Multiple sequence alignment - TraesCS3A01G116400

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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 TraesCS3A01G116400 chr3A 100.000 3605 0 0 1 3605 84648308 84651912 0.000000e+00 6658
1 TraesCS3A01G116400 chr3A 90.752 984 62 10 858 1837 85270551 85271509 0.000000e+00 1286
2 TraesCS3A01G116400 chr3A 90.556 953 60 13 899 1846 85371393 85372320 0.000000e+00 1234
3 TraesCS3A01G116400 chr3A 86.525 987 100 16 858 1839 85464171 85465129 0.000000e+00 1055
4 TraesCS3A01G116400 chr3A 86.117 994 105 16 858 1846 85533434 85534399 0.000000e+00 1040
5 TraesCS3A01G116400 chr3A 91.039 558 44 3 1926 2480 85271526 85272080 0.000000e+00 749
6 TraesCS3A01G116400 chr3A 90.553 561 42 6 1927 2480 85372329 85372885 0.000000e+00 732
7 TraesCS3A01G116400 chr3A 85.155 613 52 22 2514 3111 85372880 85373468 3.100000e-165 592
8 TraesCS3A01G116400 chr3A 84.839 620 54 23 2507 3111 85475534 85476128 4.010000e-164 588
9 TraesCS3A01G116400 chr3A 84.839 620 54 23 2507 3111 85544404 85544998 4.010000e-164 588
10 TraesCS3A01G116400 chr3A 90.046 432 37 4 1928 2356 85475095 85475523 4.070000e-154 555
11 TraesCS3A01G116400 chr3A 88.426 432 44 4 1928 2356 85543965 85544393 1.920000e-142 516
12 TraesCS3A01G116400 chr3A 86.230 305 21 12 2507 2798 85272069 85272365 9.720000e-81 311
13 TraesCS3A01G116400 chr3A 92.920 113 5 2 3001 3110 85272516 85272628 1.040000e-35 161
14 TraesCS3A01G116400 chr3A 82.812 128 16 5 667 792 85270428 85270551 3.810000e-20 110
15 TraesCS3A01G116400 chr3D 94.462 3232 111 29 2 3180 72251007 72254223 0.000000e+00 4915
16 TraesCS3A01G116400 chr3D 89.871 1007 68 12 858 1856 72648689 72649669 0.000000e+00 1264
17 TraesCS3A01G116400 chr3D 86.290 620 46 22 2507 3111 72650193 72650788 3.930000e-179 638
18 TraesCS3A01G116400 chr3D 90.722 388 30 3 2099 2480 72649817 72650204 2.480000e-141 512
19 TraesCS3A01G116400 chr3D 93.750 160 7 1 1888 2047 72649663 72649819 1.670000e-58 237
20 TraesCS3A01G116400 chr3D 83.108 148 18 2 645 792 72648549 72648689 1.050000e-25 128
21 TraesCS3A01G116400 chr3B 94.000 2500 93 14 555 3006 118136178 118138668 0.000000e+00 3733
22 TraesCS3A01G116400 chr3B 88.247 970 70 18 1517 2479 118251778 118252710 0.000000e+00 1120
23 TraesCS3A01G116400 chr3B 86.228 835 65 12 669 1497 118250998 118251788 0.000000e+00 859
24 TraesCS3A01G116400 chr3B 85.484 620 48 24 2507 3111 118252700 118253292 3.080000e-170 608
25 TraesCS3A01G116400 chr3B 89.398 415 25 6 1 414 118135756 118136152 4.150000e-139 505
26 TraesCS3A01G116400 chr2B 88.785 214 24 0 3222 3435 108508552 108508339 2.760000e-66 263
27 TraesCS3A01G116400 chr2B 88.889 162 18 0 3444 3605 108508369 108508208 2.200000e-47 200
28 TraesCS3A01G116400 chr2A 84.615 260 32 2 3255 3506 104770032 104770291 5.980000e-63 252
29 TraesCS3A01G116400 chr2D 85.537 242 23 1 3224 3465 160329336 160329565 3.600000e-60 243
30 TraesCS3A01G116400 chr2D 89.189 148 15 1 118 265 211148631 211148485 2.210000e-42 183
31 TraesCS3A01G116400 chr1D 81.218 197 23 7 3224 3419 99701588 99701771 2.900000e-31 147
32 TraesCS3A01G116400 chr5B 89.286 84 7 2 3297 3378 92238627 92238710 1.770000e-18 104


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 TraesCS3A01G116400 chr3A 84648308 84651912 3604 False 6658.000000 6658 100.000000 1 3605 1 chr3A.!!$F1 3604
1 TraesCS3A01G116400 chr3A 85464171 85465129 958 False 1055.000000 1055 86.525000 858 1839 1 chr3A.!!$F2 981
2 TraesCS3A01G116400 chr3A 85533434 85534399 965 False 1040.000000 1040 86.117000 858 1846 1 chr3A.!!$F3 988
3 TraesCS3A01G116400 chr3A 85371393 85373468 2075 False 852.666667 1234 88.754667 899 3111 3 chr3A.!!$F5 2212
4 TraesCS3A01G116400 chr3A 85475095 85476128 1033 False 571.500000 588 87.442500 1928 3111 2 chr3A.!!$F6 1183
5 TraesCS3A01G116400 chr3A 85543965 85544998 1033 False 552.000000 588 86.632500 1928 3111 2 chr3A.!!$F7 1183
6 TraesCS3A01G116400 chr3A 85270428 85272628 2200 False 523.400000 1286 88.750600 667 3110 5 chr3A.!!$F4 2443
7 TraesCS3A01G116400 chr3D 72251007 72254223 3216 False 4915.000000 4915 94.462000 2 3180 1 chr3D.!!$F1 3178
8 TraesCS3A01G116400 chr3D 72648549 72650788 2239 False 555.800000 1264 88.748200 645 3111 5 chr3D.!!$F2 2466
9 TraesCS3A01G116400 chr3B 118135756 118138668 2912 False 2119.000000 3733 91.699000 1 3006 2 chr3B.!!$F1 3005
10 TraesCS3A01G116400 chr3B 118250998 118253292 2294 False 862.333333 1120 86.653000 669 3111 3 chr3B.!!$F2 2442

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
496 538 0.783850 CTTCCCTTTTCCCTTCCCCA 59.216 55.0 0.0 0.0 0.00 4.96 F
1401 1488 0.173481 GTCTGCTCATCGCTGTGGTA 59.827 55.0 0.0 0.0 40.11 3.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1539 1659 0.602905 GGGACACGGACTTCCACTTG 60.603 60.0 0.0 0.0 33.01 3.16 R
3212 3427 0.040781 CGACCCAAACGAAAACGCAT 60.041 50.0 0.0 0.0 0.00 4.73 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 32 2.832129 AGTCCTATTGACCAAGAAGCGA 59.168 45.455 0.00 0.00 45.68 4.93
56 58 2.494870 AGCCGACGGTACTTCTTAATGT 59.505 45.455 16.73 0.00 0.00 2.71
67 69 7.750458 CGGTACTTCTTAATGTTGTACGTAAGA 59.250 37.037 0.00 0.00 43.62 2.10
116 118 6.183347 CCATGCTTAGATTTAGGGATTAGGG 58.817 44.000 0.00 0.00 0.00 3.53
131 133 6.395845 AGGGATTAGGGATTCTTATTGGGAAA 59.604 38.462 0.00 0.00 0.00 3.13
144 146 8.710749 TCTTATTGGGAAATAGATTGGATTGG 57.289 34.615 0.00 0.00 0.00 3.16
155 157 5.334724 AGATTGGATTGGCATTCAAGTTC 57.665 39.130 11.14 2.27 38.95 3.01
192 194 4.202101 TGGTTCAACTTAGGCATTGTTGTG 60.202 41.667 13.71 0.00 41.05 3.33
244 246 6.410243 AAGCGCTAAGATTCTAGTTCAAAC 57.590 37.500 12.05 0.00 0.00 2.93
322 324 9.383519 TGCTTTGAGTAATAGAAGTCATTTAGG 57.616 33.333 0.00 0.00 0.00 2.69
341 344 6.834168 TTAGGAAAAAGATTGCTACCAAGG 57.166 37.500 0.00 0.00 33.80 3.61
384 387 2.023404 TGGTAGTGAGGGGCTCTTCATA 60.023 50.000 0.01 0.00 0.00 2.15
398 440 9.373450 GGGGCTCTTCATATAGAGATGAATATA 57.627 37.037 6.69 0.00 43.22 0.86
494 536 1.147191 ACACTTCCCTTTTCCCTTCCC 59.853 52.381 0.00 0.00 0.00 3.97
496 538 0.783850 CTTCCCTTTTCCCTTCCCCA 59.216 55.000 0.00 0.00 0.00 4.96
535 577 8.840833 TTATTTTTCCTCAATAAAAAGGCACC 57.159 30.769 0.00 0.00 38.72 5.01
691 737 2.163815 GCAGCAGCTGATTCAACAATCT 59.836 45.455 27.39 0.00 39.49 2.40
701 747 5.739959 TGATTCAACAATCTTCCACGGATA 58.260 37.500 0.00 0.00 39.49 2.59
710 756 0.874175 TTCCACGGATATTCTGCGCG 60.874 55.000 0.00 0.00 43.35 6.86
728 774 2.961669 GCACGCCCACCTACAAACG 61.962 63.158 0.00 0.00 0.00 3.60
743 789 0.818040 AAACGGTGCCACAGAGGAAC 60.818 55.000 0.92 0.00 46.41 3.62
1009 1066 0.254178 GGCTTTGCAGATGGAGAGGA 59.746 55.000 0.00 0.00 0.00 3.71
1212 1275 4.648626 GTGAGGCAGCAGCACCCA 62.649 66.667 2.65 0.00 44.61 4.51
1401 1488 0.173481 GTCTGCTCATCGCTGTGGTA 59.827 55.000 0.00 0.00 40.11 3.25
1910 2051 4.379243 CAACTCGTCTGCCGGCCT 62.379 66.667 26.77 0.00 37.11 5.19
2647 2831 7.445402 GGACACCATGCATACATTAGATTTAGT 59.555 37.037 0.00 0.00 32.87 2.24
2686 2870 6.974622 CACCATGCATACTCCATTTTTACTTC 59.025 38.462 0.00 0.00 0.00 3.01
2803 2987 7.251704 TGAGTTGAGAAGTTTCAGAATTCAC 57.748 36.000 8.44 0.00 0.00 3.18
2874 3058 1.529865 GCCTGTACTTTGTCACCGTTC 59.470 52.381 0.00 0.00 0.00 3.95
2878 3069 4.116961 CTGTACTTTGTCACCGTTCAGAA 58.883 43.478 0.00 0.00 30.58 3.02
3111 3312 2.213499 CTGGTCAAATGCGTATCCTCC 58.787 52.381 0.00 0.00 0.00 4.30
3152 3367 4.006989 CGACTCCAACACCCAAATGAATA 58.993 43.478 0.00 0.00 0.00 1.75
3164 3379 9.936759 ACACCCAAATGAATAACGATTTTATTT 57.063 25.926 0.00 0.00 0.00 1.40
3166 3381 8.878769 ACCCAAATGAATAACGATTTTATTTGC 58.121 29.630 14.88 0.00 37.86 3.68
3179 3394 8.878769 ACGATTTTATTTGCTTTTTGTCTGTTT 58.121 25.926 0.00 0.00 0.00 2.83
3191 3406 8.238481 CTTTTTGTCTGTTTAAAGCAACTTCA 57.762 30.769 0.00 0.00 0.00 3.02
3192 3407 8.594881 TTTTTGTCTGTTTAAAGCAACTTCAA 57.405 26.923 0.00 0.00 0.00 2.69
3193 3408 7.575332 TTTGTCTGTTTAAAGCAACTTCAAC 57.425 32.000 0.00 0.00 0.00 3.18
3194 3409 5.328691 TGTCTGTTTAAAGCAACTTCAACG 58.671 37.500 0.00 0.00 0.00 4.10
3195 3410 4.733405 GTCTGTTTAAAGCAACTTCAACGG 59.267 41.667 0.00 0.00 30.49 4.44
3196 3411 4.035278 TGTTTAAAGCAACTTCAACGGG 57.965 40.909 0.00 0.00 0.00 5.28
3197 3412 2.785713 TTAAAGCAACTTCAACGGGC 57.214 45.000 0.00 0.00 0.00 6.13
3198 3413 1.975660 TAAAGCAACTTCAACGGGCT 58.024 45.000 0.00 0.00 36.13 5.19
3199 3414 0.385390 AAAGCAACTTCAACGGGCTG 59.615 50.000 0.00 0.00 34.56 4.85
3200 3415 0.465460 AAGCAACTTCAACGGGCTGA 60.465 50.000 0.00 0.00 34.56 4.26
3201 3416 0.250901 AGCAACTTCAACGGGCTGAT 60.251 50.000 0.00 0.00 32.76 2.90
3202 3417 0.169009 GCAACTTCAACGGGCTGATC 59.831 55.000 0.00 0.00 0.00 2.92
3203 3418 0.804989 CAACTTCAACGGGCTGATCC 59.195 55.000 0.00 0.00 0.00 3.36
3204 3419 0.400213 AACTTCAACGGGCTGATCCA 59.600 50.000 0.00 0.00 36.21 3.41
3205 3420 0.400213 ACTTCAACGGGCTGATCCAA 59.600 50.000 0.00 0.00 36.21 3.53
3206 3421 1.202879 ACTTCAACGGGCTGATCCAAA 60.203 47.619 0.00 0.00 36.21 3.28
3207 3422 1.200020 CTTCAACGGGCTGATCCAAAC 59.800 52.381 0.00 0.00 36.21 2.93
3208 3423 0.109532 TCAACGGGCTGATCCAAACA 59.890 50.000 0.00 0.00 36.21 2.83
3209 3424 0.523072 CAACGGGCTGATCCAAACAG 59.477 55.000 0.00 0.00 38.27 3.16
3210 3425 0.400213 AACGGGCTGATCCAAACAGA 59.600 50.000 0.00 0.00 37.54 3.41
3211 3426 0.321653 ACGGGCTGATCCAAACAGAC 60.322 55.000 0.00 0.00 42.10 3.51
3212 3427 0.321564 CGGGCTGATCCAAACAGACA 60.322 55.000 0.00 0.00 44.34 3.41
3213 3428 1.679944 CGGGCTGATCCAAACAGACAT 60.680 52.381 0.00 0.00 44.34 3.06
3214 3429 1.747355 GGGCTGATCCAAACAGACATG 59.253 52.381 0.00 0.00 44.34 3.21
3215 3430 1.133790 GGCTGATCCAAACAGACATGC 59.866 52.381 0.00 0.00 42.35 4.06
3216 3431 1.202110 GCTGATCCAAACAGACATGCG 60.202 52.381 0.00 0.00 37.54 4.73
3217 3432 2.079158 CTGATCCAAACAGACATGCGT 58.921 47.619 0.00 0.00 37.54 5.24
3218 3433 2.485426 CTGATCCAAACAGACATGCGTT 59.515 45.455 0.00 0.00 37.54 4.84
3219 3434 2.884012 TGATCCAAACAGACATGCGTTT 59.116 40.909 0.00 0.00 35.76 3.60
3220 3435 3.317711 TGATCCAAACAGACATGCGTTTT 59.682 39.130 5.92 0.00 33.14 2.43
3221 3436 3.347958 TCCAAACAGACATGCGTTTTC 57.652 42.857 5.92 0.00 33.14 2.29
3223 3438 2.540769 CCAAACAGACATGCGTTTTCGT 60.541 45.455 5.92 0.00 46.03 3.85
3224 3439 3.105203 CAAACAGACATGCGTTTTCGTT 58.895 40.909 5.92 0.00 46.03 3.85
3225 3440 3.414549 AACAGACATGCGTTTTCGTTT 57.585 38.095 0.00 0.00 46.03 3.60
3226 3441 2.715268 ACAGACATGCGTTTTCGTTTG 58.285 42.857 0.00 0.00 46.03 2.93
3227 3442 2.043411 CAGACATGCGTTTTCGTTTGG 58.957 47.619 0.00 0.00 46.03 3.28
3228 3443 1.001815 AGACATGCGTTTTCGTTTGGG 60.002 47.619 0.00 0.00 46.03 4.12
3229 3444 0.741915 ACATGCGTTTTCGTTTGGGT 59.258 45.000 0.00 0.00 46.03 4.51
3230 3445 1.268845 ACATGCGTTTTCGTTTGGGTC 60.269 47.619 0.00 0.00 46.03 4.46
3231 3446 0.040781 ATGCGTTTTCGTTTGGGTCG 60.041 50.000 0.00 0.00 46.03 4.79
3232 3447 1.369568 GCGTTTTCGTTTGGGTCGG 60.370 57.895 0.00 0.00 46.03 4.79
3233 3448 1.369568 CGTTTTCGTTTGGGTCGGC 60.370 57.895 0.00 0.00 38.65 5.54
3234 3449 1.008194 GTTTTCGTTTGGGTCGGCC 60.008 57.895 0.00 0.00 0.00 6.13
3235 3450 1.453379 TTTTCGTTTGGGTCGGCCA 60.453 52.632 9.07 0.00 36.17 5.36
3236 3451 1.035932 TTTTCGTTTGGGTCGGCCAA 61.036 50.000 9.07 0.00 36.17 4.52
3237 3452 1.035932 TTTCGTTTGGGTCGGCCAAA 61.036 50.000 9.07 0.00 36.17 3.28
3239 3454 2.333581 GTTTGGGTCGGCCAAACG 59.666 61.111 9.07 0.00 44.44 3.60
3240 3455 2.188161 GTTTGGGTCGGCCAAACGA 61.188 57.895 9.07 0.00 44.44 3.85
3241 3456 1.453379 TTTGGGTCGGCCAAACGAA 60.453 52.632 9.07 0.00 45.38 3.85
3242 3457 0.824182 TTTGGGTCGGCCAAACGAAT 60.824 50.000 9.07 0.00 45.38 3.34
3243 3458 0.036448 TTGGGTCGGCCAAACGAATA 59.964 50.000 9.07 0.00 45.38 1.75
3244 3459 0.253610 TGGGTCGGCCAAACGAATAT 59.746 50.000 9.07 0.00 45.38 1.28
3245 3460 0.942252 GGGTCGGCCAAACGAATATC 59.058 55.000 9.07 0.00 45.38 1.63
3246 3461 0.942252 GGTCGGCCAAACGAATATCC 59.058 55.000 0.00 0.00 45.38 2.59
3247 3462 1.658994 GTCGGCCAAACGAATATCCA 58.341 50.000 2.24 0.00 45.38 3.41
3248 3463 1.329599 GTCGGCCAAACGAATATCCAC 59.670 52.381 2.24 0.00 45.38 4.02
3249 3464 0.303493 CGGCCAAACGAATATCCACG 59.697 55.000 2.24 0.00 35.47 4.94
3250 3465 1.375551 GGCCAAACGAATATCCACGT 58.624 50.000 0.00 0.00 44.57 4.49
3251 3466 1.329599 GGCCAAACGAATATCCACGTC 59.670 52.381 0.00 0.00 41.87 4.34
3252 3467 1.329599 GCCAAACGAATATCCACGTCC 59.670 52.381 0.00 0.00 41.87 4.79
3253 3468 2.623535 CCAAACGAATATCCACGTCCA 58.376 47.619 0.00 0.00 41.87 4.02
3254 3469 2.350498 CCAAACGAATATCCACGTCCAC 59.650 50.000 0.00 0.00 41.87 4.02
3255 3470 3.259064 CAAACGAATATCCACGTCCACT 58.741 45.455 0.00 0.00 41.87 4.00
3256 3471 3.604875 AACGAATATCCACGTCCACTT 57.395 42.857 0.00 0.00 41.87 3.16
3257 3472 3.604875 ACGAATATCCACGTCCACTTT 57.395 42.857 0.00 0.00 38.34 2.66
3258 3473 3.934068 ACGAATATCCACGTCCACTTTT 58.066 40.909 0.00 0.00 38.34 2.27
3259 3474 4.320870 ACGAATATCCACGTCCACTTTTT 58.679 39.130 0.00 0.00 38.34 1.94
3260 3475 4.153475 ACGAATATCCACGTCCACTTTTTG 59.847 41.667 0.00 0.00 38.34 2.44
3262 3477 2.358322 ATCCACGTCCACTTTTTGGT 57.642 45.000 0.00 0.00 46.97 3.67
3263 3478 2.131776 TCCACGTCCACTTTTTGGTT 57.868 45.000 0.00 0.00 46.97 3.67
3264 3479 2.448453 TCCACGTCCACTTTTTGGTTT 58.552 42.857 0.00 0.00 46.97 3.27
3265 3480 2.164624 TCCACGTCCACTTTTTGGTTTG 59.835 45.455 0.00 0.00 46.97 2.93
3266 3481 2.535331 CACGTCCACTTTTTGGTTTGG 58.465 47.619 0.00 0.00 46.97 3.28
3267 3482 1.478916 ACGTCCACTTTTTGGTTTGGG 59.521 47.619 0.00 0.00 46.97 4.12
3268 3483 1.478916 CGTCCACTTTTTGGTTTGGGT 59.521 47.619 0.00 0.00 46.97 4.51
3269 3484 2.480587 CGTCCACTTTTTGGTTTGGGTC 60.481 50.000 0.00 0.00 46.97 4.46
3270 3485 2.764010 GTCCACTTTTTGGTTTGGGTCT 59.236 45.455 0.00 0.00 46.97 3.85
3271 3486 2.763448 TCCACTTTTTGGTTTGGGTCTG 59.237 45.455 0.00 0.00 46.97 3.51
3272 3487 2.549926 CACTTTTTGGTTTGGGTCTGC 58.450 47.619 0.00 0.00 0.00 4.26
3273 3488 2.093764 CACTTTTTGGTTTGGGTCTGCA 60.094 45.455 0.00 0.00 0.00 4.41
3274 3489 2.771372 ACTTTTTGGTTTGGGTCTGCAT 59.229 40.909 0.00 0.00 0.00 3.96
3275 3490 2.906691 TTTTGGTTTGGGTCTGCATG 57.093 45.000 0.00 0.00 0.00 4.06
3276 3491 0.392336 TTTGGTTTGGGTCTGCATGC 59.608 50.000 11.82 11.82 0.00 4.06
3277 3492 1.804396 TTGGTTTGGGTCTGCATGCG 61.804 55.000 14.09 8.20 0.00 4.73
3278 3493 2.126346 GTTTGGGTCTGCATGCGC 60.126 61.111 14.09 0.00 39.24 6.09
3279 3494 3.736100 TTTGGGTCTGCATGCGCG 61.736 61.111 14.09 0.00 42.97 6.86
3284 3499 3.422303 GTCTGCATGCGCGTCCAA 61.422 61.111 14.09 0.00 42.97 3.53
3285 3500 3.422303 TCTGCATGCGCGTCCAAC 61.422 61.111 14.09 0.00 42.97 3.77
3286 3501 4.799473 CTGCATGCGCGTCCAACG 62.799 66.667 14.09 0.00 45.88 4.10
3303 3518 2.676471 GGGTGGCCTGACGCATTT 60.676 61.111 3.32 0.00 40.31 2.32
3304 3519 2.275380 GGGTGGCCTGACGCATTTT 61.275 57.895 3.32 0.00 40.31 1.82
3305 3520 1.665442 GGTGGCCTGACGCATTTTT 59.335 52.632 3.32 0.00 40.31 1.94
3306 3521 0.667184 GGTGGCCTGACGCATTTTTG 60.667 55.000 3.32 0.00 40.31 2.44
3307 3522 1.006337 TGGCCTGACGCATTTTTGC 60.006 52.632 3.32 0.00 40.31 3.68
3308 3523 1.006337 GGCCTGACGCATTTTTGCA 60.006 52.632 0.00 0.00 40.31 4.08
3309 3524 0.390209 GGCCTGACGCATTTTTGCAT 60.390 50.000 0.00 0.00 40.31 3.96
3310 3525 0.717224 GCCTGACGCATTTTTGCATG 59.283 50.000 0.00 0.00 37.47 4.06
3311 3526 1.936203 GCCTGACGCATTTTTGCATGT 60.936 47.619 0.00 0.00 37.47 3.21
3312 3527 1.987770 CCTGACGCATTTTTGCATGTC 59.012 47.619 0.00 0.00 34.41 3.06
3313 3528 1.987770 CTGACGCATTTTTGCATGTCC 59.012 47.619 0.00 0.00 34.41 4.02
3314 3529 0.984109 GACGCATTTTTGCATGTCCG 59.016 50.000 0.00 0.00 34.41 4.79
3315 3530 0.313672 ACGCATTTTTGCATGTCCGT 59.686 45.000 0.00 0.00 34.41 4.69
3316 3531 0.984109 CGCATTTTTGCATGTCCGTC 59.016 50.000 0.00 0.00 34.41 4.79
3317 3532 1.401409 CGCATTTTTGCATGTCCGTCT 60.401 47.619 0.00 0.00 34.41 4.18
3318 3533 2.676076 GCATTTTTGCATGTCCGTCTT 58.324 42.857 0.00 0.00 34.41 3.01
3319 3534 2.409378 GCATTTTTGCATGTCCGTCTTG 59.591 45.455 0.00 0.00 34.41 3.02
3320 3535 2.791383 TTTTTGCATGTCCGTCTTGG 57.209 45.000 0.00 0.00 40.09 3.61
3321 3536 0.313672 TTTTGCATGTCCGTCTTGGC 59.686 50.000 0.00 0.00 37.80 4.52
3322 3537 0.821301 TTTGCATGTCCGTCTTGGCA 60.821 50.000 0.00 0.00 37.80 4.92
3323 3538 0.608856 TTGCATGTCCGTCTTGGCAT 60.609 50.000 0.00 0.00 37.80 4.40
3324 3539 0.608856 TGCATGTCCGTCTTGGCATT 60.609 50.000 0.00 0.00 37.80 3.56
3325 3540 0.527565 GCATGTCCGTCTTGGCATTT 59.472 50.000 0.00 0.00 37.80 2.32
3326 3541 1.468054 GCATGTCCGTCTTGGCATTTC 60.468 52.381 0.00 0.00 37.80 2.17
3327 3542 1.086696 ATGTCCGTCTTGGCATTTCG 58.913 50.000 0.00 0.00 37.80 3.46
3328 3543 0.250124 TGTCCGTCTTGGCATTTCGT 60.250 50.000 0.00 0.00 37.80 3.85
3329 3544 0.442699 GTCCGTCTTGGCATTTCGTC 59.557 55.000 0.00 0.00 37.80 4.20
3330 3545 1.011968 TCCGTCTTGGCATTTCGTCG 61.012 55.000 0.00 0.00 37.80 5.12
3331 3546 1.011968 CCGTCTTGGCATTTCGTCGA 61.012 55.000 0.00 0.00 0.00 4.20
3332 3547 0.787787 CGTCTTGGCATTTCGTCGAA 59.212 50.000 2.90 2.90 0.00 3.71
3333 3548 1.461888 CGTCTTGGCATTTCGTCGAAC 60.462 52.381 7.29 0.00 0.00 3.95
3334 3549 1.529438 GTCTTGGCATTTCGTCGAACA 59.471 47.619 7.29 0.00 0.00 3.18
3335 3550 1.529438 TCTTGGCATTTCGTCGAACAC 59.471 47.619 7.29 0.00 0.00 3.32
3343 3558 3.750162 CGTCGAACACGTAGCAGG 58.250 61.111 0.00 0.00 44.07 4.85
3344 3559 2.434134 CGTCGAACACGTAGCAGGC 61.434 63.158 0.00 0.00 44.07 4.85
3345 3560 1.372499 GTCGAACACGTAGCAGGCA 60.372 57.895 0.00 0.00 0.00 4.75
3346 3561 1.080772 TCGAACACGTAGCAGGCAG 60.081 57.895 0.00 0.00 0.00 4.85
3347 3562 2.730672 CGAACACGTAGCAGGCAGC 61.731 63.158 0.00 0.00 46.19 5.25
3364 3579 4.408821 CGGGGTTGGCAGCAGCTA 62.409 66.667 3.14 0.00 41.70 3.32
3365 3580 2.439156 GGGGTTGGCAGCAGCTAG 60.439 66.667 3.14 0.00 41.70 3.42
3366 3581 2.671070 GGGTTGGCAGCAGCTAGA 59.329 61.111 3.14 0.00 41.70 2.43
3367 3582 1.746991 GGGTTGGCAGCAGCTAGAC 60.747 63.158 3.14 0.00 41.70 2.59
3368 3583 2.103042 GGTTGGCAGCAGCTAGACG 61.103 63.158 3.14 0.00 41.70 4.18
3369 3584 2.103042 GTTGGCAGCAGCTAGACGG 61.103 63.158 0.00 0.00 41.70 4.79
3370 3585 3.958147 TTGGCAGCAGCTAGACGGC 62.958 63.158 0.00 0.00 41.70 5.68
3373 3588 4.880537 CAGCAGCTAGACGGCCGG 62.881 72.222 31.76 12.94 40.83 6.13
3468 3683 4.813526 CGACCTGGACGAGCGTCG 62.814 72.222 13.19 11.74 45.41 5.12
3503 3718 4.124943 CGGAGGGGAGAGGGACGA 62.125 72.222 0.00 0.00 0.00 4.20
3504 3719 2.123640 GGAGGGGAGAGGGACGAG 60.124 72.222 0.00 0.00 0.00 4.18
3505 3720 2.835895 GAGGGGAGAGGGACGAGC 60.836 72.222 0.00 0.00 0.00 5.03
3506 3721 3.351885 AGGGGAGAGGGACGAGCT 61.352 66.667 0.00 0.00 0.00 4.09
3507 3722 2.835895 GGGGAGAGGGACGAGCTC 60.836 72.222 2.73 2.73 0.00 4.09
3508 3723 2.835895 GGGAGAGGGACGAGCTCC 60.836 72.222 8.47 0.00 45.88 4.70
3509 3724 2.277404 GGAGAGGGACGAGCTCCT 59.723 66.667 8.47 0.00 43.79 3.69
3510 3725 2.124693 GGAGAGGGACGAGCTCCTG 61.125 68.421 8.47 0.00 43.79 3.86
3511 3726 2.757917 AGAGGGACGAGCTCCTGC 60.758 66.667 8.47 1.36 39.39 4.85
3512 3727 4.200283 GAGGGACGAGCTCCTGCG 62.200 72.222 8.47 0.00 45.42 5.18
3546 3761 3.441290 CCGGGAAGAGCGTCGTCT 61.441 66.667 0.00 0.00 0.00 4.18
3547 3762 2.100603 CGGGAAGAGCGTCGTCTC 59.899 66.667 8.15 8.15 0.00 3.36
3548 3763 2.490685 GGGAAGAGCGTCGTCTCC 59.509 66.667 11.45 4.81 33.66 3.71
3549 3764 2.047443 GGGAAGAGCGTCGTCTCCT 61.047 63.158 11.45 1.44 33.66 3.69
3550 3765 1.137825 GGAAGAGCGTCGTCTCCTG 59.862 63.158 11.45 0.00 33.66 3.86
3551 3766 1.137825 GAAGAGCGTCGTCTCCTGG 59.862 63.158 11.45 0.00 33.66 4.45
3552 3767 2.272918 GAAGAGCGTCGTCTCCTGGG 62.273 65.000 11.45 0.00 33.66 4.45
3553 3768 4.500116 GAGCGTCGTCTCCTGGGC 62.500 72.222 0.00 0.00 0.00 5.36
3579 3794 4.803426 GCACGGCCTGGACGAGAG 62.803 72.222 31.73 18.47 35.20 3.20
3590 3805 4.315588 ACGAGAGTCACCTACGGG 57.684 61.111 0.00 0.00 44.19 5.28
3591 3806 1.378250 ACGAGAGTCACCTACGGGG 60.378 63.158 0.00 0.00 44.19 5.73
3592 3807 1.077930 CGAGAGTCACCTACGGGGA 60.078 63.158 3.71 0.00 38.76 4.81
3593 3808 1.375098 CGAGAGTCACCTACGGGGAC 61.375 65.000 7.19 7.19 38.76 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 42 5.772521 ACGTACAACATTAAGAAGTACCGT 58.227 37.500 0.00 0.00 33.34 4.83
56 58 5.300286 GCTAGGATAACCCTCTTACGTACAA 59.700 44.000 0.00 0.00 43.31 2.41
78 80 2.662866 AGCATGGCATGATTGTTAGCT 58.337 42.857 30.69 14.76 0.00 3.32
131 133 6.238842 CGAACTTGAATGCCAATCCAATCTAT 60.239 38.462 0.00 0.00 33.68 1.98
144 146 2.935201 AGATCTGCTCGAACTTGAATGC 59.065 45.455 0.00 0.00 0.00 3.56
155 157 4.872691 AGTTGAACCAATAAGATCTGCTCG 59.127 41.667 0.00 0.00 0.00 5.03
205 207 7.495606 TCTTAGCGCTTATTTGATGAAGATTGA 59.504 33.333 18.68 0.00 0.00 2.57
219 221 7.764443 TGTTTGAACTAGAATCTTAGCGCTTAT 59.236 33.333 18.68 4.23 0.00 1.73
310 312 9.561270 GTAGCAATCTTTTTCCTAAATGACTTC 57.439 33.333 0.00 0.00 32.31 3.01
322 324 4.790765 AGCCTTGGTAGCAATCTTTTTC 57.209 40.909 7.98 0.00 0.00 2.29
341 344 5.221126 CCAACAATTAATCCTAGCCTCAAGC 60.221 44.000 0.00 0.00 44.25 4.01
351 354 5.340027 CCCCTCACTACCAACAATTAATCCT 60.340 44.000 0.00 0.00 0.00 3.24
357 360 1.710809 AGCCCCTCACTACCAACAATT 59.289 47.619 0.00 0.00 0.00 2.32
551 594 2.435372 TTTTCACAAGTGCCTCACCT 57.565 45.000 0.00 0.00 34.49 4.00
615 658 7.106439 TGGCAAAGTTTTCTTTCTTACATGA 57.894 32.000 0.00 0.00 46.89 3.07
691 737 0.874175 CGCGCAGAATATCCGTGGAA 60.874 55.000 8.75 0.00 0.00 3.53
710 756 2.951458 GTTTGTAGGTGGGCGTGC 59.049 61.111 0.00 0.00 0.00 5.34
930 978 2.972348 AGGGACTCTTGTGGTCAACTA 58.028 47.619 0.00 0.00 35.61 2.24
1009 1066 2.270205 CAGCCCTGCTCCGTCAAT 59.730 61.111 0.00 0.00 36.40 2.57
1395 1482 1.218585 CCCGGCGTTGTATACCACA 59.781 57.895 6.01 0.00 34.51 4.17
1401 1488 3.069946 TCGTCCCCGGCGTTGTAT 61.070 61.111 6.01 0.00 33.95 2.29
1539 1659 0.602905 GGGACACGGACTTCCACTTG 60.603 60.000 0.00 0.00 33.01 3.16
1910 2051 1.305802 ACCATCGCTACCACCTGGA 60.306 57.895 0.00 0.00 38.94 3.86
2647 2831 2.534990 CATGGTGGCCTAAGGGAAAAA 58.465 47.619 3.32 0.00 33.58 1.94
2686 2870 1.381928 AATGCATGCTGGCGAAGGAG 61.382 55.000 20.33 0.00 36.28 3.69
2803 2987 3.877559 TCAACAAGAGACCATAGGCATG 58.122 45.455 0.00 0.00 0.00 4.06
2874 3058 5.299531 TCGAGGTAGATACTCCAATGTTCTG 59.700 44.000 0.00 0.00 0.00 3.02
2878 3069 4.456222 CGATCGAGGTAGATACTCCAATGT 59.544 45.833 10.26 0.00 0.00 2.71
3111 3312 4.659172 TGAAAGGCGGCCACTGGG 62.659 66.667 23.09 0.00 37.18 4.45
3126 3333 1.691195 TTGGGTGTTGGAGTCGCTGA 61.691 55.000 0.00 0.00 0.00 4.26
3127 3334 0.817634 TTTGGGTGTTGGAGTCGCTG 60.818 55.000 0.00 0.00 0.00 5.18
3131 3338 5.619086 CGTTATTCATTTGGGTGTTGGAGTC 60.619 44.000 0.00 0.00 0.00 3.36
3152 3367 8.419076 ACAGACAAAAAGCAAATAAAATCGTT 57.581 26.923 0.00 0.00 0.00 3.85
3166 3381 8.238481 TGAAGTTGCTTTAAACAGACAAAAAG 57.762 30.769 0.00 0.00 32.21 2.27
3172 3387 4.733405 CCGTTGAAGTTGCTTTAAACAGAC 59.267 41.667 0.00 0.00 32.21 3.51
3173 3388 4.201970 CCCGTTGAAGTTGCTTTAAACAGA 60.202 41.667 0.00 0.00 32.21 3.41
3174 3389 4.041723 CCCGTTGAAGTTGCTTTAAACAG 58.958 43.478 0.00 0.00 32.21 3.16
3175 3390 3.735514 GCCCGTTGAAGTTGCTTTAAACA 60.736 43.478 0.00 0.00 32.21 2.83
3176 3391 2.792674 GCCCGTTGAAGTTGCTTTAAAC 59.207 45.455 0.00 0.00 0.00 2.01
3179 3394 1.606668 CAGCCCGTTGAAGTTGCTTTA 59.393 47.619 0.00 0.00 0.00 1.85
3180 3395 0.385390 CAGCCCGTTGAAGTTGCTTT 59.615 50.000 0.00 0.00 0.00 3.51
3181 3396 0.465460 TCAGCCCGTTGAAGTTGCTT 60.465 50.000 0.00 0.00 0.00 3.91
3182 3397 0.250901 ATCAGCCCGTTGAAGTTGCT 60.251 50.000 0.00 0.00 0.00 3.91
3183 3398 0.169009 GATCAGCCCGTTGAAGTTGC 59.831 55.000 0.00 0.00 0.00 4.17
3184 3399 0.804989 GGATCAGCCCGTTGAAGTTG 59.195 55.000 0.00 0.00 0.00 3.16
3185 3400 0.400213 TGGATCAGCCCGTTGAAGTT 59.600 50.000 0.00 0.00 34.97 2.66
3186 3401 0.400213 TTGGATCAGCCCGTTGAAGT 59.600 50.000 0.00 0.00 34.97 3.01
3187 3402 1.200020 GTTTGGATCAGCCCGTTGAAG 59.800 52.381 0.00 0.00 34.97 3.02
3188 3403 1.243902 GTTTGGATCAGCCCGTTGAA 58.756 50.000 0.00 0.00 34.97 2.69
3189 3404 0.109532 TGTTTGGATCAGCCCGTTGA 59.890 50.000 0.00 0.00 34.97 3.18
3190 3405 0.523072 CTGTTTGGATCAGCCCGTTG 59.477 55.000 0.00 0.00 34.97 4.10
3191 3406 0.400213 TCTGTTTGGATCAGCCCGTT 59.600 50.000 0.00 0.00 34.97 4.44
3192 3407 0.321653 GTCTGTTTGGATCAGCCCGT 60.322 55.000 0.00 0.00 34.97 5.28
3193 3408 0.321564 TGTCTGTTTGGATCAGCCCG 60.322 55.000 0.00 0.00 34.97 6.13
3194 3409 1.747355 CATGTCTGTTTGGATCAGCCC 59.253 52.381 0.00 0.00 34.97 5.19
3195 3410 1.133790 GCATGTCTGTTTGGATCAGCC 59.866 52.381 0.00 0.00 33.48 4.85
3196 3411 1.202110 CGCATGTCTGTTTGGATCAGC 60.202 52.381 0.00 0.00 33.48 4.26
3197 3412 2.079158 ACGCATGTCTGTTTGGATCAG 58.921 47.619 0.00 0.00 0.00 2.90
3198 3413 2.183478 ACGCATGTCTGTTTGGATCA 57.817 45.000 0.00 0.00 0.00 2.92
3199 3414 3.559238 AAACGCATGTCTGTTTGGATC 57.441 42.857 10.64 0.00 36.96 3.36
3200 3415 3.609175 CGAAAACGCATGTCTGTTTGGAT 60.609 43.478 11.72 0.32 38.26 3.41
3201 3416 2.286713 CGAAAACGCATGTCTGTTTGGA 60.287 45.455 11.72 0.00 38.26 3.53
3202 3417 2.043411 CGAAAACGCATGTCTGTTTGG 58.957 47.619 11.72 5.83 38.26 3.28
3203 3418 2.715268 ACGAAAACGCATGTCTGTTTG 58.285 42.857 11.72 5.43 38.26 2.93
3204 3419 3.414549 AACGAAAACGCATGTCTGTTT 57.585 38.095 6.93 6.93 39.84 2.83
3205 3420 3.105203 CAAACGAAAACGCATGTCTGTT 58.895 40.909 0.00 0.00 0.00 3.16
3206 3421 2.540769 CCAAACGAAAACGCATGTCTGT 60.541 45.455 0.00 0.00 0.00 3.41
3207 3422 2.043411 CCAAACGAAAACGCATGTCTG 58.957 47.619 0.00 0.00 0.00 3.51
3208 3423 1.001815 CCCAAACGAAAACGCATGTCT 60.002 47.619 0.00 0.00 0.00 3.41
3209 3424 1.268845 ACCCAAACGAAAACGCATGTC 60.269 47.619 0.00 0.00 0.00 3.06
3210 3425 0.741915 ACCCAAACGAAAACGCATGT 59.258 45.000 0.00 0.00 0.00 3.21
3211 3426 1.404477 GACCCAAACGAAAACGCATG 58.596 50.000 0.00 0.00 0.00 4.06
3212 3427 0.040781 CGACCCAAACGAAAACGCAT 60.041 50.000 0.00 0.00 0.00 4.73
3213 3428 1.352404 CGACCCAAACGAAAACGCA 59.648 52.632 0.00 0.00 0.00 5.24
3214 3429 1.369568 CCGACCCAAACGAAAACGC 60.370 57.895 0.00 0.00 0.00 4.84
3215 3430 1.369568 GCCGACCCAAACGAAAACG 60.370 57.895 0.00 0.00 0.00 3.60
3216 3431 1.008194 GGCCGACCCAAACGAAAAC 60.008 57.895 0.00 0.00 0.00 2.43
3217 3432 1.453379 TGGCCGACCCAAACGAAAA 60.453 52.632 0.00 0.00 41.82 2.29
3218 3433 2.192443 TGGCCGACCCAAACGAAA 59.808 55.556 0.00 0.00 41.82 3.46
3225 3440 0.253610 ATATTCGTTTGGCCGACCCA 59.746 50.000 0.00 0.00 43.51 4.51
3226 3441 0.942252 GATATTCGTTTGGCCGACCC 59.058 55.000 0.00 0.00 36.42 4.46
3227 3442 0.942252 GGATATTCGTTTGGCCGACC 59.058 55.000 0.00 0.00 36.42 4.79
3228 3443 1.329599 GTGGATATTCGTTTGGCCGAC 59.670 52.381 0.00 0.00 36.42 4.79
3229 3444 1.658994 GTGGATATTCGTTTGGCCGA 58.341 50.000 0.00 0.00 34.52 5.54
3230 3445 0.303493 CGTGGATATTCGTTTGGCCG 59.697 55.000 0.00 0.00 0.00 6.13
3231 3446 1.329599 GACGTGGATATTCGTTTGGCC 59.670 52.381 0.00 0.00 40.39 5.36
3232 3447 1.329599 GGACGTGGATATTCGTTTGGC 59.670 52.381 0.00 0.00 40.39 4.52
3233 3448 2.350498 GTGGACGTGGATATTCGTTTGG 59.650 50.000 0.00 0.00 40.39 3.28
3234 3449 3.259064 AGTGGACGTGGATATTCGTTTG 58.741 45.455 0.00 0.00 40.39 2.93
3235 3450 3.604875 AGTGGACGTGGATATTCGTTT 57.395 42.857 0.00 0.00 40.39 3.60
3236 3451 3.604875 AAGTGGACGTGGATATTCGTT 57.395 42.857 0.00 0.00 40.39 3.85
3237 3452 3.604875 AAAGTGGACGTGGATATTCGT 57.395 42.857 0.00 0.00 43.00 3.85
3238 3453 4.647964 CAAAAAGTGGACGTGGATATTCG 58.352 43.478 0.00 0.00 0.00 3.34
3252 3467 2.093764 TGCAGACCCAAACCAAAAAGTG 60.094 45.455 0.00 0.00 0.00 3.16
3253 3468 2.183679 TGCAGACCCAAACCAAAAAGT 58.816 42.857 0.00 0.00 0.00 2.66
3254 3469 2.977772 TGCAGACCCAAACCAAAAAG 57.022 45.000 0.00 0.00 0.00 2.27
3255 3470 2.744494 GCATGCAGACCCAAACCAAAAA 60.744 45.455 14.21 0.00 0.00 1.94
3256 3471 1.202627 GCATGCAGACCCAAACCAAAA 60.203 47.619 14.21 0.00 0.00 2.44
3257 3472 0.392336 GCATGCAGACCCAAACCAAA 59.608 50.000 14.21 0.00 0.00 3.28
3258 3473 1.804396 CGCATGCAGACCCAAACCAA 61.804 55.000 19.57 0.00 0.00 3.67
3259 3474 2.267351 CGCATGCAGACCCAAACCA 61.267 57.895 19.57 0.00 0.00 3.67
3260 3475 2.568090 CGCATGCAGACCCAAACC 59.432 61.111 19.57 0.00 0.00 3.27
3261 3476 2.126346 GCGCATGCAGACCCAAAC 60.126 61.111 19.57 0.00 42.15 2.93
3262 3477 3.736100 CGCGCATGCAGACCCAAA 61.736 61.111 19.57 0.00 42.97 3.28
3267 3482 3.422303 TTGGACGCGCATGCAGAC 61.422 61.111 19.57 10.98 42.97 3.51
3268 3483 3.422303 GTTGGACGCGCATGCAGA 61.422 61.111 19.57 0.00 42.97 4.26
3269 3484 4.799473 CGTTGGACGCGCATGCAG 62.799 66.667 19.57 13.48 42.97 4.41
3286 3501 1.815817 AAAAATGCGTCAGGCCACCC 61.816 55.000 5.01 0.00 42.61 4.61
3287 3502 0.667184 CAAAAATGCGTCAGGCCACC 60.667 55.000 5.01 0.00 42.61 4.61
3288 3503 1.284297 GCAAAAATGCGTCAGGCCAC 61.284 55.000 5.01 0.00 42.61 5.01
3289 3504 1.006337 GCAAAAATGCGTCAGGCCA 60.006 52.632 5.01 0.00 42.61 5.36
3290 3505 0.390209 ATGCAAAAATGCGTCAGGCC 60.390 50.000 0.00 0.00 42.61 5.19
3291 3506 0.717224 CATGCAAAAATGCGTCAGGC 59.283 50.000 0.00 0.00 43.96 4.85
3292 3507 1.987770 GACATGCAAAAATGCGTCAGG 59.012 47.619 0.00 0.00 37.69 3.86
3293 3508 1.987770 GGACATGCAAAAATGCGTCAG 59.012 47.619 0.00 0.00 37.69 3.51
3294 3509 1.665448 CGGACATGCAAAAATGCGTCA 60.665 47.619 0.00 0.00 37.69 4.35
3295 3510 0.984109 CGGACATGCAAAAATGCGTC 59.016 50.000 0.00 0.00 37.69 5.19
3296 3511 0.313672 ACGGACATGCAAAAATGCGT 59.686 45.000 0.00 0.00 37.69 5.24
3297 3512 0.984109 GACGGACATGCAAAAATGCG 59.016 50.000 0.00 0.00 37.69 4.73
3298 3513 2.352503 AGACGGACATGCAAAAATGC 57.647 45.000 0.00 0.00 0.00 3.56
3299 3514 2.988493 CCAAGACGGACATGCAAAAATG 59.012 45.455 0.00 0.00 36.56 2.32
3300 3515 2.610232 GCCAAGACGGACATGCAAAAAT 60.610 45.455 0.00 0.00 36.56 1.82
3301 3516 1.269517 GCCAAGACGGACATGCAAAAA 60.270 47.619 0.00 0.00 36.56 1.94
3302 3517 0.313672 GCCAAGACGGACATGCAAAA 59.686 50.000 0.00 0.00 36.56 2.44
3303 3518 0.821301 TGCCAAGACGGACATGCAAA 60.821 50.000 0.00 0.00 36.56 3.68
3304 3519 0.608856 ATGCCAAGACGGACATGCAA 60.609 50.000 0.00 0.00 36.56 4.08
3305 3520 0.608856 AATGCCAAGACGGACATGCA 60.609 50.000 0.00 0.00 36.56 3.96
3306 3521 0.527565 AAATGCCAAGACGGACATGC 59.472 50.000 0.00 0.00 36.56 4.06
3307 3522 1.202065 CGAAATGCCAAGACGGACATG 60.202 52.381 0.00 0.00 36.56 3.21
3308 3523 1.086696 CGAAATGCCAAGACGGACAT 58.913 50.000 0.00 0.00 36.56 3.06
3309 3524 0.250124 ACGAAATGCCAAGACGGACA 60.250 50.000 0.00 0.00 36.56 4.02
3310 3525 0.442699 GACGAAATGCCAAGACGGAC 59.557 55.000 0.00 0.00 36.56 4.79
3311 3526 1.011968 CGACGAAATGCCAAGACGGA 61.012 55.000 0.00 0.00 36.56 4.69
3312 3527 1.011968 TCGACGAAATGCCAAGACGG 61.012 55.000 0.00 0.00 38.11 4.79
3313 3528 0.787787 TTCGACGAAATGCCAAGACG 59.212 50.000 8.05 0.00 0.00 4.18
3314 3529 1.529438 TGTTCGACGAAATGCCAAGAC 59.471 47.619 12.67 0.00 0.00 3.01
3315 3530 1.529438 GTGTTCGACGAAATGCCAAGA 59.471 47.619 12.67 0.00 0.00 3.02
3316 3531 1.950472 GTGTTCGACGAAATGCCAAG 58.050 50.000 12.67 0.00 0.00 3.61
3327 3542 1.344942 CTGCCTGCTACGTGTTCGAC 61.345 60.000 0.00 0.00 40.62 4.20
3328 3543 1.080772 CTGCCTGCTACGTGTTCGA 60.081 57.895 0.00 0.00 40.62 3.71
3329 3544 2.730672 GCTGCCTGCTACGTGTTCG 61.731 63.158 0.00 0.00 39.84 3.95
3330 3545 2.730672 CGCTGCCTGCTACGTGTTC 61.731 63.158 0.00 0.00 40.11 3.18
3331 3546 2.738521 CGCTGCCTGCTACGTGTT 60.739 61.111 0.00 0.00 40.11 3.32
3332 3547 4.742201 CCGCTGCCTGCTACGTGT 62.742 66.667 0.00 0.00 40.11 4.49
3336 3551 4.410400 AACCCCGCTGCCTGCTAC 62.410 66.667 0.00 0.00 40.11 3.58
3337 3552 4.408821 CAACCCCGCTGCCTGCTA 62.409 66.667 0.00 0.00 40.11 3.49
3347 3562 4.408821 TAGCTGCTGCCAACCCCG 62.409 66.667 13.43 0.00 40.80 5.73
3348 3563 2.439156 CTAGCTGCTGCCAACCCC 60.439 66.667 13.43 0.00 40.80 4.95
3349 3564 1.746991 GTCTAGCTGCTGCCAACCC 60.747 63.158 13.43 0.00 40.80 4.11
3350 3565 2.103042 CGTCTAGCTGCTGCCAACC 61.103 63.158 13.43 0.00 40.80 3.77
3351 3566 2.103042 CCGTCTAGCTGCTGCCAAC 61.103 63.158 13.43 7.18 40.80 3.77
3352 3567 2.265739 CCGTCTAGCTGCTGCCAA 59.734 61.111 13.43 0.00 40.80 4.52
3353 3568 4.457496 GCCGTCTAGCTGCTGCCA 62.457 66.667 13.43 0.00 40.80 4.92
3356 3571 4.880537 CCGGCCGTCTAGCTGCTG 62.881 72.222 26.12 0.00 37.84 4.41
3451 3666 4.813526 CGACGCTCGTCCAGGTCG 62.814 72.222 15.64 0.00 44.92 4.79
3486 3701 4.124943 TCGTCCCTCTCCCCTCCG 62.125 72.222 0.00 0.00 0.00 4.63
3487 3702 2.123640 CTCGTCCCTCTCCCCTCC 60.124 72.222 0.00 0.00 0.00 4.30
3488 3703 2.835895 GCTCGTCCCTCTCCCCTC 60.836 72.222 0.00 0.00 0.00 4.30
3489 3704 3.351885 AGCTCGTCCCTCTCCCCT 61.352 66.667 0.00 0.00 0.00 4.79
3490 3705 2.835895 GAGCTCGTCCCTCTCCCC 60.836 72.222 0.00 0.00 0.00 4.81
3491 3706 2.835895 GGAGCTCGTCCCTCTCCC 60.836 72.222 7.83 0.00 40.29 4.30
3529 3744 3.398353 GAGACGACGCTCTTCCCGG 62.398 68.421 10.71 0.00 32.16 5.73
3530 3745 2.100603 GAGACGACGCTCTTCCCG 59.899 66.667 10.71 0.00 32.16 5.14
3531 3746 2.047443 AGGAGACGACGCTCTTCCC 61.047 63.158 15.52 7.68 35.26 3.97
3532 3747 1.137825 CAGGAGACGACGCTCTTCC 59.862 63.158 15.52 8.67 35.26 3.46
3533 3748 1.137825 CCAGGAGACGACGCTCTTC 59.862 63.158 15.52 7.99 35.26 2.87
3534 3749 2.344203 CCCAGGAGACGACGCTCTT 61.344 63.158 15.52 8.18 35.26 2.85
3535 3750 2.752238 CCCAGGAGACGACGCTCT 60.752 66.667 15.52 8.84 35.26 4.09
3536 3751 4.500116 GCCCAGGAGACGACGCTC 62.500 72.222 9.81 9.81 0.00 5.03
3562 3777 4.803426 CTCTCGTCCAGGCCGTGC 62.803 72.222 0.00 0.00 0.00 5.34
3563 3778 3.343788 GACTCTCGTCCAGGCCGTG 62.344 68.421 0.00 0.00 33.98 4.94
3564 3779 3.063084 GACTCTCGTCCAGGCCGT 61.063 66.667 0.00 0.00 33.98 5.68
3565 3780 3.062466 TGACTCTCGTCCAGGCCG 61.062 66.667 0.00 0.00 39.47 6.13
3566 3781 2.574399 GTGACTCTCGTCCAGGCC 59.426 66.667 0.00 0.00 39.47 5.19
3567 3782 0.680280 TAGGTGACTCTCGTCCAGGC 60.680 60.000 0.00 0.00 43.67 4.85
3568 3783 1.096416 GTAGGTGACTCTCGTCCAGG 58.904 60.000 0.00 0.00 43.67 4.45
3569 3784 0.727970 CGTAGGTGACTCTCGTCCAG 59.272 60.000 0.00 0.00 43.67 3.86
3570 3785 2.850439 CGTAGGTGACTCTCGTCCA 58.150 57.895 0.00 0.00 43.67 4.02


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

AutoCloner maintained by Alex Coulton.