AutoCloner

Multiple sequence alignment - TraesCS7D01G166600

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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	TraesCS7D01G166600	chr7D	100.000	2210	0	0	1	2210	117271318	117269109	0.000000e+00	4082.0
1	TraesCS7D01G166600	chr7D	89.474	380	33	5	880	1258	117472409	117472036	7.140000e-130	473.0
2	TraesCS7D01G166600	chr7D	82.909	275	18	10	598	843	117472687	117472413	1.030000e-53	220.0
3	TraesCS7D01G166600	chr7D	86.207	87	8	3	1638	1720	174830481	174830395	8.400000e-15	91.6
4	TraesCS7D01G166600	chr7B	90.115	1659	151	7	561	2210	77569980	77568326	0.000000e+00	2143.0
5	TraesCS7D01G166600	chr7B	88.158	380	38	5	880	1258	77818387	77818014	1.560000e-121	446.0
6	TraesCS7D01G166600	chr7B	81.395	301	22	15	576	843	77818691	77818392	4.780000e-52	215.0
7	TraesCS7D01G166600	chr7B	87.179	78	10	0	1604	1681	577673159	577673082	3.020000e-14	89.8
8	TraesCS7D01G166600	chr7A	85.645	1658	180	20	561	2191	121563206	121561580	0.000000e+00	1690.0
9	TraesCS7D01G166600	chr7A	89.663	919	37	17	561	1454	121611745	121610860	0.000000e+00	1118.0
10	TraesCS7D01G166600	chr7A	87.073	820	67	12	561	1377	121558662	121557879	0.000000e+00	891.0
11	TraesCS7D01G166600	chr7A	83.481	678	67	27	606	1250	121859137	121858472	6.800000e-165	590.0
12	TraesCS7D01G166600	chr6D	88.204	568	40	11	1	566	445280655	445281197	0.000000e+00	652.0
13	TraesCS7D01G166600	chr6D	87.676	568	43	10	1	566	445212429	445212971	8.610000e-179	636.0
14	TraesCS7D01G166600	chr6D	84.441	572	62	11	1	567	434946734	434947283	2.500000e-149	538.0
15	TraesCS7D01G166600	chr6D	81.345	461	80	4	1754	2210	317861023	317860565	9.640000e-99	370.0
16	TraesCS7D01G166600	chr2D	87.478	567	44	7	1	565	595208775	595209316	1.440000e-176	628.0
17	TraesCS7D01G166600	chr2D	86.420	567	43	15	1	565	3002372	3001838	6.800000e-165	590.0
18	TraesCS7D01G166600	chr2D	85.461	564	63	13	3	563	580617130	580617677	8.850000e-159	569.0
19	TraesCS7D01G166600	chr2D	82.991	535	79	11	1646	2172	560325346	560324816	7.140000e-130	473.0
20	TraesCS7D01G166600	chr1D	87.234	564	41	11	1	560	240987926	240988462	4.030000e-172	614.0
21	TraesCS7D01G166600	chr1D	86.127	519	43	10	45	562	431050664	431050174	1.160000e-147	532.0
22	TraesCS7D01G166600	chr1D	84.155	568	62	21	1	561	439114625	439114079	1.940000e-145	525.0
23	TraesCS7D01G166600	chr1A	86.042	566	54	12	1	562	202084622	202085166	3.160000e-163	584.0
24	TraesCS7D01G166600	chr1A	79.618	628	109	15	1594	2210	444426359	444425740	1.210000e-117	433.0
25	TraesCS7D01G166600	chr1A	80.470	553	94	11	1586	2129	590617556	590618103	5.680000e-111	411.0
26	TraesCS7D01G166600	chr5D	85.035	568	58	13	1	562	35290886	35291432	8.920000e-154	553.0
27	TraesCS7D01G166600	chr5D	90.179	224	20	2	346	568	424798627	424798849	7.720000e-75	291.0
28	TraesCS7D01G166600	chr3D	84.331	568	51	15	1	565	298983257	298983789	2.510000e-144	521.0
29	TraesCS7D01G166600	chr5A	85.069	509	60	11	62	566	356138333	356137837	2.530000e-139	505.0
30	TraesCS7D01G166600	chr5A	78.261	575	102	19	1646	2210	302298913	302299474	4.520000e-92	348.0
31	TraesCS7D01G166600	chr5A	90.909	220	16	3	346	564	665702995	665702779	2.150000e-75	292.0
32	TraesCS7D01G166600	chr1B	82.783	575	69	16	1	565	599517172	599516618	9.170000e-134	486.0
33	TraesCS7D01G166600	chr2B	78.906	640	109	20	1586	2210	200480853	200481481	5.680000e-111	411.0
34	TraesCS7D01G166600	chr4D	77.445	634	130	12	1586	2210	337428821	337428192	1.250000e-97	366.0
35	TraesCS7D01G166600	chr2A	76.379	707	151	12	1516	2210	766493705	766493003	1.250000e-97	366.0
36	TraesCS7D01G166600	chr3A	83.333	150	25	0	1006	1155	57007797	57007946	2.960000e-29	139.0

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	TraesCS7D01G166600	chr7D	117269109	117271318	2209	True	4082.0	4082	100.0000	1	2210	1	chr7D.!!$R1	2209
1	TraesCS7D01G166600	chr7D	117472036	117472687	651	True	346.5	473	86.1915	598	1258	2	chr7D.!!$R3	660
2	TraesCS7D01G166600	chr7B	77568326	77569980	1654	True	2143.0	2143	90.1150	561	2210	1	chr7B.!!$R1	1649
3	TraesCS7D01G166600	chr7B	77818014	77818691	677	True	330.5	446	84.7765	576	1258	2	chr7B.!!$R3	682
4	TraesCS7D01G166600	chr7A	121557879	121563206	5327	True	1290.5	1690	86.3590	561	2191	2	chr7A.!!$R3	1630
5	TraesCS7D01G166600	chr7A	121610860	121611745	885	True	1118.0	1118	89.6630	561	1454	1	chr7A.!!$R1	893
6	TraesCS7D01G166600	chr7A	121858472	121859137	665	True	590.0	590	83.4810	606	1250	1	chr7A.!!$R2	644
7	TraesCS7D01G166600	chr6D	445280655	445281197	542	False	652.0	652	88.2040	1	566	1	chr6D.!!$F3	565
8	TraesCS7D01G166600	chr6D	445212429	445212971	542	False	636.0	636	87.6760	1	566	1	chr6D.!!$F2	565
9	TraesCS7D01G166600	chr6D	434946734	434947283	549	False	538.0	538	84.4410	1	567	1	chr6D.!!$F1	566
10	TraesCS7D01G166600	chr2D	595208775	595209316	541	False	628.0	628	87.4780	1	565	1	chr2D.!!$F2	564
11	TraesCS7D01G166600	chr2D	3001838	3002372	534	True	590.0	590	86.4200	1	565	1	chr2D.!!$R1	564
12	TraesCS7D01G166600	chr2D	580617130	580617677	547	False	569.0	569	85.4610	3	563	1	chr2D.!!$F1	560
13	TraesCS7D01G166600	chr2D	560324816	560325346	530	True	473.0	473	82.9910	1646	2172	1	chr2D.!!$R2	526
14	TraesCS7D01G166600	chr1D	240987926	240988462	536	False	614.0	614	87.2340	1	560	1	chr1D.!!$F1	559
15	TraesCS7D01G166600	chr1D	439114079	439114625	546	True	525.0	525	84.1550	1	561	1	chr1D.!!$R2	560
16	TraesCS7D01G166600	chr1A	202084622	202085166	544	False	584.0	584	86.0420	1	562	1	chr1A.!!$F1	561
17	TraesCS7D01G166600	chr1A	444425740	444426359	619	True	433.0	433	79.6180	1594	2210	1	chr1A.!!$R1	616
18	TraesCS7D01G166600	chr1A	590617556	590618103	547	False	411.0	411	80.4700	1586	2129	1	chr1A.!!$F2	543
19	TraesCS7D01G166600	chr5D	35290886	35291432	546	False	553.0	553	85.0350	1	562	1	chr5D.!!$F1	561
20	TraesCS7D01G166600	chr3D	298983257	298983789	532	False	521.0	521	84.3310	1	565	1	chr3D.!!$F1	564
21	TraesCS7D01G166600	chr5A	302298913	302299474	561	False	348.0	348	78.2610	1646	2210	1	chr5A.!!$F1	564
22	TraesCS7D01G166600	chr1B	599516618	599517172	554	True	486.0	486	82.7830	1	565	1	chr1B.!!$R1	564
23	TraesCS7D01G166600	chr2B	200480853	200481481	628	False	411.0	411	78.9060	1586	2210	1	chr2B.!!$F1	624
24	TraesCS7D01G166600	chr4D	337428192	337428821	629	True	366.0	366	77.4450	1586	2210	1	chr4D.!!$R1	624
25	TraesCS7D01G166600	chr2A	766493003	766493705	702	True	366.0	366	76.3790	1516	2210	1	chr2A.!!$R1	694

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
828	922	0.386838	AGTGAAGCACTTGCCTTTGC	59.613	50.0	0.0	0.0	42.59	3.68	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1976	2108	0.034574	TGCATTTAGTGTCGGCCCAT	60.035	50.0	0.0	0.0	0.0	4.0	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
28	29	0.669625	GGACGAACCTGTACCTGCAC	60.670	60.000	0.00	0.00	35.41	4.57
151	154	3.849951	GAAGGGCCGCAGATCCGA	61.850	66.667	0.00	0.00	0.00	4.55
493	512	0.610785	TGATCGGGCAGGTTTTTCCC	60.611	55.000	0.00	0.00	36.75	3.97
530	549	0.519961	GCGGTTATTTTGCAGGTCGT	59.480	50.000	0.00	0.00	0.00	4.34
647	678	7.486647	AGATAGTTTTCGGACAATACATACGT	58.513	34.615	0.00	0.00	0.00	3.57
667	709	0.934496	GTGTTGTTGCTGTCAGCGTA	59.066	50.000	19.68	7.80	46.26	4.42
828	922	0.386838	AGTGAAGCACTTGCCTTTGC	59.613	50.000	0.00	0.00	42.59	3.68
829	923	2.296334	AGTGAAGCACTTGCCTTTGCA	61.296	47.619	0.00	0.00	42.59	4.08
830	924	4.160899	AGTGAAGCACTTGCCTTTGCAG	62.161	50.000	0.00	0.00	42.59	4.41
955	1055	3.303791	GGTCTAACGTTTTTGCAGACTGG	60.304	47.826	21.38	0.00	36.65	4.00
1118	1227	3.430862	CAATGGCACCACCGTCGG	61.431	66.667	10.48	10.48	43.94	4.79
1231	1349	4.778143	CGCCTTACCTTGCCGCCT	62.778	66.667	0.00	0.00	0.00	5.52
1343	1461	6.205784	TGAAATCTCGTTTACTTTTGGCAAG	58.794	36.000	0.00	0.00	0.00	4.01
1359	1477	2.407090	GCAAGTTGGCAAAGGAATCAC	58.593	47.619	0.00	0.00	0.00	3.06
1410	1528	7.639162	AAAAATAACTCGCTGTCTATATCCG	57.361	36.000	0.00	0.00	0.00	4.18
1431	1549	2.094906	GTGAAACGCATTTAAGTCCCCC	60.095	50.000	0.00	0.00	0.00	5.40
1479	1598	2.489073	CCCCCTTCCGAAATATTGGGAG	60.489	54.545	7.67	1.23	38.83	4.30
1535	1656	0.620556	AGGGCATCTCCAACGTCAAT	59.379	50.000	0.00	0.00	36.21	2.57
1549	1670	1.177401	GTCAATCCTCAAACCTGCCC	58.823	55.000	0.00	0.00	0.00	5.36
1554	1675	1.139498	TCCTCAAACCTGCCCCATCA	61.139	55.000	0.00	0.00	0.00	3.07
1556	1677	1.631405	CTCAAACCTGCCCCATCAAA	58.369	50.000	0.00	0.00	0.00	2.69
1563	1684	2.355115	GCCCCATCAAACCGGACT	59.645	61.111	9.46	0.00	0.00	3.85
1591	1716	1.595929	GGACCGTGAAAGCCAACGA	60.596	57.895	0.00	0.00	0.00	3.85
1613	1738	2.743928	CTGTTCTGGTCTGCGGCC	60.744	66.667	0.00	0.00	0.00	6.13
1641	1766	0.240945	ACGCATTTTCTCCGGCAAAG	59.759	50.000	0.00	0.00	0.00	2.77
1675	1801	1.761174	GGAGGTTTGCAGGAGTCCA	59.239	57.895	12.86	0.00	0.00	4.02
1730	1860	0.893727	CAAAAACCCTCCCCCTGTCG	60.894	60.000	0.00	0.00	0.00	4.35
1760	1891	2.111043	CACCTGTCGCCCAGTTGT	59.889	61.111	1.99	0.00	39.74	3.32
1790	1921	4.907034	CGATGTAGAGCGCGCCGT	62.907	66.667	30.33	18.37	0.00	5.68
1917	2049	0.787787	TCTTCGTCGCATTCAAACGG	59.212	50.000	0.00	0.00	37.05	4.44
1935	2067	1.405797	CGGCTCCATTAAACCCGTGTA	60.406	52.381	0.00	0.00	34.56	2.90
1947	2079	0.460311	CCCGTGTAGAAGCCGAGAAT	59.540	55.000	0.00	0.00	0.00	2.40
1956	2088	3.637769	AGAAGCCGAGAATCCTACTTCT	58.362	45.455	0.00	0.00	39.12	2.85
1976	2108	1.225855	GCCACACATCTGTTCACGAA	58.774	50.000	0.00	0.00	0.00	3.85
1987	2119	1.669760	TTCACGAATGGGCCGACAC	60.670	57.895	0.00	0.00	0.00	3.67
1999	2131	0.515564	GCCGACACTAAATGCAACGT	59.484	50.000	0.00	0.00	0.00	3.99
2034	2166	3.714798	TCCTGTCCGCCCTCTATTTAAAT	59.285	43.478	5.89	5.89	0.00	1.40
2039	2171	4.455877	GTCCGCCCTCTATTTAAATGATGG	59.544	45.833	11.05	12.27	0.00	3.51
2150	2286	1.432270	GCAGAGCAGTTCGGGCATAC	61.432	60.000	0.00	0.00	33.11	2.39

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
330	343	2.118404	GGTGTGTGTGTGTGTGGGG	61.118	63.158	0.00	0.00	0.00	4.96
334	347	1.302383	CGGTTGGTGTGTGTGTGTGT	61.302	55.000	0.00	0.00	0.00	3.72
335	348	1.427419	CGGTTGGTGTGTGTGTGTG	59.573	57.895	0.00	0.00	0.00	3.82
336	349	2.403378	GCGGTTGGTGTGTGTGTGT	61.403	57.895	0.00	0.00	0.00	3.72
337	350	1.653094	AAGCGGTTGGTGTGTGTGTG	61.653	55.000	0.00	0.00	0.00	3.82
338	351	1.373590	GAAGCGGTTGGTGTGTGTGT	61.374	55.000	3.70	0.00	0.00	3.72
339	352	1.355210	GAAGCGGTTGGTGTGTGTG	59.645	57.895	3.70	0.00	0.00	3.82
340	353	1.822186	GGAAGCGGTTGGTGTGTGT	60.822	57.895	3.70	0.00	0.00	3.72
341	354	2.892334	CGGAAGCGGTTGGTGTGTG	61.892	63.158	3.70	0.00	0.00	3.82
342	355	2.590575	CGGAAGCGGTTGGTGTGT	60.591	61.111	3.70	0.00	0.00	3.72
410	429	2.710902	GGCAAAATCTCGGCCCCAC	61.711	63.158	0.00	0.00	41.90	4.61
493	512	3.448340	CAAAATGCGGGTCGGGGG	61.448	66.667	0.00	0.00	0.00	5.40
647	678	1.024046	ACGCTGACAGCAACAACACA	61.024	50.000	26.32	0.00	42.58	3.72
667	709	1.342174	TCGTCGTCCCTTGTTAAGCTT	59.658	47.619	3.48	3.48	0.00	3.74
830	924	2.165845	CCTGGCTAGTAGTGTGTACCAC	59.834	54.545	0.00	6.42	44.89	4.16
831	925	2.225192	ACCTGGCTAGTAGTGTGTACCA	60.225	50.000	0.00	0.00	0.00	3.25
832	926	2.426381	GACCTGGCTAGTAGTGTGTACC	59.574	54.545	0.00	0.00	0.00	3.34
833	927	2.097142	CGACCTGGCTAGTAGTGTGTAC	59.903	54.545	0.00	0.00	0.00	2.90
834	928	2.362736	CGACCTGGCTAGTAGTGTGTA	58.637	52.381	0.00	0.00	0.00	2.90
835	929	1.174783	CGACCTGGCTAGTAGTGTGT	58.825	55.000	0.00	0.00	0.00	3.72
836	930	0.456221	CCGACCTGGCTAGTAGTGTG	59.544	60.000	0.00	0.00	0.00	3.82
837	931	0.039326	ACCGACCTGGCTAGTAGTGT	59.961	55.000	0.00	0.00	43.94	3.55
838	932	0.739561	GACCGACCTGGCTAGTAGTG	59.260	60.000	0.00	0.00	43.94	2.74
839	933	0.747283	CGACCGACCTGGCTAGTAGT	60.747	60.000	0.00	0.00	43.94	2.73
840	934	1.445716	CCGACCGACCTGGCTAGTAG	61.446	65.000	0.00	0.00	43.94	2.57
955	1055	2.811317	CGGACCTGCAAGCTCGAC	60.811	66.667	0.00	0.00	0.00	4.20
1231	1349	0.823356	GCTTCAACCCTTGACCTGCA	60.823	55.000	0.00	0.00	39.87	4.41
1320	1438	6.206498	ACTTGCCAAAAGTAAACGAGATTTC	58.794	36.000	0.00	0.00	0.00	2.17
1337	1455	1.344114	GATTCCTTTGCCAACTTGCCA	59.656	47.619	0.00	0.00	0.00	4.92
1343	1461	2.415893	CGATGGTGATTCCTTTGCCAAC	60.416	50.000	0.00	0.00	37.07	3.77
1352	1470	0.890996	GATGCCCCGATGGTGATTCC	60.891	60.000	0.00	0.00	36.04	3.01
1359	1477	0.399454	AATCAGAGATGCCCCGATGG	59.601	55.000	0.00	0.00	37.09	3.51
1410	1528	2.094906	GGGGGACTTAAATGCGTTTCAC	60.095	50.000	7.29	0.00	0.00	3.18
1417	1535	5.395214	CCTGTATTTTGGGGGACTTAAATGC	60.395	44.000	0.00	0.00	0.00	3.56
1431	1549	4.709397	TGTATTTGGCTCCCCTGTATTTTG	59.291	41.667	0.00	0.00	0.00	2.44
1479	1598	1.523154	TTCCCGCTGTGTGCCATTTC	61.523	55.000	0.00	0.00	38.78	2.17
1511	1632	1.026718	CGTTGGAGATGCCCTTGGTC	61.027	60.000	0.00	0.00	34.97	4.02
1535	1656	1.139498	TGATGGGGCAGGTTTGAGGA	61.139	55.000	0.00	0.00	0.00	3.71
1549	1670	0.606401	AGCACAGTCCGGTTTGATGG	60.606	55.000	13.55	5.30	0.00	3.51
1554	1675	4.456806	GACAGCACAGTCCGGTTT	57.543	55.556	0.00	0.00	32.36	3.27
1563	1684	4.293648	CACGGTCCGGACAGCACA	62.294	66.667	34.40	0.00	0.00	4.57
1591	1716	0.034059	CGCAGACCAGAACAGGACTT	59.966	55.000	0.00	0.00	31.25	3.01
1641	1766	0.310854	CTCCCCACGTTTGTCTTTGC	59.689	55.000	0.00	0.00	0.00	3.68
1760	1891	4.614946	CTCTACATCGACATGAATGCAGA	58.385	43.478	0.00	5.16	33.72	4.26
1790	1921	1.071542	TGAGCCGTCTTCAATGTGGAA	59.928	47.619	0.00	0.00	0.00	3.53
1917	2049	3.255969	TCTACACGGGTTTAATGGAGC	57.744	47.619	0.00	0.00	0.00	4.70
1935	2067	3.383185	CAGAAGTAGGATTCTCGGCTTCT	59.617	47.826	8.71	8.71	42.02	2.85
1947	2079	2.234661	CAGATGTGTGGCAGAAGTAGGA	59.765	50.000	0.00	0.00	0.00	2.94
1956	2088	0.105778	TCGTGAACAGATGTGTGGCA	59.894	50.000	0.00	0.00	36.84	4.92
1976	2108	0.034574	TGCATTTAGTGTCGGCCCAT	60.035	50.000	0.00	0.00	0.00	4.00
1987	2119	0.096976	CTGCCCGACGTTGCATTTAG	59.903	55.000	9.37	0.00	36.79	1.85
2034	2166	4.408821	GCCCGGTGTCTGCCATCA	62.409	66.667	0.00	0.00	0.00	3.07
2039	2171	1.244019	AATTCTTGCCCGGTGTCTGC	61.244	55.000	0.00	0.00	0.00	4.26
2130	2264	1.898330	TATGCCCGAACTGCTCTGCA	61.898	55.000	0.00	0.00	34.97	4.41
2132	2266	0.108186	TGTATGCCCGAACTGCTCTG	60.108	55.000	0.00	0.00	0.00	3.35
2177	2313	4.569023	CCTCGCGCGTATCTGCCA	62.569	66.667	30.98	6.53	0.00	4.92

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.