AutoCloner

Multiple sequence alignment - TraesCS2D01G355700

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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	TraesCS2D01G355700	chr2D	100.000	9142	0	0	1	9142	458151308	458160449	0.000000e+00	16883.0
1	TraesCS2D01G355700	chr2D	93.045	762	35	10	1	745	485841873	485841113	0.000000e+00	1098.0
2	TraesCS2D01G355700	chr2D	92.490	759	43	7	1	745	446962343	446961585	0.000000e+00	1074.0
3	TraesCS2D01G355700	chr2D	89.432	757	64	9	1	742	167008010	167007255	0.000000e+00	941.0
4	TraesCS2D01G355700	chr2D	89.735	604	44	11	1	588	427319372	427318771	0.000000e+00	756.0
5	TraesCS2D01G355700	chr2D	89.172	157	16	1	3814	3970	592621660	592621815	2.600000e-45	195.0
6	TraesCS2D01G355700	chr2D	91.667	60	5	0	5419	5478	458156651	458156710	5.880000e-12	84.2
7	TraesCS2D01G355700	chr2D	91.667	60	5	0	5344	5403	458156726	458156785	5.880000e-12	84.2
8	TraesCS2D01G355700	chr2A	96.396	6493	155	21	2680	9142	601704710	601711153	0.000000e+00	10621.0
9	TraesCS2D01G355700	chr2A	95.502	1912	29	19	824	2681	601702702	601704610	0.000000e+00	3001.0
10	TraesCS2D01G355700	chr2A	88.199	161	17	2	3814	3974	727176027	727176185	3.370000e-44	191.0
11	TraesCS2D01G355700	chr2A	92.188	64	5	0	5415	5478	601707349	601707412	3.520000e-14	91.6
12	TraesCS2D01G355700	chr2A	91.667	60	5	0	5344	5403	601707427	601707486	5.880000e-12	84.2
13	TraesCS2D01G355700	chr2B	96.111	5760	145	38	2962	8692	539278897	539284606	0.000000e+00	9323.0
14	TraesCS2D01G355700	chr2B	95.059	2044	40	21	745	2740	539276870	539278900	0.000000e+00	3158.0
15	TraesCS2D01G355700	chr2B	88.415	751	72	10	1	739	230913419	230914166	0.000000e+00	891.0
16	TraesCS2D01G355700	chr2B	85.276	163	17	6	4787	4945	133025577	133025418	2.640000e-35	161.0
17	TraesCS2D01G355700	chr6B	90.571	753	57	4	1	739	500644184	500644936	0.000000e+00	985.0
18	TraesCS2D01G355700	chr6B	91.575	273	22	1	193	465	664894554	664894283	8.670000e-100	375.0
19	TraesCS2D01G355700	chr6B	92.715	151	11	0	461	611	664863615	664863465	1.550000e-52	219.0
20	TraesCS2D01G355700	chr6B	92.086	139	11	0	607	745	664854831	664854693	7.240000e-46	196.0
21	TraesCS2D01G355700	chr1A	85.008	627	75	11	1	611	42600475	42599852	3.630000e-173	619.0
22	TraesCS2D01G355700	chr7B	91.954	174	11	1	1	174	9324062	9324232	3.300000e-59	241.0
23	TraesCS2D01G355700	chr7B	87.500	160	11	7	4787	4942	323200938	323200784	9.430000e-40	176.0
24	TraesCS2D01G355700	chr7B	82.895	76	12	1	8557	8631	118814398	118814473	5.920000e-07	67.6
25	TraesCS2D01G355700	chr7B	92.308	39	2	1	699	737	519915400	519915363	5.000000e-03	54.7
26	TraesCS2D01G355700	chr3D	88.525	183	17	3	4787	4966	579584662	579584843	1.550000e-52	219.0
27	TraesCS2D01G355700	chr3D	89.172	157	17	0	3820	3976	254103010	254103166	7.240000e-46	196.0
28	TraesCS2D01G355700	chr1D	94.366	142	4	3	4826	4965	394864402	394864541	2.000000e-51	215.0
29	TraesCS2D01G355700	chr7D	94.203	138	5	2	4831	4966	263946215	263946351	3.350000e-49	207.0
30	TraesCS2D01G355700	chr7D	80.851	94	16	2	8557	8649	156447757	156447849	1.270000e-08	73.1
31	TraesCS2D01G355700	chr7A	87.113	194	10	7	4787	4966	13343759	13343567	1.200000e-48	206.0
32	TraesCS2D01G355700	chr7A	89.506	162	15	2	1	162	544264564	544264723	4.330000e-48	204.0
33	TraesCS2D01G355700	chr7A	86.905	168	20	1	3811	3976	701493464	701493631	4.360000e-43	187.0
34	TraesCS2D01G355700	chr6D	89.506	162	16	1	3815	3976	470996264	470996424	4.330000e-48	204.0
35	TraesCS2D01G355700	chr6A	89.506	162	16	1	3815	3976	615803800	615803960	4.330000e-48	204.0
36	TraesCS2D01G355700	chr6A	92.308	143	7	3	4827	4967	465615571	465615711	5.600000e-47	200.0
37	TraesCS2D01G355700	chr4B	92.254	142	6	4	4827	4966	8413747	8413609	7.240000e-46	196.0
38	TraesCS2D01G355700	chr3A	89.103	156	15	1	3826	3979	335478020	335477865	9.370000e-45	193.0
39	TraesCS2D01G355700	chr5A	78.448	116	19	5	8518	8629	230548236	230548123	4.580000e-08	71.3
40	TraesCS2D01G355700	chr5A	78.448	116	19	5	8518	8629	230549699	230549586	4.580000e-08	71.3

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	TraesCS2D01G355700	chr2D	458151308	458160449	9141	False	5683.80	16883	94.444667	1	9142	3	chr2D.!!$F2	9141
1	TraesCS2D01G355700	chr2D	485841113	485841873	760	True	1098.00	1098	93.045000	1	745	1	chr2D.!!$R4	744
2	TraesCS2D01G355700	chr2D	446961585	446962343	758	True	1074.00	1074	92.490000	1	745	1	chr2D.!!$R3	744
3	TraesCS2D01G355700	chr2D	167007255	167008010	755	True	941.00	941	89.432000	1	742	1	chr2D.!!$R1	741
4	TraesCS2D01G355700	chr2D	427318771	427319372	601	True	756.00	756	89.735000	1	588	1	chr2D.!!$R2	587
5	TraesCS2D01G355700	chr2A	601702702	601711153	8451	False	3449.45	10621	93.938250	824	9142	4	chr2A.!!$F2	8318
6	TraesCS2D01G355700	chr2B	539276870	539284606	7736	False	6240.50	9323	95.585000	745	8692	2	chr2B.!!$F2	7947
7	TraesCS2D01G355700	chr2B	230913419	230914166	747	False	891.00	891	88.415000	1	739	1	chr2B.!!$F1	738
8	TraesCS2D01G355700	chr6B	500644184	500644936	752	False	985.00	985	90.571000	1	739	1	chr6B.!!$F1	738
9	TraesCS2D01G355700	chr1A	42599852	42600475	623	True	619.00	619	85.008000	1	611	1	chr1A.!!$R1	610

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
174	180	0.618458	CCTTCGGTTCCCATCCTGAA	59.382	55.000	0.00	0.00	3.02	F
1562	1614	0.039326	ATGGCTCTTGCTCTTTGGCT	59.961	50.000	0.00	39.59	4.75	F
1563	1615	0.692476	TGGCTCTTGCTCTTTGGCTA	59.308	50.000	0.00	39.59	3.93	F
2746	2933	1.681264	ACCCCTTTTGCTTTTCACGAG	59.319	47.619	0.00	0.00	4.18	F
4604	4791	0.325671	ATCCCCTCACGTCATGGAGT	60.326	55.000	0.00	0.00	3.85	F
4822	5009	1.137479	ACGAGTTGTTCCGAGGTTGAA	59.863	47.619	0.00	0.00	2.69	F
6322	6523	0.914644	AGCCTGGCATCTTAGCTTGA	59.085	50.000	22.65	34.17	3.02	F
7784	7990	0.105039	CGTCCTCTGGGCTGGTAATC	59.895	60.000	0.00	0.00	1.75	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1732	1791	1.444933	TCCAGGTGTCTTGGAATGGT	58.555	50.000	0.00	0.00	3.55	R
3390	3577	0.038166	ACCGGTCACTGGCATCAATT	59.962	50.000	0.00	0.00	2.32	R
3637	3824	8.438513	CAATTAATCAATCCTCAGCATACTACG	58.561	37.037	0.00	0.00	3.51	R
4808	4995	1.137479	ACGAGTTTCAACCTCGGAACA	59.863	47.619	9.36	43.90	3.18	R
6322	6523	2.097825	GCCATCTGCTTCCAAATCTGT	58.902	47.619	0.00	36.87	3.41	R
6411	6612	3.925630	ATCCTGCAACCCACCAGCG	62.926	63.158	0.00	0.00	5.18	R
8039	8245	0.948623	CACGAAGAACATCCGTGGCA	60.949	55.000	0.00	46.72	4.92	R
9077	9326	2.487934	CATGAGCTCGAACCCAATAGG	58.512	52.381	9.64	43.78	2.57	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
37	40	3.691609	GGTGGCCAGAATCTAAAGAACTG	59.308	47.826	5.11	9.24	34.64	3.16
109	115	1.869132	GTGATATCGCATGCAGCAAGA	59.131	47.619	19.57	6.59	46.13	3.02
116	122	2.944349	TCGCATGCAGCAAGATCATTTA	59.056	40.909	19.57	0.00	46.13	1.40
147	153	4.261801	ACAATCTCCTTCACAATAACCGG	58.738	43.478	0.00	0.00	0.00	5.28
174	180	0.618458	CCTTCGGTTCCCATCCTGAA	59.382	55.000	0.00	0.00	0.00	3.02
175	181	1.212935	CCTTCGGTTCCCATCCTGAAT	59.787	52.381	0.00	0.00	0.00	2.57
178	184	0.839946	CGGTTCCCATCCTGAATCCT	59.160	55.000	0.00	0.00	0.00	3.24
181	187	2.444766	GGTTCCCATCCTGAATCCTGAT	59.555	50.000	0.00	0.00	0.00	2.90
182	188	3.484407	GTTCCCATCCTGAATCCTGATG	58.516	50.000	3.09	3.09	36.49	3.07
184	190	1.144298	CCCATCCTGAATCCTGATGCA	59.856	52.381	0.00	0.00	35.62	3.96
238	258	2.689983	CAAGTGCAAGTGAAAGTCCCTT	59.310	45.455	0.00	0.00	0.00	3.95
269	289	0.912486	AAGCTTCAAGGATAGCCGGT	59.088	50.000	1.90	0.00	38.14	5.28
295	315	2.367241	TGATTCCGGAGACAACAAGTGA	59.633	45.455	3.34	0.00	0.00	3.41
365	385	1.623811	GCACCTCTTTCACCTGTCCTA	59.376	52.381	0.00	0.00	0.00	2.94
456	476	2.662596	CTGCCCTACTCGGTGCAA	59.337	61.111	0.00	0.00	38.13	4.08
742	762	3.401577	TCGACATCGAGCACTTCAC	57.598	52.632	0.00	0.00	44.22	3.18
750	770	4.997395	ACATCGAGCACTTCACTATGTTTT	59.003	37.500	0.00	0.00	0.00	2.43
751	771	4.990543	TCGAGCACTTCACTATGTTTTG	57.009	40.909	0.00	0.00	0.00	2.44
779	799	1.026718	GTGAGCCGAATTGACCCAGG	61.027	60.000	0.00	0.00	0.00	4.45
780	800	1.452108	GAGCCGAATTGACCCAGGG	60.452	63.158	2.85	2.85	0.00	4.45
1439	1466	2.839632	TGCCCCGATCGCATCTCT	60.840	61.111	10.32	0.00	0.00	3.10
1444	1471	1.742146	CCGATCGCATCTCTTCCCA	59.258	57.895	10.32	0.00	0.00	4.37
1445	1472	0.319383	CCGATCGCATCTCTTCCCAG	60.319	60.000	10.32	0.00	0.00	4.45
1449	1497	0.965866	TCGCATCTCTTCCCAGACGT	60.966	55.000	0.00	0.00	0.00	4.34
1561	1613	1.674962	CTATGGCTCTTGCTCTTTGGC	59.325	52.381	0.00	0.00	39.59	4.52
1562	1614	0.039326	ATGGCTCTTGCTCTTTGGCT	59.961	50.000	0.00	0.00	39.59	4.75
1563	1615	0.692476	TGGCTCTTGCTCTTTGGCTA	59.308	50.000	0.00	0.00	39.59	3.93
1692	1749	8.593945	AATTTTATCCCACTAGCATTTCAAGA	57.406	30.769	0.00	0.00	0.00	3.02
1808	1870	5.871396	TTATTTACTACTCCAGAGGCAGG	57.129	43.478	0.00	0.00	0.00	4.85
2537	2623	6.183361	TGGCATTAATCAGGTTGATAGGATGA	60.183	38.462	10.67	0.00	35.76	2.92
2538	2624	6.888632	GGCATTAATCAGGTTGATAGGATGAT	59.111	38.462	10.67	0.00	35.76	2.45
2539	2625	7.148120	GGCATTAATCAGGTTGATAGGATGATG	60.148	40.741	10.67	0.00	35.76	3.07
2672	2758	9.615295	TTGGCGTGTTATCTTTCTTAATTTAAC	57.385	29.630	0.00	0.00	0.00	2.01
2743	2930	3.118775	AGTGAACCCCTTTTGCTTTTCAC	60.119	43.478	4.47	4.47	41.98	3.18
2746	2933	1.681264	ACCCCTTTTGCTTTTCACGAG	59.319	47.619	0.00	0.00	0.00	4.18
2945	3132	6.926630	AGTGTTTCTCTGTTCTATCCTTCT	57.073	37.500	0.00	0.00	0.00	2.85
3201	3388	4.859245	GCATAGCCAGTTTACTTTTCTTGC	59.141	41.667	0.00	0.00	0.00	4.01
3240	3427	4.963276	TTCTTATGGAATGAGCAAACCG	57.037	40.909	0.00	0.00	28.56	4.44
3390	3577	2.066393	AGATGGCGCCAAGGCTCTA	61.066	57.895	36.33	7.40	46.88	2.43
3637	3824	6.985059	ACTGAAGGTGAGTTTGTTACTTACTC	59.015	38.462	9.38	9.38	41.71	2.59
3799	3986	6.202570	TGCCAACTTCAAAATTTTGCTGTATC	59.797	34.615	23.36	15.46	38.05	2.24
3940	4127	4.781775	TTGGTTGAACTAAGAAGGGTCA	57.218	40.909	0.00	0.00	0.00	4.02
4604	4791	0.325671	ATCCCCTCACGTCATGGAGT	60.326	55.000	0.00	0.00	0.00	3.85
4694	4881	3.186205	GCTCTCTTTCAAACTCTGCTGAC	59.814	47.826	0.00	0.00	0.00	3.51
4808	4995	3.722728	AGGTTTACGAGTTGACGAGTT	57.277	42.857	0.00	0.00	37.03	3.01
4822	5009	1.137479	ACGAGTTGTTCCGAGGTTGAA	59.863	47.619	0.00	0.00	0.00	2.69
4839	5026	5.413833	AGGTTGAAACTCGTAGACTAATCGA	59.586	40.000	0.00	0.00	0.00	3.59
4840	5027	5.511025	GGTTGAAACTCGTAGACTAATCGAC	59.489	44.000	0.00	0.00	0.00	4.20
4856	5052	1.154197	CGACACTAGTCCGACACTGA	58.846	55.000	8.13	0.00	41.87	3.41
5156	5356	8.882282	AGAGCCTGAGTGATATAAGTACTACTA	58.118	37.037	0.00	0.00	0.00	1.82
5158	5358	7.603404	AGCCTGAGTGATATAAGTACTACTACG	59.397	40.741	0.00	0.00	0.00	3.51
5220	5420	2.760092	TCTCCAATATGCAACTTTGGCC	59.240	45.455	16.70	0.00	39.79	5.36
5335	5535	6.879458	ACCTAGTCAACCTAATTACTTTGCTG	59.121	38.462	0.00	0.00	0.00	4.41
5342	5542	7.880713	TCAACCTAATTACTTTGCTGTATGTCA	59.119	33.333	0.00	0.00	0.00	3.58
5368	5568	9.965902	ATCAAAGATAGAAAAGTTGGAGTACAT	57.034	29.630	0.00	0.00	0.00	2.29
5439	5639	5.690865	TGTCAAAGATAACAAAGTGGGAGT	58.309	37.500	0.00	0.00	0.00	3.85
6239	6440	8.203485	GGATTCTGTTATTTCAATTGCCCATAA	58.797	33.333	0.00	0.66	0.00	1.90
6322	6523	0.914644	AGCCTGGCATCTTAGCTTGA	59.085	50.000	22.65	0.00	34.17	3.02
6342	6543	2.097825	ACAGATTTGGAAGCAGATGGC	58.902	47.619	0.00	0.00	45.30	4.40
6411	6612	8.964476	TCAATCCCTTCTTGAATATTCACTAC	57.036	34.615	17.76	0.00	36.83	2.73
6431	6632	1.187567	GCTGGTGGGTTGCAGGATTT	61.188	55.000	0.00	0.00	0.00	2.17
6682	6887	5.316327	AGTGCTTGCTTCCTTAAATTAGC	57.684	39.130	0.00	0.00	0.00	3.09
6685	6890	5.346011	GTGCTTGCTTCCTTAAATTAGCAAC	59.654	40.000	6.92	5.82	45.63	4.17
6706	6911	4.595986	ACCATGTTTACCATTGACCTACC	58.404	43.478	0.00	0.00	0.00	3.18
6755	6960	3.084039	GGCATGTGGAGAAGATTTGTCA	58.916	45.455	0.00	0.00	0.00	3.58
7569	7774	2.621998	CCAAGCCTGCTAATGATTCCAG	59.378	50.000	0.00	0.37	0.00	3.86
7784	7990	0.105039	CGTCCTCTGGGCTGGTAATC	59.895	60.000	0.00	0.00	0.00	1.75
7824	8030	6.041423	AGCCCATTTTCTTTCTTTACCATG	57.959	37.500	0.00	0.00	0.00	3.66
7825	8031	5.046376	AGCCCATTTTCTTTCTTTACCATGG	60.046	40.000	11.19	11.19	0.00	3.66
7833	8039	7.654022	TTCTTTCTTTACCATGGTCTGTTTT	57.346	32.000	23.76	0.00	0.00	2.43
7837	8043	5.690865	TCTTTACCATGGTCTGTTTTGAGT	58.309	37.500	23.76	0.00	0.00	3.41
7843	8049	5.891551	ACCATGGTCTGTTTTGAGTTTTAGT	59.108	36.000	13.00	0.00	0.00	2.24
7895	8101	9.890629	TTTACATTATTCAGCATCTGTTCTACT	57.109	29.630	0.00	0.00	32.61	2.57
8078	8284	3.121030	CGGGCAAAGGCAGAGTCG	61.121	66.667	0.00	0.00	43.71	4.18
8079	8285	2.032681	GGGCAAAGGCAGAGTCGT	59.967	61.111	0.00	0.00	43.71	4.34
8202	8408	1.130561	CATGACATGTGCAGCTGTGAG	59.869	52.381	16.64	4.02	0.00	3.51
8383	8604	8.587111	GCTCTTTGATTCAACGGATTTTTATTC	58.413	33.333	0.00	0.00	0.00	1.75
8479	8704	6.151480	GGGACTTTTGTACGGGATTTATTTGA	59.849	38.462	0.00	0.00	32.88	2.69
8759	8993	4.158394	GGATTGCAAGCAAAGAAGACCATA	59.842	41.667	17.68	0.00	39.55	2.74
8760	8994	4.771590	TTGCAAGCAAAGAAGACCATAG	57.228	40.909	4.79	0.00	32.44	2.23
8798	9032	7.690952	GGTTTATATTCCTACAAACCACACA	57.309	36.000	9.67	0.00	45.98	3.72
8904	9138	7.063074	AGGAAAACGTAAGATTTAGATGTCACG	59.937	37.037	0.00	0.00	42.74	4.35
8923	9157	7.602753	TGTCACGTATCATGAAATCCTATAGG	58.397	38.462	13.07	13.07	0.00	2.57
8993	9227	2.296073	TTTTGCGGGGTTGTATTCCT	57.704	45.000	0.00	0.00	0.00	3.36
9077	9326	6.397272	TGTATGCAATTTCATTGGGAACTTC	58.603	36.000	0.00	0.00	40.57	3.01
9078	9327	4.270245	TGCAATTTCATTGGGAACTTCC	57.730	40.909	0.00	0.00	40.57	3.46
9098	9347	2.487934	CTATTGGGTTCGAGCTCATGG	58.512	52.381	15.40	0.00	0.00	3.66
9099	9348	0.107017	ATTGGGTTCGAGCTCATGGG	60.107	55.000	15.40	0.00	0.00	4.00
9100	9349	2.190578	GGGTTCGAGCTCATGGGG	59.809	66.667	15.40	0.00	0.00	4.96
9115	9364	4.230455	TCATGGGGAATTTCCACTGTTTT	58.770	39.130	18.36	0.00	41.69	2.43
9116	9365	5.398236	TCATGGGGAATTTCCACTGTTTTA	58.602	37.500	18.36	0.00	41.69	1.52

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
17	19	3.587061	TCCAGTTCTTTAGATTCTGGCCA	59.413	43.478	4.71	4.71	41.67	5.36
37	40	7.767250	AGCCCATAATCTAGCTAAATTTTCC	57.233	36.000	0.00	0.00	32.73	3.13
109	115	5.820947	GGAGATTGTAACACGGGTAAATGAT	59.179	40.000	0.00	0.00	0.00	2.45
116	122	2.635915	TGAAGGAGATTGTAACACGGGT	59.364	45.455	0.00	0.00	0.00	5.28
182	188	0.245539	AAGTGGTGATTGCATGCTGC	59.754	50.000	20.33	8.58	45.29	5.25
184	190	1.965643	ACAAAGTGGTGATTGCATGCT	59.034	42.857	20.33	0.00	0.00	3.79
238	258	2.283101	AAGCTTTGGCATGCCGGA	60.283	55.556	30.87	19.66	41.70	5.14
269	289	2.367241	TGTTGTCTCCGGAATCACTGAA	59.633	45.455	5.23	0.00	0.00	3.02
295	315	0.765510	AACTTTTCTGGGCTCCTCGT	59.234	50.000	0.00	0.00	0.00	4.18
365	385	2.053244	CATGTAGATGGGGGCTTCTCT	58.947	52.381	0.00	0.00	0.00	3.10
456	476	0.617820	AGGCCGGATACAGACAAGGT	60.618	55.000	5.05	0.00	0.00	3.50
700	720	1.065854	GTGTCTGGGCATTAGCTGACT	60.066	52.381	0.00	0.00	41.70	3.41
739	759	2.890311	CTGCCCCAACAAAACATAGTGA	59.110	45.455	0.00	0.00	0.00	3.41
742	762	2.890311	TCACTGCCCCAACAAAACATAG	59.110	45.455	0.00	0.00	0.00	2.23
779	799	0.962855	GAAAGCTTCTCACAGGGGCC	60.963	60.000	0.00	0.00	0.00	5.80
780	800	1.301677	CGAAAGCTTCTCACAGGGGC	61.302	60.000	0.00	0.00	0.00	5.80
821	841	1.376683	CGGGCCATTCTCGGTTGAA	60.377	57.895	4.39	0.00	0.00	2.69
1439	1466	2.669113	CGATACAAACGACGTCTGGGAA	60.669	50.000	14.70	0.00	0.00	3.97
1561	1613	8.888579	ATCTCGGGTCAGTTTAATTGTAATAG	57.111	34.615	0.00	0.00	0.00	1.73
1562	1614	8.701895	AGATCTCGGGTCAGTTTAATTGTAATA	58.298	33.333	0.00	0.00	0.00	0.98
1563	1615	7.565680	AGATCTCGGGTCAGTTTAATTGTAAT	58.434	34.615	0.00	0.00	0.00	1.89
1675	1732	2.290896	TGGGTCTTGAAATGCTAGTGGG	60.291	50.000	0.00	0.00	0.00	4.61
1732	1791	1.444933	TCCAGGTGTCTTGGAATGGT	58.555	50.000	0.00	0.00	0.00	3.55
1762	1821	4.224147	TGTCATTCCTTCCATCTCGGTTAA	59.776	41.667	0.00	0.00	35.57	2.01
2537	2623	0.706433	ACAGGATCACTTTGGCCCAT	59.294	50.000	0.00	0.00	0.00	4.00
2538	2624	0.482446	AACAGGATCACTTTGGCCCA	59.518	50.000	0.00	0.00	0.00	5.36
2539	2625	1.632589	AAACAGGATCACTTTGGCCC	58.367	50.000	0.00	0.00	0.00	5.80
2670	2756	9.410556	GCAAGATGTTTGTACATAGAAATTGTT	57.589	29.630	0.00	0.00	44.90	2.83
2672	2758	9.630098	AAGCAAGATGTTTGTACATAGAAATTG	57.370	29.630	0.00	2.02	44.90	2.32
2833	3020	4.333372	GCAAATGCCCTGGTGAAATAAATG	59.667	41.667	0.00	0.00	34.31	2.32
2834	3021	4.225717	AGCAAATGCCCTGGTGAAATAAAT	59.774	37.500	0.94	0.00	43.38	1.40
2897	3084	4.359971	TGAAGCCATCATGAATTTGTCG	57.640	40.909	0.00	0.00	31.50	4.35
3060	3247	4.524714	AGACATACAGCTCAGTGTTAGTGT	59.475	41.667	0.00	0.00	31.46	3.55
3390	3577	0.038166	ACCGGTCACTGGCATCAATT	59.962	50.000	0.00	0.00	0.00	2.32
3637	3824	8.438513	CAATTAATCAATCCTCAGCATACTACG	58.561	37.037	0.00	0.00	0.00	3.51
4208	4395	5.405571	CGCATATATTTTCCTAGTCAACGCT	59.594	40.000	0.00	0.00	0.00	5.07
4694	4881	2.677875	GTGCCCCAAGGAAGCCTG	60.678	66.667	0.00	0.00	32.13	4.85
4808	4995	1.137479	ACGAGTTTCAACCTCGGAACA	59.863	47.619	9.36	0.00	43.90	3.18
4822	5009	6.105333	ACTAGTGTCGATTAGTCTACGAGTT	58.895	40.000	0.00	0.00	36.74	3.01
4827	5014	5.046529	TCGGACTAGTGTCGATTAGTCTAC	58.953	45.833	22.72	13.09	43.31	2.59
4836	5023	1.154197	CAGTGTCGGACTAGTGTCGA	58.846	55.000	9.88	6.98	43.79	4.20
4839	5026	2.584236	ACTTCAGTGTCGGACTAGTGT	58.416	47.619	9.88	0.00	31.73	3.55
4840	5027	3.309388	CAACTTCAGTGTCGGACTAGTG	58.691	50.000	9.88	8.91	31.73	2.74
4856	5052	3.562567	GACTAGTCTGAGTCGCAACTT	57.437	47.619	15.91	0.00	36.76	2.66
5038	5238	8.699749	GTTTAACCAACTTTTTGATACTCATGC	58.300	33.333	0.00	0.00	34.24	4.06
5156	5356	4.849883	TGCATCAATTTACAAACGAACGT	58.150	34.783	0.00	0.00	0.00	3.99
5158	5358	6.747659	AACTGCATCAATTTACAAACGAAC	57.252	33.333	0.00	0.00	0.00	3.95
5335	5535	9.994432	CCAACTTTTCTATCTTTGATGACATAC	57.006	33.333	0.00	0.00	0.00	2.39
5342	5542	9.965902	ATGTACTCCAACTTTTCTATCTTTGAT	57.034	29.630	0.00	0.00	0.00	2.57
5368	5568	6.882656	TGAAACAGATGACATTTTTGGGAAA	58.117	32.000	0.00	0.00	0.00	3.13
5409	5609	7.255104	CCACTTTGTTATCTTTGACAACTAGCA	60.255	37.037	0.00	0.00	35.66	3.49
5439	5639	7.581213	ACAGATGACATTTTTGGAAAGTGTA	57.419	32.000	2.22	0.00	0.00	2.90
6322	6523	2.097825	GCCATCTGCTTCCAAATCTGT	58.902	47.619	0.00	0.00	36.87	3.41
6396	6597	4.271049	CCACCAGCGTAGTGAATATTCAAG	59.729	45.833	19.55	12.11	39.21	3.02
6411	6612	3.925630	ATCCTGCAACCCACCAGCG	62.926	63.158	0.00	0.00	0.00	5.18
6446	6647	8.078060	TCACACATATTAAAGGATGACAGAGA	57.922	34.615	3.21	0.00	0.00	3.10
6447	6648	8.722480	TTCACACATATTAAAGGATGACAGAG	57.278	34.615	3.21	0.00	0.00	3.35
6479	6682	6.435277	AGTGGCAAGATGTTCATTTGAGTAAT	59.565	34.615	0.00	0.00	0.00	1.89
6682	6887	5.105917	GGTAGGTCAATGGTAAACATGGTTG	60.106	44.000	6.16	0.00	40.44	3.77
6685	6890	4.398044	GTGGTAGGTCAATGGTAAACATGG	59.602	45.833	0.00	0.00	40.44	3.66
6755	6960	6.384015	TGAGGATATCTACAACAGGTCACAAT	59.616	38.462	2.05	0.00	0.00	2.71
7824	8030	7.484959	CACAGAAACTAAAACTCAAAACAGACC	59.515	37.037	0.00	0.00	0.00	3.85
7825	8031	8.021396	ACACAGAAACTAAAACTCAAAACAGAC	58.979	33.333	0.00	0.00	0.00	3.51
7833	8039	6.411376	TCCTGAACACAGAAACTAAAACTCA	58.589	36.000	0.00	0.00	33.94	3.41
7837	8043	8.974060	ACTATTCCTGAACACAGAAACTAAAA	57.026	30.769	0.00	0.00	33.94	1.52
7843	8049	6.931838	ACGATACTATTCCTGAACACAGAAA	58.068	36.000	0.00	0.00	33.94	2.52
7895	8101	6.817765	ACACAGAAAAAGAAACTTGTCAGA	57.182	33.333	0.00	0.00	0.00	3.27
8039	8245	0.948623	CACGAAGAACATCCGTGGCA	60.949	55.000	0.00	0.00	46.72	4.92
8078	8284	4.246458	GGCATAGAATAGGTTCATCCGAC	58.754	47.826	0.00	0.00	41.99	4.79
8079	8285	3.056821	CGGCATAGAATAGGTTCATCCGA	60.057	47.826	0.00	0.00	41.99	4.55
8202	8408	6.150140	GGGAATAATGCTCTTGTACATGATCC	59.850	42.308	11.50	12.50	0.00	3.36
8383	8604	9.632638	TCTGAGAATTATAATCCTCCCAAAAAG	57.367	33.333	9.01	0.00	0.00	2.27
8479	8704	6.434340	GGTGGATGAAACTTTTCCTATGAGTT	59.566	38.462	0.00	0.00	36.36	3.01
8714	8947	7.061566	TCCAAAGGAAAATTTTAGGTCCAAG	57.938	36.000	2.75	0.00	32.19	3.61
8884	9118	7.700505	TGATACGTGACATCTAAATCTTACGT	58.299	34.615	0.00	0.00	44.39	3.57
8923	9157	8.660373	CACAAACCTCTTCTGTGTTCTATAATC	58.340	37.037	0.00	0.00	36.52	1.75
8937	9171	4.712122	TTTGAACCACACAAACCTCTTC	57.288	40.909	0.00	0.00	33.25	2.87
8980	9214	3.451402	ACTTCCAAGGAATACAACCCC	57.549	47.619	1.35	0.00	33.28	4.95
8993	9227	5.906113	TGCTACACAAGAAAAACTTCCAA	57.094	34.783	0.00	0.00	36.61	3.53
9077	9326	2.487934	CATGAGCTCGAACCCAATAGG	58.512	52.381	9.64	0.00	43.78	2.57
9078	9327	2.487934	CCATGAGCTCGAACCCAATAG	58.512	52.381	9.64	0.00	0.00	1.73
9098	9347	5.411361	GGCATTTAAAACAGTGGAAATTCCC	59.589	40.000	9.87	0.99	35.03	3.97
9099	9348	5.994668	TGGCATTTAAAACAGTGGAAATTCC	59.005	36.000	4.79	4.79	36.96	3.01
9100	9349	7.226523	AGTTGGCATTTAAAACAGTGGAAATTC	59.773	33.333	0.00	0.00	0.00	2.17

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.