AutoCloner

Multiple sequence alignment - TraesCS7B01G472000

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	TraesCS7B01G472000	chr7B	100.000	2552	0	0	1	2552	728004719	728007270	0.000000e+00	4713
1	TraesCS7B01G472000	chr7B	84.589	1434	146	43	1178	2552	728012978	728014395	0.000000e+00	1354
2	TraesCS7B01G472000	chr7B	90.449	178	13	3	277	450	728011870	728012047	5.490000e-57	231
3	TraesCS7B01G472000	chr7A	92.791	1845	79	26	742	2552	722877192	722879016	0.000000e+00	2621
4	TraesCS7B01G472000	chr7A	92.633	1846	81	26	742	2552	722792657	722794482	0.000000e+00	2604
5	TraesCS7B01G472000	chr7A	83.869	1432	156	38	1178	2552	723074961	723076374	0.000000e+00	1295
6	TraesCS7B01G472000	chr7A	83.473	1434	163	42	1178	2552	722898728	722900146	0.000000e+00	1267
7	TraesCS7B01G472000	chr7A	83.194	1434	167	41	1178	2552	722988239	722989657	0.000000e+00	1245
8	TraesCS7B01G472000	chr7A	91.543	473	31	6	1	466	722792120	722792590	0.000000e+00	643
9	TraesCS7B01G472000	chr7A	91.121	473	33	6	1	466	722876655	722877125	1.290000e-177	632
10	TraesCS7B01G472000	chr7A	87.119	295	23	1	1178	1457	723031082	723031376	1.140000e-83	320
11	TraesCS7B01G472000	chr7A	91.284	218	12	5	955	1166	722936586	722936802	8.930000e-75	291
12	TraesCS7B01G472000	chr7A	91.284	218	12	2	955	1166	723030883	723031099	8.930000e-75	291
13	TraesCS7B01G472000	chr7A	90.826	218	13	2	955	1166	723074762	723074978	4.160000e-73	285
14	TraesCS7B01G472000	chr7A	91.080	213	13	1	955	1161	722898529	722898741	1.490000e-72	283
15	TraesCS7B01G472000	chr7A	91.080	213	13	1	955	1161	722988040	722988252	1.490000e-72	283
16	TraesCS7B01G472000	chr7A	84.133	271	30	8	330	597	722798962	722799222	1.520000e-62	250
17	TraesCS7B01G472000	chr7A	94.355	124	7	0	1334	1457	722938443	722938566	9.320000e-45	191
18	TraesCS7B01G472000	chr7A	91.791	134	11	0	1178	1311	722936785	722936918	1.210000e-43	187
19	TraesCS7B01G472000	chr7A	77.487	191	35	5	2365	2549	722829847	722830035	9.650000e-20	108
20	TraesCS7B01G472000	chr7D	91.976	1807	97	27	747	2539	627298122	627299894	0.000000e+00	2490
21	TraesCS7B01G472000	chr7D	89.373	734	55	11	1	718	627297153	627297879	0.000000e+00	902
22	TraesCS7B01G472000	chr7D	81.149	435	46	16	756	1166	627304921	627305343	1.470000e-82	316
23	TraesCS7B01G472000	chr7D	89.326	178	13	3	277	451	627304406	627304580	4.270000e-53	219

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	TraesCS7B01G472000	chr7B	728004719	728007270	2551	False	4713.0	4713	100.000000	1	2552	1	chr7B.!!$F1	2551
1	TraesCS7B01G472000	chr7B	728011870	728014395	2525	False	792.5	1354	87.519000	277	2552	2	chr7B.!!$F2	2275
2	TraesCS7B01G472000	chr7A	722876655	722879016	2361	False	1626.5	2621	91.956000	1	2552	2	chr7A.!!$F4	2551
3	TraesCS7B01G472000	chr7A	722792120	722794482	2362	False	1623.5	2604	92.088000	1	2552	2	chr7A.!!$F3	2551
4	TraesCS7B01G472000	chr7A	723074762	723076374	1612	False	790.0	1295	87.347500	955	2552	2	chr7A.!!$F9	1597
5	TraesCS7B01G472000	chr7A	722898529	722900146	1617	False	775.0	1267	87.276500	955	2552	2	chr7A.!!$F5	1597
6	TraesCS7B01G472000	chr7A	722988040	722989657	1617	False	764.0	1245	87.137000	955	2552	2	chr7A.!!$F7	1597
7	TraesCS7B01G472000	chr7A	722936586	722938566	1980	False	223.0	291	92.476667	955	1457	3	chr7A.!!$F6	502
8	TraesCS7B01G472000	chr7D	627297153	627299894	2741	False	1696.0	2490	90.674500	1	2539	2	chr7D.!!$F1	2538
9	TraesCS7B01G472000	chr7D	627304406	627305343	937	False	267.5	316	85.237500	277	1166	2	chr7D.!!$F2	889

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
130	131	0.777446	ATACCAAACCAGCCCACAGT	59.223	50.0	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
1696	3734	0.734889	CCAGAGCTATTTGCAACCCG	59.265	55.0	0.0	0.0	45.94	5.28	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
28	29	3.192422	CGCTCTAGGAGGGTAAGATCATG	59.808	52.174	0.00	0.00	37.75	3.07
38	39	3.741344	GGGTAAGATCATGAAATCCGACG	59.259	47.826	0.00	0.00	0.00	5.12
41	42	1.414181	AGATCATGAAATCCGACGGCT	59.586	47.619	9.66	0.00	0.00	5.52
130	131	0.777446	ATACCAAACCAGCCCACAGT	59.223	50.000	0.00	0.00	0.00	3.55
131	132	1.436326	TACCAAACCAGCCCACAGTA	58.564	50.000	0.00	0.00	0.00	2.74
150	151	5.105351	ACAGTATTTTGCAAAATCTAGGGGC	60.105	40.000	34.40	18.58	39.24	5.80
160	161	0.830023	ATCTAGGGGCGGCTTCTCTC	60.830	60.000	9.56	0.00	0.00	3.20
196	198	6.715464	ACTGAATTACAAACACTTTCGTCTG	58.285	36.000	0.00	0.00	0.00	3.51
197	199	5.507077	TGAATTACAAACACTTTCGTCTGC	58.493	37.500	0.00	0.00	0.00	4.26
232	234	5.163447	ACGATATACCAACATCGGATATGGG	60.163	44.000	20.06	7.42	46.40	4.00
339	342	3.474600	CAATGCTTACATAGGCTCAGCT	58.525	45.455	0.00	0.00	34.62	4.24
345	348	4.507710	CTTACATAGGCTCAGCTTTGACA	58.492	43.478	0.00	0.00	0.00	3.58
400	408	5.163652	ACCTTTTGTTGTCTCCTTTTCTTCG	60.164	40.000	0.00	0.00	0.00	3.79
435	445	2.018542	TGTTCCTTTTCCTATCCGCG	57.981	50.000	0.00	0.00	0.00	6.46
456	466	2.870411	GTTAATAGTTAGGGCGCTGTGG	59.130	50.000	14.51	0.00	0.00	4.17
498	508	7.446625	CCTGGTCATATTGAAAAAGCTAGCTAT	59.553	37.037	19.70	9.20	0.00	2.97
500	510	7.992608	TGGTCATATTGAAAAAGCTAGCTATCA	59.007	33.333	19.70	19.02	0.00	2.15
502	512	8.014517	GTCATATTGAAAAAGCTAGCTATCAGC	58.985	37.037	19.70	7.57	42.84	4.26
503	513	7.716560	TCATATTGAAAAAGCTAGCTATCAGCA	59.283	33.333	19.70	13.49	45.56	4.41
507	543	1.403814	AAGCTAGCTATCAGCACGGA	58.596	50.000	19.70	0.00	45.56	4.69
510	546	2.366916	AGCTAGCTATCAGCACGGATTT	59.633	45.455	17.69	0.00	45.56	2.17
517	553	4.260538	GCTATCAGCACGGATTTTCTTCAG	60.261	45.833	0.00	0.00	41.89	3.02
518	554	2.426522	TCAGCACGGATTTTCTTCAGG	58.573	47.619	0.00	0.00	0.00	3.86
519	555	1.470098	CAGCACGGATTTTCTTCAGGG	59.530	52.381	0.00	0.00	0.00	4.45
571	607	7.986889	ACTTGAAACTAATTTTGCAGGTTTGAT	59.013	29.630	0.00	0.00	31.51	2.57
579	615	3.296322	TTGCAGGTTTGATTTTAGCCG	57.704	42.857	0.00	0.00	0.00	5.52
658	694	5.938438	AAAAATCAGCTCTGAGACTTGAC	57.062	39.130	9.28	0.00	43.61	3.18
665	870	2.803451	CTCTGAGACTTGACGGTATGC	58.197	52.381	0.00	0.00	0.00	3.14
673	884	1.952102	TTGACGGTATGCGAGGGGAC	61.952	60.000	0.00	0.00	0.00	4.46
726	1161	3.049708	TCTCTCTTTCCACTGCACATG	57.950	47.619	0.00	0.00	0.00	3.21
740	1175	2.114670	ACATGCCGGCATCTTTCCG	61.115	57.895	38.60	27.15	46.05	4.30
754	1199	1.544246	CTTTCCGCCAAGTAAAAGGGG	59.456	52.381	0.00	0.00	37.57	4.79
778	1223	8.357402	GGGAATGTTTCTTAGAAAAGCTTACAA	58.643	33.333	9.14	0.00	32.36	2.41
984	1479	1.283793	CAGAAACGGCAGCCACAAG	59.716	57.895	13.30	0.00	0.00	3.16
985	1480	2.050077	GAAACGGCAGCCACAAGC	60.050	61.111	13.30	0.00	44.25	4.01
991	1486	3.225798	GCAGCCACAAGCCCACAA	61.226	61.111	0.00	0.00	45.47	3.33
998	1493	1.455587	ACAAGCCCACAACCCACAG	60.456	57.895	0.00	0.00	0.00	3.66
1125	1634	3.965888	GACCTTCAAGTCCCTGCAT	57.034	52.632	0.00	0.00	0.00	3.96
1449	3475	1.553690	CCTGGCTCGAAAGGGAGGAA	61.554	60.000	1.34	0.00	34.56	3.36
1451	3477	1.078356	GGCTCGAAAGGGAGGAACC	60.078	63.158	0.00	0.00	34.56	3.62
1535	3561	1.198713	GAGGCAGATCAGGAACAGGA	58.801	55.000	0.00	0.00	0.00	3.86
1536	3562	1.138661	GAGGCAGATCAGGAACAGGAG	59.861	57.143	0.00	0.00	0.00	3.69
1696	3734	5.291128	TCTTTGACTTTGTGTTTCGAGACTC	59.709	40.000	7.68	4.46	0.00	3.36
1714	3754	1.667724	CTCGGGTTGCAAATAGCTCTG	59.332	52.381	0.00	0.00	45.94	3.35
1788	3840	6.097554	AGCTGCTATATATATGTGGGTCAGAC	59.902	42.308	0.00	0.00	0.00	3.51
1998	4083	9.403110	GCATTAATCCATAACTAGCTTGATTTG	57.597	33.333	1.04	0.00	0.00	2.32
2018	4106	8.022550	TGATTTGGCACGCATATATCTTATTTG	58.977	33.333	0.00	0.00	0.00	2.32
2019	4107	5.878332	TGGCACGCATATATCTTATTTGG	57.122	39.130	0.00	0.00	0.00	3.28
2021	4109	5.643348	TGGCACGCATATATCTTATTTGGAG	59.357	40.000	0.00	0.00	0.00	3.86
2022	4110	5.447818	GGCACGCATATATCTTATTTGGAGC	60.448	44.000	0.00	0.00	0.00	4.70
2023	4111	5.352569	GCACGCATATATCTTATTTGGAGCT	59.647	40.000	0.00	0.00	0.00	4.09
2024	4112	6.674037	GCACGCATATATCTTATTTGGAGCTG	60.674	42.308	0.00	0.00	0.00	4.24
2025	4113	6.591448	CACGCATATATCTTATTTGGAGCTGA	59.409	38.462	0.00	0.00	0.00	4.26
2147	4252	1.196012	AAAGGGTCGATCCAGTCCTC	58.804	55.000	19.03	0.00	38.11	3.71
2160	4265	6.985059	CGATCCAGTCCTCGTATGATATACTA	59.015	42.308	0.00	0.00	0.00	1.82
2331	4438	7.436118	AGTTAATGATGTTGCTTCACAATGTT	58.564	30.769	0.00	0.00	41.27	2.71
2386	4493	9.851686	TTGGAGTAATTAATGCATTCTATCTGT	57.148	29.630	16.86	0.00	0.00	3.41
2447	4558	0.693049	ATGAGAAGAACAACGGGGCT	59.307	50.000	0.00	0.00	0.00	5.19

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
6	7	2.865079	TGATCTTACCCTCCTAGAGCG	58.135	52.381	0.00	0.00	0.00	5.03
24	25	0.534873	TCAGCCGTCGGATTTCATGA	59.465	50.000	17.49	0.00	0.00	3.07
28	29	1.128692	CACTTTCAGCCGTCGGATTTC	59.871	52.381	17.49	0.00	0.00	2.17
59	60	0.971447	AGCACCGTCCTAACCCTCTC	60.971	60.000	0.00	0.00	0.00	3.20
130	131	3.383185	CCGCCCCTAGATTTTGCAAAATA	59.617	43.478	31.79	19.24	38.64	1.40
131	132	2.168313	CCGCCCCTAGATTTTGCAAAAT	59.832	45.455	32.11	32.11	41.06	1.82
150	151	0.461961	CTAGTTGGGGAGAGAAGCCG	59.538	60.000	0.00	0.00	0.00	5.52
160	161	7.013846	TGTTTGTAATTCAGTTTCTAGTTGGGG	59.986	37.037	0.00	0.00	0.00	4.96
196	198	7.690228	TGTTGGTATATCGTAATTTCACTTGC	58.310	34.615	0.00	0.00	0.00	4.01
197	199	9.864034	GATGTTGGTATATCGTAATTTCACTTG	57.136	33.333	0.00	0.00	0.00	3.16
232	234	2.810852	GGAAGCTTCCATATAGTGCAGC	59.189	50.000	35.71	7.61	46.76	5.25
339	342	2.627699	GTTGGCTTCCAGGATTGTCAAA	59.372	45.455	10.50	0.00	33.81	2.69
345	348	0.400213	TGACGTTGGCTTCCAGGATT	59.600	50.000	0.00	0.00	33.81	3.01
432	442	0.505655	GCGCCCTAACTATTAACGCG	59.494	55.000	3.53	3.53	40.97	6.01
435	445	2.870411	CCACAGCGCCCTAACTATTAAC	59.130	50.000	2.29	0.00	0.00	2.01
498	508	2.426522	CCTGAAGAAAATCCGTGCTGA	58.573	47.619	0.00	0.00	0.00	4.26
500	510	1.351017	TCCCTGAAGAAAATCCGTGCT	59.649	47.619	0.00	0.00	0.00	4.40
502	512	4.846779	TTTTCCCTGAAGAAAATCCGTG	57.153	40.909	0.00	0.00	40.04	4.94
631	667	4.021016	AGTCTCAGAGCTGATTTTTACCGT	60.021	41.667	0.00	0.00	39.13	4.83
632	668	4.499183	AGTCTCAGAGCTGATTTTTACCG	58.501	43.478	0.00	0.00	39.13	4.02
658	694	1.658673	GTAGTCCCCTCGCATACCG	59.341	63.158	0.00	0.00	38.61	4.02
665	870	1.263356	TTCAGTTGGTAGTCCCCTCG	58.737	55.000	0.00	0.00	0.00	4.63
699	915	3.369451	GCAGTGGAAAGAGAGAAATCGTC	59.631	47.826	0.00	0.00	0.00	4.20
702	918	4.067896	TGTGCAGTGGAAAGAGAGAAATC	58.932	43.478	0.00	0.00	0.00	2.17
740	1175	4.283467	AGAAACATTCCCCTTTTACTTGGC	59.717	41.667	0.00	0.00	0.00	4.52
778	1223	2.121832	TGTCACCGGTGGGGAGAT	59.878	61.111	33.40	0.00	34.84	2.75
851	1300	9.011095	GCACCATCTATCAATGTACTACTAGTA	57.989	37.037	1.89	1.89	0.00	1.82
854	1303	7.523873	GCAGCACCATCTATCAATGTACTACTA	60.524	40.741	0.00	0.00	0.00	1.82
855	1304	6.739843	GCAGCACCATCTATCAATGTACTACT	60.740	42.308	0.00	0.00	0.00	2.57
856	1305	5.406780	GCAGCACCATCTATCAATGTACTAC	59.593	44.000	0.00	0.00	0.00	2.73
984	1479	2.601367	ATGCTGTGGGTTGTGGGC	60.601	61.111	0.00	0.00	0.00	5.36
985	1480	2.934570	GCATGCTGTGGGTTGTGGG	61.935	63.158	11.37	0.00	0.00	4.61
986	1481	1.870055	GAGCATGCTGTGGGTTGTGG	61.870	60.000	28.27	0.00	0.00	4.17
987	1482	1.174078	TGAGCATGCTGTGGGTTGTG	61.174	55.000	28.27	0.00	0.00	3.33
988	1483	0.467844	TTGAGCATGCTGTGGGTTGT	60.468	50.000	28.27	0.00	0.00	3.32
989	1484	0.038892	GTTGAGCATGCTGTGGGTTG	60.039	55.000	28.27	0.00	0.00	3.77
990	1485	1.518056	CGTTGAGCATGCTGTGGGTT	61.518	55.000	28.27	0.00	0.00	4.11
991	1486	1.968017	CGTTGAGCATGCTGTGGGT	60.968	57.895	28.27	0.00	0.00	4.51
998	1493	1.930100	CTCGATCCGTTGAGCATGC	59.070	57.895	10.51	10.51	0.00	4.06
1535	3561	1.275357	ACTCCTACTCCTCCTCCTCCT	60.275	57.143	0.00	0.00	0.00	3.69
1536	3562	1.133606	CACTCCTACTCCTCCTCCTCC	60.134	61.905	0.00	0.00	0.00	4.30
1696	3734	0.734889	CCAGAGCTATTTGCAACCCG	59.265	55.000	0.00	0.00	45.94	5.28
1781	3833	5.758296	TCAAAGTATCAAACACAGTCTGACC	59.242	40.000	6.91	0.00	0.00	4.02
1788	3840	4.855388	GCTGCATCAAAGTATCAAACACAG	59.145	41.667	0.00	0.00	0.00	3.66
1985	4070	0.804989	GCGTGCCAAATCAAGCTAGT	59.195	50.000	0.00	0.00	38.21	2.57
1998	4083	5.447818	GCTCCAAATAAGATATATGCGTGCC	60.448	44.000	0.00	0.00	0.00	5.01
2046	4143	1.818674	GAAATAGGCACAACACCTGGG	59.181	52.381	0.00	0.00	38.26	4.45
2160	4265	5.126869	TGGAAATCACGGTGCAATTAATGAT	59.873	36.000	2.51	0.00	0.00	2.45
2174	4281	8.986477	AAGGAAGAAAATATTTGGAAATCACG	57.014	30.769	0.39	0.00	0.00	4.35
2214	4321	1.133407	TGTTCTTTTTCGCAAAGCCGT	59.867	42.857	2.83	0.00	0.00	5.68
2215	4322	1.780860	CTGTTCTTTTTCGCAAAGCCG	59.219	47.619	2.83	0.00	0.00	5.52
2351	4458	6.154445	GCATTAATTACTCCAATGATGCCAG	58.846	40.000	2.70	0.00	39.14	4.85
2472	4585	8.759641	CATGGTTTTGTTTCACGAAAATATGAA	58.240	29.630	0.00	0.00	33.61	2.57
2473	4586	7.923344	ACATGGTTTTGTTTCACGAAAATATGA	59.077	29.630	14.94	0.00	33.61	2.15
2483	4599	7.276658	TGTTTGACATACATGGTTTTGTTTCAC	59.723	33.333	0.00	0.00	0.00	3.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.