AutoCloner

Multiple sequence alignment - TraesCS1D01G189200

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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	TraesCS1D01G189200	chr1D	100.000	3973	0	0	1	3973	261733232	261737204	0.000000e+00	7337.0
1	TraesCS1D01G189200	chr1D	86.705	346	34	7	3639	3973	449280218	449279874	1.350000e-99	374.0
2	TraesCS1D01G189200	chr1B	96.993	3326	79	10	664	3973	350399706	350396386	0.000000e+00	5568.0
3	TraesCS1D01G189200	chr1B	89.105	514	36	9	180	680	350412908	350412402	4.360000e-174	621.0
4	TraesCS1D01G189200	chr1B	88.235	306	29	3	3674	3973	614794452	614794148	3.780000e-95	359.0
5	TraesCS1D01G189200	chr1B	90.909	77	5	2	78	154	350439011	350438937	7.020000e-18	102.0
6	TraesCS1D01G189200	chr1A	93.918	3305	111	36	692	3973	338591099	338587862	0.000000e+00	4907.0
7	TraesCS1D01G189200	chr1A	87.536	345	31	7	3640	3973	544475141	544474798	4.810000e-104	388.0
8	TraesCS1D01G189200	chr1A	88.028	284	29	5	88	369	338592585	338592305	8.230000e-87	331.0
9	TraesCS1D01G189200	chr1A	90.000	90	8	1	1	90	338592887	338592799	9.020000e-22	115.0
10	TraesCS1D01G189200	chr5A	85.554	623	80	8	1243	1857	683233552	683232932	0.000000e+00	643.0
11	TraesCS1D01G189200	chr5A	83.362	583	81	12	2271	2842	683232308	683231731	3.520000e-145	525.0
12	TraesCS1D01G189200	chr5A	88.116	345	35	5	1881	2222	683232808	683232467	4.780000e-109	405.0
13	TraesCS1D01G189200	chr4D	85.096	624	81	10	1243	1857	500851803	500851183	9.370000e-176	627.0
14	TraesCS1D01G189200	chr4D	82.333	583	87	12	2271	2842	500850558	500849981	3.570000e-135	492.0
15	TraesCS1D01G189200	chr4D	86.628	344	42	3	1881	2222	500851059	500850718	1.040000e-100	377.0
16	TraesCS1D01G189200	chr4B	84.591	623	84	8	1244	1857	644828282	644827663	3.390000e-170	608.0
17	TraesCS1D01G189200	chr4B	83.162	582	82	11	2272	2842	644827051	644826475	5.890000e-143	518.0
18	TraesCS1D01G189200	chr4B	85.279	394	49	6	1881	2271	644827559	644827172	8.000000e-107	398.0
19	TraesCS1D01G189200	chr6A	74.561	912	197	28	1957	2843	479636584	479637485	2.260000e-97	366.0
20	TraesCS1D01G189200	chr2D	77.797	581	121	8	2272	2848	507826125	507825549	6.320000e-93	351.0
21	TraesCS1D01G189200	chr2B	77.893	579	116	9	2272	2844	596650466	596649894	2.270000e-92	350.0
22	TraesCS1D01G189200	chr6D	74.123	912	201	31	1957	2843	338933877	338934778	1.060000e-90	344.0
23	TraesCS1D01G189200	chr3D	100.000	31	0	0	93	123	152856029	152856059	1.540000e-04	58.4
24	TraesCS1D01G189200	chr7B	100.000	28	0	0	92	119	694258869	694258896	7.000000e-03	52.8

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	TraesCS1D01G189200	chr1D	261733232	261737204	3972	False	7337.000000	7337	100.000000	1	3973	1	chr1D.!!$F1	3972
1	TraesCS1D01G189200	chr1B	350396386	350399706	3320	True	5568.000000	5568	96.993000	664	3973	1	chr1B.!!$R1	3309
2	TraesCS1D01G189200	chr1B	350412402	350412908	506	True	621.000000	621	89.105000	180	680	1	chr1B.!!$R2	500
3	TraesCS1D01G189200	chr1A	338587862	338592887	5025	True	1784.333333	4907	90.648667	1	3973	3	chr1A.!!$R2	3972
4	TraesCS1D01G189200	chr5A	683231731	683233552	1821	True	524.333333	643	85.677333	1243	2842	3	chr5A.!!$R1	1599
5	TraesCS1D01G189200	chr4D	500849981	500851803	1822	True	498.666667	627	84.685667	1243	2842	3	chr4D.!!$R1	1599
6	TraesCS1D01G189200	chr4B	644826475	644828282	1807	True	508.000000	608	84.344000	1244	2842	3	chr4B.!!$R1	1598
7	TraesCS1D01G189200	chr6A	479636584	479637485	901	False	366.000000	366	74.561000	1957	2843	1	chr6A.!!$F1	886
8	TraesCS1D01G189200	chr2D	507825549	507826125	576	True	351.000000	351	77.797000	2272	2848	1	chr2D.!!$R1	576
9	TraesCS1D01G189200	chr2B	596649894	596650466	572	True	350.000000	350	77.893000	2272	2844	1	chr2B.!!$R1	572
10	TraesCS1D01G189200	chr6D	338933877	338934778	901	False	344.000000	344	74.123000	1957	2843	1	chr6D.!!$F1	886

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
450	1370	0.107800	GTTAGGAAACCGGAGAGGGC	60.108	60.0	9.46	0.00	46.96	5.19	F
1213	2338	0.112025	TGTGATGACCAATGGTGCCA	59.888	50.0	10.84	2.27	35.25	4.92	F
1762	2893	0.798776	GGCACCATCTTCGACAACAG	59.201	55.0	0.00	0.00	0.00	3.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1949	3185	1.749634	AGTATCACCTCGTTCTTCCCG	59.250	52.381	0.00	0.00	5.14	R
2813	4240	1.078214	CATCATGACGGTGGCCTGT	60.078	57.895	3.32	0.00	4.00	R
3491	4927	0.031994	CTGCCTTTTGGTTGTTCCCG	59.968	55.000	0.00	42.99	5.14	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
49	50	5.509501	CGTCCATTTATTTTGATCCCATGGG	60.510	44.000	26.30	26.30	32.13	4.00
54	55	0.709397	TTTTGATCCCATGGGCCAGA	59.291	50.000	27.41	17.61	34.68	3.86
67	68	2.025321	TGGGCCAGATTTTAGAACTCCC	60.025	50.000	0.00	0.00	0.00	4.30
68	69	2.289565	GGCCAGATTTTAGAACTCCCG	58.710	52.381	0.00	0.00	0.00	5.14
90	91	5.604565	CGGTCCCGGAACTAAACTAATATT	58.395	41.667	0.73	0.00	35.56	1.28
92	93	7.209475	CGGTCCCGGAACTAAACTAATATTTA	58.791	38.462	0.73	0.00	35.56	1.40
93	94	7.874528	CGGTCCCGGAACTAAACTAATATTTAT	59.125	37.037	0.73	0.00	35.56	1.40
124	343	9.213777	TCTATAAAGAATGTTGGAGTATCAGGT	57.786	33.333	0.00	0.00	36.25	4.00
125	344	9.482627	CTATAAAGAATGTTGGAGTATCAGGTC	57.517	37.037	0.00	0.00	36.25	3.85
126	345	6.380079	AAAGAATGTTGGAGTATCAGGTCT	57.620	37.500	0.00	0.00	36.25	3.85
128	347	5.983540	AGAATGTTGGAGTATCAGGTCTTC	58.016	41.667	0.00	0.00	36.25	2.87
138	357	2.122954	AGGTCTTCGGGGAGCCTT	59.877	61.111	4.63	0.00	34.64	4.35
162	381	0.250124	TGTGAAAATGTCCTCCGCGT	60.250	50.000	4.92	0.00	0.00	6.01
167	386	0.872388	AAATGTCCTCCGCGTTGTTC	59.128	50.000	4.92	0.00	0.00	3.18
174	393	2.170260	CTCCGCGTTGTTCGTTGCAT	62.170	55.000	4.92	0.00	42.13	3.96
316	535	2.226602	TCGTGATGTGGTGTTTTCGA	57.773	45.000	0.00	0.00	0.00	3.71
349	568	1.531602	GCCCTCTTGTTGGTTGCCT	60.532	57.895	0.00	0.00	0.00	4.75
387	1226	1.542547	CCCTGTTGGTGTAGTTCGCTT	60.543	52.381	0.00	0.00	0.00	4.68
388	1227	1.531149	CCTGTTGGTGTAGTTCGCTTG	59.469	52.381	0.00	0.00	0.00	4.01
390	1229	1.937223	TGTTGGTGTAGTTCGCTTGTG	59.063	47.619	0.00	0.00	0.00	3.33
440	1360	1.205820	GTGGCGCGTGTTAGGAAAC	59.794	57.895	8.43	0.00	36.07	2.78
450	1370	0.107800	GTTAGGAAACCGGAGAGGGC	60.108	60.000	9.46	0.00	46.96	5.19
451	1371	1.269703	TTAGGAAACCGGAGAGGGCC	61.270	60.000	9.46	0.00	46.96	5.80
452	1372	2.465010	TAGGAAACCGGAGAGGGCCA	62.465	60.000	9.46	0.00	46.96	5.36
453	1373	2.680370	GGAAACCGGAGAGGGCCAT	61.680	63.158	9.46	0.00	46.96	4.40
454	1374	1.153147	GAAACCGGAGAGGGCCATC	60.153	63.158	10.05	10.05	46.96	3.51
455	1375	2.610532	GAAACCGGAGAGGGCCATCC	62.611	65.000	15.12	15.89	46.96	3.51
530	1585	5.569059	GCAAATTTCTTTAGTGACATCCGTG	59.431	40.000	0.00	0.00	0.00	4.94
532	1587	3.678056	TTCTTTAGTGACATCCGTGCT	57.322	42.857	0.00	0.00	0.00	4.40
542	1597	2.742116	ATCCGTGCTATGGGGCGTT	61.742	57.895	0.00	0.00	34.52	4.84
543	1598	2.265467	ATCCGTGCTATGGGGCGTTT	62.265	55.000	0.00	0.00	34.52	3.60
545	1600	2.489751	GTGCTATGGGGCGTTTGC	59.510	61.111	0.00	0.00	41.71	3.68
561	1616	3.161866	GTTTGCTGGGGATTGGTTTCTA	58.838	45.455	0.00	0.00	0.00	2.10
594	1649	4.318831	CGCCAGATTATCTTTACCGCTTTC	60.319	45.833	0.00	0.00	0.00	2.62
687	1790	7.606073	TCAGAATGTCAAATGTAATCCTTTCGA	59.394	33.333	0.00	0.00	37.40	3.71
708	1811	2.085532	AAAAATATAGTGCACGCGCG	57.914	45.000	30.96	30.96	42.97	6.86
742	1845	1.285078	GATTGGCCAGTAAACCCTCCT	59.715	52.381	5.11	0.00	0.00	3.69
747	1850	1.280998	GCCAGTAAACCCTCCTGCTTA	59.719	52.381	0.00	0.00	0.00	3.09
769	1872	4.898320	ACTGCTCCATCGCATTTGATATA	58.102	39.130	0.00	0.00	39.52	0.86
775	1891	6.114187	TCCATCGCATTTGATATACTCCTT	57.886	37.500	0.00	0.00	0.00	3.36
780	1896	5.985530	TCGCATTTGATATACTCCTTCTGTG	59.014	40.000	0.00	0.00	0.00	3.66
802	1918	9.520204	CTGTGTAAAAAGAATGTTCATCACTTT	57.480	29.630	9.94	9.94	33.18	2.66
880	1996	0.618458	AAGTTTATGGGCTCCTCGCA	59.382	50.000	0.00	0.00	41.67	5.10
921	2037	2.032030	CCGCCTCCGCATTATTTAACAG	60.032	50.000	0.00	0.00	34.03	3.16
1107	2223	2.486042	GTCGCACTCTCGGAGGAC	59.514	66.667	4.96	0.52	33.35	3.85
1169	2294	1.930816	CGTCAGCTACGTGCGTTGTC	61.931	60.000	1.66	0.00	46.72	3.18
1186	2311	6.183360	TGCGTTGTCTCTTTTATCATGATCAC	60.183	38.462	12.53	0.00	0.00	3.06
1213	2338	0.112025	TGTGATGACCAATGGTGCCA	59.888	50.000	10.84	2.27	35.25	4.92
1215	2340	2.025510	TGTGATGACCAATGGTGCCATA	60.026	45.455	10.84	0.00	35.25	2.74
1421	2552	1.194781	ACCAGGAGCACTTCACGGAT	61.195	55.000	0.00	0.00	0.00	4.18
1762	2893	0.798776	GGCACCATCTTCGACAACAG	59.201	55.000	0.00	0.00	0.00	3.16
2900	4332	8.047911	ACTGATCTGAATGAATGAATCAACTCT	58.952	33.333	6.60	0.00	42.54	3.24
3004	4436	4.268405	GGAGCCAAATTTGCATGTAATTCG	59.732	41.667	12.92	0.00	0.00	3.34
3105	4538	7.378728	GTCTTTTAGTGCCTGTTTGTTGATTAC	59.621	37.037	0.00	0.00	0.00	1.89
3160	4593	8.714179	CATTTCTCTGCATTGCAAAATAAGAAA	58.286	29.630	21.68	21.68	38.41	2.52
3234	4670	2.990066	AAAAATGGAAACCGGTTGCA	57.010	40.000	26.79	18.60	42.34	4.08
3297	4733	1.070445	CAAGGCCCAACATTGCTTCAA	59.930	47.619	0.00	0.00	0.00	2.69
3300	4736	2.172293	AGGCCCAACATTGCTTCAAAAA	59.828	40.909	0.00	0.00	0.00	1.94
3672	5113	3.404899	CCAAGAAGCCAACAATTGCATT	58.595	40.909	5.05	0.00	0.00	3.56
3848	5289	4.441773	CCTCTCATCTCAGTCACCTCATTG	60.442	50.000	0.00	0.00	0.00	2.82

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
11	12	0.474614	TGGACGGTGGACAATGGAAA	59.525	50.000	0.00	0.00	0.00	3.13
16	17	5.478679	TCAAAATAAATGGACGGTGGACAAT	59.521	36.000	0.00	0.00	0.00	2.71
49	50	2.289565	CCGGGAGTTCTAAAATCTGGC	58.710	52.381	0.00	0.00	0.00	4.85
54	55	1.208776	CGGGACCGGGAGTTCTAAAAT	59.791	52.381	6.32	0.00	35.56	1.82
67	68	3.531934	ATTAGTTTAGTTCCGGGACCG	57.468	47.619	10.03	3.25	39.44	4.79
68	69	9.565090	AATAAATATTAGTTTAGTTCCGGGACC	57.435	33.333	10.03	0.00	0.00	4.46
99	318	9.482627	GACCTGATACTCCAACATTCTTTATAG	57.517	37.037	0.00	0.00	0.00	1.31
119	338	2.683933	GGCTCCCCGAAGACCTGA	60.684	66.667	0.00	0.00	0.00	3.86
121	340	1.539124	AAAGGCTCCCCGAAGACCT	60.539	57.895	0.00	0.00	35.76	3.85
122	341	1.377333	CAAAGGCTCCCCGAAGACC	60.377	63.158	0.00	0.00	35.76	3.85
123	342	2.041115	GCAAAGGCTCCCCGAAGAC	61.041	63.158	0.00	0.00	36.96	3.01
124	343	2.351276	GCAAAGGCTCCCCGAAGA	59.649	61.111	0.00	0.00	36.96	2.87
125	344	3.127533	CGCAAAGGCTCCCCGAAG	61.128	66.667	0.00	0.00	38.10	3.79
126	345	3.948719	ACGCAAAGGCTCCCCGAA	61.949	61.111	7.48	0.00	38.10	4.30
138	357	1.606668	GGAGGACATTTTCACACGCAA	59.393	47.619	0.00	0.00	0.00	4.85
162	381	0.249238	GGCCAACATGCAACGAACAA	60.249	50.000	0.00	0.00	0.00	2.83
167	386	2.049248	GGTGGCCAACATGCAACG	60.049	61.111	18.33	0.00	35.95	4.10
284	503	1.550130	ATCACGATGGACCCAACCGT	61.550	55.000	12.00	12.00	0.00	4.83
379	1218	2.980233	GCCTGGCACAAGCGAACT	60.980	61.111	15.17	0.00	43.41	3.01
428	1348	1.403780	CCTCTCCGGTTTCCTAACACG	60.404	57.143	0.00	0.00	35.92	4.49
433	1353	1.688187	GGCCCTCTCCGGTTTCCTA	60.688	63.158	0.00	0.00	0.00	2.94
479	1399	1.535204	AAATGAACCTTGGCCGGCTG	61.535	55.000	28.56	16.47	0.00	4.85
480	1400	0.039035	TAAATGAACCTTGGCCGGCT	59.961	50.000	28.56	4.40	0.00	5.52
482	1402	3.194542	TCAAATAAATGAACCTTGGCCGG	59.805	43.478	0.00	0.00	0.00	6.13
483	1403	4.423732	CTCAAATAAATGAACCTTGGCCG	58.576	43.478	0.00	0.00	0.00	6.13
486	1406	5.404466	TGCCTCAAATAAATGAACCTTGG	57.596	39.130	0.00	0.00	0.00	3.61
487	1407	7.910441	ATTTGCCTCAAATAAATGAACCTTG	57.090	32.000	3.22	0.00	41.50	3.61
488	1408	8.922931	AAATTTGCCTCAAATAAATGAACCTT	57.077	26.923	5.35	0.00	42.32	3.50
489	1409	8.377799	AGAAATTTGCCTCAAATAAATGAACCT	58.622	29.630	0.00	0.00	42.32	3.50
490	1410	8.552083	AGAAATTTGCCTCAAATAAATGAACC	57.448	30.769	0.00	0.00	42.32	3.62
517	1568	1.686587	CCCATAGCACGGATGTCACTA	59.313	52.381	0.00	0.00	0.00	2.74
530	1585	2.774799	CCAGCAAACGCCCCATAGC	61.775	63.158	0.00	0.00	0.00	2.97
532	1587	2.044451	CCCAGCAAACGCCCCATA	60.044	61.111	0.00	0.00	0.00	2.74
542	1597	2.883888	GCTAGAAACCAATCCCCAGCAA	60.884	50.000	0.00	0.00	0.00	3.91
543	1598	1.340991	GCTAGAAACCAATCCCCAGCA	60.341	52.381	0.00	0.00	0.00	4.41
545	1600	1.209504	TCGCTAGAAACCAATCCCCAG	59.790	52.381	0.00	0.00	0.00	4.45
633	1688	3.637229	GGAGATCGGTCCAAACTATGAGA	59.363	47.826	0.00	0.00	36.51	3.27
634	1689	3.639094	AGGAGATCGGTCCAAACTATGAG	59.361	47.826	3.98	0.00	39.34	2.90
636	1691	3.384789	TGAGGAGATCGGTCCAAACTATG	59.615	47.826	3.98	0.00	39.34	2.23
708	1811	2.095212	GGCCAATCTTGAGACGGTTTTC	60.095	50.000	0.00	0.00	0.00	2.29
769	1872	7.556275	TGAACATTCTTTTTACACAGAAGGAGT	59.444	33.333	0.92	0.00	34.99	3.85
775	1891	8.450578	AGTGATGAACATTCTTTTTACACAGA	57.549	30.769	0.00	0.00	0.00	3.41
780	1896	8.816144	TGCAAAAGTGATGAACATTCTTTTTAC	58.184	29.630	18.50	15.82	35.39	2.01
790	1906	5.658468	TGTGAAATGCAAAAGTGATGAACA	58.342	33.333	0.00	0.00	0.00	3.18
880	1996	1.105457	TTGCAGTGCAAAGAACAGCT	58.895	45.000	27.79	0.00	45.96	4.24
921	2037	2.358015	CGGGTAGATCGAGGGTAGATC	58.642	57.143	0.00	0.00	43.48	2.75
1169	2294	5.050499	GCGTCCAGTGATCATGATAAAAGAG	60.050	44.000	8.54	0.00	0.00	2.85
1186	2311	0.320683	TTGGTCATCACAGCGTCCAG	60.321	55.000	0.00	0.00	0.00	3.86
1213	2338	1.432514	CAGTTGCTCTGCACACGTAT	58.567	50.000	0.00	0.00	38.71	3.06
1215	2340	1.889105	CCAGTTGCTCTGCACACGT	60.889	57.895	4.40	0.00	42.38	4.49
1949	3185	1.749634	AGTATCACCTCGTTCTTCCCG	59.250	52.381	0.00	0.00	0.00	5.14
2813	4240	1.078214	CATCATGACGGTGGCCTGT	60.078	57.895	3.32	0.00	0.00	4.00
2856	4283	3.074412	CAGTATAATTGCGGGGGTCATC	58.926	50.000	0.00	0.00	0.00	2.92
2920	4352	6.605471	TTATGCCCATATACCTGTACAGAG	57.395	41.667	24.68	15.90	0.00	3.35
3004	4436	5.777732	TCCCCCAAATACAATATTATGCCAC	59.222	40.000	0.00	0.00	0.00	5.01
3105	4538	4.510167	AAGGGATGTCTGGGTTTCATAG	57.490	45.455	0.00	0.00	0.00	2.23
3160	4593	5.275067	TGCCTTTGCAACATAAGTTTTCT	57.725	34.783	0.00	0.00	46.66	2.52
3234	4670	2.256306	GGAAATTGGTGGGTGGATGTT	58.744	47.619	0.00	0.00	0.00	2.71
3491	4927	0.031994	CTGCCTTTTGGTTGTTCCCG	59.968	55.000	0.00	0.00	42.99	5.14

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.