Multiple sequence alignment - TraesCS3A01G049400

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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 TraesCS3A01G049400 chr3A 100.000 4779 0 0 1 4779 26193495 26198273 0.000000e+00 8826.0
1 TraesCS3A01G049400 chr3A 91.593 1594 112 11 2277 3856 26141561 26143146 0.000000e+00 2182.0
2 TraesCS3A01G049400 chr3A 88.956 824 79 12 3959 4779 58845805 58844991 0.000000e+00 1007.0
3 TraesCS3A01G049400 chr3A 76.543 324 68 6 1358 1677 19290810 19291129 2.290000e-38 171.0
4 TraesCS3A01G049400 chr3D 93.971 1841 101 6 2059 3892 18659387 18661224 0.000000e+00 2776.0
5 TraesCS3A01G049400 chr3D 93.124 1716 109 4 2139 3849 18926509 18928220 0.000000e+00 2507.0
6 TraesCS3A01G049400 chr3D 95.066 1297 63 1 605 1900 18657742 18659038 0.000000e+00 2039.0
7 TraesCS3A01G049400 chr3D 92.210 1181 67 16 899 2059 18911024 18912199 0.000000e+00 1648.0
8 TraesCS3A01G049400 chr3D 91.713 543 37 3 2059 2593 18740592 18741134 0.000000e+00 747.0
9 TraesCS3A01G049400 chr3D 92.292 506 29 6 1475 1972 18739710 18740213 0.000000e+00 710.0
10 TraesCS3A01G049400 chr3D 88.548 489 31 7 325 790 18910529 18911015 1.930000e-158 569.0
11 TraesCS3A01G049400 chr3D 88.308 325 15 5 325 626 18657403 18657727 7.560000e-98 368.0
12 TraesCS3A01G049400 chr3D 82.822 163 10 13 1900 2059 18659149 18659296 3.880000e-26 130.0
13 TraesCS3A01G049400 chr3D 74.517 259 47 14 949 1201 18779002 18779247 1.420000e-15 95.3
14 TraesCS3A01G049400 chr3B 94.134 1824 99 4 2059 3875 29592885 29591063 0.000000e+00 2769.0
15 TraesCS3A01G049400 chr3B 92.733 1844 106 11 2059 3892 30091598 30089773 0.000000e+00 2638.0
16 TraesCS3A01G049400 chr3B 94.796 1422 72 2 2472 3892 30409435 30410855 0.000000e+00 2215.0
17 TraesCS3A01G049400 chr3B 89.801 1657 111 7 352 1977 30406664 30408293 0.000000e+00 2071.0
18 TraesCS3A01G049400 chr3B 93.595 1374 75 7 610 1975 29594621 29593253 0.000000e+00 2037.0
19 TraesCS3A01G049400 chr3B 87.926 1615 142 15 2277 3856 29379793 29381389 0.000000e+00 1853.0
20 TraesCS3A01G049400 chr3B 91.367 1309 82 11 650 1950 30093339 30092054 0.000000e+00 1762.0
21 TraesCS3A01G049400 chr3B 88.195 881 74 17 905 1767 29640843 29641711 0.000000e+00 1024.0
22 TraesCS3A01G049400 chr3B 89.083 458 44 2 2059 2510 30408983 30409440 8.980000e-157 564.0
23 TraesCS3A01G049400 chr3B 92.208 308 24 0 3546 3853 29787730 29788037 2.040000e-118 436.0
24 TraesCS3A01G049400 chr3B 94.898 196 10 0 541 736 29640649 29640844 1.670000e-79 307.0
25 TraesCS3A01G049400 chr3B 85.159 283 37 4 3327 3606 29354644 29354364 7.830000e-73 285.0
26 TraesCS3A01G049400 chr3B 85.965 285 18 5 352 614 29595616 29595332 7.830000e-73 285.0
27 TraesCS3A01G049400 chr3B 85.965 285 18 5 352 614 30095679 30095395 7.830000e-73 285.0
28 TraesCS3A01G049400 chr3B 91.525 59 5 0 1 59 30406227 30406285 1.100000e-11 82.4
29 TraesCS3A01G049400 chr3B 94.000 50 3 0 1 50 29598788 29598739 5.130000e-10 76.8
30 TraesCS3A01G049400 chr7D 89.277 830 81 6 3957 4779 567654151 567654979 0.000000e+00 1033.0
31 TraesCS3A01G049400 chr7D 91.336 277 22 2 57 331 638033364 638033088 1.260000e-100 377.0
32 TraesCS3A01G049400 chr7D 90.975 277 22 3 57 330 465265034 465264758 2.100000e-98 370.0
33 TraesCS3A01G049400 chr7D 90.942 276 23 2 57 330 530758278 530758553 2.100000e-98 370.0
34 TraesCS3A01G049400 chr7A 88.862 826 84 7 3960 4779 632530031 632530854 0.000000e+00 1009.0
35 TraesCS3A01G049400 chr7A 88.578 823 83 11 3959 4779 68342618 68341805 0.000000e+00 989.0
36 TraesCS3A01G049400 chr2A 88.341 832 85 12 3955 4779 683537857 683538683 0.000000e+00 989.0
37 TraesCS3A01G049400 chr2A 88.092 823 83 13 3961 4779 7511197 7510386 0.000000e+00 963.0
38 TraesCS3A01G049400 chr4A 88.228 824 83 11 3962 4779 48892579 48893394 0.000000e+00 972.0
39 TraesCS3A01G049400 chr4A 87.726 831 91 10 3957 4779 503480177 503479350 0.000000e+00 959.0
40 TraesCS3A01G049400 chr1A 88.092 823 81 12 3961 4779 47518879 47518070 0.000000e+00 961.0
41 TraesCS3A01G049400 chr5D 92.803 264 18 1 66 328 554510227 554510490 9.710000e-102 381.0
42 TraesCS3A01G049400 chr5D 90.909 264 23 1 66 328 339984014 339984277 2.120000e-93 353.0
43 TraesCS3A01G049400 chr1D 90.780 282 23 3 54 332 414927993 414928274 1.620000e-99 374.0
44 TraesCS3A01G049400 chr6D 92.075 265 20 1 67 330 438936279 438936543 5.840000e-99 372.0
45 TraesCS3A01G049400 chr6D 89.892 277 22 5 66 337 98020805 98020530 7.610000e-93 351.0
46 TraesCS3A01G049400 chrUn 89.046 283 23 6 57 336 36485865 36485588 1.270000e-90 344.0
47 TraesCS3A01G049400 chrUn 82.530 166 29 0 1512 1677 282462319 282462154 3.850000e-31 147.0
48 TraesCS3A01G049400 chr5B 97.222 36 1 0 671 706 28755760 28755795 1.440000e-05 62.1


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 TraesCS3A01G049400 chr3A 26193495 26198273 4778 False 8826.000000 8826 100.000000 1 4779 1 chr3A.!!$F3 4778
1 TraesCS3A01G049400 chr3A 26141561 26143146 1585 False 2182.000000 2182 91.593000 2277 3856 1 chr3A.!!$F2 1579
2 TraesCS3A01G049400 chr3A 58844991 58845805 814 True 1007.000000 1007 88.956000 3959 4779 1 chr3A.!!$R1 820
3 TraesCS3A01G049400 chr3D 18926509 18928220 1711 False 2507.000000 2507 93.124000 2139 3849 1 chr3D.!!$F2 1710
4 TraesCS3A01G049400 chr3D 18657403 18661224 3821 False 1328.250000 2776 90.041750 325 3892 4 chr3D.!!$F3 3567
5 TraesCS3A01G049400 chr3D 18910529 18912199 1670 False 1108.500000 1648 90.379000 325 2059 2 chr3D.!!$F5 1734
6 TraesCS3A01G049400 chr3D 18739710 18741134 1424 False 728.500000 747 92.002500 1475 2593 2 chr3D.!!$F4 1118
7 TraesCS3A01G049400 chr3B 29379793 29381389 1596 False 1853.000000 1853 87.926000 2277 3856 1 chr3B.!!$F1 1579
8 TraesCS3A01G049400 chr3B 30089773 30095679 5906 True 1561.666667 2638 90.021667 352 3892 3 chr3B.!!$R3 3540
9 TraesCS3A01G049400 chr3B 29591063 29598788 7725 True 1291.950000 2769 91.923500 1 3875 4 chr3B.!!$R2 3874
10 TraesCS3A01G049400 chr3B 30406227 30410855 4628 False 1233.100000 2215 91.301250 1 3892 4 chr3B.!!$F4 3891
11 TraesCS3A01G049400 chr3B 29640649 29641711 1062 False 665.500000 1024 91.546500 541 1767 2 chr3B.!!$F3 1226
12 TraesCS3A01G049400 chr7D 567654151 567654979 828 False 1033.000000 1033 89.277000 3957 4779 1 chr7D.!!$F2 822
13 TraesCS3A01G049400 chr7A 632530031 632530854 823 False 1009.000000 1009 88.862000 3960 4779 1 chr7A.!!$F1 819
14 TraesCS3A01G049400 chr7A 68341805 68342618 813 True 989.000000 989 88.578000 3959 4779 1 chr7A.!!$R1 820
15 TraesCS3A01G049400 chr2A 683537857 683538683 826 False 989.000000 989 88.341000 3955 4779 1 chr2A.!!$F1 824
16 TraesCS3A01G049400 chr2A 7510386 7511197 811 True 963.000000 963 88.092000 3961 4779 1 chr2A.!!$R1 818
17 TraesCS3A01G049400 chr4A 48892579 48893394 815 False 972.000000 972 88.228000 3962 4779 1 chr4A.!!$F1 817
18 TraesCS3A01G049400 chr4A 503479350 503480177 827 True 959.000000 959 87.726000 3957 4779 1 chr4A.!!$R1 822
19 TraesCS3A01G049400 chr1A 47518070 47518879 809 True 961.000000 961 88.092000 3961 4779 1 chr1A.!!$R1 818

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
59 60 0.038526 CCGCTAGCCACCGGTATAAG 60.039 60.000 6.87 3.72 39.67 1.73 F
1132 6332 0.824109 CGGCAACCTGACCATCTCTA 59.176 55.000 0.00 0.00 0.00 2.43 F
1993 7373 1.361993 CTCTAGAGCGGCGCTGATT 59.638 57.895 41.51 25.33 39.88 2.57 F
2053 7439 0.036010 CCAGGGATGTCAGACGCTTT 60.036 55.000 0.00 0.00 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1851 7078 0.035317 ATTGACAGAGCTTCCACGCA 59.965 50.0 0.00 0.0 0.00 5.24 R
2023 7409 0.557729 CATCCCTGGCCTACCCAAAT 59.442 55.0 3.32 0.0 44.81 2.32 R
3571 9682 0.602905 GTATGCACCATAGGCCGACC 60.603 60.0 0.00 0.0 0.00 4.79 R
3993 10110 2.095372 GGGACCAAATCTAAACTTCGCG 59.905 50.0 0.00 0.0 0.00 5.87 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
57 58 3.767816 CCGCTAGCCACCGGTATA 58.232 61.111 6.87 0.00 39.67 1.47
58 59 2.043625 CCGCTAGCCACCGGTATAA 58.956 57.895 6.87 0.00 39.67 0.98
59 60 0.038526 CCGCTAGCCACCGGTATAAG 60.039 60.000 6.87 3.72 39.67 1.73
60 61 0.956633 CGCTAGCCACCGGTATAAGA 59.043 55.000 6.87 0.00 0.00 2.10
61 62 1.335689 CGCTAGCCACCGGTATAAGAC 60.336 57.143 6.87 0.00 0.00 3.01
65 66 3.470645 AGCCACCGGTATAAGACATTC 57.529 47.619 6.87 0.00 0.00 2.67
67 68 2.870411 GCCACCGGTATAAGACATTCAC 59.130 50.000 6.87 0.00 0.00 3.18
68 69 3.680475 GCCACCGGTATAAGACATTCACA 60.680 47.826 6.87 0.00 0.00 3.58
69 70 4.119862 CCACCGGTATAAGACATTCACAG 58.880 47.826 6.87 0.00 0.00 3.66
70 71 4.382685 CCACCGGTATAAGACATTCACAGT 60.383 45.833 6.87 0.00 0.00 3.55
71 72 4.566759 CACCGGTATAAGACATTCACAGTG 59.433 45.833 6.87 0.00 0.00 3.66
72 73 4.222145 ACCGGTATAAGACATTCACAGTGT 59.778 41.667 4.49 0.00 0.00 3.55
73 74 4.566759 CCGGTATAAGACATTCACAGTGTG 59.433 45.833 17.53 17.53 34.45 3.82
74 75 5.407502 CGGTATAAGACATTCACAGTGTGA 58.592 41.667 22.06 22.06 41.09 3.58
75 76 5.516696 CGGTATAAGACATTCACAGTGTGAG 59.483 44.000 24.25 16.88 43.69 3.51
76 77 6.398918 GGTATAAGACATTCACAGTGTGAGT 58.601 40.000 24.25 19.72 43.69 3.41
77 78 7.544622 GGTATAAGACATTCACAGTGTGAGTA 58.455 38.462 24.25 12.71 43.69 2.59
79 80 9.587772 GTATAAGACATTCACAGTGTGAGTAAT 57.412 33.333 24.25 13.73 43.69 1.89
83 84 9.809096 AAGACATTCACAGTGTGAGTAATATAG 57.191 33.333 24.25 11.95 43.69 1.31
84 85 8.417106 AGACATTCACAGTGTGAGTAATATAGG 58.583 37.037 24.25 12.98 43.69 2.57
85 86 8.079211 ACATTCACAGTGTGAGTAATATAGGT 57.921 34.615 24.25 13.59 43.69 3.08
87 88 9.684448 CATTCACAGTGTGAGTAATATAGGTAG 57.316 37.037 24.25 3.92 43.69 3.18
89 90 9.470399 TTCACAGTGTGAGTAATATAGGTAGAA 57.530 33.333 24.25 2.77 43.69 2.10
90 91 9.121658 TCACAGTGTGAGTAATATAGGTAGAAG 57.878 37.037 22.06 0.00 37.67 2.85
91 92 9.121658 CACAGTGTGAGTAATATAGGTAGAAGA 57.878 37.037 18.83 0.00 35.23 2.87
96 97 9.862149 TGTGAGTAATATAGGTAGAAGATCACA 57.138 33.333 0.00 0.00 39.65 3.58
168 2355 6.452494 AAGACATGTGATAACGTAGCTAGT 57.548 37.500 1.15 0.00 0.00 2.57
169 2356 6.452494 AGACATGTGATAACGTAGCTAGTT 57.548 37.500 1.15 11.59 35.75 2.24
171 2358 7.416022 AGACATGTGATAACGTAGCTAGTTAC 58.584 38.462 1.15 6.68 36.96 2.50
172 2359 7.282675 AGACATGTGATAACGTAGCTAGTTACT 59.717 37.037 1.15 0.23 36.96 2.24
173 2360 8.442632 ACATGTGATAACGTAGCTAGTTACTA 57.557 34.615 13.96 2.36 36.96 1.82
174 2361 8.341173 ACATGTGATAACGTAGCTAGTTACTAC 58.659 37.037 13.96 14.86 36.96 2.73
175 2362 8.557864 CATGTGATAACGTAGCTAGTTACTACT 58.442 37.037 13.96 2.26 38.27 2.57
196 2383 9.409918 ACTACTAGTATGAGTAACATCACACAT 57.590 33.333 2.33 0.00 40.07 3.21
202 2389 9.755804 AGTATGAGTAACATCACACATATCAAG 57.244 33.333 0.00 0.00 40.07 3.02
203 2390 8.982685 GTATGAGTAACATCACACATATCAAGG 58.017 37.037 0.00 0.00 40.07 3.61
204 2391 5.817296 TGAGTAACATCACACATATCAAGGC 59.183 40.000 0.00 0.00 0.00 4.35
207 2394 5.571784 AACATCACACATATCAAGGCAAG 57.428 39.130 0.00 0.00 0.00 4.01
210 2397 5.298527 ACATCACACATATCAAGGCAAGATG 59.701 40.000 0.00 0.00 36.24 2.90
211 2398 5.101648 TCACACATATCAAGGCAAGATGA 57.898 39.130 2.43 0.00 0.00 2.92
213 2400 4.880120 CACACATATCAAGGCAAGATGAGT 59.120 41.667 2.43 0.00 0.00 3.41
214 2401 5.007430 CACACATATCAAGGCAAGATGAGTC 59.993 44.000 2.43 0.00 0.00 3.36
215 2402 5.104610 ACACATATCAAGGCAAGATGAGTCT 60.105 40.000 2.43 0.00 35.82 3.24
216 2403 6.098838 ACACATATCAAGGCAAGATGAGTCTA 59.901 38.462 2.43 0.00 33.30 2.59
217 2404 7.160049 CACATATCAAGGCAAGATGAGTCTAT 58.840 38.462 2.43 0.00 33.30 1.98
218 2405 8.309656 CACATATCAAGGCAAGATGAGTCTATA 58.690 37.037 2.43 0.00 33.30 1.31
219 2406 8.530311 ACATATCAAGGCAAGATGAGTCTATAG 58.470 37.037 0.00 0.00 33.30 1.31
220 2407 5.207110 TCAAGGCAAGATGAGTCTATAGC 57.793 43.478 0.00 0.00 33.30 2.97
221 2408 4.039730 TCAAGGCAAGATGAGTCTATAGCC 59.960 45.833 0.00 0.00 42.62 3.93
222 2409 3.855668 AGGCAAGATGAGTCTATAGCCT 58.144 45.455 11.05 11.05 45.15 4.58
223 2410 5.004361 AGGCAAGATGAGTCTATAGCCTA 57.996 43.478 13.74 0.00 46.63 3.93
224 2411 5.398236 AGGCAAGATGAGTCTATAGCCTAA 58.602 41.667 13.74 0.00 46.63 2.69
226 2413 7.185565 AGGCAAGATGAGTCTATAGCCTAATA 58.814 38.462 13.74 0.00 46.63 0.98
228 2415 8.314751 GGCAAGATGAGTCTATAGCCTAATAAA 58.685 37.037 0.00 0.00 40.78 1.40
229 2416 9.883142 GCAAGATGAGTCTATAGCCTAATAAAT 57.117 33.333 0.00 0.00 33.30 1.40
239 2426 9.273016 TCTATAGCCTAATAAATGAAGTGTTGC 57.727 33.333 0.00 0.00 0.00 4.17
240 2427 7.880160 ATAGCCTAATAAATGAAGTGTTGCA 57.120 32.000 0.00 0.00 0.00 4.08
241 2428 6.780457 AGCCTAATAAATGAAGTGTTGCAT 57.220 33.333 0.00 0.00 0.00 3.96
242 2429 6.567050 AGCCTAATAAATGAAGTGTTGCATG 58.433 36.000 0.00 0.00 0.00 4.06
243 2430 6.153340 AGCCTAATAAATGAAGTGTTGCATGT 59.847 34.615 0.00 0.00 0.00 3.21
244 2431 6.813152 GCCTAATAAATGAAGTGTTGCATGTT 59.187 34.615 0.00 0.00 0.00 2.71
245 2432 7.973388 GCCTAATAAATGAAGTGTTGCATGTTA 59.027 33.333 0.00 0.00 0.00 2.41
246 2433 9.289303 CCTAATAAATGAAGTGTTGCATGTTAC 57.711 33.333 0.00 0.00 0.00 2.50
247 2434 9.289303 CTAATAAATGAAGTGTTGCATGTTACC 57.711 33.333 0.00 0.00 0.00 2.85
248 2435 5.528043 AAATGAAGTGTTGCATGTTACCA 57.472 34.783 0.00 0.00 0.00 3.25
249 2436 3.980646 TGAAGTGTTGCATGTTACCAC 57.019 42.857 0.00 0.00 0.00 4.16
250 2437 3.282885 TGAAGTGTTGCATGTTACCACA 58.717 40.909 0.00 0.00 37.31 4.17
251 2438 3.066064 TGAAGTGTTGCATGTTACCACAC 59.934 43.478 7.36 7.36 35.03 3.82
252 2439 2.649190 AGTGTTGCATGTTACCACACA 58.351 42.857 15.74 0.00 35.03 3.72
253 2440 3.221771 AGTGTTGCATGTTACCACACAT 58.778 40.909 15.74 1.51 37.93 3.21
254 2441 4.393834 AGTGTTGCATGTTACCACACATA 58.606 39.130 15.74 0.00 35.51 2.29
257 2444 4.764308 TGTTGCATGTTACCACACATATGT 59.236 37.500 1.41 1.41 40.80 2.29
259 2446 6.431234 TGTTGCATGTTACCACACATATGTTA 59.569 34.615 5.37 0.00 36.72 2.41
260 2447 6.429791 TGCATGTTACCACACATATGTTAC 57.570 37.500 5.37 0.00 36.72 2.50
263 2450 7.148323 TGCATGTTACCACACATATGTTACTTC 60.148 37.037 5.37 0.00 36.72 3.01
264 2451 7.678690 GCATGTTACCACACATATGTTACTTCC 60.679 40.741 5.37 0.00 36.72 3.46
265 2452 6.174760 TGTTACCACACATATGTTACTTCCC 58.825 40.000 5.37 0.00 36.72 3.97
266 2453 4.919774 ACCACACATATGTTACTTCCCA 57.080 40.909 5.37 0.00 36.72 4.37
267 2454 4.585879 ACCACACATATGTTACTTCCCAC 58.414 43.478 5.37 0.00 36.72 4.61
269 2456 5.486063 ACCACACATATGTTACTTCCCACTA 59.514 40.000 5.37 0.00 36.72 2.74
270 2457 6.157994 ACCACACATATGTTACTTCCCACTAT 59.842 38.462 5.37 0.00 36.72 2.12
271 2458 7.346175 ACCACACATATGTTACTTCCCACTATA 59.654 37.037 5.37 0.00 36.72 1.31
272 2459 7.872993 CCACACATATGTTACTTCCCACTATAG 59.127 40.741 5.37 0.00 36.72 1.31
273 2460 8.638873 CACACATATGTTACTTCCCACTATAGA 58.361 37.037 5.37 0.00 36.72 1.98
274 2461 8.861086 ACACATATGTTACTTCCCACTATAGAG 58.139 37.037 5.37 0.00 34.46 2.43
275 2462 9.078990 CACATATGTTACTTCCCACTATAGAGA 57.921 37.037 5.37 0.00 0.00 3.10
276 2463 9.830186 ACATATGTTACTTCCCACTATAGAGAT 57.170 33.333 6.78 0.00 0.00 2.75
285 2472 9.303116 ACTTCCCACTATAGAGATAGTAACATG 57.697 37.037 6.78 0.00 45.42 3.21
286 2473 9.303116 CTTCCCACTATAGAGATAGTAACATGT 57.697 37.037 6.78 0.00 45.42 3.21
287 2474 8.637196 TCCCACTATAGAGATAGTAACATGTG 57.363 38.462 6.78 0.00 45.42 3.21
288 2475 7.176865 TCCCACTATAGAGATAGTAACATGTGC 59.823 40.741 6.78 0.00 45.42 4.57
289 2476 7.039714 CCCACTATAGAGATAGTAACATGTGCA 60.040 40.741 6.78 0.00 45.42 4.57
291 2478 9.351570 CACTATAGAGATAGTAACATGTGCATG 57.648 37.037 6.78 10.31 45.42 4.06
320 2507 8.416329 ACTACTTTATATTACTACCCGTTGTGG 58.584 37.037 0.00 0.00 37.55 4.17
321 2508 6.051074 ACTTTATATTACTACCCGTTGTGGC 58.949 40.000 0.00 0.00 35.87 5.01
323 2510 6.975196 TTATATTACTACCCGTTGTGGCTA 57.025 37.500 0.00 0.00 35.87 3.93
326 3054 0.893447 ACTACCCGTTGTGGCTAGTC 59.107 55.000 0.00 0.00 35.87 2.59
343 3071 6.221858 GCTAGTCTAATAGCATTGTTCAGC 57.778 41.667 4.66 0.00 46.12 4.26
399 3484 6.000219 AGATTAATTAGCTGGCGATGTGATT 59.000 36.000 0.00 0.00 0.00 2.57
412 3497 1.079405 GTGATTTCTGTCCGGCCGA 60.079 57.895 30.73 10.38 0.00 5.54
538 3646 3.619233 ATGTGCGTAGTTGGTTTTGTC 57.381 42.857 0.00 0.00 0.00 3.18
724 5923 1.927895 AGTATCTTCTTGCTTCGGCG 58.072 50.000 0.00 0.00 45.37 6.46
750 5949 1.666872 GCGCTAGGACAACAACCGT 60.667 57.895 0.00 0.00 0.00 4.83
762 5961 5.050091 GGACAACAACCGTGATATCATCATC 60.050 44.000 9.02 0.00 42.04 2.92
805 6004 2.910199 TGATCTGCAGCCACTCATAAC 58.090 47.619 9.47 0.00 0.00 1.89
810 6009 1.717937 CAGCCACTCATAACTGCGC 59.282 57.895 0.00 0.00 0.00 6.09
824 6023 3.706373 GCGCTCCAGGTCTTCCCA 61.706 66.667 0.00 0.00 34.66 4.37
863 6062 5.148502 AGATACGGAGTTCCCATGTTAGAT 58.851 41.667 0.00 0.00 37.78 1.98
1035 6234 4.087182 ACTGGTTCTTAGTCTTCATCGGA 58.913 43.478 0.00 0.00 0.00 4.55
1132 6332 0.824109 CGGCAACCTGACCATCTCTA 59.176 55.000 0.00 0.00 0.00 2.43
1140 6340 3.775316 ACCTGACCATCTCTAATCCGTTT 59.225 43.478 0.00 0.00 0.00 3.60
1248 6456 4.414956 TCCGTGCCCCTCATCCCT 62.415 66.667 0.00 0.00 0.00 4.20
1317 6525 2.413765 CGTTGATGAAGGCAAGCAGAAG 60.414 50.000 0.00 0.00 0.00 2.85
1443 6651 1.514678 ATTGCACGAAGGAAAGCGCA 61.515 50.000 11.47 0.00 0.00 6.09
1467 6675 2.284798 CTGCTGCACGTCGGGATAGT 62.285 60.000 0.00 0.00 0.00 2.12
1563 6786 1.991121 TCGGGAACTACGCCAGATAT 58.009 50.000 0.00 0.00 0.00 1.63
1611 6834 3.066190 CCGGTACTGGGCTCGTCA 61.066 66.667 13.47 0.00 0.00 4.35
1799 7025 4.130857 TGTTTGCACTTCCTAATCGAACA 58.869 39.130 0.00 0.00 0.00 3.18
1882 7111 5.991861 AGCTCTGTCAATCAATTGAGATCT 58.008 37.500 14.54 0.00 46.44 2.75
1992 7372 3.038280 CTCTAGAGCGGCGCTGAT 58.962 61.111 41.51 28.50 39.88 2.90
1993 7373 1.361993 CTCTAGAGCGGCGCTGATT 59.638 57.895 41.51 25.33 39.88 2.57
2013 7399 4.715523 TTCAGGCGGGAAAGGGCG 62.716 66.667 0.00 0.00 34.74 6.13
2023 7409 1.258445 GGAAAGGGCGAGTGAGAGGA 61.258 60.000 0.00 0.00 0.00 3.71
2053 7439 0.036010 CCAGGGATGTCAGACGCTTT 60.036 55.000 0.00 0.00 0.00 3.51
2054 7440 1.081892 CAGGGATGTCAGACGCTTTG 58.918 55.000 0.00 0.00 0.00 2.77
2056 7442 0.798776 GGGATGTCAGACGCTTTGTG 59.201 55.000 0.00 0.00 0.00 3.33
2057 7443 1.512926 GGATGTCAGACGCTTTGTGT 58.487 50.000 0.00 0.00 0.00 3.72
2066 8083 1.649815 CGCTTTGTGTGGCGGTTTA 59.350 52.632 0.00 0.00 46.42 2.01
2069 8086 1.335496 GCTTTGTGTGGCGGTTTAAGA 59.665 47.619 0.00 0.00 0.00 2.10
2150 8169 4.582869 TGTTGAGAGATGCTGCTATTTGT 58.417 39.130 0.00 0.00 0.00 2.83
2152 8171 6.351711 TGTTGAGAGATGCTGCTATTTGTAT 58.648 36.000 0.00 0.00 0.00 2.29
2163 8182 6.703165 TGCTGCTATTTGTATCTACATGACAG 59.297 38.462 0.00 0.00 35.89 3.51
2193 8212 6.959639 AACTACAGGTTTTGATGTGATGTT 57.040 33.333 0.00 0.00 33.90 2.71
2242 8267 0.387565 TGATCTGCTTATGCCGCGTA 59.612 50.000 4.92 0.00 38.71 4.42
2375 8403 1.604604 TGGTAGGCACAACAAGAAGC 58.395 50.000 0.00 0.00 0.00 3.86
2413 8441 3.390311 TGTCTATCATGGCTTCTGCTCAT 59.610 43.478 0.00 0.00 39.59 2.90
2453 8492 9.226345 CTTTGTCTCAAACTTTCATACTTTGAC 57.774 33.333 0.00 0.00 32.84 3.18
2582 8685 7.285858 AGGGATAGTTTACAGAGTCTCATACAC 59.714 40.741 1.94 0.00 0.00 2.90
2680 8791 4.498241 TCAGCTTGCTAACATGTCTAGTG 58.502 43.478 0.00 0.00 0.00 2.74
2735 8846 2.978156 TTTCATCCTCCCAAAGCAGT 57.022 45.000 0.00 0.00 0.00 4.40
2771 8882 1.407979 GCATGGAAGAAATGCTGAGGG 59.592 52.381 0.00 0.00 45.62 4.30
2785 8896 3.266772 TGCTGAGGGTGTATGGATCTTTT 59.733 43.478 0.00 0.00 0.00 2.27
2878 8989 4.262721 GGTGGATATGGCACGGTATTTAGA 60.263 45.833 0.00 0.00 0.00 2.10
2950 9061 3.512724 CCAAAGGCAATGGAGATGAGTTT 59.487 43.478 2.66 0.00 40.56 2.66
3139 9250 9.581861 TGGGACAAGTTACAGCAAATAGCACTA 62.582 40.741 0.00 0.00 40.88 2.74
3181 9292 6.016024 TGGAATATTTGCATCAAGGATGTAGC 60.016 38.462 7.92 0.00 41.60 3.58
3325 9436 1.215647 CGCCGAAGCAAGAGGTACT 59.784 57.895 0.00 0.00 40.46 2.73
3385 9496 3.635331 TGGAGTCGTTTCTACAAAGTCG 58.365 45.455 0.00 0.00 0.00 4.18
3437 9548 4.658901 TGGAAATGGTAGGAGGAAGGATAC 59.341 45.833 0.00 0.00 0.00 2.24
3453 9564 7.131069 AGGAAGGATACATAAAGGAAAAGGGAT 59.869 37.037 0.00 0.00 41.41 3.85
3458 9569 8.002459 GGATACATAAAGGAAAAGGGATTACCA 58.998 37.037 0.00 0.00 43.89 3.25
3488 9599 6.744112 TCAAGTGATGTGTATTTTCCAAACC 58.256 36.000 0.00 0.00 0.00 3.27
3506 9617 7.566569 TCCAAACCGGATTTATGACAGTATAA 58.433 34.615 9.46 0.00 39.64 0.98
3533 9644 4.196971 ACAGGTACAAAGTTGTGAAGTCC 58.803 43.478 6.94 2.58 42.31 3.85
3534 9645 3.564225 CAGGTACAAAGTTGTGAAGTCCC 59.436 47.826 6.94 0.00 42.31 4.46
3535 9646 3.201266 AGGTACAAAGTTGTGAAGTCCCA 59.799 43.478 6.94 0.00 42.31 4.37
3606 9717 3.754323 TGCATACAAACTAACCCCGAAAG 59.246 43.478 0.00 0.00 0.00 2.62
3659 9770 4.097135 TGTTGGAAAAGAGCATCAACGAAA 59.903 37.500 0.00 0.00 40.13 3.46
3764 9875 0.179018 GTATTGCTCCGCATCCCCTT 60.179 55.000 0.00 0.00 38.76 3.95
3779 9894 4.348020 TCCCCTTCTCTGTTACCATAGT 57.652 45.455 0.00 0.00 0.00 2.12
3888 10005 7.706281 TTATTTTCAAACATCGCATTGTGTT 57.294 28.000 0.00 0.00 40.06 3.32
3892 10009 5.681337 TCAAACATCGCATTGTGTTTCTA 57.319 34.783 0.91 0.00 44.27 2.10
3893 10010 5.448438 TCAAACATCGCATTGTGTTTCTAC 58.552 37.500 0.91 0.00 44.27 2.59
3894 10011 5.238432 TCAAACATCGCATTGTGTTTCTACT 59.762 36.000 0.91 0.00 44.27 2.57
3895 10012 6.425417 TCAAACATCGCATTGTGTTTCTACTA 59.575 34.615 0.91 0.00 44.27 1.82
3896 10013 6.795098 AACATCGCATTGTGTTTCTACTAA 57.205 33.333 0.00 0.00 35.13 2.24
3897 10014 6.408858 ACATCGCATTGTGTTTCTACTAAG 57.591 37.500 0.00 0.00 0.00 2.18
3898 10015 6.163476 ACATCGCATTGTGTTTCTACTAAGA 58.837 36.000 0.00 0.00 0.00 2.10
3899 10016 6.649141 ACATCGCATTGTGTTTCTACTAAGAA 59.351 34.615 0.00 0.00 40.03 2.52
3900 10017 7.334421 ACATCGCATTGTGTTTCTACTAAGAAT 59.666 33.333 0.00 0.00 41.36 2.40
3901 10018 7.060600 TCGCATTGTGTTTCTACTAAGAATG 57.939 36.000 0.00 0.00 41.36 2.67
3902 10019 6.092122 TCGCATTGTGTTTCTACTAAGAATGG 59.908 38.462 0.00 0.00 41.36 3.16
3903 10020 6.128282 CGCATTGTGTTTCTACTAAGAATGGT 60.128 38.462 0.00 0.00 41.36 3.55
3904 10021 7.573096 CGCATTGTGTTTCTACTAAGAATGGTT 60.573 37.037 0.00 0.00 41.36 3.67
3905 10022 7.538678 GCATTGTGTTTCTACTAAGAATGGTTG 59.461 37.037 0.00 0.00 41.36 3.77
3906 10023 6.554334 TGTGTTTCTACTAAGAATGGTTGC 57.446 37.500 0.00 0.00 41.36 4.17
3907 10024 5.178623 TGTGTTTCTACTAAGAATGGTTGCG 59.821 40.000 0.00 0.00 41.36 4.85
3908 10025 4.153475 TGTTTCTACTAAGAATGGTTGCGC 59.847 41.667 0.00 0.00 41.36 6.09
3909 10026 3.603158 TCTACTAAGAATGGTTGCGCA 57.397 42.857 5.66 5.66 0.00 6.09
3910 10027 3.932822 TCTACTAAGAATGGTTGCGCAA 58.067 40.909 21.02 21.02 0.00 4.85
3911 10028 4.513442 TCTACTAAGAATGGTTGCGCAAT 58.487 39.130 27.79 10.36 0.00 3.56
3912 10029 4.941263 TCTACTAAGAATGGTTGCGCAATT 59.059 37.500 27.79 16.94 0.00 2.32
3913 10030 4.519540 ACTAAGAATGGTTGCGCAATTT 57.480 36.364 27.79 19.44 0.00 1.82
3914 10031 4.236935 ACTAAGAATGGTTGCGCAATTTG 58.763 39.130 27.79 17.36 0.00 2.32
3915 10032 3.383620 AAGAATGGTTGCGCAATTTGA 57.616 38.095 27.79 10.81 0.00 2.69
3916 10033 3.598019 AGAATGGTTGCGCAATTTGAT 57.402 38.095 27.79 12.66 0.00 2.57
3917 10034 4.717233 AGAATGGTTGCGCAATTTGATA 57.283 36.364 27.79 9.51 0.00 2.15
3918 10035 5.070770 AGAATGGTTGCGCAATTTGATAA 57.929 34.783 27.79 7.39 0.00 1.75
3919 10036 5.104374 AGAATGGTTGCGCAATTTGATAAG 58.896 37.500 27.79 0.00 0.00 1.73
3920 10037 3.229276 TGGTTGCGCAATTTGATAAGG 57.771 42.857 27.79 0.00 0.00 2.69
3921 10038 2.822561 TGGTTGCGCAATTTGATAAGGA 59.177 40.909 27.79 0.00 0.00 3.36
3922 10039 3.256879 TGGTTGCGCAATTTGATAAGGAA 59.743 39.130 27.79 0.00 0.00 3.36
3923 10040 4.241681 GGTTGCGCAATTTGATAAGGAAA 58.758 39.130 27.79 0.00 0.00 3.13
3924 10041 4.688413 GGTTGCGCAATTTGATAAGGAAAA 59.312 37.500 27.79 0.00 0.00 2.29
3925 10042 5.163963 GGTTGCGCAATTTGATAAGGAAAAG 60.164 40.000 27.79 0.00 0.00 2.27
3926 10043 5.132897 TGCGCAATTTGATAAGGAAAAGT 57.867 34.783 8.16 0.00 0.00 2.66
3927 10044 5.160641 TGCGCAATTTGATAAGGAAAAGTC 58.839 37.500 8.16 0.00 0.00 3.01
3928 10045 5.160641 GCGCAATTTGATAAGGAAAAGTCA 58.839 37.500 0.30 0.00 0.00 3.41
3929 10046 5.807011 GCGCAATTTGATAAGGAAAAGTCAT 59.193 36.000 0.30 0.00 0.00 3.06
3930 10047 6.311200 GCGCAATTTGATAAGGAAAAGTCATT 59.689 34.615 0.30 0.00 0.00 2.57
3931 10048 7.148590 GCGCAATTTGATAAGGAAAAGTCATTT 60.149 33.333 0.30 0.00 0.00 2.32
3932 10049 8.164153 CGCAATTTGATAAGGAAAAGTCATTTG 58.836 33.333 0.00 0.00 0.00 2.32
3933 10050 9.206870 GCAATTTGATAAGGAAAAGTCATTTGA 57.793 29.630 0.00 0.00 0.00 2.69
3993 10110 6.581171 ACACTTTTCATCCCTCAATTCTTC 57.419 37.500 0.00 0.00 0.00 2.87
4001 10118 2.076863 CCCTCAATTCTTCGCGAAGTT 58.923 47.619 39.17 27.98 39.38 2.66
4035 10152 3.317993 CCTCAACTTCAAAACCGGACAAT 59.682 43.478 9.46 0.00 0.00 2.71
4040 10157 3.118956 ACTTCAAAACCGGACAATTTGCA 60.119 39.130 9.46 3.85 34.77 4.08
4043 10160 1.115467 AAACCGGACAATTTGCACCA 58.885 45.000 9.46 0.00 0.00 4.17
4061 10178 4.571919 CACCATTAACTACTGAAACCGGA 58.428 43.478 9.46 0.00 0.00 5.14
4108 10225 1.528309 CCGGTTTTGGTGCTGTCCT 60.528 57.895 0.00 0.00 0.00 3.85
4110 10227 0.872388 CGGTTTTGGTGCTGTCCTAC 59.128 55.000 0.00 0.00 0.00 3.18
4114 10231 1.063070 TTTGGTGCTGTCCTACCCCA 61.063 55.000 0.00 0.00 36.10 4.96
4139 10256 2.571212 TGACTGTGCCGACTCAAATTT 58.429 42.857 0.00 0.00 0.00 1.82
4155 10272 5.848406 TCAAATTTGCGTACCTTTTCCAAT 58.152 33.333 13.54 0.00 0.00 3.16
4166 10283 6.037391 CGTACCTTTTCCAATTCCGCTTAATA 59.963 38.462 0.00 0.00 0.00 0.98
4238 10356 5.849604 GTGTGTACTTTTTCTAAATCCACGC 59.150 40.000 0.00 0.00 0.00 5.34
4248 10366 2.415697 AAATCCACGCACTTTTTCCG 57.584 45.000 0.00 0.00 0.00 4.30
4351 10474 6.742999 TGACGTACTTATTCATATTCACGC 57.257 37.500 0.00 0.00 0.00 5.34
4352 10475 5.397240 TGACGTACTTATTCATATTCACGCG 59.603 40.000 3.53 3.53 0.00 6.01
4354 10477 5.397534 ACGTACTTATTCATATTCACGCGTC 59.602 40.000 9.86 0.00 0.00 5.19
4397 10521 4.503734 TCATTCGAACTTGAAAACGTACGT 59.496 37.500 16.72 16.72 0.00 3.57
4408 10532 6.062434 TGAAAACGTACGTGGATTTGAATT 57.938 33.333 23.57 6.00 0.00 2.17
4419 10543 5.627367 CGTGGATTTGAATTTCTTTTACGCA 59.373 36.000 0.00 0.00 0.00 5.24
4462 10589 9.658799 TGTGGATTTGAAAAATTTTGTCAACTA 57.341 25.926 13.17 2.31 31.21 2.24
4568 10697 8.836268 AAGTATACGGATTTGAAACAAGTACA 57.164 30.769 0.00 0.00 0.00 2.90
4584 10713 7.500807 ACAAGTACACGAATTTCAAAAACAC 57.499 32.000 0.00 0.00 0.00 3.32
4595 10724 8.216453 CGAATTTCAAAAACACTTCATGGATTC 58.784 33.333 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 6.609212 TGCCAATAATCAGCCCAGTAATTAAA 59.391 34.615 0.00 0.00 0.00 1.52
50 51 4.566759 CACACTGTGAATGTCTTATACCGG 59.433 45.833 15.86 0.00 35.23 5.28
51 52 5.407502 TCACACTGTGAATGTCTTATACCG 58.592 41.667 15.86 0.00 39.78 4.02
52 53 6.398918 ACTCACACTGTGAATGTCTTATACC 58.601 40.000 15.86 0.00 42.26 2.73
53 54 8.981724 TTACTCACACTGTGAATGTCTTATAC 57.018 34.615 15.86 0.00 42.26 1.47
57 58 9.809096 CTATATTACTCACACTGTGAATGTCTT 57.191 33.333 15.86 3.36 42.26 3.01
58 59 8.417106 CCTATATTACTCACACTGTGAATGTCT 58.583 37.037 15.86 3.50 42.26 3.41
59 60 8.198109 ACCTATATTACTCACACTGTGAATGTC 58.802 37.037 15.86 0.00 42.26 3.06
60 61 8.079211 ACCTATATTACTCACACTGTGAATGT 57.921 34.615 15.86 10.53 42.26 2.71
61 62 9.684448 CTACCTATATTACTCACACTGTGAATG 57.316 37.037 15.86 3.28 42.26 2.67
65 66 9.121658 TCTTCTACCTATATTACTCACACTGTG 57.878 37.037 6.19 6.19 34.45 3.66
70 71 9.862149 TGTGATCTTCTACCTATATTACTCACA 57.138 33.333 0.00 0.00 36.66 3.58
72 73 9.862149 TGTGTGATCTTCTACCTATATTACTCA 57.138 33.333 0.00 0.00 0.00 3.41
147 335 7.416022 AGTAACTAGCTACGTTATCACATGTC 58.584 38.462 14.69 0.00 0.00 3.06
149 337 8.557864 AGTAGTAACTAGCTACGTTATCACATG 58.442 37.037 14.69 0.00 42.49 3.21
169 2356 9.895138 TGTGTGATGTTACTCATACTAGTAGTA 57.105 33.333 12.38 12.38 37.92 1.82
177 2364 8.982685 CCTTGATATGTGTGATGTTACTCATAC 58.017 37.037 0.00 5.35 38.84 2.39
178 2365 7.657354 GCCTTGATATGTGTGATGTTACTCATA 59.343 37.037 0.00 0.00 39.73 2.15
181 2368 5.817296 TGCCTTGATATGTGTGATGTTACTC 59.183 40.000 0.00 0.00 0.00 2.59
183 2370 6.316140 TCTTGCCTTGATATGTGTGATGTTAC 59.684 38.462 0.00 0.00 0.00 2.50
185 2372 5.255687 TCTTGCCTTGATATGTGTGATGTT 58.744 37.500 0.00 0.00 0.00 2.71
187 2374 5.529800 TCATCTTGCCTTGATATGTGTGATG 59.470 40.000 0.00 0.00 0.00 3.07
189 2376 5.101648 TCATCTTGCCTTGATATGTGTGA 57.898 39.130 0.00 0.00 0.00 3.58
190 2377 4.880120 ACTCATCTTGCCTTGATATGTGTG 59.120 41.667 0.00 0.00 0.00 3.82
191 2378 5.104610 AGACTCATCTTGCCTTGATATGTGT 60.105 40.000 0.00 0.00 0.00 3.72
192 2379 5.366460 AGACTCATCTTGCCTTGATATGTG 58.634 41.667 0.00 0.00 0.00 3.21
193 2380 5.627182 AGACTCATCTTGCCTTGATATGT 57.373 39.130 0.00 0.00 0.00 2.29
194 2381 7.492020 GCTATAGACTCATCTTGCCTTGATATG 59.508 40.741 3.21 0.00 36.29 1.78
196 2383 6.071108 GGCTATAGACTCATCTTGCCTTGATA 60.071 42.308 3.21 0.00 39.50 2.15
197 2384 5.279910 GGCTATAGACTCATCTTGCCTTGAT 60.280 44.000 3.21 0.00 39.50 2.57
199 2386 4.040217 AGGCTATAGACTCATCTTGCCTTG 59.960 45.833 0.83 0.00 45.01 3.61
200 2387 4.230455 AGGCTATAGACTCATCTTGCCTT 58.770 43.478 0.83 0.00 45.01 4.35
201 2388 3.855668 AGGCTATAGACTCATCTTGCCT 58.144 45.455 0.83 0.00 43.78 4.75
202 2389 5.730296 TTAGGCTATAGACTCATCTTGCC 57.270 43.478 12.64 0.00 41.26 4.52
203 2390 9.883142 ATTTATTAGGCTATAGACTCATCTTGC 57.117 33.333 12.64 0.00 36.29 4.01
213 2400 9.273016 GCAACACTTCATTTATTAGGCTATAGA 57.727 33.333 3.21 0.00 0.00 1.98
214 2401 9.056005 TGCAACACTTCATTTATTAGGCTATAG 57.944 33.333 0.00 0.00 0.00 1.31
215 2402 8.972458 TGCAACACTTCATTTATTAGGCTATA 57.028 30.769 0.00 0.00 0.00 1.31
216 2403 7.880160 TGCAACACTTCATTTATTAGGCTAT 57.120 32.000 0.00 0.00 0.00 2.97
217 2404 7.339212 ACATGCAACACTTCATTTATTAGGCTA 59.661 33.333 0.00 0.00 0.00 3.93
218 2405 6.153340 ACATGCAACACTTCATTTATTAGGCT 59.847 34.615 0.00 0.00 0.00 4.58
219 2406 6.332630 ACATGCAACACTTCATTTATTAGGC 58.667 36.000 0.00 0.00 0.00 3.93
220 2407 9.289303 GTAACATGCAACACTTCATTTATTAGG 57.711 33.333 0.00 0.00 0.00 2.69
221 2408 9.289303 GGTAACATGCAACACTTCATTTATTAG 57.711 33.333 0.00 0.00 0.00 1.73
222 2409 8.797438 TGGTAACATGCAACACTTCATTTATTA 58.203 29.630 0.00 0.00 46.17 0.98
223 2410 7.665690 TGGTAACATGCAACACTTCATTTATT 58.334 30.769 0.00 0.00 46.17 1.40
224 2411 7.225784 TGGTAACATGCAACACTTCATTTAT 57.774 32.000 0.00 0.00 46.17 1.40
226 2413 5.528043 TGGTAACATGCAACACTTCATTT 57.472 34.783 0.00 0.00 46.17 2.32
242 2429 6.093082 GTGGGAAGTAACATATGTGTGGTAAC 59.907 42.308 9.63 1.91 38.92 2.50
243 2430 6.013206 AGTGGGAAGTAACATATGTGTGGTAA 60.013 38.462 9.63 0.00 38.92 2.85
244 2431 5.486063 AGTGGGAAGTAACATATGTGTGGTA 59.514 40.000 9.63 0.00 38.92 3.25
245 2432 4.288626 AGTGGGAAGTAACATATGTGTGGT 59.711 41.667 9.63 0.00 38.92 4.16
246 2433 4.843728 AGTGGGAAGTAACATATGTGTGG 58.156 43.478 9.63 0.00 38.92 4.17
247 2434 8.638873 TCTATAGTGGGAAGTAACATATGTGTG 58.361 37.037 9.63 0.00 38.92 3.82
248 2435 8.777578 TCTATAGTGGGAAGTAACATATGTGT 57.222 34.615 9.63 2.63 41.28 3.72
249 2436 9.078990 TCTCTATAGTGGGAAGTAACATATGTG 57.921 37.037 9.63 0.00 0.00 3.21
250 2437 9.830186 ATCTCTATAGTGGGAAGTAACATATGT 57.170 33.333 1.41 1.41 0.00 2.29
259 2446 9.303116 CATGTTACTATCTCTATAGTGGGAAGT 57.697 37.037 8.04 5.11 46.28 3.01
260 2447 9.303116 ACATGTTACTATCTCTATAGTGGGAAG 57.697 37.037 8.04 0.00 46.28 3.46
263 2450 7.039714 TGCACATGTTACTATCTCTATAGTGGG 60.040 40.741 0.00 0.00 46.28 4.61
264 2451 7.886338 TGCACATGTTACTATCTCTATAGTGG 58.114 38.462 0.00 0.00 46.28 4.00
265 2452 9.351570 CATGCACATGTTACTATCTCTATAGTG 57.648 37.037 0.00 0.00 39.93 2.74
296 2483 7.069826 AGCCACAACGGGTAGTAATATAAAGTA 59.930 37.037 0.00 0.00 46.31 2.24
297 2484 6.051074 GCCACAACGGGTAGTAATATAAAGT 58.949 40.000 0.00 0.00 34.06 2.66
298 2485 6.285990 AGCCACAACGGGTAGTAATATAAAG 58.714 40.000 0.00 0.00 46.31 1.85
300 2487 5.874897 AGCCACAACGGGTAGTAATATAA 57.125 39.130 0.00 0.00 46.31 0.98
309 2496 2.512692 TAGACTAGCCACAACGGGTA 57.487 50.000 0.00 0.00 46.31 3.69
311 2498 2.981859 ATTAGACTAGCCACAACGGG 57.018 50.000 0.00 0.00 34.06 5.28
312 2499 3.181479 TGCTATTAGACTAGCCACAACGG 60.181 47.826 0.00 0.00 42.85 4.44
313 2500 4.041740 TGCTATTAGACTAGCCACAACG 57.958 45.455 0.00 0.00 42.85 4.10
315 2502 5.989477 ACAATGCTATTAGACTAGCCACAA 58.011 37.500 0.00 0.00 42.85 3.33
317 2504 6.049149 TGAACAATGCTATTAGACTAGCCAC 58.951 40.000 0.00 0.00 42.85 5.01
319 2506 5.178438 GCTGAACAATGCTATTAGACTAGCC 59.822 44.000 0.00 0.00 42.85 3.93
320 2507 5.755375 TGCTGAACAATGCTATTAGACTAGC 59.245 40.000 0.00 0.00 43.61 3.42
321 2508 6.201806 GGTGCTGAACAATGCTATTAGACTAG 59.798 42.308 0.00 0.00 0.00 2.57
323 2510 4.878397 GGTGCTGAACAATGCTATTAGACT 59.122 41.667 0.00 0.00 0.00 3.24
326 3054 4.637534 ACAGGTGCTGAACAATGCTATTAG 59.362 41.667 0.00 0.00 35.18 1.73
343 3071 3.116073 CACATGCATGCAACAGGTG 57.884 52.632 26.68 23.79 42.52 4.00
431 3516 6.892658 AAGCATAACACCAAGTTTCACATA 57.107 33.333 0.00 0.00 41.64 2.29
538 3646 3.947910 ACAGGCAACCAAATCATCTTG 57.052 42.857 0.00 0.00 37.17 3.02
724 5923 1.086696 TTGTCCTAGCGCTTTCATGC 58.913 50.000 18.68 2.09 0.00 4.06
750 5949 8.148999 CAGGACTTTTCAGAGATGATGATATCA 58.851 37.037 8.10 8.10 44.55 2.15
762 5961 1.202806 TGGGTGCAGGACTTTTCAGAG 60.203 52.381 0.00 0.00 0.00 3.35
805 6004 2.125350 GGAAGACCTGGAGCGCAG 60.125 66.667 11.47 0.00 0.00 5.18
810 6009 0.622665 AGCAATGGGAAGACCTGGAG 59.377 55.000 0.00 0.00 41.11 3.86
824 6023 5.907197 CGTATCTTAATTGACGGAGCAAT 57.093 39.130 0.00 0.00 40.04 3.56
863 6062 6.096282 TGGAATCATCTCATAGTTGTCGTACA 59.904 38.462 0.00 0.00 0.00 2.90
1122 6322 3.312697 GCCAAAACGGATTAGAGATGGTC 59.687 47.826 0.00 0.00 36.56 4.02
1132 6332 0.605319 TCAGCGAGCCAAAACGGATT 60.605 50.000 0.00 0.00 36.56 3.01
1140 6340 1.290324 GTCTGTCTCAGCGAGCCAA 59.710 57.895 0.00 0.00 0.00 4.52
1206 6406 1.149627 TAGGGTTGCACTGCGGTTT 59.850 52.632 0.00 0.00 0.00 3.27
1248 6456 4.081406 AGATACTGTTGATTGCAAAGCCA 58.919 39.130 1.71 0.00 35.42 4.75
1341 6549 3.096092 GGTGTTCCCAATCTTTATGCCA 58.904 45.455 0.00 0.00 0.00 4.92
1388 6596 2.202892 GGTTGCCGAGGTCGATCC 60.203 66.667 0.00 0.00 43.02 3.36
1467 6675 2.113774 CTTGTCTGCACCAGGCCA 59.886 61.111 5.01 0.00 43.89 5.36
1611 6834 0.602638 TTGCGTTCGTCTTGCCTGAT 60.603 50.000 0.00 0.00 0.00 2.90
1699 6922 1.069906 GTTGAACTTACGTGCTGCTGG 60.070 52.381 0.00 0.00 0.00 4.85
1751 6976 1.151668 GCACTGCTTGTCCTAGTGTG 58.848 55.000 0.00 0.00 42.79 3.82
1799 7025 6.672147 GTCACTGACATGACTAATTTGCTTT 58.328 36.000 0.00 0.00 44.71 3.51
1851 7078 0.035317 ATTGACAGAGCTTCCACGCA 59.965 50.000 0.00 0.00 0.00 5.24
1964 7344 1.136872 GCTCTAGAGCGTTCAGTGCG 61.137 60.000 28.04 0.00 45.29 5.34
1992 7372 1.603455 CCTTTCCCGCCTGAAGCAA 60.603 57.895 0.00 0.00 44.04 3.91
1993 7373 2.034066 CCTTTCCCGCCTGAAGCA 59.966 61.111 0.00 0.00 44.04 3.91
2013 7399 2.158885 GCCTACCCAAATCCTCTCACTC 60.159 54.545 0.00 0.00 0.00 3.51
2016 7402 1.213296 GGCCTACCCAAATCCTCTCA 58.787 55.000 0.00 0.00 0.00 3.27
2023 7409 0.557729 CATCCCTGGCCTACCCAAAT 59.442 55.000 3.32 0.00 44.81 2.32
2053 7439 1.541670 GGACTCTTAAACCGCCACACA 60.542 52.381 0.00 0.00 0.00 3.72
2054 7440 1.154197 GGACTCTTAAACCGCCACAC 58.846 55.000 0.00 0.00 0.00 3.82
2056 7442 2.452767 CGGACTCTTAAACCGCCAC 58.547 57.895 0.00 0.00 40.19 5.01
2066 8083 1.338200 GCATCTCCAACACGGACTCTT 60.338 52.381 0.00 0.00 39.64 2.85
2069 8086 1.296715 GGCATCTCCAACACGGACT 59.703 57.895 0.00 0.00 39.64 3.85
2126 8145 6.351711 ACAAATAGCAGCATCTCTCAACATA 58.648 36.000 0.00 0.00 0.00 2.29
2150 8169 9.185680 TGTAGTTTCTAAGCTGTCATGTAGATA 57.814 33.333 0.00 0.00 0.00 1.98
2152 8171 7.363007 CCTGTAGTTTCTAAGCTGTCATGTAGA 60.363 40.741 0.00 0.00 0.00 2.59
2216 8240 4.026310 GCGGCATAAGCAGATCAAAATTTG 60.026 41.667 0.00 0.00 44.61 2.32
2242 8267 5.360591 AGCGCAACTAGCTATTAGAAATGT 58.639 37.500 11.47 0.00 44.05 2.71
2310 8338 8.540492 GGTTAGTCAATGTAAGTATCAATCACG 58.460 37.037 0.00 0.00 0.00 4.35
2453 8492 2.939103 AGCAGTTTGCCTTTAGATAGCG 59.061 45.455 0.00 0.00 46.52 4.26
2533 8635 9.454859 CCCTTTTCTAATATAGCCATTTAGGAG 57.545 37.037 0.00 0.00 41.22 3.69
2557 8659 7.068348 TGTGTATGAGACTCTGTAAACTATCCC 59.932 40.741 3.68 0.00 0.00 3.85
2735 8846 5.692115 TCCATGCTTGATTTACTACCAGA 57.308 39.130 0.22 0.00 0.00 3.86
2771 8882 3.531538 TCGGAGCAAAAGATCCATACAC 58.468 45.455 0.45 0.00 35.14 2.90
2785 8896 2.922740 ACTTGTACCTTTTCGGAGCA 57.077 45.000 0.00 0.00 36.31 4.26
2944 9055 6.658816 TGCTAATTGCCTCATTTAGAAACTCA 59.341 34.615 10.77 0.30 42.00 3.41
2950 9061 7.408756 ACAAATGCTAATTGCCTCATTTAGA 57.591 32.000 10.77 0.00 42.00 2.10
3139 9250 1.522355 CAATCCTCGTGCGATGCCT 60.522 57.895 0.00 0.00 0.00 4.75
3181 9292 3.127376 TGTCAAAATGGATGATGCGAGTG 59.873 43.478 0.00 0.00 0.00 3.51
3325 9436 5.759059 ACTTCTGGAGCAATGAATCCAATA 58.241 37.500 8.61 0.00 44.82 1.90
3385 9496 6.705381 GCATCATTCCATAGCTATAGACATCC 59.295 42.308 5.77 0.00 0.00 3.51
3437 9548 8.360390 GCTATTGGTAATCCCTTTTCCTTTATG 58.640 37.037 0.00 0.00 0.00 1.90
3453 9564 5.804639 ACACATCACTTGAGCTATTGGTAA 58.195 37.500 0.00 0.00 0.00 2.85
3458 9569 7.611467 TGGAAAATACACATCACTTGAGCTATT 59.389 33.333 0.00 0.00 0.00 1.73
3488 9599 8.642908 TGTTCTGTTATACTGTCATAAATCCG 57.357 34.615 0.00 0.00 0.00 4.18
3506 9617 4.839121 TCACAACTTTGTACCTGTTCTGT 58.161 39.130 0.00 0.00 39.91 3.41
3533 9644 2.772739 CCTCTTCAAGGTCGCATGG 58.227 57.895 0.00 0.00 40.67 3.66
3571 9682 0.602905 GTATGCACCATAGGCCGACC 60.603 60.000 0.00 0.00 0.00 4.79
3606 9717 4.838152 TGCTCATCGAAGGGCGGC 62.838 66.667 8.15 0.00 41.33 6.53
3779 9894 6.381498 TGTCCACATAATCCTACTTTTGGA 57.619 37.500 0.00 0.00 38.06 3.53
3795 9910 6.364706 GCAATTCGAATTTACATTTGTCCACA 59.635 34.615 20.56 0.00 0.00 4.17
3876 9993 7.201644 CCATTCTTAGTAGAAACACAATGCGAT 60.202 37.037 0.00 0.00 43.32 4.58
3878 9995 6.128282 ACCATTCTTAGTAGAAACACAATGCG 60.128 38.462 0.00 0.00 43.32 4.73
3883 10000 5.178623 CGCAACCATTCTTAGTAGAAACACA 59.821 40.000 0.00 0.00 43.32 3.72
3888 10005 3.932822 TGCGCAACCATTCTTAGTAGAA 58.067 40.909 8.16 0.00 44.16 2.10
3892 10009 4.022416 TCAAATTGCGCAACCATTCTTAGT 60.022 37.500 27.64 1.66 0.00 2.24
3893 10010 4.484236 TCAAATTGCGCAACCATTCTTAG 58.516 39.130 27.64 9.04 0.00 2.18
3894 10011 4.511617 TCAAATTGCGCAACCATTCTTA 57.488 36.364 27.64 0.00 0.00 2.10
3895 10012 3.383620 TCAAATTGCGCAACCATTCTT 57.616 38.095 27.64 12.07 0.00 2.52
3896 10013 3.598019 ATCAAATTGCGCAACCATTCT 57.402 38.095 27.64 5.20 0.00 2.40
3897 10014 4.268405 CCTTATCAAATTGCGCAACCATTC 59.732 41.667 27.64 0.00 0.00 2.67
3898 10015 4.081752 TCCTTATCAAATTGCGCAACCATT 60.082 37.500 27.64 17.70 0.00 3.16
3899 10016 3.446873 TCCTTATCAAATTGCGCAACCAT 59.553 39.130 27.64 16.37 0.00 3.55
3900 10017 2.822561 TCCTTATCAAATTGCGCAACCA 59.177 40.909 27.64 9.85 0.00 3.67
3901 10018 3.502191 TCCTTATCAAATTGCGCAACC 57.498 42.857 27.64 0.00 0.00 3.77
3902 10019 5.405269 ACTTTTCCTTATCAAATTGCGCAAC 59.595 36.000 27.64 0.00 0.00 4.17
3903 10020 5.537188 ACTTTTCCTTATCAAATTGCGCAA 58.463 33.333 27.24 27.24 0.00 4.85
3904 10021 5.132897 ACTTTTCCTTATCAAATTGCGCA 57.867 34.783 5.66 5.66 0.00 6.09
3905 10022 5.160641 TGACTTTTCCTTATCAAATTGCGC 58.839 37.500 0.00 0.00 0.00 6.09
3906 10023 7.816945 AATGACTTTTCCTTATCAAATTGCG 57.183 32.000 0.00 0.00 0.00 4.85
3907 10024 9.206870 TCAAATGACTTTTCCTTATCAAATTGC 57.793 29.630 0.00 0.00 0.00 3.56
3950 10067 9.758651 AAAGTGTACTTTTGTCTTTTTGTTTCT 57.241 25.926 4.25 0.00 43.07 2.52
3971 10088 5.634896 CGAAGAATTGAGGGATGAAAAGTG 58.365 41.667 0.00 0.00 0.00 3.16
3993 10110 2.095372 GGGACCAAATCTAAACTTCGCG 59.905 50.000 0.00 0.00 0.00 5.87
4001 10118 5.576563 TGAAGTTGAGGGACCAAATCTAA 57.423 39.130 0.00 0.00 0.00 2.10
4035 10152 5.278071 CGGTTTCAGTAGTTAATGGTGCAAA 60.278 40.000 0.00 0.00 0.00 3.68
4040 10157 4.040706 TGTCCGGTTTCAGTAGTTAATGGT 59.959 41.667 0.00 0.00 0.00 3.55
4043 10160 6.105397 TCTTGTCCGGTTTCAGTAGTTAAT 57.895 37.500 0.00 0.00 0.00 1.40
4061 10178 2.355108 CGTGACCAGGGATGAATCTTGT 60.355 50.000 0.00 0.00 0.00 3.16
4114 10231 1.134521 TGAGTCGGCACAGTCAAAACT 60.135 47.619 0.00 0.00 35.60 2.66
4139 10256 1.807742 CGGAATTGGAAAAGGTACGCA 59.192 47.619 0.00 0.00 0.00 5.24
4155 10272 6.975772 CCCGAATTTGAAAATATTAAGCGGAA 59.024 34.615 0.00 0.00 36.21 4.30
4196 10313 9.915629 AGTACACACATTTTTAAAAAGTTCACA 57.084 25.926 17.72 0.00 0.00 3.58
4214 10331 5.849604 GCGTGGATTTAGAAAAAGTACACAC 59.150 40.000 0.00 0.00 31.33 3.82
4228 10346 3.139850 TCGGAAAAAGTGCGTGGATTTA 58.860 40.909 0.00 0.00 42.55 1.40
4234 10352 1.329292 TGAACTCGGAAAAAGTGCGTG 59.671 47.619 0.00 0.00 42.55 5.34
4235 10353 1.329599 GTGAACTCGGAAAAAGTGCGT 59.670 47.619 0.00 0.00 42.55 5.24
4238 10356 3.800506 AGTACGTGAACTCGGAAAAAGTG 59.199 43.478 0.00 0.00 34.94 3.16
4332 10455 5.919141 AGGACGCGTGAATATGAATAAGTAC 59.081 40.000 20.70 0.00 0.00 2.73
4365 10488 9.623687 GTTTTCAAGTTCGAATGAATTTTCAAG 57.376 29.630 13.43 0.00 41.13 3.02
4375 10498 4.601522 CACGTACGTTTTCAAGTTCGAATG 59.398 41.667 20.23 0.00 35.61 2.67
4376 10499 4.318263 CCACGTACGTTTTCAAGTTCGAAT 60.318 41.667 20.23 0.00 35.61 3.34
4377 10500 3.000122 CCACGTACGTTTTCAAGTTCGAA 60.000 43.478 20.23 0.00 35.61 3.71
4397 10521 8.600449 ATTTGCGTAAAAGAAATTCAAATCCA 57.400 26.923 1.94 0.00 29.81 3.41
4435 10562 9.176460 AGTTGACAAAATTTTTCAAATCCACAT 57.824 25.926 20.31 7.20 31.21 3.21
4480 10607 6.669125 TCCAGTCCATGAAATTTGTTTGAT 57.331 33.333 0.00 0.00 0.00 2.57
4490 10617 4.803452 AGTTCCTTTTCCAGTCCATGAAA 58.197 39.130 0.00 0.00 0.00 2.69
4549 10678 4.121317 TCGTGTACTTGTTTCAAATCCGT 58.879 39.130 0.00 0.00 0.00 4.69
4568 10697 6.568869 TCCATGAAGTGTTTTTGAAATTCGT 58.431 32.000 0.00 0.00 0.00 3.85
4697 10836 6.419413 TCCGTGAACTATTTTGAAATTTGTGC 59.581 34.615 0.00 0.00 0.00 4.57


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.