AutoCloner

Multiple sequence alignment - TraesCS7A01G233100

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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	TraesCS7A01G233100	chr7A	100.000	2255	0	0	1	2255	204669176	204666922	0.000000e+00	4165
1	TraesCS7A01G233100	chr7A	89.002	1182	74	17	558	1708	205124074	205125230	0.000000e+00	1411
2	TraesCS7A01G233100	chr7A	92.184	499	36	2	2	498	649879236	649879733	0.000000e+00	702
3	TraesCS7A01G233100	chr7B	89.541	1788	111	36	493	2255	158555745	158554009	0.000000e+00	2196
4	TraesCS7A01G233100	chr7B	89.539	1281	74	17	490	1742	158936597	158937845	0.000000e+00	1568
5	TraesCS7A01G233100	chr7D	92.021	940	47	8	631	1562	195279112	195280031	0.000000e+00	1295
6	TraesCS7A01G233100	chr7D	88.939	895	45	22	493	1356	194795153	194794282	0.000000e+00	1055
7	TraesCS7A01G233100	chr7D	92.585	499	33	4	1	498	413242415	413241920	0.000000e+00	713
8	TraesCS7A01G233100	chr7D	95.522	335	15	0	1921	2255	194791248	194790914	9.170000e-149	536
9	TraesCS7A01G233100	chr7D	80.457	788	70	41	756	1517	194792618	194791889	1.980000e-145	525
10	TraesCS7A01G233100	chr7D	82.418	455	30	17	1325	1745	194794229	194793791	3.560000e-93	351
11	TraesCS7A01G233100	chr7D	82.933	375	24	9	1569	1935	194791606	194791264	3.640000e-78	302
12	TraesCS7A01G233100	chr5A	94.024	502	26	3	1	500	258117917	258118416	0.000000e+00	758
13	TraesCS7A01G233100	chr4A	93.574	498	31	1	1	498	511076151	511076647	0.000000e+00	741
14	TraesCS7A01G233100	chr6A	92.829	502	31	2	1	498	286337030	286337530	0.000000e+00	723
15	TraesCS7A01G233100	chr2D	95.364	453	19	1	1	453	624300280	624300730	0.000000e+00	719
16	TraesCS7A01G233100	chr2D	92.032	502	35	2	1	498	69146707	69147207	0.000000e+00	701
17	TraesCS7A01G233100	chr5D	91.849	503	35	4	1	501	41228085	41228583	0.000000e+00	697
18	TraesCS7A01G233100	chr3D	91.036	502	41	2	1	500	458318035	458318534	0.000000e+00	675

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	TraesCS7A01G233100	chr7A	204666922	204669176	2254	True	4165.0	4165	100.0000	1	2255	1	chr7A.!!$R1	2254
1	TraesCS7A01G233100	chr7A	205124074	205125230	1156	False	1411.0	1411	89.0020	558	1708	1	chr7A.!!$F1	1150
2	TraesCS7A01G233100	chr7B	158554009	158555745	1736	True	2196.0	2196	89.5410	493	2255	1	chr7B.!!$R1	1762
3	TraesCS7A01G233100	chr7B	158936597	158937845	1248	False	1568.0	1568	89.5390	490	1742	1	chr7B.!!$F1	1252
4	TraesCS7A01G233100	chr7D	195279112	195280031	919	False	1295.0	1295	92.0210	631	1562	1	chr7D.!!$F1	931
5	TraesCS7A01G233100	chr7D	194790914	194795153	4239	True	553.8	1055	86.0538	493	2255	5	chr7D.!!$R2	1762
6	TraesCS7A01G233100	chr6A	286337030	286337530	500	False	723.0	723	92.8290	1	498	1	chr6A.!!$F1	497
7	TraesCS7A01G233100	chr2D	69146707	69147207	500	False	701.0	701	92.0320	1	498	1	chr2D.!!$F1	497

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
892	926	0.179076	AAACACAAGCCAAGCCAAGC	60.179	50.0	0.0	0.0	0.0	4.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1745	4339	5.670485	AGTGTTGAAGTGTAAGTGACATCA	58.33	37.5	0.0	0.0	41.14	3.07	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
67	68	3.689161	CGTTTTGTTGCCTCCTATCATGA	59.311	43.478	0.00	0.00	0.00	3.07
156	157	3.189080	TGGACGACAAAGAGCATGATTTG	59.811	43.478	13.68	13.68	41.22	2.32
171	172	1.643810	GATTTGTGCGTTCGACATTGC	59.356	47.619	0.00	0.00	0.00	3.56
190	191	9.571810	GACATTGCATTGTTCATGAACTATTTA	57.428	29.630	32.57	20.39	41.67	1.40
261	262	8.696175	GTTTGGGTTGTAATAACGAAATTGAAG	58.304	33.333	0.00	0.00	0.00	3.02
391	396	2.873851	GCGCGCGCTGCATTTTAA	60.874	55.556	44.38	0.00	46.97	1.52
400	405	1.405469	CTGCATTTTAACGCGGCTGC	61.405	55.000	12.47	7.70	37.91	5.25
406	411	2.725203	TTTAACGCGGCTGCTGGAGT	62.725	55.000	17.03	2.54	39.65	3.85
434	439	2.280524	CGTCACGCCAAACCAGGA	60.281	61.111	0.00	0.00	0.00	3.86
437	442	0.321653	GTCACGCCAAACCAGGAGAT	60.322	55.000	0.00	0.00	32.29	2.75
438	443	0.321564	TCACGCCAAACCAGGAGATG	60.322	55.000	0.00	0.00	32.29	2.90
505	510	5.282055	TGTTGGAGATGCTCTTAGGTATG	57.718	43.478	0.00	0.00	0.00	2.39
516	521	5.070047	TGCTCTTAGGTATGTTTAGCCTACC	59.930	44.000	0.00	0.00	38.25	3.18
639	645	2.043852	ACCCGAGGAGACGATGCT	60.044	61.111	0.00	0.00	35.09	3.79
662	695	2.230130	TCTCCCCGGCATTTCATTTT	57.770	45.000	0.00	0.00	0.00	1.82
746	779	2.009042	GCTCCTATGCAAGCTTGTCGT	61.009	52.381	26.55	20.67	35.60	4.34
758	791	1.067635	GCTTGTCGTTGATTTGCCCAT	60.068	47.619	0.00	0.00	0.00	4.00
888	922	2.676076	CATACAAACACAAGCCAAGCC	58.324	47.619	0.00	0.00	0.00	4.35
889	923	1.769026	TACAAACACAAGCCAAGCCA	58.231	45.000	0.00	0.00	0.00	4.75
890	924	0.901124	ACAAACACAAGCCAAGCCAA	59.099	45.000	0.00	0.00	0.00	4.52
891	925	1.134729	ACAAACACAAGCCAAGCCAAG	60.135	47.619	0.00	0.00	0.00	3.61
892	926	0.179076	AAACACAAGCCAAGCCAAGC	60.179	50.000	0.00	0.00	0.00	4.01
910	944	1.227263	CCCGGTGATCTAGCAACCG	60.227	63.158	18.40	18.40	42.91	4.44
925	962	4.012374	AGCAACCGTAGTAGCACTAGTAA	58.988	43.478	0.00	0.00	30.12	2.24
929	987	5.938438	ACCGTAGTAGCACTAGTAATAGC	57.062	43.478	0.00	0.00	30.12	2.97
1064	1126	1.389106	GGCGCTAAACAAGTACGACAG	59.611	52.381	7.64	0.00	0.00	3.51
1141	1203	1.003580	TGGAGGATGTGAAGAAGCACC	59.996	52.381	0.00	0.00	37.99	5.01
1208	1273	2.412525	CGGCAGCAGCAACAACAA	59.587	55.556	2.65	0.00	44.61	2.83
1210	1276	1.592400	GGCAGCAGCAACAACAACC	60.592	57.895	2.65	0.00	44.61	3.77
1212	1278	0.459934	GCAGCAGCAACAACAACCAA	60.460	50.000	0.00	0.00	41.58	3.67
1278	1344	6.883217	AGTAAGTAGTCTGTCCGAAACTCATA	59.117	38.462	0.00	0.00	0.00	2.15
1330	1493	2.292569	GCATCATCACATAAGTGGCCAG	59.707	50.000	5.11	0.00	45.91	4.85
1403	1573	1.911471	GGCCTGGCTAGCTTTCTCT	59.089	57.895	19.68	0.00	0.00	3.10
1474	1647	6.763715	TTCCCTCTACTAATATGCATGGTT	57.236	37.500	10.16	6.92	0.00	3.67
1638	1866	4.763793	TGGCTTCTTTTCCATTCTTGAGAG	59.236	41.667	0.00	0.00	0.00	3.20
1655	1883	5.314923	TGAGAGGCAAATTTTAGCATGAC	57.685	39.130	0.00	0.00	0.00	3.06
1745	4339	3.513680	TCACTTACGTATCATTGCGGT	57.486	42.857	0.00	0.00	35.03	5.68
1752	4346	2.200899	CGTATCATTGCGGTGATGTCA	58.799	47.619	12.42	0.00	39.13	3.58
1765	4359	4.084537	CGGTGATGTCACTTACACTTCAAC	60.085	45.833	12.43	0.00	45.73	3.18
1826	4420	8.411683	TCCTAGTTGTAAGCTAATTACTACAGC	58.588	37.037	12.50	5.81	46.31	4.40
1841	4435	0.320946	ACAGCAAAACATGGCATGCC	60.321	50.000	30.54	30.54	39.59	4.40
1873	4467	5.573337	AATTGCAAGCTAAACAGATCTCC	57.427	39.130	4.94	0.00	0.00	3.71
2071	4695	3.310193	AGGTGTATTTCTAGGAGCCCTC	58.690	50.000	0.00	0.00	34.61	4.30
2124	4748	5.992217	ACCTTTAGTGAGAGTAACTTGCTTG	59.008	40.000	0.00	0.00	0.00	4.01
2127	4751	4.899352	AGTGAGAGTAACTTGCTTGGAT	57.101	40.909	0.00	0.00	0.00	3.41
2168	4792	7.581213	AATTCAGTCAAACTGGTCATAAACA	57.419	32.000	7.21	0.00	45.94	2.83
2198	4822	4.873817	TGGTTTCTGAAATCAACATGCAG	58.126	39.130	13.40	0.00	0.00	4.41
2250	4875	9.528018	ACGTTTTATCATCTTTTGTTTTGTGAT	57.472	25.926	0.00	0.00	0.00	3.06

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
156	157	0.976963	CAATGCAATGTCGAACGCAC	59.023	50.000	0.00	0.00	37.17	5.34
190	191	8.885494	ACAACAAATAGTGCAATAAACACAAT	57.115	26.923	0.00	0.00	40.59	2.71
415	420	3.353836	CTGGTTTGGCGTGACGGG	61.354	66.667	7.25	0.00	0.00	5.28
417	422	2.280524	TCCTGGTTTGGCGTGACG	60.281	61.111	0.00	0.00	0.00	4.35
419	424	0.321564	CATCTCCTGGTTTGGCGTGA	60.322	55.000	0.00	0.00	0.00	4.35
421	426	1.002134	CCATCTCCTGGTTTGGCGT	60.002	57.895	0.00	0.00	40.49	5.68
425	430	2.409870	GCGCCCATCTCCTGGTTTG	61.410	63.158	0.00	0.00	44.30	2.93
452	457	1.083593	GCCGCGCGCTAAAATCTAC	60.084	57.895	30.48	3.51	0.00	2.59
474	479	2.954684	ATCTCCAACAGCCGCCGAA	61.955	57.895	0.00	0.00	0.00	4.30
475	480	3.390521	ATCTCCAACAGCCGCCGA	61.391	61.111	0.00	0.00	0.00	5.54
476	481	3.197790	CATCTCCAACAGCCGCCG	61.198	66.667	0.00	0.00	0.00	6.46
477	482	3.512516	GCATCTCCAACAGCCGCC	61.513	66.667	0.00	0.00	0.00	6.13
505	510	9.702494	ATGATTAGTAATTACGGTAGGCTAAAC	57.298	33.333	9.91	2.00	0.00	2.01
536	541	8.823220	ATTTGTACTTTAACCAGGCTAATGAT	57.177	30.769	3.12	0.00	0.00	2.45
632	638	1.443407	CGGGGAGAATCAGCATCGT	59.557	57.895	0.00	0.00	36.25	3.73
639	645	0.623194	TGAAATGCCGGGGAGAATCA	59.377	50.000	2.18	0.00	36.25	2.57
746	779	2.233431	GCAGTACCAATGGGCAAATCAA	59.767	45.455	3.55	0.00	37.90	2.57
758	791	1.697432	AGGTGTTAGCAGCAGTACCAA	59.303	47.619	11.47	0.00	44.89	3.67
888	922	0.107703	TTGCTAGATCACCGGGCTTG	60.108	55.000	6.32	0.00	0.00	4.01
889	923	0.107654	GTTGCTAGATCACCGGGCTT	60.108	55.000	6.32	0.00	0.00	4.35
890	924	1.522569	GTTGCTAGATCACCGGGCT	59.477	57.895	6.32	0.00	0.00	5.19
891	925	1.523938	GGTTGCTAGATCACCGGGC	60.524	63.158	6.32	0.00	0.00	6.13
892	926	1.227263	CGGTTGCTAGATCACCGGG	60.227	63.158	16.24	0.00	39.96	5.73
910	944	6.016943	ACTGCTGCTATTACTAGTGCTACTAC	60.017	42.308	5.39	0.00	32.01	2.73
925	962	5.860941	ATGACTACTGTTACTGCTGCTAT	57.139	39.130	0.00	0.00	0.00	2.97
929	987	3.996363	TGCAATGACTACTGTTACTGCTG	59.004	43.478	0.00	0.00	0.00	4.41
1101	1163	2.665185	GACTTGCCGTCGCCAACT	60.665	61.111	0.00	0.00	32.04	3.16
1141	1203	2.158449	CGTCTTTTACCAGCTCTGCAAG	59.842	50.000	0.00	0.00	0.00	4.01
1146	1208	1.968493	TCCACGTCTTTTACCAGCTCT	59.032	47.619	0.00	0.00	0.00	4.09
1242	1308	2.617774	GACTACTTACTACCTCTGCCCG	59.382	54.545	0.00	0.00	0.00	6.13
1323	1398	0.747852	GAGTAGTAGAGGCTGGCCAC	59.252	60.000	14.39	7.67	38.92	5.01
1330	1493	2.761208	ACACCACATGAGTAGTAGAGGC	59.239	50.000	0.00	0.00	0.00	4.70
1448	1621	7.398024	ACCATGCATATTAGTAGAGGGAAATC	58.602	38.462	0.00	0.00	0.00	2.17
1474	1647	1.075482	CCCAAGGGAGCAGCAAGAA	59.925	57.895	0.00	0.00	37.50	2.52
1545	1718	8.954350	CAGTCAAGATTCAAGAGATAACCAAAT	58.046	33.333	0.00	0.00	0.00	2.32
1625	1853	6.350445	GCTAAAATTTGCCTCTCAAGAATGGA	60.350	38.462	0.00	0.00	35.84	3.41
1638	1866	6.572519	TGGATTAGTCATGCTAAAATTTGCC	58.427	36.000	11.80	8.35	42.35	4.52
1655	1883	9.537192	ACAAAAATATGTTCATGCATGGATTAG	57.463	29.630	25.97	7.73	0.00	1.73
1691	1924	1.292223	GGTTGGCTACGCTCAGTGA	59.708	57.895	0.00	0.00	0.00	3.41
1745	4339	5.670485	AGTGTTGAAGTGTAAGTGACATCA	58.330	37.500	0.00	0.00	41.14	3.07
1752	4346	7.985184	TGAACATAGAAGTGTTGAAGTGTAAGT	59.015	33.333	0.00	0.00	42.08	2.24
1765	4359	6.638610	ACTTGATCTCCTGAACATAGAAGTG	58.361	40.000	0.00	0.00	0.00	3.16
1841	4435	8.464770	TGTTTAGCTTGCAATTAATTAAGCAG	57.535	30.769	26.29	15.95	45.90	4.24
1961	4585	7.568267	TGATATCGCGAAAAGAAGATCATAC	57.432	36.000	15.24	0.00	0.00	2.39
2071	4695	7.106239	ACCAGATTGGCTAATATTTATCGGAG	58.894	38.462	0.00	0.00	42.67	4.63
2168	4792	8.961294	TGTTGATTTCAGAAACCAATGATTTT	57.039	26.923	5.94	0.00	0.00	1.82

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.