AutoCloner

Multiple sequence alignment - TraesCS1B01G090900

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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	TraesCS1B01G090900	chr1B	100.000	2432	0	0	1	2432	92077489	92079920	0.000000e+00	4492
1	TraesCS1B01G090900	chr1B	97.059	1054	25	3	1296	2346	198113560	198112510	0.000000e+00	1770
2	TraesCS1B01G090900	chr1B	94.796	807	41	1	1	807	198114452	198113647	0.000000e+00	1256
3	TraesCS1B01G090900	chr1B	92.937	807	57	0	1	807	149122538	149121732	0.000000e+00	1175
4	TraesCS1B01G090900	chr1A	95.486	2348	103	3	1	2346	365221261	365223607	0.000000e+00	3746
5	TraesCS1B01G090900	chr5B	95.315	2348	108	2	1	2346	290877340	290879687	0.000000e+00	3725
6	TraesCS1B01G090900	chr5B	96.869	1054	30	2	1296	2346	658347092	658348145	0.000000e+00	1760
7	TraesCS1B01G090900	chr5B	94.424	807	45	0	1	807	658346199	658347005	0.000000e+00	1242
8	TraesCS1B01G090900	chr5B	98.485	66	1	0	2365	2430	648128141	648128076	1.530000e-22	117
9	TraesCS1B01G090900	chr2B	94.672	2365	106	10	1	2346	86850056	86847693	0.000000e+00	3651
10	TraesCS1B01G090900	chr6B	94.381	2349	128	3	1	2346	396296083	396298430	0.000000e+00	3603
11	TraesCS1B01G090900	chr6B	94.672	807	43	0	1	807	651661950	651661144	0.000000e+00	1253
12	TraesCS1B01G090900	chr6B	97.015	67	2	0	2366	2432	20518024	20518090	1.980000e-21	113
13	TraesCS1B01G090900	chr7D	93.753	1905	114	4	446	2346	79046620	79044717	0.000000e+00	2854
14	TraesCS1B01G090900	chr7D	96.078	1071	40	2	1278	2346	59691542	59690472	0.000000e+00	1744
15	TraesCS1B01G090900	chr7D	91.557	533	45	0	552	1084	184931063	184931595	0.000000e+00	736
16	TraesCS1B01G090900	chr7D	98.438	64	1	0	2369	2432	62338136	62338199	1.980000e-21	113
17	TraesCS1B01G090900	chr7D	95.652	69	3	0	2364	2432	369902230	369902298	7.110000e-21	111
18	TraesCS1B01G090900	chr5D	96.089	1074	40	2	1275	2346	170711797	170712870	0.000000e+00	1749
19	TraesCS1B01G090900	chr6D	92.806	987	62	2	1	987	343521960	343522937	0.000000e+00	1421
20	TraesCS1B01G090900	chr6D	97.059	68	2	0	2365	2432	470788352	470788419	5.490000e-22	115
21	TraesCS1B01G090900	chr7B	91.008	645	56	2	552	1194	154766027	154766671	0.000000e+00	869
22	TraesCS1B01G090900	chr7A	88.509	644	72	2	552	1194	191902916	191903558	0.000000e+00	778
23	TraesCS1B01G090900	chr1D	95.890	73	2	1	2361	2432	228951353	228951281	1.530000e-22	117
24	TraesCS1B01G090900	chr1D	92.683	82	4	2	2351	2432	455648041	455647962	1.530000e-22	117
25	TraesCS1B01G090900	chr2D	97.059	68	2	0	2365	2432	67563920	67563987	5.490000e-22	115
26	TraesCS1B01G090900	chr6A	93.333	75	3	2	2359	2432	522036151	522036078	2.560000e-20	110

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	TraesCS1B01G090900	chr1B	92077489	92079920	2431	False	4492	4492	100.0000	1	2432	1	chr1B.!!$F1	2431
1	TraesCS1B01G090900	chr1B	198112510	198114452	1942	True	1513	1770	95.9275	1	2346	2	chr1B.!!$R2	2345
2	TraesCS1B01G090900	chr1B	149121732	149122538	806	True	1175	1175	92.9370	1	807	1	chr1B.!!$R1	806
3	TraesCS1B01G090900	chr1A	365221261	365223607	2346	False	3746	3746	95.4860	1	2346	1	chr1A.!!$F1	2345
4	TraesCS1B01G090900	chr5B	290877340	290879687	2347	False	3725	3725	95.3150	1	2346	1	chr5B.!!$F1	2345
5	TraesCS1B01G090900	chr5B	658346199	658348145	1946	False	1501	1760	95.6465	1	2346	2	chr5B.!!$F2	2345
6	TraesCS1B01G090900	chr2B	86847693	86850056	2363	True	3651	3651	94.6720	1	2346	1	chr2B.!!$R1	2345
7	TraesCS1B01G090900	chr6B	396296083	396298430	2347	False	3603	3603	94.3810	1	2346	1	chr6B.!!$F2	2345
8	TraesCS1B01G090900	chr6B	651661144	651661950	806	True	1253	1253	94.6720	1	807	1	chr6B.!!$R1	806
9	TraesCS1B01G090900	chr7D	79044717	79046620	1903	True	2854	2854	93.7530	446	2346	1	chr7D.!!$R2	1900
10	TraesCS1B01G090900	chr7D	59690472	59691542	1070	True	1744	1744	96.0780	1278	2346	1	chr7D.!!$R1	1068
11	TraesCS1B01G090900	chr7D	184931063	184931595	532	False	736	736	91.5570	552	1084	1	chr7D.!!$F2	532
12	TraesCS1B01G090900	chr5D	170711797	170712870	1073	False	1749	1749	96.0890	1275	2346	1	chr5D.!!$F1	1071
13	TraesCS1B01G090900	chr6D	343521960	343522937	977	False	1421	1421	92.8060	1	987	1	chr6D.!!$F1	986
14	TraesCS1B01G090900	chr7B	154766027	154766671	644	False	869	869	91.0080	552	1194	1	chr7B.!!$F1	642
15	TraesCS1B01G090900	chr7A	191902916	191903558	642	False	778	778	88.5090	552	1194	1	chr7A.!!$F1	642

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
588	603	1.0567	CCTCCATCCACCCTGGTAGG	61.057	65.0	0.0	0.0	39.03	3.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1462	1482	0.178967	TGTGCTGCCTTTTGATCCCA	60.179	50.0	0.0	0.0	0.0	4.37	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
368	383	4.116585	TCCTCCTCCTCGAGCGCT	62.117	66.667	11.27	11.27	0.00	5.92
382	397	4.796231	CGCTACGCCGCAGACCTT	62.796	66.667	0.00	0.00	0.00	3.50
464	479	3.197790	CCCGCAACATCAGCTCGG	61.198	66.667	0.97	0.97	39.79	4.63
585	600	3.017581	GCCTCCATCCACCCTGGT	61.018	66.667	0.00	0.00	39.03	4.00
588	603	1.056700	CCTCCATCCACCCTGGTAGG	61.057	65.000	0.00	0.00	39.03	3.18
701	716	2.427245	CCCAGAGGCGACGATTCCT	61.427	63.158	0.00	0.00	34.90	3.36
714	729	2.579684	GATTCCTTGTCGCCTCGGCT	62.580	60.000	6.35	0.00	39.32	5.52
813	828	1.269723	GTTAGCCCCAACTTTGCTCAC	59.730	52.381	0.00	0.00	36.57	3.51
850	867	5.977635	TGGTTGTATATGAGTTGGAGAGTG	58.022	41.667	0.00	0.00	0.00	3.51
852	869	5.104900	GGTTGTATATGAGTTGGAGAGTGGT	60.105	44.000	0.00	0.00	0.00	4.16
878	895	5.902613	ATTCTGTAATGTGGGATGTTGTG	57.097	39.130	0.00	0.00	0.00	3.33
881	898	3.070748	TGTAATGTGGGATGTTGTGTCG	58.929	45.455	0.00	0.00	0.00	4.35
906	924	3.875125	TCTGTGCGATGAGTAGACTAGT	58.125	45.455	0.00	0.00	0.00	2.57
909	927	4.733850	TGTGCGATGAGTAGACTAGTTTG	58.266	43.478	0.00	0.00	0.00	2.93
946	964	7.284489	TGATGAATTGATGCTTGATTCTGATGA	59.716	33.333	0.00	0.00	32.41	2.92
1178	1196	3.948473	TGCCAAAGCTTAACAACTACACA	59.052	39.130	0.00	0.00	40.80	3.72
1203	1221	9.000486	CATTCAGTAATCATGAACTGCAGATAT	58.000	33.333	23.35	8.48	42.31	1.63
1221	1241	1.120530	ATAGAGTTCCGGGCGATGTT	58.879	50.000	0.00	0.00	0.00	2.71
1258	1278	1.304509	GGAAGTGCAGAGGCTCAAGC	61.305	60.000	18.26	19.71	41.91	4.01
1402	1422	3.240134	GACGAGACCCTGGCTGCAA	62.240	63.158	0.50	0.00	0.00	4.08
1429	1449	0.601311	GTTCAGAGCACTGCTTCGGT	60.601	55.000	4.67	0.00	39.88	4.69
1462	1482	2.251642	GCCTTCGCGTCACAGGTTT	61.252	57.895	5.77	0.00	0.00	3.27
1496	1516	4.274950	GGCAGCACAAAACTGACTAGTTAA	59.725	41.667	0.00	0.00	46.14	2.01
1511	1532	9.321562	CTGACTAGTTAAGTGGTACAAGAAAAA	57.678	33.333	0.00	0.00	44.16	1.94
1537	1558	7.937942	AGACATTCATTAGCTAGCTCATCAATT	59.062	33.333	23.26	5.34	0.00	2.32
1622	1643	8.349983	ACAAATGTAGTGTTACTTTTAGGCAAG	58.650	33.333	0.00	0.00	35.91	4.01
1663	1684	3.652057	AATGGATGAGTTTCGTGGGAT	57.348	42.857	0.00	0.00	0.00	3.85
1935	1956	5.820423	TCCATGAATTGGTAGTTATTGGTCG	59.180	40.000	0.00	0.00	46.52	4.79
1948	1969	7.068692	AGTTATTGGTCGTATTTAGTTGCAC	57.931	36.000	0.00	0.00	0.00	4.57
2017	2038	5.068460	GTGCTAGATCTGTCATGTAGGAGTT	59.932	44.000	5.18	0.00	0.00	3.01
2348	2375	5.721232	GCGTCCAGCTATTATATTAGTGGT	58.279	41.667	15.36	0.00	44.04	4.16
2349	2376	6.164176	GCGTCCAGCTATTATATTAGTGGTT	58.836	40.000	15.36	0.00	44.04	3.67
2350	2377	6.649557	GCGTCCAGCTATTATATTAGTGGTTT	59.350	38.462	15.36	0.00	44.04	3.27
2351	2378	7.148623	GCGTCCAGCTATTATATTAGTGGTTTC	60.149	40.741	15.36	10.40	44.04	2.78
2352	2379	7.331193	CGTCCAGCTATTATATTAGTGGTTTCC	59.669	40.741	15.36	0.00	0.00	3.13
2353	2380	8.154856	GTCCAGCTATTATATTAGTGGTTTCCA	58.845	37.037	15.36	0.00	0.00	3.53
2354	2381	8.890472	TCCAGCTATTATATTAGTGGTTTCCAT	58.110	33.333	15.36	0.00	35.28	3.41
2355	2382	9.167311	CCAGCTATTATATTAGTGGTTTCCATC	57.833	37.037	0.00	0.00	35.28	3.51
2356	2383	9.950496	CAGCTATTATATTAGTGGTTTCCATCT	57.050	33.333	0.00	0.00	35.28	2.90
2358	2385	9.944376	GCTATTATATTAGTGGTTTCCATCTCA	57.056	33.333	4.12	0.00	35.28	3.27
2360	2387	8.854614	ATTATATTAGTGGTTTCCATCTCAGC	57.145	34.615	0.00	0.00	35.28	4.26
2361	2388	4.851639	ATTAGTGGTTTCCATCTCAGCT	57.148	40.909	0.00	0.00	35.28	4.24
2362	2389	2.777832	AGTGGTTTCCATCTCAGCTC	57.222	50.000	0.00	0.00	35.28	4.09
2363	2390	1.280421	AGTGGTTTCCATCTCAGCTCC	59.720	52.381	0.00	0.00	35.28	4.70
2364	2391	0.620556	TGGTTTCCATCTCAGCTCCC	59.379	55.000	0.00	0.00	0.00	4.30
2365	2392	0.620556	GGTTTCCATCTCAGCTCCCA	59.379	55.000	0.00	0.00	0.00	4.37
2366	2393	1.407989	GGTTTCCATCTCAGCTCCCAG	60.408	57.143	0.00	0.00	0.00	4.45
2367	2394	0.914644	TTTCCATCTCAGCTCCCAGG	59.085	55.000	0.00	0.00	0.00	4.45
2368	2395	1.630126	TTCCATCTCAGCTCCCAGGC	61.630	60.000	0.00	0.00	0.00	4.85
2369	2396	2.509916	CATCTCAGCTCCCAGGCC	59.490	66.667	0.00	0.00	0.00	5.19
2370	2397	2.771762	ATCTCAGCTCCCAGGCCC	60.772	66.667	0.00	0.00	0.00	5.80
2387	2414	4.742201	CCCGCGTCACTCCCACAG	62.742	72.222	4.92	0.00	0.00	3.66
2388	2415	4.742201	CCGCGTCACTCCCACAGG	62.742	72.222	4.92	0.00	0.00	4.00
2389	2416	4.742201	CGCGTCACTCCCACAGGG	62.742	72.222	0.00	0.00	46.11	4.45
2413	2440	4.580551	CGGGCGGCGTAACCCTAG	62.581	72.222	17.21	1.31	44.63	3.02
2414	2441	4.904900	GGGCGGCGTAACCCTAGC	62.905	72.222	13.07	0.00	43.36	3.42
2415	2442	4.904900	GGCGGCGTAACCCTAGCC	62.905	72.222	9.37	0.00	46.88	3.93
2418	2445	4.904900	GGCGTAACCCTAGCCCGC	62.905	72.222	0.00	0.00	44.80	6.13
2419	2446	4.904900	GCGTAACCCTAGCCCGCC	62.905	72.222	0.00	0.00	38.52	6.13
2420	2447	4.580551	CGTAACCCTAGCCCGCCG	62.581	72.222	0.00	0.00	0.00	6.46
2421	2448	4.904900	GTAACCCTAGCCCGCCGC	62.905	72.222	0.00	0.00	37.98	6.53

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
19	20	7.148689	CGGCCGTTAGATACATTAGGTTATTTC	60.149	40.741	19.50	0.00	0.00	2.17
87	88	2.031919	GTGTGCATCGTGGGTGGA	59.968	61.111	0.00	0.00	0.00	4.02
122	123	0.527565	GATCCAATGTGGGTGTGTGC	59.472	55.000	0.00	0.00	38.32	4.57
346	361	1.152567	CTCGAGGAGGAGGAGGCAT	60.153	63.158	3.91	0.00	0.00	4.40
347	362	2.277072	CTCGAGGAGGAGGAGGCA	59.723	66.667	3.91	0.00	0.00	4.75
351	366	2.743179	TAGCGCTCGAGGAGGAGGA	61.743	63.158	16.34	0.00	34.56	3.71
401	416	4.796231	GTCGATGTCAGCGCGGGT	62.796	66.667	8.83	0.00	0.00	5.28
452	467	2.034879	CGTTGGCCGAGCTGATGTT	61.035	57.895	0.00	0.00	39.56	2.71
464	479	2.956964	CTCGATCTCGCCGTTGGC	60.957	66.667	0.00	0.00	46.75	4.52
513	528	3.436577	TCCTCTTGGACTCGTAGAAGT	57.563	47.619	0.00	0.00	37.46	3.01
585	600	1.276622	GGGTTGAGAAGTGGCTCCTA	58.723	55.000	0.00	0.00	33.95	2.94
588	603	0.606673	GTGGGGTTGAGAAGTGGCTC	60.607	60.000	0.00	0.00	35.46	4.70
714	729	2.750237	TCGCAGAGCTCTACGGCA	60.750	61.111	30.77	14.12	33.76	5.69
850	867	5.885912	ACATCCCACATTACAGAATTACACC	59.114	40.000	0.00	0.00	0.00	4.16
852	869	6.945435	ACAACATCCCACATTACAGAATTACA	59.055	34.615	0.00	0.00	0.00	2.41
878	895	0.716108	CTCATCGCACAGAAACCGAC	59.284	55.000	0.00	0.00	33.46	4.79
881	898	2.924290	GTCTACTCATCGCACAGAAACC	59.076	50.000	0.00	0.00	0.00	3.27
906	924	6.259893	TCAATTCATCAGTTTATCCCCCAAA	58.740	36.000	0.00	0.00	0.00	3.28
909	927	5.279156	GCATCAATTCATCAGTTTATCCCCC	60.279	44.000	0.00	0.00	0.00	5.40
946	964	0.245539	GCAAAGCAGCACACCATGAT	59.754	50.000	0.00	0.00	0.00	2.45
994	1012	3.244700	GGTAGCACTCCTGGCATATCAAT	60.245	47.826	0.00	0.00	0.00	2.57
1170	1188	8.939929	CAGTTCATGATTACTGAATGTGTAGTT	58.060	33.333	18.82	0.00	43.45	2.24
1203	1221	0.174845	CAACATCGCCCGGAACTCTA	59.825	55.000	0.73	0.00	0.00	2.43
1258	1278	2.777969	GCAGTTGAGATGCAGAGGG	58.222	57.895	0.00	0.00	43.31	4.30
1265	1285	1.654954	GGCTGCCTGCAGTTGAGATG	61.655	60.000	19.45	0.00	45.24	2.90
1266	1286	1.378250	GGCTGCCTGCAGTTGAGAT	60.378	57.895	19.45	0.00	45.24	2.75
1354	1374	1.482593	CTTCTTAGCCATGAGGTCGGT	59.517	52.381	0.00	0.00	37.19	4.69
1402	1422	3.241530	TGCTCTGAACTGGCGGGT	61.242	61.111	0.00	0.00	0.00	5.28
1429	1449	2.427453	CGAAGGCTTTCTGGAGCTACTA	59.573	50.000	0.00	0.00	42.32	1.82
1462	1482	0.178967	TGTGCTGCCTTTTGATCCCA	60.179	50.000	0.00	0.00	0.00	4.37
1496	1516	7.823745	ATGAATGTCTTTTTCTTGTACCACT	57.176	32.000	0.00	0.00	0.00	4.00
1511	1532	6.416631	TGATGAGCTAGCTAATGAATGTCT	57.583	37.500	19.97	0.00	0.00	3.41
1537	1558	2.708216	TGCATCCTTAATCCGAAGCA	57.292	45.000	0.00	0.00	30.84	3.91
1622	1643	7.437862	TCCATTAGTTCAAAATTTGCTCAACAC	59.562	33.333	0.00	0.00	0.00	3.32
1774	1795	2.396955	GCAGCAACAGCAGCTCGAT	61.397	57.895	0.00	0.00	41.14	3.59
1824	1845	0.393537	AGAATCTTGAAGGGCTGCGG	60.394	55.000	0.00	0.00	0.00	5.69
1935	1956	6.567891	GGACTGACCAAAGTGCAACTAAATAC	60.568	42.308	0.00	0.00	42.78	1.89
1948	1969	0.944386	CACAACCGGACTGACCAAAG	59.056	55.000	9.46	0.00	38.90	2.77
2346	2373	0.620556	TGGGAGCTGAGATGGAAACC	59.379	55.000	0.00	0.00	0.00	3.27
2347	2374	1.407989	CCTGGGAGCTGAGATGGAAAC	60.408	57.143	0.00	0.00	0.00	2.78
2348	2375	0.914644	CCTGGGAGCTGAGATGGAAA	59.085	55.000	0.00	0.00	0.00	3.13
2349	2376	1.630126	GCCTGGGAGCTGAGATGGAA	61.630	60.000	0.00	0.00	0.00	3.53
2350	2377	2.068821	GCCTGGGAGCTGAGATGGA	61.069	63.158	0.00	0.00	0.00	3.41
2351	2378	2.509916	GCCTGGGAGCTGAGATGG	59.490	66.667	0.00	0.00	0.00	3.51
2352	2379	2.509916	GGCCTGGGAGCTGAGATG	59.490	66.667	0.00	0.00	0.00	2.90
2353	2380	2.771762	GGGCCTGGGAGCTGAGAT	60.772	66.667	0.84	0.00	0.00	2.75
2370	2397	4.742201	CTGTGGGAGTGACGCGGG	62.742	72.222	12.47	0.00	0.00	6.13
2371	2398	4.742201	CCTGTGGGAGTGACGCGG	62.742	72.222	12.47	0.00	33.58	6.46
2397	2424	4.904900	GCTAGGGTTACGCCGCCC	62.905	72.222	0.00	0.95	45.16	6.13
2398	2425	4.904900	GGCTAGGGTTACGCCGCC	62.905	72.222	12.81	12.81	38.44	6.13
2399	2426	4.904900	GGGCTAGGGTTACGCCGC	62.905	72.222	0.00	0.00	44.68	6.53
2400	2427	4.580551	CGGGCTAGGGTTACGCCG	62.581	72.222	0.00	0.00	44.68	6.46
2401	2428	4.904900	GCGGGCTAGGGTTACGCC	62.905	72.222	0.00	0.00	44.01	5.68
2403	2430	4.580551	CGGCGGGCTAGGGTTACG	62.581	72.222	0.00	0.00	0.00	3.18
2404	2431	4.904900	GCGGCGGGCTAGGGTTAC	62.905	72.222	9.78	0.00	39.11	2.50

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.