AutoCloner

Multiple sequence alignment - TraesCS2A01G570600

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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	TraesCS2A01G570600	chr2A	100.000	3393	0	0	1	3393	767987332	767983940	0.000000e+00	6266
1	TraesCS2A01G570600	chr2A	79.681	251	40	7	32	273	680270681	680270433	1.620000e-38	171
2	TraesCS2A01G570600	chr2D	92.811	3422	205	20	1	3393	643007768	643004359	0.000000e+00	4918
3	TraesCS2A01G570600	chr2D	92.922	1879	92	10	834	2699	643124112	643122262	0.000000e+00	2695
4	TraesCS2A01G570600	chr2D	91.898	864	58	4	1615	2469	642955319	642956179	0.000000e+00	1197
5	TraesCS2A01G570600	chr2D	91.628	215	13	4	432	642	643082206	643081993	3.310000e-75	292
6	TraesCS2A01G570600	chr2D	90.455	220	11	7	432	642	643124392	643124174	7.170000e-72	281
7	TraesCS2A01G570600	chr2D	91.515	165	10	1	3230	3390	642956220	642956384	1.230000e-54	224
8	TraesCS2A01G570600	chr2D	79.273	275	57	0	1016	1290	636354750	636355024	3.460000e-45	193
9	TraesCS2A01G570600	chrUn	92.590	2753	162	14	678	3393	31626763	31624016	0.000000e+00	3916
10	TraesCS2A01G570600	chrUn	91.494	870	68	2	1615	2481	31553762	31554628	0.000000e+00	1192
11	TraesCS2A01G570600	chrUn	82.699	578	82	12	2640	3211	274028352	274028917	6.540000e-137	497
12	TraesCS2A01G570600	chrUn	94.403	268	15	0	991	1258	183059007	183058740	2.440000e-111	412
13	TraesCS2A01G570600	chrUn	84.024	169	26	1	772	939	31578536	31578704	9.740000e-36	161
14	TraesCS2A01G570600	chr2B	79.036	1369	221	37	1012	2350	787533950	787532618	0.000000e+00	878
15	TraesCS2A01G570600	chr2B	79.592	245	40	5	41	277	640609490	640609248	2.090000e-37	167
16	TraesCS2A01G570600	chr2B	80.090	221	33	6	69	281	89330860	89331077	1.630000e-33	154
17	TraesCS2A01G570600	chr7B	85.739	575	63	8	2640	3210	246629335	246628776	1.050000e-164	590
18	TraesCS2A01G570600	chr7B	85.615	577	64	9	2640	3212	246624451	246623890	3.770000e-164	588
19	TraesCS2A01G570600	chr1A	85.069	576	73	7	2640	3212	521293055	521293620	2.940000e-160	575
20	TraesCS2A01G570600	chr1A	84.655	580	73	9	2640	3212	586337197	586337767	6.360000e-157	564
21	TraesCS2A01G570600	chr1A	94.624	93	4	1	572	664	582711859	582711950	3.530000e-30	143
22	TraesCS2A01G570600	chr7A	84.359	601	69	12	2640	3231	423569469	423570053	1.770000e-157	566
23	TraesCS2A01G570600	chr7A	77.875	913	178	19	1444	2341	101433564	101434467	2.300000e-151	545
24	TraesCS2A01G570600	chr4A	84.165	581	79	6	2636	3212	718955929	718955358	4.950000e-153	551
25	TraesCS2A01G570600	chr4B	77.514	925	175	22	1444	2350	588788190	588787281	3.000000e-145	525
26	TraesCS2A01G570600	chr4B	78.405	301	63	2	1022	1321	588788623	588788324	9.610000e-46	195
27	TraesCS2A01G570600	chr6D	83.305	581	81	8	2637	3212	376907719	376908288	3.880000e-144	521
28	TraesCS2A01G570600	chr4D	77.454	927	174	24	1444	2351	469073567	469072657	3.880000e-144	521
29	TraesCS2A01G570600	chr4D	79.399	233	36	6	57	281	509277988	509277760	1.630000e-33	154
30	TraesCS2A01G570600	chr6A	80.567	247	37	5	43	281	547305347	547305590	2.690000e-41	180
31	TraesCS2A01G570600	chr1D	78.947	247	40	9	37	281	116944	116708	1.260000e-34	158
32	TraesCS2A01G570600	chr3B	82.911	158	25	2	46	202	41798407	41798251	1.270000e-29	141
33	TraesCS2A01G570600	chr3B	82.609	161	26	2	43	202	42050110	42050269	1.270000e-29	141
34	TraesCS2A01G570600	chr1B	93.548	93	5	1	572	664	675877827	675877918	1.640000e-28	137

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	TraesCS2A01G570600	chr2A	767983940	767987332	3392	True	6266.0	6266	100.0000	1	3393	1	chr2A.!!$R2	3392
1	TraesCS2A01G570600	chr2D	643004359	643007768	3409	True	4918.0	4918	92.8110	1	3393	1	chr2D.!!$R1	3392
2	TraesCS2A01G570600	chr2D	643122262	643124392	2130	True	1488.0	2695	91.6885	432	2699	2	chr2D.!!$R3	2267
3	TraesCS2A01G570600	chr2D	642955319	642956384	1065	False	710.5	1197	91.7065	1615	3390	2	chr2D.!!$F2	1775
4	TraesCS2A01G570600	chrUn	31624016	31626763	2747	True	3916.0	3916	92.5900	678	3393	1	chrUn.!!$R1	2715
5	TraesCS2A01G570600	chrUn	31553762	31554628	866	False	1192.0	1192	91.4940	1615	2481	1	chrUn.!!$F1	866
6	TraesCS2A01G570600	chrUn	274028352	274028917	565	False	497.0	497	82.6990	2640	3211	1	chrUn.!!$F3	571
7	TraesCS2A01G570600	chr2B	787532618	787533950	1332	True	878.0	878	79.0360	1012	2350	1	chr2B.!!$R2	1338
8	TraesCS2A01G570600	chr7B	246628776	246629335	559	True	590.0	590	85.7390	2640	3210	1	chr7B.!!$R2	570
9	TraesCS2A01G570600	chr7B	246623890	246624451	561	True	588.0	588	85.6150	2640	3212	1	chr7B.!!$R1	572
10	TraesCS2A01G570600	chr1A	521293055	521293620	565	False	575.0	575	85.0690	2640	3212	1	chr1A.!!$F1	572
11	TraesCS2A01G570600	chr1A	586337197	586337767	570	False	564.0	564	84.6550	2640	3212	1	chr1A.!!$F3	572
12	TraesCS2A01G570600	chr7A	423569469	423570053	584	False	566.0	566	84.3590	2640	3231	1	chr7A.!!$F2	591
13	TraesCS2A01G570600	chr7A	101433564	101434467	903	False	545.0	545	77.8750	1444	2341	1	chr7A.!!$F1	897
14	TraesCS2A01G570600	chr4A	718955358	718955929	571	True	551.0	551	84.1650	2636	3212	1	chr4A.!!$R1	576
15	TraesCS2A01G570600	chr4B	588787281	588788623	1342	True	360.0	525	77.9595	1022	2350	2	chr4B.!!$R1	1328
16	TraesCS2A01G570600	chr6D	376907719	376908288	569	False	521.0	521	83.3050	2637	3212	1	chr6D.!!$F1	575
17	TraesCS2A01G570600	chr4D	469072657	469073567	910	True	521.0	521	77.4540	1444	2351	1	chr4D.!!$R1	907

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
770	784	0.250295	TGGTGGCTCTTTCTCCGTTG	60.250	55.0	0.0	0.0	0.0	4.10	F
1009	1035	0.249489	CTAGGTCGAAATGGAGGCGG	60.249	60.0	0.0	0.0	0.0	6.13	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2092	2167	0.377554	CGTCTACGATGCCGAAGTCT	59.622	55.0	0.0	0.0	43.02	3.24	R
2866	2957	0.692476	CTTCCACCCTGTGATGTCCA	59.308	55.0	0.0	0.0	35.23	4.02	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
87	88	2.487918	GCATATGGCAACCCGAACA	58.512	52.632	4.56	0.00	43.97	3.18
88	89	1.032014	GCATATGGCAACCCGAACAT	58.968	50.000	4.56	0.00	43.97	2.71
122	123	7.168637	TGACAAGTTTAGTTACACGAAGATGAC	59.831	37.037	0.00	0.00	0.00	3.06
142	143	6.785488	TGACAACTTTAGTTAGCAGACATG	57.215	37.500	0.00	0.00	36.32	3.21
152	153	4.449068	AGTTAGCAGACATGACAACTTTCG	59.551	41.667	0.00	0.00	0.00	3.46
172	173	7.920682	ACTTTCGTGCTTCAGTTTATTTTTGAT	59.079	29.630	0.00	0.00	0.00	2.57
235	236	3.624326	TTGCCATCAAAGAAACGTCAG	57.376	42.857	0.00	0.00	0.00	3.51
238	239	2.808543	GCCATCAAAGAAACGTCAGAGT	59.191	45.455	0.00	0.00	0.00	3.24
247	248	2.143594	AACGTCAGAGTCGGAGTGCC	62.144	60.000	0.00	0.00	0.00	5.01
248	249	2.626780	CGTCAGAGTCGGAGTGCCA	61.627	63.158	0.00	0.00	0.00	4.92
250	251	1.530655	TCAGAGTCGGAGTGCCACA	60.531	57.895	0.00	0.00	0.00	4.17
272	273	4.324669	CACATCTGACACGTGACACTTATC	59.675	45.833	25.01	7.90	32.23	1.75
286	287	5.724370	TGACACTTATCATTTAGGGAGTCCA	59.276	40.000	12.30	0.00	34.83	4.02
287	288	6.214615	TGACACTTATCATTTAGGGAGTCCAA	59.785	38.462	12.30	0.00	34.83	3.53
328	329	0.529378	GCAAAAGAGCAGGGTGGATG	59.471	55.000	0.00	0.00	0.00	3.51
468	469	7.111247	TCATTGAAAGTTGAAACCACAAGAT	57.889	32.000	0.00	0.00	0.00	2.40
632	644	2.753043	GGGTCGGCCTCGTAGTCA	60.753	66.667	5.77	0.00	37.69	3.41
644	656	2.520982	TAGTCATAGGCCGCCGCT	60.521	61.111	3.05	1.62	34.44	5.52
670	683	4.475135	GCTTCGCCTCCCTGTCCC	62.475	72.222	0.00	0.00	0.00	4.46
671	684	3.787001	CTTCGCCTCCCTGTCCCC	61.787	72.222	0.00	0.00	0.00	4.81
675	688	3.493303	GCCTCCCTGTCCCCCATC	61.493	72.222	0.00	0.00	0.00	3.51
676	689	2.374342	CCTCCCTGTCCCCCATCT	59.626	66.667	0.00	0.00	0.00	2.90
735	749	2.038557	GCCACTTTGGAGACTTGGAGTA	59.961	50.000	0.00	0.00	40.96	2.59
761	775	2.113243	GAGTTCCGGTGGTGGCTCTT	62.113	60.000	0.00	0.00	0.00	2.85
763	777	1.072505	TTCCGGTGGTGGCTCTTTC	59.927	57.895	0.00	0.00	0.00	2.62
770	784	0.250295	TGGTGGCTCTTTCTCCGTTG	60.250	55.000	0.00	0.00	0.00	4.10
791	805	0.901580	ATGGCTTTGCTGGGGACTTG	60.902	55.000	0.00	0.00	0.00	3.16
800	814	2.610859	GGGGACTTGGGAGCCTCA	60.611	66.667	0.00	0.00	0.00	3.86
802	816	2.266055	GGACTTGGGAGCCTCACG	59.734	66.667	0.00	0.00	0.00	4.35
882	898	4.201901	GGTTTTCTCGTCGGTTTGGTAAAA	60.202	41.667	0.00	0.00	0.00	1.52
1009	1035	0.249489	CTAGGTCGAAATGGAGGCGG	60.249	60.000	0.00	0.00	0.00	6.13
1428	1454	2.191400	TCTGGATGCTAACTGGCTCTT	58.809	47.619	0.00	0.00	0.00	2.85
1825	1900	1.195442	TGGGAATCCGGTGTAGCACA	61.195	55.000	0.00	0.00	35.86	4.57
1831	1906	0.687920	TCCGGTGTAGCACATTCCAA	59.312	50.000	0.00	0.00	35.86	3.53
2092	2167	2.349580	CGAGTACATCCAGTCGTTCGTA	59.650	50.000	0.00	0.00	36.76	3.43
2106	2184	0.806868	TTCGTAGACTTCGGCATCGT	59.193	50.000	1.44	0.00	34.32	3.73
2107	2185	1.655484	TCGTAGACTTCGGCATCGTA	58.345	50.000	1.44	0.00	37.69	3.43
2499	2586	3.362706	TCTGAGATAAACAGGTACCGCT	58.637	45.455	6.18	0.00	36.22	5.52
2500	2587	3.767673	TCTGAGATAAACAGGTACCGCTT	59.232	43.478	6.18	3.89	36.22	4.68
2519	2606	3.689649	GCTTGTTCCGGTCTATTGACAAT	59.310	43.478	9.51	5.87	44.61	2.71
2523	2610	5.175859	TGTTCCGGTCTATTGACAATCTTC	58.824	41.667	3.36	0.00	44.61	2.87
2606	2694	2.061773	CTGCGAATTCACGAGTGTCTT	58.938	47.619	6.22	0.00	35.09	3.01
2659	2747	7.100458	ACTTTGTTGGATATTTATGTGGCTC	57.900	36.000	0.00	0.00	0.00	4.70
2742	2831	6.528537	TTAATGTTTGTGATGGGGAATGAG	57.471	37.500	0.00	0.00	0.00	2.90
2758	2847	5.361857	GGGAATGAGTGATGTGGAATTTCAT	59.638	40.000	0.00	0.00	0.00	2.57
2773	2862	9.057089	GTGGAATTTCATTCGAGGAAGTAATAT	57.943	33.333	0.00	0.00	40.17	1.28
2805	2894	5.047377	GCCCAAAAGAAGTGTGATGGAATAA	60.047	40.000	0.00	0.00	0.00	1.40
2841	2932	7.170554	TGATAGGGGGACTCTACTGTAATTA	57.829	40.000	0.00	0.00	0.00	1.40
3030	3142	8.606040	ACTAGTATATTTAGACTCGGTCACTC	57.394	38.462	0.00	0.00	34.60	3.51
3038	3150	1.450905	GACTCGGTCACTCGAAAAACG	59.549	52.381	0.00	0.00	38.77	3.60
3086	3198	7.634671	ACATTGCTCATGAGTCATATGAAAA	57.365	32.000	23.38	6.31	36.24	2.29
3170	3289	6.272324	ACCCTCTAGCCTTATTATGCATTGTA	59.728	38.462	3.54	0.00	0.00	2.41
3173	3292	7.880195	CCTCTAGCCTTATTATGCATTGTAAGT	59.120	37.037	20.38	11.41	0.00	2.24
3190	3309	2.410466	GTGGCACCACGGAAAAGAA	58.590	52.632	6.29	0.00	37.19	2.52
3299	3428	2.231964	TGCAAGATTAGGCTTTGCTTGG	59.768	45.455	19.15	5.91	37.14	3.61
3370	3508	5.968387	AGCTTGATAATAAGTGTACGTGC	57.032	39.130	0.00	0.00	0.00	5.34

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
17	18	7.065923	AGGTTCCTCGATTAATTAGCTCAAAAC	59.934	37.037	0.00	0.00	0.00	2.43
35	36	6.803642	ACGTATGACACTTATTAGGTTCCTC	58.196	40.000	0.00	0.00	0.00	3.71
67	68	0.663153	GTTCGGGTTGCCATATGCTC	59.337	55.000	0.00	0.00	42.00	4.26
99	100	7.402811	TGTCATCTTCGTGTAACTAAACTTG	57.597	36.000	0.00	0.00	31.75	3.16
122	123	6.785488	TGTCATGTCTGCTAACTAAAGTTG	57.215	37.500	5.62	0.00	38.90	3.16
142	143	3.675467	AACTGAAGCACGAAAGTTGTC	57.325	42.857	0.00	0.00	46.40	3.18
172	173	9.739276	ATTCCATTTACTCATGACAAGTTTCTA	57.261	29.630	0.00	0.00	0.00	2.10
179	180	6.867816	GCACAAATTCCATTTACTCATGACAA	59.132	34.615	0.00	0.00	0.00	3.18
202	203	2.279741	GATGGCAATTCTAGTCACGCA	58.720	47.619	0.00	0.00	0.00	5.24
235	236	0.737715	GATGTGTGGCACTCCGACTC	60.738	60.000	19.83	6.13	35.11	3.36
238	239	1.184970	TCAGATGTGTGGCACTCCGA	61.185	55.000	19.83	3.19	35.11	4.55
247	248	1.522676	GTGTCACGTGTCAGATGTGTG	59.477	52.381	15.79	0.00	41.70	3.82
248	249	1.409064	AGTGTCACGTGTCAGATGTGT	59.591	47.619	15.79	0.00	41.70	3.72
250	251	2.890808	AAGTGTCACGTGTCAGATGT	57.109	45.000	15.79	0.00	0.00	3.06
272	273	5.677319	TCTACAGTTGGACTCCCTAAATG	57.323	43.478	0.00	0.00	0.00	2.32
286	287	6.438763	GCTTTTGCTTACAACATCTACAGTT	58.561	36.000	0.00	0.00	43.35	3.16
287	288	6.002062	GCTTTTGCTTACAACATCTACAGT	57.998	37.500	0.00	0.00	43.35	3.55
328	329	1.228552	TCAAGTCCCCAGCAAAGCC	60.229	57.895	0.00	0.00	0.00	4.35
468	469	3.750512	CACAAGAGCACGTACGTATGTA	58.249	45.455	22.34	0.00	0.00	2.29
667	680	2.285368	AGCAACCGAGATGGGGGA	60.285	61.111	0.00	0.00	44.64	4.81
673	686	2.045926	GCCACCAGCAACCGAGAT	60.046	61.111	0.00	0.00	42.97	2.75
674	687	4.680237	CGCCACCAGCAACCGAGA	62.680	66.667	0.00	0.00	44.04	4.04
735	749	2.516888	CCACCGGAACTCACCCACT	61.517	63.158	9.46	0.00	0.00	4.00
761	775	1.533625	CAAAGCCATCCAACGGAGAA	58.466	50.000	0.00	0.00	34.05	2.87
763	777	0.962356	AGCAAAGCCATCCAACGGAG	60.962	55.000	0.00	0.00	34.05	4.63
770	784	2.054453	GTCCCCAGCAAAGCCATCC	61.054	63.158	0.00	0.00	0.00	3.51
800	814	3.560251	AGCAGCTGGTCCAACCGT	61.560	61.111	13.85	0.00	42.58	4.83
802	816	3.368571	GCAGCAGCTGGTCCAACC	61.369	66.667	24.13	1.20	39.22	3.77
882	898	0.687354	ATGTGCACGTCCCTTTCTCT	59.313	50.000	13.13	0.00	0.00	3.10
926	944	5.012664	AGCACGTATATATGAACCCATTGGA	59.987	40.000	8.98	0.00	34.31	3.53
1231	1257	2.034879	CGTGGATGAAACGCCTGCT	61.035	57.895	0.00	0.00	33.79	4.24
1423	1449	7.680730	TCTCCTATATTTTATGTCCCAAGAGC	58.319	38.462	0.00	0.00	0.00	4.09
1428	1454	5.542635	ACGCTCTCCTATATTTTATGTCCCA	59.457	40.000	0.00	0.00	0.00	4.37
1557	1623	2.266055	CCCACGTGGAGAGGAAGC	59.734	66.667	36.07	0.00	37.39	3.86
1825	1900	2.475466	CGCGAGCAGGCATTGGAAT	61.475	57.895	0.00	0.00	0.00	3.01
2092	2167	0.377554	CGTCTACGATGCCGAAGTCT	59.622	55.000	0.00	0.00	43.02	3.24
2106	2184	3.072468	CCTCCCCGTTGGCGTCTA	61.072	66.667	0.00	0.00	36.15	2.59
2452	2536	1.134699	GTCTTGAGATGATCGTGCCCA	60.135	52.381	0.00	0.00	0.00	5.36
2499	2586	5.160607	AGATTGTCAATAGACCGGAACAA	57.839	39.130	9.46	7.16	44.33	2.83
2500	2587	4.819105	AGATTGTCAATAGACCGGAACA	57.181	40.909	9.46	0.00	44.33	3.18
2523	2610	8.647226	GGGAAATCAAAATACAGAAAAATCACG	58.353	33.333	0.00	0.00	0.00	4.35
2576	2664	7.580523	CACTCGTGAATTCGCAGATTTATTTAG	59.419	37.037	18.57	5.69	35.04	1.85
2606	2694	7.085746	CACATGAGATTTATTTGCAAGACACA	58.914	34.615	0.00	0.00	0.00	3.72
2758	2847	5.735354	GCACCTCGAATATTACTTCCTCGAA	60.735	44.000	0.00	0.00	38.01	3.71
2805	2894	7.034724	AGAGTCCCCCTATCAATTCCTCTATAT	60.035	40.741	0.00	0.00	0.00	0.86
2866	2957	0.692476	CTTCCACCCTGTGATGTCCA	59.308	55.000	0.00	0.00	35.23	4.02
2964	3059	7.503230	TGTGAGTCATGTGCCATGATTATATTT	59.497	33.333	17.33	2.95	0.00	1.40
3030	3142	2.126914	TCAAACATGCCCGTTTTTCG	57.873	45.000	0.00	0.00	36.98	3.46
3038	3150	2.166254	CCAACCACTATCAAACATGCCC	59.834	50.000	0.00	0.00	0.00	5.36
3170	3289	0.106918	TCTTTTCCGTGGTGCCACTT	60.107	50.000	17.96	0.00	44.16	3.16
3173	3292	1.028905	CTTTCTTTTCCGTGGTGCCA	58.971	50.000	0.00	0.00	0.00	4.92
3190	3309	7.036863	TGGATGGTCTACCCTTTAATTTCTCTT	60.037	37.037	0.00	0.00	34.29	2.85
3370	3508	1.601419	TAAAGGCACTCCGGAGTCCG	61.601	60.000	34.28	24.25	43.33	4.79

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.