AutoCloner

Multiple sequence alignment - TraesCS2A01G443600

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	TraesCS2A01G443600	chr2A	100.000	3921	0	0	1	3921	693430928	693427008	0.000000e+00	7241.0
1	TraesCS2A01G443600	chr2A	79.200	125	21	5	3430	3552	93996612	93996491	9.030000e-12	82.4
2	TraesCS2A01G443600	chr2D	96.387	2159	58	10	989	3136	553253585	553251436	0.000000e+00	3537.0
3	TraesCS2A01G443600	chr2D	89.914	347	15	4	1	335	553258987	553258649	2.800000e-116	429.0
4	TraesCS2A01G443600	chr2D	85.169	445	19	12	516	917	553254072	553253632	2.820000e-111	412.0
5	TraesCS2A01G443600	chr2D	85.644	202	10	6	482	672	553258242	553258049	1.110000e-45	195.0
6	TraesCS2A01G443600	chr2D	85.470	117	15	2	3434	3549	69254168	69254283	1.910000e-23	121.0
7	TraesCS2A01G443600	chr2B	94.382	2225	99	18	989	3195	659003838	659001622	0.000000e+00	3393.0
8	TraesCS2A01G443600	chr2B	99.207	1388	11	0	2534	3921	658997077	658995690	0.000000e+00	2503.0
9	TraesCS2A01G443600	chr2B	85.144	451	22	15	508	917	659004332	659003886	1.680000e-113	420.0
10	TraesCS2A01G443600	chr2B	89.308	159	13	1	303	457	659012740	659012582	3.090000e-46	196.0
11	TraesCS2A01G443600	chr2B	86.061	165	6	6	482	639	659012590	659012436	1.130000e-35	161.0
12	TraesCS2A01G443600	chr2B	95.745	94	4	0	3726	3819	659001080	659000987	6.790000e-33	152.0
13	TraesCS2A01G443600	chr2B	77.647	170	23	9	3304	3464	6374055	6373892	5.400000e-14	89.8
14	TraesCS2A01G443600	chr2B	78.906	128	22	5	3430	3556	121483772	121483649	9.030000e-12	82.4
15	TraesCS2A01G443600	chr6A	81.187	1297	207	23	1642	2924	493842838	493844111	0.000000e+00	1009.0
16	TraesCS2A01G443600	chr6A	80.493	1297	216	22	1642	2924	493756655	493757928	0.000000e+00	959.0
17	TraesCS2A01G443600	chr6A	80.363	1268	212	22	1671	2924	495153701	495152457	0.000000e+00	928.0
18	TraesCS2A01G443600	chr6A	79.923	1295	223	23	1642	2922	494047348	494048619	0.000000e+00	917.0
19	TraesCS2A01G443600	chr6A	80.371	917	145	19	1645	2548	494880285	494879391	0.000000e+00	664.0
20	TraesCS2A01G443600	chr6A	90.278	216	21	0	1237	1452	493842518	493842733	2.310000e-72	283.0
21	TraesCS2A01G443600	chr6A	89.815	216	22	0	1237	1452	495154050	495153835	1.070000e-70	278.0
22	TraesCS2A01G443600	chr6A	89.767	215	22	0	1238	1452	493756339	493756553	3.860000e-70	276.0
23	TraesCS2A01G443600	chr6D	81.280	1266	200	20	1671	2922	350204727	350203485	0.000000e+00	990.0
24	TraesCS2A01G443600	chr6D	80.648	1297	214	22	1642	2924	349031771	349033044	0.000000e+00	970.0
25	TraesCS2A01G443600	chr6D	80.262	1297	219	24	1642	2924	348861708	348862981	0.000000e+00	942.0
26	TraesCS2A01G443600	chr6D	79.306	807	132	21	1671	2464	350083564	350082780	2.070000e-147	532.0
27	TraesCS2A01G443600	chr6D	89.177	231	24	1	1222	1452	28244891	28244662	1.780000e-73	287.0
28	TraesCS2A01G443600	chr6D	89.352	216	23	0	1237	1452	350205034	350204819	4.990000e-69	272.0
29	TraesCS2A01G443600	chr6D	76.444	225	50	3	2165	2387	348961972	348962195	6.880000e-23	119.0
30	TraesCS2A01G443600	chr6B	81.005	1274	205	22	1665	2924	529774418	529775668	0.000000e+00	977.0
31	TraesCS2A01G443600	chr6B	80.309	1295	218	21	1642	2922	529890222	529891493	0.000000e+00	944.0
32	TraesCS2A01G443600	chr6B	80.216	1294	219	23	1645	2924	530851842	530850572	0.000000e+00	937.0
33	TraesCS2A01G443600	chr6B	90.698	215	20	0	1235	1449	52086469	52086683	1.780000e-73	287.0
34	TraesCS2A01G443600	chr6B	89.815	216	22	0	1237	1452	529889902	529890117	1.070000e-70	278.0
35	TraesCS2A01G443600	chr7D	87.279	566	46	14	1933	2498	523827036	523826497	1.200000e-174	623.0
36	TraesCS2A01G443600	chr7D	78.281	221	40	7	3333	3549	602667036	602667252	6.830000e-28	135.0
37	TraesCS2A01G443600	chr7D	76.647	167	32	5	3306	3466	46945839	46946004	6.980000e-13	86.1
38	TraesCS2A01G443600	chr1B	78.313	249	47	3	3297	3538	440518305	440518553	1.890000e-33	154.0
39	TraesCS2A01G443600	chrUn	84.828	145	18	4	2171	2313	100090466	100090608	4.080000e-30	143.0
40	TraesCS2A01G443600	chr5A	84.828	145	18	4	2182	2324	658990159	658990301	4.080000e-30	143.0
41	TraesCS2A01G443600	chr7B	80.000	185	35	2	3354	3536	686635086	686635270	6.830000e-28	135.0
42	TraesCS2A01G443600	chr5B	83.942	137	18	4	3415	3548	560448917	560448782	1.140000e-25	128.0
43	TraesCS2A01G443600	chr5B	81.884	138	19	3	3260	3392	546776670	546776806	1.150000e-20	111.0
44	TraesCS2A01G443600	chr4D	75.581	258	57	4	3295	3547	261256834	261256578	5.320000e-24	122.0
45	TraesCS2A01G443600	chr3D	77.064	218	39	8	3260	3467	73894458	73894242	8.900000e-22	115.0
46	TraesCS2A01G443600	chr1A	78.125	192	30	9	3286	3468	578249845	578249657	1.150000e-20	111.0

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	TraesCS2A01G443600	chr2A	693427008	693430928	3920	True	7241.00	7241	100.0000	1	3921	1	chr2A.!!$R2	3920
1	TraesCS2A01G443600	chr2D	553251436	553258987	7551	True	1143.25	3537	89.2785	1	3136	4	chr2D.!!$R1	3135
2	TraesCS2A01G443600	chr2B	658995690	659004332	8642	True	1617.00	3393	93.6195	508	3921	4	chr2B.!!$R3	3413
3	TraesCS2A01G443600	chr6A	494047348	494048619	1271	False	917.00	917	79.9230	1642	2922	1	chr6A.!!$F1	1280
4	TraesCS2A01G443600	chr6A	494879391	494880285	894	True	664.00	664	80.3710	1645	2548	1	chr6A.!!$R1	903
5	TraesCS2A01G443600	chr6A	493842518	493844111	1593	False	646.00	1009	85.7325	1237	2924	2	chr6A.!!$F3	1687
6	TraesCS2A01G443600	chr6A	493756339	493757928	1589	False	617.50	959	85.1300	1238	2924	2	chr6A.!!$F2	1686
7	TraesCS2A01G443600	chr6A	495152457	495154050	1593	True	603.00	928	85.0890	1237	2924	2	chr6A.!!$R2	1687
8	TraesCS2A01G443600	chr6D	349031771	349033044	1273	False	970.00	970	80.6480	1642	2924	1	chr6D.!!$F3	1282
9	TraesCS2A01G443600	chr6D	348861708	348862981	1273	False	942.00	942	80.2620	1642	2924	1	chr6D.!!$F1	1282
10	TraesCS2A01G443600	chr6D	350203485	350205034	1549	True	631.00	990	85.3160	1237	2922	2	chr6D.!!$R3	1685
11	TraesCS2A01G443600	chr6D	350082780	350083564	784	True	532.00	532	79.3060	1671	2464	1	chr6D.!!$R2	793
12	TraesCS2A01G443600	chr6B	529774418	529775668	1250	False	977.00	977	81.0050	1665	2924	1	chr6B.!!$F2	1259
13	TraesCS2A01G443600	chr6B	530850572	530851842	1270	True	937.00	937	80.2160	1645	2924	1	chr6B.!!$R1	1279
14	TraesCS2A01G443600	chr6B	529889902	529891493	1591	False	611.00	944	85.0620	1237	2922	2	chr6B.!!$F3	1685
15	TraesCS2A01G443600	chr7D	523826497	523827036	539	True	623.00	623	87.2790	1933	2498	1	chr7D.!!$R1	565

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	End Stability	Orientation
996	5483	0.032678	AGGAGCTTGATATCGGTGCG	59.967	55.0	5.34	F
1508	6011	0.034670	GTGGCAGCTTCTTCCTCCAT	60.035	55.0	3.41	F
1509	6012	0.034767	TGGCAGCTTCTTCCTCCATG	60.035	55.0	3.66	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2089	6619	0.313043	TGTCGAGGAACGTGAACTCC	59.687	55.0	8.31	2.78	43.13	3.85	R
2524	7057	0.980231	GCCTCCTCATCTCCACCAGT	60.980	60.0	0.00	0.00	0.00	4.00	R
3283	13029	2.169832	ATGCGCGTAAATAGGAGCAT	57.830	45.0	15.41	15.41	46.84	3.79	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
22	23	3.725010	CGCAGTAAAGCTCGATGGAAAAC	60.725	47.826	0.00	0.00	0.00	2.43
99	112	4.360563	CCTGATGTAACAGTTAGTAGCCG	58.639	47.826	0.00	0.00	36.30	5.52
128	141	2.569059	CTAGGTGCATGGAATCACAGG	58.431	52.381	0.00	0.00	35.04	4.00
149	162	0.753262	ACGGTCCTCTGGTGCATATC	59.247	55.000	0.00	0.00	0.00	1.63
154	167	1.895798	TCCTCTGGTGCATATCCGATC	59.104	52.381	0.00	0.00	0.00	3.69
155	168	1.403382	CCTCTGGTGCATATCCGATCG	60.403	57.143	8.51	8.51	0.00	3.69
156	169	1.541588	CTCTGGTGCATATCCGATCGA	59.458	52.381	18.66	2.91	0.00	3.59
157	170	1.269723	TCTGGTGCATATCCGATCGAC	59.730	52.381	18.66	4.35	0.00	4.20
177	190	0.798776	GTCTTTCTGGATGGTGTGCG	59.201	55.000	0.00	0.00	0.00	5.34
182	195	1.003355	CTGGATGGTGTGCGTCCTT	60.003	57.895	0.00	0.00	33.15	3.36
194	207	0.735287	GCGTCCTTCCTCGTTGTACC	60.735	60.000	0.00	0.00	0.00	3.34
196	209	0.735287	GTCCTTCCTCGTTGTACCGC	60.735	60.000	0.00	0.00	0.00	5.68
199	212	2.814183	CTTCCTCGTTGTACCGCGCT	62.814	60.000	5.56	0.00	0.00	5.92
243	256	5.178996	GCATGTAGCATTTCATCTCTACTGG	59.821	44.000	0.00	0.00	44.79	4.00
270	283	5.701290	CCGATCACCAAATACTTATCTTCCC	59.299	44.000	0.00	0.00	0.00	3.97
271	284	5.405571	CGATCACCAAATACTTATCTTCCCG	59.594	44.000	0.00	0.00	0.00	5.14
272	285	4.448210	TCACCAAATACTTATCTTCCCGC	58.552	43.478	0.00	0.00	0.00	6.13
273	286	3.564225	CACCAAATACTTATCTTCCCGCC	59.436	47.826	0.00	0.00	0.00	6.13
280	293	2.299297	ACTTATCTTCCCGCCTTATCCG	59.701	50.000	0.00	0.00	0.00	4.18
318	331	6.622549	ACTTATCCGAGAGTGAAAGTAACAG	58.377	40.000	0.00	0.00	0.00	3.16
335	348	0.106819	CAGGGCCAGATCCTTCCTTG	60.107	60.000	6.18	0.00	31.06	3.61
340	646	1.813477	GCCAGATCCTTCCTTGCTAGC	60.813	57.143	8.10	8.10	0.00	3.42
345	651	1.377202	CCTTCCTTGCTAGCGCCAA	60.377	57.895	10.77	0.00	34.43	4.52
369	675	5.236478	AGGCATATCAAGCACGTTTACATAC	59.764	40.000	0.00	0.00	0.00	2.39
370	676	5.007234	GGCATATCAAGCACGTTTACATACA	59.993	40.000	0.00	0.00	0.00	2.29
378	684	3.364565	GCACGTTTACATACACAAGTGGG	60.365	47.826	5.08	0.00	34.19	4.61
379	685	2.809696	ACGTTTACATACACAAGTGGGC	59.190	45.455	5.08	0.00	34.19	5.36
380	686	3.071479	CGTTTACATACACAAGTGGGCT	58.929	45.455	5.08	0.00	34.19	5.19
384	690	1.000896	ATACACAAGTGGGCTGGGC	60.001	57.895	5.08	0.00	34.19	5.36
398	704	1.302993	TGGGCGCAGTAAAGTTCCC	60.303	57.895	10.83	0.00	0.00	3.97
403	709	1.378119	GCAGTAAAGTTCCCCCGGG	60.378	63.158	15.80	15.80	0.00	5.73
455	761	2.902423	AAGTGCAGACCCCACGCAAA	62.902	55.000	0.00	0.00	37.41	3.68
456	762	2.124109	TGCAGACCCCACGCAAAA	60.124	55.556	0.00	0.00	31.46	2.44
457	763	2.192861	TGCAGACCCCACGCAAAAG	61.193	57.895	0.00	0.00	31.46	2.27
458	764	2.644992	CAGACCCCACGCAAAAGC	59.355	61.111	0.00	0.00	0.00	3.51
459	765	1.898574	CAGACCCCACGCAAAAGCT	60.899	57.895	0.00	0.00	0.00	3.74
460	766	1.152756	AGACCCCACGCAAAAGCTT	60.153	52.632	0.00	0.00	0.00	3.74
461	767	0.755327	AGACCCCACGCAAAAGCTTT	60.755	50.000	5.69	5.69	0.00	3.51
462	768	0.318699	GACCCCACGCAAAAGCTTTC	60.319	55.000	13.10	0.00	0.00	2.62
463	769	1.371635	CCCCACGCAAAAGCTTTCG	60.372	57.895	13.10	14.96	0.00	3.46
464	770	1.358759	CCCACGCAAAAGCTTTCGT	59.641	52.632	17.38	17.38	35.35	3.85
468	774	2.105323	ACGCAAAAGCTTTCGTGAAG	57.895	45.000	21.03	12.79	38.45	3.02
480	786	5.814314	CTTTCGTGAAGCTAGGATTATCG	57.186	43.478	0.00	0.00	0.00	2.92
481	787	3.284323	TCGTGAAGCTAGGATTATCGC	57.716	47.619	0.00	0.00	0.00	4.58
482	788	2.621526	TCGTGAAGCTAGGATTATCGCA	59.378	45.455	0.00	0.00	0.00	5.10
483	789	2.726760	CGTGAAGCTAGGATTATCGCAC	59.273	50.000	0.00	0.00	0.00	5.34
484	790	2.726760	GTGAAGCTAGGATTATCGCACG	59.273	50.000	0.00	0.00	0.00	5.34
485	791	1.721926	GAAGCTAGGATTATCGCACGC	59.278	52.381	0.00	0.00	0.00	5.34
486	792	0.673985	AGCTAGGATTATCGCACGCA	59.326	50.000	0.00	0.00	0.00	5.24
487	793	1.068588	AGCTAGGATTATCGCACGCAA	59.931	47.619	0.00	0.00	0.00	4.85
488	794	1.864711	GCTAGGATTATCGCACGCAAA	59.135	47.619	0.00	0.00	0.00	3.68
602	5053	0.733909	GCGGGCAAAAGCACAAGATC	60.734	55.000	0.00	0.00	0.00	2.75
610	5061	2.431954	AAGCACAAGATCCATCAGGG	57.568	50.000	0.00	0.00	34.83	4.45
616	5067	4.650377	GATCCATCAGGGCCGGGC	62.650	72.222	22.00	22.00	36.21	6.13
650	5101	2.086869	GTACCACTACGACCACAGCTA	58.913	52.381	0.00	0.00	0.00	3.32
659	5110	4.087892	CCACAGCTACCGCCTGCT	62.088	66.667	0.00	0.00	40.54	4.24
727	5178	0.173935	ACGCATGTGCCCATTTCATG	59.826	50.000	6.08	0.00	40.98	3.07
745	5197	1.110442	TGCATTTATCCTTTGCCGGG	58.890	50.000	2.18	0.00	35.51	5.73
802	5285	4.078516	CACCGGGACCCGTTCTCC	62.079	72.222	30.60	0.00	46.80	3.71
849	5335	2.429610	CCTGCGTATATATAAGCCCCGT	59.570	50.000	22.65	0.00	37.02	5.28
870	5356	0.607489	GCTCTGCCTCTTGCTTCCAA	60.607	55.000	0.00	0.00	42.00	3.53
878	5365	2.487986	CCTCTTGCTTCCAACTCACCTT	60.488	50.000	0.00	0.00	0.00	3.50
921	5408	0.895530	AAGTCACAAGGCGCTAGCTA	59.104	50.000	13.93	0.00	44.37	3.32
922	5409	1.115467	AGTCACAAGGCGCTAGCTAT	58.885	50.000	13.93	0.00	44.37	2.97
940	5427	4.120589	GCTATAGCTTAATATCGGTGGCC	58.879	47.826	17.75	0.00	38.21	5.36
941	5428	4.382685	GCTATAGCTTAATATCGGTGGCCA	60.383	45.833	17.75	0.00	38.21	5.36
943	5430	5.950544	ATAGCTTAATATCGGTGGCCATA	57.049	39.130	9.72	0.00	0.00	2.74
944	5431	4.844349	AGCTTAATATCGGTGGCCATAT	57.156	40.909	9.72	6.04	0.00	1.78
945	5432	5.179452	AGCTTAATATCGGTGGCCATATT	57.821	39.130	9.72	11.69	0.00	1.28
946	5433	5.570320	AGCTTAATATCGGTGGCCATATTT	58.430	37.500	9.72	0.00	0.00	1.40
947	5434	6.010219	AGCTTAATATCGGTGGCCATATTTT	58.990	36.000	9.72	7.58	0.00	1.82
948	5435	6.071952	AGCTTAATATCGGTGGCCATATTTTG	60.072	38.462	9.72	6.56	0.00	2.44
949	5436	6.294508	GCTTAATATCGGTGGCCATATTTTGT	60.295	38.462	9.72	0.00	0.00	2.83
950	5437	7.589958	TTAATATCGGTGGCCATATTTTGTT	57.410	32.000	9.72	1.93	0.00	2.83
951	5438	5.705609	ATATCGGTGGCCATATTTTGTTC	57.294	39.130	9.72	0.00	0.00	3.18
952	5439	1.740585	TCGGTGGCCATATTTTGTTCG	59.259	47.619	9.72	2.56	0.00	3.95
953	5440	1.740585	CGGTGGCCATATTTTGTTCGA	59.259	47.619	9.72	0.00	0.00	3.71
954	5441	2.357637	CGGTGGCCATATTTTGTTCGAT	59.642	45.455	9.72	0.00	0.00	3.59
956	5443	4.359706	GGTGGCCATATTTTGTTCGATTC	58.640	43.478	9.72	0.00	0.00	2.52
957	5444	4.142271	GGTGGCCATATTTTGTTCGATTCA	60.142	41.667	9.72	0.00	0.00	2.57
958	5445	4.798387	GTGGCCATATTTTGTTCGATTCAC	59.202	41.667	9.72	0.00	0.00	3.18
959	5446	4.704540	TGGCCATATTTTGTTCGATTCACT	59.295	37.500	0.00	0.00	0.00	3.41
960	5447	5.184864	TGGCCATATTTTGTTCGATTCACTT	59.815	36.000	0.00	0.00	0.00	3.16
961	5448	5.743872	GGCCATATTTTGTTCGATTCACTTC	59.256	40.000	0.00	0.00	0.00	3.01
962	5449	6.321717	GCCATATTTTGTTCGATTCACTTCA	58.678	36.000	0.00	0.00	0.00	3.02
963	5450	6.974622	GCCATATTTTGTTCGATTCACTTCAT	59.025	34.615	0.00	0.00	0.00	2.57
964	5451	7.166473	GCCATATTTTGTTCGATTCACTTCATC	59.834	37.037	0.00	0.00	0.00	2.92
965	5452	7.645340	CCATATTTTGTTCGATTCACTTCATCC	59.355	37.037	0.00	0.00	0.00	3.51
966	5453	6.824305	ATTTTGTTCGATTCACTTCATCCT	57.176	33.333	0.00	0.00	0.00	3.24
967	5454	5.611796	TTTGTTCGATTCACTTCATCCTG	57.388	39.130	0.00	0.00	0.00	3.86
968	5455	4.535526	TGTTCGATTCACTTCATCCTGA	57.464	40.909	0.00	0.00	0.00	3.86
969	5456	4.498241	TGTTCGATTCACTTCATCCTGAG	58.502	43.478	0.00	0.00	0.00	3.35
970	5457	3.808466	TCGATTCACTTCATCCTGAGG	57.192	47.619	0.00	0.00	0.00	3.86
971	5458	3.099905	TCGATTCACTTCATCCTGAGGT	58.900	45.455	0.00	0.00	37.15	3.85
972	5459	3.515502	TCGATTCACTTCATCCTGAGGTT	59.484	43.478	0.00	0.00	34.25	3.50
973	5460	4.020218	TCGATTCACTTCATCCTGAGGTTT	60.020	41.667	0.00	0.00	34.25	3.27
974	5461	5.186992	TCGATTCACTTCATCCTGAGGTTTA	59.813	40.000	0.00	0.00	34.25	2.01
975	5462	5.521735	CGATTCACTTCATCCTGAGGTTTAG	59.478	44.000	0.00	0.00	34.25	1.85
976	5463	4.207891	TCACTTCATCCTGAGGTTTAGC	57.792	45.455	0.00	0.00	34.25	3.09
977	5464	3.582647	TCACTTCATCCTGAGGTTTAGCA	59.417	43.478	0.00	0.00	34.25	3.49
978	5465	3.937706	CACTTCATCCTGAGGTTTAGCAG	59.062	47.826	0.00	0.00	34.25	4.24
996	5483	0.032678	AGGAGCTTGATATCGGTGCG	59.967	55.000	0.00	0.00	0.00	5.34
1014	5501	3.602103	GCAATGGACGCCATGGAA	58.398	55.556	18.40	0.00	44.40	3.53
1024	5511	0.745845	CGCCATGGAAAGAGGACAGG	60.746	60.000	18.40	0.00	0.00	4.00
1029	5516	1.219393	GGAAAGAGGACAGGGCTCG	59.781	63.158	0.00	0.00	0.00	5.03
1134	5626	1.196808	CTAACGAACTTGCGGCACAAT	59.803	47.619	0.05	0.00	37.72	2.71
1203	5695	2.739932	GCCGCTGATAGAGAGCAAGAAA	60.740	50.000	0.00	0.00	36.12	2.52
1302	5794	2.672414	GGTGCTGTACCTGGAGAGT	58.328	57.895	7.75	0.00	46.51	3.24
1375	5867	4.020617	CCAGCTTCCTCACGCCCA	62.021	66.667	0.00	0.00	0.00	5.36
1503	6006	3.435186	GGCGTGGCAGCTTCTTCC	61.435	66.667	8.45	0.00	37.29	3.46
1504	6007	2.359230	GCGTGGCAGCTTCTTCCT	60.359	61.111	0.00	0.00	0.00	3.36
1505	6008	2.394563	GCGTGGCAGCTTCTTCCTC	61.395	63.158	0.00	0.00	0.00	3.71
1506	6009	1.743252	CGTGGCAGCTTCTTCCTCC	60.743	63.158	0.00	0.00	0.00	4.30
1507	6010	1.376466	GTGGCAGCTTCTTCCTCCA	59.624	57.895	0.00	0.00	0.00	3.86
1508	6011	0.034670	GTGGCAGCTTCTTCCTCCAT	60.035	55.000	0.00	0.00	0.00	3.41
1509	6012	0.034767	TGGCAGCTTCTTCCTCCATG	60.035	55.000	0.00	0.00	0.00	3.66
1510	6013	1.382692	GGCAGCTTCTTCCTCCATGC	61.383	60.000	0.00	0.00	0.00	4.06
1586	6089	1.427592	GCTCATCACCTTCTCTGCGC	61.428	60.000	0.00	0.00	0.00	6.09
2089	6619	2.434884	AGGATCGCGCACACCAAG	60.435	61.111	8.75	0.00	0.00	3.61
2417	6947	3.417275	CTGCTCTACGGCTCGGTGG	62.417	68.421	0.00	0.00	0.00	4.61
2885	12625	1.080705	GTCGTGTACAGCGCCTTCT	60.081	57.895	2.29	0.00	0.00	2.85
3337	13083	2.235155	TGAACACATACGCACACCCTAT	59.765	45.455	0.00	0.00	0.00	2.57
3540	13286	1.087771	CGCCTAACCATCCAACCGAC	61.088	60.000	0.00	0.00	0.00	4.79
3637	13383	3.454375	GTGGGTTACATACTCGGTCATG	58.546	50.000	0.00	0.00	0.00	3.07
3644	13390	6.812160	GGTTACATACTCGGTCATGGATATTC	59.188	42.308	0.00	0.00	0.00	1.75
3863	13609	0.393402	GCATGCATGAGAGGTGGACA	60.393	55.000	30.64	0.00	0.00	4.02
3875	13621	5.830457	TGAGAGGTGGACAGAGATACAATAG	59.170	44.000	0.00	0.00	0.00	1.73

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
22	23	2.872557	CCATGACAGCGTGGCAAG	59.127	61.111	0.00	0.00	39.86	4.01
128	141	1.327690	TATGCACCAGAGGACCGTCC	61.328	60.000	9.81	9.81	36.58	4.79
149	162	0.450583	TCCAGAAAGACGTCGATCGG	59.549	55.000	16.41	16.00	44.69	4.18
154	167	1.336887	ACACCATCCAGAAAGACGTCG	60.337	52.381	10.46	0.00	0.00	5.12
155	168	2.069273	CACACCATCCAGAAAGACGTC	58.931	52.381	7.70	7.70	0.00	4.34
156	169	1.878102	GCACACCATCCAGAAAGACGT	60.878	52.381	0.00	0.00	0.00	4.34
157	170	0.798776	GCACACCATCCAGAAAGACG	59.201	55.000	0.00	0.00	0.00	4.18
177	190	0.735287	GCGGTACAACGAGGAAGGAC	60.735	60.000	0.00	0.00	35.47	3.85
182	195	3.367743	AGCGCGGTACAACGAGGA	61.368	61.111	10.12	0.00	34.18	3.71
194	207	0.861837	AAGTTCAGACTTTCAGCGCG	59.138	50.000	0.00	0.00	43.48	6.86
196	209	4.384247	CAGACTAAGTTCAGACTTTCAGCG	59.616	45.833	0.00	0.00	43.48	5.18
199	212	5.276461	TGCAGACTAAGTTCAGACTTTCA	57.724	39.130	0.00	0.00	43.48	2.69
243	256	5.057149	AGATAAGTATTTGGTGATCGGCAC	58.943	41.667	1.37	1.37	46.98	5.01
254	267	6.371825	GGATAAGGCGGGAAGATAAGTATTTG	59.628	42.308	0.00	0.00	0.00	2.32
271	284	1.153429	AGTTCACCGCGGATAAGGC	60.153	57.895	35.90	15.99	0.00	4.35
272	285	0.810031	CCAGTTCACCGCGGATAAGG	60.810	60.000	35.90	20.69	0.00	2.69
273	286	0.174845	TCCAGTTCACCGCGGATAAG	59.825	55.000	35.90	18.27	0.00	1.73
301	314	2.338500	GCCCTGTTACTTTCACTCTCG	58.662	52.381	0.00	0.00	0.00	4.04
318	331	1.454663	GCAAGGAAGGATCTGGCCC	60.455	63.158	0.00	0.00	0.00	5.80
335	348	0.603707	TGATATGCCTTGGCGCTAGC	60.604	55.000	7.64	4.06	44.18	3.42
340	646	0.029834	GTGCTTGATATGCCTTGGCG	59.970	55.000	7.18	0.00	0.00	5.69
345	651	3.605634	TGTAAACGTGCTTGATATGCCT	58.394	40.909	0.00	0.00	0.00	4.75
378	684	1.502190	GAACTTTACTGCGCCCAGC	59.498	57.895	4.18	0.00	43.02	4.85
379	685	1.305930	GGGAACTTTACTGCGCCCAG	61.306	60.000	4.18	0.00	44.80	4.45
380	686	1.302993	GGGAACTTTACTGCGCCCA	60.303	57.895	4.18	0.00	35.63	5.36
384	690	1.743995	CCGGGGGAACTTTACTGCG	60.744	63.158	0.00	0.00	0.00	5.18
398	704	3.361977	CGTGGCAACTTTCCCGGG	61.362	66.667	16.85	16.85	37.61	5.73
433	739	1.734388	GCGTGGGGTCTGCACTTTTT	61.734	55.000	0.00	0.00	0.00	1.94
458	764	4.149046	GCGATAATCCTAGCTTCACGAAAG	59.851	45.833	0.00	0.00	38.08	2.62
459	765	4.049186	GCGATAATCCTAGCTTCACGAAA	58.951	43.478	0.00	0.00	0.00	3.46
460	766	3.067601	TGCGATAATCCTAGCTTCACGAA	59.932	43.478	0.00	0.00	0.00	3.85
461	767	2.621526	TGCGATAATCCTAGCTTCACGA	59.378	45.455	0.00	0.00	0.00	4.35
462	768	2.726760	GTGCGATAATCCTAGCTTCACG	59.273	50.000	0.00	0.00	0.00	4.35
463	769	2.726760	CGTGCGATAATCCTAGCTTCAC	59.273	50.000	0.00	0.00	0.00	3.18
464	770	2.862530	GCGTGCGATAATCCTAGCTTCA	60.863	50.000	0.00	0.00	0.00	3.02
465	771	1.721926	GCGTGCGATAATCCTAGCTTC	59.278	52.381	0.00	0.00	0.00	3.86
466	772	1.068588	TGCGTGCGATAATCCTAGCTT	59.931	47.619	0.00	0.00	0.00	3.74
467	773	0.673985	TGCGTGCGATAATCCTAGCT	59.326	50.000	0.00	0.00	0.00	3.32
468	774	1.497991	TTGCGTGCGATAATCCTAGC	58.502	50.000	0.00	0.00	0.00	3.42
469	775	3.303132	GGTTTTGCGTGCGATAATCCTAG	60.303	47.826	0.00	0.00	0.00	3.02
470	776	2.610374	GGTTTTGCGTGCGATAATCCTA	59.390	45.455	0.00	0.00	0.00	2.94
471	777	1.400494	GGTTTTGCGTGCGATAATCCT	59.600	47.619	0.00	0.00	0.00	3.24
472	778	1.533129	GGGTTTTGCGTGCGATAATCC	60.533	52.381	0.00	0.00	0.00	3.01
473	779	1.533129	GGGGTTTTGCGTGCGATAATC	60.533	52.381	0.00	0.00	0.00	1.75
474	780	0.454196	GGGGTTTTGCGTGCGATAAT	59.546	50.000	0.00	0.00	0.00	1.28
475	781	0.606944	AGGGGTTTTGCGTGCGATAA	60.607	50.000	0.00	0.00	0.00	1.75
476	782	1.003112	AGGGGTTTTGCGTGCGATA	60.003	52.632	0.00	0.00	0.00	2.92
477	783	2.282180	AGGGGTTTTGCGTGCGAT	60.282	55.556	0.00	0.00	0.00	4.58
478	784	2.975799	GAGGGGTTTTGCGTGCGA	60.976	61.111	0.00	0.00	0.00	5.10
479	785	4.038080	GGAGGGGTTTTGCGTGCG	62.038	66.667	0.00	0.00	0.00	5.34
480	786	3.680786	GGGAGGGGTTTTGCGTGC	61.681	66.667	0.00	0.00	0.00	5.34
481	787	3.361977	CGGGAGGGGTTTTGCGTG	61.362	66.667	0.00	0.00	0.00	5.34
482	788	3.837570	GACGGGAGGGGTTTTGCGT	62.838	63.158	0.00	0.00	0.00	5.24
483	789	3.053896	GACGGGAGGGGTTTTGCG	61.054	66.667	0.00	0.00	0.00	4.85
484	790	1.674651	GAGACGGGAGGGGTTTTGC	60.675	63.158	0.00	0.00	0.00	3.68
485	791	0.605589	GTGAGACGGGAGGGGTTTTG	60.606	60.000	0.00	0.00	0.00	2.44
486	792	1.057851	TGTGAGACGGGAGGGGTTTT	61.058	55.000	0.00	0.00	0.00	2.43
487	793	1.057851	TTGTGAGACGGGAGGGGTTT	61.058	55.000	0.00	0.00	0.00	3.27
488	794	1.460689	TTGTGAGACGGGAGGGGTT	60.461	57.895	0.00	0.00	0.00	4.11
545	853	3.686760	GGAAGTTTCCCTGCTGCC	58.313	61.111	0.00	0.00	41.62	4.85
616	5067	5.106791	CGTAGTGGTACTAGAATATGACCGG	60.107	48.000	0.00	0.00	30.12	5.28
650	5101	3.075005	ATCGTGGTAGCAGGCGGT	61.075	61.111	9.69	0.00	0.00	5.68
727	5178	0.389025	CCCCGGCAAAGGATAAATGC	59.611	55.000	0.00	0.00	39.33	3.56
802	5285	3.465296	ATTAGCCGACGACGCGAGG	62.465	63.158	15.93	6.33	38.29	4.63
870	5356	1.346068	GTGAGAGCCTTGAAGGTGAGT	59.654	52.381	13.58	0.00	37.80	3.41
878	5365	3.700109	CTCGGGTGAGAGCCTTGA	58.300	61.111	0.00	0.00	45.57	3.02
905	5392	1.000163	GCTATAGCTAGCGCCTTGTGA	60.000	52.381	17.75	0.00	40.95	3.58
918	5405	4.120589	GGCCACCGATATTAAGCTATAGC	58.879	47.826	17.33	17.33	42.49	2.97
921	5408	4.844349	ATGGCCACCGATATTAAGCTAT	57.156	40.909	8.16	0.00	0.00	2.97
922	5409	5.950544	ATATGGCCACCGATATTAAGCTA	57.049	39.130	8.16	0.00	0.00	3.32
927	5414	6.072948	CGAACAAAATATGGCCACCGATATTA	60.073	38.462	8.16	0.00	0.00	0.98
928	5415	5.278266	CGAACAAAATATGGCCACCGATATT	60.278	40.000	8.16	5.40	0.00	1.28
930	5417	3.562141	CGAACAAAATATGGCCACCGATA	59.438	43.478	8.16	0.00	0.00	2.92
931	5418	2.357637	CGAACAAAATATGGCCACCGAT	59.642	45.455	8.16	0.00	0.00	4.18
934	5421	4.142271	TGAATCGAACAAAATATGGCCACC	60.142	41.667	8.16	0.00	0.00	4.61
935	5422	4.798387	GTGAATCGAACAAAATATGGCCAC	59.202	41.667	8.16	0.00	0.00	5.01
936	5423	4.704540	AGTGAATCGAACAAAATATGGCCA	59.295	37.500	8.56	8.56	0.00	5.36
939	5426	7.645340	GGATGAAGTGAATCGAACAAAATATGG	59.355	37.037	0.00	0.00	0.00	2.74
940	5427	8.400947	AGGATGAAGTGAATCGAACAAAATATG	58.599	33.333	0.00	0.00	0.00	1.78
941	5428	8.400947	CAGGATGAAGTGAATCGAACAAAATAT	58.599	33.333	0.00	0.00	39.69	1.28
943	5430	6.430925	TCAGGATGAAGTGAATCGAACAAAAT	59.569	34.615	0.00	0.00	45.97	1.82
944	5431	5.762711	TCAGGATGAAGTGAATCGAACAAAA	59.237	36.000	0.00	0.00	45.97	2.44
945	5432	5.304778	TCAGGATGAAGTGAATCGAACAAA	58.695	37.500	0.00	0.00	45.97	2.83
946	5433	4.893608	TCAGGATGAAGTGAATCGAACAA	58.106	39.130	0.00	0.00	45.97	2.83
947	5434	4.535526	TCAGGATGAAGTGAATCGAACA	57.464	40.909	0.00	0.00	45.97	3.18
975	5462	1.506493	CACCGATATCAAGCTCCTGC	58.494	55.000	3.12	0.00	40.05	4.85
976	5463	1.506493	GCACCGATATCAAGCTCCTG	58.494	55.000	3.12	0.00	0.00	3.86
977	5464	0.032678	CGCACCGATATCAAGCTCCT	59.967	55.000	3.12	0.00	0.00	3.69
978	5465	0.946221	CCGCACCGATATCAAGCTCC	60.946	60.000	3.12	0.00	0.00	4.70
979	5466	1.560860	GCCGCACCGATATCAAGCTC	61.561	60.000	3.12	0.00	0.00	4.09
980	5467	1.595382	GCCGCACCGATATCAAGCT	60.595	57.895	3.12	0.00	0.00	3.74
981	5468	1.436195	TTGCCGCACCGATATCAAGC	61.436	55.000	3.12	2.46	0.00	4.01
985	5472	0.602638	TCCATTGCCGCACCGATATC	60.603	55.000	0.00	0.00	0.00	1.63
987	5474	1.522806	GTCCATTGCCGCACCGATA	60.523	57.895	0.00	0.00	0.00	2.92
1014	5501	3.394836	GGCGAGCCCTGTCCTCTT	61.395	66.667	1.97	0.00	0.00	2.85
1375	5867	3.620785	GAGGATGGCGCCGAGGAT	61.621	66.667	23.90	9.73	0.00	3.24
1510	6013	5.121811	AGTTAGTTAAGCTCATGCATGGAG	58.878	41.667	25.97	20.73	42.74	3.86
1586	6089	4.135153	CTCGGTGGTCGGCAGGAG	62.135	72.222	0.00	0.00	39.77	3.69
2089	6619	0.313043	TGTCGAGGAACGTGAACTCC	59.687	55.000	8.31	2.78	43.13	3.85
2401	6931	3.412879	GACCACCGAGCCGTAGAGC	62.413	68.421	0.00	0.00	0.00	4.09
2524	7057	0.980231	GCCTCCTCATCTCCACCAGT	60.980	60.000	0.00	0.00	0.00	4.00
2885	12625	4.342359	GTCTTCACCTGGTAGTTCCTAGA	58.658	47.826	0.00	0.00	37.07	2.43
3283	13029	2.169832	ATGCGCGTAAATAGGAGCAT	57.830	45.000	15.41	15.41	46.84	3.79
3337	13083	2.363018	CTCTCCCAGGTGCTCGGA	60.363	66.667	0.00	0.00	0.00	4.55
3540	13286	2.192624	CAAAAGACAGCAAACCAACCG	58.807	47.619	0.00	0.00	0.00	4.44
3637	13383	6.936900	TCTACAAAATAGCTGGCTGAATATCC	59.063	38.462	5.25	0.00	0.00	2.59
3863	13609	9.250246	GTATCTTCCTAAGCCTATTGTATCTCT	57.750	37.037	0.00	0.00	0.00	3.10
3875	13621	4.500035	CCGAGACAAGTATCTTCCTAAGCC	60.500	50.000	0.00	0.00	0.00	4.35

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.