AutoCloner

Multiple sequence alignment - TraesCS6A01G095200

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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	TraesCS6A01G095200	chr6A	100.000	3693	0	0	1	3693	61877445	61873753	0.000000e+00	6820
1	TraesCS6A01G095200	chr6B	95.116	3112	122	17	1	3101	118188758	118185666	0.000000e+00	4878
2	TraesCS6A01G095200	chr6D	93.951	3141	113	27	1	3101	53563579	53566682	0.000000e+00	4676
3	TraesCS6A01G095200	chr3A	95.377	584	24	3	3111	3693	279426516	279427097	0.000000e+00	926
4	TraesCS6A01G095200	chr5A	94.692	584	30	1	3111	3693	689173210	689172627	0.000000e+00	905
5	TraesCS6A01G095200	chr5A	93.537	588	29	9	3111	3693	32722472	32721889	0.000000e+00	867
6	TraesCS6A01G095200	chr5A	91.837	588	38	9	3111	3693	457527411	457527993	0.000000e+00	811
7	TraesCS6A01G095200	chr5A	83.502	594	79	13	3113	3693	635932287	635931700	1.510000e-148	536
8	TraesCS6A01G095200	chr2B	90.460	587	50	6	3111	3693	63217269	63216685	0.000000e+00	769
9	TraesCS6A01G095200	chr7D	91.003	578	35	11	3120	3693	522874241	522874805	0.000000e+00	763
10	TraesCS6A01G095200	chr5D	88.047	594	56	10	3111	3693	45119382	45119971	0.000000e+00	689
11	TraesCS6A01G095200	chr3B	85.522	594	67	12	3111	3693	727315637	727315052	1.470000e-168	603
12	TraesCS6A01G095200	chr7A	100.000	76	0	0	784	859	217584112	217584187	1.380000e-29	141

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	TraesCS6A01G095200	chr6A	61873753	61877445	3692	True	6820	6820	100.000	1	3693	1	chr6A.!!$R1	3692
1	TraesCS6A01G095200	chr6B	118185666	118188758	3092	True	4878	4878	95.116	1	3101	1	chr6B.!!$R1	3100
2	TraesCS6A01G095200	chr6D	53563579	53566682	3103	False	4676	4676	93.951	1	3101	1	chr6D.!!$F1	3100
3	TraesCS6A01G095200	chr3A	279426516	279427097	581	False	926	926	95.377	3111	3693	1	chr3A.!!$F1	582
4	TraesCS6A01G095200	chr5A	689172627	689173210	583	True	905	905	94.692	3111	3693	1	chr5A.!!$R3	582
5	TraesCS6A01G095200	chr5A	32721889	32722472	583	True	867	867	93.537	3111	3693	1	chr5A.!!$R1	582
6	TraesCS6A01G095200	chr5A	457527411	457527993	582	False	811	811	91.837	3111	3693	1	chr5A.!!$F1	582
7	TraesCS6A01G095200	chr5A	635931700	635932287	587	True	536	536	83.502	3113	3693	1	chr5A.!!$R2	580
8	TraesCS6A01G095200	chr2B	63216685	63217269	584	True	769	769	90.460	3111	3693	1	chr2B.!!$R1	582
9	TraesCS6A01G095200	chr7D	522874241	522874805	564	False	763	763	91.003	3120	3693	1	chr7D.!!$F1	573
10	TraesCS6A01G095200	chr5D	45119382	45119971	589	False	689	689	88.047	3111	3693	1	chr5D.!!$F1	582
11	TraesCS6A01G095200	chr3B	727315052	727315637	585	True	603	603	85.522	3111	3693	1	chr3B.!!$R1	582

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
603	611	0.689055	AAGAGACTGTGCTGCCATGA	59.311	50.0	0.0	0.0	0.0	3.07	F
1309	1325	0.250295	TCAGACCCTTTTCGCACCAG	60.250	55.0	0.0	0.0	0.0	4.00	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2503	2535	0.391661	GCCTTCTCATGACCGAAGCA	60.392	55.0	15.84	0.0	36.25	3.91	R
3108	3154	0.310543	GGCGATGCAAGTGTGACAAA	59.689	50.0	0.00	0.0	0.00	2.83	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
88	90	4.680237	CCTCGGCAAGCGTGTCCA	62.680	66.667	12.00	0.00	0.00	4.02
114	116	2.124983	CTGGTGCCGTCCTCATGG	60.125	66.667	0.00	0.00	0.00	3.66
362	370	3.986134	AGCTCCATCTCAATATTCCCCTT	59.014	43.478	0.00	0.00	0.00	3.95
363	371	4.077822	GCTCCATCTCAATATTCCCCTTG	58.922	47.826	0.00	0.00	0.00	3.61
479	487	4.202567	GGATGGCCTTGGATGGTAATTCTA	60.203	45.833	3.32	0.00	0.00	2.10
603	611	0.689055	AAGAGACTGTGCTGCCATGA	59.311	50.000	0.00	0.00	0.00	3.07
691	699	7.279313	GTCTGAAATTTTGCATAATGGCATCTT	59.721	33.333	0.00	0.00	44.48	2.40
706	714	3.887716	GGCATCTTCAGGAGTATTGCAAT	59.112	43.478	17.56	17.56	32.40	3.56
712	720	5.181811	TCTTCAGGAGTATTGCAATGTTGTG	59.818	40.000	22.27	12.15	0.00	3.33
723	731	4.118410	TGCAATGTTGTGGTGTCATTTTC	58.882	39.130	0.00	0.00	30.74	2.29
724	732	4.141981	TGCAATGTTGTGGTGTCATTTTCT	60.142	37.500	0.00	0.00	30.74	2.52
732	740	4.036734	TGTGGTGTCATTTTCTCAAAGAGC	59.963	41.667	0.00	0.00	0.00	4.09
872	880	5.521906	TCTGAGATGTGAACTAGTATGCC	57.478	43.478	0.00	0.00	0.00	4.40
913	921	4.243270	ACAGTTTGATTCGTACAGCCTAC	58.757	43.478	0.00	0.00	0.00	3.18
984	996	5.251764	AGAAGATTCACTGGTGATTTGGAG	58.748	41.667	4.19	0.00	39.64	3.86
1076	1088	3.137544	ACCACTCACCCAATTTGACTACA	59.862	43.478	0.00	0.00	0.00	2.74
1204	1220	4.561735	TCGTGACAAAATTTCAGTTCCC	57.438	40.909	0.00	0.00	0.00	3.97
1227	1243	2.689983	ACCTCTGCTTGTGGAAACAAAG	59.310	45.455	5.62	0.00	46.06	2.77
1228	1244	2.951642	CCTCTGCTTGTGGAAACAAAGA	59.048	45.455	0.00	0.00	46.06	2.52
1261	1277	1.340889	TGCTTGCCTTTTTAGCACCAG	59.659	47.619	0.00	0.00	40.69	4.00
1272	1288	7.201522	GCCTTTTTAGCACCAGCATATTTTTAC	60.202	37.037	0.00	0.00	45.49	2.01
1273	1289	8.034804	CCTTTTTAGCACCAGCATATTTTTACT	58.965	33.333	0.00	0.00	45.49	2.24
1274	1290	9.423061	CTTTTTAGCACCAGCATATTTTTACTT	57.577	29.630	0.00	0.00	45.49	2.24
1275	1291	9.771534	TTTTTAGCACCAGCATATTTTTACTTT	57.228	25.926	0.00	0.00	45.49	2.66
1276	1292	9.771534	TTTTAGCACCAGCATATTTTTACTTTT	57.228	25.926	0.00	0.00	45.49	2.27
1277	1293	9.771534	TTTAGCACCAGCATATTTTTACTTTTT	57.228	25.926	0.00	0.00	45.49	1.94
1303	1319	8.712285	TTAGTGTATAAATCAGACCCTTTTCG	57.288	34.615	0.00	0.00	0.00	3.46
1309	1325	0.250295	TCAGACCCTTTTCGCACCAG	60.250	55.000	0.00	0.00	0.00	4.00
1364	1380	7.095695	AGGTTACATATTTTTAGCGCACAAT	57.904	32.000	11.47	4.35	0.00	2.71
1370	1386	8.532977	ACATATTTTTAGCGCACAATCTTTTT	57.467	26.923	11.47	0.00	0.00	1.94
1371	1387	8.647226	ACATATTTTTAGCGCACAATCTTTTTC	58.353	29.630	11.47	0.00	0.00	2.29
1394	1413	9.528489	TTTCATATAGAATAAAATAGGTGGCCC	57.472	33.333	0.00	0.00	35.83	5.80
1418	1437	3.401033	TCACTTTCTCATTCTTCGGCA	57.599	42.857	0.00	0.00	0.00	5.69
1421	1440	3.499918	CACTTTCTCATTCTTCGGCAACT	59.500	43.478	0.00	0.00	0.00	3.16
1422	1441	4.690748	CACTTTCTCATTCTTCGGCAACTA	59.309	41.667	0.00	0.00	0.00	2.24
1423	1442	4.932200	ACTTTCTCATTCTTCGGCAACTAG	59.068	41.667	0.00	0.00	0.00	2.57
1794	1814	4.101448	CTCACGGGGCAAGGAGGG	62.101	72.222	0.00	0.00	0.00	4.30
1812	1835	2.444895	GGAGGGGCTGATCCGTCT	60.445	66.667	0.00	0.00	40.46	4.18
1848	1871	1.826024	CCTCCCTTCCGACATCCTG	59.174	63.158	0.00	0.00	0.00	3.86
1872	1895	2.456119	GGTGACTGCCAGAATCGCG	61.456	63.158	0.00	0.00	0.00	5.87
1938	1961	6.201425	GGCGATCGTAAGTGACCAATTAATTA	59.799	38.462	17.81	0.00	39.48	1.40
1961	1984	5.789643	TTCCTTTCCTTTCTGATGTTTGG	57.210	39.130	0.00	0.00	0.00	3.28
2301	2333	2.205022	CAGGAGGAAATCTGCAACCA	57.795	50.000	0.00	0.00	36.17	3.67
2416	2448	3.060473	GTGACGCTTACAATATCGAAGGC	60.060	47.826	0.00	0.00	0.00	4.35
2503	2535	1.658686	CTTCCGTACGCAGAGAGGCT	61.659	60.000	10.49	0.00	0.00	4.58
2796	2828	3.740321	GCTTCTCCAATTCTAGATCTGCG	59.260	47.826	5.18	0.00	0.00	5.18
2812	2844	2.677836	TCTGCGATCCCAATTTTTCTCG	59.322	45.455	0.00	0.00	0.00	4.04
2820	2852	6.292919	CGATCCCAATTTTTCTCGTTCCTATC	60.293	42.308	0.00	0.00	0.00	2.08
2821	2855	4.873827	TCCCAATTTTTCTCGTTCCTATCG	59.126	41.667	0.00	0.00	0.00	2.92
2875	2914	7.201705	GGTGGTTAGGTAGTGATATTTTCTTGC	60.202	40.741	0.00	0.00	0.00	4.01
2935	2975	6.571154	CGATATGCTTGTATTTTGTGACATCG	59.429	38.462	0.00	0.00	0.00	3.84
2975	3015	7.148590	GGCCATTTTTGTGAATACTGACAAATC	60.149	37.037	0.00	0.00	40.73	2.17
3064	3110	5.221541	GGTTTGTGTCAATGAAAATGGGGTA	60.222	40.000	0.00	0.00	0.00	3.69
3103	3149	2.002505	ACGAGAGTATCATGGAGGGG	57.997	55.000	0.00	0.00	46.88	4.79
3104	3150	0.605589	CGAGAGTATCATGGAGGGGC	59.394	60.000	0.00	0.00	37.82	5.80
3105	3151	1.825242	CGAGAGTATCATGGAGGGGCT	60.825	57.143	0.00	0.00	37.82	5.19
3106	3152	1.622811	GAGAGTATCATGGAGGGGCTG	59.377	57.143	0.00	0.00	37.82	4.85
3107	3153	1.061812	AGAGTATCATGGAGGGGCTGT	60.062	52.381	0.00	0.00	37.82	4.40
3108	3154	1.771255	GAGTATCATGGAGGGGCTGTT	59.229	52.381	0.00	0.00	33.17	3.16
3109	3155	2.173569	GAGTATCATGGAGGGGCTGTTT	59.826	50.000	0.00	0.00	33.17	2.83
3118	3164	0.258774	AGGGGCTGTTTTGTCACACT	59.741	50.000	0.00	0.00	0.00	3.55
3168	3214	3.338250	GATGGTGGGTCCCCTGCA	61.338	66.667	5.13	0.00	36.94	4.41
3351	3401	4.324874	CCAAGTCTTGATCTCATCCCCTTT	60.325	45.833	14.42	0.00	0.00	3.11
3359	3410	1.308746	TCATCCCCTTTCCCCTCCC	60.309	63.158	0.00	0.00	0.00	4.30
3452	3516	2.622977	GCCCTCATATCCTCTCGATCCT	60.623	54.545	0.00	0.00	31.92	3.24
3466	3530	1.270305	CGATCCTGCCGTAACATCCAT	60.270	52.381	0.00	0.00	0.00	3.41
3540	3604	0.405198	TGGCCTGATTTGGAGCAAGA	59.595	50.000	3.32	0.00	0.00	3.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
114	116	0.107459	GGGCAGAGGAAGATGGACAC	60.107	60.000	0.00	0.00	0.00	3.67
479	487	5.655532	CCATCACAATTTCTTCCCAGAGATT	59.344	40.000	0.00	0.00	34.81	2.40
603	611	4.043310	TCCACTGACCTCATTTTCCTCAAT	59.957	41.667	0.00	0.00	0.00	2.57
691	699	3.758023	CCACAACATTGCAATACTCCTGA	59.242	43.478	12.53	0.00	0.00	3.86
706	714	5.417266	TCTTTGAGAAAATGACACCACAACA	59.583	36.000	0.00	0.00	0.00	3.33
712	720	4.836125	TGCTCTTTGAGAAAATGACACC	57.164	40.909	0.00	0.00	0.00	4.16
723	731	5.106038	TGCCATCACTATTTTGCTCTTTGAG	60.106	40.000	0.00	0.00	0.00	3.02
724	732	4.766373	TGCCATCACTATTTTGCTCTTTGA	59.234	37.500	0.00	0.00	0.00	2.69
732	740	7.092137	TCAGAGAAATGCCATCACTATTTTG	57.908	36.000	0.00	0.00	0.00	2.44
948	960	7.140705	CAGTGAATCTTCTCTCTATACAGCAG	58.859	42.308	0.00	0.00	0.00	4.24
984	996	3.247648	ACAACATTCGTGACAGCAACTAC	59.752	43.478	0.00	0.00	0.00	2.73
1171	1187	3.378911	TTGTCACGATGTAGCTGTGAA	57.621	42.857	5.48	0.00	43.58	3.18
1204	1220	2.023673	TGTTTCCACAAGCAGAGGTTG	58.976	47.619	7.33	7.33	45.13	3.77
1227	1243	3.005155	AGGCAAGCACAAATGTCTCTTTC	59.995	43.478	0.00	0.00	0.00	2.62
1228	1244	2.961062	AGGCAAGCACAAATGTCTCTTT	59.039	40.909	0.00	0.00	0.00	2.52
1277	1293	9.158233	CGAAAAGGGTCTGATTTATACACTAAA	57.842	33.333	0.00	0.00	0.00	1.85
1278	1294	7.279313	GCGAAAAGGGTCTGATTTATACACTAA	59.721	37.037	0.00	0.00	0.00	2.24
1279	1295	6.759827	GCGAAAAGGGTCTGATTTATACACTA	59.240	38.462	0.00	0.00	0.00	2.74
1280	1296	5.585047	GCGAAAAGGGTCTGATTTATACACT	59.415	40.000	0.00	0.00	0.00	3.55
1394	1413	4.377841	GCCGAAGAATGAGAAAGTGAACAG	60.378	45.833	0.00	0.00	0.00	3.16
1418	1437	6.940739	AGAACAGTGATGCATTCTACTAGTT	58.059	36.000	0.00	12.10	29.63	2.24
1421	1440	6.782082	AGAGAACAGTGATGCATTCTACTA	57.218	37.500	0.00	0.00	31.58	1.82
1422	1441	5.674052	AGAGAACAGTGATGCATTCTACT	57.326	39.130	0.00	3.45	31.58	2.57
1423	1442	6.568869	ACTAGAGAACAGTGATGCATTCTAC	58.431	40.000	0.00	0.88	31.58	2.59
1794	1814	3.551407	GACGGATCAGCCCCTCCC	61.551	72.222	0.00	0.00	0.00	4.30
1848	1871	1.768684	TTCTGGCAGTCACCTCCACC	61.769	60.000	15.27	0.00	0.00	4.61
1938	1961	5.279657	GCCAAACATCAGAAAGGAAAGGAAT	60.280	40.000	0.00	0.00	0.00	3.01
1959	1982	3.367600	GCATCATTTCACAATCACAGCCA	60.368	43.478	0.00	0.00	0.00	4.75
1961	1984	3.840468	TGCATCATTTCACAATCACAGC	58.160	40.909	0.00	0.00	0.00	4.40
2200	2231	8.735692	TGAACATGATGCAATTCTGTAAGATA	57.264	30.769	0.00	0.00	46.36	1.98
2301	2333	0.764752	CCCGCTCTCCTTTCCCCTAT	60.765	60.000	0.00	0.00	0.00	2.57
2395	2427	3.120792	GCCTTCGATATTGTAAGCGTCA	58.879	45.455	0.00	0.00	0.00	4.35
2416	2448	0.399454	ATCCCATTGCCTCCTCGATG	59.601	55.000	0.00	0.00	0.00	3.84
2485	2517	1.677966	AGCCTCTCTGCGTACGGAA	60.678	57.895	18.39	4.52	36.02	4.30
2503	2535	0.391661	GCCTTCTCATGACCGAAGCA	60.392	55.000	15.84	0.00	36.25	3.91
2796	2828	6.292919	CGATAGGAACGAGAAAAATTGGGATC	60.293	42.308	0.00	0.00	0.00	3.36
2812	2844	2.317530	AAGCCAGCTTCGATAGGAAC	57.682	50.000	0.00	0.00	0.00	3.62
2875	2914	4.988598	ACGCAAGCCAGTGACCCG	62.989	66.667	0.00	0.00	45.62	5.28
2935	2975	2.959507	ATGGCCGAAATAAAAGCACC	57.040	45.000	0.00	0.00	0.00	5.01
2975	3015	0.331278	TACAATGAGTTGGGGCAGGG	59.669	55.000	0.00	0.00	39.70	4.45
3017	3063	6.375455	ACCGCTGAAGAATATGAAAAACTGAT	59.625	34.615	0.00	0.00	0.00	2.90
3033	3079	2.290367	TCATTGACACAAACCGCTGAAG	59.710	45.455	0.00	0.00	0.00	3.02
3101	3147	1.802508	GCAAGTGTGACAAAACAGCCC	60.803	52.381	0.00	0.00	0.00	5.19
3102	3148	1.135141	TGCAAGTGTGACAAAACAGCC	60.135	47.619	0.00	0.00	0.00	4.85
3103	3149	2.276472	TGCAAGTGTGACAAAACAGC	57.724	45.000	0.00	0.00	0.00	4.40
3104	3150	3.038017	CGATGCAAGTGTGACAAAACAG	58.962	45.455	0.00	0.00	0.00	3.16
3105	3151	2.794282	GCGATGCAAGTGTGACAAAACA	60.794	45.455	0.00	0.00	0.00	2.83
3106	3152	1.780860	GCGATGCAAGTGTGACAAAAC	59.219	47.619	0.00	0.00	0.00	2.43
3107	3153	1.268999	GGCGATGCAAGTGTGACAAAA	60.269	47.619	0.00	0.00	0.00	2.44
3108	3154	0.310543	GGCGATGCAAGTGTGACAAA	59.689	50.000	0.00	0.00	0.00	2.83
3109	3155	0.817229	TGGCGATGCAAGTGTGACAA	60.817	50.000	0.00	0.00	0.00	3.18
3118	3164	1.913951	ATCACCTCCTGGCGATGCAA	61.914	55.000	0.00	0.00	34.14	4.08
3351	3401	0.698886	CAGGATTGGATGGGAGGGGA	60.699	60.000	0.00	0.00	0.00	4.81
3452	3516	0.809636	CAGCGATGGATGTTACGGCA	60.810	55.000	0.00	0.00	0.00	5.69

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.