AutoCloner

Multiple sequence alignment - TraesCS2A01G538400

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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	TraesCS2A01G538400	chr2A	100.000	2666	0	0	1	2666	751370550	751373215	0.000000e+00	4924
1	TraesCS2A01G538400	chr2A	80.615	650	120	4	1021	1664	752297651	752297002	5.130000e-137	497
2	TraesCS2A01G538400	chr2A	79.645	619	110	12	1016	1623	752395197	752395810	5.270000e-117	431
3	TraesCS2A01G538400	chr2A	82.162	370	42	14	572	938	82049369	82049717	2.010000e-76	296
4	TraesCS2A01G538400	chr3A	97.009	936	26	2	1	934	740813736	740812801	0.000000e+00	1572
5	TraesCS2A01G538400	chr3A	96.265	937	32	2	1	934	690938199	690939135	0.000000e+00	1533
6	TraesCS2A01G538400	chr3A	95.910	929	37	1	7	934	11032277	11031349	0.000000e+00	1504
7	TraesCS2A01G538400	chr3A	96.333	900	30	2	1	899	7332728	7331831	0.000000e+00	1476
8	TraesCS2A01G538400	chr3A	95.321	919	37	5	1	916	8238419	8237504	0.000000e+00	1454
9	TraesCS2A01G538400	chr5A	95.314	939	41	3	1	938	554051362	554052298	0.000000e+00	1487
10	TraesCS2A01G538400	chr5A	76.144	612	113	24	1024	1623	691531542	691530952	9.340000e-75	291
11	TraesCS2A01G538400	chr4A	95.075	934	39	4	1	932	593658126	593659054	0.000000e+00	1463
12	TraesCS2A01G538400	chr4A	91.822	966	73	3	1701	2666	650837366	650838325	0.000000e+00	1341
13	TraesCS2A01G538400	chr7A	94.804	943	32	8	1	942	704692631	704691705	0.000000e+00	1454
14	TraesCS2A01G538400	chr7A	95.376	865	33	4	1	863	32401239	32402098	0.000000e+00	1369
15	TraesCS2A01G538400	chr3B	92.784	970	65	3	1701	2666	666611618	666612586	0.000000e+00	1399
16	TraesCS2A01G538400	chr3B	91.503	965	76	3	1702	2666	662442222	662441264	0.000000e+00	1323
17	TraesCS2A01G538400	chr1A	92.547	966	66	3	1701	2666	406150853	406149894	0.000000e+00	1380
18	TraesCS2A01G538400	chr2B	91.959	970	71	4	1698	2666	476403120	476402157	0.000000e+00	1352
19	TraesCS2A01G538400	chr2B	91.727	967	73	4	1701	2666	53141678	53140718	0.000000e+00	1336
20	TraesCS2A01G538400	chr2B	92.208	693	51	3	1013	1702	759445391	759446083	0.000000e+00	977
21	TraesCS2A01G538400	chr2B	79.429	666	120	13	1014	1665	761709355	761710017	3.130000e-124	455
22	TraesCS2A01G538400	chr2B	79.642	614	109	12	1021	1623	761700351	761700959	6.820000e-116	427
23	TraesCS2A01G538400	chr2B	76.967	699	135	18	1012	1694	761718755	761719443	2.510000e-100	375
24	TraesCS2A01G538400	chr7B	91.822	966	73	3	1701	2666	674192042	674191083	0.000000e+00	1341
25	TraesCS2A01G538400	chr1B	91.822	966	72	4	1701	2666	8172825	8171867	0.000000e+00	1339
26	TraesCS2A01G538400	chr5B	91.538	969	76	3	1698	2666	94272525	94273487	0.000000e+00	1330
27	TraesCS2A01G538400	chr2D	95.696	395	12	5	933	1326	619706099	619706489	4.840000e-177	630
28	TraesCS2A01G538400	chr2D	94.580	369	20	0	1322	1690	619706918	619707286	2.980000e-159	571
29	TraesCS2A01G538400	chr2D	81.762	647	111	5	1012	1653	620640425	620639781	3.910000e-148	534
30	TraesCS2A01G538400	chr2D	79.341	668	117	15	1013	1664	620742755	620743417	1.460000e-122	449
31	TraesCS2A01G538400	chr4B	75.851	617	126	17	1014	1623	653955911	653955311	2.600000e-75	292
32	TraesCS2A01G538400	chrUn	75.822	608	122	21	1024	1623	126691396	126691986	4.340000e-73	285

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	TraesCS2A01G538400	chr2A	751370550	751373215	2665	False	4924.0	4924	100.000	1	2666	1	chr2A.!!$F2	2665
1	TraesCS2A01G538400	chr2A	752297002	752297651	649	True	497.0	497	80.615	1021	1664	1	chr2A.!!$R1	643
2	TraesCS2A01G538400	chr2A	752395197	752395810	613	False	431.0	431	79.645	1016	1623	1	chr2A.!!$F3	607
3	TraesCS2A01G538400	chr3A	740812801	740813736	935	True	1572.0	1572	97.009	1	934	1	chr3A.!!$R4	933
4	TraesCS2A01G538400	chr3A	690938199	690939135	936	False	1533.0	1533	96.265	1	934	1	chr3A.!!$F1	933
5	TraesCS2A01G538400	chr3A	11031349	11032277	928	True	1504.0	1504	95.910	7	934	1	chr3A.!!$R3	927
6	TraesCS2A01G538400	chr3A	7331831	7332728	897	True	1476.0	1476	96.333	1	899	1	chr3A.!!$R1	898
7	TraesCS2A01G538400	chr3A	8237504	8238419	915	True	1454.0	1454	95.321	1	916	1	chr3A.!!$R2	915
8	TraesCS2A01G538400	chr5A	554051362	554052298	936	False	1487.0	1487	95.314	1	938	1	chr5A.!!$F1	937
9	TraesCS2A01G538400	chr5A	691530952	691531542	590	True	291.0	291	76.144	1024	1623	1	chr5A.!!$R1	599
10	TraesCS2A01G538400	chr4A	593658126	593659054	928	False	1463.0	1463	95.075	1	932	1	chr4A.!!$F1	931
11	TraesCS2A01G538400	chr4A	650837366	650838325	959	False	1341.0	1341	91.822	1701	2666	1	chr4A.!!$F2	965
12	TraesCS2A01G538400	chr7A	704691705	704692631	926	True	1454.0	1454	94.804	1	942	1	chr7A.!!$R1	941
13	TraesCS2A01G538400	chr7A	32401239	32402098	859	False	1369.0	1369	95.376	1	863	1	chr7A.!!$F1	862
14	TraesCS2A01G538400	chr3B	666611618	666612586	968	False	1399.0	1399	92.784	1701	2666	1	chr3B.!!$F1	965
15	TraesCS2A01G538400	chr3B	662441264	662442222	958	True	1323.0	1323	91.503	1702	2666	1	chr3B.!!$R1	964
16	TraesCS2A01G538400	chr1A	406149894	406150853	959	True	1380.0	1380	92.547	1701	2666	1	chr1A.!!$R1	965
17	TraesCS2A01G538400	chr2B	476402157	476403120	963	True	1352.0	1352	91.959	1698	2666	1	chr2B.!!$R2	968
18	TraesCS2A01G538400	chr2B	53140718	53141678	960	True	1336.0	1336	91.727	1701	2666	1	chr2B.!!$R1	965
19	TraesCS2A01G538400	chr2B	759445391	759446083	692	False	977.0	977	92.208	1013	1702	1	chr2B.!!$F1	689
20	TraesCS2A01G538400	chr2B	761709355	761710017	662	False	455.0	455	79.429	1014	1665	1	chr2B.!!$F3	651
21	TraesCS2A01G538400	chr2B	761700351	761700959	608	False	427.0	427	79.642	1021	1623	1	chr2B.!!$F2	602
22	TraesCS2A01G538400	chr2B	761718755	761719443	688	False	375.0	375	76.967	1012	1694	1	chr2B.!!$F4	682
23	TraesCS2A01G538400	chr7B	674191083	674192042	959	True	1341.0	1341	91.822	1701	2666	1	chr7B.!!$R1	965
24	TraesCS2A01G538400	chr1B	8171867	8172825	958	True	1339.0	1339	91.822	1701	2666	1	chr1B.!!$R1	965
25	TraesCS2A01G538400	chr5B	94272525	94273487	962	False	1330.0	1330	91.538	1698	2666	1	chr5B.!!$F1	968
26	TraesCS2A01G538400	chr2D	619706099	619707286	1187	False	600.5	630	95.138	933	1690	2	chr2D.!!$F2	757
27	TraesCS2A01G538400	chr2D	620639781	620640425	644	True	534.0	534	81.762	1012	1653	1	chr2D.!!$R1	641
28	TraesCS2A01G538400	chr2D	620742755	620743417	662	False	449.0	449	79.341	1013	1664	1	chr2D.!!$F1	651
29	TraesCS2A01G538400	chr4B	653955311	653955911	600	True	292.0	292	75.851	1014	1623	1	chr4B.!!$R1	609
30	TraesCS2A01G538400	chrUn	126691396	126691986	590	False	285.0	285	75.822	1024	1623	1	chrUn.!!$F1	599

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
642	653	1.032794	CTATGCCGACAGCTAGACCA	58.967	55.0	0.0	0.0	44.23	4.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2552	3029	0.03759	CCCGGGTGAAATCCTCAACA	59.962	55.0	14.18	0.0	44.35	3.33	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
108	109	9.243637	GCTTGTGATGTTTCTTATTGTTGTTTA	57.756	29.630	0.00	0.00	0.00	2.01
642	653	1.032794	CTATGCCGACAGCTAGACCA	58.967	55.000	0.00	0.00	44.23	4.02
755	767	1.411246	GGCATAGATGTACGGACACCA	59.589	52.381	0.33	0.00	38.76	4.17
790	802	1.153429	GCCGACGGCCTTTCTATGT	60.153	57.895	28.74	0.00	44.06	2.29
810	822	1.381928	CGACGGCCTTCCTAGCTACA	61.382	60.000	3.22	0.00	0.00	2.74
938	950	1.153901	CGATTCCGGTAGTGCGTGT	60.154	57.895	0.00	0.00	0.00	4.49
953	965	3.927552	GCGTGTAGCTTAATTCTGGAC	57.072	47.619	0.00	0.00	44.04	4.02
955	967	3.682858	GCGTGTAGCTTAATTCTGGACAA	59.317	43.478	0.00	0.00	44.04	3.18
956	968	4.435651	GCGTGTAGCTTAATTCTGGACAAC	60.436	45.833	0.00	0.00	44.04	3.32
957	969	4.688879	CGTGTAGCTTAATTCTGGACAACA	59.311	41.667	0.00	0.00	0.00	3.33
958	970	8.514362	GCGTGTAGCTTAATTCTGGACAACAG	62.514	46.154	0.00	0.00	45.21	3.16
979	991	3.248602	AGCTAATTAACATGCTAGCGTGC	59.751	43.478	32.12	18.02	41.33	5.34
996	1008	3.181511	GCGTGCATCTACAATTTAGTGCA	60.182	43.478	0.00	13.76	39.94	4.57
998	1010	5.572211	CGTGCATCTACAATTTAGTGCATT	58.428	37.500	17.05	0.00	43.43	3.56
1050	1064	3.455469	GGCAGCTGTTGGGCCATC	61.455	66.667	16.64	7.51	46.92	3.51
1289	1314	4.826274	AAACAGTAGCAGCAAGGATAGA	57.174	40.909	0.00	0.00	0.00	1.98
1442	1903	1.004918	AAGACTACACCGGCAGCAC	60.005	57.895	0.00	0.00	0.00	4.40
1465	1929	4.216042	CACATGCTGTCTTGATTGTTGGTA	59.784	41.667	0.00	0.00	0.00	3.25
1606	2072	2.165437	GGTATTTTCATGCGCCAAGGAA	59.835	45.455	4.18	0.00	0.00	3.36
1686	2158	7.640597	AAAAATTATCCCCTTCCTAGTTTCG	57.359	36.000	0.00	0.00	0.00	3.46
1774	2246	0.252197	ACCGGCCAGGATTACAACTC	59.748	55.000	18.74	0.00	45.00	3.01
1793	2265	6.169094	CAACTCTGGAATACAATCACACTCT	58.831	40.000	0.00	0.00	0.00	3.24
1816	2288	9.452065	CTCTAACTAAAAGGAAAGAAAACAAGC	57.548	33.333	0.00	0.00	0.00	4.01
1871	2343	3.515502	ACAGAGGCATACAACAAGCTAGA	59.484	43.478	0.00	0.00	0.00	2.43
1874	2346	6.127054	ACAGAGGCATACAACAAGCTAGATAA	60.127	38.462	0.00	0.00	0.00	1.75
1876	2348	5.989477	AGGCATACAACAAGCTAGATAACA	58.011	37.500	0.00	0.00	0.00	2.41
1877	2349	5.817816	AGGCATACAACAAGCTAGATAACAC	59.182	40.000	0.00	0.00	0.00	3.32
1894	2370	6.493115	AGATAACACACATAGCTAGAGATGCT	59.507	38.462	0.00	0.00	43.79	3.79
1912	2388	0.828022	CTAGGAACCCCATACACGCA	59.172	55.000	0.00	0.00	33.88	5.24
1937	2413	3.744238	ACCAAGGCAAAAACGCTAAAT	57.256	38.095	0.00	0.00	0.00	1.40
2002	2478	1.152756	AAACGCCTGGGCTTGAAGT	60.153	52.632	10.04	0.00	39.32	3.01
2026	2502	3.050835	ACACATCCATCCAGATCCATCA	58.949	45.455	0.00	0.00	0.00	3.07
2100	2576	1.489481	TGGACATGCTCACCCTAGAG	58.511	55.000	0.00	0.00	38.68	2.43
2118	2594	2.120765	GCCTGCATGAATGGCATCA	58.879	52.632	15.91	0.95	45.46	3.07
2131	2607	1.327303	GGCATCACAGGAAACCACAA	58.673	50.000	0.00	0.00	0.00	3.33
2186	2662	2.989840	CGACTTACCTGAAACAGAGCAG	59.010	50.000	0.00	0.00	32.44	4.24
2216	2692	1.743996	GAGAGTCCAGGCATGAAACC	58.256	55.000	0.00	0.00	0.00	3.27
2352	2828	2.284625	TGGAGAGTCCACGGGCAT	60.285	61.111	0.00	0.00	42.67	4.40
2403	2879	1.102154	CAAACCAGCTTGACCACACA	58.898	50.000	0.00	0.00	0.00	3.72
2406	2882	1.152984	CCAGCTTGACCACACACCA	60.153	57.895	0.00	0.00	0.00	4.17
2435	2911	4.221422	GCCGCCGCTGGAGACATA	62.221	66.667	5.57	0.00	41.51	2.29
2438	2914	1.452953	CCGCCGCTGGAGACATACTA	61.453	60.000	0.00	0.00	41.51	1.82
2447	2924	1.731433	GAGACATACTACCGCCGCCA	61.731	60.000	0.00	0.00	0.00	5.69
2494	2971	0.678950	CCCGCAACCCATCTTTGTTT	59.321	50.000	0.00	0.00	0.00	2.83
2588	3065	1.140772	GGGAGACAAAGGGGAAGGGT	61.141	60.000	0.00	0.00	0.00	4.34

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
108	109	6.713903	CACCACCAAGCATATAAGAATCTCAT	59.286	38.462	0.00	0.00	0.00	2.90
160	165	7.501225	TCATCATCACACATCATAAGAAGCATT	59.499	33.333	0.00	0.00	0.00	3.56
790	802	1.099879	GTAGCTAGGAAGGCCGTCGA	61.100	60.000	12.79	2.23	39.96	4.20
810	822	1.227147	CGGCAACATATCCGTCGGT	60.227	57.895	11.88	1.23	40.72	4.69
938	950	5.165961	AGCTGTTGTCCAGAATTAAGCTA	57.834	39.130	0.00	0.00	44.49	3.32
953	965	5.200454	CGCTAGCATGTTAATTAGCTGTTG	58.800	41.667	16.45	1.65	37.94	3.33
955	967	4.271049	CACGCTAGCATGTTAATTAGCTGT	59.729	41.667	16.45	0.00	37.94	4.40
956	968	4.766007	CACGCTAGCATGTTAATTAGCTG	58.234	43.478	16.45	0.00	37.94	4.24
957	969	3.248602	GCACGCTAGCATGTTAATTAGCT	59.751	43.478	16.45	0.00	40.92	3.32
958	970	3.002246	TGCACGCTAGCATGTTAATTAGC	59.998	43.478	16.45	4.75	40.11	3.09
959	971	4.794248	TGCACGCTAGCATGTTAATTAG	57.206	40.909	16.45	0.00	40.11	1.73
996	1008	4.736611	AGTTAGGGATCCATGCATGAAT	57.263	40.909	28.31	14.34	0.00	2.57
998	1010	3.202818	ACAAGTTAGGGATCCATGCATGA	59.797	43.478	28.31	14.16	0.00	3.07
1050	1064	2.434884	ACCGAGGATGCAACAGCG	60.435	61.111	0.00	0.00	0.00	5.18
1289	1314	3.454082	TGGGTTGACAAATTGAAAGCCTT	59.546	39.130	23.57	0.00	36.67	4.35
1465	1929	1.134220	ACCGTCGGAATATGTGCCATT	60.134	47.619	20.51	0.00	0.00	3.16
1474	1938	3.084039	AGTACTTGACACCGTCGGAATA	58.916	45.455	20.51	0.00	34.95	1.75
1606	2072	7.455953	TGATCAGTCCTTAAGCACTGGATATAT	59.544	37.037	23.31	11.16	40.49	0.86
1774	2246	9.653287	TTTAGTTAGAGTGTGATTGTATTCCAG	57.347	33.333	0.00	0.00	0.00	3.86
1785	2257	9.675464	TTTTCTTTCCTTTTAGTTAGAGTGTGA	57.325	29.630	0.00	0.00	0.00	3.58
1793	2265	7.197703	CCGCTTGTTTTCTTTCCTTTTAGTTA	58.802	34.615	0.00	0.00	0.00	2.24
1815	2287	1.433471	GCCCTTGTATCTTTGCCGC	59.567	57.895	0.00	0.00	0.00	6.53
1816	2288	1.721487	CGCCCTTGTATCTTTGCCG	59.279	57.895	0.00	0.00	0.00	5.69
1871	2343	6.662865	AGCATCTCTAGCTATGTGTGTTAT	57.337	37.500	0.00	0.00	41.32	1.89
1874	2346	4.522405	CCTAGCATCTCTAGCTATGTGTGT	59.478	45.833	0.00	0.00	43.08	3.72
1876	2348	4.991776	TCCTAGCATCTCTAGCTATGTGT	58.008	43.478	0.00	0.00	43.08	3.72
1877	2349	5.336372	GGTTCCTAGCATCTCTAGCTATGTG	60.336	48.000	0.00	0.00	43.08	3.21
1894	2370	0.828022	CTGCGTGTATGGGGTTCCTA	59.172	55.000	0.00	0.00	0.00	2.94
1912	2388	1.067060	GCGTTTTTGCCTTGGTTCTCT	59.933	47.619	0.00	0.00	0.00	3.10
1968	2444	1.300775	TTTGGCAATGGCGTGCTTG	60.301	52.632	12.07	0.00	44.31	4.01
2002	2478	3.927476	TGGATCTGGATGGATGTGTCTA	58.073	45.455	0.00	0.00	0.00	2.59
2026	2502	2.679716	GCAGGGGCCTTCTGTGAT	59.320	61.111	21.57	0.00	34.89	3.06
2076	2552	2.182842	GGTGAGCATGTCCATCGCC	61.183	63.158	0.00	0.57	36.53	5.54
2131	2607	3.175710	AACGCCTGGTTCCACCCT	61.176	61.111	0.00	0.00	37.50	4.34
2197	2673	1.743996	GGTTTCATGCCTGGACTCTC	58.256	55.000	0.00	0.00	0.00	3.20
2232	2708	0.739462	CTGCTGCCCATTTGTGCATG	60.739	55.000	0.00	0.00	36.79	4.06
2341	2817	2.511600	CCTTCGATGCCCGTGGAC	60.512	66.667	0.00	0.00	39.75	4.02
2352	2828	4.087892	GCTGCAGGGCTCCTTCGA	62.088	66.667	17.12	0.00	0.00	3.71
2434	2910	2.262292	GTGTTGGCGGCGGTAGTA	59.738	61.111	9.78	0.00	0.00	1.82
2435	2911	3.931247	TGTGTTGGCGGCGGTAGT	61.931	61.111	9.78	0.00	0.00	2.73
2447	2924	1.140252	GTGGTGTAGGTGGAGTGTGTT	59.860	52.381	0.00	0.00	0.00	3.32
2494	2971	2.370349	TCTTGAAGGCGTTGTTTTGGA	58.630	42.857	0.00	0.00	0.00	3.53
2552	3029	0.037590	CCCGGGTGAAATCCTCAACA	59.962	55.000	14.18	0.00	44.35	3.33

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.