AutoCloner

Multiple sequence alignment - TraesCS4A01G247500

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	TraesCS4A01G247500	chr4A	100.000	3369	0	0	1	3369	558647418	558650786	0.000000e+00	6222
1	TraesCS4A01G247500	chr4D	88.700	1708	85	45	920	2569	40956646	40954989	0.000000e+00	1986
2	TraesCS4A01G247500	chr4D	89.070	796	31	25	2621	3369	40954849	40954063	0.000000e+00	937
3	TraesCS4A01G247500	chr4B	87.523	1659	80	61	1018	2591	60086239	60084623	0.000000e+00	1799
4	TraesCS4A01G247500	chr4B	87.698	821	41	21	2593	3367	60084584	60083778	0.000000e+00	902
5	TraesCS4A01G247500	chr2A	96.630	920	30	1	1	920	753014492	753013574	0.000000e+00	1526
6	TraesCS4A01G247500	chr2A	93.807	872	34	2	1	872	80994365	80995216	0.000000e+00	1293
7	TraesCS4A01G247500	chr2A	95.096	571	20	3	1	571	53448781	53449343	0.000000e+00	893
8	TraesCS4A01G247500	chr2A	94.872	351	17	1	571	920	53449212	53449562	6.360000e-152	547
9	TraesCS4A01G247500	chr5A	95.978	920	36	1	1	920	5699359	5700277	0.000000e+00	1493
10	TraesCS4A01G247500	chr5A	94.783	920	35	2	1	920	493823671	493824577	0.000000e+00	1421
11	TraesCS4A01G247500	chr5A	93.804	920	42	4	1	919	704840930	704840025	0.000000e+00	1369
12	TraesCS4A01G247500	chr5A	94.484	417	18	4	506	920	493824576	493824989	3.670000e-179	638
13	TraesCS4A01G247500	chr1A	95.662	922	34	5	1	920	478359496	478358579	0.000000e+00	1476
14	TraesCS4A01G247500	chr1A	91.146	576	46	1	1	571	146178955	146178380	0.000000e+00	776
15	TraesCS4A01G247500	chr1A	90.657	578	49	1	1	573	146181368	146180791	0.000000e+00	763
16	TraesCS4A01G247500	chr6A	96.673	571	19	0	1	571	551859858	551860428	0.000000e+00	950
17	TraesCS4A01G247500	chr6A	96.327	490	17	1	432	920	551858725	551859214	0.000000e+00	804
18	TraesCS4A01G247500	chr7B	93.820	178	11	0	1829	2006	467542471	467542648	5.540000e-68	268
19	TraesCS4A01G247500	chr7A	95.238	105	5	0	816	920	246272344	246272240	2.080000e-37	167
20	TraesCS4A01G247500	chr1B	94.393	107	4	2	815	920	24106882	24106987	2.690000e-36	163
21	TraesCS4A01G247500	chr5B	88.148	135	7	9	793	920	502375896	502376028	5.820000e-33	152
22	TraesCS4A01G247500	chr5B	92.222	90	7	0	1457	1546	134309003	134309092	9.810000e-26	128
23	TraesCS4A01G247500	chr5B	91.304	92	8	0	1455	1546	382569412	382569503	3.530000e-25	126
24	TraesCS4A01G247500	chr2B	94.565	92	5	0	1455	1546	132036113	132036022	3.500000e-30	143
25	TraesCS4A01G247500	chr6D	94.505	91	5	0	1455	1545	224452647	224452737	1.260000e-29	141
26	TraesCS4A01G247500	chr6D	92.391	92	7	0	1455	1546	35450439	35450348	7.580000e-27	132
27	TraesCS4A01G247500	chr2D	93.333	90	6	0	1457	1546	323756428	323756517	2.110000e-27	134
28	TraesCS4A01G247500	chr7D	93.258	89	6	0	1457	1545	427131745	427131657	7.580000e-27	132

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	TraesCS4A01G247500	chr4A	558647418	558650786	3368	False	6222.0	6222	100.0000	1	3369	1	chr4A.!!$F1	3368
1	TraesCS4A01G247500	chr4D	40954063	40956646	2583	True	1461.5	1986	88.8850	920	3369	2	chr4D.!!$R1	2449
2	TraesCS4A01G247500	chr4B	60083778	60086239	2461	True	1350.5	1799	87.6105	1018	3367	2	chr4B.!!$R1	2349
3	TraesCS4A01G247500	chr2A	753013574	753014492	918	True	1526.0	1526	96.6300	1	920	1	chr2A.!!$R1	919
4	TraesCS4A01G247500	chr2A	80994365	80995216	851	False	1293.0	1293	93.8070	1	872	1	chr2A.!!$F1	871
5	TraesCS4A01G247500	chr2A	53448781	53449562	781	False	720.0	893	94.9840	1	920	2	chr2A.!!$F2	919
6	TraesCS4A01G247500	chr5A	5699359	5700277	918	False	1493.0	1493	95.9780	1	920	1	chr5A.!!$F1	919
7	TraesCS4A01G247500	chr5A	704840025	704840930	905	True	1369.0	1369	93.8040	1	919	1	chr5A.!!$R1	918
8	TraesCS4A01G247500	chr5A	493823671	493824989	1318	False	1029.5	1421	94.6335	1	920	2	chr5A.!!$F2	919
9	TraesCS4A01G247500	chr1A	478358579	478359496	917	True	1476.0	1476	95.6620	1	920	1	chr1A.!!$R1	919
10	TraesCS4A01G247500	chr1A	146178380	146181368	2988	True	769.5	776	90.9015	1	573	2	chr1A.!!$R2	572
11	TraesCS4A01G247500	chr6A	551858725	551860428	1703	False	877.0	950	96.5000	1	920	2	chr6A.!!$F1	919

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
418	1557	0.034198	TTGTGCGATCGAGGTTTGGA	59.966	50.0	21.57	0.0	0.0	3.53	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2396	4638	0.249489	AACCGGAGCTTATAGCAGCG	60.249	55.0	9.46	0.0	45.56	5.18	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
17	1151	2.034687	GCAGCCACCATGGACTGT	59.965	61.111	21.47	0.00	40.96	3.55
126	1260	0.976641	TCCTCGCACTCCTGAACATT	59.023	50.000	0.00	0.00	0.00	2.71
183	1317	2.265739	CCTCTGCCGTAGCTGCAA	59.734	61.111	1.02	0.00	38.46	4.08
418	1557	0.034198	TTGTGCGATCGAGGTTTGGA	59.966	50.000	21.57	0.00	0.00	3.53
619	1758	8.934023	AAAGGTAAGAATCAATGTGTTAGGAA	57.066	30.769	0.00	0.00	0.00	3.36
686	1825	6.156748	TGTAACGTGATATCAATACCTGCT	57.843	37.500	7.07	0.00	0.00	4.24
804	2086	7.839680	AAGGTGAGACAAAAATAAACCAGAT	57.160	32.000	0.00	0.00	0.00	2.90
895	3033	1.120530	AATTGACCGGCGGAGACTAT	58.879	50.000	35.78	20.51	0.00	2.12
911	3049	5.303078	GGAGACTATCAACTGCTCCATTAGA	59.697	44.000	0.00	0.00	43.55	2.10
942	3080	0.180406	GGGCCCTTATCGCTTTCAGA	59.820	55.000	17.04	0.00	0.00	3.27
951	3089	4.703703	GCTTTCAGAGCCGAACCT	57.296	55.556	0.00	0.00	46.01	3.50
953	3091	1.646189	GCTTTCAGAGCCGAACCTAG	58.354	55.000	0.00	0.00	46.01	3.02
954	3092	1.204941	GCTTTCAGAGCCGAACCTAGA	59.795	52.381	0.00	0.00	46.01	2.43
959	3097	4.855715	TCAGAGCCGAACCTAGAATATG	57.144	45.455	0.00	0.00	0.00	1.78
960	3098	4.215908	TCAGAGCCGAACCTAGAATATGT	58.784	43.478	0.00	0.00	0.00	2.29
961	3099	4.038042	TCAGAGCCGAACCTAGAATATGTG	59.962	45.833	0.00	0.00	0.00	3.21
964	3102	2.767505	CCGAACCTAGAATATGTGCCC	58.232	52.381	0.00	0.00	0.00	5.36
967	3105	3.322254	CGAACCTAGAATATGTGCCCTCT	59.678	47.826	0.00	0.00	0.00	3.69
972	3110	7.394144	ACCTAGAATATGTGCCCTCTAAAAT	57.606	36.000	0.00	0.00	0.00	1.82
973	3111	7.227156	ACCTAGAATATGTGCCCTCTAAAATG	58.773	38.462	0.00	0.00	0.00	2.32
981	3119	1.064979	GCCCTCTAAAATGGAACCGGA	60.065	52.381	9.46	0.00	0.00	5.14
1000	3142	0.250793	ATTCCGTATGGCGTTCACCA	59.749	50.000	0.00	0.00	45.82	4.17
1012	3154	1.676916	CGTTCACCATGATCCAGTGCT	60.677	52.381	0.00	0.00	0.00	4.40
1027	3171	3.414700	GCTGCACGTTCAGTCGGG	61.415	66.667	16.52	0.00	36.49	5.14
1119	3283	3.431415	CGGAGATCCCAGATATACCACA	58.569	50.000	0.00	0.00	34.14	4.17
1127	3291	3.326006	CCCAGATATACCACATGTCTGCT	59.674	47.826	0.00	0.00	36.39	4.24
1128	3292	4.313282	CCAGATATACCACATGTCTGCTG	58.687	47.826	0.00	0.00	36.39	4.41
1129	3293	4.313282	CAGATATACCACATGTCTGCTGG	58.687	47.826	0.00	0.00	32.14	4.85
1131	3295	0.462581	ATACCACATGTCTGCTGGCG	60.463	55.000	0.00	0.00	30.92	5.69
1132	3296	1.826340	TACCACATGTCTGCTGGCGT	61.826	55.000	0.00	0.00	30.92	5.68
1133	3297	1.079197	CCACATGTCTGCTGGCGTA	60.079	57.895	0.00	0.00	0.00	4.42
1135	3299	0.390340	CACATGTCTGCTGGCGTACT	60.390	55.000	0.00	0.00	0.00	2.73
1155	3324	1.067669	TGTATCTCGATCAGCTGCACC	59.932	52.381	9.47	0.00	0.00	5.01
1319	3501	0.598680	CATTCCTCCTCATCCGTCGC	60.599	60.000	0.00	0.00	0.00	5.19
1321	3503	3.147595	CCTCCTCATCCGTCGCCA	61.148	66.667	0.00	0.00	0.00	5.69
1325	3507	1.595382	CCTCATCCGTCGCCAATCC	60.595	63.158	0.00	0.00	0.00	3.01
1337	3519	0.819259	GCCAATCCGCATAAGGCAGA	60.819	55.000	0.00	0.00	44.59	4.26
1344	3526	0.879400	CGCATAAGGCAGAGCTCCAG	60.879	60.000	10.93	4.58	45.17	3.86
1351	3533	2.348998	CAGAGCTCCAGCCCGTTT	59.651	61.111	10.93	0.00	43.38	3.60
1364	3546	0.958091	CCCGTTTCATTGCAGAACCA	59.042	50.000	0.00	0.00	0.00	3.67
1365	3547	1.068333	CCCGTTTCATTGCAGAACCAG	60.068	52.381	0.00	0.00	0.00	4.00
1369	3551	3.745975	CGTTTCATTGCAGAACCAGACTA	59.254	43.478	0.00	0.00	0.00	2.59
1516	3713	2.281900	GGCAACCCCTACGTGCAA	60.282	61.111	0.00	0.00	0.00	4.08
1563	3760	2.325082	CCTGCCAGTGTGCGTAACC	61.325	63.158	0.00	0.00	0.00	2.85
1564	3761	2.663520	TGCCAGTGTGCGTAACCG	60.664	61.111	0.00	0.00	37.07	4.44
1565	3762	2.663852	GCCAGTGTGCGTAACCGT	60.664	61.111	0.00	0.00	36.15	4.83
1566	3763	2.664436	GCCAGTGTGCGTAACCGTC	61.664	63.158	0.00	0.00	36.15	4.79
1567	3764	2.025418	CCAGTGTGCGTAACCGTCC	61.025	63.158	0.00	0.00	36.15	4.79
1568	3765	1.006571	CAGTGTGCGTAACCGTCCT	60.007	57.895	0.00	0.00	36.15	3.85
1569	3766	0.241749	CAGTGTGCGTAACCGTCCTA	59.758	55.000	0.00	0.00	36.15	2.94
1570	3767	0.242017	AGTGTGCGTAACCGTCCTAC	59.758	55.000	0.00	0.00	36.15	3.18
1571	3768	0.039256	GTGTGCGTAACCGTCCTACA	60.039	55.000	0.00	0.00	36.15	2.74
1601	3798	4.735822	GTCTCGTTCGATTCCTCAATACTG	59.264	45.833	0.00	0.00	0.00	2.74
1760	3957	0.874390	CAACATCTGGAACCACCGTG	59.126	55.000	0.00	0.00	42.61	4.94
1798	4019	1.489881	TTCGGATCATGATGCACGCG	61.490	55.000	24.65	3.53	0.00	6.01
2164	4397	3.213206	TCACTTGGCACTCTCAACAAT	57.787	42.857	0.00	0.00	0.00	2.71
2165	4398	3.141398	TCACTTGGCACTCTCAACAATC	58.859	45.455	0.00	0.00	0.00	2.67
2166	4399	3.144506	CACTTGGCACTCTCAACAATCT	58.855	45.455	0.00	0.00	0.00	2.40
2167	4400	3.188048	CACTTGGCACTCTCAACAATCTC	59.812	47.826	0.00	0.00	0.00	2.75
2378	4611	2.491022	CGTCCCTGACCGATCTCCC	61.491	68.421	0.00	0.00	0.00	4.30
2379	4612	2.123854	TCCCTGACCGATCTCCCG	60.124	66.667	0.00	0.00	0.00	5.14
2412	4660	2.024319	GCCGCTGCTATAAGCTCCG	61.024	63.158	0.00	3.15	42.97	4.63
2418	4666	2.864489	GCTGCTATAAGCTCCGGTTCTC	60.864	54.545	0.00	0.00	42.97	2.87
2441	4689	0.602106	CAGTGGCACTGTCCTGTCAG	60.602	60.000	34.00	10.19	41.19	3.51
2467	4715	6.040955	TGACTGATCAGTGTTTGTACTCTTCT	59.959	38.462	32.50	1.82	42.66	2.85
2555	4810	3.116531	GTTGCCTGCCGTCGGTAC	61.117	66.667	13.94	0.00	0.00	3.34
2572	4827	3.256558	GGTACGTATCACCAACCACTTC	58.743	50.000	0.00	0.00	36.01	3.01
2578	4833	2.590575	ACCAACCACTTCGCACCG	60.591	61.111	0.00	0.00	0.00	4.94
2642	5446	4.952335	GGCTCCCTCCAATCCATATTAATG	59.048	45.833	0.00	0.00	0.00	1.90
2699	5507	1.623811	GGGAGCAGTAGGTTTCTCACA	59.376	52.381	0.00	0.00	0.00	3.58
2701	5509	2.613223	GGAGCAGTAGGTTTCTCACACC	60.613	54.545	0.00	0.00	34.06	4.16
2702	5510	2.037251	GAGCAGTAGGTTTCTCACACCA	59.963	50.000	0.00	0.00	36.67	4.17
2703	5511	2.037772	AGCAGTAGGTTTCTCACACCAG	59.962	50.000	0.00	0.00	36.67	4.00
2706	5514	1.348036	GTAGGTTTCTCACACCAGCCT	59.652	52.381	0.00	0.00	36.67	4.58
2750	5571	2.093869	TGTAACCCTGAACCTCGCATAC	60.094	50.000	0.00	0.00	0.00	2.39
2781	5602	2.674852	CTGCAGCTTGTACAGTACCATG	59.325	50.000	0.00	3.29	0.00	3.66
2783	5604	2.009774	CAGCTTGTACAGTACCATGGC	58.990	52.381	13.04	7.12	0.00	4.40
2873	5698	5.744666	ACGTTACATAGCAAAACTGTTGT	57.255	34.783	0.00	0.00	32.63	3.32
2881	5706	0.653323	CAAAACTGTTGTCGTCGGCG	60.653	55.000	1.15	1.15	39.92	6.46
2882	5707	0.806884	AAAACTGTTGTCGTCGGCGA	60.807	50.000	8.66	8.66	45.79	5.54
2906	5731	4.433615	GAACTTGCAGTCGATCCATCTTA	58.566	43.478	0.00	0.00	0.00	2.10
3021	5880	6.167685	GGTATGTGTTGTGTGTGGAACTATA	58.832	40.000	0.00	0.00	38.04	1.31
3022	5881	6.821665	GGTATGTGTTGTGTGTGGAACTATAT	59.178	38.462	0.00	0.00	38.04	0.86
3035	5894	9.216117	GTGTGGAACTATATGGGTATAATTGAC	57.784	37.037	0.00	0.00	38.04	3.18
3038	5897	7.046033	GGAACTATATGGGTATAATTGACGGG	58.954	42.308	0.00	0.00	0.00	5.28
3095	5971	3.507009	GGTCGTCGAGGTCGGAGG	61.507	72.222	4.85	0.00	40.29	4.30
3096	5972	2.435586	GTCGTCGAGGTCGGAGGA	60.436	66.667	4.85	0.00	40.29	3.71

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
17	1151	2.428925	GGGTTGGCGTATCCGAGGA	61.429	63.158	0.00	0.00	37.80	3.71
126	1260	0.457853	GCAGTGCGGTTATCGAGACA	60.458	55.000	0.00	0.00	42.43	3.41
183	1317	2.040278	CCTCAGAGGCCCTGGAGT	59.960	66.667	17.89	0.00	43.12	3.85
418	1557	3.132467	GGTGGTATCTTCGCTTCCTACTT	59.868	47.826	0.00	0.00	0.00	2.24
534	1673	5.488341	GGGCAGGTATTGATATCACGTTAT	58.512	41.667	4.48	0.00	0.00	1.89
552	1691	1.081242	GCATGTCACAAACGGGCAG	60.081	57.895	0.00	0.00	31.79	4.85
644	1783	8.819015	ACGTTACAAACAATAAAACCCATTTTC	58.181	29.630	0.00	0.00	38.91	2.29
686	1825	1.603456	ACCATGCATGTCACAAACGA	58.397	45.000	24.58	0.00	0.00	3.85
758	2029	9.096823	ACCTTTCATTATTATATCCTCACGGTA	57.903	33.333	0.00	0.00	0.00	4.02
779	2050	7.654022	TCTGGTTTATTTTTGTCTCACCTTT	57.346	32.000	0.00	0.00	0.00	3.11
856	2240	1.970092	TTCGTCCCACCATTTTCGTT	58.030	45.000	0.00	0.00	0.00	3.85
863	2609	2.167662	GGTCAATTTTCGTCCCACCAT	58.832	47.619	0.00	0.00	0.00	3.55
895	3033	5.952347	TCTCTACTTCTAATGGAGCAGTTGA	59.048	40.000	0.00	0.00	0.00	3.18
942	3080	2.224305	GGCACATATTCTAGGTTCGGCT	60.224	50.000	0.00	0.00	0.00	5.52
951	3089	7.387265	TCCATTTTAGAGGGCACATATTCTA	57.613	36.000	0.00	0.00	0.00	2.10
953	3091	6.239036	GGTTCCATTTTAGAGGGCACATATTC	60.239	42.308	0.00	0.00	0.00	1.75
954	3092	5.598417	GGTTCCATTTTAGAGGGCACATATT	59.402	40.000	0.00	0.00	0.00	1.28
959	3097	1.743394	CGGTTCCATTTTAGAGGGCAC	59.257	52.381	0.00	0.00	0.00	5.01
960	3098	1.340600	CCGGTTCCATTTTAGAGGGCA	60.341	52.381	0.00	0.00	0.00	5.36
961	3099	1.064979	TCCGGTTCCATTTTAGAGGGC	60.065	52.381	0.00	0.00	0.00	5.19
981	3119	1.134220	ATGGTGAACGCCATACGGAAT	60.134	47.619	16.80	0.00	46.58	3.01
986	3124	1.873591	GGATCATGGTGAACGCCATAC	59.126	52.381	17.68	12.39	46.71	2.39
987	3125	1.488393	TGGATCATGGTGAACGCCATA	59.512	47.619	17.68	8.63	46.71	2.74
989	3127	0.392863	CTGGATCATGGTGAACGCCA	60.393	55.000	9.53	9.53	43.48	5.69
1000	3142	0.321919	AACGTGCAGCACTGGATCAT	60.322	50.000	23.15	0.00	32.40	2.45
1012	3154	4.980805	GGCCCGACTGAACGTGCA	62.981	66.667	0.00	0.00	38.28	4.57
1099	3244	4.780021	ACATGTGGTATATCTGGGATCTCC	59.220	45.833	0.00	0.00	0.00	3.71
1119	3283	1.182667	TACAGTACGCCAGCAGACAT	58.817	50.000	0.00	0.00	0.00	3.06
1127	3291	2.548480	CTGATCGAGATACAGTACGCCA	59.452	50.000	0.00	0.00	0.00	5.69
1128	3292	2.666069	GCTGATCGAGATACAGTACGCC	60.666	54.545	11.31	0.00	34.60	5.68
1129	3293	2.224549	AGCTGATCGAGATACAGTACGC	59.775	50.000	11.31	0.00	34.60	4.42
1131	3295	3.003793	TGCAGCTGATCGAGATACAGTAC	59.996	47.826	20.43	0.00	34.60	2.73
1132	3296	3.003793	GTGCAGCTGATCGAGATACAGTA	59.996	47.826	20.43	0.00	34.60	2.74
1133	3297	2.027385	TGCAGCTGATCGAGATACAGT	58.973	47.619	20.43	0.00	34.60	3.55
1135	3299	1.067669	GGTGCAGCTGATCGAGATACA	59.932	52.381	20.43	0.00	0.00	2.29
1325	3507	0.879400	CTGGAGCTCTGCCTTATGCG	60.879	60.000	14.64	0.00	45.60	4.73
1337	3519	0.962356	CAATGAAACGGGCTGGAGCT	60.962	55.000	0.00	0.00	41.70	4.09
1344	3526	0.388520	GGTTCTGCAATGAAACGGGC	60.389	55.000	0.00	0.00	0.00	6.13
1351	3533	4.973168	AGTTTAGTCTGGTTCTGCAATGA	58.027	39.130	0.00	0.00	0.00	2.57
1364	3546	1.630148	GCACGCGATGAGTTTAGTCT	58.370	50.000	15.93	0.00	0.00	3.24
1365	3547	0.645868	GGCACGCGATGAGTTTAGTC	59.354	55.000	15.93	0.00	0.00	2.59
1369	3551	1.647545	CCATGGCACGCGATGAGTTT	61.648	55.000	15.93	0.00	34.70	2.66
1563	3760	1.375098	GAGACGAGGGGTGTAGGACG	61.375	65.000	0.00	0.00	0.00	4.79
1564	3761	1.375098	CGAGACGAGGGGTGTAGGAC	61.375	65.000	0.00	0.00	0.00	3.85
1565	3762	1.077930	CGAGACGAGGGGTGTAGGA	60.078	63.158	0.00	0.00	0.00	2.94
1566	3763	0.964358	AACGAGACGAGGGGTGTAGG	60.964	60.000	0.00	0.00	0.00	3.18
1567	3764	0.450983	GAACGAGACGAGGGGTGTAG	59.549	60.000	0.00	0.00	0.00	2.74
1568	3765	1.300971	CGAACGAGACGAGGGGTGTA	61.301	60.000	0.00	0.00	0.00	2.90
1569	3766	2.623915	CGAACGAGACGAGGGGTGT	61.624	63.158	0.00	0.00	0.00	4.16
1570	3767	1.654954	ATCGAACGAGACGAGGGGTG	61.655	60.000	2.94	0.00	42.81	4.61
1571	3768	0.964358	AATCGAACGAGACGAGGGGT	60.964	55.000	2.94	0.00	42.81	4.95
1760	3957	4.551388	CGAAGCAGGGATGAGTAATACTC	58.449	47.826	13.20	13.20	45.26	2.59
1798	4019	2.317685	AAAACGTGCGGTGTCAGTGC	62.318	55.000	0.00	0.00	0.00	4.40
2164	4397	0.820226	CAGCCGGTGAATGAGAGAGA	59.180	55.000	1.90	0.00	0.00	3.10
2165	4398	0.809241	GCAGCCGGTGAATGAGAGAG	60.809	60.000	1.90	0.00	0.00	3.20
2166	4399	1.219124	GCAGCCGGTGAATGAGAGA	59.781	57.895	1.90	0.00	0.00	3.10
2167	4400	2.169789	CGCAGCCGGTGAATGAGAG	61.170	63.158	1.90	0.00	0.00	3.20
2286	4519	0.798776	CATGAACCAGAACTCGTGGC	59.201	55.000	0.00	0.00	38.83	5.01
2396	4638	0.249489	AACCGGAGCTTATAGCAGCG	60.249	55.000	9.46	0.00	45.56	5.18
2412	4660	4.329545	TGCCACTGCCGGAGAACC	62.330	66.667	5.05	0.00	36.33	3.62
2432	4680	2.560542	ACTGATCAGTCACTGACAGGAC	59.439	50.000	27.17	11.05	43.63	3.85
2441	4689	5.533482	AGAGTACAAACACTGATCAGTCAC	58.467	41.667	25.58	14.99	40.20	3.67
2467	4715	0.947180	GCGAGTTGCGGTACAGGAAA	60.947	55.000	0.86	0.00	41.29	3.13
2555	4810	0.719465	GCGAAGTGGTTGGTGATACG	59.281	55.000	0.00	0.00	0.00	3.06
2556	4811	1.463444	GTGCGAAGTGGTTGGTGATAC	59.537	52.381	0.00	0.00	0.00	2.24
2557	4812	1.609580	GGTGCGAAGTGGTTGGTGATA	60.610	52.381	0.00	0.00	0.00	2.15
2558	4813	0.889186	GGTGCGAAGTGGTTGGTGAT	60.889	55.000	0.00	0.00	0.00	3.06
2572	4827	0.788391	GGTAACACTTTCTCGGTGCG	59.212	55.000	0.00	0.00	38.14	5.34
2578	4833	7.617041	ATGAAATAGCTGGTAACACTTTCTC	57.383	36.000	0.00	0.00	46.17	2.87
2649	5453	7.385778	TCCATACTAAAAGTTGCGCTAAATT	57.614	32.000	9.73	4.13	0.00	1.82
2703	5511	1.210478	TGTAATCCCAGAGCAGAAGGC	59.790	52.381	0.00	0.00	45.30	4.35
2781	5602	4.828829	ACCAAGTGTACTGTAATACTGCC	58.171	43.478	6.72	0.00	0.00	4.85
2887	5712	4.047822	GACTAAGATGGATCGACTGCAAG	58.952	47.826	0.00	0.00	42.29	4.01
2888	5713	3.701542	AGACTAAGATGGATCGACTGCAA	59.298	43.478	0.00	0.00	0.00	4.08
2889	5714	3.067320	CAGACTAAGATGGATCGACTGCA	59.933	47.826	0.00	0.00	0.00	4.41
2890	5715	3.067461	ACAGACTAAGATGGATCGACTGC	59.933	47.826	0.00	0.00	0.00	4.40
2891	5716	4.909696	ACAGACTAAGATGGATCGACTG	57.090	45.455	0.00	0.00	0.00	3.51
2892	5717	7.681679	TCTATACAGACTAAGATGGATCGACT	58.318	38.462	0.00	0.00	0.00	4.18
2906	5731	6.721704	TGCATGATGAACTCTATACAGACT	57.278	37.500	0.00	0.00	0.00	3.24
2969	5825	4.389576	CCACTTCGCCGTGCTTGC	62.390	66.667	0.00	0.00	33.60	4.01
3021	5880	3.050089	TCCACCCGTCAATTATACCCAT	58.950	45.455	0.00	0.00	0.00	4.00
3022	5881	2.479340	TCCACCCGTCAATTATACCCA	58.521	47.619	0.00	0.00	0.00	4.51
3035	5894	1.889105	CGCTCCATTGATCCACCCG	60.889	63.158	0.00	0.00	0.00	5.28
3038	5897	2.537560	CGCCGCTCCATTGATCCAC	61.538	63.158	0.00	0.00	0.00	4.02
3095	5971	1.066114	CTCAAGAACCGCGTCGACTC	61.066	60.000	14.70	4.41	0.00	3.36
3096	5972	1.081376	CTCAAGAACCGCGTCGACT	60.081	57.895	14.70	0.00	0.00	4.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.