AutoCloner

Multiple sequence alignment - TraesCS5A01G183300

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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	TraesCS5A01G183300	chr5A	100.000	2495	0	0	1	2495	382779428	382776934	0.000000e+00	4608
1	TraesCS5A01G183300	chr5D	91.896	2073	100	21	454	2495	290395483	290393448	0.000000e+00	2835
2	TraesCS5A01G183300	chr5D	91.304	230	13	3	3	231	290395750	290395527	8.670000e-80	307
3	TraesCS5A01G183300	chr5B	92.777	1426	49	15	391	1805	331248714	331247332	0.000000e+00	2013
4	TraesCS5A01G183300	chr5B	91.429	700	41	14	1802	2495	331247220	331246534	0.000000e+00	942
5	TraesCS5A01G183300	chr5B	87.709	358	20	12	3	356	331249037	331248700	1.800000e-106	396
6	TraesCS5A01G183300	chr5B	77.519	258	48	8	1220	1468	616026601	616026345	2.000000e-31	147
7	TraesCS5A01G183300	chr7D	93.504	508	30	3	996	1502	111114543	111115048	0.000000e+00	752
8	TraesCS5A01G183300	chr7D	84.277	477	58	10	489	963	111213971	111214432	1.360000e-122	449
9	TraesCS5A01G183300	chr7D	86.792	265	28	5	940	1203	111092047	111092305	3.140000e-74	289
10	TraesCS5A01G183300	chr7D	82.482	274	38	8	1198	1468	160534357	160534623	5.370000e-57	231
11	TraesCS5A01G183300	chr7D	91.975	162	10	2	717	876	111091870	111092030	8.980000e-55	224
12	TraesCS5A01G183300	chr7D	76.854	445	47	22	473	905	111114096	111114496	1.510000e-47	200
13	TraesCS5A01G183300	chr7D	84.772	197	18	7	464	652	111091665	111091857	1.180000e-43	187
14	TraesCS5A01G183300	chr7D	82.581	155	22	4	1586	1738	111115105	111115256	5.600000e-27	132
15	TraesCS5A01G183300	chr7B	93.960	447	25	2	1058	1503	70825192	70825637	0.000000e+00	675
16	TraesCS5A01G183300	chr7B	81.818	418	40	22	507	905	70824701	70825101	4.000000e-83	318
17	TraesCS5A01G183300	chr7B	82.847	274	37	8	1198	1468	121496232	121496498	1.150000e-58	237
18	TraesCS5A01G183300	chr7A	85.493	517	45	6	1000	1514	116509282	116509770	1.710000e-141	512
19	TraesCS5A01G183300	chr7A	80.835	407	43	18	467	864	116508475	116508855	1.130000e-73	287
20	TraesCS5A01G183300	chr7A	82.847	274	37	8	1198	1468	161650832	161651098	1.150000e-58	237

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	TraesCS5A01G183300	chr5A	382776934	382779428	2494	True	4608.000000	4608	100.000000	1	2495	1	chr5A.!!$R1	2494
1	TraesCS5A01G183300	chr5D	290393448	290395750	2302	True	1571.000000	2835	91.600000	3	2495	2	chr5D.!!$R1	2492
2	TraesCS5A01G183300	chr5B	331246534	331249037	2503	True	1117.000000	2013	90.638333	3	2495	3	chr5B.!!$R2	2492
3	TraesCS5A01G183300	chr7D	111114096	111115256	1160	False	361.333333	752	84.313000	473	1738	3	chr7D.!!$F4	1265
4	TraesCS5A01G183300	chr7D	111091665	111092305	640	False	233.333333	289	87.846333	464	1203	3	chr7D.!!$F3	739
5	TraesCS5A01G183300	chr7B	70824701	70825637	936	False	496.500000	675	87.889000	507	1503	2	chr7B.!!$F2	996
6	TraesCS5A01G183300	chr7A	116508475	116509770	1295	False	399.500000	512	83.164000	467	1514	2	chr7A.!!$F2	1047

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
304	306	0.24746	GCCTGAATTTTGTCCCTGCC	59.753	55.0	0.0	0.0	0.0	4.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1568	1961	2.104967	CATGAATCCTTGCATGGGTGT	58.895	47.619	17.95	4.3	38.52	4.16	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
206	208	3.454082	TGGTTGATTTGTTTCCTTTGCCT	59.546	39.130	0.00	0.00	0.00	4.75
245	247	9.985730	ATATTTATTTTAACGGTCGGTCATAGA	57.014	29.630	0.00	0.00	0.00	1.98
246	248	8.897872	ATTTATTTTAACGGTCGGTCATAGAT	57.102	30.769	0.00	0.00	0.00	1.98
249	251	4.987408	TTAACGGTCGGTCATAGATTCA	57.013	40.909	0.00	0.00	0.00	2.57
250	252	2.865343	ACGGTCGGTCATAGATTCAC	57.135	50.000	0.00	0.00	0.00	3.18
252	254	2.099263	ACGGTCGGTCATAGATTCACAG	59.901	50.000	0.00	0.00	0.00	3.66
253	255	2.543861	CGGTCGGTCATAGATTCACAGG	60.544	54.545	0.00	0.00	0.00	4.00
254	256	2.224066	GGTCGGTCATAGATTCACAGGG	60.224	54.545	0.00	0.00	0.00	4.45
255	257	2.431057	GTCGGTCATAGATTCACAGGGT	59.569	50.000	0.00	0.00	0.00	4.34
256	258	2.693591	TCGGTCATAGATTCACAGGGTC	59.306	50.000	0.00	0.00	0.00	4.46
261	263	5.710099	GGTCATAGATTCACAGGGTCAAAAA	59.290	40.000	0.00	0.00	0.00	1.94
304	306	0.247460	GCCTGAATTTTGTCCCTGCC	59.753	55.000	0.00	0.00	0.00	4.85
319	321	4.672251	GCCCATGACTCAGGCAAT	57.328	55.556	5.18	0.00	46.34	3.56
331	333	2.421424	CTCAGGCAATACAGTTGCTTCC	59.579	50.000	11.92	0.00	44.36	3.46
338	340	2.151881	TACAGTTGCTTCCGCGTAAA	57.848	45.000	4.92	0.00	39.65	2.01
339	341	1.519408	ACAGTTGCTTCCGCGTAAAT	58.481	45.000	4.92	0.00	39.65	1.40
340	342	1.877443	ACAGTTGCTTCCGCGTAAATT	59.123	42.857	4.92	0.00	39.65	1.82
341	343	2.292292	ACAGTTGCTTCCGCGTAAATTT	59.708	40.909	4.92	0.00	39.65	1.82
342	344	3.243267	ACAGTTGCTTCCGCGTAAATTTT	60.243	39.130	4.92	0.00	39.65	1.82
343	345	3.733727	CAGTTGCTTCCGCGTAAATTTTT	59.266	39.130	4.92	0.00	39.65	1.94
484	486	4.659111	TTTCCTACAGAAAGTGACGTCA	57.341	40.909	15.76	15.76	39.60	4.35
487	489	3.057734	CCTACAGAAAGTGACGTCAACC	58.942	50.000	21.95	9.12	0.00	3.77
542	552	1.298413	CGGCAGTACACGATCTCCG	60.298	63.158	0.00	0.00	45.44	4.63
553	567	4.814294	ATCTCCGGCGTTCGTGGC	62.814	66.667	6.01	0.00	37.11	5.01
613	631	1.993653	CATGCTCCTCCTGGAACCA	59.006	57.895	0.00	0.00	42.66	3.67
614	632	0.549950	CATGCTCCTCCTGGAACCAT	59.450	55.000	0.00	0.00	42.66	3.55
681	707	3.117625	TCCTTCTGGATAGGAGCGTAGAA	60.118	47.826	0.00	0.00	36.88	2.10
691	717	6.295123	GGATAGGAGCGTAGAATTAACCATGA	60.295	42.308	0.00	0.00	0.00	3.07
692	718	5.353394	AGGAGCGTAGAATTAACCATGAA	57.647	39.130	0.00	0.00	0.00	2.57
698	724	6.653320	AGCGTAGAATTAACCATGAAAGTTGA	59.347	34.615	0.00	0.00	0.00	3.18
713	742	3.393089	AGTTGAATGGGCTAGCTATCG	57.607	47.619	15.72	0.00	0.00	2.92
727	756	3.581755	AGCTATCGCTGTTCGTAACAAA	58.418	40.909	0.00	0.00	46.86	2.83
742	771	5.411361	TCGTAACAAAGATCCAAATGACAGG	59.589	40.000	0.00	0.00	0.00	4.00
869	915	8.632906	TTTCCCGTACAAATCCACTATAAAAA	57.367	30.769	0.00	0.00	0.00	1.94
985	1032	8.830580	CATACATAGTAGAAACCATTTGGACAG	58.169	37.037	3.01	0.00	38.94	3.51
989	1036	2.154462	AGAAACCATTTGGACAGCGAG	58.846	47.619	3.01	0.00	38.94	5.03
1098	1486	1.440938	CGCCTCAGGACTACCTCTCG	61.441	65.000	0.00	0.00	45.94	4.04
1506	1899	6.595716	AGAAACCATACTAACTGTGATTGCTC	59.404	38.462	0.00	0.00	0.00	4.26
1515	1908	0.320050	TGTGATTGCTCCGCAGTACA	59.680	50.000	0.00	0.00	40.61	2.90
1516	1909	1.066215	TGTGATTGCTCCGCAGTACAT	60.066	47.619	0.00	0.00	40.61	2.29
1517	1910	2.167487	TGTGATTGCTCCGCAGTACATA	59.833	45.455	0.00	0.00	40.61	2.29
1518	1911	3.181466	TGTGATTGCTCCGCAGTACATAT	60.181	43.478	0.00	0.00	40.61	1.78
1519	1912	4.038642	TGTGATTGCTCCGCAGTACATATA	59.961	41.667	0.00	0.00	40.61	0.86
1520	1913	5.171476	GTGATTGCTCCGCAGTACATATAT	58.829	41.667	0.00	0.00	40.61	0.86
1521	1914	6.071616	TGTGATTGCTCCGCAGTACATATATA	60.072	38.462	0.00	0.00	40.61	0.86
1522	1915	6.980978	GTGATTGCTCCGCAGTACATATATAT	59.019	38.462	0.00	0.00	40.61	0.86
1523	1916	8.135529	GTGATTGCTCCGCAGTACATATATATA	58.864	37.037	0.00	0.00	40.61	0.86
1524	1917	8.860088	TGATTGCTCCGCAGTACATATATATAT	58.140	33.333	0.00	0.00	40.61	0.86
1568	1961	1.243342	CCTCGTTCCTTGCATGGCAA	61.243	55.000	13.75	3.40	46.80	4.52
1729	2142	8.739972	ACCTTGAAACATATATGAACCTTTCAC	58.260	33.333	19.63	0.27	43.48	3.18
1741	2162	7.964604	ATGAACCTTTCACTACAGTTAGTTC	57.035	36.000	0.00	0.00	43.48	3.01
1757	2178	8.410141	ACAGTTAGTTCAATCTCTAGCTGATAC	58.590	37.037	17.81	0.00	43.27	2.24
1758	2179	8.629158	CAGTTAGTTCAATCTCTAGCTGATACT	58.371	37.037	0.00	0.00	43.27	2.12
1759	2180	8.846211	AGTTAGTTCAATCTCTAGCTGATACTC	58.154	37.037	0.00	0.00	0.00	2.59
1760	2181	6.648879	AGTTCAATCTCTAGCTGATACTCC	57.351	41.667	0.00	0.00	0.00	3.85
1761	2182	6.372931	AGTTCAATCTCTAGCTGATACTCCT	58.627	40.000	0.00	0.00	0.00	3.69
1762	2183	7.522542	AGTTCAATCTCTAGCTGATACTCCTA	58.477	38.462	0.00	0.00	0.00	2.94
1844	2380	5.006386	ACCTGAAAAATCCAAGCAGAGTAG	58.994	41.667	0.00	0.00	0.00	2.57
1992	2532	7.953493	AGAATGTTTTAATTCTCTACCCCCAAA	59.047	33.333	0.00	0.00	42.01	3.28
1998	2538	5.348259	AATTCTCTACCCCCAAAAAGGAA	57.652	39.130	0.00	0.00	41.22	3.36
2003	2543	6.147473	TCTCTACCCCCAAAAAGGAAAAATT	58.853	36.000	0.00	0.00	41.22	1.82
2126	2667	6.493458	GGCTATTGATTAGGGATAAGGCAAAA	59.507	38.462	0.00	0.00	0.00	2.44
2132	2673	7.358263	TGATTAGGGATAAGGCAAAAATACCA	58.642	34.615	0.00	0.00	0.00	3.25
2135	2676	4.956075	AGGGATAAGGCAAAAATACCACAG	59.044	41.667	0.00	0.00	0.00	3.66
2165	2708	5.975988	ATAGAAGGACTAAATTGCCCTCA	57.024	39.130	0.00	0.00	34.56	3.86
2226	2769	2.973694	TGAGGATTACCAAGTACCGC	57.026	50.000	0.00	0.00	38.94	5.68
2283	2826	0.041839	GCCTATCAATGCAAGACGCG	60.042	55.000	3.53	3.53	46.97	6.01
2310	2853	1.076024	ACCACATCCACCAGCTCAAAT	59.924	47.619	0.00	0.00	0.00	2.32
2321	2864	4.213270	CACCAGCTCAAATAGAAACAACGA	59.787	41.667	0.00	0.00	0.00	3.85
2330	2874	8.025243	TCAAATAGAAACAACGAGTGGATTAC	57.975	34.615	0.00	0.00	0.00	1.89
2337	2881	6.903883	AACAACGAGTGGATTACATATCAC	57.096	37.500	0.00	0.00	0.00	3.06
2342	2886	6.273825	ACGAGTGGATTACATATCACAAGAC	58.726	40.000	0.00	0.00	33.01	3.01
2347	2891	6.597672	GTGGATTACATATCACAAGACCAACA	59.402	38.462	0.00	0.00	0.00	3.33
2363	2907	3.888930	ACCAACAAGGAAATCATTCACGT	59.111	39.130	0.00	0.00	41.22	4.49
2393	2942	0.550147	AGTGCCTTGGGTCCACCTAT	60.550	55.000	0.00	0.00	41.11	2.57
2397	2946	1.281925	CCTTGGGTCCACCTATGCCT	61.282	60.000	0.00	0.00	41.11	4.75
2398	2947	0.107017	CTTGGGTCCACCTATGCCTG	60.107	60.000	0.00	0.00	41.11	4.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
26	27	8.834004	ACCCTCAATATGTACTACAGTCTAAA	57.166	34.615	0.00	0.00	0.00	1.85
27	28	8.692710	CAACCCTCAATATGTACTACAGTCTAA	58.307	37.037	0.00	0.00	0.00	2.10
28	29	7.287005	CCAACCCTCAATATGTACTACAGTCTA	59.713	40.741	0.00	0.00	0.00	2.59
29	30	6.098409	CCAACCCTCAATATGTACTACAGTCT	59.902	42.308	0.00	0.00	0.00	3.24
30	31	6.097839	TCCAACCCTCAATATGTACTACAGTC	59.902	42.308	0.00	0.00	0.00	3.51
31	32	5.962031	TCCAACCCTCAATATGTACTACAGT	59.038	40.000	0.00	0.00	0.00	3.55
83	84	5.012893	TCTGTTTAGCTCTGATCTGACAGA	58.987	41.667	17.77	17.77	43.39	3.41
173	175	5.391312	ACAAATCAACCAATACCAGCTTC	57.609	39.130	0.00	0.00	0.00	3.86
174	176	5.806654	AACAAATCAACCAATACCAGCTT	57.193	34.783	0.00	0.00	0.00	3.74
231	233	2.097036	TGTGAATCTATGACCGACCGT	58.903	47.619	0.00	0.00	0.00	4.83
267	269	0.108138	GCATAGTGGAGGCGAAGTGT	60.108	55.000	0.00	0.00	0.00	3.55
269	271	0.978146	AGGCATAGTGGAGGCGAAGT	60.978	55.000	0.00	0.00	34.98	3.01
304	306	3.272574	ACTGTATTGCCTGAGTCATGG	57.727	47.619	0.00	0.00	0.00	3.66
484	486	5.104900	ACGCATTACTGGATTCTTCTAGGTT	60.105	40.000	0.00	0.00	34.90	3.50
487	489	5.625721	CGTACGCATTACTGGATTCTTCTAG	59.374	44.000	0.52	0.00	36.57	2.43
553	567	3.826157	TGTTTGCCCTCAAAGTTGATAGG	59.174	43.478	0.00	0.63	42.31	2.57
681	707	5.484998	AGCCCATTCAACTTTCATGGTTAAT	59.515	36.000	0.00	0.00	36.47	1.40
691	717	4.130118	CGATAGCTAGCCCATTCAACTTT	58.870	43.478	12.13	0.00	0.00	2.66
692	718	3.733337	CGATAGCTAGCCCATTCAACTT	58.267	45.455	12.13	0.00	0.00	2.66
713	742	4.742438	TTGGATCTTTGTTACGAACAGC	57.258	40.909	0.00	0.00	43.27	4.40
715	744	6.261158	TGTCATTTGGATCTTTGTTACGAACA	59.739	34.615	0.00	0.00	40.21	3.18
727	756	1.833630	TCGAGCCTGTCATTTGGATCT	59.166	47.619	0.00	0.00	36.68	2.75
848	894	6.183360	GGGGTTTTTATAGTGGATTTGTACGG	60.183	42.308	0.00	0.00	0.00	4.02
869	915	4.768807	ATAGCTTGAGTATAGAGGGGGT	57.231	45.455	0.00	0.00	0.00	4.95
913	959	2.107141	GTAGGCCGTGGCTAGCTG	59.893	66.667	15.72	4.94	41.26	4.24
921	967	1.145759	CTGCGTATGTGTAGGCCGTG	61.146	60.000	0.00	0.00	40.16	4.94
965	1011	4.020928	TCGCTGTCCAAATGGTTTCTACTA	60.021	41.667	0.00	0.00	36.34	1.82
966	1012	3.074412	CGCTGTCCAAATGGTTTCTACT	58.926	45.455	0.00	0.00	36.34	2.57
985	1032	1.227674	CCATTACTCCCTGGCTCGC	60.228	63.158	0.00	0.00	0.00	5.03
989	1036	0.105039	CGTCTCCATTACTCCCTGGC	59.895	60.000	0.00	0.00	32.30	4.85
1021	1409	1.032114	ATGGCTAGGGCGAGCAAAAC	61.032	55.000	11.55	0.00	44.76	2.43
1356	1745	3.238497	ACCTGCGTGTAGTGCCCA	61.238	61.111	0.00	0.00	0.00	5.36
1528	1921	9.444668	ACGAGGGACTACTGGACTATATATATA	57.555	37.037	2.49	2.49	41.55	0.86
1529	1922	8.334522	ACGAGGGACTACTGGACTATATATAT	57.665	38.462	0.00	0.00	41.55	0.86
1530	1923	7.746243	ACGAGGGACTACTGGACTATATATA	57.254	40.000	0.00	0.00	41.55	0.86
1568	1961	2.104967	CATGAATCCTTGCATGGGTGT	58.895	47.619	17.95	4.30	38.52	4.16
1729	2142	7.990917	TCAGCTAGAGATTGAACTAACTGTAG	58.009	38.462	0.00	0.00	35.57	2.74
1741	2162	8.347004	TCAATAGGAGTATCAGCTAGAGATTG	57.653	38.462	0.00	0.00	36.25	2.67
1758	2179	7.839705	AGAGTACCAGTCAATAACTCAATAGGA	59.160	37.037	0.00	0.00	39.20	2.94
1759	2180	8.012957	AGAGTACCAGTCAATAACTCAATAGG	57.987	38.462	0.00	0.00	39.20	2.57
1760	2181	9.953697	GTAGAGTACCAGTCAATAACTCAATAG	57.046	37.037	0.00	0.00	39.20	1.73
1761	2182	9.470399	TGTAGAGTACCAGTCAATAACTCAATA	57.530	33.333	0.00	0.00	39.20	1.90
1762	2183	8.362464	TGTAGAGTACCAGTCAATAACTCAAT	57.638	34.615	0.00	0.00	39.20	2.57
1844	2380	7.547722	CCTTTTTATTTACCCCTAAACACATGC	59.452	37.037	0.00	0.00	0.00	4.06
2165	2708	9.872684	ACCAATGAAATCTAACCATTCATCTAT	57.127	29.630	1.18	0.00	41.58	1.98
2283	2826	2.162681	CTGGTGGATGTGGTTCTTTCC	58.837	52.381	0.00	0.00	0.00	3.13
2310	2853	8.471609	TGATATGTAATCCACTCGTTGTTTCTA	58.528	33.333	0.00	0.00	0.00	2.10
2321	2864	6.560003	TGGTCTTGTGATATGTAATCCACT	57.440	37.500	0.00	0.00	33.09	4.00
2330	2874	6.573664	TTTCCTTGTTGGTCTTGTGATATG	57.426	37.500	0.00	0.00	37.07	1.78
2337	2881	5.922544	GTGAATGATTTCCTTGTTGGTCTTG	59.077	40.000	0.00	0.00	37.07	3.02
2342	2886	4.503741	ACGTGAATGATTTCCTTGTTGG	57.496	40.909	0.00	0.00	37.10	3.77
2347	2891	6.039270	TCAAAGTGAACGTGAATGATTTCCTT	59.961	34.615	0.00	0.00	0.00	3.36
2393	2942	1.301623	CGGTTAATGTCCCCAGGCA	59.698	57.895	0.00	0.00	0.00	4.75
2397	2946	0.252789	TCTCCCGGTTAATGTCCCCA	60.253	55.000	0.00	0.00	0.00	4.96
2398	2947	0.913924	TTCTCCCGGTTAATGTCCCC	59.086	55.000	0.00	0.00	0.00	4.81

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.