AutoCloner

Multiple sequence alignment - TraesCS4A01G164700

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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	TraesCS4A01G164700	chr4A	100.000	2372	0	0	1	2372	383181995	383179624	0.000000e+00	4381.0
1	TraesCS4A01G164700	chr4A	94.918	610	31	0	1760	2369	440634047	440634656	0.000000e+00	955.0
2	TraesCS4A01G164700	chr4A	94.156	616	36	0	1757	2372	440643841	440644456	0.000000e+00	939.0
3	TraesCS4A01G164700	chr4A	94.127	613	36	0	1760	2372	383170229	383169617	0.000000e+00	933.0
4	TraesCS4A01G164700	chr4A	94.108	611	35	1	1760	2369	451763729	451763119	0.000000e+00	928.0
5	TraesCS4A01G164700	chr4A	88.787	544	52	8	4	538	232097182	232097725	0.000000e+00	658.0
6	TraesCS4A01G164700	chr4A	92.353	340	24	2	649	987	498242474	498242812	1.270000e-132	483.0
7	TraesCS4A01G164700	chr4A	89.076	119	13	0	1641	1759	261975870	261975988	5.280000e-32	148.0
8	TraesCS4A01G164700	chr6A	88.518	1768	166	26	11	1759	237501847	237500098	0.000000e+00	2106.0
9	TraesCS4A01G164700	chr6A	89.426	1655	149	22	10	1646	319328665	319327019	0.000000e+00	2063.0
10	TraesCS4A01G164700	chr6A	87.952	1768	176	25	10	1759	319320626	319318878	0.000000e+00	2050.0
11	TraesCS4A01G164700	chr6A	91.105	742	63	3	825	1564	121367797	121367057	0.000000e+00	1002.0
12	TraesCS4A01G164700	chr6A	92.489	466	30	4	4	465	106913130	106913594	0.000000e+00	662.0
13	TraesCS4A01G164700	chr7A	87.778	1571	165	21	10	1566	670994980	670993423	0.000000e+00	1812.0
14	TraesCS4A01G164700	chr7A	84.830	1325	156	30	4	1306	577348366	577347065	0.000000e+00	1291.0
15	TraesCS4A01G164700	chr7A	92.346	797	60	1	553	1349	671011853	671011058	0.000000e+00	1133.0
16	TraesCS4A01G164700	chr7A	89.732	224	21	2	1345	1566	671009395	671009172	3.860000e-73	285.0
17	TraesCS4A01G164700	chr7A	92.553	94	7	0	1666	1759	670993356	670993263	4.110000e-28	135.0
18	TraesCS4A01G164700	chr7A	91.045	67	6	0	1639	1705	496470613	496470547	9.030000e-15	91.6
19	TraesCS4A01G164700	chr3D	90.744	1102	73	16	383	1481	49329086	49330161	0.000000e+00	1443.0
20	TraesCS4A01G164700	chr3D	91.948	621	45	4	863	1481	49364007	49364624	0.000000e+00	865.0
21	TraesCS4A01G164700	chr3A	91.339	762	60	5	739	1497	377723989	377723231	0.000000e+00	1037.0
22	TraesCS4A01G164700	chr3A	93.964	613	37	0	1760	2372	72719514	72718902	0.000000e+00	928.0
23	TraesCS4A01G164700	chr3A	80.317	757	111	32	7	734	362183319	362184066	2.680000e-149	538.0
24	TraesCS4A01G164700	chr3A	92.647	68	4	1	1634	1700	488128744	488128677	1.940000e-16	97.1
25	TraesCS4A01G164700	chr5A	93.974	614	34	2	1759	2372	466623998	466623388	0.000000e+00	926.0
26	TraesCS4A01G164700	chr5A	88.889	117	11	2	1644	1759	460331194	460331309	2.460000e-30	143.0
27	TraesCS4A01G164700	chr5A	90.667	75	5	2	1630	1704	196708394	196708322	5.400000e-17	99.0
28	TraesCS4A01G164700	chr2A	93.964	613	35	2	1760	2372	21083049	21082439	0.000000e+00	926.0
29	TraesCS4A01G164700	chr2A	93.801	613	38	0	1760	2372	21069294	21068682	0.000000e+00	922.0
30	TraesCS4A01G164700	chr2A	80.713	757	108	33	10	737	431644275	431643528	2.660000e-154	555.0
31	TraesCS4A01G164700	chr2A	80.053	757	113	32	10	737	431627666	431626919	5.810000e-146	527.0
32	TraesCS4A01G164700	chr2A	85.227	88	7	6	1629	1714	545938028	545938111	4.200000e-13	86.1
33	TraesCS4A01G164700	chr1A	93.506	616	39	1	1757	2372	454602727	454603341	0.000000e+00	915.0
34	TraesCS4A01G164700	chr1A	90.538	465	38	6	4	463	38485893	38485430	5.610000e-171	610.0
35	TraesCS4A01G164700	chr1A	89.914	466	43	4	4	465	38515244	38514779	4.360000e-167	597.0
36	TraesCS4A01G164700	chr1A	79.657	757	116	32	10	737	157937022	157936275	5.850000e-141	510.0
37	TraesCS4A01G164700	chr1A	85.882	170	24	0	1476	1645	157582451	157582620	5.210000e-42	182.0

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	TraesCS4A01G164700	chr4A	383179624	383181995	2371	True	4381.0	4381	100.0000	1	2372	1	chr4A.!!$R2	2371
1	TraesCS4A01G164700	chr4A	440634047	440634656	609	False	955.0	955	94.9180	1760	2369	1	chr4A.!!$F3	609
2	TraesCS4A01G164700	chr4A	440643841	440644456	615	False	939.0	939	94.1560	1757	2372	1	chr4A.!!$F4	615
3	TraesCS4A01G164700	chr4A	383169617	383170229	612	True	933.0	933	94.1270	1760	2372	1	chr4A.!!$R1	612
4	TraesCS4A01G164700	chr4A	451763119	451763729	610	True	928.0	928	94.1080	1760	2369	1	chr4A.!!$R3	609
5	TraesCS4A01G164700	chr4A	232097182	232097725	543	False	658.0	658	88.7870	4	538	1	chr4A.!!$F1	534
6	TraesCS4A01G164700	chr6A	237500098	237501847	1749	True	2106.0	2106	88.5180	11	1759	1	chr6A.!!$R2	1748
7	TraesCS4A01G164700	chr6A	319327019	319328665	1646	True	2063.0	2063	89.4260	10	1646	1	chr6A.!!$R4	1636
8	TraesCS4A01G164700	chr6A	319318878	319320626	1748	True	2050.0	2050	87.9520	10	1759	1	chr6A.!!$R3	1749
9	TraesCS4A01G164700	chr6A	121367057	121367797	740	True	1002.0	1002	91.1050	825	1564	1	chr6A.!!$R1	739
10	TraesCS4A01G164700	chr7A	577347065	577348366	1301	True	1291.0	1291	84.8300	4	1306	1	chr7A.!!$R2	1302
11	TraesCS4A01G164700	chr7A	670993263	670994980	1717	True	973.5	1812	90.1655	10	1759	2	chr7A.!!$R3	1749
12	TraesCS4A01G164700	chr7A	671009172	671011853	2681	True	709.0	1133	91.0390	553	1566	2	chr7A.!!$R4	1013
13	TraesCS4A01G164700	chr3D	49329086	49330161	1075	False	1443.0	1443	90.7440	383	1481	1	chr3D.!!$F1	1098
14	TraesCS4A01G164700	chr3D	49364007	49364624	617	False	865.0	865	91.9480	863	1481	1	chr3D.!!$F2	618
15	TraesCS4A01G164700	chr3A	377723231	377723989	758	True	1037.0	1037	91.3390	739	1497	1	chr3A.!!$R2	758
16	TraesCS4A01G164700	chr3A	72718902	72719514	612	True	928.0	928	93.9640	1760	2372	1	chr3A.!!$R1	612
17	TraesCS4A01G164700	chr3A	362183319	362184066	747	False	538.0	538	80.3170	7	734	1	chr3A.!!$F1	727
18	TraesCS4A01G164700	chr5A	466623388	466623998	610	True	926.0	926	93.9740	1759	2372	1	chr5A.!!$R2	613
19	TraesCS4A01G164700	chr2A	21082439	21083049	610	True	926.0	926	93.9640	1760	2372	1	chr2A.!!$R2	612
20	TraesCS4A01G164700	chr2A	21068682	21069294	612	True	922.0	922	93.8010	1760	2372	1	chr2A.!!$R1	612
21	TraesCS4A01G164700	chr2A	431643528	431644275	747	True	555.0	555	80.7130	10	737	1	chr2A.!!$R4	727
22	TraesCS4A01G164700	chr2A	431626919	431627666	747	True	527.0	527	80.0530	10	737	1	chr2A.!!$R3	727
23	TraesCS4A01G164700	chr1A	454602727	454603341	614	False	915.0	915	93.5060	1757	2372	1	chr1A.!!$F2	615
24	TraesCS4A01G164700	chr1A	157936275	157937022	747	True	510.0	510	79.6570	10	737	1	chr1A.!!$R3	727

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
622	666	0.325933	TCGTCGGTAGAGGTTCTCCA	59.674	55.0	0.0	0.0	35.89	3.86	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2252	3992	0.605319	TGTCCAAATGAGGTGCGGTC	60.605	55.0	0.0	0.0	0.0	4.79	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
172	178	9.738832	TTATGCAAATGTTGATATGAACATGAG	57.261	29.630	19.39	15.48	44.15	2.90
208	221	1.000359	ATGGCGGAAGGAAAAGGGG	60.000	57.895	0.00	0.00	0.00	4.79
267	282	1.065854	ACAGTTCTGGTAGCTCATGGC	60.066	52.381	0.00	0.00	42.19	4.40
281	296	1.148273	ATGGCGATACCGGTGCAAT	59.852	52.632	19.93	8.60	43.94	3.56
282	297	1.165907	ATGGCGATACCGGTGCAATG	61.166	55.000	19.93	3.42	43.94	2.82
322	347	2.806434	CAAAAGATGGTGGGGTGATCA	58.194	47.619	0.00	0.00	0.00	2.92
336	362	2.619590	GGTGATCATGGTTACCGGGTTT	60.620	50.000	4.31	0.00	0.00	3.27
434	468	1.204062	CGCAAGCATTCGTTCACGT	59.796	52.632	0.00	0.00	40.80	4.49
465	501	1.410153	GGGGTTATACCTTCGAAGCGA	59.590	52.381	19.99	9.55	38.64	4.93
518	562	0.455005	GGAAGTAGACGTTCTCGGGG	59.545	60.000	0.00	0.00	41.85	5.73
527	571	1.620413	CGTTCTCGGGGCGTTTGTAC	61.620	60.000	0.00	0.00	0.00	2.90
559	603	1.126846	GTTCATGTTCGAGAAGCGGTG	59.873	52.381	0.00	0.00	41.33	4.94
585	629	0.739813	CGGGTCTTCGACAATGGTCC	60.740	60.000	0.00	0.00	41.13	4.46
622	666	0.325933	TCGTCGGTAGAGGTTCTCCA	59.674	55.000	0.00	0.00	35.89	3.86
623	667	1.171308	CGTCGGTAGAGGTTCTCCAA	58.829	55.000	0.00	0.00	35.89	3.53
746	791	4.270008	GGTACTTGGCATCATGGTACTTT	58.730	43.478	0.00	0.00	35.18	2.66
783	828	1.078759	GTCTCGTCCTTGCGATGGTG	61.079	60.000	0.00	0.00	40.29	4.17
813	858	4.399004	TGAAGTTTTTGGTTCATGGGTG	57.601	40.909	0.00	0.00	0.00	4.61
874	919	1.067295	TGCATCCAAGTCCTTCAGGT	58.933	50.000	0.00	0.00	36.34	4.00
987	1032	2.494471	CCATGGTGTAGTCGTACTTGGA	59.506	50.000	2.57	0.00	0.00	3.53
988	1033	3.056393	CCATGGTGTAGTCGTACTTGGAA	60.056	47.826	2.57	0.00	0.00	3.53
1008	1053	1.456296	TCTGCAGCAACATGTCCATC	58.544	50.000	9.47	0.00	0.00	3.51
1161	1208	0.548510	TCAGGATCGAGCTCCTCTCA	59.451	55.000	8.47	0.00	44.04	3.27
1243	1290	1.675310	CTCCATGGTGGCAGCGAAA	60.675	57.895	12.58	0.00	37.47	3.46
1298	1345	1.381463	GCCGTAGAGGAAGGGGAGT	60.381	63.158	0.00	0.00	45.00	3.85
1370	3085	4.853142	ATGGAGGACGGGGCGCTA	62.853	66.667	7.64	0.00	0.00	4.26
1419	3136	2.694616	GTGGGGATGGTAGGGGCA	60.695	66.667	0.00	0.00	0.00	5.36
1498	3216	2.345760	GCGTCGGGGTCCTGTAGAA	61.346	63.158	0.00	0.00	0.00	2.10
1499	3217	1.880819	GCGTCGGGGTCCTGTAGAAA	61.881	60.000	0.00	0.00	0.00	2.52
1504	3222	1.551019	GGGGTCCTGTAGAAAGCGGT	61.551	60.000	0.00	0.00	0.00	5.68
1646	3364	0.491371	GAGGGAGGGATGAGAGGGAT	59.509	60.000	0.00	0.00	0.00	3.85
1650	3368	2.476199	GGAGGGATGAGAGGGATATGG	58.524	57.143	0.00	0.00	0.00	2.74
1653	3371	1.203492	GGGATGAGAGGGATATGGGGT	60.203	57.143	0.00	0.00	0.00	4.95
1654	3372	2.192263	GGATGAGAGGGATATGGGGTC	58.808	57.143	0.00	0.00	0.00	4.46
1657	3375	0.905337	GAGAGGGATATGGGGTCGGG	60.905	65.000	0.00	0.00	0.00	5.14
1658	3376	2.529389	AGGGATATGGGGTCGGGC	60.529	66.667	0.00	0.00	0.00	6.13
1705	3445	1.152226	GGGATCGAGGAGATGGGGT	60.152	63.158	0.00	0.00	40.26	4.95
1722	3462	1.598685	GTTTCGGGCGAAGGGTTCA	60.599	57.895	0.00	0.00	35.38	3.18
1731	3471	0.105964	CGAAGGGTTCACTGGTGACA	59.894	55.000	2.65	0.00	39.66	3.58
1932	3672	6.700081	GCATTTGCATACATGTTCATCTCATT	59.300	34.615	2.30	0.00	41.59	2.57
1949	3689	5.188434	TCTCATTCATTCGAGCATTTTCCT	58.812	37.500	0.00	0.00	0.00	3.36
1951	3691	4.943093	TCATTCATTCGAGCATTTTCCTCA	59.057	37.500	0.00	0.00	0.00	3.86
2024	3764	1.890876	TTCTTTCGTGTGTGGGGATG	58.109	50.000	0.00	0.00	0.00	3.51
2061	3801	4.697756	CGGGACTTGCCAAGCGGA	62.698	66.667	3.88	0.00	38.95	5.54
2086	3826	2.603173	GGTTTACTACCGATAGACCGCG	60.603	54.545	0.00	0.00	37.12	6.46
2129	3869	3.003275	GGACTTCGTTTGATGCTTCAACA	59.997	43.478	14.11	4.29	41.50	3.33
2170	3910	2.179547	CCTCGTGTGTGTTGCAGCA	61.180	57.895	0.00	0.00	0.00	4.41
2230	3970	3.383185	CCTCTCCATCTTCTAGAGCGTTT	59.617	47.826	0.00	0.00	36.29	3.60

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	2.463876	GCCTCATTTAAAATGCCTCGC	58.536	47.619	0.00	0.00	0.00	5.03
1	2	2.426738	TGGCCTCATTTAAAATGCCTCG	59.573	45.455	3.32	0.00	39.60	4.63
103	106	4.880696	TGTCATCCGCATCATGATAACAAA	59.119	37.500	8.15	0.00	32.86	2.83
151	157	8.626526	TCCATCTCATGTTCATATCAACATTTG	58.373	33.333	1.71	0.00	43.17	2.32
208	221	3.848272	TTTTCGGATTCATTCCTGTGC	57.152	42.857	0.00	0.00	42.99	4.57
249	262	0.176680	CGCCATGAGCTACCAGAACT	59.823	55.000	0.00	0.00	40.39	3.01
267	282	0.937304	CTTCCATTGCACCGGTATCG	59.063	55.000	6.87	0.00	0.00	2.92
281	296	4.329545	GCTCCCGCCACACTTCCA	62.330	66.667	0.00	0.00	0.00	3.53
282	297	3.628646	ATGCTCCCGCCACACTTCC	62.629	63.158	0.00	0.00	34.43	3.46
322	347	1.341581	CCATGGAAACCCGGTAACCAT	60.342	52.381	17.64	17.64	41.25	3.55
336	362	1.148949	CATGCCATCGACCCATGGA	59.851	57.895	15.22	0.00	45.79	3.41
434	468	1.668751	GTATAACCCCGACACGACGTA	59.331	52.381	0.00	0.00	0.00	3.57
465	501	1.674322	CCGAACCATCCCGTTTGCT	60.674	57.895	0.00	0.00	0.00	3.91
518	562	2.603953	GACTACCTCCAGTACAAACGC	58.396	52.381	0.00	0.00	0.00	4.84
527	571	3.512680	GAACATGAACGACTACCTCCAG	58.487	50.000	0.00	0.00	0.00	3.86
559	603	4.326255	TCGAAGACCCGTACCTCC	57.674	61.111	0.00	0.00	0.00	4.30
622	666	1.135083	CCACTACTGTCGCCGAGATTT	60.135	52.381	0.00	0.00	0.00	2.17
623	667	0.456221	CCACTACTGTCGCCGAGATT	59.544	55.000	0.00	0.00	0.00	2.40
783	828	4.365899	ACCAAAAACTTCAAGTTCGACC	57.634	40.909	2.45	0.00	37.47	4.79
874	919	5.814705	CCAAAATGCAAGTACAACAAGGAAA	59.185	36.000	0.00	0.00	0.00	3.13
987	1032	1.913778	TGGACATGTTGCTGCAGATT	58.086	45.000	20.43	0.00	0.00	2.40
988	1033	2.022195	GATGGACATGTTGCTGCAGAT	58.978	47.619	20.43	0.00	0.00	2.90
1008	1053	3.002102	GCTATTGGTTTGTTTGGCCATG	58.998	45.455	6.09	0.00	31.71	3.66
1216	1263	1.639635	CCACCATGGAGGCCTAAGCT	61.640	60.000	21.47	0.00	40.96	3.74
1282	1329	1.677637	GCCACTCCCCTTCCTCTACG	61.678	65.000	0.00	0.00	0.00	3.51
1284	1331	1.003051	GGCCACTCCCCTTCCTCTA	59.997	63.158	0.00	0.00	0.00	2.43
1370	3085	1.657804	CCTCTGTTCTACCCCACCTT	58.342	55.000	0.00	0.00	0.00	3.50
1374	3089	0.042731	CCTCCCTCTGTTCTACCCCA	59.957	60.000	0.00	0.00	0.00	4.96
1579	3297	4.947147	TTCGCCGCCAAGCAGGTT	62.947	61.111	0.00	0.00	40.61	3.50
1646	3364	3.158648	CCTTCGCCCGACCCCATA	61.159	66.667	0.00	0.00	0.00	2.74
1705	3445	1.598685	GTGAACCCTTCGCCCGAAA	60.599	57.895	4.58	0.00	34.17	3.46
1731	3471	1.382420	CCTGCCTCCTCCTAGCACT	60.382	63.158	0.00	0.00	32.06	4.40
1932	3672	4.701651	ACAATGAGGAAAATGCTCGAATGA	59.298	37.500	0.00	0.00	37.69	2.57
1949	3689	2.351253	CGGAATGCAAAACGGACAATGA	60.351	45.455	0.00	0.00	0.00	2.57
1951	3691	2.346099	CGGAATGCAAAACGGACAAT	57.654	45.000	0.00	0.00	0.00	2.71
2046	3786	1.600916	AAGTCCGCTTGGCAAGTCC	60.601	57.895	26.71	11.47	32.92	3.85
2086	3826	4.273969	TCCAAATGGTACGAAACTTGACAC	59.726	41.667	0.00	0.00	36.34	3.67
2129	3869	1.341080	TTTCGGTCCCTCGGTTAACT	58.659	50.000	5.42	0.00	0.00	2.24
2170	3910	1.715785	CCAAAATGGAGGGGTGTTGT	58.284	50.000	0.00	0.00	40.96	3.32
2252	3992	0.605319	TGTCCAAATGAGGTGCGGTC	60.605	55.000	0.00	0.00	0.00	4.79

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.