AutoCloner

Multiple sequence alignment - TraesCS6B01G076000

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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	TraesCS6B01G076000	chr6B	100.000	1982	0	0	337	2318	52074404	52076385	0.000000e+00	3661.0
1	TraesCS6B01G076000	chr6B	91.626	812	49	8	1522	2318	52138209	52137402	0.000000e+00	1105.0
2	TraesCS6B01G076000	chr6B	98.425	508	8	0	337	844	74470866	74471373	0.000000e+00	894.0
3	TraesCS6B01G076000	chr6B	98.232	509	8	1	337	845	694367044	694367551	0.000000e+00	889.0
4	TraesCS6B01G076000	chr6B	97.674	516	10	2	337	851	681781003	681781517	0.000000e+00	885.0
5	TraesCS6B01G076000	chr6B	100.000	38	0	0	1	38	52074068	52074105	1.150000e-08	71.3
6	TraesCS6B01G076000	chr6A	89.033	848	61	8	1502	2318	29806951	29806105	0.000000e+00	1022.0
7	TraesCS6B01G076000	chr6A	88.537	410	23	12	1449	1844	29716501	29716900	2.080000e-130	475.0
8	TraesCS6B01G076000	chr6A	93.822	259	11	4	2063	2317	29755278	29755535	3.610000e-103	385.0
9	TraesCS6B01G076000	chr6A	90.741	216	18	1	1854	2069	29737748	29737961	1.050000e-73	287.0
10	TraesCS6B01G076000	chr6D	87.907	860	60	16	1502	2318	28153794	28154652	0.000000e+00	972.0
11	TraesCS6B01G076000	chr6D	93.523	633	35	3	1691	2318	28266070	28265439	0.000000e+00	937.0
12	TraesCS6B01G076000	chr6D	82.515	509	78	10	844	1346	25817769	25817266	9.830000e-119	436.0
13	TraesCS6B01G076000	chr6D	87.293	181	13	6	1484	1656	28266250	28266072	5.050000e-47	198.0
14	TraesCS6B01G076000	chr5B	98.625	509	7	0	337	845	383770858	383770350	0.000000e+00	902.0
15	TraesCS6B01G076000	chr5B	98.239	511	9	0	337	847	593510024	593509514	0.000000e+00	894.0
16	TraesCS6B01G076000	chr5B	98.228	508	9	0	337	844	505181698	505181191	0.000000e+00	889.0
17	TraesCS6B01G076000	chr1B	98.622	508	6	1	337	844	163178620	163178114	0.000000e+00	898.0
18	TraesCS6B01G076000	chr1B	97.368	38	1	0	1	38	19541798	19541761	5.350000e-07	65.8
19	TraesCS6B01G076000	chr1B	97.368	38	1	0	1	38	68520392	68520355	5.350000e-07	65.8
20	TraesCS6B01G076000	chr1B	97.368	38	1	0	1	38	163178714	163178677	5.350000e-07	65.8
21	TraesCS6B01G076000	chr4A	98.614	505	7	0	341	845	717886931	717886427	0.000000e+00	894.0
22	TraesCS6B01G076000	chr4A	98.425	508	7	1	337	844	691176568	691176062	0.000000e+00	893.0
23	TraesCS6B01G076000	chr3D	90.873	504	45	1	841	1343	305483392	305483895	0.000000e+00	675.0
24	TraesCS6B01G076000	chr3D	91.182	499	39	4	845	1342	141195253	141194759	0.000000e+00	673.0
25	TraesCS6B01G076000	chr3A	90.637	502	46	1	844	1344	411276417	411275916	0.000000e+00	665.0
26	TraesCS6B01G076000	chr3A	87.251	502	63	1	844	1344	732918167	732917666	2.580000e-159	571.0
27	TraesCS6B01G076000	chr2B	86.882	465	58	3	882	1344	736792225	736791762	3.410000e-143	518.0
28	TraesCS6B01G076000	chr2B	100.000	38	0	0	1	38	226136238	226136275	1.150000e-08	71.3
29	TraesCS6B01G076000	chr7D	83.633	501	73	8	849	1344	474501435	474500939	1.620000e-126	462.0
30	TraesCS6B01G076000	chr7A	83.300	503	76	7	844	1342	73512289	73512787	7.550000e-125	457.0
31	TraesCS6B01G076000	chr5D	82.460	496	86	1	850	1344	491568366	491568861	1.270000e-117	433.0
32	TraesCS6B01G076000	chrUn	97.368	38	1	0	1	38	365293836	365293799	5.350000e-07	65.8
33	TraesCS6B01G076000	chrUn	97.368	38	1	0	1	38	405862013	405862050	5.350000e-07	65.8
34	TraesCS6B01G076000	chr4B	97.368	38	1	0	1	38	3602584	3602621	5.350000e-07	65.8
35	TraesCS6B01G076000	chr4B	97.368	38	1	0	1	38	430835924	430835887	5.350000e-07	65.8
36	TraesCS6B01G076000	chr4B	97.368	38	1	0	1	38	579595688	579595651	5.350000e-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	TraesCS6B01G076000	chr6B	52074068	52076385	2317	False	1866.15	3661	100.000	1	2318	2	chr6B.!!$F4	2317
1	TraesCS6B01G076000	chr6B	52137402	52138209	807	True	1105.00	1105	91.626	1522	2318	1	chr6B.!!$R1	796
2	TraesCS6B01G076000	chr6B	74470866	74471373	507	False	894.00	894	98.425	337	844	1	chr6B.!!$F1	507
3	TraesCS6B01G076000	chr6B	694367044	694367551	507	False	889.00	889	98.232	337	845	1	chr6B.!!$F3	508
4	TraesCS6B01G076000	chr6B	681781003	681781517	514	False	885.00	885	97.674	337	851	1	chr6B.!!$F2	514
5	TraesCS6B01G076000	chr6A	29806105	29806951	846	True	1022.00	1022	89.033	1502	2318	1	chr6A.!!$R1	816
6	TraesCS6B01G076000	chr6D	28153794	28154652	858	False	972.00	972	87.907	1502	2318	1	chr6D.!!$F1	816
7	TraesCS6B01G076000	chr6D	28265439	28266250	811	True	567.50	937	90.408	1484	2318	2	chr6D.!!$R2	834
8	TraesCS6B01G076000	chr6D	25817266	25817769	503	True	436.00	436	82.515	844	1346	1	chr6D.!!$R1	502
9	TraesCS6B01G076000	chr5B	383770350	383770858	508	True	902.00	902	98.625	337	845	1	chr5B.!!$R1	508
10	TraesCS6B01G076000	chr5B	593509514	593510024	510	True	894.00	894	98.239	337	847	1	chr5B.!!$R3	510
11	TraesCS6B01G076000	chr5B	505181191	505181698	507	True	889.00	889	98.228	337	844	1	chr5B.!!$R2	507
12	TraesCS6B01G076000	chr1B	163178114	163178714	600	True	481.90	898	97.995	1	844	2	chr1B.!!$R3	843
13	TraesCS6B01G076000	chr4A	717886427	717886931	504	True	894.00	894	98.614	341	845	1	chr4A.!!$R2	504
14	TraesCS6B01G076000	chr4A	691176062	691176568	506	True	893.00	893	98.425	337	844	1	chr4A.!!$R1	507
15	TraesCS6B01G076000	chr3D	305483392	305483895	503	False	675.00	675	90.873	841	1343	1	chr3D.!!$F1	502
16	TraesCS6B01G076000	chr3A	411275916	411276417	501	True	665.00	665	90.637	844	1344	1	chr3A.!!$R1	500
17	TraesCS6B01G076000	chr3A	732917666	732918167	501	True	571.00	571	87.251	844	1344	1	chr3A.!!$R2	500

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
928	929	0.556258	TCCTGAGGAATAGCGAGGGA	59.444	55.0	0.0	0.0	0.0	4.2	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2182	2248	2.241176	CTGGTAAATGCTTCCCTGGGTA	59.759	50.0	13.56	1.39	0.0	3.69	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
496	497	1.903783	GCGCGGGACATAAAACACGT	61.904	55.000	8.83	0.00	35.25	4.49
865	866	4.736896	GTGGCCCTGTCCGTCGAC	62.737	72.222	5.18	5.18	39.66	4.20
928	929	0.556258	TCCTGAGGAATAGCGAGGGA	59.444	55.000	0.00	0.00	0.00	4.20
935	936	1.273886	GGAATAGCGAGGGAGTGATCC	59.726	57.143	0.00	0.00	0.00	3.36
942	943	2.103263	GCGAGGGAGTGATCCTATTTGT	59.897	50.000	0.00	0.00	34.21	2.83
950	951	4.718961	AGTGATCCTATTTGTGGCATACC	58.281	43.478	0.00	0.00	0.00	2.73
991	992	1.757699	GATCCACTAGAGGCGGAACTT	59.242	52.381	0.53	0.00	31.18	2.66
994	995	1.134965	CCACTAGAGGCGGAACTTCAG	60.135	57.143	0.00	0.00	0.00	3.02
995	996	1.546476	CACTAGAGGCGGAACTTCAGT	59.454	52.381	0.00	0.00	0.00	3.41
1037	1039	3.820467	CTGGCCATTCAACACTCAAACTA	59.180	43.478	5.51	0.00	0.00	2.24
1042	1044	4.695455	CCATTCAACACTCAAACTATCCGT	59.305	41.667	0.00	0.00	0.00	4.69
1050	1052	4.992319	CACTCAAACTATCCGTTGGTGTTA	59.008	41.667	0.00	0.00	32.42	2.41
1065	1067	3.517901	TGGTGTTACAATCGGATTCCTCT	59.482	43.478	0.00	0.00	0.00	3.69
1077	1079	3.490933	CGGATTCCTCTGAAGCGTTATCA	60.491	47.826	0.30	0.00	37.77	2.15
1092	1094	3.326747	GTTATCATGCCTATCCACGGAC	58.673	50.000	0.00	0.00	0.00	4.79
1100	1102	2.004808	CTATCCACGGACGCTCTGCA	62.005	60.000	0.00	0.00	0.00	4.41
1241	1243	3.665675	GATTGGAGCGAGCCACCGT	62.666	63.158	0.00	0.00	37.75	4.83
1254	1256	2.665185	ACCGTTGTCTGGCTTCGC	60.665	61.111	0.00	0.00	0.00	4.70
1255	1257	2.664851	CCGTTGTCTGGCTTCGCA	60.665	61.111	0.00	0.00	0.00	5.10
1258	1260	1.771073	CGTTGTCTGGCTTCGCACAA	61.771	55.000	0.00	0.00	0.00	3.33
1263	1265	0.739462	TCTGGCTTCGCACAATACCG	60.739	55.000	0.00	0.00	0.00	4.02
1279	1281	0.390735	ACCGCCTTGTATTGACGACC	60.391	55.000	0.00	0.00	0.00	4.79
1360	1362	4.830826	AAAAAGACCACGTCCTTCATTC	57.169	40.909	0.00	0.00	32.18	2.67
1361	1363	2.080286	AAGACCACGTCCTTCATTCG	57.920	50.000	0.00	0.00	32.18	3.34
1362	1364	0.966920	AGACCACGTCCTTCATTCGT	59.033	50.000	0.00	0.00	38.34	3.85
1365	1367	1.787847	CACGTCCTTCATTCGTGCC	59.212	57.895	4.16	0.00	45.66	5.01
1366	1368	1.375523	ACGTCCTTCATTCGTGCCC	60.376	57.895	0.00	0.00	36.46	5.36
1367	1369	2.452813	CGTCCTTCATTCGTGCCCG	61.453	63.158	0.00	0.00	0.00	6.13
1368	1370	1.079405	GTCCTTCATTCGTGCCCGA	60.079	57.895	0.00	0.00	42.41	5.14
1369	1371	1.084370	GTCCTTCATTCGTGCCCGAG	61.084	60.000	0.00	0.00	45.24	4.63
1370	1372	1.079127	CCTTCATTCGTGCCCGAGT	60.079	57.895	0.00	0.00	45.24	4.18
1371	1373	0.673644	CCTTCATTCGTGCCCGAGTT	60.674	55.000	0.00	0.00	45.24	3.01
1372	1374	1.404986	CCTTCATTCGTGCCCGAGTTA	60.405	52.381	0.00	0.00	45.24	2.24
1373	1375	2.550978	CTTCATTCGTGCCCGAGTTAT	58.449	47.619	0.00	0.00	45.24	1.89
1374	1376	1.934589	TCATTCGTGCCCGAGTTATG	58.065	50.000	0.00	0.00	45.24	1.90
1375	1377	1.206132	TCATTCGTGCCCGAGTTATGT	59.794	47.619	2.45	0.00	45.24	2.29
1376	1378	2.427812	TCATTCGTGCCCGAGTTATGTA	59.572	45.455	2.45	0.00	45.24	2.29
1377	1379	2.572191	TTCGTGCCCGAGTTATGTAG	57.428	50.000	0.00	0.00	45.24	2.74
1378	1380	0.742505	TCGTGCCCGAGTTATGTAGG	59.257	55.000	0.00	0.00	38.40	3.18
1379	1381	0.742505	CGTGCCCGAGTTATGTAGGA	59.257	55.000	0.00	0.00	35.63	2.94
1380	1382	1.340248	CGTGCCCGAGTTATGTAGGAT	59.660	52.381	0.00	0.00	35.63	3.24
1381	1383	2.555325	CGTGCCCGAGTTATGTAGGATA	59.445	50.000	0.00	0.00	35.63	2.59
1382	1384	3.005050	CGTGCCCGAGTTATGTAGGATAA	59.995	47.826	0.00	0.00	35.63	1.75
1383	1385	4.304939	GTGCCCGAGTTATGTAGGATAAC	58.695	47.826	0.00	0.00	35.36	1.89
1384	1386	3.322828	TGCCCGAGTTATGTAGGATAACC	59.677	47.826	0.00	0.00	35.65	2.85
1386	1388	4.768968	GCCCGAGTTATGTAGGATAACCTA	59.231	45.833	0.00	0.00	45.83	3.08
1394	1396	1.272807	TAGGATAACCTATGGGGCGC	58.727	55.000	0.00	0.00	45.83	6.53
1395	1397	0.473886	AGGATAACCTATGGGGCGCT	60.474	55.000	7.64	0.00	45.83	5.92
1396	1398	0.036294	GGATAACCTATGGGGCGCTC	60.036	60.000	7.64	1.18	39.10	5.03
1397	1399	0.977395	GATAACCTATGGGGCGCTCT	59.023	55.000	7.48	0.00	39.10	4.09
1398	1400	0.977395	ATAACCTATGGGGCGCTCTC	59.023	55.000	7.48	0.00	39.10	3.20
1399	1401	0.397957	TAACCTATGGGGCGCTCTCA	60.398	55.000	7.48	3.61	39.10	3.27
1400	1402	1.972660	AACCTATGGGGCGCTCTCAC	61.973	60.000	7.48	0.00	39.10	3.51
1401	1403	2.423446	CTATGGGGCGCTCTCACC	59.577	66.667	7.48	0.00	0.00	4.02
1402	1404	3.161450	TATGGGGCGCTCTCACCC	61.161	66.667	7.48	9.83	46.24	4.61
1406	1408	2.282180	GGGCGCTCTCACCCAAAA	60.282	61.111	7.64	0.00	46.22	2.44
1407	1409	1.901464	GGGCGCTCTCACCCAAAAA	60.901	57.895	7.64	0.00	46.22	1.94
1463	1465	3.164576	GCAATGCTGCGTACGTGA	58.835	55.556	17.90	2.94	39.20	4.35
1464	1466	1.059369	GCAATGCTGCGTACGTGAG	59.941	57.895	17.90	13.89	39.20	3.51
1465	1467	1.059369	CAATGCTGCGTACGTGAGC	59.941	57.895	25.50	25.50	0.00	4.26
1466	1468	1.079819	AATGCTGCGTACGTGAGCT	60.080	52.632	29.30	18.29	33.66	4.09
1467	1469	0.670546	AATGCTGCGTACGTGAGCTT	60.671	50.000	29.30	23.76	33.66	3.74
1468	1470	1.078759	ATGCTGCGTACGTGAGCTTC	61.079	55.000	29.30	10.41	33.66	3.86
1469	1471	1.733041	GCTGCGTACGTGAGCTTCA	60.733	57.895	25.16	10.65	0.00	3.02
1470	1472	1.282248	GCTGCGTACGTGAGCTTCAA	61.282	55.000	25.16	0.00	0.00	2.69
1471	1473	0.435008	CTGCGTACGTGAGCTTCAAC	59.565	55.000	17.90	0.00	0.00	3.18
1472	1474	0.249114	TGCGTACGTGAGCTTCAACA	60.249	50.000	17.90	0.00	0.00	3.33
1473	1475	0.435008	GCGTACGTGAGCTTCAACAG	59.565	55.000	17.90	0.00	0.00	3.16
1474	1476	1.929038	GCGTACGTGAGCTTCAACAGA	60.929	52.381	17.90	0.00	0.00	3.41
1475	1477	1.714460	CGTACGTGAGCTTCAACAGAC	59.286	52.381	7.22	0.00	0.00	3.51
1476	1478	2.604855	CGTACGTGAGCTTCAACAGACT	60.605	50.000	7.22	0.00	0.00	3.24
1477	1479	1.858091	ACGTGAGCTTCAACAGACTG	58.142	50.000	0.00	0.00	0.00	3.51
1478	1480	1.143305	CGTGAGCTTCAACAGACTGG	58.857	55.000	7.51	0.00	0.00	4.00
1479	1481	0.871057	GTGAGCTTCAACAGACTGGC	59.129	55.000	7.51	0.00	0.00	4.85
1480	1482	0.469494	TGAGCTTCAACAGACTGGCA	59.531	50.000	7.51	0.00	0.00	4.92
1481	1483	1.155042	GAGCTTCAACAGACTGGCAG	58.845	55.000	14.16	14.16	0.00	4.85
1482	1484	0.761187	AGCTTCAACAGACTGGCAGA	59.239	50.000	23.66	0.00	0.00	4.26
1495	1497	2.893489	ACTGGCAGAAGTCAATTTTCCC	59.107	45.455	23.66	0.00	0.00	3.97
1496	1498	2.892852	CTGGCAGAAGTCAATTTTCCCA	59.107	45.455	9.42	0.00	0.00	4.37
1513	1515	1.492133	CCAGCCCAGGAGTTCAGGAA	61.492	60.000	0.00	0.00	0.00	3.36
1520	1522	4.151883	CCCAGGAGTTCAGGAATTTTGAA	58.848	43.478	0.00	3.10	32.44	2.69
1561	1563	6.534079	AGAAGAGGAAACATAAACGTATTCGG	59.466	38.462	0.00	0.00	41.85	4.30
1600	1612	8.991275	AGATAAAGAGAGACAGAGATGGAATTT	58.009	33.333	0.00	0.00	0.00	1.82
1610	1622	7.505585	AGACAGAGATGGAATTTGGTTTAAACA	59.494	33.333	19.57	3.79	0.00	2.83
1629	1650	5.755330	AACAAACAAAAACTTGCGTACTG	57.245	34.783	0.00	0.00	0.00	2.74
1639	1660	2.703409	GCGTACTGCATCCAAGCG	59.297	61.111	5.07	0.00	45.45	4.68
1653	1678	1.675641	AAGCGTCTCCCCACATTGC	60.676	57.895	0.00	0.00	0.00	3.56
1664	1701	4.092279	TCCCCACATTGCATGTATTCAAA	58.908	39.130	0.00	0.00	42.70	2.69
1671	1708	5.643348	ACATTGCATGTATTCAAAGAGACGA	59.357	36.000	0.00	0.00	42.78	4.20
1676	1713	4.866508	TGTATTCAAAGAGACGACCTGT	57.133	40.909	0.00	0.00	0.00	4.00
1708	1763	0.652592	CCAACGAAGATGATGGCGAC	59.347	55.000	0.00	0.00	29.10	5.19
2018	2082	3.415087	GGCCTCACCCTCCTGCAT	61.415	66.667	0.00	0.00	0.00	3.96
2259	2325	2.444895	GGAGGCCCATCTCCGTCT	60.445	66.667	0.00	0.00	43.19	4.18
2260	2326	2.066999	GGAGGCCCATCTCCGTCTT	61.067	63.158	0.00	0.00	43.19	3.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
6	7	4.755266	ACATAACTACACCACCTCCATC	57.245	45.455	0.00	0.00	0.00	3.51
910	911	0.965439	CTCCCTCGCTATTCCTCAGG	59.035	60.000	0.00	0.00	0.00	3.86
913	914	1.693627	TCACTCCCTCGCTATTCCTC	58.306	55.000	0.00	0.00	0.00	3.71
928	929	4.718961	GGTATGCCACAAATAGGATCACT	58.281	43.478	0.00	0.00	34.09	3.41
935	936	6.801539	AATGTATCGGTATGCCACAAATAG	57.198	37.500	0.00	0.00	34.09	1.73
942	943	4.157849	TGGAAAATGTATCGGTATGCCA	57.842	40.909	0.00	0.00	34.09	4.92
950	951	6.364165	GGATCATTGCAATGGAAAATGTATCG	59.636	38.462	33.22	8.64	37.03	2.92
991	992	3.812262	CCATACCTTGCATCATCACTGA	58.188	45.455	0.00	0.00	35.41	3.41
994	995	1.610522	GGCCATACCTTGCATCATCAC	59.389	52.381	0.00	0.00	34.51	3.06
995	996	1.479205	GGGCCATACCTTGCATCATCA	60.479	52.381	4.39	0.00	39.10	3.07
1023	1025	4.062293	CCAACGGATAGTTTGAGTGTTGA	58.938	43.478	3.94	0.00	42.02	3.18
1037	1039	2.027929	TCCGATTGTAACACCAACGGAT	60.028	45.455	0.00	0.00	40.11	4.18
1042	1044	4.019681	AGAGGAATCCGATTGTAACACCAA	60.020	41.667	0.00	0.00	0.00	3.67
1050	1052	2.739932	CGCTTCAGAGGAATCCGATTGT	60.740	50.000	0.00	0.00	32.62	2.71
1065	1067	3.070878	TGGATAGGCATGATAACGCTTCA	59.929	43.478	0.00	0.00	0.00	3.02
1077	1079	2.088674	GAGCGTCCGTGGATAGGCAT	62.089	60.000	10.72	0.00	0.00	4.40
1119	1121	9.384764	GCTAAGTGTTTAATCTCCAAGACTAAT	57.615	33.333	0.00	0.00	0.00	1.73
1212	1214	2.364324	TCGCTCCAATCGGCTATAGTTT	59.636	45.455	0.84	0.00	0.00	2.66
1218	1220	2.417516	GCTCGCTCCAATCGGCTA	59.582	61.111	0.00	0.00	0.00	3.93
1225	1227	3.936203	AACGGTGGCTCGCTCCAA	61.936	61.111	0.00	0.00	37.96	3.53
1226	1228	4.680237	CAACGGTGGCTCGCTCCA	62.680	66.667	0.00	0.00	0.00	3.86
1258	1260	2.482490	GGTCGTCAATACAAGGCGGTAT	60.482	50.000	0.00	0.00	35.53	2.73
1263	1265	1.732259	CACAGGTCGTCAATACAAGGC	59.268	52.381	0.00	0.00	0.00	4.35
1275	1277	3.062466	TCGAGAGGCCACAGGTCG	61.062	66.667	5.01	4.56	29.39	4.79
1279	1281	0.888619	TTACAGTCGAGAGGCCACAG	59.111	55.000	5.01	0.00	35.23	3.66
1348	1350	1.375523	GGGCACGAATGAAGGACGT	60.376	57.895	0.00	0.00	40.87	4.34
1349	1351	2.452813	CGGGCACGAATGAAGGACG	61.453	63.158	0.00	0.00	44.60	4.79
1350	1352	3.486263	CGGGCACGAATGAAGGAC	58.514	61.111	0.00	0.00	44.60	3.85
1360	1362	0.742505	TCCTACATAACTCGGGCACG	59.257	55.000	0.00	0.00	42.74	5.34
1361	1363	4.304939	GTTATCCTACATAACTCGGGCAC	58.695	47.826	0.00	0.00	33.11	5.01
1362	1364	3.322828	GGTTATCCTACATAACTCGGGCA	59.677	47.826	4.85	0.00	35.46	5.36
1363	1365	3.577415	AGGTTATCCTACATAACTCGGGC	59.423	47.826	4.85	0.00	43.12	6.13
1377	1379	0.036294	GAGCGCCCCATAGGTTATCC	60.036	60.000	2.29	0.00	38.26	2.59
1378	1380	0.977395	AGAGCGCCCCATAGGTTATC	59.023	55.000	2.29	0.00	38.26	1.75
1379	1381	0.977395	GAGAGCGCCCCATAGGTTAT	59.023	55.000	2.29	0.00	38.26	1.89
1380	1382	0.397957	TGAGAGCGCCCCATAGGTTA	60.398	55.000	2.29	0.00	38.26	2.85
1381	1383	1.689233	TGAGAGCGCCCCATAGGTT	60.689	57.895	2.29	0.00	38.26	3.50
1382	1384	2.041922	TGAGAGCGCCCCATAGGT	60.042	61.111	2.29	0.00	38.26	3.08
1383	1385	2.423446	GTGAGAGCGCCCCATAGG	59.577	66.667	2.29	0.00	39.47	2.57
1384	1386	2.423446	GGTGAGAGCGCCCCATAG	59.577	66.667	2.29	0.00	38.80	2.23
1390	1392	3.758172	TTTTTGGGTGAGAGCGCC	58.242	55.556	2.29	0.00	44.14	6.53
1447	1449	1.059369	GCTCACGTACGCAGCATTG	59.941	57.895	26.69	13.43	33.06	2.82
1448	1450	0.670546	AAGCTCACGTACGCAGCATT	60.671	50.000	30.67	21.65	35.46	3.56
1449	1451	1.078759	GAAGCTCACGTACGCAGCAT	61.079	55.000	30.67	23.58	35.46	3.79
1450	1452	1.733041	GAAGCTCACGTACGCAGCA	60.733	57.895	30.67	8.73	35.46	4.41
1451	1453	1.282248	TTGAAGCTCACGTACGCAGC	61.282	55.000	25.13	25.13	0.00	5.25
1452	1454	0.435008	GTTGAAGCTCACGTACGCAG	59.565	55.000	16.72	12.74	0.00	5.18
1453	1455	0.249114	TGTTGAAGCTCACGTACGCA	60.249	50.000	16.72	0.58	0.00	5.24
1454	1456	0.435008	CTGTTGAAGCTCACGTACGC	59.565	55.000	16.72	0.00	0.00	4.42
1455	1457	1.714460	GTCTGTTGAAGCTCACGTACG	59.286	52.381	15.01	15.01	0.00	3.67
1456	1458	2.726760	CAGTCTGTTGAAGCTCACGTAC	59.273	50.000	0.00	0.00	0.00	3.67
1457	1459	2.288213	CCAGTCTGTTGAAGCTCACGTA	60.288	50.000	0.00	0.00	0.00	3.57
1458	1460	1.539065	CCAGTCTGTTGAAGCTCACGT	60.539	52.381	0.00	0.00	0.00	4.49
1459	1461	1.143305	CCAGTCTGTTGAAGCTCACG	58.857	55.000	0.00	0.00	0.00	4.35
1460	1462	0.871057	GCCAGTCTGTTGAAGCTCAC	59.129	55.000	0.00	0.00	0.00	3.51
1461	1463	0.469494	TGCCAGTCTGTTGAAGCTCA	59.531	50.000	0.00	0.00	0.00	4.26
1462	1464	1.155042	CTGCCAGTCTGTTGAAGCTC	58.845	55.000	0.00	0.00	0.00	4.09
1463	1465	0.761187	TCTGCCAGTCTGTTGAAGCT	59.239	50.000	0.00	0.00	0.00	3.74
1464	1466	1.534595	CTTCTGCCAGTCTGTTGAAGC	59.465	52.381	11.28	3.39	0.00	3.86
1465	1467	2.805099	GACTTCTGCCAGTCTGTTGAAG	59.195	50.000	17.65	17.65	40.23	3.02
1466	1468	2.170397	TGACTTCTGCCAGTCTGTTGAA	59.830	45.455	8.72	0.01	43.32	2.69
1467	1469	1.762370	TGACTTCTGCCAGTCTGTTGA	59.238	47.619	8.72	0.00	43.32	3.18
1468	1470	2.245159	TGACTTCTGCCAGTCTGTTG	57.755	50.000	8.72	0.00	43.32	3.33
1469	1471	3.498774	ATTGACTTCTGCCAGTCTGTT	57.501	42.857	8.72	0.00	43.32	3.16
1470	1472	3.498774	AATTGACTTCTGCCAGTCTGT	57.501	42.857	8.72	0.00	43.32	3.41
1471	1473	4.320788	GGAAAATTGACTTCTGCCAGTCTG	60.321	45.833	8.72	0.00	43.32	3.51
1472	1474	3.823304	GGAAAATTGACTTCTGCCAGTCT	59.177	43.478	8.72	0.00	43.32	3.24
1473	1475	3.057245	GGGAAAATTGACTTCTGCCAGTC	60.057	47.826	0.00	1.69	43.23	3.51
1474	1476	2.893489	GGGAAAATTGACTTCTGCCAGT	59.107	45.455	0.00	0.00	0.00	4.00
1475	1477	2.892852	TGGGAAAATTGACTTCTGCCAG	59.107	45.455	0.00	0.00	0.00	4.85
1476	1478	2.892852	CTGGGAAAATTGACTTCTGCCA	59.107	45.455	0.00	0.00	0.00	4.92
1477	1479	2.353109	GCTGGGAAAATTGACTTCTGCC	60.353	50.000	0.00	0.00	0.00	4.85
1478	1480	2.353109	GGCTGGGAAAATTGACTTCTGC	60.353	50.000	0.00	0.00	0.00	4.26
1479	1481	2.232208	GGGCTGGGAAAATTGACTTCTG	59.768	50.000	0.00	0.00	0.00	3.02
1480	1482	2.158325	TGGGCTGGGAAAATTGACTTCT	60.158	45.455	0.00	0.00	0.00	2.85
1481	1483	2.232208	CTGGGCTGGGAAAATTGACTTC	59.768	50.000	0.00	0.00	0.00	3.01
1482	1484	2.250924	CTGGGCTGGGAAAATTGACTT	58.749	47.619	0.00	0.00	0.00	3.01
1495	1497	0.622665	ATTCCTGAACTCCTGGGCTG	59.377	55.000	0.00	0.00	34.88	4.85
1496	1498	1.376649	AATTCCTGAACTCCTGGGCT	58.623	50.000	0.00	0.00	34.88	5.19
1513	1515	4.819630	TGTAGTCCTTCGCAACTTCAAAAT	59.180	37.500	0.00	0.00	0.00	1.82
1520	1522	2.891580	TCTTCTGTAGTCCTTCGCAACT	59.108	45.455	0.00	0.00	0.00	3.16
1567	1569	8.958119	TCTCTGTCTCTCTTTATCTCTAAGAC	57.042	38.462	0.00	0.00	33.86	3.01
1600	1612	6.363473	CGCAAGTTTTTGTTTGTTTAAACCA	58.637	32.000	15.59	1.62	44.37	3.67
1622	1634	2.025359	GACGCTTGGATGCAGTACGC	62.025	60.000	0.00	3.22	42.89	4.42
1629	1650	2.514824	GGGGAGACGCTTGGATGC	60.515	66.667	0.00	0.00	40.76	3.91
1653	1678	5.171476	ACAGGTCGTCTCTTTGAATACATG	58.829	41.667	0.00	0.00	32.85	3.21
1664	1701	0.601311	GCAGCAAACAGGTCGTCTCT	60.601	55.000	0.00	0.00	0.00	3.10
1676	1713	1.098869	TCGTTGGTTTGAGCAGCAAA	58.901	45.000	0.00	1.19	43.89	3.68
1708	1763	2.374830	AATCATCTCCTCCGGCAGCG	62.375	60.000	0.00	0.00	0.00	5.18
1729	1784	4.357947	GACGCACGAGCACCTCCA	62.358	66.667	5.50	0.00	42.27	3.86
1859	1920	2.368548	TGAGAGGAACAGCAGCTTAACA	59.631	45.455	0.00	0.00	0.00	2.41
2086	2150	4.498241	TGTCGAATGAAGGATCTTGTCTG	58.502	43.478	0.00	0.00	0.00	3.51
2182	2248	2.241176	CTGGTAAATGCTTCCCTGGGTA	59.759	50.000	13.56	1.39	0.00	3.69

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.