AutoCloner

Multiple sequence alignment - TraesCS3A01G063200

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	TraesCS3A01G063200	chr3A	100.000	2669	0	0	1	2669	37828399	37825731	0.000000e+00	4929.0
1	TraesCS3A01G063200	chr3A	85.705	1574	131	41	704	2202	37651502	37649948	0.000000e+00	1574.0
2	TraesCS3A01G063200	chr3A	84.854	1096	89	29	804	1831	38124779	38125865	0.000000e+00	1033.0
3	TraesCS3A01G063200	chr3A	85.070	355	32	3	2327	2661	37648864	37648511	2.540000e-90	342.0
4	TraesCS3A01G063200	chr3A	86.532	297	36	4	1885	2179	38125971	38126265	9.220000e-85	324.0
5	TraesCS3A01G063200	chr3D	92.602	2744	119	24	1	2669	27943047	27945781	0.000000e+00	3866.0
6	TraesCS3A01G063200	chr3D	87.207	1704	143	32	704	2333	27551482	27549780	0.000000e+00	1869.0
7	TraesCS3A01G063200	chr3D	85.953	299	20	4	2327	2604	27549744	27549447	1.550000e-77	300.0
8	TraesCS3A01G063200	chr3D	79.286	140	13	6	159	298	28208118	28208241	1.700000e-12	84.2
9	TraesCS3A01G063200	chr3B	91.331	1142	76	15	524	1664	46903632	46904751	0.000000e+00	1539.0
10	TraesCS3A01G063200	chr3B	91.632	968	65	5	704	1667	46033629	46032674	0.000000e+00	1325.0
11	TraesCS3A01G063200	chr3B	86.047	1204	82	38	5	1184	46792488	46793629	0.000000e+00	1214.0
12	TraesCS3A01G063200	chr3B	88.326	651	56	3	1014	1664	46932191	46932821	0.000000e+00	763.0
13	TraesCS3A01G063200	chr3B	89.107	459	44	5	1880	2333	46032399	46031942	1.390000e-157	566.0
14	TraesCS3A01G063200	chr3B	87.986	283	22	9	150	432	46797200	46797470	9.220000e-85	324.0
15	TraesCS3A01G063200	chr3B	94.839	155	8	0	659	813	46932038	46932192	2.650000e-60	243.0
16	TraesCS3A01G063200	chr3B	89.175	194	20	1	2327	2520	46031906	46031714	9.550000e-60	241.0
17	TraesCS3A01G063200	chrUn	88.940	651	58	8	1017	1667	287642994	287642358	0.000000e+00	791.0
18	TraesCS3A01G063200	chrUn	88.710	124	14	0	859	982	287643115	287642992	4.600000e-33	152.0
19	TraesCS3A01G063200	chrUn	78.767	146	19	6	2028	2162	347229041	347229185	1.320000e-13	87.9
20	TraesCS3A01G063200	chr1B	94.118	51	3	0	2599	2649	420234592	420234642	7.920000e-11	78.7
21	TraesCS3A01G063200	chr5B	100.000	28	0	0	2617	2644	291385759	291385786	5.000000e-03	52.8
22	TraesCS3A01G063200	chr5B	96.774	31	1	0	2617	2647	291385816	291385786	5.000000e-03	52.8

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	TraesCS3A01G063200	chr3A	37825731	37828399	2668	True	4929.000000	4929	100.000000	1	2669	1	chr3A.!!$R1	2668
1	TraesCS3A01G063200	chr3A	37648511	37651502	2991	True	958.000000	1574	85.387500	704	2661	2	chr3A.!!$R2	1957
2	TraesCS3A01G063200	chr3A	38124779	38126265	1486	False	678.500000	1033	85.693000	804	2179	2	chr3A.!!$F1	1375
3	TraesCS3A01G063200	chr3D	27943047	27945781	2734	False	3866.000000	3866	92.602000	1	2669	1	chr3D.!!$F1	2668
4	TraesCS3A01G063200	chr3D	27549447	27551482	2035	True	1084.500000	1869	86.580000	704	2604	2	chr3D.!!$R1	1900
5	TraesCS3A01G063200	chr3B	46903632	46904751	1119	False	1539.000000	1539	91.331000	524	1664	1	chr3B.!!$F1	1140
6	TraesCS3A01G063200	chr3B	46792488	46797470	4982	False	769.000000	1214	87.016500	5	1184	2	chr3B.!!$F2	1179
7	TraesCS3A01G063200	chr3B	46031714	46033629	1915	True	710.666667	1325	89.971333	704	2520	3	chr3B.!!$R1	1816
8	TraesCS3A01G063200	chr3B	46932038	46932821	783	False	503.000000	763	91.582500	659	1664	2	chr3B.!!$F3	1005
9	TraesCS3A01G063200	chrUn	287642358	287643115	757	True	471.500000	791	88.825000	859	1667	2	chrUn.!!$R1	808

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
237	255	0.728466	CTCTCACGAAACCGTCCGTC	60.728	60.000	0.00	0.0	38.35	4.79	F
390	408	1.153823	CCGGTGATGTCGACTGGTC	60.154	63.158	17.92	12.4	35.41	4.02	F
1254	1352	1.104630	TATACATCGTCACCACCGCA	58.895	50.000	0.00	0.0	0.00	5.69	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1254	1352	0.768221	TGTTGAGGCCAGGGAACTCT	60.768	55.000	5.01	0.00	40.21	3.24	R
1512	1618	1.202698	GGGTTCTGACTGTTGAGCACT	60.203	52.381	0.00	0.00	0.00	4.40	R
2352	4320	1.203050	CCACTGGGGTGAATTCAAGGT	60.203	52.381	10.35	2.32	45.61	3.50	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
29	30	7.274686	GTGGTGGATTATTTTAAATGGACGTTG	59.725	37.037	0.00	0.00	0.00	4.10
38	39	8.791355	ATTTTAAATGGACGTTGTGTTTCTAC	57.209	30.769	0.00	0.00	0.00	2.59
40	41	5.821516	AAATGGACGTTGTGTTTCTACAA	57.178	34.783	0.00	0.00	38.17	2.41
46	56	7.188157	TGGACGTTGTGTTTCTACAATTTTAC	58.812	34.615	0.00	0.00	42.02	2.01
112	130	2.499205	CTAATCGTGCGCTGGGGA	59.501	61.111	9.73	0.29	0.00	4.81
167	185	2.618794	CTTCCTCTGCCTCCCTATCAT	58.381	52.381	0.00	0.00	0.00	2.45
237	255	0.728466	CTCTCACGAAACCGTCCGTC	60.728	60.000	0.00	0.00	38.35	4.79
238	256	1.731969	CTCACGAAACCGTCCGTCC	60.732	63.158	0.00	0.00	38.35	4.79
239	257	3.101428	CACGAAACCGTCCGTCCG	61.101	66.667	0.00	0.00	38.35	4.79
240	258	3.595758	ACGAAACCGTCCGTCCGT	61.596	61.111	0.00	0.00	34.90	4.69
284	302	1.187087	CCACCGCTCTCCTCTACTTT	58.813	55.000	0.00	0.00	0.00	2.66
359	377	2.681848	CAGCATCCACAAGGTGAATCTC	59.318	50.000	0.00	0.00	35.23	2.75
390	408	1.153823	CCGGTGATGTCGACTGGTC	60.154	63.158	17.92	12.40	35.41	4.02
403	421	1.517257	CTGGTCGGTGATGACTCGC	60.517	63.158	0.00	0.00	38.91	5.03
432	450	3.124636	CCGTGACAATTTCTTACCTTCGG	59.875	47.826	0.00	0.00	0.00	4.30
462	487	4.827304	TTTGCGAACTGATGTGAAATCA	57.173	36.364	0.00	0.00	0.00	2.57
484	512	7.215719	TCAGATGTTATCATACTACCTTCGG	57.784	40.000	0.00	0.00	34.06	4.30
510	540	3.489355	TCATTCCATGTTCACAAGCAGT	58.511	40.909	0.00	0.00	0.00	4.40
521	551	2.867109	ACAAGCAGTGAAGCTACCAT	57.133	45.000	0.00	0.00	45.89	3.55
522	552	2.704572	ACAAGCAGTGAAGCTACCATC	58.295	47.619	0.00	0.00	45.89	3.51
549	605	9.108284	ACTTTGGTTTTTAAACAATCAATGAGG	57.892	29.630	18.13	9.92	40.63	3.86
702	758	3.281727	ACTGAAGACTTGCCAAGTGAA	57.718	42.857	16.14	0.00	43.03	3.18
1215	1313	3.136443	TCAATCATGCCGGGAAACTAGAT	59.864	43.478	0.00	0.00	0.00	1.98
1221	1319	4.497291	TGCCGGGAAACTAGATAACATT	57.503	40.909	2.18	0.00	0.00	2.71
1222	1320	4.448210	TGCCGGGAAACTAGATAACATTC	58.552	43.478	2.18	0.00	0.00	2.67
1251	1349	1.677576	TCGGTATACATCGTCACCACC	59.322	52.381	5.01	0.00	0.00	4.61
1254	1352	1.104630	TATACATCGTCACCACCGCA	58.895	50.000	0.00	0.00	0.00	5.69
1512	1618	0.659417	GTCTTGCGACGACGTTCTCA	60.659	55.000	9.33	0.00	41.98	3.27
1584	1690	2.131183	GCGCCAGATTCAGATGTAGTC	58.869	52.381	0.00	0.00	0.00	2.59
1587	1693	3.637432	GCCAGATTCAGATGTAGTCGAG	58.363	50.000	0.00	0.00	0.00	4.04
1613	1720	3.548770	TGATGGCCAGAATGATGAAGTC	58.451	45.455	13.05	0.00	39.69	3.01
1647	1786	5.646793	GGAAATCCCTAACAACAAGACTACC	59.353	44.000	0.00	0.00	0.00	3.18
1749	2620	7.062322	AGTCATGTATATGGGCAGAATTTCAA	58.938	34.615	0.00	0.00	34.97	2.69
2116	3118	1.469767	GCGGAACTCCATGCCATTTTC	60.470	52.381	0.00	0.00	35.14	2.29
2118	3120	2.159338	CGGAACTCCATGCCATTTTCTG	60.159	50.000	0.00	0.00	35.14	3.02
2128	3130	6.038356	CCATGCCATTTTCTGAGTATTGTTC	58.962	40.000	0.00	0.00	0.00	3.18
2172	3176	2.291024	GGAGGTCCCTTTCTTTTCCCTC	60.291	54.545	0.00	0.00	36.99	4.30
2257	4178	2.638480	TGCCTATGATGCCACTTACC	57.362	50.000	0.00	0.00	0.00	2.85
2259	4180	1.202651	GCCTATGATGCCACTTACCGT	60.203	52.381	0.00	0.00	0.00	4.83
2352	4320	3.610040	ATGAATGGTTACTCGACTGCA	57.390	42.857	0.00	0.00	0.00	4.41
2626	6165	3.933332	CCTTCGTCTGGAATTACTTGTCC	59.067	47.826	0.00	0.00	33.26	4.02
2650	6189	4.811908	TCAAACGGATGTATCTTGACGAA	58.188	39.130	0.00	0.00	0.00	3.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
3	4	6.859017	ACGTCCATTTAAAATAATCCACCAC	58.141	36.000	0.00	0.00	0.00	4.16
205	223	2.826738	GAGAGGCTCGAGGTCGCT	60.827	66.667	15.58	3.43	39.60	4.93
284	302	1.691976	ACTCACCGGAGACAAATGTGA	59.308	47.619	9.46	0.00	44.26	3.58
321	339	2.232298	CTGAGGAGCCCAAGGTCGAC	62.232	65.000	7.13	7.13	41.62	4.20
390	408	2.510948	GCATAGCGAGTCATCACCG	58.489	57.895	0.00	0.00	0.00	4.94
403	421	1.665679	AGAAATTGTCACGGCGCATAG	59.334	47.619	10.83	1.82	0.00	2.23
432	450	2.998772	TCAGTTCGCAAATCAGCAAAC	58.001	42.857	0.00	0.00	0.00	2.93
521	551	9.658799	TCATTGATTGTTTAAAAACCAAAGTGA	57.341	25.926	3.27	1.10	38.11	3.41
522	552	9.919348	CTCATTGATTGTTTAAAAACCAAAGTG	57.081	29.630	3.27	0.00	38.11	3.16
549	605	2.287547	TGGCGTGTTTCAGAAATTGCTC	60.288	45.455	13.45	7.30	0.00	4.26
702	758	3.633525	TGCTGAAAATGCTTCAGACTTGT	59.366	39.130	16.12	0.00	46.57	3.16
736	792	5.177696	CCCTACGCTGCAAATCTAGATAAAC	59.822	44.000	5.46	0.00	0.00	2.01
1235	1333	1.066454	CTGCGGTGGTGACGATGTATA	59.934	52.381	0.00	0.00	0.00	1.47
1251	1349	3.672295	GAGGCCAGGGAACTCTGCG	62.672	68.421	5.01	0.00	40.21	5.18
1254	1352	0.768221	TGTTGAGGCCAGGGAACTCT	60.768	55.000	5.01	0.00	40.21	3.24
1512	1618	1.202698	GGGTTCTGACTGTTGAGCACT	60.203	52.381	0.00	0.00	0.00	4.40
1613	1720	4.410228	TGTTAGGGATTTCCATCTCTCTGG	59.590	45.833	0.00	0.00	39.75	3.86
1647	1786	6.338146	TCACTAGTAAGTCCATGGAAAATCG	58.662	40.000	18.20	3.38	31.97	3.34
2116	3118	6.429385	AGGAGCAAAAAGAGAACAATACTCAG	59.571	38.462	0.00	0.00	36.91	3.35
2118	3120	6.809630	AGGAGCAAAAAGAGAACAATACTC	57.190	37.500	0.00	0.00	34.95	2.59
2172	3176	4.926140	AGCTTCACTTTCAAAAGAAGGG	57.074	40.909	9.39	0.00	39.31	3.95
2257	4178	3.074412	AGGATAGTCCTTGCACAAAACG	58.926	45.455	0.00	0.00	46.91	3.60
2259	4180	4.042311	TGGTAGGATAGTCCTTGCACAAAA	59.958	41.667	3.49	0.00	46.91	2.44
2352	4320	1.203050	CCACTGGGGTGAATTCAAGGT	60.203	52.381	10.35	2.32	45.61	3.50
2626	6165	3.551890	CGTCAAGATACATCCGTTTGAGG	59.448	47.826	0.00	0.00	0.00	3.86

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.