AutoCloner

Multiple sequence alignment - TraesCS4D01G222500

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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	TraesCS4D01G222500	chr4D	100.000	3312	0	0	1	3312	379502405	379499094	0.000000e+00	6117
1	TraesCS4D01G222500	chr4B	94.303	1018	50	2	1315	2324	466695502	466694485	0.000000e+00	1552
2	TraesCS4D01G222500	chr4B	92.405	395	19	5	10	399	466697249	466696861	1.340000e-153	553
3	TraesCS4D01G222500	chr4B	95.873	315	13	0	970	1284	466695815	466695501	8.200000e-141	510
4	TraesCS4D01G222500	chr4B	97.647	255	4	1	2325	2577	466694366	466694112	1.410000e-118	436
5	TraesCS4D01G222500	chr4B	94.553	257	14	0	2658	2914	466693833	466693577	6.660000e-107	398
6	TraesCS4D01G222500	chr4B	89.562	297	7	6	444	720	466696363	466696071	4.070000e-94	355
7	TraesCS4D01G222500	chr4B	90.732	205	6	3	760	952	466696077	466695874	9.120000e-66	261
8	TraesCS4D01G222500	chr4B	93.151	146	8	2	3085	3229	466691556	466691412	2.590000e-51	213
9	TraesCS4D01G222500	chr4A	90.709	1001	30	13	1	952	84933822	84934808	0.000000e+00	1275
10	TraesCS4D01G222500	chr4A	95.238	462	22	0	1053	1514	84934818	84935279	0.000000e+00	732
11	TraesCS4D01G222500	chr4A	90.378	582	20	7	2067	2628	84943006	84943571	0.000000e+00	732
12	TraesCS4D01G222500	chr4A	95.374	281	13	0	1797	2077	84935285	84935565	6.520000e-122	448
13	TraesCS4D01G222500	chr4A	94.942	257	13	0	2655	2911	84943635	84943891	1.430000e-108	403
14	TraesCS4D01G222500	chr4A	92.202	218	17	0	2911	3128	84943941	84944158	3.210000e-80	309
15	TraesCS4D01G222500	chr4A	94.340	159	8	1	3155	3312	84944217	84944375	3.300000e-60	243
16	TraesCS4D01G222500	chr7D	76.017	1205	227	42	1062	2228	581271652	581272832	4.800000e-158	568
17	TraesCS4D01G222500	chr7D	76.035	1135	216	35	1075	2172	548617165	548618280	3.760000e-149	538
18	TraesCS4D01G222500	chr7D	74.896	1203	240	36	1062	2226	548608978	548610156	2.970000e-135	492
19	TraesCS4D01G222500	chr7D	74.492	1180	250	32	1071	2214	581284202	581285366	6.470000e-127	464
20	TraesCS4D01G222500	chr7D	73.929	1120	233	45	1070	2160	581086510	581087599	2.400000e-106	396
21	TraesCS4D01G222500	chr7D	74.464	513	103	14	1738	2231	582043691	582044194	2.610000e-46	196
22	TraesCS4D01G222500	chr7D	78.109	201	41	2	1188	1385	575613840	575613640	1.250000e-24	124
23	TraesCS4D01G222500	chr7B	75.241	1143	240	26	1071	2187	648909397	648910522	1.370000e-138	503
24	TraesCS4D01G222500	chr7B	73.196	873	163	40	1381	2226	648905322	648906150	1.970000e-62	250
25	TraesCS4D01G222500	chr7B	77.880	217	44	3	1749	1963	649246650	649246864	7.460000e-27	132
26	TraesCS4D01G222500	chr7B	80.247	162	28	3	1307	1465	637303648	637303488	5.810000e-23	119
27	TraesCS4D01G222500	chr5D	74.122	1225	243	40	1057	2228	289687144	289688347	3.920000e-119	438
28	TraesCS4D01G222500	chr7A	74.713	870	183	26	1305	2160	673013276	673014122	1.460000e-93	353
29	TraesCS4D01G222500	chr7A	77.577	388	81	6	1058	1443	672153024	672153407	2.570000e-56	230
30	TraesCS4D01G222500	chr7A	76.042	384	84	7	1595	1974	648211148	648210769	3.370000e-45	193

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	TraesCS4D01G222500	chr4D	379499094	379502405	3311	True	6117.000000	6117	100.000000	1	3312	1	chr4D.!!$R1	3311
1	TraesCS4D01G222500	chr4B	466691412	466697249	5837	True	534.750000	1552	93.528250	10	3229	8	chr4B.!!$R1	3219
2	TraesCS4D01G222500	chr4A	84933822	84935565	1743	False	818.333333	1275	93.773667	1	2077	3	chr4A.!!$F1	2076
3	TraesCS4D01G222500	chr4A	84943006	84944375	1369	False	421.750000	732	92.965500	2067	3312	4	chr4A.!!$F2	1245
4	TraesCS4D01G222500	chr7D	581271652	581272832	1180	False	568.000000	568	76.017000	1062	2228	1	chr7D.!!$F4	1166
5	TraesCS4D01G222500	chr7D	548617165	548618280	1115	False	538.000000	538	76.035000	1075	2172	1	chr7D.!!$F2	1097
6	TraesCS4D01G222500	chr7D	548608978	548610156	1178	False	492.000000	492	74.896000	1062	2226	1	chr7D.!!$F1	1164
7	TraesCS4D01G222500	chr7D	581284202	581285366	1164	False	464.000000	464	74.492000	1071	2214	1	chr7D.!!$F5	1143
8	TraesCS4D01G222500	chr7D	581086510	581087599	1089	False	396.000000	396	73.929000	1070	2160	1	chr7D.!!$F3	1090
9	TraesCS4D01G222500	chr7B	648905322	648910522	5200	False	376.500000	503	74.218500	1071	2226	2	chr7B.!!$F2	1155
10	TraesCS4D01G222500	chr5D	289687144	289688347	1203	False	438.000000	438	74.122000	1057	2228	1	chr5D.!!$F1	1171
11	TraesCS4D01G222500	chr7A	673013276	673014122	846	False	353.000000	353	74.713000	1305	2160	1	chr7A.!!$F2	855

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
959	1478	0.107508	CATGTCCATGCCGTCTCCTT	60.108	55.0	0.0	0.0	31.39	3.36	F
960	1479	0.179000	ATGTCCATGCCGTCTCCTTC	59.821	55.0	0.0	0.0	0.00	3.46	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2036	5129	0.618107	TGGTATCCCAACCCGCAGTA	60.618	55.000	0.0	0.0	37.98	2.74	R
2429	5642	1.198637	GAAACTGACTGCATCACCAGC	59.801	52.381	0.0	0.0	36.29	4.85	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
44	45	2.086251	CTCAGAGGAGAGGATGCCGC	62.086	65.000	0.00	0.00	44.26	6.53
45	46	3.222855	AGAGGAGAGGATGCCGCG	61.223	66.667	0.00	0.00	0.00	6.46
46	47	3.532155	GAGGAGAGGATGCCGCGT	61.532	66.667	4.92	0.00	0.00	6.01
47	48	3.077556	AGGAGAGGATGCCGCGTT	61.078	61.111	4.92	0.00	0.00	4.84
48	49	2.125106	GGAGAGGATGCCGCGTTT	60.125	61.111	4.92	0.00	0.00	3.60
49	50	2.174319	GGAGAGGATGCCGCGTTTC	61.174	63.158	4.92	0.00	0.00	2.78
50	51	2.509336	AGAGGATGCCGCGTTTCG	60.509	61.111	4.92	0.00	38.08	3.46
51	52	2.813908	GAGGATGCCGCGTTTCGT	60.814	61.111	4.92	0.00	36.19	3.85
52	53	2.358247	AGGATGCCGCGTTTCGTT	60.358	55.556	4.92	0.00	36.19	3.85
53	54	1.908066	GAGGATGCCGCGTTTCGTTT	61.908	55.000	4.92	0.00	36.19	3.60
89	95	3.922375	TGGTTGGGAGGAAATTGAACTT	58.078	40.909	0.00	0.00	0.00	2.66
153	160	2.434185	GCCATTGTCGTCCTCGCA	60.434	61.111	0.00	0.00	36.96	5.10
382	393	0.393673	TGCTGGAGAGAGACGAGGAG	60.394	60.000	0.00	0.00	0.00	3.69
385	396	0.544223	TGGAGAGAGACGAGGAGGAG	59.456	60.000	0.00	0.00	0.00	3.69
552	1020	3.318275	TCTCAGTTATCCGTGTGCTATCC	59.682	47.826	0.00	0.00	0.00	2.59
553	1021	3.296854	TCAGTTATCCGTGTGCTATCCT	58.703	45.455	0.00	0.00	0.00	3.24
554	1022	3.318275	TCAGTTATCCGTGTGCTATCCTC	59.682	47.826	0.00	0.00	0.00	3.71
555	1023	2.628657	AGTTATCCGTGTGCTATCCTCC	59.371	50.000	0.00	0.00	0.00	4.30
648	1127	2.800881	AAAGGAAAAAGAAGCAGCGG	57.199	45.000	0.00	0.00	0.00	5.52
702	1199	2.099652	CTGTCGGTGGCTGAACTGGA	62.100	60.000	0.00	0.00	0.00	3.86
908	1421	1.595993	CCTTCTCCCTCGCTCGAACA	61.596	60.000	0.00	0.00	0.00	3.18
954	1473	2.764314	GCACCATGTCCATGCCGTC	61.764	63.158	1.64	0.00	37.49	4.79
955	1474	1.078214	CACCATGTCCATGCCGTCT	60.078	57.895	1.64	0.00	37.49	4.18
956	1475	1.091771	CACCATGTCCATGCCGTCTC	61.092	60.000	1.64	0.00	37.49	3.36
959	1478	0.107508	CATGTCCATGCCGTCTCCTT	60.108	55.000	0.00	0.00	31.39	3.36
960	1479	0.179000	ATGTCCATGCCGTCTCCTTC	59.821	55.000	0.00	0.00	0.00	3.46
961	1480	1.153349	GTCCATGCCGTCTCCTTCC	60.153	63.158	0.00	0.00	0.00	3.46
963	1482	2.202932	CATGCCGTCTCCTTCCGG	60.203	66.667	0.00	0.00	46.90	5.14
993	1553	0.243907	TTCCTTCTCCTTCGTCGCTG	59.756	55.000	0.00	0.00	0.00	5.18
1035	1595	0.680280	TCCGTCTCCCTAGTGCAGAC	60.680	60.000	0.00	3.81	34.36	3.51
1279	4322	2.197605	TCCACTTCACCAGCGTCGA	61.198	57.895	0.00	0.00	0.00	4.20
1312	4355	1.216710	CTCTGGTCCGCACCTCTTC	59.783	63.158	0.00	0.00	44.17	2.87
1322	4365	1.004918	CACCTCTTCCGCGTTCCTT	60.005	57.895	4.92	0.00	0.00	3.36
1388	4431	2.571757	CTCTGCCGCTGGTACGAA	59.428	61.111	0.00	0.00	34.06	3.85
1402	4445	2.209064	TACGAAGTCTCTGCCCGTGC	62.209	60.000	0.00	0.00	43.93	5.34
1553	4605	0.843309	TTGAGTTGGTGGAGCAGGAA	59.157	50.000	0.00	0.00	0.00	3.36
1555	4607	1.425066	TGAGTTGGTGGAGCAGGAATT	59.575	47.619	0.00	0.00	0.00	2.17
1639	4699	4.723309	AGATGGGTTCATAATGAGAAGGC	58.277	43.478	0.00	0.00	32.98	4.35
1670	4730	1.394917	CATATTAGGCTCGCCAATCGC	59.605	52.381	11.02	0.00	38.92	4.58
1978	5065	2.038952	CTGGAGGGACACATGTTCTTGA	59.961	50.000	0.00	0.00	0.00	3.02
2161	5254	3.435671	GTGCCATTGTACACAGAGTTACC	59.564	47.826	0.00	0.00	36.77	2.85
2204	5298	5.587443	TCAATATCACACTTCTGATGCCTTG	59.413	40.000	0.00	0.00	32.86	3.61
2262	5357	2.159627	CGTGGCTTGGTATGTCTGTTTC	59.840	50.000	0.00	0.00	0.00	2.78
2429	5642	5.296151	TGCCCTGATTCTAGGATTTGTAG	57.704	43.478	0.00	0.00	40.42	2.74
2503	5718	5.497635	TTTTGCCTTTTGATTTTGAAGCC	57.502	34.783	0.00	0.00	0.00	4.35
2558	5793	5.584649	TGAGTCATTCGAAGTTTCTGTTGTT	59.415	36.000	3.35	0.00	0.00	2.83
2594	5991	8.246430	TCTACTACATACCAATAGTTTCTGGG	57.754	38.462	0.00	0.00	37.00	4.45
2610	6007	1.550524	CTGGGCACTGCTACTCAACTA	59.449	52.381	0.00	0.00	0.00	2.24
2628	6025	8.962679	ACTCAACTATTTTGGTTGACTTTGTAA	58.037	29.630	5.35	0.00	45.14	2.41
2656	6091	3.091545	GGTGAAAGGCCTGAATCAATGA	58.908	45.455	5.69	0.00	0.00	2.57
2718	6153	3.562973	CCTAGTAAACGACGCCATCTCTA	59.437	47.826	0.00	0.00	0.00	2.43
2725	6160	2.287668	ACGACGCCATCTCTACTAATGC	60.288	50.000	0.00	0.00	0.00	3.56
2839	6274	6.367422	CGGCATGCTTTAAATTGGAAAAGTTA	59.633	34.615	18.92	2.24	35.56	2.24
2862	6297	1.202855	AGCAGAACATCACCAAGCTGT	60.203	47.619	0.00	0.00	0.00	4.40
2879	6314	7.875041	ACCAAGCTGTGATTAGATCATACATAC	59.125	37.037	0.00	0.00	42.04	2.39
2928	6413	2.949644	CCTTTCGTGGGTTTTCTTCAGT	59.050	45.455	0.00	0.00	0.00	3.41
2935	6420	4.496840	CGTGGGTTTTCTTCAGTTTGGTAC	60.497	45.833	0.00	0.00	0.00	3.34
2975	6460	2.352651	CAGTAATGACATGCACTTCCCG	59.647	50.000	0.00	0.00	0.00	5.14
3018	6503	4.133013	AGTTGTACGAGACCTGTTGTTT	57.867	40.909	0.00	0.00	0.00	2.83
3046	6636	7.981102	AGTACAACTTTCCTCCTGAATTAAC	57.019	36.000	0.00	0.00	31.67	2.01
3059	6649	6.403049	TCCTGAATTAACTGTCGCTGAAATA	58.597	36.000	0.00	0.00	0.00	1.40
3130	8415	7.696453	ACTTTACGGCATTATTTCTGAATTTCG	59.304	33.333	0.00	0.00	0.00	3.46
3132	8417	6.377327	ACGGCATTATTTCTGAATTTCGAT	57.623	33.333	0.00	0.00	0.00	3.59
3133	8418	6.795399	ACGGCATTATTTCTGAATTTCGATT	58.205	32.000	0.00	0.00	0.00	3.34
3270	8588	8.148351	ACATCCTTATTAGAGTTAGCGCAAATA	58.852	33.333	11.47	0.00	0.00	1.40
3308	8626	9.167311	GAGGAGAAAGATCTTAAACTTGCATTA	57.833	33.333	8.75	0.00	35.54	1.90

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
44	45	2.143661	CGAAACGAAACGAAACGAAACG	59.856	45.455	0.00	0.00	0.00	3.60
45	46	3.083569	ACGAAACGAAACGAAACGAAAC	58.916	40.909	0.00	0.00	0.00	2.78
46	47	3.366808	ACGAAACGAAACGAAACGAAA	57.633	38.095	0.00	0.00	0.00	3.46
47	48	3.366808	AACGAAACGAAACGAAACGAA	57.633	38.095	0.00	0.00	0.00	3.85
48	49	3.082860	CAAACGAAACGAAACGAAACGA	58.917	40.909	0.00	0.00	0.00	3.85
49	50	2.209393	CCAAACGAAACGAAACGAAACG	59.791	45.455	0.00	0.00	0.00	3.60
50	51	3.162831	ACCAAACGAAACGAAACGAAAC	58.837	40.909	0.00	0.00	0.00	2.78
51	52	3.468304	ACCAAACGAAACGAAACGAAA	57.532	38.095	0.00	0.00	0.00	3.46
52	53	3.162068	CAACCAAACGAAACGAAACGAA	58.838	40.909	0.00	0.00	0.00	3.85
53	54	2.475852	CCAACCAAACGAAACGAAACGA	60.476	45.455	0.00	0.00	0.00	3.85
153	160	4.923415	AGAATTTCGAGTTCTGGGGATTT	58.077	39.130	12.62	0.00	34.77	2.17
382	393	3.764972	CCTCCGTATTCTATTCCTCCTCC	59.235	52.174	0.00	0.00	0.00	4.30
385	396	3.764972	CTCCCTCCGTATTCTATTCCTCC	59.235	52.174	0.00	0.00	0.00	4.30
552	1020	1.246737	GGAGCCCAGCAAAACAGGAG	61.247	60.000	0.00	0.00	0.00	3.69
553	1021	1.228552	GGAGCCCAGCAAAACAGGA	60.229	57.895	0.00	0.00	0.00	3.86
554	1022	2.278330	GGGAGCCCAGCAAAACAGG	61.278	63.158	0.00	0.00	35.81	4.00
555	1023	2.629656	CGGGAGCCCAGCAAAACAG	61.630	63.158	6.34	0.00	35.37	3.16
702	1199	3.322466	CCAACGACCTGGCTCCCT	61.322	66.667	0.00	0.00	0.00	4.20
823	1328	3.367321	TGACCCACTCATATGTCCGTTA	58.633	45.455	1.90	0.00	0.00	3.18
959	1478	2.975799	GAAACGCTTGGTGCCGGA	60.976	61.111	5.05	0.00	38.78	5.14
960	1479	4.038080	GGAAACGCTTGGTGCCGG	62.038	66.667	0.00	0.00	38.78	6.13
961	1480	2.458006	GAAGGAAACGCTTGGTGCCG	62.458	60.000	0.00	0.00	38.78	5.69
963	1482	0.238553	GAGAAGGAAACGCTTGGTGC	59.761	55.000	0.00	0.00	38.57	5.01
964	1483	0.875059	GGAGAAGGAAACGCTTGGTG	59.125	55.000	0.00	0.00	0.00	4.17
965	1484	0.765510	AGGAGAAGGAAACGCTTGGT	59.234	50.000	0.00	0.00	0.00	3.67
993	1553	4.026357	AGGAGGGGTCAGGGGGTC	62.026	72.222	0.00	0.00	0.00	4.46
1005	1565	0.825840	GGAGACGGAGATGGAGGAGG	60.826	65.000	0.00	0.00	0.00	4.30
1007	1567	1.230497	GGGAGACGGAGATGGAGGA	59.770	63.158	0.00	0.00	0.00	3.71
1133	4139	0.944386	GCTTGGAGACGCACTTGAAA	59.056	50.000	0.00	0.00	0.00	2.69
1436	4482	1.212229	GACGACCCACTTCTCCGTC	59.788	63.158	0.00	0.00	41.85	4.79
1520	4572	3.631686	CCAACTCAAACACATGGAAGTGA	59.368	43.478	0.00	0.00	42.05	3.41
1565	4617	2.233305	TGAGGTAGACAGGGAAGTCC	57.767	55.000	0.00	0.00	39.34	3.85
1639	4699	4.232188	AGCCTAATATGCTCATCCCATG	57.768	45.455	0.00	0.00	32.41	3.66
1867	4939	1.131883	CTACTAGTCGAACCACACGGG	59.868	57.143	0.00	0.00	44.81	5.28
2036	5129	0.618107	TGGTATCCCAACCCGCAGTA	60.618	55.000	0.00	0.00	37.98	2.74
2161	5254	5.744666	TTGATATCATGTGTGCAGTGATG	57.255	39.130	6.17	3.97	34.62	3.07
2189	5282	5.879223	ACTTCTTATCAAGGCATCAGAAGTG	59.121	40.000	10.76	0.00	42.16	3.16
2262	5357	9.023967	CAAGTTAGAGAAAACAAGAACCAATTG	57.976	33.333	0.00	0.00	0.00	2.32
2429	5642	1.198637	GAAACTGACTGCATCACCAGC	59.801	52.381	0.00	0.00	36.29	4.85
2503	5718	3.057596	AGCAAACATAATGAACCACCACG	60.058	43.478	0.00	0.00	0.00	4.94
2594	5991	4.455877	ACCAAAATAGTTGAGTAGCAGTGC	59.544	41.667	7.13	7.13	0.00	4.40
2610	6007	8.672815	CCAAATGTTTACAAAGTCAACCAAAAT	58.327	29.630	0.00	0.00	0.00	1.82
2628	6025	2.676748	TCAGGCCTTTCACCAAATGTT	58.323	42.857	0.00	0.00	0.00	2.71
2718	6153	7.511959	TGATCTCAGACGTTATAGCATTAGT	57.488	36.000	0.00	0.00	0.00	2.24
2839	6274	1.531423	CTTGGTGATGTTCTGCTGCT	58.469	50.000	0.00	0.00	0.00	4.24
2879	6314	5.065731	AGCTGTCTGACAAAAGAAAGAACAG	59.934	40.000	12.16	0.00	33.89	3.16
2885	6320	4.130118	GGAGAGCTGTCTGACAAAAGAAA	58.870	43.478	12.16	0.00	30.97	2.52
2957	6442	2.355197	CACGGGAAGTGCATGTCATTA	58.645	47.619	0.00	0.00	44.72	1.90
3018	6503	5.623956	TCAGGAGGAAAGTTGTACTTGAA	57.376	39.130	0.00	0.00	38.66	2.69
3034	6624	3.849911	TCAGCGACAGTTAATTCAGGAG	58.150	45.455	0.00	0.00	0.00	3.69
3046	6636	6.682863	CCGAAATTAACTTATTTCAGCGACAG	59.317	38.462	9.09	0.00	42.14	3.51
3059	6649	2.038820	TCCCACCGTCCGAAATTAACTT	59.961	45.455	0.00	0.00	0.00	2.66
3241	8559	6.040054	TGCGCTAACTCTAATAAGGATGTGTA	59.960	38.462	9.73	0.00	0.00	2.90
3245	8563	6.844696	TTTGCGCTAACTCTAATAAGGATG	57.155	37.500	9.73	0.00	0.00	3.51
3270	8588	4.326826	TCTTTCTCCTCGTTCATGCAAAT	58.673	39.130	0.00	0.00	0.00	2.32
3281	8599	5.639506	TGCAAGTTTAAGATCTTTCTCCTCG	59.360	40.000	14.36	0.00	0.00	4.63

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.