AutoCloner

Multiple sequence alignment - TraesCS6A01G248000

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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	TraesCS6A01G248000	chr6A	100.000	3575	0	0	1	3575	460007454	460003880	0.000000e+00	6602.0
1	TraesCS6A01G248000	chr6A	91.265	1557	108	16	1032	2565	459878438	459876887	0.000000e+00	2097.0
2	TraesCS6A01G248000	chr6A	90.566	106	9	1	2901	3005	460004385	460004280	4.810000e-29	139.0
3	TraesCS6A01G248000	chr6A	90.566	106	9	1	3070	3175	460004554	460004450	4.810000e-29	139.0
4	TraesCS6A01G248000	chr6A	100.000	32	0	0	2881	2912	460004427	460004396	3.850000e-05	60.2
5	TraesCS6A01G248000	chr6B	94.911	2751	71	11	1	2743	500893234	500895923	0.000000e+00	4241.0
6	TraesCS6A01G248000	chr6B	90.792	1553	114	15	1032	2556	501062655	501064206	0.000000e+00	2049.0
7	TraesCS6A01G248000	chr6B	91.971	411	26	3	3000	3407	500896304	500896710	1.440000e-158	569.0
8	TraesCS6A01G248000	chr6B	84.828	290	15	8	2742	3002	500896183	500896472	7.610000e-67	265.0
9	TraesCS6A01G248000	chr6B	84.746	177	6	7	3417	3575	500898142	500898315	1.330000e-34	158.0
10	TraesCS6A01G248000	chr6B	93.103	58	4	0	3420	3477	702422688	702422631	6.360000e-13	86.1
11	TraesCS6A01G248000	chr6D	97.320	1940	40	5	710	2645	322587315	322585384	0.000000e+00	3284.0
12	TraesCS6A01G248000	chr6D	90.983	1730	113	25	1032	2727	322572298	322570578	0.000000e+00	2290.0
13	TraesCS6A01G248000	chr6D	93.255	682	29	6	1	673	322587987	322587314	0.000000e+00	989.0
14	TraesCS6A01G248000	chr6D	87.418	612	31	11	3006	3575	322582245	322581638	0.000000e+00	662.0
15	TraesCS6A01G248000	chr6D	93.772	289	5	6	2641	2920	322583007	322582723	4.270000e-114	422.0
16	TraesCS6A01G248000	chr6D	92.857	98	5	2	3085	3181	322582411	322582315	1.340000e-29	141.0
17	TraesCS6A01G248000	chr6D	87.736	106	12	1	2901	3005	322582183	322582078	4.850000e-24	122.0
18	TraesCS6A01G248000	chr6D	100.000	32	0	0	2881	2912	322582223	322582192	3.850000e-05	60.2
19	TraesCS6A01G248000	chr2D	89.664	1190	110	9	1086	2270	15133811	15134992	0.000000e+00	1504.0
20	TraesCS6A01G248000	chr3D	87.782	1195	142	4	1085	2277	213996921	213998113	0.000000e+00	1395.0
21	TraesCS6A01G248000	chr3B	87.688	1194	143	4	1085	2276	330800921	330799730	0.000000e+00	1387.0
22	TraesCS6A01G248000	chr3A	87.583	1200	145	4	1080	2277	279436896	279435699	0.000000e+00	1387.0
23	TraesCS6A01G248000	chr4D	84.831	178	22	4	3200	3373	165887474	165887298	1.320000e-39	174.0
24	TraesCS6A01G248000	chr5B	81.250	176	27	4	3200	3370	27840697	27840871	1.730000e-28	137.0
25	TraesCS6A01G248000	chr2A	86.792	106	8	4	3070	3172	561558099	561558201	2.920000e-21	113.0
26	TraesCS6A01G248000	chr7A	87.013	77	10	0	3246	3322	33974919	33974843	1.770000e-13	87.9
27	TraesCS6A01G248000	chr7A	82.278	79	13	1	3095	3172	131122528	131122606	2.300000e-07	67.6
28	TraesCS6A01G248000	chr7D	84.091	88	13	1	3095	3181	132747121	132747034	2.290000e-12	84.2

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	TraesCS6A01G248000	chr6A	460003880	460007454	3574	True	1735.050000	6602	95.283	1	3575	4	chr6A.!!$R2	3574
1	TraesCS6A01G248000	chr6A	459876887	459878438	1551	True	2097.000000	2097	91.265	1032	2565	1	chr6A.!!$R1	1533
2	TraesCS6A01G248000	chr6B	501062655	501064206	1551	False	2049.000000	2049	90.792	1032	2556	1	chr6B.!!$F1	1524
3	TraesCS6A01G248000	chr6B	500893234	500898315	5081	False	1308.250000	4241	89.114	1	3575	4	chr6B.!!$F2	3574
4	TraesCS6A01G248000	chr6D	322570578	322572298	1720	True	2290.000000	2290	90.983	1032	2727	1	chr6D.!!$R1	1695
5	TraesCS6A01G248000	chr6D	322581638	322587987	6349	True	811.457143	3284	93.194	1	3575	7	chr6D.!!$R2	3574
6	TraesCS6A01G248000	chr2D	15133811	15134992	1181	False	1504.000000	1504	89.664	1086	2270	1	chr2D.!!$F1	1184
7	TraesCS6A01G248000	chr3D	213996921	213998113	1192	False	1395.000000	1395	87.782	1085	2277	1	chr3D.!!$F1	1192
8	TraesCS6A01G248000	chr3B	330799730	330800921	1191	True	1387.000000	1387	87.688	1085	2276	1	chr3B.!!$R1	1191
9	TraesCS6A01G248000	chr3A	279435699	279436896	1197	True	1387.000000	1387	87.583	1080	2277	1	chr3A.!!$R1	1197

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
841	861	0.407918	TTGACCAATCAACCCCCTCC	59.592	55.0	0.00	0.00	40.01	4.30	F
1613	1641	0.763223	ACGGAAAGACCCAGGTCACT	60.763	55.0	18.77	5.07	46.76	3.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2283	2311	2.035442	GGCGGCAGACCAAGAGAAC	61.035	63.158	3.07	0.0	34.57	3.01	R
3182	6323	0.795735	GCATCAACATGCGACACTGC	60.796	55.000	0.00	0.0	46.06	4.40	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
17	18	4.351054	CGCAAGGTTGGCCTCCCT	62.351	66.667	3.32	6.07	46.33	4.20
58	60	8.397906	TCATGTTTCGATCTTCCATGTTTAATC	58.602	33.333	0.00	0.00	35.54	1.75
110	117	9.392021	GTGGCGTAATTACTAGTACTAGATTTC	57.608	37.037	31.93	18.94	36.97	2.17
137	156	2.346803	TGCGAAGAACATGGCTAGTTC	58.653	47.619	12.61	12.61	44.32	3.01
145	164	5.643339	GAACATGGCTAGTTCGTTATGAG	57.357	43.478	0.00	0.00	36.40	2.90
146	165	4.737855	ACATGGCTAGTTCGTTATGAGT	57.262	40.909	0.00	0.00	0.00	3.41
272	291	2.588201	GCCCCGGATCATCTCTCCC	61.588	68.421	0.73	0.00	0.00	4.30
282	301	2.427245	ATCTCTCCCCCGCTTGTCG	61.427	63.158	0.00	0.00	38.08	4.35
370	389	4.961511	GTGTGGGTCGCGCTGTCA	62.962	66.667	5.56	0.00	0.00	3.58
401	420	0.865769	CTACGTCCAACAAGTGTGCC	59.134	55.000	0.00	0.00	0.00	5.01
736	756	1.016130	CACAGTGAGATGTGTCCCGC	61.016	60.000	0.00	0.00	44.49	6.13
737	757	1.448540	CAGTGAGATGTGTCCCGCC	60.449	63.158	0.00	0.00	0.00	6.13
738	758	2.509336	GTGAGATGTGTCCCGCCG	60.509	66.667	0.00	0.00	0.00	6.46
739	759	4.451150	TGAGATGTGTCCCGCCGC	62.451	66.667	0.00	0.00	0.00	6.53
841	861	0.407918	TTGACCAATCAACCCCCTCC	59.592	55.000	0.00	0.00	40.01	4.30
876	896	5.586643	TGTTATTTTTCTTGTTTTGGGGTGC	59.413	36.000	0.00	0.00	0.00	5.01
921	944	3.720193	CTGTGAGGCGTGTGCTGC	61.720	66.667	0.00	0.00	42.25	5.25
922	945	4.240103	TGTGAGGCGTGTGCTGCT	62.240	61.111	0.00	0.00	42.25	4.24
923	946	3.720193	GTGAGGCGTGTGCTGCTG	61.720	66.667	0.00	0.00	42.25	4.41
936	959	4.024556	GTGTGCTGCTGTATATTGGTCATC	60.025	45.833	0.00	0.00	0.00	2.92
1087	1111	1.090052	GGCACCGCTAGCACTAAAGG	61.090	60.000	16.45	9.04	0.00	3.11
1130	1154	1.244816	TCACGTCCGAGTCTGTGAAT	58.755	50.000	0.00	0.00	38.32	2.57
1226	1254	1.302033	CAAGGTTGCCTGCGAGACT	60.302	57.895	0.00	0.00	32.13	3.24
1271	1299	0.904865	TCTTGGGCGAGATCACCACT	60.905	55.000	0.00	0.00	33.20	4.00
1613	1641	0.763223	ACGGAAAGACCCAGGTCACT	60.763	55.000	18.77	5.07	46.76	3.41
2360	2405	5.190528	TGGGAAGTGAGAAGAAGCATTAGAT	59.809	40.000	0.00	0.00	0.00	1.98
2418	2463	7.241042	TGGTAGTCAGTGCTAAGTTTCTTAT	57.759	36.000	0.00	0.00	0.00	1.73
2470	2523	0.948141	AGTCGCTGAAACTGCTGAGC	60.948	55.000	0.00	0.00	0.00	4.26
2471	2524	0.948141	GTCGCTGAAACTGCTGAGCT	60.948	55.000	5.83	0.00	0.00	4.09
2513	2566	3.318275	AGTCGCTCTGTCACTTTCACTTA	59.682	43.478	0.00	0.00	0.00	2.24
2565	2635	4.906747	ATGCTCTTTCTTCCTGAGTCTT	57.093	40.909	0.00	0.00	0.00	3.01
2830	5548	5.048294	GGTTTGGTGTAAACTACAAGGATGG	60.048	44.000	0.00	0.00	46.26	3.51
2877	5595	7.382218	GGTTGGTGTTGTTGAGAATTCATAAAG	59.618	37.037	8.44	0.00	32.27	1.85
2886	5613	8.912988	TGTTGAGAATTCATAAAGAAGTTTGGT	58.087	29.630	8.44	0.00	40.15	3.67
2945	5989	8.515695	TGAAGTATTTGATAGTCTCTTACCGA	57.484	34.615	0.00	0.00	0.00	4.69
2967	6011	9.841295	ACCGAGGTATAATTATGTGTTATTTGT	57.159	29.630	8.28	0.00	0.00	2.83
3115	6235	8.156820	TGAAGTATTTTGATGGTCTCTTTCTGA	58.843	33.333	0.00	0.00	0.00	3.27
3335	6479	7.225341	GCTTCTTGAGAAATTGTTGACCAAAAT	59.775	33.333	0.00	0.00	36.44	1.82
3358	6502	9.506018	AAATAAAATTGGGAACTCAATCCAAAG	57.494	29.630	0.22	0.00	42.86	2.77
3387	6531	2.453638	GCTACAAAGAGCGTCCGCC	61.454	63.158	8.23	0.06	43.17	6.13
3389	6533	0.669318	CTACAAAGAGCGTCCGCCAA	60.669	55.000	8.23	0.00	43.17	4.52
3482	8048	9.959749	TGAACTAAATTTAAAATTGAAGAGCGT	57.040	25.926	0.00	0.00	0.00	5.07
3539	8123	4.163078	ACCCAATCAAAAACACCAATGTCA	59.837	37.500	0.00	0.00	38.45	3.58
3565	8149	2.000048	TGAATGGGAGGCCTTTAACCT	59.000	47.619	6.77	0.00	41.41	3.50

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
58	60	5.959527	CACGTATGATGAAGAAAAACGATGG	59.040	40.000	0.00	0.00	33.40	3.51
137	156	2.348666	GTGCTACTGCCAACTCATAACG	59.651	50.000	0.00	0.00	38.71	3.18
138	157	2.348666	CGTGCTACTGCCAACTCATAAC	59.651	50.000	0.00	0.00	38.71	1.89
139	158	2.028476	ACGTGCTACTGCCAACTCATAA	60.028	45.455	0.00	0.00	38.71	1.90
140	159	1.548719	ACGTGCTACTGCCAACTCATA	59.451	47.619	0.00	0.00	38.71	2.15
141	160	0.321671	ACGTGCTACTGCCAACTCAT	59.678	50.000	0.00	0.00	38.71	2.90
142	161	0.319555	GACGTGCTACTGCCAACTCA	60.320	55.000	0.00	0.00	38.71	3.41
143	162	1.014564	GGACGTGCTACTGCCAACTC	61.015	60.000	0.00	0.00	38.71	3.01
144	163	1.004918	GGACGTGCTACTGCCAACT	60.005	57.895	0.00	0.00	38.71	3.16
145	164	1.004918	AGGACGTGCTACTGCCAAC	60.005	57.895	8.23	0.00	38.71	3.77
146	165	1.005037	CAGGACGTGCTACTGCCAA	60.005	57.895	10.03	0.00	38.71	4.52
227	246	2.506438	GGCGAACGAGGAAGACGG	60.506	66.667	0.00	0.00	34.93	4.79
256	275	1.915769	GGGGGAGAGATGATCCGGG	60.916	68.421	0.00	0.00	37.75	5.73
257	276	2.279069	CGGGGGAGAGATGATCCGG	61.279	68.421	0.00	0.00	37.75	5.14
258	277	2.936912	GCGGGGGAGAGATGATCCG	61.937	68.421	0.00	0.00	37.75	4.18
261	280	0.692419	ACAAGCGGGGGAGAGATGAT	60.692	55.000	0.00	0.00	0.00	2.45
701	721	3.716195	TGGCACATCGTCTGGGGG	61.716	66.667	0.00	0.00	0.00	5.40
841	861	8.980143	ACAAGAAAAATAACAAATATGTCCCG	57.020	30.769	0.00	0.00	39.40	5.14
876	896	3.863142	ATAAGCCAGAGCAGCAAAAAG	57.137	42.857	0.00	0.00	43.56	2.27
921	944	4.876125	ACGCTCTGATGACCAATATACAG	58.124	43.478	0.00	0.00	0.00	2.74
922	945	4.584743	AGACGCTCTGATGACCAATATACA	59.415	41.667	0.00	0.00	0.00	2.29
923	946	5.127693	AGACGCTCTGATGACCAATATAC	57.872	43.478	0.00	0.00	0.00	1.47
1087	1111	4.814294	ACGTCTCGGCCGCCATTC	62.814	66.667	23.51	7.89	0.00	2.67
1271	1299	2.183409	GTAGTCGACGGTGGCCTTA	58.817	57.895	10.46	0.00	0.00	2.69
1586	1614	1.262640	GGGTCTTTCCGTCAGGCCTA	61.263	60.000	3.98	0.00	36.17	3.93
1613	1641	3.057969	TCCTCGTTTAGGTACTCGACA	57.942	47.619	0.00	0.00	46.62	4.35
2283	2311	2.035442	GGCGGCAGACCAAGAGAAC	61.035	63.158	3.07	0.00	34.57	3.01
2360	2405	2.422479	AGTGTAGAGCGTCGCTTCAATA	59.578	45.455	22.67	9.48	39.88	1.90
2513	2566	8.109634	AGGGAACTACACAACAAAGAATATGAT	58.890	33.333	0.00	0.00	40.61	2.45
2565	2635	7.047891	ACACATCGCTCTTTATTATCTTTCCA	58.952	34.615	0.00	0.00	0.00	3.53
2584	2655	8.430801	AGAACAGAGCAATAGAATTACACATC	57.569	34.615	0.00	0.00	0.00	3.06
2665	5119	5.360714	ACACCAATTGGACATAACCATGATC	59.639	40.000	31.22	0.00	39.82	2.92
2675	5129	2.225242	TGGGCTTACACCAATTGGACAT	60.225	45.455	31.22	16.78	38.94	3.06
2877	5595	3.476552	TCATCTCCACACACCAAACTTC	58.523	45.455	0.00	0.00	0.00	3.01
2886	5613	4.356405	AACACTTCATCATCTCCACACA	57.644	40.909	0.00	0.00	0.00	3.72
2967	6011	9.674068	TTTCCTGCATATGTGTGTATTAGTTTA	57.326	29.630	4.29	0.00	0.00	2.01
2971	6015	7.792374	ACTTTCCTGCATATGTGTGTATTAG	57.208	36.000	4.29	0.00	0.00	1.73
2975	6019	6.237901	AGAAACTTTCCTGCATATGTGTGTA	58.762	36.000	4.29	0.00	0.00	2.90
2976	6020	5.072741	AGAAACTTTCCTGCATATGTGTGT	58.927	37.500	4.29	0.00	0.00	3.72
3182	6323	0.795735	GCATCAACATGCGACACTGC	60.796	55.000	0.00	0.00	46.06	4.40
3335	6479	7.288852	TGACTTTGGATTGAGTTCCCAATTTTA	59.711	33.333	0.00	0.00	39.43	1.52
3358	6502	4.260375	CGCTCTTTGTAGCACCAATATGAC	60.260	45.833	0.00	0.00	42.91	3.06
3408	6552	6.429692	TCTCAAATCAATCGGTAACAACATGT	59.570	34.615	0.00	0.00	0.00	3.21
3474	8040	7.692705	GGTCAATAATTTTTCTACACGCTCTTC	59.307	37.037	0.00	0.00	0.00	2.87
3477	8043	6.837992	TGGTCAATAATTTTTCTACACGCTC	58.162	36.000	0.00	0.00	0.00	5.03
3479	8045	7.081976	ACTTGGTCAATAATTTTTCTACACGC	58.918	34.615	0.00	0.00	0.00	5.34
3481	8047	9.959749	TTGACTTGGTCAATAATTTTTCTACAC	57.040	29.630	8.75	0.00	45.88	2.90
3524	8108	6.083098	TCAATCGATGACATTGGTGTTTTT	57.917	33.333	0.00	0.00	39.09	1.94
3529	8113	4.498513	CCCATTCAATCGATGACATTGGTG	60.499	45.833	0.00	2.56	37.92	4.17
3539	8123	1.143813	AGGCCTCCCATTCAATCGAT	58.856	50.000	0.00	0.00	0.00	3.59

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.