AutoCloner

Multiple sequence alignment - TraesCS6D01G279300

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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	TraesCS6D01G279300	chr6D	100.000	7248	0	0	1	7248	387638515	387645762	0.000000e+00	13385
1	TraesCS6D01G279300	chr6D	86.780	2292	249	31	4314	6583	147665125	147667384	0.000000e+00	2505
2	TraesCS6D01G279300	chr6D	87.798	1008	106	10	3299	4293	147664065	147665068	0.000000e+00	1164
3	TraesCS6D01G279300	chr6D	83.846	910	100	27	2379	3254	147654438	147655334	0.000000e+00	822
4	TraesCS6D01G279300	chr6D	77.744	656	112	22	1535	2172	147650358	147650997	8.880000e-99	372
5	TraesCS6D01G279300	chr6D	90.406	271	15	5	1271	1538	387639527	387639789	5.380000e-91	346
6	TraesCS6D01G279300	chr6D	90.406	271	15	4	1013	1275	387639785	387640052	5.380000e-91	346
7	TraesCS6D01G279300	chr6A	96.282	6563	162	32	1	6511	532645508	532652040	0.000000e+00	10693
8	TraesCS6D01G279300	chr6A	90.391	1176	106	5	4314	5488	199999926	199998757	0.000000e+00	1539
9	TraesCS6D01G279300	chr6A	97.035	742	14	3	6508	7248	532652880	532653614	0.000000e+00	1242
10	TraesCS6D01G279300	chr6A	88.755	747	78	5	5522	6262	199995473	199994727	0.000000e+00	909
11	TraesCS6D01G279300	chr6A	82.708	1012	117	29	2331	3309	200003977	200002991	0.000000e+00	846
12	TraesCS6D01G279300	chr6A	88.448	580	52	7	3732	4302	200000547	199999974	0.000000e+00	686
13	TraesCS6D01G279300	chr6A	86.726	452	55	3	3302	3749	200002970	200002520	1.400000e-136	497
14	TraesCS6D01G279300	chr6A	91.353	266	16	3	1013	1274	532646807	532647069	2.490000e-94	357
15	TraesCS6D01G279300	chr6A	89.744	273	21	5	1271	1538	532646541	532646811	6.960000e-90	342
16	TraesCS6D01G279300	chr6B	95.039	6612	202	32	3	6546	578511872	578518425	0.000000e+00	10277
17	TraesCS6D01G279300	chr6B	90.366	1941	173	11	4314	6247	260109035	260110968	0.000000e+00	2536
18	TraesCS6D01G279300	chr6B	88.289	982	99	7	3322	4293	260108003	260108978	0.000000e+00	1162
19	TraesCS6D01G279300	chr6B	93.796	677	31	4	6578	7248	578518424	578519095	0.000000e+00	1007
20	TraesCS6D01G279300	chr6B	82.970	963	114	27	2379	3309	260106853	260107797	0.000000e+00	824
21	TraesCS6D01G279300	chr6B	90.545	275	19	4	1006	1276	578513150	578513421	2.490000e-94	357
22	TraesCS6D01G279300	chr6B	89.558	249	12	2	1271	1519	578512923	578513157	3.290000e-78	303
23	TraesCS6D01G279300	chr1D	84.072	835	99	16	3487	4307	462493972	462493158	0.000000e+00	774
24	TraesCS6D01G279300	chr1D	89.865	148	14	1	4315	4461	462493101	462492954	9.600000e-44	189
25	TraesCS6D01G279300	chr1D	83.495	206	27	3	4531	4736	462492950	462492752	1.240000e-42	185
26	TraesCS6D01G279300	chr1D	88.235	153	10	5	6264	6412	473742321	473742173	7.470000e-40	176
27	TraesCS6D01G279300	chr1B	81.016	827	94	18	4743	5567	637635838	637635073	3.740000e-167	599
28	TraesCS6D01G279300	chr1B	84.466	206	25	3	4531	4736	637636163	637635965	5.740000e-46	196
29	TraesCS6D01G279300	chr1B	83.173	208	23	4	4109	4307	637636555	637636351	5.780000e-41	180
30	TraesCS6D01G279300	chr1B	92.157	102	8	0	4360	4461	637636268	637636167	2.110000e-30	145
31	TraesCS6D01G279300	chr1A	85.846	325	38	6	6585	6907	28704972	28705290	9.010000e-89	339
32	TraesCS6D01G279300	chr1A	87.912	182	21	1	6675	6855	28664699	28664880	5.700000e-51	213
33	TraesCS6D01G279300	chr3D	85.985	264	24	9	6628	6886	608477287	608477032	3.330000e-68	270
34	TraesCS6D01G279300	chr3D	86.777	121	11	3	6585	6705	608477407	608477292	5.900000e-26	130
35	TraesCS6D01G279300	chr7B	77.088	467	97	10	5820	6282	490686286	490685826	2.010000e-65	261
36	TraesCS6D01G279300	chr7B	74.634	410	86	17	3254	3653	490686717	490686316	1.620000e-36	165

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	TraesCS6D01G279300	chr6D	387638515	387645762	7247	False	13385.000000	13385	100.000000	1	7248	1	chr6D.!!$F1	7247
1	TraesCS6D01G279300	chr6D	147664065	147667384	3319	False	1834.500000	2505	87.289000	3299	6583	2	chr6D.!!$F3	3284
2	TraesCS6D01G279300	chr6D	147650358	147655334	4976	False	597.000000	822	80.795000	1535	3254	2	chr6D.!!$F2	1719
3	TraesCS6D01G279300	chr6D	387639527	387640052	525	False	346.000000	346	90.406000	1013	1538	2	chr6D.!!$F4	525
4	TraesCS6D01G279300	chr6A	532645508	532652040	6532	False	10693.000000	10693	96.282000	1	6511	1	chr6A.!!$F1	6510
5	TraesCS6D01G279300	chr6A	532652880	532653614	734	False	1242.000000	1242	97.035000	6508	7248	1	chr6A.!!$F2	740
6	TraesCS6D01G279300	chr6A	199994727	200003977	9250	True	895.400000	1539	87.405600	2331	6262	5	chr6A.!!$R1	3931
7	TraesCS6D01G279300	chr6A	532646541	532647069	528	False	349.500000	357	90.548500	1013	1538	2	chr6A.!!$F3	525
8	TraesCS6D01G279300	chr6B	578511872	578518425	6553	False	10277.000000	10277	95.039000	3	6546	1	chr6B.!!$F1	6543
9	TraesCS6D01G279300	chr6B	260106853	260110968	4115	False	1507.333333	2536	87.208333	2379	6247	3	chr6B.!!$F3	3868
10	TraesCS6D01G279300	chr6B	578518424	578519095	671	False	1007.000000	1007	93.796000	6578	7248	1	chr6B.!!$F2	670
11	TraesCS6D01G279300	chr1D	462492752	462493972	1220	True	382.666667	774	85.810667	3487	4736	3	chr1D.!!$R2	1249
12	TraesCS6D01G279300	chr1B	637635073	637636555	1482	True	280.000000	599	85.203000	4109	5567	4	chr1B.!!$R1	1458
13	TraesCS6D01G279300	chr7B	490685826	490686717	891	True	213.000000	261	75.861000	3254	6282	2	chr7B.!!$R1	3028

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	Hairpin	End Stability	Orientation
302	326	0.464373	ACGACCTAATCCCTACGCGA	60.464	55.000	15.93	0.00	5.87	F
950	1012	0.524816	CGCCTTACTCGCATACGTGT	60.525	55.000	0.00	46.70	4.49	F
2055	2139	0.660300	GTTCAGGCCGCGAAACTTTG	60.660	55.000	8.23	0.00	2.77	F
2587	5914	1.271001	ACGGGCTGTGGTAAAACTACC	60.271	52.381	0.00	40.48	3.18	F
3916	9465	1.138247	GAGCATCCAAGCGGCAAAG	59.862	57.895	1.45	40.15	2.77	F
4028	9577	1.701847	ACTGAACCTGAGCACCAAGAT	59.298	47.619	0.00	0.00	2.40	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1602	1672	0.376502	GAGCTTGCATCGCCTTCTTC	59.623	55.000	5.02	0.00	2.87	R
2244	5491	0.534877	TGGCACAGATGAACGCACTT	60.535	50.000	0.00	0.00	3.16	R
3916	9465	3.421844	ACCATTTCAGGCTTCTTACCAC	58.578	45.455	0.00	0.00	4.16	R
4071	9620	4.331168	AGCATCAGAAGAAGCGACATTTAC	59.669	41.667	0.00	42.96	2.01	R
5434	11169	2.840753	GGTTTCACTCCCCCAGGCA	61.841	63.158	0.00	0.00	4.75	R
6402	15399	8.668510	AGCTATATCAACCTTACTGTTCATTG	57.331	34.615	0.00	0.00	2.82	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
42	43	8.750515	TCAGAATTAGGATATGCAATTCAACA	57.249	30.769	21.91	10.80	39.86	3.33
104	112	8.129161	TGCATTTTTCTTACAAATGTGAAGTG	57.871	30.769	7.11	0.00	41.72	3.16
167	179	2.568956	AGAACTGAGATAGCACAAGCCA	59.431	45.455	0.00	0.00	43.56	4.75
210	229	6.418101	ACTACCAATCAGTTAATGAGCACAT	58.582	36.000	0.00	0.00	42.53	3.21
302	326	0.464373	ACGACCTAATCCCTACGCGA	60.464	55.000	15.93	0.00	0.00	5.87
311	335	1.881252	CCCTACGCGAATTCACCCG	60.881	63.158	15.93	7.36	0.00	5.28
389	413	8.169268	CGACTGGACTCAATTCTTACATAAAAC	58.831	37.037	0.00	0.00	0.00	2.43
590	614	2.519541	CGATCTGAGGCTCGGGGA	60.520	66.667	22.67	14.17	0.00	4.81
661	685	1.545706	GGAAGGCGGAAGAGACCACT	61.546	60.000	0.00	0.00	0.00	4.00
702	729	1.525442	GGCTAGTGGGCCGTTATGT	59.475	57.895	0.00	0.00	42.82	2.29
703	730	0.814010	GGCTAGTGGGCCGTTATGTG	60.814	60.000	0.00	0.00	42.82	3.21
713	740	0.875728	CCGTTATGTGGCCGTTTTCA	59.124	50.000	0.00	0.00	0.00	2.69
717	744	3.119990	CGTTATGTGGCCGTTTTCATCTT	60.120	43.478	0.00	0.00	0.00	2.40
950	1012	0.524816	CGCCTTACTCGCATACGTGT	60.525	55.000	0.00	0.00	46.70	4.49
970	1032	2.701006	CGCTGTATCCGCGGTTTG	59.299	61.111	27.15	12.94	46.32	2.93
974	1036	0.719465	CTGTATCCGCGGTTTGTGAC	59.281	55.000	27.15	12.33	0.00	3.67
1602	1672	0.868406	GTTCGCAGGAGGACAAACAG	59.132	55.000	0.00	0.00	0.00	3.16
1612	1682	1.416401	AGGACAAACAGAAGAAGGCGA	59.584	47.619	0.00	0.00	0.00	5.54
1650	1720	4.486090	TCGAGACTTTGCAGTATGTCTTC	58.514	43.478	8.00	2.85	39.53	2.87
1837	1921	3.378427	GGATTAGTTCCTTTCGCATTGCT	59.622	43.478	7.12	0.00	41.78	3.91
1903	1987	2.673976	TGAAAGAAAAACGTAGGCGC	57.326	45.000	0.00	0.00	42.83	6.53
2055	2139	0.660300	GTTCAGGCCGCGAAACTTTG	60.660	55.000	8.23	0.00	0.00	2.77
2161	2245	8.655092	CAGAAAACTGAAGAGACTAATGATGAC	58.345	37.037	0.00	0.00	0.00	3.06
2244	5491	5.249420	TGATGACATTTTGGTACATCCGAA	58.751	37.500	0.00	0.00	39.30	4.30
2587	5914	1.271001	ACGGGCTGTGGTAAAACTACC	60.271	52.381	0.00	0.00	40.48	3.18
3294	6656	5.624081	GCTGTTCTGAAATTCATATGCATCG	59.376	40.000	0.19	0.00	0.00	3.84
3776	9325	1.795768	TCGCAAAGAGGACACATGAC	58.204	50.000	0.00	0.00	0.00	3.06
3916	9465	1.138247	GAGCATCCAAGCGGCAAAG	59.862	57.895	1.45	0.00	40.15	2.77
3948	9497	3.285484	CCTGAAATGGTTGGAGATGAGG	58.715	50.000	0.00	0.00	0.00	3.86
4028	9577	1.701847	ACTGAACCTGAGCACCAAGAT	59.298	47.619	0.00	0.00	0.00	2.40
4071	9620	4.272018	GTGAAGATGAAACGGATGATGAGG	59.728	45.833	0.00	0.00	0.00	3.86
4378	9986	2.101582	AGCAGCTTAGAGTATTCCACGG	59.898	50.000	0.00	0.00	0.00	4.94
4906	10638	6.183360	GCTTGAAGATATTGGAAGCAGTTGAT	60.183	38.462	0.00	0.00	39.09	2.57
5018	10752	3.753294	TGTTGAAGAGTCAGGAAGGAC	57.247	47.619	0.00	0.00	34.49	3.85
5099	10833	9.010029	GTTATACCAATCCTTTTCAAGTTCAGA	57.990	33.333	0.00	0.00	0.00	3.27
5434	11169	4.260170	GAGGCTCTCAAGATGTTGAACAT	58.740	43.478	11.10	11.10	42.27	2.71
5674	14659	6.491383	TCCACCAGACTATGTAGTTTACTCT	58.509	40.000	0.00	0.00	36.50	3.24
6573	15579	0.965363	AGTTATTTGTGCCCCTGCCG	60.965	55.000	0.00	0.00	36.33	5.69
6663	15669	3.319972	AGCCATCGGATTGGAATTGAATG	59.680	43.478	9.68	0.00	39.25	2.67
6664	15670	3.318839	GCCATCGGATTGGAATTGAATGA	59.681	43.478	9.68	0.00	39.25	2.57
6665	15671	4.202141	GCCATCGGATTGGAATTGAATGAA	60.202	41.667	9.68	0.00	39.25	2.57
6666	15672	5.510179	GCCATCGGATTGGAATTGAATGAAT	60.510	40.000	9.68	0.00	39.25	2.57
6907	15914	2.281900	GCCCGGGTTGTGCAACTA	60.282	61.111	24.63	0.00	40.94	2.24
7051	16058	0.620121	CCTCCTTTCTCTCCCAGGCT	60.620	60.000	0.00	0.00	0.00	4.58
7052	16059	0.829990	CTCCTTTCTCTCCCAGGCTC	59.170	60.000	0.00	0.00	0.00	4.70
7053	16060	0.618968	TCCTTTCTCTCCCAGGCTCC	60.619	60.000	0.00	0.00	0.00	4.70

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
42	43	5.355910	ACAACTACGAATGTTTGAGTTTGGT	59.644	36.000	0.00	0.00	0.00	3.67
104	112	2.631545	ACTACACTAGAACCACACCCAC	59.368	50.000	0.00	0.00	0.00	4.61
167	179	2.094182	AGTTGCTTCGATATGTGTCCGT	60.094	45.455	0.00	0.00	0.00	4.69
234	255	2.500504	AGTGGGCCTTGTTAGCTACTAC	59.499	50.000	4.53	0.00	0.00	2.73
302	326	2.027192	TGCTAAGCTTCTCGGGTGAATT	60.027	45.455	0.00	0.00	0.00	2.17
389	413	2.740714	GCCTAGTTCGCCGTGCTTG	61.741	63.158	0.00	0.00	0.00	4.01
431	455	1.732259	CATCCAAAACCCTCGTTCTCG	59.268	52.381	0.00	0.00	38.55	4.04
462	486	1.246056	CGGTGAGTTGGTCCTCCGTA	61.246	60.000	0.00	0.00	37.09	4.02
656	680	2.569404	CCTTTCTCTCTAGCCAAGTGGT	59.431	50.000	0.00	0.00	37.57	4.16
661	685	2.897969	ACGAACCTTTCTCTCTAGCCAA	59.102	45.455	0.00	0.00	0.00	4.52
696	723	4.434713	AAGATGAAAACGGCCACATAAC	57.565	40.909	2.24	0.00	0.00	1.89
702	729	4.380444	GCAAGAATAAGATGAAAACGGCCA	60.380	41.667	2.24	0.00	0.00	5.36
703	730	4.105486	GCAAGAATAAGATGAAAACGGCC	58.895	43.478	0.00	0.00	0.00	6.13
713	740	1.412710	TCGCGGAGGCAAGAATAAGAT	59.587	47.619	6.13	0.00	39.92	2.40
717	744	0.459585	GTGTCGCGGAGGCAAGAATA	60.460	55.000	6.13	0.00	35.50	1.75
765	794	4.347453	GTGTGGCGCTTGGCTTGG	62.347	66.667	7.64	0.00	42.94	3.61
766	795	4.347453	GGTGTGGCGCTTGGCTTG	62.347	66.667	7.64	0.00	42.94	4.01
970	1032	1.828832	CGACCTGAGATAAGCGTCAC	58.171	55.000	0.00	0.00	0.00	3.67
974	1036	0.101399	ACTGCGACCTGAGATAAGCG	59.899	55.000	0.00	0.00	0.00	4.68
979	1041	0.453793	CTCGAACTGCGACCTGAGAT	59.546	55.000	0.00	0.00	45.59	2.75
1602	1672	0.376502	GAGCTTGCATCGCCTTCTTC	59.623	55.000	5.02	0.00	0.00	2.87
1650	1720	7.080099	CCACAGAAAATAGACATCACAAGTTG	58.920	38.462	0.00	0.00	0.00	3.16
1837	1921	9.265862	ACAAAATACCATGAGGAAAATAATCCA	57.734	29.630	0.00	0.00	42.27	3.41
1903	1987	0.664761	CCTTGGATAACTGCATGGCG	59.335	55.000	0.00	0.00	32.52	5.69
2055	2139	3.587797	TTCGTTCACTACCAGGATGAC	57.412	47.619	0.00	0.00	39.69	3.06
2161	2245	1.068402	TGATGTGCCAAAATGTCAGCG	60.068	47.619	0.00	0.00	0.00	5.18
2244	5491	0.534877	TGGCACAGATGAACGCACTT	60.535	50.000	0.00	0.00	0.00	3.16
2248	5495	0.593128	AACTTGGCACAGATGAACGC	59.407	50.000	0.00	0.00	42.39	4.84
2587	5914	1.229336	ACTCACCTGAGGGACCTGG	60.229	63.158	2.38	0.00	46.13	4.45
2712	6041	5.468072	CGGCTTCATATAAGAACTGCAGAAT	59.532	40.000	23.35	8.80	0.00	2.40
3916	9465	3.421844	ACCATTTCAGGCTTCTTACCAC	58.578	45.455	0.00	0.00	0.00	4.16
4028	9577	8.493607	TCTTCACCATATGAGGAAAATATGTCA	58.506	33.333	3.65	0.00	40.29	3.58
4071	9620	4.331168	AGCATCAGAAGAAGCGACATTTAC	59.669	41.667	0.00	0.00	42.96	2.01
4906	10638	8.364142	CCCATTGATGTAAGTTTTTCTTGGTTA	58.636	33.333	0.00	0.00	37.56	2.85
5018	10752	6.096036	CCAATATGAGGTTAGATCTAGCACG	58.904	44.000	17.19	0.00	0.00	5.34
5099	10833	6.712095	TCATTTGTTTCTCTATCAGTGTTGCT	59.288	34.615	0.00	0.00	0.00	3.91
5434	11169	2.840753	GGTTTCACTCCCCCAGGCA	61.841	63.158	0.00	0.00	0.00	4.75
6402	15399	8.668510	AGCTATATCAACCTTACTGTTCATTG	57.331	34.615	0.00	0.00	0.00	2.82
6460	15464	3.195396	ACAAAATGTGCAGGTTCAACAGT	59.805	39.130	0.00	0.00	0.00	3.55
6573	15579	1.515954	TCGCTCCCGAAAGATCACC	59.484	57.895	0.00	0.00	41.17	4.02
6663	15669	3.084039	TCCACAAAGATCTGTGCCATTC	58.916	45.455	13.13	0.00	44.47	2.67
6664	15670	3.087031	CTCCACAAAGATCTGTGCCATT	58.913	45.455	13.13	0.00	44.47	3.16
6665	15671	2.619849	CCTCCACAAAGATCTGTGCCAT	60.620	50.000	13.13	0.00	44.47	4.40
6666	15672	1.271543	CCTCCACAAAGATCTGTGCCA	60.272	52.381	13.13	0.00	44.47	4.92
6788	15795	3.430236	CCATTAGGTTTGGGGAATTTCGC	60.430	47.826	4.95	4.95	0.00	4.70
6907	15914	1.138568	CCTCAGATGGGGAAGATGCT	58.861	55.000	0.00	0.00	0.00	3.79
7051	16058	2.439507	ACTGCAGAAAAGTTGAGGAGGA	59.560	45.455	23.35	0.00	0.00	3.71
7052	16059	2.551459	CACTGCAGAAAAGTTGAGGAGG	59.449	50.000	23.35	0.00	0.00	4.30
7053	16060	2.031333	GCACTGCAGAAAAGTTGAGGAG	60.031	50.000	23.35	0.00	0.00	3.69

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.