AutoCloner

Multiple sequence alignment - TraesCS5B01G388400

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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	TraesCS5B01G388400	chr5B	100.000	3559	0	0	1	3559	567243117	567239559	0.000000e+00	6573.0
1	TraesCS5B01G388400	chr5B	97.743	886	18	1	2674	3559	567295821	567296704	0.000000e+00	1524.0
2	TraesCS5B01G388400	chr5B	96.753	154	5	0	2663	2816	490050494	490050341	1.270000e-64	257.0
3	TraesCS5B01G388400	chr2B	97.402	2656	55	3	1	2644	391098663	391101316	0.000000e+00	4510.0
4	TraesCS5B01G388400	chr2B	97.993	897	18	0	2663	3559	391174731	391173835	0.000000e+00	1557.0
5	TraesCS5B01G388400	chr2B	98.387	62	1	0	2756	2817	539363437	539363498	3.760000e-20	110.0
6	TraesCS5B01G388400	chr2A	97.838	2451	41	1	1	2439	755478557	755481007	0.000000e+00	4222.0
7	TraesCS5B01G388400	chr2A	87.889	289	25	5	2817	3097	69261667	69261381	7.360000e-87	331.0
8	TraesCS5B01G388400	chr2A	94.771	153	8	0	2663	2815	25257647	25257799	4.590000e-59	239.0
9	TraesCS5B01G388400	chr2A	94.771	153	8	0	2663	2815	25324108	25324260	4.590000e-59	239.0
10	TraesCS5B01G388400	chr2A	94.118	153	9	0	2663	2815	25306915	25307067	2.140000e-57	233.0
11	TraesCS5B01G388400	chr2A	96.947	131	4	0	2685	2815	25275698	25275828	1.660000e-53	220.0
12	TraesCS5B01G388400	chr7B	97.838	2451	40	2	1	2439	742950729	742948280	0.000000e+00	4220.0
13	TraesCS5B01G388400	chr7B	97.511	2451	48	2	1	2439	716782616	716785065	0.000000e+00	4176.0
14	TraesCS5B01G388400	chr7A	97.797	2451	41	2	1	2439	60170758	60168309	0.000000e+00	4215.0
15	TraesCS5B01G388400	chr7A	97.716	2277	37	4	175	2439	60083121	60085394	0.000000e+00	3903.0
16	TraesCS5B01G388400	chr5A	97.715	2451	42	3	1	2439	420183712	420186160	0.000000e+00	4204.0
17	TraesCS5B01G388400	chr5A	97.884	2410	38	2	42	2439	16542604	16545012	0.000000e+00	4156.0
18	TraesCS5B01G388400	chr5A	95.455	154	7	0	2663	2816	514406268	514406115	2.740000e-61	246.0
19	TraesCS5B01G388400	chr1B	97.389	2451	50	3	1	2439	583563539	583561091	0.000000e+00	4159.0
20	TraesCS5B01G388400	chr4D	97.266	2451	53	3	1	2439	123348131	123350579	0.000000e+00	4143.0
21	TraesCS5B01G388400	chr4D	94.476	2607	120	10	1	2592	241177508	241180105	0.000000e+00	3995.0
22	TraesCS5B01G388400	chr4D	94.574	129	7	0	2791	2919	148609217	148609089	2.170000e-47	200.0
23	TraesCS5B01G388400	chr4D	95.200	125	6	0	2754	2878	39144248	39144124	7.790000e-47	198.0
24	TraesCS5B01G388400	chr1D	97.103	2451	48	4	1	2439	275776946	275779385	0.000000e+00	4111.0
25	TraesCS5B01G388400	chr1D	94.872	78	4	0	3075	3152	199131061	199131138	4.830000e-24	122.0
26	TraesCS5B01G388400	chr7D	98.603	1575	22	0	1	1575	579039779	579041353	0.000000e+00	2787.0
27	TraesCS5B01G388400	chr7D	100.000	32	0	0	2878	2909	32321117	32321148	3.840000e-05	60.2
28	TraesCS5B01G388400	chr3D	93.645	1841	98	10	769	2595	193436111	193434276	0.000000e+00	2734.0
29	TraesCS5B01G388400	chrUn	97.270	1282	23	1	1170	2439	378555716	378556997	0.000000e+00	2163.0
30	TraesCS5B01G388400	chr2D	97.073	410	12	0	3150	3559	115464450	115464041	0.000000e+00	691.0
31	TraesCS5B01G388400	chr2D	88.837	215	19	2	2817	3027	65537957	65538170	3.520000e-65	259.0
32	TraesCS5B01G388400	chr2D	89.873	79	6	2	3021	3097	65538934	65539012	2.260000e-17	100.0
33	TraesCS5B01G388400	chr5D	98.643	221	2	1	3199	3418	72495107	72495327	1.200000e-104	390.0
34	TraesCS5B01G388400	chr5D	98.052	154	3	0	2663	2816	408481242	408481089	5.860000e-68	268.0
35	TraesCS5B01G388400	chr5D	96.512	86	2	1	3420	3505	72495379	72495463	1.330000e-29	141.0
36	TraesCS5B01G388400	chr6B	96.226	106	4	0	3328	3433	146390661	146390766	1.310000e-39	174.0
37	TraesCS5B01G388400	chr6A	98.611	72	1	0	2679	2750	401410080	401410009	1.040000e-25	128.0
38	TraesCS5B01G388400	chr6A	94.737	76	4	0	3127	3202	456484276	456484201	6.240000e-23	119.0
39	TraesCS5B01G388400	chr1A	96.154	52	2	0	3214	3265	561597208	561597259	6.330000e-13	86.1

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	TraesCS5B01G388400	chr5B	567239559	567243117	3558	True	6573	6573	100.000	1	3559	1	chr5B.!!$R2	3558
1	TraesCS5B01G388400	chr5B	567295821	567296704	883	False	1524	1524	97.743	2674	3559	1	chr5B.!!$F1	885
2	TraesCS5B01G388400	chr2B	391098663	391101316	2653	False	4510	4510	97.402	1	2644	1	chr2B.!!$F1	2643
3	TraesCS5B01G388400	chr2B	391173835	391174731	896	True	1557	1557	97.993	2663	3559	1	chr2B.!!$R1	896
4	TraesCS5B01G388400	chr2A	755478557	755481007	2450	False	4222	4222	97.838	1	2439	1	chr2A.!!$F5	2438
5	TraesCS5B01G388400	chr7B	742948280	742950729	2449	True	4220	4220	97.838	1	2439	1	chr7B.!!$R1	2438
6	TraesCS5B01G388400	chr7B	716782616	716785065	2449	False	4176	4176	97.511	1	2439	1	chr7B.!!$F1	2438
7	TraesCS5B01G388400	chr7A	60168309	60170758	2449	True	4215	4215	97.797	1	2439	1	chr7A.!!$R1	2438
8	TraesCS5B01G388400	chr7A	60083121	60085394	2273	False	3903	3903	97.716	175	2439	1	chr7A.!!$F1	2264
9	TraesCS5B01G388400	chr5A	420183712	420186160	2448	False	4204	4204	97.715	1	2439	1	chr5A.!!$F2	2438
10	TraesCS5B01G388400	chr5A	16542604	16545012	2408	False	4156	4156	97.884	42	2439	1	chr5A.!!$F1	2397
11	TraesCS5B01G388400	chr1B	583561091	583563539	2448	True	4159	4159	97.389	1	2439	1	chr1B.!!$R1	2438
12	TraesCS5B01G388400	chr4D	123348131	123350579	2448	False	4143	4143	97.266	1	2439	1	chr4D.!!$F1	2438
13	TraesCS5B01G388400	chr4D	241177508	241180105	2597	False	3995	3995	94.476	1	2592	1	chr4D.!!$F2	2591
14	TraesCS5B01G388400	chr1D	275776946	275779385	2439	False	4111	4111	97.103	1	2439	1	chr1D.!!$F2	2438
15	TraesCS5B01G388400	chr7D	579039779	579041353	1574	False	2787	2787	98.603	1	1575	1	chr7D.!!$F2	1574
16	TraesCS5B01G388400	chr3D	193434276	193436111	1835	True	2734	2734	93.645	769	2595	1	chr3D.!!$R1	1826
17	TraesCS5B01G388400	chrUn	378555716	378556997	1281	False	2163	2163	97.270	1170	2439	1	chrUn.!!$F1	1269

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
532	533	4.382040	GGAAGACTCGGAATCATTCTCACA	60.382	45.833	0.00	0.00	0.0	3.58	F
1133	1135	1.201181	TGGGATTGCACGTGTTTATGC	59.799	47.619	18.38	12.57	42.4	3.14	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1866	1880	0.976073	CCCCTAGGAAAGCCTCACGA	60.976	60.0	11.48	0.0	45.54	4.35	R
3074	3089	0.608856	TGGTGTTTCGCAGGCATGAT	60.609	50.0	0.62	0.0	0.00	2.45	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
246	247	9.396022	GAAATGAGATTCTGGGTTTGATTACTA	57.604	33.333	0.00	0.00	0.00	1.82
353	354	6.263168	ACTTATTCAAAATGGGCTATCCGAAG	59.737	38.462	0.00	0.00	38.76	3.79
532	533	4.382040	GGAAGACTCGGAATCATTCTCACA	60.382	45.833	0.00	0.00	0.00	3.58
645	647	6.741992	ACAGTTGCTCAATTCATTCGATTA	57.258	33.333	0.00	0.00	0.00	1.75
1133	1135	1.201181	TGGGATTGCACGTGTTTATGC	59.799	47.619	18.38	12.57	42.40	3.14
1272	1274	8.608317	GCTATTAAAGAAGGAGATCTTGTCAAC	58.392	37.037	0.00	0.00	39.54	3.18
1546	1548	5.945784	ACTGGAAAAACTGCAATAGCTATCA	59.054	36.000	6.72	0.65	42.74	2.15
1633	1647	2.512485	TGGACAAAAACGCTCGACTA	57.488	45.000	0.00	0.00	0.00	2.59
1634	1648	2.823984	TGGACAAAAACGCTCGACTAA	58.176	42.857	0.00	0.00	0.00	2.24
1791	1805	2.975193	CGATAATGGAATGCACGCATTG	59.025	45.455	21.29	1.44	45.50	2.82
1848	1862	7.862372	GTGGCATATCGACAAATGTCATTATTT	59.138	33.333	13.51	0.00	44.99	1.40
2046	2060	7.284034	GTGATCTCCATTACAGATGGACAAATT	59.716	37.037	3.70	0.00	42.81	1.82
2218	2232	1.512694	GCCTTCGCTCAATTTGGGG	59.487	57.895	0.00	0.00	0.00	4.96
2267	2281	1.065126	ACTCAATAGAGGTGCAAGGCC	60.065	52.381	0.00	0.00	46.44	5.19
2290	2304	1.480137	CAGAAGTGCCCAAACAACCAA	59.520	47.619	0.00	0.00	0.00	3.67
2540	2555	0.237235	TTTTCATGCTCAACGGTCGC	59.763	50.000	0.00	0.00	0.00	5.19
2578	2593	2.184088	TTGGATGACGGGGAATCCTA	57.816	50.000	0.00	0.00	42.51	2.94
2644	2659	7.947890	AGGTAAAAGATGGAATTGACAACCTTA	59.052	33.333	0.00	0.00	0.00	2.69
2645	2660	8.027189	GGTAAAAGATGGAATTGACAACCTTAC	58.973	37.037	0.00	0.00	0.00	2.34
2646	2661	7.839680	AAAAGATGGAATTGACAACCTTACT	57.160	32.000	0.00	0.00	0.00	2.24
2647	2662	8.934023	AAAAGATGGAATTGACAACCTTACTA	57.066	30.769	0.00	0.00	0.00	1.82
2648	2663	9.533831	AAAAGATGGAATTGACAACCTTACTAT	57.466	29.630	0.00	0.00	0.00	2.12
2649	2664	9.533831	AAAGATGGAATTGACAACCTTACTATT	57.466	29.630	0.00	0.00	0.00	1.73
2650	2665	9.533831	AAGATGGAATTGACAACCTTACTATTT	57.466	29.630	0.00	0.00	0.00	1.40
2651	2666	9.178758	AGATGGAATTGACAACCTTACTATTTC	57.821	33.333	0.00	0.00	0.00	2.17
2652	2667	9.178758	GATGGAATTGACAACCTTACTATTTCT	57.821	33.333	0.00	0.00	0.00	2.52
2653	2668	8.561738	TGGAATTGACAACCTTACTATTTCTC	57.438	34.615	0.00	0.00	0.00	2.87
2654	2669	8.383175	TGGAATTGACAACCTTACTATTTCTCT	58.617	33.333	0.00	0.00	0.00	3.10
2655	2670	8.669243	GGAATTGACAACCTTACTATTTCTCTG	58.331	37.037	0.00	0.00	0.00	3.35
2656	2671	9.436957	GAATTGACAACCTTACTATTTCTCTGA	57.563	33.333	0.00	0.00	0.00	3.27
2657	2672	9.965902	AATTGACAACCTTACTATTTCTCTGAT	57.034	29.630	0.00	0.00	0.00	2.90
2658	2673	9.606631	ATTGACAACCTTACTATTTCTCTGATC	57.393	33.333	0.00	0.00	0.00	2.92
2659	2674	8.134202	TGACAACCTTACTATTTCTCTGATCA	57.866	34.615	0.00	0.00	0.00	2.92
2660	2675	8.253810	TGACAACCTTACTATTTCTCTGATCAG	58.746	37.037	17.07	17.07	0.00	2.90
2661	2676	8.367660	ACAACCTTACTATTTCTCTGATCAGA	57.632	34.615	23.75	23.75	35.85	3.27
2847	2862	6.231211	ACGATTTCAATGAGGAAGTAGTGTT	58.769	36.000	0.00	0.00	0.00	3.32
3011	3026	1.612035	ACCAATCCCAGGTGATCCAT	58.388	50.000	0.00	0.00	38.13	3.41
3074	3089	5.523916	GTGAGTTTTCTGAAGCAGTAGTTCA	59.476	40.000	0.00	0.00	32.61	3.18
3093	3108	0.608856	ATCATGCCTGCGAAACACCA	60.609	50.000	0.00	0.00	0.00	4.17
3175	3190	4.748102	CGCTGTCTTTACTCACTAAAACCA	59.252	41.667	0.00	0.00	0.00	3.67
3197	3212	5.245531	CAGTATTCTGGTACCAACACATGT	58.754	41.667	17.11	0.00	37.97	3.21
3482	3497	1.736681	GCATTGAGCACCAGTTCTCTC	59.263	52.381	0.00	0.00	44.79	3.20
3514	3529	3.056607	CCCCTCATCAAAATGGTGTTGTC	60.057	47.826	0.00	0.00	33.42	3.18

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
246	247	5.277345	CGCTAGCTTTGAACTTGTTTGTACT	60.277	40.000	13.93	0.00	0.00	2.73
283	284	2.614057	CCAGTTGAATGGAATCTACCGC	59.386	50.000	0.00	0.00	43.57	5.68
370	371	4.263068	GCAGCCTACCCATATTGATAGTGT	60.263	45.833	0.00	0.00	0.00	3.55
458	459	9.969001	AAATAAATAGGTTTGTAAGTGCCTAGA	57.031	29.630	0.00	0.00	37.07	2.43
645	647	8.540492	CAAGAATCACTTTATACGCTATTTCGT	58.460	33.333	0.00	0.00	40.35	3.85
864	866	5.049680	TCGGACAAAGACAATAACAAGAAGC	60.050	40.000	0.00	0.00	0.00	3.86
1272	1274	3.548745	TCCACAATAGATCCAGTGCAG	57.451	47.619	0.00	0.00	0.00	4.41
1633	1647	6.715347	AAGAATTTGAACTAGTTGTGCCTT	57.285	33.333	14.14	5.90	0.00	4.35
1634	1648	6.321181	TGAAAGAATTTGAACTAGTTGTGCCT	59.679	34.615	14.14	0.00	39.27	4.75
1848	1862	2.344500	CCTGGTGGTCGGCGTAAA	59.656	61.111	6.85	0.00	0.00	2.01
1866	1880	0.976073	CCCCTAGGAAAGCCTCACGA	60.976	60.000	11.48	0.00	45.54	4.35
1880	1894	8.002459	GGGAATGTAAATAGAAAACATCCCCTA	58.998	37.037	2.07	0.00	43.04	3.53
2235	2249	5.426833	ACCTCTATTGAGTAATGCCTGAGTT	59.573	40.000	3.47	0.00	38.61	3.01
2267	2281	2.293399	GGTTGTTTGGGCACTTCTGTAG	59.707	50.000	0.00	0.00	0.00	2.74
2290	2304	9.844257	TTTTTCAATTGGAAGTGGTTCATATTT	57.156	25.926	5.42	0.00	36.72	1.40
2514	2528	4.759693	ACCGTTGAGCATGAAAACAAGATA	59.240	37.500	0.00	0.00	0.00	1.98
2578	2593	1.049289	GTCCGGAGTAGGGCCTCATT	61.049	60.000	10.74	0.00	32.91	2.57
2644	2659	7.180051	GGGTATCCATCTGATCAGAGAAATAGT	59.820	40.741	28.26	9.09	41.33	2.12
2645	2660	7.179872	TGGGTATCCATCTGATCAGAGAAATAG	59.820	40.741	28.26	13.84	41.33	1.73
2646	2661	7.018769	TGGGTATCCATCTGATCAGAGAAATA	58.981	38.462	28.26	20.52	41.33	1.40
2647	2662	5.848369	TGGGTATCCATCTGATCAGAGAAAT	59.152	40.000	28.26	21.39	41.33	2.17
2648	2663	5.070981	GTGGGTATCCATCTGATCAGAGAAA	59.929	44.000	28.26	16.70	46.09	2.52
2649	2664	4.590647	GTGGGTATCCATCTGATCAGAGAA	59.409	45.833	28.26	17.03	46.09	2.87
2650	2665	4.155709	GTGGGTATCCATCTGATCAGAGA	58.844	47.826	28.26	21.30	46.09	3.10
2651	2666	3.260380	GGTGGGTATCCATCTGATCAGAG	59.740	52.174	28.26	19.57	46.09	3.35
2652	2667	3.242867	GGTGGGTATCCATCTGATCAGA	58.757	50.000	27.03	27.03	46.09	3.27
2653	2668	2.304180	GGGTGGGTATCCATCTGATCAG	59.696	54.545	17.07	17.07	46.09	2.90
2654	2669	2.338809	GGGTGGGTATCCATCTGATCA	58.661	52.381	4.97	0.00	46.09	2.92
2655	2670	2.039084	GTGGGTGGGTATCCATCTGATC	59.961	54.545	4.97	0.00	46.09	2.92
2656	2671	2.057922	GTGGGTGGGTATCCATCTGAT	58.942	52.381	4.97	0.00	46.09	2.90
2657	2672	1.274126	TGTGGGTGGGTATCCATCTGA	60.274	52.381	4.97	0.00	46.09	3.27
2658	2673	1.141657	CTGTGGGTGGGTATCCATCTG	59.858	57.143	4.97	0.00	46.09	2.90
2659	2674	1.009552	TCTGTGGGTGGGTATCCATCT	59.990	52.381	4.97	0.00	46.09	2.90
2660	2675	1.507140	TCTGTGGGTGGGTATCCATC	58.493	55.000	0.00	0.00	46.09	3.51
2661	2676	1.979809	TTCTGTGGGTGGGTATCCAT	58.020	50.000	0.00	0.00	46.09	3.41
2847	2862	6.903534	ACCATCCTCACTAGAAAAATCCTCTA	59.096	38.462	0.00	0.00	0.00	2.43
3011	3026	5.247110	GCTCTGATGGATGTAGGAAATCCTA	59.753	44.000	5.05	5.05	46.48	2.94
3074	3089	0.608856	TGGTGTTTCGCAGGCATGAT	60.609	50.000	0.62	0.00	0.00	2.45
3175	3190	5.012664	TGACATGTGTTGGTACCAGAATACT	59.987	40.000	15.65	0.00	0.00	2.12
3197	3212	2.812358	TGTTCGACTAGCTTGCTTGA	57.188	45.000	10.67	0.00	0.00	3.02
3482	3497	1.879575	TGATGAGGGGTGTAAGGAGG	58.120	55.000	0.00	0.00	0.00	4.30
3514	3529	1.136984	CGTCCGGTTCTTCCTCTCG	59.863	63.158	0.00	0.00	0.00	4.04

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.