AutoCloner

Multiple sequence alignment - TraesCS1B01G191300

Loading Multiple Alignment...

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	TraesCS1B01G191300	chr1B	100.000	2273	0	0	1	2273	342121447	342123719	0.000000e+00	4198.0
1	TraesCS1B01G191300	chr1B	99.346	153	1	0	363	515	342121756	342121908	6.180000e-71	278.0
2	TraesCS1B01G191300	chr1B	99.346	153	1	0	310	462	342121809	342121961	6.180000e-71	278.0
3	TraesCS1B01G191300	chr1B	85.897	234	32	1	1	233	613948816	613948583	4.850000e-62	248.0
4	TraesCS1B01G191300	chr1B	92.029	138	11	0	1376	1513	176763749	176763612	6.410000e-46	195.0
5	TraesCS1B01G191300	chr1B	99.010	101	1	0	416	516	342121756	342121856	4.990000e-42	182.0
6	TraesCS1B01G191300	chr1B	99.010	101	1	0	310	410	342121862	342121962	4.990000e-42	182.0
7	TraesCS1B01G191300	chr1B	100.000	48	0	0	310	357	342121915	342121962	3.110000e-14	89.8
8	TraesCS1B01G191300	chr1D	92.462	597	26	9	803	1381	236808653	236809248	0.000000e+00	835.0
9	TraesCS1B01G191300	chr1D	92.157	408	15	4	1507	1913	236809242	236809633	5.480000e-156	560.0
10	TraesCS1B01G191300	chr5B	98.704	463	5	1	1	462	692366887	692367349	0.000000e+00	821.0
11	TraesCS1B01G191300	chr5B	98.387	434	5	1	363	794	692367197	692367630	0.000000e+00	761.0
12	TraesCS1B01G191300	chr5B	100.000	101	0	0	310	410	692367250	692367350	1.070000e-43	187.0
13	TraesCS1B01G191300	chr5B	100.000	48	0	0	310	357	692367303	692367350	3.110000e-14	89.8
14	TraesCS1B01G191300	chr1A	90.070	574	31	11	804	1369	308811608	308811053	0.000000e+00	721.0
15	TraesCS1B01G191300	chr1A	94.225	329	18	1	468	795	323962646	323962318	3.370000e-138	501.0
16	TraesCS1B01G191300	chr1A	91.643	347	21	2	1575	1913	308810991	308810645	7.350000e-130	473.0
17	TraesCS1B01G191300	chr1A	93.671	316	17	3	1	313	323962984	323962669	9.510000e-129	470.0
18	TraesCS1B01G191300	chr5A	95.266	338	15	1	464	800	612160345	612160008	3.320000e-148	534.0
19	TraesCS1B01G191300	chr5A	93.994	333	19	1	464	795	612160742	612160410	9.370000e-139	503.0
20	TraesCS1B01G191300	chr5A	93.949	314	18	1	1	313	612161074	612160761	7.350000e-130	473.0
21	TraesCS1B01G191300	chr5A	91.111	225	17	3	573	796	612160009	612159787	3.670000e-78	302.0
22	TraesCS1B01G191300	chr5A	83.183	333	49	4	472	800	481101252	481101581	4.750000e-77	298.0
23	TraesCS1B01G191300	chr5A	84.681	235	34	2	4	237	513969564	513969331	1.360000e-57	233.0
24	TraesCS1B01G191300	chr5A	92.647	136	10	0	1375	1510	32937938	32938073	1.780000e-46	196.0
25	TraesCS1B01G191300	chr5A	100.000	55	0	0	356	410	612160347	612160293	3.990000e-18	102.0
26	TraesCS1B01G191300	chr5A	100.000	54	0	0	409	462	612160347	612160294	1.440000e-17	100.0
27	TraesCS1B01G191300	chr5A	98.182	55	1	0	356	410	612160744	612160690	1.860000e-16	97.1
28	TraesCS1B01G191300	chr5A	98.148	54	1	0	409	462	612160744	612160691	6.680000e-16	95.3
29	TraesCS1B01G191300	chr5A	100.000	48	0	0	310	357	612160340	612160293	3.110000e-14	89.8
30	TraesCS1B01G191300	chr5A	97.917	48	1	0	310	357	612160737	612160690	1.450000e-12	84.2
31	TraesCS1B01G191300	chr5A	95.556	45	2	0	267	311	612160410	612160366	3.130000e-09	73.1
32	TraesCS1B01G191300	chr4A	94.721	341	14	2	464	800	6020190	6019850	5.560000e-146	527.0
33	TraesCS1B01G191300	chr4A	93.750	320	13	4	1	313	6020528	6020209	7.350000e-130	473.0
34	TraesCS1B01G191300	chr6D	90.769	260	15	4	2022	2273	439414648	439414390	2.800000e-89	339.0
35	TraesCS1B01G191300	chr7B	85.163	337	34	11	464	794	583929901	583930227	4.680000e-87	331.0
36	TraesCS1B01G191300	chr7B	84.615	338	36	11	464	795	583929228	583929555	2.820000e-84	322.0
37	TraesCS1B01G191300	chr7B	78.723	423	57	10	1	408	583928874	583929278	3.750000e-63	252.0
38	TraesCS1B01G191300	chr7B	78.302	424	58	11	1	408	583928236	583928641	2.260000e-60	243.0
39	TraesCS1B01G191300	chr7B	85.455	165	13	6	464	625	583928591	583928747	6.500000e-36	161.0
40	TraesCS1B01G191300	chr7B	93.478	46	3	0	310	355	583928596	583928641	4.050000e-08	69.4
41	TraesCS1B01G191300	chr5D	88.341	223	16	3	2059	2272	230420787	230420566	2.240000e-65	259.0
42	TraesCS1B01G191300	chr5D	91.549	142	10	2	1375	1514	485934442	485934583	6.410000e-46	195.0
43	TraesCS1B01G191300	chr5D	85.027	187	27	1	2021	2206	230419113	230419299	2.980000e-44	189.0
44	TraesCS1B01G191300	chr5D	83.838	198	26	4	2022	2215	518916752	518916557	1.390000e-42	183.0
45	TraesCS1B01G191300	chr5D	92.683	41	3	0	1942	1982	456566111	456566151	2.440000e-05	60.2
46	TraesCS1B01G191300	chr4B	78.538	424	57	10	1	408	47656119	47656524	4.850000e-62	248.0
47	TraesCS1B01G191300	chr4B	92.086	139	11	0	1375	1513	403331547	403331409	1.780000e-46	196.0
48	TraesCS1B01G191300	chr4B	92.086	139	10	1	1375	1512	214045489	214045351	6.410000e-46	195.0
49	TraesCS1B01G191300	chr2A	87.027	185	23	1	2022	2205	742303860	742303676	8.230000e-50	207.0
50	TraesCS1B01G191300	chr3A	93.893	131	8	0	1378	1508	732394967	732394837	4.950000e-47	198.0
51	TraesCS1B01G191300	chr2D	85.128	195	28	1	2022	2215	17160582	17160388	4.950000e-47	198.0
52	TraesCS1B01G191300	chr2D	85.263	190	22	4	2021	2206	13618916	13619103	8.290000e-45	191.0
53	TraesCS1B01G191300	chr7D	92.029	138	11	0	1375	1512	564074973	564074836	6.410000e-46	195.0
54	TraesCS1B01G191300	chr7A	90.541	148	13	1	1376	1522	681028441	681028294	6.410000e-46	195.0
55	TraesCS1B01G191300	chr7A	83.871	186	29	1	2022	2206	200598134	200598319	2.320000e-40	176.0
56	TraesCS1B01G191300	chr7A	82.383	193	30	4	2017	2206	149419980	149420171	5.020000e-37	165.0
57	TraesCS1B01G191300	chr3D	90.845	142	11	2	1375	1514	405859327	405859186	2.980000e-44	189.0
58	TraesCS1B01G191300	chr3B	91.429	105	9	0	1915	2019	467893167	467893271	6.540000e-31	145.0

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	TraesCS1B01G191300	chr1B	342121447	342123719	2272	False	867.966667	4198	99.452000	1	2273	6	chr1B.!!$F1	2272
1	TraesCS1B01G191300	chr1D	236808653	236809633	980	False	697.500000	835	92.309500	803	1913	2	chr1D.!!$F1	1110
2	TraesCS1B01G191300	chr5B	692366887	692367630	743	False	464.700000	821	99.272750	1	794	4	chr5B.!!$F1	793
3	TraesCS1B01G191300	chr1A	308810645	308811608	963	True	597.000000	721	90.856500	804	1913	2	chr1A.!!$R1	1109
4	TraesCS1B01G191300	chr1A	323962318	323962984	666	True	485.500000	501	93.948000	1	795	2	chr1A.!!$R2	794
5	TraesCS1B01G191300	chr5A	612159787	612161074	1287	True	223.045455	534	96.738455	1	800	11	chr5A.!!$R2	799
6	TraesCS1B01G191300	chr4A	6019850	6020528	678	True	500.000000	527	94.235500	1	800	2	chr4A.!!$R1	799
7	TraesCS1B01G191300	chr7B	583928236	583930227	1991	False	229.733333	331	84.289333	1	795	6	chr7B.!!$F1	794

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
441	1097	0.035439	TTTCCACCGATTGCTCCTCC	60.035	55.0	0.0	0.0	0.0	4.3	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1494	3257	0.037734	CCCCTAAGGCTTTGTTCGGT	59.962	55.0	4.45	0.0	0.0	4.69	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
171	175	3.702555	GAACACGTTCGCTGCGCT	61.703	61.111	18.65	0.00	0.00	5.92
434	1090	3.824414	GTGGTAAGTTTCCACCGATTG	57.176	47.619	18.35	0.00	46.63	2.67
435	1091	2.095415	GTGGTAAGTTTCCACCGATTGC	60.095	50.000	18.35	0.00	46.63	3.56
436	1092	2.224670	TGGTAAGTTTCCACCGATTGCT	60.225	45.455	0.00	0.00	37.66	3.91
437	1093	2.418976	GGTAAGTTTCCACCGATTGCTC	59.581	50.000	0.00	0.00	0.00	4.26
438	1094	1.534729	AAGTTTCCACCGATTGCTCC	58.465	50.000	0.00	0.00	0.00	4.70
439	1095	0.693049	AGTTTCCACCGATTGCTCCT	59.307	50.000	0.00	0.00	0.00	3.69
440	1096	1.087501	GTTTCCACCGATTGCTCCTC	58.912	55.000	0.00	0.00	0.00	3.71
441	1097	0.035439	TTTCCACCGATTGCTCCTCC	60.035	55.000	0.00	0.00	0.00	4.30
442	1098	2.202932	CCACCGATTGCTCCTCCG	60.203	66.667	0.00	0.00	0.00	4.63
443	1099	2.892425	CACCGATTGCTCCTCCGC	60.892	66.667	0.00	0.00	0.00	5.54
444	1100	3.390521	ACCGATTGCTCCTCCGCA	61.391	61.111	0.00	0.00	38.31	5.69
445	1101	2.109799	CCGATTGCTCCTCCGCAT	59.890	61.111	0.00	0.00	40.04	4.73
446	1102	2.249535	CCGATTGCTCCTCCGCATG	61.250	63.158	0.00	0.00	40.04	4.06
447	1103	2.890109	CGATTGCTCCTCCGCATGC	61.890	63.158	7.91	7.91	40.04	4.06
448	1104	1.820906	GATTGCTCCTCCGCATGCA	60.821	57.895	19.57	0.00	40.04	3.96
449	1105	1.152819	ATTGCTCCTCCGCATGCAT	60.153	52.632	19.57	0.00	40.04	3.96
450	1106	1.452953	ATTGCTCCTCCGCATGCATG	61.453	55.000	22.70	22.70	40.04	4.06
451	1107	3.285215	GCTCCTCCGCATGCATGG	61.285	66.667	27.34	16.87	0.00	3.66
452	1108	2.191375	CTCCTCCGCATGCATGGT	59.809	61.111	27.34	0.00	0.00	3.55
453	1109	1.447217	CTCCTCCGCATGCATGGTA	59.553	57.895	27.34	4.69	0.00	3.25
454	1110	0.602106	CTCCTCCGCATGCATGGTAG	60.602	60.000	27.34	13.47	0.00	3.18
455	1111	1.146930	CCTCCGCATGCATGGTAGT	59.853	57.895	27.34	0.00	0.00	2.73
456	1112	0.464373	CCTCCGCATGCATGGTAGTT	60.464	55.000	27.34	0.00	0.00	2.24
457	1113	1.202639	CCTCCGCATGCATGGTAGTTA	60.203	52.381	27.34	0.00	0.00	2.24

Showing 1 to 25 of 377 entries

Previous1 2 3 4 5…16Next

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
171	175	1.285950	CTCTTCACGTCGCTCACCA	59.714	57.895	0.00	0.00	0.00	4.17
434	1090	2.665008	TACCATGCATGCGGAGGAGC	62.665	60.000	21.69	0.00	37.71	4.70
435	1091	0.602106	CTACCATGCATGCGGAGGAG	60.602	60.000	21.69	9.73	0.00	3.69
436	1092	1.337384	ACTACCATGCATGCGGAGGA	61.337	55.000	21.69	3.19	0.00	3.71
437	1093	0.464373	AACTACCATGCATGCGGAGG	60.464	55.000	21.69	17.75	0.00	4.30
438	1094	2.238942	TAACTACCATGCATGCGGAG	57.761	50.000	21.69	20.65	0.00	4.63
439	1095	2.928801	ATAACTACCATGCATGCGGA	57.071	45.000	21.69	10.30	0.00	5.54
440	1096	3.988379	AAATAACTACCATGCATGCGG	57.012	42.857	21.69	11.41	0.00	5.69
441	1097	4.739716	GGAAAAATAACTACCATGCATGCG	59.260	41.667	21.69	16.19	0.00	4.73
442	1098	4.739716	CGGAAAAATAACTACCATGCATGC	59.260	41.667	21.69	11.82	0.00	4.06
443	1099	4.739716	GCGGAAAAATAACTACCATGCATG	59.260	41.667	20.19	20.19	0.00	4.06
444	1100	4.497340	CGCGGAAAAATAACTACCATGCAT	60.497	41.667	0.00	0.00	0.00	3.96
445	1101	3.181505	CGCGGAAAAATAACTACCATGCA	60.182	43.478	0.00	0.00	0.00	3.96
446	1102	3.181504	ACGCGGAAAAATAACTACCATGC	60.182	43.478	12.47	0.00	0.00	4.06
447	1103	4.339429	CACGCGGAAAAATAACTACCATG	58.661	43.478	12.47	0.00	0.00	3.66
448	1104	3.375922	CCACGCGGAAAAATAACTACCAT	59.624	43.478	12.47	0.00	0.00	3.55
449	1105	2.743126	CCACGCGGAAAAATAACTACCA	59.257	45.455	12.47	0.00	0.00	3.25
450	1106	2.743664	ACCACGCGGAAAAATAACTACC	59.256	45.455	12.47	0.00	35.59	3.18
451	1107	5.120674	ACTTACCACGCGGAAAAATAACTAC	59.879	40.000	12.47	0.00	35.59	2.73
452	1108	5.237048	ACTTACCACGCGGAAAAATAACTA	58.763	37.500	12.47	0.00	35.59	2.24
453	1109	4.067192	ACTTACCACGCGGAAAAATAACT	58.933	39.130	12.47	0.00	35.59	2.24
454	1110	4.408993	ACTTACCACGCGGAAAAATAAC	57.591	40.909	12.47	0.00	35.59	1.89
455	1111	5.435820	AAACTTACCACGCGGAAAAATAA	57.564	34.783	12.47	0.00	35.59	1.40
456	1112	4.083377	GGAAACTTACCACGCGGAAAAATA	60.083	41.667	12.47	0.00	35.59	1.40
457	1113	3.304861	GGAAACTTACCACGCGGAAAAAT	60.305	43.478	12.47	0.00	35.59	1.82

Showing 1 to 25 of 375 entries

Previous1 2 3 4 5…15Next

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.