AutoCloner

Multiple sequence alignment - TraesCS7B01G438500

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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	TraesCS7B01G438500	chr7B	100.000	2654	0	0	1	2654	704318415	704315762	0.000000e+00	4902.0
1	TraesCS7B01G438500	chr7B	86.804	970	85	17	7	954	704289381	704290329	0.000000e+00	1042.0
2	TraesCS7B01G438500	chr7B	91.469	715	56	3	950	1663	704290359	704291069	0.000000e+00	977.0
3	TraesCS7B01G438500	chr7B	89.214	751	69	6	952	1700	704548645	704549385	0.000000e+00	928.0
4	TraesCS7B01G438500	chr7B	87.005	808	102	1	147	954	704547806	704548610	0.000000e+00	907.0
5	TraesCS7B01G438500	chr7B	86.829	782	100	2	173	954	728933706	728934484	0.000000e+00	870.0
6	TraesCS7B01G438500	chr7B	83.438	954	120	23	21	954	704637674	704636739	0.000000e+00	852.0
7	TraesCS7B01G438500	chr7B	88.314	676	74	3	988	1663	729217433	729218103	0.000000e+00	806.0
8	TraesCS7B01G438500	chr7B	86.722	723	69	13	950	1648	704636709	704635990	0.000000e+00	778.0
9	TraesCS7B01G438500	chr7B	95.833	48	2	0	1758	1805	704551378	704551425	7.880000e-11	78.7
10	TraesCS7B01G438500	chr7B	93.023	43	3	0	73	115	704289319	704289361	2.210000e-06	63.9
11	TraesCS7B01G438500	chr7D	94.235	954	48	2	1	954	613626084	613627030	0.000000e+00	1450.0
12	TraesCS7B01G438500	chr7D	95.604	728	27	3	938	1665	613627056	613627778	0.000000e+00	1162.0
13	TraesCS7B01G438500	chr7D	85.426	940	117	10	22	954	627449593	627450519	0.000000e+00	959.0
14	TraesCS7B01G438500	chr7D	90.669	718	59	5	950	1663	627450549	627451262	0.000000e+00	948.0
15	TraesCS7B01G438500	chr7D	86.471	850	100	8	1810	2654	155284006	155284845	0.000000e+00	918.0
16	TraesCS7B01G438500	chr7D	88.286	700	77	4	950	1648	613660781	613660086	0.000000e+00	833.0
17	TraesCS7B01G438500	chr7D	85.235	745	106	4	213	954	613661554	613660811	0.000000e+00	763.0
18	TraesCS7B01G438500	chr7D	87.025	316	32	7	110	423	613649414	613649722	5.440000e-92	348.0
19	TraesCS7B01G438500	chr3B	90.281	854	70	9	1805	2654	498662338	498663182	0.000000e+00	1105.0
20	TraesCS7B01G438500	chr3B	84.628	631	90	5	2028	2654	203341303	203340676	2.900000e-174	621.0
21	TraesCS7B01G438500	chr3B	77.299	859	180	10	1802	2654	778993057	778993906	2.370000e-135	492.0
22	TraesCS7B01G438500	chr6D	88.014	851	91	4	1805	2651	6377905	6378748	0.000000e+00	996.0
23	TraesCS7B01G438500	chr7A	85.150	936	125	10	22	954	705296893	705297817	0.000000e+00	946.0
24	TraesCS7B01G438500	chr7A	90.014	721	66	4	950	1667	705297847	705298564	0.000000e+00	928.0
25	TraesCS7B01G438500	chr7A	88.269	699	79	2	950	1648	705331847	705331152	0.000000e+00	833.0
26	TraesCS7B01G438500	chr7A	84.962	798	113	7	161	954	705332671	705331877	0.000000e+00	802.0
27	TraesCS7B01G438500	chr6A	87.909	794	91	4	1865	2654	5947259	5948051	0.000000e+00	929.0
28	TraesCS7B01G438500	chr3D	87.719	798	85	7	1809	2601	141238797	141238008	0.000000e+00	918.0
29	TraesCS7B01G438500	chr3A	85.933	654	88	2	1886	2535	159803974	159803321	0.000000e+00	695.0
30	TraesCS7B01G438500	chr4B	79.812	852	153	13	1807	2650	172525644	172526484	1.050000e-168	603.0

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	TraesCS7B01G438500	chr7B	704315762	704318415	2653	True	4902.0	4902	100.0000	1	2654	1	chr7B.!!$R1	2653
1	TraesCS7B01G438500	chr7B	728933706	728934484	778	False	870.0	870	86.8290	173	954	1	chr7B.!!$F1	781
2	TraesCS7B01G438500	chr7B	704635990	704637674	1684	True	815.0	852	85.0800	21	1648	2	chr7B.!!$R2	1627
3	TraesCS7B01G438500	chr7B	729217433	729218103	670	False	806.0	806	88.3140	988	1663	1	chr7B.!!$F2	675
4	TraesCS7B01G438500	chr7B	704289319	704291069	1750	False	694.3	1042	90.4320	7	1663	3	chr7B.!!$F3	1656
5	TraesCS7B01G438500	chr7B	704547806	704551425	3619	False	637.9	928	90.6840	147	1805	3	chr7B.!!$F4	1658
6	TraesCS7B01G438500	chr7D	613626084	613627778	1694	False	1306.0	1450	94.9195	1	1665	2	chr7D.!!$F3	1664
7	TraesCS7B01G438500	chr7D	627449593	627451262	1669	False	953.5	959	88.0475	22	1663	2	chr7D.!!$F4	1641
8	TraesCS7B01G438500	chr7D	155284006	155284845	839	False	918.0	918	86.4710	1810	2654	1	chr7D.!!$F1	844
9	TraesCS7B01G438500	chr7D	613660086	613661554	1468	True	798.0	833	86.7605	213	1648	2	chr7D.!!$R1	1435
10	TraesCS7B01G438500	chr3B	498662338	498663182	844	False	1105.0	1105	90.2810	1805	2654	1	chr3B.!!$F1	849
11	TraesCS7B01G438500	chr3B	203340676	203341303	627	True	621.0	621	84.6280	2028	2654	1	chr3B.!!$R1	626
12	TraesCS7B01G438500	chr3B	778993057	778993906	849	False	492.0	492	77.2990	1802	2654	1	chr3B.!!$F2	852
13	TraesCS7B01G438500	chr6D	6377905	6378748	843	False	996.0	996	88.0140	1805	2651	1	chr6D.!!$F1	846
14	TraesCS7B01G438500	chr7A	705296893	705298564	1671	False	937.0	946	87.5820	22	1667	2	chr7A.!!$F1	1645
15	TraesCS7B01G438500	chr7A	705331152	705332671	1519	True	817.5	833	86.6155	161	1648	2	chr7A.!!$R1	1487
16	TraesCS7B01G438500	chr6A	5947259	5948051	792	False	929.0	929	87.9090	1865	2654	1	chr6A.!!$F1	789
17	TraesCS7B01G438500	chr3D	141238008	141238797	789	True	918.0	918	87.7190	1809	2601	1	chr3D.!!$R1	792
18	TraesCS7B01G438500	chr3A	159803321	159803974	653	True	695.0	695	85.9330	1886	2535	1	chr3A.!!$R1	649
19	TraesCS7B01G438500	chr4B	172525644	172526484	840	False	603.0	603	79.8120	1807	2650	1	chr4B.!!$F1	843

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
934	1030	0.108329	GGGTCATGGACGACGTCATT	60.108	55.0	27.77	12.63	36.73	2.57	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2123	4222	0.037017	CACGGAAACCCATACCACCA	59.963	55.0	0.0	0.0	0.0	4.17	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
37	90	6.646267	TCTGTTAATTTTGGTACGGAGCTAT	58.354	36.000	0.00	0.00	0.00	2.97
41	94	5.813080	AATTTTGGTACGGAGCTATCAAC	57.187	39.130	0.00	0.00	0.00	3.18
75	131	1.335810	CTCAAATGGCATCCATCACCG	59.664	52.381	0.00	0.00	44.40	4.94
136	208	6.014771	TCCTACATATACGCTCCATAGGAT	57.985	41.667	0.00	0.00	33.43	3.24
182	259	0.605319	GAACCACGAGAACCATGGCA	60.605	55.000	13.04	0.00	36.96	4.92
183	260	0.606401	AACCACGAGAACCATGGCAG	60.606	55.000	13.04	1.08	36.96	4.85
184	261	2.401766	CCACGAGAACCATGGCAGC	61.402	63.158	13.04	0.68	0.00	5.25
232	311	2.169561	GCTCCCTCTTTTCCTCCTAGTG	59.830	54.545	0.00	0.00	0.00	2.74
271	361	1.376683	GAAGTATGGTGGCGTGCCA	60.377	57.895	10.06	10.06	45.02	4.92
511	601	3.027170	GAACACCATCGCCACGCTG	62.027	63.158	0.00	0.00	0.00	5.18
600	690	4.121669	GACAGAGCTGCTCGGCGA	62.122	66.667	26.08	10.14	35.36	5.54
913	1009	1.142748	GACAGCCCAGGAGATGTCG	59.857	63.158	9.67	0.00	33.42	4.35
927	1023	0.683179	ATGTCGAGGGTCATGGACGA	60.683	55.000	0.00	0.00	32.65	4.20
934	1030	0.108329	GGGTCATGGACGACGTCATT	60.108	55.000	27.77	12.63	36.73	2.57
1042	1181	0.757188	GAGGGATCTCTTCGGAGCCA	60.757	60.000	0.00	0.00	42.92	4.75
1192	1331	1.591703	CTTGAGGAGCTGCCGTACA	59.408	57.895	0.00	0.00	43.43	2.90
1399	1538	0.753848	GGAGAGGTTCGAGGAGGAGG	60.754	65.000	0.00	0.00	0.00	4.30
1455	1594	4.070552	GAGCTCCTGCCGTTCGGT	62.071	66.667	12.81	0.00	40.80	4.69
1537	1676	1.208052	CGAGCCTCCTCTTCCATTTCA	59.792	52.381	0.00	0.00	35.90	2.69
1667	1830	9.736023	GCCACCTCTCTAAATAAATTTGTATTG	57.264	33.333	0.00	0.00	0.00	1.90
1711	1874	2.696989	AATAAAAATGCCAGCCCAGC	57.303	45.000	0.00	0.00	0.00	4.85
1746	2272	1.611851	ATGGGGCCCGAAAAATGCA	60.612	52.632	19.83	5.49	0.00	3.96
1747	2273	0.982326	ATGGGGCCCGAAAAATGCAT	60.982	50.000	19.83	7.97	0.00	3.96
1769	3867	1.063942	CCCCACCCTCCCAAATAAGTC	60.064	57.143	0.00	0.00	0.00	3.01
1801	3899	2.681097	GCCCCACTAACAAGTGAGATCC	60.681	54.545	7.09	0.00	42.02	3.36
1845	3943	0.826062	CCCTTTCATGATTGGGGTGC	59.174	55.000	20.16	0.00	36.15	5.01
1846	3944	0.826062	CCTTTCATGATTGGGGTGCC	59.174	55.000	0.00	0.00	0.00	5.01
1847	3945	0.457035	CTTTCATGATTGGGGTGCCG	59.543	55.000	0.00	0.00	0.00	5.69
1848	3946	0.969917	TTTCATGATTGGGGTGCCGG	60.970	55.000	0.00	0.00	0.00	6.13
1849	3947	3.530260	CATGATTGGGGTGCCGGC	61.530	66.667	22.73	22.73	0.00	6.13
1850	3948	4.059304	ATGATTGGGGTGCCGGCA	62.059	61.111	29.03	29.03	0.00	5.69
1851	3949	3.598747	ATGATTGGGGTGCCGGCAA	62.599	57.895	34.66	16.88	0.00	4.52
1852	3950	2.759560	GATTGGGGTGCCGGCAAT	60.760	61.111	34.66	21.60	0.00	3.56
1853	3951	2.759560	ATTGGGGTGCCGGCAATC	60.760	61.111	34.66	25.60	0.00	2.67
1893	3991	7.748677	TCAAGCATATTATTGAGAGGATCCAA	58.251	34.615	15.82	0.00	33.66	3.53
1898	3996	8.510505	GCATATTATTGAGAGGATCCAAAAGAC	58.489	37.037	15.82	0.00	33.66	3.01
1914	4012	5.047660	CCAAAAGACGATAAATGGGTGGAAA	60.048	40.000	0.00	0.00	0.00	3.13
1936	4034	7.065923	GGAAAGAAAGAACGCTATCTTATGGTT	59.934	37.037	1.81	0.00	38.69	3.67
1941	4039	7.535489	AAGAACGCTATCTTATGGTTGTAAC	57.465	36.000	0.00	0.00	37.88	2.50
2042	4141	2.569059	CGGATCACTGATGCCATTTCT	58.431	47.619	5.05	0.00	0.00	2.52
2096	4195	1.825090	AGATGCATTGGTTCGCTTGA	58.175	45.000	0.00	0.00	0.00	3.02
2118	4217	3.153130	TGGAAAATGTGCATTCCGAAGA	58.847	40.909	11.27	0.00	46.58	2.87
2123	4222	4.853924	AATGTGCATTCCGAAGAAAAGT	57.146	36.364	0.00	0.00	35.09	2.66
2230	4333	2.203084	TGCGAGGGTTTTGCGTGA	60.203	55.556	0.00	0.00	39.21	4.35
2305	4408	5.435686	TCCTATGTGTGGCAGAGTATTTT	57.564	39.130	0.00	0.00	34.78	1.82
2419	4522	2.751806	GCTCCTCCAGGAAAATTGTCAG	59.248	50.000	0.00	0.00	44.91	3.51
2453	4556	5.927281	ATAGAGTGCTTACCCGAGTTAAA	57.073	39.130	0.00	0.00	0.00	1.52
2503	4606	5.543405	AGTGGGATGAGAATCTTATCAGAGG	59.457	44.000	15.48	0.00	31.23	3.69
2536	4639	3.058016	CCCATTGATGTTGATCGCATACC	60.058	47.826	3.04	0.00	0.00	2.73
2549	4652	5.825151	TGATCGCATACCACAAATTCCATTA	59.175	36.000	0.00	0.00	0.00	1.90
2635	4738	9.070179	TGTACGATCTGCCTATTATAAACAGTA	57.930	33.333	0.00	0.00	0.00	2.74

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
10	11	7.280356	AGCTCCGTACCAAAATTAACAGATAT	58.720	34.615	0.00	0.00	0.00	1.63
12	13	5.497474	AGCTCCGTACCAAAATTAACAGAT	58.503	37.500	0.00	0.00	0.00	2.90
13	14	4.901868	AGCTCCGTACCAAAATTAACAGA	58.098	39.130	0.00	0.00	0.00	3.41
14	15	6.537301	TGATAGCTCCGTACCAAAATTAACAG	59.463	38.462	0.00	0.00	0.00	3.16
15	16	6.408035	TGATAGCTCCGTACCAAAATTAACA	58.592	36.000	0.00	0.00	0.00	2.41
16	17	6.913873	TGATAGCTCCGTACCAAAATTAAC	57.086	37.500	0.00	0.00	0.00	2.01
17	18	6.316890	GGTTGATAGCTCCGTACCAAAATTAA	59.683	38.462	0.00	0.00	0.00	1.40
18	19	5.818857	GGTTGATAGCTCCGTACCAAAATTA	59.181	40.000	0.00	0.00	0.00	1.40
27	80	2.035961	GCAGATGGTTGATAGCTCCGTA	59.964	50.000	0.00	0.00	0.00	4.02
75	131	1.337118	TGTTGCTCCCAAAATGGACC	58.663	50.000	0.00	0.00	40.96	4.46
136	208	2.840753	GGCTTGGGAGTTGGGACCA	61.841	63.158	0.00	0.00	0.00	4.02
141	213	2.353610	GCCATGGCTTGGGAGTTGG	61.354	63.158	29.98	0.00	46.55	3.77
443	533	2.572284	GGTCTTGAGGACGTCCCG	59.428	66.667	30.82	16.54	45.35	5.14
583	673	4.121669	TCGCCGAGCAGCTCTGTC	62.122	66.667	20.39	9.08	0.00	3.51
696	792	3.691744	CTGACGAGGGAGCTCACGC	62.692	68.421	17.19	13.62	0.00	5.34
913	1009	1.139095	GACGTCGTCCATGACCCTC	59.861	63.158	14.60	0.00	35.40	4.30
927	1023	1.429463	GCGTTTCTCCTCAATGACGT	58.571	50.000	0.00	0.00	33.46	4.34
934	1030	2.126463	CTCGCGCGTTTCTCCTCA	60.126	61.111	30.98	5.69	0.00	3.86
1176	1315	1.517361	CATGTACGGCAGCTCCTCA	59.483	57.895	0.00	0.00	0.00	3.86
1177	1316	1.884926	GCATGTACGGCAGCTCCTC	60.885	63.158	4.61	0.00	0.00	3.71
1192	1331	1.452651	CCTTGATCACCAGCCGCAT	60.453	57.895	0.00	0.00	0.00	4.73
1667	1830	0.804933	GCGGGTGAATCTCCACGTAC	60.805	60.000	3.61	0.00	37.91	3.67
1668	1831	1.252215	TGCGGGTGAATCTCCACGTA	61.252	55.000	3.61	2.01	37.91	3.57
1669	1832	2.107041	TTGCGGGTGAATCTCCACGT	62.107	55.000	3.61	0.00	37.91	4.49
1694	1857	0.896923	CTGCTGGGCTGGCATTTTTA	59.103	50.000	2.88	0.00	39.07	1.52
1746	2272	2.617207	TATTTGGGAGGGTGGGGTAT	57.383	50.000	0.00	0.00	0.00	2.73
1747	2273	2.210644	CTTATTTGGGAGGGTGGGGTA	58.789	52.381	0.00	0.00	0.00	3.69
1769	3867	0.249120	TAGTGGGGCAATGAGACGTG	59.751	55.000	0.00	0.00	0.00	4.49
1801	3899	5.654650	AGACCCAAGTACTTATCAGAGACTG	59.345	44.000	8.04	0.00	0.00	3.51
1845	3943	2.359354	TCAACACGGGATTGCCGG	60.359	61.111	21.11	11.89	40.16	6.13
1846	3944	1.671054	AGTCAACACGGGATTGCCG	60.671	57.895	15.64	15.64	33.83	5.69
1847	3945	0.889186	ACAGTCAACACGGGATTGCC	60.889	55.000	0.00	0.00	0.00	4.52
1848	3946	0.951558	AACAGTCAACACGGGATTGC	59.048	50.000	0.00	0.00	0.00	3.56
1849	3947	2.616376	TGAAACAGTCAACACGGGATTG	59.384	45.455	0.00	0.00	31.51	2.67
1850	3948	2.925724	TGAAACAGTCAACACGGGATT	58.074	42.857	0.00	0.00	31.51	3.01
1851	3949	2.631160	TGAAACAGTCAACACGGGAT	57.369	45.000	0.00	0.00	31.51	3.85
1852	3950	2.285083	CTTGAAACAGTCAACACGGGA	58.715	47.619	0.00	0.00	41.47	5.14
1853	3951	1.268539	GCTTGAAACAGTCAACACGGG	60.269	52.381	0.00	0.00	41.47	5.28
1893	3991	5.566469	TCTTTCCACCCATTTATCGTCTTT	58.434	37.500	0.00	0.00	0.00	2.52
1898	3996	6.322491	GTTCTTTCTTTCCACCCATTTATCG	58.678	40.000	0.00	0.00	0.00	2.92
1914	4012	6.407202	ACAACCATAAGATAGCGTTCTTTCT	58.593	36.000	9.09	0.00	37.20	2.52
1936	4034	4.668941	CGCTTTGATCAATGCTTCGTTACA	60.669	41.667	31.65	6.37	38.75	2.41
1941	4039	1.131126	ACCGCTTTGATCAATGCTTCG	59.869	47.619	31.65	23.68	38.75	3.79
2022	4121	2.547211	GAGAAATGGCATCAGTGATCCG	59.453	50.000	1.56	0.00	0.00	4.18
2042	4141	0.611200	CGTCACCCCACCAGTAATGA	59.389	55.000	0.00	0.00	0.00	2.57
2096	4195	3.763360	TCTTCGGAATGCACATTTTCCAT	59.237	39.130	15.35	0.00	41.25	3.41
2118	4217	3.236047	GGAAACCCATACCACCACTTTT	58.764	45.455	0.00	0.00	0.00	2.27
2123	4222	0.037017	CACGGAAACCCATACCACCA	59.963	55.000	0.00	0.00	0.00	4.17
2305	4408	2.172483	GAAAGTCTGAGCTCCCGCCA	62.172	60.000	12.15	0.00	36.60	5.69
2375	4478	2.883828	CGGCACCCAACAGTCCTCT	61.884	63.158	0.00	0.00	0.00	3.69
2419	4522	1.587034	GCACTCTATTTCCGCGTGTAC	59.413	52.381	4.92	0.00	0.00	2.90
2453	4556	5.839063	TCCGGATACTGGATCAATAAGTTCT	59.161	40.000	0.00	0.00	36.12	3.01
2536	4639	7.337480	TCATCCTGATGTAATGGAATTTGTG	57.663	36.000	7.00	0.00	39.72	3.33
2549	4652	9.319060	ACATAATACTCAGTATCATCCTGATGT	57.681	33.333	0.00	0.00	37.70	3.06
2568	4671	3.631686	GTCAAGTGCCATGCCACATAATA	59.368	43.478	9.78	0.00	38.18	0.98

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.