AutoCloner

Multiple sequence alignment - TraesCS7D01G448200

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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	TraesCS7D01G448200	chr7D	100.000	2510	0	0	1	2510	568236745	568234236	0.000000e+00	4636
1	TraesCS7D01G448200	chr7D	84.478	1340	177	24	580	1896	568185804	568184473	0.000000e+00	1293
2	TraesCS7D01G448200	chr7B	91.809	2051	138	18	477	2510	623059775	623057738	0.000000e+00	2830
3	TraesCS7D01G448200	chr7B	91.172	2039	126	24	477	2503	623102520	623100524	0.000000e+00	2719
4	TraesCS7D01G448200	chr7B	92.853	1861	104	17	478	2322	623271368	623269521	0.000000e+00	2673
5	TraesCS7D01G448200	chr7B	92.759	1740	90	22	478	2198	623485774	623484052	0.000000e+00	2483
6	TraesCS7D01G448200	chr7B	92.332	1291	80	12	1224	2503	586929659	586930941	0.000000e+00	1818
7	TraesCS7D01G448200	chr7B	92.606	1109	66	9	1404	2503	623522372	623521271	0.000000e+00	1580
8	TraesCS7D01G448200	chr7B	92.370	1114	71	8	1404	2510	623504495	623503389	0.000000e+00	1574
9	TraesCS7D01G448200	chr7B	92.108	1115	73	9	1404	2510	623536811	623535704	0.000000e+00	1557
10	TraesCS7D01G448200	chr7B	91.722	1051	64	12	478	1508	623373475	623372428	0.000000e+00	1437
11	TraesCS7D01G448200	chr7B	92.865	911	57	5	487	1390	623537790	623536881	0.000000e+00	1315
12	TraesCS7D01G448200	chr7B	92.341	927	55	10	477	1390	623523351	623522428	0.000000e+00	1304
13	TraesCS7D01G448200	chr7B	91.026	858	48	8	1521	2367	623566419	623565580	0.000000e+00	1131
14	TraesCS7D01G448200	chr7B	91.099	764	49	8	1561	2322	623372415	623371669	0.000000e+00	1016
15	TraesCS7D01G448200	chr7B	92.364	681	37	10	477	1146	623540027	623539351	0.000000e+00	955
16	TraesCS7D01G448200	chr7B	92.444	675	37	9	477	1140	623508239	623507568	0.000000e+00	952
17	TraesCS7D01G448200	chr7B	92.696	575	38	2	4	574	623506472	623505898	0.000000e+00	826
18	TraesCS7D01G448200	chr7B	92.683	574	37	3	4	574	623523921	623523350	0.000000e+00	822
19	TraesCS7D01G448200	chr7B	92.522	575	37	3	4	574	623540598	623540026	0.000000e+00	819
20	TraesCS7D01G448200	chr7B	92.348	575	38	3	4	574	623508810	623508238	0.000000e+00	813
21	TraesCS7D01G448200	chr7B	92.188	576	41	2	1	574	623486421	623485848	0.000000e+00	811
22	TraesCS7D01G448200	chr7B	92.443	569	40	2	7	574	623538359	623537793	0.000000e+00	809
23	TraesCS7D01G448200	chr7B	91.581	582	41	4	1	574	623103116	623102535	0.000000e+00	797
24	TraesCS7D01G448200	chr7B	91.638	574	46	1	1	574	623374072	623373501	0.000000e+00	793
25	TraesCS7D01G448200	chr7B	90.674	579	47	4	1	574	623272136	623271560	0.000000e+00	763
26	TraesCS7D01G448200	chr7B	89.342	319	34	0	2192	2510	623473095	623472777	3.890000e-108	401
27	TraesCS7D01G448200	chr7B	88.940	217	24	0	2287	2503	623371665	623371449	4.120000e-68	268
28	TraesCS7D01G448200	chr7B	83.186	226	17	2	2286	2510	623269518	623269313	1.190000e-43	187

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	TraesCS7D01G448200	chr7D	568234236	568236745	2509	True	4636.000000	4636	100.000000	1	2510	1	chr7D.!!$R2	2509
1	TraesCS7D01G448200	chr7D	568184473	568185804	1331	True	1293.000000	1293	84.478000	580	1896	1	chr7D.!!$R1	1316
2	TraesCS7D01G448200	chr7B	623057738	623059775	2037	True	2830.000000	2830	91.809000	477	2510	1	chr7B.!!$R1	2033
3	TraesCS7D01G448200	chr7B	586929659	586930941	1282	False	1818.000000	1818	92.332000	1224	2503	1	chr7B.!!$F1	1279
4	TraesCS7D01G448200	chr7B	623100524	623103116	2592	True	1758.000000	2719	91.376500	1	2503	2	chr7B.!!$R4	2502
5	TraesCS7D01G448200	chr7B	623484052	623486421	2369	True	1647.000000	2483	92.473500	1	2198	2	chr7B.!!$R7	2197
6	TraesCS7D01G448200	chr7B	623521271	623523921	2650	True	1235.333333	1580	92.543333	4	2503	3	chr7B.!!$R9	2499
7	TraesCS7D01G448200	chr7B	623269313	623272136	2823	True	1207.666667	2673	88.904333	1	2510	3	chr7B.!!$R5	2509
8	TraesCS7D01G448200	chr7B	623565580	623566419	839	True	1131.000000	1131	91.026000	1521	2367	1	chr7B.!!$R3	846
9	TraesCS7D01G448200	chr7B	623535704	623540598	4894	True	1091.000000	1557	92.460400	4	2510	5	chr7B.!!$R10	2506
10	TraesCS7D01G448200	chr7B	623503389	623508810	5421	True	1041.250000	1574	92.464500	4	2510	4	chr7B.!!$R8	2506
11	TraesCS7D01G448200	chr7B	623371449	623374072	2623	True	878.500000	1437	90.849750	1	2503	4	chr7B.!!$R6	2502

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
50	51	0.674895	GGTGCCGGCAGATATCCATC	60.675	60.0	33.73	14.9	0.00	3.51	F
1185	6061	0.032416	AGTACCCGCCACTCCATAGT	60.032	55.0	0.00	0.0	35.91	2.12	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1325	6201	0.246635	ATACCGACCTGCACAGTGAC	59.753	55.0	4.15	0.0	0.0	3.67	R
2397	7843	0.250234	CATCCACCTCTCCGCTTTGA	59.750	55.0	0.00	0.0	0.0	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
50	51	0.674895	GGTGCCGGCAGATATCCATC	60.675	60.000	33.73	14.90	0.00	3.51
61	62	4.561530	GCAGATATCCATCGCTAGGAACAA	60.562	45.833	0.00	0.00	38.93	2.83
62	63	4.926238	CAGATATCCATCGCTAGGAACAAC	59.074	45.833	0.00	0.00	38.93	3.32
139	140	2.619074	GCATAGTTCCTCCAAGCCAAGT	60.619	50.000	0.00	0.00	0.00	3.16
217	218	6.648310	CGAATCAGGTCGTATCTAGGTTAGTA	59.352	42.308	0.00	0.00	36.26	1.82
262	263	3.337358	TGACAATTGCATGACGTCTCAT	58.663	40.909	17.92	0.00	37.65	2.90
273	274	0.725686	ACGTCTCATCTACCGTGTCG	59.274	55.000	0.00	0.00	31.43	4.35
288	289	2.532973	CGTGTCGAATCTGAACGATTGC	60.533	50.000	11.91	6.39	42.31	3.56
307	308	8.037166	ACGATTGCTTAGATTGCATCATATCTA	58.963	33.333	2.34	2.34	40.34	1.98
688	1012	3.126001	ACTACAAGGACCACACATGTG	57.874	47.619	24.25	24.25	45.23	3.21
801	1126	2.234896	TCCACATCCATTGCCACAAT	57.765	45.000	0.00	0.00	0.00	2.71
804	1129	3.004171	CCACATCCATTGCCACAATTTG	58.996	45.455	0.00	0.00	0.00	2.32
962	3517	1.291588	CTGAGTGGCGCAGAAGTCT	59.708	57.895	10.83	0.00	33.20	3.24
1069	3626	2.094752	GCTCTCTCTTCTTGTTCGCTCT	60.095	50.000	0.00	0.00	0.00	4.09
1185	6061	0.032416	AGTACCCGCCACTCCATAGT	60.032	55.000	0.00	0.00	35.91	2.12
1325	6201	2.074230	AATGGGTTGCGCACACACAG	62.074	55.000	24.54	0.00	43.58	3.66
1365	6283	3.079078	GTCATATTTGCGCGCGCG	61.079	61.111	45.73	45.73	45.51	6.86
1381	6307	2.351097	CGCGCACACACACACAAG	60.351	61.111	8.75	0.00	0.00	3.16
1668	7047	6.393990	TGTTGTTTGCATTGGTATGATAACC	58.606	36.000	0.00	0.00	40.19	2.85
1850	7244	6.925211	TCTCGACTCTACAGAAATGAACATT	58.075	36.000	0.00	0.00	0.00	2.71
1934	7328	3.833732	AGATATTCACAGCTACGGGAGA	58.166	45.455	0.00	0.00	0.00	3.71
1978	7372	1.960689	CCGAAGGCCCAAAGAAAGAAA	59.039	47.619	0.00	0.00	46.14	2.52
2045	7447	7.970061	ACATACATGCAACATCACATTTTACTC	59.030	33.333	0.00	0.00	0.00	2.59
2066	7472	4.180817	TCCTACTCACAACAATATGCACG	58.819	43.478	0.00	0.00	0.00	5.34
2100	7506	4.576053	CACACAAATCTCACAAGAACTCCA	59.424	41.667	0.00	0.00	34.49	3.86
2124	7530	2.952310	ACTACGATCTAGCATGCTGTGA	59.048	45.455	30.42	25.37	0.00	3.58
2156	7562	2.631160	AAGTGGATCAACGTGTGGAA	57.369	45.000	0.00	0.00	0.00	3.53
2247	7653	1.437573	GCGGACTCGGTGATCATGA	59.562	57.895	0.00	0.00	36.79	3.07
2276	7682	3.398920	GATGTCACGGCCACATCG	58.601	61.111	16.43	0.00	40.53	3.84
2294	7700	2.934107	CGTCATCAAACGAACGGAAA	57.066	45.000	0.00	0.00	45.37	3.13
2375	7821	2.929592	GCTTGCATTGCCCTTTTCTGAG	60.930	50.000	6.12	0.00	0.00	3.35
2386	7832	3.614616	CCCTTTTCTGAGAACGAAGATCG	59.385	47.826	7.93	0.00	46.93	3.69
2387	7833	3.614616	CCTTTTCTGAGAACGAAGATCGG	59.385	47.826	7.93	0.00	45.59	4.18
2388	7834	3.936372	TTTCTGAGAACGAAGATCGGT	57.064	42.857	0.00	0.00	45.79	4.69
2389	7835	5.381174	TTTTCTGAGAACGAAGATCGGTA	57.619	39.130	0.00	0.00	41.51	4.02
2390	7836	5.578005	TTTCTGAGAACGAAGATCGGTAT	57.422	39.130	0.00	0.00	41.51	2.73
2391	7837	4.553756	TCTGAGAACGAAGATCGGTATG	57.446	45.455	4.66	0.00	41.51	2.39
2392	7838	3.315470	TCTGAGAACGAAGATCGGTATGG	59.685	47.826	4.66	0.00	41.51	2.74
2393	7839	2.361119	TGAGAACGAAGATCGGTATGGG	59.639	50.000	4.66	0.00	41.51	4.00
2394	7840	2.361438	GAGAACGAAGATCGGTATGGGT	59.639	50.000	4.66	0.00	41.51	4.51
2395	7841	2.764572	AGAACGAAGATCGGTATGGGTT	59.235	45.455	4.66	0.00	41.51	4.11
2396	7842	2.596904	ACGAAGATCGGTATGGGTTG	57.403	50.000	4.66	0.00	45.59	3.77
2397	7843	1.829222	ACGAAGATCGGTATGGGTTGT	59.171	47.619	4.66	0.00	45.59	3.32
2398	7844	2.159142	ACGAAGATCGGTATGGGTTGTC	60.159	50.000	4.66	0.00	45.59	3.18
2399	7845	2.159156	CGAAGATCGGTATGGGTTGTCA	60.159	50.000	0.00	0.00	36.00	3.58
2400	7846	3.677700	CGAAGATCGGTATGGGTTGTCAA	60.678	47.826	0.00	0.00	36.00	3.18
2401	7847	3.992943	AGATCGGTATGGGTTGTCAAA	57.007	42.857	0.00	0.00	0.00	2.69
2402	7848	3.873910	AGATCGGTATGGGTTGTCAAAG	58.126	45.455	0.00	0.00	0.00	2.77
2403	7849	1.816074	TCGGTATGGGTTGTCAAAGC	58.184	50.000	0.00	0.00	0.00	3.51
2404	7850	0.446222	CGGTATGGGTTGTCAAAGCG	59.554	55.000	0.00	0.00	34.50	4.68
2405	7851	0.808755	GGTATGGGTTGTCAAAGCGG	59.191	55.000	0.00	0.00	34.50	5.52
2418	7884	1.201429	AAAGCGGAGAGGTGGATGGT	61.201	55.000	0.00	0.00	0.00	3.55
2429	7895	2.242196	AGGTGGATGGTACAATTCCAGG	59.758	50.000	10.05	0.00	46.69	4.45
2440	7906	8.096621	TGGTACAATTCCAGGATAGAAACATA	57.903	34.615	0.00	0.00	31.92	2.29

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
50	51	2.388232	GCCACGGTTGTTCCTAGCG	61.388	63.158	0.00	0.00	41.83	4.26
61	62	2.434884	CTCAGCATTCGCCACGGT	60.435	61.111	0.00	0.00	39.83	4.83
62	63	1.699656	CTTCTCAGCATTCGCCACGG	61.700	60.000	0.00	0.00	39.83	4.94
153	154	2.083774	GCAGTCCATCGATTGTTCCAA	58.916	47.619	0.00	0.00	0.00	3.53
159	160	3.441163	CCAATTTGCAGTCCATCGATTG	58.559	45.455	0.00	0.00	0.00	2.67
217	218	7.920151	TCAAAATCATGATCGTGTTTCTTTGTT	59.080	29.630	14.52	1.65	0.00	2.83
262	263	2.159612	CGTTCAGATTCGACACGGTAGA	60.160	50.000	0.00	0.00	0.00	2.59
273	274	5.906285	GCAATCTAAGCAATCGTTCAGATTC	59.094	40.000	0.00	0.00	45.95	2.52
355	361	9.672673	ACGATCTATTAATAAATCCCTTGGATG	57.327	33.333	3.68	0.00	42.27	3.51
443	449	9.720769	ATAACGGACTCCCTACATATTAAAATG	57.279	33.333	0.00	0.00	0.00	2.32
570	894	7.854916	GGTAACGGATATGTAGATAAGCGTATC	59.145	40.741	11.25	11.25	37.04	2.24
574	898	5.946298	TGGTAACGGATATGTAGATAAGCG	58.054	41.667	0.00	0.00	42.51	4.68
651	975	9.613428	TCCTTGTAGTATCAAATTGATGGTAAG	57.387	33.333	17.93	13.29	37.70	2.34
660	984	6.539173	TGTGTGGTCCTTGTAGTATCAAATT	58.461	36.000	0.00	0.00	0.00	1.82
663	987	5.012664	ACATGTGTGGTCCTTGTAGTATCAA	59.987	40.000	0.00	0.00	0.00	2.57
801	1126	8.668353	GTTTGCACATCTAGATCTTGTATCAAA	58.332	33.333	1.03	10.20	0.00	2.69
804	1129	7.776933	TGTTTGCACATCTAGATCTTGTATC	57.223	36.000	1.03	0.00	0.00	2.24
868	1193	7.494625	TCGATCGCTTAATTGGACTCTTTTAAT	59.505	33.333	11.09	0.00	0.00	1.40
962	3517	4.522405	AGCACTTGGTATGTGTTTATGCAA	59.478	37.500	0.00	0.00	37.70	4.08
1325	6201	0.246635	ATACCGACCTGCACAGTGAC	59.753	55.000	4.15	0.00	0.00	3.67
1365	6283	2.651863	GCTTGTGTGTGTGTGCGC	60.652	61.111	0.00	0.00	0.00	6.09
1668	7047	7.502120	AAATCCTATGAATCAATGAGAACCG	57.498	36.000	0.00	0.00	0.00	4.44
1923	7317	2.040178	CCCTTATGTTCTCCCGTAGCT	58.960	52.381	0.00	0.00	0.00	3.32
1934	7328	5.949952	GTGTCACCTTATTTCCCCTTATGTT	59.050	40.000	0.00	0.00	0.00	2.71
2026	7428	6.237901	AGTAGGAGTAAAATGTGATGTTGCA	58.762	36.000	0.00	0.00	0.00	4.08
2045	7447	3.242413	GCGTGCATATTGTTGTGAGTAGG	60.242	47.826	0.00	0.00	0.00	3.18
2066	7472	5.117592	GTGAGATTTGTGTGCTTAAACATGC	59.882	40.000	0.00	0.00	31.49	4.06
2100	7506	1.959985	AGCATGCTAGATCGTAGTGCT	59.040	47.619	21.21	8.99	36.69	4.40
2124	7530	2.177580	CCACTTTCGTGCACACCGT	61.178	57.895	18.64	4.96	39.86	4.83
2156	7562	3.525800	AGCTCCATTTACACCAACCTT	57.474	42.857	0.00	0.00	0.00	3.50
2276	7682	2.219216	TCGTTTCCGTTCGTTTGATGAC	59.781	45.455	0.00	0.00	35.01	3.06
2357	7803	2.291209	TCTCAGAAAAGGGCAATGCA	57.709	45.000	7.79	0.00	0.00	3.96
2375	7821	2.864343	CAACCCATACCGATCTTCGTTC	59.136	50.000	0.00	0.00	38.40	3.95
2386	7832	0.808755	CCGCTTTGACAACCCATACC	59.191	55.000	0.00	0.00	0.00	2.73
2387	7833	1.737793	CTCCGCTTTGACAACCCATAC	59.262	52.381	0.00	0.00	0.00	2.39
2388	7834	1.626321	TCTCCGCTTTGACAACCCATA	59.374	47.619	0.00	0.00	0.00	2.74
2389	7835	0.400213	TCTCCGCTTTGACAACCCAT	59.600	50.000	0.00	0.00	0.00	4.00
2390	7836	0.250295	CTCTCCGCTTTGACAACCCA	60.250	55.000	0.00	0.00	0.00	4.51
2391	7837	0.955919	CCTCTCCGCTTTGACAACCC	60.956	60.000	0.00	0.00	0.00	4.11
2392	7838	0.250338	ACCTCTCCGCTTTGACAACC	60.250	55.000	0.00	0.00	0.00	3.77
2393	7839	0.868406	CACCTCTCCGCTTTGACAAC	59.132	55.000	0.00	0.00	0.00	3.32
2394	7840	0.250295	CCACCTCTCCGCTTTGACAA	60.250	55.000	0.00	0.00	0.00	3.18
2395	7841	1.118965	TCCACCTCTCCGCTTTGACA	61.119	55.000	0.00	0.00	0.00	3.58
2396	7842	0.250513	ATCCACCTCTCCGCTTTGAC	59.749	55.000	0.00	0.00	0.00	3.18
2397	7843	0.250234	CATCCACCTCTCCGCTTTGA	59.750	55.000	0.00	0.00	0.00	2.69
2398	7844	0.745845	CCATCCACCTCTCCGCTTTG	60.746	60.000	0.00	0.00	0.00	2.77
2399	7845	1.201429	ACCATCCACCTCTCCGCTTT	61.201	55.000	0.00	0.00	0.00	3.51
2400	7846	0.325296	TACCATCCACCTCTCCGCTT	60.325	55.000	0.00	0.00	0.00	4.68
2401	7847	1.043673	GTACCATCCACCTCTCCGCT	61.044	60.000	0.00	0.00	0.00	5.52
2402	7848	1.327690	TGTACCATCCACCTCTCCGC	61.328	60.000	0.00	0.00	0.00	5.54
2403	7849	1.191535	TTGTACCATCCACCTCTCCG	58.808	55.000	0.00	0.00	0.00	4.63
2404	7850	3.433740	GGAATTGTACCATCCACCTCTCC	60.434	52.174	4.33	0.00	33.30	3.71
2405	7851	3.199946	TGGAATTGTACCATCCACCTCTC	59.800	47.826	7.15	0.00	38.30	3.20
2440	7906	7.759886	CCAATGTATATCGTTTCGGTGATAGAT	59.240	37.037	0.00	0.00	31.10	1.98

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.