AutoCloner

Multiple sequence alignment - TraesCS7A01G492500

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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	TraesCS7A01G492500	chr7A	100.000	3708	0	0	1	3708	681253691	681257398	0.000000e+00	6848.0
1	TraesCS7A01G492500	chr7A	94.969	159	7	1	822	979	681260662	681260504	7.950000e-62	248.0
2	TraesCS7A01G492500	chr7A	83.275	287	23	15	548	821	681387136	681387410	1.330000e-59	241.0
3	TraesCS7A01G492500	chr7A	80.328	244	14	21	581	802	681614436	681614205	1.780000e-33	154.0
4	TraesCS7A01G492500	chr7A	90.625	96	7	2	24	119	681386393	681386486	3.890000e-25	126.0
5	TraesCS7A01G492500	chr7A	89.552	67	6	1	254	319	681614925	681614859	2.370000e-12	84.2
6	TraesCS7A01G492500	chr6A	95.675	2081	64	6	825	2880	32921831	32923910	0.000000e+00	3321.0
7	TraesCS7A01G492500	chr6A	97.842	834	17	1	2876	3708	32932991	32933824	0.000000e+00	1439.0
8	TraesCS7A01G492500	chr3D	93.330	1814	82	12	1919	3708	599395798	599394000	0.000000e+00	2643.0
9	TraesCS7A01G492500	chr3D	91.558	1078	55	13	825	1893	599396919	599395869	0.000000e+00	1454.0
10	TraesCS7A01G492500	chr3D	81.970	1675	221	37	1458	3058	99803751	99802084	0.000000e+00	1345.0
11	TraesCS7A01G492500	chr2A	97.887	1325	26	2	1389	2711	4049809	4048485	0.000000e+00	2290.0
12	TraesCS7A01G492500	chr2A	95.336	536	24	1	825	1360	4050342	4049808	0.000000e+00	850.0
13	TraesCS7A01G492500	chr4B	91.397	1081	82	5	823	1893	602034650	602035729	0.000000e+00	1471.0
14	TraesCS7A01G492500	chr4B	83.087	1626	213	32	1917	3483	71231443	71229821	0.000000e+00	1423.0
15	TraesCS7A01G492500	chr6B	83.333	1626	210	31	1917	3483	25585204	25583581	0.000000e+00	1445.0
16	TraesCS7A01G492500	chr1B	83.531	1603	204	30	1908	3483	74500715	74502284	0.000000e+00	1443.0
17	TraesCS7A01G492500	chr5B	90.616	1087	84	4	825	1893	682198897	682199983	0.000000e+00	1426.0
18	TraesCS7A01G492500	chr5B	82.120	1415	193	27	1458	2818	70359584	70358176	0.000000e+00	1157.0
19	TraesCS7A01G492500	chr5D	82.876	1641	207	42	1907	3483	9580690	9582320	0.000000e+00	1406.0
20	TraesCS7A01G492500	chr5D	80.407	393	65	10	1458	1844	9580199	9580585	4.690000e-74	289.0
21	TraesCS7A01G492500	chr5A	82.220	1676	215	35	1458	3058	675155710	675157377	0.000000e+00	1367.0
22	TraesCS7A01G492500	chr5A	85.078	1213	146	15	1917	3096	622415522	622414312	0.000000e+00	1205.0
23	TraesCS7A01G492500	chr5A	85.113	309	45	1	3176	3483	622414155	622413847	7.730000e-82	315.0
24	TraesCS7A01G492500	chr2D	84.333	1251	156	18	1907	3120	607815754	607817001	0.000000e+00	1188.0
25	TraesCS7A01G492500	chr2D	81.525	341	48	13	825	1158	607814923	607815255	2.200000e-67	267.0
26	TraesCS7A01G492500	chr2D	85.906	149	21	0	3163	3311	607817158	607817306	3.830000e-35	159.0
27	TraesCS7A01G492500	chr2B	84.202	1247	154	27	1907	3120	175942857	175941621	0.000000e+00	1171.0
28	TraesCS7A01G492500	chr1A	94.624	372	19	1	1244	1614	22361227	22361598	3.210000e-160	575.0
29	TraesCS7A01G492500	chr1A	89.975	399	20	3	856	1250	22351095	22351477	7.150000e-137	497.0
30	TraesCS7A01G492500	chr1A	80.802	349	41	25	825	1161	497265762	497265428	2.210000e-62	250.0
31	TraesCS7A01G492500	chr7B	84.368	467	26	22	1	438	665285753	665285305	7.410000e-112	414.0
32	TraesCS7A01G492500	chr7B	91.603	262	11	7	1	252	665139984	665139724	5.890000e-93	351.0
33	TraesCS7A01G492500	chr7B	78.756	386	32	26	440	810	664796988	664797338	2.900000e-51	213.0
34	TraesCS7A01G492500	chr7B	83.756	197	23	7	581	774	664936509	664936699	1.060000e-40	178.0
35	TraesCS7A01G492500	chr7B	80.349	229	27	12	553	774	665284729	665284512	1.380000e-34	158.0
36	TraesCS7A01G492500	chr7B	78.351	291	27	29	410	670	664353804	664354088	4.960000e-34	156.0
37	TraesCS7A01G492500	chr7B	90.000	100	8	2	24	122	664796355	664796453	1.080000e-25	128.0
38	TraesCS7A01G492500	chr7D	94.068	236	11	2	1	235	590330484	590330251	4.550000e-94	355.0
39	TraesCS7A01G492500	chr7D	81.100	418	39	34	409	802	589857559	589857960	7.790000e-77	298.0
40	TraesCS7A01G492500	chr7D	75.566	618	70	54	245	810	590064627	590064039	2.880000e-56	230.0
41	TraesCS7A01G492500	chr7D	77.922	385	34	30	335	703	590218423	590218074	3.780000e-45	193.0
42	TraesCS7A01G492500	chr7D	78.491	265	28	21	552	802	589869495	589869246	2.980000e-31	147.0
43	TraesCS7A01G492500	chr7D	90.291	103	8	2	27	128	590064992	590064891	2.320000e-27	134.0
44	TraesCS7A01G492500	chr7D	90.291	103	8	2	27	128	590218928	590218827	2.320000e-27	134.0
45	TraesCS7A01G492500	chr7D	88.350	103	7	4	24	122	589857060	589857161	6.510000e-23	119.0
46	TraesCS7A01G492500	chr4A	89.000	100	10	1	24	122	416900847	416900946	5.030000e-24	122.0

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	TraesCS7A01G492500	chr7A	681253691	681257398	3707	False	6848.0	6848	100.000000	1	3708	1	chr7A.!!$F1	3707
1	TraesCS7A01G492500	chr6A	32921831	32923910	2079	False	3321.0	3321	95.675000	825	2880	1	chr6A.!!$F1	2055
2	TraesCS7A01G492500	chr6A	32932991	32933824	833	False	1439.0	1439	97.842000	2876	3708	1	chr6A.!!$F2	832
3	TraesCS7A01G492500	chr3D	599394000	599396919	2919	True	2048.5	2643	92.444000	825	3708	2	chr3D.!!$R2	2883
4	TraesCS7A01G492500	chr3D	99802084	99803751	1667	True	1345.0	1345	81.970000	1458	3058	1	chr3D.!!$R1	1600
5	TraesCS7A01G492500	chr2A	4048485	4050342	1857	True	1570.0	2290	96.611500	825	2711	2	chr2A.!!$R1	1886
6	TraesCS7A01G492500	chr4B	602034650	602035729	1079	False	1471.0	1471	91.397000	823	1893	1	chr4B.!!$F1	1070
7	TraesCS7A01G492500	chr4B	71229821	71231443	1622	True	1423.0	1423	83.087000	1917	3483	1	chr4B.!!$R1	1566
8	TraesCS7A01G492500	chr6B	25583581	25585204	1623	True	1445.0	1445	83.333000	1917	3483	1	chr6B.!!$R1	1566
9	TraesCS7A01G492500	chr1B	74500715	74502284	1569	False	1443.0	1443	83.531000	1908	3483	1	chr1B.!!$F1	1575
10	TraesCS7A01G492500	chr5B	682198897	682199983	1086	False	1426.0	1426	90.616000	825	1893	1	chr5B.!!$F1	1068
11	TraesCS7A01G492500	chr5B	70358176	70359584	1408	True	1157.0	1157	82.120000	1458	2818	1	chr5B.!!$R1	1360
12	TraesCS7A01G492500	chr5D	9580199	9582320	2121	False	847.5	1406	81.641500	1458	3483	2	chr5D.!!$F1	2025
13	TraesCS7A01G492500	chr5A	675155710	675157377	1667	False	1367.0	1367	82.220000	1458	3058	1	chr5A.!!$F1	1600
14	TraesCS7A01G492500	chr5A	622413847	622415522	1675	True	760.0	1205	85.095500	1917	3483	2	chr5A.!!$R1	1566
15	TraesCS7A01G492500	chr2D	607814923	607817306	2383	False	538.0	1188	83.921333	825	3311	3	chr2D.!!$F1	2486
16	TraesCS7A01G492500	chr2B	175941621	175942857	1236	True	1171.0	1171	84.202000	1907	3120	1	chr2B.!!$R1	1213
17	TraesCS7A01G492500	chr7B	665284512	665285753	1241	True	286.0	414	82.358500	1	774	2	chr7B.!!$R2	773
18	TraesCS7A01G492500	chr7D	589857060	589857960	900	False	208.5	298	84.725000	24	802	2	chr7D.!!$F1	778

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	End Stability	Orientation
766	1459	0.029834	GACCACACACAAGCAAGCAG	59.970	55.0	4.24	F
812	1506	0.107017	CCCACCTCAGGCAATTCGAT	60.107	55.0	3.59	F
1125	1835	0.396417	CGATGGGAGAGGAGACAGGT	60.396	60.0	4.00	F
1504	2235	0.921166	ATGTGGAGGTGCATCATGGA	59.079	50.0	3.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	End Stability	Orientation
2149	2954	2.165357	TCATCCTCTTCTGGCAGCTA	57.835	50.000	10.34	3.32	R
2349	3158	3.569194	TTTGCACCCTGTTCTTCACTA	57.431	42.857	0.00	2.74	R
2661	3470	3.698040	CACTTCCAATGCTGCTTTCCTAT	59.302	43.478	0.00	2.57	R
3305	4340	3.593442	AGGTTGGAGTGGTTGATTTGA	57.407	42.857	0.00	2.69	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
122	130	5.297029	GCAATTAACCATACTTGTCCTCCTC	59.703	44.000	0.00	0.00	0.00	3.71
125	133	0.824109	CCATACTTGTCCTCCTCGCA	59.176	55.000	0.00	0.00	0.00	5.10
191	199	1.203052	CATGCATCGTCCTTTTGCCTT	59.797	47.619	0.00	0.00	35.51	4.35
192	200	1.327303	TGCATCGTCCTTTTGCCTTT	58.673	45.000	0.00	0.00	35.51	3.11
193	201	2.509569	TGCATCGTCCTTTTGCCTTTA	58.490	42.857	0.00	0.00	35.51	1.85
194	202	2.227865	TGCATCGTCCTTTTGCCTTTAC	59.772	45.455	0.00	0.00	35.51	2.01
195	203	2.488153	GCATCGTCCTTTTGCCTTTACT	59.512	45.455	0.00	0.00	0.00	2.24
196	204	3.687698	GCATCGTCCTTTTGCCTTTACTA	59.312	43.478	0.00	0.00	0.00	1.82
197	205	4.436986	GCATCGTCCTTTTGCCTTTACTAC	60.437	45.833	0.00	0.00	0.00	2.73
198	206	4.612264	TCGTCCTTTTGCCTTTACTACT	57.388	40.909	0.00	0.00	0.00	2.57
199	207	4.312443	TCGTCCTTTTGCCTTTACTACTG	58.688	43.478	0.00	0.00	0.00	2.74
200	208	4.062991	CGTCCTTTTGCCTTTACTACTGT	58.937	43.478	0.00	0.00	0.00	3.55
201	209	4.151867	CGTCCTTTTGCCTTTACTACTGTC	59.848	45.833	0.00	0.00	0.00	3.51
202	210	5.306394	GTCCTTTTGCCTTTACTACTGTCT	58.694	41.667	0.00	0.00	0.00	3.41
203	211	6.461640	GTCCTTTTGCCTTTACTACTGTCTA	58.538	40.000	0.00	0.00	0.00	2.59
204	212	6.368243	GTCCTTTTGCCTTTACTACTGTCTAC	59.632	42.308	0.00	0.00	0.00	2.59
321	501	4.711949	CTCAGCCTGCCTGCCGTT	62.712	66.667	0.00	0.00	41.50	4.44
340	520	3.063180	CGTTATCCTTCTGCTTCTTGCTG	59.937	47.826	0.00	0.00	43.37	4.41
354	543	4.511617	TCTTGCTGATCTGATCCGTATC	57.488	45.455	14.71	1.07	0.00	2.24
355	544	4.148079	TCTTGCTGATCTGATCCGTATCT	58.852	43.478	14.71	0.00	32.93	1.98
359	548	3.129638	GCTGATCTGATCCGTATCTACCC	59.870	52.174	14.71	0.00	32.93	3.69
360	549	3.697045	CTGATCTGATCCGTATCTACCCC	59.303	52.174	14.71	0.00	32.93	4.95
361	550	3.333980	TGATCTGATCCGTATCTACCCCT	59.666	47.826	14.71	0.00	32.93	4.79
368	557	7.001099	TGATCCGTATCTACCCCTTTTTATC	57.999	40.000	0.00	0.00	32.93	1.75
373	568	5.995897	CGTATCTACCCCTTTTTATCCAAGG	59.004	44.000	0.00	0.00	40.67	3.61
381	576	3.373110	CCTTTTTATCCAAGGGAGGGAGG	60.373	52.174	0.00	0.00	37.71	4.30
385	580	2.277126	ATCCAAGGGAGGGAGGGAGG	62.277	65.000	0.00	0.00	37.96	4.30
386	581	2.456840	CAAGGGAGGGAGGGAGGT	59.543	66.667	0.00	0.00	0.00	3.85
438	640	4.653341	AGAGAGAAGAGAGAGAGAGAGAGG	59.347	50.000	0.00	0.00	0.00	3.69
439	641	4.624913	AGAGAAGAGAGAGAGAGAGAGGA	58.375	47.826	0.00	0.00	0.00	3.71
440	642	4.407296	AGAGAAGAGAGAGAGAGAGAGGAC	59.593	50.000	0.00	0.00	0.00	3.85
441	643	4.104086	AGAAGAGAGAGAGAGAGAGGACA	58.896	47.826	0.00	0.00	0.00	4.02
444	646	3.137176	AGAGAGAGAGAGAGAGGACATGG	59.863	52.174	0.00	0.00	0.00	3.66
445	647	3.122480	AGAGAGAGAGAGAGGACATGGA	58.878	50.000	0.00	0.00	0.00	3.41
446	648	3.527253	AGAGAGAGAGAGAGGACATGGAA	59.473	47.826	0.00	0.00	0.00	3.53
447	649	3.885297	GAGAGAGAGAGAGGACATGGAAG	59.115	52.174	0.00	0.00	0.00	3.46
448	650	2.362077	GAGAGAGAGAGGACATGGAAGC	59.638	54.545	0.00	0.00	0.00	3.86
455	657	3.037549	AGAGGACATGGAAGCTTAGGAG	58.962	50.000	0.00	0.00	0.00	3.69
460	662	1.419387	CATGGAAGCTTAGGAGGAGGG	59.581	57.143	0.00	0.00	0.00	4.30
461	663	0.417841	TGGAAGCTTAGGAGGAGGGT	59.582	55.000	0.00	0.00	0.00	4.34
463	665	1.574263	GAAGCTTAGGAGGAGGGTGT	58.426	55.000	0.00	0.00	0.00	4.16
464	666	2.626149	GGAAGCTTAGGAGGAGGGTGTA	60.626	54.545	0.00	0.00	0.00	2.90
494	938	2.100197	TCGATCCGAGAGTTTCACCAT	58.900	47.619	0.00	0.00	0.00	3.55
503	947	4.382470	CGAGAGTTTCACCATCCTCTCATT	60.382	45.833	13.96	0.00	46.60	2.57
505	949	4.080638	AGAGTTTCACCATCCTCTCATTCC	60.081	45.833	0.00	0.00	28.22	3.01
506	950	3.588842	AGTTTCACCATCCTCTCATTCCA	59.411	43.478	0.00	0.00	0.00	3.53
522	969	2.006805	TCCACCCACAATCATTTGCA	57.993	45.000	0.00	0.00	36.22	4.08
527	974	1.619827	CCCACAATCATTTGCACCACT	59.380	47.619	0.00	0.00	36.22	4.00
528	975	2.037511	CCCACAATCATTTGCACCACTT	59.962	45.455	0.00	0.00	36.22	3.16
534	981	5.697633	ACAATCATTTGCACCACTTCATTTC	59.302	36.000	0.00	0.00	36.22	2.17
535	982	4.255833	TCATTTGCACCACTTCATTTCC	57.744	40.909	0.00	0.00	0.00	3.13
538	985	2.064434	TGCACCACTTCATTTCCACA	57.936	45.000	0.00	0.00	0.00	4.17
595	1270	5.106555	CCATGGGCGATGATCTATTTAACAC	60.107	44.000	11.37	0.00	33.31	3.32
601	1276	3.173668	TGATCTATTTAACACGCGCCT	57.826	42.857	5.73	0.00	0.00	5.52
653	1328	0.036952	TCCTCGCTTGCTTCTCCTTG	60.037	55.000	0.00	0.00	0.00	3.61
654	1329	0.321122	CCTCGCTTGCTTCTCCTTGT	60.321	55.000	0.00	0.00	0.00	3.16
655	1330	1.517242	CTCGCTTGCTTCTCCTTGTT	58.483	50.000	0.00	0.00	0.00	2.83
657	1332	3.067106	CTCGCTTGCTTCTCCTTGTTTA	58.933	45.455	0.00	0.00	0.00	2.01
658	1333	3.067106	TCGCTTGCTTCTCCTTGTTTAG	58.933	45.455	0.00	0.00	0.00	1.85
659	1334	3.067106	CGCTTGCTTCTCCTTGTTTAGA	58.933	45.455	0.00	0.00	0.00	2.10
661	1336	4.870426	CGCTTGCTTCTCCTTGTTTAGATA	59.130	41.667	0.00	0.00	0.00	1.98
662	1337	5.006165	CGCTTGCTTCTCCTTGTTTAGATAG	59.994	44.000	0.00	0.00	0.00	2.08
663	1338	5.220758	GCTTGCTTCTCCTTGTTTAGATAGC	60.221	44.000	0.00	0.00	31.88	2.97
664	1339	4.770795	TGCTTCTCCTTGTTTAGATAGCC	58.229	43.478	0.00	0.00	31.02	3.93
665	1340	4.471386	TGCTTCTCCTTGTTTAGATAGCCT	59.529	41.667	0.00	0.00	31.02	4.58
666	1341	5.053811	GCTTCTCCTTGTTTAGATAGCCTC	58.946	45.833	0.00	0.00	0.00	4.70
667	1342	5.606505	CTTCTCCTTGTTTAGATAGCCTCC	58.393	45.833	0.00	0.00	0.00	4.30
668	1343	4.884961	TCTCCTTGTTTAGATAGCCTCCT	58.115	43.478	0.00	0.00	0.00	3.69
669	1344	4.896482	TCTCCTTGTTTAGATAGCCTCCTC	59.104	45.833	0.00	0.00	0.00	3.71
670	1345	3.967987	TCCTTGTTTAGATAGCCTCCTCC	59.032	47.826	0.00	0.00	0.00	4.30
671	1346	3.970640	CCTTGTTTAGATAGCCTCCTCCT	59.029	47.826	0.00	0.00	0.00	3.69
672	1347	4.039852	CCTTGTTTAGATAGCCTCCTCCTC	59.960	50.000	0.00	0.00	0.00	3.71
699	1385	0.105593	CTCCATCATCACCTCCACGG	59.894	60.000	0.00	0.00	39.35	4.94
701	1387	1.221566	CATCATCACCTCCACGGCA	59.778	57.895	0.00	0.00	35.61	5.69
740	1433	0.942410	GTCCTTCACGCAACGCTACA	60.942	55.000	0.00	0.00	0.00	2.74
762	1455	2.560542	ACAAAAGACCACACACAAGCAA	59.439	40.909	0.00	0.00	0.00	3.91
763	1456	3.181397	CAAAAGACCACACACAAGCAAG	58.819	45.455	0.00	0.00	0.00	4.01
764	1457	0.740737	AAGACCACACACAAGCAAGC	59.259	50.000	0.00	0.00	0.00	4.01
765	1458	0.394216	AGACCACACACAAGCAAGCA	60.394	50.000	0.00	0.00	0.00	3.91
766	1459	0.029834	GACCACACACAAGCAAGCAG	59.970	55.000	0.00	0.00	0.00	4.24
768	1461	0.309922	CCACACACAAGCAAGCAGAG	59.690	55.000	0.00	0.00	0.00	3.35
780	1474	1.123077	AAGCAGAGTCACACCACTGA	58.877	50.000	0.00	0.00	32.90	3.41
802	1496	2.439104	GGCTAGCTCCCCACCTCAG	61.439	68.421	15.72	0.00	0.00	3.35
803	1497	2.439104	GCTAGCTCCCCACCTCAGG	61.439	68.421	7.70	0.00	0.00	3.86
804	1498	2.365635	TAGCTCCCCACCTCAGGC	60.366	66.667	0.00	0.00	0.00	4.85
805	1499	3.252585	TAGCTCCCCACCTCAGGCA	62.253	63.158	0.00	0.00	0.00	4.75
806	1500	2.763988	TAGCTCCCCACCTCAGGCAA	62.764	60.000	0.00	0.00	0.00	4.52
807	1501	2.988839	GCTCCCCACCTCAGGCAAT	61.989	63.158	0.00	0.00	0.00	3.56
808	1502	1.693640	CTCCCCACCTCAGGCAATT	59.306	57.895	0.00	0.00	0.00	2.32
809	1503	0.394899	CTCCCCACCTCAGGCAATTC	60.395	60.000	0.00	0.00	0.00	2.17
810	1504	1.750399	CCCCACCTCAGGCAATTCG	60.750	63.158	0.00	0.00	0.00	3.34
811	1505	1.299648	CCCACCTCAGGCAATTCGA	59.700	57.895	0.00	0.00	0.00	3.71
812	1506	0.107017	CCCACCTCAGGCAATTCGAT	60.107	55.000	0.00	0.00	0.00	3.59
813	1507	1.303309	CCACCTCAGGCAATTCGATC	58.697	55.000	0.00	0.00	0.00	3.69
814	1508	1.134280	CCACCTCAGGCAATTCGATCT	60.134	52.381	0.00	0.00	0.00	2.75
815	1509	2.103094	CCACCTCAGGCAATTCGATCTA	59.897	50.000	0.00	0.00	0.00	1.98
816	1510	3.244353	CCACCTCAGGCAATTCGATCTAT	60.244	47.826	0.00	0.00	0.00	1.98
817	1511	3.993081	CACCTCAGGCAATTCGATCTATC	59.007	47.826	0.00	0.00	0.00	2.08
854	1548	2.353406	GCACTGGCGGTCTAAGAACTTA	60.353	50.000	0.00	0.00	0.00	2.24
943	1637	2.294233	GGTGCAATCAAGTCACACACAT	59.706	45.455	0.00	0.00	32.89	3.21
957	1651	2.029288	CACATCAGCTGAACCGCGT	61.029	57.895	22.50	10.13	34.40	6.01
1125	1835	0.396417	CGATGGGAGAGGAGACAGGT	60.396	60.000	0.00	0.00	0.00	4.00
1129	1839	1.610673	GGAGAGGAGACAGGTGGCA	60.611	63.158	0.00	0.00	0.00	4.92
1135	1845	2.603473	AGACAGGTGGCACCGCTA	60.603	61.111	29.76	0.00	44.90	4.26
1172	1882	1.079819	CGGCAAGTCAGTCATCGGT	60.080	57.895	0.00	0.00	0.00	4.69
1193	1903	2.280186	GATGGTGGATCCGGCGAC	60.280	66.667	9.30	0.00	39.52	5.19
1298	2027	3.942130	TCGGCAATAGATGATGATCGT	57.058	42.857	0.00	0.00	33.34	3.73
1485	2216	9.513906	TGTAGGTTATGAATCAGTGAAATTCAA	57.486	29.630	12.05	1.85	44.05	2.69
1504	2235	0.921166	ATGTGGAGGTGCATCATGGA	59.079	50.000	0.00	0.00	0.00	3.41
1578	2309	4.499183	TGTTGGTTTGACAATTTGGACAC	58.501	39.130	0.78	0.00	32.24	3.67
2063	2866	5.065914	ACAAGAATGTAGATGCTGTTGTGT	58.934	37.500	0.00	0.00	38.24	3.72
2149	2954	8.837389	CAGATGATGTGTATGAAGATGATTTGT	58.163	33.333	0.00	0.00	0.00	2.83
2169	2974	1.509373	AGCTGCCAGAAGAGGATGAT	58.491	50.000	0.00	0.00	0.00	2.45
2244	3053	8.966155	AAAAAGAAGGAGAACCCCATTTATAA	57.034	30.769	0.00	0.00	36.73	0.98
2253	3062	9.251440	GGAGAACCCCATTTATAAGTTTAAACT	57.749	33.333	15.22	15.22	42.04	2.66
2446	3255	2.489073	CCCTTGGAAACTAGTGGCTGTT	60.489	50.000	0.00	0.00	0.00	3.16
2661	3470	2.755655	GCAGACACAAGCTAGGTAGAGA	59.244	50.000	0.00	0.00	0.00	3.10
2705	3514	0.257039	GCATGGGGATGAGGTGAAGT	59.743	55.000	0.00	0.00	0.00	3.01
3085	3990	8.375506	AGTTCAGTTATTGTTCATAGGTTCAGA	58.624	33.333	0.00	0.00	0.00	3.27
3114	4035	8.597662	TGTTCATAGGTTCAGTTACTGTTTAC	57.402	34.615	12.41	8.90	32.61	2.01
3120	4041	9.959721	ATAGGTTCAGTTACTGTTTACATTCAT	57.040	29.630	12.41	0.00	32.61	2.57
3305	4340	4.816385	CAGACAACAACTATGGACTTGTGT	59.184	41.667	0.00	0.00	30.88	3.72
3327	4362	4.099419	GTCAAATCAACCACTCCAACCTTT	59.901	41.667	0.00	0.00	0.00	3.11
3476	4512	9.868277	TTGAATAACACTTGTGAAGTTTTCAAT	57.132	25.926	7.83	0.00	42.15	2.57
3567	4610	8.450578	TTGTCTGAAAATGAACAGTAACTGAT	57.549	30.769	0.00	0.00	35.18	2.90
3661	4704	3.383185	GCTAGAGAGCTACCTGTGTTGAT	59.617	47.826	0.00	0.00	45.98	2.57

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
15	16	2.094675	GGATGCTTTATGTGGTGTGCT	58.905	47.619	0.00	0.00	0.00	4.40
72	73	5.677091	GCCATGTGTATTGCTTGTTTAGAGG	60.677	44.000	0.00	0.00	0.00	3.69
79	83	0.810648	CCGCCATGTGTATTGCTTGT	59.189	50.000	0.00	0.00	0.00	3.16
122	130	1.570813	TCTCAAGACAGTGTGTTGCG	58.429	50.000	24.43	19.76	36.86	4.85
125	133	3.055094	AGTGGTTCTCAAGACAGTGTGTT	60.055	43.478	0.00	0.00	0.00	3.32
191	199	4.744570	GCACATGCAGTAGACAGTAGTAA	58.255	43.478	0.00	0.00	41.59	2.24
192	200	4.371855	GCACATGCAGTAGACAGTAGTA	57.628	45.455	0.00	0.00	41.59	1.82
193	201	3.238108	GCACATGCAGTAGACAGTAGT	57.762	47.619	0.00	0.00	41.59	2.73
304	480	2.599645	ATAACGGCAGGCAGGCTGAG	62.600	60.000	27.69	20.69	42.91	3.35
305	481	2.593468	GATAACGGCAGGCAGGCTGA	62.593	60.000	27.69	6.47	42.91	4.26
340	520	3.970842	AGGGGTAGATACGGATCAGATC	58.029	50.000	10.99	1.18	34.17	2.75
359	548	3.373110	CCTCCCTCCCTTGGATAAAAAGG	60.373	52.174	0.00	0.00	43.33	3.11
360	549	3.373110	CCCTCCCTCCCTTGGATAAAAAG	60.373	52.174	0.00	0.00	0.00	2.27
361	550	2.585432	CCCTCCCTCCCTTGGATAAAAA	59.415	50.000	0.00	0.00	0.00	1.94
368	557	1.898190	TACCTCCCTCCCTCCCTTGG	61.898	65.000	0.00	0.00	0.00	3.61
373	568	1.000041	TCTCCTACCTCCCTCCCTCC	61.000	65.000	0.00	0.00	0.00	4.30
377	572	1.423921	CTCTCTCTCCTACCTCCCTCC	59.576	61.905	0.00	0.00	0.00	4.30
381	576	3.314693	TCTCTCTCTCTCTCCTACCTCC	58.685	54.545	0.00	0.00	0.00	4.30
385	580	5.871396	TCTTCTCTCTCTCTCTCTCCTAC	57.129	47.826	0.00	0.00	0.00	3.18
386	581	6.672218	TCTTTCTTCTCTCTCTCTCTCTCCTA	59.328	42.308	0.00	0.00	0.00	2.94
438	640	2.103941	CCTCCTCCTAAGCTTCCATGTC	59.896	54.545	0.00	0.00	0.00	3.06
439	641	2.122768	CCTCCTCCTAAGCTTCCATGT	58.877	52.381	0.00	0.00	0.00	3.21
440	642	1.419387	CCCTCCTCCTAAGCTTCCATG	59.581	57.143	0.00	0.00	0.00	3.66
441	643	1.010170	ACCCTCCTCCTAAGCTTCCAT	59.990	52.381	0.00	0.00	0.00	3.41
444	646	1.574263	ACACCCTCCTCCTAAGCTTC	58.426	55.000	0.00	0.00	0.00	3.86
445	647	2.753247	CTACACCCTCCTCCTAAGCTT	58.247	52.381	3.48	3.48	0.00	3.74
446	648	1.689892	GCTACACCCTCCTCCTAAGCT	60.690	57.143	0.00	0.00	0.00	3.74
447	649	0.753867	GCTACACCCTCCTCCTAAGC	59.246	60.000	0.00	0.00	0.00	3.09
448	650	1.033574	CGCTACACCCTCCTCCTAAG	58.966	60.000	0.00	0.00	0.00	2.18
494	938	1.741028	TTGTGGGTGGAATGAGAGGA	58.259	50.000	0.00	0.00	0.00	3.71
503	947	1.617850	GTGCAAATGATTGTGGGTGGA	59.382	47.619	0.00	0.00	38.85	4.02
505	949	1.343789	TGGTGCAAATGATTGTGGGTG	59.656	47.619	0.00	0.00	38.85	4.61
506	950	1.344114	GTGGTGCAAATGATTGTGGGT	59.656	47.619	0.00	0.00	38.85	4.51
522	969	1.620822	GGCTGTGGAAATGAAGTGGT	58.379	50.000	0.00	0.00	0.00	4.16
527	974	2.376518	AGAGAAGGGCTGTGGAAATGAA	59.623	45.455	0.00	0.00	0.00	2.57
528	975	1.988107	AGAGAAGGGCTGTGGAAATGA	59.012	47.619	0.00	0.00	0.00	2.57
534	981	0.617249	AGGAGAGAGAAGGGCTGTGG	60.617	60.000	0.00	0.00	0.00	4.17
535	982	0.823460	GAGGAGAGAGAAGGGCTGTG	59.177	60.000	0.00	0.00	0.00	3.66
538	985	1.215423	GAGAGAGGAGAGAGAAGGGCT	59.785	57.143	0.00	0.00	0.00	5.19
601	1276	1.761667	AGGCAACAAGCAAAGGCCA	60.762	52.632	5.01	0.00	46.96	5.36
653	1328	2.029739	GCGAGGAGGAGGCTATCTAAAC	60.030	54.545	0.00	0.00	0.00	2.01
654	1329	2.240279	GCGAGGAGGAGGCTATCTAAA	58.760	52.381	0.00	0.00	0.00	1.85
655	1330	1.548128	GGCGAGGAGGAGGCTATCTAA	60.548	57.143	0.00	0.00	0.00	2.10
657	1332	1.228737	GGCGAGGAGGAGGCTATCT	60.229	63.158	0.00	0.00	0.00	1.98
658	1333	1.531840	TGGCGAGGAGGAGGCTATC	60.532	63.158	0.00	0.00	0.00	2.08
659	1334	1.834822	GTGGCGAGGAGGAGGCTAT	60.835	63.158	0.00	0.00	0.00	2.97
661	1336	3.914551	AAGTGGCGAGGAGGAGGCT	62.915	63.158	0.00	0.00	0.00	4.58
662	1337	3.378399	GAAGTGGCGAGGAGGAGGC	62.378	68.421	0.00	0.00	0.00	4.70
663	1338	1.671901	GAGAAGTGGCGAGGAGGAGG	61.672	65.000	0.00	0.00	0.00	4.30
664	1339	1.671901	GGAGAAGTGGCGAGGAGGAG	61.672	65.000	0.00	0.00	0.00	3.69
665	1340	1.682684	GGAGAAGTGGCGAGGAGGA	60.683	63.158	0.00	0.00	0.00	3.71
666	1341	1.333636	ATGGAGAAGTGGCGAGGAGG	61.334	60.000	0.00	0.00	0.00	4.30
667	1342	0.103937	GATGGAGAAGTGGCGAGGAG	59.896	60.000	0.00	0.00	0.00	3.69
668	1343	0.614697	TGATGGAGAAGTGGCGAGGA	60.615	55.000	0.00	0.00	0.00	3.71
669	1344	0.467384	ATGATGGAGAAGTGGCGAGG	59.533	55.000	0.00	0.00	0.00	4.63
670	1345	1.137675	TGATGATGGAGAAGTGGCGAG	59.862	52.381	0.00	0.00	0.00	5.03
671	1346	1.134699	GTGATGATGGAGAAGTGGCGA	60.135	52.381	0.00	0.00	0.00	5.54
672	1347	1.293924	GTGATGATGGAGAAGTGGCG	58.706	55.000	0.00	0.00	0.00	5.69
699	1385	1.376553	GAGGAACAGAGGCAGGTGC	60.377	63.158	0.00	0.00	41.14	5.01
701	1387	0.907230	GAGGAGGAACAGAGGCAGGT	60.907	60.000	0.00	0.00	0.00	4.00
710	1396	0.966920	GTGAAGGACGAGGAGGAACA	59.033	55.000	0.00	0.00	0.00	3.18
711	1397	3.816580	GTGAAGGACGAGGAGGAAC	57.183	57.895	0.00	0.00	0.00	3.62
732	1425	3.011119	TGTGGTCTTTTGTTGTAGCGTT	58.989	40.909	0.00	0.00	0.00	4.84
740	1433	2.560542	TGCTTGTGTGTGGTCTTTTGTT	59.439	40.909	0.00	0.00	0.00	2.83
762	1455	0.390860	GTCAGTGGTGTGACTCTGCT	59.609	55.000	0.00	0.00	43.10	4.24
763	1456	2.906047	GTCAGTGGTGTGACTCTGC	58.094	57.895	0.00	0.00	43.10	4.26
768	1461	0.179045	AGCCAAGTCAGTGGTGTGAC	60.179	55.000	0.00	0.00	46.22	3.67
780	1474	2.301738	GGTGGGGAGCTAGCCAAGT	61.302	63.158	12.13	0.00	0.00	3.16
810	1504	6.863645	TGCTATTTACTCTTGTGCGATAGATC	59.136	38.462	0.00	0.00	39.76	2.75
811	1505	6.642950	GTGCTATTTACTCTTGTGCGATAGAT	59.357	38.462	0.00	0.00	39.76	1.98
812	1506	5.977725	GTGCTATTTACTCTTGTGCGATAGA	59.022	40.000	0.00	0.00	39.76	1.98
813	1507	5.980116	AGTGCTATTTACTCTTGTGCGATAG	59.020	40.000	0.00	0.00	0.00	2.08
814	1508	5.748630	CAGTGCTATTTACTCTTGTGCGATA	59.251	40.000	0.00	0.00	0.00	2.92
815	1509	4.568359	CAGTGCTATTTACTCTTGTGCGAT	59.432	41.667	0.00	0.00	0.00	4.58
816	1510	3.926527	CAGTGCTATTTACTCTTGTGCGA	59.073	43.478	0.00	0.00	0.00	5.10
817	1511	3.062639	CCAGTGCTATTTACTCTTGTGCG	59.937	47.826	0.00	0.00	0.00	5.34
818	1512	3.181506	GCCAGTGCTATTTACTCTTGTGC	60.182	47.826	0.00	0.00	33.53	4.57
819	1513	3.062639	CGCCAGTGCTATTTACTCTTGTG	59.937	47.826	0.00	0.00	34.43	3.33
820	1514	3.262420	CGCCAGTGCTATTTACTCTTGT	58.738	45.455	0.00	0.00	34.43	3.16
821	1515	2.609459	CCGCCAGTGCTATTTACTCTTG	59.391	50.000	0.00	0.00	34.43	3.02
943	1637	1.954146	GACAACGCGGTTCAGCTGA	60.954	57.895	13.74	13.74	34.40	4.26
1000	1694	0.987081	ATGCAGTCCAGAGGCCTCAT	60.987	55.000	33.90	16.57	0.00	2.90
1172	1882	3.088941	GCCGGATCCACCATCGTCA	62.089	63.158	13.41	0.00	38.90	4.35
1298	2027	8.486210	AGTCATAAAACTACTATGATGCTCCAA	58.514	33.333	0.00	0.00	37.91	3.53
1308	2038	9.890629	TGCTCATTGAAGTCATAAAACTACTAT	57.109	29.630	0.00	0.00	0.00	2.12
1485	2216	0.921166	TCCATGATGCACCTCCACAT	59.079	50.000	0.00	0.00	0.00	3.21
1517	2248	2.619931	TGTCAGATTCACTCCCTTCCA	58.380	47.619	0.00	0.00	0.00	3.53
1674	2405	6.000246	TGATTTCCACCATATCTGCAAGTA	58.000	37.500	0.00	0.00	33.76	2.24
1861	2592	7.554118	AGTTTCTCTGTTTTCATCTTCTTGTCA	59.446	33.333	0.00	0.00	0.00	3.58
2063	2866	5.653330	TGCCTTTCTCAATCAAAGCATCATA	59.347	36.000	0.00	0.00	30.61	2.15
2149	2954	2.165357	TCATCCTCTTCTGGCAGCTA	57.835	50.000	10.34	0.00	0.00	3.32
2169	2974	8.934023	AGTCACTTTTATGTTTTCTATCCCAA	57.066	30.769	0.00	0.00	0.00	4.12
2244	3053	8.357402	CAACAGCTGGGTTAAATAGTTTAAACT	58.643	33.333	23.58	23.58	41.44	2.66
2253	3062	4.704540	CCATGTCAACAGCTGGGTTAAATA	59.295	41.667	19.93	0.00	0.00	1.40
2349	3158	3.569194	TTTGCACCCTGTTCTTCACTA	57.431	42.857	0.00	0.00	0.00	2.74
2446	3255	9.739276	AGAAAAGATTGTGTCCTATTGTCATTA	57.261	29.630	0.00	0.00	0.00	1.90
2661	3470	3.698040	CACTTCCAATGCTGCTTTCCTAT	59.302	43.478	0.00	0.00	0.00	2.57
2705	3514	6.931281	GCATATCTCCAAAGCAATGAGTACTA	59.069	38.462	0.00	0.00	0.00	1.82
3085	3990	9.959721	AACAGTAACTGAACCTATGAACATTAT	57.040	29.630	0.00	0.00	35.18	1.28
3088	3993	9.216117	GTAAACAGTAACTGAACCTATGAACAT	57.784	33.333	0.00	0.00	35.18	2.71
3114	4035	9.252962	AGTAAGAAGCAAAACAAGAAATGAATG	57.747	29.630	0.00	0.00	0.00	2.67
3120	4041	6.310224	GTGCAAGTAAGAAGCAAAACAAGAAA	59.690	34.615	0.00	0.00	40.35	2.52
3305	4340	3.593442	AGGTTGGAGTGGTTGATTTGA	57.407	42.857	0.00	0.00	0.00	2.69
3353	4388	5.414144	GCATAAGCTTCTGGATTATCTTCCC	59.586	44.000	13.15	0.00	34.71	3.97
3661	4704	6.417258	TGTGATTTAATCCTCTCAAGCATGA	58.583	36.000	0.00	0.00	0.00	3.07

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.