Multiple sequence alignment - TraesCS3D01G369700

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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 TraesCS3D01G369700 chr3D 100.000 3871 0 0 1 3871 482587725 482591595 0.000000e+00 7149.0
1 TraesCS3D01G369700 chr3D 96.978 364 11 0 3382 3745 89027894 89028257 2.560000e-171 612.0
2 TraesCS3D01G369700 chr3D 94.194 155 9 0 39 193 517387813 517387967 1.800000e-58 237.0
3 TraesCS3D01G369700 chr7D 96.669 3512 94 11 235 3746 59692514 59689026 0.000000e+00 5816.0
4 TraesCS3D01G369700 chr7D 97.253 364 10 0 3382 3745 75212553 75212916 5.490000e-173 617.0
5 TraesCS3D01G369700 chr7D 96.986 365 11 0 3382 3746 532448172 532448536 7.110000e-172 614.0
6 TraesCS3D01G369700 chr7D 85.992 257 25 8 38 286 478405733 478405986 8.250000e-67 265.0
7 TraesCS3D01G369700 chr7D 97.403 154 4 0 40 193 59692778 59692625 2.970000e-66 263.0
8 TraesCS3D01G369700 chr7D 91.339 127 11 0 3745 3871 255308166 255308040 1.430000e-39 174.0
9 TraesCS3D01G369700 chr7D 100.000 34 0 0 193 226 59692571 59692538 3.230000e-06 63.9
10 TraesCS3D01G369700 chr6D 96.984 3150 81 9 235 3379 343521954 343525094 0.000000e+00 5278.0
11 TraesCS3D01G369700 chr6D 96.953 361 11 0 3385 3745 462449711 462450071 1.190000e-169 606.0
12 TraesCS3D01G369700 chr6D 96.774 155 5 0 39 193 343521682 343521836 3.840000e-65 259.0
13 TraesCS3D01G369700 chr2D 96.086 3194 86 14 193 3385 621171109 621167954 0.000000e+00 5169.0
14 TraesCS3D01G369700 chr2D 96.995 366 11 0 3382 3747 131501219 131501584 1.980000e-172 616.0
15 TraesCS3D01G369700 chr2D 95.484 155 7 0 39 193 621171324 621171170 8.310000e-62 248.0
16 TraesCS3D01G369700 chr2D 94.839 155 8 0 39 193 425601358 425601512 3.860000e-60 243.0
17 TraesCS3D01G369700 chr5D 96.627 2994 89 8 235 3227 170710819 170713801 0.000000e+00 4959.0
18 TraesCS3D01G369700 chr5D 95.946 370 13 2 3382 3751 4521164 4521531 1.990000e-167 599.0
19 TraesCS3D01G369700 chr5D 96.894 161 4 1 34 193 170710541 170710701 6.370000e-68 268.0
20 TraesCS3D01G369700 chr5D 94.488 127 7 0 3745 3871 261894345 261894471 3.050000e-46 196.0
21 TraesCS3D01G369700 chr5B 96.200 2237 73 9 1151 3385 658347010 658349236 0.000000e+00 3650.0
22 TraesCS3D01G369700 chr5B 95.680 2176 81 9 1213 3385 290878614 290880779 0.000000e+00 3485.0
23 TraesCS3D01G369700 chr5B 93.857 993 52 2 235 1218 290877334 290878326 0.000000e+00 1487.0
24 TraesCS3D01G369700 chr5B 93.481 813 44 2 235 1038 658346193 658347005 0.000000e+00 1199.0
25 TraesCS3D01G369700 chr5B 94.681 282 15 0 3104 3385 17593718 17593999 4.590000e-119 438.0
26 TraesCS3D01G369700 chr5B 79.148 681 95 34 3095 3745 474962028 474962691 9.940000e-116 427.0
27 TraesCS3D01G369700 chr6B 95.664 2237 82 10 1151 3385 651661139 651658916 0.000000e+00 3579.0
28 TraesCS3D01G369700 chr6B 92.346 993 67 2 235 1218 396296077 396297069 0.000000e+00 1404.0
29 TraesCS3D01G369700 chr6B 93.850 813 41 3 235 1038 651661956 651661144 0.000000e+00 1216.0
30 TraesCS3D01G369700 chr6B 94.304 158 9 0 36 193 238301335 238301492 3.860000e-60 243.0
31 TraesCS3D01G369700 chr6B 91.339 127 11 0 3745 3871 488557742 488557616 1.430000e-39 174.0
32 TraesCS3D01G369700 chr1B 95.576 2238 83 10 1151 3385 198113642 198111418 0.000000e+00 3570.0
33 TraesCS3D01G369700 chr1B 92.850 993 62 2 235 1218 92077483 92078475 0.000000e+00 1432.0
34 TraesCS3D01G369700 chr1B 93.358 813 44 4 235 1038 198114458 198113647 0.000000e+00 1194.0
35 TraesCS3D01G369700 chr1A 95.678 2175 82 8 1213 3385 365222534 365224698 0.000000e+00 3485.0
36 TraesCS3D01G369700 chr1A 93.958 993 50 3 235 1218 365221255 365222246 0.000000e+00 1493.0
37 TraesCS3D01G369700 chr1A 92.063 126 10 0 3746 3871 265539430 265539305 1.110000e-40 178.0
38 TraesCS3D01G369700 chr7B 92.490 1478 102 6 235 1711 241347996 241346527 0.000000e+00 2106.0
39 TraesCS3D01G369700 chr7B 92.126 127 10 0 3745 3871 355976129 355976003 3.070000e-41 180.0
40 TraesCS3D01G369700 chr2B 92.131 1004 55 10 238 1218 86850059 86849057 0.000000e+00 1395.0
41 TraesCS3D01G369700 chr4D 96.703 364 12 0 3382 3745 266864139 266864502 1.190000e-169 606.0
42 TraesCS3D01G369700 chr4D 96.429 364 13 0 3382 3745 411701435 411701798 5.530000e-168 601.0
43 TraesCS3D01G369700 chr7A 87.185 437 45 4 792 1218 191902916 191903351 1.620000e-133 486.0
44 TraesCS3D01G369700 chr1D 96.154 156 6 0 38 193 425079405 425079560 4.960000e-64 255.0
45 TraesCS3D01G369700 chr1D 93.600 125 8 0 3745 3869 199475994 199475870 1.840000e-43 187.0
46 TraesCS3D01G369700 chr3A 93.701 127 8 0 3745 3871 185313450 185313576 1.420000e-44 191.0
47 TraesCS3D01G369700 chr6A 91.339 127 11 0 3745 3871 123772205 123772331 1.430000e-39 174.0
48 TraesCS3D01G369700 chr2A 91.935 124 10 0 3748 3871 381593250 381593127 1.430000e-39 174.0


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 TraesCS3D01G369700 chr3D 482587725 482591595 3870 False 7149.000000 7149 100.0000 1 3871 1 chr3D.!!$F2 3870
1 TraesCS3D01G369700 chr7D 59689026 59692778 3752 True 2047.633333 5816 98.0240 40 3746 3 chr7D.!!$R2 3706
2 TraesCS3D01G369700 chr6D 343521682 343525094 3412 False 2768.500000 5278 96.8790 39 3379 2 chr6D.!!$F2 3340
3 TraesCS3D01G369700 chr2D 621167954 621171324 3370 True 2708.500000 5169 95.7850 39 3385 2 chr2D.!!$R1 3346
4 TraesCS3D01G369700 chr5D 170710541 170713801 3260 False 2613.500000 4959 96.7605 34 3227 2 chr5D.!!$F3 3193
5 TraesCS3D01G369700 chr5B 290877334 290880779 3445 False 2486.000000 3485 94.7685 235 3385 2 chr5B.!!$F3 3150
6 TraesCS3D01G369700 chr5B 658346193 658349236 3043 False 2424.500000 3650 94.8405 235 3385 2 chr5B.!!$F4 3150
7 TraesCS3D01G369700 chr5B 474962028 474962691 663 False 427.000000 427 79.1480 3095 3745 1 chr5B.!!$F2 650
8 TraesCS3D01G369700 chr6B 651658916 651661956 3040 True 2397.500000 3579 94.7570 235 3385 2 chr6B.!!$R2 3150
9 TraesCS3D01G369700 chr6B 396296077 396297069 992 False 1404.000000 1404 92.3460 235 1218 1 chr6B.!!$F2 983
10 TraesCS3D01G369700 chr1B 198111418 198114458 3040 True 2382.000000 3570 94.4670 235 3385 2 chr1B.!!$R1 3150
11 TraesCS3D01G369700 chr1B 92077483 92078475 992 False 1432.000000 1432 92.8500 235 1218 1 chr1B.!!$F1 983
12 TraesCS3D01G369700 chr1A 365221255 365224698 3443 False 2489.000000 3485 94.8180 235 3385 2 chr1A.!!$F1 3150
13 TraesCS3D01G369700 chr7B 241346527 241347996 1469 True 2106.000000 2106 92.4900 235 1711 1 chr7B.!!$R1 1476
14 TraesCS3D01G369700 chr2B 86849057 86850059 1002 True 1395.000000 1395 92.1310 238 1218 1 chr2B.!!$R1 980

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
233 295 0.037605 CGGCCACTTTCTAACGACCT 60.038 55.000 2.24 0.0 0.0 3.85 F
751 851 2.041265 AAGGCGGAGGAGTGGGAT 59.959 61.111 0.00 0.0 0.0 3.85 F
1674 2087 3.832490 TGTCTCTACATGCAAGTACCTGT 59.168 43.478 0.00 0.0 0.0 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1698 2111 2.676265 GCCGGGGCCTCCTCTAAAA 61.676 63.158 2.18 0.00 34.56 1.52 R
2634 3051 0.883833 AGGCGCTCCAAATCAAACTG 59.116 50.000 7.64 0.00 33.74 3.16 R
3454 3939 0.171903 CAAAGAGCATCCGGCCTTTG 59.828 55.000 0.00 7.55 45.46 2.77 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 5.220710 GACACATCCATCTATTGCTAGGT 57.779 43.478 0.00 0.00 0.00 3.08
23 24 5.220710 ACACATCCATCTATTGCTAGGTC 57.779 43.478 0.00 0.00 0.00 3.85
24 25 4.904251 ACACATCCATCTATTGCTAGGTCT 59.096 41.667 0.00 0.00 0.00 3.85
25 26 5.367937 ACACATCCATCTATTGCTAGGTCTT 59.632 40.000 0.00 0.00 0.00 3.01
26 27 6.126652 ACACATCCATCTATTGCTAGGTCTTT 60.127 38.462 0.00 0.00 0.00 2.52
27 28 6.769822 CACATCCATCTATTGCTAGGTCTTTT 59.230 38.462 0.00 0.00 0.00 2.27
28 29 7.933577 CACATCCATCTATTGCTAGGTCTTTTA 59.066 37.037 0.00 0.00 0.00 1.52
29 30 8.664079 ACATCCATCTATTGCTAGGTCTTTTAT 58.336 33.333 0.00 0.00 0.00 1.40
30 31 9.160496 CATCCATCTATTGCTAGGTCTTTTATC 57.840 37.037 0.00 0.00 0.00 1.75
31 32 7.680730 TCCATCTATTGCTAGGTCTTTTATCC 58.319 38.462 0.00 0.00 0.00 2.59
32 33 6.881602 CCATCTATTGCTAGGTCTTTTATCCC 59.118 42.308 0.00 0.00 0.00 3.85
33 34 7.453393 CATCTATTGCTAGGTCTTTTATCCCA 58.547 38.462 0.00 0.00 0.00 4.37
34 35 7.067496 TCTATTGCTAGGTCTTTTATCCCAG 57.933 40.000 0.00 0.00 0.00 4.45
35 36 3.560636 TGCTAGGTCTTTTATCCCAGC 57.439 47.619 0.00 0.00 0.00 4.85
36 37 2.843730 TGCTAGGTCTTTTATCCCAGCA 59.156 45.455 0.74 0.74 33.23 4.41
37 38 3.265737 TGCTAGGTCTTTTATCCCAGCAA 59.734 43.478 2.28 0.00 32.95 3.91
191 253 4.076244 CAGCCTGCTCTTTGCTGT 57.924 55.556 2.69 0.00 45.69 4.40
226 288 1.203052 CGACCTAACGGCCACTTTCTA 59.797 52.381 2.24 0.00 0.00 2.10
227 289 2.353011 CGACCTAACGGCCACTTTCTAA 60.353 50.000 2.24 0.00 0.00 2.10
228 290 2.998670 GACCTAACGGCCACTTTCTAAC 59.001 50.000 2.24 0.00 0.00 2.34
229 291 1.997606 CCTAACGGCCACTTTCTAACG 59.002 52.381 2.24 0.00 0.00 3.18
230 292 2.353011 CCTAACGGCCACTTTCTAACGA 60.353 50.000 2.24 0.00 0.00 3.85
231 293 1.505425 AACGGCCACTTTCTAACGAC 58.495 50.000 2.24 0.00 0.00 4.34
232 294 0.320160 ACGGCCACTTTCTAACGACC 60.320 55.000 2.24 0.00 0.00 4.79
233 295 0.037605 CGGCCACTTTCTAACGACCT 60.038 55.000 2.24 0.00 0.00 3.85
242 319 2.519771 TCTAACGACCTAAGAGCCCA 57.480 50.000 0.00 0.00 0.00 5.36
414 491 2.111384 TCTTCCTCGATCCCCTTTCTG 58.889 52.381 0.00 0.00 0.00 3.02
751 851 2.041265 AAGGCGGAGGAGTGGGAT 59.959 61.111 0.00 0.00 0.00 3.85
1560 1970 8.718102 ACAAATGTAGTGTTACTTATAGGCAG 57.282 34.615 0.00 0.00 0.00 4.85
1667 2080 6.492007 ACTTCAAATGTCTCTACATGCAAG 57.508 37.500 0.00 0.00 45.79 4.01
1670 2083 6.968131 TCAAATGTCTCTACATGCAAGTAC 57.032 37.500 0.00 0.00 45.79 2.73
1671 2084 5.874810 TCAAATGTCTCTACATGCAAGTACC 59.125 40.000 0.00 0.00 45.79 3.34
1672 2085 5.683876 AATGTCTCTACATGCAAGTACCT 57.316 39.130 0.00 0.00 45.79 3.08
1673 2086 4.456280 TGTCTCTACATGCAAGTACCTG 57.544 45.455 0.00 0.00 0.00 4.00
1674 2087 3.832490 TGTCTCTACATGCAAGTACCTGT 59.168 43.478 0.00 0.00 0.00 4.00
1675 2088 4.082190 TGTCTCTACATGCAAGTACCTGTC 60.082 45.833 0.00 0.00 0.00 3.51
1676 2089 4.158764 GTCTCTACATGCAAGTACCTGTCT 59.841 45.833 0.00 0.00 0.00 3.41
1698 2111 8.632679 TGTCTCATGCTTTTTATTTCAGTCTTT 58.367 29.630 0.00 0.00 0.00 2.52
2057 2470 6.109156 TGCTACTTGTACTCCTTTCATGAA 57.891 37.500 3.38 3.38 0.00 2.57
2658 3075 0.036732 TGATTTGGAGCGCCTCTTGT 59.963 50.000 8.34 0.00 34.31 3.16
2726 3144 2.006873 TGGATTGGGAGGGGAAAATGA 58.993 47.619 0.00 0.00 0.00 2.57
2767 3186 2.307496 AGTCAAACCCATCCATGCAA 57.693 45.000 0.00 0.00 0.00 4.08
3308 3731 9.643693 GTTTTTATGGATGATCTTGTGATGTTT 57.356 29.630 0.00 0.00 32.19 2.83
3309 3732 9.859427 TTTTTATGGATGATCTTGTGATGTTTC 57.141 29.630 0.00 0.00 32.19 2.78
3388 3811 7.528481 TGAATATGAATTGCTGAACATTTGC 57.472 32.000 0.00 0.00 0.00 3.68
3418 3903 2.597510 ACGGCAAAGGCTTGTCCC 60.598 61.111 0.00 0.49 40.87 4.46
3426 3911 3.050275 GGCTTGTCCCGCAGTGAC 61.050 66.667 0.00 0.00 0.00 3.67
3434 3919 4.363990 CCGCAGTGACGTCCAGCT 62.364 66.667 14.12 5.83 0.00 4.24
3435 3920 3.108289 CGCAGTGACGTCCAGCTG 61.108 66.667 20.46 20.46 0.00 4.24
3437 3922 2.024319 GCAGTGACGTCCAGCTGAC 61.024 63.158 25.71 10.62 40.81 3.51
3457 3942 3.427425 CATTCGGCGGACGGCAAA 61.427 61.111 18.20 6.59 46.16 3.68
3553 4077 2.126850 GCCGTCGGCTTTCTTTGC 60.127 61.111 28.98 0.00 46.69 3.68
3570 4094 2.659897 CCGTCAGCCGCTGATAGC 60.660 66.667 25.41 12.28 42.73 2.97
3708 4233 0.618458 ATCCTTGCCTTTGCCGTCTA 59.382 50.000 0.00 0.00 36.33 2.59
3711 4236 1.635663 CTTGCCTTTGCCGTCTACCG 61.636 60.000 0.00 0.00 36.33 4.02
3730 4255 1.752198 TGGCAGACGGCAAAGTAGT 59.248 52.632 0.00 0.00 46.20 2.73
3746 4271 5.483685 AAGTAGTTGATTCCTGTAGTGCA 57.516 39.130 0.00 0.00 0.00 4.57
3747 4272 5.483685 AGTAGTTGATTCCTGTAGTGCAA 57.516 39.130 0.00 0.00 0.00 4.08
3748 4273 5.482908 AGTAGTTGATTCCTGTAGTGCAAG 58.517 41.667 0.00 0.00 0.00 4.01
3749 4274 3.679389 AGTTGATTCCTGTAGTGCAAGG 58.321 45.455 0.00 0.00 0.00 3.61
3750 4275 3.327757 AGTTGATTCCTGTAGTGCAAGGA 59.672 43.478 0.46 0.46 0.00 3.36
3751 4276 3.334583 TGATTCCTGTAGTGCAAGGAC 57.665 47.619 4.28 0.00 0.00 3.85
3752 4277 2.637382 TGATTCCTGTAGTGCAAGGACA 59.363 45.455 4.28 0.66 0.00 4.02
3753 4278 2.839486 TTCCTGTAGTGCAAGGACAG 57.161 50.000 14.16 14.16 40.26 3.51
3754 4279 1.717032 TCCTGTAGTGCAAGGACAGT 58.283 50.000 17.81 0.00 39.16 3.55
3755 4280 1.618837 TCCTGTAGTGCAAGGACAGTC 59.381 52.381 17.81 0.00 39.16 3.51
3756 4281 1.620819 CCTGTAGTGCAAGGACAGTCT 59.379 52.381 17.81 0.00 39.16 3.24
3757 4282 2.611473 CCTGTAGTGCAAGGACAGTCTG 60.611 54.545 17.81 0.00 39.16 3.51
3758 4283 1.270305 TGTAGTGCAAGGACAGTCTGC 60.270 52.381 7.67 7.67 0.00 4.26
3759 4284 1.001406 GTAGTGCAAGGACAGTCTGCT 59.999 52.381 14.18 0.48 0.00 4.24
3760 4285 1.342074 AGTGCAAGGACAGTCTGCTA 58.658 50.000 14.18 1.16 0.00 3.49
3761 4286 1.905215 AGTGCAAGGACAGTCTGCTAT 59.095 47.619 14.18 2.56 0.00 2.97
3762 4287 2.005451 GTGCAAGGACAGTCTGCTATG 58.995 52.381 14.18 0.00 0.00 2.23
3763 4288 1.901833 TGCAAGGACAGTCTGCTATGA 59.098 47.619 14.18 0.00 0.00 2.15
3764 4289 2.093816 TGCAAGGACAGTCTGCTATGAG 60.094 50.000 14.18 0.00 0.00 2.90
3765 4290 2.741228 GCAAGGACAGTCTGCTATGAGG 60.741 54.545 7.40 0.00 0.00 3.86
3766 4291 2.499289 CAAGGACAGTCTGCTATGAGGT 59.501 50.000 0.00 0.00 0.00 3.85
3767 4292 2.106566 AGGACAGTCTGCTATGAGGTG 58.893 52.381 0.00 0.00 0.00 4.00
3768 4293 2.103373 GGACAGTCTGCTATGAGGTGA 58.897 52.381 0.00 0.00 0.00 4.02
3769 4294 2.159170 GGACAGTCTGCTATGAGGTGAC 60.159 54.545 0.00 0.00 0.00 3.67
3770 4295 1.827969 ACAGTCTGCTATGAGGTGACC 59.172 52.381 0.00 0.00 0.00 4.02
3771 4296 1.107114 AGTCTGCTATGAGGTGACCG 58.893 55.000 0.00 0.00 0.00 4.79
3772 4297 1.103803 GTCTGCTATGAGGTGACCGA 58.896 55.000 0.00 0.00 0.00 4.69
3773 4298 1.476891 GTCTGCTATGAGGTGACCGAA 59.523 52.381 0.00 0.00 0.00 4.30
3774 4299 2.101582 GTCTGCTATGAGGTGACCGAAT 59.898 50.000 0.00 0.00 0.00 3.34
3775 4300 2.766263 TCTGCTATGAGGTGACCGAATT 59.234 45.455 0.00 0.00 0.00 2.17
3776 4301 2.868583 CTGCTATGAGGTGACCGAATTG 59.131 50.000 0.00 0.00 0.00 2.32
3777 4302 2.236146 TGCTATGAGGTGACCGAATTGT 59.764 45.455 0.00 0.00 0.00 2.71
3778 4303 3.270877 GCTATGAGGTGACCGAATTGTT 58.729 45.455 0.00 0.00 0.00 2.83
3779 4304 3.689649 GCTATGAGGTGACCGAATTGTTT 59.310 43.478 0.00 0.00 0.00 2.83
3780 4305 4.437390 GCTATGAGGTGACCGAATTGTTTG 60.437 45.833 0.00 0.00 0.00 2.93
3781 4306 1.606668 TGAGGTGACCGAATTGTTTGC 59.393 47.619 0.00 0.00 0.00 3.68
3782 4307 1.606668 GAGGTGACCGAATTGTTTGCA 59.393 47.619 0.00 0.00 0.00 4.08
3783 4308 1.336755 AGGTGACCGAATTGTTTGCAC 59.663 47.619 0.00 0.00 0.00 4.57
3784 4309 1.336755 GGTGACCGAATTGTTTGCACT 59.663 47.619 0.00 0.00 0.00 4.40
3785 4310 2.223711 GGTGACCGAATTGTTTGCACTT 60.224 45.455 0.00 0.00 0.00 3.16
3786 4311 2.788786 GTGACCGAATTGTTTGCACTTG 59.211 45.455 0.00 0.00 0.00 3.16
3787 4312 2.685388 TGACCGAATTGTTTGCACTTGA 59.315 40.909 0.00 0.00 0.00 3.02
3788 4313 3.129462 TGACCGAATTGTTTGCACTTGAA 59.871 39.130 0.00 0.00 0.00 2.69
3789 4314 3.705604 ACCGAATTGTTTGCACTTGAAG 58.294 40.909 0.00 0.00 0.00 3.02
3790 4315 2.472488 CCGAATTGTTTGCACTTGAAGC 59.528 45.455 0.00 0.00 0.00 3.86
3791 4316 3.114809 CGAATTGTTTGCACTTGAAGCA 58.885 40.909 0.00 0.00 40.85 3.91
3792 4317 3.061006 CGAATTGTTTGCACTTGAAGCAC 60.061 43.478 0.00 0.00 42.54 4.40
3793 4318 3.806625 ATTGTTTGCACTTGAAGCACT 57.193 38.095 0.00 0.00 42.54 4.40
3794 4319 3.591196 TTGTTTGCACTTGAAGCACTT 57.409 38.095 0.00 0.00 42.54 3.16
3795 4320 3.591196 TGTTTGCACTTGAAGCACTTT 57.409 38.095 0.00 0.00 42.54 2.66
3796 4321 4.710423 TGTTTGCACTTGAAGCACTTTA 57.290 36.364 0.00 0.00 42.54 1.85
3797 4322 5.261209 TGTTTGCACTTGAAGCACTTTAT 57.739 34.783 0.00 0.00 42.54 1.40
3798 4323 5.659463 TGTTTGCACTTGAAGCACTTTATT 58.341 33.333 0.00 0.00 42.54 1.40
3799 4324 6.105333 TGTTTGCACTTGAAGCACTTTATTT 58.895 32.000 0.00 0.00 42.54 1.40
3800 4325 6.255453 TGTTTGCACTTGAAGCACTTTATTTC 59.745 34.615 0.00 0.00 42.54 2.17
3801 4326 5.772825 TGCACTTGAAGCACTTTATTTCT 57.227 34.783 0.00 0.00 37.02 2.52
3802 4327 6.147864 TGCACTTGAAGCACTTTATTTCTT 57.852 33.333 0.00 0.00 37.02 2.52
3803 4328 6.572519 TGCACTTGAAGCACTTTATTTCTTT 58.427 32.000 0.00 0.00 37.02 2.52
3804 4329 7.041107 TGCACTTGAAGCACTTTATTTCTTTT 58.959 30.769 0.00 0.00 37.02 2.27
3805 4330 7.010367 TGCACTTGAAGCACTTTATTTCTTTTG 59.990 33.333 0.00 0.00 37.02 2.44
3806 4331 7.517259 GCACTTGAAGCACTTTATTTCTTTTGG 60.517 37.037 0.00 0.00 0.00 3.28
3807 4332 7.706179 CACTTGAAGCACTTTATTTCTTTTGGA 59.294 33.333 0.00 0.00 0.00 3.53
3808 4333 7.922811 ACTTGAAGCACTTTATTTCTTTTGGAG 59.077 33.333 0.00 0.00 0.00 3.86
3809 4334 6.748132 TGAAGCACTTTATTTCTTTTGGAGG 58.252 36.000 0.00 0.00 0.00 4.30
3810 4335 6.323739 TGAAGCACTTTATTTCTTTTGGAGGT 59.676 34.615 0.00 0.00 0.00 3.85
3811 4336 7.504238 TGAAGCACTTTATTTCTTTTGGAGGTA 59.496 33.333 0.00 0.00 0.00 3.08
3812 4337 7.833285 AGCACTTTATTTCTTTTGGAGGTAA 57.167 32.000 0.00 0.00 0.00 2.85
3813 4338 7.658261 AGCACTTTATTTCTTTTGGAGGTAAC 58.342 34.615 0.00 0.00 0.00 2.50
3831 4356 5.944013 GGTAACTTTCTTGAAGATTCAGGC 58.056 41.667 0.00 0.00 38.61 4.85
3832 4357 5.473504 GGTAACTTTCTTGAAGATTCAGGCA 59.526 40.000 0.00 0.00 38.61 4.75
3833 4358 6.016276 GGTAACTTTCTTGAAGATTCAGGCAA 60.016 38.462 0.00 0.00 38.61 4.52
3834 4359 5.702349 ACTTTCTTGAAGATTCAGGCAAG 57.298 39.130 12.95 12.95 41.05 4.01
3835 4360 5.136105 ACTTTCTTGAAGATTCAGGCAAGT 58.864 37.500 13.97 13.97 42.50 3.16
3836 4361 5.240403 ACTTTCTTGAAGATTCAGGCAAGTC 59.760 40.000 13.97 0.00 43.29 3.01
3837 4362 4.356405 TCTTGAAGATTCAGGCAAGTCA 57.644 40.909 0.00 0.00 38.95 3.41
3838 4363 4.717877 TCTTGAAGATTCAGGCAAGTCAA 58.282 39.130 0.00 0.00 38.95 3.18
3839 4364 5.132502 TCTTGAAGATTCAGGCAAGTCAAA 58.867 37.500 0.00 0.00 38.95 2.69
3840 4365 5.771666 TCTTGAAGATTCAGGCAAGTCAAAT 59.228 36.000 0.00 0.00 38.95 2.32
3841 4366 6.266103 TCTTGAAGATTCAGGCAAGTCAAATT 59.734 34.615 0.00 0.00 38.95 1.82
3842 4367 6.409524 TGAAGATTCAGGCAAGTCAAATTT 57.590 33.333 0.00 0.00 32.50 1.82
3843 4368 6.218019 TGAAGATTCAGGCAAGTCAAATTTG 58.782 36.000 12.15 12.15 32.50 2.32
3844 4369 5.796424 AGATTCAGGCAAGTCAAATTTGT 57.204 34.783 17.47 0.00 0.00 2.83
3845 4370 5.776744 AGATTCAGGCAAGTCAAATTTGTC 58.223 37.500 17.47 12.30 0.00 3.18
3846 4371 4.998671 TTCAGGCAAGTCAAATTTGTCA 57.001 36.364 17.47 0.00 32.71 3.58
3847 4372 5.534207 TTCAGGCAAGTCAAATTTGTCAT 57.466 34.783 17.47 2.75 32.71 3.06
3848 4373 5.125100 TCAGGCAAGTCAAATTTGTCATC 57.875 39.130 17.47 7.48 32.71 2.92
3849 4374 4.583907 TCAGGCAAGTCAAATTTGTCATCA 59.416 37.500 17.47 0.00 32.71 3.07
3850 4375 5.244402 TCAGGCAAGTCAAATTTGTCATCAT 59.756 36.000 17.47 1.45 32.71 2.45
3851 4376 6.433716 TCAGGCAAGTCAAATTTGTCATCATA 59.566 34.615 17.47 0.00 32.71 2.15
3852 4377 7.039853 TCAGGCAAGTCAAATTTGTCATCATAA 60.040 33.333 17.47 0.00 32.71 1.90
3853 4378 7.762615 CAGGCAAGTCAAATTTGTCATCATAAT 59.237 33.333 17.47 0.00 32.71 1.28
3854 4379 8.316214 AGGCAAGTCAAATTTGTCATCATAATT 58.684 29.630 17.47 0.00 32.71 1.40
3855 4380 8.385111 GGCAAGTCAAATTTGTCATCATAATTG 58.615 33.333 17.47 12.37 30.72 2.32
3856 4381 9.142515 GCAAGTCAAATTTGTCATCATAATTGA 57.857 29.630 17.47 0.00 36.00 2.57
3860 4385 9.844790 GTCAAATTTGTCATCATAATTGAGACA 57.155 29.630 17.47 0.00 37.80 3.41
3861 4386 9.844790 TCAAATTTGTCATCATAATTGAGACAC 57.155 29.630 17.47 0.00 38.54 3.67
3862 4387 9.628746 CAAATTTGTCATCATAATTGAGACACA 57.371 29.630 10.15 0.00 38.54 3.72
3863 4388 9.850628 AAATTTGTCATCATAATTGAGACACAG 57.149 29.630 0.00 0.00 38.54 3.66
3864 4389 8.797350 ATTTGTCATCATAATTGAGACACAGA 57.203 30.769 0.00 0.00 38.54 3.41
3865 4390 8.797350 TTTGTCATCATAATTGAGACACAGAT 57.203 30.769 0.00 0.00 38.54 2.90
3866 4391 8.797350 TTGTCATCATAATTGAGACACAGATT 57.203 30.769 0.00 0.00 38.54 2.40
3867 4392 8.429493 TGTCATCATAATTGAGACACAGATTC 57.571 34.615 0.00 0.00 36.24 2.52
3868 4393 8.262933 TGTCATCATAATTGAGACACAGATTCT 58.737 33.333 0.00 0.00 36.24 2.40
3869 4394 8.549548 GTCATCATAATTGAGACACAGATTCTG 58.450 37.037 12.17 12.17 34.73 3.02
3870 4395 8.262933 TCATCATAATTGAGACACAGATTCTGT 58.737 33.333 13.61 13.61 39.28 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.011533 AGACCTAGCAATAGATGGATGTGTC 59.988 44.000 0.00 0.00 0.00 3.67
4 5 9.160496 GATAAAAGACCTAGCAATAGATGGATG 57.840 37.037 0.00 0.00 0.00 3.51
6 7 7.256691 GGGATAAAAGACCTAGCAATAGATGGA 60.257 40.741 0.00 0.00 0.00 3.41
7 8 6.881602 GGGATAAAAGACCTAGCAATAGATGG 59.118 42.308 0.00 0.00 0.00 3.51
8 9 7.453393 TGGGATAAAAGACCTAGCAATAGATG 58.547 38.462 0.00 0.00 0.00 2.90
9 10 7.633018 TGGGATAAAAGACCTAGCAATAGAT 57.367 36.000 0.00 0.00 0.00 1.98
10 11 7.067496 CTGGGATAAAAGACCTAGCAATAGA 57.933 40.000 0.00 0.00 0.00 1.98
17 18 4.636206 GTGTTGCTGGGATAAAAGACCTAG 59.364 45.833 0.00 0.00 37.73 3.02
18 19 4.288626 AGTGTTGCTGGGATAAAAGACCTA 59.711 41.667 0.00 0.00 0.00 3.08
19 20 3.074538 AGTGTTGCTGGGATAAAAGACCT 59.925 43.478 0.00 0.00 0.00 3.85
20 21 3.421844 AGTGTTGCTGGGATAAAAGACC 58.578 45.455 0.00 0.00 0.00 3.85
21 22 5.122396 CAGTAGTGTTGCTGGGATAAAAGAC 59.878 44.000 0.00 0.00 33.86 3.01
22 23 5.245531 CAGTAGTGTTGCTGGGATAAAAGA 58.754 41.667 0.00 0.00 33.86 2.52
23 24 5.551760 CAGTAGTGTTGCTGGGATAAAAG 57.448 43.478 0.00 0.00 33.86 2.27
32 33 3.005554 CCTGATTCCAGTAGTGTTGCTG 58.994 50.000 0.00 0.00 38.74 4.41
33 34 2.906389 TCCTGATTCCAGTAGTGTTGCT 59.094 45.455 0.00 0.00 38.74 3.91
34 35 3.334583 TCCTGATTCCAGTAGTGTTGC 57.665 47.619 0.00 0.00 38.74 4.17
35 36 4.899502 AGTTCCTGATTCCAGTAGTGTTG 58.100 43.478 0.00 0.00 38.74 3.33
36 37 5.568620 AAGTTCCTGATTCCAGTAGTGTT 57.431 39.130 0.00 0.00 38.74 3.32
37 38 5.308825 CAAAGTTCCTGATTCCAGTAGTGT 58.691 41.667 0.00 0.00 38.74 3.55
191 253 5.240121 GTTAGGTCGTTCTTGTTAATGGGA 58.760 41.667 0.00 0.00 0.00 4.37
226 288 2.779506 CTTTTGGGCTCTTAGGTCGTT 58.220 47.619 0.00 0.00 0.00 3.85
227 289 1.610886 GCTTTTGGGCTCTTAGGTCGT 60.611 52.381 0.00 0.00 0.00 4.34
228 290 1.087501 GCTTTTGGGCTCTTAGGTCG 58.912 55.000 0.00 0.00 0.00 4.79
229 291 2.087646 CTGCTTTTGGGCTCTTAGGTC 58.912 52.381 0.00 0.00 0.00 3.85
230 292 1.705186 TCTGCTTTTGGGCTCTTAGGT 59.295 47.619 0.00 0.00 0.00 3.08
231 293 2.087646 GTCTGCTTTTGGGCTCTTAGG 58.912 52.381 0.00 0.00 0.00 2.69
232 294 1.734465 CGTCTGCTTTTGGGCTCTTAG 59.266 52.381 0.00 0.00 0.00 2.18
233 295 1.346395 TCGTCTGCTTTTGGGCTCTTA 59.654 47.619 0.00 0.00 0.00 2.10
242 319 6.695713 GGTTATTTTCTTTGTCGTCTGCTTTT 59.304 34.615 0.00 0.00 0.00 2.27
298 375 4.882396 TGTGGGTCGTGGGTGGGA 62.882 66.667 0.00 0.00 0.00 4.37
751 851 1.738350 CTCTTGGACTCGTAGAAGCGA 59.262 52.381 0.00 0.00 39.22 4.93
796 896 0.689080 ATGGAGGCTGTGGAGACGAT 60.689 55.000 0.00 0.00 29.20 3.73
830 930 0.761323 TCGTGGGGTTGAGAAGTGGA 60.761 55.000 0.00 0.00 0.00 4.02
1553 1963 5.927281 AAATTTGCTCAACATCTGCCTAT 57.073 34.783 0.00 0.00 0.00 2.57
1560 1970 8.437742 CCATTAGTTCAAAATTTGCTCAACATC 58.562 33.333 0.00 0.00 0.00 3.06
1667 2080 7.816640 TGAAATAAAAAGCATGAGACAGGTAC 58.183 34.615 0.00 0.00 0.00 3.34
1670 2083 6.917533 ACTGAAATAAAAAGCATGAGACAGG 58.082 36.000 0.00 0.00 0.00 4.00
1671 2084 7.814642 AGACTGAAATAAAAAGCATGAGACAG 58.185 34.615 0.00 0.00 0.00 3.51
1672 2085 7.750229 AGACTGAAATAAAAAGCATGAGACA 57.250 32.000 0.00 0.00 0.00 3.41
1673 2086 9.468532 AAAAGACTGAAATAAAAAGCATGAGAC 57.531 29.630 0.00 0.00 0.00 3.36
1698 2111 2.676265 GCCGGGGCCTCCTCTAAAA 61.676 63.158 2.18 0.00 34.56 1.52
2394 2810 2.176273 CACTACCTGGATGCAGCGC 61.176 63.158 9.03 0.00 0.00 5.92
2634 3051 0.883833 AGGCGCTCCAAATCAAACTG 59.116 50.000 7.64 0.00 33.74 3.16
2658 3075 5.367945 AAGAGAAGGAACTGTGGTACAAA 57.632 39.130 0.00 0.00 38.04 2.83
2726 3144 5.792741 CTTCAACAGAGACTGAAGGAAGAT 58.207 41.667 17.30 0.00 43.15 2.40
2887 3306 3.002042 CGTCATCATCAGTCTGATTTGCC 59.998 47.826 12.88 3.48 34.28 4.52
3281 3704 8.585471 ACATCACAAGATCATCCATAAAAACT 57.415 30.769 0.00 0.00 30.20 2.66
3388 3811 2.510238 GCCGTCTGCTGCTGTAGG 60.510 66.667 8.74 14.61 36.87 3.18
3418 3903 3.108289 CAGCTGGACGTCACTGCG 61.108 66.667 18.91 13.25 37.78 5.18
3434 3919 2.126228 GTCCGCCGAATGACGTCA 60.126 61.111 22.48 22.48 40.78 4.35
3435 3920 3.245315 CGTCCGCCGAATGACGTC 61.245 66.667 9.11 9.11 46.83 4.34
3454 3939 0.171903 CAAAGAGCATCCGGCCTTTG 59.828 55.000 0.00 7.55 45.46 2.77
3457 3942 2.439156 GCAAAGAGCATCCGGCCT 60.439 61.111 0.00 0.00 46.50 5.19
3553 4077 2.659897 GCTATCAGCGGCTGACGG 60.660 66.667 32.96 26.47 43.63 4.79
3591 4115 2.490328 TTGCCGTCTGCTTTTTGAAG 57.510 45.000 0.00 0.00 42.00 3.02
3711 4236 0.602905 ACTACTTTGCCGTCTGCCAC 60.603 55.000 0.00 0.00 40.16 5.01
3730 4255 3.072330 TGTCCTTGCACTACAGGAATCAA 59.928 43.478 6.43 0.00 30.47 2.57
3746 4271 2.499289 CACCTCATAGCAGACTGTCCTT 59.501 50.000 3.76 0.00 0.00 3.36
3747 4272 2.106566 CACCTCATAGCAGACTGTCCT 58.893 52.381 3.76 0.00 0.00 3.85
3748 4273 2.103373 TCACCTCATAGCAGACTGTCC 58.897 52.381 3.76 0.00 0.00 4.02
3749 4274 2.159170 GGTCACCTCATAGCAGACTGTC 60.159 54.545 3.99 0.00 0.00 3.51
3750 4275 1.827969 GGTCACCTCATAGCAGACTGT 59.172 52.381 3.99 0.00 0.00 3.55
3751 4276 1.202348 CGGTCACCTCATAGCAGACTG 60.202 57.143 0.00 0.00 0.00 3.51
3752 4277 1.107114 CGGTCACCTCATAGCAGACT 58.893 55.000 0.00 0.00 0.00 3.24
3753 4278 1.103803 TCGGTCACCTCATAGCAGAC 58.896 55.000 0.00 0.00 0.00 3.51
3754 4279 1.847328 TTCGGTCACCTCATAGCAGA 58.153 50.000 0.00 0.00 0.00 4.26
3755 4280 2.868583 CAATTCGGTCACCTCATAGCAG 59.131 50.000 0.00 0.00 0.00 4.24
3756 4281 2.236146 ACAATTCGGTCACCTCATAGCA 59.764 45.455 0.00 0.00 0.00 3.49
3757 4282 2.906354 ACAATTCGGTCACCTCATAGC 58.094 47.619 0.00 0.00 0.00 2.97
3758 4283 4.437390 GCAAACAATTCGGTCACCTCATAG 60.437 45.833 0.00 0.00 0.00 2.23
3759 4284 3.438781 GCAAACAATTCGGTCACCTCATA 59.561 43.478 0.00 0.00 0.00 2.15
3760 4285 2.228822 GCAAACAATTCGGTCACCTCAT 59.771 45.455 0.00 0.00 0.00 2.90
3761 4286 1.606668 GCAAACAATTCGGTCACCTCA 59.393 47.619 0.00 0.00 0.00 3.86
3762 4287 1.606668 TGCAAACAATTCGGTCACCTC 59.393 47.619 0.00 0.00 0.00 3.85
3763 4288 1.336755 GTGCAAACAATTCGGTCACCT 59.663 47.619 0.00 0.00 0.00 4.00
3764 4289 1.336755 AGTGCAAACAATTCGGTCACC 59.663 47.619 0.00 0.00 0.00 4.02
3765 4290 2.774439 AGTGCAAACAATTCGGTCAC 57.226 45.000 0.00 0.00 0.00 3.67
3766 4291 2.685388 TCAAGTGCAAACAATTCGGTCA 59.315 40.909 0.00 0.00 30.15 4.02
3767 4292 3.347958 TCAAGTGCAAACAATTCGGTC 57.652 42.857 0.00 0.00 30.15 4.79
3768 4293 3.705604 CTTCAAGTGCAAACAATTCGGT 58.294 40.909 0.00 0.00 30.15 4.69
3769 4294 2.472488 GCTTCAAGTGCAAACAATTCGG 59.528 45.455 0.00 0.00 30.15 4.30
3770 4295 3.061006 GTGCTTCAAGTGCAAACAATTCG 60.061 43.478 0.00 0.00 42.41 3.34
3771 4296 4.114794 AGTGCTTCAAGTGCAAACAATTC 58.885 39.130 0.00 0.00 42.41 2.17
3772 4297 4.127566 AGTGCTTCAAGTGCAAACAATT 57.872 36.364 0.00 0.00 42.41 2.32
3773 4298 3.806625 AGTGCTTCAAGTGCAAACAAT 57.193 38.095 0.00 0.00 42.41 2.71
3774 4299 3.591196 AAGTGCTTCAAGTGCAAACAA 57.409 38.095 0.00 0.00 42.41 2.83
3775 4300 3.591196 AAAGTGCTTCAAGTGCAAACA 57.409 38.095 0.00 0.00 42.41 2.83
3776 4301 6.476706 AGAAATAAAGTGCTTCAAGTGCAAAC 59.523 34.615 0.00 0.00 42.41 2.93
3777 4302 6.572519 AGAAATAAAGTGCTTCAAGTGCAAA 58.427 32.000 0.00 0.00 42.41 3.68
3778 4303 6.147864 AGAAATAAAGTGCTTCAAGTGCAA 57.852 33.333 0.00 0.00 42.41 4.08
3779 4304 5.772825 AGAAATAAAGTGCTTCAAGTGCA 57.227 34.783 0.00 0.00 38.19 4.57
3780 4305 7.339953 CAAAAGAAATAAAGTGCTTCAAGTGC 58.660 34.615 0.00 0.00 0.00 4.40
3781 4306 7.706179 TCCAAAAGAAATAAAGTGCTTCAAGTG 59.294 33.333 0.00 0.00 0.00 3.16
3782 4307 7.781056 TCCAAAAGAAATAAAGTGCTTCAAGT 58.219 30.769 0.00 0.00 0.00 3.16
3783 4308 7.383300 CCTCCAAAAGAAATAAAGTGCTTCAAG 59.617 37.037 0.00 0.00 0.00 3.02
3784 4309 7.147742 ACCTCCAAAAGAAATAAAGTGCTTCAA 60.148 33.333 0.00 0.00 0.00 2.69
3785 4310 6.323739 ACCTCCAAAAGAAATAAAGTGCTTCA 59.676 34.615 0.00 0.00 0.00 3.02
3786 4311 6.749139 ACCTCCAAAAGAAATAAAGTGCTTC 58.251 36.000 0.00 0.00 0.00 3.86
3787 4312 6.731292 ACCTCCAAAAGAAATAAAGTGCTT 57.269 33.333 0.00 0.00 0.00 3.91
3788 4313 7.505923 AGTTACCTCCAAAAGAAATAAAGTGCT 59.494 33.333 0.00 0.00 0.00 4.40
3789 4314 7.658261 AGTTACCTCCAAAAGAAATAAAGTGC 58.342 34.615 0.00 0.00 0.00 4.40
3795 4320 9.635404 TCAAGAAAGTTACCTCCAAAAGAAATA 57.365 29.630 0.00 0.00 0.00 1.40
3796 4321 8.533569 TCAAGAAAGTTACCTCCAAAAGAAAT 57.466 30.769 0.00 0.00 0.00 2.17
3797 4322 7.948034 TCAAGAAAGTTACCTCCAAAAGAAA 57.052 32.000 0.00 0.00 0.00 2.52
3798 4323 7.832187 TCTTCAAGAAAGTTACCTCCAAAAGAA 59.168 33.333 0.00 0.00 36.31 2.52
3799 4324 7.343357 TCTTCAAGAAAGTTACCTCCAAAAGA 58.657 34.615 0.00 0.00 36.31 2.52
3800 4325 7.568199 TCTTCAAGAAAGTTACCTCCAAAAG 57.432 36.000 0.00 0.00 36.31 2.27
3801 4326 8.533569 AATCTTCAAGAAAGTTACCTCCAAAA 57.466 30.769 0.00 0.00 36.31 2.44
3802 4327 7.777910 TGAATCTTCAAGAAAGTTACCTCCAAA 59.222 33.333 0.00 0.00 36.31 3.28
3803 4328 7.287061 TGAATCTTCAAGAAAGTTACCTCCAA 58.713 34.615 0.00 0.00 36.31 3.53
3804 4329 6.837312 TGAATCTTCAAGAAAGTTACCTCCA 58.163 36.000 0.00 0.00 36.31 3.86
3805 4330 6.372937 CCTGAATCTTCAAGAAAGTTACCTCC 59.627 42.308 0.00 0.00 36.64 4.30
3806 4331 6.128145 GCCTGAATCTTCAAGAAAGTTACCTC 60.128 42.308 0.00 0.00 36.64 3.85
3807 4332 5.707764 GCCTGAATCTTCAAGAAAGTTACCT 59.292 40.000 0.00 0.00 36.64 3.08
3808 4333 5.473504 TGCCTGAATCTTCAAGAAAGTTACC 59.526 40.000 0.00 0.00 36.64 2.85
3809 4334 6.560253 TGCCTGAATCTTCAAGAAAGTTAC 57.440 37.500 0.00 0.00 36.64 2.50
3810 4335 6.772716 ACTTGCCTGAATCTTCAAGAAAGTTA 59.227 34.615 8.51 0.00 42.25 2.24
3811 4336 5.595952 ACTTGCCTGAATCTTCAAGAAAGTT 59.404 36.000 8.51 0.00 42.25 2.66
3812 4337 5.136105 ACTTGCCTGAATCTTCAAGAAAGT 58.864 37.500 8.51 8.51 40.85 2.66
3813 4338 5.240183 TGACTTGCCTGAATCTTCAAGAAAG 59.760 40.000 13.38 7.45 39.28 2.62
3814 4339 5.132502 TGACTTGCCTGAATCTTCAAGAAA 58.867 37.500 13.38 0.00 39.22 2.52
3815 4340 4.717877 TGACTTGCCTGAATCTTCAAGAA 58.282 39.130 13.38 0.00 39.22 2.52
3816 4341 4.356405 TGACTTGCCTGAATCTTCAAGA 57.644 40.909 13.38 0.00 39.22 3.02
3817 4342 5.443185 TTTGACTTGCCTGAATCTTCAAG 57.557 39.130 0.00 0.00 41.07 3.02
3818 4343 6.409524 AATTTGACTTGCCTGAATCTTCAA 57.590 33.333 0.00 0.00 36.64 2.69
3819 4344 6.183360 ACAAATTTGACTTGCCTGAATCTTCA 60.183 34.615 24.64 0.00 35.57 3.02
3820 4345 6.218746 ACAAATTTGACTTGCCTGAATCTTC 58.781 36.000 24.64 0.00 0.00 2.87
3821 4346 6.165700 ACAAATTTGACTTGCCTGAATCTT 57.834 33.333 24.64 0.00 0.00 2.40
3822 4347 5.302568 TGACAAATTTGACTTGCCTGAATCT 59.697 36.000 24.64 0.00 0.00 2.40
3823 4348 5.531634 TGACAAATTTGACTTGCCTGAATC 58.468 37.500 24.64 7.51 0.00 2.52
3824 4349 5.534207 TGACAAATTTGACTTGCCTGAAT 57.466 34.783 24.64 0.00 0.00 2.57
3825 4350 4.998671 TGACAAATTTGACTTGCCTGAA 57.001 36.364 24.64 0.00 0.00 3.02
3826 4351 4.583907 TGATGACAAATTTGACTTGCCTGA 59.416 37.500 24.64 1.40 0.00 3.86
3827 4352 4.873817 TGATGACAAATTTGACTTGCCTG 58.126 39.130 24.64 0.00 0.00 4.85
3828 4353 5.733620 ATGATGACAAATTTGACTTGCCT 57.266 34.783 24.64 0.00 0.00 4.75
3829 4354 8.385111 CAATTATGATGACAAATTTGACTTGCC 58.615 33.333 24.64 9.40 0.00 4.52
3830 4355 9.142515 TCAATTATGATGACAAATTTGACTTGC 57.857 29.630 24.64 11.74 0.00 4.01
3834 4359 9.844790 TGTCTCAATTATGATGACAAATTTGAC 57.155 29.630 24.64 18.43 39.04 3.18
3835 4360 9.844790 GTGTCTCAATTATGATGACAAATTTGA 57.155 29.630 24.64 3.48 41.26 2.69
3836 4361 9.628746 TGTGTCTCAATTATGATGACAAATTTG 57.371 29.630 16.67 16.67 41.26 2.32
3837 4362 9.850628 CTGTGTCTCAATTATGATGACAAATTT 57.149 29.630 10.50 0.00 41.26 1.82
3838 4363 9.234827 TCTGTGTCTCAATTATGATGACAAATT 57.765 29.630 10.50 0.00 41.26 1.82
3839 4364 8.797350 TCTGTGTCTCAATTATGATGACAAAT 57.203 30.769 10.50 0.00 41.26 2.32
3840 4365 8.797350 ATCTGTGTCTCAATTATGATGACAAA 57.203 30.769 10.50 6.79 41.26 2.83
3841 4366 8.797350 AATCTGTGTCTCAATTATGATGACAA 57.203 30.769 10.50 1.24 41.26 3.18
3842 4367 8.262933 AGAATCTGTGTCTCAATTATGATGACA 58.737 33.333 0.00 0.00 39.35 3.58
3843 4368 8.549548 CAGAATCTGTGTCTCAATTATGATGAC 58.450 37.037 1.31 0.00 35.79 3.06
3844 4369 8.262933 ACAGAATCTGTGTCTCAATTATGATGA 58.737 33.333 15.96 0.00 43.63 2.92
3845 4370 8.434733 ACAGAATCTGTGTCTCAATTATGATG 57.565 34.615 15.96 0.00 43.63 3.07


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

AutoCloner maintained by Alex Coulton.