AutoCloner

Multiple sequence alignment - TraesCS2A01G358700

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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	TraesCS2A01G358700	chr2A	100.000	2579	0	0	1	2579	602767708	602765130	0.000000e+00	4763.0
1	TraesCS2A01G358700	chr2A	92.081	985	61	10	785	1763	602718865	602717892	0.000000e+00	1371.0
2	TraesCS2A01G358700	chr2A	91.587	939	52	11	737	1663	602689013	602688090	0.000000e+00	1271.0
3	TraesCS2A01G358700	chr2A	97.268	732	14	1	1	732	747151738	747152463	0.000000e+00	1236.0
4	TraesCS2A01G358700	chr2A	82.935	586	78	12	136	718	562359894	562360460	2.290000e-140	508.0
5	TraesCS2A01G358700	chr2A	87.206	383	44	5	1837	2216	639524657	639524277	5.100000e-117	431.0
6	TraesCS2A01G358700	chr2A	90.498	221	18	3	2359	2579	639524258	639524041	3.250000e-74	289.0
7	TraesCS2A01G358700	chr2A	94.737	38	1	1	85	121	562359825	562359862	9.970000e-05	58.4
8	TraesCS2A01G358700	chr2D	91.721	918	54	9	859	1763	459344131	459343223	0.000000e+00	1254.0
9	TraesCS2A01G358700	chr2D	88.052	385	38	7	1837	2216	494473501	494473882	1.410000e-122	449.0
10	TraesCS2A01G358700	chr2D	89.140	221	21	3	2359	2579	494473901	494474118	3.270000e-69	272.0
11	TraesCS2A01G358700	chr3A	97.401	731	18	1	1	730	11567110	11567840	0.000000e+00	1243.0
12	TraesCS2A01G358700	chr2B	90.747	843	56	11	824	1663	540813869	540813046	0.000000e+00	1105.0
13	TraesCS2A01G358700	chr6D	89.050	758	49	7	1	728	126021140	126020387	0.000000e+00	909.0
14	TraesCS2A01G358700	chr6D	82.838	606	72	20	136	730	35466439	35467023	4.920000e-142	514.0
15	TraesCS2A01G358700	chr6D	100.000	32	0	0	1782	1813	207236861	207236830	2.770000e-05	60.2
16	TraesCS2A01G358700	chr3B	88.509	644	64	6	89	728	817793166	817793803	0.000000e+00	771.0
17	TraesCS2A01G358700	chr3B	88.596	114	11	2	2268	2380	264012973	264013085	1.240000e-28	137.0
18	TraesCS2A01G358700	chr3B	95.238	42	2	0	46	87	817793070	817793111	1.660000e-07	67.6
19	TraesCS2A01G358700	chr7D	92.445	503	32	6	1780	2277	13925224	13924723	0.000000e+00	713.0
20	TraesCS2A01G358700	chr7D	96.380	221	8	0	2359	2579	13924724	13924504	5.240000e-97	364.0
21	TraesCS2A01G358700	chr7D	92.308	221	16	1	2359	2579	360202667	360202448	1.930000e-81	313.0
22	TraesCS2A01G358700	chr7D	92.000	100	8	0	2276	2375	59099530	59099629	9.620000e-30	141.0
23	TraesCS2A01G358700	chr7D	100.000	33	0	0	1780	1812	21789677	21789709	7.710000e-06	62.1
24	TraesCS2A01G358700	chr7B	81.696	672	90	19	964	1622	699562563	699561912	1.760000e-146	529.0
25	TraesCS2A01G358700	chr7B	80.448	670	90	24	1003	1659	699354569	699355210	8.350000e-130	473.0
26	TraesCS2A01G358700	chr7B	82.555	321	46	7	1305	1622	699530705	699530392	9.090000e-70	274.0
27	TraesCS2A01G358700	chr7B	89.844	128	13	0	2359	2486	185607268	185607395	5.710000e-37	165.0
28	TraesCS2A01G358700	chr5A	82.833	600	77	16	136	731	59441255	59441832	4.920000e-142	514.0
29	TraesCS2A01G358700	chr5A	83.069	378	53	6	344	718	44559469	44559838	1.480000e-87	333.0
30	TraesCS2A01G358700	chr5A	82.289	367	50	10	350	711	157859795	157860151	1.160000e-78	303.0
31	TraesCS2A01G358700	chr5A	80.892	157	17	10	136	292	59439467	59439610	7.540000e-21	111.0
32	TraesCS2A01G358700	chr5A	80.892	157	17	10	136	292	59440361	59440504	7.540000e-21	111.0
33	TraesCS2A01G358700	chr5A	94.737	38	1	1	85	121	59441186	59441223	9.970000e-05	58.4
34	TraesCS2A01G358700	chr1D	81.063	602	76	21	136	734	21533653	21534219	1.820000e-121	446.0
35	TraesCS2A01G358700	chr7A	82.398	517	70	9	997	1507	700685332	700684831	5.100000e-117	431.0
36	TraesCS2A01G358700	chr7A	98.214	56	1	0	1530	1585	700684835	700684780	5.870000e-17	99.0
37	TraesCS2A01G358700	chr7A	100.000	33	0	0	1780	1812	668817718	668817750	7.710000e-06	62.1
38	TraesCS2A01G358700	chrUn	94.681	94	5	0	2268	2361	71515192	71515099	2.070000e-31	147.0
39	TraesCS2A01G358700	chrUn	93.258	89	5	1	2276	2363	132121232	132121144	2.080000e-26	130.0
40	TraesCS2A01G358700	chrUn	88.288	111	9	4	2269	2377	326633043	326632935	2.080000e-26	130.0
41	TraesCS2A01G358700	chrUn	88.288	111	9	4	2269	2377	382902201	382902093	2.080000e-26	130.0
42	TraesCS2A01G358700	chrUn	100.000	32	0	0	1780	1811	471059384	471059353	2.770000e-05	60.2
43	TraesCS2A01G358700	chr4A	89.091	110	10	2	2269	2377	712646223	712646331	4.480000e-28	135.0
44	TraesCS2A01G358700	chr4A	89.091	110	10	2	2269	2377	712809625	712809733	4.480000e-28	135.0
45	TraesCS2A01G358700	chr4A	89.091	110	10	2	2269	2377	712834708	712834816	4.480000e-28	135.0
46	TraesCS2A01G358700	chr4D	100.000	32	0	0	1780	1811	10404373	10404342	2.770000e-05	60.2
47	TraesCS2A01G358700	chr4D	100.000	32	0	0	1780	1811	121846364	121846395	2.770000e-05	60.2
48	TraesCS2A01G358700	chr4D	100.000	32	0	0	1782	1813	437046804	437046773	2.770000e-05	60.2
49	TraesCS2A01G358700	chr1A	100.000	32	0	0	1782	1813	100366082	100366113	2.770000e-05	60.2

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	TraesCS2A01G358700	chr2A	602765130	602767708	2578	True	4763.0	4763	100.0000	1	2579	1	chr2A.!!$R3	2578
1	TraesCS2A01G358700	chr2A	602717892	602718865	973	True	1371.0	1371	92.0810	785	1763	1	chr2A.!!$R2	978
2	TraesCS2A01G358700	chr2A	602688090	602689013	923	True	1271.0	1271	91.5870	737	1663	1	chr2A.!!$R1	926
3	TraesCS2A01G358700	chr2A	747151738	747152463	725	False	1236.0	1236	97.2680	1	732	1	chr2A.!!$F1	731
4	TraesCS2A01G358700	chr2A	639524041	639524657	616	True	360.0	431	88.8520	1837	2579	2	chr2A.!!$R4	742
5	TraesCS2A01G358700	chr2A	562359825	562360460	635	False	283.2	508	88.8360	85	718	2	chr2A.!!$F2	633
6	TraesCS2A01G358700	chr2D	459343223	459344131	908	True	1254.0	1254	91.7210	859	1763	1	chr2D.!!$R1	904
7	TraesCS2A01G358700	chr2D	494473501	494474118	617	False	360.5	449	88.5960	1837	2579	2	chr2D.!!$F1	742
8	TraesCS2A01G358700	chr3A	11567110	11567840	730	False	1243.0	1243	97.4010	1	730	1	chr3A.!!$F1	729
9	TraesCS2A01G358700	chr2B	540813046	540813869	823	True	1105.0	1105	90.7470	824	1663	1	chr2B.!!$R1	839
10	TraesCS2A01G358700	chr6D	126020387	126021140	753	True	909.0	909	89.0500	1	728	1	chr6D.!!$R1	727
11	TraesCS2A01G358700	chr6D	35466439	35467023	584	False	514.0	514	82.8380	136	730	1	chr6D.!!$F1	594
12	TraesCS2A01G358700	chr3B	817793070	817793803	733	False	419.3	771	91.8735	46	728	2	chr3B.!!$F2	682
13	TraesCS2A01G358700	chr7D	13924504	13925224	720	True	538.5	713	94.4125	1780	2579	2	chr7D.!!$R2	799
14	TraesCS2A01G358700	chr7B	699561912	699562563	651	True	529.0	529	81.6960	964	1622	1	chr7B.!!$R2	658
15	TraesCS2A01G358700	chr7B	699354569	699355210	641	False	473.0	473	80.4480	1003	1659	1	chr7B.!!$F2	656
16	TraesCS2A01G358700	chr1D	21533653	21534219	566	False	446.0	446	81.0630	136	734	1	chr1D.!!$F1	598
17	TraesCS2A01G358700	chr7A	700684780	700685332	552	True	265.0	431	90.3060	997	1585	2	chr7A.!!$R1	588

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
944	1037	0.306228	AGTCATCGCTCGATCTCGTG	59.694	55.0	1.3	0.0	40.8	4.35	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2504	2655	1.039856	ACATGCACCTTTGGGTTGAC	58.96	50.0	0.0	0.0	44.73	3.18	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
335	411	9.160412	AGGCAAAGACTTAGTCCTACATATATT	57.840	33.333	8.96	0.00	32.18	1.28
533	618	5.684550	AAAAATAGAGTTGTTCACCCGAC	57.315	39.130	0.00	0.00	0.00	4.79
735	823	6.110411	ACAGGCATGTTTACTAGTTGTAGT	57.890	37.500	0.00	0.00	38.70	2.73
739	827	7.601130	CAGGCATGTTTACTAGTTGTAGTACAA	59.399	37.037	11.75	11.75	40.76	2.41
773	861	3.439476	AGCACTAGTTCGTCTCGTACATT	59.561	43.478	0.00	0.00	29.93	2.71
775	863	5.296283	AGCACTAGTTCGTCTCGTACATTAT	59.704	40.000	0.00	0.00	29.93	1.28
776	864	6.481313	AGCACTAGTTCGTCTCGTACATTATA	59.519	38.462	0.00	0.00	29.93	0.98
777	865	7.011763	AGCACTAGTTCGTCTCGTACATTATAA	59.988	37.037	0.00	0.00	29.93	0.98
778	866	7.111317	GCACTAGTTCGTCTCGTACATTATAAC	59.889	40.741	0.00	0.00	29.93	1.89
779	867	8.333908	CACTAGTTCGTCTCGTACATTATAACT	58.666	37.037	0.00	0.00	29.93	2.24
780	868	9.534565	ACTAGTTCGTCTCGTACATTATAACTA	57.465	33.333	0.00	0.00	29.93	2.24
783	871	9.875675	AGTTCGTCTCGTACATTATAACTAATC	57.124	33.333	0.00	0.00	29.93	1.75
820	908	7.159372	TGGACTTGTCTAAGAAACACTAATCC	58.841	38.462	0.61	0.00	37.36	3.01
886	975	1.891919	TGCCTGTCGCACAACTTCC	60.892	57.895	0.00	0.00	44.64	3.46
905	994	0.664166	CAAGCCCACAAATCGCACAC	60.664	55.000	0.00	0.00	0.00	3.82
908	997	1.580942	CCCACAAATCGCACACCAG	59.419	57.895	0.00	0.00	0.00	4.00
944	1037	0.306228	AGTCATCGCTCGATCTCGTG	59.694	55.000	1.30	0.00	40.80	4.35
1230	1326	1.988956	CCAGCTGGAGAGACAGGCT	60.989	63.158	29.88	0.00	38.90	4.58
1443	1572	4.760047	TTCGGAGCGCCAAGGAGC	62.760	66.667	7.44	6.73	41.21	4.70
1451	1580	3.756727	GCCAAGGAGCCAGCAAGC	61.757	66.667	0.00	0.00	0.00	4.01
1452	1581	3.066814	CCAAGGAGCCAGCAAGCC	61.067	66.667	0.00	0.00	0.00	4.35
1453	1582	2.282674	CAAGGAGCCAGCAAGCCA	60.283	61.111	0.00	0.00	0.00	4.75
1528	1657	2.364317	CCCAGAAGGCTCCTCCGA	60.364	66.667	0.00	0.00	40.77	4.55
1609	1745	7.494952	AGACGATAGCTTTCCCTTTTAACATAC	59.505	37.037	0.00	0.00	42.67	2.39
1727	1871	1.202154	CGATCGACTGGTCTGTGGTAC	60.202	57.143	10.26	0.00	0.00	3.34
1730	1874	0.526662	CGACTGGTCTGTGGTACCTC	59.473	60.000	14.36	10.53	37.91	3.85
1776	1920	8.904099	AATTATCACCTACTAGTAAATGTGCC	57.096	34.615	16.44	0.00	0.00	5.01
1777	1921	4.748277	TCACCTACTAGTAAATGTGCCC	57.252	45.455	16.44	0.00	0.00	5.36
1778	1922	3.131577	TCACCTACTAGTAAATGTGCCCG	59.868	47.826	16.44	0.00	0.00	6.13
1812	1956	1.611491	TGCAACGGGAGAAACAAATCC	59.389	47.619	0.00	0.00	34.64	3.01
1822	1967	5.181433	GGGAGAAACAAATCCAAGTGACTAC	59.819	44.000	0.00	0.00	37.33	2.73
2016	2163	0.316689	GCGGAAGTCAACAAACCACG	60.317	55.000	0.00	0.00	0.00	4.94
2039	2186	6.764560	ACGCCGTAAATTAGAGGACAATAAAT	59.235	34.615	0.00	0.00	0.00	1.40
2083	2231	8.511321	TCTTTGTTATTAGCAAACATGGTACTG	58.489	33.333	0.00	0.00	36.75	2.74
2193	2344	6.347483	CCTCAAGATATCGAGTCATGCAAATG	60.347	42.308	0.00	0.00	0.00	2.32
2355	2506	9.953697	AACGCTCTTATATTAGTTTACAGAGAG	57.046	33.333	0.00	0.00	34.15	3.20
2356	2507	9.339850	ACGCTCTTATATTAGTTTACAGAGAGA	57.660	33.333	4.35	0.00	32.80	3.10
2357	2508	9.820229	CGCTCTTATATTAGTTTACAGAGAGAG	57.180	37.037	0.00	0.00	30.76	3.20
2464	2615	7.509141	TGAACAACTCAACATGATGTAACAT	57.491	32.000	0.00	0.00	0.00	2.71
2494	2645	1.856629	ATGAAATGAGGTTGCCCCTG	58.143	50.000	0.00	0.00	46.51	4.45
2504	2655	3.086282	AGGTTGCCCCTGTATAAAAACG	58.914	45.455	0.00	0.00	44.08	3.60

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
335	411	7.834068	TGTTTTAAGTTGCTATTTTGTTGCA	57.166	28.000	0.00	0.00	36.79	4.08
370	452	3.007831	TGTGTGCTGACCATGAAGTCATA	59.992	43.478	5.41	0.00	45.39	2.15
372	454	1.140652	TGTGTGCTGACCATGAAGTCA	59.859	47.619	0.00	0.00	44.38	3.41
380	462	3.865446	CTTCTATCATGTGTGCTGACCA	58.135	45.455	0.00	0.00	0.00	4.02
514	599	4.771054	ACTAGTCGGGTGAACAACTCTATT	59.229	41.667	0.00	0.00	0.00	1.73
533	618	7.361457	TGGGACATGAATCCTAGTTAACTAG	57.639	40.000	28.63	28.63	44.22	2.57
711	799	7.601508	GTACTACAACTAGTAAACATGCCTGTT	59.398	37.037	1.04	1.04	39.40	3.16
714	802	7.235935	TGTACTACAACTAGTAAACATGCCT	57.764	36.000	0.00	0.00	37.24	4.75
732	820	2.354704	GCTGGGTCTGCATGTTGTACTA	60.355	50.000	0.00	0.00	0.00	1.82
733	821	1.611673	GCTGGGTCTGCATGTTGTACT	60.612	52.381	0.00	0.00	0.00	2.73
734	822	0.804989	GCTGGGTCTGCATGTTGTAC	59.195	55.000	0.00	0.00	0.00	2.90
735	823	0.399833	TGCTGGGTCTGCATGTTGTA	59.600	50.000	0.00	0.00	33.63	2.41
739	827	0.251354	CTAGTGCTGGGTCTGCATGT	59.749	55.000	0.00	0.00	40.15	3.21
799	887	8.499162	CAACTGGATTAGTGTTTCTTAGACAAG	58.501	37.037	0.00	0.00	40.26	3.16
820	908	2.094906	TCGTACAATCCGAGTCCAACTG	60.095	50.000	0.00	0.00	0.00	3.16
881	970	1.247567	CGATTTGTGGGCTTGGAAGT	58.752	50.000	0.00	0.00	0.00	3.01
886	975	0.664166	GTGTGCGATTTGTGGGCTTG	60.664	55.000	0.00	0.00	0.00	4.01
905	994	2.991076	GCTCCTTGCTTGCTGCTGG	61.991	63.158	0.00	6.29	43.37	4.85
908	997	1.080705	CTTGCTCCTTGCTTGCTGC	60.081	57.895	0.00	0.00	43.37	5.25
1144	1240	1.573108	AGATCCTTGGTGTGATCCGT	58.427	50.000	0.00	0.00	38.50	4.69
1146	1242	3.243569	CGAGTAGATCCTTGGTGTGATCC	60.244	52.174	0.00	0.00	38.50	3.36
1230	1326	4.060667	GCCCTTGCCTTGGCCCTA	62.061	66.667	9.35	0.00	41.97	3.53
1249	1345	3.842925	TTGCCTTCGCCTCCGCTTT	62.843	57.895	0.00	0.00	0.00	3.51
1386	1515	0.602372	GCTGATTCCTCGATGCTCCC	60.602	60.000	0.00	0.00	0.00	4.30
1443	1572	3.068691	ATGCTGCTGGCTTGCTGG	61.069	61.111	0.00	3.47	42.39	4.85
1451	1580	0.454600	GTTCATGGACATGCTGCTGG	59.545	55.000	7.41	0.00	38.65	4.85
1452	1581	0.098200	CGTTCATGGACATGCTGCTG	59.902	55.000	4.68	0.00	38.65	4.41
1453	1582	0.036105	TCGTTCATGGACATGCTGCT	60.036	50.000	4.68	0.00	38.65	4.24
1696	1840	2.542178	CCAGTCGATCGAGTAGTCTCAG	59.458	54.545	24.28	10.65	40.44	3.35
1699	1843	2.168936	AGACCAGTCGATCGAGTAGTCT	59.831	50.000	34.09	34.09	40.12	3.24
1763	1907	1.396996	GCACACGGGCACATTTACTAG	59.603	52.381	0.00	0.00	0.00	2.57
1764	1908	1.444836	GCACACGGGCACATTTACTA	58.555	50.000	0.00	0.00	0.00	1.82
1765	1909	1.241315	GGCACACGGGCACATTTACT	61.241	55.000	0.00	0.00	42.77	2.24
1766	1910	1.211709	GGCACACGGGCACATTTAC	59.788	57.895	0.00	0.00	42.77	2.01
1767	1911	1.974343	GGGCACACGGGCACATTTA	60.974	57.895	0.00	0.00	45.66	1.40
1768	1912	3.302344	GGGCACACGGGCACATTT	61.302	61.111	0.00	0.00	45.66	2.32
2016	2163	9.048446	TGTATTTATTGTCCTCTAATTTACGGC	57.952	33.333	0.00	0.00	0.00	5.68
2039	2186	6.707290	ACAAAGATGGTAGCTTACATGTGTA	58.293	36.000	9.11	0.00	0.00	2.90
2083	2231	8.349983	AGTTCACCAATTTTTACATGAGTGTAC	58.650	33.333	0.00	0.00	40.40	2.90
2329	2480	9.953697	CTCTCTGTAAACTAATATAAGAGCGTT	57.046	33.333	0.00	0.00	0.00	4.84
2330	2481	9.339850	TCTCTCTGTAAACTAATATAAGAGCGT	57.660	33.333	0.00	0.00	0.00	5.07
2331	2482	9.820229	CTCTCTCTGTAAACTAATATAAGAGCG	57.180	37.037	0.00	0.00	0.00	5.03
2411	2562	9.031537	TGTATGTCGTGGTAAGATAATGGATAT	57.968	33.333	0.00	0.00	0.00	1.63
2429	2580	5.050431	TGTTGAGTTGTTCATGTGTATGTCG	60.050	40.000	0.00	0.00	35.27	4.35
2464	2615	6.424509	GCAACCTCATTTCATTCATCAAACAA	59.575	34.615	0.00	0.00	0.00	2.83
2494	2645	5.916320	CACCTTTGGGTTGACGTTTTTATAC	59.084	40.000	0.00	0.00	44.73	1.47
2504	2655	1.039856	ACATGCACCTTTGGGTTGAC	58.960	50.000	0.00	0.00	44.73	3.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.