AutoCloner

Multiple sequence alignment - TraesCS5D01G523600

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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	TraesCS5D01G523600	chr5D	100.000	2801	0	0	1	2801	543338384	543341184	0.000000e+00	5173.0
1	TraesCS5D01G523600	chr5D	95.455	66	3	0	2022	2087	120339643	120339578	3.820000e-19	106.0
2	TraesCS5D01G523600	chr5D	95.455	66	2	1	2022	2087	542272450	542272386	1.370000e-18	104.0
3	TraesCS5D01G523600	chr4A	90.917	2180	94	29	134	2290	695911340	695913438	0.000000e+00	2833.0
4	TraesCS5D01G523600	chr4A	95.280	1695	71	8	833	2523	625863265	625861576	0.000000e+00	2678.0
5	TraesCS5D01G523600	chr4A	83.453	417	29	15	2361	2739	695913434	695913848	4.440000e-93	351.0
6	TraesCS5D01G523600	chr4A	78.959	442	58	19	21	449	484366857	484367276	4.600000e-68	268.0
7	TraesCS5D01G523600	chr4A	76.071	560	66	38	45	592	625864084	625863581	2.170000e-56	230.0
8	TraesCS5D01G523600	chr4A	89.706	68	3	1	618	681	625863579	625863512	1.790000e-12	84.2
9	TraesCS5D01G523600	chr5B	94.692	1639	78	9	823	2455	557137428	557139063	0.000000e+00	2536.0
10	TraesCS5D01G523600	chr5B	90.368	353	12	10	2461	2801	557139137	557139479	7.120000e-121	444.0
11	TraesCS5D01G523600	chr5B	81.628	430	48	14	45	457	557150793	557150378	7.480000e-86	327.0
12	TraesCS5D01G523600	chr5B	79.276	497	64	25	1	465	557148842	557148353	7.530000e-81	311.0
13	TraesCS5D01G523600	chr5B	85.425	247	19	6	45	287	557158043	557158276	1.000000e-59	241.0
14	TraesCS5D01G523600	chr5B	75.702	605	53	46	24	592	557136578	557137124	1.690000e-52	217.0
15	TraesCS5D01G523600	chr1B	89.811	1217	103	13	821	2025	654922929	654921722	0.000000e+00	1541.0
16	TraesCS5D01G523600	chr1B	81.853	259	37	6	2085	2339	654921843	654921591	2.830000e-50	209.0
17	TraesCS5D01G523600	chr1D	89.655	754	72	2	1059	1812	204988446	204987699	0.000000e+00	955.0
18	TraesCS5D01G523600	chr6A	80.268	522	56	23	438	948	289826088	289826573	1.600000e-92	350.0
19	TraesCS5D01G523600	chr2A	79.279	444	52	14	19	449	435609323	435609739	9.880000e-70	274.0
20	TraesCS5D01G523600	chr6B	80.460	261	19	15	1	239	81732385	81732635	1.330000e-38	171.0
21	TraesCS5D01G523600	chr7B	73.934	422	49	35	277	681	31433233	31432856	2.280000e-21	113.0
22	TraesCS5D01G523600	chr5A	95.588	68	3	0	2022	2089	130535256	130535323	2.950000e-20	110.0
23	TraesCS5D01G523600	chr7D	95.522	67	2	1	2022	2087	186402882	186402948	3.820000e-19	106.0
24	TraesCS5D01G523600	chr1A	95.455	66	3	0	2022	2087	454330747	454330812	3.820000e-19	106.0
25	TraesCS5D01G523600	chr2B	89.873	79	6	1	2009	2087	752834948	752835024	1.780000e-17	100.0

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	TraesCS5D01G523600	chr5D	543338384	543341184	2800	False	5173.000000	5173	100.000000	1	2801	1	chr5D.!!$F1	2800
1	TraesCS5D01G523600	chr4A	695911340	695913848	2508	False	1592.000000	2833	87.185000	134	2739	2	chr4A.!!$F2	2605
2	TraesCS5D01G523600	chr4A	625861576	625864084	2508	True	997.400000	2678	87.019000	45	2523	3	chr4A.!!$R1	2478
3	TraesCS5D01G523600	chr5B	557136578	557139479	2901	False	1065.666667	2536	86.920667	24	2801	3	chr5B.!!$F2	2777
4	TraesCS5D01G523600	chr5B	557148353	557150793	2440	True	319.000000	327	80.452000	1	465	2	chr5B.!!$R1	464
5	TraesCS5D01G523600	chr1B	654921591	654922929	1338	True	875.000000	1541	85.832000	821	2339	2	chr1B.!!$R1	1518
6	TraesCS5D01G523600	chr1D	204987699	204988446	747	True	955.000000	955	89.655000	1059	1812	1	chr1D.!!$R1	753

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
383	409	0.243365	TGGATTTGAATGCCACGCAC	59.757	50.0	0.0	0.0	43.04	5.34	F
797	2616	0.950116	GCTCATGTGATTGCCTAGCC	59.050	55.0	0.0	0.0	0.00	3.93	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1599	3573	0.664466	TCAAGAGCGTTGACTCTGCG	60.664	55.0	0.8	0.0	46.38	5.18	R
2455	4446	1.279496	TCAGAGGTGGGGATGAGTTG	58.721	55.0	0.0	0.0	0.00	3.16	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
262	277	5.244785	TCCAGTATGCGTGTCTTTAGTAG	57.755	43.478	0.00	0.00	31.97	2.57
272	290	5.107951	GCGTGTCTTTAGTAGTTCAACTGTC	60.108	44.000	0.00	0.00	0.00	3.51
308	327	5.659463	AGAAATCGATGCCTCTATCTATGC	58.341	41.667	0.00	0.00	0.00	3.14
366	392	3.071874	TCAGATTAGGTTGGTGCTTGG	57.928	47.619	0.00	0.00	0.00	3.61
383	409	0.243365	TGGATTTGAATGCCACGCAC	59.757	50.000	0.00	0.00	43.04	5.34
513	722	1.522258	GTGGCGATTGCTGTTTGTTTG	59.478	47.619	4.59	0.00	42.25	2.93
538	747	3.295093	TGTTCAGGAAATTGCCAGTTCA	58.705	40.909	4.92	0.00	0.00	3.18
567	777	5.257262	TGCTGCCATGTAAGGTTAAATGTA	58.743	37.500	0.00	0.00	28.30	2.29
570	1426	7.012894	TGCTGCCATGTAAGGTTAAATGTATAC	59.987	37.037	0.00	0.00	28.30	1.47
571	1427	7.521585	GCTGCCATGTAAGGTTAAATGTATACC	60.522	40.741	0.00	0.00	28.30	2.73
624	1480	9.450807	TTTCTCATTCGAAAAGAGTTTCATTTC	57.549	29.630	22.56	0.00	42.90	2.17
649	1509	6.101650	TCAACTGGGCTACATCATGTATAG	57.898	41.667	0.00	0.00	31.66	1.31
696	2511	8.589338	CAGAGTATTACCTAGGAATTGCTGTAT	58.411	37.037	17.98	0.00	0.00	2.29
697	2512	8.589338	AGAGTATTACCTAGGAATTGCTGTATG	58.411	37.037	17.98	0.00	0.00	2.39
698	2513	8.263854	AGTATTACCTAGGAATTGCTGTATGT	57.736	34.615	17.98	4.06	0.00	2.29
699	2514	8.714906	AGTATTACCTAGGAATTGCTGTATGTT	58.285	33.333	17.98	0.00	0.00	2.71
700	2515	9.991906	GTATTACCTAGGAATTGCTGTATGTTA	57.008	33.333	17.98	0.00	0.00	2.41
702	2517	8.958119	TTACCTAGGAATTGCTGTATGTTAAG	57.042	34.615	17.98	0.00	0.00	1.85
703	2518	6.357367	ACCTAGGAATTGCTGTATGTTAAGG	58.643	40.000	17.98	8.06	0.00	2.69
704	2519	6.157994	ACCTAGGAATTGCTGTATGTTAAGGA	59.842	38.462	17.98	0.00	0.00	3.36
705	2520	7.054124	CCTAGGAATTGCTGTATGTTAAGGAA	58.946	38.462	10.10	0.00	0.00	3.36
706	2521	7.721399	CCTAGGAATTGCTGTATGTTAAGGAAT	59.279	37.037	10.10	0.00	36.17	3.01
707	2522	7.961326	AGGAATTGCTGTATGTTAAGGAATT	57.039	32.000	0.00	2.36	44.18	2.17
708	2523	7.775120	AGGAATTGCTGTATGTTAAGGAATTG	58.225	34.615	0.00	0.00	42.35	2.32
731	2546	1.272212	CAACTGGGTTACATGGTTGCC	59.728	52.381	0.00	0.00	32.50	4.52
770	2589	7.201821	GCTGTATGTTAAGGAATTGGTTGCTAT	60.202	37.037	0.00	0.00	34.65	2.97
796	2615	1.964552	AGCTCATGTGATTGCCTAGC	58.035	50.000	0.00	0.00	0.00	3.42
797	2616	0.950116	GCTCATGTGATTGCCTAGCC	59.050	55.000	0.00	0.00	0.00	3.93
798	2617	1.476471	GCTCATGTGATTGCCTAGCCT	60.476	52.381	0.00	0.00	0.00	4.58
799	2618	2.224378	GCTCATGTGATTGCCTAGCCTA	60.224	50.000	0.00	0.00	0.00	3.93
801	2620	2.149578	CATGTGATTGCCTAGCCTAGC	58.850	52.381	0.00	0.00	0.00	3.42
900	2865	1.785041	ATGTTCCACGCACACAGCAC	61.785	55.000	0.00	0.00	46.13	4.40
924	2892	7.214449	CACGATGTTTCTCATACAAAACGAATC	59.786	37.037	0.00	0.00	38.03	2.52
982	2951	3.047796	CAGTGACACATTTCTGCTTTGC	58.952	45.455	8.59	0.00	0.00	3.68
983	2952	2.689471	AGTGACACATTTCTGCTTTGCA	59.311	40.909	8.59	0.00	36.92	4.08
1036	3009	1.145803	GTTCCGACGTCTTTCCAAGG	58.854	55.000	14.70	5.51	0.00	3.61
1599	3573	2.326550	CACCGTGCACGTCAAACC	59.673	61.111	34.81	0.00	37.74	3.27
1846	3824	4.100808	AGAGTCTTCTCCATACAAGATGCC	59.899	45.833	0.00	0.00	41.26	4.40
1859	3838	3.258372	ACAAGATGCCGAGAGTTTAGACA	59.742	43.478	0.00	0.00	0.00	3.41
1892	3871	5.128663	TGCTCCTTTAATTAATTCTTGGCCC	59.871	40.000	3.39	1.49	0.00	5.80
1893	3872	5.736207	GCTCCTTTAATTAATTCTTGGCCCG	60.736	44.000	3.39	0.00	0.00	6.13
1928	3909	6.611381	TGATGACTACTTTGTGCTATTTTGC	58.389	36.000	0.00	0.00	0.00	3.68
1998	3979	4.340381	GCAAGATCCTGCCATGTTATTCTT	59.660	41.667	4.87	0.00	36.25	2.52
2113	4094	5.107491	GCTACTTTGTGCTATTTTGGTTTGC	60.107	40.000	0.00	0.00	0.00	3.68
2126	4107	5.389859	TTTGGTTTGCGATGATCAGATTT	57.610	34.783	0.09	0.00	0.00	2.17
2144	4125	4.331717	AGATTTTGGTAATAAGCCGTCACG	59.668	41.667	0.00	0.00	0.00	4.35
2214	4195	7.494211	TCTACTTCAGTTTTGCTGTGTACTAA	58.506	34.615	0.00	0.00	45.23	2.24
2455	4446	6.672147	ACATGCAACTGAAAGAACTATGTTC	58.328	36.000	0.00	2.54	37.43	3.18
2484	4544	1.425448	CCCACCTCTGAACCCTTTCTT	59.575	52.381	0.00	0.00	32.36	2.52
2488	4548	4.207165	CACCTCTGAACCCTTTCTTGAAA	58.793	43.478	0.00	0.00	32.36	2.69
2491	4551	4.279420	CCTCTGAACCCTTTCTTGAAAAGG	59.721	45.833	9.18	9.18	46.24	3.11
2503	4563	4.717877	TCTTGAAAAGGAATCTGCTGTGA	58.282	39.130	0.00	0.00	46.24	3.58
2504	4564	5.319453	TCTTGAAAAGGAATCTGCTGTGAT	58.681	37.500	0.00	0.00	46.24	3.06
2505	4565	5.771666	TCTTGAAAAGGAATCTGCTGTGATT	59.228	36.000	0.00	0.00	46.24	2.57
2549	4624	6.183360	GCTGTTCCTTTATCTCCTTTCATGTC	60.183	42.308	0.00	0.00	0.00	3.06
2592	4667	0.911769	TCCTGCGGGATCTGATTGTT	59.088	50.000	11.27	0.00	36.57	2.83
2702	4798	0.178973	TTGTCGAGGGTCAGGTCTCA	60.179	55.000	0.00	0.00	0.00	3.27
2778	4882	7.639113	TTTCTCTCTTTGGCAAGTTAAAAGA	57.361	32.000	0.00	0.00	37.54	2.52

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
131	138	4.593864	GGGCGGAGGATCGAGCAC	62.594	72.222	1.84	0.00	40.44	4.40
262	277	5.227908	TCAGATTAACCTCGACAGTTGAAC	58.772	41.667	6.38	0.00	0.00	3.18
272	290	5.107683	GCATCGATTTCTCAGATTAACCTCG	60.108	44.000	0.00	0.00	0.00	4.63
366	392	0.109781	ACGTGCGTGGCATTCAAATC	60.110	50.000	0.00	0.00	41.91	2.17
383	409	1.135731	GAGCAGTCAGTCTCCGACG	59.864	63.158	0.00	0.00	38.46	5.12
454	496	6.914757	GGCATTTGCATGAAGTAGAATTCTAC	59.085	38.462	30.31	30.31	44.69	2.59
513	722	4.886579	ACTGGCAATTTCCTGAACAAATC	58.113	39.130	7.96	0.00	0.00	2.17
538	747	2.304092	CCTTACATGGCAGCATCACAT	58.696	47.619	0.00	0.00	0.00	3.21
567	777	4.320023	TGTGCAGAACATACAAACGGTAT	58.680	39.130	0.00	0.00	43.53	2.73
570	1426	2.548057	ACTGTGCAGAACATACAAACGG	59.452	45.455	6.17	0.00	38.39	4.44
571	1427	3.878086	ACTGTGCAGAACATACAAACG	57.122	42.857	6.17	0.00	38.39	3.60
624	1480	3.548770	ACATGATGTAGCCCAGTTGATG	58.451	45.455	0.00	0.00	0.00	3.07
649	1509	5.871524	TCTGAAGAGAAATGTGTCACTATGC	59.128	40.000	4.27	0.00	0.00	3.14
696	2511	4.148838	CCCAGTTGGTCAATTCCTTAACA	58.851	43.478	0.00	0.00	0.00	2.41
697	2512	4.783764	CCCAGTTGGTCAATTCCTTAAC	57.216	45.455	0.00	0.00	0.00	2.01
731	2546	0.732571	ATACAGCAACCGCCGAAATG	59.267	50.000	0.00	0.00	39.83	2.32
770	2589	5.933617	AGGCAATCACATGAGCTAGAATTA	58.066	37.500	0.00	0.00	0.00	1.40
796	2615	3.895232	AACCAGTATGACACAGCTAGG	57.105	47.619	0.00	0.00	39.69	3.02
797	2616	3.372206	GCAAACCAGTATGACACAGCTAG	59.628	47.826	0.00	0.00	39.69	3.42
798	2617	3.007940	AGCAAACCAGTATGACACAGCTA	59.992	43.478	0.00	0.00	39.69	3.32
799	2618	2.154462	GCAAACCAGTATGACACAGCT	58.846	47.619	0.00	0.00	39.69	4.24
801	2620	3.141398	ACAGCAAACCAGTATGACACAG	58.859	45.455	0.00	0.00	39.69	3.66
888	2853	1.436195	AAACATCGTGCTGTGTGCGT	61.436	50.000	0.00	0.00	46.63	5.24
900	2865	7.456253	AGATTCGTTTTGTATGAGAAACATCG	58.544	34.615	0.00	0.00	40.07	3.84
924	2892	2.886862	AGCTCGGTTCATCAGATGAG	57.113	50.000	12.97	2.77	40.94	2.90
982	2951	1.466025	ATTGCACCACCTTGGCTGTG	61.466	55.000	0.00	5.20	42.67	3.66
983	2952	1.152483	ATTGCACCACCTTGGCTGT	60.152	52.632	0.00	0.00	42.67	4.40
1036	3009	1.748122	CTGGGCTCATGGTGAGTGC	60.748	63.158	8.58	0.00	45.94	4.40
1599	3573	0.664466	TCAAGAGCGTTGACTCTGCG	60.664	55.000	0.80	0.00	46.38	5.18
1846	3824	6.809196	AGCATAAGAAAGTGTCTAAACTCTCG	59.191	38.462	0.00	0.00	34.56	4.04
1892	3871	5.312120	AGTAGTCATCAAACCTAGACACG	57.688	43.478	0.00	0.00	33.56	4.49
1893	3872	6.929606	ACAAAGTAGTCATCAAACCTAGACAC	59.070	38.462	0.00	0.00	33.56	3.67
1928	3909	4.375272	ACCAGAATCTGATTATCACAGCG	58.625	43.478	12.53	0.00	35.61	5.18
2113	4094	7.301054	GGCTTATTACCAAAATCTGATCATCG	58.699	38.462	0.00	0.00	0.00	3.84
2126	4107	2.012937	CCGTGACGGCTTATTACCAA	57.987	50.000	12.53	0.00	41.17	3.67
2214	4195	6.004574	AGCTCAACATGATATCAAGATGCAT	58.995	36.000	14.59	0.00	0.00	3.96
2251	4233	6.684613	GCATAAGCATCATTCAAGGGAAACAT	60.685	38.462	0.00	0.00	41.58	2.71
2412	4403	3.760738	TGTACCATGTCTGAAAATGCCA	58.239	40.909	0.00	0.00	0.00	4.92
2421	4412	3.337358	TCAGTTGCATGTACCATGTCTG	58.663	45.455	6.13	10.99	0.00	3.51
2455	4446	1.279496	TCAGAGGTGGGGATGAGTTG	58.721	55.000	0.00	0.00	0.00	3.16
2484	4544	7.828717	TGTATAATCACAGCAGATTCCTTTTCA	59.171	33.333	2.84	0.00	38.97	2.69
2488	4548	6.543831	GGTTGTATAATCACAGCAGATTCCTT	59.456	38.462	2.84	0.00	38.97	3.36
2491	4551	6.989169	AGAGGTTGTATAATCACAGCAGATTC	59.011	38.462	2.84	0.00	38.97	2.52
2503	4563	7.951591	ACAGCAAAAACAAGAGGTTGTATAAT	58.048	30.769	0.00	0.00	46.68	1.28
2504	4564	7.341445	ACAGCAAAAACAAGAGGTTGTATAA	57.659	32.000	0.00	0.00	46.68	0.98
2505	4565	6.952773	ACAGCAAAAACAAGAGGTTGTATA	57.047	33.333	0.00	0.00	46.68	1.47
2549	4624	6.835819	AATCATCATTGAGGGCATATGAAG	57.164	37.500	6.97	0.00	34.73	3.02
2592	4667	4.997395	CAGCAAAGCTAGGTACTTCTTTCA	59.003	41.667	0.00	0.00	41.75	2.69
2702	4798	5.511202	CCATTTGCACATAACAAAACTCCCT	60.511	40.000	0.00	0.00	40.19	4.20
2762	4866	3.769844	TGTGGGTCTTTTAACTTGCCAAA	59.230	39.130	0.00	0.00	0.00	3.28
2778	4882	2.172505	TGATGCCGAAATCTATGTGGGT	59.827	45.455	0.00	0.00	0.00	4.51

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.