Multiple sequence alignment - TraesCS5B01G241100

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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 TraesCS5B01G241100 chr5B 100.000 4930 0 0 1 4930 421181778 421186707 0.000000e+00 9105
1 TraesCS5B01G241100 chr5B 92.063 126 9 1 3103 3227 516474959 516475084 5.070000e-40 176
2 TraesCS5B01G241100 chr5D 97.851 3118 47 8 1 3107 356200912 356204020 0.000000e+00 5369
3 TraesCS5B01G241100 chr5D 92.655 1729 94 17 3218 4930 356204021 356205732 0.000000e+00 2459
4 TraesCS5B01G241100 chr5D 86.792 265 26 6 3628 3891 235908693 235908437 2.250000e-73 287
5 TraesCS5B01G241100 chr5D 92.248 129 9 1 3094 3222 361510227 361510354 1.090000e-41 182
6 TraesCS5B01G241100 chr5A 97.566 3122 46 12 1 3107 457899907 457903013 0.000000e+00 5317
7 TraesCS5B01G241100 chr5A 90.982 1752 100 24 3218 4930 457903014 457904746 0.000000e+00 2307
8 TraesCS5B01G241100 chr5A 89.529 191 12 4 4740 4930 457906207 457906389 8.250000e-58 235
9 TraesCS5B01G241100 chr6D 80.298 873 93 39 3718 4572 38239378 38238567 1.980000e-163 586
10 TraesCS5B01G241100 chr6D 85.854 205 16 9 3708 3905 38235453 38235255 6.470000e-49 206
11 TraesCS5B01G241100 chr6D 93.388 121 8 0 3104 3224 136474598 136474718 3.920000e-41 180
12 TraesCS5B01G241100 chr6B 83.359 643 60 25 3945 4572 89142622 89142012 7.210000e-153 551
13 TraesCS5B01G241100 chr6B 84.878 205 18 9 3708 3905 89141285 89141087 1.400000e-45 195
14 TraesCS5B01G241100 chr6B 90.625 128 12 0 3097 3224 299964374 299964247 2.360000e-38 171
15 TraesCS5B01G241100 chr3A 85.766 274 28 8 3621 3891 110680931 110680666 3.760000e-71 279
16 TraesCS5B01G241100 chr3A 83.212 274 35 8 3621 3891 377488287 377488022 1.770000e-59 241
17 TraesCS5B01G241100 chr4B 85.660 265 29 5 3628 3891 175638543 175638287 2.260000e-68 270
18 TraesCS5B01G241100 chr4B 86.111 180 19 4 3621 3800 422773128 422772955 6.510000e-44 189
19 TraesCS5B01G241100 chr1B 86.667 180 18 4 3621 3800 368095820 368095993 1.400000e-45 195
20 TraesCS5B01G241100 chr1B 86.111 180 19 4 3621 3800 499391995 499391822 6.510000e-44 189
21 TraesCS5B01G241100 chr3B 92.683 123 9 0 3099 3221 694025011 694025133 1.410000e-40 178
22 TraesCS5B01G241100 chr3B 91.406 128 11 0 3094 3221 154470983 154471110 5.070000e-40 176
23 TraesCS5B01G241100 chr2B 91.473 129 11 0 3103 3231 39373057 39372929 1.410000e-40 178
24 TraesCS5B01G241100 chr2B 91.339 127 11 0 3104 3230 401283053 401282927 1.820000e-39 174
25 TraesCS5B01G241100 chr2B 90.840 131 10 2 3093 3222 529598826 529598697 1.820000e-39 174
26 TraesCS5B01G241100 chr2A 91.011 89 7 1 3804 3891 192622033 192622121 8.670000e-23 119
27 TraesCS5B01G241100 chr4A 85.714 70 10 0 2587 2656 660080547 660080616 1.900000e-09 75


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 TraesCS5B01G241100 chr5B 421181778 421186707 4929 False 9105.000000 9105 100.000000 1 4930 1 chr5B.!!$F1 4929
1 TraesCS5B01G241100 chr5D 356200912 356205732 4820 False 3914.000000 5369 95.253000 1 4930 2 chr5D.!!$F2 4929
2 TraesCS5B01G241100 chr5A 457899907 457906389 6482 False 2619.666667 5317 92.692333 1 4930 3 chr5A.!!$F1 4929
3 TraesCS5B01G241100 chr6D 38235255 38239378 4123 True 396.000000 586 83.076000 3708 4572 2 chr6D.!!$R1 864
4 TraesCS5B01G241100 chr6B 89141087 89142622 1535 True 373.000000 551 84.118500 3708 4572 2 chr6B.!!$R2 864

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
300 308 4.022603 TCATTTGGGTACAACATGGATGG 58.977 43.478 0.0 0.0 36.06 3.51 F
1059 1067 4.012374 CAACTTATGGCAACCTCATCACT 58.988 43.478 0.0 0.0 0.00 3.41 F
2897 2916 2.231964 TGGCACAGGCTCATCAAAATTC 59.768 45.455 0.0 0.0 40.87 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1682 1690 4.031652 AGCGTCAATTGAAAATTAATGCGC 59.968 37.5 20.16 20.16 35.86 6.09 R
3023 3042 2.781945 AGGCTTTGAAAACAGAAGCG 57.218 45.0 0.00 0.00 45.04 4.68 R
4561 4629 0.248990 CACACTGCGCATTGTTGGTT 60.249 50.0 28.32 6.32 0.00 3.67 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
293 301 7.446106 ACTAGGATATCATTTGGGTACAACA 57.554 36.000 4.83 0.00 36.06 3.33
300 308 4.022603 TCATTTGGGTACAACATGGATGG 58.977 43.478 0.00 0.00 36.06 3.51
327 335 4.065088 ACGTAATCAGTGATGCAACAACT 58.935 39.130 6.34 0.00 0.00 3.16
610 618 7.761038 AATTTAGGTCAACTTTCTAACAGGG 57.239 36.000 0.00 0.00 0.00 4.45
785 793 7.816640 TGCAACTTTAATTCTACACATCTTCC 58.183 34.615 0.00 0.00 0.00 3.46
1059 1067 4.012374 CAACTTATGGCAACCTCATCACT 58.988 43.478 0.00 0.00 0.00 3.41
1283 1291 9.524106 CATCAGATGAAATAAGCTTGCAATTTA 57.476 29.630 9.86 2.72 0.00 1.40
1320 1328 7.931578 TTGTTTAAAGTTCAAACTCTCAGGA 57.068 32.000 3.34 0.00 38.57 3.86
1328 1336 8.753497 AAGTTCAAACTCTCAGGATTTAACTT 57.247 30.769 0.00 0.00 38.57 2.66
1570 1578 7.870509 TCAGTTCAATATTCTGCTAATGCTT 57.129 32.000 0.00 0.00 40.48 3.91
1973 1981 9.528018 GTTTTTGACTTCTTGTTGATTGGATTA 57.472 29.630 0.00 0.00 0.00 1.75
2897 2916 2.231964 TGGCACAGGCTCATCAAAATTC 59.768 45.455 0.00 0.00 40.87 2.17
2952 2971 2.652348 TGGGGAGTGTTGGATTGGTTAT 59.348 45.455 0.00 0.00 0.00 1.89
2953 2972 3.023832 GGGGAGTGTTGGATTGGTTATG 58.976 50.000 0.00 0.00 0.00 1.90
3023 3042 6.093219 GTGCAGATATGGTGGATATTCACATC 59.907 42.308 16.12 10.08 39.27 3.06
3050 3069 6.959639 TCTGTTTTCAAAGCCTTACATTCT 57.040 33.333 0.00 0.00 0.00 2.40
3093 3112 5.627499 TCAAGTAAGTAAAATGCAGGCAG 57.373 39.130 0.00 0.00 0.00 4.85
3101 3120 6.041423 AGTAAAATGCAGGCAGCTTATTTT 57.959 33.333 14.30 14.30 45.94 1.82
3102 3121 5.870978 AGTAAAATGCAGGCAGCTTATTTTG 59.129 36.000 17.43 0.00 45.94 2.44
3103 3122 3.967332 AATGCAGGCAGCTTATTTTGT 57.033 38.095 2.86 0.00 45.94 2.83
3104 3123 5.404466 AAATGCAGGCAGCTTATTTTGTA 57.596 34.783 2.86 0.00 45.94 2.41
3105 3124 3.848272 TGCAGGCAGCTTATTTTGTAC 57.152 42.857 2.86 0.00 45.94 2.90
3106 3125 3.420893 TGCAGGCAGCTTATTTTGTACT 58.579 40.909 2.86 0.00 45.94 2.73
3107 3126 3.440173 TGCAGGCAGCTTATTTTGTACTC 59.560 43.478 2.86 0.00 45.94 2.59
3108 3127 3.181496 GCAGGCAGCTTATTTTGTACTCC 60.181 47.826 0.00 0.00 41.15 3.85
3109 3128 3.378427 CAGGCAGCTTATTTTGTACTCCC 59.622 47.826 0.00 0.00 0.00 4.30
3110 3129 3.267031 AGGCAGCTTATTTTGTACTCCCT 59.733 43.478 0.00 0.00 0.00 4.20
3111 3130 3.628032 GGCAGCTTATTTTGTACTCCCTC 59.372 47.826 0.00 0.00 0.00 4.30
3112 3131 3.628032 GCAGCTTATTTTGTACTCCCTCC 59.372 47.826 0.00 0.00 0.00 4.30
3113 3132 3.871594 CAGCTTATTTTGTACTCCCTCCG 59.128 47.826 0.00 0.00 0.00 4.63
3114 3133 3.518303 AGCTTATTTTGTACTCCCTCCGT 59.482 43.478 0.00 0.00 0.00 4.69
3115 3134 3.869832 GCTTATTTTGTACTCCCTCCGTC 59.130 47.826 0.00 0.00 0.00 4.79
3116 3135 4.439968 CTTATTTTGTACTCCCTCCGTCC 58.560 47.826 0.00 0.00 0.00 4.79
3117 3136 0.604578 TTTTGTACTCCCTCCGTCCG 59.395 55.000 0.00 0.00 0.00 4.79
3118 3137 1.252904 TTTGTACTCCCTCCGTCCGG 61.253 60.000 0.00 0.00 0.00 5.14
3119 3138 2.141011 TTGTACTCCCTCCGTCCGGA 62.141 60.000 0.00 0.00 42.90 5.14
3120 3139 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
3121 3140 0.967380 GTACTCCCTCCGTCCGGAAA 60.967 60.000 5.23 0.00 44.66 3.13
3122 3141 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
3123 3142 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
3124 3143 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
3125 3144 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
3126 3145 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
3127 3146 1.202498 CCCTCCGTCCGGAAATACTTC 60.202 57.143 5.23 0.00 44.66 3.01
3128 3147 1.755380 CCTCCGTCCGGAAATACTTCT 59.245 52.381 5.23 0.00 44.66 2.85
3129 3148 2.167900 CCTCCGTCCGGAAATACTTCTT 59.832 50.000 5.23 0.00 44.66 2.52
3130 3149 3.187700 CTCCGTCCGGAAATACTTCTTG 58.812 50.000 5.23 0.00 44.66 3.02
3131 3150 2.093869 TCCGTCCGGAAATACTTCTTGG 60.094 50.000 5.23 0.00 42.05 3.61
3132 3151 2.093869 CCGTCCGGAAATACTTCTTGGA 60.094 50.000 5.23 0.00 35.23 3.53
3133 3152 3.187700 CGTCCGGAAATACTTCTTGGAG 58.812 50.000 5.23 0.00 37.00 3.86
3134 3153 3.119245 CGTCCGGAAATACTTCTTGGAGA 60.119 47.826 5.23 0.00 37.00 3.71
3135 3154 4.619863 CGTCCGGAAATACTTCTTGGAGAA 60.620 45.833 5.23 0.00 37.00 2.87
3136 3155 5.243207 GTCCGGAAATACTTCTTGGAGAAA 58.757 41.667 5.23 0.00 37.00 2.52
3137 3156 5.880887 GTCCGGAAATACTTCTTGGAGAAAT 59.119 40.000 5.23 0.00 37.00 2.17
3138 3157 5.880332 TCCGGAAATACTTCTTGGAGAAATG 59.120 40.000 0.00 0.00 33.19 2.32
3139 3158 5.066505 CCGGAAATACTTCTTGGAGAAATGG 59.933 44.000 0.00 0.00 33.19 3.16
3140 3159 5.880332 CGGAAATACTTCTTGGAGAAATGGA 59.120 40.000 0.00 0.00 33.19 3.41
3141 3160 6.543831 CGGAAATACTTCTTGGAGAAATGGAT 59.456 38.462 0.00 0.00 33.19 3.41
3142 3161 7.467811 CGGAAATACTTCTTGGAGAAATGGATG 60.468 40.741 0.00 0.00 33.19 3.51
3143 3162 7.340487 GGAAATACTTCTTGGAGAAATGGATGT 59.660 37.037 0.00 0.00 33.19 3.06
3144 3163 9.396022 GAAATACTTCTTGGAGAAATGGATGTA 57.604 33.333 0.00 0.00 33.19 2.29
3145 3164 9.927081 AAATACTTCTTGGAGAAATGGATGTAT 57.073 29.630 0.00 0.00 33.19 2.29
3146 3165 9.566432 AATACTTCTTGGAGAAATGGATGTATC 57.434 33.333 0.00 0.00 33.19 2.24
3147 3166 7.205515 ACTTCTTGGAGAAATGGATGTATCT 57.794 36.000 0.00 0.00 33.19 1.98
3148 3167 8.324191 ACTTCTTGGAGAAATGGATGTATCTA 57.676 34.615 0.00 0.00 33.19 1.98
3149 3168 8.428063 ACTTCTTGGAGAAATGGATGTATCTAG 58.572 37.037 0.00 0.00 33.19 2.43
3150 3169 8.553085 TTCTTGGAGAAATGGATGTATCTAGA 57.447 34.615 0.00 0.00 29.99 2.43
3151 3170 7.957002 TCTTGGAGAAATGGATGTATCTAGAC 58.043 38.462 0.00 0.00 0.00 2.59
3152 3171 7.565029 TCTTGGAGAAATGGATGTATCTAGACA 59.435 37.037 0.00 0.00 0.00 3.41
3153 3172 7.862274 TGGAGAAATGGATGTATCTAGACAT 57.138 36.000 0.00 0.00 42.82 3.06
3154 3173 8.956446 TGGAGAAATGGATGTATCTAGACATA 57.044 34.615 0.00 0.00 40.18 2.29
3155 3174 9.552695 TGGAGAAATGGATGTATCTAGACATAT 57.447 33.333 0.00 0.00 40.18 1.78
3194 3213 8.760980 ACATTCATTTTTATCTATTTCCCCGA 57.239 30.769 0.00 0.00 0.00 5.14
3195 3214 8.630037 ACATTCATTTTTATCTATTTCCCCGAC 58.370 33.333 0.00 0.00 0.00 4.79
3196 3215 8.629158 CATTCATTTTTATCTATTTCCCCGACA 58.371 33.333 0.00 0.00 0.00 4.35
3197 3216 8.582657 TTCATTTTTATCTATTTCCCCGACAA 57.417 30.769 0.00 0.00 0.00 3.18
3198 3217 8.220755 TCATTTTTATCTATTTCCCCGACAAG 57.779 34.615 0.00 0.00 0.00 3.16
3199 3218 7.832187 TCATTTTTATCTATTTCCCCGACAAGT 59.168 33.333 0.00 0.00 0.00 3.16
3200 3219 9.116067 CATTTTTATCTATTTCCCCGACAAGTA 57.884 33.333 0.00 0.00 0.00 2.24
3201 3220 9.862149 ATTTTTATCTATTTCCCCGACAAGTAT 57.138 29.630 0.00 0.00 0.00 2.12
3202 3221 9.689501 TTTTTATCTATTTCCCCGACAAGTATT 57.310 29.630 0.00 0.00 0.00 1.89
3203 3222 9.689501 TTTTATCTATTTCCCCGACAAGTATTT 57.310 29.630 0.00 0.00 0.00 1.40
3204 3223 8.897872 TTATCTATTTCCCCGACAAGTATTTC 57.102 34.615 0.00 0.00 0.00 2.17
3205 3224 6.555463 TCTATTTCCCCGACAAGTATTTCT 57.445 37.500 0.00 0.00 0.00 2.52
3206 3225 6.346096 TCTATTTCCCCGACAAGTATTTCTG 58.654 40.000 0.00 0.00 0.00 3.02
3207 3226 3.343941 TTCCCCGACAAGTATTTCTGG 57.656 47.619 0.00 0.00 0.00 3.86
3208 3227 2.542550 TCCCCGACAAGTATTTCTGGA 58.457 47.619 0.00 0.00 0.00 3.86
3209 3228 2.235402 TCCCCGACAAGTATTTCTGGAC 59.765 50.000 0.00 0.00 0.00 4.02
3210 3229 2.268298 CCCGACAAGTATTTCTGGACG 58.732 52.381 0.00 0.00 35.64 4.79
3211 3230 2.268298 CCGACAAGTATTTCTGGACGG 58.732 52.381 0.00 0.00 45.37 4.79
3212 3231 3.226346 CGACAAGTATTTCTGGACGGA 57.774 47.619 0.00 0.00 33.12 4.69
3213 3232 3.179830 CGACAAGTATTTCTGGACGGAG 58.820 50.000 0.00 0.00 33.12 4.63
3214 3233 3.522553 GACAAGTATTTCTGGACGGAGG 58.477 50.000 0.00 0.00 0.00 4.30
3215 3234 2.236395 ACAAGTATTTCTGGACGGAGGG 59.764 50.000 0.00 0.00 0.00 4.30
3216 3235 2.500098 CAAGTATTTCTGGACGGAGGGA 59.500 50.000 0.00 0.00 0.00 4.20
3229 3248 3.504375 ACGGAGGGAGTACAAAGTAACT 58.496 45.455 0.00 0.00 0.00 2.24
3233 3252 6.212187 ACGGAGGGAGTACAAAGTAACTAATT 59.788 38.462 0.00 0.00 0.00 1.40
3245 3264 9.515226 ACAAAGTAACTAATTAATCAGCTTCCA 57.485 29.630 0.00 0.00 0.00 3.53
3285 3304 7.220030 ACCATTTCTACATGACAGGATGATAC 58.780 38.462 0.00 0.00 39.69 2.24
3290 3309 6.805150 TCTACATGACAGGATGATACCCTAT 58.195 40.000 0.00 0.00 39.69 2.57
3359 3378 5.440610 AGAAACTTGTCAATGTTGGAGAGT 58.559 37.500 2.48 0.00 0.00 3.24
3451 3470 1.836802 GAGGAGACCAATGAGGAAGCT 59.163 52.381 0.00 0.00 41.22 3.74
3473 3492 1.956477 TCAAGAGGTGAGCTTTTTGGC 59.044 47.619 9.05 0.00 0.00 4.52
3474 3493 1.959282 CAAGAGGTGAGCTTTTTGGCT 59.041 47.619 0.00 0.00 46.11 4.75
3475 3494 2.363359 CAAGAGGTGAGCTTTTTGGCTT 59.637 45.455 0.00 0.00 43.20 4.35
3478 3497 0.601046 GGTGAGCTTTTTGGCTTGCC 60.601 55.000 4.43 4.43 43.20 4.52
3578 3597 1.465354 GCTGCTGTCTGATGAAAAGCG 60.465 52.381 0.00 0.00 37.12 4.68
3594 3613 4.771684 CGAATTCGCCAAGCAAGG 57.228 55.556 15.93 0.00 0.00 3.61
3612 3631 1.202879 AGGTCGCCAAAATGAAGTCCA 60.203 47.619 0.00 0.00 0.00 4.02
3617 3638 2.160417 CGCCAAAATGAAGTCCAGTCTC 59.840 50.000 0.00 0.00 0.00 3.36
3620 3641 5.003804 GCCAAAATGAAGTCCAGTCTCTTA 58.996 41.667 0.00 0.00 0.00 2.10
3625 3646 6.865834 AATGAAGTCCAGTCTCTTATGTCT 57.134 37.500 0.00 0.00 0.00 3.41
3637 3658 4.038522 TCTCTTATGTCTATGCTCTGCCAC 59.961 45.833 0.00 0.00 0.00 5.01
3640 3661 0.107993 TGTCTATGCTCTGCCACAGC 60.108 55.000 0.00 0.00 40.48 4.40
3641 3662 1.142531 TCTATGCTCTGCCACAGCG 59.857 57.895 0.00 0.00 44.31 5.18
3642 3663 1.142531 CTATGCTCTGCCACAGCGA 59.857 57.895 0.00 0.00 44.31 4.93
3643 3664 0.460811 CTATGCTCTGCCACAGCGAA 60.461 55.000 0.00 0.00 44.31 4.70
3644 3665 0.036483 TATGCTCTGCCACAGCGAAA 60.036 50.000 0.00 0.00 44.31 3.46
3649 3671 2.322161 CTCTGCCACAGCGAAATTTTG 58.678 47.619 0.59 0.59 44.31 2.44
3652 3674 1.406898 TGCCACAGCGAAATTTTGTCA 59.593 42.857 7.27 0.00 44.31 3.58
3678 3700 3.245803 TGGCATACCCCAGTTACCAATTT 60.246 43.478 0.00 0.00 33.59 1.82
3685 3707 4.283212 ACCCCAGTTACCAATTTGTTGATG 59.717 41.667 0.00 0.00 0.00 3.07
3703 3725 7.095910 TGTTGATGTGTTTGTTGAAGTTTCAT 58.904 30.769 0.00 0.00 37.00 2.57
3709 3731 8.233692 TGTGTTTGTTGAAGTTTCATTGTAAC 57.766 30.769 0.00 0.00 37.00 2.50
3772 3794 3.945285 AGTTTGATAATGTTAGGTGCCGG 59.055 43.478 0.00 0.00 0.00 6.13
3776 3798 0.985760 TAATGTTAGGTGCCGGTGGT 59.014 50.000 1.90 0.00 0.00 4.16
3792 3816 6.038825 TGCCGGTGGTTTTAGATATGTAAATG 59.961 38.462 1.90 0.00 0.00 2.32
3891 3919 4.444022 CCGATGAGTTCTGAAGGATTCCAT 60.444 45.833 5.29 0.00 46.93 3.41
3894 3922 3.265221 TGAGTTCTGAAGGATTCCATGCT 59.735 43.478 5.29 0.00 46.93 3.79
3907 3935 2.862738 CATGCTGACCATGCAGTGA 58.137 52.632 0.00 0.00 44.34 3.41
3935 3963 2.288825 CGGAATAAAGAGATAGCCGCCA 60.289 50.000 0.00 0.00 0.00 5.69
4180 4229 3.386768 AGCGCTTCACTAACTCAAAGA 57.613 42.857 2.64 0.00 0.00 2.52
4436 4493 6.211587 TGGCTGGAACTGAATATTTTGATG 57.788 37.500 0.00 0.00 0.00 3.07
4467 4533 0.251165 GTGGGTAGCCTTCCAAAGCA 60.251 55.000 13.11 0.00 34.47 3.91
4561 4629 4.401022 AGCACCAAAAGATCTGATCAACA 58.599 39.130 19.12 0.00 0.00 3.33
4699 4768 4.016444 TCCAAGTGGATGGTAGCAAAATC 58.984 43.478 0.00 0.00 39.78 2.17
4704 4773 5.815581 AGTGGATGGTAGCAAAATCTGTTA 58.184 37.500 0.00 0.00 0.00 2.41
4798 4869 7.116519 GCTACATTAGATCGACCATAGGTTTTC 59.883 40.741 0.00 0.00 35.25 2.29
4843 4914 3.701664 AGCATTTCTTCAAACCCCTAGG 58.298 45.455 0.06 0.06 40.04 3.02
4848 4919 3.895704 TCTTCAAACCCCTAGGCTTTT 57.104 42.857 2.05 1.38 36.11 2.27
4849 4920 4.193240 TCTTCAAACCCCTAGGCTTTTT 57.807 40.909 2.05 0.00 36.11 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
293 301 5.306937 TCACTGATTACGTATTCCCATCCAT 59.693 40.000 13.39 0.00 0.00 3.41
300 308 5.293324 TGTTGCATCACTGATTACGTATTCC 59.707 40.000 13.39 0.00 0.00 3.01
587 595 5.710567 GCCCTGTTAGAAAGTTGACCTAAAT 59.289 40.000 0.00 0.00 0.00 1.40
1570 1578 9.793259 AGATAAAAGAACCAGAAATACAGAACA 57.207 29.630 0.00 0.00 0.00 3.18
1682 1690 4.031652 AGCGTCAATTGAAAATTAATGCGC 59.968 37.500 20.16 20.16 35.86 6.09
1973 1981 7.665559 ACAATATGTGTTACTGGACAAGTTCAT 59.334 33.333 0.00 0.00 37.01 2.57
2897 2916 2.863739 TGTGCATCGTACTTCTCTTCG 58.136 47.619 0.00 0.00 0.00 3.79
2952 2971 2.815158 TGGTGTAGATCCACTGCTACA 58.185 47.619 0.00 0.00 43.26 2.74
2953 2972 4.408182 AATGGTGTAGATCCACTGCTAC 57.592 45.455 2.68 0.00 37.81 3.58
3023 3042 2.781945 AGGCTTTGAAAACAGAAGCG 57.218 45.000 0.00 0.00 45.04 4.68
3083 3102 3.967332 ACAAAATAAGCTGCCTGCATT 57.033 38.095 0.00 0.00 45.94 3.56
3093 3112 3.869832 GACGGAGGGAGTACAAAATAAGC 59.130 47.826 0.00 0.00 0.00 3.09
3101 3120 2.044650 CCGGACGGAGGGAGTACA 60.045 66.667 4.40 0.00 37.50 2.90
3102 3121 0.967380 TTTCCGGACGGAGGGAGTAC 60.967 60.000 13.64 0.00 46.06 2.73
3103 3122 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
3104 3123 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
3105 3124 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
3106 3125 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
3107 3126 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
3108 3127 1.755380 AGAAGTATTTCCGGACGGAGG 59.245 52.381 13.64 0.00 46.06 4.30
3109 3128 3.187700 CAAGAAGTATTTCCGGACGGAG 58.812 50.000 13.64 0.00 46.06 4.63
3110 3129 2.093869 CCAAGAAGTATTTCCGGACGGA 60.094 50.000 1.83 9.76 43.52 4.69
3111 3130 2.093869 TCCAAGAAGTATTTCCGGACGG 60.094 50.000 1.83 3.96 32.99 4.79
3112 3131 3.119245 TCTCCAAGAAGTATTTCCGGACG 60.119 47.826 1.83 0.00 33.86 4.79
3113 3132 4.467198 TCTCCAAGAAGTATTTCCGGAC 57.533 45.455 1.83 0.00 33.86 4.79
3114 3133 5.492855 TTTCTCCAAGAAGTATTTCCGGA 57.507 39.130 0.00 0.00 35.37 5.14
3115 3134 5.066505 CCATTTCTCCAAGAAGTATTTCCGG 59.933 44.000 0.00 0.00 35.37 5.14
3116 3135 5.880332 TCCATTTCTCCAAGAAGTATTTCCG 59.120 40.000 0.00 0.00 35.37 4.30
3117 3136 7.340487 ACATCCATTTCTCCAAGAAGTATTTCC 59.660 37.037 0.00 0.00 35.37 3.13
3118 3137 8.286191 ACATCCATTTCTCCAAGAAGTATTTC 57.714 34.615 0.00 0.00 35.37 2.17
3119 3138 9.927081 ATACATCCATTTCTCCAAGAAGTATTT 57.073 29.630 0.00 0.00 35.37 1.40
3120 3139 9.566432 GATACATCCATTTCTCCAAGAAGTATT 57.434 33.333 0.00 0.00 35.37 1.89
3121 3140 8.943085 AGATACATCCATTTCTCCAAGAAGTAT 58.057 33.333 0.00 0.00 35.37 2.12
3122 3141 8.324191 AGATACATCCATTTCTCCAAGAAGTA 57.676 34.615 0.00 0.00 35.37 2.24
3123 3142 7.205515 AGATACATCCATTTCTCCAAGAAGT 57.794 36.000 0.00 0.00 35.37 3.01
3124 3143 8.646004 TCTAGATACATCCATTTCTCCAAGAAG 58.354 37.037 0.00 0.00 35.37 2.85
3125 3144 8.424918 GTCTAGATACATCCATTTCTCCAAGAA 58.575 37.037 0.00 0.00 31.28 2.52
3126 3145 7.565029 TGTCTAGATACATCCATTTCTCCAAGA 59.435 37.037 0.00 0.00 0.00 3.02
3127 3146 7.730084 TGTCTAGATACATCCATTTCTCCAAG 58.270 38.462 0.00 0.00 0.00 3.61
3128 3147 7.675161 TGTCTAGATACATCCATTTCTCCAA 57.325 36.000 0.00 0.00 0.00 3.53
3129 3148 7.862274 ATGTCTAGATACATCCATTTCTCCA 57.138 36.000 0.00 0.00 35.08 3.86
3168 3187 9.854668 TCGGGGAAATAGATAAAAATGAATGTA 57.145 29.630 0.00 0.00 0.00 2.29
3169 3188 8.630037 GTCGGGGAAATAGATAAAAATGAATGT 58.370 33.333 0.00 0.00 0.00 2.71
3170 3189 8.629158 TGTCGGGGAAATAGATAAAAATGAATG 58.371 33.333 0.00 0.00 0.00 2.67
3171 3190 8.760980 TGTCGGGGAAATAGATAAAAATGAAT 57.239 30.769 0.00 0.00 0.00 2.57
3172 3191 8.582657 TTGTCGGGGAAATAGATAAAAATGAA 57.417 30.769 0.00 0.00 0.00 2.57
3173 3192 7.832187 ACTTGTCGGGGAAATAGATAAAAATGA 59.168 33.333 0.00 0.00 0.00 2.57
3174 3193 7.996385 ACTTGTCGGGGAAATAGATAAAAATG 58.004 34.615 0.00 0.00 0.00 2.32
3175 3194 9.862149 ATACTTGTCGGGGAAATAGATAAAAAT 57.138 29.630 0.00 0.00 0.00 1.82
3176 3195 9.689501 AATACTTGTCGGGGAAATAGATAAAAA 57.310 29.630 0.00 0.00 0.00 1.94
3177 3196 9.689501 AAATACTTGTCGGGGAAATAGATAAAA 57.310 29.630 0.00 0.00 0.00 1.52
3178 3197 9.333724 GAAATACTTGTCGGGGAAATAGATAAA 57.666 33.333 0.00 0.00 0.00 1.40
3179 3198 8.711170 AGAAATACTTGTCGGGGAAATAGATAA 58.289 33.333 0.00 0.00 0.00 1.75
3180 3199 8.148351 CAGAAATACTTGTCGGGGAAATAGATA 58.852 37.037 0.00 0.00 0.00 1.98
3181 3200 6.992715 CAGAAATACTTGTCGGGGAAATAGAT 59.007 38.462 0.00 0.00 0.00 1.98
3182 3201 6.346096 CAGAAATACTTGTCGGGGAAATAGA 58.654 40.000 0.00 0.00 0.00 1.98
3183 3202 5.527582 CCAGAAATACTTGTCGGGGAAATAG 59.472 44.000 0.00 0.00 0.00 1.73
3184 3203 5.190132 TCCAGAAATACTTGTCGGGGAAATA 59.810 40.000 0.00 0.00 30.83 1.40
3185 3204 4.018779 TCCAGAAATACTTGTCGGGGAAAT 60.019 41.667 0.00 0.00 30.83 2.17
3186 3205 3.328343 TCCAGAAATACTTGTCGGGGAAA 59.672 43.478 0.00 0.00 30.83 3.13
3187 3206 2.907696 TCCAGAAATACTTGTCGGGGAA 59.092 45.455 0.00 0.00 30.83 3.97
3188 3207 2.235402 GTCCAGAAATACTTGTCGGGGA 59.765 50.000 0.00 0.00 30.83 4.81
3189 3208 2.629051 GTCCAGAAATACTTGTCGGGG 58.371 52.381 0.00 0.00 30.83 5.73
3190 3209 2.268298 CGTCCAGAAATACTTGTCGGG 58.732 52.381 0.00 0.00 0.00 5.14
3191 3210 2.094390 TCCGTCCAGAAATACTTGTCGG 60.094 50.000 0.00 0.00 41.47 4.79
3192 3211 3.179830 CTCCGTCCAGAAATACTTGTCG 58.820 50.000 0.00 0.00 0.00 4.35
3193 3212 3.522553 CCTCCGTCCAGAAATACTTGTC 58.477 50.000 0.00 0.00 0.00 3.18
3194 3213 2.236395 CCCTCCGTCCAGAAATACTTGT 59.764 50.000 0.00 0.00 0.00 3.16
3195 3214 2.500098 TCCCTCCGTCCAGAAATACTTG 59.500 50.000 0.00 0.00 0.00 3.16
3196 3215 2.766828 CTCCCTCCGTCCAGAAATACTT 59.233 50.000 0.00 0.00 0.00 2.24
3197 3216 2.292323 ACTCCCTCCGTCCAGAAATACT 60.292 50.000 0.00 0.00 0.00 2.12
3198 3217 2.108970 ACTCCCTCCGTCCAGAAATAC 58.891 52.381 0.00 0.00 0.00 1.89
3199 3218 2.544844 ACTCCCTCCGTCCAGAAATA 57.455 50.000 0.00 0.00 0.00 1.40
3200 3219 2.108970 GTACTCCCTCCGTCCAGAAAT 58.891 52.381 0.00 0.00 0.00 2.17
3201 3220 1.203087 TGTACTCCCTCCGTCCAGAAA 60.203 52.381 0.00 0.00 0.00 2.52
3202 3221 0.406750 TGTACTCCCTCCGTCCAGAA 59.593 55.000 0.00 0.00 0.00 3.02
3203 3222 0.406750 TTGTACTCCCTCCGTCCAGA 59.593 55.000 0.00 0.00 0.00 3.86
3204 3223 1.204941 CTTTGTACTCCCTCCGTCCAG 59.795 57.143 0.00 0.00 0.00 3.86
3205 3224 1.263356 CTTTGTACTCCCTCCGTCCA 58.737 55.000 0.00 0.00 0.00 4.02
3206 3225 1.264295 ACTTTGTACTCCCTCCGTCC 58.736 55.000 0.00 0.00 0.00 4.79
3207 3226 3.509184 AGTTACTTTGTACTCCCTCCGTC 59.491 47.826 0.00 0.00 0.00 4.79
3208 3227 3.504375 AGTTACTTTGTACTCCCTCCGT 58.496 45.455 0.00 0.00 0.00 4.69
3209 3228 5.649782 TTAGTTACTTTGTACTCCCTCCG 57.350 43.478 0.00 0.00 0.00 4.63
3233 3252 7.423844 TCTCTGAGTAAATGGAAGCTGATTA 57.576 36.000 4.32 0.00 0.00 1.75
3359 3378 3.815401 GAGACAGGTTTCTTTAGCAGCAA 59.185 43.478 0.00 0.00 0.00 3.91
3470 3489 1.302949 GATAGGTGGTGGCAAGCCA 59.697 57.895 10.24 10.24 45.02 4.75
3471 3490 0.749454 CTGATAGGTGGTGGCAAGCC 60.749 60.000 3.61 3.61 0.00 4.35
3472 3491 0.749454 CCTGATAGGTGGTGGCAAGC 60.749 60.000 0.00 0.00 0.00 4.01
3473 3492 3.483954 CCTGATAGGTGGTGGCAAG 57.516 57.895 0.00 0.00 0.00 4.01
3532 3551 5.260424 TGCAAATCTGGAAATAAGGTGCTA 58.740 37.500 0.00 0.00 0.00 3.49
3562 3581 4.329489 CGAATTCGCTTTTCATCAGACAG 58.671 43.478 15.93 0.00 0.00 3.51
3578 3597 0.179189 CGACCTTGCTTGGCGAATTC 60.179 55.000 0.00 0.00 0.00 2.17
3594 3613 1.880027 ACTGGACTTCATTTTGGCGAC 59.120 47.619 0.00 0.00 0.00 5.19
3612 3631 4.280677 GGCAGAGCATAGACATAAGAGACT 59.719 45.833 0.00 0.00 0.00 3.24
3617 3638 4.056740 CTGTGGCAGAGCATAGACATAAG 58.943 47.826 0.00 0.00 32.44 1.73
3620 3641 1.474677 GCTGTGGCAGAGCATAGACAT 60.475 52.381 29.40 0.00 36.40 3.06
3625 3646 0.036483 TTTCGCTGTGGCAGAGCATA 60.036 50.000 32.21 19.05 36.12 3.14
3637 3658 2.664568 CCATGCTGACAAAATTTCGCTG 59.335 45.455 0.00 0.00 0.00 5.18
3640 3661 2.674954 TGCCATGCTGACAAAATTTCG 58.325 42.857 0.00 0.00 0.00 3.46
3641 3662 4.567959 GGTATGCCATGCTGACAAAATTTC 59.432 41.667 0.00 0.00 34.09 2.17
3642 3663 4.506758 GGTATGCCATGCTGACAAAATTT 58.493 39.130 0.00 0.00 34.09 1.82
3643 3664 3.118665 GGGTATGCCATGCTGACAAAATT 60.119 43.478 1.04 0.00 36.17 1.82
3644 3665 2.431782 GGGTATGCCATGCTGACAAAAT 59.568 45.455 1.04 0.00 36.17 1.82
3649 3671 0.820891 CTGGGGTATGCCATGCTGAC 60.821 60.000 1.04 0.00 36.17 3.51
3652 3674 1.133792 GTAACTGGGGTATGCCATGCT 60.134 52.381 1.04 0.00 36.17 3.79
3664 3686 5.221422 ACACATCAACAAATTGGTAACTGGG 60.221 40.000 0.00 0.00 36.39 4.45
3678 3700 6.450545 TGAAACTTCAACAAACACATCAACA 58.549 32.000 0.00 0.00 33.55 3.33
3685 3707 7.061326 ACGTTACAATGAAACTTCAACAAACAC 59.939 33.333 0.00 0.00 41.13 3.32
3709 3731 7.901377 GCCACACTACACATTTATTTAACTACG 59.099 37.037 0.00 0.00 0.00 3.51
3767 3789 3.637911 ACATATCTAAAACCACCGGCA 57.362 42.857 0.00 0.00 0.00 5.69
3891 3919 0.321034 GTCTCACTGCATGGTCAGCA 60.321 55.000 0.00 0.00 40.19 4.41
3894 3922 2.703416 GAATGTCTCACTGCATGGTCA 58.297 47.619 0.00 0.00 0.00 4.02
3907 3935 6.459923 GGCTATCTCTTTATTCCGAATGTCT 58.540 40.000 3.73 0.00 0.00 3.41
3935 3963 2.154462 GTACTTGTTCCATGCAGCAGT 58.846 47.619 0.00 0.00 0.00 4.40
4180 4229 7.169140 GGAAAGCGTGTCAATAAAAATGAACTT 59.831 33.333 0.00 0.00 0.00 2.66
4259 4312 6.993079 TGCAAGAGAGTAGTAATGAGTTTGA 58.007 36.000 0.00 0.00 0.00 2.69
4436 4493 1.339291 GCTACCCACCGTAGTATCCAC 59.661 57.143 0.00 0.00 45.51 4.02
4460 4526 2.163010 CACATGCTTAGACCTGCTTTGG 59.837 50.000 0.00 0.00 0.00 3.28
4561 4629 0.248990 CACACTGCGCATTGTTGGTT 60.249 50.000 28.32 6.32 0.00 3.67
4704 4773 9.746457 AAGAGCTCCAAGATTTCTACTTAATTT 57.254 29.630 10.93 0.00 0.00 1.82
4770 4840 5.184096 ACCTATGGTCGATCTAATGTAGCAG 59.816 44.000 0.00 0.00 0.00 4.24
4798 4869 1.551883 CAGATTTGCCTTTTCCCCCAG 59.448 52.381 0.00 0.00 0.00 4.45
4848 4919 2.161855 CAGGCCACTAACATGAGCAAA 58.838 47.619 5.01 0.00 0.00 3.68
4849 4920 1.825090 CAGGCCACTAACATGAGCAA 58.175 50.000 5.01 0.00 0.00 3.91
4850 4921 0.677731 GCAGGCCACTAACATGAGCA 60.678 55.000 5.01 0.00 0.00 4.26
4851 4922 0.677731 TGCAGGCCACTAACATGAGC 60.678 55.000 5.01 0.00 0.00 4.26
4852 4923 1.089920 GTGCAGGCCACTAACATGAG 58.910 55.000 5.01 0.00 41.35 2.90


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

AutoCloner maintained by Alex Coulton.