTACGCA 59.866 52.381 0.00 0.0 0.00 5.24
2361 2747 2.182825 CACCGATACAACTCTACGCAC 58.817 52.381 0.00 0.0 0.00 5.34
2362 2748 1.814394 ACCGATACAACTCTACGCACA 59.186 47.619 0.00 0.0 0.00 4.57
2363 2749 2.182825 CCGATACAACTCTACGCACAC 58.817 52.381 0.00 0.0 0.00 3.82
2364 2750 2.159421 CCGATACAACTCTACGCACACT 60.159 50.000 0.00 0.0 0.00 3.55
2365 2751 3.499048 CGATACAACTCTACGCACACTT 58.501 45.455 0.00 0.0 0.00 3.16
2366 2752 3.300853 CGATACAACTCTACGCACACTTG 59.699 47.826 0.00 0.0 0.00 3.16
2367 2753 2.882927 ACAACTCTACGCACACTTGA 57.117 45.000 0.00 0.0 0.00 3.02
2368 2754 2.470821 ACAACTCTACGCACACTTGAC 58.529 47.619 0.00 0.0 0.00 3.18
2369 2755 1.452025 CAACTCTACGCACACTTGACG 59.548 52.381 0.00 0.0 0.00 4.35
2370 2756 0.666913 ACTCTACGCACACTTGACGT 59.333 50.000 0.00 0.0 38.47 4.34
2371 2757 1.066605 ACTCTACGCACACTTGACGTT 59.933 47.619 7.22 0.0 36.97 3.99
2372 2758 1.714460 CTCTACGCACACTTGACGTTC 59.286 52.381 7.22 0.0 36.97 3.95
2373 2759 0.429736 CTACGCACACTTGACGTTCG 59.570 55.000 7.22 0.0 36.97 3.95
2374 2760 1.542272 TACGCACACTTGACGTTCGC 61.542 55.000 7.22 0.0 36.97 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
104 105 2.492019 GACAAACCTTGTGTCTTGGC 57.508 50.000 0.00 0.00 45.52 4.52
347 349 9.932207 ATCAAAATGTTATTCAGCAAGAATCAA 57.068 25.926 7.57 0.70 43.42 2.57
1024 1148 2.551270 TGGCTCTTCACCTTCTGGTAT 58.449 47.619 0.00 0.00 46.60 2.73
1404 1538 1.920574 CTACGACAAACTGCATCGGAG 59.079 52.381 11.03 7.93 40.22 4.63
1487 1652 0.179018 GTGCTCCCAGGTTCACTTGT 60.179 55.000 0.00 0.00 0.00 3.16
1518 1768 1.280421 GCTCCCAGGTTCACAAGATCT 59.720 52.381 0.00 0.00 0.00 2.75
1865 2227 3.795688 TGGAGCCTTTTTCTGATGACT 57.204 42.857 0.00 0.00 0.00 3.41
2072 2445 1.213678 CCCACACCATGTCAGATCCAT 59.786 52.381 0.00 0.00 0.00 3.41
2311 2697 9.620259 GATAGAACTTGAGGGAATATTTGTTCT 57.380 33.333 0.00 0.00 43.21 3.01
2337 2723 2.538333 CGTAGAGTTGTATCGGTGGTCG 60.538 54.545 0.00 0.00 40.90 4.79
2338 2724 2.793933 GCGTAGAGTTGTATCGGTGGTC 60.794 54.545 0.00 0.00 0.00 4.02
2339 2725 1.133790 GCGTAGAGTTGTATCGGTGGT 59.866 52.381 0.00 0.00 0.00 4.16
2340 2726 1.133598 TGCGTAGAGTTGTATCGGTGG 59.866 52.381 0.00 0.00 0.00 4.61
2341 2727 2.182825 GTGCGTAGAGTTGTATCGGTG 58.817 52.381 0.00 0.00 0.00 4.94
2342 2728 1.814394 TGTGCGTAGAGTTGTATCGGT 59.186 47.619 0.00 0.00 0.00 4.69
2343 2729 2.159421 AGTGTGCGTAGAGTTGTATCGG 60.159 50.000 0.00 0.00 0.00 4.18
2344 2730 3.132629 AGTGTGCGTAGAGTTGTATCG 57.867 47.619 0.00 0.00 0.00 2.92
2345 2731 4.323868 GTCAAGTGTGCGTAGAGTTGTATC 59.676 45.833 15.91 6.59 33.50 2.24
2346 2732 4.235360 GTCAAGTGTGCGTAGAGTTGTAT 58.765 43.478 15.91 0.00 33.50 2.29
2347 2733 3.635331 GTCAAGTGTGCGTAGAGTTGTA 58.365 45.455 15.91 3.09 33.50 2.41
2348 2734 2.470821 GTCAAGTGTGCGTAGAGTTGT 58.529 47.619 15.91 0.00 33.50 3.32
2349 2735 1.452025 CGTCAAGTGTGCGTAGAGTTG 59.548 52.381 11.29 11.29 33.14 3.16
2350 2736 1.066605 ACGTCAAGTGTGCGTAGAGTT 59.933 47.619 0.00 0.00 36.29 3.01
2351 2737 0.666913 ACGTCAAGTGTGCGTAGAGT 59.333 50.000 0.00 0.00 36.29 3.24
2352 2738 1.714460 GAACGTCAAGTGTGCGTAGAG 59.286 52.381 0.00 0.00 36.79 2.43
2353 2739 1.762419 GAACGTCAAGTGTGCGTAGA 58.238 50.000 0.00 0.00 36.79 2.59
2354 2740 0.429736 CGAACGTCAAGTGTGCGTAG 59.570 55.000 0.00 0.00 36.79 3.51
2355 2741 1.542272 GCGAACGTCAAGTGTGCGTA 61.542 55.000 0.00 0.00 36.79 4.42
2356 2742 2.867091 GCGAACGTCAAGTGTGCGT 61.867 57.895 0.00 0.00 38.54 5.24
2357 2743 2.128128 GCGAACGTCAAGTGTGCG 60.128 61.111 0.00 0.00 0.00 5.34


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

AutoCloner maintained by Alex Coulton.