Multiple sequence alignment - TraesCS4D01G188300

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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 TraesCS4D01G188300 chr4D 100.000 3496 0 0 1 3496 327722065 327718570 0.000000e+00 6457
1 TraesCS4D01G188300 chr4D 100.000 403 0 0 3702 4104 327718364 327717962 0.000000e+00 745
2 TraesCS4D01G188300 chr4D 95.813 406 14 2 3702 4104 150906258 150905853 0.000000e+00 652
3 TraesCS4D01G188300 chr4D 95.567 406 15 2 3702 4104 344840667 344840262 0.000000e+00 647
4 TraesCS4D01G188300 chr4B 95.956 3190 80 18 46 3196 407059593 407056414 0.000000e+00 5131
5 TraesCS4D01G188300 chr4B 97.087 103 1 1 1 101 407059691 407059589 5.450000e-39 172
6 TraesCS4D01G188300 chr4A 96.195 2444 58 9 1 2432 143249643 143252063 0.000000e+00 3965
7 TraesCS4D01G188300 chr4A 96.547 782 22 2 2417 3193 143252079 143252860 0.000000e+00 1290
8 TraesCS4D01G188300 chr3B 95.028 724 19 7 2030 2751 554899968 554900676 0.000000e+00 1122
9 TraesCS4D01G188300 chr3B 94.191 723 25 7 2030 2751 303334400 303333694 0.000000e+00 1086
10 TraesCS4D01G188300 chr3B 77.679 224 37 11 2637 2852 419965947 419965729 1.550000e-24 124
11 TraesCS4D01G188300 chr2B 94.329 723 25 6 2030 2751 188856425 188855718 0.000000e+00 1094
12 TraesCS4D01G188300 chr5B 94.191 723 25 9 2030 2751 299679337 299680043 0.000000e+00 1086
13 TraesCS4D01G188300 chr7D 96.305 406 12 2 3702 4104 618686409 618686004 0.000000e+00 664
14 TraesCS4D01G188300 chr7D 95.813 406 13 3 3702 4104 413996391 413996795 0.000000e+00 652
15 TraesCS4D01G188300 chr7A 96.305 406 11 3 3702 4104 157405516 157405920 0.000000e+00 664
16 TraesCS4D01G188300 chr7A 92.174 115 9 0 3382 3496 324585349 324585235 3.280000e-36 163
17 TraesCS4D01G188300 chr3D 96.296 405 13 2 3702 4104 15914023 15914427 0.000000e+00 664
18 TraesCS4D01G188300 chr3D 96.059 406 13 2 3702 4104 29694029 29694434 0.000000e+00 658
19 TraesCS4D01G188300 chr3D 78.222 225 40 8 2634 2852 301414172 301414393 7.160000e-28 135
20 TraesCS4D01G188300 chr6D 95.813 406 13 3 3702 4104 285037271 285036867 0.000000e+00 652
21 TraesCS4D01G188300 chr6D 92.063 126 10 0 3371 3496 285037440 285037315 1.170000e-40 178
22 TraesCS4D01G188300 chr6D 92.174 115 9 0 3382 3496 366976045 366975931 3.280000e-36 163
23 TraesCS4D01G188300 chr1B 95.813 406 13 3 3702 4103 662244201 662244606 0.000000e+00 652
24 TraesCS4D01G188300 chr1B 80.093 216 32 8 2644 2852 665061697 665061908 2.560000e-32 150
25 TraesCS4D01G188300 chr5D 90.226 133 12 1 3364 3496 395297123 395296992 5.450000e-39 172
26 TraesCS4D01G188300 chr5D 93.043 115 8 0 3382 3496 375321469 375321355 7.060000e-38 169
27 TraesCS4D01G188300 chr2D 92.373 118 9 0 3379 3496 259756552 259756669 7.060000e-38 169
28 TraesCS4D01G188300 chr1D 91.597 119 10 0 3378 3496 268154432 268154314 9.130000e-37 165
29 TraesCS4D01G188300 chr1D 91.597 119 10 0 3378 3496 340669137 340669019 9.130000e-37 165
30 TraesCS4D01G188300 chr1D 92.174 115 9 0 3382 3496 16391132 16391018 3.280000e-36 163
31 TraesCS4D01G188300 chr1D 80.556 216 31 8 2644 2852 477480552 477480763 5.490000e-34 156
32 TraesCS4D01G188300 chr1A 80.556 216 31 8 2644 2852 573921813 573922024 5.490000e-34 156
33 TraesCS4D01G188300 chr3A 79.310 232 38 9 2637 2861 434069284 434069056 1.980000e-33 154


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 TraesCS4D01G188300 chr4D 327717962 327722065 4103 True 3601.0 6457 100.0000 1 4104 2 chr4D.!!$R3 4103
1 TraesCS4D01G188300 chr4B 407056414 407059691 3277 True 2651.5 5131 96.5215 1 3196 2 chr4B.!!$R1 3195
2 TraesCS4D01G188300 chr4A 143249643 143252860 3217 False 2627.5 3965 96.3710 1 3193 2 chr4A.!!$F1 3192
3 TraesCS4D01G188300 chr3B 554899968 554900676 708 False 1122.0 1122 95.0280 2030 2751 1 chr3B.!!$F1 721
4 TraesCS4D01G188300 chr3B 303333694 303334400 706 True 1086.0 1086 94.1910 2030 2751 1 chr3B.!!$R1 721
5 TraesCS4D01G188300 chr2B 188855718 188856425 707 True 1094.0 1094 94.3290 2030 2751 1 chr2B.!!$R1 721
6 TraesCS4D01G188300 chr5B 299679337 299680043 706 False 1086.0 1086 94.1910 2030 2751 1 chr5B.!!$F1 721
7 TraesCS4D01G188300 chr6D 285036867 285037440 573 True 415.0 652 93.9380 3371 4104 2 chr6D.!!$R2 733

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
816 872 0.911769 TTGATTCATCTCCACGGCCT 59.088 50.0 0.0 0.00 0.00 5.19 F
817 873 0.911769 TGATTCATCTCCACGGCCTT 59.088 50.0 0.0 0.00 0.00 4.35 F
862 933 0.924090 GCTGGTCGCGTCAGATAAAG 59.076 55.0 26.9 9.24 34.36 1.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2676 2800 0.540365 CCCTCCCACTTGTTGCACAT 60.540 55.000 0.0 0.0 0.0 3.21 R
2912 3036 1.112113 ACACGGCAATAGGAGACGAT 58.888 50.000 0.0 0.0 0.0 3.73 R
3165 3293 1.817740 GCCACTACTGTTTTCCTGCCA 60.818 52.381 0.0 0.0 0.0 4.92 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
141 195 1.529438 TGCGACTCAAAAGCTTAACCG 59.471 47.619 0.00 0.00 0.00 4.44
406 460 7.925483 CCTCACCTGAAGAATATCTAGAAACTG 59.075 40.741 0.00 0.00 0.00 3.16
455 509 2.307098 AGAGCCTGTTATTTGCAGACCT 59.693 45.455 0.00 0.00 36.12 3.85
469 523 3.202097 GCAGACCTTAGCTCTGATTTCC 58.798 50.000 8.59 0.00 37.90 3.13
501 555 7.867305 TCAACAACAGAACAACAATACCTTA 57.133 32.000 0.00 0.00 0.00 2.69
647 701 1.890510 GTGGTGTCCAACGGTGACC 60.891 63.158 0.00 1.53 34.18 4.02
806 862 7.149569 TCTGGTCATTTTCACTTGATTCATC 57.850 36.000 0.00 0.00 0.00 2.92
809 865 6.151648 TGGTCATTTTCACTTGATTCATCTCC 59.848 38.462 0.00 0.00 0.00 3.71
813 869 3.251479 TCACTTGATTCATCTCCACGG 57.749 47.619 0.00 0.00 0.00 4.94
814 870 1.667724 CACTTGATTCATCTCCACGGC 59.332 52.381 0.00 0.00 0.00 5.68
815 871 1.303309 CTTGATTCATCTCCACGGCC 58.697 55.000 0.00 0.00 0.00 6.13
816 872 0.911769 TTGATTCATCTCCACGGCCT 59.088 50.000 0.00 0.00 0.00 5.19
817 873 0.911769 TGATTCATCTCCACGGCCTT 59.088 50.000 0.00 0.00 0.00 4.35
818 874 1.303309 GATTCATCTCCACGGCCTTG 58.697 55.000 1.29 1.29 0.00 3.61
862 933 0.924090 GCTGGTCGCGTCAGATAAAG 59.076 55.000 26.90 9.24 34.36 1.85
864 935 2.455032 CTGGTCGCGTCAGATAAAGAG 58.545 52.381 21.26 0.00 34.36 2.85
999 1077 3.952628 CTTCCGAACCCGACAGGCC 62.953 68.421 0.00 0.00 40.58 5.19
1053 1131 2.105930 CGCTCTCTGCTACCCTGC 59.894 66.667 0.00 0.00 40.11 4.85
1707 1795 2.103601 GGTAAGCCCGCAAATCCTACTA 59.896 50.000 0.00 0.00 0.00 1.82
1785 1873 2.741517 TCGAAAATCTGCGCTGAATTCA 59.258 40.909 28.60 19.65 0.00 2.57
2037 2125 1.714414 CAGAGTCGCTTGATGCAGC 59.286 57.895 0.00 0.00 43.06 5.25
2136 2225 2.376808 ATCAGACGAAACTCTGGCAG 57.623 50.000 8.58 8.58 38.62 4.85
2238 2327 4.814771 ACAGTTGTAGCTTTGAACCTACAC 59.185 41.667 0.00 2.51 42.43 2.90
2310 2399 6.984740 TTTTAATTTACGCTGCAACTTGAG 57.015 33.333 0.00 0.00 0.00 3.02
2676 2800 2.283529 GGCACCCAGAAGACGGAGA 61.284 63.158 0.00 0.00 0.00 3.71
2852 2976 1.367471 CTGCCACTTCCGTCACTCA 59.633 57.895 0.00 0.00 0.00 3.41
2912 3036 0.751277 CCACCAACACCAACTGCTCA 60.751 55.000 0.00 0.00 0.00 4.26
2923 3047 2.363680 CCAACTGCTCATCGTCTCCTAT 59.636 50.000 0.00 0.00 0.00 2.57
3187 3315 1.953686 GCAGGAAAACAGTAGTGGCAA 59.046 47.619 1.92 0.00 0.00 4.52
3193 3321 5.001232 GGAAAACAGTAGTGGCAATGTCTA 58.999 41.667 0.00 0.00 0.00 2.59
3196 3324 2.567169 ACAGTAGTGGCAATGTCTAGCA 59.433 45.455 0.00 0.00 0.00 3.49
3197 3325 3.007940 ACAGTAGTGGCAATGTCTAGCAA 59.992 43.478 0.00 0.00 0.00 3.91
3198 3326 3.620374 CAGTAGTGGCAATGTCTAGCAAG 59.380 47.826 0.00 0.00 0.00 4.01
3199 3327 2.867109 AGTGGCAATGTCTAGCAAGT 57.133 45.000 0.00 0.00 0.00 3.16
3200 3328 2.430465 AGTGGCAATGTCTAGCAAGTG 58.570 47.619 0.00 0.00 0.00 3.16
3201 3329 2.038952 AGTGGCAATGTCTAGCAAGTGA 59.961 45.455 0.00 0.00 0.00 3.41
3202 3330 3.012518 GTGGCAATGTCTAGCAAGTGAT 58.987 45.455 0.00 0.00 0.00 3.06
3203 3331 3.011818 TGGCAATGTCTAGCAAGTGATG 58.988 45.455 0.00 0.00 0.00 3.07
3204 3332 2.357009 GGCAATGTCTAGCAAGTGATGG 59.643 50.000 0.00 0.00 0.00 3.51
3205 3333 2.357009 GCAATGTCTAGCAAGTGATGGG 59.643 50.000 0.00 0.00 0.00 4.00
3206 3334 2.338577 ATGTCTAGCAAGTGATGGGC 57.661 50.000 0.00 0.00 0.00 5.36
3207 3335 0.253044 TGTCTAGCAAGTGATGGGCC 59.747 55.000 0.00 0.00 0.00 5.80
3208 3336 0.253044 GTCTAGCAAGTGATGGGCCA 59.747 55.000 9.61 9.61 0.00 5.36
3209 3337 0.991146 TCTAGCAAGTGATGGGCCAA 59.009 50.000 11.89 0.00 0.00 4.52
3210 3338 1.354031 TCTAGCAAGTGATGGGCCAAA 59.646 47.619 11.89 0.00 0.00 3.28
3211 3339 1.474077 CTAGCAAGTGATGGGCCAAAC 59.526 52.381 11.89 12.82 0.00 2.93
3212 3340 1.080569 GCAAGTGATGGGCCAAACG 60.081 57.895 11.89 1.79 0.00 3.60
3213 3341 1.586028 CAAGTGATGGGCCAAACGG 59.414 57.895 11.89 6.67 0.00 4.44
3214 3342 1.606313 AAGTGATGGGCCAAACGGG 60.606 57.895 11.89 0.00 40.85 5.28
3223 3351 4.418401 CCAAACGGGCCGTGCATG 62.418 66.667 34.87 28.51 39.99 4.06
3224 3352 3.361158 CAAACGGGCCGTGCATGA 61.361 61.111 34.87 0.00 39.99 3.07
3225 3353 3.361977 AAACGGGCCGTGCATGAC 61.362 61.111 34.87 0.00 39.99 3.06
3229 3357 4.722700 GGGCCGTGCATGACCTGT 62.723 66.667 11.37 0.00 0.00 4.00
3230 3358 3.434319 GGCCGTGCATGACCTGTG 61.434 66.667 7.72 0.00 0.00 3.66
3231 3359 2.669569 GCCGTGCATGACCTGTGT 60.670 61.111 7.72 0.00 0.00 3.72
3232 3360 1.375396 GCCGTGCATGACCTGTGTA 60.375 57.895 7.72 0.00 0.00 2.90
3233 3361 0.744414 GCCGTGCATGACCTGTGTAT 60.744 55.000 7.72 0.00 0.00 2.29
3234 3362 1.290203 CCGTGCATGACCTGTGTATC 58.710 55.000 7.72 0.00 0.00 2.24
3235 3363 0.923403 CGTGCATGACCTGTGTATCG 59.077 55.000 0.00 0.00 0.00 2.92
3236 3364 1.290203 GTGCATGACCTGTGTATCGG 58.710 55.000 0.00 0.00 0.00 4.18
3237 3365 0.901827 TGCATGACCTGTGTATCGGT 59.098 50.000 0.00 0.00 35.90 4.69
3238 3366 1.277842 TGCATGACCTGTGTATCGGTT 59.722 47.619 0.00 0.00 32.62 4.44
3239 3367 1.933853 GCATGACCTGTGTATCGGTTC 59.066 52.381 0.00 0.00 32.62 3.62
3240 3368 2.193447 CATGACCTGTGTATCGGTTCG 58.807 52.381 0.00 0.00 32.62 3.95
3241 3369 1.250328 TGACCTGTGTATCGGTTCGT 58.750 50.000 0.00 0.00 32.62 3.85
3242 3370 1.200716 TGACCTGTGTATCGGTTCGTC 59.799 52.381 0.00 0.00 32.62 4.20
3243 3371 0.169672 ACCTGTGTATCGGTTCGTCG 59.830 55.000 0.00 0.00 0.00 5.12
3244 3372 1.138047 CCTGTGTATCGGTTCGTCGC 61.138 60.000 0.00 0.00 0.00 5.19
3245 3373 0.179171 CTGTGTATCGGTTCGTCGCT 60.179 55.000 0.00 0.00 0.00 4.93
3246 3374 1.063027 CTGTGTATCGGTTCGTCGCTA 59.937 52.381 0.00 0.00 0.00 4.26
3247 3375 1.672363 TGTGTATCGGTTCGTCGCTAT 59.328 47.619 0.00 0.00 0.00 2.97
3248 3376 2.286595 TGTGTATCGGTTCGTCGCTATC 60.287 50.000 0.00 0.00 0.00 2.08
3249 3377 2.032204 GTGTATCGGTTCGTCGCTATCT 60.032 50.000 0.00 0.00 0.00 1.98
3250 3378 2.615447 TGTATCGGTTCGTCGCTATCTT 59.385 45.455 0.00 0.00 0.00 2.40
3251 3379 2.121116 ATCGGTTCGTCGCTATCTTG 57.879 50.000 0.00 0.00 0.00 3.02
3252 3380 0.806868 TCGGTTCGTCGCTATCTTGT 59.193 50.000 0.00 0.00 0.00 3.16
3253 3381 1.200716 TCGGTTCGTCGCTATCTTGTT 59.799 47.619 0.00 0.00 0.00 2.83
3254 3382 1.320555 CGGTTCGTCGCTATCTTGTTG 59.679 52.381 0.00 0.00 0.00 3.33
3255 3383 2.602878 GGTTCGTCGCTATCTTGTTGA 58.397 47.619 0.00 0.00 0.00 3.18
3256 3384 3.187700 GGTTCGTCGCTATCTTGTTGAT 58.812 45.455 0.00 0.00 39.11 2.57
3257 3385 3.243177 GGTTCGTCGCTATCTTGTTGATC 59.757 47.826 0.00 0.00 36.65 2.92
3258 3386 4.106197 GTTCGTCGCTATCTTGTTGATCT 58.894 43.478 0.00 0.00 36.65 2.75
3259 3387 3.695816 TCGTCGCTATCTTGTTGATCTG 58.304 45.455 0.00 0.00 36.65 2.90
3260 3388 3.377172 TCGTCGCTATCTTGTTGATCTGA 59.623 43.478 0.00 0.00 36.65 3.27
3261 3389 4.105486 CGTCGCTATCTTGTTGATCTGAA 58.895 43.478 0.00 0.00 36.65 3.02
3262 3390 4.027295 CGTCGCTATCTTGTTGATCTGAAC 60.027 45.833 0.00 0.00 36.65 3.18
3263 3391 5.105752 GTCGCTATCTTGTTGATCTGAACT 58.894 41.667 0.00 0.00 36.65 3.01
3264 3392 6.266323 GTCGCTATCTTGTTGATCTGAACTA 58.734 40.000 0.00 0.00 36.65 2.24
3265 3393 6.416455 GTCGCTATCTTGTTGATCTGAACTAG 59.584 42.308 0.00 0.00 36.65 2.57
3266 3394 5.174761 CGCTATCTTGTTGATCTGAACTAGC 59.825 44.000 0.00 0.47 36.65 3.42
3267 3395 5.465056 GCTATCTTGTTGATCTGAACTAGCC 59.535 44.000 0.00 0.00 36.65 3.93
3268 3396 4.207891 TCTTGTTGATCTGAACTAGCCC 57.792 45.455 0.00 0.00 31.25 5.19
3269 3397 3.582647 TCTTGTTGATCTGAACTAGCCCA 59.417 43.478 0.00 0.00 31.25 5.36
3270 3398 3.334583 TGTTGATCTGAACTAGCCCAC 57.665 47.619 0.00 0.00 0.00 4.61
3271 3399 2.637382 TGTTGATCTGAACTAGCCCACA 59.363 45.455 0.00 0.00 0.00 4.17
3272 3400 3.264193 TGTTGATCTGAACTAGCCCACAT 59.736 43.478 0.00 0.00 0.00 3.21
3273 3401 4.469586 TGTTGATCTGAACTAGCCCACATA 59.530 41.667 0.00 0.00 0.00 2.29
3274 3402 5.045942 TGTTGATCTGAACTAGCCCACATAA 60.046 40.000 0.00 0.00 0.00 1.90
3275 3403 5.282055 TGATCTGAACTAGCCCACATAAG 57.718 43.478 0.00 0.00 0.00 1.73
3276 3404 4.101585 TGATCTGAACTAGCCCACATAAGG 59.898 45.833 0.00 0.00 0.00 2.69
3277 3405 3.450904 TCTGAACTAGCCCACATAAGGT 58.549 45.455 0.00 0.00 0.00 3.50
3290 3418 4.065088 CACATAAGGTGGACGGATATTGG 58.935 47.826 0.00 0.00 44.04 3.16
3291 3419 3.971305 ACATAAGGTGGACGGATATTGGA 59.029 43.478 0.00 0.00 0.00 3.53
3292 3420 4.202326 ACATAAGGTGGACGGATATTGGAC 60.202 45.833 0.00 0.00 0.00 4.02
3293 3421 2.176247 AGGTGGACGGATATTGGACT 57.824 50.000 0.00 0.00 0.00 3.85
3294 3422 3.323774 AGGTGGACGGATATTGGACTA 57.676 47.619 0.00 0.00 0.00 2.59
3295 3423 3.231818 AGGTGGACGGATATTGGACTAG 58.768 50.000 0.00 0.00 0.00 2.57
3296 3424 2.299297 GGTGGACGGATATTGGACTAGG 59.701 54.545 0.00 0.00 0.00 3.02
3297 3425 1.968493 TGGACGGATATTGGACTAGGC 59.032 52.381 0.00 0.00 0.00 3.93
3298 3426 1.275573 GGACGGATATTGGACTAGGCC 59.724 57.143 8.06 8.06 0.00 5.19
3299 3427 1.275573 GACGGATATTGGACTAGGCCC 59.724 57.143 13.60 4.15 0.00 5.80
3300 3428 1.348064 CGGATATTGGACTAGGCCCA 58.652 55.000 13.60 0.00 0.00 5.36
3301 3429 1.276421 CGGATATTGGACTAGGCCCAG 59.724 57.143 13.60 0.00 34.77 4.45
3302 3430 1.003696 GGATATTGGACTAGGCCCAGC 59.996 57.143 13.60 0.00 34.77 4.85
3303 3431 1.699634 GATATTGGACTAGGCCCAGCA 59.300 52.381 13.60 2.21 34.77 4.41
3304 3432 1.819753 TATTGGACTAGGCCCAGCAT 58.180 50.000 13.60 1.33 34.77 3.79
3305 3433 0.184451 ATTGGACTAGGCCCAGCATG 59.816 55.000 13.60 0.00 34.77 4.06
3306 3434 2.203266 GGACTAGGCCCAGCATGC 60.203 66.667 10.51 10.51 31.97 4.06
3313 3441 3.078836 GCCCAGCATGCCCAACAT 61.079 61.111 15.66 0.00 40.66 2.71
3314 3442 2.662070 GCCCAGCATGCCCAACATT 61.662 57.895 15.66 0.00 36.64 2.71
3315 3443 1.984817 CCCAGCATGCCCAACATTT 59.015 52.632 15.66 0.00 36.64 2.32
3316 3444 0.108041 CCCAGCATGCCCAACATTTC 60.108 55.000 15.66 0.00 36.64 2.17
3317 3445 0.899720 CCAGCATGCCCAACATTTCT 59.100 50.000 15.66 0.00 36.64 2.52
3318 3446 1.134907 CCAGCATGCCCAACATTTCTC 60.135 52.381 15.66 0.00 36.64 2.87
3319 3447 1.822990 CAGCATGCCCAACATTTCTCT 59.177 47.619 15.66 0.00 36.64 3.10
3320 3448 2.232941 CAGCATGCCCAACATTTCTCTT 59.767 45.455 15.66 0.00 36.64 2.85
3321 3449 3.444742 CAGCATGCCCAACATTTCTCTTA 59.555 43.478 15.66 0.00 36.64 2.10
3322 3450 3.445096 AGCATGCCCAACATTTCTCTTAC 59.555 43.478 15.66 0.00 36.64 2.34
3323 3451 3.429410 GCATGCCCAACATTTCTCTTACC 60.429 47.826 6.36 0.00 36.64 2.85
3324 3452 3.806949 TGCCCAACATTTCTCTTACCT 57.193 42.857 0.00 0.00 0.00 3.08
3325 3453 4.112634 TGCCCAACATTTCTCTTACCTT 57.887 40.909 0.00 0.00 0.00 3.50
3326 3454 5.249780 TGCCCAACATTTCTCTTACCTTA 57.750 39.130 0.00 0.00 0.00 2.69
3327 3455 5.826643 TGCCCAACATTTCTCTTACCTTAT 58.173 37.500 0.00 0.00 0.00 1.73
3328 3456 6.252995 TGCCCAACATTTCTCTTACCTTATT 58.747 36.000 0.00 0.00 0.00 1.40
3329 3457 7.406916 TGCCCAACATTTCTCTTACCTTATTA 58.593 34.615 0.00 0.00 0.00 0.98
3330 3458 7.891183 TGCCCAACATTTCTCTTACCTTATTAA 59.109 33.333 0.00 0.00 0.00 1.40
3331 3459 8.914011 GCCCAACATTTCTCTTACCTTATTAAT 58.086 33.333 0.00 0.00 0.00 1.40
3402 3530 5.840940 ATCTACCGAATAATAAAGCACGC 57.159 39.130 0.00 0.00 0.00 5.34
3427 3555 4.457496 CTGCCCGTCCATCGCACT 62.457 66.667 0.00 0.00 38.35 4.40
3431 3559 2.100631 CCCGTCCATCGCACTGTTC 61.101 63.158 0.00 0.00 38.35 3.18
3435 3563 0.950555 GTCCATCGCACTGTTCTGCA 60.951 55.000 0.00 0.00 36.94 4.41
3473 3601 2.513753 TCATGAAATCAACCCGCAGTT 58.486 42.857 0.00 0.00 40.16 3.16
3475 3603 1.974265 TGAAATCAACCCGCAGTTCA 58.026 45.000 0.00 0.00 36.18 3.18
3490 3618 4.377431 CGCAGTTCAGATTTAAGTCACACC 60.377 45.833 0.44 0.00 0.00 4.16
3727 3855 4.951254 TCCGCGGATCATATTTAAGTCAA 58.049 39.130 27.28 0.00 0.00 3.18
3734 3862 9.944663 GCGGATCATATTTAAGTCAAACAAATA 57.055 29.630 0.00 0.00 0.00 1.40
3775 3903 7.440255 CCATATCTTTTAAACCGTAACTCCGAT 59.560 37.037 0.00 0.00 0.00 4.18
4061 4190 6.497785 ACTTATAACTATAGCGCACGATCT 57.502 37.500 11.47 0.00 0.00 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
141 195 2.363683 CCTGAGGTGGAAGAGAAATGC 58.636 52.381 0.00 0.00 0.00 3.56
406 460 8.891671 AATACAATGCCAATGAAATAATCCAC 57.108 30.769 0.00 0.00 0.00 4.02
455 509 3.988976 ACAGCAGGAAATCAGAGCTAA 57.011 42.857 0.00 0.00 33.59 3.09
647 701 2.738846 ACAGTAAAGAGCACTGCATTCG 59.261 45.455 3.30 0.00 45.96 3.34
806 862 1.066143 ACAAGTATCAAGGCCGTGGAG 60.066 52.381 19.08 5.31 0.00 3.86
809 865 2.422597 TGAACAAGTATCAAGGCCGTG 58.577 47.619 13.08 13.08 0.00 4.94
813 869 6.603095 CACTAAGTTGAACAAGTATCAAGGC 58.397 40.000 0.00 0.00 37.46 4.35
814 870 6.204688 TGCACTAAGTTGAACAAGTATCAAGG 59.795 38.462 0.00 0.00 37.46 3.61
815 871 7.189693 TGCACTAAGTTGAACAAGTATCAAG 57.810 36.000 0.00 0.00 37.46 3.02
816 872 6.204688 CCTGCACTAAGTTGAACAAGTATCAA 59.795 38.462 0.00 0.00 34.56 2.57
817 873 5.700832 CCTGCACTAAGTTGAACAAGTATCA 59.299 40.000 0.00 2.38 0.00 2.15
818 874 5.932303 TCCTGCACTAAGTTGAACAAGTATC 59.068 40.000 0.00 0.00 0.00 2.24
862 933 2.070028 GCAGGAACGACTTTTCTCCTC 58.930 52.381 0.00 0.00 0.00 3.71
864 935 1.157585 GGCAGGAACGACTTTTCTCC 58.842 55.000 0.00 0.00 0.00 3.71
924 995 2.417719 GTCGAAGTGACTTGATTGCCT 58.582 47.619 0.90 0.00 44.58 4.75
999 1077 2.030958 GGGCGGTTACCTTCGTGTG 61.031 63.158 0.00 0.00 0.00 3.82
1245 1333 2.202544 GAGTGGAGCTGCGTCTCG 60.203 66.667 12.62 0.00 33.98 4.04
1707 1795 6.183360 CGGAATAAAGCAGTGAATTCGTAAGT 60.183 38.462 0.04 0.00 39.48 2.24
1785 1873 5.547465 TGGAACTATTGAACTGTGTTCGAT 58.453 37.500 15.01 15.01 38.20 3.59
1930 2018 4.098654 ACTCTGCTACTTGATGCTATCGTT 59.901 41.667 0.00 0.00 0.00 3.85
2037 2125 3.168963 TCAATTAAGCGACTTCGACTCG 58.831 45.455 2.02 7.22 43.02 4.18
2136 2225 7.061634 GCCAAATCGTTTATAGAACGTCATAC 58.938 38.462 10.57 0.00 43.47 2.39
2238 2327 0.740149 TCAAGCAACTGCCAACACTG 59.260 50.000 0.00 0.00 43.38 3.66
2297 2386 1.795768 TTCCTACTCAAGTTGCAGCG 58.204 50.000 0.00 0.00 0.00 5.18
2676 2800 0.540365 CCCTCCCACTTGTTGCACAT 60.540 55.000 0.00 0.00 0.00 3.21
2912 3036 1.112113 ACACGGCAATAGGAGACGAT 58.888 50.000 0.00 0.00 0.00 3.73
3165 3293 1.817740 GCCACTACTGTTTTCCTGCCA 60.818 52.381 0.00 0.00 0.00 4.92
3187 3315 1.133976 GGCCCATCACTTGCTAGACAT 60.134 52.381 1.04 0.00 0.00 3.06
3193 3321 1.526575 CGTTTGGCCCATCACTTGCT 61.527 55.000 0.00 0.00 0.00 3.91
3196 3324 1.606313 CCCGTTTGGCCCATCACTT 60.606 57.895 0.00 0.00 0.00 3.16
3197 3325 2.035626 CCCGTTTGGCCCATCACT 59.964 61.111 0.00 0.00 0.00 3.41
3206 3334 4.418401 CATGCACGGCCCGTTTGG 62.418 66.667 5.76 0.00 38.32 3.28
3207 3335 3.361158 TCATGCACGGCCCGTTTG 61.361 61.111 5.76 5.05 38.32 2.93
3208 3336 3.361977 GTCATGCACGGCCCGTTT 61.362 61.111 5.76 0.00 38.32 3.60
3212 3340 4.722700 ACAGGTCATGCACGGCCC 62.723 66.667 0.00 0.00 0.00 5.80
3213 3341 2.796483 TACACAGGTCATGCACGGCC 62.796 60.000 0.00 0.00 0.00 6.13
3214 3342 0.744414 ATACACAGGTCATGCACGGC 60.744 55.000 0.00 0.00 0.00 5.68
3215 3343 1.290203 GATACACAGGTCATGCACGG 58.710 55.000 0.00 0.00 0.00 4.94
3216 3344 0.923403 CGATACACAGGTCATGCACG 59.077 55.000 0.00 0.00 0.00 5.34
3217 3345 1.290203 CCGATACACAGGTCATGCAC 58.710 55.000 0.00 0.00 0.00 4.57
3218 3346 0.901827 ACCGATACACAGGTCATGCA 59.098 50.000 0.00 0.00 35.50 3.96
3219 3347 1.933853 GAACCGATACACAGGTCATGC 59.066 52.381 0.00 0.00 40.37 4.06
3220 3348 2.193447 CGAACCGATACACAGGTCATG 58.807 52.381 0.00 0.00 40.37 3.07
3221 3349 1.822990 ACGAACCGATACACAGGTCAT 59.177 47.619 0.00 0.00 40.37 3.06
3222 3350 1.200716 GACGAACCGATACACAGGTCA 59.799 52.381 0.00 0.00 40.37 4.02
3223 3351 1.792993 CGACGAACCGATACACAGGTC 60.793 57.143 0.00 0.00 40.37 3.85
3224 3352 0.169672 CGACGAACCGATACACAGGT 59.830 55.000 0.00 0.00 43.68 4.00
3225 3353 1.138047 GCGACGAACCGATACACAGG 61.138 60.000 0.00 0.00 0.00 4.00
3226 3354 0.179171 AGCGACGAACCGATACACAG 60.179 55.000 0.00 0.00 0.00 3.66
3227 3355 1.085893 TAGCGACGAACCGATACACA 58.914 50.000 0.00 0.00 0.00 3.72
3228 3356 2.032204 AGATAGCGACGAACCGATACAC 60.032 50.000 0.00 0.00 33.10 2.90
3229 3357 2.216046 AGATAGCGACGAACCGATACA 58.784 47.619 0.00 0.00 33.10 2.29
3230 3358 2.965477 AGATAGCGACGAACCGATAC 57.035 50.000 0.00 0.00 33.10 2.24
3231 3359 2.615447 ACAAGATAGCGACGAACCGATA 59.385 45.455 0.00 0.00 34.84 2.92
3232 3360 1.404391 ACAAGATAGCGACGAACCGAT 59.596 47.619 0.00 0.00 0.00 4.18
3233 3361 0.806868 ACAAGATAGCGACGAACCGA 59.193 50.000 0.00 0.00 0.00 4.69
3234 3362 1.320555 CAACAAGATAGCGACGAACCG 59.679 52.381 0.00 0.00 0.00 4.44
3235 3363 2.602878 TCAACAAGATAGCGACGAACC 58.397 47.619 0.00 0.00 0.00 3.62
3236 3364 4.027295 CAGATCAACAAGATAGCGACGAAC 60.027 45.833 0.00 0.00 37.00 3.95
3237 3365 4.105486 CAGATCAACAAGATAGCGACGAA 58.895 43.478 0.00 0.00 37.00 3.85
3238 3366 3.377172 TCAGATCAACAAGATAGCGACGA 59.623 43.478 0.00 0.00 37.00 4.20
3239 3367 3.695816 TCAGATCAACAAGATAGCGACG 58.304 45.455 0.00 0.00 37.00 5.12
3240 3368 5.105752 AGTTCAGATCAACAAGATAGCGAC 58.894 41.667 0.00 0.00 37.00 5.19
3241 3369 5.330455 AGTTCAGATCAACAAGATAGCGA 57.670 39.130 0.00 0.00 37.00 4.93
3242 3370 5.174761 GCTAGTTCAGATCAACAAGATAGCG 59.825 44.000 0.00 0.00 37.00 4.26
3243 3371 5.465056 GGCTAGTTCAGATCAACAAGATAGC 59.535 44.000 0.00 1.60 37.00 2.97
3244 3372 5.988561 GGGCTAGTTCAGATCAACAAGATAG 59.011 44.000 0.00 0.00 37.00 2.08
3245 3373 5.425217 TGGGCTAGTTCAGATCAACAAGATA 59.575 40.000 0.00 0.00 37.00 1.98
3246 3374 4.225942 TGGGCTAGTTCAGATCAACAAGAT 59.774 41.667 0.00 0.00 40.48 2.40
3247 3375 3.582647 TGGGCTAGTTCAGATCAACAAGA 59.417 43.478 0.00 0.00 0.00 3.02
3248 3376 3.686726 GTGGGCTAGTTCAGATCAACAAG 59.313 47.826 0.00 0.00 0.00 3.16
3249 3377 3.072330 TGTGGGCTAGTTCAGATCAACAA 59.928 43.478 0.00 0.00 0.00 2.83
3250 3378 2.637382 TGTGGGCTAGTTCAGATCAACA 59.363 45.455 0.00 0.00 0.00 3.33
3251 3379 3.334583 TGTGGGCTAGTTCAGATCAAC 57.665 47.619 0.00 0.00 0.00 3.18
3252 3380 5.396772 CCTTATGTGGGCTAGTTCAGATCAA 60.397 44.000 0.00 0.00 0.00 2.57
3253 3381 4.101585 CCTTATGTGGGCTAGTTCAGATCA 59.898 45.833 0.00 0.00 0.00 2.92
3254 3382 4.101741 ACCTTATGTGGGCTAGTTCAGATC 59.898 45.833 0.00 0.00 0.00 2.75
3255 3383 4.040755 ACCTTATGTGGGCTAGTTCAGAT 58.959 43.478 0.00 0.00 0.00 2.90
3256 3384 3.197766 CACCTTATGTGGGCTAGTTCAGA 59.802 47.826 0.00 0.00 41.52 3.27
3257 3385 3.535561 CACCTTATGTGGGCTAGTTCAG 58.464 50.000 0.00 0.00 41.52 3.02
3258 3386 3.627395 CACCTTATGTGGGCTAGTTCA 57.373 47.619 0.00 0.00 41.52 3.18
3268 3396 4.065088 CCAATATCCGTCCACCTTATGTG 58.935 47.826 0.00 0.00 45.01 3.21
3269 3397 3.971305 TCCAATATCCGTCCACCTTATGT 59.029 43.478 0.00 0.00 0.00 2.29
3270 3398 4.040461 AGTCCAATATCCGTCCACCTTATG 59.960 45.833 0.00 0.00 0.00 1.90
3271 3399 4.232091 AGTCCAATATCCGTCCACCTTAT 58.768 43.478 0.00 0.00 0.00 1.73
3272 3400 3.649843 AGTCCAATATCCGTCCACCTTA 58.350 45.455 0.00 0.00 0.00 2.69
3273 3401 2.478292 AGTCCAATATCCGTCCACCTT 58.522 47.619 0.00 0.00 0.00 3.50
3274 3402 2.176247 AGTCCAATATCCGTCCACCT 57.824 50.000 0.00 0.00 0.00 4.00
3275 3403 2.299297 CCTAGTCCAATATCCGTCCACC 59.701 54.545 0.00 0.00 0.00 4.61
3276 3404 2.288886 GCCTAGTCCAATATCCGTCCAC 60.289 54.545 0.00 0.00 0.00 4.02
3277 3405 1.968493 GCCTAGTCCAATATCCGTCCA 59.032 52.381 0.00 0.00 0.00 4.02
3278 3406 1.275573 GGCCTAGTCCAATATCCGTCC 59.724 57.143 0.00 0.00 0.00 4.79
3279 3407 1.275573 GGGCCTAGTCCAATATCCGTC 59.724 57.143 0.84 0.00 0.00 4.79
3280 3408 1.349067 GGGCCTAGTCCAATATCCGT 58.651 55.000 0.84 0.00 0.00 4.69
3281 3409 1.276421 CTGGGCCTAGTCCAATATCCG 59.724 57.143 8.21 0.00 36.63 4.18
3282 3410 1.003696 GCTGGGCCTAGTCCAATATCC 59.996 57.143 18.47 0.00 36.63 2.59
3283 3411 1.699634 TGCTGGGCCTAGTCCAATATC 59.300 52.381 18.47 0.00 36.63 1.63
3284 3412 1.819753 TGCTGGGCCTAGTCCAATAT 58.180 50.000 18.47 0.00 36.63 1.28
3285 3413 1.421268 CATGCTGGGCCTAGTCCAATA 59.579 52.381 18.47 0.00 36.63 1.90
3286 3414 0.184451 CATGCTGGGCCTAGTCCAAT 59.816 55.000 18.47 4.11 36.63 3.16
3287 3415 1.609239 CATGCTGGGCCTAGTCCAA 59.391 57.895 18.47 1.74 36.63 3.53
3288 3416 3.047807 GCATGCTGGGCCTAGTCCA 62.048 63.158 18.47 8.46 35.34 4.02
3289 3417 2.203266 GCATGCTGGGCCTAGTCC 60.203 66.667 18.47 2.14 0.00 3.85
3296 3424 2.187896 AAATGTTGGGCATGCTGGGC 62.188 55.000 18.92 6.77 37.96 5.36
3297 3425 0.108041 GAAATGTTGGGCATGCTGGG 60.108 55.000 18.92 0.00 37.96 4.45
3298 3426 0.899720 AGAAATGTTGGGCATGCTGG 59.100 50.000 18.92 0.00 37.96 4.85
3299 3427 1.822990 AGAGAAATGTTGGGCATGCTG 59.177 47.619 18.92 0.00 37.96 4.41
3300 3428 2.226962 AGAGAAATGTTGGGCATGCT 57.773 45.000 18.92 0.00 37.96 3.79
3301 3429 3.429410 GGTAAGAGAAATGTTGGGCATGC 60.429 47.826 9.90 9.90 37.96 4.06
3302 3430 4.019174 AGGTAAGAGAAATGTTGGGCATG 58.981 43.478 0.00 0.00 37.96 4.06
3303 3431 4.322057 AGGTAAGAGAAATGTTGGGCAT 57.678 40.909 0.00 0.00 40.03 4.40
3304 3432 3.806949 AGGTAAGAGAAATGTTGGGCA 57.193 42.857 0.00 0.00 0.00 5.36
3305 3433 6.775594 AATAAGGTAAGAGAAATGTTGGGC 57.224 37.500 0.00 0.00 0.00 5.36
3376 3504 8.744011 GCGTGCTTTATTATTCGGTAGATATAG 58.256 37.037 0.00 0.00 0.00 1.31
3382 3510 4.084537 CCTGCGTGCTTTATTATTCGGTAG 60.085 45.833 0.00 0.00 0.00 3.18
3387 3515 4.632538 AACCCTGCGTGCTTTATTATTC 57.367 40.909 0.00 0.00 0.00 1.75
3473 3601 4.312443 GGTTCGGTGTGACTTAAATCTGA 58.688 43.478 0.00 0.00 0.00 3.27
3910 4039 5.969423 TCGGAGTTACGGTTGAAAAGATAT 58.031 37.500 0.00 0.00 0.00 1.63
3919 4048 5.594724 TGTTAAAATCGGAGTTACGGTTG 57.405 39.130 0.00 0.00 37.25 3.77
4034 4163 5.174398 TCGTGCGCTATAGTTATAAGTTTGC 59.826 40.000 9.73 0.84 0.00 3.68


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

AutoCloner maintained by Alex Coulton.