AutoCloner

Multiple sequence alignment - TraesCS2D01G181000

Loading Multiple Alignment...

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	TraesCS2D01G181000	chr2D	100.000	3020	0	0	1	3020	125342739	125345758	0.000000e+00	5578
1	TraesCS2D01G181000	chr2D	77.946	331	52	18	1201	1522	37245409	37245727	1.430000e-43	187
2	TraesCS2D01G181000	chr2D	78.495	279	55	4	1202	1476	537415371	537415094	8.600000e-41	178
3	TraesCS2D01G181000	chr2B	91.234	1791	101	32	259	2041	178730207	178731949	0.000000e+00	2386
4	TraesCS2D01G181000	chr2B	82.463	536	77	9	2256	2779	583107736	583108266	1.280000e-123	453
5	TraesCS2D01G181000	chr2B	74.688	881	184	30	1143	2008	759176396	759175540	3.700000e-94	355
6	TraesCS2D01G181000	chr2B	78.443	334	48	16	1201	1522	64864084	64863763	2.380000e-46	196
7	TraesCS2D01G181000	chr2A	94.461	1372	46	13	879	2245	131711114	131712460	0.000000e+00	2085
8	TraesCS2D01G181000	chr2A	86.621	882	73	22	1	872	131710157	131711003	0.000000e+00	933
9	TraesCS2D01G181000	chr2A	74.651	860	171	37	1154	1994	24002389	24003220	1.340000e-88	337
10	TraesCS2D01G181000	chr2A	80.147	272	49	4	1202	1469	679971755	679971485	6.600000e-47	198
11	TraesCS2D01G181000	chr2A	80.000	275	42	10	1201	1467	42027458	42027189	1.110000e-44	191
12	TraesCS2D01G181000	chr7B	93.548	558	24	7	2249	2795	363232387	363231831	0.000000e+00	821
13	TraesCS2D01G181000	chr7B	96.930	228	5	1	2793	3020	363231791	363231566	6.110000e-102	381
14	TraesCS2D01G181000	chr3D	93.548	558	24	7	2249	2795	570537914	570538470	0.000000e+00	821
15	TraesCS2D01G181000	chr3D	92.832	558	28	7	2249	2795	478426966	478426410	0.000000e+00	798
16	TraesCS2D01G181000	chr3D	83.240	537	74	11	2256	2779	584682168	584682701	2.110000e-131	479
17	TraesCS2D01G181000	chr3D	96.053	228	7	1	2793	3020	570538510	570538735	1.320000e-98	370
18	TraesCS2D01G181000	chr3D	94.737	228	10	1	2793	3020	478426370	478426145	1.330000e-93	353
19	TraesCS2D01G181000	chr5D	91.039	558	38	7	2249	2795	564237163	564237719	0.000000e+00	743
20	TraesCS2D01G181000	chr5D	97.368	228	4	1	2793	3020	564237759	564237984	1.310000e-103	387
21	TraesCS2D01G181000	chr5D	96.491	228	6	1	2793	3020	399974425	399974200	2.840000e-100	375
22	TraesCS2D01G181000	chr4D	82.276	536	78	11	2256	2779	297375959	297376489	5.940000e-122	448
23	TraesCS2D01G181000	chr4D	91.228	228	18	1	2793	3020	297376545	297376770	2.920000e-80	309
24	TraesCS2D01G181000	chr7A	81.495	535	85	10	2256	2779	380509187	380509718	7.740000e-116	427
25	TraesCS2D01G181000	chr7A	95.575	226	8	1	2793	3018	640368279	640368502	7.960000e-96	361
26	TraesCS2D01G181000	chr7A	75.121	824	161	32	1194	2000	46911007	46911803	2.230000e-91	346
27	TraesCS2D01G181000	chr7A	78.022	273	53	6	1197	1464	1273390	1273660	6.700000e-37	165
28	TraesCS2D01G181000	chr7A	74.142	379	87	9	1634	2008	163915913	163916284	2.430000e-31	147
29	TraesCS2D01G181000	chr6A	83.298	467	68	8	2338	2795	23218235	23217770	3.600000e-114	422
30	TraesCS2D01G181000	chr1B	75.930	860	178	24	1154	1994	664611470	664610621	6.020000e-112	414
31	TraesCS2D01G181000	chr1A	79.852	541	93	7	2259	2788	27317991	27317456	6.110000e-102	381
32	TraesCS2D01G181000	chr1A	77.152	639	122	20	1204	1833	11530446	11531069	1.720000e-92	350
33	TraesCS2D01G181000	chr7D	74.858	879	180	29	1143	2008	163010620	163011470	7.960000e-96	361
34	TraesCS2D01G181000	chr3B	94.737	228	10	1	2793	3020	664535273	664535498	1.330000e-93	353
35	TraesCS2D01G181000	chr6B	92.237	219	15	1	2802	3020	705859121	705858905	2.920000e-80	309

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	TraesCS2D01G181000	chr2D	125342739	125345758	3019	False	5578.0	5578	100.0000	1	3020	1	chr2D.!!$F2	3019
1	TraesCS2D01G181000	chr2B	178730207	178731949	1742	False	2386.0	2386	91.2340	259	2041	1	chr2B.!!$F1	1782
2	TraesCS2D01G181000	chr2B	583107736	583108266	530	False	453.0	453	82.4630	2256	2779	1	chr2B.!!$F2	523
3	TraesCS2D01G181000	chr2B	759175540	759176396	856	True	355.0	355	74.6880	1143	2008	1	chr2B.!!$R2	865
4	TraesCS2D01G181000	chr2A	131710157	131712460	2303	False	1509.0	2085	90.5410	1	2245	2	chr2A.!!$F2	2244
5	TraesCS2D01G181000	chr2A	24002389	24003220	831	False	337.0	337	74.6510	1154	1994	1	chr2A.!!$F1	840
6	TraesCS2D01G181000	chr7B	363231566	363232387	821	True	601.0	821	95.2390	2249	3020	2	chr7B.!!$R1	771
7	TraesCS2D01G181000	chr3D	570537914	570538735	821	False	595.5	821	94.8005	2249	3020	2	chr3D.!!$F2	771
8	TraesCS2D01G181000	chr3D	478426145	478426966	821	True	575.5	798	93.7845	2249	3020	2	chr3D.!!$R1	771
9	TraesCS2D01G181000	chr3D	584682168	584682701	533	False	479.0	479	83.2400	2256	2779	1	chr3D.!!$F1	523
10	TraesCS2D01G181000	chr5D	564237163	564237984	821	False	565.0	743	94.2035	2249	3020	2	chr5D.!!$F1	771
11	TraesCS2D01G181000	chr4D	297375959	297376770	811	False	378.5	448	86.7520	2256	3020	2	chr4D.!!$F1	764
12	TraesCS2D01G181000	chr7A	380509187	380509718	531	False	427.0	427	81.4950	2256	2779	1	chr7A.!!$F4	523
13	TraesCS2D01G181000	chr7A	46911007	46911803	796	False	346.0	346	75.1210	1194	2000	1	chr7A.!!$F2	806
14	TraesCS2D01G181000	chr1B	664610621	664611470	849	True	414.0	414	75.9300	1154	1994	1	chr1B.!!$R1	840
15	TraesCS2D01G181000	chr1A	27317456	27317991	535	True	381.0	381	79.8520	2259	2788	1	chr1A.!!$R1	529
16	TraesCS2D01G181000	chr1A	11530446	11531069	623	False	350.0	350	77.1520	1204	1833	1	chr1A.!!$F1	629
17	TraesCS2D01G181000	chr7D	163010620	163011470	850	False	361.0	361	74.8580	1143	2008	1	chr7D.!!$F1	865

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
88	89	0.240945	CTCCGAAACTTGGCGCAATT	59.759	50.0	10.83	0.0	0.0	2.32	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2022	2179	0.321475	TCACGCATGCAGATTGTCCA	60.321	50.0	19.57	0.0	0.0	4.02	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
46	47	4.088634	TGCAAAGATAGATGTTGGGCTTT	58.911	39.130	0.00	0.00	0.00	3.51
58	59	4.922206	TGTTGGGCTTTATTCTGATGAGT	58.078	39.130	0.00	0.00	0.00	3.41
63	64	5.189180	GGGCTTTATTCTGATGAGTGTCTT	58.811	41.667	0.00	0.00	0.00	3.01
72	73	2.229062	TGATGAGTGTCTTGACGACTCC	59.771	50.000	19.94	12.16	43.25	3.85
73	74	0.591659	TGAGTGTCTTGACGACTCCG	59.408	55.000	19.94	0.00	43.25	4.63
88	89	0.240945	CTCCGAAACTTGGCGCAATT	59.759	50.000	10.83	0.00	0.00	2.32
99	100	4.034048	ACTTGGCGCAATTAGAATAACTCG	59.966	41.667	10.83	0.00	0.00	4.18
105	106	6.292873	GCGCAATTAGAATAACTCGAAGATC	58.707	40.000	0.30	0.00	33.89	2.75
107	108	6.142480	CGCAATTAGAATAACTCGAAGATCGT	59.858	38.462	0.00	0.00	41.35	3.73
113	114	4.832590	ATAACTCGAAGATCGTACCCTG	57.167	45.455	0.00	0.00	41.35	4.45
118	119	1.134367	CGAAGATCGTACCCTGCTTGA	59.866	52.381	0.00	0.00	34.72	3.02
119	120	2.223829	CGAAGATCGTACCCTGCTTGAT	60.224	50.000	0.00	0.00	34.72	2.57
120	121	3.004419	CGAAGATCGTACCCTGCTTGATA	59.996	47.826	0.00	0.00	34.72	2.15
142	143	0.667993	CCACTGGACGTTGTTGCAAT	59.332	50.000	0.59	0.00	0.00	3.56
153	154	3.485378	CGTTGTTGCAATAAACACACCAG	59.515	43.478	21.05	6.42	39.70	4.00
155	156	3.027412	TGTTGCAATAAACACACCAGGT	58.973	40.909	0.59	0.00	35.16	4.00
195	196	0.393808	TGCCGTCTAATTTCAGGCCC	60.394	55.000	0.00	0.00	46.67	5.80
210	211	3.125376	GCCCCGGAGCATCAATCCT	62.125	63.158	1.65	0.00	36.25	3.24
212	213	1.895707	CCCGGAGCATCAATCCTGC	60.896	63.158	0.73	0.00	39.97	4.85
225	226	5.235850	TCAATCCTGCCTACAAACAGTAA	57.764	39.130	0.00	0.00	30.92	2.24
237	239	1.722011	AACAGTAATGCCCGAGAACG	58.278	50.000	0.00	0.00	39.43	3.95
239	241	1.480954	ACAGTAATGCCCGAGAACGAT	59.519	47.619	0.00	0.00	42.66	3.73
245	247	1.144057	GCCCGAGAACGATGACCAT	59.856	57.895	0.00	0.00	42.66	3.55
250	252	2.128035	CGAGAACGATGACCATAAGGC	58.872	52.381	0.00	0.00	42.66	4.35
306	308	3.067106	TCATGCCAGTCGAAGAAGTTTC	58.933	45.455	0.00	0.00	39.69	2.78
347	350	2.260869	AAAGCCACAGACGCGCATT	61.261	52.632	5.73	0.00	0.00	3.56
348	351	2.462255	AAAGCCACAGACGCGCATTG	62.462	55.000	5.73	4.56	0.00	2.82
377	380	1.762460	ATCCGAGCTCCCCGACAAT	60.762	57.895	8.47	0.00	0.00	2.71
414	417	1.597195	TGACACAACATGACAAGACGC	59.403	47.619	0.00	0.00	29.61	5.19
415	418	1.867233	GACACAACATGACAAGACGCT	59.133	47.619	0.00	0.00	0.00	5.07
447	453	6.904626	AGAACATACTAGGATTTTCAGCCAT	58.095	36.000	14.84	0.00	0.00	4.40
454	460	1.134610	GGATTTTCAGCCATGCCCAAG	60.135	52.381	0.00	0.00	0.00	3.61
515	522	7.571919	ACAAGTCAGAGATCCACAATATTCAT	58.428	34.615	0.00	0.00	0.00	2.57
516	523	7.714377	ACAAGTCAGAGATCCACAATATTCATC	59.286	37.037	0.00	0.00	0.00	2.92
519	526	5.013495	TCAGAGATCCACAATATTCATCCCC	59.987	44.000	0.00	0.00	0.00	4.81
522	529	4.416513	AGATCCACAATATTCATCCCCACA	59.583	41.667	0.00	0.00	0.00	4.17
665	675	9.371136	TGTATTTCATCATTCTCACTCTTGTAC	57.629	33.333	0.00	0.00	0.00	2.90
674	684	9.688091	TCATTCTCACTCTTGTACTATTCTAGT	57.312	33.333	0.00	0.00	42.68	2.57
689	699	8.577048	ACTATTCTAGTACTACAAGACTGCAA	57.423	34.615	0.00	0.00	37.23	4.08
690	700	8.460428	ACTATTCTAGTACTACAAGACTGCAAC	58.540	37.037	0.00	0.00	37.23	4.17
691	701	6.896021	TTCTAGTACTACAAGACTGCAACT	57.104	37.500	0.00	0.00	0.00	3.16
692	702	7.991084	TTCTAGTACTACAAGACTGCAACTA	57.009	36.000	0.00	0.00	0.00	2.24
693	703	8.577048	TTCTAGTACTACAAGACTGCAACTAT	57.423	34.615	0.00	0.00	0.00	2.12
694	704	7.986562	TCTAGTACTACAAGACTGCAACTATG	58.013	38.462	0.00	0.00	0.00	2.23
715	725	8.160106	ACTATGCATAATCCCTTTCTTTAGGAG	58.840	37.037	8.00	0.00	37.50	3.69
721	731	8.687242	CATAATCCCTTTCTTTAGGAGGAAAAC	58.313	37.037	0.00	0.00	37.50	2.43
722	732	5.656549	TCCCTTTCTTTAGGAGGAAAACA	57.343	39.130	0.00	0.00	37.50	2.83
723	733	6.020881	TCCCTTTCTTTAGGAGGAAAACAA	57.979	37.500	0.00	0.00	37.50	2.83
724	734	6.436890	TCCCTTTCTTTAGGAGGAAAACAAA	58.563	36.000	0.00	0.00	37.50	2.83
725	735	6.898521	TCCCTTTCTTTAGGAGGAAAACAAAA	59.101	34.615	0.00	0.00	37.50	2.44
726	736	6.984474	CCCTTTCTTTAGGAGGAAAACAAAAC	59.016	38.462	0.00	0.00	37.50	2.43
727	737	7.147724	CCCTTTCTTTAGGAGGAAAACAAAACT	60.148	37.037	0.00	0.00	37.50	2.66
728	738	8.909923	CCTTTCTTTAGGAGGAAAACAAAACTA	58.090	33.333	0.00	0.00	37.50	2.24
793	806	2.676342	GGTACCATTTCGCTTTCGACAT	59.324	45.455	7.15	0.00	45.43	3.06
1011	1129	1.228367	ATCTCCAATGGCCGCCATC	60.228	57.895	25.27	0.00	44.40	3.51
1022	1140	3.803082	CGCCATCGCCACCAAGTG	61.803	66.667	0.00	0.00	0.00	3.16
1099	1217	2.291043	GCCAAGGAGGAGTTCGGGA	61.291	63.158	0.00	0.00	41.22	5.14
1107	1225	2.182030	GAGTTCGGGAGCCTCGTG	59.818	66.667	0.00	0.00	0.00	4.35
1710	1861	1.544691	GTGCTCTTCCTCAGGTACGAA	59.455	52.381	0.00	0.00	0.00	3.85
1866	2023	1.699634	CTGGAGGTGAACAAGAAGGGA	59.300	52.381	0.00	0.00	0.00	4.20
2071	2228	0.679002	CTGTATGCTTGGCTGCTGGT	60.679	55.000	0.00	0.00	0.00	4.00
2118	2278	0.035317	TTCTCGGCACAATCACTGCT	59.965	50.000	0.00	0.00	34.84	4.24
2170	2331	3.295785	TGTCGATTGCAACATTTTGACG	58.704	40.909	0.00	0.00	34.24	4.35
2181	2342	5.339611	GCAACATTTTGACGATAAGTGACAC	59.660	40.000	0.00	0.00	34.24	3.67
2216	2377	2.549754	ACCGAACTTGTCAGCATCAAAG	59.450	45.455	0.00	0.00	0.00	2.77
2245	2406	2.791868	GCACAAGCCCCACGGTTTT	61.792	57.895	0.00	0.00	28.42	2.43
2246	2407	1.457009	GCACAAGCCCCACGGTTTTA	61.457	55.000	0.00	0.00	28.42	1.52
2247	2408	0.312729	CACAAGCCCCACGGTTTTAC	59.687	55.000	0.00	0.00	28.42	2.01
2386	2552	2.570582	CTTCTCCTCTGCTGACGGGC	62.571	65.000	8.49	0.00	0.00	6.13
2390	2556	2.759973	CTCTGCTGACGGGCCCTA	60.760	66.667	22.43	5.02	0.00	3.53
2406	2572	1.390565	CCTAGACCACGGACGAGAAT	58.609	55.000	0.00	0.00	0.00	2.40
2511	2680	8.441312	TTTTCTTCTGGTACTCGTATTTGTTT	57.559	30.769	0.00	0.00	0.00	2.83
2596	2765	2.223340	GGCGCTAAAACACATGGAGATG	60.223	50.000	7.64	0.00	35.49	2.90
2633	2802	1.351017	CTCCTAAGTGTTCAAGCCCCA	59.649	52.381	0.00	0.00	0.00	4.96
2675	2844	3.969250	GAGGAATCGGCGGCCACAA	62.969	63.158	20.71	3.83	0.00	3.33
2676	2845	3.508840	GGAATCGGCGGCCACAAG	61.509	66.667	20.71	2.16	0.00	3.16
2746	2918	1.267574	ATGATGCACGACCAGGGTCT	61.268	55.000	15.95	1.31	42.54	3.85
2789	2961	4.167268	GTCTTCGCGTAAGTCTGAATCTT	58.833	43.478	5.77	0.00	41.68	2.40
2869	3083	8.349983	GTCTTTCAGACTTGGCTAAACATAAAA	58.650	33.333	0.00	0.00	41.88	1.52
2870	3084	8.908903	TCTTTCAGACTTGGCTAAACATAAAAA	58.091	29.630	0.00	0.00	0.00	1.94
2879	3093	3.600786	GCTAAACATAAAAACACGTCGGC	59.399	43.478	0.00	0.00	0.00	5.54

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
36	37	4.701651	CACTCATCAGAATAAAGCCCAACA	59.298	41.667	0.00	0.00	0.00	3.33
38	39	4.922206	ACACTCATCAGAATAAAGCCCAA	58.078	39.130	0.00	0.00	0.00	4.12
46	47	5.897377	TCGTCAAGACACTCATCAGAATA	57.103	39.130	0.72	0.00	0.00	1.75
63	64	0.599204	GCCAAGTTTCGGAGTCGTCA	60.599	55.000	0.00	0.00	37.69	4.35
72	73	2.892373	TCTAATTGCGCCAAGTTTCG	57.108	45.000	4.18	0.00	0.00	3.46
73	74	6.322491	AGTTATTCTAATTGCGCCAAGTTTC	58.678	36.000	4.18	0.00	0.00	2.78
88	89	6.204301	CAGGGTACGATCTTCGAGTTATTCTA	59.796	42.308	3.62	0.00	43.74	2.10
99	100	2.961526	TCAAGCAGGGTACGATCTTC	57.038	50.000	0.00	0.00	0.00	2.87
105	106	2.676342	GTGGTTTATCAAGCAGGGTACG	59.324	50.000	0.00	0.00	41.08	3.67
107	108	3.308117	CCAGTGGTTTATCAAGCAGGGTA	60.308	47.826	0.00	0.00	41.08	3.69
113	114	2.423577	ACGTCCAGTGGTTTATCAAGC	58.576	47.619	9.54	0.00	0.00	4.01
118	119	2.292292	GCAACAACGTCCAGTGGTTTAT	59.708	45.455	9.54	0.00	44.28	1.40
119	120	1.671845	GCAACAACGTCCAGTGGTTTA	59.328	47.619	9.54	0.00	44.28	2.01
120	121	0.454196	GCAACAACGTCCAGTGGTTT	59.546	50.000	9.54	0.00	44.28	3.27
142	143	0.746063	ACGACGACCTGGTGTGTTTA	59.254	50.000	2.82	0.00	0.00	2.01
153	154	1.646624	GACCCTCTCAGACGACGACC	61.647	65.000	0.00	0.00	0.00	4.79
155	156	0.954449	GTGACCCTCTCAGACGACGA	60.954	60.000	0.00	0.00	0.00	4.20
184	185	2.043953	GCTCCGGGGCCTGAAATT	60.044	61.111	18.17	0.00	0.00	1.82
195	196	1.895707	GGCAGGATTGATGCTCCGG	60.896	63.158	0.00	0.00	43.35	5.14
210	211	2.442413	GGGCATTACTGTTTGTAGGCA	58.558	47.619	0.00	0.00	35.99	4.75
212	213	2.936498	CTCGGGCATTACTGTTTGTAGG	59.064	50.000	0.00	0.00	32.08	3.18
225	226	1.144057	GGTCATCGTTCTCGGGCAT	59.856	57.895	0.00	0.00	37.69	4.40
245	247	2.934886	ACCTTTTACACGTGGCCTTA	57.065	45.000	21.57	0.00	0.00	2.69
250	252	3.006110	TGTCTCCTACCTTTTACACGTGG	59.994	47.826	21.57	2.73	0.00	4.94
306	308	1.135199	GCATGCTTTGATCCTGGTGTG	60.135	52.381	11.37	0.00	0.00	3.82
347	350	0.106708	GCTCGGATGCCTATTGGTCA	59.893	55.000	0.00	0.00	35.27	4.02
348	351	0.394565	AGCTCGGATGCCTATTGGTC	59.605	55.000	0.00	0.00	35.27	4.02
372	375	1.205417	CACATTCTTGGGGGCATTGTC	59.795	52.381	0.00	0.00	0.00	3.18
377	380	0.703488	TCATCACATTCTTGGGGGCA	59.297	50.000	0.00	0.00	0.00	5.36
414	417	5.250235	TCCTAGTATGTTCTTTCGCTCAG	57.750	43.478	0.00	0.00	0.00	3.35
415	418	5.854010	ATCCTAGTATGTTCTTTCGCTCA	57.146	39.130	0.00	0.00	0.00	4.26
447	453	4.303794	ACCCTAGTATGTTATCTTGGGCA	58.696	43.478	10.55	0.00	45.75	5.36
496	503	5.221986	TGGGGATGAATATTGTGGATCTCTG	60.222	44.000	0.00	0.00	0.00	3.35
497	504	4.915809	TGGGGATGAATATTGTGGATCTCT	59.084	41.667	0.00	0.00	0.00	3.10
502	509	4.812403	ATGTGGGGATGAATATTGTGGA	57.188	40.909	0.00	0.00	0.00	4.02
557	566	9.267084	GTTAGGAAATGCAAATTGAAAAAGGTA	57.733	29.630	0.00	0.00	0.00	3.08
596	606	8.015185	AGGGTTATAAATACGAGTTTAGCTCA	57.985	34.615	0.00	0.00	44.33	4.26
665	675	8.679100	AGTTGCAGTCTTGTAGTACTAGAATAG	58.321	37.037	14.79	10.22	46.50	1.73
667	677	7.469537	AGTTGCAGTCTTGTAGTACTAGAAT	57.530	36.000	14.79	11.67	32.19	2.40
669	679	7.986562	CATAGTTGCAGTCTTGTAGTACTAGA	58.013	38.462	9.97	9.97	0.00	2.43
688	698	8.502738	TCCTAAAGAAAGGGATTATGCATAGTT	58.497	33.333	6.50	0.00	37.24	2.24
689	699	8.045720	TCCTAAAGAAAGGGATTATGCATAGT	57.954	34.615	6.50	3.64	37.24	2.12
690	700	7.609532	CCTCCTAAAGAAAGGGATTATGCATAG	59.390	40.741	6.50	0.00	37.24	2.23
691	701	7.294720	TCCTCCTAAAGAAAGGGATTATGCATA	59.705	37.037	1.16	1.16	37.24	3.14
692	702	6.103205	TCCTCCTAAAGAAAGGGATTATGCAT	59.897	38.462	3.79	3.79	37.24	3.96
693	703	5.431731	TCCTCCTAAAGAAAGGGATTATGCA	59.568	40.000	0.00	0.00	37.24	3.96
694	704	5.941788	TCCTCCTAAAGAAAGGGATTATGC	58.058	41.667	0.00	0.00	37.24	3.14
695	705	8.687242	GTTTTCCTCCTAAAGAAAGGGATTATG	58.313	37.037	0.00	0.00	37.24	1.90
696	706	8.398743	TGTTTTCCTCCTAAAGAAAGGGATTAT	58.601	33.333	0.00	0.00	37.24	1.28
697	707	7.761608	TGTTTTCCTCCTAAAGAAAGGGATTA	58.238	34.615	0.00	0.00	37.24	1.75
698	708	6.620429	TGTTTTCCTCCTAAAGAAAGGGATT	58.380	36.000	0.00	0.00	37.24	3.01
699	709	6.214177	TGTTTTCCTCCTAAAGAAAGGGAT	57.786	37.500	0.00	0.00	37.24	3.85
700	710	5.656549	TGTTTTCCTCCTAAAGAAAGGGA	57.343	39.130	0.00	0.00	37.24	4.20
707	717	8.194769	TGCTTTAGTTTTGTTTTCCTCCTAAAG	58.805	33.333	0.00	0.00	40.98	1.85
710	720	7.504238	TCATGCTTTAGTTTTGTTTTCCTCCTA	59.496	33.333	0.00	0.00	0.00	2.94
715	725	7.116805	CCTCATCATGCTTTAGTTTTGTTTTCC	59.883	37.037	0.00	0.00	0.00	3.13
721	731	5.865552	CCAACCTCATCATGCTTTAGTTTTG	59.134	40.000	0.00	0.00	0.00	2.44
722	732	5.047092	CCCAACCTCATCATGCTTTAGTTTT	60.047	40.000	0.00	0.00	0.00	2.43
723	733	4.463891	CCCAACCTCATCATGCTTTAGTTT	59.536	41.667	0.00	0.00	0.00	2.66
724	734	4.019174	CCCAACCTCATCATGCTTTAGTT	58.981	43.478	0.00	0.00	0.00	2.24
725	735	3.624777	CCCAACCTCATCATGCTTTAGT	58.375	45.455	0.00	0.00	0.00	2.24
726	736	2.954318	CCCCAACCTCATCATGCTTTAG	59.046	50.000	0.00	0.00	0.00	1.85
727	737	2.311542	ACCCCAACCTCATCATGCTTTA	59.688	45.455	0.00	0.00	0.00	1.85
728	738	1.077663	ACCCCAACCTCATCATGCTTT	59.922	47.619	0.00	0.00	0.00	3.51
731	741	0.257039	AGACCCCAACCTCATCATGC	59.743	55.000	0.00	0.00	0.00	4.06
793	806	7.925483	ACGATGGATCAAATTTTGACTTTGAAA	59.075	29.630	13.80	0.00	43.61	2.69
828	841	3.549827	CGCATGTGCCTTTTGTTCACTTA	60.550	43.478	0.00	0.00	37.91	2.24
873	886	9.327731	CTCCTTTGGGGAAGAATATATAGTAGT	57.672	37.037	0.00	0.00	44.58	2.73
874	887	9.327731	ACTCCTTTGGGGAAGAATATATAGTAG	57.672	37.037	0.00	0.00	44.58	2.57
875	888	9.101325	CACTCCTTTGGGGAAGAATATATAGTA	57.899	37.037	0.00	0.00	44.58	1.82
877	890	7.237679	TCCACTCCTTTGGGGAAGAATATATAG	59.762	40.741	0.00	0.00	44.58	1.31
888	1005	0.771127	CACTTCCACTCCTTTGGGGA	59.229	55.000	0.00	0.00	42.77	4.81
896	1013	0.321122	CAGGCTGACACTTCCACTCC	60.321	60.000	9.42	0.00	0.00	3.85
986	1104	0.479815	GGCCATTGGAGATGGATGGA	59.520	55.000	6.95	0.00	42.31	3.41
987	1105	0.892358	CGGCCATTGGAGATGGATGG	60.892	60.000	6.95	0.00	41.64	3.51
988	1106	1.521450	GCGGCCATTGGAGATGGATG	61.521	60.000	6.95	1.67	41.64	3.51
989	1107	1.228367	GCGGCCATTGGAGATGGAT	60.228	57.895	6.95	0.00	41.64	3.41
1020	1138	3.192103	AACAGGGCCGGAAGTCCAC	62.192	63.158	11.67	0.00	35.14	4.02
1021	1139	2.852075	AACAGGGCCGGAAGTCCA	60.852	61.111	11.67	0.00	35.14	4.02
1022	1140	2.046217	GAACAGGGCCGGAAGTCC	60.046	66.667	11.67	0.00	0.00	3.85
1023	1141	2.046217	GGAACAGGGCCGGAAGTC	60.046	66.667	11.67	4.52	0.00	3.01
1077	1195	1.377856	GAACTCCTCCTTGGCTGGC	60.378	63.158	0.00	0.00	35.26	4.85
1225	1343	2.278013	GAGGATCACGTCGTCGGC	60.278	66.667	7.05	0.00	41.85	5.54
1500	1651	1.198408	CTGCAGACGTACACGACCTTA	59.802	52.381	8.42	0.00	43.02	2.69
1683	1834	0.471780	TGAGGAAGAGCACCCTGTCA	60.472	55.000	0.00	0.00	31.84	3.58
1710	1861	2.746359	GTGTCCAGCAGCAGGTCT	59.254	61.111	3.35	0.00	0.00	3.85
2022	2179	0.321475	TCACGCATGCAGATTGTCCA	60.321	50.000	19.57	0.00	0.00	4.02
2071	2228	6.459573	GCATCTTTATTCTAAATCAACGGGCA	60.460	38.462	0.00	0.00	0.00	5.36
2074	2231	7.697691	ACAGCATCTTTATTCTAAATCAACGG	58.302	34.615	0.00	0.00	0.00	4.44
2145	2306	4.616381	TCAAAATGTTGCAATCGACAATCG	59.384	37.500	0.59	0.00	39.85	3.34
2170	2331	5.074430	ACGAAACAAACGTGTCACTTATC	57.926	39.130	0.65	0.00	42.37	1.75
2216	2377	1.136891	GGGCTTGTGCACCAATAATCC	59.863	52.381	15.69	6.68	41.91	3.01
2245	2406	2.364579	CAGGCCCCGGTGGTAGTA	60.365	66.667	0.00	0.00	36.04	1.82
2386	2552	0.679002	TTCTCGTCCGTGGTCTAGGG	60.679	60.000	0.00	0.00	35.61	3.53
2390	2556	1.473278	GAGAATTCTCGTCCGTGGTCT	59.527	52.381	19.31	0.00	32.78	3.85
2441	2607	4.049186	CCTATCGGTGAGTCCAAATTACG	58.951	47.826	0.00	0.00	35.57	3.18
2447	2613	2.756760	GTGTACCTATCGGTGAGTCCAA	59.243	50.000	0.00	0.00	45.18	3.53
2633	2802	0.981183	TCAGTTTCAGGGTACGGCAT	59.019	50.000	0.00	0.00	0.00	4.40
2675	2844	1.985116	GGGAGAGAAGCGGACCACT	60.985	63.158	0.00	0.00	0.00	4.00
2676	2845	2.283529	TGGGAGAGAAGCGGACCAC	61.284	63.158	0.00	0.00	0.00	4.16
2783	2955	3.380320	CGGGTTGGGTTGGAATAAGATTC	59.620	47.826	0.00	0.00	0.00	2.52
2789	2961	1.364269	ACTCGGGTTGGGTTGGAATA	58.636	50.000	0.00	0.00	0.00	1.75
2869	3083	1.593209	ACACAATCGCCGACGTGTT	60.593	52.632	15.99	3.87	39.49	3.32
2870	3084	2.028484	ACACAATCGCCGACGTGT	59.972	55.556	15.99	15.99	41.18	4.49
2879	3093	3.860717	TGCTCTCGCACACAATCG	58.139	55.556	0.00	0.00	42.25	3.34

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.