Multiple sequence alignment - TraesCS6A01G209800

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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 TraesCS6A01G209800 chr6A 100.000 3413 0 0 1 3413 380109280 380112692 0.000000e+00 6303
1 TraesCS6A01G209800 chr6A 94.175 103 5 1 3311 3413 85673384 85673485 4.560000e-34 156
2 TraesCS6A01G209800 chr6D 94.965 2820 66 23 524 3319 267200090 267202857 0.000000e+00 4351
3 TraesCS6A01G209800 chr6D 93.333 285 16 1 1 282 267199473 267199757 5.270000e-113 418
4 TraesCS6A01G209800 chr6D 84.912 285 17 3 280 539 267199786 267200069 7.260000e-67 265
5 TraesCS6A01G209800 chr6B 91.518 2794 128 51 1 2735 415728950 415731693 0.000000e+00 3746
6 TraesCS6A01G209800 chr6B 94.248 226 11 1 2927 3150 415732212 415732437 9.070000e-91 344
7 TraesCS6A01G209800 chr6B 93.836 146 9 0 2777 2922 415731901 415732046 1.590000e-53 220
8 TraesCS6A01G209800 chr6B 79.452 219 17 13 3110 3319 415732431 415732630 2.760000e-26 130
9 TraesCS6A01G209800 chr1A 95.960 99 4 0 3315 3413 178597165 178597067 9.800000e-36 161
10 TraesCS6A01G209800 chr1A 92.661 109 6 2 3307 3413 472426090 472425982 4.560000e-34 156
11 TraesCS6A01G209800 chr4A 95.050 101 5 0 3313 3413 298416519 298416619 3.530000e-35 159
12 TraesCS6A01G209800 chr4A 94.118 102 6 0 3312 3413 523396025 523395924 4.560000e-34 156
13 TraesCS6A01G209800 chr4A 90.517 116 8 3 3298 3413 278913439 278913551 2.120000e-32 150
14 TraesCS6A01G209800 chr4A 90.909 77 7 0 1211 1287 615212962 615213038 1.680000e-18 104
15 TraesCS6A01G209800 chr3A 92.593 108 7 1 3307 3413 632576977 632576870 1.640000e-33 154
16 TraesCS6A01G209800 chr3A 88.710 124 9 5 3295 3413 693495741 693495864 2.740000e-31 147
17 TraesCS6A01G209800 chr2A 90.351 114 10 1 3300 3413 294893629 294893741 7.630000e-32 148
18 TraesCS6A01G209800 chr5D 93.243 74 5 0 1214 1287 552784600 552784527 3.600000e-20 110
19 TraesCS6A01G209800 chr5B 92.208 77 6 0 1211 1287 697679891 697679967 3.600000e-20 110
20 TraesCS6A01G209800 chr5B 89.610 77 8 0 1211 1287 697778088 697778164 7.790000e-17 99


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 TraesCS6A01G209800 chr6A 380109280 380112692 3412 False 6303 6303 100.0000 1 3413 1 chr6A.!!$F2 3412
1 TraesCS6A01G209800 chr6D 267199473 267202857 3384 False 1678 4351 91.0700 1 3319 3 chr6D.!!$F1 3318
2 TraesCS6A01G209800 chr6B 415728950 415732630 3680 False 1110 3746 89.7635 1 3319 4 chr6B.!!$F1 3318

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
261 265 0.461516 TCGCTCGTAGGAGATGACGT 60.462 55.0 16.47 0.0 43.27 4.34 F
645 782 0.468226 AAACAGAGAACGTGGAGCCA 59.532 50.0 0.00 0.0 0.00 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2253 2400 0.614697 TCGCCTCCTCATCCTTGTCA 60.615 55.000 0.0 0.0 0.0 3.58 R
2489 2636 4.657814 TTCACAAGAGCCTTCCCTAAAT 57.342 40.909 0.0 0.0 0.0 1.40 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
22 23 3.708403 ACTTGTGCAGATCAAGGATCA 57.292 42.857 17.06 0.00 44.29 2.92
41 42 1.153086 CAAGCCCTCCTTGCGCTAT 60.153 57.895 9.73 0.00 43.98 2.97
67 68 0.469917 ACATACCTTCTCCCATGCCG 59.530 55.000 0.00 0.00 0.00 5.69
126 127 5.055812 GCCCAAAGAATGTTGTGAATTGAA 58.944 37.500 0.00 0.00 0.00 2.69
205 206 7.716998 AGTCCTAAATTTATCATGAATGCTCGT 59.283 33.333 0.00 0.00 0.00 4.18
248 252 1.135972 CCTTTTGGTGATGTTCGCTCG 60.136 52.381 0.00 0.00 34.07 5.03
261 265 0.461516 TCGCTCGTAGGAGATGACGT 60.462 55.000 16.47 0.00 43.27 4.34
340 375 6.705825 AGTGCATATGCGTGTATGAGATAAAA 59.294 34.615 22.21 0.00 45.83 1.52
371 408 7.886338 TGCATATAAATGTTTGTGTTGGTGTA 58.114 30.769 0.00 0.00 35.38 2.90
503 565 6.761731 AATTCGCAAAATCAATTGTCGAAA 57.238 29.167 16.66 0.00 44.06 3.46
517 579 2.159352 TGTCGAAAATACCGCGAGATGA 60.159 45.455 8.23 0.00 34.41 2.92
528 626 0.855349 GCGAGATGATGCGTAAGTGG 59.145 55.000 0.00 0.00 41.68 4.00
555 653 2.162008 GTCACGGTCACTCCTCTAGAAC 59.838 54.545 0.00 0.00 0.00 3.01
566 664 3.900601 CTCCTCTAGAACATATGCACCCT 59.099 47.826 1.58 0.00 0.00 4.34
607 744 2.640316 AGAGAACGTGGAGCCTTTTT 57.360 45.000 0.00 0.00 0.00 1.94
608 745 2.495084 AGAGAACGTGGAGCCTTTTTC 58.505 47.619 0.00 0.00 0.00 2.29
609 746 2.104963 AGAGAACGTGGAGCCTTTTTCT 59.895 45.455 0.00 0.00 0.00 2.52
610 747 2.879026 GAGAACGTGGAGCCTTTTTCTT 59.121 45.455 0.00 0.00 0.00 2.52
611 748 3.288092 AGAACGTGGAGCCTTTTTCTTT 58.712 40.909 0.00 0.00 0.00 2.52
645 782 0.468226 AAACAGAGAACGTGGAGCCA 59.532 50.000 0.00 0.00 0.00 4.75
736 873 0.529378 GCCCAGAAGCACCAGATTTG 59.471 55.000 0.00 0.00 0.00 2.32
1092 1239 2.043450 CTCCCGCTCTCCACCTCT 60.043 66.667 0.00 0.00 0.00 3.69
1566 1713 2.345991 GCCAAGCAGGTCGGTGTA 59.654 61.111 0.00 0.00 40.61 2.90
1653 1800 3.816524 CTCGAGGTCCGCGAGCTT 61.817 66.667 28.47 0.00 45.17 3.74
1713 1860 3.368190 CTCCGGCTCTGCACTCAGG 62.368 68.421 0.00 0.00 40.69 3.86
1794 1941 3.614092 TGGCATCTTCTCCTTGATTGAC 58.386 45.455 0.00 0.00 0.00 3.18
1839 1986 2.052690 GCAGAGGCAGACCGACCTA 61.053 63.158 0.00 0.00 42.76 3.08
1965 2112 2.418910 CGTCGGCATCAGGGAGACT 61.419 63.158 0.00 0.00 0.00 3.24
2619 2766 0.606401 ATGTCCTTGACTGTTGGCCG 60.606 55.000 0.00 0.00 33.15 6.13
2731 2899 8.792830 AGCTTATTTGTTTACTGCTTCAGATA 57.207 30.769 0.29 0.00 35.18 1.98
2748 2916 5.303165 TCAGATATATGCTTGCTTGACAGG 58.697 41.667 0.00 0.00 0.00 4.00
2767 2935 9.793259 TTGACAGGTTTATCTTAATCTTGAAGT 57.207 29.630 0.00 0.00 0.00 3.01
2801 3123 3.988379 TCATATTGATTTTCCGCTGGC 57.012 42.857 0.00 0.00 0.00 4.85
2841 3163 3.624410 GCAATCATGTGTGTGCTCATCTA 59.376 43.478 0.00 0.00 34.13 1.98
2853 3175 6.127563 TGTGTGCTCATCTATTTCAATGCAAT 60.128 34.615 0.00 0.00 0.00 3.56
2873 3195 5.752955 GCAATAACAGTTTCATGTGTTGGTT 59.247 36.000 9.11 5.26 37.46 3.67
3142 3630 1.985473 TGTGCTGCTTCTGGATGTTT 58.015 45.000 0.00 0.00 0.00 2.83
3143 3631 1.881973 TGTGCTGCTTCTGGATGTTTC 59.118 47.619 0.00 0.00 0.00 2.78
3149 3669 2.552315 TGCTTCTGGATGTTTCGTTTCC 59.448 45.455 0.00 0.00 0.00 3.13
3156 3676 4.677584 TGGATGTTTCGTTTCCTTTTGTG 58.322 39.130 0.00 0.00 0.00 3.33
3157 3677 4.158764 TGGATGTTTCGTTTCCTTTTGTGT 59.841 37.500 0.00 0.00 0.00 3.72
3158 3678 4.502645 GGATGTTTCGTTTCCTTTTGTGTG 59.497 41.667 0.00 0.00 0.00 3.82
3159 3679 4.506886 TGTTTCGTTTCCTTTTGTGTGT 57.493 36.364 0.00 0.00 0.00 3.72
3161 3681 4.918583 TGTTTCGTTTCCTTTTGTGTGTTC 59.081 37.500 0.00 0.00 0.00 3.18
3162 3682 3.768468 TCGTTTCCTTTTGTGTGTTCC 57.232 42.857 0.00 0.00 0.00 3.62
3163 3683 3.082548 TCGTTTCCTTTTGTGTGTTCCA 58.917 40.909 0.00 0.00 0.00 3.53
3164 3684 3.127895 TCGTTTCCTTTTGTGTGTTCCAG 59.872 43.478 0.00 0.00 0.00 3.86
3166 3686 4.617298 CGTTTCCTTTTGTGTGTTCCAGTT 60.617 41.667 0.00 0.00 0.00 3.16
3168 3688 3.963129 TCCTTTTGTGTGTTCCAGTTCT 58.037 40.909 0.00 0.00 0.00 3.01
3176 3696 4.826733 TGTGTGTTCCAGTTCTAAATGCAT 59.173 37.500 0.00 0.00 0.00 3.96
3183 3703 7.446931 TGTTCCAGTTCTAAATGCATACTCAAA 59.553 33.333 0.00 0.00 0.00 2.69
3184 3704 8.462016 GTTCCAGTTCTAAATGCATACTCAAAT 58.538 33.333 0.00 0.00 0.00 2.32
3185 3705 9.679661 TTCCAGTTCTAAATGCATACTCAAATA 57.320 29.630 0.00 0.00 0.00 1.40
3203 3726 5.529430 TCAAATATTTCGTGTCTTGTGGTGT 59.471 36.000 0.00 0.00 0.00 4.16
3210 3733 2.132762 GTGTCTTGTGGTGTAGTTCCG 58.867 52.381 0.00 0.00 0.00 4.30
3211 3734 1.145803 GTCTTGTGGTGTAGTTCCGC 58.854 55.000 0.00 0.00 36.18 5.54
3212 3735 0.753867 TCTTGTGGTGTAGTTCCGCA 59.246 50.000 0.00 0.00 42.62 5.69
3213 3736 1.346395 TCTTGTGGTGTAGTTCCGCAT 59.654 47.619 0.00 0.00 43.55 4.73
3214 3737 2.151202 CTTGTGGTGTAGTTCCGCATT 58.849 47.619 0.00 0.00 43.55 3.56
3215 3738 2.264005 TGTGGTGTAGTTCCGCATTT 57.736 45.000 0.00 0.00 40.01 2.32
3216 3739 2.577700 TGTGGTGTAGTTCCGCATTTT 58.422 42.857 0.00 0.00 40.01 1.82
3217 3740 2.292016 TGTGGTGTAGTTCCGCATTTTG 59.708 45.455 0.00 0.00 40.01 2.44
3218 3741 1.268352 TGGTGTAGTTCCGCATTTTGC 59.732 47.619 0.00 0.00 40.69 3.68
3219 3742 1.539827 GGTGTAGTTCCGCATTTTGCT 59.460 47.619 0.00 0.00 42.25 3.91
3220 3743 2.414161 GGTGTAGTTCCGCATTTTGCTC 60.414 50.000 0.00 0.00 42.25 4.26
3221 3744 2.484264 GTGTAGTTCCGCATTTTGCTCT 59.516 45.455 0.00 0.00 42.25 4.09
3222 3745 2.483877 TGTAGTTCCGCATTTTGCTCTG 59.516 45.455 0.00 0.00 42.25 3.35
3234 3757 6.075205 CGCATTTTGCTCTGTTCTAATAATGC 60.075 38.462 0.00 0.00 42.25 3.56
3235 3758 6.199719 GCATTTTGCTCTGTTCTAATAATGCC 59.800 38.462 0.00 0.00 40.96 4.40
3236 3759 7.486647 CATTTTGCTCTGTTCTAATAATGCCT 58.513 34.615 0.00 0.00 0.00 4.75
3237 3760 6.683974 TTTGCTCTGTTCTAATAATGCCTC 57.316 37.500 0.00 0.00 0.00 4.70
3238 3761 4.708177 TGCTCTGTTCTAATAATGCCTCC 58.292 43.478 0.00 0.00 0.00 4.30
3239 3762 4.164030 TGCTCTGTTCTAATAATGCCTCCA 59.836 41.667 0.00 0.00 0.00 3.86
3287 3810 6.947733 TGATTTGAACTCCATTAACATCACCT 59.052 34.615 0.00 0.00 0.00 4.00
3288 3811 6.573664 TTTGAACTCCATTAACATCACCTG 57.426 37.500 0.00 0.00 0.00 4.00
3321 3849 6.780706 AGTAACATGCTGTGTAGTTGTAAC 57.219 37.500 0.00 0.00 41.14 2.50
3322 3850 6.285224 AGTAACATGCTGTGTAGTTGTAACA 58.715 36.000 0.00 0.00 41.14 2.41
3323 3851 5.418310 AACATGCTGTGTAGTTGTAACAC 57.582 39.130 0.00 0.00 45.96 3.32
3324 3852 3.813166 ACATGCTGTGTAGTTGTAACACC 59.187 43.478 4.09 0.00 45.33 4.16
3325 3853 2.841215 TGCTGTGTAGTTGTAACACCC 58.159 47.619 4.09 0.00 45.33 4.61
3326 3854 2.170817 TGCTGTGTAGTTGTAACACCCA 59.829 45.455 4.09 0.00 45.33 4.51
3327 3855 2.546789 GCTGTGTAGTTGTAACACCCAC 59.453 50.000 4.09 2.01 45.33 4.61
3328 3856 2.798283 CTGTGTAGTTGTAACACCCACG 59.202 50.000 4.09 0.00 45.33 4.94
3329 3857 2.429971 TGTGTAGTTGTAACACCCACGA 59.570 45.455 4.09 0.00 45.33 4.35
3330 3858 3.069872 TGTGTAGTTGTAACACCCACGAT 59.930 43.478 4.09 0.00 45.33 3.73
3331 3859 3.430895 GTGTAGTTGTAACACCCACGATG 59.569 47.826 0.00 0.00 41.10 3.84
3332 3860 1.519408 AGTTGTAACACCCACGATGC 58.481 50.000 0.00 0.00 0.00 3.91
3333 3861 0.165079 GTTGTAACACCCACGATGCG 59.835 55.000 0.00 0.00 0.00 4.73
3334 3862 0.951525 TTGTAACACCCACGATGCGG 60.952 55.000 0.00 0.00 0.00 5.69
3335 3863 2.435234 TAACACCCACGATGCGGC 60.435 61.111 0.00 0.00 0.00 6.53
3336 3864 2.949909 TAACACCCACGATGCGGCT 61.950 57.895 0.00 0.00 0.00 5.52
3337 3865 1.605971 TAACACCCACGATGCGGCTA 61.606 55.000 0.00 0.00 0.00 3.93
3338 3866 2.108976 CACCCACGATGCGGCTAT 59.891 61.111 0.00 0.00 0.00 2.97
3339 3867 1.365999 CACCCACGATGCGGCTATA 59.634 57.895 0.00 0.00 0.00 1.31
3340 3868 0.037326 CACCCACGATGCGGCTATAT 60.037 55.000 0.00 0.00 0.00 0.86
3341 3869 0.246635 ACCCACGATGCGGCTATATC 59.753 55.000 0.00 0.00 0.00 1.63
3342 3870 0.532573 CCCACGATGCGGCTATATCT 59.467 55.000 0.00 0.00 0.00 1.98
3343 3871 1.469940 CCCACGATGCGGCTATATCTC 60.470 57.143 0.00 0.00 0.00 2.75
3344 3872 1.469940 CCACGATGCGGCTATATCTCC 60.470 57.143 0.00 0.00 0.00 3.71
3345 3873 0.818296 ACGATGCGGCTATATCTCCC 59.182 55.000 0.00 0.00 0.00 4.30
3346 3874 0.817654 CGATGCGGCTATATCTCCCA 59.182 55.000 0.00 0.00 0.00 4.37
3347 3875 1.469940 CGATGCGGCTATATCTCCCAC 60.470 57.143 0.00 0.00 0.00 4.61
3348 3876 0.532573 ATGCGGCTATATCTCCCACG 59.467 55.000 0.00 0.00 0.00 4.94
3349 3877 0.826256 TGCGGCTATATCTCCCACGT 60.826 55.000 0.00 0.00 0.00 4.49
3350 3878 0.388649 GCGGCTATATCTCCCACGTG 60.389 60.000 9.08 9.08 0.00 4.49
3351 3879 0.959553 CGGCTATATCTCCCACGTGT 59.040 55.000 15.65 0.00 0.00 4.49
3352 3880 1.068472 CGGCTATATCTCCCACGTGTC 60.068 57.143 15.65 0.00 0.00 3.67
3353 3881 1.068472 GGCTATATCTCCCACGTGTCG 60.068 57.143 15.65 4.04 0.00 4.35
3354 3882 1.068472 GCTATATCTCCCACGTGTCGG 60.068 57.143 15.65 9.74 0.00 4.79
3355 3883 2.501261 CTATATCTCCCACGTGTCGGA 58.499 52.381 15.65 13.73 0.00 4.55
3356 3884 1.319541 ATATCTCCCACGTGTCGGAG 58.680 55.000 26.30 26.30 46.07 4.63
3357 3885 1.381928 TATCTCCCACGTGTCGGAGC 61.382 60.000 27.01 0.00 44.61 4.70
3358 3886 3.680786 CTCCCACGTGTCGGAGCA 61.681 66.667 22.68 0.35 39.36 4.26
3359 3887 3.916392 CTCCCACGTGTCGGAGCAC 62.916 68.421 22.68 0.00 39.36 4.40
3375 3903 5.891810 GGAGCACGATTTAGAGACATAAC 57.108 43.478 0.00 0.00 0.00 1.89
3376 3904 4.745620 GGAGCACGATTTAGAGACATAACC 59.254 45.833 0.00 0.00 0.00 2.85
3377 3905 4.360563 AGCACGATTTAGAGACATAACCG 58.639 43.478 0.00 0.00 0.00 4.44
3378 3906 3.060473 GCACGATTTAGAGACATAACCGC 60.060 47.826 0.00 0.00 0.00 5.68
3379 3907 4.109766 CACGATTTAGAGACATAACCGCA 58.890 43.478 0.00 0.00 0.00 5.69
3380 3908 4.745125 CACGATTTAGAGACATAACCGCAT 59.255 41.667 0.00 0.00 0.00 4.73
3381 3909 5.234329 CACGATTTAGAGACATAACCGCATT 59.766 40.000 0.00 0.00 0.00 3.56
3382 3910 5.234329 ACGATTTAGAGACATAACCGCATTG 59.766 40.000 0.00 0.00 0.00 2.82
3383 3911 5.234329 CGATTTAGAGACATAACCGCATTGT 59.766 40.000 0.00 0.00 0.00 2.71
3384 3912 6.419710 CGATTTAGAGACATAACCGCATTGTA 59.580 38.462 0.00 0.00 0.00 2.41
3385 3913 7.358435 CGATTTAGAGACATAACCGCATTGTAG 60.358 40.741 0.00 0.00 0.00 2.74
3386 3914 4.060038 AGAGACATAACCGCATTGTAGG 57.940 45.455 0.00 0.00 0.00 3.18
3387 3915 3.451178 AGAGACATAACCGCATTGTAGGT 59.549 43.478 0.98 0.98 43.68 3.08
3388 3916 4.647853 AGAGACATAACCGCATTGTAGGTA 59.352 41.667 6.42 0.00 40.37 3.08
3389 3917 5.304614 AGAGACATAACCGCATTGTAGGTAT 59.695 40.000 6.42 0.00 40.37 2.73
3390 3918 5.297547 AGACATAACCGCATTGTAGGTATG 58.702 41.667 9.99 9.99 40.37 2.39
3391 3919 5.031066 ACATAACCGCATTGTAGGTATGT 57.969 39.130 10.95 10.95 40.37 2.29
3392 3920 5.054477 ACATAACCGCATTGTAGGTATGTC 58.946 41.667 10.95 0.00 40.37 3.06
3393 3921 2.218953 ACCGCATTGTAGGTATGTCG 57.781 50.000 4.50 0.00 39.30 4.35
3394 3922 1.479323 ACCGCATTGTAGGTATGTCGT 59.521 47.619 4.50 0.00 39.30 4.34
3395 3923 2.689471 ACCGCATTGTAGGTATGTCGTA 59.311 45.455 4.50 0.00 39.30 3.43
3396 3924 3.130869 ACCGCATTGTAGGTATGTCGTAA 59.869 43.478 4.50 0.00 39.30 3.18
3397 3925 4.114073 CCGCATTGTAGGTATGTCGTAAA 58.886 43.478 0.00 0.00 0.00 2.01
3398 3926 4.567558 CCGCATTGTAGGTATGTCGTAAAA 59.432 41.667 0.00 0.00 0.00 1.52
3399 3927 5.276678 CCGCATTGTAGGTATGTCGTAAAAG 60.277 44.000 0.00 0.00 0.00 2.27
3400 3928 5.276678 CGCATTGTAGGTATGTCGTAAAAGG 60.277 44.000 0.00 0.00 0.00 3.11
3401 3929 5.007332 GCATTGTAGGTATGTCGTAAAAGGG 59.993 44.000 0.00 0.00 0.00 3.95
3402 3930 4.741321 TGTAGGTATGTCGTAAAAGGGG 57.259 45.455 0.00 0.00 0.00 4.79
3403 3931 4.095946 TGTAGGTATGTCGTAAAAGGGGT 58.904 43.478 0.00 0.00 0.00 4.95
3404 3932 5.268387 TGTAGGTATGTCGTAAAAGGGGTA 58.732 41.667 0.00 0.00 0.00 3.69
3405 3933 5.719085 TGTAGGTATGTCGTAAAAGGGGTAA 59.281 40.000 0.00 0.00 0.00 2.85
3406 3934 5.963214 AGGTATGTCGTAAAAGGGGTAAT 57.037 39.130 0.00 0.00 0.00 1.89
3407 3935 5.922053 AGGTATGTCGTAAAAGGGGTAATC 58.078 41.667 0.00 0.00 0.00 1.75
3408 3936 5.664457 AGGTATGTCGTAAAAGGGGTAATCT 59.336 40.000 0.00 0.00 0.00 2.40
3409 3937 6.157471 AGGTATGTCGTAAAAGGGGTAATCTT 59.843 38.462 0.00 0.00 0.00 2.40
3410 3938 6.825213 GGTATGTCGTAAAAGGGGTAATCTTT 59.175 38.462 0.00 0.00 36.15 2.52
3411 3939 7.986889 GGTATGTCGTAAAAGGGGTAATCTTTA 59.013 37.037 0.00 0.00 33.80 1.85
3412 3940 7.854557 ATGTCGTAAAAGGGGTAATCTTTAC 57.145 36.000 0.00 0.00 33.80 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 3.522759 TGGGAGAAGGTATGTACACCAA 58.477 45.455 0.00 0.00 41.40 3.67
67 68 2.819608 TCACTGGAGGCAAATGTAAAGC 59.180 45.455 0.00 0.00 0.00 3.51
90 91 1.338020 CTTTGGGCACAAGAGGACAAC 59.662 52.381 0.00 0.00 37.97 3.32
92 93 0.843309 TCTTTGGGCACAAGAGGACA 59.157 50.000 0.00 0.00 37.97 4.02
126 127 8.739972 CAAAGAAACCTAACCTATTTGCTATGT 58.260 33.333 0.00 0.00 0.00 2.29
195 196 6.757897 AATCCAATAAAAGACGAGCATTCA 57.242 33.333 0.00 0.00 0.00 2.57
226 230 2.293399 GAGCGAACATCACCAAAAGGTT 59.707 45.455 0.00 0.00 0.00 3.50
248 252 4.563184 GTCAACATGAACGTCATCTCCTAC 59.437 45.833 0.00 0.00 34.28 3.18
261 265 5.550290 TCAGCATCTTGTAGTCAACATGAA 58.450 37.500 0.00 0.00 43.28 2.57
282 286 5.452078 AGCATTTTCGAAAGACCAAATCA 57.548 34.783 10.98 0.00 41.84 2.57
283 287 5.691754 ACAAGCATTTTCGAAAGACCAAATC 59.308 36.000 10.98 0.00 41.84 2.17
517 579 2.806244 GTGACTGTTTCCACTTACGCAT 59.194 45.455 0.00 0.00 0.00 4.73
521 583 2.798847 GACCGTGACTGTTTCCACTTAC 59.201 50.000 0.00 0.00 0.00 2.34
528 626 1.068741 AGGAGTGACCGTGACTGTTTC 59.931 52.381 0.00 0.00 44.74 2.78
566 664 2.099263 TCATTTCACGGGAAAACGCAAA 59.901 40.909 18.20 0.00 45.52 3.68
622 759 2.476997 GCTCCACGTTCTCTGTTTTCTC 59.523 50.000 0.00 0.00 0.00 2.87
623 760 2.484889 GCTCCACGTTCTCTGTTTTCT 58.515 47.619 0.00 0.00 0.00 2.52
629 766 0.318441 TTCTGGCTCCACGTTCTCTG 59.682 55.000 0.00 0.00 0.00 3.35
736 873 4.690159 GGAACGCGAAATGGATGC 57.310 55.556 15.93 0.00 0.00 3.91
1035 1182 3.157949 GAGGGCGGGAAGAGGAGG 61.158 72.222 0.00 0.00 0.00 4.30
1212 1359 2.345991 CCGATGTTGACGTGGGGT 59.654 61.111 0.00 0.00 0.00 4.95
1566 1713 2.365293 GAGGAAAACAACAATGCTGGGT 59.635 45.455 0.00 0.00 0.00 4.51
1653 1800 1.134310 TCGTACTCATAGGCCGTGAGA 60.134 52.381 33.91 20.81 44.57 3.27
1839 1986 0.886490 CAACAGCGAGCAAGAAGGGT 60.886 55.000 0.00 0.00 0.00 4.34
1965 2112 3.047280 GTGACCGTGGCATTGCGA 61.047 61.111 1.91 0.00 0.00 5.10
2184 2331 1.546589 ATTGCGGACGGTAACCAGGA 61.547 55.000 0.00 0.00 0.00 3.86
2253 2400 0.614697 TCGCCTCCTCATCCTTGTCA 60.615 55.000 0.00 0.00 0.00 3.58
2489 2636 4.657814 TTCACAAGAGCCTTCCCTAAAT 57.342 40.909 0.00 0.00 0.00 1.40
2619 2766 7.653311 AGCATATCAACAAGAGGAAAACAAAAC 59.347 33.333 0.00 0.00 0.00 2.43
2665 2812 0.921896 AACCAGTCCCTGCAGCATAT 59.078 50.000 8.66 0.00 0.00 1.78
2731 2899 6.125029 AGATAAACCTGTCAAGCAAGCATAT 58.875 36.000 0.00 0.00 0.00 1.78
2771 2939 7.757624 GCGGAAAATCAATATGAACTACCAAAA 59.242 33.333 0.00 0.00 0.00 2.44
2841 3163 8.714179 CACATGAAACTGTTATTGCATTGAAAT 58.286 29.630 0.00 0.00 0.00 2.17
2853 3175 7.918033 CACAATAACCAACACATGAAACTGTTA 59.082 33.333 0.00 2.22 0.00 2.41
2899 3221 7.307042 CCAGCAGAAAATCGATATGAACTACAG 60.307 40.741 0.00 0.00 0.00 2.74
2900 3222 6.479990 CCAGCAGAAAATCGATATGAACTACA 59.520 38.462 0.00 0.00 0.00 2.74
3134 3622 4.158764 ACACAAAAGGAAACGAAACATCCA 59.841 37.500 0.00 0.00 35.62 3.41
3142 3630 3.082548 TGGAACACACAAAAGGAAACGA 58.917 40.909 0.00 0.00 0.00 3.85
3143 3631 3.119637 ACTGGAACACACAAAAGGAAACG 60.120 43.478 0.00 0.00 0.00 3.60
3149 3669 6.198966 GCATTTAGAACTGGAACACACAAAAG 59.801 38.462 0.00 0.00 0.00 2.27
3156 3676 6.371548 TGAGTATGCATTTAGAACTGGAACAC 59.628 38.462 3.54 0.00 0.00 3.32
3157 3677 6.472016 TGAGTATGCATTTAGAACTGGAACA 58.528 36.000 3.54 0.00 0.00 3.18
3158 3678 6.985188 TGAGTATGCATTTAGAACTGGAAC 57.015 37.500 3.54 0.00 0.00 3.62
3159 3679 7.994425 TTTGAGTATGCATTTAGAACTGGAA 57.006 32.000 3.54 0.00 0.00 3.53
3168 3688 9.929722 GACACGAAATATTTGAGTATGCATTTA 57.070 29.630 3.54 0.00 0.00 1.40
3176 3696 6.932400 ACCACAAGACACGAAATATTTGAGTA 59.068 34.615 5.17 0.00 0.00 2.59
3183 3703 5.790593 ACTACACCACAAGACACGAAATAT 58.209 37.500 0.00 0.00 0.00 1.28
3184 3704 5.204409 ACTACACCACAAGACACGAAATA 57.796 39.130 0.00 0.00 0.00 1.40
3185 3705 4.067972 ACTACACCACAAGACACGAAAT 57.932 40.909 0.00 0.00 0.00 2.17
3189 3709 2.132762 GGAACTACACCACAAGACACG 58.867 52.381 0.00 0.00 0.00 4.49
3190 3710 2.132762 CGGAACTACACCACAAGACAC 58.867 52.381 0.00 0.00 0.00 3.67
3210 3733 6.199719 GGCATTATTAGAACAGAGCAAAATGC 59.800 38.462 7.48 7.48 45.46 3.56
3211 3734 7.486647 AGGCATTATTAGAACAGAGCAAAATG 58.513 34.615 0.00 0.00 0.00 2.32
3212 3735 7.201857 GGAGGCATTATTAGAACAGAGCAAAAT 60.202 37.037 0.00 0.00 0.00 1.82
3213 3736 6.095440 GGAGGCATTATTAGAACAGAGCAAAA 59.905 38.462 0.00 0.00 0.00 2.44
3214 3737 5.590259 GGAGGCATTATTAGAACAGAGCAAA 59.410 40.000 0.00 0.00 0.00 3.68
3215 3738 5.126067 GGAGGCATTATTAGAACAGAGCAA 58.874 41.667 0.00 0.00 0.00 3.91
3216 3739 4.164030 TGGAGGCATTATTAGAACAGAGCA 59.836 41.667 0.00 0.00 0.00 4.26
3217 3740 4.513318 GTGGAGGCATTATTAGAACAGAGC 59.487 45.833 0.00 0.00 0.00 4.09
3218 3741 5.059833 GGTGGAGGCATTATTAGAACAGAG 58.940 45.833 0.00 0.00 0.00 3.35
3219 3742 4.721776 AGGTGGAGGCATTATTAGAACAGA 59.278 41.667 0.00 0.00 0.00 3.41
3220 3743 5.041191 AGGTGGAGGCATTATTAGAACAG 57.959 43.478 0.00 0.00 0.00 3.16
3221 3744 4.721776 AGAGGTGGAGGCATTATTAGAACA 59.278 41.667 0.00 0.00 0.00 3.18
3222 3745 5.297569 AGAGGTGGAGGCATTATTAGAAC 57.702 43.478 0.00 0.00 0.00 3.01
3239 3762 0.615331 ATGCGGATGTCACAAGAGGT 59.385 50.000 0.00 0.00 0.00 3.85
3319 3847 2.252072 ATAGCCGCATCGTGGGTGTT 62.252 55.000 8.47 0.00 44.01 3.32
3320 3848 1.396607 TATAGCCGCATCGTGGGTGT 61.397 55.000 8.47 4.53 44.01 4.16
3321 3849 0.037326 ATATAGCCGCATCGTGGGTG 60.037 55.000 8.47 0.00 44.01 4.61
3322 3850 0.246635 GATATAGCCGCATCGTGGGT 59.753 55.000 3.52 3.52 46.10 4.51
3323 3851 0.532573 AGATATAGCCGCATCGTGGG 59.467 55.000 0.00 0.00 33.18 4.61
3324 3852 1.469940 GGAGATATAGCCGCATCGTGG 60.470 57.143 0.00 0.00 36.10 4.94
3325 3853 1.469940 GGGAGATATAGCCGCATCGTG 60.470 57.143 0.00 0.00 0.00 4.35
3326 3854 0.818296 GGGAGATATAGCCGCATCGT 59.182 55.000 0.00 0.00 0.00 3.73
3327 3855 0.817654 TGGGAGATATAGCCGCATCG 59.182 55.000 0.00 0.00 0.00 3.84
3328 3856 1.469940 CGTGGGAGATATAGCCGCATC 60.470 57.143 0.00 0.00 0.00 3.91
3329 3857 0.532573 CGTGGGAGATATAGCCGCAT 59.467 55.000 0.00 0.00 0.00 4.73
3330 3858 0.826256 ACGTGGGAGATATAGCCGCA 60.826 55.000 0.00 0.00 0.00 5.69
3331 3859 0.388649 CACGTGGGAGATATAGCCGC 60.389 60.000 7.95 0.00 0.00 6.53
3332 3860 0.959553 ACACGTGGGAGATATAGCCG 59.040 55.000 21.57 0.00 0.00 5.52
3333 3861 1.068472 CGACACGTGGGAGATATAGCC 60.068 57.143 21.57 0.00 0.00 3.93
3334 3862 1.068472 CCGACACGTGGGAGATATAGC 60.068 57.143 21.57 0.00 0.00 2.97
3335 3863 2.501261 TCCGACACGTGGGAGATATAG 58.499 52.381 21.57 0.00 32.32 1.31
3336 3864 2.643995 TCCGACACGTGGGAGATATA 57.356 50.000 21.57 0.00 32.32 0.86
3337 3865 3.507675 TCCGACACGTGGGAGATAT 57.492 52.632 21.57 0.00 32.32 1.63
3342 3870 3.986006 GTGCTCCGACACGTGGGA 61.986 66.667 21.57 16.34 36.07 4.37
3352 3880 2.561733 TGTCTCTAAATCGTGCTCCG 57.438 50.000 0.00 0.00 38.13 4.63
3353 3881 4.745620 GGTTATGTCTCTAAATCGTGCTCC 59.254 45.833 0.00 0.00 0.00 4.70
3354 3882 4.441415 CGGTTATGTCTCTAAATCGTGCTC 59.559 45.833 0.00 0.00 0.00 4.26
3355 3883 4.360563 CGGTTATGTCTCTAAATCGTGCT 58.639 43.478 0.00 0.00 0.00 4.40
3356 3884 3.060473 GCGGTTATGTCTCTAAATCGTGC 60.060 47.826 0.00 0.00 0.00 5.34
3357 3885 4.109766 TGCGGTTATGTCTCTAAATCGTG 58.890 43.478 0.00 0.00 0.00 4.35
3358 3886 4.380841 TGCGGTTATGTCTCTAAATCGT 57.619 40.909 0.00 0.00 0.00 3.73
3359 3887 5.234329 ACAATGCGGTTATGTCTCTAAATCG 59.766 40.000 0.00 0.00 0.00 3.34
3360 3888 6.604735 ACAATGCGGTTATGTCTCTAAATC 57.395 37.500 0.00 0.00 0.00 2.17
3361 3889 6.706270 CCTACAATGCGGTTATGTCTCTAAAT 59.294 38.462 0.00 0.00 0.00 1.40
3362 3890 6.046593 CCTACAATGCGGTTATGTCTCTAAA 58.953 40.000 0.00 0.00 0.00 1.85
3363 3891 5.128171 ACCTACAATGCGGTTATGTCTCTAA 59.872 40.000 0.00 0.00 0.00 2.10
3364 3892 4.647853 ACCTACAATGCGGTTATGTCTCTA 59.352 41.667 0.00 0.00 0.00 2.43
3365 3893 3.451178 ACCTACAATGCGGTTATGTCTCT 59.549 43.478 0.00 0.00 0.00 3.10
3366 3894 3.793559 ACCTACAATGCGGTTATGTCTC 58.206 45.455 0.00 0.00 0.00 3.36
3367 3895 3.906720 ACCTACAATGCGGTTATGTCT 57.093 42.857 0.00 0.00 0.00 3.41
3368 3896 5.054477 ACATACCTACAATGCGGTTATGTC 58.946 41.667 0.18 0.00 34.76 3.06
3369 3897 5.031066 ACATACCTACAATGCGGTTATGT 57.969 39.130 0.18 6.07 34.76 2.29
3370 3898 4.149922 CGACATACCTACAATGCGGTTATG 59.850 45.833 0.18 5.59 34.76 1.90
3371 3899 4.202182 ACGACATACCTACAATGCGGTTAT 60.202 41.667 0.18 0.00 34.76 1.89
3372 3900 3.130869 ACGACATACCTACAATGCGGTTA 59.869 43.478 0.18 0.00 34.76 2.85
3373 3901 2.093869 ACGACATACCTACAATGCGGTT 60.094 45.455 0.18 0.00 34.76 4.44
3374 3902 1.479323 ACGACATACCTACAATGCGGT 59.521 47.619 0.00 0.62 37.31 5.68
3375 3903 2.218953 ACGACATACCTACAATGCGG 57.781 50.000 0.00 0.00 32.17 5.69
3376 3904 5.276678 CCTTTTACGACATACCTACAATGCG 60.277 44.000 0.00 0.00 33.28 4.73
3377 3905 5.007332 CCCTTTTACGACATACCTACAATGC 59.993 44.000 0.00 0.00 0.00 3.56
3378 3906 5.526111 CCCCTTTTACGACATACCTACAATG 59.474 44.000 0.00 0.00 0.00 2.82
3379 3907 5.190330 ACCCCTTTTACGACATACCTACAAT 59.810 40.000 0.00 0.00 0.00 2.71
3380 3908 4.531732 ACCCCTTTTACGACATACCTACAA 59.468 41.667 0.00 0.00 0.00 2.41
3381 3909 4.095946 ACCCCTTTTACGACATACCTACA 58.904 43.478 0.00 0.00 0.00 2.74
3382 3910 4.743057 ACCCCTTTTACGACATACCTAC 57.257 45.455 0.00 0.00 0.00 3.18
3383 3911 6.840705 AGATTACCCCTTTTACGACATACCTA 59.159 38.462 0.00 0.00 0.00 3.08
3384 3912 5.664457 AGATTACCCCTTTTACGACATACCT 59.336 40.000 0.00 0.00 0.00 3.08
3385 3913 5.922053 AGATTACCCCTTTTACGACATACC 58.078 41.667 0.00 0.00 0.00 2.73
3386 3914 7.854557 AAAGATTACCCCTTTTACGACATAC 57.145 36.000 0.00 0.00 30.32 2.39
3387 3915 8.947055 GTAAAGATTACCCCTTTTACGACATA 57.053 34.615 0.00 0.00 35.65 2.29
3388 3916 7.854557 GTAAAGATTACCCCTTTTACGACAT 57.145 36.000 0.00 0.00 35.65 3.06


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

AutoCloner maintained by Alex Coulton.