AutoCloner

Multiple sequence alignment - TraesCS7D01G319800

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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	TraesCS7D01G319800	chr7D	100.000	6996	0	0	1	6996	409463758	409456763	0.000000e+00	12920
1	TraesCS7D01G319800	chr7D	95.402	87	3	1	5946	6032	409457726	409457641	3.400000e-28	137
2	TraesCS7D01G319800	chr7D	95.402	87	3	1	6033	6118	409457813	409457727	3.400000e-28	137
3	TraesCS7D01G319800	chr7B	96.282	5057	163	12	992	6028	423772249	423767198	0.000000e+00	8274
4	TraesCS7D01G319800	chr7B	95.101	939	17	5	6028	6940	423767092	423766157	0.000000e+00	1452
5	TraesCS7D01G319800	chr7B	92.574	781	43	10	230	1007	423773036	423772268	0.000000e+00	1107
6	TraesCS7D01G319800	chr7B	93.506	231	12	3	1	228	423773431	423773201	2.420000e-89	340
7	TraesCS7D01G319800	chr7B	80.882	272	30	17	568	827	116121786	116121525	1.990000e-45	195
8	TraesCS7D01G319800	chr7B	97.333	75	1	1	5958	6032	423767078	423767005	7.370000e-25	126
9	TraesCS7D01G319800	chr7B	93.976	83	5	0	6033	6115	423767280	423767198	7.370000e-25	126
10	TraesCS7D01G319800	chr7A	96.168	3314	61	14	3719	6987	469987294	469984002	0.000000e+00	5356
11	TraesCS7D01G319800	chr7A	97.950	2927	51	6	809	3728	469990248	469987324	0.000000e+00	5064
12	TraesCS7D01G319800	chr7A	89.078	824	63	14	1	820	470119801	470119001	0.000000e+00	998
13	TraesCS7D01G319800	chr7A	81.008	258	34	11	568	822	78658055	78657810	2.580000e-44	191
14	TraesCS7D01G319800	chr7A	91.765	85	2	3	6035	6118	469985041	469984961	5.740000e-21	113
15	TraesCS7D01G319800	chr4A	93.529	170	9	1	4476	4643	448515226	448515057	1.160000e-62	252
16	TraesCS7D01G319800	chr4A	81.250	272	31	13	561	822	132995276	132995537	1.190000e-47	202
17	TraesCS7D01G319800	chr5D	91.304	184	12	3	4469	4649	508111951	508112133	1.510000e-61	248
18	TraesCS7D01G319800	chr5D	91.954	174	12	1	4469	4640	119768976	119768803	7.010000e-60	243
19	TraesCS7D01G319800	chr5D	88.108	185	20	1	4458	4640	559427206	559427022	1.180000e-52	219
20	TraesCS7D01G319800	chr2D	93.491	169	8	2	4476	4641	628591814	628591982	1.510000e-61	248
21	TraesCS7D01G319800	chr2D	82.051	273	24	18	568	826	158246198	158245937	7.110000e-50	209
22	TraesCS7D01G319800	chr4D	92.442	172	9	2	4473	4640	122199878	122200049	7.010000e-60	243
23	TraesCS7D01G319800	chr4D	81.203	266	31	10	568	822	339065105	339064848	5.540000e-46	196
24	TraesCS7D01G319800	chr1D	90.341	176	11	5	4458	4629	394864345	394864518	7.060000e-55	226
25	TraesCS7D01G319800	chr3B	86.364	198	16	8	567	760	394097759	394097949	9.200000e-49	206
26	TraesCS7D01G319800	chr3D	84.925	199	18	8	567	760	298594867	298595058	2.580000e-44	191

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	TraesCS7D01G319800	chr7D	409456763	409463758	6995	True	12920.0	12920	100.000000	1	6996	1	chr7D.!!$R1	6995
1	TraesCS7D01G319800	chr7B	423766157	423772249	6092	True	3284.0	8274	96.238667	992	6940	3	chr7B.!!$R3	5948
2	TraesCS7D01G319800	chr7B	423772268	423773431	1163	True	723.5	1107	93.040000	1	1007	2	chr7B.!!$R4	1006
3	TraesCS7D01G319800	chr7A	469984002	469990248	6246	True	3511.0	5356	95.294333	809	6987	3	chr7A.!!$R3	6178
4	TraesCS7D01G319800	chr7A	470119001	470119801	800	True	998.0	998	89.078000	1	820	1	chr7A.!!$R2	819

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
514	682	2.044123	AAAGGAGTTCGATGATGGCC	57.956	50.000	0.00	0.00	5.36	F
1096	1271	0.512952	GCGATTTTCGATCCATCCCG	59.487	55.000	0.32	43.74	5.14	F
2231	2408	0.110104	AGCTGGAAAGCTGCTGAACT	59.890	50.000	1.35	44.44	3.01	F
3246	3425	2.574322	CACGTGCACACAATTTAGCTC	58.426	47.619	18.64	0.00	4.09	F
3939	4157	0.760945	CCCCGCTAGGAGGTTCTCAT	60.761	60.000	0.00	41.02	2.90	F
4381	4601	5.832539	ATTCCCTTTTCTGTCTTCTCTCA	57.167	39.130	0.00	0.00	3.27	F
5201	5450	1.066143	AGTAACATGCAACCGCTAGCT	60.066	47.619	13.93	39.64	3.32	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1696	1871	1.523758	GACGCCAGATTTTCACCTGT	58.476	50.000	0.00	0.00	4.00	R
2629	2808	1.019673	CATCCTTGCGATGGAACCTG	58.980	55.000	0.00	44.14	4.00	R
3693	3872	3.751175	CGTGTATCCAGAAACCACACAAT	59.249	43.478	0.00	39.52	2.71	R
4381	4601	1.000896	CAAACCGCCCTCCCAGAAT	60.001	57.895	0.00	0.00	2.40	R
4800	5023	1.133790	GCATGTGACATTTCCCTCTGC	59.866	52.381	0.00	0.00	4.26	R
5847	6110	2.761208	AGAGTGGATTTCTGGGACTACG	59.239	50.000	0.00	0.00	3.51	R
6446	6844	1.078497	TCACCGGACACATCCATGC	60.078	57.895	9.46	46.67	4.06	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
141	144	8.846607	GTTAAAGTACAAAATAATTGAGTGCCG	58.153	33.333	0.00	0.00	0.00	5.69
190	193	5.014123	TGTTTCCCATTGAATCTGTAGGAGT	59.986	40.000	0.00	0.00	31.67	3.85
201	204	6.552725	TGAATCTGTAGGAGTTGAGCTATCAT	59.447	38.462	0.00	0.00	34.73	2.45
202	205	7.725844	TGAATCTGTAGGAGTTGAGCTATCATA	59.274	37.037	0.00	0.00	34.73	2.15
206	209	8.580720	TCTGTAGGAGTTGAGCTATCATATTTC	58.419	37.037	0.00	0.00	34.73	2.17
258	425	3.136443	TGGATTTATGACCGAAGAGGCAT	59.864	43.478	0.00	0.00	46.52	4.40
318	485	7.168637	GGTTCCGAGTCTTTTGTTTATTTTTCC	59.831	37.037	0.00	0.00	0.00	3.13
319	486	7.336161	TCCGAGTCTTTTGTTTATTTTTCCA	57.664	32.000	0.00	0.00	0.00	3.53
373	540	9.696917	GGTTTCCAATATGATGAAATACAATCC	57.303	33.333	0.00	0.00	31.35	3.01
408	575	6.428771	CCGTTCCTACCTTCTTGAATTTTGTA	59.571	38.462	0.00	0.00	0.00	2.41
413	580	8.726988	TCCTACCTTCTTGAATTTTGTAAATCG	58.273	33.333	0.00	0.00	0.00	3.34
514	682	2.044123	AAAGGAGTTCGATGATGGCC	57.956	50.000	0.00	0.00	0.00	5.36
637	807	7.064016	GTCAACTTTGCAAAATTTGACCAAGTA	59.936	33.333	32.63	14.65	40.01	2.24
760	930	7.090173	CGGATGTAAATGTTTTCTCCACAAAT	58.910	34.615	0.00	0.00	0.00	2.32
835	1005	4.263594	GGAGGGAGTACTATAGAGTCAGGG	60.264	54.167	6.78	0.00	37.10	4.45
1096	1271	0.512952	GCGATTTTCGATCCATCCCG	59.487	55.000	0.32	0.00	43.74	5.14
1105	1280	2.040009	GATCCATCCCGCCGGAGAAA	62.040	60.000	5.05	0.00	43.12	2.52
1531	1706	5.237048	TGGTAGGTGGTAACGTAATTTCAC	58.763	41.667	0.00	0.00	42.51	3.18
1696	1871	4.704540	CCCATCTTTTGCACTGGTTACATA	59.295	41.667	0.00	0.00	0.00	2.29
1781	1956	0.811281	GCTGTTATGGAAGGCACCAC	59.189	55.000	5.63	0.00	43.03	4.16
1799	1975	4.523943	CACCACTTCTCCCAATTCAATGAA	59.476	41.667	0.00	0.00	0.00	2.57
1843	2019	3.418047	CCATACGGAGGGTTTGAAGTTT	58.582	45.455	0.00	0.00	30.07	2.66
1909	2085	2.037772	CACTCTGCTTGGTCCTGTAGTT	59.962	50.000	0.00	0.00	0.00	2.24
2092	2268	7.571080	TGTAAACTGGTTTCTTCGGTAATTT	57.429	32.000	1.77	0.00	34.23	1.82
2093	2269	7.419204	TGTAAACTGGTTTCTTCGGTAATTTG	58.581	34.615	1.77	0.00	34.23	2.32
2188	2365	5.821995	TGTTTGGTTGTACAAGTTAGGGTAC	59.178	40.000	8.98	0.00	40.15	3.34
2204	2381	7.500227	AGTTAGGGTACAAAGTTCTACAAAACC	59.500	37.037	0.00	0.00	0.00	3.27
2213	2390	6.451064	AAGTTCTACAAAACCAAGACCAAG	57.549	37.500	0.00	0.00	0.00	3.61
2231	2408	0.110104	AGCTGGAAAGCTGCTGAACT	59.890	50.000	1.35	0.00	44.44	3.01
2629	2808	2.829741	TTTGGCCTTGTTTGTATGGC	57.170	45.000	3.32	0.00	44.22	4.40
2770	2949	5.402270	CCAAAAACAGGTGATTCGATGTTTC	59.598	40.000	11.72	0.00	43.17	2.78
3060	3239	5.386958	TCGTCTGATGTACTTTAACTGCT	57.613	39.130	0.00	0.00	0.00	4.24
3246	3425	2.574322	CACGTGCACACAATTTAGCTC	58.426	47.619	18.64	0.00	0.00	4.09
3727	3945	9.274065	GTTTCTGGATACACGCTAAATTTTTAG	57.726	33.333	0.00	5.83	46.17	1.85
3781	3999	9.577110	TTCCAGTATACATAGTTTTGTAGTTCG	57.423	33.333	5.50	0.00	35.65	3.95
3939	4157	0.760945	CCCCGCTAGGAGGTTCTCAT	60.761	60.000	0.00	0.00	41.02	2.90
4173	4392	6.365970	TTGCTTCTAGAGTCTTCTCCATTT	57.634	37.500	0.00	0.00	41.26	2.32
4381	4601	5.832539	ATTCCCTTTTCTGTCTTCTCTCA	57.167	39.130	0.00	0.00	0.00	3.27
5201	5450	1.066143	AGTAACATGCAACCGCTAGCT	60.066	47.619	13.93	0.00	39.64	3.32
5470	5733	5.448654	TCCTGCATACATTGGCTATCTTTT	58.551	37.500	0.00	0.00	0.00	2.27
5807	6070	8.617290	ACTGGAAACTACAAATTAGGTTACTG	57.383	34.615	0.00	0.00	32.38	2.74
5847	6110	1.000938	CTGCTGTTTTCACCTTCTGCC	60.001	52.381	0.00	0.00	0.00	4.85
6119	6491	9.618890	AGACATAAATTGCTCATATGTAACTGT	57.381	29.630	1.90	1.16	39.64	3.55
6163	6535	5.500234	TCGATTCAATCAAATTGGGTCTCT	58.500	37.500	0.00	0.00	40.61	3.10
6446	6844	3.004629	CCCTGACTCGATCTTCTCATCAG	59.995	52.174	0.00	0.00	33.45	2.90
6838	7236	1.489560	GGCTAGGTGGAGGTGTTGGT	61.490	60.000	0.00	0.00	0.00	3.67

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
141	144	8.450180	CAAAATTAAATCAAAGGGGTTGCATAC	58.550	33.333	0.00	0.00	37.13	2.39
181	184	8.584157	AGAAATATGATAGCTCAACTCCTACAG	58.416	37.037	0.00	0.00	34.37	2.74
243	410	1.153086	GGCATGCCTCTTCGGTCAT	60.153	57.895	29.98	0.00	34.25	3.06
270	437	5.126067	CCACGAGAATAGGGAAAATGATGT	58.874	41.667	0.00	0.00	0.00	3.06
368	535	3.070018	GGAACGGAGATATGCAGGATTG	58.930	50.000	0.00	0.00	0.00	2.67
373	540	2.894126	AGGTAGGAACGGAGATATGCAG	59.106	50.000	0.00	0.00	0.00	4.41
408	575	2.839486	TCCAAGTGACTCTGCGATTT	57.161	45.000	0.00	0.00	0.00	2.17
413	580	3.064545	GTGCATAATCCAAGTGACTCTGC	59.935	47.826	0.00	0.00	0.00	4.26
557	725	8.515927	TGGAACTGAGGGAGTATAGTATAGTA	57.484	38.462	0.00	0.00	33.09	1.82
558	726	7.403837	TGGAACTGAGGGAGTATAGTATAGT	57.596	40.000	0.00	0.00	33.09	2.12
561	729	9.261035	CAATATGGAACTGAGGGAGTATAGTAT	57.739	37.037	0.00	0.00	33.09	2.12
713	883	8.512966	TCCGGAATGTCAAACATATTTCATTA	57.487	30.769	0.00	0.00	37.97	1.90
714	884	7.403312	TCCGGAATGTCAAACATATTTCATT	57.597	32.000	0.00	0.00	37.97	2.57
788	958	7.445096	TCCGTTTCGTAATGTAGTCCATATAGA	59.555	37.037	0.00	0.00	31.97	1.98
789	959	7.587629	TCCGTTTCGTAATGTAGTCCATATAG	58.412	38.462	0.00	0.00	31.97	1.31
790	960	7.308770	CCTCCGTTTCGTAATGTAGTCCATATA	60.309	40.741	0.00	0.00	31.97	0.86
796	966	3.129287	TCCCTCCGTTTCGTAATGTAGTC	59.871	47.826	0.00	0.00	0.00	2.59
806	976	4.384056	TCTATAGTACTCCCTCCGTTTCG	58.616	47.826	0.00	0.00	0.00	3.46
875	1046	0.954452	CCTATTTTCATGGGCTCGGC	59.046	55.000	0.00	0.00	0.00	5.54
897	1072	2.732619	CCCACTACCTCCTTCCGGC	61.733	68.421	0.00	0.00	0.00	6.13
905	1080	3.119209	GCTATATTACGGCCCACTACCTC	60.119	52.174	0.00	0.00	0.00	3.85
1043	1218	1.116536	TTTGGGGAAGGCGGGAAAAC	61.117	55.000	0.00	0.00	0.00	2.43
1096	1271	1.623973	CCGTCGTCTTTTTCTCCGGC	61.624	60.000	0.00	0.00	0.00	6.13
1105	1280	0.173708	GCATCCTCTCCGTCGTCTTT	59.826	55.000	0.00	0.00	0.00	2.52
1358	1533	2.376695	AATCGGAGGGGATAAGTCGA	57.623	50.000	0.00	0.00	0.00	4.20
1531	1706	5.333645	GCCTACGCTGACATTGAAGATATTG	60.334	44.000	0.00	0.00	0.00	1.90
1696	1871	1.523758	GACGCCAGATTTTCACCTGT	58.476	50.000	0.00	0.00	0.00	4.00
1781	1956	5.948162	TCTTCCTTCATTGAATTGGGAGAAG	59.052	40.000	11.51	10.77	33.96	2.85
1799	1975	8.909423	TGGGAATAACCAATAAATTTCTTCCT	57.091	30.769	0.00	0.00	41.20	3.36
1818	1994	2.201830	TCAAACCCTCCGTATGGGAAT	58.798	47.619	10.95	0.00	46.61	3.01
1843	2019	9.953697	GTTTTCTATTGTGTTGGTTATGTTGTA	57.046	29.630	0.00	0.00	0.00	2.41
1909	2085	2.029020	AGAGCTCGTGACAAACATGCTA	60.029	45.455	8.37	0.00	34.57	3.49
2092	2268	6.397272	GGTCAAATTTAAACCATCAGATGCA	58.603	36.000	14.20	0.00	33.11	3.96
2093	2269	5.516339	CGGTCAAATTTAAACCATCAGATGC	59.484	40.000	17.54	0.00	32.35	3.91
2188	2365	6.202516	TGGTCTTGGTTTTGTAGAACTTTG	57.797	37.500	0.00	0.00	0.00	2.77
2231	2408	2.655090	TTGGTGATTGGCTGAACAGA	57.345	45.000	5.97	0.00	0.00	3.41
2449	2628	1.723608	CCTGTCACACAAAGGCGCAA	61.724	55.000	10.83	0.00	0.00	4.85
2629	2808	1.019673	CATCCTTGCGATGGAACCTG	58.980	55.000	0.00	0.00	44.14	4.00
2770	2949	2.787473	TACAGAAGCCAAGATGGTGG	57.213	50.000	0.00	0.00	40.46	4.61
3246	3425	4.446371	GGATAGAGAATGTGGTGAAGGTG	58.554	47.826	0.00	0.00	0.00	4.00
3626	3805	8.934023	TCAAAGGTTAGAATGTTAGTTCCATT	57.066	30.769	0.00	0.00	35.30	3.16
3638	3817	6.773638	TCAAAGAGCTCTCAAAGGTTAGAAT	58.226	36.000	18.55	0.00	35.33	2.40
3693	3872	3.751175	CGTGTATCCAGAAACCACACAAT	59.249	43.478	0.00	0.00	39.52	2.71
3781	3999	6.605995	AGGGCCAAACAAATTAGTATCCTAAC	59.394	38.462	6.18	0.00	36.03	2.34
3939	4157	5.303333	TCACTGTAACAGATCAGTAACACCA	59.697	40.000	0.00	0.00	42.05	4.17
4173	4392	7.444183	CCAAATAGACTGAGTTCCTGTTTAACA	59.556	37.037	0.00	0.00	0.00	2.41
4381	4601	1.000896	CAAACCGCCCTCCCAGAAT	60.001	57.895	0.00	0.00	0.00	2.40
4793	5016	3.181440	TGACATTTCCCTCTGCAACTTCT	60.181	43.478	0.00	0.00	0.00	2.85
4800	5023	1.133790	GCATGTGACATTTCCCTCTGC	59.866	52.381	0.00	0.00	0.00	4.26
4930	5153	7.047891	AGGCTTACTCAATGTGATATTTTCGA	58.952	34.615	0.00	0.00	0.00	3.71
4939	5162	6.109156	TCAAAGTAGGCTTACTCAATGTGA	57.891	37.500	9.19	5.76	39.20	3.58
5131	5368	2.879103	TTCTTCCATGTGGTTCCTCC	57.121	50.000	0.00	0.00	36.34	4.30
5423	5684	4.282957	TGCAGATTCAGACTGAAACTCTCT	59.717	41.667	21.41	16.34	37.39	3.10
5424	5685	4.564041	TGCAGATTCAGACTGAAACTCTC	58.436	43.478	21.41	16.72	37.39	3.20
5470	5733	3.243839	GGAAAGTGCATGCAAGAAGGAAA	60.244	43.478	24.58	0.00	0.00	3.13
5807	6070	4.672801	GCAGCAGGCTACATTTCTTTACAC	60.673	45.833	0.00	0.00	40.25	2.90
5847	6110	2.761208	AGAGTGGATTTCTGGGACTACG	59.239	50.000	0.00	0.00	0.00	3.51
6119	6491	7.371126	TCGATATGCAAACTATTGTTGTCAA	57.629	32.000	0.00	0.00	38.85	3.18
6163	6535	3.438781	GTGTGATTGAAATAAGGGCGTCA	59.561	43.478	0.00	0.00	0.00	4.35
6232	6627	4.557296	GCAATGATCAAATCCATACCCACG	60.557	45.833	0.00	0.00	0.00	4.94
6446	6844	1.078497	TCACCGGACACATCCATGC	60.078	57.895	9.46	0.00	46.67	4.06
6838	7236	2.043604	CTCCGCCACATATCAGCCCA	62.044	60.000	0.00	0.00	0.00	5.36

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.