AutoCloner

Multiple sequence alignment - TraesCS2A01G459500

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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	TraesCS2A01G459500	chr2A	100.000	3012	0	0	1	3012	706531534	706528523	0.000000e+00	5563.0
1	TraesCS2A01G459500	chr2A	82.321	1465	164	53	730	2136	706489655	706488228	0.000000e+00	1182.0
2	TraesCS2A01G459500	chr2A	85.276	978	78	27	1075	2014	706510969	706510020	0.000000e+00	948.0
3	TraesCS2A01G459500	chr2A	79.267	791	98	42	2235	2994	706509370	706508615	2.700000e-135	492.0
4	TraesCS2A01G459500	chr2D	90.340	2557	153	35	1	2507	566657683	566655171	0.000000e+00	3267.0
5	TraesCS2A01G459500	chr2D	86.814	1130	120	16	1	1111	566481841	566480722	0.000000e+00	1234.0
6	TraesCS2A01G459500	chr2D	86.802	1129	119	17	1	1111	566455519	566454403	0.000000e+00	1232.0
7	TraesCS2A01G459500	chr2D	85.714	1127	107	24	1	1111	558374126	558375214	0.000000e+00	1140.0
8	TraesCS2A01G459500	chr2D	81.499	1481	164	60	730	2136	566263145	566261701	0.000000e+00	1116.0
9	TraesCS2A01G459500	chr2D	83.279	927	121	19	1159	2066	566480725	566479814	0.000000e+00	822.0
10	TraesCS2A01G459500	chr2D	90.476	630	41	8	1440	2066	566302461	566301848	0.000000e+00	813.0
11	TraesCS2A01G459500	chr2D	86.709	632	75	6	1417	2047	558376146	558376769	0.000000e+00	693.0
12	TraesCS2A01G459500	chr2D	90.945	508	35	2	2505	3012	566655085	566654589	0.000000e+00	673.0
13	TraesCS2A01G459500	chr2D	84.816	461	47	11	2433	2891	566300905	566300466	2.760000e-120	442.0
14	TraesCS2A01G459500	chr2D	82.126	414	39	17	1073	1452	566302935	566302523	3.750000e-84	322.0
15	TraesCS2A01G459500	chr2D	89.474	76	8	0	134	209	566263666	566263591	2.470000e-16	97.1
16	TraesCS2A01G459500	chr2B	90.308	1527	90	25	1	1491	679729019	679730523	0.000000e+00	1947.0
17	TraesCS2A01G459500	chr2B	89.861	1440	82	23	716	2111	679696201	679697620	0.000000e+00	1792.0
18	TraesCS2A01G459500	chr2B	82.097	1469	172	57	730	2151	679031612	679030188	0.000000e+00	1171.0
19	TraesCS2A01G459500	chr2B	86.770	1028	83	20	1072	2066	679071596	679070589	0.000000e+00	1096.0
20	TraesCS2A01G459500	chr2B	92.308	728	44	8	1	724	679694060	679694779	0.000000e+00	1024.0
21	TraesCS2A01G459500	chr2B	92.407	619	36	5	1498	2111	679743801	679744413	0.000000e+00	872.0
22	TraesCS2A01G459500	chr2B	82.088	910	130	14	1161	2048	679305179	679304281	0.000000e+00	747.0
23	TraesCS2A01G459500	chr2B	89.880	583	39	7	2430	3012	679745655	679746217	0.000000e+00	732.0
24	TraesCS2A01G459500	chr2B	89.365	583	42	7	2430	3012	679698736	679699298	0.000000e+00	715.0
25	TraesCS2A01G459500	chr2B	85.132	491	57	11	2522	3012	679069091	679068617	3.490000e-134	488.0
26	TraesCS2A01G459500	chr2B	91.743	218	13	4	2097	2312	679698287	679698501	6.310000e-77	298.0
27	TraesCS2A01G459500	chr7B	80.786	229	36	7	2511	2736	634294559	634294782	3.990000e-39	172.0
28	TraesCS2A01G459500	chrUn	80.435	230	35	9	2511	2736	92640066	92640289	1.860000e-37	167.0
29	TraesCS2A01G459500	chr7A	78.355	231	37	10	2511	2736	664212660	664212882	1.460000e-28	137.0
30	TraesCS2A01G459500	chr5D	85.556	90	11	2	522	611	73802208	73802295	3.200000e-15	93.5
31	TraesCS2A01G459500	chr5B	81.188	101	16	2	514	614	78705048	78704951	8.950000e-11	78.7

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	TraesCS2A01G459500	chr2A	706528523	706531534	3011	True	5563.000000	5563	100.00000	1	3012	1	chr2A.!!$R2	3011
1	TraesCS2A01G459500	chr2A	706488228	706489655	1427	True	1182.000000	1182	82.32100	730	2136	1	chr2A.!!$R1	1406
2	TraesCS2A01G459500	chr2A	706508615	706510969	2354	True	720.000000	948	82.27150	1075	2994	2	chr2A.!!$R3	1919
3	TraesCS2A01G459500	chr2D	566654589	566657683	3094	True	1970.000000	3267	90.64250	1	3012	2	chr2D.!!$R5	3011
4	TraesCS2A01G459500	chr2D	566454403	566455519	1116	True	1232.000000	1232	86.80200	1	1111	1	chr2D.!!$R1	1110
5	TraesCS2A01G459500	chr2D	566479814	566481841	2027	True	1028.000000	1234	85.04650	1	2066	2	chr2D.!!$R4	2065
6	TraesCS2A01G459500	chr2D	558374126	558376769	2643	False	916.500000	1140	86.21150	1	2047	2	chr2D.!!$F1	2046
7	TraesCS2A01G459500	chr2D	566261701	566263666	1965	True	606.550000	1116	85.48650	134	2136	2	chr2D.!!$R2	2002
8	TraesCS2A01G459500	chr2D	566300466	566302935	2469	True	525.666667	813	85.80600	1073	2891	3	chr2D.!!$R3	1818
9	TraesCS2A01G459500	chr2B	679729019	679730523	1504	False	1947.000000	1947	90.30800	1	1491	1	chr2B.!!$F1	1490
10	TraesCS2A01G459500	chr2B	679030188	679031612	1424	True	1171.000000	1171	82.09700	730	2151	1	chr2B.!!$R1	1421
11	TraesCS2A01G459500	chr2B	679694060	679699298	5238	False	957.250000	1792	90.81925	1	3012	4	chr2B.!!$F2	3011
12	TraesCS2A01G459500	chr2B	679743801	679746217	2416	False	802.000000	872	91.14350	1498	3012	2	chr2B.!!$F3	1514
13	TraesCS2A01G459500	chr2B	679068617	679071596	2979	True	792.000000	1096	85.95100	1072	3012	2	chr2B.!!$R3	1940
14	TraesCS2A01G459500	chr2B	679304281	679305179	898	True	747.000000	747	82.08800	1161	2048	1	chr2B.!!$R2	887

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
937	2502	0.768622	TCAAACACCCCACCGATCTT	59.231	50.0	0.0	0.0	0.0	2.4	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2695	7610	0.445436	CTTGCTTCTCGTGTGCATCC	59.555	55.0	0.0	0.0	36.55	3.51	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
44	45	1.175983	TCCATTCCCGCAACAACACC	61.176	55.000	0.00	0.00	0.00	4.16
52	53	1.512156	CGCAACAACACCTGGGGTAC	61.512	60.000	0.00	0.00	32.11	3.34
189	195	8.892723	AGAATCAATTAGACATTAATCGTTGCA	58.107	29.630	0.00	0.00	0.00	4.08
278	372	2.867793	TACCACGCGGCAATGCTCAT	62.868	55.000	12.47	0.00	34.57	2.90
345	445	6.473455	GCAATGAATTTAGTGGTTGTATCTGC	59.527	38.462	0.00	0.00	0.00	4.26
479	587	2.348872	CGTTCATGTAATGCGGATGAGC	60.349	50.000	0.00	0.00	46.21	4.26
551	660	2.818130	AGCATGGCAAAACGAATGTT	57.182	40.000	0.00	0.00	40.98	2.71
629	741	5.119898	TGACAAATCCGCAAAATTATGTTGC	59.880	36.000	9.90	9.90	46.34	4.17
634	746	2.590073	CGCAAAATTATGTTGCCACGA	58.410	42.857	13.79	0.00	46.98	4.35
635	747	2.593775	CGCAAAATTATGTTGCCACGAG	59.406	45.455	13.79	0.00	46.98	4.18
636	748	2.923020	GCAAAATTATGTTGCCACGAGG	59.077	45.455	8.83	0.00	44.53	4.63
637	749	3.366883	GCAAAATTATGTTGCCACGAGGA	60.367	43.478	8.83	0.00	44.53	3.71
807	2350	9.624697	GCGATGCCAATTAATATGATCTTTAAA	57.375	29.630	0.00	0.00	0.00	1.52
918	2479	2.594592	GCCCAACCTCGCAACTGT	60.595	61.111	0.00	0.00	0.00	3.55
937	2502	0.768622	TCAAACACCCCACCGATCTT	59.231	50.000	0.00	0.00	0.00	2.40
1001	2569	3.263937	AGAAAAGAGGAAGCAGAGCAGAT	59.736	43.478	0.00	0.00	0.00	2.90
1022	2591	1.448013	CCGCCGAGAAAGGGAAGAC	60.448	63.158	0.00	0.00	0.00	3.01
1347	2970	4.574759	CTTAATTAATTCGCGCTCGTGTT	58.425	39.130	5.56	0.00	36.96	3.32
1356	2979	0.654472	GCGCTCGTGTTGTTTCTGTG	60.654	55.000	0.00	0.00	0.00	3.66
1361	2984	0.650512	CGTGTTGTTTCTGTGCGAGT	59.349	50.000	0.00	0.00	0.00	4.18
1362	2985	1.855978	CGTGTTGTTTCTGTGCGAGTA	59.144	47.619	0.00	0.00	0.00	2.59
1363	2986	2.475111	CGTGTTGTTTCTGTGCGAGTAT	59.525	45.455	0.00	0.00	0.00	2.12
1395	3040	4.500603	AGTAGGTTAGATTATGTCCGCG	57.499	45.455	0.00	0.00	0.00	6.46
1404	3691	1.282817	TTATGTCCGCGGATCAAACG	58.717	50.000	33.58	0.00	0.00	3.60
1427	3714	6.922957	ACGCATGTTGTTTGATTGATTTAACT	59.077	30.769	0.00	0.00	0.00	2.24
1491	3851	4.330074	CAGAGTTCTGTGTTCTTCGTGTTT	59.670	41.667	0.91	0.00	39.09	2.83
1650	4030	2.897846	CGTTGCCGTCACCACCAA	60.898	61.111	0.00	0.00	0.00	3.67
1675	4055	2.125512	GCGTTCTGCACCCTCGAT	60.126	61.111	0.00	0.00	45.45	3.59
1976	4357	1.306226	AGCGGGAAGAAGCCTAGGT	60.306	57.895	11.31	0.00	0.00	3.08
2167	5463	6.550854	AGGGACAAAAGATGAAAGACAAATGA	59.449	34.615	0.00	0.00	0.00	2.57
2265	6076	3.428870	ACGCTACAATGTTCTTCTTCACG	59.571	43.478	0.00	0.00	0.00	4.35
2317	6128	1.613630	ATGAGCTCCCCGTCCTTGT	60.614	57.895	12.15	0.00	0.00	3.16
2327	6138	1.897802	CCCGTCCTTGTGTACCTACTT	59.102	52.381	0.00	0.00	0.00	2.24
2329	6140	2.559668	CCGTCCTTGTGTACCTACTTCA	59.440	50.000	0.00	0.00	0.00	3.02
2424	6443	0.038166	CTGCCCCCAGTGCTTCTTTA	59.962	55.000	0.00	0.00	34.31	1.85
2428	6585	0.321653	CCCCAGTGCTTCTTTACGCT	60.322	55.000	0.00	0.00	0.00	5.07
2695	7610	3.525537	AGAAGTAGATGGTGCGTTGATG	58.474	45.455	0.00	0.00	0.00	3.07
2698	7613	2.435805	AGTAGATGGTGCGTTGATGGAT	59.564	45.455	0.00	0.00	0.00	3.41
2777	7702	6.315144	GCAAGCCCAAAGAAAGAAACTTTAAA	59.685	34.615	0.00	0.00	36.09	1.52
2870	7795	7.994425	TCTTTTTATGGAAGTCATTGCACTA	57.006	32.000	0.00	0.00	39.79	2.74
2892	7817	5.485662	AATGATGTTCTTACTTTAGGCGC	57.514	39.130	0.00	0.00	0.00	6.53
2894	7819	2.843401	TGTTCTTACTTTAGGCGCCA	57.157	45.000	31.54	12.31	0.00	5.69
2896	7821	3.681593	TGTTCTTACTTTAGGCGCCAAT	58.318	40.909	31.54	12.06	0.00	3.16
2901	7826	1.739067	ACTTTAGGCGCCAATGAGTC	58.261	50.000	31.54	0.00	0.00	3.36
2915	7840	5.288952	GCCAATGAGTCGAGTTAACTAGAAC	59.711	44.000	18.49	15.43	29.60	3.01
2923	7848	8.666580	AGTCGAGTTAACTAGAACGTATTTTC	57.333	34.615	18.49	4.90	34.36	2.29
2963	7888	8.318412	TCTTAATGCTTGACCTAGTTTGATGTA	58.682	33.333	0.00	0.00	0.00	2.29

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
12	13	2.097825	GGAATGGATGCAGTTGCTTCT	58.902	47.619	16.44	1.24	42.66	2.85
16	17	1.434696	CGGGAATGGATGCAGTTGC	59.565	57.895	0.00	0.00	42.50	4.17
44	45	7.724506	TGTTGAATACTAGAGATAGTACCCCAG	59.275	40.741	0.00	0.00	35.60	4.45
278	372	8.826710	CCGCTGATCTATATTTTAGTTCACAAA	58.173	33.333	0.00	0.00	0.00	2.83
345	445	9.197694	CTTCGTCCATCCATATTTTAGTAGAAG	57.802	37.037	0.00	0.00	0.00	2.85
400	505	2.287644	CGCCGCTGAAATATCATGTTCA	59.712	45.455	0.00	0.00	34.37	3.18
629	741	0.035056	ATTGCCTTCCTTCCTCGTGG	60.035	55.000	0.00	0.00	0.00	4.94
807	2350	6.601217	GGCAGAGAGAACCTTAAAGATCATTT	59.399	38.462	0.00	0.00	0.00	2.32
808	2351	6.118852	GGCAGAGAGAACCTTAAAGATCATT	58.881	40.000	0.00	0.00	0.00	2.57
809	2352	5.397334	GGGCAGAGAGAACCTTAAAGATCAT	60.397	44.000	0.00	0.00	0.00	2.45
810	2353	4.080863	GGGCAGAGAGAACCTTAAAGATCA	60.081	45.833	0.00	0.00	0.00	2.92
811	2354	4.447290	GGGCAGAGAGAACCTTAAAGATC	58.553	47.826	0.00	0.00	0.00	2.75
813	2356	2.572104	GGGGCAGAGAGAACCTTAAAGA	59.428	50.000	0.00	0.00	0.00	2.52
817	2374	1.622725	GGAGGGGCAGAGAGAACCTTA	60.623	57.143	0.00	0.00	0.00	2.69
819	2376	1.306568	GGAGGGGCAGAGAGAACCT	60.307	63.158	0.00	0.00	0.00	3.50
905	2466	1.400494	GTGTTTGACAGTTGCGAGGTT	59.600	47.619	0.00	0.00	0.00	3.50
909	2470	1.098712	GGGGTGTTTGACAGTTGCGA	61.099	55.000	0.00	0.00	0.00	5.10
918	2479	0.768622	AAGATCGGTGGGGTGTTTGA	59.231	50.000	0.00	0.00	0.00	2.69
937	2502	4.078922	AGAGAGAGAGAGAGAGAGAGGAGA	60.079	50.000	0.00	0.00	0.00	3.71
1001	2569	2.167398	CTTCCCTTTCTCGGCGGTCA	62.167	60.000	7.21	0.00	0.00	4.02
1164	2736	0.738762	CCTCTAGGTCGACGACGTCA	60.739	60.000	24.84	12.97	40.69	4.35
1347	2970	6.598525	CAAATTACATACTCGCACAGAAACA	58.401	36.000	0.00	0.00	0.00	2.83
1356	2979	6.214399	ACCTACTAGCAAATTACATACTCGC	58.786	40.000	0.00	0.00	0.00	5.03
1404	3691	7.011189	GCAGTTAAATCAATCAAACAACATGC	58.989	34.615	0.00	0.00	0.00	4.06
1411	3698	8.692110	TCATCATGCAGTTAAATCAATCAAAC	57.308	30.769	0.00	0.00	0.00	2.93
1427	3714	7.747155	AAACCAAAATTTTGATCATCATGCA	57.253	28.000	28.44	0.00	40.55	3.96
1477	3837	6.145534	TCTGTATGATGAAACACGAAGAACAC	59.854	38.462	0.00	0.00	0.00	3.32
1491	3851	9.599866	CACCTTGTTAAGTAATCTGTATGATGA	57.400	33.333	0.00	0.00	35.21	2.92
1521	3895	5.277825	CGGACTGCACAAAAACAAGAATTA	58.722	37.500	0.00	0.00	0.00	1.40
1581	3955	3.636231	CCTGGTGGCCGTCTTGGA	61.636	66.667	0.00	0.00	42.00	3.53
1635	4009	1.525077	GAGTTGGTGGTGACGGCAA	60.525	57.895	0.00	0.00	0.00	4.52
1636	4010	2.110213	GAGTTGGTGGTGACGGCA	59.890	61.111	0.00	0.00	0.00	5.69
1637	4011	2.668550	GGAGTTGGTGGTGACGGC	60.669	66.667	0.00	0.00	0.00	5.68
1650	4030	3.303135	TGCAGAACGCGGAGGAGT	61.303	61.111	12.47	0.00	46.97	3.85
1976	4357	0.874390	GCGTCAGCATTCAGGTCAAA	59.126	50.000	0.00	0.00	44.35	2.69
2095	4489	3.866651	ACATGTAACTGCTCCTGATGAC	58.133	45.455	0.00	0.00	0.00	3.06
2103	4497	9.282247	CATAATTTTCTGAACATGTAACTGCTC	57.718	33.333	0.00	0.00	0.00	4.26
2143	5439	6.748132	TCATTTGTCTTTCATCTTTTGTCCC	58.252	36.000	0.00	0.00	0.00	4.46
2180	5477	7.769272	TGATGACATGAAAAACTTTTCCAAC	57.231	32.000	11.42	3.49	44.48	3.77
2197	5914	2.988636	TCCCCAACCAATTGATGACA	57.011	45.000	7.12	0.00	38.15	3.58
2317	6128	7.450074	ACAAATGATTCACTGAAGTAGGTACA	58.550	34.615	0.00	0.00	0.00	2.90
2327	6138	5.705902	CAGATGCAACAAATGATTCACTGA	58.294	37.500	0.00	0.00	0.00	3.41
2329	6140	4.491676	GCAGATGCAACAAATGATTCACT	58.508	39.130	0.00	0.00	41.59	3.41
2357	6170	1.148273	GCAATGGGCGGACCTGATA	59.852	57.895	0.00	0.00	41.11	2.15
2413	6242	2.802816	CAACAGAGCGTAAAGAAGCACT	59.197	45.455	0.00	0.00	34.77	4.40
2424	6443	5.353123	TGAAGTTTCTTAAACAACAGAGCGT	59.647	36.000	5.42	0.00	43.79	5.07
2428	6585	7.302524	GTGTGTGAAGTTTCTTAAACAACAGA	58.697	34.615	5.42	3.12	43.79	3.41
2487	6646	6.003950	ACATATACATCGCTTTTATGGCCTT	58.996	36.000	3.32	0.00	0.00	4.35
2535	7450	4.394729	ACGGGATTCGCATACCAAATTAT	58.605	39.130	0.00	0.00	43.89	1.28
2547	7462	0.459585	TAGTGAGCAACGGGATTCGC	60.460	55.000	0.00	0.00	43.89	4.70
2650	7565	8.858094	TCTCTATCAGTAATCGACAGTAGTAGA	58.142	37.037	0.00	0.00	33.84	2.59
2695	7610	0.445436	CTTGCTTCTCGTGTGCATCC	59.555	55.000	0.00	0.00	36.55	3.51
2698	7613	0.880278	GGACTTGCTTCTCGTGTGCA	60.880	55.000	4.44	4.44	34.69	4.57
2777	7702	4.402474	ACTCAAAGTGCAAGGTAAAGCTTT	59.598	37.500	17.30	17.30	0.00	3.51
2870	7795	4.335594	GGCGCCTAAAGTAAGAACATCATT	59.664	41.667	22.15	0.00	0.00	2.57
2892	7817	5.512082	CGTTCTAGTTAACTCGACTCATTGG	59.488	44.000	12.39	0.00	0.00	3.16
2894	7819	6.251655	ACGTTCTAGTTAACTCGACTCATT	57.748	37.500	12.39	0.00	0.00	2.57
2896	7821	6.974932	ATACGTTCTAGTTAACTCGACTCA	57.025	37.500	12.39	0.00	0.00	3.41
2981	7910	6.744537	GCATAATTGAACAACTCAGTGCTTAG	59.255	38.462	0.00	0.00	34.81	2.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.