AutoCloner

Multiple sequence alignment - TraesCS2A01G175800

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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	TraesCS2A01G175800	chr2A	100.000	3197	0	0	1	3197	134868373	134865177	0.000000e+00	5904.0
1	TraesCS2A01G175800	chr2A	88.429	2342	186	47	477	2783	83984601	83986892	0.000000e+00	2745.0
2	TraesCS2A01G175800	chr2A	89.324	2173	160	22	672	2822	83989925	83992047	0.000000e+00	2662.0
3	TraesCS2A01G175800	chr2A	88.280	1988	153	36	858	2822	84143618	84145548	0.000000e+00	2307.0
4	TraesCS2A01G175800	chr2A	95.882	170	7	0	622	791	733423647	733423478	3.140000e-70	276.0
5	TraesCS2A01G175800	chr2A	83.333	294	20	9	2844	3132	84146006	84146275	8.860000e-61	244.0
6	TraesCS2A01G175800	chr2A	96.667	60	2	0	733	792	84143484	84143543	2.030000e-17	100.0
7	TraesCS2A01G175800	chr2D	95.387	2840	90	8	367	3197	127821891	127819084	0.000000e+00	4481.0
8	TraesCS2A01G175800	chr2D	87.240	2359	193	54	577	2862	83224896	83227219	0.000000e+00	2590.0
9	TraesCS2A01G175800	chr2D	89.815	2003	135	31	858	2822	83529898	83531869	0.000000e+00	2505.0
10	TraesCS2A01G175800	chr2D	84.421	1977	178	34	997	2933	85251793	85249907	0.000000e+00	1825.0
11	TraesCS2A01G175800	chr2D	89.814	1237	86	26	477	1690	83187978	83189197	0.000000e+00	1550.0
12	TraesCS2A01G175800	chr2D	90.884	362	25	3	1	355	127822439	127822079	2.230000e-131	479.0
13	TraesCS2A01G175800	chr2D	100.000	28	0	0	765	792	83529796	83529823	6.000000e-03	52.8
14	TraesCS2A01G175800	chr5A	90.356	2105	126	25	650	2722	326438158	326436099	0.000000e+00	2691.0
15	TraesCS2A01G175800	chr2B	89.775	2044	146	29	863	2862	135357952	135359976	0.000000e+00	2558.0
16	TraesCS2A01G175800	chr2B	88.464	1803	156	29	889	2663	137349337	137347559	0.000000e+00	2130.0
17	TraesCS2A01G175800	chr2B	90.146	1299	88	13	408	1690	135126232	135127506	0.000000e+00	1653.0
18	TraesCS2A01G175800	chr2B	90.253	1108	80	17	602	1690	135463372	135464470	0.000000e+00	1423.0
19	TraesCS2A01G175800	chr2B	88.841	1156	98	22	1684	2822	135464494	135465635	0.000000e+00	1391.0
20	TraesCS2A01G175800	chr2B	91.389	929	73	6	1898	2822	182132936	182132011	0.000000e+00	1266.0
21	TraesCS2A01G175800	chr2B	87.893	1082	99	13	1899	2953	136813863	136812787	0.000000e+00	1243.0
22	TraesCS2A01G175800	chr2B	87.783	221	27	0	2	222	135125620	135125840	3.160000e-65	259.0
23	TraesCS2A01G175800	chr2B	78.125	288	21	17	2844	3129	182131591	182131344	9.240000e-31	145.0
24	TraesCS2A01G175800	chr2B	82.123	179	13	4	2954	3132	135128953	135129112	5.560000e-28	135.0
25	TraesCS2A01G175800	chr2B	82.386	176	12	4	2954	3129	135466151	135466307	5.560000e-28	135.0
26	TraesCS2A01G175800	chr5D	92.351	1582	101	10	535	2113	230368712	230370276	0.000000e+00	2233.0
27	TraesCS2A01G175800	chr7A	86.613	1860	151	37	889	2703	618195367	618193561	0.000000e+00	1965.0
28	TraesCS2A01G175800	chrUn	92.627	963	62	3	858	1820	25419699	25418746	0.000000e+00	1376.0
29	TraesCS2A01G175800	chrUn	87.912	91	8	3	702	792	25419861	25419774	1.570000e-18	104.0
30	TraesCS2A01G175800	chrUn	84.375	64	9	1	647	709	312486021	312485958	9.580000e-06	62.1
31	TraesCS2A01G175800	chrUn	83.582	67	10	1	641	706	321744756	321744822	9.580000e-06	62.1
32	TraesCS2A01G175800	chrUn	84.375	64	9	1	647	709	387218396	387218333	9.580000e-06	62.1
33	TraesCS2A01G175800	chrUn	84.375	64	9	1	647	709	394422171	394422108	9.580000e-06	62.1
34	TraesCS2A01G175800	chr3A	80.612	98	14	4	614	706	688945330	688945427	1.590000e-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	TraesCS2A01G175800	chr2A	134865177	134868373	3196	True	5904.000000	5904	100.000000	1	3197	1	chr2A.!!$R1	3196
1	TraesCS2A01G175800	chr2A	83984601	83992047	7446	False	2703.500000	2745	88.876500	477	2822	2	chr2A.!!$F1	2345
2	TraesCS2A01G175800	chr2A	84143484	84146275	2791	False	883.666667	2307	89.426667	733	3132	3	chr2A.!!$F2	2399
3	TraesCS2A01G175800	chr2D	83224896	83227219	2323	False	2590.000000	2590	87.240000	577	2862	1	chr2D.!!$F2	2285
4	TraesCS2A01G175800	chr2D	127819084	127822439	3355	True	2480.000000	4481	93.135500	1	3197	2	chr2D.!!$R2	3196
5	TraesCS2A01G175800	chr2D	85249907	85251793	1886	True	1825.000000	1825	84.421000	997	2933	1	chr2D.!!$R1	1936
6	TraesCS2A01G175800	chr2D	83187978	83189197	1219	False	1550.000000	1550	89.814000	477	1690	1	chr2D.!!$F1	1213
7	TraesCS2A01G175800	chr2D	83529796	83531869	2073	False	1278.900000	2505	94.907500	765	2822	2	chr2D.!!$F3	2057
8	TraesCS2A01G175800	chr5A	326436099	326438158	2059	True	2691.000000	2691	90.356000	650	2722	1	chr5A.!!$R1	2072
9	TraesCS2A01G175800	chr2B	135357952	135359976	2024	False	2558.000000	2558	89.775000	863	2862	1	chr2B.!!$F1	1999
10	TraesCS2A01G175800	chr2B	137347559	137349337	1778	True	2130.000000	2130	88.464000	889	2663	1	chr2B.!!$R2	1774
11	TraesCS2A01G175800	chr2B	136812787	136813863	1076	True	1243.000000	1243	87.893000	1899	2953	1	chr2B.!!$R1	1054
12	TraesCS2A01G175800	chr2B	135463372	135466307	2935	False	983.000000	1423	87.160000	602	3129	3	chr2B.!!$F3	2527
13	TraesCS2A01G175800	chr2B	182131344	182132936	1592	True	705.500000	1266	84.757000	1898	3129	2	chr2B.!!$R3	1231
14	TraesCS2A01G175800	chr2B	135125620	135129112	3492	False	682.333333	1653	86.684000	2	3132	3	chr2B.!!$F2	3130
15	TraesCS2A01G175800	chr5D	230368712	230370276	1564	False	2233.000000	2233	92.351000	535	2113	1	chr5D.!!$F1	1578
16	TraesCS2A01G175800	chr7A	618193561	618195367	1806	True	1965.000000	1965	86.613000	889	2703	1	chr7A.!!$R1	1814
17	TraesCS2A01G175800	chrUn	25418746	25419861	1115	True	740.000000	1376	90.269500	702	1820	2	chrUn.!!$R4	1118

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
903	1206	0.537188	GAGCTCGAGTTGGATCCCAA	59.463	55.0	15.13	0.58	41.69	4.12	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2491	7964	0.178995	TCACCAACCAATGCTGCTCA	60.179	50.0	0.0	0.0	0.0	4.26	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
67	68	2.757212	CGTAAGCCACATACGCCAA	58.243	52.632	0.00	0.00	39.56	4.52
94	95	2.092592	CCCACTAACCGCTTATCCCTTT	60.093	50.000	0.00	0.00	0.00	3.11
165	166	2.959465	TCTCCCGCATCTCTCTCATA	57.041	50.000	0.00	0.00	0.00	2.15
189	190	2.615747	CGTCTCACACCTCTCACCTAGA	60.616	54.545	0.00	0.00	0.00	2.43
196	197	4.221703	CACACCTCTCACCTAGAAGTTCAT	59.778	45.833	5.50	0.00	32.46	2.57
231	232	1.668793	CACTCCATGCGCACTGTCA	60.669	57.895	14.90	0.69	0.00	3.58
236	237	1.579964	CCATGCGCACTGTCATGTGT	61.580	55.000	14.90	0.00	38.63	3.72
273	274	1.543642	TGTCATGATGGGGTGGGGT	60.544	57.895	0.00	0.00	0.00	4.95
356	562	1.015109	GAGACGACGAGCTATGACCA	58.985	55.000	0.00	0.00	0.00	4.02
360	566	1.663379	CGACGAGCTATGACCACCCA	61.663	60.000	0.00	0.00	0.00	4.51
394	600	4.322385	GTCGGTGCGTTGCAACCC	62.322	66.667	23.42	15.59	44.30	4.11
395	601	4.858680	TCGGTGCGTTGCAACCCA	62.859	61.111	23.42	18.21	44.30	4.51
397	603	3.522731	GGTGCGTTGCAACCCACA	61.523	61.111	35.58	23.88	40.86	4.17
474	718	2.363306	TTTGCTGGGCTTCTCTTTCA	57.637	45.000	0.00	0.00	0.00	2.69
491	735	8.709386	TCTCTTTCAGAAGCACATTTAGTATC	57.291	34.615	0.00	0.00	32.75	2.24
511	755	8.934023	AGTATCAGAAGGGAAAATTTGTGTAA	57.066	30.769	0.00	0.00	0.00	2.41
599	860	8.323140	CAGAAATTTATGCGATTTGCCTAAAAG	58.677	33.333	9.52	0.00	43.69	2.27
600	861	8.034804	AGAAATTTATGCGATTTGCCTAAAAGT	58.965	29.630	9.52	2.80	43.69	2.66
612	873	6.458232	TTGCCTAAAAGTACAATTGTGTGT	57.542	33.333	21.42	4.21	38.82	3.72
658	919	7.573843	GCTGTGCTCAAGAACAATACAAACTAT	60.574	37.037	0.00	0.00	32.17	2.12
661	922	7.746475	GTGCTCAAGAACAATACAAACTATGAC	59.254	37.037	0.00	0.00	0.00	3.06
677	938	8.349245	CAAACTATGACTGATTTTTGTACCACA	58.651	33.333	0.00	0.00	0.00	4.17
850	1147	4.511826	AGACGTTCCATTTGTTCTTCAGTC	59.488	41.667	0.00	0.00	0.00	3.51
903	1206	0.537188	GAGCTCGAGTTGGATCCCAA	59.463	55.000	15.13	0.58	41.69	4.12
1246	1562	2.039137	GAGTCCCGGGAGTCCCTT	59.961	66.667	38.69	15.71	42.67	3.95
1279	1595	2.048127	GACTTCCAGCGCCGTCTT	60.048	61.111	2.29	0.00	0.00	3.01
1281	1597	3.121030	CTTCCAGCGCCGTCTTGG	61.121	66.667	2.29	4.72	42.50	3.61
1429	1745	3.319198	ACCCGTGCTGATCCCGTT	61.319	61.111	0.00	0.00	0.00	4.44
1444	1770	2.904866	GTTCGTGCCTGGTGCCAA	60.905	61.111	0.00	0.00	40.16	4.52
1445	1771	2.904866	TTCGTGCCTGGTGCCAAC	60.905	61.111	0.00	0.00	40.16	3.77
1446	1772	3.414136	TTCGTGCCTGGTGCCAACT	62.414	57.895	0.00	0.00	40.16	3.16
1447	1773	3.357079	CGTGCCTGGTGCCAACTC	61.357	66.667	0.00	0.00	40.16	3.01
1448	1774	3.357079	GTGCCTGGTGCCAACTCG	61.357	66.667	0.00	0.00	40.16	4.18
1449	1775	3.872603	TGCCTGGTGCCAACTCGT	61.873	61.111	0.00	0.00	40.16	4.18
1450	1776	2.594592	GCCTGGTGCCAACTCGTT	60.595	61.111	0.00	0.00	0.00	3.85
1451	1777	2.617274	GCCTGGTGCCAACTCGTTC	61.617	63.158	0.00	0.00	0.00	3.95
1798	7254	2.746277	GCGCCCGGTGTGAAGAAT	60.746	61.111	0.00	0.00	0.00	2.40
1806	7265	2.289072	CCGGTGTGAAGAATGTGACTCT	60.289	50.000	0.00	0.00	0.00	3.24
1822	7281	1.203523	ACTCTAGCTTCAACTCTGCGG	59.796	52.381	0.00	0.00	0.00	5.69
1863	7322	1.380524	CTCAGCTGCAAGATTCCCAG	58.619	55.000	9.47	0.00	34.07	4.45
1887	7346	0.609662	AACCAATCACCATTGCCTGC	59.390	50.000	0.00	0.00	38.53	4.85
1983	7445	8.297426	GTCTTTTTACCTTCCTAAACCATTCAG	58.703	37.037	0.00	0.00	0.00	3.02
2435	7906	6.945435	TGGCTGTCCTGTAAAATTAATCTTGA	59.055	34.615	0.00	0.00	0.00	3.02
2491	7964	6.273071	GTGAGTTAAAGTTGCAGTTTCCAAT	58.727	36.000	0.00	0.00	0.00	3.16
2495	7968	3.375782	AAGTTGCAGTTTCCAATGAGC	57.624	42.857	0.00	0.00	0.00	4.26
2565	8038	4.223923	AGCTAAGCAAGTCCTTGATGTACT	59.776	41.667	11.12	0.66	42.93	2.73
2717	8260	3.403038	TCTGCTGCTCTAGTTGGAAAAC	58.597	45.455	0.00	0.00	0.00	2.43
2849	8848	3.656559	GCAATCAAATTGGCAAGAGTGT	58.343	40.909	14.21	0.00	40.57	3.55
2850	8849	3.430895	GCAATCAAATTGGCAAGAGTGTG	59.569	43.478	14.21	6.34	40.57	3.82
2918	8926	9.242477	GGCTTTTTCATATCTTAGCTTTTCATC	57.758	33.333	0.00	0.00	0.00	2.92
3018	9034	0.032130	TCATCGCTCCAAGTATCCGC	59.968	55.000	0.00	0.00	0.00	5.54
3037	9053	0.320073	CCGTGCCGTTCCAGTCTAAA	60.320	55.000	0.00	0.00	0.00	1.85
3134	9150	0.602905	AGCGCTGGAACTGGTTGTAC	60.603	55.000	10.39	0.00	0.00	2.90
3135	9151	0.602905	GCGCTGGAACTGGTTGTACT	60.603	55.000	0.00	0.00	0.00	2.73
3136	9152	1.337447	GCGCTGGAACTGGTTGTACTA	60.337	52.381	0.00	0.00	0.00	1.82
3177	9193	3.909995	CACTCCCCCAACATATCCTATCA	59.090	47.826	0.00	0.00	0.00	2.15

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
67	68	0.843984	AAGCGGTTAGTGGGCCATAT	59.156	50.000	10.70	4.15	0.00	1.78
165	166	1.240256	GTGAGAGGTGTGAGACGAGT	58.760	55.000	0.00	0.00	0.00	4.18
189	190	1.207329	GCTACCACCTCCGATGAACTT	59.793	52.381	0.00	0.00	0.00	2.66
196	197	1.001120	TGATGGCTACCACCTCCGA	59.999	57.895	0.00	0.00	35.80	4.55
236	237	1.079681	GGGGAATACGTGTGTGCGA	60.080	57.895	0.00	0.00	35.59	5.10
244	245	2.104792	CCATCATGACAGGGGAATACGT	59.895	50.000	0.00	0.00	0.00	3.57
305	313	2.426023	GGTGCAACACGAGGTCCT	59.574	61.111	0.00	0.00	39.98	3.85
338	346	0.733729	GTGGTCATAGCTCGTCGTCT	59.266	55.000	0.00	0.00	0.00	4.18
360	566	4.379243	CGGTTGCAGCTCCCTCGT	62.379	66.667	0.00	0.00	0.00	4.18
394	600	3.801050	CCATCATAGCTCTTCTCGTTGTG	59.199	47.826	0.00	0.00	0.00	3.33
395	601	3.181471	CCCATCATAGCTCTTCTCGTTGT	60.181	47.826	0.00	0.00	0.00	3.32
397	603	3.034635	ACCCATCATAGCTCTTCTCGTT	58.965	45.455	0.00	0.00	0.00	3.85
444	688	0.667184	CCCAGCAAAAATGGTCGTGC	60.667	55.000	0.00	0.00	35.96	5.34
474	718	6.156949	TCCCTTCTGATACTAAATGTGCTTCT	59.843	38.462	0.00	0.00	0.00	2.85
489	733	8.477419	TTCTTACACAAATTTTCCCTTCTGAT	57.523	30.769	0.00	0.00	0.00	2.90
490	734	7.014230	CCTTCTTACACAAATTTTCCCTTCTGA	59.986	37.037	0.00	0.00	0.00	3.27
491	735	7.014230	TCCTTCTTACACAAATTTTCCCTTCTG	59.986	37.037	0.00	0.00	0.00	3.02
612	873	7.973388	GCACAGCCTAAAATGATGTGTATAAAA	59.027	33.333	9.93	0.00	42.48	1.52
630	891	2.283145	ATTGTTCTTGAGCACAGCCT	57.717	45.000	0.00	0.00	0.00	4.58
658	919	7.581213	AATTCTGTGGTACAAAAATCAGTCA	57.419	32.000	0.00	0.00	44.16	3.41
661	922	6.868339	GGGAAATTCTGTGGTACAAAAATCAG	59.132	38.462	0.00	0.00	44.16	2.90
677	938	6.053632	CCAATTTGGCTTTAGGGAAATTCT	57.946	37.500	1.71	0.00	0.00	2.40
713	974	8.757982	ATAAAATAGGATGTGCAAGACAGAAT	57.242	30.769	0.00	0.00	38.23	2.40
756	1025	1.068250	GGACGCCTCTGCATCCTAC	59.932	63.158	0.00	0.00	46.31	3.18
850	1147	2.583739	TCACGCGCTCATTCATTTTTG	58.416	42.857	5.73	0.00	0.00	2.44
992	1296	1.277557	AGCAGATCGAAGTGGAGCTTT	59.722	47.619	0.00	0.00	37.59	3.51
993	1297	0.901124	AGCAGATCGAAGTGGAGCTT	59.099	50.000	0.00	0.00	40.76	3.74
1250	1566	4.373116	GAAGTCGGCGTCCCAGCA	62.373	66.667	6.85	0.00	39.27	4.41
1442	1768	1.867233	CTTGAGGTGGTGAACGAGTTG	59.133	52.381	0.00	0.00	0.00	3.16
1443	1769	1.202651	CCTTGAGGTGGTGAACGAGTT	60.203	52.381	0.00	0.00	0.00	3.01
1444	1770	0.393077	CCTTGAGGTGGTGAACGAGT	59.607	55.000	0.00	0.00	0.00	4.18
1445	1771	0.320771	CCCTTGAGGTGGTGAACGAG	60.321	60.000	0.00	0.00	0.00	4.18
1446	1772	1.752198	CCCTTGAGGTGGTGAACGA	59.248	57.895	0.00	0.00	0.00	3.85
1447	1773	4.379174	CCCTTGAGGTGGTGAACG	57.621	61.111	0.00	0.00	0.00	3.95
1798	7254	3.305676	GCAGAGTTGAAGCTAGAGTCACA	60.306	47.826	0.00	0.00	0.00	3.58
1806	7265	1.079127	GCCCGCAGAGTTGAAGCTA	60.079	57.895	0.00	0.00	0.00	3.32
1822	7281	1.130678	CCCTCATCCCCCTTCTAGCC	61.131	65.000	0.00	0.00	0.00	3.93
1863	7322	1.805943	GCAATGGTGATTGGTTTTGCC	59.194	47.619	0.00	0.00	39.62	4.52
1983	7445	8.031277	AGGCAAAGATTAAATGAAACTCATGTC	58.969	33.333	0.00	0.00	37.15	3.06
2211	7676	4.637534	TGGCTCATCTGCTTTACTTTGATC	59.362	41.667	0.00	0.00	0.00	2.92
2241	7708	5.392380	GGAATTGCAGTACATGAGTTTCCAG	60.392	44.000	0.00	0.00	34.30	3.86
2435	7906	4.851639	ATGCCTAAGAATCCAAGTCAGT	57.148	40.909	0.00	0.00	0.00	3.41
2491	7964	0.178995	TCACCAACCAATGCTGCTCA	60.179	50.000	0.00	0.00	0.00	4.26
2495	7968	2.233271	AGAGTTCACCAACCAATGCTG	58.767	47.619	0.00	0.00	32.22	4.41
2717	8260	2.263077	GATTCGTGCCTCAGTACACAG	58.737	52.381	0.00	0.00	36.57	3.66
2789	8580	5.229423	CAATAACTGTCCCAAACATGGTTG	58.771	41.667	16.91	16.91	37.23	3.77
2849	8848	4.100707	GCACTATGATGCAAGCTTTTCA	57.899	40.909	0.00	0.67	45.39	2.69
2918	8926	4.083324	AGACTGTTGTTGCACATAATTCGG	60.083	41.667	0.00	0.00	0.00	4.30
3018	9034	4.799502	AGTTTAGACTGGAACGGCACGG	62.800	54.545	0.00	0.00	46.93	4.94

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.