AutoCloner

Multiple sequence alignment - TraesCS2D01G325600

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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	TraesCS2D01G325600	chr2D	100.000	4041	0	0	1	4041	419039497	419043537	0.000000e+00	7463.0
1	TraesCS2D01G325600	chr2B	92.130	1512	92	17	2100	3596	491182645	491184144	0.000000e+00	2108.0
2	TraesCS2D01G325600	chr2B	94.527	1352	46	12	761	2095	491181093	491182433	0.000000e+00	2061.0
3	TraesCS2D01G325600	chr2B	89.406	623	51	5	1	609	491180478	491181099	0.000000e+00	771.0
4	TraesCS2D01G325600	chr2B	84.419	353	33	10	3707	4041	159609709	159610057	1.080000e-85	327.0
5	TraesCS2D01G325600	chr2B	83.562	365	29	15	3706	4041	33527206	33527568	3.030000e-81	313.0
6	TraesCS2D01G325600	chr2A	95.217	1338	42	5	775	2095	570785407	570784075	0.000000e+00	2097.0
7	TraesCS2D01G325600	chr2A	92.741	1295	76	11	2103	3384	570783858	570782569	0.000000e+00	1855.0
8	TraesCS2D01G325600	chr2A	93.760	609	37	1	1	609	570786028	570785421	0.000000e+00	913.0
9	TraesCS2D01G325600	chr2A	85.753	365	21	10	3707	4041	761296577	761296940	1.380000e-94	357.0
10	TraesCS2D01G325600	chr2A	84.658	365	24	14	3707	4041	6099494	6099856	6.470000e-88	335.0
11	TraesCS2D01G325600	chr3A	80.641	873	120	34	996	1844	32151800	32150953	7.370000e-177	630.0
12	TraesCS2D01G325600	chr3B	79.725	873	135	26	995	1844	40245592	40244739	9.670000e-166	593.0
13	TraesCS2D01G325600	chr3B	86.895	351	27	8	3709	4041	22357389	22357040	3.810000e-100	375.0
14	TraesCS2D01G325600	chr3B	100.000	151	0	0	608	758	815207173	815207023	3.080000e-71	279.0
15	TraesCS2D01G325600	chr3B	80.636	346	40	12	3711	4041	726993769	726994102	4.040000e-60	243.0
16	TraesCS2D01G325600	chr3D	84.380	589	70	16	996	1569	23063560	23062979	3.530000e-155	558.0
17	TraesCS2D01G325600	chr3D	87.393	349	23	9	3707	4037	504417657	504418002	8.200000e-102	381.0
18	TraesCS2D01G325600	chr3D	100.000	149	0	0	610	758	30037540	30037392	3.980000e-70	276.0
19	TraesCS2D01G325600	chr3D	86.620	142	19	0	1703	1844	23062854	23062713	1.500000e-34	158.0
20	TraesCS2D01G325600	chr4A	85.279	394	54	3	1023	1414	580908038	580907647	1.750000e-108	403.0
21	TraesCS2D01G325600	chr4A	86.607	112	15	0	2760	2871	580906795	580906684	1.520000e-24	124.0
22	TraesCS2D01G325600	chr4D	85.025	394	55	3	1023	1414	21888296	21887905	8.140000e-107	398.0
23	TraesCS2D01G325600	chr4D	87.252	353	24	9	3707	4041	495899777	495900126	2.280000e-102	383.0
24	TraesCS2D01G325600	chr4D	82.740	365	19	18	3707	4041	508497257	508497607	6.610000e-73	285.0
25	TraesCS2D01G325600	chr4D	87.500	112	14	0	2760	2871	21887023	21886912	3.280000e-26	130.0
26	TraesCS2D01G325600	chr4B	85.063	395	53	6	1023	1414	32806104	32806495	8.140000e-107	398.0
27	TraesCS2D01G325600	chr4B	87.500	112	14	0	2760	2871	32807359	32807470	3.280000e-26	130.0
28	TraesCS2D01G325600	chr7B	85.352	355	33	10	3701	4037	739964274	739963921	2.310000e-92	350.0
29	TraesCS2D01G325600	chr7B	82.727	110	19	0	1728	1837	292829136	292829245	9.240000e-17	99.0
30	TraesCS2D01G325600	chrUn	85.205	365	22	15	3707	4041	212969397	212969759	2.990000e-91	346.0
31	TraesCS2D01G325600	chrUn	84.932	365	24	13	3707	4041	194718236	194718599	1.390000e-89	340.0
32	TraesCS2D01G325600	chrUn	84.932	365	24	13	3707	4041	205408978	205409341	1.390000e-89	340.0
33	TraesCS2D01G325600	chrUn	84.932	365	24	13	3707	4041	348485549	348485912	1.390000e-89	340.0
34	TraesCS2D01G325600	chr6B	85.227	352	34	8	3707	4041	698112197	698111847	2.990000e-91	346.0
35	TraesCS2D01G325600	chr6B	91.111	225	16	3	3695	3917	702380679	702380901	6.560000e-78	302.0
36	TraesCS2D01G325600	chr6B	100.000	149	0	0	610	758	222858720	222858572	3.980000e-70	276.0
37	TraesCS2D01G325600	chr6B	99.333	150	1	0	609	758	177745591	177745442	5.150000e-69	272.0
38	TraesCS2D01G325600	chr1A	84.658	365	25	14	3707	4041	512344700	512344337	6.470000e-88	335.0
39	TraesCS2D01G325600	chr5B	83.621	348	36	6	3707	4036	599308433	599308089	1.410000e-79	307.0
40	TraesCS2D01G325600	chr5B	98.718	156	2	0	603	758	642290435	642290590	1.110000e-70	278.0
41	TraesCS2D01G325600	chr7A	83.526	346	37	5	3711	4037	620364138	620364482	5.070000e-79	305.0
42	TraesCS2D01G325600	chr7A	99.338	151	1	0	608	758	89629665	89629515	1.430000e-69	274.0
43	TraesCS2D01G325600	chr7A	82.727	110	19	0	1728	1837	386357098	386356989	9.240000e-17	99.0
44	TraesCS2D01G325600	chr6D	100.000	151	0	0	609	759	237770719	237770569	3.080000e-71	279.0
45	TraesCS2D01G325600	chr6A	96.053	152	6	0	607	758	615695896	615696047	8.670000e-62	248.0
46	TraesCS2D01G325600	chr7D	95.302	149	6	1	610	757	30855650	30855502	6.750000e-58	235.0
47	TraesCS2D01G325600	chr7D	81.818	110	20	0	1728	1837	356897476	356897585	4.300000e-15	93.5

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	TraesCS2D01G325600	chr2D	419039497	419043537	4040	False	7463.000000	7463	100.0000	1	4041	1	chr2D.!!$F1	4040
1	TraesCS2D01G325600	chr2B	491180478	491184144	3666	False	1646.666667	2108	92.0210	1	3596	3	chr2B.!!$F3	3595
2	TraesCS2D01G325600	chr2A	570782569	570786028	3459	True	1621.666667	2097	93.9060	1	3384	3	chr2A.!!$R1	3383
3	TraesCS2D01G325600	chr3A	32150953	32151800	847	True	630.000000	630	80.6410	996	1844	1	chr3A.!!$R1	848
4	TraesCS2D01G325600	chr3B	40244739	40245592	853	True	593.000000	593	79.7250	995	1844	1	chr3B.!!$R2	849
5	TraesCS2D01G325600	chr3D	23062713	23063560	847	True	358.000000	558	85.5000	996	1844	2	chr3D.!!$R2	848
6	TraesCS2D01G325600	chr4A	580906684	580908038	1354	True	263.500000	403	85.9430	1023	2871	2	chr4A.!!$R1	1848
7	TraesCS2D01G325600	chr4D	21886912	21888296	1384	True	264.000000	398	86.2625	1023	2871	2	chr4D.!!$R1	1848
8	TraesCS2D01G325600	chr4B	32806104	32807470	1366	False	264.000000	398	86.2815	1023	2871	2	chr4B.!!$F1	1848

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
634	649	0.178301	TGCTACACAAACGACACCCA	59.822	50.0	0.00	0.00	0.00	4.51	F
752	767	0.179137	TCGCATCGGCTGTGAAGTAG	60.179	55.0	0.00	0.00	41.34	2.57	F
2529	2986	0.310854	GAACTTGGCCAACAGTTCGG	59.689	55.0	26.72	14.19	32.04	4.30	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2367	2824	0.741915	AACAAACACCCGCGTTCAAT	59.258	45.000	4.92	0.00	0.00	2.57	R
2643	3101	2.618794	TGAAAGTCCAAAATGGGCCAT	58.381	42.857	14.78	14.78	45.08	4.40	R
3453	3979	0.597568	CCCATTTTGTCAGCGCTTCA	59.402	50.000	7.50	7.70	0.00	3.02	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
126	137	4.520846	CAAATCTCGCCGCCGCAC	62.521	66.667	0.00	0.00	34.03	5.34
205	216	0.547712	CCCTTCCTCCCCTTCTGTCA	60.548	60.000	0.00	0.00	0.00	3.58
218	229	1.812922	CTGTCACCCTGATCTGCGC	60.813	63.158	0.00	0.00	0.00	6.09
259	271	1.327764	CGCTGAATTCTCGGGCTAAAC	59.672	52.381	7.05	0.00	0.00	2.01
283	295	5.681105	CCTGTTGTTTCGTACAGAATTGTTG	59.319	40.000	0.00	0.00	43.45	3.33
317	329	6.017109	AGTGAATGGTATTGTTATTGGATCGC	60.017	38.462	0.00	0.00	0.00	4.58
331	343	2.808598	ATCGCTGTGATCTACCCGT	58.191	52.632	0.00	0.00	28.49	5.28
372	384	2.808315	CACGTCGGATCCCCTCAG	59.192	66.667	6.06	0.00	0.00	3.35
425	437	4.842376	GGGAATTTCGTTACTTCGTTTTCG	59.158	41.667	0.00	0.00	45.64	3.46
471	486	4.060900	GCAGATTAGATCCGATGCTTTGA	58.939	43.478	0.00	0.00	0.00	2.69
513	528	3.157949	TCGGATATGCGGGGCACA	61.158	61.111	16.98	0.00	43.04	4.57
560	575	8.044309	TGTTATTTGTGCCAGTGTACAGTATAT	58.956	33.333	2.08	0.00	38.37	0.86
601	616	6.184789	TGTTTTCTGTATTTGGGGTCTATCC	58.815	40.000	0.00	0.00	0.00	2.59
609	624	3.622166	TTGGGGTCTATCCGAAAGAAC	57.378	47.619	0.00	0.00	37.00	3.01
610	625	2.542550	TGGGGTCTATCCGAAAGAACA	58.457	47.619	0.00	0.00	37.00	3.18
611	626	2.500098	TGGGGTCTATCCGAAAGAACAG	59.500	50.000	0.00	0.00	37.00	3.16
612	627	2.500504	GGGGTCTATCCGAAAGAACAGT	59.499	50.000	0.00	0.00	37.00	3.55
616	631	5.341617	GGTCTATCCGAAAGAACAGTAGTG	58.658	45.833	0.00	0.00	0.00	2.74
617	632	4.799428	GTCTATCCGAAAGAACAGTAGTGC	59.201	45.833	0.00	0.00	0.00	4.40
619	634	5.884232	TCTATCCGAAAGAACAGTAGTGCTA	59.116	40.000	0.00	0.00	30.07	3.49
620	635	4.170292	TCCGAAAGAACAGTAGTGCTAC	57.830	45.455	0.00	1.33	30.07	3.58
621	636	3.570975	TCCGAAAGAACAGTAGTGCTACA	59.429	43.478	11.39	0.00	38.48	2.74
622	637	3.673809	CCGAAAGAACAGTAGTGCTACAC	59.326	47.826	11.39	0.00	38.48	2.90
623	638	4.295870	CGAAAGAACAGTAGTGCTACACA	58.704	43.478	11.39	0.00	38.48	3.72
624	639	4.743151	CGAAAGAACAGTAGTGCTACACAA	59.257	41.667	11.39	0.00	38.48	3.33

Showing 1 to 25 of 393 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
126	137	1.428869	ATCGGAGGAGAATTGAGGGG	58.571	55.000	0.00	0.00	0.00	4.79
192	203	0.545309	TCAGGGTGACAGAAGGGGAG	60.545	60.000	0.00	0.00	0.00	4.30
199	210	1.893062	CGCAGATCAGGGTGACAGA	59.107	57.895	0.00	0.00	0.00	3.41
205	216	1.078848	GAACAGCGCAGATCAGGGT	60.079	57.895	11.47	0.00	0.00	4.34
218	229	2.350772	GCAACAAATCCCGTCAGAACAG	60.351	50.000	0.00	0.00	0.00	3.16
259	271	5.418310	ACAATTCTGTACGAAACAACAGG	57.582	39.130	2.91	0.00	42.72	4.00
283	295	0.458889	TACCATTCACTACGCACGGC	60.459	55.000	0.00	0.00	0.00	5.68
317	329	1.135139	CCAGTCACGGGTAGATCACAG	59.865	57.143	0.00	0.00	0.00	3.66
331	343	3.620488	GCAAATCCTATCAACCCAGTCA	58.380	45.455	0.00	0.00	0.00	3.41
338	350	1.268032	CGTGCGGCAAATCCTATCAAC	60.268	52.381	3.23	0.00	0.00	3.18
368	380	0.607489	CACCAAACCCAGGCTCTGAG	60.607	60.000	0.00	0.00	32.44	3.35
372	384	1.271926	ACATACACCAAACCCAGGCTC	60.272	52.381	0.00	0.00	0.00	4.70
425	437	3.851976	AATATATCGACACGAGAGGGC	57.148	47.619	0.00	0.00	39.91	5.19
471	486	4.398044	CGAAATACAACCCCTGCAATACTT	59.602	41.667	0.00	0.00	0.00	2.24
513	528	5.083821	ACAAGGCCAATTTTGTATACCACT	58.916	37.500	5.01	0.00	35.86	4.00
560	575	9.883142	ACAGAAAACAGGTTTGATTTTGAATTA	57.117	25.926	0.00	0.00	30.49	1.40
584	599	4.717778	TCTTTCGGATAGACCCCAAATACA	59.282	41.667	0.00	0.00	34.64	2.29
601	616	4.295870	TGTGTAGCACTACTGTTCTTTCG	58.704	43.478	9.12	0.00	37.00	3.46
609	624	3.181774	GTGTCGTTTGTGTAGCACTACTG	59.818	47.826	9.12	0.00	37.00	2.74
610	625	3.378339	GTGTCGTTTGTGTAGCACTACT	58.622	45.455	9.12	0.00	37.00	2.57
611	626	2.473984	GGTGTCGTTTGTGTAGCACTAC	59.526	50.000	0.70	0.70	35.11	2.73
612	627	2.546373	GGGTGTCGTTTGTGTAGCACTA	60.546	50.000	0.90	0.00	35.11	2.74
616	631	1.196808	CATGGGTGTCGTTTGTGTAGC	59.803	52.381	0.00	0.00	0.00	3.58
617	632	1.196808	GCATGGGTGTCGTTTGTGTAG	59.803	52.381	0.00	0.00	0.00	2.74
619	634	0.749818	TGCATGGGTGTCGTTTGTGT	60.750	50.000	0.00	0.00	0.00	3.72

Showing 1 to 25 of 369 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.