AutoCloner

Multiple sequence alignment - TraesCS2A01G213300

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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	TraesCS2A01G213300	chr2A	100.000	2413	0	0	1	2413	197923464	197925876	0.000000e+00	4457.0
1	TraesCS2A01G213300	chr2A	100.000	33	0	0	2184	2216	637223126	637223158	7.200000e-06	62.1
2	TraesCS2A01G213300	chr2D	97.077	1300	30	5	1119	2413	183629472	183630768	0.000000e+00	2183.0
3	TraesCS2A01G213300	chr2D	89.904	624	46	13	468	1090	183619179	183619786	0.000000e+00	787.0
4	TraesCS2A01G213300	chr2D	93.263	475	22	7	6	475	183618137	183618606	0.000000e+00	691.0
5	TraesCS2A01G213300	chr2D	100.000	33	0	0	2184	2216	492022697	492022729	7.200000e-06	62.1
6	TraesCS2A01G213300	chr2B	93.243	740	30	7	770	1509	239465357	239466076	0.000000e+00	1072.0
7	TraesCS2A01G213300	chr2B	87.827	649	62	11	1	638	239464694	239465336	0.000000e+00	745.0
8	TraesCS2A01G213300	chr2B	85.854	410	53	3	2005	2413	656599023	656598618	4.770000e-117	431.0
9	TraesCS2A01G213300	chr2B	81.046	459	46	21	1957	2407	23111223	23111648	6.430000e-86	327.0
10	TraesCS2A01G213300	chr2B	95.536	112	3	2	1498	1607	239482561	239482672	6.860000e-41	178.0
11	TraesCS2A01G213300	chr2B	100.000	33	0	0	2184	2216	576744978	576745010	7.200000e-06	62.1
12	TraesCS2A01G213300	chr4B	90.123	81	8	0	691	771	371286400	371286320	3.280000e-19	106.0
13	TraesCS2A01G213300	chr4B	78.218	101	20	2	674	773	532257568	532257469	2.000000e-06	63.9
14	TraesCS2A01G213300	chr6B	92.647	68	5	0	1627	1694	140365640	140365707	5.490000e-17	99.0
15	TraesCS2A01G213300	chr3A	81.553	103	17	2	673	773	724552522	724552624	1.540000e-12	84.2
16	TraesCS2A01G213300	chr7A	85.714	77	6	4	319	392	671443315	671443389	2.570000e-10	76.8
17	TraesCS2A01G213300	chr7D	93.023	43	2	1	278	319	559295299	559295257	7.200000e-06	62.1
18	TraesCS2A01G213300	chr4D	91.111	45	3	1	348	392	471991851	471991894	2.590000e-05	60.2

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	TraesCS2A01G213300	chr2A	197923464	197925876	2412	False	4457.0	4457	100.0000	1	2413	1	chr2A.!!$F1	2412
1	TraesCS2A01G213300	chr2D	183629472	183630768	1296	False	2183.0	2183	97.0770	1119	2413	1	chr2D.!!$F1	1294
2	TraesCS2A01G213300	chr2D	183618137	183619786	1649	False	739.0	787	91.5835	6	1090	2	chr2D.!!$F3	1084
3	TraesCS2A01G213300	chr2B	239464694	239466076	1382	False	908.5	1072	90.5350	1	1509	2	chr2B.!!$F4	1508

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
858	1450	0.962855	GCTGGCCTTGGTTTCTCTCC	60.963	60.0	3.32	0.0	0.0	3.71	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1871	2466	0.03759	TCCTTGGTGAATTGGACGGG	59.962	55.0	0.0	0.0	0.0	5.28	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
74	76	8.657387	TTGTTCATGTAATCAATTTTCCCCTA	57.343	30.769	0.00	0.00	0.00	3.53
453	463	4.538746	AGACACCTAGGAAACTAACAGC	57.461	45.455	17.98	0.00	43.83	4.40
455	465	2.895404	ACACCTAGGAAACTAACAGCGA	59.105	45.455	17.98	0.00	43.83	4.93
497	1088	1.691976	ACTGTCAGACCAACGGATGAA	59.308	47.619	6.91	0.00	0.00	2.57
503	1094	1.210478	AGACCAACGGATGAAGGATGG	59.790	52.381	0.00	0.00	0.00	3.51
506	1097	1.462616	CAACGGATGAAGGATGGCAA	58.537	50.000	0.00	0.00	0.00	4.52
544	1135	3.954200	TGAGCAATTCAAGATAGGCACA	58.046	40.909	0.00	0.00	31.34	4.57
555	1146	6.690530	TCAAGATAGGCACAAAAAGGATTTG	58.309	36.000	0.00	0.00	39.02	2.32
598	1190	5.466393	CCACATTTAAACTTGGCCAAAGAAG	59.534	40.000	20.91	10.37	39.38	2.85
663	1255	2.099098	CCCAACTCGGTGGCATTTAATC	59.901	50.000	0.00	0.00	37.34	1.75
664	1256	2.752354	CCAACTCGGTGGCATTTAATCA	59.248	45.455	0.00	0.00	0.00	2.57
665	1257	3.192422	CCAACTCGGTGGCATTTAATCAA	59.808	43.478	0.00	0.00	0.00	2.57
666	1258	4.414852	CAACTCGGTGGCATTTAATCAAG	58.585	43.478	0.00	0.00	0.00	3.02
667	1259	3.950397	ACTCGGTGGCATTTAATCAAGA	58.050	40.909	0.00	0.00	0.00	3.02
668	1260	3.941483	ACTCGGTGGCATTTAATCAAGAG	59.059	43.478	0.00	0.00	0.00	2.85
672	1264	4.427312	GGTGGCATTTAATCAAGAGCTTG	58.573	43.478	3.87	3.87	41.71	4.01
675	1267	4.221262	TGGCATTTAATCAAGAGCTTGCTT	59.779	37.500	5.37	5.12	40.24	3.91
678	1270	5.742926	GCATTTAATCAAGAGCTTGCTTCTC	59.257	40.000	5.37	0.00	40.24	2.87
679	1271	6.404513	GCATTTAATCAAGAGCTTGCTTCTCT	60.405	38.462	5.37	0.00	42.31	3.10
681	1273	6.734104	TTAATCAAGAGCTTGCTTCTCTTC	57.266	37.500	5.37	0.00	46.01	2.87
682	1274	4.556592	ATCAAGAGCTTGCTTCTCTTCT	57.443	40.909	5.37	2.63	46.01	2.85
683	1275	3.661944	TCAAGAGCTTGCTTCTCTTCTG	58.338	45.455	5.37	4.96	46.01	3.02
684	1276	3.070734	TCAAGAGCTTGCTTCTCTTCTGT	59.929	43.478	5.37	0.00	46.01	3.41
685	1277	3.317603	AGAGCTTGCTTCTCTTCTGTC	57.682	47.619	0.00	0.00	37.63	3.51
686	1278	2.632028	AGAGCTTGCTTCTCTTCTGTCA	59.368	45.455	0.00	0.00	37.63	3.58
687	1279	3.261390	AGAGCTTGCTTCTCTTCTGTCAT	59.739	43.478	0.00	0.00	37.63	3.06
688	1280	3.598299	AGCTTGCTTCTCTTCTGTCATC	58.402	45.455	0.00	0.00	0.00	2.92
689	1281	2.677337	GCTTGCTTCTCTTCTGTCATCC	59.323	50.000	0.00	0.00	0.00	3.51
690	1282	3.269178	CTTGCTTCTCTTCTGTCATCCC	58.731	50.000	0.00	0.00	0.00	3.85
696	1288	3.370104	TCTCTTCTGTCATCCCTTCTCC	58.630	50.000	0.00	0.00	0.00	3.71
697	1289	2.433970	CTCTTCTGTCATCCCTTCTCCC	59.566	54.545	0.00	0.00	0.00	4.30
702	1294	1.081174	TGTCATCCCTTCTCCCTCCTT	59.919	52.381	0.00	0.00	0.00	3.36
703	1295	2.317900	TGTCATCCCTTCTCCCTCCTTA	59.682	50.000	0.00	0.00	0.00	2.69
858	1450	0.962855	GCTGGCCTTGGTTTCTCTCC	60.963	60.000	3.32	0.00	0.00	3.71
878	1470	5.126545	TCTCCTCGAAACGAATTAATCCTCA	59.873	40.000	0.00	0.00	34.74	3.86
1021	1613	2.682893	GCGTACAGCCTGAAGATGG	58.317	57.895	0.00	0.00	40.81	3.51
1075	1667	0.833287	CCTCTTCACCATCCCACGAT	59.167	55.000	0.00	0.00	0.00	3.73
1109	1701	3.323136	CGTAGCGGCTCGACATGC	61.323	66.667	5.39	0.00	0.00	4.06
1311	1903	2.210013	TGCTGCTCCAGGTCGAACT	61.210	57.895	0.00	0.00	31.21	3.01
1489	2081	7.557358	AGGAGCCAAATGTTTTCTTTGAAAAAT	59.443	29.630	6.99	2.36	35.99	1.82
1633	2228	6.365970	TTGCAAGAAGGGGCAATTAAATTA	57.634	33.333	0.00	0.00	44.41	1.40
1681	2276	2.235891	GTTGAAACCTCCCCGTGAATT	58.764	47.619	0.00	0.00	0.00	2.17
1684	2279	3.681593	TGAAACCTCCCCGTGAATTTAG	58.318	45.455	0.00	0.00	0.00	1.85
1709	2304	8.928733	AGTATTATCGTTTTCAAACTCGCTTTA	58.071	29.630	1.13	0.00	36.77	1.85
1717	2312	3.972403	TCAAACTCGCTTTAAAAAGGGC	58.028	40.909	13.10	0.00	45.41	5.19
1720	2315	1.161843	CTCGCTTTAAAAAGGGCGGA	58.838	50.000	16.48	5.91	45.41	5.54
1721	2316	1.743394	CTCGCTTTAAAAAGGGCGGAT	59.257	47.619	16.48	0.00	45.41	4.18
1722	2317	2.163613	CTCGCTTTAAAAAGGGCGGATT	59.836	45.455	16.48	0.00	45.41	3.01
1723	2318	2.559231	TCGCTTTAAAAAGGGCGGATTT	59.441	40.909	16.48	0.00	45.41	2.17
1725	2320	3.122780	CGCTTTAAAAAGGGCGGATTTTG	59.877	43.478	10.70	0.00	43.25	2.44
1726	2321	4.311606	GCTTTAAAAAGGGCGGATTTTGA	58.688	39.130	4.71	0.00	36.53	2.69
1727	2322	4.935205	GCTTTAAAAAGGGCGGATTTTGAT	59.065	37.500	4.71	0.00	36.53	2.57
1728	2323	5.411361	GCTTTAAAAAGGGCGGATTTTGATT	59.589	36.000	4.71	0.00	36.53	2.57
1802	2397	3.059166	GTGTTTGCTTATTTGCCACTGG	58.941	45.455	0.00	0.00	0.00	4.00
1860	2455	0.250727	ACCCGTGTGGAAATCACCAG	60.251	55.000	0.00	0.00	45.48	4.00
1871	2466	1.117150	AATCACCAGATTGCCCATGC	58.883	50.000	0.00	0.00	42.72	4.06
2031	2626	2.343506	CAGGTGATGCTGTTTGCCA	58.656	52.632	0.00	0.00	42.00	4.92
2082	2677	2.202932	CTCTGTTATGCCGCCGCT	60.203	61.111	0.00	0.00	35.36	5.52
2164	2759	0.953471	TTCGTGGCCATGTGTGCTAC	60.953	55.000	24.24	0.00	36.91	3.58
2294	2889	2.282674	CTTTGCTGCTGCTCCCCA	60.283	61.111	17.00	0.00	40.48	4.96
2392	2987	4.200287	CGTGCGAACATGGGATGA	57.800	55.556	0.00	0.00	0.00	2.92

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
453	463	2.711542	ACTGTCCTAAATTTGCCCTCG	58.288	47.619	0.00	0.00	0.00	4.63
455	465	5.044846	AGTCATACTGTCCTAAATTTGCCCT	60.045	40.000	0.00	0.00	0.00	5.19
518	1109	5.061853	GCCTATCTTGAATTGCTCATCTGA	58.938	41.667	0.00	0.00	32.78	3.27
522	1113	4.529897	TGTGCCTATCTTGAATTGCTCAT	58.470	39.130	0.00	0.00	32.78	2.90
525	1116	5.726980	TTTTGTGCCTATCTTGAATTGCT	57.273	34.783	0.00	0.00	0.00	3.91
532	1123	6.690530	TCAAATCCTTTTTGTGCCTATCTTG	58.309	36.000	0.00	0.00	0.00	3.02
539	1130	5.700373	TGCTAAATCAAATCCTTTTTGTGCC	59.300	36.000	0.00	0.00	0.00	5.01
576	1167	6.233905	ACTTCTTTGGCCAAGTTTAAATGT	57.766	33.333	19.48	8.04	33.66	2.71
640	1232	0.893727	AAATGCCACCGAGTTGGGTC	60.894	55.000	0.24	0.00	44.64	4.46
642	1234	1.540267	TTAAATGCCACCGAGTTGGG	58.460	50.000	0.24	0.00	44.64	4.12
643	1235	2.752354	TGATTAAATGCCACCGAGTTGG	59.248	45.455	0.00	0.00	46.41	3.77
644	1236	4.155826	TCTTGATTAAATGCCACCGAGTTG	59.844	41.667	0.00	0.00	0.00	3.16
665	1257	2.632028	TGACAGAAGAGAAGCAAGCTCT	59.368	45.455	0.00	0.00	44.25	4.09
666	1258	3.037431	TGACAGAAGAGAAGCAAGCTC	57.963	47.619	0.00	0.00	0.00	4.09
667	1259	3.598299	GATGACAGAAGAGAAGCAAGCT	58.402	45.455	0.00	0.00	0.00	3.74
668	1260	2.677337	GGATGACAGAAGAGAAGCAAGC	59.323	50.000	0.00	0.00	0.00	4.01
672	1264	3.197549	AGAAGGGATGACAGAAGAGAAGC	59.802	47.826	0.00	0.00	0.00	3.86
675	1267	3.370104	GGAGAAGGGATGACAGAAGAGA	58.630	50.000	0.00	0.00	0.00	3.10
678	1270	2.433970	GAGGGAGAAGGGATGACAGAAG	59.566	54.545	0.00	0.00	0.00	2.85
679	1271	2.472029	GAGGGAGAAGGGATGACAGAA	58.528	52.381	0.00	0.00	0.00	3.02
680	1272	1.343478	GGAGGGAGAAGGGATGACAGA	60.343	57.143	0.00	0.00	0.00	3.41
681	1273	1.127343	GGAGGGAGAAGGGATGACAG	58.873	60.000	0.00	0.00	0.00	3.51
682	1274	0.719015	AGGAGGGAGAAGGGATGACA	59.281	55.000	0.00	0.00	0.00	3.58
683	1275	1.886422	AAGGAGGGAGAAGGGATGAC	58.114	55.000	0.00	0.00	0.00	3.06
684	1276	3.780850	GTTTAAGGAGGGAGAAGGGATGA	59.219	47.826	0.00	0.00	0.00	2.92
685	1277	3.783082	AGTTTAAGGAGGGAGAAGGGATG	59.217	47.826	0.00	0.00	0.00	3.51
686	1278	4.095616	AGTTTAAGGAGGGAGAAGGGAT	57.904	45.455	0.00	0.00	0.00	3.85
687	1279	3.579742	AGTTTAAGGAGGGAGAAGGGA	57.420	47.619	0.00	0.00	0.00	4.20
688	1280	4.783763	ACTTAGTTTAAGGAGGGAGAAGGG	59.216	45.833	1.40	0.00	40.08	3.95
689	1281	7.492077	TTACTTAGTTTAAGGAGGGAGAAGG	57.508	40.000	0.00	0.00	40.08	3.46
690	1282	8.813951	TCTTTACTTAGTTTAAGGAGGGAGAAG	58.186	37.037	0.00	0.00	40.08	2.85
765	1357	5.422331	TCCTGAGATCAAACCGAATAAGAGT	59.578	40.000	0.00	0.00	0.00	3.24
766	1358	5.907207	TCCTGAGATCAAACCGAATAAGAG	58.093	41.667	0.00	0.00	0.00	2.85
858	1450	6.589830	ACATGAGGATTAATTCGTTTCGAG	57.410	37.500	0.00	0.00	37.14	4.04
905	1497	3.066760	TGATCGATCTGCTATGACGTTGT	59.933	43.478	25.02	0.00	0.00	3.32
1075	1667	3.488047	GCTACGCGTGTTATACCTTGAGA	60.488	47.826	24.59	0.00	0.00	3.27
1104	1696	1.775039	ATATTTGCTCGCGCGCATGT	61.775	50.000	32.61	17.97	40.04	3.21
1108	1700	1.832913	CAAATATTTGCTCGCGCGC	59.167	52.632	27.95	23.91	39.65	6.86
1489	2081	8.316214	AGTACACAAAATAGACGGGAGATTTTA	58.684	33.333	0.00	0.00	32.79	1.52
1633	2228	1.000396	GGGCTGAAGAATGTGGCCT	60.000	57.895	3.32	0.00	42.14	5.19
1681	2276	8.470040	AGCGAGTTTGAAAACGATAATACTAA	57.530	30.769	9.28	0.00	43.51	2.24
1684	2279	9.532697	TTAAAGCGAGTTTGAAAACGATAATAC	57.467	29.630	9.28	0.00	43.51	1.89
1802	2397	5.462068	GCAAAACATCCAAGTCCAAACTAAC	59.538	40.000	0.00	0.00	33.48	2.34
1860	2455	3.219198	GGACGGGCATGGGCAATC	61.219	66.667	0.00	0.00	43.71	2.67
1871	2466	0.037590	TCCTTGGTGAATTGGACGGG	59.962	55.000	0.00	0.00	0.00	5.28
2082	2677	0.677731	CGGGAAGGCATGAAGAAGCA	60.678	55.000	0.00	0.00	0.00	3.91
2164	2759	1.016130	CGACCACCAGTAAGCAGCAG	61.016	60.000	0.00	0.00	0.00	4.24
2238	2833	0.388907	TACACGCTAAGGCCGAACAC	60.389	55.000	0.00	0.00	34.44	3.32
2248	2843	1.469595	GCCCATGTACGTACACGCTAA	60.470	52.381	29.54	7.10	44.43	3.09
2337	2932	3.723235	CTCTACACGCAGCGGGCAT	62.723	63.158	19.42	0.00	45.17	4.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.