AutoCloner

Multiple sequence alignment - TraesCS6D01G376300

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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	TraesCS6D01G376300	chr6D	100.000	3131	0	0	1	3131	459064533	459061403	0.000000e+00	5782.0
1	TraesCS6D01G376300	chr6D	91.828	1603	98	19	1550	3131	458989366	458987776	0.000000e+00	2204.0
2	TraesCS6D01G376300	chr6D	88.235	1428	126	21	1	1411	458990914	458989512	0.000000e+00	1668.0
3	TraesCS6D01G376300	chr6B	96.163	1642	42	7	1496	3118	698114882	698113243	0.000000e+00	2663.0
4	TraesCS6D01G376300	chr6B	90.186	1508	130	8	1	1504	698121941	698120448	0.000000e+00	1949.0
5	TraesCS6D01G376300	chr6A	90.055	1458	110	15	1328	2768	605344024	605342585	0.000000e+00	1857.0
6	TraesCS6D01G376300	chr6A	93.548	217	13	1	2916	3131	605342312	605342096	3.900000e-84	322.0
7	TraesCS6D01G376300	chr2B	80.961	2206	324	53	132	2271	781149736	781151911	0.000000e+00	1659.0
8	TraesCS6D01G376300	chr2B	81.146	1623	230	40	669	2239	781085479	781083881	0.000000e+00	1232.0
9	TraesCS6D01G376300	chr2B	91.111	90	8	0	1	90	781149549	781149638	4.240000e-24	122.0
10	TraesCS6D01G376300	chr2A	80.723	2184	315	56	138	2256	776170762	776168620	0.000000e+00	1604.0
11	TraesCS6D01G376300	chr2A	79.840	2257	358	55	132	2338	776212964	776215173	0.000000e+00	1557.0
12	TraesCS6D01G376300	chr2A	87.778	90	11	0	1	90	776170955	776170866	4.270000e-19	106.0
13	TraesCS6D01G376300	chr2D	80.761	1944	301	44	132	2020	651431766	651433691	0.000000e+00	1450.0
14	TraesCS6D01G376300	chr2D	82.009	1334	167	38	998	2271	651422700	651421380	0.000000e+00	1066.0
15	TraesCS6D01G376300	chr5B	78.587	2293	344	74	143	2338	703859418	703857176	0.000000e+00	1378.0
16	TraesCS6D01G376300	chr5B	83.555	827	91	21	1550	2338	699612420	699611601	0.000000e+00	732.0
17	TraesCS6D01G376300	chr5B	82.027	829	103	20	1550	2338	703798395	703797573	0.000000e+00	664.0
18	TraesCS6D01G376300	chr5B	75.088	1140	215	37	142	1241	697869074	697867964	4.730000e-128	468.0
19	TraesCS6D01G376300	chr5B	75.926	756	165	8	142	884	697832195	697831444	3.810000e-99	372.0
20	TraesCS6D01G376300	chr5B	71.806	1135	258	50	139	1232	697808072	697809185	1.850000e-67	267.0
21	TraesCS6D01G376300	chr5B	83.007	153	26	0	142	294	699616251	699616099	4.210000e-29	139.0
22	TraesCS6D01G376300	chr5D	83.415	820	95	20	1553	2338	551408331	551407519	0.000000e+00	723.0
23	TraesCS6D01G376300	chr5D	77.692	780	134	23	1550	2305	552128014	552127251	1.030000e-119	440.0
24	TraesCS6D01G376300	chr5D	84.298	242	36	2	132	372	429865012	429864772	5.220000e-58	235.0
25	TraesCS6D01G376300	chr5D	83.908	87	12	2	2	86	552741841	552741755	7.200000e-12	82.4
26	TraesCS6D01G376300	chrUn	79.243	925	164	22	373	1281	23720245	23719333	1.230000e-173	619.0
27	TraesCS6D01G376300	chr4A	83.286	700	79	18	1673	2338	616702577	616703272	7.420000e-171	610.0
28	TraesCS6D01G376300	chr4A	85.304	592	72	9	1552	2130	632617214	632617803	5.780000e-167	597.0
29	TraesCS6D01G376300	chr7B	84.615	91	8	4	2	88	146046056	146046144	5.560000e-13	86.1
30	TraesCS6D01G376300	chr7B	92.857	42	3	0	35	76	151062515	151062556	9.380000e-06	62.1
31	TraesCS6D01G376300	chr7A	82.418	91	10	4	2	88	184569183	184569271	1.200000e-09	75.0
32	TraesCS6D01G376300	chr1B	86.957	69	2	4	17	78	53082874	53082806	1.560000e-08	71.3

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	TraesCS6D01G376300	chr6D	459061403	459064533	3130	True	5782.0	5782	100.0000	1	3131	1	chr6D.!!$R1	3130
1	TraesCS6D01G376300	chr6D	458987776	458990914	3138	True	1936.0	2204	90.0315	1	3131	2	chr6D.!!$R2	3130
2	TraesCS6D01G376300	chr6B	698113243	698114882	1639	True	2663.0	2663	96.1630	1496	3118	1	chr6B.!!$R1	1622
3	TraesCS6D01G376300	chr6B	698120448	698121941	1493	True	1949.0	1949	90.1860	1	1504	1	chr6B.!!$R2	1503
4	TraesCS6D01G376300	chr6A	605342096	605344024	1928	True	1089.5	1857	91.8015	1328	3131	2	chr6A.!!$R1	1803
5	TraesCS6D01G376300	chr2B	781083881	781085479	1598	True	1232.0	1232	81.1460	669	2239	1	chr2B.!!$R1	1570
6	TraesCS6D01G376300	chr2B	781149549	781151911	2362	False	890.5	1659	86.0360	1	2271	2	chr2B.!!$F1	2270
7	TraesCS6D01G376300	chr2A	776212964	776215173	2209	False	1557.0	1557	79.8400	132	2338	1	chr2A.!!$F1	2206
8	TraesCS6D01G376300	chr2A	776168620	776170955	2335	True	855.0	1604	84.2505	1	2256	2	chr2A.!!$R1	2255
9	TraesCS6D01G376300	chr2D	651431766	651433691	1925	False	1450.0	1450	80.7610	132	2020	1	chr2D.!!$F1	1888
10	TraesCS6D01G376300	chr2D	651421380	651422700	1320	True	1066.0	1066	82.0090	998	2271	1	chr2D.!!$R1	1273
11	TraesCS6D01G376300	chr5B	703857176	703859418	2242	True	1378.0	1378	78.5870	143	2338	1	chr5B.!!$R4	2195
12	TraesCS6D01G376300	chr5B	703797573	703798395	822	True	664.0	664	82.0270	1550	2338	1	chr5B.!!$R3	788
13	TraesCS6D01G376300	chr5B	697867964	697869074	1110	True	468.0	468	75.0880	142	1241	1	chr5B.!!$R2	1099
14	TraesCS6D01G376300	chr5B	699611601	699616251	4650	True	435.5	732	83.2810	142	2338	2	chr5B.!!$R5	2196
15	TraesCS6D01G376300	chr5B	697831444	697832195	751	True	372.0	372	75.9260	142	884	1	chr5B.!!$R1	742
16	TraesCS6D01G376300	chr5B	697808072	697809185	1113	False	267.0	267	71.8060	139	1232	1	chr5B.!!$F1	1093
17	TraesCS6D01G376300	chr5D	551407519	551408331	812	True	723.0	723	83.4150	1553	2338	1	chr5D.!!$R2	785
18	TraesCS6D01G376300	chr5D	552127251	552128014	763	True	440.0	440	77.6920	1550	2305	1	chr5D.!!$R3	755
19	TraesCS6D01G376300	chrUn	23719333	23720245	912	True	619.0	619	79.2430	373	1281	1	chrUn.!!$R1	908
20	TraesCS6D01G376300	chr4A	616702577	616703272	695	False	610.0	610	83.2860	1673	2338	1	chr4A.!!$F1	665
21	TraesCS6D01G376300	chr4A	632617214	632617803	589	False	597.0	597	85.3040	1552	2130	1	chr4A.!!$F2	578

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
974	1802	0.820891	AGTGCCAGCAACCTGTTGAG	60.821	55.0	13.94	5.27	42.93	3.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2660	5815	0.682209	CACCCTCCTGGCTGAAATGG	60.682	60.0	0.0	0.0	37.83	3.16	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
165	227	3.206211	GATCAGCGCTCTCCCCGAG	62.206	68.421	7.13	0.00	42.88	4.63
375	1164	4.516195	GTTCCCCTCGCCGAGAGC	62.516	72.222	17.19	0.00	45.54	4.09
677	1493	1.448540	CTTGTGGTAGGCTCAGGCG	60.449	63.158	0.00	0.00	39.81	5.52
886	1702	1.740380	GCTATGTTCCTGAGCTTCGCA	60.740	52.381	0.00	0.00	33.28	5.10
971	1799	1.529244	GGAGTGCCAGCAACCTGTT	60.529	57.895	0.00	0.00	37.38	3.16
974	1802	0.820891	AGTGCCAGCAACCTGTTGAG	60.821	55.000	13.94	5.27	42.93	3.02
975	1803	1.103398	GTGCCAGCAACCTGTTGAGT	61.103	55.000	13.94	0.00	42.93	3.41
979	1807	1.876156	CCAGCAACCTGTTGAGTCTTC	59.124	52.381	13.94	0.00	42.93	2.87
996	1824	3.498397	GTCTTCATCTTGGTTTCGAGCAA	59.502	43.478	0.00	0.00	0.00	3.91
1059	1908	7.606349	TCTTCTGCATCTACATACCATATGTC	58.394	38.462	4.77	0.00	33.76	3.06
1065	1915	6.815641	GCATCTACATACCATATGTCCTTCTG	59.184	42.308	4.77	0.54	33.76	3.02
1079	1930	3.440522	GTCCTTCTGTACCAATTTCAGCC	59.559	47.826	0.00	0.00	0.00	4.85
1084	1935	1.876799	TGTACCAATTTCAGCCGTGTG	59.123	47.619	0.00	0.00	0.00	3.82
1467	2333	1.199789	GCGAGACAATGTCCATGCAAA	59.800	47.619	10.12	0.00	32.18	3.68
2116	5229	3.746432	GCATGGATCATCCTCATGTGTGA	60.746	47.826	4.96	0.00	40.07	3.58
2319	5468	1.377725	CTGGCCGCATGGTTCTCTT	60.378	57.895	0.00	0.00	37.67	2.85
2384	5533	7.516198	AGTATATGATGATTTGTTTGCCCTC	57.484	36.000	0.00	0.00	0.00	4.30
2614	5768	5.535030	GTGTAGGAAAGGGAAATTGTGAACT	59.465	40.000	0.00	0.00	0.00	3.01
2660	5815	3.505680	TCACAAACTCCATGTTGTATGCC	59.494	43.478	0.00	0.00	39.13	4.40
2785	5951	0.247736	GATGAGTGGAAGCCTGTCGT	59.752	55.000	0.00	0.00	0.00	4.34
2788	5954	1.000506	TGAGTGGAAGCCTGTCGTAAC	59.999	52.381	0.00	0.00	0.00	2.50
2797	5963	0.172578	CCTGTCGTAACGCTCATGGA	59.827	55.000	0.00	0.00	0.00	3.41
2812	5978	4.142513	GCTCATGGAAAATGGAAGACAGTC	60.143	45.833	0.00	0.00	0.00	3.51
2813	5979	4.335416	TCATGGAAAATGGAAGACAGTCC	58.665	43.478	0.00	0.00	38.27	3.85
2815	5981	3.754965	TGGAAAATGGAAGACAGTCCTG	58.245	45.455	0.00	0.00	38.62	3.86
2816	5982	3.084786	GGAAAATGGAAGACAGTCCTGG	58.915	50.000	0.00	0.00	38.62	4.45
2818	5984	3.710209	AAATGGAAGACAGTCCTGGAG	57.290	47.619	0.00	0.00	38.62	3.86
2820	5986	2.630889	TGGAAGACAGTCCTGGAGAT	57.369	50.000	0.00	0.00	38.62	2.75
2821	5987	2.182827	TGGAAGACAGTCCTGGAGATG	58.817	52.381	0.00	1.55	38.62	2.90
2861	6037	4.221703	CCAGAGATACACAACAAGAGGTCT	59.778	45.833	0.00	0.00	0.00	3.85
2978	6309	1.714794	CTCCAGCAGGAACTTGTACG	58.285	55.000	0.00	0.00	45.19	3.67
3052	6383	9.478238	TGATTTTTGGATGATCAGAGGATTTAA	57.522	29.630	0.09	0.00	32.67	1.52
3125	6456	8.660373	CAGAGCCAACTAAAGAAACATAACTAG	58.340	37.037	0.00	0.00	0.00	2.57

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
165	227	1.460273	GGATCTCGAGGAGGAGGTGC	61.460	65.000	13.56	0.00	34.74	5.01
375	1164	3.710722	AGGGACTTGAGGGCGCTG	61.711	66.667	8.56	0.00	45.06	5.18
677	1493	3.391382	AGGTACGCAGGGTGAGGC	61.391	66.667	0.00	0.00	0.00	4.70
688	1504	0.317160	TCAACCAGTCTGCAGGTACG	59.683	55.000	15.13	2.00	37.07	3.67
713	1529	1.272781	GTCGATCTTGAGCACGAAGG	58.727	55.000	0.00	0.00	36.57	3.46
792	1608	3.922171	AGCTTAGGGACAGAAATGAGG	57.078	47.619	0.00	0.00	0.00	3.86
838	1654	1.480137	CAGTGGAAGCTTCTCGGAGAT	59.520	52.381	25.05	3.16	33.89	2.75
849	1665	1.006922	GCCAAAGTGCAGTGGAAGC	60.007	57.895	13.87	3.24	37.03	3.86
851	1667	2.161855	CATAGCCAAAGTGCAGTGGAA	58.838	47.619	13.87	2.92	37.03	3.53
886	1702	5.058490	GGCTCTAGAATCGAGTAGTACACT	58.942	45.833	2.52	0.00	41.47	3.55
971	1799	4.560128	CTCGAAACCAAGATGAAGACTCA	58.440	43.478	0.00	0.00	35.56	3.41
974	1802	3.067106	TGCTCGAAACCAAGATGAAGAC	58.933	45.455	0.00	0.00	0.00	3.01
975	1803	3.401033	TGCTCGAAACCAAGATGAAGA	57.599	42.857	0.00	0.00	0.00	2.87
979	1807	3.624326	TTGTTGCTCGAAACCAAGATG	57.376	42.857	0.00	0.00	0.00	2.90
996	1824	6.310224	GCGCAGAAATTAATTGTACCATTTGT	59.690	34.615	0.30	0.00	0.00	2.83
1059	1908	2.420022	CGGCTGAAATTGGTACAGAAGG	59.580	50.000	0.00	0.00	42.39	3.46
1065	1915	1.877443	ACACACGGCTGAAATTGGTAC	59.123	47.619	0.00	0.00	0.00	3.34
1079	1930	4.209452	ACAGCAAGAACATAAACACACG	57.791	40.909	0.00	0.00	0.00	4.49
1084	1935	7.816640	TCCAAATCTACAGCAAGAACATAAAC	58.183	34.615	0.00	0.00	0.00	2.01
1491	2376	9.847224	AAGAACTTTTGGAGAACTCTTAACATA	57.153	29.630	1.86	0.00	0.00	2.29
2319	5468	8.284693	GCAATTAGTTACTCGGTAAACTGAAAA	58.715	33.333	0.00	0.00	29.42	2.29
2384	5533	8.970691	AAACAAGTCAAGAATTTGAATATCCG	57.029	30.769	3.49	0.00	44.49	4.18
2629	5784	9.733556	ACAACATGGAGTTTGTGAGTATATAAA	57.266	29.630	0.00	0.00	38.74	1.40
2660	5815	0.682209	CACCCTCCTGGCTGAAATGG	60.682	60.000	0.00	0.00	37.83	3.16
2785	5951	4.394920	GTCTTCCATTTTCCATGAGCGTTA	59.605	41.667	0.00	0.00	0.00	3.18
2788	5954	2.749076	TGTCTTCCATTTTCCATGAGCG	59.251	45.455	0.00	0.00	0.00	5.03
2797	5963	3.652869	TCTCCAGGACTGTCTTCCATTTT	59.347	43.478	7.85	0.00	38.25	1.82
2812	5978	5.466728	CGAATGTAACAATACCATCTCCAGG	59.533	44.000	0.00	0.00	0.00	4.45
2813	5979	5.466728	CCGAATGTAACAATACCATCTCCAG	59.533	44.000	0.00	0.00	0.00	3.86
2815	5981	4.213482	GCCGAATGTAACAATACCATCTCC	59.787	45.833	0.00	0.00	0.00	3.71
2816	5982	4.213482	GGCCGAATGTAACAATACCATCTC	59.787	45.833	0.00	0.00	0.00	2.75
2818	5984	3.880490	TGGCCGAATGTAACAATACCATC	59.120	43.478	0.00	0.00	0.00	3.51
2820	5986	3.055021	TCTGGCCGAATGTAACAATACCA	60.055	43.478	0.00	0.00	0.00	3.25
2821	5987	3.537580	TCTGGCCGAATGTAACAATACC	58.462	45.455	0.00	0.00	0.00	2.73
2861	6037	5.632764	CACATTGACAAAAATTCGCACCATA	59.367	36.000	0.00	0.00	0.00	2.74
2978	6309	2.287188	CGCAGGTTGGCATATTGATGTC	60.287	50.000	0.00	0.00	38.24	3.06
3033	6364	7.348274	AGGTAGTTTAAATCCTCTGATCATCCA	59.652	37.037	0.00	0.00	0.00	3.41
3052	6383	6.904654	TCCCCTGTAATGTAACATAGGTAGTT	59.095	38.462	0.00	0.00	0.00	2.24
3062	6393	2.504175	TCTGCCTCCCCTGTAATGTAAC	59.496	50.000	0.00	0.00	0.00	2.50

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.