Multiple sequence alignment - TraesCS3B01G142400

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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 TraesCS3B01G142400 chr3B 100.000 3442 0 0 1 3442 129942386 129938945 0.000000e+00 6357
1 TraesCS3B01G142400 chr3B 95.871 3318 120 15 1 3311 300387412 300390719 0.000000e+00 5352
2 TraesCS3B01G142400 chr3B 94.471 3328 162 13 1 3311 252185466 252188788 0.000000e+00 5107
3 TraesCS3B01G142400 chr3B 93.890 1915 102 7 1 1904 477769065 477770975 0.000000e+00 2874
4 TraesCS3B01G142400 chr4B 96.721 3233 103 3 1 3231 494405641 494408872 0.000000e+00 5380
5 TraesCS3B01G142400 chr4B 94.388 3332 147 19 1 3311 310225953 310222641 0.000000e+00 5081
6 TraesCS3B01G142400 chr4B 94.349 3327 155 21 1 3311 407695552 407692243 0.000000e+00 5072
7 TraesCS3B01G142400 chr4B 94.109 3327 154 20 3 3311 380783996 380787298 0.000000e+00 5020
8 TraesCS3B01G142400 chr4B 91.902 3334 221 25 1 3311 173397504 173394197 0.000000e+00 4615
9 TraesCS3B01G142400 chr4B 93.412 425 14 5 1 416 365097085 365097504 4.880000e-173 617
10 TraesCS3B01G142400 chr4B 94.326 141 7 1 3303 3442 189727106 189727246 7.480000e-52 215
11 TraesCS3B01G142400 chr1B 95.275 3323 140 12 1 3311 330756293 330759610 0.000000e+00 5251
12 TraesCS3B01G142400 chr1B 93.483 3330 176 24 2 3311 256706751 256710059 0.000000e+00 4909
13 TraesCS3B01G142400 chr1B 92.849 3328 203 19 1 3311 206308164 206311473 0.000000e+00 4795
14 TraesCS3B01G142400 chr1B 93.718 2706 130 26 1 2696 163070616 163067941 0.000000e+00 4019
15 TraesCS3B01G142400 chr1B 93.868 1223 59 8 1 1212 290946678 290947895 0.000000e+00 1829
16 TraesCS3B01G142400 chr1B 96.970 132 4 0 3311 3442 544015195 544015064 4.470000e-54 222
17 TraesCS3B01G142400 chr1B 96.923 130 4 0 3313 3442 246523803 246523932 5.780000e-53 219
18 TraesCS3B01G142400 chr2B 95.158 3325 143 12 1 3314 209876001 209872684 0.000000e+00 5232
19 TraesCS3B01G142400 chr2B 94.919 3326 149 14 1 3311 75310986 75307666 0.000000e+00 5188
20 TraesCS3B01G142400 chr2B 94.854 3323 149 14 1 3311 259485627 259482315 0.000000e+00 5169
21 TraesCS3B01G142400 chr2B 94.797 3325 153 15 1 3311 261018123 261021441 0.000000e+00 5164
22 TraesCS3B01G142400 chr2B 94.797 3325 153 11 1 3311 379155441 379158759 0.000000e+00 5164
23 TraesCS3B01G142400 chr2B 94.677 3325 144 21 1 3311 506424438 506421133 0.000000e+00 5129
24 TraesCS3B01G142400 chr2B 93.699 3333 174 20 1 3311 179064051 179067369 0.000000e+00 4959
25 TraesCS3B01G142400 chr2B 87.273 220 16 8 1 216 205284756 205284545 1.230000e-59 241
26 TraesCS3B01G142400 chr2B 97.692 130 3 0 3313 3442 343773468 343773339 1.240000e-54 224
27 TraesCS3B01G142400 chr2B 96.923 130 4 0 3313 3442 343781485 343781356 5.780000e-53 219
28 TraesCS3B01G142400 chr7B 94.800 3327 146 20 1 3314 381026460 381023148 0.000000e+00 5160
29 TraesCS3B01G142400 chr7B 94.434 3324 163 12 1 3311 430145630 430148944 0.000000e+00 5094
30 TraesCS3B01G142400 chr7B 94.351 3328 157 18 1 3309 207971317 207974632 0.000000e+00 5075
31 TraesCS3B01G142400 chr7B 96.923 130 4 0 3313 3442 181452491 181452620 5.780000e-53 219
32 TraesCS3B01G142400 chr6B 94.404 3324 156 16 3 3311 379095870 379092562 0.000000e+00 5081
33 TraesCS3B01G142400 chr6B 94.358 3332 152 21 1 3310 247392368 247395685 0.000000e+00 5079
34 TraesCS3B01G142400 chr6B 93.750 144 5 3 3303 3442 396258885 396259028 2.690000e-51 213
35 TraesCS3B01G142400 chr6B 95.420 131 6 0 3312 3442 653410547 653410417 3.480000e-50 209
36 TraesCS3B01G142400 chr5A 92.370 3329 210 28 1 3311 141902098 141905400 0.000000e+00 4700
37 TraesCS3B01G142400 chr6A 92.053 3322 212 30 1 3311 158983443 158980163 0.000000e+00 4625
38 TraesCS3B01G142400 chr7A 91.945 3327 211 25 1 3311 245449793 245446508 0.000000e+00 4606
39 TraesCS3B01G142400 chr5B 93.673 2924 156 20 1 2903 524597116 524600031 0.000000e+00 4348
40 TraesCS3B01G142400 chr5B 95.556 135 6 0 3308 3442 415522299 415522165 2.080000e-52 217
41 TraesCS3B01G142400 chr5D 91.528 2774 185 31 1 2755 378825553 378822811 0.000000e+00 3775
42 TraesCS3B01G142400 chr5D 87.838 222 16 5 2 216 378825793 378825576 2.050000e-62 250
43 TraesCS3B01G142400 chr5D 86.239 218 25 5 2 216 108670317 108670102 7.430000e-57 231
44 TraesCS3B01G142400 chr2D 87.387 222 15 8 2 216 259248000 259247785 3.430000e-60 243
45 TraesCS3B01G142400 chr2D 93.151 146 8 2 1 146 254956675 254956532 2.690000e-51 213
46 TraesCS3B01G142400 chr3D 86.996 223 17 8 2 216 353281018 353281236 1.230000e-59 241
47 TraesCS3B01G142400 chr6D 86.547 223 18 8 2 216 249245762 249245980 5.740000e-58 235
48 TraesCS3B01G142400 chr1A 86.547 223 19 6 2 216 404652695 404652914 5.740000e-58 235
49 TraesCS3B01G142400 chr1A 85.981 214 18 6 2 206 75532176 75532386 5.780000e-53 219
50 TraesCS3B01G142400 chr4D 86.239 218 25 5 2 216 426270319 426270104 7.430000e-57 231
51 TraesCS3B01G142400 chr4D 84.862 218 28 5 2 216 79271696 79271481 7.480000e-52 215
52 TraesCS3B01G142400 chr4D 85.135 222 19 9 2 216 201239042 201239256 7.480000e-52 215
53 TraesCS3B01G142400 chr1D 86.099 223 19 8 2 216 95412314 95412096 2.670000e-56 230
54 TraesCS3B01G142400 chr1D 85.321 218 27 5 2 216 296768330 296768545 1.610000e-53 220
55 TraesCS3B01G142400 chr1D 85.202 223 17 9 2 216 285934975 285935189 7.480000e-52 215
56 TraesCS3B01G142400 chr1D 84.404 218 29 5 2 216 78755065 78754850 3.480000e-50 209
57 TraesCS3B01G142400 chr1D 83.945 218 30 5 2 216 88013294 88013079 1.620000e-48 204
58 TraesCS3B01G142400 chr1D 88.112 143 14 3 2 144 266169689 266169550 2.120000e-37 167


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 TraesCS3B01G142400 chr3B 129938945 129942386 3441 True 6357.0 6357 100.000 1 3442 1 chr3B.!!$R1 3441
1 TraesCS3B01G142400 chr3B 300387412 300390719 3307 False 5352.0 5352 95.871 1 3311 1 chr3B.!!$F2 3310
2 TraesCS3B01G142400 chr3B 252185466 252188788 3322 False 5107.0 5107 94.471 1 3311 1 chr3B.!!$F1 3310
3 TraesCS3B01G142400 chr3B 477769065 477770975 1910 False 2874.0 2874 93.890 1 1904 1 chr3B.!!$F3 1903
4 TraesCS3B01G142400 chr4B 494405641 494408872 3231 False 5380.0 5380 96.721 1 3231 1 chr4B.!!$F4 3230
5 TraesCS3B01G142400 chr4B 310222641 310225953 3312 True 5081.0 5081 94.388 1 3311 1 chr4B.!!$R2 3310
6 TraesCS3B01G142400 chr4B 407692243 407695552 3309 True 5072.0 5072 94.349 1 3311 1 chr4B.!!$R3 3310
7 TraesCS3B01G142400 chr4B 380783996 380787298 3302 False 5020.0 5020 94.109 3 3311 1 chr4B.!!$F3 3308
8 TraesCS3B01G142400 chr4B 173394197 173397504 3307 True 4615.0 4615 91.902 1 3311 1 chr4B.!!$R1 3310
9 TraesCS3B01G142400 chr1B 330756293 330759610 3317 False 5251.0 5251 95.275 1 3311 1 chr1B.!!$F5 3310
10 TraesCS3B01G142400 chr1B 256706751 256710059 3308 False 4909.0 4909 93.483 2 3311 1 chr1B.!!$F3 3309
11 TraesCS3B01G142400 chr1B 206308164 206311473 3309 False 4795.0 4795 92.849 1 3311 1 chr1B.!!$F1 3310
12 TraesCS3B01G142400 chr1B 163067941 163070616 2675 True 4019.0 4019 93.718 1 2696 1 chr1B.!!$R1 2695
13 TraesCS3B01G142400 chr1B 290946678 290947895 1217 False 1829.0 1829 93.868 1 1212 1 chr1B.!!$F4 1211
14 TraesCS3B01G142400 chr2B 209872684 209876001 3317 True 5232.0 5232 95.158 1 3314 1 chr2B.!!$R3 3313
15 TraesCS3B01G142400 chr2B 75307666 75310986 3320 True 5188.0 5188 94.919 1 3311 1 chr2B.!!$R1 3310
16 TraesCS3B01G142400 chr2B 259482315 259485627 3312 True 5169.0 5169 94.854 1 3311 1 chr2B.!!$R4 3310
17 TraesCS3B01G142400 chr2B 261018123 261021441 3318 False 5164.0 5164 94.797 1 3311 1 chr2B.!!$F2 3310
18 TraesCS3B01G142400 chr2B 379155441 379158759 3318 False 5164.0 5164 94.797 1 3311 1 chr2B.!!$F3 3310
19 TraesCS3B01G142400 chr2B 506421133 506424438 3305 True 5129.0 5129 94.677 1 3311 1 chr2B.!!$R7 3310
20 TraesCS3B01G142400 chr2B 179064051 179067369 3318 False 4959.0 4959 93.699 1 3311 1 chr2B.!!$F1 3310
21 TraesCS3B01G142400 chr7B 381023148 381026460 3312 True 5160.0 5160 94.800 1 3314 1 chr7B.!!$R1 3313
22 TraesCS3B01G142400 chr7B 430145630 430148944 3314 False 5094.0 5094 94.434 1 3311 1 chr7B.!!$F3 3310
23 TraesCS3B01G142400 chr7B 207971317 207974632 3315 False 5075.0 5075 94.351 1 3309 1 chr7B.!!$F2 3308
24 TraesCS3B01G142400 chr6B 379092562 379095870 3308 True 5081.0 5081 94.404 3 3311 1 chr6B.!!$R1 3308
25 TraesCS3B01G142400 chr6B 247392368 247395685 3317 False 5079.0 5079 94.358 1 3310 1 chr6B.!!$F1 3309
26 TraesCS3B01G142400 chr5A 141902098 141905400 3302 False 4700.0 4700 92.370 1 3311 1 chr5A.!!$F1 3310
27 TraesCS3B01G142400 chr6A 158980163 158983443 3280 True 4625.0 4625 92.053 1 3311 1 chr6A.!!$R1 3310
28 TraesCS3B01G142400 chr7A 245446508 245449793 3285 True 4606.0 4606 91.945 1 3311 1 chr7A.!!$R1 3310
29 TraesCS3B01G142400 chr5B 524597116 524600031 2915 False 4348.0 4348 93.673 1 2903 1 chr5B.!!$F1 2902
30 TraesCS3B01G142400 chr5D 378822811 378825793 2982 True 2012.5 3775 89.683 1 2755 2 chr5D.!!$R2 2754

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
28 29 1.597854 CCCGCTGAAGCAGTGACAA 60.598 57.895 9.38 0.00 43.78 3.18 F
853 1134 2.031465 GAACGAACCGCCTCCCAA 59.969 61.111 0.00 0.00 0.00 4.12 F
948 1234 2.288152 GCCGCTTCCATTTCAACTGAAA 60.288 45.455 7.31 7.31 46.60 2.69 F
2310 2625 2.492088 CCAGACAACCTCATCGAGTACA 59.508 50.000 0.00 0.00 0.00 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1217 1504 0.179156 GCCGACGATCCTACGAAACA 60.179 55.000 0.0 0.0 37.03 2.83 R
2415 2730 0.260523 GTAAAGGGGCAATAGGGGCA 59.739 55.000 0.0 0.0 34.52 5.36 R
2435 2750 4.906664 AGGCTCTGATGTTATCTTCATCCT 59.093 41.667 0.0 0.0 40.38 3.24 R
3354 3709 0.032815 TGACATGGCAACGAAGACGA 59.967 50.000 0.0 0.0 42.66 4.20 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
28 29 1.597854 CCCGCTGAAGCAGTGACAA 60.598 57.895 9.38 0.00 43.78 3.18
618 894 3.702330 CTTGACTATACGAATCGGTGCA 58.298 45.455 7.80 0.00 0.00 4.57
853 1134 2.031465 GAACGAACCGCCTCCCAA 59.969 61.111 0.00 0.00 0.00 4.12
948 1234 2.288152 GCCGCTTCCATTTCAACTGAAA 60.288 45.455 7.31 7.31 46.60 2.69
979 1266 4.445557 AAACTTCTCTCTCCAAAAGCCT 57.554 40.909 0.00 0.00 0.00 4.58
1106 1393 4.795795 CGAGAAGCATGAGTACACTACAAG 59.204 45.833 0.00 0.00 0.00 3.16
1592 1894 7.654568 TGAAGTTGATCGACTAGTGAAGTTTA 58.345 34.615 16.19 0.00 39.07 2.01
1803 2108 7.361971 CCAATGCAGAACATACAACATTGACTA 60.362 37.037 13.49 0.00 44.38 2.59
2087 2400 2.975410 TCAGCATTGAAAGCGACAAG 57.025 45.000 0.00 0.00 37.01 3.16
2310 2625 2.492088 CCAGACAACCTCATCGAGTACA 59.508 50.000 0.00 0.00 0.00 2.90
2349 2664 2.747446 GCCACGTACAAATCATGGTTCT 59.253 45.455 0.00 0.00 32.71 3.01
2415 2730 3.306156 GGAGGCTGAAAACTTCTACGACT 60.306 47.826 0.00 0.00 0.00 4.18
2435 2750 0.260523 GCCCCTATTGCCCCTTTACA 59.739 55.000 0.00 0.00 0.00 2.41
2615 2931 9.630098 AAGTACAATGTTTTGCTTATCTCATTG 57.370 29.630 12.16 12.16 43.99 2.82
2655 2971 7.282224 TGGTAGCTTCATATGTTGTTAATCCAC 59.718 37.037 1.90 0.00 0.00 4.02
2844 3169 5.940192 CGTAAGGGCTAATATGAATGCAA 57.060 39.130 0.00 0.00 0.00 4.08
3311 3666 1.203994 GGACTAAACCTAGAGCGCACA 59.796 52.381 11.47 0.00 0.00 4.57
3314 3669 2.233922 ACTAAACCTAGAGCGCACATGT 59.766 45.455 11.47 0.00 0.00 3.21
3315 3670 3.446161 ACTAAACCTAGAGCGCACATGTA 59.554 43.478 11.47 0.00 0.00 2.29
3316 3671 3.328382 AAACCTAGAGCGCACATGTAA 57.672 42.857 11.47 0.00 0.00 2.41
3317 3672 2.295253 ACCTAGAGCGCACATGTAAC 57.705 50.000 11.47 0.00 0.00 2.50
3318 3673 1.200483 CCTAGAGCGCACATGTAACG 58.800 55.000 11.47 14.33 0.00 3.18
3322 3677 4.174129 GCGCACATGTAACGCCCC 62.174 66.667 26.54 7.28 46.63 5.80
3323 3678 3.860125 CGCACATGTAACGCCCCG 61.860 66.667 0.00 0.00 0.00 5.73
3324 3679 3.505184 GCACATGTAACGCCCCGG 61.505 66.667 0.00 0.00 0.00 5.73
3325 3680 2.266372 CACATGTAACGCCCCGGA 59.734 61.111 0.73 0.00 0.00 5.14
3326 3681 1.153249 CACATGTAACGCCCCGGAT 60.153 57.895 0.73 0.00 0.00 4.18
3327 3682 0.746563 CACATGTAACGCCCCGGATT 60.747 55.000 0.73 0.00 0.00 3.01
3328 3683 0.463116 ACATGTAACGCCCCGGATTC 60.463 55.000 0.73 0.00 0.00 2.52
3329 3684 1.227438 ATGTAACGCCCCGGATTCG 60.227 57.895 0.73 5.63 0.00 3.34
3330 3685 1.678598 ATGTAACGCCCCGGATTCGA 61.679 55.000 0.73 0.00 39.00 3.71
3331 3686 1.068585 GTAACGCCCCGGATTCGAT 59.931 57.895 0.73 0.02 39.00 3.59
3332 3687 1.068417 TAACGCCCCGGATTCGATG 59.932 57.895 0.73 0.00 39.00 3.84
3333 3688 2.981977 TAACGCCCCGGATTCGATGC 62.982 60.000 0.73 0.00 39.00 3.91
3337 3692 4.908687 CCCGGATTCGATGCGCCA 62.909 66.667 0.73 0.00 43.11 5.69
3338 3693 3.341043 CCGGATTCGATGCGCCAG 61.341 66.667 4.18 0.00 43.11 4.85
3339 3694 3.341043 CGGATTCGATGCGCCAGG 61.341 66.667 4.18 0.00 37.28 4.45
3340 3695 2.203070 GGATTCGATGCGCCAGGT 60.203 61.111 4.18 0.00 0.00 4.00
3341 3696 2.537560 GGATTCGATGCGCCAGGTG 61.538 63.158 4.18 0.00 0.00 4.00
3342 3697 1.815421 GATTCGATGCGCCAGGTGT 60.815 57.895 4.18 0.00 0.00 4.16
3343 3698 1.766143 GATTCGATGCGCCAGGTGTC 61.766 60.000 4.18 0.00 0.00 3.67
3344 3699 2.244117 ATTCGATGCGCCAGGTGTCT 62.244 55.000 4.18 0.00 0.00 3.41
3345 3700 3.190849 CGATGCGCCAGGTGTCTG 61.191 66.667 4.18 0.00 40.59 3.51
3346 3701 3.503363 GATGCGCCAGGTGTCTGC 61.503 66.667 4.18 0.00 39.61 4.26
3350 3705 2.360350 CGCCAGGTGTCTGCCAAT 60.360 61.111 0.00 0.00 39.61 3.16
3351 3706 1.973281 CGCCAGGTGTCTGCCAATT 60.973 57.895 0.00 0.00 39.61 2.32
3352 3707 0.676466 CGCCAGGTGTCTGCCAATTA 60.676 55.000 0.00 0.00 39.61 1.40
3353 3708 1.767759 GCCAGGTGTCTGCCAATTAT 58.232 50.000 0.00 0.00 39.61 1.28
3354 3709 2.102578 GCCAGGTGTCTGCCAATTATT 58.897 47.619 0.00 0.00 39.61 1.40
3355 3710 2.099756 GCCAGGTGTCTGCCAATTATTC 59.900 50.000 0.00 0.00 39.61 1.75
3356 3711 2.355756 CCAGGTGTCTGCCAATTATTCG 59.644 50.000 0.00 0.00 39.61 3.34
3357 3712 3.009723 CAGGTGTCTGCCAATTATTCGT 58.990 45.455 0.00 0.00 33.86 3.85
3358 3713 3.063997 CAGGTGTCTGCCAATTATTCGTC 59.936 47.826 0.00 0.00 33.86 4.20
3359 3714 3.055094 AGGTGTCTGCCAATTATTCGTCT 60.055 43.478 0.00 0.00 0.00 4.18
3360 3715 3.689649 GGTGTCTGCCAATTATTCGTCTT 59.310 43.478 0.00 0.00 0.00 3.01
3361 3716 4.201822 GGTGTCTGCCAATTATTCGTCTTC 60.202 45.833 0.00 0.00 0.00 2.87
3362 3717 3.616821 TGTCTGCCAATTATTCGTCTTCG 59.383 43.478 0.00 0.00 38.55 3.79
3363 3718 3.617263 GTCTGCCAATTATTCGTCTTCGT 59.383 43.478 0.00 0.00 38.33 3.85
3364 3719 4.092968 GTCTGCCAATTATTCGTCTTCGTT 59.907 41.667 0.00 0.00 38.33 3.85
3365 3720 4.092821 TCTGCCAATTATTCGTCTTCGTTG 59.907 41.667 0.00 0.00 38.33 4.10
3366 3721 3.098636 GCCAATTATTCGTCTTCGTTGC 58.901 45.455 0.00 0.00 38.33 4.17
3367 3722 3.680789 CCAATTATTCGTCTTCGTTGCC 58.319 45.455 0.00 0.00 38.33 4.52
3368 3723 3.126171 CCAATTATTCGTCTTCGTTGCCA 59.874 43.478 0.00 0.00 38.33 4.92
3369 3724 4.201910 CCAATTATTCGTCTTCGTTGCCAT 60.202 41.667 0.00 0.00 38.33 4.40
3370 3725 4.536364 ATTATTCGTCTTCGTTGCCATG 57.464 40.909 0.00 0.00 38.33 3.66
3371 3726 1.808411 ATTCGTCTTCGTTGCCATGT 58.192 45.000 0.00 0.00 38.33 3.21
3372 3727 1.144969 TTCGTCTTCGTTGCCATGTC 58.855 50.000 0.00 0.00 38.33 3.06
3373 3728 0.032815 TCGTCTTCGTTGCCATGTCA 59.967 50.000 0.00 0.00 38.33 3.58
3374 3729 1.078709 CGTCTTCGTTGCCATGTCAT 58.921 50.000 0.00 0.00 0.00 3.06
3375 3730 1.464608 CGTCTTCGTTGCCATGTCATT 59.535 47.619 0.00 0.00 0.00 2.57
3376 3731 2.095768 CGTCTTCGTTGCCATGTCATTT 60.096 45.455 0.00 0.00 0.00 2.32
3377 3732 3.236816 GTCTTCGTTGCCATGTCATTTG 58.763 45.455 0.00 0.00 0.00 2.32
3378 3733 1.987770 CTTCGTTGCCATGTCATTTGC 59.012 47.619 0.00 0.00 0.00 3.68
3379 3734 1.246649 TCGTTGCCATGTCATTTGCT 58.753 45.000 5.85 0.00 0.00 3.91
3380 3735 1.612950 TCGTTGCCATGTCATTTGCTT 59.387 42.857 5.85 0.00 0.00 3.91
3381 3736 1.722464 CGTTGCCATGTCATTTGCTTG 59.278 47.619 5.85 0.00 0.00 4.01
3382 3737 1.461897 GTTGCCATGTCATTTGCTTGC 59.538 47.619 5.85 0.00 0.00 4.01
3383 3738 0.388778 TGCCATGTCATTTGCTTGCG 60.389 50.000 5.85 0.00 0.00 4.85
3384 3739 0.388907 GCCATGTCATTTGCTTGCGT 60.389 50.000 0.00 0.00 0.00 5.24
3385 3740 1.342555 CCATGTCATTTGCTTGCGTG 58.657 50.000 0.00 0.00 0.00 5.34
3386 3741 1.336148 CCATGTCATTTGCTTGCGTGT 60.336 47.619 0.00 0.00 0.00 4.49
3387 3742 2.396601 CATGTCATTTGCTTGCGTGTT 58.603 42.857 0.00 0.00 0.00 3.32
3388 3743 1.837648 TGTCATTTGCTTGCGTGTTG 58.162 45.000 0.00 0.00 0.00 3.33
3389 3744 0.503961 GTCATTTGCTTGCGTGTTGC 59.496 50.000 0.00 0.00 46.70 4.17
3398 3753 4.024698 GCGTGTTGCATTTTGCCA 57.975 50.000 0.00 0.00 44.23 4.92
3399 3754 2.531055 GCGTGTTGCATTTTGCCAT 58.469 47.368 0.00 0.00 44.23 4.40
3400 3755 0.164217 GCGTGTTGCATTTTGCCATG 59.836 50.000 0.00 0.00 44.23 3.66
3401 3756 1.500108 CGTGTTGCATTTTGCCATGT 58.500 45.000 0.00 0.00 44.23 3.21
3402 3757 1.456544 CGTGTTGCATTTTGCCATGTC 59.543 47.619 0.00 0.00 44.23 3.06
3403 3758 2.481854 GTGTTGCATTTTGCCATGTCA 58.518 42.857 0.00 0.00 44.23 3.58
3404 3759 3.068560 GTGTTGCATTTTGCCATGTCAT 58.931 40.909 0.00 0.00 44.23 3.06
3405 3760 3.123959 GTGTTGCATTTTGCCATGTCATC 59.876 43.478 0.00 0.00 44.23 2.92
3406 3761 3.244112 TGTTGCATTTTGCCATGTCATCA 60.244 39.130 0.00 0.00 44.23 3.07
3407 3762 3.897141 TGCATTTTGCCATGTCATCAT 57.103 38.095 0.00 0.00 44.23 2.45
3408 3763 3.787785 TGCATTTTGCCATGTCATCATC 58.212 40.909 0.00 0.00 44.23 2.92
3409 3764 3.449377 TGCATTTTGCCATGTCATCATCT 59.551 39.130 0.00 0.00 44.23 2.90
3410 3765 3.802139 GCATTTTGCCATGTCATCATCTG 59.198 43.478 0.00 0.00 37.42 2.90
3411 3766 3.513680 TTTTGCCATGTCATCATCTGC 57.486 42.857 0.00 0.00 31.15 4.26
3412 3767 2.131776 TTGCCATGTCATCATCTGCA 57.868 45.000 0.00 0.00 37.20 4.41
3413 3768 2.358322 TGCCATGTCATCATCTGCAT 57.642 45.000 0.00 0.00 35.40 3.96
3414 3769 2.661718 TGCCATGTCATCATCTGCATT 58.338 42.857 0.00 0.00 35.40 3.56
3415 3770 3.822940 TGCCATGTCATCATCTGCATTA 58.177 40.909 0.00 0.00 35.40 1.90
3416 3771 3.566742 TGCCATGTCATCATCTGCATTAC 59.433 43.478 0.00 0.00 35.40 1.89
3417 3772 3.566742 GCCATGTCATCATCTGCATTACA 59.433 43.478 0.00 0.00 32.46 2.41
3418 3773 4.217767 GCCATGTCATCATCTGCATTACAT 59.782 41.667 0.00 0.00 32.46 2.29
3419 3774 5.619309 GCCATGTCATCATCTGCATTACATC 60.619 44.000 0.00 0.00 32.46 3.06
3420 3775 5.106277 CCATGTCATCATCTGCATTACATCC 60.106 44.000 0.00 0.00 31.15 3.51
3421 3776 4.060205 TGTCATCATCTGCATTACATCCG 58.940 43.478 0.00 0.00 0.00 4.18
3422 3777 3.069289 TCATCATCTGCATTACATCCGC 58.931 45.455 0.00 0.00 0.00 5.54
3423 3778 2.618442 TCATCTGCATTACATCCGCA 57.382 45.000 0.00 0.00 0.00 5.69
3424 3779 3.130280 TCATCTGCATTACATCCGCAT 57.870 42.857 0.00 0.00 34.63 4.73
3425 3780 2.809696 TCATCTGCATTACATCCGCATG 59.190 45.455 0.00 0.00 34.63 4.06
3426 3781 2.330440 TCTGCATTACATCCGCATGT 57.670 45.000 0.00 0.00 45.73 3.21
3427 3782 2.642427 TCTGCATTACATCCGCATGTT 58.358 42.857 0.00 0.00 40.66 2.71
3428 3783 3.016031 TCTGCATTACATCCGCATGTTT 58.984 40.909 0.00 0.00 40.66 2.83
3429 3784 3.443329 TCTGCATTACATCCGCATGTTTT 59.557 39.130 0.00 0.00 40.66 2.43
3430 3785 4.082300 TCTGCATTACATCCGCATGTTTTT 60.082 37.500 0.00 0.00 40.66 1.94
3431 3786 4.172505 TGCATTACATCCGCATGTTTTTC 58.827 39.130 0.00 0.00 40.66 2.29
3432 3787 4.172505 GCATTACATCCGCATGTTTTTCA 58.827 39.130 0.00 0.00 40.66 2.69
3433 3788 4.624882 GCATTACATCCGCATGTTTTTCAA 59.375 37.500 0.00 0.00 40.66 2.69
3434 3789 5.119898 GCATTACATCCGCATGTTTTTCAAA 59.880 36.000 0.00 0.00 40.66 2.69
3435 3790 6.347240 GCATTACATCCGCATGTTTTTCAAAA 60.347 34.615 0.00 0.00 40.66 2.44
3436 3791 6.517914 TTACATCCGCATGTTTTTCAAAAC 57.482 33.333 0.00 8.02 40.66 2.43
3437 3792 4.692228 ACATCCGCATGTTTTTCAAAACT 58.308 34.783 14.63 0.55 46.37 2.66
3438 3793 5.115480 ACATCCGCATGTTTTTCAAAACTT 58.885 33.333 14.63 7.11 46.37 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
456 731 2.562738 CCAGTGAGACTATGTGTGGTGA 59.437 50.000 0.00 0.00 0.00 4.02
618 894 6.108015 GTGGTGATGATGGCATTTTATTGTT 58.892 36.000 0.00 0.00 34.11 2.83
773 1050 0.254462 TGCAGTCCCTTGTGTCAACA 59.746 50.000 0.00 0.00 0.00 3.33
853 1134 0.894835 GTGCGTGGATGGGGATTTTT 59.105 50.000 0.00 0.00 0.00 1.94
979 1266 2.050350 CCTTCCTCCGGCGACTGTA 61.050 63.158 9.30 0.00 0.00 2.74
1035 1322 0.820482 TCCTCTTGTCCGACGTGTCA 60.820 55.000 0.00 0.00 0.00 3.58
1217 1504 0.179156 GCCGACGATCCTACGAAACA 60.179 55.000 0.00 0.00 37.03 2.83
2087 2400 1.433534 CGGACAACTTCAGCTTCTCC 58.566 55.000 0.00 0.00 0.00 3.71
2288 2603 1.924731 ACTCGATGAGGTTGTCTGGA 58.075 50.000 0.00 0.00 33.35 3.86
2310 2625 0.381089 GCGTACGCATCTACTCCTGT 59.619 55.000 33.90 0.00 41.49 4.00
2349 2664 4.402474 ACCATCAGTGATGTAGTCGATCAA 59.598 41.667 27.27 0.00 38.28 2.57
2415 2730 0.260523 GTAAAGGGGCAATAGGGGCA 59.739 55.000 0.00 0.00 34.52 5.36
2435 2750 4.906664 AGGCTCTGATGTTATCTTCATCCT 59.093 41.667 0.00 0.00 40.38 3.24
2615 2931 7.443259 TGAAGCTACCAAACCAAACTTATAC 57.557 36.000 0.00 0.00 0.00 1.47
2696 3015 7.033791 TCATAACTAGTTCTTTAGAGCAACGG 58.966 38.462 12.39 0.00 0.00 4.44
2844 3169 7.968956 CGTGTAGACTGAGTTTTGTACTGATAT 59.031 37.037 0.00 0.00 37.17 1.63
3287 3642 1.822990 CGCTCTAGGTTTAGTCCCACA 59.177 52.381 0.00 0.00 0.00 4.17
3311 3666 1.227438 CGAATCCGGGGCGTTACAT 60.227 57.895 0.00 0.00 0.00 2.29
3314 3669 1.068417 CATCGAATCCGGGGCGTTA 59.932 57.895 0.00 0.00 36.24 3.18
3315 3670 2.203015 CATCGAATCCGGGGCGTT 60.203 61.111 0.00 0.00 36.24 4.84
3316 3671 4.910585 GCATCGAATCCGGGGCGT 62.911 66.667 0.00 0.00 36.24 5.68
3320 3675 4.908687 TGGCGCATCGAATCCGGG 62.909 66.667 10.83 0.00 36.24 5.73
3321 3676 3.341043 CTGGCGCATCGAATCCGG 61.341 66.667 10.83 0.00 36.24 5.14
3322 3677 3.341043 CCTGGCGCATCGAATCCG 61.341 66.667 10.83 0.00 37.07 4.18
3323 3678 2.203070 ACCTGGCGCATCGAATCC 60.203 61.111 10.83 0.00 0.00 3.01
3324 3679 1.766143 GACACCTGGCGCATCGAATC 61.766 60.000 10.83 0.00 0.00 2.52
3325 3680 1.815421 GACACCTGGCGCATCGAAT 60.815 57.895 10.83 0.00 0.00 3.34
3326 3681 2.434185 GACACCTGGCGCATCGAA 60.434 61.111 10.83 0.00 0.00 3.71
3327 3682 3.381983 AGACACCTGGCGCATCGA 61.382 61.111 10.83 0.00 0.00 3.59
3328 3683 3.190849 CAGACACCTGGCGCATCG 61.191 66.667 10.83 0.00 36.77 3.84
3329 3684 3.503363 GCAGACACCTGGCGCATC 61.503 66.667 10.83 0.00 40.72 3.91
3335 3690 2.355756 CGAATAATTGGCAGACACCTGG 59.644 50.000 0.00 0.00 40.72 4.45
3336 3691 3.009723 ACGAATAATTGGCAGACACCTG 58.990 45.455 0.00 0.00 43.22 4.00
3337 3692 3.055094 AGACGAATAATTGGCAGACACCT 60.055 43.478 0.00 0.00 0.00 4.00
3338 3693 3.270877 AGACGAATAATTGGCAGACACC 58.729 45.455 0.00 0.00 0.00 4.16
3339 3694 4.492570 CGAAGACGAATAATTGGCAGACAC 60.493 45.833 0.00 0.00 42.66 3.67
3340 3695 3.616821 CGAAGACGAATAATTGGCAGACA 59.383 43.478 0.00 0.00 42.66 3.41
3341 3696 3.617263 ACGAAGACGAATAATTGGCAGAC 59.383 43.478 0.00 0.00 42.66 3.51
3342 3697 3.857052 ACGAAGACGAATAATTGGCAGA 58.143 40.909 0.00 0.00 42.66 4.26
3343 3698 4.334443 CAACGAAGACGAATAATTGGCAG 58.666 43.478 0.00 0.00 42.66 4.85
3344 3699 3.425625 GCAACGAAGACGAATAATTGGCA 60.426 43.478 0.00 0.00 42.66 4.92
3345 3700 3.098636 GCAACGAAGACGAATAATTGGC 58.901 45.455 0.00 0.00 42.66 4.52
3346 3701 3.126171 TGGCAACGAAGACGAATAATTGG 59.874 43.478 0.00 0.00 42.66 3.16
3347 3702 4.335082 TGGCAACGAAGACGAATAATTG 57.665 40.909 0.00 0.00 42.66 2.32
3348 3703 4.394920 ACATGGCAACGAAGACGAATAATT 59.605 37.500 0.00 0.00 42.66 1.40
3349 3704 3.938963 ACATGGCAACGAAGACGAATAAT 59.061 39.130 0.00 0.00 42.66 1.28
3350 3705 3.331150 ACATGGCAACGAAGACGAATAA 58.669 40.909 0.00 0.00 42.66 1.40
3351 3706 2.927477 GACATGGCAACGAAGACGAATA 59.073 45.455 0.00 0.00 42.66 1.75
3352 3707 1.732259 GACATGGCAACGAAGACGAAT 59.268 47.619 0.00 0.00 42.66 3.34
3353 3708 1.144969 GACATGGCAACGAAGACGAA 58.855 50.000 0.00 0.00 42.66 3.85
3354 3709 0.032815 TGACATGGCAACGAAGACGA 59.967 50.000 0.00 0.00 42.66 4.20
3355 3710 1.078709 ATGACATGGCAACGAAGACG 58.921 50.000 4.70 0.00 45.75 4.18
3356 3711 3.236816 CAAATGACATGGCAACGAAGAC 58.763 45.455 4.70 0.00 42.51 3.01
3357 3712 2.351641 GCAAATGACATGGCAACGAAGA 60.352 45.455 4.70 0.00 42.51 2.87
3358 3713 1.987770 GCAAATGACATGGCAACGAAG 59.012 47.619 4.70 0.00 42.51 3.79
3359 3714 1.612950 AGCAAATGACATGGCAACGAA 59.387 42.857 4.70 0.00 42.51 3.85
3360 3715 1.246649 AGCAAATGACATGGCAACGA 58.753 45.000 4.70 0.00 42.51 3.85
3361 3716 1.722464 CAAGCAAATGACATGGCAACG 59.278 47.619 4.70 0.00 42.51 4.10
3362 3717 1.461897 GCAAGCAAATGACATGGCAAC 59.538 47.619 4.70 0.00 0.00 4.17
3363 3718 1.798283 GCAAGCAAATGACATGGCAA 58.202 45.000 4.70 0.00 0.00 4.52
3364 3719 0.388778 CGCAAGCAAATGACATGGCA 60.389 50.000 2.18 2.18 0.00 4.92
3365 3720 0.388907 ACGCAAGCAAATGACATGGC 60.389 50.000 0.00 0.00 45.62 4.40
3366 3721 1.336148 ACACGCAAGCAAATGACATGG 60.336 47.619 0.00 0.00 45.62 3.66
3367 3722 2.054687 ACACGCAAGCAAATGACATG 57.945 45.000 0.00 0.00 45.62 3.21
3368 3723 2.396601 CAACACGCAAGCAAATGACAT 58.603 42.857 0.00 0.00 45.62 3.06
3369 3724 1.837648 CAACACGCAAGCAAATGACA 58.162 45.000 0.00 0.00 45.62 3.58
3370 3725 0.503961 GCAACACGCAAGCAAATGAC 59.496 50.000 0.00 0.00 45.62 3.06
3371 3726 2.884146 GCAACACGCAAGCAAATGA 58.116 47.368 0.00 0.00 45.62 2.57
3383 3738 8.304424 GATGATGACATGGCAAAATGCAACAC 62.304 42.308 4.70 0.00 40.11 3.32
3384 3739 6.364545 GATGATGACATGGCAAAATGCAACA 61.365 40.000 4.70 0.00 40.11 3.33
3385 3740 4.033587 GATGATGACATGGCAAAATGCAAC 59.966 41.667 4.70 0.00 40.11 4.17
3386 3741 4.081365 AGATGATGACATGGCAAAATGCAA 60.081 37.500 4.70 0.00 40.11 4.08
3387 3742 3.449377 AGATGATGACATGGCAAAATGCA 59.551 39.130 4.70 0.00 40.11 3.96
3388 3743 3.802139 CAGATGATGACATGGCAAAATGC 59.198 43.478 4.70 0.00 38.66 3.56
3389 3744 3.802139 GCAGATGATGACATGGCAAAATG 59.198 43.478 4.70 1.53 36.82 2.32
3390 3745 3.449377 TGCAGATGATGACATGGCAAAAT 59.551 39.130 4.70 1.31 39.08 1.82
3391 3746 2.826725 TGCAGATGATGACATGGCAAAA 59.173 40.909 4.70 0.00 39.08 2.44
3392 3747 2.448453 TGCAGATGATGACATGGCAAA 58.552 42.857 4.70 0.00 39.08 3.68
3393 3748 2.131776 TGCAGATGATGACATGGCAA 57.868 45.000 4.70 0.00 39.08 4.52
3394 3749 2.358322 ATGCAGATGATGACATGGCA 57.642 45.000 2.18 2.18 42.91 4.92
3395 3750 3.566742 TGTAATGCAGATGATGACATGGC 59.433 43.478 0.00 0.00 36.82 4.40
3396 3751 5.106277 GGATGTAATGCAGATGATGACATGG 60.106 44.000 0.00 0.00 33.73 3.66
3397 3752 5.390567 CGGATGTAATGCAGATGATGACATG 60.391 44.000 0.00 0.00 33.33 3.21
3398 3753 4.694037 CGGATGTAATGCAGATGATGACAT 59.306 41.667 0.00 0.00 35.07 3.06
3399 3754 4.060205 CGGATGTAATGCAGATGATGACA 58.940 43.478 0.00 0.00 32.20 3.58
3400 3755 3.120408 GCGGATGTAATGCAGATGATGAC 60.120 47.826 0.00 0.00 32.20 3.06
3401 3756 3.069289 GCGGATGTAATGCAGATGATGA 58.931 45.455 0.00 0.00 32.20 2.92
3402 3757 2.809696 TGCGGATGTAATGCAGATGATG 59.190 45.455 0.00 0.00 32.20 3.07
3403 3758 3.130280 TGCGGATGTAATGCAGATGAT 57.870 42.857 0.00 0.00 32.20 2.45
3404 3759 2.618442 TGCGGATGTAATGCAGATGA 57.382 45.000 0.00 0.00 32.20 2.92
3405 3760 2.551032 ACATGCGGATGTAATGCAGATG 59.449 45.455 21.92 0.00 41.27 2.90
3406 3761 2.854963 ACATGCGGATGTAATGCAGAT 58.145 42.857 21.92 0.00 41.27 2.90
3407 3762 2.330440 ACATGCGGATGTAATGCAGA 57.670 45.000 21.92 0.00 41.27 4.26
3408 3763 3.425577 AAACATGCGGATGTAATGCAG 57.574 42.857 23.47 0.00 42.30 4.41
3409 3764 3.865011 AAAACATGCGGATGTAATGCA 57.135 38.095 23.47 0.00 42.30 3.96
3410 3765 4.172505 TGAAAAACATGCGGATGTAATGC 58.827 39.130 23.47 13.66 42.30 3.56
3411 3766 6.702972 TTTGAAAAACATGCGGATGTAATG 57.297 33.333 23.47 0.00 42.30 1.90
3412 3767 7.116061 GTTTTGAAAAACATGCGGATGTAAT 57.884 32.000 23.47 12.40 45.72 1.89
3413 3768 6.517914 GTTTTGAAAAACATGCGGATGTAA 57.482 33.333 23.47 10.42 45.72 2.41


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

AutoCloner maintained by Alex Coulton.