AutoCloner

Multiple sequence alignment - TraesCS1B01G033800

Loading Multiple Alignment...

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	TraesCS1B01G033800	chr1B	100.000	2231	0	0	1	2231	16461616	16463846	0.000000e+00	4120.0
1	TraesCS1B01G033800	chr1A	91.416	1561	112	11	682	2231	22660299	22658750	0.000000e+00	2121.0
2	TraesCS1B01G033800	chr1A	98.793	580	7	0	1	580	111984882	111985461	0.000000e+00	1033.0
3	TraesCS1B01G033800	chr1A	97.938	97	2	0	578	674	22660739	22660643	3.810000e-38	169.0
4	TraesCS1B01G033800	chr5A	99.135	578	5	0	1	578	29644	30221	0.000000e+00	1040.0
5	TraesCS1B01G033800	chr5A	83.607	244	29	4	351	583	675531100	675531343	3.730000e-53	219.0
6	TraesCS1B01G033800	chr7B	98.469	588	3	4	1	587	5928874	5929456	0.000000e+00	1031.0
7	TraesCS1B01G033800	chr7B	84.685	222	15	6	578	798	94809525	94809322	1.040000e-48	204.0
8	TraesCS1B01G033800	chr4A	98.787	577	6	1	1	576	641295868	641295292	0.000000e+00	1026.0
9	TraesCS1B01G033800	chr4A	78.095	420	69	18	166	572	116327570	116327979	6.150000e-61	244.0
10	TraesCS1B01G033800	chr3B	98.246	570	10	0	1	570	647899114	647898545	0.000000e+00	998.0
11	TraesCS1B01G033800	chr2B	98.893	542	5	1	1	541	587240324	587240865	0.000000e+00	966.0
12	TraesCS1B01G033800	chr2B	93.274	223	13	2	578	799	636759423	636759202	5.940000e-86	327.0
13	TraesCS1B01G033800	chr1D	88.280	657	65	10	798	1449	10955773	10956422	0.000000e+00	776.0
14	TraesCS1B01G033800	chr1D	83.502	691	76	19	1503	2178	10956567	10957234	5.270000e-171	610.0
15	TraesCS1B01G033800	chr1D	91.441	222	13	3	583	799	188444272	188444052	1.290000e-77	300.0
16	TraesCS1B01G033800	chr1D	90.583	223	19	2	578	799	391288770	391288991	6.020000e-76	294.0
17	TraesCS1B01G033800	chr1D	89.545	220	12	4	580	798	33580551	33580760	3.650000e-68	268.0
18	TraesCS1B01G033800	chr6A	93.373	498	30	2	76	570	40918505	40919002	0.000000e+00	734.0
19	TraesCS1B01G033800	chr6A	97.619	42	1	0	6	47	40918462	40918503	3.070000e-09	73.1
20	TraesCS1B01G033800	chr4D	91.143	350	14	4	221	567	503520252	503520587	2.020000e-125	459.0
21	TraesCS1B01G033800	chr4D	86.643	277	28	8	42	310	188708025	188707750	4.660000e-77	298.0
22	TraesCS1B01G033800	chr3D	91.928	223	14	4	578	799	458296771	458296552	2.150000e-80	309.0
23	TraesCS1B01G033800	chr7A	91.818	220	16	2	578	796	706428642	706428860	2.780000e-79	305.0
24	TraesCS1B01G033800	chr4B	86.643	277	28	8	42	310	203204141	203203866	4.660000e-77	298.0
25	TraesCS1B01G033800	chr5D	88.739	222	22	3	578	798	439657356	439657575	3.650000e-68	268.0

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	TraesCS1B01G033800	chr1B	16461616	16463846	2230	False	4120.00	4120	100.000	1	2231	1	chr1B.!!$F1	2230
1	TraesCS1B01G033800	chr1A	22658750	22660739	1989	True	1145.00	2121	94.677	578	2231	2	chr1A.!!$R1	1653
2	TraesCS1B01G033800	chr1A	111984882	111985461	579	False	1033.00	1033	98.793	1	580	1	chr1A.!!$F1	579
3	TraesCS1B01G033800	chr5A	29644	30221	577	False	1040.00	1040	99.135	1	578	1	chr5A.!!$F1	577
4	TraesCS1B01G033800	chr7B	5928874	5929456	582	False	1031.00	1031	98.469	1	587	1	chr7B.!!$F1	586
5	TraesCS1B01G033800	chr4A	641295292	641295868	576	True	1026.00	1026	98.787	1	576	1	chr4A.!!$R1	575
6	TraesCS1B01G033800	chr3B	647898545	647899114	569	True	998.00	998	98.246	1	570	1	chr3B.!!$R1	569
7	TraesCS1B01G033800	chr2B	587240324	587240865	541	False	966.00	966	98.893	1	541	1	chr2B.!!$F1	540
8	TraesCS1B01G033800	chr1D	10955773	10957234	1461	False	693.00	776	85.891	798	2178	2	chr1D.!!$F3	1380
9	TraesCS1B01G033800	chr6A	40918462	40919002	540	False	403.55	734	95.496	6	570	2	chr6A.!!$F1	564

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
898	1242	0.032017	ATCCCGTCTAGCCCTTGACT	60.032	55.0	7.95	0.0	34.08	3.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1980	2434	0.975887	ACACAATGGCCAATGGTTCC	59.024	50.0	24.49	0.0	0.0	3.62	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
103	104	1.349357	GGAGCTTCTTGGTCTGGTTCT	59.651	52.381	0.00	0.00	42.40	3.01
639	643	7.435488	CCAGAATAGATACCTAGACAAAACACG	59.565	40.741	0.00	0.00	0.00	4.49
651	655	6.903883	AGACAAAACACGCTCGATATATTT	57.096	33.333	0.00	0.00	0.00	1.40
689	1029	7.439056	TGCATCTTATATGTCATGTATATGCCG	59.561	37.037	21.67	4.98	34.21	5.69
705	1045	0.246086	GCCGCACAATTCCATTTCCA	59.754	50.000	0.00	0.00	0.00	3.53
757	1097	7.410174	TGTCTATCTTGGGTGGTAATTTGATT	58.590	34.615	0.00	0.00	0.00	2.57
831	1171	7.672983	AAGTTATATGCCGATATCAACCAAG	57.327	36.000	3.12	0.00	0.00	3.61
867	1209	3.002791	CAAGCTCGAGGTTCATTTAGCA	58.997	45.455	26.13	0.00	32.86	3.49
872	1214	3.997021	CTCGAGGTTCATTTAGCAACAGT	59.003	43.478	3.91	0.00	0.00	3.55
873	1215	4.385825	TCGAGGTTCATTTAGCAACAGTT	58.614	39.130	0.00	0.00	0.00	3.16
884	1228	2.699954	AGCAACAGTTTGAGTATCCCG	58.300	47.619	0.00	0.00	34.24	5.14
892	1236	1.700955	TTGAGTATCCCGTCTAGCCC	58.299	55.000	0.00	0.00	0.00	5.19
896	1240	1.217183	AGTATCCCGTCTAGCCCTTGA	59.783	52.381	0.00	0.00	0.00	3.02
898	1242	0.032017	ATCCCGTCTAGCCCTTGACT	60.032	55.000	7.95	0.00	34.08	3.41
902	1246	1.267261	CCGTCTAGCCCTTGACTATCG	59.733	57.143	7.95	0.00	34.08	2.92
961	1305	9.906660	TTAATTAGAAACACAACTTGCTATTGG	57.093	29.630	0.00	0.00	0.00	3.16
990	1334	3.813166	AGTGTATTGTTTTGTAGCGTGCT	59.187	39.130	0.00	0.00	0.00	4.40
996	1340	3.920446	TGTTTTGTAGCGTGCTAGATCA	58.080	40.909	0.96	0.00	0.00	2.92
1015	1359	1.532604	AACGATGAGCTCCACGGACA	61.533	55.000	25.28	3.39	0.00	4.02
1039	1383	2.285668	CCCCTGGAGGCCTCTTCA	60.286	66.667	31.36	20.56	0.00	3.02
1096	1440	1.082766	TCCATCAAGGAGGCCAGGA	59.917	57.895	5.01	0.00	43.07	3.86
1106	1450	1.492176	GGAGGCCAGGAAGATCATTCA	59.508	52.381	5.01	0.00	0.00	2.57
1111	1455	3.614092	GCCAGGAAGATCATTCACAAGA	58.386	45.455	0.00	0.00	0.00	3.02
1122	1466	3.565482	TCATTCACAAGAACAAGCCTGAC	59.435	43.478	0.00	0.00	36.39	3.51
1127	1471	2.146342	CAAGAACAAGCCTGACGATGT	58.854	47.619	0.00	0.00	0.00	3.06
1147	1491	1.179152	TATCGTCGTTCTCCCAGCAA	58.821	50.000	0.00	0.00	0.00	3.91
1181	1525	0.178992	CTGGACTTGAGGCCCAAACA	60.179	55.000	0.00	2.76	33.76	2.83
1189	1533	3.683937	GGCCCAAACATGTGCGCT	61.684	61.111	9.73	0.00	0.00	5.92
1206	1550	1.332904	CGCTTCTTTGTTGACACCGTC	60.333	52.381	0.00	0.00	0.00	4.79
1267	1611	2.492881	CAAAGGAATGTATGCCTGCACA	59.507	45.455	0.00	0.00	34.00	4.57
1293	1637	7.789341	TGCATGTTCGTGAATACATTTTTAC	57.211	32.000	0.00	0.00	32.88	2.01
1326	1670	1.656652	AATACAGGCATGTCGAGCAC	58.343	50.000	7.56	0.00	41.01	4.40
1376	1725	9.405587	ACTTATGTGTATGTTTTTGCATTGTAC	57.594	29.630	0.00	0.00	0.00	2.90
1401	1750	8.317679	ACTTTTAGTTTGATGAGAGAGTGCTAT	58.682	33.333	0.00	0.00	0.00	2.97
1405	1754	6.676950	AGTTTGATGAGAGAGTGCTATATCG	58.323	40.000	0.00	0.00	0.00	2.92
1406	1755	6.488344	AGTTTGATGAGAGAGTGCTATATCGA	59.512	38.462	0.00	0.00	0.00	3.59
1460	1809	3.465296	GAGTGGCATGCGCAGATGC	62.465	63.158	24.31	24.31	46.82	3.91
1477	1826	0.478072	TGCAGTCCATTTGGTGTCCT	59.522	50.000	0.00	0.00	36.34	3.85
1516	1956	4.007659	ACATGTGACCGGAAAAACCTATC	58.992	43.478	9.46	0.00	36.31	2.08
1527	1967	7.336176	ACCGGAAAAACCTATCTTAATGACTTC	59.664	37.037	9.46	0.00	36.31	3.01
1545	1985	5.880332	TGACTTCAGCTATAAAATGTCACCC	59.120	40.000	0.00	0.00	0.00	4.61
1575	2015	5.584253	TCTAGAGTTCTTACATGGACTGC	57.416	43.478	0.00	0.00	0.00	4.40
1580	2020	0.172578	TCTTACATGGACTGCGACCG	59.827	55.000	0.00	0.00	0.00	4.79
1610	2050	6.346518	CGCTGTTGTTTTGTTTTGTTTTCTCT	60.347	34.615	0.00	0.00	0.00	3.10
1640	2088	8.622948	TTCCTTTCTTTATCTTGTCTCTTTCC	57.377	34.615	0.00	0.00	0.00	3.13
1791	2242	8.006298	TCCAGAAATGTGTCAACAACTTAATT	57.994	30.769	0.00	0.00	40.46	1.40
1894	2345	3.305676	CGTCATCTCGGATGAAGCCTATT	60.306	47.826	15.34	0.00	0.00	1.73
1951	2404	1.853963	ACATCGACTAGAAGTGGGCT	58.146	50.000	0.00	0.00	28.50	5.19
2007	2461	2.988684	GCCATTGTGTTCGCCCCA	60.989	61.111	0.00	0.00	0.00	4.96
2115	2569	9.693739	ATGTCATAAACTATATGGTTTGGTGAA	57.306	29.630	23.14	16.60	39.39	3.18
2123	2582	6.780522	ACTATATGGTTTGGTGAAGGTTGTTT	59.219	34.615	0.00	0.00	0.00	2.83
2206	2666	0.957888	GAAGCCCACTGCAACTCCTC	60.958	60.000	0.00	0.00	44.83	3.71
2227	2687	8.315391	TCCTCAAGAAATTTAGCGATGATATG	57.685	34.615	0.00	0.00	0.00	1.78

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
103	104	3.165875	AGATCAAGAACCAGACCTTCGA	58.834	45.455	0.00	0.00	0.00	3.71
639	643	7.356476	GCAAAAGCACGTAAAAATATATCGAGC	60.356	37.037	5.45	5.45	38.08	5.03
651	655	7.757526	ACATATAAGATGCAAAAGCACGTAAA	58.242	30.769	0.00	0.00	0.00	2.01
674	678	2.611225	TGTGCGGCATATACATGACA	57.389	45.000	5.72	0.00	40.60	3.58
675	679	4.466828	GAATTGTGCGGCATATACATGAC	58.533	43.478	5.72	0.00	36.76	3.06
679	683	2.924421	TGGAATTGTGCGGCATATACA	58.076	42.857	5.72	0.00	0.00	2.29
680	684	4.503741	AATGGAATTGTGCGGCATATAC	57.496	40.909	5.72	0.00	33.44	1.47
689	1029	8.891671	ATTATAACATGGAAATGGAATTGTGC	57.108	30.769	0.00	0.00	36.10	4.57
723	1063	7.182060	ACCACCCAAGATAGACATATTTGTTT	58.818	34.615	0.00	0.00	35.79	2.83
727	1067	9.936329	AAATTACCACCCAAGATAGACATATTT	57.064	29.630	0.00	0.00	0.00	1.40
746	1086	8.651588	CGTCAGAGCTCATATAATCAAATTACC	58.348	37.037	17.77	0.00	0.00	2.85
757	1097	4.379918	GCATAGCACGTCAGAGCTCATATA	60.380	45.833	17.77	0.00	43.14	0.86
794	1134	9.559732	TCGGCATATAACTTACTACAAGTACTA	57.440	33.333	0.00	0.00	28.93	1.82
795	1135	8.455903	TCGGCATATAACTTACTACAAGTACT	57.544	34.615	0.00	0.00	28.93	2.73
805	1145	8.542497	TTGGTTGATATCGGCATATAACTTAC	57.458	34.615	0.00	0.00	0.00	2.34
818	1158	1.934589	TCGTGGCTTGGTTGATATCG	58.065	50.000	0.00	0.00	0.00	2.92
831	1171	3.685058	GAGCTTGTTAATTGATCGTGGC	58.315	45.455	0.00	0.00	0.00	5.01
867	1209	4.381718	GCTAGACGGGATACTCAAACTGTT	60.382	45.833	0.00	0.00	0.00	3.16
872	1214	2.037144	GGGCTAGACGGGATACTCAAA	58.963	52.381	0.00	0.00	0.00	2.69
873	1215	1.217183	AGGGCTAGACGGGATACTCAA	59.783	52.381	0.00	0.00	0.00	3.02
884	1228	4.076394	AGATCGATAGTCAAGGGCTAGAC	58.924	47.826	0.00	0.00	35.02	2.59
896	1240	8.638629	ATGCTAACTAGGTAAAGATCGATAGT	57.361	34.615	0.00	0.00	37.40	2.12
898	1242	8.304596	CCAATGCTAACTAGGTAAAGATCGATA	58.695	37.037	0.00	0.00	0.00	2.92
902	1246	9.609346	TTTACCAATGCTAACTAGGTAAAGATC	57.391	33.333	10.16	0.00	45.06	2.75
961	1305	6.534934	GCTACAAAACAATACACTGAGCTAC	58.465	40.000	0.00	0.00	0.00	3.58
990	1334	2.033424	CGTGGAGCTCATCGTTGATCTA	59.967	50.000	17.19	0.00	28.65	1.98
996	1340	1.215647	GTCCGTGGAGCTCATCGTT	59.784	57.895	17.19	0.00	0.00	3.85
1015	1359	3.580319	GCCTCCAGGGGTGGTGTT	61.580	66.667	5.37	0.00	38.49	3.32
1039	1383	1.202582	CCACGACTTCGACTCCTCAAT	59.797	52.381	5.47	0.00	43.02	2.57
1096	1440	5.048224	CAGGCTTGTTCTTGTGAATGATCTT	60.048	40.000	0.00	0.00	34.40	2.40
1106	1450	2.146342	CATCGTCAGGCTTGTTCTTGT	58.854	47.619	0.00	0.00	0.00	3.16
1127	1471	1.179152	TGCTGGGAGAACGACGATAA	58.821	50.000	0.00	0.00	0.00	1.75
1181	1525	1.675483	TGTCAACAAAGAAGCGCACAT	59.325	42.857	11.47	0.00	0.00	3.21
1189	1533	0.653636	GCGACGGTGTCAACAAAGAA	59.346	50.000	0.00	0.00	32.09	2.52
1206	1550	1.597027	AGTGAAGGGTGTTTCGGCG	60.597	57.895	0.00	0.00	0.00	6.46
1242	1586	1.288932	AGGCATACATTCCTTTGGGCT	59.711	47.619	0.00	0.00	0.00	5.19
1246	1590	2.492881	TGTGCAGGCATACATTCCTTTG	59.507	45.455	0.00	0.00	0.00	2.77
1267	1611	7.887996	AAAAATGTATTCACGAACATGCATT	57.112	28.000	0.00	0.00	36.47	3.56
1293	1637	8.145767	ACATGCCTGTATTTATTCATTCATTGG	58.854	33.333	0.00	0.00	32.49	3.16
1310	1654	0.174389	CTAGTGCTCGACATGCCTGT	59.826	55.000	0.00	0.00	38.67	4.00
1334	1683	5.642491	CACATAAGTAGAGATCCATGCCATG	59.358	44.000	0.00	0.00	0.00	3.66
1376	1725	8.715191	ATAGCACTCTCTCATCAAACTAAAAG	57.285	34.615	0.00	0.00	0.00	2.27
1425	1774	3.612860	CCACTCTAATTTTGAGGACGACG	59.387	47.826	11.63	0.00	35.98	5.12
1460	1809	2.867109	AGAGGACACCAAATGGACTG	57.133	50.000	6.42	0.00	38.94	3.51
1465	1814	2.076863	GGTCGAAGAGGACACCAAATG	58.923	52.381	0.00	0.00	36.95	2.32
1477	1826	3.383505	ACATGTATGAATCCGGTCGAAGA	59.616	43.478	0.00	0.00	0.00	2.87
1527	1967	5.331902	CGTTTGGGTGACATTTTATAGCTG	58.668	41.667	0.00	0.00	0.00	4.24
1545	1985	6.183360	CCATGTAAGAACTCTAGAAGCGTTTG	60.183	42.308	0.00	0.00	0.00	2.93
1580	2020	2.271821	AACAAAACAACAGCGGACAC	57.728	45.000	0.00	0.00	0.00	3.67
1640	2088	6.861572	GGAGAATAGGAAAAGAAAAACCAACG	59.138	38.462	0.00	0.00	0.00	4.10
1894	2345	1.731613	GTCGTGGCGTGTCGATTGA	60.732	57.895	0.00	0.00	38.32	2.57
1951	2404	1.500474	CCTACCATTGCAGAGGAGGA	58.500	55.000	12.87	0.00	0.00	3.71
1980	2434	0.975887	ACACAATGGCCAATGGTTCC	59.024	50.000	24.49	0.00	0.00	3.62
2007	2461	5.263599	TCCTTTTTGTACATGATGCCAGAT	58.736	37.500	0.00	0.00	0.00	2.90
2059	2513	6.485313	CGTTTCAATTGGATTGGCTAGGTATA	59.515	38.462	5.42	0.00	40.61	1.47

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.