AutoCloner

Multiple sequence alignment - TraesCS6A01G318200

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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	TraesCS6A01G318200	chr6A	100.000	4057	0	0	1	4057	554460381	554456325	0.000000e+00	7492.0
1	TraesCS6A01G318200	chr6A	78.876	1032	130	33	2515	3518	596341704	596342675	5.760000e-173	617.0
2	TraesCS6A01G318200	chr6A	77.705	1072	158	48	2478	3518	596363645	596364666	7.560000e-162	580.0
3	TraesCS6A01G318200	chr6A	83.405	464	49	16	1160	1602	596354166	596354622	4.880000e-109	405.0
4	TraesCS6A01G318200	chr6A	84.545	330	25	9	2172	2484	596354783	596355103	1.830000e-78	303.0
5	TraesCS6A01G318200	chr6A	85.263	285	18	7	2167	2435	596341417	596341693	5.170000e-69	272.0
6	TraesCS6A01G318200	chr6A	83.981	206	23	7	1167	1362	596340914	596341119	5.350000e-44	189.0
7	TraesCS6A01G318200	chr6B	95.430	2910	93	17	1159	4057	613111544	613108664	0.000000e+00	4601.0
8	TraesCS6A01G318200	chr6B	92.821	1198	39	12	1	1168	613112816	613111636	0.000000e+00	1692.0
9	TraesCS6A01G318200	chr6D	94.595	2812	104	20	1159	3962	408650932	408648161	0.000000e+00	4307.0
10	TraesCS6A01G318200	chr6D	93.031	1191	37	15	1	1168	408652182	408651015	0.000000e+00	1698.0
11	TraesCS6A01G318200	chr6D	85.906	447	52	6	1167	1607	450820279	450820720	2.210000e-127	466.0
12	TraesCS6A01G318200	chr6D	80.777	515	46	16	1953	2446	450821046	450821528	1.790000e-93	353.0
13	TraesCS6A01G318200	chr6D	96.104	77	3	0	3981	4057	408646896	408646820	4.260000e-25	126.0
14	TraesCS6A01G318200	chr6D	86.250	80	9	2	1890	1968	450820953	450821031	7.220000e-13	86.1
15	TraesCS6A01G318200	chr3D	80.316	950	113	46	1796	2702	335629033	335629951	0.000000e+00	651.0
16	TraesCS6A01G318200	chr3D	82.000	400	49	14	1210	1602	335628609	335628992	6.540000e-83	318.0
17	TraesCS6A01G318200	chr3D	88.889	198	17	4	2863	3059	335630235	335630428	5.240000e-59	239.0
18	TraesCS6A01G318200	chr3D	94.340	53	3	0	1712	1764	17876352	17876404	9.350000e-12	82.4
19	TraesCS6A01G318200	chr3D	83.333	90	13	2	1691	1778	486153997	486153908	9.350000e-12	82.4
20	TraesCS6A01G318200	chr3B	79.577	945	124	35	1795	2693	434048919	434049840	2.680000e-171	612.0
21	TraesCS6A01G318200	chr3B	81.047	401	51	17	1210	1602	434048498	434048881	3.070000e-76	296.0
22	TraesCS6A01G318200	chr3B	88.265	196	18	4	2863	3057	434050169	434050360	3.150000e-56	230.0
23	TraesCS6A01G318200	chr3B	93.506	77	5	0	3981	4057	825002412	825002488	9.210000e-22	115.0
24	TraesCS6A01G318200	chr3B	82.418	91	13	3	1691	1778	648925351	648925261	4.350000e-10	76.8
25	TraesCS6A01G318200	chr3A	79.000	700	87	32	2044	2702	453602231	453602911	1.350000e-114	424.0
26	TraesCS6A01G318200	chr3A	81.000	400	53	14	1210	1602	453601583	453601966	3.070000e-76	296.0
27	TraesCS6A01G318200	chr3A	79.744	390	38	23	2707	3084	453603052	453603412	1.130000e-60	244.0
28	TraesCS6A01G318200	chr7D	94.805	77	4	0	3981	4057	105507660	105507736	1.980000e-23	121.0
29	TraesCS6A01G318200	chr7D	87.838	74	8	1	1701	1774	622233903	622233975	7.220000e-13	86.1
30	TraesCS6A01G318200	chr7D	100.000	28	0	0	3960	3987	105507680	105507707	7.000000e-03	52.8
31	TraesCS6A01G318200	chr5A	94.805	77	4	0	3981	4057	545714519	545714595	1.980000e-23	121.0
32	TraesCS6A01G318200	chr2A	94.805	77	4	0	3981	4057	726993235	726993311	1.980000e-23	121.0
33	TraesCS6A01G318200	chr1B	94.805	77	4	0	3981	4057	181305600	181305524	1.980000e-23	121.0
34	TraesCS6A01G318200	chrUn	93.506	77	5	0	3981	4057	158061995	158062071	9.210000e-22	115.0
35	TraesCS6A01G318200	chr4A	93.506	77	5	0	3981	4057	111078887	111078963	9.210000e-22	115.0

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	TraesCS6A01G318200	chr6A	554456325	554460381	4056	True	7492.000000	7492	100.000000	1	4057	1	chr6A.!!$R1	4056
1	TraesCS6A01G318200	chr6A	596363645	596364666	1021	False	580.000000	580	77.705000	2478	3518	1	chr6A.!!$F1	1040
2	TraesCS6A01G318200	chr6A	596340914	596342675	1761	False	359.333333	617	82.706667	1167	3518	3	chr6A.!!$F2	2351
3	TraesCS6A01G318200	chr6A	596354166	596355103	937	False	354.000000	405	83.975000	1160	2484	2	chr6A.!!$F3	1324
4	TraesCS6A01G318200	chr6B	613108664	613112816	4152	True	3146.500000	4601	94.125500	1	4057	2	chr6B.!!$R1	4056
5	TraesCS6A01G318200	chr6D	408646820	408652182	5362	True	2043.666667	4307	94.576667	1	4057	3	chr6D.!!$R1	4056
6	TraesCS6A01G318200	chr6D	450820279	450821528	1249	False	301.700000	466	84.311000	1167	2446	3	chr6D.!!$F1	1279
7	TraesCS6A01G318200	chr3D	335628609	335630428	1819	False	402.666667	651	83.735000	1210	3059	3	chr3D.!!$F2	1849
8	TraesCS6A01G318200	chr3B	434048498	434050360	1862	False	379.333333	612	82.963000	1210	3057	3	chr3B.!!$F2	1847
9	TraesCS6A01G318200	chr3A	453601583	453603412	1829	False	321.333333	424	79.914667	1210	3084	3	chr3A.!!$F1	1874

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	Hairpin	End Stability	Orientation
770	785	0.108329	CAGAACTGTACGGGGCGAAT	60.108	55.000	6.65	0.00	3.34	F
819	834	0.771127	GGCTGGCCCTATGGAATGTA	59.229	55.000	0.00	0.00	2.29	F
1198	1341	1.004560	TTCTGAGCTTGAGGCCACG	60.005	57.895	5.01	43.05	4.94	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1612	1780	1.903877	ATGCGGTGAGAACAGGGGAG	61.904	60.000	0.00	0.0	0.00	4.30	R
1998	2251	2.271944	AACAGTTTAGGAGGTGCCAC	57.728	50.000	0.00	0.0	40.02	5.01	R
3093	3615	1.601162	GGAGCGGCATATGCAATTGTG	60.601	52.381	28.07	11.5	44.36	3.33	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
592	593	4.459089	GCCTGGTCCTCGTCCTGC	62.459	72.222	0.00	0.00	0.00	4.85
685	695	3.406595	CTCCATTGGGGTCTCCGGC	62.407	68.421	2.09	0.00	38.76	6.13
760	775	2.340731	TGGTTTAGGGCCAGAACTGTA	58.659	47.619	17.80	6.21	0.00	2.74
770	785	0.108329	CAGAACTGTACGGGGCGAAT	60.108	55.000	6.65	0.00	0.00	3.34
772	787	1.702491	GAACTGTACGGGGCGAATGC	61.702	60.000	6.65	0.00	41.71	3.56
783	798	2.167861	GCGAATGCAGAGTCGGGAC	61.168	63.158	16.18	0.00	40.03	4.46
784	799	1.513158	CGAATGCAGAGTCGGGACT	59.487	57.895	0.00	0.00	45.84	3.85
801	816	2.038975	TCGGGAGGGAAGAGGTGG	59.961	66.667	0.00	0.00	0.00	4.61
819	834	0.771127	GGCTGGCCCTATGGAATGTA	59.229	55.000	0.00	0.00	0.00	2.29
820	835	1.545651	GGCTGGCCCTATGGAATGTAC	60.546	57.143	0.00	0.00	0.00	2.90
821	836	1.421646	GCTGGCCCTATGGAATGTACT	59.578	52.381	0.00	0.00	0.00	2.73
822	837	2.637872	GCTGGCCCTATGGAATGTACTA	59.362	50.000	0.00	0.00	0.00	1.82
823	838	3.557264	GCTGGCCCTATGGAATGTACTAC	60.557	52.174	0.00	0.00	0.00	2.73
824	839	3.904339	CTGGCCCTATGGAATGTACTACT	59.096	47.826	0.00	0.00	0.00	2.57
825	840	3.901844	TGGCCCTATGGAATGTACTACTC	59.098	47.826	0.00	0.00	0.00	2.59
826	841	3.056749	GGCCCTATGGAATGTACTACTCG	60.057	52.174	0.00	0.00	0.00	4.18
827	842	3.573110	GCCCTATGGAATGTACTACTCGT	59.427	47.826	0.00	0.00	0.00	4.18
828	843	4.763793	GCCCTATGGAATGTACTACTCGTA	59.236	45.833	0.00	0.00	0.00	3.43
844	859	5.789710	ACTCGTATTTCCGTAAAACATGG	57.210	39.130	0.00	0.00	34.18	3.66
1170	1309	1.153989	CTCGATCTAGGCCTCCCCA	59.846	63.158	9.68	0.00	35.39	4.96
1198	1341	1.004560	TTCTGAGCTTGAGGCCACG	60.005	57.895	5.01	0.00	43.05	4.94
1218	1361	2.544694	CGGATCACTATGCAGTCCTGTC	60.545	54.545	0.00	0.00	30.46	3.51
1227	1373	1.949525	TGCAGTCCTGTCAAAAGAAGC	59.050	47.619	0.00	0.00	0.00	3.86
1368	1526	8.654230	TCTTCTCATGCTTTGCTATAGTAAAG	57.346	34.615	28.91	28.91	46.13	1.85
1452	1615	2.171003	GGAGGTGAAAAATGAGGGTGG	58.829	52.381	0.00	0.00	0.00	4.61
1458	1621	2.566724	TGAAAAATGAGGGTGGCATTCC	59.433	45.455	0.00	0.00	35.06	3.01
1558	1722	5.235850	AGGAAGAAGGTCTCCTTTCTTTC	57.764	43.478	2.48	6.68	44.82	2.62
1612	1780	8.734030	CGTTGTTCAGAATTCAGTTTTCTAAAC	58.266	33.333	8.44	0.00	33.65	2.01
1826	2047	1.282157	ACAGTCCTAAATCCCCACTGC	59.718	52.381	0.00	0.00	38.44	4.40
1885	2106	6.024049	GCAACAAGTAAATGCTGCTAACTAG	58.976	40.000	0.00	0.00	38.91	2.57
1986	2239	2.166907	AGACAGCATAGCTACCCAGT	57.833	50.000	0.00	0.00	36.40	4.00
1998	2251	0.682852	TACCCAGTCCTCACCAAACG	59.317	55.000	0.00	0.00	0.00	3.60
2212	2479	2.289631	CCCCTGAAATTGGCCAAGAAAC	60.290	50.000	24.94	14.78	0.00	2.78
2237	2504	4.006989	TGTATTTCACCCAGAATCCAACG	58.993	43.478	0.00	0.00	35.83	4.10
2629	2947	2.167693	TCTATTCCGAACAGCGATGGTT	59.832	45.455	5.32	0.00	44.57	3.67
2630	2948	1.821216	ATTCCGAACAGCGATGGTTT	58.179	45.000	5.32	0.00	44.57	3.27
2631	2949	2.459060	TTCCGAACAGCGATGGTTTA	57.541	45.000	5.32	0.00	44.57	2.01
2632	2950	1.717194	TCCGAACAGCGATGGTTTAC	58.283	50.000	5.32	0.00	44.57	2.01
2633	2951	1.274167	TCCGAACAGCGATGGTTTACT	59.726	47.619	5.32	0.00	44.57	2.24
2634	2952	2.492881	TCCGAACAGCGATGGTTTACTA	59.507	45.455	5.32	0.00	44.57	1.82
3019	3530	5.660417	AGATCAATGAACTCAAGCTAGGAGA	59.340	40.000	19.10	0.85	36.26	3.71
3130	3652	2.076863	CTCCAAAAGCAGGTACTTCGG	58.923	52.381	0.00	0.00	34.60	4.30
3299	3825	5.979517	TGCATAGATATATGATGTAGCGTGC	59.020	40.000	11.53	9.53	0.00	5.34
3340	3867	7.039082	AGCCTTTTTAGGATCTGTTTTGCATTA	60.039	33.333	0.00	0.00	0.00	1.90
3348	3875	6.774170	AGGATCTGTTTTGCATTATGATAGCA	59.226	34.615	0.00	0.00	36.32	3.49
3352	3879	9.826574	ATCTGTTTTGCATTATGATAGCATTTT	57.173	25.926	0.00	0.00	38.19	1.82
3358	3885	9.616156	TTTGCATTATGATAGCATTTTGGATTT	57.384	25.926	0.00	0.00	38.19	2.17
3361	3888	9.263538	GCATTATGATAGCATTTTGGATTTGAA	57.736	29.630	0.00	0.00	35.94	2.69
3541	4074	7.082972	ACCTGGATCCTACATAGATTACCTTT	58.917	38.462	14.23	0.00	0.00	3.11
3620	4153	1.065199	AGAATCCGATCTTGCAGGCAA	60.065	47.619	6.53	6.53	0.00	4.52
3622	4155	1.386533	ATCCGATCTTGCAGGCAAAG	58.613	50.000	8.20	3.12	35.33	2.77
4000	5779	5.462398	GGTTATAACAACTCAGCTGTATCCG	59.538	44.000	14.67	2.60	0.00	4.18

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
178	179	2.022129	CGCCGTCATCCCGCTTATC	61.022	63.158	0.00	0.00	0.00	1.75
574	575	2.997315	CAGGACGAGGACCAGGCA	60.997	66.667	0.00	0.00	0.00	4.75
592	593	0.468214	TAGCTCTCGTCCCCATGGAG	60.468	60.000	15.22	0.00	42.85	3.86
685	695	4.514577	ACCTCGCCGCATCCTTCG	62.515	66.667	0.00	0.00	0.00	3.79
701	711	0.458669	TCCCAAATCTAGTCGCCGAC	59.541	55.000	9.71	9.71	0.00	4.79
760	775	3.665675	GACTCTGCATTCGCCCCGT	62.666	63.158	0.00	0.00	37.32	5.28
783	798	2.060980	CCACCTCTTCCCTCCCGAG	61.061	68.421	0.00	0.00	0.00	4.63
784	799	2.038975	CCACCTCTTCCCTCCCGA	59.961	66.667	0.00	0.00	0.00	5.14
801	816	1.421646	AGTACATTCCATAGGGCCAGC	59.578	52.381	6.18	0.00	0.00	4.85
819	834	6.532657	CCATGTTTTACGGAAATACGAGTAGT	59.467	38.462	0.00	0.00	37.61	2.73
820	835	6.753279	TCCATGTTTTACGGAAATACGAGTAG	59.247	38.462	0.00	0.00	37.61	2.57
821	836	6.629128	TCCATGTTTTACGGAAATACGAGTA	58.371	36.000	0.00	0.00	37.61	2.59
822	837	5.481105	TCCATGTTTTACGGAAATACGAGT	58.519	37.500	0.00	0.00	37.61	4.18
823	838	6.256975	TCATCCATGTTTTACGGAAATACGAG	59.743	38.462	0.00	0.00	37.61	4.18
824	839	6.107343	TCATCCATGTTTTACGGAAATACGA	58.893	36.000	0.00	0.00	37.61	3.43
825	840	6.352682	TCATCCATGTTTTACGGAAATACG	57.647	37.500	0.00	0.00	40.31	3.06
826	841	7.220108	GCTTTCATCCATGTTTTACGGAAATAC	59.780	37.037	0.00	0.00	31.18	1.89
827	842	7.254852	GCTTTCATCCATGTTTTACGGAAATA	58.745	34.615	0.00	0.00	31.18	1.40
828	843	6.099341	GCTTTCATCCATGTTTTACGGAAAT	58.901	36.000	0.00	0.00	31.18	2.17
904	919	3.520290	TTTGAGACACGTGTTCAGAGT	57.480	42.857	24.26	3.52	0.00	3.24
929	944	7.387948	GGTGAAGCTTCTATGTTCAGAGTTTTA	59.612	37.037	26.09	0.00	30.94	1.52
990	1019	2.146061	CCCCTCCATCCCTGAGCTC	61.146	68.421	6.82	6.82	0.00	4.09
1011	1047	3.064987	CTGGTCGCGGAGTAGGGTG	62.065	68.421	6.13	0.00	0.00	4.61
1127	1164	1.964552	TTTAGAAAACGAACGGGGCA	58.035	45.000	0.00	0.00	0.00	5.36
1198	1341	2.432146	TGACAGGACTGCATAGTGATCC	59.568	50.000	0.00	0.00	37.25	3.36
1392	1552	2.060050	AGGGAGGTCAGTCGACATAG	57.940	55.000	19.50	7.34	44.54	2.23
1452	1615	1.632422	CCTGTGCAATTTCGGAATGC	58.368	50.000	8.93	8.93	0.00	3.56
1558	1722	3.859961	ACGTGAATATGAAGAACAGAGCG	59.140	43.478	0.00	0.00	0.00	5.03
1612	1780	1.903877	ATGCGGTGAGAACAGGGGAG	61.904	60.000	0.00	0.00	0.00	4.30
1749	1970	6.920569	ACTCCATCCGTATCAAAATACAAC	57.079	37.500	0.00	0.00	38.11	3.32
1998	2251	2.271944	AACAGTTTAGGAGGTGCCAC	57.728	50.000	0.00	0.00	40.02	5.01
2212	2479	6.389906	GTTGGATTCTGGGTGAAATACAAAG	58.610	40.000	0.00	0.00	38.29	2.77
2605	2915	3.185188	CCATCGCTGTTCGGAATAGAATG	59.815	47.826	17.36	16.77	39.05	2.67
3093	3615	1.601162	GGAGCGGCATATGCAATTGTG	60.601	52.381	28.07	11.50	44.36	3.33
3299	3825	4.335400	AAAGGCTACAATGTTTTGGTGG	57.665	40.909	0.00	0.00	37.15	4.61
3340	3867	9.158233	CAAACTTCAAATCCAAAATGCTATCAT	57.842	29.630	0.00	0.00	33.53	2.45
3348	3875	6.245890	TGGGTCAAACTTCAAATCCAAAAT	57.754	33.333	0.00	0.00	0.00	1.82
3352	3879	5.683876	TTTTGGGTCAAACTTCAAATCCA	57.316	34.783	0.00	0.00	32.79	3.41
3358	3885	7.595819	AGTGATATTTTTGGGTCAAACTTCA	57.404	32.000	0.00	0.00	32.79	3.02
3361	3888	8.357402	GTTGTAGTGATATTTTTGGGTCAAACT	58.643	33.333	0.00	0.00	32.79	2.66
3605	4138	1.386533	ATCTTTGCCTGCAAGATCGG	58.613	50.000	4.58	0.00	37.24	4.18
3620	4153	3.266772	TGAGGCCAAGTCCATGTAATCTT	59.733	43.478	5.01	0.00	0.00	2.40
3622	4155	3.281727	TGAGGCCAAGTCCATGTAATC	57.718	47.619	5.01	0.00	0.00	1.75
3718	4251	7.693969	ACTTGAAGCTAGCTCACAATAATTT	57.306	32.000	26.23	7.65	0.00	1.82
4000	5779	8.637986	TGTTATAACCAATGAATAGGAAATGCC	58.362	33.333	13.01	0.00	0.00	4.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.