AutoCloner

Multiple sequence alignment - TraesCS3D01G464400

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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	TraesCS3D01G464400	chr3D	100.000	2690	0	0	1	2690	568180581	568183270	0.000000e+00	4968.0
1	TraesCS3D01G464400	chr3D	85.468	1913	225	28	554	2429	569888686	569886790	0.000000e+00	1943.0
2	TraesCS3D01G464400	chr3D	81.886	403	44	13	480	870	569467351	569466966	2.010000e-81	313.0
3	TraesCS3D01G464400	chr3D	72.392	1112	261	36	590	1670	565641954	565643050	7.230000e-81	311.0
4	TraesCS3D01G464400	chr3D	82.447	376	46	7	2211	2574	569126850	569126483	7.230000e-81	311.0
5	TraesCS3D01G464400	chr3D	82.789	337	49	2	540	870	569132378	569132711	2.620000e-75	292.0
6	TraesCS3D01G464400	chr3D	77.902	448	94	4	1219	1665	566609555	566609998	9.490000e-70	274.0
7	TraesCS3D01G464400	chr3D	77.538	463	99	4	1219	1680	568018082	568018540	9.490000e-70	274.0
8	TraesCS3D01G464400	chr3D	90.338	207	18	1	1	207	12382355	12382559	1.230000e-68	270.0
9	TraesCS3D01G464400	chr3D	74.403	586	113	22	551	1126	566608907	566609465	1.620000e-52	217.0
10	TraesCS3D01G464400	chr3D	76.633	398	79	11	1291	1681	566629274	566629664	9.760000e-50	207.0
11	TraesCS3D01G464400	chr3D	76.559	401	74	12	1291	1681	569133140	569133530	4.540000e-48	202.0
12	TraesCS3D01G464400	chr3D	75.907	386	51	23	479	864	568017415	568017758	2.770000e-35	159.0
13	TraesCS3D01G464400	chr3D	91.765	85	5	2	787	870	567906259	567906342	1.690000e-22	117.0
14	TraesCS3D01G464400	chr3D	80.000	145	23	4	2119	2258	567688665	567688522	4.740000e-18	102.0
15	TraesCS3D01G464400	chr3D	79.137	139	25	3	2118	2254	568113232	568113368	2.850000e-15	93.5
16	TraesCS3D01G464400	chr3A	93.704	2732	125	18	1	2690	700423996	700421270	0.000000e+00	4048.0
17	TraesCS3D01G464400	chr3A	78.440	1141	186	30	580	1680	700352278	700351158	0.000000e+00	689.0
18	TraesCS3D01G464400	chr3A	70.130	462	120	15	1213	1662	701644065	701644520	3.710000e-09	73.1
19	TraesCS3D01G464400	chr3A	93.182	44	3	0	1232	1275	701834614	701834657	6.220000e-07	65.8
20	TraesCS3D01G464400	chr1D	87.629	388	36	6	1	384	485492027	485492406	8.840000e-120	440.0
21	TraesCS3D01G464400	chr4A	86.154	390	41	6	1	384	733923392	733923774	2.490000e-110	409.0
22	TraesCS3D01G464400	chr4A	78.977	176	33	4	1507	1680	648794357	648794184	1.690000e-22	117.0
23	TraesCS3D01G464400	chr4A	79.355	155	23	6	1536	1684	80159	80008	1.700000e-17	100.0
24	TraesCS3D01G464400	chr4A	100.000	30	0	0	1853	1882	611417127	611417098	3.740000e-04	56.5
25	TraesCS3D01G464400	chrUn	87.273	330	28	7	60	384	88913445	88913765	5.470000e-97	364.0
26	TraesCS3D01G464400	chrUn	82.398	392	48	11	485	870	250747455	250747831	3.340000e-84	322.0
27	TraesCS3D01G464400	chrUn	82.398	392	48	11	485	870	258534255	258533879	3.340000e-84	322.0
28	TraesCS3D01G464400	chrUn	82.398	392	48	11	485	870	329510149	329510525	3.340000e-84	322.0
29	TraesCS3D01G464400	chrUn	76.709	395	78	13	1297	1684	284162522	284162135	9.760000e-50	207.0
30	TraesCS3D01G464400	chrUn	76.842	380	77	10	1291	1666	41057776	41058148	1.260000e-48	204.0
31	TraesCS3D01G464400	chrUn	76.037	217	38	9	2040	2254	40895093	40895297	1.700000e-17	100.0
32	TraesCS3D01G464400	chrUn	89.474	76	7	1	485	560	217837239	217837313	7.930000e-16	95.3
33	TraesCS3D01G464400	chrUn	89.474	76	7	1	485	560	227101507	227101581	7.930000e-16	95.3
34	TraesCS3D01G464400	chrUn	93.333	45	3	0	1232	1276	40879328	40879284	1.730000e-07	67.6
35	TraesCS3D01G464400	chrUn	84.848	66	8	2	1853	1916	48323074	48323009	6.220000e-07	65.8
36	TraesCS3D01G464400	chrUn	83.333	66	9	2	1853	1916	48292747	48292682	2.890000e-05	60.2
37	TraesCS3D01G464400	chr3B	82.620	397	48	11	480	870	756379550	756379169	5.550000e-87	331.0
38	TraesCS3D01G464400	chr3B	84.122	296	39	3	554	847	202001164	202000875	2.040000e-71	279.0
39	TraesCS3D01G464400	chr3B	76.962	395	77	13	1297	1684	754849465	754849078	2.100000e-51	213.0
40	TraesCS3D01G464400	chr3B	72.867	457	98	22	1232	1681	754303008	754303445	1.680000e-27	134.0
41	TraesCS3D01G464400	chr3B	86.842	76	10	0	1609	1684	684636524	684636449	4.770000e-13	86.1
42	TraesCS3D01G464400	chr4B	79.355	155	23	6	1536	1684	121476	121325	1.700000e-17	100.0
43	TraesCS3D01G464400	chr2B	95.000	40	2	0	345	384	26981525	26981486	2.240000e-06	63.9

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	TraesCS3D01G464400	chr3D	568180581	568183270	2689	False	4968.0	4968	100.0000	1	2690	1	chr3D.!!$F6	2689
1	TraesCS3D01G464400	chr3D	569886790	569888686	1896	True	1943.0	1943	85.4680	554	2429	1	chr3D.!!$R4	1875
2	TraesCS3D01G464400	chr3D	565641954	565643050	1096	False	311.0	311	72.3920	590	1670	1	chr3D.!!$F2	1080
3	TraesCS3D01G464400	chr3D	569132378	569133530	1152	False	247.0	292	79.6740	540	1681	2	chr3D.!!$F9	1141
4	TraesCS3D01G464400	chr3D	566608907	566609998	1091	False	245.5	274	76.1525	551	1665	2	chr3D.!!$F7	1114
5	TraesCS3D01G464400	chr3D	568017415	568018540	1125	False	216.5	274	76.7225	479	1680	2	chr3D.!!$F8	1201
6	TraesCS3D01G464400	chr3A	700421270	700423996	2726	True	4048.0	4048	93.7040	1	2690	1	chr3A.!!$R2	2689
7	TraesCS3D01G464400	chr3A	700351158	700352278	1120	True	689.0	689	78.4400	580	1680	1	chr3A.!!$R1	1100

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
440	441	0.327191	ATCCCTGGTGGTTCCCGTAT	60.327	55.0	0.0	0.0	34.77	3.06	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2385	2571	0.032952	ACTTCAACGAGCGGTGCTTA	59.967	50.0	2.51	0.0	39.88	3.09	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
192	193	4.250464	TGCTCGGTCCAACTAAAATACAG	58.750	43.478	0.00	0.00	0.00	2.74
295	296	7.907389	TGGGTTGCACATATGGTAAATTTTAA	58.093	30.769	7.80	0.00	0.00	1.52
344	345	9.010029	TCTTAACTTAATTAGGCCTGAACTTTG	57.990	33.333	17.99	2.59	0.00	2.77
354	355	4.067192	GGCCTGAACTTTGATTTTGCATT	58.933	39.130	0.00	0.00	0.00	3.56
372	373	1.387737	TGGGCCCCCAAATTCTCAG	59.612	57.895	22.27	0.00	44.12	3.35
382	383	1.065418	CAAATTCTCAGGTACGGCCCT	60.065	52.381	0.00	0.00	38.26	5.19
396	397	2.439701	CCCTGTGGCCATGCTCTG	60.440	66.667	9.72	0.00	0.00	3.35
434	435	1.141858	GGATCAGATCCCTGGTGGTTC	59.858	57.143	17.97	0.00	43.88	3.62
435	436	1.141858	GATCAGATCCCTGGTGGTTCC	59.858	57.143	0.00	0.00	40.76	3.62
436	437	0.914417	TCAGATCCCTGGTGGTTCCC	60.914	60.000	0.00	0.00	40.76	3.97
437	438	1.995626	AGATCCCTGGTGGTTCCCG	60.996	63.158	0.00	0.00	33.89	5.14
439	440	0.979187	GATCCCTGGTGGTTCCCGTA	60.979	60.000	0.00	0.00	34.77	4.02
440	441	0.327191	ATCCCTGGTGGTTCCCGTAT	60.327	55.000	0.00	0.00	34.77	3.06
442	443	1.061967	TCCCTGGTGGTTCCCGTATAT	60.062	52.381	0.00	0.00	34.77	0.86
444	445	3.178865	CCCTGGTGGTTCCCGTATATAT	58.821	50.000	0.00	0.00	34.77	0.86
446	447	4.966805	CCCTGGTGGTTCCCGTATATATAT	59.033	45.833	0.00	0.00	34.77	0.86
448	449	6.785963	CCCTGGTGGTTCCCGTATATATATAT	59.214	42.308	10.10	10.10	34.77	0.86
509	527	2.806745	CGTCACTTCCACTTCACACCAT	60.807	50.000	0.00	0.00	0.00	3.55
544	562	3.675775	GCTATCGAGATCCAGATTGAGCC	60.676	52.174	11.56	0.00	0.00	4.70
547	565	1.433121	GAGATCCAGATTGAGCCCCT	58.567	55.000	0.00	0.00	0.00	4.79
597	615	3.961414	GGTTCCCCTCCACCGCAA	61.961	66.667	0.00	0.00	0.00	4.85
679	697	3.538028	CTGTCGTGCCGTCTGTCGT	62.538	63.158	0.00	0.00	37.94	4.34
711	741	2.343758	CACCTCCACCCACGACTG	59.656	66.667	0.00	0.00	0.00	3.51
781	811	1.588674	ACAATTTCAAGTGCGACGGA	58.411	45.000	0.00	0.00	0.00	4.69
831	867	3.834799	CGACCACCGAGTAGGGGC	61.835	72.222	0.00	0.00	44.00	5.80
887	929	4.834406	ATTGACCTCTCCTATCCTGGTA	57.166	45.455	0.00	0.00	0.00	3.25
1032	1089	3.246112	TACCCGCACAGCCCAACT	61.246	61.111	0.00	0.00	0.00	3.16
1072	1141	6.389830	TGTTGTACTTGAGTGATGCAAATT	57.610	33.333	0.00	0.00	0.00	1.82
1393	1547	3.365220	GTCACAAGACTATGACAACGAGC	59.635	47.826	12.71	0.00	43.89	5.03
1412	1566	2.785857	AGCTATGGGCCTTGAAATACCT	59.214	45.455	4.53	0.00	43.05	3.08
1499	1653	1.486726	GGTCACTTCTAGGGATGGTGG	59.513	57.143	0.00	0.00	25.81	4.61
1672	1829	6.267471	ACAGGGTTATGTTGTGAACAATTCAT	59.733	34.615	0.00	2.40	45.86	2.57
1686	1845	6.375174	TGAACAATTCATCTTTCATCGGATGT	59.625	34.615	17.01	0.00	39.93	3.06
1716	1875	1.065854	AGTGAGGCAGCGCTTCTAAAT	60.066	47.619	7.50	0.00	35.64	1.40
1787	1946	4.151157	GGCTTTTCTTTGTTGATGCATGTC	59.849	41.667	2.46	0.00	0.00	3.06
1826	1985	2.744202	CTCTCACTGTTATGTGGTTGCC	59.256	50.000	0.00	0.00	38.40	4.52
1884	2043	5.410067	AGTCATTTTGGTGTGTGTTTGAAG	58.590	37.500	0.00	0.00	0.00	3.02
1993	2170	6.004574	ACTGGAGGATTGACTTTACCTTTTC	58.995	40.000	0.00	0.00	32.53	2.29
2105	2287	3.669251	AGTTCTGTTCTAGCTGACCAC	57.331	47.619	0.00	0.00	0.00	4.16
2188	2374	8.994429	ATACTCATGAGCTGCTATGTATAAAC	57.006	34.615	22.83	0.00	0.00	2.01
2314	2500	1.202770	GGCTACCAGTTCTGTTGTGGT	60.203	52.381	0.00	0.00	46.54	4.16
2315	2501	1.873591	GCTACCAGTTCTGTTGTGGTG	59.126	52.381	3.46	0.00	44.52	4.17
2385	2571	6.941857	TGAACTTGGGTTTTTAAAGAGCTTT	58.058	32.000	7.73	0.74	35.58	3.51
2392	2578	5.694910	GGGTTTTTAAAGAGCTTTAAGCACC	59.305	40.000	19.63	22.33	45.56	5.01
2458	2644	3.436704	TGTTCGTTCATTCCTCTTCATGC	59.563	43.478	0.00	0.00	0.00	4.06
2461	2647	3.873361	TCGTTCATTCCTCTTCATGCATC	59.127	43.478	0.00	0.00	0.00	3.91
2462	2648	3.875727	CGTTCATTCCTCTTCATGCATCT	59.124	43.478	0.00	0.00	0.00	2.90
2463	2649	4.260661	CGTTCATTCCTCTTCATGCATCTG	60.261	45.833	0.00	0.00	0.00	2.90
2464	2650	3.816994	TCATTCCTCTTCATGCATCTGG	58.183	45.455	0.00	0.00	0.00	3.86
2641	2844	2.496070	TCGAGTACCATTGGTCTCAAGG	59.504	50.000	23.36	13.89	37.09	3.61
2676	2879	9.288576	TCAAGTTCACTCTGATCATTTGTTATT	57.711	29.630	0.00	0.00	0.00	1.40

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
6	7	2.093783	CGCGATCCTTTGGTAGTTGAAC	59.906	50.000	0.00	0.00	0.00	3.18
12	13	1.287425	GGAACGCGATCCTTTGGTAG	58.713	55.000	26.40	0.00	36.50	3.18
55	56	4.340381	AGCAATTTCCATCTATTCCACTGC	59.660	41.667	0.00	0.00	0.00	4.40
56	57	6.461110	AAGCAATTTCCATCTATTCCACTG	57.539	37.500	0.00	0.00	0.00	3.66
83	84	8.506437	CACAATTTTGAAGTGCTATCTCTGTAA	58.494	33.333	0.00	0.00	0.00	2.41
148	149	6.828785	AGCAACTTTTCTAGAACTTCCTTTCA	59.171	34.615	4.18	0.00	0.00	2.69
154	155	4.750598	ACCGAGCAACTTTTCTAGAACTTC	59.249	41.667	4.18	0.00	0.00	3.01
167	168	2.922740	TTTAGTTGGACCGAGCAACT	57.077	45.000	0.00	0.00	41.41	3.16
168	169	4.453136	TGTATTTTAGTTGGACCGAGCAAC	59.547	41.667	0.00	0.00	0.00	4.17
324	325	9.143631	CAAAATCAAAGTTCAGGCCTAATTAAG	57.856	33.333	3.98	0.00	0.00	1.85
344	345	1.224315	GGGGGCCCAATGCAAAATC	59.776	57.895	26.86	0.59	43.89	2.17
354	355	1.387737	CTGAGAATTTGGGGGCCCA	59.612	57.895	26.86	7.88	45.63	5.36
391	392	0.107459	GGGTTCCATCAGACCAGAGC	60.107	60.000	0.00	0.00	37.68	4.09
396	397	1.132500	CCCTAGGGTTCCATCAGACC	58.868	60.000	20.88	0.00	35.14	3.85
457	475	2.591923	TGGAGCTCTAGTGCAGATAGG	58.408	52.381	18.36	0.08	34.99	2.57
466	484	1.834822	GGGGCGATGGAGCTCTAGT	60.835	63.158	14.64	0.00	37.84	2.57
509	527	3.195610	TCTCGATAGCAAAGCAAGAGGAA	59.804	43.478	0.00	0.00	0.00	3.36
711	741	4.803426	CGTGGTGAGCGAGGAGGC	62.803	72.222	0.00	0.00	0.00	4.70
781	811	0.526662	CTAGGAACTTGACGCGGTCT	59.473	55.000	12.47	0.00	41.75	3.85
864	900	4.375313	ACCAGGATAGGAGAGGTCAATTT	58.625	43.478	0.00	0.00	0.00	1.82
1032	1089	4.827692	ACAACAATAATCTGTACTCGCCA	58.172	39.130	0.00	0.00	0.00	5.69
1072	1141	0.616395	TAGGAGCCATCGTGTCCCAA	60.616	55.000	0.00	0.00	0.00	4.12
1277	1395	0.175989	GTGAGCGGGGTAAGGAAGAG	59.824	60.000	0.00	0.00	0.00	2.85
1393	1547	3.117512	ACCAGGTATTTCAAGGCCCATAG	60.118	47.826	0.00	0.00	0.00	2.23
1672	1829	4.433615	GACAGCTAACATCCGATGAAAGA	58.566	43.478	15.47	0.00	0.00	2.52
1686	1845	0.610174	CTGCCTCACTGGACAGCTAA	59.390	55.000	0.00	0.00	38.35	3.09
1716	1875	1.899814	CATAAGGATACCGCTAGGCCA	59.100	52.381	5.01	0.00	42.76	5.36
1767	1926	6.339730	ACTTGACATGCATCAACAAAGAAAA	58.660	32.000	0.00	0.00	34.84	2.29
1768	1927	5.904941	ACTTGACATGCATCAACAAAGAAA	58.095	33.333	0.00	0.00	34.84	2.52
1787	1946	4.753610	TGAGAGCTTCTTGATCACAACTTG	59.246	41.667	0.00	0.00	32.67	3.16
1826	1985	6.974622	GGTACCAAAACATGCATAGATTTCAG	59.025	38.462	7.15	0.00	0.00	3.02
1884	2043	2.512515	GCAGACCGGAGCACATCC	60.513	66.667	9.46	0.00	45.64	3.51
1993	2170	6.539649	TTCATGTAAAACGAAGACCAAGAG	57.460	37.500	0.00	0.00	0.00	2.85
2057	2239	4.329392	ACATGAGACACATCAAGATTGCA	58.671	39.130	0.00	0.00	37.07	4.08
2105	2287	5.697178	TGCCACATTCAATTTTCACATTCAG	59.303	36.000	0.00	0.00	0.00	3.02
2165	2349	6.927936	CAGTTTATACATAGCAGCTCATGAGT	59.072	38.462	23.38	8.16	0.00	3.41
2206	2392	9.261180	TCTTGATCATAATAAAGAAACTAGCCG	57.739	33.333	0.00	0.00	30.57	5.52
2385	2571	0.032952	ACTTCAACGAGCGGTGCTTA	59.967	50.000	2.51	0.00	39.88	3.09
2392	2578	0.723414	ATCATGCACTTCAACGAGCG	59.277	50.000	0.00	0.00	0.00	5.03
2461	2647	7.989826	AGCATAGCTTTTTAACATCTAACCAG	58.010	34.615	0.00	0.00	33.89	4.00
2462	2648	7.938140	AGCATAGCTTTTTAACATCTAACCA	57.062	32.000	0.00	0.00	33.89	3.67
2481	2684	8.615211	CAACAGCAAAGACAGATTTATAGCATA	58.385	33.333	0.00	0.00	0.00	3.14
2492	2695	1.063912	CAACGCAACAGCAAAGACAGA	59.936	47.619	0.00	0.00	0.00	3.41
2641	2844	5.777802	TCAGAGTGAACTTGAGACAATCTC	58.222	41.667	0.00	0.00	43.65	2.75

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.