AutoCloner

Multiple sequence alignment - TraesCS7B01G040900

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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	TraesCS7B01G040900	chr7B	100.000	3047	0	0	1	3047	40444734	40441688	0.000000e+00	5627
1	TraesCS7B01G040900	chr7B	95.459	1079	25	12	983	2060	40346741	40347796	0.000000e+00	1700
2	TraesCS7B01G040900	chr7B	82.124	386	37	20	2427	2789	40353035	40353411	4.940000e-78	302
3	TraesCS7B01G040900	chr7A	92.083	2122	94	26	959	3047	90665047	90662967	0.000000e+00	2920
4	TraesCS7B01G040900	chr7A	93.153	1110	62	5	959	2060	90586463	90587566	0.000000e+00	1616
5	TraesCS7B01G040900	chr7A	86.525	1462	151	31	991	2431	91017271	91015835	0.000000e+00	1567
6	TraesCS7B01G040900	chr7A	92.737	537	32	5	60	592	90665908	90665375	0.000000e+00	769
7	TraesCS7B01G040900	chr7A	88.697	522	52	6	1	519	90585680	90586197	5.540000e-177	630
8	TraesCS7B01G040900	chr7A	87.665	227	18	6	630	853	90665372	90665153	3.900000e-64	255
9	TraesCS7B01G040900	chr7A	90.395	177	15	2	17	191	90613906	90614082	6.570000e-57	231
10	TraesCS7B01G040900	chr7A	89.726	146	11	3	710	853	90586214	90586357	1.870000e-42	183
11	TraesCS7B01G040900	chr7A	92.857	126	9	0	728	853	90614964	90615089	1.870000e-42	183
12	TraesCS7B01G040900	chr7A	88.966	145	14	1	711	853	90615833	90615977	8.680000e-41	178
13	TraesCS7B01G040900	chr7A	93.694	111	7	0	743	853	90614089	90614199	1.880000e-37	167
14	TraesCS7B01G040900	chr7D	84.330	2993	284	110	1	2918	89792379	89789497	0.000000e+00	2758
15	TraesCS7B01G040900	chr7D	90.588	2093	128	33	991	3047	89731734	89729675	0.000000e+00	2710
16	TraesCS7B01G040900	chr7D	88.823	1512	110	28	566	2060	89521892	89523361	0.000000e+00	1801
17	TraesCS7B01G040900	chr7D	95.176	1078	52	0	983	2060	89486419	89487496	0.000000e+00	1703
18	TraesCS7B01G040900	chr7D	88.632	475	48	5	87	559	89521285	89521755	9.480000e-160	573
19	TraesCS7B01G040900	chr7D	82.206	399	35	24	2427	2800	89598958	89599345	8.200000e-81	311
20	TraesCS7B01G040900	chr7D	95.455	88	4	0	1	88	89521055	89521142	1.140000e-29	141
21	TraesCS7B01G040900	chrUn	85.588	1471	174	26	981	2432	91490447	91491898	0.000000e+00	1507

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	TraesCS7B01G040900	chr7B	40441688	40444734	3046	True	5627.000000	5627	100.000000	1	3047	1	chr7B.!!$R1	3046
1	TraesCS7B01G040900	chr7B	40346741	40347796	1055	False	1700.000000	1700	95.459000	983	2060	1	chr7B.!!$F1	1077
2	TraesCS7B01G040900	chr7A	91015835	91017271	1436	True	1567.000000	1567	86.525000	991	2431	1	chr7A.!!$R1	1440
3	TraesCS7B01G040900	chr7A	90662967	90665908	2941	True	1314.666667	2920	90.828333	60	3047	3	chr7A.!!$R2	2987
4	TraesCS7B01G040900	chr7A	90585680	90587566	1886	False	809.666667	1616	90.525333	1	2060	3	chr7A.!!$F1	2059
5	TraesCS7B01G040900	chr7D	89789497	89792379	2882	True	2758.000000	2758	84.330000	1	2918	1	chr7D.!!$R2	2917
6	TraesCS7B01G040900	chr7D	89729675	89731734	2059	True	2710.000000	2710	90.588000	991	3047	1	chr7D.!!$R1	2056
7	TraesCS7B01G040900	chr7D	89486419	89487496	1077	False	1703.000000	1703	95.176000	983	2060	1	chr7D.!!$F1	1077
8	TraesCS7B01G040900	chr7D	89521055	89523361	2306	False	838.333333	1801	90.970000	1	2060	3	chr7D.!!$F3	2059
9	TraesCS7B01G040900	chrUn	91490447	91491898	1451	False	1507.000000	1507	85.588000	981	2432	1	chrUn.!!$F1	1451

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
876	1194	0.033796	TCAGACCCCTCCGTCGTTAT	60.034	55.0	0.0	0.0	37.85	1.89	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2843	3284	0.671781	GTTCGTCACAGGCATCAGCT	60.672	55.0	0.0	0.0	41.7	4.24	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
119	265	7.178741	TGACGCAATTTTCTCAAAACAATTTG	58.821	30.769	0.00	0.00	45.92	2.32
191	337	9.642327	TTTGATATGCATGGAATATGTTAATGC	57.358	29.630	10.16	12.67	43.08	3.56
356	503	7.642071	AAAATATTCATGTGTGTTCAACAGC	57.358	32.000	0.00	0.00	40.26	4.40
364	511	3.171277	GTGTGTTCAACAGCTGTTCAAC	58.829	45.455	32.07	32.07	39.09	3.18
418	567	4.496895	GTGTTTCGCATGAGATAAATGTGC	59.503	41.667	0.00	0.00	35.86	4.57
495	644	1.555477	CCAAGCAAAACGTTCACACC	58.445	50.000	0.00	0.00	0.00	4.16
498	647	0.100503	AGCAAAACGTTCACACCAGC	59.899	50.000	0.00	0.00	0.00	4.85
502	651	2.844122	AAACGTTCACACCAGCTTTC	57.156	45.000	0.00	0.00	0.00	2.62
515	664	8.801299	TCACACCAGCTTTCAAATATTATTCAA	58.199	29.630	0.00	0.00	0.00	2.69
726	1009	8.527810	TGTGTTCTAATTTTTATCCCATCAACC	58.472	33.333	0.00	0.00	0.00	3.77
815	1104	0.459759	GGACCAGGTCGAATCGGAAC	60.460	60.000	13.80	0.00	32.65	3.62
816	1105	0.531200	GACCAGGTCGAATCGGAACT	59.469	55.000	3.05	0.00	33.18	3.01
821	1110	2.022934	AGGTCGAATCGGAACTACTCC	58.977	52.381	1.76	0.00	41.40	3.85
859	1177	1.592400	CGTACTCTTGCCGGGACTCA	61.592	60.000	2.18	0.00	0.00	3.41
875	1193	0.679002	CTCAGACCCCTCCGTCGTTA	60.679	60.000	0.00	0.00	37.85	3.18
876	1194	0.033796	TCAGACCCCTCCGTCGTTAT	60.034	55.000	0.00	0.00	37.85	1.89
877	1195	0.384669	CAGACCCCTCCGTCGTTATC	59.615	60.000	0.00	0.00	37.85	1.75
878	1196	1.099879	AGACCCCTCCGTCGTTATCG	61.100	60.000	0.00	0.00	37.85	2.92
879	1197	1.379044	ACCCCTCCGTCGTTATCGT	60.379	57.895	0.00	0.00	38.33	3.73
918	1236	1.873591	CCTTGTTCTCTCCACCAAACG	59.126	52.381	0.00	0.00	0.00	3.60
920	1238	2.992124	TGTTCTCTCCACCAAACGAA	57.008	45.000	0.00	0.00	0.00	3.85
921	1239	2.557317	TGTTCTCTCCACCAAACGAAC	58.443	47.619	0.00	0.00	33.34	3.95
923	1241	1.124780	TCTCTCCACCAAACGAACCA	58.875	50.000	0.00	0.00	0.00	3.67
924	1242	1.487142	TCTCTCCACCAAACGAACCAA	59.513	47.619	0.00	0.00	0.00	3.67
925	1243	2.092861	TCTCTCCACCAAACGAACCAAA	60.093	45.455	0.00	0.00	0.00	3.28
927	1245	1.746220	CTCCACCAAACGAACCAAACA	59.254	47.619	0.00	0.00	0.00	2.83
939	1257	3.058570	CGAACCAAACAACAATCCATCGA	60.059	43.478	0.00	0.00	0.00	3.59
940	1258	4.475944	GAACCAAACAACAATCCATCGAG	58.524	43.478	0.00	0.00	0.00	4.04
941	1259	2.228822	ACCAAACAACAATCCATCGAGC	59.771	45.455	0.00	0.00	0.00	5.03
942	1260	2.508867	CAAACAACAATCCATCGAGCG	58.491	47.619	0.00	0.00	0.00	5.03
943	1261	2.093306	AACAACAATCCATCGAGCGA	57.907	45.000	0.00	0.00	0.00	4.93
944	1262	2.093306	ACAACAATCCATCGAGCGAA	57.907	45.000	0.00	0.00	0.00	4.70
945	1263	2.002586	ACAACAATCCATCGAGCGAAG	58.997	47.619	0.00	0.00	0.00	3.79
985	1303	3.257393	CACAAGCTCTCGAAACAGCTAT	58.743	45.455	12.31	3.50	45.58	2.97
1077	1396	3.009723	CCTAATCTTTTGCTTCTCGCCA	58.990	45.455	0.00	0.00	38.05	5.69
1212	1531	2.585247	GGTCCATACAGCGGCGTC	60.585	66.667	9.37	0.13	0.00	5.19
1548	1874	1.739562	CTTCACGGACAGCTCCAGC	60.740	63.158	0.00	0.00	36.12	4.85
1851	2180	1.768870	GGATACTGGGTGGCACTACAT	59.231	52.381	18.45	9.47	0.00	2.29
2046	2375	0.785378	CCGTCGTCACACGCAAATAA	59.215	50.000	0.00	0.00	42.21	1.40
2228	2599	9.284594	TGTATCAAATTATCTTTGTTTAAGCGC	57.715	29.630	0.00	0.00	33.66	5.92
2307	2693	7.124347	AGCATTGTTGTGAAATAAATTGCTG	57.876	32.000	0.00	0.00	0.00	4.41
2576	3016	2.417651	GGCACACCAATGACCATGAATG	60.418	50.000	0.00	0.00	35.26	2.67
2581	3021	3.004002	CACCAATGACCATGAATGATCCG	59.996	47.826	0.00	0.00	0.00	4.18
2647	3087	7.095695	ACACCATATACAAAATACACAAGCC	57.904	36.000	0.00	0.00	0.00	4.35
2727	3167	1.134371	GCCATGTCAGTCCTTCCTACC	60.134	57.143	0.00	0.00	0.00	3.18
2843	3284	1.063266	AGTTGGCCTCAGGGTTTTTCA	60.063	47.619	3.32	0.00	34.45	2.69
2845	3286	0.827507	TGGCCTCAGGGTTTTTCAGC	60.828	55.000	3.32	0.00	34.45	4.26
2878	3319	2.288334	ACGAACAGTACATACAACCGCA	60.288	45.455	0.00	0.00	0.00	5.69
2964	3413	7.202016	TGAATCACCAAACATCTACAACTTC	57.798	36.000	0.00	0.00	0.00	3.01
2979	3428	7.618137	TCTACAACTTCATTAACTAGAACCCC	58.382	38.462	0.00	0.00	0.00	4.95
2993	3442	3.771160	CCCCAAGCGCCGTAGTCT	61.771	66.667	2.29	0.00	0.00	3.24

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
119	265	8.923683	GTTACACACTAACAATTTCTCTCCTAC	58.076	37.037	0.00	0.00	0.00	3.18
166	312	8.804204	TGCATTAACATATTCCATGCATATCAA	58.196	29.630	0.00	0.00	44.07	2.57
267	414	8.773033	ATACTTGAAAGATATTCATTTGCCCT	57.227	30.769	0.00	0.00	0.00	5.19
269	416	9.455847	GTGATACTTGAAAGATATTCATTTGCC	57.544	33.333	0.00	0.00	0.00	4.52
286	433	5.049828	TCATAACTGATGCCGTGATACTTG	58.950	41.667	0.00	0.00	35.29	3.16
437	586	5.477510	TGTTGAAACTTGCATGAACACTTT	58.522	33.333	6.60	0.00	0.00	2.66
456	605	7.095313	TGCTTGGCACACATTTATATTTTGTTG	60.095	33.333	0.00	0.00	39.29	3.33
559	711	4.520179	TCATGGACTGCGTAGTACTAGAA	58.480	43.478	17.27	0.00	38.66	2.10
563	715	3.257375	TGTTTCATGGACTGCGTAGTACT	59.743	43.478	17.27	0.00	38.66	2.73
564	716	3.581755	TGTTTCATGGACTGCGTAGTAC	58.418	45.455	9.22	9.22	37.25	2.73
696	979	9.586435	GATGGGATAAAAATTAGAACACAAAGG	57.414	33.333	0.00	0.00	0.00	3.11
815	1104	2.231529	CCTATCCGTGTCCTGGAGTAG	58.768	57.143	0.00	0.00	39.30	2.57
816	1105	1.133575	CCCTATCCGTGTCCTGGAGTA	60.134	57.143	0.00	0.00	39.30	2.59
821	1110	1.033574	GAGTCCCTATCCGTGTCCTG	58.966	60.000	0.00	0.00	0.00	3.86
859	1177	1.099879	CGATAACGACGGAGGGGTCT	61.100	60.000	0.00	0.00	42.66	3.85
875	1193	4.443034	GGGTGCCTCTGTTCTTATAACGAT	60.443	45.833	0.00	0.00	0.00	3.73
876	1194	3.118884	GGGTGCCTCTGTTCTTATAACGA	60.119	47.826	0.00	0.00	0.00	3.85
877	1195	3.195661	GGGTGCCTCTGTTCTTATAACG	58.804	50.000	0.00	0.00	0.00	3.18
878	1196	3.200165	AGGGGTGCCTCTGTTCTTATAAC	59.800	47.826	0.00	0.00	0.00	1.89
879	1197	3.460825	AGGGGTGCCTCTGTTCTTATAA	58.539	45.455	0.00	0.00	0.00	0.98
918	1236	4.475944	CTCGATGGATTGTTGTTTGGTTC	58.524	43.478	0.00	0.00	0.00	3.62
920	1238	2.228822	GCTCGATGGATTGTTGTTTGGT	59.771	45.455	0.00	0.00	0.00	3.67
921	1239	2.728846	CGCTCGATGGATTGTTGTTTGG	60.729	50.000	0.00	0.00	0.00	3.28
923	1241	2.422597	TCGCTCGATGGATTGTTGTTT	58.577	42.857	0.00	0.00	0.00	2.83
924	1242	2.093306	TCGCTCGATGGATTGTTGTT	57.907	45.000	0.00	0.00	0.00	2.83
925	1243	2.002586	CTTCGCTCGATGGATTGTTGT	58.997	47.619	0.00	0.00	0.00	3.32
927	1245	1.009829	GCTTCGCTCGATGGATTGTT	58.990	50.000	7.18	0.00	0.00	2.83
939	1257	0.036732	TCTGGTGGATTTGCTTCGCT	59.963	50.000	0.00	0.00	0.00	4.93
940	1258	0.881118	TTCTGGTGGATTTGCTTCGC	59.119	50.000	0.00	0.00	0.00	4.70
941	1259	2.426522	TCTTCTGGTGGATTTGCTTCG	58.573	47.619	0.00	0.00	0.00	3.79
942	1260	4.037923	TGTTTCTTCTGGTGGATTTGCTTC	59.962	41.667	0.00	0.00	0.00	3.86
943	1261	3.960102	TGTTTCTTCTGGTGGATTTGCTT	59.040	39.130	0.00	0.00	0.00	3.91
944	1262	3.319122	GTGTTTCTTCTGGTGGATTTGCT	59.681	43.478	0.00	0.00	0.00	3.91
945	1263	3.068024	TGTGTTTCTTCTGGTGGATTTGC	59.932	43.478	0.00	0.00	0.00	3.68
946	1264	4.916983	TGTGTTTCTTCTGGTGGATTTG	57.083	40.909	0.00	0.00	0.00	2.32
947	1265	4.202151	GCTTGTGTTTCTTCTGGTGGATTT	60.202	41.667	0.00	0.00	0.00	2.17
948	1266	3.319122	GCTTGTGTTTCTTCTGGTGGATT	59.681	43.478	0.00	0.00	0.00	3.01
949	1267	2.887152	GCTTGTGTTTCTTCTGGTGGAT	59.113	45.455	0.00	0.00	0.00	3.41
950	1268	2.092429	AGCTTGTGTTTCTTCTGGTGGA	60.092	45.455	0.00	0.00	0.00	4.02
951	1269	2.291741	GAGCTTGTGTTTCTTCTGGTGG	59.708	50.000	0.00	0.00	0.00	4.61
952	1270	3.209410	AGAGCTTGTGTTTCTTCTGGTG	58.791	45.455	0.00	0.00	0.00	4.17
985	1303	0.726827	GCCATGTCGATTTGCTTCGA	59.273	50.000	0.00	3.42	45.27	3.71
1548	1874	4.629634	TCATGTTGCGACCTATTGTAGTTG	59.370	41.667	0.45	0.00	0.00	3.16
1851	2180	1.599606	GGAGCTCAGCCTTCTCACGA	61.600	60.000	17.19	0.00	0.00	4.35
2141	2505	5.057149	TCTCCACTTAACAACAGAAAGCTC	58.943	41.667	0.00	0.00	0.00	4.09
2219	2590	8.807667	TGTACTTTCCTATATAGCGCTTAAAC	57.192	34.615	18.68	0.00	0.00	2.01
2220	2591	8.636213	ACTGTACTTTCCTATATAGCGCTTAAA	58.364	33.333	18.68	0.00	0.00	1.52
2227	2598	7.711339	ACTTGCAACTGTACTTTCCTATATAGC	59.289	37.037	4.04	0.00	0.00	2.97
2228	2599	9.601217	AACTTGCAACTGTACTTTCCTATATAG	57.399	33.333	2.46	2.46	0.00	1.31
2231	2602	6.148811	GCAACTTGCAACTGTACTTTCCTATA	59.851	38.462	8.97	0.00	44.26	1.31
2232	2603	5.048713	GCAACTTGCAACTGTACTTTCCTAT	60.049	40.000	8.97	0.00	44.26	2.57
2307	2693	4.113354	CTCTAGACCGTCTTATTTGTGCC	58.887	47.826	6.31	0.00	0.00	5.01
2576	3016	5.416013	TGTGTATACATCTGGAGATCGGATC	59.584	44.000	9.18	10.02	39.36	3.36
2581	3021	6.488344	TGAGTCTGTGTATACATCTGGAGATC	59.512	42.308	9.18	7.03	35.97	2.75
2727	3167	1.071605	GTGACGGCTTTGTAGCTCAG	58.928	55.000	0.00	0.00	46.90	3.35
2843	3284	0.671781	GTTCGTCACAGGCATCAGCT	60.672	55.000	0.00	0.00	41.70	4.24
2845	3286	3.215642	TGTTCGTCACAGGCATCAG	57.784	52.632	0.00	0.00	0.00	2.90
2864	3305	1.066716	TGGACCTGCGGTTGTATGTAC	60.067	52.381	1.80	0.00	35.25	2.90
2865	3306	1.268066	TGGACCTGCGGTTGTATGTA	58.732	50.000	1.80	0.00	35.25	2.29
2878	3319	7.405292	TGAGTATTTTCTGAAATGATGGACCT	58.595	34.615	3.31	0.00	36.22	3.85
2881	3322	7.339976	TGCATGAGTATTTTCTGAAATGATGGA	59.660	33.333	3.31	0.00	36.22	3.41
2882	3323	7.485810	TGCATGAGTATTTTCTGAAATGATGG	58.514	34.615	3.31	0.00	36.22	3.51
2964	3413	2.354821	GCGCTTGGGGTTCTAGTTAATG	59.645	50.000	0.00	0.00	0.00	1.90
2979	3428	2.493713	AATCTAGACTACGGCGCTTG	57.506	50.000	6.90	2.40	0.00	4.01
2993	3442	8.097038	GGTCCAGCATAGATCATACAAAATCTA	58.903	37.037	0.00	0.00	38.49	1.98

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.