AutoCloner

Multiple sequence alignment - TraesCS1A01G123500

Loading Multiple Alignment...

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	TraesCS1A01G123500	chr1A	100.000	2598	0	0	1	2598	143380553	143377956	0.000000e+00	4798.0
1	TraesCS1A01G123500	chr1A	93.437	1417	76	5	1182	2598	480976394	480974995	0.000000e+00	2085.0
2	TraesCS1A01G123500	chr1A	90.265	678	57	6	511	1187	480984172	480983503	0.000000e+00	878.0
3	TraesCS1A01G123500	chr1A	100.000	31	0	0	675	705	58297033	58297003	1.000000e-04	58.4
4	TraesCS1A01G123500	chr2B	91.702	2109	131	15	491	2594	488700738	488702807	0.000000e+00	2885.0
5	TraesCS1A01G123500	chr2B	96.184	1258	46	2	1342	2598	631590	632846	0.000000e+00	2056.0
6	TraesCS1A01G123500	chr2B	89.920	377	34	4	1636	2011	485685733	485685360	1.400000e-132	483.0
7	TraesCS1A01G123500	chr2B	92.366	262	17	3	491	749	631326	631587	1.140000e-98	370.0
8	TraesCS1A01G123500	chr7A	90.982	2118	160	14	491	2598	346770678	346768582	0.000000e+00	2824.0
9	TraesCS1A01G123500	chr7A	81.285	529	56	24	712	1232	299583233	299582740	3.140000e-104	388.0
10	TraesCS1A01G123500	chr7A	84.375	128	19	1	716	842	417545715	417545588	9.760000e-25	124.0
11	TraesCS1A01G123500	chr3D	93.519	1836	105	11	491	2321	124496888	124495062	0.000000e+00	2719.0
12	TraesCS1A01G123500	chr3D	96.047	506	20	0	1	506	269393783	269393278	0.000000e+00	824.0
13	TraesCS1A01G123500	chr3D	97.464	276	7	0	2323	2598	124495011	124494736	3.030000e-129	472.0
14	TraesCS1A01G123500	chr3D	89.583	96	2	5	1547	1634	348484997	348485092	5.880000e-22	115.0
15	TraesCS1A01G123500	chr3D	88.542	96	5	4	1547	1637	589850007	589850101	7.600000e-21	111.0
16	TraesCS1A01G123500	chr4A	96.439	1320	40	3	1282	2598	622161061	622162376	0.000000e+00	2170.0
17	TraesCS1A01G123500	chr4A	94.981	797	39	1	491	1286	622133992	622134788	0.000000e+00	1249.0
18	TraesCS1A01G123500	chr4A	78.278	755	88	38	491	1232	374360400	374361091	1.440000e-112	416.0
19	TraesCS1A01G123500	chr4A	83.619	409	44	14	1227	1634	501978832	501979218	1.900000e-96	363.0
20	TraesCS1A01G123500	chr7B	94.099	1254	68	6	923	2174	511464566	511463317	0.000000e+00	1901.0
21	TraesCS1A01G123500	chr7B	91.980	399	29	2	505	900	511464954	511464556	8.120000e-155	556.0
22	TraesCS1A01G123500	chr1D	97.177	496	14	0	1	496	476996485	476995990	0.000000e+00	839.0
23	TraesCS1A01G123500	chr1D	96.982	497	14	1	1	496	352296827	352297323	0.000000e+00	833.0
24	TraesCS1A01G123500	chr5D	96.976	496	15	0	1	496	370875144	370874649	0.000000e+00	833.0
25	TraesCS1A01G123500	chr5D	82.386	176	25	6	491	663	44500282	44500454	5.790000e-32	148.0
26	TraesCS1A01G123500	chr2D	96.976	496	15	0	1	496	81900609	81900114	0.000000e+00	833.0
27	TraesCS1A01G123500	chr2D	96.982	497	14	1	1	496	634197906	634197410	0.000000e+00	833.0
28	TraesCS1A01G123500	chr1B	96.976	496	15	0	1	496	570380878	570381373	0.000000e+00	833.0
29	TraesCS1A01G123500	chr1B	90.451	377	32	4	1636	2011	200035722	200035349	6.460000e-136	494.0
30	TraesCS1A01G123500	chr1B	79.330	179	30	7	491	666	646746068	646746242	4.540000e-23	119.0
31	TraesCS1A01G123500	chr6D	96.774	496	16	0	1	496	460537545	460537050	0.000000e+00	828.0
32	TraesCS1A01G123500	chr4D	96.781	497	15	1	1	496	467090968	467091464	0.000000e+00	828.0
33	TraesCS1A01G123500	chr5A	78.153	769	91	39	477	1232	42137672	42136968	4.000000e-113	418.0
34	TraesCS1A01G123500	chr5A	83.744	406	43	11	1230	1634	42136866	42136483	1.900000e-96	363.0
35	TraesCS1A01G123500	chr6A	77.690	762	86	43	488	1232	52901900	52902594	3.140000e-104	388.0
36	TraesCS1A01G123500	chr6A	83.619	409	44	11	1227	1634	52902693	52903079	1.900000e-96	363.0
37	TraesCS1A01G123500	chr3B	83.619	409	44	11	1227	1634	51764697	51765083	1.900000e-96	363.0
38	TraesCS1A01G123500	chr3B	84.956	113	16	1	1052	1164	800424463	800424352	2.110000e-21	113.0
39	TraesCS1A01G123500	chr6B	79.054	296	37	13	675	959	159796510	159796791	2.050000e-41	180.0
40	TraesCS1A01G123500	chr6B	84.672	137	20	1	707	842	432519469	432519605	4.510000e-28	135.0
41	TraesCS1A01G123500	chr5B	77.528	178	35	5	491	666	237819582	237819408	4.570000e-18	102.0
42	TraesCS1A01G123500	chr4B	100.000	31	0	0	675	705	173329633	173329663	1.000000e-04	58.4

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	TraesCS1A01G123500	chr1A	143377956	143380553	2597	True	4798.0	4798	100.0000	1	2598	1	chr1A.!!$R2	2597
1	TraesCS1A01G123500	chr1A	480974995	480976394	1399	True	2085.0	2085	93.4370	1182	2598	1	chr1A.!!$R3	1416
2	TraesCS1A01G123500	chr1A	480983503	480984172	669	True	878.0	878	90.2650	511	1187	1	chr1A.!!$R4	676
3	TraesCS1A01G123500	chr2B	488700738	488702807	2069	False	2885.0	2885	91.7020	491	2594	1	chr2B.!!$F1	2103
4	TraesCS1A01G123500	chr2B	631326	632846	1520	False	1213.0	2056	94.2750	491	2598	2	chr2B.!!$F2	2107
5	TraesCS1A01G123500	chr7A	346768582	346770678	2096	True	2824.0	2824	90.9820	491	2598	1	chr7A.!!$R2	2107
6	TraesCS1A01G123500	chr3D	124494736	124496888	2152	True	1595.5	2719	95.4915	491	2598	2	chr3D.!!$R2	2107
7	TraesCS1A01G123500	chr3D	269393278	269393783	505	True	824.0	824	96.0470	1	506	1	chr3D.!!$R1	505
8	TraesCS1A01G123500	chr4A	622161061	622162376	1315	False	2170.0	2170	96.4390	1282	2598	1	chr4A.!!$F4	1316
9	TraesCS1A01G123500	chr4A	622133992	622134788	796	False	1249.0	1249	94.9810	491	1286	1	chr4A.!!$F3	795
10	TraesCS1A01G123500	chr4A	374360400	374361091	691	False	416.0	416	78.2780	491	1232	1	chr4A.!!$F1	741
11	TraesCS1A01G123500	chr7B	511463317	511464954	1637	True	1228.5	1901	93.0395	505	2174	2	chr7B.!!$R1	1669
12	TraesCS1A01G123500	chr5A	42136483	42137672	1189	True	390.5	418	80.9485	477	1634	2	chr5A.!!$R1	1157
13	TraesCS1A01G123500	chr6A	52901900	52903079	1179	False	375.5	388	80.6545	488	1634	2	chr6A.!!$F1	1146

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
173	174	0.312729	TGTTGACGCTGCTACTTCGA	59.687	50.0	0.00	0.0	0.00	3.71	F
1131	1151	0.311790	GGTGACCGACGGCGATAATA	59.688	55.0	15.16	0.0	40.82	0.98	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1201	1221	1.001974	CTCACGGGATTCAAGTGGTCA	59.998	52.381	0.00	0.0	36.60	4.02	R
2167	2303	2.158928	ACAAAATGGAGCTGCAAAGCAA	60.159	40.909	13.45	0.0	38.41	3.91	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
33	34	2.566010	GCCGGCGAAAAGATTGCA	59.434	55.556	12.58	0.00	0.00	4.08
38	39	1.135717	CGGCGAAAAGATTGCATGTCA	60.136	47.619	0.00	0.00	0.00	3.58
77	78	4.759183	AGAGTTGATCAAGAAGAAGCCAAC	59.241	41.667	8.80	0.00	36.36	3.77
115	116	3.306088	GGACGAAGAAGAAGATGACACCA	60.306	47.826	0.00	0.00	0.00	4.17
126	127	5.135020	AGAAGATGACACCATGGGGAATTAT	59.865	40.000	24.27	8.86	38.05	1.28
167	168	1.629013	CGAAGATGTTGACGCTGCTA	58.371	50.000	0.00	0.00	0.00	3.49
170	171	2.751166	AGATGTTGACGCTGCTACTT	57.249	45.000	0.00	0.00	0.00	2.24
173	174	0.312729	TGTTGACGCTGCTACTTCGA	59.687	50.000	0.00	0.00	0.00	3.71
211	212	4.615912	GCTTTTGTCGTATTTGCCTGTCAT	60.616	41.667	0.00	0.00	0.00	3.06
249	250	7.503521	TCTACTATGTGAAATTGTGTTTGCA	57.496	32.000	0.00	0.00	0.00	4.08
353	354	9.691362	GTTTGGTGATTGTATGACAACTAAAAT	57.309	29.630	0.00	0.00	41.40	1.82
425	426	7.307694	TGAATTTGATGACATAGTTTGCTGTC	58.692	34.615	0.00	0.00	41.69	3.51
615	624	4.617253	AAGTGGCTAATTTGGGAAAACC	57.383	40.909	0.00	0.00	40.81	3.27
719	730	4.400961	GCGAGGTGGCTGGAGCTT	62.401	66.667	0.00	0.00	41.70	3.74
720	731	2.435586	CGAGGTGGCTGGAGCTTG	60.436	66.667	0.00	0.00	41.70	4.01
721	732	2.749441	GAGGTGGCTGGAGCTTGC	60.749	66.667	0.00	0.00	41.70	4.01
980	995	3.050275	GGCAGCGCGAAGTCCTTT	61.050	61.111	12.10	0.00	0.00	3.11
1102	1121	1.445942	GCGCTGGATAACCTAGCCA	59.554	57.895	0.00	0.00	42.94	4.75
1128	1148	2.122797	ATGGTGACCGACGGCGATA	61.123	57.895	15.16	0.00	40.82	2.92
1131	1151	0.311790	GGTGACCGACGGCGATAATA	59.688	55.000	15.16	0.00	40.82	0.98
1174	1194	1.850441	CGGCGGTATGACTTAGAAACG	59.150	52.381	0.00	0.00	0.00	3.60
1201	1221	1.306226	CCTTCCCTTCTCCCTCGGT	60.306	63.158	0.00	0.00	0.00	4.69
1271	1396	2.556766	CTCTTCTTTCCTCCCCTTCCT	58.443	52.381	0.00	0.00	0.00	3.36
1290	1415	6.728164	CCTTCCTTGATGATATTCTCTCCCTA	59.272	42.308	0.00	0.00	0.00	3.53
1296	1421	5.481824	TGATGATATTCTCTCCCTAACGCAT	59.518	40.000	0.00	0.00	0.00	4.73
1412	1537	1.626356	GCCTCCACCATCTGCAGGTA	61.626	60.000	15.13	0.00	37.23	3.08
1428	1555	6.998074	TCTGCAGGTATTTCTTCTTTTCTTCA	59.002	34.615	15.13	0.00	0.00	3.02
1433	1560	7.445402	CAGGTATTTCTTCTTTTCTTCACCTCA	59.555	37.037	0.00	0.00	30.40	3.86
1437	1564	4.130118	TCTTCTTTTCTTCACCTCACTGC	58.870	43.478	0.00	0.00	0.00	4.40
1486	1614	5.365025	TGCAGGTGAAGCTCTATCTATTCTT	59.635	40.000	0.00	0.00	0.00	2.52
1502	1630	2.169832	TCTTTGCTGCAGTGTCTACC	57.830	50.000	16.64	0.00	0.00	3.18
1503	1631	1.416030	TCTTTGCTGCAGTGTCTACCA	59.584	47.619	16.64	0.00	0.00	3.25
1523	1651	4.227300	ACCATGGACTATTTGCACCTTCTA	59.773	41.667	21.47	0.00	0.00	2.10
1806	1941	7.119992	TGCAAGCAATTCTCGGTTTAAATACTA	59.880	33.333	0.00	0.00	0.00	1.82
2017	2153	0.919710	GGTAGGGGGAAATCACTGCT	59.080	55.000	0.00	0.00	0.00	4.24
2058	2194	6.918067	TCTATTTGTGAGTATGATCGGGAT	57.082	37.500	0.00	0.00	0.00	3.85
2158	2294	3.821033	GCTAAGTTTGGATGTGGAGTTGT	59.179	43.478	0.00	0.00	0.00	3.32
2167	2303	8.357402	GTTTGGATGTGGAGTTGTAATTTAACT	58.643	33.333	7.31	7.31	40.84	2.24
2289	2425	1.448013	GGGTCCACGCTGCTTAGAC	60.448	63.158	0.00	0.00	0.00	2.59
2299	2435	4.090642	CACGCTGCTTAGACTGTCTAAAAG	59.909	45.833	25.52	24.16	38.38	2.27
2439	2625	8.971321	GTTAGCACATATTTCCTTGCAATTATG	58.029	33.333	0.00	5.88	37.44	1.90
2476	2676	3.752747	GCATCCTTTTTCCATTTTGGTGG	59.247	43.478	0.00	0.00	39.03	4.61
2477	2677	4.504689	GCATCCTTTTTCCATTTTGGTGGA	60.505	41.667	0.00	0.00	46.28	4.02
2486	2686	4.991776	TCCATTTTGGTGGAATGTAGACA	58.008	39.130	0.00	0.00	45.03	3.41
2487	2687	5.579047	TCCATTTTGGTGGAATGTAGACAT	58.421	37.500	0.00	0.00	45.03	3.06
2488	2688	6.015918	TCCATTTTGGTGGAATGTAGACATT	58.984	36.000	7.61	7.61	45.03	2.71
2489	2689	6.071447	TCCATTTTGGTGGAATGTAGACATTG	60.071	38.462	12.50	0.00	45.03	2.82

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
38	39	3.876274	ACTCTTGTATGTCGACAGCAT	57.124	42.857	24.41	9.95	0.00	3.79
45	46	6.808704	TCTTCTTGATCAACTCTTGTATGTCG	59.191	38.462	3.38	0.00	0.00	4.35
115	116	6.520021	TCAGTCTGAATCATAATTCCCCAT	57.480	37.500	0.00	0.00	40.57	4.00
126	127	4.445453	GCCATGTGTATCAGTCTGAATCA	58.555	43.478	6.64	6.45	0.00	2.57
167	168	6.932356	AGCAATGTAATCATCATTCGAAGT	57.068	33.333	3.35	0.00	33.92	3.01
170	171	7.537715	ACAAAAGCAATGTAATCATCATTCGA	58.462	30.769	0.00	0.00	33.92	3.71
173	174	7.315142	ACGACAAAAGCAATGTAATCATCATT	58.685	30.769	0.00	0.00	36.16	2.57
249	250	5.593909	TGTTCATCAGGTTTCAGTTGTCATT	59.406	36.000	0.00	0.00	0.00	2.57
460	461	1.672356	CCCTGTCGGGTCAGCTTTG	60.672	63.158	0.00	0.00	46.12	2.77
615	624	7.264947	ACATGGTCCTTTTTGTAAAGTGAAAG	58.735	34.615	0.00	0.00	39.29	2.62
708	718	4.355720	CCCTGCAAGCTCCAGCCA	62.356	66.667	8.44	0.00	43.38	4.75
719	730	4.100084	CACAGATCCGCCCCTGCA	62.100	66.667	0.00	0.00	37.32	4.41
721	732	3.411114	ATGCACAGATCCGCCCCTG	62.411	63.158	0.00	0.00	36.53	4.45
789	801	2.595463	TTCCTCGTCGTCACCGGT	60.595	61.111	0.00	0.00	33.95	5.28
980	995	2.609610	AGGCCCGCCTCCAACTAA	60.610	61.111	1.26	0.00	44.43	2.24
1020	1035	2.973899	GCGGCCACAGAGAGAAGA	59.026	61.111	2.24	0.00	0.00	2.87
1102	1121	4.033776	CGGTCACCATGGCCCAGT	62.034	66.667	13.04	0.00	39.48	4.00
1128	1148	3.867549	GGTAGCCACCACCGTTATT	57.132	52.632	0.00	0.00	45.04	1.40
1174	1194	3.342477	AAGGGAAGGGGCAGAGGC	61.342	66.667	0.00	0.00	40.13	4.70
1201	1221	1.001974	CTCACGGGATTCAAGTGGTCA	59.998	52.381	0.00	0.00	36.60	4.02
1271	1396	5.304357	TGCGTTAGGGAGAGAATATCATCAA	59.696	40.000	0.00	0.00	0.00	2.57
1290	1415	2.124060	TTGGGTGTGTGCATGCGTT	61.124	52.632	14.09	0.00	0.00	4.84
1296	1421	2.551006	GCGATGTTGGGTGTGTGCA	61.551	57.895	0.00	0.00	0.00	4.57
1412	1537	6.238869	GCAGTGAGGTGAAGAAAAGAAGAAAT	60.239	38.462	0.00	0.00	0.00	2.17
1428	1555	1.293062	ATGGAATCCAGCAGTGAGGT	58.707	50.000	8.40	0.00	36.75	3.85
1433	1560	3.118112	AGAATCGAATGGAATCCAGCAGT	60.118	43.478	8.40	0.00	36.75	4.40
1437	1564	3.497640	GCAGAGAATCGAATGGAATCCAG	59.502	47.826	8.40	0.00	42.67	3.86
1486	1614	1.611410	CCATGGTAGACACTGCAGCAA	60.611	52.381	15.27	0.00	0.00	3.91
1502	1630	5.278169	GCATAGAAGGTGCAAATAGTCCATG	60.278	44.000	0.00	0.00	42.08	3.66
1503	1631	4.823989	GCATAGAAGGTGCAAATAGTCCAT	59.176	41.667	0.00	0.00	42.08	3.41
1819	1954	2.746362	AGCATGACAGTTTAGCTCTTGC	59.254	45.455	0.00	0.00	40.05	4.01
1822	1957	5.350504	ACATAGCATGACAGTTTAGCTCT	57.649	39.130	0.00	0.00	36.80	4.09
1961	2096	5.852282	ACAGCTTTAAACTGAACCAACAT	57.148	34.783	18.56	0.00	38.55	2.71
2058	2194	4.829064	ACATACTTTCAGAAAAGCGCAA	57.171	36.364	11.47	0.00	44.82	4.85
2113	2249	5.565439	GCATGGCACTACATCTTTCTTGTTT	60.565	40.000	0.00	0.00	0.00	2.83
2158	2294	5.010516	TGGAGCTGCAAAGCAAGTTAAATTA	59.989	36.000	5.01	0.00	38.41	1.40
2167	2303	2.158928	ACAAAATGGAGCTGCAAAGCAA	60.159	40.909	13.45	0.00	38.41	3.91
2439	2625	7.425577	AAAAGGATGCAAACAGAAATTTAGC	57.574	32.000	0.00	0.00	0.00	3.09
2476	2676	9.319143	ACTACATCTTAAGCAATGTCTACATTC	57.681	33.333	11.86	2.22	44.10	2.67
2477	2677	9.672673	AACTACATCTTAAGCAATGTCTACATT	57.327	29.630	11.86	2.47	46.62	2.71
2478	2678	9.672673	AAACTACATCTTAAGCAATGTCTACAT	57.327	29.630	11.86	0.00	37.33	2.29
2479	2679	8.935844	CAAACTACATCTTAAGCAATGTCTACA	58.064	33.333	11.86	0.00	37.33	2.74
2480	2680	9.151471	TCAAACTACATCTTAAGCAATGTCTAC	57.849	33.333	11.86	0.00	37.33	2.59
2481	2681	9.890629	ATCAAACTACATCTTAAGCAATGTCTA	57.109	29.630	11.86	0.00	37.33	2.59
2482	2682	8.798859	ATCAAACTACATCTTAAGCAATGTCT	57.201	30.769	11.86	0.00	37.33	3.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.