AutoCloner

Multiple sequence alignment - TraesCS5D01G194100

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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	TraesCS5D01G194100	chr5D	100.000	1605	0	0	958	2562	298123720	298125324	0.000000e+00	2964.0
1	TraesCS5D01G194100	chr5D	100.000	667	0	0	1	667	298122763	298123429	0.000000e+00	1232.0
2	TraesCS5D01G194100	chr5D	95.811	549	21	2	1	548	469726143	469726690	0.000000e+00	885.0
3	TraesCS5D01G194100	chr5B	97.580	1157	20	7	958	2107	339100991	339099836	0.000000e+00	1975.0
4	TraesCS5D01G194100	chr5B	98.022	455	9	0	2108	2562	339099756	339099302	0.000000e+00	791.0
5	TraesCS5D01G194100	chr5B	97.468	79	2	0	589	667	339102093	339102015	4.450000e-28	135.0
6	TraesCS5D01G194100	chr5B	77.707	157	20	9	1673	1819	672817402	672817251	5.880000e-12	82.4
7	TraesCS5D01G194100	chr7A	85.070	1286	118	42	958	2227	63398807	63397580	0.000000e+00	1243.0
8	TraesCS5D01G194100	chr7A	82.023	1552	193	62	958	2476	63427644	63426146	0.000000e+00	1242.0
9	TraesCS5D01G194100	chr7A	80.920	1043	109	52	1359	2375	63356057	63357035	0.000000e+00	741.0
10	TraesCS5D01G194100	chr7A	93.501	477	22	6	963	1430	63117662	63118138	0.000000e+00	701.0
11	TraesCS5D01G194100	chr7D	80.410	1511	183	69	1023	2488	58793630	58795072	0.000000e+00	1046.0
12	TraesCS5D01G194100	chr7D	90.483	704	45	12	958	1645	58863688	58862991	0.000000e+00	909.0
13	TraesCS5D01G194100	chr7D	92.723	481	22	8	963	1430	58768360	58768840	0.000000e+00	682.0
14	TraesCS5D01G194100	chr7D	75.829	422	60	18	2116	2521	105383503	105383898	2.620000e-40	176.0
15	TraesCS5D01G194100	chr7D	79.365	252	37	7	2108	2358	58821307	58821544	2.040000e-36	163.0
16	TraesCS5D01G194100	chr1D	96.998	533	16	0	1	533	228950531	228949999	0.000000e+00	896.0
17	TraesCS5D01G194100	chr1D	95.255	548	26	0	1	548	455647212	455646665	0.000000e+00	869.0
18	TraesCS5D01G194100	chr1D	95.387	542	23	1	1	542	244555934	244556473	0.000000e+00	861.0
19	TraesCS5D01G194100	chr2D	96.435	533	19	0	1	533	174243239	174242707	0.000000e+00	880.0
20	TraesCS5D01G194100	chr2D	95.685	533	23	0	1	533	67564736	67565268	0.000000e+00	857.0
21	TraesCS5D01G194100	chr6D	95.756	542	19	3	1	541	8029842	8030380	0.000000e+00	870.0
22	TraesCS5D01G194100	chr6D	95.896	536	18	3	1	533	363871465	363871999	0.000000e+00	865.0
23	TraesCS5D01G194100	chr1B	96.060	533	21	0	1	533	421459866	421460398	0.000000e+00	869.0
24	TraesCS5D01G194100	chr7B	91.865	504	34	4	976	1479	63934944	63935440	0.000000e+00	697.0
25	TraesCS5D01G194100	chr7B	73.259	359	57	21	1482	1819	63935468	63935808	7.550000e-16	95.3
26	TraesCS5D01G194100	chr7B	78.344	157	19	11	1673	1819	648275496	648275647	1.260000e-13	87.9
27	TraesCS5D01G194100	chr7B	77.070	157	21	8	1673	1819	126787908	126788059	2.730000e-10	76.8
28	TraesCS5D01G194100	chrUn	91.023	479	35	6	999	1474	84317810	84317337	7.730000e-180	640.0
29	TraesCS5D01G194100	chr4D	73.109	357	59	22	1482	1819	321816002	321816340	2.710000e-15	93.5

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	TraesCS5D01G194100	chr5D	298122763	298125324	2561	False	2098.00	2964	100.000	1	2562	2	chr5D.!!$F2	2561
1	TraesCS5D01G194100	chr5D	469726143	469726690	547	False	885.00	885	95.811	1	548	1	chr5D.!!$F1	547
2	TraesCS5D01G194100	chr5B	339099302	339102093	2791	True	967.00	1975	97.690	589	2562	3	chr5B.!!$R2	1973
3	TraesCS5D01G194100	chr7A	63397580	63398807	1227	True	1243.00	1243	85.070	958	2227	1	chr7A.!!$R1	1269
4	TraesCS5D01G194100	chr7A	63426146	63427644	1498	True	1242.00	1242	82.023	958	2476	1	chr7A.!!$R2	1518
5	TraesCS5D01G194100	chr7A	63356057	63357035	978	False	741.00	741	80.920	1359	2375	1	chr7A.!!$F2	1016
6	TraesCS5D01G194100	chr7D	58793630	58795072	1442	False	1046.00	1046	80.410	1023	2488	1	chr7D.!!$F2	1465
7	TraesCS5D01G194100	chr7D	58862991	58863688	697	True	909.00	909	90.483	958	1645	1	chr7D.!!$R1	687
8	TraesCS5D01G194100	chr1D	228949999	228950531	532	True	896.00	896	96.998	1	533	1	chr1D.!!$R1	532
9	TraesCS5D01G194100	chr1D	455646665	455647212	547	True	869.00	869	95.255	1	548	1	chr1D.!!$R2	547
10	TraesCS5D01G194100	chr1D	244555934	244556473	539	False	861.00	861	95.387	1	542	1	chr1D.!!$F1	541
11	TraesCS5D01G194100	chr2D	174242707	174243239	532	True	880.00	880	96.435	1	533	1	chr2D.!!$R1	532
12	TraesCS5D01G194100	chr2D	67564736	67565268	532	False	857.00	857	95.685	1	533	1	chr2D.!!$F1	532
13	TraesCS5D01G194100	chr6D	8029842	8030380	538	False	870.00	870	95.756	1	541	1	chr6D.!!$F1	540
14	TraesCS5D01G194100	chr6D	363871465	363871999	534	False	865.00	865	95.896	1	533	1	chr6D.!!$F2	532
15	TraesCS5D01G194100	chr1B	421459866	421460398	532	False	869.00	869	96.060	1	533	1	chr1B.!!$F1	532
16	TraesCS5D01G194100	chr7B	63934944	63935808	864	False	396.15	697	82.562	976	1819	2	chr7B.!!$F3	843

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
574	578	0.530744	TCATGCCTGACACGAGGTAC	59.469	55.0	0.0	0.0	35.29	3.34	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2247	3164	0.109597	GATGTTTGCAAGGTGAGGCG	60.11	55.0	0.0	0.0	0.0	5.52	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
227	228	2.968697	GCGTCGGACCGGTTTGTT	60.969	61.111	15.25	0.00	0.00	2.83
402	404	6.994496	CCTTCATCATTTGGATAGAAGTAGCA	59.006	38.462	0.00	0.00	38.31	3.49
409	411	7.992608	TCATTTGGATAGAAGTAGCAGCAAATA	59.007	33.333	0.00	0.00	0.00	1.40
533	537	5.130705	GGGGTCATCCTCCTTTTCTAAAT	57.869	43.478	0.00	0.00	35.33	1.40
534	538	5.519808	GGGGTCATCCTCCTTTTCTAAATT	58.480	41.667	0.00	0.00	35.33	1.82
560	564	1.007849	AAAAACGGGCGTGTCATGC	60.008	52.632	8.63	8.63	0.00	4.06
572	576	3.791640	TCATGCCTGACACGAGGT	58.208	55.556	0.00	0.00	35.29	3.85
573	577	2.970205	TCATGCCTGACACGAGGTA	58.030	52.632	0.00	0.00	35.29	3.08
574	578	0.530744	TCATGCCTGACACGAGGTAC	59.469	55.000	0.00	0.00	35.29	3.34
607	611	2.457598	GTACACTCCTCACCTCATCCA	58.542	52.381	0.00	0.00	0.00	3.41
625	629	3.273434	TCCAGCCAATGATTCTCGAAAG	58.727	45.455	0.00	0.00	0.00	2.62
1432	2170	1.740296	GAGCGCGCCTAGGTTTTCA	60.740	57.895	30.33	0.00	0.00	2.69
1556	2332	6.289745	TGAAATTGCAATGAAAAGTTCAGC	57.710	33.333	13.82	0.00	43.98	4.26
1669	2458	3.063452	CAGTGACGGGGTTGAATAATTCG	59.937	47.826	0.00	0.00	0.00	3.34
1691	2480	4.440758	CGCATGGATTTTATTACTTTGCCG	59.559	41.667	0.00	0.00	0.00	5.69
1773	2579	2.837947	ACAGGGATCTGATGAACTCCA	58.162	47.619	0.00	0.00	43.49	3.86
1952	2768	1.838913	TTGCAAACGAAAGCTGAAGC	58.161	45.000	0.00	0.00	42.49	3.86
1953	2769	0.030638	TGCAAACGAAAGCTGAAGCC	59.969	50.000	0.00	0.00	43.38	4.35
1967	2790	4.581824	AGCTGAAGCCAATGTGGTTATATG	59.418	41.667	0.00	0.00	40.46	1.78
1968	2791	4.794003	GCTGAAGCCAATGTGGTTATATGC	60.794	45.833	0.00	0.00	40.46	3.14
1969	2792	4.276642	TGAAGCCAATGTGGTTATATGCA	58.723	39.130	0.00	0.00	40.46	3.96
1970	2793	4.894705	TGAAGCCAATGTGGTTATATGCAT	59.105	37.500	3.79	3.79	40.46	3.96
1974	2798	4.552355	CCAATGTGGTTATATGCATGCTG	58.448	43.478	20.33	3.46	31.35	4.41
1975	2799	4.038282	CCAATGTGGTTATATGCATGCTGT	59.962	41.667	20.33	10.26	31.35	4.40
1976	2800	5.241285	CCAATGTGGTTATATGCATGCTGTA	59.759	40.000	20.33	12.22	31.35	2.74
2123	3040	4.627467	CGCAGTAGAGTACAATTCAAGCTT	59.373	41.667	0.00	0.00	0.00	3.74
2398	3332	1.604593	GCTGTGACCATTGCCAGGT	60.605	57.895	0.00	0.00	43.46	4.00
2407	3341	1.304381	ATTGCCAGGTGAATGCGGT	60.304	52.632	0.00	0.00	0.00	5.68
2423	3358	1.293924	CGGTATGAGCAGGAGCAAAG	58.706	55.000	0.00	0.00	45.49	2.77
2489	3424	7.232127	ACAAATGAGCTTTGCCTTATATGCTAT	59.768	33.333	0.00	0.00	46.81	2.97

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
227	228	1.687840	CACATACCGGGTCTGGGGA	60.688	63.158	15.92	0.00	0.00	4.81
555	559	0.530744	GTACCTCGTGTCAGGCATGA	59.469	55.000	0.00	0.00	40.54	3.07
556	560	0.802222	CGTACCTCGTGTCAGGCATG	60.802	60.000	0.00	0.00	36.98	4.06
557	561	1.511305	CGTACCTCGTGTCAGGCAT	59.489	57.895	0.00	0.00	36.98	4.40
558	562	2.632544	CCGTACCTCGTGTCAGGCA	61.633	63.158	0.00	0.00	36.98	4.75
559	563	2.181021	CCGTACCTCGTGTCAGGC	59.819	66.667	0.00	0.00	36.98	4.85
560	564	2.882876	CCCGTACCTCGTGTCAGG	59.117	66.667	0.00	0.00	39.80	3.86
561	565	2.181021	GCCCGTACCTCGTGTCAG	59.819	66.667	0.00	0.00	37.94	3.51
562	566	2.282674	AGCCCGTACCTCGTGTCA	60.283	61.111	0.00	0.00	37.94	3.58
563	567	2.181021	CAGCCCGTACCTCGTGTC	59.819	66.667	0.00	0.00	37.94	3.67
564	568	3.379445	CCAGCCCGTACCTCGTGT	61.379	66.667	0.00	0.00	37.94	4.49
565	569	4.814294	GCCAGCCCGTACCTCGTG	62.814	72.222	0.00	0.00	37.94	4.35
577	581	4.468689	GAGTGTACCCGGGCCAGC	62.469	72.222	24.08	9.20	0.00	4.85
578	582	3.782443	GGAGTGTACCCGGGCCAG	61.782	72.222	24.08	0.00	0.00	4.85
579	583	4.326227	AGGAGTGTACCCGGGCCA	62.326	66.667	24.08	15.79	0.00	5.36
580	584	3.468140	GAGGAGTGTACCCGGGCC	61.468	72.222	24.08	13.10	0.00	5.80
581	585	2.682494	TGAGGAGTGTACCCGGGC	60.682	66.667	24.08	5.60	0.00	6.13
582	586	2.356780	GGTGAGGAGTGTACCCGGG	61.357	68.421	22.25	22.25	0.00	5.73
583	587	1.305046	AGGTGAGGAGTGTACCCGG	60.305	63.158	0.00	0.00	35.03	5.73
584	588	0.611062	TGAGGTGAGGAGTGTACCCG	60.611	60.000	0.00	0.00	35.03	5.28
585	589	1.757699	GATGAGGTGAGGAGTGTACCC	59.242	57.143	0.00	0.00	35.03	3.69
586	590	1.757699	GGATGAGGTGAGGAGTGTACC	59.242	57.143	0.00	0.00	34.68	3.34
587	591	2.428890	CTGGATGAGGTGAGGAGTGTAC	59.571	54.545	0.00	0.00	0.00	2.90
607	611	4.478206	TCTCTTTCGAGAATCATTGGCT	57.522	40.909	0.00	0.00	43.10	4.75
1432	2170	0.741574	TATTGTCAACGGCGGCGAAT	60.742	50.000	38.93	26.38	0.00	3.34
1556	2332	6.769822	AGGACAAAATTAGCACCAGATGATAG	59.230	38.462	0.00	0.00	28.97	2.08
1669	2458	4.744631	CCGGCAAAGTAATAAAATCCATGC	59.255	41.667	0.00	0.00	0.00	4.06
1691	2480	7.382218	CACCAATCAAAAATAACAGAGAACACC	59.618	37.037	0.00	0.00	0.00	4.16
1952	2768	4.038282	ACAGCATGCATATAACCACATTGG	59.962	41.667	21.98	0.00	42.53	3.16
1953	2769	5.190992	ACAGCATGCATATAACCACATTG	57.809	39.130	21.98	6.82	42.53	2.82
1967	2790	6.260936	ACATTATAGACAGGTTTACAGCATGC	59.739	38.462	10.51	10.51	42.53	4.06
1968	2791	7.792374	ACATTATAGACAGGTTTACAGCATG	57.208	36.000	0.00	0.00	46.00	4.06
1969	2792	8.807948	AAACATTATAGACAGGTTTACAGCAT	57.192	30.769	0.00	0.00	30.55	3.79
1970	2793	9.727859	TTAAACATTATAGACAGGTTTACAGCA	57.272	29.630	0.00	0.00	34.67	4.41
2123	3040	2.444010	GGCCAAATACCCATACCACCTA	59.556	50.000	0.00	0.00	0.00	3.08
2247	3164	0.109597	GATGTTTGCAAGGTGAGGCG	60.110	55.000	0.00	0.00	0.00	5.52
2398	3332	0.829990	TCCTGCTCATACCGCATTCA	59.170	50.000	0.00	0.00	36.70	2.57
2407	3341	2.573462	AGGAACTTTGCTCCTGCTCATA	59.427	45.455	0.00	0.00	41.96	2.15

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.