AutoCloner

Multiple sequence alignment - TraesCS7D01G004900

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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	TraesCS7D01G004900	chr7D	100.000	5228	0	0	1	5228	2444573	2439346	0.000000e+00	9655.0
1	TraesCS7D01G004900	chr7D	83.042	2176	337	28	1620	3780	19050678	19052836	0.000000e+00	1945.0
2	TraesCS7D01G004900	chr7D	87.368	95	10	2	4811	4905	3843403	3843311	1.990000e-19	108.0
3	TraesCS7D01G004900	chr7D	100.000	44	0	0	5179	5222	30905259	30905302	1.210000e-11	82.4
4	TraesCS7D01G004900	chr7D	100.000	35	0	0	5140	5174	200767212	200767178	1.220000e-06	65.8
5	TraesCS7D01G004900	chr7D	88.462	52	4	2	4487	4538	3845290	3845241	1.570000e-05	62.1
6	TraesCS7D01G004900	chr4A	92.531	4539	283	25	1	4501	742142952	742147472	0.000000e+00	6453.0
7	TraesCS7D01G004900	chr4A	92.602	4136	264	17	393	4501	739905074	739909194	0.000000e+00	5904.0
8	TraesCS7D01G004900	chr4A	93.816	3412	201	6	1092	4501	733872383	733868980	0.000000e+00	5123.0
9	TraesCS7D01G004900	chr4A	96.018	2813	66	12	2405	5190	741864795	741867588	0.000000e+00	4532.0
10	TraesCS7D01G004900	chr4A	94.565	1656	62	10	753	2407	741850217	741851845	0.000000e+00	2534.0
11	TraesCS7D01G004900	chr4A	86.301	2168	284	11	1620	3782	733991046	733993205	0.000000e+00	2346.0
12	TraesCS7D01G004900	chr4A	86.064	2167	291	9	1620	3782	741159988	741162147	0.000000e+00	2318.0
13	TraesCS7D01G004900	chr4A	95.238	651	29	2	1262	1911	741273102	741273751	0.000000e+00	1029.0
14	TraesCS7D01G004900	chr4A	93.681	364	17	5	1	362	739904716	739905075	1.660000e-149	540.0
15	TraesCS7D01G004900	chr4A	91.392	395	17	4	94	484	741849348	741849729	4.640000e-145	525.0
16	TraesCS7D01G004900	chr4A	89.019	428	16	5	4772	5190	741274070	741274475	7.820000e-138	501.0
17	TraesCS7D01G004900	chr4A	91.257	366	25	5	4	365	733878561	733878199	4.700000e-135	492.0
18	TraesCS7D01G004900	chr4A	93.309	269	17	1	131	399	741266647	741266914	3.790000e-106	396.0
19	TraesCS7D01G004900	chr4A	83.471	363	54	2	3864	4220	739783218	739783580	3.020000e-87	333.0
20	TraesCS7D01G004900	chr4A	77.941	340	71	4	1726	2063	739740684	739741021	5.310000e-50	209.0
21	TraesCS7D01G004900	chr4A	86.471	170	20	2	930	1096	733873299	733873130	3.220000e-42	183.0
22	TraesCS7D01G004900	chr4A	78.667	300	35	12	473	758	741849909	741850193	6.960000e-39	172.0
23	TraesCS7D01G004900	chr4A	74.929	351	68	13	1096	1430	739779780	739780126	5.460000e-30	143.0
24	TraesCS7D01G004900	chr4A	88.889	90	7	2	4816	4905	741283568	741283654	1.990000e-19	108.0
25	TraesCS7D01G004900	chr4A	92.857	42	3	0	880	921	733875625	733875584	1.570000e-05	62.1
26	TraesCS7D01G004900	chr7A	94.183	1444	79	3	2159	3600	3827920	3826480	0.000000e+00	2196.0
27	TraesCS7D01G004900	chr7A	93.574	1245	74	3	2761	4005	3603311	3602073	0.000000e+00	1851.0
28	TraesCS7D01G004900	chr7A	81.718	2177	377	15	1615	3782	2959168	2957004	0.000000e+00	1796.0
29	TraesCS7D01G004900	chr7A	87.819	509	33	5	3993	4501	3594899	3594420	2.110000e-158	569.0
30	TraesCS7D01G004900	chrUn	92.493	1119	72	6	794	1911	221199424	221198317	0.000000e+00	1591.0
31	TraesCS7D01G004900	chrUn	92.404	1119	73	6	794	1911	318474322	318475429	0.000000e+00	1585.0
32	TraesCS7D01G004900	chrUn	95.238	651	29	2	1262	1911	232070716	232071365	0.000000e+00	1029.0
33	TraesCS7D01G004900	chrUn	89.019	428	16	5	4772	5190	221197998	221197593	7.820000e-138	501.0
34	TraesCS7D01G004900	chrUn	89.019	428	16	5	4772	5190	232071684	232072089	7.820000e-138	501.0
35	TraesCS7D01G004900	chrUn	89.019	428	16	5	4772	5190	318475748	318476153	7.820000e-138	501.0
36	TraesCS7D01G004900	chrUn	92.565	269	19	1	131	399	221205127	221204860	8.210000e-103	385.0
37	TraesCS7D01G004900	chrUn	92.565	269	19	1	131	399	232064931	232065198	8.210000e-103	385.0
38	TraesCS7D01G004900	chrUn	88.506	87	7	3	4819	4905	455664789	455664706	9.260000e-18	102.0
39	TraesCS7D01G004900	chr3D	89.051	137	6	1	5035	5162	20750877	20751013	1.510000e-35	161.0
40	TraesCS7D01G004900	chr5B	97.778	45	1	0	5184	5228	218214439	218214395	1.560000e-10	78.7
41	TraesCS7D01G004900	chr5B	92.308	52	3	1	5177	5228	181638236	181638186	7.260000e-09	73.1
42	TraesCS7D01G004900	chr5B	92.308	52	3	1	5177	5228	331754278	331754328	7.260000e-09	73.1
43	TraesCS7D01G004900	chr1B	95.918	49	1	1	5180	5228	555627374	555627327	1.560000e-10	78.7
44	TraesCS7D01G004900	chr6A	95.745	47	2	0	5182	5228	102998494	102998540	5.610000e-10	76.8
45	TraesCS7D01G004900	chr4B	94.000	50	3	0	5179	5228	252015132	252015181	5.610000e-10	76.8
46	TraesCS7D01G004900	chr1A	95.833	48	1	1	5181	5228	508631005	508630959	5.610000e-10	76.8
47	TraesCS7D01G004900	chr5A	92.453	53	1	3	5179	5228	670270026	670269974	7.260000e-09	73.1
48	TraesCS7D01G004900	chr5D	93.617	47	3	0	364	410	45145960	45145914	2.610000e-08	71.3
49	TraesCS7D01G004900	chr2A	87.097	62	5	2	359	420	99160513	99160455	3.380000e-07	67.6

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	TraesCS7D01G004900	chr7D	2439346	2444573	5227	True	9655.000	9655	100.00000	1	5228	1	chr7D.!!$R1	5227
1	TraesCS7D01G004900	chr7D	19050678	19052836	2158	False	1945.000	1945	83.04200	1620	3780	1	chr7D.!!$F1	2160
2	TraesCS7D01G004900	chr4A	742142952	742147472	4520	False	6453.000	6453	92.53100	1	4501	1	chr4A.!!$F7	4500
3	TraesCS7D01G004900	chr4A	741864795	741867588	2793	False	4532.000	4532	96.01800	2405	5190	1	chr4A.!!$F6	2785
4	TraesCS7D01G004900	chr4A	739904716	739909194	4478	False	3222.000	5904	93.14150	1	4501	2	chr4A.!!$F9	4500
5	TraesCS7D01G004900	chr4A	733991046	733993205	2159	False	2346.000	2346	86.30100	1620	3782	1	chr4A.!!$F1	2162
6	TraesCS7D01G004900	chr4A	741159988	741162147	2159	False	2318.000	2318	86.06400	1620	3782	1	chr4A.!!$F3	2162
7	TraesCS7D01G004900	chr4A	733868980	733878561	9581	True	1465.025	5123	91.10025	4	4501	4	chr4A.!!$R1	4497
8	TraesCS7D01G004900	chr4A	741849348	741851845	2497	False	1077.000	2534	88.20800	94	2407	3	chr4A.!!$F11	2313
9	TraesCS7D01G004900	chr4A	741273102	741274475	1373	False	765.000	1029	92.12850	1262	5190	2	chr4A.!!$F10	3928
10	TraesCS7D01G004900	chr4A	739779780	739783580	3800	False	238.000	333	79.20000	1096	4220	2	chr4A.!!$F8	3124
11	TraesCS7D01G004900	chr7A	3826480	3827920	1440	True	2196.000	2196	94.18300	2159	3600	1	chr7A.!!$R4	1441
12	TraesCS7D01G004900	chr7A	3602073	3603311	1238	True	1851.000	1851	93.57400	2761	4005	1	chr7A.!!$R3	1244
13	TraesCS7D01G004900	chr7A	2957004	2959168	2164	True	1796.000	1796	81.71800	1615	3782	1	chr7A.!!$R1	2167
14	TraesCS7D01G004900	chrUn	221197593	221199424	1831	True	1046.000	1591	90.75600	794	5190	2	chrUn.!!$R3	4396
15	TraesCS7D01G004900	chrUn	318474322	318476153	1831	False	1043.000	1585	90.71150	794	5190	2	chrUn.!!$F3	4396
16	TraesCS7D01G004900	chrUn	232070716	232072089	1373	False	765.000	1029	92.12850	1262	5190	2	chrUn.!!$F2	3928

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
22	24	0.390492	CAGCGATCCATGCTACTCCA	59.610	55.0	0.00	41.72	3.86	F
1171	6387	0.176680	CCTGATGTCCTGGGAGAACG	59.823	60.0	0.00	0.00	3.95	F
1272	6500	0.833287	GGATGCAGCTTAGAGGGACA	59.167	55.0	0.22	0.00	4.02	F
2151	7887	0.244721	GTGCCTTGCCATTCAACCTC	59.755	55.0	0.00	0.00	3.85	F
3680	9425	1.673168	AAGGCTTGCATCTCGGATTC	58.327	50.0	0.00	0.00	2.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1554	6857	0.178967	TGTTGCTTGGGATTGAGCCA	60.179	50.000	0.00	0.00	38.11	4.75	R
2151	7887	0.247736	GTAGCTGACCTCCCACACAG	59.752	60.000	0.00	0.00	0.00	3.66	R
2801	8545	3.887716	GGCTTCAAGCATACCAAGATCAT	59.112	43.478	12.53	0.00	44.75	2.45	R
3896	9998	1.273606	CATCACACTTCTCGGTCACCT	59.726	52.381	0.00	0.00	0.00	4.00	R
4734	10860	0.668401	ATCGGTCCAAACGACGAACC	60.668	55.000	0.00	0.13	43.78	3.62	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
19	21	4.766970	GCAGCGATCCATGCTACT	57.233	55.556	9.07	0.00	41.72	2.57
20	22	2.526545	GCAGCGATCCATGCTACTC	58.473	57.895	9.07	0.00	41.72	2.59
22	24	0.390492	CAGCGATCCATGCTACTCCA	59.610	55.000	0.00	0.00	41.72	3.86
23	25	1.123077	AGCGATCCATGCTACTCCAA	58.877	50.000	0.00	0.00	41.87	3.53
55	59	5.424757	ACTGTGTGTGTGTATGTAACAAGT	58.575	37.500	0.00	0.00	40.63	3.16
127	131	4.933330	TGGCTCGATAACTTATGACACTC	58.067	43.478	0.00	0.00	0.00	3.51
174	178	4.438880	GCTGATAGCGTGTGAGAGTAGAAA	60.439	45.833	0.00	0.00	0.00	2.52
245	251	1.559682	AGTCAACCAATATGAGCGGGT	59.440	47.619	0.00	0.00	34.43	5.28
465	2377	3.587797	TGTGTCAATAGTCTTCGTCCC	57.412	47.619	0.00	0.00	0.00	4.46
536	2652	3.430862	CACCATCAACCGGCACCG	61.431	66.667	0.00	1.02	39.44	4.94
563	2679	3.488569	CCGGGCTGCCCAGGAATA	61.489	66.667	35.22	0.00	45.83	1.75
595	2719	4.522789	GGAGGAGTAAATTTTTGTGGAGCA	59.477	41.667	0.00	0.00	0.00	4.26
600	2724	5.842907	AGTAAATTTTTGTGGAGCAAGACC	58.157	37.500	0.00	0.00	38.47	3.85
616	2740	2.743928	CCCAGAGGTCGTTGCAGC	60.744	66.667	0.00	0.00	0.00	5.25
630	2754	2.998279	GCAGCGATGCCTTGGCTTT	61.998	57.895	16.30	0.34	34.13	3.51
692	2817	1.204231	GTAGGGAGGTCGTTGGTCTTC	59.796	57.143	0.00	0.00	0.00	2.87
709	2848	5.193679	GGTCTTCCCCTAGTACGTAGTTTA	58.806	45.833	8.48	0.00	37.78	2.01
720	2859	3.756933	ACGTAGTTTAGGTGAAAGCCA	57.243	42.857	0.00	0.00	37.78	4.75
785	2953	4.146443	GCTTGACGAATTCAAAGTTTTCCG	59.854	41.667	6.22	0.00	43.90	4.30
840	3025	4.651503	AGTCAATGGATTAGATGACGAGGT	59.348	41.667	0.00	0.00	45.21	3.85
883	3069	3.005554	CACAAGCTACCAAGGACATGAG	58.994	50.000	0.00	0.00	0.00	2.90
917	3103	1.320344	CCTACTGCGTGGACCTAGCA	61.320	60.000	12.61	12.61	39.25	3.49
923	3109	0.876342	GCGTGGACCTAGCATGCTAC	60.876	60.000	23.52	14.16	0.00	3.58
924	3110	0.459899	CGTGGACCTAGCATGCTACA	59.540	55.000	23.52	16.46	0.00	2.74
925	3111	1.134818	CGTGGACCTAGCATGCTACAA	60.135	52.381	23.52	5.85	0.00	2.41
926	3112	2.555199	GTGGACCTAGCATGCTACAAG	58.445	52.381	23.52	15.65	0.00	3.16
927	3113	1.486310	TGGACCTAGCATGCTACAAGG	59.514	52.381	26.70	26.70	0.00	3.61
928	3114	1.587547	GACCTAGCATGCTACAAGGC	58.412	55.000	27.77	19.02	0.00	4.35
950	5415	5.125097	GGCACAAGCTCTAAGTACTAGTACA	59.875	44.000	29.87	13.16	41.70	2.90
963	5428	2.093106	CTAGTACACCTCTCGCCAACT	58.907	52.381	0.00	0.00	0.00	3.16
965	5430	2.736347	AGTACACCTCTCGCCAACTAT	58.264	47.619	0.00	0.00	0.00	2.12
971	5436	1.309950	CTCTCGCCAACTATCGGAGA	58.690	55.000	0.00	0.00	45.75	3.71
1149	6365	0.469494	TCAGCAACCAGAGTCAGCAA	59.531	50.000	0.00	0.00	31.33	3.91
1157	6373	0.252479	CAGAGTCAGCAAGCCCTGAT	59.748	55.000	3.10	0.00	43.19	2.90
1171	6387	0.176680	CCTGATGTCCTGGGAGAACG	59.823	60.000	0.00	0.00	0.00	3.95
1173	6389	1.153349	GATGTCCTGGGAGAACGCC	60.153	63.158	0.00	0.00	0.00	5.68
1239	6461	4.457496	CGGCCTGTGATCAGCGGT	62.457	66.667	0.00	0.00	40.09	5.68
1272	6500	0.833287	GGATGCAGCTTAGAGGGACA	59.167	55.000	0.22	0.00	0.00	4.02
1446	6749	9.032420	GTACCACTAGATAAAATGAGTAGCAAC	57.968	37.037	0.00	0.00	0.00	4.17
1907	7643	2.304761	TCTTACGCCTTTGGGAGAACAT	59.695	45.455	0.00	0.00	36.25	2.71
2058	7794	5.494632	ACCTTTACAAGAACCAACTTTCG	57.505	39.130	0.00	0.00	0.00	3.46
2151	7887	0.244721	GTGCCTTGCCATTCAACCTC	59.755	55.000	0.00	0.00	0.00	3.85
2369	8111	5.068636	CAGATTATCTCATCTTTGGGGTGG	58.931	45.833	0.00	0.00	30.50	4.61
2801	8545	5.023452	TGGCTCTATTCCAAGTCTGTTAGA	58.977	41.667	0.00	0.00	0.00	2.10
3217	8961	4.284178	CATCTGGAACTTTGATGGGGAAT	58.716	43.478	0.00	0.00	35.32	3.01
3222	8966	6.159575	TCTGGAACTTTGATGGGGAATATGTA	59.840	38.462	0.00	0.00	0.00	2.29
3391	9136	4.650545	TTTAACCGTGAAATACACTCGC	57.349	40.909	0.00	0.00	46.24	5.03
3680	9425	1.673168	AAGGCTTGCATCTCGGATTC	58.327	50.000	0.00	0.00	0.00	2.52
3849	9951	7.659390	GCACTTAGATGATAGAGGTAGCAAAAT	59.341	37.037	0.00	0.00	0.00	1.82
3896	9998	3.882288	TCAGAGCTTGCATACACAACAAA	59.118	39.130	0.00	0.00	0.00	2.83
3990	10092	5.781818	AGGTGATTTCCTTTCATCCATTGTT	59.218	36.000	0.00	0.00	33.52	2.83
3991	10093	6.071165	AGGTGATTTCCTTTCATCCATTGTTC	60.071	38.462	0.00	0.00	33.52	3.18
4002	10110	6.325919	TCATCCATTGTTCACAAAACTACC	57.674	37.500	0.00	0.00	39.55	3.18
4016	10124	6.359617	CACAAAACTACCTTACTTCGCAATTG	59.640	38.462	0.00	0.00	0.00	2.32
4125	10233	0.690192	ATCCATCACACCGTCCAACA	59.310	50.000	0.00	0.00	0.00	3.33
4504	10620	1.768870	GCCTCTCACTTGGGGCTTATA	59.231	52.381	0.00	0.00	41.20	0.98
4586	10702	2.715749	TGTGGCGGAGATGATTTGAT	57.284	45.000	0.00	0.00	0.00	2.57
4620	10736	0.752658	GGCAAAACAGAGGGCTTTGT	59.247	50.000	0.00	0.00	33.51	2.83
4621	10737	1.960689	GGCAAAACAGAGGGCTTTGTA	59.039	47.619	0.00	0.00	33.51	2.41
4622	10738	2.364002	GGCAAAACAGAGGGCTTTGTAA	59.636	45.455	0.00	0.00	33.51	2.41
4623	10739	3.381045	GCAAAACAGAGGGCTTTGTAAC	58.619	45.455	0.00	0.00	33.51	2.50
4624	10740	3.181480	GCAAAACAGAGGGCTTTGTAACA	60.181	43.478	0.00	0.00	33.51	2.41
4625	10741	4.501400	GCAAAACAGAGGGCTTTGTAACAT	60.501	41.667	0.00	0.00	33.51	2.71
4626	10742	4.853924	AAACAGAGGGCTTTGTAACATG	57.146	40.909	0.00	0.00	0.00	3.21
4748	10874	3.294079	GAAGGGTTCGTCGTTTGGA	57.706	52.632	0.00	0.00	0.00	3.53
4761	10887	3.495753	GTCGTTTGGACCGATAACTTGTT	59.504	43.478	0.00	0.00	39.90	2.83
4764	10890	2.773993	TGGACCGATAACTTGTTCCC	57.226	50.000	0.00	0.00	0.00	3.97
4766	10892	2.640826	TGGACCGATAACTTGTTCCCTT	59.359	45.455	0.00	0.00	0.00	3.95
4768	10894	3.268330	GACCGATAACTTGTTCCCTTCC	58.732	50.000	0.00	0.00	0.00	3.46
4909	11035	4.180946	CGGAGCAGAGTAGCGCGT	62.181	66.667	8.43	0.00	40.15	6.01
4950	11078	0.038310	TGCCGGAGAGAGACAGAGAA	59.962	55.000	5.05	0.00	0.00	2.87
4957	11085	3.701040	GGAGAGAGACAGAGAAAGATGCT	59.299	47.826	0.00	0.00	0.00	3.79
5071	11199	1.512694	GCCAGCTCCAAAAATCCCG	59.487	57.895	0.00	0.00	0.00	5.14
5117	11245	1.234821	CTCCGCTGTTTTTACCTGCA	58.765	50.000	0.00	0.00	0.00	4.41
5162	11299	3.003763	GAGGGGCTCCGAACAGGT	61.004	66.667	0.00	0.00	41.99	4.00
5177	11314	2.132686	ACAGGTCCTAAGTGTTGGGTT	58.867	47.619	0.00	0.00	32.34	4.11
5190	11327	3.999001	GTGTTGGGTTTGTACCTAGCTAC	59.001	47.826	0.00	0.00	44.38	3.58
5191	11328	3.905591	TGTTGGGTTTGTACCTAGCTACT	59.094	43.478	0.00	0.00	44.38	2.57
5192	11329	4.020839	TGTTGGGTTTGTACCTAGCTACTC	60.021	45.833	0.00	0.00	44.38	2.59
5193	11330	3.102204	TGGGTTTGTACCTAGCTACTCC	58.898	50.000	0.00	0.00	44.38	3.85
5194	11331	2.433604	GGGTTTGTACCTAGCTACTCCC	59.566	54.545	0.00	3.39	44.38	4.30
5195	11332	3.372897	GGTTTGTACCTAGCTACTCCCT	58.627	50.000	0.00	0.00	41.53	4.20
5196	11333	3.384146	GGTTTGTACCTAGCTACTCCCTC	59.616	52.174	0.00	0.00	41.53	4.30
5197	11334	3.309600	TTGTACCTAGCTACTCCCTCC	57.690	52.381	0.00	0.00	0.00	4.30
5198	11335	1.142465	TGTACCTAGCTACTCCCTCCG	59.858	57.143	0.00	0.00	0.00	4.63
5199	11336	1.142667	GTACCTAGCTACTCCCTCCGT	59.857	57.143	0.00	0.00	0.00	4.69
5200	11337	0.183252	ACCTAGCTACTCCCTCCGTC	59.817	60.000	0.00	0.00	0.00	4.79
5201	11338	0.537828	CCTAGCTACTCCCTCCGTCC	60.538	65.000	0.00	0.00	0.00	4.79
5202	11339	0.537828	CTAGCTACTCCCTCCGTCCC	60.538	65.000	0.00	0.00	0.00	4.46
5203	11340	1.284111	TAGCTACTCCCTCCGTCCCA	61.284	60.000	0.00	0.00	0.00	4.37
5204	11341	1.457831	GCTACTCCCTCCGTCCCAT	60.458	63.158	0.00	0.00	0.00	4.00
5205	11342	0.178970	GCTACTCCCTCCGTCCCATA	60.179	60.000	0.00	0.00	0.00	2.74
5206	11343	1.756690	GCTACTCCCTCCGTCCCATAA	60.757	57.143	0.00	0.00	0.00	1.90
5207	11344	2.890814	CTACTCCCTCCGTCCCATAAT	58.109	52.381	0.00	0.00	0.00	1.28
5208	11345	1.424638	ACTCCCTCCGTCCCATAATG	58.575	55.000	0.00	0.00	0.00	1.90
5209	11346	1.344087	ACTCCCTCCGTCCCATAATGT	60.344	52.381	0.00	0.00	0.00	2.71
5210	11347	2.090943	ACTCCCTCCGTCCCATAATGTA	60.091	50.000	0.00	0.00	0.00	2.29
5211	11348	2.969950	CTCCCTCCGTCCCATAATGTAA	59.030	50.000	0.00	0.00	0.00	2.41
5212	11349	2.969950	TCCCTCCGTCCCATAATGTAAG	59.030	50.000	0.00	0.00	0.00	2.34
5213	11350	2.969950	CCCTCCGTCCCATAATGTAAGA	59.030	50.000	0.00	0.00	0.00	2.10
5214	11351	3.244112	CCCTCCGTCCCATAATGTAAGAC	60.244	52.174	0.00	0.00	0.00	3.01
5216	11353	3.025978	TCCGTCCCATAATGTAAGACGT	58.974	45.455	9.63	0.00	46.62	4.34
5217	11354	3.448301	TCCGTCCCATAATGTAAGACGTT	59.552	43.478	9.63	0.00	46.62	3.99
5218	11355	4.081531	TCCGTCCCATAATGTAAGACGTTT	60.082	41.667	9.63	0.00	46.62	3.60
5219	11356	4.632688	CCGTCCCATAATGTAAGACGTTTT	59.367	41.667	9.63	0.00	46.62	2.43
5220	11357	5.122711	CCGTCCCATAATGTAAGACGTTTTT	59.877	40.000	9.63	0.00	46.62	1.94

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
14	16	5.238650	ACACAGTATTTGTTGTTGGAGTAGC	59.761	40.000	0.00	0.00	38.16	3.58
16	18	6.037720	CACACACAGTATTTGTTGTTGGAGTA	59.962	38.462	0.00	0.00	38.16	2.59
17	19	4.947388	ACACACAGTATTTGTTGTTGGAGT	59.053	37.500	0.00	0.00	38.16	3.85
18	20	5.163663	ACACACACAGTATTTGTTGTTGGAG	60.164	40.000	0.00	0.00	38.16	3.86
19	21	4.702612	ACACACACAGTATTTGTTGTTGGA	59.297	37.500	0.00	0.00	38.16	3.53
20	22	4.797868	CACACACACAGTATTTGTTGTTGG	59.202	41.667	0.00	0.00	38.16	3.77
22	24	5.637006	ACACACACACAGTATTTGTTGTT	57.363	34.783	0.00	0.00	38.16	2.83
23	25	6.317642	ACATACACACACACAGTATTTGTTGT	59.682	34.615	0.00	0.00	38.16	3.32
127	131	1.931841	CTCTGACTGATGCCATTCACG	59.068	52.381	0.00	0.00	30.27	4.35
174	178	9.520515	ACTTGACCATTCACTAAACATATCTTT	57.479	29.630	0.00	0.00	0.00	2.52
322	331	7.469181	GCTTATGAGACCCATTTCTATTGTTGG	60.469	40.741	0.00	0.00	36.71	3.77
389	398	1.063654	AAAGGAGGTCGAAACCCCCA	61.064	55.000	0.00	0.00	45.88	4.96
425	2337	3.884693	ACAAGTGCATGTGAGATTGTTCA	59.115	39.130	6.59	0.00	30.82	3.18
465	2377	8.854979	TTGATCACTATTGACACAAGTTTTTG	57.145	30.769	0.00	0.00	35.98	2.44
513	2629	2.034066	CGGTTGATGGTGGCCACT	59.966	61.111	33.91	17.10	35.80	4.00
557	2673	1.059913	CCTCCCGCTTGGATATTCCT	58.940	55.000	0.00	0.00	44.07	3.36
563	2679	1.580059	TTTACTCCTCCCGCTTGGAT	58.420	50.000	0.00	0.00	44.07	3.41
600	2724	2.842394	ATCGCTGCAACGACCTCTGG	62.842	60.000	15.37	0.00	46.28	3.86
616	2740	0.169672	CACTCAAAGCCAAGGCATCG	59.830	55.000	14.40	0.58	44.88	3.84
644	2769	1.850377	CCAGCGTTGACAAATTTGCA	58.150	45.000	18.12	13.57	0.00	4.08
672	2797	1.204231	GAAGACCAACGACCTCCCTAC	59.796	57.143	0.00	0.00	0.00	3.18
692	2817	4.526970	TCACCTAAACTACGTACTAGGGG	58.473	47.826	18.33	15.97	36.44	4.79
709	2848	2.032681	GTCGCCTGGCTTTCACCT	59.967	61.111	17.92	0.00	0.00	4.00
720	2859	2.198827	TTCCAATCAATGTGTCGCCT	57.801	45.000	0.00	0.00	0.00	5.52
785	2953	2.747989	TCACGATCACAGTCTAGTCACC	59.252	50.000	0.00	0.00	0.00	4.02
883	3069	3.561725	GCAGTAGGTAAATGATCAGCCAC	59.438	47.826	0.09	0.00	0.00	5.01
917	3103	1.004044	AGAGCTTGTGCCTTGTAGCAT	59.996	47.619	0.00	0.00	46.24	3.79
923	3109	3.931578	AGTACTTAGAGCTTGTGCCTTG	58.068	45.455	0.00	0.00	40.80	3.61
924	3110	4.773149	ACTAGTACTTAGAGCTTGTGCCTT	59.227	41.667	0.00	0.00	34.75	4.35
925	3111	4.345854	ACTAGTACTTAGAGCTTGTGCCT	58.654	43.478	0.00	0.00	34.75	4.75
926	3112	4.722361	ACTAGTACTTAGAGCTTGTGCC	57.278	45.455	0.00	0.00	34.75	5.01
927	3113	6.028987	GTGTACTAGTACTTAGAGCTTGTGC	58.971	44.000	28.56	3.05	37.00	4.57
928	3114	6.374894	AGGTGTACTAGTACTTAGAGCTTGTG	59.625	42.308	28.56	0.00	37.00	3.33
950	5415	0.395311	TCCGATAGTTGGCGAGAGGT	60.395	55.000	0.00	0.00	0.00	3.85
963	5428	5.588648	GGTTTTGATGGAAATGTCTCCGATA	59.411	40.000	0.00	0.00	38.44	2.92
965	5430	3.756434	GGTTTTGATGGAAATGTCTCCGA	59.244	43.478	0.00	0.00	38.44	4.55
971	5436	6.063404	AGCATTTTGGTTTTGATGGAAATGT	58.937	32.000	0.00	0.00	37.03	2.71
1088	5553	0.966179	TGCTCTTGCTTGTACTCCGA	59.034	50.000	0.00	0.00	40.48	4.55
1149	6365	1.692042	CTCCCAGGACATCAGGGCT	60.692	63.158	4.23	0.00	42.52	5.19
1157	6373	2.203788	AGGCGTTCTCCCAGGACA	60.204	61.111	0.00	0.00	0.00	4.02
1446	6749	2.222027	GACAAGTTGAGGGTCACAAGG	58.778	52.381	10.54	0.00	0.00	3.61
1468	6771	6.183360	GGGATGTGACCAACTAAATGATTGAG	60.183	42.308	0.00	0.00	0.00	3.02
1554	6857	0.178967	TGTTGCTTGGGATTGAGCCA	60.179	50.000	0.00	0.00	38.11	4.75
1907	7643	6.361433	TCTTGTGGAATTTGACCAGAAAGTA	58.639	36.000	0.00	0.00	39.52	2.24
2058	7794	4.412528	ACAATTCCTTGAGGTATAGGTCCC	59.587	45.833	0.00	0.00	36.20	4.46
2151	7887	0.247736	GTAGCTGACCTCCCACACAG	59.752	60.000	0.00	0.00	0.00	3.66
2334	8076	6.122850	TGAGATAATCTGCCGAACAATTTG	57.877	37.500	0.00	0.00	0.00	2.32
2369	8111	5.332808	CGTAACACAGTAAGTTTGTAGCACC	60.333	44.000	0.00	0.00	0.00	5.01
2801	8545	3.887716	GGCTTCAAGCATACCAAGATCAT	59.112	43.478	12.53	0.00	44.75	2.45
3222	8966	6.757237	TGTGGCATCAACAATTTTCTTGTAT	58.243	32.000	0.00	0.00	31.50	2.29
3391	9136	1.332640	GCGATGTCGAATGTGCATCAG	60.333	52.381	6.60	6.95	43.02	2.90
3680	9425	7.981789	TCACATCTAGTATTTTTGCTAGACCAG	59.018	37.037	0.00	1.15	44.18	4.00
3849	9951	7.534085	AGAAATATCAACATTCGAGCGTAAA	57.466	32.000	0.00	0.00	0.00	2.01
3851	9953	6.754675	TGAAGAAATATCAACATTCGAGCGTA	59.245	34.615	0.00	0.00	0.00	4.42
3896	9998	1.273606	CATCACACTTCTCGGTCACCT	59.726	52.381	0.00	0.00	0.00	4.00
3990	10092	4.695396	TGCGAAGTAAGGTAGTTTTGTGA	58.305	39.130	0.00	0.00	0.00	3.58
3991	10093	5.412526	TTGCGAAGTAAGGTAGTTTTGTG	57.587	39.130	0.00	0.00	0.00	3.33
4045	10153	2.159128	ACATCTCACTTGCGATCTCAGG	60.159	50.000	0.00	0.00	0.00	3.86
4125	10233	3.004734	GCACCTTGAGTACTTGTTGCATT	59.995	43.478	0.00	0.00	0.00	3.56
4450	10565	8.843262	CATGGCTTGAGAATCTTATAATGTTCA	58.157	33.333	10.72	0.00	34.92	3.18
4504	10620	8.877864	TCATTGTACCCATCTTATTCTTGTTT	57.122	30.769	0.00	0.00	0.00	2.83
4586	10702	2.689553	TTGCCGAGCATATGAACTCA	57.310	45.000	6.97	0.00	38.76	3.41
4677	10793	1.219124	CATGAGGCTGTACCGCTGT	59.781	57.895	9.25	0.00	46.52	4.40
4734	10860	0.668401	ATCGGTCCAAACGACGAACC	60.668	55.000	0.00	0.13	43.78	3.62
4742	10868	3.189910	GGGAACAAGTTATCGGTCCAAAC	59.810	47.826	0.00	0.00	0.00	2.93
4748	10874	2.640826	TGGAAGGGAACAAGTTATCGGT	59.359	45.455	0.00	0.00	0.00	4.69
4761	10887	7.098845	ACCTAGTAGAAATTTTTGGAAGGGA	57.901	36.000	0.00	0.00	0.00	4.20
4913	11039	1.004560	ATCTCTGTGTGTGTGCCCG	60.005	57.895	0.00	0.00	0.00	6.13
4914	11040	1.580845	GCATCTCTGTGTGTGTGCCC	61.581	60.000	0.00	0.00	0.00	5.36
4915	11041	1.580845	GGCATCTCTGTGTGTGTGCC	61.581	60.000	0.00	0.00	44.37	5.01
4916	11042	1.871772	GGCATCTCTGTGTGTGTGC	59.128	57.895	0.00	0.00	0.00	4.57
5071	11199	1.926108	ATAGCTACTCCGTGGATCCC	58.074	55.000	9.90	0.00	0.00	3.85
5162	11299	4.089408	GGTACAAACCCAACACTTAGGA	57.911	45.455	0.00	0.00	40.21	2.94
5177	11314	2.422519	CGGAGGGAGTAGCTAGGTACAA	60.423	54.545	28.68	0.00	0.00	2.41
5190	11327	1.424638	ACATTATGGGACGGAGGGAG	58.575	55.000	0.00	0.00	0.00	4.30
5191	11328	2.779429	TACATTATGGGACGGAGGGA	57.221	50.000	0.00	0.00	0.00	4.20
5192	11329	2.969950	TCTTACATTATGGGACGGAGGG	59.030	50.000	0.00	0.00	0.00	4.30
5193	11330	3.552273	CGTCTTACATTATGGGACGGAGG	60.552	52.174	20.50	5.87	43.69	4.30
5194	11331	3.639538	CGTCTTACATTATGGGACGGAG	58.360	50.000	20.50	2.74	43.69	4.63
5195	11332	3.720949	CGTCTTACATTATGGGACGGA	57.279	47.619	20.50	2.30	43.69	4.69

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.