AutoCloner

Multiple sequence alignment - TraesCS7A01G503500

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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	TraesCS7A01G503500	chr7A	100.000	2228	0	0	1	2228	692310758	692308531	0.000000e+00	4115
1	TraesCS7A01G503500	chr1D	86.637	2275	186	57	3	2228	5454670	5456875	0.000000e+00	2409
2	TraesCS7A01G503500	chr1B	86.151	2159	174	51	133	2228	17832553	17830457	0.000000e+00	2215
3	TraesCS7A01G503500	chr1B	86.625	1443	105	33	689	2098	8193224	8194611	0.000000e+00	1515
4	TraesCS7A01G503500	chr1B	86.947	1379	103	28	133	1462	639480886	639482236	0.000000e+00	1478
5	TraesCS7A01G503500	chr1B	86.808	849	54	29	3	818	8183492	8184315	0.000000e+00	894
6	TraesCS7A01G503500	chr1B	87.738	734	57	16	1512	2228	639482344	639483061	0.000000e+00	826
7	TraesCS7A01G503500	chr1B	83.806	741	71	21	1512	2228	8184589	8185304	0.000000e+00	658
8	TraesCS7A01G503500	chr1B	92.400	250	12	3	1224	1466	8184321	8184570	1.270000e-92	350
9	TraesCS7A01G503500	chr1B	93.458	107	7	0	2122	2228	8194608	8194714	2.290000e-35	159
10	TraesCS7A01G503500	chr1A	88.804	1563	137	25	689	2228	6634475	6632928	0.000000e+00	1882
11	TraesCS7A01G503500	chr1A	88.455	1178	91	18	1064	2228	6762087	6760942	0.000000e+00	1380
12	TraesCS7A01G503500	chr1A	85.114	1189	122	36	689	1845	6721098	6719933	0.000000e+00	1164
13	TraesCS7A01G503500	chr1A	85.668	935	72	21	3	893	6763244	6762328	0.000000e+00	928
14	TraesCS7A01G503500	chr1A	92.373	118	9	0	1984	2101	6719860	6719743	3.800000e-38	169
15	TraesCS7A01G503500	chr1A	94.393	107	6	0	2122	2228	6719749	6719643	4.920000e-37	165
16	TraesCS7A01G503500	chr6D	91.605	405	30	3	819	1222	389252782	389253183	6.950000e-155	556
17	TraesCS7A01G503500	chr5D	91.980	399	28	3	825	1222	503240895	503241290	6.950000e-155	556
18	TraesCS7A01G503500	chrUn	91.729	399	30	1	825	1223	397078686	397078291	3.230000e-153	551

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	TraesCS7A01G503500	chr7A	692308531	692310758	2227	True	4115.000000	4115	100.000000	1	2228	1	chr7A.!!$R1	2227
1	TraesCS7A01G503500	chr1D	5454670	5456875	2205	False	2409.000000	2409	86.637000	3	2228	1	chr1D.!!$F1	2225
2	TraesCS7A01G503500	chr1B	17830457	17832553	2096	True	2215.000000	2215	86.151000	133	2228	1	chr1B.!!$R1	2095
3	TraesCS7A01G503500	chr1B	639480886	639483061	2175	False	1152.000000	1478	87.342500	133	2228	2	chr1B.!!$F3	2095
4	TraesCS7A01G503500	chr1B	8193224	8194714	1490	False	837.000000	1515	90.041500	689	2228	2	chr1B.!!$F2	1539
5	TraesCS7A01G503500	chr1B	8183492	8185304	1812	False	634.000000	894	87.671333	3	2228	3	chr1B.!!$F1	2225
6	TraesCS7A01G503500	chr1A	6632928	6634475	1547	True	1882.000000	1882	88.804000	689	2228	1	chr1A.!!$R1	1539
7	TraesCS7A01G503500	chr1A	6760942	6763244	2302	True	1154.000000	1380	87.061500	3	2228	2	chr1A.!!$R3	2225
8	TraesCS7A01G503500	chr1A	6719643	6721098	1455	True	499.333333	1164	90.626667	689	2228	3	chr1A.!!$R2	1539

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
280	301	0.76489	TTGCTGGGCTTATCGGCTAT	59.235	50.0	0.0	0.0	37.4	2.97	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1466	1711	0.797579	AGAGGAAGGGGAAGGGTGTA	59.202	55.0	0.0	0.0	0.0	2.9	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	3.184379	TCGCTTGTTTTCTTGTCTCGATG	59.816	43.478	0.00	0.00	0.00	3.84
47	48	7.714813	TCTCGATGCTCAACCAAATTGATTATA	59.285	33.333	0.00	0.00	46.37	0.98
108	112	2.563620	TCATGCCCTTTAGACGTACACA	59.436	45.455	0.00	0.00	0.00	3.72
117	125	6.921857	CCCTTTAGACGTACACAGTTATATGG	59.078	42.308	0.00	0.00	0.00	2.74
280	301	0.764890	TTGCTGGGCTTATCGGCTAT	59.235	50.000	0.00	0.00	37.40	2.97
318	339	9.232473	GTGGAAGGTAAACTCTCATTCTTTTAT	57.768	33.333	0.00	0.00	0.00	1.40
319	340	9.807921	TGGAAGGTAAACTCTCATTCTTTTATT	57.192	29.630	0.00	0.00	0.00	1.40
370	415	3.682372	GCTGTAATTCTAGTTGCAGGC	57.318	47.619	11.42	3.14	40.68	4.85
399	444	6.596888	TCTGCTTTTTGAAGTCATATCCAGAG	59.403	38.462	0.00	0.00	0.00	3.35
409	454	7.712639	TGAAGTCATATCCAGAGTTGCTAATTC	59.287	37.037	0.00	0.00	0.00	2.17
410	455	7.129457	AGTCATATCCAGAGTTGCTAATTCA	57.871	36.000	0.00	0.00	0.00	2.57
545	597	9.764870	CAGTTAGATGATGTTTCAAATACAGTG	57.235	33.333	0.00	0.00	34.96	3.66
554	606	5.825679	TGTTTCAAATACAGTGCAGGTAAGT	59.174	36.000	2.57	0.00	0.00	2.24
556	608	6.952773	TTCAAATACAGTGCAGGTAAGTTT	57.047	33.333	2.57	0.00	0.00	2.66
557	609	6.952773	TCAAATACAGTGCAGGTAAGTTTT	57.047	33.333	2.57	0.00	0.00	2.43
601	659	3.062639	GCACATTATGGACTGTCTGAACG	59.937	47.826	7.85	0.00	0.00	3.95
686	754	5.047235	AGGTTACGAAGAAACATCTAGCTGT	60.047	40.000	0.00	0.00	0.00	4.40
687	755	5.638234	GGTTACGAAGAAACATCTAGCTGTT	59.362	40.000	6.14	6.14	41.01	3.16
843	915	5.698089	CGATACCTCTACAGAACCGTACATA	59.302	44.000	0.00	0.00	0.00	2.29
844	916	6.370994	CGATACCTCTACAGAACCGTACATAT	59.629	42.308	0.00	0.00	0.00	1.78
847	919	5.531659	ACCTCTACAGAACCGTACATATGAG	59.468	44.000	10.38	0.24	0.00	2.90
874	948	1.101635	TCATACGGCTCCTCGGTCAG	61.102	60.000	0.00	0.00	0.00	3.51
908	982	6.958767	AGGAATCCTTTTCCTTATTCGAGAA	58.041	36.000	0.00	0.00	46.21	2.87
917	991	2.297597	CCTTATTCGAGAATCTCCGCCT	59.702	50.000	4.47	0.00	32.50	5.52
930	1004	1.741770	CCGCCTTTCTTCCACTCCG	60.742	63.158	0.00	0.00	0.00	4.63
931	1005	1.741770	CGCCTTTCTTCCACTCCGG	60.742	63.158	0.00	0.00	0.00	5.14
935	1009	2.124507	CTTTCTTCCACTCCGGCCCA	62.125	60.000	0.00	0.00	33.14	5.36
1098	1305	2.047061	TCTCGGTATCAATCCCCTTGG	58.953	52.381	0.00	0.00	35.43	3.61
1154	1362	6.875948	TCGAGTTTCCATTTCTTCATTTGA	57.124	33.333	0.00	0.00	0.00	2.69
1170	1378	4.703575	TCATTTGAAATCTGGGCTCTTCTG	59.296	41.667	0.00	0.00	0.00	3.02
1326	1542	2.867975	CCGTACGGTTGAAATATGGGTC	59.132	50.000	26.39	0.00	0.00	4.46
1345	1563	1.414919	TCGGTGCCTTGTACTGAAACT	59.585	47.619	0.00	0.00	31.10	2.66
1348	1566	2.949644	GGTGCCTTGTACTGAAACTTGT	59.050	45.455	0.00	0.00	0.00	3.16
1349	1567	4.131596	GGTGCCTTGTACTGAAACTTGTA	58.868	43.478	0.00	0.00	0.00	2.41
1381	1609	6.830912	TGCTTATTGGAGCTACATATCACTT	58.169	36.000	0.00	0.00	43.11	3.16
1462	1707	2.292267	CCAGGTAAGCACATGTCCATC	58.708	52.381	0.00	0.00	34.63	3.51
1466	1711	5.311265	CAGGTAAGCACATGTCCATCATAT	58.689	41.667	0.00	0.00	34.67	1.78
1467	1712	6.466812	CAGGTAAGCACATGTCCATCATATA	58.533	40.000	0.00	0.00	34.67	0.86
1560	1862	2.353357	ACCGGTATCAGGATCGTACA	57.647	50.000	4.49	0.00	0.00	2.90
1581	1883	0.533978	TGCGTGCAACTGAAGCCTTA	60.534	50.000	0.00	0.00	31.75	2.69
1715	2026	4.823989	GGCTATTGGTTCTGCATCAACTAT	59.176	41.667	8.22	5.74	0.00	2.12
1796	2121	3.721575	AGCTCTAGGATCCTCTTCAGAGA	59.278	47.826	31.07	21.12	44.74	3.10
1881	2211	2.753446	GGCTCTGCCTTTCCAGCC	60.753	66.667	0.73	0.00	46.69	4.85
1967	2298	6.329496	CAGTCTCCTCTTGTATCTCTTCAAC	58.671	44.000	0.00	0.00	0.00	3.18
2061	2398	4.706842	ATGACCCCTTTTATCTATGCGT	57.293	40.909	0.00	0.00	0.00	5.24
2069	2406	6.258160	CCCTTTTATCTATGCGTTCTGTTTG	58.742	40.000	0.00	0.00	0.00	2.93

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	0.307760	AAGAAAACAAGCGAGCACCG	59.692	50.000	0.00	0.00	42.21	4.94
1	2	1.065551	ACAAGAAAACAAGCGAGCACC	59.934	47.619	0.00	0.00	0.00	5.01
108	112	4.881157	AGAGGGCCAAAACCATATAACT	57.119	40.909	6.18	0.00	0.00	2.24
117	125	4.139038	TGTACAAACTAGAGGGCCAAAAC	58.861	43.478	6.18	0.00	0.00	2.43
280	301	0.249120	CCTTCCACCTGACGTATGCA	59.751	55.000	0.00	0.00	0.00	3.96
318	339	5.575157	TGTGTAATCTTGGATGGCCTAAAA	58.425	37.500	3.32	0.00	34.31	1.52
319	340	5.186256	TGTGTAATCTTGGATGGCCTAAA	57.814	39.130	3.32	0.00	34.31	1.85
320	341	4.853468	TGTGTAATCTTGGATGGCCTAA	57.147	40.909	3.32	0.00	34.31	2.69
321	342	4.018870	TGTTGTGTAATCTTGGATGGCCTA	60.019	41.667	3.32	0.00	34.31	3.93
322	343	3.245229	TGTTGTGTAATCTTGGATGGCCT	60.245	43.478	3.32	0.00	34.31	5.19
326	347	5.122869	CCTCAGTGTTGTGTAATCTTGGATG	59.877	44.000	0.00	0.00	0.00	3.51
370	415	6.976925	GGATATGACTTCAAAAAGCAGAATGG	59.023	38.462	0.00	0.00	35.81	3.16
383	428	6.544928	TTAGCAACTCTGGATATGACTTCA	57.455	37.500	0.00	0.00	0.00	3.02
399	444	6.284459	AGATACTAGCAGGTGAATTAGCAAC	58.716	40.000	0.00	0.00	0.00	4.17
409	454	4.740695	GCGAACTTTAGATACTAGCAGGTG	59.259	45.833	0.00	0.00	0.00	4.00
410	455	4.497674	CGCGAACTTTAGATACTAGCAGGT	60.498	45.833	0.00	0.00	0.00	4.00
588	642	1.337260	ACAGCATCGTTCAGACAGTCC	60.337	52.381	0.00	0.00	0.00	3.85
619	680	6.968131	TCTTCATGTAAGATGAAAAGGTCG	57.032	37.500	0.00	0.00	39.36	4.79
646	714	6.411376	TCGTAACCTGAAATGGACACATATT	58.589	36.000	0.00	0.00	35.94	1.28
647	715	5.984725	TCGTAACCTGAAATGGACACATAT	58.015	37.500	0.00	0.00	35.94	1.78
847	919	1.207329	AGGAGCCGTATGAGGTGAAAC	59.793	52.381	0.00	0.00	0.00	2.78
874	948	5.473846	AGGAAAAGGATTCCTTCGAAAGAAC	59.526	40.000	18.21	6.07	46.21	3.01
908	982	1.208293	GAGTGGAAGAAAGGCGGAGAT	59.792	52.381	0.00	0.00	0.00	2.75
917	991	1.710996	TTGGGCCGGAGTGGAAGAAA	61.711	55.000	5.05	0.00	42.00	2.52
930	1004	3.008704	TGGTCTTAGTTAGTCTTTGGGCC	59.991	47.826	0.00	0.00	0.00	5.80
931	1005	4.281898	TGGTCTTAGTTAGTCTTTGGGC	57.718	45.455	0.00	0.00	0.00	5.36
935	1009	5.303845	ACTCGGTTGGTCTTAGTTAGTCTTT	59.696	40.000	0.00	0.00	0.00	2.52
1013	1113	8.925161	TTGTTTGGTAAAAGAACAATCTTCTG	57.075	30.769	0.00	0.00	45.19	3.02
1154	1362	3.055240	CAGAGACAGAAGAGCCCAGATTT	60.055	47.826	0.00	0.00	0.00	2.17
1241	1457	2.000447	GGATCACTGCGACCTACAAAC	59.000	52.381	0.00	0.00	0.00	2.93
1326	1542	1.878953	AGTTTCAGTACAAGGCACCG	58.121	50.000	0.00	0.00	0.00	4.94
1345	1563	7.745717	AGCTCCAATAAGCAAGGTATATACAA	58.254	34.615	14.70	0.00	45.00	2.41
1348	1566	8.430573	TGTAGCTCCAATAAGCAAGGTATATA	57.569	34.615	0.00	0.00	45.00	0.86
1349	1567	7.316393	TGTAGCTCCAATAAGCAAGGTATAT	57.684	36.000	0.00	0.00	45.00	0.86
1381	1609	5.979993	TCAAGATAAATAAGTGCACCCGTA	58.020	37.500	14.63	3.96	0.00	4.02
1462	1707	3.327439	AGGAAGGGGAAGGGTGTATATG	58.673	50.000	0.00	0.00	0.00	1.78
1466	1711	0.797579	AGAGGAAGGGGAAGGGTGTA	59.202	55.000	0.00	0.00	0.00	2.90
1467	1712	0.797579	TAGAGGAAGGGGAAGGGTGT	59.202	55.000	0.00	0.00	0.00	4.16
1525	1824	8.657074	TGATACCGGTTTGAAAGTAGATAATG	57.343	34.615	15.04	0.00	0.00	1.90
1560	1862	2.546494	GGCTTCAGTTGCACGCACT	61.546	57.895	0.00	0.00	0.00	4.40
1691	2000	3.019564	GTTGATGCAGAACCAATAGCCT	58.980	45.455	0.00	0.00	0.00	4.58
1693	2002	5.333645	CGATAGTTGATGCAGAACCAATAGC	60.334	44.000	7.58	0.00	0.00	2.97
1694	2003	6.220579	CGATAGTTGATGCAGAACCAATAG	57.779	41.667	7.58	0.97	0.00	1.73
1764	2086	2.623418	TCCTAGAGCTGGAAGGAACA	57.377	50.000	5.94	0.00	36.47	3.18
1881	2211	9.125026	ACATAAATTAGATTCCCAGTAGCAAAG	57.875	33.333	0.00	0.00	0.00	2.77
1890	2221	8.250332	GCAAGAAACACATAAATTAGATTCCCA	58.750	33.333	0.00	0.00	0.00	4.37
1967	2298	2.279517	GGCTACTGATGCGACCGG	60.280	66.667	0.00	0.00	0.00	5.28
2000	2331	4.817318	TCTGAAACCAAACCTTGCTTTT	57.183	36.364	0.00	0.00	0.00	2.27
2061	2398	4.869297	CCAACTTGATTTGTGCAAACAGAA	59.131	37.500	0.00	0.00	32.51	3.02
2069	2406	3.622612	AGCAAAACCAACTTGATTTGTGC	59.377	39.130	15.54	12.48	35.68	4.57

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.