AutoCloner

Multiple sequence alignment - TraesCS7A01G456200

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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	TraesCS7A01G456200	chr7A	100.000	3246	0	0	1	3246	652338793	652342038	0.000000e+00	5995
1	TraesCS7A01G456200	chr7A	84.812	2344	275	30	3	2313	652357723	652360018	0.000000e+00	2281
2	TraesCS7A01G456200	chr7A	97.957	783	16	0	2464	3246	6321005	6321787	0.000000e+00	1358
3	TraesCS7A01G456200	chr7A	81.706	1618	255	25	28	1619	652287280	652288882	0.000000e+00	1310
4	TraesCS7A01G456200	chr7A	80.497	1569	254	28	77	1620	652196058	652197599	0.000000e+00	1155
5	TraesCS7A01G456200	chr7D	94.397	2463	119	10	1	2453	566038269	566040722	0.000000e+00	3766
6	TraesCS7A01G456200	chr7D	84.490	1599	219	15	19	1600	565618214	565619800	0.000000e+00	1552
7	TraesCS7A01G456200	chr7D	82.910	1615	240	22	28	1620	566014814	566016414	0.000000e+00	1421
8	TraesCS7A01G456200	chr7D	80.923	1625	267	29	20	1620	565644476	565646081	0.000000e+00	1243
9	TraesCS7A01G456200	chr7B	93.042	1696	100	6	1	1684	617578534	617580223	0.000000e+00	2462
10	TraesCS7A01G456200	chr7B	84.135	1601	221	18	19	1600	616837069	616838655	0.000000e+00	1519
11	TraesCS7A01G456200	chr7B	82.105	1615	253	23	28	1620	617557103	617555503	0.000000e+00	1349
12	TraesCS7A01G456200	chr7B	80.961	1665	281	21	3	1644	616903894	616905545	0.000000e+00	1286
13	TraesCS7A01G456200	chr7B	81.172	1604	240	33	45	1631	616822405	616820847	0.000000e+00	1232
14	TraesCS7A01G456200	chr7B	80.279	1648	271	33	21	1643	616749083	616747465	0.000000e+00	1194
15	TraesCS7A01G456200	chr7B	80.292	411	58	18	1810	2212	143059333	143058938	4.100000e-74	289
16	TraesCS7A01G456200	chr3A	98.462	780	12	0	2467	3246	740874710	740875489	0.000000e+00	1375
17	TraesCS7A01G456200	chr3B	96.051	785	28	1	2464	3245	812719844	812719060	0.000000e+00	1275
18	TraesCS7A01G456200	chr6A	95.044	787	29	4	2464	3246	13727812	13728592	0.000000e+00	1229
19	TraesCS7A01G456200	chr6D	94.917	787	35	4	2464	3246	314021807	314021022	0.000000e+00	1227
20	TraesCS7A01G456200	chr5B	94.027	519	19	3	2731	3246	699456749	699456240	0.000000e+00	776
21	TraesCS7A01G456200	chr5B	95.536	224	10	0	2464	2687	699456973	699456750	3.080000e-95	359
22	TraesCS7A01G456200	chr2B	88.319	351	35	2	2899	3246	708192839	708193186	1.800000e-112	416
23	TraesCS7A01G456200	chr4B	82.262	389	69	0	2858	3246	585727683	585727295	1.440000e-88	337
24	TraesCS7A01G456200	chr5A	74.430	790	186	14	2468	3246	47975626	47974842	3.120000e-85	326
25	TraesCS7A01G456200	chrUn	80.729	384	59	13	1826	2205	251536964	251537336	5.300000e-73	285
26	TraesCS7A01G456200	chr1A	80.357	392	56	16	1832	2211	49148932	49148550	8.870000e-71	278
27	TraesCS7A01G456200	chr4D	83.562	292	31	13	1812	2100	62295503	62295226	1.160000e-64	257
28	TraesCS7A01G456200	chr3D	78.325	406	74	11	1812	2211	68432467	68432070	1.930000e-62	250
29	TraesCS7A01G456200	chr2D	77.506	409	79	11	1812	2211	644141136	644141540	1.950000e-57	233
30	TraesCS7A01G456200	chr4A	80.690	290	37	15	1812	2098	535814204	535813931	1.180000e-49	207
31	TraesCS7A01G456200	chr5D	76.284	409	79	11	1812	2214	302838030	302837634	5.490000e-48	202

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	TraesCS7A01G456200	chr7A	652338793	652342038	3245	False	5995.0	5995	100.0000	1	3246	1	chr7A.!!$F4	3245
1	TraesCS7A01G456200	chr7A	652357723	652360018	2295	False	2281.0	2281	84.8120	3	2313	1	chr7A.!!$F5	2310
2	TraesCS7A01G456200	chr7A	6321005	6321787	782	False	1358.0	1358	97.9570	2464	3246	1	chr7A.!!$F1	782
3	TraesCS7A01G456200	chr7A	652287280	652288882	1602	False	1310.0	1310	81.7060	28	1619	1	chr7A.!!$F3	1591
4	TraesCS7A01G456200	chr7A	652196058	652197599	1541	False	1155.0	1155	80.4970	77	1620	1	chr7A.!!$F2	1543
5	TraesCS7A01G456200	chr7D	566038269	566040722	2453	False	3766.0	3766	94.3970	1	2453	1	chr7D.!!$F4	2452
6	TraesCS7A01G456200	chr7D	565618214	565619800	1586	False	1552.0	1552	84.4900	19	1600	1	chr7D.!!$F1	1581
7	TraesCS7A01G456200	chr7D	566014814	566016414	1600	False	1421.0	1421	82.9100	28	1620	1	chr7D.!!$F3	1592
8	TraesCS7A01G456200	chr7D	565644476	565646081	1605	False	1243.0	1243	80.9230	20	1620	1	chr7D.!!$F2	1600
9	TraesCS7A01G456200	chr7B	617578534	617580223	1689	False	2462.0	2462	93.0420	1	1684	1	chr7B.!!$F3	1683
10	TraesCS7A01G456200	chr7B	616837069	616838655	1586	False	1519.0	1519	84.1350	19	1600	1	chr7B.!!$F1	1581
11	TraesCS7A01G456200	chr7B	617555503	617557103	1600	True	1349.0	1349	82.1050	28	1620	1	chr7B.!!$R4	1592
12	TraesCS7A01G456200	chr7B	616903894	616905545	1651	False	1286.0	1286	80.9610	3	1644	1	chr7B.!!$F2	1641
13	TraesCS7A01G456200	chr7B	616820847	616822405	1558	True	1232.0	1232	81.1720	45	1631	1	chr7B.!!$R3	1586
14	TraesCS7A01G456200	chr7B	616747465	616749083	1618	True	1194.0	1194	80.2790	21	1643	1	chr7B.!!$R2	1622
15	TraesCS7A01G456200	chr3A	740874710	740875489	779	False	1375.0	1375	98.4620	2467	3246	1	chr3A.!!$F1	779
16	TraesCS7A01G456200	chr3B	812719060	812719844	784	True	1275.0	1275	96.0510	2464	3245	1	chr3B.!!$R1	781
17	TraesCS7A01G456200	chr6A	13727812	13728592	780	False	1229.0	1229	95.0440	2464	3246	1	chr6A.!!$F1	782
18	TraesCS7A01G456200	chr6D	314021022	314021807	785	True	1227.0	1227	94.9170	2464	3246	1	chr6D.!!$R1	782
19	TraesCS7A01G456200	chr5B	699456240	699456973	733	True	567.5	776	94.7815	2464	3246	2	chr5B.!!$R1	782
20	TraesCS7A01G456200	chr5A	47974842	47975626	784	True	326.0	326	74.4300	2468	3246	1	chr5A.!!$R1	778

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
610	627	0.106149	GGGGCATCGGTGTTACTAGG	59.894	60.0	0.00	0.0	0.0	3.02	F
773	793	0.598158	TGTACCGCGGTGTTCTGAAC	60.598	55.0	40.02	27.3	0.0	3.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1829	1883	0.030705	TAAGGCCTCCATGGAGCTCT	60.031	55.000	32.97	26.77	40.69	4.09	R
2324	2383	1.127582	GCTCGTCTTGTGATGCTTGAC	59.872	52.381	0.00	0.00	0.00	3.18	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
259	260	1.019278	CACAACGGATCAAGGACGGG	61.019	60.000	0.00	0.00	0.00	5.28
293	294	2.507484	CTGCCAGACATGAAACTTCCA	58.493	47.619	0.00	0.00	0.00	3.53
294	295	2.227388	CTGCCAGACATGAAACTTCCAC	59.773	50.000	0.00	0.00	0.00	4.02
351	352	2.046892	AGTGCGAATCGGCTTGCT	60.047	55.556	4.35	0.00	0.00	3.91
400	408	3.790437	CTCTGCCGGGGAGTGCAT	61.790	66.667	15.63	0.00	36.79	3.96
444	452	1.367659	GCTTCAGCAGCTCTACTTGG	58.632	55.000	0.00	0.00	46.27	3.61
445	453	1.066573	GCTTCAGCAGCTCTACTTGGA	60.067	52.381	0.00	0.00	46.27	3.53
446	454	2.613977	GCTTCAGCAGCTCTACTTGGAA	60.614	50.000	0.00	0.00	46.27	3.53
452	460	3.009473	AGCAGCTCTACTTGGAATTGGAA	59.991	43.478	0.00	0.00	0.00	3.53
454	462	5.104360	AGCAGCTCTACTTGGAATTGGAATA	60.104	40.000	0.00	0.00	0.00	1.75
470	478	0.694444	AATATGACAGCCCCGGGTCT	60.694	55.000	21.85	9.82	35.11	3.85
471	479	0.190069	ATATGACAGCCCCGGGTCTA	59.810	55.000	21.85	0.00	35.11	2.59
476	484	1.382146	CAGCCCCGGGTCTAACCTA	60.382	63.158	21.85	0.00	38.64	3.08
603	620	4.033776	CAGTGGGGGCATCGGTGT	62.034	66.667	0.00	0.00	0.00	4.16
610	627	0.106149	GGGGCATCGGTGTTACTAGG	59.894	60.000	0.00	0.00	0.00	3.02
627	644	1.568504	AGGCTGGAGGATTGTTCGTA	58.431	50.000	0.00	0.00	0.00	3.43
773	793	0.598158	TGTACCGCGGTGTTCTGAAC	60.598	55.000	40.02	27.30	0.00	3.18
842	865	0.753479	TTGAAAGTCTTGGGCGGCAA	60.753	50.000	12.47	0.00	0.00	4.52
905	935	1.174078	TCCAGCACGTGAACCTCGTA	61.174	55.000	22.23	0.00	39.55	3.43
1041	1079	1.450848	CATCATGCTCGGTGTGGCT	60.451	57.895	0.00	0.00	0.00	4.75
1114	1152	1.556911	ACATCAAGCCGGAGAACATCT	59.443	47.619	5.05	0.00	0.00	2.90
1577	1621	1.146485	TGGAAGGCGTCGTCCAAAA	59.854	52.632	22.68	0.00	45.99	2.44
1624	1668	1.374758	GAGCACCTTGTCACCCTCG	60.375	63.158	0.00	0.00	0.00	4.63
1791	1845	7.922278	TGCAATTATTTAAAGATAGCTGCCTTG	59.078	33.333	0.00	0.00	0.00	3.61
1810	1864	6.209589	TGCCTTGTATAACAAAAACCATAGCA	59.790	34.615	0.00	0.00	37.69	3.49
1819	1873	5.375773	ACAAAAACCATAGCAAAAATGCCT	58.624	33.333	0.00	0.00	34.90	4.75
1829	1883	5.726980	AGCAAAAATGCCTAATGAAGACA	57.273	34.783	0.00	0.00	34.90	3.41
1951	2008	6.638063	ACATTTGTGTGAATTTTCATGTCGAG	59.362	34.615	0.00	0.00	39.73	4.04
1955	2012	4.055360	TGTGAATTTTCATGTCGAGACGT	58.945	39.130	0.00	0.00	39.73	4.34
1973	2030	4.857588	AGACGTGTTAAAATGAGAGCTACG	59.142	41.667	0.00	0.00	35.40	3.51
2122	2180	4.023622	CGTGTGAACATGGGTATTGTTTCA	60.024	41.667	0.00	0.00	37.43	2.69
2300	2359	3.338249	CGAACAGGTGAACCTCATGATT	58.662	45.455	0.00	0.00	46.65	2.57
2316	2375	4.223255	TCATGATTTTTGTGCACCCATGAT	59.777	37.500	15.69	1.87	35.45	2.45
2319	2378	2.721274	TTTTGTGCACCCATGATTCG	57.279	45.000	15.69	0.00	0.00	3.34
2324	2383	1.024046	TGCACCCATGATTCGAACCG	61.024	55.000	0.00	0.00	0.00	4.44
2364	2423	4.256920	AGCATTCACACTACAGGAATCAC	58.743	43.478	0.00	0.00	0.00	3.06
2368	2427	2.028112	TCACACTACAGGAATCACTGGC	60.028	50.000	0.00	0.00	42.75	4.85
2370	2429	3.195610	CACACTACAGGAATCACTGGCTA	59.804	47.826	0.00	0.00	42.75	3.93
2447	2506	3.399181	GACCTCCCGTGCCCATCA	61.399	66.667	0.00	0.00	0.00	3.07
2453	2512	1.598962	CCCGTGCCCATCAGCATAG	60.599	63.158	0.00	0.00	46.24	2.23
2454	2513	1.146930	CCGTGCCCATCAGCATAGT	59.853	57.895	0.00	0.00	46.24	2.12
2455	2514	0.392706	CCGTGCCCATCAGCATAGTA	59.607	55.000	0.00	0.00	46.24	1.82
2456	2515	1.202639	CCGTGCCCATCAGCATAGTAA	60.203	52.381	0.00	0.00	46.24	2.24
2457	2516	2.550855	CCGTGCCCATCAGCATAGTAAT	60.551	50.000	0.00	0.00	46.24	1.89
2458	2517	2.481568	CGTGCCCATCAGCATAGTAATG	59.518	50.000	0.00	0.00	46.24	1.90
2810	2869	6.515832	CCAAAGGAAAGTGCAGTATTTCTTT	58.484	36.000	14.99	13.93	36.59	2.52
2910	2979	6.270231	AGCTAAATACGGATGGTTCCTATTCT	59.730	38.462	0.00	0.00	40.17	2.40
3082	3152	2.752903	TCTGATCGTCCAATCGAAGTCA	59.247	45.455	0.00	0.00	42.99	3.41
3151	3222	3.243636	GGATCGGTCGGTTTATGCTTCTA	60.244	47.826	0.00	0.00	0.00	2.10

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
123	124	0.107459	CAAGGTAGCTTGCCTCCCTC	60.107	60.000	20.79	0.00	34.81	4.30
259	260	4.166011	GCAGCATCACGAACCCGC	62.166	66.667	0.00	0.00	39.95	6.13
293	294	1.080501	CACGGTGAGCGAGTCATGT	60.081	57.895	12.27	0.00	37.56	3.21
294	295	1.807165	CCACGGTGAGCGAGTCATG	60.807	63.158	12.27	0.00	37.56	3.07
441	449	3.960102	GGGCTGTCATATTCCAATTCCAA	59.040	43.478	0.00	0.00	0.00	3.53
442	450	3.565307	GGGCTGTCATATTCCAATTCCA	58.435	45.455	0.00	0.00	0.00	3.53
443	451	2.893489	GGGGCTGTCATATTCCAATTCC	59.107	50.000	0.00	0.00	0.00	3.01
444	452	2.554032	CGGGGCTGTCATATTCCAATTC	59.446	50.000	0.00	0.00	0.00	2.17
445	453	2.586425	CGGGGCTGTCATATTCCAATT	58.414	47.619	0.00	0.00	0.00	2.32
446	454	1.202927	CCGGGGCTGTCATATTCCAAT	60.203	52.381	0.00	0.00	0.00	3.16
452	460	0.190069	TAGACCCGGGGCTGTCATAT	59.810	55.000	40.61	14.13	33.89	1.78
454	462	1.306654	TTAGACCCGGGGCTGTCAT	60.307	57.895	40.61	15.92	33.89	3.06
603	620	3.132289	CGAACAATCCTCCAGCCTAGTAA	59.868	47.826	0.00	0.00	0.00	2.24
610	627	1.653151	GGTACGAACAATCCTCCAGC	58.347	55.000	0.00	0.00	0.00	4.85
627	644	1.355043	ACTGACTAGTCTCCTTCGGGT	59.645	52.381	23.01	6.89	31.66	5.28
773	793	0.541863	AGTTGTCTCCCTTATGCCGG	59.458	55.000	0.00	0.00	0.00	6.13
842	865	2.040544	CCGGAATTGCTTGTCGCCT	61.041	57.895	0.00	0.00	38.05	5.52
905	935	3.382832	CAGAACCCGAGGAGCCGT	61.383	66.667	0.00	0.00	0.00	5.68
1041	1079	1.075226	CAGGTAGGCCAGCCCTCTA	60.075	63.158	5.01	0.00	44.96	2.43
1077	1115	1.643880	TGTCGCAGTGTATGATGCAG	58.356	50.000	0.00	0.00	42.68	4.41
1114	1152	0.037326	GACATGTCCTCGTCCAGCAA	60.037	55.000	15.31	0.00	0.00	3.91
1447	1491	3.863543	CATCACATCGCCGCGCAA	61.864	61.111	8.75	0.00	0.00	4.85
1624	1668	0.638746	CCGCGACGTGAGAATTACAC	59.361	55.000	8.23	5.50	35.26	2.90
1673	1718	1.788308	GCGCGTACAGTTGTCTTGTTA	59.212	47.619	8.43	0.00	0.00	2.41
1691	1736	3.521220	GCAGTCGACGTGTACGCG	61.521	66.667	26.18	26.18	44.43	6.01
1703	1748	2.005971	AGTAATTTCGGTCGGCAGTC	57.994	50.000	0.00	0.00	0.00	3.51
1791	1845	9.753669	GCATTTTTGCTATGGTTTTTGTTATAC	57.246	29.630	0.00	0.00	0.00	1.47
1810	1864	5.713861	AGCTCTGTCTTCATTAGGCATTTTT	59.286	36.000	0.00	0.00	37.96	1.94
1819	1873	4.033009	TCCATGGAGCTCTGTCTTCATTA	58.967	43.478	11.44	0.00	29.99	1.90
1829	1883	0.030705	TAAGGCCTCCATGGAGCTCT	60.031	55.000	32.97	26.77	40.69	4.09
1910	1967	9.586435	CACACAAATGTACATTATGTCTCTAGA	57.414	33.333	24.99	0.00	36.72	2.43
1945	2002	4.862350	TCTCATTTTAACACGTCTCGACA	58.138	39.130	0.00	0.00	0.00	4.35
1951	2008	4.855388	TCGTAGCTCTCATTTTAACACGTC	59.145	41.667	0.00	0.00	0.00	4.34
1955	2012	7.442969	TCCTTTTTCGTAGCTCTCATTTTAACA	59.557	33.333	0.00	0.00	0.00	2.41
2039	2097	4.764679	ATTTTGAATTGCGAGCTACACA	57.235	36.364	0.00	0.00	0.00	3.72
2300	2359	2.234143	TCGAATCATGGGTGCACAAAA	58.766	42.857	20.43	3.23	0.00	2.44
2316	2375	1.144969	GTGATGCTTGACGGTTCGAA	58.855	50.000	0.00	0.00	0.00	3.71
2319	2378	2.096218	GTCTTGTGATGCTTGACGGTTC	60.096	50.000	0.00	0.00	0.00	3.62
2324	2383	1.127582	GCTCGTCTTGTGATGCTTGAC	59.872	52.381	0.00	0.00	0.00	3.18
2375	2434	2.886124	GCTGACCGCTTAGCCGAC	60.886	66.667	0.00	0.00	33.89	4.79
2376	2435	2.443260	TTTGCTGACCGCTTAGCCGA	62.443	55.000	0.00	0.00	39.15	5.54
2377	2436	1.970917	CTTTGCTGACCGCTTAGCCG	61.971	60.000	0.00	0.00	39.15	5.52
2413	2472	2.036475	AGGTCAGCCAACGCTATCTATG	59.964	50.000	0.00	0.00	46.25	2.23
2414	2473	2.297597	GAGGTCAGCCAACGCTATCTAT	59.702	50.000	0.00	0.00	46.25	1.98
2430	2489	3.391665	CTGATGGGCACGGGAGGTC	62.392	68.421	0.00	0.00	0.00	3.85
2433	2492	2.043604	TATGCTGATGGGCACGGGAG	62.044	60.000	0.00	0.00	45.36	4.30
2437	2496	2.238942	TTACTATGCTGATGGGCACG	57.761	50.000	0.00	0.00	45.36	5.34
2459	2518	2.819595	CCACTTCCATGCCGACGG	60.820	66.667	10.29	10.29	0.00	4.79
2460	2519	1.811266	CTCCACTTCCATGCCGACG	60.811	63.158	0.00	0.00	0.00	5.12
2461	2520	1.450312	CCTCCACTTCCATGCCGAC	60.450	63.158	0.00	0.00	0.00	4.79
2462	2521	1.612146	TCCTCCACTTCCATGCCGA	60.612	57.895	0.00	0.00	0.00	5.54
2607	2666	4.285020	TCTGAATATCACTCAGCTCACCT	58.715	43.478	0.00	0.00	40.18	4.00
2810	2869	1.131638	AAGAGGTGTGGCAGTGAGAA	58.868	50.000	0.00	0.00	0.00	2.87
2910	2979	4.263572	CCCGCACCACCACCAGAA	62.264	66.667	0.00	0.00	0.00	3.02
3082	3152	0.739561	GCCGTACTCGAGTCCATCTT	59.260	55.000	23.89	0.00	39.71	2.40
3151	3222	7.833285	ACAGTAACTTAATTTCACCAACCAT	57.167	32.000	0.00	0.00	0.00	3.55

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.