AutoCloner

Multiple sequence alignment - TraesCS5D01G208000

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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	TraesCS5D01G208000	chr5D	100.000	5245	0	0	1	5245	314381690	314386934	0.000000e+00	9686.0
1	TraesCS5D01G208000	chr5A	95.563	4530	125	22	768	5243	408180614	408185121	0.000000e+00	7182.0
2	TraesCS5D01G208000	chr5A	90.541	740	62	5	1	733	408179875	408180613	0.000000e+00	972.0
3	TraesCS5D01G208000	chr5B	94.035	4644	153	34	677	5243	362117237	362121833	0.000000e+00	6927.0
4	TraesCS5D01G208000	chr5B	82.520	492	80	6	1	487	290131985	290132475	1.350000e-115	427.0
5	TraesCS5D01G208000	chr5B	97.674	43	1	0	2941	2983	215889683	215889725	2.030000e-09	75.0
6	TraesCS5D01G208000	chr7D	86.084	618	65	14	1640	2249	40486836	40486232	0.000000e+00	645.0
7	TraesCS5D01G208000	chr7D	83.146	178	14	4	4430	4595	560912978	560912805	1.180000e-31	148.0
8	TraesCS5D01G208000	chr7D	89.474	57	6	0	2940	2996	242779551	242779495	7.290000e-09	73.1
9	TraesCS5D01G208000	chr6A	84.384	666	84	15	1586	2249	68578443	68577796	2.060000e-178	636.0
10	TraesCS5D01G208000	chr6A	86.085	539	65	5	3015	3547	21392569	21392035	5.890000e-159	571.0
11	TraesCS5D01G208000	chr6A	82.203	118	12	3	4432	4540	251145175	251145058	5.590000e-15	93.5
12	TraesCS5D01G208000	chr6A	89.062	64	5	2	2940	3002	145131722	145131660	1.570000e-10	78.7
13	TraesCS5D01G208000	chr6B	86.751	551	62	8	3015	3559	36045521	36044976	2.090000e-168	603.0
14	TraesCS5D01G208000	chr6D	86.431	538	63	7	3015	3547	21364505	21363973	9.790000e-162	580.0
15	TraesCS5D01G208000	chr6D	87.678	422	44	5	3015	3431	21059437	21059019	7.900000e-133	484.0
16	TraesCS5D01G208000	chr6D	87.500	424	43	7	3015	3431	21820564	21820144	1.020000e-131	481.0
17	TraesCS5D01G208000	chr6D	97.674	43	1	0	2941	2983	292073372	292073414	2.030000e-09	75.0
18	TraesCS5D01G208000	chr6D	97.674	43	1	0	2941	2983	304279412	304279454	2.030000e-09	75.0
19	TraesCS5D01G208000	chr6D	97.368	38	1	0	3015	3052	20961190	20961227	1.220000e-06	65.8
20	TraesCS5D01G208000	chr2D	86.431	538	60	8	3015	3547	24677702	24677173	1.270000e-160	577.0
21	TraesCS5D01G208000	chr2D	80.357	280	46	3	1	280	305935100	305935370	2.480000e-48	204.0
22	TraesCS5D01G208000	chr2D	88.757	169	11	5	4464	4631	341694017	341693856	3.200000e-47	200.0
23	TraesCS5D01G208000	chr2D	88.757	169	11	5	4464	4631	378729244	378729405	3.200000e-47	200.0
24	TraesCS5D01G208000	chr4A	80.491	692	111	14	1	682	593824673	593825350	4.690000e-140	508.0
25	TraesCS5D01G208000	chr1D	79.913	687	125	10	8	683	355127555	355126871	4.720000e-135	492.0
26	TraesCS5D01G208000	chr1D	81.239	565	98	8	43	601	38297299	38296737	2.880000e-122	449.0
27	TraesCS5D01G208000	chr1D	87.719	171	15	3	4464	4634	11141189	11141353	1.490000e-45	195.0
28	TraesCS5D01G208000	chr4D	84.263	502	69	8	1	499	458089058	458089552	1.020000e-131	481.0
29	TraesCS5D01G208000	chr4D	88.166	169	14	3	4464	4632	370775520	370775682	4.140000e-46	196.0
30	TraesCS5D01G208000	chr4D	97.674	43	1	0	2941	2983	107698228	107698270	2.030000e-09	75.0
31	TraesCS5D01G208000	chr1A	78.623	697	127	14	1	683	454740510	454739822	4.820000e-120	442.0
32	TraesCS5D01G208000	chr1A	76.471	221	36	12	4970	5174	497854799	497855019	7.180000e-19	106.0
33	TraesCS5D01G208000	chr1A	81.513	119	16	2	571	683	300923400	300923282	5.590000e-15	93.5
34	TraesCS5D01G208000	chr3A	79.398	631	119	9	1	624	468656624	468657250	8.070000e-118	435.0
35	TraesCS5D01G208000	chr3A	84.390	205	21	8	4431	4632	725447635	725447831	1.930000e-44	191.0
36	TraesCS5D01G208000	chr3A	83.000	100	12	4	526	622	743845380	743845477	9.360000e-13	86.1
37	TraesCS5D01G208000	chr3A	95.455	44	2	0	2940	2983	645150476	645150519	2.620000e-08	71.3
38	TraesCS5D01G208000	chr3D	79.114	632	115	14	2	627	517116657	517117277	2.260000e-113	420.0
39	TraesCS5D01G208000	chr3D	88.506	174	14	4	4464	4637	505407903	505407736	6.880000e-49	206.0
40	TraesCS5D01G208000	chr3D	100.000	33	0	0	4432	4464	319867758	319867726	1.580000e-05	62.1
41	TraesCS5D01G208000	chr3B	84.615	221	16	4	4423	4631	353997211	353997425	2.480000e-48	204.0
42	TraesCS5D01G208000	chr2A	79.231	130	14	6	4423	4540	373521183	373521055	1.570000e-10	78.7
43	TraesCS5D01G208000	chr2A	77.519	129	16	10	5062	5177	515941044	515940916	1.220000e-06	65.8
44	TraesCS5D01G208000	chr2B	80.899	89	8	1	4432	4511	373693063	373692975	1.580000e-05	62.1

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	TraesCS5D01G208000	chr5D	314381690	314386934	5244	False	9686	9686	100.000	1	5245	1	chr5D.!!$F1	5244
1	TraesCS5D01G208000	chr5A	408179875	408185121	5246	False	4077	7182	93.052	1	5243	2	chr5A.!!$F1	5242
2	TraesCS5D01G208000	chr5B	362117237	362121833	4596	False	6927	6927	94.035	677	5243	1	chr5B.!!$F3	4566
3	TraesCS5D01G208000	chr7D	40486232	40486836	604	True	645	645	86.084	1640	2249	1	chr7D.!!$R1	609
4	TraesCS5D01G208000	chr6A	68577796	68578443	647	True	636	636	84.384	1586	2249	1	chr6A.!!$R2	663
5	TraesCS5D01G208000	chr6A	21392035	21392569	534	True	571	571	86.085	3015	3547	1	chr6A.!!$R1	532
6	TraesCS5D01G208000	chr6B	36044976	36045521	545	True	603	603	86.751	3015	3559	1	chr6B.!!$R1	544
7	TraesCS5D01G208000	chr6D	21363973	21364505	532	True	580	580	86.431	3015	3547	1	chr6D.!!$R2	532
8	TraesCS5D01G208000	chr2D	24677173	24677702	529	True	577	577	86.431	3015	3547	1	chr2D.!!$R1	532
9	TraesCS5D01G208000	chr4A	593824673	593825350	677	False	508	508	80.491	1	682	1	chr4A.!!$F1	681
10	TraesCS5D01G208000	chr1D	355126871	355127555	684	True	492	492	79.913	8	683	1	chr1D.!!$R2	675
11	TraesCS5D01G208000	chr1D	38296737	38297299	562	True	449	449	81.239	43	601	1	chr1D.!!$R1	558
12	TraesCS5D01G208000	chr1A	454739822	454740510	688	True	442	442	78.623	1	683	1	chr1A.!!$R2	682
13	TraesCS5D01G208000	chr3A	468656624	468657250	626	False	435	435	79.398	1	624	1	chr3A.!!$F1	623
14	TraesCS5D01G208000	chr3D	517116657	517117277	620	False	420	420	79.114	2	627	1	chr3D.!!$F1	625

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	Hairpin	End Stability	Orientation
853	883	0.105224	TGACGGAGAAGACGCCAAAA	59.895	50.000	0.00	35.72	2.44	F
1193	1242	1.509463	CTGCTGCATCGCCATTTGT	59.491	52.632	1.31	0.00	2.83	F
2175	2232	1.004044	CTCATGTCTGTGAAAGGGCCT	59.996	52.381	0.00	0.00	5.19	F
3348	3434	1.119684	AAAGTTGGTGGTTCTTGCCC	58.880	50.000	0.00	0.00	5.36	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1803	1858	1.885887	CCACCAAACCGACAACATCAT	59.114	47.619	0.00	0.00	0.00	2.45	R
3136	3216	2.499756	TAGCACAATCCGCGCACAGA	62.500	55.000	8.75	0.19	0.00	3.41	R
3506	3593	0.609131	GTAAGGCTGCTTGGCAAGGA	60.609	55.000	27.25	23.99	44.55	3.36	R
4893	5008	1.672898	CGAGGTTCCCACGGGTAAA	59.327	57.895	1.07	0.00	34.18	2.01	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
224	226	2.203126	CTCCTCCATTGCGGCCTC	60.203	66.667	0.00	0.00	33.14	4.70
305	307	1.187087	GGATCCTCCGACACTTCTGT	58.813	55.000	3.84	0.00	0.00	3.41
503	512	0.968393	GGTTGGCCAGGCGGATAAAA	60.968	55.000	5.11	0.00	34.09	1.52
569	581	1.450312	CTTCGGCTTGCGGGAGAAT	60.450	57.895	2.74	0.00	0.00	2.40
583	595	0.179084	GAGAATTCGCATCCGGACCA	60.179	55.000	6.12	0.00	34.56	4.02
752	775	3.911661	ACACGGTGTGACTAGAACTAC	57.088	47.619	13.92	0.00	36.96	2.73
795	825	0.738762	CGTGGAGTGCTCTGTCCATG	60.739	60.000	0.00	0.00	44.71	3.66
853	883	0.105224	TGACGGAGAAGACGCCAAAA	59.895	50.000	0.00	0.00	35.72	2.44
1192	1241	1.876714	GCTGCTGCATCGCCATTTG	60.877	57.895	11.11	0.00	39.41	2.32
1193	1242	1.509463	CTGCTGCATCGCCATTTGT	59.491	52.632	1.31	0.00	0.00	2.83
1197	1246	2.580326	GCATCGCCATTTGTGCCG	60.580	61.111	0.00	0.00	0.00	5.69
1566	1615	4.681978	GCCACCGGAGCGTTCACT	62.682	66.667	9.46	0.00	0.00	3.41
1803	1858	4.037565	TCTTCTTGTCAGAGTTTACGCAGA	59.962	41.667	0.00	0.00	0.00	4.26
2065	2121	1.307097	GCCTGATGCTCCACATTCTC	58.693	55.000	0.00	0.00	39.84	2.87
2175	2232	1.004044	CTCATGTCTGTGAAAGGGCCT	59.996	52.381	0.00	0.00	0.00	5.19
2301	2358	5.822132	AAGTATTGAGCTGGCTCTGATAT	57.178	39.130	20.97	12.31	43.12	1.63
2335	2398	3.197983	TCCCTGTGGAATACTTGGGAAT	58.802	45.455	0.00	0.00	44.11	3.01
2362	2425	6.311200	GCATATTGGATGTTTCTTTGGTGTTC	59.689	38.462	0.00	0.00	0.00	3.18
2396	2465	4.703093	TGACCTTTTTCCAACTTCGAAAGT	59.297	37.500	0.00	0.00	45.46	2.66
2413	2482	9.370126	CTTCGAAAGTTGTTTGAACTACATAAG	57.630	33.333	0.00	3.90	37.16	1.73
2551	2624	2.566952	ATCTGCGGTTAAAGCATTGC	57.433	45.000	0.00	0.00	44.26	3.56
2937	3017	6.034256	GCATACAGAACATTCAGCAACAAATC	59.966	38.462	0.00	0.00	0.00	2.17
2939	3019	3.916172	CAGAACATTCAGCAACAAATCGG	59.084	43.478	0.00	0.00	0.00	4.18
3013	3093	5.103000	AGTATTTAGTACTGTGCTGCTTCG	58.897	41.667	5.39	0.00	42.06	3.79
3047	3127	6.012658	TGTTGACCTTCTTTATTCACATGC	57.987	37.500	0.00	0.00	0.00	4.06
3348	3434	1.119684	AAAGTTGGTGGTTCTTGCCC	58.880	50.000	0.00	0.00	0.00	5.36
3441	3528	4.454678	TGCTGTCATGAGTTCTTTGAGTT	58.545	39.130	0.00	0.00	0.00	3.01
3506	3593	7.328277	TGTGTTTGCAGAACATTAGTTAGTT	57.672	32.000	14.59	0.00	38.30	2.24
4153	4254	3.538591	TGTGTGAATGGATGATGAGCTC	58.461	45.455	6.82	6.82	0.00	4.09
4213	4314	0.034756	TGAACTGGTGACCATGACGG	59.965	55.000	4.03	0.00	42.50	4.79
4299	4400	7.015682	TGTTTATTCCCAAGTTGCCTGAAATTA	59.984	33.333	0.00	0.00	0.00	1.40
4357	4458	9.636879	AGATCAACATCTAAATCATCATCGTAG	57.363	33.333	0.00	0.00	37.63	3.51
4372	4473	2.849942	TCGTAGATGCCCCATTTCATG	58.150	47.619	0.00	0.00	0.00	3.07
4395	4496	9.303116	CATGTACTCCCTCTATCCATATATACC	57.697	40.741	0.00	0.00	0.00	2.73
4406	4509	5.525454	TCCATATATACCGGGTCTAGTGT	57.475	43.478	6.32	0.00	0.00	3.55
4451	4554	9.712359	ATTACGTTTTTCAAGACTAACTTTGAC	57.288	29.630	0.00	0.00	36.61	3.18
4488	4603	6.348498	ACATGCAAGTTACATAGAGCATACA	58.652	36.000	0.00	0.00	40.38	2.29
4594	4709	3.253432	GTCAAAGGGCAGTCTCGAAAAAT	59.747	43.478	0.00	0.00	0.00	1.82
4599	4714	3.199946	AGGGCAGTCTCGAAAAATGGATA	59.800	43.478	0.00	0.00	0.00	2.59
4602	4717	4.876107	GGCAGTCTCGAAAAATGGATAAGA	59.124	41.667	0.00	0.00	0.00	2.10
4606	4721	5.189934	AGTCTCGAAAAATGGATAAGACCCT	59.810	40.000	0.00	0.00	33.76	4.34
4607	4722	6.383147	AGTCTCGAAAAATGGATAAGACCCTA	59.617	38.462	0.00	0.00	33.76	3.53
4608	4723	7.071321	AGTCTCGAAAAATGGATAAGACCCTAT	59.929	37.037	0.00	0.00	33.76	2.57
4609	4724	8.365647	GTCTCGAAAAATGGATAAGACCCTATA	58.634	37.037	0.00	0.00	0.00	1.31
4722	4837	3.726557	TGAGGGAAGGAACTACTACGA	57.273	47.619	0.00	0.00	38.49	3.43
4739	4854	8.343366	ACTACTACGATTCATGTACACACATAG	58.657	37.037	0.00	0.00	43.73	2.23
4893	5008	6.489603	TGGCCAACAAATATATAATCGGGAT	58.510	36.000	0.61	0.00	0.00	3.85
4942	5057	8.641498	AGATCACCCACATTGATAAAATATCC	57.359	34.615	0.00	0.00	33.70	2.59
4944	5059	8.780616	ATCACCCACATTGATAAAATATCCAA	57.219	30.769	0.00	0.00	31.68	3.53
5033	5160	8.993404	AGGGATATATTCCTATTCCTACGTAC	57.007	38.462	11.24	0.00	44.75	3.67

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
152	154	2.988684	GTGGCAATGGGCGTGGAA	60.989	61.111	0.00	0.00	46.16	3.53
300	302	2.202866	GGAGATGGAGCCGACAGAA	58.797	57.895	0.00	0.00	0.00	3.02
642	658	2.049618	GCAAATTTCCCGCGTGCA	60.050	55.556	4.92	0.00	35.28	4.57
750	773	2.801063	CGGACTATTTTTCTCGCCGTA	58.199	47.619	0.00	0.00	33.14	4.02
752	775	1.587034	GACGGACTATTTTTCTCGCCG	59.413	52.381	0.00	0.00	42.64	6.46
795	825	2.094700	GCCTTTCCCATTTCTCGAAACC	60.095	50.000	0.00	0.00	32.51	3.27
853	883	0.400213	TCCGATTGGAGCAGGTTTGT	59.600	50.000	0.00	0.00	40.17	2.83
1192	1241	1.880027	ACAAAGACCAAATCTCGGCAC	59.120	47.619	0.00	0.00	36.27	5.01
1193	1242	2.270352	ACAAAGACCAAATCTCGGCA	57.730	45.000	0.00	0.00	36.27	5.69
1197	1246	5.205565	GTCGTCAAACAAAGACCAAATCTC	58.794	41.667	0.00	0.00	36.27	2.75
1803	1858	1.885887	CCACCAAACCGACAACATCAT	59.114	47.619	0.00	0.00	0.00	2.45
2141	2197	7.714813	TCACAGACATGAGACAAAATTGTTCTA	59.285	33.333	0.00	0.00	42.43	2.10
2148	2204	5.242393	CCCTTTCACAGACATGAGACAAAAT	59.758	40.000	0.00	0.00	0.00	1.82
2175	2232	9.160496	GAGATTGCTGAATTTTCTAAGAGAGAA	57.840	33.333	0.00	0.00	42.69	2.87
2335	2398	6.164876	CACCAAAGAAACATCCAATATGCAA	58.835	36.000	0.00	0.00	0.00	4.08
2362	2425	5.782047	TGGAAAAAGGTCAAAGTATGCATG	58.218	37.500	10.16	0.00	0.00	4.06
2396	2465	9.748708	ACTTACGTACTTATGTAGTTCAAACAA	57.251	29.630	0.00	0.00	38.33	2.83
2413	2482	5.695816	TGGTATGTCCAAAACACTTACGTAC	59.304	40.000	0.00	0.00	44.12	3.67
2551	2624	8.080417	CCTTGCAACAAATATAAGGATGAGATG	58.920	37.037	0.00	0.00	40.18	2.90
2868	2948	8.364142	GCCATGCCTATATATAGAAAGTAGGAG	58.636	40.741	19.51	2.66	35.08	3.69
2939	3019	5.303845	ACTTATTATGGAACGGAGGGAGTAC	59.696	44.000	0.00	0.00	0.00	2.73
3013	3093	4.381411	AGAAGGTCAACAGTAGCAGAAAC	58.619	43.478	0.00	0.00	0.00	2.78
3136	3216	2.499756	TAGCACAATCCGCGCACAGA	62.500	55.000	8.75	0.19	0.00	3.41
3348	3434	8.807948	TTTCCTAGGAATATTGAAGGAACAAG	57.192	34.615	24.82	0.00	44.04	3.16
3441	3528	7.327214	TGACAAAGTACTATACACATGCATGA	58.673	34.615	32.75	11.53	0.00	3.07
3506	3593	0.609131	GTAAGGCTGCTTGGCAAGGA	60.609	55.000	27.25	23.99	44.55	3.36
3622	3709	7.760794	CAGCTTAGTGCATTCAATTATTCCAAA	59.239	33.333	0.00	0.00	45.94	3.28
3632	3719	4.516323	TGATAGCAGCTTAGTGCATTCAA	58.484	39.130	0.00	0.00	46.60	2.69
3786	3882	8.486210	GGCCAAAATTAAAGAGGGATAGAAAAT	58.514	33.333	0.00	0.00	0.00	1.82
4312	4413	9.209175	GTTGATCTAACGATTTATGAAGGCTAT	57.791	33.333	0.00	0.00	0.00	2.97
4313	4414	8.201464	TGTTGATCTAACGATTTATGAAGGCTA	58.799	33.333	0.00	0.00	42.34	3.93
4372	4473	6.941436	CCGGTATATATGGATAGAGGGAGTAC	59.059	46.154	0.00	0.00	0.00	2.73
4426	4529	8.177013	GGTCAAAGTTAGTCTTGAAAAACGTAA	58.823	33.333	0.00	0.00	36.40	3.18
4488	4603	5.122396	GCTCCTTTCACGTATGAATTTGACT	59.878	40.000	0.00	0.00	44.36	3.41
4602	4717	8.568556	TCCCTCCATCCATATATATATAGGGT	57.431	38.462	25.41	14.52	40.15	4.34
4722	4837	6.115446	CCCAGAACTATGTGTGTACATGAAT	58.885	40.000	0.00	0.00	46.63	2.57
4739	4854	6.374333	TGCAATTCTATTCAGTAACCCAGAAC	59.626	38.462	0.00	0.00	0.00	3.01
4893	5008	1.672898	CGAGGTTCCCACGGGTAAA	59.327	57.895	1.07	0.00	34.18	2.01
4902	5017	2.101082	GTGATCTTAGACCGAGGTTCCC	59.899	54.545	0.00	0.00	0.00	3.97
4919	5034	8.780616	TTGGATATTTTATCAATGTGGGTGAT	57.219	30.769	0.00	0.00	39.12	3.06
4920	5035	7.201902	GCTTGGATATTTTATCAATGTGGGTGA	60.202	37.037	0.00	0.00	0.00	4.02
4942	5057	4.865776	TCAAAATTCCTGTAAACGGCTTG	58.134	39.130	0.00	0.00	0.00	4.01
4944	5059	4.825085	TCTTCAAAATTCCTGTAAACGGCT	59.175	37.500	0.00	0.00	0.00	5.52

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.