AutoCloner

Multiple sequence alignment - TraesCS5A01G541500

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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	TraesCS5A01G541500	chr5A	100.000	2471	0	0	1	2471	698218024	698215554	0.000000e+00	4564.0
1	TraesCS5A01G541500	chr5A	80.081	738	121	17	1	729	698230805	698230085	2.180000e-145	525.0
2	TraesCS5A01G541500	chr5A	89.627	241	24	1	2232	2471	698228880	698228640	3.090000e-79	305.0
3	TraesCS5A01G541500	chr5A	72.681	1186	225	65	7	1143	698319061	698317926	1.110000e-78	303.0
4	TraesCS5A01G541500	chr5A	80.964	394	51	11	1217	1606	698229997	698229624	8.640000e-75	291.0
5	TraesCS5A01G541500	chr5A	73.882	559	139	5	40	597	698250936	698250384	1.490000e-52	217.0
6	TraesCS5A01G541500	chr5A	85.119	168	19	4	1990	2154	698229037	698228873	1.520000e-37	167.0
7	TraesCS5A01G541500	chr4D	89.323	1255	69	23	278	1499	509374343	509373121	0.000000e+00	1515.0
8	TraesCS5A01G541500	chr4D	93.503	862	36	9	1626	2470	509372893	509372035	0.000000e+00	1264.0
9	TraesCS5A01G541500	chr4D	82.041	735	112	10	938	1669	509383875	509383158	2.100000e-170	608.0
10	TraesCS5A01G541500	chr4D	90.625	192	18	0	1	192	509374528	509374337	3.150000e-64	255.0
11	TraesCS5A01G541500	chr4D	83.390	295	24	11	1937	2228	509382917	509382645	1.470000e-62	250.0
12	TraesCS5A01G541500	chr4D	96.396	111	4	0	1537	1647	509373123	509373013	1.510000e-42	183.0
13	TraesCS5A01G541500	chr4B	79.521	1670	253	44	1	1647	657459112	657460715	0.000000e+00	1107.0
14	TraesCS5A01G541500	chr4B	90.041	241	23	1	2232	2471	657466779	657467019	6.640000e-81	311.0
15	TraesCS5A01G541500	chr7D	79.260	1514	254	38	6	1488	31369521	31368037	0.000000e+00	1002.0
16	TraesCS5A01G541500	chr7D	83.673	98	14	2	1940	2036	31365686	31365590	9.410000e-15	91.6
17	TraesCS5A01G541500	chr4A	75.309	729	145	24	1	710	697334274	697333562	1.430000e-82	316.0
18	TraesCS5A01G541500	chr5B	75.738	610	128	15	1	601	43895430	43894832	3.110000e-74	289.0
19	TraesCS5A01G541500	chr5B	75.478	628	127	19	840	1458	43894663	43894054	5.200000e-72	281.0
20	TraesCS5A01G541500	chr5B	83.962	212	27	5	1	207	43900067	43899858	1.940000e-46	196.0

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	TraesCS5A01G541500	chr5A	698215554	698218024	2470	True	4564.00	4564	100.00000	1	2471	1	chr5A.!!$R1	2470
1	TraesCS5A01G541500	chr5A	698228640	698230805	2165	True	322.00	525	83.94775	1	2471	4	chr5A.!!$R4	2470
2	TraesCS5A01G541500	chr5A	698317926	698319061	1135	True	303.00	303	72.68100	7	1143	1	chr5A.!!$R3	1136
3	TraesCS5A01G541500	chr5A	698250384	698250936	552	True	217.00	217	73.88200	40	597	1	chr5A.!!$R2	557
4	TraesCS5A01G541500	chr4D	509372035	509374528	2493	True	804.25	1515	92.46175	1	2470	4	chr4D.!!$R1	2469
5	TraesCS5A01G541500	chr4D	509382645	509383875	1230	True	429.00	608	82.71550	938	2228	2	chr4D.!!$R2	1290
6	TraesCS5A01G541500	chr4B	657459112	657460715	1603	False	1107.00	1107	79.52100	1	1647	1	chr4B.!!$F1	1646
7	TraesCS5A01G541500	chr7D	31365590	31369521	3931	True	546.80	1002	81.46650	6	2036	2	chr7D.!!$R1	2030
8	TraesCS5A01G541500	chr4A	697333562	697334274	712	True	316.00	316	75.30900	1	710	1	chr4A.!!$R1	709
9	TraesCS5A01G541500	chr5B	43894054	43895430	1376	True	285.00	289	75.60800	1	1458	2	chr5B.!!$R2	1457

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
93	94	0.252421	TGACCTGCTCCCACTCTCAT	60.252	55.0	0.0	0.0	0.0	2.90	F
290	312	0.830444	TCCTGACCAGCCTGTACGTT	60.830	55.0	0.0	0.0	0.0	3.99	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1158	1296	0.458543	CGTCATTGTCGGAGTCCCAG	60.459	60.000	2.8	0.0	0.0	4.45	R
1782	4169	2.095969	TCGTGTTTGGTCGATGCAAATC	60.096	45.455	0.0	0.0	0.0	2.17	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
92	93	0.902048	CTGACCTGCTCCCACTCTCA	60.902	60.000	0.00	0.00	0.00	3.27
93	94	0.252421	TGACCTGCTCCCACTCTCAT	60.252	55.000	0.00	0.00	0.00	2.90
102	106	2.185350	CACTCTCATTCGCCGGCT	59.815	61.111	26.68	1.82	0.00	5.52
122	126	3.615110	GCTTCTTCATCCAGTTCGACTCA	60.615	47.826	0.00	0.00	0.00	3.41
164	177	2.066393	CCGCCCCTCTTCCTCATCA	61.066	63.158	0.00	0.00	0.00	3.07
214	230	2.491455	CCCCCATGTATCCCTTTGATGG	60.491	54.545	0.00	0.00	34.76	3.51
227	249	3.925090	GATGGGGTAGGCGACGGG	61.925	72.222	0.00	0.00	0.00	5.28
245	267	3.181472	ACGGGTTTGACGAAGACTACTTT	60.181	43.478	0.00	0.00	36.39	2.66
273	295	1.751927	CACTGCAATGGCCTCCTCC	60.752	63.158	3.32	0.00	40.13	4.30
283	305	2.040278	CCTCCTCCTGACCAGCCT	59.960	66.667	0.00	0.00	0.00	4.58
290	312	0.830444	TCCTGACCAGCCTGTACGTT	60.830	55.000	0.00	0.00	0.00	3.99
354	380	4.256180	GCCCGGCCGATCCAGAAT	62.256	66.667	30.73	0.00	34.01	2.40
406	438	0.896479	TCTTCGATCCCACCGTGTCA	60.896	55.000	0.00	0.00	0.00	3.58
434	466	1.133513	ACCAAGTGTTCAGCATTCCCA	60.134	47.619	0.00	0.00	0.00	4.37
459	491	2.884663	CGCGAGCAGAGTACCTATAG	57.115	55.000	0.00	0.00	0.00	1.31
462	494	2.552591	GCGAGCAGAGTACCTATAGGGA	60.553	54.545	22.91	12.31	40.27	4.20
471	506	0.957305	ACCTATAGGGACATGGGGGT	59.043	55.000	22.91	0.00	40.27	4.95
473	508	1.152271	CCTATAGGGACATGGGGGTCT	59.848	57.143	11.33	0.00	37.91	3.85
476	511	2.484868	TAGGGACATGGGGGTCTGCA	62.485	60.000	0.00	0.00	37.91	4.41
495	536	3.131396	GCAGTACCATCCAATTAGACCG	58.869	50.000	0.00	0.00	0.00	4.79
555	596	3.729108	TCCTGGATGTCTTCTCCTCAAT	58.271	45.455	0.00	0.00	33.69	2.57
872	976	1.659098	CTTTCCGATGACAAGTACCGC	59.341	52.381	0.00	0.00	0.00	5.68
925	1063	6.101734	ACCATGGCTTATCTAGGAAGATCAAA	59.898	38.462	13.04	0.00	41.71	2.69
1404	1555	7.012421	GGCTTCAGATCTACCGAACAAAATTAT	59.988	37.037	0.00	0.00	0.00	1.28
1473	1624	9.134734	AGCAACAACAAATGTAATTTATAACGG	57.865	29.630	0.00	0.00	46.64	4.44
1488	3505	0.396435	AACGGCAGTCATCTGGAACA	59.604	50.000	0.00	0.00	41.57	3.18
1535	3552	9.745323	GTTTTGATTATTTATTTTCTGCAGTGC	57.255	29.630	14.67	8.58	0.00	4.40
1719	4001	9.478768	AAAACTAGCTAGAAACTCTTAACTGAC	57.521	33.333	27.45	0.00	0.00	3.51
1781	4168	2.862536	CGCGAGAAACATCACATCATCT	59.137	45.455	0.00	0.00	0.00	2.90
1782	4169	3.302286	CGCGAGAAACATCACATCATCTG	60.302	47.826	0.00	0.00	0.00	2.90
2085	4522	4.628333	AGGAAATGAAAAATGAATGCTGCG	59.372	37.500	0.00	0.00	0.00	5.18
2104	4541	5.333798	GCTGCGTTATAGAGAAACAACAACA	60.334	40.000	0.00	0.00	0.00	3.33
2279	4716	2.742428	ACATCCATGGTCCCTGATTG	57.258	50.000	12.58	1.10	0.00	2.67
2282	4719	3.245730	ACATCCATGGTCCCTGATTGTTT	60.246	43.478	12.58	0.00	0.00	2.83
2299	4736	2.166664	TGTTTTTGTGGCCAGGTTACAC	59.833	45.455	5.11	0.00	35.75	2.90
2320	4757	4.103153	CACCAGGAACATCCCTACATACAT	59.897	45.833	0.00	0.00	37.19	2.29
2328	4765	4.846367	ACATCCCTACATACATGGCTACAT	59.154	41.667	0.00	0.00	37.99	2.29
2345	4782	2.461695	ACATGTAGCTAGGCTGAGTGT	58.538	47.619	0.00	1.85	40.10	3.55
2347	4784	4.023980	ACATGTAGCTAGGCTGAGTGTTA	58.976	43.478	0.00	0.00	40.10	2.41
2351	4788	5.235516	TGTAGCTAGGCTGAGTGTTAAAAC	58.764	41.667	0.00	0.00	40.10	2.43
2352	4789	4.351874	AGCTAGGCTGAGTGTTAAAACA	57.648	40.909	0.00	0.00	37.57	2.83

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
74	75	0.252421	ATGAGAGTGGGAGCAGGTCA	60.252	55.000	1.20	0.00	0.00	4.02
92	93	0.815615	GGATGAAGAAGCCGGCGAAT	60.816	55.000	23.20	11.97	0.00	3.34
93	94	1.449601	GGATGAAGAAGCCGGCGAA	60.450	57.895	23.20	4.39	0.00	4.70
102	106	3.320826	TGTGAGTCGAACTGGATGAAGAA	59.679	43.478	0.00	0.00	0.00	2.52
164	177	0.905357	AGTCGAGCTTGGTATTGGCT	59.095	50.000	0.00	0.00	39.16	4.75
214	230	2.435410	CAAACCCGTCGCCTACCC	60.435	66.667	0.00	0.00	0.00	3.69
227	249	5.230726	TCGAACAAAGTAGTCTTCGTCAAAC	59.769	40.000	0.00	0.00	32.90	2.93
245	267	1.511850	CATTGCAGTGGTCTCGAACA	58.488	50.000	0.32	0.00	0.00	3.18
273	295	0.033504	ACAACGTACAGGCTGGTCAG	59.966	55.000	20.34	9.51	0.00	3.51
283	305	0.533308	GGCAGGGTTGACAACGTACA	60.533	55.000	12.07	0.00	30.39	2.90
351	377	5.467035	TTGAACCAAAAGGTCATCCATTC	57.533	39.130	0.00	0.00	35.89	2.67
354	380	7.147915	GCTTATATTGAACCAAAAGGTCATCCA	60.148	37.037	0.00	0.00	35.89	3.41
377	409	4.503991	GGTGGGATCGAAGATTAGATGCTT	60.504	45.833	7.02	0.00	45.12	3.91
378	410	3.007398	GGTGGGATCGAAGATTAGATGCT	59.993	47.826	7.02	0.00	45.12	3.79
379	411	3.330267	GGTGGGATCGAAGATTAGATGC	58.670	50.000	0.00	0.00	45.12	3.91
380	412	3.005897	ACGGTGGGATCGAAGATTAGATG	59.994	47.826	0.00	0.00	45.12	2.90
386	418	0.460311	GACACGGTGGGATCGAAGAT	59.540	55.000	13.48	0.00	45.12	2.40
387	419	0.896479	TGACACGGTGGGATCGAAGA	60.896	55.000	13.48	0.00	45.75	2.87
446	478	4.090090	CCCATGTCCCTATAGGTACTCTG	58.910	52.174	17.72	12.75	41.75	3.35
457	489	1.692749	GCAGACCCCCATGTCCCTA	60.693	63.158	0.00	0.00	35.83	3.53
459	491	3.338250	TGCAGACCCCCATGTCCC	61.338	66.667	0.00	0.00	35.83	4.46
462	494	1.562672	GGTACTGCAGACCCCCATGT	61.563	60.000	23.35	0.00	0.00	3.21
469	504	2.717639	ATTGGATGGTACTGCAGACC	57.282	50.000	23.35	22.23	37.49	3.85
471	506	4.141711	GGTCTAATTGGATGGTACTGCAGA	60.142	45.833	23.35	0.48	0.00	4.26
473	508	3.431626	CGGTCTAATTGGATGGTACTGCA	60.432	47.826	0.00	0.00	0.00	4.41
476	511	3.039011	AGCGGTCTAATTGGATGGTACT	58.961	45.455	0.00	0.00	0.00	2.73
495	536	3.561725	CCATTCGGATTTCTCCACTAAGC	59.438	47.826	0.00	0.00	42.19	3.09
555	596	3.147595	CCTCCCAGCGATCCGACA	61.148	66.667	0.00	0.00	0.00	4.35
872	976	3.989167	TGTCGGTTGGTAGTTTAATCACG	59.011	43.478	0.00	0.00	0.00	4.35
1158	1296	0.458543	CGTCATTGTCGGAGTCCCAG	60.459	60.000	2.80	0.00	0.00	4.45
1181	1319	2.604914	GCCATGTCTACGATGTTGTCTG	59.395	50.000	0.00	0.00	0.00	3.51
1404	1555	3.597255	TGGCGTGTACGGAAAATATTCA	58.403	40.909	6.55	0.00	40.23	2.57
1473	1624	2.227388	CAGGTTTGTTCCAGATGACTGC	59.773	50.000	0.00	0.00	42.25	4.40
1719	4001	6.403049	TGTGTATCCATTAGTTAGTGGTGTG	58.597	40.000	1.29	0.00	34.93	3.82
1781	4168	2.350293	CGTGTTTGGTCGATGCAAATCA	60.350	45.455	0.00	0.00	0.00	2.57
1782	4169	2.095969	TCGTGTTTGGTCGATGCAAATC	60.096	45.455	0.00	0.00	0.00	2.17
1901	4292	2.687935	ACCAGACCATTGTGTTTGTGAC	59.312	45.455	0.00	0.00	0.00	3.67
2085	4522	6.080406	GCAGCTGTTGTTGTTTCTCTATAAC	58.920	40.000	16.64	0.00	0.00	1.89
2104	4541	3.954258	ACCTTTAACTTCAGTTTGCAGCT	59.046	39.130	0.00	0.00	39.31	4.24
2279	4716	2.816689	GTGTAACCTGGCCACAAAAAC	58.183	47.619	0.00	0.00	0.00	2.43
2299	4736	4.505566	CCATGTATGTAGGGATGTTCCTGG	60.506	50.000	0.00	0.00	37.75	4.45
2328	4765	5.221561	TGTTTTAACACTCAGCCTAGCTACA	60.222	40.000	0.00	0.00	33.13	2.74
2345	4782	9.793259	ACTCAGATTAATCCTTGTCTGTTTTAA	57.207	29.630	11.92	0.00	39.22	1.52
2347	4784	8.160106	AGACTCAGATTAATCCTTGTCTGTTTT	58.840	33.333	22.74	8.48	39.22	2.43
2351	4788	6.047870	CCAGACTCAGATTAATCCTTGTCTG	58.952	44.000	30.58	30.58	41.63	3.51
2352	4789	5.396213	GCCAGACTCAGATTAATCCTTGTCT	60.396	44.000	20.02	20.02	33.41	3.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.