AutoCloner

Multiple sequence alignment - TraesCS5A01G195400

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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	TraesCS5A01G195400	chr5A	100.000	2875	0	0	1	2875	398677351	398674477	0.000000e+00	5310.0
1	TraesCS5A01G195400	chr5A	93.353	1715	71	26	1167	2875	219433791	219435468	0.000000e+00	2495.0
2	TraesCS5A01G195400	chr5A	86.073	876	76	26	1069	1934	492836835	492835996	0.000000e+00	900.0
3	TraesCS5A01G195400	chr5A	82.496	577	61	20	2023	2571	492835915	492835351	1.210000e-128	470.0
4	TraesCS5A01G195400	chr5A	92.722	316	23	0	2560	2875	492835331	492835016	9.390000e-125	457.0
5	TraesCS5A01G195400	chr5A	89.305	187	18	2	672	857	18724039	18723854	1.720000e-57	233.0
6	TraesCS5A01G195400	chr5D	95.623	1965	69	14	615	2571	198459484	198461439	0.000000e+00	3136.0
7	TraesCS5A01G195400	chr5D	87.066	518	17	25	2390	2875	198392426	198392925	9.060000e-150	540.0
8	TraesCS5A01G195400	chr5D	91.456	316	9	1	2560	2875	198461459	198461756	4.430000e-113	418.0
9	TraesCS5A01G195400	chr4A	93.236	1715	73	26	1167	2875	60353802	60352125	0.000000e+00	2484.0
10	TraesCS5A01G195400	chr4A	98.374	615	10	0	1	615	389501774	389502388	0.000000e+00	1081.0
11	TraesCS5A01G195400	chr4A	98.046	614	12	0	1	614	381548940	381548327	0.000000e+00	1068.0
12	TraesCS5A01G195400	chr4A	97.883	614	13	0	1	614	374566189	374566802	0.000000e+00	1062.0
13	TraesCS5A01G195400	chr4A	82.807	285	28	7	1532	1796	174993433	174993716	4.790000e-58	235.0
14	TraesCS5A01G195400	chr3A	92.867	1458	78	13	615	2068	89361387	89362822	0.000000e+00	2093.0
15	TraesCS5A01G195400	chr3A	91.648	455	36	2	615	1067	575765650	575766104	1.880000e-176	628.0
16	TraesCS5A01G195400	chr3A	92.857	168	12	0	9	176	562872588	562872755	7.960000e-61	244.0
17	TraesCS5A01G195400	chr2A	95.365	1316	46	13	1261	2571	191920789	191922094	0.000000e+00	2078.0
18	TraesCS5A01G195400	chr2A	97.785	316	7	0	2560	2875	191922114	191922429	1.950000e-151	545.0
19	TraesCS5A01G195400	chr2A	92.511	227	16	1	615	840	409143370	409143596	9.940000e-85	324.0
20	TraesCS5A01G195400	chr7B	94.084	1217	60	9	1041	2254	83104661	83103454	0.000000e+00	1838.0
21	TraesCS5A01G195400	chr7B	91.533	437	34	3	615	1049	83107349	83106914	1.470000e-167	599.0
22	TraesCS5A01G195400	chr7B	91.022	323	23	3	2250	2571	83060558	83060241	5.690000e-117	431.0
23	TraesCS5A01G195400	chr7B	97.166	247	7	0	2629	2875	83049298	83049052	4.430000e-113	418.0
24	TraesCS5A01G195400	chr7B	94.521	73	4	0	2560	2632	83060221	83060149	2.340000e-21	113.0
25	TraesCS5A01G195400	chr3D	85.762	1482	142	26	1069	2499	418327421	418325958	0.000000e+00	1504.0
26	TraesCS5A01G195400	chr3D	90.374	187	17	1	672	857	113998202	113998016	7.960000e-61	244.0
27	TraesCS5A01G195400	chr3D	82.955	264	32	7	2621	2875	38035940	38036199	2.880000e-55	226.0
28	TraesCS5A01G195400	chr1B	90.452	1173	65	26	1708	2875	684141841	684142971	0.000000e+00	1502.0
29	TraesCS5A01G195400	chr1B	92.925	523	35	2	615	1135	684141007	684141529	0.000000e+00	760.0
30	TraesCS5A01G195400	chr1B	92.489	466	10	2	173	614	524502998	524503462	0.000000e+00	643.0
31	TraesCS5A01G195400	chr1B	96.166	313	9	3	1286	1597	684141526	684141836	2.560000e-140	508.0
32	TraesCS5A01G195400	chr7A	97.712	612	14	0	3	614	483859812	483860423	0.000000e+00	1053.0
33	TraesCS5A01G195400	chr7A	92.045	176	10	1	1	176	148778124	148777953	7.960000e-61	244.0
34	TraesCS5A01G195400	chr7A	87.374	198	23	2	2376	2571	114280843	114281040	2.880000e-55	226.0
35	TraesCS5A01G195400	chr3B	92.704	466	10	8	173	614	766700924	766700459	0.000000e+00	651.0
36	TraesCS5A01G195400	chr3B	97.159	176	5	0	1	176	766704786	766704611	6.020000e-77	298.0
37	TraesCS5A01G195400	chr4B	92.688	465	11	11	173	614	223367356	223367820	0.000000e+00	649.0
38	TraesCS5A01G195400	chr4B	94.886	176	9	0	1	176	223344352	223344527	2.820000e-70	276.0
39	TraesCS5A01G195400	chr6A	96.992	266	8	0	173	438	579288414	579288679	5.650000e-122	448.0
40	TraesCS5A01G195400	chr6A	94.318	176	10	0	1	176	579284728	579284903	1.310000e-68	270.0
41	TraesCS5A01G195400	chr6A	98.765	81	1	0	531	611	579288767	579288847	8.300000e-31	145.0
42	TraesCS5A01G195400	chr7D	90.110	273	14	9	354	614	27561365	27561636	2.740000e-90	342.0
43	TraesCS5A01G195400	chr7D	89.189	148	12	2	173	316	27560665	27560812	6.330000e-42	182.0
44	TraesCS5A01G195400	chr7D	100.000	33	0	0	321	353	27561342	27561374	8.600000e-06	62.1
45	TraesCS5A01G195400	chr4D	88.571	175	14	4	650	822	24097607	24097777	1.040000e-49	207.0
46	TraesCS5A01G195400	chr4D	81.579	152	16	8	2116	2262	359682896	359682752	6.510000e-22	115.0

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	TraesCS5A01G195400	chr5A	398674477	398677351	2874	True	5310.000000	5310	100.000000	1	2875	1	chr5A.!!$R2	2874
1	TraesCS5A01G195400	chr5A	219433791	219435468	1677	False	2495.000000	2495	93.353000	1167	2875	1	chr5A.!!$F1	1708
2	TraesCS5A01G195400	chr5A	492835016	492836835	1819	True	609.000000	900	87.097000	1069	2875	3	chr5A.!!$R3	1806
3	TraesCS5A01G195400	chr5D	198459484	198461756	2272	False	1777.000000	3136	93.539500	615	2875	2	chr5D.!!$F2	2260
4	TraesCS5A01G195400	chr4A	60352125	60353802	1677	True	2484.000000	2484	93.236000	1167	2875	1	chr4A.!!$R1	1708
5	TraesCS5A01G195400	chr4A	389501774	389502388	614	False	1081.000000	1081	98.374000	1	615	1	chr4A.!!$F3	614
6	TraesCS5A01G195400	chr4A	381548327	381548940	613	True	1068.000000	1068	98.046000	1	614	1	chr4A.!!$R2	613
7	TraesCS5A01G195400	chr4A	374566189	374566802	613	False	1062.000000	1062	97.883000	1	614	1	chr4A.!!$F2	613
8	TraesCS5A01G195400	chr3A	89361387	89362822	1435	False	2093.000000	2093	92.867000	615	2068	1	chr3A.!!$F1	1453
9	TraesCS5A01G195400	chr2A	191920789	191922429	1640	False	1311.500000	2078	96.575000	1261	2875	2	chr2A.!!$F2	1614
10	TraesCS5A01G195400	chr7B	83103454	83107349	3895	True	1218.500000	1838	92.808500	615	2254	2	chr7B.!!$R3	1639
11	TraesCS5A01G195400	chr3D	418325958	418327421	1463	True	1504.000000	1504	85.762000	1069	2499	1	chr3D.!!$R2	1430
12	TraesCS5A01G195400	chr1B	684141007	684142971	1964	False	923.333333	1502	93.181000	615	2875	3	chr1B.!!$F2	2260
13	TraesCS5A01G195400	chr7A	483859812	483860423	611	False	1053.000000	1053	97.712000	3	614	1	chr7A.!!$F2	611
14	TraesCS5A01G195400	chr3B	766700459	766704786	4327	True	474.500000	651	94.931500	1	614	2	chr3B.!!$R1	613
15	TraesCS5A01G195400	chr6A	579284728	579288847	4119	False	287.666667	448	96.691667	1	611	3	chr6A.!!$F1	610

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
953	4687	0.109365	TGACGCATTTGATTTGCCCG	60.109	50.0	0.0	0.0	36.75	6.13	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2038	8093	0.527565	CCGCATGCCTTAACTGCTTT	59.472	50.0	13.15	0.0	33.75	3.51	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
47	48	5.368145	TCAGGATATAACTTGCATGGTCAC	58.632	41.667	4.44	0.00	0.00	3.67
52	53	2.831685	AACTTGCATGGTCACGTCTA	57.168	45.000	4.44	0.00	0.00	2.59
293	4002	3.364460	TCTATGTGTTCCCATTGGTGG	57.636	47.619	1.20	0.00	45.61	4.61
311	4020	4.832266	TGGTGGCTGAATAATTTGTCACTT	59.168	37.500	0.00	0.00	0.00	3.16
640	4373	3.188100	CGAGCGAGCCGATTTGCA	61.188	61.111	0.00	0.00	0.00	4.08
648	4381	2.042831	GCCGATTTGCACAGAGGCT	61.043	57.895	12.48	0.00	41.21	4.58
670	4403	1.378911	GATGGGATGGTGTGCTGCA	60.379	57.895	0.00	0.00	0.00	4.41
818	4552	1.203492	AGGTTGAGGATGGGAAGAGGT	60.203	52.381	0.00	0.00	0.00	3.85
859	4593	4.400961	GAGGAGGGCACGCAGCTT	62.401	66.667	0.00	0.00	44.79	3.74
952	4686	1.632422	CTGACGCATTTGATTTGCCC	58.368	50.000	0.00	0.00	36.75	5.36
953	4687	0.109365	TGACGCATTTGATTTGCCCG	60.109	50.000	0.00	0.00	36.75	6.13
1034	4769	2.094494	TGCAGGAAGTCGAGAATGTCTC	60.094	50.000	0.00	0.00	40.06	3.36
1048	7043	0.986019	TGTCTCCACCACCCTTGTGT	60.986	55.000	0.00	0.00	41.09	3.72
1184	7179	1.847506	AGGTGGCATCACTGGTCCA	60.848	57.895	0.00	0.00	43.17	4.02
1207	7202	7.124448	TCCATGTAAAACAGGTTTAAACTTGGT	59.876	33.333	27.83	22.09	40.29	3.67
1258	7254	6.708285	TCTTCTGTTAGGACCCTTTATCAAC	58.292	40.000	0.00	0.00	0.00	3.18
1367	7364	9.971922	TTCTTTTGAATTCCTGAAATTTCTCTC	57.028	29.630	18.64	7.12	37.70	3.20
1436	7434	8.619546	TCAGCTACGATCATCTAATCTCATATG	58.380	37.037	0.00	0.00	0.00	1.78
1739	7739	7.822822	CCAACCTAGGGAACTATAAATATTCCG	59.177	40.741	14.81	0.00	43.39	4.30
1786	7787	5.645497	ACCAGCAATATTGTTCAGAGACTTC	59.355	40.000	16.61	0.00	0.00	3.01
1858	7867	2.122167	CGTCGGAGGGGGAGAAGAG	61.122	68.421	0.00	0.00	0.00	2.85
1873	7882	5.988561	GGGAGAAGAGCTTGTTATCTACATG	59.011	44.000	0.00	0.00	36.44	3.21
1874	7883	6.183360	GGGAGAAGAGCTTGTTATCTACATGA	60.183	42.308	0.00	0.00	36.44	3.07
1875	7884	6.699642	GGAGAAGAGCTTGTTATCTACATGAC	59.300	42.308	0.00	0.00	36.44	3.06
1876	7885	7.416964	AGAAGAGCTTGTTATCTACATGACT	57.583	36.000	0.00	0.00	36.44	3.41
1877	7886	8.526667	AGAAGAGCTTGTTATCTACATGACTA	57.473	34.615	0.00	0.00	36.44	2.59
1878	7887	8.410141	AGAAGAGCTTGTTATCTACATGACTAC	58.590	37.037	0.00	0.00	36.44	2.73
1879	7888	7.646548	AGAGCTTGTTATCTACATGACTACA	57.353	36.000	0.00	0.00	36.44	2.74
1880	7889	8.243961	AGAGCTTGTTATCTACATGACTACAT	57.756	34.615	0.00	0.00	36.44	2.29
1884	7893	9.265901	GCTTGTTATCTACATGACTACATCAAT	57.734	33.333	0.00	0.00	41.93	2.57
1983	7992	0.035458	AAGACCGGAAACAGAGCAGG	59.965	55.000	9.46	0.00	0.00	4.85
2038	8093	1.920325	CTCTGGGAGGGAGTTGCCA	60.920	63.158	0.00	0.00	38.95	4.92
2068	8123	0.109132	GGCATGCGGAGGTTTGAAAG	60.109	55.000	12.44	0.00	0.00	2.62
2291	8392	4.621274	GCCAAAGCACACAACAATCCATAT	60.621	41.667	0.00	0.00	39.53	1.78
2353	8454	0.175302	TTGTGGGCAACAGCAGTTTG	59.825	50.000	0.00	0.00	40.74	2.93
2354	8455	0.682532	TGTGGGCAACAGCAGTTTGA	60.683	50.000	0.00	0.00	35.28	2.69
2462	8569	4.095483	CAGTATTCAGCCTTGCGAGAAAAT	59.905	41.667	1.22	0.00	33.16	1.82
2522	8684	7.232127	CCTTGAATGCCAGGATTTTATGAGTAT	59.768	37.037	0.00	0.00	0.00	2.12

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
254	3963	8.660373	CACATAGAAAACAGTATTTCCAGAGAC	58.340	37.037	0.00	0.00	39.59	3.36
293	4002	9.801714	CATTGAAAAAGTGACAAATTATTCAGC	57.198	29.630	0.00	0.00	0.00	4.26
629	4362	2.042831	GCCTCTGTGCAAATCGGCT	61.043	57.895	8.86	0.00	34.80	5.52
636	4369	0.035725	CATCCTCAGCCTCTGTGCAA	60.036	55.000	0.00	0.00	32.61	4.08
640	4373	0.030297	ATCCCATCCTCAGCCTCTGT	60.030	55.000	0.00	0.00	32.61	3.41
648	4381	0.915872	AGCACACCATCCCATCCTCA	60.916	55.000	0.00	0.00	0.00	3.86
682	4415	1.421646	CAATCCCCTTAATCGAGCCCT	59.578	52.381	0.00	0.00	0.00	5.19
691	4424	1.304891	CCACCCTCCAATCCCCTTAA	58.695	55.000	0.00	0.00	0.00	1.85
859	4593	3.551846	TGTATCTACACATGGCGAGAGA	58.448	45.455	0.00	0.00	0.00	3.10
952	4686	1.227674	GCCCTTCCTAGATGGCACG	60.228	63.158	0.00	0.00	43.46	5.34
953	4687	0.179034	CAGCCCTTCCTAGATGGCAC	60.179	60.000	12.32	0.00	46.45	5.01
1048	7043	0.102844	GTGTTGCTTGCCTTCTTGCA	59.897	50.000	0.00	0.00	40.07	4.08
1184	7179	8.068892	TCACCAAGTTTAAACCTGTTTTACAT	57.931	30.769	14.72	0.00	34.23	2.29
1207	7202	3.554934	AGAGTGTTGTTCAATGGCTTCA	58.445	40.909	0.00	0.00	0.00	3.02
1258	7254	1.526575	AACTTGGCGTGGCTCAATGG	61.527	55.000	0.00	0.00	0.00	3.16
1367	7364	6.748132	TCTGGCAAAGAAAGACTTATTTTGG	58.252	36.000	18.49	8.42	37.93	3.28
1381	7379	4.464008	ACAGTTCAATCTTCTGGCAAAGA	58.536	39.130	12.33	12.33	39.49	2.52
1436	7434	8.831000	AGTAAATAAAGTTCAAACGAACACAC	57.169	30.769	7.96	0.00	44.40	3.82
1739	7739	8.308207	TGGTCTATTAAAATAGTTTGGCAAACC	58.692	33.333	33.07	17.74	42.34	3.27
1786	7787	4.135153	CGCTGTGGAGGAGGACCG	62.135	72.222	0.00	0.00	41.83	4.79
1858	7867	8.648557	TTGATGTAGTCATGTAGATAACAAGC	57.351	34.615	0.00	0.00	42.70	4.01
1873	7882	5.163953	CGGTTCACTCAACATTGATGTAGTC	60.164	44.000	0.00	0.00	40.80	2.59
1874	7883	4.690748	CGGTTCACTCAACATTGATGTAGT	59.309	41.667	0.00	0.00	40.80	2.73
1875	7884	4.436050	GCGGTTCACTCAACATTGATGTAG	60.436	45.833	0.00	0.00	40.80	2.74
1876	7885	3.435327	GCGGTTCACTCAACATTGATGTA	59.565	43.478	0.00	0.00	40.80	2.29
1877	7886	2.226437	GCGGTTCACTCAACATTGATGT	59.774	45.455	0.00	0.00	44.20	3.06
1878	7887	2.414559	GGCGGTTCACTCAACATTGATG	60.415	50.000	0.00	0.00	36.61	3.07
1879	7888	1.812571	GGCGGTTCACTCAACATTGAT	59.187	47.619	0.00	0.00	36.61	2.57
1880	7889	1.234821	GGCGGTTCACTCAACATTGA	58.765	50.000	0.00	0.00	36.61	2.57
1884	7893	1.593209	GACGGCGGTTCACTCAACA	60.593	57.895	13.24	0.00	36.61	3.33
2038	8093	0.527565	CCGCATGCCTTAACTGCTTT	59.472	50.000	13.15	0.00	33.75	3.51
2095	8150	1.027357	TAGAGGGATTGTACGCCGTC	58.973	55.000	0.00	11.67	38.89	4.79
2150	8214	2.435372	TTTCTGCCTGAAACACCTGT	57.565	45.000	0.00	0.00	39.50	4.00
2237	8302	4.221422	GGCGGGCATCGTAGCAGA	62.221	66.667	0.00	0.00	41.72	4.26
2353	8454	6.088824	TCACGTTTCTACTACCGATTCTTTC	58.911	40.000	0.00	0.00	0.00	2.62
2354	8455	6.017400	TCACGTTTCTACTACCGATTCTTT	57.983	37.500	0.00	0.00	0.00	2.52
2462	8569	0.687757	AGCTTCTATCCCGAGGCACA	60.688	55.000	0.00	0.00	38.35	4.57
2522	8684	5.775195	TGTAATGAGAACAGAAGAGTCAGGA	59.225	40.000	0.00	0.00	0.00	3.86

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.