AutoCloner

Multiple sequence alignment - TraesCS4A01G381000

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	TraesCS4A01G381000	chr4A	100.000	2828	0	0	1	2828	658607620	658610447	0.000000e+00	5223
1	TraesCS4A01G381000	chr4D	95.775	2793	110	5	41	2828	198581769	198584558	0.000000e+00	4497
2	TraesCS4A01G381000	chr7A	95.342	2834	122	7	1	2828	613710773	613713602	0.000000e+00	4494
3	TraesCS4A01G381000	chr7A	96.235	903	32	2	1928	2828	712101793	712102695	0.000000e+00	1478
4	TraesCS4A01G381000	chr7A	95.126	636	28	2	9	641	712099163	712099798	0.000000e+00	1000
5	TraesCS4A01G381000	chr7A	94.788	614	31	1	662	1274	712099787	712100400	0.000000e+00	955
6	TraesCS4A01G381000	chr7A	92.614	176	9	4	2574	2747	449710831	449711004	1.680000e-62	250
7	TraesCS4A01G381000	chr5B	94.140	2833	141	10	1	2828	386152700	386155512	0.000000e+00	4289
8	TraesCS4A01G381000	chr2A	94.006	2002	113	7	830	2828	596501776	596499779	0.000000e+00	3025
9	TraesCS4A01G381000	chr2A	93.214	840	41	6	1	834	595998370	595999199	0.000000e+00	1221
10	TraesCS4A01G381000	chr2A	89.264	503	41	10	1808	2305	207107984	207108478	4.000000e-173	617
11	TraesCS4A01G381000	chr2A	82.677	254	34	6	1238	1490	595998955	595999199	1.710000e-52	217
12	TraesCS4A01G381000	chr3B	94.010	1586	91	4	1	1583	534149551	534147967	0.000000e+00	2399
13	TraesCS4A01G381000	chr3B	90.556	180	17	0	1571	1750	534143206	534143027	3.640000e-59	239
14	TraesCS4A01G381000	chr6A	88.503	1844	158	23	400	2206	36691061	36692887	0.000000e+00	2182
15	TraesCS4A01G381000	chr6B	89.160	1642	150	20	581	2207	67994962	67996590	0.000000e+00	2021
16	TraesCS4A01G381000	chr6B	94.395	892	49	1	1	891	254030447	254029556	0.000000e+00	1369
17	TraesCS4A01G381000	chr5A	95.903	903	35	2	1928	2828	605038449	605039351	0.000000e+00	1461
18	TraesCS4A01G381000	chr5A	94.811	636	30	2	9	641	605035819	605036454	0.000000e+00	989
19	TraesCS4A01G381000	chr5A	94.463	614	33	1	662	1274	605036443	605037056	0.000000e+00	944
20	TraesCS4A01G381000	chr5A	88.927	587	54	9	1249	1831	174257309	174257888	0.000000e+00	713
21	TraesCS4A01G381000	chr5A	92.045	176	10	4	2574	2747	641407272	641407445	7.830000e-61	244
22	TraesCS4A01G381000	chr2D	89.641	502	38	10	1808	2305	107760340	107760831	6.650000e-176	627
23	TraesCS4A01G381000	chr1A	90.451	377	31	5	2206	2579	218981623	218981997	2.530000e-135	492
24	TraesCS4A01G381000	chr2B	88.298	376	36	6	1	372	66809235	66808864	7.190000e-121	444
25	TraesCS4A01G381000	chr2B	93.976	249	14	1	2209	2456	190041024	190040776	2.660000e-100	375
26	TraesCS4A01G381000	chr2B	84.636	371	40	10	16	372	89702578	89702945	1.250000e-93	353
27	TraesCS4A01G381000	chr3A	93.927	247	13	2	2206	2451	120239689	120239934	3.440000e-99	372
28	TraesCS4A01G381000	chrUn	92.398	171	12	1	2578	2747	39528803	39528633	2.810000e-60	243

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	TraesCS4A01G381000	chr4A	658607620	658610447	2827	False	5223.000000	5223	100.0000	1	2828	1	chr4A.!!$F1	2827
1	TraesCS4A01G381000	chr4D	198581769	198584558	2789	False	4497.000000	4497	95.7750	41	2828	1	chr4D.!!$F1	2787
2	TraesCS4A01G381000	chr7A	613710773	613713602	2829	False	4494.000000	4494	95.3420	1	2828	1	chr7A.!!$F2	2827
3	TraesCS4A01G381000	chr7A	712099163	712102695	3532	False	1144.333333	1478	95.3830	9	2828	3	chr7A.!!$F3	2819
4	TraesCS4A01G381000	chr5B	386152700	386155512	2812	False	4289.000000	4289	94.1400	1	2828	1	chr5B.!!$F1	2827
5	TraesCS4A01G381000	chr2A	596499779	596501776	1997	True	3025.000000	3025	94.0060	830	2828	1	chr2A.!!$R1	1998
6	TraesCS4A01G381000	chr2A	595998370	595999199	829	False	719.000000	1221	87.9455	1	1490	2	chr2A.!!$F2	1489
7	TraesCS4A01G381000	chr3B	534147967	534149551	1584	True	2399.000000	2399	94.0100	1	1583	1	chr3B.!!$R2	1582
8	TraesCS4A01G381000	chr6A	36691061	36692887	1826	False	2182.000000	2182	88.5030	400	2206	1	chr6A.!!$F1	1806
9	TraesCS4A01G381000	chr6B	67994962	67996590	1628	False	2021.000000	2021	89.1600	581	2207	1	chr6B.!!$F1	1626
10	TraesCS4A01G381000	chr6B	254029556	254030447	891	True	1369.000000	1369	94.3950	1	891	1	chr6B.!!$R1	890
11	TraesCS4A01G381000	chr5A	605035819	605039351	3532	False	1131.333333	1461	95.0590	9	2828	3	chr5A.!!$F3	2819
12	TraesCS4A01G381000	chr5A	174257309	174257888	579	False	713.000000	713	88.9270	1249	1831	1	chr5A.!!$F1	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
243	259	0.450583	TTGACTCGGCTGTAGCTACG	59.549	55.000	18.74	14.02	41.7	3.51	F
994	1051	1.957877	CTTTACTTGGTTTCCCGGCAA	59.042	47.619	0.00	0.00	0.0	4.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1193	1254	1.463444	GTTACTAACAAGCGGTGGCAG	59.537	52.381	0.0	0.0	43.41	4.85	R
2777	3874	2.094390	CCAAATCAGGCACAGTCAATGG	60.094	50.000	0.0	0.0	0.00	3.16	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
89	90	2.213499	GTCGGCTGGATGAATCGATTT	58.787	47.619	12.81	0.00	32.46	2.17
113	115	1.134699	TCGATGCTCTGCCTACCTTTG	60.135	52.381	0.00	0.00	0.00	2.77
117	119	1.685224	CTCTGCCTACCTTTGCCCA	59.315	57.895	0.00	0.00	0.00	5.36
193	201	6.790232	TCTGTGGATTTCCTTTTTGTCTTT	57.210	33.333	0.00	0.00	36.82	2.52
242	258	1.473278	AGTTGACTCGGCTGTAGCTAC	59.527	52.381	17.30	17.30	41.70	3.58
243	259	0.450583	TTGACTCGGCTGTAGCTACG	59.549	55.000	18.74	14.02	41.70	3.51
269	289	4.463186	GGATACCTACCAGCGACATAGAAT	59.537	45.833	0.00	0.00	0.00	2.40
297	317	3.275617	AAGCACTACTTGGTTGTGTGA	57.724	42.857	12.09	0.00	44.44	3.58
324	345	6.413018	TCATGTCGAATTCAGATTTCTGTG	57.587	37.500	6.22	0.00	44.12	3.66
341	362	8.827177	ATTTCTGTGATCGTTCAGTTACTTAA	57.173	30.769	0.00	0.00	33.89	1.85
357	378	4.036941	ACTTAAGGCCGACCCAAAATTA	57.963	40.909	7.53	0.00	36.11	1.40
365	386	2.556622	CCGACCCAAAATTACTTGCAGT	59.443	45.455	0.00	0.00	0.00	4.40
517	538	4.471904	TGAACATTCGAGAGCATTACCT	57.528	40.909	0.00	0.00	0.00	3.08
539	562	8.147244	ACCTAGAGAAATGTACATACAAAGGT	57.853	34.615	9.21	13.70	39.99	3.50
711	768	4.738998	TGCCCTGCCCCATTGACG	62.739	66.667	0.00	0.00	0.00	4.35
741	798	7.478520	AATAACGCTATTGACAATCACCTAC	57.521	36.000	3.36	0.00	0.00	3.18
991	1048	2.738314	CGTACTTTACTTGGTTTCCCGG	59.262	50.000	0.00	0.00	0.00	5.73
994	1051	1.957877	CTTTACTTGGTTTCCCGGCAA	59.042	47.619	0.00	0.00	0.00	4.52
1066	1123	5.843019	TTTCTCTTTTGATGGGGACTACT	57.157	39.130	0.00	0.00	0.00	2.57
1101	1159	6.986231	CAGCAAAGGTTCTTATTTTTCCTTGT	59.014	34.615	0.00	0.00	38.33	3.16
1104	1163	7.254761	GCAAAGGTTCTTATTTTTCCTTGTTGG	60.255	37.037	0.00	0.00	38.33	3.77
1140	1199	4.255833	TGGCTGTCATCAATGAAAAACC	57.744	40.909	0.00	0.00	38.75	3.27
1150	1209	7.277098	GTCATCAATGAAAAACCCAAGATCATG	59.723	37.037	0.00	0.00	38.75	3.07
1155	1214	9.439500	CAATGAAAAACCCAAGATCATGTAATT	57.561	29.630	0.00	0.00	31.49	1.40
1157	1216	7.385267	TGAAAAACCCAAGATCATGTAATTGG	58.615	34.615	14.64	14.64	41.55	3.16
1177	1238	7.817418	ATTGGTTACTCTGCTTTTTCTACAA	57.183	32.000	0.00	0.00	0.00	2.41
1193	1254	6.569179	TTCTACAAGACTTTTGGTAATGCC	57.431	37.500	0.00	0.00	37.90	4.40
1246	1307	2.671896	AATCAATGATCCTGCCTCCC	57.328	50.000	0.00	0.00	0.00	4.30
1453	2450	6.940867	AGAAGAAATTAGTTGAAGGGTGTACC	59.059	38.462	0.00	0.00	40.67	3.34
1612	2671	6.317140	GGATTGTGAGATGAGAATTTGCACTA	59.683	38.462	0.00	0.00	0.00	2.74
1614	2673	7.509141	TTGTGAGATGAGAATTTGCACTAAA	57.491	32.000	0.00	0.00	0.00	1.85
1691	2750	9.823647	AGATTCAACGATATTCTTACATCAACT	57.176	29.630	0.00	0.00	0.00	3.16
1717	2776	4.424626	CATTACTTGCAAGCTCGAGTAGA	58.575	43.478	26.27	2.97	35.15	2.59
1847	2909	9.696917	GCATTAATAAATCTCCTTTGGTTATGG	57.303	33.333	0.00	0.00	0.00	2.74
1861	2923	7.147672	CCTTTGGTTATGGGATGCTAAGATTTT	60.148	37.037	0.00	0.00	0.00	1.82
1943	3031	8.579850	AGAACCTCATTTTGTTATATTCAGCA	57.420	30.769	0.00	0.00	0.00	4.41
1961	3052	5.479306	TCAGCATTGTACCAACTTCTAGAC	58.521	41.667	0.00	0.00	0.00	2.59
2095	3189	7.545615	GTGAAAAGGAACATTTGAAGTTCTTGT	59.454	33.333	4.17	2.99	43.67	3.16
2110	3204	5.930135	AGTTCTTGTGCCTTCTTCTTAAGA	58.070	37.500	0.00	0.00	35.26	2.10
2234	3328	4.761227	TGTCTGCATGCTTAATTCACTCAA	59.239	37.500	20.33	0.00	0.00	3.02
2373	3469	3.911989	CAGCAGATGCACCGAAATC	57.088	52.632	7.68	0.00	45.16	2.17
2445	3541	4.065789	AGTACTTGTAGAAGCACTTTGCC	58.934	43.478	0.00	0.00	46.52	4.52
2470	3566	3.194861	GCACCGTGCATATAACTTGAGA	58.805	45.455	18.79	0.00	44.26	3.27
2533	3629	0.394762	GCCCTCATCTGTTCATGGCA	60.395	55.000	0.00	0.00	37.36	4.92

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
89	90	0.741326	GTAGGCAGAGCATCGAGACA	59.259	55.000	0.00	0.00	42.67	3.41
113	115	1.379642	CGAGAGGAAAAGGCATGGGC	61.380	60.000	0.00	0.00	40.13	5.36
193	201	1.525197	CTGAAAAACTGCTACACGCGA	59.475	47.619	15.93	0.00	43.27	5.87
243	259	0.388294	GTCGCTGGTAGGTATCCACC	59.612	60.000	0.00	0.00	46.19	4.61
269	289	8.537016	ACACAACCAAGTAGTGCTTATTATCTA	58.463	33.333	0.00	0.00	36.76	1.98
297	317	5.879223	AGAAATCTGAATTCGACATGAGCTT	59.121	36.000	0.00	0.00	32.04	3.74
324	345	3.550678	CGGCCTTAAGTAACTGAACGATC	59.449	47.826	0.00	0.00	0.00	3.69
341	362	2.167662	CAAGTAATTTTGGGTCGGCCT	58.832	47.619	5.77	0.00	34.45	5.19
357	378	5.310182	GCCCTAGCTAAGCTACTGCAAGT	62.310	52.174	7.94	0.00	43.85	3.16
365	386	0.826672	GGTCGGCCCTAGCTAAGCTA	60.827	60.000	13.51	0.00	40.44	3.32
711	768	9.845305	GTGATTGTCAATAGCGTTATTAACTAC	57.155	33.333	4.07	2.54	0.00	2.73
732	789	1.840635	GAGCCTCTTGGGTAGGTGATT	59.159	52.381	0.00	0.00	45.24	2.57
741	798	1.376037	GTTCGGTGAGCCTCTTGGG	60.376	63.158	0.00	0.00	38.36	4.12
909	966	5.496556	TCCGGAACATCAACATAAAGACAT	58.503	37.500	0.00	0.00	0.00	3.06
991	1048	3.937706	AGCACAATAGTCATGTCTCTTGC	59.062	43.478	14.82	10.65	0.00	4.01
994	1051	3.197333	AGCAGCACAATAGTCATGTCTCT	59.803	43.478	0.00	0.00	0.00	3.10
1066	1123	4.410099	AGAACCTTTGCTGGATCATTGAA	58.590	39.130	0.00	0.00	32.18	2.69
1101	1159	2.825532	GCCAAATCTTAAGGAGCACCAA	59.174	45.455	2.07	0.00	38.94	3.67
1104	1163	3.084786	ACAGCCAAATCTTAAGGAGCAC	58.915	45.455	1.85	0.00	0.00	4.40
1140	1199	7.467811	GCAGAGTAACCAATTACATGATCTTGG	60.468	40.741	17.46	17.46	42.83	3.61
1150	1209	8.780249	TGTAGAAAAAGCAGAGTAACCAATTAC	58.220	33.333	0.00	0.00	41.00	1.89
1155	1214	6.482308	GTCTTGTAGAAAAAGCAGAGTAACCA	59.518	38.462	0.00	0.00	0.00	3.67
1157	1216	7.716768	AGTCTTGTAGAAAAAGCAGAGTAAC	57.283	36.000	0.00	0.00	0.00	2.50
1177	1238	2.171003	GGCAGGCATTACCAAAAGTCT	58.829	47.619	0.00	0.00	43.14	3.24
1193	1254	1.463444	GTTACTAACAAGCGGTGGCAG	59.537	52.381	0.00	0.00	43.41	4.85
1322	1386	9.232082	CGTCTCATTTTGTACAAATTCTTTCAA	57.768	29.630	21.17	4.80	0.00	2.69
1492	2489	8.846211	ACAAGCAACAAGAAAGCTTATAAAGTA	58.154	29.630	0.00	0.00	46.01	2.24
1612	2671	2.514803	AGTACGCATGGGCTTCTTTTT	58.485	42.857	10.10	0.00	38.10	1.94
1614	2673	2.200373	AAGTACGCATGGGCTTCTTT	57.800	45.000	10.10	0.00	38.10	2.52
1714	2773	4.873010	AGGACAAGAGGTAAGCTCATCTA	58.127	43.478	0.00	0.00	0.00	1.98
1715	2774	3.718723	AGGACAAGAGGTAAGCTCATCT	58.281	45.455	0.00	0.00	0.00	2.90
1717	2776	3.198853	GGAAGGACAAGAGGTAAGCTCAT	59.801	47.826	0.00	0.00	0.00	2.90
1847	2909	8.897752	ACAATAAGTCAGAAAATCTTAGCATCC	58.102	33.333	0.00	0.00	0.00	3.51
1882	2970	8.404000	ACTTACAGTACGGTATGTCTATCAAAG	58.596	37.037	15.68	7.39	28.77	2.77
1886	2974	7.854916	GTGAACTTACAGTACGGTATGTCTATC	59.145	40.741	19.75	15.42	32.41	2.08
2207	3301	6.118170	AGTGAATTAAGCATGCAGACATACT	58.882	36.000	21.98	12.34	33.67	2.12
2248	3343	6.875076	TCAGTAATTTCTAGCAACTACTCCC	58.125	40.000	0.00	0.00	0.00	4.30
2283	3379	8.846943	TTCTTTGAAATTCAGTGCATCTACTA	57.153	30.769	0.00	0.00	0.00	1.82
2358	3454	3.785486	TCAGTAGATTTCGGTGCATCTG	58.215	45.455	0.00	0.00	31.89	2.90
2367	3463	7.379529	ACTGCAAACAAAATTCAGTAGATTTCG	59.620	33.333	0.00	0.00	36.37	3.46
2470	3566	8.462016	GTGCATATAAATTCAGAGGACACTTTT	58.538	33.333	0.00	0.00	0.00	2.27
2533	3629	8.527810	TGTTTGTTCCTTTTCTTTTACTCATGT	58.472	29.630	0.00	0.00	0.00	3.21
2594	3690	7.557358	AGATGGTCAAAGCAACAATGATATACA	59.443	33.333	0.00	0.00	0.00	2.29
2777	3874	2.094390	CCAAATCAGGCACAGTCAATGG	60.094	50.000	0.00	0.00	0.00	3.16

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.