AutoCloner

Multiple sequence alignment - TraesCS2A01G568600

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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	TraesCS2A01G568600	chr2A	100.000	4078	0	0	1	4078	766850101	766846024	0.000000e+00	7531.0
1	TraesCS2A01G568600	chr2A	90.909	396	33	3	184	578	767444157	767444550	2.790000e-146	529.0
2	TraesCS2A01G568600	chr2A	85.526	304	37	6	1984	2283	767131471	767131771	1.100000e-80	311.0
3	TraesCS2A01G568600	chr2A	94.737	133	7	0	1255	1387	767463301	767463433	1.490000e-49	207.0
4	TraesCS2A01G568600	chr2A	84.553	123	11	3	3580	3701	767551912	767552027	9.260000e-22	115.0
5	TraesCS2A01G568600	chr2A	84.694	98	15	0	3705	3802	767552063	767552160	9.330000e-17	99.0
6	TraesCS2A01G568600	chr2A	96.875	32	1	0	688	719	773381090	773381121	2.000000e-03	54.7
7	TraesCS2A01G568600	chr2D	94.355	3118	82	31	964	4071	641882126	641879093	0.000000e+00	4697.0
8	TraesCS2A01G568600	chr2D	94.920	2008	61	13	1093	3097	597826528	597824559	0.000000e+00	3105.0
9	TraesCS2A01G568600	chr2D	80.598	1170	184	19	1973	3131	597895224	597894087	0.000000e+00	863.0
10	TraesCS2A01G568600	chr2D	76.677	1312	197	69	1023	2287	642442289	642441040	9.620000e-176	627.0
11	TraesCS2A01G568600	chr2D	76.789	1258	180	75	1039	2251	642478962	642477772	1.620000e-168	603.0
12	TraesCS2A01G568600	chr2D	79.778	811	132	12	2317	3126	641948860	641948081	9.900000e-156	560.0
13	TraesCS2A01G568600	chr2D	85.342	307	38	6	1984	2286	598374523	598374220	1.100000e-80	311.0
14	TraesCS2A01G568600	chr2D	78.601	486	71	20	1414	1892	641950217	641949758	1.430000e-74	291.0
15	TraesCS2A01G568600	chr2D	84.848	297	29	8	3165	3451	641948014	641947724	6.670000e-73	285.0
16	TraesCS2A01G568600	chr2D	80.612	392	54	10	1490	1878	597896224	597895852	2.400000e-72	283.0
17	TraesCS2A01G568600	chr2D	83.594	256	30	6	3204	3451	597893885	597893634	3.170000e-56	230.0
18	TraesCS2A01G568600	chr2D	91.304	138	8	1	964	1097	597827862	597827725	6.960000e-43	185.0
19	TraesCS2A01G568600	chr2D	94.118	119	7	0	3471	3589	641947735	641947617	9.000000e-42	182.0
20	TraesCS2A01G568600	chr2D	82.990	194	23	6	780	965	597828194	597828003	2.520000e-37	167.0
21	TraesCS2A01G568600	chr2D	97.561	82	2	0	3471	3552	597893645	597893564	1.530000e-29	141.0
22	TraesCS2A01G568600	chr2D	85.385	130	15	4	3806	3932	10907140	10907268	9.200000e-27	132.0
23	TraesCS2A01G568600	chr2D	83.929	112	11	5	861	965	641882378	641882267	2.590000e-17	100.0
24	TraesCS2A01G568600	chr2D	89.091	55	6	0	780	834	641882438	641882384	7.310000e-08	69.4
25	TraesCS2A01G568600	chr2B	88.664	988	71	17	998	1966	799288716	799289681	0.000000e+00	1166.0
26	TraesCS2A01G568600	chr2B	89.433	776	71	7	3	775	799298189	799297422	0.000000e+00	968.0
27	TraesCS2A01G568600	chr2B	80.362	1161	181	22	1977	3123	799970787	799971914	0.000000e+00	837.0
28	TraesCS2A01G568600	chr2B	96.644	447	14	1	3204	3650	799972071	799972516	0.000000e+00	741.0
29	TraesCS2A01G568600	chr2B	96.690	423	10	2	3653	4071	799974922	799975344	0.000000e+00	701.0
30	TraesCS2A01G568600	chr2B	94.946	277	12	2	2009	2285	799289787	799290061	2.250000e-117	433.0
31	TraesCS2A01G568600	chr2B	87.147	389	32	7	1490	1875	799969529	799969902	3.770000e-115	425.0
32	TraesCS2A01G568600	chr2B	75.902	859	117	48	1039	1873	799258678	799259470	1.390000e-94	357.0
33	TraesCS2A01G568600	chr2B	85.668	307	37	6	1984	2286	799360097	799359794	2.370000e-82	316.0
34	TraesCS2A01G568600	chr2B	77.273	418	57	25	1482	1891	799254570	799254957	1.150000e-50	211.0
35	TraesCS2A01G568600	chr2B	86.325	117	13	3	3818	3932	796866538	796866653	1.540000e-24	124.0
36	TraesCS2A01G568600	chrUn	89.708	719	60	7	1	717	183020639	183019933	0.000000e+00	905.0
37	TraesCS2A01G568600	chrUn	95.307	277	11	2	2009	2285	183018632	183018358	4.840000e-119	438.0
38	TraesCS2A01G568600	chrUn	87.158	366	20	6	964	1317	183019170	183018820	1.370000e-104	390.0
39	TraesCS2A01G568600	chrUn	87.075	147	8	5	757	894	183019546	183019402	5.460000e-34	156.0
40	TraesCS2A01G568600	chrUn	94.118	85	5	0	1882	1966	183018822	183018738	3.310000e-26	130.0
41	TraesCS2A01G568600	chr5B	92.308	104	7	1	3	106	18714506	18714608	3.280000e-31	147.0
42	TraesCS2A01G568600	chr6B	86.154	130	15	3	3806	3932	22559837	22559966	1.980000e-28	137.0
43	TraesCS2A01G568600	chr6B	90.099	101	10	0	1	101	69720887	69720987	9.200000e-27	132.0
44	TraesCS2A01G568600	chr7A	85.385	130	15	4	3806	3932	254431840	254431712	9.200000e-27	132.0
45	TraesCS2A01G568600	chr7A	88.679	106	12	0	1	106	53893692	53893587	3.310000e-26	130.0
46	TraesCS2A01G568600	chr6D	88.679	106	12	0	1	106	454884373	454884268	3.310000e-26	130.0
47	TraesCS2A01G568600	chr6D	87.736	106	13	0	1	106	454886682	454886577	1.540000e-24	124.0
48	TraesCS2A01G568600	chr5D	84.848	132	14	4	3806	3932	484701572	484701702	1.190000e-25	128.0
49	TraesCS2A01G568600	chr3B	89.109	101	11	0	1	101	770336522	770336422	4.280000e-25	126.0
50	TraesCS2A01G568600	chr1B	87.273	110	13	1	1	109	633103307	633103198	1.540000e-24	124.0
51	TraesCS2A01G568600	chr1B	94.737	38	2	0	683	720	323944562	323944599	4.400000e-05	60.2
52	TraesCS2A01G568600	chr3A	83.846	130	17	4	3806	3932	165095635	165095763	1.990000e-23	121.0
53	TraesCS2A01G568600	chr5A	83.077	130	18	4	3806	3932	682897127	682896999	9.260000e-22	115.0

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	TraesCS2A01G568600	chr2A	766846024	766850101	4077	True	7531.000000	7531	100.00000	1	4078	1	chr2A.!!$R1	4077
1	TraesCS2A01G568600	chr2D	641879093	641882438	3345	True	1622.133333	4697	89.12500	780	4071	3	chr2D.!!$R6	3291
2	TraesCS2A01G568600	chr2D	597824559	597828194	3635	True	1152.333333	3105	89.73800	780	3097	3	chr2D.!!$R4	2317
3	TraesCS2A01G568600	chr2D	642441040	642442289	1249	True	627.000000	627	76.67700	1023	2287	1	chr2D.!!$R2	1264
4	TraesCS2A01G568600	chr2D	642477772	642478962	1190	True	603.000000	603	76.78900	1039	2251	1	chr2D.!!$R3	1212
5	TraesCS2A01G568600	chr2D	597893564	597896224	2660	True	379.250000	863	85.59125	1490	3552	4	chr2D.!!$R5	2062
6	TraesCS2A01G568600	chr2D	641947617	641950217	2600	True	329.500000	560	84.33625	1414	3589	4	chr2D.!!$R7	2175
7	TraesCS2A01G568600	chr2B	799297422	799298189	767	True	968.000000	968	89.43300	3	775	1	chr2B.!!$R1	772
8	TraesCS2A01G568600	chr2B	799288716	799290061	1345	False	799.500000	1166	91.80500	998	2285	2	chr2B.!!$F3	1287
9	TraesCS2A01G568600	chr2B	799969529	799975344	5815	False	676.000000	837	90.21075	1490	4071	4	chr2B.!!$F4	2581
10	TraesCS2A01G568600	chr2B	799254570	799259470	4900	False	284.000000	357	76.58750	1039	1891	2	chr2B.!!$F2	852
11	TraesCS2A01G568600	chrUn	183018358	183020639	2281	True	403.800000	905	90.67320	1	2285	5	chrUn.!!$R1	2284

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
407	409	0.107508	CCATCACATCTCTTGCCCGT	60.108	55.0	0.00	0.00	5.28	F
1673	3458	0.035915	AGAAGAAAGAAGCGGAGGCC	60.036	55.0	0.00	41.24	5.19	F
1724	3515	0.394565	GTGGAGGAGAAGCACAGTGT	59.605	55.0	1.61	0.00	3.55	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
1906	3699	0.039165	GCAAGCGGACCAAGGAAAAG	60.039	55.000	0.00	2.27	R
2987	5870	2.159085	GGTAATCTCCACCTCAGAACCG	60.159	54.545	32.98	4.44	R
3114	6078	2.171237	AGCTGATACATGCTACTTGCCA	59.829	45.455	42.00	4.92	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
27	28	2.029828	AGCCATATCGATGAACCTCGTC	60.030	50.000	8.54	0.00	39.62	4.20
35	36	4.062293	TCGATGAACCTCGTCAACAAATT	58.938	39.130	0.00	0.00	39.62	1.82
38	39	5.559991	CGATGAACCTCGTCAACAAATTTCA	60.560	40.000	0.00	0.00	32.03	2.69
63	64	1.002576	CGTGCTTGTGTGATTGCTTGA	60.003	47.619	0.00	0.00	0.00	3.02
70	71	2.028203	TGTGTGATTGCTTGATCCTCGA	60.028	45.455	0.00	0.00	0.00	4.04
75	76	3.873361	TGATTGCTTGATCCTCGAATGAC	59.127	43.478	0.00	0.00	0.00	3.06
76	77	3.616956	TTGCTTGATCCTCGAATGACT	57.383	42.857	0.00	0.00	0.00	3.41
79	80	3.133542	TGCTTGATCCTCGAATGACTGAT	59.866	43.478	0.00	0.00	0.00	2.90
80	81	4.342092	TGCTTGATCCTCGAATGACTGATA	59.658	41.667	0.00	0.00	0.00	2.15
91	92	5.301805	TCGAATGACTGATAGTATGCCTCAA	59.698	40.000	0.00	0.00	0.00	3.02
105	107	8.579850	AGTATGCCTCAAATTTATTCTGACAA	57.420	30.769	0.00	0.00	0.00	3.18
117	119	2.028420	TCTGACAATCATTGAGCCGG	57.972	50.000	3.79	0.00	0.00	6.13
129	131	2.413310	TGAGCCGGAATTTTACCTCC	57.587	50.000	5.05	0.00	0.00	4.30
223	225	0.717196	AGTAGGGGCTGTAGGGTTCT	59.283	55.000	0.00	0.00	0.00	3.01
298	300	2.094545	GCTTTCATCAACCACCACATCC	60.095	50.000	0.00	0.00	0.00	3.51
311	313	2.118679	CCACATCCACTAGGTCATCCA	58.881	52.381	0.00	0.00	35.89	3.41
362	364	2.884207	GTCGTTGATCGGCGGGTC	60.884	66.667	7.21	6.66	40.32	4.46
407	409	0.107508	CCATCACATCTCTTGCCCGT	60.108	55.000	0.00	0.00	0.00	5.28
412	414	2.565391	TCACATCTCTTGCCCGTAGAAA	59.435	45.455	0.00	0.00	0.00	2.52
415	417	2.762535	TCTCTTGCCCGTAGAAAAGG	57.237	50.000	0.00	0.00	0.00	3.11
451	453	1.608717	AAATCCCGAGCAGCGAGTCT	61.609	55.000	0.21	0.00	44.57	3.24
520	522	0.732880	CTCCACGATCGTTGCGAAGT	60.733	55.000	20.14	0.00	39.99	3.01
527	529	4.409588	CGTTGCGAAGTGCCGTCG	62.410	66.667	6.25	6.25	45.60	5.12
594	597	0.833949	GCTAGGTCTTCTCCAAGGGG	59.166	60.000	0.00	0.00	0.00	4.79
595	598	1.622725	GCTAGGTCTTCTCCAAGGGGA	60.623	57.143	0.00	0.00	42.29	4.81
630	633	4.624882	CACTGAATTCTTTCCTCAGAGACG	59.375	45.833	7.05	0.00	39.15	4.18
666	670	1.662517	TTGTGCTTCTCGTGCAAGAA	58.337	45.000	3.39	2.11	42.41	2.52
672	676	4.331168	GTGCTTCTCGTGCAAGAATAGATT	59.669	41.667	3.39	0.00	42.41	2.40
680	684	3.887716	GTGCAAGAATAGATTGAGGGCAT	59.112	43.478	0.00	0.00	0.00	4.40
681	685	5.065914	GTGCAAGAATAGATTGAGGGCATA	58.934	41.667	0.00	0.00	0.00	3.14
685	689	6.881065	GCAAGAATAGATTGAGGGCATATGTA	59.119	38.462	4.29	0.00	0.00	2.29
695	699	6.933514	TGAGGGCATATGTATGTTCATAGA	57.066	37.500	4.29	0.00	36.11	1.98
721	1063	5.925907	TGAGTGTACGCGCGTATATATAAA	58.074	37.500	40.91	19.66	32.82	1.40
725	1067	5.003684	GTGTACGCGCGTATATATAAATGCA	59.996	40.000	40.91	27.28	32.82	3.96
729	1071	4.549871	CGCGCGTATATATAAATGCATGCA	60.550	41.667	25.04	25.04	0.00	3.96
735	1077	7.585210	GCGTATATATAAATGCATGCATCTGTG	59.415	37.037	32.25	14.66	35.31	3.66
743	1085	1.538512	GCATGCATCTGTGTTGTGTCT	59.461	47.619	14.21	0.00	0.00	3.41
775	1127	5.740290	TCAGAGTCCGGAAGTTCTAAAAT	57.260	39.130	5.23	0.00	0.00	1.82
776	1128	6.845758	TCAGAGTCCGGAAGTTCTAAAATA	57.154	37.500	5.23	0.00	0.00	1.40
778	1130	7.321153	TCAGAGTCCGGAAGTTCTAAAATAAG	58.679	38.462	5.23	0.00	0.00	1.73
785	1137	8.550585	TCCGGAAGTTCTAAAATAAGGGAAATA	58.449	33.333	0.00	0.00	0.00	1.40
820	1172	1.737793	CTTGTAGTTGTGGCCGAATCC	59.262	52.381	0.00	0.00	0.00	3.01
821	1173	0.687920	TGTAGTTGTGGCCGAATCCA	59.312	50.000	0.00	0.00	0.00	3.41
822	1174	1.280710	TGTAGTTGTGGCCGAATCCAT	59.719	47.619	0.00	0.00	38.57	3.41
890	1255	2.420967	CCCTGTAAACCCCGATCGAAAT	60.421	50.000	18.66	0.00	0.00	2.17
893	1258	4.877251	CCTGTAAACCCCGATCGAAATAAA	59.123	41.667	18.66	0.00	0.00	1.40
895	1260	5.490159	TGTAAACCCCGATCGAAATAAACT	58.510	37.500	18.66	0.00	0.00	2.66
896	1261	4.957759	AAACCCCGATCGAAATAAACTG	57.042	40.909	18.66	0.00	0.00	3.16
897	1262	3.899052	ACCCCGATCGAAATAAACTGA	57.101	42.857	18.66	0.00	0.00	3.41
898	1263	4.417426	ACCCCGATCGAAATAAACTGAT	57.583	40.909	18.66	0.00	0.00	2.90
900	1265	5.539048	ACCCCGATCGAAATAAACTGATAG	58.461	41.667	18.66	0.00	0.00	2.08
901	1266	4.929808	CCCCGATCGAAATAAACTGATAGG	59.070	45.833	18.66	3.40	34.54	2.57
903	1268	5.634020	CCCGATCGAAATAAACTGATAGGTC	59.366	44.000	18.66	0.00	33.37	3.85
905	1270	6.144080	CCGATCGAAATAAACTGATAGGTCAC	59.856	42.308	18.66	0.00	31.41	3.67
918	1316	3.036084	GTCACAGGTGCGACCGTG	61.036	66.667	16.30	16.30	44.90	4.94
948	1346	3.564027	CGATCGAACAAGCCGGCC	61.564	66.667	26.15	6.12	0.00	6.13
968	1509	2.671396	CCGCTAGTTGCTTCGTACAAAT	59.329	45.455	0.00	0.00	40.11	2.32
1021	1562	1.982226	TGGACTCCGGGAAAGATCAAA	59.018	47.619	0.00	0.00	0.00	2.69
1050	1591	3.499157	AGTTATCGACGCTGATAGAGGAC	59.501	47.826	0.00	0.00	32.70	3.85
1174	2935	0.733566	CATGGCCGACAACACAATGC	60.734	55.000	0.00	0.00	0.00	3.56
1231	2992	3.490399	CAGGTTAGAGACGACGAGAAAC	58.510	50.000	0.00	0.00	0.00	2.78
1321	3091	3.595758	GGATTTCCCATGCCCGCG	61.596	66.667	0.00	0.00	34.14	6.46
1351	3121	2.436646	CGGCCGATGAGCTGGTTT	60.437	61.111	24.07	0.00	35.37	3.27
1442	3227	4.909355	AGAGGAAGGAAGATAAGGAGGA	57.091	45.455	0.00	0.00	0.00	3.71
1444	3229	4.484270	AGAGGAAGGAAGATAAGGAGGAGA	59.516	45.833	0.00	0.00	0.00	3.71
1446	3231	3.901222	GGAAGGAAGATAAGGAGGAGAGG	59.099	52.174	0.00	0.00	0.00	3.69
1447	3232	3.628832	AGGAAGATAAGGAGGAGAGGG	57.371	52.381	0.00	0.00	0.00	4.30
1448	3233	3.143406	AGGAAGATAAGGAGGAGAGGGA	58.857	50.000	0.00	0.00	0.00	4.20
1449	3234	3.737613	AGGAAGATAAGGAGGAGAGGGAT	59.262	47.826	0.00	0.00	0.00	3.85
1451	3236	5.016245	AGGAAGATAAGGAGGAGAGGGATAG	59.984	48.000	0.00	0.00	0.00	2.08
1472	3257	1.674962	GATGAGGAACAAGGATGCAGC	59.325	52.381	0.00	0.00	0.00	5.25
1527	3312	1.470051	GTCTCTCCTCCAGTGTCCTC	58.530	60.000	0.00	0.00	0.00	3.71
1538	3323	0.681564	AGTGTCCTCGCTAGACCCAG	60.682	60.000	0.00	0.00	33.09	4.45
1621	3406	2.937959	GATGGAGGCGGAGAGGGAGT	62.938	65.000	0.00	0.00	0.00	3.85
1666	3451	1.972027	GCGGCGGAGAAGAAAGAAGC	61.972	60.000	9.78	0.00	0.00	3.86
1669	3454	0.389948	GCGGAGAAGAAAGAAGCGGA	60.390	55.000	0.00	0.00	0.00	5.54
1670	3455	1.634702	CGGAGAAGAAAGAAGCGGAG	58.365	55.000	0.00	0.00	0.00	4.63
1672	3457	1.364721	GAGAAGAAAGAAGCGGAGGC	58.635	55.000	0.00	0.00	40.37	4.70
1673	3458	0.035915	AGAAGAAAGAAGCGGAGGCC	60.036	55.000	0.00	0.00	41.24	5.19
1684	3469	2.750237	GGAGGCCGCGGATTGTTT	60.750	61.111	33.48	6.23	0.00	2.83
1685	3470	2.340328	GGAGGCCGCGGATTGTTTT	61.340	57.895	33.48	4.57	0.00	2.43
1686	3471	1.154035	GAGGCCGCGGATTGTTTTG	60.154	57.895	33.48	0.00	0.00	2.44
1693	3478	1.701704	GCGGATTGTTTTGCAGAAGG	58.298	50.000	0.00	0.00	0.00	3.46
1695	3480	2.922335	GCGGATTGTTTTGCAGAAGGAC	60.922	50.000	0.00	0.00	0.00	3.85
1697	3482	2.893489	GGATTGTTTTGCAGAAGGACCT	59.107	45.455	0.00	0.00	0.00	3.85
1720	3508	1.980765	AGATTGTGGAGGAGAAGCACA	59.019	47.619	0.00	0.00	0.00	4.57
1721	3509	2.027377	AGATTGTGGAGGAGAAGCACAG	60.027	50.000	0.00	0.00	0.00	3.66
1724	3515	0.394565	GTGGAGGAGAAGCACAGTGT	59.605	55.000	1.61	0.00	0.00	3.55
1726	3517	0.681733	GGAGGAGAAGCACAGTGTCA	59.318	55.000	1.61	0.00	0.00	3.58
1737	3528	1.334869	CACAGTGTCAAGCAGGAAACC	59.665	52.381	0.00	0.00	0.00	3.27
1822	3613	0.461548	TAGCATCTGGGAACGCTCTG	59.538	55.000	0.00	0.00	35.93	3.35
1903	3696	2.941720	GCTGCAGCTTAGCTTACTCAAT	59.058	45.455	31.33	0.00	36.40	2.57
1906	3699	5.551760	TGCAGCTTAGCTTACTCAATTTC	57.448	39.130	3.00	0.00	36.40	2.17
1921	3714	3.005367	TCAATTTCTTTTCCTTGGTCCGC	59.995	43.478	0.00	0.00	0.00	5.54
2330	5126	7.923414	ATATACTTTGTTGTCCTCTGTTTCC	57.077	36.000	0.00	0.00	0.00	3.13
2374	5205	6.685527	ACTTCTTTGTCCTCTGTTTCTTTC	57.314	37.500	0.00	0.00	0.00	2.62
2461	5310	1.376466	GCTTGACTGGCCCTTCTCA	59.624	57.895	0.00	0.00	0.00	3.27
2642	5491	3.003482	CGTTCGATAGTCCCTTCTGTAGG	59.997	52.174	0.00	0.00	39.88	3.18
2987	5870	3.371285	GTCAGGGTAGATTTTTCGTCTGC	59.629	47.826	0.00	0.00	0.00	4.26
3072	5955	5.766590	TGATTGAGGGATACACTACTCAGA	58.233	41.667	0.00	0.00	40.63	3.27
3114	6078	6.483307	CGATCAGGATGTGGTATTTGTATGTT	59.517	38.462	0.00	0.00	37.40	2.71
3229	6347	6.255453	GCAGTTGTGTTGTGTGAAATATTTGT	59.745	34.615	5.17	0.00	0.00	2.83
3279	6397	7.608376	TGCTTGTACTGGCATTATGTTTACTTA	59.392	33.333	8.75	0.00	33.23	2.24
3718	11190	4.576463	ACTTCAAGTTCGCCATATCCAATC	59.424	41.667	0.00	0.00	0.00	2.67
3744	11216	0.389296	TCGTCGTCGCCAATCACATT	60.389	50.000	0.00	0.00	36.96	2.71
3781	11253	2.004120	AACCTGTCCACACCACCCA	61.004	57.895	0.00	0.00	0.00	4.51
3885	11357	7.736893	AGATCCGCCAATACTAGTAGAAAAAT	58.263	34.615	8.85	0.00	0.00	1.82
4032	11508	1.723003	GAGCGCAATTTCAGGCAAAAG	59.277	47.619	11.47	0.00	0.00	2.27
4062	11538	1.394917	CGTCTGCTTCCTTTCCATTCG	59.605	52.381	0.00	0.00	0.00	3.34
4071	11547	2.092323	CCTTTCCATTCGGTTTCCCTC	58.908	52.381	0.00	0.00	0.00	4.30
4072	11548	2.554344	CCTTTCCATTCGGTTTCCCTCA	60.554	50.000	0.00	0.00	0.00	3.86
4073	11549	3.356290	CTTTCCATTCGGTTTCCCTCAT	58.644	45.455	0.00	0.00	0.00	2.90
4074	11550	2.710096	TCCATTCGGTTTCCCTCATC	57.290	50.000	0.00	0.00	0.00	2.92
4075	11551	1.134521	TCCATTCGGTTTCCCTCATCG	60.135	52.381	0.00	0.00	0.00	3.84
4076	11552	1.134521	CCATTCGGTTTCCCTCATCGA	60.135	52.381	0.00	0.00	0.00	3.59
4077	11553	2.627945	CATTCGGTTTCCCTCATCGAA	58.372	47.619	0.00	0.00	42.63	3.71

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
27	28	3.694734	AGCACGACACTGAAATTTGTTG	58.305	40.909	0.00	0.00	33.85	3.33
35	36	1.006086	CACACAAGCACGACACTGAA	58.994	50.000	0.00	0.00	0.00	3.02
38	39	1.599071	CAATCACACAAGCACGACACT	59.401	47.619	0.00	0.00	0.00	3.55
63	64	5.105554	GGCATACTATCAGTCATTCGAGGAT	60.106	44.000	0.00	0.00	0.00	3.24
70	71	8.757982	AAATTTGAGGCATACTATCAGTCATT	57.242	30.769	0.00	0.00	0.00	2.57
79	80	9.679661	TTGTCAGAATAAATTTGAGGCATACTA	57.320	29.630	0.00	0.00	0.00	1.82
80	81	8.579850	TTGTCAGAATAAATTTGAGGCATACT	57.420	30.769	0.00	0.00	0.00	2.12
91	92	7.198390	CGGCTCAATGATTGTCAGAATAAATT	58.802	34.615	4.93	0.00	0.00	1.82
101	103	4.376340	AAATTCCGGCTCAATGATTGTC	57.624	40.909	4.93	0.00	0.00	3.18
105	107	4.536765	AGGTAAAATTCCGGCTCAATGAT	58.463	39.130	0.00	0.00	0.00	2.45
117	119	3.686016	TCTGGTGCAGGAGGTAAAATTC	58.314	45.455	0.00	0.00	31.51	2.17
129	131	1.030488	CAGCTTGGGATCTGGTGCAG	61.030	60.000	0.00	0.00	0.00	4.41
171	173	4.621034	GGAACATGCGTGAGGTAAAATTTG	59.379	41.667	14.17	0.00	0.00	2.32
223	225	0.106894	TTGCCCGTGTACACATGACA	59.893	50.000	24.98	14.06	34.90	3.58
261	263	5.193663	TGAAAGCGATCTCCTAGAAGATG	57.806	43.478	0.00	0.00	36.13	2.90
311	313	9.359653	CCATGATGAAGGAATTAGGTCTTAAAT	57.640	33.333	0.00	0.00	0.00	1.40
336	338	1.084370	CGATCAACGACAAGGAGGCC	61.084	60.000	0.00	0.00	45.77	5.19
365	367	2.203832	TCTCAGTCAGCAGGGGCA	60.204	61.111	0.00	0.00	44.61	5.36
407	409	1.874872	CCGGCGAAACAACCTTTTCTA	59.125	47.619	9.30	0.00	33.93	2.10
412	414	3.656045	CGCCGGCGAAACAACCTT	61.656	61.111	44.86	0.00	42.83	3.50
451	453	2.992689	TGGTAGCCGGCGTCTTCA	60.993	61.111	23.20	13.52	0.00	3.02
594	597	1.469335	TTCAGTGTCACCGTCCCCTC	61.469	60.000	0.00	0.00	0.00	4.30
595	598	0.836400	ATTCAGTGTCACCGTCCCCT	60.836	55.000	0.00	0.00	0.00	4.79
596	599	0.036306	AATTCAGTGTCACCGTCCCC	59.964	55.000	0.00	0.00	0.00	4.81
597	600	1.002087	AGAATTCAGTGTCACCGTCCC	59.998	52.381	8.44	0.00	0.00	4.46
598	601	2.457366	AGAATTCAGTGTCACCGTCC	57.543	50.000	8.44	0.00	0.00	4.79
599	602	3.186613	GGAAAGAATTCAGTGTCACCGTC	59.813	47.826	8.44	0.00	37.29	4.79
600	603	3.139077	GGAAAGAATTCAGTGTCACCGT	58.861	45.455	8.44	0.00	37.29	4.83
601	604	3.403038	AGGAAAGAATTCAGTGTCACCG	58.597	45.455	8.44	0.00	37.29	4.94
630	633	8.145122	AGAAGCACAAATTAGGCTACTAGATAC	58.855	37.037	0.00	0.00	36.76	2.24
666	670	7.921304	TGAACATACATATGCCCTCAATCTAT	58.079	34.615	1.58	0.00	37.19	1.98
672	676	6.725834	TCTCTATGAACATACATATGCCCTCA	59.274	38.462	1.58	0.00	37.19	3.86
681	685	8.293157	CGTACACTCATCTCTATGAACATACAT	58.707	37.037	0.00	0.00	41.57	2.29
685	689	5.524284	GCGTACACTCATCTCTATGAACAT	58.476	41.667	0.00	0.00	41.57	2.71
695	699	0.661552	ATACGCGCGTACACTCATCT	59.338	50.000	41.36	22.43	33.01	2.90
706	710	3.894288	GCATGCATTTATATATACGCGCG	59.106	43.478	30.96	30.96	0.00	6.86
721	1063	1.890489	ACACAACACAGATGCATGCAT	59.110	42.857	32.66	32.66	39.69	3.96
725	1067	6.389830	TTTTAAGACACAACACAGATGCAT	57.610	33.333	0.00	0.00	0.00	3.96
752	1104	5.540400	TTTTAGAACTTCCGGACTCTGAA	57.460	39.130	1.83	7.07	0.00	3.02
755	1107	6.351966	CCCTTATTTTAGAACTTCCGGACTCT	60.352	42.308	1.83	9.48	0.00	3.24
775	1127	2.754465	TGCCGGACTCTATTTCCCTTA	58.246	47.619	5.05	0.00	0.00	2.69
776	1128	1.580059	TGCCGGACTCTATTTCCCTT	58.420	50.000	5.05	0.00	0.00	3.95
778	1130	1.543429	CCATGCCGGACTCTATTTCCC	60.543	57.143	5.05	0.00	36.56	3.97
820	1172	8.758633	AGTAGCTATTTAACCTATACGCAATG	57.241	34.615	0.00	0.00	0.00	2.82
821	1173	9.852091	GTAGTAGCTATTTAACCTATACGCAAT	57.148	33.333	0.00	0.00	0.00	3.56
822	1174	9.071276	AGTAGTAGCTATTTAACCTATACGCAA	57.929	33.333	0.00	0.00	0.00	4.85
890	1255	3.368013	CGCACCTGTGACCTATCAGTTTA	60.368	47.826	0.51	0.00	34.75	2.01
893	1258	0.532573	CGCACCTGTGACCTATCAGT	59.467	55.000	0.51	0.00	34.75	3.41
895	1260	0.530744	GTCGCACCTGTGACCTATCA	59.469	55.000	7.63	0.00	46.65	2.15
896	1261	3.347411	GTCGCACCTGTGACCTATC	57.653	57.895	7.63	0.00	46.65	2.08
903	1268	4.293648	TCCACGGTCGCACCTGTG	62.294	66.667	15.86	15.86	40.17	3.66
905	1270	3.515316	AAGTCCACGGTCGCACCTG	62.515	63.158	4.21	2.36	35.66	4.00
918	1316	2.060326	TCGATCGAACACACAAGTCC	57.940	50.000	16.99	0.00	0.00	3.85
952	1350	2.671396	CCGCTATTTGTACGAAGCAACT	59.329	45.455	7.42	0.00	34.60	3.16
1005	1546	3.334583	TCAGTTTGATCTTTCCCGGAG	57.665	47.619	0.73	0.00	0.00	4.63
1021	1562	2.683362	TCAGCGTCGATAACTCATCAGT	59.317	45.455	0.00	0.00	32.71	3.41
1050	1591	0.317799	CCCTCTCCAGCGAGATGATG	59.682	60.000	0.00	0.00	44.25	3.07
1174	2935	0.682852	TTCTTGTGTACAGGGACGGG	59.317	55.000	0.00	0.00	0.00	5.28
1231	2992	2.464865	GAGGATGGAATCGACGAGTTG	58.535	52.381	3.01	0.00	46.86	3.16
1321	3091	1.445582	CGGCCGTGTACAAGGAGAC	60.446	63.158	29.16	17.09	31.21	3.36
1351	3121	7.831691	TTTTCTTTAATCTGGATGTTGTGGA	57.168	32.000	0.00	0.00	0.00	4.02
1442	3227	4.230455	CTTGTTCCTCATCCTATCCCTCT	58.770	47.826	0.00	0.00	0.00	3.69
1444	3229	3.051032	TCCTTGTTCCTCATCCTATCCCT	60.051	47.826	0.00	0.00	0.00	4.20
1446	3231	4.805609	GCATCCTTGTTCCTCATCCTATCC	60.806	50.000	0.00	0.00	0.00	2.59
1447	3232	4.202398	TGCATCCTTGTTCCTCATCCTATC	60.202	45.833	0.00	0.00	0.00	2.08
1448	3233	3.718434	TGCATCCTTGTTCCTCATCCTAT	59.282	43.478	0.00	0.00	0.00	2.57
1449	3234	3.114606	TGCATCCTTGTTCCTCATCCTA	58.885	45.455	0.00	0.00	0.00	2.94
1451	3236	2.295885	CTGCATCCTTGTTCCTCATCC	58.704	52.381	0.00	0.00	0.00	3.51
1472	3257	1.617357	TCAGCATCATCTGATCCCTCG	59.383	52.381	0.00	0.00	38.11	4.63
1527	3312	0.535335	TGTAAAGGCTGGGTCTAGCG	59.465	55.000	0.00	0.00	44.60	4.26
1538	3323	3.670627	CGCCAACTCATTCTTGTAAAGGC	60.671	47.826	0.00	0.00	46.24	4.35
1621	3406	0.117140	TTCTCCCTCTGCCTCTCCAA	59.883	55.000	0.00	0.00	0.00	3.53
1669	3454	2.961768	CAAAACAATCCGCGGCCT	59.038	55.556	23.51	7.36	0.00	5.19
1670	3455	2.809174	GCAAAACAATCCGCGGCC	60.809	61.111	23.51	0.00	0.00	6.13
1672	3457	0.039617	TTCTGCAAAACAATCCGCGG	60.040	50.000	22.12	22.12	0.00	6.46
1673	3458	1.330306	CTTCTGCAAAACAATCCGCG	58.670	50.000	0.00	0.00	0.00	6.46
1674	3459	1.269448	TCCTTCTGCAAAACAATCCGC	59.731	47.619	0.00	0.00	0.00	5.54
1675	3460	2.351738	GGTCCTTCTGCAAAACAATCCG	60.352	50.000	0.00	0.00	0.00	4.18
1676	3461	2.893489	AGGTCCTTCTGCAAAACAATCC	59.107	45.455	0.00	0.00	0.00	3.01
1677	3462	3.905784	CAGGTCCTTCTGCAAAACAATC	58.094	45.455	0.00	0.00	0.00	2.67
1693	3478	0.615331	TCCTCCACAATCTGCAGGTC	59.385	55.000	15.13	0.00	0.00	3.85
1695	3480	0.907486	TCTCCTCCACAATCTGCAGG	59.093	55.000	15.13	0.00	0.00	4.85
1697	3482	1.339438	GCTTCTCCTCCACAATCTGCA	60.339	52.381	0.00	0.00	0.00	4.41
1714	3502	0.181114	TCCTGCTTGACACTGTGCTT	59.819	50.000	7.90	0.00	0.00	3.91
1720	3508	2.435372	TTGGTTTCCTGCTTGACACT	57.565	45.000	0.00	0.00	0.00	3.55
1721	3509	3.552890	GGATTTGGTTTCCTGCTTGACAC	60.553	47.826	0.00	0.00	0.00	3.67
1724	3515	2.247358	GGGATTTGGTTTCCTGCTTGA	58.753	47.619	0.00	0.00	33.53	3.02
1726	3517	1.132881	TGGGGATTTGGTTTCCTGCTT	60.133	47.619	0.00	0.00	33.53	3.91
1737	3528	0.243636	GTTGCTCCGTTGGGGATTTG	59.756	55.000	0.00	0.00	46.04	2.32
1822	3613	2.182842	GTCCGGACATGCTGCCATC	61.183	63.158	29.75	0.00	0.00	3.51
1903	3696	2.358322	AGCGGACCAAGGAAAAGAAA	57.642	45.000	0.00	0.00	0.00	2.52
1906	3699	0.039165	GCAAGCGGACCAAGGAAAAG	60.039	55.000	0.00	0.00	0.00	2.27
1921	3714	7.606858	TTTCTTGAGACATGAATAGAGCAAG	57.393	36.000	0.00	0.00	34.41	4.01
2314	5110	5.751586	ACTTAAAGGAAACAGAGGACAACA	58.248	37.500	0.00	0.00	0.00	3.33
2461	5310	3.641434	AGTCCACAGCTAGAATTGCAT	57.359	42.857	0.00	0.00	0.00	3.96
2642	5491	2.421619	CTCTCAAACCTCAACTCTGCC	58.578	52.381	0.00	0.00	0.00	4.85
2805	5673	9.702253	ATCTAGACCTACTTCATGTTCTTTAGA	57.298	33.333	0.00	0.00	0.00	2.10
2806	5674	9.743057	CATCTAGACCTACTTCATGTTCTTTAG	57.257	37.037	0.00	0.00	0.00	1.85
2807	5675	8.696374	CCATCTAGACCTACTTCATGTTCTTTA	58.304	37.037	0.00	0.00	0.00	1.85
2808	5676	7.181125	ACCATCTAGACCTACTTCATGTTCTTT	59.819	37.037	0.00	0.00	0.00	2.52
2987	5870	2.159085	GGTAATCTCCACCTCAGAACCG	60.159	54.545	0.00	0.00	32.98	4.44
3072	5955	3.319122	TGATCGCAGATAGCACACTACAT	59.681	43.478	0.00	0.00	45.12	2.29
3114	6078	2.171237	AGCTGATACATGCTACTTGCCA	59.829	45.455	0.00	0.00	42.00	4.92
4047	11523	2.094700	GGAAACCGAATGGAAAGGAAGC	60.095	50.000	0.00	0.00	39.21	3.86

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.