AutoCloner

Multiple sequence alignment - TraesCS5A01G389600

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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	TraesCS5A01G389600	chr5A	100.000	2441	0	0	1	2441	585423855	585421415	0.000000e+00	4508.0
1	TraesCS5A01G389600	chr3A	98.415	2271	35	1	1	2271	40289298	40287029	0.000000e+00	3993.0
2	TraesCS5A01G389600	chr3A	83.281	1597	243	17	1	1593	309005171	309006747	0.000000e+00	1448.0
3	TraesCS5A01G389600	chr3B	95.725	2269	66	8	1	2268	718683879	718686117	0.000000e+00	3624.0
4	TraesCS5A01G389600	chr3B	94.825	1681	79	3	1	1674	752380848	752382527	0.000000e+00	2615.0
5	TraesCS5A01G389600	chr3B	95.070	1582	68	3	1	1582	296063236	296061665	0.000000e+00	2481.0
6	TraesCS5A01G389600	chr3B	94.216	1072	52	3	511	1582	20829463	20828402	0.000000e+00	1628.0
7	TraesCS5A01G389600	chr3B	94.952	416	18	2	1857	2271	296061329	296060916	0.000000e+00	649.0
8	TraesCS5A01G389600	chr5B	95.062	2268	89	1	1	2268	599324817	599327061	0.000000e+00	3546.0
9	TraesCS5A01G389600	chr5B	94.928	138	7	0	2272	2409	572364492	572364355	1.470000e-52	217.0
10	TraesCS5A01G389600	chr5B	89.855	138	14	0	2272	2409	572390783	572390646	6.940000e-41	178.0
11	TraesCS5A01G389600	chr5B	100.000	38	0	0	2380	2417	572379301	572379264	1.210000e-08	71.3
12	TraesCS5A01G389600	chr2B	91.103	1551	126	6	1	1548	678014479	678016020	0.000000e+00	2089.0
13	TraesCS5A01G389600	chr4B	95.680	1250	52	2	1022	2271	14571825	14570578	0.000000e+00	2008.0
14	TraesCS5A01G389600	chr4B	93.780	1254	58	8	1019	2271	80008967	80007733	0.000000e+00	1866.0
15	TraesCS5A01G389600	chr2D	96.446	1210	42	1	1071	2280	591541901	591540693	0.000000e+00	1995.0
16	TraesCS5A01G389600	chr2D	97.980	198	4	0	882	1079	591547411	591547214	6.460000e-91	344.0
17	TraesCS5A01G389600	chr2A	96.501	543	19	0	1729	2271	570149245	570148703	0.000000e+00	898.0
18	TraesCS5A01G389600	chr6D	95.262	401	19	0	1679	2079	446644219	446643819	9.520000e-179	636.0
19	TraesCS5A01G389600	chr7B	97.059	374	11	0	1627	2000	592742026	592741653	4.430000e-177	630.0
20	TraesCS5A01G389600	chr5D	97.945	146	3	0	2272	2417	465022488	465022343	1.120000e-63	254.0
21	TraesCS5A01G389600	chr5D	96.269	134	5	0	2272	2405	465012696	465012563	1.140000e-53	220.0

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	TraesCS5A01G389600	chr5A	585421415	585423855	2440	True	4508	4508	100.000	1	2441	1	chr5A.!!$R1	2440
1	TraesCS5A01G389600	chr3A	40287029	40289298	2269	True	3993	3993	98.415	1	2271	1	chr3A.!!$R1	2270
2	TraesCS5A01G389600	chr3A	309005171	309006747	1576	False	1448	1448	83.281	1	1593	1	chr3A.!!$F1	1592
3	TraesCS5A01G389600	chr3B	718683879	718686117	2238	False	3624	3624	95.725	1	2268	1	chr3B.!!$F1	2267
4	TraesCS5A01G389600	chr3B	752380848	752382527	1679	False	2615	2615	94.825	1	1674	1	chr3B.!!$F2	1673
5	TraesCS5A01G389600	chr3B	20828402	20829463	1061	True	1628	1628	94.216	511	1582	1	chr3B.!!$R1	1071
6	TraesCS5A01G389600	chr3B	296060916	296063236	2320	True	1565	2481	95.011	1	2271	2	chr3B.!!$R2	2270
7	TraesCS5A01G389600	chr5B	599324817	599327061	2244	False	3546	3546	95.062	1	2268	1	chr5B.!!$F1	2267
8	TraesCS5A01G389600	chr2B	678014479	678016020	1541	False	2089	2089	91.103	1	1548	1	chr2B.!!$F1	1547
9	TraesCS5A01G389600	chr4B	14570578	14571825	1247	True	2008	2008	95.680	1022	2271	1	chr4B.!!$R1	1249
10	TraesCS5A01G389600	chr4B	80007733	80008967	1234	True	1866	1866	93.780	1019	2271	1	chr4B.!!$R2	1252
11	TraesCS5A01G389600	chr2D	591540693	591541901	1208	True	1995	1995	96.446	1071	2280	1	chr2D.!!$R1	1209
12	TraesCS5A01G389600	chr2A	570148703	570149245	542	True	898	898	96.501	1729	2271	1	chr2A.!!$R1	542

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
706	709	1.067425	TGGCTGAATCTGCATGCAAAC	60.067	47.619	22.88	13.04	0.0	2.93	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2418	2546	0.105039	GGCCGAGTTCATAGAGTGGG	59.895	60.0	0.0	0.0	0.0	4.61	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
147	149	2.086869	ACCTGCCACTTGATTGATTCG	58.913	47.619	0.00	0.00	0.00	3.34
499	502	3.152341	AGTTCACAATCAAGAGGCCAAG	58.848	45.455	5.01	0.00	0.00	3.61
706	709	1.067425	TGGCTGAATCTGCATGCAAAC	60.067	47.619	22.88	13.04	0.00	2.93
739	742	5.815222	GGATTTTACACAGCAACCAAACTTT	59.185	36.000	0.00	0.00	0.00	2.66
929	932	4.390264	TGTGTTCCGGTTGTATTTGATCA	58.610	39.130	0.00	0.00	0.00	2.92
998	1002	7.395772	TGGAAGTGAAATTGAAGCCAATACATA	59.604	33.333	0.00	0.00	41.84	2.29
1093	1097	3.107601	CAAGAGGATTGTGGGAGTCCTA	58.892	50.000	9.58	0.00	42.27	2.94
1199	1205	5.188434	TGAGCTGGATCAGTATTTGAAAGG	58.812	41.667	0.00	0.00	39.77	3.11
1321	1330	0.319083	TATTTCTGCGTCCACGGTGT	59.681	50.000	7.45	0.00	40.23	4.16
1709	1726	2.633967	TGCAAAATGTTCATCTGCCCTT	59.366	40.909	13.46	0.00	31.92	3.95
2050	2178	9.770097	CAGATTATGTACTTGTTGTATCCTGAT	57.230	33.333	0.00	0.00	33.23	2.90
2115	2243	5.907207	TGCTCTATCCTGACATGTACTTTC	58.093	41.667	0.00	0.00	0.00	2.62
2121	2249	8.851145	TCTATCCTGACATGTACTTTCTGTATC	58.149	37.037	0.00	0.00	33.23	2.24
2256	2384	0.681887	TGGGACTTCCGCGTCTCATA	60.682	55.000	4.92	0.00	39.38	2.15
2268	2396	1.672737	CGTCTCATACCACTTGCAGCA	60.673	52.381	0.00	0.00	0.00	4.41
2271	2399	1.674441	CTCATACCACTTGCAGCATGG	59.326	52.381	12.80	12.80	39.57	3.66
2273	2401	2.093890	CATACCACTTGCAGCATGGAA	58.906	47.619	20.09	0.00	47.00	3.53
2278	2406	4.100479	TTGCAGCATGGAAGGTGG	57.900	55.556	0.00	0.00	43.23	4.61
2279	2407	1.153524	TTGCAGCATGGAAGGTGGT	59.846	52.632	0.00	0.00	43.23	4.16
2280	2408	1.180456	TTGCAGCATGGAAGGTGGTG	61.180	55.000	0.00	1.31	43.23	4.17
2281	2409	2.345760	GCAGCATGGAAGGTGGTGG	61.346	63.158	7.33	0.00	43.35	4.61
2282	2410	1.075482	CAGCATGGAAGGTGGTGGT	59.925	57.895	0.00	0.00	40.41	4.16
2283	2411	1.075482	AGCATGGAAGGTGGTGGTG	59.925	57.895	0.00	0.00	0.00	4.17
2284	2412	1.978617	GCATGGAAGGTGGTGGTGG	60.979	63.158	0.00	0.00	0.00	4.61
2285	2413	1.978617	CATGGAAGGTGGTGGTGGC	60.979	63.158	0.00	0.00	0.00	5.01
2286	2414	3.224007	ATGGAAGGTGGTGGTGGCC	62.224	63.158	0.00	0.00	0.00	5.36
2288	2416	4.265056	GAAGGTGGTGGTGGCCGT	62.265	66.667	0.00	0.00	0.00	5.68
2289	2417	4.579384	AAGGTGGTGGTGGCCGTG	62.579	66.667	0.00	0.00	0.00	4.94
2304	2432	4.838486	GTGGACGCGAGCGAGGAG	62.838	72.222	24.72	0.00	42.83	3.69
2306	2434	4.244802	GGACGCGAGCGAGGAGAG	62.245	72.222	24.72	0.00	42.83	3.20
2307	2435	4.897856	GACGCGAGCGAGGAGAGC	62.898	72.222	24.72	0.84	42.83	4.09
2309	2437	4.263209	CGCGAGCGAGGAGAGCAT	62.263	66.667	12.58	0.00	42.83	3.79
2310	2438	2.657944	GCGAGCGAGGAGAGCATG	60.658	66.667	0.00	0.00	37.01	4.06
2311	2439	2.657944	CGAGCGAGGAGAGCATGC	60.658	66.667	10.51	10.51	37.01	4.06
2312	2440	2.498248	GAGCGAGGAGAGCATGCA	59.502	61.111	21.98	0.00	37.01	3.96
2313	2441	1.882167	GAGCGAGGAGAGCATGCAC	60.882	63.158	21.98	14.59	37.01	4.57
2314	2442	3.260483	GCGAGGAGAGCATGCACG	61.260	66.667	21.98	15.11	36.45	5.34
2315	2443	3.260483	CGAGGAGAGCATGCACGC	61.260	66.667	21.98	15.75	0.00	5.34
2316	2444	3.260483	GAGGAGAGCATGCACGCG	61.260	66.667	21.98	3.53	36.85	6.01
2319	2447	4.219846	GAGAGCATGCACGCGCTG	62.220	66.667	17.49	5.02	42.48	5.18
2321	2449	4.511443	GAGCATGCACGCGCTGTC	62.511	66.667	21.98	1.57	38.99	3.51
2376	2504	4.808238	GCGTCCGTCGTCGTCCTC	62.808	72.222	0.71	0.00	42.13	3.71
2377	2505	4.157958	CGTCCGTCGTCGTCCTCC	62.158	72.222	0.71	0.00	35.01	4.30
2378	2506	3.052082	GTCCGTCGTCGTCCTCCA	61.052	66.667	0.71	0.00	35.01	3.86
2379	2507	3.052082	TCCGTCGTCGTCCTCCAC	61.052	66.667	0.71	0.00	35.01	4.02
2409	2537	3.593794	GTCGACCGCTCCGCCTAT	61.594	66.667	3.51	0.00	0.00	2.57
2410	2538	3.592814	TCGACCGCTCCGCCTATG	61.593	66.667	0.00	0.00	0.00	2.23
2411	2539	4.647615	CGACCGCTCCGCCTATGG	62.648	72.222	0.00	0.00	0.00	2.74
2412	2540	3.537874	GACCGCTCCGCCTATGGT	61.538	66.667	0.00	0.00	35.14	3.55
2413	2541	2.123597	ACCGCTCCGCCTATGGTA	60.124	61.111	0.00	0.00	0.00	3.25
2414	2542	2.338984	CCGCTCCGCCTATGGTAC	59.661	66.667	0.00	0.00	0.00	3.34
2415	2543	2.338984	CGCTCCGCCTATGGTACC	59.661	66.667	4.43	4.43	0.00	3.34
2416	2544	2.495409	CGCTCCGCCTATGGTACCA	61.495	63.158	18.99	18.99	0.00	3.25
2417	2545	1.827394	GCTCCGCCTATGGTACCAA	59.173	57.895	20.76	7.62	0.00	3.67
2418	2546	0.532196	GCTCCGCCTATGGTACCAAC	60.532	60.000	20.76	8.06	0.00	3.77
2419	2547	0.106149	CTCCGCCTATGGTACCAACC	59.894	60.000	20.76	6.54	46.98	3.77
2420	2548	1.147600	CCGCCTATGGTACCAACCC	59.852	63.158	20.76	6.90	46.16	4.11
2421	2549	1.628238	CCGCCTATGGTACCAACCCA	61.628	60.000	20.76	3.69	46.16	4.51
2422	2550	0.463116	CGCCTATGGTACCAACCCAC	60.463	60.000	20.76	6.95	46.16	4.61
2423	2551	0.916809	GCCTATGGTACCAACCCACT	59.083	55.000	20.76	3.33	46.16	4.00
2424	2552	1.134189	GCCTATGGTACCAACCCACTC	60.134	57.143	20.76	0.99	46.16	3.51
2425	2553	2.478292	CCTATGGTACCAACCCACTCT	58.522	52.381	20.76	1.65	46.16	3.24
2426	2554	3.649843	CCTATGGTACCAACCCACTCTA	58.350	50.000	20.76	2.91	46.16	2.43
2427	2555	4.232091	CCTATGGTACCAACCCACTCTAT	58.768	47.826	20.76	0.00	46.16	1.98
2428	2556	4.040461	CCTATGGTACCAACCCACTCTATG	59.960	50.000	20.76	0.00	46.16	2.23
2429	2557	3.193395	TGGTACCAACCCACTCTATGA	57.807	47.619	13.60	0.00	46.16	2.15
2430	2558	3.522759	TGGTACCAACCCACTCTATGAA	58.477	45.455	13.60	0.00	46.16	2.57
2431	2559	3.262405	TGGTACCAACCCACTCTATGAAC	59.738	47.826	13.60	0.00	46.16	3.18
2432	2560	3.518303	GGTACCAACCCACTCTATGAACT	59.482	47.826	7.15	0.00	40.21	3.01
2433	2561	3.983044	ACCAACCCACTCTATGAACTC	57.017	47.619	0.00	0.00	0.00	3.01
2434	2562	2.233922	ACCAACCCACTCTATGAACTCG	59.766	50.000	0.00	0.00	0.00	4.18
2435	2563	2.418746	CCAACCCACTCTATGAACTCGG	60.419	54.545	0.00	0.00	0.00	4.63
2436	2564	0.824759	ACCCACTCTATGAACTCGGC	59.175	55.000	0.00	0.00	0.00	5.54
2437	2565	0.105039	CCCACTCTATGAACTCGGCC	59.895	60.000	0.00	0.00	0.00	6.13
2438	2566	0.105039	CCACTCTATGAACTCGGCCC	59.895	60.000	0.00	0.00	0.00	5.80
2439	2567	0.249073	CACTCTATGAACTCGGCCCG	60.249	60.000	0.00	0.00	0.00	6.13
2440	2568	1.300233	CTCTATGAACTCGGCCCGC	60.300	63.158	0.00	0.00	0.00	6.13

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
169	171	7.937394	TGTCTGCATCATGAAGAATCTTATGAT	59.063	33.333	15.62	15.62	40.00	2.45
373	376	5.478332	AGACATGAGGAGCATATCGACAATA	59.522	40.000	0.00	0.00	35.56	1.90
383	386	3.996921	AGTTGAAGACATGAGGAGCAT	57.003	42.857	0.00	0.00	37.85	3.79
706	709	6.012658	TGCTGTGTAAAATCCTTTTAGCAG	57.987	37.500	13.71	13.71	39.58	4.24
739	742	5.314529	AGTCGGATACTTCGATCCAGATAA	58.685	41.667	3.80	0.00	45.08	1.75
998	1002	7.275560	GGATTGCTTTGTTTAATTTACGCATCT	59.724	33.333	0.00	0.00	0.00	2.90
1093	1097	0.324738	TCTTCATCCTCCTCGGCACT	60.325	55.000	0.00	0.00	0.00	4.40
1321	1330	4.281182	AGAACTAAAAGCGGACTCAGAAGA	59.719	41.667	0.00	0.00	0.00	2.87
1521	1537	6.621613	ACGCCTTTAAATTTTTCTGGATCTC	58.378	36.000	0.00	0.00	0.00	2.75
1709	1726	9.520204	GAAACATTCATCTTTTCTTCAGAACAA	57.480	29.630	0.00	0.00	33.13	2.83
1850	1867	5.611374	TCTTCAAGTAGCAAACTAGCAACT	58.389	37.500	0.00	0.00	37.50	3.16
2083	2211	6.737720	TGTCAGGATAGAGCAAGTTCATAT	57.262	37.500	0.00	0.00	0.00	1.78
2256	2384	0.896940	CCTTCCATGCTGCAAGTGGT	60.897	55.000	18.88	0.00	35.30	4.16
2268	2396	2.440599	GCCACCACCACCTTCCAT	59.559	61.111	0.00	0.00	0.00	3.41
2271	2399	4.265056	ACGGCCACCACCACCTTC	62.265	66.667	2.24	0.00	0.00	3.46
2287	2415	4.838486	CTCCTCGCTCGCGTCCAC	62.838	72.222	5.77	0.00	40.74	4.02
2289	2417	4.244802	CTCTCCTCGCTCGCGTCC	62.245	72.222	5.77	0.00	40.74	4.79
2290	2418	4.897856	GCTCTCCTCGCTCGCGTC	62.898	72.222	5.77	0.00	40.74	5.19
2292	2420	4.263209	ATGCTCTCCTCGCTCGCG	62.263	66.667	0.00	0.00	41.35	5.87
2293	2421	2.657944	CATGCTCTCCTCGCTCGC	60.658	66.667	0.00	0.00	0.00	5.03
2294	2422	2.657944	GCATGCTCTCCTCGCTCG	60.658	66.667	11.37	0.00	0.00	5.03
2295	2423	1.882167	GTGCATGCTCTCCTCGCTC	60.882	63.158	20.33	0.00	0.00	5.03
2296	2424	2.186384	GTGCATGCTCTCCTCGCT	59.814	61.111	20.33	0.00	0.00	4.93
2297	2425	3.260483	CGTGCATGCTCTCCTCGC	61.260	66.667	20.33	0.00	0.00	5.03
2298	2426	3.260483	GCGTGCATGCTCTCCTCG	61.260	66.667	23.72	13.81	0.00	4.63
2299	2427	3.260483	CGCGTGCATGCTCTCCTC	61.260	66.667	27.33	4.01	0.00	3.71
2302	2430	4.219846	CAGCGCGTGCATGCTCTC	62.220	66.667	27.33	16.16	46.23	3.20
2304	2432	4.511443	GACAGCGCGTGCATGCTC	62.511	66.667	27.33	20.62	46.23	4.26
2359	2487	4.808238	GAGGACGACGACGGACGC	62.808	72.222	12.58	2.01	46.94	5.19
2361	2489	3.052082	TGGAGGACGACGACGGAC	61.052	66.667	12.58	3.84	44.46	4.79
2362	2490	3.052082	GTGGAGGACGACGACGGA	61.052	66.667	12.58	0.00	44.46	4.69
2400	2528	0.106149	GGTTGGTACCATAGGCGGAG	59.894	60.000	17.17	0.00	44.36	4.63
2401	2529	1.339644	GGGTTGGTACCATAGGCGGA	61.340	60.000	17.17	0.00	46.96	5.54
2402	2530	1.147600	GGGTTGGTACCATAGGCGG	59.852	63.158	17.17	0.00	46.96	6.13
2403	2531	0.463116	GTGGGTTGGTACCATAGGCG	60.463	60.000	17.17	0.00	46.96	5.52
2404	2532	0.916809	AGTGGGTTGGTACCATAGGC	59.083	55.000	17.17	6.58	46.96	3.93
2405	2533	2.478292	AGAGTGGGTTGGTACCATAGG	58.522	52.381	17.17	0.00	46.96	2.57
2406	2534	4.899457	TCATAGAGTGGGTTGGTACCATAG	59.101	45.833	17.17	0.00	46.96	2.23
2407	2535	4.886163	TCATAGAGTGGGTTGGTACCATA	58.114	43.478	17.17	2.45	46.96	2.74
2408	2536	3.731431	TCATAGAGTGGGTTGGTACCAT	58.269	45.455	17.17	0.00	46.96	3.55
2409	2537	3.193395	TCATAGAGTGGGTTGGTACCA	57.807	47.619	11.60	11.60	46.96	3.25
2410	2538	3.518303	AGTTCATAGAGTGGGTTGGTACC	59.482	47.826	4.43	4.43	44.22	3.34
2411	2539	4.677250	CGAGTTCATAGAGTGGGTTGGTAC	60.677	50.000	0.00	0.00	0.00	3.34
2412	2540	3.446161	CGAGTTCATAGAGTGGGTTGGTA	59.554	47.826	0.00	0.00	0.00	3.25
2413	2541	2.233922	CGAGTTCATAGAGTGGGTTGGT	59.766	50.000	0.00	0.00	0.00	3.67
2414	2542	2.418746	CCGAGTTCATAGAGTGGGTTGG	60.419	54.545	0.00	0.00	0.00	3.77
2415	2543	2.893637	CCGAGTTCATAGAGTGGGTTG	58.106	52.381	0.00	0.00	0.00	3.77
2416	2544	1.207329	GCCGAGTTCATAGAGTGGGTT	59.793	52.381	0.00	0.00	0.00	4.11
2417	2545	0.824759	GCCGAGTTCATAGAGTGGGT	59.175	55.000	0.00	0.00	0.00	4.51
2418	2546	0.105039	GGCCGAGTTCATAGAGTGGG	59.895	60.000	0.00	0.00	0.00	4.61
2419	2547	0.105039	GGGCCGAGTTCATAGAGTGG	59.895	60.000	0.00	0.00	0.00	4.00
2420	2548	0.249073	CGGGCCGAGTTCATAGAGTG	60.249	60.000	24.41	0.00	0.00	3.51
2421	2549	2.017559	GCGGGCCGAGTTCATAGAGT	62.018	60.000	33.44	0.00	0.00	3.24
2422	2550	1.300233	GCGGGCCGAGTTCATAGAG	60.300	63.158	33.44	0.00	0.00	2.43
2423	2551	2.812499	GCGGGCCGAGTTCATAGA	59.188	61.111	33.44	0.00	0.00	1.98

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.