AutoCloner

Multiple sequence alignment - TraesCS4B01G119000

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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	TraesCS4B01G119000	chr4B	100.000	3797	0	0	1	3797	139550186	139546390	0.000000e+00	7012
1	TraesCS4B01G119000	chr4B	85.192	2323	252	48	870	3155	139572279	139570012	0.000000e+00	2300
2	TraesCS4B01G119000	chr4B	82.922	931	143	10	1402	2327	460156617	460155698	0.000000e+00	824
3	TraesCS4B01G119000	chr4D	96.696	2270	52	7	868	3135	97962538	97960290	0.000000e+00	3755
4	TraesCS4B01G119000	chr4D	86.670	2033	200	32	906	2929	97970281	97968311	0.000000e+00	2187
5	TraesCS4B01G119000	chr4D	80.684	1346	221	26	1402	2729	98015418	98014094	0.000000e+00	1009
6	TraesCS4B01G119000	chr4D	77.592	1379	233	43	1402	2760	435198755	435197433	0.000000e+00	765
7	TraesCS4B01G119000	chr4D	90.280	607	26	9	3217	3797	97960308	97959709	0.000000e+00	763
8	TraesCS4B01G119000	chr4D	80.142	282	24	13	3212	3471	97966955	97966684	8.380000e-42	182
9	TraesCS4B01G119000	chr4D	95.062	81	4	0	789	869	97962650	97962570	1.110000e-25	128
10	TraesCS4B01G119000	chr4A	96.721	1403	37	7	870	2271	478209463	478210857	0.000000e+00	2327
11	TraesCS4B01G119000	chr4A	97.274	917	24	1	2267	3183	478216299	478217214	0.000000e+00	1554
12	TraesCS4B01G119000	chr4A	80.000	1425	239	29	1402	2800	478191411	478192815	0.000000e+00	1011
13	TraesCS4B01G119000	chr4A	88.491	643	30	10	3196	3797	478217198	478217837	0.000000e+00	737
14	TraesCS4B01G119000	chr1B	84.042	2306	276	47	907	3176	487405524	487407773	0.000000e+00	2135
15	TraesCS4B01G119000	chr1D	84.255	2242	268	47	969	3178	363861164	363863352	0.000000e+00	2106
16	TraesCS4B01G119000	chr1A	84.190	2062	262	33	896	2932	463218522	463220544	0.000000e+00	1943
17	TraesCS4B01G119000	chr7B	96.503	772	27	0	1	772	507833071	507833842	0.000000e+00	1277
18	TraesCS4B01G119000	chr7B	96.364	385	14	0	388	772	507834032	507834416	5.350000e-178	634
19	TraesCS4B01G119000	chr6B	95.602	773	32	2	1	773	151915520	151916290	0.000000e+00	1238
20	TraesCS4B01G119000	chr6B	78.567	1451	221	49	885	2305	134838183	134839573	0.000000e+00	874
21	TraesCS4B01G119000	chr6B	92.058	277	21	1	45	321	494480096	494479821	4.600000e-104	388
22	TraesCS4B01G119000	chr5D	91.624	776	44	5	1	773	463359664	463358907	0.000000e+00	1053
23	TraesCS4B01G119000	chr6D	91.440	771	47	4	1	770	441964702	441963950	0.000000e+00	1040
24	TraesCS4B01G119000	chr6D	83.544	474	62	11	885	1344	61002816	61003287	2.710000e-116	429
25	TraesCS4B01G119000	chr6A	91.747	727	54	5	50	775	607847263	607847984	0.000000e+00	1005
26	TraesCS4B01G119000	chr2D	89.276	774	41	13	1	773	168137734	168137002	0.000000e+00	931
27	TraesCS4B01G119000	chr3D	89.971	678	45	8	98	775	290177891	290177237	0.000000e+00	854
28	TraesCS4B01G119000	chr7A	88.599	728	48	5	1	728	289135652	289134960	0.000000e+00	852
29	TraesCS4B01G119000	chr3B	78.766	1248	205	38	1402	2614	706754884	706756106	0.000000e+00	782
30	TraesCS4B01G119000	chr3B	78.180	912	152	29	1716	2602	706185594	706186483	4.320000e-149	538
31	TraesCS4B01G119000	chr5B	95.000	300	15	0	1	300	65540853	65540554	4.440000e-129	472
32	TraesCS4B01G119000	chr7D	91.961	311	25	0	45	355	580667191	580667501	1.620000e-118	436
33	TraesCS4B01G119000	chr3A	83.731	461	61	9	885	1344	149717131	149716684	1.260000e-114	424

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	TraesCS4B01G119000	chr4B	139546390	139550186	3796	True	7012.000000	7012	100.000000	1	3797	1	chr4B.!!$R1	3796
1	TraesCS4B01G119000	chr4B	139570012	139572279	2267	True	2300.000000	2300	85.192000	870	3155	1	chr4B.!!$R2	2285
2	TraesCS4B01G119000	chr4B	460155698	460156617	919	True	824.000000	824	82.922000	1402	2327	1	chr4B.!!$R3	925
3	TraesCS4B01G119000	chr4D	97959709	97962650	2941	True	1548.666667	3755	94.012667	789	3797	3	chr4D.!!$R3	3008
4	TraesCS4B01G119000	chr4D	97966684	97970281	3597	True	1184.500000	2187	83.406000	906	3471	2	chr4D.!!$R4	2565
5	TraesCS4B01G119000	chr4D	98014094	98015418	1324	True	1009.000000	1009	80.684000	1402	2729	1	chr4D.!!$R1	1327
6	TraesCS4B01G119000	chr4D	435197433	435198755	1322	True	765.000000	765	77.592000	1402	2760	1	chr4D.!!$R2	1358
7	TraesCS4B01G119000	chr4A	478209463	478210857	1394	False	2327.000000	2327	96.721000	870	2271	1	chr4A.!!$F2	1401
8	TraesCS4B01G119000	chr4A	478216299	478217837	1538	False	1145.500000	1554	92.882500	2267	3797	2	chr4A.!!$F3	1530
9	TraesCS4B01G119000	chr4A	478191411	478192815	1404	False	1011.000000	1011	80.000000	1402	2800	1	chr4A.!!$F1	1398
10	TraesCS4B01G119000	chr1B	487405524	487407773	2249	False	2135.000000	2135	84.042000	907	3176	1	chr1B.!!$F1	2269
11	TraesCS4B01G119000	chr1D	363861164	363863352	2188	False	2106.000000	2106	84.255000	969	3178	1	chr1D.!!$F1	2209
12	TraesCS4B01G119000	chr1A	463218522	463220544	2022	False	1943.000000	1943	84.190000	896	2932	1	chr1A.!!$F1	2036
13	TraesCS4B01G119000	chr7B	507833071	507834416	1345	False	955.500000	1277	96.433500	1	772	2	chr7B.!!$F1	771
14	TraesCS4B01G119000	chr6B	151915520	151916290	770	False	1238.000000	1238	95.602000	1	773	1	chr6B.!!$F2	772
15	TraesCS4B01G119000	chr6B	134838183	134839573	1390	False	874.000000	874	78.567000	885	2305	1	chr6B.!!$F1	1420
16	TraesCS4B01G119000	chr5D	463358907	463359664	757	True	1053.000000	1053	91.624000	1	773	1	chr5D.!!$R1	772
17	TraesCS4B01G119000	chr6D	441963950	441964702	752	True	1040.000000	1040	91.440000	1	770	1	chr6D.!!$R1	769
18	TraesCS4B01G119000	chr6A	607847263	607847984	721	False	1005.000000	1005	91.747000	50	775	1	chr6A.!!$F1	725
19	TraesCS4B01G119000	chr2D	168137002	168137734	732	True	931.000000	931	89.276000	1	773	1	chr2D.!!$R1	772
20	TraesCS4B01G119000	chr3D	290177237	290177891	654	True	854.000000	854	89.971000	98	775	1	chr3D.!!$R1	677
21	TraesCS4B01G119000	chr7A	289134960	289135652	692	True	852.000000	852	88.599000	1	728	1	chr7A.!!$R1	727
22	TraesCS4B01G119000	chr3B	706754884	706756106	1222	False	782.000000	782	78.766000	1402	2614	1	chr3B.!!$F2	1212
23	TraesCS4B01G119000	chr3B	706185594	706186483	889	False	538.000000	538	78.180000	1716	2602	1	chr3B.!!$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
888	1509	0.252239	GGACATTGGGCCTTTTCCCT	60.252	55.0	4.53	0.0	46.67	4.20	F
2014	2703	0.738975	TCATGTCCTAGAGTTCGGCG	59.261	55.0	0.00	0.0	0.00	6.46	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2646	3381	2.005451	CGCAGAGGATTCACTTTGGAG	58.995	52.381	0.0	0.0	0.00	3.86	R
3666	5635	1.964373	GTACGTTGTGCCTGGTGGG	60.964	63.158	0.0	0.0	38.36	4.61	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
22	23	1.566298	GCCTCCAAGATGGTGTCCCT	61.566	60.000	0.00	0.00	39.03	4.20
576	587	3.173965	AGGGGAGAAAGAAAGATGACGA	58.826	45.455	0.00	0.00	0.00	4.20
628	639	6.347725	GCCGATAACGAGATATGAAAATTGCT	60.348	38.462	0.00	0.00	42.66	3.91
636	647	1.197812	ATGAAAATTGCTGAGGGGGC	58.802	50.000	0.00	0.00	0.00	5.80
653	664	2.192605	GCAATGAGCGGGGTCAAAT	58.807	52.632	4.53	0.00	0.00	2.32
670	681	6.402442	GGGTCAAATAATGATTTTGTTGCTGC	60.402	38.462	0.00	0.00	40.97	5.25
674	685	7.603024	TCAAATAATGATTTTGTTGCTGCATGA	59.397	29.630	1.84	0.00	35.90	3.07
680	691	5.992829	TGATTTTGTTGCTGCATGAAAGAAT	59.007	32.000	1.84	0.00	0.00	2.40
767	1355	2.114411	AACCCACGGGCGTTCAAT	59.886	55.556	0.69	0.00	39.32	2.57
775	1363	3.001939	CCACGGGCGTTCAATTAGTAATC	59.998	47.826	0.00	0.00	0.00	1.75
776	1364	2.861935	ACGGGCGTTCAATTAGTAATCG	59.138	45.455	0.00	0.00	0.00	3.34
777	1365	2.861935	CGGGCGTTCAATTAGTAATCGT	59.138	45.455	0.00	0.00	0.00	3.73
778	1366	3.307782	CGGGCGTTCAATTAGTAATCGTT	59.692	43.478	0.00	0.00	0.00	3.85
779	1367	4.503734	CGGGCGTTCAATTAGTAATCGTTA	59.496	41.667	0.00	0.00	0.00	3.18
780	1368	5.005586	CGGGCGTTCAATTAGTAATCGTTAA	59.994	40.000	0.00	0.00	0.00	2.01
781	1369	6.455380	CGGGCGTTCAATTAGTAATCGTTAAA	60.455	38.462	0.00	0.00	0.00	1.52
782	1370	7.242783	GGGCGTTCAATTAGTAATCGTTAAAA	58.757	34.615	0.00	0.00	0.00	1.52
783	1371	7.427318	GGGCGTTCAATTAGTAATCGTTAAAAG	59.573	37.037	0.00	0.00	0.00	2.27
784	1372	7.959109	GGCGTTCAATTAGTAATCGTTAAAAGT	59.041	33.333	0.00	0.00	0.00	2.66
785	1373	9.956797	GCGTTCAATTAGTAATCGTTAAAAGTA	57.043	29.630	0.00	0.00	0.00	2.24
840	1428	4.121669	GCTCCTCAGCGTGCTCGA	62.122	66.667	13.13	0.00	39.71	4.04
888	1509	0.252239	GGACATTGGGCCTTTTCCCT	60.252	55.000	4.53	0.00	46.67	4.20
926	1551	4.129737	TTCTCTTCCGCCGCTCCG	62.130	66.667	0.00	0.00	0.00	4.63
2014	2703	0.738975	TCATGTCCTAGAGTTCGGCG	59.261	55.000	0.00	0.00	0.00	6.46
2310	3027	1.067354	CCCTGATGCTTCTTTTGGCAC	60.067	52.381	0.88	0.00	41.39	5.01
2742	3477	0.256752	CTGAAGATGGTGGCATGGGA	59.743	55.000	0.00	0.00	0.00	4.37
3127	4982	2.214920	GGGGCCGGGGATAGTAGTG	61.215	68.421	2.18	0.00	0.00	2.74
3132	5043	2.027949	GCCGGGGATAGTAGTGACAGT	61.028	57.143	2.18	0.00	0.00	3.55
3187	5098	9.944376	TTGATAATTTCCTCTAGATATTTCCCG	57.056	33.333	0.00	0.00	30.04	5.14
3188	5099	8.041323	TGATAATTTCCTCTAGATATTTCCCGC	58.959	37.037	0.00	0.00	30.04	6.13
3189	5100	5.825593	ATTTCCTCTAGATATTTCCCGCA	57.174	39.130	0.00	0.00	0.00	5.69
3190	5101	5.623956	TTTCCTCTAGATATTTCCCGCAA	57.376	39.130	0.00	0.00	0.00	4.85
3191	5102	5.623956	TTCCTCTAGATATTTCCCGCAAA	57.376	39.130	0.00	0.00	0.00	3.68
3192	5103	5.623956	TCCTCTAGATATTTCCCGCAAAA	57.376	39.130	0.00	0.00	0.00	2.44
3193	5104	5.996644	TCCTCTAGATATTTCCCGCAAAAA	58.003	37.500	0.00	0.00	0.00	1.94
3281	5192	2.094286	TGTGCCCTTTTGTGTTCTGTTG	60.094	45.455	0.00	0.00	0.00	3.33
3290	5201	6.418819	CCTTTTGTGTTCTGTTGTGATTGATC	59.581	38.462	0.00	0.00	0.00	2.92
3391	5318	1.333931	TGGTTATTTTCGCAACGTGCA	59.666	42.857	9.95	0.00	45.36	4.57
3481	5443	6.563037	ATGATATGCAGCATCCTAGATCTT	57.437	37.500	12.38	4.53	0.00	2.40
3549	5511	1.610102	CCAGAGGGTCACAGCTTCTTG	60.610	57.143	0.00	0.00	29.16	3.02
3575	5543	4.199310	GCCTATATGGTTCTTCAGTTGCA	58.801	43.478	0.00	0.00	38.35	4.08
3605	5573	1.005975	GTTATCATGTCGTCGTGCTGC	60.006	52.381	0.00	0.00	0.00	5.25
3666	5635	5.982356	AGACGGGGTAGACCTTTTATTAAC	58.018	41.667	0.00	0.00	40.03	2.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
35	37	1.227263	CCTTGGTCGCTATCGTGGG	60.227	63.158	0.00	0.00	36.96	4.61
181	191	0.550147	TCTCCTTAGCCAGGGCCTTT	60.550	55.000	1.32	0.00	44.12	3.11
274	285	2.937959	CTTCCCCTCCTCCTCCCTCG	62.938	70.000	0.00	0.00	0.00	4.63
357	368	1.069378	GACGTGCGAGGAAAGGTACG	61.069	60.000	0.00	0.00	45.66	3.67
628	639	4.113815	CCGCTCATTGCCCCCTCA	62.114	66.667	0.00	0.00	38.78	3.86
636	647	3.631686	TCATTATTTGACCCCGCTCATTG	59.368	43.478	0.00	0.00	0.00	2.82
653	664	7.153315	TCTTTCATGCAGCAACAAAATCATTA	58.847	30.769	0.00	0.00	0.00	1.90
753	1341	2.012937	TACTAATTGAACGCCCGTGG	57.987	50.000	0.00	0.00	0.00	4.94
779	1367	9.662947	AGACCGCAAAATTATACTACTACTTTT	57.337	29.630	0.00	0.00	0.00	2.27
780	1368	9.095065	CAGACCGCAAAATTATACTACTACTTT	57.905	33.333	0.00	0.00	0.00	2.66
781	1369	7.709613	CCAGACCGCAAAATTATACTACTACTT	59.290	37.037	0.00	0.00	0.00	2.24
782	1370	7.147776	ACCAGACCGCAAAATTATACTACTACT	60.148	37.037	0.00	0.00	0.00	2.57
783	1371	6.982724	ACCAGACCGCAAAATTATACTACTAC	59.017	38.462	0.00	0.00	0.00	2.73
784	1372	7.116075	ACCAGACCGCAAAATTATACTACTA	57.884	36.000	0.00	0.00	0.00	1.82
785	1373	5.985911	ACCAGACCGCAAAATTATACTACT	58.014	37.500	0.00	0.00	0.00	2.57
786	1374	5.051240	CGACCAGACCGCAAAATTATACTAC	60.051	44.000	0.00	0.00	0.00	2.73
787	1375	5.045215	CGACCAGACCGCAAAATTATACTA	58.955	41.667	0.00	0.00	0.00	1.82
825	1413	2.258591	GTTCGAGCACGCTGAGGA	59.741	61.111	0.00	0.00	39.58	3.71
834	1422	2.031919	AATGGGCACGTTCGAGCA	59.968	55.556	15.14	0.00	0.00	4.26
840	1428	2.035626	CCTCCCAATGGGCACGTT	59.964	61.111	14.88	0.00	43.94	3.99
1045	1677	1.445410	CGTCGAGCCGGAACATCAA	60.445	57.895	5.05	0.00	0.00	2.57
1077	1709	1.753368	CGAAGAGGGCCTCCATCTCC	61.753	65.000	29.62	11.39	34.83	3.71
2310	3027	6.260714	TGCTAGTACATTATGGTGCAAATGAG	59.739	38.462	14.27	4.09	36.73	2.90
2646	3381	2.005451	CGCAGAGGATTCACTTTGGAG	58.995	52.381	0.00	0.00	0.00	3.86
2742	3477	2.704572	CCCGATGCTCTCTTGAAGTTT	58.295	47.619	0.00	0.00	0.00	2.66
3127	4982	6.749118	GCAAAACATGGATTATCTCAACTGTC	59.251	38.462	0.00	0.00	0.00	3.51
3132	5043	8.461222	CAGTAAGCAAAACATGGATTATCTCAA	58.539	33.333	0.00	0.00	0.00	3.02
3193	5104	9.237706	TCCCAGGTAATATCTAGAGGAATTTTT	57.762	33.333	0.00	0.00	0.00	1.94
3194	5105	8.814448	TCCCAGGTAATATCTAGAGGAATTTT	57.186	34.615	0.00	0.00	0.00	1.82
3195	5106	8.997301	ATCCCAGGTAATATCTAGAGGAATTT	57.003	34.615	0.00	0.00	0.00	1.82
3199	5110	9.494055	CAAATATCCCAGGTAATATCTAGAGGA	57.506	37.037	0.00	0.00	0.00	3.71
3200	5111	9.273137	ACAAATATCCCAGGTAATATCTAGAGG	57.727	37.037	0.00	0.00	0.00	3.69
3203	5114	9.892130	GGAACAAATATCCCAGGTAATATCTAG	57.108	37.037	0.00	0.00	0.00	2.43
3204	5115	9.400208	TGGAACAAATATCCCAGGTAATATCTA	57.600	33.333	0.00	0.00	36.04	1.98
3205	5116	8.287904	TGGAACAAATATCCCAGGTAATATCT	57.712	34.615	0.00	0.00	36.04	1.98
3206	5117	7.121315	GCTGGAACAAATATCCCAGGTAATATC	59.879	40.741	0.00	0.00	44.70	1.63
3281	5192	5.032100	GCACATCTATGCAGATCAATCAC	57.968	43.478	0.00	0.00	45.39	3.06
3320	5231	2.146342	CGCAACTGAAGAACCAGATGT	58.854	47.619	0.00	0.00	38.64	3.06
3391	5318	9.110502	GCAGCTCAAGTTACTATTATTACCTTT	57.889	33.333	0.00	0.00	0.00	3.11
3481	5443	7.171508	GCGTGTGGAAGATCATAGAATAAATGA	59.828	37.037	0.00	0.00	37.73	2.57
3501	5463	5.927030	ACAACTACTTTATCATTGCGTGTG	58.073	37.500	0.00	0.00	0.00	3.82
3502	5464	5.163992	CGACAACTACTTTATCATTGCGTGT	60.164	40.000	0.00	0.00	0.00	4.49
3549	5511	5.234466	ACTGAAGAACCATATAGGCCATC	57.766	43.478	5.01	0.00	43.14	3.51
3582	5550	2.686405	AGCACGACGACATGATAACCTA	59.314	45.455	0.00	0.00	0.00	3.08
3605	5573	3.799281	TGGTGAAAACTGAAAAGCCTG	57.201	42.857	0.00	0.00	0.00	4.85
3666	5635	1.964373	GTACGTTGTGCCTGGTGGG	60.964	63.158	0.00	0.00	38.36	4.61

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.