AutoCloner

Multiple sequence alignment - TraesCS2B01G234500

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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	TraesCS2B01G234500	chr2B	100.000	2982	0	0	1	2982	233270057	233267076	0.000000e+00	5507.0
1	TraesCS2B01G234500	chr2D	90.399	1979	84	40	672	2586	176164533	176162597	0.000000e+00	2505.0
2	TraesCS2B01G234500	chr2D	90.785	586	25	9	1	567	176165391	176164816	0.000000e+00	756.0
3	TraesCS2B01G234500	chr2D	98.515	404	1	1	2584	2982	176162535	176162132	0.000000e+00	708.0
4	TraesCS2B01G234500	chr2D	91.753	97	6	1	569	663	176164780	176164684	1.860000e-27	134.0
5	TraesCS2B01G234500	chr2A	90.759	1515	69	38	1088	2578	187953385	187951918	0.000000e+00	1956.0
6	TraesCS2B01G234500	chr2A	87.023	655	32	12	62	666	187955525	187954874	0.000000e+00	689.0
7	TraesCS2B01G234500	chr2A	96.535	404	9	2	2584	2982	187951847	187951444	0.000000e+00	664.0
8	TraesCS2B01G234500	chr2A	81.868	364	14	9	741	1083	187953815	187953483	2.950000e-65	259.0
9	TraesCS2B01G234500	chr2A	96.226	53	2	0	1	53	187955642	187955590	1.470000e-13	87.9
10	TraesCS2B01G234500	chr2A	94.595	37	2	0	82	118	187955585	187955549	1.150000e-04	58.4
11	TraesCS2B01G234500	chr2A	100.000	29	0	0	569	597	24689912	24689940	1.000000e-03	54.7
12	TraesCS2B01G234500	chr2A	100.000	29	0	0	569	597	537253122	537253094	1.000000e-03	54.7
13	TraesCS2B01G234500	chr7D	84.749	1154	100	36	1318	2452	581035091	581036187	0.000000e+00	1086.0
14	TraesCS2B01G234500	chr3D	85.216	487	32	18	1983	2452	604598317	604597854	5.820000e-127	464.0
15	TraesCS2B01G234500	chr3D	88.449	303	20	5	1647	1949	604598600	604598313	4.730000e-93	351.0
16	TraesCS2B01G234500	chr3D	97.143	35	0	1	569	602	67481301	67481267	1.150000e-04	58.4
17	TraesCS2B01G234500	chr6B	94.792	192	6	1	669	860	594649497	594649684	2.250000e-76	296.0
18	TraesCS2B01G234500	chr6B	94.792	192	6	1	669	860	594650787	594650600	2.250000e-76	296.0
19	TraesCS2B01G234500	chr3B	97.143	35	0	1	569	602	112281254	112281220	1.150000e-04	58.4
20	TraesCS2B01G234500	chr1B	94.595	37	2	0	561	597	646128874	646128910	1.150000e-04	58.4
21	TraesCS2B01G234500	chr7A	100.000	29	0	0	569	597	731652194	731652222	1.000000e-03	54.7
22	TraesCS2B01G234500	chr5B	96.970	33	0	1	571	602	300097182	300097214	1.000000e-03	54.7
23	TraesCS2B01G234500	chr1D	100.000	28	0	0	569	596	112472006	112471979	5.000000e-03	52.8

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	TraesCS2B01G234500	chr2B	233267076	233270057	2981	True	5507.00	5507	100.000000	1	2982	1	chr2B.!!$R1	2981
1	TraesCS2B01G234500	chr2D	176162132	176165391	3259	True	1025.75	2505	92.863000	1	2982	4	chr2D.!!$R1	2981
2	TraesCS2B01G234500	chr2A	187951444	187955642	4198	True	619.05	1956	91.167667	1	2982	6	chr2A.!!$R2	2981
3	TraesCS2B01G234500	chr7D	581035091	581036187	1096	False	1086.00	1086	84.749000	1318	2452	1	chr7D.!!$F1	1134
4	TraesCS2B01G234500	chr3D	604597854	604598600	746	True	407.50	464	86.832500	1647	2452	2	chr3D.!!$R2	805

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
765	1886	0.449786	TCGTAAATGTGCATTGCCCG	59.55	50.0	6.12	2.39	0.0	6.13	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2315	3609	0.391661	TCGACTCTGCATTGCCCTTC	60.392	55.0	6.12	0.0	0.0	3.46	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
58	59	3.928211	CAGTGTCGCTGCAAATACATAC	58.072	45.455	0.00	0.00	38.52	2.39
74	133	9.868389	CAAATACATACACTTGTATATGCTGTG	57.132	33.333	12.86	12.86	40.94	3.66
140	199	1.903183	AGGAAGAACTGGACTGCTACC	59.097	52.381	0.00	0.00	0.00	3.18
195	254	2.144482	GCATCTTGTTGCTTGTTGCT	57.856	45.000	0.00	0.00	43.37	3.91
234	293	3.825585	TGCATTAAGATCACTTTGCCACA	59.174	39.130	0.00	0.00	38.40	4.17
238	315	5.885230	TTAAGATCACTTTGCCACATCAG	57.115	39.130	0.00	0.00	37.53	2.90
297	381	3.137544	AGTTTACAACATCTGGTGGACCA	59.862	43.478	0.00	0.00	45.30	4.02
390	485	7.461182	TTTATATTGTTTCCCAAGACACCAG	57.539	36.000	0.00	0.00	36.25	4.00
412	507	1.888215	AGATGAATGCCAGGCGTATG	58.112	50.000	6.58	0.00	0.00	2.39
522	617	2.567615	GTGGGAGCCTTTCTCAGAGTTA	59.432	50.000	0.00	0.00	43.70	2.24
597	728	7.222999	ACATAAGAGCGTTTAGATCACTAAAGC	59.777	37.037	0.00	0.00	45.42	3.51
603	734	4.031426	CGTTTAGATCACTAAAGCGTGACC	59.969	45.833	0.00	0.00	45.74	4.02
618	749	3.325870	CGTGACCACTAGCAAAATCTCA	58.674	45.455	0.00	0.00	0.00	3.27
649	780	0.686224	GCTATGCATCTCAGGGAGCT	59.314	55.000	0.19	0.00	0.00	4.09
656	787	2.744494	GCATCTCAGGGAGCTTAACTGG	60.744	54.545	11.69	5.07	33.19	4.00
670	955	2.833631	AACTGGACCGACCTTTGTAG	57.166	50.000	0.00	0.00	39.86	2.74
681	966	1.148310	CCTTTGTAGGCACTGTCACG	58.852	55.000	0.00	0.00	41.52	4.35
706	991	2.568003	GGTCCAAACCAGCTTAGCC	58.432	57.895	0.00	0.00	45.68	3.93
738	1173	1.472878	GAGACGAGCACCACTACATCA	59.527	52.381	0.00	0.00	0.00	3.07
754	1875	7.401860	CACTACATCATCTGGTTTCGTAAATG	58.598	38.462	0.00	0.00	0.00	2.32
765	1886	0.449786	TCGTAAATGTGCATTGCCCG	59.550	50.000	6.12	2.39	0.00	6.13
825	1949	4.033776	GCAGCCTAGCCACCCACA	62.034	66.667	0.00	0.00	0.00	4.17
826	1950	2.270205	CAGCCTAGCCACCCACAG	59.730	66.667	0.00	0.00	0.00	3.66
827	1951	3.011517	AGCCTAGCCACCCACAGG	61.012	66.667	0.00	0.00	40.04	4.00
853	1977	0.810648	AGGCACGCAATATGTGGTTG	59.189	50.000	0.00	0.00	37.80	3.77
857	1981	1.729517	CACGCAATATGTGGTTGTCGA	59.270	47.619	8.72	0.00	33.69	4.20
866	1990	1.153127	TGGTTGTCGAAGCCGGTTT	60.153	52.632	1.95	1.95	36.24	3.27
982	2124	4.315122	CGATCGTCCTCTCCGCCG	62.315	72.222	7.03	0.00	0.00	6.46
985	2127	3.989838	ATCGTCCTCTCCGCCGTGA	62.990	63.158	0.00	0.00	0.00	4.35
986	2128	4.477975	CGTCCTCTCCGCCGTGAC	62.478	72.222	0.00	0.00	0.00	3.67
1083	2225	1.880340	GCCGCCGTCTGATCTCTTG	60.880	63.158	0.00	0.00	0.00	3.02
1084	2226	1.513158	CCGCCGTCTGATCTCTTGT	59.487	57.895	0.00	0.00	0.00	3.16
1085	2227	0.738975	CCGCCGTCTGATCTCTTGTA	59.261	55.000	0.00	0.00	0.00	2.41
1086	2228	1.134367	CCGCCGTCTGATCTCTTGTAA	59.866	52.381	0.00	0.00	0.00	2.41
1096	2331	6.476380	GTCTGATCTCTTGTAATTGCTGAGAG	59.524	42.308	18.27	17.13	37.24	3.20
1461	2696	1.417890	CCAGGGGCTCAAGGTATGTAG	59.582	57.143	0.00	0.00	0.00	2.74
1462	2697	2.119495	CAGGGGCTCAAGGTATGTAGT	58.881	52.381	0.00	0.00	0.00	2.73
1463	2698	3.305720	CAGGGGCTCAAGGTATGTAGTA	58.694	50.000	0.00	0.00	0.00	1.82
1464	2699	3.069729	CAGGGGCTCAAGGTATGTAGTAC	59.930	52.174	0.00	0.00	0.00	2.73
1465	2700	2.035576	GGGGCTCAAGGTATGTAGTACG	59.964	54.545	0.00	0.00	33.94	3.67
1467	2702	3.131755	GGGCTCAAGGTATGTAGTACGTT	59.868	47.826	0.00	0.00	40.88	3.99
1468	2703	4.357996	GGCTCAAGGTATGTAGTACGTTC	58.642	47.826	0.00	0.00	38.86	3.95
1469	2704	4.033684	GCTCAAGGTATGTAGTACGTTCG	58.966	47.826	0.00	0.00	38.86	3.95
1470	2705	4.595116	CTCAAGGTATGTAGTACGTTCGG	58.405	47.826	0.00	0.00	38.86	4.30
1471	2706	4.260985	TCAAGGTATGTAGTACGTTCGGA	58.739	43.478	0.00	0.00	38.86	4.55
1479	2714	4.978186	TGTAGTACGTTCGGAAGATTCAG	58.022	43.478	0.00	0.00	41.60	3.02
1493	2728	1.731433	ATTCAGACGGCCATGCATGC	61.731	55.000	21.69	11.82	0.00	4.06
1494	2729	3.135457	CAGACGGCCATGCATGCA	61.135	61.111	25.04	25.04	0.00	3.96
1516	2773	5.690816	CAAAGCTATATGCAAGCAGAGATG	58.309	41.667	11.29	0.00	45.94	2.90
1517	2774	4.886496	AGCTATATGCAAGCAGAGATGA	57.114	40.909	11.29	0.00	45.94	2.92
1518	2775	5.224821	AGCTATATGCAAGCAGAGATGAA	57.775	39.130	11.29	0.00	45.94	2.57
1563	2820	3.372206	CCCAGAGTAAGTTGCTGAAATCG	59.628	47.826	0.00	0.00	0.00	3.34
1564	2821	3.997021	CCAGAGTAAGTTGCTGAAATCGT	59.003	43.478	0.00	0.00	0.00	3.73
1565	2822	4.143030	CCAGAGTAAGTTGCTGAAATCGTG	60.143	45.833	0.00	0.00	0.00	4.35
1794	3059	4.322057	AACAAACATGCCCTCCTATCTT	57.678	40.909	0.00	0.00	0.00	2.40
1815	3080	7.787725	TCTTAACTGAACCTTTCTGAAGAAC	57.212	36.000	0.00	0.00	34.71	3.01
1827	3092	5.581126	TTCTGAAGAACACATTGTTTGCT	57.419	34.783	0.00	0.00	41.28	3.91
1828	3093	5.581126	TCTGAAGAACACATTGTTTGCTT	57.419	34.783	0.00	0.00	41.28	3.91
1829	3094	6.691754	TCTGAAGAACACATTGTTTGCTTA	57.308	33.333	0.00	0.00	41.28	3.09
2170	3453	2.472695	TCACATTTTGAGGACTCGGG	57.527	50.000	0.00	0.00	0.00	5.14
2315	3609	1.000506	AGGCTGCAGCATTTGTTTCAG	59.999	47.619	37.63	0.00	44.36	3.02
2371	3665	5.016831	TGATACAAGCCACTGTCTCTAGAA	58.983	41.667	0.00	0.00	0.00	2.10
2395	3689	9.213799	GAAGCTATTCTCTCAAGTATATTTGGG	57.786	37.037	7.99	4.90	32.33	4.12
2407	3701	8.589338	TCAAGTATATTTGGGATAGCTTCTCTC	58.411	37.037	7.99	0.00	0.00	3.20
2498	3793	2.002586	CGAAGATCGAAGCCAACATGT	58.997	47.619	0.00	0.00	43.74	3.21
2531	3826	9.480861	AATAAGTAGAGAATCATCCGGATATGA	57.519	33.333	18.63	13.93	40.07	2.15
2578	3873	5.391312	ACATGTTAATGCCAGGAAAAGAC	57.609	39.130	0.00	0.00	37.29	3.01
2580	3875	4.112634	TGTTAATGCCAGGAAAAGACCT	57.887	40.909	0.00	0.00	41.43	3.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
9	10	3.726607	CATCTTGCAGCCTACCTTAGAG	58.273	50.000	0.00	0.00	0.00	2.43
140	199	3.493503	GGAAATAGAAGGGCGACAATACG	59.506	47.826	0.00	0.00	0.00	3.06
234	293	7.445402	ACAAGCAGTTGTCTTAACAATACTGAT	59.555	33.333	12.32	5.34	43.88	2.90
297	381	3.055891	GGAATGGGCTGTTTACATGCTTT	60.056	43.478	0.00	0.00	0.00	3.51
390	485	0.749454	ACGCCTGGCATTCATCTTCC	60.749	55.000	20.29	0.00	0.00	3.46
412	507	5.403766	CGATGCATTGGTCTCATCTAACTAC	59.596	44.000	5.98	0.00	35.64	2.73
572	701	7.559845	GCTTTAGTGATCTAAACGCTCTTATG	58.440	38.462	0.00	0.00	40.05	1.90
597	728	3.325870	TGAGATTTTGCTAGTGGTCACG	58.674	45.455	0.00	0.00	36.20	4.35
603	734	2.540361	GCCGCATGAGATTTTGCTAGTG	60.540	50.000	0.00	0.00	36.71	2.74
649	780	3.007182	CCTACAAAGGTCGGTCCAGTTAA	59.993	47.826	0.00	0.00	38.19	2.01
656	787	0.320697	AGTGCCTACAAAGGTCGGTC	59.679	55.000	0.00	0.00	45.64	4.79
670	955	2.031163	AGGCTTCGTGACAGTGCC	59.969	61.111	0.00	0.00	43.52	5.01
738	1173	5.401550	CAATGCACATTTACGAAACCAGAT	58.598	37.500	0.00	0.00	0.00	2.90
853	1977	2.556287	CAGCAAACCGGCTTCGAC	59.444	61.111	0.00	0.00	42.71	4.20
910	2052	1.378119	CAGGCTTGCAGATGAGGCA	60.378	57.895	11.74	0.00	40.58	4.75
951	2093	4.306471	ATCGAGCGAGCGAGCGAG	62.306	66.667	13.62	0.41	44.26	5.03
952	2094	4.300743	GATCGAGCGAGCGAGCGA	62.301	66.667	11.47	11.47	44.26	4.93
1096	2331	3.958822	GAGCTGCGCACCAACATGC	62.959	63.158	5.66	6.73	42.48	4.06
1461	2696	2.844804	CGTCTGAATCTTCCGAACGTAC	59.155	50.000	0.00	0.00	0.00	3.67
1462	2697	2.159476	CCGTCTGAATCTTCCGAACGTA	60.159	50.000	0.00	0.00	0.00	3.57
1463	2698	1.402456	CCGTCTGAATCTTCCGAACGT	60.402	52.381	0.00	0.00	0.00	3.99
1464	2699	1.269166	CCGTCTGAATCTTCCGAACG	58.731	55.000	0.00	0.00	0.00	3.95
1465	2700	1.000145	GCCGTCTGAATCTTCCGAAC	59.000	55.000	0.00	0.00	0.00	3.95
1467	2702	1.254975	TGGCCGTCTGAATCTTCCGA	61.255	55.000	0.00	0.00	0.00	4.55
1468	2703	0.179073	ATGGCCGTCTGAATCTTCCG	60.179	55.000	0.00	0.00	0.00	4.30
1469	2704	1.303309	CATGGCCGTCTGAATCTTCC	58.697	55.000	0.00	0.00	0.00	3.46
1470	2705	0.659957	GCATGGCCGTCTGAATCTTC	59.340	55.000	0.00	0.00	0.00	2.87
1471	2706	0.035152	TGCATGGCCGTCTGAATCTT	60.035	50.000	0.00	0.00	0.00	2.40
1479	2714	1.517694	CTTTGCATGCATGGCCGTC	60.518	57.895	27.34	11.23	0.00	4.79
1493	2728	5.469084	TCATCTCTGCTTGCATATAGCTTTG	59.531	40.000	10.10	1.69	45.94	2.77
1494	2729	5.618236	TCATCTCTGCTTGCATATAGCTTT	58.382	37.500	10.10	0.00	45.94	3.51
1563	2820	0.311790	CTGCAACATCCACACCACAC	59.688	55.000	0.00	0.00	0.00	3.82
1564	2821	0.822944	CCTGCAACATCCACACCACA	60.823	55.000	0.00	0.00	0.00	4.17
1565	2822	1.526575	CCCTGCAACATCCACACCAC	61.527	60.000	0.00	0.00	0.00	4.16
1794	3059	6.411376	TGTGTTCTTCAGAAAGGTTCAGTTA	58.589	36.000	0.00	0.00	35.58	2.24
1815	3080	8.075574	TCAGTTCAGTAATAAGCAAACAATGTG	58.924	33.333	0.00	0.00	0.00	3.21
1827	3092	6.426937	GTCAGCTTGGTTCAGTTCAGTAATAA	59.573	38.462	0.00	0.00	0.00	1.40
1828	3093	5.932303	GTCAGCTTGGTTCAGTTCAGTAATA	59.068	40.000	0.00	0.00	0.00	0.98
1829	3094	4.757149	GTCAGCTTGGTTCAGTTCAGTAAT	59.243	41.667	0.00	0.00	0.00	1.89
2170	3453	4.987285	TCGTCTACATCGTAGTACCAGATC	59.013	45.833	1.36	0.00	0.00	2.75
2276	3570	2.836372	CCTGCAGATATGCCATCCTAGA	59.164	50.000	17.39	0.00	0.00	2.43
2277	3571	2.680221	GCCTGCAGATATGCCATCCTAG	60.680	54.545	17.39	0.00	0.00	3.02
2297	3591	2.427232	TCTGAAACAAATGCTGCAGC	57.573	45.000	31.89	31.89	42.50	5.25
2298	3592	3.314553	CCTTCTGAAACAAATGCTGCAG	58.685	45.455	10.11	10.11	0.00	4.41
2299	3593	2.036217	CCCTTCTGAAACAAATGCTGCA	59.964	45.455	4.13	4.13	0.00	4.41
2300	3594	2.680577	CCCTTCTGAAACAAATGCTGC	58.319	47.619	0.00	0.00	0.00	5.25
2301	3595	2.036217	TGCCCTTCTGAAACAAATGCTG	59.964	45.455	0.00	0.00	0.00	4.41
2302	3596	2.318908	TGCCCTTCTGAAACAAATGCT	58.681	42.857	0.00	0.00	0.00	3.79
2303	3597	2.818130	TGCCCTTCTGAAACAAATGC	57.182	45.000	0.00	0.00	0.00	3.56
2304	3598	3.434299	GCATTGCCCTTCTGAAACAAATG	59.566	43.478	0.00	7.10	0.00	2.32
2305	3599	3.071312	TGCATTGCCCTTCTGAAACAAAT	59.929	39.130	6.12	0.00	0.00	2.32
2306	3600	2.433604	TGCATTGCCCTTCTGAAACAAA	59.566	40.909	6.12	0.00	0.00	2.83
2315	3609	0.391661	TCGACTCTGCATTGCCCTTC	60.392	55.000	6.12	0.00	0.00	3.46
2371	3665	8.497910	TCCCAAATATACTTGAGAGAATAGCT	57.502	34.615	0.00	0.00	0.00	3.32
2395	3689	7.222611	GTGTCATTTCTGAAGAGAGAAGCTATC	59.777	40.741	0.00	0.00	33.50	2.08
2407	3701	6.484643	TCAAGAGGAAAGTGTCATTTCTGAAG	59.515	38.462	0.00	0.00	38.86	3.02
2578	3873	5.782047	TGTATGCCAGAAATTTTGAACAGG	58.218	37.500	0.00	0.00	0.00	4.00
2580	3875	7.048629	TCTTGTATGCCAGAAATTTTGAACA	57.951	32.000	0.00	0.00	0.00	3.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.