AutoCloner

Multiple sequence alignment - TraesCS4A01G217300

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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	TraesCS4A01G217300	chr4A	100.000	2579	0	0	1	2579	516582296	516584874	0.000000e+00	4763
1	TraesCS4A01G217300	chr4A	81.669	791	110	19	819	1588	641443074	641442298	2.180000e-175	625
2	TraesCS4A01G217300	chr4D	90.150	2061	148	22	536	2579	67326644	67324622	0.000000e+00	2630
3	TraesCS4A01G217300	chr4B	90.297	2020	152	22	579	2579	99593705	99595699	0.000000e+00	2604
4	TraesCS4A01G217300	chr5B	79.800	802	116	25	800	1584	670074450	670075222	2.260000e-150	542
5	TraesCS4A01G217300	chr5D	80.234	769	111	19	819	1573	530834514	530835255	8.120000e-150	540
6	TraesCS4A01G217300	chr5D	83.117	539	78	10	1	537	376718308	376717781	1.800000e-131	479
7	TraesCS4A01G217300	chr5D	84.667	150	18	4	2374	2518	13713700	13713849	7.440000e-31	145
8	TraesCS4A01G217300	chr2D	83.507	479	70	9	31	506	445705314	445704842	3.050000e-119	438
9	TraesCS4A01G217300	chr2D	81.149	557	82	18	1	546	649588432	649587888	2.370000e-115	425
10	TraesCS4A01G217300	chr2D	96.667	60	2	0	2373	2432	564070291	564070350	1.630000e-17	100
11	TraesCS4A01G217300	chr7D	81.550	542	83	14	1	537	383231317	383230788	5.100000e-117	431
12	TraesCS4A01G217300	chr7D	79.024	553	94	18	1	542	159709653	159709112	2.440000e-95	359
13	TraesCS4A01G217300	chr5A	81.181	542	88	12	1	537	440952091	440952623	8.530000e-115	424
14	TraesCS4A01G217300	chr1D	80.515	544	96	9	1	541	477426198	477426734	2.390000e-110	409
15	TraesCS4A01G217300	chr3B	80.519	539	94	9	1	537	405958623	405959152	1.110000e-108	403
16	TraesCS4A01G217300	chr7B	80.347	519	92	10	1	515	692618047	692617535	4.030000e-103	385
17	TraesCS4A01G217300	chr7A	80.556	216	28	11	2373	2577	735514852	735515064	1.240000e-33	154

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	TraesCS4A01G217300	chr4A	516582296	516584874	2578	False	4763	4763	100.000	1	2579	1	chr4A.!!$F1	2578
1	TraesCS4A01G217300	chr4A	641442298	641443074	776	True	625	625	81.669	819	1588	1	chr4A.!!$R1	769
2	TraesCS4A01G217300	chr4D	67324622	67326644	2022	True	2630	2630	90.150	536	2579	1	chr4D.!!$R1	2043
3	TraesCS4A01G217300	chr4B	99593705	99595699	1994	False	2604	2604	90.297	579	2579	1	chr4B.!!$F1	2000
4	TraesCS4A01G217300	chr5B	670074450	670075222	772	False	542	542	79.800	800	1584	1	chr5B.!!$F1	784
5	TraesCS4A01G217300	chr5D	530834514	530835255	741	False	540	540	80.234	819	1573	1	chr5D.!!$F2	754
6	TraesCS4A01G217300	chr5D	376717781	376718308	527	True	479	479	83.117	1	537	1	chr5D.!!$R1	536
7	TraesCS4A01G217300	chr2D	649587888	649588432	544	True	425	425	81.149	1	546	1	chr2D.!!$R2	545
8	TraesCS4A01G217300	chr7D	383230788	383231317	529	True	431	431	81.550	1	537	1	chr7D.!!$R2	536
9	TraesCS4A01G217300	chr7D	159709112	159709653	541	True	359	359	79.024	1	542	1	chr7D.!!$R1	541
10	TraesCS4A01G217300	chr5A	440952091	440952623	532	False	424	424	81.181	1	537	1	chr5A.!!$F1	536
11	TraesCS4A01G217300	chr1D	477426198	477426734	536	False	409	409	80.515	1	541	1	chr1D.!!$F1	540
12	TraesCS4A01G217300	chr3B	405958623	405959152	529	False	403	403	80.519	1	537	1	chr3B.!!$F1	536
13	TraesCS4A01G217300	chr7B	692617535	692618047	512	True	385	385	80.347	1	515	1	chr7B.!!$R1	514

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
284	298	0.108138	GACATGGTCCAACGGAGGAG	60.108	60.0	0.00	0.0	38.64	3.69	F
515	531	0.179023	ACGTTTAAGGCGGGTTTGGA	60.179	50.0	6.49	0.0	0.00	3.53	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1306	1355	0.031917	TGGTCCGCCCCTATGTAGAA	60.032	55.000	0.00	0.0	0.00	2.10	R
2368	2433	1.135803	CCCATAGACCAAACGTTTGCG	60.136	52.381	31.02	25.3	44.93	4.85	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
62	63	2.350134	CTCAAGGAGCTGCAGCCA	59.650	61.111	34.39	11.07	43.38	4.75
107	109	4.215742	CCTTATCCGGCGGCGTGA	62.216	66.667	30.09	24.97	0.00	4.35
176	179	4.468689	GCGGACGGGGGAAGGAAG	62.469	72.222	0.00	0.00	0.00	3.46
275	287	1.958715	CACGCAACGACATGGTCCA	60.959	57.895	0.00	0.00	0.00	4.02
284	298	0.108138	GACATGGTCCAACGGAGGAG	60.108	60.000	0.00	0.00	38.64	3.69
285	299	0.544357	ACATGGTCCAACGGAGGAGA	60.544	55.000	0.00	0.00	38.64	3.71
299	313	2.634600	GAGGAGACGAGCTTCAGACTA	58.365	52.381	0.00	0.00	0.00	2.59
301	315	2.085320	GGAGACGAGCTTCAGACTACA	58.915	52.381	0.00	0.00	0.00	2.74
304	318	0.528470	ACGAGCTTCAGACTACAGGC	59.472	55.000	0.00	0.00	0.00	4.85
408	423	1.068121	GGCTGGATATAAGGGGTGCT	58.932	55.000	0.00	0.00	0.00	4.40
480	495	1.080298	CGTGACCGGTTAGTGACCC	60.080	63.158	9.42	0.00	46.35	4.46
502	517	2.349755	GGCCTGCCCAGACGTTTA	59.650	61.111	0.00	0.00	0.00	2.01
515	531	0.179023	ACGTTTAAGGCGGGTTTGGA	60.179	50.000	6.49	0.00	0.00	3.53
516	532	0.953003	CGTTTAAGGCGGGTTTGGAA	59.047	50.000	0.00	0.00	0.00	3.53
539	556	3.263170	TGCCCAGTTGTAGATGCTCTTAA	59.737	43.478	0.00	0.00	0.00	1.85
547	564	3.965347	TGTAGATGCTCTTAACCCTACCC	59.035	47.826	0.00	0.00	0.00	3.69
548	565	2.040178	AGATGCTCTTAACCCTACCCG	58.960	52.381	0.00	0.00	0.00	5.28
585	602	4.785346	ACCATCCTATGCTTGATCTTGT	57.215	40.909	0.00	0.00	0.00	3.16
612	629	3.209410	GCCAAGTATTCATCCTCCACAG	58.791	50.000	0.00	0.00	0.00	3.66
613	630	3.813443	CCAAGTATTCATCCTCCACAGG	58.187	50.000	0.00	0.00	42.01	4.00
615	632	1.414181	AGTATTCATCCTCCACAGGCG	59.586	52.381	0.00	0.00	40.12	5.52
617	634	0.467384	ATTCATCCTCCACAGGCGAG	59.533	55.000	0.00	0.00	40.12	5.03
657	674	2.041081	ACGATTTGATTTCCACCCCAGA	59.959	45.455	0.00	0.00	0.00	3.86
670	687	7.465900	TTCCACCCCAGAGATTAATATTTCT	57.534	36.000	0.00	0.00	0.00	2.52
683	700	9.751542	AGATTAATATTTCTCCGTAGTTGACTG	57.248	33.333	0.00	0.00	0.00	3.51
687	704	1.153823	CTCCGTAGTTGACTGGCCG	60.154	63.158	0.00	0.00	0.00	6.13
690	707	2.345991	GTAGTTGACTGGCCGCCA	59.654	61.111	12.67	12.67	0.00	5.69
691	708	2.033194	GTAGTTGACTGGCCGCCAC	61.033	63.158	8.43	0.00	0.00	5.01
692	709	3.248446	TAGTTGACTGGCCGCCACC	62.248	63.158	8.43	3.96	0.00	4.61
863	894	1.822990	CTGAATCCCAATTGCTGCACT	59.177	47.619	0.00	0.00	0.00	4.40
885	916	0.874607	ACGTGTCGCTTGTGTTCCTC	60.875	55.000	0.00	0.00	0.00	3.71
1003	1040	8.918116	ACACATATTACTTAGCTCAAGAGATGA	58.082	33.333	0.32	0.00	37.71	2.92
1037	1077	4.699257	GGTGATGCTTCTTGTTCTCTTCAT	59.301	41.667	0.88	0.00	0.00	2.57
1038	1078	5.163774	GGTGATGCTTCTTGTTCTCTTCATC	60.164	44.000	0.88	0.00	0.00	2.92
1039	1079	5.410746	GTGATGCTTCTTGTTCTCTTCATCA	59.589	40.000	0.88	0.00	37.37	3.07
1164	1213	0.889638	ACTTCCACGACAGCTCGAGA	60.890	55.000	18.75	0.00	43.06	4.04
1168	1217	2.673341	ACGACAGCTCGAGAGGCA	60.673	61.111	18.75	0.00	43.06	4.75
1171	1220	4.427661	ACAGCTCGAGAGGCACGC	62.428	66.667	18.75	0.00	0.00	5.34
1224	1273	2.954753	GCCGTCGTTGCAGACCTTG	61.955	63.158	0.86	0.00	37.85	3.61
1428	1477	3.998672	AACTTCCCGCTCGCCGAA	61.999	61.111	0.00	0.00	40.02	4.30
1510	1559	1.826921	GCCCGGACCTACTCGATGA	60.827	63.158	0.73	0.00	0.00	2.92
1513	1562	1.100510	CCGGACCTACTCGATGAACA	58.899	55.000	0.00	0.00	0.00	3.18
1514	1563	1.202268	CCGGACCTACTCGATGAACAC	60.202	57.143	0.00	0.00	0.00	3.32
1584	1634	6.729690	AAGCATGCAAATATTTAAGGGCTA	57.270	33.333	21.98	1.99	0.00	3.93
1624	1674	9.090692	CTTCACAGAGTGTTTTCATTTCATTTT	57.909	29.630	0.00	0.00	34.79	1.82
1625	1675	9.434420	TTCACAGAGTGTTTTCATTTCATTTTT	57.566	25.926	0.00	0.00	34.79	1.94
1664	1722	3.365364	CCGTGCTTTGAGATTTGGACTTC	60.365	47.826	0.00	0.00	0.00	3.01
1675	1733	5.565509	AGATTTGGACTTCTCCTTTTCCTC	58.434	41.667	0.00	0.00	37.48	3.71
1702	1760	0.530431	GTGTGCCTTTGCTTGGGTTG	60.530	55.000	0.00	0.00	38.71	3.77
1776	1834	9.558396	TGTGCTTTTTCTTAAATCAATGGAAAT	57.442	25.926	0.00	0.00	0.00	2.17
1976	2035	5.029807	TGCCATCACCGATGTAGATTTTA	57.970	39.130	3.47	0.00	38.28	1.52
1994	2053	7.937649	AGATTTTAAAGTCGGTTTTAAGCTGT	58.062	30.769	5.20	0.00	34.87	4.40
2142	2202	4.499526	CCCTCGAATCATGTCAGAGAAGAG	60.500	50.000	10.24	0.00	0.00	2.85
2197	2262	2.496070	CACTATGACCCGGTCTTCAGAA	59.504	50.000	18.54	0.00	33.15	3.02
2305	2370	1.971167	GCAACATTGGAGACGCCCA	60.971	57.895	0.00	0.00	34.97	5.36
2367	2432	9.344772	ACAATAATGTATTAGGCCAAATTACGA	57.655	29.630	5.01	0.00	38.24	3.43
2368	2433	9.607285	CAATAATGTATTAGGCCAAATTACGAC	57.393	33.333	5.01	0.00	0.00	4.34
2372	2439	2.096220	TAGGCCAAATTACGACGCAA	57.904	45.000	5.01	0.00	0.00	4.85
2563	2636	5.418840	GGGTCAAAATAGTGTGAATGGTGAT	59.581	40.000	0.00	0.00	0.00	3.06

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
62	63	0.172803	ATTTCTAACGACGGAGCGCT	59.827	50.000	11.27	11.27	33.86	5.92
71	72	0.034863	GGGCCACCCATTTCTAACGA	60.035	55.000	4.39	0.00	44.65	3.85
107	109	1.056700	CCACTAGTAGCCATGCCCCT	61.057	60.000	0.00	0.00	0.00	4.79
168	171	0.548510	CCCCTCCACATCTTCCTTCC	59.451	60.000	0.00	0.00	0.00	3.46
176	179	2.224305	CGAAATCCTACCCCTCCACATC	60.224	54.545	0.00	0.00	0.00	3.06
223	230	3.142393	CCGCATAGTGCCTAGCCT	58.858	61.111	0.00	0.00	41.12	4.58
270	279	1.935327	CTCGTCTCCTCCGTTGGACC	61.935	65.000	0.00	0.00	31.94	4.46
275	287	0.894184	TGAAGCTCGTCTCCTCCGTT	60.894	55.000	0.00	0.00	0.00	4.44
284	298	1.468395	GCCTGTAGTCTGAAGCTCGTC	60.468	57.143	0.00	0.00	0.00	4.20
285	299	0.528470	GCCTGTAGTCTGAAGCTCGT	59.472	55.000	0.00	0.00	0.00	4.18
328	342	2.126424	GTCAGACTGACGTCGGGC	60.126	66.667	27.33	25.49	44.93	6.13
374	389	1.523758	CAGCCCAAATATAGGACGGC	58.476	55.000	0.00	0.00	36.62	5.68
408	423	0.460722	TCAAACGTCCGAACTGACCA	59.539	50.000	0.00	0.00	31.35	4.02
443	458	3.184178	CACGAAATTTTGACCATGTTGGC	59.816	43.478	12.54	0.00	42.67	4.52
502	517	2.282783	GGCATTCCAAACCCGCCTT	61.283	57.895	0.00	0.00	39.73	4.35
515	531	2.648059	GAGCATCTACAACTGGGCATT	58.352	47.619	0.00	0.00	0.00	3.56
516	532	2.338577	GAGCATCTACAACTGGGCAT	57.661	50.000	0.00	0.00	0.00	4.40
539	556	0.632835	TCCATAGTGACGGGTAGGGT	59.367	55.000	0.00	0.00	0.00	4.34
564	581	4.164796	TGACAAGATCAAGCATAGGATGGT	59.835	41.667	0.00	0.00	43.93	3.55
585	602	4.517285	GAGGATGAATACTTGGCAACTGA	58.483	43.478	0.00	0.00	37.61	3.41
612	629	2.493973	CTCACAGCCTCTCTCGCC	59.506	66.667	0.00	0.00	0.00	5.54
613	630	2.493973	CCTCACAGCCTCTCTCGC	59.506	66.667	0.00	0.00	0.00	5.03
615	632	0.612744	AAAGCCTCACAGCCTCTCTC	59.387	55.000	0.00	0.00	0.00	3.20
617	634	2.351455	GTTAAAGCCTCACAGCCTCTC	58.649	52.381	0.00	0.00	0.00	3.20
657	674	9.751542	CAGTCAACTACGGAGAAATATTAATCT	57.248	33.333	0.00	0.00	0.00	2.40
670	687	2.967397	CGGCCAGTCAACTACGGA	59.033	61.111	2.24	0.00	0.00	4.69
687	704	0.674895	AGATTTCAGCTGTCGGTGGC	60.675	55.000	14.67	0.00	39.09	5.01
690	707	0.687354	ACCAGATTTCAGCTGTCGGT	59.313	50.000	14.67	12.37	0.00	4.69
691	708	1.081892	CACCAGATTTCAGCTGTCGG	58.918	55.000	14.67	11.78	0.00	4.79
692	709	2.084610	TCACCAGATTTCAGCTGTCG	57.915	50.000	14.67	1.21	0.00	4.35
693	710	2.941720	GGATCACCAGATTTCAGCTGTC	59.058	50.000	14.67	3.95	33.72	3.51
694	711	2.306805	TGGATCACCAGATTTCAGCTGT	59.693	45.455	14.67	0.00	41.77	4.40
695	712	2.995283	TGGATCACCAGATTTCAGCTG	58.005	47.619	7.63	7.63	41.77	4.24
721	745	3.505680	TGATGTTACTTGTGGATTGTGGC	59.494	43.478	0.00	0.00	0.00	5.01
863	894	1.149361	GAACACAAGCGACACGTGGA	61.149	55.000	21.57	0.00	34.91	4.02
885	916	1.482593	AGTGGATGGAAGGAGCGTAAG	59.517	52.381	0.00	0.00	43.44	2.34
1003	1040	2.671070	CATCACCGCTCCCTTGGT	59.329	61.111	0.00	0.00	39.66	3.67
1206	1255	2.665185	AAGGTCTGCAACGACGGC	60.665	61.111	0.00	0.00	34.75	5.68
1224	1273	4.362476	ACGTACACCGCCCCGAAC	62.362	66.667	0.00	0.00	41.42	3.95
1306	1355	0.031917	TGGTCCGCCCCTATGTAGAA	60.032	55.000	0.00	0.00	0.00	2.10
1434	1483	2.029666	CCGACGATGGGCATCTCC	59.970	66.667	0.00	0.00	35.72	3.71
1510	1559	2.280592	GTCGCCGGTCTTGGTGTT	60.281	61.111	1.90	0.00	40.48	3.32
1561	1610	5.619132	AGCCCTTAAATATTTGCATGCTT	57.381	34.783	20.33	6.03	0.00	3.91
1584	1634	6.000219	ACTCTGTGAAGCATTACAATCAGTT	59.000	36.000	0.00	0.00	0.00	3.16
1624	1674	1.543802	CGGCCAACCTGAAGCAATAAA	59.456	47.619	2.24	0.00	0.00	1.40
1625	1675	1.173043	CGGCCAACCTGAAGCAATAA	58.827	50.000	2.24	0.00	0.00	1.40
1627	1677	1.228552	ACGGCCAACCTGAAGCAAT	60.229	52.632	2.24	0.00	0.00	3.56
1630	1688	4.043200	GCACGGCCAACCTGAAGC	62.043	66.667	2.24	0.00	0.00	3.86
1664	1722	5.393461	GCACACCAATATTGAGGAAAAGGAG	60.393	44.000	17.23	0.00	0.00	3.69
1675	1733	3.598019	AGCAAAGGCACACCAATATTG	57.402	42.857	8.58	8.58	44.61	1.90
1702	1760	1.929836	CTTGCCACTTGCTAGACGATC	59.070	52.381	1.04	0.00	44.38	3.69
1976	2035	4.976224	AACACAGCTTAAAACCGACTTT	57.024	36.364	0.00	0.00	0.00	2.66
1994	2053	6.318648	AGTGAAAAATAGCACTGACTGAAACA	59.681	34.615	0.00	0.00	43.26	2.83
2047	2106	5.656416	ACCCATGTGAGTATTAAACATTGGG	59.344	40.000	15.74	15.74	39.98	4.12
2171	2236	2.463752	AGACCGGGTCATAGTGCTAAA	58.536	47.619	27.87	0.00	34.60	1.85
2265	2330	2.990740	AGACATGGGGTTTAAGCCAA	57.009	45.000	15.41	3.79	37.54	4.52
2266	2331	2.896685	CAAAGACATGGGGTTTAAGCCA	59.103	45.455	15.41	1.91	37.54	4.75
2276	2341	2.299582	TCCAATGTTGCAAAGACATGGG	59.700	45.455	14.95	14.95	45.96	4.00
2305	2370	6.598850	GCTAGGTAGTAGTGAACTAGTGACTT	59.401	42.308	11.93	0.48	41.42	3.01
2306	2371	6.114767	GCTAGGTAGTAGTGAACTAGTGACT	58.885	44.000	11.51	11.51	41.42	3.41
2352	2417	2.096220	TGCGTCGTAATTTGGCCTAA	57.904	45.000	3.32	2.09	0.00	2.69
2368	2433	1.135803	CCCATAGACCAAACGTTTGCG	60.136	52.381	31.02	25.30	44.93	4.85
2372	2439	2.943036	ACACCCATAGACCAAACGTT	57.057	45.000	0.00	0.00	0.00	3.99
2459	2528	6.128634	CGAGTACAATGGAAGGTCAAGTTTAC	60.129	42.308	0.00	0.00	0.00	2.01
2535	2608	6.098982	ACCATTCACACTATTTTGACCCAAAA	59.901	34.615	7.23	7.23	45.41	2.44
2539	2612	4.764823	TCACCATTCACACTATTTTGACCC	59.235	41.667	0.00	0.00	0.00	4.46

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.