AutoCloner

Multiple sequence alignment - TraesCS3B01G242400

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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	TraesCS3B01G242400	chr3B	100.000	3034	0	0	1	3034	382316950	382319983	0.000000e+00	5603.0
1	TraesCS3B01G242400	chr3D	98.222	1406	13	3	1634	3034	290015632	290017030	0.000000e+00	2447.0
2	TraesCS3B01G242400	chr3D	98.385	991	12	2	649	1636	290014561	290015550	0.000000e+00	1738.0
3	TraesCS3B01G242400	chr3D	89.596	644	42	10	83	707	290012900	290013537	0.000000e+00	795.0
4	TraesCS3B01G242400	chr3D	85.920	348	32	2	225	555	31098953	31099300	3.720000e-94	355.0
5	TraesCS3B01G242400	chr3D	93.902	82	4	1	2	83	326701490	326701410	4.110000e-24	122.0
6	TraesCS3B01G242400	chr3D	100.000	40	0	0	700	739	290014517	290014556	1.170000e-09	75.0
7	TraesCS3B01G242400	chr3A	95.745	1457	46	5	1587	3034	381293299	381294748	0.000000e+00	2333.0
8	TraesCS3B01G242400	chr3A	98.013	755	15	0	799	1553	381292543	381293297	0.000000e+00	1312.0
9	TraesCS3B01G242400	chr3A	95.385	260	12	0	557	816	381292266	381292525	6.050000e-112	414.0
10	TraesCS3B01G242400	chr3A	86.577	149	13	6	83	224	381292133	381292281	1.130000e-34	158.0
11	TraesCS3B01G242400	chr3A	97.590	83	2	0	1	83	534189461	534189379	3.150000e-30	143.0
12	TraesCS3B01G242400	chr3A	94.048	84	4	1	1	84	213239443	213239361	3.180000e-25	126.0
13	TraesCS3B01G242400	chr3A	92.771	83	6	0	1	83	584094329	584094411	1.480000e-23	121.0
14	TraesCS3B01G242400	chr1D	86.969	353	28	3	225	559	334455369	334455721	6.140000e-102	381.0
15	TraesCS3B01G242400	chr1D	93.023	43	3	0	1549	1591	473785734	473785776	2.530000e-06	63.9
16	TraesCS3B01G242400	chr4B	86.932	352	28	3	225	559	168151591	168151941	2.210000e-101	379.0
17	TraesCS3B01G242400	chr4A	86.313	358	31	3	225	564	640912351	640912708	1.030000e-99	374.0
18	TraesCS3B01G242400	chr4A	85.933	327	27	4	251	558	32409911	32409585	6.270000e-87	331.0
19	TraesCS3B01G242400	chr4A	85.417	336	30	6	251	567	677125110	677125445	6.270000e-87	331.0
20	TraesCS3B01G242400	chr6A	85.795	352	33	4	225	559	49742703	49742352	1.030000e-94	357.0
21	TraesCS3B01G242400	chr2A	84.986	353	36	7	225	560	519349602	519349954	2.900000e-90	342.0
22	TraesCS3B01G242400	chr2A	97.727	44	1	0	1549	1592	31984558	31984601	3.240000e-10	76.8
23	TraesCS3B01G242400	chr7A	84.943	352	35	4	225	558	643253025	643253376	1.040000e-89	340.0
24	TraesCS3B01G242400	chr7A	84.375	352	36	5	225	558	635371383	635371033	8.110000e-86	327.0
25	TraesCS3B01G242400	chr7A	88.525	61	5	2	1538	1597	732036874	732036815	4.200000e-09	73.1
26	TraesCS3B01G242400	chr5A	84.286	350	38	3	225	557	404011843	404012192	2.920000e-85	326.0
27	TraesCS3B01G242400	chr5A	95.122	41	2	0	1549	1589	656937068	656937028	7.020000e-07	65.8
28	TraesCS3B01G242400	chr1B	85.366	328	30	3	251	560	363451112	363450785	1.050000e-84	324.0
29	TraesCS3B01G242400	chr1B	93.976	83	5	0	1	83	558549621	558549703	3.180000e-25	126.0
30	TraesCS3B01G242400	chr5D	81.654	387	35	7	206	558	435968279	435967895	3.830000e-74	289.0
31	TraesCS3B01G242400	chr5D	85.388	219	15	7	362	563	53873810	53874028	8.520000e-51	211.0
32	TraesCS3B01G242400	chr5D	97.674	43	1	0	1548	1590	173753662	173753620	1.170000e-09	75.0
33	TraesCS3B01G242400	chr6B	97.590	83	2	0	1	83	100869138	100869056	3.150000e-30	143.0
34	TraesCS3B01G242400	chr6B	91.489	47	2	1	1549	1593	678748021	678748067	2.530000e-06	63.9
35	TraesCS3B01G242400	chr5B	96.471	85	3	0	1	85	98504271	98504187	1.130000e-29	141.0
36	TraesCS3B01G242400	chr7D	93.902	82	3	2	2	83	88371717	88371638	4.110000e-24	122.0
37	TraesCS3B01G242400	chr4D	91.463	82	6	1	2	83	17255523	17255603	8.890000e-21	111.0
38	TraesCS3B01G242400	chr6D	94.340	53	2	1	1538	1590	469221232	469221283	2.510000e-11	80.5
39	TraesCS3B01G242400	chr1A	95.556	45	2	0	1549	1593	513890300	513890256	4.200000e-09	73.1

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	TraesCS3B01G242400	chr3B	382316950	382319983	3033	False	5603.00	5603	100.00000	1	3034	1	chr3B.!!$F1	3033
1	TraesCS3B01G242400	chr3D	290012900	290017030	4130	False	1263.75	2447	96.55075	83	3034	4	chr3D.!!$F2	2951
2	TraesCS3B01G242400	chr3A	381292133	381294748	2615	False	1054.25	2333	93.93000	83	3034	4	chr3A.!!$F2	2951

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
307	315	0.036388	GCTCATCCTCACGGTTTGGA	60.036	55.000	1.96	1.96	0.0	3.53	F
807	1914	1.154413	CGCATCACCAACGTCTTGC	60.154	57.895	0.00	0.00	0.0	4.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1179	2321	3.077556	CTCGGAGGGGTGGACAGG	61.078	72.222	0.0	0.0	0.0	4.00	R
2779	4017	2.427753	CGCCTCCCTATCCCAAGC	59.572	66.667	0.0	0.0	0.0	4.01	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
54	55	8.472007	TTCCTCTCTCTTCTATAAAGCTAAGG	57.528	38.462	0.00	0.00	0.00	2.69
55	56	7.588169	TCCTCTCTCTTCTATAAAGCTAAGGT	58.412	38.462	0.00	0.00	0.00	3.50
56	57	8.725256	TCCTCTCTCTTCTATAAAGCTAAGGTA	58.275	37.037	0.00	0.00	0.00	3.08
57	58	8.789762	CCTCTCTCTTCTATAAAGCTAAGGTAC	58.210	40.741	0.00	0.00	0.00	3.34
58	59	8.380743	TCTCTCTTCTATAAAGCTAAGGTACG	57.619	38.462	0.00	0.00	0.00	3.67
59	60	6.968250	TCTCTTCTATAAAGCTAAGGTACGC	58.032	40.000	0.00	0.00	0.00	4.42
60	61	6.016443	TCTCTTCTATAAAGCTAAGGTACGCC	60.016	42.308	0.00	0.00	0.00	5.68
75	76	3.782042	GCCTTTGGCGTACTCTCG	58.218	61.111	0.00	0.00	39.62	4.04
76	77	1.810030	GCCTTTGGCGTACTCTCGG	60.810	63.158	0.00	0.00	39.62	4.63
77	78	1.888018	CCTTTGGCGTACTCTCGGA	59.112	57.895	0.00	0.00	0.00	4.55
78	79	0.245539	CCTTTGGCGTACTCTCGGAA	59.754	55.000	0.00	0.00	0.00	4.30
79	80	1.337447	CCTTTGGCGTACTCTCGGAAA	60.337	52.381	0.00	0.00	0.00	3.13
80	81	2.409975	CTTTGGCGTACTCTCGGAAAA	58.590	47.619	0.00	0.00	0.00	2.29
81	82	2.529780	TTGGCGTACTCTCGGAAAAA	57.470	45.000	0.00	0.00	0.00	1.94
113	114	2.611292	GCATCTCAATGTAGTGGCTCAC	59.389	50.000	0.00	0.00	35.18	3.51
126	127	2.939103	GTGGCTCACATGTTAGCTAAGG	59.061	50.000	26.60	2.34	38.80	2.69
150	151	9.569122	AGGCTTGTAAGAATCTTAGTGTTTTTA	57.431	29.630	2.48	0.00	0.00	1.52
167	173	9.705290	AGTGTTTTTATGTTTTTGTTCTGTTCT	57.295	25.926	0.00	0.00	0.00	3.01
243	251	1.486310	TCAAGAAGAGTGGCGCCATAT	59.514	47.619	35.23	24.91	0.00	1.78
244	252	1.600957	CAAGAAGAGTGGCGCCATATG	59.399	52.381	35.23	18.68	0.00	1.78
255	263	1.228124	GCCATATGTAAGGCGCCCA	60.228	57.895	26.15	15.43	41.70	5.36
274	282	3.220110	CCACAGCTGCTTAATGGATGAT	58.780	45.455	15.27	0.00	31.69	2.45
281	289	1.541588	GCTTAATGGATGATTCCCGGC	59.458	52.381	0.00	0.00	41.83	6.13
282	290	2.815589	GCTTAATGGATGATTCCCGGCT	60.816	50.000	0.00	0.00	41.83	5.52
284	292	1.143813	AATGGATGATTCCCGGCTCT	58.856	50.000	0.00	0.00	41.83	4.09
294	302	2.279784	CCGGCTCTTCGGCTCATC	60.280	66.667	0.00	0.00	43.71	2.92
297	305	1.068921	GGCTCTTCGGCTCATCCTC	59.931	63.158	0.00	0.00	34.85	3.71
307	315	0.036388	GCTCATCCTCACGGTTTGGA	60.036	55.000	1.96	1.96	0.00	3.53
310	318	1.905894	TCATCCTCACGGTTTGGATCA	59.094	47.619	8.26	0.00	38.41	2.92
339	347	1.467342	GTTTTGGCGTGGTCCACTATC	59.533	52.381	19.82	9.35	35.50	2.08
355	363	4.700213	CCACTATCTTTTGTCGGGATGTTT	59.300	41.667	0.00	0.00	0.00	2.83
359	367	3.546724	TCTTTTGTCGGGATGTTTGTGA	58.453	40.909	0.00	0.00	0.00	3.58
393	401	2.289382	TGTGGTGTACAAGCATGACGAT	60.289	45.455	0.00	0.00	38.84	3.73
435	459	2.560861	CGGGTTGCACGTGATTGG	59.439	61.111	22.23	0.00	0.00	3.16
465	489	9.131791	GTAACCCAATTATGGTCTGATTGTATT	57.868	33.333	0.00	0.00	46.01	1.89
478	502	7.277098	GGTCTGATTGTATTAGTTTTAGCACGA	59.723	37.037	0.00	0.00	0.00	4.35
494	518	5.713822	AGCACGATTTTCCGTAGATTAAC	57.286	39.130	0.00	0.00	41.29	2.01
495	519	5.172934	AGCACGATTTTCCGTAGATTAACA	58.827	37.500	0.00	0.00	41.29	2.41
505	529	4.163458	TCCGTAGATTAACAGGGCAATTCT	59.837	41.667	0.00	0.00	0.00	2.40
506	530	4.881850	CCGTAGATTAACAGGGCAATTCTT	59.118	41.667	0.00	0.00	0.00	2.52
507	531	5.357032	CCGTAGATTAACAGGGCAATTCTTT	59.643	40.000	0.00	0.00	0.00	2.52
517	541	7.544804	ACAGGGCAATTCTTTTCTTCTTAAT	57.455	32.000	0.00	0.00	0.00	1.40
535	559	9.956720	CTTCTTAATTAATCGATGAGGCAATTT	57.043	29.630	0.00	0.00	0.00	1.82
807	1914	1.154413	CGCATCACCAACGTCTTGC	60.154	57.895	0.00	0.00	0.00	4.01
919	2061	1.990614	GCGTTCCCTCCTTCCCTCT	60.991	63.158	0.00	0.00	0.00	3.69
982	2124	2.693069	AGAGACAATCAAGAACGCCAG	58.307	47.619	0.00	0.00	0.00	4.85
1179	2321	4.785453	CCTCCCAAGACGCCAGCC	62.785	72.222	0.00	0.00	0.00	4.85
1338	2483	1.204113	AGAGGAAGGTGGCCAAGGAG	61.204	60.000	7.24	0.00	0.00	3.69
1699	2930	6.509418	TGTAATTAGTTCTTGGGCATGTTC	57.491	37.500	0.00	0.00	0.00	3.18
1745	2976	5.212532	TGGTGAAGTTGCTGCAAATTATT	57.787	34.783	25.45	13.98	31.79	1.40
2064	3295	2.264005	TGGCGGTGTTGTTCTGTATT	57.736	45.000	0.00	0.00	0.00	1.89
2065	3296	2.577700	TGGCGGTGTTGTTCTGTATTT	58.422	42.857	0.00	0.00	0.00	1.40
2066	3297	2.550606	TGGCGGTGTTGTTCTGTATTTC	59.449	45.455	0.00	0.00	0.00	2.17
2067	3298	2.812011	GGCGGTGTTGTTCTGTATTTCT	59.188	45.455	0.00	0.00	0.00	2.52
2068	3299	3.998341	GGCGGTGTTGTTCTGTATTTCTA	59.002	43.478	0.00	0.00	0.00	2.10
2069	3300	4.634443	GGCGGTGTTGTTCTGTATTTCTAT	59.366	41.667	0.00	0.00	0.00	1.98
2779	4017	4.619160	GCAAGGTTAGGGATCTTTTTGCAG	60.619	45.833	0.00	0.00	39.41	4.41
2863	4101	8.366401	TGAATAGCAAAAATGACCTCAAATTCA	58.634	29.630	0.00	0.00	0.00	2.57
2931	4170	3.550678	GTCCGAAGAGGTTAACAATAGCG	59.449	47.826	8.10	5.32	41.99	4.26

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
28	29	8.919145	CCTTAGCTTTATAGAAGAGAGAGGAAA	58.081	37.037	0.00	0.0	0.00	3.13
29	30	8.062536	ACCTTAGCTTTATAGAAGAGAGAGGAA	58.937	37.037	0.00	0.0	0.00	3.36
30	31	7.588169	ACCTTAGCTTTATAGAAGAGAGAGGA	58.412	38.462	0.00	0.0	0.00	3.71
31	32	7.833285	ACCTTAGCTTTATAGAAGAGAGAGG	57.167	40.000	0.00	0.0	0.00	3.69
32	33	8.500773	CGTACCTTAGCTTTATAGAAGAGAGAG	58.499	40.741	0.00	0.0	0.00	3.20
33	34	7.041235	GCGTACCTTAGCTTTATAGAAGAGAGA	60.041	40.741	0.00	0.0	0.00	3.10
34	35	7.079475	GCGTACCTTAGCTTTATAGAAGAGAG	58.921	42.308	0.00	0.0	0.00	3.20
35	36	6.016443	GGCGTACCTTAGCTTTATAGAAGAGA	60.016	42.308	0.00	0.0	0.00	3.10
36	37	6.151004	GGCGTACCTTAGCTTTATAGAAGAG	58.849	44.000	0.00	0.0	0.00	2.85
37	38	6.081872	GGCGTACCTTAGCTTTATAGAAGA	57.918	41.667	0.00	0.0	0.00	2.87
58	59	1.810030	CCGAGAGTACGCCAAAGGC	60.810	63.158	0.00	0.0	46.75	4.35
59	60	0.245539	TTCCGAGAGTACGCCAAAGG	59.754	55.000	0.00	0.0	0.00	3.11
60	61	2.074547	TTTCCGAGAGTACGCCAAAG	57.925	50.000	0.00	0.0	0.00	2.77
61	62	2.529780	TTTTCCGAGAGTACGCCAAA	57.470	45.000	0.00	0.0	0.00	3.28
62	63	2.529780	TTTTTCCGAGAGTACGCCAA	57.470	45.000	0.00	0.0	0.00	4.52
78	79	7.322664	ACATTGAGATGCCGATAAACATTTTT	58.677	30.769	0.00	0.0	36.72	1.94
79	80	6.866480	ACATTGAGATGCCGATAAACATTTT	58.134	32.000	0.00	0.0	36.72	1.82
80	81	6.455360	ACATTGAGATGCCGATAAACATTT	57.545	33.333	0.00	0.0	36.72	2.32
81	82	6.767902	ACTACATTGAGATGCCGATAAACATT	59.232	34.615	0.00	0.0	36.72	2.71
87	88	3.554960	GCCACTACATTGAGATGCCGATA	60.555	47.826	0.00	0.0	36.72	2.92
88	89	2.808202	GCCACTACATTGAGATGCCGAT	60.808	50.000	0.00	0.0	36.72	4.18
150	151	6.877236	ACAATCCAGAACAGAACAAAAACAT	58.123	32.000	0.00	0.0	0.00	2.71
255	263	3.887716	GGAATCATCCATTAAGCAGCTGT	59.112	43.478	16.64	0.0	45.79	4.40
281	289	0.248825	CGTGAGGATGAGCCGAAGAG	60.249	60.000	0.00	0.0	43.43	2.85
282	290	1.809869	CGTGAGGATGAGCCGAAGA	59.190	57.895	0.00	0.0	43.43	2.87
297	305	3.427909	CCACAATGATGATCCAAACCGTG	60.428	47.826	0.00	0.0	0.00	4.94
307	315	2.562298	ACGCCAAAACCACAATGATGAT	59.438	40.909	0.00	0.0	0.00	2.45
310	318	1.000731	CCACGCCAAAACCACAATGAT	59.999	47.619	0.00	0.0	0.00	2.45
339	347	3.628017	GTCACAAACATCCCGACAAAAG	58.372	45.455	0.00	0.0	0.00	2.27
355	363	2.099921	CCACAATTTTGAACCCGTCACA	59.900	45.455	0.00	0.0	35.39	3.58
359	367	2.104170	ACACCACAATTTTGAACCCGT	58.896	42.857	0.00	0.0	0.00	5.28
393	401	5.010213	GCAAACCCTCCTAACACACAATAAA	59.990	40.000	0.00	0.0	0.00	1.40
450	474	8.893727	GTGCTAAAACTAATACAATCAGACCAT	58.106	33.333	0.00	0.0	0.00	3.55
465	489	6.389091	TCTACGGAAAATCGTGCTAAAACTA	58.611	36.000	0.00	0.0	43.70	2.24
466	490	5.232463	TCTACGGAAAATCGTGCTAAAACT	58.768	37.500	0.00	0.0	43.70	2.66
478	502	4.850680	TGCCCTGTTAATCTACGGAAAAT	58.149	39.130	0.00	0.0	0.00	1.82
494	518	9.927668	TTAATTAAGAAGAAAAGAATTGCCCTG	57.072	29.630	0.00	0.0	0.00	4.45
505	529	9.173021	TGCCTCATCGATTAATTAAGAAGAAAA	57.827	29.630	3.94	0.0	0.00	2.29
506	530	8.731275	TGCCTCATCGATTAATTAAGAAGAAA	57.269	30.769	3.94	0.0	0.00	2.52
507	531	8.731275	TTGCCTCATCGATTAATTAAGAAGAA	57.269	30.769	3.94	0.0	0.00	2.52
585	610	5.518847	CACTTTTCTGAACGTGAGACTTACA	59.481	40.000	11.53	0.0	37.23	2.41
919	2061	0.323542	GACGGAGGGGAAGAGAGTGA	60.324	60.000	0.00	0.0	0.00	3.41
982	2124	0.319405	ATTGCTTGGTTTGAGCTGCC	59.681	50.000	0.00	0.0	40.75	4.85
1179	2321	3.077556	CTCGGAGGGGTGGACAGG	61.078	72.222	0.00	0.0	0.00	4.00
1338	2483	7.532682	CTTCTTCTTGAAGTATTCCTGTAGC	57.467	40.000	9.80	0.0	46.93	3.58
1745	2976	6.636454	AGTACATGAGGGGAAAAGAACATA	57.364	37.500	0.00	0.0	0.00	2.29
1865	3096	5.911752	TGCAGGAACAAGCAATCTTAAAAA	58.088	33.333	0.00	0.0	38.58	1.94
1866	3097	5.528043	TGCAGGAACAAGCAATCTTAAAA	57.472	34.783	0.00	0.0	38.58	1.52
2117	3353	8.668510	AAACTCAAGGATATAATAGTGTGCAG	57.331	34.615	0.00	0.0	0.00	4.41
2169	3405	6.332630	AGCTGGAAATTGGATTTTACATTCG	58.667	36.000	0.00	0.0	31.47	3.34
2779	4017	2.427753	CGCCTCCCTATCCCAAGC	59.572	66.667	0.00	0.0	0.00	4.01
2863	4101	9.582648	AGGTACATGGTGTTTTTAACTTATCTT	57.417	29.630	0.00	0.0	0.00	2.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.