AutoCloner

Multiple sequence alignment - TraesCS2A01G374600

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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	TraesCS2A01G374600	chr2A	100.000	5170	0	0	1	5170	617643464	617638295	0.000000e+00	9548.0
1	TraesCS2A01G374600	chr2D	96.840	3165	66	9	2025	5170	475083500	475080351	0.000000e+00	5260.0
2	TraesCS2A01G374600	chr2D	92.098	1063	45	19	762	1815	475084989	475083957	0.000000e+00	1461.0
3	TraesCS2A01G374600	chr2D	90.762	801	30	17	1	771	475085827	475085041	0.000000e+00	1029.0
4	TraesCS2A01G374600	chr2D	90.308	227	17	3	1817	2039	475083881	475083656	5.060000e-75	292.0
5	TraesCS2A01G374600	chr2B	90.033	1846	91	32	1459	3295	556194562	556192801	0.000000e+00	2303.0
6	TraesCS2A01G374600	chr2B	93.694	1459	55	13	1	1424	556196018	556194562	0.000000e+00	2150.0
7	TraesCS2A01G374600	chr2B	92.130	1080	53	16	3579	4630	556191221	556190146	0.000000e+00	1495.0
8	TraesCS2A01G374600	chr2B	93.053	475	31	2	4696	5170	556190134	556189662	0.000000e+00	693.0
9	TraesCS2A01G374600	chr2B	89.130	138	12	3	4543	4678	141562166	141562302	8.900000e-38	169.0
10	TraesCS2A01G374600	chr2B	86.861	137	16	2	4547	4681	601696142	601696006	8.970000e-33	152.0
11	TraesCS2A01G374600	chr7A	87.748	555	53	7	3516	4058	108869406	108868855	7.300000e-178	634.0
12	TraesCS2A01G374600	chr7A	88.674	362	25	8	2482	2840	108869831	108869483	1.330000e-115	427.0
13	TraesCS2A01G374600	chr5A	87.455	558	55	7	3513	4058	666111533	666112087	3.400000e-176	628.0
14	TraesCS2A01G374600	chr5A	88.398	362	26	8	2482	2840	666111111	666111459	6.190000e-114	422.0
15	TraesCS2A01G374600	chr1D	84.211	551	57	13	3516	4058	451050861	451050333	4.620000e-140	508.0
16	TraesCS2A01G374600	chr1D	85.405	370	29	12	2482	2840	451051293	451050938	1.370000e-95	361.0
17	TraesCS2A01G374600	chr1D	87.770	139	16	1	4540	4678	7349697	7349834	1.490000e-35	161.0
18	TraesCS2A01G374600	chr1A	83.813	556	66	13	3516	4061	9750500	9749959	1.660000e-139	507.0
19	TraesCS2A01G374600	chr1A	94.444	90	5	0	2682	2771	9750783	9750694	6.980000e-29	139.0
20	TraesCS2A01G374600	chr5B	83.544	553	68	10	3516	4058	430288222	430287683	3.600000e-136	496.0
21	TraesCS2A01G374600	chr5B	94.000	150	7	2	2626	2775	430288737	430288590	5.210000e-55	226.0
22	TraesCS2A01G374600	chr5B	87.931	58	6	1	2785	2842	430288353	430288297	3.340000e-07	67.6
23	TraesCS2A01G374600	chr5D	83.574	554	62	16	3513	4058	557974870	557975402	4.650000e-135	492.0
24	TraesCS2A01G374600	chr5D	88.122	362	27	8	2482	2840	557974448	557974796	2.880000e-112	416.0
25	TraesCS2A01G374600	chr6A	86.898	374	39	8	2481	2846	97773736	97773365	1.340000e-110	411.0
26	TraesCS2A01G374600	chr6A	80.952	567	64	21	3516	4052	97773292	97772740	4.820000e-110	409.0
27	TraesCS2A01G374600	chr4B	87.857	140	15	2	4544	4681	22464608	22464747	4.140000e-36	163.0
28	TraesCS2A01G374600	chr4A	87.591	137	15	2	4547	4681	30742886	30742750	1.930000e-34	158.0
29	TraesCS2A01G374600	chr4A	87.500	136	17	0	4543	4678	296323799	296323934	1.930000e-34	158.0
30	TraesCS2A01G374600	chr3D	86.429	140	17	2	4547	4685	535782670	535782532	8.970000e-33	152.0
31	TraesCS2A01G374600	chr6D	95.000	40	2	0	4246	4285	431056147	431056186	4.320000e-06	63.9

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	TraesCS2A01G374600	chr2A	617638295	617643464	5169	True	9548.00	9548	100.000000	1	5170	1	chr2A.!!$R1	5169
1	TraesCS2A01G374600	chr2D	475080351	475085827	5476	True	2010.50	5260	92.502000	1	5170	4	chr2D.!!$R1	5169
2	TraesCS2A01G374600	chr2B	556189662	556196018	6356	True	1660.25	2303	92.227500	1	5170	4	chr2B.!!$R2	5169
3	TraesCS2A01G374600	chr7A	108868855	108869831	976	True	530.50	634	88.211000	2482	4058	2	chr7A.!!$R1	1576
4	TraesCS2A01G374600	chr5A	666111111	666112087	976	False	525.00	628	87.926500	2482	4058	2	chr5A.!!$F1	1576
5	TraesCS2A01G374600	chr1D	451050333	451051293	960	True	434.50	508	84.808000	2482	4058	2	chr1D.!!$R1	1576
6	TraesCS2A01G374600	chr1A	9749959	9750783	824	True	323.00	507	89.128500	2682	4061	2	chr1A.!!$R1	1379
7	TraesCS2A01G374600	chr5B	430287683	430288737	1054	True	263.20	496	88.491667	2626	4058	3	chr5B.!!$R1	1432
8	TraesCS2A01G374600	chr5D	557974448	557975402	954	False	454.00	492	85.848000	2482	4058	2	chr5D.!!$F1	1576
9	TraesCS2A01G374600	chr6A	97772740	97773736	996	True	410.00	411	83.925000	2481	4052	2	chr6A.!!$R1	1571

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
735	793	1.332195	GCAAGAGCTTTTGGGGAAGT	58.668	50.000	17.82	0.00	37.91	3.01	F
1540	1666	1.002468	ACATGTTGCTTGTGCTTCGTC	60.002	47.619	0.00	0.00	40.48	4.20	F
1706	1834	0.038159	AAGGCGTTCAAGGACTCGAG	60.038	55.000	11.84	11.84	0.00	4.04	F
2543	2921	1.950630	GTTGTTGGCCGCAAAGCTG	60.951	57.895	13.19	0.00	0.00	4.24	F
3606	5613	2.954989	CACTGCTAGAGTGCTGAGGATA	59.045	50.000	8.70	0.00	45.72	2.59	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1675	1803	0.887933	AACGCCTTTAGCACCCAATG	59.112	50.000	0.00	0.00	44.04	2.82	R
3063	3723	1.991430	CGACGAGCGGATTTGACAG	59.009	57.895	0.00	0.00	36.03	3.51	R
3392	5052	4.089408	AGGTTCGTAGCAACCCTAAAAA	57.911	40.909	0.24	0.00	46.39	1.94	R
3991	6054	4.818546	AGTATTGGATGCATCAGTTGTAGC	59.181	41.667	27.25	8.54	0.00	3.58	R
4875	6983	2.505118	GACGACGCTCCTGTCAGC	60.505	66.667	0.00	0.00	38.84	4.26	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
272	273	6.268617	CCTGATACAGAGATTACCCTGATTCA	59.731	42.308	0.00	0.00	32.44	2.57
460	473	5.308825	AGACATCAGTTTCTGAACGGATTT	58.691	37.500	3.58	0.00	44.68	2.17
590	637	5.885912	AGTGACAGTTATTTGACCTTGTTGT	59.114	36.000	0.00	0.00	0.00	3.32
601	656	4.203226	TGACCTTGTTGTGAATGTTGCTA	58.797	39.130	0.00	0.00	0.00	3.49
602	657	4.826733	TGACCTTGTTGTGAATGTTGCTAT	59.173	37.500	0.00	0.00	0.00	2.97
603	658	5.048782	TGACCTTGTTGTGAATGTTGCTATC	60.049	40.000	0.00	0.00	0.00	2.08
604	659	5.072741	ACCTTGTTGTGAATGTTGCTATCT	58.927	37.500	0.00	0.00	0.00	1.98
605	660	5.048504	ACCTTGTTGTGAATGTTGCTATCTG	60.049	40.000	0.00	0.00	0.00	2.90
606	661	5.048504	CCTTGTTGTGAATGTTGCTATCTGT	60.049	40.000	0.00	0.00	0.00	3.41
607	662	5.611796	TGTTGTGAATGTTGCTATCTGTC	57.388	39.130	0.00	0.00	0.00	3.51
608	663	5.308014	TGTTGTGAATGTTGCTATCTGTCT	58.692	37.500	0.00	0.00	0.00	3.41
620	675	6.691754	TGCTATCTGTCTCTTAACTCTGAG	57.308	41.667	2.45	2.45	0.00	3.35
660	718	2.671396	GTCATTACACGACATGTCCACC	59.329	50.000	20.03	0.00	42.09	4.61
661	719	2.300437	TCATTACACGACATGTCCACCA	59.700	45.455	20.03	1.27	42.09	4.17
662	720	2.912690	TTACACGACATGTCCACCAA	57.087	45.000	20.03	6.86	42.09	3.67
663	721	2.912690	TACACGACATGTCCACCAAA	57.087	45.000	20.03	0.00	42.09	3.28
735	793	1.332195	GCAAGAGCTTTTGGGGAAGT	58.668	50.000	17.82	0.00	37.91	3.01
757	815	2.414691	GCTCAACGATTTTCCTTCTGGC	60.415	50.000	0.00	0.00	0.00	4.85
1022	1147	1.599797	CGACCACCACCACCCTTTC	60.600	63.158	0.00	0.00	0.00	2.62
1026	1151	1.530655	CACCACCACCCTTTCCCAC	60.531	63.158	0.00	0.00	0.00	4.61
1191	1316	3.069318	GAGGCGGACGAGGAGGTT	61.069	66.667	0.00	0.00	0.00	3.50
1197	1322	1.592223	GGACGAGGAGGTTGAGGTG	59.408	63.158	0.00	0.00	0.00	4.00
1428	1553	1.251527	GGGTGAGCCTTCGAGTCTGA	61.252	60.000	0.00	0.00	34.45	3.27
1431	1556	2.548067	GGTGAGCCTTCGAGTCTGAAAA	60.548	50.000	0.00	0.00	0.00	2.29
1432	1557	3.330267	GTGAGCCTTCGAGTCTGAAAAT	58.670	45.455	0.00	0.00	0.00	1.82
1433	1558	3.369451	GTGAGCCTTCGAGTCTGAAAATC	59.631	47.826	0.00	0.00	0.00	2.17
1434	1559	3.006859	TGAGCCTTCGAGTCTGAAAATCA	59.993	43.478	0.00	0.00	0.00	2.57
1435	1560	4.187694	GAGCCTTCGAGTCTGAAAATCAT	58.812	43.478	0.00	0.00	0.00	2.45
1436	1561	3.937706	AGCCTTCGAGTCTGAAAATCATG	59.062	43.478	0.00	0.00	0.00	3.07
1437	1562	3.686726	GCCTTCGAGTCTGAAAATCATGT	59.313	43.478	0.00	0.00	0.00	3.21
1438	1563	4.436584	GCCTTCGAGTCTGAAAATCATGTG	60.437	45.833	0.00	0.00	0.00	3.21
1442	1567	6.267496	TCGAGTCTGAAAATCATGTGTAGA	57.733	37.500	0.00	0.00	0.00	2.59
1495	1621	8.245491	TGATACGATTAGCAGTTTAGTTACACA	58.755	33.333	0.00	0.00	0.00	3.72
1496	1622	6.701432	ACGATTAGCAGTTTAGTTACACAC	57.299	37.500	0.00	0.00	0.00	3.82
1540	1666	1.002468	ACATGTTGCTTGTGCTTCGTC	60.002	47.619	0.00	0.00	40.48	4.20
1545	1671	3.179048	GTTGCTTGTGCTTCGTCTTTTT	58.821	40.909	0.00	0.00	40.48	1.94
1546	1672	2.796304	TGCTTGTGCTTCGTCTTTTTG	58.204	42.857	0.00	0.00	40.48	2.44
1656	1784	2.307049	CAGCGGTTCGTTTGTTCAATC	58.693	47.619	0.00	0.00	0.00	2.67
1659	1787	2.541999	GCGGTTCGTTTGTTCAATCCAA	60.542	45.455	0.00	0.00	0.00	3.53
1662	1790	4.678622	GGTTCGTTTGTTCAATCCAAACT	58.321	39.130	12.51	0.00	45.94	2.66
1671	1799	8.573035	GTTTGTTCAATCCAAACTCCAATAGTA	58.427	33.333	8.36	0.00	45.13	1.82
1675	1803	8.451748	GTTCAATCCAAACTCCAATAGTAGTTC	58.548	37.037	0.00	0.00	37.50	3.01
1688	1816	6.601613	CCAATAGTAGTTCATTGGGTGCTAAA	59.398	38.462	5.59	0.00	44.97	1.85
1690	1818	4.589908	AGTAGTTCATTGGGTGCTAAAGG	58.410	43.478	0.00	0.00	0.00	3.11
1704	1832	1.993370	CTAAAGGCGTTCAAGGACTCG	59.007	52.381	0.00	0.00	0.00	4.18
1705	1833	0.391597	AAAGGCGTTCAAGGACTCGA	59.608	50.000	0.00	0.00	0.00	4.04
1706	1834	0.038159	AAGGCGTTCAAGGACTCGAG	60.038	55.000	11.84	11.84	0.00	4.04
1779	1907	9.234384	GTTGCAATTTCATCTCTATTCATCAAG	57.766	33.333	0.59	0.00	0.00	3.02
1815	2017	8.370940	ACCATGAGTCATGACCATACTAAATAG	58.629	37.037	30.63	13.14	43.81	1.73
1845	2047	9.836076	AGTTTGTTTCAGTTAGTTGTTACTTTC	57.164	29.630	0.00	0.00	35.78	2.62
1915	2119	6.551385	AGTTTCTGTTGATCACAAGCTAAG	57.449	37.500	0.00	0.00	36.64	2.18
1917	2121	4.277515	TCTGTTGATCACAAGCTAAGCT	57.722	40.909	0.00	0.00	42.56	3.74
1937	2141	6.575162	AGCTTACCTTTTTATTGACCACTG	57.425	37.500	0.00	0.00	0.00	3.66
1938	2142	6.303839	AGCTTACCTTTTTATTGACCACTGA	58.696	36.000	0.00	0.00	0.00	3.41
1990	2194	4.467795	TCACAAGCTAGGCTCATCTTTACT	59.532	41.667	0.00	0.00	38.25	2.24
2026	2232	3.349927	TCTTGCTGATGTTCTTGATGGG	58.650	45.455	0.00	0.00	0.00	4.00
2032	2238	5.128919	GCTGATGTTCTTGATGGGACTATT	58.871	41.667	0.00	0.00	0.00	1.73
2039	2245	8.737168	TGTTCTTGATGGGACTATTAATTCTG	57.263	34.615	0.00	0.00	0.00	3.02
2047	2422	6.721318	TGGGACTATTAATTCTGTTGCTCTT	58.279	36.000	0.00	0.00	0.00	2.85
2049	2424	7.987458	TGGGACTATTAATTCTGTTGCTCTTAG	59.013	37.037	0.00	0.00	0.00	2.18
2269	2647	7.981789	TCTGAACTTATATTGGACTGCTGTTAG	59.018	37.037	0.00	0.00	0.00	2.34
2424	2802	8.203485	TGCAAAGATCTAAACCAGAAATTTTGT	58.797	29.630	0.00	0.00	36.67	2.83
2465	2843	9.979578	TTTGACATATGAAACTGTAATGCTTTT	57.020	25.926	10.38	0.00	0.00	2.27
2543	2921	1.950630	GTTGTTGGCCGCAAAGCTG	60.951	57.895	13.19	0.00	0.00	4.24
3063	3723	4.151157	GCATTTGTCTGTTTCTTCCATTGC	59.849	41.667	0.00	0.00	0.00	3.56
3360	5020	5.913137	AGTTCAATTTGACACCTTCAACA	57.087	34.783	0.00	0.00	44.28	3.33
3363	5023	6.096705	AGTTCAATTTGACACCTTCAACATGA	59.903	34.615	0.00	0.00	44.28	3.07
3606	5613	2.954989	CACTGCTAGAGTGCTGAGGATA	59.045	50.000	8.70	0.00	45.72	2.59
3866	5909	4.412199	TCCCTGTTCCTCCATTATAACTGG	59.588	45.833	0.00	0.00	39.38	4.00
4026	6089	9.224267	GATGCATCCAATACTATTGTCATAACT	57.776	33.333	16.23	0.00	0.00	2.24
4133	6196	3.508793	AGTCGTTAGAAAGGATGGTCGAA	59.491	43.478	0.00	0.00	0.00	3.71
4480	6568	1.812571	CCTACATTGGGTGTGAGTTGC	59.187	52.381	0.00	0.00	42.24	4.17
4649	6737	7.148950	GCACACTAAACTGCGTCTATATACATC	60.149	40.741	0.00	0.00	0.00	3.06
4708	6816	2.905415	TGAAGCCATTCTGAACCCAT	57.095	45.000	0.00	0.00	36.33	4.00
4740	6848	1.202989	TGTGGGTAGCAAAGCATCCAA	60.203	47.619	0.00	0.00	0.00	3.53
4784	6892	8.886719	CATGAGCAATCAAGTCTGTAAAAGATA	58.113	33.333	0.00	0.00	37.23	1.98
4875	6983	7.782049	TCCAACTTCTATGGTGACTTGTATAG	58.218	38.462	0.00	0.00	39.09	1.31
4923	7031	0.719015	AGGAATGGACCTCCTGGAGA	59.281	55.000	25.18	5.22	41.96	3.71
4924	7032	1.296523	AGGAATGGACCTCCTGGAGAT	59.703	52.381	25.18	8.09	41.96	2.75

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
272	273	3.456277	AGGAGAAACAAGGTGAAGAGTGT	59.544	43.478	0.00	0.00	0.00	3.55
460	473	1.295792	GACAACAAACCAGCTCGTCA	58.704	50.000	0.00	0.00	0.00	4.35
590	637	7.615403	AGTTAAGAGACAGATAGCAACATTCA	58.385	34.615	0.00	0.00	0.00	2.57
601	656	8.644374	AGTAAACTCAGAGTTAAGAGACAGAT	57.356	34.615	16.46	0.00	37.47	2.90
602	657	9.570468	TTAGTAAACTCAGAGTTAAGAGACAGA	57.430	33.333	16.46	1.09	37.47	3.41
646	704	1.264020	CACTTTGGTGGACATGTCGTG	59.736	52.381	19.33	14.96	39.59	4.35
662	720	9.751542	CGAGAATAATTAAGACTATGTCCACTT	57.248	33.333	0.00	0.00	32.18	3.16
663	721	9.132923	TCGAGAATAATTAAGACTATGTCCACT	57.867	33.333	0.00	0.00	32.18	4.00
735	793	2.813754	CCAGAAGGAAAATCGTTGAGCA	59.186	45.455	0.00	0.00	36.89	4.26
771	829	6.478016	CCAGCTCTCAAAAGAAAAAGGAAAAG	59.522	38.462	0.00	0.00	0.00	2.27
808	927	2.802247	GACAACATGCTTTTTGGGCTTC	59.198	45.455	0.00	0.00	0.00	3.86
809	928	2.435437	AGACAACATGCTTTTTGGGCTT	59.565	40.909	0.00	0.00	0.00	4.35
848	968	4.163268	GGGAGAGAGGAAGAGCAGTAAAAT	59.837	45.833	0.00	0.00	0.00	1.82
1191	1316	1.305633	CAGCTCCTCCTCCACCTCA	60.306	63.158	0.00	0.00	0.00	3.86
1197	1322	4.154347	CACGGCAGCTCCTCCTCC	62.154	72.222	0.00	0.00	0.00	4.30
1428	1553	6.932356	AAGCATCGATCTACACATGATTTT	57.068	33.333	0.00	0.00	0.00	1.82
1431	1556	6.155136	CACTAAGCATCGATCTACACATGAT	58.845	40.000	0.00	0.00	0.00	2.45
1432	1557	5.507985	CCACTAAGCATCGATCTACACATGA	60.508	44.000	0.00	0.00	0.00	3.07
1433	1558	4.683320	CCACTAAGCATCGATCTACACATG	59.317	45.833	0.00	0.00	0.00	3.21
1434	1559	4.262207	CCCACTAAGCATCGATCTACACAT	60.262	45.833	0.00	0.00	0.00	3.21
1435	1560	3.068165	CCCACTAAGCATCGATCTACACA	59.932	47.826	0.00	0.00	0.00	3.72
1436	1561	3.553096	CCCCACTAAGCATCGATCTACAC	60.553	52.174	0.00	0.00	0.00	2.90
1437	1562	2.628178	CCCCACTAAGCATCGATCTACA	59.372	50.000	0.00	0.00	0.00	2.74
1438	1563	2.028930	CCCCCACTAAGCATCGATCTAC	60.029	54.545	0.00	0.00	0.00	2.59
1442	1567	0.759346	GTCCCCCACTAAGCATCGAT	59.241	55.000	0.00	0.00	0.00	3.59
1495	1621	3.544698	TCTTAGAGAGGAACCACCAGT	57.455	47.619	0.00	0.00	42.04	4.00
1496	1622	4.383552	CCAATCTTAGAGAGGAACCACCAG	60.384	50.000	0.00	0.00	42.04	4.00
1501	1627	5.104735	ACATGTCCAATCTTAGAGAGGAACC	60.105	44.000	6.95	0.00	0.00	3.62
1540	1666	6.687081	TTATTATCTACCGCCACCAAAAAG	57.313	37.500	0.00	0.00	0.00	2.27
1545	1671	4.406326	TCACTTTATTATCTACCGCCACCA	59.594	41.667	0.00	0.00	0.00	4.17
1546	1672	4.952460	TCACTTTATTATCTACCGCCACC	58.048	43.478	0.00	0.00	0.00	4.61
1591	1717	7.710676	TTTTGGCATGGCTAAAACTCTATTA	57.289	32.000	22.73	1.19	42.32	0.98
1671	1799	2.171003	GCCTTTAGCACCCAATGAACT	58.829	47.619	0.00	0.00	42.97	3.01
1675	1803	0.887933	AACGCCTTTAGCACCCAATG	59.112	50.000	0.00	0.00	44.04	2.82
1688	1816	0.894184	TCTCGAGTCCTTGAACGCCT	60.894	55.000	13.13	0.00	0.00	5.52
1690	1818	1.997669	ATTCTCGAGTCCTTGAACGC	58.002	50.000	13.13	0.00	0.00	4.84
1704	1832	8.744568	AAAAAGAGTCAATCTCCCATATTCTC	57.255	34.615	0.00	0.00	43.71	2.87
1733	1861	3.300388	ACATAGAATCCCTCGCTGAGAA	58.700	45.455	7.07	0.00	0.00	2.87
1735	1863	3.388308	CAACATAGAATCCCTCGCTGAG	58.612	50.000	0.00	0.00	0.00	3.35
1737	1865	1.869767	GCAACATAGAATCCCTCGCTG	59.130	52.381	0.00	0.00	0.00	5.18
1738	1866	1.486310	TGCAACATAGAATCCCTCGCT	59.514	47.619	0.00	0.00	0.00	4.93
1739	1867	1.953559	TGCAACATAGAATCCCTCGC	58.046	50.000	0.00	0.00	0.00	5.03
1740	1868	5.066375	TGAAATTGCAACATAGAATCCCTCG	59.934	40.000	0.00	0.00	0.00	4.63
1741	1869	6.455360	TGAAATTGCAACATAGAATCCCTC	57.545	37.500	0.00	0.00	0.00	4.30
1742	1870	6.837568	AGATGAAATTGCAACATAGAATCCCT	59.162	34.615	0.00	0.00	0.00	4.20
1776	1904	8.146412	TCATGACTCATGGTTCTATGATACTTG	58.854	37.037	17.33	6.06	41.66	3.16
1779	1907	6.870965	GGTCATGACTCATGGTTCTATGATAC	59.129	42.308	24.50	5.65	41.66	2.24
1815	2017	9.058424	GTAACAACTAACTGAAACAAACTGAAC	57.942	33.333	0.00	0.00	0.00	3.18
1845	2047	6.229733	AGTTCTCCTGATTCTTTCTCACTTG	58.770	40.000	0.00	0.00	0.00	3.16
1915	2119	6.206829	AGTCAGTGGTCAATAAAAAGGTAAGC	59.793	38.462	0.00	0.00	0.00	3.09
1917	2121	9.280174	CTTAGTCAGTGGTCAATAAAAAGGTAA	57.720	33.333	0.00	0.00	0.00	2.85
1927	2131	6.054860	ACATAAGCTTAGTCAGTGGTCAAT	57.945	37.500	12.54	0.00	0.00	2.57
1932	2136	6.560253	ACAAAACATAAGCTTAGTCAGTGG	57.440	37.500	12.54	1.84	0.00	4.00
1937	2141	9.118236	GTGATCAAACAAAACATAAGCTTAGTC	57.882	33.333	12.54	0.00	0.00	2.59
1938	2142	8.629158	TGTGATCAAACAAAACATAAGCTTAGT	58.371	29.630	12.54	7.44	0.00	2.24
2039	2245	7.617041	AATGGTTATGACTTCTAAGAGCAAC	57.383	36.000	0.00	0.00	0.00	4.17
2269	2647	4.229876	GAGAAAATAAAGCAGGTGTGTGC	58.770	43.478	0.00	0.00	44.35	4.57
2384	2762	6.347696	AGATCTTTGCAAGGAGATAGTCTTG	58.652	40.000	16.88	0.00	42.19	3.02
2424	2802	9.904198	TCATATGTCAAAATCTATTCTGACCAA	57.096	29.630	1.90	0.00	37.90	3.67
2543	2921	4.462133	TGTAGTCCTCACTATAGCCAGAC	58.538	47.826	0.00	2.47	37.45	3.51
2786	3442	8.287439	TCTAAGAGTACCAGAATCAGAAGAAG	57.713	38.462	0.00	0.00	0.00	2.85
2886	3546	7.831691	TCCACAAATTTCATAGGAAGTCAAA	57.168	32.000	0.00	0.00	33.82	2.69
2987	3647	9.952188	GAAAGTAATCTTCTAAAAGTTTGCAGT	57.048	29.630	0.00	0.00	32.41	4.40
3063	3723	1.991430	CGACGAGCGGATTTGACAG	59.009	57.895	0.00	0.00	36.03	3.51
3333	4993	6.329496	TGAAGGTGTCAAATTGAACTTCAAC	58.671	36.000	23.97	11.83	39.10	3.18
3392	5052	4.089408	AGGTTCGTAGCAACCCTAAAAA	57.911	40.909	0.24	0.00	46.39	1.94
3457	5247	5.068855	CCACAGCTCTTGATCATCTTCTAGA	59.931	44.000	0.00	0.00	0.00	2.43
3606	5613	7.981225	GGACCTGCAATATCATAAAACACAAAT	59.019	33.333	0.00	0.00	0.00	2.32
3866	5909	6.112058	GGGAGCTGGATAATTCACAGATATC	58.888	44.000	0.00	0.00	34.21	1.63
3991	6054	4.818546	AGTATTGGATGCATCAGTTGTAGC	59.181	41.667	27.25	8.54	0.00	3.58
4026	6089	5.730296	TGAAAACAGGGAAAGAAACAACA	57.270	34.783	0.00	0.00	0.00	3.33
4601	6689	7.970061	TGTGCTTATTCACTTATTTCAATCTGC	59.030	33.333	0.00	0.00	37.81	4.26
4633	6721	6.971756	CCTGATTCAGATGTATATAGACGCAG	59.028	42.308	15.36	0.00	32.44	5.18
4649	6737	6.147864	TGTTCCAACTTTTTCCTGATTCAG	57.852	37.500	6.70	6.70	0.00	3.02
4708	6816	2.752354	GCTACCCACATATTGTGCACAA	59.248	45.455	32.78	32.78	46.51	3.33
4731	6839	8.674263	TGTTTTACATTCAAATTTGGATGCTT	57.326	26.923	31.11	19.35	46.03	3.91
4740	6848	8.659925	TGCTCATGTTGTTTTACATTCAAATT	57.340	26.923	0.00	0.00	36.64	1.82
4861	6969	3.195610	CCTGTCAGCTATACAAGTCACCA	59.804	47.826	0.00	0.00	0.00	4.17
4875	6983	2.505118	GACGACGCTCCTGTCAGC	60.505	66.667	0.00	0.00	38.84	4.26
4912	7020	6.042552	CACAATTGTATAGATCTCCAGGAGGT	59.957	42.308	17.10	9.82	35.89	3.85
4923	7031	8.896744	CATGACCTGAAACACAATTGTATAGAT	58.103	33.333	11.53	0.00	33.55	1.98
4924	7032	8.100164	TCATGACCTGAAACACAATTGTATAGA	58.900	33.333	11.53	0.00	33.55	1.98

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.