AutoCloner

Multiple sequence alignment - TraesCS2B01G396500

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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	TraesCS2B01G396500	chr2B	100.000	2456	0	0	1	2456	563031363	563028908	0.000000e+00	4536
1	TraesCS2B01G396500	chr2B	82.822	652	92	12	25	672	13973427	13972792	1.270000e-157	566
2	TraesCS2B01G396500	chr2A	93.290	1699	75	16	770	2456	622699857	622698186	0.000000e+00	2470
3	TraesCS2B01G396500	chr2A	82.556	665	96	15	1	660	10632734	10633383	3.540000e-158	568
4	TraesCS2B01G396500	chr2D	89.842	1585	72	36	876	2456	480165510	480164011	0.000000e+00	1953
5	TraesCS2B01G396500	chr2D	86.068	768	92	9	1	766	480166631	480165877	0.000000e+00	811
6	TraesCS2B01G396500	chr2D	87.241	627	57	8	1125	1729	651321323	651320698	0.000000e+00	693
7	TraesCS2B01G396500	chr2D	98.305	118	2	0	768	885	480165841	480165724	8.900000e-50	207
8	TraesCS2B01G396500	chr1A	84.776	624	63	13	1135	1729	525021546	525020926	4.520000e-167	597
9	TraesCS2B01G396500	chr1A	82.655	663	100	15	3	660	65236021	65236673	7.620000e-160	573
10	TraesCS2B01G396500	chr5B	80.605	562	103	5	60	615	577348428	577347867	1.750000e-116	429
11	TraesCS2B01G396500	chr6D	79.140	628	118	10	1	620	153814042	153814664	2.920000e-114	422
12	TraesCS2B01G396500	chr4B	80.712	534	91	9	71	597	374708283	374708811	2.940000e-109	405
13	TraesCS2B01G396500	chr1D	78.956	613	107	17	3	601	460419978	460420582	4.920000e-107	398
14	TraesCS2B01G396500	chr3A	80.318	503	86	8	70	562	51598699	51599198	3.860000e-98	368

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	TraesCS2B01G396500	chr2B	563028908	563031363	2455	True	4536.000000	4536	100.000	1	2456	1	chr2B.!!$R2	2455
1	TraesCS2B01G396500	chr2B	13972792	13973427	635	True	566.000000	566	82.822	25	672	1	chr2B.!!$R1	647
2	TraesCS2B01G396500	chr2A	622698186	622699857	1671	True	2470.000000	2470	93.290	770	2456	1	chr2A.!!$R1	1686
3	TraesCS2B01G396500	chr2A	10632734	10633383	649	False	568.000000	568	82.556	1	660	1	chr2A.!!$F1	659
4	TraesCS2B01G396500	chr2D	480164011	480166631	2620	True	990.333333	1953	91.405	1	2456	3	chr2D.!!$R2	2455
5	TraesCS2B01G396500	chr2D	651320698	651321323	625	True	693.000000	693	87.241	1125	1729	1	chr2D.!!$R1	604
6	TraesCS2B01G396500	chr1A	525020926	525021546	620	True	597.000000	597	84.776	1135	1729	1	chr1A.!!$R1	594
7	TraesCS2B01G396500	chr1A	65236021	65236673	652	False	573.000000	573	82.655	3	660	1	chr1A.!!$F1	657
8	TraesCS2B01G396500	chr5B	577347867	577348428	561	True	429.000000	429	80.605	60	615	1	chr5B.!!$R1	555
9	TraesCS2B01G396500	chr6D	153814042	153814664	622	False	422.000000	422	79.140	1	620	1	chr6D.!!$F1	619
10	TraesCS2B01G396500	chr4B	374708283	374708811	528	False	405.000000	405	80.712	71	597	1	chr4B.!!$F1	526
11	TraesCS2B01G396500	chr1D	460419978	460420582	604	False	398.000000	398	78.956	3	601	1	chr1D.!!$F1	598

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
225	228	1.227205	GCAGGACATCTCTCCAGCG	60.227	63.158	0.0	0.0	33.60	5.18	F
413	424	1.324005	GCTGGCTCCTAGACGAAGGT	61.324	60.000	0.0	0.0	37.91	3.50	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1206	1510	0.107508	CCATGGGCTGATCGTTGTCT	60.108	55.000	2.85	0.0	0.0	3.41	R
1473	1779	1.400629	CCAATCAGCACGTCAAAGCAG	60.401	52.381	0.00	0.0	0.0	4.24	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
53	55	1.682684	CCCCACTCCTACGCTCTGT	60.683	63.158	0.00	0.00	0.00	3.41
79	81	5.858581	GTCAAAAAGATAAGGACACACATGC	59.141	40.000	0.00	0.00	0.00	4.06
137	140	5.010617	TGTGGCTTTGAGTATCGCTATATGA	59.989	40.000	0.00	0.00	38.61	2.15
217	220	2.110901	CTGAGCAAAGCAGGACATCT	57.889	50.000	0.00	0.00	0.00	2.90
225	228	1.227205	GCAGGACATCTCTCCAGCG	60.227	63.158	0.00	0.00	33.60	5.18
252	255	5.261216	ACACAAAGAAGGAGGAAGAACAAA	58.739	37.500	0.00	0.00	0.00	2.83
275	285	9.734620	CAAAAACAGAAAATCATACTGACAAGA	57.265	29.630	0.00	0.00	35.85	3.02
310	320	2.904866	CCACACAACCACCACCCG	60.905	66.667	0.00	0.00	0.00	5.28
311	321	3.591835	CACACAACCACCACCCGC	61.592	66.667	0.00	0.00	0.00	6.13
358	368	2.039084	GCCAACCTCCAGATACCATAGG	59.961	54.545	0.00	0.00	0.00	2.57
375	386	3.112709	GCCGCACCTCAACGAGAC	61.113	66.667	0.00	0.00	0.00	3.36
413	424	1.324005	GCTGGCTCCTAGACGAAGGT	61.324	60.000	0.00	0.00	37.91	3.50
427	438	1.381463	AAGGTAGGAGCCCCGTCTC	60.381	63.158	0.00	0.00	37.58	3.36
468	479	4.600012	AAAACTTATTCAGATGCGTCGG	57.400	40.909	0.00	0.00	0.00	4.79
524	535	4.960469	CCCTAACCCTACTGAGAACACATA	59.040	45.833	0.00	0.00	0.00	2.29
533	545	3.245797	CTGAGAACACATAGGACACACG	58.754	50.000	0.00	0.00	0.00	4.49
537	549	4.021229	AGAACACATAGGACACACGGATA	58.979	43.478	0.00	0.00	0.00	2.59
623	645	2.281484	GGCGCACAAAGGGACTCA	60.281	61.111	10.83	0.00	38.49	3.41
680	702	3.176708	GCTCGAAGCGTTATTGTCTACA	58.823	45.455	0.00	0.00	0.00	2.74
681	703	3.611113	GCTCGAAGCGTTATTGTCTACAA	59.389	43.478	0.00	0.00	40.51	2.41
684	706	5.165676	TCGAAGCGTTATTGTCTACAACAT	58.834	37.500	0.00	0.00	38.86	2.71
689	711	8.991243	AAGCGTTATTGTCTACAACATAACTA	57.009	30.769	13.41	0.00	38.86	2.24
699	721	8.676401	TGTCTACAACATAACTATGCGTAAGTA	58.324	33.333	0.00	0.00	37.19	2.24
722	744	4.761235	ATGATTTGCATTCTGATAGGCG	57.239	40.909	0.00	0.00	31.73	5.52
723	745	3.807553	TGATTTGCATTCTGATAGGCGA	58.192	40.909	0.00	0.00	0.00	5.54
725	747	4.274214	TGATTTGCATTCTGATAGGCGAAG	59.726	41.667	0.00	0.00	33.50	3.79
726	748	2.245159	TGCATTCTGATAGGCGAAGG	57.755	50.000	0.00	0.00	0.00	3.46
733	755	3.157881	TCTGATAGGCGAAGGATACCAG	58.842	50.000	0.00	0.00	37.17	4.00
749	771	6.983984	GGATACCAGTGTCCTTCTAACTATC	58.016	44.000	6.34	0.00	37.81	2.08
755	777	6.295916	CCAGTGTCCTTCTAACTATCCAACTT	60.296	42.308	0.00	0.00	0.00	2.66
756	778	7.093465	CCAGTGTCCTTCTAACTATCCAACTTA	60.093	40.741	0.00	0.00	0.00	2.24
757	779	7.976734	CAGTGTCCTTCTAACTATCCAACTTAG	59.023	40.741	0.00	0.00	0.00	2.18
758	780	7.894364	AGTGTCCTTCTAACTATCCAACTTAGA	59.106	37.037	0.00	0.00	0.00	2.10
760	782	9.268282	TGTCCTTCTAACTATCCAACTTAGATT	57.732	33.333	0.00	0.00	0.00	2.40
761	783	9.535878	GTCCTTCTAACTATCCAACTTAGATTG	57.464	37.037	0.00	0.00	0.00	2.67
1019	1323	3.984749	GGAGCTCGATCTCCCGCC	61.985	72.222	22.24	0.04	45.40	6.13
1020	1324	4.335584	GAGCTCGATCTCCCGCCG	62.336	72.222	4.91	0.00	0.00	6.46
1473	1779	2.777832	AGGATGAAGGTGACTCTTGC	57.222	50.000	0.00	0.00	42.68	4.01
1486	1792	0.385223	CTCTTGCTGCTTTGACGTGC	60.385	55.000	0.00	0.00	0.00	5.34
1498	1804	3.829886	TTGACGTGCTGATTGGAATTC	57.170	42.857	0.00	0.00	0.00	2.17
1605	1915	1.728490	GGGAATGGCCGAATGAGCAC	61.728	60.000	0.00	0.00	37.63	4.40
1623	1933	1.805943	CACGGTGACAGAATGATTGCA	59.194	47.619	0.74	0.00	39.69	4.08
1634	1944	7.390162	TGACAGAATGATTGCATTACTGTTGTA	59.610	33.333	16.84	9.63	44.47	2.41
1675	2007	6.127338	CCCCCAGATAAACCAAATTTTCTCTC	60.127	42.308	0.00	0.00	0.00	3.20
1841	2174	7.801716	TTATGAATTCTCTTATCCCGTTTGG	57.198	36.000	7.05	0.00	0.00	3.28
2002	2338	7.066645	GGCGGTGACTAGGAATATAAAACTTTT	59.933	37.037	0.00	0.00	0.00	2.27
2062	2398	6.386927	AGTCAACCACATTGGAATATAGGAGA	59.613	38.462	0.00	0.00	40.96	3.71
2119	2455	7.148672	TGCAAATTCGCAACATTAATAAGTTGG	60.149	33.333	16.26	9.31	43.94	3.77
2125	2461	7.915508	TCGCAACATTAATAAGTTGGTATCAG	58.084	34.615	16.26	2.64	43.94	2.90
2149	2485	9.849166	CAGTTTGTCCAAAGTTTAGTAGAAAAA	57.151	29.630	0.00	0.00	32.02	1.94
2199	2536	2.474410	AAGGAAGGGCTTGTTAGTCG	57.526	50.000	0.00	0.00	0.00	4.18
2200	2537	1.640917	AGGAAGGGCTTGTTAGTCGA	58.359	50.000	0.00	0.00	0.00	4.20
2201	2538	2.188817	AGGAAGGGCTTGTTAGTCGAT	58.811	47.619	0.00	0.00	0.00	3.59
2202	2539	2.572104	AGGAAGGGCTTGTTAGTCGATT	59.428	45.455	0.00	0.00	0.00	3.34
2203	2540	3.009143	AGGAAGGGCTTGTTAGTCGATTT	59.991	43.478	0.00	0.00	0.00	2.17
2204	2541	3.127030	GGAAGGGCTTGTTAGTCGATTTG	59.873	47.826	0.00	0.00	0.00	2.32
2331	2668	5.338463	GGCTTATGTTGGAAGTCCTCTTAGT	60.338	44.000	0.00	0.00	36.82	2.24
2332	2669	6.174049	GCTTATGTTGGAAGTCCTCTTAGTT	58.826	40.000	0.00	0.00	36.82	2.24
2333	2670	6.092807	GCTTATGTTGGAAGTCCTCTTAGTTG	59.907	42.308	0.00	0.00	36.82	3.16
2334	2671	3.740115	TGTTGGAAGTCCTCTTAGTTGC	58.260	45.455	0.00	0.00	36.82	4.17
2335	2672	3.391296	TGTTGGAAGTCCTCTTAGTTGCT	59.609	43.478	0.00	0.00	36.82	3.91
2358	2695	5.644188	TGATGGGGAAGATCTTGAAGTTTT	58.356	37.500	14.00	0.00	0.00	2.43
2417	2754	9.268282	ACTTAGTTATCAACCTATTTCTCCAGA	57.732	33.333	0.00	0.00	0.00	3.86
2439	2776	6.643770	CAGAAATTCATTTGTGCTAGCAACTT	59.356	34.615	21.29	0.00	34.87	2.66

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
18	19	0.328258	GGGGAGTAACATGGCAGTGT	59.672	55.000	0.00	0.00	0.00	3.55
53	55	5.361427	TGTGTGTCCTTATCTTTTTGACGA	58.639	37.500	0.00	0.00	0.00	4.20
79	81	4.465512	GCAGGCGTGTTGGATGCG	62.466	66.667	8.40	0.00	37.48	4.73
137	140	2.501723	TCTCTTTTATCTGGAAGGCGCT	59.498	45.455	7.64	0.00	0.00	5.92
140	143	6.052360	CCTAGTTCTCTTTTATCTGGAAGGC	58.948	44.000	0.00	0.00	0.00	4.35
199	202	1.627329	AGAGATGTCCTGCTTTGCTCA	59.373	47.619	0.00	0.00	0.00	4.26
217	220	1.138069	TCTTTGTGTTGTCGCTGGAGA	59.862	47.619	0.00	0.00	0.00	3.71
225	228	4.451900	TCTTCCTCCTTCTTTGTGTTGTC	58.548	43.478	0.00	0.00	0.00	3.18
275	285	4.991687	GTGTGGAGACGAAGATTCTTCTTT	59.008	41.667	21.03	10.16	42.34	2.52
358	368	3.112709	GTCTCGTTGAGGTGCGGC	61.113	66.667	0.00	0.00	0.00	6.53
413	424	2.043248	GGTGAGACGGGGCTCCTA	60.043	66.667	0.00	0.00	33.95	2.94
427	438	2.398554	CCGGGCTTCGTTCATGGTG	61.399	63.158	0.00	0.00	37.11	4.17
524	535	0.323178	ACCTCGTATCCGTGTGTCCT	60.323	55.000	0.00	0.00	35.01	3.85
621	643	1.803998	CGATCTCAAGGCGAGCAATGA	60.804	52.381	0.00	0.00	41.98	2.57
623	645	0.176680	ACGATCTCAAGGCGAGCAAT	59.823	50.000	0.00	0.00	41.98	3.56
684	706	9.699703	TGCAAATCATATACTTACGCATAGTTA	57.300	29.630	0.00	0.00	0.00	2.24
689	711	8.232513	CAGAATGCAAATCATATACTTACGCAT	58.767	33.333	0.00	0.00	39.12	4.73
699	721	6.175471	TCGCCTATCAGAATGCAAATCATAT	58.825	36.000	0.00	0.00	34.33	1.78
702	724	3.807553	TCGCCTATCAGAATGCAAATCA	58.192	40.909	0.00	0.00	34.76	2.57
705	727	2.945008	CCTTCGCCTATCAGAATGCAAA	59.055	45.455	0.00	0.00	34.76	3.68
709	731	4.021104	TGGTATCCTTCGCCTATCAGAATG	60.021	45.833	0.00	0.00	37.54	2.67
718	740	0.824759	GACACTGGTATCCTTCGCCT	59.175	55.000	0.00	0.00	0.00	5.52
720	742	0.824759	AGGACACTGGTATCCTTCGC	59.175	55.000	0.00	0.00	43.09	4.70
725	747	6.015265	GGATAGTTAGAAGGACACTGGTATCC	60.015	46.154	0.00	0.00	34.98	2.59
726	748	6.550108	TGGATAGTTAGAAGGACACTGGTATC	59.450	42.308	0.00	0.00	0.00	2.24
733	755	8.064336	TCTAAGTTGGATAGTTAGAAGGACAC	57.936	38.462	0.00	0.00	42.89	3.67
755	777	8.713708	TGTCCCTTAAAATTTGAACCAATCTA	57.286	30.769	0.00	0.00	0.00	1.98
756	778	7.610580	TGTCCCTTAAAATTTGAACCAATCT	57.389	32.000	0.00	0.00	0.00	2.40
757	779	8.147704	TCTTGTCCCTTAAAATTTGAACCAATC	58.852	33.333	0.00	0.00	0.00	2.67
758	780	8.028652	TCTTGTCCCTTAAAATTTGAACCAAT	57.971	30.769	0.00	0.00	0.00	3.16
760	782	7.418483	CCTTCTTGTCCCTTAAAATTTGAACCA	60.418	37.037	0.00	0.00	0.00	3.67
761	783	6.929049	CCTTCTTGTCCCTTAAAATTTGAACC	59.071	38.462	0.00	0.00	0.00	3.62
762	784	7.722363	TCCTTCTTGTCCCTTAAAATTTGAAC	58.278	34.615	0.00	0.00	0.00	3.18
764	786	7.469456	CGTTCCTTCTTGTCCCTTAAAATTTGA	60.469	37.037	0.00	0.00	0.00	2.69
765	787	6.640907	CGTTCCTTCTTGTCCCTTAAAATTTG	59.359	38.462	0.00	0.00	0.00	2.32
766	788	6.322969	ACGTTCCTTCTTGTCCCTTAAAATTT	59.677	34.615	0.00	0.00	0.00	1.82
776	831	4.830826	ATCAAAACGTTCCTTCTTGTCC	57.169	40.909	0.00	0.00	0.00	4.02
1206	1510	0.107508	CCATGGGCTGATCGTTGTCT	60.108	55.000	2.85	0.00	0.00	3.41
1473	1779	1.400629	CCAATCAGCACGTCAAAGCAG	60.401	52.381	0.00	0.00	0.00	4.24
1605	1915	3.770263	AATGCAATCATTCTGTCACCG	57.230	42.857	0.00	0.00	38.47	4.94
1623	1933	3.055385	ACATCAGCGGGTACAACAGTAAT	60.055	43.478	0.00	0.00	0.00	1.89
1634	1944	2.672996	GGCACAACATCAGCGGGT	60.673	61.111	0.00	0.00	0.00	5.28
1841	2174	3.577805	AACAATATGGCCAGTACCCTC	57.422	47.619	13.05	0.00	0.00	4.30
2002	2338	6.691754	TCAACAAGAAGCAATACACAGAAA	57.308	33.333	0.00	0.00	0.00	2.52
2062	2398	3.071874	TCCCAGATTTCAGCGTTCAAT	57.928	42.857	0.00	0.00	0.00	2.57
2119	2455	9.485206	TCTACTAAACTTTGGACAAACTGATAC	57.515	33.333	0.00	0.00	0.00	2.24
2149	2485	6.145696	GCAACATTTCTCTGTCGTAGTACTTT	59.854	38.462	0.00	0.00	0.00	2.66
2150	2486	5.634020	GCAACATTTCTCTGTCGTAGTACTT	59.366	40.000	0.00	0.00	0.00	2.24
2183	2520	3.751698	ACAAATCGACTAACAAGCCCTTC	59.248	43.478	0.00	0.00	0.00	3.46
2194	2531	6.570672	ACTGAGACACTTACAAATCGACTA	57.429	37.500	0.00	0.00	0.00	2.59
2195	2532	5.455056	ACTGAGACACTTACAAATCGACT	57.545	39.130	0.00	0.00	0.00	4.18
2196	2533	6.421202	AGAAACTGAGACACTTACAAATCGAC	59.579	38.462	0.00	0.00	0.00	4.20
2197	2534	6.420903	CAGAAACTGAGACACTTACAAATCGA	59.579	38.462	0.00	0.00	32.44	3.59
2198	2535	6.584954	CAGAAACTGAGACACTTACAAATCG	58.415	40.000	0.00	0.00	32.44	3.34
2199	2536	6.203723	AGCAGAAACTGAGACACTTACAAATC	59.796	38.462	2.81	0.00	32.44	2.17
2200	2537	6.058183	AGCAGAAACTGAGACACTTACAAAT	58.942	36.000	2.81	0.00	32.44	2.32
2201	2538	5.428253	AGCAGAAACTGAGACACTTACAAA	58.572	37.500	2.81	0.00	32.44	2.83
2202	2539	5.023533	AGCAGAAACTGAGACACTTACAA	57.976	39.130	2.81	0.00	32.44	2.41
2203	2540	4.672587	AGCAGAAACTGAGACACTTACA	57.327	40.909	2.81	0.00	32.44	2.41
2204	2541	4.811557	ACAAGCAGAAACTGAGACACTTAC	59.188	41.667	2.81	0.00	32.44	2.34
2256	2593	4.281435	ACTGATGCATTTGATGTTGTTCCA	59.719	37.500	0.00	0.00	0.00	3.53
2264	2601	3.991121	TGCACAAACTGATGCATTTGATG	59.009	39.130	15.53	11.12	46.63	3.07
2300	2637	5.047377	GGACTTCCAACATAAGCCATTTCAA	60.047	40.000	0.00	0.00	35.64	2.69
2316	2653	3.239449	TCAGCAACTAAGAGGACTTCCA	58.761	45.455	0.00	0.00	38.89	3.53
2317	2654	3.963428	TCAGCAACTAAGAGGACTTCC	57.037	47.619	0.00	0.00	37.53	3.46
2331	2668	2.577563	TCAAGATCTTCCCCATCAGCAA	59.422	45.455	4.57	0.00	0.00	3.91
2332	2669	2.199208	TCAAGATCTTCCCCATCAGCA	58.801	47.619	4.57	0.00	0.00	4.41
2333	2670	3.212685	CTTCAAGATCTTCCCCATCAGC	58.787	50.000	4.57	0.00	0.00	4.26
2334	2671	4.500499	ACTTCAAGATCTTCCCCATCAG	57.500	45.455	4.57	0.00	0.00	2.90
2335	2672	4.934797	AACTTCAAGATCTTCCCCATCA	57.065	40.909	4.57	0.00	0.00	3.07
2413	2750	5.063180	TGCTAGCACAAATGAATTTCTGG	57.937	39.130	14.93	0.00	0.00	3.86
2414	2751	6.154445	AGTTGCTAGCACAAATGAATTTCTG	58.846	36.000	19.17	0.00	0.00	3.02
2417	2754	8.928733	CATTAAGTTGCTAGCACAAATGAATTT	58.071	29.630	19.17	6.61	28.54	1.82

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.