AutoCloner

Multiple sequence alignment - TraesCS3D01G472900

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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	TraesCS3D01G472900	chr3D	100.000	2869	0	0	603	3471	574783251	574780383	0.000000e+00	5299.0
1	TraesCS3D01G472900	chr3D	87.480	1270	140	8	2219	3471	575479921	575481188	0.000000e+00	1447.0
2	TraesCS3D01G472900	chr3D	85.019	1295	171	11	2172	3446	575527340	575528631	0.000000e+00	1295.0
3	TraesCS3D01G472900	chr3D	83.373	1269	188	17	2198	3446	575546577	575547842	0.000000e+00	1153.0
4	TraesCS3D01G472900	chr3D	81.594	1217	197	21	750	1947	574771492	574770284	0.000000e+00	981.0
5	TraesCS3D01G472900	chr3D	81.594	1217	197	21	750	1947	575486685	575487893	0.000000e+00	981.0
6	TraesCS3D01G472900	chr3D	77.114	1206	222	39	2269	3445	612858834	612857654	0.000000e+00	649.0
7	TraesCS3D01G472900	chr3D	100.000	230	0	0	1	230	574783853	574783624	3.200000e-115	425.0
8	TraesCS3D01G472900	chr3D	92.917	240	7	1	1	230	397387076	397387315	1.190000e-89	340.0
9	TraesCS3D01G472900	chr3D	92.917	240	7	1	1	230	579177726	579177487	1.190000e-89	340.0
10	TraesCS3D01G472900	chr3A	97.369	2737	66	3	740	3471	710836756	710839491	0.000000e+00	4650.0
11	TraesCS3D01G472900	chr3A	86.222	2475	295	23	1001	3446	711056723	711059180	0.000000e+00	2639.0
12	TraesCS3D01G472900	chr3A	85.760	1566	191	15	1906	3446	710937207	710938765	0.000000e+00	1628.0
13	TraesCS3D01G472900	chr3A	86.002	1243	140	22	2238	3452	710948358	710949594	0.000000e+00	1301.0
14	TraesCS3D01G472900	chr3A	84.720	1178	159	15	750	1914	710935351	710936520	0.000000e+00	1158.0
15	TraesCS3D01G472900	chr3A	78.631	1198	216	28	2269	3445	747573371	747572193	0.000000e+00	758.0
16	TraesCS3D01G472900	chr3A	80.952	651	119	4	2269	2915	747610106	747609457	8.590000e-141	510.0
17	TraesCS3D01G472900	chr3B	95.004	1381	61	3	740	2117	765547661	765549036	0.000000e+00	2161.0
18	TraesCS3D01G472900	chr3B	94.250	1374	68	6	2107	3471	765549080	765550451	0.000000e+00	2089.0
19	TraesCS3D01G472900	chr3B	85.358	1564	196	20	1906	3445	765669983	765671537	0.000000e+00	1589.0
20	TraesCS3D01G472900	chr3B	85.266	1561	200	17	1906	3446	765623269	765624819	0.000000e+00	1581.0
21	TraesCS3D01G472900	chr3B	84.133	1563	201	24	1906	3446	765658031	765659568	0.000000e+00	1469.0
22	TraesCS3D01G472900	chr3B	86.062	1191	139	15	740	1915	765667946	765669124	0.000000e+00	1254.0
23	TraesCS3D01G472900	chr3B	87.184	1108	119	16	816	1908	765621768	765622867	0.000000e+00	1238.0
24	TraesCS3D01G472900	chr3B	88.725	949	99	6	898	1841	765656643	765657588	0.000000e+00	1153.0
25	TraesCS3D01G472900	chr3B	83.163	1271	188	19	2198	3446	765928465	765929731	0.000000e+00	1138.0
26	TraesCS3D01G472900	chr2D	94.583	240	3	1	1	230	555392190	555391951	2.550000e-96	363.0
27	TraesCS3D01G472900	chr2D	94.393	107	4	1	603	709	555391746	555391642	2.770000e-36	163.0
28	TraesCS3D01G472900	chrUn	94.167	240	4	1	1	230	29649822	29649583	1.180000e-94	357.0
29	TraesCS3D01G472900	chr6D	94.167	240	4	1	1	230	3734866	3734627	1.180000e-94	357.0
30	TraesCS3D01G472900	chr6D	93.644	236	5	1	4	229	413052298	413052063	9.220000e-91	344.0
31	TraesCS3D01G472900	chr6D	80.851	94	10	5	603	696	26119167	26119252	2.240000e-07	67.6
32	TraesCS3D01G472900	chr1D	94.167	240	4	1	1	230	407470	407709	1.180000e-94	357.0
33	TraesCS3D01G472900	chr1D	93.750	240	5	1	1	230	427593102	427592863	5.510000e-93	351.0
34	TraesCS3D01G472900	chr1D	93.939	231	4	1	1	221	468102589	468102819	1.190000e-89	340.0
35	TraesCS3D01G472900	chr1D	93.678	174	1	5	1	164	417370500	417370673	5.750000e-63	252.0
36	TraesCS3D01G472900	chr1D	96.190	105	4	0	603	707	427592105	427592001	4.610000e-39	172.0
37	TraesCS3D01G472900	chr5D	93.627	204	3	1	1	194	334018357	334018560	2.620000e-76	296.0
38	TraesCS3D01G472900	chr5D	100.000	93	0	0	1	93	334014527	334014435	4.610000e-39	172.0

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	TraesCS3D01G472900	chr3D	574780383	574783853	3470	True	2862.0	5299	100.000	1	3471	2	chr3D.!!$R4	3470
1	TraesCS3D01G472900	chr3D	575479921	575481188	1267	False	1447.0	1447	87.480	2219	3471	1	chr3D.!!$F2	1252
2	TraesCS3D01G472900	chr3D	575527340	575528631	1291	False	1295.0	1295	85.019	2172	3446	1	chr3D.!!$F4	1274
3	TraesCS3D01G472900	chr3D	575546577	575547842	1265	False	1153.0	1153	83.373	2198	3446	1	chr3D.!!$F5	1248
4	TraesCS3D01G472900	chr3D	574770284	574771492	1208	True	981.0	981	81.594	750	1947	1	chr3D.!!$R1	1197
5	TraesCS3D01G472900	chr3D	575486685	575487893	1208	False	981.0	981	81.594	750	1947	1	chr3D.!!$F3	1197
6	TraesCS3D01G472900	chr3D	612857654	612858834	1180	True	649.0	649	77.114	2269	3445	1	chr3D.!!$R3	1176
7	TraesCS3D01G472900	chr3A	710836756	710839491	2735	False	4650.0	4650	97.369	740	3471	1	chr3A.!!$F1	2731
8	TraesCS3D01G472900	chr3A	711056723	711059180	2457	False	2639.0	2639	86.222	1001	3446	1	chr3A.!!$F3	2445
9	TraesCS3D01G472900	chr3A	710935351	710938765	3414	False	1393.0	1628	85.240	750	3446	2	chr3A.!!$F4	2696
10	TraesCS3D01G472900	chr3A	710948358	710949594	1236	False	1301.0	1301	86.002	2238	3452	1	chr3A.!!$F2	1214
11	TraesCS3D01G472900	chr3A	747572193	747573371	1178	True	758.0	758	78.631	2269	3445	1	chr3A.!!$R1	1176
12	TraesCS3D01G472900	chr3A	747609457	747610106	649	True	510.0	510	80.952	2269	2915	1	chr3A.!!$R2	646
13	TraesCS3D01G472900	chr3B	765547661	765550451	2790	False	2125.0	2161	94.627	740	3471	2	chr3B.!!$F2	2731
14	TraesCS3D01G472900	chr3B	765667946	765671537	3591	False	1421.5	1589	85.710	740	3445	2	chr3B.!!$F5	2705
15	TraesCS3D01G472900	chr3B	765621768	765624819	3051	False	1409.5	1581	86.225	816	3446	2	chr3B.!!$F3	2630
16	TraesCS3D01G472900	chr3B	765656643	765659568	2925	False	1311.0	1469	86.429	898	3446	2	chr3B.!!$F4	2548
17	TraesCS3D01G472900	chr3B	765928465	765929731	1266	False	1138.0	1138	83.163	2198	3446	1	chr3B.!!$F1	1248
18	TraesCS3D01G472900	chr2D	555391642	555392190	548	True	263.0	363	94.488	1	709	2	chr2D.!!$R1	708
19	TraesCS3D01G472900	chr1D	427592001	427593102	1101	True	261.5	351	94.970	1	707	2	chr1D.!!$R1	706

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
714	1110	0.102481	GAGGATAAGTTCGCCGCTGA	59.898	55.0	0.00	0.0	0.0	4.26	F
717	1113	0.102481	GATAAGTTCGCCGCTGAGGA	59.898	55.0	0.09	0.0	45.0	3.71	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2356	4026	2.339418	TGCGGGTTGTCGTAATTAGTG	58.661	47.619	0.0	0.0	0.00	2.74	R
2482	4155	2.368875	TCTTGAGGACACCCTTTCTCAC	59.631	50.000	0.0	0.0	44.53	3.51	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
632	1028	1.233369	GGGAGGAGATCGAGGGGAA	59.767	63.158	0.00	0.00	0.00	3.97
710	1106	3.165559	CGAGAGGATAAGTTCGCCG	57.834	57.895	0.00	0.00	0.00	6.46
711	1107	0.935366	CGAGAGGATAAGTTCGCCGC	60.935	60.000	0.00	0.00	0.00	6.53
712	1108	0.386113	GAGAGGATAAGTTCGCCGCT	59.614	55.000	0.74	0.74	34.42	5.52
713	1109	0.103208	AGAGGATAAGTTCGCCGCTG	59.897	55.000	0.39	0.00	30.39	5.18
714	1110	0.102481	GAGGATAAGTTCGCCGCTGA	59.898	55.000	0.00	0.00	0.00	4.26
715	1111	0.103208	AGGATAAGTTCGCCGCTGAG	59.897	55.000	0.00	0.00	0.00	3.35
716	1112	0.876342	GGATAAGTTCGCCGCTGAGG	60.876	60.000	0.00	0.00	44.97	3.86
717	1113	0.102481	GATAAGTTCGCCGCTGAGGA	59.898	55.000	0.09	0.00	45.00	3.71
718	1114	0.103208	ATAAGTTCGCCGCTGAGGAG	59.897	55.000	0.09	0.00	45.00	3.69
719	1115	1.945354	TAAGTTCGCCGCTGAGGAGG	61.945	60.000	0.09	0.00	45.00	4.30
720	1116	4.070552	GTTCGCCGCTGAGGAGGT	62.071	66.667	0.09	0.00	45.00	3.85
721	1117	4.069232	TTCGCCGCTGAGGAGGTG	62.069	66.667	0.09	0.00	45.00	4.00
723	1119	3.449227	CGCCGCTGAGGAGGTGTA	61.449	66.667	0.09	0.00	45.00	2.90
724	1120	2.496817	GCCGCTGAGGAGGTGTAG	59.503	66.667	0.09	0.00	45.00	2.74
725	1121	2.052690	GCCGCTGAGGAGGTGTAGA	61.053	63.158	0.09	0.00	45.00	2.59
726	1122	1.395826	GCCGCTGAGGAGGTGTAGAT	61.396	60.000	0.09	0.00	45.00	1.98
727	1123	0.387202	CCGCTGAGGAGGTGTAGATG	59.613	60.000	0.00	0.00	45.00	2.90
728	1124	0.387202	CGCTGAGGAGGTGTAGATGG	59.613	60.000	0.00	0.00	0.00	3.51
729	1125	0.755686	GCTGAGGAGGTGTAGATGGG	59.244	60.000	0.00	0.00	0.00	4.00
730	1126	1.689575	GCTGAGGAGGTGTAGATGGGA	60.690	57.143	0.00	0.00	0.00	4.37
731	1127	2.969628	CTGAGGAGGTGTAGATGGGAT	58.030	52.381	0.00	0.00	0.00	3.85
732	1128	2.896685	CTGAGGAGGTGTAGATGGGATC	59.103	54.545	0.00	0.00	0.00	3.36
733	1129	1.889829	GAGGAGGTGTAGATGGGATCG	59.110	57.143	0.00	0.00	0.00	3.69
734	1130	0.318762	GGAGGTGTAGATGGGATCGC	59.681	60.000	2.14	2.14	0.00	4.58
735	1131	0.318762	GAGGTGTAGATGGGATCGCC	59.681	60.000	7.38	0.12	0.00	5.54
736	1132	1.006102	GGTGTAGATGGGATCGCCG	60.006	63.158	7.38	0.00	33.83	6.46
737	1133	1.664965	GTGTAGATGGGATCGCCGC	60.665	63.158	7.38	0.00	33.83	6.53
738	1134	2.048127	GTAGATGGGATCGCCGCC	60.048	66.667	7.38	0.00	33.83	6.13
767	1163	5.945784	TGTCTACTATTACTACCACAACCGT	59.054	40.000	0.00	0.00	0.00	4.83
892	1295	3.332034	ACAACGCTGGTTTCTATACCAC	58.668	45.455	0.00	0.00	43.14	4.16
894	1297	3.688694	ACGCTGGTTTCTATACCACAA	57.311	42.857	0.00	0.00	43.14	3.33
930	1336	1.552792	TGACACGATCATTGCCCAGTA	59.447	47.619	0.00	0.00	29.99	2.74
1662	2074	3.691609	AGAAGATCAAAGGGCAATTCGAC	59.308	43.478	0.00	0.00	0.00	4.20
1701	2113	3.157087	GGTTTCTCAGAATCCCAGCAAA	58.843	45.455	3.30	0.00	0.00	3.68
2147	3806	4.340381	AGGTCTCAGAATATGCAATTTGGC	59.660	41.667	0.00	0.00	0.00	4.52
2356	4026	0.988063	AAGAAGAGTCCTGGAAGCCC	59.012	55.000	0.00	0.00	0.00	5.19
2401	4071	6.220930	TCGTTAGTGTCTCTAAAGCATGTTT	58.779	36.000	0.00	0.00	39.88	2.83
2510	4183	1.270893	GGGTGTCCTCAAGAGTTGGTC	60.271	57.143	0.00	0.00	0.00	4.02
2623	4297	5.835819	TGAAAACAAAGGACCAATGGTATGA	59.164	36.000	4.23	0.00	35.25	2.15
2755	4429	9.905713	TTGTTTGTTATATCTTAGCATCTTCCT	57.094	29.630	0.00	0.00	0.00	3.36

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
612	1008	2.784654	CCCCTCGATCTCCTCCCCT	61.785	68.421	0.00	0.00	0.00	4.79
709	1105	0.387202	CCATCTACACCTCCTCAGCG	59.613	60.000	0.00	0.00	0.00	5.18
710	1106	0.755686	CCCATCTACACCTCCTCAGC	59.244	60.000	0.00	0.00	0.00	4.26
711	1107	2.461300	TCCCATCTACACCTCCTCAG	57.539	55.000	0.00	0.00	0.00	3.35
712	1108	2.753168	CGATCCCATCTACACCTCCTCA	60.753	54.545	0.00	0.00	0.00	3.86
713	1109	1.889829	CGATCCCATCTACACCTCCTC	59.110	57.143	0.00	0.00	0.00	3.71
714	1110	2.002505	CGATCCCATCTACACCTCCT	57.997	55.000	0.00	0.00	0.00	3.69
715	1111	0.318762	GCGATCCCATCTACACCTCC	59.681	60.000	0.00	0.00	0.00	4.30
716	1112	0.318762	GGCGATCCCATCTACACCTC	59.681	60.000	0.00	0.00	0.00	3.85
717	1113	1.464376	CGGCGATCCCATCTACACCT	61.464	60.000	0.00	0.00	0.00	4.00
718	1114	1.006102	CGGCGATCCCATCTACACC	60.006	63.158	0.00	0.00	0.00	4.16
719	1115	1.664965	GCGGCGATCCCATCTACAC	60.665	63.158	12.98	0.00	0.00	2.90
720	1116	2.734591	GCGGCGATCCCATCTACA	59.265	61.111	12.98	0.00	0.00	2.74
721	1117	2.048127	GGCGGCGATCCCATCTAC	60.048	66.667	12.98	0.00	0.00	2.59
722	1118	2.523168	TGGCGGCGATCCCATCTA	60.523	61.111	12.98	0.00	0.00	1.98
723	1119	4.241555	GTGGCGGCGATCCCATCT	62.242	66.667	12.98	0.00	32.95	2.90
724	1120	4.545706	TGTGGCGGCGATCCCATC	62.546	66.667	12.98	4.52	32.95	3.51
725	1121	4.856801	GTGTGGCGGCGATCCCAT	62.857	66.667	12.98	0.00	32.95	4.00
728	1124	4.760047	ACAGTGTGGCGGCGATCC	62.760	66.667	12.98	3.21	0.00	3.36
729	1125	2.279502	TAGACAGTGTGGCGGCGATC	62.280	60.000	12.98	1.66	0.00	3.69
730	1126	2.348104	TAGACAGTGTGGCGGCGAT	61.348	57.895	12.98	0.00	0.00	4.58
731	1127	2.986979	TAGACAGTGTGGCGGCGA	60.987	61.111	12.98	0.00	0.00	5.54
732	1128	1.929806	TAGTAGACAGTGTGGCGGCG	61.930	60.000	0.00	0.51	0.00	6.46
733	1129	0.460311	ATAGTAGACAGTGTGGCGGC	59.540	55.000	0.00	0.00	0.00	6.53
734	1130	2.961526	AATAGTAGACAGTGTGGCGG	57.038	50.000	0.00	0.00	0.00	6.13
735	1131	4.634184	AGTAATAGTAGACAGTGTGGCG	57.366	45.455	0.00	0.00	0.00	5.69
736	1132	5.359009	TGGTAGTAATAGTAGACAGTGTGGC	59.641	44.000	0.00	0.00	0.00	5.01
737	1133	6.376299	TGTGGTAGTAATAGTAGACAGTGTGG	59.624	42.308	0.00	0.00	0.00	4.17
738	1134	7.387119	TGTGGTAGTAATAGTAGACAGTGTG	57.613	40.000	0.00	0.00	0.00	3.82
767	1163	0.986019	AGCGGGGTCCCATGTATCAA	60.986	55.000	10.98	0.00	35.37	2.57
892	1295	4.455877	GTGTCATAAGGGAGAAACTGGTTG	59.544	45.833	0.00	0.00	0.00	3.77
894	1297	3.306780	CGTGTCATAAGGGAGAAACTGGT	60.307	47.826	0.00	0.00	0.00	4.00
1504	1916	4.256110	TCATCTCGTGTTTCATCAATGCT	58.744	39.130	0.00	0.00	0.00	3.79
1662	2074	8.397906	TGAGAAACCGAAATAAAAGCATCATAG	58.602	33.333	0.00	0.00	0.00	2.23
1731	2143	3.128465	GCATACTTGCTCTTGTCAAGC	57.872	47.619	7.78	0.00	45.77	4.01
1903	2323	9.524496	AACAATATGGTATCAAGATGCATATGT	57.476	29.630	0.00	0.00	0.00	2.29
1946	3541	8.101654	ACTAACTACATCATTTACGCCAAAAA	57.898	30.769	0.00	0.00	0.00	1.94
2356	4026	2.339418	TGCGGGTTGTCGTAATTAGTG	58.661	47.619	0.00	0.00	0.00	2.74
2401	4071	8.553085	TTTGTAGATATCATCCTTGGAAGAGA	57.447	34.615	5.32	0.00	0.00	3.10
2482	4155	2.368875	TCTTGAGGACACCCTTTCTCAC	59.631	50.000	0.00	0.00	44.53	3.51
2510	4183	8.885494	TTTTCAAAATGTCTTTGGATACTTGG	57.115	30.769	0.00	0.00	37.61	3.61
2755	4429	7.632861	TCCTTTCATAATCTTGTGATCTTCCA	58.367	34.615	0.00	0.00	31.51	3.53
2932	4619	2.299013	ACCATGTCATGTACACGACACT	59.701	45.455	25.49	12.79	44.45	3.55
3014	4701	6.686484	ACCAAATTATGCCTTTTTCTTCCT	57.314	33.333	0.00	0.00	0.00	3.36
3025	4712	3.715628	ATCTGCGAACCAAATTATGCC	57.284	42.857	0.00	0.00	0.00	4.40
3301	5000	5.887754	ACCTCTTAAATCCAAGGTAAGCAA	58.112	37.500	0.00	0.00	40.33	3.91

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.