Multiple sequence alignment - TraesCS5B01G302800

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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 TraesCS5B01G302800 chr5B 100.000 3887 0 0 1 3887 487347220 487343334 0.000000e+00 7179
1 TraesCS5B01G302800 chr5B 95.492 488 17 4 3404 3887 155711933 155711447 0.000000e+00 774
2 TraesCS5B01G302800 chr5B 95.122 492 18 5 3400 3887 681661089 681660600 0.000000e+00 771
3 TraesCS5B01G302800 chr5B 77.555 548 110 12 1711 2250 487438568 487439110 6.270000e-83 318
4 TraesCS5B01G302800 chr5B 94.969 159 7 1 521 679 476006006 476005849 8.340000e-62 248
5 TraesCS5B01G302800 chr5B 91.772 158 11 2 521 678 708662883 708663038 6.540000e-53 219
6 TraesCS5B01G302800 chr5D 94.147 2785 95 28 679 3411 406395560 406392792 0.000000e+00 4178
7 TraesCS5B01G302800 chr5D 77.455 550 111 12 1711 2252 406416356 406416900 2.250000e-82 316
8 TraesCS5B01G302800 chr5A 93.021 2794 110 39 679 3411 512052432 512049663 0.000000e+00 4000
9 TraesCS5B01G302800 chr5A 80.745 483 47 17 84 520 512052907 512052425 6.220000e-88 335
10 TraesCS5B01G302800 chr5A 81.818 143 23 3 2916 3055 235649496 235649638 2.450000e-22 117
11 TraesCS5B01G302800 chr3D 86.817 1957 191 41 988 2887 613056905 613058851 0.000000e+00 2122
12 TraesCS5B01G302800 chr3D 86.928 153 17 3 2916 3066 66248229 66248380 6.680000e-38 169
13 TraesCS5B01G302800 chr3B 86.043 1956 205 43 994 2888 825994297 825992349 0.000000e+00 2037
14 TraesCS5B01G302800 chr3B 95.876 485 16 3 3407 3887 22550458 22549974 0.000000e+00 782
15 TraesCS5B01G302800 chr3B 96.066 483 14 4 3410 3887 247808972 247809454 0.000000e+00 782
16 TraesCS5B01G302800 chr3B 88.281 128 11 4 2943 3068 773147651 773147776 2.420000e-32 150
17 TraesCS5B01G302800 chr3A 88.384 1696 170 17 1218 2888 747723739 747725432 0.000000e+00 2015
18 TraesCS5B01G302800 chr3A 85.000 140 16 5 2916 3051 615144226 615144088 1.880000e-28 137
19 TraesCS5B01G302800 chr2B 95.893 487 16 3 3405 3887 116381231 116380745 0.000000e+00 785
20 TraesCS5B01G302800 chr2B 96.258 481 13 4 3412 3887 683096049 683096529 0.000000e+00 784
21 TraesCS5B01G302800 chr2B 95.344 494 18 4 3399 3887 675208177 675208670 0.000000e+00 780
22 TraesCS5B01G302800 chr2B 94.194 155 8 1 521 675 198537199 198537352 6.490000e-58 235
23 TraesCS5B01G302800 chr2B 94.245 139 8 0 540 678 2485199 2485061 3.040000e-51 213
24 TraesCS5B01G302800 chr2B 92.958 142 10 0 537 678 2364073 2364214 1.420000e-49 207
25 TraesCS5B01G302800 chr7B 95.510 490 17 4 3402 3887 624955626 624956114 0.000000e+00 778
26 TraesCS5B01G302800 chr7B 94.455 505 19 8 3390 3887 586933490 586932988 0.000000e+00 769
27 TraesCS5B01G302800 chr7B 81.269 331 54 7 1227 1556 685360922 685360599 1.070000e-65 261
28 TraesCS5B01G302800 chr7B 92.405 158 11 1 521 678 507215948 507216104 1.410000e-54 224
29 TraesCS5B01G302800 chr7D 84.571 525 77 4 2365 2887 555233265 555232743 5.760000e-143 518
30 TraesCS5B01G302800 chr7D 91.139 158 12 2 521 678 560288039 560287884 3.040000e-51 213
31 TraesCS5B01G302800 chr7D 84.615 143 19 3 2916 3055 17945081 17944939 5.240000e-29 139
32 TraesCS5B01G302800 chr1A 78.364 550 106 13 1711 2252 537346917 537346373 1.030000e-90 344
33 TraesCS5B01G302800 chr1B 77.878 556 104 17 1708 2252 598191549 598192096 1.040000e-85 327
34 TraesCS5B01G302800 chr1B 90.987 233 21 0 1173 1405 616824823 616825055 8.110000e-82 315
35 TraesCS5B01G302800 chr1B 93.820 178 11 0 2268 2445 616824819 616824642 6.400000e-68 268
36 TraesCS5B01G302800 chr1B 96.575 146 5 0 2301 2446 616963177 616963032 3.880000e-60 243
37 TraesCS5B01G302800 chr1B 91.720 157 10 2 2301 2456 616958867 616959021 8.460000e-52 215
38 TraesCS5B01G302800 chr1D 82.911 316 41 11 1227 1537 440718648 440718955 4.950000e-69 272
39 TraesCS5B01G302800 chr1D 85.235 149 16 4 2466 2611 265986820 265986675 8.700000e-32 148
40 TraesCS5B01G302800 chr2A 91.250 160 14 0 520 679 14055591 14055750 6.540000e-53 219
41 TraesCS5B01G302800 chr2A 86.000 150 18 3 2920 3066 326257881 326258030 1.450000e-34 158
42 TraesCS5B01G302800 chr7A 91.195 159 12 2 520 678 701197168 701197324 8.460000e-52 215
43 TraesCS5B01G302800 chr6B 82.911 158 22 5 2913 3066 247029326 247029482 1.880000e-28 137
44 TraesCS5B01G302800 chr2D 83.916 143 20 3 2916 3055 645242064 645241922 2.440000e-27 134


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 TraesCS5B01G302800 chr5B 487343334 487347220 3886 True 7179.0 7179 100.000 1 3887 1 chr5B.!!$R3 3886
1 TraesCS5B01G302800 chr5B 487438568 487439110 542 False 318.0 318 77.555 1711 2250 1 chr5B.!!$F1 539
2 TraesCS5B01G302800 chr5D 406392792 406395560 2768 True 4178.0 4178 94.147 679 3411 1 chr5D.!!$R1 2732
3 TraesCS5B01G302800 chr5D 406416356 406416900 544 False 316.0 316 77.455 1711 2252 1 chr5D.!!$F1 541
4 TraesCS5B01G302800 chr5A 512049663 512052907 3244 True 2167.5 4000 86.883 84 3411 2 chr5A.!!$R1 3327
5 TraesCS5B01G302800 chr3D 613056905 613058851 1946 False 2122.0 2122 86.817 988 2887 1 chr3D.!!$F2 1899
6 TraesCS5B01G302800 chr3B 825992349 825994297 1948 True 2037.0 2037 86.043 994 2888 1 chr3B.!!$R2 1894
7 TraesCS5B01G302800 chr3A 747723739 747725432 1693 False 2015.0 2015 88.384 1218 2888 1 chr3A.!!$F1 1670
8 TraesCS5B01G302800 chr7B 586932988 586933490 502 True 769.0 769 94.455 3390 3887 1 chr7B.!!$R1 497
9 TraesCS5B01G302800 chr7D 555232743 555233265 522 True 518.0 518 84.571 2365 2887 1 chr7D.!!$R2 522
10 TraesCS5B01G302800 chr1A 537346373 537346917 544 True 344.0 344 78.364 1711 2252 1 chr1A.!!$R1 541
11 TraesCS5B01G302800 chr1B 598191549 598192096 547 False 327.0 327 77.878 1708 2252 1 chr1B.!!$F1 544

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
633 680 0.036765 TTACTGTTACCTGCAGCCGG 60.037 55.0 8.66 0.0 37.47 6.13 F
652 699 0.255033 GCCCTCCCCAACGTCTAATT 59.745 55.0 0.00 0.0 0.00 1.40 F
701 748 0.470766 AGTTTCCCCGTAACACAGCA 59.529 50.0 0.00 0.0 0.00 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2484 2629 4.394712 AGGTTCGCGCCCTTCTGG 62.395 66.667 10.91 0.0 37.09 3.86 R
2791 2942 2.747686 GTCCGCCTCCAGGAACAA 59.252 61.111 0.00 0.0 39.84 2.83 R
2903 3054 6.476380 GGAAAATGCAAAGCAAATCGATGATA 59.524 34.615 0.00 0.0 43.62 2.15 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
22 23 5.947228 CTGTAGACAAATCTGCCTTTTGA 57.053 39.130 9.32 0.00 36.78 2.69
23 24 5.936054 CTGTAGACAAATCTGCCTTTTGAG 58.064 41.667 9.32 0.00 36.78 3.02
24 25 3.930634 AGACAAATCTGCCTTTTGAGC 57.069 42.857 9.32 0.00 37.48 4.26
25 26 2.560105 AGACAAATCTGCCTTTTGAGCC 59.440 45.455 9.32 1.03 37.48 4.70
26 27 1.270550 ACAAATCTGCCTTTTGAGCCG 59.729 47.619 9.32 0.00 37.48 5.52
27 28 1.541147 CAAATCTGCCTTTTGAGCCGA 59.459 47.619 0.00 0.00 36.40 5.54
28 29 2.134789 AATCTGCCTTTTGAGCCGAT 57.865 45.000 0.00 0.00 35.96 4.18
29 30 1.386533 ATCTGCCTTTTGAGCCGATG 58.613 50.000 0.00 0.00 33.58 3.84
30 31 0.324614 TCTGCCTTTTGAGCCGATGA 59.675 50.000 0.00 0.00 0.00 2.92
31 32 1.167851 CTGCCTTTTGAGCCGATGAA 58.832 50.000 0.00 0.00 0.00 2.57
32 33 1.541147 CTGCCTTTTGAGCCGATGAAA 59.459 47.619 0.00 0.00 0.00 2.69
33 34 2.165030 CTGCCTTTTGAGCCGATGAAAT 59.835 45.455 0.00 0.00 0.00 2.17
34 35 2.094597 TGCCTTTTGAGCCGATGAAATG 60.095 45.455 0.00 0.00 0.00 2.32
35 36 2.736400 GCCTTTTGAGCCGATGAAATGG 60.736 50.000 0.00 0.00 0.00 3.16
36 37 2.493278 CCTTTTGAGCCGATGAAATGGT 59.507 45.455 0.00 0.00 0.00 3.55
37 38 3.428045 CCTTTTGAGCCGATGAAATGGTC 60.428 47.826 0.00 0.00 0.00 4.02
38 39 1.750193 TTGAGCCGATGAAATGGTCC 58.250 50.000 0.00 0.00 0.00 4.46
39 40 0.617935 TGAGCCGATGAAATGGTCCA 59.382 50.000 0.00 0.00 0.00 4.02
40 41 1.212688 TGAGCCGATGAAATGGTCCAT 59.787 47.619 0.00 0.00 0.00 3.41
41 42 1.876156 GAGCCGATGAAATGGTCCATC 59.124 52.381 4.39 0.00 36.67 3.51
45 46 2.763249 GATGAAATGGTCCATCGCAC 57.237 50.000 4.39 0.00 31.20 5.34
46 47 2.016318 GATGAAATGGTCCATCGCACA 58.984 47.619 4.39 4.02 31.20 4.57
47 48 2.127271 TGAAATGGTCCATCGCACAT 57.873 45.000 4.39 0.00 0.00 3.21
48 49 1.744522 TGAAATGGTCCATCGCACATG 59.255 47.619 4.39 0.00 0.00 3.21
49 50 2.016318 GAAATGGTCCATCGCACATGA 58.984 47.619 4.39 0.00 0.00 3.07
50 51 1.382522 AATGGTCCATCGCACATGAC 58.617 50.000 4.39 0.00 0.00 3.06
51 52 0.811219 ATGGTCCATCGCACATGACG 60.811 55.000 0.00 2.72 0.00 4.35
52 53 2.173669 GGTCCATCGCACATGACGG 61.174 63.158 0.00 0.00 0.00 4.79
53 54 1.153647 GTCCATCGCACATGACGGA 60.154 57.895 0.00 0.00 0.00 4.69
54 55 1.141665 TCCATCGCACATGACGGAG 59.858 57.895 0.00 0.00 0.00 4.63
55 56 2.528743 CCATCGCACATGACGGAGC 61.529 63.158 0.00 0.00 0.00 4.70
56 57 1.520120 CATCGCACATGACGGAGCT 60.520 57.895 0.00 0.00 0.00 4.09
57 58 1.520120 ATCGCACATGACGGAGCTG 60.520 57.895 0.00 0.00 0.00 4.24
58 59 1.948721 ATCGCACATGACGGAGCTGA 61.949 55.000 0.00 0.00 0.00 4.26
59 60 2.163390 CGCACATGACGGAGCTGAG 61.163 63.158 0.00 0.00 0.00 3.35
60 61 1.079543 GCACATGACGGAGCTGAGT 60.080 57.895 0.00 0.00 0.00 3.41
61 62 1.080995 GCACATGACGGAGCTGAGTC 61.081 60.000 0.00 10.35 37.85 3.36
62 63 0.529833 CACATGACGGAGCTGAGTCT 59.470 55.000 16.26 3.21 38.16 3.24
63 64 1.067283 CACATGACGGAGCTGAGTCTT 60.067 52.381 16.26 9.34 38.16 3.01
64 65 1.620819 ACATGACGGAGCTGAGTCTTT 59.379 47.619 16.26 4.72 38.16 2.52
65 66 1.998315 CATGACGGAGCTGAGTCTTTG 59.002 52.381 16.26 11.25 38.16 2.77
66 67 1.040646 TGACGGAGCTGAGTCTTTGT 58.959 50.000 16.26 0.00 38.16 2.83
67 68 2.235891 TGACGGAGCTGAGTCTTTGTA 58.764 47.619 16.26 0.00 38.16 2.41
68 69 2.229062 TGACGGAGCTGAGTCTTTGTAG 59.771 50.000 16.26 0.00 38.16 2.74
69 70 1.067495 ACGGAGCTGAGTCTTTGTAGC 60.067 52.381 0.00 0.00 36.45 3.58
70 71 1.634702 GGAGCTGAGTCTTTGTAGCG 58.365 55.000 0.00 0.00 40.92 4.26
71 72 0.995728 GAGCTGAGTCTTTGTAGCGC 59.004 55.000 0.00 0.00 40.92 5.92
72 73 0.734253 AGCTGAGTCTTTGTAGCGCG 60.734 55.000 0.00 0.00 40.92 6.86
73 74 1.009389 GCTGAGTCTTTGTAGCGCGT 61.009 55.000 8.43 0.00 0.00 6.01
74 75 0.985549 CTGAGTCTTTGTAGCGCGTC 59.014 55.000 8.43 0.00 0.00 5.19
75 76 0.312729 TGAGTCTTTGTAGCGCGTCA 59.687 50.000 8.43 2.02 0.00 4.35
76 77 1.269361 TGAGTCTTTGTAGCGCGTCAA 60.269 47.619 8.43 14.25 0.00 3.18
77 78 1.124477 GAGTCTTTGTAGCGCGTCAAC 59.876 52.381 16.99 4.20 0.00 3.18
78 79 0.163146 GTCTTTGTAGCGCGTCAACC 59.837 55.000 16.99 7.30 0.00 3.77
79 80 1.129809 CTTTGTAGCGCGTCAACCG 59.870 57.895 16.99 9.57 40.40 4.44
80 81 2.222953 CTTTGTAGCGCGTCAACCGG 62.223 60.000 16.99 0.00 36.94 5.28
87 88 2.818274 GCGTCAACCGGGGATCAC 60.818 66.667 6.32 0.00 36.94 3.06
100 101 0.832135 GGATCACCCCTATCTCCGCA 60.832 60.000 0.00 0.00 0.00 5.69
109 110 1.625315 CCTATCTCCGCATGATCCCAA 59.375 52.381 0.00 0.00 0.00 4.12
111 112 0.839277 ATCTCCGCATGATCCCAACA 59.161 50.000 0.00 0.00 0.00 3.33
113 114 1.202687 TCTCCGCATGATCCCAACATC 60.203 52.381 0.00 0.00 0.00 3.06
153 154 0.611062 TTGGAGGAGATCACCGTCGT 60.611 55.000 3.31 0.00 34.73 4.34
154 155 0.611062 TGGAGGAGATCACCGTCGTT 60.611 55.000 3.31 0.00 34.73 3.85
161 162 0.944311 GATCACCGTCGTTGCACACT 60.944 55.000 0.00 0.00 0.00 3.55
182 183 0.758123 CCATTTGCACACCCCACTTT 59.242 50.000 0.00 0.00 0.00 2.66
192 193 4.407365 CACACCCCACTTTAAATCCTTCT 58.593 43.478 0.00 0.00 0.00 2.85
202 203 5.703130 ACTTTAAATCCTTCTCACACTCTGC 59.297 40.000 0.00 0.00 0.00 4.26
207 208 1.085091 CTTCTCACACTCTGCCATGC 58.915 55.000 0.00 0.00 0.00 4.06
247 249 1.369625 GTGACCCTAAACATCAGCCG 58.630 55.000 0.00 0.00 0.00 5.52
248 250 0.981183 TGACCCTAAACATCAGCCGT 59.019 50.000 0.00 0.00 0.00 5.68
252 254 1.338674 CCCTAAACATCAGCCGTCACA 60.339 52.381 0.00 0.00 0.00 3.58
266 268 2.290464 CGTCACAACCTAAAACCACCA 58.710 47.619 0.00 0.00 0.00 4.17
269 271 4.142038 GTCACAACCTAAAACCACCAGAT 58.858 43.478 0.00 0.00 0.00 2.90
270 272 4.583073 GTCACAACCTAAAACCACCAGATT 59.417 41.667 0.00 0.00 0.00 2.40
278 280 0.620556 AACCACCAGATTCGATGCCT 59.379 50.000 0.00 0.00 0.00 4.75
289 291 0.665298 TCGATGCCTCATGAGACGAG 59.335 55.000 24.62 8.29 0.00 4.18
290 292 0.665298 CGATGCCTCATGAGACGAGA 59.335 55.000 24.62 0.00 31.84 4.04
291 293 1.334870 CGATGCCTCATGAGACGAGAG 60.335 57.143 24.62 7.15 31.84 3.20
295 297 1.039785 CCTCATGAGACGAGAGGCCA 61.040 60.000 24.62 0.00 43.69 5.36
296 298 0.102120 CTCATGAGACGAGAGGCCAC 59.898 60.000 18.34 0.00 43.69 5.01
307 313 0.547712 AGAGGCCACCTTCCTAGCAA 60.548 55.000 5.01 0.00 31.76 3.91
311 317 1.019805 GCCACCTTCCTAGCAACGTC 61.020 60.000 0.00 0.00 0.00 4.34
316 322 1.927174 CCTTCCTAGCAACGTCGATTG 59.073 52.381 0.00 1.13 0.00 2.67
322 328 0.865769 AGCAACGTCGATTGGAACAC 59.134 50.000 0.00 0.00 39.29 3.32
326 332 2.024868 CGTCGATTGGAACACCGCA 61.025 57.895 0.00 0.00 39.29 5.69
327 333 1.561717 CGTCGATTGGAACACCGCAA 61.562 55.000 0.00 0.00 39.29 4.85
346 369 4.142902 CGCAAGACCAAATTATTCTCACGT 60.143 41.667 0.00 0.00 43.02 4.49
402 425 1.063567 ACAAACCCCAACCTAGCAACA 60.064 47.619 0.00 0.00 0.00 3.33
403 426 1.339929 CAAACCCCAACCTAGCAACAC 59.660 52.381 0.00 0.00 0.00 3.32
411 434 2.677003 CCTAGCAACACCAACGCCG 61.677 63.158 0.00 0.00 0.00 6.46
446 493 4.063967 CGTAGAGCCACGGCCACA 62.064 66.667 2.24 0.00 43.17 4.17
470 517 3.615592 CGACGAAGATGGGGAAAGTTACA 60.616 47.826 0.00 0.00 0.00 2.41
495 542 1.010419 AGGTTGGCGTTACGTTAGCG 61.010 55.000 6.63 0.00 44.93 4.26
510 557 3.120338 CGTTAGCGCCATCAAAAGAAAGA 60.120 43.478 2.29 0.00 0.00 2.52
512 559 1.541588 AGCGCCATCAAAAGAAAGACC 59.458 47.619 2.29 0.00 0.00 3.85
513 560 1.541588 GCGCCATCAAAAGAAAGACCT 59.458 47.619 0.00 0.00 0.00 3.85
514 561 2.414691 GCGCCATCAAAAGAAAGACCTC 60.415 50.000 0.00 0.00 0.00 3.85
515 562 2.162408 CGCCATCAAAAGAAAGACCTCC 59.838 50.000 0.00 0.00 0.00 4.30
516 563 3.157087 GCCATCAAAAGAAAGACCTCCA 58.843 45.455 0.00 0.00 0.00 3.86
517 564 3.192212 GCCATCAAAAGAAAGACCTCCAG 59.808 47.826 0.00 0.00 0.00 3.86
518 565 4.401925 CCATCAAAAGAAAGACCTCCAGT 58.598 43.478 0.00 0.00 0.00 4.00
519 566 4.829492 CCATCAAAAGAAAGACCTCCAGTT 59.171 41.667 0.00 0.00 0.00 3.16
520 567 5.048434 CCATCAAAAGAAAGACCTCCAGTTC 60.048 44.000 0.00 0.00 0.00 3.01
521 568 5.110814 TCAAAAGAAAGACCTCCAGTTCA 57.889 39.130 0.00 0.00 0.00 3.18
522 569 5.126067 TCAAAAGAAAGACCTCCAGTTCAG 58.874 41.667 0.00 0.00 0.00 3.02
523 570 4.779993 AAAGAAAGACCTCCAGTTCAGT 57.220 40.909 0.00 0.00 0.00 3.41
524 571 3.760580 AGAAAGACCTCCAGTTCAGTG 57.239 47.619 0.00 0.00 0.00 3.66
525 572 2.370189 AGAAAGACCTCCAGTTCAGTGG 59.630 50.000 0.00 0.00 39.19 4.00
526 573 0.398318 AAGACCTCCAGTTCAGTGGC 59.602 55.000 0.00 0.00 37.53 5.01
527 574 1.374758 GACCTCCAGTTCAGTGGCG 60.375 63.158 0.00 0.00 37.53 5.69
528 575 2.046892 CCTCCAGTTCAGTGGCGG 60.047 66.667 0.00 0.00 36.13 6.13
529 576 2.583441 CCTCCAGTTCAGTGGCGGA 61.583 63.158 3.84 0.00 44.24 5.54
530 577 1.079543 CTCCAGTTCAGTGGCGGAG 60.080 63.158 0.00 0.00 37.53 4.63
531 578 2.046892 CCAGTTCAGTGGCGGAGG 60.047 66.667 0.00 0.00 0.00 4.30
549 596 3.569210 CACAGGTGGGGCCAGACA 61.569 66.667 4.39 0.00 40.61 3.41
550 597 3.252284 ACAGGTGGGGCCAGACAG 61.252 66.667 4.39 0.55 40.61 3.51
551 598 4.039092 CAGGTGGGGCCAGACAGG 62.039 72.222 4.39 0.00 40.61 4.00
573 620 4.191015 GGGCCCTCCCGAACATCC 62.191 72.222 17.04 0.00 43.94 3.51
574 621 3.090532 GGCCCTCCCGAACATCCT 61.091 66.667 0.00 0.00 0.00 3.24
575 622 1.764854 GGCCCTCCCGAACATCCTA 60.765 63.158 0.00 0.00 0.00 2.94
576 623 1.342672 GGCCCTCCCGAACATCCTAA 61.343 60.000 0.00 0.00 0.00 2.69
577 624 0.765510 GCCCTCCCGAACATCCTAAT 59.234 55.000 0.00 0.00 0.00 1.73
578 625 1.543429 GCCCTCCCGAACATCCTAATG 60.543 57.143 0.00 0.00 38.93 1.90
580 627 2.224305 CCCTCCCGAACATCCTAATGTC 60.224 54.545 0.00 0.00 45.48 3.06
581 628 2.224305 CCTCCCGAACATCCTAATGTCC 60.224 54.545 0.00 0.00 45.48 4.02
582 629 2.700897 CTCCCGAACATCCTAATGTCCT 59.299 50.000 0.00 0.00 45.48 3.85
583 630 3.112263 TCCCGAACATCCTAATGTCCTT 58.888 45.455 0.00 0.00 45.48 3.36
584 631 3.118408 TCCCGAACATCCTAATGTCCTTG 60.118 47.826 0.00 0.00 45.48 3.61
585 632 3.206150 CCGAACATCCTAATGTCCTTGG 58.794 50.000 0.00 0.00 45.48 3.61
586 633 3.370527 CCGAACATCCTAATGTCCTTGGT 60.371 47.826 0.00 0.00 45.48 3.67
587 634 4.141801 CCGAACATCCTAATGTCCTTGGTA 60.142 45.833 0.00 0.00 45.48 3.25
588 635 5.424757 CGAACATCCTAATGTCCTTGGTAA 58.575 41.667 0.00 0.00 45.48 2.85
589 636 6.055588 CGAACATCCTAATGTCCTTGGTAAT 58.944 40.000 0.00 0.00 45.48 1.89
590 637 7.214381 CGAACATCCTAATGTCCTTGGTAATA 58.786 38.462 0.00 0.00 45.48 0.98
591 638 7.878127 CGAACATCCTAATGTCCTTGGTAATAT 59.122 37.037 0.00 0.00 45.48 1.28
592 639 9.574516 GAACATCCTAATGTCCTTGGTAATATT 57.425 33.333 0.00 0.00 45.48 1.28
593 640 9.574516 AACATCCTAATGTCCTTGGTAATATTC 57.425 33.333 0.00 0.00 45.48 1.75
594 641 8.723365 ACATCCTAATGTCCTTGGTAATATTCA 58.277 33.333 0.00 0.00 42.59 2.57
595 642 9.745018 CATCCTAATGTCCTTGGTAATATTCAT 57.255 33.333 0.00 0.00 0.00 2.57
603 650 9.559732 TGTCCTTGGTAATATTCATATGAACAG 57.440 33.333 20.19 3.16 36.80 3.16
604 651 9.561069 GTCCTTGGTAATATTCATATGAACAGT 57.439 33.333 20.19 11.08 36.80 3.55
605 652 9.559732 TCCTTGGTAATATTCATATGAACAGTG 57.440 33.333 20.19 9.07 36.80 3.66
606 653 9.559732 CCTTGGTAATATTCATATGAACAGTGA 57.440 33.333 20.19 4.58 36.80 3.41
632 679 1.803334 TTTACTGTTACCTGCAGCCG 58.197 50.000 8.66 0.00 37.47 5.52
633 680 0.036765 TTACTGTTACCTGCAGCCGG 60.037 55.000 8.66 0.00 37.47 6.13
634 681 2.515996 TACTGTTACCTGCAGCCGGC 62.516 60.000 21.89 21.89 45.13 6.13
635 682 4.715523 TGTTACCTGCAGCCGGCC 62.716 66.667 26.15 9.73 43.89 6.13
649 696 2.686106 GGCCCTCCCCAACGTCTA 60.686 66.667 0.00 0.00 0.00 2.59
650 697 2.295602 GGCCCTCCCCAACGTCTAA 61.296 63.158 0.00 0.00 0.00 2.10
651 698 1.632965 GGCCCTCCCCAACGTCTAAT 61.633 60.000 0.00 0.00 0.00 1.73
652 699 0.255033 GCCCTCCCCAACGTCTAATT 59.745 55.000 0.00 0.00 0.00 1.40
653 700 1.487558 GCCCTCCCCAACGTCTAATTA 59.512 52.381 0.00 0.00 0.00 1.40
654 701 2.105993 GCCCTCCCCAACGTCTAATTAT 59.894 50.000 0.00 0.00 0.00 1.28
655 702 3.325716 GCCCTCCCCAACGTCTAATTATA 59.674 47.826 0.00 0.00 0.00 0.98
656 703 4.019591 GCCCTCCCCAACGTCTAATTATAT 60.020 45.833 0.00 0.00 0.00 0.86
657 704 5.488341 CCCTCCCCAACGTCTAATTATATG 58.512 45.833 0.00 0.00 0.00 1.78
658 705 4.935808 CCTCCCCAACGTCTAATTATATGC 59.064 45.833 0.00 0.00 0.00 3.14
659 706 5.512404 CCTCCCCAACGTCTAATTATATGCA 60.512 44.000 0.00 0.00 0.00 3.96
660 707 6.121776 TCCCCAACGTCTAATTATATGCAT 57.878 37.500 3.79 3.79 0.00 3.96
661 708 6.539173 TCCCCAACGTCTAATTATATGCATT 58.461 36.000 3.54 0.00 0.00 3.56
662 709 6.653320 TCCCCAACGTCTAATTATATGCATTC 59.347 38.462 3.54 0.00 0.00 2.67
663 710 6.128007 CCCCAACGTCTAATTATATGCATTCC 60.128 42.308 3.54 0.00 0.00 3.01
664 711 6.655003 CCCAACGTCTAATTATATGCATTCCT 59.345 38.462 3.54 0.00 0.00 3.36
665 712 7.361201 CCCAACGTCTAATTATATGCATTCCTG 60.361 40.741 3.54 0.00 0.00 3.86
674 721 4.802051 GCATTCCTGCCTCCGCCA 62.802 66.667 0.00 0.00 42.88 5.69
675 722 2.825836 CATTCCTGCCTCCGCCAC 60.826 66.667 0.00 0.00 0.00 5.01
676 723 3.011517 ATTCCTGCCTCCGCCACT 61.012 61.111 0.00 0.00 0.00 4.00
677 724 3.335356 ATTCCTGCCTCCGCCACTG 62.335 63.158 0.00 0.00 0.00 3.66
690 737 1.303643 CCACTGCTCCAGTTTCCCC 60.304 63.158 0.00 0.00 42.59 4.81
701 748 0.470766 AGTTTCCCCGTAACACAGCA 59.529 50.000 0.00 0.00 0.00 4.41
814 866 2.253758 CGGTTCCCCTGCATATGCG 61.254 63.158 22.21 16.10 45.83 4.73
908 960 0.839946 CCGATCCAACCTCCCAATCT 59.160 55.000 0.00 0.00 0.00 2.40
914 966 1.849039 CCAACCTCCCAATCTCATCCT 59.151 52.381 0.00 0.00 0.00 3.24
951 1005 2.574955 CCACCTCGATCGATCCCCC 61.575 68.421 19.78 0.00 0.00 5.40
986 1044 4.835891 CTCCTCCCCGCGGTACCT 62.836 72.222 26.12 0.00 0.00 3.08
1071 1135 3.799755 GACATGGCCGACCGCAAC 61.800 66.667 0.00 0.00 40.31 4.17
1168 1268 2.675423 AGGGCGACTACAGCGACA 60.675 61.111 0.00 0.00 38.88 4.35
2791 2942 2.030562 CGAAGAACCTGGTGCGGT 59.969 61.111 0.00 0.00 39.48 5.68
2903 3054 1.073444 CTGATAGCCCAGCCATGATGT 59.927 52.381 0.00 0.00 0.00 3.06
2922 3073 4.961435 TGTATCATCGATTTGCTTTGCA 57.039 36.364 0.00 0.00 36.47 4.08
2928 3079 4.626604 TCATCGATTTGCTTTGCATTTTCC 59.373 37.500 0.00 0.00 38.76 3.13
2932 3083 4.687483 CGATTTGCTTTGCATTTTCCTTCT 59.313 37.500 0.00 0.00 38.76 2.85
2937 3088 3.059393 GCTTTGCATTTTCCTTCTGTTGC 60.059 43.478 0.00 0.00 0.00 4.17
2960 3122 5.586643 GCTTTGCTACTAGCTAGGTGAAATT 59.413 40.000 24.35 4.44 42.97 1.82
2990 3152 2.962786 TGAACCGAACGCGTGTGG 60.963 61.111 23.91 23.91 35.23 4.17
3068 3235 4.346129 CTTGCTTGTGACTGTTTGAACTC 58.654 43.478 0.00 0.00 0.00 3.01
3101 3268 6.614694 TGGTTATTCTTCAGTTACAGCCTA 57.385 37.500 0.00 0.00 0.00 3.93
3102 3269 6.640518 TGGTTATTCTTCAGTTACAGCCTAG 58.359 40.000 0.00 0.00 0.00 3.02
3103 3270 6.212791 TGGTTATTCTTCAGTTACAGCCTAGT 59.787 38.462 0.00 0.00 0.00 2.57
3104 3271 7.398047 TGGTTATTCTTCAGTTACAGCCTAGTA 59.602 37.037 0.00 0.00 0.00 1.82
3105 3272 8.255905 GGTTATTCTTCAGTTACAGCCTAGTAA 58.744 37.037 0.00 0.00 0.00 2.24
3106 3273 9.819267 GTTATTCTTCAGTTACAGCCTAGTAAT 57.181 33.333 0.00 0.00 36.47 1.89
3107 3274 9.817809 TTATTCTTCAGTTACAGCCTAGTAATG 57.182 33.333 0.00 0.00 36.47 1.90
3108 3275 7.476540 TTCTTCAGTTACAGCCTAGTAATGA 57.523 36.000 0.00 0.00 36.47 2.57
3121 3301 6.552350 AGCCTAGTAATGAAATCCAATTGCAT 59.448 34.615 0.00 0.00 40.27 3.96
3219 3409 6.515832 ACCTCCAAAATGATTCAGTTTTGTC 58.484 36.000 20.44 0.00 41.43 3.18
3273 3464 2.016318 CTGGTCGGCTGAAATGCATAA 58.984 47.619 0.00 0.00 34.04 1.90
3292 3516 6.582672 TGCATAATTCGTTCTATAGCTTCTCG 59.417 38.462 0.00 0.00 0.00 4.04
3320 3544 1.084289 GAATGTAGCGGTTCACCACC 58.916 55.000 0.00 0.00 43.16 4.61
3339 3575 1.826720 CCCACCAAAGTGCAGCATTAT 59.173 47.619 0.00 0.00 43.09 1.28
3349 3604 7.009815 CCAAAGTGCAGCATTATAATTTCTGTG 59.990 37.037 18.49 11.90 0.00 3.66
3350 3605 7.395190 AAGTGCAGCATTATAATTTCTGTGA 57.605 32.000 18.49 8.85 0.00 3.58
3351 3606 7.578310 AGTGCAGCATTATAATTTCTGTGAT 57.422 32.000 18.49 8.03 0.00 3.06
3352 3607 7.646314 AGTGCAGCATTATAATTTCTGTGATC 58.354 34.615 18.49 8.43 0.00 2.92
3353 3608 6.576313 GTGCAGCATTATAATTTCTGTGATCG 59.424 38.462 18.49 0.00 0.00 3.69
3354 3609 6.260714 TGCAGCATTATAATTTCTGTGATCGT 59.739 34.615 18.49 0.00 0.00 3.73
3355 3610 6.576313 GCAGCATTATAATTTCTGTGATCGTG 59.424 38.462 18.49 0.02 0.00 4.35
3356 3611 6.576313 CAGCATTATAATTTCTGTGATCGTGC 59.424 38.462 12.90 4.32 0.00 5.34
3357 3612 5.561499 GCATTATAATTTCTGTGATCGTGCG 59.439 40.000 0.00 0.00 0.00 5.34
3358 3613 6.649436 CATTATAATTTCTGTGATCGTGCGT 58.351 36.000 0.00 0.00 0.00 5.24
3418 3675 7.954447 TGAATTTATTTAATTTTTGGGTCGCG 58.046 30.769 0.00 0.00 36.59 5.87
3625 3884 6.785337 TCTTCGAAACTAGATCCCATGTTA 57.215 37.500 0.00 0.00 0.00 2.41
3639 3898 9.645128 AGATCCCATGTTAATATGTTTTGATGA 57.355 29.630 10.82 0.00 0.00 2.92
3710 3971 5.159273 TGATGTACACTGAAGTTGCCATA 57.841 39.130 0.00 0.00 0.00 2.74
3798 4059 3.997021 AGAAACTAGACTTGCCATGAACG 59.003 43.478 0.00 0.00 0.00 3.95
3837 4098 6.264832 CCATGATACATGCACGTAAAATTGT 58.735 36.000 0.00 0.00 0.00 2.71
3848 4109 6.072452 TGCACGTAAAATTGTCATGGTTCATA 60.072 34.615 0.00 0.00 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 3.758554 GGCTCAAAAGGCAGATTTGTCTA 59.241 43.478 0.00 0.00 46.99 2.59
5 6 2.951726 GGCTCAAAAGGCAGATTTGTC 58.048 47.619 9.30 0.00 46.99 3.18
14 15 2.533266 CATTTCATCGGCTCAAAAGGC 58.467 47.619 0.00 0.00 44.42 4.35
15 16 2.493278 ACCATTTCATCGGCTCAAAAGG 59.507 45.455 0.00 0.00 0.00 3.11
16 17 3.428045 GGACCATTTCATCGGCTCAAAAG 60.428 47.826 0.00 0.00 0.00 2.27
17 18 2.491693 GGACCATTTCATCGGCTCAAAA 59.508 45.455 0.00 0.00 0.00 2.44
18 19 2.091541 GGACCATTTCATCGGCTCAAA 58.908 47.619 0.00 0.00 0.00 2.69
19 20 1.004161 TGGACCATTTCATCGGCTCAA 59.996 47.619 0.00 0.00 0.00 3.02
20 21 0.617935 TGGACCATTTCATCGGCTCA 59.382 50.000 0.00 0.00 0.00 4.26
21 22 1.876156 GATGGACCATTTCATCGGCTC 59.124 52.381 8.78 0.00 31.83 4.70
22 23 1.972872 GATGGACCATTTCATCGGCT 58.027 50.000 8.78 0.00 31.83 5.52
26 27 2.016318 TGTGCGATGGACCATTTCATC 58.984 47.619 8.78 0.00 37.12 2.92
27 28 2.127271 TGTGCGATGGACCATTTCAT 57.873 45.000 8.78 0.00 0.00 2.57
28 29 1.744522 CATGTGCGATGGACCATTTCA 59.255 47.619 8.78 6.95 0.00 2.69
29 30 2.016318 TCATGTGCGATGGACCATTTC 58.984 47.619 8.78 4.28 0.00 2.17
30 31 1.745087 GTCATGTGCGATGGACCATTT 59.255 47.619 8.78 0.00 0.00 2.32
31 32 1.382522 GTCATGTGCGATGGACCATT 58.617 50.000 8.78 0.00 0.00 3.16
32 33 0.811219 CGTCATGTGCGATGGACCAT 60.811 55.000 6.71 6.71 0.00 3.55
33 34 1.447663 CGTCATGTGCGATGGACCA 60.448 57.895 0.00 0.00 0.00 4.02
34 35 2.173669 CCGTCATGTGCGATGGACC 61.174 63.158 12.49 0.00 43.72 4.46
35 36 1.148157 CTCCGTCATGTGCGATGGAC 61.148 60.000 12.49 0.00 44.49 4.02
36 37 1.141665 CTCCGTCATGTGCGATGGA 59.858 57.895 12.49 2.11 46.65 3.41
37 38 2.528743 GCTCCGTCATGTGCGATGG 61.529 63.158 12.49 0.00 42.57 3.51
38 39 1.520120 AGCTCCGTCATGTGCGATG 60.520 57.895 12.49 6.98 0.00 3.84
39 40 1.520120 CAGCTCCGTCATGTGCGAT 60.520 57.895 12.49 0.00 0.00 4.58
40 41 2.125952 CAGCTCCGTCATGTGCGA 60.126 61.111 12.49 0.00 0.00 5.10
41 42 2.125952 TCAGCTCCGTCATGTGCG 60.126 61.111 0.00 0.00 0.00 5.34
42 43 1.079543 ACTCAGCTCCGTCATGTGC 60.080 57.895 0.00 0.00 0.00 4.57
43 44 0.529833 AGACTCAGCTCCGTCATGTG 59.470 55.000 12.89 0.00 32.68 3.21
44 45 1.261480 AAGACTCAGCTCCGTCATGT 58.739 50.000 12.89 0.00 32.68 3.21
45 46 1.998315 CAAAGACTCAGCTCCGTCATG 59.002 52.381 12.89 8.32 32.68 3.07
46 47 1.620819 ACAAAGACTCAGCTCCGTCAT 59.379 47.619 12.89 0.26 32.68 3.06
47 48 1.040646 ACAAAGACTCAGCTCCGTCA 58.959 50.000 12.89 0.00 32.68 4.35
48 49 2.869897 CTACAAAGACTCAGCTCCGTC 58.130 52.381 4.16 4.16 0.00 4.79
49 50 1.067495 GCTACAAAGACTCAGCTCCGT 60.067 52.381 0.00 0.00 0.00 4.69
50 51 1.634702 GCTACAAAGACTCAGCTCCG 58.365 55.000 0.00 0.00 0.00 4.63
51 52 1.634702 CGCTACAAAGACTCAGCTCC 58.365 55.000 0.00 0.00 31.74 4.70
52 53 0.995728 GCGCTACAAAGACTCAGCTC 59.004 55.000 0.00 0.00 31.74 4.09
53 54 0.734253 CGCGCTACAAAGACTCAGCT 60.734 55.000 5.56 0.00 31.74 4.24
54 55 1.009389 ACGCGCTACAAAGACTCAGC 61.009 55.000 5.73 0.00 0.00 4.26
55 56 0.985549 GACGCGCTACAAAGACTCAG 59.014 55.000 5.73 0.00 0.00 3.35
56 57 0.312729 TGACGCGCTACAAAGACTCA 59.687 50.000 5.73 0.00 0.00 3.41
57 58 1.124477 GTTGACGCGCTACAAAGACTC 59.876 52.381 5.73 0.00 0.00 3.36
58 59 1.137513 GTTGACGCGCTACAAAGACT 58.862 50.000 5.73 0.00 0.00 3.24
59 60 0.163146 GGTTGACGCGCTACAAAGAC 59.837 55.000 5.73 6.58 0.00 3.01
60 61 1.279527 CGGTTGACGCGCTACAAAGA 61.280 55.000 5.73 0.00 34.82 2.52
61 62 1.129809 CGGTTGACGCGCTACAAAG 59.870 57.895 5.73 10.25 34.82 2.77
62 63 2.311701 CCGGTTGACGCGCTACAAA 61.312 57.895 5.73 0.00 42.52 2.83
63 64 2.735478 CCGGTTGACGCGCTACAA 60.735 61.111 5.73 8.03 42.52 2.41
64 65 4.728102 CCCGGTTGACGCGCTACA 62.728 66.667 5.73 0.68 42.52 2.74
69 70 4.444838 TGATCCCCGGTTGACGCG 62.445 66.667 3.53 3.53 42.52 6.01
70 71 2.818274 GTGATCCCCGGTTGACGC 60.818 66.667 0.00 0.00 42.52 5.19
71 72 2.125269 GGTGATCCCCGGTTGACG 60.125 66.667 0.00 0.00 43.80 4.35
81 82 0.832135 TGCGGAGATAGGGGTGATCC 60.832 60.000 0.00 0.00 0.00 3.36
82 83 1.066573 CATGCGGAGATAGGGGTGATC 60.067 57.143 0.00 0.00 0.00 2.92
87 88 0.539051 GGATCATGCGGAGATAGGGG 59.461 60.000 0.00 0.00 0.00 4.79
90 91 2.037641 TGTTGGGATCATGCGGAGATAG 59.962 50.000 0.00 0.00 0.00 2.08
100 101 1.757118 AGTCGACGATGTTGGGATCAT 59.243 47.619 10.46 0.00 0.00 2.45
109 110 2.519377 TTGGTTGAAGTCGACGATGT 57.481 45.000 10.46 0.00 0.00 3.06
111 112 1.732259 GCATTGGTTGAAGTCGACGAT 59.268 47.619 10.46 2.88 0.00 3.73
113 114 0.865111 TGCATTGGTTGAAGTCGACG 59.135 50.000 10.46 0.00 0.00 5.12
140 141 0.666274 TGTGCAACGACGGTGATCTC 60.666 55.000 18.96 0.00 42.39 2.75
146 147 3.269347 GCAGTGTGCAACGACGGT 61.269 61.111 0.00 0.00 44.26 4.83
178 179 5.703130 GCAGAGTGTGAGAAGGATTTAAAGT 59.297 40.000 0.00 0.00 0.00 2.66
182 183 3.582647 TGGCAGAGTGTGAGAAGGATTTA 59.417 43.478 0.00 0.00 0.00 1.40
192 193 2.046988 CGGCATGGCAGAGTGTGA 60.047 61.111 20.37 0.00 0.00 3.58
233 235 2.093306 TGTGACGGCTGATGTTTAGG 57.907 50.000 0.00 0.00 0.00 2.69
242 244 1.265905 GGTTTTAGGTTGTGACGGCTG 59.734 52.381 0.00 0.00 0.00 4.85
247 249 3.547746 TCTGGTGGTTTTAGGTTGTGAC 58.452 45.455 0.00 0.00 0.00 3.67
248 250 3.935818 TCTGGTGGTTTTAGGTTGTGA 57.064 42.857 0.00 0.00 0.00 3.58
252 254 4.360951 TCGAATCTGGTGGTTTTAGGTT 57.639 40.909 0.00 0.00 0.00 3.50
266 268 2.288091 CGTCTCATGAGGCATCGAATCT 60.288 50.000 26.10 0.00 31.14 2.40
269 271 1.066152 CTCGTCTCATGAGGCATCGAA 59.934 52.381 26.10 5.77 31.14 3.71
270 272 0.665298 CTCGTCTCATGAGGCATCGA 59.335 55.000 26.10 23.25 31.14 3.59
278 280 1.323271 GGTGGCCTCTCGTCTCATGA 61.323 60.000 3.32 0.00 0.00 3.07
289 291 0.393132 GTTGCTAGGAAGGTGGCCTC 60.393 60.000 3.32 0.00 36.96 4.70
290 292 1.685820 GTTGCTAGGAAGGTGGCCT 59.314 57.895 3.32 0.00 39.56 5.19
291 293 1.745489 CGTTGCTAGGAAGGTGGCC 60.745 63.158 8.37 0.00 0.00 5.36
293 295 0.736325 CGACGTTGCTAGGAAGGTGG 60.736 60.000 24.33 19.50 0.00 4.61
295 297 1.183549 ATCGACGTTGCTAGGAAGGT 58.816 50.000 20.34 20.34 0.00 3.50
296 298 1.927174 CAATCGACGTTGCTAGGAAGG 59.073 52.381 14.24 14.24 0.00 3.46
307 313 2.025418 GCGGTGTTCCAATCGACGT 61.025 57.895 0.00 0.00 0.00 4.34
311 317 0.165944 GTCTTGCGGTGTTCCAATCG 59.834 55.000 0.00 0.00 0.00 3.34
316 322 0.958822 ATTTGGTCTTGCGGTGTTCC 59.041 50.000 0.00 0.00 0.00 3.62
322 328 4.662145 GTGAGAATAATTTGGTCTTGCGG 58.338 43.478 0.00 0.00 0.00 5.69
326 332 4.156008 GCCACGTGAGAATAATTTGGTCTT 59.844 41.667 19.30 0.00 0.00 3.01
327 333 3.689649 GCCACGTGAGAATAATTTGGTCT 59.310 43.478 19.30 0.00 0.00 3.85
367 390 4.700692 GGGGTTTGTTTTCATAGAGGAGTC 59.299 45.833 0.00 0.00 0.00 3.36
370 393 4.733077 TGGGGTTTGTTTTCATAGAGGA 57.267 40.909 0.00 0.00 0.00 3.71
372 395 4.832823 AGGTTGGGGTTTGTTTTCATAGAG 59.167 41.667 0.00 0.00 0.00 2.43
446 493 0.249398 CTTTCCCCATCTTCGTCGGT 59.751 55.000 0.00 0.00 0.00 4.69
495 542 3.157087 TGGAGGTCTTTCTTTTGATGGC 58.843 45.455 0.00 0.00 0.00 4.40
510 557 2.743718 CGCCACTGAACTGGAGGT 59.256 61.111 0.00 0.00 32.30 3.85
512 559 1.079543 CTCCGCCACTGAACTGGAG 60.080 63.158 0.00 0.00 40.19 3.86
513 560 2.583441 CCTCCGCCACTGAACTGGA 61.583 63.158 0.00 0.00 32.30 3.86
514 561 2.046892 CCTCCGCCACTGAACTGG 60.047 66.667 0.00 0.00 0.00 4.00
515 562 2.743928 GCCTCCGCCACTGAACTG 60.744 66.667 0.00 0.00 0.00 3.16
516 563 3.241530 TGCCTCCGCCACTGAACT 61.242 61.111 0.00 0.00 0.00 3.01
517 564 3.050275 GTGCCTCCGCCACTGAAC 61.050 66.667 0.00 0.00 0.00 3.18
518 565 3.535629 CTGTGCCTCCGCCACTGAA 62.536 63.158 0.00 0.00 0.00 3.02
519 566 4.007644 CTGTGCCTCCGCCACTGA 62.008 66.667 0.00 0.00 0.00 3.41
532 579 3.557903 CTGTCTGGCCCCACCTGTG 62.558 68.421 0.00 0.00 40.22 3.66
533 580 3.252284 CTGTCTGGCCCCACCTGT 61.252 66.667 0.00 0.00 40.22 4.00
534 581 4.039092 CCTGTCTGGCCCCACCTG 62.039 72.222 0.00 0.00 40.22 4.00
557 604 1.342672 TTAGGATGTTCGGGAGGGCC 61.343 60.000 0.00 0.00 0.00 5.80
558 605 0.765510 ATTAGGATGTTCGGGAGGGC 59.234 55.000 0.00 0.00 0.00 5.19
559 606 1.768870 ACATTAGGATGTTCGGGAGGG 59.231 52.381 0.00 0.00 43.92 4.30
560 607 2.224305 GGACATTAGGATGTTCGGGAGG 60.224 54.545 0.00 0.00 46.27 4.30
561 608 2.700897 AGGACATTAGGATGTTCGGGAG 59.299 50.000 0.00 0.00 46.27 4.30
562 609 2.759355 AGGACATTAGGATGTTCGGGA 58.241 47.619 0.00 0.00 46.27 5.14
563 610 3.206150 CAAGGACATTAGGATGTTCGGG 58.794 50.000 0.00 0.00 46.27 5.14
564 611 3.206150 CCAAGGACATTAGGATGTTCGG 58.794 50.000 0.00 0.00 46.27 4.30
565 612 3.873910 ACCAAGGACATTAGGATGTTCG 58.126 45.455 0.00 0.00 46.27 3.95
566 613 9.574516 AATATTACCAAGGACATTAGGATGTTC 57.425 33.333 0.00 0.00 46.27 3.18
567 614 9.574516 GAATATTACCAAGGACATTAGGATGTT 57.425 33.333 0.00 0.00 46.27 2.71
569 616 9.745018 ATGAATATTACCAAGGACATTAGGATG 57.255 33.333 0.00 0.00 39.25 3.51
577 624 9.559732 CTGTTCATATGAATATTACCAAGGACA 57.440 33.333 20.65 9.18 36.33 4.02
578 625 9.561069 ACTGTTCATATGAATATTACCAAGGAC 57.439 33.333 20.65 5.07 36.33 3.85
579 626 9.559732 CACTGTTCATATGAATATTACCAAGGA 57.440 33.333 20.65 0.00 36.33 3.36
580 627 9.559732 TCACTGTTCATATGAATATTACCAAGG 57.440 33.333 20.65 6.81 36.33 3.61
611 658 2.550606 CGGCTGCAGGTAACAGTAAAAA 59.449 45.455 17.12 0.00 37.47 1.94
612 659 2.147958 CGGCTGCAGGTAACAGTAAAA 58.852 47.619 17.12 0.00 37.47 1.52
613 660 1.609580 CCGGCTGCAGGTAACAGTAAA 60.610 52.381 17.12 0.00 37.47 2.01
614 661 0.036765 CCGGCTGCAGGTAACAGTAA 60.037 55.000 17.12 0.00 37.47 2.24
615 662 1.594833 CCGGCTGCAGGTAACAGTA 59.405 57.895 17.12 0.00 37.47 2.74
616 663 2.347490 CCGGCTGCAGGTAACAGT 59.653 61.111 17.12 0.00 37.47 3.55
617 664 3.127533 GCCGGCTGCAGGTAACAG 61.128 66.667 22.15 0.00 40.77 3.16
618 665 4.715523 GGCCGGCTGCAGGTAACA 62.716 66.667 28.56 0.00 43.89 2.41
632 679 1.632965 ATTAGACGTTGGGGAGGGCC 61.633 60.000 0.00 0.00 0.00 5.80
633 680 0.255033 AATTAGACGTTGGGGAGGGC 59.745 55.000 0.00 0.00 0.00 5.19
634 681 5.488341 CATATAATTAGACGTTGGGGAGGG 58.512 45.833 0.00 0.00 0.00 4.30
635 682 4.935808 GCATATAATTAGACGTTGGGGAGG 59.064 45.833 0.00 0.00 0.00 4.30
636 683 5.547465 TGCATATAATTAGACGTTGGGGAG 58.453 41.667 0.00 0.00 0.00 4.30
637 684 5.554437 TGCATATAATTAGACGTTGGGGA 57.446 39.130 0.00 0.00 0.00 4.81
638 685 6.128007 GGAATGCATATAATTAGACGTTGGGG 60.128 42.308 0.00 0.00 0.00 4.96
639 686 6.655003 AGGAATGCATATAATTAGACGTTGGG 59.345 38.462 0.00 0.00 0.00 4.12
640 687 7.521529 CAGGAATGCATATAATTAGACGTTGG 58.478 38.462 0.00 0.00 0.00 3.77
641 688 7.017645 GCAGGAATGCATATAATTAGACGTTG 58.982 38.462 0.00 0.00 34.41 4.10
642 689 6.149474 GGCAGGAATGCATATAATTAGACGTT 59.851 38.462 0.00 0.00 36.33 3.99
643 690 5.643777 GGCAGGAATGCATATAATTAGACGT 59.356 40.000 0.00 0.00 36.33 4.34
644 691 5.877012 AGGCAGGAATGCATATAATTAGACG 59.123 40.000 0.00 0.00 36.33 4.18
645 692 6.317391 GGAGGCAGGAATGCATATAATTAGAC 59.683 42.308 0.00 0.00 36.33 2.59
646 693 6.418101 GGAGGCAGGAATGCATATAATTAGA 58.582 40.000 0.00 0.00 36.33 2.10
647 694 5.295292 CGGAGGCAGGAATGCATATAATTAG 59.705 44.000 0.00 0.00 36.33 1.73
648 695 5.185454 CGGAGGCAGGAATGCATATAATTA 58.815 41.667 0.00 0.00 36.33 1.40
649 696 4.012374 CGGAGGCAGGAATGCATATAATT 58.988 43.478 0.00 0.00 36.33 1.40
650 697 3.614092 CGGAGGCAGGAATGCATATAAT 58.386 45.455 0.00 0.00 36.33 1.28
651 698 2.875672 GCGGAGGCAGGAATGCATATAA 60.876 50.000 0.00 0.00 39.62 0.98
652 699 1.339055 GCGGAGGCAGGAATGCATATA 60.339 52.381 0.00 0.00 39.62 0.86
653 700 0.607489 GCGGAGGCAGGAATGCATAT 60.607 55.000 0.00 0.00 39.62 1.78
654 701 1.227943 GCGGAGGCAGGAATGCATA 60.228 57.895 0.00 0.00 39.62 3.14
655 702 2.517875 GCGGAGGCAGGAATGCAT 60.518 61.111 0.00 0.00 39.62 3.96
667 714 2.738213 AAACTGGAGCAGTGGCGGAG 62.738 60.000 0.00 0.00 44.62 4.63
668 715 2.731691 GAAACTGGAGCAGTGGCGGA 62.732 60.000 0.00 0.00 44.62 5.54
669 716 2.281761 AAACTGGAGCAGTGGCGG 60.282 61.111 0.00 0.00 44.62 6.13
670 717 2.328099 GGAAACTGGAGCAGTGGCG 61.328 63.158 0.00 0.00 44.62 5.69
671 718 1.973812 GGGAAACTGGAGCAGTGGC 60.974 63.158 0.00 0.00 44.62 5.01
672 719 1.303643 GGGGAAACTGGAGCAGTGG 60.304 63.158 0.00 0.00 44.62 4.00
673 720 1.672356 CGGGGAAACTGGAGCAGTG 60.672 63.158 0.00 0.00 44.62 3.66
675 722 0.323629 TTACGGGGAAACTGGAGCAG 59.676 55.000 0.00 0.00 37.52 4.24
676 723 0.035739 GTTACGGGGAAACTGGAGCA 59.964 55.000 0.00 0.00 0.00 4.26
677 724 0.035739 TGTTACGGGGAAACTGGAGC 59.964 55.000 0.00 0.00 0.00 4.70
701 748 8.542497 TTCTCAAAATACGTTTAGCACTACAT 57.458 30.769 0.00 0.00 0.00 2.29
717 764 5.455392 GCTGCGCATGTATATTCTCAAAAT 58.545 37.500 12.24 0.00 0.00 1.82
734 783 2.486966 GATCCTTTGTGGCTGCGC 59.513 61.111 0.00 0.00 35.26 6.09
814 866 2.440247 CCGGGATCCTTTGTGGCC 60.440 66.667 12.58 0.00 35.26 5.36
908 960 1.294986 TGATTGGAGGAGGGAGGATGA 59.705 52.381 0.00 0.00 0.00 2.92
914 966 1.522900 GGGATTGATTGGAGGAGGGA 58.477 55.000 0.00 0.00 0.00 4.20
951 1005 0.845102 AGGTGGGGGTCTAGGGTTTG 60.845 60.000 0.00 0.00 0.00 2.93
982 1037 1.565390 ATGGCTGGCTTGCTGAGGTA 61.565 55.000 2.00 0.00 0.00 3.08
986 1044 2.361992 CCATGGCTGGCTTGCTGA 60.362 61.111 0.00 0.00 35.23 4.26
2484 2629 4.394712 AGGTTCGCGCCCTTCTGG 62.395 66.667 10.91 0.00 37.09 3.86
2791 2942 2.747686 GTCCGCCTCCAGGAACAA 59.252 61.111 0.00 0.00 39.84 2.83
2903 3054 6.476380 GGAAAATGCAAAGCAAATCGATGATA 59.524 34.615 0.00 0.00 43.62 2.15
2922 3073 4.677673 AGCAAAGCAACAGAAGGAAAAT 57.322 36.364 0.00 0.00 0.00 1.82
2928 3079 3.999663 AGCTAGTAGCAAAGCAACAGAAG 59.000 43.478 23.77 0.00 45.56 2.85
2932 3083 3.260884 ACCTAGCTAGTAGCAAAGCAACA 59.739 43.478 23.77 0.00 45.56 3.33
2937 3088 7.550906 AGAAATTTCACCTAGCTAGTAGCAAAG 59.449 37.037 23.77 18.57 45.56 2.77
2960 3122 1.686587 TCGGTTCACAGCTTCAGAGAA 59.313 47.619 0.00 0.00 0.00 2.87
2990 3152 7.548427 TCATTCATTCAGTTCAGAGATTCAGAC 59.452 37.037 0.00 0.00 0.00 3.51
3068 3235 5.295292 ACTGAAGAATAACCATGCAATCGAG 59.705 40.000 0.00 0.00 0.00 4.04
3238 3429 5.044558 GCCGACCAGAATACAAAACAAAAA 58.955 37.500 0.00 0.00 0.00 1.94
3239 3430 4.339814 AGCCGACCAGAATACAAAACAAAA 59.660 37.500 0.00 0.00 0.00 2.44
3240 3431 3.886505 AGCCGACCAGAATACAAAACAAA 59.113 39.130 0.00 0.00 0.00 2.83
3241 3432 3.252215 CAGCCGACCAGAATACAAAACAA 59.748 43.478 0.00 0.00 0.00 2.83
3242 3433 2.811431 CAGCCGACCAGAATACAAAACA 59.189 45.455 0.00 0.00 0.00 2.83
3243 3434 3.071479 TCAGCCGACCAGAATACAAAAC 58.929 45.455 0.00 0.00 0.00 2.43
3244 3435 3.410631 TCAGCCGACCAGAATACAAAA 57.589 42.857 0.00 0.00 0.00 2.44
3245 3436 3.410631 TTCAGCCGACCAGAATACAAA 57.589 42.857 0.00 0.00 0.00 2.83
3246 3437 3.410631 TTTCAGCCGACCAGAATACAA 57.589 42.857 0.00 0.00 0.00 2.41
3247 3438 3.270027 CATTTCAGCCGACCAGAATACA 58.730 45.455 0.00 0.00 0.00 2.29
3248 3439 2.032178 GCATTTCAGCCGACCAGAATAC 59.968 50.000 0.00 0.00 0.00 1.89
3249 3440 2.288666 GCATTTCAGCCGACCAGAATA 58.711 47.619 0.00 0.00 0.00 1.75
3250 3441 1.098050 GCATTTCAGCCGACCAGAAT 58.902 50.000 0.00 0.00 0.00 2.40
3251 3442 0.250684 TGCATTTCAGCCGACCAGAA 60.251 50.000 0.00 0.00 0.00 3.02
3252 3443 0.035152 ATGCATTTCAGCCGACCAGA 60.035 50.000 0.00 0.00 0.00 3.86
3257 3448 2.942376 ACGAATTATGCATTTCAGCCGA 59.058 40.909 3.54 0.00 0.00 5.54
3258 3449 3.338818 ACGAATTATGCATTTCAGCCG 57.661 42.857 3.54 4.51 0.00 5.52
3273 3464 5.278071 CCTCACGAGAAGCTATAGAACGAAT 60.278 44.000 3.21 0.00 0.00 3.34
3292 3516 3.454371 ACCGCTACATTCATACCTCAC 57.546 47.619 0.00 0.00 0.00 3.51
3320 3544 4.717233 TTATAATGCTGCACTTTGGTGG 57.283 40.909 3.57 0.00 43.18 4.61
3339 3575 4.924462 TGTTACGCACGATCACAGAAATTA 59.076 37.500 0.00 0.00 0.00 1.40
3349 3604 5.144359 ACATTTTTCTTGTTACGCACGATC 58.856 37.500 0.00 0.00 0.00 3.69
3350 3605 5.103290 ACATTTTTCTTGTTACGCACGAT 57.897 34.783 0.00 0.00 0.00 3.73
3351 3606 4.539509 ACATTTTTCTTGTTACGCACGA 57.460 36.364 0.00 0.00 0.00 4.35
3352 3607 5.672051 TCTACATTTTTCTTGTTACGCACG 58.328 37.500 0.00 0.00 0.00 5.34
3353 3608 6.523201 CCATCTACATTTTTCTTGTTACGCAC 59.477 38.462 0.00 0.00 0.00 5.34
3354 3609 6.428465 TCCATCTACATTTTTCTTGTTACGCA 59.572 34.615 0.00 0.00 0.00 5.24
3355 3610 6.837992 TCCATCTACATTTTTCTTGTTACGC 58.162 36.000 0.00 0.00 0.00 4.42
3356 3611 8.029642 ACTCCATCTACATTTTTCTTGTTACG 57.970 34.615 0.00 0.00 0.00 3.18
3357 3612 9.827411 GAACTCCATCTACATTTTTCTTGTTAC 57.173 33.333 0.00 0.00 0.00 2.50
3358 3613 9.567776 TGAACTCCATCTACATTTTTCTTGTTA 57.432 29.630 0.00 0.00 0.00 2.41
3418 3675 1.569493 CACACGTGTGGCAGTTAGC 59.431 57.895 35.65 0.00 42.10 3.09
3649 3908 6.476706 GCAATAGACATGGCAACTTTTAATCC 59.523 38.462 0.00 0.00 30.66 3.01
3766 4027 7.037873 TGGCAAGTCTAGTTTCTTAATTCCCTA 60.038 37.037 0.00 0.00 0.00 3.53
3767 4028 6.181190 GGCAAGTCTAGTTTCTTAATTCCCT 58.819 40.000 0.00 0.00 0.00 4.20


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

AutoCloner maintained by Alex Coulton.