AutoCloner

Multiple sequence alignment - TraesCS3B01G225200

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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	TraesCS3B01G225200	chr3B	100.000	2744	0	0	1	2744	309408514	309411257	0.000000e+00	5068.0
1	TraesCS3B01G225200	chr3B	94.444	36	1	1	2505	2540	123121327	123121361	1.000000e-03	54.7
2	TraesCS3B01G225200	chr3A	89.962	2112	68	64	723	2744	336612653	336610596	0.000000e+00	2593.0
3	TraesCS3B01G225200	chr3A	88.965	734	47	9	1	728	336613732	336613027	0.000000e+00	876.0
4	TraesCS3B01G225200	chr3A	95.238	42	1	1	2499	2540	496990041	496990081	6.340000e-07	65.8
5	TraesCS3B01G225200	chr3A	80.460	87	12	4	2458	2540	527938618	527938703	8.200000e-06	62.1
6	TraesCS3B01G225200	chr2A	87.301	2071	96	59	768	2744	712064651	712066648	0.000000e+00	2213.0
7	TraesCS3B01G225200	chr2A	83.001	753	35	26	1	745	712063992	712064659	1.820000e-166	595.0
8	TraesCS3B01G225200	chr2D	87.854	1869	64	59	768	2520	572804641	572806462	0.000000e+00	2043.0
9	TraesCS3B01G225200	chr2D	83.777	752	30	23	1	745	572803983	572804649	1.790000e-176	628.0
10	TraesCS3B01G225200	chr2D	96.907	97	3	0	2648	2744	572806653	572806749	2.190000e-36	163.0
11	TraesCS3B01G225200	chr2D	92.857	84	6	0	2530	2613	572806568	572806651	3.710000e-24	122.0
12	TraesCS3B01G225200	chr3D	91.483	1362	64	23	1	1355	253565129	253563813	0.000000e+00	1825.0
13	TraesCS3B01G225200	chr3D	94.040	453	14	7	1431	1874	253556952	253556504	0.000000e+00	675.0
14	TraesCS3B01G225200	chr3D	89.928	417	14	4	2167	2556	253554342	253553927	1.880000e-141	512.0
15	TraesCS3B01G225200	chr3D	95.806	310	6	4	1866	2174	253556414	253556111	6.830000e-136	494.0
16	TraesCS3B01G225200	chr3D	97.744	133	3	0	2612	2744	253553806	253553674	2.130000e-56	230.0
17	TraesCS3B01G225200	chr3D	100.000	38	0	0	1371	1408	253556988	253556951	1.360000e-08	71.3
18	TraesCS3B01G225200	chr3D	95.238	42	1	1	2499	2540	374358800	374358840	6.340000e-07	65.8
19	TraesCS3B01G225200	chr1A	83.451	284	22	10	768	1027	457344230	457344512	9.820000e-60	241.0
20	TraesCS3B01G225200	chr1A	82.517	286	8	12	464	745	457343991	457344238	2.140000e-51	213.0
21	TraesCS3B01G225200	chr1A	81.250	128	6	7	383	509	457344639	457344529	1.350000e-13	87.9
22	TraesCS3B01G225200	chr4A	92.857	42	2	1	2499	2540	684505053	684505013	2.950000e-05	60.2
23	TraesCS3B01G225200	chr5B	92.308	39	2	1	2506	2544	50646857	50646894	1.000000e-03	54.7
24	TraesCS3B01G225200	chr5D	100.000	28	0	0	634	661	342702682	342702709	5.000000e-03	52.8

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	TraesCS3B01G225200	chr3B	309408514	309411257	2743	False	5068.00	5068	100.00000	1	2744	1	chr3B.!!$F2	2743
1	TraesCS3B01G225200	chr3A	336610596	336613732	3136	True	1734.50	2593	89.46350	1	2744	2	chr3A.!!$R1	2743
2	TraesCS3B01G225200	chr2A	712063992	712066648	2656	False	1404.00	2213	85.15100	1	2744	2	chr2A.!!$F1	2743
3	TraesCS3B01G225200	chr2D	572803983	572806749	2766	False	739.00	2043	90.34875	1	2744	4	chr2D.!!$F1	2743
4	TraesCS3B01G225200	chr3D	253563813	253565129	1316	True	1825.00	1825	91.48300	1	1355	1	chr3D.!!$R1	1354
5	TraesCS3B01G225200	chr3D	253553674	253556988	3314	True	396.46	675	95.50360	1371	2744	5	chr3D.!!$R2	1373
6	TraesCS3B01G225200	chr1A	457343991	457344512	521	False	227.00	241	82.98400	464	1027	2	chr1A.!!$F1	563

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
577	614	0.311165	GCATGATGCATGAGCCAGAC	59.689	55.0	13.36	0.0	43.81	3.51	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1956	2661	0.035458	CGGATATTGGTCCTCAGCCC	59.965	60.0	0.0	0.0	36.07	5.19	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	2.034305	CCGTTCTATAGGACTTGTCCGG	59.966	54.545	13.41	0.00	34.28	5.14
102	103	1.006832	GGCGTCGATTTGCTACACAT	58.993	50.000	0.00	0.00	0.00	3.21
157	158	0.667792	AACTTCTCGGACGCTGCTTC	60.668	55.000	0.00	0.00	0.00	3.86
163	164	2.250939	CGGACGCTGCTTCCACAAA	61.251	57.895	22.88	0.00	31.94	2.83
175	176	3.118775	GCTTCCACAAACTCTTGGGTTTT	60.119	43.478	0.00	0.00	37.32	2.43
230	235	1.098869	TTGCCACGAGTTTTGCTCAA	58.901	45.000	0.00	0.00	44.33	3.02
390	419	6.377146	AGGAAAACTGAGTAGCACAAAAGAAA	59.623	34.615	0.00	0.00	0.00	2.52
456	485	3.391382	CGGAGGAGGCGGGAACTT	61.391	66.667	0.00	0.00	0.00	2.66
491	520	3.794717	CACAGTGATCTCTAGCTTGCAT	58.205	45.455	0.00	0.00	0.00	3.96
577	614	0.311165	GCATGATGCATGAGCCAGAC	59.689	55.000	13.36	0.00	43.81	3.51
582	619	0.461516	ATGCATGAGCCAGACAGACG	60.462	55.000	0.00	0.00	41.13	4.18
602	645	2.724977	GCTACTGAGCTACACACACA	57.275	50.000	0.00	0.00	45.98	3.72
603	646	2.329379	GCTACTGAGCTACACACACAC	58.671	52.381	0.00	0.00	45.98	3.82
604	647	2.029828	GCTACTGAGCTACACACACACT	60.030	50.000	0.00	0.00	45.98	3.55
605	648	2.802787	ACTGAGCTACACACACACTC	57.197	50.000	0.00	0.00	0.00	3.51
606	649	2.031870	ACTGAGCTACACACACACTCA	58.968	47.619	0.00	0.00	36.08	3.41
607	650	2.223829	ACTGAGCTACACACACACTCAC	60.224	50.000	0.00	0.00	33.95	3.51
608	651	2.031870	TGAGCTACACACACACTCACT	58.968	47.619	0.00	0.00	32.65	3.41
745	1167	2.814023	GCTAGCCAGCTCTACTCCA	58.186	57.895	2.29	0.00	44.93	3.86
754	1176	0.757561	GCTCTACTCCACTCCTCCCC	60.758	65.000	0.00	0.00	0.00	4.81
755	1177	0.466555	CTCTACTCCACTCCTCCCCG	60.467	65.000	0.00	0.00	0.00	5.73
756	1178	1.455959	CTACTCCACTCCTCCCCGG	60.456	68.421	0.00	0.00	0.00	5.73
757	1179	3.674050	TACTCCACTCCTCCCCGGC	62.674	68.421	0.00	0.00	0.00	6.13
761	1183	4.787280	CACTCCTCCCCGGCCTCT	62.787	72.222	0.00	0.00	0.00	3.69
762	1184	4.467107	ACTCCTCCCCGGCCTCTC	62.467	72.222	0.00	0.00	0.00	3.20
774	1196	2.520741	CCTCTCCGGCCTCTCCTC	60.521	72.222	0.00	0.00	0.00	3.71
807	1258	5.354792	GCACCAAACCGTATATAAAAGACCA	59.645	40.000	0.00	0.00	0.00	4.02
834	1293	1.355720	CTCCCATCTCCAAACCAACCT	59.644	52.381	0.00	0.00	0.00	3.50
861	1324	3.616219	TCCAACACAACACAAGCTAAGT	58.384	40.909	0.00	0.00	0.00	2.24
905	1368	6.420913	TTGGGTTAGATTGATAGCTAGACC	57.579	41.667	0.00	0.00	0.00	3.85
915	1378	2.195741	TAGCTAGACCAGACACACGT	57.804	50.000	0.00	0.00	0.00	4.49
916	1379	2.195741	AGCTAGACCAGACACACGTA	57.804	50.000	0.00	0.00	0.00	3.57
917	1380	1.811359	AGCTAGACCAGACACACGTAC	59.189	52.381	0.00	0.00	0.00	3.67
918	1381	1.465354	GCTAGACCAGACACACGTACG	60.465	57.143	15.01	15.01	0.00	3.67
929	1403	2.182825	CACACGTACGCTAGATTGACC	58.817	52.381	16.72	0.00	0.00	4.02
1254	1744	1.373497	CGCAAAGACAGACTCCGCT	60.373	57.895	0.00	0.00	0.00	5.52
1357	1869	1.977544	CTCCGGCCCCCTATCTACG	60.978	68.421	0.00	0.00	0.00	3.51
1400	1934	2.159324	GCTAGCTTTCCAAGGAATGTGC	60.159	50.000	7.70	12.69	33.79	4.57
1401	1935	1.999648	AGCTTTCCAAGGAATGTGCA	58.000	45.000	17.70	0.00	33.79	4.57
1403	1937	2.232941	AGCTTTCCAAGGAATGTGCATG	59.767	45.455	17.70	0.00	33.79	4.06
1404	1938	2.613691	CTTTCCAAGGAATGTGCATGC	58.386	47.619	11.82	11.82	33.79	4.06
1405	1939	1.630223	TTCCAAGGAATGTGCATGCA	58.370	45.000	18.46	18.46	0.00	3.96
1454	2004	7.169140	CCTGAAAAGAAAGAAAATTAACCACGG	59.831	37.037	0.00	0.00	0.00	4.94
1597	2161	3.554524	CACGGCACATTTACACTTCTTG	58.445	45.455	0.00	0.00	0.00	3.02
1600	2164	4.097286	ACGGCACATTTACACTTCTTGTTT	59.903	37.500	0.00	0.00	39.91	2.83
1609	2180	1.593006	CACTTCTTGTTTGCGACGAGT	59.407	47.619	0.00	0.00	40.20	4.18
1615	2186	1.367665	GTTTGCGACGAGTGCACAC	60.368	57.895	21.04	12.49	43.10	3.82
1623	2200	1.597195	GACGAGTGCACACATTGACAA	59.403	47.619	21.04	0.00	0.00	3.18
1691	2279	1.276421	ACTGGTCTGGTGCTGTATGTC	59.724	52.381	0.00	0.00	0.00	3.06
1705	2293	7.150640	GTGCTGTATGTCATCTCATCTAATCA	58.849	38.462	0.00	0.00	0.00	2.57
1956	2661	0.041751	TACATGTGCGCGTGTGTTTG	60.042	50.000	30.53	3.13	43.95	2.93
2028	2737	6.418057	AATTCCAGTTTGGCTTCATTTGTA	57.582	33.333	0.00	0.00	37.47	2.41
2030	2739	3.252215	TCCAGTTTGGCTTCATTTGTACG	59.748	43.478	0.00	0.00	37.47	3.67
2031	2740	3.004315	CCAGTTTGGCTTCATTTGTACGT	59.996	43.478	0.00	0.00	0.00	3.57
2032	2741	4.499019	CCAGTTTGGCTTCATTTGTACGTT	60.499	41.667	0.00	0.00	0.00	3.99
2033	2742	4.675114	CAGTTTGGCTTCATTTGTACGTTC	59.325	41.667	0.00	0.00	0.00	3.95
2034	2743	4.336993	AGTTTGGCTTCATTTGTACGTTCA	59.663	37.500	0.00	0.00	0.00	3.18
2162	2880	2.559840	CTTGCTTGTGCCTGCTCG	59.440	61.111	0.00	0.00	38.71	5.03
2254	4750	2.053627	GCCACAAGCGAATGTTTCTTG	58.946	47.619	0.00	0.00	41.99	3.02
2497	5032	2.825086	AAGACGTTTTGTGACACTGC	57.175	45.000	7.20	0.00	0.00	4.40
2595	5228	5.246981	AGTCACAATCTTTCCTCCATGAA	57.753	39.130	0.00	0.00	0.00	2.57
2599	5232	7.555554	AGTCACAATCTTTCCTCCATGAATTAG	59.444	37.037	0.00	0.00	0.00	1.73

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
67	68	1.081175	GCCCTGAAGAAGCAAACGC	60.081	57.895	0.00	0.00	0.00	4.84
157	158	6.876789	ACTTTTTAAAACCCAAGAGTTTGTGG	59.123	34.615	0.00	0.00	39.83	4.17
163	164	7.604927	GGAACAAACTTTTTAAAACCCAAGAGT	59.395	33.333	0.00	0.00	0.00	3.24
175	176	5.561993	CGTCTCAACGGAACAAACTTTTTA	58.438	37.500	0.00	0.00	45.21	1.52
230	235	2.156098	ATCCACCCACAGTGCACCT	61.156	57.895	14.63	0.00	45.83	4.00
347	375	3.218453	TCCTTCATTTGCGAAAAGGACA	58.782	40.909	13.75	0.00	41.74	4.02
390	419	7.498443	TCTCGTCTTCTCTTTCCTTAGTTTTT	58.502	34.615	0.00	0.00	0.00	1.94
491	520	0.400381	TGATGGGCCTCTCCATGCTA	60.400	55.000	4.53	0.00	46.67	3.49
597	640	2.099756	TGAGTGAGTGAGTGAGTGTGTG	59.900	50.000	0.00	0.00	0.00	3.82
598	641	2.360483	CTGAGTGAGTGAGTGAGTGTGT	59.640	50.000	0.00	0.00	0.00	3.72
599	642	2.861750	GCTGAGTGAGTGAGTGAGTGTG	60.862	54.545	0.00	0.00	0.00	3.82
600	643	1.339610	GCTGAGTGAGTGAGTGAGTGT	59.660	52.381	0.00	0.00	0.00	3.55
601	644	1.336702	GGCTGAGTGAGTGAGTGAGTG	60.337	57.143	0.00	0.00	0.00	3.51
602	645	0.965439	GGCTGAGTGAGTGAGTGAGT	59.035	55.000	0.00	0.00	0.00	3.41
603	646	1.067706	CAGGCTGAGTGAGTGAGTGAG	60.068	57.143	9.42	0.00	0.00	3.51
604	647	0.964700	CAGGCTGAGTGAGTGAGTGA	59.035	55.000	9.42	0.00	0.00	3.41
605	648	0.669932	GCAGGCTGAGTGAGTGAGTG	60.670	60.000	20.86	0.00	0.00	3.51
606	649	1.670590	GCAGGCTGAGTGAGTGAGT	59.329	57.895	20.86	0.00	0.00	3.41
607	650	1.079266	GGCAGGCTGAGTGAGTGAG	60.079	63.158	20.86	0.00	0.00	3.51
608	651	2.587247	GGGCAGGCTGAGTGAGTGA	61.587	63.158	20.86	0.00	0.00	3.41
745	1167	4.467107	GAGAGGCCGGGGAGGAGT	62.467	72.222	2.18	0.00	45.00	3.85
757	1179	2.520741	GAGGAGAGGCCGGAGAGG	60.521	72.222	5.05	0.00	43.43	3.69
758	1180	2.520741	GGAGGAGAGGCCGGAGAG	60.521	72.222	5.05	0.00	43.43	3.20
759	1181	3.024356	AGGAGGAGAGGCCGGAGA	61.024	66.667	5.05	0.00	43.43	3.71
760	1182	2.837291	CAGGAGGAGAGGCCGGAG	60.837	72.222	5.05	0.00	43.43	4.63
761	1183	4.465446	CCAGGAGGAGAGGCCGGA	62.465	72.222	5.05	0.00	43.43	5.14
762	1184	4.787280	ACCAGGAGGAGAGGCCGG	62.787	72.222	0.00	0.00	43.43	6.13
763	1185	3.465403	CACCAGGAGGAGAGGCCG	61.465	72.222	0.00	0.00	43.43	6.13
764	1186	3.791586	GCACCAGGAGGAGAGGCC	61.792	72.222	0.00	0.00	38.69	5.19
765	1187	3.005539	TGCACCAGGAGGAGAGGC	61.006	66.667	0.00	0.00	38.69	4.70
766	1188	3.028921	GCTGCACCAGGAGGAGAGG	62.029	68.421	9.72	0.00	38.69	3.69
767	1189	2.288778	TGCTGCACCAGGAGGAGAG	61.289	63.158	9.72	0.00	38.69	3.20
768	1190	2.203832	TGCTGCACCAGGAGGAGA	60.204	61.111	9.72	0.00	38.69	3.71
769	1191	2.046507	GTGCTGCACCAGGAGGAG	60.047	66.667	21.78	0.59	33.46	3.69
807	1258	0.119155	TTGGAGATGGGAGGTGGAGT	59.881	55.000	0.00	0.00	0.00	3.85
834	1293	2.647683	TGTGTTGTGTTGGATGGCTA	57.352	45.000	0.00	0.00	0.00	3.93
861	1324	1.556911	GGAGAAGGTGATGAGAGGCAA	59.443	52.381	0.00	0.00	0.00	4.52
905	1368	2.826979	ATCTAGCGTACGTGTGTCTG	57.173	50.000	17.90	1.15	0.00	3.51
915	1378	1.674441	CAGACCGGTCAATCTAGCGTA	59.326	52.381	35.00	0.00	38.65	4.42
916	1379	0.456221	CAGACCGGTCAATCTAGCGT	59.544	55.000	35.00	9.45	38.65	5.07
917	1380	0.738975	TCAGACCGGTCAATCTAGCG	59.261	55.000	35.00	12.97	39.95	4.26
918	1381	3.821600	TCTATCAGACCGGTCAATCTAGC	59.178	47.826	35.00	7.51	0.00	3.42
980	1456	7.224753	TCTCCATCGCTGTTAATAATCAGAAAC	59.775	37.037	6.73	0.00	34.02	2.78
995	1485	1.137675	TCATCACCTTCTCCATCGCTG	59.862	52.381	0.00	0.00	0.00	5.18
1032	1522	1.734477	CGACCTGCAACTCCAGTCG	60.734	63.158	0.00	0.00	33.56	4.18
1092	1582	3.854669	AGCTTAGCCTCGCCGCAT	61.855	61.111	0.00	0.00	0.00	4.73
1357	1869	9.344309	CTAGCTTTAATCTAACCGATTAGCTAC	57.656	37.037	11.97	0.00	45.51	3.58
1454	2004	0.109597	CAGTCTGCATCGCCAAAACC	60.110	55.000	0.00	0.00	0.00	3.27
1597	2161	1.367665	GTGTGCACTCGTCGCAAAC	60.368	57.895	19.41	0.00	41.97	2.93
1600	2164	1.594021	AATGTGTGCACTCGTCGCA	60.594	52.632	19.41	3.99	36.94	5.10
1609	2180	4.717233	AGAAAAGTTGTCAATGTGTGCA	57.283	36.364	0.00	0.00	0.00	4.57
1615	2186	6.329838	TCGCAAAAAGAAAAGTTGTCAATG	57.670	33.333	0.00	0.00	0.00	2.82
1623	2200	3.989817	GCCATCATCGCAAAAAGAAAAGT	59.010	39.130	0.00	0.00	0.00	2.66
1718	2306	4.469657	ACCTGCAAAGGAAGTAAACATCA	58.530	39.130	0.00	0.00	0.00	3.07
1719	2307	5.453567	AACCTGCAAAGGAAGTAAACATC	57.546	39.130	0.00	0.00	0.00	3.06
1720	2308	6.969993	TTAACCTGCAAAGGAAGTAAACAT	57.030	33.333	0.00	0.00	0.00	2.71
1837	2436	2.624364	GGGTTGGCGAAGGTTTTTCTTA	59.376	45.455	0.00	0.00	0.00	2.10
1956	2661	0.035458	CGGATATTGGTCCTCAGCCC	59.965	60.000	0.00	0.00	36.07	5.19
2031	2740	5.123820	CAGGAGTTCACTCAAAAGTTGTGAA	59.876	40.000	9.18	0.06	44.96	3.18
2032	2741	4.635765	CAGGAGTTCACTCAAAAGTTGTGA	59.364	41.667	9.18	0.00	44.60	3.58
2033	2742	4.396166	ACAGGAGTTCACTCAAAAGTTGTG	59.604	41.667	9.18	0.00	44.60	3.33
2034	2743	4.396166	CACAGGAGTTCACTCAAAAGTTGT	59.604	41.667	9.18	1.33	44.60	3.32
2254	4750	0.167470	GCGGCGACTAAAGGTTTTCC	59.833	55.000	12.98	0.00	41.05	3.13
2281	4778	1.822371	GCTCCCGGAATCTCTCTATCC	59.178	57.143	0.73	0.00	0.00	2.59
2467	5002	9.360093	TGTCACAAAACGTCTTTTATTTTGATT	57.640	25.926	13.87	0.00	43.07	2.57
2528	5161	2.292918	ACATACCAAGCTACTCCCTCCA	60.293	50.000	0.00	0.00	0.00	3.86
2657	5355	1.890876	TTACACCGTGCAGCTTTGAT	58.109	45.000	0.00	0.00	0.00	2.57

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.