AutoCloner

Multiple sequence alignment - TraesCS2D01G015400

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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	TraesCS2D01G015400	chr2D	100.000	3325	0	0	1	3325	7526315	7522991	0.000000e+00	6141.0
1	TraesCS2D01G015400	chr2D	96.239	2765	38	4	627	3325	147381591	147378827	0.000000e+00	4470.0
2	TraesCS2D01G015400	chr2D	78.899	545	54	34	43	574	7302789	7302293	2.490000e-81	313.0
3	TraesCS2D01G015400	chr5D	97.511	2732	35	3	627	3325	430983990	430981259	0.000000e+00	4638.0
4	TraesCS2D01G015400	chr5D	94.467	994	37	4	625	1600	494245454	494244461	0.000000e+00	1515.0
5	TraesCS2D01G015400	chr6D	98.514	2624	33	1	627	3244	438338928	438336305	0.000000e+00	4625.0
6	TraesCS2D01G015400	chr6D	97.543	2645	38	6	627	3248	175423683	175426323	0.000000e+00	4499.0
7	TraesCS2D01G015400	chr6D	98.947	95	1	0	3210	3304	438336311	438336217	1.590000e-38	171.0
8	TraesCS2D01G015400	chr3D	96.942	2747	36	3	627	3325	532071287	532068541	0.000000e+00	4564.0
9	TraesCS2D01G015400	chr7D	96.834	2748	35	5	626	3325	526288224	526290967	0.000000e+00	4545.0
10	TraesCS2D01G015400	chr7D	97.137	2655	42	6	627	3248	540442133	540444786	0.000000e+00	4451.0
11	TraesCS2D01G015400	chr4D	97.657	2646	34	6	623	3244	391455568	391458209	0.000000e+00	4518.0
12	TraesCS2D01G015400	chr4D	93.630	989	38	5	627	1598	498718570	498717590	0.000000e+00	1454.0
13	TraesCS2D01G015400	chr4D	99.138	116	1	0	3210	3325	391458203	391458318	3.360000e-50	209.0
14	TraesCS2D01G015400	chr4D	98.901	91	1	0	3235	3325	498703199	498703109	2.650000e-36	163.0
15	TraesCS2D01G015400	chr1D	94.362	2696	73	17	627	3248	30073891	30071201	0.000000e+00	4063.0
16	TraesCS2D01G015400	chr3B	92.136	1653	62	27	1719	3325	470856769	470858399	0.000000e+00	2270.0
17	TraesCS2D01G015400	chr2B	91.160	1629	83	25	1719	3325	69353006	69354595	0.000000e+00	2154.0
18	TraesCS2D01G015400	chr2B	89.932	586	28	14	41	626	1361698	1362252	0.000000e+00	726.0
19	TraesCS2D01G015400	chr2B	95.122	41	2	0	3088	3128	750451984	750451944	7.700000e-07	65.8
20	TraesCS2D01G015400	chr2B	93.023	43	0	2	1	40	1361555	1361597	3.580000e-05	60.2
21	TraesCS2D01G015400	chr5A	93.648	677	31	9	2574	3248	647553084	647553750	0.000000e+00	1002.0

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	TraesCS2D01G015400	chr2D	7522991	7526315	3324	True	6141.0	6141	100.0000	1	3325	1	chr2D.!!$R2	3324
1	TraesCS2D01G015400	chr2D	147378827	147381591	2764	True	4470.0	4470	96.2390	627	3325	1	chr2D.!!$R3	2698
2	TraesCS2D01G015400	chr5D	430981259	430983990	2731	True	4638.0	4638	97.5110	627	3325	1	chr5D.!!$R1	2698
3	TraesCS2D01G015400	chr5D	494244461	494245454	993	True	1515.0	1515	94.4670	625	1600	1	chr5D.!!$R2	975
4	TraesCS2D01G015400	chr6D	175423683	175426323	2640	False	4499.0	4499	97.5430	627	3248	1	chr6D.!!$F1	2621
5	TraesCS2D01G015400	chr6D	438336217	438338928	2711	True	2398.0	4625	98.7305	627	3304	2	chr6D.!!$R1	2677
6	TraesCS2D01G015400	chr3D	532068541	532071287	2746	True	4564.0	4564	96.9420	627	3325	1	chr3D.!!$R1	2698
7	TraesCS2D01G015400	chr7D	526288224	526290967	2743	False	4545.0	4545	96.8340	626	3325	1	chr7D.!!$F1	2699
8	TraesCS2D01G015400	chr7D	540442133	540444786	2653	False	4451.0	4451	97.1370	627	3248	1	chr7D.!!$F2	2621
9	TraesCS2D01G015400	chr4D	391455568	391458318	2750	False	2363.5	4518	98.3975	623	3325	2	chr4D.!!$F1	2702
10	TraesCS2D01G015400	chr4D	498717590	498718570	980	True	1454.0	1454	93.6300	627	1598	1	chr4D.!!$R2	971
11	TraesCS2D01G015400	chr1D	30071201	30073891	2690	True	4063.0	4063	94.3620	627	3248	1	chr1D.!!$R1	2621
12	TraesCS2D01G015400	chr3B	470856769	470858399	1630	False	2270.0	2270	92.1360	1719	3325	1	chr3B.!!$F1	1606
13	TraesCS2D01G015400	chr2B	69353006	69354595	1589	False	2154.0	2154	91.1600	1719	3325	1	chr2B.!!$F1	1606
14	TraesCS2D01G015400	chr2B	1361555	1362252	697	False	393.1	726	91.4775	1	626	2	chr2B.!!$F2	625
15	TraesCS2D01G015400	chr5A	647553084	647553750	666	False	1002.0	1002	93.6480	2574	3248	1	chr5A.!!$F1	674

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
938	1094	0.039472	TGCTCTCACTCCTCTGCTCT	59.961	55.0	0.00	0.00	0.00	4.09	F
954	1110	1.152989	CTCTAGTACGAGCTCGCCGT	61.153	60.0	34.83	21.14	44.43	5.68	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2255	2427	0.321122	ACCCTTCTTTCAGCAGCTCG	60.321	55.000	0.0	0.0	0.0	5.03	R
3004	3243	2.988839	GCCCTCATCCTTGCCCACT	61.989	63.158	0.0	0.0	0.0	4.00	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	148	4.751600	CAGAAGACTGCACACAATTCTGTA	59.248	41.667	11.47	0.00	36.79	2.74
50	154	5.304778	ACTGCACACAATTCTGTACACATA	58.695	37.500	0.00	0.00	33.22	2.29
64	168	8.856153	TCTGTACACATACATAACCATGTTTT	57.144	30.769	0.00	0.00	42.98	2.43
110	214	4.309950	ACGGACGTGTTCCAGGCC	62.310	66.667	0.00	0.00	46.29	5.19
169	273	5.105877	CCTTAGTCCTCACTGTACATTTCGA	60.106	44.000	0.00	0.00	33.62	3.71
199	303	2.626743	GCAGACTATTTAGCCTACGGGA	59.373	50.000	0.00	0.00	33.58	5.14
208	312	4.208686	CCTACGGGAGTGCCGCTC	62.209	72.222	24.30	0.00	46.80	5.03
229	333	5.597594	GCTCCTGTACAGTAATAACCCTAGT	59.402	44.000	21.18	0.00	0.00	2.57
281	385	1.078426	GCGTGCTCTTGGGGTGTAT	60.078	57.895	0.00	0.00	0.00	2.29
325	429	3.008049	GGACCTGTGTGACCTTGAATAGT	59.992	47.826	0.00	0.00	0.00	2.12
341	445	2.969821	TAGTTGTTCTGGCATGGGTT	57.030	45.000	0.00	0.00	0.00	4.11
369	473	6.492007	TGCTCTCTCTTTTGTGATGAAATC	57.508	37.500	0.00	0.00	45.83	2.17
399	503	1.405105	TGTGCAGTTGAGAACTTTGCC	59.595	47.619	0.00	0.00	40.46	4.52
403	507	2.735823	CAGTTGAGAACTTTGCCTTGC	58.264	47.619	0.00	0.00	40.46	4.01
407	511	1.682854	TGAGAACTTTGCCTTGCTTGG	59.317	47.619	0.00	0.00	0.00	3.61
413	517	2.091102	TTTGCCTTGCTTGGAGCTGC	62.091	55.000	0.00	0.00	42.97	5.25
429	533	3.033184	AGCTGCTCTGCTATCTCTCTTT	58.967	45.455	0.00	0.00	42.10	2.52
430	534	3.068590	AGCTGCTCTGCTATCTCTCTTTC	59.931	47.826	0.00	0.00	42.10	2.62
431	535	3.181477	GCTGCTCTGCTATCTCTCTTTCA	60.181	47.826	0.00	0.00	0.00	2.69
435	539	5.595952	TGCTCTGCTATCTCTCTTTCATGTA	59.404	40.000	0.00	0.00	0.00	2.29
436	540	6.097412	TGCTCTGCTATCTCTCTTTCATGTAA	59.903	38.462	0.00	0.00	0.00	2.41
437	541	6.420604	GCTCTGCTATCTCTCTTTCATGTAAC	59.579	42.308	0.00	0.00	0.00	2.50
438	542	7.410120	TCTGCTATCTCTCTTTCATGTAACA	57.590	36.000	0.00	0.00	0.00	2.41
439	543	7.487484	TCTGCTATCTCTCTTTCATGTAACAG	58.513	38.462	0.00	0.00	0.00	3.16
440	544	7.340487	TCTGCTATCTCTCTTTCATGTAACAGA	59.660	37.037	0.00	0.00	0.00	3.41
441	545	8.016301	TGCTATCTCTCTTTCATGTAACAGAT	57.984	34.615	0.00	0.00	0.00	2.90
442	546	7.924947	TGCTATCTCTCTTTCATGTAACAGATG	59.075	37.037	0.00	0.00	0.00	2.90
443	547	7.095691	GCTATCTCTCTTTCATGTAACAGATGC	60.096	40.741	0.00	0.00	0.00	3.91
444	548	6.291648	TCTCTCTTTCATGTAACAGATGCT	57.708	37.500	0.00	0.00	0.00	3.79
445	549	6.336566	TCTCTCTTTCATGTAACAGATGCTC	58.663	40.000	0.00	0.00	0.00	4.26
446	550	6.154192	TCTCTCTTTCATGTAACAGATGCTCT	59.846	38.462	0.00	0.00	0.00	4.09
447	551	6.336566	TCTCTTTCATGTAACAGATGCTCTC	58.663	40.000	0.00	0.00	0.00	3.20
448	552	5.423015	TCTTTCATGTAACAGATGCTCTCC	58.577	41.667	0.00	0.00	0.00	3.71
449	553	3.443099	TCATGTAACAGATGCTCTCCG	57.557	47.619	0.00	0.00	0.00	4.63
450	554	3.023832	TCATGTAACAGATGCTCTCCGA	58.976	45.455	0.00	0.00	0.00	4.55
451	555	3.447229	TCATGTAACAGATGCTCTCCGAA	59.553	43.478	0.00	0.00	0.00	4.30
452	556	3.510388	TGTAACAGATGCTCTCCGAAG	57.490	47.619	0.00	0.00	0.00	3.79
453	557	2.197577	GTAACAGATGCTCTCCGAAGC	58.802	52.381	0.00	0.00	42.82	3.86
454	558	0.901124	AACAGATGCTCTCCGAAGCT	59.099	50.000	6.09	0.00	42.94	3.74
455	559	0.175302	ACAGATGCTCTCCGAAGCTG	59.825	55.000	0.00	0.00	42.94	4.24
456	560	0.459078	CAGATGCTCTCCGAAGCTGA	59.541	55.000	0.00	0.00	42.94	4.26
457	561	1.134877	CAGATGCTCTCCGAAGCTGAA	60.135	52.381	0.00	0.00	42.94	3.02
458	562	1.136695	AGATGCTCTCCGAAGCTGAAG	59.863	52.381	0.00	0.00	42.94	3.02
459	563	0.901124	ATGCTCTCCGAAGCTGAAGT	59.099	50.000	0.00	0.00	42.94	3.01
460	564	0.681733	TGCTCTCCGAAGCTGAAGTT	59.318	50.000	0.00	0.00	42.94	2.66
461	565	1.337260	TGCTCTCCGAAGCTGAAGTTC	60.337	52.381	0.00	0.00	42.94	3.01
462	566	1.337260	GCTCTCCGAAGCTGAAGTTCA	60.337	52.381	5.25	5.25	39.27	3.18
463	567	2.676463	GCTCTCCGAAGCTGAAGTTCAT	60.676	50.000	5.91	0.00	39.27	2.57
575	679	4.655649	TGCCTCTTACAGTATCCATGTGAT	59.344	41.667	0.00	0.00	37.49	3.06
603	707	4.687483	CGATTTGCCAGAAATTTTGAGCTT	59.313	37.500	0.00	0.00	0.00	3.74
712	817	1.884579	TCTCAGAAAGCTACCGAACGT	59.115	47.619	0.00	0.00	0.00	3.99
848	954	1.933115	TAACGGCCGTTAGTCGACCC	61.933	60.000	39.67	3.93	38.87	4.46
938	1094	0.039472	TGCTCTCACTCCTCTGCTCT	59.961	55.000	0.00	0.00	0.00	4.09
954	1110	1.152989	CTCTAGTACGAGCTCGCCGT	61.153	60.000	34.83	21.14	44.43	5.68
1082	1238	5.727279	TGGACATGGGACTTATGGTAAGTTA	59.273	40.000	0.00	0.00	0.00	2.24
1151	1319	3.346315	CCATGGATGTTGCTGAGTGTAA	58.654	45.455	5.56	0.00	0.00	2.41
1358	1527	7.206687	CAGTGTTTGTTGGTTATTATGGTTGT	58.793	34.615	0.00	0.00	0.00	3.32
2209	2381	3.351740	TGAAGGCTGTTGAAGTTGACAA	58.648	40.909	0.00	0.00	0.00	3.18
2255	2427	1.006922	GCTTGAGCTTGTGGTTGCC	60.007	57.895	0.00	0.00	38.21	4.52
3004	3243	7.944554	GGGAAGGTCATTCATGGAGATAATTAA	59.055	37.037	0.00	0.00	39.91	1.40
3076	3315	0.181587	TGGGTCCGTTTCTTTGAGCA	59.818	50.000	0.00	0.00	0.00	4.26

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
37	40	9.461312	AAACATGGTTATGTATGTGTACAGAAT	57.539	29.630	0.00	0.00	46.54	2.40
38	41	8.856153	AAACATGGTTATGTATGTGTACAGAA	57.144	30.769	0.00	0.00	46.54	3.02
64	168	2.224523	ACGATCCCTGCTTGTCAGAAAA	60.225	45.455	0.00	0.00	45.72	2.29
138	242	2.114616	AGTGAGGACTAAGGATGCAGG	58.885	52.381	0.00	0.00	0.00	4.85
169	273	2.521958	AAATAGTCTGCTGCCGCCGT	62.522	55.000	0.00	0.00	34.43	5.68
199	303	0.611062	TACTGTACAGGAGCGGCACT	60.611	55.000	26.12	5.03	0.00	4.40
208	312	6.158023	CCACTAGGGTTATTACTGTACAGG	57.842	45.833	26.12	9.07	0.00	4.00
229	333	1.072965	TGGCATGTACACATCACACCA	59.927	47.619	0.00	0.00	33.61	4.17
238	342	0.811281	GAAGGCCTTGGCATGTACAC	59.189	55.000	26.25	0.00	0.00	2.90
281	385	1.596752	AACACATGGCGCGACTCAA	60.597	52.632	15.80	0.00	0.00	3.02
325	429	1.786937	ACAAACCCATGCCAGAACAA	58.213	45.000	0.00	0.00	0.00	2.83
341	445	5.589855	TCATCACAAAAGAGAGAGCAAACAA	59.410	36.000	0.00	0.00	0.00	2.83
369	473	3.740832	TCTCAACTGCACAAATACTCACG	59.259	43.478	0.00	0.00	0.00	4.35
399	503	1.924320	GCAGAGCAGCTCCAAGCAAG	61.924	60.000	19.40	2.06	45.56	4.01
403	507	1.413445	AGATAGCAGAGCAGCTCCAAG	59.587	52.381	19.40	10.50	45.26	3.61
407	511	2.233271	AGAGAGATAGCAGAGCAGCTC	58.767	52.381	15.25	15.25	45.26	4.09
413	517	7.487484	TGTTACATGAAAGAGAGATAGCAGAG	58.513	38.462	0.00	0.00	0.00	3.35
439	543	1.134848	ACTTCAGCTTCGGAGAGCATC	60.135	52.381	0.00	0.00	38.43	3.91
440	544	0.901124	ACTTCAGCTTCGGAGAGCAT	59.099	50.000	0.00	0.00	38.43	3.79
441	545	0.681733	AACTTCAGCTTCGGAGAGCA	59.318	50.000	0.00	0.00	38.43	4.26
442	546	1.337260	TGAACTTCAGCTTCGGAGAGC	60.337	52.381	0.00	0.00	38.43	4.09
443	547	2.732412	TGAACTTCAGCTTCGGAGAG	57.268	50.000	0.00	0.00	38.43	3.20
444	548	3.685139	AATGAACTTCAGCTTCGGAGA	57.315	42.857	0.00	0.00	0.00	3.71
445	549	3.748048	TCAAATGAACTTCAGCTTCGGAG	59.252	43.478	0.00	0.00	0.00	4.63
446	550	3.738982	TCAAATGAACTTCAGCTTCGGA	58.261	40.909	0.00	0.00	0.00	4.55
447	551	4.488126	TTCAAATGAACTTCAGCTTCGG	57.512	40.909	0.00	0.00	0.00	4.30
459	563	7.918033	TGCTAAAACGATCAAAGTTCAAATGAA	59.082	29.630	0.00	0.00	0.00	2.57
460	564	7.421599	TGCTAAAACGATCAAAGTTCAAATGA	58.578	30.769	0.00	0.00	0.00	2.57
461	565	7.621832	TGCTAAAACGATCAAAGTTCAAATG	57.378	32.000	0.00	0.00	0.00	2.32
462	566	7.867403	ACATGCTAAAACGATCAAAGTTCAAAT	59.133	29.630	0.00	0.00	0.00	2.32
463	567	7.199766	ACATGCTAAAACGATCAAAGTTCAAA	58.800	30.769	0.00	0.00	0.00	2.69
510	614	0.251341	GGACAGCCTTCCCACATGTT	60.251	55.000	0.00	0.00	0.00	2.71
522	626	1.327303	TTGTTTCCACATGGACAGCC	58.673	50.000	0.00	0.00	45.39	4.85
545	649	7.618019	TGGATACTGTAAGAGGCAGATAAAT	57.382	36.000	0.00	0.00	37.43	1.40
546	650	7.071196	ACATGGATACTGTAAGAGGCAGATAAA	59.929	37.037	0.00	0.00	37.43	1.40
575	679	3.872511	AATTTCTGGCAAATCGCATGA	57.127	38.095	0.00	0.00	45.17	3.07
580	684	4.240096	AGCTCAAAATTTCTGGCAAATCG	58.760	39.130	10.36	0.00	0.00	3.34
603	707	7.016153	TCCTGGTTCTCAAGCTCTAATTTAA	57.984	36.000	0.00	0.00	0.00	1.52
615	719	5.755409	TGCTATTTACTCCTGGTTCTCAA	57.245	39.130	0.00	0.00	0.00	3.02
616	720	5.957771	ATGCTATTTACTCCTGGTTCTCA	57.042	39.130	0.00	0.00	0.00	3.27
736	841	0.244450	CGCTAGTCACCACGGGTTTA	59.756	55.000	0.00	0.00	31.02	2.01
744	850	2.417651	CGGGTTAAATCGCTAGTCACCA	60.418	50.000	0.00	0.00	0.00	4.17
938	1094	2.520039	CGACGGCGAGCTCGTACTA	61.520	63.158	34.46	0.00	41.22	1.82
982	1138	2.257409	ATTGCGGCAAGGAGGTCGAT	62.257	55.000	21.11	0.00	38.35	3.59
1082	1238	1.569072	CCCTAACCCTAGGTGGCAAAT	59.431	52.381	8.29	0.00	43.08	2.32
1151	1319	4.717233	ATCACACACACAACAACAACAT	57.283	36.364	0.00	0.00	0.00	2.71
1358	1527	1.149288	AGTGGTGTCTGGTTCCTCCTA	59.851	52.381	0.00	0.00	37.07	2.94
2091	2263	0.325933	TCCATCTGCACCTCCAACAG	59.674	55.000	0.00	0.00	0.00	3.16
2209	2381	6.176896	GCCTTCTCCTTCTTAAGAACATCTT	58.823	40.000	13.99	0.00	40.35	2.40
2255	2427	0.321122	ACCCTTCTTTCAGCAGCTCG	60.321	55.000	0.00	0.00	0.00	5.03
3004	3243	2.988839	GCCCTCATCCTTGCCCACT	61.989	63.158	0.00	0.00	0.00	4.00
3076	3315	9.334947	CCAAATCTCACAAATATCAGTCATAGT	57.665	33.333	0.00	0.00	0.00	2.12

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.