AutoCloner

Multiple sequence alignment - TraesCS7D01G377400

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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	TraesCS7D01G377400	chr7D	100.000	3566	0	0	1	3566	488781553	488785118	0.000000e+00	6586.0
1	TraesCS7D01G377400	chr7D	85.733	764	55	16	2696	3450	488792136	488792854	0.000000e+00	758.0
2	TraesCS7D01G377400	chr7D	92.857	56	4	0	3510	3565	488792886	488792941	8.210000e-12	82.4
3	TraesCS7D01G377400	chr7B	93.904	3035	124	31	445	3452	517309916	517312916	0.000000e+00	4523.0
4	TraesCS7D01G377400	chr7B	83.363	1106	82	42	2378	3450	517322950	517323986	0.000000e+00	929.0
5	TraesCS7D01G377400	chr7B	94.572	479	22	2	1	479	517309442	517309916	0.000000e+00	737.0
6	TraesCS7D01G377400	chr7B	91.837	49	4	0	3510	3558	517324018	517324066	6.390000e-08	69.4
7	TraesCS7D01G377400	chr7A	94.641	2034	71	18	619	2630	556159073	556161090	0.000000e+00	3118.0
8	TraesCS7D01G377400	chr7A	93.135	874	48	6	2696	3566	556161625	556162489	0.000000e+00	1271.0
9	TraesCS7D01G377400	chr7A	86.369	873	64	19	2696	3565	556170147	556170967	0.000000e+00	902.0
10	TraesCS7D01G377400	chr7A	90.000	250	22	1	1	250	556158425	556158671	1.600000e-83	320.0
11	TraesCS7D01G377400	chr7A	87.264	212	23	3	412	620	556158676	556158886	4.600000e-59	239.0
12	TraesCS7D01G377400	chr7A	85.965	114	14	2	2440	2552	556169909	556170021	1.740000e-23	121.0
13	TraesCS7D01G377400	chr7A	100.000	42	0	0	2654	2695	556161357	556161398	1.060000e-10	78.7
14	TraesCS7D01G377400	chr6B	96.894	161	4	1	250	410	111688650	111688809	5.870000e-68	268.0
15	TraesCS7D01G377400	chr6B	93.714	175	8	3	237	410	111694163	111694335	3.530000e-65	259.0
16	TraesCS7D01G377400	chrUn	93.820	178	8	3	237	413	245704220	245704045	7.590000e-67	265.0
17	TraesCS7D01G377400	chrUn	94.286	175	7	3	237	410	348898998	348899170	7.590000e-67	265.0
18	TraesCS7D01G377400	chrUn	94.286	175	7	3	237	410	448431959	448432131	7.590000e-67	265.0
19	TraesCS7D01G377400	chrUn	96.273	161	5	1	250	410	67502869	67503028	2.730000e-66	263.0
20	TraesCS7D01G377400	chrUn	96.273	161	5	1	250	410	67512634	67512793	2.730000e-66	263.0
21	TraesCS7D01G377400	chr5A	93.714	175	8	3	237	410	706866747	706866919	3.530000e-65	259.0
22	TraesCS7D01G377400	chr5A	71.904	541	128	20	1229	1760	191092281	191092806	6.210000e-28	135.0
23	TraesCS7D01G377400	chr5D	72.426	544	126	20	1229	1763	177676792	177676264	6.170000e-33	152.0
24	TraesCS7D01G377400	chr5B	73.902	387	87	11	1381	1763	192349801	192349425	3.710000e-30	143.0

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	TraesCS7D01G377400	chr7D	488781553	488785118	3565	False	6586.00	6586	100.000	1	3566	1	chr7D.!!$F1	3565
1	TraesCS7D01G377400	chr7D	488792136	488792941	805	False	420.20	758	89.295	2696	3565	2	chr7D.!!$F2	869
2	TraesCS7D01G377400	chr7B	517309442	517312916	3474	False	2630.00	4523	94.238	1	3452	2	chr7B.!!$F1	3451
3	TraesCS7D01G377400	chr7B	517322950	517324066	1116	False	499.20	929	87.600	2378	3558	2	chr7B.!!$F2	1180
4	TraesCS7D01G377400	chr7A	556158425	556162489	4064	False	1005.34	3118	93.008	1	3566	5	chr7A.!!$F1	3565
5	TraesCS7D01G377400	chr7A	556169909	556170967	1058	False	511.50	902	86.167	2440	3565	2	chr7A.!!$F2	1125

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
951	1188	0.109412	GCCGTTCGGTATATCCTCCG	60.109	60.0	12.81	7.35	46.93	4.63	F
1914	2164	0.105401	CCCTCCCTCTCCCTACTTCC	60.105	65.0	0.00	0.00	0.00	3.46	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2173	2426	0.537828	TTGATGGTGCTCTGCTGCAA	60.538	50.000	3.02	0.0	45.12	4.08	R
2930	3669	1.477558	GCAAGGGGAATGTGGATCGAT	60.478	52.381	0.00	0.0	0.00	3.59	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
202	203	4.202050	GGAATGTTGTGGTATGATGCCTTC	60.202	45.833	0.30	0.00	0.00	3.46
224	225	8.237949	CCTTCTATTCGATCTTGTATCGTGTAT	58.762	37.037	7.22	3.53	41.77	2.29
263	264	5.580022	ACATTACCCTTATTGCCTCAAACT	58.420	37.500	0.00	0.00	0.00	2.66
265	266	6.152831	ACATTACCCTTATTGCCTCAAACTTC	59.847	38.462	0.00	0.00	0.00	3.01
299	300	2.029739	GGCGATAGTCCCTCTAAGAAGC	60.030	54.545	0.00	0.00	39.35	3.86
306	307	2.035632	TCCCTCTAAGAAGCTAGCTGC	58.964	52.381	20.16	17.84	43.29	5.25
320	321	3.160047	CTGCGGAGGGATGGCTCT	61.160	66.667	0.00	0.00	0.00	4.09
322	323	3.474570	GCGGAGGGATGGCTCTGT	61.475	66.667	0.00	0.00	0.00	3.41
348	349	1.190643	AGTTAGCAGGCTGAGGTCTC	58.809	55.000	20.86	0.00	0.00	3.36
353	354	1.674057	CAGGCTGAGGTCTCCGTTT	59.326	57.895	9.42	0.00	0.00	3.60
397	398	1.683790	CGCTCCGCCAACTAAGAACG	61.684	60.000	0.00	0.00	0.00	3.95
410	411	1.647545	AAGAACGGCCATGCATCACG	61.648	55.000	2.24	4.30	0.00	4.35
431	432	2.681344	GACTTACCGAAAATTGGGCGAT	59.319	45.455	0.00	0.00	0.00	4.58
462	464	0.529378	GCCCTGGACTGCATCAAAAG	59.471	55.000	0.00	0.00	0.00	2.27
670	903	6.809689	TGATACATTCGTGTCGTGTAAGAAAT	59.190	34.615	0.00	0.00	36.11	2.17
703	936	1.134401	ACGTTCACCCTGCATGGATAG	60.134	52.381	15.66	4.47	38.35	2.08
722	955	0.396435	GAGTCCACATCACCACCACA	59.604	55.000	0.00	0.00	0.00	4.17
723	956	0.843309	AGTCCACATCACCACCACAA	59.157	50.000	0.00	0.00	0.00	3.33
724	957	0.951558	GTCCACATCACCACCACAAC	59.048	55.000	0.00	0.00	0.00	3.32
781	1017	5.738619	TGGTGTCTACATGTATGTGTTCT	57.261	39.130	5.91	0.00	41.89	3.01
951	1188	0.109412	GCCGTTCGGTATATCCTCCG	60.109	60.000	12.81	7.35	46.93	4.63
1131	1378	2.813061	CAGGTTCTTGCCTTGTGTTTG	58.187	47.619	0.00	0.00	36.58	2.93
1914	2164	0.105401	CCCTCCCTCTCCCTACTTCC	60.105	65.000	0.00	0.00	0.00	3.46
2129	2382	1.228245	ACGCCATGAACAAGCTGGT	60.228	52.632	0.00	0.00	32.42	4.00
2331	2584	4.189188	GCCGCGTCCGAGAGCTTA	62.189	66.667	4.92	0.00	36.29	3.09
2787	3522	5.575157	TGCAAATGTCTTCCTAATGGGTTA	58.425	37.500	0.00	0.00	36.25	2.85
2795	3533	6.389869	TGTCTTCCTAATGGGTTAATCCTGAT	59.610	38.462	6.28	0.00	36.25	2.90
3109	3850	4.258702	ACTTCTTCAGTATTGACAGCGT	57.741	40.909	0.00	0.00	31.97	5.07
3235	3976	6.292381	CCGCAGTCATAGCAAGTCTAAATTAC	60.292	42.308	0.00	0.00	0.00	1.89
3251	3992	7.369026	GTCTAAATTACGCGTGTTAGCAATTAC	59.631	37.037	24.59	14.64	36.85	1.89
3460	4209	7.253420	GCACAAACTTTGTCAGCATTATATTCG	60.253	37.037	4.06	0.00	43.23	3.34
3527	4276	2.320745	TGATCTGCATGTAGGCACAG	57.679	50.000	11.15	0.19	39.25	3.66

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
188	189	5.481824	AGATCGAATAGAAGGCATCATACCA	59.518	40.000	0.00	0.00	0.00	3.25
202	203	7.201359	GGCAATACACGATACAAGATCGAATAG	60.201	40.741	13.45	3.71	43.59	1.73
224	225	4.461081	GGTAATGTCATGTAACCAAGGCAA	59.539	41.667	7.18	0.00	26.40	4.52
299	300	2.739784	CCATCCCTCCGCAGCTAG	59.260	66.667	0.00	0.00	0.00	3.42
306	307	1.821753	CTATACAGAGCCATCCCTCCG	59.178	57.143	0.00	0.00	32.17	4.63
336	337	1.122019	ACAAACGGAGACCTCAGCCT	61.122	55.000	0.00	0.00	0.00	4.58
397	398	0.657840	GTAAGTCGTGATGCATGGCC	59.342	55.000	2.46	0.00	0.00	5.36
410	411	2.078392	TCGCCCAATTTTCGGTAAGTC	58.922	47.619	0.00	0.00	0.00	3.01
431	432	1.063070	TCCAGGGCTTTGGTGTACCA	61.063	55.000	0.00	0.00	45.94	3.25
703	936	0.396435	TGTGGTGGTGATGTGGACTC	59.604	55.000	0.00	0.00	0.00	3.36
722	955	7.616313	TCCAAATAAAAACTGAACAAGTGGTT	58.384	30.769	0.00	0.00	44.10	3.67
723	956	7.176589	TCCAAATAAAAACTGAACAAGTGGT	57.823	32.000	0.00	0.00	39.81	4.16
724	957	7.114811	CGATCCAAATAAAAACTGAACAAGTGG	59.885	37.037	0.00	0.00	39.81	4.00
781	1017	6.821665	ACTAGGAATACAATTTTCGCAGCTAA	59.178	34.615	0.00	0.00	0.00	3.09
1016	1253	4.093952	CCAAACGCTCGGCTGCTG	62.094	66.667	0.95	0.95	0.00	4.41
1024	1261	1.063031	GCTGCAAAATCCAAACGCTC	58.937	50.000	0.00	0.00	0.00	5.03
1133	1380	4.849926	GCGCATGAAAAGCATACAGATATG	59.150	41.667	0.30	0.00	41.16	1.78
1134	1381	4.758674	AGCGCATGAAAAGCATACAGATAT	59.241	37.500	11.47	0.00	34.82	1.63
1135	1382	4.129380	AGCGCATGAAAAGCATACAGATA	58.871	39.130	11.47	0.00	34.82	1.98
1136	1383	2.947652	AGCGCATGAAAAGCATACAGAT	59.052	40.909	11.47	0.00	34.82	2.90
1137	1384	2.352651	GAGCGCATGAAAAGCATACAGA	59.647	45.455	11.47	0.00	34.82	3.41
1138	1385	2.713011	GAGCGCATGAAAAGCATACAG	58.287	47.619	11.47	0.00	34.82	2.74
1139	1386	1.062440	CGAGCGCATGAAAAGCATACA	59.938	47.619	11.47	0.00	34.82	2.29
1140	1387	1.062587	ACGAGCGCATGAAAAGCATAC	59.937	47.619	11.47	0.00	34.82	2.39
1141	1388	1.062440	CACGAGCGCATGAAAAGCATA	59.938	47.619	11.47	0.00	34.82	3.14
1142	1389	0.179181	CACGAGCGCATGAAAAGCAT	60.179	50.000	11.47	0.00	37.85	3.79
1145	1392	0.453282	CACCACGAGCGCATGAAAAG	60.453	55.000	11.47	0.00	0.00	2.27
1185	1433	1.014044	ATCTGCACATTTCGCGACGT	61.014	50.000	9.15	3.25	0.00	4.34
1187	1435	0.721154	TCATCTGCACATTTCGCGAC	59.279	50.000	9.15	0.00	0.00	5.19
1189	1437	0.588233	GCTCATCTGCACATTTCGCG	60.588	55.000	0.00	0.00	0.00	5.87
1190	1438	0.731417	AGCTCATCTGCACATTTCGC	59.269	50.000	0.00	0.00	34.99	4.70
1914	2164	9.205719	CCATGAAGATCATACATAACTCTGAAG	57.794	37.037	0.00	0.00	34.28	3.02
2173	2426	0.537828	TTGATGGTGCTCTGCTGCAA	60.538	50.000	3.02	0.00	45.12	4.08
2331	2584	3.562779	CTTGTACCCCGCGACGTGT	62.563	63.158	8.23	0.80	0.00	4.49
2821	3559	8.518702	ACATATTGCTTTCCTTTCTTTCTCTTC	58.481	33.333	0.00	0.00	0.00	2.87
2860	3598	9.740239	CCATACAAACCATTGAAGAATATTCTG	57.260	33.333	18.61	7.60	38.94	3.02
2861	3599	9.699410	TCCATACAAACCATTGAAGAATATTCT	57.301	29.630	12.37	12.37	38.94	2.40
2865	3604	7.888021	ACTGTCCATACAAACCATTGAAGAATA	59.112	33.333	0.00	0.00	38.94	1.75
2874	3613	5.186198	GCTCTTACTGTCCATACAAACCAT	58.814	41.667	0.00	0.00	34.49	3.55
2877	3616	3.939592	GGGCTCTTACTGTCCATACAAAC	59.060	47.826	0.00	0.00	34.49	2.93
2878	3617	3.844211	AGGGCTCTTACTGTCCATACAAA	59.156	43.478	0.00	0.00	34.49	2.83
2930	3669	1.477558	GCAAGGGGAATGTGGATCGAT	60.478	52.381	0.00	0.00	0.00	3.59
3235	3976	7.557036	TGTATATAGTAATTGCTAACACGCG	57.443	36.000	3.53	3.53	0.00	6.01
3474	4223	4.836825	TCCTCTTCCTAATGCTGACAAAG	58.163	43.478	0.00	0.00	0.00	2.77
3477	4226	3.582647	TGTTCCTCTTCCTAATGCTGACA	59.417	43.478	0.00	0.00	0.00	3.58
3527	4276	4.216257	ACTTTGACACATACACTTGCATCC	59.784	41.667	0.00	0.00	0.00	3.51

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.