AutoCloner

Multiple sequence alignment - TraesCS7D01G509100

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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	TraesCS7D01G509100	chr7D	100.000	2851	0	0	1	2851	612776504	612773654	0.000000e+00	5265.0
1	TraesCS7D01G509100	chr7D	85.155	1226	149	19	1519	2732	612709262	612708058	0.000000e+00	1225.0
2	TraesCS7D01G509100	chr7D	77.386	880	140	36	2005	2850	612405461	612404607	4.300000e-128	468.0
3	TraesCS7D01G509100	chr7D	77.331	622	126	12	2067	2679	612936457	612935842	1.260000e-93	353.0
4	TraesCS7D01G509100	chr7D	83.758	314	40	7	686	994	612709932	612709625	1.290000e-73	287.0
5	TraesCS7D01G509100	chr7D	89.080	174	10	4	1144	1316	612709502	612709337	1.040000e-49	207.0
6	TraesCS7D01G509100	chr7D	92.500	80	5	1	1002	1081	612709582	612709504	2.320000e-21	113.0
7	TraesCS7D01G509100	chr7A	93.389	2859	142	22	6	2851	703563279	703560455	0.000000e+00	4189.0
8	TraesCS7D01G509100	chr7A	84.627	644	62	20	1519	2152	703546417	703545801	8.740000e-170	606.0
9	TraesCS7D01G509100	chr7A	82.484	314	48	5	686	994	703547081	703546770	4.680000e-68	268.0
10	TraesCS7D01G509100	chr7A	86.857	175	14	6	1143	1316	703546658	703546492	1.350000e-43	187.0
11	TraesCS7D01G509100	chr7B	93.561	1584	87	7	7	1584	702235260	702233686	0.000000e+00	2346.0
12	TraesCS7D01G509100	chr7B	94.598	833	36	5	1860	2689	702229376	702228550	0.000000e+00	1280.0
13	TraesCS7D01G509100	chr7B	83.943	1202	143	22	1519	2709	702179024	702177862	0.000000e+00	1105.0
14	TraesCS7D01G509100	chr7B	92.797	236	11	2	1634	1863	702233673	702233438	1.270000e-88	337.0
15	TraesCS7D01G509100	chr7B	84.177	316	39	6	686	994	702179681	702179370	2.150000e-76	296.0
16	TraesCS7D01G509100	chr7B	74.880	625	118	15	2067	2679	702461711	702461114	6.100000e-62	248.0
17	TraesCS7D01G509100	chr7B	87.831	189	7	4	2671	2851	702227406	702227226	1.040000e-49	207.0
18	TraesCS7D01G509100	chr7B	90.361	83	6	2	984	1064	702179350	702179268	1.080000e-19	108.0
19	TraesCS7D01G509100	chr1B	79.572	1121	168	41	1769	2846	10046569	10047671	0.000000e+00	745.0
20	TraesCS7D01G509100	chr1B	90.411	73	3	2	1359	1428	571834624	571834695	3.020000e-15	93.5
21	TraesCS7D01G509100	chr1D	80.064	943	148	27	1769	2681	7237492	7236560	0.000000e+00	664.0
22	TraesCS7D01G509100	chr1D	90.411	73	3	2	1359	1428	422984214	422984285	3.020000e-15	93.5
23	TraesCS7D01G509100	chr2A	79.935	309	55	6	2143	2449	698178296	698177993	1.330000e-53	220.0
24	TraesCS7D01G509100	chr1A	91.781	73	2	3	1359	1428	518935065	518935136	6.500000e-17	99.0

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	TraesCS7D01G509100	chr7D	612773654	612776504	2850	True	5265.000000	5265	100.000000	1	2851	1	chr7D.!!$R2	2850
1	TraesCS7D01G509100	chr7D	612404607	612405461	854	True	468.000000	468	77.386000	2005	2850	1	chr7D.!!$R1	845
2	TraesCS7D01G509100	chr7D	612708058	612709932	1874	True	458.000000	1225	87.623250	686	2732	4	chr7D.!!$R4	2046
3	TraesCS7D01G509100	chr7D	612935842	612936457	615	True	353.000000	353	77.331000	2067	2679	1	chr7D.!!$R3	612
4	TraesCS7D01G509100	chr7A	703560455	703563279	2824	True	4189.000000	4189	93.389000	6	2851	1	chr7A.!!$R1	2845
5	TraesCS7D01G509100	chr7A	703545801	703547081	1280	True	353.666667	606	84.656000	686	2152	3	chr7A.!!$R2	1466
6	TraesCS7D01G509100	chr7B	702233438	702235260	1822	True	1341.500000	2346	93.179000	7	1863	2	chr7B.!!$R4	1856
7	TraesCS7D01G509100	chr7B	702227226	702229376	2150	True	743.500000	1280	91.214500	1860	2851	2	chr7B.!!$R3	991
8	TraesCS7D01G509100	chr7B	702177862	702179681	1819	True	503.000000	1105	86.160333	686	2709	3	chr7B.!!$R2	2023
9	TraesCS7D01G509100	chr7B	702461114	702461711	597	True	248.000000	248	74.880000	2067	2679	1	chr7B.!!$R1	612
10	TraesCS7D01G509100	chr1B	10046569	10047671	1102	False	745.000000	745	79.572000	1769	2846	1	chr1B.!!$F1	1077
11	TraesCS7D01G509100	chr1D	7236560	7237492	932	True	664.000000	664	80.064000	1769	2681	1	chr1D.!!$R1	912

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	Hairpin	End Stability	Orientation
322	326	0.856982	TTCCTTTTCCAGCTTGGGGA	59.143	50.000	2.86	38.32	4.81	F
624	628	1.134580	AGCAGACAAGATGATCGGTGG	60.135	52.381	4.58	0.00	4.61	F
1282	1370	1.392853	CGCTCTCAGCAGTGTGAATTC	59.607	52.381	0.00	42.58	2.17	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1599	1714	0.327259	ACAGGCTGACACATGAGCAT	59.673	50.0	23.66	0.00	36.9	3.79	R
1600	1715	0.604511	CACAGGCTGACACATGAGCA	60.605	55.0	23.66	0.00	36.9	4.26	R
2349	2502	1.458398	TCTCCTTGACTGCTCTCGAG	58.542	55.0	5.93	5.93	0.0	4.04	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
40	42	4.098349	AGACAAAAGATGCAAGTGAAAGCA	59.902	37.500	0.00	0.00	45.92	3.91
74	76	4.778534	AGGATCATTGCAACAAGACAAG	57.221	40.909	0.00	0.00	0.00	3.16
81	84	1.464608	TGCAACAAGACAAGCTATCGC	59.535	47.619	0.00	0.00	0.00	4.58
113	116	2.287373	GCCTCGCTTTCAGATTCAGATG	59.713	50.000	0.00	0.00	0.00	2.90
199	202	1.597027	CTGAAAACGCCACCTCCGT	60.597	57.895	0.00	0.00	41.24	4.69
322	326	0.856982	TTCCTTTTCCAGCTTGGGGA	59.143	50.000	2.86	0.00	38.32	4.81
354	358	2.408050	GACGTGCTCAACTGACTGATT	58.592	47.619	0.00	0.00	0.00	2.57
363	367	5.392380	GCTCAACTGACTGATTACAAATGGG	60.392	44.000	0.00	0.00	0.00	4.00
405	409	3.058914	CGTGCCACTCTTTCTAACTTTGG	60.059	47.826	0.00	0.00	0.00	3.28
407	411	4.023963	GTGCCACTCTTTCTAACTTTGGTC	60.024	45.833	0.00	0.00	0.00	4.02
418	422	6.801539	TCTAACTTTGGTCTGCTTTATGTG	57.198	37.500	0.00	0.00	0.00	3.21
523	527	2.203126	CAGATCTTCTGGGGCCGC	60.203	66.667	14.01	14.01	40.71	6.53
542	546	3.384668	CGCGATATGACCATTGTTCTCT	58.615	45.455	0.00	0.00	0.00	3.10
566	570	5.954752	TGTTTCAGGTGGATTATTTGCCATA	59.045	36.000	0.00	0.00	36.41	2.74
567	571	6.610830	TGTTTCAGGTGGATTATTTGCCATAT	59.389	34.615	0.00	0.00	36.41	1.78
624	628	1.134580	AGCAGACAAGATGATCGGTGG	60.135	52.381	4.58	0.00	0.00	4.61
690	694	8.974060	ACTACTTCCATTTTAGACAAACTGAA	57.026	30.769	0.00	0.00	0.00	3.02
705	709	6.815089	ACAAACTGAAAAGCCACAATATTCA	58.185	32.000	0.00	0.00	0.00	2.57
755	759	4.081406	TCACTTGCAGCCTACAATTGAAT	58.919	39.130	13.59	0.00	34.83	2.57
759	763	3.156293	TGCAGCCTACAATTGAATGTGT	58.844	40.909	13.59	0.00	34.75	3.72
792	797	6.506464	TTCGTCTCAAAAAGAAGTACGAAG	57.494	37.500	0.00	0.00	39.21	3.79
834	842	3.259374	AGTGTCCACTGATTGTACCTGAG	59.741	47.826	0.00	0.00	40.75	3.35
835	843	3.258372	GTGTCCACTGATTGTACCTGAGA	59.742	47.826	0.00	0.00	0.00	3.27
848	862	4.962362	TGTACCTGAGAGAGGATATGCAAA	59.038	41.667	0.00	0.00	46.33	3.68
857	871	3.201708	AGAGGATATGCAAAAGCCAGACT	59.798	43.478	9.14	3.32	0.00	3.24
906	920	2.040679	GGAGTCTACCTAGCTCCCCTAG	59.959	59.091	0.00	0.00	42.68	3.02
1068	1152	6.887626	TTAACAATTCCCTAACAGACCAAC	57.112	37.500	0.00	0.00	0.00	3.77
1282	1370	1.392853	CGCTCTCAGCAGTGTGAATTC	59.607	52.381	0.00	0.00	42.58	2.17
1343	1431	2.672908	CTGGCATGTGAGCAGGGA	59.327	61.111	0.00	0.00	35.83	4.20
1481	1569	1.536766	GTTTACCCACCGGTTTACTGC	59.463	52.381	2.97	0.00	40.58	4.40
1584	1699	2.210116	GTCGGTTGTGTGAGTGAATGT	58.790	47.619	0.00	0.00	0.00	2.71
1585	1700	2.612212	GTCGGTTGTGTGAGTGAATGTT	59.388	45.455	0.00	0.00	0.00	2.71
1587	1702	4.451096	GTCGGTTGTGTGAGTGAATGTTAT	59.549	41.667	0.00	0.00	0.00	1.89
1588	1703	4.450757	TCGGTTGTGTGAGTGAATGTTATG	59.549	41.667	0.00	0.00	0.00	1.90
1593	1708	5.129634	TGTGTGAGTGAATGTTATGGTGTT	58.870	37.500	0.00	0.00	0.00	3.32
1594	1709	5.238432	TGTGTGAGTGAATGTTATGGTGTTC	59.762	40.000	0.00	0.00	0.00	3.18
1595	1710	5.470098	GTGTGAGTGAATGTTATGGTGTTCT	59.530	40.000	0.00	0.00	0.00	3.01
1596	1711	6.017109	GTGTGAGTGAATGTTATGGTGTTCTT	60.017	38.462	0.00	0.00	0.00	2.52
1597	1712	6.017192	TGTGAGTGAATGTTATGGTGTTCTTG	60.017	38.462	0.00	0.00	0.00	3.02
1598	1713	6.204688	GTGAGTGAATGTTATGGTGTTCTTGA	59.795	38.462	0.00	0.00	0.00	3.02
1599	1714	6.770303	TGAGTGAATGTTATGGTGTTCTTGAA	59.230	34.615	0.00	0.00	0.00	2.69
1600	1715	7.448161	TGAGTGAATGTTATGGTGTTCTTGAAT	59.552	33.333	0.00	0.00	0.00	2.57
1601	1716	7.596494	AGTGAATGTTATGGTGTTCTTGAATG	58.404	34.615	0.00	0.00	0.00	2.67
1602	1717	6.308766	GTGAATGTTATGGTGTTCTTGAATGC	59.691	38.462	0.00	0.00	0.00	3.56
1614	1729	2.745821	TCTTGAATGCTCATGTGTCAGC	59.254	45.455	0.00	0.00	36.08	4.26
1630	1745	1.065491	TCAGCCTGTGTGTTGACTGTT	60.065	47.619	0.00	0.00	0.00	3.16
1857	1989	4.202567	ACATATGTGAAAGGAAGGGTGTGT	60.203	41.667	7.78	0.00	0.00	3.72
1897	2031	0.243636	ATGCAAAAGTAAGCCCACGC	59.756	50.000	0.00	0.00	0.00	5.34
1991	2133	7.549842	TGTTGGATCATAATTTTGGCAGAAATG	59.450	33.333	0.00	0.00	30.06	2.32
2012	2154	9.840427	GAAATGTAGCATTTTGACTTAGCTAAA	57.160	29.630	7.74	0.00	39.26	1.85
2020	2162	9.034544	GCATTTTGACTTAGCTAAATAATTGGG	57.965	33.333	7.74	0.00	0.00	4.12
2023	2165	7.548196	TTGACTTAGCTAAATAATTGGGACG	57.452	36.000	7.74	0.00	0.00	4.79
2081	2229	6.092092	TGCCACATATTCAACAAATCTTTCG	58.908	36.000	0.00	0.00	0.00	3.46
2163	2316	9.486123	AACATATACTCACCAGAGCTATGATAT	57.514	33.333	10.62	1.13	46.09	1.63
2289	2442	2.001357	CATCGGTGCACATCTGACG	58.999	57.895	20.43	11.84	0.00	4.35
2349	2502	2.725221	AGCCATTGATCTCCACTTCC	57.275	50.000	0.00	0.00	0.00	3.46
2687	4038	3.511934	AGTTATCCGCCTCATCCTGATAC	59.488	47.826	0.00	0.00	0.00	2.24
2702	4053	3.961480	TGATACACAGACAAGTCCTGG	57.039	47.619	0.00	0.00	36.03	4.45
2714	4069	5.656416	AGACAAGTCCTGGAAAAACAATTGA	59.344	36.000	13.59	0.00	0.00	2.57
2717	4072	3.004734	AGTCCTGGAAAAACAATTGAGCG	59.995	43.478	13.59	0.00	0.00	5.03
2836	4205	0.980423	GGGAGCTGTCCTTGTCTCTT	59.020	55.000	0.00	0.00	43.36	2.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	2.668212	TGCCTTTTCCTCACGCGG	60.668	61.111	12.47	0.00	0.00	6.46
1	2	1.667830	TCTGCCTTTTCCTCACGCG	60.668	57.895	3.53	3.53	0.00	6.01
2	3	0.884704	TGTCTGCCTTTTCCTCACGC	60.885	55.000	0.00	0.00	0.00	5.34
3	4	1.593196	TTGTCTGCCTTTTCCTCACG	58.407	50.000	0.00	0.00	0.00	4.35
5	6	3.897239	TCTTTTGTCTGCCTTTTCCTCA	58.103	40.909	0.00	0.00	0.00	3.86
40	42	5.130975	TGCAATGATCCTATCACCACTAACT	59.869	40.000	0.00	0.00	43.01	2.24
81	84	3.842869	AGCGAGGCTTTCCACTAAG	57.157	52.632	0.00	0.00	33.89	2.18
113	116	5.009210	AGCTTACACCGAACTCTATCTGATC	59.991	44.000	0.00	0.00	0.00	2.92
224	227	0.548031	ATCCACCATCGTCCAATGCT	59.452	50.000	0.00	0.00	0.00	3.79
322	326	0.978146	AGCACGTCCCTGCTAGGAAT	60.978	55.000	0.00	0.00	46.03	3.01
354	358	0.040942	AGCACCATGGCCCATTTGTA	59.959	50.000	13.04	0.00	0.00	2.41
363	367	1.799544	CTTTTGGAAAGCACCATGGC	58.200	50.000	13.04	0.00	39.82	4.40
405	409	3.372206	CAGTACAGCCACATAAAGCAGAC	59.628	47.826	0.00	0.00	0.00	3.51
407	411	2.096496	GCAGTACAGCCACATAAAGCAG	59.904	50.000	0.00	0.00	0.00	4.24
418	422	2.099141	TCATCAAGTGCAGTACAGCC	57.901	50.000	7.87	0.00	0.00	4.85
506	510	2.203126	GCGGCCCCAGAAGATCTG	60.203	66.667	0.00	0.32	43.91	2.90
507	511	3.854669	CGCGGCCCCAGAAGATCT	61.855	66.667	0.00	0.00	0.00	2.75
523	527	6.313658	TGAAACAGAGAACAATGGTCATATCG	59.686	38.462	0.00	0.00	0.00	2.92
542	546	4.155709	TGGCAAATAATCCACCTGAAACA	58.844	39.130	0.00	0.00	0.00	2.83
617	621	2.569059	CTTGCAGATCAATCCACCGAT	58.431	47.619	0.00	0.00	33.57	4.18
624	628	4.789012	TGTTTTCCCTTGCAGATCAATC	57.211	40.909	0.00	0.00	33.57	2.67
679	683	6.655078	ATATTGTGGCTTTTCAGTTTGTCT	57.345	33.333	0.00	0.00	0.00	3.41
690	694	5.948162	AGTCTCACATGAATATTGTGGCTTT	59.052	36.000	0.00	0.00	43.67	3.51
705	709	2.757868	GTCTCCAGCTACAGTCTCACAT	59.242	50.000	0.00	0.00	0.00	3.21
755	759	4.951254	TGAGACGAATGTAAGGAAACACA	58.049	39.130	0.00	0.00	30.75	3.72
759	763	7.795482	TCTTTTTGAGACGAATGTAAGGAAA	57.205	32.000	0.00	0.00	0.00	3.13
792	797	3.441572	ACTTGTCCATCAATAACAGCAGC	59.558	43.478	0.00	0.00	35.35	5.25
857	871	3.009033	GGCATTATATGAGTGGTGGCCTA	59.991	47.826	3.32	0.00	36.04	3.93
906	920	2.688446	GGCCTTACCACTTTCTTATGCC	59.312	50.000	0.00	0.00	38.86	4.40
1068	1152	2.790791	CCCAGGTCTCTGCTAGCGG	61.791	68.421	17.99	17.99	39.61	5.52
1481	1569	2.754472	TGATCACAACTCACAAGGACG	58.246	47.619	0.00	0.00	0.00	4.79
1584	1699	5.711506	ACATGAGCATTCAAGAACACCATAA	59.288	36.000	0.00	0.00	36.78	1.90
1585	1700	5.124297	CACATGAGCATTCAAGAACACCATA	59.876	40.000	0.00	0.00	36.78	2.74
1587	1702	3.253921	CACATGAGCATTCAAGAACACCA	59.746	43.478	0.00	0.00	36.78	4.17
1588	1703	3.254166	ACACATGAGCATTCAAGAACACC	59.746	43.478	0.00	0.00	36.78	4.16
1593	1708	2.745821	GCTGACACATGAGCATTCAAGA	59.254	45.455	0.00	0.00	36.78	3.02
1594	1709	2.159421	GGCTGACACATGAGCATTCAAG	60.159	50.000	0.00	0.00	36.78	3.02
1595	1710	1.814394	GGCTGACACATGAGCATTCAA	59.186	47.619	0.00	0.00	36.78	2.69
1596	1711	1.003928	AGGCTGACACATGAGCATTCA	59.996	47.619	0.00	0.00	36.90	2.57
1597	1712	1.400846	CAGGCTGACACATGAGCATTC	59.599	52.381	9.42	0.00	36.90	2.67
1598	1713	1.271762	ACAGGCTGACACATGAGCATT	60.272	47.619	23.66	0.00	36.90	3.56
1599	1714	0.327259	ACAGGCTGACACATGAGCAT	59.673	50.000	23.66	0.00	36.90	3.79
1600	1715	0.604511	CACAGGCTGACACATGAGCA	60.605	55.000	23.66	0.00	36.90	4.26
1601	1716	0.604780	ACACAGGCTGACACATGAGC	60.605	55.000	23.66	0.00	34.23	4.26
1602	1717	1.154197	CACACAGGCTGACACATGAG	58.846	55.000	23.66	3.18	0.00	2.90
1614	1729	3.309682	CACAGTAACAGTCAACACACAGG	59.690	47.826	0.00	0.00	0.00	4.00
1630	1745	9.424319	CTTCTTTTAGCTAATTGACTCACAGTA	57.576	33.333	7.08	0.00	0.00	2.74
2012	2154	4.776349	TGTGCTTGTATCGTCCCAATTAT	58.224	39.130	0.00	0.00	0.00	1.28
2013	2155	4.209307	TGTGCTTGTATCGTCCCAATTA	57.791	40.909	0.00	0.00	0.00	1.40
2020	2162	7.751047	TTATAGAGTTTGTGCTTGTATCGTC	57.249	36.000	0.00	0.00	0.00	4.20
2021	2163	8.604035	CAATTATAGAGTTTGTGCTTGTATCGT	58.396	33.333	0.00	0.00	0.00	3.73
2022	2164	8.064222	CCAATTATAGAGTTTGTGCTTGTATCG	58.936	37.037	0.00	0.00	0.00	2.92
2023	2165	7.857885	GCCAATTATAGAGTTTGTGCTTGTATC	59.142	37.037	0.00	0.00	0.00	2.24
2111	2259	2.727777	TGTATGATTAGCGTGCTCGTC	58.272	47.619	10.18	2.47	39.49	4.20
2163	2316	3.755112	TCTTCGGTGGAATGTTGTGTA	57.245	42.857	0.00	0.00	0.00	2.90
2349	2502	1.458398	TCTCCTTGACTGCTCTCGAG	58.542	55.000	5.93	5.93	0.00	4.04
2386	2539	4.020617	TCCTTGCGAGGCCACAGG	62.021	66.667	16.01	1.46	43.21	4.00
2687	4038	3.694072	TGTTTTTCCAGGACTTGTCTGTG	59.306	43.478	0.00	0.00	0.00	3.66
2702	4053	6.791303	TGTATATCCCGCTCAATTGTTTTTC	58.209	36.000	5.13	0.00	0.00	2.29
2714	4069	6.833933	TGTGAGTGATATATGTATATCCCGCT	59.166	38.462	14.38	10.77	42.35	5.52

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.