AutoCloner

Multiple sequence alignment - TraesCS4A01G137700

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	TraesCS4A01G137700	chr4A	100.000	2402	0	0	1	2402	197939146	197941547	0.000000e+00	4436.0
1	TraesCS4A01G137700	chr7A	91.477	2370	166	22	1	2348	412375684	412373329	0.000000e+00	3225.0
2	TraesCS4A01G137700	chr7A	87.432	366	41	2	1	366	239423819	239424179	1.330000e-112	416.0
3	TraesCS4A01G137700	chr7A	90.698	172	14	2	378	549	239424263	239424432	6.680000e-56	228.0
4	TraesCS4A01G137700	chr7A	90.000	130	13	0	579	708	239424428	239424557	4.110000e-38	169.0
5	TraesCS4A01G137700	chr7A	100.000	31	0	0	338	368	642695729	642695759	9.270000e-05	58.4
6	TraesCS4A01G137700	chr2D	92.839	1983	132	5	368	2348	110570273	110572247	0.000000e+00	2867.0
7	TraesCS4A01G137700	chr2D	96.739	368	12	0	1	368	110569834	110570201	4.390000e-172	614.0
8	TraesCS4A01G137700	chr4B	86.897	1740	179	23	694	2402	607366061	607367782	0.000000e+00	1905.0
9	TraesCS4A01G137700	chr4B	90.256	195	16	1	174	368	607354894	607355085	3.960000e-63	252.0
10	TraesCS4A01G137700	chr4B	95.425	153	7	0	27	179	607353277	607353429	6.630000e-61	244.0
11	TraesCS4A01G137700	chr4B	94.815	135	6	1	368	502	607365930	607366063	2.420000e-50	209.0
12	TraesCS4A01G137700	chr1D	93.851	1171	69	3	368	1537	352080069	352081237	0.000000e+00	1760.0
13	TraesCS4A01G137700	chr1D	88.723	1339	117	19	1068	2399	352090105	352091416	0.000000e+00	1605.0
14	TraesCS4A01G137700	chr1D	91.985	1098	75	3	590	1683	300078893	300079981	0.000000e+00	1528.0
15	TraesCS4A01G137700	chr1D	88.618	615	61	8	1793	2402	233200776	233201386	0.000000e+00	739.0
16	TraesCS4A01G137700	chr3B	85.706	1700	192	21	694	2362	538249290	538250969	0.000000e+00	1746.0
17	TraesCS4A01G137700	chr3B	88.072	1006	88	20	1	1006	787736107	787735134	0.000000e+00	1164.0
18	TraesCS4A01G137700	chr3B	91.520	342	26	1	27	368	538248749	538249087	3.620000e-128	468.0
19	TraesCS4A01G137700	chr3B	89.877	326	32	1	999	1323	787734369	787734044	3.690000e-113	418.0
20	TraesCS4A01G137700	chr3B	94.815	135	6	1	368	502	538249159	538249292	2.420000e-50	209.0
21	TraesCS4A01G137700	chr6B	87.017	1448	132	23	1	1423	515726039	515727455	0.000000e+00	1581.0
22	TraesCS4A01G137700	chr4D	85.321	763	92	11	1615	2375	475415789	475416533	0.000000e+00	771.0
23	TraesCS4A01G137700	chr4D	84.625	787	101	11	1615	2399	475452295	475453063	0.000000e+00	765.0
24	TraesCS4A01G137700	chr4D	84.015	782	104	16	1630	2402	58620968	58620199	0.000000e+00	732.0
25	TraesCS4A01G137700	chr4D	89.756	205	21	0	1	205	141828165	141827961	1.830000e-66	263.0
26	TraesCS4A01G137700	chr2A	87.855	634	60	11	1775	2402	557985966	557986588	0.000000e+00	728.0
27	TraesCS4A01G137700	chr3D	86.567	670	68	16	1742	2402	177763167	177763823	0.000000e+00	719.0
28	TraesCS4A01G137700	chr3A	82.730	608	85	11	940	1530	517372922	517372318	7.610000e-145	523.0
29	TraesCS4A01G137700	chr3A	83.455	550	56	25	1	549	517373573	517373058	1.670000e-131	479.0
30	TraesCS4A01G137700	chr3A	87.970	133	16	0	579	711	517373062	517372930	8.890000e-35	158.0
31	TraesCS4A01G137700	chr6D	84.839	310	30	6	1	302	350475546	350475246	1.810000e-76	296.0
32	TraesCS4A01G137700	chr5B	87.160	257	31	2	18	272	519607354	519607098	8.400000e-75	291.0
33	TraesCS4A01G137700	chrUn	88.235	85	9	1	1317	1400	421339337	421339421	1.520000e-17	100.0

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	TraesCS4A01G137700	chr4A	197939146	197941547	2401	False	4436.000000	4436	100.000000	1	2402	1	chr4A.!!$F1	2401
1	TraesCS4A01G137700	chr7A	412373329	412375684	2355	True	3225.000000	3225	91.477000	1	2348	1	chr7A.!!$R1	2347
2	TraesCS4A01G137700	chr7A	239423819	239424557	738	False	271.000000	416	89.376667	1	708	3	chr7A.!!$F2	707
3	TraesCS4A01G137700	chr2D	110569834	110572247	2413	False	1740.500000	2867	94.789000	1	2348	2	chr2D.!!$F1	2347
4	TraesCS4A01G137700	chr4B	607365930	607367782	1852	False	1057.000000	1905	90.856000	368	2402	2	chr4B.!!$F2	2034
5	TraesCS4A01G137700	chr4B	607353277	607355085	1808	False	248.000000	252	92.840500	27	368	2	chr4B.!!$F1	341
6	TraesCS4A01G137700	chr1D	352080069	352081237	1168	False	1760.000000	1760	93.851000	368	1537	1	chr1D.!!$F3	1169
7	TraesCS4A01G137700	chr1D	352090105	352091416	1311	False	1605.000000	1605	88.723000	1068	2399	1	chr1D.!!$F4	1331
8	TraesCS4A01G137700	chr1D	300078893	300079981	1088	False	1528.000000	1528	91.985000	590	1683	1	chr1D.!!$F2	1093
9	TraesCS4A01G137700	chr1D	233200776	233201386	610	False	739.000000	739	88.618000	1793	2402	1	chr1D.!!$F1	609
10	TraesCS4A01G137700	chr3B	538248749	538250969	2220	False	807.666667	1746	90.680333	27	2362	3	chr3B.!!$F1	2335
11	TraesCS4A01G137700	chr3B	787734044	787736107	2063	True	791.000000	1164	88.974500	1	1323	2	chr3B.!!$R1	1322
12	TraesCS4A01G137700	chr6B	515726039	515727455	1416	False	1581.000000	1581	87.017000	1	1423	1	chr6B.!!$F1	1422
13	TraesCS4A01G137700	chr4D	475415789	475416533	744	False	771.000000	771	85.321000	1615	2375	1	chr4D.!!$F1	760
14	TraesCS4A01G137700	chr4D	475452295	475453063	768	False	765.000000	765	84.625000	1615	2399	1	chr4D.!!$F2	784
15	TraesCS4A01G137700	chr4D	58620199	58620968	769	True	732.000000	732	84.015000	1630	2402	1	chr4D.!!$R1	772
16	TraesCS4A01G137700	chr2A	557985966	557986588	622	False	728.000000	728	87.855000	1775	2402	1	chr2A.!!$F1	627
17	TraesCS4A01G137700	chr3D	177763167	177763823	656	False	719.000000	719	86.567000	1742	2402	1	chr3D.!!$F1	660
18	TraesCS4A01G137700	chr3A	517372318	517373573	1255	True	386.666667	523	84.718333	1	1530	3	chr3A.!!$R1	1529

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
277	1748	0.321564	CAGACGCATGAAACAGGGGA	60.322	55.0	0.0	0.0	32.66	4.81	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1966	4656	0.035439	TCTTGATTCCGCTCAACCCC	60.035	55.0	0.0	0.0	31.98	4.95	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
191	1662	5.296780	CAGCACCTTTGTCTTTTTCTGTCTA	59.703	40.000	0.00	0.00	0.00	2.59
239	1710	2.780149	CTTTTTCCACCGCGGCTTCG	62.780	60.000	28.58	11.54	33.14	3.79
265	1736	3.438781	CCAAAAGGTAATAAGCAGACGCA	59.561	43.478	0.00	0.00	42.27	5.24
277	1748	0.321564	CAGACGCATGAAACAGGGGA	60.322	55.000	0.00	0.00	32.66	4.81
327	1803	1.377725	AGCAGAAACAGGCCATCCG	60.378	57.895	5.01	0.00	37.47	4.18
328	1804	2.409870	GCAGAAACAGGCCATCCGG	61.410	63.158	5.01	0.00	37.47	5.14
411	2060	6.864342	TCCGTTCTTCTAATACTTTCCAGAG	58.136	40.000	0.00	0.00	0.00	3.35
553	2202	3.120683	ACACGCACGTTGAATTGATACAG	60.121	43.478	0.00	0.00	0.00	2.74
733	2575	2.050754	ATATCCCATACAGCAGCCCT	57.949	50.000	0.00	0.00	0.00	5.19
734	2576	2.713828	TATCCCATACAGCAGCCCTA	57.286	50.000	0.00	0.00	0.00	3.53
859	2701	1.004679	GGCCACTCCGTACGGAAAA	60.005	57.895	34.77	15.81	44.66	2.29
981	2823	1.141019	GGAGAGTATGGCGCAACGA	59.859	57.895	10.83	0.00	0.00	3.85
1061	3675	1.302511	GTGCAGTGGTTGACCCGAT	60.303	57.895	0.00	0.00	35.15	4.18
1178	3793	3.834799	GCGACCCCGAACGGAGAT	61.835	66.667	15.07	0.00	38.22	2.75
1212	3829	0.679505	GCGGATATGTAGGTGGCTCA	59.320	55.000	0.00	0.00	0.00	4.26
1219	3836	1.127567	TGTAGGTGGCTCAAGGCTGT	61.128	55.000	5.11	0.00	41.69	4.40
1226	3843	1.227943	GCTCAAGGCTGTGGTGTCA	60.228	57.895	0.00	0.00	38.06	3.58
1277	3900	2.665185	GTGGCTCGGCGACAACTT	60.665	61.111	4.99	0.00	37.24	2.66
1454	4130	2.507102	CGCGGCGACTGACTTGAT	60.507	61.111	19.16	0.00	0.00	2.57
1457	4133	1.737735	CGGCGACTGACTTGATGCA	60.738	57.895	0.00	0.00	0.00	3.96
1458	4134	1.086067	CGGCGACTGACTTGATGCAT	61.086	55.000	0.00	0.00	0.00	3.96
1463	4139	2.341257	GACTGACTTGATGCATCACGT	58.659	47.619	31.99	31.99	41.27	4.49
1475	4151	2.942796	ATCACGTGGAAGCGAGGCA	61.943	57.895	17.00	0.00	35.59	4.75
1480	4156	1.004440	GTGGAAGCGAGGCAGACTT	60.004	57.895	0.00	0.00	0.00	3.01
1555	4234	0.694771	TCAAGAACAGCAGGCAGGAT	59.305	50.000	0.00	0.00	0.00	3.24
1572	4251	5.128919	GCAGGATCATGAGATTGGTAGTTT	58.871	41.667	12.39	0.00	33.72	2.66
1584	4263	7.038302	TGAGATTGGTAGTTTAGATCCTTGTGT	60.038	37.037	0.00	0.00	0.00	3.72
1592	4271	1.573108	AGATCCTTGTGTCACCCGAT	58.427	50.000	0.00	0.00	0.00	4.18
1675	4357	3.034635	ACTCTTATCTCGGTCTTGGCAT	58.965	45.455	0.00	0.00	0.00	4.40
1758	4442	1.464023	CGCACACGCTATTTCAACTGG	60.464	52.381	0.00	0.00	35.30	4.00
1764	4448	2.029290	ACGCTATTTCAACTGGTCGTCT	60.029	45.455	0.00	0.00	0.00	4.18
1904	4592	2.357637	CCAACTGTCGTGGTTTTGTCAT	59.642	45.455	0.00	0.00	0.00	3.06
1907	4595	2.217750	CTGTCGTGGTTTTGTCATGGA	58.782	47.619	0.00	0.00	0.00	3.41
1909	4597	3.218453	TGTCGTGGTTTTGTCATGGAAT	58.782	40.909	0.00	0.00	0.00	3.01
1954	4644	0.815213	TGAGGCCAACGCATCTATGC	60.815	55.000	5.01	4.82	46.01	3.14
1966	4656	2.478134	GCATCTATGCGGTAGCTTGAAG	59.522	50.000	0.00	0.00	44.67	3.02
1998	4711	3.003275	GGAATCAAGAGACGCAACACAAA	59.997	43.478	0.00	0.00	0.00	2.83
2000	4713	4.836125	ATCAAGAGACGCAACACAAAAT	57.164	36.364	0.00	0.00	0.00	1.82
2021	4734	3.983044	AAGGATTTAGACAGCTTCGGT	57.017	42.857	0.00	0.00	0.00	4.69
2026	4739	0.543410	TTAGACAGCTTCGGTCCCCA	60.543	55.000	0.00	0.00	35.89	4.96
2106	4821	0.810016	GAGAGAGTCGCCGGTAAACT	59.190	55.000	1.90	4.04	0.00	2.66
2146	4876	5.047731	GCCCTAAAGATTGTTTCTTCTTGCT	60.048	40.000	0.00	0.00	44.09	3.91
2151	4881	6.455360	AAGATTGTTTCTTCTTGCTTGTCA	57.545	33.333	0.00	0.00	40.86	3.58
2155	4885	5.235305	TGTTTCTTCTTGCTTGTCACTTC	57.765	39.130	0.00	0.00	0.00	3.01
2284	5022	4.094476	CAAGTCCAGGTCTTAACTCCCTA	58.906	47.826	0.00	0.00	0.00	3.53

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
191	1662	2.562738	TGATCACATGACGACCAGAGTT	59.437	45.455	0.00	0.00	0.00	3.01
239	1710	8.750403	GCGTCTGCTTATTACCTTTTGGTTCC	62.750	46.154	0.00	0.00	44.54	3.62
265	1736	1.754234	GCCGCATCCCCTGTTTCAT	60.754	57.895	0.00	0.00	0.00	2.57
327	1803	0.247736	ACGGAGTTGATCTGCTGTCC	59.752	55.000	0.00	0.00	37.78	4.02
328	1804	3.822607	ACGGAGTTGATCTGCTGTC	57.177	52.632	0.00	0.00	37.78	3.51
411	2060	2.485814	GGAGGACAGACAATTGTTGAGC	59.514	50.000	13.36	9.99	0.00	4.26
553	2202	4.038402	CCAATTTCTGCATAAGGGATCCAC	59.962	45.833	15.23	2.86	0.00	4.02
671	2513	1.202533	CGAGCTGGACCGTTGGAATAT	60.203	52.381	0.00	0.00	0.00	1.28
733	2575	6.472887	CCTCTTCAATTTGTTACTCCACCTA	58.527	40.000	0.00	0.00	0.00	3.08
734	2576	5.316987	CCTCTTCAATTTGTTACTCCACCT	58.683	41.667	0.00	0.00	0.00	4.00
859	2701	2.593436	CCGGACGTGGCCAAGTTT	60.593	61.111	25.53	3.28	0.00	2.66
917	2759	2.289694	CCATCGGTCTGTCTTTGGTTCT	60.290	50.000	0.00	0.00	0.00	3.01
981	2823	1.296715	GGTTCACCTCGAGCCATGT	59.703	57.895	6.99	0.00	44.23	3.21
1031	3645	3.536917	CTGCACCCCGATCCGCTA	61.537	66.667	0.00	0.00	0.00	4.26
1037	3651	2.034066	CAACCACTGCACCCCGAT	59.966	61.111	0.00	0.00	0.00	4.18
1061	3675	3.006728	CCGAAGCCACCCCTACCA	61.007	66.667	0.00	0.00	0.00	3.25
1064	3678	1.536907	TGTTCCGAAGCCACCCCTA	60.537	57.895	0.00	0.00	0.00	3.53
1070	3684	4.697756	CGCCCTGTTCCGAAGCCA	62.698	66.667	0.00	0.00	0.00	4.75
1108	3722	2.727392	CGTCAAGCCACCCCGGATA	61.727	63.158	0.73	0.00	36.56	2.59
1178	3793	3.443925	CGCTGGTCTCTGCCTCGA	61.444	66.667	0.00	0.00	34.85	4.04
1212	3829	1.151450	CCCTTGACACCACAGCCTT	59.849	57.895	0.00	0.00	0.00	4.35
1219	3836	4.329545	GCCTCGCCCTTGACACCA	62.330	66.667	0.00	0.00	0.00	4.17
1226	3843	3.771160	CACCTACGCCTCGCCCTT	61.771	66.667	0.00	0.00	0.00	3.95
1394	4070	1.121407	TATGCCCTGCTATCACCGCT	61.121	55.000	0.00	0.00	0.00	5.52
1454	4130	1.737735	CTCGCTTCCACGTGATGCA	60.738	57.895	19.30	7.93	42.68	3.96
1457	4133	2.125512	GCCTCGCTTCCACGTGAT	60.126	61.111	19.30	0.00	0.00	3.06
1458	4134	3.573772	CTGCCTCGCTTCCACGTGA	62.574	63.158	19.30	0.00	0.00	4.35
1463	4139	0.603707	CAAAGTCTGCCTCGCTTCCA	60.604	55.000	0.00	0.00	0.00	3.53
1475	4151	3.649986	GCACCGCGCACAAAGTCT	61.650	61.111	8.75	0.00	41.79	3.24
1508	4184	2.280524	CAAACCGAGCACGACCCA	60.281	61.111	4.70	0.00	42.66	4.51
1538	4214	0.694771	TGATCCTGCCTGCTGTTCTT	59.305	50.000	0.00	0.00	0.00	2.52
1548	4227	2.653234	ACCAATCTCATGATCCTGCC	57.347	50.000	0.00	0.00	31.51	4.85
1555	4234	7.921041	AGGATCTAAACTACCAATCTCATGA	57.079	36.000	0.00	0.00	0.00	3.07
1572	4251	2.225382	TCGGGTGACACAAGGATCTA	57.775	50.000	8.08	0.00	0.00	1.98
1584	4263	6.549736	TCAGAATAATACTCTTCATCGGGTGA	59.450	38.462	0.00	0.00	34.25	4.02
1592	4271	7.288621	TGCAGGAGATCAGAATAATACTCTTCA	59.711	37.037	0.00	0.00	0.00	3.02
1675	4357	1.407299	GCTGCACACACCATGGAGATA	60.407	52.381	21.47	0.00	37.70	1.98
1758	4442	5.333492	CAGAAGGATCTACGTCATAGACGAC	60.333	48.000	24.20	10.37	45.40	4.34
1764	4448	4.275196	CGGTTCAGAAGGATCTACGTCATA	59.725	45.833	0.00	0.00	33.50	2.15
1954	4644	0.323629	TCAACCCCTTCAAGCTACCG	59.676	55.000	0.00	0.00	0.00	4.02
1966	4656	0.035439	TCTTGATTCCGCTCAACCCC	60.035	55.000	0.00	0.00	31.98	4.95
1998	4711	5.990668	ACCGAAGCTGTCTAAATCCTTATT	58.009	37.500	0.00	0.00	0.00	1.40
2000	4713	4.142004	GGACCGAAGCTGTCTAAATCCTTA	60.142	45.833	3.02	0.00	33.22	2.69
2021	4734	0.546122	CGGATGATGTTTCCTGGGGA	59.454	55.000	0.00	0.00	0.00	4.81
2026	4739	4.505039	GGCTATTACCGGATGATGTTTCCT	60.505	45.833	9.46	0.00	0.00	3.36
2100	4815	4.568760	GCTAGACATGAAGAGCCAGTTTAC	59.431	45.833	0.00	0.00	0.00	2.01
2146	4876	3.492102	CCAAAGAGGGAGAAGTGACAA	57.508	47.619	0.00	0.00	0.00	3.18
2171	4907	4.503685	ACTTATATAAGGAGGGGCAGGA	57.496	45.455	23.24	0.00	37.62	3.86
2255	4993	2.233305	AGACCTGGACTTGTATCCGT	57.767	50.000	0.00	0.00	42.24	4.69
2298	5036	4.336280	GGTTTAAGAGGAAAGGCATGAGT	58.664	43.478	0.00	0.00	0.00	3.41
2357	5096	1.288188	TCCAGATGGATGACAAGGCA	58.712	50.000	0.00	0.00	39.78	4.75

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.