AutoCloner

Multiple sequence alignment - TraesCS2A01G393300

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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	TraesCS2A01G393300	chr2A	100.000	2877	0	0	1	2877	642966142	642969018	0.000000e+00	5313
1	TraesCS2A01G393300	chr2A	87.963	324	30	5	1559	1877	143245182	143244863	9.730000e-100	374
2	TraesCS2A01G393300	chr5A	94.705	1964	90	11	729	2683	237952938	237950980	0.000000e+00	3038
3	TraesCS2A01G393300	chr5A	92.535	576	35	6	1	573	606464489	606463919	0.000000e+00	819
4	TraesCS2A01G393300	chr5A	85.542	166	4	1	2732	2877	237950991	237950826	3.840000e-34	156
5	TraesCS2A01G393300	chr6A	96.021	1156	44	2	576	1730	585305472	585304318	0.000000e+00	1879
6	TraesCS2A01G393300	chr6A	93.576	576	32	5	1	575	522375240	522375811	0.000000e+00	854
7	TraesCS2A01G393300	chr6A	93.092	579	33	5	1	575	31801864	31801289	0.000000e+00	841
8	TraesCS2A01G393300	chr6A	92.683	574	35	6	3	575	493879238	493879805	0.000000e+00	821
9	TraesCS2A01G393300	chr4B	89.650	1285	122	8	1505	2787	259785219	259783944	0.000000e+00	1626
10	TraesCS2A01G393300	chr4B	85.045	662	92	4	1877	2536	642688178	642687522	0.000000e+00	667
11	TraesCS2A01G393300	chr4B	76.946	989	144	54	576	1497	259786235	259785264	1.200000e-133	486
12	TraesCS2A01G393300	chr4B	81.942	587	67	19	924	1494	430377613	430378176	7.260000e-126	460
13	TraesCS2A01G393300	chr4B	88.618	123	13	1	1505	1627	430378223	430378344	6.420000e-32	148
14	TraesCS2A01G393300	chr4B	83.333	90	5	3	2788	2877	259783923	259783844	1.110000e-09	75
15	TraesCS2A01G393300	chr1A	94.087	575	31	3	1	575	34329121	34328550	0.000000e+00	870
16	TraesCS2A01G393300	chr1A	92.424	594	35	7	1	589	420599339	420599927	0.000000e+00	839
17	TraesCS2A01G393300	chr3A	92.882	576	37	4	1	576	487799536	487798965	0.000000e+00	833
18	TraesCS2A01G393300	chr3A	82.589	649	66	19	877	1494	352457795	352458427	1.960000e-146	529
19	TraesCS2A01G393300	chr3A	91.057	123	10	1	1505	1627	352458474	352458595	6.380000e-37	165
20	TraesCS2A01G393300	chr7A	92.612	582	32	6	1	575	69230518	69229941	0.000000e+00	826
21	TraesCS2A01G393300	chr7A	79.742	775	90	32	576	1300	315305716	315304959	1.540000e-137	499
22	TraesCS2A01G393300	chr7A	79.934	603	63	28	743	1294	342810869	342811464	9.670000e-105	390
23	TraesCS2A01G393300	chr4A	92.522	575	37	5	1	575	572479658	572479090	0.000000e+00	819
24	TraesCS2A01G393300	chr5B	87.048	664	81	5	1877	2536	678449991	678450653	0.000000e+00	745
25	TraesCS2A01G393300	chr6B	85.714	595	73	4	1944	2536	176245766	176245182	4.070000e-173	617
26	TraesCS2A01G393300	chr6B	85.403	596	74	4	1944	2536	176220954	176220369	8.820000e-170	606
27	TraesCS2A01G393300	chr6B	85.235	596	75	4	1944	2536	176183649	176183064	4.100000e-168	601
28	TraesCS2A01G393300	chrUn	85.546	595	74	4	1944	2536	78311683	78312267	1.890000e-171	612
29	TraesCS2A01G393300	chrUn	85.378	595	75	4	1944	2536	274935710	274936294	8.820000e-170	606
30	TraesCS2A01G393300	chrUn	86.498	237	24	6	576	805	360321861	360322096	1.320000e-63	254
31	TraesCS2A01G393300	chr2D	81.458	782	81	40	576	1300	564596102	564596876	1.490000e-162	582
32	TraesCS2A01G393300	chr2D	87.077	325	32	6	1559	1877	135384086	135383766	2.730000e-95	359
33	TraesCS2A01G393300	chr1D	84.127	378	41	13	926	1288	209974807	209975180	5.900000e-92	348
34	TraesCS2A01G393300	chr2B	86.792	318	33	5	1566	1877	192440909	192440595	2.120000e-91	346
35	TraesCS2A01G393300	chr7B	83.421	380	42	12	926	1288	447988531	447988906	1.650000e-87	333
36	TraesCS2A01G393300	chr7B	86.498	237	24	6	576	805	680753929	680754164	1.320000e-63	254

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	TraesCS2A01G393300	chr2A	642966142	642969018	2876	False	5313	5313	100.000000	1	2877	1	chr2A.!!$F1	2876
1	TraesCS2A01G393300	chr5A	237950826	237952938	2112	True	1597	3038	90.123500	729	2877	2	chr5A.!!$R2	2148
2	TraesCS2A01G393300	chr5A	606463919	606464489	570	True	819	819	92.535000	1	573	1	chr5A.!!$R1	572
3	TraesCS2A01G393300	chr6A	585304318	585305472	1154	True	1879	1879	96.021000	576	1730	1	chr6A.!!$R2	1154
4	TraesCS2A01G393300	chr6A	522375240	522375811	571	False	854	854	93.576000	1	575	1	chr6A.!!$F2	574
5	TraesCS2A01G393300	chr6A	31801289	31801864	575	True	841	841	93.092000	1	575	1	chr6A.!!$R1	574
6	TraesCS2A01G393300	chr6A	493879238	493879805	567	False	821	821	92.683000	3	575	1	chr6A.!!$F1	572
7	TraesCS2A01G393300	chr4B	259783844	259786235	2391	True	729	1626	83.309667	576	2877	3	chr4B.!!$R2	2301
8	TraesCS2A01G393300	chr4B	642687522	642688178	656	True	667	667	85.045000	1877	2536	1	chr4B.!!$R1	659
9	TraesCS2A01G393300	chr4B	430377613	430378344	731	False	304	460	85.280000	924	1627	2	chr4B.!!$F1	703
10	TraesCS2A01G393300	chr1A	34328550	34329121	571	True	870	870	94.087000	1	575	1	chr1A.!!$R1	574
11	TraesCS2A01G393300	chr1A	420599339	420599927	588	False	839	839	92.424000	1	589	1	chr1A.!!$F1	588
12	TraesCS2A01G393300	chr3A	487798965	487799536	571	True	833	833	92.882000	1	576	1	chr3A.!!$R1	575
13	TraesCS2A01G393300	chr3A	352457795	352458595	800	False	347	529	86.823000	877	1627	2	chr3A.!!$F1	750
14	TraesCS2A01G393300	chr7A	69229941	69230518	577	True	826	826	92.612000	1	575	1	chr7A.!!$R1	574
15	TraesCS2A01G393300	chr7A	315304959	315305716	757	True	499	499	79.742000	576	1300	1	chr7A.!!$R2	724
16	TraesCS2A01G393300	chr7A	342810869	342811464	595	False	390	390	79.934000	743	1294	1	chr7A.!!$F1	551
17	TraesCS2A01G393300	chr4A	572479090	572479658	568	True	819	819	92.522000	1	575	1	chr4A.!!$R1	574
18	TraesCS2A01G393300	chr5B	678449991	678450653	662	False	745	745	87.048000	1877	2536	1	chr5B.!!$F1	659
19	TraesCS2A01G393300	chr6B	176245182	176245766	584	True	617	617	85.714000	1944	2536	1	chr6B.!!$R3	592
20	TraesCS2A01G393300	chr6B	176220369	176220954	585	True	606	606	85.403000	1944	2536	1	chr6B.!!$R2	592
21	TraesCS2A01G393300	chr6B	176183064	176183649	585	True	601	601	85.235000	1944	2536	1	chr6B.!!$R1	592
22	TraesCS2A01G393300	chrUn	78311683	78312267	584	False	612	612	85.546000	1944	2536	1	chrUn.!!$F1	592
23	TraesCS2A01G393300	chrUn	274935710	274936294	584	False	606	606	85.378000	1944	2536	1	chrUn.!!$F2	592
24	TraesCS2A01G393300	chr2D	564596102	564596876	774	False	582	582	81.458000	576	1300	1	chr2D.!!$F1	724

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
939	1074	0.107214	TGTCAGAATCCAATCGCCCC	60.107	55.0	0.0	0.0	0.0	5.8	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2848	3107	0.680921	ACCTCAAATCCACATGCCCG	60.681	55.0	0.0	0.0	0.0	6.13	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
21	23	2.158143	AGCTATCCCCCTCTTATTCCGT	60.158	50.000	0.00	0.00	0.00	4.69
136	142	3.188159	TGAGTACTCACGGTTGCTTTT	57.812	42.857	21.74	0.00	34.14	2.27
140	146	2.622064	ACTCACGGTTGCTTTTCTCT	57.378	45.000	0.00	0.00	0.00	3.10
179	186	3.589988	CTTCTACCTGATTGTCGCAACT	58.410	45.455	0.00	0.00	0.00	3.16
330	343	2.621526	TGCGCCTCTTTCGATCTGTATA	59.378	45.455	4.18	0.00	0.00	1.47
334	347	4.499188	CGCCTCTTTCGATCTGTATACCAA	60.499	45.833	0.00	0.00	0.00	3.67
400	414	5.428253	TGTACTCAGATATTGTTGCTTCCC	58.572	41.667	0.00	0.00	0.00	3.97
442	463	0.830648	CTTGTATTCGAGCCCCCTGA	59.169	55.000	0.00	0.00	0.00	3.86
530	551	4.964897	AGTCCCTGATCTTGATCATACACA	59.035	41.667	12.94	0.00	0.00	3.72
618	639	2.028020	GGATCCTCGGTGAAAGTCAACT	60.028	50.000	3.84	0.00	30.24	3.16
731	753	4.168871	CCCTAGATTCTTTTCCCCCAATCT	59.831	45.833	0.00	0.00	38.74	2.40
817	919	3.461773	CCTCCCACATCGGACGCT	61.462	66.667	0.00	0.00	36.56	5.07
939	1074	0.107214	TGTCAGAATCCAATCGCCCC	60.107	55.000	0.00	0.00	0.00	5.80
975	1117	0.460459	GTAGCACCGCTTCTTCCCTC	60.460	60.000	0.00	0.00	40.44	4.30
1087	1251	1.053835	TGCTCCTCTTCACCACCACA	61.054	55.000	0.00	0.00	0.00	4.17
1235	1401	9.658799	CTCAGTCTAGATTTAATGAAGGAAACA	57.341	33.333	0.00	0.00	0.00	2.83
1304	1470	2.291540	TGGATGAAGGGTTGGATGGAAC	60.292	50.000	0.00	0.00	0.00	3.62
1402	1594	9.226606	TCAGAATAAGAACCATTCGTGTTATTT	57.773	29.630	0.00	0.00	37.45	1.40
1475	1667	4.989875	AATCAGGAGGGACCATCTAATG	57.010	45.455	6.05	3.46	42.04	1.90
1497	1689	8.409358	AATGGTTGCTAAAGTTACTTCTGAAT	57.591	30.769	0.00	0.00	0.00	2.57
1591	1820	6.983307	GCATCTCTGAACTCTTGCTCTAATTA	59.017	38.462	0.00	0.00	0.00	1.40
1630	1859	4.115199	ATCGGGCTGGGCTTGACC	62.115	66.667	0.00	0.00	37.93	4.02
1802	2031	3.310246	GTTCTCTTCGTCTCTGGTGTTC	58.690	50.000	0.00	0.00	0.00	3.18
1804	2033	0.596577	TCTTCGTCTCTGGTGTTCCG	59.403	55.000	0.00	0.00	36.30	4.30
1819	2048	2.492881	TGTTCCGCTAACGATTGGACTA	59.507	45.455	0.00	0.00	43.93	2.59
1820	2049	3.056678	TGTTCCGCTAACGATTGGACTAA	60.057	43.478	0.00	0.00	43.93	2.24
1907	2137	2.128771	GCACTTTTGCTATCCCTGGA	57.871	50.000	0.00	0.00	46.17	3.86
1955	2185	7.757941	TGTTCATCATTGTTTCTGGATTGTA	57.242	32.000	0.00	0.00	0.00	2.41
2004	2234	5.000591	TCCTATTGTCTGCAAATGAAACGA	58.999	37.500	0.00	0.00	38.21	3.85
2026	2257	5.359194	AACTTGATGTACCTCTGGTATGG	57.641	43.478	0.00	0.00	40.54	2.74
2172	2404	3.761218	TGGTGTATAAATGTTGCACCTGG	59.239	43.478	12.36	0.00	46.92	4.45
2211	2443	8.828644	AGGATATACGAATGAAGCTATAGTACG	58.171	37.037	0.84	0.00	0.00	3.67
2271	2506	7.179269	AGTAAAAATGATAACCTACCAGGCAA	58.821	34.615	0.00	0.00	39.63	4.52
2319	2554	3.156293	TGTGCATGTTAGGTGAGCATTT	58.844	40.909	0.00	0.00	37.56	2.32
2662	2901	0.675633	AAATGTGTTGCACTCTGGGC	59.324	50.000	0.00	0.00	35.11	5.36
2671	2910	0.250234	GCACTCTGGGCTGTGATACA	59.750	55.000	0.00	0.00	36.38	2.29
2687	2926	6.280643	TGTGATACATGTACATCTAAGTGGC	58.719	40.000	7.96	0.00	0.00	5.01
2695	2934	3.834489	ACATCTAAGTGGCTGATGAGG	57.166	47.619	8.86	0.00	39.72	3.86
2699	2938	4.737855	TCTAAGTGGCTGATGAGGTAAC	57.262	45.455	0.00	0.00	0.00	2.50
2840	3099	4.203950	TGTGAAGTGCGTGTTTAATCAC	57.796	40.909	6.60	6.60	36.97	3.06
2848	3107	2.661195	GCGTGTTTAATCACCATGCAAC	59.339	45.455	10.37	0.00	40.11	4.17

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
68	74	7.670364	AGCTACACTACATATGTATGCATTGA	58.330	34.615	15.81	0.00	37.19	2.57
136	142	1.993301	GAAAGGGGGAAAAGGGAGAGA	59.007	52.381	0.00	0.00	0.00	3.10
140	146	0.405852	AGGGAAAGGGGGAAAAGGGA	60.406	55.000	0.00	0.00	0.00	4.20
179	186	2.050144	GATCCTGGGCTCCAACATCTA	58.950	52.381	0.00	0.00	30.80	1.98
330	343	3.160679	AGAAGGCTAGCACAAATTGGT	57.839	42.857	18.24	0.00	39.92	3.67
400	414	3.804518	CTCGATCATAGACGAGTCAGG	57.195	52.381	5.99	0.00	46.90	3.86
442	463	9.618890	AAGTCATACAAGCATCATATTACAAGT	57.381	29.630	0.00	0.00	0.00	3.16
530	551	6.037726	TCGTACACTAATCATACACGCAAAT	58.962	36.000	0.00	0.00	0.00	2.32
567	588	1.416813	CGAAGGATCAGCTGTGACGC	61.417	60.000	14.67	0.00	34.75	5.19
731	753	3.311110	GTGGGAGACGGCTGTGGA	61.311	66.667	0.80	0.00	0.00	4.02
817	919	3.094062	GCCATGGACGAGCCTAGCA	62.094	63.158	18.40	0.00	37.63	3.49
1235	1401	2.401583	TTGGCGATGTATGAACAGCT	57.598	45.000	0.00	0.00	39.92	4.24
1304	1470	9.566432	AATAATACCTAGAGGAAGCAATTCTTG	57.434	33.333	1.60	0.00	38.94	3.02
1402	1594	9.877178	AACCAATGAACAAACAATAAAACACTA	57.123	25.926	0.00	0.00	0.00	2.74
1475	1667	6.086871	GCATTCAGAAGTAACTTTAGCAACC	58.913	40.000	0.00	0.00	0.00	3.77
1497	1689	4.743057	ACATGCATACTTAGAGAGTGCA	57.257	40.909	0.00	11.86	40.33	4.57
1591	1820	7.086376	CGATCTCTGTTGGAAAAATGTGAAAT	58.914	34.615	0.00	0.00	0.00	2.17
1603	1832	1.617018	CCAGCCCGATCTCTGTTGGA	61.617	60.000	3.74	0.00	0.00	3.53
1630	1859	3.477530	AGAAGAGAACTCCAAAAACCCG	58.522	45.455	0.00	0.00	0.00	5.28
1802	2031	3.518590	ACTTTAGTCCAATCGTTAGCGG	58.481	45.455	0.00	0.00	38.89	5.52
1804	2033	5.638234	AGTTGACTTTAGTCCAATCGTTAGC	59.362	40.000	7.39	0.00	44.15	3.09
1820	2049	5.253330	TGTGAAGAACTGGAAAGTTGACTT	58.747	37.500	0.00	0.00	37.91	3.01
1889	2119	3.690460	AGTTCCAGGGATAGCAAAAGTG	58.310	45.455	0.00	0.00	0.00	3.16
1907	2137	6.346477	TCAGCTCTATTGACTTGTGTAGTT	57.654	37.500	0.00	0.00	37.17	2.24
1955	2185	7.839680	AAACCTTAATCCAACTGAAAGATGT	57.160	32.000	0.00	0.00	34.53	3.06
2004	2234	4.783227	ACCATACCAGAGGTACATCAAGTT	59.217	41.667	10.58	0.00	41.31	2.66
2026	2257	5.712446	AGGAAAGGGCAATCTCTTCTTTTAC	59.288	40.000	0.00	0.00	0.00	2.01
2172	2404	8.660373	CATTCGTATATCCTTGGAAAATAGAGC	58.340	37.037	0.00	0.00	0.00	4.09
2211	2443	2.246719	AGAGGAGTCACAGTTTGCAC	57.753	50.000	0.00	0.00	0.00	4.57
2271	2506	8.757982	AACAGAGATCAGCCATGTAATTTTAT	57.242	30.769	0.00	0.00	0.00	1.40
2332	2567	9.327628	GAGGAAAATACACTCTATTAAGGGAAC	57.672	37.037	0.00	0.00	0.00	3.62
2662	2901	6.422100	GCCACTTAGATGTACATGTATCACAG	59.578	42.308	14.43	10.11	0.00	3.66
2671	2910	5.221601	CCTCATCAGCCACTTAGATGTACAT	60.222	44.000	8.43	8.43	39.96	2.29
2699	2938	9.764363	TTGTGCAGACTAATCATAATACCTAAG	57.236	33.333	0.00	0.00	0.00	2.18
2710	2949	6.701340	ACAGACTAATTGTGCAGACTAATCA	58.299	36.000	0.00	0.00	0.00	2.57
2718	2957	7.545615	TGTTAGATGTACAGACTAATTGTGCAG	59.454	37.037	20.43	0.00	42.83	4.41
2848	3107	0.680921	ACCTCAAATCCACATGCCCG	60.681	55.000	0.00	0.00	0.00	6.13

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.