AutoCloner

Multiple sequence alignment - TraesCS5B01G535000

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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	TraesCS5B01G535000	chr5B	100.000	2959	0	0	1	2959	691128477	691131435	0.000000e+00	5465.0
1	TraesCS5B01G535000	chr5B	98.516	2157	23	2	812	2959	691484962	691487118	0.000000e+00	3797.0
2	TraesCS5B01G535000	chr5B	83.780	1566	218	27	905	2449	690972618	690974168	0.000000e+00	1452.0
3	TraesCS5B01G535000	chr5B	79.021	1940	272	67	545	2448	691570076	691571916	0.000000e+00	1203.0
4	TraesCS5B01G535000	chr5B	80.927	928	123	34	1550	2448	691265296	691266198	0.000000e+00	684.0
5	TraesCS5B01G535000	chr5D	86.577	2369	230	42	1	2336	547500805	547503118	0.000000e+00	2532.0
6	TraesCS5B01G535000	chr5D	80.167	1553	215	42	827	2337	547437591	547439092	0.000000e+00	1075.0
7	TraesCS5B01G535000	chr4A	82.908	1527	198	32	930	2429	618158506	618159996	0.000000e+00	1315.0
8	TraesCS5B01G535000	chr4A	82.114	1599	227	30	882	2450	618101941	618103510	0.000000e+00	1314.0
9	TraesCS5B01G535000	chr4A	82.112	1487	195	40	885	2338	621465921	621464473	0.000000e+00	1206.0
10	TraesCS5B01G535000	chr4A	89.855	69	2	2	2694	2757	659496276	659496344	1.890000e-12	84.2
11	TraesCS5B01G535000	chr4A	88.406	69	3	2	2694	2757	660083297	660083365	8.790000e-11	78.7
12	TraesCS5B01G535000	chrUn	82.112	1487	194	41	885	2338	296641804	296640357	0.000000e+00	1206.0
13	TraesCS5B01G535000	chrUn	82.857	1365	167	36	885	2219	319797645	319798972	0.000000e+00	1162.0
14	TraesCS5B01G535000	chrUn	100.000	390	0	0	1353	1742	479948203	479947814	0.000000e+00	721.0
15	TraesCS5B01G535000	chrUn	88.406	69	3	2	2694	2757	335934555	335934623	8.790000e-11	78.7
16	TraesCS5B01G535000	chr6B	71.734	796	161	48	1217	1976	59739185	59739952	6.560000e-37	165.0
17	TraesCS5B01G535000	chr2B	85.185	81	11	1	2693	2772	615784863	615784943	6.800000e-12	82.4
18	TraesCS5B01G535000	chr7A	88.406	69	4	3	2691	2759	711827743	711827679	2.440000e-11	80.5
19	TraesCS5B01G535000	chr3D	82.927	82	10	2	2694	2775	401679150	401679073	1.470000e-08	71.3
20	TraesCS5B01G535000	chr3A	82.927	82	10	2	2694	2775	522063611	522063534	1.470000e-08	71.3
21	TraesCS5B01G535000	chr7D	81.319	91	11	6	2692	2776	341477080	341477170	5.290000e-08	69.4

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	TraesCS5B01G535000	chr5B	691128477	691131435	2958	False	5465	5465	100.000	1	2959	1	chr5B.!!$F2	2958
1	TraesCS5B01G535000	chr5B	691484962	691487118	2156	False	3797	3797	98.516	812	2959	1	chr5B.!!$F4	2147
2	TraesCS5B01G535000	chr5B	690972618	690974168	1550	False	1452	1452	83.780	905	2449	1	chr5B.!!$F1	1544
3	TraesCS5B01G535000	chr5B	691570076	691571916	1840	False	1203	1203	79.021	545	2448	1	chr5B.!!$F5	1903
4	TraesCS5B01G535000	chr5B	691265296	691266198	902	False	684	684	80.927	1550	2448	1	chr5B.!!$F3	898
5	TraesCS5B01G535000	chr5D	547500805	547503118	2313	False	2532	2532	86.577	1	2336	1	chr5D.!!$F2	2335
6	TraesCS5B01G535000	chr5D	547437591	547439092	1501	False	1075	1075	80.167	827	2337	1	chr5D.!!$F1	1510
7	TraesCS5B01G535000	chr4A	618158506	618159996	1490	False	1315	1315	82.908	930	2429	1	chr4A.!!$F2	1499
8	TraesCS5B01G535000	chr4A	618101941	618103510	1569	False	1314	1314	82.114	882	2450	1	chr4A.!!$F1	1568
9	TraesCS5B01G535000	chr4A	621464473	621465921	1448	True	1206	1206	82.112	885	2338	1	chr4A.!!$R1	1453
10	TraesCS5B01G535000	chrUn	296640357	296641804	1447	True	1206	1206	82.112	885	2338	1	chrUn.!!$R1	1453
11	TraesCS5B01G535000	chrUn	319797645	319798972	1327	False	1162	1162	82.857	885	2219	1	chrUn.!!$F1	1334

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
130	131	0.611062	AGACAATCCGACTCCCGACA	60.611	55.000	0.0	0.0	41.76	4.35	F
436	438	1.339438	TGCTCACCTCTTCTCCATTGC	60.339	52.381	0.0	0.0	0.00	3.56	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1262	1304	3.412386	GTCAAGCCCTGTGTGATTAAGT	58.588	45.455	0.0	0.0	0.0	2.24	R
2614	2747	6.435277	AGGAAAATGTTGTGCTGAGATATTGT	59.565	34.615	0.0	0.0	0.0	2.71	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
73	74	3.759618	GTCACCACTACTGACTCTAGCTT	59.240	47.826	0.00	0.00	35.99	3.74
74	75	4.942483	GTCACCACTACTGACTCTAGCTTA	59.058	45.833	0.00	0.00	35.99	3.09
75	76	5.065474	GTCACCACTACTGACTCTAGCTTAG	59.935	48.000	0.00	0.00	35.99	2.18
76	77	3.949113	ACCACTACTGACTCTAGCTTAGC	59.051	47.826	0.00	0.00	0.00	3.09
77	78	4.204012	CCACTACTGACTCTAGCTTAGCT	58.796	47.826	12.67	12.67	43.41	3.32
91	92	6.948309	TCTAGCTTAGCTATATCATCCACACA	59.052	38.462	14.78	0.00	40.54	3.72
95	96	6.756074	GCTTAGCTATATCATCCACACATCTC	59.244	42.308	0.00	0.00	0.00	2.75
102	103	3.434309	TCATCCACACATCTCAGAGACA	58.566	45.455	0.91	0.00	0.00	3.41
130	131	0.611062	AGACAATCCGACTCCCGACA	60.611	55.000	0.00	0.00	41.76	4.35
211	212	3.252215	CAGTTTCGTGTGCCTCCATTTTA	59.748	43.478	0.00	0.00	0.00	1.52
212	213	4.079253	AGTTTCGTGTGCCTCCATTTTAT	58.921	39.130	0.00	0.00	0.00	1.40
213	214	5.123186	CAGTTTCGTGTGCCTCCATTTTATA	59.877	40.000	0.00	0.00	0.00	0.98
214	215	5.885912	AGTTTCGTGTGCCTCCATTTTATAT	59.114	36.000	0.00	0.00	0.00	0.86
215	216	6.377146	AGTTTCGTGTGCCTCCATTTTATATT	59.623	34.615	0.00	0.00	0.00	1.28
216	217	6.767524	TTCGTGTGCCTCCATTTTATATTT	57.232	33.333	0.00	0.00	0.00	1.40
217	218	6.767524	TCGTGTGCCTCCATTTTATATTTT	57.232	33.333	0.00	0.00	0.00	1.82
246	247	3.542712	TTGACAAGGACGTACGTACTC	57.457	47.619	32.21	20.64	38.57	2.59
251	252	3.373439	ACAAGGACGTACGTACTCATCTC	59.627	47.826	32.21	12.00	38.57	2.75
286	287	1.753368	CTCTCGGCCTCCCATTCTCC	61.753	65.000	0.00	0.00	0.00	3.71
318	319	8.798859	TTATCTTTAAGCTTGCATTTCTCTCT	57.201	30.769	9.86	0.00	0.00	3.10
332	333	5.862924	TTTCTCTCTTGTAAGAAATGGCG	57.137	39.130	0.00	0.00	36.76	5.69
335	336	3.596214	TCTCTTGTAAGAAATGGCGACC	58.404	45.455	0.00	0.00	34.03	4.79
340	341	4.920640	TGTAAGAAATGGCGACCAAAAA	57.079	36.364	2.68	0.00	36.95	1.94
402	403	9.443283	CATATAATTTCTCTTCTTTTCTTGCCG	57.557	33.333	0.00	0.00	0.00	5.69
405	406	7.454260	AATTTCTCTTCTTTTCTTGCCGTAT	57.546	32.000	0.00	0.00	0.00	3.06
436	438	1.339438	TGCTCACCTCTTCTCCATTGC	60.339	52.381	0.00	0.00	0.00	3.56
453	455	6.597562	TCCATTGCTACTAACCGGAAATATT	58.402	36.000	9.46	0.00	0.00	1.28
458	460	4.023450	GCTACTAACCGGAAATATTTGCCC	60.023	45.833	9.46	5.16	0.00	5.36
478	480	3.093172	GGAAGGGCCCTCTCCAGG	61.093	72.222	32.14	0.00	39.98	4.45
528	530	7.888021	TGTTCCTCTATCCTTTTGCTTGATTTA	59.112	33.333	0.00	0.00	0.00	1.40
561	563	2.094675	TGCTAGCTGCTTCCATTTTCC	58.905	47.619	17.23	0.00	43.37	3.13
653	656	9.921637	CTTTTGAAGGTTATTACTTTGCCAATA	57.078	29.630	0.00	0.00	0.00	1.90
689	692	9.920946	TGGATTTTACATCCTCTTAATTAGCTT	57.079	29.630	0.00	0.00	38.95	3.74
720	728	4.681744	TCTTGCCACAAACAAATGAAGAC	58.318	39.130	0.00	0.00	0.00	3.01
721	729	3.077229	TGCCACAAACAAATGAAGACG	57.923	42.857	0.00	0.00	0.00	4.18
722	730	2.425312	TGCCACAAACAAATGAAGACGT	59.575	40.909	0.00	0.00	0.00	4.34
723	731	3.119316	TGCCACAAACAAATGAAGACGTT	60.119	39.130	0.00	0.00	0.00	3.99
725	733	4.328712	GCCACAAACAAATGAAGACGTTTT	59.671	37.500	0.00	0.00	33.60	2.43
726	734	5.517054	GCCACAAACAAATGAAGACGTTTTA	59.483	36.000	0.00	0.00	33.60	1.52
731	739	8.964150	ACAAACAAATGAAGACGTTTTATTAGC	58.036	29.630	0.00	0.00	33.60	3.09
732	740	9.180678	CAAACAAATGAAGACGTTTTATTAGCT	57.819	29.630	0.00	0.00	33.60	3.32
779	787	7.225538	CACCTCATCAAAGTAGGTCAATATGAC	59.774	40.741	1.88	1.88	46.23	3.06
823	832	2.099405	ACCTAGCTTCTGAGTCAGAGC	58.901	52.381	25.05	25.05	41.75	4.09
926	948	3.764885	ACAACATTTCCGCTTATCTGC	57.235	42.857	0.00	0.00	0.00	4.26
1216	1258	7.362660	CCCATGTGCCATATGATGAAGAAATAG	60.363	40.741	3.65	0.00	0.00	1.73
1262	1304	3.562176	GGGAAGAGATTGCCCTGAAGAAA	60.562	47.826	0.00	0.00	38.85	2.52
2562	2695	6.155827	CGAAAGAGAGGGAGCAATTAGATAG	58.844	44.000	0.00	0.00	0.00	2.08
2573	2706	7.449086	GGGAGCAATTAGATAGTACTCTGTAGT	59.551	40.741	0.00	0.00	39.91	2.73
2614	2747	1.700739	ACCCCGTTGTTGGATCTACAA	59.299	47.619	9.05	9.05	33.37	2.41
2641	2774	5.886960	ATCTCAGCACAACATTTTCCTAC	57.113	39.130	0.00	0.00	0.00	3.18
2648	2781	7.392953	TCAGCACAACATTTTCCTACATGAATA	59.607	33.333	0.00	0.00	0.00	1.75
2833	2974	7.116233	CAGTTTGCCACCTAAATATTTTGTGAC	59.884	37.037	22.41	15.83	0.00	3.67

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
7	8	0.104120	ACGCAAGCATATACGAGGCA	59.896	50.000	0.00	0.00	45.62	4.75
9	10	2.423926	AGACGCAAGCATATACGAGG	57.576	50.000	0.00	0.00	45.62	4.63
55	56	4.204012	AGCTAAGCTAGAGTCAGTAGTGG	58.796	47.826	0.00	0.00	36.99	4.00
61	62	7.555914	TGGATGATATAGCTAAGCTAGAGTCAG	59.444	40.741	0.00	0.00	44.66	3.51
73	74	7.177878	TCTGAGATGTGTGGATGATATAGCTA	58.822	38.462	0.00	0.00	0.00	3.32
74	75	6.015282	TCTGAGATGTGTGGATGATATAGCT	58.985	40.000	0.00	0.00	0.00	3.32
75	76	6.152492	TCTCTGAGATGTGTGGATGATATAGC	59.848	42.308	2.58	0.00	0.00	2.97
76	77	7.176340	TGTCTCTGAGATGTGTGGATGATATAG	59.824	40.741	11.07	0.00	0.00	1.31
77	78	7.006509	TGTCTCTGAGATGTGTGGATGATATA	58.993	38.462	11.07	0.00	0.00	0.86
91	92	8.759481	TTGTCTATCTACAATGTCTCTGAGAT	57.241	34.615	11.07	0.00	34.50	2.75
130	131	3.709653	TCTTGGACTAGGACCGCAATAAT	59.290	43.478	0.00	0.00	0.00	1.28
211	212	9.801873	CGTCCTTGTCAAATAATTGGAAAATAT	57.198	29.630	0.00	0.00	37.15	1.28
212	213	8.798402	ACGTCCTTGTCAAATAATTGGAAAATA	58.202	29.630	0.00	0.00	37.15	1.40
213	214	7.666623	ACGTCCTTGTCAAATAATTGGAAAAT	58.333	30.769	0.00	0.00	37.15	1.82
214	215	7.045126	ACGTCCTTGTCAAATAATTGGAAAA	57.955	32.000	0.00	0.00	37.15	2.29
215	216	6.642707	ACGTCCTTGTCAAATAATTGGAAA	57.357	33.333	0.00	0.00	37.15	3.13
216	217	6.128499	CGTACGTCCTTGTCAAATAATTGGAA	60.128	38.462	7.22	0.00	37.15	3.53
217	218	5.349270	CGTACGTCCTTGTCAAATAATTGGA	59.651	40.000	7.22	0.00	37.15	3.53
224	225	4.022935	TGAGTACGTACGTCCTTGTCAAAT	60.023	41.667	26.53	3.32	0.00	2.32
229	230	3.341823	AGATGAGTACGTACGTCCTTGT	58.658	45.455	26.53	11.31	0.00	3.16
267	268	1.745264	GAGAATGGGAGGCCGAGAG	59.255	63.158	0.00	0.00	0.00	3.20
268	269	1.762460	GGAGAATGGGAGGCCGAGA	60.762	63.158	0.00	0.00	0.00	4.04
286	287	9.852091	AAATGCAAGCTTAAAGATAAAGAAGAG	57.148	29.630	0.00	0.00	0.00	2.85
318	319	4.920640	TTTTGGTCGCCATTTCTTACAA	57.079	36.364	0.00	0.00	31.53	2.41
353	354	5.699001	TGGTGATATTTCCGGTTAATGATCG	59.301	40.000	0.00	0.00	0.00	3.69
398	399	1.406887	GCAAGAGAAGGGAATACGGCA	60.407	52.381	0.00	0.00	0.00	5.69
402	403	3.198853	AGGTGAGCAAGAGAAGGGAATAC	59.801	47.826	0.00	0.00	0.00	1.89
405	406	1.625818	GAGGTGAGCAAGAGAAGGGAA	59.374	52.381	0.00	0.00	0.00	3.97
436	438	5.374071	AGGGCAAATATTTCCGGTTAGTAG	58.626	41.667	0.00	0.00	0.00	2.57
458	460	1.919600	CTGGAGAGGGCCCTTCCAAG	61.920	65.000	35.57	28.64	36.21	3.61
478	480	6.371825	CAGAGAAACCATTACCCTTGACTAAC	59.628	42.308	0.00	0.00	0.00	2.34
528	530	2.164624	CAGCTAGCAGGTTCTTAGACGT	59.835	50.000	18.83	0.00	0.00	4.34
561	563	9.463443	AAAATCAAACTATCGAAGAAAACCAAG	57.537	29.630	0.00	0.00	43.58	3.61
689	692	0.822811	TTGTGGCAAGAGCAGCAAAA	59.177	45.000	0.00	0.00	44.61	2.44
690	693	0.822811	TTTGTGGCAAGAGCAGCAAA	59.177	45.000	0.00	0.00	44.61	3.68
720	728	8.298140	ACTAGCACCTAGATAGCTAATAAAACG	58.702	37.037	0.00	0.00	39.86	3.60
721	729	9.413048	CACTAGCACCTAGATAGCTAATAAAAC	57.587	37.037	0.00	0.00	39.86	2.43
722	730	8.088981	GCACTAGCACCTAGATAGCTAATAAAA	58.911	37.037	0.00	0.00	39.86	1.52
723	731	7.451877	AGCACTAGCACCTAGATAGCTAATAAA	59.548	37.037	0.00	0.00	45.49	1.40
725	733	6.486056	AGCACTAGCACCTAGATAGCTAATA	58.514	40.000	0.00	0.00	45.49	0.98
726	734	5.329399	AGCACTAGCACCTAGATAGCTAAT	58.671	41.667	0.00	0.00	45.49	1.73
731	739	4.460731	TGCATAGCACTAGCACCTAGATAG	59.539	45.833	6.29	0.00	45.49	2.08
732	740	4.407365	TGCATAGCACTAGCACCTAGATA	58.593	43.478	6.29	0.00	45.49	1.98
734	742	2.666317	TGCATAGCACTAGCACCTAGA	58.334	47.619	6.29	0.00	45.49	2.43
764	772	9.125026	GGATTGAAAATGTCATATTGACCTACT	57.875	33.333	5.27	0.00	46.40	2.57
779	787	9.520204	GGTATTGTTATGTCAGGATTGAAAATG	57.480	33.333	0.00	0.00	34.49	2.32
823	832	2.767505	ACCTTGTTCTTCTTACAGGCG	58.232	47.619	0.00	0.00	0.00	5.52
911	929	2.627945	TCGTTGCAGATAAGCGGAAAT	58.372	42.857	0.00	0.00	37.31	2.17
1216	1258	5.357032	CCATTGTCCAATACTCCCTGTTAAC	59.643	44.000	0.00	0.00	0.00	2.01
1262	1304	3.412386	GTCAAGCCCTGTGTGATTAAGT	58.588	45.455	0.00	0.00	0.00	2.24
2614	2747	6.435277	AGGAAAATGTTGTGCTGAGATATTGT	59.565	34.615	0.00	0.00	0.00	2.71
2648	2781	7.094205	GCTGTCCGGGATAAATATTCATGATTT	60.094	37.037	0.00	0.00	0.00	2.17
2833	2974	0.389817	TGCACCTGTTAGCGCACTAG	60.390	55.000	11.47	1.72	0.00	2.57
2924	3065	7.337436	ACTTTGTAAGTTTGTAGCCTGTAAACA	59.663	33.333	7.92	0.00	39.04	2.83

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.