AutoCloner

Multiple sequence alignment - TraesCS1B01G162600

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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	TraesCS1B01G162600	chr1B	100.000	2789	0	0	1	2789	280208832	280211620	0.000000e+00	5151.0
1	TraesCS1B01G162600	chr1B	87.372	784	80	14	1	766	11906983	11907765	0.000000e+00	881.0
2	TraesCS1B01G162600	chr1B	84.485	767	82	20	1	766	518905759	518905029	0.000000e+00	723.0
3	TraesCS1B01G162600	chr1B	98.077	104	2	0	2190	2293	280211124	280211021	6.140000e-42	182.0
4	TraesCS1B01G162600	chr1B	100.000	48	0	0	2190	2237	51907872	51907825	3.830000e-14	89.8
5	TraesCS1B01G162600	chr1D	95.385	1105	27	3	803	1897	199671618	199672708	0.000000e+00	1736.0
6	TraesCS1B01G162600	chr1D	88.618	492	46	5	1	490	356071588	356072071	8.600000e-165	590.0
7	TraesCS1B01G162600	chr1D	88.438	493	47	8	1	490	411024758	411025243	1.110000e-163	586.0
8	TraesCS1B01G162600	chr1D	98.039	51	0	1	2187	2236	170824442	170824492	1.380000e-13	87.9
9	TraesCS1B01G162600	chr1A	94.064	1095	27	7	814	1897	251936080	251937147	0.000000e+00	1628.0
10	TraesCS1B01G162600	chr5B	97.586	787	12	3	2001	2781	314468212	314468997	0.000000e+00	1341.0
11	TraesCS1B01G162600	chr5B	98.711	543	7	0	2247	2789	314469101	314469643	0.000000e+00	965.0
12	TraesCS1B01G162600	chr5B	86.198	768	82	17	1	767	454027619	454026875	0.000000e+00	809.0
13	TraesCS1B01G162600	chr5B	86.198	768	81	18	1	766	452023065	452022321	0.000000e+00	808.0
14	TraesCS1B01G162600	chr5B	97.704	392	5	2	2401	2789	23050911	23050521	0.000000e+00	671.0
15	TraesCS1B01G162600	chr5B	99.065	321	2	1	2469	2789	295199952	295199633	2.410000e-160	575.0
16	TraesCS1B01G162600	chr5B	97.859	327	3	1	1941	2263	314467760	314468086	1.880000e-156	562.0
17	TraesCS1B01G162600	chr5B	96.400	250	7	2	1934	2182	295200176	295199928	7.190000e-111	411.0
18	TraesCS1B01G162600	chr5B	92.857	252	15	3	1933	2182	539797593	539797843	2.040000e-96	363.0
19	TraesCS1B01G162600	chr5B	85.401	274	38	2	493	766	250538700	250538971	1.640000e-72	283.0
20	TraesCS1B01G162600	chr5B	94.393	107	3	2	2190	2293	314468507	314468401	7.990000e-36	161.0
21	TraesCS1B01G162600	chr4A	86.900	771	73	14	1	766	727802924	727803671	0.000000e+00	839.0
22	TraesCS1B01G162600	chr4A	85.971	278	37	2	493	770	723465420	723465145	2.100000e-76	296.0
23	TraesCS1B01G162600	chr2B	85.899	773	84	15	1	770	703324459	703323709	0.000000e+00	800.0
24	TraesCS1B01G162600	chr2B	85.789	767	85	16	1	766	340130720	340131463	0.000000e+00	791.0
25	TraesCS1B01G162600	chr2B	98.305	236	4	0	2248	2483	38277096	38276861	5.560000e-112	414.0
26	TraesCS1B01G162600	chr2B	98.298	235	3	1	2247	2480	31490839	31490605	7.190000e-111	411.0
27	TraesCS1B01G162600	chr2B	98.696	230	3	0	2247	2476	483588137	483587908	2.590000e-110	409.0
28	TraesCS1B01G162600	chr2B	85.766	274	37	2	493	766	506859729	506859458	3.510000e-74	289.0
29	TraesCS1B01G162600	chrUn	97.449	392	6	2	2401	2789	470569347	470568957	0.000000e+00	665.0
30	TraesCS1B01G162600	chrUn	86.182	275	36	2	493	767	31681544	31681816	2.100000e-76	296.0
31	TraesCS1B01G162600	chr7B	97.576	330	7	1	2460	2789	374430215	374430543	5.210000e-157	564.0
32	TraesCS1B01G162600	chr7B	97.510	241	6	0	1942	2182	374430008	374430248	2.000000e-111	412.0
33	TraesCS1B01G162600	chr3B	98.442	321	4	1	2469	2789	780554109	780553790	5.210000e-157	564.0
34	TraesCS1B01G162600	chr3B	97.541	244	4	2	1941	2182	780554328	780554085	1.550000e-112	416.0
35	TraesCS1B01G162600	chr3B	97.521	242	5	1	2248	2489	370042418	370042178	2.000000e-111	412.0
36	TraesCS1B01G162600	chr3B	87.591	274	31	3	493	766	182637354	182637084	5.800000e-82	315.0
37	TraesCS1B01G162600	chr3B	100.000	48	0	0	2190	2237	275341917	275341870	3.830000e-14	89.8
38	TraesCS1B01G162600	chr3A	97.273	330	8	1	2460	2789	67428177	67428505	2.430000e-155	558.0
39	TraesCS1B01G162600	chr3A	97.273	330	7	2	2460	2789	191862057	191862384	2.430000e-155	558.0
40	TraesCS1B01G162600	chr3A	97.521	242	4	1	1943	2182	191861849	191862090	2.000000e-111	412.0
41	TraesCS1B01G162600	chr3A	98.707	232	2	1	1952	2182	67427979	67428210	7.190000e-111	411.0
42	TraesCS1B01G162600	chr3A	95.510	245	7	2	1942	2182	724294382	724294626	3.370000e-104	388.0
43	TraesCS1B01G162600	chr6B	98.298	235	4	0	2248	2482	46958925	46959159	2.000000e-111	412.0
44	TraesCS1B01G162600	chr6B	98.276	232	4	0	2248	2479	96639057	96638826	9.300000e-110	407.0
45	TraesCS1B01G162600	chr6B	87.179	273	33	2	490	762	650807211	650807481	2.700000e-80	309.0
46	TraesCS1B01G162600	chr5A	98.283	233	3	1	2248	2479	412524248	412524480	9.300000e-110	407.0
47	TraesCS1B01G162600	chr2D	87.365	277	33	2	493	769	514872523	514872249	1.610000e-82	316.0
48	TraesCS1B01G162600	chr2D	87.179	273	31	4	493	764	465568585	465568316	9.700000e-80	307.0
49	TraesCS1B01G162600	chr5D	86.909	275	33	3	493	766	480455957	480456229	3.490000e-79	305.0
50	TraesCS1B01G162600	chr5D	98.000	50	1	0	2187	2236	502514558	502514509	1.380000e-13	87.9
51	TraesCS1B01G162600	chr5D	93.333	60	1	2	2190	2246	268958517	268958458	4.950000e-13	86.1

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	TraesCS1B01G162600	chr1B	280208832	280211620	2788	False	5151.0	5151	100.0000	1	2789	1	chr1B.!!$F2	2788
1	TraesCS1B01G162600	chr1B	11906983	11907765	782	False	881.0	881	87.3720	1	766	1	chr1B.!!$F1	765
2	TraesCS1B01G162600	chr1B	518905029	518905759	730	True	723.0	723	84.4850	1	766	1	chr1B.!!$R3	765
3	TraesCS1B01G162600	chr1D	199671618	199672708	1090	False	1736.0	1736	95.3850	803	1897	1	chr1D.!!$F2	1094
4	TraesCS1B01G162600	chr1A	251936080	251937147	1067	False	1628.0	1628	94.0640	814	1897	1	chr1A.!!$F1	1083
5	TraesCS1B01G162600	chr5B	314467760	314469643	1883	False	956.0	1341	98.0520	1941	2789	3	chr5B.!!$F3	848
6	TraesCS1B01G162600	chr5B	454026875	454027619	744	True	809.0	809	86.1980	1	767	1	chr5B.!!$R4	766
7	TraesCS1B01G162600	chr5B	452022321	452023065	744	True	808.0	808	86.1980	1	766	1	chr5B.!!$R3	765
8	TraesCS1B01G162600	chr5B	295199633	295200176	543	True	493.0	575	97.7325	1934	2789	2	chr5B.!!$R5	855
9	TraesCS1B01G162600	chr4A	727802924	727803671	747	False	839.0	839	86.9000	1	766	1	chr4A.!!$F1	765
10	TraesCS1B01G162600	chr2B	703323709	703324459	750	True	800.0	800	85.8990	1	770	1	chr2B.!!$R5	769
11	TraesCS1B01G162600	chr2B	340130720	340131463	743	False	791.0	791	85.7890	1	766	1	chr2B.!!$F1	765
12	TraesCS1B01G162600	chr7B	374430008	374430543	535	False	488.0	564	97.5430	1942	2789	2	chr7B.!!$F1	847
13	TraesCS1B01G162600	chr3B	780553790	780554328	538	True	490.0	564	97.9915	1941	2789	2	chr3B.!!$R4	848
14	TraesCS1B01G162600	chr3A	191861849	191862384	535	False	485.0	558	97.3970	1943	2789	2	chr3A.!!$F3	846
15	TraesCS1B01G162600	chr3A	67427979	67428505	526	False	484.5	558	97.9900	1952	2789	2	chr3A.!!$F2	837

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
601	658	0.038526	CGCCGACTAACTTCACCACT	60.039	55.0	0.0	0.0	0.0	4.0	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1939	2009	0.035725	ACGGGCCCTTTTGCTAGTAC	60.036	55.0	22.43	0.0	0.0	2.73	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
58	59	6.173339	TGGACAAAACCAACTCATCTATCTC	58.827	40.000	0.00	0.00	36.96	2.75
59	60	6.173339	GGACAAAACCAACTCATCTATCTCA	58.827	40.000	0.00	0.00	0.00	3.27
60	61	6.825721	GGACAAAACCAACTCATCTATCTCAT	59.174	38.462	0.00	0.00	0.00	2.90
111	112	5.464389	CGAACTTTATAGTAAATCCCCACCG	59.536	44.000	0.00	0.00	33.17	4.94
126	129	2.206750	CCACCGGTTTGTATATGTCCG	58.793	52.381	2.97	0.00	40.72	4.79
153	156	7.716612	AGGTTGTCTGAAAATAAGAAGTTTGG	58.283	34.615	0.00	0.00	0.00	3.28
243	247	3.308438	AGCTTGCAAGTGCCAATAAAG	57.692	42.857	26.55	0.00	41.18	1.85
251	255	5.125417	TGCAAGTGCCAATAAAGGAGAATAC	59.875	40.000	0.00	0.00	41.18	1.89
256	260	5.353123	GTGCCAATAAAGGAGAATACGTTGA	59.647	40.000	0.00	0.00	0.00	3.18
295	304	0.321564	TGTGGGCACATGAGCACTAC	60.322	55.000	18.42	14.21	39.15	2.73
298	307	1.004628	TGGGCACATGAGCACTACAAT	59.995	47.619	18.42	0.00	39.15	2.71
301	310	3.885297	GGGCACATGAGCACTACAATAAT	59.115	43.478	17.11	0.00	34.32	1.28
302	311	4.023707	GGGCACATGAGCACTACAATAATC	60.024	45.833	17.11	0.00	34.32	1.75
303	312	4.576053	GGCACATGAGCACTACAATAATCA	59.424	41.667	17.11	0.00	35.83	2.57
304	313	5.277683	GGCACATGAGCACTACAATAATCAG	60.278	44.000	17.11	0.00	35.83	2.90
411	420	2.037144	AGTAATCCATCCGGTTACGCT	58.963	47.619	0.00	0.00	39.22	5.07
428	437	1.264557	CGCTATCGTAGGAGACAGTGG	59.735	57.143	0.00	0.00	0.00	4.00
509	554	2.201732	CGTCGCATAGCTACCAAATGT	58.798	47.619	0.00	0.00	0.00	2.71
529	574	2.369532	GTGGTAGTAGACACAACCCCAA	59.630	50.000	0.00	0.00	37.54	4.12
533	578	4.713321	GGTAGTAGACACAACCCCAAGATA	59.287	45.833	0.00	0.00	0.00	1.98
534	579	5.188359	GGTAGTAGACACAACCCCAAGATAA	59.812	44.000	0.00	0.00	0.00	1.75
543	588	0.546598	CCCCAAGATAAAGGCGGACT	59.453	55.000	0.00	0.00	0.00	3.85
593	650	4.430765	CCGCCACGCCGACTAACT	62.431	66.667	0.00	0.00	0.00	2.24
594	651	2.431942	CGCCACGCCGACTAACTT	60.432	61.111	0.00	0.00	0.00	2.66
595	652	2.442188	CGCCACGCCGACTAACTTC	61.442	63.158	0.00	0.00	0.00	3.01
596	653	1.373748	GCCACGCCGACTAACTTCA	60.374	57.895	0.00	0.00	0.00	3.02
597	654	1.623973	GCCACGCCGACTAACTTCAC	61.624	60.000	0.00	0.00	0.00	3.18
598	655	1.012486	CCACGCCGACTAACTTCACC	61.012	60.000	0.00	0.00	0.00	4.02
599	656	0.319211	CACGCCGACTAACTTCACCA	60.319	55.000	0.00	0.00	0.00	4.17
600	657	0.319297	ACGCCGACTAACTTCACCAC	60.319	55.000	0.00	0.00	0.00	4.16
601	658	0.038526	CGCCGACTAACTTCACCACT	60.039	55.000	0.00	0.00	0.00	4.00
602	659	1.200716	CGCCGACTAACTTCACCACTA	59.799	52.381	0.00	0.00	0.00	2.74
623	680	3.762407	TCAAGATCTCACGGGACAAAA	57.238	42.857	0.00	0.00	0.00	2.44
634	691	0.879090	GGGACAAAACATGACCGGTC	59.121	55.000	28.17	28.17	43.77	4.79
706	764	6.065976	TGGTGGACACATCAATTATCTCTT	57.934	37.500	4.69	0.00	34.04	2.85
707	765	6.484288	TGGTGGACACATCAATTATCTCTTT	58.516	36.000	4.69	0.00	34.04	2.52
738	797	2.038426	TCGCAAAGAAATGTCTCTCCCA	59.962	45.455	0.00	0.00	30.70	4.37
778	837	8.437360	CATATGTGCTAGTTCTATCCAACAAA	57.563	34.615	0.00	0.00	0.00	2.83
779	838	8.892723	CATATGTGCTAGTTCTATCCAACAAAA	58.107	33.333	0.00	0.00	0.00	2.44
780	839	7.759489	ATGTGCTAGTTCTATCCAACAAAAA	57.241	32.000	0.00	0.00	0.00	1.94
781	840	7.759489	TGTGCTAGTTCTATCCAACAAAAAT	57.241	32.000	0.00	0.00	0.00	1.82
782	841	8.856153	TGTGCTAGTTCTATCCAACAAAAATA	57.144	30.769	0.00	0.00	0.00	1.40
783	842	8.726988	TGTGCTAGTTCTATCCAACAAAAATAC	58.273	33.333	0.00	0.00	0.00	1.89
784	843	7.903431	GTGCTAGTTCTATCCAACAAAAATACG	59.097	37.037	0.00	0.00	0.00	3.06
785	844	6.905609	GCTAGTTCTATCCAACAAAAATACGC	59.094	38.462	0.00	0.00	0.00	4.42
786	845	5.864986	AGTTCTATCCAACAAAAATACGCG	58.135	37.500	3.53	3.53	0.00	6.01
787	846	4.267357	TCTATCCAACAAAAATACGCGC	57.733	40.909	5.73	0.00	0.00	6.86
788	847	1.889891	ATCCAACAAAAATACGCGCG	58.110	45.000	30.96	30.96	0.00	6.86
789	848	0.587285	TCCAACAAAAATACGCGCGT	59.413	45.000	39.05	39.05	0.00	6.01
790	849	0.700226	CCAACAAAAATACGCGCGTG	59.300	50.000	42.78	27.77	0.00	5.34
791	850	1.390820	CAACAAAAATACGCGCGTGT	58.609	45.000	42.78	35.29	0.00	4.49
792	851	1.119847	CAACAAAAATACGCGCGTGTG	59.880	47.619	42.78	30.53	0.00	3.82
793	852	0.384974	ACAAAAATACGCGCGTGTGG	60.385	50.000	42.78	27.14	0.00	4.17
794	853	1.441349	AAAAATACGCGCGTGTGGC	60.441	52.632	42.78	2.52	38.69	5.01
795	854	2.119147	AAAAATACGCGCGTGTGGCA	62.119	50.000	42.78	25.21	43.84	4.92
796	855	1.917782	AAAATACGCGCGTGTGGCAT	61.918	50.000	42.78	26.34	43.84	4.40
797	856	1.917782	AAATACGCGCGTGTGGCATT	61.918	50.000	42.78	30.19	43.84	3.56
798	857	2.576287	AATACGCGCGTGTGGCATTG	62.576	55.000	42.78	7.98	43.84	2.82
853	912	1.515521	AAAGGCGCTTCAGGAAACCG	61.516	55.000	7.64	0.00	0.00	4.44
924	983	0.995024	CCATCTTCTCCACCACCCTT	59.005	55.000	0.00	0.00	0.00	3.95
1098	1158	3.279875	GGGAACGGCATCGGCATC	61.280	66.667	0.00	0.00	43.71	3.91
1209	1269	3.755628	GCACTCTCCCACGCCGTA	61.756	66.667	0.00	0.00	0.00	4.02
1239	1299	1.137872	GACGACATCCTGCTTCTCCAT	59.862	52.381	0.00	0.00	0.00	3.41
1595	1655	1.680735	GATCTCCTCATCGCACAGACT	59.319	52.381	0.00	0.00	0.00	3.24
1615	1675	5.413833	AGACTCGACCGAAACAACTAATCTA	59.586	40.000	0.00	0.00	0.00	1.98
1686	1746	1.298859	GCACGGCGGAGTTCTTGATT	61.299	55.000	13.24	0.00	0.00	2.57
1772	1832	4.497291	ACACAAAGACCCACAAGAACTA	57.503	40.909	0.00	0.00	0.00	2.24
1778	1838	1.348036	GACCCACAAGAACTACTGGCT	59.652	52.381	0.00	0.00	0.00	4.75
1779	1839	1.348036	ACCCACAAGAACTACTGGCTC	59.652	52.381	0.00	0.00	0.00	4.70
1819	1889	1.209128	CACGTGCCCATCGATTAGAC	58.791	55.000	0.82	0.00	0.00	2.59
1908	1978	3.250464	GATTGCATCGATGAGTTCTGC	57.750	47.619	29.20	13.69	0.00	4.26
1909	1979	1.372582	TTGCATCGATGAGTTCTGCC	58.627	50.000	29.20	8.89	31.89	4.85
1910	1980	0.538584	TGCATCGATGAGTTCTGCCT	59.461	50.000	29.20	0.00	31.89	4.75
1911	1981	0.935898	GCATCGATGAGTTCTGCCTG	59.064	55.000	29.20	0.00	0.00	4.85
1912	1982	0.935898	CATCGATGAGTTCTGCCTGC	59.064	55.000	21.02	0.00	0.00	4.85
1913	1983	0.179062	ATCGATGAGTTCTGCCTGCC	60.179	55.000	0.00	0.00	0.00	4.85
1914	1984	1.078918	CGATGAGTTCTGCCTGCCA	60.079	57.895	0.00	0.00	0.00	4.92
1915	1985	0.674581	CGATGAGTTCTGCCTGCCAA	60.675	55.000	0.00	0.00	0.00	4.52
1916	1986	1.538047	GATGAGTTCTGCCTGCCAAA	58.462	50.000	0.00	0.00	0.00	3.28
1917	1987	1.888512	GATGAGTTCTGCCTGCCAAAA	59.111	47.619	0.00	0.00	0.00	2.44
1918	1988	1.774110	TGAGTTCTGCCTGCCAAAAA	58.226	45.000	0.00	0.00	0.00	1.94
1939	2009	5.970317	AAAGGTTTCCCCGTTTTATACTG	57.030	39.130	0.00	0.00	38.74	2.74
2112	2187	7.254556	CGTATCATAGCAATGTTTGTCATGACT	60.255	37.037	25.55	2.94	36.51	3.41
2226	2693	1.381327	CTACCCCGCCCTCTCTTGA	60.381	63.158	0.00	0.00	0.00	3.02
2240	2707	5.251764	CCTCTCTTGACATTCTCCATGTTT	58.748	41.667	0.00	0.00	46.96	2.83
2272	2742	3.003173	TCAAGAGAGGGCGGGGTG	61.003	66.667	0.00	0.00	0.00	4.61
2351	2821	2.362397	CCGAAGAGCTAGCTATGGACAA	59.638	50.000	19.38	0.00	0.00	3.18
2383	2853	1.133575	AGCTTGCTATCCATGTGCCAT	60.134	47.619	0.00	0.00	0.00	4.40
2390	2860	1.919240	ATCCATGTGCCATAGCCATG	58.081	50.000	7.33	7.33	42.54	3.66

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
111	112	5.422145	ACAACCTACGGACATATACAAACC	58.578	41.667	0.00	0.00	0.00	3.27
126	129	9.665264	CAAACTTCTTATTTTCAGACAACCTAC	57.335	33.333	0.00	0.00	0.00	3.18
168	172	8.991026	CCTTCTGCTCATGATTCTTAAGATAAG	58.009	37.037	5.89	0.00	0.00	1.73
214	218	1.672356	CTTGCAAGCTAGCACCGGT	60.672	57.895	18.83	0.00	45.61	5.28
243	247	3.001330	CGAGCCAAATCAACGTATTCTCC	59.999	47.826	0.00	0.00	0.00	3.71
315	324	7.466804	ACAACAATGTCCCTTCTTTATTAGGA	58.533	34.615	0.00	0.00	33.41	2.94
337	346	5.277779	GCATATTTAGCGCATAACCAGACAA	60.278	40.000	11.47	0.00	0.00	3.18
378	387	3.735591	TGGATTACTAATTGTAGCGCCC	58.264	45.455	2.29	0.00	32.08	6.13
379	388	4.392138	GGATGGATTACTAATTGTAGCGCC	59.608	45.833	2.29	0.00	32.08	6.53
411	420	2.169144	TCGACCACTGTCTCCTACGATA	59.831	50.000	0.00	0.00	39.47	2.92
418	427	0.033504	TTGCTTCGACCACTGTCTCC	59.966	55.000	0.00	0.00	39.47	3.71
462	471	3.135348	TGTCTGCCTCCTCATTTGATAGG	59.865	47.826	5.23	5.23	32.94	2.57
513	558	5.280521	CCTTTATCTTGGGGTTGTGTCTACT	60.281	44.000	0.00	0.00	0.00	2.57
515	560	4.566907	GCCTTTATCTTGGGGTTGTGTCTA	60.567	45.833	0.00	0.00	0.00	2.59
526	571	1.136305	TCGAGTCCGCCTTTATCTTGG	59.864	52.381	0.00	0.00	35.37	3.61
529	574	1.409427	CCTTCGAGTCCGCCTTTATCT	59.591	52.381	0.00	0.00	35.37	1.98
533	578	0.395312	TTTCCTTCGAGTCCGCCTTT	59.605	50.000	0.00	0.00	35.37	3.11
534	579	0.395312	TTTTCCTTCGAGTCCGCCTT	59.605	50.000	0.00	0.00	35.37	4.35
557	602	0.108138	GCAACCATCCTACTCGTGCT	60.108	55.000	0.00	0.00	0.00	4.40
591	648	5.393569	CGTGAGATCTTGATAGTGGTGAAGT	60.394	44.000	0.00	0.00	0.00	3.01
592	649	5.039984	CGTGAGATCTTGATAGTGGTGAAG	58.960	45.833	0.00	0.00	0.00	3.02
593	650	4.142160	CCGTGAGATCTTGATAGTGGTGAA	60.142	45.833	0.00	0.00	0.00	3.18
594	651	3.381590	CCGTGAGATCTTGATAGTGGTGA	59.618	47.826	0.00	0.00	0.00	4.02
595	652	3.491619	CCCGTGAGATCTTGATAGTGGTG	60.492	52.174	0.00	0.00	0.00	4.17
596	653	2.695666	CCCGTGAGATCTTGATAGTGGT	59.304	50.000	0.00	0.00	0.00	4.16
597	654	2.959030	TCCCGTGAGATCTTGATAGTGG	59.041	50.000	0.00	0.00	0.00	4.00
598	655	3.381590	TGTCCCGTGAGATCTTGATAGTG	59.618	47.826	0.00	0.00	0.00	2.74
599	656	3.632333	TGTCCCGTGAGATCTTGATAGT	58.368	45.455	0.00	0.00	0.00	2.12
600	657	4.655762	TTGTCCCGTGAGATCTTGATAG	57.344	45.455	0.00	0.00	0.00	2.08
601	658	5.175859	GTTTTGTCCCGTGAGATCTTGATA	58.824	41.667	0.00	0.00	0.00	2.15
602	659	3.981071	TTTGTCCCGTGAGATCTTGAT	57.019	42.857	0.00	0.00	0.00	2.57
634	691	1.937108	GCGAGGAGTTGTGGTCTTCTG	60.937	57.143	0.00	0.00	0.00	3.02
767	826	3.026349	CGCGCGTATTTTTGTTGGATAG	58.974	45.455	24.19	0.00	0.00	2.08
768	827	2.415857	ACGCGCGTATTTTTGTTGGATA	59.584	40.909	37.08	0.00	0.00	2.59
769	828	1.198178	ACGCGCGTATTTTTGTTGGAT	59.802	42.857	37.08	3.21	0.00	3.41
770	829	0.587285	ACGCGCGTATTTTTGTTGGA	59.413	45.000	37.08	0.00	0.00	3.53
771	830	0.700226	CACGCGCGTATTTTTGTTGG	59.300	50.000	37.24	15.45	0.00	3.77
772	831	1.119847	CACACGCGCGTATTTTTGTTG	59.880	47.619	37.24	21.83	0.00	3.33
773	832	1.390820	CACACGCGCGTATTTTTGTT	58.609	45.000	37.24	6.52	0.00	2.83
774	833	0.384974	CCACACGCGCGTATTTTTGT	60.385	50.000	37.24	24.91	0.00	2.83
775	834	1.661052	GCCACACGCGCGTATTTTTG	61.661	55.000	37.24	24.18	0.00	2.44
776	835	1.441349	GCCACACGCGCGTATTTTT	60.441	52.632	37.24	14.60	0.00	1.94
777	836	1.917782	ATGCCACACGCGCGTATTTT	61.918	50.000	37.24	17.33	42.08	1.82
778	837	1.917782	AATGCCACACGCGCGTATTT	61.918	50.000	37.24	20.12	42.08	1.40
779	838	2.395360	AATGCCACACGCGCGTATT	61.395	52.632	37.24	26.94	42.08	1.89
780	839	2.817834	AATGCCACACGCGCGTAT	60.818	55.556	37.24	24.94	42.08	3.06
781	840	3.783327	CAATGCCACACGCGCGTA	61.783	61.111	37.24	21.01	42.08	4.42
819	878	3.295228	CTTTGGTGGAAGACGCGCG	62.295	63.158	30.96	30.96	0.00	6.86
820	879	2.556287	CTTTGGTGGAAGACGCGC	59.444	61.111	5.73	0.00	0.00	6.86
831	890	0.467290	TTTCCTGAAGCGCCTTTGGT	60.467	50.000	2.29	0.00	0.00	3.67
893	952	3.044894	GAGAAGATGGAGGGGAGACATT	58.955	50.000	0.00	0.00	0.00	2.71
1128	1188	0.815095	TCATCACGAGCCGCTTCTTA	59.185	50.000	0.00	0.00	0.00	2.10
1239	1299	2.741985	CTCGGCGGCATGTTGACA	60.742	61.111	10.53	0.00	0.00	3.58
1326	1386	4.308458	CCGCCACCGAGGAACACA	62.308	66.667	0.00	0.00	41.22	3.72
1353	1413	0.041238	TCTCCATGAACTCCCCGTCT	59.959	55.000	0.00	0.00	0.00	4.18
1595	1655	4.418392	GCTAGATTAGTTGTTTCGGTCGA	58.582	43.478	0.00	0.00	0.00	4.20
1778	1838	3.541996	ATGTACATGTTCATGCGAGGA	57.458	42.857	16.22	0.00	0.00	3.71
1779	1839	4.025730	GTGTATGTACATGTTCATGCGAGG	60.026	45.833	23.66	0.00	38.63	4.63
1836	1906	1.461512	ACACGCACGCGATAATTGAAA	59.538	42.857	19.66	0.00	42.83	2.69
1897	1967	1.538047	TTTGGCAGGCAGAACTCATC	58.462	50.000	0.00	0.00	0.00	2.92
1898	1968	1.999648	TTTTGGCAGGCAGAACTCAT	58.000	45.000	0.00	0.00	0.00	2.90
1899	1969	1.774110	TTTTTGGCAGGCAGAACTCA	58.226	45.000	0.00	0.00	0.00	3.41
1921	1991	6.256539	GCTAGTACAGTATAAAACGGGGAAAC	59.743	42.308	0.00	0.00	0.00	2.78
1922	1992	6.070881	TGCTAGTACAGTATAAAACGGGGAAA	60.071	38.462	0.00	0.00	0.00	3.13
1923	1993	5.421693	TGCTAGTACAGTATAAAACGGGGAA	59.578	40.000	0.00	0.00	0.00	3.97
1924	1994	4.955450	TGCTAGTACAGTATAAAACGGGGA	59.045	41.667	0.00	0.00	0.00	4.81
1925	1995	5.266733	TGCTAGTACAGTATAAAACGGGG	57.733	43.478	0.00	0.00	0.00	5.73
1926	1996	7.201582	CCTTTTGCTAGTACAGTATAAAACGGG	60.202	40.741	0.00	0.00	0.00	5.28
1927	1997	7.201582	CCCTTTTGCTAGTACAGTATAAAACGG	60.202	40.741	0.00	0.00	0.00	4.44
1928	1998	7.675637	GCCCTTTTGCTAGTACAGTATAAAACG	60.676	40.741	0.00	0.00	0.00	3.60
1929	1999	7.414873	GGCCCTTTTGCTAGTACAGTATAAAAC	60.415	40.741	0.00	0.00	0.00	2.43
1930	2000	6.600427	GGCCCTTTTGCTAGTACAGTATAAAA	59.400	38.462	0.00	0.00	0.00	1.52
1931	2001	6.117488	GGCCCTTTTGCTAGTACAGTATAAA	58.883	40.000	0.00	0.00	0.00	1.40
1932	2002	5.397109	GGGCCCTTTTGCTAGTACAGTATAA	60.397	44.000	17.04	0.00	0.00	0.98
1933	2003	4.102054	GGGCCCTTTTGCTAGTACAGTATA	59.898	45.833	17.04	0.00	0.00	1.47
1934	2004	3.118000	GGGCCCTTTTGCTAGTACAGTAT	60.118	47.826	17.04	0.00	0.00	2.12
1935	2005	2.237893	GGGCCCTTTTGCTAGTACAGTA	59.762	50.000	17.04	0.00	0.00	2.74
1936	2006	1.004394	GGGCCCTTTTGCTAGTACAGT	59.996	52.381	17.04	0.00	0.00	3.55
1937	2007	1.751437	GGGCCCTTTTGCTAGTACAG	58.249	55.000	17.04	0.00	0.00	2.74
1938	2008	0.035820	CGGGCCCTTTTGCTAGTACA	60.036	55.000	22.43	0.00	0.00	2.90
1939	2009	0.035725	ACGGGCCCTTTTGCTAGTAC	60.036	55.000	22.43	0.00	0.00	2.73
2112	2187	3.525537	GTTCATCGGAGAGCTGAAATGA	58.474	45.455	0.00	0.00	43.63	2.57
2240	2707	6.409704	CCTCTCTTGACATTCTCCATGTTTA	58.590	40.000	0.00	0.00	46.96	2.01
2272	2742	2.017049	CTCCCATGTCAAATTCGGTCC	58.983	52.381	0.00	0.00	0.00	4.46
2351	2821	1.980772	GCAAGCTTCCATGCACCCT	60.981	57.895	0.00	0.00	42.12	4.34
2390	2860	3.557595	CCATAAGATCTCGCAACCAACTC	59.442	47.826	0.00	0.00	0.00	3.01

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.