AutoCloner

Multiple sequence alignment - TraesCS5A01G101100

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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	TraesCS5A01G101100	chr5A	100.000	3472	0	0	1	3472	147589513	147592984	0.000000e+00	6412
1	TraesCS5A01G101100	chr5A	95.489	2505	108	5	971	3472	210234484	210231982	0.000000e+00	3995
2	TraesCS5A01G101100	chr5A	94.655	2507	127	7	968	3472	213233991	213231490	0.000000e+00	3880
3	TraesCS5A01G101100	chr5A	96.591	968	31	1	1	968	147581147	147582112	0.000000e+00	1604
4	TraesCS5A01G101100	chr5A	95.389	976	38	2	1	969	147517784	147518759	0.000000e+00	1546
5	TraesCS5A01G101100	chr5A	84.424	443	51	9	1180	1607	35913222	35913661	1.490000e-113	420
6	TraesCS5A01G101100	chr1A	95.371	2506	109	7	971	3472	147728879	147726377	0.000000e+00	3978
7	TraesCS5A01G101100	chr6A	94.007	2503	120	13	991	3472	206133791	206136284	0.000000e+00	3764
8	TraesCS5A01G101100	chr4D	92.767	1991	119	9	968	2939	215033548	215035532	0.000000e+00	2856
9	TraesCS5A01G101100	chr4D	94.063	977	52	5	2501	3472	313783419	313782444	0.000000e+00	1478
10	TraesCS5A01G101100	chr4D	85.896	943	83	31	1602	2503	15874836	15873903	0.000000e+00	959
11	TraesCS5A01G101100	chr4D	90.581	637	50	4	971	1607	313784527	313783901	0.000000e+00	835
12	TraesCS5A01G101100	chr4D	92.066	542	31	6	2934	3472	215046728	215047260	0.000000e+00	752
13	TraesCS5A01G101100	chr4D	82.695	861	115	28	120	967	395276718	395277557	0.000000e+00	734
14	TraesCS5A01G101100	chr3A	94.456	938	45	6	26	962	245946111	245947042	0.000000e+00	1437
15	TraesCS5A01G101100	chr3A	87.695	642	65	5	979	1607	281209418	281208778	0.000000e+00	736
16	TraesCS5A01G101100	chr2A	92.008	976	68	9	2501	3472	404058329	404059298	0.000000e+00	1362
17	TraesCS5A01G101100	chr2A	91.906	976	69	9	2501	3472	402113211	402114180	0.000000e+00	1356
18	TraesCS5A01G101100	chr2A	81.106	434	48	12	1206	1607	404057436	404057867	2.010000e-82	316
19	TraesCS5A01G101100	chr2A	80.645	434	50	12	1206	1607	402112318	402112749	4.350000e-79	305
20	TraesCS5A01G101100	chr7A	91.505	977	72	9	2501	3472	195277216	195276246	0.000000e+00	1334
21	TraesCS5A01G101100	chr7A	89.848	197	19	1	971	1167	17043724	17043529	5.750000e-63	252
22	TraesCS5A01G101100	chr4B	84.762	945	88	31	1602	2503	27398917	27397986	0.000000e+00	896
23	TraesCS5A01G101100	chr4A	84.921	882	116	16	91	967	126361652	126362521	0.000000e+00	876
24	TraesCS5A01G101100	chr4A	90.535	486	40	4	2022	2503	584697312	584696829	3.780000e-179	638
25	TraesCS5A01G101100	chr1B	83.916	858	115	22	120	967	255549106	255548262	0.000000e+00	798
26	TraesCS5A01G101100	chrUn	83.702	859	116	23	120	967	281084711	281083866	0.000000e+00	789
27	TraesCS5A01G101100	chr3B	83.566	858	118	22	120	967	397830837	397829993	0.000000e+00	782
28	TraesCS5A01G101100	chr3B	77.451	714	106	28	1771	2466	822552222	822552898	3.270000e-100	375
29	TraesCS5A01G101100	chr7D	83.061	856	115	24	120	967	506748939	506749772	0.000000e+00	750
30	TraesCS5A01G101100	chr3D	85.239	481	48	3	971	1451	604116989	604116532	1.130000e-129	473

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	TraesCS5A01G101100	chr5A	147589513	147592984	3471	False	6412.0	6412	100.0000	1	3472	1	chr5A.!!$F4	3471
1	TraesCS5A01G101100	chr5A	210231982	210234484	2502	True	3995.0	3995	95.4890	971	3472	1	chr5A.!!$R1	2501
2	TraesCS5A01G101100	chr5A	213231490	213233991	2501	True	3880.0	3880	94.6550	968	3472	1	chr5A.!!$R2	2504
3	TraesCS5A01G101100	chr5A	147581147	147582112	965	False	1604.0	1604	96.5910	1	968	1	chr5A.!!$F3	967
4	TraesCS5A01G101100	chr5A	147517784	147518759	975	False	1546.0	1546	95.3890	1	969	1	chr5A.!!$F2	968
5	TraesCS5A01G101100	chr1A	147726377	147728879	2502	True	3978.0	3978	95.3710	971	3472	1	chr1A.!!$R1	2501
6	TraesCS5A01G101100	chr6A	206133791	206136284	2493	False	3764.0	3764	94.0070	991	3472	1	chr6A.!!$F1	2481
7	TraesCS5A01G101100	chr4D	215033548	215035532	1984	False	2856.0	2856	92.7670	968	2939	1	chr4D.!!$F1	1971
8	TraesCS5A01G101100	chr4D	313782444	313784527	2083	True	1156.5	1478	92.3220	971	3472	2	chr4D.!!$R2	2501
9	TraesCS5A01G101100	chr4D	15873903	15874836	933	True	959.0	959	85.8960	1602	2503	1	chr4D.!!$R1	901
10	TraesCS5A01G101100	chr4D	215046728	215047260	532	False	752.0	752	92.0660	2934	3472	1	chr4D.!!$F2	538
11	TraesCS5A01G101100	chr4D	395276718	395277557	839	False	734.0	734	82.6950	120	967	1	chr4D.!!$F3	847
12	TraesCS5A01G101100	chr3A	245946111	245947042	931	False	1437.0	1437	94.4560	26	962	1	chr3A.!!$F1	936
13	TraesCS5A01G101100	chr3A	281208778	281209418	640	True	736.0	736	87.6950	979	1607	1	chr3A.!!$R1	628
14	TraesCS5A01G101100	chr2A	404057436	404059298	1862	False	839.0	1362	86.5570	1206	3472	2	chr2A.!!$F2	2266
15	TraesCS5A01G101100	chr2A	402112318	402114180	1862	False	830.5	1356	86.2755	1206	3472	2	chr2A.!!$F1	2266
16	TraesCS5A01G101100	chr7A	195276246	195277216	970	True	1334.0	1334	91.5050	2501	3472	1	chr7A.!!$R2	971
17	TraesCS5A01G101100	chr4B	27397986	27398917	931	True	896.0	896	84.7620	1602	2503	1	chr4B.!!$R1	901
18	TraesCS5A01G101100	chr4A	126361652	126362521	869	False	876.0	876	84.9210	91	967	1	chr4A.!!$F1	876
19	TraesCS5A01G101100	chr1B	255548262	255549106	844	True	798.0	798	83.9160	120	967	1	chr1B.!!$R1	847
20	TraesCS5A01G101100	chrUn	281083866	281084711	845	True	789.0	789	83.7020	120	967	1	chrUn.!!$R1	847
21	TraesCS5A01G101100	chr3B	397829993	397830837	844	True	782.0	782	83.5660	120	967	1	chr3B.!!$R1	847
22	TraesCS5A01G101100	chr3B	822552222	822552898	676	False	375.0	375	77.4510	1771	2466	1	chr3B.!!$F1	695
23	TraesCS5A01G101100	chr7D	506748939	506749772	833	False	750.0	750	83.0610	120	967	1	chr7D.!!$F1	847

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
675	689	0.252513	TTCCTTCGGGGTCTCCATCA	60.253	55.0	0.0	0.0	36.25	3.07	F
1772	2168	0.768221	ACCCATCCCCGCACATATCT	60.768	55.0	0.0	0.0	0.00	1.98	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2310	2743	0.029700	GTTTTTGTTGGGGGTCGACG	59.970	55.000	9.92	0.00	32.34	5.12	R
2806	3252	2.265367	TCCATGGACTAGCTGGTTTCA	58.735	47.619	11.44	6.91	0.00	2.69	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
17	18	2.121228	TGGCCCAGGGGTAAAGGT	60.121	61.111	7.91	0.00	37.65	3.50
114	124	8.843262	ACTTAGTTTAAGTAAAATGCGAACCTT	58.157	29.630	0.00	0.00	46.53	3.50
472	486	6.327626	ACTGTAGCATAAATATCCAGGTGTCT	59.672	38.462	0.00	0.00	0.00	3.41
619	633	6.233434	GGTCCATAGCATTGATGTCTTCATA	58.767	40.000	0.00	0.00	33.34	2.15
675	689	0.252513	TTCCTTCGGGGTCTCCATCA	60.253	55.000	0.00	0.00	36.25	3.07
685	699	3.256136	GGGGTCTCCATCATACTTACGAG	59.744	52.174	0.00	0.00	35.00	4.18
690	704	6.642950	GGTCTCCATCATACTTACGAGAAATG	59.357	42.308	0.00	0.00	0.00	2.32
796	811	6.017852	ACCTCTCGAGTTGAAATTCAAGAAAC	60.018	38.462	13.13	0.00	37.00	2.78
903	918	3.691609	GGTTCAGAGCAATGGGAAAGTAG	59.308	47.826	0.00	0.00	0.00	2.57
946	961	1.280133	CATCTCAAGGAAGGTGGCTCA	59.720	52.381	0.00	0.00	0.00	4.26
1158	1173	3.596046	TCCTCTTCTCCTTCTCTTCCTCT	59.404	47.826	0.00	0.00	0.00	3.69
1190	1205	1.153086	GGATCCTGCTGCCGTCAAT	60.153	57.895	3.84	0.00	0.00	2.57
1191	1206	1.442526	GGATCCTGCTGCCGTCAATG	61.443	60.000	3.84	0.00	0.00	2.82
1193	1208	2.547640	ATCCTGCTGCCGTCAATGCT	62.548	55.000	0.00	0.00	0.00	3.79
1247	1262	1.939769	GCGCCCTCTCTTCTTCTCGT	61.940	60.000	0.00	0.00	0.00	4.18
1332	1359	1.572085	CGCTGCTGGTTGACCTTCTG	61.572	60.000	1.34	0.00	36.82	3.02
1382	1410	1.753073	GGTTACTTTCGAGGATCCGGA	59.247	52.381	6.61	6.61	0.00	5.14
1434	1466	0.894835	TGCTGTGTGAAGATCCGCTA	59.105	50.000	0.00	0.00	0.00	4.26
1451	1483	2.799917	CGCTAGCCTAAAGACGCAAGAT	60.800	50.000	9.66	0.00	43.62	2.40
1495	1557	7.499232	TGCTAATGCTATTTTCTTCCTCCTAAC	59.501	37.037	0.00	0.00	40.48	2.34
1708	2094	8.825745	CAATTATAAAACAACAAGTTGCAGGTT	58.174	29.630	12.54	2.28	44.03	3.50
1724	2119	4.156556	TGCAGGTTTCATCAGTTTGATAGC	59.843	41.667	0.00	0.00	34.28	2.97
1765	2161	1.570857	AAGAATCACCCATCCCCGCA	61.571	55.000	0.00	0.00	0.00	5.69
1772	2168	0.768221	ACCCATCCCCGCACATATCT	60.768	55.000	0.00	0.00	0.00	1.98
1784	2181	3.911365	CGCACATATCTGAATCTCTCGAC	59.089	47.826	0.00	0.00	0.00	4.20
1962	2386	8.560576	ACAAACTGAAATATGTTTTTCTCACG	57.439	30.769	0.00	0.00	36.71	4.35
1975	2399	6.490721	TGTTTTTCTCACGGGTTAATTGGTAT	59.509	34.615	0.00	0.00	0.00	2.73
2044	2468	3.699038	GACTGAGTAGTCCTGCTTCTCAT	59.301	47.826	4.50	0.00	46.01	2.90
2053	2477	4.042187	AGTCCTGCTTCTCATAGGTTTTGT	59.958	41.667	0.00	0.00	33.30	2.83
2170	2597	1.592400	AACAATCTCCGAGGCGACGA	61.592	55.000	0.00	0.00	35.09	4.20
2173	2600	1.384989	AATCTCCGAGGCGACGACAT	61.385	55.000	2.19	0.00	35.09	3.06
2298	2731	1.238615	AGAACTCCCCTATCCCCGTA	58.761	55.000	0.00	0.00	0.00	4.02
2307	2740	1.909302	CCTATCCCCGTATTGGCAGAT	59.091	52.381	0.00	0.00	35.87	2.90
2310	2743	1.048601	TCCCCGTATTGGCAGATCTC	58.951	55.000	0.00	0.00	35.87	2.75
2312	2745	0.389391	CCCGTATTGGCAGATCTCGT	59.611	55.000	0.00	0.00	35.87	4.18
2340	2773	2.223479	CCAACAAAAACAGGTGAGTCCG	60.223	50.000	0.00	0.00	41.99	4.79
2432	2872	3.065925	GGGATTTGATCTTTTCGCCAGAG	59.934	47.826	0.00	0.00	0.00	3.35
2567	3007	9.667607	ATTTAATCATCCTAGGAGAGAAGAAGA	57.332	33.333	18.34	5.23	0.00	2.87
2606	3052	4.148348	GTGTGAGAGAACACGTACAATGAC	59.852	45.833	1.26	0.00	40.96	3.06
2758	3204	3.923017	ACTTACAATTGCAACTCTGGC	57.077	42.857	0.00	0.00	0.00	4.85
2806	3252	7.595819	TGTAAAGAAAATGGAAGTTCATGGT	57.404	32.000	5.01	0.00	0.00	3.55
2987	3436	8.385898	ACTATGGTATTTTCACACGAAGAAAA	57.614	30.769	13.55	13.55	45.68	2.29
3298	3757	4.258543	TGAAACATGGATTCCTCGTTACC	58.741	43.478	3.95	4.38	0.00	2.85
3302	3761	4.658063	ACATGGATTCCTCGTTACCAAAA	58.342	39.130	3.95	0.00	34.28	2.44
3426	3889	9.619316	TTAAATAACGGAGATGTTGAATGTTTG	57.381	29.630	0.00	0.00	33.32	2.93
3439	3902	8.635877	TGTTGAATGTTTGTTACAATACCAAC	57.364	30.769	0.00	9.63	40.89	3.77

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
149	159	3.708563	TGAGTACCAAGCTTTTTGTGC	57.291	42.857	0.00	0.00	0.00	4.57
379	391	6.145338	TCTCGCTTAGATTCTAATCGGTTT	57.855	37.500	22.47	0.00	40.35	3.27
406	420	4.130857	ACACGTCACCATTGTTATTGTGA	58.869	39.130	0.00	0.00	34.92	3.58
455	469	8.160106	GGAGAATTGAGACACCTGGATATTTAT	58.840	37.037	0.00	0.00	0.00	1.40
472	486	6.433847	TTTCTTGTAGTGGAGGAGAATTGA	57.566	37.500	0.00	0.00	0.00	2.57
619	633	7.464273	TCATCATGATTACCTGAAGCCAATAT	58.536	34.615	5.16	0.00	0.00	1.28
623	637	4.776435	TCATCATGATTACCTGAAGCCA	57.224	40.909	5.16	0.00	0.00	4.75
675	689	5.901276	TCCCCCTTACATTTCTCGTAAGTAT	59.099	40.000	8.72	0.00	42.77	2.12
685	699	3.439129	CACGAGTTTCCCCCTTACATTTC	59.561	47.826	0.00	0.00	0.00	2.17
690	704	2.038164	ACTTCACGAGTTTCCCCCTTAC	59.962	50.000	0.00	0.00	33.92	2.34
903	918	8.804688	ATGATCTATTCTAGTTTTAGACGCAC	57.195	34.615	0.00	0.00	35.67	5.34
946	961	7.178274	TGGTGTTTGGCTTCATAAGTAATTCAT	59.822	33.333	0.00	0.00	0.00	2.57
1158	1173	3.432749	GCAGGATCCAGCAAAGATCACTA	60.433	47.826	23.20	0.00	41.64	2.74
1190	1205	2.742116	GGGGTTCCGATGCCTAGCA	61.742	63.158	0.00	0.00	44.86	3.49
1191	1206	2.111251	GGGGTTCCGATGCCTAGC	59.889	66.667	0.00	0.00	0.00	3.42
1210	1225	4.101448	GGCGATGGAGTGCAGGGT	62.101	66.667	0.00	0.00	0.00	4.34
1235	1250	0.389166	AGCCGCAACGAGAAGAAGAG	60.389	55.000	0.00	0.00	0.00	2.85
1370	1397	1.032794	CTTGTGATCCGGATCCTCGA	58.967	55.000	35.72	26.34	37.02	4.04
1434	1466	2.770164	ACATCTTGCGTCTTTAGGCT	57.230	45.000	0.00	0.00	37.40	4.58
1495	1557	1.068474	AAATCAAGGCGTCGACTTCG	58.932	50.000	11.28	7.14	41.45	3.79
1708	2094	8.213679	AGCCTATTAAGCTATCAAACTGATGAA	58.786	33.333	0.00	0.00	39.29	2.57
1765	2161	4.279671	GTGGGTCGAGAGATTCAGATATGT	59.720	45.833	0.00	0.00	45.19	2.29
1772	2168	2.248248	AGTTGTGGGTCGAGAGATTCA	58.752	47.619	0.00	0.00	45.19	2.57
1962	2386	7.949690	AAACAGGACTAATACCAATTAACCC	57.050	36.000	0.00	0.00	30.58	4.11
1975	2399	5.560724	CTCTGGGATTGAAAACAGGACTAA	58.439	41.667	0.00	0.00	0.00	2.24
2044	2468	9.575783	GTGACAGATAAACAAAAACAAAACCTA	57.424	29.630	0.00	0.00	0.00	3.08
2136	2563	6.093219	CGGAGATTGTTGAGTTCATCTTTGAT	59.907	38.462	0.00	0.00	0.00	2.57
2170	2597	6.231211	CACTCCTTGTACTTTCTGGTTATGT	58.769	40.000	0.00	0.00	0.00	2.29
2173	2600	4.041198	CCCACTCCTTGTACTTTCTGGTTA	59.959	45.833	0.00	0.00	0.00	2.85
2209	2636	4.807834	CGAGGTCGTTGTAGTAGTCATAGA	59.192	45.833	0.00	0.00	34.11	1.98
2298	2731	0.103208	GGTCGACGAGATCTGCCAAT	59.897	55.000	9.92	0.00	0.00	3.16
2307	2740	1.401318	TTTGTTGGGGGTCGACGAGA	61.401	55.000	9.92	0.00	32.34	4.04
2310	2743	0.029700	GTTTTTGTTGGGGGTCGACG	59.970	55.000	9.92	0.00	32.34	5.12
2312	2745	1.394618	CTGTTTTTGTTGGGGGTCGA	58.605	50.000	0.00	0.00	0.00	4.20
2340	2773	5.880054	AGAACAAACATATACACTGCACC	57.120	39.130	0.00	0.00	0.00	5.01
2432	2872	3.767902	ATTCTGCTCTCCAATCTAGGC	57.232	47.619	0.00	0.00	0.00	3.93
2539	2979	9.667607	TTCTTCTCTCCTAGGATGATTAAATCT	57.332	33.333	13.12	0.00	0.00	2.40
2758	3204	6.295039	AGTTTACAAACATTACACAGACGG	57.705	37.500	7.53	0.00	41.30	4.79
2806	3252	2.265367	TCCATGGACTAGCTGGTTTCA	58.735	47.619	11.44	6.91	0.00	2.69
2926	3375	5.589050	ACTTTTAACAGTGAAGGTTCAGACC	59.411	40.000	0.00	0.00	46.92	3.85
3086	3542	3.986996	AGATGGGGAAAAGCCATTTTG	57.013	42.857	0.00	0.00	38.74	2.44
3439	3902	8.600449	TGCTTGGTTTATTTAATTTGACCTTG	57.400	30.769	0.00	0.00	0.00	3.61

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.