AutoCloner

Multiple sequence alignment - TraesCS7B01G425500

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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	TraesCS7B01G425500	chr7B	100.000	3729	0	0	1	3729	694358532	694362260	0.000000e+00	6887.0
1	TraesCS7B01G425500	chr7B	96.765	2998	77	9	1	2992	693616654	693619637	0.000000e+00	4981.0
2	TraesCS7B01G425500	chr7B	92.950	3007	152	22	1	2992	699135781	699138742	0.000000e+00	4324.0
3	TraesCS7B01G425500	chr7B	91.922	2154	129	19	862	2992	699177492	699179623	0.000000e+00	2972.0
4	TraesCS7B01G425500	chr7B	91.212	2162	128	24	859	2992	698649994	698652121	0.000000e+00	2883.0
5	TraesCS7B01G425500	chr7B	88.117	1338	100	19	859	2160	696140168	696141482	0.000000e+00	1535.0
6	TraesCS7B01G425500	chr7B	84.861	1440	151	23	2189	3600	696141481	696142881	0.000000e+00	1389.0
7	TraesCS7B01G425500	chr7B	97.600	750	5	2	2986	3722	698652158	698652907	0.000000e+00	1273.0
8	TraesCS7B01G425500	chr7B	95.515	758	6	4	2986	3729	693619674	693620417	0.000000e+00	1186.0
9	TraesCS7B01G425500	chr7B	84.449	1061	145	17	1864	2913	697027536	697026485	0.000000e+00	1027.0
10	TraesCS7B01G425500	chr7B	89.961	767	36	10	2986	3716	699138779	699139540	0.000000e+00	952.0
11	TraesCS7B01G425500	chr7B	98.760	484	5	1	3240	3722	699142734	699143217	0.000000e+00	859.0
12	TraesCS7B01G425500	chr7B	91.422	443	21	2	3291	3716	699180016	699180458	3.210000e-165	592.0
13	TraesCS7B01G425500	chr7B	90.741	162	14	1	3071	3232	699179861	699180021	8.110000e-52	215.0
14	TraesCS7B01G425500	chr4A	90.779	2169	154	18	843	2992	661819450	661821591	0.000000e+00	2856.0
15	TraesCS7B01G425500	chr4A	85.733	764	50	20	2986	3716	661821628	661822365	0.000000e+00	752.0
16	TraesCS7B01G425500	chr7A	86.857	2176	202	37	1243	3367	700508867	700506725	0.000000e+00	2357.0
17	TraesCS7B01G425500	chr7A	86.885	1281	114	22	916	2160	700204351	700205613	0.000000e+00	1386.0
18	TraesCS7B01G425500	chr7A	89.239	762	50	13	2986	3716	700206448	700207208	0.000000e+00	924.0
19	TraesCS7B01G425500	chr7A	88.520	392	28	6	862	1246	700509518	700509137	3.390000e-125	459.0
20	TraesCS7B01G425500	chr7A	90.769	65	6	0	162	226	42283159	42283095	1.850000e-13	87.9
21	TraesCS7B01G425500	chr7D	92.435	1573	90	8	1353	2920	608194801	608196349	0.000000e+00	2218.0
22	TraesCS7B01G425500	chr7D	88.721	1321	98	16	869	2160	514744254	514745552	0.000000e+00	1567.0
23	TraesCS7B01G425500	chr7D	85.948	1530	134	42	2189	3680	514745551	514747037	0.000000e+00	1559.0
24	TraesCS7B01G425500	chr7D	88.024	1336	109	20	862	2160	600237982	600236661	0.000000e+00	1533.0
25	TraesCS7B01G425500	chr7D	87.631	1334	109	14	862	2160	610537470	610536158	0.000000e+00	1498.0
26	TraesCS7B01G425500	chr7D	85.902	1447	140	28	2189	3600	610536159	610534742	0.000000e+00	1483.0
27	TraesCS7B01G425500	chr7D	87.805	1066	102	16	2189	3241	600236662	600235612	0.000000e+00	1223.0
28	TraesCS7B01G425500	chr7D	84.551	1068	143	18	1861	2913	609333457	609334517	0.000000e+00	1038.0
29	TraesCS7B01G425500	chr7D	87.373	887	69	13	1046	1902	79325957	79326830	0.000000e+00	977.0
30	TraesCS7B01G425500	chr7D	88.889	738	61	9	1046	1775	62576513	62577237	0.000000e+00	889.0
31	TraesCS7B01G425500	chr7D	88.753	738	62	9	1046	1775	62520075	62520799	0.000000e+00	883.0
32	TraesCS7B01G425500	chr7D	84.150	612	40	21	3131	3722	608196608	608197182	1.180000e-149	540.0
33	TraesCS7B01G425500	chr7D	90.397	302	13	1	3315	3600	600235579	600235278	2.100000e-102	383.0
34	TraesCS7B01G425500	chr7D	85.227	176	24	1	575	748	610537649	610537474	2.960000e-41	180.0
35	TraesCS7B01G425500	chr7D	88.889	54	6	0	386	439	628199454	628199507	2.400000e-07	67.6
36	TraesCS7B01G425500	chr1D	88.222	866	63	11	1046	1902	16257678	16258513	0.000000e+00	998.0
37	TraesCS7B01G425500	chr1D	87.356	87	9	2	150	236	453793028	453792944	8.520000e-17	99.0
38	TraesCS7B01G425500	chrUn	83.651	893	111	23	1861	2738	343622224	343623096	0.000000e+00	808.0
39	TraesCS7B01G425500	chr3B	91.026	78	7	0	150	227	500658376	500658299	5.090000e-19	106.0
40	TraesCS7B01G425500	chr2A	90.909	77	7	0	150	226	689015331	689015407	1.830000e-18	104.0
41	TraesCS7B01G425500	chr2A	100.000	30	0	0	403	432	28821300	28821329	5.200000e-04	56.5
42	TraesCS7B01G425500	chr5B	90.667	75	7	0	152	226	128805802	128805876	2.370000e-17	100.0
43	TraesCS7B01G425500	chr5B	89.610	77	8	0	150	226	6920243	6920319	8.520000e-17	99.0
44	TraesCS7B01G425500	chr2B	81.148	122	20	3	745	863	318204331	318204452	1.100000e-15	95.3
45	TraesCS7B01G425500	chr2B	87.013	77	9	1	150	226	110066118	110066193	6.640000e-13	86.1
46	TraesCS7B01G425500	chr6B	80.833	120	16	4	768	880	52982219	52982100	1.850000e-13	87.9
47	TraesCS7B01G425500	chr6D	90.244	41	4	0	392	432	115329903	115329943	2.000000e-03	54.7

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	TraesCS7B01G425500	chr7B	694358532	694362260	3728	False	6887.000000	6887	100.000000	1	3729	1	chr7B.!!$F1	3728
1	TraesCS7B01G425500	chr7B	693616654	693620417	3763	False	3083.500000	4981	96.140000	1	3729	2	chr7B.!!$F2	3728
2	TraesCS7B01G425500	chr7B	698649994	698652907	2913	False	2078.000000	2883	94.406000	859	3722	2	chr7B.!!$F4	2863
3	TraesCS7B01G425500	chr7B	699135781	699143217	7436	False	2045.000000	4324	93.890333	1	3722	3	chr7B.!!$F5	3721
4	TraesCS7B01G425500	chr7B	696140168	696142881	2713	False	1462.000000	1535	86.489000	859	3600	2	chr7B.!!$F3	2741
5	TraesCS7B01G425500	chr7B	699177492	699180458	2966	False	1259.666667	2972	91.361667	862	3716	3	chr7B.!!$F6	2854
6	TraesCS7B01G425500	chr7B	697026485	697027536	1051	True	1027.000000	1027	84.449000	1864	2913	1	chr7B.!!$R1	1049
7	TraesCS7B01G425500	chr4A	661819450	661822365	2915	False	1804.000000	2856	88.256000	843	3716	2	chr4A.!!$F1	2873
8	TraesCS7B01G425500	chr7A	700506725	700509518	2793	True	1408.000000	2357	87.688500	862	3367	2	chr7A.!!$R2	2505
9	TraesCS7B01G425500	chr7A	700204351	700207208	2857	False	1155.000000	1386	88.062000	916	3716	2	chr7A.!!$F1	2800
10	TraesCS7B01G425500	chr7D	514744254	514747037	2783	False	1563.000000	1567	87.334500	869	3680	2	chr7D.!!$F6	2811
11	TraesCS7B01G425500	chr7D	608194801	608197182	2381	False	1379.000000	2218	88.292500	1353	3722	2	chr7D.!!$F7	2369
12	TraesCS7B01G425500	chr7D	610534742	610537649	2907	True	1053.666667	1498	86.253333	575	3600	3	chr7D.!!$R2	3025
13	TraesCS7B01G425500	chr7D	600235278	600237982	2704	True	1046.333333	1533	88.742000	862	3600	3	chr7D.!!$R1	2738
14	TraesCS7B01G425500	chr7D	609333457	609334517	1060	False	1038.000000	1038	84.551000	1861	2913	1	chr7D.!!$F4	1052
15	TraesCS7B01G425500	chr7D	79325957	79326830	873	False	977.000000	977	87.373000	1046	1902	1	chr7D.!!$F3	856
16	TraesCS7B01G425500	chr7D	62576513	62577237	724	False	889.000000	889	88.889000	1046	1775	1	chr7D.!!$F2	729
17	TraesCS7B01G425500	chr7D	62520075	62520799	724	False	883.000000	883	88.753000	1046	1775	1	chr7D.!!$F1	729
18	TraesCS7B01G425500	chr1D	16257678	16258513	835	False	998.000000	998	88.222000	1046	1902	1	chr1D.!!$F1	856
19	TraesCS7B01G425500	chrUn	343622224	343623096	872	False	808.000000	808	83.651000	1861	2738	1	chrUn.!!$F1	877

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
508	509	1.202663	AGCTCAGCCAGTGCATCATAG	60.203	52.381	0.00	0.00	41.13	2.23	F
1044	1071	0.533755	CCATCTTGGCCGATCCACTC	60.534	60.000	0.00	0.00	46.55	3.51	F
1462	1799	0.393673	TGTGGATTACGGCACCATGG	60.394	55.000	11.19	11.19	36.09	3.66	F
2288	2706	1.874299	ATGGGGTTGGACCATGGACC	61.874	60.000	24.48	24.48	46.57	4.46	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1460	1797	0.409092	AAAGTCCATGGTGCCATCCA	59.591	50.0	12.58	0.00	42.01	3.41	R
2094	2512	1.607801	CTCAGACGACCTCCATGCCA	61.608	60.0	0.00	0.00	0.00	4.92	R
2622	3065	5.786975	ACATTTCCCTGGAATCCAAGAAATT	59.213	36.0	25.39	17.96	40.99	1.82	R
3577	8057	6.333416	TGACTCTGATGAACAATAGTAGCAC	58.667	40.0	0.00	0.00	0.00	4.40	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
140	141	3.552875	TGTCTTAGTCATACTCCCTCCG	58.447	50.000	0.00	0.00	0.00	4.63
161	162	6.498304	TCCGTCCAAAAATATCTAGACGTAC	58.502	40.000	9.20	0.00	44.06	3.67
241	242	6.329460	GGAGGGAGTATATTTTAGTGGACCTT	59.671	42.308	0.00	0.00	0.00	3.50
508	509	1.202663	AGCTCAGCCAGTGCATCATAG	60.203	52.381	0.00	0.00	41.13	2.23
598	600	6.037786	AGTAGAATAGTTTGCACTGCAGTA	57.962	37.500	21.20	1.09	40.61	2.74
755	760	4.000325	TCGTGCATGCATGTAAAGTACTT	59.000	39.130	33.08	1.12	34.75	2.24
784	789	4.076394	TCCAAAAATACTTGTCGGGGAAG	58.924	43.478	0.00	0.00	0.00	3.46
797	802	4.263550	TGTCGGGGAAGTGGATAAAAATGA	60.264	41.667	0.00	0.00	0.00	2.57
1044	1071	0.533755	CCATCTTGGCCGATCCACTC	60.534	60.000	0.00	0.00	46.55	3.51
1050	1077	2.367202	GGCCGATCCACTCCCAAGA	61.367	63.158	0.00	0.00	34.01	3.02
1062	1089	3.753272	CACTCCCAAGACAACAGGTATTG	59.247	47.826	0.00	0.00	45.93	1.90
1274	1606	9.691362	GGTTTATTCAAGCTTCATTTTAACTGA	57.309	29.630	0.00	0.00	0.00	3.41
1315	1647	7.394016	ACAAGCATAATTCATATACGATCCCA	58.606	34.615	0.00	0.00	0.00	4.37
1316	1648	7.334421	ACAAGCATAATTCATATACGATCCCAC	59.666	37.037	0.00	0.00	0.00	4.61
1322	1654	7.792364	AATTCATATACGATCCCACCTCTTA	57.208	36.000	0.00	0.00	0.00	2.10
1323	1655	6.835819	TTCATATACGATCCCACCTCTTAG	57.164	41.667	0.00	0.00	0.00	2.18
1329	1663	3.952967	ACGATCCCACCTCTTAGTCTTAC	59.047	47.826	0.00	0.00	0.00	2.34
1359	1693	8.134202	TCTGACTTGGATATAGAGTTCACAAA	57.866	34.615	0.00	0.00	0.00	2.83
1388	1724	4.196626	TCGAAATCCCGACACAATAACT	57.803	40.909	0.00	0.00	33.14	2.24
1426	1763	0.749091	TTGATGGCAGGCGGAGATTG	60.749	55.000	0.00	0.00	0.00	2.67
1431	1768	1.372087	GGCAGGCGGAGATTGAAGTG	61.372	60.000	0.00	0.00	0.00	3.16
1451	1788	5.744171	AGTGCACTCAACATATGTGGATTA	58.256	37.500	15.25	0.00	34.80	1.75
1452	1789	5.586243	AGTGCACTCAACATATGTGGATTAC	59.414	40.000	15.25	9.88	34.80	1.89
1453	1790	4.570369	TGCACTCAACATATGTGGATTACG	59.430	41.667	13.44	4.69	32.85	3.18
1454	1791	4.024893	GCACTCAACATATGTGGATTACGG	60.025	45.833	13.44	4.34	32.85	4.02
1455	1792	4.024893	CACTCAACATATGTGGATTACGGC	60.025	45.833	13.44	0.00	0.00	5.68
1456	1793	4.126437	CTCAACATATGTGGATTACGGCA	58.874	43.478	13.44	0.00	0.00	5.69
1457	1794	3.874543	TCAACATATGTGGATTACGGCAC	59.125	43.478	9.63	0.00	0.00	5.01
1458	1795	2.846193	ACATATGTGGATTACGGCACC	58.154	47.619	7.78	0.00	0.00	5.01
1459	1796	2.171659	ACATATGTGGATTACGGCACCA	59.828	45.455	7.78	0.00	0.00	4.17
1460	1797	3.181445	ACATATGTGGATTACGGCACCAT	60.181	43.478	7.78	0.00	36.09	3.55
1461	1798	1.679139	ATGTGGATTACGGCACCATG	58.321	50.000	0.00	0.00	36.09	3.66
1462	1799	0.393673	TGTGGATTACGGCACCATGG	60.394	55.000	11.19	11.19	36.09	3.66
1567	1904	8.357402	GTTGTGGTCTATTCCAAACTTTGTTAT	58.643	33.333	0.88	0.00	39.34	1.89
1725	2063	5.448926	AACTTGCAAAACAAATGAACGTC	57.551	34.783	0.00	0.00	37.96	4.34
2288	2706	1.874299	ATGGGGTTGGACCATGGACC	61.874	60.000	24.48	24.48	46.57	4.46
2406	2829	2.301296	ACATGCTCTCACTGCTTAGTGT	59.699	45.455	7.25	0.00	40.45	3.55
2568	3007	8.260114	AGGCCCACATCTAAAAATAAGATTTTG	58.740	33.333	0.00	0.00	34.51	2.44
2616	3059	3.896888	TGGAGCACCACTGATTTTTCATT	59.103	39.130	0.00	0.00	41.77	2.57
2622	3065	7.725251	AGCACCACTGATTTTTCATTTCTTAA	58.275	30.769	0.00	0.00	0.00	1.85
2743	3186	3.885484	AAATGAAGTTGCACTCGTGAG	57.115	42.857	0.39	0.00	0.00	3.51
3577	8057	2.005451	CGATGCCTGAACCTGAAGAAG	58.995	52.381	0.00	0.00	0.00	2.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
211	212	5.303589	CACTAAAATATACTCCCTCCGTCCA	59.696	44.000	0.00	0.00	0.00	4.02
241	242	2.256158	CGACGCGTGGTTACAGGA	59.744	61.111	20.70	0.00	34.50	3.86
367	368	7.274603	AGTATTTTTACTAGAGCTACCTCGG	57.725	40.000	0.00	0.00	43.05	4.63
508	509	3.670627	GCGTTTTGAATCTCCATCACCAC	60.671	47.826	0.00	0.00	0.00	4.16
718	723	5.163854	GCATGCACGATAAATCCAGGTATAC	60.164	44.000	14.21	0.00	0.00	1.47
755	760	5.414454	CCGACAAGTATTTTTGGATGAAGGA	59.586	40.000	0.00	0.00	32.32	3.36
1044	1071	4.021102	AGTCAATACCTGTTGTCTTGGG	57.979	45.455	0.00	0.00	33.21	4.12
1050	1077	6.545666	TGATCAACAAAGTCAATACCTGTTGT	59.454	34.615	11.69	2.02	43.65	3.32
1062	1089	8.261492	AGATATGTGAACTGATCAACAAAGTC	57.739	34.615	2.23	2.26	40.50	3.01
1136	1188	2.152016	GGCCGGCTCCACTTTTATATC	58.848	52.381	28.56	0.00	0.00	1.63
1315	1647	6.726764	AGTCAGATTTGGTAAGACTAAGAGGT	59.273	38.462	0.00	0.00	37.75	3.85
1316	1648	7.176589	AGTCAGATTTGGTAAGACTAAGAGG	57.823	40.000	0.00	0.00	37.75	3.69
1322	1654	5.825593	TCCAAGTCAGATTTGGTAAGACT	57.174	39.130	21.02	0.00	44.35	3.24
1323	1655	9.482627	CTATATCCAAGTCAGATTTGGTAAGAC	57.517	37.037	21.02	0.00	44.35	3.01
1329	1663	8.206867	TGAACTCTATATCCAAGTCAGATTTGG	58.793	37.037	16.95	16.95	45.17	3.28
1359	1693	1.108776	TCGGGATTTCGACGATCCTT	58.891	50.000	20.61	0.00	42.23	3.36
1388	1724	8.556194	GCCATCAAGAACAACGAAATATATGTA	58.444	33.333	0.00	0.00	0.00	2.29
1426	1763	4.002982	TCCACATATGTTGAGTGCACTTC	58.997	43.478	22.65	14.43	32.09	3.01
1431	1768	4.024893	CCGTAATCCACATATGTTGAGTGC	60.025	45.833	17.35	15.19	32.09	4.40
1460	1797	0.409092	AAAGTCCATGGTGCCATCCA	59.591	50.000	12.58	0.00	42.01	3.41
1461	1798	1.106285	GAAAGTCCATGGTGCCATCC	58.894	55.000	12.58	0.00	33.90	3.51
1462	1799	1.838112	TGAAAGTCCATGGTGCCATC	58.162	50.000	12.58	6.05	33.90	3.51
1567	1904	5.421693	ACCATGGATAAATTGCTTGCTTGTA	59.578	36.000	21.47	0.00	0.00	2.41
1654	1991	3.181471	CCTCATGTGTTAGATTCGCCTCT	60.181	47.826	0.00	0.00	0.00	3.69
1725	2063	5.721876	ACATATTTTCAATGCCATTTGCG	57.278	34.783	0.00	0.00	45.60	4.85
2094	2512	1.607801	CTCAGACGACCTCCATGCCA	61.608	60.000	0.00	0.00	0.00	4.92
2288	2706	6.572519	TGGAAACCTTTCATTCTTCAACTTG	58.427	36.000	0.40	0.00	38.92	3.16
2616	3059	7.245292	TCCCTGGAATCCAAGAAATTTAAGAA	58.755	34.615	2.61	0.00	30.80	2.52
2622	3065	5.786975	ACATTTCCCTGGAATCCAAGAAATT	59.213	36.000	25.39	17.96	40.99	1.82
3577	8057	6.333416	TGACTCTGATGAACAATAGTAGCAC	58.667	40.000	0.00	0.00	0.00	4.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.