AutoCloner

Multiple sequence alignment - TraesCS7D01G550400

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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	TraesCS7D01G550400	chr7D	100.000	3344	0	0	1	3344	634658567	634661910	0.000000e+00	6176.0
1	TraesCS7D01G550400	chr7D	94.752	1429	54	11	964	2380	634751433	634750014	0.000000e+00	2204.0
2	TraesCS7D01G550400	chr7D	83.762	1515	193	34	961	2443	583548565	583550058	0.000000e+00	1386.0
3	TraesCS7D01G550400	chr7D	80.947	887	118	27	2457	3318	583550335	583551195	0.000000e+00	654.0
4	TraesCS7D01G550400	chr7D	83.849	582	83	8	959	1533	634454618	634455195	8.160000e-151	544.0
5	TraesCS7D01G550400	chr7D	86.848	479	45	9	2460	2932	634759501	634759035	1.380000e-143	520.0
6	TraesCS7D01G550400	chr4B	90.096	1565	134	12	882	2443	625072739	625074285	0.000000e+00	2012.0
7	TraesCS7D01G550400	chr4B	89.531	917	60	10	2448	3341	625074461	625075364	0.000000e+00	1129.0
8	TraesCS7D01G550400	chr7A	90.045	1557	112	19	893	2440	731126032	731127554	0.000000e+00	1977.0
9	TraesCS7D01G550400	chr7A	90.473	1522	107	22	929	2440	731186462	731187955	0.000000e+00	1973.0
10	TraesCS7D01G550400	chr7A	89.595	1557	119	19	893	2440	731157471	731158993	0.000000e+00	1938.0
11	TraesCS7D01G550400	chr7A	88.644	1585	147	15	867	2443	731095930	731097489	0.000000e+00	1899.0
12	TraesCS7D01G550400	chr7A	88.780	1533	98	28	1	1517	731540387	731538913	0.000000e+00	1810.0
13	TraesCS7D01G550400	chr7A	92.958	994	58	4	1453	2446	731397763	731396782	0.000000e+00	1437.0
14	TraesCS7D01G550400	chr7A	84.050	1511	199	27	959	2443	675021924	675023418	0.000000e+00	1417.0
15	TraesCS7D01G550400	chr7A	93.396	954	62	1	1490	2443	731220342	731221294	0.000000e+00	1411.0
16	TraesCS7D01G550400	chr7A	91.872	935	72	4	1513	2446	731506620	731505689	0.000000e+00	1303.0
17	TraesCS7D01G550400	chr7A	88.326	908	63	21	2452	3341	731221341	731222223	0.000000e+00	1050.0
18	TraesCS7D01G550400	chr7A	87.500	904	86	19	2450	3341	731097534	731098422	0.000000e+00	1018.0
19	TraesCS7D01G550400	chr7A	90.247	769	50	11	2450	3209	731012480	731013232	0.000000e+00	981.0
20	TraesCS7D01G550400	chr7A	86.374	866	91	19	2450	3303	731013401	731014251	0.000000e+00	920.0
21	TraesCS7D01G550400	chr7A	91.896	617	34	8	2738	3344	731430374	731429764	0.000000e+00	848.0
22	TraesCS7D01G550400	chr7A	89.984	629	44	9	2729	3341	731159564	731160189	0.000000e+00	795.0
23	TraesCS7D01G550400	chr7A	89.825	629	45	9	2729	3341	731129860	731130485	0.000000e+00	789.0
24	TraesCS7D01G550400	chr7A	89.825	629	45	10	2729	3341	731188526	731189151	0.000000e+00	789.0
25	TraesCS7D01G550400	chr7A	91.628	430	30	4	2497	2921	731505616	731505188	1.030000e-164	590.0
26	TraesCS7D01G550400	chr7A	81.653	714	89	20	2457	3154	675026421	675027108	3.770000e-154	555.0
27	TraesCS7D01G550400	chr7B	86.689	1525	163	21	951	2446	741624990	741623477	0.000000e+00	1655.0
28	TraesCS7D01G550400	chr7B	85.696	1545	158	32	915	2443	741482087	741483584	0.000000e+00	1570.0
29	TraesCS7D01G550400	chr7B	90.105	475	41	5	2450	2921	741542896	741543367	2.210000e-171	612.0
30	TraesCS7D01G550400	chr7B	89.041	438	40	4	2450	2883	741623435	741623002	1.370000e-148	536.0
31	TraesCS7D01G550400	chr7B	92.954	369	23	2	1023	1388	741541527	741541895	4.910000e-148	534.0
32	TraesCS7D01G550400	chr7B	93.983	349	18	1	2996	3341	741543370	741543718	2.960000e-145	525.0
33	TraesCS7D01G550400	chr7B	82.587	201	22	7	2460	2654	651141934	651142127	7.420000e-37	165.0
34	TraesCS7D01G550400	chr4D	82.278	79	12	1	45	121	379498551	379498473	2.150000e-07	67.6

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	TraesCS7D01G550400	chr7D	634658567	634661910	3343	False	6176.0	6176	100.000000	1	3344	1	chr7D.!!$F2	3343
1	TraesCS7D01G550400	chr7D	634750014	634751433	1419	True	2204.0	2204	94.752000	964	2380	1	chr7D.!!$R1	1416
2	TraesCS7D01G550400	chr7D	583548565	583551195	2630	False	1020.0	1386	82.354500	961	3318	2	chr7D.!!$F3	2357
3	TraesCS7D01G550400	chr7D	634454618	634455195	577	False	544.0	544	83.849000	959	1533	1	chr7D.!!$F1	574
4	TraesCS7D01G550400	chr4B	625072739	625075364	2625	False	1570.5	2012	89.813500	882	3341	2	chr4B.!!$F1	2459
5	TraesCS7D01G550400	chr7A	731538913	731540387	1474	True	1810.0	1810	88.780000	1	1517	1	chr7A.!!$R3	1516
6	TraesCS7D01G550400	chr7A	731095930	731098422	2492	False	1458.5	1899	88.072000	867	3341	2	chr7A.!!$F3	2474
7	TraesCS7D01G550400	chr7A	731396782	731397763	981	True	1437.0	1437	92.958000	1453	2446	1	chr7A.!!$R1	993
8	TraesCS7D01G550400	chr7A	731126032	731130485	4453	False	1383.0	1977	89.935000	893	3341	2	chr7A.!!$F4	2448
9	TraesCS7D01G550400	chr7A	731186462	731189151	2689	False	1381.0	1973	90.149000	929	3341	2	chr7A.!!$F6	2412
10	TraesCS7D01G550400	chr7A	731157471	731160189	2718	False	1366.5	1938	89.789500	893	3341	2	chr7A.!!$F5	2448
11	TraesCS7D01G550400	chr7A	731220342	731222223	1881	False	1230.5	1411	90.861000	1490	3341	2	chr7A.!!$F7	1851
12	TraesCS7D01G550400	chr7A	675021924	675027108	5184	False	986.0	1417	82.851500	959	3154	2	chr7A.!!$F1	2195
13	TraesCS7D01G550400	chr7A	731012480	731014251	1771	False	950.5	981	88.310500	2450	3303	2	chr7A.!!$F2	853
14	TraesCS7D01G550400	chr7A	731505188	731506620	1432	True	946.5	1303	91.750000	1513	2921	2	chr7A.!!$R4	1408
15	TraesCS7D01G550400	chr7A	731429764	731430374	610	True	848.0	848	91.896000	2738	3344	1	chr7A.!!$R2	606
16	TraesCS7D01G550400	chr7B	741482087	741483584	1497	False	1570.0	1570	85.696000	915	2443	1	chr7B.!!$F2	1528
17	TraesCS7D01G550400	chr7B	741623002	741624990	1988	True	1095.5	1655	87.865000	951	2883	2	chr7B.!!$R1	1932
18	TraesCS7D01G550400	chr7B	741541527	741543718	2191	False	557.0	612	92.347333	1023	3341	3	chr7B.!!$F3	2318

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
948	972	0.965866	TCACTGGTCGCTCCCACTAG	60.966	60.0	0.0	0.0	34.77	2.57	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2792	5257	0.521291	GGAGTTAAGCATGCACGCAA	59.479	50.0	21.98	4.82	0.0	4.85	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
110	111	3.098636	GGCGAACATTTCTTGAATACGC	58.901	45.455	0.00	0.00	40.13	4.42
135	136	7.043059	GCGAACATTTTTGTCCTGAACATTTTA	60.043	33.333	0.00	0.00	37.82	1.52
172	173	5.342433	ACATTGTTTGAATATGCGGACATG	58.658	37.500	0.00	0.00	37.04	3.21
184	185	7.807977	ATATGCGGACATGTTTTCTAATTCT	57.192	32.000	0.00	0.00	37.04	2.40
191	192	8.400947	CGGACATGTTTTCTAATTCTTGATGAT	58.599	33.333	0.00	0.00	0.00	2.45
432	436	9.987272	ATGGAAAATGAAAAAGGAGAAGTAAAG	57.013	29.630	0.00	0.00	0.00	1.85
526	534	4.547367	GATCCCTGGCCCGAACCG	62.547	72.222	0.00	0.00	0.00	4.44
546	554	3.047735	CCAAAAAGTGGGTCCCGC	58.952	61.111	14.16	14.16	44.64	6.13
569	577	3.146182	GCATCGGCCTCTCCTGAT	58.854	61.111	0.00	0.00	0.00	2.90
582	590	1.773391	CCTGATGCATCCCCCTCCT	60.773	63.158	23.67	0.00	0.00	3.69
591	599	1.698532	CATCCCCCTCCTCAATCTCTG	59.301	57.143	0.00	0.00	0.00	3.35
638	646	2.137523	CATGCCCAAGAAAACAAGTGC	58.862	47.619	0.00	0.00	0.00	4.40
673	681	2.037136	CGAGCACCTCCAAAGCCTG	61.037	63.158	0.00	0.00	0.00	4.85
694	702	1.339291	CTCAGCAGATCCGTGAGCATA	59.661	52.381	4.19	0.00	31.83	3.14
717	725	1.538047	GCACCAAATCTGCTTCTCCA	58.462	50.000	0.00	0.00	0.00	3.86
750	758	7.602265	CGGATTGATTCCAAAAGGTAAAACATT	59.398	33.333	0.00	0.00	45.78	2.71
766	774	8.458052	GGTAAAACATTCACATGTACATGATGA	58.542	33.333	36.36	29.62	43.34	2.92
815	823	4.569719	AGCCCCTTTTATATATCCCACG	57.430	45.455	0.00	0.00	0.00	4.94
926	940	1.203063	AGCTCACTGTCCCACTCACTA	60.203	52.381	0.00	0.00	0.00	2.74
927	941	1.067495	GCTCACTGTCCCACTCACTAC	60.067	57.143	0.00	0.00	0.00	2.73
948	972	0.965866	TCACTGGTCGCTCCCACTAG	60.966	60.000	0.00	0.00	34.77	2.57
949	973	1.682684	ACTGGTCGCTCCCACTAGG	60.683	63.158	0.00	0.00	34.77	3.02
950	974	3.075005	TGGTCGCTCCCACTAGGC	61.075	66.667	0.00	0.00	34.51	3.93
956	980	1.823976	GCTCCCACTAGGCCACTAC	59.176	63.158	5.01	0.00	34.51	2.73
1114	1166	2.270205	CCTGCACATCCTTCCGCT	59.730	61.111	0.00	0.00	0.00	5.52
1201	1265	2.367202	ATGGACGTGGGCGGATTCT	61.367	57.895	0.00	0.00	43.45	2.40
1341	1408	1.111116	TCCAAGACGACGGTGAAGGT	61.111	55.000	0.00	0.00	0.00	3.50
1413	1481	0.388294	GATCCTTCTACCCCCGTTCG	59.612	60.000	0.00	0.00	0.00	3.95
1418	1486	2.363406	CTACCCCCGTTCGGTCCT	60.363	66.667	10.36	0.00	34.66	3.85
1421	1489	3.771160	CCCCCGTTCGGTCCTGAG	61.771	72.222	10.36	0.00	0.00	3.35
1567	1641	4.988716	TCGCCGTCTGTGACCCCT	62.989	66.667	0.00	0.00	0.00	4.79
1569	1643	2.642254	CGCCGTCTGTGACCCCTTA	61.642	63.158	0.00	0.00	0.00	2.69
1753	1827	1.738099	CTCTTTGTGCTCCCGTCCG	60.738	63.158	0.00	0.00	0.00	4.79
2033	2108	2.232208	CCCTTGAGATGTTTTCCCTTGC	59.768	50.000	0.00	0.00	0.00	4.01
2130	2206	0.902531	TACAGCTTCCTGGGCAGTAC	59.097	55.000	0.00	0.00	43.53	2.73
2476	2868	5.830912	TGGTTTTAAGCTGATGTTTGAGTG	58.169	37.500	0.00	0.00	0.00	3.51
2487	2879	6.865205	GCTGATGTTTGAGTGCTCTTTATTTT	59.135	34.615	0.68	0.00	0.00	1.82
2488	2880	7.383300	GCTGATGTTTGAGTGCTCTTTATTTTT	59.617	33.333	0.68	0.00	0.00	1.94
2499	2891	8.474831	AGTGCTCTTTATTTTTACCTTGTTGTT	58.525	29.630	0.00	0.00	0.00	2.83
2534	4661	7.069950	AGCATAGAGTTCACATGTTATGGTCTA	59.930	37.037	10.44	7.62	33.60	2.59
2573	4716	3.770263	TGCTTCACTGCAATAAGATGC	57.230	42.857	6.55	7.19	46.58	3.91
2587	4733	8.166061	TGCAATAAGATGCCTCTAGGATTATTT	58.834	33.333	0.00	0.00	45.83	1.40
2596	4742	5.684704	CCTCTAGGATTATTTGGAAGCACA	58.315	41.667	0.00	0.00	37.39	4.57
2659	4815	8.814038	ACTCTGTAATTTTGCAGATAGGAAAT	57.186	30.769	10.83	0.00	46.31	2.17
2677	4835	5.299949	GGAAATATTCCCATTGCATCAACC	58.700	41.667	0.00	0.00	44.30	3.77
2690	4850	4.929198	CAACCGCAGTTGCTTCAG	57.071	55.556	0.00	0.00	46.43	3.02
2770	5224	4.021016	CCTTGTCAAACTAGCTAGGACAGT	60.021	45.833	24.35	2.68	39.39	3.55
2796	5261	7.350110	AGTCAATTCATGGTTTTATTTTGCG	57.650	32.000	0.00	0.00	0.00	4.85
2803	5268	2.478134	TGGTTTTATTTTGCGTGCATGC	59.522	40.909	24.20	24.20	0.00	4.06
2838	5309	9.264719	CATGTATGTGATTGAGAATGCTAACTA	57.735	33.333	0.00	0.00	0.00	2.24
2865	5336	7.653767	AAGAAAGATTACACACTAGTTTCGG	57.346	36.000	0.00	0.00	0.00	4.30
2921	5393	2.419057	AATGGCTTTCGCGCTTGCAA	62.419	50.000	5.56	0.00	39.07	4.08
2927	5415	2.584791	CTTTCGCGCTTGCAACTTTAT	58.415	42.857	5.56	0.00	39.07	1.40
3249	6740	6.756270	AGAAATTGGGATAGGGAAATTTCCT	58.244	36.000	31.23	21.00	44.47	3.36
3341	6836	0.752658	GTTTTGGTCTTGCTTGGGCT	59.247	50.000	0.00	0.00	39.59	5.19

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
110	111	6.826893	AAATGTTCAGGACAAAAATGTTCG	57.173	33.333	0.00	0.00	42.62	3.95
135	136	9.859427	ATTCAAACAATGTTCACGATTTCATAT	57.141	25.926	0.00	0.00	0.00	1.78
478	486	3.400054	CCCTCCCTTCCCCGACAC	61.400	72.222	0.00	0.00	0.00	3.67
569	577	0.327867	AGATTGAGGAGGGGGATGCA	60.328	55.000	0.00	0.00	0.00	3.96
582	590	0.914644	CCAGCCTTCCCAGAGATTGA	59.085	55.000	0.00	0.00	0.00	2.57
652	660	1.743252	GCTTTGGAGGTGCTCGAGG	60.743	63.158	15.58	0.00	0.00	4.63
673	681	4.416533	CTCACGGATCTGCTGAGC	57.583	61.111	16.25	0.00	0.00	4.26
686	694	0.878416	TTTGGTGCCGTTATGCTCAC	59.122	50.000	0.00	0.00	0.00	3.51
694	702	0.598065	GAAGCAGATTTGGTGCCGTT	59.402	50.000	0.00	0.00	42.24	4.44
750	758	4.515361	TGCACATCATCATGTACATGTGA	58.485	39.130	30.03	28.75	46.08	3.58
795	803	3.617284	CCGTGGGATATATAAAAGGGGC	58.383	50.000	0.00	0.00	0.00	5.80
806	814	5.067283	GTGTTAAATTTCAGCCGTGGGATAT	59.933	40.000	0.00	0.00	0.00	1.63
815	823	8.863049	CATAAATCTGTGTGTTAAATTTCAGCC	58.137	33.333	0.00	0.00	0.00	4.85
927	941	2.997315	TGGGAGCGACCAGTGAGG	60.997	66.667	0.00	0.00	45.67	3.86
948	972	4.056584	GGGTTGGGGGTAGTGGCC	62.057	72.222	0.00	0.00	0.00	5.36
949	973	1.209523	TTAGGGTTGGGGGTAGTGGC	61.210	60.000	0.00	0.00	0.00	5.01
950	974	0.622136	GTTAGGGTTGGGGGTAGTGG	59.378	60.000	0.00	0.00	0.00	4.00
956	980	3.352748	GGGGGTTAGGGTTGGGGG	61.353	72.222	0.00	0.00	0.00	5.40
1114	1166	3.561429	GCGACCTTTGATGACGCA	58.439	55.556	0.00	0.00	46.75	5.24
1335	1402	4.069232	CGCCAGCGAGGACCTTCA	62.069	66.667	6.06	0.00	42.83	3.02
1413	1481	1.331399	GGTAGCTCCACCTCAGGACC	61.331	65.000	0.00	0.00	35.55	4.46
1418	1486	2.363795	CCGGGTAGCTCCACCTCA	60.364	66.667	5.65	0.00	38.73	3.86
1421	1489	1.684734	TCTTCCGGGTAGCTCCACC	60.685	63.158	0.00	0.00	38.11	4.61
1567	1641	3.118775	AGCAACACGTATCTGCTGGATAA	60.119	43.478	15.15	0.00	44.56	1.75
1569	1643	1.208052	AGCAACACGTATCTGCTGGAT	59.792	47.619	15.15	0.00	44.56	3.41
2033	2108	2.350772	GCAAAGGATCCGTGTTGACTTG	60.351	50.000	22.59	8.86	0.00	3.16
2130	2206	2.094078	ACCGATTGTGCAAATGGAATGG	60.094	45.455	11.18	0.00	0.00	3.16
2392	2485	2.833794	TGCGAGTAGAACAAGCAAAGT	58.166	42.857	0.00	0.00	31.80	2.66
2443	2536	4.022935	TCAGCTTAAAACCATCAACTGCAG	60.023	41.667	13.48	13.48	0.00	4.41
2446	2539	6.017400	ACATCAGCTTAAAACCATCAACTG	57.983	37.500	0.00	0.00	0.00	3.16
2499	2891	7.229306	ACATGTGAACTCTATGCTCTTGAAAAA	59.771	33.333	0.00	0.00	0.00	1.94
2573	4716	5.684704	TGTGCTTCCAAATAATCCTAGAGG	58.315	41.667	0.00	0.00	0.00	3.69
2596	4742	3.988819	TGAAAGGCGCAAAAGCTTATTT	58.011	36.364	10.83	0.00	37.29	1.40
2659	4815	1.680735	GCGGTTGATGCAATGGGAATA	59.319	47.619	0.00	0.00	0.00	1.75
2770	5224	8.920665	CGCAAAATAAAACCATGAATTGACTAA	58.079	29.630	0.00	0.00	0.00	2.24
2792	5257	0.521291	GGAGTTAAGCATGCACGCAA	59.479	50.000	21.98	4.82	0.00	4.85
2796	5261	2.094675	ACATGGGAGTTAAGCATGCAC	58.905	47.619	21.98	9.67	0.00	4.57
2803	5268	7.275183	TCTCAATCACATACATGGGAGTTAAG	58.725	38.462	0.00	0.00	44.55	1.85
2838	5309	9.931210	CGAAACTAGTGTGTAATCTTTCTTTTT	57.069	29.630	0.00	0.00	0.00	1.94
2865	5336	4.701956	TGGAGCAATAAAAACTAGCTGC	57.298	40.909	0.00	0.00	42.89	5.25
2921	5393	8.517062	ACTAACGATGTACTCCTACATAAAGT	57.483	34.615	0.00	0.00	42.66	2.66
2927	5415	7.278135	AGTATGACTAACGATGTACTCCTACA	58.722	38.462	0.00	0.00	37.28	2.74
3295	6790	0.179105	AAGCGAGCTCAGATCTGCAG	60.179	55.000	18.36	15.95	0.00	4.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.