Multiple sequence alignment - TraesCS2B01G332100

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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 TraesCS2B01G332100 chr2B 100.000 3251 0 0 1 3251 475128944 475125694 0.000000e+00 6004.0
1 TraesCS2B01G332100 chr2A 95.281 3136 109 20 7 3131 537684941 537681834 0.000000e+00 4935.0
2 TraesCS2B01G332100 chr2A 84.848 99 14 1 88 185 702077367 702077465 7.420000e-17 99.0
3 TraesCS2B01G332100 chr2A 100.000 28 0 0 116 143 537638058 537638031 6.000000e-03 52.8
4 TraesCS2B01G332100 chr2D 94.754 3126 114 28 7 3125 401115402 401112320 0.000000e+00 4819.0
5 TraesCS2B01G332100 chr2D 87.719 57 6 1 88 143 362924108 362924164 7.530000e-07 65.8
6 TraesCS2B01G332100 chr7B 99.206 126 1 0 3126 3251 706479268 706479393 9.070000e-56 228.0
7 TraesCS2B01G332100 chr3A 89.873 79 8 0 104 182 445523109 445523187 5.740000e-18 102.0
8 TraesCS2B01G332100 chr4D 96.491 57 2 0 3157 3213 63580614 63580558 9.600000e-16 95.3
9 TraesCS2B01G332100 chrUn 89.231 65 6 1 129 192 32053808 32053744 2.690000e-11 80.5
10 TraesCS2B01G332100 chrUn 97.436 39 1 0 3213 3251 50437490 50437528 2.090000e-07 67.6
11 TraesCS2B01G332100 chrUn 97.436 39 1 0 3213 3251 263186141 263186103 2.090000e-07 67.6
12 TraesCS2B01G332100 chrUn 97.436 39 1 0 3213 3251 345495523 345495561 2.090000e-07 67.6
13 TraesCS2B01G332100 chr4B 97.436 39 1 0 3213 3251 654981405 654981443 2.090000e-07 67.6
14 TraesCS2B01G332100 chr4B 97.436 39 1 0 3213 3251 655017135 655017173 2.090000e-07 67.6
15 TraesCS2B01G332100 chr4B 97.436 39 1 0 3213 3251 655052541 655052579 2.090000e-07 67.6
16 TraesCS2B01G332100 chr4B 97.368 38 1 0 343 380 150016643 150016606 7.530000e-07 65.8
17 TraesCS2B01G332100 chr4A 97.436 39 1 0 3213 3251 670558828 670558866 2.090000e-07 67.6
18 TraesCS2B01G332100 chr4A 97.368 38 1 0 343 380 75612426 75612463 7.530000e-07 65.8
19 TraesCS2B01G332100 chr3D 86.885 61 7 1 320 380 120561274 120561215 2.090000e-07 67.6
20 TraesCS2B01G332100 chr3D 97.297 37 1 0 344 380 185006623 185006659 2.710000e-06 63.9
21 TraesCS2B01G332100 chr7D 91.489 47 3 1 3206 3251 207603587 207603541 2.710000e-06 63.9
22 TraesCS2B01G332100 chr5D 97.297 37 1 0 344 380 546145301 546145337 2.710000e-06 63.9
23 TraesCS2B01G332100 chr5A 97.297 37 1 0 344 380 419766426 419766390 2.710000e-06 63.9
24 TraesCS2B01G332100 chr1D 97.297 37 1 0 344 380 343607338 343607302 2.710000e-06 63.9
25 TraesCS2B01G332100 chr1B 100.000 32 0 0 154 185 652281905 652281936 3.500000e-05 60.2
26 TraesCS2B01G332100 chr6D 100.000 28 0 0 116 143 166241933 166241960 6.000000e-03 52.8
27 TraesCS2B01G332100 chr6A 100.000 28 0 0 116 143 362241633 362241606 6.000000e-03 52.8


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 TraesCS2B01G332100 chr2B 475125694 475128944 3250 True 6004 6004 100.000 1 3251 1 chr2B.!!$R1 3250
1 TraesCS2B01G332100 chr2A 537681834 537684941 3107 True 4935 4935 95.281 7 3131 1 chr2A.!!$R2 3124
2 TraesCS2B01G332100 chr2D 401112320 401115402 3082 True 4819 4819 94.754 7 3125 1 chr2D.!!$R1 3118

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
325 328 0.679505 AAAGTGTGTGGAGCTCGCTA 59.320 50.000 7.83 0.00 31.98 4.26 F
328 331 1.276421 AGTGTGTGGAGCTCGCTATTT 59.724 47.619 7.83 0.00 30.65 1.40 F
586 593 1.378155 CGAAAAGACGACGACGAGAAC 59.622 52.381 15.32 2.73 42.66 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2130 2143 0.949105 GGTACTGATAATGCGGGCGG 60.949 60.000 0.00 0.00 0.00 6.13 R
2166 2179 2.663796 CTGGCAGCTGCAGAGTCT 59.336 61.111 37.63 1.42 44.36 3.24 R
2557 2570 0.912486 AACCCTGATAGAGGCCACAC 59.088 55.000 5.01 0.00 41.19 3.82 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
84 85 6.603599 TGTAGATTCTCTAAGACTGCTAGCAA 59.396 38.462 19.86 1.95 29.58 3.91
98 99 2.860735 GCTAGCAATAGGAAGTGTCGTG 59.139 50.000 10.63 0.00 0.00 4.35
108 109 8.404000 CAATAGGAAGTGTCGTGTACTACTATT 58.596 37.037 0.00 0.00 38.08 1.73
117 118 6.915843 TGTCGTGTACTACTATTATGCACATG 59.084 38.462 0.00 0.00 0.00 3.21
152 153 6.247229 TGATACCACCTTTACAGTGCATAT 57.753 37.500 0.00 0.00 33.75 1.78
186 187 6.548251 TGATCTCATTTATTGTCATGCATGGT 59.452 34.615 25.97 12.38 0.00 3.55
296 298 4.136051 CGGTTTAACCAACACCTTCCTAA 58.864 43.478 14.97 0.00 38.47 2.69
323 326 1.160329 ACAAAGTGTGTGGAGCTCGC 61.160 55.000 7.83 3.71 39.72 5.03
324 327 0.882042 CAAAGTGTGTGGAGCTCGCT 60.882 55.000 7.83 0.00 33.42 4.93
325 328 0.679505 AAAGTGTGTGGAGCTCGCTA 59.320 50.000 7.83 0.00 31.98 4.26
328 331 1.276421 AGTGTGTGGAGCTCGCTATTT 59.724 47.619 7.83 0.00 30.65 1.40
334 337 6.202954 GTGTGTGGAGCTCGCTATTTTATAAT 59.797 38.462 7.83 0.00 0.00 1.28
365 368 8.341903 TCATGTTTACCGATGCATTAATTACAG 58.658 33.333 0.00 0.00 0.00 2.74
393 396 6.866010 TGCATACATGATCACTAAATGACC 57.134 37.500 0.00 0.00 41.24 4.02
405 408 7.979444 TCACTAAATGACCAAGGACTTTTAG 57.021 36.000 22.63 22.63 40.05 1.85
569 576 2.202743 CCGGAGCGAGCAATCGAA 60.203 61.111 0.00 0.00 34.64 3.71
586 593 1.378155 CGAAAAGACGACGACGAGAAC 59.622 52.381 15.32 2.73 42.66 3.01
941 951 4.329545 CACCACCACCGACCCCTG 62.330 72.222 0.00 0.00 0.00 4.45
1023 1033 2.623915 CGACGACGACAACTCCCCT 61.624 63.158 0.00 0.00 42.66 4.79
1779 1792 2.429236 CTAGCGCAGGCGATACGG 60.429 66.667 18.96 0.58 46.35 4.02
1875 1888 2.048222 TTCGCACGGGAGCTTGAG 60.048 61.111 0.00 0.00 0.00 3.02
2130 2143 4.864334 CATCACCGCCCTGCCCTC 62.864 72.222 0.00 0.00 0.00 4.30
2166 2179 5.104569 TCAGTACCATGAGAACAATATGGCA 60.105 40.000 0.00 0.00 44.06 4.92
2291 2304 2.963432 CCAGGCATTGGTGATTCAAAC 58.037 47.619 0.00 0.00 42.41 2.93
2536 2549 2.884012 TGATGTCGTTTGTGCCAAGAAT 59.116 40.909 0.00 0.00 0.00 2.40
2552 2565 2.226330 AGAATTGTGGCGTGTTTGCTA 58.774 42.857 0.00 0.00 34.52 3.49
2557 2570 1.069568 TGTGGCGTGTTTGCTAAATCG 60.070 47.619 0.00 0.00 34.52 3.34
2581 2594 2.378547 TGGCCTCTATCAGGGTTGTTTT 59.621 45.455 3.32 0.00 43.70 2.43
2620 2633 1.677966 AGCACCAGCAGCCTGAATG 60.678 57.895 0.00 0.00 45.49 2.67
2661 2674 8.391075 AGTACTCTTATCATCAGCTTCTACTC 57.609 38.462 0.00 0.00 0.00 2.59
2774 2790 3.979101 TGCAGATGTCATGAACCTGTA 57.021 42.857 16.63 12.02 0.00 2.74
2784 2800 3.383505 TCATGAACCTGTATGTAGTCCGG 59.616 47.826 0.00 0.00 0.00 5.14
2830 2846 4.240103 AGGTGCTGCTGACGTGCA 62.240 61.111 0.00 0.00 41.05 4.57
2937 2953 4.821805 TGTTTCCTTCTCTGATTGTTGACC 59.178 41.667 0.00 0.00 0.00 4.02
2998 3014 2.627699 TGTCACTACATGCACAGAGTCA 59.372 45.455 0.00 0.00 0.00 3.41
3127 3145 2.074547 CAAGCATGCTGTTTTGGAGG 57.925 50.000 23.48 0.00 0.00 4.30
3128 3146 0.319405 AAGCATGCTGTTTTGGAGGC 59.681 50.000 23.48 0.00 35.40 4.70
3129 3147 0.828762 AGCATGCTGTTTTGGAGGCA 60.829 50.000 21.98 0.00 37.53 4.75
3130 3148 0.248289 GCATGCTGTTTTGGAGGCAT 59.752 50.000 11.37 0.00 44.77 4.40
3131 3149 1.738030 GCATGCTGTTTTGGAGGCATC 60.738 52.381 11.37 0.00 42.49 3.91
3132 3150 1.546923 CATGCTGTTTTGGAGGCATCA 59.453 47.619 0.00 0.00 42.49 3.07
3133 3151 1.250328 TGCTGTTTTGGAGGCATCAG 58.750 50.000 0.00 0.00 0.00 2.90
3134 3152 0.529378 GCTGTTTTGGAGGCATCAGG 59.471 55.000 0.00 0.00 0.00 3.86
3135 3153 1.887956 GCTGTTTTGGAGGCATCAGGA 60.888 52.381 0.00 0.00 0.00 3.86
3136 3154 2.517959 CTGTTTTGGAGGCATCAGGAA 58.482 47.619 0.00 0.00 0.00 3.36
3137 3155 2.892852 CTGTTTTGGAGGCATCAGGAAA 59.107 45.455 0.00 0.00 0.00 3.13
3138 3156 2.627699 TGTTTTGGAGGCATCAGGAAAC 59.372 45.455 0.00 8.38 0.00 2.78
3139 3157 1.923356 TTTGGAGGCATCAGGAAACC 58.077 50.000 0.00 0.00 0.00 3.27
3140 3158 0.776810 TTGGAGGCATCAGGAAACCA 59.223 50.000 0.00 0.00 0.00 3.67
3141 3159 0.038166 TGGAGGCATCAGGAAACCAC 59.962 55.000 0.00 0.00 0.00 4.16
3142 3160 0.038166 GGAGGCATCAGGAAACCACA 59.962 55.000 0.00 0.00 0.00 4.17
3143 3161 1.168714 GAGGCATCAGGAAACCACAC 58.831 55.000 0.00 0.00 0.00 3.82
3144 3162 0.478072 AGGCATCAGGAAACCACACA 59.522 50.000 0.00 0.00 0.00 3.72
3145 3163 0.598065 GGCATCAGGAAACCACACAC 59.402 55.000 0.00 0.00 0.00 3.82
3146 3164 1.317613 GCATCAGGAAACCACACACA 58.682 50.000 0.00 0.00 0.00 3.72
3147 3165 1.680735 GCATCAGGAAACCACACACAA 59.319 47.619 0.00 0.00 0.00 3.33
3148 3166 2.100584 GCATCAGGAAACCACACACAAA 59.899 45.455 0.00 0.00 0.00 2.83
3149 3167 3.705604 CATCAGGAAACCACACACAAAC 58.294 45.455 0.00 0.00 0.00 2.93
3150 3168 3.080300 TCAGGAAACCACACACAAACT 57.920 42.857 0.00 0.00 0.00 2.66
3151 3169 2.752354 TCAGGAAACCACACACAAACTG 59.248 45.455 0.00 0.00 0.00 3.16
3152 3170 2.491693 CAGGAAACCACACACAAACTGT 59.508 45.455 0.00 0.00 0.00 3.55
3153 3171 3.692101 CAGGAAACCACACACAAACTGTA 59.308 43.478 0.00 0.00 0.00 2.74
3154 3172 3.945285 AGGAAACCACACACAAACTGTAG 59.055 43.478 0.00 0.00 0.00 2.74
3155 3173 3.692593 GGAAACCACACACAAACTGTAGT 59.307 43.478 0.00 0.00 0.00 2.73
3156 3174 4.157105 GGAAACCACACACAAACTGTAGTT 59.843 41.667 0.00 0.00 40.50 2.24
3157 3175 4.695217 AACCACACACAAACTGTAGTTG 57.305 40.909 0.00 0.00 38.44 3.16
3158 3176 3.945346 ACCACACACAAACTGTAGTTGA 58.055 40.909 0.00 0.00 38.44 3.18
3159 3177 3.938963 ACCACACACAAACTGTAGTTGAG 59.061 43.478 0.00 0.00 38.44 3.02
3160 3178 3.938963 CCACACACAAACTGTAGTTGAGT 59.061 43.478 0.00 0.00 38.44 3.41
3161 3179 4.394920 CCACACACAAACTGTAGTTGAGTT 59.605 41.667 0.00 0.00 38.44 3.01
3162 3180 5.323900 CACACACAAACTGTAGTTGAGTTG 58.676 41.667 0.00 0.00 38.44 3.16
3163 3181 4.394920 ACACACAAACTGTAGTTGAGTTGG 59.605 41.667 0.00 0.00 38.44 3.77
3164 3182 4.394920 CACACAAACTGTAGTTGAGTTGGT 59.605 41.667 0.00 0.00 37.98 3.67
3165 3183 4.634443 ACACAAACTGTAGTTGAGTTGGTC 59.366 41.667 0.00 0.00 35.73 4.02
3166 3184 3.869246 ACAAACTGTAGTTGAGTTGGTCG 59.131 43.478 0.00 0.00 33.04 4.79
3167 3185 2.150397 ACTGTAGTTGAGTTGGTCGC 57.850 50.000 0.00 0.00 0.00 5.19
3168 3186 1.687123 ACTGTAGTTGAGTTGGTCGCT 59.313 47.619 0.00 0.00 0.00 4.93
3169 3187 2.061773 CTGTAGTTGAGTTGGTCGCTG 58.938 52.381 0.00 0.00 0.00 5.18
3170 3188 0.790814 GTAGTTGAGTTGGTCGCTGC 59.209 55.000 0.00 0.00 0.00 5.25
3171 3189 0.666274 TAGTTGAGTTGGTCGCTGCG 60.666 55.000 17.25 17.25 0.00 5.18
3172 3190 2.664851 TTGAGTTGGTCGCTGCGG 60.665 61.111 23.03 3.55 0.00 5.69
3177 3195 4.927782 TTGGTCGCTGCGGCTGTT 62.928 61.111 26.53 0.00 36.09 3.16
3178 3196 4.927782 TGGTCGCTGCGGCTGTTT 62.928 61.111 26.53 0.00 36.09 2.83
3179 3197 4.090057 GGTCGCTGCGGCTGTTTC 62.090 66.667 26.53 5.27 36.09 2.78
3180 3198 4.090057 GTCGCTGCGGCTGTTTCC 62.090 66.667 20.64 0.00 36.09 3.13
3181 3199 4.617520 TCGCTGCGGCTGTTTCCA 62.618 61.111 23.03 0.00 36.09 3.53
3182 3200 3.659092 CGCTGCGGCTGTTTCCAA 61.659 61.111 17.03 0.00 36.09 3.53
3183 3201 2.256461 GCTGCGGCTGTTTCCAAG 59.744 61.111 11.21 0.00 35.22 3.61
3184 3202 2.256461 CTGCGGCTGTTTCCAAGC 59.744 61.111 0.00 0.00 0.00 4.01
3185 3203 3.273080 CTGCGGCTGTTTCCAAGCC 62.273 63.158 4.32 4.32 44.69 4.35
3186 3204 4.056125 GCGGCTGTTTCCAAGCCC 62.056 66.667 8.79 0.00 45.30 5.19
3187 3205 2.282462 CGGCTGTTTCCAAGCCCT 60.282 61.111 8.79 0.00 45.30 5.19
3188 3206 1.903404 CGGCTGTTTCCAAGCCCTT 60.903 57.895 8.79 0.00 45.30 3.95
3189 3207 1.667722 GGCTGTTTCCAAGCCCTTG 59.332 57.895 2.95 1.05 42.52 3.61
3190 3208 1.005748 GCTGTTTCCAAGCCCTTGC 60.006 57.895 2.51 0.00 39.16 4.01
3191 3209 1.286880 CTGTTTCCAAGCCCTTGCG 59.713 57.895 2.51 0.00 44.33 4.85
3192 3210 1.454847 TGTTTCCAAGCCCTTGCGT 60.455 52.632 2.51 0.00 44.33 5.24
3193 3211 1.040339 TGTTTCCAAGCCCTTGCGTT 61.040 50.000 2.51 0.00 44.33 4.84
3194 3212 0.597377 GTTTCCAAGCCCTTGCGTTG 60.597 55.000 2.51 0.00 44.33 4.10
3195 3213 2.362329 TTTCCAAGCCCTTGCGTTGC 62.362 55.000 2.51 0.00 44.33 4.17
3196 3214 3.297620 CCAAGCCCTTGCGTTGCT 61.298 61.111 2.51 0.00 44.33 3.91
3197 3215 2.049802 CAAGCCCTTGCGTTGCTG 60.050 61.111 0.00 0.00 44.33 4.41
3198 3216 3.982241 AAGCCCTTGCGTTGCTGC 61.982 61.111 0.00 0.00 44.33 5.25
3199 3217 4.962836 AGCCCTTGCGTTGCTGCT 62.963 61.111 0.00 0.00 44.33 4.24
3200 3218 3.982241 GCCCTTGCGTTGCTGCTT 61.982 61.111 0.00 0.00 35.36 3.91
3201 3219 2.625823 GCCCTTGCGTTGCTGCTTA 61.626 57.895 0.00 0.00 35.36 3.09
3202 3220 1.210155 CCCTTGCGTTGCTGCTTAC 59.790 57.895 0.00 0.00 35.36 2.34
3203 3221 1.210155 CCTTGCGTTGCTGCTTACC 59.790 57.895 0.00 0.00 35.36 2.85
3204 3222 1.514678 CCTTGCGTTGCTGCTTACCA 61.515 55.000 0.00 0.00 35.36 3.25
3205 3223 0.310543 CTTGCGTTGCTGCTTACCAA 59.689 50.000 0.00 5.50 35.36 3.67
3206 3224 0.958091 TTGCGTTGCTGCTTACCAAT 59.042 45.000 0.00 0.00 35.36 3.16
3207 3225 1.814793 TGCGTTGCTGCTTACCAATA 58.185 45.000 0.00 0.00 35.36 1.90
3208 3226 1.466950 TGCGTTGCTGCTTACCAATAC 59.533 47.619 0.00 0.00 35.36 1.89
3209 3227 1.529010 GCGTTGCTGCTTACCAATACG 60.529 52.381 0.00 0.00 0.00 3.06
3210 3228 1.730064 CGTTGCTGCTTACCAATACGT 59.270 47.619 0.00 0.00 0.00 3.57
3211 3229 2.473868 CGTTGCTGCTTACCAATACGTG 60.474 50.000 0.00 0.00 0.00 4.49
3212 3230 2.465860 TGCTGCTTACCAATACGTGT 57.534 45.000 0.00 0.00 0.00 4.49
3213 3231 2.343101 TGCTGCTTACCAATACGTGTC 58.657 47.619 0.00 0.00 0.00 3.67
3214 3232 1.664151 GCTGCTTACCAATACGTGTCC 59.336 52.381 0.00 0.00 0.00 4.02
3215 3233 2.677037 GCTGCTTACCAATACGTGTCCT 60.677 50.000 0.00 0.00 0.00 3.85
3216 3234 3.187700 CTGCTTACCAATACGTGTCCTC 58.812 50.000 0.00 0.00 0.00 3.71
3217 3235 2.829720 TGCTTACCAATACGTGTCCTCT 59.170 45.455 0.00 0.00 0.00 3.69
3218 3236 3.119245 TGCTTACCAATACGTGTCCTCTC 60.119 47.826 0.00 0.00 0.00 3.20
3219 3237 3.692576 CTTACCAATACGTGTCCTCTCG 58.307 50.000 0.00 0.00 36.75 4.04
3220 3238 1.542492 ACCAATACGTGTCCTCTCGT 58.458 50.000 0.00 0.00 44.14 4.18
3221 3239 2.715046 ACCAATACGTGTCCTCTCGTA 58.285 47.619 0.00 0.00 45.40 3.43
3222 3240 2.421424 ACCAATACGTGTCCTCTCGTAC 59.579 50.000 0.00 0.00 44.60 3.67
3223 3241 2.223433 CCAATACGTGTCCTCTCGTACC 60.223 54.545 0.00 0.00 44.60 3.34
3224 3242 2.681848 CAATACGTGTCCTCTCGTACCT 59.318 50.000 0.00 0.00 44.60 3.08
3225 3243 1.730501 TACGTGTCCTCTCGTACCTG 58.269 55.000 0.00 0.00 42.40 4.00
3226 3244 0.959372 ACGTGTCCTCTCGTACCTGG 60.959 60.000 0.00 0.00 41.01 4.45
3227 3245 1.511768 GTGTCCTCTCGTACCTGGC 59.488 63.158 0.00 0.00 0.00 4.85
3228 3246 2.044555 TGTCCTCTCGTACCTGGCG 61.045 63.158 0.00 0.00 0.00 5.69
3229 3247 2.439701 TCCTCTCGTACCTGGCGG 60.440 66.667 0.00 0.00 0.00 6.13
3230 3248 4.208686 CCTCTCGTACCTGGCGGC 62.209 72.222 0.00 0.00 0.00 6.53
3231 3249 3.141488 CTCTCGTACCTGGCGGCT 61.141 66.667 11.43 0.00 0.00 5.52
3232 3250 3.417275 CTCTCGTACCTGGCGGCTG 62.417 68.421 11.43 10.13 0.00 4.85
3236 3254 3.431725 GTACCTGGCGGCTGCAAC 61.432 66.667 21.31 2.92 45.35 4.17
3237 3255 4.715523 TACCTGGCGGCTGCAACC 62.716 66.667 21.31 2.08 45.35 3.77
3240 3258 4.408821 CTGGCGGCTGCAACCCTA 62.409 66.667 21.31 0.00 45.35 3.53
3241 3259 4.408821 TGGCGGCTGCAACCCTAG 62.409 66.667 21.31 0.00 45.35 3.02
3246 3264 4.785453 GCTGCAACCCTAGCCGCT 62.785 66.667 0.00 0.00 38.86 5.52
3247 3265 2.821366 CTGCAACCCTAGCCGCTG 60.821 66.667 2.16 0.00 0.00 5.18
3250 3268 4.408821 CAACCCTAGCCGCTGCCA 62.409 66.667 2.16 0.00 38.69 4.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 4.778143 GACGCATCCGGGTGGCTT 62.778 66.667 18.38 4.10 38.64 4.35
20 21 0.110678 ATCTCCTAGATGTCCGCGGA 59.889 55.000 27.28 27.28 32.80 5.54
66 67 5.696030 TCCTATTGCTAGCAGTCTTAGAGA 58.304 41.667 16.85 12.23 0.00 3.10
84 85 9.790344 ATAATAGTAGTACACGACACTTCCTAT 57.210 33.333 2.52 0.00 0.00 2.57
125 126 5.046231 TGCACTGTAAAGGTGGTATCATACA 60.046 40.000 0.00 0.00 35.47 2.29
134 135 7.750229 ATGATAATATGCACTGTAAAGGTGG 57.250 36.000 0.00 0.00 35.47 4.61
269 271 2.158579 AGGTGTTGGTTAAACCGGTCAT 60.159 45.455 8.04 2.07 42.58 3.06
296 298 4.275936 GCTCCACACACTTTGTTACAGAAT 59.724 41.667 0.00 0.00 35.67 2.40
392 395 5.902613 TCAATGCATCTAAAAGTCCTTGG 57.097 39.130 0.00 0.00 0.00 3.61
393 396 7.092137 TCATCAATGCATCTAAAAGTCCTTG 57.908 36.000 0.00 0.00 0.00 3.61
529 532 7.255695 CCGGTTTAAAGGTCCTGTCTTATTTTT 60.256 37.037 0.00 0.00 0.00 1.94
569 576 1.398198 CGAGTTCTCGTCGTCGTCTTT 60.398 52.381 13.18 0.00 38.33 2.52
941 951 0.464452 CCGATCTGGGGTTGTAGGTC 59.536 60.000 0.00 0.00 0.00 3.85
1676 1689 4.408821 TCTTGCCATTCGCCGCCT 62.409 61.111 0.00 0.00 36.24 5.52
1737 1750 1.811266 CATGCCCTGAGAACGGTCG 60.811 63.158 0.00 0.00 0.00 4.79
1783 1796 1.153549 GCTCGTAGGCCTCACCAAG 60.154 63.158 9.68 1.98 43.14 3.61
2130 2143 0.949105 GGTACTGATAATGCGGGCGG 60.949 60.000 0.00 0.00 0.00 6.13
2166 2179 2.663796 CTGGCAGCTGCAGAGTCT 59.336 61.111 37.63 1.42 44.36 3.24
2272 2285 3.006110 ACTGTTTGAATCACCAATGCCTG 59.994 43.478 0.00 0.00 0.00 4.85
2291 2304 7.110155 ACCCTAACACATACCAATAGAAACTG 58.890 38.462 0.00 0.00 0.00 3.16
2536 2549 2.603412 CGATTTAGCAAACACGCCACAA 60.603 45.455 0.00 0.00 0.00 3.33
2552 2565 2.158900 CCTGATAGAGGCCACACGATTT 60.159 50.000 5.01 0.00 34.01 2.17
2557 2570 0.912486 AACCCTGATAGAGGCCACAC 59.088 55.000 5.01 0.00 41.19 3.82
2656 2669 9.317936 TGCAGATAAATATTTCACACAGAGTAG 57.682 33.333 3.39 0.00 0.00 2.57
2661 2674 8.671921 AGTTCTGCAGATAAATATTTCACACAG 58.328 33.333 19.04 11.00 0.00 3.66
2774 2790 1.337071 CTCGCATACACCGGACTACAT 59.663 52.381 9.46 0.00 0.00 2.29
2937 2953 1.346378 CCGCGCCAAATGCAGAAAAG 61.346 55.000 0.00 0.00 41.33 2.27
3125 3143 0.478072 TGTGTGGTTTCCTGATGCCT 59.522 50.000 0.00 0.00 0.00 4.75
3126 3144 0.598065 GTGTGTGGTTTCCTGATGCC 59.402 55.000 0.00 0.00 0.00 4.40
3127 3145 1.317613 TGTGTGTGGTTTCCTGATGC 58.682 50.000 0.00 0.00 0.00 3.91
3128 3146 3.381272 AGTTTGTGTGTGGTTTCCTGATG 59.619 43.478 0.00 0.00 0.00 3.07
3129 3147 3.381272 CAGTTTGTGTGTGGTTTCCTGAT 59.619 43.478 0.00 0.00 0.00 2.90
3130 3148 2.752354 CAGTTTGTGTGTGGTTTCCTGA 59.248 45.455 0.00 0.00 0.00 3.86
3131 3149 2.491693 ACAGTTTGTGTGTGGTTTCCTG 59.508 45.455 0.00 0.00 38.28 3.86
3132 3150 2.802719 ACAGTTTGTGTGTGGTTTCCT 58.197 42.857 0.00 0.00 38.28 3.36
3133 3151 3.692593 ACTACAGTTTGTGTGTGGTTTCC 59.307 43.478 0.00 0.00 40.69 3.13
3134 3152 4.957759 ACTACAGTTTGTGTGTGGTTTC 57.042 40.909 0.00 0.00 40.69 2.78
3135 3153 4.762765 TCAACTACAGTTTGTGTGTGGTTT 59.237 37.500 2.61 0.00 44.46 3.27
3136 3154 4.328536 TCAACTACAGTTTGTGTGTGGTT 58.671 39.130 0.00 0.00 46.84 3.67
3137 3155 3.938963 CTCAACTACAGTTTGTGTGTGGT 59.061 43.478 0.00 0.00 40.97 4.16
3138 3156 3.938963 ACTCAACTACAGTTTGTGTGTGG 59.061 43.478 0.00 0.00 40.69 4.17
3139 3157 5.323900 CAACTCAACTACAGTTTGTGTGTG 58.676 41.667 0.00 0.00 40.69 3.82
3140 3158 4.394920 CCAACTCAACTACAGTTTGTGTGT 59.605 41.667 0.00 0.00 40.69 3.72
3141 3159 4.394920 ACCAACTCAACTACAGTTTGTGTG 59.605 41.667 0.00 0.00 40.69 3.82
3142 3160 4.585879 ACCAACTCAACTACAGTTTGTGT 58.414 39.130 0.00 0.00 43.86 3.72
3143 3161 4.260212 CGACCAACTCAACTACAGTTTGTG 60.260 45.833 0.00 0.00 35.83 3.33
3144 3162 3.869246 CGACCAACTCAACTACAGTTTGT 59.131 43.478 0.00 0.00 35.83 2.83
3145 3163 3.303132 GCGACCAACTCAACTACAGTTTG 60.303 47.826 0.00 0.00 35.83 2.93
3146 3164 2.870411 GCGACCAACTCAACTACAGTTT 59.130 45.455 0.00 0.00 35.83 2.66
3147 3165 2.102588 AGCGACCAACTCAACTACAGTT 59.897 45.455 0.00 0.00 39.12 3.16
3148 3166 1.687123 AGCGACCAACTCAACTACAGT 59.313 47.619 0.00 0.00 0.00 3.55
3149 3167 2.061773 CAGCGACCAACTCAACTACAG 58.938 52.381 0.00 0.00 0.00 2.74
3150 3168 1.872237 GCAGCGACCAACTCAACTACA 60.872 52.381 0.00 0.00 0.00 2.74
3151 3169 0.790814 GCAGCGACCAACTCAACTAC 59.209 55.000 0.00 0.00 0.00 2.73
3152 3170 0.666274 CGCAGCGACCAACTCAACTA 60.666 55.000 9.98 0.00 0.00 2.24
3153 3171 1.956170 CGCAGCGACCAACTCAACT 60.956 57.895 9.98 0.00 0.00 3.16
3154 3172 2.551270 CGCAGCGACCAACTCAAC 59.449 61.111 9.98 0.00 0.00 3.18
3155 3173 2.664851 CCGCAGCGACCAACTCAA 60.665 61.111 18.75 0.00 0.00 3.02
3160 3178 4.927782 AACAGCCGCAGCGACCAA 62.928 61.111 18.75 0.00 46.67 3.67
3161 3179 4.927782 AAACAGCCGCAGCGACCA 62.928 61.111 18.75 0.00 46.67 4.02
3162 3180 4.090057 GAAACAGCCGCAGCGACC 62.090 66.667 18.75 6.86 46.67 4.79
3163 3181 4.090057 GGAAACAGCCGCAGCGAC 62.090 66.667 18.75 3.99 46.67 5.19
3164 3182 4.617520 TGGAAACAGCCGCAGCGA 62.618 61.111 18.75 0.00 46.67 4.93
3165 3183 3.599792 CTTGGAAACAGCCGCAGCG 62.600 63.158 8.18 8.18 46.67 5.18
3166 3184 2.256461 CTTGGAAACAGCCGCAGC 59.744 61.111 0.00 0.00 44.54 5.25
3167 3185 2.256461 GCTTGGAAACAGCCGCAG 59.744 61.111 0.00 0.00 44.54 5.18
3168 3186 3.294493 GGCTTGGAAACAGCCGCA 61.294 61.111 0.00 0.00 44.54 5.69
3172 3190 1.005748 GCAAGGGCTTGGAAACAGC 60.006 57.895 0.00 0.00 44.54 4.40
3173 3191 1.286880 CGCAAGGGCTTGGAAACAG 59.713 57.895 0.00 0.00 44.54 3.16
3174 3192 1.040339 AACGCAAGGGCTTGGAAACA 61.040 50.000 0.00 0.00 46.39 2.83
3175 3193 0.597377 CAACGCAAGGGCTTGGAAAC 60.597 55.000 0.00 0.00 46.39 2.78
3176 3194 1.739049 CAACGCAAGGGCTTGGAAA 59.261 52.632 0.00 0.00 46.39 3.13
3177 3195 2.855514 GCAACGCAAGGGCTTGGAA 61.856 57.895 0.00 0.00 46.39 3.53
3178 3196 3.294493 GCAACGCAAGGGCTTGGA 61.294 61.111 0.00 0.00 46.39 3.53
3183 3201 2.625823 TAAGCAGCAACGCAAGGGC 61.626 57.895 0.00 0.00 46.39 5.19
3184 3202 1.210155 GTAAGCAGCAACGCAAGGG 59.790 57.895 0.00 0.00 46.39 3.95
3185 3203 1.210155 GGTAAGCAGCAACGCAAGG 59.790 57.895 0.00 0.00 46.39 3.61
3186 3204 0.310543 TTGGTAAGCAGCAACGCAAG 59.689 50.000 0.00 0.00 37.24 4.01
3187 3205 0.958091 ATTGGTAAGCAGCAACGCAA 59.042 45.000 0.00 0.36 44.43 4.85
3188 3206 1.466950 GTATTGGTAAGCAGCAACGCA 59.533 47.619 0.00 0.00 44.43 5.24
3189 3207 1.529010 CGTATTGGTAAGCAGCAACGC 60.529 52.381 0.00 0.00 44.43 4.84
3190 3208 1.730064 ACGTATTGGTAAGCAGCAACG 59.270 47.619 0.00 0.00 44.43 4.10
3191 3209 2.482721 ACACGTATTGGTAAGCAGCAAC 59.517 45.455 0.00 0.00 44.43 4.17
3192 3210 2.739913 GACACGTATTGGTAAGCAGCAA 59.260 45.455 0.00 0.00 45.60 3.91
3193 3211 2.343101 GACACGTATTGGTAAGCAGCA 58.657 47.619 0.00 0.00 0.00 4.41
3194 3212 1.664151 GGACACGTATTGGTAAGCAGC 59.336 52.381 0.00 0.00 0.00 5.25
3195 3213 3.119101 AGAGGACACGTATTGGTAAGCAG 60.119 47.826 0.00 0.00 0.00 4.24
3196 3214 2.829720 AGAGGACACGTATTGGTAAGCA 59.170 45.455 0.00 0.00 0.00 3.91
3197 3215 3.445857 GAGAGGACACGTATTGGTAAGC 58.554 50.000 0.00 0.00 0.00 3.09
3198 3216 3.128242 ACGAGAGGACACGTATTGGTAAG 59.872 47.826 0.00 0.00 40.97 2.34
3199 3217 3.084039 ACGAGAGGACACGTATTGGTAA 58.916 45.455 0.00 0.00 40.97 2.85
3200 3218 2.715046 ACGAGAGGACACGTATTGGTA 58.285 47.619 0.00 0.00 40.97 3.25
3201 3219 1.542492 ACGAGAGGACACGTATTGGT 58.458 50.000 0.00 0.00 40.97 3.67
3202 3220 3.062323 GTACGAGAGGACACGTATTGG 57.938 52.381 0.00 0.00 46.92 3.16
3212 3230 2.439701 CCGCCAGGTACGAGAGGA 60.440 66.667 0.00 0.00 0.00 3.71
3213 3231 4.208686 GCCGCCAGGTACGAGAGG 62.209 72.222 0.00 0.00 40.50 3.69
3214 3232 3.141488 AGCCGCCAGGTACGAGAG 61.141 66.667 0.00 0.00 40.50 3.20
3215 3233 3.449227 CAGCCGCCAGGTACGAGA 61.449 66.667 0.00 0.00 40.50 4.04
3219 3237 3.431725 GTTGCAGCCGCCAGGTAC 61.432 66.667 0.00 0.00 40.50 3.34
3220 3238 4.715523 GGTTGCAGCCGCCAGGTA 62.716 66.667 2.95 0.00 40.50 3.08
3223 3241 4.408821 TAGGGTTGCAGCCGCCAG 62.409 66.667 13.95 0.00 41.56 4.85
3224 3242 4.408821 CTAGGGTTGCAGCCGCCA 62.409 66.667 13.95 0.00 41.56 5.69
3230 3248 2.821366 CAGCGGCTAGGGTTGCAG 60.821 66.667 0.26 0.00 0.00 4.41
3233 3251 4.408821 TGGCAGCGGCTAGGGTTG 62.409 66.667 9.17 0.00 40.87 3.77


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

AutoCloner maintained by Alex Coulton.