Multiple sequence alignment - TraesCS3D01G327800

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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 TraesCS3D01G327800 chr3D 100.000 5418 0 0 1 5418 441123161 441128578 0.000000e+00 10006.0
1 TraesCS3D01G327800 chr3D 90.323 62 4 2 1801 1861 326698957 326699017 4.500000e-11 80.5
2 TraesCS3D01G327800 chr3A 94.024 3062 114 23 1870 4899 581251959 581254983 0.000000e+00 4577.0
3 TraesCS3D01G327800 chr3A 87.280 1761 102 50 1 1715 581249791 581251475 0.000000e+00 1899.0
4 TraesCS3D01G327800 chr3A 84.816 461 36 20 4986 5418 581256623 581257077 3.000000e-117 433.0
5 TraesCS3D01G327800 chr3A 89.655 58 5 1 4888 4945 581256555 581256611 7.530000e-09 73.1
6 TraesCS3D01G327800 chr3B 88.840 2061 174 29 1873 3901 578276036 578278072 0.000000e+00 2481.0
7 TraesCS3D01G327800 chr3B 88.109 1396 103 38 332 1712 578274430 578275777 0.000000e+00 1600.0
8 TraesCS3D01G327800 chr3B 89.006 1046 62 23 4198 5233 578278383 578279385 0.000000e+00 1245.0
9 TraesCS3D01G327800 chr3B 94.477 344 10 5 1 335 578273991 578274334 6.220000e-144 521.0
10 TraesCS3D01G327800 chr3B 86.594 276 21 6 3928 4189 578278064 578278337 1.910000e-74 291.0
11 TraesCS3D01G327800 chr3B 93.750 192 11 1 5227 5418 578279800 578279990 2.470000e-73 287.0
12 TraesCS3D01G327800 chr3B 92.188 64 5 0 1799 1862 783474156 783474093 2.080000e-14 91.6
13 TraesCS3D01G327800 chr3B 100.000 28 0 0 1760 1787 227667967 227667994 1.000000e-02 52.8
14 TraesCS3D01G327800 chrUn 87.977 524 40 11 963 1482 355025655 355025151 1.000000e-166 597.0
15 TraesCS3D01G327800 chrUn 86.190 420 35 11 1067 1482 442532468 442532868 3.000000e-117 433.0
16 TraesCS3D01G327800 chrUn 96.226 106 3 1 1511 1615 355025154 355025049 7.210000e-39 172.0
17 TraesCS3D01G327800 chrUn 96.226 106 3 1 1511 1615 442532865 442532970 7.210000e-39 172.0
18 TraesCS3D01G327800 chrUn 94.444 90 5 0 963 1052 453488487 453488576 7.320000e-29 139.0
19 TraesCS3D01G327800 chr7A 83.716 479 35 23 417 879 634922981 634922530 3.910000e-111 412.0
20 TraesCS3D01G327800 chr7A 84.286 140 20 2 1070 1208 617853440 617853578 9.470000e-28 135.0
21 TraesCS3D01G327800 chr7A 90.164 61 6 0 1800 1860 347151279 347151219 4.500000e-11 80.5
22 TraesCS3D01G327800 chr7A 88.372 43 5 0 1802 1844 650614482 650614524 1.000000e-02 52.8
23 TraesCS3D01G327800 chr7D 84.314 306 14 13 572 873 549307581 549307306 8.950000e-68 268.0
24 TraesCS3D01G327800 chr7D 85.000 140 19 2 1070 1208 535730155 535730017 2.030000e-29 141.0
25 TraesCS3D01G327800 chr7B 85.714 140 18 2 1070 1208 577565770 577565632 4.370000e-31 147.0
26 TraesCS3D01G327800 chr6D 91.803 61 5 0 1799 1859 302193809 302193869 9.670000e-13 86.1
27 TraesCS3D01G327800 chr2D 91.667 60 5 0 834 893 620269429 620269488 3.480000e-12 84.2
28 TraesCS3D01G327800 chr1B 96.078 51 2 0 1799 1849 277455224 277455174 3.480000e-12 84.2
29 TraesCS3D01G327800 chr1B 86.792 53 6 1 1811 1862 653827108 653827056 2.110000e-04 58.4
30 TraesCS3D01G327800 chr5D 85.938 64 9 0 1799 1862 11309327 11309264 9.740000e-08 69.4
31 TraesCS3D01G327800 chr1A 89.583 48 5 0 1796 1843 564146559 564146606 1.630000e-05 62.1
32 TraesCS3D01G327800 chr2B 94.118 34 2 0 1760 1793 29741051 29741018 1.000000e-02 52.8
33 TraesCS3D01G327800 chr2B 94.118 34 2 0 1760 1793 29741102 29741069 1.000000e-02 52.8


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 TraesCS3D01G327800 chr3D 441123161 441128578 5417 False 10006.000000 10006 100.000000 1 5418 1 chr3D.!!$F2 5417
1 TraesCS3D01G327800 chr3A 581249791 581257077 7286 False 1745.525000 4577 88.943750 1 5418 4 chr3A.!!$F1 5417
2 TraesCS3D01G327800 chr3B 578273991 578279990 5999 False 1070.833333 2481 90.129333 1 5418 6 chr3B.!!$F2 5417
3 TraesCS3D01G327800 chrUn 355025049 355025655 606 True 384.500000 597 92.101500 963 1615 2 chrUn.!!$R1 652
4 TraesCS3D01G327800 chrUn 442532468 442532970 502 False 302.500000 433 91.208000 1067 1615 2 chrUn.!!$F2 548

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
700 862 0.251634 AAGACTTAGCAGGAGCAGGC 59.748 55.000 0.0 0.0 45.49 4.85 F
701 863 0.617249 AGACTTAGCAGGAGCAGGCT 60.617 55.000 0.0 0.0 45.49 4.58 F
1290 1459 0.689745 TCCGTGGAAGGGGAATCGAT 60.690 55.000 0.0 0.0 43.54 3.59 F
1404 1582 1.069204 AGGTGCATCTGCGTAATCGAT 59.931 47.619 0.0 0.0 45.83 3.59 F
1658 1846 2.084546 GTGCTGGGATAGTTGGTGTTC 58.915 52.381 0.0 0.0 0.00 3.18 F
3455 4042 1.376424 CGAGTGCAGTTGGCTCCAT 60.376 57.895 0.2 0.0 45.15 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2633 3216 1.211457 AGCCATGGTTAGCTCCTTCTG 59.789 52.381 14.67 0.00 32.71 3.02 R
2635 3218 2.293170 GAAGCCATGGTTAGCTCCTTC 58.707 52.381 14.67 11.49 38.74 3.46 R
2873 3458 0.828022 TCGGGCCTAAACGTCATCAT 59.172 50.000 0.84 0.00 0.00 2.45 R
2880 3465 1.415374 CGATACATCGGGCCTAAACG 58.585 55.000 0.84 0.00 45.93 3.60 R
3589 4176 4.307443 TCTCCATGTCGCAGTACATTAG 57.693 45.455 0.00 0.00 38.01 1.73 R
4936 7191 0.036294 GGAACTGACAGGGGCAGTAC 60.036 60.000 4.96 0.00 45.27 2.73 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
99 113 3.639162 CGGAAGCAGCAACAACAAA 57.361 47.368 0.00 0.00 0.00 2.83
242 259 0.674581 CATGTCGATGCCACCACACT 60.675 55.000 0.00 0.00 0.00 3.55
243 260 0.391661 ATGTCGATGCCACCACACTC 60.392 55.000 0.00 0.00 0.00 3.51
244 261 1.005037 GTCGATGCCACCACACTCA 60.005 57.895 0.00 0.00 0.00 3.41
245 262 1.005037 TCGATGCCACCACACTCAC 60.005 57.895 0.00 0.00 0.00 3.51
335 359 3.941483 GTGGAAATGCAGCAGTGTAGTAT 59.059 43.478 0.00 0.00 0.00 2.12
336 360 5.104941 AGTGGAAATGCAGCAGTGTAGTATA 60.105 40.000 0.00 0.00 0.00 1.47
337 361 5.584649 GTGGAAATGCAGCAGTGTAGTATAA 59.415 40.000 0.00 0.00 0.00 0.98
341 365 7.494625 GGAAATGCAGCAGTGTAGTATAAACTA 59.505 37.037 0.00 0.00 36.90 2.24
342 366 8.425577 AAATGCAGCAGTGTAGTATAAACTAG 57.574 34.615 0.00 0.00 36.90 2.57
344 368 4.441415 GCAGCAGTGTAGTATAAACTAGCG 59.559 45.833 0.00 0.00 36.90 4.26
359 483 1.739466 CTAGCGCAAGAAATTGGAGCA 59.261 47.619 11.47 0.00 43.02 4.26
375 499 8.767478 AATTGGAGCAAAGAAAAAGTATGATG 57.233 30.769 0.00 0.00 0.00 3.07
390 514 6.287107 AGTATGATGCGCATGTAGTAAAAC 57.713 37.500 30.76 10.44 37.87 2.43
391 515 4.552166 ATGATGCGCATGTAGTAAAACC 57.448 40.909 30.76 9.63 35.42 3.27
422 553 8.873215 ATATGTTTCTACATCTTCAACCTACG 57.127 34.615 0.00 0.00 43.81 3.51
489 625 3.854856 GCTGAGGGCCAAACACAA 58.145 55.556 6.18 0.00 34.27 3.33
490 626 1.662044 GCTGAGGGCCAAACACAAG 59.338 57.895 6.18 0.00 34.27 3.16
491 627 1.662044 CTGAGGGCCAAACACAAGC 59.338 57.895 6.18 0.00 0.00 4.01
492 628 1.076412 TGAGGGCCAAACACAAGCA 60.076 52.632 6.18 0.00 0.00 3.91
521 657 3.610040 TGTTTAGCACATCTCCGTCAT 57.390 42.857 0.00 0.00 0.00 3.06
522 658 4.729227 TGTTTAGCACATCTCCGTCATA 57.271 40.909 0.00 0.00 0.00 2.15
562 698 2.264109 TAGCGAAGAAGCTCAGTTCG 57.736 50.000 16.60 16.60 45.67 3.95
581 717 1.304381 GGCCAATCAGGTTCAGGCA 60.304 57.895 0.00 0.00 46.96 4.75
687 849 2.370189 AGAACAGCCTAGCACAAGACTT 59.630 45.455 0.00 0.00 0.00 3.01
688 850 3.578716 AGAACAGCCTAGCACAAGACTTA 59.421 43.478 0.00 0.00 0.00 2.24
689 851 3.601443 ACAGCCTAGCACAAGACTTAG 57.399 47.619 0.00 0.00 0.00 2.18
690 852 2.275318 CAGCCTAGCACAAGACTTAGC 58.725 52.381 4.14 4.14 0.00 3.09
691 853 1.902508 AGCCTAGCACAAGACTTAGCA 59.097 47.619 12.65 1.25 0.00 3.49
692 854 2.093764 AGCCTAGCACAAGACTTAGCAG 60.094 50.000 12.65 8.48 0.00 4.24
693 855 2.898705 CCTAGCACAAGACTTAGCAGG 58.101 52.381 12.65 12.21 0.00 4.85
694 856 2.497675 CCTAGCACAAGACTTAGCAGGA 59.502 50.000 16.56 4.14 31.40 3.86
695 857 2.758736 AGCACAAGACTTAGCAGGAG 57.241 50.000 12.65 0.00 0.00 3.69
696 858 1.082690 GCACAAGACTTAGCAGGAGC 58.917 55.000 6.87 0.00 42.56 4.70
697 859 1.609061 GCACAAGACTTAGCAGGAGCA 60.609 52.381 6.87 0.00 45.49 4.26
698 860 2.344950 CACAAGACTTAGCAGGAGCAG 58.655 52.381 0.00 0.00 45.49 4.24
699 861 1.277557 ACAAGACTTAGCAGGAGCAGG 59.722 52.381 0.00 0.00 45.49 4.85
700 862 0.251634 AAGACTTAGCAGGAGCAGGC 59.748 55.000 0.00 0.00 45.49 4.85
701 863 0.617249 AGACTTAGCAGGAGCAGGCT 60.617 55.000 0.00 0.00 45.49 4.58
766 929 3.943691 CCCACGAACCCAACCCGA 61.944 66.667 0.00 0.00 0.00 5.14
767 930 2.667199 CCACGAACCCAACCCGAC 60.667 66.667 0.00 0.00 0.00 4.79
768 931 2.109387 CACGAACCCAACCCGACA 59.891 61.111 0.00 0.00 0.00 4.35
898 1061 3.633094 CTGGACCGGAGCAGACACG 62.633 68.421 9.46 0.00 0.00 4.49
915 1078 4.416738 GCCGCTGCTTCCTTCCCT 62.417 66.667 0.00 0.00 33.53 4.20
931 1096 1.857348 CCTTCCCCTTTCCCCACCT 60.857 63.158 0.00 0.00 0.00 4.00
1032 1198 2.363795 CTGGTCCTGGCCCTCGTA 60.364 66.667 0.00 0.00 0.00 3.43
1221 1387 1.674057 CCTGTGCGTTTCCCTCTCT 59.326 57.895 0.00 0.00 0.00 3.10
1240 1406 1.153469 CCTCTCTTGCTCGCCCTTC 60.153 63.158 0.00 0.00 0.00 3.46
1242 1408 1.892819 CTCTCTTGCTCGCCCTTCCA 61.893 60.000 0.00 0.00 0.00 3.53
1256 1422 3.057245 GCCCTTCCATTTCTGTTTGAGTC 60.057 47.826 0.00 0.00 0.00 3.36
1273 1442 4.394712 CGGGGCTGTGGTCTGTCC 62.395 72.222 0.00 0.00 36.70 4.02
1277 1446 2.357517 GCTGTGGTCTGTCCGTGG 60.358 66.667 0.00 0.00 39.52 4.94
1279 1448 1.745890 CTGTGGTCTGTCCGTGGAA 59.254 57.895 0.00 0.00 39.52 3.53
1289 1458 1.305465 TCCGTGGAAGGGGAATCGA 60.305 57.895 0.00 0.00 43.54 3.59
1290 1459 0.689745 TCCGTGGAAGGGGAATCGAT 60.690 55.000 0.00 0.00 43.54 3.59
1312 1490 4.647615 CGGGCTCGCGTCTATGGG 62.648 72.222 5.77 0.00 0.00 4.00
1317 1495 2.123854 TCGCGTCTATGGGGAGCT 60.124 61.111 5.77 0.00 0.00 4.09
1319 1497 1.170919 TCGCGTCTATGGGGAGCTAC 61.171 60.000 5.77 0.00 0.00 3.58
1326 1504 3.830755 GTCTATGGGGAGCTACCGATTTA 59.169 47.826 18.77 3.81 40.11 1.40
1327 1505 4.282703 GTCTATGGGGAGCTACCGATTTAA 59.717 45.833 18.77 0.00 40.11 1.52
1341 1519 4.600012 CGATTTAACAGCGGATGAGTTT 57.400 40.909 0.00 0.00 0.00 2.66
1404 1582 1.069204 AGGTGCATCTGCGTAATCGAT 59.931 47.619 0.00 0.00 45.83 3.59
1411 1589 5.639082 TGCATCTGCGTAATCGATGATTTAT 59.361 36.000 0.00 0.00 45.83 1.40
1412 1590 6.147656 TGCATCTGCGTAATCGATGATTTATT 59.852 34.615 0.00 0.00 45.83 1.40
1413 1591 7.330700 TGCATCTGCGTAATCGATGATTTATTA 59.669 33.333 0.00 0.00 45.83 0.98
1484 1662 2.975851 CTGCGTGAATCAAAACAAGAGC 59.024 45.455 0.00 0.00 0.00 4.09
1487 1665 3.814945 CGTGAATCAAAACAAGAGCCTC 58.185 45.455 0.00 0.00 0.00 4.70
1658 1846 2.084546 GTGCTGGGATAGTTGGTGTTC 58.915 52.381 0.00 0.00 0.00 3.18
1677 1865 6.145535 GTGTTCTTTGTGTTCTCCATGAATC 58.854 40.000 0.00 0.00 36.99 2.52
1700 1889 2.464682 CTGCCTAGTGCTTGCAGTC 58.535 57.895 6.19 0.00 45.69 3.51
1768 2204 7.761608 AGTAGCTAATTCACTATACTCCCTCT 58.238 38.462 0.00 0.00 0.00 3.69
1787 2230 9.539825 CTCCCTCTGATTCATATTAATTATCGG 57.460 37.037 0.00 0.00 0.00 4.18
1814 2283 8.995220 TGATTTAGTACCATATTAATTGTCGCC 58.005 33.333 0.00 0.00 0.00 5.54
1851 2325 3.348119 TGTACCAAATCAGCGGCAATTA 58.652 40.909 1.45 0.00 0.00 1.40
1862 2336 3.436704 CAGCGGCAATTAATATGGATCGT 59.563 43.478 1.45 0.00 0.00 3.73
1863 2337 4.072131 AGCGGCAATTAATATGGATCGTT 58.928 39.130 1.45 0.00 0.00 3.85
1864 2338 4.154195 AGCGGCAATTAATATGGATCGTTC 59.846 41.667 1.45 0.00 0.00 3.95
1865 2339 4.154195 GCGGCAATTAATATGGATCGTTCT 59.846 41.667 0.00 0.00 0.00 3.01
1866 2340 5.671329 GCGGCAATTAATATGGATCGTTCTC 60.671 44.000 0.00 0.00 0.00 2.87
1867 2341 5.639506 CGGCAATTAATATGGATCGTTCTCT 59.360 40.000 0.00 0.00 0.00 3.10
1868 2342 6.147821 CGGCAATTAATATGGATCGTTCTCTT 59.852 38.462 0.00 0.00 0.00 2.85
1870 2344 8.352942 GGCAATTAATATGGATCGTTCTCTTTT 58.647 33.333 0.00 0.00 0.00 2.27
1871 2345 9.736023 GCAATTAATATGGATCGTTCTCTTTTT 57.264 29.630 0.00 0.00 0.00 1.94
1912 2439 7.859377 AGCTATTGATGATTTCTTGTATTTGCG 59.141 33.333 0.00 0.00 0.00 4.85
1991 2518 5.163395 CCCCTCTTACAGAGATCTTGGTAAC 60.163 48.000 13.23 0.00 45.07 2.50
1997 2524 8.816894 TCTTACAGAGATCTTGGTAACTTGAAT 58.183 33.333 13.23 0.00 37.61 2.57
2097 2624 9.216117 GTTTGGTTCTTATTGCTAGTTTCTCTA 57.784 33.333 0.00 0.00 0.00 2.43
2235 2783 5.671742 GCAATTTGCAAAACACCAATAGT 57.328 34.783 17.19 0.00 44.26 2.12
2236 2784 6.777526 GCAATTTGCAAAACACCAATAGTA 57.222 33.333 17.19 0.00 44.26 1.82
2237 2785 6.820459 GCAATTTGCAAAACACCAATAGTAG 58.180 36.000 17.19 0.00 44.26 2.57
2238 2786 6.618379 GCAATTTGCAAAACACCAATAGTAGC 60.618 38.462 17.19 2.16 44.26 3.58
2239 2787 5.521906 TTTGCAAAACACCAATAGTAGCA 57.478 34.783 10.02 0.00 0.00 3.49
2240 2788 5.720371 TTGCAAAACACCAATAGTAGCAT 57.280 34.783 0.00 0.00 0.00 3.79
2241 2789 5.309323 TGCAAAACACCAATAGTAGCATC 57.691 39.130 0.00 0.00 0.00 3.91
2242 2790 5.009631 TGCAAAACACCAATAGTAGCATCT 58.990 37.500 0.00 0.00 0.00 2.90
2243 2791 5.106197 TGCAAAACACCAATAGTAGCATCTG 60.106 40.000 0.00 0.00 0.00 2.90
2244 2792 5.123820 GCAAAACACCAATAGTAGCATCTGA 59.876 40.000 0.00 0.00 0.00 3.27
2245 2793 6.183360 GCAAAACACCAATAGTAGCATCTGAT 60.183 38.462 0.00 0.00 0.00 2.90
2246 2794 7.412853 CAAAACACCAATAGTAGCATCTGATC 58.587 38.462 0.00 0.00 0.00 2.92
2247 2795 4.876125 ACACCAATAGTAGCATCTGATCG 58.124 43.478 0.00 0.00 0.00 3.69
2293 2841 2.189594 TTTGGTCTGAGATGTGGCTG 57.810 50.000 0.00 0.00 0.00 4.85
2298 2846 2.498167 GTCTGAGATGTGGCTGTTGTT 58.502 47.619 0.00 0.00 0.00 2.83
2517 3099 8.049655 AGTAGCTTTACAGTACTACAACCTAC 57.950 38.462 0.00 6.37 37.94 3.18
2787 3371 7.279981 TGTGTAACTGAATACCTAATGCACATC 59.720 37.037 0.00 0.00 38.04 3.06
2808 3392 6.094603 ACATCATCCTATTTTGAACTGCTGTC 59.905 38.462 0.00 0.00 0.00 3.51
2833 3417 4.223477 AGGATCCATTTCCATTGTTGTTGG 59.777 41.667 15.82 0.00 38.32 3.77
2850 3435 3.195610 TGTTGGTGGTGCATTTGTTTACA 59.804 39.130 0.00 0.00 0.00 2.41
2890 3475 3.537580 TGTTATGATGACGTTTAGGCCC 58.462 45.455 0.00 0.00 0.00 5.80
3144 3730 6.317789 TCTTGTAAGTTTCATGCCTTCAAG 57.682 37.500 15.53 15.53 32.83 3.02
3163 3749 9.522804 CCTTCAAGTACTCTCTACATATGAAAC 57.477 37.037 10.38 0.00 0.00 2.78
3251 3837 3.048337 TGTTCTAATGGTGTCGGGTTC 57.952 47.619 0.00 0.00 0.00 3.62
3264 3850 3.158676 GTCGGGTTCTGCTAGGATATCT 58.841 50.000 2.05 0.00 0.00 1.98
3285 3871 4.460034 TCTGTTCGTAGGTGCTATGTACAA 59.540 41.667 0.00 0.00 34.54 2.41
3292 3878 6.753279 TCGTAGGTGCTATGTACAAATGTAAC 59.247 38.462 0.00 0.00 31.52 2.50
3455 4042 1.376424 CGAGTGCAGTTGGCTCCAT 60.376 57.895 0.20 0.00 45.15 3.41
3589 4176 3.326836 AGTAAGTCTGCTTGCCTTCTC 57.673 47.619 0.00 0.00 37.94 2.87
3618 4205 3.820467 ACTGCGACATGGAGATTTTCAAA 59.180 39.130 0.00 0.00 38.54 2.69
3645 4232 7.716799 ATGCCCATAATAGAAGTTTCAAACA 57.283 32.000 2.41 0.00 0.00 2.83
3713 4300 6.644347 AGGATGTGTGTCTCTTAACCAATAG 58.356 40.000 0.00 0.00 0.00 1.73
3715 4302 7.399191 AGGATGTGTGTCTCTTAACCAATAGTA 59.601 37.037 0.00 0.00 0.00 1.82
3716 4303 7.491696 GGATGTGTGTCTCTTAACCAATAGTAC 59.508 40.741 0.00 0.00 0.00 2.73
3718 4305 7.959175 TGTGTGTCTCTTAACCAATAGTACTT 58.041 34.615 0.00 0.00 0.00 2.24
3719 4306 7.870954 TGTGTGTCTCTTAACCAATAGTACTTG 59.129 37.037 0.00 0.00 0.00 3.16
3721 4308 7.870954 TGTGTCTCTTAACCAATAGTACTTGTG 59.129 37.037 0.00 0.00 0.00 3.33
3722 4309 8.086522 GTGTCTCTTAACCAATAGTACTTGTGA 58.913 37.037 0.00 0.00 0.00 3.58
3725 4312 9.706691 TCTCTTAACCAATAGTACTTGTGAAAG 57.293 33.333 0.00 5.14 0.00 2.62
3738 4325 7.807907 AGTACTTGTGAAAGGCAAATTAAATCG 59.192 33.333 0.00 0.00 0.00 3.34
3759 4346 3.531538 GCTCCTGTGATTATTTGACCGA 58.468 45.455 0.00 0.00 0.00 4.69
3890 4483 3.055675 TGTTTCCGTGATAAGGTGGGTAG 60.056 47.826 0.00 0.00 0.00 3.18
3892 4485 2.381911 TCCGTGATAAGGTGGGTAGTC 58.618 52.381 0.00 0.00 0.00 2.59
3893 4486 2.104967 CCGTGATAAGGTGGGTAGTCA 58.895 52.381 0.00 0.00 0.00 3.41
3894 4487 2.159142 CCGTGATAAGGTGGGTAGTCAC 60.159 54.545 0.00 0.00 36.95 3.67
3895 4488 2.758979 CGTGATAAGGTGGGTAGTCACT 59.241 50.000 0.00 0.00 37.75 3.41
3896 4489 3.949754 CGTGATAAGGTGGGTAGTCACTA 59.050 47.826 0.00 0.00 37.75 2.74
3897 4490 4.583489 CGTGATAAGGTGGGTAGTCACTAT 59.417 45.833 0.00 0.00 37.75 2.12
3898 4491 5.068723 CGTGATAAGGTGGGTAGTCACTATT 59.931 44.000 0.00 0.00 37.75 1.73
3899 4492 6.406624 CGTGATAAGGTGGGTAGTCACTATTT 60.407 42.308 0.00 0.00 37.75 1.40
3900 4493 6.985059 GTGATAAGGTGGGTAGTCACTATTTC 59.015 42.308 0.00 0.00 37.75 2.17
3901 4494 6.670464 TGATAAGGTGGGTAGTCACTATTTCA 59.330 38.462 0.00 0.00 37.75 2.69
3902 4495 5.836024 AAGGTGGGTAGTCACTATTTCAA 57.164 39.130 0.00 0.00 37.75 2.69
3905 4498 7.504926 AGGTGGGTAGTCACTATTTCAATTA 57.495 36.000 0.00 0.00 37.75 1.40
4185 4792 0.178068 CCTAGTGGGCACATAACGCT 59.822 55.000 0.00 0.00 0.00 5.07
4190 4797 0.107897 TGGGCACATAACGCTGTAGG 60.108 55.000 0.00 0.00 0.00 3.18
4194 4801 1.739035 GCACATAACGCTGTAGGCTCA 60.739 52.381 0.00 0.00 39.13 4.26
4233 4877 6.078202 TGTTTTCTTTCCATAACGATGCAA 57.922 33.333 0.00 0.00 0.00 4.08
4265 4911 1.676967 CCAGCCTCCACTTTCCAGC 60.677 63.158 0.00 0.00 0.00 4.85
4279 4925 2.462456 TCCAGCTCATGTTCTCACAC 57.538 50.000 0.00 0.00 35.03 3.82
4363 5009 1.153745 CAGCTTCGAGAGGAACCCG 60.154 63.158 0.00 0.00 0.00 5.28
4493 5140 3.316588 CGGAGATCGGGGTGATATAGATG 59.683 52.174 0.00 0.00 37.47 2.90
4498 5145 6.444704 AGATCGGGGTGATATAGATGGTTAT 58.555 40.000 0.00 0.00 37.47 1.89
4554 5201 1.512996 ATAGCGCTGTCATGCCATGC 61.513 55.000 22.90 0.00 0.00 4.06
4696 5357 8.694540 GTCATCTACTCATCTCTATTATGGCAT 58.305 37.037 4.88 4.88 0.00 4.40
4755 5417 4.704965 TCTACGAGTAGCATTCTAGCTGA 58.295 43.478 0.00 0.00 46.11 4.26
4782 5444 4.630644 AACTGATGTAGGGCTGATATGG 57.369 45.455 0.00 0.00 0.00 2.74
4882 5550 2.032680 TTCTTATAGCGGTGCCAACC 57.967 50.000 0.00 0.00 43.76 3.77
4884 5552 1.138266 TCTTATAGCGGTGCCAACCTC 59.862 52.381 0.00 0.00 45.17 3.85
4886 5554 0.906066 TATAGCGGTGCCAACCTCAA 59.094 50.000 0.00 0.00 45.17 3.02
4919 7174 6.920758 CCAAAACAATTGAAGTAAACGGATGA 59.079 34.615 13.59 0.00 0.00 2.92
4924 7179 6.932400 ACAATTGAAGTAAACGGATGACTGTA 59.068 34.615 13.59 0.00 34.90 2.74
4929 7184 3.762288 AGTAAACGGATGACTGTAGCTGA 59.238 43.478 0.00 0.00 34.90 4.26
4930 7185 3.895232 AAACGGATGACTGTAGCTGAT 57.105 42.857 0.00 0.00 34.90 2.90
4936 7191 5.755375 ACGGATGACTGTAGCTGATATTTTG 59.245 40.000 0.00 0.00 33.41 2.44
4942 7197 6.535150 TGACTGTAGCTGATATTTTGTACTGC 59.465 38.462 0.00 0.00 0.00 4.40
4943 7198 5.817816 ACTGTAGCTGATATTTTGTACTGCC 59.182 40.000 0.00 0.00 0.00 4.85
4944 7199 5.123227 TGTAGCTGATATTTTGTACTGCCC 58.877 41.667 0.00 0.00 0.00 5.36
4945 7200 3.555966 AGCTGATATTTTGTACTGCCCC 58.444 45.455 0.00 0.00 0.00 5.80
4946 7201 3.203040 AGCTGATATTTTGTACTGCCCCT 59.797 43.478 0.00 0.00 0.00 4.79
4947 7202 3.316308 GCTGATATTTTGTACTGCCCCTG 59.684 47.826 0.00 0.00 0.00 4.45
4948 7203 4.526970 CTGATATTTTGTACTGCCCCTGT 58.473 43.478 0.00 0.00 0.00 4.00
4949 7204 4.523083 TGATATTTTGTACTGCCCCTGTC 58.477 43.478 0.00 0.00 0.00 3.51
4950 7205 2.969821 ATTTTGTACTGCCCCTGTCA 57.030 45.000 0.00 0.00 0.00 3.58
4951 7206 2.270352 TTTTGTACTGCCCCTGTCAG 57.730 50.000 0.00 0.00 37.56 3.51
4952 7207 1.136828 TTTGTACTGCCCCTGTCAGT 58.863 50.000 0.00 1.18 45.71 3.41
4953 7208 1.136828 TTGTACTGCCCCTGTCAGTT 58.863 50.000 0.77 0.00 41.61 3.16
4954 7209 0.685097 TGTACTGCCCCTGTCAGTTC 59.315 55.000 0.77 0.00 41.61 3.01
4955 7210 0.036294 GTACTGCCCCTGTCAGTTCC 60.036 60.000 0.77 0.00 41.61 3.62
4956 7211 0.472925 TACTGCCCCTGTCAGTTCCA 60.473 55.000 0.77 0.00 41.61 3.53
4957 7212 1.136329 ACTGCCCCTGTCAGTTCCAT 61.136 55.000 0.00 0.00 41.61 3.41
4958 7213 0.393537 CTGCCCCTGTCAGTTCCATC 60.394 60.000 0.00 0.00 0.00 3.51
4959 7214 1.133181 TGCCCCTGTCAGTTCCATCA 61.133 55.000 0.00 0.00 0.00 3.07
4960 7215 0.257039 GCCCCTGTCAGTTCCATCAT 59.743 55.000 0.00 0.00 0.00 2.45
4961 7216 1.490490 GCCCCTGTCAGTTCCATCATA 59.510 52.381 0.00 0.00 0.00 2.15
5072 7327 4.883585 TGTCTCAAAAGCATCTTCACAACT 59.116 37.500 0.00 0.00 0.00 3.16
5078 7333 6.094742 TCAAAAGCATCTTCACAACTTGTACA 59.905 34.615 0.00 0.00 0.00 2.90
5129 7385 7.404671 AAAAGTTACCAGTGACAGTGATTTT 57.595 32.000 12.04 7.72 0.00 1.82
5138 7394 6.206243 CCAGTGACAGTGATTTTCTTCAGAAT 59.794 38.462 12.04 0.00 33.54 2.40
5160 7444 8.695456 AGAATAAGTTAGTGGGGCAATTATTTG 58.305 33.333 0.00 0.00 35.85 2.32
5163 7447 4.956075 AGTTAGTGGGGCAATTATTTGGAG 59.044 41.667 0.00 0.00 33.22 3.86
5168 7452 3.960102 TGGGGCAATTATTTGGAGATGAC 59.040 43.478 0.00 0.00 33.22 3.06
5190 7478 2.212900 CTGTCAGACACGATCGGGCA 62.213 60.000 19.30 6.34 34.49 5.36
5191 7479 1.141881 GTCAGACACGATCGGGCAT 59.858 57.895 19.30 2.56 0.00 4.40
5192 7480 0.460284 GTCAGACACGATCGGGCATT 60.460 55.000 19.30 0.00 0.00 3.56
5193 7481 0.179111 TCAGACACGATCGGGCATTC 60.179 55.000 19.30 7.92 0.00 2.67
5194 7482 1.226974 AGACACGATCGGGCATTCG 60.227 57.895 19.30 0.00 41.04 3.34
5195 7483 2.202878 ACACGATCGGGCATTCGG 60.203 61.111 19.30 0.00 39.61 4.30
5196 7484 2.967076 CACGATCGGGCATTCGGG 60.967 66.667 20.98 0.16 39.61 5.14
5197 7485 4.910585 ACGATCGGGCATTCGGGC 62.911 66.667 20.98 0.00 39.61 6.13
5198 7486 4.609018 CGATCGGGCATTCGGGCT 62.609 66.667 7.38 0.00 42.84 5.19
5215 7504 1.729881 CTTAGGCTTGGGCGATTGC 59.270 57.895 0.00 0.00 39.81 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
99 113 2.623416 CCTCTGCTTTTCCGTTTTCCTT 59.377 45.455 0.00 0.00 0.00 3.36
153 170 1.819632 CTACACGCCTTGCCATCCC 60.820 63.158 0.00 0.00 0.00 3.85
274 297 0.108233 GCAGGAGAGACAAGAGCAGG 60.108 60.000 0.00 0.00 0.00 4.85
335 359 4.142687 GCTCCAATTTCTTGCGCTAGTTTA 60.143 41.667 18.20 5.86 0.00 2.01
336 360 3.366374 GCTCCAATTTCTTGCGCTAGTTT 60.366 43.478 18.20 8.36 0.00 2.66
337 361 2.162408 GCTCCAATTTCTTGCGCTAGTT 59.838 45.455 18.20 3.16 0.00 2.24
341 365 0.961019 TTGCTCCAATTTCTTGCGCT 59.039 45.000 9.73 0.00 32.06 5.92
342 366 1.723003 CTTTGCTCCAATTTCTTGCGC 59.277 47.619 0.00 0.00 0.00 6.09
344 368 5.989551 TTTTCTTTGCTCCAATTTCTTGC 57.010 34.783 0.00 0.00 0.00 4.01
359 483 5.713025 ACATGCGCATCATACTTTTTCTTT 58.287 33.333 22.51 0.00 33.19 2.52
375 499 2.158058 TCGTTGGTTTTACTACATGCGC 59.842 45.455 0.00 0.00 0.00 6.09
422 553 1.539157 CCTTCCCACTCTTTGCCTTC 58.461 55.000 0.00 0.00 0.00 3.46
426 557 0.332972 ATCCCCTTCCCACTCTTTGC 59.667 55.000 0.00 0.00 0.00 3.68
481 617 3.129287 ACAAAGAGACCTGCTTGTGTTTG 59.871 43.478 0.00 0.00 0.00 2.93
484 620 2.717639 ACAAAGAGACCTGCTTGTGT 57.282 45.000 0.00 0.00 0.00 3.72
485 621 4.555511 GCTAAACAAAGAGACCTGCTTGTG 60.556 45.833 0.00 0.00 0.00 3.33
486 622 3.565902 GCTAAACAAAGAGACCTGCTTGT 59.434 43.478 0.00 0.00 0.00 3.16
487 623 3.565482 TGCTAAACAAAGAGACCTGCTTG 59.435 43.478 0.00 0.00 0.00 4.01
489 625 3.142174 GTGCTAAACAAAGAGACCTGCT 58.858 45.455 0.00 0.00 0.00 4.24
490 626 2.878406 TGTGCTAAACAAAGAGACCTGC 59.122 45.455 0.00 0.00 35.24 4.85
491 627 4.999950 AGATGTGCTAAACAAAGAGACCTG 59.000 41.667 0.00 0.00 43.61 4.00
492 628 5.234466 AGATGTGCTAAACAAAGAGACCT 57.766 39.130 0.00 0.00 43.61 3.85
521 657 9.512435 CGCTAAGCTAGTTATTTAGTCTTGTTA 57.488 33.333 0.00 0.00 0.00 2.41
522 658 8.248945 TCGCTAAGCTAGTTATTTAGTCTTGTT 58.751 33.333 0.00 0.00 0.00 2.83
562 698 2.054453 GCCTGAACCTGATTGGCCC 61.054 63.158 0.00 0.00 40.22 5.80
601 746 4.443457 GGCTGCTATAGGTGTGAATCTTCA 60.443 45.833 1.04 0.00 34.20 3.02
659 804 1.190643 GCTAGGCTGTTCTCTGTCCT 58.809 55.000 0.00 0.00 0.00 3.85
660 805 0.898320 TGCTAGGCTGTTCTCTGTCC 59.102 55.000 0.00 0.00 0.00 4.02
687 849 2.362369 GGTCAGCCTGCTCCTGCTA 61.362 63.158 0.00 0.00 40.48 3.49
688 850 3.715097 GGTCAGCCTGCTCCTGCT 61.715 66.667 0.00 0.00 40.48 4.24
689 851 4.792804 GGGTCAGCCTGCTCCTGC 62.793 72.222 5.91 0.00 40.20 4.85
690 852 2.816601 CTTGGGTCAGCCTGCTCCTG 62.817 65.000 0.00 0.00 34.45 3.86
691 853 2.530151 TTGGGTCAGCCTGCTCCT 60.530 61.111 0.00 0.00 34.45 3.69
692 854 2.045536 CTTGGGTCAGCCTGCTCC 60.046 66.667 0.00 0.00 34.45 4.70
693 855 1.376553 GACTTGGGTCAGCCTGCTC 60.377 63.158 0.00 0.00 41.75 4.26
694 856 2.149383 TGACTTGGGTCAGCCTGCT 61.149 57.895 0.00 0.00 46.19 4.24
695 857 2.431683 TGACTTGGGTCAGCCTGC 59.568 61.111 0.00 0.00 46.19 4.85
764 927 1.153046 AGTTGGGTGGGTTGTGTCG 60.153 57.895 0.00 0.00 0.00 4.35
765 928 1.164041 CGAGTTGGGTGGGTTGTGTC 61.164 60.000 0.00 0.00 0.00 3.67
766 929 1.153046 CGAGTTGGGTGGGTTGTGT 60.153 57.895 0.00 0.00 0.00 3.72
767 930 1.896660 CCGAGTTGGGTGGGTTGTG 60.897 63.158 0.00 0.00 0.00 3.33
768 931 2.333701 GACCGAGTTGGGTGGGTTGT 62.334 60.000 0.24 0.00 44.64 3.32
898 1061 3.927481 AAGGGAAGGAAGCAGCGGC 62.927 63.158 0.00 0.00 41.61 6.53
899 1062 1.746991 GAAGGGAAGGAAGCAGCGG 60.747 63.158 0.00 0.00 0.00 5.52
914 1077 1.384191 CAGGTGGGGAAAGGGGAAG 59.616 63.158 0.00 0.00 0.00 3.46
915 1078 2.852281 GCAGGTGGGGAAAGGGGAA 61.852 63.158 0.00 0.00 0.00 3.97
1213 1379 1.006813 AGCAAGAGAGGAGAGAGGGA 58.993 55.000 0.00 0.00 0.00 4.20
1221 1387 1.608717 GAAGGGCGAGCAAGAGAGGA 61.609 60.000 0.00 0.00 0.00 3.71
1240 1406 1.812571 CCCCGACTCAAACAGAAATGG 59.187 52.381 0.00 0.00 0.00 3.16
1242 1408 1.073923 AGCCCCGACTCAAACAGAAAT 59.926 47.619 0.00 0.00 0.00 2.17
1256 1422 4.394712 GGACAGACCACAGCCCCG 62.395 72.222 0.00 0.00 38.79 5.73
1273 1442 1.583054 GAATCGATTCCCCTTCCACG 58.417 55.000 24.74 0.00 0.00 4.94
1277 1446 1.222115 CGGCGAATCGATTCCCCTTC 61.222 60.000 29.85 16.06 33.57 3.46
1279 1448 2.421739 CGGCGAATCGATTCCCCT 59.578 61.111 29.85 3.34 33.57 4.79
1296 1474 4.301027 CCCCATAGACGCGAGCCC 62.301 72.222 15.93 0.00 0.00 5.19
1308 1486 2.775384 TGTTAAATCGGTAGCTCCCCAT 59.225 45.455 0.00 0.00 0.00 4.00
1312 1490 1.859080 CGCTGTTAAATCGGTAGCTCC 59.141 52.381 0.00 0.00 32.43 4.70
1317 1495 3.131577 ACTCATCCGCTGTTAAATCGGTA 59.868 43.478 10.00 0.87 43.35 4.02
1319 1497 2.550978 ACTCATCCGCTGTTAAATCGG 58.449 47.619 5.28 5.28 44.16 4.18
1326 1504 4.222124 AGGAATAAACTCATCCGCTGTT 57.778 40.909 0.00 0.00 38.31 3.16
1327 1505 3.914426 AGGAATAAACTCATCCGCTGT 57.086 42.857 0.00 0.00 38.31 4.40
1341 1519 8.092687 GTCGGGAACAAATTATAGCTAGGAATA 58.907 37.037 0.00 0.00 0.00 1.75
1484 1662 7.320443 TCAAACAGATTAATTTCCGATGAGG 57.680 36.000 0.00 0.00 42.97 3.86
1487 1665 6.554419 TGCTCAAACAGATTAATTTCCGATG 58.446 36.000 0.00 0.00 0.00 3.84
1615 1803 5.046520 ACAGTAACTTATCTTCTCCGCCTTT 60.047 40.000 0.00 0.00 0.00 3.11
1616 1804 4.466726 ACAGTAACTTATCTTCTCCGCCTT 59.533 41.667 0.00 0.00 0.00 4.35
1617 1805 4.024670 ACAGTAACTTATCTTCTCCGCCT 58.975 43.478 0.00 0.00 0.00 5.52
1627 1815 6.163135 ACTATCCCAGCACAGTAACTTATC 57.837 41.667 0.00 0.00 0.00 1.75
1658 1846 6.206243 AGTGAAGATTCATGGAGAACACAAAG 59.794 38.462 0.00 0.00 39.49 2.77
1746 2182 6.615617 TCAGAGGGAGTATAGTGAATTAGCT 58.384 40.000 0.00 0.00 0.00 3.32
1787 2230 9.807386 GCGACAATTAATATGGTACTAAATCAC 57.193 33.333 0.00 0.00 0.00 3.06
1885 2412 8.965172 GCAAATACAAGAAATCATCAATAGCTG 58.035 33.333 0.00 0.00 0.00 4.24
1955 2482 5.788533 TCTGTAAGAGGGGGTATTTGAAGAA 59.211 40.000 0.00 0.00 38.67 2.52
1991 2518 6.459298 GCACCAGATGACCAGATAAATTCAAG 60.459 42.308 0.00 0.00 0.00 3.02
1997 2524 3.281727 GGCACCAGATGACCAGATAAA 57.718 47.619 0.00 0.00 0.00 1.40
2097 2624 6.667558 ACAGTAGGTTTGAGCTTACTACTT 57.332 37.500 11.53 0.00 41.58 2.24
2228 2776 5.126396 TGACGATCAGATGCTACTATTGG 57.874 43.478 0.00 0.00 0.00 3.16
2229 2777 6.212235 AGTTGACGATCAGATGCTACTATTG 58.788 40.000 0.00 0.00 0.00 1.90
2230 2778 6.398234 AGTTGACGATCAGATGCTACTATT 57.602 37.500 0.00 0.00 0.00 1.73
2231 2779 6.398234 AAGTTGACGATCAGATGCTACTAT 57.602 37.500 0.00 0.00 0.00 2.12
2232 2780 5.836821 AAGTTGACGATCAGATGCTACTA 57.163 39.130 0.00 0.00 0.00 1.82
2233 2781 4.727507 AAGTTGACGATCAGATGCTACT 57.272 40.909 0.00 0.00 0.00 2.57
2234 2782 5.457148 CACTAAGTTGACGATCAGATGCTAC 59.543 44.000 0.00 0.00 0.00 3.58
2235 2783 5.582550 CACTAAGTTGACGATCAGATGCTA 58.417 41.667 0.00 0.00 0.00 3.49
2236 2784 4.428209 CACTAAGTTGACGATCAGATGCT 58.572 43.478 0.00 0.00 0.00 3.79
2237 2785 3.000724 GCACTAAGTTGACGATCAGATGC 59.999 47.826 0.00 0.00 0.00 3.91
2238 2786 4.267214 CAGCACTAAGTTGACGATCAGATG 59.733 45.833 0.00 0.00 0.00 2.90
2239 2787 4.158579 TCAGCACTAAGTTGACGATCAGAT 59.841 41.667 0.00 0.00 32.06 2.90
2240 2788 3.506067 TCAGCACTAAGTTGACGATCAGA 59.494 43.478 0.00 0.00 32.06 3.27
2241 2789 3.838120 TCAGCACTAAGTTGACGATCAG 58.162 45.455 0.00 0.00 32.06 2.90
2242 2790 3.934457 TCAGCACTAAGTTGACGATCA 57.066 42.857 0.00 0.00 32.06 2.92
2243 2791 4.864806 TCAATCAGCACTAAGTTGACGATC 59.135 41.667 0.00 0.00 40.42 3.69
2244 2792 4.820897 TCAATCAGCACTAAGTTGACGAT 58.179 39.130 0.00 0.00 40.42 3.73
2245 2793 4.251543 TCAATCAGCACTAAGTTGACGA 57.748 40.909 0.00 0.00 40.42 4.20
2246 2794 5.536554 AATCAATCAGCACTAAGTTGACG 57.463 39.130 0.00 0.00 40.42 4.35
2247 2795 6.672147 ACAAATCAATCAGCACTAAGTTGAC 58.328 36.000 0.00 0.00 40.42 3.18
2293 2841 5.086058 CGCACATGATTTGGTAGTAACAAC 58.914 41.667 0.00 0.00 0.00 3.32
2298 2846 3.260475 AGCGCACATGATTTGGTAGTA 57.740 42.857 11.47 0.00 0.00 1.82
2491 3073 7.536159 AGGTTGTAGTACTGTAAAGCTACTT 57.464 36.000 5.39 0.00 35.95 2.24
2633 3216 1.211457 AGCCATGGTTAGCTCCTTCTG 59.789 52.381 14.67 0.00 32.71 3.02
2635 3218 2.293170 GAAGCCATGGTTAGCTCCTTC 58.707 52.381 14.67 11.49 38.74 3.46
2787 3371 6.259608 CCTAGACAGCAGTTCAAAATAGGATG 59.740 42.308 0.00 0.00 30.93 3.51
2808 3392 6.406177 CCAACAACAATGGAAATGGATCCTAG 60.406 42.308 14.23 0.00 40.56 3.02
2833 3417 8.532977 AAATAGAATGTAAACAAATGCACCAC 57.467 30.769 0.00 0.00 0.00 4.16
2873 3458 0.828022 TCGGGCCTAAACGTCATCAT 59.172 50.000 0.84 0.00 0.00 2.45
2880 3465 1.415374 CGATACATCGGGCCTAAACG 58.585 55.000 0.84 0.00 45.93 3.60
2940 3525 6.558009 AGTCAATACAACTGCATTGCATTAG 58.442 36.000 12.53 7.24 42.62 1.73
2941 3526 6.513806 AGTCAATACAACTGCATTGCATTA 57.486 33.333 12.53 2.18 42.62 1.90
3017 3602 4.651778 TCTTCAAATCACCAAGTTCCGAT 58.348 39.130 0.00 0.00 0.00 4.18
3163 3749 9.874215 CATTCAGTTGCTAATATGTGATAACTG 57.126 33.333 0.00 0.00 42.77 3.16
3251 3837 4.762765 ACCTACGAACAGATATCCTAGCAG 59.237 45.833 0.00 0.00 0.00 4.24
3264 3850 4.787260 TTGTACATAGCACCTACGAACA 57.213 40.909 0.00 0.00 0.00 3.18
3455 4042 7.119407 CCAAAATTATCACATGGCAAATTCACA 59.881 33.333 0.00 0.00 0.00 3.58
3589 4176 4.307443 TCTCCATGTCGCAGTACATTAG 57.693 45.455 0.00 0.00 38.01 1.73
3713 4300 7.410407 GCGATTTAATTTGCCTTTCACAAGTAC 60.410 37.037 0.00 0.00 0.00 2.73
3715 4302 5.405269 GCGATTTAATTTGCCTTTCACAAGT 59.595 36.000 0.00 0.00 0.00 3.16
3716 4303 5.634859 AGCGATTTAATTTGCCTTTCACAAG 59.365 36.000 6.05 0.00 0.00 3.16
3718 4305 5.132897 AGCGATTTAATTTGCCTTTCACA 57.867 34.783 6.05 0.00 0.00 3.58
3719 4306 4.562789 GGAGCGATTTAATTTGCCTTTCAC 59.437 41.667 6.05 0.00 0.00 3.18
3721 4308 4.800471 CAGGAGCGATTTAATTTGCCTTTC 59.200 41.667 6.05 0.00 0.00 2.62
3722 4309 4.220602 ACAGGAGCGATTTAATTTGCCTTT 59.779 37.500 6.05 0.00 0.00 3.11
3725 4312 3.128589 TCACAGGAGCGATTTAATTTGCC 59.871 43.478 6.05 0.00 0.00 4.52
3738 4325 3.309954 GTCGGTCAAATAATCACAGGAGC 59.690 47.826 0.00 0.00 0.00 4.70
3759 4346 6.040842 GCATGTTTTAGGATCCACATATTGGT 59.959 38.462 15.82 0.00 46.97 3.67
3914 4507 3.197116 AGAAATAGTGACTACCCAACCCG 59.803 47.826 0.00 0.00 0.00 5.28
3969 4562 0.818445 CTGCACTCAGATGATGCCCC 60.818 60.000 11.89 0.00 42.95 5.80
4185 4792 5.894298 ATGGTTGAGATTATGAGCCTACA 57.106 39.130 0.00 0.00 0.00 2.74
4190 4797 9.455847 GAAAACATAATGGTTGAGATTATGAGC 57.544 33.333 15.88 3.03 42.64 4.26
4265 4911 2.549064 TGGTGGTGTGAGAACATGAG 57.451 50.000 0.00 0.00 0.00 2.90
4279 4925 1.515081 ACGGAACAACGTAATGGTGG 58.485 50.000 0.00 0.00 46.58 4.61
4321 4967 1.860676 TAAAACAGAACGCTCGCACT 58.139 45.000 0.00 0.00 0.00 4.40
4325 4971 2.096466 TGCACATAAAACAGAACGCTCG 60.096 45.455 0.00 0.00 0.00 5.03
4327 4973 2.350772 GCTGCACATAAAACAGAACGCT 60.351 45.455 0.00 0.00 33.10 5.07
4363 5009 4.722700 TCTGGGCCTTCCAAGCGC 62.723 66.667 4.53 0.00 46.51 5.92
4493 5140 0.170339 GGCAAACTGCGGACATAACC 59.830 55.000 0.00 0.00 46.21 2.85
4498 5145 1.034838 AAAGTGGCAAACTGCGGACA 61.035 50.000 0.00 0.00 46.21 4.02
4755 5417 4.234550 TCAGCCCTACATCAGTTATCCAT 58.765 43.478 0.00 0.00 0.00 3.41
4782 5444 1.825090 TGGACATCTCACACCAATGC 58.175 50.000 0.00 0.00 0.00 3.56
4882 5550 5.296283 TCAATTGTTTTGGTTGGCATTTGAG 59.704 36.000 5.13 0.00 31.74 3.02
4884 5552 5.496133 TCAATTGTTTTGGTTGGCATTTG 57.504 34.783 5.13 0.00 0.00 2.32
4886 5554 5.192176 ACTTCAATTGTTTTGGTTGGCATT 58.808 33.333 5.13 0.00 0.00 3.56
4919 7174 5.817816 GGCAGTACAAAATATCAGCTACAGT 59.182 40.000 0.00 0.00 0.00 3.55
4924 7179 3.203040 AGGGGCAGTACAAAATATCAGCT 59.797 43.478 0.00 0.00 0.00 4.24
4929 7184 4.018415 ACTGACAGGGGCAGTACAAAATAT 60.018 41.667 2.21 0.00 44.27 1.28
4930 7185 3.329520 ACTGACAGGGGCAGTACAAAATA 59.670 43.478 2.21 0.00 44.27 1.40
4936 7191 0.036294 GGAACTGACAGGGGCAGTAC 60.036 60.000 4.96 0.00 45.27 2.73
4942 7197 2.158755 GGTATGATGGAACTGACAGGGG 60.159 54.545 7.51 0.00 0.00 4.79
4943 7198 2.774234 AGGTATGATGGAACTGACAGGG 59.226 50.000 7.51 0.00 0.00 4.45
4944 7199 3.198635 ACAGGTATGATGGAACTGACAGG 59.801 47.826 7.51 0.00 33.57 4.00
4945 7200 4.437239 GACAGGTATGATGGAACTGACAG 58.563 47.826 0.00 0.00 33.57 3.51
4946 7201 3.197766 GGACAGGTATGATGGAACTGACA 59.802 47.826 0.00 0.00 33.57 3.58
4947 7202 3.452627 AGGACAGGTATGATGGAACTGAC 59.547 47.826 0.00 0.00 33.57 3.51
4948 7203 3.724478 AGGACAGGTATGATGGAACTGA 58.276 45.455 0.00 0.00 33.57 3.41
4949 7204 4.494091 AAGGACAGGTATGATGGAACTG 57.506 45.455 0.00 0.00 35.40 3.16
4950 7205 5.256474 CAAAAGGACAGGTATGATGGAACT 58.744 41.667 0.00 0.00 0.00 3.01
4951 7206 4.399303 CCAAAAGGACAGGTATGATGGAAC 59.601 45.833 0.00 0.00 0.00 3.62
4952 7207 4.290985 TCCAAAAGGACAGGTATGATGGAA 59.709 41.667 0.00 0.00 31.87 3.53
4953 7208 3.849574 TCCAAAAGGACAGGTATGATGGA 59.150 43.478 0.00 0.00 32.33 3.41
4954 7209 4.080356 TCTCCAAAAGGACAGGTATGATGG 60.080 45.833 0.00 0.00 0.00 3.51
4955 7210 5.102953 TCTCCAAAAGGACAGGTATGATG 57.897 43.478 0.00 0.00 0.00 3.07
4956 7211 5.398353 CCATCTCCAAAAGGACAGGTATGAT 60.398 44.000 0.00 0.00 0.00 2.45
4957 7212 4.080356 CCATCTCCAAAAGGACAGGTATGA 60.080 45.833 0.00 0.00 0.00 2.15
4958 7213 4.202441 CCATCTCCAAAAGGACAGGTATG 58.798 47.826 0.00 0.00 0.00 2.39
4959 7214 3.203040 CCCATCTCCAAAAGGACAGGTAT 59.797 47.826 0.00 0.00 0.00 2.73
4960 7215 2.576191 CCCATCTCCAAAAGGACAGGTA 59.424 50.000 0.00 0.00 0.00 3.08
4961 7216 1.355720 CCCATCTCCAAAAGGACAGGT 59.644 52.381 0.00 0.00 0.00 4.00
5106 7361 6.828785 AGAAAATCACTGTCACTGGTAACTTT 59.171 34.615 0.00 0.00 37.61 2.66
5110 7365 6.353323 TGAAGAAAATCACTGTCACTGGTAA 58.647 36.000 0.00 0.00 0.00 2.85
5129 7385 4.534500 TGCCCCACTAACTTATTCTGAAGA 59.466 41.667 0.00 0.00 0.00 2.87
5138 7394 6.494952 TCCAAATAATTGCCCCACTAACTTA 58.505 36.000 0.00 0.00 35.10 2.24
5145 7401 3.960102 TCATCTCCAAATAATTGCCCCAC 59.040 43.478 0.00 0.00 35.10 4.61
5168 7452 1.534805 CCCGATCGTGTCTGACAGATG 60.535 57.143 20.06 11.15 0.00 2.90
5190 7478 1.227383 CCCAAGCCTAAGCCCGAAT 59.773 57.895 0.00 0.00 41.25 3.34
5191 7479 2.674754 CCCAAGCCTAAGCCCGAA 59.325 61.111 0.00 0.00 41.25 4.30
5192 7480 4.109675 GCCCAAGCCTAAGCCCGA 62.110 66.667 0.00 0.00 41.25 5.14
5194 7482 2.911221 AATCGCCCAAGCCTAAGCCC 62.911 60.000 0.00 0.00 41.25 5.19
5195 7483 1.453928 AATCGCCCAAGCCTAAGCC 60.454 57.895 0.00 0.00 41.25 4.35
5196 7484 1.729881 CAATCGCCCAAGCCTAAGC 59.270 57.895 0.00 0.00 40.32 3.09
5197 7485 1.031571 TGCAATCGCCCAAGCCTAAG 61.032 55.000 0.00 0.00 37.32 2.18
5198 7486 1.001517 TGCAATCGCCCAAGCCTAA 60.002 52.632 0.00 0.00 37.32 2.69
5225 7514 1.815613 CACCAGTCGATCACTCTCAGT 59.184 52.381 0.00 0.00 30.26 3.41


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

AutoCloner maintained by Alex Coulton.