AutoCloner

Multiple sequence alignment - TraesCS7D01G378600

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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	TraesCS7D01G378600	chr7D	100.000	4067	0	0	1	4067	489904624	489900558	0.000000e+00	7511.0
1	TraesCS7D01G378600	chr7D	84.375	128	15	5	3862	3987	590520170	590520294	1.990000e-23	121.0
2	TraesCS7D01G378600	chr7D	100.000	32	0	0	4036	4067	489785189	489785158	4.390000e-05	60.2
3	TraesCS7D01G378600	chr7B	94.060	3350	138	31	1	3301	518408157	518404820	0.000000e+00	5027.0
4	TraesCS7D01G378600	chr7B	94.000	3350	140	31	1	3301	518399786	518396449	0.000000e+00	5016.0
5	TraesCS7D01G378600	chr7B	95.099	2979	113	17	343	3301	518415453	518412488	0.000000e+00	4662.0
6	TraesCS7D01G378600	chr7B	96.412	1923	52	7	1153	3062	518395290	518393372	0.000000e+00	3153.0
7	TraesCS7D01G378600	chr7B	89.240	855	57	18	68	888	518419993	518419140	0.000000e+00	1037.0
8	TraesCS7D01G378600	chr7B	87.131	474	23	18	3624	4062	518393055	518392585	1.690000e-138	503.0
9	TraesCS7D01G378600	chr7B	95.804	286	10	2	3285	3569	518396382	518396098	1.030000e-125	460.0
10	TraesCS7D01G378600	chr7B	98.266	173	3	0	3285	3457	518404753	518404581	1.840000e-78	303.0
11	TraesCS7D01G378600	chr7B	98.266	173	3	0	3285	3457	518412421	518412249	1.840000e-78	303.0
12	TraesCS7D01G378600	chr7A	90.127	1965	120	25	1	1930	556554909	556552984	0.000000e+00	2486.0
13	TraesCS7D01G378600	chr7A	75.510	294	43	17	2212	2497	556556307	556556035	2.570000e-22	117.0
14	TraesCS7D01G378600	chrUn	82.083	480	59	15	836	1308	31327202	31326743	6.380000e-103	385.0
15	TraesCS7D01G378600	chrUn	78.106	644	104	23	1346	1977	31326735	31326117	1.380000e-99	374.0
16	TraesCS7D01G378600	chrUn	85.185	351	50	2	964	1313	31312971	31312622	3.870000e-95	359.0
17	TraesCS7D01G378600	chrUn	75.963	649	114	29	1347	1977	31312618	31311994	3.070000e-76	296.0
18	TraesCS7D01G378600	chrUn	75.796	628	102	31	1370	1977	31370974	31370377	5.180000e-69	272.0
19	TraesCS7D01G378600	chr2D	86.325	351	46	2	964	1313	648120800	648121149	8.250000e-102	381.0
20	TraesCS7D01G378600	chr2D	77.868	619	101	21	1346	1952	648102863	648103457	6.470000e-93	351.0
21	TraesCS7D01G378600	chr2D	76.852	648	110	24	1338	1968	648121144	648121768	3.030000e-86	329.0
22	TraesCS7D01G378600	chr2D	84.848	132	17	3	3862	3992	598725233	598725104	3.300000e-26	130.0
23	TraesCS7D01G378600	chr2D	75.127	197	32	12	350	532	648120297	648120490	4.360000e-10	76.8
24	TraesCS7D01G378600	chr2B	86.000	350	48	1	964	1313	781796136	781795788	1.380000e-99	374.0
25	TraesCS7D01G378600	chr2B	81.174	494	63	19	823	1308	781807282	781806811	1.790000e-98	370.0
26	TraesCS7D01G378600	chr2B	76.579	649	110	26	1347	1977	781795784	781795160	6.560000e-83	318.0
27	TraesCS7D01G378600	chr2B	75.878	655	118	26	1338	1977	781828230	781827601	8.550000e-77	298.0
28	TraesCS7D01G378600	chr5D	84.049	163	24	2	2163	2324	5568774	5568935	5.440000e-34	156.0
29	TraesCS7D01G378600	chr5D	83.951	162	26	0	2163	2324	6354833	6354672	5.440000e-34	156.0
30	TraesCS7D01G378600	chr5B	83.436	163	27	0	2162	2324	6602060	6601898	7.040000e-33	152.0
31	TraesCS7D01G378600	chr5A	83.436	163	25	2	2163	2324	3314666	3314827	2.530000e-32	150.0
32	TraesCS7D01G378600	chr5A	85.075	134	13	6	3862	3992	123979657	123979528	3.300000e-26	130.0
33	TraesCS7D01G378600	chr1D	85.926	135	12	6	3862	3994	318557404	318557275	1.970000e-28	137.0
34	TraesCS7D01G378600	chr6B	87.719	114	13	1	3880	3992	444284587	444284474	9.170000e-27	132.0
35	TraesCS7D01G378600	chr3A	84.559	136	13	7	3862	3994	583580636	583580766	1.190000e-25	128.0
36	TraesCS7D01G378600	chr6A	84.328	134	14	6	3862	3992	350839553	350839682	1.530000e-24	124.0
37	TraesCS7D01G378600	chr3D	83.206	131	19	3	3862	3991	496045291	496045163	2.570000e-22	117.0
38	TraesCS7D01G378600	chr6D	87.500	56	3	4	3091	3146	389701269	389701320	1.220000e-05	62.1
39	TraesCS7D01G378600	chr1B	92.683	41	2	1	3106	3146	667078615	667078654	1.580000e-04	58.4

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	TraesCS7D01G378600	chr7D	489900558	489904624	4066	True	7511.000000	7511	100.000000	1	4067	1	chr7D.!!$R2	4066
1	TraesCS7D01G378600	chr7B	518404581	518408157	3576	True	2665.000000	5027	96.163000	1	3457	2	chr7B.!!$R2	3456
2	TraesCS7D01G378600	chr7B	518392585	518399786	7201	True	2283.000000	5016	93.336750	1	4062	4	chr7B.!!$R1	4061
3	TraesCS7D01G378600	chr7B	518412249	518419993	7744	True	2000.666667	4662	94.201667	68	3457	3	chr7B.!!$R3	3389
4	TraesCS7D01G378600	chr7A	556552984	556556307	3323	True	1301.500000	2486	82.818500	1	2497	2	chr7A.!!$R1	2496
5	TraesCS7D01G378600	chrUn	31326117	31327202	1085	True	379.500000	385	80.094500	836	1977	2	chrUn.!!$R3	1141
6	TraesCS7D01G378600	chrUn	31311994	31312971	977	True	327.500000	359	80.574000	964	1977	2	chrUn.!!$R2	1013
7	TraesCS7D01G378600	chrUn	31370377	31370974	597	True	272.000000	272	75.796000	1370	1977	1	chrUn.!!$R1	607
8	TraesCS7D01G378600	chr2D	648102863	648103457	594	False	351.000000	351	77.868000	1346	1952	1	chr2D.!!$F1	606
9	TraesCS7D01G378600	chr2D	648120297	648121768	1471	False	262.266667	381	79.434667	350	1968	3	chr2D.!!$F2	1618
10	TraesCS7D01G378600	chr2B	781795160	781796136	976	True	346.000000	374	81.289500	964	1977	2	chr2B.!!$R3	1013
11	TraesCS7D01G378600	chr2B	781827601	781828230	629	True	298.000000	298	75.878000	1338	1977	1	chr2B.!!$R2	639

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
33	1432	0.519519	AAGTGAGTGAGAGCGAGACG	59.480	55.000	0.00	0.00	0.00	4.18	F
170	1569	0.662085	GTACCATCTCTCCGACGGTC	59.338	60.000	14.79	0.00	0.00	4.79	F
181	1580	1.134075	CGACGGTCAGGTCAGTACG	59.866	63.158	9.10	0.00	36.73	3.67	F
1240	6933	1.202568	CGTGCGCACAAGTCTTCTG	59.797	57.895	37.03	15.87	0.00	3.02	F
2370	8079	0.953727	CTGGCACTGCTTTGCTACAA	59.046	50.000	9.55	0.00	42.56	2.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1360	7053	1.227943	GAGCAGCAAGTGGTCCACA	60.228	57.895	24.02	46.33	4.17	R
2168	7877	0.960364	TGCAAACCCCTCTCGAATGC	60.960	55.000	0.00	0.00	3.56	R
2304	8013	8.494016	AAGTATTACCATCTTGAGCTTAACAC	57.506	34.615	0.00	0.00	3.32	R
2416	8125	0.107263	TGTTTCACAGTGCTCCTGCA	60.107	50.000	0.00	45.68	4.41	R
3383	9188	0.252696	TGGGCATACCACTCCAGTCT	60.253	55.000	0.00	46.80	3.24	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
33	1432	0.519519	AAGTGAGTGAGAGCGAGACG	59.480	55.000	0.00	0.00	0.00	4.18
157	1556	2.046700	CCACCGCCGTTGTACCAT	60.047	61.111	0.00	0.00	0.00	3.55
161	1560	1.255667	ACCGCCGTTGTACCATCTCT	61.256	55.000	0.00	0.00	0.00	3.10
167	1566	1.531264	CGTTGTACCATCTCTCCGACG	60.531	57.143	0.00	0.00	0.00	5.12
170	1569	0.662085	GTACCATCTCTCCGACGGTC	59.338	60.000	14.79	0.00	0.00	4.79
181	1580	1.134075	CGACGGTCAGGTCAGTACG	59.866	63.158	9.10	0.00	36.73	3.67
287	1713	2.225242	TGGGGTATTTGCAGAATGGTGT	60.225	45.455	4.89	0.00	35.86	4.16
317	1743	4.585162	TGTTACCTAGAGATTGCTAGCTCC	59.415	45.833	17.23	4.91	37.52	4.70
349	1775	8.985315	AATTTGGTCAATCTCTAGATTATGCA	57.015	30.769	4.93	0.00	42.41	3.96
350	1776	8.985315	ATTTGGTCAATCTCTAGATTATGCAA	57.015	30.769	4.93	0.00	42.41	4.08
352	1778	8.442632	TTGGTCAATCTCTAGATTATGCAAAG	57.557	34.615	4.93	0.00	42.41	2.77
362	1790	8.824159	TCTAGATTATGCAAAGATACTGAAGC	57.176	34.615	0.00	0.00	0.00	3.86
364	1792	5.468072	AGATTATGCAAAGATACTGAAGCGG	59.532	40.000	0.00	0.00	0.00	5.52
429	1862	6.425735	TCACATAATGATCACCACATTTCCT	58.574	36.000	0.00	0.00	38.61	3.36
433	1866	8.253113	ACATAATGATCACCACATTTCCTTTTC	58.747	33.333	0.00	0.00	38.61	2.29
458	1893	1.843368	CCAGATGAAGTGGGCACAAT	58.157	50.000	0.00	0.00	0.00	2.71
512	1951	2.233431	TGCATCTACCACCATTTTTGCC	59.767	45.455	0.00	0.00	0.00	4.52
549	1988	6.736853	GCTTATGTTTAACTGTCGTCAATCAC	59.263	38.462	0.00	0.00	0.00	3.06
652	2096	7.976175	TCAGTATCTTAGACAACATAACTGCTG	59.024	37.037	0.00	0.00	0.00	4.41
655	2099	6.590234	TCTTAGACAACATAACTGCTGAGA	57.410	37.500	0.00	0.00	0.00	3.27
711	2155	4.327680	CCCTACCTCTTTCTTTTCAGTGG	58.672	47.826	0.00	0.00	0.00	4.00
847	2299	3.921119	TGTTGGCATTTACAGCTGAAG	57.079	42.857	23.35	6.01	0.00	3.02
894	6581	5.215160	GCTGCATATGTATTTTCCTTTCCG	58.785	41.667	4.29	0.00	0.00	4.30
918	6609	7.201884	CCGAGACTATCCTTTTACATAAGGTCA	60.202	40.741	0.00	0.00	44.19	4.02
995	6686	5.526506	AATCATCTCATCTCATCGTGTGA	57.473	39.130	0.00	0.00	35.05	3.58

Showing 1 to 25 of 97 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability
145	1544	4.958907	GTCGGAGAGATGGTACAACGGC	62.959	59.091	0.00	39.56	5.68
157	1556	1.376942	GACCTGACCGTCGGAGAGA	60.377	63.158	20.51	36.95	3.10
161	1560	0.957395	GTACTGACCTGACCGTCGGA	60.957	60.000	20.51	40.96	4.55
167	1566	0.108756	GAAGGCGTACTGACCTGACC	60.109	60.000	0.26	36.07	4.02
170	1569	0.603569	ACTGAAGGCGTACTGACCTG	59.396	55.000	0.26	36.07	4.00
181	1580	1.079503	CGCTGGTAGAAACTGAAGGC	58.920	55.000	0.00	0.00	4.35
287	1713	5.189736	AGCAATCTCTAGGTAACACCAATGA	59.810	40.000	0.00	41.95	2.57
317	1743	3.370978	AGAGATTGACCAAATTACGCACG	59.629	43.478	0.00	0.00	5.34
347	1773	1.739067	ACCCGCTTCAGTATCTTTGC	58.261	50.000	0.00	0.00	3.68
348	1774	3.857052	TGTACCCGCTTCAGTATCTTTG	58.143	45.455	0.00	0.00	2.77
349	1775	4.161565	TCATGTACCCGCTTCAGTATCTTT	59.838	41.667	0.00	0.00	2.52
350	1776	3.704566	TCATGTACCCGCTTCAGTATCTT	59.295	43.478	0.00	0.00	2.40
352	1778	3.728076	TCATGTACCCGCTTCAGTATC	57.272	47.619	0.00	0.00	2.24
358	1786	2.094762	ACAGTTCATGTACCCGCTTC	57.905	50.000	0.00	41.60	3.86
362	1790	7.605410	AATAAGTTAACAGTTCATGTACCCG	57.395	36.000	8.61	43.00	5.28
406	1839	6.704289	AGGAAATGTGGTGATCATTATGTG	57.296	37.500	0.00	34.92	3.21
433	1866	1.745141	GCCCACTTCATCTGGCTACAG	60.745	57.143	0.00	46.30	2.74
458	1893	5.368145	AGTCAGTCTGCAACAAACAGAATA	58.632	37.500	0.00	45.32	1.75
512	1951	8.223769	CAGTTAAACATAAGCTCAACAGTAGTG	58.776	37.037	0.00	0.00	2.74
652	2096	7.748847	TCAACGCACTAATAGGAATTTTTCTC	58.251	34.615	0.00	0.00	2.87
655	2099	7.882179	ACTTCAACGCACTAATAGGAATTTTT	58.118	30.769	0.00	0.00	1.94
918	6609	3.485394	TGTACTGGCAATCACACAATGT	58.515	40.909	0.00	0.00	2.71
1047	6740	2.433604	TGAATCAACAAAGGGCAAAGCA	59.566	40.909	0.00	0.00	3.91
1126	6819	2.108157	TCGTTGCCTCGCACACTT	59.892	55.556	0.00	38.71	3.16
1360	7053	1.227943	GAGCAGCAAGTGGTCCACA	60.228	57.895	24.02	46.33	4.17

Showing 1 to 25 of 87 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.