AutoCloner

Multiple sequence alignment - TraesCS6D01G182500

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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	TraesCS6D01G182500	chr6D	100.000	3801	0	0	1	3801	213389438	213393238	0.000000e+00	7020.0
1	TraesCS6D01G182500	chr4A	97.117	3815	79	25	1	3801	687550392	687546595	0.000000e+00	6407.0
2	TraesCS6D01G182500	chr3A	97.457	2989	64	9	818	3801	515899458	515902439	0.000000e+00	5088.0
3	TraesCS6D01G182500	chrUn	97.337	2441	53	9	1274	3707	340582217	340579782	0.000000e+00	4137.0
4	TraesCS6D01G182500	chrUn	97.063	1975	48	8	1834	3801	316114597	316112626	0.000000e+00	3317.0
5	TraesCS6D01G182500	chrUn	96.028	2014	36	22	29	2034	360648151	360646174	0.000000e+00	3236.0
6	TraesCS6D01G182500	chrUn	97.423	1552	24	13	244	1787	390548977	390550520	0.000000e+00	2630.0
7	TraesCS6D01G182500	chrUn	97.668	1501	23	10	541	2034	394645244	394643749	0.000000e+00	2567.0
8	TraesCS6D01G182500	chrUn	96.821	1101	20	14	1	1093	384677894	384676801	0.000000e+00	1825.0
9	TraesCS6D01G182500	chrUn	97.940	971	19	1	2832	3801	39516389	39515419	0.000000e+00	1681.0
10	TraesCS6D01G182500	chrUn	96.890	643	17	3	1893	2533	39517041	39516400	0.000000e+00	1074.0
11	TraesCS6D01G182500	chrUn	100.000	35	0	0	1	35	387671942	387671908	8.810000e-07	65.8
12	TraesCS6D01G182500	chr1B	97.533	1216	26	3	2391	3605	208995772	208996984	0.000000e+00	2076.0
13	TraesCS6D01G182500	chr6B	96.912	1101	19	13	1	1093	716513129	716514222	0.000000e+00	1831.0
14	TraesCS6D01G182500	chr6B	96.586	498	11	5	273	768	32921161	32921654	0.000000e+00	821.0
15	TraesCS6D01G182500	chr2B	96.730	1101	21	14	1	1093	8409377	8410470	0.000000e+00	1820.0
16	TraesCS6D01G182500	chr2B	96.388	443	10	6	329	769	8407369	8407807	0.000000e+00	725.0
17	TraesCS6D01G182500	chr7D	85.423	343	27	11	15	336	84250801	84251141	6.080000e-88	335.0
18	TraesCS6D01G182500	chr7A	84.478	335	25	13	23	332	85606979	85607311	4.770000e-79	305.0
19	TraesCS6D01G182500	chr4B	100.000	35	0	0	1	35	367935743	367935777	8.810000e-07	65.8

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	TraesCS6D01G182500	chr6D	213389438	213393238	3800	False	7020.0	7020	100.000	1	3801	1	chr6D.!!$F1	3800
1	TraesCS6D01G182500	chr4A	687546595	687550392	3797	True	6407.0	6407	97.117	1	3801	1	chr4A.!!$R1	3800
2	TraesCS6D01G182500	chr3A	515899458	515902439	2981	False	5088.0	5088	97.457	818	3801	1	chr3A.!!$F1	2983
3	TraesCS6D01G182500	chrUn	340579782	340582217	2435	True	4137.0	4137	97.337	1274	3707	1	chrUn.!!$R2	2433
4	TraesCS6D01G182500	chrUn	316112626	316114597	1971	True	3317.0	3317	97.063	1834	3801	1	chrUn.!!$R1	1967
5	TraesCS6D01G182500	chrUn	360646174	360648151	1977	True	3236.0	3236	96.028	29	2034	1	chrUn.!!$R3	2005
6	TraesCS6D01G182500	chrUn	390548977	390550520	1543	False	2630.0	2630	97.423	244	1787	1	chrUn.!!$F1	1543
7	TraesCS6D01G182500	chrUn	394643749	394645244	1495	True	2567.0	2567	97.668	541	2034	1	chrUn.!!$R6	1493
8	TraesCS6D01G182500	chrUn	384676801	384677894	1093	True	1825.0	1825	96.821	1	1093	1	chrUn.!!$R4	1092
9	TraesCS6D01G182500	chrUn	39515419	39517041	1622	True	1377.5	1681	97.415	1893	3801	2	chrUn.!!$R7	1908
10	TraesCS6D01G182500	chr1B	208995772	208996984	1212	False	2076.0	2076	97.533	2391	3605	1	chr1B.!!$F1	1214
11	TraesCS6D01G182500	chr6B	716513129	716514222	1093	False	1831.0	1831	96.912	1	1093	1	chr6B.!!$F2	1092
12	TraesCS6D01G182500	chr2B	8407369	8410470	3101	False	1272.5	1820	96.559	1	1093	2	chr2B.!!$F1	1092

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	End Stability	Orientation
476	2489	0.395862	CTCCTCCCAGTAGCCGAAGA	60.396	60.000	2.87	F
479	2492	1.115467	CTCCCAGTAGCCGAAGATGT	58.885	55.000	3.06	F
2111	4135	1.144936	CCATCCTCGCACTCTTCCC	59.855	63.158	3.97	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	End Stability	Orientation
2087	4110	3.914426	AGAGTGCGAGGATGGTTAAAT	57.086	42.857	0.00	1.40	R
2448	4474	4.241590	TGCATTGAATCAAAAAGCTCGT	57.758	36.364	15.62	4.18	R
2922	4950	0.323087	TGTAGTGCGGCAGGTCTAGA	60.323	55.000	1.18	2.43	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
51	2062	5.032170	AGAATGGCCAATTATTCAGGGTTT	58.968	37.500	10.96	0.00	36.11	3.27
151	2163	2.359230	GAGGGCCACTGAGTGCAC	60.359	66.667	9.40	9.40	31.34	4.57
215	2227	2.361757	TGCCACTTTGACCTGAACAATG	59.638	45.455	0.00	0.00	0.00	2.82
362	2375	4.305989	TGTGCACCTTCATCAACTTTTC	57.694	40.909	15.69	0.00	0.00	2.29
367	2380	6.019559	GTGCACCTTCATCAACTTTTCTTTTC	60.020	38.462	5.22	0.00	0.00	2.29
395	2408	5.444122	GTGTTGAGCAGAGATGTGTTAAAC	58.556	41.667	0.00	0.00	0.00	2.01
476	2489	0.395862	CTCCTCCCAGTAGCCGAAGA	60.396	60.000	0.00	0.00	0.00	2.87
479	2492	1.115467	CTCCCAGTAGCCGAAGATGT	58.885	55.000	0.00	0.00	0.00	3.06
480	2493	1.482593	CTCCCAGTAGCCGAAGATGTT	59.517	52.381	0.00	0.00	0.00	2.71
522	2535	2.772287	AGTGTTGCTTCTACTTGCTCC	58.228	47.619	0.00	0.00	0.00	4.70
581	2594	6.294361	TCTGCTACCTATCTGCTGTTTTTA	57.706	37.500	0.00	0.00	0.00	1.52
683	2700	6.016777	ACTCATGTTGACCTTTGTTCTTCATC	60.017	38.462	0.00	0.00	0.00	2.92
730	2747	4.271696	TGCTGTACTGCACTAAAGATGT	57.728	40.909	21.93	0.00	38.12	3.06
732	2749	5.789521	TGCTGTACTGCACTAAAGATGTTA	58.210	37.500	21.93	0.00	38.12	2.41
866	2884	6.861065	TCCTTTTGAGTACTGTCATTTCAC	57.139	37.500	0.00	0.00	0.00	3.18
1114	3135	1.661341	ATTCCTTGCACTCGCTGATC	58.339	50.000	0.00	0.00	39.64	2.92
1164	3185	2.982470	GGATTTTGCAACAAAGCTCTCG	59.018	45.455	0.00	0.00	34.99	4.04
1403	3424	3.562397	GGATACCACTTGGCGGAAA	57.438	52.632	0.00	0.00	39.32	3.13
1479	3500	3.934457	AAATGCAAAGGAAACTACCCG	57.066	42.857	0.00	0.00	42.68	5.28
1576	3597	2.601666	TCACCGTGCTCCTCTGCT	60.602	61.111	0.00	0.00	0.00	4.24
1816	3837	7.937394	TCTCTCTTTCATATCCACATACGTCTA	59.063	37.037	0.00	0.00	0.00	2.59
2061	4084	5.591067	CAGGCTCCCGGTAATTATTTTTGTA	59.409	40.000	0.00	0.00	0.00	2.41
2067	4090	8.174733	TCCCGGTAATTATTTTTGTAAACACA	57.825	30.769	0.00	0.00	0.00	3.72
2106	4130	2.872858	GGATTTAACCATCCTCGCACTC	59.127	50.000	0.00	0.00	39.93	3.51
2111	4135	1.144936	CCATCCTCGCACTCTTCCC	59.855	63.158	0.00	0.00	0.00	3.97
2193	4217	4.099266	ACAAAACTTATGGCAGACAAAGCA	59.901	37.500	0.00	0.00	0.00	3.91
2197	4221	3.192001	ACTTATGGCAGACAAAGCATGTG	59.808	43.478	0.00	0.00	44.12	3.21
2226	4250	2.031157	CACCCTTCGGTCAAATCAACAC	60.031	50.000	0.00	0.00	42.04	3.32
2231	4255	2.912771	TCGGTCAAATCAACACACAGT	58.087	42.857	0.00	0.00	0.00	3.55
2257	4281	3.715854	CACACTAGGTGCCTCGTAC	57.284	57.895	0.00	0.00	41.36	3.67
2347	4372	2.703416	TGTCTTTAGAGGTGCAGCATG	58.297	47.619	19.63	0.00	40.87	4.06
2471	4497	4.445385	ACGAGCTTTTTGATTCAATGCAAC	59.555	37.500	16.35	11.14	0.00	4.17
2513	4539	1.881973	TGAACCTGCTGAAACTGATGC	59.118	47.619	0.00	0.00	0.00	3.91
2589	4615	0.823356	AGTTGCGTGCCCATTTCAGT	60.823	50.000	0.00	0.00	0.00	3.41
2654	4680	2.146342	CAAGTACCACACTGGCTGAAG	58.854	52.381	0.00	0.00	42.67	3.02
2660	4686	1.610522	CCACACTGGCTGAAGGAAAAG	59.389	52.381	0.00	0.00	0.00	2.27
2668	4694	5.044550	ACTGGCTGAAGGAAAAGAGGATAAT	60.045	40.000	0.00	0.00	0.00	1.28
2719	4746	1.973812	GGGCAGGAAACAGAGCACC	60.974	63.158	0.00	0.00	0.00	5.01
2720	4747	1.228245	GGCAGGAAACAGAGCACCA	60.228	57.895	0.00	0.00	0.00	4.17
2721	4748	1.518903	GGCAGGAAACAGAGCACCAC	61.519	60.000	0.00	0.00	0.00	4.16
2911	4939	7.974675	ACTTCGAATAATTGACACAATACCAG	58.025	34.615	0.00	0.00	0.00	4.00
2922	4950	3.259064	CACAATACCAGTTTCGACCGAT	58.741	45.455	0.00	0.00	0.00	4.18
2936	4964	2.490148	CCGATCTAGACCTGCCGCA	61.490	63.158	0.00	0.00	0.00	5.69
2939	4967	1.319541	GATCTAGACCTGCCGCACTA	58.680	55.000	0.00	0.00	0.00	2.74
3003	5031	1.112113	GAGATACCGAGGCTGAACCA	58.888	55.000	0.00	0.00	43.14	3.67
3062	5090	0.318614	AAAGCATTTTGGCACCGACG	60.319	50.000	0.00	0.00	31.62	5.12
3095	5123	5.463724	CACGAGAGCCAGATTTATTAACCTC	59.536	44.000	0.00	0.00	0.00	3.85
3131	5159	5.694995	TCTGTTTGAAGAATGGAAGGTCTT	58.305	37.500	0.00	0.00	36.80	3.01
3168	5196	1.228245	TGAAGGTCCAACCAGCAGC	60.228	57.895	0.00	0.00	41.95	5.25
3239	5267	4.517285	ACATGCATGTCCTTAAACGAGAT	58.483	39.130	26.61	0.00	35.87	2.75
3479	5507	0.388649	GACCCTGATATGGTAGCGCG	60.389	60.000	0.00	0.00	35.85	6.86
3567	5595	4.756642	ACCACATCAGTTACACAAGACATG	59.243	41.667	0.00	0.00	0.00	3.21
3605	5633	2.232941	AGCCCAATGAGATTTGTTGCAG	59.767	45.455	0.00	0.00	0.00	4.41
3611	5639	3.909776	TGAGATTTGTTGCAGCTTCAG	57.090	42.857	1.17	0.00	0.00	3.02
3641	5669	3.181501	CCAGTCGAAAGTGCTGTTTTCAA	60.182	43.478	0.00	0.00	34.90	2.69
3764	5793	4.034510	GGATGCACTGTCTGTATAACAAGC	59.965	45.833	0.00	0.00	0.00	4.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
51	2062	1.034356	AAATGCAGCAGCTCAACACA	58.966	45.000	0.00	0.00	42.74	3.72
102	2114	0.539438	TGACCCACTGTGCATTTCCC	60.539	55.000	1.29	0.00	0.00	3.97
151	2163	5.401550	CAAATGCTAACCTGTGTGTATTGG	58.598	41.667	0.00	0.00	0.00	3.16
362	2375	0.821711	TGCTCAACACCCGGGAAAAG	60.822	55.000	32.02	17.22	0.00	2.27
367	2380	1.903877	ATCTCTGCTCAACACCCGGG	61.904	60.000	22.25	22.25	0.00	5.73
408	2421	8.992073	ACTCATAAACAAATGCAAAAGGAAATC	58.008	29.630	0.00	0.00	0.00	2.17
409	2422	8.776470	CACTCATAAACAAATGCAAAAGGAAAT	58.224	29.630	0.00	0.00	0.00	2.17
417	2430	6.041409	TCCTTTCCACTCATAAACAAATGCAA	59.959	34.615	0.00	0.00	0.00	4.08
522	2535	5.305585	AGAACAGGTAACACATGGTTAGTG	58.694	41.667	0.00	6.32	42.44	2.74
581	2594	7.048512	AGCCTAGCTTGATTACTACGAAAAAT	58.951	34.615	0.00	0.00	33.89	1.82
599	2614	6.017523	GGATAAGATGTTTCTTGAAGCCTAGC	60.018	42.308	0.00	0.00	42.25	3.42
683	2700	6.035866	TGCTGAGCATTGTTAGTTTGTTTTTG	59.964	34.615	1.40	0.00	31.71	2.44
1141	3162	4.625028	GAGAGCTTTGTTGCAAAATCCTT	58.375	39.130	0.00	0.00	34.99	3.36
1164	3185	1.003866	GTCGCCATGAATTTCCGTAGC	60.004	52.381	0.00	0.00	0.00	3.58
1193	3214	5.130145	AGCTGCCTTTGATCTAGAGTTACAT	59.870	40.000	0.00	0.00	0.00	2.29
1401	3422	7.210174	GGTTTTGCTTCTTCTCTATGGTTTTT	58.790	34.615	0.00	0.00	0.00	1.94
1403	3424	5.243954	GGGTTTTGCTTCTTCTCTATGGTTT	59.756	40.000	0.00	0.00	0.00	3.27
1452	3473	4.122046	AGTTTCCTTTGCATTTTGTCTGC	58.878	39.130	0.00	0.00	40.10	4.26
1479	3500	4.694339	AGTTATCCAGCTCGTTTATGGTC	58.306	43.478	0.00	0.00	35.51	4.02
1832	3853	9.646522	AATATTGTGCTTGAAGAAACCCTATAT	57.353	29.630	0.00	0.00	0.00	0.86
1837	3858	6.691508	AGAAATATTGTGCTTGAAGAAACCC	58.308	36.000	0.00	0.00	0.00	4.11
2087	4110	3.914426	AGAGTGCGAGGATGGTTAAAT	57.086	42.857	0.00	0.00	0.00	1.40
2106	4130	5.772169	AGAAACCATCTTTCTTCAAGGGAAG	59.228	40.000	0.00	0.00	43.04	3.46
2111	4135	6.348376	GCTGAGAGAAACCATCTTTCTTCAAG	60.348	42.308	0.00	0.00	39.46	3.02
2226	4250	4.442706	ACCTAGTGTGACTTTTGACTGTG	58.557	43.478	0.00	0.00	0.00	3.66
2448	4474	4.241590	TGCATTGAATCAAAAAGCTCGT	57.758	36.364	15.62	0.00	0.00	4.18
2471	4497	5.580691	TCATAAAGTTCTTGGCGAGTACATG	59.419	40.000	13.24	8.55	0.00	3.21
2513	4539	2.852143	GCGATGAAGAATGCATTGACGG	60.852	50.000	18.59	0.60	37.79	4.79
2589	4615	2.920912	AAGGAACCGTCGGAGCCA	60.921	61.111	20.51	0.00	0.00	4.75
2619	4645	3.253188	GGTACTTGTCATTTGCAAGCTGA	59.747	43.478	9.10	9.10	45.09	4.26
2654	4680	6.253946	TCCTTCAGGATTATCCTCTTTTCC	57.746	41.667	11.38	0.00	45.66	3.13
2660	4686	5.825151	CCTGTTTTCCTTCAGGATTATCCTC	59.175	44.000	11.38	0.00	45.66	3.71
2676	4702	1.273327	CCACATTCTGCCCCTGTTTTC	59.727	52.381	0.00	0.00	0.00	2.29
2719	4746	5.328691	TGTTTCTTCAGCTGTAAAAACGTG	58.671	37.500	22.84	2.94	31.06	4.49
2720	4747	5.554822	TGTTTCTTCAGCTGTAAAAACGT	57.445	34.783	22.84	0.00	31.06	3.99
2721	4748	6.506357	GCTTTGTTTCTTCAGCTGTAAAAACG	60.506	38.462	22.84	15.54	31.06	3.60
2911	4939	2.795331	GCAGGTCTAGATCGGTCGAAAC	60.795	54.545	5.01	0.00	0.00	2.78
2922	4950	0.323087	TGTAGTGCGGCAGGTCTAGA	60.323	55.000	1.18	0.00	0.00	2.43
2936	4964	1.066143	CCTCCAATGCTTCCGTGTAGT	60.066	52.381	0.00	0.00	0.00	2.73
2939	4967	1.002134	CCCTCCAATGCTTCCGTGT	60.002	57.895	0.00	0.00	0.00	4.49
3003	5031	2.666317	AGCAAGCTAAAAGTGTGGGTT	58.334	42.857	0.00	0.00	0.00	4.11
3062	5090	2.183046	GCTCTCGTGGACTCAGCC	59.817	66.667	0.00	0.00	0.00	4.85
3095	5123	2.089980	CAAACAGATTGAGCTCCCTGG	58.910	52.381	23.12	9.42	41.85	4.45
3131	5159	5.514136	CCTTCACTACCATCAACCTTGGTAA	60.514	44.000	4.31	0.00	46.35	2.85
3168	5196	0.663688	CTGTCGTCCTGATAGGGTCG	59.336	60.000	0.00	0.00	35.59	4.79
3298	5326	4.002316	TCATGATGAATGTTGCTCGACAA	58.998	39.130	0.00	0.00	37.56	3.18
3479	5507	3.188873	CCTATCGGTAGACTCGATCAACC	59.811	52.174	3.68	0.00	44.82	3.77
3567	5595	3.072944	GGGCTTGATCTCTGATATGTGC	58.927	50.000	0.00	0.00	0.00	4.57
3605	5633	1.396301	CGACTGGATTTGAGCTGAAGC	59.604	52.381	0.00	0.00	42.49	3.86
3611	5639	2.413371	GCACTTTCGACTGGATTTGAGC	60.413	50.000	0.00	0.00	0.00	4.26
3764	5793	9.933723	AGAGGAATGAAAAAGGACAAAATATTG	57.066	29.630	0.00	0.00	42.46	1.90

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.