AutoCloner

Multiple sequence alignment - TraesCS6D01G347200

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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	TraesCS6D01G347200	chr6D	100.000	3437	0	0	1	3437	445977965	445981401	0.000000e+00	6348.0
1	TraesCS6D01G347200	chr6D	95.058	2853	94	15	44	2874	445963519	445966346	0.000000e+00	4444.0
2	TraesCS6D01G347200	chr6D	84.247	2279	286	33	808	3049	445788971	445786729	0.000000e+00	2152.0
3	TraesCS6D01G347200	chr6D	85.728	2011	219	26	886	2846	445778872	445776880	0.000000e+00	2061.0
4	TraesCS6D01G347200	chr6D	87.785	1580	187	6	845	2420	411470943	411469366	0.000000e+00	1844.0
5	TraesCS6D01G347200	chr6D	80.968	1860	305	30	791	2624	445793878	445792042	0.000000e+00	1428.0
6	TraesCS6D01G347200	chr6D	89.135	451	28	11	2956	3388	445966378	445966825	3.020000e-150	542.0
7	TraesCS6D01G347200	chr6D	86.550	171	16	3	318	481	445789398	445789228	7.580000e-42	182.0
8	TraesCS6D01G347200	chr6D	84.397	141	13	5	365	498	445789920	445789782	2.780000e-26	130.0
9	TraesCS6D01G347200	chr6D	77.184	206	31	8	252	447	411471505	411471306	4.690000e-19	106.0
10	TraesCS6D01G347200	chr6D	100.000	49	0	0	1	49	467149893	467149845	1.310000e-14	91.6
11	TraesCS6D01G347200	chr6A	94.494	3342	123	22	130	3434	592617455	592620772	0.000000e+00	5096.0
12	TraesCS6D01G347200	chr6A	84.656	2281	283	37	809	3049	592458970	592456717	0.000000e+00	2211.0
13	TraesCS6D01G347200	chr6A	85.682	1767	213	18	828	2556	592464456	592462692	0.000000e+00	1825.0
14	TraesCS6D01G347200	chr6A	87.014	1594	200	7	832	2420	556038468	556036877	0.000000e+00	1790.0
15	TraesCS6D01G347200	chr6A	83.636	1650	239	26	796	2427	592599449	592601085	0.000000e+00	1522.0
16	TraesCS6D01G347200	chr6A	81.322	348	42	18	2702	3042	592462546	592462215	9.460000e-66	261.0
17	TraesCS6D01G347200	chr6A	94.286	105	4	2	44	147	592617341	592617444	3.550000e-35	159.0
18	TraesCS6D01G347200	chr6A	81.818	165	20	6	342	498	592465539	592465377	2.780000e-26	130.0
19	TraesCS6D01G347200	chr6A	96.491	57	2	0	425	481	592464803	592464747	1.020000e-15	95.3
20	TraesCS6D01G347200	chr6B	86.555	1614	201	14	813	2420	618670273	618668670	0.000000e+00	1764.0
21	TraesCS6D01G347200	chr6B	91.523	1274	77	12	249	1497	673875618	673876885	0.000000e+00	1725.0
22	TraesCS6D01G347200	chr6B	84.514	1595	224	18	813	2399	673764195	673765774	0.000000e+00	1555.0
23	TraesCS6D01G347200	chr6B	86.709	1407	174	11	812	2213	672457703	672456305	0.000000e+00	1550.0
24	TraesCS6D01G347200	chr6B	80.608	1119	195	16	1305	2419	673931388	673930288	0.000000e+00	845.0
25	TraesCS6D01G347200	chr6B	89.024	656	58	6	2277	2921	673897941	673898593	0.000000e+00	800.0
26	TraesCS6D01G347200	chr6B	81.180	356	37	20	2699	3042	672490761	672490424	3.400000e-65	259.0
27	TraesCS6D01G347200	chr6B	89.011	182	18	2	44	224	673855016	673855196	1.240000e-54	224.0
28	TraesCS6D01G347200	chr6B	83.333	210	26	5	339	541	672493411	672493204	5.860000e-43	185.0
29	TraesCS6D01G347200	chr6B	77.729	229	30	13	2918	3134	673918008	673918227	1.680000e-23	121.0
30	TraesCS6D01G347200	chr6B	77.880	217	30	11	295	498	672493952	672493741	6.030000e-23	119.0
31	TraesCS6D01G347200	chr6B	92.982	57	4	0	1	57	586638921	586638977	2.200000e-12	84.2
32	TraesCS6D01G347200	chr5D	98.113	53	1	0	1	53	61485408	61485460	3.650000e-15	93.5
33	TraesCS6D01G347200	chr5D	100.000	49	0	0	1	49	72615034	72614986	1.310000e-14	91.6
34	TraesCS6D01G347200	chr4D	92.188	64	3	2	1	63	119923616	119923554	4.720000e-14	89.8
35	TraesCS6D01G347200	chr2B	98.039	51	1	0	1	51	579684176	579684126	4.720000e-14	89.8
36	TraesCS6D01G347200	chr7B	98.039	51	0	1	1	51	332310882	332310931	1.700000e-13	87.9
37	TraesCS6D01G347200	chr5A	90.476	63	4	2	1	62	4117129	4117068	7.910000e-12	82.4
38	TraesCS6D01G347200	chr5B	90.323	62	5	1	1	61	393570535	393570474	2.840000e-11	80.5

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	TraesCS6D01G347200	chr6D	445977965	445981401	3436	False	6348.00	6348	100.0000	1	3437	1	chr6D.!!$F1	3436
1	TraesCS6D01G347200	chr6D	445963519	445966825	3306	False	2493.00	4444	92.0965	44	3388	2	chr6D.!!$F2	3344
2	TraesCS6D01G347200	chr6D	445776880	445778872	1992	True	2061.00	2061	85.7280	886	2846	1	chr6D.!!$R1	1960
3	TraesCS6D01G347200	chr6D	411469366	411471505	2139	True	975.00	1844	82.4845	252	2420	2	chr6D.!!$R3	2168
4	TraesCS6D01G347200	chr6D	445786729	445793878	7149	True	973.00	2152	84.0405	318	3049	4	chr6D.!!$R4	2731
5	TraesCS6D01G347200	chr6A	592617341	592620772	3431	False	2627.50	5096	94.3900	44	3434	2	chr6A.!!$F2	3390
6	TraesCS6D01G347200	chr6A	556036877	556038468	1591	True	1790.00	1790	87.0140	832	2420	1	chr6A.!!$R1	1588
7	TraesCS6D01G347200	chr6A	592599449	592601085	1636	False	1522.00	1522	83.6360	796	2427	1	chr6A.!!$F1	1631
8	TraesCS6D01G347200	chr6A	592456717	592465539	8822	True	904.46	2211	85.9938	342	3049	5	chr6A.!!$R2	2707
9	TraesCS6D01G347200	chr6B	618668670	618670273	1603	True	1764.00	1764	86.5550	813	2420	1	chr6B.!!$R1	1607
10	TraesCS6D01G347200	chr6B	673875618	673876885	1267	False	1725.00	1725	91.5230	249	1497	1	chr6B.!!$F4	1248
11	TraesCS6D01G347200	chr6B	673764195	673765774	1579	False	1555.00	1555	84.5140	813	2399	1	chr6B.!!$F2	1586
12	TraesCS6D01G347200	chr6B	672456305	672457703	1398	True	1550.00	1550	86.7090	812	2213	1	chr6B.!!$R2	1401
13	TraesCS6D01G347200	chr6B	673930288	673931388	1100	True	845.00	845	80.6080	1305	2419	1	chr6B.!!$R3	1114
14	TraesCS6D01G347200	chr6B	673897941	673898593	652	False	800.00	800	89.0240	2277	2921	1	chr6B.!!$F5	644

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
334	4499	1.836999	CTCCGTCCAATCCACCCACA	61.837	60.0	0.0	0.0	0.0	4.17	F
1430	11893	0.840722	ACTGGGATCTTTCGGGTGGT	60.841	55.0	0.0	0.0	0.0	4.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1874	12339	1.000163	GCCTGAGTCGAAGTGAGACAA	60.000	52.381	0.0	0.0	40.84	3.18	R
2869	13400	0.033781	GCCATGTGTTGTGTTGCCAT	59.966	50.000	0.0	0.0	0.00	4.40	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
41	42	7.870826	TGAATAGATTGAAAGTTTTTCTCGCA	58.129	30.769	3.53	0.00	0.00	5.10
42	43	8.349245	TGAATAGATTGAAAGTTTTTCTCGCAA	58.651	29.630	3.53	0.00	0.00	4.85
45	46	7.826260	AGATTGAAAGTTTTTCTCGCAAAAA	57.174	28.000	3.53	1.87	0.00	1.94
334	4499	1.836999	CTCCGTCCAATCCACCCACA	61.837	60.000	0.00	0.00	0.00	4.17
351	4516	3.379445	ACGATCACCGCCGTTCCT	61.379	61.111	0.00	0.00	43.32	3.36
600	5426	9.087424	GAAATGGCCTGCTTTAATTTTAGTAAG	57.913	33.333	3.32	0.00	0.00	2.34
601	5427	6.524101	TGGCCTGCTTTAATTTTAGTAAGG	57.476	37.500	3.32	0.00	0.00	2.69
602	5428	5.420739	TGGCCTGCTTTAATTTTAGTAAGGG	59.579	40.000	3.32	0.00	0.00	3.95
604	5430	5.681437	GCCTGCTTTAATTTTAGTAAGGGCC	60.681	44.000	0.00	0.00	0.00	5.80
605	5431	5.163447	CCTGCTTTAATTTTAGTAAGGGCCC	60.163	44.000	16.46	16.46	0.00	5.80
606	5432	5.334421	TGCTTTAATTTTAGTAAGGGCCCA	58.666	37.500	27.56	0.00	0.00	5.36
607	5433	5.420739	TGCTTTAATTTTAGTAAGGGCCCAG	59.579	40.000	27.56	8.20	0.00	4.45
610	5450	7.310175	GCTTTAATTTTAGTAAGGGCCCAGAAA	60.310	37.037	27.56	14.71	0.00	2.52
780	5672	2.931969	GCTTTTGCATTAGGTGATTGCC	59.068	45.455	0.00	0.00	46.58	4.52
912	5875	6.656314	TCGTACAGCTGTTATTTGGTTATG	57.344	37.500	27.06	9.00	0.00	1.90
1338	11801	4.974591	TCTGCTCATACATCGATGATACG	58.025	43.478	31.33	15.73	35.32	3.06
1360	11823	3.181464	GGGTCTTGGTTATCTAGCTGACC	60.181	52.174	0.00	0.69	42.36	4.02
1361	11824	3.707102	GGTCTTGGTTATCTAGCTGACCT	59.293	47.826	8.78	0.00	41.19	3.85
1430	11893	0.840722	ACTGGGATCTTTCGGGTGGT	60.841	55.000	0.00	0.00	0.00	4.16
1459	11922	3.435275	TGCAGGTATCTGTCAGTTCTCT	58.565	45.455	4.60	0.00	42.78	3.10
1912	12377	3.323115	CAGGCCTCTGCACTATGAAGATA	59.677	47.826	0.00	0.00	40.13	1.98
1980	12445	0.181114	TTAGCTGCCCGATGCTTCAT	59.819	50.000	0.00	0.00	42.00	2.57
2024	12489	4.770874	CGACCCCGATTGGCCGTT	62.771	66.667	0.00	0.00	38.22	4.44
2440	12911	8.791605	CAATGAACATGAACATAAAATGACTCG	58.208	33.333	0.00	0.00	0.00	4.18
2574	13066	3.091545	TCCAATTGGCTTCAGATGTTCC	58.908	45.455	20.33	0.00	34.44	3.62
2834	13350	9.262358	GATTAGATCTGCTAACCGTTTCTTTAT	57.738	33.333	5.18	0.00	41.64	1.40
2856	13387	8.718102	TTATAGTGGTTCTTGCTCATAACTTC	57.282	34.615	0.00	0.00	0.00	3.01
2863	13394	6.366630	GTTCTTGCTCATAACTTCTCAACAC	58.633	40.000	0.00	0.00	0.00	3.32
2864	13395	5.610398	TCTTGCTCATAACTTCTCAACACA	58.390	37.500	0.00	0.00	0.00	3.72
2865	13396	6.054941	TCTTGCTCATAACTTCTCAACACAA	58.945	36.000	0.00	0.00	0.00	3.33
2866	13397	5.673337	TGCTCATAACTTCTCAACACAAC	57.327	39.130	0.00	0.00	0.00	3.32
2867	13398	5.122519	TGCTCATAACTTCTCAACACAACA	58.877	37.500	0.00	0.00	0.00	3.33
2868	13399	5.007626	TGCTCATAACTTCTCAACACAACAC	59.992	40.000	0.00	0.00	0.00	3.32
2869	13400	5.007626	GCTCATAACTTCTCAACACAACACA	59.992	40.000	0.00	0.00	0.00	3.72
2870	13401	6.293626	GCTCATAACTTCTCAACACAACACAT	60.294	38.462	0.00	0.00	0.00	3.21
2871	13402	6.958255	TCATAACTTCTCAACACAACACATG	58.042	36.000	0.00	0.00	0.00	3.21
2872	13403	4.637483	AACTTCTCAACACAACACATGG	57.363	40.909	0.00	0.00	0.00	3.66
2873	13404	2.358898	ACTTCTCAACACAACACATGGC	59.641	45.455	0.00	0.00	0.00	4.40
2874	13405	2.049888	TCTCAACACAACACATGGCA	57.950	45.000	0.00	0.00	0.00	4.92
2875	13406	2.373224	TCTCAACACAACACATGGCAA	58.627	42.857	0.00	0.00	0.00	4.52
2876	13407	2.098934	TCTCAACACAACACATGGCAAC	59.901	45.455	0.00	0.00	0.00	4.17
2889	13420	1.325476	TGGCAACACAACACATGGCA	61.325	50.000	0.00	0.00	46.17	4.92
2924	13455	9.852091	ATGAAAGAAAGCAAAGAGATTATGAAC	57.148	29.630	0.00	0.00	0.00	3.18
2925	13456	8.849168	TGAAAGAAAGCAAAGAGATTATGAACA	58.151	29.630	0.00	0.00	0.00	3.18
2926	13457	9.339492	GAAAGAAAGCAAAGAGATTATGAACAG	57.661	33.333	0.00	0.00	0.00	3.16
2927	13458	7.388460	AGAAAGCAAAGAGATTATGAACAGG	57.612	36.000	0.00	0.00	0.00	4.00
2928	13459	6.376581	AGAAAGCAAAGAGATTATGAACAGGG	59.623	38.462	0.00	0.00	0.00	4.45
2929	13460	5.441718	AGCAAAGAGATTATGAACAGGGA	57.558	39.130	0.00	0.00	0.00	4.20
2930	13461	5.819991	AGCAAAGAGATTATGAACAGGGAA	58.180	37.500	0.00	0.00	0.00	3.97
2931	13462	5.649831	AGCAAAGAGATTATGAACAGGGAAC	59.350	40.000	0.00	0.00	0.00	3.62
2932	13463	5.415701	GCAAAGAGATTATGAACAGGGAACA	59.584	40.000	0.00	0.00	0.00	3.18
2933	13464	6.404074	GCAAAGAGATTATGAACAGGGAACAG	60.404	42.308	0.00	0.00	0.00	3.16
2934	13465	6.627087	AAGAGATTATGAACAGGGAACAGA	57.373	37.500	0.00	0.00	0.00	3.41
2935	13466	6.821616	AGAGATTATGAACAGGGAACAGAT	57.178	37.500	0.00	0.00	0.00	2.90
2936	13467	6.590068	AGAGATTATGAACAGGGAACAGATG	58.410	40.000	0.00	0.00	0.00	2.90
2937	13468	5.128919	AGATTATGAACAGGGAACAGATGC	58.871	41.667	0.00	0.00	0.00	3.91
2938	13469	2.134789	ATGAACAGGGAACAGATGCC	57.865	50.000	0.00	0.00	40.55	4.40
2948	13479	5.060662	GGGAACAGATGCCTTTTTCTTAC	57.939	43.478	0.00	0.00	36.40	2.34
2949	13480	4.522789	GGGAACAGATGCCTTTTTCTTACA	59.477	41.667	0.00	0.00	36.40	2.41
2950	13481	5.461526	GGAACAGATGCCTTTTTCTTACAC	58.538	41.667	0.00	0.00	0.00	2.90
2951	13482	5.241728	GGAACAGATGCCTTTTTCTTACACT	59.758	40.000	0.00	0.00	0.00	3.55
2952	13483	5.695851	ACAGATGCCTTTTTCTTACACTG	57.304	39.130	0.00	0.00	0.00	3.66
2953	13484	5.376625	ACAGATGCCTTTTTCTTACACTGA	58.623	37.500	0.00	0.00	0.00	3.41
2954	13485	5.239525	ACAGATGCCTTTTTCTTACACTGAC	59.760	40.000	0.00	0.00	0.00	3.51
3027	13594	3.375610	AGATATGGTATAGCGACTCAGCG	59.624	47.826	0.00	0.00	43.00	5.18
3071	13638	1.679977	TCTTCATGCTGCTTGGCCC	60.680	57.895	14.55	0.00	0.00	5.80
3073	13640	1.945354	CTTCATGCTGCTTGGCCCTG	61.945	60.000	14.55	0.00	0.00	4.45
3074	13641	4.143333	CATGCTGCTTGGCCCTGC	62.143	66.667	0.00	4.99	0.00	4.85
3092	13659	4.142315	CCCTGCCAAATGTCTTCATGTAAG	60.142	45.833	0.00	0.00	34.19	2.34
3134	13701	3.807622	CGTTACACACAAGAACCAGTGAT	59.192	43.478	0.00	0.00	39.03	3.06
3136	13703	2.851195	ACACACAAGAACCAGTGATCC	58.149	47.619	0.00	0.00	39.03	3.36
3147	13726	0.798776	CAGTGATCCCTTCGCAACAC	59.201	55.000	0.00	0.00	37.31	3.32
3186	13765	4.753233	AGAAGAACTGACGAATGATCAGG	58.247	43.478	0.09	0.00	46.60	3.86
3187	13766	2.898705	AGAACTGACGAATGATCAGGC	58.101	47.619	0.09	0.00	46.60	4.85
3188	13767	2.234661	AGAACTGACGAATGATCAGGCA	59.765	45.455	0.09	0.00	46.60	4.75
3189	13768	2.306341	ACTGACGAATGATCAGGCAG	57.694	50.000	13.37	13.37	46.60	4.85
3269	13855	8.763356	GTTACAGATCAGCTCATGAAGATAAAG	58.237	37.037	0.00	0.00	42.53	1.85
3270	13856	7.122138	ACAGATCAGCTCATGAAGATAAAGA	57.878	36.000	0.00	0.00	42.53	2.52
3271	13857	7.211573	ACAGATCAGCTCATGAAGATAAAGAG	58.788	38.462	0.00	0.00	42.53	2.85
3273	13859	4.701765	TCAGCTCATGAAGATAAAGAGGC	58.298	43.478	0.00	0.00	34.02	4.70
3308	13897	2.820178	TGCCAGGACAACAGAGAGATA	58.180	47.619	0.00	0.00	0.00	1.98
3337	13926	2.632512	TGACAAGCATGTGTAGACCAGA	59.367	45.455	0.00	0.00	40.74	3.86
3338	13927	3.261643	TGACAAGCATGTGTAGACCAGAT	59.738	43.478	0.00	0.00	40.74	2.90
3339	13928	4.466015	TGACAAGCATGTGTAGACCAGATA	59.534	41.667	0.00	0.00	40.74	1.98
3341	13930	5.804639	ACAAGCATGTGTAGACCAGATAAA	58.195	37.500	0.00	0.00	38.69	1.40
3389	13978	7.309133	CCTGATTCCAGTTACAATGTTAAGCAA	60.309	37.037	0.00	0.00	38.74	3.91
3390	13979	8.121305	TGATTCCAGTTACAATGTTAAGCAAT	57.879	30.769	0.00	0.00	0.00	3.56
3391	13980	9.237187	TGATTCCAGTTACAATGTTAAGCAATA	57.763	29.630	0.00	0.00	0.00	1.90
3409	13998	4.499183	CAATATACATTCTCGCTCTCCCC	58.501	47.826	0.00	0.00	0.00	4.81
3427	14016	2.419198	GCCAGCCATCGATCGTCT	59.581	61.111	15.94	5.64	0.00	4.18
3436	14025	3.943034	CGATCGTCTCGCCTCGCT	61.943	66.667	7.03	0.00	41.14	4.93

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
14	15	9.004146	GCGAGAAAAACTTTCAATCTATTCATC	57.996	33.333	2.25	0.00	0.00	2.92
15	16	8.514594	TGCGAGAAAAACTTTCAATCTATTCAT	58.485	29.630	2.25	0.00	0.00	2.57
17	18	8.728088	TTGCGAGAAAAACTTTCAATCTATTC	57.272	30.769	2.25	0.00	0.00	1.75
18	19	9.528018	TTTTGCGAGAAAAACTTTCAATCTATT	57.472	25.926	2.25	0.00	0.00	1.73
19	20	9.528018	TTTTTGCGAGAAAAACTTTCAATCTAT	57.472	25.926	2.25	0.00	0.00	1.98
20	21	8.918961	TTTTTGCGAGAAAAACTTTCAATCTA	57.081	26.923	2.25	0.00	0.00	1.98
21	22	7.826260	TTTTTGCGAGAAAAACTTTCAATCT	57.174	28.000	2.25	0.00	0.00	2.40
45	46	5.491323	TTGCGGGGATAAAAGGAATTTTT	57.509	34.783	0.00	0.00	41.68	1.94
157	188	1.003116	GACTTGATGATGATGCGTGCC	60.003	52.381	0.00	0.00	0.00	5.01
320	355	0.251916	GATCGTGTGGGTGGATTGGA	59.748	55.000	0.00	0.00	0.00	3.53
334	4499	3.379445	AGGAACGGCGGTGATCGT	61.379	61.111	13.24	2.73	41.72	3.73
351	4516	3.661648	GAAGGGGGAAGCTGGGCA	61.662	66.667	0.00	0.00	0.00	5.36
600	5426	1.607801	GCAAGGACATTTCTGGGCCC	61.608	60.000	17.59	17.59	0.00	5.80
601	5427	0.899717	TGCAAGGACATTTCTGGGCC	60.900	55.000	0.00	0.00	0.00	5.80
602	5428	0.529378	CTGCAAGGACATTTCTGGGC	59.471	55.000	0.00	0.00	0.00	5.36
604	5430	3.087031	ACATCTGCAAGGACATTTCTGG	58.913	45.455	0.00	0.00	0.00	3.86
605	5431	3.754850	TCACATCTGCAAGGACATTTCTG	59.245	43.478	0.00	0.00	0.00	3.02
606	5432	4.008330	CTCACATCTGCAAGGACATTTCT	58.992	43.478	0.00	0.00	0.00	2.52
607	5433	3.755378	ACTCACATCTGCAAGGACATTTC	59.245	43.478	0.00	0.00	0.00	2.17
610	5450	3.244665	TGAACTCACATCTGCAAGGACAT	60.245	43.478	0.00	0.00	0.00	3.06
780	5672	5.868801	CACCAAATTATGTGCTTAACTTGGG	59.131	40.000	16.70	7.20	40.85	4.12
912	5875	2.676342	AGTCAGAACGGAACACAACAAC	59.324	45.455	0.00	0.00	0.00	3.32
1152	11615	4.472833	AGAGATACCAAGGCTTCTGTTGAT	59.527	41.667	0.00	0.00	0.00	2.57
1338	11801	3.181464	GGTCAGCTAGATAACCAAGACCC	60.181	52.174	0.00	0.00	38.62	4.46
1430	11893	1.423541	ACAGATACCTGCAACCAACCA	59.576	47.619	0.00	0.00	44.16	3.67
1459	11922	4.002906	CTGCCTTACAGTCAACAAGGTA	57.997	45.455	2.41	0.00	41.86	3.08
1874	12339	1.000163	GCCTGAGTCGAAGTGAGACAA	60.000	52.381	0.00	0.00	40.84	3.18
1912	12377	4.959210	AGTCAGTGCTGTCCTATACTCAAT	59.041	41.667	0.00	0.00	0.00	2.57
1980	12445	1.264020	GCGAATGTGAGCTCAACAACA	59.736	47.619	20.19	12.80	0.00	3.33
2440	12911	0.535335	TACTGGATTCAGGGCGACAC	59.465	55.000	5.84	0.00	44.99	3.67
2574	13066	1.398451	CGCGCTACCAAAACAAGTCTG	60.398	52.381	5.56	0.00	0.00	3.51
2774	13290	0.674895	GCTCAATGACGCCTGAACCT	60.675	55.000	0.00	0.00	0.00	3.50
2834	13350	6.014584	TGAGAAGTTATGAGCAAGAACCACTA	60.015	38.462	0.00	0.00	0.00	2.74
2856	13387	2.159268	TGTTGCCATGTGTTGTGTTGAG	60.159	45.455	0.00	0.00	0.00	3.02
2863	13394	1.925847	GTGTTGTGTTGCCATGTGTTG	59.074	47.619	0.00	0.00	0.00	3.33
2864	13395	1.547820	TGTGTTGTGTTGCCATGTGTT	59.452	42.857	0.00	0.00	0.00	3.32
2865	13396	1.180907	TGTGTTGTGTTGCCATGTGT	58.819	45.000	0.00	0.00	0.00	3.72
2866	13397	2.128821	CATGTGTTGTGTTGCCATGTG	58.871	47.619	0.00	0.00	0.00	3.21
2867	13398	1.068895	CCATGTGTTGTGTTGCCATGT	59.931	47.619	0.00	0.00	32.87	3.21
2868	13399	1.785768	CCATGTGTTGTGTTGCCATG	58.214	50.000	0.00	0.00	34.18	3.66
2869	13400	0.033781	GCCATGTGTTGTGTTGCCAT	59.966	50.000	0.00	0.00	0.00	4.40
2870	13401	1.325476	TGCCATGTGTTGTGTTGCCA	61.325	50.000	0.00	0.00	0.00	4.92
2871	13402	0.875474	GTGCCATGTGTTGTGTTGCC	60.875	55.000	0.00	0.00	0.00	4.52
2872	13403	0.179116	TGTGCCATGTGTTGTGTTGC	60.179	50.000	0.00	0.00	0.00	4.17
2873	13404	1.135170	TGTGTGCCATGTGTTGTGTTG	60.135	47.619	0.00	0.00	0.00	3.33
2874	13405	1.180907	TGTGTGCCATGTGTTGTGTT	58.819	45.000	0.00	0.00	0.00	3.32
2875	13406	1.067364	CATGTGTGCCATGTGTTGTGT	59.933	47.619	0.00	0.00	44.96	3.72
2876	13407	1.773410	CATGTGTGCCATGTGTTGTG	58.227	50.000	0.00	0.00	44.96	3.33
2889	13420	7.715657	TCTTTGCTTTCTTTCATAACATGTGT	58.284	30.769	0.00	0.00	0.00	3.72
2904	13435	6.375455	TCCCTGTTCATAATCTCTTTGCTTTC	59.625	38.462	0.00	0.00	0.00	2.62
2920	13451	1.067295	AGGCATCTGTTCCCTGTTCA	58.933	50.000	0.00	0.00	0.00	3.18
2921	13452	2.206576	AAGGCATCTGTTCCCTGTTC	57.793	50.000	0.00	0.00	0.00	3.18
2922	13453	2.683211	AAAGGCATCTGTTCCCTGTT	57.317	45.000	0.00	0.00	0.00	3.16
2923	13454	2.683211	AAAAGGCATCTGTTCCCTGT	57.317	45.000	0.00	0.00	0.00	4.00
2924	13455	3.160269	AGAAAAAGGCATCTGTTCCCTG	58.840	45.455	0.00	0.00	0.00	4.45
2925	13456	3.532641	AGAAAAAGGCATCTGTTCCCT	57.467	42.857	0.00	0.00	0.00	4.20
2926	13457	4.522789	TGTAAGAAAAAGGCATCTGTTCCC	59.477	41.667	0.00	0.00	0.00	3.97
2927	13458	5.241728	AGTGTAAGAAAAAGGCATCTGTTCC	59.758	40.000	0.00	0.00	0.00	3.62
2928	13459	6.017109	TCAGTGTAAGAAAAAGGCATCTGTTC	60.017	38.462	0.00	0.00	0.00	3.18
2929	13460	5.827797	TCAGTGTAAGAAAAAGGCATCTGTT	59.172	36.000	0.00	0.00	0.00	3.16
2930	13461	5.239525	GTCAGTGTAAGAAAAAGGCATCTGT	59.760	40.000	0.00	0.00	0.00	3.41
2931	13462	5.471456	AGTCAGTGTAAGAAAAAGGCATCTG	59.529	40.000	0.00	0.00	0.00	2.90
2932	13463	5.471456	CAGTCAGTGTAAGAAAAAGGCATCT	59.529	40.000	0.00	0.00	0.00	2.90
2933	13464	5.470098	TCAGTCAGTGTAAGAAAAAGGCATC	59.530	40.000	0.00	0.00	0.00	3.91
2934	13465	5.376625	TCAGTCAGTGTAAGAAAAAGGCAT	58.623	37.500	0.00	0.00	0.00	4.40
2935	13466	4.776349	TCAGTCAGTGTAAGAAAAAGGCA	58.224	39.130	0.00	0.00	0.00	4.75
2936	13467	5.065988	TGTTCAGTCAGTGTAAGAAAAAGGC	59.934	40.000	0.00	0.00	0.00	4.35
2937	13468	6.677781	TGTTCAGTCAGTGTAAGAAAAAGG	57.322	37.500	0.00	0.00	0.00	3.11
2938	13469	8.826710	TGTATGTTCAGTCAGTGTAAGAAAAAG	58.173	33.333	0.00	0.00	0.00	2.27
2939	13470	8.725405	TGTATGTTCAGTCAGTGTAAGAAAAA	57.275	30.769	0.00	0.00	0.00	1.94
2940	13471	8.773645	CATGTATGTTCAGTCAGTGTAAGAAAA	58.226	33.333	0.00	0.00	0.00	2.29
2941	13472	7.931407	ACATGTATGTTCAGTCAGTGTAAGAAA	59.069	33.333	0.00	0.00	37.90	2.52
2942	13473	7.441836	ACATGTATGTTCAGTCAGTGTAAGAA	58.558	34.615	0.00	0.00	37.90	2.52
2943	13474	6.993079	ACATGTATGTTCAGTCAGTGTAAGA	58.007	36.000	0.00	0.00	37.90	2.10
2944	13475	7.812669	TGTACATGTATGTTCAGTCAGTGTAAG	59.187	37.037	9.18	0.00	41.97	2.34
2945	13476	7.662897	TGTACATGTATGTTCAGTCAGTGTAA	58.337	34.615	9.18	0.00	41.97	2.41
2946	13477	7.222000	TGTACATGTATGTTCAGTCAGTGTA	57.778	36.000	9.18	0.00	41.97	2.90
2947	13478	6.096673	TGTACATGTATGTTCAGTCAGTGT	57.903	37.500	9.18	0.00	41.97	3.55
2948	13479	6.036408	CCATGTACATGTATGTTCAGTCAGTG	59.964	42.308	29.25	8.70	40.54	3.66
2949	13480	6.108687	CCATGTACATGTATGTTCAGTCAGT	58.891	40.000	29.25	0.00	40.54	3.41
2950	13481	6.036408	CACCATGTACATGTATGTTCAGTCAG	59.964	42.308	29.25	14.48	40.54	3.51
2951	13482	5.874261	CACCATGTACATGTATGTTCAGTCA	59.126	40.000	29.25	0.00	40.54	3.41
2952	13483	6.106003	TCACCATGTACATGTATGTTCAGTC	58.894	40.000	29.25	0.00	40.54	3.51
2953	13484	6.048732	TCACCATGTACATGTATGTTCAGT	57.951	37.500	29.25	16.88	40.54	3.41
2954	13485	7.928167	ACTATCACCATGTACATGTATGTTCAG	59.072	37.037	29.25	23.17	40.54	3.02
3043	13610	3.131933	AGCAGCATGAAGACTACACTAGG	59.868	47.826	0.00	0.00	39.69	3.02
3071	13638	5.885230	TCTTACATGAAGACATTTGGCAG	57.115	39.130	0.00	0.00	39.36	4.85
3092	13659	2.225467	GCCTCTGATGCCCTTACAATC	58.775	52.381	0.00	0.00	0.00	2.67
3134	13701	1.673920	GAGTTTTGTGTTGCGAAGGGA	59.326	47.619	0.00	0.00	0.00	4.20
3136	13703	3.420839	AAGAGTTTTGTGTTGCGAAGG	57.579	42.857	0.00	0.00	0.00	3.46
3147	13726	4.207165	TCTTCTCCACCCAAAGAGTTTTG	58.793	43.478	0.00	0.00	42.66	2.44
3186	13765	6.609237	TTCTGTAAATCAGCATGTATCTGC	57.391	37.500	0.00	0.00	43.32	4.26
3187	13766	8.429493	TCTTTCTGTAAATCAGCATGTATCTG	57.571	34.615	0.00	0.00	43.32	2.90
3269	13855	2.858646	GCAAAGGTTCAGAAAACGCCTC	60.859	50.000	0.00	0.00	0.00	4.70
3270	13856	1.067060	GCAAAGGTTCAGAAAACGCCT	59.933	47.619	0.00	0.00	0.00	5.52
3271	13857	1.487482	GCAAAGGTTCAGAAAACGCC	58.513	50.000	0.00	0.00	0.00	5.68
3273	13859	2.543653	CCTGGCAAAGGTTCAGAAAACG	60.544	50.000	0.00	0.00	41.74	3.60
3327	13916	8.483758	GGAATTACTTCCTTTATCTGGTCTACA	58.516	37.037	4.64	0.00	46.44	2.74
3328	13917	8.890124	GGAATTACTTCCTTTATCTGGTCTAC	57.110	38.462	4.64	0.00	46.44	2.59
3389	13978	2.755655	CGGGGAGAGCGAGAATGTATAT	59.244	50.000	0.00	0.00	0.00	0.86
3390	13979	2.160205	CGGGGAGAGCGAGAATGTATA	58.840	52.381	0.00	0.00	0.00	1.47
3391	13980	0.962489	CGGGGAGAGCGAGAATGTAT	59.038	55.000	0.00	0.00	0.00	2.29
3409	13998	3.032609	GACGATCGATGGCTGGCG	61.033	66.667	24.34	0.77	0.00	5.69

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.