AutoCloner

Multiple sequence alignment - TraesCS7D01G402300

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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	TraesCS7D01G402300	chr7D	100.000	3167	0	0	1	3167	519269991	519273157	0.000000e+00	5849
1	TraesCS7D01G402300	chr7D	86.733	799	106	0	1240	2038	519261821	519261023	0.000000e+00	889
2	TraesCS7D01G402300	chr7D	80.802	349	34	20	2434	2777	519406979	519407299	3.160000e-60	243
3	TraesCS7D01G402300	chr7D	77.198	364	39	23	2806	3149	519291303	519291642	4.200000e-39	172
4	TraesCS7D01G402300	chr7A	94.975	2388	61	30	791	3150	595198381	595200737	0.000000e+00	3690
5	TraesCS7D01G402300	chr7A	88.110	799	95	0	1240	2038	595069695	595068897	0.000000e+00	950
6	TraesCS7D01G402300	chr7A	89.474	551	44	6	1	551	595197277	595197813	0.000000e+00	684
7	TraesCS7D01G402300	chr7A	81.646	316	36	13	2465	2777	595281366	595281662	3.160000e-60	243
8	TraesCS7D01G402300	chr7A	98.551	69	1	0	728	796	595197868	595197936	4.290000e-24	122
9	TraesCS7D01G402300	chr7B	94.601	2408	69	20	793	3167	552665193	552667572	0.000000e+00	3670
10	TraesCS7D01G402300	chr7B	87.000	800	102	2	1240	2038	552560863	552560065	0.000000e+00	900
11	TraesCS7D01G402300	chr7B	86.933	375	39	5	247	620	552664259	552664624	2.270000e-111	412
12	TraesCS7D01G402300	chr7B	89.723	253	22	2	1	252	552594447	552594696	1.420000e-83	320
13	TraesCS7D01G402300	chr7B	79.539	347	37	20	2433	2777	552707052	552707366	1.910000e-52	217
14	TraesCS7D01G402300	chr7B	79.539	347	37	20	2433	2777	552754038	552754352	1.910000e-52	217
15	TraesCS7D01G402300	chr7B	85.315	143	12	6	2981	3123	552707758	552707891	4.260000e-29	139
16	TraesCS7D01G402300	chr7B	85.507	138	11	6	2981	3118	552754744	552754872	5.510000e-28	135
17	TraesCS7D01G402300	chr7B	97.368	76	1	1	722	796	552664872	552664947	9.220000e-26	128
18	TraesCS7D01G402300	chr2D	81.879	447	70	8	1	443	565138214	565138653	1.790000e-97	366
19	TraesCS7D01G402300	chr2A	81.562	461	68	12	1	456	705548566	705548118	6.460000e-97	364
20	TraesCS7D01G402300	chrUn	79.339	484	87	11	1	477	45888610	45888133	8.470000e-86	327
21	TraesCS7D01G402300	chr5D	82.133	347	53	8	116	457	544151456	544151798	4.000000e-74	289
22	TraesCS7D01G402300	chr4A	80.814	344	60	6	116	457	625127100	625126761	6.740000e-67	265
23	TraesCS7D01G402300	chr5B	76.471	374	65	15	116	481	686204038	686204396	6.980000e-42	182

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	TraesCS7D01G402300	chr7D	519269991	519273157	3166	False	5849.000000	5849	100.000000	1	3167	1	chr7D.!!$F1	3166
1	TraesCS7D01G402300	chr7D	519261023	519261821	798	True	889.000000	889	86.733000	1240	2038	1	chr7D.!!$R1	798
2	TraesCS7D01G402300	chr7A	595197277	595200737	3460	False	1498.666667	3690	94.333333	1	3150	3	chr7A.!!$F2	3149
3	TraesCS7D01G402300	chr7A	595068897	595069695	798	True	950.000000	950	88.110000	1240	2038	1	chr7A.!!$R1	798
4	TraesCS7D01G402300	chr7B	552664259	552667572	3313	False	1403.333333	3670	92.967333	247	3167	3	chr7B.!!$F2	2920
5	TraesCS7D01G402300	chr7B	552560065	552560863	798	True	900.000000	900	87.000000	1240	2038	1	chr7B.!!$R1	798

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
487	489	0.039798	GTGCACCAAGTAGACGACGA	60.040	55.0	5.22	0.00	0.00	4.20	F
608	610	1.046204	CGGGGTAGGGAAGTACATCC	58.954	60.0	8.69	8.69	38.86	3.51	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1566	2248	0.179000	GGGTGCAGAGGATGTCGAAT	59.821	55.0	0.0	0.0	0.00	3.34	R
2328	3017	0.673437	TGCAAGCTTTTCTTTCCCCG	59.327	50.0	0.0	0.0	31.27	5.73	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
29	30	4.823790	AACTCACAACCAATAACCGAAC	57.176	40.909	0.00	0.00	0.00	3.95
33	34	2.486592	CACAACCAATAACCGAACCTCC	59.513	50.000	0.00	0.00	0.00	4.30
87	88	7.664731	CACAATCATAGCAATATCTTCCTCCTT	59.335	37.037	0.00	0.00	0.00	3.36
97	98	3.721087	TCTTCCTCCTTGGTCAAATCC	57.279	47.619	0.00	0.00	37.07	3.01
140	141	3.961182	TCATCGTAATAGTTGGAGTCGC	58.039	45.455	0.00	0.00	0.00	5.19
143	144	3.702330	TCGTAATAGTTGGAGTCGCATG	58.298	45.455	0.00	0.00	0.00	4.06
156	157	2.159503	AGTCGCATGAACTCGTCTACAG	60.160	50.000	0.00	0.00	0.00	2.74
317	319	2.285442	GCTACTGGGAGGGGGTGT	60.285	66.667	0.00	0.00	0.00	4.16
357	359	1.002134	CCTTGACGTGGGGAAGCAT	60.002	57.895	0.00	0.00	0.00	3.79
417	419	0.324943	CCAAATGTCACCGGACCTCT	59.675	55.000	9.46	0.00	43.65	3.69
421	423	1.194781	ATGTCACCGGACCTCTGCTT	61.195	55.000	9.46	0.00	43.65	3.91
429	431	4.379243	ACCTCTGCTTGGTCGCGG	62.379	66.667	6.13	0.00	37.63	6.46
460	462	4.025858	GGCTGTGGAGCTCCTGCA	62.026	66.667	32.28	26.85	45.44	4.41
469	471	2.232298	GAGCTCCTGCAACCGCTAGT	62.232	60.000	0.87	0.00	42.74	2.57
485	487	2.864968	CTAGTGCACCAAGTAGACGAC	58.135	52.381	14.63	0.00	0.00	4.34
487	489	0.039798	GTGCACCAAGTAGACGACGA	60.040	55.000	5.22	0.00	0.00	4.20
496	498	3.655276	AGTAGACGACGACAAATTGGT	57.345	42.857	0.00	0.00	0.00	3.67
509	511	2.288961	AATTGGTAGCGAATCGACGT	57.711	45.000	6.91	0.00	35.59	4.34
543	545	2.119029	GTCGGTGGCTAAATGGGGC	61.119	63.158	0.00	0.00	0.00	5.80
605	607	1.686800	GGCGGGGTAGGGAAGTACA	60.687	63.158	0.00	0.00	0.00	2.90
608	610	1.046204	CGGGGTAGGGAAGTACATCC	58.954	60.000	8.69	8.69	38.86	3.51
614	616	2.728435	GGGAAGTACATCCGGGCGT	61.728	63.158	10.87	0.98	40.62	5.68
635	648	2.815647	GCAGTGGCCTACGAGTGC	60.816	66.667	3.32	4.32	0.00	4.40
636	649	2.973899	CAGTGGCCTACGAGTGCT	59.026	61.111	3.32	0.00	0.00	4.40
638	651	2.815647	GTGGCCTACGAGTGCTGC	60.816	66.667	3.32	0.00	0.00	5.25
673	793	5.979288	TTTTTGGGCTAGCCGTTTATTTA	57.021	34.783	27.24	5.09	36.85	1.40
674	794	6.532988	TTTTTGGGCTAGCCGTTTATTTAT	57.467	33.333	27.24	0.00	36.85	1.40
677	797	6.532988	TTGGGCTAGCCGTTTATTTATTTT	57.467	33.333	27.24	0.00	36.85	1.82
717	867	3.257375	TGAGCTGCTCTAAAAACGTCCTA	59.743	43.478	28.04	2.43	0.00	2.94
718	868	4.243270	GAGCTGCTCTAAAAACGTCCTAA	58.757	43.478	21.93	0.00	0.00	2.69
719	869	4.638304	AGCTGCTCTAAAAACGTCCTAAA	58.362	39.130	0.00	0.00	0.00	1.85
720	870	5.246307	AGCTGCTCTAAAAACGTCCTAAAT	58.754	37.500	0.00	0.00	0.00	1.40
800	1467	5.412594	TGCTTCACTTGCTTGGAGTAATAAG	59.587	40.000	0.00	0.00	0.00	1.73
805	1472	6.094048	TCACTTGCTTGGAGTAATAAGCATTC	59.906	38.462	11.81	0.00	46.15	2.67
856	1523	3.304911	TTGTTTGGAGGACATGTTGGA	57.695	42.857	0.00	0.00	0.00	3.53
888	1564	1.692148	CCGCAGCGTCGCATCTAAAA	61.692	55.000	21.09	0.00	0.00	1.52
924	1600	1.881252	CGAAGCCCATACCCGAACG	60.881	63.158	0.00	0.00	0.00	3.95
953	1629	2.205462	ACACCAGAGGCCCAGACT	59.795	61.111	0.00	0.00	0.00	3.24
990	1669	2.024022	CGGAAGCGAGCGAGAGAG	59.976	66.667	0.00	0.00	0.00	3.20
1941	2623	4.385825	TCATGTACAACAAGAACTCCACC	58.614	43.478	0.00	0.00	0.00	4.61
2151	2833	2.123640	CCCACCCCCAACAACGTT	60.124	61.111	0.00	0.00	0.00	3.99
2174	2856	0.325765	GTCCCCAAGTAGCCTCCTCT	60.326	60.000	0.00	0.00	0.00	3.69
2175	2857	0.032017	TCCCCAAGTAGCCTCCTCTC	60.032	60.000	0.00	0.00	0.00	3.20
2176	2858	0.031616	CCCCAAGTAGCCTCCTCTCT	60.032	60.000	0.00	0.00	0.00	3.10
2177	2859	1.408969	CCCAAGTAGCCTCCTCTCTC	58.591	60.000	0.00	0.00	0.00	3.20
2178	2860	1.408969	CCAAGTAGCCTCCTCTCTCC	58.591	60.000	0.00	0.00	0.00	3.71
2179	2861	1.408969	CAAGTAGCCTCCTCTCTCCC	58.591	60.000	0.00	0.00	0.00	4.30
2180	2862	1.063266	CAAGTAGCCTCCTCTCTCCCT	60.063	57.143	0.00	0.00	0.00	4.20
2181	2863	0.850784	AGTAGCCTCCTCTCTCCCTC	59.149	60.000	0.00	0.00	0.00	4.30
2182	2864	0.178973	GTAGCCTCCTCTCTCCCTCC	60.179	65.000	0.00	0.00	0.00	4.30
2217	2899	2.669849	CTGGCTTGCTCTGCTCCT	59.330	61.111	0.00	0.00	0.00	3.69
2218	2900	1.745864	CTGGCTTGCTCTGCTCCTG	60.746	63.158	0.00	0.00	0.00	3.86
2236	2918	2.283298	CTGTGCTCCATGGTGATGTAC	58.717	52.381	17.98	12.86	0.00	2.90
2251	2934	8.437360	TGGTGATGTACTATGATCAATTTCAC	57.563	34.615	0.00	6.62	30.45	3.18
2328	3017	2.749800	GCCAAGAGTGATTCCCCCATAC	60.750	54.545	0.00	0.00	0.00	2.39
2479	3171	6.212187	TGAGGATATCTCGTGGATGATTTCAT	59.788	38.462	2.05	0.00	45.32	2.57
2508	3200	5.819991	AGATCAAAATCAGTGGGCTTTCTA	58.180	37.500	0.00	0.00	34.07	2.10
2705	3398	1.136336	GTGCCATCGAACGAAACTGTC	60.136	52.381	0.12	0.00	0.00	3.51
2742	3436	7.459795	TTGTTAATTACACATCATGGAAGCA	57.540	32.000	0.00	0.00	33.39	3.91
2754	3448	1.729586	TGGAAGCAGTAACCACTCCT	58.270	50.000	0.00	0.00	30.46	3.69
2839	3539	2.189594	TGGTCAGCAAGTCATCCAAG	57.810	50.000	0.00	0.00	0.00	3.61
2963	3678	5.008911	TCGATGATTTGCCAATACCAATCTG	59.991	40.000	0.00	0.00	0.00	2.90
2964	3679	5.008911	CGATGATTTGCCAATACCAATCTGA	59.991	40.000	0.00	0.00	0.00	3.27
2966	3681	6.795144	TGATTTGCCAATACCAATCTGATT	57.205	33.333	0.00	0.00	0.00	2.57
2968	3683	6.608405	TGATTTGCCAATACCAATCTGATTCT	59.392	34.615	0.00	0.00	0.00	2.40
2969	3684	6.455360	TTTGCCAATACCAATCTGATTCTC	57.545	37.500	0.00	0.00	0.00	2.87
2970	3685	5.114764	TGCCAATACCAATCTGATTCTCA	57.885	39.130	0.00	0.00	0.00	3.27
2971	3686	5.508567	TGCCAATACCAATCTGATTCTCAA	58.491	37.500	0.00	0.00	0.00	3.02
2972	3687	6.131264	TGCCAATACCAATCTGATTCTCAAT	58.869	36.000	0.00	0.00	0.00	2.57
3074	3789	5.467035	TGGATTGTTTGCCTTCCTTTTAG	57.533	39.130	0.00	0.00	0.00	1.85
3141	3856	2.190578	CATCCGCTCCAACCTCCC	59.809	66.667	0.00	0.00	0.00	4.30
3155	3872	0.842467	CCTCCCCTTCCACTTCCACT	60.842	60.000	0.00	0.00	0.00	4.00

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
18	19	0.725117	GCACGGAGGTTCGGTTATTG	59.275	55.000	0.00	0.00	0.00	1.90
33	34	1.961277	AACAAGAGGCCGAAGCACG	60.961	57.895	0.00	0.00	42.56	5.34
87	88	4.951715	CAGATGAGGAATTGGATTTGACCA	59.048	41.667	0.00	0.00	38.24	4.02
140	141	6.641314	AGTTTTGTACTGTAGACGAGTTCATG	59.359	38.462	0.00	0.00	35.19	3.07
143	144	7.484324	GGATAGTTTTGTACTGTAGACGAGTTC	59.516	40.741	0.00	0.00	37.73	3.01
199	200	9.536558	GTAAAAGAAAAGTTCATTTGCGTTTTT	57.463	25.926	2.39	0.00	38.56	1.94
200	201	8.172484	GGTAAAAGAAAAGTTCATTTGCGTTTT	58.828	29.630	2.39	0.00	38.56	2.43
201	202	7.547722	AGGTAAAAGAAAAGTTCATTTGCGTTT	59.452	29.630	2.39	0.00	40.14	3.60
204	205	7.463469	AAGGTAAAAGAAAAGTTCATTTGCG	57.537	32.000	2.39	0.00	35.01	4.85
240	241	0.530744	TGCACACTAGGTGTCCGATC	59.469	55.000	11.47	0.00	43.92	3.69
460	462	0.682852	TACTTGGTGCACTAGCGGTT	59.317	50.000	17.98	1.77	46.23	4.44
469	471	0.039798	GTCGTCGTCTACTTGGTGCA	60.040	55.000	0.00	0.00	0.00	4.57
485	487	2.601314	TCGATTCGCTACCAATTTGTCG	59.399	45.455	0.00	0.00	0.00	4.35
487	489	2.347452	CGTCGATTCGCTACCAATTTGT	59.653	45.455	0.00	0.00	0.00	2.83
496	498	2.277692	CGCCACGTCGATTCGCTA	60.278	61.111	0.00	0.00	0.00	4.26
522	524	0.106719	CCCATTTAGCCACCGACCAT	60.107	55.000	0.00	0.00	0.00	3.55
523	525	1.301623	CCCATTTAGCCACCGACCA	59.698	57.895	0.00	0.00	0.00	4.02
530	532	2.043046	GCCAGCCCCATTTAGCCA	60.043	61.111	0.00	0.00	0.00	4.75
620	622	2.973899	CAGCACTCGTAGGCCACT	59.026	61.111	5.01	0.00	0.00	4.00
655	774	6.532988	AAAAATAAATAAACGGCTAGCCCA	57.467	33.333	28.09	11.14	0.00	5.36
688	808	6.595716	ACGTTTTTAGAGCAGCTCAATAGATT	59.404	34.615	24.64	4.24	32.06	2.40
689	809	6.109359	ACGTTTTTAGAGCAGCTCAATAGAT	58.891	36.000	24.64	5.00	32.06	1.98
699	819	5.324697	GCATTTAGGACGTTTTTAGAGCAG	58.675	41.667	0.00	0.00	0.00	4.24
703	853	4.653868	TGGGCATTTAGGACGTTTTTAGA	58.346	39.130	0.00	0.00	0.00	2.10
800	1467	1.632589	ACCCCTCCAAACAAGAATGC	58.367	50.000	0.00	0.00	0.00	3.56
805	1472	1.039856	CCACAACCCCTCCAAACAAG	58.960	55.000	0.00	0.00	0.00	3.16
903	1579	2.124901	CGGGTATGGGCTTCGCAA	60.125	61.111	0.00	0.00	0.00	4.85
924	1600	1.064621	CTGGTGTGTTGTGTGCTGC	59.935	57.895	0.00	0.00	0.00	5.25
1090	1772	3.508840	GGGCGACTGGAATTGGCG	61.509	66.667	0.00	0.00	0.00	5.69
1566	2248	0.179000	GGGTGCAGAGGATGTCGAAT	59.821	55.000	0.00	0.00	0.00	3.34
1941	2623	4.379243	AGGCGGTTGAGCAGGTCG	62.379	66.667	0.00	0.00	39.27	4.79
2151	2833	0.685458	GAGGCTACTTGGGGACGGTA	60.685	60.000	0.00	0.00	0.00	4.02
2174	2856	3.036959	GAGGGGAGGGGAGGGAGA	61.037	72.222	0.00	0.00	0.00	3.71
2175	2857	4.179599	GGAGGGGAGGGGAGGGAG	62.180	77.778	0.00	0.00	0.00	4.30
2202	2884	2.039405	CACAGGAGCAGAGCAAGCC	61.039	63.158	0.00	0.00	0.00	4.35
2217	2899	1.908619	AGTACATCACCATGGAGCACA	59.091	47.619	21.47	0.00	33.82	4.57
2218	2900	2.698855	AGTACATCACCATGGAGCAC	57.301	50.000	21.47	6.83	33.82	4.40
2236	2918	7.701078	CCAGCAAAGAAGTGAAATTGATCATAG	59.299	37.037	0.00	0.00	0.00	2.23
2251	2934	7.094634	ACACAATGTATAAGACCAGCAAAGAAG	60.095	37.037	0.00	0.00	0.00	2.85
2287	2970	5.133941	TGGCAGAAATACAAACTGGTACAA	58.866	37.500	0.00	0.00	38.70	2.41
2328	3017	0.673437	TGCAAGCTTTTCTTTCCCCG	59.327	50.000	0.00	0.00	31.27	5.73
2479	3171	4.943705	GCCCACTGATTTTGATCTAAGACA	59.056	41.667	0.00	0.00	0.00	3.41
2508	3200	5.366477	ACAAGGACTTTCAAATCCCAATGTT	59.634	36.000	0.00	0.00	35.38	2.71
2742	3436	3.239449	TGACATGACAGGAGTGGTTACT	58.761	45.455	0.00	0.00	40.66	2.24
2754	3448	9.208022	GTATTAAGCAAGCTATATGACATGACA	57.792	33.333	0.00	0.00	0.00	3.58
2839	3539	2.063266	CATGTGTTGTTCCAATGCTGC	58.937	47.619	0.00	0.00	0.00	5.25
2963	3678	7.650903	GGCATGGTTTATGAGAAATTGAGAATC	59.349	37.037	0.00	0.00	39.21	2.52
2964	3679	7.343833	AGGCATGGTTTATGAGAAATTGAGAAT	59.656	33.333	0.00	0.00	39.21	2.40
2966	3681	6.189859	AGGCATGGTTTATGAGAAATTGAGA	58.810	36.000	0.00	0.00	39.21	3.27
2968	3683	6.855763	AAGGCATGGTTTATGAGAAATTGA	57.144	33.333	0.00	0.00	39.21	2.57
2969	3684	7.999679	TCTAAGGCATGGTTTATGAGAAATTG	58.000	34.615	0.00	0.00	39.21	2.32
2970	3685	8.593945	TTCTAAGGCATGGTTTATGAGAAATT	57.406	30.769	0.00	0.00	39.21	1.82
2971	3686	8.773033	ATTCTAAGGCATGGTTTATGAGAAAT	57.227	30.769	0.00	0.00	39.21	2.17
2972	3687	8.593945	AATTCTAAGGCATGGTTTATGAGAAA	57.406	30.769	0.00	0.00	39.21	2.52
3035	3750	4.595762	ATCCAATGATTGCAACCATAGC	57.404	40.909	6.75	0.00	0.00	2.97
3065	3780	7.290714	TCCCTCGTATATAAAGGCTAAAAGGAA	59.709	37.037	6.84	0.00	0.00	3.36
3066	3781	6.783977	TCCCTCGTATATAAAGGCTAAAAGGA	59.216	38.462	6.84	0.00	0.00	3.36
3074	3789	7.349412	AGTATCATCCCTCGTATATAAAGGC	57.651	40.000	6.84	0.00	0.00	4.35
3141	3856	2.350522	CGAATGAGTGGAAGTGGAAGG	58.649	52.381	0.00	0.00	0.00	3.46

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.