AutoCloner

Multiple sequence alignment - TraesCS6D01G093100

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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	TraesCS6D01G093100	chr6D	100.000	3254	0	0	1	3254	58094205	58097458	0.000000e+00	6010.0
1	TraesCS6D01G093100	chr6D	83.597	1329	179	24	989	2311	58242521	58243816	0.000000e+00	1210.0
2	TraesCS6D01G093100	chr6D	78.280	1128	185	42	1330	2444	58230696	58231776	0.000000e+00	671.0
3	TraesCS6D01G093100	chr6D	73.877	1447	284	61	956	2381	58418082	58419455	2.920000e-135	492.0
4	TraesCS6D01G093100	chr6D	76.934	711	106	35	961	1663	57215876	57216536	5.170000e-93	351.0
5	TraesCS6D01G093100	chr6D	82.461	382	58	6	2449	2824	58244121	58244499	3.130000e-85	326.0
6	TraesCS6D01G093100	chr6D	74.154	650	127	31	1029	1668	58047126	58047744	7.020000e-57	231.0
7	TraesCS6D01G093100	chr6B	93.134	2403	126	18	1	2393	130323397	130325770	0.000000e+00	3487.0
8	TraesCS6D01G093100	chr6B	79.628	1507	239	45	917	2408	77746748	77748201	0.000000e+00	1020.0
9	TraesCS6D01G093100	chr6B	97.830	553	11	1	2391	2943	130325863	130326414	0.000000e+00	953.0
10	TraesCS6D01G093100	chr6B	97.834	277	6	0	2978	3254	130326414	130326690	2.270000e-131	479.0
11	TraesCS6D01G093100	chr6B	77.614	679	102	27	992	1663	129268684	129269319	1.840000e-97	366.0
12	TraesCS6D01G093100	chr6B	84.016	244	32	5	1	241	275483567	275483328	9.080000e-56	228.0
13	TraesCS6D01G093100	chr6B	80.797	276	51	1	398	673	707819319	707819592	7.070000e-52	215.0
14	TraesCS6D01G093100	chr6B	80.385	260	49	1	398	657	707819821	707820078	2.560000e-46	196.0
15	TraesCS6D01G093100	chr6B	78.000	350	36	25	2778	3122	130565857	130566170	7.170000e-42	182.0
16	TraesCS6D01G093100	chr6A	90.974	842	62	8	1	837	73445784	73446616	0.000000e+00	1122.0
17	TraesCS6D01G093100	chr6A	80.598	1371	204	28	950	2311	73559268	73560585	0.000000e+00	1002.0
18	TraesCS6D01G093100	chr6A	76.338	710	112	31	961	1663	72429399	72430059	2.420000e-86	329.0
19	TraesCS6D01G093100	chr6A	80.155	388	59	7	2449	2824	73560794	73561175	1.150000e-69	274.0
20	TraesCS6D01G093100	chr6A	84.274	248	29	9	1	243	420467357	420467115	1.950000e-57	233.0
21	TraesCS6D01G093100	chr6A	74.114	649	129	26	1029	1668	73379375	73379993	7.020000e-57	231.0
22	TraesCS6D01G093100	chr6A	83.607	244	29	9	3	243	55304193	55304428	5.470000e-53	219.0
23	TraesCS6D01G093100	chr6A	78.477	302	34	16	2457	2740	73511874	73512162	5.580000e-38	169.0
24	TraesCS6D01G093100	chr6A	84.559	136	14	3	2961	3094	73525488	73525618	9.480000e-26	128.0
25	TraesCS6D01G093100	chrUn	80.286	1537	252	36	917	2443	112686720	112685225	0.000000e+00	1112.0
26	TraesCS6D01G093100	chrUn	78.971	1555	249	40	917	2444	112925609	112927112	0.000000e+00	989.0
27	TraesCS6D01G093100	chrUn	81.588	277	46	4	398	673	47560569	47560841	1.170000e-54	224.0
28	TraesCS6D01G093100	chrUn	83.186	226	38	0	419	644	47560086	47560311	1.180000e-49	207.0
29	TraesCS6D01G093100	chrUn	100.000	28	0	0	1334	1361	373622708	373622735	6.000000e-03	52.8
30	TraesCS6D01G093100	chr1A	84.211	247	30	8	1	243	425961933	425961692	7.020000e-57	231.0
31	TraesCS6D01G093100	chr2A	85.520	221	27	4	25	242	477728488	477728706	3.270000e-55	226.0
32	TraesCS6D01G093100	chr7A	83.539	243	30	8	3	242	492786491	492786256	5.470000e-53	219.0
33	TraesCS6D01G093100	chr2B	82.927	246	34	7	1	243	448110569	448110809	7.070000e-52	215.0
34	TraesCS6D01G093100	chr2B	79.783	277	52	4	398	673	584817175	584816902	7.120000e-47	198.0
35	TraesCS6D01G093100	chr1B	82.773	238	35	4	410	644	14495166	14494932	1.180000e-49	207.0
36	TraesCS6D01G093100	chr1B	94.737	38	2	0	799	836	343921591	343921628	3.510000e-05	60.2
37	TraesCS6D01G093100	chr1B	94.444	36	2	0	796	831	343665300	343665335	4.540000e-04	56.5
38	TraesCS6D01G093100	chr3B	80.000	280	51	3	397	673	743127442	743127165	5.510000e-48	202.0
39	TraesCS6D01G093100	chr7D	92.453	53	4	0	798	850	506506210	506506262	3.480000e-10	76.8
40	TraesCS6D01G093100	chr7B	89.583	48	5	0	801	848	677164089	677164136	9.750000e-06	62.1
41	TraesCS6D01G093100	chr7B	94.444	36	2	0	796	831	701637037	701637072	4.540000e-04	56.5
42	TraesCS6D01G093100	chr7B	89.130	46	2	1	804	849	683166894	683166852	2.000000e-03	54.7
43	TraesCS6D01G093100	chr3D	94.595	37	2	0	800	836	588869705	588869741	1.260000e-04	58.4
44	TraesCS6D01G093100	chr2D	100.000	29	0	0	1334	1362	628996519	628996491	2.000000e-03	54.7
45	TraesCS6D01G093100	chr5B	96.875	32	0	1	2580	2611	462323444	462323414	6.000000e-03	52.8
46	TraesCS6D01G093100	chr6D	100.000	3254	0	0	1	3254	58094205	58097458	0.000000e+00	6010.0
47	TraesCS6D01G093100	chr6D	83.597	1329	179	24	989	2311	58242521	58243816	0.000000e+00	1210.0
48	TraesCS6D01G093100	chr6D	78.280	1128	185	42	1330	2444	58230696	58231776	0.000000e+00	671.0
49	TraesCS6D01G093100	chr6D	73.877	1447	284	61	956	2381	58418082	58419455	2.920000e-135	492.0
50	TraesCS6D01G093100	chr6D	76.934	711	106	35	961	1663	57215876	57216536	5.170000e-93	351.0
51	TraesCS6D01G093100	chr6D	82.461	382	58	6	2449	2824	58244121	58244499	3.130000e-85	326.0
52	TraesCS6D01G093100	chr6D	74.154	650	127	31	1029	1668	58047126	58047744	7.020000e-57	231.0
53	TraesCS6D01G093100	chr6B	93.134	2403	126	18	1	2393	130323397	130325770	0.000000e+00	3487.0
54	TraesCS6D01G093100	chr6B	79.628	1507	239	45	917	2408	77746748	77748201	0.000000e+00	1020.0
55	TraesCS6D01G093100	chr6B	97.830	553	11	1	2391	2943	130325863	130326414	0.000000e+00	953.0
56	TraesCS6D01G093100	chr6B	97.834	277	6	0	2978	3254	130326414	130326690	2.270000e-131	479.0
57	TraesCS6D01G093100	chr6B	77.614	679	102	27	992	1663	129268684	129269319	1.840000e-97	366.0
58	TraesCS6D01G093100	chr6B	84.016	244	32	5	1	241	275483567	275483328	9.080000e-56	228.0
59	TraesCS6D01G093100	chr6B	80.797	276	51	1	398	673	707819319	707819592	7.070000e-52	215.0
60	TraesCS6D01G093100	chr6B	80.385	260	49	1	398	657	707819821	707820078	2.560000e-46	196.0
61	TraesCS6D01G093100	chr6B	78.000	350	36	25	2778	3122	130565857	130566170	7.170000e-42	182.0
62	TraesCS6D01G093100	chr6A	90.974	842	62	8	1	837	73445784	73446616	0.000000e+00	1122.0
63	TraesCS6D01G093100	chr6A	80.598	1371	204	28	950	2311	73559268	73560585	0.000000e+00	1002.0
64	TraesCS6D01G093100	chr6A	76.338	710	112	31	961	1663	72429399	72430059	2.420000e-86	329.0
65	TraesCS6D01G093100	chr6A	80.155	388	59	7	2449	2824	73560794	73561175	1.150000e-69	274.0
66	TraesCS6D01G093100	chr6A	84.274	248	29	9	1	243	420467357	420467115	1.950000e-57	233.0
67	TraesCS6D01G093100	chr6A	74.114	649	129	26	1029	1668	73379375	73379993	7.020000e-57	231.0
68	TraesCS6D01G093100	chr6A	83.607	244	29	9	3	243	55304193	55304428	5.470000e-53	219.0
69	TraesCS6D01G093100	chr6A	78.477	302	34	16	2457	2740	73511874	73512162	5.580000e-38	169.0
70	TraesCS6D01G093100	chr6A	84.559	136	14	3	2961	3094	73525488	73525618	9.480000e-26	128.0
71	TraesCS6D01G093100	chrUn	80.286	1537	252	36	917	2443	112686720	112685225	0.000000e+00	1112.0
72	TraesCS6D01G093100	chrUn	78.971	1555	249	40	917	2444	112925609	112927112	0.000000e+00	989.0
73	TraesCS6D01G093100	chrUn	81.588	277	46	4	398	673	47560569	47560841	1.170000e-54	224.0
74	TraesCS6D01G093100	chrUn	83.186	226	38	0	419	644	47560086	47560311	1.180000e-49	207.0
75	TraesCS6D01G093100	chrUn	100.000	28	0	0	1334	1361	373622708	373622735	6.000000e-03	52.8
76	TraesCS6D01G093100	chr1A	84.211	247	30	8	1	243	425961933	425961692	7.020000e-57	231.0
77	TraesCS6D01G093100	chr2A	85.520	221	27	4	25	242	477728488	477728706	3.270000e-55	226.0
78	TraesCS6D01G093100	chr7A	83.539	243	30	8	3	242	492786491	492786256	5.470000e-53	219.0
79	TraesCS6D01G093100	chr2B	82.927	246	34	7	1	243	448110569	448110809	7.070000e-52	215.0
80	TraesCS6D01G093100	chr2B	79.783	277	52	4	398	673	584817175	584816902	7.120000e-47	198.0
81	TraesCS6D01G093100	chr1B	82.773	238	35	4	410	644	14495166	14494932	1.180000e-49	207.0
82	TraesCS6D01G093100	chr1B	94.737	38	2	0	799	836	343921591	343921628	3.510000e-05	60.2
83	TraesCS6D01G093100	chr1B	94.444	36	2	0	796	831	343665300	343665335	4.540000e-04	56.5
84	TraesCS6D01G093100	chr3B	80.000	280	51	3	397	673	743127442	743127165	5.510000e-48	202.0
85	TraesCS6D01G093100	chr7D	92.453	53	4	0	798	850	506506210	506506262	3.480000e-10	76.8
86	TraesCS6D01G093100	chr7B	89.583	48	5	0	801	848	677164089	677164136	9.750000e-06	62.1
87	TraesCS6D01G093100	chr7B	94.444	36	2	0	796	831	701637037	701637072	4.540000e-04	56.5
88	TraesCS6D01G093100	chr7B	89.130	46	2	1	804	849	683166894	683166852	2.000000e-03	54.7
89	TraesCS6D01G093100	chr3D	94.595	37	2	0	800	836	588869705	588869741	1.260000e-04	58.4
90	TraesCS6D01G093100	chr2D	100.000	29	0	0	1334	1362	628996519	628996491	2.000000e-03	54.7
91	TraesCS6D01G093100	chr5B	96.875	32	0	1	2580	2611	462323444	462323414	6.000000e-03	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	TraesCS6D01G093100	chr6D	58094205	58097458	3253	False	6010.000000	6010	100.0000	1	3254	2	chr6D.!!$F3	3253
1	TraesCS6D01G093100	chr6D	58242521	58244499	1978	False	768.000000	1210	83.0290	989	2824	4	chr6D.!!$F5	1835
2	TraesCS6D01G093100	chr6D	58230696	58231776	1080	False	671.000000	671	78.2800	1330	2444	2	chr6D.!!$F4	1114
3	TraesCS6D01G093100	chr6D	58418082	58419455	1373	False	492.000000	492	73.8770	956	2381	2	chr6D.!!$F6	1425
4	TraesCS6D01G093100	chr6D	57215876	57216536	660	False	351.000000	351	76.9340	961	1663	2	chr6D.!!$F1	702
5	TraesCS6D01G093100	chr6D	58047126	58047744	618	False	231.000000	231	74.1540	1029	1668	2	chr6D.!!$F2	639
6	TraesCS6D01G093100	chr6B	130323397	130326690	3293	False	1639.666667	3487	96.2660	1	3254	6	chr6B.!!$F3	3253
7	TraesCS6D01G093100	chr6B	77746748	77748201	1453	False	1020.000000	1020	79.6280	917	2408	2	chr6B.!!$F1	1491
8	TraesCS6D01G093100	chr6B	129268684	129269319	635	False	366.000000	366	77.6140	992	1663	2	chr6B.!!$F2	671
9	TraesCS6D01G093100	chr6B	707819319	707820078	759	False	205.500000	215	80.5910	398	673	4	chr6B.!!$F5	275
10	TraesCS6D01G093100	chr6A	73445784	73446616	832	False	1122.000000	1122	90.9740	1	837	2	chr6A.!!$F4	836
11	TraesCS6D01G093100	chr6A	73559268	73561175	1907	False	638.000000	1002	80.3765	950	2824	4	chr6A.!!$F7	1874
12	TraesCS6D01G093100	chr6A	72429399	72430059	660	False	329.000000	329	76.3380	961	1663	2	chr6A.!!$F2	702
13	TraesCS6D01G093100	chr6A	73379375	73379993	618	False	231.000000	231	74.1140	1029	1668	2	chr6A.!!$F3	639
14	TraesCS6D01G093100	chrUn	112685225	112686720	1495	True	1112.000000	1112	80.2860	917	2443	2	chrUn.!!$R1	1526
15	TraesCS6D01G093100	chrUn	112925609	112927112	1503	False	989.000000	989	78.9710	917	2444	2	chrUn.!!$F2	1527
16	TraesCS6D01G093100	chrUn	47560086	47560841	755	False	215.500000	224	82.3870	398	673	4	chrUn.!!$F1	275

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
881	1391	0.32005	TTTTTGAAATGGGCCGCCTC	59.68	50.0	9.86	0.0	0.0	4.7	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2422	3450	2.03187	ACCTTTCCTGGTTTGACAAGC	58.968	47.619	0.0	0.0	36.89	4.01	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
142	143	8.491331	TTCCCTTTCATTCAACTTTCAAAAAG	57.509	30.769	0.00	0.00	0.00	2.27
467	970	3.342719	TGTCTCAAATATTGCAAGCGGA	58.657	40.909	4.94	0.00	0.00	5.54
538	1042	3.574826	AGAGTACGAGAAGTTTTGAGGCT	59.425	43.478	0.00	0.00	0.00	4.58
586	1090	3.959535	TTATAAACCGGACACGTTCCT	57.040	42.857	9.46	0.48	43.25	3.36
590	1094	0.466963	AACCGGACACGTTCCTTCTT	59.533	50.000	9.46	0.00	43.25	2.52
644	1148	0.601558	TACAAGCGGTCTCAGGTGAC	59.398	55.000	0.00	0.00	36.31	3.67
659	1163	3.818773	CAGGTGACCCTTATTCAAAACGT	59.181	43.478	0.00	0.00	39.89	3.99
665	1169	3.818773	ACCCTTATTCAAAACGTGTCCAG	59.181	43.478	0.00	0.00	0.00	3.86
689	1193	9.401058	CAGACTTTTATGAAGGGAAAGATGTAT	57.599	33.333	2.45	0.00	35.09	2.29
740	1244	1.153449	CCCATATGCGTGACGGTGT	60.153	57.895	7.25	0.00	0.00	4.16
754	1258	0.944311	CGGTGTGAGAGGTGTTTCCG	60.944	60.000	0.00	0.00	41.99	4.30
817	1321	3.723260	ACATACAACGTGACACATGTGA	58.277	40.909	31.94	8.09	33.54	3.58
826	1330	4.093408	ACGTGACACATGTGATAAGCAATC	59.907	41.667	31.94	16.13	31.87	2.67
881	1391	0.320050	TTTTTGAAATGGGCCGCCTC	59.680	50.000	9.86	0.00	0.00	4.70
890	1400	1.976474	GGGCCGCCTCAAATTGTGA	60.976	57.895	9.86	0.00	34.17	3.58
898	1408	5.687285	GCCGCCTCAAATTGTGAAATTATAG	59.313	40.000	0.00	0.00	35.22	1.31
938	1454	2.180204	GCACAACACACCACGCTCT	61.180	57.895	0.00	0.00	0.00	4.09
1027	1571	2.098871	CGGCGTCGTACATCGTCA	59.901	61.111	0.00	0.00	40.80	4.35
1193	1740	1.243902	GGATTCGCCCTTGACAAACA	58.756	50.000	0.00	0.00	0.00	2.83
1399	2178	2.924290	GACATCGAGCCAGTCTTTACAC	59.076	50.000	0.00	0.00	0.00	2.90
1530	2319	0.399454	CCATTGGCGAGGATGAGGAT	59.601	55.000	0.00	0.00	0.00	3.24
1534	2323	0.106015	TGGCGAGGATGAGGATGAGA	60.106	55.000	0.00	0.00	0.00	3.27
1614	2403	3.314913	TCACGTTTGTGTACTCTTCCGTA	59.685	43.478	0.00	0.00	46.49	4.02
1678	2470	2.191641	GCACAGATGAGCCCCCTC	59.808	66.667	0.00	0.00	38.62	4.30
1692	2485	1.305930	CCCCTCGGAAAGGCTTTTCG	61.306	60.000	30.18	30.18	44.71	3.46
2086	2882	1.496060	AGCTCGGTGGGATGACAATA	58.504	50.000	0.00	0.00	0.00	1.90
2094	2890	3.136443	GGTGGGATGACAATAGACATGGA	59.864	47.826	0.00	0.00	30.38	3.41
2422	3450	5.862924	AACGGTTCATGTGATTGTTAGAG	57.137	39.130	0.00	0.00	0.00	2.43
2476	3596	7.055667	TCTGACCAATCTATGATAACACTCC	57.944	40.000	0.00	0.00	0.00	3.85
2513	3637	8.379331	AGTTTTAGCTAAGACCTTTGAAGATCT	58.621	33.333	20.34	0.00	0.00	2.75
2608	3740	2.525105	ATCCCACAACCAATACCCAC	57.475	50.000	0.00	0.00	0.00	4.61
2678	3812	3.296842	ATTTTCCCGTCCCAGCCCC	62.297	63.158	0.00	0.00	0.00	5.80
2712	3846	1.676615	GGCCATTTTGGTCCTTGCATG	60.677	52.381	0.00	0.00	40.46	4.06
2945	4079	7.430992	TCATGCTGATAAGATTGTTGATAGC	57.569	36.000	0.00	0.00	0.00	2.97
2946	4080	6.429078	TCATGCTGATAAGATTGTTGATAGCC	59.571	38.462	0.00	0.00	0.00	3.93
2947	4081	5.065914	TGCTGATAAGATTGTTGATAGCCC	58.934	41.667	0.00	0.00	0.00	5.19
2948	4082	5.163163	TGCTGATAAGATTGTTGATAGCCCT	60.163	40.000	0.00	0.00	0.00	5.19
2949	4083	5.411053	GCTGATAAGATTGTTGATAGCCCTC	59.589	44.000	0.00	0.00	0.00	4.30
2950	4084	6.499106	TGATAAGATTGTTGATAGCCCTCA	57.501	37.500	0.00	0.00	0.00	3.86
2951	4085	6.899089	TGATAAGATTGTTGATAGCCCTCAA	58.101	36.000	0.00	0.00	32.84	3.02
2955	4089	3.496675	GTTGATAGCCCTCAACCCC	57.503	57.895	14.94	0.00	46.00	4.95
2956	4090	0.919710	GTTGATAGCCCTCAACCCCT	59.080	55.000	14.94	0.00	46.00	4.79
2957	4091	0.918983	TTGATAGCCCTCAACCCCTG	59.081	55.000	0.00	0.00	30.34	4.45
2958	4092	0.988145	TGATAGCCCTCAACCCCTGG	60.988	60.000	0.00	0.00	0.00	4.45
2959	4093	0.694444	GATAGCCCTCAACCCCTGGA	60.694	60.000	0.00	0.00	0.00	3.86
2960	4094	0.695803	ATAGCCCTCAACCCCTGGAG	60.696	60.000	0.00	0.00	0.00	3.86
2961	4095	1.821966	TAGCCCTCAACCCCTGGAGA	61.822	60.000	0.00	0.00	32.87	3.71
2962	4096	2.003548	GCCCTCAACCCCTGGAGAT	61.004	63.158	0.00	0.00	32.87	2.75
2963	4097	1.575447	GCCCTCAACCCCTGGAGATT	61.575	60.000	0.00	0.00	32.87	2.40
2964	4098	1.002857	CCCTCAACCCCTGGAGATTT	58.997	55.000	0.00	0.00	32.87	2.17
2965	4099	1.359130	CCCTCAACCCCTGGAGATTTT	59.641	52.381	0.00	0.00	32.87	1.82
2966	4100	2.450476	CCTCAACCCCTGGAGATTTTG	58.550	52.381	0.00	0.00	32.87	2.44
2967	4101	2.225117	CCTCAACCCCTGGAGATTTTGT	60.225	50.000	0.00	0.00	32.87	2.83
2968	4102	3.010138	CCTCAACCCCTGGAGATTTTGTA	59.990	47.826	0.00	0.00	32.87	2.41
2969	4103	4.265073	CTCAACCCCTGGAGATTTTGTAG	58.735	47.826	0.00	0.00	32.87	2.74
2970	4104	3.655777	TCAACCCCTGGAGATTTTGTAGT	59.344	43.478	0.00	0.00	0.00	2.73
2971	4105	3.721087	ACCCCTGGAGATTTTGTAGTG	57.279	47.619	0.00	0.00	0.00	2.74
2972	4106	2.308866	ACCCCTGGAGATTTTGTAGTGG	59.691	50.000	0.00	0.00	0.00	4.00
2973	4107	2.357154	CCCCTGGAGATTTTGTAGTGGG	60.357	54.545	0.00	0.00	0.00	4.61
2974	4108	2.576191	CCCTGGAGATTTTGTAGTGGGA	59.424	50.000	0.00	0.00	34.34	4.37
2975	4109	3.010138	CCCTGGAGATTTTGTAGTGGGAA	59.990	47.826	0.00	0.00	34.34	3.97
2976	4110	4.010349	CCTGGAGATTTTGTAGTGGGAAC	58.990	47.826	0.00	0.00	0.00	3.62
2977	4111	4.263506	CCTGGAGATTTTGTAGTGGGAACT	60.264	45.833	0.00	0.00	0.00	3.01
3009	4143	6.827727	TCATAATTCTGGCCTTAGGAGTTAC	58.172	40.000	3.32	0.00	0.00	2.50
3181	4315	4.423625	ACAATCAATGGTCCTACCTAGC	57.576	45.455	0.00	0.00	39.58	3.42
3195	4329	0.892755	CCTAGCTGTGTCACCGGTAA	59.107	55.000	6.87	0.00	0.00	2.85
3208	4342	5.258456	TCACCGGTAACAAGTGATCTATC	57.742	43.478	6.87	0.00	42.68	2.08
3226	4360	5.674525	TCTATCTTATGCACTTTGTGAGGG	58.325	41.667	1.52	0.00	35.23	4.30

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
108	109	8.670521	AGTTGAATGAAAGGGAATAAAAGGAT	57.329	30.769	0.00	0.00	0.00	3.24
346	347	4.144297	TCTGTTTTTGCTGCAGGATTACT	58.856	39.130	17.12	0.00	0.00	2.24
416	417	2.044555	GTTAGGGTTTCAGCGCCCC	61.045	63.158	10.42	10.42	45.95	5.80
462	463	1.721487	CGCATTTTTCGGATCCGCT	59.279	52.632	29.62	8.13	39.59	5.52
515	1019	4.039366	AGCCTCAAAACTTCTCGTACTCTT	59.961	41.667	0.00	0.00	0.00	2.85
520	1024	4.232221	CGTTAGCCTCAAAACTTCTCGTA	58.768	43.478	0.00	0.00	0.00	3.43
556	1060	4.004982	GTCCGGTTTATAAAGGAAGTGCA	58.995	43.478	0.00	0.00	34.17	4.57
586	1090	5.899547	TGAGCTAATCTCTGGGTATCAAGAA	59.100	40.000	0.00	0.00	42.38	2.52
590	1094	5.066913	TCTGAGCTAATCTCTGGGTATCA	57.933	43.478	0.00	0.00	42.38	2.15
644	1148	4.069304	TCTGGACACGTTTTGAATAAGGG	58.931	43.478	0.00	0.00	0.00	3.95
659	1163	5.576563	TTCCCTTCATAAAAGTCTGGACA	57.423	39.130	3.51	0.00	0.00	4.02
665	1169	8.131731	GCATACATCTTTCCCTTCATAAAAGTC	58.868	37.037	0.00	0.00	32.94	3.01
689	1193	0.165727	GTTCGACGCATCACATTGCA	59.834	50.000	0.00	0.00	42.91	4.08
707	1211	2.325583	ATGGGCATATCGTCGTTTGT	57.674	45.000	0.00	0.00	0.00	2.83
740	1244	1.663739	CGACCGGAAACACCTCTCA	59.336	57.895	9.46	0.00	36.31	3.27
774	1278	4.280436	TCCCGAAGCTATTTGTGAAAGA	57.720	40.909	0.00	0.00	0.00	2.52
848	1352	6.478344	CCATTTCAAAAATGTTCGAACCTTCA	59.522	34.615	24.78	7.25	0.00	3.02
852	1356	4.084066	GCCCATTTCAAAAATGTTCGAACC	60.084	41.667	24.78	8.19	0.00	3.62
854	1358	4.061596	GGCCCATTTCAAAAATGTTCGAA	58.938	39.130	10.55	0.00	0.00	3.71
855	1359	3.658709	GGCCCATTTCAAAAATGTTCGA	58.341	40.909	10.55	0.00	0.00	3.71
856	1360	2.411409	CGGCCCATTTCAAAAATGTTCG	59.589	45.455	0.00	7.75	0.00	3.95
858	1362	2.150390	GCGGCCCATTTCAAAAATGTT	58.850	42.857	0.00	0.00	0.00	2.71
859	1363	1.610363	GGCGGCCCATTTCAAAAATGT	60.610	47.619	8.12	0.00	0.00	2.71
860	1364	1.085893	GGCGGCCCATTTCAAAAATG	58.914	50.000	8.12	5.60	0.00	2.32
861	1365	0.983467	AGGCGGCCCATTTCAAAAAT	59.017	45.000	17.02	0.00	0.00	1.82
862	1366	0.320050	GAGGCGGCCCATTTCAAAAA	59.680	50.000	17.02	0.00	0.00	1.94
881	1391	5.459762	CAGCGGGCTATAATTTCACAATTTG	59.540	40.000	0.00	0.00	34.29	2.32
957	1473	2.683933	GCCGGGTGGAGAGGAAGA	60.684	66.667	2.18	0.00	37.49	2.87
1027	1571	2.176798	AGATCTCCTCCAGGATCTCGTT	59.823	50.000	0.00	0.00	43.31	3.85
1602	2391	1.470098	TCAACGGCTACGGAAGAGTAC	59.530	52.381	0.00	0.00	46.48	2.73
1614	2403	2.170607	AGCTATACACCATTCAACGGCT	59.829	45.455	0.00	0.00	0.00	5.52
1692	2485	2.345341	GCCACGCAAATAGTTGAAATGC	59.655	45.455	7.18	0.00	36.83	3.56
1878	2671	6.357367	ACCAACAAGAGTAAACATCTCAAGT	58.643	36.000	0.00	0.00	34.73	3.16
2094	2890	6.319048	ACATCATTATCCACAGGAAAGACT	57.681	37.500	0.00	0.00	34.34	3.24
2330	3163	2.742053	GACGAACAGAATAAGCTTGCCA	59.258	45.455	9.86	0.00	0.00	4.92
2422	3450	2.031870	ACCTTTCCTGGTTTGACAAGC	58.968	47.619	0.00	0.00	36.89	4.01
2476	3596	6.197468	GTCTTAGCTAAAACTATGCACTCGAG	59.803	42.308	11.84	11.84	0.00	4.04
2608	3740	4.240096	CCTGAGTAAATTTGCAAAGCTGG	58.760	43.478	18.19	10.91	0.00	4.85
2694	3828	2.299582	TCACATGCAAGGACCAAAATGG	59.700	45.455	0.00	0.00	45.02	3.16
2712	3846	2.289002	CAGTTGCACCAGAGAAACTCAC	59.711	50.000	0.00	0.00	30.59	3.51
2847	3981	7.222000	ACTAGTTTTTCACCTGTTTGACAAA	57.778	32.000	0.00	0.00	0.00	2.83
2853	3987	6.871492	CCAACAAACTAGTTTTTCACCTGTTT	59.129	34.615	18.25	1.78	33.87	2.83
2923	4057	5.709164	GGGCTATCAACAATCTTATCAGCAT	59.291	40.000	0.00	0.00	0.00	3.79
2943	4077	2.498820	ATCTCCAGGGGTTGAGGGCT	62.499	60.000	0.00	0.00	0.00	5.19
2944	4078	1.575447	AATCTCCAGGGGTTGAGGGC	61.575	60.000	0.00	0.00	0.00	5.19
2945	4079	1.002857	AAATCTCCAGGGGTTGAGGG	58.997	55.000	0.00	0.00	0.00	4.30
2946	4080	2.225117	ACAAAATCTCCAGGGGTTGAGG	60.225	50.000	0.00	0.00	0.00	3.86
2947	4081	3.160679	ACAAAATCTCCAGGGGTTGAG	57.839	47.619	0.00	0.00	0.00	3.02
2948	4082	3.655777	ACTACAAAATCTCCAGGGGTTGA	59.344	43.478	0.00	0.00	0.00	3.18
2949	4083	3.758554	CACTACAAAATCTCCAGGGGTTG	59.241	47.826	0.00	0.00	0.00	3.77
2950	4084	3.245264	CCACTACAAAATCTCCAGGGGTT	60.245	47.826	0.00	0.00	0.00	4.11
2951	4085	2.308866	CCACTACAAAATCTCCAGGGGT	59.691	50.000	0.00	0.00	0.00	4.95
2952	4086	2.357154	CCCACTACAAAATCTCCAGGGG	60.357	54.545	0.00	0.00	0.00	4.79
2953	4087	2.576191	TCCCACTACAAAATCTCCAGGG	59.424	50.000	0.00	0.00	35.09	4.45
2954	4088	4.010349	GTTCCCACTACAAAATCTCCAGG	58.990	47.826	0.00	0.00	0.00	4.45
2955	4089	4.697352	CAGTTCCCACTACAAAATCTCCAG	59.303	45.833	0.00	0.00	0.00	3.86
2956	4090	4.349636	TCAGTTCCCACTACAAAATCTCCA	59.650	41.667	0.00	0.00	0.00	3.86
2957	4091	4.906618	TCAGTTCCCACTACAAAATCTCC	58.093	43.478	0.00	0.00	0.00	3.71
2958	4092	6.877611	TTTCAGTTCCCACTACAAAATCTC	57.122	37.500	0.00	0.00	0.00	2.75
2959	4093	6.833933	AGTTTTCAGTTCCCACTACAAAATCT	59.166	34.615	0.00	0.00	31.36	2.40
2960	4094	7.039313	AGTTTTCAGTTCCCACTACAAAATC	57.961	36.000	0.00	0.00	31.36	2.17
2961	4095	7.123547	TGAAGTTTTCAGTTCCCACTACAAAAT	59.876	33.333	0.00	0.00	34.08	1.82
2962	4096	6.434652	TGAAGTTTTCAGTTCCCACTACAAAA	59.565	34.615	0.00	0.00	34.08	2.44
2963	4097	5.946972	TGAAGTTTTCAGTTCCCACTACAAA	59.053	36.000	0.00	0.00	34.08	2.83
2964	4098	5.502079	TGAAGTTTTCAGTTCCCACTACAA	58.498	37.500	0.00	0.00	34.08	2.41
2965	4099	5.105567	TGAAGTTTTCAGTTCCCACTACA	57.894	39.130	0.00	0.00	34.08	2.74
2966	4100	7.739498	TTATGAAGTTTTCAGTTCCCACTAC	57.261	36.000	0.00	0.00	43.98	2.73
2967	4101	8.934023	AATTATGAAGTTTTCAGTTCCCACTA	57.066	30.769	0.00	0.00	43.98	2.74
2968	4102	7.725844	AGAATTATGAAGTTTTCAGTTCCCACT	59.274	33.333	0.00	0.00	43.98	4.00
2969	4103	7.809806	CAGAATTATGAAGTTTTCAGTTCCCAC	59.190	37.037	0.00	0.00	43.98	4.61
2970	4104	7.039784	CCAGAATTATGAAGTTTTCAGTTCCCA	60.040	37.037	0.54	0.00	43.98	4.37
2971	4105	7.315890	CCAGAATTATGAAGTTTTCAGTTCCC	58.684	38.462	0.54	0.00	43.98	3.97
2972	4106	6.808704	GCCAGAATTATGAAGTTTTCAGTTCC	59.191	38.462	0.54	0.00	43.98	3.62
2973	4107	6.808704	GGCCAGAATTATGAAGTTTTCAGTTC	59.191	38.462	0.54	3.08	43.98	3.01
2974	4108	6.494835	AGGCCAGAATTATGAAGTTTTCAGTT	59.505	34.615	5.01	0.00	43.98	3.16
2975	4109	6.012745	AGGCCAGAATTATGAAGTTTTCAGT	58.987	36.000	5.01	0.00	43.98	3.41
2976	4110	6.521151	AGGCCAGAATTATGAAGTTTTCAG	57.479	37.500	5.01	0.00	43.98	3.02
2977	4111	6.916360	AAGGCCAGAATTATGAAGTTTTCA	57.084	33.333	5.01	0.00	45.01	2.69
3009	4143	4.427096	ACAAGACACACGATGAGAGTAG	57.573	45.455	0.00	0.00	0.00	2.57
3066	4200	4.742438	TGAAAAGACGCCTATTGTGTTC	57.258	40.909	0.00	0.00	37.96	3.18
3181	4315	1.864711	CACTTGTTACCGGTGACACAG	59.135	52.381	29.85	27.29	33.32	3.66
3195	4329	7.826252	ACAAAGTGCATAAGATAGATCACTTGT	59.174	33.333	6.24	4.84	41.98	3.16
3208	4342	3.438087	CACTCCCTCACAAAGTGCATAAG	59.562	47.826	0.00	0.00	34.55	1.73

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.