AutoCloner

Multiple sequence alignment - TraesCS1B01G101300

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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	TraesCS1B01G101300	chr1B	100.000	3739	0	0	1	3739	111053464	111049726	0.000000e+00	6905.0
1	TraesCS1B01G101300	chr1B	82.781	755	107	15	2851	3599	111033065	111032328	0.000000e+00	652.0
2	TraesCS1B01G101300	chr1B	89.286	168	16	2	723	890	171844166	171844331	3.780000e-50	209.0
3	TraesCS1B01G101300	chr1A	92.569	1090	53	12	1866	2952	68459800	68458736	0.000000e+00	1539.0
4	TraesCS1B01G101300	chr1A	91.945	869	46	16	914	1772	68460647	68459793	0.000000e+00	1195.0
5	TraesCS1B01G101300	chr1A	94.354	673	24	4	2954	3625	68457845	68457186	0.000000e+00	1020.0
6	TraesCS1B01G101300	chr1A	81.444	900	139	19	1	893	349219922	349220800	0.000000e+00	712.0
7	TraesCS1B01G101300	chr1A	82.407	756	108	14	2851	3599	68418697	68417960	1.460000e-178	636.0
8	TraesCS1B01G101300	chr1D	93.039	1020	39	18	2749	3739	69196369	69195353	0.000000e+00	1461.0
9	TraesCS1B01G101300	chr1D	94.118	884	40	4	1866	2743	69197307	69196430	0.000000e+00	1334.0
10	TraesCS1B01G101300	chr1D	92.823	836	42	10	953	1772	69198133	69197300	0.000000e+00	1195.0
11	TraesCS1B01G101300	chr1D	82.115	766	114	13	2843	3599	69189482	69188731	5.270000e-178	634.0
12	TraesCS1B01G101300	chr5B	94.774	861	40	5	1	859	195371405	195372262	0.000000e+00	1336.0
13	TraesCS1B01G101300	chr5B	90.419	167	14	2	723	889	37720646	37720482	6.290000e-53	219.0
14	TraesCS1B01G101300	chr6B	92.584	890	54	5	1	889	56038289	56039167	0.000000e+00	1267.0
15	TraesCS1B01G101300	chr6B	89.593	663	57	8	231	889	674715673	674715019	0.000000e+00	832.0
16	TraesCS1B01G101300	chr6B	89.820	167	15	2	723	889	79514205	79514369	2.930000e-51	213.0
17	TraesCS1B01G101300	chr6B	100.000	36	0	0	1830	1865	669350021	669350056	2.410000e-07	67.6
18	TraesCS1B01G101300	chr3B	92.174	575	44	1	1	574	762434799	762435373	0.000000e+00	811.0
19	TraesCS1B01G101300	chr3B	88.820	322	27	4	572	889	762447982	762448298	1.630000e-103	387.0
20	TraesCS1B01G101300	chr3B	90.476	168	14	2	723	890	737252843	737253008	1.750000e-53	220.0
21	TraesCS1B01G101300	chr3B	80.970	268	47	4	3152	3417	66820866	66820601	3.780000e-50	209.0
22	TraesCS1B01G101300	chr7D	82.828	891	130	12	1	889	96640446	96639577	0.000000e+00	776.0
23	TraesCS1B01G101300	chr7D	100.000	33	0	0	1833	1865	5486571	5486539	1.120000e-05	62.1
24	TraesCS1B01G101300	chr4D	82.399	892	133	14	1	889	101649009	101649879	0.000000e+00	756.0
25	TraesCS1B01G101300	chr7B	77.778	891	163	24	4	889	169379438	169378578	1.990000e-142	516.0
26	TraesCS1B01G101300	chr7B	73.671	414	92	15	3205	3604	640513844	640513434	1.080000e-30	145.0
27	TraesCS1B01G101300	chr4A	89.881	168	15	2	723	890	647854032	647853867	8.130000e-52	215.0
28	TraesCS1B01G101300	chr4A	95.000	60	3	0	1772	1831	626725528	626725469	1.110000e-15	95.3
29	TraesCS1B01G101300	chr2B	72.792	566	124	25	2197	2739	691416621	691416063	8.310000e-37	165.0
30	TraesCS1B01G101300	chr2B	73.381	417	87	17	2188	2586	691271457	691271867	2.340000e-27	134.0
31	TraesCS1B01G101300	chr2A	72.948	536	117	17	2188	2703	713532062	713532589	1.070000e-35	161.0
32	TraesCS1B01G101300	chr2D	72.474	574	130	23	2188	2739	575239742	575240309	3.870000e-35	159.0
33	TraesCS1B01G101300	chr7A	73.671	414	92	15	3205	3604	669406338	669405928	1.080000e-30	145.0
34	TraesCS1B01G101300	chr3A	96.667	60	2	0	1772	1831	472549	472490	2.380000e-17	100.0
35	TraesCS1B01G101300	chr6D	98.113	53	1	0	1774	1826	318993651	318993703	3.980000e-15	93.5
36	TraesCS1B01G101300	chr5D	93.333	60	4	0	1772	1831	542411951	542412010	5.140000e-14	89.8
37	TraesCS1B01G101300	chr4B	97.368	38	1	0	1832	1869	235388292	235388255	8.670000e-07	65.8

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	TraesCS1B01G101300	chr1B	111049726	111053464	3738	True	6905.000000	6905	100.000000	1	3739	1	chr1B.!!$R2	3738
1	TraesCS1B01G101300	chr1B	111032328	111033065	737	True	652.000000	652	82.781000	2851	3599	1	chr1B.!!$R1	748
2	TraesCS1B01G101300	chr1A	68457186	68460647	3461	True	1251.333333	1539	92.956000	914	3625	3	chr1A.!!$R2	2711
3	TraesCS1B01G101300	chr1A	349219922	349220800	878	False	712.000000	712	81.444000	1	893	1	chr1A.!!$F1	892
4	TraesCS1B01G101300	chr1A	68417960	68418697	737	True	636.000000	636	82.407000	2851	3599	1	chr1A.!!$R1	748
5	TraesCS1B01G101300	chr1D	69195353	69198133	2780	True	1330.000000	1461	93.326667	953	3739	3	chr1D.!!$R2	2786
6	TraesCS1B01G101300	chr1D	69188731	69189482	751	True	634.000000	634	82.115000	2843	3599	1	chr1D.!!$R1	756
7	TraesCS1B01G101300	chr5B	195371405	195372262	857	False	1336.000000	1336	94.774000	1	859	1	chr5B.!!$F1	858
8	TraesCS1B01G101300	chr6B	56038289	56039167	878	False	1267.000000	1267	92.584000	1	889	1	chr6B.!!$F1	888
9	TraesCS1B01G101300	chr6B	674715019	674715673	654	True	832.000000	832	89.593000	231	889	1	chr6B.!!$R1	658
10	TraesCS1B01G101300	chr3B	762434799	762435373	574	False	811.000000	811	92.174000	1	574	1	chr3B.!!$F2	573
11	TraesCS1B01G101300	chr7D	96639577	96640446	869	True	776.000000	776	82.828000	1	889	1	chr7D.!!$R2	888
12	TraesCS1B01G101300	chr4D	101649009	101649879	870	False	756.000000	756	82.399000	1	889	1	chr4D.!!$F1	888
13	TraesCS1B01G101300	chr7B	169378578	169379438	860	True	516.000000	516	77.778000	4	889	1	chr7B.!!$R1	885

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
109	111	0.108804	GAGCACCGGACGAGATCAAA	60.109	55.0	9.46	0.00	2.69	F
937	951	0.234884	GTGTTTTGAAGACGGCCTCG	59.765	55.0	0.00	43.02	4.63	F
1213	1229	0.376152	GGTTGCATGCTGATCGAGTG	59.624	55.0	20.33	0.00	3.51	F
1263	1291	0.467384	CATCAGGCGATCACCTCCTT	59.533	55.0	0.00	38.26	3.36	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1864	1899	0.322546	GACCTGGATCACCACCAACC	60.323	60.000	0.00	0.00	41.77	3.77	R
1956	1991	1.346395	ACGGCTGACATGAACAGGTAA	59.654	47.619	19.70	0.00	36.09	2.85	R
2496	2551	1.550976	GGAGAGGAGGAACATGTTCGT	59.449	52.381	28.67	28.67	40.37	3.85	R
3018	4064	2.203337	GTTGGTGCTGGTGCCTGA	60.203	61.111	0.00	0.00	38.71	3.86	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
31	33	0.804989	GCAACCTCACCGAAATCCTG	59.195	55.000	0.00	0.00	0.00	3.86
85	87	3.309410	GGCTGGCTGGGATTATATTGGAT	60.309	47.826	0.00	0.00	0.00	3.41
109	111	0.108804	GAGCACCGGACGAGATCAAA	60.109	55.000	9.46	0.00	0.00	2.69
168	170	1.274447	GGCCTACGACCTACAGTTTGT	59.726	52.381	0.00	0.00	0.00	2.83
174	176	4.330944	ACGACCTACAGTTTGTTGATCA	57.669	40.909	0.00	0.00	0.00	2.92
400	404	1.134580	CAGTATGGAGTCAGGTGGCAG	60.135	57.143	0.00	0.00	0.00	4.85
441	445	1.228245	GAACCCAAGCAGCCAGACA	60.228	57.895	0.00	0.00	0.00	3.41
622	626	2.115427	TGATCAGCCAAATCCGGAGTA	58.885	47.619	11.34	0.00	0.00	2.59
707	711	5.346281	CCGTGAGAGTGTAGAAATCAGTTTC	59.654	44.000	0.00	0.00	43.24	2.78
738	747	3.813166	CGCCTTTTGTCTCTGTTTTCCTA	59.187	43.478	0.00	0.00	0.00	2.94
751	762	8.908903	TCTCTGTTTTCCTATCTTCAGAGATAC	58.091	37.037	15.56	0.00	46.77	2.24
906	920	4.489679	AAAAGAACCAGCGATTCTGAAC	57.510	40.909	0.00	0.00	45.72	3.18
907	921	1.714794	AGAACCAGCGATTCTGAACG	58.285	50.000	0.00	0.24	45.72	3.95
928	942	3.490526	CGCCTCAAAATGGTGTTTTGAAG	59.509	43.478	14.54	10.86	44.67	3.02
937	951	0.234884	GTGTTTTGAAGACGGCCTCG	59.765	55.000	0.00	0.00	43.02	4.63
941	955	1.469335	TTTGAAGACGGCCTCGAGGT	61.469	55.000	31.43	13.35	40.11	3.85
945	959	4.070552	GACGGCCTCGAGGTGCTT	62.071	66.667	31.43	14.37	40.11	3.91
946	960	3.591254	GACGGCCTCGAGGTGCTTT	62.591	63.158	31.43	12.57	40.11	3.51
999	1013	8.981647	ACATGCTTTTTCTTTACAATCATTGAC	58.018	29.630	3.79	0.00	0.00	3.18
1039	1053	6.179906	ACTCCCCATTGATACATGAACTAG	57.820	41.667	0.00	0.00	0.00	2.57
1121	1136	7.347222	TCCATTAGTAAGAGAAATCAGGGCTAA	59.653	37.037	0.00	0.00	0.00	3.09
1126	1141	2.501723	AGAGAAATCAGGGCTAAGCGAA	59.498	45.455	0.00	0.00	0.00	4.70
1213	1229	0.376152	GGTTGCATGCTGATCGAGTG	59.624	55.000	20.33	0.00	0.00	3.51
1261	1289	1.596477	GCATCAGGCGATCACCTCC	60.596	63.158	0.00	0.00	38.26	4.30
1262	1290	2.037620	GCATCAGGCGATCACCTCCT	62.038	60.000	0.00	0.00	38.26	3.69
1263	1291	0.467384	CATCAGGCGATCACCTCCTT	59.533	55.000	0.00	0.00	38.26	3.36
1264	1292	0.755686	ATCAGGCGATCACCTCCTTC	59.244	55.000	0.00	0.00	38.26	3.46
1265	1293	0.614697	TCAGGCGATCACCTCCTTCA	60.615	55.000	0.00	0.00	38.26	3.02
1413	1448	0.889186	GGGAAACAAAGCGCCTCTCA	60.889	55.000	2.29	0.00	0.00	3.27
1525	1560	3.131478	TCATCGACCGAGCGCTGA	61.131	61.111	18.48	5.53	34.50	4.26
1749	1784	2.107141	GATTGCTCTAGCGGCGGT	59.893	61.111	18.21	18.21	45.83	5.68
1765	1800	4.626081	GTGTGCTCACCTGGCCGT	62.626	66.667	7.70	0.00	38.51	5.68
1766	1801	3.872603	TGTGCTCACCTGGCCGTT	61.873	61.111	0.00	0.00	0.00	4.44
1767	1802	3.357079	GTGCTCACCTGGCCGTTG	61.357	66.667	0.00	0.00	0.00	4.10
1768	1803	4.641645	TGCTCACCTGGCCGTTGG	62.642	66.667	0.00	2.53	0.00	3.77
1769	1804	4.643387	GCTCACCTGGCCGTTGGT	62.643	66.667	8.83	8.83	36.96	3.67
1781	1816	2.281208	GTTGGTGGCAGTGGCGTA	60.281	61.111	12.58	0.00	42.47	4.42
1782	1817	2.031919	TTGGTGGCAGTGGCGTAG	59.968	61.111	12.58	0.00	42.47	3.51
1783	1818	3.545124	TTGGTGGCAGTGGCGTAGG	62.545	63.158	12.58	0.00	42.47	3.18
1796	1831	1.257743	GCGTAGGCAGGATATCTCCA	58.742	55.000	1.75	0.00	44.79	3.86
1797	1832	1.067495	GCGTAGGCAGGATATCTCCAC	60.067	57.143	1.75	3.31	44.79	4.02
1798	1833	1.200252	CGTAGGCAGGATATCTCCACG	59.800	57.143	2.05	9.90	44.79	4.94
1799	1834	1.067495	GTAGGCAGGATATCTCCACGC	60.067	57.143	2.05	1.81	44.79	5.34
1800	1835	4.683432	GCAGGATATCTCCACGCC	57.317	61.111	2.05	0.00	44.79	5.68
1801	1836	1.004440	GCAGGATATCTCCACGCCC	60.004	63.158	2.05	0.00	44.79	6.13
1802	1837	1.674057	CAGGATATCTCCACGCCCC	59.326	63.158	2.05	0.00	44.79	5.80
1803	1838	1.908793	AGGATATCTCCACGCCCCG	60.909	63.158	2.05	0.00	44.79	5.73
1804	1839	2.657237	GATATCTCCACGCCCCGG	59.343	66.667	0.00	0.00	0.00	5.73
1805	1840	2.923035	ATATCTCCACGCCCCGGG	60.923	66.667	15.80	15.80	0.00	5.73
1835	1870	2.745884	GCACAGTGCATACGGCCA	60.746	61.111	21.22	0.00	44.26	5.36
1836	1871	2.753966	GCACAGTGCATACGGCCAG	61.754	63.158	21.22	0.00	44.26	4.85
1837	1872	2.108514	CACAGTGCATACGGCCAGG	61.109	63.158	2.24	0.00	43.89	4.45
1838	1873	2.514592	CAGTGCATACGGCCAGGG	60.515	66.667	2.24	0.00	43.89	4.45
1839	1874	4.489771	AGTGCATACGGCCAGGGC	62.490	66.667	2.24	1.81	43.89	5.19
1840	1875	4.794648	GTGCATACGGCCAGGGCA	62.795	66.667	14.59	3.58	43.89	5.36
1841	1876	4.488136	TGCATACGGCCAGGGCAG	62.488	66.667	14.59	10.97	43.89	4.85
1971	2006	3.260884	GGGAGTCTTACCTGTTCATGTCA	59.739	47.826	0.00	0.00	0.00	3.58
2165	2200	1.073216	ACATCGCGTCGCTGAAGAAG	61.073	55.000	16.36	4.68	0.00	2.85
2173	2208	2.821810	GCTGAAGAAGCGCCTCCC	60.822	66.667	2.29	0.00	43.45	4.30
2429	2484	2.890808	TGATACAGAAGGCTAAGGCG	57.109	50.000	0.00	0.00	39.81	5.52
2576	2631	4.157120	GGCGAGCCGGTGTATGGT	62.157	66.667	1.90	0.00	0.00	3.55
2744	2799	6.811253	TGATTACACGCCTGAAAAATAACT	57.189	33.333	0.00	0.00	0.00	2.24
2746	2801	7.745015	TGATTACACGCCTGAAAAATAACTAC	58.255	34.615	0.00	0.00	0.00	2.73
2755	2865	7.118680	CGCCTGAAAAATAACTACTCCAGTTTA	59.881	37.037	0.00	0.00	45.54	2.01
2766	2876	7.482169	ACTACTCCAGTTTATTCACAGATCA	57.518	36.000	0.00	0.00	31.59	2.92
2870	3026	6.127535	ACAAATGATTAAAGCTCTGATGGTGG	60.128	38.462	0.00	0.00	0.00	4.61
2900	3056	2.480419	GGAAGTTCAGACAACATCCACG	59.520	50.000	5.01	0.00	37.80	4.94
3018	4064	6.536582	CGAGATGAGAACTACAAAATGACCAT	59.463	38.462	0.00	0.00	0.00	3.55
3038	4084	3.964875	GGCACCAGCACCAACACG	61.965	66.667	0.00	0.00	44.61	4.49
3671	4724	6.811253	TTAACCTTAGGCCATTATTATGCG	57.189	37.500	5.01	0.00	0.00	4.73
3674	4727	4.760204	ACCTTAGGCCATTATTATGCGTTC	59.240	41.667	5.01	0.00	0.00	3.95
3711	4764	5.835113	AACACATGTCCCAAGCATATTAC	57.165	39.130	0.00	0.00	0.00	1.89

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
25	27	1.251251	GCACAAACTGAGGCAGGATT	58.749	50.000	0.00	0.00	35.51	3.01
31	33	0.595825	GCAAGTGCACAAACTGAGGC	60.596	55.000	21.04	6.47	41.59	4.70
65	67	5.183530	TCATCCAATATAATCCCAGCCAG	57.816	43.478	0.00	0.00	0.00	4.85
85	87	2.678580	TCGTCCGGTGCTCCATCA	60.679	61.111	0.00	0.00	0.00	3.07
109	111	1.229625	TCCTCCACCTGCTGTCCAT	60.230	57.895	0.00	0.00	0.00	3.41
168	170	0.669318	GTTCGTCGCAGGGTGATCAA	60.669	55.000	0.00	0.00	0.00	2.57
174	176	3.692406	GGAGGTTCGTCGCAGGGT	61.692	66.667	0.00	0.00	0.00	4.34
503	507	0.537188	GATCGACCTCAGCCCTTTCA	59.463	55.000	0.00	0.00	0.00	2.69
622	626	1.181098	AAACGCCATTGCTCCAGCTT	61.181	50.000	0.00	0.00	42.66	3.74
707	711	1.681264	AGACAAAAGGCGGACCAAAAG	59.319	47.619	0.00	0.00	39.06	2.27
738	747	4.695396	CTGCTGCAAGTATCTCTGAAGAT	58.305	43.478	3.02	0.00	44.57	2.40
774	785	4.527583	GGAGAGCAGCGAGGCCAG	62.528	72.222	5.01	0.00	0.00	4.85
896	910	3.419915	CATTTTGAGGCGTTCAGAATCG	58.580	45.455	5.33	0.00	38.25	3.34
897	911	3.191371	ACCATTTTGAGGCGTTCAGAATC	59.809	43.478	5.33	0.00	38.25	2.52
898	912	3.057315	CACCATTTTGAGGCGTTCAGAAT	60.057	43.478	3.21	3.21	40.25	2.40
899	913	2.293122	CACCATTTTGAGGCGTTCAGAA	59.707	45.455	0.00	0.00	37.07	3.02
900	914	1.879380	CACCATTTTGAGGCGTTCAGA	59.121	47.619	0.00	0.00	37.07	3.27
901	915	1.608590	ACACCATTTTGAGGCGTTCAG	59.391	47.619	0.00	0.00	37.07	3.02
902	916	1.686355	ACACCATTTTGAGGCGTTCA	58.314	45.000	0.00	0.00	0.00	3.18
903	917	2.793278	AACACCATTTTGAGGCGTTC	57.207	45.000	0.00	0.00	25.26	3.95
904	918	3.118956	TCAAAACACCATTTTGAGGCGTT	60.119	39.130	10.06	0.00	41.74	4.84
905	919	2.428890	TCAAAACACCATTTTGAGGCGT	59.571	40.909	10.06	0.00	41.74	5.68
906	920	3.090952	TCAAAACACCATTTTGAGGCG	57.909	42.857	10.06	0.00	41.74	5.52
907	921	4.507756	GTCTTCAAAACACCATTTTGAGGC	59.492	41.667	15.52	9.56	45.55	4.70
908	922	4.739716	CGTCTTCAAAACACCATTTTGAGG	59.260	41.667	14.62	14.62	45.55	3.86
909	923	4.739716	CCGTCTTCAAAACACCATTTTGAG	59.260	41.667	12.96	8.97	45.55	3.02
910	924	4.677584	CCGTCTTCAAAACACCATTTTGA	58.322	39.130	10.06	10.06	43.99	2.69
911	925	3.245048	GCCGTCTTCAAAACACCATTTTG	59.755	43.478	5.89	5.89	39.90	2.44
912	926	3.453424	GCCGTCTTCAAAACACCATTTT	58.547	40.909	0.00	0.00	0.00	1.82
928	942	3.591254	AAAGCACCTCGAGGCCGTC	62.591	63.158	31.56	16.83	39.32	4.79
941	955	3.379880	GCCAATGGAGCCAAAGCA	58.620	55.556	2.05	0.00	43.56	3.91
959	973	2.544685	AGCATGTCGATCTCGGAAAAG	58.455	47.619	0.00	0.00	40.29	2.27
1026	1040	3.247173	GCAGTGCAGCTAGTTCATGTATC	59.753	47.826	11.09	0.00	0.00	2.24
1039	1053	1.138247	GCATTACTGGCAGTGCAGC	59.862	57.895	29.65	23.59	37.52	5.25
1078	1092	1.005924	TGGAAATTGGAGAGGAAGGCC	59.994	52.381	0.00	0.00	0.00	5.19
1080	1094	5.760131	ACTAATGGAAATTGGAGAGGAAGG	58.240	41.667	0.00	0.00	0.00	3.46
1121	1136	2.159014	TGGAATTAGGTACGCATTCGCT	60.159	45.455	0.00	0.00	39.84	4.93
1126	1141	2.093181	TGCAGTGGAATTAGGTACGCAT	60.093	45.455	0.00	0.00	0.00	4.73
1213	1229	4.093998	TCTCGTCGTCACTACTGTATTTCC	59.906	45.833	0.00	0.00	0.00	3.13
1271	1299	2.168496	GTAGGTCAGGTGCTCTGTGTA	58.832	52.381	7.35	0.00	43.76	2.90
1385	1420	0.466555	CTTTGTTTCCCGGGGTGTCA	60.467	55.000	23.50	12.37	0.00	3.58
1413	1448	1.203523	GACTCCTTGCTGTCGATGTCT	59.796	52.381	0.00	0.00	0.00	3.41
1749	1784	3.872603	AACGGCCAGGTGAGCACA	61.873	61.111	2.24	0.00	0.00	4.57
1764	1799	2.281208	TACGCCACTGCCACCAAC	60.281	61.111	0.00	0.00	0.00	3.77
1765	1800	2.031919	CTACGCCACTGCCACCAA	59.968	61.111	0.00	0.00	0.00	3.67
1766	1801	4.015406	CCTACGCCACTGCCACCA	62.015	66.667	0.00	0.00	0.00	4.17
1768	1803	4.697756	TGCCTACGCCACTGCCAC	62.698	66.667	0.00	0.00	0.00	5.01
1769	1804	4.393155	CTGCCTACGCCACTGCCA	62.393	66.667	0.00	0.00	0.00	4.92
1771	1806	2.028125	TATCCTGCCTACGCCACTGC	62.028	60.000	0.00	0.00	0.00	4.40
1772	1807	0.681733	ATATCCTGCCTACGCCACTG	59.318	55.000	0.00	0.00	0.00	3.66
1773	1808	0.969894	GATATCCTGCCTACGCCACT	59.030	55.000	0.00	0.00	0.00	4.00
1774	1809	0.969894	AGATATCCTGCCTACGCCAC	59.030	55.000	0.00	0.00	0.00	5.01
1775	1810	1.257743	GAGATATCCTGCCTACGCCA	58.742	55.000	0.00	0.00	0.00	5.69
1776	1811	0.533032	GGAGATATCCTGCCTACGCC	59.467	60.000	0.00	0.00	0.00	5.68
1777	1812	1.067495	GTGGAGATATCCTGCCTACGC	60.067	57.143	8.09	0.00	31.46	4.42
1778	1813	1.200252	CGTGGAGATATCCTGCCTACG	59.800	57.143	8.09	4.89	31.46	3.51
1779	1814	1.067495	GCGTGGAGATATCCTGCCTAC	60.067	57.143	8.09	0.00	31.46	3.18
1780	1815	1.257743	GCGTGGAGATATCCTGCCTA	58.742	55.000	8.09	0.00	31.46	3.93
1781	1816	1.476007	GGCGTGGAGATATCCTGCCT	61.476	60.000	26.33	0.00	43.68	4.75
1782	1817	1.004440	GGCGTGGAGATATCCTGCC	60.004	63.158	21.93	21.93	41.89	4.85
1783	1818	1.004440	GGGCGTGGAGATATCCTGC	60.004	63.158	8.09	11.36	0.00	4.85
1784	1819	1.674057	GGGGCGTGGAGATATCCTG	59.326	63.158	8.09	1.36	0.00	3.86
1785	1820	1.908793	CGGGGCGTGGAGATATCCT	60.909	63.158	8.09	0.00	0.00	3.24
1786	1821	2.657237	CGGGGCGTGGAGATATCC	59.343	66.667	0.00	0.00	0.00	2.59
1787	1822	2.657237	CCGGGGCGTGGAGATATC	59.343	66.667	0.00	0.00	0.00	1.63
1788	1823	2.923035	CCCGGGGCGTGGAGATAT	60.923	66.667	14.71	0.00	0.00	1.63
1810	1845	0.673333	TATGCACTGTGCCAACGAGG	60.673	55.000	28.17	0.00	44.23	4.63
1811	1846	0.443869	GTATGCACTGTGCCAACGAG	59.556	55.000	28.17	0.00	44.23	4.18
1812	1847	1.288419	CGTATGCACTGTGCCAACGA	61.288	55.000	34.29	18.33	46.50	3.85
1813	1848	1.132436	CGTATGCACTGTGCCAACG	59.868	57.895	29.44	29.44	44.23	4.10
1814	1849	1.501741	CCGTATGCACTGTGCCAAC	59.498	57.895	28.17	23.00	44.23	3.77
1815	1850	2.331893	GCCGTATGCACTGTGCCAA	61.332	57.895	28.17	14.46	44.23	4.52
1816	1851	2.745884	GCCGTATGCACTGTGCCA	60.746	61.111	28.17	17.10	44.23	4.92
1817	1852	3.508840	GGCCGTATGCACTGTGCC	61.509	66.667	28.17	13.19	44.23	5.01
1818	1853	2.745884	TGGCCGTATGCACTGTGC	60.746	61.111	25.15	25.15	45.29	4.57
1819	1854	2.108514	CCTGGCCGTATGCACTGTG	61.109	63.158	2.76	2.76	43.89	3.66
1820	1855	2.268920	CCTGGCCGTATGCACTGT	59.731	61.111	0.00	0.00	43.89	3.55
1821	1856	2.514592	CCCTGGCCGTATGCACTG	60.515	66.667	0.00	0.00	43.89	3.66
1822	1857	4.489771	GCCCTGGCCGTATGCACT	62.490	66.667	0.00	0.00	43.89	4.40
1823	1858	4.794648	TGCCCTGGCCGTATGCAC	62.795	66.667	5.57	0.00	43.89	4.57
1824	1859	4.488136	CTGCCCTGGCCGTATGCA	62.488	66.667	5.57	3.35	43.89	3.96
1854	1889	2.046314	CACCAACCAGGGGCGTAG	60.046	66.667	0.00	0.00	43.89	3.51
1855	1890	3.642503	CCACCAACCAGGGGCGTA	61.643	66.667	0.00	0.00	40.60	4.42
1858	1893	3.224007	ATCACCACCAACCAGGGGC	62.224	63.158	0.00	0.00	40.60	5.80
1859	1894	1.000896	GATCACCACCAACCAGGGG	60.001	63.158	0.00	0.00	43.89	4.79
1860	1895	1.000896	GGATCACCACCAACCAGGG	60.001	63.158	0.00	0.00	43.89	4.45
1861	1896	0.322816	CTGGATCACCACCAACCAGG	60.323	60.000	0.00	0.00	42.77	4.45
1862	1897	0.322816	CCTGGATCACCACCAACCAG	60.323	60.000	0.00	0.00	45.09	4.00
1863	1898	1.065410	ACCTGGATCACCACCAACCA	61.065	55.000	0.00	0.00	41.77	3.67
1864	1899	0.322546	GACCTGGATCACCACCAACC	60.323	60.000	0.00	0.00	41.77	3.77
1956	1991	1.346395	ACGGCTGACATGAACAGGTAA	59.654	47.619	19.70	0.00	36.09	2.85
2408	2463	3.062763	CGCCTTAGCCTTCTGTATCATG	58.937	50.000	0.00	0.00	34.57	3.07
2496	2551	1.550976	GGAGAGGAGGAACATGTTCGT	59.449	52.381	28.67	28.67	40.37	3.85
2744	2799	7.239763	TGTGATCTGTGAATAAACTGGAGTA	57.760	36.000	0.00	0.00	0.00	2.59
2746	2801	7.984050	AGTATGTGATCTGTGAATAAACTGGAG	59.016	37.037	0.00	0.00	0.00	3.86
2755	2865	7.725818	CATAAGCAGTATGTGATCTGTGAAT	57.274	36.000	0.00	0.00	39.31	2.57
2844	2962	7.318141	CACCATCAGAGCTTTAATCATTTGTT	58.682	34.615	0.00	0.00	0.00	2.83
3018	4064	2.203337	GTTGGTGCTGGTGCCTGA	60.203	61.111	0.00	0.00	38.71	3.86
3417	4465	3.629087	AGCTGATATGCTCCTTGCTTTT	58.371	40.909	0.00	0.00	39.34	2.27
3418	4466	3.294038	AGCTGATATGCTCCTTGCTTT	57.706	42.857	0.00	0.00	39.34	3.51
3634	4687	7.041984	GGCCTAAGGTTAATTAAGATCTCGTTG	60.042	40.741	0.00	0.00	0.00	4.10
3650	4703	4.725490	ACGCATAATAATGGCCTAAGGTT	58.275	39.130	3.32	0.00	33.38	3.50
3668	4721	4.411993	TTTAAAAGATCGCATGAACGCA	57.588	36.364	0.00	0.00	0.00	5.24
3671	4724	6.984740	TGTGTTTTAAAAGATCGCATGAAC	57.015	33.333	0.00	0.00	0.00	3.18
3674	4727	6.033831	GGACATGTGTTTTAAAAGATCGCATG	59.966	38.462	26.15	26.15	46.00	4.06

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.