AutoCloner

Multiple sequence alignment - TraesCS3B01G197000

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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	TraesCS3B01G197000	chr3B	100.000	3483	0	0	1	3483	224165885	224162403	0.000000e+00	6433.0
1	TraesCS3B01G197000	chr3B	95.717	3292	100	18	227	3483	224288145	224284860	0.000000e+00	5260.0
2	TraesCS3B01G197000	chr3B	90.879	3037	149	59	505	3483	223678853	223675887	0.000000e+00	3956.0
3	TraesCS3B01G197000	chr3B	92.919	692	25	6	1277	1952	223558923	223558240	0.000000e+00	985.0
4	TraesCS3B01G197000	chr3B	92.593	432	22	3	2179	2606	223558129	223557704	2.300000e-171	612.0
5	TraesCS3B01G197000	chr3B	91.192	386	30	3	92	474	223679237	223678853	3.980000e-144	521.0
6	TraesCS3B01G197000	chr3B	89.327	431	22	10	3077	3483	224319052	224318622	1.430000e-143	520.0
7	TraesCS3B01G197000	chr3B	89.074	421	30	6	1287	1692	223690763	223690344	3.100000e-140	508.0
8	TraesCS3B01G197000	chr3B	91.237	194	15	2	1026	1218	224191297	224191105	2.670000e-66	263.0
9	TraesCS3B01G197000	chr3B	90.206	194	17	2	1026	1218	224201689	224201497	5.770000e-63	252.0
10	TraesCS3B01G197000	chr3B	94.783	115	6	0	1323	1437	223653794	223653680	2.760000e-41	180.0
11	TraesCS3B01G197000	chr3B	88.889	90	10	0	1	90	223679362	223679273	1.020000e-20	111.0
12	TraesCS3B01G197000	chr3B	93.846	65	4	0	2611	2675	223557675	223557611	7.960000e-17	99.0
13	TraesCS3B01G197000	chr3B	93.220	59	4	0	2226	2284	469631876	469631934	1.720000e-13	87.9
14	TraesCS3B01G197000	chr3D	92.782	2286	104	23	1253	3483	152852273	152849994	0.000000e+00	3251.0
15	TraesCS3B01G197000	chr3D	92.381	945	55	4	1294	2224	152702619	152701678	0.000000e+00	1330.0
16	TraesCS3B01G197000	chr3D	84.507	1278	124	32	1435	2674	149769996	149768755	0.000000e+00	1195.0
17	TraesCS3B01G197000	chr3D	89.941	845	54	17	2669	3483	153084044	153083201	0.000000e+00	1061.0
18	TraesCS3B01G197000	chr3D	87.100	876	72	15	1429	2284	141410556	141411410	0.000000e+00	953.0
19	TraesCS3B01G197000	chr3D	89.494	514	19	8	2196	2675	152701781	152701269	4.940000e-173	617.0
20	TraesCS3B01G197000	chr3D	85.484	310	38	5	816	1122	435710936	435710631	2.020000e-82	316.0
21	TraesCS3B01G197000	chr3D	83.923	311	43	6	816	1122	47207969	47208276	1.220000e-74	291.0
22	TraesCS3B01G197000	chr3D	77.938	417	70	14	107	511	47194448	47194042	1.250000e-59	241.0
23	TraesCS3B01G197000	chr3D	86.792	53	7	0	2	54	364658710	364658762	3.750000e-05	60.2
24	TraesCS3B01G197000	chr3A	93.303	1329	63	4	1320	2634	177671314	177672630	0.000000e+00	1938.0
25	TraesCS3B01G197000	chr3A	93.156	1125	61	4	1487	2606	177888055	177889168	0.000000e+00	1637.0
26	TraesCS3B01G197000	chr3A	83.921	1219	105	40	1429	2611	159831955	159833118	0.000000e+00	1081.0
27	TraesCS3B01G197000	chr3A	82.827	1252	113	46	1491	2678	181104902	181106115	0.000000e+00	1027.0
28	TraesCS3B01G197000	chr3A	89.048	840	45	18	2669	3481	177105075	177105894	0.000000e+00	998.0
29	TraesCS3B01G197000	chr3A	87.522	561	55	10	1253	1808	177647061	177647611	4.900000e-178	634.0
30	TraesCS3B01G197000	chr3A	95.092	163	6	2	2631	2791	177672706	177672868	4.460000e-64	255.0
31	TraesCS3B01G197000	chr3A	85.621	153	16	2	2099	2248	177888739	177888888	4.650000e-34	156.0
32	TraesCS3B01G197000	chr3A	90.769	65	3	1	2611	2675	177889197	177889258	2.230000e-12	84.2
33	TraesCS3B01G197000	chr5D	88.710	310	30	4	816	1122	344690139	344690446	1.180000e-99	374.0
34	TraesCS3B01G197000	chr5D	84.936	312	37	8	816	1124	137052595	137052291	1.210000e-79	307.0
35	TraesCS3B01G197000	chr5D	84.810	316	36	9	813	1123	237258649	237258957	1.210000e-79	307.0
36	TraesCS3B01G197000	chr5D	83.333	282	29	12	189	460	353518101	353517828	9.660000e-61	244.0
37	TraesCS3B01G197000	chr6D	87.908	306	30	6	816	1117	177797254	177796952	1.540000e-93	353.0
38	TraesCS3B01G197000	chr6B	84.639	319	43	5	809	1123	632504937	632505253	2.610000e-81	313.0
39	TraesCS3B01G197000	chr6B	77.024	457	86	14	115	556	122954115	122953663	9.660000e-61	244.0
40	TraesCS3B01G197000	chr2D	83.654	312	41	8	816	1121	340691299	340691606	5.690000e-73	285.0
41	TraesCS3B01G197000	chr2D	83.582	67	7	3	2	68	539235744	539235806	3.750000e-05	60.2
42	TraesCS3B01G197000	chr1D	79.398	432	65	17	92	514	479781889	479781473	2.050000e-72	283.0
43	TraesCS3B01G197000	chr7D	76.443	433	83	14	92	514	629540019	629539596	2.110000e-52	217.0
44	TraesCS3B01G197000	chr7D	75.490	408	75	17	88	475	365384141	365384543	3.570000e-40	176.0
45	TraesCS3B01G197000	chr2B	77.089	371	59	17	114	471	463478534	463478177	1.280000e-44	191.0
46	TraesCS3B01G197000	chr2B	75.276	453	75	22	92	523	227680090	227680526	7.680000e-42	182.0
47	TraesCS3B01G197000	chr4A	78.700	277	41	12	190	460	707054814	707055078	5.980000e-38	169.0
48	TraesCS3B01G197000	chr5A	73.939	165	39	3	130	290	696246832	696246996	2.900000e-06	63.9
49	TraesCS3B01G197000	chr7B	83.333	66	11	0	1	66	579451488	579451553	1.040000e-05	62.1

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	TraesCS3B01G197000	chr3B	224162403	224165885	3482	True	6433.000000	6433	100.000000	1	3483	1	chr3B.!!$R3	3482
1	TraesCS3B01G197000	chr3B	224284860	224288145	3285	True	5260.000000	5260	95.717000	227	3483	1	chr3B.!!$R6	3256
2	TraesCS3B01G197000	chr3B	223675887	223679362	3475	True	1529.333333	3956	90.320000	1	3483	3	chr3B.!!$R9	3482
3	TraesCS3B01G197000	chr3B	223557611	223558923	1312	True	565.333333	985	93.119333	1277	2675	3	chr3B.!!$R8	1398
4	TraesCS3B01G197000	chr3D	152849994	152852273	2279	True	3251.000000	3251	92.782000	1253	3483	1	chr3D.!!$R3	2230
5	TraesCS3B01G197000	chr3D	149768755	149769996	1241	True	1195.000000	1195	84.507000	1435	2674	1	chr3D.!!$R2	1239
6	TraesCS3B01G197000	chr3D	153083201	153084044	843	True	1061.000000	1061	89.941000	2669	3483	1	chr3D.!!$R4	814
7	TraesCS3B01G197000	chr3D	152701269	152702619	1350	True	973.500000	1330	90.937500	1294	2675	2	chr3D.!!$R6	1381
8	TraesCS3B01G197000	chr3D	141410556	141411410	854	False	953.000000	953	87.100000	1429	2284	1	chr3D.!!$F2	855
9	TraesCS3B01G197000	chr3A	177671314	177672868	1554	False	1096.500000	1938	94.197500	1320	2791	2	chr3A.!!$F5	1471
10	TraesCS3B01G197000	chr3A	159831955	159833118	1163	False	1081.000000	1081	83.921000	1429	2611	1	chr3A.!!$F1	1182
11	TraesCS3B01G197000	chr3A	181104902	181106115	1213	False	1027.000000	1027	82.827000	1491	2678	1	chr3A.!!$F4	1187
12	TraesCS3B01G197000	chr3A	177105075	177105894	819	False	998.000000	998	89.048000	2669	3481	1	chr3A.!!$F2	812
13	TraesCS3B01G197000	chr3A	177647061	177647611	550	False	634.000000	634	87.522000	1253	1808	1	chr3A.!!$F3	555
14	TraesCS3B01G197000	chr3A	177888055	177889258	1203	False	625.733333	1637	89.848667	1487	2675	3	chr3A.!!$F6	1188

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
56	57	0.531974	GCATGCCTCGAATTCCGGTA	60.532	55.0	6.36	0.81	39.14	4.02	F
518	556	0.681733	GGCTCGATATGAAGGCTCCA	59.318	55.0	0.00	0.00	0.00	3.86	F
1164	1205	0.876777	AACGACAAATGGACGCGTGA	60.877	50.0	20.70	2.33	35.16	4.35	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1100	1141	0.381445	TTGTGTGTGCTGACATGTGC	59.619	50.000	1.15	1.24	33.63	4.57	R
2161	2260	2.046892	GTGCAGATGAGCCACCGT	60.047	61.111	0.00	0.00	0.00	4.83	R
2792	3174	5.703592	TGCGTGTTCTGGAAACATAAACTAT	59.296	36.000	0.00	0.00	41.51	2.12	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
55	56	1.819632	GCATGCCTCGAATTCCGGT	60.820	57.895	6.36	0.00	39.14	5.28
56	57	0.531974	GCATGCCTCGAATTCCGGTA	60.532	55.000	6.36	0.81	39.14	4.02
90	91	0.995803	TATGGGTAGGGCACAAGCAA	59.004	50.000	0.00	0.00	44.61	3.91
101	136	0.896940	CACAAGCAAGGGCAGGTGAT	60.897	55.000	5.23	0.00	44.29	3.06
103	138	1.075374	ACAAGCAAGGGCAGGTGATAA	59.925	47.619	0.00	0.00	44.61	1.75
104	139	1.474077	CAAGCAAGGGCAGGTGATAAC	59.526	52.381	0.00	0.00	44.61	1.89
112	147	1.090052	GCAGGTGATAACGTGGGAGC	61.090	60.000	5.07	0.00	0.00	4.70
116	151	2.960129	GATAACGTGGGAGCGGCG	60.960	66.667	0.51	0.51	35.98	6.46
136	171	3.414700	GACTGTGCAACCCTCGCG	61.415	66.667	0.00	0.00	34.36	5.87
178	213	3.869272	CAACTCTGGCATCCGCGC	61.869	66.667	0.00	0.00	39.92	6.86
198	233	2.825836	CGCTGGTGGGGAAGATGC	60.826	66.667	0.00	0.00	0.00	3.91
331	369	3.589988	GACATGGTCGTCAGAGTCATTT	58.410	45.455	0.00	0.00	35.62	2.32
356	394	2.223971	TGGATCGAAATCGGAGTAAGGC	60.224	50.000	2.63	0.00	40.29	4.35
432	470	1.452801	GGTTTTGTGGGGACGGAGA	59.547	57.895	0.00	0.00	0.00	3.71
511	549	4.346709	TCCTACATTTGGGCTCGATATGAA	59.653	41.667	0.03	0.00	0.00	2.57
518	556	0.681733	GGCTCGATATGAAGGCTCCA	59.318	55.000	0.00	0.00	0.00	3.86
525	563	3.941483	CGATATGAAGGCTCCAAACAACT	59.059	43.478	0.00	0.00	0.00	3.16
542	580	3.256631	ACAACTTGATGATTTGAGGGCAC	59.743	43.478	0.00	0.00	0.00	5.01
556	594	2.357034	GCACTTTGAGACGCCCGA	60.357	61.111	0.00	0.00	0.00	5.14
614	653	1.373590	CCCAGACATTTAACGCGGGG	61.374	60.000	12.47	2.72	0.00	5.73
628	667	3.572222	GGGGTTGGGGTGTTCGGA	61.572	66.667	0.00	0.00	0.00	4.55
646	685	1.001860	GGATGTAGATGCTCTCAGGCC	59.998	57.143	0.00	0.00	0.00	5.19
694	733	7.225538	CCAGTAGCGAGATACATCAAAAAGAAT	59.774	37.037	1.28	0.00	0.00	2.40
808	848	1.750778	CATCCATTGGTCCTTTTCCCG	59.249	52.381	1.86	0.00	0.00	5.14
829	869	3.604582	GCTAATCAGAGCAACTCCAACT	58.395	45.455	0.00	0.00	42.36	3.16
1099	1140	4.363990	CACTCGCCAGCGGTCAGT	62.364	66.667	12.71	5.62	40.25	3.41
1100	1141	4.363990	ACTCGCCAGCGGTCAGTG	62.364	66.667	12.71	0.00	40.25	3.66
1117	1158	2.024117	TGCACATGTCAGCACACAC	58.976	52.632	6.75	0.00	34.48	3.82
1154	1195	2.677003	CGGCAGGCGAACGACAAAT	61.677	57.895	11.78	0.00	0.00	2.32
1162	1203	1.857364	GAACGACAAATGGACGCGT	59.143	52.632	13.85	13.85	36.68	6.01
1164	1205	0.876777	AACGACAAATGGACGCGTGA	60.877	50.000	20.70	2.33	35.16	4.35
1182	1223	3.273834	CCGTTTTGGTCGGTGCGT	61.274	61.111	0.00	0.00	42.62	5.24
1453	1530	2.766828	AGTTTCCCCGATCTCGATTCTT	59.233	45.455	0.22	0.00	43.02	2.52
2177	2276	0.108186	CTTACGGTGGCTCATCTGCA	60.108	55.000	0.00	0.00	34.04	4.41
3023	3437	7.863375	CGGTTAGAATCGATAAGTCATTCTCTT	59.137	37.037	0.00	0.00	35.62	2.85
3224	3661	2.288948	TGCATGCTTTGTTTCCATGTCC	60.289	45.455	20.33	0.00	38.79	4.02
3285	3722	7.601886	TCTGTTTGTTTTTCTTGAATGCTTCAA	59.398	29.630	9.84	9.84	46.68	2.69
3367	3804	4.963318	TCAGATCTTTTGTCTGGACAGT	57.037	40.909	0.00	0.00	42.94	3.55
3388	3835	5.461407	CAGTTGTCTCATATCGAAGGACATG	59.539	44.000	0.00	0.00	36.90	3.21
3408	3855	2.306805	TGATGAAGCTGTCACCCTCAAT	59.693	45.455	0.00	0.00	39.72	2.57

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
39	40	1.878102	GCATACCGGAATTCGAGGCAT	60.878	52.381	9.46	8.11	42.43	4.40
40	41	0.531974	GCATACCGGAATTCGAGGCA	60.532	55.000	9.46	6.30	42.43	4.75
46	47	1.563173	GACGCGCATACCGGAATTC	59.437	57.895	9.46	0.00	37.44	2.17
72	73	0.323725	CTTGCTTGTGCCCTACCCAT	60.324	55.000	0.00	0.00	38.71	4.00
73	74	1.074775	CTTGCTTGTGCCCTACCCA	59.925	57.895	0.00	0.00	38.71	4.51
77	78	2.035626	GCCCTTGCTTGTGCCCTA	59.964	61.111	0.00	0.00	38.71	3.53
90	91	1.602237	CCACGTTATCACCTGCCCT	59.398	57.895	0.00	0.00	0.00	5.19
118	153	2.031163	GCGAGGGTTGCACAGTCT	59.969	61.111	0.00	0.00	0.00	3.24
119	154	3.414700	CGCGAGGGTTGCACAGTC	61.415	66.667	0.00	0.00	0.00	3.51
144	179	4.717313	GGCCCCTTCGACCCACAC	62.717	72.222	0.00	0.00	0.00	3.82
151	186	2.592993	CCAGAGTTGGCCCCTTCGA	61.593	63.158	0.00	0.00	37.73	3.71
178	213	3.335356	ATCTTCCCCACCAGCGCAG	62.335	63.158	11.47	0.00	0.00	5.18
181	216	2.825836	GCATCTTCCCCACCAGCG	60.826	66.667	0.00	0.00	0.00	5.18
198	233	1.084370	GTTTCGGATCTGCCACCTCG	61.084	60.000	0.00	0.00	35.94	4.63
212	247	1.966451	GACACAGGGGGCAGTTTCG	60.966	63.158	0.00	0.00	0.00	3.46
222	257	2.825982	TCCAACGTGGACACAGGG	59.174	61.111	3.12	1.03	42.67	4.45
274	312	2.024871	CGACTCCGACCTCGATGC	59.975	66.667	0.00	0.00	43.02	3.91
331	369	2.100197	ACTCCGATTTCGATCCACTCA	58.900	47.619	0.67	0.00	43.02	3.41
356	394	4.000325	TCTCACTCTGTCTCTTCTTCTCG	59.000	47.826	0.00	0.00	0.00	4.04
475	513	3.827817	ATGTAGGACCGATATGGGAGA	57.172	47.619	11.20	0.00	44.64	3.71
511	549	3.228188	TCATCAAGTTGTTTGGAGCCT	57.772	42.857	2.11	0.00	37.39	4.58
518	556	4.344679	TGCCCTCAAATCATCAAGTTGTTT	59.655	37.500	2.11	0.00	34.59	2.83
525	563	4.151121	TCAAAGTGCCCTCAAATCATCAA	58.849	39.130	0.00	0.00	0.00	2.57
542	580	0.179134	CCTACTCGGGCGTCTCAAAG	60.179	60.000	0.00	0.00	0.00	2.77
588	627	2.070783	GTTAAATGTCTGGGCGAACGA	58.929	47.619	0.00	0.00	0.00	3.85
614	653	1.276989	TCTACATCCGAACACCCCAAC	59.723	52.381	0.00	0.00	0.00	3.77
646	685	5.072058	TGGGCTACTTCTACTCTACTCTAGG	59.928	48.000	0.00	0.00	0.00	3.02
736	776	6.018588	CCACTTTCACGTGTTCATGTTTAGTA	60.019	38.462	16.51	0.00	33.07	1.82
808	848	3.373439	CAGTTGGAGTTGCTCTGATTAGC	59.627	47.826	0.00	0.00	43.08	3.09
829	869	2.112297	GTCTGTTTGGGTCGGCCA	59.888	61.111	9.07	0.00	36.17	5.36
1099	1140	0.747283	TGTGTGTGCTGACATGTGCA	60.747	50.000	1.15	4.60	33.63	4.57
1100	1141	0.381445	TTGTGTGTGCTGACATGTGC	59.619	50.000	1.15	1.24	33.63	4.57
1154	1195	2.202905	AAAACGGTCACGCGTCCA	60.203	55.556	9.86	0.00	46.04	4.02
1182	1223	3.818787	GAGCGACTCCGGGCGTAA	61.819	66.667	0.00	0.00	36.06	3.18
1195	1236	3.438087	ACAAATCAAAGGATGTGAGAGCG	59.562	43.478	2.04	0.00	40.62	5.03
1453	1530	4.927782	AGGTGCGCGCAAACTCCA	62.928	61.111	38.24	8.49	0.00	3.86
2161	2260	2.046892	GTGCAGATGAGCCACCGT	60.047	61.111	0.00	0.00	0.00	4.83
2792	3174	5.703592	TGCGTGTTCTGGAAACATAAACTAT	59.296	36.000	0.00	0.00	41.51	2.12
3224	3661	5.277538	GGCCTCTTTAGTTATGCTGAATTCG	60.278	44.000	0.00	0.00	0.00	3.34
3335	3772	8.579863	CAGACAAAAGATCTGAAACCCTAAAAT	58.420	33.333	0.00	0.00	45.46	1.82
3367	3804	5.852282	TCATGTCCTTCGATATGAGACAA	57.148	39.130	7.33	0.00	40.52	3.18
3388	3835	2.479566	TTGAGGGTGACAGCTTCATC	57.520	50.000	18.66	6.54	36.32	2.92
3408	3855	4.756642	CAGCAGAGACCAAAAACTGTGATA	59.243	41.667	0.00	0.00	33.57	2.15
3439	3886	8.328758	CCATATATAGGTTTTATGCTCCAAGGA	58.671	37.037	0.00	0.00	0.00	3.36

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.