AutoCloner

Multiple sequence alignment - TraesCS2D01G073800

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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	TraesCS2D01G073800	chr2D	100.000	3509	0	0	1	3509	31510666	31514174	0.000000e+00	6481.0
1	TraesCS2D01G073800	chr2D	95.179	643	21	4	1292	1933	31476417	31477050	0.000000e+00	1007.0
2	TraesCS2D01G073800	chr2D	95.192	104	4	1	2760	2862	31477054	31477157	2.800000e-36	163.0
3	TraesCS2D01G073800	chr2A	93.763	1459	63	6	1049	2491	33334687	33336133	0.000000e+00	2165.0
4	TraesCS2D01G073800	chr2A	90.390	718	59	6	2797	3509	33336672	33337384	0.000000e+00	935.0
5	TraesCS2D01G073800	chr2A	91.783	572	30	7	1	567	33327646	33327087	0.000000e+00	780.0
6	TraesCS2D01G073800	chr2A	78.571	420	65	19	423	827	662895500	662895091	1.620000e-63	254.0
7	TraesCS2D01G073800	chr2A	77.292	480	73	30	362	827	494947608	494947151	2.090000e-62	250.0
8	TraesCS2D01G073800	chr2A	82.812	256	37	7	312	563	33327474	33327222	4.560000e-54	222.0
9	TraesCS2D01G073800	chrUn	91.974	1408	51	14	1213	2597	17259027	17257659	0.000000e+00	1917.0
10	TraesCS2D01G073800	chrUn	89.323	665	47	5	2626	3271	17257662	17257003	0.000000e+00	813.0
11	TraesCS2D01G073800	chrUn	92.871	505	32	4	3006	3508	17270335	17269833	0.000000e+00	730.0
12	TraesCS2D01G073800	chrUn	92.949	156	11	0	2849	3004	17270573	17270418	9.800000e-56	228.0
13	TraesCS2D01G073800	chrUn	89.205	176	19	0	1049	1224	17259813	17259638	1.640000e-53	220.0
14	TraesCS2D01G073800	chr2B	95.017	883	43	1	2626	3508	51085295	51084414	0.000000e+00	1386.0
15	TraesCS2D01G073800	chr2B	90.919	947	43	11	1622	2549	51086419	51085497	0.000000e+00	1232.0
16	TraesCS2D01G073800	chr2B	93.282	774	37	11	183	951	51102539	51101776	0.000000e+00	1127.0
17	TraesCS2D01G073800	chr2B	91.561	474	40	0	3036	3509	52527741	52528214	0.000000e+00	654.0
18	TraesCS2D01G073800	chr2B	90.234	471	38	1	3039	3509	52150790	52150328	3.000000e-170	608.0
19	TraesCS2D01G073800	chr2B	84.590	610	71	14	1	605	51102839	51102248	5.050000e-163	584.0
20	TraesCS2D01G073800	chr2B	74.354	1470	294	53	1052	2475	50742055	50740623	1.840000e-152	549.0
21	TraesCS2D01G073800	chr2B	78.496	944	112	45	1251	2158	52219277	52218389	5.160000e-148	534.0
22	TraesCS2D01G073800	chr2B	90.118	425	19	6	964	1373	51099258	51098842	6.670000e-147	531.0
23	TraesCS2D01G073800	chr2B	90.237	379	28	2	2113	2491	52526339	52526708	1.460000e-133	486.0
24	TraesCS2D01G073800	chr2B	82.487	571	59	20	984	1545	52517656	52518194	2.470000e-126	462.0
25	TraesCS2D01G073800	chr2B	82.809	477	65	15	159	626	52514863	52515331	9.070000e-111	411.0
26	TraesCS2D01G073800	chr2B	91.085	258	11	3	1378	1626	51091920	51091666	4.340000e-89	339.0
27	TraesCS2D01G073800	chr2B	88.172	186	13	4	2815	2991	52182584	52182399	2.740000e-51	213.0
28	TraesCS2D01G073800	chr2B	87.097	186	13	6	2797	2981	52527361	52527536	2.140000e-47	200.0
29	TraesCS2D01G073800	chr2B	78.033	305	56	11	180	478	52515016	52515315	7.740000e-42	182.0
30	TraesCS2D01G073800	chr2B	81.720	186	22	6	1073	1256	52219628	52219453	1.020000e-30	145.0
31	TraesCS2D01G073800	chr2B	78.238	193	32	8	423	608	572551988	572551799	7.960000e-22	115.0
32	TraesCS2D01G073800	chr2B	97.297	37	1	0	2561	2597	51085328	51085292	2.920000e-06	63.9
33	TraesCS2D01G073800	chr5B	79.452	438	67	19	309	738	244740337	244740759	4.430000e-74	289.0
34	TraesCS2D01G073800	chr5B	73.986	296	55	18	339	620	485079015	485078728	2.230000e-17	100.0
35	TraesCS2D01G073800	chr3A	78.571	434	57	19	423	852	336047655	336048056	1.620000e-63	254.0
36	TraesCS2D01G073800	chr7D	81.231	325	43	17	534	850	467681985	467682299	2.710000e-61	246.0
37	TraesCS2D01G073800	chr7D	78.171	339	46	15	489	825	69376485	69376797	1.290000e-44	191.0
38	TraesCS2D01G073800	chr6B	79.787	282	48	9	534	811	461995989	461996265	2.760000e-46	196.0
39	TraesCS2D01G073800	chr6B	74.081	517	97	23	198	686	699027115	699026608	1.000000e-40	178.0
40	TraesCS2D01G073800	chr6B	92.188	64	5	0	175	238	279193739	279193676	1.340000e-14	91.6
41	TraesCS2D01G073800	chr4A	75.688	436	72	25	179	589	734070738	734071164	1.660000e-43	187.0
42	TraesCS2D01G073800	chr6A	77.976	336	41	22	495	820	52308826	52308514	2.780000e-41	180.0
43	TraesCS2D01G073800	chr6A	80.909	110	14	3	135	244	460453737	460453635	2.900000e-11	80.5
44	TraesCS2D01G073800	chr1A	80.176	227	36	9	429	654	456447046	456446828	1.010000e-35	161.0
45	TraesCS2D01G073800	chr4D	82.353	153	20	7	680	827	473805164	473805314	3.680000e-25	126.0
46	TraesCS2D01G073800	chr4B	80.240	167	21	9	667	831	596364859	596365015	7.960000e-22	115.0
47	TraesCS2D01G073800	chr7B	72.334	347	71	21	307	641	527959829	527960162	6.240000e-13	86.1
48	TraesCS2D01G073800	chr3D	87.500	72	7	2	305	375	582993022	582993092	8.070000e-12	82.4

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	TraesCS2D01G073800	chr2D	31510666	31514174	3508	False	6481.000000	6481	100.000000	1	3509	1	chr2D.!!$F1	3508
1	TraesCS2D01G073800	chr2D	31476417	31477157	740	False	585.000000	1007	95.185500	1292	2862	2	chr2D.!!$F2	1570
2	TraesCS2D01G073800	chr2A	33334687	33337384	2697	False	1550.000000	2165	92.076500	1049	3509	2	chr2A.!!$F1	2460
3	TraesCS2D01G073800	chr2A	33327087	33327646	559	True	501.000000	780	87.297500	1	567	2	chr2A.!!$R3	566
4	TraesCS2D01G073800	chrUn	17257003	17259813	2810	True	983.333333	1917	90.167333	1049	3271	3	chrUn.!!$R1	2222
5	TraesCS2D01G073800	chrUn	17269833	17270573	740	True	479.000000	730	92.910000	2849	3508	2	chrUn.!!$R2	659
6	TraesCS2D01G073800	chr2B	51084414	51086419	2005	True	893.966667	1386	94.411000	1622	3508	3	chr2B.!!$R6	1886
7	TraesCS2D01G073800	chr2B	51098842	51102839	3997	True	747.333333	1127	89.330000	1	1373	3	chr2B.!!$R7	1372
8	TraesCS2D01G073800	chr2B	50740623	50742055	1432	True	549.000000	549	74.354000	1052	2475	1	chr2B.!!$R1	1423
9	TraesCS2D01G073800	chr2B	52526339	52528214	1875	False	446.666667	654	89.631667	2113	3509	3	chr2B.!!$F2	1396
10	TraesCS2D01G073800	chr2B	52514863	52518194	3331	False	351.666667	462	81.109667	159	1545	3	chr2B.!!$F1	1386
11	TraesCS2D01G073800	chr2B	52218389	52219628	1239	True	339.500000	534	80.108000	1073	2158	2	chr2B.!!$R8	1085

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
779	923	6.418819	CAGTGTTCTATGGAAAGTGCTTTTTG	59.581	38.462	0.0	0.0	32.81	2.44	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2566	8404	0.397816	AGGCGGTTGATCCTCTAGCT	60.398	55.0	0.0	0.0	0.0	3.32	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
71	73	7.320384	AGATGGGAAAATCAGAAAAACCAAT	57.680	32.000	0.00	0.00	0.00	3.16
276	281	6.485313	ACCATTGTTATAATACATGGTCACCG	59.515	38.462	15.49	0.00	36.27	4.94
410	548	9.258826	CATTTTCTGAAAACATGGTGAACATTA	57.741	29.630	17.06	0.00	32.15	1.90
414	553	9.829507	TTCTGAAAACATGGTGAACATTATTTT	57.170	25.926	0.00	2.71	37.84	1.82
779	923	6.418819	CAGTGTTCTATGGAAAGTGCTTTTTG	59.581	38.462	0.00	0.00	32.81	2.44
864	3033	6.885735	AAATAAAAACAGAATACATGCGGC	57.114	33.333	0.00	0.00	0.00	6.53
961	5631	6.910972	GCTCAACAAACCTAAAAAGTAGTCAC	59.089	38.462	0.00	0.00	0.00	3.67
1015	5693	2.093816	AGCTGATCATCGCACAAGAAGA	60.094	45.455	9.38	0.00	0.00	2.87
1016	5694	2.871022	GCTGATCATCGCACAAGAAGAT	59.129	45.455	0.00	0.00	32.09	2.40
1017	5695	4.053983	GCTGATCATCGCACAAGAAGATA	58.946	43.478	0.00	0.00	29.90	1.98
1018	5696	4.689812	GCTGATCATCGCACAAGAAGATAT	59.310	41.667	0.00	0.00	29.90	1.63
1031	5709	6.428159	CACAAGAAGATATATGGCAACCTACC	59.572	42.308	0.00	0.00	0.00	3.18
1038	5716	4.796495	GGCAACCTACCGGCAGGG	62.796	72.222	24.99	15.31	43.47	4.45
1204	5898	2.284699	CGGGGACTCAACCTCCCT	60.285	66.667	3.51	0.00	46.27	4.20
1240	6556	3.195698	GTGACGGGCGCCATCTTC	61.196	66.667	30.85	18.00	0.00	2.87
1241	6557	3.390521	TGACGGGCGCCATCTTCT	61.391	61.111	30.85	2.18	0.00	2.85
1242	6558	2.586357	GACGGGCGCCATCTTCTC	60.586	66.667	30.85	7.76	0.00	2.87
1243	6559	4.162690	ACGGGCGCCATCTTCTCC	62.163	66.667	30.85	6.91	0.00	3.71
1313	6814	1.742880	CCGGACGACCTACTCGACA	60.743	63.158	0.00	0.00	46.14	4.35
1373	6874	3.343788	GACCTCGCGCTGCAGTACT	62.344	63.158	16.64	0.00	0.00	2.73
1374	6875	2.882777	CCTCGCGCTGCAGTACTG	60.883	66.667	18.93	18.93	0.00	2.74
1756	7296	2.591715	GACACAGTGCCTGCGGTT	60.592	61.111	0.00	0.00	34.37	4.44
1913	7462	0.035152	TCATCAGCCGGTGCAAGAAT	60.035	50.000	1.90	0.00	41.13	2.40
1936	7486	2.104530	GTACCTTCGCCTCGAGCC	59.895	66.667	6.99	0.00	37.14	4.70
1957	7507	1.152881	GCCCCTCAATGGCCTACTG	60.153	63.158	3.32	0.00	43.33	2.74
1983	7533	1.270826	GCGAGATCACAGCTATAGCCA	59.729	52.381	21.17	3.50	43.38	4.75
1984	7534	2.288457	GCGAGATCACAGCTATAGCCAA	60.288	50.000	21.17	4.85	43.38	4.52
2140	7705	5.518128	CCGAGACATTGAAGAAGACATACTG	59.482	44.000	0.00	0.00	0.00	2.74
2230	7804	2.034685	ACGACGACACCTATGATGATGG	59.965	50.000	0.00	0.00	0.00	3.51
2385	7959	2.751806	GCTTTGGAGGAATTCTCAGTGG	59.248	50.000	5.23	0.00	44.19	4.00
2404	7978	1.448540	CCTTAGCGGCTCCACTGTG	60.449	63.158	5.39	0.00	0.00	3.66
2477	8051	4.715297	CCCAGGACCATAGTAACTTGTACT	59.285	45.833	0.00	0.00	0.00	2.73
2478	8052	5.895534	CCCAGGACCATAGTAACTTGTACTA	59.104	44.000	0.00	0.00	34.88	1.82
2479	8053	6.040616	CCCAGGACCATAGTAACTTGTACTAG	59.959	46.154	2.56	2.56	34.01	2.57
2507	8170	5.404096	ACAAGGGTTACACTTTGTTTTTCG	58.596	37.500	0.00	0.00	0.00	3.46
2519	8193	6.034150	CACTTTGTTTTTCGGAAACCAACTAC	59.966	38.462	15.31	0.00	28.51	2.73
2520	8194	5.640189	TTGTTTTTCGGAAACCAACTACA	57.360	34.783	15.31	0.00	0.00	2.74
2521	8195	5.640189	TGTTTTTCGGAAACCAACTACAA	57.360	34.783	15.31	0.00	0.00	2.41
2522	8196	5.400703	TGTTTTTCGGAAACCAACTACAAC	58.599	37.500	15.31	10.02	0.00	3.32
2523	8197	5.183522	TGTTTTTCGGAAACCAACTACAACT	59.816	36.000	15.31	0.00	0.00	3.16
2524	8198	6.373774	TGTTTTTCGGAAACCAACTACAACTA	59.626	34.615	15.31	1.58	0.00	2.24
2557	8395	2.703536	TGGCCGGAATGTATATGACACT	59.296	45.455	5.05	0.00	42.17	3.55
2559	8397	4.530553	TGGCCGGAATGTATATGACACTAT	59.469	41.667	5.05	0.00	42.17	2.12
2566	8404	9.908152	CGGAATGTATATGACACTATACAGAAA	57.092	33.333	16.16	2.41	43.93	2.52
2603	8441	3.683847	CGCCTTCCTGAGATTTCATCCTT	60.684	47.826	0.00	0.00	31.68	3.36
2606	8444	5.053145	CCTTCCTGAGATTTCATCCTTACG	58.947	45.833	0.00	0.00	31.68	3.18
2714	8827	1.527311	GGACTTTCTTGACGACAGCAC	59.473	52.381	0.00	0.00	0.00	4.40
3175	9521	0.171903	CGATTGCTTTGCCCTTCTGG	59.828	55.000	0.00	0.00	37.09	3.86
3214	9560	1.227527	CAGTGTGACACCGGCTTCA	60.228	57.895	12.81	0.12	34.49	3.02
3341	9687	0.615850	CCCCTCCTTCCTCAACTGAC	59.384	60.000	0.00	0.00	0.00	3.51
3409	9756	0.257328	TGAGGTCAGGTTTGTTGCCA	59.743	50.000	0.00	0.00	0.00	4.92
3463	9810	1.434555	CAACGCCTTCAACCGATGTA	58.565	50.000	0.00	0.00	0.00	2.29
3493	9840	2.185608	GGGAGCTTCTGCCGAGAC	59.814	66.667	0.00	0.00	40.80	3.36

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
33	35	7.847711	TTTTCCCATCTTGTTTCTTTCCATA	57.152	32.000	0.00	0.00	0.00	2.74
48	50	9.500785	TTTATTGGTTTTTCTGATTTTCCCATC	57.499	29.630	0.00	0.00	0.00	3.51
302	311	8.406172	TCAGAAAATGTTAAACTTGTTTCTGC	57.594	30.769	18.73	0.00	45.85	4.26
330	339	8.620416	TGTGTATAGATAAAATGTTGACCATGC	58.380	33.333	0.00	0.00	32.82	4.06
456	597	6.832804	TCGCAAAAATGTTGACGATGTATTA	58.167	32.000	0.00	0.00	0.00	0.98
524	665	7.855904	GCGTATAGGAAAAATGTTGACCATTAG	59.144	37.037	0.00	0.00	43.04	1.73
1015	5693	1.982226	TGCCGGTAGGTTGCCATATAT	59.018	47.619	1.90	0.00	40.50	0.86
1016	5694	1.346395	CTGCCGGTAGGTTGCCATATA	59.654	52.381	12.40	0.00	40.50	0.86
1017	5695	0.108585	CTGCCGGTAGGTTGCCATAT	59.891	55.000	12.40	0.00	40.50	1.78
1018	5696	1.524961	CTGCCGGTAGGTTGCCATA	59.475	57.895	12.40	0.00	40.50	2.74
1193	5887	0.109342	AAGCACACAGGGAGGTTGAG	59.891	55.000	0.00	0.00	0.00	3.02
1240	6556	4.366684	GTGGTGGGGCCCTTGGAG	62.367	72.222	25.93	0.00	36.04	3.86
1306	6807	2.492090	GCGATCCAGCTGTCGAGT	59.508	61.111	25.70	2.49	40.11	4.18
1373	6874	4.023137	GGGAGTAGTGCCGGTACA	57.977	61.111	25.19	8.05	0.00	2.90
1913	7462	1.642037	CGAGGCGAAGGTACGTCAGA	61.642	60.000	0.00	0.00	40.49	3.27
1957	7507	2.811066	GCTGTGATCTCGCTGCTGC	61.811	63.158	13.35	5.34	44.43	5.25
1983	7533	1.125711	AGCTGGGGTAAGTGGTCGTT	61.126	55.000	0.00	0.00	0.00	3.85
1984	7534	1.535687	AGCTGGGGTAAGTGGTCGT	60.536	57.895	0.00	0.00	0.00	4.34
2140	7705	0.592754	GCCGTACTCATCGTCAGAGC	60.593	60.000	0.00	0.00	36.58	4.09
2230	7804	1.022735	CATGCTCCTGAACATCCAGC	58.977	55.000	0.00	0.00	32.97	4.85
2408	7982	2.899339	GCAATCTCCTCCCTGCGC	60.899	66.667	0.00	0.00	0.00	6.09
2477	8051	5.306160	ACAAAGTGTAACCCTTGTCTAGCTA	59.694	40.000	0.00	0.00	38.56	3.32
2478	8052	4.102681	ACAAAGTGTAACCCTTGTCTAGCT	59.897	41.667	0.00	0.00	38.56	3.32
2479	8053	4.386711	ACAAAGTGTAACCCTTGTCTAGC	58.613	43.478	0.00	0.00	38.56	3.42
2507	8170	5.046807	TCCTAGCTAGTTGTAGTTGGTTTCC	60.047	44.000	19.31	0.00	0.00	3.13
2519	8193	3.997021	CGGCCATATTTCCTAGCTAGTTG	59.003	47.826	19.31	5.38	0.00	3.16
2520	8194	3.008049	CCGGCCATATTTCCTAGCTAGTT	59.992	47.826	19.31	4.30	0.00	2.24
2521	8195	2.567615	CCGGCCATATTTCCTAGCTAGT	59.432	50.000	19.31	3.48	0.00	2.57
2522	8196	2.832129	TCCGGCCATATTTCCTAGCTAG	59.168	50.000	14.20	14.20	0.00	3.42
2523	8197	2.897350	TCCGGCCATATTTCCTAGCTA	58.103	47.619	2.24	0.00	0.00	3.32
2524	8198	1.729586	TCCGGCCATATTTCCTAGCT	58.270	50.000	2.24	0.00	0.00	3.32
2557	8395	6.016192	CGGTTGATCCTCTAGCTTTCTGTATA	60.016	42.308	0.00	0.00	0.00	1.47
2559	8397	4.098044	CGGTTGATCCTCTAGCTTTCTGTA	59.902	45.833	0.00	0.00	0.00	2.74
2566	8404	0.397816	AGGCGGTTGATCCTCTAGCT	60.398	55.000	0.00	0.00	0.00	3.32
2603	8441	2.234414	GTTGGGTGTGGGATCTTACGTA	59.766	50.000	0.00	0.00	0.00	3.57
2606	8444	2.871096	TGTTGGGTGTGGGATCTTAC	57.129	50.000	0.00	0.00	0.00	2.34
2714	8827	2.775911	TGCCAGAATCTGAACTCCAG	57.224	50.000	12.53	0.00	44.27	3.86
3004	9200	5.392767	TGAAGGTTCGCTCATATATCCTC	57.607	43.478	0.00	0.00	0.00	3.71
3013	9356	6.112734	ACAAATGTATATGAAGGTTCGCTCA	58.887	36.000	0.00	0.00	0.00	4.26
3130	9476	2.556287	CGCTTCGGTTCAAGTGCC	59.444	61.111	0.00	0.00	0.00	5.01
3175	9521	2.168728	GGGATGGGAGAAGTATATCGGC	59.831	54.545	0.00	0.00	0.00	5.54
3214	9560	5.685075	CGAGGTTACTTCCAGGATTAGCATT	60.685	44.000	0.00	0.00	0.00	3.56
3341	9687	1.926511	ATCGCAGAAAAAGCAGCCGG	61.927	55.000	0.00	0.00	43.58	6.13

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.