AutoCloner

Multiple sequence alignment - TraesCS1B01G179800

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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	TraesCS1B01G179800	chr1B	100.000	3094	0	0	1	3094	326005480	326002387	0.000000e+00	5714
1	TraesCS1B01G179800	chr1B	96.037	757	26	3	2340	3094	328277624	328278378	0.000000e+00	1229
2	TraesCS1B01G179800	chr1B	96.252	747	24	3	2350	3094	604427962	604428706	0.000000e+00	1221
3	TraesCS1B01G179800	chr1B	96.113	746	27	1	2349	3094	325991488	325990745	0.000000e+00	1216
4	TraesCS1B01G179800	chr1A	93.647	1889	74	24	490	2350	291973979	291975849	0.000000e+00	2782
5	TraesCS1B01G179800	chr1A	92.760	221	13	3	2130	2350	291979113	291979330	1.790000e-82	316
6	TraesCS1B01G179800	chr1D	93.573	1867	77	19	490	2346	225861190	225859357	0.000000e+00	2743
7	TraesCS1B01G179800	chr5B	96.252	747	25	2	2349	3094	630109579	630110323	0.000000e+00	1221
8	TraesCS1B01G179800	chr6B	95.984	747	26	3	2349	3094	521227872	521228615	0.000000e+00	1210
9	TraesCS1B01G179800	chr6B	95.984	747	26	3	2349	3094	534022642	534023385	0.000000e+00	1210
10	TraesCS1B01G179800	chr6B	95.984	747	26	3	2349	3094	534032360	534033103	0.000000e+00	1210
11	TraesCS1B01G179800	chr6B	96.976	496	7	4	1	490	478462664	478462171	0.000000e+00	826
12	TraesCS1B01G179800	chr3B	95.984	747	26	3	2350	3094	487062293	487061549	0.000000e+00	1210
13	TraesCS1B01G179800	chr3B	95.979	746	27	2	2349	3094	145089864	145089122	0.000000e+00	1208
14	TraesCS1B01G179800	chr3B	97.358	492	11	2	1	490	8790767	8791258	0.000000e+00	835
15	TraesCS1B01G179800	chr3B	97.172	495	9	3	1	490	54608467	54608961	0.000000e+00	832
16	TraesCS1B01G179800	chr3B	96.988	498	5	4	1	490	765595938	765595443	0.000000e+00	828
17	TraesCS1B01G179800	chr3A	97.590	498	8	2	1	494	474444918	474444421	0.000000e+00	850
18	TraesCS1B01G179800	chr3A	97.206	501	10	1	1	497	66351757	66352257	0.000000e+00	845
19	TraesCS1B01G179800	chrUn	97.586	497	8	2	1	493	53744478	53744974	0.000000e+00	848
20	TraesCS1B01G179800	chr7B	97.166	494	10	1	1	490	54777529	54778022	0.000000e+00	832
21	TraesCS1B01G179800	chr2B	97.166	494	8	3	1	490	73114183	73114674	0.000000e+00	830

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	TraesCS1B01G179800	chr1B	326002387	326005480	3093	True	5714	5714	100.0000	1	3094	1	chr1B.!!$R2	3093
1	TraesCS1B01G179800	chr1B	328277624	328278378	754	False	1229	1229	96.0370	2340	3094	1	chr1B.!!$F1	754
2	TraesCS1B01G179800	chr1B	604427962	604428706	744	False	1221	1221	96.2520	2350	3094	1	chr1B.!!$F2	744
3	TraesCS1B01G179800	chr1B	325990745	325991488	743	True	1216	1216	96.1130	2349	3094	1	chr1B.!!$R1	745
4	TraesCS1B01G179800	chr1A	291973979	291979330	5351	False	1549	2782	93.2035	490	2350	2	chr1A.!!$F1	1860
5	TraesCS1B01G179800	chr1D	225859357	225861190	1833	True	2743	2743	93.5730	490	2346	1	chr1D.!!$R1	1856
6	TraesCS1B01G179800	chr5B	630109579	630110323	744	False	1221	1221	96.2520	2349	3094	1	chr5B.!!$F1	745
7	TraesCS1B01G179800	chr6B	521227872	521228615	743	False	1210	1210	95.9840	2349	3094	1	chr6B.!!$F1	745
8	TraesCS1B01G179800	chr6B	534022642	534023385	743	False	1210	1210	95.9840	2349	3094	1	chr6B.!!$F2	745
9	TraesCS1B01G179800	chr6B	534032360	534033103	743	False	1210	1210	95.9840	2349	3094	1	chr6B.!!$F3	745
10	TraesCS1B01G179800	chr3B	487061549	487062293	744	True	1210	1210	95.9840	2350	3094	1	chr3B.!!$R2	744
11	TraesCS1B01G179800	chr3B	145089122	145089864	742	True	1208	1208	95.9790	2349	3094	1	chr3B.!!$R1	745
12	TraesCS1B01G179800	chr3A	66351757	66352257	500	False	845	845	97.2060	1	497	1	chr3A.!!$F1	496

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	Hairpin	End Stability	Orientation
336	337	0.106217	GAGGGGGAGAGAGAGTGAGG	60.106	65.0	0.00	3.86	F
338	339	0.336737	GGGGGAGAGAGAGTGAGGAA	59.663	60.0	0.00	3.36	F
1118	1131	0.906282	CCCCTGCCTTCCTTTGCATT	60.906	55.0	36.79	3.56	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1325	1338	1.474077	CCTTGAAGCCCTGCATGTAAC	59.526	52.381	0.00	0.00	2.50	R
1538	1562	2.832129	TCGGAAGTATTGCCTGAAGACT	59.168	45.455	0.00	37.74	3.24	R
2752	4975	0.530744	TACCGCTAGTGAGGCAAGTG	59.469	55.000	4.44	36.56	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
155	156	2.838736	TCTTGTCTTCAGTGCAGAACC	58.161	47.619	0.00	0.00	0.00	3.62
214	215	8.803397	ACTACCTTGAACCTGTTTTATAATCC	57.197	34.615	0.00	0.00	0.00	3.01
258	259	4.808895	GTGTGCGTGTGAAATAGATGGATA	59.191	41.667	0.00	0.00	0.00	2.59
259	260	5.466728	GTGTGCGTGTGAAATAGATGGATAT	59.533	40.000	0.00	0.00	0.00	1.63
336	337	0.106217	GAGGGGGAGAGAGAGTGAGG	60.106	65.000	0.00	0.00	0.00	3.86
338	339	0.336737	GGGGGAGAGAGAGTGAGGAA	59.663	60.000	0.00	0.00	0.00	3.36
346	351	1.287739	AGAGAGTGAGGAAGAGGGAGG	59.712	57.143	0.00	0.00	0.00	4.30
562	567	2.835156	GCCTTACCTTCCTCTTCACTCT	59.165	50.000	0.00	0.00	0.00	3.24
581	586	2.581246	TCTCCAGTTCCCACTAGCTAGA	59.419	50.000	27.45	1.63	0.00	2.43
604	609	2.631160	TTTCCTTCGCTGAAAGGTGA	57.369	45.000	8.66	0.00	45.16	4.02
637	642	1.377725	ATTCAGGAAGGCGCCACAG	60.378	57.895	31.54	15.25	0.00	3.66
660	665	7.095910	CAGACTACTCCATGGATCATGATAAC	58.904	42.308	16.63	5.56	43.81	1.89
691	701	4.999950	CCCTGCATGTTCTCCTATCAATAC	59.000	45.833	0.00	0.00	0.00	1.89
692	702	5.455183	CCCTGCATGTTCTCCTATCAATACA	60.455	44.000	0.00	0.00	0.00	2.29
693	703	6.057533	CCTGCATGTTCTCCTATCAATACAA	58.942	40.000	0.00	0.00	0.00	2.41
694	704	6.017605	CCTGCATGTTCTCCTATCAATACAAC	60.018	42.308	0.00	0.00	0.00	3.32
753	763	7.125507	ACTCATCAACTTCTCTTATCATGGACT	59.874	37.037	0.00	0.00	0.00	3.85
841	851	1.967597	GCTGAACGCCGCTCCTTTAC	61.968	60.000	0.00	0.00	0.00	2.01
1118	1131	0.906282	CCCCTGCCTTCCTTTGCATT	60.906	55.000	0.00	0.00	36.79	3.56
1136	1149	3.548818	GCATTTGCTGACGAGAAAACACT	60.549	43.478	0.00	0.00	38.21	3.55
1193	1206	5.221342	ACAAGGGTAATGATCTCACGATCTC	60.221	44.000	0.00	0.00	45.10	2.75
1229	1242	4.761739	TCTTCTCCCAACTGCTGTAATTTG	59.238	41.667	0.00	0.00	0.00	2.32
1250	1263	8.697846	ATTTGTATGTCAATGCTGATTTTCTG	57.302	30.769	0.00	0.00	35.84	3.02
1281	1294	1.268778	GCGCCGCAGACAAAAAGAAC	61.269	55.000	3.15	0.00	0.00	3.01
1311	1324	4.672587	TTATCGGATGAGCAAGCTAAGT	57.327	40.909	0.00	0.00	0.00	2.24
1325	1338	6.593382	AGCAAGCTAAGTCAGAAAACAGATAG	59.407	38.462	0.00	0.00	0.00	2.08
1394	1407	8.984764	GGAGTAATATATGTGTATCGCAACAAA	58.015	33.333	0.00	0.00	0.00	2.83
1426	1449	6.635030	AACTAACCAGGAAACAATTCTCAC	57.365	37.500	0.00	0.00	35.79	3.51
1470	1494	1.798813	CAGTAGCACTTGGACCGAAAC	59.201	52.381	0.00	0.00	0.00	2.78
1538	1562	2.161855	CAAGCTGGTAGCATGGACAAA	58.838	47.619	3.43	0.00	45.56	2.83
1646	1670	3.022406	AGCTGGAATGCTTTTCATCTCC	58.978	45.455	0.00	0.00	40.93	3.71
1650	1674	4.012374	TGGAATGCTTTTCATCTCCACTC	58.988	43.478	0.00	0.00	37.40	3.51
1651	1675	3.064545	GGAATGCTTTTCATCTCCACTCG	59.935	47.826	3.03	0.00	34.90	4.18
1748	1772	3.964411	GGTAACTAAAGCACAATCCCCT	58.036	45.455	0.00	0.00	0.00	4.79
1759	1783	1.215423	ACAATCCCCTGGTCAATAGCC	59.785	52.381	0.00	0.00	0.00	3.93
2033	2058	2.419297	GGAGATGAGATGACACACCCAC	60.419	54.545	0.00	0.00	0.00	4.61
2053	2078	3.820467	CACTTCTGTAATCCCAAGCACAA	59.180	43.478	0.00	0.00	0.00	3.33
2189	2223	3.813166	TCTTCAAGATGTTTTCCACGGTC	59.187	43.478	0.00	0.00	0.00	4.79
2246	2280	9.559732	CATCATGTTAATACCTCTTCATTACCA	57.440	33.333	0.00	0.00	0.00	3.25
2252	2286	9.043079	GTTAATACCTCTTCATTACCAAGTAGC	57.957	37.037	0.00	0.00	0.00	3.58
2334	2368	5.249393	ACAGGAGAGTGATAATGTTGAAGGT	59.751	40.000	0.00	0.00	0.00	3.50
2346	2380	5.717078	ATGTTGAAGGTCGTCTAGTGTTA	57.283	39.130	0.00	0.00	0.00	2.41
2363	2398	8.653191	TCTAGTGTTATTTGTAGGACCTTGAAA	58.347	33.333	0.00	0.00	0.00	2.69
2472	2508	3.988379	TTGGACAAGTCAAGCAATCAC	57.012	42.857	2.29	0.00	0.00	3.06
2577	2733	3.848272	TGGAGGATTCAAACGCAATTC	57.152	42.857	0.00	0.00	0.00	2.17
2632	3617	2.104170	TGGTGCTATCGTACATCCACA	58.896	47.619	0.00	0.00	0.00	4.17
2701	4924	2.283529	GGGCTCCACTCACGAAGGA	61.284	63.158	0.00	0.00	0.00	3.36
2800	5075	1.405821	CGAAGTAGGCGATCTCCTTGT	59.594	52.381	10.08	0.00	37.66	3.16
2801	5076	2.159226	CGAAGTAGGCGATCTCCTTGTT	60.159	50.000	10.08	3.81	37.66	2.83
2835	5110	7.037586	ACTCCTTGGTTCAACTCCATAATCTTA	60.038	37.037	0.00	0.00	34.75	2.10
2890	5165	3.753294	GAGACACCACTCTCCAAGAAA	57.247	47.619	0.00	0.00	31.88	2.52
2913	5188	6.691754	ATAACAAATGGTGCGTTGATGATA	57.308	33.333	0.00	0.00	0.00	2.15
2922	5197	4.873827	GGTGCGTTGATGATAAACTCCTTA	59.126	41.667	0.00	0.00	0.00	2.69
2970	5245	3.056891	CCCAACACTCAACTCTCTCTCTC	60.057	52.174	0.00	0.00	0.00	3.20
2994	5356	4.402616	AGGATTTGGATCTGGTGGAAAA	57.597	40.909	0.00	0.00	32.66	2.29

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
4	5	3.496884	TCCTAGACAAACGCAACATCAAC	59.503	43.478	0.00	0.00	0.00	3.18
214	215	3.184379	ACGCGCTAGTGCATAACAATATG	59.816	43.478	26.75	9.62	41.59	1.78
278	279	6.946340	TCTCTAACACACACACATATCCATT	58.054	36.000	0.00	0.00	0.00	3.16
336	337	0.610687	CACACACTCCCTCCCTCTTC	59.389	60.000	0.00	0.00	0.00	2.87
338	339	0.833834	CACACACACTCCCTCCCTCT	60.834	60.000	0.00	0.00	0.00	3.69
346	351	4.083110	CCATCAAATTCTCACACACACTCC	60.083	45.833	0.00	0.00	0.00	3.85
519	524	0.526739	GCACGTTGGTTGGTTTGGAC	60.527	55.000	0.00	0.00	0.00	4.02
562	567	3.097614	GTTCTAGCTAGTGGGAACTGGA	58.902	50.000	20.10	0.00	36.24	3.86
604	609	2.035832	CCTGAATGCCGGTTGTTCTTTT	59.964	45.455	1.90	0.00	0.00	2.27
637	642	7.238486	AGTTATCATGATCCATGGAGTAGTC	57.762	40.000	21.33	13.13	41.66	2.59
660	665	4.080863	AGGAGAACATGCAGGGTTTACTAG	60.081	45.833	2.31	0.00	0.00	2.57
691	701	6.539649	TGCTTACAGTTAGCTTTACAGTTG	57.460	37.500	12.62	0.00	39.38	3.16
692	702	6.348540	GCATGCTTACAGTTAGCTTTACAGTT	60.349	38.462	11.37	0.00	39.38	3.16
693	703	5.122396	GCATGCTTACAGTTAGCTTTACAGT	59.878	40.000	11.37	0.00	39.38	3.55
694	704	5.447818	GGCATGCTTACAGTTAGCTTTACAG	60.448	44.000	18.92	0.00	39.38	2.74
833	843	4.278419	CACACTTTTCTTGGGGTAAAGGAG	59.722	45.833	0.00	0.00	34.10	3.69
841	851	1.069049	CAAGGCACACTTTTCTTGGGG	59.931	52.381	0.00	0.00	37.29	4.96
1118	1131	3.069016	TCCTAGTGTTTTCTCGTCAGCAA	59.931	43.478	0.00	0.00	0.00	3.91
1136	1149	7.039784	CCAAAGAAGAACATGATGGTTTTCCTA	60.040	37.037	9.80	0.00	41.38	2.94
1193	1206	2.373224	GGAGAAGAGAATTGGGCAAGG	58.627	52.381	0.00	0.00	0.00	3.61
1229	1242	6.094603	AGGACAGAAAATCAGCATTGACATAC	59.905	38.462	0.00	0.00	35.83	2.39
1250	1263	3.431725	CGGCGCCAAGGAAAGGAC	61.432	66.667	28.98	0.00	0.00	3.85
1281	1294	2.989840	GCTCATCCGATAAACGATGGAG	59.010	50.000	0.00	0.00	45.77	3.86
1311	1324	6.595326	CCTGCATGTAACTATCTGTTTTCTGA	59.405	38.462	0.00	0.00	39.89	3.27
1325	1338	1.474077	CCTTGAAGCCCTGCATGTAAC	59.526	52.381	0.00	0.00	0.00	2.50
1357	1370	9.715119	ACACATATATTACTCCTAGATGGCATA	57.285	33.333	0.00	0.00	35.26	3.14
1366	1379	9.016438	TGTTGCGATACACATATATTACTCCTA	57.984	33.333	0.00	0.00	0.00	2.94
1367	1380	7.892609	TGTTGCGATACACATATATTACTCCT	58.107	34.615	0.00	0.00	0.00	3.69
1368	1381	8.528917	TTGTTGCGATACACATATATTACTCC	57.471	34.615	0.00	0.00	0.00	3.85
1387	1400	9.301153	CCTGGTTAGTTTATATCAATTTGTTGC	57.699	33.333	0.00	0.00	0.00	4.17
1538	1562	2.832129	TCGGAAGTATTGCCTGAAGACT	59.168	45.455	0.00	0.00	37.74	3.24
1748	1772	4.764823	CCAGTAAACTTTGGCTATTGACCA	59.235	41.667	0.00	0.00	34.65	4.02
1759	1783	8.047413	ACCGGTATTTAATCCAGTAAACTTTG	57.953	34.615	4.49	0.00	0.00	2.77
1779	1803	3.379057	CGCCCAAATATTTCTTAACCGGT	59.621	43.478	0.00	0.00	0.00	5.28
2033	2058	4.142315	CCATTGTGCTTGGGATTACAGAAG	60.142	45.833	0.00	0.00	0.00	2.85
2168	2202	3.563808	TGACCGTGGAAAACATCTTGAAG	59.436	43.478	0.00	0.00	0.00	3.02
2189	2223	5.411977	CCTTTCAGCATATCCTAAGCTCATG	59.588	44.000	0.00	0.00	36.26	3.07
2334	2368	5.948162	AGGTCCTACAAATAACACTAGACGA	59.052	40.000	0.00	0.00	0.00	4.20
2346	2380	9.838339	CTAGACATATTTCAAGGTCCTACAAAT	57.162	33.333	11.14	11.14	0.00	2.32
2414	2450	6.269769	TCTGCCAAACTCTAAAATTGGGAAAT	59.730	34.615	5.97	0.00	42.81	2.17
2472	2508	2.512485	TGCTTGCTTGAATTGTGTGG	57.488	45.000	0.00	0.00	0.00	4.17
2577	2733	2.285602	CGCCAAAAATATCCGTGTCTCG	60.286	50.000	0.00	0.00	39.52	4.04
2632	3617	3.074390	TGTGGGTTGAAGTCTCCATCAAT	59.926	43.478	0.00	0.00	37.82	2.57
2692	4915	1.541379	TCTTCGTGGATCCTTCGTGA	58.459	50.000	22.09	18.80	0.00	4.35
2701	4924	2.154462	CAAGGTTGCTTCTTCGTGGAT	58.846	47.619	0.00	0.00	0.00	3.41
2752	4975	0.530744	TACCGCTAGTGAGGCAAGTG	59.469	55.000	4.44	0.00	36.56	3.16
2800	5075	6.184789	AGTTGAACCAAGGAGTTTGTAAGAA	58.815	36.000	0.00	0.00	34.87	2.52
2801	5076	5.751586	AGTTGAACCAAGGAGTTTGTAAGA	58.248	37.500	0.00	0.00	34.87	2.10
2835	5110	1.306141	TCACTTGGGAGCCTCCGAT	60.306	57.895	4.29	0.00	37.43	4.18
2890	5165	5.581126	ATCATCAACGCACCATTTGTTAT	57.419	34.783	0.00	0.00	0.00	1.89
2913	5188	5.036117	TGAAGCACAAGAGTAAGGAGTTT	57.964	39.130	0.00	0.00	0.00	2.66
2922	5197	6.471146	AGACTATCATTTGAAGCACAAGAGT	58.529	36.000	0.00	0.00	39.77	3.24
2970	5245	4.712051	TCCACCAGATCCAAATCCTATG	57.288	45.455	0.00	0.00	31.78	2.23
2994	5356	5.859205	AGTTGCTTTCCACTCAAATCTTT	57.141	34.783	0.00	0.00	0.00	2.52

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.