AutoCloner

Multiple sequence alignment - TraesCS7A01G440800

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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	TraesCS7A01G440800	chr7A	100.000	3167	0	0	1	3167	635074005	635077171	0.000000e+00	5849.0
1	TraesCS7A01G440800	chr7A	82.917	2400	294	64	138	2511	635093491	635095800	0.000000e+00	2054.0
2	TraesCS7A01G440800	chr7A	85.994	1735	213	16	734	2448	635241133	635242857	0.000000e+00	1831.0
3	TraesCS7A01G440800	chr7A	84.625	1626	211	24	844	2448	635270704	635272311	0.000000e+00	1581.0
4	TraesCS7A01G440800	chr7A	84.014	1689	210	32	791	2448	635051461	635053120	0.000000e+00	1568.0
5	TraesCS7A01G440800	chr7A	85.079	764	98	9	1675	2428	635238791	635239548	0.000000e+00	765.0
6	TraesCS7A01G440800	chr7D	96.193	2154	72	4	414	2565	549696963	549699108	0.000000e+00	3515.0
7	TraesCS7A01G440800	chr7D	86.330	1763	208	18	707	2448	549770437	549772187	0.000000e+00	1890.0
8	TraesCS7A01G440800	chr7D	85.128	1802	216	30	705	2492	549705317	549707080	0.000000e+00	1796.0
9	TraesCS7A01G440800	chr7D	86.704	361	35	7	330	681	549770016	549770372	3.830000e-104	388.0
10	TraesCS7A01G440800	chr7D	90.559	286	17	6	1	276	549696590	549696875	1.390000e-98	370.0
11	TraesCS7A01G440800	chr7D	79.167	120	21	4	2448	2565	549763018	549763135	2.620000e-11	80.5
12	TraesCS7A01G440800	chr7B	85.690	1761	221	17	707	2448	594063521	594065269	0.000000e+00	1827.0
13	TraesCS7A01G440800	chr7B	95.971	1092	35	2	816	1898	594035399	594036490	0.000000e+00	1764.0
14	TraesCS7A01G440800	chr7B	83.908	1827	217	42	706	2511	594048255	594050025	0.000000e+00	1674.0
15	TraesCS7A01G440800	chr7B	95.262	591	27	1	2577	3167	529153120	529152531	0.000000e+00	935.0
16	TraesCS7A01G440800	chr7B	93.960	596	30	2	2577	3167	663733641	663733047	0.000000e+00	896.0
17	TraesCS7A01G440800	chr7B	93.919	592	34	2	2577	3167	533794802	533794212	0.000000e+00	893.0
18	TraesCS7A01G440800	chr7B	90.401	573	37	8	252	815	594034750	594035313	0.000000e+00	737.0
19	TraesCS7A01G440800	chr7B	85.873	361	38	7	330	681	594063100	594063456	3.860000e-99	372.0
20	TraesCS7A01G440800	chr7B	86.742	264	23	9	1	254	594029144	594029405	1.860000e-72	283.0
21	TraesCS7A01G440800	chr7B	92.000	200	15	1	2367	2565	594043924	594044123	2.410000e-71	279.0
22	TraesCS7A01G440800	chr7B	86.147	231	26	2	124	353	594047650	594047875	8.770000e-61	244.0
23	TraesCS7A01G440800	chr1B	96.108	591	21	2	2577	3167	638301748	638302336	0.000000e+00	963.0
24	TraesCS7A01G440800	chr1B	95.262	591	27	1	2577	3167	638376525	638377114	0.000000e+00	935.0
25	TraesCS7A01G440800	chrUn	95.623	594	21	3	2577	3167	7978589	7979180	0.000000e+00	948.0
26	TraesCS7A01G440800	chr3B	94.595	592	28	4	2577	3167	767791794	767791206	0.000000e+00	913.0
27	TraesCS7A01G440800	chr4B	93.058	605	36	6	2563	3167	386408964	386409562	0.000000e+00	880.0
28	TraesCS7A01G440800	chr6D	93.570	591	34	4	2578	3167	10692569	10693156	0.000000e+00	878.0
29	TraesCS7A01G440800	chr1A	75.796	157	31	7	498	649	521642701	521642855	4.380000e-09	73.1

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	TraesCS7A01G440800	chr7A	635074005	635077171	3166	False	5849.000000	5849	100.000000	1	3167	1	chr7A.!!$F2	3166
1	TraesCS7A01G440800	chr7A	635093491	635095800	2309	False	2054.000000	2054	82.917000	138	2511	1	chr7A.!!$F3	2373
2	TraesCS7A01G440800	chr7A	635270704	635272311	1607	False	1581.000000	1581	84.625000	844	2448	1	chr7A.!!$F4	1604
3	TraesCS7A01G440800	chr7A	635051461	635053120	1659	False	1568.000000	1568	84.014000	791	2448	1	chr7A.!!$F1	1657
4	TraesCS7A01G440800	chr7A	635238791	635242857	4066	False	1298.000000	1831	85.536500	734	2448	2	chr7A.!!$F5	1714
5	TraesCS7A01G440800	chr7D	549696590	549699108	2518	False	1942.500000	3515	93.376000	1	2565	2	chr7D.!!$F3	2564
6	TraesCS7A01G440800	chr7D	549705317	549707080	1763	False	1796.000000	1796	85.128000	705	2492	1	chr7D.!!$F1	1787
7	TraesCS7A01G440800	chr7D	549770016	549772187	2171	False	1139.000000	1890	86.517000	330	2448	2	chr7D.!!$F4	2118
8	TraesCS7A01G440800	chr7B	594034750	594036490	1740	False	1250.500000	1764	93.186000	252	1898	2	chr7B.!!$F2	1646
9	TraesCS7A01G440800	chr7B	594063100	594065269	2169	False	1099.500000	1827	85.781500	330	2448	2	chr7B.!!$F4	2118
10	TraesCS7A01G440800	chr7B	529152531	529153120	589	True	935.000000	935	95.262000	2577	3167	1	chr7B.!!$R1	590
11	TraesCS7A01G440800	chr7B	663733047	663733641	594	True	896.000000	896	93.960000	2577	3167	1	chr7B.!!$R3	590
12	TraesCS7A01G440800	chr7B	533794212	533794802	590	True	893.000000	893	93.919000	2577	3167	1	chr7B.!!$R2	590
13	TraesCS7A01G440800	chr7B	594043924	594050025	6101	False	732.333333	1674	87.351667	124	2565	3	chr7B.!!$F3	2441
14	TraesCS7A01G440800	chr1B	638301748	638302336	588	False	963.000000	963	96.108000	2577	3167	1	chr1B.!!$F1	590
15	TraesCS7A01G440800	chr1B	638376525	638377114	589	False	935.000000	935	95.262000	2577	3167	1	chr1B.!!$F2	590
16	TraesCS7A01G440800	chrUn	7978589	7979180	591	False	948.000000	948	95.623000	2577	3167	1	chrUn.!!$F1	590
17	TraesCS7A01G440800	chr3B	767791206	767791794	588	True	913.000000	913	94.595000	2577	3167	1	chr3B.!!$R1	590
18	TraesCS7A01G440800	chr4B	386408964	386409562	598	False	880.000000	880	93.058000	2563	3167	1	chr4B.!!$F1	604
19	TraesCS7A01G440800	chr6D	10692569	10693156	587	False	878.000000	878	93.570000	2578	3167	1	chr6D.!!$F1	589

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
89	92	0.394216	CATCATTTCTGGCCGGGTCA	60.394	55.0	12.87	0.0	0.0	4.02	F
704	4325	0.450184	ACATTGAAATGGTACGCCGC	59.550	50.0	7.87	0.0	40.7	6.53	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1510	7176	1.045407	AACCTGAGAACGTAGCCACA	58.955	50.0	0.0	0.0	0.0	4.17	R
2564	8258	1.253100	CAAGGGGGCGTATTGTGTTT	58.747	50.0	0.0	0.0	0.0	2.83	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
89	92	0.394216	CATCATTTCTGGCCGGGTCA	60.394	55.000	12.87	0.00	0.00	4.02
127	130	2.964389	GCGGCGCAGAAGATCCTC	60.964	66.667	29.21	0.00	0.00	3.71
128	131	2.279784	CGGCGCAGAAGATCCTCC	60.280	66.667	10.83	0.00	0.00	4.30
130	133	1.068921	GGCGCAGAAGATCCTCCTC	59.931	63.158	10.83	0.00	0.00	3.71
151	3756	1.819753	CCCCCTCCCAATATCTGTCA	58.180	55.000	0.00	0.00	0.00	3.58
216	3822	4.689549	TCCTTCCCCTCGACGGCA	62.690	66.667	0.00	0.00	29.74	5.69
306	3913	2.758130	ACACCCCACAAATTCACCTTT	58.242	42.857	0.00	0.00	0.00	3.11
360	3967	6.712095	AGATTTCAGTTATGAGCAACACAGAA	59.288	34.615	0.00	0.00	36.61	3.02
496	4116	5.674525	TGCAGATTAGTCAACAGGGATTAG	58.325	41.667	0.00	0.00	0.00	1.73
498	4118	5.988561	GCAGATTAGTCAACAGGGATTAGAG	59.011	44.000	0.00	0.00	0.00	2.43
616	4237	4.097589	TGTGATCACAACAAGCACATGAAA	59.902	37.500	26.02	0.00	38.56	2.69
654	4275	9.798994	TCGTTTAACCTTCTATTCATTAGTCTC	57.201	33.333	0.00	0.00	0.00	3.36
704	4325	0.450184	ACATTGAAATGGTACGCCGC	59.550	50.000	7.87	0.00	40.70	6.53
1041	6688	3.063084	GTCCTCGACGACCTGCCT	61.063	66.667	3.43	0.00	0.00	4.75
1193	6841	1.386533	CCATTGCTCCCTGTCATCAC	58.613	55.000	0.00	0.00	0.00	3.06
1337	6991	4.401022	TGTGATGGCTTTCTCATCTTGTT	58.599	39.130	0.00	0.00	41.01	2.83
1488	7154	1.921869	CTGGGGAATACCGGGTGCTT	61.922	60.000	10.66	3.04	41.60	3.91
1510	7176	1.148273	TTCTCACGTGGCTGCCTTT	59.852	52.632	21.03	0.43	0.00	3.11
1976	7654	0.756294	TGTTGTCACACTCCATCGGT	59.244	50.000	0.00	0.00	0.00	4.69
2301	7995	4.569943	TGTTCTAGCTCTTTTGCTACCAG	58.430	43.478	0.00	0.00	43.74	4.00
2326	8020	1.405105	TGCCTTTTGTGCTGTCTTGAC	59.595	47.619	0.00	0.00	0.00	3.18
2392	8086	5.064834	GCTACTTCTTCCCCATTTACTTTCG	59.935	44.000	0.00	0.00	0.00	3.46
2397	8091	2.718563	TCCCCATTTACTTTCGCTTCC	58.281	47.619	0.00	0.00	0.00	3.46
2521	8215	4.326826	TCTAGGAAAACAGTGCCATCAAG	58.673	43.478	0.00	0.00	0.00	3.02
2548	8242	3.494045	TGAGAGATGCAGTTGTAGTCG	57.506	47.619	0.00	0.00	0.00	4.18
2554	8248	4.632153	AGATGCAGTTGTAGTCGTTTTCT	58.368	39.130	0.00	0.00	0.00	2.52
2560	8254	6.134061	GCAGTTGTAGTCGTTTTCTTTTAGG	58.866	40.000	0.00	0.00	0.00	2.69
2562	8256	6.480981	CAGTTGTAGTCGTTTTCTTTTAGGGA	59.519	38.462	0.00	0.00	0.00	4.20
2563	8257	7.172703	CAGTTGTAGTCGTTTTCTTTTAGGGAT	59.827	37.037	0.00	0.00	0.00	3.85
2564	8258	8.370182	AGTTGTAGTCGTTTTCTTTTAGGGATA	58.630	33.333	0.00	0.00	0.00	2.59
2566	8260	9.558396	TTGTAGTCGTTTTCTTTTAGGGATAAA	57.442	29.630	0.00	0.00	0.00	1.40
2567	8261	8.992073	TGTAGTCGTTTTCTTTTAGGGATAAAC	58.008	33.333	0.00	0.00	0.00	2.01
2568	8262	8.992073	GTAGTCGTTTTCTTTTAGGGATAAACA	58.008	33.333	0.00	0.00	0.00	2.83
2569	8263	7.868775	AGTCGTTTTCTTTTAGGGATAAACAC	58.131	34.615	0.00	0.00	0.00	3.32
2570	8264	7.499895	AGTCGTTTTCTTTTAGGGATAAACACA	59.500	33.333	0.00	0.00	0.00	3.72
2571	8265	8.130469	GTCGTTTTCTTTTAGGGATAAACACAA	58.870	33.333	0.00	0.00	0.00	3.33
2572	8266	8.852135	TCGTTTTCTTTTAGGGATAAACACAAT	58.148	29.630	0.00	0.00	0.00	2.71
2668	8367	2.364317	CTTCCTCCTCCCGCCTCA	60.364	66.667	0.00	0.00	0.00	3.86
3083	8786	4.400961	GCAGCGCCCTTCTGTCCT	62.401	66.667	2.29	0.00	34.21	3.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
37	40	3.575351	CTATAGGGCCGGAGTGCGC	62.575	68.421	5.05	0.00	43.89	6.09
40	43	2.201022	ACGCTATAGGGCCGGAGTG	61.201	63.158	16.22	12.50	0.00	3.51
89	92	2.128507	GGGAGAGGAGGCGACGAAT	61.129	63.158	0.00	0.00	0.00	3.34
111	114	2.279784	GGAGGATCTTCTGCGCCG	60.280	66.667	4.18	0.00	33.73	6.46
112	115	1.068921	GAGGAGGATCTTCTGCGCC	59.931	63.158	4.18	0.00	38.33	6.53
117	120	1.458588	GGGGCGAGGAGGATCTTCT	60.459	63.158	4.68	0.00	39.36	2.85
118	121	2.512355	GGGGGCGAGGAGGATCTTC	61.512	68.421	0.00	0.00	37.94	2.87
119	122	2.446802	GGGGGCGAGGAGGATCTT	60.447	66.667	0.00	0.00	33.73	2.40
120	123	3.443479	AGGGGGCGAGGAGGATCT	61.443	66.667	0.00	0.00	33.73	2.75
121	124	2.920384	GAGGGGGCGAGGAGGATC	60.920	72.222	0.00	0.00	0.00	3.36
125	128	2.965226	TATTGGGAGGGGGCGAGGAG	62.965	65.000	0.00	0.00	0.00	3.69
127	130	1.842381	GATATTGGGAGGGGGCGAGG	61.842	65.000	0.00	0.00	0.00	4.63
128	131	0.838122	AGATATTGGGAGGGGGCGAG	60.838	60.000	0.00	0.00	0.00	5.03
130	133	1.376466	CAGATATTGGGAGGGGGCG	59.624	63.158	0.00	0.00	0.00	6.13
141	3746	0.598680	GCTCGCCGCTGACAGATATT	60.599	55.000	6.65	0.00	35.14	1.28
189	3795	3.834799	GGGAAGGACGACGGCGAT	61.835	66.667	22.49	0.00	41.64	4.58
259	3865	3.106672	GTGCAGTTCGTCTTACCGATAG	58.893	50.000	0.00	0.00	36.62	2.08
326	3933	9.702494	TGCTCATAACTGAAATCTCATATACTG	57.298	33.333	0.00	0.00	0.00	2.74
334	3941	6.369890	TCTGTGTTGCTCATAACTGAAATCTC	59.630	38.462	0.00	0.00	0.00	2.75
360	3967	9.178758	CTAATAGTGGCTTCTTTTCTACCAATT	57.821	33.333	0.00	0.00	30.32	2.32
406	4013	1.305381	AGAGGAGACAGGGGTTCCG	60.305	63.158	0.00	0.00	38.33	4.30
409	4016	1.081277	GGGAGAGGAGACAGGGGTT	59.919	63.158	0.00	0.00	0.00	4.11
496	4116	3.305629	CACGAATCAGCTAGCAGAAACTC	59.694	47.826	18.83	11.49	0.00	3.01
498	4118	2.222908	GCACGAATCAGCTAGCAGAAAC	60.223	50.000	18.83	11.47	0.00	2.78
552	4172	4.768448	TCAGTTGAGATGCCATCAAACATT	59.232	37.500	19.31	3.77	38.34	2.71
616	4237	7.712797	AGAAGGTTAAACGAATGAACAAATGT	58.287	30.769	0.00	0.00	0.00	2.71
653	4274	7.561021	TTTACTGCAAAAACATGTCAGTAGA	57.439	32.000	18.37	14.04	39.15	2.59
695	4316	1.014352	AGAAAATCATGCGGCGTACC	58.986	50.000	9.37	0.00	0.00	3.34
1041	6688	3.763897	TCTCTTCGATCACAATCCACTCA	59.236	43.478	0.00	0.00	0.00	3.41
1488	7154	1.891919	GCAGCCACGTGAGAACCAA	60.892	57.895	19.30	0.00	0.00	3.67
1510	7176	1.045407	AACCTGAGAACGTAGCCACA	58.955	50.000	0.00	0.00	0.00	4.17
1801	7467	3.736720	TCTCTATGCTGGCATCATTGTC	58.263	45.455	9.35	0.00	37.82	3.18
1976	7654	2.575735	TGCAACAGATAATCAGGACCCA	59.424	45.455	0.00	0.00	0.00	4.51
2301	7995	3.605664	AGCACAAAAGGCACCCGC	61.606	61.111	0.00	0.00	37.44	6.13
2326	8020	4.635223	ACTCCAACATATCATGATGACGG	58.365	43.478	18.72	10.98	35.33	4.79
2392	8086	5.001232	TCACACTACTTAACAATGGGAAGC	58.999	41.667	0.00	0.00	0.00	3.86
2397	8091	5.182950	TGCCATTCACACTACTTAACAATGG	59.817	40.000	0.00	0.00	41.14	3.16
2521	8215	8.430801	ACTACAACTGCATCTCTCATATTTTC	57.569	34.615	0.00	0.00	0.00	2.29
2554	8248	5.357596	GGGCGTATTGTGTTTATCCCTAAAA	59.642	40.000	0.00	0.00	0.00	1.52
2560	8254	1.951602	GGGGGCGTATTGTGTTTATCC	59.048	52.381	0.00	0.00	0.00	2.59
2562	8256	3.020984	CAAGGGGGCGTATTGTGTTTAT	58.979	45.455	0.00	0.00	0.00	1.40
2563	8257	2.438411	CAAGGGGGCGTATTGTGTTTA	58.562	47.619	0.00	0.00	0.00	2.01
2564	8258	1.253100	CAAGGGGGCGTATTGTGTTT	58.747	50.000	0.00	0.00	0.00	2.83
2566	8260	1.677633	GCAAGGGGGCGTATTGTGT	60.678	57.895	0.00	0.00	0.00	3.72
2567	8261	2.414785	GGCAAGGGGGCGTATTGTG	61.415	63.158	0.00	0.00	33.57	3.33
2568	8262	2.044352	GGCAAGGGGGCGTATTGT	60.044	61.111	0.00	0.00	33.57	2.71
2569	8263	2.833121	GGGCAAGGGGGCGTATTG	60.833	66.667	0.00	0.00	44.56	1.90
2570	8264	4.137615	GGGGCAAGGGGGCGTATT	62.138	66.667	0.00	0.00	44.56	1.89
2807	8506	4.840005	CCGAAGAAGGAGCCGCCC	62.840	72.222	0.00	0.00	37.37	6.13
2936	8639	1.227380	CGCGATGGGGAAGGAAGAG	60.227	63.158	0.00	0.00	0.00	2.85
3068	8771	0.397816	ATCTAGGACAGAAGGGCGCT	60.398	55.000	7.64	0.00	36.67	5.92
3080	8783	1.846439	CAAAAGGGCCCAGATCTAGGA	59.154	52.381	27.56	0.00	0.00	2.94
3083	8786	0.926293	CCCAAAAGGGCCCAGATCTA	59.074	55.000	27.56	0.00	34.21	1.98

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.