AutoCloner

Multiple sequence alignment - TraesCS5A01G095200

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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	TraesCS5A01G095200	chr5A	100.000	3350	0	0	1	3350	132597468	132594119	0.000000e+00	6187
1	TraesCS5A01G095200	chr5B	94.920	3071	99	24	309	3350	134449339	134446297	0.000000e+00	4754
2	TraesCS5A01G095200	chr5B	83.544	553	66	12	2738	3272	215845885	215846430	8.350000e-136	494
3	TraesCS5A01G095200	chr5D	96.599	2617	71	10	207	2821	121175220	121172620	0.000000e+00	4324
4	TraesCS5A01G095200	chr5D	91.916	569	21	8	2803	3350	121172606	121172042	0.000000e+00	773
5	TraesCS5A01G095200	chr5D	87.437	199	24	1	16	214	121176472	121176275	9.350000e-56	228
6	TraesCS5A01G095200	chr3D	89.852	1015	92	6	1316	2326	17792237	17793244	0.000000e+00	1293
7	TraesCS5A01G095200	chr3D	88.870	575	58	3	1752	2326	17807509	17808077	0.000000e+00	702
8	TraesCS5A01G095200	chr3D	86.557	610	70	6	1754	2361	17793682	17794281	0.000000e+00	662
9	TraesCS5A01G095200	chr3D	88.506	522	60	0	1753	2274	17796382	17796903	1.700000e-177	632
10	TraesCS5A01G095200	chr3D	87.768	466	46	8	1899	2361	17834713	17835170	4.920000e-148	534
11	TraesCS5A01G095200	chrUn	90.556	540	39	8	1826	2361	37157942	37157411	0.000000e+00	704
12	TraesCS5A01G095200	chrUn	85.366	615	64	13	2756	3350	244072313	244072921	6.140000e-172	614
13	TraesCS5A01G095200	chrUn	85.366	615	64	13	2756	3350	256066504	256065896	6.140000e-172	614
14	TraesCS5A01G095200	chrUn	85.366	615	64	13	2756	3350	268677062	268676454	6.140000e-172	614
15	TraesCS5A01G095200	chrUn	85.450	378	28	11	1421	1798	37158287	37157937	5.280000e-98	368
16	TraesCS5A01G095200	chr7A	84.727	622	64	16	2755	3350	727513178	727513794	8.000000e-166	593
17	TraesCS5A01G095200	chr2A	84.516	620	67	14	2755	3350	394800921	394800307	1.340000e-163	586
18	TraesCS5A01G095200	chr2A	84.355	620	68	14	2755	3350	406408612	406409226	6.230000e-162	580
19	TraesCS5A01G095200	chr2A	83.885	453	73	0	1144	1596	133671038	133671490	1.850000e-117	433
20	TraesCS5A01G095200	chr2A	80.591	474	58	25	1602	2055	133671627	133672086	5.360000e-88	335
21	TraesCS5A01G095200	chr2B	84.106	453	72	0	1144	1596	180558781	180559233	3.970000e-119	438
22	TraesCS5A01G095200	chr2B	81.328	482	53	30	1594	2055	180559327	180559791	1.140000e-94	357
23	TraesCS5A01G095200	chr2D	83.885	453	73	0	1144	1596	126968377	126968829	1.850000e-117	433
24	TraesCS5A01G095200	chr2D	80.672	476	70	18	1594	2055	126968941	126969408	1.910000e-92	350
25	TraesCS5A01G095200	chr6D	76.104	385	72	16	1161	1535	454231330	454231704	2.050000e-42	183
26	TraesCS5A01G095200	chr6A	75.584	385	74	18	1161	1535	600404314	600404688	4.440000e-39	172
27	TraesCS5A01G095200	chr6B	90.152	132	11	2	1161	1291	690560723	690560593	1.600000e-38	171

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	TraesCS5A01G095200	chr5A	132594119	132597468	3349	True	6187.000000	6187	100.0000	1	3350	1	chr5A.!!$R1	3349
1	TraesCS5A01G095200	chr5B	134446297	134449339	3042	True	4754.000000	4754	94.9200	309	3350	1	chr5B.!!$R1	3041
2	TraesCS5A01G095200	chr5B	215845885	215846430	545	False	494.000000	494	83.5440	2738	3272	1	chr5B.!!$F1	534
3	TraesCS5A01G095200	chr5D	121172042	121176472	4430	True	1775.000000	4324	91.9840	16	3350	3	chr5D.!!$R1	3334
4	TraesCS5A01G095200	chr3D	17792237	17796903	4666	False	862.333333	1293	88.3050	1316	2361	3	chr3D.!!$F3	1045
5	TraesCS5A01G095200	chr3D	17807509	17808077	568	False	702.000000	702	88.8700	1752	2326	1	chr3D.!!$F1	574
6	TraesCS5A01G095200	chrUn	244072313	244072921	608	False	614.000000	614	85.3660	2756	3350	1	chrUn.!!$F1	594
7	TraesCS5A01G095200	chrUn	256065896	256066504	608	True	614.000000	614	85.3660	2756	3350	1	chrUn.!!$R1	594
8	TraesCS5A01G095200	chrUn	268676454	268677062	608	True	614.000000	614	85.3660	2756	3350	1	chrUn.!!$R2	594
9	TraesCS5A01G095200	chrUn	37157411	37158287	876	True	536.000000	704	88.0030	1421	2361	2	chrUn.!!$R3	940
10	TraesCS5A01G095200	chr7A	727513178	727513794	616	False	593.000000	593	84.7270	2755	3350	1	chr7A.!!$F1	595
11	TraesCS5A01G095200	chr2A	394800307	394800921	614	True	586.000000	586	84.5160	2755	3350	1	chr2A.!!$R1	595
12	TraesCS5A01G095200	chr2A	406408612	406409226	614	False	580.000000	580	84.3550	2755	3350	1	chr2A.!!$F1	595
13	TraesCS5A01G095200	chr2A	133671038	133672086	1048	False	384.000000	433	82.2380	1144	2055	2	chr2A.!!$F2	911
14	TraesCS5A01G095200	chr2B	180558781	180559791	1010	False	397.500000	438	82.7170	1144	2055	2	chr2B.!!$F1	911
15	TraesCS5A01G095200	chr2D	126968377	126969408	1031	False	391.500000	433	82.2785	1144	2055	2	chr2D.!!$F1	911

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
829	1892	0.036105	TGTGACATGCCATCTCGCTT	60.036	50.0	0.0	0.0	0.0	4.68	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2783	7745	0.323302	TGGTCGGCATGCTAAAGTCA	59.677	50.0	18.92	6.3	0.0	3.41	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
57	58	8.943002	AGTGGTTGTTACATTTGTATAACTAGC	58.057	33.333	13.43	9.12	36.06	3.42
58	59	7.901377	GTGGTTGTTACATTTGTATAACTAGCG	59.099	37.037	13.43	0.00	37.35	4.26
61	62	9.632969	GTTGTTACATTTGTATAACTAGCGATG	57.367	33.333	0.00	0.00	33.32	3.84
64	65	5.364778	ACATTTGTATAACTAGCGATGCCA	58.635	37.500	0.00	0.00	0.00	4.92
65	66	5.997746	ACATTTGTATAACTAGCGATGCCAT	59.002	36.000	0.00	0.00	0.00	4.40
74	75	2.648724	CGATGCCATGCGCGTTTC	60.649	61.111	8.43	0.00	42.08	2.78
79	80	3.050166	GCCATGCGCGTTTCCATGA	62.050	57.895	21.23	0.00	40.92	3.07
84	85	0.595588	TGCGCGTTTCCATGAATTGT	59.404	45.000	8.43	0.00	0.00	2.71
91	92	6.482835	CGCGTTTCCATGAATTGTAGATTTA	58.517	36.000	0.00	0.00	0.00	1.40
155	156	6.777580	AGGTGTAAACCATGTGAGAAATTTCT	59.222	34.615	20.60	20.60	41.00	2.52
163	164	5.632347	CCATGTGAGAAATTTCTGCAGAAAC	59.368	40.000	37.28	26.35	45.55	2.78
164	165	4.847633	TGTGAGAAATTTCTGCAGAAACG	58.152	39.130	37.28	3.54	45.55	3.60
175	176	3.692101	TCTGCAGAAACGGAAAAACAGAA	59.308	39.130	15.67	0.00	30.46	3.02
186	187	8.496707	AACGGAAAAACAGAAGTCTTAACTTA	57.503	30.769	0.00	0.00	45.80	2.24
187	188	8.496707	ACGGAAAAACAGAAGTCTTAACTTAA	57.503	30.769	0.00	0.00	45.80	1.85
188	189	8.949177	ACGGAAAAACAGAAGTCTTAACTTAAA	58.051	29.630	0.00	0.00	45.80	1.52
282	1345	2.820178	TCTGCATGGTAGGAAGACAGA	58.180	47.619	0.00	0.00	0.00	3.41
304	1367	2.027385	TCTCATGACCAGATCAGACGG	58.973	52.381	0.00	0.00	41.91	4.79
440	1503	8.730948	TGTAGTAGGGGTTGTCTAAGATACTAT	58.269	37.037	0.00	0.00	29.93	2.12
441	1504	9.012161	GTAGTAGGGGTTGTCTAAGATACTATG	57.988	40.741	0.00	0.00	29.93	2.23
442	1505	7.011382	AGTAGGGGTTGTCTAAGATACTATGG	58.989	42.308	0.00	0.00	0.00	2.74
443	1506	6.039415	AGGGGTTGTCTAAGATACTATGGA	57.961	41.667	0.00	0.00	0.00	3.41
444	1507	6.078664	AGGGGTTGTCTAAGATACTATGGAG	58.921	44.000	0.00	0.00	0.00	3.86
445	1508	5.839606	GGGGTTGTCTAAGATACTATGGAGT	59.160	44.000	0.00	0.00	39.92	3.85
446	1509	7.008941	GGGGTTGTCTAAGATACTATGGAGTA	58.991	42.308	0.00	0.00	42.41	2.59
829	1892	0.036105	TGTGACATGCCATCTCGCTT	60.036	50.000	0.00	0.00	0.00	4.68
852	1915	4.213270	TGTTGTTGATGCTTCTTCTTACCG	59.787	41.667	0.88	0.00	0.00	4.02
1062	2125	4.357947	GTCACCTGCTCCGTCGCA	62.358	66.667	0.00	0.00	38.40	5.10
1293	2356	0.846693	ACTGCTCCAAGTTCAAGGGT	59.153	50.000	0.00	0.00	0.00	4.34
2043	6998	1.780919	AGCTTCCAGTACAAACCCCTT	59.219	47.619	0.00	0.00	0.00	3.95
2262	7217	1.155624	GCCCGACTCCTACCCCTAT	59.844	63.158	0.00	0.00	0.00	2.57
2457	7416	0.038618	GGGGCATTTTGGTTGTCGAC	60.039	55.000	9.11	9.11	0.00	4.20
2529	7490	7.284489	ACATATTTTGTTTAGGAGTGTGTGTGT	59.716	33.333	0.00	0.00	33.74	3.72
2530	7491	4.955925	TTTGTTTAGGAGTGTGTGTGTG	57.044	40.909	0.00	0.00	0.00	3.82
2531	7492	3.620427	TGTTTAGGAGTGTGTGTGTGT	57.380	42.857	0.00	0.00	0.00	3.72
2532	7493	3.266636	TGTTTAGGAGTGTGTGTGTGTG	58.733	45.455	0.00	0.00	0.00	3.82
2533	7494	3.267483	GTTTAGGAGTGTGTGTGTGTGT	58.733	45.455	0.00	0.00	0.00	3.72
2534	7495	2.595124	TAGGAGTGTGTGTGTGTGTG	57.405	50.000	0.00	0.00	0.00	3.82
2613	7574	7.757526	TGTATTTTATGGAATGAGTCAAACGG	58.242	34.615	0.00	0.00	0.00	4.44
2731	7693	2.904434	AGAGTTTGACACCGGGTATTCT	59.096	45.455	6.32	0.00	0.00	2.40
2736	7698	3.880047	TGACACCGGGTATTCTAAGTG	57.120	47.619	6.32	0.00	0.00	3.16
2742	7704	3.450096	ACCGGGTATTCTAAGTGTCTTCC	59.550	47.826	6.32	0.00	0.00	3.46
2749	7711	8.975295	GGGTATTCTAAGTGTCTTCCTAACTTA	58.025	37.037	0.00	0.00	35.77	2.24
2761	7723	9.529823	TGTCTTCCTAACTTATCTCAACTAGAA	57.470	33.333	0.00	0.00	37.89	2.10
2787	7749	3.726517	GCACGTTGCCGCATGACT	61.727	61.111	0.00	0.00	37.42	3.41
2826	7820	5.494724	ACTCAGTGACAGATGCACATTAAT	58.505	37.500	0.00	0.00	38.70	1.40
2874	7871	1.679680	CAACATCTGCCCACATCCATC	59.320	52.381	0.00	0.00	0.00	3.51
2908	7906	6.924111	ACCTGAAGGCAATTGTACTAAAATG	58.076	36.000	7.40	0.00	39.32	2.32
2997	7995	7.597386	AGATTAACTTTGAGAACATTCCTTGC	58.403	34.615	0.00	0.00	0.00	4.01
3115	8116	7.941919	ACACAGAGAAATTGCTATACTCGATA	58.058	34.615	0.00	0.00	33.53	2.92
3117	8118	9.416794	CACAGAGAAATTGCTATACTCGATATT	57.583	33.333	0.00	0.00	33.53	1.28
3170	8172	3.793797	AGAAACAACCAAAAACCCTCG	57.206	42.857	0.00	0.00	0.00	4.63
3331	8355	6.349944	GCAGAAGAACATCAAAGGACAATCAT	60.350	38.462	0.00	0.00	0.00	2.45

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
9	10	9.778741	CCACTATAAGCTTATAAAGAATCCACA	57.221	33.333	23.14	2.97	0.00	4.17
10	11	9.780186	ACCACTATAAGCTTATAAAGAATCCAC	57.220	33.333	23.14	0.00	0.00	4.02
32	33	7.901377	CGCTAGTTATACAAATGTAACAACCAC	59.099	37.037	13.48	6.74	35.45	4.16
42	43	5.922739	TGGCATCGCTAGTTATACAAATG	57.077	39.130	0.00	0.00	0.00	2.32
43	44	5.106555	GCATGGCATCGCTAGTTATACAAAT	60.107	40.000	12.62	0.00	0.00	2.32
57	58	2.648724	GAAACGCGCATGGCATCG	60.649	61.111	5.73	12.80	43.84	3.84
58	59	2.278142	GGAAACGCGCATGGCATC	60.278	61.111	5.73	0.00	43.84	3.91
61	62	2.540736	TTCATGGAAACGCGCATGGC	62.541	55.000	19.69	0.00	38.69	4.40
64	65	1.202114	ACAATTCATGGAAACGCGCAT	59.798	42.857	5.73	0.00	0.00	4.73
65	66	0.595588	ACAATTCATGGAAACGCGCA	59.404	45.000	5.73	0.00	0.00	6.09
120	121	7.721842	TCACATGGTTTACACCTTAAGAAATGA	59.278	33.333	3.36	0.00	44.61	2.57
132	133	6.363357	GCAGAAATTTCTCACATGGTTTACAC	59.637	38.462	17.91	0.00	34.74	2.90
155	156	3.442273	ACTTCTGTTTTTCCGTTTCTGCA	59.558	39.130	0.00	0.00	0.00	4.41
163	164	9.777575	TTTTAAGTTAAGACTTCTGTTTTTCCG	57.222	29.630	0.00	0.00	44.75	4.30
199	200	9.944663	TCCGAGCAAAATTAATTATAACATGTC	57.055	29.630	0.00	0.00	0.00	3.06
215	1278	7.429633	TCAAGTGATTTTAAATCCGAGCAAAA	58.570	30.769	14.22	0.00	0.00	2.44
229	1292	5.300034	TGCACTCAATGACTCAAGTGATTTT	59.700	36.000	11.89	0.00	41.26	1.82
282	1345	2.687425	CGTCTGATCTGGTCATGAGAGT	59.313	50.000	0.00	0.00	35.97	3.24
304	1367	7.761249	GGATTTGCTACATTGCCCATTATTATC	59.239	37.037	0.00	0.00	0.00	1.75
443	1506	9.819267	GCCATCTTTCATTTACTAAGTAGTACT	57.181	33.333	0.00	0.00	38.43	2.73
444	1507	8.753175	CGCCATCTTTCATTTACTAAGTAGTAC	58.247	37.037	0.00	0.00	38.43	2.73
445	1508	8.689061	TCGCCATCTTTCATTTACTAAGTAGTA	58.311	33.333	0.00	0.00	37.73	1.82
446	1509	7.553334	TCGCCATCTTTCATTTACTAAGTAGT	58.447	34.615	0.00	0.00	40.24	2.73
638	1701	3.222126	TTGCGTCGTTGCTCTTGCG	62.222	57.895	0.00	0.00	43.34	4.85
829	1892	4.213270	CGGTAAGAAGAAGCATCAACAACA	59.787	41.667	0.00	0.00	0.00	3.33
852	1915	6.470160	CATCGGCGAAGAATAATAATACAGC	58.530	40.000	15.93	0.00	0.00	4.40
1131	2194	1.949133	CATGGCCACGTATCCGTCG	60.949	63.158	8.16	0.00	46.28	5.12
2163	7118	3.055094	GGCTGAAGGTGAAGGTTCTATCA	60.055	47.826	0.00	0.00	0.00	2.15
2457	7416	7.360575	ACCACTCAGCTAGTTTTAATAAACG	57.639	36.000	0.00	0.00	46.54	3.60
2529	7490	7.867305	TTAATCTTAACTTGACAACCACACA	57.133	32.000	0.00	0.00	0.00	3.72
2613	7574	7.792374	TGAAGATCTAAGTAACAATGCCATC	57.208	36.000	0.00	0.00	0.00	3.51
2731	7693	9.310449	AGTTGAGATAAGTTAGGAAGACACTTA	57.690	33.333	0.00	0.00	37.40	2.24
2742	7704	9.974980	GGGAATCTTCTAGTTGAGATAAGTTAG	57.025	37.037	6.50	0.00	32.88	2.34
2749	7711	3.070302	GCGGGGAATCTTCTAGTTGAGAT	59.930	47.826	0.00	0.00	32.88	2.75
2761	7723	2.746277	GCAACGTGCGGGGAATCT	60.746	61.111	0.00	0.00	31.71	2.40
2783	7745	0.323302	TGGTCGGCATGCTAAAGTCA	59.677	50.000	18.92	6.30	0.00	3.41
2787	7749	1.271108	TGAGTTGGTCGGCATGCTAAA	60.271	47.619	18.92	0.00	0.00	1.85
2798	7760	2.072298	GCATCTGTCACTGAGTTGGTC	58.928	52.381	0.00	0.00	0.00	4.02
2874	7871	5.665916	ATTGCCTTCAGGTTAATCCTTTG	57.334	39.130	0.00	0.00	45.67	2.77
3115	8116	9.034544	GTTTGTCTTGCAAGATTTCAGTTAAAT	57.965	29.630	30.65	0.00	38.47	1.40
3117	8118	7.542890	TGTTTGTCTTGCAAGATTTCAGTTAA	58.457	30.769	30.65	13.21	38.47	2.01
3170	8172	7.544915	ACTCCGTTTATTTTAGCTCTTCAGTAC	59.455	37.037	0.00	0.00	0.00	2.73
3210	8232	7.413166	ACATTAACTGTTCAGGTTTGGACCTC	61.413	42.308	0.00	0.00	43.97	3.85
3226	8248	6.057533	TGGCCATTCTCATAGACATTAACTG	58.942	40.000	0.00	0.00	0.00	3.16

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.