AutoCloner

Multiple sequence alignment - TraesCS1B01G241000

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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	TraesCS1B01G241000	chr1B	100.000	2654	0	0	1	2654	428638753	428636100	0.000000e+00	4902.0
1	TraesCS1B01G241000	chr1B	93.388	121	4	2	429	549	428616691	428616575	2.720000e-40	176.0
2	TraesCS1B01G241000	chr1D	95.666	2238	58	16	429	2652	316602400	316600188	0.000000e+00	3559.0
3	TraesCS1B01G241000	chr1D	97.500	40	0	1	2614	2652	301334853	301334814	1.700000e-07	67.6
4	TraesCS1B01G241000	chr1A	93.715	1607	68	18	1058	2652	397669477	397667892	0.000000e+00	2377.0
5	TraesCS1B01G241000	chr1A	90.269	668	35	12	413	1060	397700564	397699907	0.000000e+00	846.0
6	TraesCS1B01G241000	chr1A	92.576	229	15	2	162	390	324503475	324503701	7.080000e-86	327.0
7	TraesCS1B01G241000	chr5D	86.867	1066	108	22	1571	2608	35803894	35804955	0.000000e+00	1164.0
8	TraesCS1B01G241000	chr5B	85.286	1067	102	34	1569	2602	26642047	26641003	0.000000e+00	1050.0
9	TraesCS1B01G241000	chr5B	87.251	855	76	22	1569	2401	26637363	26636520	0.000000e+00	944.0
10	TraesCS1B01G241000	chr5B	91.727	411	12	3	1	390	261258001	261257592	3.860000e-153	551.0
11	TraesCS1B01G241000	chr5B	79.211	558	107	7	1085	1639	26637914	26637363	1.930000e-101	379.0
12	TraesCS1B01G241000	chr5B	79.211	558	107	7	1085	1639	26642598	26642047	1.930000e-101	379.0
13	TraesCS1B01G241000	chr5A	84.981	1052	109	31	1584	2614	24354082	24355105	0.000000e+00	1022.0
14	TraesCS1B01G241000	chr5A	88.564	411	29	10	1722	2122	23900968	23900566	1.430000e-132	483.0
15	TraesCS1B01G241000	chr5A	86.702	188	25	0	1463	1650	23901275	23901088	2.680000e-50	209.0
16	TraesCS1B01G241000	chrUn	85.305	524	62	9	2097	2605	389867533	389867010	6.510000e-146	527.0
17	TraesCS1B01G241000	chrUn	84.048	420	47	18	1569	1975	323956503	323956091	1.150000e-103	387.0
18	TraesCS1B01G241000	chrUn	79.211	558	107	7	1085	1639	323957054	323956503	1.930000e-101	379.0
19	TraesCS1B01G241000	chr2B	92.857	238	15	2	1	237	8992604	8992368	7.030000e-91	344.0
20	TraesCS1B01G241000	chr2B	97.391	115	3	0	276	390	8991844	8991730	2.080000e-46	196.0
21	TraesCS1B01G241000	chr4B	82.821	390	52	11	1	386	149064664	149065042	4.230000e-88	335.0
22	TraesCS1B01G241000	chr6B	94.366	213	10	2	183	394	607490254	607490465	2.550000e-85	326.0
23	TraesCS1B01G241000	chr6B	95.192	104	5	0	1	104	607489831	607489934	5.880000e-37	165.0
24	TraesCS1B01G241000	chr3B	97.326	187	4	1	204	390	463466741	463466926	1.530000e-82	316.0
25	TraesCS1B01G241000	chr3B	96.190	105	4	0	1	105	463466148	463466252	3.510000e-39	172.0
26	TraesCS1B01G241000	chr3B	100.000	40	0	0	188	227	463466704	463466743	1.020000e-09	75.0
27	TraesCS1B01G241000	chr3B	90.909	55	5	0	324	378	752208988	752209042	1.020000e-09	75.0
28	TraesCS1B01G241000	chr3D	91.111	225	19	1	162	386	593127145	593126922	1.190000e-78	303.0
29	TraesCS1B01G241000	chr3D	90.588	85	7	1	1	85	600107015	600106932	7.770000e-21	111.0
30	TraesCS1B01G241000	chr4D	87.113	194	22	2	1	194	483988296	483988486	1.600000e-52	217.0
31	TraesCS1B01G241000	chr4D	100.000	32	0	0	2618	2649	417478018	417478049	2.850000e-05	60.2
32	TraesCS1B01G241000	chr6D	85.326	184	21	4	1	183	331202569	331202747	4.510000e-43	185.0
33	TraesCS1B01G241000	chr3A	89.655	58	5	1	324	381	21272146	21272202	3.660000e-09	73.1
34	TraesCS1B01G241000	chr4A	93.333	45	3	0	324	368	27192806	27192850	1.700000e-07	67.6
35	TraesCS1B01G241000	chr2A	100.000	35	0	0	2618	2652	456080308	456080342	6.130000e-07	65.8
36	TraesCS1B01G241000	chr2A	100.000	35	0	0	2618	2652	456095730	456095764	6.130000e-07	65.8
37	TraesCS1B01G241000	chr2A	100.000	33	0	0	2620	2652	744087990	744087958	7.930000e-06	62.1
38	TraesCS1B01G241000	chr7D	97.143	35	1	0	2618	2652	246754541	246754507	2.850000e-05	60.2
39	TraesCS1B01G241000	chr7B	94.737	38	2	0	2617	2654	180666948	180666911	2.850000e-05	60.2

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	TraesCS1B01G241000	chr1B	428636100	428638753	2653	True	4902.0	4902	100.00000	1	2654	1	chr1B.!!$R2	2653
1	TraesCS1B01G241000	chr1D	316600188	316602400	2212	True	3559.0	3559	95.66600	429	2652	1	chr1D.!!$R2	2223
2	TraesCS1B01G241000	chr1A	397667892	397669477	1585	True	2377.0	2377	93.71500	1058	2652	1	chr1A.!!$R1	1594
3	TraesCS1B01G241000	chr1A	397699907	397700564	657	True	846.0	846	90.26900	413	1060	1	chr1A.!!$R2	647
4	TraesCS1B01G241000	chr5D	35803894	35804955	1061	False	1164.0	1164	86.86700	1571	2608	1	chr5D.!!$F1	1037
5	TraesCS1B01G241000	chr5B	26636520	26642598	6078	True	688.0	1050	82.73975	1085	2602	4	chr5B.!!$R2	1517
6	TraesCS1B01G241000	chr5A	24354082	24355105	1023	False	1022.0	1022	84.98100	1584	2614	1	chr5A.!!$F1	1030
7	TraesCS1B01G241000	chr5A	23900566	23901275	709	True	346.0	483	87.63300	1463	2122	2	chr5A.!!$R1	659
8	TraesCS1B01G241000	chrUn	389867010	389867533	523	True	527.0	527	85.30500	2097	2605	1	chrUn.!!$R1	508
9	TraesCS1B01G241000	chrUn	323956091	323957054	963	True	383.0	387	81.62950	1085	1975	2	chrUn.!!$R2	890
10	TraesCS1B01G241000	chr2B	8991730	8992604	874	True	270.0	344	95.12400	1	390	2	chr2B.!!$R1	389
11	TraesCS1B01G241000	chr6B	607489831	607490465	634	False	245.5	326	94.77900	1	394	2	chr6B.!!$F1	393

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
571	1314	0.037326	ATTGTGTCCGATCGTGTGCT	60.037	50.0	15.09	0.0	0.0	4.4	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2071	2959	0.038983	GCAAACGGGCGTTTTACCAT	60.039	50.0	0.0	0.0	44.84	3.55	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	2.824041	GACCATGACGGCGGCAAT	60.824	61.111	23.82	8.74	39.03	3.56
138	140	3.656045	GGTGGGTTTGCGGTGTCG	61.656	66.667	0.00	0.00	39.81	4.35
162	164	1.464608	CTGTAGCAACACATCCAACGG	59.535	52.381	0.00	0.00	0.00	4.44
165	167	2.560861	CAACACATCCAACGGCGG	59.439	61.111	13.24	0.00	0.00	6.13
390	1118	4.129737	GACGCCTAGCAGTCGCCA	62.130	66.667	1.01	0.00	39.83	5.69
391	1119	3.432051	GACGCCTAGCAGTCGCCAT	62.432	63.158	1.01	0.00	39.83	4.40
392	1120	2.071844	GACGCCTAGCAGTCGCCATA	62.072	60.000	1.01	0.00	39.83	2.74
394	1122	0.319900	CGCCTAGCAGTCGCCATAAT	60.320	55.000	0.00	0.00	39.83	1.28
395	1123	1.433534	GCCTAGCAGTCGCCATAATC	58.566	55.000	0.00	0.00	39.83	1.75
396	1124	1.001406	GCCTAGCAGTCGCCATAATCT	59.999	52.381	0.00	0.00	39.83	2.40
397	1125	2.548920	GCCTAGCAGTCGCCATAATCTT	60.549	50.000	0.00	0.00	39.83	2.40
398	1126	3.062763	CCTAGCAGTCGCCATAATCTTG	58.937	50.000	0.00	0.00	39.83	3.02
399	1127	2.698855	AGCAGTCGCCATAATCTTGT	57.301	45.000	0.00	0.00	39.83	3.16
400	1128	2.991250	AGCAGTCGCCATAATCTTGTT	58.009	42.857	0.00	0.00	39.83	2.83
401	1129	4.137116	AGCAGTCGCCATAATCTTGTTA	57.863	40.909	0.00	0.00	39.83	2.41
402	1130	4.122776	AGCAGTCGCCATAATCTTGTTAG	58.877	43.478	0.00	0.00	39.83	2.34
403	1131	3.871594	GCAGTCGCCATAATCTTGTTAGT	59.128	43.478	0.00	0.00	0.00	2.24
404	1132	5.047847	GCAGTCGCCATAATCTTGTTAGTA	58.952	41.667	0.00	0.00	0.00	1.82
405	1133	5.050972	GCAGTCGCCATAATCTTGTTAGTAC	60.051	44.000	0.00	0.00	0.00	2.73
406	1134	6.040247	CAGTCGCCATAATCTTGTTAGTACA	58.960	40.000	0.00	0.00	0.00	2.90
407	1135	6.701841	CAGTCGCCATAATCTTGTTAGTACAT	59.298	38.462	0.00	0.00	33.44	2.29
408	1136	6.701841	AGTCGCCATAATCTTGTTAGTACATG	59.298	38.462	0.00	0.00	33.44	3.21
409	1137	5.465390	TCGCCATAATCTTGTTAGTACATGC	59.535	40.000	0.00	0.00	33.44	4.06
410	1138	5.612492	CGCCATAATCTTGTTAGTACATGCG	60.612	44.000	0.00	0.00	33.44	4.73
411	1139	5.679906	CCATAATCTTGTTAGTACATGCGC	58.320	41.667	0.00	0.00	33.44	6.09
437	1171	3.119743	TCGTACGAATGTCGGATTTGTCT	60.120	43.478	17.11	0.00	45.59	3.41
556	1299	5.365021	AGTGAAATGGAGCTAGCTATTGT	57.635	39.130	19.38	6.01	0.00	2.71
571	1314	0.037326	ATTGTGTCCGATCGTGTGCT	60.037	50.000	15.09	0.00	0.00	4.40
586	1329	0.101399	GTGCTGGACGATCGATGAGT	59.899	55.000	24.34	2.12	0.00	3.41
623	1366	2.671396	CGAACGAAACCCAATCGAATCT	59.329	45.455	2.65	0.00	42.76	2.40
628	1371	4.506654	ACGAAACCCAATCGAATCTAATCG	59.493	41.667	2.65	0.00	42.76	3.34
891	1641	2.033550	AGCTAAGCAACTCGATCTACCG	59.966	50.000	0.00	0.00	0.00	4.02
907	1657	0.171903	ACCGCTTACAATACGTCGCT	59.828	50.000	0.00	0.00	0.00	4.93
908	1658	0.844503	CCGCTTACAATACGTCGCTC	59.155	55.000	0.00	0.00	0.00	5.03
940	1690	3.713764	TCTCTTCCTTCCAATCCATCTCC	59.286	47.826	0.00	0.00	0.00	3.71
1053	1803	3.849951	CTCCCGCGCCACCATACT	61.850	66.667	0.00	0.00	0.00	2.12
1200	1950	3.986006	GTCCACCACGACGGCTCA	61.986	66.667	0.00	0.00	39.03	4.26
1338	2088	3.793144	CTCAACCTCGCGCTTGCC	61.793	66.667	5.56	0.00	34.11	4.52
1340	2090	4.389576	CAACCTCGCGCTTGCCAC	62.390	66.667	5.56	0.00	34.11	5.01
1545	2295	1.591594	CCATGAAGCGTATCGGCGT	60.592	57.895	6.85	0.00	38.18	5.68
1733	2604	7.886629	TTTCCTTTCTACGCTTCCTATACTA	57.113	36.000	0.00	0.00	0.00	1.82
1734	2605	8.474710	TTTCCTTTCTACGCTTCCTATACTAT	57.525	34.615	0.00	0.00	0.00	2.12
1735	2606	9.578576	TTTCCTTTCTACGCTTCCTATACTATA	57.421	33.333	0.00	0.00	0.00	1.31
1736	2607	9.750783	TTCCTTTCTACGCTTCCTATACTATAT	57.249	33.333	0.00	0.00	0.00	0.86
1737	2608	9.175312	TCCTTTCTACGCTTCCTATACTATATG	57.825	37.037	0.00	0.00	0.00	1.78
1738	2609	7.916450	CCTTTCTACGCTTCCTATACTATATGC	59.084	40.741	0.00	0.00	0.00	3.14
1874	2746	2.663826	AGAGCTTTAGCAAGTCTCCG	57.336	50.000	4.33	0.00	45.16	4.63
2025	2908	7.029563	GGAAAACTCATTTATGTACTGCAAGG	58.970	38.462	0.00	0.00	39.30	3.61
2092	2986	0.662077	GGTAAAACGCCCGTTTGCTG	60.662	55.000	18.08	0.00	46.22	4.41
2122	3016	3.451178	TGTAGCAGGATTGGGAGTAGAAC	59.549	47.826	0.00	0.00	0.00	3.01
2152	3046	2.338500	TGATGCACGCGTAATTGTGTA	58.662	42.857	13.44	0.00	38.36	2.90
2174	3068	1.488393	GCTGCCTAAAGGTCTGGAGAT	59.512	52.381	0.00	0.00	37.57	2.75
2257	3151	5.424121	TCTTTCAGCTAAAACTGCAGTTC	57.576	39.130	31.20	18.83	37.25	3.01
2348	3252	5.049405	GTCCTTGATGTAACCAGTCAAGTTG	60.049	44.000	11.88	0.00	44.50	3.16
2354	3258	4.121317	TGTAACCAGTCAAGTTGTAACCG	58.879	43.478	2.11	0.00	0.00	4.44
2614	3544	0.535335	ATATGACACCGACAAGGCGT	59.465	50.000	0.00	0.00	46.52	5.68
2652	3582	0.178855	TAGGGGGTGCTAACCTGGTT	60.179	55.000	17.44	17.44	46.70	3.67
2653	3583	1.304134	GGGGGTGCTAACCTGGTTG	60.304	63.158	22.04	12.54	46.70	3.77

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
33	34	3.003173	CTCACCGAGGCCCCTCAA	61.003	66.667	14.28	0.00	42.86	3.02
43	44	4.034258	GTGGTCGACGCTCACCGA	62.034	66.667	9.92	0.00	41.02	4.69
138	140	1.425428	GATGTGTTGCTACAGCCGC	59.575	57.895	0.00	0.00	41.18	6.53
390	1118	5.051039	CGTGCGCATGTACTAACAAGATTAT	60.051	40.000	21.57	0.00	39.58	1.28
391	1119	4.266739	CGTGCGCATGTACTAACAAGATTA	59.733	41.667	21.57	0.00	39.58	1.75
392	1120	3.062099	CGTGCGCATGTACTAACAAGATT	59.938	43.478	21.57	0.00	39.58	2.40
394	1122	1.989864	CGTGCGCATGTACTAACAAGA	59.010	47.619	21.57	0.00	39.58	3.02
395	1123	1.724623	ACGTGCGCATGTACTAACAAG	59.275	47.619	32.82	0.58	39.58	3.16
396	1124	1.722464	GACGTGCGCATGTACTAACAA	59.278	47.619	33.68	0.00	39.58	2.83
397	1125	1.342555	GACGTGCGCATGTACTAACA	58.657	50.000	33.68	0.00	40.69	2.41
398	1126	0.293723	CGACGTGCGCATGTACTAAC	59.706	55.000	33.68	19.96	0.00	2.34
399	1127	0.109643	ACGACGTGCGCATGTACTAA	60.110	50.000	33.68	0.00	46.04	2.24
400	1128	0.726256	TACGACGTGCGCATGTACTA	59.274	50.000	33.68	21.87	46.04	1.82
401	1129	0.795735	GTACGACGTGCGCATGTACT	60.796	55.000	33.68	22.86	46.04	2.73
402	1130	1.622269	GTACGACGTGCGCATGTAC	59.378	57.895	33.68	26.13	46.04	2.90
403	1131	1.864314	CGTACGACGTGCGCATGTA	60.864	57.895	33.68	20.33	46.04	2.29
404	1132	3.169924	CGTACGACGTGCGCATGT	61.170	61.111	34.10	34.10	46.04	3.21
405	1133	1.739093	ATTCGTACGACGTGCGCATG	61.739	55.000	29.69	27.53	46.04	4.06
406	1134	1.515519	ATTCGTACGACGTGCGCAT	60.516	52.632	29.69	23.22	46.04	4.73
407	1135	2.126773	ATTCGTACGACGTGCGCA	60.127	55.556	29.69	22.02	46.04	6.09
408	1136	2.312061	CATTCGTACGACGTGCGC	59.688	61.111	29.69	0.00	46.04	6.09
409	1137	1.617179	GACATTCGTACGACGTGCG	59.383	57.895	28.86	28.86	43.14	5.34
410	1138	1.617179	CGACATTCGTACGACGTGC	59.383	57.895	19.36	8.63	43.14	5.34
411	1139	0.179217	TCCGACATTCGTACGACGTG	60.179	55.000	19.36	20.85	43.14	4.49
556	1299	2.261361	CCAGCACACGATCGGACA	59.739	61.111	20.98	0.00	0.00	4.02
571	1314	1.064134	CGCACTCATCGATCGTCCA	59.936	57.895	15.94	0.00	0.00	4.02
586	1329	2.452105	GTTCGGTTTGTTTTAAGCGCA	58.548	42.857	11.47	0.00	45.64	6.09
623	1366	5.168569	AGAGACAGCAAAACGATTCGATTA	58.831	37.500	13.95	0.00	0.00	1.75
628	1371	2.473049	GCGAGAGACAGCAAAACGATTC	60.473	50.000	0.00	0.00	0.00	2.52
733	1476	1.268437	GCAAGCTTGCGATTCATCTCC	60.268	52.381	33.75	6.12	45.11	3.71
891	1641	3.436496	AGAAGAGCGACGTATTGTAAGC	58.564	45.455	0.00	0.00	35.32	3.09
907	1657	5.398236	TGGAAGGAAGAGAGAAGAAGAAGA	58.602	41.667	0.00	0.00	0.00	2.87
908	1658	5.736951	TGGAAGGAAGAGAGAAGAAGAAG	57.263	43.478	0.00	0.00	0.00	2.85
940	1690	2.613223	GGTGGGAAGGAGAAGAAGAACG	60.613	54.545	0.00	0.00	0.00	3.95
1053	1803	2.699768	CGACGTGGCGGTAGGGTAA	61.700	63.158	0.00	0.00	0.00	2.85
1310	2060	1.653151	GAGGTTGAGCCCACGAATAC	58.347	55.000	0.00	0.00	38.26	1.89
1338	2088	2.514592	AGCCGATTGCATCCGGTG	60.515	61.111	22.74	0.00	46.84	4.94
1749	2620	9.298250	AGCGACAAAGGATAAAGAGACTATATA	57.702	33.333	0.00	0.00	0.00	0.86
1750	2621	8.184304	AGCGACAAAGGATAAAGAGACTATAT	57.816	34.615	0.00	0.00	0.00	0.86
1751	2622	7.502895	AGAGCGACAAAGGATAAAGAGACTATA	59.497	37.037	0.00	0.00	0.00	1.31
1874	2746	0.963355	TTATGGTTTGCTGCCCGGTC	60.963	55.000	0.00	0.00	0.00	4.79
1981	2854	9.959721	AGTTTTCCTCAGTTATCTGCTATTTTA	57.040	29.630	0.00	0.00	41.10	1.52
2071	2959	0.038983	GCAAACGGGCGTTTTACCAT	60.039	50.000	0.00	0.00	44.84	3.55
2072	2960	1.102222	AGCAAACGGGCGTTTTACCA	61.102	50.000	0.00	0.00	44.84	3.25
2092	2986	2.893682	AATCCTGCTACAAGCCGGGC	62.894	60.000	12.11	12.11	44.53	6.13
2122	3016	1.678360	GCGTGCATCAACAAGTTCAG	58.322	50.000	0.00	0.00	0.00	3.02
2152	3046	1.280421	CTCCAGACCTTTAGGCAGCTT	59.720	52.381	0.00	0.00	39.32	3.74
2348	3252	6.441274	TCGTTCCATTACATAGATCGGTTAC	58.559	40.000	0.00	0.00	0.00	2.50
2354	3258	8.612619	ACAATGTTTCGTTCCATTACATAGATC	58.387	33.333	0.00	0.00	30.41	2.75
2454	3373	3.181480	ACACATTTCCGACCAAAACAAGG	60.181	43.478	0.00	0.00	0.00	3.61
2461	3380	1.539388	GATGCACACATTTCCGACCAA	59.461	47.619	0.00	0.00	36.35	3.67
2614	3544	0.762418	AATCCAGGACACCGTCACAA	59.238	50.000	0.00	0.00	33.68	3.33

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.