Multiple sequence alignment - TraesCS7D01G438900

Loading Multiple Alignment...

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 TraesCS7D01G438900 chr7D 100.000 3457 0 0 1 3457 558325136 558328592 0.000000e+00 6384
1 TraesCS7D01G438900 chr7D 95.923 3238 85 9 1 3209 558342389 558339170 0.000000e+00 5204
2 TraesCS7D01G438900 chr7D 96.563 2153 64 8 1061 3209 558352273 558350127 0.000000e+00 3557
3 TraesCS7D01G438900 chr7D 94.901 1059 24 4 1 1034 558353323 558352270 0.000000e+00 1629
4 TraesCS7D01G438900 chr7D 96.181 707 24 2 2504 3209 558337134 558336430 0.000000e+00 1153
5 TraesCS7D01G438900 chr7D 96.181 707 24 2 2504 3209 558338504 558337800 0.000000e+00 1153
6 TraesCS7D01G438900 chr7D 95.769 709 27 1 2504 3209 558348086 558347378 0.000000e+00 1140
7 TraesCS7D01G438900 chr7D 95.480 708 31 1 2504 3210 558335764 558335057 0.000000e+00 1129
8 TraesCS7D01G438900 chr7D 95.339 708 31 1 2504 3209 558349460 558348753 0.000000e+00 1123
9 TraesCS7D01G438900 chr1D 96.226 3233 97 8 1 3209 116465946 116469177 0.000000e+00 5271
10 TraesCS7D01G438900 chr1D 95.014 722 33 2 2490 3209 116460253 116460973 0.000000e+00 1131
11 TraesCS7D01G438900 chr1D 96.094 256 7 3 3205 3457 370603257 370603002 6.900000e-112 414
12 TraesCS7D01G438900 chr6D 93.263 3236 166 24 4 3209 19451947 19455160 0.000000e+00 4721
13 TraesCS7D01G438900 chr6D 92.970 2973 157 17 1 2937 349539308 349536352 0.000000e+00 4285
14 TraesCS7D01G438900 chr6D 92.611 2964 157 22 1 2937 349549550 349552478 0.000000e+00 4204
15 TraesCS7D01G438900 chr6D 96.863 255 6 1 3205 3457 112447294 112447548 3.190000e-115 425
16 TraesCS7D01G438900 chr6D 96.850 254 5 2 3205 3455 447980312 447980565 4.130000e-114 422
17 TraesCS7D01G438900 chr6D 96.429 252 6 2 3205 3453 35157862 35158113 2.480000e-111 412
18 TraesCS7D01G438900 chr6D 96.429 252 6 2 3205 3454 410069051 410069301 2.480000e-111 412
19 TraesCS7D01G438900 chr3B 93.849 3024 144 19 1 2990 808051292 808048277 0.000000e+00 4516
20 TraesCS7D01G438900 chr2B 91.949 3242 211 26 1 3209 791869357 791866133 0.000000e+00 4495
21 TraesCS7D01G438900 chr5D 93.529 2967 142 12 1 2937 407681276 407678330 0.000000e+00 4370
22 TraesCS7D01G438900 chr2D 93.315 2962 155 14 1 2937 38585846 38588789 0.000000e+00 4333
23 TraesCS7D01G438900 chr2D 93.113 2962 158 18 1 2937 38597128 38600068 0.000000e+00 4298
24 TraesCS7D01G438900 chr2D 96.094 256 5 5 3205 3457 546336118 546335865 2.480000e-111 412
25 TraesCS7D01G438900 chr1A 90.929 3263 222 41 1 3209 574378705 574375463 0.000000e+00 4318
26 TraesCS7D01G438900 chr7A 92.814 2978 163 17 1 2952 80552552 80555504 0.000000e+00 4266
27 TraesCS7D01G438900 chr5B 92.874 2975 146 19 1 2934 544187939 544184990 0.000000e+00 4259
28 TraesCS7D01G438900 chr4A 93.898 1098 42 9 1 1073 327612516 327611419 0.000000e+00 1633
29 TraesCS7D01G438900 chr3D 96.875 256 5 2 3205 3457 4929553 4929298 3.190000e-115 425
30 TraesCS7D01G438900 chr3D 96.094 256 6 3 3205 3457 605982476 605982730 6.900000e-112 414
31 TraesCS7D01G438900 chr3D 95.703 256 8 3 3205 3457 609735999 609736254 3.210000e-110 409


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 TraesCS7D01G438900 chr7D 558325136 558328592 3456 False 6384.00 6384 100.00000 1 3457 1 chr7D.!!$F1 3456
1 TraesCS7D01G438900 chr7D 558335057 558342389 7332 True 2159.75 5204 95.94125 1 3210 4 chr7D.!!$R1 3209
2 TraesCS7D01G438900 chr7D 558347378 558353323 5945 True 1862.25 3557 95.64300 1 3209 4 chr7D.!!$R2 3208
3 TraesCS7D01G438900 chr1D 116465946 116469177 3231 False 5271.00 5271 96.22600 1 3209 1 chr1D.!!$F2 3208
4 TraesCS7D01G438900 chr1D 116460253 116460973 720 False 1131.00 1131 95.01400 2490 3209 1 chr1D.!!$F1 719
5 TraesCS7D01G438900 chr6D 19451947 19455160 3213 False 4721.00 4721 93.26300 4 3209 1 chr6D.!!$F1 3205
6 TraesCS7D01G438900 chr6D 349536352 349539308 2956 True 4285.00 4285 92.97000 1 2937 1 chr6D.!!$R1 2936
7 TraesCS7D01G438900 chr6D 349549550 349552478 2928 False 4204.00 4204 92.61100 1 2937 1 chr6D.!!$F4 2936
8 TraesCS7D01G438900 chr3B 808048277 808051292 3015 True 4516.00 4516 93.84900 1 2990 1 chr3B.!!$R1 2989
9 TraesCS7D01G438900 chr2B 791866133 791869357 3224 True 4495.00 4495 91.94900 1 3209 1 chr2B.!!$R1 3208
10 TraesCS7D01G438900 chr5D 407678330 407681276 2946 True 4370.00 4370 93.52900 1 2937 1 chr5D.!!$R1 2936
11 TraesCS7D01G438900 chr2D 38585846 38588789 2943 False 4333.00 4333 93.31500 1 2937 1 chr2D.!!$F1 2936
12 TraesCS7D01G438900 chr2D 38597128 38600068 2940 False 4298.00 4298 93.11300 1 2937 1 chr2D.!!$F2 2936
13 TraesCS7D01G438900 chr1A 574375463 574378705 3242 True 4318.00 4318 90.92900 1 3209 1 chr1A.!!$R1 3208
14 TraesCS7D01G438900 chr7A 80552552 80555504 2952 False 4266.00 4266 92.81400 1 2952 1 chr7A.!!$F1 2951
15 TraesCS7D01G438900 chr5B 544184990 544187939 2949 True 4259.00 4259 92.87400 1 2934 1 chr5B.!!$R1 2933
16 TraesCS7D01G438900 chr4A 327611419 327612516 1097 True 1633.00 1633 93.89800 1 1073 1 chr4A.!!$R1 1072

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
436 458 1.144936 CAGAAGCCCTCATCGGTCC 59.855 63.158 0.0 0.0 0.00 4.46 F
1378 1408 3.523157 TGATAGGGAAATCCTTGCAGTCA 59.477 43.478 0.0 0.0 45.47 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1958 1994 6.450845 TTTGCATCTAATTTTTCAAGCGTG 57.549 33.333 0.00 0.00 0.00 5.34 R
3153 10143 0.037326 AACTCTTGGCGATCGAAGCA 60.037 50.000 21.57 4.27 36.08 3.91 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
52 53 9.884465 CAAAGAAAGTCCTTACAAAATGTAGAG 57.116 33.333 0.00 0.00 33.92 2.43
141 142 9.041354 AGAACTTAGTGAGACCATAGAAGAATT 57.959 33.333 0.00 0.00 0.00 2.17
280 281 8.567948 AGCATACAAATTATTGGAGAAATACCG 58.432 33.333 0.00 0.00 41.01 4.02
299 300 3.632145 ACCGATGAAACATTGGGATAAGC 59.368 43.478 18.54 0.00 0.00 3.09
315 316 6.183361 TGGGATAAGCACTCTATAGTTTGCAT 60.183 38.462 22.22 16.17 31.97 3.96
436 458 1.144936 CAGAAGCCCTCATCGGTCC 59.855 63.158 0.00 0.00 0.00 4.46
1267 1296 5.373812 AGGATGGGGTGTGATACTAAAAG 57.626 43.478 0.00 0.00 0.00 2.27
1377 1407 4.156455 TGATAGGGAAATCCTTGCAGTC 57.844 45.455 0.00 0.00 45.47 3.51
1378 1408 3.523157 TGATAGGGAAATCCTTGCAGTCA 59.477 43.478 0.00 0.00 45.47 3.41
1845 1880 7.285172 TGAATAGCTTGGCAGAATATTTTAGCA 59.715 33.333 0.00 0.00 0.00 3.49
1958 1994 9.822185 GGCATATATTTGGAATGGGAAAATATC 57.178 33.333 3.78 0.00 37.54 1.63
1962 1998 4.647424 TTGGAATGGGAAAATATCACGC 57.353 40.909 0.00 0.00 32.41 5.34
2394 2430 8.498192 AGAATGCGATCAAAAATATGATTTCG 57.502 30.769 0.00 0.00 40.08 3.46
2831 4321 4.191544 CAGCCAATTATTCACCGAGAGAA 58.808 43.478 0.00 0.00 0.00 2.87
2861 5727 5.179368 CACGTGAAGAAAGCAAAGATTCCTA 59.821 40.000 10.90 0.00 0.00 2.94
2924 9909 6.727824 ATATTATTAGAAGGACACGCATGC 57.272 37.500 7.91 7.91 0.00 4.06
2931 9916 1.376683 GGACACGCATGCACCCTAA 60.377 57.895 19.57 0.00 0.00 2.69
3035 10020 0.690762 TAAAAGGAGACGCTGGGCTT 59.309 50.000 0.00 0.00 0.00 4.35
3148 10138 4.469945 ACCACTGCTAGTAGAATAGCCAAA 59.530 41.667 15.37 0.00 46.27 3.28
3153 10143 6.062258 TGCTAGTAGAATAGCCAAAAAGGT 57.938 37.500 0.00 0.00 46.27 3.50
3221 10211 3.592059 TCCCTTCGGATGTAACTTTTCG 58.408 45.455 0.00 0.00 31.13 3.46
3222 10212 3.258872 TCCCTTCGGATGTAACTTTTCGA 59.741 43.478 0.00 0.00 31.13 3.71
3223 10213 3.617263 CCCTTCGGATGTAACTTTTCGAG 59.383 47.826 0.00 0.00 0.00 4.04
3224 10214 4.243270 CCTTCGGATGTAACTTTTCGAGT 58.757 43.478 0.00 0.00 41.47 4.18
3225 10215 5.404946 CCTTCGGATGTAACTTTTCGAGTA 58.595 41.667 0.00 0.00 37.72 2.59
3226 10216 5.515626 CCTTCGGATGTAACTTTTCGAGTAG 59.484 44.000 0.00 0.00 37.72 2.57
3227 10217 5.885230 TCGGATGTAACTTTTCGAGTAGA 57.115 39.130 3.22 0.00 37.72 2.59
3228 10218 6.446781 TCGGATGTAACTTTTCGAGTAGAT 57.553 37.500 3.22 0.00 37.72 1.98
3229 10219 6.263344 TCGGATGTAACTTTTCGAGTAGATG 58.737 40.000 3.22 0.00 37.72 2.90
3230 10220 6.094464 TCGGATGTAACTTTTCGAGTAGATGA 59.906 38.462 3.22 0.00 37.72 2.92
3231 10221 6.918569 CGGATGTAACTTTTCGAGTAGATGAT 59.081 38.462 3.22 0.00 37.72 2.45
3232 10222 7.435488 CGGATGTAACTTTTCGAGTAGATGATT 59.565 37.037 3.22 0.00 37.72 2.57
3233 10223 9.099454 GGATGTAACTTTTCGAGTAGATGATTT 57.901 33.333 3.22 0.00 37.72 2.17
3259 10249 9.787532 TTTCATATAAAAGCTTTTTCATCCGAG 57.212 29.630 28.21 11.34 0.00 4.63
3260 10250 8.506168 TCATATAAAAGCTTTTTCATCCGAGT 57.494 30.769 28.21 3.90 0.00 4.18
3261 10251 8.956426 TCATATAAAAGCTTTTTCATCCGAGTT 58.044 29.630 28.21 3.37 0.00 3.01
3262 10252 9.226345 CATATAAAAGCTTTTTCATCCGAGTTC 57.774 33.333 28.21 0.00 0.00 3.01
3263 10253 3.813529 AAGCTTTTTCATCCGAGTTCG 57.186 42.857 0.00 0.00 39.44 3.95
3264 10254 2.767505 AGCTTTTTCATCCGAGTTCGT 58.232 42.857 0.48 0.00 37.74 3.85
3265 10255 3.921677 AGCTTTTTCATCCGAGTTCGTA 58.078 40.909 0.48 0.00 37.74 3.43
3266 10256 4.504858 AGCTTTTTCATCCGAGTTCGTAT 58.495 39.130 0.48 0.00 37.74 3.06
3267 10257 4.330074 AGCTTTTTCATCCGAGTTCGTATG 59.670 41.667 1.22 1.22 37.09 2.39
3268 10258 4.578601 CTTTTTCATCCGAGTTCGTATGC 58.421 43.478 2.65 0.00 35.95 3.14
3269 10259 2.951457 TTCATCCGAGTTCGTATGCA 57.049 45.000 2.65 0.00 35.95 3.96
3270 10260 2.951457 TCATCCGAGTTCGTATGCAA 57.049 45.000 2.65 0.00 35.95 4.08
3271 10261 3.239587 TCATCCGAGTTCGTATGCAAA 57.760 42.857 2.65 0.00 35.95 3.68
3272 10262 3.591023 TCATCCGAGTTCGTATGCAAAA 58.409 40.909 2.65 0.00 35.95 2.44
3273 10263 3.616821 TCATCCGAGTTCGTATGCAAAAG 59.383 43.478 2.65 0.00 35.95 2.27
3274 10264 3.034721 TCCGAGTTCGTATGCAAAAGT 57.965 42.857 0.00 0.00 37.74 2.66
3275 10265 3.395639 TCCGAGTTCGTATGCAAAAGTT 58.604 40.909 0.00 0.00 37.74 2.66
3276 10266 4.558178 TCCGAGTTCGTATGCAAAAGTTA 58.442 39.130 0.00 0.00 37.74 2.24
3277 10267 5.172934 TCCGAGTTCGTATGCAAAAGTTAT 58.827 37.500 0.00 0.00 37.74 1.89
3278 10268 5.062934 TCCGAGTTCGTATGCAAAAGTTATG 59.937 40.000 0.00 0.00 37.74 1.90
3279 10269 4.723862 CGAGTTCGTATGCAAAAGTTATGC 59.276 41.667 0.00 0.00 38.20 3.14
3280 10270 5.670094 CGAGTTCGTATGCAAAAGTTATGCA 60.670 40.000 3.45 3.45 45.01 3.96
3281 10271 7.628446 CGAGTTCGTATGCAAAAGTTATGCAC 61.628 42.308 2.99 0.00 44.36 4.57
3282 10272 9.860567 CGAGTTCGTATGCAAAAGTTATGCACA 62.861 40.741 2.99 0.00 44.36 4.57
3293 10283 9.662545 GCAAAAGTTATGCACATTTTACAAATT 57.337 25.926 0.00 0.00 43.29 1.82
3296 10286 9.553064 AAAGTTATGCACATTTTACAAATTCCA 57.447 25.926 0.00 0.00 0.00 3.53
3297 10287 8.761575 AGTTATGCACATTTTACAAATTCCAG 57.238 30.769 0.00 0.00 0.00 3.86
3298 10288 8.584157 AGTTATGCACATTTTACAAATTCCAGA 58.416 29.630 0.00 0.00 0.00 3.86
3299 10289 8.863049 GTTATGCACATTTTACAAATTCCAGAG 58.137 33.333 0.00 0.00 0.00 3.35
3300 10290 6.647334 TGCACATTTTACAAATTCCAGAGA 57.353 33.333 0.00 0.00 0.00 3.10
3301 10291 6.446318 TGCACATTTTACAAATTCCAGAGAC 58.554 36.000 0.00 0.00 0.00 3.36
3302 10292 6.040278 TGCACATTTTACAAATTCCAGAGACA 59.960 34.615 0.00 0.00 0.00 3.41
3303 10293 7.092716 GCACATTTTACAAATTCCAGAGACAT 58.907 34.615 0.00 0.00 0.00 3.06
3304 10294 7.599998 GCACATTTTACAAATTCCAGAGACATT 59.400 33.333 0.00 0.00 0.00 2.71
3305 10295 9.480053 CACATTTTACAAATTCCAGAGACATTT 57.520 29.630 0.00 0.00 0.00 2.32
3308 10298 7.945033 TTTACAAATTCCAGAGACATTTTGC 57.055 32.000 0.00 0.00 0.00 3.68
3309 10299 5.534207 ACAAATTCCAGAGACATTTTGCA 57.466 34.783 0.00 0.00 0.00 4.08
3310 10300 5.916318 ACAAATTCCAGAGACATTTTGCAA 58.084 33.333 0.00 0.00 0.00 4.08
3311 10301 6.347696 ACAAATTCCAGAGACATTTTGCAAA 58.652 32.000 8.05 8.05 0.00 3.68
3312 10302 6.993902 ACAAATTCCAGAGACATTTTGCAAAT 59.006 30.769 13.65 0.00 0.00 2.32
3313 10303 8.149647 ACAAATTCCAGAGACATTTTGCAAATA 58.850 29.630 13.65 4.65 0.00 1.40
3314 10304 8.991026 CAAATTCCAGAGACATTTTGCAAATAA 58.009 29.630 13.65 0.00 0.00 1.40
3315 10305 9.558396 AAATTCCAGAGACATTTTGCAAATAAA 57.442 25.926 13.65 0.00 0.00 1.40
3316 10306 8.767478 ATTCCAGAGACATTTTGCAAATAAAG 57.233 30.769 13.65 5.97 0.00 1.85
3317 10307 7.288810 TCCAGAGACATTTTGCAAATAAAGT 57.711 32.000 13.65 9.15 0.00 2.66
3318 10308 7.370383 TCCAGAGACATTTTGCAAATAAAGTC 58.630 34.615 13.65 16.70 0.00 3.01
3319 10309 6.306356 CCAGAGACATTTTGCAAATAAAGTCG 59.694 38.462 13.65 6.50 0.00 4.18
3320 10310 7.077605 CAGAGACATTTTGCAAATAAAGTCGA 58.922 34.615 13.65 0.00 0.00 4.20
3321 10311 7.591057 CAGAGACATTTTGCAAATAAAGTCGAA 59.409 33.333 13.65 0.00 0.00 3.71
3322 10312 8.134895 AGAGACATTTTGCAAATAAAGTCGAAA 58.865 29.630 13.65 0.00 0.00 3.46
3323 10313 8.816640 AGACATTTTGCAAATAAAGTCGAAAT 57.183 26.923 13.65 0.00 0.00 2.17
3324 10314 9.260002 AGACATTTTGCAAATAAAGTCGAAATT 57.740 25.926 13.65 0.83 0.00 1.82
3325 10315 9.516091 GACATTTTGCAAATAAAGTCGAAATTC 57.484 29.630 13.65 0.00 0.00 2.17
3326 10316 9.039870 ACATTTTGCAAATAAAGTCGAAATTCA 57.960 25.926 13.65 0.00 0.00 2.57
3329 10319 8.586570 TTTGCAAATAAAGTCGAAATTCATGT 57.413 26.923 8.05 0.00 0.00 3.21
3330 10320 8.586570 TTGCAAATAAAGTCGAAATTCATGTT 57.413 26.923 0.00 0.00 0.00 2.71
3331 10321 8.586570 TGCAAATAAAGTCGAAATTCATGTTT 57.413 26.923 0.00 0.00 0.00 2.83
3332 10322 8.486383 TGCAAATAAAGTCGAAATTCATGTTTG 58.514 29.630 0.00 0.00 0.00 2.93
3333 10323 8.487176 GCAAATAAAGTCGAAATTCATGTTTGT 58.513 29.630 0.00 0.00 0.00 2.83
3342 10332 9.791838 GTCGAAATTCATGTTTGTAAATTTTCC 57.208 29.630 0.00 0.00 32.90 3.13
3343 10333 8.983724 TCGAAATTCATGTTTGTAAATTTTCCC 58.016 29.630 0.00 0.00 32.90 3.97
3344 10334 8.768955 CGAAATTCATGTTTGTAAATTTTCCCA 58.231 29.630 0.00 0.00 32.90 4.37
3347 10337 8.970859 ATTCATGTTTGTAAATTTTCCCAACA 57.029 26.923 0.00 4.29 0.00 3.33
3348 10338 8.792830 TTCATGTTTGTAAATTTTCCCAACAA 57.207 26.923 11.29 6.57 0.00 2.83
3349 10339 8.202745 TCATGTTTGTAAATTTTCCCAACAAC 57.797 30.769 11.29 5.64 30.28 3.32
3350 10340 8.043710 TCATGTTTGTAAATTTTCCCAACAACT 58.956 29.630 11.29 0.00 30.28 3.16
3351 10341 9.319143 CATGTTTGTAAATTTTCCCAACAACTA 57.681 29.630 11.29 2.94 30.28 2.24
3352 10342 8.934507 TGTTTGTAAATTTTCCCAACAACTAG 57.065 30.769 0.00 0.00 30.28 2.57
3353 10343 8.750298 TGTTTGTAAATTTTCCCAACAACTAGA 58.250 29.630 0.00 0.00 30.28 2.43
3354 10344 9.027129 GTTTGTAAATTTTCCCAACAACTAGAC 57.973 33.333 0.00 0.00 30.28 2.59
3355 10345 7.279750 TGTAAATTTTCCCAACAACTAGACC 57.720 36.000 0.00 0.00 0.00 3.85
3356 10346 6.834451 TGTAAATTTTCCCAACAACTAGACCA 59.166 34.615 0.00 0.00 0.00 4.02
3357 10347 5.784578 AATTTTCCCAACAACTAGACCAC 57.215 39.130 0.00 0.00 0.00 4.16
3358 10348 3.935818 TTTCCCAACAACTAGACCACA 57.064 42.857 0.00 0.00 0.00 4.17
3359 10349 4.447138 TTTCCCAACAACTAGACCACAT 57.553 40.909 0.00 0.00 0.00 3.21
3360 10350 5.570205 TTTCCCAACAACTAGACCACATA 57.430 39.130 0.00 0.00 0.00 2.29
3361 10351 5.772393 TTCCCAACAACTAGACCACATAT 57.228 39.130 0.00 0.00 0.00 1.78
3362 10352 5.353394 TCCCAACAACTAGACCACATATC 57.647 43.478 0.00 0.00 0.00 1.63
3363 10353 4.780554 TCCCAACAACTAGACCACATATCA 59.219 41.667 0.00 0.00 0.00 2.15
3364 10354 4.876107 CCCAACAACTAGACCACATATCAC 59.124 45.833 0.00 0.00 0.00 3.06
3365 10355 5.487433 CCAACAACTAGACCACATATCACA 58.513 41.667 0.00 0.00 0.00 3.58
3366 10356 6.115446 CCAACAACTAGACCACATATCACAT 58.885 40.000 0.00 0.00 0.00 3.21
3367 10357 6.037500 CCAACAACTAGACCACATATCACATG 59.962 42.308 0.00 0.00 0.00 3.21
3368 10358 5.674525 ACAACTAGACCACATATCACATGG 58.325 41.667 0.00 0.00 39.57 3.66
3369 10359 4.963318 ACTAGACCACATATCACATGGG 57.037 45.455 0.00 0.00 37.86 4.00
3370 10360 4.556697 ACTAGACCACATATCACATGGGA 58.443 43.478 0.00 0.00 37.86 4.37
3371 10361 4.968719 ACTAGACCACATATCACATGGGAA 59.031 41.667 0.00 0.00 37.86 3.97
3372 10362 4.860802 AGACCACATATCACATGGGAAA 57.139 40.909 0.00 0.00 37.86 3.13
3373 10363 4.526970 AGACCACATATCACATGGGAAAC 58.473 43.478 0.00 0.00 37.86 2.78
3374 10364 4.228210 AGACCACATATCACATGGGAAACT 59.772 41.667 0.00 0.00 37.86 2.66
3375 10365 4.934356 ACCACATATCACATGGGAAACTT 58.066 39.130 0.00 0.00 37.86 2.66
3376 10366 6.069673 AGACCACATATCACATGGGAAACTTA 60.070 38.462 0.00 0.00 37.86 2.24
3377 10367 6.672593 ACCACATATCACATGGGAAACTTAT 58.327 36.000 0.00 0.00 37.86 1.73
3378 10368 7.125391 ACCACATATCACATGGGAAACTTATT 58.875 34.615 0.00 0.00 37.86 1.40
3379 10369 7.619302 ACCACATATCACATGGGAAACTTATTT 59.381 33.333 0.00 0.00 37.86 1.40
3380 10370 8.477256 CCACATATCACATGGGAAACTTATTTT 58.523 33.333 0.00 0.00 0.00 1.82
3439 10429 5.585820 TTTTCTAAAACTGAAAAGGCGGT 57.414 34.783 0.00 0.00 38.15 5.68
3440 10430 4.823790 TTCTAAAACTGAAAAGGCGGTC 57.176 40.909 0.00 0.00 0.00 4.79
3441 10431 3.143728 TCTAAAACTGAAAAGGCGGTCC 58.856 45.455 0.00 0.00 0.00 4.46
3442 10432 1.770294 AAAACTGAAAAGGCGGTCCA 58.230 45.000 0.00 0.00 33.74 4.02
3443 10433 1.029681 AAACTGAAAAGGCGGTCCAC 58.970 50.000 0.00 0.00 33.74 4.02
3444 10434 0.822121 AACTGAAAAGGCGGTCCACC 60.822 55.000 0.00 0.00 33.74 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
167 168 4.336433 AGAGAATGATTGTAACCCAATGCG 59.664 41.667 0.00 0.00 43.87 4.73
280 281 5.591877 AGAGTGCTTATCCCAATGTTTCATC 59.408 40.000 0.00 0.00 0.00 2.92
436 458 6.291067 TGATTTCTAACTATGAATGCAGCG 57.709 37.500 0.00 0.00 0.00 5.18
1267 1296 7.404671 TTGGAGAGTATTTATTGGGCTTTTC 57.595 36.000 0.00 0.00 0.00 2.29
1311 1341 9.905713 AATTTGTAACTTCCTGAAGCATATCTA 57.094 29.630 6.81 0.00 41.99 1.98
1930 1966 7.630005 TTTTCCCATTCCAAATATATGCCAT 57.370 32.000 0.00 0.00 0.00 4.40
1958 1994 6.450845 TTTGCATCTAATTTTTCAAGCGTG 57.549 33.333 0.00 0.00 0.00 5.34
1960 1996 7.786114 TCTTTTTGCATCTAATTTTTCAAGCG 58.214 30.769 0.00 0.00 0.00 4.68
2577 2615 1.494721 GGTCTTCCCTGCCCATATGAA 59.505 52.381 3.65 0.00 0.00 2.57
2743 2863 2.284190 GCGATTAGCCTTCAGAGCTTT 58.716 47.619 0.00 0.00 41.83 3.51
2831 4321 1.680735 TGCTTTCTTCACGTGGCATTT 59.319 42.857 17.00 0.00 0.00 2.32
2861 5727 3.632145 AGTGCCGACAAACTTCAATCTTT 59.368 39.130 0.00 0.00 0.00 2.52
2924 9909 0.458669 ACGCGTGTCCTATTAGGGTG 59.541 55.000 12.93 3.25 35.59 4.61
2931 9916 0.744874 AGTATGCACGCGTGTCCTAT 59.255 50.000 36.80 26.37 0.00 2.57
2982 9967 2.759114 CTGCAAGGGAGGCCTTCA 59.241 61.111 14.70 1.24 0.00 3.02
3035 10020 3.893200 TCCCGTCTTGTGTTCTCTTCTTA 59.107 43.478 0.00 0.00 0.00 2.10
3148 10138 0.605319 TTGGCGATCGAAGCACCTTT 60.605 50.000 21.57 0.00 36.08 3.11
3153 10143 0.037326 AACTCTTGGCGATCGAAGCA 60.037 50.000 21.57 4.27 36.08 3.91
3233 10223 9.787532 CTCGGATGAAAAAGCTTTTATATGAAA 57.212 29.630 24.11 8.21 0.00 2.69
3234 10224 8.956426 ACTCGGATGAAAAAGCTTTTATATGAA 58.044 29.630 24.11 7.55 0.00 2.57
3235 10225 8.506168 ACTCGGATGAAAAAGCTTTTATATGA 57.494 30.769 24.11 15.37 0.00 2.15
3236 10226 9.226345 GAACTCGGATGAAAAAGCTTTTATATG 57.774 33.333 24.11 12.33 0.00 1.78
3237 10227 8.122952 CGAACTCGGATGAAAAAGCTTTTATAT 58.877 33.333 24.11 19.63 35.37 0.86
3238 10228 7.118680 ACGAACTCGGATGAAAAAGCTTTTATA 59.881 33.333 24.11 16.06 44.95 0.98
3239 10229 6.072673 ACGAACTCGGATGAAAAAGCTTTTAT 60.073 34.615 24.11 15.07 44.95 1.40
3240 10230 5.237779 ACGAACTCGGATGAAAAAGCTTTTA 59.762 36.000 24.11 10.73 44.95 1.52
3241 10231 4.036380 ACGAACTCGGATGAAAAAGCTTTT 59.964 37.500 18.74 18.74 44.95 2.27
3242 10232 3.564225 ACGAACTCGGATGAAAAAGCTTT 59.436 39.130 5.69 5.69 44.95 3.51
3243 10233 3.139077 ACGAACTCGGATGAAAAAGCTT 58.861 40.909 3.88 0.00 44.95 3.74
3244 10234 2.767505 ACGAACTCGGATGAAAAAGCT 58.232 42.857 3.88 0.00 44.95 3.74
3245 10235 4.859629 ATACGAACTCGGATGAAAAAGC 57.140 40.909 3.88 0.00 42.14 3.51
3253 10243 3.596214 ACTTTTGCATACGAACTCGGAT 58.404 40.909 3.88 0.00 45.12 4.18
3254 10244 3.034721 ACTTTTGCATACGAACTCGGA 57.965 42.857 3.88 0.00 44.95 4.55
3255 10245 3.806316 AACTTTTGCATACGAACTCGG 57.194 42.857 3.88 0.00 44.95 4.63
3256 10246 4.723862 GCATAACTTTTGCATACGAACTCG 59.276 41.667 0.00 0.00 41.50 4.18
3257 10247 5.627172 TGCATAACTTTTGCATACGAACTC 58.373 37.500 3.05 0.00 44.73 3.01
3258 10248 5.621197 TGCATAACTTTTGCATACGAACT 57.379 34.783 3.05 0.00 44.73 3.01
3267 10257 9.662545 AATTTGTAAAATGTGCATAACTTTTGC 57.337 25.926 5.36 4.79 36.54 3.68
3270 10260 9.553064 TGGAATTTGTAAAATGTGCATAACTTT 57.447 25.926 0.00 0.00 0.00 2.66
3271 10261 9.206870 CTGGAATTTGTAAAATGTGCATAACTT 57.793 29.630 0.00 0.00 0.00 2.66
3272 10262 8.584157 TCTGGAATTTGTAAAATGTGCATAACT 58.416 29.630 0.00 0.00 0.00 2.24
3273 10263 8.755696 TCTGGAATTTGTAAAATGTGCATAAC 57.244 30.769 0.00 0.00 0.00 1.89
3274 10264 8.801299 TCTCTGGAATTTGTAAAATGTGCATAA 58.199 29.630 0.00 0.00 0.00 1.90
3275 10265 8.243426 GTCTCTGGAATTTGTAAAATGTGCATA 58.757 33.333 0.00 0.00 0.00 3.14
3276 10266 7.092716 GTCTCTGGAATTTGTAAAATGTGCAT 58.907 34.615 0.00 0.00 0.00 3.96
3277 10267 6.040278 TGTCTCTGGAATTTGTAAAATGTGCA 59.960 34.615 0.00 0.00 0.00 4.57
3278 10268 6.446318 TGTCTCTGGAATTTGTAAAATGTGC 58.554 36.000 0.00 0.00 0.00 4.57
3279 10269 9.480053 AAATGTCTCTGGAATTTGTAAAATGTG 57.520 29.630 0.00 0.00 0.00 3.21
3282 10272 8.992073 GCAAAATGTCTCTGGAATTTGTAAAAT 58.008 29.630 0.00 0.00 32.03 1.82
3283 10273 7.984050 TGCAAAATGTCTCTGGAATTTGTAAAA 59.016 29.630 0.00 0.00 32.03 1.52
3284 10274 7.495901 TGCAAAATGTCTCTGGAATTTGTAAA 58.504 30.769 0.00 0.00 32.03 2.01
3285 10275 7.048629 TGCAAAATGTCTCTGGAATTTGTAA 57.951 32.000 0.00 0.00 32.03 2.41
3286 10276 6.647334 TGCAAAATGTCTCTGGAATTTGTA 57.353 33.333 0.00 0.00 32.03 2.41
3287 10277 5.534207 TGCAAAATGTCTCTGGAATTTGT 57.466 34.783 0.00 0.00 32.03 2.83
3288 10278 6.847956 TTTGCAAAATGTCTCTGGAATTTG 57.152 33.333 10.02 0.00 0.00 2.32
3289 10279 9.558396 TTTATTTGCAAAATGTCTCTGGAATTT 57.442 25.926 17.19 0.00 0.00 1.82
3290 10280 9.211485 CTTTATTTGCAAAATGTCTCTGGAATT 57.789 29.630 17.19 0.00 0.00 2.17
3291 10281 8.370182 ACTTTATTTGCAAAATGTCTCTGGAAT 58.630 29.630 17.19 0.00 0.00 3.01
3292 10282 7.725251 ACTTTATTTGCAAAATGTCTCTGGAA 58.275 30.769 17.19 0.00 0.00 3.53
3293 10283 7.288810 ACTTTATTTGCAAAATGTCTCTGGA 57.711 32.000 17.19 0.00 0.00 3.86
3294 10284 6.306356 CGACTTTATTTGCAAAATGTCTCTGG 59.694 38.462 17.19 5.91 0.00 3.86
3295 10285 7.077605 TCGACTTTATTTGCAAAATGTCTCTG 58.922 34.615 17.19 9.23 0.00 3.35
3296 10286 7.202016 TCGACTTTATTTGCAAAATGTCTCT 57.798 32.000 17.19 0.00 0.00 3.10
3297 10287 7.851822 TTCGACTTTATTTGCAAAATGTCTC 57.148 32.000 17.19 7.59 0.00 3.36
3298 10288 8.816640 ATTTCGACTTTATTTGCAAAATGTCT 57.183 26.923 17.19 1.30 0.00 3.41
3299 10289 9.516091 GAATTTCGACTTTATTTGCAAAATGTC 57.484 29.630 17.19 18.13 0.00 3.06
3300 10290 9.039870 TGAATTTCGACTTTATTTGCAAAATGT 57.960 25.926 17.19 12.01 0.00 2.71
3303 10293 9.039870 ACATGAATTTCGACTTTATTTGCAAAA 57.960 25.926 17.19 2.96 0.00 2.44
3304 10294 8.586570 ACATGAATTTCGACTTTATTTGCAAA 57.413 26.923 15.44 15.44 0.00 3.68
3305 10295 8.586570 AACATGAATTTCGACTTTATTTGCAA 57.413 26.923 0.00 0.00 0.00 4.08
3306 10296 8.486383 CAAACATGAATTTCGACTTTATTTGCA 58.514 29.630 0.00 0.00 0.00 4.08
3307 10297 8.487176 ACAAACATGAATTTCGACTTTATTTGC 58.513 29.630 0.00 0.00 0.00 3.68
3316 10306 9.791838 GGAAAATTTACAAACATGAATTTCGAC 57.208 29.630 0.00 0.00 32.29 4.20
3317 10307 8.983724 GGGAAAATTTACAAACATGAATTTCGA 58.016 29.630 0.00 0.00 32.29 3.71
3318 10308 8.768955 TGGGAAAATTTACAAACATGAATTTCG 58.231 29.630 0.00 0.00 32.29 3.46
3321 10311 9.401058 TGTTGGGAAAATTTACAAACATGAATT 57.599 25.926 6.80 0.00 0.00 2.17
3322 10312 8.970859 TGTTGGGAAAATTTACAAACATGAAT 57.029 26.923 6.80 0.00 0.00 2.57
3323 10313 8.669243 GTTGTTGGGAAAATTTACAAACATGAA 58.331 29.630 11.38 0.00 31.29 2.57
3324 10314 8.043710 AGTTGTTGGGAAAATTTACAAACATGA 58.956 29.630 11.38 0.00 31.29 3.07
3325 10315 8.207521 AGTTGTTGGGAAAATTTACAAACATG 57.792 30.769 11.38 0.00 31.29 3.21
3326 10316 9.541143 CTAGTTGTTGGGAAAATTTACAAACAT 57.459 29.630 11.38 1.24 31.29 2.71
3327 10317 8.750298 TCTAGTTGTTGGGAAAATTTACAAACA 58.250 29.630 6.80 6.80 31.29 2.83
3328 10318 9.027129 GTCTAGTTGTTGGGAAAATTTACAAAC 57.973 33.333 1.22 1.22 31.29 2.93
3329 10319 8.198778 GGTCTAGTTGTTGGGAAAATTTACAAA 58.801 33.333 5.30 0.00 31.29 2.83
3330 10320 7.342284 TGGTCTAGTTGTTGGGAAAATTTACAA 59.658 33.333 0.00 0.00 0.00 2.41
3331 10321 6.834451 TGGTCTAGTTGTTGGGAAAATTTACA 59.166 34.615 0.00 0.00 0.00 2.41
3332 10322 7.143340 GTGGTCTAGTTGTTGGGAAAATTTAC 58.857 38.462 0.00 0.00 0.00 2.01
3333 10323 6.834451 TGTGGTCTAGTTGTTGGGAAAATTTA 59.166 34.615 0.00 0.00 0.00 1.40
3334 10324 5.659079 TGTGGTCTAGTTGTTGGGAAAATTT 59.341 36.000 0.00 0.00 0.00 1.82
3335 10325 5.205056 TGTGGTCTAGTTGTTGGGAAAATT 58.795 37.500 0.00 0.00 0.00 1.82
3336 10326 4.798882 TGTGGTCTAGTTGTTGGGAAAAT 58.201 39.130 0.00 0.00 0.00 1.82
3337 10327 4.237976 TGTGGTCTAGTTGTTGGGAAAA 57.762 40.909 0.00 0.00 0.00 2.29
3338 10328 3.935818 TGTGGTCTAGTTGTTGGGAAA 57.064 42.857 0.00 0.00 0.00 3.13
3339 10329 5.249622 TGATATGTGGTCTAGTTGTTGGGAA 59.750 40.000 0.00 0.00 0.00 3.97
3340 10330 4.780554 TGATATGTGGTCTAGTTGTTGGGA 59.219 41.667 0.00 0.00 0.00 4.37
3341 10331 4.876107 GTGATATGTGGTCTAGTTGTTGGG 59.124 45.833 0.00 0.00 0.00 4.12
3342 10332 5.487433 TGTGATATGTGGTCTAGTTGTTGG 58.513 41.667 0.00 0.00 0.00 3.77
3343 10333 6.037500 CCATGTGATATGTGGTCTAGTTGTTG 59.962 42.308 0.00 0.00 0.00 3.33
3344 10334 6.115446 CCATGTGATATGTGGTCTAGTTGTT 58.885 40.000 0.00 0.00 0.00 2.83
3345 10335 5.396772 CCCATGTGATATGTGGTCTAGTTGT 60.397 44.000 0.00 0.00 0.00 3.32
3346 10336 5.059161 CCCATGTGATATGTGGTCTAGTTG 58.941 45.833 0.00 0.00 0.00 3.16
3347 10337 4.968719 TCCCATGTGATATGTGGTCTAGTT 59.031 41.667 0.00 0.00 0.00 2.24
3348 10338 4.556697 TCCCATGTGATATGTGGTCTAGT 58.443 43.478 0.00 0.00 0.00 2.57
3349 10339 5.551305 TTCCCATGTGATATGTGGTCTAG 57.449 43.478 0.00 0.00 0.00 2.43
3350 10340 5.428457 AGTTTCCCATGTGATATGTGGTCTA 59.572 40.000 0.00 0.00 0.00 2.59
3351 10341 4.228210 AGTTTCCCATGTGATATGTGGTCT 59.772 41.667 0.00 0.00 0.00 3.85
3352 10342 4.526970 AGTTTCCCATGTGATATGTGGTC 58.473 43.478 0.00 0.00 0.00 4.02
3353 10343 4.591321 AGTTTCCCATGTGATATGTGGT 57.409 40.909 0.00 0.00 0.00 4.16
3354 10344 7.587037 AATAAGTTTCCCATGTGATATGTGG 57.413 36.000 0.00 0.00 0.00 4.17
3416 10406 5.968254 ACCGCCTTTTCAGTTTTAGAAAAA 58.032 33.333 0.00 0.00 42.45 1.94
3417 10407 5.450826 GGACCGCCTTTTCAGTTTTAGAAAA 60.451 40.000 0.00 0.00 41.27 2.29
3418 10408 4.037089 GGACCGCCTTTTCAGTTTTAGAAA 59.963 41.667 0.00 0.00 33.48 2.52
3419 10409 3.566742 GGACCGCCTTTTCAGTTTTAGAA 59.433 43.478 0.00 0.00 0.00 2.10
3420 10410 3.143728 GGACCGCCTTTTCAGTTTTAGA 58.856 45.455 0.00 0.00 0.00 2.10
3421 10411 2.882137 TGGACCGCCTTTTCAGTTTTAG 59.118 45.455 0.00 0.00 34.31 1.85
3422 10412 2.619646 GTGGACCGCCTTTTCAGTTTTA 59.380 45.455 0.00 0.00 34.31 1.52
3423 10413 1.407618 GTGGACCGCCTTTTCAGTTTT 59.592 47.619 0.00 0.00 34.31 2.43
3424 10414 1.029681 GTGGACCGCCTTTTCAGTTT 58.970 50.000 0.00 0.00 34.31 2.66
3425 10415 0.822121 GGTGGACCGCCTTTTCAGTT 60.822 55.000 17.39 0.00 34.31 3.16
3426 10416 1.228154 GGTGGACCGCCTTTTCAGT 60.228 57.895 17.39 0.00 34.31 3.41
3427 10417 3.668386 GGTGGACCGCCTTTTCAG 58.332 61.111 17.39 0.00 34.31 3.02


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

AutoCloner maintained by Alex Coulton.