AutoCloner

Multiple sequence alignment - TraesCS3B01G362800

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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	TraesCS3B01G362800	chr3B	100.000	3572	0	0	1	3572	574339865	574343436	0.000000e+00	6597.0
1	TraesCS3B01G362800	chr3B	89.698	1058	95	9	1642	2698	574379666	574380710	0.000000e+00	1338.0
2	TraesCS3B01G362800	chr3B	92.511	681	46	3	850	1530	574378966	574379641	0.000000e+00	970.0
3	TraesCS3B01G362800	chr3B	82.555	963	144	18	1657	2606	574523882	574524833	0.000000e+00	826.0
4	TraesCS3B01G362800	chr3B	83.053	832	70	29	1	824	574378201	574378969	0.000000e+00	689.0
5	TraesCS3B01G362800	chr3B	83.026	542	72	10	1000	1534	574523270	574523798	1.160000e-129	473.0
6	TraesCS3B01G362800	chr3B	77.066	593	101	27	15	593	354949274	354949845	3.460000e-80	309.0
7	TraesCS3B01G362800	chr3B	78.862	369	57	17	2	356	144489875	144489514	2.770000e-56	230.0
8	TraesCS3B01G362800	chr3A	91.459	1124	83	8	1536	2653	577077281	577078397	0.000000e+00	1531.0
9	TraesCS3B01G362800	chr3A	93.878	686	42	0	2886	3571	235443480	235444165	0.000000e+00	1035.0
10	TraesCS3B01G362800	chr3A	91.680	637	51	1	902	1538	577076616	577077250	0.000000e+00	881.0
11	TraesCS3B01G362800	chr3A	83.248	979	138	20	1643	2607	577239686	577240652	0.000000e+00	876.0
12	TraesCS3B01G362800	chr3A	77.597	616	103	27	2	603	323106417	323107011	1.230000e-89	340.0
13	TraesCS3B01G362800	chr3A	81.851	281	47	4	1250	1529	577239301	577239578	2.140000e-57	233.0
14	TraesCS3B01G362800	chr3A	86.700	203	27	0	965	1167	577238720	577238922	3.590000e-55	226.0
15	TraesCS3B01G362800	chr3A	87.629	194	17	5	607	796	577076318	577076508	6.000000e-53	219.0
16	TraesCS3B01G362800	chr3D	91.021	1058	85	8	1642	2698	438543427	438544475	0.000000e+00	1419.0
17	TraesCS3B01G362800	chr3D	88.984	935	82	12	600	1530	438542485	438543402	0.000000e+00	1136.0
18	TraesCS3B01G362800	chr3D	77.744	328	51	18	4	320	608399059	608399375	7.880000e-42	182.0
19	TraesCS3B01G362800	chr5B	95.779	687	29	0	2886	3572	377214092	377213406	0.000000e+00	1109.0
20	TraesCS3B01G362800	chr5B	92.422	673	49	2	2887	3559	270887619	270886949	0.000000e+00	959.0
21	TraesCS3B01G362800	chr5B	78.652	356	58	13	99	441	676171894	676171544	1.670000e-53	220.0
22	TraesCS3B01G362800	chr5B	73.752	621	122	31	2	605	506970809	506971405	4.670000e-49	206.0
23	TraesCS3B01G362800	chr4B	95.051	687	34	0	2886	3572	454998482	454997796	0.000000e+00	1081.0
24	TraesCS3B01G362800	chr4B	79.245	159	30	3	2727	2884	498633532	498633688	1.360000e-19	108.0
25	TraesCS3B01G362800	chr4B	82.540	126	16	5	2	124	33318365	33318243	4.880000e-19	106.0
26	TraesCS3B01G362800	chr2A	92.868	687	49	0	2886	3572	60717081	60717767	0.000000e+00	998.0
27	TraesCS3B01G362800	chrUn	92.576	687	51	0	2886	3572	306236632	306235946	0.000000e+00	987.0
28	TraesCS3B01G362800	chrUn	92.576	687	50	1	2886	3572	204502304	204501619	0.000000e+00	985.0
29	TraesCS3B01G362800	chrUn	91.849	687	56	0	2886	3572	219678764	219678078	0.000000e+00	959.0
30	TraesCS3B01G362800	chr7B	91.543	674	57	0	2886	3559	583590825	583591498	0.000000e+00	929.0
31	TraesCS3B01G362800	chr7B	79.911	896	160	7	1666	2545	574486884	574485993	1.080000e-179	640.0
32	TraesCS3B01G362800	chr7B	82.331	532	64	11	994	1520	574487536	574487030	5.480000e-118	435.0
33	TraesCS3B01G362800	chr7A	80.937	619	90	23	2	603	121934289	121934896	6.980000e-127	464.0
34	TraesCS3B01G362800	chr6A	80.606	495	68	22	8	489	600371394	600370915	1.220000e-94	357.0
35	TraesCS3B01G362800	chr6A	84.397	141	20	2	2727	2867	497931376	497931238	1.730000e-28	137.0
36	TraesCS3B01G362800	chr6B	77.868	619	104	21	2	602	3715133	3714530	1.580000e-93	353.0
37	TraesCS3B01G362800	chr2B	77.740	584	109	17	2	574	373091453	373092026	4.420000e-89	339.0
38	TraesCS3B01G362800	chr4A	75.662	604	115	23	2	586	539146148	539146738	4.540000e-69	272.0
39	TraesCS3B01G362800	chr5A	75.893	560	103	25	2	544	698241	698785	1.270000e-64	257.0
40	TraesCS3B01G362800	chr5D	81.500	200	27	8	2	199	420917490	420917299	4.770000e-34	156.0
41	TraesCS3B01G362800	chr5D	85.106	141	20	1	2727	2867	109013892	109014031	3.720000e-30	143.0
42	TraesCS3B01G362800	chr6D	83.544	158	24	2	2727	2884	407585567	407585722	2.870000e-31	147.0
43	TraesCS3B01G362800	chr6D	81.890	127	22	1	2727	2853	457467211	457467336	4.880000e-19	106.0
44	TraesCS3B01G362800	chr6D	81.579	114	14	6	2727	2836	122364452	122364562	1.770000e-13	87.9
45	TraesCS3B01G362800	chr1D	83.333	150	23	2	2719	2867	247844178	247844326	1.730000e-28	137.0
46	TraesCS3B01G362800	chr4D	81.132	159	29	1	2727	2884	372203439	372203281	3.740000e-25	126.0
47	TraesCS3B01G362800	chr4D	80.357	168	30	3	2718	2884	175809722	175809557	1.350000e-24	124.0

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	TraesCS3B01G362800	chr3B	574339865	574343436	3571	False	6597.0	6597	100.000000	1	3572	1	chr3B.!!$F2	3571
1	TraesCS3B01G362800	chr3B	574378201	574380710	2509	False	999.0	1338	88.420667	1	2698	3	chr3B.!!$F3	2697
2	TraesCS3B01G362800	chr3B	574523270	574524833	1563	False	649.5	826	82.790500	1000	2606	2	chr3B.!!$F4	1606
3	TraesCS3B01G362800	chr3B	354949274	354949845	571	False	309.0	309	77.066000	15	593	1	chr3B.!!$F1	578
4	TraesCS3B01G362800	chr3A	235443480	235444165	685	False	1035.0	1035	93.878000	2886	3571	1	chr3A.!!$F1	685
5	TraesCS3B01G362800	chr3A	577076318	577078397	2079	False	877.0	1531	90.256000	607	2653	3	chr3A.!!$F3	2046
6	TraesCS3B01G362800	chr3A	577238720	577240652	1932	False	445.0	876	83.933000	965	2607	3	chr3A.!!$F4	1642
7	TraesCS3B01G362800	chr3A	323106417	323107011	594	False	340.0	340	77.597000	2	603	1	chr3A.!!$F2	601
8	TraesCS3B01G362800	chr3D	438542485	438544475	1990	False	1277.5	1419	90.002500	600	2698	2	chr3D.!!$F2	2098
9	TraesCS3B01G362800	chr5B	377213406	377214092	686	True	1109.0	1109	95.779000	2886	3572	1	chr5B.!!$R2	686
10	TraesCS3B01G362800	chr5B	270886949	270887619	670	True	959.0	959	92.422000	2887	3559	1	chr5B.!!$R1	672
11	TraesCS3B01G362800	chr5B	506970809	506971405	596	False	206.0	206	73.752000	2	605	1	chr5B.!!$F1	603
12	TraesCS3B01G362800	chr4B	454997796	454998482	686	True	1081.0	1081	95.051000	2886	3572	1	chr4B.!!$R2	686
13	TraesCS3B01G362800	chr2A	60717081	60717767	686	False	998.0	998	92.868000	2886	3572	1	chr2A.!!$F1	686
14	TraesCS3B01G362800	chrUn	306235946	306236632	686	True	987.0	987	92.576000	2886	3572	1	chrUn.!!$R3	686
15	TraesCS3B01G362800	chrUn	204501619	204502304	685	True	985.0	985	92.576000	2886	3572	1	chrUn.!!$R1	686
16	TraesCS3B01G362800	chrUn	219678078	219678764	686	True	959.0	959	91.849000	2886	3572	1	chrUn.!!$R2	686
17	TraesCS3B01G362800	chr7B	583590825	583591498	673	False	929.0	929	91.543000	2886	3559	1	chr7B.!!$F1	673
18	TraesCS3B01G362800	chr7B	574485993	574487536	1543	True	537.5	640	81.121000	994	2545	2	chr7B.!!$R1	1551
19	TraesCS3B01G362800	chr7A	121934289	121934896	607	False	464.0	464	80.937000	2	603	1	chr7A.!!$F1	601
20	TraesCS3B01G362800	chr6B	3714530	3715133	603	True	353.0	353	77.868000	2	602	1	chr6B.!!$R1	600
21	TraesCS3B01G362800	chr2B	373091453	373092026	573	False	339.0	339	77.740000	2	574	1	chr2B.!!$F1	572
22	TraesCS3B01G362800	chr4A	539146148	539146738	590	False	272.0	272	75.662000	2	586	1	chr4A.!!$F1	584
23	TraesCS3B01G362800	chr5A	698241	698785	544	False	257.0	257	75.893000	2	544	1	chr5A.!!$F1	542

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
675	728	0.105593	CACTCATGCAGATACGGGCT	59.894	55.0	0.0	0.0	0.0	5.19	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2609	3176	0.107831	TTGACCCGCAAACAGCTACT	59.892	50.0	0.0	0.0	42.61	2.57	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
96	105	2.484065	CCTTTCGTGGTGTGGTTCTGTA	60.484	50.000	0.00	0.00	0.00	2.74
159	185	4.031765	GCGTCCATGTACTATATTGATGCG	59.968	45.833	0.00	0.00	0.00	4.73
272	304	7.228308	GGTTGATTTGAAAAATCATTGACCCAA	59.772	33.333	17.00	1.65	36.63	4.12
388	426	5.239525	AGAAAACTCCGAGAGAAATTGTTGG	59.760	40.000	1.33	0.00	33.32	3.77
401	439	3.979101	ATTGTTGGCCCGATCAAAATT	57.021	38.095	0.00	0.00	0.00	1.82
407	445	2.289320	TGGCCCGATCAAAATTTGGTTG	60.289	45.455	0.00	2.42	0.00	3.77
603	650	7.855784	ATGGACCATAGTGTGTAGATGATTA	57.144	36.000	4.75	0.00	0.00	1.75
612	663	6.499172	AGTGTGTAGATGATTACTGATGTCG	58.501	40.000	0.00	0.00	0.00	4.35
675	728	0.105593	CACTCATGCAGATACGGGCT	59.894	55.000	0.00	0.00	0.00	5.19
691	744	2.795329	GGGCTTGATTCTTCTGTTGGA	58.205	47.619	0.00	0.00	0.00	3.53
721	774	2.097825	GGGAATCAGACAGCTGCATTT	58.902	47.619	15.27	0.32	42.01	2.32
782	840	9.720769	AGATTTAGGAGAGAAATGTAAACGAAA	57.279	29.630	0.00	0.00	0.00	3.46
898	1024	2.735134	CGACAACCGGAAAGTAAAGAGG	59.265	50.000	9.46	0.00	33.91	3.69
934	1060	4.377022	CCCAAAAAGTATGACAACGTCTCG	60.377	45.833	0.00	0.00	33.15	4.04
972	1098	5.202004	ACATAAGAGTACTCCACCGATCTT	58.798	41.667	19.38	7.07	0.00	2.40
1077	1208	1.259840	GCCACATCAACCCCATGCTT	61.260	55.000	0.00	0.00	0.00	3.91
1230	1364	2.297895	CCCCAACGTCATCCCCTCA	61.298	63.158	0.00	0.00	0.00	3.86
1447	1883	4.699522	AGCCGGCCACGTTCTTCC	62.700	66.667	26.15	0.00	38.78	3.46
1468	1904	2.787249	CGCTCTGCCATTTGGACG	59.213	61.111	0.00	0.00	37.39	4.79
1493	1932	3.134127	GCCGGTGGATGAAGGTGC	61.134	66.667	1.90	0.00	0.00	5.01
1508	1947	0.107654	GGTGCCAGCGAAGAAGGTAT	60.108	55.000	0.00	0.00	0.00	2.73
1509	1948	1.138266	GGTGCCAGCGAAGAAGGTATA	59.862	52.381	0.00	0.00	0.00	1.47
1530	1975	7.661847	GGTATACTAGCTAATTTGACCATGCTT	59.338	37.037	2.25	0.00	32.72	3.91
1538	1983	7.035004	GCTAATTTGACCATGCTTCAACATTA	58.965	34.615	7.33	11.64	32.65	1.90
1541	2018	4.299586	TGACCATGCTTCAACATTAGGA	57.700	40.909	0.00	0.00	0.00	2.94

Showing 1 to 25 of 168 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
132	141	6.013842	TCAATATAGTACATGGACGCAGAG	57.986	41.667	1.41	0.00	0.00	3.35
159	185	5.243207	TCATCATCATCATGTGATACTGCC	58.757	41.667	9.50	0.00	45.76	4.85
272	304	9.500785	AATTTTGGATTTGGTTACGATTTTGAT	57.499	25.926	0.00	0.00	0.00	2.57
369	402	2.427506	GCCAACAATTTCTCTCGGAGT	58.572	47.619	4.69	0.00	0.00	3.85
375	411	2.290896	TGATCGGGCCAACAATTTCTCT	60.291	45.455	4.39	0.00	0.00	3.10
388	426	1.731709	GCAACCAAATTTTGATCGGGC	59.268	47.619	10.72	3.70	0.00	6.13
407	445	5.921962	AAGGTCTTCATTTAGAATTGGGC	57.078	39.130	0.00	0.00	35.25	5.36
419	459	7.824779	GGTCTCACAACTAATTAAGGTCTTCAT	59.175	37.037	0.00	0.00	0.00	2.57
555	602	9.897744	CATAGTTTTAAAAAGCTCACATTCAGA	57.102	29.630	1.31	0.00	31.69	3.27
556	603	9.132521	CCATAGTTTTAAAAAGCTCACATTCAG	57.867	33.333	1.31	0.00	31.69	3.02
580	627	6.839134	AGTAATCATCTACACACTATGGTCCA	59.161	38.462	0.00	0.00	0.00	4.02
593	640	7.142021	ACATCACGACATCAGTAATCATCTAC	58.858	38.462	0.00	0.00	0.00	2.59
594	641	7.013274	TGACATCACGACATCAGTAATCATCTA	59.987	37.037	0.00	0.00	0.00	1.98
595	642	6.154203	ACATCACGACATCAGTAATCATCT	57.846	37.500	0.00	0.00	0.00	2.90
596	643	5.979517	TGACATCACGACATCAGTAATCATC	59.020	40.000	0.00	0.00	0.00	2.92
598	645	5.323371	TGACATCACGACATCAGTAATCA	57.677	39.130	0.00	0.00	0.00	2.57
603	650	1.273327	TGCTGACATCACGACATCAGT	59.727	47.619	9.82	0.00	40.61	3.41
612	663	6.367686	TGATAACATCATTGCTGACATCAC	57.632	37.500	0.00	0.00	33.59	3.06
675	728	6.331369	GGACAAATCCAACAGAAGAATCAA	57.669	37.500	0.00	0.00	45.47	2.57
691	744	4.275810	CTGTCTGATTCCCATGGACAAAT	58.724	43.478	15.22	9.93	36.65	2.32
724	780	5.168569	AGACGTGAATTAGCAGATCGAAAA	58.831	37.500	0.00	0.00	0.00	2.29
728	784	5.096954	TCTAGACGTGAATTAGCAGATCG	57.903	43.478	0.00	0.00	0.00	3.69
729	785	8.035165	TCTATCTAGACGTGAATTAGCAGATC	57.965	38.462	0.00	0.00	0.00	2.75
730	786	7.987750	TCTATCTAGACGTGAATTAGCAGAT	57.012	36.000	0.00	0.00	0.00	2.90
731	787	7.987750	ATCTATCTAGACGTGAATTAGCAGA	57.012	36.000	0.00	0.00	34.72	4.26

Showing 1 to 25 of 182 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.