AutoCloner

Multiple sequence alignment - TraesCS1D01G008600

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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	TraesCS1D01G008600	chr1D	100.000	2880	0	0	1	2880	4340666	4343545	0.000000e+00	5319
1	TraesCS1D01G008600	chr1D	97.052	2883	58	18	1	2880	7157708	7154850	0.000000e+00	4828
2	TraesCS1D01G008600	chr1D	86.893	1236	104	33	741	1952	99010	100211	0.000000e+00	1332
3	TraesCS1D01G008600	chr1D	82.570	1572	208	42	1237	2778	5139230	5140765	0.000000e+00	1325
4	TraesCS1D01G008600	chr1D	83.019	1431	176	32	1367	2778	5356876	5358258	0.000000e+00	1234
5	TraesCS1D01G008600	chr1D	81.845	1377	169	44	1414	2778	3710385	3709078	0.000000e+00	1083
6	TraesCS1D01G008600	chr1D	84.230	818	95	8	1996	2808	100219	101007	0.000000e+00	765
7	TraesCS1D01G008600	chr1D	83.175	844	114	20	742	1563	5138785	5139622	0.000000e+00	747
8	TraesCS1D01G008600	chr1D	86.284	401	47	5	339	732	98696	99095	2.330000e-116	429
9	TraesCS1D01G008600	chr1D	100.000	129	0	0	3144	3272	4343809	4343937	4.220000e-59	239
10	TraesCS1D01G008600	chr1D	99.130	115	1	0	3158	3272	7154615	7154501	1.190000e-49	207
11	TraesCS1D01G008600	chr1D	91.667	96	7	1	742	836	4341312	4341407	7.370000e-27	132
12	TraesCS1D01G008600	chr1D	91.667	96	7	1	742	836	7157063	7156968	7.370000e-27	132
13	TraesCS1D01G008600	chr1B	94.740	1597	81	2	1	1597	22184644	22186237	0.000000e+00	2481
14	TraesCS1D01G008600	chr1B	94.779	1494	75	2	1	1491	6438564	6437071	0.000000e+00	2324
15	TraesCS1D01G008600	chr1B	92.040	1608	110	15	1282	2880	6437343	6435745	0.000000e+00	2244
16	TraesCS1D01G008600	chr1B	90.909	1628	106	26	1282	2880	22185862	22187476	0.000000e+00	2148
17	TraesCS1D01G008600	chr1B	87.286	1227	117	21	742	1955	5521102	5519902	0.000000e+00	1365
18	TraesCS1D01G008600	chr1B	84.395	1256	160	23	742	1973	5688038	5686795	0.000000e+00	1201
19	TraesCS1D01G008600	chr1B	89.748	634	47	9	742	1360	5585822	5585192	0.000000e+00	795
20	TraesCS1D01G008600	chr1B	84.005	819	96	8	1995	2808	5584365	5583577	0.000000e+00	754
21	TraesCS1D01G008600	chr1B	84.772	591	76	10	1372	1955	5584952	5584369	6.090000e-162	580
22	TraesCS1D01G008600	chr1B	87.282	401	44	6	339	733	5688351	5687952	4.980000e-123	451
23	TraesCS1D01G008600	chr1B	96.875	128	4	0	3144	3271	6435695	6435568	7.110000e-52	215
24	TraesCS1D01G008600	chr1B	94.531	128	7	0	3144	3271	22187525	22187652	7.160000e-47	198
25	TraesCS1D01G008600	chr1B	88.816	152	15	2	583	733	5585886	5585736	5.580000e-43	185
26	TraesCS1D01G008600	chr1B	84.000	200	21	9	346	536	5586084	5585887	7.210000e-42	182
27	TraesCS1D01G008600	chr1B	87.273	110	10	4	3144	3252	7314347	7314241	4.430000e-24	122
28	TraesCS1D01G008600	chr1A	83.615	1422	166	35	1369	2778	6517555	6518921	0.000000e+00	1273
29	TraesCS1D01G008600	chr1A	82.507	1029	123	28	1414	2429	6561935	6562919	0.000000e+00	850
30	TraesCS1D01G008600	chr1A	84.644	801	86	13	2017	2808	4095906	4095134	0.000000e+00	763
31	TraesCS1D01G008600	chr1A	83.784	740	106	9	1	733	6516431	6517163	0.000000e+00	689
32	TraesCS1D01G008600	chr1A	85.435	666	76	15	742	1399	6561451	6562103	0.000000e+00	673
33	TraesCS1D01G008600	chr1A	84.987	393	50	7	347	733	4097476	4097087	1.100000e-104	390
34	TraesCS1D01G008600	chr1A	86.176	340	43	4	397	733	6561199	6561537	6.670000e-97	364
35	TraesCS1D01G008600	chrUn	100.000	385	0	0	2312	2696	480721449	480721833	0.000000e+00	712

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	TraesCS1D01G008600	chr1D	4340666	4343937	3271	False	1896.666667	5319	97.222333	1	3272	3	chr1D.!!$F3	3271
1	TraesCS1D01G008600	chr1D	7154501	7157708	3207	True	1722.333333	4828	95.949667	1	3272	3	chr1D.!!$R2	3271
2	TraesCS1D01G008600	chr1D	5356876	5358258	1382	False	1234.000000	1234	83.019000	1367	2778	1	chr1D.!!$F1	1411
3	TraesCS1D01G008600	chr1D	3709078	3710385	1307	True	1083.000000	1083	81.845000	1414	2778	1	chr1D.!!$R1	1364
4	TraesCS1D01G008600	chr1D	5138785	5140765	1980	False	1036.000000	1325	82.872500	742	2778	2	chr1D.!!$F4	2036
5	TraesCS1D01G008600	chr1D	98696	101007	2311	False	842.000000	1332	85.802333	339	2808	3	chr1D.!!$F2	2469
6	TraesCS1D01G008600	chr1B	22184644	22187652	3008	False	1609.000000	2481	93.393333	1	3271	3	chr1B.!!$F1	3270
7	TraesCS1D01G008600	chr1B	6435568	6438564	2996	True	1594.333333	2324	94.564667	1	3271	3	chr1B.!!$R5	3270
8	TraesCS1D01G008600	chr1B	5519902	5521102	1200	True	1365.000000	1365	87.286000	742	1955	1	chr1B.!!$R1	1213
9	TraesCS1D01G008600	chr1B	5686795	5688351	1556	True	826.000000	1201	85.838500	339	1973	2	chr1B.!!$R4	1634
10	TraesCS1D01G008600	chr1B	5583577	5586084	2507	True	499.200000	795	86.268200	346	2808	5	chr1B.!!$R3	2462
11	TraesCS1D01G008600	chr1A	6516431	6518921	2490	False	981.000000	1273	83.699500	1	2778	2	chr1A.!!$F1	2777
12	TraesCS1D01G008600	chr1A	6561199	6562919	1720	False	629.000000	850	84.706000	397	2429	3	chr1A.!!$F2	2032
13	TraesCS1D01G008600	chr1A	4095134	4097476	2342	True	576.500000	763	84.815500	347	2808	2	chr1A.!!$R1	2461

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
127	130	4.319477	CCTGAACATGAACCACAGTAAACG	60.319	45.833	0.0	0.0	0.0	3.60	F
1329	2097	3.513515	ACAACAACCACCATTTTCACAGT	59.486	39.130	0.0	0.0	0.0	3.55	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1515	2406	0.242286	TGTTGTTGCTGTTGTTGCGT	59.758	45.000	0.0	0.0	0.00	5.24	R
2708	3692	5.659440	AAAGCTGGACTTTTTCTTGACAA	57.341	34.783	0.0	0.0	46.73	3.18	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
127	130	4.319477	CCTGAACATGAACCACAGTAAACG	60.319	45.833	0.00	0.00	0.00	3.60
412	425	6.831769	AGTGACTTGTAAGCAATTACAATCG	58.168	36.000	12.51	6.39	43.80	3.34
877	904	8.270799	CACAACTAAAAAGCAACTTTGATGATG	58.729	33.333	0.00	0.00	33.64	3.07
1329	2097	3.513515	ACAACAACCACCATTTTCACAGT	59.486	39.130	0.00	0.00	0.00	3.55
1515	2406	1.693627	ACCGCAACAACCACCATTTA	58.306	45.000	0.00	0.00	0.00	1.40
1524	2418	2.785713	ACCACCATTTACGCAACAAC	57.214	45.000	0.00	0.00	0.00	3.32
1525	2419	2.025155	ACCACCATTTACGCAACAACA	58.975	42.857	0.00	0.00	0.00	3.33
1526	2420	2.034053	ACCACCATTTACGCAACAACAG	59.966	45.455	0.00	0.00	0.00	3.16
1527	2421	2.050691	CACCATTTACGCAACAACAGC	58.949	47.619	0.00	0.00	0.00	4.40
1528	2422	1.678627	ACCATTTACGCAACAACAGCA	59.321	42.857	0.00	0.00	0.00	4.41
1529	2423	2.099921	ACCATTTACGCAACAACAGCAA	59.900	40.909	0.00	0.00	0.00	3.91
1530	2424	2.470999	CCATTTACGCAACAACAGCAAC	59.529	45.455	0.00	0.00	0.00	4.17
1531	2425	2.921634	TTTACGCAACAACAGCAACA	57.078	40.000	0.00	0.00	0.00	3.33
1532	2426	2.921634	TTACGCAACAACAGCAACAA	57.078	40.000	0.00	0.00	0.00	2.83
1533	2427	2.181426	TACGCAACAACAGCAACAAC	57.819	45.000	0.00	0.00	0.00	3.32
1534	2428	0.242286	ACGCAACAACAGCAACAACA	59.758	45.000	0.00	0.00	0.00	3.33
1535	2429	1.336332	ACGCAACAACAGCAACAACAA	60.336	42.857	0.00	0.00	0.00	2.83
1536	2430	1.058979	CGCAACAACAGCAACAACAAC	59.941	47.619	0.00	0.00	0.00	3.32
1537	2431	2.064762	GCAACAACAGCAACAACAACA	58.935	42.857	0.00	0.00	0.00	3.33
1538	2432	2.478134	GCAACAACAGCAACAACAACAA	59.522	40.909	0.00	0.00	0.00	2.83
1539	2433	3.664014	GCAACAACAGCAACAACAACAAC	60.664	43.478	0.00	0.00	0.00	3.32
1540	2434	3.377346	ACAACAGCAACAACAACAACA	57.623	38.095	0.00	0.00	0.00	3.33
1541	2435	3.722147	ACAACAGCAACAACAACAACAA	58.278	36.364	0.00	0.00	0.00	2.83
1542	2436	3.492756	ACAACAGCAACAACAACAACAAC	59.507	39.130	0.00	0.00	0.00	3.32
1543	2437	3.377346	ACAGCAACAACAACAACAACA	57.623	38.095	0.00	0.00	0.00	3.33
1544	2438	3.722147	ACAGCAACAACAACAACAACAA	58.278	36.364	0.00	0.00	0.00	2.83
1545	2439	3.492756	ACAGCAACAACAACAACAACAAC	59.507	39.130	0.00	0.00	0.00	3.32
1546	2440	3.492383	CAGCAACAACAACAACAACAACA	59.508	39.130	0.00	0.00	0.00	3.33
1547	2441	4.025396	CAGCAACAACAACAACAACAACAA	60.025	37.500	0.00	0.00	0.00	2.83
1548	2442	4.025313	AGCAACAACAACAACAACAACAAC	60.025	37.500	0.00	0.00	0.00	3.32
1549	2443	4.260375	GCAACAACAACAACAACAACAACA	60.260	37.500	0.00	0.00	0.00	3.33
1550	2444	5.727791	GCAACAACAACAACAACAACAACAA	60.728	36.000	0.00	0.00	0.00	2.83
1551	2445	5.396750	ACAACAACAACAACAACAACAAC	57.603	34.783	0.00	0.00	0.00	3.32
1552	2446	4.870426	ACAACAACAACAACAACAACAACA	59.130	33.333	0.00	0.00	0.00	3.33
1553	2447	5.351465	ACAACAACAACAACAACAACAACAA	59.649	32.000	0.00	0.00	0.00	2.83
1554	2448	5.396750	ACAACAACAACAACAACAACAAC	57.603	34.783	0.00	0.00	0.00	3.32
1555	2449	4.870426	ACAACAACAACAACAACAACAACA	59.130	33.333	0.00	0.00	0.00	3.33
1556	2450	5.351465	ACAACAACAACAACAACAACAACAA	59.649	32.000	0.00	0.00	0.00	2.83
1557	2451	5.396750	ACAACAACAACAACAACAACAAC	57.603	34.783	0.00	0.00	0.00	3.32
1558	2452	4.870426	ACAACAACAACAACAACAACAACA	59.130	33.333	0.00	0.00	0.00	3.33
1559	2453	5.351465	ACAACAACAACAACAACAACAACAA	59.649	32.000	0.00	0.00	0.00	2.83
1560	2454	5.396750	ACAACAACAACAACAACAACAAC	57.603	34.783	0.00	0.00	0.00	3.32
1561	2455	4.870426	ACAACAACAACAACAACAACAACA	59.130	33.333	0.00	0.00	0.00	3.33
1562	2456	5.351465	ACAACAACAACAACAACAACAACAA	59.649	32.000	0.00	0.00	0.00	2.83
1563	2457	5.396750	ACAACAACAACAACAACAACAAC	57.603	34.783	0.00	0.00	0.00	3.32
1564	2458	4.870426	ACAACAACAACAACAACAACAACA	59.130	33.333	0.00	0.00	0.00	3.33
1565	2459	5.351465	ACAACAACAACAACAACAACAACAA	59.649	32.000	0.00	0.00	0.00	2.83
1628	2552	1.099689	AACACCAACAACCGGTTCTG	58.900	50.000	19.24	17.27	37.72	3.02
1978	2923	0.179045	AAGCAGCTCGGACAGTGTTT	60.179	50.000	0.00	0.00	0.00	2.83

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
127	130	8.758633	ACTATGACGGCAACATATATAGTTTC	57.241	34.615	0.00	0.00	30.01	2.78
412	425	7.981142	TCATCGAATTCCCTTTACATGTAAAC	58.019	34.615	23.91	13.07	32.26	2.01
1329	2097	2.422597	CTGCGAGAATGGTGGTTGTTA	58.577	47.619	0.00	0.00	0.00	2.41
1515	2406	0.242286	TGTTGTTGCTGTTGTTGCGT	59.758	45.000	0.00	0.00	0.00	5.24
1524	2418	3.492383	TGTTGTTGTTGTTGTTGTTGCTG	59.508	39.130	0.00	0.00	0.00	4.41
1525	2419	3.722147	TGTTGTTGTTGTTGTTGTTGCT	58.278	36.364	0.00	0.00	0.00	3.91
1526	2420	4.207599	GTTGTTGTTGTTGTTGTTGTTGC	58.792	39.130	0.00	0.00	0.00	4.17
1527	2421	5.395325	TGTTGTTGTTGTTGTTGTTGTTG	57.605	34.783	0.00	0.00	0.00	3.33
1528	2422	5.351465	TGTTGTTGTTGTTGTTGTTGTTGTT	59.649	32.000	0.00	0.00	0.00	2.83
1529	2423	4.870426	TGTTGTTGTTGTTGTTGTTGTTGT	59.130	33.333	0.00	0.00	0.00	3.32
1530	2424	5.395325	TGTTGTTGTTGTTGTTGTTGTTG	57.605	34.783	0.00	0.00	0.00	3.33
1531	2425	5.351465	TGTTGTTGTTGTTGTTGTTGTTGTT	59.649	32.000	0.00	0.00	0.00	2.83
1532	2426	4.870426	TGTTGTTGTTGTTGTTGTTGTTGT	59.130	33.333	0.00	0.00	0.00	3.32
1533	2427	5.395325	TGTTGTTGTTGTTGTTGTTGTTG	57.605	34.783	0.00	0.00	0.00	3.33
1534	2428	5.351465	TGTTGTTGTTGTTGTTGTTGTTGTT	59.649	32.000	0.00	0.00	0.00	2.83
1535	2429	4.870426	TGTTGTTGTTGTTGTTGTTGTTGT	59.130	33.333	0.00	0.00	0.00	3.32
1536	2430	5.395325	TGTTGTTGTTGTTGTTGTTGTTG	57.605	34.783	0.00	0.00	0.00	3.33
1537	2431	5.351465	TGTTGTTGTTGTTGTTGTTGTTGTT	59.649	32.000	0.00	0.00	0.00	2.83
1538	2432	4.870426	TGTTGTTGTTGTTGTTGTTGTTGT	59.130	33.333	0.00	0.00	0.00	3.32
1539	2433	5.395325	TGTTGTTGTTGTTGTTGTTGTTG	57.605	34.783	0.00	0.00	0.00	3.33
1540	2434	5.351465	TGTTGTTGTTGTTGTTGTTGTTGTT	59.649	32.000	0.00	0.00	0.00	2.83
1541	2435	4.870426	TGTTGTTGTTGTTGTTGTTGTTGT	59.130	33.333	0.00	0.00	0.00	3.32
1542	2436	5.395325	TGTTGTTGTTGTTGTTGTTGTTG	57.605	34.783	0.00	0.00	0.00	3.33
1543	2437	5.351465	TGTTGTTGTTGTTGTTGTTGTTGTT	59.649	32.000	0.00	0.00	0.00	2.83
1544	2438	4.870426	TGTTGTTGTTGTTGTTGTTGTTGT	59.130	33.333	0.00	0.00	0.00	3.32
1545	2439	5.395325	TGTTGTTGTTGTTGTTGTTGTTG	57.605	34.783	0.00	0.00	0.00	3.33
1546	2440	5.351465	TGTTGTTGTTGTTGTTGTTGTTGTT	59.649	32.000	0.00	0.00	0.00	2.83
1547	2441	4.870426	TGTTGTTGTTGTTGTTGTTGTTGT	59.130	33.333	0.00	0.00	0.00	3.32
1548	2442	5.395325	TGTTGTTGTTGTTGTTGTTGTTG	57.605	34.783	0.00	0.00	0.00	3.33
1549	2443	5.351465	TGTTGTTGTTGTTGTTGTTGTTGTT	59.649	32.000	0.00	0.00	0.00	2.83
1550	2444	4.870426	TGTTGTTGTTGTTGTTGTTGTTGT	59.130	33.333	0.00	0.00	0.00	3.32
1551	2445	5.395325	TGTTGTTGTTGTTGTTGTTGTTG	57.605	34.783	0.00	0.00	0.00	3.33
1552	2446	5.351465	TGTTGTTGTTGTTGTTGTTGTTGTT	59.649	32.000	0.00	0.00	0.00	2.83
1553	2447	4.870426	TGTTGTTGTTGTTGTTGTTGTTGT	59.130	33.333	0.00	0.00	0.00	3.32
1554	2448	5.395325	TGTTGTTGTTGTTGTTGTTGTTG	57.605	34.783	0.00	0.00	0.00	3.33
1555	2449	5.220681	GGTTGTTGTTGTTGTTGTTGTTGTT	60.221	36.000	0.00	0.00	0.00	2.83
1556	2450	4.271291	GGTTGTTGTTGTTGTTGTTGTTGT	59.729	37.500	0.00	0.00	0.00	3.32
1557	2451	4.271049	TGGTTGTTGTTGTTGTTGTTGTTG	59.729	37.500	0.00	0.00	0.00	3.33
1558	2452	4.442706	TGGTTGTTGTTGTTGTTGTTGTT	58.557	34.783	0.00	0.00	0.00	2.83
1559	2453	4.060038	TGGTTGTTGTTGTTGTTGTTGT	57.940	36.364	0.00	0.00	0.00	3.32
1560	2454	5.604010	ATTGGTTGTTGTTGTTGTTGTTG	57.396	34.783	0.00	0.00	0.00	3.33
1561	2455	5.994668	AGAATTGGTTGTTGTTGTTGTTGTT	59.005	32.000	0.00	0.00	0.00	2.83
1562	2456	5.546526	AGAATTGGTTGTTGTTGTTGTTGT	58.453	33.333	0.00	0.00	0.00	3.32
1563	2457	6.035542	GGTAGAATTGGTTGTTGTTGTTGTTG	59.964	38.462	0.00	0.00	0.00	3.33
1564	2458	6.103330	GGTAGAATTGGTTGTTGTTGTTGTT	58.897	36.000	0.00	0.00	0.00	2.83
1565	2459	5.656480	GGTAGAATTGGTTGTTGTTGTTGT	58.344	37.500	0.00	0.00	0.00	3.32
1628	2552	2.362169	ATGGTATTTGTTGTTGCGGC	57.638	45.000	0.00	0.00	0.00	6.53
1978	2923	3.082548	TGTTGTTGAGGTCGTTGGAAAA	58.917	40.909	0.00	0.00	0.00	2.29
2708	3692	5.659440	AAAGCTGGACTTTTTCTTGACAA	57.341	34.783	0.00	0.00	46.73	3.18
2825	3815	7.975058	CACAATAATTGTTGGATTGATGTAGCA	59.025	33.333	17.83	0.00	43.23	3.49

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.