AutoCloner

Multiple sequence alignment - TraesCS3B01G283500

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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	TraesCS3B01G283500	chr3B	100.000	2785	0	0	1	2785	454648538	454651322	0.000000e+00	5144
1	TraesCS3B01G283500	chr4B	92.405	2699	122	43	130	2785	24068793	24066135	0.000000e+00	3771
2	TraesCS3B01G283500	chr7A	93.344	2494	94	31	346	2785	141302656	141305131	0.000000e+00	3620
3	TraesCS3B01G283500	chr7A	91.922	2513	112	43	346	2785	141893394	141895888	0.000000e+00	3432
4	TraesCS3B01G283500	chr7A	95.606	2071	59	13	739	2785	140759386	140761448	0.000000e+00	3291
5	TraesCS3B01G283500	chr7A	96.868	1724	42	4	1072	2785	141048618	141050339	0.000000e+00	2874
6	TraesCS3B01G283500	chr7A	94.335	1324	44	9	739	2039	141643112	141644427	0.000000e+00	2001
7	TraesCS3B01G283500	chr7A	83.936	498	45	22	346	828	141642672	141643149	7.080000e-121	444
8	TraesCS3B01G283500	chr7A	84.141	454	42	18	346	783	141047621	141048060	2.000000e-111	412
9	TraesCS3B01G283500	chr7A	83.250	400	37	18	346	730	140758472	140758856	9.550000e-90	340
10	TraesCS3B01G283500	chr7A	86.196	326	15	8	739	1041	141048299	141048617	2.680000e-85	326
11	TraesCS3B01G283500	chr4D	94.818	2065	61	15	747	2785	13352609	13350565	0.000000e+00	3179
12	TraesCS3B01G283500	chr4D	86.423	1532	167	17	745	2249	13363008	13361491	0.000000e+00	1639
13	TraesCS3B01G283500	chr4D	82.271	863	84	34	3	828	13363857	13363027	0.000000e+00	682
14	TraesCS3B01G283500	chr4D	80.765	863	84	31	3	828	13353398	13352581	1.430000e-167	599
15	TraesCS3B01G283500	chr6A	96.870	1725	50	3	1063	2785	201638501	201640223	0.000000e+00	2883
16	TraesCS3B01G283500	chr6A	81.311	412	36	18	221	615	201631285	201631672	2.100000e-76	296
17	TraesCS3B01G283500	chr6A	95.420	131	5	1	655	785	201631967	201632096	1.010000e-49	207
18	TraesCS3B01G283500	chr4A	94.154	1454	54	9	739	2169	588633335	588634780	0.000000e+00	2185
19	TraesCS3B01G283500	chr4A	86.225	1539	170	19	739	2249	571359500	571361024	0.000000e+00	1629
20	TraesCS3B01G283500	chr4A	86.160	1539	171	19	739	2249	588584566	588586090	0.000000e+00	1624
21	TraesCS3B01G283500	chr4A	81.512	860	87	33	3	828	571358716	571359537	2.340000e-180	641
22	TraesCS3B01G283500	chr4A	82.583	666	62	28	184	828	588583971	588584603	3.160000e-149	538
23	TraesCS3B01G283500	chr4A	83.624	287	31	11	346	621	588600100	588600381	3.560000e-64	255
24	TraesCS3B01G283500	chr4A	94.805	77	3	1	655	731	588632869	588632944	4.870000e-23	119

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	TraesCS3B01G283500	chr3B	454648538	454651322	2784	False	5144.0	5144	100.000000	1	2785	1	chr3B.!!$F1	2784
1	TraesCS3B01G283500	chr4B	24066135	24068793	2658	True	3771.0	3771	92.405000	130	2785	1	chr4B.!!$R1	2655
2	TraesCS3B01G283500	chr7A	141302656	141305131	2475	False	3620.0	3620	93.344000	346	2785	1	chr7A.!!$F1	2439
3	TraesCS3B01G283500	chr7A	141893394	141895888	2494	False	3432.0	3432	91.922000	346	2785	1	chr7A.!!$F2	2439
4	TraesCS3B01G283500	chr7A	140758472	140761448	2976	False	1815.5	3291	89.428000	346	2785	2	chr7A.!!$F3	2439
5	TraesCS3B01G283500	chr7A	141642672	141644427	1755	False	1222.5	2001	89.135500	346	2039	2	chr7A.!!$F5	1693
6	TraesCS3B01G283500	chr7A	141047621	141050339	2718	False	1204.0	2874	89.068333	346	2785	3	chr7A.!!$F4	2439
7	TraesCS3B01G283500	chr4D	13350565	13353398	2833	True	1889.0	3179	87.791500	3	2785	2	chr4D.!!$R1	2782
8	TraesCS3B01G283500	chr4D	13361491	13363857	2366	True	1160.5	1639	84.347000	3	2249	2	chr4D.!!$R2	2246
9	TraesCS3B01G283500	chr6A	201638501	201640223	1722	False	2883.0	2883	96.870000	1063	2785	1	chr6A.!!$F1	1722
10	TraesCS3B01G283500	chr6A	201631285	201632096	811	False	251.5	296	88.365500	221	785	2	chr6A.!!$F2	564
11	TraesCS3B01G283500	chr4A	588632869	588634780	1911	False	1152.0	2185	94.479500	655	2169	2	chr4A.!!$F4	1514
12	TraesCS3B01G283500	chr4A	571358716	571361024	2308	False	1135.0	1629	83.868500	3	2249	2	chr4A.!!$F2	2246
13	TraesCS3B01G283500	chr4A	588583971	588586090	2119	False	1081.0	1624	84.371500	184	2249	2	chr4A.!!$F3	2065

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
253	273	1.070445	CCAGGGAGAATAGCAGCCG	59.930	63.158	0.00	0.0	0.00	5.52	F
1194	2357	0.950555	TGGTCAGCTGCGTTGATCAC	60.951	55.000	9.47	0.0	29.42	3.06	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1215	2378	1.215655	CGCCAAGTATACGAGGCTGC	61.216	60.0	27.66	13.34	44.85	5.25	R
2436	3611	1.098050	CGGCCCTTCCTTGATTTCAG	58.902	55.0	0.00	0.00	0.00	3.02	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
61	62	2.047179	GGTGAGTGGGAGCGGTTC	60.047	66.667	0.00	0.00	0.00	3.62
118	119	2.867975	TGCATGCGACTCAATCTATGTG	59.132	45.455	14.09	0.00	0.00	3.21
122	123	1.863454	GCGACTCAATCTATGTGCAGG	59.137	52.381	0.00	0.00	0.00	4.85
123	124	2.481969	GCGACTCAATCTATGTGCAGGA	60.482	50.000	0.00	0.00	0.00	3.86
125	126	3.726607	GACTCAATCTATGTGCAGGAGG	58.273	50.000	0.00	0.00	0.00	4.30
148	165	2.583319	CTGTCATCCGCGTCGCAT	60.583	61.111	18.75	0.48	0.00	4.73
159	177	1.492873	CGTCGCATGTTGGTCACTG	59.507	57.895	0.00	0.00	0.00	3.66
173	191	4.631131	TGGTCACTGTGTCTACAAATCAG	58.369	43.478	7.79	0.00	36.14	2.90
185	203	2.433436	ACAAATCAGGAACGTAAGCCC	58.567	47.619	0.00	0.00	45.62	5.19
205	225	3.144871	GCCCCATAACCCCAACGC	61.145	66.667	0.00	0.00	0.00	4.84
206	226	2.357056	CCCCATAACCCCAACGCA	59.643	61.111	0.00	0.00	0.00	5.24
210	230	2.044352	ATAACCCCAACGCAGCCC	60.044	61.111	0.00	0.00	0.00	5.19
249	269	1.271840	AACCGCCAGGGAGAATAGCA	61.272	55.000	0.00	0.00	43.47	3.49
253	273	1.070445	CCAGGGAGAATAGCAGCCG	59.930	63.158	0.00	0.00	0.00	5.52
272	292	2.159366	CCGCTAGATAGGCATTAGACGG	60.159	54.545	0.00	0.00	32.32	4.79
292	312	2.297597	GGTTCTGGAGACTCCCATATCG	59.702	54.545	19.11	1.01	35.03	2.92
333	355	5.743026	TTGTCATTTACAAAAGTCGCTGA	57.257	34.783	0.00	0.00	45.11	4.26
334	356	5.743026	TGTCATTTACAAAAGTCGCTGAA	57.257	34.783	0.00	0.00	34.29	3.02
335	357	6.125327	TGTCATTTACAAAAGTCGCTGAAA	57.875	33.333	0.00	0.00	34.29	2.69
336	358	6.556212	TGTCATTTACAAAAGTCGCTGAAAA	58.444	32.000	0.00	0.00	34.29	2.29
337	359	7.030165	TGTCATTTACAAAAGTCGCTGAAAAA	58.970	30.769	0.00	0.00	34.29	1.94
338	360	7.704472	TGTCATTTACAAAAGTCGCTGAAAAAT	59.296	29.630	0.00	0.00	34.29	1.82
339	361	7.998212	GTCATTTACAAAAGTCGCTGAAAAATG	59.002	33.333	0.00	0.00	34.47	2.32
340	362	7.704472	TCATTTACAAAAGTCGCTGAAAAATGT	59.296	29.630	0.00	0.00	34.61	2.71
341	363	7.820044	TTTACAAAAGTCGCTGAAAAATGTT	57.180	28.000	0.00	0.00	0.00	2.71
342	364	5.949233	ACAAAAGTCGCTGAAAAATGTTC	57.051	34.783	0.00	0.00	0.00	3.18
343	365	5.406649	ACAAAAGTCGCTGAAAAATGTTCA	58.593	33.333	0.00	0.00	0.00	3.18
344	366	5.288472	ACAAAAGTCGCTGAAAAATGTTCAC	59.712	36.000	0.00	0.00	0.00	3.18
345	367	4.900635	AAGTCGCTGAAAAATGTTCACT	57.099	36.364	0.00	0.00	0.00	3.41
346	368	4.900635	AGTCGCTGAAAAATGTTCACTT	57.099	36.364	0.00	0.00	0.00	3.16
347	369	6.371809	AAGTCGCTGAAAAATGTTCACTTA	57.628	33.333	0.00	0.00	0.00	2.24
348	370	6.560253	AGTCGCTGAAAAATGTTCACTTAT	57.440	33.333	0.00	0.00	0.00	1.73
349	371	6.970484	AGTCGCTGAAAAATGTTCACTTATT	58.030	32.000	0.00	0.00	0.00	1.40
350	372	8.094798	AGTCGCTGAAAAATGTTCACTTATTA	57.905	30.769	0.00	0.00	0.00	0.98
353	375	9.906660	TCGCTGAAAAATGTTCACTTATTAAAT	57.093	25.926	0.00	0.00	0.00	1.40
581	618	1.795286	CTCACAGGAAACAACTCGCTC	59.205	52.381	0.00	0.00	0.00	5.03
584	621	1.968493	ACAGGAAACAACTCGCTCCTA	59.032	47.619	0.00	0.00	36.10	2.94
585	622	2.288886	ACAGGAAACAACTCGCTCCTAC	60.289	50.000	0.00	0.00	36.10	3.18
598	637	1.268437	GCTCCTACGCCTTACACTACG	60.268	57.143	0.00	0.00	0.00	3.51
632	934	2.289072	CCGAGTGTTCCACAATCTGTCT	60.289	50.000	3.15	0.00	40.67	3.41
633	935	2.989840	CGAGTGTTCCACAATCTGTCTC	59.010	50.000	3.15	0.00	40.67	3.36
634	936	3.305676	CGAGTGTTCCACAATCTGTCTCT	60.306	47.826	3.15	0.00	40.67	3.10
635	937	4.636249	GAGTGTTCCACAATCTGTCTCTT	58.364	43.478	0.00	0.00	39.81	2.85
636	938	5.041191	AGTGTTCCACAATCTGTCTCTTT	57.959	39.130	0.00	0.00	36.74	2.52
639	941	4.103153	TGTTCCACAATCTGTCTCTTTCCT	59.897	41.667	0.00	0.00	0.00	3.36
640	942	4.982241	TCCACAATCTGTCTCTTTCCTT	57.018	40.909	0.00	0.00	0.00	3.36
641	943	6.183361	TGTTCCACAATCTGTCTCTTTCCTTA	60.183	38.462	0.00	0.00	0.00	2.69
642	944	6.627087	TCCACAATCTGTCTCTTTCCTTAT	57.373	37.500	0.00	0.00	0.00	1.73
644	946	8.146053	TCCACAATCTGTCTCTTTCCTTATTA	57.854	34.615	0.00	0.00	0.00	0.98
645	947	8.041323	TCCACAATCTGTCTCTTTCCTTATTAC	58.959	37.037	0.00	0.00	0.00	1.89
647	949	7.824289	CACAATCTGTCTCTTTCCTTATTACCA	59.176	37.037	0.00	0.00	0.00	3.25
648	950	8.552296	ACAATCTGTCTCTTTCCTTATTACCAT	58.448	33.333	0.00	0.00	0.00	3.55
679	981	3.764466	CTGCCTCGCTCCTTCGGT	61.764	66.667	0.00	0.00	0.00	4.69
997	2160	2.282180	GGCGCCCTTTCACTTCCA	60.282	61.111	18.11	0.00	0.00	3.53
1194	2357	0.950555	TGGTCAGCTGCGTTGATCAC	60.951	55.000	9.47	0.00	29.42	3.06
1289	2452	0.105964	TCGGACAGTGTCAACCCTTG	59.894	55.000	24.20	5.38	33.68	3.61
1290	2453	0.179056	CGGACAGTGTCAACCCTTGT	60.179	55.000	24.20	0.00	33.68	3.16
1707	2879	1.655959	CCGTTTTGTTCCGTTGCCG	60.656	57.895	0.00	0.00	0.00	5.69
1726	2898	2.922779	GTTCCGGAACCGTGTGATT	58.077	52.632	33.02	0.00	37.81	2.57
1745	2917	5.179368	GTGATTCGTCTGAGTTCCATTTGAA	59.821	40.000	0.00	0.00	0.00	2.69
1746	2918	5.762711	TGATTCGTCTGAGTTCCATTTGAAA	59.237	36.000	0.00	0.00	33.94	2.69
1747	2919	6.430925	TGATTCGTCTGAGTTCCATTTGAAAT	59.569	34.615	0.00	0.00	33.94	2.17
1872	3044	3.609853	TGAAGCGAGCAAAGGATTATGT	58.390	40.909	0.00	0.00	0.00	2.29
2005	3177	2.423947	GCCTGGGATGTTTGATGAGGAT	60.424	50.000	0.00	0.00	0.00	3.24
2436	3611	8.314021	AGAATTTGAAACCAAAGGGACAATATC	58.686	33.333	0.00	0.00	37.01	1.63
2642	3817	2.341101	CGCGTACCACTCTCCACCT	61.341	63.158	0.00	0.00	0.00	4.00
2714	3889	0.447801	CTTTGGCTCCGATTTGTCCG	59.552	55.000	0.00	0.00	0.00	4.79
2716	3891	0.250553	TTGGCTCCGATTTGTCCGTT	60.251	50.000	0.00	0.00	0.00	4.44

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	6.074888	GGTTCGCATATTCAATTTGGAAATCG	60.075	38.462	0.00	0.00	0.00	3.34
1	2	6.200854	GGGTTCGCATATTCAATTTGGAAATC	59.799	38.462	0.00	0.00	0.00	2.17
16	17	1.788229	TCATCTCAGGGGTTCGCATA	58.212	50.000	0.00	0.00	0.00	3.14
61	62	1.068832	TTGACTTCGATTCGACGGCG	61.069	55.000	2.87	2.87	35.89	6.46
63	64	3.431856	TGTATTGACTTCGATTCGACGG	58.568	45.455	15.76	10.99	34.89	4.79
101	102	2.543641	CTGCACATAGATTGAGTCGCA	58.456	47.619	0.00	0.00	0.00	5.10
122	123	4.554036	GGATGACAGGCCCGCCTC	62.554	72.222	4.92	0.00	46.28	4.70
148	165	3.897141	TTGTAGACACAGTGACCAACA	57.103	42.857	7.81	6.16	35.67	3.33
159	177	5.163982	GCTTACGTTCCTGATTTGTAGACAC	60.164	44.000	0.00	0.00	0.00	3.67
173	191	3.122971	GGCGTGGGCTTACGTTCC	61.123	66.667	14.23	6.32	45.36	3.62
185	203	2.049767	GTTGGGGTTATGGGGCGTG	61.050	63.158	0.00	0.00	0.00	5.34
188	206	3.144871	GCGTTGGGGTTATGGGGC	61.145	66.667	0.00	0.00	0.00	5.80
217	237	1.007502	GCGGTTCAGTGCATGCAAA	60.008	52.632	24.58	10.93	0.00	3.68
249	269	2.494073	GTCTAATGCCTATCTAGCGGCT	59.506	50.000	7.98	7.98	46.42	5.52
253	273	4.218852	AGAACCGTCTAATGCCTATCTAGC	59.781	45.833	0.00	0.00	29.93	3.42
266	286	1.340795	GGGAGTCTCCAGAACCGTCTA	60.341	57.143	20.72	0.00	38.64	2.59
272	292	2.959707	ACGATATGGGAGTCTCCAGAAC	59.040	50.000	20.72	3.64	40.56	3.01
312	334	5.743026	TTCAGCGACTTTTGTAAATGACA	57.257	34.783	0.00	0.00	35.78	3.58
326	348	8.722342	TTAATAAGTGAACATTTTTCAGCGAC	57.278	30.769	0.00	0.00	0.00	5.19
474	497	9.492973	CCTGGAAAACACAAGATTTATTTCAAT	57.507	29.630	0.00	0.00	0.00	2.57
475	498	8.700051	TCCTGGAAAACACAAGATTTATTTCAA	58.300	29.630	0.00	0.00	0.00	2.69
476	499	8.243961	TCCTGGAAAACACAAGATTTATTTCA	57.756	30.769	0.00	0.00	0.00	2.69
477	500	9.541143	TTTCCTGGAAAACACAAGATTTATTTC	57.459	29.630	19.14	0.00	0.00	2.17
560	597	1.412710	AGCGAGTTGTTTCCTGTGAGA	59.587	47.619	0.00	0.00	0.00	3.27
566	603	1.067776	CGTAGGAGCGAGTTGTTTCCT	60.068	52.381	9.64	9.64	42.50	3.36
621	661	7.824289	TGGTAATAAGGAAAGAGACAGATTGTG	59.176	37.037	0.00	0.00	0.00	3.33
623	663	8.970859	ATGGTAATAAGGAAAGAGACAGATTG	57.029	34.615	0.00	0.00	0.00	2.67
659	961	1.142748	CGAAGGAGCGAGGCAGATT	59.857	57.895	0.00	0.00	0.00	2.40
679	981	1.909302	AGATTGAGCGAGGGGAAGAAA	59.091	47.619	0.00	0.00	0.00	2.52
1011	2174	0.108138	CACACGGAGAAGGATGGTCC	60.108	60.000	0.00	0.00	36.58	4.46
1215	2378	1.215655	CGCCAAGTATACGAGGCTGC	61.216	60.000	27.66	13.34	44.85	5.25
1289	2452	4.336532	AAATAGTCGATGAACCGCAAAC	57.663	40.909	0.00	0.00	0.00	2.93
1290	2453	4.214545	ACAAAATAGTCGATGAACCGCAAA	59.785	37.500	0.00	0.00	0.00	3.68
1726	2898	6.565811	CGAAATTTCAAATGGAACTCAGACGA	60.566	38.462	17.99	0.00	34.56	4.20
1745	2917	5.872070	GTCTTGGAGTGAGATTCTCGAAATT	59.128	40.000	9.07	0.00	31.50	1.82
1746	2918	5.415221	GTCTTGGAGTGAGATTCTCGAAAT	58.585	41.667	9.07	0.00	31.50	2.17
1747	2919	4.322049	GGTCTTGGAGTGAGATTCTCGAAA	60.322	45.833	9.07	0.00	31.50	3.46
1872	3044	3.266772	AGTCCATGTTTTAGCCATCCAGA	59.733	43.478	0.00	0.00	0.00	3.86
2005	3177	9.528018	GTCAATTTCTTCCAAGTCAAATTGTTA	57.472	29.630	17.41	5.54	42.76	2.41
2281	3453	6.711645	ACTAGTGCTTTTCCGGTTATTACAAA	59.288	34.615	0.00	0.00	0.00	2.83
2436	3611	1.098050	CGGCCCTTCCTTGATTTCAG	58.902	55.000	0.00	0.00	0.00	3.02
2642	3817	1.618345	GGAGAGCTCCTTGGTGAGAGA	60.618	57.143	10.93	0.00	46.16	3.10

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.