AutoCloner

Multiple sequence alignment - TraesCS2D01G415400

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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	TraesCS2D01G415400	chr2D	100.000	2714	0	0	1	2714	529044088	529041375	0.000000e+00	5012
1	TraesCS2D01G415400	chr2D	81.915	282	31	8	472	740	245533780	245533506	1.270000e-53	220
2	TraesCS2D01G415400	chr2A	95.543	718	32	0	1212	1929	673990565	673989848	0.000000e+00	1149
3	TraesCS2D01G415400	chr2A	93.311	598	26	8	1923	2515	673967679	673967091	0.000000e+00	870
4	TraesCS2D01G415400	chr2A	76.014	1109	226	26	1042	2132	673957606	673956520	3.070000e-149	538
5	TraesCS2D01G415400	chr2A	89.346	413	20	6	472	874	673997141	673996743	5.220000e-137	497
6	TraesCS2D01G415400	chr2A	97.417	271	6	1	892	1161	673995569	673995299	6.850000e-126	460
7	TraesCS2D01G415400	chr2A	79.930	284	31	11	472	737	334889111	334889386	4.610000e-43	185
8	TraesCS2D01G415400	chr2B	88.768	917	62	16	1	894	628420843	628419945	0.000000e+00	1085
9	TraesCS2D01G415400	chr2B	93.225	738	26	7	892	1629	628419902	628419189	0.000000e+00	1064
10	TraesCS2D01G415400	chr2B	93.696	698	39	3	1626	2323	628416931	628416239	0.000000e+00	1040
11	TraesCS2D01G415400	chr2B	92.092	392	24	2	2317	2701	628412978	628412587	1.840000e-151	545
12	TraesCS2D01G415400	chr2B	81.949	277	31	10	473	737	310941267	310941536	1.640000e-52	217
13	TraesCS2D01G415400	chr6D	87.927	381	39	5	2337	2714	253841958	253841582	2.480000e-120	442
14	TraesCS2D01G415400	chr7A	87.368	380	40	6	2338	2714	561892408	561892782	1.930000e-116	429
15	TraesCS2D01G415400	chr4B	87.273	385	38	8	2335	2714	184591258	184590880	1.930000e-116	429
16	TraesCS2D01G415400	chr1D	86.719	384	42	8	2334	2714	382215675	382215298	4.180000e-113	418
17	TraesCS2D01G415400	chr5A	86.614	381	43	6	2337	2714	606313073	606312698	5.410000e-112	414
18	TraesCS2D01G415400	chr7B	87.429	350	33	5	2336	2674	117786862	117787211	2.530000e-105	392
19	TraesCS2D01G415400	chr7B	79.654	231	35	11	518	736	616498552	616498782	3.620000e-34	156
20	TraesCS2D01G415400	chr7D	87.452	263	24	6	2336	2590	156012887	156013148	7.350000e-76	294
21	TraesCS2D01G415400	chr5B	88.073	218	22	4	2497	2714	166644823	166645036	3.470000e-64	255
22	TraesCS2D01G415400	chr1B	85.780	218	25	4	2497	2714	670039465	670039254	2.720000e-55	226
23	TraesCS2D01G415400	chr4A	84.024	169	13	9	508	662	73994009	73993841	1.680000e-32	150

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	TraesCS2D01G415400	chr2D	529041375	529044088	2713	True	5012.0	5012	100.00000	1	2714	1	chr2D.!!$R2	2713
1	TraesCS2D01G415400	chr2A	673989848	673990565	717	True	1149.0	1149	95.54300	1212	1929	1	chr2A.!!$R3	717
2	TraesCS2D01G415400	chr2A	673967091	673967679	588	True	870.0	870	93.31100	1923	2515	1	chr2A.!!$R2	592
3	TraesCS2D01G415400	chr2A	673956520	673957606	1086	True	538.0	538	76.01400	1042	2132	1	chr2A.!!$R1	1090
4	TraesCS2D01G415400	chr2A	673995299	673997141	1842	True	478.5	497	93.38150	472	1161	2	chr2A.!!$R4	689
5	TraesCS2D01G415400	chr2B	628412587	628420843	8256	True	933.5	1085	91.94525	1	2701	4	chr2B.!!$R1	2700

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
820	852	0.179056	CCGGATGGATTACAACGGCT	60.179	55.0	0.0	0.0	43.45	5.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1862	5324	0.114168	ACCAGCCAAAGCCCATGTAA	59.886	50.0	0.0	0.0	41.25	2.41	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
118	119	9.651913	AATGTCATGAATTGGTTTTAATGGTAC	57.348	29.630	0.00	0.00	0.00	3.34
119	120	7.309177	TGTCATGAATTGGTTTTAATGGTACG	58.691	34.615	0.00	0.00	0.00	3.67
122	123	6.085555	TGAATTGGTTTTAATGGTACGCAA	57.914	33.333	0.00	0.00	0.00	4.85
238	244	7.119116	TCACGGATATATTTTAAATGCTCGCAT	59.881	33.333	0.00	0.00	38.46	4.73
278	284	7.119605	TGCAAATAAATCTTTGACAATGCAC	57.880	32.000	3.79	0.00	38.17	4.57
290	296	3.064207	GACAATGCACGAACACTTCCTA	58.936	45.455	0.00	0.00	0.00	2.94
297	303	3.810373	CACGAACACTTCCTAAATGTGC	58.190	45.455	0.00	0.00	35.33	4.57
299	305	2.159707	CGAACACTTCCTAAATGTGCGG	60.160	50.000	0.00	0.00	40.93	5.69
421	439	1.269569	CGTATACAAGCAGATCGGCCA	60.270	52.381	14.56	0.00	0.00	5.36
465	483	6.681729	TCCCAGACAGTTAGTTTAGTGAAT	57.318	37.500	0.00	0.00	0.00	2.57
466	484	7.074653	TCCCAGACAGTTAGTTTAGTGAATT	57.925	36.000	0.00	0.00	0.00	2.17
467	485	6.934645	TCCCAGACAGTTAGTTTAGTGAATTG	59.065	38.462	0.00	0.00	0.00	2.32
468	486	6.149474	CCCAGACAGTTAGTTTAGTGAATTGG	59.851	42.308	0.00	0.00	0.00	3.16
469	487	6.710744	CCAGACAGTTAGTTTAGTGAATTGGT	59.289	38.462	0.00	0.00	0.00	3.67
470	488	7.876068	CCAGACAGTTAGTTTAGTGAATTGGTA	59.124	37.037	0.00	0.00	0.00	3.25
484	502	4.972568	TGAATTGGTATAGGAGCTAACCCA	59.027	41.667	0.00	0.00	0.00	4.51
601	619	3.196901	AGCCATGCATGATTTGTTGATGT	59.803	39.130	28.31	0.00	0.00	3.06
652	670	4.460263	GGTGGTAGATTAATGACATGGCA	58.540	43.478	2.18	2.18	0.00	4.92
724	743	9.828039	AATAGTTAGTGGGTTGCTACTATTTAC	57.172	33.333	0.00	0.00	29.37	2.01
727	746	5.410355	AGTGGGTTGCTACTATTTACGAA	57.590	39.130	0.00	0.00	0.00	3.85
820	852	0.179056	CCGGATGGATTACAACGGCT	60.179	55.000	0.00	0.00	43.45	5.52
824	856	3.554129	CGGATGGATTACAACGGCTGATA	60.554	47.826	0.00	0.00	32.18	2.15
827	859	4.955811	TGGATTACAACGGCTGATAGAT	57.044	40.909	0.00	0.00	0.00	1.98
871	903	7.555087	TGCCTATTTATTTTCTGTTGGGAATG	58.445	34.615	0.00	0.00	0.00	2.67
939	2127	3.077359	AGAAACAAAGAATCTGCTCCGG	58.923	45.455	0.00	0.00	0.00	5.14
1260	2458	1.823041	GGCATCCTTCCAGCTCAGC	60.823	63.158	0.00	0.00	0.00	4.26
1343	2541	1.816074	ACCACCGATAAAACATGCGT	58.184	45.000	0.00	0.00	0.00	5.24
1446	2644	1.227002	GGAGATCGCCCTCGTCAAC	60.227	63.158	3.71	0.00	36.96	3.18
1459	2657	1.264826	TCGTCAACGATGTGAAGTCGA	59.735	47.619	0.22	0.00	44.22	4.20
1645	5107	3.777106	TGAGAGCAAAGGACATGAGTT	57.223	42.857	0.00	0.00	0.00	3.01
1657	5119	5.601662	AGGACATGAGTTGTATTACCATCG	58.398	41.667	0.00	0.00	39.18	3.84
1841	5303	3.406764	AGAGCATCCTTTGTGAGAACAC	58.593	45.455	0.00	0.00	41.17	3.32
1911	5373	2.355197	TGTGGTAGGTTGAATGATGCG	58.645	47.619	0.00	0.00	0.00	4.73
2276	5742	5.850557	TCACAAATTCACAATTGACCACT	57.149	34.783	13.59	0.00	0.00	4.00
2280	5746	6.524239	CACAAATTCACAATTGACCACTATCG	59.476	38.462	13.59	0.00	0.00	2.92
2289	5755	9.040939	CACAATTGACCACTATCGTATCATAAA	57.959	33.333	13.59	0.00	0.00	1.40
2331	9064	9.765795	CCAAAAACAAATTATAGGTGGTGTTTA	57.234	29.630	0.00	0.00	38.01	2.01
2390	9126	4.380843	TGGTATCCACACCACTCATTTT	57.619	40.909	0.00	0.00	43.76	1.82
2470	9206	7.147828	CGGATAATAGATGAGTATGGTCCACAT	60.148	40.741	0.00	0.00	43.68	3.21
2531	9267	5.045651	ACACTGATCCCACACTATTGATCAA	60.046	40.000	11.26	11.26	42.04	2.57
2545	9281	9.307121	CACTATTGATCAAACGAGTTATTCTCT	57.693	33.333	13.09	0.00	40.75	3.10
2569	9309	3.906014	TTGCTTGCAGCGTACATTAAA	57.094	38.095	0.00	0.00	46.26	1.52
2572	9312	2.418628	GCTTGCAGCGTACATTAAAGGA	59.581	45.455	0.00	0.00	0.00	3.36
2618	9358	1.287739	TCCCCATCCCTTGTTCATTCC	59.712	52.381	0.00	0.00	0.00	3.01
2626	9366	0.449388	CTTGTTCATTCCGCAGCTCC	59.551	55.000	0.00	0.00	0.00	4.70
2643	9383	2.760092	GCTCCTCTCTCACTCATCTTGT	59.240	50.000	0.00	0.00	0.00	3.16
2652	9392	6.945435	TCTCTCACTCATCTTGTTTCTCTAGT	59.055	38.462	0.00	0.00	0.00	2.57
2674	9414	2.294233	TCTTGCTCTTTGTTCATGGCAC	59.706	45.455	0.00	0.00	0.00	5.01
2698	9438	5.278512	CGGCTAAGCTAGAACTCATACATGA	60.279	44.000	0.00	0.00	35.16	3.07
2701	9441	7.495934	GGCTAAGCTAGAACTCATACATGAAAA	59.504	37.037	0.00	0.00	36.18	2.29
2702	9442	9.050601	GCTAAGCTAGAACTCATACATGAAAAT	57.949	33.333	0.00	0.00	36.18	1.82

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
73	74	8.152582	TGACATTTAAAATATTCACGCGTTTC	57.847	30.769	10.22	0.00	0.00	2.78
77	78	7.890879	TCATGACATTTAAAATATTCACGCG	57.109	32.000	3.53	3.53	0.00	6.01
215	220	9.935682	AATATGCGAGCATTTAAAATATATCCG	57.064	29.630	16.15	0.00	37.82	4.18
250	256	8.231837	GCATTGTCAAAGATTTATTTGCACAAT	58.768	29.630	15.06	15.06	42.89	2.71
253	259	7.011189	GTGCATTGTCAAAGATTTATTTGCAC	58.989	34.615	15.44	15.44	39.51	4.57
260	266	5.912396	GTGTTCGTGCATTGTCAAAGATTTA	59.088	36.000	0.00	0.00	0.00	1.40
262	268	4.036734	AGTGTTCGTGCATTGTCAAAGATT	59.963	37.500	0.00	0.00	0.00	2.40
265	271	3.338818	AGTGTTCGTGCATTGTCAAAG	57.661	42.857	0.00	0.00	0.00	2.77
269	275	1.873591	AGGAAGTGTTCGTGCATTGTC	59.126	47.619	0.00	0.00	0.00	3.18
278	284	2.159707	CCGCACATTTAGGAAGTGTTCG	60.160	50.000	1.18	1.18	35.75	3.95
290	296	1.305201	AAGACGTTCACCGCACATTT	58.695	45.000	0.00	0.00	41.42	2.32
297	303	5.942325	AAAATTTTCAAAGACGTTCACCG	57.058	34.783	0.00	0.00	44.03	4.94
386	404	5.689927	TGTATACGTGACACATTAAAGCG	57.310	39.130	6.37	0.00	0.00	4.68
400	418	1.269621	GGCCGATCTGCTTGTATACGT	60.270	52.381	9.11	0.00	0.00	3.57
401	419	1.269569	TGGCCGATCTGCTTGTATACG	60.270	52.381	9.11	0.00	0.00	3.06
465	483	2.696707	CGTGGGTTAGCTCCTATACCAA	59.303	50.000	0.00	0.00	32.20	3.67
466	484	2.313317	CGTGGGTTAGCTCCTATACCA	58.687	52.381	0.00	0.00	32.20	3.25
467	485	2.035576	CACGTGGGTTAGCTCCTATACC	59.964	54.545	7.95	0.00	0.00	2.73
468	486	2.692041	ACACGTGGGTTAGCTCCTATAC	59.308	50.000	21.57	0.00	0.00	1.47
469	487	3.022557	ACACGTGGGTTAGCTCCTATA	57.977	47.619	21.57	0.00	0.00	1.31
470	488	1.861982	ACACGTGGGTTAGCTCCTAT	58.138	50.000	21.57	0.00	0.00	2.57
484	502	1.447838	CTATCAGCCGGCAACACGT	60.448	57.895	31.54	10.54	0.00	4.49
652	670	7.362920	GCTTCCATAAACAAACCATACATGTCT	60.363	37.037	0.00	0.00	0.00	3.41
723	742	3.731264	CGACGCTCCTATCTTCTTTTCGT	60.731	47.826	0.00	0.00	0.00	3.85
724	743	2.784380	CGACGCTCCTATCTTCTTTTCG	59.216	50.000	0.00	0.00	0.00	3.46
727	746	1.751924	AGCGACGCTCCTATCTTCTTT	59.248	47.619	18.46	0.00	30.62	2.52
769	801	2.506472	GCCTAGCCCAGTAGTGCC	59.494	66.667	0.00	0.00	0.00	5.01
820	852	1.000607	GGCGCAGTCCGTTATCTATCA	60.001	52.381	10.83	0.00	39.71	2.15
824	856	2.104331	CGGCGCAGTCCGTTATCT	59.896	61.111	10.83	0.00	41.02	1.98
827	859	1.940883	AATCTCGGCGCAGTCCGTTA	61.941	55.000	10.83	0.00	44.85	3.18
947	2135	4.088762	GTGTGATGGCGTGCCGTG	62.089	66.667	10.97	0.00	39.42	4.94
1343	2541	1.071542	TCATGAACTTGTGAAGGCCGA	59.928	47.619	0.00	0.00	0.00	5.54
1428	2626	1.227002	GTTGACGAGGGCGATCTCC	60.227	63.158	0.00	0.00	41.64	3.71
1446	2644	3.243877	CCTTAGCAATCGACTTCACATCG	59.756	47.826	0.00	0.00	41.00	3.84
1622	2823	3.518705	ACTCATGTCCTTTGCTCTCATCT	59.481	43.478	0.00	0.00	0.00	2.90
1645	5107	3.118592	TGCATGTCACCGATGGTAATACA	60.119	43.478	0.00	0.00	32.11	2.29
1862	5324	0.114168	ACCAGCCAAAGCCCATGTAA	59.886	50.000	0.00	0.00	41.25	2.41
1911	5373	3.143728	AGACCCAATAAACCGAACACAC	58.856	45.455	0.00	0.00	0.00	3.82
2107	5569	6.749923	ATATTTTTCTGAGCAAGACACTCC	57.250	37.500	0.00	0.00	33.46	3.85
2289	5755	6.987386	TGTTTTTGGAACCGATGATTAACAT	58.013	32.000	0.00	0.00	42.47	2.71
2302	5768	7.929245	ACACCACCTATAATTTGTTTTTGGAAC	59.071	33.333	0.00	0.00	0.00	3.62
2331	9064	7.329471	CACGTCCACTCATGATTTATCGATAAT	59.671	37.037	18.18	8.87	0.00	1.28
2336	9069	3.060272	GCACGTCCACTCATGATTTATCG	60.060	47.826	0.00	2.18	0.00	2.92
2390	9126	8.716646	ATGTAAATACAACACGAATCATGAGA	57.283	30.769	0.09	0.00	39.99	3.27
2445	9181	7.482169	TGTGGACCATACTCATCTATTATCC	57.518	40.000	0.00	0.00	0.00	2.59
2569	9309	1.675641	GCGATGGTGCAGGTTTCCT	60.676	57.895	0.00	0.00	34.15	3.36
2618	9358	1.311651	TGAGTGAGAGAGGAGCTGCG	61.312	60.000	0.00	0.00	0.00	5.18
2626	9366	6.271488	AGAGAAACAAGATGAGTGAGAGAG	57.729	41.667	0.00	0.00	0.00	3.20
2643	9383	7.047891	TGAACAAAGAGCAAGAACTAGAGAAA	58.952	34.615	0.00	0.00	0.00	2.52
2652	9392	2.957680	TGCCATGAACAAAGAGCAAGAA	59.042	40.909	0.00	0.00	0.00	2.52
2674	9414	4.569761	TGTATGAGTTCTAGCTTAGCCG	57.430	45.455	0.00	0.00	0.00	5.52

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.