AutoCloner

Multiple sequence alignment - TraesCS1B01G449400

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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	TraesCS1B01G449400	chr1B	100.000	1935	0	0	1	1935	668032183	668030249	0.000000e+00	3574.0
1	TraesCS1B01G449400	chr1B	92.292	1479	61	24	495	1929	667997851	667996382	0.000000e+00	2050.0
2	TraesCS1B01G449400	chr1B	100.000	746	0	0	2190	2935	668029994	668029249	0.000000e+00	1378.0
3	TraesCS1B01G449400	chr1B	90.663	996	55	17	954	1935	667975901	667974930	0.000000e+00	1290.0
4	TraesCS1B01G449400	chr1B	94.125	834	43	6	1092	1924	667930918	667931746	0.000000e+00	1264.0
5	TraesCS1B01G449400	chr1B	90.510	706	59	5	2190	2892	667974926	667974226	0.000000e+00	926.0
6	TraesCS1B01G449400	chr1B	86.024	830	80	15	36	844	667976993	667976179	0.000000e+00	857.0
7	TraesCS1B01G449400	chr1B	87.500	712	58	16	2191	2892	667932027	667932717	0.000000e+00	793.0
8	TraesCS1B01G449400	chr1B	94.538	476	24	2	32	507	667998843	667998370	0.000000e+00	734.0
9	TraesCS1B01G449400	chr1B	85.153	687	62	11	5	654	667929783	667930466	0.000000e+00	667.0
10	TraesCS1B01G449400	chr1B	90.566	424	36	2	2190	2613	667996245	667995826	2.550000e-155	558.0
11	TraesCS1B01G449400	chr1B	86.614	381	32	8	701	1068	667930469	667930843	1.270000e-108	403.0
12	TraesCS1B01G449400	chr1B	91.968	249	19	1	2644	2892	667995560	667995313	6.020000e-92	348.0
13	TraesCS1B01G449400	chr1B	88.073	218	26	0	1128	1345	667918574	667918357	2.900000e-65	259.0
14	TraesCS1B01G449400	chr1B	78.607	201	33	2	197	388	667919389	667919190	1.100000e-24	124.0
15	TraesCS1B01G449400	chr1A	89.238	1115	82	20	5	1087	576204722	576203614	0.000000e+00	1360.0
16	TraesCS1B01G449400	chr1A	89.559	862	33	13	1091	1935	576203558	576202737	0.000000e+00	1040.0
17	TraesCS1B01G449400	chr1A	90.133	750	61	7	2190	2931	576202730	576201986	0.000000e+00	963.0
18	TraesCS1B01G449400	chr1A	82.311	1125	103	41	25	1087	576140322	576139232	0.000000e+00	887.0
19	TraesCS1B01G449400	chr1A	90.435	690	33	16	1100	1771	576139167	576138493	0.000000e+00	878.0
20	TraesCS1B01G449400	chr1A	91.297	563	43	4	2190	2752	576138373	576137817	0.000000e+00	763.0
21	TraesCS1B01G449400	chr1A	91.304	230	18	2	2706	2935	576137824	576137597	2.200000e-81	313.0
22	TraesCS1B01G449400	chr1A	86.574	216	29	0	1130	1345	576065867	576065652	3.780000e-59	239.0
23	TraesCS1B01G449400	chr1A	80.597	201	29	2	197	388	576066754	576066555	2.360000e-31	147.0
24	TraesCS1B01G449400	chr1A	87.500	128	4	5	1808	1935	576138494	576138379	1.420000e-28	137.0
25	TraesCS1B01G449400	chr1A	75.934	241	29	17	1655	1889	576077757	576077540	2.410000e-16	97.1
26	TraesCS1B01G449400	chr1D	87.238	1097	95	31	5	1080	479751976	479750904	0.000000e+00	1208.0
27	TraesCS1B01G449400	chr1D	85.205	1122	115	27	5	1087	479760569	479759460	0.000000e+00	1105.0
28	TraesCS1B01G449400	chr1D	92.246	748	53	4	2190	2935	479750000	479749256	0.000000e+00	1055.0
29	TraesCS1B01G449400	chr1D	89.217	881	39	19	1091	1935	479759406	479758546	0.000000e+00	1050.0
30	TraesCS1B01G449400	chr1D	91.323	703	56	4	2190	2892	479758539	479757842	0.000000e+00	955.0
31	TraesCS1B01G449400	chr1D	86.972	852	85	19	1092	1935	479750840	479750007	0.000000e+00	935.0
32	TraesCS1B01G449400	chr1D	90.801	337	26	4	2433	2766	479722102	479721768	2.080000e-121	446.0
33	TraesCS1B01G449400	chr1D	81.250	160	20	3	197	347	479686822	479686980	1.430000e-23	121.0
34	TraesCS1B01G449400	chr1D	75.833	240	31	15	1655	1889	479737354	479737137	2.410000e-16	97.1

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	TraesCS1B01G449400	chr1B	668029249	668032183	2934	True	2476.000000	3574	100.000000	1	2935	2	chr1B.!!$R4	2934
1	TraesCS1B01G449400	chr1B	667974226	667976993	2767	True	1024.333333	1290	89.065667	36	2892	3	chr1B.!!$R2	2856
2	TraesCS1B01G449400	chr1B	667995313	667998843	3530	True	922.500000	2050	92.341000	32	2892	4	chr1B.!!$R3	2860
3	TraesCS1B01G449400	chr1B	667929783	667932717	2934	False	781.750000	1264	88.348000	5	2892	4	chr1B.!!$F1	2887
4	TraesCS1B01G449400	chr1A	576201986	576204722	2736	True	1121.000000	1360	89.643333	5	2931	3	chr1A.!!$R4	2926
5	TraesCS1B01G449400	chr1A	576137597	576140322	2725	True	595.600000	887	88.569400	25	2935	5	chr1A.!!$R3	2910
6	TraesCS1B01G449400	chr1D	479749256	479751976	2720	True	1066.000000	1208	88.818667	5	2935	3	chr1D.!!$R3	2930
7	TraesCS1B01G449400	chr1D	479757842	479760569	2727	True	1036.666667	1105	88.581667	5	2892	3	chr1D.!!$R4	2887

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
107	108	0.955428	AATGAGCCGCGACACACATT	60.955	50.0	8.23	10.42	0.00	2.71	F
1269	2179	0.179065	TCAGGCGCTACTACGAGCTA	60.179	55.0	7.64	0.00	40.51	3.32	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1619	2534	0.532640	TGCCCGCTAGTGCATGTATG	60.533	55.0	0.0	0.0	39.64	2.39	R
2566	3681	0.320374	ACAAGCAGTTGCCTAGCGTA	59.680	50.0	0.0	0.0	43.38	4.42	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	75	2.305343	CCCAAATTGCCAAAATGGAGGA	59.695	45.455	12.09	0.00	40.96	3.71
76	77	4.568169	CCCAAATTGCCAAAATGGAGGAAT	60.568	41.667	12.09	0.00	40.96	3.01
99	100	2.595124	TTAGAATCAATGAGCCGCGA	57.405	45.000	8.23	0.00	0.00	5.87
107	108	0.955428	AATGAGCCGCGACACACATT	60.955	50.000	8.23	10.42	0.00	2.71
268	291	1.202806	CCTGGATCGTATGGCCAACAT	60.203	52.381	10.96	0.00	43.68	2.71
269	292	2.146342	CTGGATCGTATGGCCAACATC	58.854	52.381	10.96	8.77	41.03	3.06
309	332	3.903090	TGGATTCCCAATCTTTGCAACTT	59.097	39.130	0.00	0.00	40.09	2.66
325	348	7.704578	TTGCAACTTACTATCTGTAGAGAGT	57.295	36.000	13.08	13.08	46.88	3.24
507	1103	2.639327	ATGCCCGCAAGAAGTTGGC	61.639	57.895	0.00	0.00	42.49	4.52
530	1126	6.238925	GGCTGAACCACAACACTAGTAAAAAT	60.239	38.462	0.00	0.00	38.86	1.82
575	1174	7.439955	TGTTGTGTAAATAAGAGTCAACATCGT	59.560	33.333	0.00	0.00	38.69	3.73
597	1196	4.581077	TGTACATGCACAATTCAAAGCA	57.419	36.364	0.00	0.00	41.73	3.91
760	1378	4.904253	TGAATGTATGGATGCACATGTG	57.096	40.909	21.83	21.83	35.59	3.21
924	1564	1.454847	CCCTCCTCACTCCTCTCGG	60.455	68.421	0.00	0.00	0.00	4.63
984	1784	4.090761	TGCACATTATCATCCTCCTTCC	57.909	45.455	0.00	0.00	0.00	3.46
1015	1817	1.065854	ACAAAGCTGAATCCTCCTCGG	60.066	52.381	0.00	0.00	0.00	4.63
1088	1998	3.323403	AGCAGCCAAGATCCTAGTGTATC	59.677	47.826	0.00	0.00	0.00	2.24
1089	1999	3.070159	GCAGCCAAGATCCTAGTGTATCA	59.930	47.826	0.00	0.00	0.00	2.15
1098	2008	1.669265	CCTAGTGTATCACGTCGAGCA	59.331	52.381	0.00	0.00	39.64	4.26
1126	2036	1.627329	TGGCTTCTCTGTCAATGAGCT	59.373	47.619	0.00	0.00	0.00	4.09
1269	2179	0.179065	TCAGGCGCTACTACGAGCTA	60.179	55.000	7.64	0.00	40.51	3.32
1296	2206	1.009335	CGACATCGCCCGTATCGAA	60.009	57.895	0.00	0.00	39.54	3.71
1371	2281	3.917760	GCCAGCTACGAGGCCGAT	61.918	66.667	0.00	0.00	45.18	4.18
1405	2315	3.310774	CCATCGCTGTGTTTCTTATCAGG	59.689	47.826	0.00	0.00	0.00	3.86
1453	2363	4.910195	AGCAGGTAATTTGTGTGATCAGA	58.090	39.130	0.00	0.00	0.00	3.27
1584	2499	7.998753	ACCTTGTAATACTTATAAGCGTGTC	57.001	36.000	12.54	2.18	34.26	3.67
1619	2534	5.415415	GACTCCATGTCATATGTCAAAGC	57.585	43.478	6.74	0.27	44.73	3.51
1908	2889	1.816224	AGACAAAACAACTGCGGTGTT	59.184	42.857	0.00	2.09	0.00	3.32
2301	3407	1.234615	CGGAGAACACGCACCCATTT	61.235	55.000	0.00	0.00	0.00	2.32
2325	3431	0.962356	AAATGGCAGAGCAGAACCGG	60.962	55.000	0.00	0.00	0.00	5.28
2344	3450	4.224370	ACCGGGAACAAATCACACTACTAT	59.776	41.667	6.32	0.00	0.00	2.12
2351	3457	8.893727	GGAACAAATCACACTACTATAAAGCAT	58.106	33.333	0.00	0.00	0.00	3.79
2374	3480	4.223700	TCCATATCATGCTAGGGTTGCTAG	59.776	45.833	7.12	0.00	0.00	3.42
2395	3501	0.911769	TCTCCTCGCATGGGTTCATT	59.088	50.000	9.86	0.00	0.00	2.57
2420	3526	1.951209	TGTTGATAGTGGAGCTCCCA	58.049	50.000	29.95	16.98	44.25	4.37
2471	3586	3.009115	CGCCTCCTCCCCTTCCAA	61.009	66.667	0.00	0.00	0.00	3.53
2475	3590	1.685820	CTCCTCCCCTTCCAACCAC	59.314	63.158	0.00	0.00	0.00	4.16
2480	3595	1.144913	CTCCCCTTCCAACCACTGAAA	59.855	52.381	0.00	0.00	0.00	2.69
2544	3659	0.617935	TTTGATGATGGTGGAGCCGA	59.382	50.000	0.00	0.00	41.21	5.54
2566	3681	4.669206	TTCATGTTGTTGTGCTTGGATT	57.331	36.364	0.00	0.00	0.00	3.01
2608	3723	2.310538	CTCCTCAAGTGCAAGGGTTTT	58.689	47.619	2.34	0.00	33.21	2.43
2618	3733	3.634910	GTGCAAGGGTTTTCAGAGGTAAA	59.365	43.478	0.00	0.00	0.00	2.01
2673	4023	1.768265	AATTTACCTGGGTCCCACCT	58.232	50.000	6.47	0.00	38.64	4.00
2762	4152	6.361433	TGGTCAACAAGTCAGAGGAAAATAA	58.639	36.000	0.00	0.00	0.00	1.40
2791	4181	5.665916	AAAAACAAGGGCATCTGGAATAG	57.334	39.130	0.00	0.00	0.00	1.73
2843	4235	1.375908	CCTAGACAGCCAAAGCGCA	60.376	57.895	11.47	0.00	46.67	6.09
2896	4291	7.394359	CCATGGACTATAAACCCTCCAATATTG	59.606	40.741	5.56	8.58	36.39	1.90
2931	4326	1.128809	TTAGGGCAACTCCAACGGGA	61.129	55.000	0.00	0.00	42.29	5.14

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	6.442952	CAAGCTCGATAAATAGAGTAGCACT	58.557	40.000	0.00	0.00	36.88	4.40
3	4	5.774630	ACCAAGCTCGATAAATAGAGTAGC	58.225	41.667	0.00	0.00	36.88	3.58
74	75	6.204688	TCGCGGCTCATTGATTCTAAATTATT	59.795	34.615	6.13	0.00	0.00	1.40
76	77	5.050363	GTCGCGGCTCATTGATTCTAAATTA	60.050	40.000	1.90	0.00	0.00	1.40
99	100	7.537596	TCCTTTAATTCCAATGAATGTGTGT	57.462	32.000	0.00	0.00	40.34	3.72
309	332	7.174080	GCATCATGTCACTCTCTACAGATAGTA	59.826	40.741	0.00	0.00	31.42	1.82
353	386	8.608844	AATTATTACATGTGAAGTAGCTAGCC	57.391	34.615	12.13	0.00	0.00	3.93
490	555	3.294493	GCCAACTTCTTGCGGGCA	61.294	61.111	0.00	0.00	44.01	5.36
542	1138	8.440059	TGACTCTTATTTACACAACAAATAGCG	58.560	33.333	0.00	0.00	31.39	4.26
552	1151	7.439955	ACAACGATGTTGACTCTTATTTACACA	59.560	33.333	15.92	0.00	35.91	3.72
575	1174	4.941657	TGCTTTGAATTGTGCATGTACAA	58.058	34.783	27.94	27.94	43.93	2.41
618	1217	7.992180	AGTGAATCAAAGCTTTTTGTTACAG	57.008	32.000	9.53	0.00	33.82	2.74
684	1285	4.790937	TGAGGCATATGCAGATACCAAAA	58.209	39.130	28.07	0.00	44.36	2.44
688	1289	4.013267	AGTTGAGGCATATGCAGATACC	57.987	45.455	28.07	10.39	44.36	2.73
690	1291	7.282585	AGTTAAAGTTGAGGCATATGCAGATA	58.717	34.615	28.07	9.28	44.36	1.98
691	1292	6.125029	AGTTAAAGTTGAGGCATATGCAGAT	58.875	36.000	28.07	13.94	44.36	2.90
693	1294	5.824904	AGTTAAAGTTGAGGCATATGCAG	57.175	39.130	28.07	0.00	44.36	4.41
737	1351	6.063404	ACACATGTGCATCCATACATTCATA	58.937	36.000	25.68	0.00	35.46	2.15
738	1352	4.891168	ACACATGTGCATCCATACATTCAT	59.109	37.500	25.68	0.00	35.46	2.57
739	1353	4.271661	ACACATGTGCATCCATACATTCA	58.728	39.130	25.68	0.00	35.46	2.57
740	1354	4.906065	ACACATGTGCATCCATACATTC	57.094	40.909	25.68	0.00	35.46	2.67
741	1355	5.412640	CAAACACATGTGCATCCATACATT	58.587	37.500	25.68	5.50	35.46	2.71
760	1378	8.819974	TCAAAGATTCAAAGAGAAAATGCAAAC	58.180	29.630	0.00	0.00	40.22	2.93
924	1564	6.868864	GGAAAAACTAGAGGAATTTTGAAGCC	59.131	38.462	0.00	0.00	0.00	4.35
1032	1834	3.454447	TGAGGAAGAAGGTGTGAGAACAA	59.546	43.478	0.00	0.00	0.00	2.83
1088	1998	1.201954	CCATTGATGTTGCTCGACGTG	60.202	52.381	0.00	0.00	0.00	4.49
1089	1999	1.078709	CCATTGATGTTGCTCGACGT	58.921	50.000	0.00	0.00	0.00	4.34
1098	2008	4.025040	TGACAGAGAAGCCATTGATGTT	57.975	40.909	0.00	0.00	0.00	2.71
1218	2128	3.883744	CTTTCCACCGCCGACAGCT	62.884	63.158	0.00	0.00	40.39	4.24
1230	2140	3.296836	TCGTCCGCCGACTTTCCA	61.297	61.111	3.71	0.00	41.60	3.53
1371	2281	2.837883	GCGATGGCGGTCGTACCTA	61.838	63.158	12.59	0.00	43.27	3.08
1405	2315	1.610522	CCAGCTTAAGCCCATGCATAC	59.389	52.381	23.71	0.00	43.38	2.39
1453	2363	5.743117	AGCTAGATCTTCAAGTGCTTCAAT	58.257	37.500	0.00	0.00	0.00	2.57
1558	2468	8.862550	ACACGCTTATAAGTATTACAAGGTAC	57.137	34.615	13.91	0.00	35.68	3.34
1619	2534	0.532640	TGCCCGCTAGTGCATGTATG	60.533	55.000	0.00	0.00	39.64	2.39
2269	3375	0.391597	TTCTCCGTCCTTGGTGACAC	59.608	55.000	0.00	0.00	42.67	3.67
2273	3379	0.944311	CGTGTTCTCCGTCCTTGGTG	60.944	60.000	0.00	0.00	0.00	4.17
2301	3407	2.751259	GTTCTGCTCTGCCATTTGATCA	59.249	45.455	0.00	0.00	0.00	2.92
2325	3431	8.263940	TGCTTTATAGTAGTGTGATTTGTTCC	57.736	34.615	0.00	0.00	0.00	3.62
2351	3457	2.981784	AGCAACCCTAGCATGATATGGA	59.018	45.455	17.82	0.00	0.00	3.41
2374	3480	1.522580	GAACCCATGCGAGGAGAGC	60.523	63.158	0.00	0.00	0.00	4.09
2395	3501	4.065088	GAGCTCCACTATCAACAACAACA	58.935	43.478	0.87	0.00	0.00	3.33
2420	3526	0.837272	CCTGGTGTCCCAATATCCGT	59.163	55.000	0.00	0.00	41.27	4.69
2475	3590	5.012239	TGGAAGAGGAACCATTGATTTCAG	58.988	41.667	0.00	0.00	0.00	3.02
2480	3595	3.369892	CGAGTGGAAGAGGAACCATTGAT	60.370	47.826	0.00	0.00	38.48	2.57
2544	3659	4.877378	ATCCAAGCACAACAACATGAAT	57.123	36.364	0.00	0.00	0.00	2.57
2566	3681	0.320374	ACAAGCAGTTGCCTAGCGTA	59.680	50.000	0.00	0.00	43.38	4.42
2581	3696	1.311859	TGCACTTGAGGAGCAACAAG	58.688	50.000	0.00	0.00	45.85	3.16
2673	4023	2.225242	ACCATTTTGCCACATAGGACCA	60.225	45.455	0.00	0.00	41.22	4.02
2772	4162	4.228210	TCTTCTATTCCAGATGCCCTTGTT	59.772	41.667	0.00	0.00	31.77	2.83
2781	4171	7.202084	CCCTTTAGCTCTTCTTCTATTCCAGAT	60.202	40.741	0.00	0.00	31.77	2.90
2786	4176	5.060506	GGCCCTTTAGCTCTTCTTCTATTC	58.939	45.833	0.00	0.00	0.00	1.75
2791	4181	1.282157	TGGGCCCTTTAGCTCTTCTTC	59.718	52.381	25.70	0.00	33.00	2.87
2843	4235	3.515562	CATCCCTCTAGCTACCCTGATT	58.484	50.000	0.00	0.00	0.00	2.57
2896	4291	6.902771	TGCCCTAATCTATGAAGACTAGTC	57.097	41.667	15.41	15.41	31.03	2.59

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.