AutoCloner

Multiple sequence alignment - TraesCS7D01G136500

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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	TraesCS7D01G136500	chr7D	100.000	4095	0	0	1	4095	87748010	87752104	0.000000e+00	7563.0
1	TraesCS7D01G136500	chr7D	95.506	623	8	2	3475	4095	2014988	2015592	0.000000e+00	977.0
2	TraesCS7D01G136500	chr7D	90.772	531	34	8	138	668	87769819	87769304	0.000000e+00	695.0
3	TraesCS7D01G136500	chr7D	86.833	281	33	2	2909	3189	87689471	87689195	1.110000e-80	311.0
4	TraesCS7D01G136500	chr7B	92.702	3138	113	48	395	3445	36509582	36506474	0.000000e+00	4420.0
5	TraesCS7D01G136500	chr7B	92.780	277	19	1	2913	3189	36505074	36504799	2.290000e-107	399.0
6	TraesCS7D01G136500	chr7B	76.703	279	42	16	205	472	481348996	481348730	2.570000e-27	134.0
7	TraesCS7D01G136500	chr7B	91.860	86	7	0	3456	3541	568794659	568794574	2.000000e-23	121.0
8	TraesCS7D01G136500	chr7B	94.231	52	3	0	3190	3241	36504780	36504729	3.390000e-11	80.5
9	TraesCS7D01G136500	chr7A	95.352	1678	53	9	1652	3310	89074009	89072338	0.000000e+00	2643.0
10	TraesCS7D01G136500	chr7A	95.257	1476	52	7	131	1597	89075566	89074100	0.000000e+00	2322.0
11	TraesCS7D01G136500	chr7A	95.833	384	14	2	3465	3848	44436918	44436537	1.620000e-173	619.0
12	TraesCS7D01G136500	chr7A	86.378	323	26	8	3464	3786	533507571	533507267	1.820000e-88	337.0
13	TraesCS7D01G136500	chr7A	96.364	165	4	1	3933	4095	44436331	44436167	1.880000e-68	270.0
14	TraesCS7D01G136500	chr7A	91.282	195	14	2	3881	4075	533507216	533507025	3.140000e-66	263.0
15	TraesCS7D01G136500	chr7A	88.406	138	10	4	1	132	89075894	89075757	1.180000e-35	161.0
16	TraesCS7D01G136500	chr3D	97.235	651	12	5	3449	4095	289809709	289810357	0.000000e+00	1098.0
17	TraesCS7D01G136500	chr1D	97.634	634	12	2	3464	4095	12310534	12309902	0.000000e+00	1085.0
18	TraesCS7D01G136500	chr1D	79.585	289	46	11	3754	4037	228022649	228022369	1.160000e-45	195.0
19	TraesCS7D01G136500	chr1D	80.000	175	23	11	3745	3915	208190484	208190650	7.190000e-23	119.0
20	TraesCS7D01G136500	chr6A	90.808	631	49	5	3464	4092	437496469	437497092	0.000000e+00	835.0
21	TraesCS7D01G136500	chr2A	89.348	629	56	5	3466	4092	385326956	385327575	0.000000e+00	780.0
22	TraesCS7D01G136500	chr2A	77.193	285	42	14	198	474	564615495	564615764	1.190000e-30	145.0
23	TraesCS7D01G136500	chrUn	86.463	458	36	10	3464	3921	71655529	71655098	2.860000e-131	479.0
24	TraesCS7D01G136500	chr4B	82.222	225	29	7	198	418	67849706	67849489	2.510000e-42	183.0
25	TraesCS7D01G136500	chr4B	93.590	78	5	0	3464	3541	13296951	13296874	2.590000e-22	117.0
26	TraesCS7D01G136500	chr6D	77.705	305	44	11	191	488	453470526	453470239	9.110000e-37	165.0
27	TraesCS7D01G136500	chr5A	80.617	227	32	7	201	421	23590543	23590763	9.110000e-37	165.0
28	TraesCS7D01G136500	chr3A	88.060	134	7	2	8	132	651596566	651596699	2.550000e-32	150.0
29	TraesCS7D01G136500	chr5B	76.596	282	42	19	205	474	510815799	510816068	2.570000e-27	134.0
30	TraesCS7D01G136500	chr1B	91.667	96	8	0	3946	4041	605008672	605008767	2.570000e-27	134.0

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	TraesCS7D01G136500	chr7D	87748010	87752104	4094	False	7563.000000	7563	100.000000	1	4095	1	chr7D.!!$F2	4094
1	TraesCS7D01G136500	chr7D	2014988	2015592	604	False	977.000000	977	95.506000	3475	4095	1	chr7D.!!$F1	620
2	TraesCS7D01G136500	chr7D	87769304	87769819	515	True	695.000000	695	90.772000	138	668	1	chr7D.!!$R2	530
3	TraesCS7D01G136500	chr7B	36504729	36509582	4853	True	1633.166667	4420	93.237667	395	3445	3	chr7B.!!$R3	3050
4	TraesCS7D01G136500	chr7A	89072338	89075894	3556	True	1708.666667	2643	93.005000	1	3310	3	chr7A.!!$R2	3309
5	TraesCS7D01G136500	chr7A	44436167	44436918	751	True	444.500000	619	96.098500	3465	4095	2	chr7A.!!$R1	630
6	TraesCS7D01G136500	chr7A	533507025	533507571	546	True	300.000000	337	88.830000	3464	4075	2	chr7A.!!$R3	611
7	TraesCS7D01G136500	chr3D	289809709	289810357	648	False	1098.000000	1098	97.235000	3449	4095	1	chr3D.!!$F1	646
8	TraesCS7D01G136500	chr1D	12309902	12310534	632	True	1085.000000	1085	97.634000	3464	4095	1	chr1D.!!$R1	631
9	TraesCS7D01G136500	chr6A	437496469	437497092	623	False	835.000000	835	90.808000	3464	4092	1	chr6A.!!$F1	628
10	TraesCS7D01G136500	chr2A	385326956	385327575	619	False	780.000000	780	89.348000	3466	4092	1	chr2A.!!$F1	626

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
234	433	0.247736	ATGAGCTCGGGTGAACAGTC	59.752	55.0	9.64	0.0	0.00	3.51	F
1620	1889	0.606604	AGTTCGCCACCACGACTTAT	59.393	50.0	0.00	0.0	42.78	1.73	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2011	2323	1.008424	CGGGAGGTCGACGATGATG	60.008	63.158	9.92	0.00	0.00	3.07	R
3461	3792	0.313043	ACGTGCACGCTTACTAGTGT	59.687	50.000	37.35	12.57	45.74	3.55	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
112	119	5.788450	AGTTGATCTTGTTCTGACGATCTT	58.212	37.500	0.00	0.00	34.75	2.40
113	120	5.866633	AGTTGATCTTGTTCTGACGATCTTC	59.133	40.000	0.00	0.00	34.75	2.87
127	134	3.879427	CGATCTTCTCGCTACGAATTCT	58.121	45.455	3.52	0.00	41.14	2.40
193	392	0.647410	CTAGCACAAATCGGACGCAG	59.353	55.000	0.00	0.00	0.00	5.18
206	405	2.689646	GGACGCAGCTATTCTAATCCC	58.310	52.381	0.00	0.00	0.00	3.85
234	433	0.247736	ATGAGCTCGGGTGAACAGTC	59.752	55.000	9.64	0.00	0.00	3.51
324	527	6.094603	TGTTTGTTGGCTTGCAAAATTACATT	59.905	30.769	0.00	0.00	36.51	2.71
353	556	0.801872	CATTCGTGGAAATCGTGGCA	59.198	50.000	0.00	0.00	0.00	4.92
502	714	8.336080	GGAAAATATTTGAAAGCTAGGAGTACG	58.664	37.037	0.39	0.00	0.00	3.67
623	862	7.765819	AGGTTATACAACTGGGAACGTTATAAC	59.234	37.037	0.00	8.35	33.52	1.89
777	1044	1.741528	ACAAACGACCCAAAACGACT	58.258	45.000	0.00	0.00	0.00	4.18
852	1120	1.617947	CCCTCTTTCCACCTCCTCCG	61.618	65.000	0.00	0.00	0.00	4.63
1109	1378	3.272334	GCGGGCGCAGGATTACAG	61.272	66.667	10.83	0.00	41.49	2.74
1407	1676	4.353437	AACGTCTCCGGTGGCGTC	62.353	66.667	33.07	7.56	38.78	5.19
1600	1869	1.452801	CCCACCCACAAAGGTACGT	59.547	57.895	0.00	0.00	38.39	3.57
1604	1873	2.224354	CCACCCACAAAGGTACGTAGTT	60.224	50.000	0.00	0.00	35.28	2.24
1606	1875	2.288395	ACCCACAAAGGTACGTAGTTCG	60.288	50.000	0.00	0.00	38.79	3.95
1609	1878	1.340889	ACAAAGGTACGTAGTTCGCCA	59.659	47.619	0.00	0.00	37.78	5.69
1620	1889	0.606604	AGTTCGCCACCACGACTTAT	59.393	50.000	0.00	0.00	42.78	1.73
1990	2302	2.049802	TTCGACTTCACGCCCGTC	60.050	61.111	0.00	0.00	0.00	4.79
2218	2530	0.462759	GGAAGATCACCGGGAAGCTG	60.463	60.000	6.32	0.00	0.00	4.24
2233	2545	1.666872	GCTGAACCCGCACTACGTT	60.667	57.895	0.00	0.00	41.42	3.99
2237	2549	1.500512	GAACCCGCACTACGTTTGCA	61.501	55.000	18.64	0.00	40.20	4.08
2272	2584	2.003548	GAGCCCCATGGAGTTCCCT	61.004	63.158	15.22	0.00	35.38	4.20
2515	2827	3.047877	GTGCCCTTCGACAACCGG	61.048	66.667	0.00	0.00	39.14	5.28
2722	3034	2.180159	AAATGGGCGAGCACTACGGT	62.180	55.000	0.00	0.00	0.00	4.83
3043	3355	0.034616	GTCTCTTGCAGGCTGTCACT	59.965	55.000	17.16	0.00	0.00	3.41
3100	3412	3.067461	ACTCCTCGTGCTTATGATCTGTC	59.933	47.826	0.00	0.00	0.00	3.51
3226	3557	1.997669	ACGAAGGAATTGCTCTCGAC	58.002	50.000	25.81	7.75	0.00	4.20
3249	3580	6.221659	ACCAACTACAGACTTACACTTTAGC	58.778	40.000	0.00	0.00	0.00	3.09
3262	3593	8.813951	ACTTACACTTTAGCTATACTTCAGGTT	58.186	33.333	0.00	0.00	0.00	3.50
3263	3594	9.303537	CTTACACTTTAGCTATACTTCAGGTTC	57.696	37.037	0.00	0.00	0.00	3.62
3264	3595	7.241042	ACACTTTAGCTATACTTCAGGTTCA	57.759	36.000	0.00	0.00	0.00	3.18
3265	3596	7.324178	ACACTTTAGCTATACTTCAGGTTCAG	58.676	38.462	0.00	0.00	0.00	3.02
3266	3597	6.758886	CACTTTAGCTATACTTCAGGTTCAGG	59.241	42.308	0.00	0.00	0.00	3.86
3267	3598	6.440965	ACTTTAGCTATACTTCAGGTTCAGGT	59.559	38.462	0.00	0.00	0.00	4.00
3315	3646	3.723764	CGATTCTGTTTTCCAAACACACG	59.276	43.478	0.00	0.04	0.00	4.49
3317	3648	1.187715	CTGTTTTCCAAACACACGCG	58.812	50.000	3.53	3.53	0.00	6.01
3318	3649	0.522180	TGTTTTCCAAACACACGCGT	59.478	45.000	5.58	5.58	0.00	6.01
3319	3650	1.736126	TGTTTTCCAAACACACGCGTA	59.264	42.857	13.44	0.00	0.00	4.42
3320	3651	2.103388	GTTTTCCAAACACACGCGTAC	58.897	47.619	13.44	0.00	0.00	3.67
3321	3652	1.366679	TTTCCAAACACACGCGTACA	58.633	45.000	13.44	0.00	0.00	2.90
3322	3653	1.366679	TTCCAAACACACGCGTACAA	58.633	45.000	13.44	0.00	0.00	2.41
3323	3654	1.366679	TCCAAACACACGCGTACAAA	58.633	45.000	13.44	0.00	0.00	2.83
3363	3694	2.120232	CAGCATAGCTAGTGCGTACAC	58.880	52.381	17.04	0.00	46.86	2.90
3404	3735	1.335810	AGAGCATTAATGGTGCATGCG	59.664	47.619	24.07	0.00	46.62	4.73
3417	3748	2.246841	CATGCGTGCTTGTGGAGAA	58.753	52.632	0.00	0.00	0.00	2.87
3428	3759	7.042051	GCGTGCTTGTGGAGAATAATTAAGATA	60.042	37.037	0.00	0.00	0.00	1.98
3429	3760	8.491152	CGTGCTTGTGGAGAATAATTAAGATAG	58.509	37.037	0.00	0.00	0.00	2.08
3445	3776	7.507733	TTAAGATAGACCTAACGACCTCATC	57.492	40.000	0.00	0.00	0.00	2.92
3447	3778	6.436738	AGATAGACCTAACGACCTCATCTA	57.563	41.667	0.00	0.00	0.00	1.98
3448	3779	7.023171	AGATAGACCTAACGACCTCATCTAT	57.977	40.000	0.00	0.00	32.06	1.98
3449	3780	7.107542	AGATAGACCTAACGACCTCATCTATC	58.892	42.308	9.37	9.37	41.71	2.08
3452	3783	5.533154	AGACCTAACGACCTCATCTATCTTG	59.467	44.000	0.00	0.00	0.00	3.02
3453	3784	5.202004	ACCTAACGACCTCATCTATCTTGT	58.798	41.667	0.00	0.00	0.00	3.16
3455	3786	7.005296	ACCTAACGACCTCATCTATCTTGTAT	58.995	38.462	0.00	0.00	0.00	2.29
3457	3788	9.011095	CCTAACGACCTCATCTATCTTGTATTA	57.989	37.037	0.00	0.00	0.00	0.98
3511	3854	7.900864	CGCACGTCTTCATTAACACATAAATTA	59.099	33.333	0.00	0.00	0.00	1.40

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
90	97	5.866633	AGAAGATCGTCAGAACAAGATCAAC	59.133	40.000	11.35	1.43	41.24	3.18
173	372	0.245266	TGCGTCCGATTTGTGCTAGA	59.755	50.000	0.00	0.00	0.00	2.43
193	392	3.944055	TGAGCTCGGGATTAGAATAGC	57.056	47.619	9.64	0.00	0.00	2.97
293	496	2.681848	TGCAAGCCAACAAACATTTTGG	59.318	40.909	3.82	0.00	44.54	3.28
324	527	2.998316	TCCACGAATGTCATATGGCA	57.002	45.000	13.32	13.32	0.00	4.92
367	574	7.011295	TGTTTGAAAAGAACATTTTGGAGCATC	59.989	33.333	0.00	0.00	32.44	3.91
423	635	6.766944	ACATTCATGAAAAATGTGGCAAGAAA	59.233	30.769	13.09	0.00	43.76	2.52
424	636	6.289834	ACATTCATGAAAAATGTGGCAAGAA	58.710	32.000	13.09	0.00	43.76	2.52
425	637	5.856156	ACATTCATGAAAAATGTGGCAAGA	58.144	33.333	13.09	0.00	43.76	3.02
426	638	5.697178	TGACATTCATGAAAAATGTGGCAAG	59.303	36.000	15.99	0.00	45.02	4.01
427	639	5.608449	TGACATTCATGAAAAATGTGGCAA	58.392	33.333	15.99	0.36	45.02	4.52
428	640	5.211174	TGACATTCATGAAAAATGTGGCA	57.789	34.783	15.99	13.01	45.02	4.92
547	759	7.294676	TCAATTTGAGTACAGACATTGATCG	57.705	36.000	0.00	0.00	30.79	3.69
708	967	4.770874	CGGAATTGGACGCCGGGT	62.771	66.667	2.18	0.00	41.29	5.28
1109	1378	1.603172	CCTCCTCGTCATCGCCATTAC	60.603	57.143	0.00	0.00	36.96	1.89
1407	1676	2.108362	GGGTATCCGGCGAAGGTG	59.892	66.667	9.30	0.00	0.00	4.00
1600	1869	1.246649	TAAGTCGTGGTGGCGAACTA	58.753	50.000	0.00	0.00	42.82	2.24
1604	1873	1.138036	CGATAAGTCGTGGTGGCGA	59.862	57.895	0.00	0.00	42.78	5.54
1677	1989	2.434658	ATCCTTGACGCAGCACACGA	62.435	55.000	0.00	0.00	0.00	4.35
1765	2077	2.567049	GTCAGCACGTCGTAGGCT	59.433	61.111	4.49	4.49	38.70	4.58
1990	2302	1.687494	GCCGCTTCTCGCAGTTGTAG	61.687	60.000	0.00	0.00	39.08	2.74
2011	2323	1.008424	CGGGAGGTCGACGATGATG	60.008	63.158	9.92	0.00	0.00	3.07
2012	2324	2.846652	GCGGGAGGTCGACGATGAT	61.847	63.158	9.92	0.00	0.00	2.45
2122	2434	3.011517	AGCTGGAAGATGGCCCGT	61.012	61.111	0.00	0.00	34.07	5.28
2218	2530	1.205820	GCAAACGTAGTGCGGGTTC	59.794	57.895	5.41	0.00	45.00	3.62
3043	3355	1.144691	TCATCACAAGAACCACCCCA	58.855	50.000	0.00	0.00	0.00	4.96
3100	3412	7.069085	ACAATGATACAATCCCCAGAGATTTTG	59.931	37.037	0.00	0.00	34.19	2.44
3139	3451	3.609853	TCAGCAAATGTAGCACCCTAAG	58.390	45.455	0.00	0.00	0.00	2.18
3226	3557	6.456501	AGCTAAAGTGTAAGTCTGTAGTTGG	58.543	40.000	0.00	0.00	0.00	3.77
3249	3580	5.419155	TCAGTCACCTGAACCTGAAGTATAG	59.581	44.000	0.00	0.00	44.67	1.31
3262	3593	8.768397	ACCATAGTAAAATATTCAGTCACCTGA	58.232	33.333	0.00	0.00	45.95	3.86
3263	3594	8.964476	ACCATAGTAAAATATTCAGTCACCTG	57.036	34.615	0.00	0.00	40.25	4.00
3264	3595	8.768397	TGACCATAGTAAAATATTCAGTCACCT	58.232	33.333	0.00	0.00	0.00	4.00
3265	3596	8.958119	TGACCATAGTAAAATATTCAGTCACC	57.042	34.615	0.00	0.00	0.00	4.02
3266	3597	9.601217	ACTGACCATAGTAAAATATTCAGTCAC	57.399	33.333	0.00	0.00	38.41	3.67
3275	3606	8.692710	ACAGAATCGACTGACCATAGTAAAATA	58.307	33.333	9.80	0.00	40.63	1.40
3277	3608	6.931838	ACAGAATCGACTGACCATAGTAAAA	58.068	36.000	9.80	0.00	40.63	1.52
3278	3609	6.525578	ACAGAATCGACTGACCATAGTAAA	57.474	37.500	9.80	0.00	40.63	2.01
3282	3613	5.292101	GGAAAACAGAATCGACTGACCATAG	59.708	44.000	9.80	0.00	40.63	2.23
3298	3629	1.187715	CGCGTGTGTTTGGAAAACAG	58.812	50.000	5.82	0.00	0.00	3.16
3315	3646	3.311106	TGCAGTAGTGTACTTTGTACGC	58.689	45.455	11.95	11.95	36.76	4.42
3317	3648	4.688879	TGCATGCAGTAGTGTACTTTGTAC	59.311	41.667	18.46	1.33	36.76	2.90
3318	3649	4.888917	TGCATGCAGTAGTGTACTTTGTA	58.111	39.130	18.46	0.00	36.76	2.41
3319	3650	3.738982	TGCATGCAGTAGTGTACTTTGT	58.261	40.909	18.46	0.00	36.76	2.83
3320	3651	4.655027	CATGCATGCAGTAGTGTACTTTG	58.345	43.478	26.69	10.67	36.76	2.77
3321	3652	4.952262	CATGCATGCAGTAGTGTACTTT	57.048	40.909	26.69	0.84	36.76	2.66
3370	3701	3.257561	CTCTCAATGGCCGCGTCG	61.258	66.667	4.92	0.00	0.00	5.12
3371	3702	3.567797	GCTCTCAATGGCCGCGTC	61.568	66.667	4.92	0.00	0.00	5.19
3372	3703	3.687321	ATGCTCTCAATGGCCGCGT	62.687	57.895	4.92	0.00	0.00	6.01
3373	3704	1.159713	TAATGCTCTCAATGGCCGCG	61.160	55.000	0.00	0.00	0.00	6.46
3374	3705	1.024271	TTAATGCTCTCAATGGCCGC	58.976	50.000	0.00	0.00	0.00	6.53
3375	3706	2.030540	CCATTAATGCTCTCAATGGCCG	60.031	50.000	10.11	0.00	41.53	6.13
3376	3707	3.655276	CCATTAATGCTCTCAATGGCC	57.345	47.619	10.11	0.00	41.53	5.36
3404	3735	9.547753	TCTATCTTAATTATTCTCCACAAGCAC	57.452	33.333	0.00	0.00	0.00	4.40
3417	3748	9.584008	TGAGGTCGTTAGGTCTATCTTAATTAT	57.416	33.333	0.00	0.00	0.00	1.28
3428	3759	5.313280	AGATAGATGAGGTCGTTAGGTCT	57.687	43.478	0.00	0.00	0.00	3.85
3429	3760	5.299782	ACAAGATAGATGAGGTCGTTAGGTC	59.700	44.000	0.00	0.00	0.00	3.85
3452	3783	9.059485	GTGCACGCTTACTAGTGTATATAATAC	57.941	37.037	5.39	0.00	43.06	1.89
3453	3784	7.959109	CGTGCACGCTTACTAGTGTATATAATA	59.041	37.037	28.16	0.00	43.06	0.98
3455	3786	6.138088	CGTGCACGCTTACTAGTGTATATAA	58.862	40.000	28.16	0.00	43.06	0.98
3457	3788	4.036027	ACGTGCACGCTTACTAGTGTATAT	59.964	41.667	37.35	10.61	43.06	0.86
3460	3791	1.536766	ACGTGCACGCTTACTAGTGTA	59.463	47.619	37.35	0.00	43.06	2.90
3461	3792	0.313043	ACGTGCACGCTTACTAGTGT	59.687	50.000	37.35	12.57	45.74	3.55
3462	3793	0.708370	CACGTGCACGCTTACTAGTG	59.292	55.000	37.35	21.79	44.43	2.74

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.