AutoCloner

Multiple sequence alignment - TraesCS7B01G015500

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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	TraesCS7B01G015500	chr7B	100.000	3431	0	0	1	3431	12720267	12716837	0.000000e+00	6336.0
1	TraesCS7B01G015500	chr7B	90.492	2356	141	27	709	3022	12951767	12954081	0.000000e+00	3033.0
2	TraesCS7B01G015500	chr7B	81.159	759	48	33	534	1225	12716053	12716783	3.920000e-144	521.0
3	TraesCS7B01G015500	chr7B	91.732	254	15	4	3070	3319	12954087	12954338	7.050000e-92	348.0
4	TraesCS7B01G015500	chr7B	83.333	180	30	0	275	454	634772088	634772267	2.120000e-37	167.0
5	TraesCS7B01G015500	chr7B	91.860	86	5	2	578	662	632179618	632179534	6.010000e-23	119.0
6	TraesCS7B01G015500	chr7B	98.182	55	1	0	3377	3431	12954371	12954425	2.820000e-16	97.1
7	TraesCS7B01G015500	chr7D	93.236	2809	127	25	622	3379	69953926	69956722	0.000000e+00	4076.0
8	TraesCS7B01G015500	chr7D	93.921	2665	119	17	1	2625	70154895	70152234	0.000000e+00	3984.0
9	TraesCS7B01G015500	chr7D	93.431	2664	123	17	1	2625	70047422	70050072	0.000000e+00	3903.0
10	TraesCS7B01G015500	chr7D	89.618	1570	67	30	575	2126	70737047	70735556	0.000000e+00	1908.0
11	TraesCS7B01G015500	chr7D	88.608	474	39	6	2155	2613	70735561	70735088	2.310000e-156	562.0
12	TraesCS7B01G015500	chr7D	87.535	361	26	9	706	1053	70361728	70362082	1.920000e-107	399.0
13	TraesCS7B01G015500	chr7D	95.882	170	7	0	1825	1994	70362283	70362114	3.370000e-70	276.0
14	TraesCS7B01G015500	chr7D	84.466	103	8	5	29	124	42551664	42551563	1.010000e-15	95.3
15	TraesCS7B01G015500	chr7A	85.878	524	43	17	2130	2625	76550200	76550720	2.340000e-146	529.0
16	TraesCS7B01G015500	chr7A	92.784	97	2	2	666	762	76819166	76819257	5.970000e-28	135.0
17	TraesCS7B01G015500	chr1B	76.203	395	64	24	273	662	408109518	408109149	7.560000e-42	182.0
18	TraesCS7B01G015500	chr1B	75.843	178	42	1	273	450	555624180	555624004	4.720000e-14	89.8
19	TraesCS7B01G015500	chr3D	76.203	395	53	24	273	662	508380040	508380398	1.640000e-38	171.0
20	TraesCS7B01G015500	chr5A	91.860	86	5	2	578	662	16416025	16415941	6.010000e-23	119.0
21	TraesCS7B01G015500	chrUn	88.421	95	9	2	569	662	136641165	136641258	2.800000e-21	113.0
22	TraesCS7B01G015500	chr5D	90.698	86	6	2	578	662	355102150	355102234	2.800000e-21	113.0
23	TraesCS7B01G015500	chr4B	90.698	86	6	2	578	662	385954295	385954211	2.800000e-21	113.0
24	TraesCS7B01G015500	chr4B	77.246	167	36	2	273	438	625959730	625959895	2.820000e-16	97.1
25	TraesCS7B01G015500	chr4A	87.097	93	11	1	29	120	649434314	649434222	1.680000e-18	104.0
26	TraesCS7B01G015500	chr6A	89.062	64	4	3	26	87	496018473	496018535	3.670000e-10	76.8
27	TraesCS7B01G015500	chr6D	88.462	52	5	1	38	88	312954220	312954271	1.030000e-05	62.1

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	TraesCS7B01G015500	chr7B	12716837	12720267	3430	True	6336.000000	6336	100.000000	1	3431	1	chr7B.!!$R1	3430
1	TraesCS7B01G015500	chr7B	12951767	12954425	2658	False	1159.366667	3033	93.468667	709	3431	3	chr7B.!!$F3	2722
2	TraesCS7B01G015500	chr7B	12716053	12716783	730	False	521.000000	521	81.159000	534	1225	1	chr7B.!!$F1	691
3	TraesCS7B01G015500	chr7D	69953926	69956722	2796	False	4076.000000	4076	93.236000	622	3379	1	chr7D.!!$F1	2757
4	TraesCS7B01G015500	chr7D	70152234	70154895	2661	True	3984.000000	3984	93.921000	1	2625	1	chr7D.!!$R2	2624
5	TraesCS7B01G015500	chr7D	70047422	70050072	2650	False	3903.000000	3903	93.431000	1	2625	1	chr7D.!!$F2	2624
6	TraesCS7B01G015500	chr7D	70735088	70737047	1959	True	1235.000000	1908	89.113000	575	2613	2	chr7D.!!$R4	2038
7	TraesCS7B01G015500	chr7A	76550200	76550720	520	False	529.000000	529	85.878000	2130	2625	1	chr7A.!!$F1	495

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
870	931	0.042731	TCGGATTTCCCCTCAGTCCT	59.957	55.0	0.0	0.0	0.0	3.85	F
876	937	0.042731	TTCCCCTCAGTCCTCGGATT	59.957	55.0	0.0	0.0	0.0	3.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1724	1838	0.401738	CTTCCTTGAGCCACCCTTGA	59.598	55.0	0.0	0.0	0.0	3.02	R
2511	2678	0.603065	GCCACACAAAGATCCCAACC	59.397	55.0	0.0	0.0	0.0	3.77	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
72	73	1.135402	GTCCGGATTGTTGAACCATGC	60.135	52.381	7.81	0.00	0.00	4.06
74	75	1.545582	CCGGATTGTTGAACCATGCTT	59.454	47.619	0.00	0.00	0.00	3.91
98	99	4.861389	TTTGCTTTGTTGCATTGTTGAG	57.139	36.364	0.00	0.00	42.96	3.02
161	162	9.394767	GCCATGAATTTGAGGGTTTAAATTTAT	57.605	29.630	0.00	0.00	36.81	1.40
172	173	5.186992	GGGTTTAAATTTATGGAGTGTGGCT	59.813	40.000	0.00	0.00	0.00	4.75
180	181	4.767255	GAGTGTGGCTGCCTCGGG	62.767	72.222	21.03	0.00	0.00	5.14
266	267	3.267031	AGTTACTTTTCCATCCCCTCCTG	59.733	47.826	0.00	0.00	0.00	3.86
286	287	0.814457	TGCAAAGCTGGTCAAACGTT	59.186	45.000	0.00	0.00	0.00	3.99
362	363	1.303317	CGGCAGGGGCTAAACAAGT	60.303	57.895	0.00	0.00	40.87	3.16
371	372	0.948678	GCTAAACAAGTTGTGCCCGA	59.051	50.000	9.79	0.00	0.00	5.14
374	375	1.398692	AAACAAGTTGTGCCCGACAT	58.601	45.000	9.79	0.00	33.40	3.06
416	417	3.415087	GTCCTGGAGGCTGGGCAT	61.415	66.667	0.00	0.00	34.44	4.40
445	446	2.415776	GGACGACACGACCCATTTAAA	58.584	47.619	0.00	0.00	35.86	1.52
478	481	8.408043	TTTTCTCCATTTGAGCTGATTTTCTA	57.592	30.769	0.00	0.00	41.18	2.10
809	861	0.827368	CACCTACCTCTTCCCTGCTC	59.173	60.000	0.00	0.00	0.00	4.26
818	870	3.442977	CCTCTTCCCTGCTCAATTTTCTG	59.557	47.826	0.00	0.00	0.00	3.02
862	923	1.384082	TCCTCCCTCGGATTTCCCC	60.384	63.158	0.00	0.00	0.00	4.81
863	924	1.384643	CCTCCCTCGGATTTCCCCT	60.385	63.158	0.00	0.00	0.00	4.79
864	925	1.411651	CCTCCCTCGGATTTCCCCTC	61.412	65.000	0.00	0.00	0.00	4.30
865	926	0.691078	CTCCCTCGGATTTCCCCTCA	60.691	60.000	0.00	0.00	0.00	3.86
866	927	0.691078	TCCCTCGGATTTCCCCTCAG	60.691	60.000	0.00	0.00	0.00	3.35
867	928	0.983378	CCCTCGGATTTCCCCTCAGT	60.983	60.000	0.00	0.00	0.00	3.41
868	929	0.466124	CCTCGGATTTCCCCTCAGTC	59.534	60.000	0.00	0.00	0.00	3.51
869	930	0.466124	CTCGGATTTCCCCTCAGTCC	59.534	60.000	0.00	0.00	0.00	3.85
870	931	0.042731	TCGGATTTCCCCTCAGTCCT	59.957	55.000	0.00	0.00	0.00	3.85
871	932	0.466124	CGGATTTCCCCTCAGTCCTC	59.534	60.000	0.00	0.00	0.00	3.71
872	933	0.466124	GGATTTCCCCTCAGTCCTCG	59.534	60.000	0.00	0.00	0.00	4.63
873	934	0.466124	GATTTCCCCTCAGTCCTCGG	59.534	60.000	0.00	0.00	0.00	4.63
874	935	0.042731	ATTTCCCCTCAGTCCTCGGA	59.957	55.000	0.00	0.00	0.00	4.55
875	936	0.042731	TTTCCCCTCAGTCCTCGGAT	59.957	55.000	0.00	0.00	0.00	4.18
876	937	0.042731	TTCCCCTCAGTCCTCGGATT	59.957	55.000	0.00	0.00	0.00	3.01
877	938	0.042731	TCCCCTCAGTCCTCGGATTT	59.957	55.000	0.00	0.00	0.00	2.17
878	939	0.466124	CCCCTCAGTCCTCGGATTTC	59.534	60.000	0.00	0.00	0.00	2.17
879	940	0.466124	CCCTCAGTCCTCGGATTTCC	59.534	60.000	0.00	0.00	0.00	3.13
903	987	1.414061	CCTCATCGGATTCCCCTGCT	61.414	60.000	0.00	0.00	33.16	4.24
1185	1293	0.099968	GCGACGTGCTGGACTACATA	59.900	55.000	0.00	0.00	41.73	2.29
1205	1313	4.394712	CTTCCGGGCCGTCTGCTT	62.395	66.667	26.32	0.00	40.92	3.91
1265	1373	2.668550	GCGCAAACCGGACCTCTT	60.669	61.111	9.46	0.00	37.44	2.85
1500	1608	2.679287	GTCGACCTCCCGTCCCTT	60.679	66.667	3.51	0.00	38.36	3.95
1724	1838	1.731969	GGCTTTACGCGACAGTCGT	60.732	57.895	23.62	8.62	42.81	4.34
2071	2212	6.016777	CAGCAACTCCATTTACTTCTCTTTGT	60.017	38.462	0.00	0.00	0.00	2.83
2199	2340	1.962807	CCTTTCACCATTGCTGACCAA	59.037	47.619	0.00	0.00	37.94	3.67
2278	2420	4.336153	TCTTTGCATGTATCATGTGCGATT	59.664	37.500	10.68	0.00	41.61	3.34
2307	2451	2.977808	TGACTGTCTTCTCTTCCCCTT	58.022	47.619	9.51	0.00	0.00	3.95
2365	2509	5.918011	CACTCTATACCTGAATCTTTCGAGC	59.082	44.000	0.00	0.00	0.00	5.03
2415	2559	5.593502	AGATTCTAAACTACGGATTCCTCGT	59.406	40.000	0.30	0.00	43.64	4.18
2471	2638	3.620374	GTCACAGCACCTCACATGAATAG	59.380	47.826	0.00	0.00	0.00	1.73
2484	2651	5.817296	TCACATGAATAGTGCCAATAGACAC	59.183	40.000	0.00	0.00	36.93	3.67
2511	2678	1.528586	CATAATTCCCTTGCTCGCTCG	59.471	52.381	0.00	0.00	0.00	5.03
2626	2800	7.106239	GCTATGCATATATAGTGGTGGTTCTT	58.894	38.462	6.92	0.00	33.99	2.52
2728	2905	6.547510	GCTCATCCCCATTAAGACAGTTAAAT	59.452	38.462	0.00	0.00	0.00	1.40
2729	2906	7.469181	GCTCATCCCCATTAAGACAGTTAAATG	60.469	40.741	0.45	0.45	0.00	2.32
2811	2988	1.206849	GAGAAGTGGGAGAGAGCCTTG	59.793	57.143	0.00	0.00	0.00	3.61
2844	3021	1.271871	ACTGGTGAAATCAATGGCGGA	60.272	47.619	0.00	0.00	0.00	5.54
2904	3081	2.041206	GCGGTGGGGGACTAGGAATC	62.041	65.000	0.00	0.00	0.00	2.52
3051	3229	3.004734	AGTCAGGTTTGCATTACAGTTGC	59.995	43.478	0.00	0.00	40.55	4.17
3129	3307	2.602878	CTGAGTTTTCGCCGCTAGTTA	58.397	47.619	0.00	0.00	0.00	2.24
3274	3456	3.484407	AGATAATTGCCTGGCTAGCTTG	58.516	45.455	21.03	7.57	0.00	4.01
3278	3460	0.035439	TTGCCTGGCTAGCTTGTACC	60.035	55.000	21.03	0.00	0.00	3.34
3298	3480	2.224621	CCATATCGGCTTTGGACCTGAT	60.225	50.000	0.00	0.00	31.94	2.90
3370	3552	4.894705	TGGCCATGTTATCAGCATTTATGT	59.105	37.500	0.00	0.00	0.00	2.29
3371	3553	5.221283	TGGCCATGTTATCAGCATTTATGTG	60.221	40.000	0.00	0.00	0.00	3.21
3372	3554	5.221303	GGCCATGTTATCAGCATTTATGTGT	60.221	40.000	0.00	0.00	0.00	3.72
3373	3555	5.688621	GCCATGTTATCAGCATTTATGTGTG	59.311	40.000	0.00	0.00	0.00	3.82
3374	3556	5.688621	CCATGTTATCAGCATTTATGTGTGC	59.311	40.000	0.00	0.00	41.57	4.57
3393	3594	5.356751	GTGTGCTTATATGATTCAACCACCA	59.643	40.000	0.00	0.00	0.00	4.17

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
17	18	2.690881	AAGTCCGGGCCATGGCTA	60.691	61.111	34.70	16.08	41.60	3.93
126	127	7.500141	ACCCTCAAATTCATGGCATTTATTAC	58.500	34.615	0.00	0.00	0.00	1.89
131	132	4.914177	AACCCTCAAATTCATGGCATTT	57.086	36.364	0.00	0.00	0.00	2.32
161	162	4.007644	CGAGGCAGCCACACTCCA	62.008	66.667	15.80	0.00	0.00	3.86
266	267	0.100503	ACGTTTGACCAGCTTTGCAC	59.899	50.000	0.00	0.00	0.00	4.57
338	339	0.905809	TTTAGCCCCTGCCGTGTCTA	60.906	55.000	0.00	0.00	38.69	2.59
341	342	2.033602	GTTTAGCCCCTGCCGTGT	59.966	61.111	0.00	0.00	38.69	4.49
426	427	4.673534	AATTTAAATGGGTCGTGTCGTC	57.326	40.909	0.39	0.00	0.00	4.20
430	431	9.990360	AAAATAGAAAATTTAAATGGGTCGTGT	57.010	25.926	0.39	0.00	0.00	4.49
457	458	9.649167	AAAAATAGAAAATCAGCTCAAATGGAG	57.351	29.630	0.00	0.00	46.93	3.86
662	668	2.507110	AATCCACACGTCGGAGCAGG	62.507	60.000	9.05	0.00	35.56	4.85
809	861	1.398041	TCGCGGATCAGCAGAAAATTG	59.602	47.619	18.07	0.00	36.85	2.32
818	870	4.531912	TCGACGTCGCGGATCAGC	62.532	66.667	32.19	7.88	39.60	4.26
872	933	0.249911	CGATGAGGGACCGGAAATCC	60.250	60.000	9.46	4.30	35.28	3.01
873	934	0.249911	CCGATGAGGGACCGGAAATC	60.250	60.000	9.46	0.53	45.58	2.17
874	935	1.830145	CCGATGAGGGACCGGAAAT	59.170	57.895	9.46	0.00	45.58	2.17
875	936	3.305314	CCGATGAGGGACCGGAAA	58.695	61.111	9.46	0.00	45.58	3.13
878	939	1.367840	GAATCCGATGAGGGACCGG	59.632	63.158	0.00	0.00	44.22	5.28
879	940	1.367840	GGAATCCGATGAGGGACCG	59.632	63.158	0.00	0.00	39.34	4.79
880	941	1.755384	GGGAATCCGATGAGGGACC	59.245	63.158	0.00	0.00	39.34	4.46
884	945	1.072159	GCAGGGGAATCCGATGAGG	59.928	63.158	6.55	0.00	41.52	3.86
888	949	0.181350	GAACAGCAGGGGAATCCGAT	59.819	55.000	0.00	0.00	41.52	4.18
903	987	2.281208	CCGGCCGGAACTTGAACA	60.281	61.111	41.82	0.00	37.50	3.18
1185	1293	3.382832	CAGACGGCCCGGAAGACT	61.383	66.667	8.57	0.00	0.00	3.24
1249	1357	2.966309	GCAAGAGGTCCGGTTTGCG	61.966	63.158	0.00	0.00	36.89	4.85
1724	1838	0.401738	CTTCCTTGAGCCACCCTTGA	59.598	55.000	0.00	0.00	0.00	3.02
1905	2019	6.966534	AATAGCTTATAGGCATTTTGCTGT	57.033	33.333	9.75	0.00	44.28	4.40
2071	2212	1.049855	ACCACAACAGGGTCACGGTA	61.050	55.000	0.00	0.00	31.49	4.02
2199	2340	3.707102	GAGGATGGCAGTAGGTTAGAAGT	59.293	47.826	0.00	0.00	0.00	3.01
2251	2393	5.271625	GCACATGATACATGCAAAGAAGAG	58.728	41.667	0.00	0.00	39.23	2.85
2278	2420	7.068839	GGGAAGAGAAGACAGTCATAATGTAGA	59.931	40.741	2.66	0.00	0.00	2.59
2307	2451	4.792068	ACATGAGTCCTTTTGTCCTTCAA	58.208	39.130	0.00	0.00	0.00	2.69
2365	2509	6.564709	TGTCTTGATGTTCTTCCTCAATTG	57.435	37.500	0.00	0.00	32.12	2.32
2386	2530	8.101419	AGGAATCCGTAGTTTAGAATCTTTTGT	58.899	33.333	0.00	0.00	0.00	2.83
2415	2559	2.293170	TCGGATCAACAAACTGCAACA	58.707	42.857	0.00	0.00	0.00	3.33
2471	2638	2.749076	TGCATCAAGTGTCTATTGGCAC	59.251	45.455	3.54	3.54	35.98	5.01
2484	2651	4.556104	CGAGCAAGGGAATTATGCATCAAG	60.556	45.833	0.19	0.00	42.45	3.02
2511	2678	0.603065	GCCACACAAAGATCCCAACC	59.397	55.000	0.00	0.00	0.00	3.77
2626	2800	4.486125	TTGCAGGCACAACTAGATATCA	57.514	40.909	5.32	0.00	0.00	2.15
2728	2905	2.004733	CTGATGAATGAGCTTCGCACA	58.995	47.619	0.00	0.00	36.60	4.57
2729	2906	1.267932	GCTGATGAATGAGCTTCGCAC	60.268	52.381	0.00	0.00	36.60	5.34
2748	2925	2.745492	GCCTCAGTGACCAGCAGC	60.745	66.667	0.00	0.00	0.00	5.25
2770	2947	1.064463	CACTGCTCCCAATACCCATGT	60.064	52.381	0.00	0.00	0.00	3.21
2811	2988	0.958822	CACCAGTACCTGCCCAAAAC	59.041	55.000	0.00	0.00	0.00	2.43
2828	3005	3.062504	GCATTTTCCGCCATTGATTTCAC	59.937	43.478	0.00	0.00	0.00	3.18
2904	3081	1.679032	CCCCTGGAGCTTTAGGTTTCG	60.679	57.143	14.08	1.82	31.99	3.46
3129	3307	0.749454	GGCAGCCGAATGAACTCCAT	60.749	55.000	0.00	0.00	36.99	3.41
3274	3456	2.104281	AGGTCCAAAGCCGATATGGTAC	59.896	50.000	0.00	0.00	41.21	3.34
3278	3460	2.620251	TCAGGTCCAAAGCCGATATG	57.380	50.000	0.00	0.00	0.00	1.78
3298	3480	3.153919	GGCTAATCACAAGTTGTCCCAA	58.846	45.455	5.27	0.00	0.00	4.12
3371	3553	5.356751	TGTGGTGGTTGAATCATATAAGCAC	59.643	40.000	6.47	6.47	46.40	4.40
3372	3554	5.504853	TGTGGTGGTTGAATCATATAAGCA	58.495	37.500	0.00	0.00	0.00	3.91
3373	3555	6.441274	CATGTGGTGGTTGAATCATATAAGC	58.559	40.000	0.00	0.00	0.00	3.09
3374	3556	6.973843	CCATGTGGTGGTTGAATCATATAAG	58.026	40.000	0.00	0.00	43.44	1.73
3375	3557	6.957920	CCATGTGGTGGTTGAATCATATAA	57.042	37.500	0.00	0.00	43.44	0.98
3393	3594	6.523840	ACATTTTTATTTGCACTCACCATGT	58.476	32.000	0.00	0.00	0.00	3.21

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.