AutoCloner

Multiple sequence alignment - TraesCS3D01G280500

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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	TraesCS3D01G280500	chr3D	100.000	4695	0	0	1	4695	388515021	388519715	0.000000e+00	8671.0
1	TraesCS3D01G280500	chr3D	97.087	103	3	0	4309	4411	388519228	388519330	1.740000e-39	174.0
2	TraesCS3D01G280500	chr3D	97.087	103	3	0	4208	4310	388519329	388519431	1.740000e-39	174.0
3	TraesCS3D01G280500	chr3A	93.769	4574	187	36	135	4656	509563322	509567849	0.000000e+00	6778.0
4	TraesCS3D01G280500	chr3A	92.424	132	10	0	1	132	717901024	717901155	6.200000e-44	189.0
5	TraesCS3D01G280500	chr3A	95.146	103	5	0	4208	4310	509567502	509567604	3.760000e-36	163.0
6	TraesCS3D01G280500	chr3A	91.398	93	8	0	3833	3925	535500192	535500284	1.370000e-25	128.0
7	TraesCS3D01G280500	chr3A	90.625	96	9	0	3833	3928	587894885	587894790	1.370000e-25	128.0
8	TraesCS3D01G280500	chr3A	89.109	101	10	1	3833	3933	144639006	144638907	1.770000e-24	124.0
9	TraesCS3D01G280500	chr3B	94.120	2194	87	19	464	2633	505517949	505520124	0.000000e+00	3299.0
10	TraesCS3D01G280500	chr3B	94.313	1776	72	16	464	2220	505514189	505515954	0.000000e+00	2693.0
11	TraesCS3D01G280500	chr3B	95.881	1651	59	6	3053	4695	505520118	505521767	0.000000e+00	2663.0
12	TraesCS3D01G280500	chr3B	90.698	215	14	4	148	362	505513579	505513787	9.950000e-72	281.0
13	TraesCS3D01G280500	chr3B	90.698	215	14	4	148	362	505517331	505517539	9.950000e-72	281.0
14	TraesCS3D01G280500	chr3B	97.087	103	3	0	4309	4411	505521281	505521383	1.740000e-39	174.0
15	TraesCS3D01G280500	chr3B	95.146	103	4	1	4208	4310	505521382	505521483	1.350000e-35	161.0
16	TraesCS3D01G280500	chrUn	94.029	2194	89	19	464	2633	40531221	40529046	0.000000e+00	3288.0
17	TraesCS3D01G280500	chrUn	96.063	1651	56	6	3053	4695	40529052	40527403	0.000000e+00	2680.0
18	TraesCS3D01G280500	chrUn	92.619	420	23	7	2635	3052	85303368	85302955	8.700000e-167	597.0
19	TraesCS3D01G280500	chrUn	91.038	212	13	4	151	362	40531828	40531623	9.950000e-72	281.0
20	TraesCS3D01G280500	chrUn	91.038	212	13	4	151	362	40533738	40533533	9.950000e-72	281.0
21	TraesCS3D01G280500	chrUn	88.125	160	15	4	3924	4081	110474257	110474414	2.230000e-43	187.0
22	TraesCS3D01G280500	chrUn	96.226	106	4	0	4309	4414	40527889	40527784	1.740000e-39	174.0
23	TraesCS3D01G280500	chrUn	94.340	106	5	1	4208	4313	40527788	40527684	1.350000e-35	161.0
24	TraesCS3D01G280500	chr2D	93.349	421	25	3	2633	3052	556347385	556347803	1.860000e-173	619.0
25	TraesCS3D01G280500	chr2D	91.538	130	11	0	1	130	562351590	562351461	3.730000e-41	180.0
26	TraesCS3D01G280500	chr4D	92.637	421	28	3	2633	3052	468904565	468904147	1.870000e-168	603.0
27	TraesCS3D01G280500	chr4D	92.593	135	8	1	1	133	451681205	451681339	4.790000e-45	193.0
28	TraesCS3D01G280500	chr1D	92.619	420	27	4	2634	3052	317595928	317596344	6.720000e-168	601.0
29	TraesCS3D01G280500	chr5D	92.037	427	28	5	2633	3056	410251871	410252294	3.130000e-166	595.0
30	TraesCS3D01G280500	chr5D	91.791	134	9	1	1	132	424820206	424820339	8.020000e-43	185.0
31	TraesCS3D01G280500	chr5B	92.000	425	29	5	2633	3053	596701679	596701256	4.050000e-165	592.0
32	TraesCS3D01G280500	chr5B	83.673	196	26	6	3926	4117	6625950	6626143	3.730000e-41	180.0
33	TraesCS3D01G280500	chr5B	82.659	173	24	6	3924	4092	31143683	31143853	1.050000e-31	148.0
34	TraesCS3D01G280500	chr6D	92.344	418	27	5	2635	3049	85793613	85794028	1.460000e-164	590.0
35	TraesCS3D01G280500	chr6D	92.188	128	10	0	6	133	86614072	86613945	1.040000e-41	182.0
36	TraesCS3D01G280500	chr6D	87.156	109	11	3	3824	3931	251235029	251235135	2.290000e-23	121.0
37	TraesCS3D01G280500	chr1A	91.142	429	32	6	2630	3054	33217090	33216664	1.130000e-160	577.0
38	TraesCS3D01G280500	chr7D	91.791	134	11	0	1	134	54991772	54991905	2.230000e-43	187.0
39	TraesCS3D01G280500	chr7D	92.188	128	10	0	6	133	599718276	599718149	1.040000e-41	182.0
40	TraesCS3D01G280500	chr6A	92.308	130	10	0	1	130	26569474	26569345	8.020000e-43	185.0
41	TraesCS3D01G280500	chr5A	83.000	200	29	5	3924	4120	3614989	3614792	4.830000e-40	176.0
42	TraesCS3D01G280500	chr5A	83.168	202	23	11	3926	4120	3516273	3516470	1.740000e-39	174.0
43	TraesCS3D01G280500	chr5A	86.667	135	10	5	3922	4053	700175650	700175521	4.900000e-30	143.0
44	TraesCS3D01G280500	chr7A	90.152	132	13	0	1	132	65033601	65033732	6.250000e-39	172.0
45	TraesCS3D01G280500	chr2A	88.889	99	11	0	3833	3931	302053492	302053394	6.380000e-24	122.0
46	TraesCS3D01G280500	chr2B	86.486	111	11	4	3824	3932	556697784	556697676	8.250000e-23	119.0
47	TraesCS3D01G280500	chr6B	91.379	58	3	2	4311	4367	704897420	704897364	1.400000e-10	78.7
48	TraesCS3D01G280500	chr4A	89.831	59	6	0	4309	4367	93563459	93563401	5.040000e-10	76.8

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	TraesCS3D01G280500	chr3D	388515021	388519715	4694	False	3006.333333	8671	98.058000	1	4695	3	chr3D.!!$F1	4694
1	TraesCS3D01G280500	chr3A	509563322	509567849	4527	False	3470.500000	6778	94.457500	135	4656	2	chr3A.!!$F3	4521
2	TraesCS3D01G280500	chr3B	505513579	505521767	8188	False	1364.571429	3299	93.991857	148	4695	7	chr3B.!!$F1	4547
3	TraesCS3D01G280500	chrUn	40527403	40533738	6335	True	1144.166667	3288	93.789000	151	4695	6	chrUn.!!$R2	4544

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	Hairpin	End Stability	Orientation
129	130	0.035630	GTGGCTGTTGGAGATGCTCT	60.036	55.000	0.00	4.09	F
130	131	0.694771	TGGCTGTTGGAGATGCTCTT	59.305	50.000	0.00	2.85	F
1109	3351	1.271271	CCCAGCTCTTCTGCTTCTGTT	60.271	52.381	41.98	3.16	F
2140	8154	2.875672	GCTTTACCTGAGTGCATGTCCA	60.876	50.000	0.00	4.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
1259	3502	0.374758	CCGTCATGTTTGCAGGATCG	59.625	55.000	37.75	3.69	R
1820	7834	2.683211	ACCCTGCAACCTCAAAGATT	57.317	45.000	0.00	2.40	R
2791	8810	1.202359	GCACAACCCACATTTCAACGT	60.202	47.619	0.00	3.99	R
3768	9796	1.674764	TTGGTGGTTGCTTGCAGTGG	61.675	55.000	0.00	4.00	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	3.878384	CGCGCGCGCTCAATTTTG	61.878	61.111	45.97	27.76	39.32	2.44
23	24	2.501650	GCGCGCGCTCAATTTTGA	60.502	55.556	44.38	0.00	38.26	2.69
24	25	2.767919	GCGCGCGCTCAATTTTGAC	61.768	57.895	44.38	13.88	38.26	3.18
25	26	2.479782	CGCGCGCTCAATTTTGACG	61.480	57.895	30.48	4.48	35.96	4.35
26	27	2.767919	GCGCGCTCAATTTTGACGC	61.768	57.895	26.67	20.29	45.32	5.19
27	28	4.531708	GCGCTCAATTTTGACGCA	57.468	50.000	22.94	0.00	46.58	5.24
28	29	3.020102	GCGCTCAATTTTGACGCAT	57.980	47.368	22.94	0.00	46.58	4.73
29	30	0.909843	GCGCTCAATTTTGACGCATC	59.090	50.000	22.94	9.67	46.58	3.91
30	31	1.538276	CGCTCAATTTTGACGCATCC	58.462	50.000	12.14	0.00	33.74	3.51
31	32	1.538276	GCTCAATTTTGACGCATCCG	58.462	50.000	8.76	0.00	41.14	4.18
41	42	3.499737	CGCATCCGTTGGAGCCAC	61.500	66.667	0.00	0.00	34.05	5.01
42	43	3.134127	GCATCCGTTGGAGCCACC	61.134	66.667	0.00	0.00	34.05	4.61
43	44	2.819595	CATCCGTTGGAGCCACCG	60.820	66.667	0.00	0.00	42.61	4.94
44	45	4.778143	ATCCGTTGGAGCCACCGC	62.778	66.667	0.51	0.00	42.61	5.68
66	67	3.723348	GGCCGCGTCAAACCAGAC	61.723	66.667	4.92	0.00	35.19	3.51
73	74	1.568025	GTCAAACCAGACGAACGGC	59.432	57.895	0.00	0.00	0.00	5.68
75	76	3.343421	AAACCAGACGAACGGCGC	61.343	61.111	6.90	0.00	46.04	6.53
118	119	4.250431	GTGCGTTGCGTGGCTGTT	62.250	61.111	0.00	0.00	0.00	3.16
119	120	4.249020	TGCGTTGCGTGGCTGTTG	62.249	61.111	0.00	0.00	0.00	3.33
120	121	4.980903	GCGTTGCGTGGCTGTTGG	62.981	66.667	0.00	0.00	0.00	3.77
121	122	3.276091	CGTTGCGTGGCTGTTGGA	61.276	61.111	0.00	0.00	0.00	3.53
122	123	2.639286	GTTGCGTGGCTGTTGGAG	59.361	61.111	0.00	0.00	0.00	3.86
123	124	1.891919	GTTGCGTGGCTGTTGGAGA	60.892	57.895	0.00	0.00	0.00	3.71
124	125	1.073025	TTGCGTGGCTGTTGGAGAT	59.927	52.632	0.00	0.00	0.00	2.75
125	126	1.236616	TTGCGTGGCTGTTGGAGATG	61.237	55.000	0.00	0.00	0.00	2.90
126	127	3.044059	GCGTGGCTGTTGGAGATGC	62.044	63.158	0.00	0.00	0.00	3.91
127	128	1.376424	CGTGGCTGTTGGAGATGCT	60.376	57.895	0.00	0.00	0.00	3.79
128	129	1.364626	CGTGGCTGTTGGAGATGCTC	61.365	60.000	0.00	0.00	0.00	4.26
129	130	0.035630	GTGGCTGTTGGAGATGCTCT	60.036	55.000	0.00	0.00	0.00	4.09
130	131	0.694771	TGGCTGTTGGAGATGCTCTT	59.305	50.000	0.00	0.00	0.00	2.85
131	132	1.908619	TGGCTGTTGGAGATGCTCTTA	59.091	47.619	0.00	0.00	0.00	2.10
132	133	2.093288	TGGCTGTTGGAGATGCTCTTAG	60.093	50.000	0.00	0.00	0.00	2.18
133	134	1.939255	GCTGTTGGAGATGCTCTTAGC	59.061	52.381	0.00	0.00	42.82	3.09
136	137	4.260170	CTGTTGGAGATGCTCTTAGCTTT	58.740	43.478	0.00	0.00	42.97	3.51
144	145	6.434018	AGATGCTCTTAGCTTTGACATTTC	57.566	37.500	0.00	0.00	42.97	2.17
168	169	4.523173	GTCCAGAACCGGAGTATCATGATA	59.477	45.833	9.46	11.49	35.10	2.15
173	174	5.420421	AGAACCGGAGTATCATGATATGAGG	59.580	44.000	18.18	18.82	43.53	3.86
202	203	2.286772	GGCGCGTCTAAAAATACCATGG	60.287	50.000	11.19	11.19	0.00	3.66
289	290	3.485711	CGTCCAATTCACATCAATCCACG	60.486	47.826	0.00	0.00	0.00	4.94
295	296	2.179427	TCACATCAATCCACGTCTCCT	58.821	47.619	0.00	0.00	0.00	3.69
305	306	3.709587	TCCACGTCTCCTCTAGGAAAAT	58.290	45.455	0.00	0.00	44.91	1.82
306	307	4.863548	TCCACGTCTCCTCTAGGAAAATA	58.136	43.478	0.00	0.00	44.91	1.40
322	323	7.989416	AGGAAAATAAAAACTATCCACGTCA	57.011	32.000	0.00	0.00	0.00	4.35
325	326	7.094506	GGAAAATAAAAACTATCCACGTCACCT	60.095	37.037	0.00	0.00	0.00	4.00
535	2746	2.833227	CCCCCAGGACGAAACACA	59.167	61.111	0.00	0.00	33.47	3.72
682	2914	4.005650	TCACGTACTGTAGATTCCGAGTT	58.994	43.478	0.00	0.00	0.00	3.01
725	2964	7.726291	TCATGGAAACCAATCTGTAACCTTTAA	59.274	33.333	0.00	0.00	36.95	1.52
746	2985	3.490439	ACAGTCATGACCATTCACACA	57.510	42.857	22.21	0.00	33.38	3.72
762	3001	2.406024	CACACAAAGAATGCGTGCAATC	59.594	45.455	0.00	0.00	35.48	2.67
1066	3308	2.871427	GCCGGTCATCGACAATCGC	61.871	63.158	1.90	0.00	40.21	4.58
1109	3351	1.271271	CCCAGCTCTTCTGCTTCTGTT	60.271	52.381	0.00	0.00	41.98	3.16
1171	3413	2.930040	GCTGCAGCTAACGAGATTTGTA	59.070	45.455	31.33	0.00	38.21	2.41
1233	3476	6.652900	TGCATGCTGTTACTGTTATCTTTGTA	59.347	34.615	20.33	0.00	0.00	2.41
1259	3502	4.505217	CATGCCGTCGCGCACTTC	62.505	66.667	8.75	0.37	42.70	3.01
1382	3625	5.868801	TGCTTATTCAACAAATTAGGCAAGC	59.131	36.000	0.00	0.00	35.72	4.01
1385	3628	5.990120	ATTCAACAAATTAGGCAAGCTCT	57.010	34.783	0.00	0.00	0.00	4.09
1389	3632	7.283625	TCAACAAATTAGGCAAGCTCTTTAA	57.716	32.000	0.00	0.00	0.00	1.52
1435	3685	6.947464	AGGCAAGCTTATTACTTCAGTAGAA	58.053	36.000	0.00	0.00	0.00	2.10
1577	3827	8.836268	TGTTCACAACTTCTTTATATTACCGT	57.164	30.769	0.00	0.00	0.00	4.83
1578	3828	9.926158	TGTTCACAACTTCTTTATATTACCGTA	57.074	29.630	0.00	0.00	0.00	4.02
1647	3900	8.153479	TGCCACAATATCAGTCAATATGTTAC	57.847	34.615	0.00	0.00	0.00	2.50
1738	7751	5.355350	CCATTTTCTGATAGCTTTCGGAGTT	59.645	40.000	14.30	3.11	32.74	3.01
1740	7753	4.537135	TTCTGATAGCTTTCGGAGTTGT	57.463	40.909	14.30	0.00	32.74	3.32
2140	8154	2.875672	GCTTTACCTGAGTGCATGTCCA	60.876	50.000	0.00	0.00	0.00	4.02
2221	8236	4.159120	GCAGTAACTCGAATTTCTTTGGC	58.841	43.478	0.00	0.00	0.00	4.52
2338	8357	6.933514	ACCATCTGTCAACCCAAAAATAAT	57.066	33.333	0.00	0.00	0.00	1.28
2637	8656	9.687210	CATGCATAGTAGTATAAGTAACGGAAA	57.313	33.333	0.00	0.00	0.00	3.13
2787	8806	4.582701	TGTGTGTAAAATTTCAGGGCAG	57.417	40.909	0.00	0.00	0.00	4.85
2791	8810	4.646945	TGTGTAAAATTTCAGGGCAGAACA	59.353	37.500	0.00	0.00	0.00	3.18
2793	8812	3.369546	AAAATTTCAGGGCAGAACACG	57.630	42.857	0.00	0.00	0.00	4.49
2802	8821	1.336755	GGGCAGAACACGTTGAAATGT	59.663	47.619	0.00	0.00	0.00	2.71
2814	8833	3.265791	GTTGAAATGTGGGTTGTGCAAA	58.734	40.909	0.00	0.00	0.00	3.68
2815	8834	3.616956	TGAAATGTGGGTTGTGCAAAA	57.383	38.095	0.00	0.00	0.00	2.44
2816	8835	3.942829	TGAAATGTGGGTTGTGCAAAAA	58.057	36.364	0.00	0.00	0.00	1.94
2863	8882	7.039152	ACACATGATACTATTCATCCTCTCAGG	60.039	40.741	0.00	0.00	34.09	3.86
2902	8921	2.839975	TGTACAGGTCGCATTTCAACA	58.160	42.857	0.00	0.00	0.00	3.33
2954	8973	5.876460	GTGGGTTACATCCTTAAATACACGT	59.124	40.000	0.00	0.00	0.00	4.49
3028	9047	2.371658	AATAAAGGCCTCCATGGAGC	57.628	50.000	32.97	26.44	40.69	4.70
3068	9090	6.231211	CCATTCTCAAGTAACACCTACTGTT	58.769	40.000	0.00	0.00	45.57	3.16
3391	9418	8.611654	TCATGGTAAGTTTTTAGTCTACCAAC	57.388	34.615	3.55	0.00	39.23	3.77
3518	9545	3.389329	AGACTCTTTGAAGTTGCCTGAGA	59.611	43.478	0.00	0.00	0.00	3.27
3768	9796	1.377725	CCACACCAGGAGTCCATGC	60.378	63.158	12.86	0.00	0.00	4.06
3786	9814	2.126596	CCACTGCAAGCAACCACCA	61.127	57.895	0.00	0.00	37.60	4.17
3799	9827	4.987912	AGCAACCACCAAATTTGAAATACG	59.012	37.500	19.86	4.15	0.00	3.06
3822	9850	8.839310	ACGTATTGTATCTCTAGTTACCGTAT	57.161	34.615	0.00	0.00	0.00	3.06
3856	9885	6.183347	CCCTCCATCTCAAAATAAGTGTCTT	58.817	40.000	0.00	0.00	0.00	3.01
3940	9969	7.783596	TGGAGGGAGTATTAGTTTAGAGTAAGG	59.216	40.741	0.00	0.00	0.00	2.69
4188	10220	8.908903	TCACCACAACTACTGTTTGAAATATTT	58.091	29.630	0.00	0.00	35.47	1.40
4549	10581	3.393687	AGAGTGGGGGCTAATATTCACA	58.606	45.455	0.00	0.00	0.00	3.58
4594	10626	9.774742	GAATTTCTACACAAGGACAATGTTATC	57.225	33.333	0.00	0.00	0.00	1.75
4595	10627	6.961359	TTCTACACAAGGACAATGTTATCG	57.039	37.500	0.00	0.00	0.00	2.92
4637	10669	7.929941	GTCATTTACCAAGAAGGAGAAGAAT	57.070	36.000	0.00	0.00	41.22	2.40
4643	10675	6.899892	ACCAAGAAGGAGAAGAATAGGAAT	57.100	37.500	0.00	0.00	41.22	3.01
4673	10705	8.042515	TCTTGATGTGATATGTGATGAACTTGA	58.957	33.333	0.00	0.00	0.00	3.02
4675	10707	8.149973	TGATGTGATATGTGATGAACTTGATG	57.850	34.615	0.00	0.00	0.00	3.07

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
6	7	2.501650	TCAAAATTGAGCGCGCGC	60.502	55.556	45.10	45.10	42.33	6.86
7	8	2.479782	CGTCAAAATTGAGCGCGCG	61.480	57.895	28.44	28.44	37.98	6.86
8	9	2.767919	GCGTCAAAATTGAGCGCGC	61.768	57.895	26.66	26.66	42.68	6.86
9	10	3.352536	GCGTCAAAATTGAGCGCG	58.647	55.556	19.31	0.00	42.68	6.86
11	12	1.538276	GGATGCGTCAAAATTGAGCG	58.462	50.000	8.47	5.20	37.98	5.03
12	13	1.135689	ACGGATGCGTCAAAATTGAGC	60.136	47.619	6.39	3.84	37.98	4.26
13	14	2.900122	ACGGATGCGTCAAAATTGAG	57.100	45.000	6.39	0.00	37.98	3.02
14	15	2.351253	CCAACGGATGCGTCAAAATTGA	60.351	45.455	14.18	0.00	34.20	2.57
15	16	1.984990	CCAACGGATGCGTCAAAATTG	59.015	47.619	14.18	6.29	0.00	2.32
16	17	1.883275	TCCAACGGATGCGTCAAAATT	59.117	42.857	14.18	0.00	0.00	1.82
17	18	1.468520	CTCCAACGGATGCGTCAAAAT	59.531	47.619	14.18	0.00	0.00	1.82
18	19	0.871722	CTCCAACGGATGCGTCAAAA	59.128	50.000	14.18	0.00	0.00	2.44
19	20	1.573829	GCTCCAACGGATGCGTCAAA	61.574	55.000	14.18	0.00	0.00	2.69
20	21	2.032634	GCTCCAACGGATGCGTCAA	61.033	57.895	14.18	0.33	0.00	3.18
21	22	2.434185	GCTCCAACGGATGCGTCA	60.434	61.111	14.18	0.00	0.00	4.35
22	23	3.195698	GGCTCCAACGGATGCGTC	61.196	66.667	14.18	0.00	30.49	5.19
23	24	4.015406	TGGCTCCAACGGATGCGT	62.015	61.111	6.39	6.39	30.49	5.24
24	25	3.499737	GTGGCTCCAACGGATGCG	61.500	66.667	4.58	4.58	30.49	4.73
25	26	3.134127	GGTGGCTCCAACGGATGC	61.134	66.667	0.00	0.00	35.97	3.91
49	50	3.723348	GTCTGGTTTGACGCGGCC	61.723	66.667	10.82	0.56	0.00	6.13
55	56	1.568025	GCCGTTCGTCTGGTTTGAC	59.432	57.895	0.00	0.00	0.00	3.18
56	57	1.952133	CGCCGTTCGTCTGGTTTGA	60.952	57.895	0.00	0.00	0.00	2.69
57	58	2.549282	CGCCGTTCGTCTGGTTTG	59.451	61.111	0.00	0.00	0.00	2.93
58	59	3.343421	GCGCCGTTCGTCTGGTTT	61.343	61.111	0.00	0.00	41.07	3.27
101	102	4.250431	AACAGCCACGCAACGCAC	62.250	61.111	0.00	0.00	0.00	5.34
102	103	4.249020	CAACAGCCACGCAACGCA	62.249	61.111	0.00	0.00	0.00	5.24
103	104	4.980903	CCAACAGCCACGCAACGC	62.981	66.667	0.00	0.00	0.00	4.84
104	105	3.240606	CTCCAACAGCCACGCAACG	62.241	63.158	0.00	0.00	0.00	4.10
105	106	1.237285	ATCTCCAACAGCCACGCAAC	61.237	55.000	0.00	0.00	0.00	4.17
106	107	1.073025	ATCTCCAACAGCCACGCAA	59.927	52.632	0.00	0.00	0.00	4.85
107	108	1.672030	CATCTCCAACAGCCACGCA	60.672	57.895	0.00	0.00	0.00	5.24
108	109	3.044059	GCATCTCCAACAGCCACGC	62.044	63.158	0.00	0.00	0.00	5.34
109	110	1.364626	GAGCATCTCCAACAGCCACG	61.365	60.000	0.00	0.00	0.00	4.94
110	111	2.475666	GAGCATCTCCAACAGCCAC	58.524	57.895	0.00	0.00	0.00	5.01
122	123	5.163814	ACGAAATGTCAAAGCTAAGAGCATC	60.164	40.000	0.64	0.00	45.56	3.91
123	124	4.697352	ACGAAATGTCAAAGCTAAGAGCAT	59.303	37.500	0.64	0.00	45.56	3.79
124	125	4.065088	ACGAAATGTCAAAGCTAAGAGCA	58.935	39.130	0.64	0.00	45.56	4.26
125	126	4.670227	ACGAAATGTCAAAGCTAAGAGC	57.330	40.909	0.00	0.00	42.84	4.09
144	145	1.100510	TGATACTCCGGTTCTGGACG	58.899	55.000	0.00	0.00	33.48	4.79
187	188	6.657541	GTGTCCAAGACCATGGTATTTTTAGA	59.342	38.462	22.03	13.22	41.46	2.10
202	203	3.612479	GCAATTCCACATGTGTCCAAGAC	60.612	47.826	23.79	4.81	0.00	3.01
295	296	9.374838	GACGTGGATAGTTTTTATTTTCCTAGA	57.625	33.333	0.00	0.00	0.00	2.43
305	306	6.158598	GTGTAGGTGACGTGGATAGTTTTTA	58.841	40.000	0.00	0.00	0.00	1.52
306	307	4.992951	GTGTAGGTGACGTGGATAGTTTTT	59.007	41.667	0.00	0.00	0.00	1.94
535	2746	1.488705	TTGACCCTGAGCCCATCGTT	61.489	55.000	0.00	0.00	0.00	3.85
657	2889	4.005650	TCGGAATCTACAGTACGTGAACT	58.994	43.478	0.00	0.00	0.00	3.01
658	2890	4.142730	ACTCGGAATCTACAGTACGTGAAC	60.143	45.833	0.00	0.00	0.00	3.18
659	2891	4.005650	ACTCGGAATCTACAGTACGTGAA	58.994	43.478	0.00	0.00	0.00	3.18
664	2896	4.491676	TGCAAACTCGGAATCTACAGTAC	58.508	43.478	0.00	0.00	0.00	2.73
725	2964	3.819368	TGTGTGAATGGTCATGACTGTT	58.181	40.909	24.50	18.42	35.80	3.16
746	2985	4.697352	ACTTCTAGATTGCACGCATTCTTT	59.303	37.500	18.45	2.36	37.66	2.52
762	3001	4.554723	CGAGGGTGCAAACAAAACTTCTAG	60.555	45.833	0.00	0.00	0.00	2.43
797	3038	2.610859	AATGTGGGCCTCGGACCT	60.611	61.111	9.71	0.00	45.59	3.85
800	3041	2.196997	CTTGGAATGTGGGCCTCGGA	62.197	60.000	4.53	0.00	0.00	4.55
904	3145	2.475487	GACACTCCGGAAGAAAACGAAG	59.525	50.000	5.23	0.00	0.00	3.79
1066	3308	2.793160	TTCAGAGAAGCCGCTGCCAG	62.793	60.000	0.00	0.00	39.61	4.85
1109	3351	5.858381	ACTTACAGTTCAAGCTGAAGATCA	58.142	37.500	0.56	0.00	37.00	2.92
1171	3413	7.575414	AGTTCTCATGATAACTCTGTACGAT	57.425	36.000	18.08	0.00	30.08	3.73
1259	3502	0.374758	CCGTCATGTTTGCAGGATCG	59.625	55.000	0.00	0.00	37.75	3.69
1401	3650	5.757850	AATAAGCTTGCCTAATTTCCTCG	57.242	39.130	9.86	0.00	0.00	4.63
1454	3704	6.590292	AGCTTCAGATGCATCATTTGAAAAAG	59.410	34.615	27.81	16.68	41.88	2.27
1551	3801	9.444600	ACGGTAATATAAAGAAGTTGTGAACAT	57.555	29.630	0.00	0.00	0.00	2.71
1612	3865	7.652909	TGACTGATATTGTGGCAAAAGAAAAAG	59.347	33.333	0.00	0.00	0.00	2.27
1647	3900	5.518487	ACTTTTGAACATTGGCAAAGTTACG	59.482	36.000	19.49	6.25	35.64	3.18
1738	7751	9.278978	TGTAGACAAGCTTTATCATTTGTTACA	57.721	29.630	0.00	0.00	34.18	2.41
1820	7834	2.683211	ACCCTGCAACCTCAAAGATT	57.317	45.000	0.00	0.00	0.00	2.40
2140	8154	9.331282	GTGGCTGATTTTACTAGATATGAAACT	57.669	33.333	0.00	0.00	0.00	2.66
2221	8236	9.774742	GTTAAACTCCATACAGATTAGCAAAAG	57.225	33.333	0.00	0.00	0.00	2.27
2338	8357	1.960040	AATGCGAGCGGTCCATCTCA	61.960	55.000	15.69	5.25	0.00	3.27
2376	8395	4.858680	GGCAGCTAGGGTTCCGCC	62.859	72.222	0.00	0.00	0.00	6.13
2629	8648	3.004944	GTCACCAAAGGCAATTTCCGTTA	59.995	43.478	0.00	0.00	0.00	3.18
2637	8656	1.244019	GCTCGGTCACCAAAGGCAAT	61.244	55.000	0.00	0.00	0.00	3.56
2776	8795	1.608590	CAACGTGTTCTGCCCTGAAAT	59.391	47.619	0.00	0.00	0.00	2.17
2787	8806	3.112580	CAACCCACATTTCAACGTGTTC	58.887	45.455	0.00	0.00	0.00	3.18
2791	8810	1.202359	GCACAACCCACATTTCAACGT	60.202	47.619	0.00	0.00	0.00	3.99
2793	8812	2.593346	TGCACAACCCACATTTCAAC	57.407	45.000	0.00	0.00	0.00	3.18
2814	8833	9.187455	GTGTTAAACATCCACGATTTGTATTTT	57.813	29.630	0.00	0.00	0.00	1.82
2815	8834	8.353684	TGTGTTAAACATCCACGATTTGTATTT	58.646	29.630	0.00	0.00	32.36	1.40
2816	8835	7.877003	TGTGTTAAACATCCACGATTTGTATT	58.123	30.769	0.00	0.00	32.36	1.89
2817	8836	7.441890	TGTGTTAAACATCCACGATTTGTAT	57.558	32.000	0.00	0.00	32.36	2.29
2818	8837	6.862711	TGTGTTAAACATCCACGATTTGTA	57.137	33.333	0.00	0.00	32.36	2.41
2819	8838	5.759506	TGTGTTAAACATCCACGATTTGT	57.240	34.783	0.00	0.00	32.36	2.83
2835	8854	9.367160	TGAGAGGATGAATAGTATCATGTGTTA	57.633	33.333	0.00	0.00	40.08	2.41
2859	8878	5.549742	AAAAAGACAAATTCATGGCCTGA	57.450	34.783	3.32	2.06	0.00	3.86
2999	9018	7.394077	CCATGGAGGCCTTTATTTTTCAAAAAT	59.606	33.333	6.77	12.69	0.00	1.82
3391	9418	5.686841	TCGAGAATGCAATTTTCACAAACAG	59.313	36.000	0.00	0.00	37.29	3.16
3455	9482	9.059023	ACCCTTTACTGAATTCCTAGTTATTCT	57.941	33.333	2.27	0.93	33.08	2.40
3518	9545	9.553064	CCTGCAGAATATAAGAGAAAATGTAGT	57.447	33.333	17.39	0.00	0.00	2.73
3768	9796	1.674764	TTGGTGGTTGCTTGCAGTGG	61.675	55.000	0.00	0.00	0.00	4.00
3776	9804	4.987912	CGTATTTCAAATTTGGTGGTTGCT	59.012	37.500	17.90	0.00	0.00	3.91
3940	9969	4.014406	ACGAACCTTTCCATATCCAAACC	58.986	43.478	0.00	0.00	0.00	3.27
4082	10114	4.587684	AGAGAGAAGACACGGTAGGAAAAA	59.412	41.667	0.00	0.00	0.00	1.94
4188	10220	9.657419	ATTATCATCACAATATCGCATGTAAGA	57.343	29.630	0.00	0.00	0.00	2.10
4549	10581	1.630369	TCAAGCCTATCACTTGCCAGT	59.370	47.619	0.00	0.00	43.40	4.00
4594	10626	3.323691	TGACCTTCCATCATGTATACCCG	59.676	47.826	0.00	0.00	0.00	5.28
4595	10627	4.974645	TGACCTTCCATCATGTATACCC	57.025	45.455	0.00	0.00	0.00	3.69
4643	10675	7.128234	TCATCACATATCACATCAAGAAGGA	57.872	36.000	0.00	0.00	0.00	3.36
4673	10705	1.275002	ACCCCCTCTCCCACATTACAT	60.275	52.381	0.00	0.00	0.00	2.29
4675	10707	0.546598	CACCCCCTCTCCCACATTAC	59.453	60.000	0.00	0.00	0.00	1.89

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.