AutoCloner

Multiple sequence alignment - TraesCS4A01G305800

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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	TraesCS4A01G305800	chr4A	100.000	2954	0	0	1	2954	600920929	600917976	0.000000e+00	5456
1	TraesCS4A01G305800	chr4A	79.782	2018	360	28	961	2954	601309765	601311758	0.000000e+00	1423
2	TraesCS4A01G305800	chr4A	77.188	754	157	14	1606	2352	601310852	601311597	2.720000e-115	425
3	TraesCS4A01G305800	chr4B	95.730	2014	77	4	941	2954	4955150	4953146	0.000000e+00	3234
4	TraesCS4A01G305800	chr4B	81.799	1456	234	25	937	2382	6055752	6057186	0.000000e+00	1192
5	TraesCS4A01G305800	chr4B	83.747	1249	180	11	1013	2245	6039137	6040378	0.000000e+00	1160
6	TraesCS4A01G305800	chr4B	87.234	752	70	11	10	756	4956418	4955688	0.000000e+00	833
7	TraesCS4A01G305800	chr4B	78.791	910	176	12	2049	2954	6056421	6057317	1.960000e-166	595
8	TraesCS4A01G305800	chr4B	76.796	1030	205	25	1625	2640	4954322	4953313	5.570000e-152	547
9	TraesCS4A01G305800	chr4B	77.763	769	165	5	1624	2389	4954035	4953270	4.460000e-128	468
10	TraesCS4A01G305800	chr4B	76.587	756	159	13	2078	2827	4954445	4953702	1.650000e-107	399
11	TraesCS4A01G305800	chr4B	80.810	469	75	10	2320	2784	6056405	6056862	1.300000e-93	353
12	TraesCS4A01G305800	chr4B	88.571	175	7	3	754	916	4955417	4955244	1.800000e-47	200
13	TraesCS4A01G305800	chr4D	93.575	2039	101	11	937	2954	3712427	3714456	0.000000e+00	3013
14	TraesCS4A01G305800	chr4D	91.592	892	57	13	1	882	3711396	3712279	0.000000e+00	1216
15	TraesCS4A01G305800	chr4D	83.531	1014	132	21	958	1950	3421771	3420772	0.000000e+00	915
16	TraesCS4A01G305800	chr4D	77.067	1016	209	18	1625	2631	3713280	3714280	5.530000e-157	564
17	TraesCS4A01G305800	chr4D	75.753	598	135	5	2225	2820	3713160	3713749	2.880000e-75	292
18	TraesCS4A01G305800	chr2D	81.605	810	114	21	966	1754	2341470	2342265	3.210000e-179	638
19	TraesCS4A01G305800	chr2D	77.221	1058	216	19	1251	2295	5394727	5395772	1.960000e-166	595
20	TraesCS4A01G305800	chr3B	80.602	665	106	15	1109	1754	52893139	52892479	2.650000e-135	492
21	TraesCS4A01G305800	chr3B	86.325	234	31	1	321	553	323409936	323409703	1.360000e-63	254
22	TraesCS4A01G305800	chr7B	86.752	234	30	1	321	553	414077180	414077413	2.920000e-65	259
23	TraesCS4A01G305800	chr5B	86.752	234	28	3	322	553	543674343	543674111	1.050000e-64	257
24	TraesCS4A01G305800	chr6B	86.383	235	31	1	320	553	583242092	583242326	3.780000e-64	255
25	TraesCS4A01G305800	chr7D	86.325	234	31	1	321	553	266504939	266504706	1.360000e-63	254
26	TraesCS4A01G305800	chr7D	85.833	240	33	1	315	553	495857307	495857546	1.360000e-63	254
27	TraesCS4A01G305800	chr6D	86.383	235	29	3	320	553	11766923	11766691	1.360000e-63	254
28	TraesCS4A01G305800	chr2A	80.714	140	17	5	1111	1242	4042635	4042772	1.870000e-17	100
29	TraesCS4A01G305800	chr2A	84.211	76	12	0	1111	1186	17100519	17100594	1.140000e-09	75

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	TraesCS4A01G305800	chr4A	600917976	600920929	2953	True	5456.000000	5456	100.000000	1	2954	1	chr4A.!!$R1	2953
1	TraesCS4A01G305800	chr4A	601309765	601311758	1993	False	924.000000	1423	78.485000	961	2954	2	chr4A.!!$F1	1993
2	TraesCS4A01G305800	chr4B	6039137	6040378	1241	False	1160.000000	1160	83.747000	1013	2245	1	chr4B.!!$F1	1232
3	TraesCS4A01G305800	chr4B	4953146	4956418	3272	True	946.833333	3234	83.780167	10	2954	6	chr4B.!!$R1	2944
4	TraesCS4A01G305800	chr4B	6055752	6057317	1565	False	713.333333	1192	80.466667	937	2954	3	chr4B.!!$F2	2017
5	TraesCS4A01G305800	chr4D	3711396	3714456	3060	False	1271.250000	3013	84.496750	1	2954	4	chr4D.!!$F1	2953
6	TraesCS4A01G305800	chr4D	3420772	3421771	999	True	915.000000	915	83.531000	958	1950	1	chr4D.!!$R1	992
7	TraesCS4A01G305800	chr2D	2341470	2342265	795	False	638.000000	638	81.605000	966	1754	1	chr2D.!!$F1	788
8	TraesCS4A01G305800	chr2D	5394727	5395772	1045	False	595.000000	595	77.221000	1251	2295	1	chr2D.!!$F2	1044
9	TraesCS4A01G305800	chr3B	52892479	52893139	660	True	492.000000	492	80.602000	1109	1754	1	chr3B.!!$R1	645

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
931	1264	0.034896	TTTCTTGGTGCCGTCTCTCC	59.965	55.0	0.0	0.0	0.0	3.71	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2298	3451	0.398098	ACGTATCGGGGATGGAACCT	60.398	55.0	0.0	0.0	0.0	3.5	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
61	62	6.525578	TGGACTCGAGTGTTCTGTATTATT	57.474	37.500	25.58	0.00	0.00	1.40
216	236	7.543520	GCTTCAAGCACATAATTAAAGAAAGCT	59.456	33.333	3.89	0.00	41.89	3.74
256	276	4.453478	TCGAAACGCCGATAGTATATGACT	59.547	41.667	0.00	0.00	36.54	3.41
259	279	6.564709	AAACGCCGATAGTATATGACTGTA	57.435	37.500	0.00	0.00	39.39	2.74
350	370	4.563140	TCGGGCTAGTTTATTGGTCTTT	57.437	40.909	0.00	0.00	0.00	2.52
468	488	7.490962	ACGAATCCAGCGATATAATTTTTGA	57.509	32.000	0.00	0.00	0.00	2.69
558	578	5.065218	CCAATAAATCAGGACGGAGAAAGTG	59.935	44.000	0.00	0.00	0.00	3.16
576	596	5.734855	AAGTGCAATACAATCGTATCCAC	57.265	39.130	0.00	0.00	37.34	4.02
597	620	4.875536	CACCATTGGTAATGAACTCGATCA	59.124	41.667	8.31	0.00	41.46	2.92
674	697	5.046520	TCACTCACTAGCTAGTCACTAGTCA	60.047	44.000	23.68	8.77	45.65	3.41
675	698	5.820423	CACTCACTAGCTAGTCACTAGTCAT	59.180	44.000	23.68	3.05	45.65	3.06
708	731	4.082245	CGGTGTATTTTTCAGCAGGGAATT	60.082	41.667	0.00	0.00	33.61	2.17
709	732	5.170748	GGTGTATTTTTCAGCAGGGAATTG	58.829	41.667	0.00	0.00	34.09	2.32
711	734	5.863935	GTGTATTTTTCAGCAGGGAATTGAC	59.136	40.000	0.00	0.00	0.00	3.18
712	735	5.774690	TGTATTTTTCAGCAGGGAATTGACT	59.225	36.000	0.00	0.00	0.00	3.41
713	736	5.813513	ATTTTTCAGCAGGGAATTGACTT	57.186	34.783	0.00	0.00	0.00	3.01
714	737	5.612725	TTTTTCAGCAGGGAATTGACTTT	57.387	34.783	0.00	0.00	0.00	2.66
716	739	4.853924	TTCAGCAGGGAATTGACTTTTC	57.146	40.909	0.00	0.00	0.00	2.29
717	740	4.104383	TCAGCAGGGAATTGACTTTTCT	57.896	40.909	0.00	0.00	0.00	2.52
719	742	3.077359	AGCAGGGAATTGACTTTTCTCG	58.923	45.455	0.00	0.00	0.00	4.04
720	743	3.074412	GCAGGGAATTGACTTTTCTCGA	58.926	45.455	0.00	0.00	0.00	4.04
911	1244	2.286127	GACAGTACGAGAGCCCAGCC	62.286	65.000	0.00	0.00	0.00	4.85
916	1249	0.614979	TACGAGAGCCCAGCCTTTCT	60.615	55.000	0.00	0.00	0.00	2.52
917	1250	1.298014	CGAGAGCCCAGCCTTTCTT	59.702	57.895	0.00	0.00	0.00	2.52
921	1254	1.228675	AGCCCAGCCTTTCTTGGTG	60.229	57.895	0.00	0.00	30.52	4.17
922	1255	2.935740	GCCCAGCCTTTCTTGGTGC	61.936	63.158	0.00	0.00	30.52	5.01
923	1256	2.278330	CCCAGCCTTTCTTGGTGCC	61.278	63.158	0.00	0.00	0.00	5.01
924	1257	2.629656	CCAGCCTTTCTTGGTGCCG	61.630	63.158	0.00	0.00	0.00	5.69
925	1258	1.898574	CAGCCTTTCTTGGTGCCGT	60.899	57.895	0.00	0.00	0.00	5.68
926	1259	1.600916	AGCCTTTCTTGGTGCCGTC	60.601	57.895	0.00	0.00	0.00	4.79
927	1260	1.600916	GCCTTTCTTGGTGCCGTCT	60.601	57.895	0.00	0.00	0.00	4.18
928	1261	1.578206	GCCTTTCTTGGTGCCGTCTC	61.578	60.000	0.00	0.00	0.00	3.36
929	1262	0.035458	CCTTTCTTGGTGCCGTCTCT	59.965	55.000	0.00	0.00	0.00	3.10
930	1263	1.433534	CTTTCTTGGTGCCGTCTCTC	58.566	55.000	0.00	0.00	0.00	3.20
931	1264	0.034896	TTTCTTGGTGCCGTCTCTCC	59.965	55.000	0.00	0.00	0.00	3.71
932	1265	1.118965	TTCTTGGTGCCGTCTCTCCA	61.119	55.000	0.00	0.00	0.00	3.86
934	1267	3.220999	TTGGTGCCGTCTCTCCACG	62.221	63.158	0.00	0.00	39.61	4.94
999	1409	2.205074	CAATAACCTACTCCAGCTGCG	58.795	52.381	8.66	3.75	0.00	5.18
1197	1607	0.251165	AATCCTGGGGAAACACCACG	60.251	55.000	0.00	0.00	47.00	4.94
1419	1854	3.790437	CGCCACCTCCTGCTCCAT	61.790	66.667	0.00	0.00	0.00	3.41
1427	1862	0.822532	CTCCTGCTCCATGGGAATGC	60.823	60.000	13.02	11.89	0.00	3.56
1473	1908	8.652290	AGACAAATAAAACACCTAGAGAGTCTT	58.348	33.333	0.00	0.00	0.00	3.01
1592	2027	0.967380	CTCACAGGCCCCATTCCAAC	60.967	60.000	0.00	0.00	0.00	3.77
1692	2127	6.385033	ACTAGGTTACATCGTGAAACTACAC	58.615	40.000	0.00	0.00	37.42	2.90
1951	3104	4.202609	ACCAATTCTCTGGACATGTTCCTT	60.203	41.667	0.46	0.00	46.10	3.36
1988	3141	5.964758	TCTTGTGAATTTGCAAGAGTTGTT	58.035	33.333	16.60	0.00	44.01	2.83
2286	3439	8.672214	ATTTTGAACATTTGTTGCTTCAAAAC	57.328	26.923	16.95	0.02	45.25	2.43
2298	3451	3.256879	TGCTTCAAAACAACCAACTCACA	59.743	39.130	0.00	0.00	0.00	3.58
2316	3469	0.033504	CAGGTTCCATCCCCGATACG	59.966	60.000	0.00	0.00	0.00	3.06
2365	3518	4.579753	CCTTGTACCTTTTCCGTAACCAAA	59.420	41.667	0.00	0.00	0.00	3.28
2406	3559	6.394345	AAAGAATTAGGATCCTTGGTGAGT	57.606	37.500	22.03	0.43	0.00	3.41
2407	3560	6.394345	AAGAATTAGGATCCTTGGTGAGTT	57.606	37.500	22.03	4.07	0.00	3.01
2408	3561	6.394345	AGAATTAGGATCCTTGGTGAGTTT	57.606	37.500	22.03	2.50	0.00	2.66
2409	3562	7.510675	AGAATTAGGATCCTTGGTGAGTTTA	57.489	36.000	22.03	0.00	0.00	2.01
2410	3563	7.928873	AGAATTAGGATCCTTGGTGAGTTTAA	58.071	34.615	22.03	3.98	0.00	1.52
2411	3564	8.049721	AGAATTAGGATCCTTGGTGAGTTTAAG	58.950	37.037	22.03	0.00	0.00	1.85
2422	3575	7.497909	CCTTGGTGAGTTTAAGTTTAGAAGACA	59.502	37.037	0.00	0.00	0.00	3.41
2637	3790	5.529800	GGGAAACTTGACAAAGCTTACTACA	59.470	40.000	0.00	0.00	36.84	2.74
2705	3858	7.674772	AGAACTAGGTTACTTGGTGAATCTAGT	59.325	37.037	2.45	2.45	38.12	2.57

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
216	236	0.748450	CGAAGGGTGCCCGTATCTAA	59.252	55.000	0.98	0.00	41.95	2.10
224	244	3.733960	GCGTTTCGAAGGGTGCCC	61.734	66.667	0.00	0.00	0.00	5.36
468	488	9.709495	AACTAACAAAATGTTAATGCATGTCAT	57.291	25.926	0.00	2.79	41.70	3.06
510	530	9.137459	TGGTCTCCTTTGTATTTTATGTCAAAA	57.863	29.630	0.00	0.00	31.07	2.44
558	578	5.451908	CAATGGTGGATACGATTGTATTGC	58.548	41.667	7.06	1.55	43.69	3.56
576	596	5.817296	TCTTGATCGAGTTCATTACCAATGG	59.183	40.000	9.87	0.00	39.38	3.16
597	620	1.291877	GACGTGCCGACATGCTTCTT	61.292	55.000	0.00	0.00	36.15	2.52
622	645	1.305201	GACTCTGACTCGAGGCTAGG	58.695	60.000	21.24	11.30	36.10	3.02
674	697	7.499321	TGAAAAATACACCGCCGATTTATAT	57.501	32.000	0.00	0.00	0.00	0.86
675	698	6.512091	GCTGAAAAATACACCGCCGATTTATA	60.512	38.462	0.00	0.00	0.00	0.98
719	742	4.211584	TCGCTGTTAGTGTAGATCGAGATC	59.788	45.833	5.00	5.00	38.09	2.75
720	743	4.024725	GTCGCTGTTAGTGTAGATCGAGAT	60.025	45.833	0.00	0.00	0.00	2.75
730	754	1.602165	CGGACAAGTCGCTGTTAGTGT	60.602	52.381	0.00	0.00	0.00	3.55
911	1244	1.433534	GAGAGACGGCACCAAGAAAG	58.566	55.000	0.00	0.00	0.00	2.62
916	1249	2.741092	GTGGAGAGACGGCACCAA	59.259	61.111	3.53	0.00	34.11	3.67
917	1250	3.680786	CGTGGAGAGACGGCACCA	61.681	66.667	0.00	0.00	35.65	4.17
921	1254	3.851976	ATATATTCGTGGAGAGACGGC	57.148	47.619	0.00	0.00	39.88	5.68
922	1255	6.738832	TCTTATATATTCGTGGAGAGACGG	57.261	41.667	0.00	0.00	39.88	4.79
923	1256	7.534578	GTGTTCTTATATATTCGTGGAGAGACG	59.465	40.741	0.00	0.00	40.83	4.18
924	1257	8.569641	AGTGTTCTTATATATTCGTGGAGAGAC	58.430	37.037	0.00	0.00	0.00	3.36
925	1258	8.693120	AGTGTTCTTATATATTCGTGGAGAGA	57.307	34.615	0.00	0.00	0.00	3.10
926	1259	8.024285	GGAGTGTTCTTATATATTCGTGGAGAG	58.976	40.741	0.00	0.00	0.00	3.20
927	1260	7.504574	TGGAGTGTTCTTATATATTCGTGGAGA	59.495	37.037	0.00	0.00	0.00	3.71
928	1261	7.595502	GTGGAGTGTTCTTATATATTCGTGGAG	59.404	40.741	0.00	0.00	0.00	3.86
929	1262	7.431249	GTGGAGTGTTCTTATATATTCGTGGA	58.569	38.462	0.00	0.00	0.00	4.02
930	1263	6.362551	CGTGGAGTGTTCTTATATATTCGTGG	59.637	42.308	0.00	0.00	0.00	4.94
931	1264	6.362551	CCGTGGAGTGTTCTTATATATTCGTG	59.637	42.308	0.00	0.00	0.00	4.35
932	1265	6.263842	TCCGTGGAGTGTTCTTATATATTCGT	59.736	38.462	0.00	0.00	0.00	3.85
934	1267	8.304596	TGATCCGTGGAGTGTTCTTATATATTC	58.695	37.037	0.00	0.00	0.00	1.75
1227	1637	2.747460	GCTGGATGCTCGCCACAA	60.747	61.111	0.00	0.00	38.95	3.33
1419	1854	1.899437	GACCGGAGAGTGCATTCCCA	61.899	60.000	9.46	0.00	0.00	4.37
1473	1908	2.494073	GTTTGACAAGTCCAACCCAACA	59.506	45.455	6.02	0.00	31.36	3.33
1592	2027	4.333926	GCTTAGTGCAATTCCCTAGACTTG	59.666	45.833	0.00	0.00	42.31	3.16
1692	2127	1.996292	TGCTGCTAAGTGCTAACTCG	58.004	50.000	0.00	0.00	43.37	4.18
1951	3104	9.219603	CAAATTCACAAGATAACCTAGTTCTCA	57.780	33.333	0.00	0.00	0.00	3.27
1988	3141	5.184864	CCCACTAATTGGTTGTTATGAAGCA	59.815	40.000	0.00	0.00	45.25	3.91
1995	3148	5.063017	TGGAACCCACTAATTGGTTGTTA	57.937	39.130	2.82	0.00	44.70	2.41
2286	3439	2.051334	TGGAACCTGTGAGTTGGTTG	57.949	50.000	1.88	0.00	45.48	3.77
2298	3451	0.398098	ACGTATCGGGGATGGAACCT	60.398	55.000	0.00	0.00	0.00	3.50
2316	3469	5.812127	AGTGAGCTTGTTCAAATTTCCAAAC	59.188	36.000	0.00	0.00	0.00	2.93
2394	3547	8.437575	TCTTCTAAACTTAAACTCACCAAGGAT	58.562	33.333	0.00	0.00	0.00	3.24
2408	3561	9.332502	TGTAAAGTTGCATGTCTTCTAAACTTA	57.667	29.630	0.00	0.00	36.98	2.24
2409	3562	8.220755	TGTAAAGTTGCATGTCTTCTAAACTT	57.779	30.769	0.00	0.00	38.99	2.66
2410	3563	7.801716	TGTAAAGTTGCATGTCTTCTAAACT	57.198	32.000	0.00	0.00	0.00	2.66
2411	3564	8.850454	TTTGTAAAGTTGCATGTCTTCTAAAC	57.150	30.769	0.00	0.00	0.00	2.01
2422	3575	8.442384	CAAGAGTTTGTTTTTGTAAAGTTGCAT	58.558	29.630	0.00	0.00	0.00	3.96
2637	3790	2.364190	TGGTTTCCCCCTAGGTTCAAT	58.636	47.619	8.29	0.00	36.75	2.57
2705	3858	7.455641	TTGTTTTTGTCAAGTTCCAAGTCTA	57.544	32.000	0.00	0.00	0.00	2.59
2859	4012	7.829211	CCAGAGAGATTGTTACCCTCAAATTAA	59.171	37.037	0.00	0.00	0.00	1.40
2860	4013	7.037586	ACCAGAGAGATTGTTACCCTCAAATTA	60.038	37.037	0.00	0.00	0.00	1.40
2861	4014	6.183347	CCAGAGAGATTGTTACCCTCAAATT	58.817	40.000	0.00	0.00	0.00	1.82
2868	4021	2.170817	GGGACCAGAGAGATTGTTACCC	59.829	54.545	0.00	0.00	0.00	3.69

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.