AutoCloner

Multiple sequence alignment - TraesCS7B01G214200

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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	TraesCS7B01G214200	chr7B	100.000	2993	0	0	1	2993	393237398	393234406	0.000000e+00	5528
1	TraesCS7B01G214200	chr7B	95.526	2928	103	21	79	2993	319716426	319719338	0.000000e+00	4656
2	TraesCS7B01G214200	chr7B	95.774	2508	70	15	492	2993	240199659	240202136	0.000000e+00	4012
3	TraesCS7B01G214200	chr2B	95.655	2923	109	13	79	2993	386132474	386135386	0.000000e+00	4678
4	TraesCS7B01G214200	chr2B	95.158	2685	115	12	88	2762	320940728	320938049	0.000000e+00	4224
5	TraesCS7B01G214200	chr2B	94.333	1641	87	6	115	1752	115619519	115617882	0.000000e+00	2510
6	TraesCS7B01G214200	chr1B	95.249	2926	116	16	79	2993	348699997	348697084	0.000000e+00	4612
7	TraesCS7B01G214200	chr1B	94.730	2922	119	21	80	2993	60863762	60860868	0.000000e+00	4510
8	TraesCS7B01G214200	chr4B	94.433	2928	135	21	79	2993	559209640	559206728	0.000000e+00	4479
9	TraesCS7B01G214200	chr4B	95.532	2574	104	8	198	2762	277835048	277832477	0.000000e+00	4106
10	TraesCS7B01G214200	chr6B	95.846	2576	100	5	192	2762	48901240	48903813	0.000000e+00	4157
11	TraesCS7B01G214200	chr5A	89.296	1009	77	19	1993	2993	606428560	606427575	0.000000e+00	1236
12	TraesCS7B01G214200	chr4A	93.750	336	8	8	2664	2993	487351063	487350735	2.680000e-135	492
13	TraesCS7B01G214200	chr7A	81.081	407	58	15	1	403	522956777	522957168	1.040000e-79	307
14	TraesCS7B01G214200	chr6D	88.800	125	14	0	1	125	238740463	238740339	1.440000e-33	154

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	TraesCS7B01G214200	chr7B	393234406	393237398	2992	True	5528	5528	100.000	1	2993	1	chr7B.!!$R1	2992
1	TraesCS7B01G214200	chr7B	319716426	319719338	2912	False	4656	4656	95.526	79	2993	1	chr7B.!!$F2	2914
2	TraesCS7B01G214200	chr7B	240199659	240202136	2477	False	4012	4012	95.774	492	2993	1	chr7B.!!$F1	2501
3	TraesCS7B01G214200	chr2B	386132474	386135386	2912	False	4678	4678	95.655	79	2993	1	chr2B.!!$F1	2914
4	TraesCS7B01G214200	chr2B	320938049	320940728	2679	True	4224	4224	95.158	88	2762	1	chr2B.!!$R2	2674
5	TraesCS7B01G214200	chr2B	115617882	115619519	1637	True	2510	2510	94.333	115	1752	1	chr2B.!!$R1	1637
6	TraesCS7B01G214200	chr1B	348697084	348699997	2913	True	4612	4612	95.249	79	2993	1	chr1B.!!$R2	2914
7	TraesCS7B01G214200	chr1B	60860868	60863762	2894	True	4510	4510	94.730	80	2993	1	chr1B.!!$R1	2913
8	TraesCS7B01G214200	chr4B	559206728	559209640	2912	True	4479	4479	94.433	79	2993	1	chr4B.!!$R2	2914
9	TraesCS7B01G214200	chr4B	277832477	277835048	2571	True	4106	4106	95.532	198	2762	1	chr4B.!!$R1	2564
10	TraesCS7B01G214200	chr6B	48901240	48903813	2573	False	4157	4157	95.846	192	2762	1	chr6B.!!$F1	2570
11	TraesCS7B01G214200	chr5A	606427575	606428560	985	True	1236	1236	89.296	1993	2993	1	chr5A.!!$R1	1000

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
74	75	0.768622	TCATGTCCCGTTGTTTCCCT	59.231	50.0	0.0	0.0	0.0	4.2	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2009	2024	5.362717	TCTCCACTCTTCTCTGTTTGTGTTA	59.637	40.0	0.0	0.0	0.0	2.41	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
22	23	4.133078	CTGTCATAGCATTCTTTCTCCCC	58.867	47.826	0.00	0.00	0.00	4.81
23	24	3.117888	TGTCATAGCATTCTTTCTCCCCC	60.118	47.826	0.00	0.00	0.00	5.40
24	25	3.137360	GTCATAGCATTCTTTCTCCCCCT	59.863	47.826	0.00	0.00	0.00	4.79
25	26	3.788142	TCATAGCATTCTTTCTCCCCCTT	59.212	43.478	0.00	0.00	0.00	3.95
26	27	4.230502	TCATAGCATTCTTTCTCCCCCTTT	59.769	41.667	0.00	0.00	0.00	3.11
27	28	2.812658	AGCATTCTTTCTCCCCCTTTG	58.187	47.619	0.00	0.00	0.00	2.77
28	29	2.110721	AGCATTCTTTCTCCCCCTTTGT	59.889	45.455	0.00	0.00	0.00	2.83
29	30	2.899900	GCATTCTTTCTCCCCCTTTGTT	59.100	45.455	0.00	0.00	0.00	2.83
30	31	4.086457	GCATTCTTTCTCCCCCTTTGTTA	58.914	43.478	0.00	0.00	0.00	2.41
31	32	4.082190	GCATTCTTTCTCCCCCTTTGTTAC	60.082	45.833	0.00	0.00	0.00	2.50
32	33	4.799715	TTCTTTCTCCCCCTTTGTTACA	57.200	40.909	0.00	0.00	0.00	2.41
33	34	5.333566	TTCTTTCTCCCCCTTTGTTACAT	57.666	39.130	0.00	0.00	0.00	2.29
34	35	4.662278	TCTTTCTCCCCCTTTGTTACATG	58.338	43.478	0.00	0.00	0.00	3.21
35	36	4.105697	TCTTTCTCCCCCTTTGTTACATGT	59.894	41.667	2.69	2.69	0.00	3.21
36	37	5.311121	TCTTTCTCCCCCTTTGTTACATGTA	59.689	40.000	0.08	0.08	0.00	2.29
37	38	5.789574	TTCTCCCCCTTTGTTACATGTAT	57.210	39.130	6.36	0.00	0.00	2.29
38	39	5.110814	TCTCCCCCTTTGTTACATGTATG	57.889	43.478	6.36	0.00	0.00	2.39
39	40	4.785914	TCTCCCCCTTTGTTACATGTATGA	59.214	41.667	6.36	0.00	0.00	2.15
40	41	5.431731	TCTCCCCCTTTGTTACATGTATGAT	59.568	40.000	6.36	0.00	0.00	2.45
41	42	6.617784	TCTCCCCCTTTGTTACATGTATGATA	59.382	38.462	6.36	0.00	0.00	2.15
42	43	6.837312	TCCCCCTTTGTTACATGTATGATAG	58.163	40.000	6.36	2.95	0.00	2.08
43	44	6.388689	TCCCCCTTTGTTACATGTATGATAGT	59.611	38.462	6.36	0.00	0.00	2.12
44	45	7.569485	TCCCCCTTTGTTACATGTATGATAGTA	59.431	37.037	6.36	0.00	0.00	1.82
45	46	8.215050	CCCCCTTTGTTACATGTATGATAGTAA	58.785	37.037	6.36	0.00	0.00	2.24
46	47	9.793259	CCCCTTTGTTACATGTATGATAGTAAT	57.207	33.333	6.36	0.00	0.00	1.89
64	65	9.302345	GATAGTAATATATGTGTTCATGTCCCG	57.698	37.037	0.00	0.00	35.70	5.14
65	66	7.062749	AGTAATATATGTGTTCATGTCCCGT	57.937	36.000	0.00	0.00	35.70	5.28
66	67	7.506114	AGTAATATATGTGTTCATGTCCCGTT	58.494	34.615	0.00	0.00	35.70	4.44
67	68	6.618287	AATATATGTGTTCATGTCCCGTTG	57.382	37.500	0.00	0.00	35.70	4.10
68	69	2.270352	ATGTGTTCATGTCCCGTTGT	57.730	45.000	0.00	0.00	32.51	3.32
69	70	2.045561	TGTGTTCATGTCCCGTTGTT	57.954	45.000	0.00	0.00	0.00	2.83
70	71	2.370349	TGTGTTCATGTCCCGTTGTTT	58.630	42.857	0.00	0.00	0.00	2.83
71	72	2.356382	TGTGTTCATGTCCCGTTGTTTC	59.644	45.455	0.00	0.00	0.00	2.78
72	73	1.950909	TGTTCATGTCCCGTTGTTTCC	59.049	47.619	0.00	0.00	0.00	3.13
73	74	1.268625	GTTCATGTCCCGTTGTTTCCC	59.731	52.381	0.00	0.00	0.00	3.97
74	75	0.768622	TCATGTCCCGTTGTTTCCCT	59.231	50.000	0.00	0.00	0.00	4.20
75	76	1.144093	TCATGTCCCGTTGTTTCCCTT	59.856	47.619	0.00	0.00	0.00	3.95
76	77	1.960689	CATGTCCCGTTGTTTCCCTTT	59.039	47.619	0.00	0.00	0.00	3.11
77	78	3.150767	CATGTCCCGTTGTTTCCCTTTA	58.849	45.455	0.00	0.00	0.00	1.85
86	87	5.151389	CGTTGTTTCCCTTTATGTTAGTGC	58.849	41.667	0.00	0.00	0.00	4.40
176	179	7.042523	GCTTATATTGCATTTTCTTTGGCGATT	60.043	33.333	0.00	0.00	32.79	3.34
181	184	5.342433	TGCATTTTCTTTGGCGATTATCTG	58.658	37.500	0.00	0.00	0.00	2.90
373	385	2.823147	CGGGGACTAGCGTCGAGT	60.823	66.667	0.00	0.00	41.16	4.18
862	877	4.142381	GGCCTGAAAACCAGAATATGTCAC	60.142	45.833	0.00	0.00	45.78	3.67
994	1009	4.804597	TCCTACTCATATACCACAGCACT	58.195	43.478	0.00	0.00	0.00	4.40
1803	1818	3.548770	TGCTGATTTCTGCCATCCTAAG	58.451	45.455	6.93	0.00	39.65	2.18
2009	2024	1.352622	TGAGGGGAGCACAAACAGGT	61.353	55.000	0.00	0.00	0.00	4.00
2562	2583	1.567357	TGTCATGTTCCCTGGATCGA	58.433	50.000	0.00	0.00	0.00	3.59
2586	2607	6.061022	TGGCTTGTGAAATCTGGTAGATTA	57.939	37.500	4.64	0.00	43.67	1.75
2767	2796	7.129660	TGGTATGTTCCTTTGGGGAGATAATAA	59.870	37.037	0.00	0.00	46.01	1.40
2966	2999	6.739331	AGCCAGCTCTTGATTATTAGTAGT	57.261	37.500	0.00	0.00	0.00	2.73
2967	3000	7.841282	AGCCAGCTCTTGATTATTAGTAGTA	57.159	36.000	0.00	0.00	0.00	1.82

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	4.133078	GGGGAGAAAGAATGCTATGACAG	58.867	47.826	0.00	0.00	0.00	3.51
1	2	3.117888	GGGGGAGAAAGAATGCTATGACA	60.118	47.826	0.00	0.00	0.00	3.58
2	3	3.137360	AGGGGGAGAAAGAATGCTATGAC	59.863	47.826	0.00	0.00	0.00	3.06
3	4	3.397527	AGGGGGAGAAAGAATGCTATGA	58.602	45.455	0.00	0.00	0.00	2.15
4	5	3.872459	AGGGGGAGAAAGAATGCTATG	57.128	47.619	0.00	0.00	0.00	2.23
5	6	4.017130	ACAAAGGGGGAGAAAGAATGCTAT	60.017	41.667	0.00	0.00	0.00	2.97
6	7	3.333680	ACAAAGGGGGAGAAAGAATGCTA	59.666	43.478	0.00	0.00	0.00	3.49
7	8	2.110721	ACAAAGGGGGAGAAAGAATGCT	59.889	45.455	0.00	0.00	0.00	3.79
8	9	2.529632	ACAAAGGGGGAGAAAGAATGC	58.470	47.619	0.00	0.00	0.00	3.56
9	10	5.076873	TGTAACAAAGGGGGAGAAAGAATG	58.923	41.667	0.00	0.00	0.00	2.67
10	11	5.333566	TGTAACAAAGGGGGAGAAAGAAT	57.666	39.130	0.00	0.00	0.00	2.40
11	12	4.799715	TGTAACAAAGGGGGAGAAAGAA	57.200	40.909	0.00	0.00	0.00	2.52
12	13	4.105697	ACATGTAACAAAGGGGGAGAAAGA	59.894	41.667	0.00	0.00	0.00	2.52
13	14	4.407365	ACATGTAACAAAGGGGGAGAAAG	58.593	43.478	0.00	0.00	0.00	2.62
14	15	4.463050	ACATGTAACAAAGGGGGAGAAA	57.537	40.909	0.00	0.00	0.00	2.52
15	16	5.251932	TCATACATGTAACAAAGGGGGAGAA	59.748	40.000	10.14	0.00	0.00	2.87
16	17	4.785914	TCATACATGTAACAAAGGGGGAGA	59.214	41.667	10.14	0.00	0.00	3.71
17	18	5.110814	TCATACATGTAACAAAGGGGGAG	57.889	43.478	10.14	0.00	0.00	4.30
18	19	5.725551	ATCATACATGTAACAAAGGGGGA	57.274	39.130	10.14	0.00	0.00	4.81
19	20	6.601332	ACTATCATACATGTAACAAAGGGGG	58.399	40.000	10.14	0.00	0.00	5.40
20	21	9.793259	ATTACTATCATACATGTAACAAAGGGG	57.207	33.333	10.14	0.00	0.00	4.79
38	39	9.302345	CGGGACATGAACACATATATTACTATC	57.698	37.037	0.00	0.00	0.00	2.08
39	40	8.812972	ACGGGACATGAACACATATATTACTAT	58.187	33.333	0.00	0.00	0.00	2.12
40	41	8.185506	ACGGGACATGAACACATATATTACTA	57.814	34.615	0.00	0.00	0.00	1.82
41	42	7.062749	ACGGGACATGAACACATATATTACT	57.937	36.000	0.00	0.00	0.00	2.24
42	43	7.225931	ACAACGGGACATGAACACATATATTAC	59.774	37.037	0.00	0.00	0.00	1.89
43	44	7.276658	ACAACGGGACATGAACACATATATTA	58.723	34.615	0.00	0.00	0.00	0.98
44	45	6.119536	ACAACGGGACATGAACACATATATT	58.880	36.000	0.00	0.00	0.00	1.28
45	46	5.680619	ACAACGGGACATGAACACATATAT	58.319	37.500	0.00	0.00	0.00	0.86
46	47	5.092554	ACAACGGGACATGAACACATATA	57.907	39.130	0.00	0.00	0.00	0.86
47	48	3.950397	ACAACGGGACATGAACACATAT	58.050	40.909	0.00	0.00	0.00	1.78
48	49	3.410631	ACAACGGGACATGAACACATA	57.589	42.857	0.00	0.00	0.00	2.29
49	50	2.270352	ACAACGGGACATGAACACAT	57.730	45.000	0.00	0.00	0.00	3.21
50	51	2.045561	AACAACGGGACATGAACACA	57.954	45.000	0.00	0.00	0.00	3.72
51	52	2.287368	GGAAACAACGGGACATGAACAC	60.287	50.000	0.00	0.00	0.00	3.32
52	53	1.950909	GGAAACAACGGGACATGAACA	59.049	47.619	0.00	0.00	0.00	3.18
53	54	1.268625	GGGAAACAACGGGACATGAAC	59.731	52.381	0.00	0.00	0.00	3.18
54	55	1.144093	AGGGAAACAACGGGACATGAA	59.856	47.619	0.00	0.00	0.00	2.57
55	56	0.768622	AGGGAAACAACGGGACATGA	59.231	50.000	0.00	0.00	0.00	3.07
56	57	1.616159	AAGGGAAACAACGGGACATG	58.384	50.000	0.00	0.00	0.00	3.21
57	58	2.375014	AAAGGGAAACAACGGGACAT	57.625	45.000	0.00	0.00	0.00	3.06
58	59	3.150767	CATAAAGGGAAACAACGGGACA	58.849	45.455	0.00	0.00	0.00	4.02
59	60	3.151554	ACATAAAGGGAAACAACGGGAC	58.848	45.455	0.00	0.00	0.00	4.46
60	61	3.512219	ACATAAAGGGAAACAACGGGA	57.488	42.857	0.00	0.00	0.00	5.14
61	62	4.763279	ACTAACATAAAGGGAAACAACGGG	59.237	41.667	0.00	0.00	0.00	5.28
62	63	5.695818	CACTAACATAAAGGGAAACAACGG	58.304	41.667	0.00	0.00	0.00	4.44
63	64	5.048991	AGCACTAACATAAAGGGAAACAACG	60.049	40.000	0.00	0.00	0.00	4.10
64	65	6.327279	AGCACTAACATAAAGGGAAACAAC	57.673	37.500	0.00	0.00	0.00	3.32
65	66	6.969993	AAGCACTAACATAAAGGGAAACAA	57.030	33.333	0.00	0.00	0.00	2.83
66	67	8.466617	TTTAAGCACTAACATAAAGGGAAACA	57.533	30.769	0.00	0.00	0.00	2.83
67	68	9.923143	AATTTAAGCACTAACATAAAGGGAAAC	57.077	29.630	0.00	0.00	0.00	2.78
70	71	9.528489	AGAAATTTAAGCACTAACATAAAGGGA	57.472	29.630	0.00	0.00	0.00	4.20
71	72	9.788960	GAGAAATTTAAGCACTAACATAAAGGG	57.211	33.333	0.00	0.00	0.00	3.95
72	73	9.490663	CGAGAAATTTAAGCACTAACATAAAGG	57.509	33.333	0.00	0.00	0.00	3.11
75	76	8.388103	GCTCGAGAAATTTAAGCACTAACATAA	58.612	33.333	18.75	0.00	33.21	1.90
76	77	7.011109	GGCTCGAGAAATTTAAGCACTAACATA	59.989	37.037	18.75	0.00	34.65	2.29
77	78	6.183360	GGCTCGAGAAATTTAAGCACTAACAT	60.183	38.462	18.75	0.00	34.65	2.71
121	123	7.038017	AGGGAGATTCAGATTTTTCTCACTGTA	60.038	37.037	2.90	0.00	45.03	2.74
130	133	6.676990	AAGCAAAGGGAGATTCAGATTTTT	57.323	33.333	0.00	0.00	0.00	1.94
373	385	4.150897	AGTCTAAAGCCTCACACAAACA	57.849	40.909	0.00	0.00	0.00	2.83
441	453	2.570386	ACAGGGGTTAGTGGCTAGAT	57.430	50.000	0.00	0.00	0.00	1.98
629	644	1.603802	CAAAAACTCCTTCTCGCTGCA	59.396	47.619	0.00	0.00	0.00	4.41
862	877	4.963318	TCTCAGGGTTATTGCTCCTATG	57.037	45.455	0.00	0.00	0.00	2.23
994	1009	3.724478	ACTCCATTGGACACATCTCCTA	58.276	45.455	0.00	0.00	0.00	2.94
2009	2024	5.362717	TCTCCACTCTTCTCTGTTTGTGTTA	59.637	40.000	0.00	0.00	0.00	2.41
2562	2583	4.574674	TCTACCAGATTTCACAAGCCAT	57.425	40.909	0.00	0.00	0.00	4.40
2631	2656	3.893200	CCCGAGAACATGGTATACACCTA	59.107	47.826	5.01	0.00	45.98	3.08
2705	2734	0.388294	GGTATACACCTGGCTCGACC	59.612	60.000	5.01	0.00	42.11	4.79
2711	2740	3.467803	GAGAACATGGTATACACCTGGC	58.532	50.000	5.01	0.00	45.98	4.85
2965	2998	4.072131	TGGCCTTGAGTCAAACTGAATAC	58.928	43.478	3.32	0.00	0.00	1.89
2966	2999	4.365514	TGGCCTTGAGTCAAACTGAATA	57.634	40.909	3.32	0.00	0.00	1.75
2967	3000	3.228188	TGGCCTTGAGTCAAACTGAAT	57.772	42.857	3.32	0.00	0.00	2.57
2972	3005	3.288809	GTCAATGGCCTTGAGTCAAAC	57.711	47.619	15.31	2.11	44.44	2.93

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.