AutoCloner

Multiple sequence alignment - TraesCS7D01G247500

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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	TraesCS7D01G247500	chr7D	100.000	2603	0	0	1	2603	217839125	217836523	0.000000e+00	4807.0
1	TraesCS7D01G247500	chr7D	93.621	533	33	1	1	532	133872236	133871704	0.000000e+00	795.0
2	TraesCS7D01G247500	chr7D	93.621	533	33	1	1	532	369265084	369264552	0.000000e+00	795.0
3	TraesCS7D01G247500	chr7D	93.433	533	33	2	1	532	263867811	263868342	0.000000e+00	789.0
4	TraesCS7D01G247500	chr5D	97.713	1749	36	2	855	2603	442843529	442845273	0.000000e+00	3005.0
5	TraesCS7D01G247500	chr5D	92.415	1358	77	6	565	1916	285330837	285329500	0.000000e+00	1914.0
6	TraesCS7D01G247500	chr5D	93.622	1176	67	5	565	1734	318014043	318012870	0.000000e+00	1749.0
7	TraesCS7D01G247500	chr5D	97.235	868	18	4	1737	2603	318011444	318010582	0.000000e+00	1465.0
8	TraesCS7D01G247500	chr5D	96.248	533	15	3	2071	2603	285324968	285324441	0.000000e+00	869.0
9	TraesCS7D01G247500	chr5D	94.747	533	26	2	1	532	385100855	385101386	0.000000e+00	828.0
10	TraesCS7D01G247500	chr5D	93.246	533	35	1	1	532	436742452	436741920	0.000000e+00	784.0
11	TraesCS7D01G247500	chr5D	96.562	349	12	0	1733	2081	285329500	285329152	1.740000e-161	579.0
12	TraesCS7D01G247500	chr5D	95.224	335	10	2	531	859	442830171	442830505	2.290000e-145	525.0
13	TraesCS7D01G247500	chr5D	89.510	286	23	3	565	844	543384102	543383818	3.190000e-94	355.0
14	TraesCS7D01G247500	chr5D	89.347	291	18	5	564	841	270109223	270109513	1.150000e-93	353.0
15	TraesCS7D01G247500	chr5D	96.410	195	7	0	1726	1920	318011638	318011444	3.230000e-84	322.0
16	TraesCS7D01G247500	chr4D	94.925	1596	70	4	1008	2603	277203327	277201743	0.000000e+00	2488.0
17	TraesCS7D01G247500	chr4D	98.507	67	1	0	530	596	455586085	455586151	4.550000e-23	119.0
18	TraesCS7D01G247500	chr6A	93.908	1067	45	11	561	1616	552986248	552987305	0.000000e+00	1592.0
19	TraesCS7D01G247500	chr6A	96.696	908	29	1	1607	2514	552988847	552989753	0.000000e+00	1509.0
20	TraesCS7D01G247500	chr6A	96.761	494	11	3	2110	2603	552989751	552990239	0.000000e+00	819.0
21	TraesCS7D01G247500	chr3D	93.820	534	30	3	1	532	376989892	376990424	0.000000e+00	800.0
22	TraesCS7D01G247500	chr1D	93.621	533	32	2	1	532	270157647	270158178	0.000000e+00	795.0
23	TraesCS7D01G247500	chr1D	93.246	533	35	1	1	532	37131000	37130468	0.000000e+00	784.0
24	TraesCS7D01G247500	chr1D	93.246	533	34	2	1	532	258621721	258621190	0.000000e+00	784.0
25	TraesCS7D01G247500	chr4A	87.685	203	16	6	577	770	727048964	727049166	7.250000e-56	228.0
26	TraesCS7D01G247500	chr7A	88.265	196	14	5	566	752	10286525	10286330	2.610000e-55	226.0
27	TraesCS7D01G247500	chr7A	94.805	77	3	1	522	597	726899522	726899598	4.550000e-23	119.0
28	TraesCS7D01G247500	chr2A	78.543	247	15	10	531	769	691539423	691539639	7.560000e-26	128.0
29	TraesCS7D01G247500	chr2A	94.737	76	2	2	516	591	16890373	16890446	1.640000e-22	117.0
30	TraesCS7D01G247500	chr1B	100.000	61	0	0	531	591	54970810	54970750	2.120000e-21	113.0
31	TraesCS7D01G247500	chr2D	95.588	68	3	0	524	591	83081560	83081493	2.740000e-20	110.0
32	TraesCS7D01G247500	chr2D	90.361	83	3	3	531	613	648359709	648359786	1.270000e-18	104.0
33	TraesCS7D01G247500	chr2D	87.692	65	1	2	774	832	43804885	43804948	4.650000e-08	69.4
34	TraesCS7D01G247500	chr6D	83.594	128	6	7	532	659	55325914	55326026	3.540000e-19	106.0

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	TraesCS7D01G247500	chr7D	217836523	217839125	2602	True	4807.000000	4807	100.000000	1	2603	1	chr7D.!!$R2	2602
1	TraesCS7D01G247500	chr7D	133871704	133872236	532	True	795.000000	795	93.621000	1	532	1	chr7D.!!$R1	531
2	TraesCS7D01G247500	chr7D	369264552	369265084	532	True	795.000000	795	93.621000	1	532	1	chr7D.!!$R3	531
3	TraesCS7D01G247500	chr7D	263867811	263868342	531	False	789.000000	789	93.433000	1	532	1	chr7D.!!$F1	531
4	TraesCS7D01G247500	chr5D	442843529	442845273	1744	False	3005.000000	3005	97.713000	855	2603	1	chr5D.!!$F4	1748
5	TraesCS7D01G247500	chr5D	285329152	285330837	1685	True	1246.500000	1914	94.488500	565	2081	2	chr5D.!!$R4	1516
6	TraesCS7D01G247500	chr5D	318010582	318014043	3461	True	1178.666667	1749	95.755667	565	2603	3	chr5D.!!$R5	2038
7	TraesCS7D01G247500	chr5D	285324441	285324968	527	True	869.000000	869	96.248000	2071	2603	1	chr5D.!!$R1	532
8	TraesCS7D01G247500	chr5D	385100855	385101386	531	False	828.000000	828	94.747000	1	532	1	chr5D.!!$F2	531
9	TraesCS7D01G247500	chr5D	436741920	436742452	532	True	784.000000	784	93.246000	1	532	1	chr5D.!!$R2	531
10	TraesCS7D01G247500	chr4D	277201743	277203327	1584	True	2488.000000	2488	94.925000	1008	2603	1	chr4D.!!$R1	1595
11	TraesCS7D01G247500	chr6A	552986248	552990239	3991	False	1306.666667	1592	95.788333	561	2603	3	chr6A.!!$F1	2042
12	TraesCS7D01G247500	chr3D	376989892	376990424	532	False	800.000000	800	93.820000	1	532	1	chr3D.!!$F1	531
13	TraesCS7D01G247500	chr1D	270157647	270158178	531	False	795.000000	795	93.621000	1	532	1	chr1D.!!$F1	531
14	TraesCS7D01G247500	chr1D	37130468	37131000	532	True	784.000000	784	93.246000	1	532	1	chr1D.!!$R1	531
15	TraesCS7D01G247500	chr1D	258621190	258621721	531	True	784.000000	784	93.246000	1	532	1	chr1D.!!$R2	531

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
673	677	0.332632	CACACAATCCCACCCATCCT	59.667	55.0	0.0	0.0	0.0	3.24	F
1197	1228	0.108138	GCACCGGTGAGCTTGTATCT	60.108	55.0	38.3	0.0	0.0	1.98	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1599	1630	2.952978	AGTTGTCGGTATCAGAGGCTAG	59.047	50.0	0.0	0.0	0.0	3.42	R
2531	5938	4.083057	ACAACAACAACAACAAAAATGGCC	60.083	37.5	0.0	0.0	0.0	5.36	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
25	26	4.762289	AACATTCAGAGGAGGATACCAC	57.238	45.455	0.00	0.00	37.17	4.16
128	129	6.774170	TGCATGGCATGAGAAACTATAATCTT	59.226	34.615	30.69	0.00	31.71	2.40
159	160	9.872721	TGTCATTGCAAACATGTTTAATCATAT	57.127	25.926	22.87	13.14	0.00	1.78
184	185	5.244851	TGAGCTGAATCATGGATACTAGGTC	59.755	44.000	0.00	0.00	37.61	3.85
283	284	4.280425	TCATTATTGCCTTTCACTTGCACA	59.720	37.500	0.00	0.00	34.16	4.57
299	300	4.153958	TGCACAACCAAACGATATGAAC	57.846	40.909	0.00	0.00	0.00	3.18
470	471	7.801783	CCTTGGTACGACTCAAATAAAAAGAAC	59.198	37.037	0.00	0.00	0.00	3.01
532	534	6.660887	TTGGTTTTCTTGAACAAGCAAATC	57.339	33.333	13.26	13.19	36.33	2.17
533	535	5.976458	TGGTTTTCTTGAACAAGCAAATCT	58.024	33.333	18.01	0.00	36.23	2.40
534	536	6.042143	TGGTTTTCTTGAACAAGCAAATCTC	58.958	36.000	18.01	11.06	36.23	2.75
535	537	6.127366	TGGTTTTCTTGAACAAGCAAATCTCT	60.127	34.615	18.01	0.00	36.23	3.10
536	538	7.068103	TGGTTTTCTTGAACAAGCAAATCTCTA	59.932	33.333	18.01	3.91	36.23	2.43
537	539	7.379797	GGTTTTCTTGAACAAGCAAATCTCTAC	59.620	37.037	13.26	3.39	36.33	2.59
538	540	7.807977	TTTCTTGAACAAGCAAATCTCTACT	57.192	32.000	9.38	0.00	38.28	2.57
539	541	8.902540	TTTCTTGAACAAGCAAATCTCTACTA	57.097	30.769	9.38	0.00	38.28	1.82
540	542	9.507329	TTTCTTGAACAAGCAAATCTCTACTAT	57.493	29.630	9.38	0.00	38.28	2.12
541	543	9.507329	TTCTTGAACAAGCAAATCTCTACTATT	57.493	29.630	9.38	0.00	38.28	1.73
547	549	8.738645	ACAAGCAAATCTCTACTATTAAAGGG	57.261	34.615	0.00	0.00	0.00	3.95
548	550	7.775561	ACAAGCAAATCTCTACTATTAAAGGGG	59.224	37.037	0.00	0.00	0.00	4.79
549	551	6.842676	AGCAAATCTCTACTATTAAAGGGGG	58.157	40.000	0.00	0.00	0.00	5.40
550	552	6.619852	AGCAAATCTCTACTATTAAAGGGGGA	59.380	38.462	0.00	0.00	0.00	4.81
551	553	7.295911	AGCAAATCTCTACTATTAAAGGGGGAT	59.704	37.037	0.00	0.00	0.00	3.85
552	554	7.608376	GCAAATCTCTACTATTAAAGGGGGATC	59.392	40.741	0.00	0.00	0.00	3.36
553	555	7.483580	AATCTCTACTATTAAAGGGGGATCG	57.516	40.000	0.00	0.00	0.00	3.69
554	556	6.210172	TCTCTACTATTAAAGGGGGATCGA	57.790	41.667	0.00	0.00	0.00	3.59
555	557	6.617538	TCTCTACTATTAAAGGGGGATCGAA	58.382	40.000	0.00	0.00	0.00	3.71
556	558	6.492772	TCTCTACTATTAAAGGGGGATCGAAC	59.507	42.308	0.00	0.00	0.00	3.95
557	559	4.332428	ACTATTAAAGGGGGATCGAACG	57.668	45.455	0.00	0.00	0.00	3.95
558	560	3.708121	ACTATTAAAGGGGGATCGAACGT	59.292	43.478	0.00	0.00	0.00	3.99
559	561	2.678471	TTAAAGGGGGATCGAACGTC	57.322	50.000	0.00	0.00	0.00	4.34
560	562	0.457035	TAAAGGGGGATCGAACGTCG	59.543	55.000	0.00	0.00	42.10	5.12
561	563	1.538687	AAAGGGGGATCGAACGTCGT	61.539	55.000	0.00	0.00	41.35	4.34
562	564	2.202703	GGGGGATCGAACGTCGTG	60.203	66.667	0.00	0.00	41.35	4.35
563	565	2.703798	GGGGGATCGAACGTCGTGA	61.704	63.158	0.00	0.00	41.35	4.35
602	606	2.840203	GATCCCCCACCTCCACCTCA	62.840	65.000	0.00	0.00	0.00	3.86
625	629	1.296002	GATAACCCAACCCTCCACCT	58.704	55.000	0.00	0.00	0.00	4.00
673	677	0.332632	CACACAATCCCACCCATCCT	59.667	55.000	0.00	0.00	0.00	3.24
682	686	0.893270	CCACCCATCCTGCACGAAAA	60.893	55.000	0.00	0.00	0.00	2.29
752	765	2.520188	ATCCATCTCCCTCAATCCCA	57.480	50.000	0.00	0.00	0.00	4.37
756	769	2.060275	CATCTCCCTCAATCCCATGGA	58.940	52.381	15.22	0.00	35.55	3.41
808	821	2.118679	ACACTGCAGCCATACCATCTA	58.881	47.619	15.27	0.00	0.00	1.98
1116	1147	2.511600	GTCGTCCCGGCCATCAAG	60.512	66.667	2.24	0.00	0.00	3.02
1197	1228	0.108138	GCACCGGTGAGCTTGTATCT	60.108	55.000	38.30	0.00	0.00	1.98
1326	1357	3.407424	TGCATGCACTTGTAAGACTCT	57.593	42.857	18.46	0.00	0.00	3.24
1374	1405	2.092429	ACTTTTCTGTCAAGGTCTGCCA	60.092	45.455	0.00	0.00	37.19	4.92
1489	1520	1.933181	GCTCTTTTGTTTGTGTTGCCC	59.067	47.619	0.00	0.00	0.00	5.36
1599	1630	5.657302	TCAGTCTCTTATAGGGGTTCTCAAC	59.343	44.000	0.00	0.00	0.00	3.18
1659	3241	1.357258	GAGCATCGCTGTCCACTGTG	61.357	60.000	0.00	0.00	39.88	3.66
1731	4554	7.272037	TCTTTGATTTGTTGAGTTAACTCCC	57.728	36.000	28.43	20.19	42.20	4.30
1911	4917	2.912956	AGAGAGGAGAGTGAGAGACTGT	59.087	50.000	0.00	0.00	33.83	3.55
2041	5047	2.370189	CCTTGTTTTTGTATTGCCCCCA	59.630	45.455	0.00	0.00	0.00	4.96
2069	5075	5.191722	AGGGTTAGGTGTGTCATATGTTCAT	59.808	40.000	1.90	0.00	0.00	2.57
2158	5164	9.976511	AAAAATCAAGCCTCATACATCATTATG	57.023	29.630	0.00	0.00	39.17	1.90
2259	5266	7.285401	AGGCTTCTTTCAACTTCAAGTTCAATA	59.715	33.333	0.00	0.00	36.03	1.90
2531	5938	4.421948	ACGGAGCGATAGTTGTTTCTTAG	58.578	43.478	0.00	0.00	39.35	2.18
2539	5946	6.625081	GCGATAGTTGTTTCTTAGGCCATTTT	60.625	38.462	5.01	0.00	39.35	1.82
2540	5947	7.312899	CGATAGTTGTTTCTTAGGCCATTTTT	58.687	34.615	5.01	0.00	0.00	1.94
2541	5948	7.273381	CGATAGTTGTTTCTTAGGCCATTTTTG	59.727	37.037	5.01	0.00	0.00	2.44

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
25	26	5.915196	ACGATTGTGATGTAGTATGACGATG	59.085	40.000	0.00	0.00	0.00	3.84
159	160	5.604231	ACCTAGTATCCATGATTCAGCTCAA	59.396	40.000	0.00	0.00	0.00	3.02
470	471	6.609237	TTCAGTGTGTTCTCTGAATTTCTG	57.391	37.500	8.11	0.00	44.11	3.02
532	534	6.569994	CGTTCGATCCCCCTTTAATAGTAGAG	60.570	46.154	0.00	0.00	0.00	2.43
533	535	5.242393	CGTTCGATCCCCCTTTAATAGTAGA	59.758	44.000	0.00	0.00	0.00	2.59
534	536	5.010415	ACGTTCGATCCCCCTTTAATAGTAG	59.990	44.000	0.00	0.00	0.00	2.57
535	537	4.895297	ACGTTCGATCCCCCTTTAATAGTA	59.105	41.667	0.00	0.00	0.00	1.82
536	538	3.708121	ACGTTCGATCCCCCTTTAATAGT	59.292	43.478	0.00	0.00	0.00	2.12
537	539	4.304939	GACGTTCGATCCCCCTTTAATAG	58.695	47.826	0.00	0.00	0.00	1.73
538	540	3.243501	CGACGTTCGATCCCCCTTTAATA	60.244	47.826	0.00	0.00	43.74	0.98
539	541	2.482490	CGACGTTCGATCCCCCTTTAAT	60.482	50.000	0.00	0.00	43.74	1.40
540	542	1.135024	CGACGTTCGATCCCCCTTTAA	60.135	52.381	0.00	0.00	43.74	1.52
541	543	0.457035	CGACGTTCGATCCCCCTTTA	59.543	55.000	0.00	0.00	43.74	1.85
542	544	1.217244	CGACGTTCGATCCCCCTTT	59.783	57.895	0.00	0.00	43.74	3.11
543	545	1.980772	ACGACGTTCGATCCCCCTT	60.981	57.895	13.06	0.00	43.74	3.95
544	546	2.362120	ACGACGTTCGATCCCCCT	60.362	61.111	13.06	0.00	43.74	4.79
545	547	2.012902	ATCACGACGTTCGATCCCCC	62.013	60.000	13.06	0.00	43.74	5.40
546	548	0.870307	CATCACGACGTTCGATCCCC	60.870	60.000	13.06	0.00	43.74	4.81
547	549	0.870307	CCATCACGACGTTCGATCCC	60.870	60.000	13.06	0.00	43.74	3.85
548	550	0.179145	ACCATCACGACGTTCGATCC	60.179	55.000	13.06	0.00	43.74	3.36
549	551	1.582502	GAACCATCACGACGTTCGATC	59.417	52.381	13.06	0.00	43.74	3.69
550	552	1.625616	GAACCATCACGACGTTCGAT	58.374	50.000	13.06	0.00	43.74	3.59
551	553	3.096541	GAACCATCACGACGTTCGA	57.903	52.632	13.06	0.00	43.74	3.71
553	555	0.706729	GTCGAACCATCACGACGTTC	59.293	55.000	0.00	0.00	46.39	3.95
554	556	2.805277	GTCGAACCATCACGACGTT	58.195	52.632	0.00	0.00	46.39	3.99
555	557	4.546637	GTCGAACCATCACGACGT	57.453	55.556	0.00	0.00	46.39	4.34
602	606	2.092592	GTGGAGGGTTGGGTTATCGAAT	60.093	50.000	0.00	0.00	0.00	3.34
659	663	1.307647	GTGCAGGATGGGTGGGATT	59.692	57.895	0.00	0.00	35.86	3.01
682	686	2.223317	GCGTACGTGGGTTGTTCTTTTT	60.223	45.455	17.90	0.00	0.00	1.94
752	765	0.832135	ATCGGCGGTGATAGGTCCAT	60.832	55.000	7.21	0.00	0.00	3.41
756	769	0.755698	AGTCATCGGCGGTGATAGGT	60.756	55.000	27.14	8.73	0.00	3.08
1116	1147	2.743928	CTGTTGGCGCCAGTCTCC	60.744	66.667	30.75	16.10	0.00	3.71
1326	1357	3.042682	TGGAGAAGACAGGGTTACACAA	58.957	45.455	0.00	0.00	0.00	3.33
1374	1405	2.742053	GCACCAGTCAACGACATACATT	59.258	45.455	0.00	0.00	34.60	2.71
1599	1630	2.952978	AGTTGTCGGTATCAGAGGCTAG	59.047	50.000	0.00	0.00	0.00	3.42
1731	4554	6.169419	TCAGAGAACATTCACAAAATAGCG	57.831	37.500	0.00	0.00	0.00	4.26
1777	4600	7.817478	CACAACACAGTAGACCATTGATAACTA	59.183	37.037	0.00	0.00	0.00	2.24
2041	5047	5.191722	ACATATGACACACCTAACCCTTCAT	59.808	40.000	10.38	0.00	0.00	2.57
2158	5164	5.938125	TCTGCAGAATACAAACTAAACCTCC	59.062	40.000	15.67	0.00	0.00	4.30
2531	5938	4.083057	ACAACAACAACAACAAAAATGGCC	60.083	37.500	0.00	0.00	0.00	5.36
2539	5946	8.184192	ACAAAAATGAAACAACAACAACAACAA	58.816	25.926	0.00	0.00	0.00	2.83
2540	5947	7.697691	ACAAAAATGAAACAACAACAACAACA	58.302	26.923	0.00	0.00	0.00	3.33
2541	5948	8.553817	AACAAAAATGAAACAACAACAACAAC	57.446	26.923	0.00	0.00	0.00	3.32

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.