AutoCloner

Multiple sequence alignment - TraesCS5B01G497500

Loading Multiple Alignment...

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	TraesCS5B01G497500	chr5B	100.000	3322	0	0	1	3322	664476891	664473570	0.000000e+00	6135
1	TraesCS5B01G497500	chr5B	97.965	1818	30	1	719	2529	664417754	664415937	0.000000e+00	3145
2	TraesCS5B01G497500	chr5B	91.071	1064	65	13	1383	2446	664503803	664502770	0.000000e+00	1411
3	TraesCS5B01G497500	chr5B	92.029	690	31	6	1	689	470626637	470627303	0.000000e+00	948
4	TraesCS5B01G497500	chr5B	97.854	233	4	1	2525	2757	664415780	664415549	5.160000e-108	401
5	TraesCS5B01G497500	chr5B	84.483	406	54	8	867	1271	664504630	664504233	3.110000e-105	392
6	TraesCS5B01G497500	chr5A	91.815	1405	91	14	1383	2780	655189357	655187970	0.000000e+00	1936
7	TraesCS5B01G497500	chr5A	91.744	1405	92	14	1383	2780	655225519	655224132	0.000000e+00	1930
8	TraesCS5B01G497500	chr5A	92.664	777	50	5	1379	2148	654851793	654851017	0.000000e+00	1112
9	TraesCS5B01G497500	chr5A	86.942	582	45	8	2174	2728	654851022	654850445	2.810000e-175	625
10	TraesCS5B01G497500	chr5A	90.283	247	16	4	2497	2743	654849942	654849704	1.920000e-82	316
11	TraesCS5B01G497500	chr3D	89.219	1076	84	16	1388	2450	2968677	2967621	0.000000e+00	1315
12	TraesCS5B01G497500	chr3D	85.818	275	27	6	1001	1265	2969414	2969142	7.020000e-72	281
13	TraesCS5B01G497500	chr3D	88.785	107	8	4	2490	2594	2967614	2967510	9.670000e-26	128
14	TraesCS5B01G497500	chr7D	87.318	1167	97	27	1398	2548	401550939	401549808	0.000000e+00	1288
15	TraesCS5B01G497500	chr7D	86.385	213	17	8	251	454	147693194	147693403	4.310000e-54	222
16	TraesCS5B01G497500	chr3B	87.918	1076	97	23	1388	2450	2878866	2879921	0.000000e+00	1236
17	TraesCS5B01G497500	chr3B	97.504	561	14	0	2759	3319	4506180	4506740	0.000000e+00	959
18	TraesCS5B01G497500	chr3B	96.809	564	17	1	2759	3322	11940184	11939622	0.000000e+00	941
19	TraesCS5B01G497500	chr3B	84.088	729	49	37	7	696	66627171	66626471	2.790000e-180	641
20	TraesCS5B01G497500	chr3B	82.778	720	59	34	7	688	767301617	767300925	1.720000e-162	582
21	TraesCS5B01G497500	chr3B	84.868	304	32	11	1024	1316	2878158	2878458	9.010000e-76	294
22	TraesCS5B01G497500	chr3B	90.566	106	9	1	2490	2594	2879928	2880033	4.470000e-29	139
23	TraesCS5B01G497500	chr7A	86.189	1173	103	32	1415	2552	459210149	459209001	0.000000e+00	1214
24	TraesCS5B01G497500	chr7A	82.868	537	91	1	2784	3319	96098075	96098611	6.450000e-132	481
25	TraesCS5B01G497500	chr7B	85.618	1189	115	30	1395	2552	411060010	411058847	0.000000e+00	1197
26	TraesCS5B01G497500	chr7B	93.795	693	16	4	1	692	124361526	124362192	0.000000e+00	1016
27	TraesCS5B01G497500	chr7B	97.549	204	5	0	458	661	452159208	452159005	1.900000e-92	350
28	TraesCS5B01G497500	chr6B	94.143	700	14	5	1	697	547694184	547693509	0.000000e+00	1040
29	TraesCS5B01G497500	chr6B	91.271	653	27	2	1	653	705759411	705758789	0.000000e+00	863
30	TraesCS5B01G497500	chr1B	97.340	564	15	0	2759	3322	680759014	680758451	0.000000e+00	959
31	TraesCS5B01G497500	chr1B	83.086	538	86	4	2784	3319	118139532	118140066	4.980000e-133	484
32	TraesCS5B01G497500	chr4B	92.086	695	31	4	1	694	585725739	585725068	0.000000e+00	957
33	TraesCS5B01G497500	chr4B	91.837	245	16	4	1	243	514609048	514609290	4.110000e-89	339
34	TraesCS5B01G497500	chr5D	91.692	662	35	11	1785	2446	527841860	527841219	0.000000e+00	900
35	TraesCS5B01G497500	chr5D	84.146	410	54	8	864	1271	527843042	527842642	1.450000e-103	387
36	TraesCS5B01G497500	chr2A	89.368	696	48	5	1	694	277179127	277178456	0.000000e+00	852
37	TraesCS5B01G497500	chr2B	92.266	556	43	0	2767	3322	25745738	25746293	0.000000e+00	789
38	TraesCS5B01G497500	chr4A	87.644	696	57	9	1	692	503623977	503624647	0.000000e+00	782

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	TraesCS5B01G497500	chr5B	664473570	664476891	3321	True	6135.000000	6135	100.000000	1	3322	1	chr5B.!!$R1	3321
1	TraesCS5B01G497500	chr5B	664415549	664417754	2205	True	1773.000000	3145	97.909500	719	2757	2	chr5B.!!$R2	2038
2	TraesCS5B01G497500	chr5B	470626637	470627303	666	False	948.000000	948	92.029000	1	689	1	chr5B.!!$F1	688
3	TraesCS5B01G497500	chr5B	664502770	664504630	1860	True	901.500000	1411	87.777000	867	2446	2	chr5B.!!$R3	1579
4	TraesCS5B01G497500	chr5A	655187970	655189357	1387	True	1936.000000	1936	91.815000	1383	2780	1	chr5A.!!$R1	1397
5	TraesCS5B01G497500	chr5A	655224132	655225519	1387	True	1930.000000	1930	91.744000	1383	2780	1	chr5A.!!$R2	1397
6	TraesCS5B01G497500	chr5A	654849704	654851793	2089	True	684.333333	1112	89.963000	1379	2743	3	chr5A.!!$R3	1364
7	TraesCS5B01G497500	chr3D	2967510	2969414	1904	True	574.666667	1315	87.940667	1001	2594	3	chr3D.!!$R1	1593
8	TraesCS5B01G497500	chr7D	401549808	401550939	1131	True	1288.000000	1288	87.318000	1398	2548	1	chr7D.!!$R1	1150
9	TraesCS5B01G497500	chr3B	4506180	4506740	560	False	959.000000	959	97.504000	2759	3319	1	chr3B.!!$F1	560
10	TraesCS5B01G497500	chr3B	11939622	11940184	562	True	941.000000	941	96.809000	2759	3322	1	chr3B.!!$R1	563
11	TraesCS5B01G497500	chr3B	66626471	66627171	700	True	641.000000	641	84.088000	7	696	1	chr3B.!!$R2	689
12	TraesCS5B01G497500	chr3B	767300925	767301617	692	True	582.000000	582	82.778000	7	688	1	chr3B.!!$R3	681
13	TraesCS5B01G497500	chr3B	2878158	2880033	1875	False	556.333333	1236	87.784000	1024	2594	3	chr3B.!!$F2	1570
14	TraesCS5B01G497500	chr7A	459209001	459210149	1148	True	1214.000000	1214	86.189000	1415	2552	1	chr7A.!!$R1	1137
15	TraesCS5B01G497500	chr7A	96098075	96098611	536	False	481.000000	481	82.868000	2784	3319	1	chr7A.!!$F1	535
16	TraesCS5B01G497500	chr7B	411058847	411060010	1163	True	1197.000000	1197	85.618000	1395	2552	1	chr7B.!!$R1	1157
17	TraesCS5B01G497500	chr7B	124361526	124362192	666	False	1016.000000	1016	93.795000	1	692	1	chr7B.!!$F1	691
18	TraesCS5B01G497500	chr6B	547693509	547694184	675	True	1040.000000	1040	94.143000	1	697	1	chr6B.!!$R1	696
19	TraesCS5B01G497500	chr6B	705758789	705759411	622	True	863.000000	863	91.271000	1	653	1	chr6B.!!$R2	652
20	TraesCS5B01G497500	chr1B	680758451	680759014	563	True	959.000000	959	97.340000	2759	3322	1	chr1B.!!$R1	563
21	TraesCS5B01G497500	chr1B	118139532	118140066	534	False	484.000000	484	83.086000	2784	3319	1	chr1B.!!$F1	535
22	TraesCS5B01G497500	chr4B	585725068	585725739	671	True	957.000000	957	92.086000	1	694	1	chr4B.!!$R1	693
23	TraesCS5B01G497500	chr5D	527841219	527843042	1823	True	643.500000	900	87.919000	864	2446	2	chr5D.!!$R1	1582
24	TraesCS5B01G497500	chr2A	277178456	277179127	671	True	852.000000	852	89.368000	1	694	1	chr2A.!!$R1	693
25	TraesCS5B01G497500	chr2B	25745738	25746293	555	False	789.000000	789	92.266000	2767	3322	1	chr2B.!!$F1	555
26	TraesCS5B01G497500	chr4A	503623977	503624647	670	False	782.000000	782	87.644000	1	692	1	chr4A.!!$F1	691

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
247	250	0.605589	AGCCGGTTGTAGCTTTCACC	60.606	55.0	1.9	0.0	35.22	4.02	F
248	251	0.887387	GCCGGTTGTAGCTTTCACCA	60.887	55.0	1.9	0.0	0.00	4.17	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1942	2465	1.501582	AGTACCTGCATCCCTTCTCC	58.498	55.0	0.00	0.0	0.00	3.71	R
2475	3058	1.572085	CTCCTTGCACAAGACTGCCG	61.572	60.0	11.94	0.0	40.79	5.69	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
241	244	0.889186	CACCAAAGCCGGTTGTAGCT	60.889	55.000	1.90	0.00	42.40	3.32
245	248	3.717842	AAGCCGGTTGTAGCTTTCA	57.282	47.368	1.90	0.00	46.99	2.69
246	249	1.235724	AAGCCGGTTGTAGCTTTCAC	58.764	50.000	1.90	0.00	46.99	3.18
247	250	0.605589	AGCCGGTTGTAGCTTTCACC	60.606	55.000	1.90	0.00	35.22	4.02
248	251	0.887387	GCCGGTTGTAGCTTTCACCA	60.887	55.000	1.90	0.00	0.00	4.17
249	252	1.600023	CCGGTTGTAGCTTTCACCAA	58.400	50.000	0.00	0.00	0.00	3.67
250	253	1.950909	CCGGTTGTAGCTTTCACCAAA	59.049	47.619	0.00	0.00	0.00	3.28
251	254	2.031157	CCGGTTGTAGCTTTCACCAAAG	60.031	50.000	0.00	0.00	41.92	2.77
308	311	1.272769	GCCCTAGTCTCGTTTGACAGT	59.727	52.381	8.19	0.00	39.27	3.55
396	409	4.891992	AGAAAGCTTGGAGTAGTAGCAA	57.108	40.909	0.00	0.00	37.37	3.91
669	715	2.049248	GCAACGGTTCGGTCGGTA	60.049	61.111	0.00	0.00	0.00	4.02
694	740	5.052481	GCCGTCTATTAACGTTTCCCTAAT	58.948	41.667	5.91	1.95	41.01	1.73
696	742	6.701400	GCCGTCTATTAACGTTTCCCTAATTA	59.299	38.462	5.91	0.00	41.01	1.40
707	753	8.828688	ACGTTTCCCTAATTATATAGTCAAGC	57.171	34.615	0.00	0.00	0.00	4.01
708	754	8.426489	ACGTTTCCCTAATTATATAGTCAAGCA	58.574	33.333	0.00	0.00	0.00	3.91
709	755	9.268268	CGTTTCCCTAATTATATAGTCAAGCAA	57.732	33.333	0.00	0.00	0.00	3.91
741	787	2.094762	ACCGAACAGTTACTCATGGC	57.905	50.000	0.00	0.00	0.00	4.40
768	814	6.538381	GCCATAATTGTCCAAACCCTTATTTG	59.462	38.462	0.00	0.00	38.96	2.32
769	815	6.538381	CCATAATTGTCCAAACCCTTATTTGC	59.462	38.462	0.00	0.00	38.10	3.68
821	867	2.424956	ACGGAACCGATTACTAGTGGAC	59.575	50.000	20.14	0.00	42.83	4.02
858	904	9.386010	CTAGGATAAGATAACTACTAGCACGAT	57.614	37.037	0.00	0.00	0.00	3.73
897	943	1.301165	GCAAGCCAAAACCCTGCTG	60.301	57.895	0.00	0.00	35.08	4.41
1022	1068	1.432270	GCGCCTCTTGGTGATACTGC	61.432	60.000	0.00	0.00	46.34	4.40
1284	1375	3.138283	CCTATCCTTTTACCATCTGGCCA	59.862	47.826	4.71	4.71	39.32	5.36
1295	1386	2.224606	CATCTGGCCACGCATTAGATT	58.775	47.619	0.00	0.00	0.00	2.40
1570	2093	2.417719	GGAGAGCGTGAGTTCATGTTT	58.582	47.619	3.51	0.00	44.48	2.83
2219	2777	0.832135	TGAGGGAGGTGCTCGAGTTT	60.832	55.000	15.13	0.00	0.00	2.66
2475	3058	2.077413	TTTGATTGCATCCGTTTGGC	57.923	45.000	0.00	0.00	34.14	4.52
2488	3075	2.844451	TTTGGCGGCAGTCTTGTGC	61.844	57.895	12.87	0.00	43.19	4.57
2528	3872	5.417580	TGTTGTAGCCTTCACCCAAATATTC	59.582	40.000	0.00	0.00	0.00	1.75
2757	4101	7.857734	TTTATTCTTCATAATTGACGAGCCA	57.142	32.000	0.00	0.00	32.39	4.75
2769	4113	1.672030	CGAGCCACTCCAACATGCA	60.672	57.895	0.00	0.00	0.00	3.96
2806	4150	3.133464	ATCGTTGCACCGCCATGG	61.133	61.111	7.63	7.63	46.41	3.66
2918	4263	2.757077	CCGGAAACCCCAGCTTCT	59.243	61.111	0.00	0.00	34.14	2.85
2924	4269	2.337879	AAACCCCAGCTTCTGCGTCA	62.338	55.000	0.00	0.00	45.42	4.35
3302	4647	1.896220	TGACATCAAGGTGGTCAAGC	58.104	50.000	0.00	0.00	38.50	4.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
241	244	2.360801	GCTACAACCAGCTTTGGTGAAA	59.639	45.455	5.08	0.00	42.20	2.69
242	245	1.953686	GCTACAACCAGCTTTGGTGAA	59.046	47.619	5.08	0.00	42.20	3.18
243	246	1.604604	GCTACAACCAGCTTTGGTGA	58.395	50.000	5.08	0.00	42.20	4.02
251	254	1.079503	CTTCGGAAGCTACAACCAGC	58.920	55.000	4.57	0.00	42.12	4.85
252	255	2.457366	ACTTCGGAAGCTACAACCAG	57.543	50.000	17.37	0.00	0.00	4.00
253	256	2.489971	CAACTTCGGAAGCTACAACCA	58.510	47.619	17.37	0.00	0.00	3.67
254	257	1.197036	GCAACTTCGGAAGCTACAACC	59.803	52.381	17.37	0.00	0.00	3.77
255	258	1.197036	GGCAACTTCGGAAGCTACAAC	59.803	52.381	17.37	2.09	0.00	3.32
256	259	1.519408	GGCAACTTCGGAAGCTACAA	58.481	50.000	17.37	0.00	0.00	2.41
257	260	0.669318	CGGCAACTTCGGAAGCTACA	60.669	55.000	17.37	0.00	0.00	2.74
258	261	2.079049	CGGCAACTTCGGAAGCTAC	58.921	57.895	17.37	6.78	0.00	3.58
259	262	4.590487	CGGCAACTTCGGAAGCTA	57.410	55.556	17.37	0.00	0.00	3.32
308	311	3.039588	GCTTCAACCGAACGGCGA	61.040	61.111	16.62	7.45	44.57	5.54
332	338	0.662374	ACGACGCTCGAACGACATTT	60.662	50.000	16.16	0.00	43.74	2.32
333	339	1.063951	GACGACGCTCGAACGACATT	61.064	55.000	16.16	0.00	43.74	2.71
669	715	2.262211	GGAAACGTTAATAGACGGCGT	58.738	47.619	14.65	14.65	46.77	5.68
699	745	7.361713	CGGTTCAATTAGGATTTTGCTTGACTA	60.362	37.037	0.00	0.00	0.00	2.59
700	746	6.570378	CGGTTCAATTAGGATTTTGCTTGACT	60.570	38.462	0.00	0.00	0.00	3.41
701	747	5.572896	CGGTTCAATTAGGATTTTGCTTGAC	59.427	40.000	0.00	0.00	0.00	3.18
702	748	5.475220	TCGGTTCAATTAGGATTTTGCTTGA	59.525	36.000	0.00	0.00	0.00	3.02
703	749	5.708948	TCGGTTCAATTAGGATTTTGCTTG	58.291	37.500	0.00	0.00	0.00	4.01
704	750	5.975693	TCGGTTCAATTAGGATTTTGCTT	57.024	34.783	0.00	0.00	0.00	3.91
705	751	5.242838	TGTTCGGTTCAATTAGGATTTTGCT	59.757	36.000	0.00	0.00	0.00	3.91
706	752	5.465935	TGTTCGGTTCAATTAGGATTTTGC	58.534	37.500	0.00	0.00	0.00	3.68
707	753	6.677913	ACTGTTCGGTTCAATTAGGATTTTG	58.322	36.000	0.00	0.00	0.00	2.44
708	754	6.894339	ACTGTTCGGTTCAATTAGGATTTT	57.106	33.333	0.00	0.00	0.00	1.82
709	755	6.894339	AACTGTTCGGTTCAATTAGGATTT	57.106	33.333	0.00	0.00	0.00	2.17
710	756	7.166167	AGTAACTGTTCGGTTCAATTAGGATT	58.834	34.615	0.00	0.00	0.00	3.01
711	757	6.708285	AGTAACTGTTCGGTTCAATTAGGAT	58.292	36.000	0.00	0.00	0.00	3.24
712	758	6.105397	AGTAACTGTTCGGTTCAATTAGGA	57.895	37.500	0.00	0.00	0.00	2.94
713	759	5.929992	TGAGTAACTGTTCGGTTCAATTAGG	59.070	40.000	0.00	0.00	0.00	2.69
714	760	7.413000	CCATGAGTAACTGTTCGGTTCAATTAG	60.413	40.741	0.00	0.00	0.00	1.73
715	761	6.370442	CCATGAGTAACTGTTCGGTTCAATTA	59.630	38.462	0.00	0.00	0.00	1.40
716	762	5.181245	CCATGAGTAACTGTTCGGTTCAATT	59.819	40.000	0.00	0.00	0.00	2.32
717	763	4.695455	CCATGAGTAACTGTTCGGTTCAAT	59.305	41.667	0.00	0.00	0.00	2.57
741	787	3.099141	AGGGTTTGGACAATTATGGCAG	58.901	45.455	0.00	0.00	35.69	4.85
768	814	5.895928	ACTCCTCTCTTGTTTTTCTTTTGC	58.104	37.500	0.00	0.00	0.00	3.68
769	815	9.670719	GATAACTCCTCTCTTGTTTTTCTTTTG	57.329	33.333	0.00	0.00	0.00	2.44
821	867	7.447853	AGTTATCTTATCCTAGTCCGGTTACAG	59.552	40.741	0.00	0.00	0.00	2.74
858	904	3.880047	CGTAGGGGCCGATTATTATCA	57.120	47.619	0.00	0.00	0.00	2.15
897	943	1.029681	CGGGCTTATAAAGGGTTGCC	58.970	55.000	3.19	3.19	39.61	4.52
1284	1375	3.572255	ACCAAACACCAAATCTAATGCGT	59.428	39.130	0.00	0.00	0.00	5.24
1295	1386	3.907474	TCTCAGATCCTACCAAACACCAA	59.093	43.478	0.00	0.00	0.00	3.67
1942	2465	1.501582	AGTACCTGCATCCCTTCTCC	58.498	55.000	0.00	0.00	0.00	3.71
2475	3058	1.572085	CTCCTTGCACAAGACTGCCG	61.572	60.000	11.94	0.00	40.79	5.69
2488	3075	3.679389	ACAACAATCAGTAGCCTCCTTG	58.321	45.455	0.00	0.00	0.00	3.61
2528	3872	5.107133	GTCCATTCATTCAAGGCTTTGATG	58.893	41.667	12.50	12.14	42.60	3.07
2656	4000	0.040067	GAAAACCACTCAAGCCAGCG	60.040	55.000	0.00	0.00	0.00	5.18
2757	4101	0.320771	GTCGGAGTGCATGTTGGAGT	60.321	55.000	0.00	0.00	0.00	3.85
2769	4113	2.060980	GCAGGGATGAGGTCGGAGT	61.061	63.158	0.00	0.00	0.00	3.85
2806	4150	0.737219	GGCTGACATCATTGACCAGC	59.263	55.000	20.43	20.43	44.43	4.85
2918	4263	4.680237	CCAAGAGCCCGTGACGCA	62.680	66.667	0.00	0.00	0.00	5.24

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.