AutoCloner

Multiple sequence alignment - TraesCS3A01G458300

Loading Multiple Alignment...

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	TraesCS3A01G458300	chr3A	100.000	3152	0	0	1	3152	695514312	695517463	0.000000e+00	5821.0
1	TraesCS3A01G458300	chr3A	81.579	1368	186	42	876	2228	692495403	692494087	0.000000e+00	1070.0
2	TraesCS3A01G458300	chr3A	80.728	1401	232	21	814	2198	692316353	692314975	0.000000e+00	1057.0
3	TraesCS3A01G458300	chr3A	73.310	1139	239	47	1056	2151	691732868	691731752	2.990000e-95	359.0
4	TraesCS3A01G458300	chr3A	84.765	361	35	9	761	1117	692491409	692491065	8.370000e-91	344.0
5	TraesCS3A01G458300	chr3A	80.488	123	13	4	2694	2806	692474426	692474305	2.010000e-12	84.2
6	TraesCS3A01G458300	chr3A	89.655	58	5	1	2429	2485	692056439	692056382	4.360000e-09	73.1
7	TraesCS3A01G458300	chr3A	89.655	58	5	1	2429	2485	692470351	692470294	4.360000e-09	73.1
8	TraesCS3A01G458300	chr3A	90.000	50	5	0	2564	2613	692488671	692488622	7.300000e-07	65.8
9	TraesCS3A01G458300	chr3D	95.507	2404	85	13	1	2387	559119294	559121691	0.000000e+00	3819.0
10	TraesCS3A01G458300	chr3D	83.093	1597	216	35	740	2316	555314672	555313110	0.000000e+00	1404.0
11	TraesCS3A01G458300	chr3D	82.882	1402	210	21	817	2194	555306219	555304824	0.000000e+00	1232.0
12	TraesCS3A01G458300	chr3D	93.736	447	16	3	2378	2813	559121766	559122211	0.000000e+00	660.0
13	TraesCS3A01G458300	chr3D	94.306	281	13	2	2873	3150	559122230	559122510	8.080000e-116	427.0
14	TraesCS3A01G458300	chr3D	94.828	58	2	1	1468	1524	554817329	554817386	4.330000e-14	89.8
15	TraesCS3A01G458300	chr3D	82.000	100	8	6	2522	2614	555310723	555310627	3.370000e-10	76.8
16	TraesCS3A01G458300	chr3D	86.207	58	7	1	2429	2485	555304595	555304538	9.440000e-06	62.1
17	TraesCS3A01G458300	chr3B	87.596	2346	175	37	740	3003	741968259	741965948	0.000000e+00	2614.0
18	TraesCS3A01G458300	chr3B	91.958	1604	93	10	693	2283	742110595	742109015	0.000000e+00	2215.0
19	TraesCS3A01G458300	chr3B	81.680	1583	226	33	740	2303	738591969	738590432	0.000000e+00	1258.0
20	TraesCS3A01G458300	chr3B	91.153	893	49	13	2280	3150	742108935	742108051	0.000000e+00	1184.0
21	TraesCS3A01G458300	chr3B	82.353	1343	183	38	876	2205	738625876	738624575	0.000000e+00	1118.0
22	TraesCS3A01G458300	chr3B	91.942	757	48	5	693	1448	742081408	742080664	0.000000e+00	1048.0
23	TraesCS3A01G458300	chr3B	91.810	757	49	5	693	1448	742061608	742060864	0.000000e+00	1042.0
24	TraesCS3A01G458300	chr3B	80.455	1407	222	26	817	2198	738289885	738288507	0.000000e+00	1026.0
25	TraesCS3A01G458300	chr3B	79.510	1469	233	39	876	2316	738156535	738155107	0.000000e+00	983.0
26	TraesCS3A01G458300	chr3B	82.407	756	103	22	780	1528	738295542	738294810	1.600000e-177	632.0
27	TraesCS3A01G458300	chr3B	89.706	68	6	1	1468	1534	738105965	738105898	5.600000e-13	86.1
28	TraesCS3A01G458300	chr3B	85.507	69	10	0	2614	2682	738154873	738154805	4.360000e-09	73.1
29	TraesCS3A01G458300	chr3B	80.612	98	14	4	2522	2614	738588021	738587924	1.570000e-08	71.3
30	TraesCS3A01G458300	chr3B	87.931	58	6	1	2429	2485	738288282	738288225	2.030000e-07	67.6
31	TraesCS3A01G458300	chr3B	90.196	51	5	0	2564	2614	738590186	738590136	2.030000e-07	67.6
32	TraesCS3A01G458300	chr4B	82.590	471	57	18	172	627	85435606	85435146	2.950000e-105	392.0
33	TraesCS3A01G458300	chrUn	72.975	1136	244	45	1058	2151	272482922	272481808	3.890000e-89	339.0
34	TraesCS3A01G458300	chrUn	72.959	1139	245	45	1052	2148	279590173	279591290	3.890000e-89	339.0
35	TraesCS3A01G458300	chr2A	97.674	43	1	0	135	177	53078512	53078470	1.210000e-09	75.0
36	TraesCS3A01G458300	chr7A	97.561	41	1	0	135	175	667343185	667343225	1.570000e-08	71.3
37	TraesCS3A01G458300	chr4D	95.349	43	2	0	135	177	341396729	341396687	5.640000e-08	69.4
38	TraesCS3A01G458300	chr4D	91.304	46	4	0	131	176	509434136	509434181	2.620000e-06	63.9
39	TraesCS3A01G458300	chr2D	95.349	43	2	0	135	177	51940852	51940810	5.640000e-08	69.4
40	TraesCS3A01G458300	chr2B	95.349	43	2	0	135	177	387071351	387071309	5.640000e-08	69.4
41	TraesCS3A01G458300	chr1A	90.385	52	3	2	125	175	547258247	547258297	2.030000e-07	67.6
42	TraesCS3A01G458300	chr6A	93.023	43	3	0	135	177	33182567	33182525	2.620000e-06	63.9

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	TraesCS3A01G458300	chr3A	695514312	695517463	3151	False	5821.000000	5821	100.000000	1	3152	1	chr3A.!!$F1	3151
1	TraesCS3A01G458300	chr3A	692314975	692316353	1378	True	1057.000000	1057	80.728000	814	2198	1	chr3A.!!$R3	1384
2	TraesCS3A01G458300	chr3A	692488622	692495403	6781	True	493.266667	1070	85.448000	761	2613	3	chr3A.!!$R5	1852
3	TraesCS3A01G458300	chr3A	691731752	691732868	1116	True	359.000000	359	73.310000	1056	2151	1	chr3A.!!$R1	1095
4	TraesCS3A01G458300	chr3D	559119294	559122510	3216	False	1635.333333	3819	94.516333	1	3150	3	chr3D.!!$F2	3149
5	TraesCS3A01G458300	chr3D	555310627	555314672	4045	True	740.400000	1404	82.546500	740	2614	2	chr3D.!!$R2	1874
6	TraesCS3A01G458300	chr3D	555304538	555306219	1681	True	647.050000	1232	84.544500	817	2485	2	chr3D.!!$R1	1668
7	TraesCS3A01G458300	chr3B	741965948	741968259	2311	True	2614.000000	2614	87.596000	740	3003	1	chr3B.!!$R4	2263
8	TraesCS3A01G458300	chr3B	742108051	742110595	2544	True	1699.500000	2215	91.555500	693	3150	2	chr3B.!!$R10	2457
9	TraesCS3A01G458300	chr3B	738624575	738625876	1301	True	1118.000000	1118	82.353000	876	2205	1	chr3B.!!$R3	1329
10	TraesCS3A01G458300	chr3B	742080664	742081408	744	True	1048.000000	1048	91.942000	693	1448	1	chr3B.!!$R6	755
11	TraesCS3A01G458300	chr3B	742060864	742061608	744	True	1042.000000	1042	91.810000	693	1448	1	chr3B.!!$R5	755
12	TraesCS3A01G458300	chr3B	738294810	738295542	732	True	632.000000	632	82.407000	780	1528	1	chr3B.!!$R2	748
13	TraesCS3A01G458300	chr3B	738288225	738289885	1660	True	546.800000	1026	84.193000	817	2485	2	chr3B.!!$R8	1668
14	TraesCS3A01G458300	chr3B	738154805	738156535	1730	True	528.050000	983	82.508500	876	2682	2	chr3B.!!$R7	1806
15	TraesCS3A01G458300	chr3B	738587924	738591969	4045	True	465.633333	1258	84.162667	740	2614	3	chr3B.!!$R9	1874
16	TraesCS3A01G458300	chrUn	272481808	272482922	1114	True	339.000000	339	72.975000	1058	2151	1	chrUn.!!$R1	1093
17	TraesCS3A01G458300	chrUn	279590173	279591290	1117	False	339.000000	339	72.959000	1052	2148	1	chrUn.!!$F1	1096

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
370	372	0.250727	TCTAGGCAAACACCAGCACC	60.251	55.0	0.0	0.0	0.0	5.01	F
458	460	0.803380	GCATCCGCCAACAAATGAGC	60.803	55.0	0.0	0.0	0.0	4.26	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1310	1352	0.755686	ATCCAAGATGTCGAGCTCCC	59.244	55.0	8.47	0.0	0.0	4.30	R
2253	7458	1.689984	TCAATCAAGCACCAACAGCA	58.310	45.0	0.00	0.0	0.0	4.41	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
46	47	7.889589	TCTCTATGAACACACACATACTTTG	57.110	36.000	0.00	0.00	0.00	2.77
47	48	6.368791	TCTCTATGAACACACACATACTTTGC	59.631	38.462	0.00	0.00	0.00	3.68
52	53	1.541147	CACACACATACTTTGCCCCTG	59.459	52.381	0.00	0.00	0.00	4.45
77	78	4.778579	AGCACATCTGAGATTGCACTATT	58.221	39.130	22.29	7.15	37.44	1.73
78	79	4.815308	AGCACATCTGAGATTGCACTATTC	59.185	41.667	22.29	0.00	37.44	1.75
119	120	7.338449	GCCTATGTAAGTAATGGTTGGAAGAAA	59.662	37.037	0.00	0.00	0.00	2.52
188	189	2.103432	TGAACTAAGGCCGTGTTCTGAA	59.897	45.455	26.52	13.03	40.27	3.02
241	243	2.023673	TGTGAAGAAACTGGGTTGCAG	58.976	47.619	0.00	0.00	0.00	4.41
339	341	4.996758	CCAAAGGAAAAGCTAATTGTTGGG	59.003	41.667	0.00	0.00	31.39	4.12
370	372	0.250727	TCTAGGCAAACACCAGCACC	60.251	55.000	0.00	0.00	0.00	5.01
376	378	3.372422	AAACACCAGCACCAGGGCA	62.372	57.895	0.00	0.00	35.83	5.36
393	395	2.418884	GGGCACAGCTAGTACCTTTCTC	60.419	54.545	5.79	0.00	33.82	2.87
403	405	6.770785	AGCTAGTACCTTTCTCTCTCACATAG	59.229	42.308	0.00	0.00	0.00	2.23
412	414	8.449397	CCTTTCTCTCTCACATAGAACATTTTG	58.551	37.037	0.00	0.00	32.46	2.44
414	416	8.539770	TTCTCTCTCACATAGAACATTTTGTC	57.460	34.615	0.00	0.00	32.46	3.18
458	460	0.803380	GCATCCGCCAACAAATGAGC	60.803	55.000	0.00	0.00	0.00	4.26
497	499	4.566004	TGTTCCTTCGGAATAGACACAAG	58.434	43.478	0.00	0.00	44.04	3.16
536	538	6.808321	TTTGGAATACTGTACTGCTATCCT	57.192	37.500	14.87	0.00	0.00	3.24
570	572	5.127682	ACACTTCAAAGGAAAAGCATTCAGT	59.872	36.000	4.87	0.00	31.35	3.41
631	633	0.975887	ACGAACGGGCCTAAGGTTAA	59.024	50.000	0.84	0.00	0.00	2.01
632	634	1.556451	ACGAACGGGCCTAAGGTTAAT	59.444	47.619	0.84	0.00	0.00	1.40
669	673	1.448985	AAAATGGCGTGCGTGTCTAT	58.551	45.000	0.00	0.00	0.00	1.98
675	679	1.413767	GCGTGCGTGTCTATCAGTGG	61.414	60.000	0.00	0.00	0.00	4.00
1158	1196	1.460305	CCTCATCTCCCACCCCGAT	60.460	63.158	0.00	0.00	0.00	4.18
1310	1352	0.174845	TCGTTCCTACCTGAATGCGG	59.825	55.000	0.00	0.00	32.45	5.69
1829	1914	6.293298	GGACAATTGTATCTCACAGATCATGC	60.293	42.308	11.95	0.00	38.72	4.06
2041	2141	6.765512	TCCGCAGATGAAATTATTGTCATACA	59.234	34.615	3.79	0.00	34.61	2.29
2233	7426	9.107177	CTTAGATCTTGAATATGAGCAACAGTT	57.893	33.333	0.00	0.00	0.00	3.16
2240	7433	6.653020	TGAATATGAGCAACAGTTATCTGGT	58.347	36.000	5.80	0.00	45.14	4.00
2253	7458	9.959721	AACAGTTATCTGGTTAAGTTGTGATAT	57.040	29.630	5.80	0.00	45.14	1.63
2330	7679	7.670364	TCAGTCAACTTCTCTGTTAATCATGA	58.330	34.615	0.00	0.00	0.00	3.07
2610	10176	3.677648	CCAGGGCTGCTGTTGCAC	61.678	66.667	0.00	0.00	45.31	4.57
2622	10211	0.531974	TGTTGCACTTCCACGGAGAC	60.532	55.000	0.00	0.00	0.00	3.36
2629	10218	2.557056	CACTTCCACGGAGACTCAGTTA	59.443	50.000	5.43	0.00	0.00	2.24
2793	10555	2.746362	GTTCCTCCAGATGCAAGTTCTG	59.254	50.000	8.56	8.56	40.25	3.02
2816	10578	1.970917	GACGAGTTGCCCGCTTCATG	61.971	60.000	0.00	0.00	0.00	3.07
2834	10596	4.991776	TCATGTTGTTAAGTCATGGGGAA	58.008	39.130	11.78	0.00	39.25	3.97
2845	10634	2.087461	ATGGGGAATGGGGCCTCTC	61.087	63.158	3.07	0.00	0.00	3.20
2920	11044	5.771469	TCTTATTGTTTGTTCCATGCTGTG	58.229	37.500	0.00	0.00	0.00	3.66
3096	12444	3.503891	TGATTTGTGCAATTCATGAGCG	58.496	40.909	0.00	0.00	0.00	5.03
3107	12455	5.004156	GCAATTCATGAGCGAAAATTGTCTC	59.996	40.000	14.10	0.00	39.90	3.36
3150	12498	1.899814	TCTTCAAGGCGTGTACCTGAT	59.100	47.619	0.00	0.00	39.93	2.90

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
27	28	3.255642	GGGCAAAGTATGTGTGTGTTCAT	59.744	43.478	0.00	0.00	0.00	2.57
46	47	0.253044	TCAGATGTGCTAACAGGGGC	59.747	55.000	0.00	0.00	40.39	5.80
47	48	1.833630	TCTCAGATGTGCTAACAGGGG	59.166	52.381	0.00	0.00	40.39	4.79
52	53	3.937706	AGTGCAATCTCAGATGTGCTAAC	59.062	43.478	17.40	11.13	37.87	2.34
77	78	2.265739	GCCGTCATGCAGGACAGA	59.734	61.111	28.84	2.06	37.66	3.41
78	79	1.960040	TAGGCCGTCATGCAGGACAG	61.960	60.000	28.84	20.19	38.23	3.51
119	120	7.858498	TCGAGGGGAGTCTTAATTAAAGAAAT	58.142	34.615	0.00	0.00	45.78	2.17
140	141	4.546570	TGCGACACTTATTATGGATCGAG	58.453	43.478	0.00	0.00	0.00	4.04
188	189	7.465900	TTCCTATGTTTTTCTATCCCTCCAT	57.534	36.000	0.00	0.00	0.00	3.41
228	230	0.478507	AGCTACCTGCAACCCAGTTT	59.521	50.000	0.00	0.00	45.94	2.66
231	233	0.036732	TCAAGCTACCTGCAACCCAG	59.963	55.000	0.00	0.00	45.94	4.45
241	243	4.911514	TCACAAAGGTTTTCAAGCTACC	57.088	40.909	0.00	0.00	38.49	3.18
273	275	2.572104	ACCTCAGTTTTAGCCGATCCTT	59.428	45.455	0.00	0.00	0.00	3.36
322	324	3.576550	TGGGTCCCAACAATTAGCTTTTC	59.423	43.478	8.65	0.00	0.00	2.29
339	341	0.690762	TGCCTAGAACTTGGTGGGTC	59.309	55.000	0.00	0.00	0.00	4.46
352	354	0.537143	TGGTGCTGGTGTTTGCCTAG	60.537	55.000	0.00	0.00	0.00	3.02
376	378	4.703093	GTGAGAGAGAAAGGTACTAGCTGT	59.297	45.833	0.00	0.00	38.49	4.40
393	395	6.093219	CCCAGACAAAATGTTCTATGTGAGAG	59.907	42.308	0.00	0.00	34.93	3.20
403	405	5.048713	CAGAAGTACCCCAGACAAAATGTTC	60.049	44.000	0.00	0.00	0.00	3.18
412	414	2.861147	AAAGCAGAAGTACCCCAGAC	57.139	50.000	0.00	0.00	0.00	3.51
414	416	2.040412	AGGAAAAGCAGAAGTACCCCAG	59.960	50.000	0.00	0.00	0.00	4.45
490	492	1.251251	AATGCTGGCTTCCTTGTGTC	58.749	50.000	0.00	0.00	0.00	3.67
497	499	2.299867	TCCAAAAGAAATGCTGGCTTCC	59.700	45.455	0.00	0.00	0.00	3.46
536	538	4.130857	TCCTTTGAAGTGTTCGCATTGTA	58.869	39.130	0.00	0.00	0.00	2.41
570	572	6.657541	AGGATTTTTACACGCAAGAATTCCTA	59.342	34.615	0.65	0.00	43.62	2.94
690	694	3.630769	GGGCTTTTTACTGGGCTGTATAC	59.369	47.826	0.00	0.00	0.00	1.47
734	738	3.489355	TGATGGATGCTGCGGAATTTAT	58.511	40.909	0.00	0.00	0.00	1.40
735	739	2.929641	TGATGGATGCTGCGGAATTTA	58.070	42.857	0.00	0.00	0.00	1.40
885	893	3.430513	GGGAAAAGAGGACGTACCAGATC	60.431	52.174	0.00	0.00	42.04	2.75
1158	1196	2.261671	GGAAGCTTCTCGCGGTGA	59.738	61.111	25.05	1.83	45.59	4.02
1228	1267	2.614481	GGTAAACATGAGGAAGCCGTGA	60.614	50.000	0.00	0.00	0.00	4.35
1310	1352	0.755686	ATCCAAGATGTCGAGCTCCC	59.244	55.000	8.47	0.00	0.00	4.30
1392	1447	2.546373	GCACACCACGTACTCCAAAGTA	60.546	50.000	0.00	0.00	36.92	2.24
1829	1914	4.694509	CCCAGATTGACAGTTCAGAAGAAG	59.305	45.833	0.00	0.00	33.63	2.85
1871	1956	6.527423	AGCTTCAATGTCCAACAATTTTCAT	58.473	32.000	0.00	0.00	0.00	2.57
2041	2141	1.747206	CGGCTCCCTCGAATCCATTTT	60.747	52.381	0.00	0.00	0.00	1.82
2233	7426	7.564793	ACAGCATATCACAACTTAACCAGATA	58.435	34.615	0.00	0.00	0.00	1.98
2240	7433	5.335583	GCACCAACAGCATATCACAACTTAA	60.336	40.000	0.00	0.00	0.00	1.85
2253	7458	1.689984	TCAATCAAGCACCAACAGCA	58.310	45.000	0.00	0.00	0.00	4.41
2351	7701	1.939934	CCAACAGGTACATGCCGTATG	59.060	52.381	7.57	0.00	42.68	2.39
2610	10176	3.697045	AGATAACTGAGTCTCCGTGGAAG	59.303	47.826	0.00	0.00	0.00	3.46
2629	10218	8.752187	ACAGCACATAAATGAAATACCAAAGAT	58.248	29.630	0.00	0.00	0.00	2.40
2793	10555	3.112709	GCGGGCAACTCGTCTGTC	61.113	66.667	0.00	0.00	33.54	3.51
2816	10578	3.447229	CCCATTCCCCATGACTTAACAAC	59.553	47.826	0.00	0.00	34.31	3.32
2834	10596	2.683933	AACGACGAGAGGCCCCAT	60.684	61.111	0.00	0.00	33.32	4.00
2845	10634	4.847365	AGATCATGAATTCACAACGACG	57.153	40.909	11.07	0.00	0.00	5.12
2920	11044	6.833342	ATCACTTGACAAACAATCAAAAGC	57.167	33.333	0.00	0.00	35.70	3.51
3096	12444	6.145048	CAGCAAGAAACCATGAGACAATTTTC	59.855	38.462	0.00	0.00	0.00	2.29
3107	12455	1.202222	GGATCGCAGCAAGAAACCATG	60.202	52.381	0.00	0.00	0.00	3.66

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.