AutoCloner

Multiple sequence alignment - TraesCS2B01G110200

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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	TraesCS2B01G110200	chr2B	100.000	2265	0	0	1	2265	71643478	71641214	0.000000e+00	4183.0
1	TraesCS2B01G110200	chr2B	87.822	1938	157	28	293	2190	292847731	292849629	0.000000e+00	2198.0
2	TraesCS2B01G110200	chr2B	90.118	1103	102	5	784	1886	15207721	15206626	0.000000e+00	1426.0
3	TraesCS2B01G110200	chr2B	91.964	784	49	5	1	771	215847199	215847981	0.000000e+00	1086.0
4	TraesCS2B01G110200	chr2B	91.709	784	52	3	1	771	430232432	430231649	0.000000e+00	1075.0
5	TraesCS2B01G110200	chr2B	88.047	343	31	8	1838	2175	71641301	71641638	4.530000e-107	398.0
6	TraesCS2B01G110200	chr2B	79.310	319	34	15	678	970	465664055	465663743	6.380000e-46	195.0
7	TraesCS2B01G110200	chr2B	100.000	28	0	0	2073	2100	546616545	546616518	4.000000e-03	52.8
8	TraesCS2B01G110200	chr2B	100.000	28	0	0	2073	2100	722909399	722909426	4.000000e-03	52.8
9	TraesCS2B01G110200	chr3B	92.119	2043	140	8	1	2030	548879092	548881126	0.000000e+00	2861.0
10	TraesCS2B01G110200	chr3B	92.617	149	8	3	2032	2178	548881078	548880931	6.340000e-51	211.0
11	TraesCS2B01G110200	chr3B	91.228	114	10	0	2077	2190	548882770	548882883	3.010000e-34	156.0
12	TraesCS2B01G110200	chr5D	91.510	1755	118	7	1	1755	358006658	358004935	0.000000e+00	2386.0
13	TraesCS2B01G110200	chr5D	91.902	778	51	6	1	766	520878628	520879405	0.000000e+00	1077.0
14	TraesCS2B01G110200	chr5D	84.293	191	19	6	1773	1953	358004872	358004683	2.310000e-40	176.0
15	TraesCS2B01G110200	chr5D	90.265	113	9	2	2064	2175	358004683	358004794	1.810000e-31	147.0
16	TraesCS2B01G110200	chr5D	88.776	98	11	0	2093	2190	358004563	358004466	1.100000e-23	121.0
17	TraesCS2B01G110200	chr1B	89.692	1591	107	19	708	2265	449941595	449943161	0.000000e+00	1977.0
18	TraesCS2B01G110200	chr1B	84.973	366	24	12	1841	2178	449943071	449942709	2.150000e-90	342.0
19	TraesCS2B01G110200	chr6A	90.879	1195	90	7	766	1944	607999744	607998553	0.000000e+00	1585.0
20	TraesCS2B01G110200	chr4B	88.406	1311	117	16	975	2265	644495844	644494549	0.000000e+00	1546.0
21	TraesCS2B01G110200	chr4B	94.370	746	39	3	1	745	644536048	644535305	0.000000e+00	1142.0
22	TraesCS2B01G110200	chr4B	79.109	359	52	15	1838	2175	644494625	644494981	2.260000e-55	226.0
23	TraesCS2B01G110200	chr6B	90.226	1197	97	8	766	1945	702946726	702945533	0.000000e+00	1544.0
24	TraesCS2B01G110200	chr6B	89.200	1250	112	14	710	1944	702991736	702990495	0.000000e+00	1539.0
25	TraesCS2B01G110200	chr6B	85.689	573	45	19	1324	1875	238287859	238288415	9.080000e-159	569.0
26	TraesCS2B01G110200	chr1D	91.489	1081	74	6	680	1756	198509272	198510338	0.000000e+00	1471.0
27	TraesCS2B01G110200	chr1D	92.318	742	51	4	1	742	198508633	198509368	0.000000e+00	1050.0
28	TraesCS2B01G110200	chr1D	86.139	101	11	3	2088	2187	198510599	198510697	3.080000e-19	106.0
29	TraesCS2B01G110200	chr5B	92.790	749	47	2	1	742	89726883	89727631	0.000000e+00	1077.0
30	TraesCS2B01G110200	chr3D	92.722	742	54	0	1	742	116061566	116062307	0.000000e+00	1072.0
31	TraesCS2B01G110200	chr3D	86.400	125	16	1	2064	2187	116072270	116072394	3.920000e-28	135.0
32	TraesCS2B01G110200	chrUn	89.333	75	7	1	1877	1950	10401198	10401272	2.400000e-15	93.5
33	TraesCS2B01G110200	chrUn	89.333	75	7	1	1877	1950	349151471	349151545	2.400000e-15	93.5

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	TraesCS2B01G110200	chr2B	71641214	71643478	2264	True	4183.000000	4183	100.0000	1	2265	1	chr2B.!!$R2	2264
1	TraesCS2B01G110200	chr2B	292847731	292849629	1898	False	2198.000000	2198	87.8220	293	2190	1	chr2B.!!$F3	1897
2	TraesCS2B01G110200	chr2B	15206626	15207721	1095	True	1426.000000	1426	90.1180	784	1886	1	chr2B.!!$R1	1102
3	TraesCS2B01G110200	chr2B	215847199	215847981	782	False	1086.000000	1086	91.9640	1	771	1	chr2B.!!$F2	770
4	TraesCS2B01G110200	chr2B	430231649	430232432	783	True	1075.000000	1075	91.7090	1	771	1	chr2B.!!$R3	770
5	TraesCS2B01G110200	chr3B	548879092	548882883	3791	False	1508.500000	2861	91.6735	1	2190	2	chr3B.!!$F1	2189
6	TraesCS2B01G110200	chr5D	520878628	520879405	777	False	1077.000000	1077	91.9020	1	766	1	chr5D.!!$F2	765
7	TraesCS2B01G110200	chr5D	358004466	358006658	2192	True	894.333333	2386	88.1930	1	2190	3	chr5D.!!$R1	2189
8	TraesCS2B01G110200	chr1B	449941595	449943161	1566	False	1977.000000	1977	89.6920	708	2265	1	chr1B.!!$F1	1557
9	TraesCS2B01G110200	chr6A	607998553	607999744	1191	True	1585.000000	1585	90.8790	766	1944	1	chr6A.!!$R1	1178
10	TraesCS2B01G110200	chr4B	644494549	644495844	1295	True	1546.000000	1546	88.4060	975	2265	1	chr4B.!!$R1	1290
11	TraesCS2B01G110200	chr4B	644535305	644536048	743	True	1142.000000	1142	94.3700	1	745	1	chr4B.!!$R2	744
12	TraesCS2B01G110200	chr6B	702945533	702946726	1193	True	1544.000000	1544	90.2260	766	1945	1	chr6B.!!$R1	1179
13	TraesCS2B01G110200	chr6B	702990495	702991736	1241	True	1539.000000	1539	89.2000	710	1944	1	chr6B.!!$R2	1234
14	TraesCS2B01G110200	chr6B	238287859	238288415	556	False	569.000000	569	85.6890	1324	1875	1	chr6B.!!$F1	551
15	TraesCS2B01G110200	chr1D	198508633	198510697	2064	False	875.666667	1471	89.9820	1	2187	3	chr1D.!!$F1	2186
16	TraesCS2B01G110200	chr5B	89726883	89727631	748	False	1077.000000	1077	92.7900	1	742	1	chr5B.!!$F1	741
17	TraesCS2B01G110200	chr3D	116061566	116062307	741	False	1072.000000	1072	92.7220	1	742	1	chr3D.!!$F1	741

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
798	889	0.245539	CGTGGCCGTAGAGGAAGAAA	59.754	55.0	0.0	0.0	45.0	2.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1644	1741	1.136305	CCGGTTACATGACGAGTCCAT	59.864	52.381	0.0	0.0	0.0	3.41	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
153	154	2.876368	GATGAGCCGGGTGGGACAAG	62.876	65.000	12.94	0.00	44.16	3.16
168	169	1.622312	GACAAGAAGGGACGGTAGGTT	59.378	52.381	0.00	0.00	0.00	3.50
285	286	0.507358	GCAACACGGACGAGAAACTC	59.493	55.000	0.00	0.00	0.00	3.01
295	296	1.153549	GAGAAACTCGCCCGCATCT	60.154	57.895	0.00	0.00	0.00	2.90
331	332	1.002900	CGGTTGCACGAGTTCACATTT	60.003	47.619	0.00	0.00	35.47	2.32
361	362	4.243008	TTGACGTGGGCGCCTTGA	62.243	61.111	28.56	7.94	42.83	3.02
373	374	3.118775	GGGCGCCTTGATTTAATCCTTTT	60.119	43.478	28.56	0.00	0.00	2.27
419	420	1.302431	CACGGCCCAGACATTGTGA	60.302	57.895	0.00	0.00	0.00	3.58
422	423	0.888736	CGGCCCAGACATTGTGACAA	60.889	55.000	0.00	0.00	0.00	3.18
425	426	2.353011	GGCCCAGACATTGTGACAAATG	60.353	50.000	0.62	4.29	42.21	2.32
453	454	1.426598	CATGGTGCCTATGAGGGGAAT	59.573	52.381	0.00	0.00	35.37	3.01
456	457	3.335748	TGGTGCCTATGAGGGGAATAAT	58.664	45.455	0.00	0.00	35.37	1.28
475	476	9.892130	GGAATAATAAGAAAGAAGAGGTTCAGA	57.108	33.333	0.00	0.00	34.82	3.27
579	580	4.789012	ATTGTGGAGAATGCAACGAAAT	57.211	36.364	0.00	0.00	39.09	2.17
613	614	1.347707	AGGAGATGCACGAAGAAACCA	59.652	47.619	0.00	0.00	0.00	3.67
754	845	1.692762	GGCCATGGAGGAAGGACTAGA	60.693	57.143	18.40	0.00	41.22	2.43
769	860	0.539051	CTAGACTTGGAGTGGGCCTG	59.461	60.000	4.53	0.00	0.00	4.85
798	889	0.245539	CGTGGCCGTAGAGGAAGAAA	59.754	55.000	0.00	0.00	45.00	2.52
799	890	1.736032	CGTGGCCGTAGAGGAAGAAAG	60.736	57.143	0.00	0.00	45.00	2.62
831	922	1.039233	GGCCATGGATCTGGTGGTTG	61.039	60.000	18.40	0.00	38.63	3.77
841	932	0.949105	CTGGTGGTTGTAGGACACGC	60.949	60.000	0.00	0.00	36.02	5.34
868	959	2.044492	TGATAGGGGAAGGCCTATCGAT	59.956	50.000	5.16	2.16	44.45	3.59
875	966	2.158957	GGAAGGCCTATCGATGTGTTGA	60.159	50.000	5.16	0.00	0.00	3.18
882	973	4.993584	GCCTATCGATGTGTTGATCAATCT	59.006	41.667	12.12	0.00	30.91	2.40
1010	1106	2.806434	TGTTGTAGGCATGGCTTCATT	58.194	42.857	28.30	5.01	0.00	2.57
1028	1124	2.905415	TTTGGTTCCATGATGAGGCT	57.095	45.000	0.00	0.00	0.00	4.58
1043	1139	1.449070	GGCTACCGTGTGCTAACCC	60.449	63.158	0.00	0.00	0.00	4.11
1055	1151	1.009829	GCTAACCCAGAAGACATGCG	58.990	55.000	0.00	0.00	0.00	4.73
1097	1193	3.458118	TCTTTGGACAAGGTGAAGGAGAA	59.542	43.478	0.00	0.00	0.00	2.87
1105	1201	5.449553	ACAAGGTGAAGGAGAAAAGATGTT	58.550	37.500	0.00	0.00	0.00	2.71
1149	1245	3.149196	GAGATGTTTGCAAGGTGAAGGA	58.851	45.455	0.00	0.00	0.00	3.36
1238	1334	0.250252	TCATGCGCTTCCAACTCACA	60.250	50.000	9.73	0.00	0.00	3.58
1371	1467	5.071384	TCATGTGGATAGATCATGAAGTGCT	59.929	40.000	0.00	0.00	42.87	4.40
1414	1510	5.760253	CCAATATGAAGATTGTCTTAGGCGT	59.240	40.000	0.00	0.00	36.73	5.68
1417	1513	4.471904	TGAAGATTGTCTTAGGCGTCAT	57.528	40.909	0.00	0.00	36.73	3.06
1418	1514	4.832248	TGAAGATTGTCTTAGGCGTCATT	58.168	39.130	0.00	0.00	36.73	2.57
1439	1535	8.941977	GTCATTGGTTGTTTAAAGAAAGGTTTT	58.058	29.630	0.00	0.00	0.00	2.43
1480	1577	1.746220	CGTCGTCAGAAGGAGAGGATT	59.254	52.381	0.00	0.00	33.17	3.01
1517	1614	3.249189	AGGAGAGGGCACGCCAAA	61.249	61.111	10.83	0.00	37.98	3.28
1609	1706	1.512926	CACGTGACAAGAAGGGGAAG	58.487	55.000	10.90	0.00	0.00	3.46
1644	1741	3.321111	ACTCTGTAAAGCCTTCACTTCGA	59.679	43.478	0.00	0.00	0.00	3.71
1681	1778	1.811860	GGATGAAGCCATGCCACAC	59.188	57.895	0.00	0.00	35.39	3.82
1687	1784	1.331756	GAAGCCATGCCACACTTATCG	59.668	52.381	0.00	0.00	0.00	2.92
1809	1978	5.978919	GTCAGCAATTTCTGTGATTTGTCAA	59.021	36.000	4.99	0.00	35.63	3.18
1962	2156	2.750350	CGGCATAGGGGGTGGATC	59.250	66.667	0.00	0.00	0.00	3.36
1963	2157	2.750350	GGCATAGGGGGTGGATCG	59.250	66.667	0.00	0.00	0.00	3.69
1968	2163	0.564171	ATAGGGGGTGGATCGGTACA	59.436	55.000	0.00	0.00	0.00	2.90
1985	2184	5.415701	TCGGTACAGTAACGAGAAATAACCT	59.584	40.000	16.97	0.00	43.93	3.50
1989	2188	6.356186	ACAGTAACGAGAAATAACCTTCCT	57.644	37.500	0.00	0.00	0.00	3.36
2030	2237	1.068250	GCCAGAGCCTATGACGGTC	59.932	63.158	0.00	0.00	0.00	4.79
2033	2240	1.101635	CAGAGCCTATGACGGTCGGA	61.102	60.000	3.34	0.00	0.00	4.55
2056	2288	6.020041	GGATTTTTCTCGTTACAGTACCGATC	60.020	42.308	0.10	0.00	0.00	3.69
2070	2302	2.750350	GATCCACCCCCTATGCCG	59.250	66.667	0.00	0.00	0.00	5.69
2143	3949	2.439409	GTGTGGCGGTAGGGTTAAAAT	58.561	47.619	0.00	0.00	0.00	1.82
2195	4001	7.888021	TCATCTAAGGCCAAATCTTAACTCAAA	59.112	33.333	5.01	0.00	0.00	2.69

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
153	154	3.054875	ACCATAAAACCTACCGTCCCTTC	60.055	47.826	0.00	0.00	0.00	3.46
168	169	4.250464	CTCGTAAGCAACTCCACCATAAA	58.750	43.478	0.00	0.00	37.18	1.40
232	233	3.466836	CGAGCAAGGCCAATGATACTTA	58.533	45.455	5.01	0.00	0.00	2.24
291	292	2.863401	CACCATTGTGCCATCAGATG	57.137	50.000	3.04	3.04	35.31	2.90
331	332	1.661617	CACGTCAACCTTGTTCGTTCA	59.338	47.619	0.00	0.00	37.56	3.18
361	362	7.178983	TGTGAGGCATCAAGAAAAGGATTAAAT	59.821	33.333	0.92	0.00	37.14	1.40
373	374	3.942351	CCACTGTGAGGCATCAAGA	57.058	52.632	9.86	0.00	37.14	3.02
419	420	0.895100	ACCATGAGTGCGGCATTTGT	60.895	50.000	5.72	0.00	0.00	2.83
422	423	3.594568	CACCATGAGTGCGGCATT	58.405	55.556	5.72	0.16	40.28	3.56
453	454	9.712305	CACTTCTGAACCTCTTCTTTCTTATTA	57.288	33.333	0.00	0.00	0.00	0.98
456	457	7.147724	TGTCACTTCTGAACCTCTTCTTTCTTA	60.148	37.037	0.00	0.00	0.00	2.10
475	476	4.202336	CCAGCTAGATCATCCATGTCACTT	60.202	45.833	0.00	0.00	0.00	3.16
579	580	4.469586	TGCATCTCCTAATGTTGTGTCCTA	59.530	41.667	0.00	0.00	0.00	2.94
613	614	0.470766	TAGTGCCCGTGTTGGTTCTT	59.529	50.000	0.00	0.00	35.15	2.52
671	672	1.002403	TCCTTCCTCCACGGCCATA	59.998	57.895	2.24	0.00	0.00	2.74
672	673	2.285368	TCCTTCCTCCACGGCCAT	60.285	61.111	2.24	0.00	0.00	4.40
702	703	2.127065	TCCTTCCTCCATGGCCCA	59.873	61.111	6.96	0.00	35.26	5.36
754	845	3.260100	CCCAGGCCCACTCCAAGT	61.260	66.667	0.00	0.00	0.00	3.16
788	879	6.140377	CCCCTCTAAGTATCTTTCTTCCTCT	58.860	44.000	0.00	0.00	0.00	3.69
798	889	2.625639	CATGGCCCCCTCTAAGTATCT	58.374	52.381	0.00	0.00	0.00	1.98
799	890	1.630878	CCATGGCCCCCTCTAAGTATC	59.369	57.143	0.00	0.00	0.00	2.24
831	922	2.234913	ATCAACCCGGCGTGTCCTAC	62.235	60.000	6.01	0.00	0.00	3.18
841	932	1.837090	CCTTCCCCTATCAACCCGG	59.163	63.158	0.00	0.00	0.00	5.73
868	959	4.305539	ACCATCCAGATTGATCAACACA	57.694	40.909	11.07	0.00	0.00	3.72
875	966	8.418662	CACATTATTTCAACCATCCAGATTGAT	58.581	33.333	0.00	0.00	32.61	2.57
882	973	6.440010	ACCATTCACATTATTTCAACCATCCA	59.560	34.615	0.00	0.00	0.00	3.41
917	1012	8.961092	GCAAATATATCAACACATGAACACATC	58.039	33.333	0.00	0.00	42.54	3.06
920	1015	7.483307	AGGCAAATATATCAACACATGAACAC	58.517	34.615	0.00	0.00	42.54	3.32
1010	1106	2.092429	GGTAGCCTCATCATGGAACCAA	60.092	50.000	0.00	0.00	34.37	3.67
1028	1124	1.274167	CTTCTGGGTTAGCACACGGTA	59.726	52.381	0.00	0.00	33.83	4.02
1043	1139	2.096565	CACTTGTGACGCATGTCTTCTG	60.097	50.000	4.66	0.00	45.70	3.02
1055	1151	0.531974	TGCGTTCTCCCACTTGTGAC	60.532	55.000	1.89	0.00	0.00	3.67
1097	1193	4.949856	ACATGGCCGAATCTTAACATCTTT	59.050	37.500	0.00	0.00	0.00	2.52
1105	1201	2.290641	ACACCAACATGGCCGAATCTTA	60.291	45.455	0.00	0.00	42.67	2.10
1149	1245	0.317479	CTTCTTTCGGTCGGTGGACT	59.683	55.000	0.00	0.00	42.97	3.85
1238	1334	1.580059	ATCGGTGGTTGGTCATAGGT	58.420	50.000	0.00	0.00	0.00	3.08
1414	1510	8.940952	CAAAACCTTTCTTTAAACAACCAATGA	58.059	29.630	0.00	0.00	0.00	2.57
1417	1513	8.904099	TTCAAAACCTTTCTTTAAACAACCAA	57.096	26.923	0.00	0.00	0.00	3.67
1418	1514	8.368668	TCTTCAAAACCTTTCTTTAAACAACCA	58.631	29.630	0.00	0.00	0.00	3.67
1439	1535	1.905215	CTCTTCCTCCAAGCCTCTTCA	59.095	52.381	0.00	0.00	31.26	3.02
1480	1577	1.664649	CTCGTGTTGCTTCCGCTCA	60.665	57.895	0.00	0.00	36.97	4.26
1494	1591	2.363147	GTGCCCTCTCCTCCTCGT	60.363	66.667	0.00	0.00	0.00	4.18
1517	1614	0.610174	TCCTCATGAGCAAGCTTCGT	59.390	50.000	17.76	0.00	0.00	3.85
1609	1706	1.144057	CAGAGTCATACGGGGCCAC	59.856	63.158	4.39	0.00	0.00	5.01
1644	1741	1.136305	CCGGTTACATGACGAGTCCAT	59.864	52.381	0.00	0.00	0.00	3.41
1703	1800	7.766278	CACATGTCTTCTTGCCTTTAGTAGTAT	59.234	37.037	0.00	0.00	0.00	2.12
1711	1811	2.549754	CGACACATGTCTTCTTGCCTTT	59.450	45.455	10.18	0.00	42.66	3.11
1962	2156	5.644644	AGGTTATTTCTCGTTACTGTACCG	58.355	41.667	0.00	0.00	0.00	4.02
1963	2157	6.533012	GGAAGGTTATTTCTCGTTACTGTACC	59.467	42.308	0.00	0.00	0.00	3.34
1968	2163	6.653740	CCAAAGGAAGGTTATTTCTCGTTACT	59.346	38.462	0.00	0.00	0.00	2.24
1980	2176	1.279846	CCTACCGCCAAAGGAAGGTTA	59.720	52.381	8.52	0.00	36.79	2.85
1985	2184	1.279846	CTTACCCTACCGCCAAAGGAA	59.720	52.381	0.00	0.00	34.58	3.36
1989	2188	1.202769	AGGCTTACCCTACCGCCAAA	61.203	55.000	0.00	0.00	44.08	3.28
2030	2237	4.030977	CGGTACTGTAACGAGAAAAATCCG	59.969	45.833	19.92	5.16	42.61	4.18
2195	4001	7.105588	TGAGTTATGTATGTGCTTGAGTTGAT	58.894	34.615	0.00	0.00	0.00	2.57

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.