AutoCloner

Multiple sequence alignment - TraesCS4D01G237600

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	TraesCS4D01G237600	chr4D	100.000	3629	0	0	1	3629	399776695	399780323	0.000000e+00	6702
1	TraesCS4D01G237600	chr4D	94.783	230	12	0	1902	2131	350265909	350266138	3.450000e-95	359
2	TraesCS4D01G237600	chr4D	90.244	246	24	0	2591	2836	350266135	350266380	4.520000e-84	322
3	TraesCS4D01G237600	chr4B	94.655	3667	129	23	1	3629	494020297	494023934	0.000000e+00	5624
4	TraesCS4D01G237600	chr4B	91.928	223	17	1	1382	1604	13276372	13276151	9.780000e-81	311
5	TraesCS4D01G237600	chr4A	90.972	3445	158	55	1	3331	57812212	57815617	0.000000e+00	4497
6	TraesCS4D01G237600	chr4A	85.648	216	9	9	3417	3628	57815636	57815833	1.320000e-49	207
7	TraesCS4D01G237600	chr2A	88.749	1351	100	17	2155	3476	697070953	697069626	0.000000e+00	1605
8	TraesCS4D01G237600	chr2A	89.053	338	22	2	1382	1718	697071458	697071135	4.360000e-109	405
9	TraesCS4D01G237600	chr2A	93.902	164	3	1	1935	2091	697071114	697070951	1.300000e-59	241
10	TraesCS4D01G237600	chr5A	89.899	891	59	9	1919	2783	667025497	667024612	0.000000e+00	1118
11	TraesCS4D01G237600	chr5A	93.889	360	22	0	1594	1953	129233694	129233335	8.860000e-151	544
12	TraesCS4D01G237600	chr5A	94.379	338	18	1	1382	1718	667025832	667025495	5.370000e-143	518
13	TraesCS4D01G237600	chr5A	96.087	230	9	0	1902	2131	52485128	52485357	3.420000e-100	375
14	TraesCS4D01G237600	chr5A	92.444	225	17	0	2612	2836	52485366	52485590	4.520000e-84	322
15	TraesCS4D01G237600	chr7B	88.127	758	51	11	2042	2777	735911800	735912540	0.000000e+00	865
16	TraesCS4D01G237600	chr7B	93.403	288	18	1	1432	1718	735909814	735910101	3.350000e-115	425
17	TraesCS4D01G237600	chr7B	90.583	223	20	1	1382	1604	22543460	22543681	9.850000e-76	294
18	TraesCS4D01G237600	chr7B	90.728	151	6	2	1919	2061	735910099	735910249	1.030000e-45	195
19	TraesCS4D01G237600	chr3D	95.845	361	15	0	1592	1952	470481483	470481843	5.220000e-163	584
20	TraesCS4D01G237600	chr2D	95.291	361	17	0	1592	1952	287142733	287143093	1.130000e-159	573
21	TraesCS4D01G237600	chr1A	93.370	362	24	0	1592	1953	505305790	505306151	1.480000e-148	536
22	TraesCS4D01G237600	chr2B	90.135	223	21	1	1382	1604	152133766	152133987	4.580000e-74	289
23	TraesCS4D01G237600	chr7D	93.684	190	9	2	1382	1571	264483516	264483330	7.670000e-72	281

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	TraesCS4D01G237600	chr4D	399776695	399780323	3628	False	6702.000000	6702	100.000000	1	3629	1	chr4D.!!$F1	3628
1	TraesCS4D01G237600	chr4B	494020297	494023934	3637	False	5624.000000	5624	94.655000	1	3629	1	chr4B.!!$F1	3628
2	TraesCS4D01G237600	chr4A	57812212	57815833	3621	False	2352.000000	4497	88.310000	1	3628	2	chr4A.!!$F1	3627
3	TraesCS4D01G237600	chr2A	697069626	697071458	1832	True	750.333333	1605	90.568000	1382	3476	3	chr2A.!!$R1	2094
4	TraesCS4D01G237600	chr5A	667024612	667025832	1220	True	818.000000	1118	92.139000	1382	2783	2	chr5A.!!$R2	1401
5	TraesCS4D01G237600	chr7B	735909814	735912540	2726	False	495.000000	865	90.752667	1432	2777	3	chr7B.!!$F2	1345

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
715	788	0.402121	GCACACCCTCCCTTCTTCTT	59.598	55.000	0.0	0.0	0.00	2.52	F
1055	1150	1.533033	TCCAGTGAGCGGTGGAAGA	60.533	57.895	0.0	0.0	40.01	2.87	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1713	1826	1.073199	CGTGAAGGGGCCAAGAAGT	59.927	57.895	4.39	0.0	0.0	3.01	R
2789	4506	0.400213	CACAGCCCAACCCTTGAGTA	59.600	55.000	0.00	0.0	0.0	2.59	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
93	99	4.386049	CGCGTGCCCTAGATTTAGATTTAG	59.614	45.833	0.00	0.00	0.00	1.85
94	100	5.539048	GCGTGCCCTAGATTTAGATTTAGA	58.461	41.667	0.00	0.00	0.00	2.10
95	101	5.635700	GCGTGCCCTAGATTTAGATTTAGAG	59.364	44.000	0.00	0.00	0.00	2.43
156	201	2.110213	GTGGTCACCGGTCAGCAA	59.890	61.111	13.35	0.00	0.00	3.91
170	215	1.148273	AGCAACCTCAAGTTCCGCA	59.852	52.632	0.00	0.00	36.18	5.69
194	239	3.470888	CGCTCCCGTTCCCCAGAT	61.471	66.667	0.00	0.00	0.00	2.90
250	298	5.104151	ACCAAATGTTGAAAAGGGGAAACAT	60.104	36.000	0.00	0.00	43.28	2.71
308	356	8.573035	TGGTAAAAATCACATCAAACCTAGAAC	58.427	33.333	0.00	0.00	0.00	3.01
373	426	0.846427	TCTTCCCCATGCCTTCCTGT	60.846	55.000	0.00	0.00	0.00	4.00
376	429	1.377690	TCCCCATGCCTTCCTGTTTA	58.622	50.000	0.00	0.00	0.00	2.01
388	441	1.606668	TCCTGTTTAGTGCTTTTGGCG	59.393	47.619	0.00	0.00	45.43	5.69
444	497	3.006217	GGCAGCACTGAAGAAAAAGGAAT	59.994	43.478	0.81	0.00	0.00	3.01
445	498	4.502087	GGCAGCACTGAAGAAAAAGGAATT	60.502	41.667	0.81	0.00	0.00	2.17
468	521	6.377327	TTTTGAGCGAGAGAAAAGAAATGT	57.623	33.333	0.00	0.00	0.00	2.71
627	698	4.742201	CTCACTCGCACCCACCCG	62.742	72.222	0.00	0.00	0.00	5.28
696	769	1.953559	CTCTCTCACTCCCTCTCTCG	58.046	60.000	0.00	0.00	0.00	4.04
715	788	0.402121	GCACACCCTCCCTTCTTCTT	59.598	55.000	0.00	0.00	0.00	2.52
716	789	1.611936	GCACACCCTCCCTTCTTCTTC	60.612	57.143	0.00	0.00	0.00	2.87
717	790	1.981495	CACACCCTCCCTTCTTCTTCT	59.019	52.381	0.00	0.00	0.00	2.85
1055	1150	1.533033	TCCAGTGAGCGGTGGAAGA	60.533	57.895	0.00	0.00	40.01	2.87
1713	1826	1.299850	CGTGTCGTTGCTGACCTCA	60.300	57.895	2.62	0.00	38.11	3.86
2307	4005	3.432051	GATGGTGCCCGAGGAGTCG	62.432	68.421	0.00	0.00	46.39	4.18
2513	4214	4.335416	ACATAGTCCTGGTTGTGATTTGG	58.665	43.478	0.00	0.00	0.00	3.28
2525	4226	1.003545	GTGATTTGGGTCGATGATGCG	60.004	52.381	0.00	0.00	0.00	4.73
2527	4228	1.447317	ATTTGGGTCGATGATGCGGC	61.447	55.000	0.00	0.00	34.63	6.53
2620	4325	4.322801	GGCCTGTGTGTAGATAAACTCAGT	60.323	45.833	0.00	0.00	36.59	3.41
2703	4412	0.537188	TCGACAGGAAGCTTGGATCC	59.463	55.000	2.10	4.20	35.88	3.36
2788	4505	5.858581	GTGTGAATTTGGTCAGCTCAATAAC	59.141	40.000	0.00	0.00	0.00	1.89
2789	4506	5.769662	TGTGAATTTGGTCAGCTCAATAACT	59.230	36.000	0.00	0.00	0.00	2.24
2866	4590	2.494870	AGAATTAAGCAAAGGCCTGCAG	59.505	45.455	18.35	6.78	45.18	4.41
2882	4606	3.674753	CCTGCAGTTTTAGATTTTTGGCG	59.325	43.478	13.81	0.00	0.00	5.69
2892	4616	1.818674	GATTTTTGGCGATGTGGGAGT	59.181	47.619	0.00	0.00	0.00	3.85
2935	4662	4.075682	CCTTTTCTTTCTTCTCCTGGGTC	58.924	47.826	0.00	0.00	0.00	4.46
3078	4808	3.058224	GGTTGTTTGATTCTCCGGTCAAG	60.058	47.826	0.00	0.00	35.91	3.02
3112	4843	6.001460	TGTACACTTTTGCCTATAGCTTGTT	58.999	36.000	0.00	0.00	44.23	2.83
3227	4970	3.149981	TCACCCTATCTCATCTACTGCG	58.850	50.000	0.00	0.00	0.00	5.18
3300	5043	5.590530	GGCAACCAATTGTTCCATATACA	57.409	39.130	4.43	0.00	38.17	2.29
3301	5044	5.348164	GGCAACCAATTGTTCCATATACAC	58.652	41.667	4.43	0.00	38.17	2.90
3305	5058	7.862372	GCAACCAATTGTTCCATATACACTATG	59.138	37.037	4.43	0.00	38.17	2.23
3331	5084	5.109903	ACCAGTGCTTAATTGACGTAGATC	58.890	41.667	0.00	0.00	0.00	2.75
3381	5136	0.465705	CTGTGTCCGTATCCTGGCAT	59.534	55.000	0.00	0.00	0.00	4.40
3382	5137	0.908910	TGTGTCCGTATCCTGGCATT	59.091	50.000	0.00	0.00	0.00	3.56
3384	5139	0.180171	TGTCCGTATCCTGGCATTGG	59.820	55.000	0.00	0.00	0.00	3.16
3385	5140	1.148273	TCCGTATCCTGGCATTGGC	59.852	57.895	2.73	2.73	40.13	4.52
3387	5142	0.751277	CCGTATCCTGGCATTGGCAA	60.751	55.000	14.35	0.68	43.71	4.52
3388	5143	0.381801	CGTATCCTGGCATTGGCAAC	59.618	55.000	14.35	8.34	43.71	4.17
3389	5144	0.381801	GTATCCTGGCATTGGCAACG	59.618	55.000	14.35	7.41	43.71	4.10
3390	5145	1.383456	TATCCTGGCATTGGCAACGC	61.383	55.000	10.24	10.24	43.71	4.84
3391	5146	3.682885	CCTGGCATTGGCAACGCA	61.683	61.111	20.60	5.50	43.71	5.24
3393	5148	1.735198	CTGGCATTGGCAACGCAAG	60.735	57.895	20.60	14.80	43.71	4.01
3394	5149	2.339712	GGCATTGGCAACGCAAGT	59.660	55.556	20.60	0.00	46.88	3.16
3422	5177	5.709164	AGTATTGCAATTCATATCAGAGGGC	59.291	40.000	18.75	0.00	0.00	5.19
3494	5249	0.249489	GTCGCACACTAGGCCATAGG	60.249	60.000	5.01	0.00	35.63	2.57
3497	5252	1.000163	CGCACACTAGGCCATAGGTAG	60.000	57.143	5.01	0.00	35.63	3.18
3498	5253	2.317040	GCACACTAGGCCATAGGTAGA	58.683	52.381	5.01	0.00	35.63	2.59
3499	5254	2.297597	GCACACTAGGCCATAGGTAGAG	59.702	54.545	5.01	0.00	35.63	2.43
3500	5255	3.833732	CACACTAGGCCATAGGTAGAGA	58.166	50.000	5.01	0.00	35.63	3.10
3501	5256	3.823873	CACACTAGGCCATAGGTAGAGAG	59.176	52.174	5.01	0.00	35.63	3.20
3502	5257	3.181427	ACACTAGGCCATAGGTAGAGAGG	60.181	52.174	5.01	0.00	35.63	3.69
3503	5258	3.074687	CACTAGGCCATAGGTAGAGAGGA	59.925	52.174	5.01	0.00	35.63	3.71
3504	5259	2.990740	AGGCCATAGGTAGAGAGGAG	57.009	55.000	5.01	0.00	0.00	3.69
3505	5260	2.148702	AGGCCATAGGTAGAGAGGAGT	58.851	52.381	5.01	0.00	0.00	3.85
3506	5261	3.337606	AGGCCATAGGTAGAGAGGAGTA	58.662	50.000	5.01	0.00	0.00	2.59
3522	5277	5.799049	AGAGGAGTATAGCTTAGGGATAGGT	59.201	44.000	0.00	0.00	0.00	3.08

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
93	99	2.222908	GCGTACTGTGTACGTACTCCTC	60.223	54.545	25.12	13.57	42.35	3.71
94	100	1.734465	GCGTACTGTGTACGTACTCCT	59.266	52.381	25.12	12.39	42.35	3.69
95	101	1.464608	TGCGTACTGTGTACGTACTCC	59.535	52.381	25.12	16.16	42.35	3.85
156	201	1.302033	CAGCTGCGGAACTTGAGGT	60.302	57.895	0.00	0.00	0.00	3.85
223	271	5.443230	TCCCCTTTTCAACATTTGGTTTT	57.557	34.783	0.00	0.00	37.72	2.43
250	298	3.132646	GGAATGAAATGCCCATGCTGTTA	59.867	43.478	0.00	0.00	35.17	2.41
308	356	5.578005	TGGTTTCCTTAGTAGTGATCTCG	57.422	43.478	0.00	0.00	0.00	4.04
373	426	0.671251	CCCACGCCAAAAGCACTAAA	59.329	50.000	0.00	0.00	44.04	1.85
376	429	3.605664	GCCCACGCCAAAAGCACT	61.606	61.111	0.00	0.00	44.04	4.40
430	483	6.568869	TCGCTCAAAAATTCCTTTTTCTTCA	58.431	32.000	0.00	0.00	41.49	3.02
444	497	6.795399	ACATTTCTTTTCTCTCGCTCAAAAA	58.205	32.000	0.00	0.00	0.00	1.94
445	498	6.377327	ACATTTCTTTTCTCTCGCTCAAAA	57.623	33.333	0.00	0.00	0.00	2.44
468	521	8.495361	TTCATTTATTTTAGCGCTGGTACTAA	57.505	30.769	22.90	8.19	0.00	2.24
627	698	9.959749	TTATTATCCGGATTTGCAATTTTACTC	57.040	29.630	24.71	0.00	0.00	2.59
696	769	0.402121	AAGAAGAAGGGAGGGTGTGC	59.598	55.000	0.00	0.00	0.00	4.57
715	788	0.704664	TGAGCTAGAGTGGGTGGAGA	59.295	55.000	0.00	0.00	0.00	3.71
716	789	1.110442	CTGAGCTAGAGTGGGTGGAG	58.890	60.000	0.00	0.00	0.00	3.86
717	790	0.972983	GCTGAGCTAGAGTGGGTGGA	60.973	60.000	0.00	0.00	0.00	4.02
765	838	2.094286	GGAGATCTGATATGCGAGGGTG	60.094	54.545	0.00	0.00	0.00	4.61
766	839	2.175202	GGAGATCTGATATGCGAGGGT	58.825	52.381	0.00	0.00	0.00	4.34
774	866	5.603395	CAGGGCATATGAGGAGATCTGATAT	59.397	44.000	6.97	0.00	33.48	1.63
1095	1194	2.033294	TGGTACTGCGGCATTGCA	59.967	55.556	11.39	0.00	43.95	4.08
1296	1395	2.268920	GGGCAGATGAAGACGGCA	59.731	61.111	0.00	0.00	0.00	5.69
1587	1686	2.532715	TTGAGGGGCTGCCTCCTT	60.533	61.111	23.84	5.12	32.74	3.36
1713	1826	1.073199	CGTGAAGGGGCCAAGAAGT	59.927	57.895	4.39	0.00	0.00	3.01
2124	3822	2.853542	TCCAAGGCTGGCTCCACA	60.854	61.111	3.48	0.00	43.17	4.17
2259	3957	2.046988	CACAGCATCGACAGGGCA	60.047	61.111	0.00	0.00	0.00	5.36
2513	4214	2.663188	GGAGCCGCATCATCGACC	60.663	66.667	0.00	0.00	0.00	4.79
2525	4226	2.440980	GGCTGACCAATGGGAGCC	60.441	66.667	23.34	23.34	42.46	4.70
2527	4228	1.153289	CGAGGCTGACCAATGGGAG	60.153	63.158	3.55	0.00	39.06	4.30
2620	4325	1.617850	CACAGCAAGTTGGGCCAATTA	59.382	47.619	23.95	0.00	0.00	1.40
2788	4505	0.693049	ACAGCCCAACCCTTGAGTAG	59.307	55.000	0.00	0.00	0.00	2.57
2789	4506	0.400213	CACAGCCCAACCCTTGAGTA	59.600	55.000	0.00	0.00	0.00	2.59
2866	4590	4.625311	CCCACATCGCCAAAAATCTAAAAC	59.375	41.667	0.00	0.00	0.00	2.43
2882	4606	0.539051	CCCTGACAGACTCCCACATC	59.461	60.000	3.32	0.00	0.00	3.06
2892	4616	2.310779	AGAACTACAGCCCTGACAGA	57.689	50.000	3.32	0.00	0.00	3.41
2935	4662	8.289618	CCAATTTATATCACCAATTACACCGAG	58.710	37.037	0.00	0.00	0.00	4.63
3098	4829	4.030913	AGTAGTGGAACAAGCTATAGGCA	58.969	43.478	1.04	0.00	44.16	4.75
3227	4970	2.604914	CTGCGAGTGGAACATGATACAC	59.395	50.000	10.26	10.26	44.52	2.90
3305	5058	5.865552	TCTACGTCAATTAAGCACTGGTAAC	59.134	40.000	0.00	0.00	0.00	2.50
3309	5062	5.109210	TGATCTACGTCAATTAAGCACTGG	58.891	41.667	0.00	0.00	0.00	4.00
3343	5096	7.201956	GGACACAGAGAATGTAGGAATCTATGT	60.202	40.741	0.00	0.00	44.06	2.29
3344	5097	7.151308	GGACACAGAGAATGTAGGAATCTATG	58.849	42.308	0.00	0.00	41.41	2.23
3355	5110	3.131223	CAGGATACGGACACAGAGAATGT	59.869	47.826	0.00	0.00	43.50	2.71
3381	5136	0.107831	ACTCCTACTTGCGTTGCCAA	59.892	50.000	0.00	0.00	0.00	4.52
3382	5137	0.970640	TACTCCTACTTGCGTTGCCA	59.029	50.000	0.00	0.00	0.00	4.92
3384	5139	2.223044	GCAATACTCCTACTTGCGTTGC	60.223	50.000	0.00	0.00	36.31	4.17
3385	5140	3.000041	TGCAATACTCCTACTTGCGTTG	59.000	45.455	0.00	0.00	46.35	4.10
3387	5142	3.328382	TTGCAATACTCCTACTTGCGT	57.672	42.857	0.00	0.00	46.35	5.24
3388	5143	4.332543	TGAATTGCAATACTCCTACTTGCG	59.667	41.667	13.39	0.00	46.35	4.85
3389	5144	5.818136	TGAATTGCAATACTCCTACTTGC	57.182	39.130	13.39	0.00	44.25	4.01
3390	5145	9.276590	TGATATGAATTGCAATACTCCTACTTG	57.723	33.333	13.39	0.00	0.00	3.16
3391	5146	9.499479	CTGATATGAATTGCAATACTCCTACTT	57.501	33.333	13.39	0.00	0.00	2.24
3393	5148	9.149225	CTCTGATATGAATTGCAATACTCCTAC	57.851	37.037	13.39	3.25	0.00	3.18
3394	5149	8.316946	CCTCTGATATGAATTGCAATACTCCTA	58.683	37.037	13.39	5.55	0.00	2.94
3395	5150	7.166851	CCTCTGATATGAATTGCAATACTCCT	58.833	38.462	13.39	3.37	0.00	3.69
3396	5151	6.373774	CCCTCTGATATGAATTGCAATACTCC	59.626	42.308	13.39	3.43	0.00	3.85
3397	5152	6.128063	GCCCTCTGATATGAATTGCAATACTC	60.128	42.308	13.39	8.28	0.00	2.59
3494	5249	6.377245	TCCCTAAGCTATACTCCTCTCTAC	57.623	45.833	0.00	0.00	0.00	2.59
3497	5252	6.069264	ACCTATCCCTAAGCTATACTCCTCTC	60.069	46.154	0.00	0.00	0.00	3.20
3498	5253	5.799049	ACCTATCCCTAAGCTATACTCCTCT	59.201	44.000	0.00	0.00	0.00	3.69
3499	5254	6.082228	ACCTATCCCTAAGCTATACTCCTC	57.918	45.833	0.00	0.00	0.00	3.71
3500	5255	6.046881	TGAACCTATCCCTAAGCTATACTCCT	59.953	42.308	0.00	0.00	0.00	3.69
3501	5256	6.254522	TGAACCTATCCCTAAGCTATACTCC	58.745	44.000	0.00	0.00	0.00	3.85
3502	5257	7.397761	ACATGAACCTATCCCTAAGCTATACTC	59.602	40.741	0.00	0.00	0.00	2.59
3503	5258	7.179338	CACATGAACCTATCCCTAAGCTATACT	59.821	40.741	0.00	0.00	0.00	2.12
3504	5259	7.038941	ACACATGAACCTATCCCTAAGCTATAC	60.039	40.741	0.00	0.00	0.00	1.47
3505	5260	7.016914	ACACATGAACCTATCCCTAAGCTATA	58.983	38.462	0.00	0.00	0.00	1.31
3506	5261	5.846714	ACACATGAACCTATCCCTAAGCTAT	59.153	40.000	0.00	0.00	0.00	2.97
3522	5277	6.160576	TCTCCGATCAATCATACACATGAA	57.839	37.500	0.00	0.00	44.27	2.57

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.