AutoCloner

Multiple sequence alignment - TraesCS7D01G484300

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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	TraesCS7D01G484300	chr7D	100.000	2886	0	0	1	2886	594546257	594543372	0.000000e+00	5330.0
1	TraesCS7D01G484300	chr7D	94.694	2582	130	5	310	2886	594636870	594634291	0.000000e+00	4002.0
2	TraesCS7D01G484300	chr7D	94.860	1712	84	3	1	1710	594662147	594660438	0.000000e+00	2671.0
3	TraesCS7D01G484300	chr7D	92.352	1229	86	4	1661	2886	594850733	594851956	0.000000e+00	1742.0
4	TraesCS7D01G484300	chr7D	92.045	704	49	6	280	976	594187903	594187200	0.000000e+00	983.0
5	TraesCS7D01G484300	chr7D	93.286	283	16	2	1	283	424859623	424859902	5.750000e-112	414.0
6	TraesCS7D01G484300	chr7D	96.154	52	0	2	280	331	242609890	242609841	1.840000e-12	84.2
7	TraesCS7D01G484300	chr7D	92.727	55	4	0	280	334	9682873	9682927	2.380000e-11	80.5
8	TraesCS7D01G484300	chr7A	92.191	2894	209	15	2	2886	687241529	687244414	0.000000e+00	4076.0
9	TraesCS7D01G484300	chr7A	91.813	2895	221	12	1	2886	687060302	687063189	0.000000e+00	4019.0
10	TraesCS7D01G484300	chr7A	92.823	1895	127	8	997	2886	687185814	687187704	0.000000e+00	2737.0
11	TraesCS7D01G484300	chr7A	92.823	1895	127	8	997	2886	687200473	687202363	0.000000e+00	2737.0
12	TraesCS7D01G484300	chr7B	91.699	2614	203	11	280	2886	666718421	666715815	0.000000e+00	3613.0
13	TraesCS7D01G484300	chr7B	91.431	2614	209	10	280	2886	667007269	667004664	0.000000e+00	3572.0
14	TraesCS7D01G484300	chr7B	91.393	2614	210	10	280	2886	667035768	667033163	0.000000e+00	3567.0
15	TraesCS7D01G484300	chr5D	92.933	283	17	2	1	283	114345461	114345182	2.680000e-110	409.0
16	TraesCS7D01G484300	chr4A	92.933	283	17	1	1	283	469285974	469285695	2.680000e-110	409.0
17	TraesCS7D01G484300	chr3D	92.933	283	17	2	1	283	138318711	138318432	2.680000e-110	409.0
18	TraesCS7D01G484300	chr1D	92.933	283	17	2	1	283	216454250	216453971	2.680000e-110	409.0

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	TraesCS7D01G484300	chr7D	594543372	594546257	2885	True	5330	5330	100.000	1	2886	1	chr7D.!!$R3	2885
1	TraesCS7D01G484300	chr7D	594634291	594636870	2579	True	4002	4002	94.694	310	2886	1	chr7D.!!$R4	2576
2	TraesCS7D01G484300	chr7D	594660438	594662147	1709	True	2671	2671	94.860	1	1710	1	chr7D.!!$R5	1709
3	TraesCS7D01G484300	chr7D	594850733	594851956	1223	False	1742	1742	92.352	1661	2886	1	chr7D.!!$F3	1225
4	TraesCS7D01G484300	chr7D	594187200	594187903	703	True	983	983	92.045	280	976	1	chr7D.!!$R2	696
5	TraesCS7D01G484300	chr7A	687241529	687244414	2885	False	4076	4076	92.191	2	2886	1	chr7A.!!$F4	2884
6	TraesCS7D01G484300	chr7A	687060302	687063189	2887	False	4019	4019	91.813	1	2886	1	chr7A.!!$F1	2885
7	TraesCS7D01G484300	chr7A	687185814	687187704	1890	False	2737	2737	92.823	997	2886	1	chr7A.!!$F2	1889
8	TraesCS7D01G484300	chr7A	687200473	687202363	1890	False	2737	2737	92.823	997	2886	1	chr7A.!!$F3	1889
9	TraesCS7D01G484300	chr7B	666715815	666718421	2606	True	3613	3613	91.699	280	2886	1	chr7B.!!$R1	2606
10	TraesCS7D01G484300	chr7B	667004664	667007269	2605	True	3572	3572	91.431	280	2886	1	chr7B.!!$R2	2606
11	TraesCS7D01G484300	chr7B	667033163	667035768	2605	True	3567	3567	91.393	280	2886	1	chr7B.!!$R3	2606

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
790	807	1.068434	AGCAAATGGAACGTGGTTTGG	59.932	47.619	13.48	0.0	33.39	3.28	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2238	2261	1.312815	GCAAGTACCATCATGAGCCC	58.687	55.0	0.09	0.0	0.0	5.19	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
186	187	6.405065	CCACAATTCATCGGATCTCAACAAAT	60.405	38.462	0.00	0.00	0.00	2.32
209	210	4.022416	TGCACCGCAAAAGAAGATTACAAT	60.022	37.500	0.00	0.00	34.76	2.71
240	241	3.421844	TCTGAGAACATCGAGGAGAACA	58.578	45.455	3.06	0.00	0.00	3.18
248	249	7.782049	AGAACATCGAGGAGAACATTGTATTA	58.218	34.615	3.06	0.00	0.00	0.98
286	290	2.969628	AGGACTAGCCATCTAGCATGT	58.030	47.619	6.07	0.00	44.83	3.21
429	434	3.813724	CCCCCACCCATCAGGAGC	61.814	72.222	0.00	0.00	39.89	4.70
517	530	6.759272	ACATGTAAGCTACTTCTTCACTTGA	58.241	36.000	0.00	0.00	0.00	3.02
522	535	8.559536	TGTAAGCTACTTCTTCACTTGAAATTG	58.440	33.333	0.00	0.00	33.07	2.32
550	565	8.668510	AGAGACAAATATAGTATGCCACTTTG	57.331	34.615	0.00	0.00	38.80	2.77
572	588	7.596749	TTGTCGTTAAGATCATCTTCCTTTC	57.403	36.000	2.18	0.00	37.89	2.62
655	672	9.130661	CCCAAATATCCCAAAAAGAAACTTTTT	57.869	29.630	13.96	13.96	32.38	1.94
673	690	9.883142	AAACTTTTTATTGAAATCACACCAAGA	57.117	25.926	0.00	0.00	0.00	3.02
790	807	1.068434	AGCAAATGGAACGTGGTTTGG	59.932	47.619	13.48	0.00	33.39	3.28
830	847	2.687935	CCATGGGCCAGTACACAAATAC	59.312	50.000	13.78	0.00	0.00	1.89
887	905	3.181493	GCTGCAACAATTATGGAGTGGAG	60.181	47.826	11.75	0.00	38.38	3.86
901	919	3.449018	GGAGTGGAGAGTATGACACATGT	59.551	47.826	0.00	0.00	36.35	3.21
1007	1025	3.019564	CCTTAGCTCTTCCCACCAATTG	58.980	50.000	0.00	0.00	0.00	2.32
1108	1126	6.941857	AGGGATGTTTTAGTGTTTTGTGTTT	58.058	32.000	0.00	0.00	0.00	2.83
1224	1244	2.449967	TAGAGGCGGTGGTTGAGGGA	62.450	60.000	0.00	0.00	0.00	4.20
1239	1259	2.243736	TGAGGGAAACTTCACAAAGGGT	59.756	45.455	0.00	0.00	42.14	4.34
1335	1355	4.933064	CGTGCGCCTCTCGATCCC	62.933	72.222	4.18	0.00	41.67	3.85
1344	1364	0.179062	CTCTCGATCCCCAGGCTTTG	60.179	60.000	0.00	0.00	0.00	2.77
1455	1475	2.353357	ACGATGGTGATGGATGCATT	57.647	45.000	0.00	0.00	0.00	3.56
1476	1496	4.314522	TGATGGAACTAAAGATGCCCAA	57.685	40.909	0.00	0.00	0.00	4.12
1619	1639	8.938883	TCTCTGCTTAATCCAATATCCTACTTT	58.061	33.333	0.00	0.00	0.00	2.66
1700	1722	9.685276	ATACAATGAGTGAATGTTCCTTGATAA	57.315	29.630	0.00	0.00	0.00	1.75
1757	1779	4.589908	ACACATCCACTCACCCTATTTTC	58.410	43.478	0.00	0.00	0.00	2.29
1861	1884	6.586344	AGTGGAGGTGTATGTGATTTCATAG	58.414	40.000	0.00	0.00	32.01	2.23
1980	2003	5.426689	AGCTCATGTGAAGAAATAGGACA	57.573	39.130	0.00	0.00	0.00	4.02
2021	2044	4.540715	TCCATCTCAAGTCTGATGAGCTA	58.459	43.478	3.86	0.00	43.19	3.32
2087	2110	1.988846	CAAACTCCTCCTTCCCCTTCT	59.011	52.381	0.00	0.00	0.00	2.85
2120	2143	2.570752	AGTGCTGTCTTCACATCCATCT	59.429	45.455	0.00	0.00	36.93	2.90
2127	2150	3.068732	GTCTTCACATCCATCTCCATCGA	59.931	47.826	0.00	0.00	0.00	3.59
2145	2168	2.603110	TCGACGCTACATCATTTTGCTC	59.397	45.455	0.00	0.00	0.00	4.26
2253	2276	1.131638	TGAGGGGCTCATGATGGTAC	58.868	55.000	0.00	0.00	35.39	3.34
2279	2302	2.825264	GCGCAAGAGGGCCTCTAT	59.175	61.111	35.23	21.88	46.99	1.98
2302	2325	1.628846	TCTTTAGGAAGACAGGGTGGC	59.371	52.381	0.00	0.00	36.99	5.01
2348	2371	3.326747	CCTTTGGGAAGTTCTAGTCACG	58.673	50.000	2.25	0.00	33.58	4.35
2357	2380	2.486636	TTCTAGTCACGCACCGCCTG	62.487	60.000	0.00	0.00	0.00	4.85
2360	2383	2.203972	TAGTCACGCACCGCCTGTAC	62.204	60.000	0.00	0.00	0.00	2.90
2394	2417	0.250727	CCTCACCAACCATCACCGTT	60.251	55.000	0.00	0.00	0.00	4.44
2404	2427	3.139077	ACCATCACCGTTTCTTCTGAAC	58.861	45.455	0.00	0.00	31.02	3.18
2542	2565	1.289160	AGGCTACAATGGCTTCCTCA	58.711	50.000	0.00	0.00	40.00	3.86
2598	2621	0.868406	CGTCCAAAGACAGAAGGTGC	59.132	55.000	0.00	0.00	43.73	5.01
2643	2668	6.548321	ACTTTCCACTCCATAATGGTTACAA	58.452	36.000	0.00	0.00	39.03	2.41
2670	2696	9.277565	CTGTAATATTTTTCAGTCGGAAATGTG	57.722	33.333	0.00	0.00	44.59	3.21
2687	2713	8.611757	CGGAAATGTGAACATGTCTATTTATGA	58.388	33.333	12.28	0.00	39.86	2.15
2692	2718	8.806429	TGTGAACATGTCTATTTATGAATGGT	57.194	30.769	0.00	0.00	0.00	3.55
2727	2753	6.269077	TCTTCAATGAGTAGGAGTAAACCACA	59.731	38.462	0.00	0.00	0.00	4.17

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
55	56	4.695217	TTGAACTATCGGTTTGGATTGC	57.305	40.909	0.00	0.00	38.41	3.56
186	187	2.881513	TGTAATCTTCTTTTGCGGTGCA	59.118	40.909	0.00	0.00	36.47	4.57
209	210	5.193679	TCGATGTTCTCAGAGTTCTATCCA	58.806	41.667	0.00	0.00	0.00	3.41
248	249	8.421002	GCTAGTCCTTCTCTCTATTTGATCTTT	58.579	37.037	0.00	0.00	0.00	2.52
258	259	5.514136	GCTAGATGGCTAGTCCTTCTCTCTA	60.514	48.000	18.45	9.94	43.63	2.43
268	272	5.201713	TGTTACATGCTAGATGGCTAGTC	57.798	43.478	0.00	0.00	44.84	2.59
269	273	5.614324	TTGTTACATGCTAGATGGCTAGT	57.386	39.130	0.00	0.00	44.84	2.57
270	274	6.226052	TGATTGTTACATGCTAGATGGCTAG	58.774	40.000	0.00	0.00	45.63	3.42
271	275	6.173427	TGATTGTTACATGCTAGATGGCTA	57.827	37.500	0.00	0.00	0.00	3.93
455	461	8.599624	AATGAATTAGTGGACATTGGAGAATT	57.400	30.769	0.00	0.00	32.79	2.17
456	462	8.599624	AAATGAATTAGTGGACATTGGAGAAT	57.400	30.769	0.00	0.00	34.02	2.40
522	535	7.897864	AGTGGCATACTATATTTGTCTCTACC	58.102	38.462	0.00	0.00	38.04	3.18
550	565	7.545965	TCAAGAAAGGAAGATGATCTTAACGAC	59.454	37.037	7.82	1.02	36.73	4.34
588	605	6.051717	GCATCCAAAGCTATCTTAGAGAACA	58.948	40.000	0.00	0.00	31.02	3.18
662	679	6.839124	TGCATTTTAGAATCTTGGTGTGAT	57.161	33.333	0.00	0.00	0.00	3.06
673	690	2.103601	GCTGGCCCATGCATTTTAGAAT	59.896	45.455	0.00	0.00	40.13	2.40
790	807	2.838202	TGGTTTCCTCCATGAGTAGGAC	59.162	50.000	10.02	2.78	41.63	3.85
830	847	2.351641	CCCATGGAAATGTCAACACGTG	60.352	50.000	15.22	15.48	0.00	4.49
887	905	4.262635	CCATCCCCTACATGTGTCATACTC	60.263	50.000	9.11	0.00	0.00	2.59
901	919	1.844296	AAGGTGACCCCCATCCCCTA	61.844	60.000	0.00	0.00	0.00	3.53
1108	1126	9.706691	TTAATACAAACACCAAGAAACAAACAA	57.293	25.926	0.00	0.00	0.00	2.83
1239	1259	2.729360	CTCAACGATGAGTACACGCAAA	59.271	45.455	14.11	0.00	46.60	3.68
1335	1355	5.684704	TCTAATGGATTAGACAAAGCCTGG	58.315	41.667	5.19	0.00	44.44	4.45
1455	1475	4.018506	TCTTGGGCATCTTTAGTTCCATCA	60.019	41.667	0.00	0.00	0.00	3.07
1476	1496	3.009584	GTCCAACTCATTCTTCCCCTTCT	59.990	47.826	0.00	0.00	0.00	2.85
1487	1507	0.991920	ATCACCCGGTCCAACTCATT	59.008	50.000	0.00	0.00	0.00	2.57
1578	1598	5.845391	AGCAGAGAGTCTACTTATGGAAC	57.155	43.478	0.00	0.00	0.00	3.62
1619	1639	4.121317	CACCACCACTAGTTCGTGTAAAA	58.879	43.478	15.44	0.00	33.07	1.52
1726	1748	5.488341	GGTGAGTGGATGTGTATGTTAAGT	58.512	41.667	0.00	0.00	0.00	2.24
1757	1779	8.733857	AGCATTCTTTCGATTTTTACAAAGAG	57.266	30.769	0.00	0.00	36.48	2.85
1781	1803	2.880890	GGATCCCGAACCAATTGATGAG	59.119	50.000	7.12	0.00	0.00	2.90
1895	1918	7.755582	TCAATATACACTGACTGAATGTTCG	57.244	36.000	0.00	0.00	0.00	3.95
1905	1928	9.245962	ACTATTAAGCGTTCAATATACACTGAC	57.754	33.333	0.00	0.00	0.00	3.51
1980	2003	3.303049	GGATCTCCCTGCAAAATCCAAT	58.697	45.455	0.00	0.00	36.67	3.16
2021	2044	2.633967	TGCCATGCTTTCATGTTCCTTT	59.366	40.909	4.80	0.00	46.64	3.11
2120	2143	3.452755	AAATGATGTAGCGTCGATGGA	57.547	42.857	6.79	0.00	0.00	3.41
2127	2150	2.017049	GGGAGCAAAATGATGTAGCGT	58.983	47.619	0.00	0.00	0.00	5.07
2145	2168	5.841810	TCTTGCTTAGTTTCATTTTGTGGG	58.158	37.500	0.00	0.00	0.00	4.61
2186	2209	5.886960	AGAATTGAGGTTGTATGAGTTGC	57.113	39.130	0.00	0.00	0.00	4.17
2238	2261	1.312815	GCAAGTACCATCATGAGCCC	58.687	55.000	0.09	0.00	0.00	5.19
2279	2302	3.519510	CCACCCTGTCTTCCTAAAGATCA	59.480	47.826	0.00	0.00	43.26	2.92
2340	2363	1.929806	TACAGGCGGTGCGTGACTAG	61.930	60.000	17.21	0.00	45.68	2.57
2343	2366	3.110178	GTACAGGCGGTGCGTGAC	61.110	66.667	17.21	8.01	45.68	3.67
2348	2371	3.562732	AAAGGGGTACAGGCGGTGC	62.563	63.158	0.00	0.00	0.00	5.01
2357	2380	3.181437	TGAGGACAAAAGGAAAGGGGTAC	60.181	47.826	0.00	0.00	0.00	3.34
2360	2383	2.239400	GTGAGGACAAAAGGAAAGGGG	58.761	52.381	0.00	0.00	0.00	4.79
2394	2417	2.418669	AGGGTGGGAAGTTCAGAAGAA	58.581	47.619	5.01	0.00	0.00	2.52
2404	2427	4.041198	TGTTGACTTTACTAGGGTGGGAAG	59.959	45.833	0.00	0.00	0.00	3.46
2609	2632	5.241403	TGGAGTGGAAAGTATCACACATT	57.759	39.130	0.00	0.00	36.43	2.71
2643	2668	9.010029	ACATTTCCGACTGAAAAATATTACAGT	57.990	29.630	16.98	16.98	45.67	3.55
2687	2713	7.616935	ACTCATTGAAGAAACCATATGACCATT	59.383	33.333	3.65	0.00	0.00	3.16
2692	2718	8.089625	TCCTACTCATTGAAGAAACCATATGA	57.910	34.615	3.65	0.00	0.00	2.15
2727	2753	7.552330	ACAAAGTGCAAAACCAGTAAATTGAAT	59.448	29.630	0.00	0.00	0.00	2.57

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.