AutoCloner

Multiple sequence alignment - TraesCS6B01G045500

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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	TraesCS6B01G045500	chr6B	100.000	3161	0	0	1	3161	27077966	27074806	0.000000e+00	5838
1	TraesCS6B01G045500	chr6B	81.712	1285	203	27	973	2236	26389182	26390455	0.000000e+00	1042
2	TraesCS6B01G045500	chr6B	76.843	1438	291	29	983	2403	26500510	26501922	0.000000e+00	773
3	TraesCS6B01G045500	chr6B	75.306	1470	293	54	969	2398	26291274	26292713	9.560000e-180	640
4	TraesCS6B01G045500	chr6B	89.143	175	19	0	1974	2148	27520148	27520322	5.310000e-53	219
5	TraesCS6B01G045500	chr6D	96.546	2287	56	9	877	3161	15358433	15356168	0.000000e+00	3764
6	TraesCS6B01G045500	chr6D	93.125	800	41	7	1	790	15359595	15358800	0.000000e+00	1160
7	TraesCS6B01G045500	chr6D	77.021	1175	246	19	1075	2240	7994185	7993026	0.000000e+00	652
8	TraesCS6B01G045500	chr6D	74.983	1439	313	39	958	2366	18001657	18000236	1.250000e-173	619
9	TraesCS6B01G045500	chr6D	75.488	1024	217	26	1430	2433	14518073	14519082	1.330000e-128	470
10	TraesCS6B01G045500	chr6A	96.463	2177	66	5	985	3161	15940118	15937953	0.000000e+00	3583
11	TraesCS6B01G045500	chr6A	78.286	1575	280	41	973	2519	15694585	15696125	0.000000e+00	957
12	TraesCS6B01G045500	chr6A	89.330	731	64	8	1	721	15941464	15940738	0.000000e+00	905
13	TraesCS6B01G045500	chr6A	77.734	1271	247	29	984	2240	15914156	15912908	0.000000e+00	747
14	TraesCS6B01G045500	chr6A	76.114	875	169	33	1578	2433	15717380	15718233	3.770000e-114	422
15	TraesCS6B01G045500	chr1A	77.620	1269	258	24	961	2222	589248532	589247283	0.000000e+00	747
16	TraesCS6B01G045500	chr3A	79.587	387	52	18	2260	2641	748565127	748565491	5.230000e-63	252

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	TraesCS6B01G045500	chr6B	27074806	27077966	3160	True	5838	5838	100.0000	1	3161	1	chr6B.!!$R1	3160
1	TraesCS6B01G045500	chr6B	26389182	26390455	1273	False	1042	1042	81.7120	973	2236	1	chr6B.!!$F2	1263
2	TraesCS6B01G045500	chr6B	26500510	26501922	1412	False	773	773	76.8430	983	2403	1	chr6B.!!$F3	1420
3	TraesCS6B01G045500	chr6B	26291274	26292713	1439	False	640	640	75.3060	969	2398	1	chr6B.!!$F1	1429
4	TraesCS6B01G045500	chr6D	15356168	15359595	3427	True	2462	3764	94.8355	1	3161	2	chr6D.!!$R3	3160
5	TraesCS6B01G045500	chr6D	7993026	7994185	1159	True	652	652	77.0210	1075	2240	1	chr6D.!!$R1	1165
6	TraesCS6B01G045500	chr6D	18000236	18001657	1421	True	619	619	74.9830	958	2366	1	chr6D.!!$R2	1408
7	TraesCS6B01G045500	chr6D	14518073	14519082	1009	False	470	470	75.4880	1430	2433	1	chr6D.!!$F1	1003
8	TraesCS6B01G045500	chr6A	15937953	15941464	3511	True	2244	3583	92.8965	1	3161	2	chr6A.!!$R2	3160
9	TraesCS6B01G045500	chr6A	15694585	15696125	1540	False	957	957	78.2860	973	2519	1	chr6A.!!$F1	1546
10	TraesCS6B01G045500	chr6A	15912908	15914156	1248	True	747	747	77.7340	984	2240	1	chr6A.!!$R1	1256
11	TraesCS6B01G045500	chr6A	15717380	15718233	853	False	422	422	76.1140	1578	2433	1	chr6A.!!$F2	855
12	TraesCS6B01G045500	chr1A	589247283	589248532	1249	True	747	747	77.6200	961	2222	1	chr1A.!!$R1	1261

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	Hairpin	End Stability	Orientation
617	631	0.031585	CTGCATGATGAAATGGCCCG	59.968	55.0	0.00	6.13	F
806	820	0.331616	AACCCATTTCCCTCGGAAGG	59.668	55.0	43.06	3.46	F
853	1136	0.527113	CGATTGCATGAGCCCAAACA	59.473	50.0	41.13	2.83	F

Position	MSA Position	Penalty	Sequence	TM	GC	End Stability	Orientation
1784	2479	0.036952	CACTTCGGCATCAGACCACT	60.037	55.000	4.00	R
2073	2768	0.250467	GTGCAGCCTTCTTGTGAGGA	60.250	55.000	3.71	R
2340	3068	1.812571	CGGGGTTCAGGAATCAAGTTG	59.187	52.381	3.16	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
74	76	6.620877	TTGGATGAAACTACTATGTGGTCT	57.379	37.500	0.00	0.00	0.00	3.85
94	96	5.601313	GGTCTAGTGGGTGATATTAGGACAA	59.399	44.000	0.00	0.00	0.00	3.18
97	99	8.211629	GTCTAGTGGGTGATATTAGGACAATTT	58.788	37.037	0.00	0.00	0.00	1.82
98	100	8.429641	TCTAGTGGGTGATATTAGGACAATTTC	58.570	37.037	0.00	0.00	0.00	2.17
131	139	7.037586	TCCTCTACATGGAAAAAGGAAGTATGT	60.038	37.037	0.00	0.00	30.19	2.29
221	230	6.449635	TGTGCTTGCTATAAAAATGGTAGG	57.550	37.500	0.00	0.00	0.00	3.18
529	540	6.067263	TGACCACTAACTATTGTTTGTTGC	57.933	37.500	4.60	0.00	39.40	4.17
539	553	6.039616	ACTATTGTTTGTTGCGTGACATTTT	58.960	32.000	0.00	0.00	0.00	1.82
577	591	7.069085	AGCAAATTAATACGGTGTACTCTCCTA	59.931	37.037	0.00	0.00	0.00	2.94
617	631	0.031585	CTGCATGATGAAATGGCCCG	59.968	55.000	0.00	0.00	0.00	6.13
754	768	8.748412	CAAACTGGAATGTAGATGGGAAATTTA	58.252	33.333	0.00	0.00	0.00	1.40
763	777	8.934023	TGTAGATGGGAAATTTAAAACAGAGT	57.066	30.769	0.00	0.00	0.00	3.24
779	793	3.496130	ACAGAGTCATGCTTGTTCTTTCG	59.504	43.478	0.00	0.00	0.00	3.46
785	799	5.049818	AGTCATGCTTGTTCTTTCGAAAGAG	60.050	40.000	32.62	24.27	45.01	2.85
790	804	4.554919	GCTTGTTCTTTCGAAAGAGGAACC	60.555	45.833	32.62	21.14	45.01	3.62
792	806	3.118186	TGTTCTTTCGAAAGAGGAACCCA	60.118	43.478	32.62	21.81	45.01	4.51
793	807	4.072839	GTTCTTTCGAAAGAGGAACCCAT	58.927	43.478	32.62	0.00	45.01	4.00
796	810	4.760204	TCTTTCGAAAGAGGAACCCATTTC	59.240	41.667	31.62	0.00	43.69	2.17
797	811	6.265402	TCTTTCGAAAGAGGAACCCATTTCC	61.265	44.000	31.62	0.00	42.26	3.13
804	818	3.970205	GAACCCATTTCCCTCGGAA	57.030	52.632	0.00	0.00	40.27	4.30
805	819	1.751437	GAACCCATTTCCCTCGGAAG	58.249	55.000	0.00	0.00	43.06	3.46
806	820	0.331616	AACCCATTTCCCTCGGAAGG	59.668	55.000	0.00	0.00	43.06	3.46
807	821	0.549169	ACCCATTTCCCTCGGAAGGA	60.549	55.000	4.64	0.00	46.67	3.36
808	822	0.623723	CCCATTTCCCTCGGAAGGAA	59.376	55.000	3.93	3.93	46.67	3.36
809	823	1.408822	CCCATTTCCCTCGGAAGGAAG	60.409	57.143	8.04	0.00	46.67	3.46
810	824	1.559682	CCATTTCCCTCGGAAGGAAGA	59.440	52.381	8.04	1.56	46.67	2.87
812	826	3.274288	CATTTCCCTCGGAAGGAAGAAG	58.726	50.000	8.04	0.14	46.67	2.85
815	829	2.111384	TCCCTCGGAAGGAAGAAGATG	58.889	52.381	0.00	0.00	46.67	2.90
817	831	1.474143	CCTCGGAAGGAAGAAGATGGC	60.474	57.143	0.00	0.00	46.67	4.40
818	832	1.208052	CTCGGAAGGAAGAAGATGGCA	59.792	52.381	0.00	0.00	0.00	4.92
819	833	1.208052	TCGGAAGGAAGAAGATGGCAG	59.792	52.381	0.00	0.00	0.00	4.85
820	834	1.745141	CGGAAGGAAGAAGATGGCAGG	60.745	57.143	0.00	0.00	0.00	4.85
853	1136	0.527113	CGATTGCATGAGCCCAAACA	59.473	50.000	0.00	0.00	41.13	2.83
871	1154	3.561120	AACGGATTCGGCCCAGCAA	62.561	57.895	0.00	0.00	41.39	3.91
921	1214	1.514678	CTGTTACGGCAGGCAAGCAA	61.515	55.000	4.37	0.00	35.83	3.91
922	1215	1.210155	GTTACGGCAGGCAAGCAAG	59.790	57.895	4.37	0.62	35.83	4.01
923	1216	2.625823	TTACGGCAGGCAAGCAAGC	61.626	57.895	4.37	0.00	35.83	4.01
924	1217	3.841137	TACGGCAGGCAAGCAAGCA	62.841	57.895	9.55	0.00	35.83	3.91
966	1259	1.529244	CCCAAATCCCTCCGCCATC	60.529	63.158	0.00	0.00	0.00	3.51
967	1260	1.893808	CCAAATCCCTCCGCCATCG	60.894	63.158	0.00	0.00	0.00	3.84
1042	1712	1.388531	GTCTCCCACCTCCTCTCCA	59.611	63.158	0.00	0.00	0.00	3.86
1050	1720	3.522731	CTCCTCTCCACTCCGGCG	61.523	72.222	0.00	0.00	33.14	6.46
1118	1806	1.322538	CCCATTTCCCCGAGCCAAAG	61.323	60.000	0.00	0.00	0.00	2.77
1121	1809	2.439553	ATTTCCCCGAGCCAAAGCCA	62.440	55.000	0.00	0.00	41.25	4.75
1122	1810	2.648613	TTTCCCCGAGCCAAAGCCAA	62.649	55.000	0.00	0.00	41.25	4.52
1153	1844	4.198625	AGGAGTACCTCGTCGACG	57.801	61.111	31.30	31.30	44.13	5.12
1344	2035	3.411517	CGGACCCTGGCCTCCAAT	61.412	66.667	3.32	0.00	30.80	3.16
1537	2231	2.264480	CATCCAACCGCGACAGGA	59.736	61.111	8.23	12.07	34.73	3.86
1632	2327	2.202932	CCAAGGATCCTCACCGCG	60.203	66.667	16.52	0.00	0.00	6.46
1784	2479	7.807907	GGCGAAGTTTTTGAAGAAGATATTCAA	59.192	33.333	2.42	0.00	43.13	2.69
1881	2576	2.417719	CAAAGGTCCGAGTTCTTCCTG	58.582	52.381	0.00	0.00	0.00	3.86
2073	2768	7.598759	AGTATTTATGGAGAGGTTCATACGT	57.401	36.000	0.00	0.00	0.00	3.57
2245	2947	4.202245	TGTATGCTGGTAACTCTTGTCC	57.798	45.455	0.00	0.00	37.61	4.02
2340	3068	8.668353	TCATTGCTAATTCTTGATGTAACTGAC	58.332	33.333	0.00	0.00	0.00	3.51
2343	3071	7.806690	TGCTAATTCTTGATGTAACTGACAAC	58.193	34.615	0.00	0.00	42.78	3.32
2596	3328	9.927668	ACATTTATTTAGAATGTCCTGTTTTGG	57.072	29.630	0.00	0.00	42.40	3.28
2734	3466	9.328845	AGTTTGCAGTTCAATGTTCAATATTTT	57.671	25.926	0.00	0.00	34.12	1.82
2820	3555	8.556589	TCCCCTTATTGTTCTAAAGATTCATCA	58.443	33.333	0.00	0.00	0.00	3.07
2821	3556	9.359653	CCCCTTATTGTTCTAAAGATTCATCAT	57.640	33.333	0.00	0.00	0.00	2.45
3158	3893	2.094957	ACACCGTTGTTCACAAAACCAG	60.095	45.455	0.00	0.00	37.63	4.00

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
44	46	8.554528	CACATAGTAGTTTCATCCAATGCTTAG	58.445	37.037	0.00	0.00	0.00	2.18
47	49	5.824624	CCACATAGTAGTTTCATCCAATGCT	59.175	40.000	0.00	0.00	0.00	3.79
74	76	7.214381	CGAAATTGTCCTAATATCACCCACTA	58.786	38.462	0.00	0.00	0.00	2.74
94	96	4.408921	TCCATGTAGAGGATCAACCGAAAT	59.591	41.667	0.00	0.00	44.74	2.17
97	99	3.026707	TCCATGTAGAGGATCAACCGA	57.973	47.619	0.00	0.00	44.74	4.69
98	100	3.819564	TTCCATGTAGAGGATCAACCG	57.180	47.619	0.00	0.00	44.74	4.44
179	188	7.844493	AGCACAATATATGGAAACCATGATT	57.156	32.000	12.78	9.34	44.84	2.57
340	350	9.167311	GAACTGGAATTAGTGAGACATAAACAT	57.833	33.333	0.00	0.00	0.00	2.71
342	352	8.547967	TGAACTGGAATTAGTGAGACATAAAC	57.452	34.615	0.00	0.00	0.00	2.01
494	505	1.888215	AGTGGTCAGTGCATGTTCAG	58.112	50.000	0.00	0.00	0.00	3.02
563	577	3.568430	TGCACATATAGGAGAGTACACCG	59.432	47.826	0.00	0.00	32.13	4.94
569	583	3.899980	TGCTCATGCACATATAGGAGAGT	59.100	43.478	0.00	0.00	45.31	3.24
570	584	4.532314	TGCTCATGCACATATAGGAGAG	57.468	45.455	0.00	0.00	45.31	3.20
732	746	9.586435	GTTTTAAATTTCCCATCTACATTCCAG	57.414	33.333	0.00	0.00	0.00	3.86
754	768	5.841957	AAGAACAAGCATGACTCTGTTTT	57.158	34.783	0.00	0.96	32.98	2.43
790	804	1.559682	TCTTCCTTCCGAGGGAAATGG	59.440	52.381	12.69	2.67	41.54	3.16
792	806	3.182152	TCTTCTTCCTTCCGAGGGAAAT	58.818	45.455	12.69	0.00	41.54	2.17
793	807	2.616524	TCTTCTTCCTTCCGAGGGAAA	58.383	47.619	12.69	0.00	41.54	3.13
796	810	1.139853	CCATCTTCTTCCTTCCGAGGG	59.860	57.143	0.00	0.00	43.72	4.30
797	811	1.474143	GCCATCTTCTTCCTTCCGAGG	60.474	57.143	0.00	0.00	45.02	4.63
798	812	1.208052	TGCCATCTTCTTCCTTCCGAG	59.792	52.381	0.00	0.00	0.00	4.63
800	814	1.661341	CTGCCATCTTCTTCCTTCCG	58.339	55.000	0.00	0.00	0.00	4.30
801	815	2.021208	GCCTGCCATCTTCTTCCTTCC	61.021	57.143	0.00	0.00	0.00	3.46
802	816	1.064832	AGCCTGCCATCTTCTTCCTTC	60.065	52.381	0.00	0.00	0.00	3.46
803	817	0.998145	AGCCTGCCATCTTCTTCCTT	59.002	50.000	0.00	0.00	0.00	3.36
804	818	1.767681	CTAGCCTGCCATCTTCTTCCT	59.232	52.381	0.00	0.00	0.00	3.36
805	819	1.813477	GCTAGCCTGCCATCTTCTTCC	60.813	57.143	2.29	0.00	0.00	3.46
806	820	1.592064	GCTAGCCTGCCATCTTCTTC	58.408	55.000	2.29	0.00	0.00	2.87
807	821	3.796764	GCTAGCCTGCCATCTTCTT	57.203	52.632	2.29	0.00	0.00	2.52
817	831	1.448540	CGTTGAGTGGGCTAGCCTG	60.449	63.158	32.18	9.14	36.10	4.85
818	832	0.978146	ATCGTTGAGTGGGCTAGCCT	60.978	55.000	32.18	14.13	36.10	4.58
819	833	0.107654	AATCGTTGAGTGGGCTAGCC	60.108	55.000	26.55	26.55	0.00	3.93
820	834	1.009829	CAATCGTTGAGTGGGCTAGC	58.990	55.000	6.04	6.04	0.00	3.42
853	1136	3.561120	TTGCTGGGCCGAATCCGTT	62.561	57.895	0.00	0.00	0.00	4.44
880	1163	1.673626	CCGTGCCCGTACAGTTAATGT	60.674	52.381	0.00	0.00	46.45	2.71
882	1165	0.741927	GCCGTGCCCGTACAGTTAAT	60.742	55.000	0.00	0.00	0.00	1.40
883	1166	1.374505	GCCGTGCCCGTACAGTTAA	60.375	57.895	0.00	0.00	0.00	2.01
921	1214	3.369400	AGCTGCGTCTCGTCTGCT	61.369	61.111	0.00	10.09	35.20	4.24
922	1215	3.177920	CAGCTGCGTCTCGTCTGC	61.178	66.667	0.00	0.00	0.00	4.26
923	1216	3.177920	GCAGCTGCGTCTCGTCTG	61.178	66.667	25.23	0.00	0.00	3.51
924	1217	3.212906	TTGCAGCTGCGTCTCGTCT	62.213	57.895	32.11	0.00	45.83	4.18
1050	1720	2.383527	CGAAGTGACGCTGAAGGCC	61.384	63.158	0.00	0.00	37.74	5.19
1233	1924	2.726351	GGCGAGGAAGGCTAGCACT	61.726	63.158	18.24	8.50	0.00	4.40
1327	2018	3.411517	ATTGGAGGCCAGGGTCCG	61.412	66.667	5.01	0.00	35.37	4.79
1766	2461	8.786898	CAGACCACTTGAATATCTTCTTCAAAA	58.213	33.333	0.00	0.00	40.89	2.44
1784	2479	0.036952	CACTTCGGCATCAGACCACT	60.037	55.000	0.00	0.00	0.00	4.00
1881	2576	2.367202	TTCCAGCCCCATCTCGGAC	61.367	63.158	0.00	0.00	36.56	4.79
2073	2768	0.250467	GTGCAGCCTTCTTGTGAGGA	60.250	55.000	0.00	0.00	0.00	3.71
2245	2947	6.319658	ACATCAAGTTAGGCAATGAATACTGG	59.680	38.462	0.00	0.00	0.00	4.00
2291	3000	3.817084	CGAAACTGGCATGTCATGGATAT	59.183	43.478	14.64	0.00	0.00	1.63
2292	3001	3.205338	CGAAACTGGCATGTCATGGATA	58.795	45.455	14.64	0.00	0.00	2.59
2293	3002	2.019249	CGAAACTGGCATGTCATGGAT	58.981	47.619	14.64	0.00	0.00	3.41
2340	3068	1.812571	CGGGGTTCAGGAATCAAGTTG	59.187	52.381	0.00	0.00	0.00	3.16
2343	3071	2.717639	ATCGGGGTTCAGGAATCAAG	57.282	50.000	0.00	0.00	0.00	3.02
2582	3314	5.988287	ACAATGAAACCAAAACAGGACATT	58.012	33.333	0.00	0.00	34.13	2.71
3057	3792	1.067071	AGCTGTAGGTTGTAGCGGAAC	60.067	52.381	0.00	0.00	42.10	3.62

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.