AutoCloner

Multiple sequence alignment - TraesCS1D01G339300

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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	TraesCS1D01G339300	chr1D	100.000	3458	0	0	1	3458	429027645	429024188	0.000000e+00	6386.0
1	TraesCS1D01G339300	chr1D	90.730	3495	194	57	5	3458	429494395	429490990	0.000000e+00	4540.0
2	TraesCS1D01G339300	chr1B	94.336	2560	119	13	1	2554	580540059	580537520	0.000000e+00	3901.0
3	TraesCS1D01G339300	chr1B	77.525	1406	270	35	1066	2460	589224616	589225986	0.000000e+00	804.0
4	TraesCS1D01G339300	chr1B	87.071	495	42	9	2975	3458	580531134	580530651	1.090000e-149	540.0
5	TraesCS1D01G339300	chr1B	90.367	218	7	5	2686	2901	580531922	580531717	1.220000e-69	274.0
6	TraesCS1D01G339300	chr1B	87.766	188	23	0	3271	3458	580532940	580532753	1.620000e-53	220.0
7	TraesCS1D01G339300	chr1A	91.648	2263	134	24	959	3191	526759050	526756813	0.000000e+00	3081.0
8	TraesCS1D01G339300	chr1A	77.163	1410	260	46	1068	2458	441033730	441032364	0.000000e+00	763.0
9	TraesCS1D01G339300	chr1A	83.750	720	76	16	2	684	526919317	526918602	0.000000e+00	643.0
10	TraesCS1D01G339300	chr1A	79.057	530	93	8	367	894	558888990	558888477	7.100000e-92	348.0
11	TraesCS1D01G339300	chr1A	93.000	100	6	1	819	918	526763483	526763385	1.000000e-30	145.0
12	TraesCS1D01G339300	chr1A	100.000	30	0	0	920	949	526763348	526763319	4.820000e-04	56.5
13	TraesCS1D01G339300	chr7D	80.259	1469	248	30	1008	2455	92763916	92762469	0.000000e+00	1068.0
14	TraesCS1D01G339300	chr7B	80.153	1436	254	23	1019	2449	45175540	45176949	0.000000e+00	1044.0
15	TraesCS1D01G339300	chr7A	80.132	1213	210	26	1262	2455	94916011	94914811	0.000000e+00	876.0
16	TraesCS1D01G339300	chr2A	74.927	1033	202	48	1118	2129	179349069	179348073	1.480000e-113	420.0
17	TraesCS1D01G339300	chr5D	72.507	1444	325	57	1039	2440	431971703	431970290	5.380000e-108	401.0
18	TraesCS1D01G339300	chr5A	72.268	1446	325	58	1039	2440	547061870	547060457	2.520000e-101	379.0
19	TraesCS1D01G339300	chr5A	87.671	73	7	2	841	911	229519249	229519177	2.210000e-12	84.2
20	TraesCS1D01G339300	chr6A	82.500	400	59	9	493	889	506323913	506324304	1.190000e-89	340.0
21	TraesCS1D01G339300	chr6A	77.876	565	84	23	95	626	49472042	49472598	2.590000e-81	313.0
22	TraesCS1D01G339300	chr6D	78.136	590	82	26	223	781	296204188	296204761	7.150000e-87	331.0
23	TraesCS1D01G339300	chr6B	75.426	704	106	38	221	889	550146006	550146677	2.630000e-71	279.0
24	TraesCS1D01G339300	chr6B	80.072	276	37	12	616	890	88733383	88733641	4.560000e-44	189.0
25	TraesCS1D01G339300	chr3B	75.276	453	92	17	447	896	428135987	428135552	7.570000e-47	198.0
26	TraesCS1D01G339300	chr5B	84.884	86	11	2	385	469	248804191	248804107	6.150000e-13	86.1
27	TraesCS1D01G339300	chr5B	84.706	85	12	1	385	469	248926867	248926950	2.210000e-12	84.2
28	TraesCS1D01G339300	chr5B	100.000	30	0	0	2994	3023	270665945	270665916	4.820000e-04	56.5
29	TraesCS1D01G339300	chr2D	88.235	51	6	0	2980	3030	27275721	27275671	1.040000e-05	62.1

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	TraesCS1D01G339300	chr1D	429024188	429027645	3457	True	6386.000000	6386	100.000000	1	3458	1	chr1D.!!$R1	3457
1	TraesCS1D01G339300	chr1D	429490990	429494395	3405	True	4540.000000	4540	90.730000	5	3458	1	chr1D.!!$R2	3453
2	TraesCS1D01G339300	chr1B	580537520	580540059	2539	True	3901.000000	3901	94.336000	1	2554	1	chr1B.!!$R1	2553
3	TraesCS1D01G339300	chr1B	589224616	589225986	1370	False	804.000000	804	77.525000	1066	2460	1	chr1B.!!$F1	1394
4	TraesCS1D01G339300	chr1B	580530651	580532940	2289	True	344.666667	540	88.401333	2686	3458	3	chr1B.!!$R2	772
5	TraesCS1D01G339300	chr1A	526756813	526759050	2237	True	3081.000000	3081	91.648000	959	3191	1	chr1A.!!$R2	2232
6	TraesCS1D01G339300	chr1A	441032364	441033730	1366	True	763.000000	763	77.163000	1068	2458	1	chr1A.!!$R1	1390
7	TraesCS1D01G339300	chr1A	526918602	526919317	715	True	643.000000	643	83.750000	2	684	1	chr1A.!!$R3	682
8	TraesCS1D01G339300	chr1A	558888477	558888990	513	True	348.000000	348	79.057000	367	894	1	chr1A.!!$R4	527
9	TraesCS1D01G339300	chr7D	92762469	92763916	1447	True	1068.000000	1068	80.259000	1008	2455	1	chr7D.!!$R1	1447
10	TraesCS1D01G339300	chr7B	45175540	45176949	1409	False	1044.000000	1044	80.153000	1019	2449	1	chr7B.!!$F1	1430
11	TraesCS1D01G339300	chr7A	94914811	94916011	1200	True	876.000000	876	80.132000	1262	2455	1	chr7A.!!$R1	1193
12	TraesCS1D01G339300	chr2A	179348073	179349069	996	True	420.000000	420	74.927000	1118	2129	1	chr2A.!!$R1	1011
13	TraesCS1D01G339300	chr5D	431970290	431971703	1413	True	401.000000	401	72.507000	1039	2440	1	chr5D.!!$R1	1401
14	TraesCS1D01G339300	chr5A	547060457	547061870	1413	True	379.000000	379	72.268000	1039	2440	1	chr5A.!!$R2	1401
15	TraesCS1D01G339300	chr6A	49472042	49472598	556	False	313.000000	313	77.876000	95	626	1	chr6A.!!$F1	531
16	TraesCS1D01G339300	chr6D	296204188	296204761	573	False	331.000000	331	78.136000	223	781	1	chr6D.!!$F1	558
17	TraesCS1D01G339300	chr6B	550146006	550146677	671	False	279.000000	279	75.426000	221	889	1	chr6B.!!$F2	668

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
788	870	0.167470	TCGTCATTGTCGTCCTCGTC	59.833	55.0	3.38	0.0	38.33	4.20	F
789	871	1.126421	CGTCATTGTCGTCCTCGTCG	61.126	60.0	0.00	0.0	38.33	5.12	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2224	2417	1.949847	ATCTCCCGGACGTCAAGCTG	61.950	60.000	18.91	4.39	0.0	4.24	R
2595	2813	3.241022	CGTTATCGTCGTTCCGTACAAAC	60.241	47.826	0.00	0.00	0.0	2.93	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
166	176	4.611119	TCGGCCCCGAATAGATCA	57.389	55.556	6.99	0.00	46.01	2.92
492	561	1.227823	TGGTCTTGTTGCCGACAGG	60.228	57.895	0.00	0.00	39.94	4.00
648	721	2.075837	CGGGGAAGAAGAAAGGGGT	58.924	57.895	0.00	0.00	0.00	4.95
723	797	7.698130	CGATTCAATTTTAACCTGTGAGATTCC	59.302	37.037	0.00	0.00	0.00	3.01
776	858	4.220693	TGGATTGGAGTTCATCGTCATT	57.779	40.909	0.00	0.00	0.00	2.57
781	863	2.029380	TGGAGTTCATCGTCATTGTCGT	60.029	45.455	3.38	0.00	0.00	4.34
782	864	2.599082	GGAGTTCATCGTCATTGTCGTC	59.401	50.000	3.38	0.00	0.00	4.20
783	865	2.599082	GAGTTCATCGTCATTGTCGTCC	59.401	50.000	3.38	0.00	0.00	4.79
784	866	2.231478	AGTTCATCGTCATTGTCGTCCT	59.769	45.455	3.38	0.00	0.00	3.85
785	867	2.561733	TCATCGTCATTGTCGTCCTC	57.438	50.000	3.38	0.00	0.00	3.71
786	868	1.191944	CATCGTCATTGTCGTCCTCG	58.808	55.000	3.38	0.00	38.55	4.63
787	869	0.809385	ATCGTCATTGTCGTCCTCGT	59.191	50.000	3.38	0.00	38.33	4.18
788	870	0.167470	TCGTCATTGTCGTCCTCGTC	59.833	55.000	3.38	0.00	38.33	4.20
789	871	1.126421	CGTCATTGTCGTCCTCGTCG	61.126	60.000	0.00	0.00	38.33	5.12
832	914	1.739338	GATCCTGGGCGACGATGTCT	61.739	60.000	0.00	0.00	0.00	3.41
918	1009	4.825634	CACTCCATTGTTGCTATGATCCAT	59.174	41.667	0.00	0.00	0.00	3.41
944	1035	6.854496	TTATTTGCCCGCAGTAATTACTAG	57.146	37.500	17.62	13.96	34.13	2.57
1021	1118	2.044848	ACGTTGGGCAACACCACA	60.045	55.556	0.00	0.00	41.03	4.17
2263	2456	3.477582	TGGAAGCGGATGTCCACA	58.522	55.556	0.00	0.00	39.04	4.17
2499	2695	2.032799	GTGGCTACTCGATCTGTCTCTG	59.967	54.545	0.00	0.00	0.00	3.35
2564	2768	0.921896	CCCATGAGTGAGACCCCATT	59.078	55.000	0.00	0.00	0.00	3.16
2577	2781	3.353557	GACCCCATTAGTTGGTCTTTCC	58.646	50.000	0.00	0.00	44.83	3.13
2579	2783	3.401342	ACCCCATTAGTTGGTCTTTCCTT	59.599	43.478	0.00	0.00	44.83	3.36
2580	2784	3.763897	CCCCATTAGTTGGTCTTTCCTTG	59.236	47.826	0.00	0.00	44.83	3.61
2581	2785	3.193479	CCCATTAGTTGGTCTTTCCTTGC	59.807	47.826	0.00	0.00	44.83	4.01
2582	2786	3.826157	CCATTAGTTGGTCTTTCCTTGCA	59.174	43.478	0.00	0.00	40.99	4.08
2583	2787	4.280677	CCATTAGTTGGTCTTTCCTTGCAA	59.719	41.667	0.00	0.00	40.99	4.08
2584	2788	5.221422	CCATTAGTTGGTCTTTCCTTGCAAA	60.221	40.000	0.00	0.00	40.99	3.68
2585	2789	6.458210	CATTAGTTGGTCTTTCCTTGCAAAT	58.542	36.000	0.00	0.00	37.07	2.32
2595	2813	7.078228	GTCTTTCCTTGCAAATAAGTACAGTG	58.922	38.462	0.00	0.00	0.00	3.66
2625	2843	1.823828	ACGACGATAACGATGTGAGC	58.176	50.000	0.00	0.00	42.66	4.26
2636	2854	1.386533	GATGTGAGCCCATGTTGGAG	58.613	55.000	0.00	0.00	40.96	3.86
2638	2856	0.994247	TGTGAGCCCATGTTGGAGAT	59.006	50.000	0.00	0.00	40.96	2.75
2669	2887	3.526534	GGTGACTTCCTAGAGTTGCATC	58.473	50.000	0.00	0.00	0.00	3.91
2784	3002	6.017605	TCCACGTACGTCCTCTTCTAATTATC	60.018	42.308	19.94	0.00	0.00	1.75
2785	3003	6.238566	CCACGTACGTCCTCTTCTAATTATCA	60.239	42.308	19.94	0.00	0.00	2.15
2786	3004	7.191551	CACGTACGTCCTCTTCTAATTATCAA	58.808	38.462	19.94	0.00	0.00	2.57
2787	3005	7.861372	CACGTACGTCCTCTTCTAATTATCAAT	59.139	37.037	19.94	0.00	0.00	2.57
2788	3006	7.861372	ACGTACGTCCTCTTCTAATTATCAATG	59.139	37.037	16.72	0.00	0.00	2.82
2789	3007	7.326305	CGTACGTCCTCTTCTAATTATCAATGG	59.674	40.741	7.22	0.00	0.00	3.16
2852	3070	1.196012	GGTCCTCTCATCGGGTCTTT	58.804	55.000	0.00	0.00	0.00	2.52
2926	3146	3.576078	TTCCACCGATAAAGATGCCAT	57.424	42.857	0.00	0.00	0.00	4.40
2927	3147	3.126001	TCCACCGATAAAGATGCCATC	57.874	47.619	0.00	0.00	0.00	3.51
2928	3148	2.705658	TCCACCGATAAAGATGCCATCT	59.294	45.455	0.08	0.08	42.61	2.90
2939	3159	3.387962	AGATGCCATCTTTACCCTCTCA	58.612	45.455	0.08	0.00	35.76	3.27
3033	3814	7.839705	AGGACAGTGATATTCCTAGTTCAAGTA	59.160	37.037	0.00	0.00	38.03	2.24
3160	3941	8.153221	TGTATTTGTAGGGATCAAAAGGACTA	57.847	34.615	0.00	0.00	38.11	2.59
3191	3972	6.317391	GTGCTCATCATCATCATCATCATCAT	59.683	38.462	0.00	0.00	0.00	2.45
3192	3973	6.540189	TGCTCATCATCATCATCATCATCATC	59.460	38.462	0.00	0.00	0.00	2.92
3193	3974	6.540189	GCTCATCATCATCATCATCATCATCA	59.460	38.462	0.00	0.00	0.00	3.07
3194	3975	7.228308	GCTCATCATCATCATCATCATCATCAT	59.772	37.037	0.00	0.00	0.00	2.45
3195	3976	8.668510	TCATCATCATCATCATCATCATCATC	57.331	34.615	0.00	0.00	0.00	2.92
3196	3977	8.267183	TCATCATCATCATCATCATCATCATCA	58.733	33.333	0.00	0.00	0.00	3.07
3197	3978	9.064706	CATCATCATCATCATCATCATCATCAT	57.935	33.333	0.00	0.00	0.00	2.45
3198	3979	8.668510	TCATCATCATCATCATCATCATCATC	57.331	34.615	0.00	0.00	0.00	2.92
3199	3980	8.267183	TCATCATCATCATCATCATCATCATCA	58.733	33.333	0.00	0.00	0.00	3.07
3264	4046	9.060347	ACTAAATTGTAATAGGCATCACATCAG	57.940	33.333	0.00	0.00	0.00	2.90
3372	4154	5.793817	TCTAAACGTGCATCATAGGCATAT	58.206	37.500	0.00	0.00	44.11	1.78
3445	4227	5.123344	AGTTGTGTAGGCGAAAAATCATACC	59.877	40.000	0.00	0.00	0.00	2.73

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
166	176	9.849166	AAAATTATGAAATGACCGATTTTACGT	57.151	25.926	0.00	0.00	34.18	3.57
208	220	1.135774	GCGGAAATGTTCGGGACTTTC	60.136	52.381	0.00	0.00	0.00	2.62
492	561	0.593008	GGTGCCGAAAACAACCGAAC	60.593	55.000	0.00	0.00	0.00	3.95
648	721	2.668212	CCGAAGCAAAGCCGACCA	60.668	61.111	0.00	0.00	0.00	4.02
723	797	2.738147	ACGCTCGTGAATTTCTCCG	58.262	52.632	0.00	0.91	0.00	4.63
782	864	1.134818	TGTCCAAATCATCCGACGAGG	60.135	52.381	0.00	0.00	42.97	4.63
783	865	2.293677	TGTCCAAATCATCCGACGAG	57.706	50.000	0.00	0.00	0.00	4.18
784	866	2.979814	ATGTCCAAATCATCCGACGA	57.020	45.000	0.00	0.00	0.00	4.20
785	867	3.977427	TCTATGTCCAAATCATCCGACG	58.023	45.455	0.00	0.00	0.00	5.12
786	868	5.601662	TCTTCTATGTCCAAATCATCCGAC	58.398	41.667	0.00	0.00	0.00	4.79
787	869	5.869649	TCTTCTATGTCCAAATCATCCGA	57.130	39.130	0.00	0.00	0.00	4.55
788	870	6.925610	TTTCTTCTATGTCCAAATCATCCG	57.074	37.500	0.00	0.00	0.00	4.18
789	871	8.455903	TCATTTCTTCTATGTCCAAATCATCC	57.544	34.615	0.00	0.00	0.00	3.51
797	879	5.163163	CCCAGGATCATTTCTTCTATGTCCA	60.163	44.000	0.00	0.00	31.39	4.02
832	914	5.804639	AGATGCAATAACACTAGGTTGTCA	58.195	37.500	0.00	0.00	40.73	3.58
918	1009	5.825679	AGTAATTACTGCGGGCAAATAATCA	59.174	36.000	17.35	0.00	34.72	2.57
944	1035	5.351465	TGATGTTTCTTCTTATTCGAGTGCC	59.649	40.000	0.00	0.00	0.00	5.01
2132	2325	3.251972	GCAGCTATAATTGGCTTGACCTC	59.748	47.826	0.00	0.00	37.63	3.85
2224	2417	1.949847	ATCTCCCGGACGTCAAGCTG	61.950	60.000	18.91	4.39	0.00	4.24
2564	2768	6.775629	ACTTATTTGCAAGGAAAGACCAACTA	59.224	34.615	18.70	0.00	42.04	2.24
2595	2813	3.241022	CGTTATCGTCGTTCCGTACAAAC	60.241	47.826	0.00	0.00	0.00	2.93
2625	2843	5.450412	CCGTTATTCAAATCTCCAACATGGG	60.450	44.000	0.00	0.00	38.32	4.00
2636	2854	7.039882	TCTAGGAAGTCACCGTTATTCAAATC	58.960	38.462	0.00	0.00	34.73	2.17
2638	2856	6.014840	ACTCTAGGAAGTCACCGTTATTCAAA	60.015	38.462	0.00	0.00	34.73	2.69
2706	2924	6.825944	ACGCTAGTGATGATGTATGATAGT	57.174	37.500	10.99	0.00	0.00	2.12
2707	2925	6.529477	CCAACGCTAGTGATGATGTATGATAG	59.471	42.308	14.53	0.00	0.00	2.08
2784	3002	3.638160	ACCTACCAATGCTAATGCCATTG	59.362	43.478	0.00	7.04	37.40	2.82
2785	3003	3.914771	ACCTACCAATGCTAATGCCATT	58.085	40.909	0.00	0.00	38.71	3.16
2786	3004	3.600448	ACCTACCAATGCTAATGCCAT	57.400	42.857	0.00	0.00	38.71	4.40
2787	3005	3.380471	AACCTACCAATGCTAATGCCA	57.620	42.857	0.00	0.00	38.71	4.92
2788	3006	3.737972	GCAAACCTACCAATGCTAATGCC	60.738	47.826	0.00	0.00	38.71	4.40
2789	3007	3.447742	GCAAACCTACCAATGCTAATGC	58.552	45.455	0.00	0.00	35.93	3.56
2852	3070	4.125124	TGGTGGAATTCATGGGAGAAAA	57.875	40.909	7.93	0.00	0.00	2.29
2931	3151	9.844257	CTTGAGAATTAGAAATAATGAGAGGGT	57.156	33.333	0.00	0.00	0.00	4.34
2932	3152	9.844257	ACTTGAGAATTAGAAATAATGAGAGGG	57.156	33.333	0.00	0.00	0.00	4.30
2970	3212	2.228138	ACGTTGGTTCGCTCTACAAA	57.772	45.000	0.00	0.00	0.00	2.83
3033	3814	4.201950	GCAAGCGTCAATATCAAGTCCAAT	60.202	41.667	0.00	0.00	0.00	3.16
3050	3831	3.436704	TGAACTCTAGGAAAATGCAAGCG	59.563	43.478	0.00	0.00	0.00	4.68
3160	3941	7.005709	TGATGATGATGATGAGCACTTAGAT	57.994	36.000	0.00	0.00	0.00	1.98
3171	3952	8.442632	TGATGATGATGATGATGATGATGATG	57.557	34.615	0.00	0.00	0.00	3.07
3192	3973	9.603298	CCGATTACAATCACTTTTATGATGATG	57.397	33.333	3.07	0.00	39.32	3.07
3193	3974	8.292448	GCCGATTACAATCACTTTTATGATGAT	58.708	33.333	3.07	0.00	39.32	2.45
3194	3975	7.281999	TGCCGATTACAATCACTTTTATGATGA	59.718	33.333	3.07	0.00	39.32	2.92
3195	3976	7.376866	GTGCCGATTACAATCACTTTTATGATG	59.623	37.037	3.07	0.00	39.32	3.07
3196	3977	7.417612	GTGCCGATTACAATCACTTTTATGAT	58.582	34.615	3.07	0.00	41.20	2.45
3197	3978	6.183360	GGTGCCGATTACAATCACTTTTATGA	60.183	38.462	3.07	0.00	35.11	2.15
3198	3979	5.971202	GGTGCCGATTACAATCACTTTTATG	59.029	40.000	3.07	0.00	35.11	1.90
3199	3980	5.885912	AGGTGCCGATTACAATCACTTTTAT	59.114	36.000	3.07	0.00	35.11	1.40
3372	4154	6.876789	ACAACAACTATTTACCGATGTGATGA	59.123	34.615	0.00	0.00	0.00	2.92

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.