AutoCloner

Multiple sequence alignment - TraesCS4D01G306400

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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	TraesCS4D01G306400	chr4D	100.000	2710	0	0	1	2710	474702269	474699560	0.000000e+00	5005.0
1	TraesCS4D01G306400	chr4D	86.477	1198	102	29	894	2082	474603212	474602066	0.000000e+00	1260.0
2	TraesCS4D01G306400	chr4D	85.366	246	25	6	2432	2667	15916640	15916884	7.500000e-61	244.0
3	TraesCS4D01G306400	chr4D	87.273	220	21	6	533	746	474603614	474603396	7.500000e-61	244.0
4	TraesCS4D01G306400	chr4B	95.170	2174	84	12	2	2169	599171487	599169329	0.000000e+00	3413.0
5	TraesCS4D01G306400	chr4B	95.368	1835	74	6	883	2710	598914020	598912190	0.000000e+00	2907.0
6	TraesCS4D01G306400	chr4B	92.317	833	50	5	2	828	598604195	598603371	0.000000e+00	1171.0
7	TraesCS4D01G306400	chr4B	92.400	829	50	6	2	828	598914846	598914029	0.000000e+00	1170.0
8	TraesCS4D01G306400	chr4B	85.714	791	77	16	1312	2081	598458866	598458091	0.000000e+00	802.0
9	TraesCS4D01G306400	chr4B	95.939	394	16	0	987	1380	598603090	598602697	8.180000e-180	640.0
10	TraesCS4D01G306400	chr4B	92.677	396	24	4	894	1285	598459254	598458860	1.410000e-157	566.0
11	TraesCS4D01G306400	chr4B	95.588	340	13	2	1832	2171	598602368	598602031	6.600000e-151	544.0
12	TraesCS4D01G306400	chr4B	96.084	332	9	2	1467	1795	598602700	598602370	3.070000e-149	538.0
13	TraesCS4D01G306400	chr4B	90.511	137	10	2	862	997	598603370	598603236	7.710000e-41	178.0
14	TraesCS4D01G306400	chr4B	87.805	123	9	6	629	746	598459601	598459480	3.640000e-29	139.0
15	TraesCS4D01G306400	chr4A	90.047	1718	126	23	391	2082	681592487	681594185	0.000000e+00	2183.0
16	TraesCS4D01G306400	chr4A	89.610	1511	103	28	584	2082	681652845	681654313	0.000000e+00	1871.0
17	TraesCS4D01G306400	chr4A	86.747	83	7	1	474	556	681652768	681652846	3.720000e-14	89.8
18	TraesCS4D01G306400	chr5B	88.199	322	25	6	2	321	229823132	229822822	3.300000e-99	372.0
19	TraesCS4D01G306400	chr5B	87.888	322	26	6	2	321	229891600	229891290	1.530000e-97	366.0
20	TraesCS4D01G306400	chrUn	87.888	322	30	5	2	322	103351223	103351536	1.190000e-98	370.0
21	TraesCS4D01G306400	chr1B	87.768	327	25	8	2	325	521185122	521185436	4.260000e-98	368.0
22	TraesCS4D01G306400	chr6B	87.888	322	26	6	2	321	371602637	371602327	1.530000e-97	366.0
23	TraesCS4D01G306400	chr6B	87.616	323	26	9	2	321	84861292	84860981	1.980000e-96	363.0
24	TraesCS4D01G306400	chr3B	78.309	627	85	25	932	1546	13731867	13732454	9.230000e-95	357.0
25	TraesCS4D01G306400	chr3B	79.462	409	73	8	1638	2042	13732588	13732989	2.050000e-71	279.0
26	TraesCS4D01G306400	chr3D	81.114	413	69	5	1638	2044	5175704	5175295	3.370000e-84	322.0
27	TraesCS4D01G306400	chr3D	78.261	437	66	18	1114	1546	9543511	9543922	1.250000e-63	254.0
28	TraesCS4D01G306400	chr3A	74.086	930	136	61	649	1546	11677804	11676948	4.420000e-73	285.0
29	TraesCS4D01G306400	chr3A	73.843	929	140	59	649	1546	11705250	11704394	9.560000e-70	274.0

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	TraesCS4D01G306400	chr4D	474699560	474702269	2709	True	5005.000000	5005	100.0000	1	2710	1	chr4D.!!$R1	2709
1	TraesCS4D01G306400	chr4D	474602066	474603614	1548	True	752.000000	1260	86.8750	533	2082	2	chr4D.!!$R2	1549
2	TraesCS4D01G306400	chr4B	599169329	599171487	2158	True	3413.000000	3413	95.1700	2	2169	1	chr4B.!!$R1	2167
3	TraesCS4D01G306400	chr4B	598912190	598914846	2656	True	2038.500000	2907	93.8840	2	2710	2	chr4B.!!$R4	2708
4	TraesCS4D01G306400	chr4B	598602031	598604195	2164	True	614.200000	1171	94.0878	2	2171	5	chr4B.!!$R3	2169
5	TraesCS4D01G306400	chr4B	598458091	598459601	1510	True	502.333333	802	88.7320	629	2081	3	chr4B.!!$R2	1452
6	TraesCS4D01G306400	chr4A	681592487	681594185	1698	False	2183.000000	2183	90.0470	391	2082	1	chr4A.!!$F1	1691
7	TraesCS4D01G306400	chr4A	681652768	681654313	1545	False	980.400000	1871	88.1785	474	2082	2	chr4A.!!$F2	1608
8	TraesCS4D01G306400	chr3B	13731867	13732989	1122	False	318.000000	357	78.8855	932	2042	2	chr3B.!!$F1	1110
9	TraesCS4D01G306400	chr3A	11676948	11677804	856	True	285.000000	285	74.0860	649	1546	1	chr3A.!!$R1	897
10	TraesCS4D01G306400	chr3A	11704394	11705250	856	True	274.000000	274	73.8430	649	1546	1	chr3A.!!$R2	897

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
409	418	1.541147	CAACCACTGTACATGCCCTTG	59.459	52.381	0.0	0.0	0.0	3.61	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2051	2435	1.969103	AAAACGTACGAGACCGCTAC	58.031	50.0	24.41	0.0	39.95	3.58	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
71	72	8.990163	ATACATTAGTACAAAATTACCCTGGG	57.010	34.615	12.28	12.28	31.96	4.45
77	78	6.257586	AGTACAAAATTACCCTGGGCAAATA	58.742	36.000	14.08	0.00	0.00	1.40
145	150	5.902431	AGATATAGGCAATCAGGGGAGATAC	59.098	44.000	0.00	0.00	0.00	2.24
255	262	4.336713	GTGAGGATTAGAAGAAATGCACCC	59.663	45.833	0.00	0.00	30.24	4.61
324	331	3.174779	GAAGGAACAGAGGGAGTAACCT	58.825	50.000	0.00	0.00	45.57	3.50
375	384	8.718102	TCTAAATTATGTGACAGGCTTAAGAC	57.282	34.615	6.67	2.43	0.00	3.01
382	391	3.743396	GTGACAGGCTTAAGACAAGACAG	59.257	47.826	11.83	0.00	0.00	3.51
392	401	6.402658	GCTTAAGACAAGACAGCCTTATCAAC	60.403	42.308	6.67	0.00	30.81	3.18
395	404	3.412386	ACAAGACAGCCTTATCAACCAC	58.588	45.455	0.00	0.00	32.86	4.16
409	418	1.541147	CAACCACTGTACATGCCCTTG	59.459	52.381	0.00	0.00	0.00	3.61
415	424	2.637872	ACTGTACATGCCCTTGTGTACT	59.362	45.455	14.44	0.00	46.70	2.73
441	450	3.328050	ACTTAGCTAGTGTTTGGGCTTCT	59.672	43.478	0.00	0.00	35.19	2.85
442	451	2.481289	AGCTAGTGTTTGGGCTTCTC	57.519	50.000	0.00	0.00	0.00	2.87
443	452	1.699634	AGCTAGTGTTTGGGCTTCTCA	59.300	47.619	0.00	0.00	0.00	3.27
602	612	7.009179	AGAGTCAAGATACACATCAGGAAAA	57.991	36.000	0.00	0.00	33.21	2.29
638	648	2.353011	CCACCACATGAATGCACCTTTC	60.353	50.000	0.00	0.00	0.00	2.62
641	651	2.173519	CACATGAATGCACCTTTCCCT	58.826	47.619	0.00	0.00	0.00	4.20
864	950	3.021695	TCACTCACCGATCGAGGTAAAT	58.978	45.455	18.66	0.00	43.89	1.40
892	997	1.996292	TCGTGCATGACTAGTTCTGC	58.004	50.000	18.64	18.64	35.21	4.26
1017	1288	2.827190	ATGGACGACTCGCGCCTA	60.827	61.111	0.00	0.00	46.04	3.93
1926	2310	5.047377	TGTGAAATAAATGGAAAGGGTCTGC	60.047	40.000	0.00	0.00	0.00	4.26
2051	2435	7.678218	GCAAAGGCAAGTTCTCATCAGTAATAG	60.678	40.741	0.00	0.00	40.72	1.73
2056	2440	6.143118	GCAAGTTCTCATCAGTAATAGTAGCG	59.857	42.308	0.00	0.00	0.00	4.26
2060	2448	5.622180	TCTCATCAGTAATAGTAGCGGTCT	58.378	41.667	0.00	0.00	0.00	3.85
2061	2449	5.701750	TCTCATCAGTAATAGTAGCGGTCTC	59.298	44.000	0.00	0.00	0.00	3.36
2185	2573	6.433093	TGCAAAGTACTACAGATAGTGAGACA	59.567	38.462	0.00	0.00	41.92	3.41
2194	2582	5.710984	ACAGATAGTGAGACAAAGTAACGG	58.289	41.667	0.00	0.00	0.00	4.44
2213	2603	4.146564	ACGGTTAAGTAGCAACCCAAAAT	58.853	39.130	0.00	0.00	42.11	1.82
2267	2658	9.150348	GTTTCATTTGGAATTAATTGTAGTGGG	57.850	33.333	5.17	0.00	34.91	4.61
2341	2732	3.585862	TCTAAGACATGGCACGTTCTTC	58.414	45.455	0.00	0.00	0.00	2.87
2352	2743	2.095059	GCACGTTCTTCAAGATGGCAAT	60.095	45.455	0.00	0.00	0.00	3.56
2372	2763	5.463061	GCAATATGACCACCAATTTATGCAC	59.537	40.000	0.00	0.00	0.00	4.57
2380	2771	6.162777	ACCACCAATTTATGCACAAACATAC	58.837	36.000	0.00	0.00	32.32	2.39
2386	2777	2.892373	ATGCACAAACATACGTTCCG	57.108	45.000	0.00	0.00	32.91	4.30
2435	2826	4.592426	CGGTTCTCTCCCGGTTTC	57.408	61.111	0.00	0.00	41.78	2.78
2472	2863	0.030235	AGGTTTTCGTTTGGCTTCGC	59.970	50.000	0.00	0.00	0.00	4.70
2530	2921	1.912043	CCTCAACTCTGGTTCCTCCAT	59.088	52.381	0.00	0.00	46.12	3.41
2531	2922	2.355513	CCTCAACTCTGGTTCCTCCATG	60.356	54.545	0.00	0.00	46.12	3.66
2560	2951	0.616371	TTATGGAGTTGGGGGACGTG	59.384	55.000	0.00	0.00	0.00	4.49
2588	2979	1.179814	AAGTCTCCTTGGAGCGACGT	61.180	55.000	11.61	0.00	0.00	4.34
2618	3009	2.892425	GTGGGCGAGATTGGCGAG	60.892	66.667	0.00	0.00	34.76	5.03
2626	3017	3.195698	GATTGGCGAGACGGTGGC	61.196	66.667	0.00	0.00	0.00	5.01
2653	3044	1.191647	CTCGTCGTTCCCTTTTGTTCG	59.808	52.381	0.00	0.00	0.00	3.95
2656	3047	1.082366	CGTTCCCTTTTGTTCGCCG	60.082	57.895	0.00	0.00	0.00	6.46
2667	3058	1.143183	GTTCGCCGGCTTCTCCATA	59.857	57.895	26.68	0.00	34.01	2.74
2690	3081	2.125106	GGCGACGCCTTCTCCAAT	60.125	61.111	31.30	0.00	46.69	3.16

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
69	70	4.099266	TGCCAGTAATCAACATATTTGCCC	59.901	41.667	0.00	0.00	0.00	5.36
71	72	6.332630	ACTTGCCAGTAATCAACATATTTGC	58.667	36.000	0.00	0.00	0.00	3.68
77	78	7.394359	ACTGATTTACTTGCCAGTAATCAACAT	59.606	33.333	10.90	2.00	43.65	2.71
167	172	7.786943	TCTTTCTCCCATTGTATGTATCTCTCT	59.213	37.037	0.00	0.00	0.00	3.10
224	230	9.007901	CATTTCTTCTAATCCTCACATAATCCC	57.992	37.037	0.00	0.00	0.00	3.85
225	231	8.510505	GCATTTCTTCTAATCCTCACATAATCC	58.489	37.037	0.00	0.00	0.00	3.01
303	310	3.174779	AGGTTACTCCCTCTGTTCCTTC	58.825	50.000	0.00	0.00	36.75	3.46
311	318	4.961099	GGTGTACAATAGGTTACTCCCTCT	59.039	45.833	0.00	0.00	35.97	3.69
375	384	3.438087	CAGTGGTTGATAAGGCTGTCTTG	59.562	47.826	4.46	0.00	36.93	3.02
382	391	3.065371	GCATGTACAGTGGTTGATAAGGC	59.935	47.826	0.33	0.00	0.00	4.35
392	401	1.167851	CACAAGGGCATGTACAGTGG	58.832	55.000	0.33	0.00	30.84	4.00
409	418	3.870633	ACTAGCTAAGTGCCAGTACAC	57.129	47.619	0.00	0.00	41.63	2.90
602	612	1.360852	TGGTGGGGCAGAAATACCAAT	59.639	47.619	0.00	0.00	34.26	3.16
641	651	6.037062	CAGTGAAAATGATATTCTACACCGCA	59.963	38.462	0.00	0.00	30.28	5.69
768	795	2.674796	GAGCGTTAAGGTCCTGTCAT	57.325	50.000	0.00	0.00	41.28	3.06
892	997	1.060713	CGTGACACCGCAGAACTAAG	58.939	55.000	0.00	0.00	0.00	2.18
1017	1288	2.048023	CACCGCCCACTGCATGAAT	61.048	57.895	0.00	0.00	41.33	2.57
1474	1781	3.775654	CTTCTCCCGGCGCTTCCT	61.776	66.667	7.64	0.00	0.00	3.36
1732	2106	2.811317	CGGTCTCAACGCTCCTGC	60.811	66.667	0.00	0.00	0.00	4.85
2003	2387	4.204012	CCATGGTGGTAATAATCACGGTT	58.796	43.478	2.57	0.00	34.93	4.44
2051	2435	1.969103	AAAACGTACGAGACCGCTAC	58.031	50.000	24.41	0.00	39.95	3.58
2185	2573	4.756642	GGGTTGCTACTTAACCGTTACTTT	59.243	41.667	0.00	0.00	46.73	2.66
2194	2582	6.208797	AGGAAGATTTTGGGTTGCTACTTAAC	59.791	38.462	0.00	0.00	0.00	2.01
2250	2641	6.893554	ACCTAAACCCCACTACAATTAATTCC	59.106	38.462	0.00	0.00	0.00	3.01
2323	2714	2.254546	TGAAGAACGTGCCATGTCTT	57.745	45.000	0.00	0.00	0.00	3.01
2341	2732	3.289836	TGGTGGTCATATTGCCATCTTG	58.710	45.455	7.01	0.00	36.84	3.02
2352	2743	6.015095	TGTTTGTGCATAAATTGGTGGTCATA	60.015	34.615	12.01	0.00	0.00	2.15
2400	2791	4.040198	GGGTTCCCTCCCCCTCCT	62.040	72.222	0.00	0.00	41.54	3.69
2435	2826	6.980416	AAACCTAACCCTACAGCTATCTAG	57.020	41.667	0.00	0.00	0.00	2.43
2486	2877	1.448985	TTTATTGGACACTGCTCCGC	58.551	50.000	0.00	0.00	32.22	5.54
2530	2921	3.673956	CTCCATAACGCCACCGCCA	62.674	63.158	0.00	0.00	38.22	5.69
2531	2922	2.895372	CTCCATAACGCCACCGCC	60.895	66.667	0.00	0.00	38.22	6.13
2540	2931	0.616891	ACGTCCCCCAACTCCATAAC	59.383	55.000	0.00	0.00	0.00	1.89
2588	2979	1.613317	CGCCCACCCACACTAGATCA	61.613	60.000	0.00	0.00	0.00	2.92
2618	3009	1.519455	CGAGATCAAGGCCACCGTC	60.519	63.158	5.01	0.00	0.00	4.79
2626	3017	0.818296	AGGGAACGACGAGATCAAGG	59.182	55.000	0.00	0.00	0.00	3.61
2627	3018	2.656560	AAGGGAACGACGAGATCAAG	57.343	50.000	0.00	0.00	0.00	3.02
2653	3044	2.281139	GCCTATGGAGAAGCCGGC	60.281	66.667	21.89	21.89	40.66	6.13
2656	3047	1.369321	CCGAGCCTATGGAGAAGCC	59.631	63.158	0.00	0.00	37.10	4.35
2683	3074	0.824109	CCACTCGTAGGCATTGGAGA	59.176	55.000	5.52	0.00	0.00	3.71
2690	3081	3.066190	CCCGACCACTCGTAGGCA	61.066	66.667	0.00	0.00	38.32	4.75

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.