AutoCloner

Multiple sequence alignment - TraesCS7A01G275500

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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	TraesCS7A01G275500	chr7A	100.000	2315	0	0	1	2315	287888007	287890321	0.000000e+00	4276
1	TraesCS7A01G275500	chr7A	86.082	1164	86	27	318	1468	287861416	287862516	0.000000e+00	1182
2	TraesCS7A01G275500	chr7D	87.109	2397	175	54	5	2315	264337181	264339529	0.000000e+00	2591
3	TraesCS7A01G275500	chr7D	85.611	1522	133	25	21	1467	264359197	264360707	0.000000e+00	1519
4	TraesCS7A01G275500	chr7D	87.638	1181	92	19	309	1468	264324605	264325752	0.000000e+00	1323
5	TraesCS7A01G275500	chr7D	95.131	842	24	5	1474	2315	264325930	264326754	0.000000e+00	1312
6	TraesCS7A01G275500	chr7D	86.273	1202	79	25	318	1467	264369413	264370580	0.000000e+00	1227
7	TraesCS7A01G275500	chr7D	89.256	847	65	23	1473	2315	264370638	264371462	0.000000e+00	1037
8	TraesCS7A01G275500	chr7D	88.353	850	67	26	1473	2313	264360765	264361591	0.000000e+00	992
9	TraesCS7A01G275500	chr7B	93.653	1481	67	11	5	1467	244649898	244651369	0.000000e+00	2189
10	TraesCS7A01G275500	chr7B	85.799	1183	86	26	336	1467	244691566	244692717	0.000000e+00	1179
11	TraesCS7A01G275500	chr7B	85.628	1155	104	30	336	1467	244715076	244716191	0.000000e+00	1157
12	TraesCS7A01G275500	chr7B	89.374	847	63	24	1473	2315	244716249	244717072	0.000000e+00	1040
13	TraesCS7A01G275500	chr7B	88.915	848	65	26	1473	2315	244644973	244645796	0.000000e+00	1018
14	TraesCS7A01G275500	chr7B	88.507	844	59	25	1473	2313	244692775	244693583	0.000000e+00	987
15	TraesCS7A01G275500	chr7B	97.431	545	14	0	1771	2315	244651643	244652187	0.000000e+00	929
16	TraesCS7A01G275500	chr7B	88.587	552	47	6	318	869	244643491	244644026	0.000000e+00	656
17	TraesCS7A01G275500	chr7B	83.725	596	34	16	904	1452	244644028	244644607	2.650000e-139	505
18	TraesCS7A01G275500	chr7B	96.364	220	7	1	1473	1692	244651426	244651644	6.080000e-96	361
19	TraesCS7A01G275500	chrUn	88.608	553	42	7	336	888	284874698	284875229	0.000000e+00	652

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	TraesCS7A01G275500	chr7A	287888007	287890321	2314	False	4276.000000	4276	100.000000	1	2315	1	chr7A.!!$F2	2314
1	TraesCS7A01G275500	chr7A	287861416	287862516	1100	False	1182.000000	1182	86.082000	318	1468	1	chr7A.!!$F1	1150
2	TraesCS7A01G275500	chr7D	264337181	264339529	2348	False	2591.000000	2591	87.109000	5	2315	1	chr7D.!!$F1	2310
3	TraesCS7A01G275500	chr7D	264324605	264326754	2149	False	1317.500000	1323	91.384500	309	2315	2	chr7D.!!$F2	2006
4	TraesCS7A01G275500	chr7D	264359197	264361591	2394	False	1255.500000	1519	86.982000	21	2313	2	chr7D.!!$F3	2292
5	TraesCS7A01G275500	chr7D	264369413	264371462	2049	False	1132.000000	1227	87.764500	318	2315	2	chr7D.!!$F4	1997
6	TraesCS7A01G275500	chr7B	244649898	244652187	2289	False	1159.666667	2189	95.816000	5	2315	3	chr7B.!!$F2	2310
7	TraesCS7A01G275500	chr7B	244715076	244717072	1996	False	1098.500000	1157	87.501000	336	2315	2	chr7B.!!$F4	1979
8	TraesCS7A01G275500	chr7B	244691566	244693583	2017	False	1083.000000	1179	87.153000	336	2313	2	chr7B.!!$F3	1977
9	TraesCS7A01G275500	chr7B	244643491	244645796	2305	False	726.333333	1018	87.075667	318	2315	3	chr7B.!!$F1	1997
10	TraesCS7A01G275500	chrUn	284874698	284875229	531	False	652.000000	652	88.608000	336	888	1	chrUn.!!$F1	552

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
789	837	0.317479	GCTTCAGGAGGTGTGTACGT	59.683	55.0	0.0	0.0	0.0	3.57	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2202	2798	1.08992	CAAGCCTCCTCAAACCATCG	58.91	55.0	0.0	0.0	0.0	3.84	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
41	42	3.436704	ACAGAATACACACCGATGCAAAG	59.563	43.478	0.00	0.00	0.00	2.77
48	49	3.198068	CACACCGATGCAAAGCTACTAT	58.802	45.455	0.00	0.00	0.00	2.12
102	103	2.745102	TGCACGTATGACGAGAACAAA	58.255	42.857	5.94	0.00	46.05	2.83
272	276	2.121291	TGCTCACCAGACAAACACAA	57.879	45.000	0.00	0.00	0.00	3.33
365	396	0.867746	GACATCAAACTGCACGCTCA	59.132	50.000	0.00	0.00	0.00	4.26
403	434	2.105477	GCCCATAGTGGAGACATGACAT	59.895	50.000	0.00	0.00	46.14	3.06
407	438	4.384537	CCATAGTGGAGACATGACATGGTT	60.385	45.833	19.39	6.99	46.14	3.67
496	528	0.836606	TCAGCTTGTTGTGGAGGTGA	59.163	50.000	1.54	1.54	45.16	4.02
524	557	2.759114	CACAGCACCCCCATCAGT	59.241	61.111	0.00	0.00	0.00	3.41
537	570	4.387598	CCCCATCAGTGATGAGATTCTTC	58.612	47.826	30.63	0.00	42.09	2.87
556	589	1.448540	CTGTCTACAAGGCCAGCCG	60.449	63.158	5.01	0.00	41.95	5.52
648	687	9.664332	CTTTTCTCTGAATCTCTCTTCCATTTA	57.336	33.333	0.00	0.00	0.00	1.40
654	693	8.766476	TCTGAATCTCTCTTCCATTTACAGATT	58.234	33.333	0.00	0.00	32.94	2.40
667	706	7.011389	TCCATTTACAGATTCATAGAAAGCACG	59.989	37.037	0.00	0.00	0.00	5.34
756	796	4.225942	TCTTCACCTTCTGCTACCATTGAT	59.774	41.667	0.00	0.00	0.00	2.57
788	836	0.389948	GGCTTCAGGAGGTGTGTACG	60.390	60.000	0.00	0.00	0.00	3.67
789	837	0.317479	GCTTCAGGAGGTGTGTACGT	59.683	55.000	0.00	0.00	0.00	3.57
790	838	1.935300	GCTTCAGGAGGTGTGTACGTG	60.935	57.143	0.00	0.00	0.00	4.49
791	839	1.611977	CTTCAGGAGGTGTGTACGTGA	59.388	52.381	0.00	0.00	0.00	4.35
792	840	0.956633	TCAGGAGGTGTGTACGTGAC	59.043	55.000	0.00	0.00	0.00	3.67
793	841	0.959553	CAGGAGGTGTGTACGTGACT	59.040	55.000	0.00	0.00	0.00	3.41
794	842	2.156917	CAGGAGGTGTGTACGTGACTA	58.843	52.381	0.00	0.00	0.00	2.59
795	843	2.095364	CAGGAGGTGTGTACGTGACTAC	60.095	54.545	0.00	0.00	0.00	2.73
921	969	1.117150	AACATCTGCAATGCCATCCC	58.883	50.000	1.53	0.00	0.00	3.85
1000	1058	5.163405	GCCAAGATACAGTCCTTCATCAGTA	60.163	44.000	0.00	0.00	0.00	2.74
1038	1096	5.766222	CCAAAACAGTGGAAGAAGATCAAG	58.234	41.667	0.00	0.00	41.65	3.02
1076	1134	0.957888	GACAAGGAGAGTTGCAGGGC	60.958	60.000	0.00	0.00	0.00	5.19
1078	1136	3.909086	AAGGAGAGTTGCAGGGCGC	62.909	63.158	0.00	0.00	42.89	6.53
1136	1202	0.745845	ATGCTTCAGTCATCCACGCC	60.746	55.000	0.00	0.00	0.00	5.68
1137	1203	1.078848	GCTTCAGTCATCCACGCCT	60.079	57.895	0.00	0.00	0.00	5.52
1139	1205	1.363744	CTTCAGTCATCCACGCCTTC	58.636	55.000	0.00	0.00	0.00	3.46
1158	1224	4.156739	CCTTCCCTACTGAAGCAAATTGTC	59.843	45.833	0.00	0.00	40.34	3.18
1279	1358	3.608008	GCAGTGCTTAGACTTTGTTGAGC	60.608	47.826	8.18	0.00	0.00	4.26
1341	1441	3.609853	TGCCTATGGTTCACTGTGATTC	58.390	45.455	11.86	7.98	0.00	2.52
1430	1545	3.953712	TGGAGCATTTAACTCAGACGA	57.046	42.857	0.00	0.00	35.79	4.20
1468	1882	6.233434	ACAGTTACTCAGAAATGCTCATCAA	58.767	36.000	0.00	0.00	0.00	2.57
1469	1883	6.148480	ACAGTTACTCAGAAATGCTCATCAAC	59.852	38.462	0.00	0.00	0.00	3.18
1470	1884	6.148315	CAGTTACTCAGAAATGCTCATCAACA	59.852	38.462	0.00	0.00	0.00	3.33
1471	1885	6.712095	AGTTACTCAGAAATGCTCATCAACAA	59.288	34.615	0.00	0.00	0.00	2.83
1518	2105	1.003928	AGATGCCATGTGTTGCTCAGA	59.996	47.619	0.00	0.00	0.00	3.27
1540	2127	2.949447	ACAAGCAAAGGATCCTTGTGT	58.051	42.857	27.71	22.96	45.22	3.72
1695	2288	2.235402	CACCAACCCATACTCGGTTAGT	59.765	50.000	0.00	0.00	41.78	2.24
1703	2296	4.828939	CCCATACTCGGTTAGTACACCATA	59.171	45.833	3.50	0.00	43.47	2.74
1704	2297	5.278660	CCCATACTCGGTTAGTACACCATAC	60.279	48.000	3.50	0.00	43.47	2.39
1705	2298	5.300034	CCATACTCGGTTAGTACACCATACA	59.700	44.000	3.50	0.00	43.47	2.29
1706	2299	6.183360	CCATACTCGGTTAGTACACCATACAA	60.183	42.308	3.50	0.00	43.47	2.41
1707	2300	5.726980	ACTCGGTTAGTACACCATACAAA	57.273	39.130	3.50	0.00	36.36	2.83
1708	2301	6.100404	ACTCGGTTAGTACACCATACAAAA	57.900	37.500	3.50	0.00	36.36	2.44
1709	2302	6.704310	ACTCGGTTAGTACACCATACAAAAT	58.296	36.000	3.50	0.00	36.36	1.82
1749	2344	5.762179	TTGTCAAGATCCACCAATAGAGT	57.238	39.130	0.00	0.00	0.00	3.24
1755	2350	6.443849	TCAAGATCCACCAATAGAGTAAACCT	59.556	38.462	0.00	0.00	0.00	3.50
2202	2798	3.192422	CCATGACCATCGAGACTATCTCC	59.808	52.174	0.00	0.00	40.34	3.71

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
102	103	5.672819	GCACGGCAGTTTACTCGATTATTTT	60.673	40.000	0.00	0.00	0.00	1.82
272	276	1.822186	GGGCTCCAACACAACACGT	60.822	57.895	0.00	0.00	0.00	4.49
403	434	7.041107	GCCTTTGCTTGAATTTATGATAACCA	58.959	34.615	0.00	0.00	33.53	3.67
407	438	6.691754	TCGCCTTTGCTTGAATTTATGATA	57.308	33.333	0.00	0.00	34.43	2.15
518	551	5.672503	ACAGGAAGAATCTCATCACTGATG	58.327	41.667	12.25	12.25	41.00	3.07
524	557	6.127225	CCTTGTAGACAGGAAGAATCTCATCA	60.127	42.308	0.00	0.00	0.00	3.07
537	570	1.078143	GGCTGGCCTTGTAGACAGG	60.078	63.158	3.32	0.00	0.00	4.00
556	589	2.660189	ATAAGCACAAGCCATGCAAC	57.340	45.000	7.14	0.00	45.92	4.17
611	648	9.473640	GAGATTCAGAGAAAAGAAATTTTGCTT	57.526	29.630	0.00	0.00	0.00	3.91
648	687	2.939103	GGCGTGCTTTCTATGAATCTGT	59.061	45.455	0.00	0.00	0.00	3.41
654	693	1.438651	GTGTGGCGTGCTTTCTATGA	58.561	50.000	0.00	0.00	0.00	2.15
667	706	1.758122	GAATGGGGGATGGTGTGGC	60.758	63.158	0.00	0.00	0.00	5.01
756	796	4.661222	TCCTGAAGCCATCAAACATTGTA	58.339	39.130	0.00	0.00	37.67	2.41
788	836	6.626488	CGATACTATTGTACACACGTAGTCAC	59.374	42.308	0.00	0.69	41.61	3.67
789	837	6.534793	TCGATACTATTGTACACACGTAGTCA	59.465	38.462	0.00	0.00	41.61	3.41
790	838	6.937457	TCGATACTATTGTACACACGTAGTC	58.063	40.000	0.00	0.00	41.61	2.59
792	840	6.201615	TCCTCGATACTATTGTACACACGTAG	59.798	42.308	0.00	0.00	0.00	3.51
793	841	6.048509	TCCTCGATACTATTGTACACACGTA	58.951	40.000	0.00	0.00	0.00	3.57
794	842	4.877823	TCCTCGATACTATTGTACACACGT	59.122	41.667	0.00	0.00	0.00	4.49
795	843	5.235831	TCTCCTCGATACTATTGTACACACG	59.764	44.000	0.00	0.00	0.00	4.49
956	1004	4.725790	GCCTGAGAGCCAATGTAATTTT	57.274	40.909	0.00	0.00	31.22	1.82
1000	1058	1.517538	TTTGGCCCCATCCTGGTCAT	61.518	55.000	0.00	0.00	37.33	3.06
1038	1096	4.573900	TGTCAGCTGAAGGAGATTTCTTC	58.426	43.478	20.19	1.27	40.57	2.87
1076	1134	1.165907	TCCAGCCAACAGTTTGAGCG	61.166	55.000	0.00	0.00	35.33	5.03
1078	1136	0.595095	GCTCCAGCCAACAGTTTGAG	59.405	55.000	0.00	0.00	34.24	3.02
1136	1202	4.761739	TGACAATTTGCTTCAGTAGGGAAG	59.238	41.667	0.00	0.00	45.58	3.46
1137	1203	4.724399	TGACAATTTGCTTCAGTAGGGAA	58.276	39.130	0.00	0.00	0.00	3.97
1139	1205	4.676196	GCATGACAATTTGCTTCAGTAGGG	60.676	45.833	0.00	0.00	35.95	3.53
1158	1224	3.938963	ACCACTTGTTATAACTCGGCATG	59.061	43.478	16.33	6.55	0.00	4.06
1202	1268	4.202141	TGTTGCATGGAAGTCTTTTCTTGG	60.202	41.667	0.00	0.00	0.00	3.61
1279	1358	1.411977	ACTCTGCTCGGGATCAATCTG	59.588	52.381	0.00	0.00	0.00	2.90
1341	1441	1.635663	CGCTCTAAAAGGTGGGTGCG	61.636	60.000	0.00	0.00	35.90	5.34
1468	1882	2.906389	TGGCCATCTTGTAGAGACTTGT	59.094	45.455	0.00	0.00	37.17	3.16
1469	1883	3.616956	TGGCCATCTTGTAGAGACTTG	57.383	47.619	0.00	0.00	37.17	3.16
1470	1884	3.521126	ACATGGCCATCTTGTAGAGACTT	59.479	43.478	17.61	0.00	37.17	3.01
1471	1885	3.110705	ACATGGCCATCTTGTAGAGACT	58.889	45.455	17.61	0.00	37.17	3.24
1714	2309	6.096705	TGGATCTTGACAAAATTGTGTGTTCT	59.903	34.615	5.84	0.00	42.43	3.01
1715	2310	6.198966	GTGGATCTTGACAAAATTGTGTGTTC	59.801	38.462	5.84	0.00	42.43	3.18
1717	2312	5.451798	GGTGGATCTTGACAAAATTGTGTGT	60.452	40.000	5.84	0.00	42.43	3.72
1727	2322	5.762179	ACTCTATTGGTGGATCTTGACAA	57.238	39.130	0.00	0.00	0.00	3.18
1755	2350	1.153353	GCGACAAGAATCAACCGGAA	58.847	50.000	9.46	0.00	0.00	4.30
1778	2373	9.060347	AGATATCACATTGTCATGTTCCATTAC	57.940	33.333	5.32	0.00	41.16	1.89
2202	2798	1.089920	CAAGCCTCCTCAAACCATCG	58.910	55.000	0.00	0.00	0.00	3.84

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.