AutoCloner

Multiple sequence alignment - TraesCS3D01G258600

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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	TraesCS3D01G258600	chr3D	100.000	1877	0	0	1	1877	360631777	360633653	0.000000e+00	3467.0
1	TraesCS3D01G258600	chr3D	100.000	289	0	0	2201	2489	360633977	360634265	3.640000e-148	534.0
2	TraesCS3D01G258600	chr3D	82.828	396	44	13	1468	1862	607244749	607245121	1.430000e-87	333.0
3	TraesCS3D01G258600	chr3D	95.652	69	2	1	2263	2330	589761280	589761212	2.620000e-20	110.0
4	TraesCS3D01G258600	chr3D	94.030	67	4	0	2263	2329	141424337	141424271	4.380000e-18	102.0
5	TraesCS3D01G258600	chr3D	97.059	34	1	0	935	968	406173566	406173599	9.620000e-05	58.4
6	TraesCS3D01G258600	chr3B	90.380	1185	63	22	1	1153	469338065	469339230	0.000000e+00	1509.0
7	TraesCS3D01G258600	chr3B	94.517	693	35	3	1185	1877	469339234	469339923	0.000000e+00	1066.0
8	TraesCS3D01G258600	chr3B	96.181	288	8	3	2201	2487	469339951	469340236	3.750000e-128	468.0
9	TraesCS3D01G258600	chr3B	75.813	922	188	28	967	1877	154798678	154797781	3.800000e-118	435.0
10	TraesCS3D01G258600	chr3A	81.910	890	83	37	74	909	480435249	480436114	0.000000e+00	680.0
11	TraesCS3D01G258600	chr3A	84.138	435	34	16	1321	1753	739683314	739683715	3.000000e-104	388.0
12	TraesCS3D01G258600	chr3A	86.525	141	11	3	2324	2462	480436290	480436424	5.550000e-32	148.0
13	TraesCS3D01G258600	chr6D	96.875	64	2	0	2263	2326	24554585	24554522	9.410000e-20	108.0
14	TraesCS3D01G258600	chr6B	95.455	66	3	0	2263	2328	508941194	508941259	3.390000e-19	106.0
15	TraesCS3D01G258600	chr5B	95.455	66	3	0	2257	2322	279098281	279098346	3.390000e-19	106.0
16	TraesCS3D01G258600	chr5A	90.909	77	6	1	2263	2339	613017679	613017754	4.380000e-18	102.0
17	TraesCS3D01G258600	chr5A	92.500	40	2	1	929	968	656668358	656668320	3.460000e-04	56.5
18	TraesCS3D01G258600	chr7B	88.889	81	5	3	2263	2341	2907459	2907537	2.040000e-16	97.1
19	TraesCS3D01G258600	chr6A	83.838	99	9	3	2263	2356	610209086	610209182	1.230000e-13	87.9
20	TraesCS3D01G258600	chr6A	90.698	43	4	0	938	980	486550829	486550787	9.620000e-05	58.4
21	TraesCS3D01G258600	chr2A	94.000	50	3	0	2215	2264	507074283	507074234	2.650000e-10	76.8
22	TraesCS3D01G258600	chr1D	95.000	40	0	2	929	968	464793223	464793186	7.430000e-06	62.1
23	TraesCS3D01G258600	chr7A	91.111	45	2	2	931	973	10085964	10086008	2.670000e-05	60.2
24	TraesCS3D01G258600	chr7D	88.000	50	5	1	938	986	552499652	552499603	9.620000e-05	58.4
25	TraesCS3D01G258600	chrUn	89.362	47	2	2	941	984	86557215	86557261	3.460000e-04	56.5
26	TraesCS3D01G258600	chr4A	89.362	47	2	2	941	984	664911287	664911241	3.460000e-04	56.5

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	TraesCS3D01G258600	chr3D	360631777	360634265	2488	False	2000.500000	3467	100.000000	1	2489	2	chr3D.!!$F3	2488
1	TraesCS3D01G258600	chr3B	469338065	469340236	2171	False	1014.333333	1509	93.692667	1	2487	3	chr3B.!!$F1	2486
2	TraesCS3D01G258600	chr3B	154797781	154798678	897	True	435.000000	435	75.813000	967	1877	1	chr3B.!!$R1	910
3	TraesCS3D01G258600	chr3A	480435249	480436424	1175	False	414.000000	680	84.217500	74	2462	2	chr3A.!!$F2	2388

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
55	56	0.380378	TCTGAAACCAGCGCAACAAC	59.62	50.0	11.47	0.0	0.0	3.32	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1712	1946	0.456221	CGGAAGCACGGTACTCTGAT	59.544	55.0	0.0	0.0	0.0	2.9	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
45	46	1.192146	CCGGGTCCTCTCTGAAACCA	61.192	60.000	0.00	0.00	33.27	3.67
54	55	0.662619	CTCTGAAACCAGCGCAACAA	59.337	50.000	11.47	0.00	0.00	2.83
55	56	0.380378	TCTGAAACCAGCGCAACAAC	59.620	50.000	11.47	0.00	0.00	3.32
56	57	0.929824	CTGAAACCAGCGCAACAACG	60.930	55.000	11.47	0.00	0.00	4.10
299	318	3.379057	GTCAGTGCTACTACCTCTCTTCC	59.621	52.174	0.00	0.00	0.00	3.46
307	326	6.066032	GCTACTACCTCTCTTCCATACTCTT	58.934	44.000	0.00	0.00	0.00	2.85
311	330	7.842982	ACTACCTCTCTTCCATACTCTTTTTC	58.157	38.462	0.00	0.00	0.00	2.29
318	337	9.277783	TCTCTTCCATACTCTTTTTCTTTTCTG	57.722	33.333	0.00	0.00	0.00	3.02
319	338	8.980481	TCTTCCATACTCTTTTTCTTTTCTGT	57.020	30.769	0.00	0.00	0.00	3.41
320	339	9.408648	TCTTCCATACTCTTTTTCTTTTCTGTT	57.591	29.630	0.00	0.00	0.00	3.16
323	342	9.408648	TCCATACTCTTTTTCTTTTCTGTTCTT	57.591	29.630	0.00	0.00	0.00	2.52
328	347	9.631452	ACTCTTTTTCTTTTCTGTTCTTTTGAG	57.369	29.630	0.00	0.00	0.00	3.02
329	348	9.846248	CTCTTTTTCTTTTCTGTTCTTTTGAGA	57.154	29.630	0.00	0.00	0.00	3.27
332	351	7.992180	TTTCTTTTCTGTTCTTTTGAGATGC	57.008	32.000	0.00	0.00	0.00	3.91
333	352	6.698008	TCTTTTCTGTTCTTTTGAGATGCA	57.302	33.333	0.00	0.00	0.00	3.96
334	353	7.099266	TCTTTTCTGTTCTTTTGAGATGCAA	57.901	32.000	0.00	0.00	33.88	4.08
335	354	7.719483	TCTTTTCTGTTCTTTTGAGATGCAAT	58.281	30.769	0.00	0.00	36.15	3.56
336	355	7.864379	TCTTTTCTGTTCTTTTGAGATGCAATC	59.136	33.333	0.00	0.00	46.04	2.67
357	376	7.574217	GCAATCCTTCCTCTCTAGTATTAGTCG	60.574	44.444	0.00	0.00	0.00	4.18
369	388	4.531332	AGTATTAGTCGCGGTTAATCGTC	58.469	43.478	10.29	1.31	0.00	4.20
371	390	0.381801	TAGTCGCGGTTAATCGTCCC	59.618	55.000	10.29	0.00	0.00	4.46
502	568	0.823356	GCTCCAACCAGTTGCTCCAA	60.823	55.000	4.96	0.00	39.16	3.53
503	569	1.915141	CTCCAACCAGTTGCTCCAAT	58.085	50.000	4.96	0.00	39.16	3.16
525	591	2.231716	TCCAAACCGATGGAGAGAGA	57.768	50.000	1.05	0.00	44.52	3.10
539	610	5.314529	TGGAGAGAGACGGGTAGTATATTG	58.685	45.833	0.00	0.00	0.00	1.90
547	618	4.439057	ACGGGTAGTATATTGCAACACAG	58.561	43.478	0.00	0.00	0.00	3.66
555	626	7.792374	AGTATATTGCAACACAGACTAATGG	57.208	36.000	0.00	0.00	0.00	3.16
573	645	0.963355	GGCTTGGATTTGCCCGTGTA	60.963	55.000	0.00	0.00	43.11	2.90
605	677	3.964875	CGCGGCTTGGCTGTTGTT	61.965	61.111	0.00	0.00	37.24	2.83
635	707	4.886579	ACAAATTGTTGAAAGCAGGATCC	58.113	39.130	2.48	2.48	38.20	3.36
641	713	0.690192	TGAAAGCAGGATCCGAACCA	59.310	50.000	5.98	0.00	0.00	3.67
734	806	5.324697	GTGCTTCGGTCATTTAGTGATTTC	58.675	41.667	0.00	0.00	39.48	2.17
736	808	5.471797	TGCTTCGGTCATTTAGTGATTTCAA	59.528	36.000	0.00	0.00	39.48	2.69
775	861	7.828223	AGATGTAATTCTCATGCTTGTTCTTCT	59.172	33.333	0.00	0.00	0.00	2.85
1155	1388	2.880268	TGACAGAGCAAAATCAGTGTGG	59.120	45.455	0.00	0.00	0.00	4.17
1156	1389	3.141398	GACAGAGCAAAATCAGTGTGGA	58.859	45.455	0.00	0.00	0.00	4.02
1164	1397	4.794003	GCAAAATCAGTGTGGAAGGAACTG	60.794	45.833	0.00	0.00	40.86	3.16
1168	1401	1.133792	CAGTGTGGAAGGAACTGGGTT	60.134	52.381	0.00	0.00	40.86	4.11
1169	1402	1.569072	AGTGTGGAAGGAACTGGGTTT	59.431	47.619	0.00	0.00	40.86	3.27
1173	1406	1.850345	TGGAAGGAACTGGGTTTGAGT	59.150	47.619	0.00	0.00	40.86	3.41
1260	1493	1.742268	GCTGAAATCTCTGGAGGCAAC	59.258	52.381	0.00	0.00	0.00	4.17
1268	1501	1.002069	TCTGGAGGCAACATCCCAAT	58.998	50.000	0.00	0.00	35.86	3.16
1322	1555	3.306780	GGATGGTACTTATGGTGGGATCG	60.307	52.174	0.00	0.00	0.00	3.69
1323	1556	1.414919	TGGTACTTATGGTGGGATCGC	59.585	52.381	2.14	2.14	0.00	4.58
1405	1639	7.585884	AGAGGTATAGTAGCTAATACCCTGA	57.414	40.000	22.84	0.00	39.77	3.86
1450	1684	3.446873	GCGATCTATGAGATGGGTCAGAT	59.553	47.826	0.00	0.00	34.53	2.90
1476	1710	5.298527	GGCTGCCGGAGTAATTAAACTAAAT	59.701	40.000	5.05	0.00	0.00	1.40
1531	1765	2.505407	AGGTGCTACTGGTGCATTGATA	59.495	45.455	0.00	0.00	42.69	2.15
1649	1883	1.914634	GCGTCTAGCCGATGATATGG	58.085	55.000	0.00	0.00	40.81	2.74
1686	1920	4.009002	TGCCATCGAATGTGATTCTTTGA	58.991	39.130	0.00	0.00	37.13	2.69
1712	1946	3.178046	TGTTCAAGCTATACTGGACCCA	58.822	45.455	0.00	0.00	0.00	4.51
1853	2087	2.202756	CGAGCGAGTTACAGGGGC	60.203	66.667	0.00	0.00	0.00	5.80
2225	2459	8.546083	AATATCCTCTCTCTTAACAGACATGT	57.454	34.615	0.00	0.00	43.15	3.21
2248	2482	7.022384	TGTTTATTGTTTAATAAAGGTCGCCG	58.978	34.615	5.68	0.00	44.87	6.46
2254	2488	5.106987	TGTTTAATAAAGGTCGCCGAAGTTC	60.107	40.000	0.00	0.00	0.00	3.01
2375	2609	5.906113	ATAAACAGTCATGACTCGACTCT	57.094	39.130	25.58	9.51	41.80	3.24
2419	2654	5.648960	GGTCACTAGCTAGATACAGATACCC	59.351	48.000	27.45	9.89	0.00	3.69

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
25	26	0.903454	GGTTTCAGAGAGGACCCGGA	60.903	60.000	0.73	0.00	0.00	5.14
45	46	2.972505	CAGGGACGTTGTTGCGCT	60.973	61.111	9.73	0.00	34.88	5.92
307	326	8.034215	TGCATCTCAAAAGAACAGAAAAGAAAA	58.966	29.630	0.00	0.00	34.49	2.29
311	330	7.115947	GGATTGCATCTCAAAAGAACAGAAAAG	59.884	37.037	0.00	0.00	38.34	2.27
318	337	5.184671	AGGAAGGATTGCATCTCAAAAGAAC	59.815	40.000	0.00	0.00	39.77	3.01
319	338	5.327732	AGGAAGGATTGCATCTCAAAAGAA	58.672	37.500	0.00	0.00	39.77	2.52
320	339	4.927049	AGGAAGGATTGCATCTCAAAAGA	58.073	39.130	0.00	0.00	39.77	2.52
323	342	4.226846	AGAGAGGAAGGATTGCATCTCAAA	59.773	41.667	11.21	0.00	40.41	2.69
325	344	3.382278	AGAGAGGAAGGATTGCATCTCA	58.618	45.455	11.21	0.00	40.41	3.27
326	345	4.588528	ACTAGAGAGGAAGGATTGCATCTC	59.411	45.833	0.00	2.17	39.77	2.75
327	346	4.555689	ACTAGAGAGGAAGGATTGCATCT	58.444	43.478	0.00	0.00	39.77	2.90
328	347	4.953940	ACTAGAGAGGAAGGATTGCATC	57.046	45.455	0.00	0.00	39.77	3.91
329	348	7.732593	ACTAATACTAGAGAGGAAGGATTGCAT	59.267	37.037	0.00	0.00	39.77	3.96
330	349	7.069986	ACTAATACTAGAGAGGAAGGATTGCA	58.930	38.462	0.00	0.00	39.77	4.08
331	350	7.533289	ACTAATACTAGAGAGGAAGGATTGC	57.467	40.000	0.00	0.00	36.28	3.56
332	351	7.574217	GCGACTAATACTAGAGAGGAAGGATTG	60.574	44.444	0.00	0.00	29.08	2.67
333	352	6.431852	GCGACTAATACTAGAGAGGAAGGATT	59.568	42.308	0.00	0.00	31.20	3.01
334	353	5.941647	GCGACTAATACTAGAGAGGAAGGAT	59.058	44.000	0.00	0.00	0.00	3.24
335	354	5.307204	GCGACTAATACTAGAGAGGAAGGA	58.693	45.833	0.00	0.00	0.00	3.36
336	355	4.152759	CGCGACTAATACTAGAGAGGAAGG	59.847	50.000	0.00	0.00	0.00	3.46
337	356	4.152759	CCGCGACTAATACTAGAGAGGAAG	59.847	50.000	8.23	0.00	32.55	3.46
338	357	4.063689	CCGCGACTAATACTAGAGAGGAA	58.936	47.826	8.23	0.00	32.55	3.36
339	358	3.070734	ACCGCGACTAATACTAGAGAGGA	59.929	47.826	8.23	0.00	33.83	3.71
340	359	3.401182	ACCGCGACTAATACTAGAGAGG	58.599	50.000	8.23	0.00	34.84	3.69
341	360	6.536731	TTAACCGCGACTAATACTAGAGAG	57.463	41.667	8.23	0.00	0.00	3.20
342	361	6.128715	CGATTAACCGCGACTAATACTAGAGA	60.129	42.308	8.23	0.00	0.00	3.10
343	362	6.014293	CGATTAACCGCGACTAATACTAGAG	58.986	44.000	8.23	0.00	0.00	2.43
344	363	5.466728	ACGATTAACCGCGACTAATACTAGA	59.533	40.000	8.23	0.00	0.00	2.43
345	364	5.683859	ACGATTAACCGCGACTAATACTAG	58.316	41.667	8.23	5.51	0.00	2.57
346	365	5.334105	GGACGATTAACCGCGACTAATACTA	60.334	44.000	8.23	0.00	0.00	1.82
347	366	4.531332	GACGATTAACCGCGACTAATACT	58.469	43.478	8.23	0.00	0.00	2.12
348	367	3.665871	GGACGATTAACCGCGACTAATAC	59.334	47.826	8.23	5.53	0.00	1.89
357	376	2.159476	GGAAAAAGGGACGATTAACCGC	60.159	50.000	0.00	0.00	0.00	5.68
369	388	1.826385	ACATCTGCTCGGAAAAAGGG	58.174	50.000	0.00	0.00	0.00	3.95
371	390	2.813754	TCCAACATCTGCTCGGAAAAAG	59.186	45.455	0.00	0.00	0.00	2.27
456	522	4.855715	TTTATTCAATGGTTTGACGGCA	57.144	36.364	0.00	0.00	41.50	5.69
471	537	6.212888	ACTGGTTGGAGCATGAATTTATTC	57.787	37.500	0.00	0.00	37.31	1.75
502	568	3.639094	CTCTCTCCATCGGTTTGGACTAT	59.361	47.826	0.00	0.00	40.90	2.12
503	569	3.024547	CTCTCTCCATCGGTTTGGACTA	58.975	50.000	0.00	0.00	40.90	2.59
525	591	4.160814	TCTGTGTTGCAATATACTACCCGT	59.839	41.667	0.59	0.00	0.00	5.28
539	610	2.095059	CCAAGCCATTAGTCTGTGTTGC	60.095	50.000	0.00	0.00	0.00	4.17
555	626	0.170339	GTACACGGGCAAATCCAAGC	59.830	55.000	0.00	0.00	36.21	4.01
569	641	1.798813	CGGTTCAGCTTTCCTGTACAC	59.201	52.381	0.00	0.00	41.91	2.90
573	645	1.961277	CGCGGTTCAGCTTTCCTGT	60.961	57.895	0.00	0.00	42.38	4.00
605	677	5.299028	TGCTTTCAACAATTTGTAGCTCTCA	59.701	36.000	18.12	5.78	39.79	3.27
635	707	0.737715	CTTCCTCCTCGCTTGGTTCG	60.738	60.000	0.00	0.00	0.00	3.95
641	713	0.899019	GGAACTCTTCCTCCTCGCTT	59.101	55.000	0.00	0.00	46.57	4.68
744	830	6.435277	ACAAGCATGAGAATTACATCTGGTTT	59.565	34.615	0.00	0.00	0.00	3.27
751	837	7.148120	CCAGAAGAACAAGCATGAGAATTACAT	60.148	37.037	0.00	0.00	0.00	2.29
775	861	1.614051	CCTGAAGCTGCACATTACCCA	60.614	52.381	1.02	0.00	0.00	4.51
932	1153	2.368875	ACAGAGGGAGTACAACACAAGG	59.631	50.000	0.00	0.00	0.00	3.61
969	1190	3.181474	GGAGGGACTGTATTCTCCGAAAG	60.181	52.174	7.49	0.00	41.55	2.62
973	1194	1.776662	TGGAGGGACTGTATTCTCCG	58.223	55.000	14.58	0.00	46.42	4.63
1155	1388	3.208747	TCACTCAAACCCAGTTCCTTC	57.791	47.619	0.00	0.00	0.00	3.46
1156	1389	3.662759	TTCACTCAAACCCAGTTCCTT	57.337	42.857	0.00	0.00	0.00	3.36
1164	1397	5.241728	AGCTTCAATAGTTTCACTCAAACCC	59.758	40.000	0.00	0.00	45.05	4.11
1168	1401	4.821260	TGCAGCTTCAATAGTTTCACTCAA	59.179	37.500	0.00	0.00	0.00	3.02
1169	1402	4.388485	TGCAGCTTCAATAGTTTCACTCA	58.612	39.130	0.00	0.00	0.00	3.41
1173	1406	2.160219	CGCTGCAGCTTCAATAGTTTCA	59.840	45.455	34.22	0.00	39.32	2.69
1198	1431	1.996191	GACTGAACCAGAACGCTCATC	59.004	52.381	0.45	0.00	35.18	2.92
1260	1493	6.041182	TCTCAATTCCATTAGCAATTGGGATG	59.959	38.462	7.72	1.86	42.19	3.51
1268	1501	8.799367	CCATAATCATCTCAATTCCATTAGCAA	58.201	33.333	0.00	0.00	0.00	3.91
1322	1555	2.556622	TCCTTGTGAGAAATTTTCCGGC	59.443	45.455	0.00	0.00	0.00	6.13
1323	1556	4.846779	TTCCTTGTGAGAAATTTTCCGG	57.153	40.909	5.52	0.00	0.00	5.14
1405	1639	5.776744	CGTTAGTACCTTCAGTTTGGTAGT	58.223	41.667	0.00	0.00	42.91	2.73
1424	1658	3.154710	ACCCATCTCATAGATCGCGTTA	58.845	45.455	5.77	0.00	31.32	3.18
1476	1710	2.104792	GGGTGATAGCTAAGCATCCACA	59.895	50.000	19.18	0.72	33.01	4.17
1486	1720	3.515059	AGCGTCAGGGTGATAGCTA	57.485	52.632	0.00	0.00	39.92	3.32
1531	1765	2.341101	CGCCCCTGTACAGTCTCGT	61.341	63.158	21.18	0.00	0.00	4.18
1621	1855	3.801129	GCTAGACGCAAGCCTTCC	58.199	61.111	0.00	0.00	45.62	3.46
1639	1873	4.940046	CAGAGAAAATCCCCCATATCATCG	59.060	45.833	0.00	0.00	0.00	3.84
1649	1883	1.923356	TGGCAACAGAGAAAATCCCC	58.077	50.000	0.00	0.00	46.17	4.81
1686	1920	6.116126	GGTCCAGTATAGCTTGAACAATCTT	58.884	40.000	0.00	0.00	0.00	2.40
1712	1946	0.456221	CGGAAGCACGGTACTCTGAT	59.544	55.000	0.00	0.00	0.00	2.90
1777	2011	2.336809	GCTCTATCGTCGCCCTGG	59.663	66.667	0.00	0.00	0.00	4.45
1853	2087	0.953960	GCCACTCCCCAGTACGTTTG	60.954	60.000	0.00	0.00	0.00	2.93
2225	2459	7.375106	TCGGCGACCTTTATTAAACAATAAA	57.625	32.000	4.99	3.34	34.51	1.40
2358	2592	7.075121	GTGATATTAGAGTCGAGTCATGACTG	58.925	42.308	32.50	22.40	46.29	3.51
2375	2609	6.550108	GTGACCTACTTCCTCCTGTGATATTA	59.450	42.308	0.00	0.00	0.00	0.98
2419	2654	9.613428	TTTACATAAGGAAGTCAATACCATGAG	57.387	33.333	0.00	0.00	0.00	2.90

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.