AutoCloner

Multiple sequence alignment - TraesCS2D01G074100

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	TraesCS2D01G074100	chr2D	100.000	3456	0	0	1	3456	31609459	31606004	0.000000e+00	6383.0
1	TraesCS2D01G074100	chr2D	86.332	1573	154	23	918	2463	31730046	31728508	0.000000e+00	1657.0
2	TraesCS2D01G074100	chr2D	89.158	1116	121	0	1351	2466	31561232	31560117	0.000000e+00	1391.0
3	TraesCS2D01G074100	chr2D	93.976	249	15	0	3201	3449	31727277	31727029	9.050000e-101	377.0
4	TraesCS2D01G074100	chr2D	88.276	145	15	1	3061	3203	31727519	31727375	4.590000e-39	172.0
5	TraesCS2D01G074100	chr2D	100.000	29	0	0	257	285	406947958	406947986	2.000000e-03	54.7
6	TraesCS2D01G074100	chr2B	94.036	2314	101	10	407	2715	51707499	51705218	0.000000e+00	3474.0
7	TraesCS2D01G074100	chr2B	90.412	1116	84	8	1353	2466	52123408	52124502	0.000000e+00	1447.0
8	TraesCS2D01G074100	chr2B	90.417	720	35	14	2738	3451	51703701	51703010	0.000000e+00	917.0
9	TraesCS2D01G074100	chr2B	93.061	245	17	0	3201	3445	52131040	52131284	3.280000e-95	359.0
10	TraesCS2D01G074100	chr2B	92.653	245	18	0	3201	3445	52133105	52133349	1.530000e-93	353.0
11	TraesCS2D01G074100	chr2B	92.653	245	18	0	3201	3445	52135069	52135313	1.530000e-93	353.0
12	TraesCS2D01G074100	chr2B	93.301	209	13	1	6	214	51708040	51707833	1.200000e-79	307.0
13	TraesCS2D01G074100	chr2B	91.089	202	18	0	2792	2993	52125278	52125479	1.220000e-69	274.0
14	TraesCS2D01G074100	chr2B	91.795	195	14	1	2738	2932	51704737	51704545	1.580000e-68	270.0
15	TraesCS2D01G074100	chr2B	86.275	204	13	12	209	402	51707771	51707573	1.260000e-49	207.0
16	TraesCS2D01G074100	chr2B	77.023	383	41	30	918	1270	52123017	52123382	3.540000e-40	176.0
17	TraesCS2D01G074100	chr2B	87.179	78	7	2	412	489	471439923	471439997	6.150000e-13	86.1
18	TraesCS2D01G074100	chr2B	100.000	44	0	0	3004	3047	52125519	52125562	7.950000e-12	82.4
19	TraesCS2D01G074100	chr2B	87.097	62	8	0	341	402	257527737	257527676	1.720000e-08	71.3
20	TraesCS2D01G074100	chr2A	92.857	1974	119	12	756	2715	33382861	33380896	0.000000e+00	2844.0
21	TraesCS2D01G074100	chr2A	90.388	1134	107	2	1333	2465	33563973	33562841	0.000000e+00	1489.0
22	TraesCS2D01G074100	chr2A	87.831	1134	135	2	1351	2484	33343988	33342858	0.000000e+00	1327.0
23	TraesCS2D01G074100	chr2A	88.571	350	34	3	415	762	33383335	33382990	1.480000e-113	420.0
24	TraesCS2D01G074100	chr2A	92.130	216	15	1	1	214	33383885	33383670	1.560000e-78	303.0
25	TraesCS2D01G074100	chr2A	84.456	193	21	6	3015	3203	33560266	33560079	7.620000e-42	182.0
26	TraesCS2D01G074100	chr2A	82.517	143	15	6	3008	3144	33552310	33552172	2.180000e-22	117.0
27	TraesCS2D01G074100	chr2A	84.000	75	5	5	225	298	670215523	670215591	8.010000e-07	65.8
28	TraesCS2D01G074100	chr2A	100.000	29	0	0	257	285	574968479	574968507	2.000000e-03	54.7
29	TraesCS2D01G074100	chrUn	83.271	1333	180	24	1396	2714	17252922	17254225	0.000000e+00	1186.0
30	TraesCS2D01G074100	chrUn	82.759	87	14	1	415	501	26261681	26261766	3.700000e-10	76.8
31	TraesCS2D01G074100	chr7D	81.481	1026	170	16	1418	2439	154376804	154377813	0.000000e+00	824.0
32	TraesCS2D01G074100	chr7D	87.156	109	14	0	412	520	4626661	4626769	1.300000e-24	124.0
33	TraesCS2D01G074100	chr7D	86.139	101	12	2	421	520	4583352	4583451	1.310000e-19	108.0
34	TraesCS2D01G074100	chr7D	83.750	80	12	1	132	211	623591553	623591475	1.330000e-09	75.0
35	TraesCS2D01G074100	chr7B	80.000	195	36	3	18	211	43704360	43704552	1.290000e-29	141.0
36	TraesCS2D01G074100	chr7B	75.410	183	45	0	27	209	613900140	613900322	4.750000e-14	89.8
37	TraesCS2D01G074100	chr7B	75.275	182	45	0	27	208	613923655	613923836	1.710000e-13	87.9
38	TraesCS2D01G074100	chr4A	86.364	88	11	1	415	502	246650097	246650183	1.020000e-15	95.3
39	TraesCS2D01G074100	chr4A	100.000	28	0	0	154	181	648381636	648381663	6.000000e-03	52.8
40	TraesCS2D01G074100	chr1B	81.720	93	15	2	117	208	336617076	336616985	3.700000e-10	76.8
41	TraesCS2D01G074100	chr6D	93.182	44	3	0	415	458	141787375	141787332	8.010000e-07	65.8
42	TraesCS2D01G074100	chr6D	91.837	49	1	3	415	463	363319412	363319367	8.010000e-07	65.8

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	TraesCS2D01G074100	chr2D	31606004	31609459	3455	True	6383.000000	6383	100.0000	1	3456	1	chr2D.!!$R2	3455
1	TraesCS2D01G074100	chr2D	31560117	31561232	1115	True	1391.000000	1391	89.1580	1351	2466	1	chr2D.!!$R1	1115
2	TraesCS2D01G074100	chr2D	31727029	31730046	3017	True	735.333333	1657	89.5280	918	3449	3	chr2D.!!$R3	2531
3	TraesCS2D01G074100	chr2B	51703010	51708040	5030	True	1035.000000	3474	91.1648	6	3451	5	chr2B.!!$R2	3445
4	TraesCS2D01G074100	chr2B	52123017	52125562	2545	False	494.850000	1447	89.6310	918	3047	4	chr2B.!!$F2	2129
5	TraesCS2D01G074100	chr2B	52131040	52135313	4273	False	355.000000	359	92.7890	3201	3445	3	chr2B.!!$F3	244
6	TraesCS2D01G074100	chr2A	33342858	33343988	1130	True	1327.000000	1327	87.8310	1351	2484	1	chr2A.!!$R1	1133
7	TraesCS2D01G074100	chr2A	33380896	33383885	2989	True	1189.000000	2844	91.1860	1	2715	3	chr2A.!!$R3	2714
8	TraesCS2D01G074100	chr2A	33560079	33563973	3894	True	835.500000	1489	87.4220	1333	3203	2	chr2A.!!$R4	1870
9	TraesCS2D01G074100	chrUn	17252922	17254225	1303	False	1186.000000	1186	83.2710	1396	2714	1	chrUn.!!$F1	1318
10	TraesCS2D01G074100	chr7D	154376804	154377813	1009	False	824.000000	824	81.4810	1418	2439	1	chr7D.!!$F3	1021

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
91	94	1.130955	GTCCATGCGTGCAACTTTTG	58.869	50.0	0.0	0.0	31.75	2.44	F
1093	1409	0.176449	TCTCCATGTGACCAGCATCG	59.824	55.0	0.0	0.0	0.00	3.84	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1439	1770	0.60813	TCCAGATGGTCGAACACCTG	59.392	55.0	18.63	18.63	46.98	4.00	R
3067	6894	0.59117	AAAATTGCGTGTCCAGGTCG	59.409	50.0	0.00	0.00	0.00	4.79	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
85	88	2.203549	TATGGGGTCCATGCGTGCAA	62.204	55.000	9.50	0.00	44.84	4.08
91	94	1.130955	GTCCATGCGTGCAACTTTTG	58.869	50.000	0.00	0.00	31.75	2.44
110	113	2.336088	CAGGTTTTGGCAGCACCG	59.664	61.111	10.56	3.95	43.94	4.94
188	191	3.378911	TTTGAACCGAAAGCCCAATTC	57.621	42.857	0.00	0.00	0.00	2.17
341	427	3.325425	GCCCCAAGCCTAAACCTTAAAAA	59.675	43.478	0.00	0.00	34.35	1.94
342	428	4.801581	GCCCCAAGCCTAAACCTTAAAAAC	60.802	45.833	0.00	0.00	34.35	2.43
343	429	4.262721	CCCCAAGCCTAAACCTTAAAAACC	60.263	45.833	0.00	0.00	0.00	3.27
344	430	4.262721	CCCAAGCCTAAACCTTAAAAACCC	60.263	45.833	0.00	0.00	0.00	4.11
345	431	4.591498	CCAAGCCTAAACCTTAAAAACCCT	59.409	41.667	0.00	0.00	0.00	4.34
346	432	5.776208	CCAAGCCTAAACCTTAAAAACCCTA	59.224	40.000	0.00	0.00	0.00	3.53
347	433	6.268158	CCAAGCCTAAACCTTAAAAACCCTAA	59.732	38.462	0.00	0.00	0.00	2.69
405	560	8.577296	ACTACTATCAAGCTTCGATATTTAGCA	58.423	33.333	14.80	0.00	37.37	3.49
442	597	7.332182	TGCAAACGAAACTTAATTTGGACTTTT	59.668	29.630	0.00	0.00	33.55	2.27
493	648	5.382618	AGAAGATGAAATGACAAAGGCAC	57.617	39.130	0.00	0.00	0.00	5.01
617	774	6.916360	AGTTTTCCAATCTTAAGCCAATCA	57.084	33.333	0.00	0.00	0.00	2.57
627	784	2.268920	GCCAATCAGACGGCCAGA	59.731	61.111	2.24	0.00	42.82	3.86
674	832	1.226746	CTACGAATTTCCGATGGCCC	58.773	55.000	0.00	0.00	0.00	5.80
860	1155	3.703556	TCTTCAATCAAAAACTGCCACCA	59.296	39.130	0.00	0.00	0.00	4.17
876	1171	3.864921	GCCACCAACCTACAGTCTGTAAG	60.865	52.174	13.63	10.24	31.67	2.34
890	1185	1.542030	CTGTAAGCTGTCCGTGACTCT	59.458	52.381	0.00	1.33	33.15	3.24
1041	1357	1.001641	GCATCCTTGTCCACTGGCT	60.002	57.895	0.00	0.00	0.00	4.75
1093	1409	0.176449	TCTCCATGTGACCAGCATCG	59.824	55.000	0.00	0.00	0.00	3.84
1153	1482	3.504863	GAAAATGTCTGCACGCAATGAT	58.495	40.909	0.00	0.00	0.00	2.45
1315	1646	2.911928	GAACTAGCAGGGGGAGCC	59.088	66.667	0.00	0.00	0.00	4.70
1331	1662	0.468400	AGCCGACCATCCTCCTAGAC	60.468	60.000	0.00	0.00	0.00	2.59
1507	1838	2.428925	CCTTAAGCCCGCCGAGGTA	61.429	63.158	0.00	0.00	38.74	3.08
1942	2273	3.023949	GCGTGCCACCTCCATCTCT	62.024	63.158	0.00	0.00	0.00	3.10
2278	2609	2.436109	GGGGTGAAAGAGCTGGCA	59.564	61.111	0.00	0.00	0.00	4.92
2597	2980	3.915437	TTTTTCTGATCGGGTTGAAGC	57.085	42.857	0.62	0.00	0.00	3.86
2604	2987	2.103094	TGATCGGGTTGAAGCTATGAGG	59.897	50.000	0.00	0.00	0.00	3.86
2688	3145	5.163713	GGGAGAGTGAAAGTTGTATTCATGC	60.164	44.000	0.00	0.00	38.89	4.06
2739	3662	2.433145	ATGTGAGGCGCAGTCGTG	60.433	61.111	10.83	0.00	36.95	4.35
2759	5024	2.586792	GGAATCTCGGTGCCAGCT	59.413	61.111	0.00	0.00	0.00	4.24
2804	5069	1.280982	CACAGTGGCACTATACGCAG	58.719	55.000	21.59	8.62	0.00	5.18
2840	5105	5.392380	CGGGAAAACAAGATGGAGATTTCTG	60.392	44.000	0.00	0.00	0.00	3.02
2866	5131	3.689649	GCCACGAGTCCAGATTTGTAATT	59.310	43.478	0.00	0.00	0.00	1.40
2872	5139	5.065218	CGAGTCCAGATTTGTAATTTCCAGG	59.935	44.000	0.00	0.00	0.00	4.45
2993	5260	3.542875	CGAAGCTTGCATACAGATGTTCG	60.543	47.826	2.10	0.00	35.30	3.95
3059	6886	2.517450	GCGAGCCAGCGTGATGTAC	61.517	63.158	0.00	0.00	0.00	2.90
3083	6910	2.047274	CCGACCTGGACACGCAAT	60.047	61.111	0.00	0.00	42.00	3.56
3084	6911	1.671054	CCGACCTGGACACGCAATT	60.671	57.895	0.00	0.00	42.00	2.32
3085	6912	1.234615	CCGACCTGGACACGCAATTT	61.235	55.000	0.00	0.00	42.00	1.82
3086	6913	0.591170	CGACCTGGACACGCAATTTT	59.409	50.000	0.00	0.00	0.00	1.82
3087	6914	1.001815	CGACCTGGACACGCAATTTTT	60.002	47.619	0.00	0.00	0.00	1.94
3155	6986	3.609373	GCTTTTATGTACGTGCGTAGTCA	59.391	43.478	4.58	1.50	0.00	3.41
3175	7006	5.068636	GTCATTGATCCTGCATTGACCTAT	58.931	41.667	0.00	0.00	40.55	2.57
3329	7263	8.257602	TGGTAGGTTAGCAAGATGACATTATA	57.742	34.615	0.00	0.00	32.53	0.98
3346	7280	5.163301	ACATTATAGATCAGAAACACGGGCT	60.163	40.000	0.00	0.00	0.00	5.19
3367	7301	5.039333	GCTAGATTGCAGTAGCCATTTTTG	58.961	41.667	11.79	0.00	41.13	2.44
3399	7333	7.092716	AGTTGAAAATTGCAGTAGCCATTTAG	58.907	34.615	0.80	0.00	43.05	1.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
16	17	5.772672	TGCAAATACCAAACCAGTTATCTGT	59.227	36.000	0.30	0.00	39.82	3.41
85	88	2.418609	GCTGCCAAAACCTGTCAAAAGT	60.419	45.455	0.00	0.00	0.00	2.66
91	94	1.363807	GGTGCTGCCAAAACCTGTC	59.636	57.895	0.00	0.00	37.17	3.51
110	113	4.961438	AAACATGAAATATGGGATGGGC	57.039	40.909	0.00	0.00	0.00	5.36
188	191	8.984764	CACCCATGAATATGCAAAAGAAATATG	58.015	33.333	0.00	0.00	32.79	1.78
297	376	4.383880	GCTTAGGGGTTTAGGGTCTTACAG	60.384	50.000	0.00	0.00	0.00	2.74
303	382	0.549950	GGGCTTAGGGGTTTAGGGTC	59.450	60.000	0.00	0.00	0.00	4.46
402	488	3.505680	TCGTTTGCATACTTCCATTTGCT	59.494	39.130	5.74	0.00	36.10	3.91
405	560	6.084326	AGTTTCGTTTGCATACTTCCATTT	57.916	33.333	5.74	0.00	0.00	2.32
472	627	4.161333	CGTGCCTTTGTCATTTCATCTTC	58.839	43.478	0.00	0.00	0.00	2.87
493	648	2.735772	CCATCCACCTCACCTCCCG	61.736	68.421	0.00	0.00	0.00	5.14
592	747	7.153985	TGATTGGCTTAAGATTGGAAAACTTG	58.846	34.615	6.67	0.00	39.41	3.16
600	757	3.313526	CCGTCTGATTGGCTTAAGATTGG	59.686	47.826	6.67	0.00	0.00	3.16
601	758	4.542662	CCGTCTGATTGGCTTAAGATTG	57.457	45.455	6.67	0.00	0.00	2.67
617	774	1.069765	CAGTTGTGTCTGGCCGTCT	59.930	57.895	0.00	0.00	0.00	4.18
674	832	2.245096	CGGTTCGTAGACTAAACCACG	58.755	52.381	13.93	3.23	42.09	4.94
860	1155	3.258622	GGACAGCTTACAGACTGTAGGTT	59.741	47.826	21.74	15.42	46.82	3.50
876	1171	1.214062	CTCCAGAGTCACGGACAGC	59.786	63.158	6.78	0.00	34.60	4.40
1041	1357	1.281867	CTTGTTCTGGTCCATGGCCTA	59.718	52.381	21.23	2.72	0.00	3.93
1093	1409	1.101331	ACGTACCAGTAGCAGTAGGC	58.899	55.000	0.00	0.00	45.30	3.93
1205	1536	2.192263	GATTCTTCCTCCTCCACTGGT	58.808	52.381	0.00	0.00	0.00	4.00
1315	1646	3.822940	ACTAAGTCTAGGAGGATGGTCG	58.177	50.000	0.00	0.00	0.00	4.79
1320	1651	7.002276	GCTTCTCTTACTAAGTCTAGGAGGAT	58.998	42.308	0.00	0.00	0.00	3.24
1331	1662	0.840729	CGCGCGCTTCTCTTACTAAG	59.159	55.000	30.48	4.24	0.00	2.18
1439	1770	0.608130	TCCAGATGGTCGAACACCTG	59.392	55.000	18.63	18.63	46.98	4.00
1624	1955	1.077501	CATGTTCCCCACGAGGCAT	60.078	57.895	0.00	0.00	0.00	4.40
1786	2117	3.624205	CGGAGAGGAAGAGGTACCTGTTA	60.624	52.174	23.37	0.00	36.57	2.41
2387	2718	2.360350	CGATGTTGCAGGCTGGGT	60.360	61.111	17.64	0.00	0.00	4.51
2579	2962	2.859165	AGCTTCAACCCGATCAGAAA	57.141	45.000	0.00	0.00	0.00	2.52
2597	2980	8.410673	ACAGTAGTACAATACCATCCTCATAG	57.589	38.462	2.52	0.00	0.00	2.23
2688	3145	9.770097	AGGATGTTACACTGATAAATAGACATG	57.230	33.333	0.00	0.00	0.00	3.21
2703	3160	4.871993	CATGCTGAAGAGGATGTTACAC	57.128	45.455	0.00	0.00	41.82	2.90
2804	5069	7.148355	TCTTGTTTTCCCGATTAAACCATAC	57.852	36.000	0.00	0.00	34.21	2.39
2814	5079	4.510167	ATCTCCATCTTGTTTTCCCGAT	57.490	40.909	0.00	0.00	0.00	4.18
2840	5105	2.673368	CAAATCTGGACTCGTGGCTTAC	59.327	50.000	0.00	0.00	0.00	2.34
2866	5131	3.565307	AGAAATGAACAAGCACCTGGAA	58.435	40.909	0.00	0.00	0.00	3.53
2872	5139	7.862372	TCAACTTGATTAGAAATGAACAAGCAC	59.138	33.333	0.00	0.00	38.42	4.40
2984	5251	1.201812	GCACTAACACGCGAACATCTG	60.202	52.381	15.93	0.68	0.00	2.90
2993	5260	2.225491	TGGATTCAAAGCACTAACACGC	59.775	45.455	0.00	0.00	0.00	5.34
3051	6878	2.357009	AGGTCGGATACACGTACATCAC	59.643	50.000	9.91	2.19	34.94	3.06
3052	6879	2.356695	CAGGTCGGATACACGTACATCA	59.643	50.000	9.91	0.00	34.94	3.07
3053	6880	2.287427	CCAGGTCGGATACACGTACATC	60.287	54.545	0.00	0.00	36.56	3.06
3054	6881	1.679680	CCAGGTCGGATACACGTACAT	59.320	52.381	0.00	0.00	36.56	2.29
3055	6882	1.097232	CCAGGTCGGATACACGTACA	58.903	55.000	0.00	0.00	36.56	2.90
3056	6883	1.382522	TCCAGGTCGGATACACGTAC	58.617	55.000	0.00	0.00	39.64	3.67
3057	6884	3.880040	TCCAGGTCGGATACACGTA	57.120	52.632	0.00	0.00	39.64	3.57
3067	6894	0.591170	AAAATTGCGTGTCCAGGTCG	59.409	50.000	0.00	0.00	0.00	4.79
3084	6911	8.888716	GGAAAGTTGCCTGAATTTTTCTAAAAA	58.111	29.630	3.29	3.29	41.59	1.94
3085	6912	8.264347	AGGAAAGTTGCCTGAATTTTTCTAAAA	58.736	29.630	0.00	0.00	29.42	1.52
3086	6913	7.791029	AGGAAAGTTGCCTGAATTTTTCTAAA	58.209	30.769	0.00	0.00	29.42	1.85
3087	6914	7.360113	AGGAAAGTTGCCTGAATTTTTCTAA	57.640	32.000	0.00	0.00	29.42	2.10
3155	6986	4.758674	CGAATAGGTCAATGCAGGATCAAT	59.241	41.667	4.45	0.00	0.00	2.57
3175	7006	1.377202	GAGGCATTGGCTGGACGAA	60.377	57.895	18.51	0.00	38.98	3.85
3204	7035	5.817296	CCGTGTGAATTAAGATCATTCCTGA	59.183	40.000	0.00	0.00	35.41	3.86
3329	7263	2.457598	TCTAGCCCGTGTTTCTGATCT	58.542	47.619	0.00	0.00	0.00	2.75
3346	7280	6.588719	AACAAAAATGGCTACTGCAATCTA	57.411	33.333	0.00	0.00	41.91	1.98
3367	7301	7.119360	GCTACTGCAATTTTCAACTCAAAAAC	58.881	34.615	0.00	0.00	39.41	2.43
3399	7333	3.602483	TCCTGTTGCCGAATAAACCTAC	58.398	45.455	0.00	0.00	0.00	3.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.