AutoCloner

Multiple sequence alignment - TraesCS4D01G191000

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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	TraesCS4D01G191000	chr4D	100.000	4568	0	0	1	4568	334157641	334153074	0.000000e+00	8436
1	TraesCS4D01G191000	chr4D	82.500	320	56	0	2454	2773	118819513	118819832	9.680000e-72	281
2	TraesCS4D01G191000	chr4A	94.627	3778	128	24	196	3942	139536895	139540628	0.000000e+00	5782
3	TraesCS4D01G191000	chr4A	92.492	626	38	5	3950	4567	715713842	715713218	0.000000e+00	887
4	TraesCS4D01G191000	chr4A	92.332	626	38	8	3951	4567	159496654	159497278	0.000000e+00	881
5	TraesCS4D01G191000	chr4A	93.782	193	11	1	1	193	139536661	139536852	5.780000e-74	289
6	TraesCS4D01G191000	chr4A	82.188	320	57	0	2454	2773	454122807	454123126	4.500000e-70	276
7	TraesCS4D01G191000	chr4B	96.449	3041	93	9	916	3952	412183828	412180799	0.000000e+00	5003
8	TraesCS4D01G191000	chr4B	89.301	916	37	17	5	884	412184999	412184109	0.000000e+00	1092
9	TraesCS4D01G191000	chr4B	81.471	340	63	0	2454	2793	181252444	181252783	3.480000e-71	279
10	TraesCS4D01G191000	chr3B	92.937	623	38	3	3945	4567	169188829	169189445	0.000000e+00	902
11	TraesCS4D01G191000	chr3B	76.709	468	87	13	2999	3463	612930982	612931430	1.640000e-59	241
12	TraesCS4D01G191000	chr3B	73.569	367	73	18	1122	1472	612912198	612912556	8.030000e-23	119
13	TraesCS4D01G191000	chrUn	92.640	625	37	7	3951	4567	55786245	55786868	0.000000e+00	891
14	TraesCS4D01G191000	chrUn	92.640	625	37	7	3951	4567	302515512	302514889	0.000000e+00	891
15	TraesCS4D01G191000	chr5D	92.395	618	46	1	3951	4567	540247866	540247249	0.000000e+00	880
16	TraesCS4D01G191000	chr3A	92.160	625	40	7	3951	4567	203841267	203840644	0.000000e+00	874
17	TraesCS4D01G191000	chr2B	92.160	625	40	7	3951	4567	64336446	64337069	0.000000e+00	874
18	TraesCS4D01G191000	chr2B	78.108	370	65	14	1122	1480	122013778	122014142	2.140000e-53	220
19	TraesCS4D01G191000	chr2A	92.160	625	40	7	3951	4567	733695661	733695038	0.000000e+00	874
20	TraesCS4D01G191000	chr2A	77.941	1020	188	26	2454	3463	79173552	79174544	1.820000e-168	603
21	TraesCS4D01G191000	chr2A	75.152	495	101	20	1122	1602	79172268	79172754	3.580000e-51	213
22	TraesCS4D01G191000	chr2D	79.976	824	102	34	2981	3776	107703599	107704387	2.400000e-152	549
23	TraesCS4D01G191000	chr2D	80.000	545	98	9	2923	3463	78757868	78758405	4.280000e-105	392
24	TraesCS4D01G191000	chr2D	91.150	226	11	5	2499	2716	107703180	107703404	9.610000e-77	298
25	TraesCS4D01G191000	chr2D	75.252	497	97	24	1122	1602	78756127	78756613	3.580000e-51	213
26	TraesCS4D01G191000	chr7A	79.878	164	23	9	1358	1516	705593844	705593686	1.340000e-20	111

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	TraesCS4D01G191000	chr4D	334153074	334157641	4567	True	8436.0	8436	100.0000	1	4568	1	chr4D.!!$R1	4567
1	TraesCS4D01G191000	chr4A	139536661	139540628	3967	False	3035.5	5782	94.2045	1	3942	2	chr4A.!!$F3	3941
2	TraesCS4D01G191000	chr4A	715713218	715713842	624	True	887.0	887	92.4920	3950	4567	1	chr4A.!!$R1	617
3	TraesCS4D01G191000	chr4A	159496654	159497278	624	False	881.0	881	92.3320	3951	4567	1	chr4A.!!$F1	616
4	TraesCS4D01G191000	chr4B	412180799	412184999	4200	True	3047.5	5003	92.8750	5	3952	2	chr4B.!!$R1	3947
5	TraesCS4D01G191000	chr3B	169188829	169189445	616	False	902.0	902	92.9370	3945	4567	1	chr3B.!!$F1	622
6	TraesCS4D01G191000	chrUn	55786245	55786868	623	False	891.0	891	92.6400	3951	4567	1	chrUn.!!$F1	616
7	TraesCS4D01G191000	chrUn	302514889	302515512	623	True	891.0	891	92.6400	3951	4567	1	chrUn.!!$R1	616
8	TraesCS4D01G191000	chr5D	540247249	540247866	617	True	880.0	880	92.3950	3951	4567	1	chr5D.!!$R1	616
9	TraesCS4D01G191000	chr3A	203840644	203841267	623	True	874.0	874	92.1600	3951	4567	1	chr3A.!!$R1	616
10	TraesCS4D01G191000	chr2B	64336446	64337069	623	False	874.0	874	92.1600	3951	4567	1	chr2B.!!$F1	616
11	TraesCS4D01G191000	chr2A	733695038	733695661	623	True	874.0	874	92.1600	3951	4567	1	chr2A.!!$R1	616
12	TraesCS4D01G191000	chr2A	79172268	79174544	2276	False	408.0	603	76.5465	1122	3463	2	chr2A.!!$F1	2341
13	TraesCS4D01G191000	chr2D	107703180	107704387	1207	False	423.5	549	85.5630	2499	3776	2	chr2D.!!$F2	1277
14	TraesCS4D01G191000	chr2D	78756127	78758405	2278	False	302.5	392	77.6260	1122	3463	2	chr2D.!!$F1	2341

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
848	932	0.322456	TGCTTTTCCTACCGCAGCAT	60.322	50.0	0.0	35.56	3.79	F
2187	2685	0.321564	TCTGTGGGTTCAATGGCTCG	60.322	55.0	0.0	0.00	5.03	F
3375	3955	0.677098	AGGAGCTCGTGAAGACGCTA	60.677	55.0	8.4	45.68	4.26	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
2193	2691	0.320771	GAGAAGAAGCGGAGGTGCAA	60.321	55.000	0.00	39.47	4.08	R
3472	4056	0.106619	AAGGACGAGGTAGCGGAGAT	60.107	55.000	0.00	35.12	2.75	R
4324	4938	1.405105	GGAGCGCTTGCCATTATTTGA	59.595	47.619	13.26	40.41	2.69	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
84	85	1.747355	GTGAAGTGAAGGATGGCCATG	59.253	52.381	26.56	0.00	36.29	3.66
162	163	1.589716	GCACATTCCTCCAGTGGTGC	61.590	60.000	9.54	5.96	43.78	5.01
266	307	7.970061	CACGAAATGAATAAAATGATGGTGTCT	59.030	33.333	0.00	0.00	0.00	3.41
267	308	8.184192	ACGAAATGAATAAAATGATGGTGTCTC	58.816	33.333	0.00	0.00	0.00	3.36
268	309	7.374228	CGAAATGAATAAAATGATGGTGTCTCG	59.626	37.037	0.00	0.00	0.00	4.04
408	449	3.726517	CCCGTTTGCTGTCTGCCG	61.727	66.667	0.00	0.00	42.00	5.69
472	518	3.135994	CTCGATGTATTAAAACCCCCGG	58.864	50.000	0.00	0.00	0.00	5.73
492	538	3.857854	CACGTGATCGCTGCTGCC	61.858	66.667	10.90	0.00	41.18	4.85
595	649	4.242602	GGATTCTTTCCGGCCCTG	57.757	61.111	0.00	0.00	33.93	4.45
596	650	2.121538	GGATTCTTTCCGGCCCTGC	61.122	63.158	0.00	0.00	33.93	4.85
597	651	2.043953	ATTCTTTCCGGCCCTGCC	60.044	61.111	0.00	0.00	46.75	4.85
791	864	8.103935	CCCTTCTGTTAATTATATTCCCTCCTC	58.896	40.741	0.00	0.00	0.00	3.71
794	867	9.447279	TTCTGTTAATTATATTCCCTCCTCTCA	57.553	33.333	0.00	0.00	0.00	3.27
795	868	8.871125	TCTGTTAATTATATTCCCTCCTCTCAC	58.129	37.037	0.00	0.00	0.00	3.51
796	869	7.974504	TGTTAATTATATTCCCTCCTCTCACC	58.025	38.462	0.00	0.00	0.00	4.02
797	870	5.746990	AATTATATTCCCTCCTCTCACCG	57.253	43.478	0.00	0.00	0.00	4.94
798	871	2.016905	ATATTCCCTCCTCTCACCGG	57.983	55.000	0.00	0.00	0.00	5.28
799	872	0.759436	TATTCCCTCCTCTCACCGGC	60.759	60.000	0.00	0.00	0.00	6.13
848	932	0.322456	TGCTTTTCCTACCGCAGCAT	60.322	50.000	0.00	0.00	35.56	3.79
905	1253	6.757947	GCTACTAGGTACGAGGATACAGATAG	59.242	46.154	0.00	0.00	34.62	2.08
924	1272	3.089784	GCAGCTGCATTGCATTGC	58.910	55.556	33.36	23.33	40.05	3.56
939	1287	2.764768	CATTGCATTGCATTGCGTTTC	58.235	42.857	24.10	3.26	45.77	2.78
969	1317	6.317893	GGATTAGATCCTAGAGCTAGTAGTGC	59.682	46.154	0.00	0.00	46.19	4.40
1046	1394	1.070786	GTGTTGGGTCAAGAGGCGA	59.929	57.895	0.00	0.00	0.00	5.54
1062	1410	3.906649	GACATGCTCGCGCTGTCG	61.907	66.667	10.46	0.00	35.87	4.35
1829	2255	0.619543	TTAGGTGGTACCCTCCCTGC	60.620	60.000	19.90	0.00	39.75	4.85
1879	2305	3.323115	AGAGATCAAGCTCGATGGCAATA	59.677	43.478	0.00	0.00	39.87	1.90
1887	2313	2.224606	CTCGATGGCAATAGCATTGGT	58.775	47.619	0.00	0.00	44.61	3.67
1932	2358	2.618045	CGGGCTCAAGAACCTAACCAAT	60.618	50.000	0.00	0.00	0.00	3.16
1947	2373	1.203364	ACCAATCTGTCCCTGAGGAGT	60.203	52.381	0.00	0.00	45.21	3.85
2031	2529	1.340248	GTCTCCGAGAACAACCTCACA	59.660	52.381	0.00	0.00	32.86	3.58
2187	2685	0.321564	TCTGTGGGTTCAATGGCTCG	60.322	55.000	0.00	0.00	0.00	5.03
2193	2691	1.463674	GGTTCAATGGCTCGGACATT	58.536	50.000	0.00	0.00	42.67	2.71
2852	3402	3.713858	TGGCTTGTTTCATTCTGTGTG	57.286	42.857	0.00	0.00	0.00	3.82
2869	3419	0.815213	GTGCTGACCACAACTCTGCA	60.815	55.000	0.00	0.00	44.06	4.41
3375	3955	0.677098	AGGAGCTCGTGAAGACGCTA	60.677	55.000	8.40	0.00	45.68	4.26
3393	3973	2.733227	GCTAAAGCTCGCATTGCATTGT	60.733	45.455	9.69	0.00	38.21	2.71
3574	4158	1.261480	CACCACAGAGTAGTCAGCCT	58.739	55.000	0.00	0.00	0.00	4.58
3780	4381	2.282462	CGGGAGTGCTGGCCTTTT	60.282	61.111	3.32	0.00	0.00	2.27
3901	4509	3.057526	GGATCCTTTTAACAGTTGCGCTT	60.058	43.478	9.73	0.00	0.00	4.68
4019	4632	6.049149	GCCTCTGCATAACTAAGATGTACAA	58.951	40.000	0.00	0.00	37.47	2.41
4033	4646	4.649218	AGATGTACAAAGCCAAACAAGGTT	59.351	37.500	0.00	0.00	0.00	3.50
4038	4651	3.769300	ACAAAGCCAAACAAGGTTCTCTT	59.231	39.130	0.00	0.00	35.79	2.85
4215	4829	0.681564	AGGTCTCGATTCTCCACGCT	60.682	55.000	0.00	0.00	0.00	5.07
4223	4837	3.057104	TCGATTCTCCACGCTTTGTAGAA	60.057	43.478	0.00	0.00	31.50	2.10
4324	4938	5.368145	TCATTTCTACATAGCCAAAGCGAT	58.632	37.500	0.00	0.00	46.67	4.58
4426	5040	3.034635	AGCAACACTACAGGGAGGATAG	58.965	50.000	0.00	0.00	0.00	2.08
4432	5046	1.889829	CTACAGGGAGGATAGAAGCCG	59.110	57.143	0.00	0.00	0.00	5.52

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
53	54	0.319900	TCACTTCACTCTGCGCCTTC	60.320	55.000	4.18	0.00	0.00	3.46
62	63	1.003580	TGGCCATCCTTCACTTCACTC	59.996	52.381	0.00	0.00	0.00	3.51
142	143	0.250858	CACCACTGGAGGAATGTGCA	60.251	55.000	0.71	0.00	0.00	4.57
268	309	2.741211	GTTTGGCGAGACCGGGAC	60.741	66.667	6.32	0.00	43.94	4.46
371	412	2.043652	CATGGGGAAGGGGCACTG	60.044	66.667	0.00	0.00	0.00	3.66
408	449	3.282885	CAGTAAAGAGGGATTTGGGAGC	58.717	50.000	0.00	0.00	0.00	4.70
498	544	0.252057	GCTATCTCTCCCCTCCCTCC	60.252	65.000	0.00	0.00	0.00	4.30
506	552	1.069935	GCCAACGGCTATCTCTCCC	59.930	63.158	0.00	0.00	46.69	4.30
507	553	4.760757	GCCAACGGCTATCTCTCC	57.239	61.111	0.00	0.00	46.69	3.71
632	686	2.510238	GCTACGGTGCAGCCTGAG	60.510	66.667	10.90	6.17	32.68	3.35
640	694	1.097547	TAGTCCTACGGCTACGGTGC	61.098	60.000	0.00	0.00	46.48	5.01
643	716	0.107456	TCCTAGTCCTACGGCTACGG	59.893	60.000	0.00	0.00	46.48	4.02
657	730	2.623878	TCAGCTCGTACTCCTCCTAG	57.376	55.000	0.00	0.00	0.00	3.02
658	731	3.579534	AATCAGCTCGTACTCCTCCTA	57.420	47.619	0.00	0.00	0.00	2.94
659	732	2.445682	AATCAGCTCGTACTCCTCCT	57.554	50.000	0.00	0.00	0.00	3.69
660	733	4.650754	TTAAATCAGCTCGTACTCCTCC	57.349	45.455	0.00	0.00	0.00	4.30
661	734	7.921745	ACTAATTTAAATCAGCTCGTACTCCTC	59.078	37.037	0.10	0.00	0.00	3.71
662	735	7.783042	ACTAATTTAAATCAGCTCGTACTCCT	58.217	34.615	0.10	0.00	0.00	3.69
663	736	7.921745	AGACTAATTTAAATCAGCTCGTACTCC	59.078	37.037	0.10	0.00	0.00	3.85
664	737	8.859517	AGACTAATTTAAATCAGCTCGTACTC	57.140	34.615	0.10	0.00	0.00	2.59
665	738	9.088512	CAAGACTAATTTAAATCAGCTCGTACT	57.911	33.333	0.10	0.00	0.00	2.73
794	867	0.250727	ATATATGCAAAGCGGCCGGT	60.251	50.000	26.97	26.97	0.00	5.28
795	868	1.665679	CTATATATGCAAAGCGGCCGG	59.334	52.381	29.38	11.47	0.00	6.13
796	869	2.604914	CTCTATATATGCAAAGCGGCCG	59.395	50.000	24.05	24.05	0.00	6.13
797	870	3.600388	ACTCTATATATGCAAAGCGGCC	58.400	45.455	0.00	0.00	0.00	6.13
798	871	3.619038	GGACTCTATATATGCAAAGCGGC	59.381	47.826	0.00	0.00	0.00	6.53
799	872	4.820897	TGGACTCTATATATGCAAAGCGG	58.179	43.478	0.00	0.00	0.00	5.52
838	922	0.457853	GACGAGTTGATGCTGCGGTA	60.458	55.000	0.00	0.00	0.00	4.02
848	932	1.267832	GCGCTGTTTTTGACGAGTTGA	60.268	47.619	0.00	0.00	0.00	3.18
876	961	0.867086	CCTCGTACCTAGTAGCTCGC	59.133	60.000	0.00	0.00	0.00	5.03
881	966	7.760794	CACTATCTGTATCCTCGTACCTAGTAG	59.239	44.444	0.00	0.00	0.00	2.57
882	967	7.609960	CACTATCTGTATCCTCGTACCTAGTA	58.390	42.308	0.00	0.00	0.00	1.82
883	968	6.465948	CACTATCTGTATCCTCGTACCTAGT	58.534	44.000	0.00	0.00	0.00	2.57
924	1272	3.493877	TCCAAAAGAAACGCAATGCAATG	59.506	39.130	5.91	0.00	0.00	2.82
925	1273	3.726607	TCCAAAAGAAACGCAATGCAAT	58.273	36.364	5.91	0.00	0.00	3.56
926	1274	3.170791	TCCAAAAGAAACGCAATGCAA	57.829	38.095	5.91	0.00	0.00	4.08
927	1275	2.879002	TCCAAAAGAAACGCAATGCA	57.121	40.000	5.91	0.00	0.00	3.96
928	1276	5.160641	TCTAATCCAAAAGAAACGCAATGC	58.839	37.500	0.00	0.00	0.00	3.56
980	1328	4.372656	CATTGGGACTAACAGCTAGCTAC	58.627	47.826	18.86	4.96	0.00	3.58
1060	1408	3.385384	CAGGAGGACCAGCAGCGA	61.385	66.667	0.00	0.00	38.94	4.93
1119	1467	4.388499	ATCACCACGCCGTCCCAC	62.388	66.667	0.00	0.00	0.00	4.61
1829	2255	1.000955	AGGTAACGTTGCAGAGTGAGG	59.999	52.381	18.24	0.00	46.39	3.86
1854	2280	2.609244	GCCATCGAGCTTGATCTCTACC	60.609	54.545	13.91	0.00	0.00	3.18
1879	2305	1.076024	AGGAATGTGACCACCAATGCT	59.924	47.619	0.00	0.00	0.00	3.79
1887	2313	0.770499	TGGCTTCAGGAATGTGACCA	59.230	50.000	0.00	0.00	0.00	4.02
1932	2358	2.111384	GCATTACTCCTCAGGGACAGA	58.889	52.381	0.00	0.00	36.57	3.41
2031	2529	3.644953	GGACTCTGGAATCCCTCCT	57.355	57.895	0.00	0.00	45.64	3.69
2045	2543	3.076092	CAAGGCTGCTCAGGGACT	58.924	61.111	0.00	0.00	43.88	3.85
2067	2565	3.458189	AGACACGTTGAAAGAGTTGAGG	58.542	45.455	0.00	0.00	0.00	3.86
2116	2614	3.909732	TGAACCTGTTGGAAAGAACCAT	58.090	40.909	0.00	0.00	39.82	3.55
2187	2685	1.244019	AAGCGGAGGTGCAAATGTCC	61.244	55.000	0.00	0.00	39.47	4.02
2193	2691	0.320771	GAGAAGAAGCGGAGGTGCAA	60.321	55.000	0.00	0.00	39.47	4.08
2742	3292	2.900716	TGGTCATGAAGTCGAACACA	57.099	45.000	0.00	0.00	0.00	3.72
2852	3402	1.068748	CATTGCAGAGTTGTGGTCAGC	60.069	52.381	0.00	0.00	0.00	4.26
2869	3419	0.675633	GTGCAAGAACAGTGGGCATT	59.324	50.000	0.00	0.00	36.79	3.56
3375	3955	1.000060	ACACAATGCAATGCGAGCTTT	60.000	42.857	0.46	0.00	0.00	3.51
3472	4056	0.106619	AAGGACGAGGTAGCGGAGAT	60.107	55.000	0.00	0.00	35.12	2.75
3480	4064	2.345760	GCCGGTGAAGGACGAGGTA	61.346	63.158	1.90	0.00	0.00	3.08
3504	4088	1.922570	CGGTCGCAGTAGTATTGCTT	58.077	50.000	14.82	0.00	39.38	3.91
3508	4092	0.179119	GTGGCGGTCGCAGTAGTATT	60.179	55.000	17.21	0.00	44.11	1.89
3574	4158	5.593909	TGGAATTTTCTTTCAGTCTGCAAGA	59.406	36.000	10.46	10.46	43.69	3.02
3780	4381	7.284489	AGCACTAAGGTTCATTGAAAGTGTAAA	59.716	33.333	21.37	0.00	32.52	2.01
3901	4509	6.109156	TGTTACCTTGCTCTTCATGACTAA	57.891	37.500	0.00	0.00	0.00	2.24
3946	4554	2.102252	AGCGCACCTTTTCAAAAATGGA	59.898	40.909	11.47	0.00	0.00	3.41
3948	4556	4.534794	AAAGCGCACCTTTTCAAAAATG	57.465	36.364	11.47	0.00	40.85	2.32
3949	4557	6.859420	AATAAAGCGCACCTTTTCAAAAAT	57.141	29.167	11.47	0.00	40.85	1.82
3993	4606	3.181450	ACATCTTAGTTATGCAGAGGCCC	60.181	47.826	0.00	0.00	40.13	5.80
4019	4632	4.532834	TGTAAGAGAACCTTGTTTGGCTT	58.467	39.130	0.00	0.00	36.34	4.35
4060	4673	8.603242	ACTCTACATGTTTCTTTGTATTTCGT	57.397	30.769	2.30	0.00	0.00	3.85
4112	4726	2.228343	GGCAGCATGATCTTAGGATTGC	59.772	50.000	0.00	3.87	39.69	3.56
4156	4770	0.461961	GATTGGAGGCTACAGCGAGT	59.538	55.000	0.00	0.00	43.26	4.18
4215	4829	7.218614	TCTTCGTTTATGGTCCTTTCTACAAA	58.781	34.615	0.00	0.00	0.00	2.83
4223	4837	3.055312	GGGACTCTTCGTTTATGGTCCTT	60.055	47.826	9.33	0.00	41.81	3.36
4324	4938	1.405105	GGAGCGCTTGCCATTATTTGA	59.595	47.619	13.26	0.00	40.41	2.69
4432	5046	3.879892	GGTCAGTCATCCAAATAGCTTCC	59.120	47.826	0.00	0.00	0.00	3.46

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.