AutoCloner

Multiple sequence alignment - TraesCS3D01G491700

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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	TraesCS3D01G491700	chr3D	100.000	4044	0	0	1	4044	585434764	585430721	0.000000e+00	7468
1	TraesCS3D01G491700	chr3D	91.328	3125	229	21	939	4044	585652059	585655160	0.000000e+00	4231
2	TraesCS3D01G491700	chr3D	91.530	2314	167	13	1743	4044	585617344	585619640	0.000000e+00	3160
3	TraesCS3D01G491700	chr3D	95.926	1571	63	1	2474	4044	585467968	585466399	0.000000e+00	2545
4	TraesCS3D01G491700	chr3D	91.321	1279	95	11	939	2210	585632879	585634148	0.000000e+00	1733
5	TraesCS3D01G491700	chr3D	83.487	1841	201	50	1538	3308	585711494	585709687	0.000000e+00	1620
6	TraesCS3D01G491700	chr3D	92.298	805	52	6	939	1738	585616222	585617021	0.000000e+00	1134
7	TraesCS3D01G491700	chr3D	87.567	933	103	10	18	941	585401066	585400138	0.000000e+00	1068
8	TraesCS3D01G491700	chr3D	88.443	623	58	6	3191	3804	585655163	585655780	0.000000e+00	739
9	TraesCS3D01G491700	chr3D	87.294	425	44	8	12	430	585636625	585637045	1.020000e-130	477
10	TraesCS3D01G491700	chr3D	83.071	254	33	6	13	256	585651043	585651296	5.260000e-54	222
11	TraesCS3D01G491700	chr3B	93.250	2963	166	17	1	2957	781672679	781669745	0.000000e+00	4333
12	TraesCS3D01G491700	chr3B	91.544	3122	234	19	939	4044	781837790	781834683	0.000000e+00	4276
13	TraesCS3D01G491700	chr3B	88.144	2716	246	37	939	3609	782342410	782339726	0.000000e+00	3162
14	TraesCS3D01G491700	chr3B	92.769	1051	72	2	2994	4044	781669745	781668699	0.000000e+00	1517
15	TraesCS3D01G491700	chr3B	86.339	937	112	12	12	941	781809309	781808382	0.000000e+00	1007
16	TraesCS3D01G491700	chr3B	88.060	335	33	3	2874	3207	782112412	782112084	1.360000e-104	390
17	TraesCS3D01G491700	chr3B	86.307	241	25	4	18	250	782343475	782343235	5.190000e-64	255
18	TraesCS3D01G491700	chr3B	85.833	240	27	4	18	250	781838796	781838557	8.680000e-62	248
19	TraesCS3D01G491700	chr3B	85.417	240	28	4	18	250	782484055	782483816	4.040000e-60	243
20	TraesCS3D01G491700	chrUn	91.573	2314	166	13	1743	4044	321264022	321266318	0.000000e+00	3166
21	TraesCS3D01G491700	chrUn	91.402	2047	150	10	2008	4044	300190850	300192880	0.000000e+00	2782
22	TraesCS3D01G491700	chrUn	92.413	804	52	5	939	1738	358609584	358610382	0.000000e+00	1138
23	TraesCS3D01G491700	chr4B	86.250	720	89	6	957	1673	422033129	422032417	0.000000e+00	773
24	TraesCS3D01G491700	chr3A	86.792	689	81	10	260	941	377484955	377484270	0.000000e+00	760
25	TraesCS3D01G491700	chr7D	86.647	689	82	10	260	941	434908804	434908119	0.000000e+00	754
26	TraesCS3D01G491700	chr7D	85.942	690	90	7	257	940	145836099	145836787	0.000000e+00	730
27	TraesCS3D01G491700	chr4A	86.357	689	84	10	260	941	311616133	311615448	0.000000e+00	743
28	TraesCS3D01G491700	chr5D	86.107	691	87	9	257	940	428424024	428424712	0.000000e+00	736
29	TraesCS3D01G491700	chr4D	85.437	721	90	9	957	1673	340551511	340550802	0.000000e+00	736
30	TraesCS3D01G491700	chr7B	86.087	690	83	12	260	941	608883716	608883032	0.000000e+00	730

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	TraesCS3D01G491700	chr3D	585430721	585434764	4043	True	7468.000000	7468	100.0000	1	4044	1	chr3D.!!$R2	4043
1	TraesCS3D01G491700	chr3D	585466399	585467968	1569	True	2545.000000	2545	95.9260	2474	4044	1	chr3D.!!$R3	1570
2	TraesCS3D01G491700	chr3D	585616222	585619640	3418	False	2147.000000	3160	91.9140	939	4044	2	chr3D.!!$F1	3105
3	TraesCS3D01G491700	chr3D	585651043	585655780	4737	False	1730.666667	4231	87.6140	13	4044	3	chr3D.!!$F3	4031
4	TraesCS3D01G491700	chr3D	585709687	585711494	1807	True	1620.000000	1620	83.4870	1538	3308	1	chr3D.!!$R4	1770
5	TraesCS3D01G491700	chr3D	585632879	585637045	4166	False	1105.000000	1733	89.3075	12	2210	2	chr3D.!!$F2	2198
6	TraesCS3D01G491700	chr3D	585400138	585401066	928	True	1068.000000	1068	87.5670	18	941	1	chr3D.!!$R1	923
7	TraesCS3D01G491700	chr3B	781668699	781672679	3980	True	2925.000000	4333	93.0095	1	4044	2	chr3B.!!$R4	4043
8	TraesCS3D01G491700	chr3B	781834683	781838796	4113	True	2262.000000	4276	88.6885	18	4044	2	chr3B.!!$R5	4026
9	TraesCS3D01G491700	chr3B	782339726	782343475	3749	True	1708.500000	3162	87.2255	18	3609	2	chr3B.!!$R6	3591
10	TraesCS3D01G491700	chr3B	781808382	781809309	927	True	1007.000000	1007	86.3390	12	941	1	chr3B.!!$R1	929
11	TraesCS3D01G491700	chrUn	321264022	321266318	2296	False	3166.000000	3166	91.5730	1743	4044	1	chrUn.!!$F2	2301
12	TraesCS3D01G491700	chrUn	300190850	300192880	2030	False	2782.000000	2782	91.4020	2008	4044	1	chrUn.!!$F1	2036
13	TraesCS3D01G491700	chrUn	358609584	358610382	798	False	1138.000000	1138	92.4130	939	1738	1	chrUn.!!$F3	799
14	TraesCS3D01G491700	chr4B	422032417	422033129	712	True	773.000000	773	86.2500	957	1673	1	chr4B.!!$R1	716
15	TraesCS3D01G491700	chr3A	377484270	377484955	685	True	760.000000	760	86.7920	260	941	1	chr3A.!!$R1	681
16	TraesCS3D01G491700	chr7D	434908119	434908804	685	True	754.000000	754	86.6470	260	941	1	chr7D.!!$R1	681
17	TraesCS3D01G491700	chr7D	145836099	145836787	688	False	730.000000	730	85.9420	257	940	1	chr7D.!!$F1	683
18	TraesCS3D01G491700	chr4A	311615448	311616133	685	True	743.000000	743	86.3570	260	941	1	chr4A.!!$R1	681
19	TraesCS3D01G491700	chr5D	428424024	428424712	688	False	736.000000	736	86.1070	257	940	1	chr5D.!!$F1	683
20	TraesCS3D01G491700	chr4D	340550802	340551511	709	True	736.000000	736	85.4370	957	1673	1	chr4D.!!$R1	716
21	TraesCS3D01G491700	chr7B	608883032	608883716	684	True	730.000000	730	86.0870	260	941	1	chr7B.!!$R1	681

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
754	1375	1.134128	AGTGGAGCATTGTGTGACACA	60.134	47.619	15.39	15.39	43.02	3.72	F
1768	2721	3.749088	ACCGAGCATTCAAATGTCGTTTA	59.251	39.130	17.85	0.00	37.79	2.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2005	2961	0.974010	CCACTAGTAGCCCGGAACCA	60.974	60.0	0.73	0.0	0.0	3.67	R
3578	6272	0.237235	GAAAAATGACGTCGCAGCCA	59.763	50.0	11.62	0.0	0.0	4.75	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
158	169	8.135382	ACACCTAGGGATATATATGTTGTGAC	57.865	38.462	14.81	0.00	0.00	3.67
490	1108	3.808174	GGTTGAGTTAGGTATTCCGATGC	59.192	47.826	0.00	0.00	39.05	3.91
516	1134	3.415457	TCATTGTGTGCACTATGACCA	57.585	42.857	19.41	0.00	44.38	4.02
619	1238	5.471424	TGATTCAGGGTCTTGATATCCTCT	58.529	41.667	0.00	0.00	0.00	3.69
681	1301	1.693606	CCCCCTGTTGCTTTGAATGTT	59.306	47.619	0.00	0.00	0.00	2.71
754	1375	1.134128	AGTGGAGCATTGTGTGACACA	60.134	47.619	15.39	15.39	43.02	3.72
762	1383	5.363101	AGCATTGTGTGACACATCTATAGG	58.637	41.667	20.15	6.94	44.16	2.57
781	1402	9.326489	TCTATAGGTAATAAATGAGTCTGCCAT	57.674	33.333	0.00	0.00	0.00	4.40
905	1526	5.920273	CGCATTCTTTGTGGTACTTGAAATT	59.080	36.000	0.00	0.00	31.94	1.82
907	1528	7.566709	GCATTCTTTGTGGTACTTGAAATTTG	58.433	34.615	0.00	0.00	0.00	2.32
917	1538	6.099341	GGTACTTGAAATTTGCACCTAATGG	58.901	40.000	0.00	0.00	39.83	3.16
955	1576	6.892485	TCATTCAATCCTGATGCTTCTTCTA	58.108	36.000	0.88	0.00	0.00	2.10
1133	1754	7.035612	CCCAAACTGTTCAATAAGATAAAGGC	58.964	38.462	0.00	0.00	0.00	4.35
1167	1788	8.511604	ACATTTGTAGATTAAGTTGGATCTGG	57.488	34.615	11.68	0.00	34.60	3.86
1343	1971	7.765695	GGATTTGATCCCAAGAATGCTTATA	57.234	36.000	0.00	0.00	43.88	0.98
1344	1972	7.597386	GGATTTGATCCCAAGAATGCTTATAC	58.403	38.462	0.00	0.00	43.88	1.47
1484	2113	4.771114	TGGTACCCCATCTATTTCACAG	57.229	45.455	10.07	0.00	35.17	3.66
1515	2144	7.821359	AGCGACTATCATATCTGCACAATAAAT	59.179	33.333	0.00	0.00	0.00	1.40
1516	2145	8.446273	GCGACTATCATATCTGCACAATAAATT	58.554	33.333	0.00	0.00	0.00	1.82
1578	2207	9.934784	TGGATGGATGATAGGAAAATTAAGAAA	57.065	29.630	0.00	0.00	0.00	2.52
1602	2231	7.656707	AAATACATTTGTTGTGAAATGCTCC	57.343	32.000	0.00	0.00	44.08	4.70
1768	2721	3.749088	ACCGAGCATTCAAATGTCGTTTA	59.251	39.130	17.85	0.00	37.79	2.01
1861	2814	5.573219	TGCCAATCTGGGATATGATAAAGG	58.427	41.667	0.00	0.00	38.19	3.11
1866	2819	7.555554	CCAATCTGGGATATGATAAAGGTCATC	59.444	40.741	0.00	0.00	35.70	2.92
2005	2961	6.377996	TGCATATTACTTGCTCTTGGACAATT	59.622	34.615	0.00	0.00	40.77	2.32
2045	3001	2.872038	GCTATTTGGGGGCTGACTATCG	60.872	54.545	0.00	0.00	0.00	2.92
2077	3033	5.504853	TGGTTAGTCCACATTTGCATCATA	58.495	37.500	0.00	0.00	41.93	2.15
2095	3051	7.094248	TGCATCATATGTGACCTATTTAATGCC	60.094	37.037	12.36	0.64	37.14	4.40
2191	3147	1.672881	GGAATCAGCAAGCGCAAGTAT	59.327	47.619	11.47	0.00	42.27	2.12
2237	3193	1.742268	GATTCTCAAGGCAGTGGCTTC	59.258	52.381	27.66	13.01	45.21	3.86
2286	3242	2.581354	CTCTTGGGCTCCAGGTCG	59.419	66.667	3.82	0.00	33.81	4.79
2295	3251	0.320421	GCTCCAGGTCGTGCAAACTA	60.320	55.000	0.00	0.00	0.00	2.24
2310	3266	6.149633	GTGCAAACTATCCACTTTACTTTGG	58.850	40.000	0.00	0.00	0.00	3.28
2323	3279	5.119434	ACTTTACTTTGGTTTGTTTTGCACG	59.881	36.000	0.00	0.00	0.00	5.34
2348	3304	3.770263	GCTGTTGAGCTAATGCATCAA	57.230	42.857	0.00	0.00	42.52	2.57
2441	3462	2.095718	GTCCGTTGGAAGAAGAATGTGC	60.096	50.000	0.00	0.00	31.38	4.57
2508	3707	6.018425	GTCAGTGATATGTTGTTAGATGCCAG	60.018	42.308	0.00	0.00	0.00	4.85
2673	4329	4.585955	TCTACTCAATATCGCCTTCACC	57.414	45.455	0.00	0.00	0.00	4.02
2769	4444	7.012704	ACCATTATTATGTCTTGCATGTGTCTC	59.987	37.037	0.00	0.00	38.47	3.36
2870	4581	8.071368	GTGTTGGTGTTAGAAATTACAATTCGA	58.929	33.333	0.00	0.00	32.04	3.71
2986	4702	2.009681	TGCAGAGAGTTACTGGACCA	57.990	50.000	0.00	0.00	36.09	4.02
3208	5103	4.035091	TGACAGAGAATCGTGTTTGTTTGG	59.965	41.667	0.00	0.00	42.67	3.28
3561	6255	2.107750	CGCGGTGATGCTCTGGAT	59.892	61.111	0.00	0.00	0.00	3.41
3577	6271	1.591703	GATCTCAGGTGTGGTGCGA	59.408	57.895	0.00	0.00	0.00	5.10
3578	6272	0.176680	GATCTCAGGTGTGGTGCGAT	59.823	55.000	0.00	0.00	0.00	4.58
3631	6325	4.410400	GGGCCGTCCTTGACCAGG	62.410	72.222	0.00	0.00	45.64	4.45
3693	6387	3.379445	GGGCGAAGAGGGTCACGA	61.379	66.667	0.00	0.00	0.00	4.35
3772	6568	3.936203	GGTGTGTGCCCAGGACGA	61.936	66.667	0.00	0.00	0.00	4.20
3816	6612	3.078836	GGTACGGGCTGCAGGGTA	61.079	66.667	17.12	0.00	0.00	3.69
4015	6811	3.580319	GAGGTGGGTGCTTGGGGT	61.580	66.667	0.00	0.00	0.00	4.95

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
8	9	8.819643	AGAAGTAAAGTGTTAGATTGAGTGTC	57.180	34.615	0.00	0.00	0.00	3.67
99	104	2.492088	CCGGATGATAGGAGCGTGAATA	59.508	50.000	0.00	0.00	0.00	1.75
158	169	4.261322	CCTCACCATTCTTGCAATATTCCG	60.261	45.833	0.00	0.00	0.00	4.30
318	392	8.434733	TTGCAGAAAACATTCAAATGATTCAA	57.565	26.923	18.74	9.33	39.67	2.69
490	1108	0.603707	AGTGCACACAATGACTCGGG	60.604	55.000	21.04	0.00	0.00	5.14
516	1134	2.520968	GCAACCTCCACCAACCCT	59.479	61.111	0.00	0.00	0.00	4.34
586	1204	4.265073	AGACCCTGAATCAGTAAATGCAC	58.735	43.478	9.63	0.00	0.00	4.57
619	1238	4.603989	TCATGATTTGGCTTCTGCAAAA	57.396	36.364	0.00	0.00	45.11	2.44
681	1301	6.042781	AGGTACCAACAAAATCACTCTACTCA	59.957	38.462	15.94	0.00	0.00	3.41
754	1375	9.326489	TGGCAGACTCATTTATTACCTATAGAT	57.674	33.333	0.00	0.00	0.00	1.98
773	1394	5.176223	GCACATTGCAAATAATATGGCAGAC	59.824	40.000	1.71	0.00	44.26	3.51
905	1526	2.300956	TTTCCAGCCATTAGGTGCAA	57.699	45.000	0.00	0.00	42.90	4.08
907	1528	2.102578	ACATTTCCAGCCATTAGGTGC	58.897	47.619	0.00	0.00	42.90	5.01
955	1576	2.396590	ATTAACCCAGACGATGCGTT	57.603	45.000	0.00	0.00	41.37	4.84
1133	1754	9.445786	AACTTAATCTACAAATGTTTTGTCACG	57.554	29.630	8.76	1.12	34.11	4.35
1343	1971	5.183530	TCTCTTCATGGGATCAACAATGT	57.816	39.130	0.00	0.00	0.00	2.71
1344	1972	6.320418	TGATTCTCTTCATGGGATCAACAATG	59.680	38.462	0.00	0.00	0.00	2.82
1428	2056	1.454847	TGTGTTTGGTGGAGGCACC	60.455	57.895	0.00	0.00	45.20	5.01
1484	2113	4.984785	TGCAGATATGATAGTCGCTTGAAC	59.015	41.667	0.00	0.00	0.00	3.18
1578	2207	6.650390	GGGAGCATTTCACAACAAATGTATTT	59.350	34.615	7.54	0.00	43.16	1.40
1584	2213	2.302733	GGGGGAGCATTTCACAACAAAT	59.697	45.455	0.00	0.00	0.00	2.32
1590	2219	2.358090	CCATAAGGGGGAGCATTTCACA	60.358	50.000	0.00	0.00	0.00	3.58
1747	2700	2.900122	AACGACATTTGAATGCTCGG	57.100	45.000	21.17	11.18	40.66	4.63
1768	2721	6.154534	AGCAAATCAGCATATCATTGCCATAT	59.845	34.615	4.82	0.00	43.83	1.78
1861	2814	3.665323	GCACAACGATTCACACAGATGAC	60.665	47.826	0.00	0.00	0.00	3.06
1866	2819	2.753989	TTGCACAACGATTCACACAG	57.246	45.000	0.00	0.00	0.00	3.66
2005	2961	0.974010	CCACTAGTAGCCCGGAACCA	60.974	60.000	0.73	0.00	0.00	3.67
2077	3033	6.777580	CCTTTAGGGCATTAAATAGGTCACAT	59.222	38.462	0.00	0.00	0.00	3.21
2121	3077	5.557576	TCCTAGAGAACCATCCATTCATG	57.442	43.478	0.00	0.00	0.00	3.07
2191	3147	4.107072	ACTTCCTGGAAGATCATTCCTGA	58.893	43.478	36.38	15.73	41.71	3.86
2286	3242	6.149633	CCAAAGTAAAGTGGATAGTTTGCAC	58.850	40.000	7.87	0.00	46.30	4.57
2295	3251	6.315144	GCAAAACAAACCAAAGTAAAGTGGAT	59.685	34.615	0.00	0.00	38.36	3.41
2310	3266	2.027926	CAGCTGAACGTGCAAAACAAAC	59.972	45.455	8.42	0.00	0.00	2.93
2348	3304	2.295909	GAGCTCGAGACTGCTGGATAAT	59.704	50.000	18.75	0.00	39.91	1.28
2411	3367	7.519032	TCTTCTTCCAACGGACATTTAATTT	57.481	32.000	0.00	0.00	0.00	1.82
2441	3462	4.478699	CACCTGCATTTCATGTTGTAGTG	58.521	43.478	0.00	0.00	0.00	2.74
2769	4444	4.634004	TCGACAATAGTTGTTGGCAATAGG	59.366	41.667	1.92	0.00	45.52	2.57
2870	4581	4.831155	ACAGTATATACAGTACCATGCCGT	59.169	41.667	15.18	0.00	0.00	5.68
2986	4702	1.963985	ATTCCAGGAAGAGGAGCTGT	58.036	50.000	8.20	0.00	36.33	4.40
3551	6245	1.485480	CACACCTGAGATCCAGAGCAT	59.515	52.381	11.48	0.00	45.78	3.79
3561	6255	1.293179	CATCGCACCACACCTGAGA	59.707	57.895	0.00	0.00	0.00	3.27
3577	6271	0.881118	AAAAATGACGTCGCAGCCAT	59.119	45.000	11.62	0.00	0.00	4.40
3578	6272	0.237235	GAAAAATGACGTCGCAGCCA	59.763	50.000	11.62	0.00	0.00	4.75
3624	6318	0.325671	GATCCCTCTGGACCTGGTCA	60.326	60.000	26.94	12.90	45.58	4.02
3631	6325	1.044611	GGCACTAGATCCCTCTGGAC	58.955	60.000	0.00	0.00	45.58	4.02
3682	6376	1.384989	CCATACGCTCGTGACCCTCT	61.385	60.000	5.05	0.00	0.00	3.69
3772	6568	4.520874	CACATGGTGAGATATAGACCTCGT	59.479	45.833	0.00	0.00	35.23	4.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.