Multiple sequence alignment - TraesCS7B01G131100

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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 TraesCS7B01G131100 chr7B 100.000 7257 0 0 1 7257 158167615 158174871 0.000000e+00 13402.0
1 TraesCS7B01G131100 chr7B 79.863 293 50 7 302 587 715263553 715263263 9.540000e-49 206.0
2 TraesCS7B01G131100 chr7D 95.093 3179 93 16 2579 5711 194245135 194248296 0.000000e+00 4948.0
3 TraesCS7B01G131100 chr7D 92.568 1803 90 18 767 2554 194243184 194244957 0.000000e+00 2547.0
4 TraesCS7B01G131100 chr7D 94.886 704 33 3 5743 6445 194248296 194248997 0.000000e+00 1098.0
5 TraesCS7B01G131100 chr7D 96.381 525 15 3 6735 7257 194249327 194249849 0.000000e+00 861.0
6 TraesCS7B01G131100 chr7D 87.774 638 62 11 1 628 194241337 194241968 0.000000e+00 732.0
7 TraesCS7B01G131100 chr7D 85.417 192 6 5 6526 6696 194249140 194249330 5.780000e-41 180.0
8 TraesCS7B01G131100 chr7D 95.238 84 4 0 6442 6525 194249025 194249108 4.570000e-27 134.0
9 TraesCS7B01G131100 chr7D 90.625 64 5 1 650 712 194241969 194242032 4.670000e-12 84.2
10 TraesCS7B01G131100 chr7A 94.587 3159 132 18 3300 6445 203965928 203969060 0.000000e+00 4850.0
11 TraesCS7B01G131100 chr7A 90.651 2610 133 40 762 3303 203963270 203965836 0.000000e+00 3365.0
12 TraesCS7B01G131100 chr7A 90.840 524 22 5 6735 7257 203969359 203969857 0.000000e+00 678.0
13 TraesCS7B01G131100 chr7A 83.276 586 66 18 144 712 203902740 203903310 1.810000e-140 510.0
14 TraesCS7B01G131100 chr7A 79.518 332 59 7 305 628 572175419 572175749 2.040000e-55 228.0
15 TraesCS7B01G131100 chr7A 82.500 80 13 1 398 477 7074975 7074897 1.310000e-07 69.4
16 TraesCS7B01G131100 chr1D 85.593 826 96 8 5634 6444 449122019 449121202 0.000000e+00 845.0
17 TraesCS7B01G131100 chr1D 88.251 366 40 2 5104 5467 449128637 449128273 1.120000e-117 435.0
18 TraesCS7B01G131100 chr1D 81.029 311 47 6 9 307 194141196 194140886 3.380000e-58 237.0
19 TraesCS7B01G131100 chr1D 80.564 319 51 3 9 316 418041743 418041425 1.220000e-57 235.0
20 TraesCS7B01G131100 chr1D 82.500 120 16 3 5497 5613 449128267 449128150 4.630000e-17 100.0
21 TraesCS7B01G131100 chr1D 95.918 49 0 2 6699 6746 252006281 252006234 2.170000e-10 78.7
22 TraesCS7B01G131100 chr1D 95.918 49 0 2 6699 6746 386746837 386746884 2.170000e-10 78.7
23 TraesCS7B01G131100 chr1A 76.836 1593 234 74 4307 5856 2664073 2662573 0.000000e+00 773.0
24 TraesCS7B01G131100 chr1A 79.503 483 80 11 1754 2230 2646701 2646232 7.020000e-85 326.0
25 TraesCS7B01G131100 chr1A 83.387 313 36 13 5183 5485 2643617 2643311 7.170000e-70 276.0
26 TraesCS7B01G131100 chr1A 86.207 145 17 3 6303 6444 115444153 115444297 3.510000e-33 154.0
27 TraesCS7B01G131100 chr1A 77.917 240 48 4 6109 6347 2642828 2642593 2.110000e-30 145.0
28 TraesCS7B01G131100 chr1A 85.849 106 14 1 3489 3594 2840821 2840717 2.140000e-20 111.0
29 TraesCS7B01G131100 chr1B 82.572 832 99 21 5629 6444 614594023 614593222 0.000000e+00 691.0
30 TraesCS7B01G131100 chr1B 82.685 514 57 12 5105 5613 614612658 614612172 1.870000e-115 427.0
31 TraesCS7B01G131100 chr1B 94.231 52 2 1 6699 6749 596247388 596247439 2.170000e-10 78.7
32 TraesCS7B01G131100 chr6A 76.763 1205 170 53 4105 5259 617403601 617404745 2.270000e-159 573.0
33 TraesCS7B01G131100 chr6A 80.529 529 79 15 1710 2230 617319291 617319803 1.140000e-102 385.0
34 TraesCS7B01G131100 chr6A 85.635 362 47 4 5124 5483 617225914 617226272 6.870000e-100 375.0
35 TraesCS7B01G131100 chr6A 79.915 468 66 16 4105 4562 617248739 617249188 1.170000e-82 318.0
36 TraesCS7B01G131100 chr6A 85.424 295 37 4 5113 5404 617239372 617239663 1.180000e-77 302.0
37 TraesCS7B01G131100 chr6A 82.759 348 51 5 5071 5416 617344022 617344362 1.180000e-77 302.0
38 TraesCS7B01G131100 chr6A 82.866 321 44 3 9 318 559338350 559338670 1.990000e-70 278.0
39 TraesCS7B01G131100 chr6A 80.278 360 37 15 3754 4110 617321463 617321791 2.620000e-59 241.0
40 TraesCS7B01G131100 chr6A 79.444 360 45 9 3754 4110 617224615 617224948 2.040000e-55 228.0
41 TraesCS7B01G131100 chr6A 87.640 178 21 1 1998 2174 617553831 617554008 9.540000e-49 206.0
42 TraesCS7B01G131100 chr6A 76.435 331 60 12 6024 6342 617352592 617352916 5.830000e-36 163.0
43 TraesCS7B01G131100 chr6A 83.929 112 16 2 3488 3599 617555722 617555831 9.960000e-19 106.0
44 TraesCS7B01G131100 chr6A 86.747 83 6 4 2320 2401 617247815 617247893 3.610000e-13 87.9
45 TraesCS7B01G131100 chr6D 76.653 968 121 61 4149 5091 472490206 472489319 8.640000e-119 438.0
46 TraesCS7B01G131100 chr6D 79.057 530 89 13 1708 2230 472501222 472500708 1.940000e-90 344.0
47 TraesCS7B01G131100 chr6D 83.281 317 37 13 5183 5489 472497873 472497563 1.990000e-70 278.0
48 TraesCS7B01G131100 chr6D 77.500 240 49 4 6109 6347 472497086 472496851 9.820000e-29 139.0
49 TraesCS7B01G131100 chr6D 85.981 107 14 1 3488 3594 472427084 472426979 5.950000e-21 113.0
50 TraesCS7B01G131100 chr6B 80.226 531 81 14 1708 2230 717419348 717418834 1.910000e-100 377.0
51 TraesCS7B01G131100 chr6B 82.532 395 52 10 4456 4841 717409008 717408622 1.510000e-86 331.0
52 TraesCS7B01G131100 chr6B 83.429 350 52 6 5071 5416 717408407 717408060 3.270000e-83 320.0
53 TraesCS7B01G131100 chr6B 85.232 237 34 1 1998 2233 717402798 717402562 7.270000e-60 243.0
54 TraesCS7B01G131100 chr6B 82.392 301 32 13 5183 5474 717416081 717415793 7.270000e-60 243.0
55 TraesCS7B01G131100 chr6B 87.079 178 21 2 1998 2174 717141602 717141426 4.440000e-47 200.0
56 TraesCS7B01G131100 chr2D 79.744 390 60 13 310 685 602662841 602663225 1.550000e-66 265.0
57 TraesCS7B01G131100 chr2D 84.836 244 26 4 4 236 8886795 8887038 1.220000e-57 235.0
58 TraesCS7B01G131100 chr5D 80.428 327 52 3 3 318 379780281 379779956 9.410000e-59 239.0
59 TraesCS7B01G131100 chr5D 79.661 295 50 9 310 596 379779486 379779194 3.430000e-48 204.0
60 TraesCS7B01G131100 chr5D 89.286 140 12 3 9 147 344949084 344948947 9.680000e-39 172.0
61 TraesCS7B01G131100 chr5D 95.918 49 0 2 6699 6746 184636640 184636687 2.170000e-10 78.7
62 TraesCS7B01G131100 chr3D 80.380 316 48 8 319 630 175505003 175505308 2.040000e-55 228.0
63 TraesCS7B01G131100 chr2A 84.146 246 27 5 4 237 223658603 223658358 2.040000e-55 228.0
64 TraesCS7B01G131100 chr2A 78.621 290 48 11 310 590 718558020 718557736 5.780000e-41 180.0
65 TraesCS7B01G131100 chr5A 80.277 289 49 6 310 591 480272191 480271904 2.050000e-50 211.0
66 TraesCS7B01G131100 chr5A 89.928 139 13 1 9 147 447154207 447154344 2.080000e-40 178.0
67 TraesCS7B01G131100 chr5B 73.913 276 47 12 21 285 529376996 529376735 3.610000e-13 87.9
68 TraesCS7B01G131100 chr5B 97.826 46 1 0 6694 6739 506317774 506317819 6.040000e-11 80.5
69 TraesCS7B01G131100 chr5B 94.118 51 3 0 6688 6738 617082493 617082543 2.170000e-10 78.7
70 TraesCS7B01G131100 chr4D 97.872 47 1 0 6699 6745 465950493 465950539 1.680000e-11 82.4
71 TraesCS7B01G131100 chr4D 95.918 49 0 2 6699 6746 412711736 412711783 2.170000e-10 78.7
72 TraesCS7B01G131100 chr3B 100.000 40 0 0 6699 6738 60585821 60585860 2.810000e-09 75.0


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 TraesCS7B01G131100 chr7B 158167615 158174871 7256 False 13402.000000 13402 100.00000 1 7257 1 chr7B.!!$F1 7256
1 TraesCS7B01G131100 chr7D 194241337 194249849 8512 False 1323.025000 4948 92.24775 1 7257 8 chr7D.!!$F1 7256
2 TraesCS7B01G131100 chr7A 203963270 203969857 6587 False 2964.333333 4850 92.02600 762 7257 3 chr7A.!!$F3 6495
3 TraesCS7B01G131100 chr7A 203902740 203903310 570 False 510.000000 510 83.27600 144 712 1 chr7A.!!$F1 568
4 TraesCS7B01G131100 chr1D 449121202 449122019 817 True 845.000000 845 85.59300 5634 6444 1 chr1D.!!$R4 810
5 TraesCS7B01G131100 chr1A 2662573 2664073 1500 True 773.000000 773 76.83600 4307 5856 1 chr1A.!!$R1 1549
6 TraesCS7B01G131100 chr1A 2642593 2646701 4108 True 249.000000 326 80.26900 1754 6347 3 chr1A.!!$R3 4593
7 TraesCS7B01G131100 chr1B 614593222 614594023 801 True 691.000000 691 82.57200 5629 6444 1 chr1B.!!$R1 815
8 TraesCS7B01G131100 chr6A 617403601 617404745 1144 False 573.000000 573 76.76300 4105 5259 1 chr6A.!!$F5 1154
9 TraesCS7B01G131100 chr6A 617319291 617321791 2500 False 313.000000 385 80.40350 1710 4110 2 chr6A.!!$F8 2400
10 TraesCS7B01G131100 chr6A 617224615 617226272 1657 False 301.500000 375 82.53950 3754 5483 2 chr6A.!!$F6 1729
11 TraesCS7B01G131100 chr6A 617247815 617249188 1373 False 202.950000 318 83.33100 2320 4562 2 chr6A.!!$F7 2242
12 TraesCS7B01G131100 chr6D 472489319 472490206 887 True 438.000000 438 76.65300 4149 5091 1 chr6D.!!$R2 942
13 TraesCS7B01G131100 chr6D 472496851 472501222 4371 True 253.666667 344 79.94600 1708 6347 3 chr6D.!!$R3 4639
14 TraesCS7B01G131100 chr6B 717408060 717409008 948 True 325.500000 331 82.98050 4456 5416 2 chr6B.!!$R3 960
15 TraesCS7B01G131100 chr6B 717415793 717419348 3555 True 310.000000 377 81.30900 1708 5474 2 chr6B.!!$R4 3766
16 TraesCS7B01G131100 chr5D 379779194 379780281 1087 True 221.500000 239 80.04450 3 596 2 chr5D.!!$R2 593

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
752 2368 0.033796 TAGATGTTCGGTCGTCCCCT 60.034 55.000 0.00 0.00 0.00 4.79 F
1250 2877 0.029059 CCCTATTTCCCCTCCCTGGA 60.029 60.000 0.00 0.00 38.35 3.86 F
1637 3266 0.109132 GTGCTGCTTATGTTGGGTGC 60.109 55.000 0.00 0.00 0.00 5.01 F
2740 4583 0.179145 AGCGAATTCAGCTGCATTGC 60.179 50.000 16.55 17.69 44.22 3.56 F
2743 4586 1.143969 GAATTCAGCTGCATTGCGCC 61.144 55.000 16.55 0.00 41.33 6.53 F
2745 4588 1.672854 ATTCAGCTGCATTGCGCCAT 61.673 50.000 9.47 0.00 41.33 4.40 F
4425 7126 2.076863 AGTTGTAATTCCAGTCTGCGC 58.923 47.619 0.00 0.00 0.00 6.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1610 3239 0.372679 CATAAGCAGCACAGCACTCG 59.627 55.000 0.00 0.00 36.85 4.18 R
2937 4782 0.322648 CCTGTGGAGCTGTCATCACA 59.677 55.000 0.00 0.00 37.73 3.58 R
3533 6012 1.776710 ACTAACCCTTGGGTGCCCA 60.777 57.895 12.67 5.73 45.63 5.36 R
4425 7126 5.883661 ACTGTCAATCACAACACTTGAAAG 58.116 37.500 0.00 0.00 39.24 2.62 R
4960 7693 4.380867 GGCACATTTAATCTCAACACCCTG 60.381 45.833 0.00 0.00 0.00 4.45 R
4963 7696 4.458989 TCAGGCACATTTAATCTCAACACC 59.541 41.667 0.00 0.00 0.00 4.16 R
6470 9404 0.027586 GAGTGTTGTGTGGTGCGTTC 59.972 55.000 0.00 0.00 0.00 3.95 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
36 37 5.482908 TCTCTTCTTACCAGAAATGCACTC 58.517 41.667 0.00 0.00 38.63 3.51
37 38 5.012046 TCTCTTCTTACCAGAAATGCACTCA 59.988 40.000 0.00 0.00 38.63 3.41
167 179 1.729586 TTGGCCCTGAGTACTTGAGT 58.270 50.000 0.00 0.00 0.00 3.41
179 191 1.967319 ACTTGAGTGCCAAATGTCGT 58.033 45.000 0.00 0.00 33.76 4.34
193 205 5.291128 CCAAATGTCGTAGATACAACCTGAC 59.709 44.000 0.00 0.00 40.67 3.51
195 207 7.255569 CAAATGTCGTAGATACAACCTGACTA 58.744 38.462 0.00 0.00 40.67 2.59
211 223 3.277715 TGACTATTGGCGATCAATGCAA 58.722 40.909 12.65 0.00 45.00 4.08
226 238 4.957954 TCAATGCAAATAGAGGCTTTCCAT 59.042 37.500 0.00 0.00 33.74 3.41
239 251 3.195396 GGCTTTCCATGAATGCTTGGTAA 59.805 43.478 5.53 1.92 40.81 2.85
240 252 4.141869 GGCTTTCCATGAATGCTTGGTAAT 60.142 41.667 5.53 0.00 40.81 1.89
292 304 2.856231 TGCCTATTTGATTGGTAGGGGT 59.144 45.455 0.00 0.00 36.36 4.95
300 312 2.905085 TGATTGGTAGGGGTCGTACAAA 59.095 45.455 0.00 0.00 0.00 2.83
301 313 3.327172 TGATTGGTAGGGGTCGTACAAAA 59.673 43.478 0.00 0.00 0.00 2.44
340 830 3.423154 GAGCACCAAGAACCGGCG 61.423 66.667 0.00 0.00 0.00 6.46
350 840 2.936498 CAAGAACCGGCGATGTTTCTAT 59.064 45.455 9.30 0.01 0.00 1.98
445 938 4.820894 ATGGACTCACCTTGGTAACTAC 57.179 45.455 0.00 0.00 39.86 2.73
446 939 2.901839 TGGACTCACCTTGGTAACTACC 59.098 50.000 0.00 0.00 42.12 3.18
467 960 4.398044 ACCACATGTATCGGTTCATTTTCC 59.602 41.667 0.00 0.00 0.00 3.13
482 975 6.757897 TCATTTTCCTTCGATGTATTTGCT 57.242 33.333 0.00 0.00 0.00 3.91
489 982 8.725405 TTCCTTCGATGTATTTGCTACAATTA 57.275 30.769 0.00 0.00 43.42 1.40
492 985 9.950680 CCTTCGATGTATTTGCTACAATTAAAT 57.049 29.630 0.00 0.00 43.42 1.40
572 1067 7.466746 ACTATGTGCTTATTTGGTTGTGAAT 57.533 32.000 0.00 0.00 0.00 2.57
636 1131 1.376166 TGTACATTTGACCGCCGGG 60.376 57.895 8.57 0.00 40.11 5.73
685 1188 0.172352 ACCGCCAACACAAACACAAG 59.828 50.000 0.00 0.00 0.00 3.16
720 1224 8.836413 ACAAGAAAATAAAAAGTGATCAGACGA 58.164 29.630 0.00 0.00 0.00 4.20
721 1225 9.663904 CAAGAAAATAAAAAGTGATCAGACGAA 57.336 29.630 0.00 0.00 0.00 3.85
725 1229 7.921786 AATAAAAAGTGATCAGACGAATCCA 57.078 32.000 0.00 0.00 0.00 3.41
733 2349 5.003160 TGATCAGACGAATCCACACAAAAT 58.997 37.500 0.00 0.00 0.00 1.82
734 2350 6.092122 GTGATCAGACGAATCCACACAAAATA 59.908 38.462 0.00 0.00 0.00 1.40
748 2364 4.387862 ACACAAAATAGATGTTCGGTCGTC 59.612 41.667 0.00 0.00 0.00 4.20
751 2367 1.038280 ATAGATGTTCGGTCGTCCCC 58.962 55.000 0.00 0.00 0.00 4.81
752 2368 0.033796 TAGATGTTCGGTCGTCCCCT 60.034 55.000 0.00 0.00 0.00 4.79
753 2369 0.033796 AGATGTTCGGTCGTCCCCTA 60.034 55.000 0.00 0.00 0.00 3.53
754 2370 0.819582 GATGTTCGGTCGTCCCCTAA 59.180 55.000 0.00 0.00 0.00 2.69
755 2371 1.205417 GATGTTCGGTCGTCCCCTAAA 59.795 52.381 0.00 0.00 0.00 1.85
756 2372 1.047002 TGTTCGGTCGTCCCCTAAAA 58.953 50.000 0.00 0.00 0.00 1.52
757 2373 1.415659 TGTTCGGTCGTCCCCTAAAAA 59.584 47.619 0.00 0.00 0.00 1.94
788 2404 1.839424 GTGGAGTTTGGCTAGGCAAT 58.161 50.000 29.87 17.82 0.00 3.56
791 2407 1.017387 GAGTTTGGCTAGGCAATCCG 58.983 55.000 29.87 0.00 37.47 4.18
815 2431 0.753111 GGATCCCGCAGAAAAGGCAT 60.753 55.000 0.00 0.00 0.00 4.40
903 2519 1.837051 TCTGCCTGTCTGAACCGGT 60.837 57.895 0.00 0.00 32.64 5.28
963 2590 3.827898 GTCGAGCCTCCTCACCGG 61.828 72.222 0.00 0.00 38.00 5.28
964 2591 4.361971 TCGAGCCTCCTCACCGGT 62.362 66.667 0.00 0.00 38.00 5.28
966 2593 2.680352 GAGCCTCCTCACCGGTCA 60.680 66.667 2.59 0.00 38.03 4.02
967 2594 2.997897 AGCCTCCTCACCGGTCAC 60.998 66.667 2.59 0.00 0.00 3.67
968 2595 4.083862 GCCTCCTCACCGGTCACC 62.084 72.222 2.59 0.00 0.00 4.02
970 2597 4.436998 CTCCTCACCGGTCACCGC 62.437 72.222 12.05 0.00 46.86 5.68
1201 2828 4.171754 CAAGCAGGTACGTACTAGGTTTC 58.828 47.826 24.07 6.72 0.00 2.78
1206 2833 2.624293 GGTACGTACTAGGTTTCCCCCT 60.624 54.545 24.07 0.00 38.70 4.79
1207 2834 1.857965 ACGTACTAGGTTTCCCCCTC 58.142 55.000 0.00 0.00 35.97 4.30
1208 2835 1.117994 CGTACTAGGTTTCCCCCTCC 58.882 60.000 0.00 0.00 35.97 4.30
1209 2836 1.117994 GTACTAGGTTTCCCCCTCCG 58.882 60.000 0.00 0.00 35.97 4.63
1210 2837 0.688749 TACTAGGTTTCCCCCTCCGC 60.689 60.000 0.00 0.00 35.97 5.54
1211 2838 3.078836 TAGGTTTCCCCCTCCGCG 61.079 66.667 0.00 0.00 35.97 6.46
1250 2877 0.029059 CCCTATTTCCCCTCCCTGGA 60.029 60.000 0.00 0.00 38.35 3.86
1282 2909 2.897969 GGGCCCGTCTTATTCTGATCTA 59.102 50.000 5.69 0.00 0.00 1.98
1283 2910 3.515901 GGGCCCGTCTTATTCTGATCTAT 59.484 47.826 5.69 0.00 0.00 1.98
1284 2911 4.382147 GGGCCCGTCTTATTCTGATCTATC 60.382 50.000 5.69 0.00 0.00 2.08
1285 2912 4.464597 GGCCCGTCTTATTCTGATCTATCT 59.535 45.833 0.00 0.00 0.00 1.98
1446 3073 3.003173 TTCAGGGCTCAGGGGTCG 61.003 66.667 0.00 0.00 0.00 4.79
1455 3082 1.658686 CTCAGGGGTCGTCCTCTTCG 61.659 65.000 0.00 0.00 42.96 3.79
1500 3127 0.733150 GCTTGAACGCCCATAACTCC 59.267 55.000 0.00 0.00 0.00 3.85
1534 3161 4.018490 TGCTGTTCATTTCCATAGCATGT 58.982 39.130 0.00 0.00 36.37 3.21
1568 3197 6.560687 TGGTGGTTAGGATGATAATGATGGTA 59.439 38.462 0.00 0.00 0.00 3.25
1637 3266 0.109132 GTGCTGCTTATGTTGGGTGC 60.109 55.000 0.00 0.00 0.00 5.01
1653 3283 1.028868 GTGCAGGGTGCCTCTGAATC 61.029 60.000 6.28 0.00 44.23 2.52
1665 3295 3.258123 GCCTCTGAATCTCTAGGGCTTAG 59.742 52.174 0.00 0.00 35.73 2.18
1666 3296 4.479158 CCTCTGAATCTCTAGGGCTTAGT 58.521 47.826 3.39 0.00 0.00 2.24
1667 3297 4.280677 CCTCTGAATCTCTAGGGCTTAGTG 59.719 50.000 3.39 1.47 0.00 2.74
1695 3328 3.065371 GTGCTGGCTGCTATAACGATTTT 59.935 43.478 17.45 0.00 43.37 1.82
1736 3370 5.982324 AGAAGATTTTCGTTTGTAACCGAC 58.018 37.500 0.00 0.00 38.38 4.79
1920 3557 7.263100 TGTATCTTTTGATGTCACATATGGC 57.737 36.000 7.80 0.00 39.88 4.40
1923 3560 6.000246 TCTTTTGATGTCACATATGGCCTA 58.000 37.500 3.32 0.00 0.00 3.93
1971 3610 1.716826 TTCGCGTGTGGGTTGGTTTC 61.717 55.000 5.77 0.00 0.00 2.78
2019 3685 9.394477 CAGTTTACTTGCATAAACCTTTTAGTC 57.606 33.333 15.92 0.00 43.28 2.59
2099 3765 1.713078 AGGCTCTTTGAAACAGGGGAT 59.287 47.619 0.00 0.00 0.00 3.85
2108 3774 3.386063 TGAAACAGGGGATCCGGTAATA 58.614 45.455 5.45 0.00 40.57 0.98
2111 3777 2.766736 ACAGGGGATCCGGTAATAACA 58.233 47.619 5.45 0.00 39.67 2.41
2284 3951 0.533308 GCCGGAACAGTGTTGGTGTA 60.533 55.000 14.57 0.00 0.00 2.90
2294 3961 7.201487 GGAACAGTGTTGGTGTAAAAACATTTC 60.201 37.037 14.57 0.00 38.47 2.17
2354 4021 0.735978 TGAGTTGGCGCAGTATCACG 60.736 55.000 10.83 0.00 0.00 4.35
2423 4090 6.998074 TGATCAGTTAACACAACTCCAAGAAT 59.002 34.615 8.61 0.00 0.00 2.40
2435 4102 8.783093 CACAACTCCAAGAATCTTGTGTATTTA 58.217 33.333 20.18 0.00 37.83 1.40
2631 4473 4.985413 TGAGAAGCGATTTTAAATGCTGG 58.015 39.130 12.65 0.00 37.81 4.85
2738 4581 1.734707 GCAAGCGAATTCAGCTGCATT 60.735 47.619 20.28 11.56 45.31 3.56
2739 4582 1.917955 CAAGCGAATTCAGCTGCATTG 59.082 47.619 16.55 9.64 45.31 2.82
2740 4583 0.179145 AGCGAATTCAGCTGCATTGC 60.179 50.000 16.55 17.69 44.22 3.56
2741 4584 1.469126 GCGAATTCAGCTGCATTGCG 61.469 55.000 16.55 17.91 38.13 4.85
2742 4585 1.469126 CGAATTCAGCTGCATTGCGC 61.469 55.000 16.55 14.73 42.89 6.09
2743 4586 1.143969 GAATTCAGCTGCATTGCGCC 61.144 55.000 16.55 0.00 41.33 6.53
2744 4587 1.879737 AATTCAGCTGCATTGCGCCA 61.880 50.000 10.95 0.00 41.33 5.69
2745 4588 1.672854 ATTCAGCTGCATTGCGCCAT 61.673 50.000 9.47 0.00 41.33 4.40
2758 4601 2.129146 CGCCATTGCCACCATGGAT 61.129 57.895 21.47 0.00 40.96 3.41
2776 4621 2.224867 GGATCCCCACTCACCCATTATG 60.225 54.545 0.00 0.00 0.00 1.90
2929 4774 4.605640 TGTCATGATCCGAGCATCAATA 57.394 40.909 0.00 0.00 36.36 1.90
2937 4782 4.406648 TCCGAGCATCAATAATGTGACT 57.593 40.909 0.00 0.00 37.71 3.41
2977 4880 3.629398 GGACTTTATCATTGTCCCTGCAG 59.371 47.826 6.78 6.78 43.10 4.41
3264 5647 4.768583 TGCCAAAGCTTTGTTTCTTGATT 58.231 34.783 31.67 0.00 40.80 2.57
3294 5677 3.488047 CCAAGCTTGACGATTTGCCATAG 60.488 47.826 28.05 1.58 0.00 2.23
3474 5953 2.489938 ACTGTGTGTGGTTGAAGTGT 57.510 45.000 0.00 0.00 0.00 3.55
3757 6247 7.736893 AGATTACTGTCAAAACCAGTCTTAGT 58.263 34.615 0.00 0.00 42.03 2.24
4117 6765 4.380531 TCACCTGACTTAGCACTTGAAAG 58.619 43.478 0.00 0.00 0.00 2.62
4120 6768 5.066505 CACCTGACTTAGCACTTGAAAGTTT 59.933 40.000 0.00 0.00 37.08 2.66
4425 7126 2.076863 AGTTGTAATTCCAGTCTGCGC 58.923 47.619 0.00 0.00 0.00 6.09
4453 7154 8.255394 TCAAGTGTTGTGATTGACAGTATATG 57.745 34.615 0.00 0.00 35.44 1.78
4454 7155 6.668541 AGTGTTGTGATTGACAGTATATGC 57.331 37.500 0.00 0.00 35.44 3.14
4960 7693 5.391629 GGACAAACACCTGGAACGATAAATC 60.392 44.000 0.00 0.00 0.00 2.17
4983 7716 3.763897 AGGGTGTTGAGATTAAATGTGCC 59.236 43.478 0.00 0.00 0.00 5.01
4990 7723 6.072508 TGTTGAGATTAAATGTGCCTGAGTTC 60.073 38.462 0.00 0.00 0.00 3.01
5038 7799 9.126151 TGTACTCAAAATTGGAGTATTGTTGAA 57.874 29.630 12.88 0.00 46.29 2.69
5045 7806 5.560722 TTGGAGTATTGTTGAAGGTCTGA 57.439 39.130 0.00 0.00 0.00 3.27
5102 7903 5.258051 TGTGAGTAAAGTTGAACAAAGGGT 58.742 37.500 0.00 0.00 0.00 4.34
5169 8029 4.630069 ACCGTTTATCCGAGTTGATTTCTG 59.370 41.667 0.00 0.00 0.00 3.02
5346 8207 7.455008 TGAGGTAATTCTCCTTCTGTCTAACTT 59.545 37.037 4.02 0.00 35.20 2.66
5384 8245 4.320494 GCATTTACTCTGGTTCCAGTGTTG 60.320 45.833 24.74 19.22 40.08 3.33
5388 8249 0.546122 TCTGGTTCCAGTGTTGCACT 59.454 50.000 17.00 0.00 46.51 4.40
5416 8282 0.252696 TGTCAGATGTGGGGCTAGGT 60.253 55.000 0.00 0.00 0.00 3.08
5427 8294 1.624391 GGGGCTAGGTTCCTGGAGTTA 60.624 57.143 6.40 0.00 0.00 2.24
5495 8362 4.674281 GGACTTTATCCTCGATTCCACT 57.326 45.455 0.00 0.00 45.22 4.00
5519 8386 4.894784 AGATTTGATGACACGTACAACCT 58.105 39.130 0.00 0.00 0.00 3.50
5527 8394 0.033504 CACGTACAACCTGAGCTGGT 59.966 55.000 0.00 0.00 43.11 4.00
5547 8414 0.786435 AAAAATCAGGCCTCCACCCT 59.214 50.000 0.00 0.00 0.00 4.34
5548 8415 0.332972 AAAATCAGGCCTCCACCCTC 59.667 55.000 0.00 0.00 0.00 4.30
5549 8416 0.551131 AAATCAGGCCTCCACCCTCT 60.551 55.000 0.00 0.00 0.00 3.69
5550 8417 1.277580 AATCAGGCCTCCACCCTCTG 61.278 60.000 0.00 0.00 0.00 3.35
5551 8418 2.186873 ATCAGGCCTCCACCCTCTGA 62.187 60.000 0.00 0.00 38.59 3.27
5552 8419 1.692042 CAGGCCTCCACCCTCTGAT 60.692 63.158 0.00 0.00 0.00 2.90
5618 8489 5.431765 CTGGACATGAATAGTTGGTAGCTT 58.568 41.667 0.00 0.00 0.00 3.74
5785 8664 5.163301 TGGGGAAGATTAGTGCAAGATACTC 60.163 44.000 0.00 0.00 0.00 2.59
5989 8887 4.592192 GCATCTAGAGCGGCGGCA 62.592 66.667 19.21 0.00 43.41 5.69
6082 8980 4.736896 GCCGAGGTGACCGTGGTC 62.737 72.222 12.17 12.17 44.77 4.02
6186 9084 0.835276 TCAGATGTGCAGATGGGGAG 59.165 55.000 0.00 0.00 0.00 4.30
6187 9085 0.818445 CAGATGTGCAGATGGGGAGC 60.818 60.000 0.00 0.00 0.00 4.70
6214 9112 5.468540 AGGTTATTCCAAAAGTTGAAGCC 57.531 39.130 0.00 0.00 39.02 4.35
6253 9151 0.396435 ACAAGATGAACGTGGGAGCA 59.604 50.000 0.00 0.00 32.54 4.26
6331 9229 0.690192 TGCTTGGGAACTTCCGATCA 59.310 50.000 1.53 0.00 37.43 2.92
6363 9261 2.098614 TCGCCCGGTAACTGTAATGTA 58.901 47.619 0.00 0.00 0.00 2.29
6412 9312 4.271533 GTGTACAAAGTGTTGGATTGTCGA 59.728 41.667 0.00 0.00 39.22 4.20
6470 9404 6.690098 CACACTCAACAATTTTGAACAGAGAG 59.310 38.462 0.00 0.00 0.00 3.20
6481 9415 0.464036 AACAGAGAGAACGCACCACA 59.536 50.000 0.00 0.00 0.00 4.17
6511 9445 2.159282 GCTCATGCACCAGAAGATTTGG 60.159 50.000 0.00 0.00 41.60 3.28
6568 9533 4.458989 CCTGGTGCATAACTTAAGCAAAGA 59.541 41.667 1.29 0.00 40.35 2.52
6608 9573 1.336148 TGCTTGCTCAATGAAAAGGCG 60.336 47.619 7.26 0.00 0.00 5.52
6648 9633 9.737427 TGCTTGAAAATAAAATGAAGTCGTAAA 57.263 25.926 0.00 0.00 0.00 2.01
6696 9681 1.571773 GGGGAATGCCACCAGGTACT 61.572 60.000 0.00 0.00 37.19 2.73
6697 9682 0.107165 GGGAATGCCACCAGGTACTC 60.107 60.000 0.00 0.00 37.19 2.59
6698 9683 0.618458 GGAATGCCACCAGGTACTCA 59.382 55.000 0.00 0.00 34.60 3.41
6699 9684 1.004277 GGAATGCCACCAGGTACTCAA 59.996 52.381 0.00 0.00 34.60 3.02
6700 9685 2.084546 GAATGCCACCAGGTACTCAAC 58.915 52.381 0.00 0.00 34.60 3.18
6701 9686 1.362224 ATGCCACCAGGTACTCAACT 58.638 50.000 0.00 0.00 34.60 3.16
6702 9687 2.018355 TGCCACCAGGTACTCAACTA 57.982 50.000 0.00 0.00 34.60 2.24
6703 9688 2.331166 TGCCACCAGGTACTCAACTAA 58.669 47.619 0.00 0.00 34.60 2.24
6704 9689 2.706723 TGCCACCAGGTACTCAACTAAA 59.293 45.455 0.00 0.00 34.60 1.85
6705 9690 3.136809 TGCCACCAGGTACTCAACTAAAA 59.863 43.478 0.00 0.00 34.60 1.52
6706 9691 3.501062 GCCACCAGGTACTCAACTAAAAC 59.499 47.826 0.00 0.00 34.60 2.43
6707 9692 4.070009 CCACCAGGTACTCAACTAAAACC 58.930 47.826 0.00 0.00 34.60 3.27
6708 9693 4.445162 CCACCAGGTACTCAACTAAAACCA 60.445 45.833 0.00 0.00 34.60 3.67
6709 9694 4.514066 CACCAGGTACTCAACTAAAACCAC 59.486 45.833 0.00 0.00 34.60 4.16
6710 9695 3.744426 CCAGGTACTCAACTAAAACCACG 59.256 47.826 0.00 0.00 34.60 4.94
6711 9696 4.501915 CCAGGTACTCAACTAAAACCACGA 60.502 45.833 0.00 0.00 34.60 4.35
6712 9697 4.446719 CAGGTACTCAACTAAAACCACGAC 59.553 45.833 0.00 0.00 34.60 4.34
6713 9698 3.426525 GGTACTCAACTAAAACCACGACG 59.573 47.826 0.00 0.00 0.00 5.12
6714 9699 3.441496 ACTCAACTAAAACCACGACGA 57.559 42.857 0.00 0.00 0.00 4.20
6715 9700 3.378339 ACTCAACTAAAACCACGACGAG 58.622 45.455 0.00 0.00 0.00 4.18
6716 9701 3.181483 ACTCAACTAAAACCACGACGAGT 60.181 43.478 0.00 0.00 0.00 4.18
6717 9702 4.036734 ACTCAACTAAAACCACGACGAGTA 59.963 41.667 0.00 0.00 29.82 2.59
6718 9703 4.930963 TCAACTAAAACCACGACGAGTAA 58.069 39.130 0.00 0.00 0.00 2.24
6719 9704 5.531634 TCAACTAAAACCACGACGAGTAAT 58.468 37.500 0.00 0.00 0.00 1.89
6720 9705 5.984926 TCAACTAAAACCACGACGAGTAATT 59.015 36.000 0.00 1.08 0.00 1.40
6721 9706 6.479660 TCAACTAAAACCACGACGAGTAATTT 59.520 34.615 0.00 0.34 0.00 1.82
6722 9707 6.219302 ACTAAAACCACGACGAGTAATTTG 57.781 37.500 0.00 2.39 0.00 2.32
6723 9708 4.477302 AAAACCACGACGAGTAATTTGG 57.523 40.909 0.00 0.00 0.00 3.28
6724 9709 3.389925 AACCACGACGAGTAATTTGGA 57.610 42.857 0.00 0.00 0.00 3.53
6725 9710 3.389925 ACCACGACGAGTAATTTGGAA 57.610 42.857 0.00 0.00 0.00 3.53
6726 9711 3.062042 ACCACGACGAGTAATTTGGAAC 58.938 45.455 0.00 0.00 0.00 3.62
6727 9712 2.091588 CCACGACGAGTAATTTGGAACG 59.908 50.000 0.00 0.00 0.00 3.95
6728 9713 2.091588 CACGACGAGTAATTTGGAACGG 59.908 50.000 0.00 0.00 0.00 4.44
6729 9714 2.030007 ACGACGAGTAATTTGGAACGGA 60.030 45.455 0.00 0.00 0.00 4.69
6730 9715 2.597305 CGACGAGTAATTTGGAACGGAG 59.403 50.000 0.00 0.00 0.00 4.63
6731 9716 2.928116 GACGAGTAATTTGGAACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
6732 9717 2.277084 CGAGTAATTTGGAACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
6733 9718 2.093869 CGAGTAATTTGGAACGGAGGGA 60.094 50.000 0.00 0.00 0.00 4.20
6734 9719 3.532542 GAGTAATTTGGAACGGAGGGAG 58.467 50.000 0.00 0.00 0.00 4.30
6735 9720 2.910977 AGTAATTTGGAACGGAGGGAGT 59.089 45.455 0.00 0.00 0.00 3.85
6736 9721 4.098894 AGTAATTTGGAACGGAGGGAGTA 58.901 43.478 0.00 0.00 0.00 2.59
6737 9722 3.345508 AATTTGGAACGGAGGGAGTAC 57.654 47.619 0.00 0.00 0.00 2.73
6740 9725 0.901580 TGGAACGGAGGGAGTACACC 60.902 60.000 0.00 0.00 0.00 4.16
6753 9738 4.439057 GGAGTACACCGCAATTATCTCAA 58.561 43.478 0.00 0.00 0.00 3.02
6760 9745 5.650266 ACACCGCAATTATCTCAATTTGGTA 59.350 36.000 0.00 0.00 29.62 3.25
6824 9810 5.216614 ACCTCTATTCCTATTTTCGCCTC 57.783 43.478 0.00 0.00 0.00 4.70
6841 9827 2.606308 GCCTCATGATTGCATAAAGCCG 60.606 50.000 11.38 0.00 44.83 5.52
6899 9885 7.857734 TGAAAAGCATATAAAGATCGAACCA 57.142 32.000 0.00 0.00 0.00 3.67
6902 9888 8.506168 AAAAGCATATAAAGATCGAACCAGAA 57.494 30.769 0.00 0.00 0.00 3.02
7049 10037 4.787381 TGACGTGTACATGAAAAGTGTG 57.213 40.909 21.82 0.00 0.00 3.82
7116 10104 5.180680 GGTCTTGGTGTACAACAGTTTATCC 59.819 44.000 14.34 8.45 34.76 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 4.543590 TTCTGGTAAGAAGAGAAGCCAG 57.456 45.455 0.00 0.00 43.37 4.85
17 18 4.326826 CCTGAGTGCATTTCTGGTAAGAA 58.673 43.478 14.89 0.00 40.76 2.52
36 37 2.212652 TGCAAGCATACGAATAGCCTG 58.787 47.619 0.00 0.00 0.00 4.85
37 38 2.620251 TGCAAGCATACGAATAGCCT 57.380 45.000 0.00 0.00 0.00 4.58
113 114 5.468072 GCAGAACCTATACATTGATGTGAGG 59.532 44.000 18.20 18.20 44.44 3.86
167 179 3.936453 GGTTGTATCTACGACATTTGGCA 59.064 43.478 9.39 0.00 41.38 4.92
179 191 4.891168 TCGCCAATAGTCAGGTTGTATCTA 59.109 41.667 0.00 0.00 0.00 1.98
193 205 6.245115 TCTATTTGCATTGATCGCCAATAG 57.755 37.500 13.93 13.93 43.27 1.73
195 207 4.022589 CCTCTATTTGCATTGATCGCCAAT 60.023 41.667 0.00 0.00 45.88 3.16
211 223 4.801164 AGCATTCATGGAAAGCCTCTATT 58.199 39.130 2.92 0.00 37.01 1.73
226 238 9.203421 CGTACAATCTATATTACCAAGCATTCA 57.797 33.333 0.00 0.00 0.00 2.57
239 251 6.040504 TCACTTCCAGTGCGTACAATCTATAT 59.959 38.462 6.38 0.00 45.54 0.86
240 252 5.358725 TCACTTCCAGTGCGTACAATCTATA 59.641 40.000 6.38 0.00 45.54 1.31
273 285 3.135895 ACGACCCCTACCAATCAAATAGG 59.864 47.826 0.00 0.00 36.07 2.57
292 304 6.320494 ACATTTTACATGCCTTTTGTACGA 57.680 33.333 0.00 0.00 29.60 3.43
374 867 9.844790 GAGTTGAATGTGATTTTGTCAATCATA 57.155 29.630 0.79 0.00 38.90 2.15
382 875 9.829507 TTATTTTGGAGTTGAATGTGATTTTGT 57.170 25.926 0.00 0.00 0.00 2.83
445 938 4.640201 AGGAAAATGAACCGATACATGTGG 59.360 41.667 9.11 3.60 0.00 4.17
446 939 5.818136 AGGAAAATGAACCGATACATGTG 57.182 39.130 9.11 0.00 0.00 3.21
505 998 9.838163 GTTTACAACCGAATAAAAATCACAAAC 57.162 29.630 0.00 0.00 0.00 2.93
615 1110 0.165079 CGGCGGTCAAATGTACACAC 59.835 55.000 0.00 0.00 0.00 3.82
616 1111 0.951525 CCGGCGGTCAAATGTACACA 60.952 55.000 19.97 0.00 0.00 3.72
636 1131 1.609555 TGGCCGACACATTTGGTTTAC 59.390 47.619 0.00 0.00 0.00 2.01
638 1133 1.115467 TTGGCCGACACATTTGGTTT 58.885 45.000 0.00 0.00 0.00 3.27
639 1134 1.337118 ATTGGCCGACACATTTGGTT 58.663 45.000 0.00 0.00 0.00 3.67
698 1202 9.278734 GGATTCGTCTGATCACTTTTTATTTTC 57.721 33.333 0.00 0.00 0.00 2.29
701 1205 7.390440 TGTGGATTCGTCTGATCACTTTTTATT 59.610 33.333 0.00 0.00 0.00 1.40
712 1216 6.406370 TCTATTTTGTGTGGATTCGTCTGAT 58.594 36.000 0.00 0.00 0.00 2.90
713 1217 5.789521 TCTATTTTGTGTGGATTCGTCTGA 58.210 37.500 0.00 0.00 0.00 3.27
714 1218 6.092670 ACATCTATTTTGTGTGGATTCGTCTG 59.907 38.462 0.00 0.00 0.00 3.51
720 1224 5.710099 ACCGAACATCTATTTTGTGTGGATT 59.290 36.000 0.00 0.00 0.00 3.01
721 1225 5.253330 ACCGAACATCTATTTTGTGTGGAT 58.747 37.500 0.00 0.00 0.00 3.41
722 1226 4.647611 ACCGAACATCTATTTTGTGTGGA 58.352 39.130 0.00 0.00 0.00 4.02
723 1227 4.435518 CGACCGAACATCTATTTTGTGTGG 60.436 45.833 0.00 0.00 0.00 4.17
725 1229 4.312443 ACGACCGAACATCTATTTTGTGT 58.688 39.130 0.00 0.00 0.00 3.72
733 2349 0.033796 AGGGGACGACCGAACATCTA 60.034 55.000 0.00 0.00 41.60 1.98
734 2350 0.033796 TAGGGGACGACCGAACATCT 60.034 55.000 0.00 0.00 41.60 2.90
756 2372 2.320745 ACTCCACGACCGAACTTTTT 57.679 45.000 0.00 0.00 0.00 1.94
757 2373 2.320745 AACTCCACGACCGAACTTTT 57.679 45.000 0.00 0.00 0.00 2.27
758 2374 1.937899 CAAACTCCACGACCGAACTTT 59.062 47.619 0.00 0.00 0.00 2.66
759 2375 1.578583 CAAACTCCACGACCGAACTT 58.421 50.000 0.00 0.00 0.00 2.66
760 2376 0.249741 CCAAACTCCACGACCGAACT 60.250 55.000 0.00 0.00 0.00 3.01
847 2463 0.678366 TCTCGCCTCTGTGTCTCCTC 60.678 60.000 0.00 0.00 0.00 3.71
885 2501 0.541063 TACCGGTTCAGACAGGCAGA 60.541 55.000 15.04 0.00 43.98 4.26
915 2531 0.249398 CGGAGTAGGGACACTTTGGG 59.751 60.000 0.00 0.00 0.00 4.12
918 2534 0.886563 CGTCGGAGTAGGGACACTTT 59.113 55.000 0.00 0.00 32.74 2.66
919 2535 0.037303 TCGTCGGAGTAGGGACACTT 59.963 55.000 0.00 0.00 32.74 3.16
920 2536 0.255318 ATCGTCGGAGTAGGGACACT 59.745 55.000 0.00 0.00 32.74 3.55
921 2537 0.662085 GATCGTCGGAGTAGGGACAC 59.338 60.000 0.00 0.00 32.74 3.67
922 2538 0.545171 AGATCGTCGGAGTAGGGACA 59.455 55.000 0.00 0.00 32.74 4.02
923 2539 2.540265 TAGATCGTCGGAGTAGGGAC 57.460 55.000 0.00 0.00 0.00 4.46
1206 2833 2.367030 TTAAATTCGAGTTCCGCGGA 57.633 45.000 27.28 27.28 38.37 5.54
1207 2834 3.545426 GGAATTAAATTCGAGTTCCGCGG 60.545 47.826 22.12 22.12 40.17 6.46
1208 2835 3.545426 GGGAATTAAATTCGAGTTCCGCG 60.545 47.826 0.00 0.00 39.33 6.46
1209 2836 3.242969 GGGGAATTAAATTCGAGTTCCGC 60.243 47.826 12.56 12.56 42.20 5.54
1210 2837 3.314357 GGGGGAATTAAATTCGAGTTCCG 59.686 47.826 0.00 0.00 39.33 4.30
1211 2838 4.913335 GGGGGAATTAAATTCGAGTTCC 57.087 45.455 0.00 6.20 40.17 3.62
1242 2869 1.231221 CGTCTCGTATCTCCAGGGAG 58.769 60.000 9.11 9.11 43.21 4.30
1250 2877 2.905880 CGGGCCCGTCTCGTATCT 60.906 66.667 36.64 0.00 34.35 1.98
1276 2903 7.720957 CCCACAAAATCCAACATAGATAGATCA 59.279 37.037 0.00 0.00 0.00 2.92
1282 2909 4.640201 CGACCCACAAAATCCAACATAGAT 59.360 41.667 0.00 0.00 0.00 1.98
1283 2910 4.006989 CGACCCACAAAATCCAACATAGA 58.993 43.478 0.00 0.00 0.00 1.98
1284 2911 3.128589 CCGACCCACAAAATCCAACATAG 59.871 47.826 0.00 0.00 0.00 2.23
1285 2912 3.085533 CCGACCCACAAAATCCAACATA 58.914 45.455 0.00 0.00 0.00 2.29
1455 3082 1.382146 TGAGTGGGATCCGGGGTAC 60.382 63.158 5.45 0.00 0.00 3.34
1534 3161 2.189676 TCCTAACCACCAGCGGAATTA 58.810 47.619 1.50 0.00 0.00 1.40
1568 3197 7.719633 CCACCAAAGCAATAGTACCAATATACT 59.280 37.037 0.00 0.00 38.89 2.12
1610 3239 0.372679 CATAAGCAGCACAGCACTCG 59.627 55.000 0.00 0.00 36.85 4.18
1613 3242 1.401931 CCAACATAAGCAGCACAGCAC 60.402 52.381 0.00 0.00 36.85 4.40
1614 3243 0.883153 CCAACATAAGCAGCACAGCA 59.117 50.000 0.00 0.00 36.85 4.41
1637 3266 1.202330 AGAGATTCAGAGGCACCCTG 58.798 55.000 0.00 0.00 34.62 4.45
1653 3283 2.572104 ACCCAAACACTAAGCCCTAGAG 59.428 50.000 0.00 0.00 0.00 2.43
1665 3295 2.730094 CAGCCAGCACCCAAACAC 59.270 61.111 0.00 0.00 0.00 3.32
1666 3296 3.225798 GCAGCCAGCACCCAAACA 61.226 61.111 0.00 0.00 44.79 2.83
1723 3356 1.571215 GGCAGGGTCGGTTACAAACG 61.571 60.000 0.00 0.00 0.00 3.60
1736 3370 2.233271 GATACATGGTTCATGGCAGGG 58.767 52.381 11.85 0.00 45.16 4.45
1916 3553 6.264292 TCAACATATACGCAAAAATAGGCCAT 59.736 34.615 5.01 0.00 0.00 4.40
1953 3592 2.124653 AAACCAACCCACACGCGA 60.125 55.556 15.93 0.00 0.00 5.87
1954 3593 2.184167 AGAAACCAACCCACACGCG 61.184 57.895 3.53 3.53 0.00 6.01
1955 3594 1.358759 CAGAAACCAACCCACACGC 59.641 57.895 0.00 0.00 0.00 5.34
1956 3595 0.380378 CACAGAAACCAACCCACACG 59.620 55.000 0.00 0.00 0.00 4.49
1971 3610 6.130298 TGGATCAACTTTTAACACACACAG 57.870 37.500 0.00 0.00 0.00 3.66
2019 3685 8.192774 ACAACAAAGATTGGTCATGCATATAAG 58.807 33.333 0.00 0.00 33.63 1.73
2157 3824 5.619981 GCGAAGTGCTTGAATAAAGAATGGT 60.620 40.000 0.00 0.00 41.73 3.55
2284 3951 6.451064 AAGACAGGTCTTCGAAATGTTTTT 57.549 33.333 8.82 0.00 46.13 1.94
2294 3961 7.062371 CACAAAGTTAGATAAGACAGGTCTTCG 59.938 40.741 17.29 0.00 46.13 3.79
2354 4021 5.488341 TGTAAAAGTGTAGAGAAGGATGGC 58.512 41.667 0.00 0.00 0.00 4.40
2435 4102 5.221402 GCTTCCCGTATAAGCCTAAAGTAGT 60.221 44.000 0.00 0.00 42.85 2.73
2452 4122 2.894126 ACCATCTAGTATCAGCTTCCCG 59.106 50.000 0.00 0.00 0.00 5.14
2577 4419 2.158385 AGGGGGTGCATTAACTTGTTCA 60.158 45.455 0.00 0.00 0.00 3.18
2631 4473 4.270008 AGGGTGTAAATAGCATTGTGGTC 58.730 43.478 0.00 0.00 0.00 4.02
2738 4581 3.761140 CATGGTGGCAATGGCGCA 61.761 61.111 21.52 8.59 42.47 6.09
2739 4582 4.517815 CCATGGTGGCAATGGCGC 62.518 66.667 12.15 12.15 42.47 6.53
2740 4583 2.079020 GATCCATGGTGGCAATGGCG 62.079 60.000 12.58 0.00 43.70 5.69
2741 4584 1.744014 GATCCATGGTGGCAATGGC 59.256 57.895 12.58 0.00 43.70 4.40
2742 4585 1.117142 GGGATCCATGGTGGCAATGG 61.117 60.000 15.23 11.29 45.13 3.16
2743 4586 1.117142 GGGGATCCATGGTGGCAATG 61.117 60.000 15.23 0.00 37.47 2.82
2744 4587 1.233949 GGGGATCCATGGTGGCAAT 59.766 57.895 15.23 0.00 37.47 3.56
2745 4588 2.244633 TGGGGATCCATGGTGGCAA 61.245 57.895 15.23 0.00 38.32 4.52
2758 4601 0.550914 GCATAATGGGTGAGTGGGGA 59.449 55.000 0.00 0.00 0.00 4.81
2776 4621 5.426504 CTGACTATAGATCATGGGATTGGC 58.573 45.833 6.78 0.00 32.67 4.52
2937 4782 0.322648 CCTGTGGAGCTGTCATCACA 59.677 55.000 0.00 0.00 37.73 3.58
2977 4880 4.342092 CAGGGTTTGATTATGAATGGACCC 59.658 45.833 0.00 0.00 44.58 4.46
3264 5647 2.509569 TCGTCAAGCTTGGGCAAATAA 58.490 42.857 25.73 1.09 41.70 1.40
3474 5953 3.401033 CACCTACAGTGGTTCACATCA 57.599 47.619 0.00 0.00 43.26 3.07
3533 6012 1.776710 ACTAACCCTTGGGTGCCCA 60.777 57.895 12.67 5.73 45.63 5.36
3619 6109 7.679783 TCTCTTCTCAAACCATACTCAAATCA 58.320 34.615 0.00 0.00 0.00 2.57
3622 6112 7.303182 TCTCTCTTCTCAAACCATACTCAAA 57.697 36.000 0.00 0.00 0.00 2.69
3686 6176 6.813649 TCCTCGATCTTTGTGAATCTTAAGTG 59.186 38.462 1.63 0.00 0.00 3.16
4120 6768 7.539366 GCGGAACATTAATAAGTTAACAAGCAA 59.461 33.333 8.61 0.00 32.91 3.91
4138 6786 7.703328 ACAGAAATAAAATAATCGCGGAACAT 58.297 30.769 6.13 0.00 0.00 2.71
4139 6787 7.079182 ACAGAAATAAAATAATCGCGGAACA 57.921 32.000 6.13 0.00 0.00 3.18
4140 6788 7.964545 AACAGAAATAAAATAATCGCGGAAC 57.035 32.000 6.13 0.00 0.00 3.62
4425 7126 5.883661 ACTGTCAATCACAACACTTGAAAG 58.116 37.500 0.00 0.00 39.24 2.62
4960 7693 4.380867 GGCACATTTAATCTCAACACCCTG 60.381 45.833 0.00 0.00 0.00 4.45
4963 7696 4.458989 TCAGGCACATTTAATCTCAACACC 59.541 41.667 0.00 0.00 0.00 4.16
4983 7716 4.683781 GTCTTGAACTAGCAGTGAACTCAG 59.316 45.833 0.00 0.00 0.00 3.35
4990 7723 5.928839 ACAATACTGTCTTGAACTAGCAGTG 59.071 40.000 12.19 0.00 40.18 3.66
5038 7799 4.412528 ACCAAAGTTCCTTACTTCAGACCT 59.587 41.667 0.00 0.00 46.34 3.85
5346 8207 1.317613 AATGCCTGAACGCTCAACAA 58.682 45.000 0.00 0.00 0.00 2.83
5384 8245 3.254166 ACATCTGACATCCAAAACAGTGC 59.746 43.478 0.00 0.00 0.00 4.40
5388 8249 3.156293 CCCACATCTGACATCCAAAACA 58.844 45.455 0.00 0.00 0.00 2.83
5416 8282 3.170717 ACCAGAATCGTAACTCCAGGAA 58.829 45.455 0.00 0.00 0.00 3.36
5427 8294 1.201429 AGCCCTGGAACCAGAATCGT 61.201 55.000 20.79 0.00 46.30 3.73
5495 8362 6.367695 CAGGTTGTACGTGTCATCAAATCTTA 59.632 38.462 0.00 0.00 0.00 2.10
5519 8386 2.041620 AGGCCTGATTTTTACCAGCTCA 59.958 45.455 3.11 0.00 0.00 4.26
5527 8394 2.000048 AGGGTGGAGGCCTGATTTTTA 59.000 47.619 12.00 0.00 0.00 1.52
5537 8404 2.222227 AAAAATCAGAGGGTGGAGGC 57.778 50.000 0.00 0.00 0.00 4.70
5547 8414 8.849168 CATGGCCAACTACATATAAAAATCAGA 58.151 33.333 10.96 0.00 0.00 3.27
5548 8415 8.084073 CCATGGCCAACTACATATAAAAATCAG 58.916 37.037 10.96 0.00 0.00 2.90
5549 8416 7.563188 ACCATGGCCAACTACATATAAAAATCA 59.437 33.333 10.96 0.00 0.00 2.57
5550 8417 7.951591 ACCATGGCCAACTACATATAAAAATC 58.048 34.615 10.96 0.00 0.00 2.17
5551 8418 7.912778 ACCATGGCCAACTACATATAAAAAT 57.087 32.000 10.96 0.00 0.00 1.82
5552 8419 7.726033 AACCATGGCCAACTACATATAAAAA 57.274 32.000 10.96 0.00 0.00 1.94
5832 8716 1.192534 CGTCACTCTGCTTTCCGTTTC 59.807 52.381 0.00 0.00 0.00 2.78
5989 8887 3.562343 ACATTCTGAGCATCTGCAGAT 57.438 42.857 23.75 23.75 45.16 2.90
6082 8980 0.745845 CTCCTTGATCTGGGTTGCGG 60.746 60.000 0.00 0.00 0.00 5.69
6186 9084 2.817844 ACTTTTGGAATAACCTCCACGC 59.182 45.455 0.00 0.00 45.37 5.34
6187 9085 4.517453 TCAACTTTTGGAATAACCTCCACG 59.483 41.667 0.00 0.00 45.37 4.94
6214 9112 1.136000 TCGTCATGTGCTTCATTTGCG 60.136 47.619 0.00 0.00 34.09 4.85
6253 9151 3.074412 CACAGGGAAGCGAAACAACTAT 58.926 45.455 0.00 0.00 0.00 2.12
6279 9177 6.548441 TTGGACTTAATAAGTTCACAACGG 57.452 37.500 13.36 0.00 46.45 4.44
6317 9215 2.781681 TTCCTTGATCGGAAGTTCCC 57.218 50.000 16.47 3.04 38.12 3.97
6373 9271 0.173255 ACACACACCAGCAAACAAGC 59.827 50.000 0.00 0.00 0.00 4.01
6470 9404 0.027586 GAGTGTTGTGTGGTGCGTTC 59.972 55.000 0.00 0.00 0.00 3.95
6481 9415 1.230635 GGTGCATGAGCGAGTGTTGT 61.231 55.000 0.00 0.00 46.23 3.32
6568 9533 4.520492 AGCAAGAGAATTGAAAACGGACAT 59.480 37.500 0.00 0.00 0.00 3.06
6648 9633 4.141482 ACCATGTCTCGGCAATAAGGTAAT 60.141 41.667 0.00 0.00 0.00 1.89
6696 9681 3.441496 ACTCGTCGTGGTTTTAGTTGA 57.559 42.857 0.00 0.00 0.00 3.18
6697 9682 5.834239 ATTACTCGTCGTGGTTTTAGTTG 57.166 39.130 0.00 0.00 0.00 3.16
6698 9683 6.293027 CCAAATTACTCGTCGTGGTTTTAGTT 60.293 38.462 0.00 0.00 0.00 2.24
6699 9684 5.178067 CCAAATTACTCGTCGTGGTTTTAGT 59.822 40.000 0.00 0.00 0.00 2.24
6700 9685 5.406175 TCCAAATTACTCGTCGTGGTTTTAG 59.594 40.000 0.00 0.00 0.00 1.85
6701 9686 5.295950 TCCAAATTACTCGTCGTGGTTTTA 58.704 37.500 0.00 0.00 0.00 1.52
6702 9687 4.128643 TCCAAATTACTCGTCGTGGTTTT 58.871 39.130 0.00 0.00 0.00 2.43
6703 9688 3.731089 TCCAAATTACTCGTCGTGGTTT 58.269 40.909 0.00 0.00 0.00 3.27
6704 9689 3.389925 TCCAAATTACTCGTCGTGGTT 57.610 42.857 0.00 0.00 0.00 3.67
6705 9690 3.062042 GTTCCAAATTACTCGTCGTGGT 58.938 45.455 0.00 0.00 0.00 4.16
6706 9691 2.091588 CGTTCCAAATTACTCGTCGTGG 59.908 50.000 0.00 0.00 0.00 4.94
6707 9692 2.091588 CCGTTCCAAATTACTCGTCGTG 59.908 50.000 0.00 0.00 0.00 4.35
6708 9693 2.030007 TCCGTTCCAAATTACTCGTCGT 60.030 45.455 0.00 0.00 0.00 4.34
6709 9694 2.597305 CTCCGTTCCAAATTACTCGTCG 59.403 50.000 0.00 0.00 0.00 5.12
6710 9695 2.928116 CCTCCGTTCCAAATTACTCGTC 59.072 50.000 0.00 0.00 0.00 4.20
6711 9696 2.354403 CCCTCCGTTCCAAATTACTCGT 60.354 50.000 0.00 0.00 0.00 4.18
6712 9697 2.093869 TCCCTCCGTTCCAAATTACTCG 60.094 50.000 0.00 0.00 0.00 4.18
6713 9698 3.055312 ACTCCCTCCGTTCCAAATTACTC 60.055 47.826 0.00 0.00 0.00 2.59
6714 9699 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
6715 9700 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
6716 9701 3.839490 TGTACTCCCTCCGTTCCAAATTA 59.161 43.478 0.00 0.00 0.00 1.40
6717 9702 2.640826 TGTACTCCCTCCGTTCCAAATT 59.359 45.455 0.00 0.00 0.00 1.82
6718 9703 2.027469 GTGTACTCCCTCCGTTCCAAAT 60.027 50.000 0.00 0.00 0.00 2.32
6719 9704 1.345415 GTGTACTCCCTCCGTTCCAAA 59.655 52.381 0.00 0.00 0.00 3.28
6720 9705 0.971386 GTGTACTCCCTCCGTTCCAA 59.029 55.000 0.00 0.00 0.00 3.53
6721 9706 0.901580 GGTGTACTCCCTCCGTTCCA 60.902 60.000 2.33 0.00 0.00 3.53
6722 9707 1.895966 GGTGTACTCCCTCCGTTCC 59.104 63.158 2.33 0.00 0.00 3.62
6723 9708 1.509923 CGGTGTACTCCCTCCGTTC 59.490 63.158 8.36 0.00 38.45 3.95
6724 9709 2.643232 GCGGTGTACTCCCTCCGTT 61.643 63.158 8.36 0.00 44.07 4.44
6725 9710 3.066814 GCGGTGTACTCCCTCCGT 61.067 66.667 8.36 0.00 44.07 4.69
6726 9711 1.956629 ATTGCGGTGTACTCCCTCCG 61.957 60.000 8.36 8.54 44.86 4.63
6727 9712 0.252197 AATTGCGGTGTACTCCCTCC 59.748 55.000 8.36 0.00 0.00 4.30
6728 9713 2.973694 TAATTGCGGTGTACTCCCTC 57.026 50.000 8.36 1.74 0.00 4.30
6729 9714 3.039011 AGATAATTGCGGTGTACTCCCT 58.961 45.455 8.36 0.00 0.00 4.20
6730 9715 3.181469 TGAGATAATTGCGGTGTACTCCC 60.181 47.826 8.36 0.44 0.00 4.30
6731 9716 4.054780 TGAGATAATTGCGGTGTACTCC 57.945 45.455 3.76 3.76 0.00 3.85
6732 9717 6.604735 AATTGAGATAATTGCGGTGTACTC 57.395 37.500 0.00 0.00 0.00 2.59
6733 9718 6.183360 CCAAATTGAGATAATTGCGGTGTACT 60.183 38.462 0.00 0.00 0.00 2.73
6734 9719 5.971202 CCAAATTGAGATAATTGCGGTGTAC 59.029 40.000 0.00 0.00 0.00 2.90
6735 9720 5.650266 ACCAAATTGAGATAATTGCGGTGTA 59.350 36.000 0.00 0.00 29.94 2.90
6736 9721 4.462483 ACCAAATTGAGATAATTGCGGTGT 59.538 37.500 0.00 0.00 29.94 4.16
6737 9722 4.997565 ACCAAATTGAGATAATTGCGGTG 58.002 39.130 0.00 0.00 29.94 4.94
6740 9725 7.967854 TGAAACTACCAAATTGAGATAATTGCG 59.032 33.333 0.00 0.00 0.00 4.85
6789 9774 4.384940 GAATAGAGGTTGAGGGAGAATGC 58.615 47.826 0.00 0.00 0.00 3.56
6824 9810 1.067364 TGCCGGCTTTATGCAATCATG 59.933 47.619 29.70 0.00 45.15 3.07
6841 9827 0.249398 ACCTGAGGTGTATCGTTGCC 59.751 55.000 1.77 0.00 32.98 4.52
6866 9852 9.624373 ATCTTTATATGCTTTTCATGTGACTCT 57.376 29.630 0.00 0.00 36.63 3.24
6867 9853 9.875675 GATCTTTATATGCTTTTCATGTGACTC 57.124 33.333 0.00 0.00 36.63 3.36
6899 9885 8.046107 CCAGAGGATTCAAGAGTTAGAATTTCT 58.954 37.037 4.03 4.03 34.79 2.52
6902 9888 7.038017 TGTCCAGAGGATTCAAGAGTTAGAATT 60.038 37.037 0.00 0.00 34.79 2.17
7049 10037 7.440523 ACATGAAGACATTCTTTTGTAGGAC 57.559 36.000 0.00 0.00 36.73 3.85
7116 10104 4.843448 GGCAAAAATTAAATTTGGAACGCG 59.157 37.500 3.53 3.53 38.04 6.01


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

AutoCloner maintained by Alex Coulton.