AutoCloner

Multiple sequence alignment - TraesCS2D01G470800

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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	TraesCS2D01G470800	chr2D	100.000	3452	0	0	1	3452	575163527	575160076	0.000000e+00	6375
1	TraesCS2D01G470800	chr2D	96.460	1582	46	3	1515	3088	575169178	575167599	0.000000e+00	2603
2	TraesCS2D01G470800	chr2D	96.571	1400	17	12	1	1399	575176323	575174954	0.000000e+00	2290
3	TraesCS2D01G470800	chr2D	89.536	927	80	6	1517	2427	574656540	574657465	0.000000e+00	1158
4	TraesCS2D01G470800	chr2D	83.451	852	125	12	1	841	575180489	575179643	0.000000e+00	778
5	TraesCS2D01G470800	chr2D	90.559	519	41	5	2941	3452	574661644	574662161	0.000000e+00	680
6	TraesCS2D01G470800	chr2D	88.664	494	55	1	2959	3452	574601587	574601095	4.930000e-168	601
7	TraesCS2D01G470800	chr2D	88.462	494	56	1	2959	3452	574572962	574572470	2.290000e-166	595
8	TraesCS2D01G470800	chr2D	88.259	494	57	1	2959	3452	574597660	574597168	1.070000e-164	590
9	TraesCS2D01G470800	chr2D	93.165	395	26	1	1443	1836	575174956	575174562	2.310000e-161	579
10	TraesCS2D01G470800	chr2D	86.500	400	35	10	1112	1511	574655825	574656205	4.120000e-114	422
11	TraesCS2D01G470800	chr2D	84.158	404	59	3	2100	2498	574979059	574978656	1.500000e-103	387
12	TraesCS2D01G470800	chr2D	84.872	390	45	6	536	921	574664938	574665317	6.990000e-102	381
13	TraesCS2D01G470800	chr2B	95.697	3021	92	16	1	3018	691051906	691048921	0.000000e+00	4824
14	TraesCS2D01G470800	chr2B	88.130	1449	124	18	1112	2535	690930463	690931888	0.000000e+00	1679
15	TraesCS2D01G470800	chr2B	84.277	795	115	7	1	790	691055858	691055069	0.000000e+00	767
16	TraesCS2D01G470800	chr2B	93.135	437	28	2	3016	3452	690940885	690941319	1.040000e-179	640
17	TraesCS2D01G470800	chr2B	86.482	577	66	8	2878	3452	691039491	691038925	1.050000e-174	623
18	TraesCS2D01G470800	chr2B	91.304	437	37	1	3016	3452	691048549	691048114	2.290000e-166	595
19	TraesCS2D01G470800	chr2A	88.880	1322	109	12	1112	2418	713015953	713017251	0.000000e+00	1592
20	TraesCS2D01G470800	chr2A	94.144	888	36	7	1	876	713218032	713217149	0.000000e+00	1338
21	TraesCS2D01G470800	chr2A	90.251	718	55	7	2742	3452	713191202	713190493	0.000000e+00	924
22	TraesCS2D01G470800	chr2A	90.944	519	39	6	2941	3452	713123610	713124127	0.000000e+00	691
23	TraesCS2D01G470800	chr2A	82.792	831	69	20	1896	2709	713204193	713203420	0.000000e+00	675
24	TraesCS2D01G470800	chr2A	85.794	359	46	4	210	567	713228726	713228372	3.250000e-100	375
25	TraesCS2D01G470800	chr2A	84.438	347	30	6	1514	1836	713216485	713216139	1.550000e-83	320
26	TraesCS2D01G470800	chr2A	80.093	216	32	6	1	213	713245990	713245783	2.150000e-32	150
27	TraesCS2D01G470800	chr2A	88.660	97	8	2	1021	1115	713015676	713015771	7.830000e-22	115
28	TraesCS2D01G470800	chr7D	83.587	658	93	4	1770	2412	152219593	152220250	1.370000e-168	603
29	TraesCS2D01G470800	chr7D	81.832	666	98	7	1776	2423	141562156	141562816	3.920000e-149	538
30	TraesCS2D01G470800	chr7D	89.498	219	23	0	1419	1637	141561589	141561807	9.440000e-71	278
31	TraesCS2D01G470800	chr7D	89.116	147	13	2	1633	1779	141561914	141562057	2.740000e-41	180
32	TraesCS2D01G470800	chr7A	82.979	658	97	4	1770	2412	152833772	152834429	6.420000e-162	580
33	TraesCS2D01G470800	chr7A	82.406	665	96	5	1776	2423	144170867	144170207	8.370000e-156	560
34	TraesCS2D01G470800	chr7A	90.141	213	21	0	1425	1637	144171388	144171176	9.440000e-71	278
35	TraesCS2D01G470800	chr7A	87.302	189	24	0	1112	1300	152832608	152832796	2.090000e-52	217
36	TraesCS2D01G470800	chr7A	89.116	147	13	2	1633	1779	144171106	144170963	2.740000e-41	180
37	TraesCS2D01G470800	chr7B	81.641	719	108	12	1770	2468	114395044	114395758	2.990000e-160	575
38	TraesCS2D01G470800	chr7B	89.498	219	23	0	1419	1637	114394435	114394653	9.440000e-71	278

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	TraesCS2D01G470800	chr2D	575160076	575163527	3451	True	6375.000000	6375	100.000000	1	3452	1	chr2D.!!$R3	3451
1	TraesCS2D01G470800	chr2D	575167599	575169178	1579	True	2603.000000	2603	96.460000	1515	3088	1	chr2D.!!$R4	1573
2	TraesCS2D01G470800	chr2D	575174562	575180489	5927	True	1215.666667	2290	91.062333	1	1836	3	chr2D.!!$R6	1835
3	TraesCS2D01G470800	chr2D	574655825	574657465	1640	False	790.000000	1158	88.018000	1112	2427	2	chr2D.!!$F1	1315
4	TraesCS2D01G470800	chr2D	574597168	574601587	4419	True	595.500000	601	88.461500	2959	3452	2	chr2D.!!$R5	493
5	TraesCS2D01G470800	chr2D	574661644	574665317	3673	False	530.500000	680	87.715500	536	3452	2	chr2D.!!$F2	2916
6	TraesCS2D01G470800	chr2B	691048114	691055858	7744	True	2062.000000	4824	90.426000	1	3452	3	chr2B.!!$R2	3451
7	TraesCS2D01G470800	chr2B	690930463	690931888	1425	False	1679.000000	1679	88.130000	1112	2535	1	chr2B.!!$F1	1423
8	TraesCS2D01G470800	chr2B	691038925	691039491	566	True	623.000000	623	86.482000	2878	3452	1	chr2B.!!$R1	574
9	TraesCS2D01G470800	chr2A	713190493	713191202	709	True	924.000000	924	90.251000	2742	3452	1	chr2A.!!$R1	710
10	TraesCS2D01G470800	chr2A	713015676	713017251	1575	False	853.500000	1592	88.770000	1021	2418	2	chr2A.!!$F2	1397
11	TraesCS2D01G470800	chr2A	713216139	713218032	1893	True	829.000000	1338	89.291000	1	1836	2	chr2A.!!$R5	1835
12	TraesCS2D01G470800	chr2A	713123610	713124127	517	False	691.000000	691	90.944000	2941	3452	1	chr2A.!!$F1	511
13	TraesCS2D01G470800	chr2A	713203420	713204193	773	True	675.000000	675	82.792000	1896	2709	1	chr2A.!!$R2	813
14	TraesCS2D01G470800	chr7D	152219593	152220250	657	False	603.000000	603	83.587000	1770	2412	1	chr7D.!!$F1	642
15	TraesCS2D01G470800	chr7D	141561589	141562816	1227	False	332.000000	538	86.815333	1419	2423	3	chr7D.!!$F2	1004
16	TraesCS2D01G470800	chr7A	152832608	152834429	1821	False	398.500000	580	85.140500	1112	2412	2	chr7A.!!$F1	1300
17	TraesCS2D01G470800	chr7A	144170207	144171388	1181	True	339.333333	560	87.221000	1425	2423	3	chr7A.!!$R1	998
18	TraesCS2D01G470800	chr7B	114394435	114395758	1323	False	426.500000	575	85.569500	1419	2468	2	chr7B.!!$F1	1049

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
740	4975	2.754375	CGGGTAACTGGCCACCTT	59.246	61.111	0.0	0.0	40.24	3.50	F
2133	7603	0.043334	AGGCTGGTATGGAGGACAGT	59.957	55.000	0.0	0.0	33.62	3.55	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2302	7784	0.403271	AACACATGAAGCTCAGGCCT	59.597	50.0	0.0	0.0	39.73	5.19	R
3203	9096	0.531974	TTGACGTGGAGACTGTTGCC	60.532	55.0	0.0	0.0	0.00	4.52	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
740	4975	2.754375	CGGGTAACTGGCCACCTT	59.246	61.111	0.00	0.00	40.24	3.50
769	5004	4.069232	CGGCGGTGAAGCTCTCCA	62.069	66.667	0.00	0.00	37.29	3.86
961	5213	3.547054	ACGACTTCTATCTCTCTCCGT	57.453	47.619	0.00	0.00	0.00	4.69
962	5214	3.460103	ACGACTTCTATCTCTCTCCGTC	58.540	50.000	0.00	0.00	0.00	4.79
964	5216	3.739300	CGACTTCTATCTCTCTCCGTCTC	59.261	52.174	0.00	0.00	0.00	3.36
965	5217	4.062991	GACTTCTATCTCTCTCCGTCTCC	58.937	52.174	0.00	0.00	0.00	3.71
966	5218	2.823924	TCTATCTCTCTCCGTCTCCG	57.176	55.000	0.00	0.00	0.00	4.63
982	5234	6.907206	CGTCTCCGGTTATAAAAACCATAA	57.093	37.500	0.00	0.00	40.28	1.90
983	5235	6.940714	CGTCTCCGGTTATAAAAACCATAAG	58.059	40.000	0.00	1.91	40.28	1.73
1033	5350	8.938883	AGTACATATAGTCATCCAATCCAAGTT	58.061	33.333	0.00	0.00	0.00	2.66
1231	5741	3.680786	CCGTGCTCCTCACCGACA	61.681	66.667	0.00	0.00	42.69	4.35
1238	5748	0.965866	CTCCTCACCGACAGCTACCA	60.966	60.000	0.00	0.00	0.00	3.25
1282	5792	4.710375	GGAAGAGGAACTACACCTACATCA	59.290	45.833	0.00	0.00	41.55	3.07
1302	5812	2.488820	GCCGTCGAGTCCTACACC	59.511	66.667	0.00	0.00	0.00	4.16
1303	5813	2.338015	GCCGTCGAGTCCTACACCA	61.338	63.158	0.00	0.00	0.00	4.17
1304	5814	1.664321	GCCGTCGAGTCCTACACCAT	61.664	60.000	0.00	0.00	0.00	3.55
1305	5815	0.381089	CCGTCGAGTCCTACACCATC	59.619	60.000	0.00	0.00	0.00	3.51
1308	5818	1.092348	TCGAGTCCTACACCATCACG	58.908	55.000	0.00	0.00	0.00	4.35
1309	5819	0.100682	CGAGTCCTACACCATCACGG	59.899	60.000	0.00	0.00	42.50	4.94
1310	5820	0.179108	GAGTCCTACACCATCACGGC	60.179	60.000	0.00	0.00	39.03	5.68
1312	5822	1.679641	TCCTACACCATCACGGCGA	60.680	57.895	16.62	0.00	39.03	5.54
1313	5823	1.216977	CCTACACCATCACGGCGAA	59.783	57.895	16.62	0.42	39.03	4.70
1314	5824	0.806102	CCTACACCATCACGGCGAAG	60.806	60.000	16.62	5.73	39.03	3.79
1315	5825	0.172578	CTACACCATCACGGCGAAGA	59.827	55.000	16.62	11.96	39.03	2.87
1316	5826	0.172578	TACACCATCACGGCGAAGAG	59.827	55.000	16.62	2.90	39.03	2.85
1318	5828	1.982395	ACCATCACGGCGAAGAGGA	60.982	57.895	16.62	3.00	39.03	3.71
1319	5829	1.330655	ACCATCACGGCGAAGAGGAT	61.331	55.000	16.62	5.44	39.03	3.24
1320	5830	0.598680	CCATCACGGCGAAGAGGATC	60.599	60.000	16.62	0.00	0.00	3.36
1503	6202	2.205074	CATGTACATGGTCCTCTTCGC	58.795	52.381	25.41	0.00	35.24	4.70
1594	6626	3.571590	GGTCATGTCCATCTCCTACTCT	58.428	50.000	3.91	0.00	0.00	3.24
1793	7242	2.599578	AGGACACGGTGTAGGCGT	60.600	61.111	14.74	0.70	0.00	5.68
1862	7313	0.687354	CACCACCACAGCCTTCTACT	59.313	55.000	0.00	0.00	0.00	2.57
1924	7390	0.832135	TCACCAGGTTCGGCTTCTCT	60.832	55.000	0.00	0.00	0.00	3.10
2133	7603	0.043334	AGGCTGGTATGGAGGACAGT	59.957	55.000	0.00	0.00	33.62	3.55
2302	7784	1.302192	GAAGTGGGTGGCGCTACAA	60.302	57.895	25.79	10.35	0.00	2.41
2413	7902	4.331968	TGTTCAAGACCAAGTTGTGAACT	58.668	39.130	25.32	9.36	45.29	3.01
3013	8518	5.372343	TGCACATATGATACCTTGACCTT	57.628	39.130	10.38	0.00	0.00	3.50
3146	9033	0.174845	TCCGTGGAGCCATAAACTCG	59.825	55.000	0.00	0.00	34.87	4.18
3200	9093	4.229876	GTTGCTCTGCTAAAACCAATGTC	58.770	43.478	0.00	0.00	0.00	3.06
3203	9096	3.667960	GCTCTGCTAAAACCAATGTCGTG	60.668	47.826	0.00	0.00	0.00	4.35
3230	9123	0.388520	TCTCCACGTCAATGCACTCG	60.389	55.000	0.00	0.00	0.00	4.18
3251	9144	6.262273	ACTCGGACAATTTACTTTCACACATT	59.738	34.615	0.00	0.00	0.00	2.71
3252	9145	6.434596	TCGGACAATTTACTTTCACACATTG	58.565	36.000	0.00	0.00	0.00	2.82
3353	13173	3.256879	GCTCATCGACTATCAGGGAATCA	59.743	47.826	0.00	0.00	0.00	2.57
3377	13197	7.123397	TCAGTGTATATGAAGTGAAGAAGAGCT	59.877	37.037	0.00	0.00	0.00	4.09
3394	13214	4.077822	AGAGCTTCAAAGATTTCAGGGTG	58.922	43.478	0.00	0.00	0.00	4.61
3412	13232	4.463891	AGGGTGGATGTCATCAATTTTGAC	59.536	41.667	14.72	10.16	43.04	3.18
3439	13259	3.323691	TGTGTTTCCTTCTCCTTCATCGA	59.676	43.478	0.00	0.00	0.00	3.59
3442	13262	4.202315	TGTTTCCTTCTCCTTCATCGAACA	60.202	41.667	0.00	0.00	0.00	3.18

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
769	5004	0.395862	ACGTCGTCCAGATCCTCCAT	60.396	55.000	0.00	0.00	0.00	3.41
961	5213	6.961042	ACCTTATGGTTTTTATAACCGGAGA	58.039	36.000	9.46	0.00	46.05	3.71
977	5229	6.818142	GGATTTGATTTGTTCCAACCTTATGG	59.182	38.462	0.00	0.00	42.12	2.74
979	5231	6.435904	TCGGATTTGATTTGTTCCAACCTTAT	59.564	34.615	0.00	0.00	0.00	1.73
980	5232	5.770663	TCGGATTTGATTTGTTCCAACCTTA	59.229	36.000	0.00	0.00	0.00	2.69
981	5233	4.586841	TCGGATTTGATTTGTTCCAACCTT	59.413	37.500	0.00	0.00	0.00	3.50
982	5234	4.148838	TCGGATTTGATTTGTTCCAACCT	58.851	39.130	0.00	0.00	0.00	3.50
983	5235	4.022329	ACTCGGATTTGATTTGTTCCAACC	60.022	41.667	0.00	0.00	0.00	3.77
1033	5350	4.507756	CAGTCGATCGAATTGCCTAAATCA	59.492	41.667	21.31	0.00	0.00	2.57
1282	5792	1.303888	TGTAGGACTCGACGGCCTT	60.304	57.895	13.55	0.00	33.28	4.35
1302	5812	0.387202	AGATCCTCTTCGCCGTGATG	59.613	55.000	0.00	0.00	0.00	3.07
1303	5813	0.671251	GAGATCCTCTTCGCCGTGAT	59.329	55.000	0.00	0.00	0.00	3.06
1304	5814	1.384989	GGAGATCCTCTTCGCCGTGA	61.385	60.000	0.00	0.00	0.00	4.35
1305	5815	1.066587	GGAGATCCTCTTCGCCGTG	59.933	63.158	0.00	0.00	0.00	4.94
1308	5818	0.827368	ACTTGGAGATCCTCTTCGCC	59.173	55.000	0.00	0.00	36.25	5.54
1309	5819	1.472376	CCACTTGGAGATCCTCTTCGC	60.472	57.143	0.00	0.00	37.39	4.70
1310	5820	1.472376	GCCACTTGGAGATCCTCTTCG	60.472	57.143	0.00	0.00	37.39	3.79
1312	5822	0.539051	CGCCACTTGGAGATCCTCTT	59.461	55.000	0.00	0.00	37.14	2.85
1313	5823	0.324738	TCGCCACTTGGAGATCCTCT	60.325	55.000	0.00	0.00	39.12	3.69
1314	5824	0.537188	TTCGCCACTTGGAGATCCTC	59.463	55.000	2.24	0.00	43.47	3.71
1315	5825	0.539051	CTTCGCCACTTGGAGATCCT	59.461	55.000	2.24	0.00	43.47	3.24
1316	5826	0.250513	ACTTCGCCACTTGGAGATCC	59.749	55.000	2.24	0.00	43.47	3.36
1318	5828	0.687354	ACACTTCGCCACTTGGAGAT	59.313	50.000	2.24	0.00	43.47	2.75
1319	5829	0.249868	CACACTTCGCCACTTGGAGA	60.250	55.000	0.00	0.00	42.33	3.71
1320	5830	1.230635	CCACACTTCGCCACTTGGAG	61.231	60.000	0.00	0.00	37.39	3.86
1321	5831	1.227823	CCACACTTCGCCACTTGGA	60.228	57.895	0.00	0.00	37.39	3.53
1324	5834	0.180406	AGAACCACACTTCGCCACTT	59.820	50.000	0.00	0.00	0.00	3.16
1327	5921	1.891919	GCAGAACCACACTTCGCCA	60.892	57.895	0.00	0.00	0.00	5.69
1417	6116	5.893518	AGCAGTTGGCCTTGTAAAGAGCA	62.894	47.826	3.32	0.00	45.77	4.26
1423	6122	1.133637	TGGAAGCAGTTGGCCTTGTAA	60.134	47.619	3.32	0.00	46.50	2.41
1503	6202	1.746220	AGAAGACGACCTTGGAGATCG	59.254	52.381	0.00	0.00	37.25	3.69
1641	6959	1.296392	CCCATGGTCGTCTTGCTGA	59.704	57.895	11.73	0.00	0.00	4.26
1643	6961	1.003355	CACCCATGGTCGTCTTGCT	60.003	57.895	11.73	0.00	31.02	3.91
2133	7603	1.656263	GTGCTCACGACGACGAACA	60.656	57.895	15.32	3.43	42.66	3.18
2302	7784	0.403271	AACACATGAAGCTCAGGCCT	59.597	50.000	0.00	0.00	39.73	5.19
3013	8518	2.419667	GCAGTGGCTAGTTCCGTTAAA	58.580	47.619	0.00	0.00	36.96	1.52
3146	9033	2.095053	GGATCTCAAAGAAGCTTGCGTC	59.905	50.000	2.10	0.44	0.00	5.19
3200	9093	3.642755	GTGGAGACTGTTGCCACG	58.357	61.111	14.45	0.00	42.20	4.94
3203	9096	0.531974	TTGACGTGGAGACTGTTGCC	60.532	55.000	0.00	0.00	0.00	4.52
3230	9123	5.982516	TGCAATGTGTGAAAGTAAATTGTCC	59.017	36.000	0.00	0.00	0.00	4.02
3251	9144	7.336679	CGATATGGATTGGATAGGTTAAATGCA	59.663	37.037	0.00	0.00	35.30	3.96
3252	9145	7.552687	TCGATATGGATTGGATAGGTTAAATGC	59.447	37.037	0.00	0.00	0.00	3.56
3353	13173	7.416964	AGCTCTTCTTCACTTCATATACACT	57.583	36.000	0.00	0.00	0.00	3.55
3377	13197	4.739793	ACATCCACCCTGAAATCTTTGAA	58.260	39.130	0.00	0.00	0.00	2.69
3394	13214	4.095410	TGCGTCAAAATTGATGACATCC	57.905	40.909	17.32	10.49	45.90	3.51
3412	13232	0.868406	GGAGAAGGAAACACACTGCG	59.132	55.000	0.00	0.00	0.00	5.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.