AutoCloner

Multiple sequence alignment - TraesCS7D01G349700

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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	TraesCS7D01G349700	chr7D	100.000	2972	0	0	1	2972	449546928	449549899	0.000000e+00	5489.0
1	TraesCS7D01G349700	chr7D	89.122	1048	77	19	783	1813	451041506	451040479	0.000000e+00	1269.0
2	TraesCS7D01G349700	chr7D	98.182	55	1	0	1778	1832	449680458	449680404	2.440000e-16	97.1
3	TraesCS7D01G349700	chr2D	98.074	1142	19	3	1832	2970	643047339	643046198	0.000000e+00	1984.0
4	TraesCS7D01G349700	chr2D	93.741	719	33	8	1	711	201389908	201390622	0.000000e+00	1068.0
5	TraesCS7D01G349700	chr2D	92.500	720	40	10	1	711	80972724	80972010	0.000000e+00	1018.0
6	TraesCS7D01G349700	chr2D	91.888	715	49	7	1	711	95172239	95171530	0.000000e+00	990.0
7	TraesCS7D01G349700	chr7A	92.967	1038	47	11	791	1803	546344222	546343186	0.000000e+00	1489.0
8	TraesCS7D01G349700	chr7A	92.191	922	48	15	906	1810	546045926	546046840	0.000000e+00	1282.0
9	TraesCS7D01G349700	chr7A	92.211	719	42	5	1	711	571095472	571096184	0.000000e+00	1005.0
10	TraesCS7D01G349700	chr7A	88.083	193	21	1	1832	2024	240678557	240678367	8.290000e-56	228.0
11	TraesCS7D01G349700	chr7A	85.000	80	10	1	782	861	546045827	546045904	2.460000e-11	80.5
12	TraesCS7D01G349700	chr7B	94.891	920	34	6	925	1832	472784808	472783890	0.000000e+00	1426.0
13	TraesCS7D01G349700	chr7B	90.019	1032	69	18	782	1798	468828310	468827298	0.000000e+00	1304.0
14	TraesCS7D01G349700	chr7B	96.390	748	25	2	1086	1832	468051030	468051776	0.000000e+00	1230.0
15	TraesCS7D01G349700	chr7B	91.806	720	42	10	1	711	200679575	200678864	0.000000e+00	987.0
16	TraesCS7D01G349700	chr7B	83.073	384	30	17	725	1074	468050513	468050895	1.720000e-82	316.0
17	TraesCS7D01G349700	chr7B	86.705	173	19	3	725	894	472785061	472784890	3.910000e-44	189.0
18	TraesCS7D01G349700	chr4D	92.577	714	38	10	1	711	233256062	233255361	0.000000e+00	1011.0
19	TraesCS7D01G349700	chr4D	91.933	719	43	10	1	711	208104383	208105094	0.000000e+00	992.0
20	TraesCS7D01G349700	chr4D	91.370	730	47	11	1	721	260227095	260227817	0.000000e+00	985.0
21	TraesCS7D01G349700	chr6D	92.340	718	39	7	1	708	71778652	71779363	0.000000e+00	1007.0
22	TraesCS7D01G349700	chr4A	85.732	785	79	19	1833	2599	381205759	381204990	0.000000e+00	798.0
23	TraesCS7D01G349700	chr4A	86.778	537	47	10	2440	2971	381205001	381204484	7.140000e-161	577.0
24	TraesCS7D01G349700	chr4A	81.250	96	17	1	2650	2744	381204677	381204582	3.180000e-10	76.8
25	TraesCS7D01G349700	chr3A	88.083	193	21	1	1832	2024	47845823	47846013	8.290000e-56	228.0
26	TraesCS7D01G349700	chrUn	81.633	196	29	7	2617	2811	85632857	85632668	3.970000e-34	156.0
27	TraesCS7D01G349700	chr3D	93.590	78	5	0	1290	1367	105196648	105196571	1.870000e-22	117.0
28	TraesCS7D01G349700	chr3D	79.394	165	23	9	2527	2686	608417647	608417805	4.050000e-19	106.0

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	TraesCS7D01G349700	chr7D	449546928	449549899	2971	False	5489.000000	5489	100.000000	1	2972	1	chr7D.!!$F1	2971
1	TraesCS7D01G349700	chr7D	451040479	451041506	1027	True	1269.000000	1269	89.122000	783	1813	1	chr7D.!!$R2	1030
2	TraesCS7D01G349700	chr2D	643046198	643047339	1141	True	1984.000000	1984	98.074000	1832	2970	1	chr2D.!!$R3	1138
3	TraesCS7D01G349700	chr2D	201389908	201390622	714	False	1068.000000	1068	93.741000	1	711	1	chr2D.!!$F1	710
4	TraesCS7D01G349700	chr2D	80972010	80972724	714	True	1018.000000	1018	92.500000	1	711	1	chr2D.!!$R1	710
5	TraesCS7D01G349700	chr2D	95171530	95172239	709	True	990.000000	990	91.888000	1	711	1	chr2D.!!$R2	710
6	TraesCS7D01G349700	chr7A	546343186	546344222	1036	True	1489.000000	1489	92.967000	791	1803	1	chr7A.!!$R2	1012
7	TraesCS7D01G349700	chr7A	571095472	571096184	712	False	1005.000000	1005	92.211000	1	711	1	chr7A.!!$F1	710
8	TraesCS7D01G349700	chr7A	546045827	546046840	1013	False	681.250000	1282	88.595500	782	1810	2	chr7A.!!$F2	1028
9	TraesCS7D01G349700	chr7B	468827298	468828310	1012	True	1304.000000	1304	90.019000	782	1798	1	chr7B.!!$R2	1016
10	TraesCS7D01G349700	chr7B	200678864	200679575	711	True	987.000000	987	91.806000	1	711	1	chr7B.!!$R1	710
11	TraesCS7D01G349700	chr7B	472783890	472785061	1171	True	807.500000	1426	90.798000	725	1832	2	chr7B.!!$R3	1107
12	TraesCS7D01G349700	chr7B	468050513	468051776	1263	False	773.000000	1230	89.731500	725	1832	2	chr7B.!!$F1	1107
13	TraesCS7D01G349700	chr4D	233255361	233256062	701	True	1011.000000	1011	92.577000	1	711	1	chr4D.!!$R1	710
14	TraesCS7D01G349700	chr4D	208104383	208105094	711	False	992.000000	992	91.933000	1	711	1	chr4D.!!$F1	710
15	TraesCS7D01G349700	chr4D	260227095	260227817	722	False	985.000000	985	91.370000	1	721	1	chr4D.!!$F2	720
16	TraesCS7D01G349700	chr6D	71778652	71779363	711	False	1007.000000	1007	92.340000	1	708	1	chr6D.!!$F1	707
17	TraesCS7D01G349700	chr4A	381204484	381205759	1275	True	483.933333	798	84.586667	1833	2971	3	chr4A.!!$R1	1138

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
761	779	0.668535	GATAAGGAATTGGGCCGTGC	59.331	55.0	0.0	0.0	0.0	5.34	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2278	2527	0.108992	GGTGATACAAGTCGACGGCA	60.109	55.0	10.46	0.0	0.0	5.69	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
157	159	9.979578	CTCAGTTTTAGCTCATATGATCTTAGT	57.020	33.333	13.95	2.05	0.00	2.24
270	278	2.138596	TCGTGGAAGTCGTGGTAAAC	57.861	50.000	0.00	0.00	0.00	2.01
272	280	2.159128	TCGTGGAAGTCGTGGTAAACAA	60.159	45.455	0.00	0.00	0.00	2.83
273	281	2.803956	CGTGGAAGTCGTGGTAAACAAT	59.196	45.455	0.00	0.00	0.00	2.71
322	335	4.533919	TTTGCCATGATTTCCACGAATT	57.466	36.364	0.00	0.00	0.00	2.17
368	381	5.083533	AGCACTCAAAACATTGGTCAAAA	57.916	34.783	0.00	0.00	0.00	2.44
379	392	3.853355	TTGGTCAAAATTTGCCACCAT	57.147	38.095	16.67	0.00	37.38	3.55
446	463	9.783081	TCATGCTAAGATCATATGAGCTAAAAA	57.217	29.630	23.05	10.64	40.30	1.94
447	464	9.823098	CATGCTAAGATCATATGAGCTAAAAAC	57.177	33.333	23.05	11.88	40.30	2.43
448	465	9.790344	ATGCTAAGATCATATGAGCTAAAAACT	57.210	29.630	23.05	9.57	40.30	2.66
461	478	6.013725	TGAGCTAAAAACTAAGATGGGACTGA	60.014	38.462	0.00	0.00	0.00	3.41
505	522	6.558771	GCAAATGACATGCACATATAGGTA	57.441	37.500	6.44	0.00	43.29	3.08
506	523	6.605849	GCAAATGACATGCACATATAGGTAG	58.394	40.000	6.44	0.00	43.29	3.18
652	670	3.131223	TGGGCAAGAACAAATGTTTTCGA	59.869	39.130	0.00	0.00	38.56	3.71
682	700	1.045407	TAAACCTGCCGAGTGTGACT	58.955	50.000	0.00	0.00	0.00	3.41
711	729	5.725490	AGGGGCATAAAATCAATTATCCCA	58.275	37.500	0.00	0.00	35.97	4.37
717	735	9.264719	GGCATAAAATCAATTATCCCAAAAGAG	57.735	33.333	0.00	0.00	0.00	2.85
734	752	9.224267	CCCAAAAGAGAATGTAGATATACATGG	57.776	37.037	13.52	9.16	40.26	3.66
735	753	8.725148	CCAAAAGAGAATGTAGATATACATGGC	58.275	37.037	13.52	9.12	40.26	4.40
736	754	9.276590	CAAAAGAGAATGTAGATATACATGGCA	57.723	33.333	13.52	0.00	40.26	4.92
737	755	9.851686	AAAAGAGAATGTAGATATACATGGCAA	57.148	29.630	13.52	0.00	40.26	4.52
751	769	2.799126	TGGCAACACGGATAAGGAAT	57.201	45.000	0.00	0.00	46.17	3.01
756	774	2.052782	ACACGGATAAGGAATTGGGC	57.947	50.000	0.00	0.00	0.00	5.36
761	779	0.668535	GATAAGGAATTGGGCCGTGC	59.331	55.000	0.00	0.00	0.00	5.34
785	803	2.126385	CGTAGTTGCCGTACGCCA	60.126	61.111	10.49	0.87	37.10	5.69
789	807	2.216750	TAGTTGCCGTACGCCAGTCC	62.217	60.000	10.49	0.00	36.24	3.85
808	826	2.201436	CTCTGGACACCACGGAGTCG	62.201	65.000	7.44	0.00	41.61	4.18
810	828	2.201436	CTGGACACCACGGAGTCGAG	62.201	65.000	10.33	10.33	41.61	4.04
888	909	4.764823	CCAAGAATTGTACCAGCCAGTAAA	59.235	41.667	0.00	0.00	46.99	2.01
894	915	9.338622	AGAATTGTACCAGCCAGTAAATAATAC	57.661	33.333	0.00	0.00	0.00	1.89
898	934	6.757947	TGTACCAGCCAGTAAATAATACGAAC	59.242	38.462	0.00	0.00	0.00	3.95
901	937	5.815740	CCAGCCAGTAAATAATACGAACACT	59.184	40.000	0.00	0.00	0.00	3.55
903	939	7.169308	CCAGCCAGTAAATAATACGAACACTAG	59.831	40.741	0.00	0.00	0.00	2.57
904	940	7.919091	CAGCCAGTAAATAATACGAACACTAGA	59.081	37.037	0.00	0.00	0.00	2.43
913	954	8.873215	ATAATACGAACACTAGAAGTCCATTG	57.127	34.615	0.00	0.00	0.00	2.82
947	1021	4.935352	AAAAGGTAATCAAACTGCTGCA	57.065	36.364	0.88	0.88	0.00	4.41
980	1054	2.049248	CGCCAAAACCTTGCGCAT	60.049	55.556	12.75	0.00	31.77	4.73
1069	1204	6.595716	ACTCCTTCCTCATCAAAGTTTAATCG	59.404	38.462	0.00	0.00	0.00	3.34
1103	1321	3.120786	GCACGTACAACTCATTACACACC	60.121	47.826	0.00	0.00	0.00	4.16
1357	1580	1.219124	GTCATCCTCGGCTGCTTCA	59.781	57.895	0.00	0.00	0.00	3.02
2025	2261	4.162690	GCCTCCAGGGTACAGCGG	62.163	72.222	0.00	0.00	37.43	5.52
2031	2267	2.683933	AGGGTACAGCGGGTGGAG	60.684	66.667	12.33	0.00	0.00	3.86
2042	2278	1.296715	GGGTGGAGATTGCACGAGT	59.703	57.895	0.00	0.00	39.79	4.18
2166	2402	1.167851	CTTTTTCGGATGCAGCTCCA	58.832	50.000	0.22	0.00	34.78	3.86
2278	2527	2.267006	CACCATGTCCAGCTCGCT	59.733	61.111	0.00	0.00	0.00	4.93
2535	2786	2.159114	GCTCCAGCAAACAAAAGTCCAA	60.159	45.455	0.00	0.00	41.59	3.53
2656	3047	4.637534	GCAAATTCAGATGCTAGTTCCAGA	59.362	41.667	0.00	0.00	39.46	3.86
2706	3098	4.780275	TGATGTGGCGAAAAATCATGAA	57.220	36.364	0.00	0.00	0.00	2.57

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
120	122	3.055094	GCTAAAACTGAGATGGGGACTGA	60.055	47.826	0.00	0.00	0.00	3.41
322	335	5.083122	TGCCAAGTTTCATAAGGGAATGAA	58.917	37.500	0.00	0.00	42.63	2.57
368	381	8.922931	AATTCTAAAGAAAAATGGTGGCAAAT	57.077	26.923	0.00	0.00	37.61	2.32
418	434	9.783081	TTTAGCTCATATGATCTTAGCATGAAA	57.217	29.630	13.95	8.70	35.63	2.69
446	463	3.008049	GTGTTGGTCAGTCCCATCTTAGT	59.992	47.826	0.00	0.00	33.60	2.24
447	464	3.261897	AGTGTTGGTCAGTCCCATCTTAG	59.738	47.826	0.00	0.00	33.60	2.18
448	465	3.248024	AGTGTTGGTCAGTCCCATCTTA	58.752	45.455	0.00	0.00	33.60	2.10
450	467	1.734655	AGTGTTGGTCAGTCCCATCT	58.265	50.000	0.00	0.00	33.60	2.90
451	468	2.568623	AAGTGTTGGTCAGTCCCATC	57.431	50.000	0.00	0.00	33.60	3.51
452	469	3.312736	AAAAGTGTTGGTCAGTCCCAT	57.687	42.857	0.00	0.00	33.60	4.00
453	470	2.818751	AAAAGTGTTGGTCAGTCCCA	57.181	45.000	0.00	0.00	34.77	4.37
576	594	6.039270	CCTTTGACTGTTTGACCATCACTTTA	59.961	38.462	0.00	0.00	0.00	1.85
652	670	2.553685	CGGCAGGTTTACCCCTAGTTTT	60.554	50.000	0.00	0.00	36.42	2.43
682	700	9.077885	GATAATTGATTTTATGCCCCTAGTTGA	57.922	33.333	0.00	0.00	0.00	3.18
711	729	9.851686	TTGCCATGTATATCTACATTCTCTTTT	57.148	29.630	1.17	0.00	44.42	2.27
717	735	6.128553	CCGTGTTGCCATGTATATCTACATTC	60.129	42.308	1.17	0.00	44.42	2.67
720	738	4.342665	TCCGTGTTGCCATGTATATCTACA	59.657	41.667	0.00	0.00	41.92	2.74
721	739	4.878439	TCCGTGTTGCCATGTATATCTAC	58.122	43.478	0.00	0.00	0.00	2.59
722	740	5.738619	ATCCGTGTTGCCATGTATATCTA	57.261	39.130	0.00	0.00	0.00	1.98
723	741	4.623932	ATCCGTGTTGCCATGTATATCT	57.376	40.909	0.00	0.00	0.00	1.98
724	742	5.351465	CCTTATCCGTGTTGCCATGTATATC	59.649	44.000	0.00	0.00	0.00	1.63
725	743	5.012664	TCCTTATCCGTGTTGCCATGTATAT	59.987	40.000	0.00	0.00	0.00	0.86
726	744	4.345547	TCCTTATCCGTGTTGCCATGTATA	59.654	41.667	0.00	0.00	0.00	1.47
727	745	3.135712	TCCTTATCCGTGTTGCCATGTAT	59.864	43.478	0.00	0.00	0.00	2.29
728	746	2.502130	TCCTTATCCGTGTTGCCATGTA	59.498	45.455	0.00	0.00	0.00	2.29
729	747	1.280710	TCCTTATCCGTGTTGCCATGT	59.719	47.619	0.00	0.00	0.00	3.21
730	748	2.036958	TCCTTATCCGTGTTGCCATG	57.963	50.000	0.00	0.00	0.00	3.66
731	749	2.799126	TTCCTTATCCGTGTTGCCAT	57.201	45.000	0.00	0.00	0.00	4.40
732	750	2.752354	CAATTCCTTATCCGTGTTGCCA	59.248	45.455	0.00	0.00	0.00	4.92
733	751	2.099098	CCAATTCCTTATCCGTGTTGCC	59.901	50.000	0.00	0.00	0.00	4.52
734	752	2.099098	CCCAATTCCTTATCCGTGTTGC	59.901	50.000	0.00	0.00	0.00	4.17
735	753	2.099098	GCCCAATTCCTTATCCGTGTTG	59.901	50.000	0.00	0.00	0.00	3.33
736	754	2.375146	GCCCAATTCCTTATCCGTGTT	58.625	47.619	0.00	0.00	0.00	3.32
737	755	1.409661	GGCCCAATTCCTTATCCGTGT	60.410	52.381	0.00	0.00	0.00	4.49
756	774	0.446222	CAACTACGGAATTGGCACGG	59.554	55.000	0.32	0.00	0.00	4.94
761	779	1.662122	GTACGGCAACTACGGAATTGG	59.338	52.381	0.00	0.00	35.23	3.16
762	780	1.322338	CGTACGGCAACTACGGAATTG	59.678	52.381	7.57	0.00	38.88	2.32
765	783	1.444212	GCGTACGGCAACTACGGAA	60.444	57.895	18.39	0.00	41.14	4.30
789	807	1.587054	GACTCCGTGGTGTCCAGAG	59.413	63.158	9.44	4.29	33.66	3.35
808	826	0.163788	CGGTGTTGCATTGACGTCTC	59.836	55.000	17.92	4.09	0.00	3.36
810	828	1.141645	TACGGTGTTGCATTGACGTC	58.858	50.000	9.11	9.11	35.97	4.34
888	909	7.926555	CCAATGGACTTCTAGTGTTCGTATTAT	59.073	37.037	0.00	0.00	0.00	1.28
894	915	3.926616	ACCAATGGACTTCTAGTGTTCG	58.073	45.455	6.16	0.00	0.00	3.95
898	934	6.702329	AGTAGAAACCAATGGACTTCTAGTG	58.298	40.000	23.00	0.00	35.34	2.74
980	1054	0.680618	TGTTCGGTCGGCTTAAGGAA	59.319	50.000	4.29	0.00	0.00	3.36
1103	1321	2.411904	GAGTTGAGTGCAGAGAACAGG	58.588	52.381	0.00	0.00	0.00	4.00
1342	1565	2.185350	CGTGAAGCAGCCGAGGAT	59.815	61.111	0.00	0.00	0.00	3.24
1357	1580	2.591753	CCATGATGTCCTGGGCGT	59.408	61.111	0.00	0.00	0.00	5.68
1550	1773	0.735978	CGGACACATCACGCAGCTTA	60.736	55.000	0.00	0.00	0.00	3.09
1630	1853	1.222113	TGCACTCCACGTGGAACAA	59.778	52.632	35.36	19.59	44.91	2.83
2014	2247	2.531483	ATCTCCACCCGCTGTACCCT	62.531	60.000	0.00	0.00	0.00	4.34
2025	2261	1.927895	CTACTCGTGCAATCTCCACC	58.072	55.000	0.00	0.00	0.00	4.61
2031	2267	1.537135	GGGAGAGCTACTCGTGCAATC	60.537	57.143	0.00	0.00	45.76	2.67
2042	2278	3.461773	GCTGCACGGGGAGAGCTA	61.462	66.667	11.71	0.00	37.34	3.32
2278	2527	0.108992	GGTGATACAAGTCGACGGCA	60.109	55.000	10.46	0.00	0.00	5.69
2372	2621	4.240096	CTGAATTTTGTTGTGCTGGATCC	58.760	43.478	4.20	4.20	0.00	3.36
2801	3193	7.783090	TTTTGCTACATCAAATTTTTGCTGA	57.217	28.000	12.39	0.00	36.65	4.26

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.