AutoCloner

Multiple sequence alignment - TraesCS7B01G049200

Loading Multiple Alignment...

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	TraesCS7B01G049200	chr7B	100.000	5851	0	0	1	5851	49190255	49184405	0.000000e+00	10805.0
1	TraesCS7B01G049200	chr7B	84.138	1387	110	52	1328	2636	49026862	49028216	0.000000e+00	1242.0
2	TraesCS7B01G049200	chr7B	90.604	596	53	1	3527	4119	49033787	49034382	0.000000e+00	787.0
3	TraesCS7B01G049200	chr7B	92.667	450	29	2	2665	3114	153181759	153182204	0.000000e+00	645.0
4	TraesCS7B01G049200	chr7B	90.222	450	41	1	2665	3114	42360439	42359993	8.450000e-163	584.0
5	TraesCS7B01G049200	chr7B	85.660	523	63	6	4156	4672	49034380	49034896	1.850000e-149	540.0
6	TraesCS7B01G049200	chr7B	88.354	395	29	14	851	1241	49026292	49026673	5.340000e-125	459.0
7	TraesCS7B01G049200	chr7B	80.038	531	63	32	106	607	49025604	49026120	2.590000e-93	353.0
8	TraesCS7B01G049200	chr7B	82.917	240	40	1	5418	5656	50680142	50680381	1.280000e-51	215.0
9	TraesCS7B01G049200	chr7B	91.525	59	2	1	2818	2876	49028247	49028302	1.750000e-10	78.7
10	TraesCS7B01G049200	chr7D	94.021	3044	132	20	2830	5850	95062875	95059859	0.000000e+00	4567.0
11	TraesCS7B01G049200	chr7D	93.096	1376	43	24	1315	2641	95064680	95063308	0.000000e+00	1967.0
12	TraesCS7B01G049200	chr7D	82.685	1646	143	77	964	2544	94936529	94938097	0.000000e+00	1330.0
13	TraesCS7B01G049200	chr7D	84.773	926	54	34	3	857	95066058	95065149	0.000000e+00	848.0
14	TraesCS7B01G049200	chr7D	81.542	856	92	26	3258	4086	94938696	94939512	0.000000e+00	645.0
15	TraesCS7B01G049200	chr7D	87.726	497	40	9	4153	4649	94939510	94939985	1.420000e-155	560.0
16	TraesCS7B01G049200	chr7D	88.836	421	44	1	3669	4086	94796895	94797315	1.120000e-141	514.0
17	TraesCS7B01G049200	chr7D	85.380	513	48	9	4153	4656	94797313	94797807	1.880000e-139	507.0
18	TraesCS7B01G049200	chr7D	95.221	272	10	1	994	1265	95065080	95064812	1.510000e-115	427.0
19	TraesCS7B01G049200	chr7D	96.257	187	7	0	2659	2845	95063323	95063137	2.050000e-79	307.0
20	TraesCS7B01G049200	chr7D	84.825	257	37	2	5401	5656	96030475	96030730	2.090000e-64	257.0
21	TraesCS7B01G049200	chr7D	84.706	255	38	1	5403	5656	95147579	95147833	2.710000e-63	254.0
22	TraesCS7B01G049200	chr7D	85.366	246	32	4	5402	5646	96081465	96081707	9.730000e-63	252.0
23	TraesCS7B01G049200	chr7D	76.161	646	49	59	143	764	94935890	94936454	5.860000e-60	243.0
24	TraesCS7B01G049200	chr7D	87.192	203	22	3	974	1174	252000832	252000632	1.640000e-55	228.0
25	TraesCS7B01G049200	chr7D	93.525	139	8	1	3486	3624	94796752	94796889	7.690000e-49	206.0
26	TraesCS7B01G049200	chr7D	80.078	256	30	12	2316	2554	94793245	94793496	2.800000e-38	171.0
27	TraesCS7B01G049200	chr7D	85.849	106	15	0	1591	1696	606302100	606302205	4.790000e-21	113.0
28	TraesCS7B01G049200	chr7D	93.333	45	3	0	1263	1307	95064750	95064706	3.780000e-07	67.6
29	TraesCS7B01G049200	chr7D	100.000	30	0	0	3230	3259	406336418	406336447	8.190000e-04	56.5
30	TraesCS7B01G049200	chr7A	87.853	2659	158	75	6	2553	98737101	98734497	0.000000e+00	2968.0
31	TraesCS7B01G049200	chr7A	91.630	1840	105	15	3274	5073	98733865	98732035	0.000000e+00	2499.0
32	TraesCS7B01G049200	chr7A	85.170	1679	139	54	925	2544	98098143	98099770	0.000000e+00	1620.0
33	TraesCS7B01G049200	chr7A	92.574	808	37	11	5064	5851	98731852	98731048	0.000000e+00	1138.0
34	TraesCS7B01G049200	chr7A	84.493	1135	88	47	1464	2544	98545933	98547033	0.000000e+00	1040.0
35	TraesCS7B01G049200	chr7A	94.852	641	29	2	2576	3215	98734503	98733866	0.000000e+00	998.0
36	TraesCS7B01G049200	chr7A	83.521	886	105	27	3258	4119	98547632	98548500	0.000000e+00	789.0
37	TraesCS7B01G049200	chr7A	81.084	1015	81	53	232	1219	98544613	98545543	0.000000e+00	708.0
38	TraesCS7B01G049200	chr7A	88.200	500	53	2	4156	4649	98102377	98102876	5.050000e-165	592.0
39	TraesCS7B01G049200	chr7A	88.000	500	47	4	4156	4649	98548498	98548990	3.930000e-161	579.0
40	TraesCS7B01G049200	chr7A	83.968	499	52	20	3328	3803	98101606	98102099	2.490000e-123	453.0
41	TraesCS7B01G049200	chr7A	82.302	582	44	31	232	802	98097563	98098096	3.220000e-122	449.0
42	TraesCS7B01G049200	chr7A	86.316	285	36	1	3838	4119	98102095	98102379	2.050000e-79	307.0
43	TraesCS7B01G049200	chr7A	88.079	151	16	1	1306	1456	98545667	98545815	1.680000e-40	178.0
44	TraesCS7B01G049200	chr7A	84.868	152	13	7	3024	3167	98547316	98547465	1.700000e-30	145.0
45	TraesCS7B01G049200	chr4A	92.430	819	40	8	1904	2712	650174612	650173806	0.000000e+00	1149.0
46	TraesCS7B01G049200	chr4A	92.000	450	33	1	2665	3114	670379070	670378624	3.850000e-176	628.0
47	TraesCS7B01G049200	chr4A	84.559	272	39	3	5401	5670	621741087	621740817	3.480000e-67	267.0
48	TraesCS7B01G049200	chr6B	92.444	450	31	1	2665	3114	672451863	672452309	1.780000e-179	640.0
49	TraesCS7B01G049200	chr6B	87.603	121	12	3	1056	1176	667074941	667074824	2.840000e-28	137.0
50	TraesCS7B01G049200	chr6B	96.774	31	1	0	3230	3260	503536350	503536320	1.100000e-02	52.8
51	TraesCS7B01G049200	chr6A	89.633	463	32	7	2665	3114	437701811	437701352	5.080000e-160	575.0
52	TraesCS7B01G049200	chr6A	90.909	110	9	1	1056	1165	590079124	590079016	4.720000e-31	147.0
53	TraesCS7B01G049200	chr1B	79.245	477	65	16	2185	2637	661036638	661037104	9.530000e-78	302.0
54	TraesCS7B01G049200	chr1B	92.857	70	5	0	2665	2734	186142714	186142783	1.040000e-17	102.0
55	TraesCS7B01G049200	chr5B	84.559	272	40	2	5401	5670	690319082	690319353	9.660000e-68	268.0
56	TraesCS7B01G049200	chr5B	100.000	29	0	0	3230	3258	21155301	21155273	3.000000e-03	54.7
57	TraesCS7B01G049200	chr1D	80.451	266	31	8	974	1223	427771827	427772087	3.600000e-42	183.0
58	TraesCS7B01G049200	chr1D	85.143	175	15	6	1491	1654	429718781	429718955	1.010000e-37	169.0
59	TraesCS7B01G049200	chr1A	78.417	278	35	12	971	1232	585036752	585036484	2.180000e-34	158.0
60	TraesCS7B01G049200	chr1A	84.177	158	15	5	1491	1638	527184808	527184965	1.700000e-30	145.0
61	TraesCS7B01G049200	chr6D	80.612	196	32	6	1511	1705	441622695	441622505	4.720000e-31	147.0
62	TraesCS7B01G049200	chr3A	100.000	31	0	0	3627	3657	714093567	714093597	2.280000e-04	58.4
63	TraesCS7B01G049200	chr3A	100.000	30	0	0	3231	3260	41615199	41615228	8.190000e-04	56.5
64	TraesCS7B01G049200	chr3A	100.000	29	0	0	3231	3259	41615134	41615106	3.000000e-03	54.7
65	TraesCS7B01G049200	chr5D	100.000	28	0	0	3232	3259	461621589	461621616	1.100000e-02	52.8
66	TraesCS7B01G049200	chr4D	100.000	28	0	0	3230	3257	6774285	6774312	1.100000e-02	52.8
67	TraesCS7B01G049200	chr3D	100.000	28	0	0	3232	3259	477826621	477826648	1.100000e-02	52.8
68	TraesCS7B01G049200	chr2A	100.000	28	0	0	400	427	300817296	300817323	1.100000e-02	52.8

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	TraesCS7B01G049200	chr7B	49184405	49190255	5850	True	10805.000000	10805	100.00000	1	5851	1	chr7B.!!$R2	5850
1	TraesCS7B01G049200	chr7B	49033787	49034896	1109	False	663.500000	787	88.13200	3527	4672	2	chr7B.!!$F4	1145
2	TraesCS7B01G049200	chr7B	49025604	49028302	2698	False	533.175000	1242	86.01375	106	2876	4	chr7B.!!$F3	2770
3	TraesCS7B01G049200	chr7D	95059859	95066058	6199	True	1363.933333	4567	92.78350	3	5850	6	chr7D.!!$R2	5847
4	TraesCS7B01G049200	chr7D	94935890	94939985	4095	False	694.500000	1330	82.02850	143	4649	4	chr7D.!!$F7	4506
5	TraesCS7B01G049200	chr7D	94793245	94797807	4562	False	349.500000	514	86.95475	2316	4656	4	chr7D.!!$F6	2340
6	TraesCS7B01G049200	chr7A	98731048	98737101	6053	True	1900.750000	2968	91.72725	6	5851	4	chr7A.!!$R1	5845
7	TraesCS7B01G049200	chr7A	98097563	98102876	5313	False	684.200000	1620	85.19120	232	4649	5	chr7A.!!$F1	4417
8	TraesCS7B01G049200	chr7A	98544613	98548990	4377	False	573.166667	1040	85.00750	232	4649	6	chr7A.!!$F2	4417
9	TraesCS7B01G049200	chr4A	650173806	650174612	806	True	1149.000000	1149	92.43000	1904	2712	1	chr4A.!!$R2	808

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	Hairpin	End Stability	Orientation
398	468	0.040067	GTGGTTTGGCTGCTTCTTCG	60.040	55.000	0.00	0.00	3.79	F
1174	1318	0.111061	TCATGGTCAGTGCCTGCTTT	59.889	50.000	0.00	0.00	3.51	F
1954	2504	0.951558	AGCCGAACAACAACCATGAC	59.048	50.000	0.00	0.00	3.06	F
2394	2978	1.068083	ATCTGCAGGTATGGCGACG	59.932	57.895	15.13	0.00	5.12	F
3678	7906	0.039618	TCATCAACCCTTTGCCCCTC	59.960	55.000	0.00	32.17	4.30	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
2274	2855	1.069636	GCAAGAGAAAGGACACAAGCG	60.070	52.381	0.00	0.00	4.68	R
2610	3407	2.930040	CTGCAACTAATAGGTGTGTCGG	59.070	50.000	7.21	34.77	4.79	R
3678	7906	0.831966	AGAGATGGAAGAGCAGCAGG	59.168	55.000	0.00	0.00	4.85	R
4122	8368	1.136774	GCAAATCGGCGGAAACTCC	59.863	57.895	7.21	0.00	3.85	R
5673	10221	0.035317	TGCCAAGCACATCGTCTTCT	59.965	50.000	0.00	31.71	2.85	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
24	25	6.767524	AAGGGAGTAGCATATATTCTCTCG	57.232	41.667	0.00	0.00	31.74	4.04
32	39	4.332543	AGCATATATTCTCTCGCTCTCTCG	59.667	45.833	0.00	0.00	0.00	4.04
49	56	1.263484	CTCGCATCACCATTCTGCATC	59.737	52.381	0.00	0.00	35.64	3.91
54	61	4.501071	GCATCACCATTCTGCATCTTTTT	58.499	39.130	0.00	0.00	35.96	1.94
55	62	4.328983	GCATCACCATTCTGCATCTTTTTG	59.671	41.667	0.00	0.00	35.96	2.44
58	65	7.485810	CATCACCATTCTGCATCTTTTTGATA	58.514	34.615	0.00	0.00	33.36	2.15
67	74	7.982224	TCTGCATCTTTTTGATATCAGTTCAG	58.018	34.615	5.39	6.51	36.83	3.02
166	175	4.974721	AAGCACCCCCAACTGCCG	62.975	66.667	0.00	0.00	33.57	5.69
199	210	4.351054	GTGGCAGGTGGGTCCCAG	62.351	72.222	12.21	0.10	32.34	4.45
209	220	2.692368	GGTCCCAGGGGCTCATCA	60.692	66.667	10.88	0.00	34.68	3.07
224	235	1.202568	TCATCATCCTGTAGCCTTGCG	60.203	52.381	0.00	0.00	0.00	4.85
347	387	0.396417	CACCTCCCCAAACAACACCA	60.396	55.000	0.00	0.00	0.00	4.17
398	468	0.040067	GTGGTTTGGCTGCTTCTTCG	60.040	55.000	0.00	0.00	0.00	3.79
400	470	0.668535	GGTTTGGCTGCTTCTTCGTT	59.331	50.000	0.00	0.00	0.00	3.85
529	615	2.807045	CGGAGTGTCGCTGTCTGC	60.807	66.667	0.00	0.00	38.57	4.26
553	639	2.881734	CCTCTGCCTTTCTTTTTCCCT	58.118	47.619	0.00	0.00	0.00	4.20
556	642	3.490348	TCTGCCTTTCTTTTTCCCTCTG	58.510	45.455	0.00	0.00	0.00	3.35
560	646	3.384789	GCCTTTCTTTTTCCCTCTGTGTT	59.615	43.478	0.00	0.00	0.00	3.32
567	653	0.391597	TTCCCTCTGTGTTCCGTGTC	59.608	55.000	0.00	0.00	0.00	3.67
740	840	4.589908	GGCAAGTTTTCCCTCTGATCTTA	58.410	43.478	0.00	0.00	0.00	2.10
741	841	4.637977	GGCAAGTTTTCCCTCTGATCTTAG	59.362	45.833	0.00	0.00	0.00	2.18
750	850	3.243704	CCCTCTGATCTTAGCTTCTTCCG	60.244	52.174	0.00	0.00	0.00	4.30
788	906	2.305927	CCCTAGCTTTCCCTTCTGTTGA	59.694	50.000	0.00	0.00	0.00	3.18
807	925	0.916086	AGTTCAGGTGGTGTTGGTGA	59.084	50.000	0.00	0.00	0.00	4.02
808	926	1.021968	GTTCAGGTGGTGTTGGTGAC	58.978	55.000	0.00	0.00	0.00	3.67
810	928	0.180171	TCAGGTGGTGTTGGTGACTG	59.820	55.000	0.00	0.00	0.00	3.51
1174	1318	0.111061	TCATGGTCAGTGCCTGCTTT	59.889	50.000	0.00	0.00	0.00	3.51
1180	1324	2.494059	GTCAGTGCCTGCTTTCACTTA	58.506	47.619	3.24	0.00	41.19	2.24
1184	1328	5.181245	GTCAGTGCCTGCTTTCACTTAATTA	59.819	40.000	3.24	0.00	41.19	1.40
1187	1331	4.800471	GTGCCTGCTTTCACTTAATTATGC	59.200	41.667	0.00	0.00	0.00	3.14
1190	1334	5.067023	GCCTGCTTTCACTTAATTATGCTCT	59.933	40.000	0.00	0.00	0.00	4.09
1193	1337	7.699812	CCTGCTTTCACTTAATTATGCTCTTTC	59.300	37.037	0.00	0.00	0.00	2.62
1228	1379	7.178712	AGAAACTTCATTCTGTTGTTAGTCG	57.821	36.000	0.00	0.00	38.22	4.18
1272	1548	8.729756	CAATTGTGGTTTCACTTATCAGTCATA	58.270	33.333	0.00	0.00	43.94	2.15
1276	1552	7.765819	TGTGGTTTCACTTATCAGTCATATGAG	59.234	37.037	5.42	0.00	43.94	2.90
1387	1745	4.168760	GAGTGTAAAACAATCTGCCATGC	58.831	43.478	0.57	0.00	39.81	4.06
1404	1762	4.082190	GCCATGCTCTGAAATGCATATCAT	60.082	41.667	0.00	0.00	46.65	2.45
1456	1824	5.573282	ACTCTTACAATGCGATGCGATATAC	59.427	40.000	0.00	0.00	0.00	1.47
1459	1827	7.309920	TCTTACAATGCGATGCGATATACTTA	58.690	34.615	0.00	0.00	0.00	2.24
1775	2324	9.463443	GTGTTAAAATATGGATGTTAATGAGGC	57.537	33.333	0.00	0.00	29.35	4.70
1912	2462	3.269347	GTGTGGCAGCACGTCGTT	61.269	61.111	0.00	0.00	0.00	3.85
1954	2504	0.951558	AGCCGAACAACAACCATGAC	59.048	50.000	0.00	0.00	0.00	3.06
2274	2855	1.672737	GGCTGCAGCAAACCCATTTAC	60.673	52.381	37.63	13.82	44.36	2.01
2394	2978	1.068083	ATCTGCAGGTATGGCGACG	59.932	57.895	15.13	0.00	0.00	5.12
2480	3091	6.151985	TGCACAGGAAGAAAAACTTTTACAGA	59.848	34.615	0.00	0.00	39.13	3.41
2610	3407	7.071572	TCCTTATCCCCTTACTGTATTTGGTAC	59.928	40.741	0.00	0.00	0.00	3.34
2646	3443	3.688673	AGTTGCAGAGCAGAGCTTAATTC	59.311	43.478	0.00	0.00	39.88	2.17
3017	4814	7.421530	AATACTGCTGTACAAGTTAACTGTG	57.578	36.000	9.34	11.74	0.00	3.66
3059	4856	9.329913	CTGCTGTACAAGTTAATGTTGTATTTC	57.670	33.333	13.50	8.26	41.28	2.17
3060	4857	8.841300	TGCTGTACAAGTTAATGTTGTATTTCA	58.159	29.630	13.50	8.41	41.28	2.69
3089	4886	7.416154	GTACTGCTGTACAAGTTTAATGTGA	57.584	36.000	24.20	0.00	46.06	3.58
3435	6030	4.946157	CAGCAAGAATCTCCATACCAAACT	59.054	41.667	0.00	0.00	0.00	2.66
3678	7906	0.039618	TCATCAACCCTTTGCCCCTC	59.960	55.000	0.00	0.00	32.17	4.30
3696	7939	0.829333	TCCTGCTGCTCTTCCATCTC	59.171	55.000	0.00	0.00	0.00	2.75
3923	8169	2.092538	CCAGCTCCATCAGAAGTGGATT	60.093	50.000	0.00	0.00	44.34	3.01
3995	8241	3.492102	AACACTATGTCTGGCACACTT	57.508	42.857	0.00	0.00	38.04	3.16
4047	8293	4.070716	AGAAGATCTTTTGGAGTGCACTG	58.929	43.478	27.27	8.86	0.00	3.66
4117	8363	0.250901	TCAGGGCTGCTTGAAAGGTC	60.251	55.000	0.00	0.00	0.00	3.85
4118	8364	0.251077	CAGGGCTGCTTGAAAGGTCT	60.251	55.000	0.00	0.00	0.00	3.85
4119	8365	0.251077	AGGGCTGCTTGAAAGGTCTG	60.251	55.000	0.00	0.00	0.00	3.51
4120	8366	0.538287	GGGCTGCTTGAAAGGTCTGT	60.538	55.000	0.00	0.00	0.00	3.41
4121	8367	0.877743	GGCTGCTTGAAAGGTCTGTC	59.122	55.000	0.00	0.00	0.00	3.51
4122	8368	0.514691	GCTGCTTGAAAGGTCTGTCG	59.485	55.000	0.00	0.00	0.00	4.35
4123	8369	1.151668	CTGCTTGAAAGGTCTGTCGG	58.848	55.000	0.00	0.00	0.00	4.79
4124	8370	0.756294	TGCTTGAAAGGTCTGTCGGA	59.244	50.000	0.00	0.00	0.00	4.55
4125	8371	1.270305	TGCTTGAAAGGTCTGTCGGAG	60.270	52.381	0.00	0.00	0.00	4.63
4126	8372	1.270358	GCTTGAAAGGTCTGTCGGAGT	60.270	52.381	0.00	0.00	0.00	3.85
4127	8373	2.807108	GCTTGAAAGGTCTGTCGGAGTT	60.807	50.000	0.00	0.00	0.00	3.01
4128	8374	3.467803	CTTGAAAGGTCTGTCGGAGTTT	58.532	45.455	0.00	0.00	0.00	2.66
4129	8375	3.107642	TGAAAGGTCTGTCGGAGTTTC	57.892	47.619	8.59	8.59	32.69	2.78
4130	8376	2.224209	TGAAAGGTCTGTCGGAGTTTCC	60.224	50.000	11.47	0.00	31.79	3.13
4140	8386	1.136774	GGAGTTTCCGCCGATTTGC	59.863	57.895	0.00	0.00	0.00	3.68
4232	8517	0.462789	ACATCCCGTTCGATGGTACC	59.537	55.000	4.43	4.43	43.34	3.34
4236	8521	2.182284	CGTTCGATGGTACCGGCA	59.818	61.111	7.57	0.00	0.00	5.69
4318	8603	4.759516	TTTCGGAAAGAATGGCTGTTAC	57.240	40.909	0.00	0.00	38.86	2.50
4417	8705	2.177016	TCCCTCCTCATGATACCGAGAA	59.823	50.000	0.00	0.00	0.00	2.87
4441	8729	8.491331	AAACATTCAAAATACTTGCAGTTTGT	57.509	26.923	0.00	0.00	35.54	2.83
4589	8889	2.005606	TTCCAAAGCTGCAGGGTGGA	62.006	55.000	17.12	5.98	36.59	4.02
4634	8934	6.152323	ACTTTGATGGTCTTCTCAATTCCATG	59.848	38.462	0.00	0.00	38.74	3.66
4888	9222	9.603189	AGTAATATTTAGGCTAGTCCACTACAT	57.397	33.333	0.00	0.04	37.29	2.29
4897	9231	5.221884	GGCTAGTCCACTACATACCTAGAGA	60.222	48.000	0.00	0.00	34.01	3.10
4902	9236	7.001674	AGTCCACTACATACCTAGAGAAGATG	58.998	42.308	0.00	0.00	0.00	2.90
4993	9327	2.659428	AGGGATTTCATGGCTTGTAGC	58.341	47.619	0.00	0.00	41.46	3.58
4996	9330	3.429410	GGGATTTCATGGCTTGTAGCAAC	60.429	47.826	0.67	0.00	44.75	4.17
5016	9350	4.625607	ACCTGTACTTTCTTTCTCCTGG	57.374	45.455	0.00	0.00	0.00	4.45
5055	9390	6.710295	AGCAAATATATGGCGTCTAATCACAA	59.290	34.615	0.00	0.00	0.00	3.33
5250	9780	6.344572	TGCTAAATGCTACAAACTACGATG	57.655	37.500	0.00	0.00	43.37	3.84
5278	9808	1.640428	GGTCGCATGATCGAAACTCA	58.360	50.000	0.00	0.00	40.43	3.41
5292	9822	3.193691	CGAAACTCAGAGATGTAGGTGGT	59.806	47.826	3.79	0.00	0.00	4.16
5316	9846	7.065923	GGTTTTTCAGTGACTAGGATGATAACC	59.934	40.741	0.00	6.23	33.47	2.85
5352	9882	5.801380	TGAAAAACCACCTACACCTATCTC	58.199	41.667	0.00	0.00	0.00	2.75
5369	9899	3.950087	TCTCGATTTTTGATCATGCGG	57.050	42.857	0.00	0.00	0.00	5.69
5377	9907	4.996434	GATCATGCGGCGGGGGAG	62.996	72.222	9.78	0.00	0.00	4.30
5388	9918	2.691252	GGGGGAGTGGGGAACGAT	60.691	66.667	0.00	0.00	0.00	3.73
5390	9920	2.590092	GGGAGTGGGGAACGATGG	59.410	66.667	0.00	0.00	0.00	3.51
5396	9933	0.249489	GTGGGGAACGATGGATCTCG	60.249	60.000	3.04	3.04	44.14	4.04
5461	9998	1.785041	CGATTGCCGGCTTGGGTATG	61.785	60.000	29.70	5.35	38.63	2.39
5467	10004	1.823899	CGGCTTGGGTATGGGCTTC	60.824	63.158	0.00	0.00	0.00	3.86
5491	10028	0.842635	GGTGAAGATCCATCCCTGCT	59.157	55.000	0.00	0.00	0.00	4.24
5578	10115	1.140407	CGTAGCGGCTTTCTTCCTCG	61.140	60.000	8.26	0.00	0.00	4.63
5673	10221	7.331026	ACGTCAGATTAAATCATCTTCAGGAA	58.669	34.615	0.00	0.00	30.50	3.36
5701	10250	4.802424	TGCTTGGCACGTTGTTTG	57.198	50.000	0.00	0.00	31.71	2.93
5702	10251	1.518133	TGCTTGGCACGTTGTTTGC	60.518	52.632	0.00	0.00	39.41	3.68
5703	10252	1.226945	GCTTGGCACGTTGTTTGCT	60.227	52.632	0.00	0.00	40.07	3.91
5705	10254	0.871163	CTTGGCACGTTGTTTGCTGG	60.871	55.000	0.00	0.00	40.07	4.85
5706	10255	1.315981	TTGGCACGTTGTTTGCTGGA	61.316	50.000	0.00	0.00	40.07	3.86
5707	10256	1.008538	GGCACGTTGTTTGCTGGAG	60.009	57.895	0.00	0.00	40.07	3.86
5708	10257	1.444119	GGCACGTTGTTTGCTGGAGA	61.444	55.000	0.00	0.00	40.07	3.71
5709	10258	0.380378	GCACGTTGTTTGCTGGAGAA	59.620	50.000	0.00	0.00	37.00	2.87

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	6.350612	GCGAGAGAATATATGCTACTCCCTTT	60.351	42.308	11.57	0.00	0.00	3.11
1	2	5.126384	GCGAGAGAATATATGCTACTCCCTT	59.874	44.000	11.57	0.00	0.00	3.95
24	25	1.202510	AGAATGGTGATGCGAGAGAGC	60.203	52.381	0.00	0.00	37.71	4.09
32	39	3.795623	AAAGATGCAGAATGGTGATGC	57.204	42.857	0.00	0.00	40.40	3.91
49	56	5.183713	TGTGGGCTGAACTGATATCAAAAAG	59.816	40.000	6.90	3.81	0.00	2.27
54	61	2.840038	ACTGTGGGCTGAACTGATATCA	59.160	45.455	5.07	5.07	0.00	2.15
55	62	3.550437	ACTGTGGGCTGAACTGATATC	57.450	47.619	0.00	0.00	0.00	1.63
58	65	3.788227	TTTACTGTGGGCTGAACTGAT	57.212	42.857	0.00	0.00	0.00	2.90
166	175	1.535204	CCACAACCCTCCAATGGCAC	61.535	60.000	0.00	0.00	0.00	5.01
199	210	0.036022	GCTACAGGATGATGAGCCCC	59.964	60.000	0.00	0.00	39.69	5.80
206	217	0.533755	GCGCAAGGCTACAGGATGAT	60.534	55.000	0.30	0.00	38.06	2.45
224	235	2.435059	GAGTGGAAGTGCTCGGGC	60.435	66.667	0.00	0.00	39.26	6.13
347	387	2.971598	CGCTTGGTGAGGTGGGGAT	61.972	63.158	0.00	0.00	0.00	3.85
398	468	1.107945	CGAGGAGGAGGAGGAAGAAC	58.892	60.000	0.00	0.00	0.00	3.01
400	470	0.256464	GACGAGGAGGAGGAGGAAGA	59.744	60.000	0.00	0.00	0.00	2.87
529	615	1.625511	AAAAGAAAGGCAGAGGCAGG	58.374	50.000	0.00	0.00	43.71	4.85
553	639	0.959553	GAGAGGACACGGAACACAGA	59.040	55.000	0.00	0.00	0.00	3.41
556	642	0.680061	AAGGAGAGGACACGGAACAC	59.320	55.000	0.00	0.00	0.00	3.32
560	646	1.827399	GCCAAAGGAGAGGACACGGA	61.827	60.000	0.00	0.00	0.00	4.69
567	653	0.605083	GCAAAAGGCCAAAGGAGAGG	59.395	55.000	5.01	0.00	36.11	3.69
637	730	2.033194	GGCCTTCAGGAACGAACCG	61.033	63.158	0.00	0.00	37.39	4.44
664	757	0.107752	GAGACGAGACTAGACGGGGT	60.108	60.000	0.00	0.00	0.00	4.95
704	799	2.365582	ACTTGCCGGTGGATTTGTATC	58.634	47.619	1.90	0.00	0.00	2.24
722	817	5.487131	AGAAGCTAAGATCAGAGGGAAAACT	59.513	40.000	0.00	0.00	0.00	2.66
723	818	5.739959	AGAAGCTAAGATCAGAGGGAAAAC	58.260	41.667	0.00	0.00	0.00	2.43
740	840	3.679083	CGAAAATACTCCCGGAAGAAGCT	60.679	47.826	0.73	0.00	0.00	3.74
741	841	2.608090	CGAAAATACTCCCGGAAGAAGC	59.392	50.000	0.73	0.00	0.00	3.86
750	850	3.794737	GGGACCCGAAAATACTCCC	57.205	57.895	0.00	0.00	33.97	4.30
788	906	0.916086	TCACCAACACCACCTGAACT	59.084	50.000	0.00	0.00	0.00	3.01
883	1027	0.247736	CAGCAAGAACGAGGCCTAGT	59.752	55.000	13.44	13.44	0.00	2.57
968	1112	2.666619	GCCAATTCAGAGCAACTTGACG	60.667	50.000	0.00	0.00	0.00	4.35
1110	1254	0.179020	CCAGAACCTTGAGGCACACA	60.179	55.000	0.00	0.00	39.32	3.72
1228	1379	3.526931	TTGACTAGCTGCAGGTGATAC	57.473	47.619	28.10	15.89	0.00	2.24
1276	1552	3.447204	GAGCAAACTCTCTGGAACAGCC	61.447	54.545	0.00	0.00	44.72	4.85
1438	1796	6.968131	AATAAGTATATCGCATCGCATTGT	57.032	33.333	0.00	0.00	0.00	2.71
1774	2313	4.847255	GCACGAGTTGAATGGTGC	57.153	55.556	3.06	3.06	45.52	5.01
1775	2324	1.069703	CACTGCACGAGTTGAATGGTG	60.070	52.381	0.00	0.00	29.75	4.17
1912	2462	1.275291	CGGTTGCTGAACTTCCTCCTA	59.725	52.381	0.00	0.00	32.15	2.94
2020	2570	4.429212	TGGTCGGACGACATGCCG	62.429	66.667	24.00	0.00	46.20	5.69
2022	2572	1.517257	CTCTGGTCGGACGACATGC	60.517	63.158	24.00	9.43	46.20	4.06
2025	2581	2.197605	TTGCTCTGGTCGGACGACA	61.198	57.895	24.00	10.94	46.20	4.35
2032	2588	2.743928	GCCCTGTTGCTCTGGTCG	60.744	66.667	0.00	0.00	33.97	4.79
2274	2855	1.069636	GCAAGAGAAAGGACACAAGCG	60.070	52.381	0.00	0.00	0.00	4.68
2394	2978	3.548818	GCGATGATGGAAGTAAATGCCAC	60.549	47.826	0.00	0.00	33.93	5.01
2499	3111	3.006859	AGGAAAATAAGGCCACTTTGCAC	59.993	43.478	5.01	0.00	38.14	4.57
2610	3407	2.930040	CTGCAACTAATAGGTGTGTCGG	59.070	50.000	7.21	0.00	34.77	4.79
2646	3443	3.312146	TGCTGTGCAACACCATAATATCG	59.688	43.478	0.00	0.00	45.67	2.92
2960	4757	6.003950	ACTCTGCATTAAACCTGTACAACAT	58.996	36.000	0.00	0.00	0.00	2.71
3011	4808	5.048083	CAGTGCATACCAAAATACCACAGTT	60.048	40.000	0.00	0.00	0.00	3.16
3017	4814	3.443681	ACAGCAGTGCATACCAAAATACC	59.556	43.478	19.20	0.00	0.00	2.73
3089	4886	5.560724	ACTCAGCAGTACATACCAAAACAT	58.439	37.500	0.00	0.00	0.00	2.71
3243	5837	2.843113	AGGTGTACTACTACCTCCGTCT	59.157	50.000	0.00	0.00	43.69	4.18
3331	5925	8.145122	CCCTTTAATGTAGGCTTGTTAACAAAA	58.855	33.333	20.89	7.25	35.15	2.44
3335	5929	6.829229	ACCCTTTAATGTAGGCTTGTTAAC	57.171	37.500	0.00	0.00	0.00	2.01
3435	6030	7.719871	ACAGTCTTAAGATAACTGCTTCCTA	57.280	36.000	18.09	0.00	43.30	2.94
3678	7906	0.831966	AGAGATGGAAGAGCAGCAGG	59.168	55.000	0.00	0.00	0.00	4.85
3911	8157	5.707298	GGTTTCTTGATGAATCCACTTCTGA	59.293	40.000	3.96	0.00	41.74	3.27
3923	8169	4.576053	CACAAGTCACTGGTTTCTTGATGA	59.424	41.667	15.84	0.00	39.39	2.92
3995	8241	5.294306	CAGTGAACTGCTTGTAACTCTTTGA	59.706	40.000	0.00	0.00	37.15	2.69
4047	8293	1.336240	GGCTCCAACTTTGATGTGTGC	60.336	52.381	0.00	0.00	0.00	4.57
4122	8368	1.136774	GCAAATCGGCGGAAACTCC	59.863	57.895	7.21	0.00	0.00	3.85
4123	8369	4.765611	GCAAATCGGCGGAAACTC	57.234	55.556	7.21	0.00	0.00	3.01
4133	8379	5.639506	AGATATACAAGAATCCCGCAAATCG	59.360	40.000	0.00	0.00	38.08	3.34
4134	8380	6.650807	TGAGATATACAAGAATCCCGCAAATC	59.349	38.462	0.00	0.00	0.00	2.17
4135	8381	6.533730	TGAGATATACAAGAATCCCGCAAAT	58.466	36.000	0.00	0.00	0.00	2.32
4136	8382	5.924356	TGAGATATACAAGAATCCCGCAAA	58.076	37.500	0.00	0.00	0.00	3.68
4137	8383	5.541845	CTGAGATATACAAGAATCCCGCAA	58.458	41.667	0.00	0.00	0.00	4.85
4138	8384	4.561530	GCTGAGATATACAAGAATCCCGCA	60.562	45.833	0.00	0.00	0.00	5.69
4139	8385	3.929610	GCTGAGATATACAAGAATCCCGC	59.070	47.826	0.00	0.00	0.00	6.13
4140	8386	5.139435	TGCTGAGATATACAAGAATCCCG	57.861	43.478	0.00	0.00	0.00	5.14
4141	8387	5.931146	CACTGCTGAGATATACAAGAATCCC	59.069	44.000	0.00	0.00	0.00	3.85
4142	8388	6.423302	CACACTGCTGAGATATACAAGAATCC	59.577	42.308	0.00	0.00	0.00	3.01
4143	8389	6.073873	GCACACTGCTGAGATATACAAGAATC	60.074	42.308	0.00	0.00	40.96	2.52
4144	8390	5.757320	GCACACTGCTGAGATATACAAGAAT	59.243	40.000	0.00	0.00	40.96	2.40
4145	8391	5.111989	GCACACTGCTGAGATATACAAGAA	58.888	41.667	0.00	0.00	40.96	2.52
4146	8392	4.686972	GCACACTGCTGAGATATACAAGA	58.313	43.478	0.00	0.00	40.96	3.02
4232	8517	1.673760	CATCAAGTTTTGTCGTGCCG	58.326	50.000	0.00	0.00	0.00	5.69
4236	8521	3.403038	AGCTAGCATCAAGTTTTGTCGT	58.597	40.909	18.83	0.00	0.00	4.34
4318	8603	2.038295	AGGCTCTCAGAAGGACAAACAG	59.962	50.000	0.00	0.00	0.00	3.16
4378	8666	2.280628	GGAGCAGCATTGTACTACCAC	58.719	52.381	0.00	0.00	0.00	4.16
4441	8729	2.158827	TGTCTAGAGTTGCTTGCAACCA	60.159	45.455	28.02	17.73	35.79	3.67
4589	8889	4.015084	AGTTGCAGCTGCTAGAATTGAAT	58.985	39.130	36.61	10.79	42.66	2.57
4634	8934	7.103641	TGACTGATGTCCTTACCACTTTTATC	58.896	38.462	0.00	0.00	42.28	1.75
4888	9222	9.352191	GAATAACTGTACCATCTTCTCTAGGTA	57.648	37.037	0.00	0.00	35.62	3.08
4897	9231	6.619852	ACCCATAGGAATAACTGTACCATCTT	59.380	38.462	0.00	0.00	36.73	2.40
4993	9327	4.757149	CCAGGAGAAAGAAAGTACAGGTTG	59.243	45.833	0.00	0.00	0.00	3.77
4996	9330	3.583086	TCCCAGGAGAAAGAAAGTACAGG	59.417	47.826	0.00	0.00	0.00	4.00
5016	9350	0.903942	TTTGCTTCCATTGCCCATCC	59.096	50.000	0.00	0.00	0.00	3.51
5055	9390	3.629398	CCAGAGTTTGTGTTTTCAGAGCT	59.371	43.478	0.00	0.00	0.00	4.09
5094	9622	4.963276	TTTGAGTTCCAGAGTTTGTGTG	57.037	40.909	0.00	0.00	0.00	3.82
5170	9700	6.434028	TCAGGTCAGGTTTATTTCCAGAATTG	59.566	38.462	0.00	0.00	0.00	2.32
5278	9808	5.071788	TCACTGAAAAACCACCTACATCTCT	59.928	40.000	0.00	0.00	0.00	3.10
5292	9822	6.816640	CGGTTATCATCCTAGTCACTGAAAAA	59.183	38.462	0.00	0.00	0.00	1.94
5352	9882	1.114842	CGCCGCATGATCAAAAATCG	58.885	50.000	0.00	0.00	0.00	3.34
5377	9907	0.249489	CGAGATCCATCGTTCCCCAC	60.249	60.000	0.00	0.00	37.91	4.61
5378	9908	1.399744	CCGAGATCCATCGTTCCCCA	61.400	60.000	3.97	0.00	41.12	4.96
5396	9933	5.569413	CAACCAAGTTAATAACTGATCGCC	58.431	41.667	6.41	0.00	41.91	5.54
5448	9985	3.358932	AAGCCCATACCCAAGCCGG	62.359	63.158	0.00	0.00	0.00	6.13
5461	9998	0.250513	ATCTTCACCTGACGAAGCCC	59.749	55.000	0.00	0.00	39.80	5.19
5467	10004	1.202580	GGGATGGATCTTCACCTGACG	60.203	57.143	0.00	0.00	0.00	4.35
5491	10028	1.300963	GCTGCAGGAGTCCATGGAA	59.699	57.895	18.20	0.00	0.00	3.53
5593	10130	2.103771	AGTGATGAATGGCTACGATGCT	59.896	45.455	0.00	0.00	0.00	3.79
5673	10221	0.035317	TGCCAAGCACATCGTCTTCT	59.965	50.000	0.00	0.00	31.71	2.85
5675	10223	4.798433	TGCCAAGCACATCGTCTT	57.202	50.000	0.00	0.00	31.71	3.01
5700	10249	3.420893	CCAGGTACATTTTTCTCCAGCA	58.579	45.455	0.00	0.00	0.00	4.41
5701	10250	2.164422	GCCAGGTACATTTTTCTCCAGC	59.836	50.000	0.00	0.00	0.00	4.85
5702	10251	3.420893	TGCCAGGTACATTTTTCTCCAG	58.579	45.455	0.00	0.00	0.00	3.86
5703	10252	3.517296	TGCCAGGTACATTTTTCTCCA	57.483	42.857	0.00	0.00	0.00	3.86
5705	10254	4.462483	TGGATTGCCAGGTACATTTTTCTC	59.538	41.667	0.00	0.00	39.92	2.87
5706	10255	4.415596	TGGATTGCCAGGTACATTTTTCT	58.584	39.130	0.00	0.00	39.92	2.52
5707	10256	4.799564	TGGATTGCCAGGTACATTTTTC	57.200	40.909	0.00	0.00	39.92	2.29

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.